Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008187.1 Hibiscus syriacus cultivar Beakdansim tig00110794_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: 1300289
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 5
Found at i:344654 original size:20 final size:20
Alignment explanation
Indices: 344605--344660 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
344595 GAATTTGGAA
344605 TAAATCGCAATGCGAACTTG
1 TAAATCGCAATGCGAACTTG
* *
344625 GACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
344646 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
344661 TAGTCGAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:344680 original size:21 final size:21
Alignment explanation
Indices: 344650--344725 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
344640 AATATGTAAA
*
344650 TCGCAATGCGATAGTCGAGGT
1 TCGCATTGCGATAGTCGAGGT
* *
344671 TCGCATTGCGATAGTCCAAGTT
1 TCGCATTGCGATAGT-CGAGGT
*
344693 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAGGT
**
344714 TCGTGTTGCGAT
1 TCGCATTGCGAT
344726 TTATTCCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 27 0.59
22 19 0.41
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAGGT
Found at i:344698 original size:22 final size:22
Alignment explanation
Indices: 344650--344714 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
344640 AATATGTAAA
* * *
344650 TCGCAATGCGATAGT-CGAGGT
1 TCGCATTGCGATAGTCCAAGTT
344671 TCGCATTGCGATAGTCCAAGTT
1 TCGCATTGCGATAGTCCAAGTT
*
344693 TCGCATTGCGATAGTCGAAGTT
1 TCGCATTGCGATAGTCCAAGTT
344715 CGTGTTGCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 14 0.36
22 25 0.64
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (22 bp):
TCGCATTGCGATAGTCCAAGTT
Found at i:344810 original size:21 final size:21
Alignment explanation
Indices: 344784--344837 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
344774 GATTTATATA
344784 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
344805 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
344826 TTCGCGTTGCGA
1 TTCGCATTGCGA
344838 ATCTGGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:349092 original size:18 final size:18
Alignment explanation
Indices: 349069--349107 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
349059 ACCATAAACA
*
349069 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
349087 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
349105 GAA
1 GAA
349108 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:349256 original size:20 final size:21
Alignment explanation
Indices: 349228--349266 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
349218 GTTTTCAAAA
*
349228 ATGA-TTTTTAAAAATATTAT
1 ATGAGTTTTCAAAAATATTAT
*
349248 ATGAGTTTTCCAAAATATT
1 ATGAGTTTTCAAAAATATT
349267 TTTAAAACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (21 bp):
ATGAGTTTTCAAAAATATTAT
Found at i:349307 original size:38 final size:36
Alignment explanation
Indices: 349157--349419 Score: 185
Period size: 33 Copynumber: 7.3 Consensus size: 36
349147 TATATCCCAA
* *
349157 AAAAATATTTTTTAAACTATATA-T-TATA--TTT-
1 AAAAATGTTTTTAAAACTATATATTATATAGTTTTC
* **
349188 AAAAATGTTTTCAAAACTATATACCATATAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAGTTTTC
349224 AAAAATGATTTTT-AAA--A-ATATTATATGAGTTTTC
1 AAAAATG-TTTTTAAAACTATATATTATAT-AGTTTTC
* * *
349258 CAAAATATTTTTAAAACTATATATTATATAAAATTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT--AGTTTTC
*
349296 AAAAATGTTTTTATTTTAAACTATACATTATAT--TTTT-
1 AAAAATGTTTTTA----AAACTATATATTATATAGTTTTC
* * * *
349333 -AAAATGATTTTCAAAAATATATGTTATATAATTTTC
1 AAAAATG-TTTTTAAAACTATATATTATATAGTTTTC
349369 -AAAATGTTTTTAAAACTTATATATTGTATATAAGTTTTC
1 AAAAATGTTTTTAAAAC-TATATA-T-TATAT-AGTTTTC
*
349408 AAAAACGTTTTT
1 AAAAATGTTTTT
349420 TTAAAAAAAA
Statistics
Matches: 184, Mismatches: 23, Indels: 41
0.74 0.09 0.17
Matches are distributed among these distances:
31 20 0.11
33 29 0.16
34 16 0.09
35 15 0.08
36 28 0.15
37 19 0.10
38 26 0.14
39 6 0.03
40 10 0.05
42 15 0.08
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
AAAAATGTTTTTAAAACTATATATTATATAGTTTTC
Found at i:359881 original size:34 final size:33
Alignment explanation
Indices: 359809--359905 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
359799 TTTTCCCTAC
* *
359809 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
359841 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
359875 TTTATTAGTGTTATTATATATATATATATAT
1 TTTATTAATTTTATTATATATGTATATATAT
359906 ATATTTATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 20 0.38
33 5 0.09
34 28 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:360047 original size:16 final size:18
Alignment explanation
Indices: 360026--360060 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
360016 TTTACTAATT
360026 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
360042 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
360060 T
1 T
360061 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:360194 original size:16 final size:16
Alignment explanation
Indices: 360156--360194 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
360146 TTATTGTTTT
360156 TTTATTTTATATTCTA
1 TTTATTTTATATTCTA
*
360172 TTCATTTTATATT-TA
1 TTTATTTTATATTCTA
360187 CTTTATTT
1 -TTTATTT
360195 CTTACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTATATTCTA
Found at i:363288 original size:20 final size:20
Alignment explanation
Indices: 363236--363305 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
363226 CAAAAAGAGG
*
363236 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
363259 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
363280 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
363300 AAAAAG
1 AAAAAG
363306 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:363936 original size:29 final size:29
Alignment explanation
Indices: 363894--363956 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
363884 CCAGTAGAGA
363894 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
363923 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
363952 AGCAT
1 AGCAT
363957 CAAATGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AGCATGCAAGCTACCCCATCAATCCTTTG
Found at i:364413 original size:18 final size:18
Alignment explanation
Indices: 364390--364425 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
364380 TCAACATCAA
* *
364390 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
364408 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
364426 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:364873 original size:36 final size:37
Alignment explanation
Indices: 364748--365164 Score: 165
Period size: 36 Copynumber: 11.8 Consensus size: 37
364738 CAGATGATTA
** * * *
364748 TCTCACTTGAGATTGCTTTT-TTAAAAC-AGACTTTG
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTTG
* * * * *
364783 TCTCACTTGGGACTGTTTTACTCGAAAGAAGATTTAT-
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTT-TG
* ** *
364820 T-TCAC-TCATGATTGTTTTTCTTAAAACAAGA-TTTG
1 TCTCACTTGA-GACAGTTTTTCTTGAAACAAGATTTTG
* * * *
364855 TCTCACTTGAGACCGTTTTCACTAG-AA-GAG-TTTT-
1 TCTCACTTGAGACAGTTTT-TCTTGAAACAAGATTTTG
* **
364889 TCTCTCTTGAGACAGTTTCCCTTGAAACAA-ATTTTG
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTTG
* * *
364925 TCTCTCTTGAGACAGTTTCTCTTGAAACAA-ATTTCG
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTTG
** *
364961 TCT-ATCTTGAGACAGTTTCCCTTGAAATAA-ATTTTG
1 TCTCA-CTTGAGACAGTTTTTCTTGAAACAAGATTTTG
* **
364997 TCTCTCTTGAGACAGTTTCCCTTGAAACAA-A-----
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTTG
* * * *
365028 -AT-ATTTGA-ATA-TGTTTTCTTTGAAACAA-ATTTCG
1 TCTCACTTGAGACAGT-TTTTC-TTGAAACAAGATTTTG
* *
365062 TCTCCCTTGAGACAGTTTCTT-TTGGAACTAAG-TTTTG
1 TCTCACTTGAGACAGTTT-TTCTTGAAAC-AAGATTTTG
* * *
365099 CCTCTCTTGAGACAGTTTCTCTTGAAAC-A-ATTTTCG
1 TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTT-G
**
365135 TCT-ATCTTGAGACAGTTTCCCTTGAAACAA
1 TCTCA-CTTGAGACAGTTTTTCTTGAAACAA
365165 AACCTTTGAA
Statistics
Matches: 293, Mismatches: 55, Indels: 66
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.00
28 5 0.02
29 14 0.05
30 1 0.00
33 3 0.01
34 19 0.06
35 36 0.12
36 167 0.57
37 43 0.15
38 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
TCTCACTTGAGACAGTTTTTCTTGAAACAAGATTTTG
Found at i:364934 original size:70 final size:73
Alignment explanation
Indices: 364843--365165 Score: 230
Period size: 72 Copynumber: 4.6 Consensus size: 73
364833 GTTTTTCTTA
* * * * * *
364843 AAACAAGA-TTTGTCTCACTTGAGACCGTTTTCACTAG-AA-GAGTTT-TTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
364904 TTTCCCTTG
65 TTTCCCTTG
* *
364913 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
364977 TTCCCTTG
66 TTCCCTTG
* * * * *
364985 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
365041 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * * *
365050 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGCCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
365114 TTTCTCTTG
65 TTTCCCTTG
* * *
365123 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
365166 ACCTTTGAAT
Statistics
Matches: 204, Mismatches: 34, Indels: 28
0.77 0.13 0.11
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
69 8 0.04
70 25 0.12
71 4 0.02
72 73 0.36
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:364986 original size:72 final size:70
Alignment explanation
Indices: 364893--365165 Score: 299
Period size: 72 Copynumber: 3.9 Consensus size: 70
364883 AGTTTTTCTC
*
364893 TCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATT
1 TCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
364958 TCGTCTA
66 T-G-CTA
*
364965 TCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA--
1 TCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
*
365028 --ATA
