Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:841990 original size:31 final size:31
Alignment explanation
Indices: 841955--842013 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
841945 TAAAAAATGA
* *
841955 AAAAAATAGAATACTAAAAATTAAAAGGAAT
1 AAAAAATAAAATAATAAAAATTAAAAGGAAT
* * *
841986 AAAAATTAAAATAATAGAAATTTAAAGG
1 AAAAAATAAAATAATAAAAATTAAAAGG
842014 TAAAATGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (31 bp):
AAAAAATAAAATAATAAAAATTAAAAGGAAT
Found at i:842001 original size:15 final size:15
Alignment explanation
Indices: 841964--842007 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
841954 AAAAAAATAG
*
841964 AATACTAAAAATTAA
1 AATAATAAAAATTAA
*
841979 AAGGAATAAAAATTAA
1 AA-TAATAAAAATTAA
*
841995 AATAATAGAAATT
1 AATAATAAAAATT
842008 TAAAGGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (15 bp):
AATAATAAAAATTAA
Found at i:846070 original size:14 final size:14
Alignment explanation
Indices: 846051--846080 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
846041 TCCTTGCAAG
846051 GTAGGAACTCTGTT
1 GTAGGAACTCTGTT
846065 GTAGGAACTCTGTT
1 GTAGGAACTCTGTT
846079 GT
1 GT
846081 TTGTTGCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (14 bp):
GTAGGAACTCTGTT
Found at i:854388 original size:12 final size:12
Alignment explanation
Indices: 854371--854437 Score: 66
Period size: 12 Copynumber: 5.6 Consensus size: 12
854361 GTGTGTTTAG
854371 TGGACTGATTGA
1 TGGACTGATTGA
*
854383 TGGACT-ATTTA
1 TGGACTGATTGA
854394 GTGGACTGATTGA
1 -TGGACTGATTGA
*
854407 TGGACTG-TTTA
1 TGGACTGATTGA
* *
854418 GTGGACTTATTGG
1 -TGGACTGATTGA
854431 TGGACTG
1 TGGACTG
854438 TTCATTGAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
11 7 0.16
12 31 0.70
13 6 0.14
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.37
Consensus pattern (12 bp):
TGGACTGATTGA
Found at i:854437 original size:24 final size:24
Alignment explanation
Indices: 854364--854439 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
854354 GTGTTTGGTG
854364 TGTTTAGTGGACTGATTGATGGAC
1 TGTTTAGTGGACTGATTGATGGAC
*
854388 TATTTAGTGGACTGATTGATGGAC
1 TGTTTAGTGGACTGATTGATGGAC
* *
854412 TGTTTAGTGGACTTATTGGTGGAC
1 TGTTTAGTGGACTGATTGATGGAC
854436 TGTT
1 TGTT
854440 CATTGAGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.41
Consensus pattern (24 bp):
TGTTTAGTGGACTGATTGATGGAC
Found at i:855998 original size:24 final size:24
Alignment explanation
Indices: 855966--856014 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
855956 ATATTGTGGC
855966 CGTTGCCCACTTTGGCCTCTACCT
1 CGTTGCCCACTTTGGCCTCTACCT
855990 CGTTGCCCACTTTGGCCTCTACCT
1 CGTTGCCCACTTTGGCCTCTACCT
856014 C
1 C
856015 TACCACGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.43, G:0.16, T:0.33
Consensus pattern (24 bp):
CGTTGCCCACTTTGGCCTCTACCT
Found at i:857432 original size:26 final size:26
Alignment explanation
Indices: 857396--857450 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
857386 TTTAATGCCA
857396 GATTGATAATAGTGATGTCTTACCAT
1 GATTGATAATAGTGATGTCTTACCAT
857422 GATTGATAATAGTGATGTCTTACCAT
1 GATTGATAATAGTGATGTCTTACCAT
857448 GAT
1 GAT
857451 CTCTTCAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (26 bp):
GATTGATAATAGTGATGTCTTACCAT
Found at i:865155 original size:23 final size:24
Alignment explanation
Indices: 865129--865189 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
865119 ATTATTTAAA
865129 TTTAATATAAAAA-AT-AATTTATT
1 TTTAATATAAAAATATCAATTT-TT
865152 TTTACAATATAAAAATATCAATTTTT
1 TTT--AATATAAAAATATCAATTTTT
865178 TTATAAT-TAAAA
1 TT-TAATATAAAA
865190 CTAACTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 3 0.09
24 5 0.15
25 13 0.39
26 6 0.18
27 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTAATATAAAAATATCAATTTTT
Found at i:865249 original size:12 final size:11
Alignment explanation
Indices: 865219--865253 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
865209 ATAATAATAA
865219 AATATCATTTAT
1 AATAT-ATTTAT
865231 AATATATTTAT
1 AATATATTTAT
865242 AATAATATTTAT
1 AAT-ATATTTAT
865254 TCAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
AATATATTTAT
Found at i:865824 original size:14 final size:14
Alignment explanation
Indices: 865805--865831 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
865795 ATTTTTTCTT
865805 TTAAAATTATTTTC
1 TTAAAATTATTTTC
865819 TTAAAATTATTTT
1 TTAAAATTATTTT
865832 AAAATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:871001 original size:28 final size:28
Alignment explanation
Indices: 870962--871016 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
870952 TCAAATTTTA
* *
870962 AAATATTTTTTAT-TTTTTAAAAAAATT
1 AAATATTCTTTATACTTTTAAAAAAATT
870989 AAATAATTCTTTATACTTTTAAAAAAAT
1 AAAT-ATTCTTTATACTTTTAAAAAAAT
871017 CAATTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 8 0.33
29 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATATTCTTTATACTTTTAAAAAAATT
Found at i:872043 original size:22 final size:20
Alignment explanation
Indices: 872017--872065 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
872007 ATATTTTTAG
872017 ATTTTAATATAATATAATATTT
1 ATTTTAATATAA-AT-ATATTT
* *
872039 ATTTTATTTTAAATATATTT
1 ATTTTAATATAAATATATTT
872059 ATATTTA
1 AT-TTTA
872066 GAATAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 6 0.25
22 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTAATATAAATATATTT
Found at i:882579 original size:189 final size:187
Alignment explanation
Indices: 882216--882583 Score: 562
Period size: 189 Copynumber: 2.0 Consensus size: 187
882206 AATTTATAAG
* **
882216 TCCTCCGGGTCATCCATAAGACCTTGGGCAGGATGTTTTCACATGTCTATCAAAATATGAGAAAG
1 TCCTCCGGGCCATCCATAAGACCTCAGGCAGGATGTTTTCACATGTCTATCAAAATATGAGAAAG
*
882281 GTTCTCATATTAAATCTGAAAATGAAATTTTGAAAAGTAAGAAAGGTTTCTACCCAATAAACTAT
66 GTTCTCATATTAAATCTGAAAATGAAATTTTGAAAAGTAAGAAAGCTTTCTA-CCAATAAACTAT
* * *
882346 TTCCAAAATTTATAATCCTTCGGGTCATCAGTAAGTCTTTTCGAGCATGTTGCTCAAA
130 TTCCAAAATTCATAATCATTCGGGCCATCAGTAAGTCTTTTCGAGCATGTTGCTCAAA
* *
882404 TCCTTCGGGCCATCCATAAGACCTCAGGCAGGATGTTTTCACATGTCTTTTC-AAATATGAGAAA
1 TCCTCCGGGCCATCCATAAGACCTCAGGCAGGATGTTTTCACATGTC-TATCAAAATATGAGAAA
* *
882468 TGTTTCTCATATTAAATCTGAAATTTGAAATTTTGAAAAGTAAGAAAGCTTTCTTA-CAATAAAC
65 -GGTTCTCATATTAAATCTGAAA-ATGAAATTTTGAAAAGTAAGAAAGCTTTC-TACCAATAAAC
882532 TATTTCCAAAATTCATAAGTCATTCGGGCCATCAGTAAGTC-TTTCGAGCATG
127 TATTTCCAAAATTCATAA-TCATTCGGGCCATCAGTAAGTCTTTTCGAGCATG
882584 ATTTTTAAAT
Statistics
Matches: 164, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
188 55 0.34
189 60 0.37
190 47 0.29
191 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (187 bp):
TCCTCCGGGCCATCCATAAGACCTCAGGCAGGATGTTTTCACATGTCTATCAAAATATGAGAAAG
GTTCTCATATTAAATCTGAAAATGAAATTTTGAAAAGTAAGAAAGCTTTCTACCAATAAACTATT
TCCAAAATTCATAATCATTCGGGCCATCAGTAAGTCTTTTCGAGCATGTTGCTCAAA
Found at i:882984 original size:132 final size:131
Alignment explanation
Indices: 882780--883102 Score: 447
Period size: 132 Copynumber: 2.5 Consensus size: 131
882770 TCAAGATTTG
* * *
882780 ATCTTCCCTGAATAACAGCGGAATGGATCAATTCAT-AATCTGTTATT-CCTTCAGAAGAAGTGG
1 ATCTTCCCTGAATGACAGCGGAAT-GATCAACTCATCAATCTGATATTCCCTTCAGAAGAAGTGG
* *
882843 AACATATCACTCTATTTCAAGATTTGATA-TCCCTGAGTGACAACGGAACAAGTCTACCATGATT
65 AACAGATCACTCTATTTCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCATGATT
882907 CA
130 CA
* * * *
882909 ATCTTCCCTGATTGATAGCGGAATGATCAACTCATCCATATATGATATTCCCTTCAAAAGAAGTG
1 ATCTTCCCTGAATGACAGCGGAATGATCAACTCAT-CA-ATCTGATATTCCCTTCAGAAGAAGTG
* * * *
882974 GAATAGATCACTCTCTTTCAAGATTTGATATTCCCTTAGTGACAGCAGAACAAGTCTACCATGAT
64 GAACAGATCACTCTATTTCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCATGAT
883039 TCA
129 TCA
*
883042 ATCTTCTCT-AAGTGACAGCGGAATGATCAACTCATCAGATCTGATATTCCCTTCAGAAGAA
1 ATCTTCCCTGAA-TGACAGCGGAATGATCAACTCATCA-ATCTGATATTCCCTTCAGAAGAA
883103 CAACATCCCC
Statistics
Matches: 169, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
128 10 0.06
129 21 0.12
130 1 0.01
131 8 0.05
132 65 0.38
133 64 0.38
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (131 bp):
ATCTTCCCTGAATGACAGCGGAATGATCAACTCATCAATCTGATATTCCCTTCAGAAGAAGTGGA
ACAGATCACTCTATTTCAAGATTTGATATTCCCTGAGTGACAACAGAACAAGTCTACCATGATTC
A
Found at i:883064 original size:133 final size:130
Alignment explanation
Indices: 882780--883102 Score: 436
Period size: 133 Copynumber: 2.5 Consensus size: 130
882770 TCAAGATTTG
* * *
882780 ATCTTCCCTGAA-TAACAGCGGAATGGATCAATTCAT-AATCTGTTATT-CCTTCAGAAGAAGTG
1 ATCTTCCCT-AAGTGACAGCGGAAT-GATCAACTCATCAATCTGATATTCCCTTCAGAAGAAGTG
* *
882842 GAACATATCACTCTATTTCAAGATTTGATATCCCTGAGTGACAACGGAACAAGTCTACCATGATT
64 GAACAGATCACTCTATTTCAAGATTTGATATCCCTGAGTGACAACAGAACAAGTCTACCATGATT
882907 CA
129 CA
* * * * *
882909 ATCTTCCCTGATTGATAGCGGAATGATCAACTCATCCATATATGATATTCCCTTCAAAAGAAGTG
1 ATCTTCCCTAAGTGACAGCGGAATGATCAACTCAT-CA-ATCTGATATTCCCTTCAGAAGAAGTG
* * * *
882974 GAATAGATCACTCTCTTTCAAGATTTGATATTCCCTTAGTGACAGCAGAACAAGTCTACCATGAT
64 GAACAGATCACTCTATTTCAAGATTTGATA-TCCCTGAGTGACAACAGAACAAGTCTACCATGAT
883039 TCA
128 TCA
*
883042 ATCTTCTCTAAGTGACAGCGGAATGATCAACTCATCAGATCTGATATTCCCTTCAGAAGAA
1 ATCTTCCCTAAGTGACAGCGGAATGATCAACTCATCA-ATCTGATATTCCCTTCAGAAGAA
883103 CAACATCCCC
Statistics
Matches: 168, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
128 11 0.07
129 19 0.11
130 1 0.01
131 8 0.05
132 64 0.38
133 65 0.39
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (130 bp):
ATCTTCCCTAAGTGACAGCGGAATGATCAACTCATCAATCTGATATTCCCTTCAGAAGAAGTGGA
ACAGATCACTCTATTTCAAGATTTGATATCCCTGAGTGACAACAGAACAAGTCTACCATGATTCA
Found at i:885319 original size:25 final size:25
Alignment explanation
Indices: 885285--885337 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
885275 CTCTTGAGAG
*
885285 TGGGGTTTTATAGAAATCGCATTTA
1 TGGGGTTTTATAGAAATCACATTTA
885310 TGGGGTTTTATAGAAATCACATTTA
1 TGGGGTTTTATAGAAATCACATTTA
885335 TGG
1 TGG
885338 ATTTGAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.40
Consensus pattern (25 bp):
TGGGGTTTTATAGAAATCACATTTA
Found at i:887423 original size:43 final size:45
Alignment explanation
Indices: 887376--887486 Score: 129
Period size: 43 Copynumber: 2.5 Consensus size: 45
887366 GGTAAGTATG
* *
887376 AAAATAAGCTTATGAGCTTATGAA-T-AATGGCAATTATATTGAT
1 AAAATAAGCTTAAGAGCTTATGAATTAAATGGCAAATATATTGAT
* * * *
887419 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAATATTTTGGT
1 AAAATAAGCTTAAGAGCTTAT-GAA-TTAAATGGCAAATATATTGAT
887466 -AAATAAGCTTAAGAGCTTATG
1 AAAATAAGCTTAAGAGCTTATG
887487 GGATAAATGG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
43 20 0.34
44 3 0.05
45 1 0.02
46 20 0.34
47 14 0.24
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (45 bp):
AAAATAAGCTTAAGAGCTTATGAATTAAATGGCAAATATATTGAT
Found at i:887474 original size:46 final size:45
Alignment explanation
Indices: 887376--887499 Score: 146
Period size: 46 Copynumber: 2.8 Consensus size: 45
887366 GGTAAGTATG
* * *
887376 AAAATAAGCTTATGAGCTTAT-GAAT-AATGGCAATTATATTGAT
1 AAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATATATTGAT
* * *