66 TGCTA
* * * * * ** *
365031 T-TTGA-ATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA-
* *
365094 TTTTGCCTC
63 ATTTG-CTA
* *
365103 TCTTGAGACAGTTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTTGAGACAGTTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
365166 ACCTTTGAAT
Statistics
Matches: 164, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
64 2 0.01
65 46 0.28
66 5 0.03
72 70 0.43
73 39 0.24
74 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (70 bp):
TCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
TGCTA
Found at i:365079 original size:101 final size:103
Alignment explanation
Indices: 364940--365128 Score: 292
Period size: 102 Copynumber: 1.9 Consensus size: 103
364930 CTTGAGACAG
* *
364940 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGCCTCTCT
365004 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
365042 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGCCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGCCTCTCT
*
365106 TGAGACAGTTTCTCTTGAAACAA
66 TGAGACAGTTTCCCTTGAAACAA
365129 TTTTCGTCTA
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 34 0.44
102 44 0.56
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGCCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:365157 original size:138 final size:137
Alignment explanation
Indices: 364904--365228 Score: 429
Period size: 138 Copynumber: 2.4 Consensus size: 137
364894 CTTGAGACAG
* *
364904 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGCCTATCTT
* *
364969 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
365034 GAATATG
131 GAATATA
* * * * * * * *
365041 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGCCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGCCTATCT
* * *
365106 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
365170 TTGAATTTA
129 TTGAATATA
* * *
365179 TTTCCCCT-AAAAATAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
365229 CAAAATCTTC
Statistics
Matches: 160, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
137 54 0.34
138 106 0.66
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGCCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:365257 original size:67 final size:68
Alignment explanation
Indices: 365140--365296 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 68
365130 TTTCGTCTAT
* **
365140 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAA-ATAATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
365202 TCC
66 TCC
* * * *
365205 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
365270 TCC
66 TCC
* * *
365273 CTTGAAACTGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
365297 ACAGATATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 26 0.33
68 33 0.42
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
TCC
Found at i:366270 original size:105 final size:104
Alignment explanation
Indices: 365931--366972 Score: 1541
Period size: 105 Copynumber: 10.0 Consensus size: 104
365921 ATATCGTGGC
* * * * * *
365931 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
365996 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
366037 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACAA-CTTCC
* *
366102 CAATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
64 CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366144 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
366209 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366249 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
366314 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366354 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
366415 ATTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366454 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
366519 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366559 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
366620 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366659 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
366724 ATCCCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366764 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
** *
366825 ATTCAGATTCAATTTCAACTTCACAACGAATGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
366864 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
366929 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
366970 ACT
1 ACT
366973 TGGAACAATG
Statistics
Matches: 863, Mismatches: 54, Indels: 38
0.90 0.06 0.04
Matches are distributed among these distances:
100 259 0.30
101 12 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 375 0.43
106 92 0.11
107 94 0.11
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:366509 original size:205 final size:205
Alignment explanation
Indices: 365931--366972 Score: 1611
Period size: 205 Copynumber: 5.0 Consensus size: 205
365921 ATATCGTGGC
* * * * *
365931 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AA-TT-TC
*
365996 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
62 -A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACT
* * * * *
366061 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCTAATTTCAACTT
125 TCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTTT-CCAATCTCAGAGCCAATTTCAACTT
*
366126 CACAGCGAAGGATATTGG
188 CACAACGAAGGATATTGG
* * *
366144 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
366209 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTT
62 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTT
366274 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCAC
126 CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCAC
366339 AACGAAGGATATTGG
191 AACGAAGGATATTGG
366354 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
* *
366419 AGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
366484 CGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGA
131 CGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGA
366549 AGGATATTGG
196 AGGATATTGG
366559 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
*
366624 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
* * *
366689 CGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAACGA
131 CGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGA
*
366754 AAGATATTGG
196 AGGATATTGG
366764 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
** * * ** *
366829 AGATTCAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
* * ** *
366894 CGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCGGT-TCCAGAGCCAATTTCAACTTCACGA
131 CGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCAATCT-CAGAGCCAATTTCAACTTCACAA
*
366957 CGGAGGATATTGG
193 CGAAGGATATTGG
366970 ACT
1 ACT
366973 TGGAACAATG
Statistics
Matches: 785, Mismatches: 40, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
205 485 0.62
206 46 0.06
207 1 0.00
208 2 0.00
209 2 0.00
210 93 0.12
211 9 0.01
212 99 0.13
213 48 0.06
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAAATTTCATTC
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGA
AGGATATTGG
Found at i:366526 original size:310 final size:312
Alignment explanation
Indices: 365931--366972 Score: 1570
Period size: 310 Copynumber: 3.3 Consensus size: 312
365921 ATATCGTGGC
* * * * *
365931 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAATTTC-C
365996 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
65 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
366061 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCTAATTTCAACTT
129 TCACGACGAAGGGACCGCTGCTTGTCAA-CAACAACTTT--CAA-TTCAGAGCCAATTTCAACTT
* *
366126 CACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTT
190 CACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTT
*
366191 GTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
255 GTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
366249 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAA-TTTCC
366313 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
65 AAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
366378 TCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAACCAATTTCAACTTCACA
129 TCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCAATTTCAACTTCACA
*
366440 GCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCA
194 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCA
366505 ACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
259 ACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
366559 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AATTT-C-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAATTTCCA
* *
366620 ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTC
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
* * *
366685 ACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACA
131 ACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-TCAAT-TCAGAGCCAATTTCAACTTCACA
* *
366750 ACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCA
194 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCA
** *
366815 ACAA-AA-TTT-C-AT-TCAGATTCAATTTCAACTTCACAACGAATGATATTGG
259 ACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
366864 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAATTT-CC
** * *
366929 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
366973 TGGAACAATG
Statistics
Matches: 674, Mismatches: 37, Indels: 33
0.91 0.05 0.04
Matches are distributed among these distances:
305 171 0.25
306 8 0.01
307 9 0.01
308 7 0.01
309 7 0.01
310 280 0.42
311 37 0.05
312 1 0.00
314 3 0.00
315 2 0.00
316 3 0.00
317 96 0.14
318 50 0.07
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (312 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAAACAATTTCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
ACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCAATTTCAACTTCACAGC
GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC
AACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:368026 original size:2 final size:2
Alignment explanation
Indices: 368021--368053 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
368011 ATTAGTGTAT
*
368021 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
368054 TTCCTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:368054 original size:8 final size:8
Alignment explanation
Indices: 367987--368055 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
367977 TTCTATTAAT
367987 TTTATATA
1 TTTATATA
*
367995 TGTATATA
1 TTTATATA
* *
368003 TGTTTTTTA
1 T-TTATATA
*
368012 -TTAGTGTA
1 TTTA-TATA
368020 TTATATATA
1 TT-TATATA
*
368029 TATATATA
1 TTTATATA
*
368037 TATATATA
1 TTTATATA
368045 TTTATATA
1 TTTATATA
368053 TTT
1 TTT
368056 CCTATTTTGC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
7 2 0.04
8 35 0.73
9 9 0.19
10 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:368168 original size:16 final size:18
Alignment explanation
Indices: 368147--368181 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
368137 TTTACTAATT
368147 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
368163 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
368181 T
1 T
368182 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:371843 original size:34 final size:34
Alignment explanation
Indices: 371800--371870 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
371790 TAGACAGACA
*
371800 TTTAGTAATGCTT-GACAACTCTTCATTGGCTTTC
1 TTTAGTAATG-TTAGACAACTCTTCATTAGCTTTC
*
371834 TTTAGTAATGTTAGACAACTCTTCCTTAGCTTTC
1 TTTAGTAATGTTAGACAACTCTTCATTAGCTTTC
371868 TTT
1 TTT
371871 GAGATTCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (34 bp):
TTTAGTAATGTTAGACAACTCTTCATTAGCTTTC
Found at i:382747 original size:73 final size:73
Alignment explanation
Indices: 382652--382807 Score: 276
Period size: 73 Copynumber: 2.1 Consensus size: 73
382642 ATGAGAAATC
* *
382652 ACGAGCTACTCGAGTTATACTCGATCAAAACTCGAATTGAAATGAACTCGACTCGAATTCTTAAC
1 ACGAGCTACTCGAGTTAGACTCGATCAAAACTCAAATTGAAATGAACTCGACTCGAATTCTTAAC
382717 GAGTCAAA
66 GAGTCAAA
*
382725 ACGAGCTACTCGAGTTCGACTCGATCAAAACTCAAATTGAAATGAACTCGACTCGAATTCTTAAC
1 ACGAGCTACTCGAGTTAGACTCGATCAAAACTCAAATTGAAATGAACTCGACTCGAATTCTTAAC
*
382790 GAGTTAAA
66 GAGTCAAA
382798 ACGAGCTACT
1 ACGAGCTACT
382808 TGATACTCGA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 79 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (73 bp):
ACGAGCTACTCGAGTTAGACTCGATCAAAACTCAAATTGAAATGAACTCGACTCGAATTCTTAAC
GAGTCAAA
Found at i:382969 original size:18 final size:18
Alignment explanation
Indices: 382946--382980 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
382936 CATATACTTA
*
382946 AAGTTTAAGTTCAAGTTT
1 AAGTTTAAATTCAAGTTT
382964 AAGTTTAAATTCAAGTT
1 AAGTTTAAATTCAAGTT
382981 CAAACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (18 bp):
AAGTTTAAATTCAAGTTT
Found at i:383189 original size:2 final size:2
Alignment explanation
Indices: 383182--383218 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
383172 TACACTCAAC
* *
383182 AT AT AT AT AA AC 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 A
383219 AAACGGAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:395520 original size:34 final size:35
Alignment explanation
Indices: 395477--395550 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 35
395467 GTCTGTTTAG
395477 TATAGAGATGGGTTC-AATCCAATCCTCTTATTAT
1 TATAGAGATGGGTTCAAATCCAATCCTCTTATTAT
395511 TATAGAGATGGGTTCAAATTAATCCAATCCTCTTATTAT
1 TATAGAGATGGGTTC--A--AATCCAATCCTCTTATTAT
395550 T
1 T
395551 TGTCAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 15 0.43
39 20 0.57
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (35 bp):
TATAGAGATGGGTTCAAATCCAATCCTCTTATTAT
Found at i:395933 original size:118 final size:118
Alignment explanation
Indices: 395789--396005 Score: 380
Period size: 118 Copynumber: 1.8 Consensus size: 118
395779 TTTGTGATAG
* * * *
395789 AATTTTCACTTCTTTTTCTGGATTTGTGATAGAATTTTCATAGTTCCATGCGAGTATTATTTTGA
1 AATTTTCACTTATTTTCCTGGATTTGTGATAGAATTTTCATAATTCCATGCGAGCATTATTTTGA
*
395854 AAGGGAATTTGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
66 AAGGGAATTCGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
395907 AATTTTCACTTATTTTCCTGGATTTGTGATAGAATTTTCATAATTCCATGCGAGCATTATTTTGA
1 AATTTTCACTTATTTTCCTGGATTTGTGATAGAATTTTCATAATTCCATGCGAGCATTATTTTGA
*
395972 AAGGGAATTCGTTGTTTTTGTTGAAATTTGTTGA
66 AAGGGAATTCGTTGTTTTTGTTGAAATTTATTGA
396006 TCCACATAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (118 bp):
AATTTTCACTTATTTTCCTGGATTTGTGATAGAATTTTCATAATTCCATGCGAGCATTATTTTGA
AAGGGAATTCGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
Found at i:405634 original size:55 final size:54
Alignment explanation
Indices: 405568--405739 Score: 186
Period size: 55 Copynumber: 3.1 Consensus size: 54
405558 ACCGAAATTA
* *
405568 AATATACTTATTAGTTGTTATCATTAATAAGCATAAAAATAGGA-CTTCGAAATCG
1 AATATATTTATTAGTTGTTATCATTAAGAAGCATAAAAATAGGATC-T-GAAATCG
* * *
405623 AGTATATTTATTAGTTGTTATCGTTAAGAAGAATAAAAATAAGGATCTGAAATCG
1 AATATATTTATTAGTTGTTATCATTAAGAAGCATAAAAAT-AGGATCTGAAATCG
* * * * * *
405678 AATATATCTATCAGCTGTT-GCTATTAAGAAGCATAAAAATAGATATCCGAAATCG
1 AATATATTTATTAGTTGTTATC-ATTAAGAAGCATAAAAATAG-GATCTGAAATCG
405733 AATATAT
1 AATATAT
405740 CTAAAAAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
54 3 0.03
55 90 0.91
56 5 0.05
57 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (54 bp):
AATATATTTATTAGTTGTTATCATTAAGAAGCATAAAAATAGGATCTGAAATCG
Found at i:408718 original size:46 final size:46
Alignment explanation
Indices: 408665--408753 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
408655 AAACGGATAT
* *
408665 AATTTCGTGGATTCCGTACCGCATCCGCTCTGATTGGGGCGGGTAC
1 AATTTCGTGGATTCCGCACCGCATCCGCTCTAATTGGGGCGGGTAC
408711 AATTTCGTGGATTCCGCACCGCATCCGCTCTAATTGGGGCGGG
1 AATTTCGTGGATTCCGCACCGCATCCGCTCTAATTGGGGCGGG
408754 AATGGGTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (46 bp):
AATTTCGTGGATTCCGCACCGCATCCGCTCTAATTGGGGCGGGTAC
Found at i:420709 original size:61 final size:61
Alignment explanation
Indices: 420614--420731 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
420604 TCGAAAAGTG
* *
420614 CAGTGCTAAAAGAGAAAACTATTTAAAAGTTCAATGACAAAATCGATACACCCCTAACGTT
1 CAGTGCTAAAAAAGAAAAATATTTAAAAGTTCAATGACAAAATCGATACACCCCTAACGTT
*
420675 CAGTGTTAAAAAAGAAAAATATTTAAAAGTTCAATGACAAAATCGATACACCCCTAA
1 CAGTGCTAAAAAAGAAAAATATTTAAAAGTTCAATGACAAAATCGATACACCCCTAA
420732 AGCTTGGATC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (61 bp):
CAGTGCTAAAAAAGAAAAATATTTAAAAGTTCAATGACAAAATCGATACACCCCTAACGTT
Found at i:420860 original size:26 final size:26
Alignment explanation
Indices: 420808--420860 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
420798 TTGGGCTACA
* * *
420808 TCCATTCTAGCCTTCGTGCATTCAAT
1 TCCATTCTAGCCTTCCTGCACTAAAT
**
420834 TCCATTCTAGTTTTCCTGCACTAAAT
1 TCCATTCTAGCCTTCCTGCACTAAAT
420860 T
1 T
420861 TTAATATCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (26 bp):
TCCATTCTAGCCTTCCTGCACTAAAT
Found at i:432136 original size:14 final size:14
Alignment explanation
Indices: 432117--432151 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
432107 AGTAGTTCTC
*
432117 TTTTTCTTGTTTTT
1 TTTTTCTGGTTTTT
432131 TTTTTCTGGTTTTT
1 TTTTTCTGGTTTTT
432145 TTTTTCT
1 TTTTTCT
432152 CCCTGAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (14 bp):
TTTTTCTGGTTTTT
Found at i:432741 original size:3 final size:3
Alignment explanation
Indices: 432733--432784 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
432723 GGCCTGTAAA
*
432733 AAT AAT AAT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT
432779 AAT AAT
1 AAT AAT
432785 TAAAATTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:433146 original size:43 final size:41
Alignment explanation
Indices: 433085--433323 Score: 157
Period size: 40 Copynumber: 5.6 Consensus size: 41
433075 GAAGGCAATA
*
433085 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGGGTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGG--ATCTAGGGGTG
* *
433128 ACACGGCTCCTACGTGATGAGGAGATCTGG-TC-GGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGATCTAGGGG-TG
* * **
433168 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGTG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGG--ATC--TAGG--GGTG
* * *
433215 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ---ACACGGCTCCTACGTGATGAGGA-GAGCTGG--ATCTAGGGGTG
*
433261 ACACGGCTCCTACGTGATGAGGAGATCTGG-TCT-GGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGATCTAGGGG-TG
** *
433301 ACACGATTCCTACATGATGAGGA
1 ACACGGCTCCTACGTGATGAGGA
433324 CGGCTGGCCA
Statistics
Matches: 158, Mismatches: 22, Indels: 35
0.73 0.10 0.16
Matches are distributed among these distances:
39 6 0.04
40 56 0.35
42 2 0.01
43 54 0.34
46 5 0.03
47 2 0.01
48 5 0.03
50 27 0.17
51 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (41 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGATCTAGGGGTG
Found at i:433267 original size:133 final size:133
Alignment explanation
Indices: 432979--433342 Score: 550
Period size: 133 Copynumber: 2.7 Consensus size: 133
432969 GAAGAGTTCG
* * * * *
432979 GGTTGTCTAAGGGTGACACGGTTCCTACGTGATGAGGAGATTTGGTCGGTGGATGACACGGCTCA
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
*
433044 TACGTGATGAAGAGTTCTTGGCCATATTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGAC
433109 GGCT
130 GGCT
433113 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
**
433178 TACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGTGATAACACGGTTCCTACGTGATGAGGACG
66 TACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGACG
433243 GCT
131 GCT
* * * ** *