887419 AAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAATATTTTGGT
1 AAAATAAGCTTAAGAGCTTATGGAA--TAAATGGTAAATATATTGAT
*
887466 -AAATAAGCTTAAGAGCTTATGGGATAAATGGTAA
1 AAAATAAGCTTAAGAGCTTATGGAATAAATGGTAA
887500 GAGATTTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
43 20 0.29
44 13 0.19
46 23 0.33
47 14 0.20
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (45 bp):
AAAATAAGCTTAAGAGCTTATGGAATAAATGGTAAATATATTGAT
Found at i:889256 original size:2 final size:2
Alignment explanation
Indices: 889249--889311 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
889239 GTACTTACCC
889249 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
889291 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
889312 ATTGTTGATC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:890201 original size:16 final size:16
Alignment explanation
Indices: 890180--890212 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
890170 TAAAAAATAA
890180 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
890196 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
890212 A
1 A
890213 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:890235 original size:43 final size:44
Alignment explanation
Indices: 890187--890274 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
890177 TAAACGAACA
890187 TAAACGAACACGAACATAAACGAACAAAA-TTTTTTTGTTCATG
1 TAAACGAACACGAACATAAACGAACAAAATTTTTTTTGTTCATG
890230 TAAACGAACACGAACATAAACGAACAAAATTTTTTTTGTTCATG
1 TAAACGAACACGAACATAAACGAACAAAATTTTTTTTGTTCATG
890274 T
1 T
890275 TCGTTTATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 29 0.66
44 15 0.34
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (44 bp):
TAAACGAACACGAACATAAACGAACAAAATTTTTTTTGTTCATG
Found at i:891118 original size:14 final size:14
Alignment explanation
Indices: 891101--891156 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
891091 AATGAACATA
*
891101 AACGAACATAATCG
1 AACGAACATAACCG
891115 AACGAACAT-A---
1 AACGAACATAACCG
*
891125 AACGAACATAACCA
1 AACGAACATAACCG
891139 AACGAACATAACCG
1 AACGAACATAACCG
891153 AACG
1 AACG
891157 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:891121 original size:24 final size:24
Alignment explanation
Indices: 891081--891155 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
891071 GATTGTGTTA
*
891081 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
891105 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
891129 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
891153 AAC
1 AAC
891156 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:900935 original size:2 final size:2
Alignment explanation
Indices: 900928--901079 Score: 295
Period size: 2 Copynumber: 75.5 Consensus size: 2
900918 TGGGTAAAAG
900928 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
900970 TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
901013 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
901055 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
901080 CAGCATTGTC
Statistics
Matches: 149, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 147 0.99
3 2 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:906600 original size:21 final size:20
Alignment explanation
Indices: 906558--906630 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
906548 TTCTCCAAGA
*
906558 GATCGATCCTTTTAAAAAGG
1 GATCGATCCTTTTCAAAAGG
**
906578 GATCGATCCTTTCTCTTAAGG
1 GATCGATCCTTT-TCAAAAGG
* *
906599 GATCGATCATTTTGAAAAGG
1 GATCGATCCTTTTCAAAAGG
906619 GATCGATCCTTT
1 GATCGATCCTTT
906631 ACTAGACAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
GATCGATCCTTTTCAAAAGG
Found at i:907497 original size:22 final size:22
Alignment explanation
Indices: 907471--907518 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
907461 AATATTATCT
907471 ATTTAAATAATATTTGT-ATTAG
1 ATTTAAA-AATATTTGTCATTAG
*
907493 ATTT-AAAATATTTTTCATTAG
1 ATTTAAAAATATTTGTCATTAG
907514 ATTTA
1 ATTTA
907519 TTTAAATCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
21 11 0.48
22 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
ATTTAAAAATATTTGTCATTAG
Found at i:907711 original size:18 final size:19
Alignment explanation
Indices: 907655--907711 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
907645 GTATTATTAT
* *
907655 TATTATTATCTTATATTAGA
1 TATTATTATATTAT-TTAAA
907675 T-TTATT-TATTA-TTATAA
1 TATTATTATATTATTTA-AA
907692 TATTATTAT-TTATTTAAA
1 TATTATTATATTATTTAAA
907710 TA
1 TA
907712 GTTTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 3 0.10
17 2 0.06
18 16 0.52
19 9 0.29
20 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTATTATATTATTTAAA
Found at i:911878 original size:22 final size:23
Alignment explanation
Indices: 911836--911884 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
911826 GGTTGATTTG
*
911836 TTTATATAATTAAACTTTTAATT
1 TTTATATAATTAAACTTTTAAAT
*
911859 TTTAT-TAATTATA-TTATTAAAT
1 TTTATATAATTAAACTT-TTAAAT
911881 TTTA
1 TTTA
911885 GTTTTACAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATATAATTAAACTTTTAAAT
Found at i:916057 original size:201 final size:202
Alignment explanation
Indices: 915709--916114 Score: 787
Period size: 201 Copynumber: 2.0 Consensus size: 202
915699 ATAAATTAAC
915709 GGGTTGAAGAGTAAAGGTCTACCTGATATCTCAAATTTTCAGCCTAAGCACCAAAGCATTGTATT
1 GGGTTGAAGAGTAAAGGTCTACCTGATATCTCAAATTTTCAGCCTAAG--CCAAAGCATTGTATT
915774 AAGTCATCATCAAGTAGTTCCTCTAGTGAACTTGTACCATCAAACGGAAGTTCAAATGGGCTGTT
64 AAGTCATCATCAAGTAGTTCCTCTAGTGAACTTGTACCATCAAACGGAAGTTCAAATGGGCTGTT