433246 GGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCC
1 GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
* * *
433311 TACATGATGAGGACG-GCTGGCCATCTTTAGGA
66 TACGTGATGAAGA-GTTCTGGCCATCTTTAGGA
433343 GTTATGGTTT
Statistics
Matches: 212, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
133 134 0.63
134 78 0.37
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (133 bp):
GGTTATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
TACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGCAATAACACGGTTCCTACGTGATGAGGACG
GCT
Found at i:433400 original size:28 final size:28
Alignment explanation
Indices: 433369--433445 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
433359 AAACCAAATT
433369 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
433397 AAAGATTCGTTTCAAGAA-AAACAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
433425 AAAGATGATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
433446 CAACTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 29 0.71
29 2 0.05
30 3 0.07
31 7 0.17
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:433540 original size:31 final size:31
Alignment explanation
Indices: 433499--433610 Score: 88
Period size: 31 Copynumber: 3.6 Consensus size: 31
433489 TCAAAGATGA
*
433499 TTTAAAGGAAACTG-TCTCAAGAAAATTTGTT
1 TTTAAGGGAAA-TGTTCTCAAGAAAATTTGTT
* ** *
433530 TTTAAGGGAAATGTTCTC-A-AAGATCGGGGT
1 TTTAAGGGAAATGTTCTCAAGAAAAT-TTGTT
* ** *
433560 TTCATTGAAAACTG-TCTCAAGAAAATTTGTT
1 TTTAAGGGAAA-TGTTCTCAAGAAAATTTGTT
433591 TTTAAGGGAAATGTTCTCAA
1 TTTAAGGGAAATGTTCTCAA
433611 AGATCGGGGT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
29 4 0.07
30 18 0.31
31 32 0.55
32 4 0.07
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (31 bp):
TTTAAGGGAAATGTTCTCAAGAAAATTTGTT
Found at i:433572 original size:61 final size:61
Alignment explanation
Indices: 433507--433640 Score: 268
Period size: 61 Copynumber: 2.2 Consensus size: 61
433497 GATTTAAAGG
433507 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
1 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
433568 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
1 AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
433629 AAACTGTCTCAA
1 AAACTGTCTCAA
433641 ATGAGACAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 73 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.34
Consensus pattern (61 bp):
AAACTGTCTCAAGAAAATTTGTTTTTAAGGGAAATGTTCTCAAAGATCGGGGTTTCATTGA
Found at i:433579 original size:30 final size:30
Alignment explanation
Indices: 433544--433641 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
433534 AGGGAAATGT
433544 TCTCAAAGATCGGGGTTTCATTGAAAACTG
1 TCTCAAAGATCGGGGTTTCATTGAAAACTG
* ** * * ** *
433574 TCTCAAGAAAAT-TTGTTTTTAAGGGAAA-TG
1 TCTC-A-AAGATCGGGGTTTCATTGAAAACTG
433604 TTCTCAAAGATCGGGGTTTCATTGAAAACTG
1 -TCTCAAAGATCGGGGTTTCATTGAAAACTG
433635 TCTCAAA
1 TCTCAAA
433642 TGAGACAAAA
Statistics
Matches: 47, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
29 4 0.09
30 23 0.49
31 16 0.34
32 4 0.09
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (30 bp):
TCTCAAAGATCGGGGTTTCATTGAAAACTG
Found at i:434285 original size:37 final size:35
Alignment explanation
Indices: 434234--434354 Score: 96
Period size: 37 Copynumber: 3.5 Consensus size: 35
434224 AGACTCGAAG
434234 ATTTT-TTTCAAAAGAAATTGTCTTAAGAGAGACAAA
1 ATTTTGTTTCAAAAGAAA-T-TCTTAAGAGAGACAAA
* **
434270 ATTTTGTTTCCAAAGAAA--C---A-A-ACTCAAA
1 ATTTTGTTTCAAAAGAAATTCTTAAGAGAGACAAA
434298 GATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAA
1 -A-TTTTGTTTCAAAAGAAA-T-TCTTAAGAGAGACAAA
*
434337 ATTTTGTTTCCAAAGAAA
1 ATTTTGTTTCAAAAGAAA
434355 CAAACTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
28 5 0.08
29 2 0.03
30 17 0.26
33 1 0.02
34 1 0.02
36 5 0.08
37 28 0.42
38 2 0.03
39 5 0.08
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (35 bp):
ATTTTGTTTCAAAAGAAATTCTTAAGAGAGACAAA
Found at i:434325 original size:67 final size:65
Alignment explanation
Indices: 434226--434387 Score: 263
Period size: 67 Copynumber: 2.5 Consensus size: 65
434216 AAGAGAAAAG
* * *
434226 ACTCGAAGATTTTTTTCAAAAGAAATTGTCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 ACTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
434291 ACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAAC
1 ACTCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAAC
434356 AA
64 AA
*
434358 ACTCAAAGA-TTTTTTCAAAAGAAACAATCT
1 ACTCAAAGATTTTTTTCAAAAGAAACTATCT
434388 CAAAGATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
64 17 0.19
65 11 0.12
66 4 0.04
67 59 0.65
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (65 bp):
ACTCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
Found at i:434376 original size:26 final size:27
Alignment explanation
Indices: 434343--434399 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
434333 CAAAATTTTG
*
434343 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
434370 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
434397 TTT
1 TTT
434400 TTCACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:434568 original size:29 final size:29
Alignment explanation
Indices: 434487--434746 Score: 207
Period size: 29 Copynumber: 9.0 Consensus size: 29
434477 AAAACTTTGT
* * *
434487 TTCAAAATAAATAGACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
434514 TTCAAAAGAAAC-AACTCAAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
434542 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
434571 TTCAAAAGGAACAAACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *** *
434598 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT-
1 TTCAAAAGAAACAAACTC-A-A-AG-----A-TTTTTA
* * *
434635 TTCAAAATAAATAGACTCAAAGA-TTTT-
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
*
434662 TTCAAAAGAAAC-AACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
* *
434690 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAAACTCAAAGATTTTTA
434719 TTCAAAATG-AACAAACTCAAAGATTTTT
1 TTCAAAA-GAAACAAACTCAAAGATTTTT
434747 TCAAGAGAAA
Statistics
Matches: 190, Mismatches: 26, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
26 18 0.09
27 43 0.23
28 27 0.14
29 78 0.41
30 3 0.02
34 2 0.01
35 2 0.01
36 1 0.01
37 16 0.08
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (29 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTA
Found at i:434637 original size:148 final size:148
Alignment explanation
Indices: 434440--434776 Score: 608
Period size: 148 Copynumber: 2.3 Consensus size: 148
434430 TTTGTTTCAG
* * *
434440 ACTCAAAGA-TTTTTC-ACA-AAATTGTCTCAAGAGATACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
*
434502 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATTTTTATTCAAAAGGAACAAACTCCAAGATT
66 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
434567 TTTATTCAAAAGGAACAA
131 TTTATTCAAAAGGAACAA
434585 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
434650 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
66 CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
*
434715 TTTATTCAAAATGAACAA
131 TTTATTCAAAAGGAACAA
434733 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
434777 AAAATCGTTT
Statistics
Matches: 184, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
145 9 0.05
146 6 0.03
147 2 0.01
148 167 0.91
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (148 bp):
ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
CTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATT
TTTATTCAAAAGGAACAA
Found at i:435084 original size:35 final size:35
Alignment explanation
Indices: 434999--435131 Score: 187
Period size: 35 Copynumber: 3.8 Consensus size: 35
434989 GGAAAAAAAA
* * * *
434999 TGTCCCAAGCGAGACGAAATTTG-TTTTCAGATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCA-A-GAAC
* *
435035 TGTCTTAAGTGAGACAAAATTTGTTTTTCAAGAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAC
435070 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAC
435105 TGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTT
435132 CGAAGGAAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
35 62 0.70
36 20 0.23
37 6 0.07
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTCAAGAAC
Found at i:435188 original size:36 final size:37
Alignment explanation
Indices: 435116--435188 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
435106 GTCTCAAGCG
* * * *
435116 AGACAAAATTTGTTTTCGAAGGAAACTACCTTAAATA
1 AGACAAAATTTGTTTTCAAAGGAAACAAACTCAAATA
*
435153 AGACAAATTTTG-TTTCAAAGGAAACAAACTCAAATA
1 AGACAAAATTTGTTTTCAAAGGAAACAAACTCAAATA
435189 TTTTTTTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 20 0.65
37 11 0.35
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (37 bp):
AGACAAAATTTGTTTTCAAAGGAAACAAACTCAAATA
Found at i:436799 original size:17 final size:17
Alignment explanation
Indices: 436757--436807 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
436747 ACTTTCTGTT
*
436757 CTTTT-TTTTCACTTTG
1 CTTTTCTTTTCTCTTTG
436773 --TTTC-TTTCTCTTTG
1 CTTTTCTTTTCTCTTTG
*
436787 CTTTTCTTTTCTCTTCG
1 CTTTTCTTTTCTCTTTG
436804 CTTT
1 CTTT
436808 AATATGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 12 0.41
16 4 0.14
17 13 0.45
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.69
Consensus pattern (17 bp):
CTTTTCTTTTCTCTTTG
Found at i:443875 original size:3 final size:3
Alignment explanation
Indices: 443867--443921 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
443857 GCCTGCAAAA
*
443867 AAT AAT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
443913 AAT AAT AAT
1 AAT AAT AAT
443922 TAAAATTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:446567 original size:29 final size:29
Alignment explanation
Indices: 446535--446629 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
446525 AATTAGTCCT
446535 TAAACTTTTAAATATTCTAATTTCATCCC