915839 AAAGCCACCATAAAACAAGGGATCATTTGTTGGCGAACCAAAGGGGTTCTGAACAGCTCTATCTT
129 AAAGCCACCATAAAACAAGGGATCATTTGTTGGCGAACCAAAGGGGTTCTGAACAGCTCTATCTT
915904 GTTCATTGT
194 GTTCATTGT
915913 GGGTTGAAGAGTAAAGGTCTACCTGATATCTCAAATTTTCAGCCTAAG-CAAAGCATTGTATTAA
1 GGGTTGAAGAGTAAAGGTCTACCTGATATCTCAAATTTTCAGCCTAAGCCAAAGCATTGTATTAA
915977 GTCATCATCAAGTAGTTCCTCTAGTGAACTTGTACCATCAAACGGAAGTTCAAATGGGCTGTTAA
66 GTCATCATCAAGTAGTTCCTCTAGTGAACTTGTACCATCAAACGGAAGTTCAAATGGGCTGTTAA
916042 AGCCACCATAAAACAAGGGATCATTTGTTGGCGAACCAAAGGGGTTCTGAACAGCTCTATCTTGT
131 AGCCACCATAAAACAAGGGATCATTTGTTGGCGAACCAAAGGGGTTCTGAACAGCTCTATCTTGT
916107 TCATTGT
196 TCATTGT
916114 G
1 G
916115 CAGTATGTCT
Statistics
Matches: 202, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
201 154 0.76
204 48 0.24
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (202 bp):
GGGTTGAAGAGTAAAGGTCTACCTGATATCTCAAATTTTCAGCCTAAGCCAAAGCATTGTATTAA
GTCATCATCAAGTAGTTCCTCTAGTGAACTTGTACCATCAAACGGAAGTTCAAATGGGCTGTTAA
AGCCACCATAAAACAAGGGATCATTTGTTGGCGAACCAAAGGGGTTCTGAACAGCTCTATCTTGT
TCATTGT
Found at i:936275 original size:16 final size:17
Alignment explanation
Indices: 936254--936288 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
936244 AAAAACATTT
936254 AAAACTA-TTATTATAA
1 AAAACTATTTATTATAA
*
936270 AAAACTATTTTTTATAA
1 AAAACTATTTATTATAA
936287 AA
1 AA
936289 TGTAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAACTATTTATTATAA
Found at i:936653 original size:7 final size:7
Alignment explanation
Indices: 936641--936670 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
936631 CGTAATTTGA
936641 TTAAAAT
1 TTAAAAT
936648 TTAAAAT
1 TTAAAAT
936655 TTAAAAT
1 TTAAAAT
936662 TTAAAAT
1 TTAAAAT
936669 TT
1 TT
936671 CGGTATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTAAAAT
Found at i:950634 original size:23 final size:23
Alignment explanation
Indices: 950608--950652 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
950598 CACCACAGCT
* *
950608 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
*
950631 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
950653 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:950890 original size:149 final size:149
Alignment explanation
Indices: 950620--950934 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
950610 TATAATTGCA
950620 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
950684 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* * *
950749 CTACAGAATATATATATATC
130 CCAAAGAATATACATATATC
* **
950769 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
950834 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
950899 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
950918 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
950935 CCCTCGACTC
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:951390 original size:2 final size:2
Alignment explanation
Indices: 951383--951412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
951373 TCTCTTAGAC
951383 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
951413 CACATGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:952380 original size:21 final size:21
Alignment explanation
Indices: 952356--952400 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
952346 TGTTGTTCGT
* *
952356 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
952377 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
952398 TTG
1 TTG
952401 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:955704 original size:23 final size:23
Alignment explanation
Indices: 955678--955722 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
955668 CACGACAGCT
*
955678 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
955701 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
955723 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:955960 original size:149 final size:149
Alignment explanation
Indices: 955690--956004 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
955680 TATAATTGCA
955690 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
955754 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
955819 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
**
955839 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
955904 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
955969 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
*
955988 CTGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
956005 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:956460 original size:2 final size:2
Alignment explanation
Indices: 956453--956480 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
956443 TCTCTTAGAC
956453 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
956481 CAGGTAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:958851 original size:103 final size:103
Alignment explanation
Indices: 958671--958885 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
958661 GTAGAGGGTC
* *
958671 TATGTGGTCCTTCAGAACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGAACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
*
958736 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTATGGCATATGTATATGATTCTTAAGGAATGA
* *
958774 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
1 TATGTGGTCATTCAGAACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
958839 TTGATCTATGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTATGGCATATGTATATGATTCTTAAGGAATGA
958877 TATGTGGTC
1 TATGTGGTC
958886 CTTATGGACA
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCAGAACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTAAGACACATAC
TTGATCTATGGCATATGTATATGATTCTTAAGGAATGA
Found at i:965049 original size:63 final size:67
Alignment explanation
Indices: 964982--965108 Score: 201
Period size: 63 Copynumber: 2.0 Consensus size: 67
964972 TTTAAAAAGA
964982 AAACATCGAATAGGATTTATGCATCGATGCATAAG-G-A-TGCATCGATGCAT-CC-CCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAA
965042 TAC
65 TAC
*
965045 AAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
965109 ATATGAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
62 1 0.02
63 33 0.57
64 1 0.02
65 13 0.22
66 2 0.03
67 8 0.14
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (67 bp):
AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAAT
AC
Found at i:965782 original size:103 final size:103
Alignment explanation
Indices: 965557--965774 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
965547 GTAGAGGGTT
* *
965557 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTAAGACACATAC
*
965622 TTGATCTTTGGCATATGTATATGATTCTTAGGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
965660 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTAAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTAAGACACATAC
*
965725 TTGGTCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
965763 TATGTGGTCCTT
1 TATGTGGTCCTT
965775 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTAAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:965817 original size:23 final size:22
Alignment explanation
Indices: 965790--965853 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
965780 CATTATTATA
965790 TGGCACTATGGTGCAATTCTACG
1 TGGCACT-TGGTGCAATTCTACG
**
965813 TGGCACTCCAGTGCAATTCTACG
1 TGGCACT-TGGTGCAATTCTACG
965836 TGGCACTTAGGTGCAATT
1 TGGCACTT-GGTGCAATT
965854 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
TGGCACTTGGTGCAATTCTACG
Found at i:969234 original size:23 final size:22
Alignment explanation
Indices: 969197--969241 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
969187 TAATTCTTAA
969197 AATTTATATAATATATTAATTT
1 AATTTATATAATATATTAATTT
969219 AATTTATAATAATATATTAATTT
1 AATTTAT-ATAATATATTAATTT
969242 TTTTGAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTATATAATATATTAATTT
Found at i:979007 original size:16 final size:16
Alignment explanation
Indices: 978982--979020 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
978972 CCACCCTTGA
*
978982 AGGCGCCAAGATTTTC
1 AGGCGTCAAGATTTTC
*
978998 AGGCGTCAAGATTTTT
1 AGGCGTCAAGATTTTC
979014 AGGCGTC
1 AGGCGTC
979021 TTTGAGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (16 bp):
AGGCGTCAAGATTTTC
Found at i:982247 original size:25 final size:25
Alignment explanation
Indices: 982218--982266 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
982208 TATAGTAAGG
*
982218 TGTTTTTAAAAGGGAGAAGTGTTAA
1 TGTTTTTAAAAGGGAGAAATGTTAA
*
982243 TGTTTTTAAAAGGGATAAATGTTA
1 TGTTTTTAAAAGGGAGAAATGTTA
982267 TAGTAAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (25 bp):
TGTTTTTAAAAGGGAGAAATGTTAA
Found at i:982721 original size:65 final size:63
Alignment explanation
Indices: 982642--982820 Score: 191
Period size: 64 Copynumber: 2.8 Consensus size: 63
982632 TTGAACATCG
* *
982642 AATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACAAC
1 AATGCATTTGATGCATCGATGCACAT-CCATGCACCGATGCACTAAGGATATTT-TG-AAACAAC
982706 A
63 A
* * ** * * *
982707 AATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCG
1 AATGCATTTGATGCATCGATGCA-CATCCATGCACCGATGCACTAAGGATATTTTGAAACAACA
* *
982771 AATGCACTTGATGCATCGATGCAC-TCTTAGTGCACCGATGCACTAAGGAT
1 AATGCATTTGATGCATCGATGCACATC-CA-TGCACCGATGCACTAAGGAT
982821 CCAACAGTCA
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 44 0.46
65 43 0.45
66 5 0.05
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (63 bp):
AATGCATTTGATGCATCGATGCACATCCATGCACCGATGCACTAAGGATATTTTGAAACAACA
Found at i:982794 original size:17 final size:19
Alignment explanation
Indices: 982766--982814 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
982756 TATTTTGAAA
982766 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
982784 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
982803 CACCGATGCACT
1 CATCGATGCACT
982815 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:984771 original size:21 final size:21
Alignment explanation
Indices: 984736--984777 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
984726 AAGACTCTAT
*
984736 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAACGATA
**
984757 TTTCAAAATTGAAAAACGATA
1 TTTCAAAATACAAAAACGATA
984778 ATAGTCTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.29
Consensus pattern (21 bp):
TTTCAAAATACAAAAACGATA
Found at i:993694 original size:43 final size:43
Alignment explanation
Indices: 993643--993933 Score: 396
Period size: 43 Copynumber: 6.8 Consensus size: 43
993633 AGGTCTTATA
* *
993643 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGGGCCTGGGGAAACTGTAAGGCTTACC
* **
993686 CTTGCACATAGCAAAAGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGGGCCTGGGGAAACTGTAAGGCTTACC
* * *
993728 CTTGCACACAAC-AAAGGAACCTGGGGAAACTATAAGGCTTACC
1 CTTGCACACAGCAAAAGG-GCCTGGGGAAACTGTAAGGCTTACC
*
993771 CTTGCACACAGC-AAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGGG-CCTGGGGAAACTGTAAGGCTTACC
993814 CTTGCACACAGC-AAAGGGACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGGG-CCTGGGGAAACTGTAAGGCTTACC