1 TAAACTTTTAAATATTCTAATTTCATCCC
* * ** * *
446564 TAAACTATGACTCTCATTCTAAATT-AGTCCT
1 TAAACTTTTA-AAT-ATTCTAATTTCA-TCCC
*
446595 TAAACTTTTGAAA-ATTCTAATTTCATCTC
1 TAAACTTTT-AAATATTCTAATTTCATCCC
446624 TAAACT
1 TAAACT
446630 ATGACCCTCT
Statistics
Matches: 48, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
29 25 0.52
30 3 0.06
31 19 0.40
32 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAACTTTTAAATATTCTAATTTCATCCC
Found at i:446584 original size:31 final size:30
Alignment explanation
Indices: 446548--446645 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
446538 ACTTTTAAAT
446548 ATTCTAATTTCATCCCTAAACTATGACTCTC
1 ATTCTAATTTCATCCCTAAACTATGAC-CTC
* * * **
446579 ATTCTAAATT-AGTCCTTAAACTTTTGA--AA
1 ATTCTAATTTCA-TCCCTAAAC-TATGACCTC
*
446608 ATTCTAATTTCATCTCTAAACTATGACCCTC
1 ATTCTAATTTCATCCCTAAACTATGA-CCTC
*
446639 TTTCTAA
1 ATTCTAA
446646 ATAAGTCCCC
Statistics
Matches: 49, Mismatches: 12, Indels: 12
0.67 0.16 0.16
Matches are distributed among these distances:
28 4 0.08
29 16 0.33
30 2 0.04
31 23 0.47
32 4 0.08
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (30 bp):
ATTCTAATTTCATCCCTAAACTATGACCTC
Found at i:446599 original size:60 final size:60
Alignment explanation
Indices: 446523--446681 Score: 221
Period size: 60 Copynumber: 2.6 Consensus size: 60
446513 ATCCTTATTT
*
446523 TAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCCCTAAACTATGACTCTCATTC
1 TAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCCCTAAACTATGACCCTCATTC
* *
446583 TAAATTAGTCCTTAAACTTTTGAAA-ATTCTAATTTCATCTCTAAACTATGACCCTCTTTC
1 TAAATTAGTCCTTAAACTTTT-AAATATTCTAATTTCATCCCTAAACTATGACCCTCATTC
* ** * * *
446643 TAAATAAGTCCCCAAACTTTTGAATCTTCCAATTTCATC
1 TAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATC
446682 ACCAAATTCA
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.02
60 83 0.94
61 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTAAATATTCTAATTTCATCCCTAAACTATGACCCTCATTC
Found at i:446908 original size:60 final size:60
Alignment explanation
Indices: 446801--446938 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
446791 GTATATACAT
*** * **
446801 ATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAAT-GAAGGTC
1 ATAGTTTGGGATGAAATCAAAATGTTCAAAAAGTATAAGGACCAATTTAGAATGGAA-GTC
* * *
446861 ATAGTTTGGGGATGAAATCAAAATGTTC-AAAAGTATAAGGACTAATTTAGATTGGTAGTC
1 ATAGTTT-GGGATGAAATCAAAATGTTCAAAAAGTATAAGGACCAATTTAGAATGGAAGTC
446921 ATAGTTTAGGGATGAAAT
1 ATAGTTT-GGGATGAAAT
446939 TATAATATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
60 47 0.71
61 19 0.29
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (60 bp):
ATAGTTTGGGATGAAATCAAAATGTTCAAAAAGTATAAGGACCAATTTAGAATGGAAGTC
Found at i:446968 original size:60 final size:60
Alignment explanation
Indices: 446801--446969 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 60
446791 GTATATACAT
*** * * *
446801 ATAGTTT-GGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAAGGTC
1 ATAGTTTAGGGATGAAATCAAAATATTC-AAAAGTATAGGGACCAATTTAGAATGAAGGTC
* * * * * *
446861 ATAGTTTGGGGATGAAATCAAAATGTTCAAAAGTATAAGGACTAATTTAGATTGGTA-GTC
1 ATAGTTTAGGGATGAAATCAAAATATTCAAAAGTATAGGGACCAATTTAGAAT-GAAGGTC
* * * * * *
446921 ATAGTTTAGGGATGAAATTATAATATTTACAATTTTAGGGACCAATTTA
1 ATAGTTTAGGGATGAAATCAAAATATTCAAAAGTATAGGGACCAATTTA
446970 AAATCGGTTC
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
60 69 0.78
61 19 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (60 bp):
ATAGTTTAGGGATGAAATCAAAATATTCAAAAGTATAGGGACCAATTTAGAATGAAGGTC
Found at i:448689 original size:14 final size:14
Alignment explanation
Indices: 448670--448715 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
448660 CGTTCGTGAA
448670 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
448684 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
448698 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
448712 CGTT
1 CGTT
448716 TATGTTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:448712 original size:24 final size:24
Alignment explanation
Indices: 448685--448735 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
448675 GGTTATGTTC
*
448685 GTTCGGTTATGTTCGTTCGA-TTAT
1 GTTCGGTTATGTTCATTC-ATTTAT
*
448709 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCATTTAT
448733 GTT
1 GTT
448736 TAACCCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCATTTAT
Found at i:448733 original size:38 final size:34
Alignment explanation
Indices: 448647--448735 Score: 88
Period size: 38 Copynumber: 2.5 Consensus size: 34
448637 CATAGGTCTC
*
448647 GTTCATTCATTTACGTTCGTGAACGTTCGGTTAT
1 GTTCATTCATTTATGTTCGTGAACGTTCGGTTAT
* ** * *
448681 GTTCGTTCGGTTATGTTCGTTCGATTATGTTCGTTTAT
1 GTTCATTCATTTATGTTCG-T-GA--ACGTTCGGTTAT
448719 GTTCATTCATTTATGTT
1 GTTCATTCATTTATGTT
448736 TAACCCAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
34 15 0.36
35 1 0.02
36 2 0.05
38 24 0.57
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (34 bp):
GTTCATTCATTTATGTTCGTGAACGTTCGGTTAT
Found at i:449377 original size:16 final size:16
Alignment explanation
Indices: 449356--449406 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
449346 GTCTCCAACG
449356 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
449372 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
449388 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
449402 TTTAT
1 TTTAT
449407 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:477081 original size:2 final size:2
Alignment explanation
Indices: 477074--477124 Score: 68
Period size: 2 Copynumber: 25.5 Consensus size: 2
477064 TTACTTTGAG
*
477074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA -A TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
*
477116 AA TA TA TA T
1 TA TA TA TA T
477125 CCCCTATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:490028 original size:16 final size:17
Alignment explanation
Indices: 489998--490032 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
489988 TATCGCCGAC
489998 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
490015 CGAAATTT-ACTATTCA
1 CGAAATTTCACTATTCA
490031 CG
1 CG
490033 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:495416 original size:2 final size:2
Alignment explanation
Indices: 495409--495462 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
495399 CAATCAGCAG
495409 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
495451 AT AT AT AT AT AT
1 AT AT AT AT AT AT
495463 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:503852 original size:42 final size:42
Alignment explanation
Indices: 503791--503880 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
503781 CATCCCAAGT
*
503791 GATAGGGCCACCGAACAACAATACCTTCAAACGACCAGAGGA
1 GATAGAGCCACCGAACAACAATACCTTCAAACGACCAGAGGA
* *
503833 GATAGAGCCACCGACCAACAATACCTTGAAACGACCAGAGGA
1 GATAGAGCCACCGAACAACAATACCTTCAAACGACCAGAGGA
*
503875 AATAGA
1 GATAGA
503881 AACAGGAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.42, C:0.27, G:0.21, T:0.10
Consensus pattern (42 bp):
GATAGAGCCACCGAACAACAATACCTTCAAACGACCAGAGGA
Found at i:505336 original size:17 final size:17
Alignment explanation
Indices: 505300--505345 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
505290 GGACCGGATA
* *
505300 AATTTATTATTTTAGAG
1 AATTTATTAATTTACAG
*
505317 AATTTATTAATTTACCG
1 AATTTATTAATTTACAG
505334 AA--TATTAATTTA
1 AATTTATTAATTTA
505346 AAGAGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 10 0.38
17 16 0.62
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (17 bp):
AATTTATTAATTTACAG
Found at i:509667 original size:15 final size:16
Alignment explanation
Indices: 509635--509667 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
509625 AAAATCTTTC
509635 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
509651 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
509666 TT
1 TT
509668 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:525925 original size:13 final size:13
Alignment explanation
Indices: 525907--525932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525897 CTGGTTAATA
525907 ATCTGTTATGCTG
1 ATCTGTTATGCTG
525920 ATCTGTTATGCTG
1 ATCTGTTATGCTG
525933 TTATGAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
ATCTGTTATGCTG
Found at i:533343 original size:24 final size:25
Alignment explanation
Indices: 533315--533363 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
533305 GAAGCTATAT
*
533315 TAAAATTTTA-AGGGTGTGAAATTA
1 TAAAATTTGAGAGGGTGTGAAATTA
*
533339 TAAAATTTGAGGGGGTGTGAAATTA
1 TAAAATTTGAGAGGGTGTGAAATTA
533364 AATTATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (25 bp):
TAAAATTTGAGAGGGTGTGAAATTA
Found at i:533365 original size:23 final size:22
Alignment explanation
Indices: 533313--533365 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
533303 AAGAAGCTAT
*
533313 ATTAAAATTTTAAGGGTGTGAA
1 ATTAAAATTTGAAGGGTGTGAA
*
533335 ATTATAAAATTTGAGGGGGTGTGAA
1 A-T-TAAAATTTGA-AGGGTGTGAA
533360 ATTAAA
1 ATTAAA
533366 TTATCAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 5 0.19
24 10 0.38
25 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.34
Consensus pattern (22 bp):
ATTAAAATTTGAAGGGTGTGAA
Found at i:536248 original size:41 final size:41
Alignment explanation
Indices: 536203--536319 Score: 143
Period size: 43 Copynumber: 2.9 Consensus size: 41
536193 GAATATATAA
*
536203 ATATTTTAAATAATTAAAATAATATTTTATAATCA-TTTATT
1 ATATTTTAAATAATTAAAATAATATTTTATAAT-ATTTTACT
**
536244 ATATTTTAAATTTTTAAAATAATATATTTTATAATATTTTACT
1 ATATTTTAAATAATTAAAAT-A-ATATTTTATAATATTTTACT
*
536287 ATATTTT-AATAATT-AAATAATATATT-TAATATT
1 ATATTTTAAATAATTAAAATAATATTTTATAATATT
536320 ATAAAAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
38 7 0.10
39 6 0.09
40 1 0.01
41 22 0.33
42 7 0.10
43 24 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (41 bp):