* *
993856 CTTGCACACAGCAAAGGGGCCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGGGCCTGGGGAAACTGTAAGGCTTACC
*
993899 CTTGCACACAGC-AAAGGGACCTGGGGTAACTGTAA
1 CTTGCACACAGCAAAAGGG-CCTGGGGAAACTGTAA
993934 CGGTAATTAA
Statistics
Matches: 228, Mismatches: 14, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
41 4 0.02
42 73 0.32
43 151 0.66
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAAGGGCCTGGGGAAACTGTAAGGCTTACC
Found at i:993735 original size:85 final size:86
Alignment explanation
Indices: 993643--993933 Score: 437
Period size: 85 Copynumber: 3.4 Consensus size: 86
993633 AGGTCTTATA
* * * *
993643 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACATAGCAAAAGAACC
1 CTTGCACACAGCAAAGAGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACC
*
993707 T-GGGAAACTGTAAGGCTTACC
65 TGGGGGAACTGTAAGGCTTACC
* *
993728 CTTGCACACAACAAAG-GAACCTGGGGAAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACC
993792 TGGGGGAACTGTAAGGCTTACC
65 TGGGGGAACTGTAAGGCTTACC
* *
993814 CTTGCACACAGCAAAGGGACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGGCCT
1 CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
993878 GGGGGAACTGTAAGGCTTACC
66 GGGGGAACTGTAAGGCTTACC
* *
993899 CTTGCACACAGCAAAGGGACCTGGGGTAACTGTAA
1 CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAA
993934 CGGTAATTAA
Statistics
Matches: 190, Mismatches: 11, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
85 139 0.73
86 50 0.26
87 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (86 bp):
CTTGCACACAGCAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
GGGGGAACTGTAAGGCTTACC
Found at i:993794 original size:128 final size:128
Alignment explanation
Indices: 993625--993933 Score: 458
Period size: 128 Copynumber: 2.4 Consensus size: 128
993615 GAGCATGCAA
* ** * *
993625 AAACGATAAGGTCTTATACTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTT
1 AAACTATAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTGTAAGGCTTACCCTT
*
993689 GCACATAGCAAAAGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
64 GCACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
*
993754 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGC
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGC
* * * **
993819 ACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGGCCTGGGG
66 ACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
* * *
993882 GAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGTAACTGTAA
1 AAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAA
993934 CGGTAATTAA
Statistics
Matches: 164, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 152 0.93
129 12 0.07
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (128 bp):
AAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGC
ACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGG
Found at i:998448 original size:21 final size:20
Alignment explanation
Indices: 998415--998490 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
998405 AAATGCCTGA
998415 GGGTATCTG-TACCTAAGTAGG
1 GGGTATC-GATACCTAA-TAGG
998436 GGGTATCGATACC-ATATCATGG
1 GGGTATCGATACCTA-AT-A-GG
*
998458 GGGTATCGATACCTACTAGG
1 GGGTATCGATACCTAATAGG
* *
998478 CGGTATCGGTACC
1 GGGTATCGATACC
998491 ATCCGAGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 16 0.34
21 14 0.30
22 16 0.34
23 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCTAATAGG
Found at i:998484 original size:20 final size:20
Alignment explanation
Indices: 998432--998492 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
998422 TGTACCTAAG
998432 TAGGGGGTATCGATACCATA
1 TAGGGGGTATCGATACCATA
998452 TCATGGGGGTATCGATACC-TA
1 T-A-GGGGGTATCGATACCATA
* *
998473 CTAGGCGGTATCGGTACCAT
1 -TAGGGGGTATCGATACCAT
998493 CCGAGCATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 14 0.40
21 5 0.14
22 16 0.46
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (20 bp):
TAGGGGGTATCGATACCATA
Found at i:998581 original size:74 final size:75
Alignment explanation
Indices: 998452--998642 Score: 305
Period size: 74 Copynumber: 2.5 Consensus size: 75
998442 CGATACCATA
* * *
998452 TCATGGGGGTATCGATA-CCTACTAGGCGGTATCGGTACCATCCGAGCATTCTGTTATTT-TCGG
1 TCATAGGGGTATCGATACCCTA-TAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGG
*
998515 AATCAAAATGT
65 AACCAAAATGT
998526 TCATAGGGGTATCGATACCCTATAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGGA
1 TCATAGGGGTATCGATACCCTATAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGGA
998591 ACCAAAATGT
66 ACCAAAATGT
*
998601 TCATAGGGGTATCGATACCCTATATGGGGGTATCGATACCAT
1 TCATAGGGGTATCGATACCCTATA-GGGGGTATCGGTACCAT
998643 ACTAAATAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
74 51 0.47
75 42 0.39
76 16 0.15
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (75 bp):
TCATAGGGGTATCGATACCCTATAGGGGGTATCGGTACCATCCGAGCATTATGTTATTTCTCGGA
ACCAAAATGT
Found at i:1001295 original size:21 final size:21
Alignment explanation
Indices: 1001226--1001350 Score: 132
Period size: 21 Copynumber: 5.8 Consensus size: 21
1001216 AACTCGACAG
*
1001226 GGGGTATCGATACC-A-TCAG
1 GGGGTATCGATACCTATTCAA
1001245 GGGGTATCGATA-CTCATTCAAA
1 GGGGTATCGATACCT-ATTC-AA
1001267 GAGGGTATCGATACCTATTCAA
1 G-GGGTATCGATACCTATTCAA
*
1001289 TGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTC-AA
*
1001311 GGGTGTATCGATACCTGTATC-A
1 GGG-GTATCGATACCTAT-TCAA
1001333 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
1001351 GCACATAAAT
Statistics
Matches: 91, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.01
19 12 0.13
20 1 0.01
21 30 0.33
22 15 0.16
23 28 0.31
24 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (21 bp):
GGGGTATCGATACCTATTCAA
Found at i:1001308 original size:44 final size:43
Alignment explanation
Indices: 1001226--1001350 Score: 150
Period size: 44 Copynumber: 2.9 Consensus size: 43
1001216 AACTCGACAG
*
1001226 GGGGTATCGATACC-A-TCAGGGGGTATCGATA-CTCATTCAAA
1 GGGGTATCGATACCTATTCAAGGGGTATCGATACCT-ATTCAAA
*
1001267 GAGGGTATCGATACCTATTCAATGGGTATCGATACCTATTCAAA
1 G-GGGTATCGATACCTATTCAAGGGGTATCGATACCTATTCAAA
*
1001311 GGGTGTATCGATACCTGTATC-AGGGGTATCGATACTCTAT
1 GGG-GTATCGATACCTAT-TCAAGGGGTATCGATAC-CTAT
1001351 GCACATAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
41 1 0.01
42 13 0.18
43 3 0.04
44 48 0.66
45 8 0.11
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
GGGGTATCGATACCTATTCAAGGGGTATCGATACCTATTCAAA
Found at i:1006443 original size:21 final size:21
Alignment explanation
Indices: 1006408--1006467 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
1006398 AGAACCTGTG
* *
1006408 GGGGGTATCGATTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
1006428 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCC--TCAAA
1006452 GGGGGAATC-GTTCCCT
1 GGGGGAATCGGTTCCCT
1006468 TATGGGGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 6 0.18
23 9 0.26
24 4 0.12
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1010561 original size:116 final size:116
Alignment explanation
Indices: 1010347--1010562 Score: 267
Period size: 116 Copynumber: 1.9 Consensus size: 116
1010337 AAATCAAAAT
* *
1010347 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATTCTTCTTCAAGATTTCATTT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
* * *
1010412 TGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTGAAA
66 TGATTTCCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAA
* * * *
1010463 TTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACATTTCAT
1 TTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTTCAT
* * **
1010526 TTTGATTTCCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTTGATTTCCAAAATCCATTTTAG-TTTCTAAAAGAAG
1010563 ATCATTTTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
115 2 0.02
116 78 0.93
117 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (116 bp):
TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
TGATTTCCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAA
Found at i:1015726 original size:20 final size:21
Alignment explanation
Indices: 1015674--1015726 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
1015664 AAATGCCTGA
*
1015674 GGGTATCGGTACCTAAGTAGG
1 GGGTATCGGTACCTAACTAGG
**
1015695 GGGTAT-TATACCT-ACTAGG
1 GGGTATCGGTACCTAACTAGG
1015714 GGGTATCGGTACC
1 GGGTATCGGTACC
1015727 ATCCGAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.42
20 9 0.35
21 6 0.23
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (21 bp):
GGGTATCGGTACCTAACTAGG
Found at i:1015781 original size:95 final size:94
Alignment explanation
Indices: 1015674--1015920 Score: 363
Period size: 95 Copynumber: 2.6 Consensus size: 94
1015664 AAATGCCTGA
*
1015674 GGGTATCGGTACCTAAGTAGGGGGTAT-TATA-CCTACTAGGGGGTATCGGTACCATCCGAGCAT
1 GGGTATCGGTACCT-A-TAGGGGGTATCGATACCCTA-TAGGGGGTATCGGTACCATCCGAGCAT
* *
1015737 TCTGTTATTTCTCGGAATCAAAATGTTCATAG
63 TCTATTATTTCTCGGAACCAAAATGTTCATAG
*
1015769 GGGTATCGGTACCCTATAGGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTC
1 GGGTATCGGTA-CCTATAGGGGGTATCGATACCCTATAGGGGGTATCGGTACCATCCGAGCATTC
1015834 TATTATTTCTCGGAACCAAAATGTTCATAG
65 TATTATTTCTCGGAACCAAAATGTTCATAG
* *
1015864 GGGTATCGGTACCCTATATGGGGGTATCGGTACCCTATATGGGGGTATCGATACCAT
1 GGGTATCGGTA-CCTATA-GGGGGTATCGATACCCTATA-GGGGGTATCGGTACCAT
1015921 ACTAAATAAA
Statistics
Matches: 142, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
94 10 0.07
95 89 0.63
96 27 0.19
97 16 0.11
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (94 bp):
GGGTATCGGTACCTATAGGGGGTATCGATACCCTATAGGGGGTATCGGTACCATCCGAGCATTCT
ATTATTTCTCGGAACCAAAATGTTCATAG
Found at i:1015793 original size:20 final size:20
Alignment explanation
Indices: 1015768--1015821 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1015758 AATGTTCATA
1015768 GGGGTATCGGTACCCTATAG
1 GGGGTATCGGTACCCTATAG
1015788 GGGGTATCGGTACCCTATAG
1 GGGGTATCGGTACCCTATAG
1015808 GGGGTATCGGTACC
1 GGGGTATCGGTACC
1015822 ATCCGAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.20, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGTATCGGTACCCTATAG
Found at i:1015888 original size:21 final size:21
Alignment explanation
Indices: 1015863--1015918 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1015853 AATGTTCATA
1015863 GGGGTATCGGTACCCTATATG
1 GGGGTATCGGTACCCTATATG
1015884 GGGGTATCGGTACCCTATATG
1 GGGGTATCGGTACCCTATATG
*
1015905 GGGGTATCGATACC
1 GGGGTATCGGTACC
1015919 ATACTAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.27
Consensus pattern (21 bp):
GGGGTATCGGTACCCTATATG
Found at i:1016806 original size:20 final size:20
Alignment explanation
Indices: 1016781--1016820 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1016771 AAATATGTTC
1016781 GTTGTTCATACACAAAGGTG
1 GTTGTTCATACACAAAGGTG
1016801 GTTGTTCATACACAAAGGTG
1 GTTGTTCATACACAAAGGTG
1016821 AGAGTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (20 bp):
GTTGTTCATACACAAAGGTG
Found at i:1016827 original size:20 final size:20
Alignment explanation