ATATTTTAAATAATTAAAATAATATTTTATAATATTTTACT
Found at i:536251 original size:10 final size:10
Alignment explanation
Indices: 536221--536299 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 10
536211 AATAATTAAA
536221 ATAATATTTT
1 ATAATATTTT
536231 ATAATCA-TTT
1 ATAAT-ATTTT
*
536241 ATTATATTTT
1 ATAATATTTT
536251 A-AAT-TTTT
1 ATAATATTTT
*
536259 A-AA-A--TA
1 ATAATATTTT
536265 AT-ATATTTT
1 ATAATATTTT
536274 ATAATATTTT
1 ATAATATTTT
536284 ACT-ATATTTT
1 A-TAATATTTT
536294 AATAAT
1 -ATAAT
536300 TAAATAATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 21
0.68 0.05 0.27
Matches are distributed among these distances:
6 3 0.06
7 1 0.02
8 7 0.13
9 6 0.11
10 32 0.59
11 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (10 bp):
ATAATATTTT
Found at i:536290 original size:43 final size:43
Alignment explanation
Indices: 536203--536313 Score: 151
Period size: 41 Copynumber: 2.7 Consensus size: 43
536193 GAATATATAA
*
536203 ATATTTTAAATAATTAAAAT-A-ATATTTTATAATCATTTATT
1 ATATTTTAAATAATTAAAATAATATATTTTATAATCATTTACT
**
536244 ATATTTTAAATTTTTAAAATAATATATTTTATAAT-ATTTTACT
1 ATATTTTAAATAATTAAAATAATATATTTTATAATCA-TTTACT
536287 ATATTTT-AATAATT-AAATAATATATTT
1 ATATTTTAAATAATTAAAATAATATATTT
536314 AATATTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 31 0.50
42 7 0.11
43 24 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (43 bp):
ATATTTTAAATAATTAAAATAATATATTTTATAATCATTTACT
Found at i:536328 original size:20 final size:21
Alignment explanation
Indices: 536286--536328 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
536276 AATATTTTAC
*
536286 TATATTTTAATAATTAAATAA
1 TATATTTTAATAATTAAAAAA
536307 TATA-TTTAAT-ATTATAAAAA
1 TATATTTTAATAATTA-AAAAA
536327 TA
1 TA
536329 AAAATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATATTTTAATAATTAAAAAA
Found at i:536546 original size:29 final size:29
Alignment explanation
Indices: 536503--536568 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
536493 AACCATCCCT
* *
536503 ACTCTTAAACACTAAAATTTAAATATTTAA
1 ACTCTAAAACACTAAAATATAAAT-TTTAA
* *
536533 AC-CTAAAACTCTAACATATAAATTTTAA
1 ACTCTAAAACACTAAAATATAAATTTTAA
536561 ACTCTAAA
1 ACTCTAAA
536569 TCTTATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 22 0.71
30 2 0.06
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (29 bp):
ACTCTAAAACACTAAAATATAAATTTTAA
Found at i:536562 original size:21 final size:23
Alignment explanation
Indices: 536538--536584 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
536528 TTTAAACCTA
536538 AAACTCT-AA-CATATAAATTTT
1 AAACTCTAAATCATATAAATTTT
*
536559 AAACTCTAAATCTTATAAATTTT
1 AAACTCTAAATCATATAAATTTT
536582 AAA
1 AAA
536585 ATATTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 2 0.09
23 14 0.61
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (23 bp):
AAACTCTAAATCATATAAATTTT
Found at i:536597 original size:24 final size:23
Alignment explanation
Indices: 536549--536597 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
536539 AACTCTAACA
*
536549 TATAAATTTTAAACTCTAAATCT
1 TATAAATTTTAAAATCTAAATCT
*
536572 TATAAATTTTAAAATATTAAATCT
1 TATAAATTTTAAAAT-CTAAATCT
536596 TA
1 TA
536598 ATTAAGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAAATTTTAAAATCTAAATCT
Found at i:541150 original size:17 final size:17
Alignment explanation
Indices: 541128--541166 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
541118 AGTGCAGAGC
541128 CATCCAACAAATCTCAT
1 CATCCAACAAATCTCAT
*
541145 CATCCAACGAATCTCAT
1 CATCCAACAAATCTCAT
541162 CATCC
1 CATCC
541167 CAGCATCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.38, G:0.03, T:0.23
Consensus pattern (17 bp):
CATCCAACAAATCTCAT
Found at i:543210 original size:20 final size:21
Alignment explanation
Indices: 543171--543213 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
543161 GGGTTTATAA
**
543171 AATTTTAAGAAATGAACTTAT
1 AATTTTAAGAAAAAAACTTAT
543192 AATTTTAA-AAAAAAACTTAT
1 AATTTTAAGAAAAAAACTTAT
543212 AA
1 AA
543214 AATTTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
AATTTTAAGAAAAAAACTTAT
Found at i:543220 original size:22 final size:22
Alignment explanation
Indices: 543165--543225 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
543155 GAAAATGGGT
**
543165 TTATAAAATTTTAAGAAATGAAC
1 TTATAAAATTTTAA-AAAAAAAC
543188 TTAT--AATTTTAAAAAAAAAC
1 TTATAAAATTTTAAAAAAAAAC
*
543208 TTATAAAATTTTAGAAAA
1 TTATAAAATTTTAAAAAA
543226 TGAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 10 0.30
21 8 0.24
22 11 0.33
23 4 0.12
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATAAAATTTTAAAAAAAAAC
Found at i:543258 original size:10 final size:9
Alignment explanation
Indices: 543246--543284 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
543236 ATTTTAATTA
543246 AAAATATTT
1 AAAATATTT
543255 AAAA-ATTT
1 AAAATATTT
*
543263 AAAATATAT
1 AAAATATTT
543272 AAAA-ATTT
1 AAAATATTT
543280 AAAAT
1 AAAAT
543285 TTATAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 15 0.58
9 11 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATATTT
Found at i:543261 original size:17 final size:17
Alignment explanation
Indices: 543241--543294 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
543231 ATAAAATTTT
* *
543241 AATTAAAAATATTTAAA
1 AATTTAAAATATATAAA
543258 AATTTAAAATATATAAA
1 AATTTAAAATATATAAA
*
543275 AATTTAAAATTTATAGAA
1 AATTTAAAATATATA-AA
543293 AA
1 AA
543295 ACGGCTGCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 29 0.88
18 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTAAAATATATAAA
Found at i:543264 original size:8 final size:8
Alignment explanation
Indices: 543241--543287 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 8
543231 ATAAAATTTT
*
543241 AATTAAAA
1 AATTTAAA
543249 ATATTTAAA
1 A-ATTTAAA
543258 AATTTAAA
1 AATTTAAA
*
543266 ATATATAAA
1 A-ATTTAAA
543275 AATTT-AA
1 AATTTAAA
543282 AATTTA
1 AATTTA
543288 TAGAAAAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 12 0.36
9 14 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATTTAAA
Found at i:545374 original size:16 final size:17
Alignment explanation
Indices: 545343--545375 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
545333 TGAAATTTGA
*
545343 TATTTTTTTATATTAAT
1 TATTTATTTATATTAAT
545360 TATTTATTT-TATTAAT
1 TATTTATTTATATTAAT
545376 AATATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATATTAAT
Found at i:545381 original size:18 final size:17
Alignment explanation
Indices: 545342--545383 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
545332 TTGAAATTTG
*
545342 ATATTT-TTTTATATTA
1 ATATTTATTTTATAATA
545358 ATTATTTATTTTATTAATA
1 A-TATTTATTTTA-TAATA
545377 ATATTTA
1 ATATTTA
545384 ATCTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 5 0.23
18 11 0.50
19 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTATTTTATAATA
Found at i:547545 original size:27 final size:27
Alignment explanation
Indices: 547511--547569 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
547501 AACAAAGGGT
547511 AAAC-TACACATTTAGTATCTCAACTA
1 AAACTTACACATTTAGTATCTCAACTA
547537 AAACTTACACATTTAGTATCTCAACTA
1 AAACTTACACATTTAGTATCTCAACTA
547564 AAACTT
1 AAACTT
547570 TTATTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.32
Consensus pattern (27 bp):
AAACTTACACATTTAGTATCTCAACTA
Found at i:555055 original size:34 final size:38
Alignment explanation
Indices: 554991--555084 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 38
554981 CCTCCTCCTC
* * *
554991 CTTCAAGAGCTTAAACTCATA-ATTGGTTC-T-TT-TT
1 CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT
*
555025 CTTCAAGAACTTAAACCCATAGCTT-ATTCTTCTTCTT
1 CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT
555062 CTTC-AGAAGCTTAAACTCATAGC
1 CTTCAAGAA-CTTAAACTCATAGC
555085 AATTAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 22 0.44
35 3 0.06
36 6 0.12
37 19 0.38
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (38 bp):
CTTCAAGAACTTAAACTCATAGCTTGATTCTTCTTCTT
Found at i:569166 original size:60 final size:60
Alignment explanation
Indices: 569053--569167 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
569043 AATGACCATT
* * * * * *
569053 TTGTAACTTTTAATAGTCGAGGGACTCAATAAATCAACACCCTATAATTAGATGATAAGG
1 TTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCATATAATCAGATGATAAGG
* * * *
569113 TTGTAACTTTTAATTGTCAATAGACTCAACAAAGCAACACCATGTAGTCAGATGA
1 TTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCATATAATCAGATGA
569168 CCATTTGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (60 bp):
TTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACACCATATAATCAGATGATAAGG
Found at i:591114 original size:34 final size:33
Alignment explanation
Indices: 591071--591161 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 33
591061 ATAGCGCTGC
591071 CATTGAACCATAGCCAAGCCGTACTCGTAAAGTT
1 CATTGAACCATA-CCAAGCCGTACTCGTAAAGTT
*
591105 CATTGAACCATCACCAAGCCGTACTTGTAAAGTT
1 CATTGAACCAT-ACCAAGCCGTACTCGTAAAGTT
*
591139 CATTGAATCATTACCAAGCCGTA
1 CATTGAACCA-TACCAAGCCGTA
591162 TTGGTGAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
34 51 0.96
35 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (33 bp):
CATTGAACCATACCAAGCCGTACTCGTAAAGTT
Found at i:593073 original size:60 final size:60
Alignment explanation
Indices: 592980--593095 Score: 205
Period size: 60 Copynumber: 1.9 Consensus size: 60
592970 AAAACAACAA
* *
592980 AGAATGAGATAAGGAAAATGCAACTTATGCGTCCACAACTAGCAGGAAGATACATATGAG
1 AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATATGAG
*
593040 AGAATGAAATAGGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATA
1 AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATA
593096 CTTGCAAAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (60 bp):
AGAATGAAATAAGGAAAATGCAACTTATGCGTCCACAACAAGCAGGAAGATACATATGAG
Found at i:597992 original size:15 final size:15
Alignment explanation
Indices: 597972--598005 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
597962 AAGATATCCC
*
597972 ACGACAACGATGATG
1 ACGACAACGAAGATG
597987 ACGACAACGAAGATG
1 ACGACAACGAAGATG
598002 ACGA
1 ACGA
598006 AAATATGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (15 bp):
ACGACAACGAAGATG
Found at i:612000 original size:6 final size:6
Alignment explanation
Indices: 611989--612015 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
611979 ATCAGGGTTT
611989 ATAGGG ATAGGG ATAGGG ATAGGG ATA
1 ATAGGG ATAGGG ATAGGG ATAGGG ATA
612016 TGTAGTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (6 bp):
ATAGGG
Found at i:612485 original size:20 final size:20
Alignment explanation
Indices: 612449--612486 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
612439 TACGAATAAT
*
612449 CTCGTTTATAAATTTATTAA
1 CTCGTTTATAAACTTATTAA
*
612469 CTCGTTTATTAACTTATT
1 CTCGTTTATAAACTTATT
612487 TATCTGATTT
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:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (20 bp):
CTCGTTTATAAACTTATTAA
Found at i:614898 original size:87 final size:86
Alignment explanation
Indices: 614731--614957 Score: 255
Period size: 87 Copynumber: 2.6 Consensus size: 86
614721 TGTGAAATAA
* * * ** *
614731 AAACGCCGCAAAAAGTCAAGTTCTATAGCGGCGTTTTTGAAACAAACATCGCAAAAGGTTGAGAT
1 AAACGCCGCAAAAAGTCAA-ATCTATAGCGGCGTTTTCGATACAAACGCCGCAAAAGGTTCAGAT
*
614796 CTATAGTGGTGTTTTTATT-TCAC
65 CTATAGCGGTGTTTTT-TTAT-AC
* *
614819 AAACGCCGCAAAATA-TCAAATCTATAGCGGCGATTTTGGATACAAACGCCGCAAAATG-TCAGA
1 AAACGCCGCAAAA-AGTCAAATCTATAGCGGCG-TTTTCGATACAAACGCCGCAAAAGGTTCAGA
614882 TCTATAGCGG-GATTTTTTTGATAC
64 TCTATAGCGGTG-TTTTTTT-ATAC
* *
614906 AAACGCCGCAAAAAGTCAAATCTATAACGGCGTTTTTCAATACAAACGCCGC
1 AAACGCCGCAAAAAGTCAAATCTATAGCGGCG-TTTTCGATACAAACGCCGC
614958 TAATTACCAT
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
86 4 0.03
87 78 0.64
88 38 0.31
89 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (86 bp):
AAACGCCGCAAAAAGTCAAATCTATAGCGGCGTTTTCGATACAAACGCCGCAAAAGGTTCAGATC
TATAGCGGTGTTTTTTTATAC
Found at i:614918 original size:44 final size:43
Alignment explanation
Indices: 614731--614957 Score: 210
Period size: 43 Copynumber: 5.2 Consensus size: 43
614721 TGTGAAATAA
* *
614731 AAACGCCGCAAAAAGTCAAGTTCTATAGCGGCG-TTTTTGAAAC
1 AAACGCCGCAAAAAGTC-AGATCTATAGCGGCGTTTTTTGATAC
** * * * * *
614774 AAACATCGCAAAAGGTTGAGATCTATAGTGGTGTTTTTAT-TTCAC
1 AAACGCCGCAAAAAG-TCAGATCTATAGCGGCGTTTTT-TGAT-AC
* * *
614819 AAACGCCGCAAAATA-TCAAATCTATAGCGGCGATTTTGGATAC
1 AAACGCCGCAAAA-AGTCAGATCTATAGCGGCGTTTTTTGATAC
*
614862 AAACGCCGCAAAATGTCAGATCTATAGCGG-GATTTTTTTGATAC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCG--TTTTTTGATAC
* * **
614906 AAACGCCGCAAAAAGTCAAATCTATAACGGCGTTTTTCAATAC
1 AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTGATAC
614949 AAACGCCGC
1 AAACGCCGC
614958 TAATTACCAT
Statistics
Matches: 146, Mismatches: 28, Indels: 20
0.75 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 71 0.49
44 59 0.40
45 15 0.10
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAAGTCAGATCTATAGCGGCGTTTTTTGATAC
Found at i:616556 original size:82 final size:82
Alignment explanation
Indices: 616419--616582 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
616409 GCTTGTCAAG
*
616419 GAATGTGATGAGGAAAGAGTAGGTGTAGAATCTCTTGCTATGGATGCAAGAAGTGGAAGCCTATT
1 GAATGTAATGAGGAAAGAGTAGGTGTAGAATCTCTTGCTATGGATGCAAGAAGTGGAAGCCTATT
616484 GGAAGACGATGGGAGTT
66 GGAAGACGATGGGAGTT
616501 GAATGTAATGAGGAAAGAGTAGGTGTAGAATCTCTTGCTATGGATGCAAGAAGTGGAAGCCTATT
1 GAATGTAATGAGGAAAGAGTAGGTGTAGAATCTCTTGCTATGGATGCAAGAAGTGGAAGCCTATT
616566 GGAAGACGATGGGAGTT
66 GGAAGACGATGGGAGTT
616583 TAGCTTTTGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.32, C:0.09, G:0.35, T:0.24
Consensus pattern (82 bp):
GAATGTAATGAGGAAAGAGTAGGTGTAGAATCTCTTGCTATGGATGCAAGAAGTGGAAGCCTATT
GGAAGACGATGGGAGTT
Found at i:627522 original size:23 final size:22
Alignment explanation
Indices: 627495--627544 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
627485 AAATTTATTT
627495 ATAAAATTTT-AATAAAAACAAA
1 ATAAAATTTTCAATAAAAA-AAA
*
627517 A-ATAAATTTTCAATATAAAAAA
1 ATA-AAATTTTCAATAAAAAAAA
627539 ATAAAA
1 ATAAAA
627545 GGAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAAATTTTCAATAAAAAAAA
Found at i:628353 original size:20 final size:19
Alignment explanation
Indices: 628330--628375 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
628320 GATATACCAT
628330 GTAAAAATATGATAAAACCG
1 GTAAAAA-ATGATAAAACCG
628350 GTAACAAAATGATAAAACCG
1 GTAA-AAAATGATAAAACCG
628370 GTAAAA
1 GTAAAA
628376 CGTTTCCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (19 bp):
GTAAAAAATGATAAAACCG
Found at i:628463 original size:181 final size:181
Alignment explanation
Indices: 628117--628589 Score: 662
Period size: 181 Copynumber: 2.6 Consensus size: 181
628107 GTTCCAAATT
* * ** *
628117 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGATAAAACCGGTATTGAAATAATA
1 AAAAATGTATCGATCCAAAACGATATAACA-GTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
628182 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATAGACACTTC
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATAGACACTTC
* *
628247 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGAC-ACTTTTA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCG-CTACTTTAA
* *
628299 AAAAATGTATCGATCCAAAACGATATACCATGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACA-GTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
628364 AAACCGGTAAAACGTTTCCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATAGACACTTC
* ** *
628428 GTGAATTTAAAAGAGAATCAGTTTTAGCGCCTATAATGTGTCGCTACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGCTACTTTAA
* *
628480 AAAAATATATCGATCCACAACGATATAACAGATAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAG-TAAAAATATGATAAAACCGGTATCAAAATGATA
* *
628545 AAACCGATAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
628590 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
180 2 0.01
181 161 0.62
182 96 0.37
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGTAAAAATATGATAAAACCGGTATCAAAATGATAA
AACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATAGACACTTCG
TGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGCTACTTTAA
Found at i:628558 original size:17 final size:20
Alignment explanation
Indices: 628519--628561 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
628509 AGATAAAAAT
628519 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGGTATCAAA
628539 ATGATAAAACC-G-AT-AAA
1 ATGATAAAACCGGTATCAAA
628556 ATGATA
1 ATGATA
628562 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 1 0.04
20 11 0.48
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (20 bp):
ATGATAAAACCGGTATCAAA
Found at i:630676 original size:17 final size:17
Alignment explanation
Indices: 630654--630687 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
630644 ATGGTTGTAT
*
630654 TGGGGGATGACGGTGAG
1 TGGGGGACGACGGTGAG
630671 TGGGGGACGACGGTGAG
1 TGGGGGACGACGGTGAG
630688 GGAAACATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.59, T:0.15
Consensus pattern (17 bp):
TGGGGGACGACGGTGAG
Found at i:630804 original size:21 final size:21
Alignment explanation
Indices: 630769--630832 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
630759 AATACAATCA
*
630769 AGAGTCGAA-AGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
630789 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
630810 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
630831 AG
1 AG
630833 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 9 0.22
21 31 0.77
ACGTcount: A:0.42, C:0.11, G:0.30, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:630908 original size:33 final size:33
Alignment explanation
Indices: 630866--630931 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
630856 AAATAGATGG
*
630866 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
630899 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
630932 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:631929 original size:21 final size:21
Alignment explanation
Indices: 631891--631953 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
631881 AATACAATCA
*
631891 AGAGTCGAAGAG-AACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
631911 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
631932 AGAG-CGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
631952 AG
1 AG
631954 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 28 0.72
21 11 0.28
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:634403 original size:23 final size:23
Alignment explanation
Indices: 634372--634435 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
634362 ATAGGTAAAA
*
634372 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
634395 ATATAATGTAATAGATAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
634418 ATATAATGTAATAAGTAG
1 ATATAATGTAATAGGTAG
634436 TGTTTAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:634887 original size:23 final size:23
Alignment explanation
Indices: 634856--634928 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
634846 ATAGGTAAAA
*
634856 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
634879 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
634902 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
634925 ATAT
1 ATAT
634929 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:635062 original size:484 final size:490
Alignment explanation
Indices: 634029--635827 Score: 3192
Period size: 491 Copynumber: 3.7 Consensus size: 490
634019 AGGTATGTAC
* *
634029 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATGATTTA-TTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
634093 GTTACGG--TATA-TATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
634155 TTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
* * *
634220 ATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
634285 AAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
*
634349 CACTTTCAATATTATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGATAGC
326 CACTTTCAATA-TATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
* * *
634414 GTTTATATAATGTAATAAGTAGTGTTTAGATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCA
390 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCA
634479 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
634515 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
634580 GTTACGGTATATATTATTATTAAATT-AAAAC-A-AAACATATAT-TTACAT-TTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
634640 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
* * *
634705 ATTTTTTGGGCAAATAAAAATATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAA
196 ATTTTTTGTGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
634770 AAAATTGAAACATAAATTACATAACTTT-AAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
634834 CACTTTCAATATATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
326 CACTTTCAATATATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
*
634899 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAT
634964 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
*
634999 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
635064 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
635129 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
*
635194 ATTTTTTGCGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
635259 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
*
635324 CACTTTCAATATAATAGATAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
326 CACTTTCAATAT-ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
*
635389 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTACA
390 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCA
*
635454 TATTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
* * * *
635490 ATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAATTATATGTATCTAATGATTTATTTTTTAT
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
* * *
635555 GTTACCGTATATATTATCATTAAATTAAAAACAATAAACATATATATTACACATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
635620 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
* *
635685 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATT--AA
196 ATTTTTTGTGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
* *
635748 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCTTTTTTATAAAAAAGTATAG
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGG
*
635813 ACACTTTCAACATAT
325 ACACTTTCAATATAT
635828 TATAATGTAA
Statistics
Matches: 1264, Mismatches: 37, Indels: 21
0.96 0.03 0.02
Matches are distributed among these distances:
484 239 0.19
485 215 0.17
486 62 0.05
487 34 0.03
488 7 0.01
489 232 0.18
490 82 0.06
491 393 0.31
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (490 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTAC
GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
TTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGCAAATGAAAATATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAACATAAATTACATAACTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
CACTTTCAATATATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAT
ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:635378 original size:23 final size:23
Alignment explanation
Indices: 635347--635419 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
635337 ATAGATAAAA
*
635347 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
635370 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
635393 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
635416 ATAT
1 ATAT
635420 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:636412 original size:85 final size:85
Alignment explanation
Indices: 636269--636432 Score: 247
Period size: 85 Copynumber: 1.9 Consensus size: 85
636259 AAAAAGACCT
* * * * * * * * *
636269 TTAAATTTTAATTTTATCATTGATCTATAATATTTTGTTTGTTTTTTTATTGTTACAATGGTAAT
1 TTAAATCTCAATTTTACCATTGATCCATAATACTTTATTTGCTTTTTTATTGTAACAATAGTAAT
636334 AAATCTAATTTTTTAGGCCC
66 AAATCTAATTTTTTAGGCCC
636354 TTAAATCTCAATTTTACCATTGATCCATAATACTTTATTTGCTTTTTTATTGTAACAATAGTAAT
1 TTAAATCTCAATTTTACCATTGATCCATAATACTTTATTTGCTTTTTTATTGTAACAATAGTAAT
636419 AAATCTAATTTTTT
66 AAATCTAATTTTTT
636433 GAAACCCTCG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (85 bp):
TTAAATCTCAATTTTACCATTGATCCATAATACTTTATTTGCTTTTTTATTGTAACAATAGTAAT
AAATCTAATTTTTTAGGCCC
Found at i:639313 original size:20 final size:20
Alignment explanation
Indices: 639276--639313 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
639266 ATTTTTATTG
*
639276 ATTTTTTATATCATTAATTA
1 ATTTTTTATAACATTAATTA
639296 ATTTTTTA-AACATATAAT
1 ATTTTTTATAACAT-TAAT
639314 ATATTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTTTATAACATTAATTA
Found at i:640321 original size:29 final size:30
Alignment explanation
Indices: 640247--640331 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
640237 CGAATATAGA
640247 TCGCCAGGTGATCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
640277 TCGCCAGGTGATCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
*
640307 T-GCCAGGTGGTCTGGGCGACCAATG
1 TCGCCAGGTGATCTGGGCGACCAATG
640332 TTGGGCGGCG
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 23 0.43
30 31 0.57
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.18
Consensus pattern (30 bp):
TCGCCAGGTGATCTGGGCGACCAATGAAGG
Found at i:640988 original size:50 final size:50
Alignment explanation
Indices: 640927--641028 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
640917 AAAATTATTG
640927 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
640977 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
641027 AA
1 AA
641029 ATAGGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:646017 original size:27 final size:27
Alignment explanation
Indices: 645986--646060 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
645976 CTGTTTGCAG
645986 TATATCGTCGAACCAATGCTTGAACAT
1 TATATCGTCGAACCAATGCTTGAACAT
* *
646013 TATATCGCCGAACCAATGCTTGAATAT
1 TATATCGTCGAACCAATGCTTGAACAT
* *
646040 TATGTTGTCGAACCAATGCTT
1 TATATCGTCGAACCAATGCTT
646061 AAAAGTAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (27 bp):
TATATCGTCGAACCAATGCTTGAACAT
Found at i:646281 original size:17 final size:17
Alignment explanation
Indices: 646259--646293 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
646249 GGAGGACCAT
646259 TTGTGTATTTTATTATC
1 TTGTGTATTTTATTATC
646276 TTGTGTATTTTATTATC
1 TTGTGTATTTTATTATC
646293 T
1 T
646294 AGTAAGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (17 bp):
TTGTGTATTTTATTATC
Found at i:646348 original size:3 final size:3
Alignment explanation
Indices: 646340--646369 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
646330 TTAAAAATAA
646340 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
646370 GGTAGAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:652576 original size:71 final size:72
Alignment explanation
Indices: 652487--652627 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 72
652477 ATTCAATAAT
*
652487 GCTTTTACTCTTTTCTTTAAGTTTTCTTAGGCTTTTCTTGGTATGATTCTTTCATGCATAAACTT
1 GCTTTTACTCTTTTCTTTAAGTTTTCTTACGCTTTTCTTGGTATGATTCTTTCATGCATAAACTT
652552 TTCTTAG
66 TTCTTAG
*
652559 GCTTTTACTC-TTTCTTTAAGTTTTCTTACGCTTTTCTTGGTATGATTCTTTCATGCATTAACTT
1 GCTTTTACTCTTTTCTTTAAGTTTTCTTACGCTTTTCTTGGTATGATTCTTTCATGCATAAACTT
652623 TTCTT
66 TTCTT
652628 GGTATGATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 57 0.85
72 10 0.15
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (72 bp):
GCTTTTACTCTTTTCTTTAAGTTTTCTTACGCTTTTCTTGGTATGATTCTTTCATGCATAAACTT
TTCTTAG
Found at i:659684 original size:2 final size:2
Alignment explanation
Indices: 659679--659725 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
659669 TAGATGTGTG
659679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
659721 TA TA T
1 TA TA T
659726 GTGAAATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:667558 original size:63 final size:63
Alignment explanation
Indices: 667477--667596 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
667467 TCGGAATCAA
** * * *
667477 ACAAACAATGAATGACATTGATGAAAATGGAAAAATAAATATAATTTTTCGAACATTGAAGTT
1 ACAAACAAAAAATAACATTAATGAAAATGGAAAAATAAATATAATTTTTCAAACATTGAAGTT
* ** *
667540 ACAAACAAAAAATAACATTAATGAAAATGGGAAAATGGATATCATTTTTCAAACATT
1 ACAAACAAAAAATAACATTAATGAAAATGGAAAAATAAATATAATTTTTCAAACATT
667597 TAAGCAATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (63 bp):
ACAAACAAAAAATAACATTAATGAAAATGGAAAAATAAATATAATTTTTCAAACATTGAAGTT
Found at i:671917 original size:13 final size:13
Alignment explanation
Indices: 671899--671924 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
671889 CAAGGTTCTT
671899 AACCTTGAGGTCG
1 AACCTTGAGGTCG
671912 AACCTTGAGGTCG
1 AACCTTGAGGTCG
671925 TGTGATCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
AACCTTGAGGTCG
Found at i:681500 original size:22 final size:19
Alignment explanation
Indices: 681439--681525 Score: 90
Period size: 19 Copynumber: 4.5 Consensus size: 19
681429 AATCTTATTT
681439 AATTTT-TTATTTTAAATA
1 AATTTTATTATTTTAAATA
*
681457 AATCTTATTATTTT-AATGA
1 AATTTTATTATTTTAAAT-A
681476 AATTTTGAAATTATTTTAAATA
1 AATTTT---ATTATTTTAAATA
681498 AATTATTATTATTTT-AATA
1 AATT-TTATTATTTTAAATA
*
681517 AATCTTATT
1 AATTTTATT
681526 TAATTTTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
18 13 0.22
19 20 0.34
20 8 0.14
22 13 0.22
23 5 0.08
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTATTATTTTAAATA
Done.