Indices: 1016784--1016830 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1016774 TATGTTCGTT
*
1016784 GTTCATACACAAAGGTGGTT
1 GTTCATACACAAAGGTGGTA
1016804 GTTCATACACAAAGGTGAG-A
1 GTTCATACACAAAGGTG-GTA
1016824 GTTCATA
1 GTTCATA
1016831 TACGGGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
GTTCATACACAAAGGTGGTA
Found at i:1017326 original size:67 final size:67
Alignment explanation
Indices: 1017218--1017355 Score: 181
Period size: 67 Copynumber: 2.1 Consensus size: 67
1017208 AAACACTAAA
* * * *
1017218 ATTAAATTAAAATATAATTTGAACATTTATTTTTACATTAAACCTT-ATAAAAATTAATATTATT
1 ATTAAATTAAAATATAATTTGAACAATTATTTATACATTAAA-CTTAAAAAAAACTAATATTATT
1017282 TAT
65 TAT
* * *
1017285 ATTAAACTTAAAATATAATTTGTACAATTA-TTATACATTAAACTTAAAAAAAACTAGTATTCTT
1 ATTAAA-TTAAAATATAATTTGAACAATTATTTATACATTAAACTTAAAAAAAACTAATATTATT
1017349 TAT
65 TAT
1017352 ATTA
1 ATTA
1017356 CAATACCCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
66 3 0.05
67 38 0.61
68 21 0.34
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (67 bp):
ATTAAATTAAAATATAATTTGAACAATTATTTATACATTAAACTTAAAAAAAACTAATATTATTT
AT
Found at i:1017331 original size:36 final size:35
Alignment explanation
Indices: 1017218--1017333 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 35
1017208 AAACACTAAA
* *
1017218 ATTAAA-TTAAAATATAATTTGAACATTTATTTTTAC
1 ATTAAACTTAAAATATAATTTGTACAATTA--TTTAC
* *
1017254 ATTAAACCTTATAA-A-AA--T-TA-ATATTATTTAT
1 ATTAAA-CTTAAAATATAATTTGTACA-ATTATTTAC
1017285 ATTAAACTTAAAATATAATTTGTACAATTATTATAC
1 ATTAAACTTAAAATATAATTTGTACAATTATT-TAC
1017321 ATTAAACTTAAAA
1 ATTAAACTTAAAA
1017334 AAAACTAGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
30 6 0.09
31 11 0.17
32 3 0.05
33 4 0.06
34 2 0.03
35 8 0.12
36 24 0.38
37 1 0.02
38 5 0.08
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (35 bp):
ATTAAACTTAAAATATAATTTGTACAATTATTTAC
Found at i:1017676 original size:14 final size:14
Alignment explanation
Indices: 1017620--1017697 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
1017610 ACGCTGTTCT
*
1017620 AACTCAAAACCATA
1 AACTCTAAACCATA
* * *
1017634 AATTATAAACCTTA
1 AACTCTAAACCATA
* *
1017648 AAC-ATAACCCCATA
1 AACTCTAA-ACCATA
*
1017662 ACCTCTAAACCATA
1 AACTCTAAACCATA
*
1017676 AATTCTAAACCATA
1 AACTCTAAACCATA
1017690 AACTCTAA
1 AACTCTAA
1017698 CTTAATATTA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
13 4 0.08
14 42 0.86
15 3 0.06
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (14 bp):
AACTCTAAACCATA
Found at i:1018199 original size:35 final size:36
Alignment explanation
Indices: 1018148--1018216 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
1018138 AACACAATCA
* *
1018148 TCAATTTTATTCTAAACCTC-AAATTCTAAAATAAT
1 TCAATTATATTCTAAACCCCTAAATTCTAAAATAAT
*
1018183 TCAATTATATTTTAAACCCCTAAATTCTAAAATA
1 TCAATTATATTCTAAACCCCTAAATTCTAAAATA
1018217 CTTTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.57
36 13 0.43
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (36 bp):
TCAATTATATTCTAAACCCCTAAATTCTAAAATAAT
Found at i:1018267 original size:35 final size:35
Alignment explanation
Indices: 1018228--1018295 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
1018218 TTTAATTTAA
*
1018228 GGTTTAGAATATAATTGAAGTATTTTGGAATTTGG
1 GGTTTAGAATATAATTGAAGTATTTTGAAATTTGG
* *
1018263 GGTTTAGAATGTAATTGAAGTGTTTTGAAATTT
1 GGTTTAGAATATAATTGAAGTATTTTGAAATTT
1018296 TGAATATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
GGTTTAGAATATAATTGAAGTATTTTGAAATTTGG
Found at i:1034481 original size:261 final size:262
Alignment explanation
Indices: 1034017--1034533 Score: 968
Period size: 261 Copynumber: 2.0 Consensus size: 262
1034007 ATGTGGCAAT
1034017 GGCATTAGTGGAAAAATGACAAATCGAATTCCCCATGGTTAGTCATAGGAGATTTCAATGAAATA
1 GGCATTAGTGGAAAAATGACAAATCGAATTCCCCATGGTTAGTCATAGGAGATTTCAATGAAATA
** *
1034082 ATGTTCTCAACTGAAAAATGAGGTGGACAGGTGTGAAGTGAAAAGCAATGTAATGCCCCAATTTT
66 ATGTTCTCAACTGAAAAACAAGGTGGACAGGTGTGAAGTGAAAAGCAATGTAACGCCCCAATTTT
1034147 CAGGTTAATATTTTTGGGTAAACTCAGGTGGTTGTAATTTAGGCTAAGAGACCATTTAGAAGTGT
131 CAGGTTAATATTTTTGGGTAAACTCAGGTGGTTGTAATTTAGGCTAAGAGACCATTTAGAAGTGT
1034212 TGTTTGAATTTTTACTTGTTATAGTTTGGACTTGAGCCCATCAAGGCTT-AAAAAGGCATTGGCG
196 TGTTTGAATTTTTACTTGTTATAGTTTGGACTTGAGCCCATCAAGGCTTGAAAAAGGCATTGGCG
1034276 AA
261 AA
1034278 GGCATTAGTGGAAAAATGACAAATCGAATTCCCCATGGTTAGTCATAGGAGATTTCAATGAAATA
1 GGCATTAGTGGAAAAATGACAAATCGAATTCCCCATGGTTAGTCATAGGAGATTTCAATGAAATA
1034343 ATGTTCTCAACTGAAAAACAAGGTGGACAGGTGTGAAGTGAAAAGCAATGTAACGCCCCAATTTT
66 ATGTTCTCAACTGAAAAACAAGGTGGACAGGTGTGAAGTGAAAAGCAATGTAACGCCCCAATTTT
1034408 CAGGTT-A-ATTTTTGGGTAAACTCAGGTGGGTTGTAATTTAGGCTAAGAGACCATTTAGAAGTG
131 CAGGTTAATATTTTTGGGTAAACTCAGGT-GGTTGTAATTTAGGCTAAGAGACCATTTAGAAGTG
1034471 TTGGTTTGAATTTTTACTTGTTATAGTTTGGACTTGAGCCCATCAAGGCTTGAAAAAGGCATT
195 TT-GTTTGAATTTTTACTTGTTATAGTTTGGACTTGAGCCCATCAAGGCTTGAAAAAGGCATT
1034534 TTTAAATTAA
Statistics
Matches: 250, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
259 20 0.08
260 38 0.15
261 181 0.72
262 11 0.04
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (262 bp):
GGCATTAGTGGAAAAATGACAAATCGAATTCCCCATGGTTAGTCATAGGAGATTTCAATGAAATA
ATGTTCTCAACTGAAAAACAAGGTGGACAGGTGTGAAGTGAAAAGCAATGTAACGCCCCAATTTT
CAGGTTAATATTTTTGGGTAAACTCAGGTGGTTGTAATTTAGGCTAAGAGACCATTTAGAAGTGT
TGTTTGAATTTTTACTTGTTATAGTTTGGACTTGAGCCCATCAAGGCTTGAAAAAGGCATTGGCG
AA
Found at i:1037574 original size:22 final size:22
Alignment explanation
Indices: 1037522--1037574 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
1037512 TTTGAGCCTT
*
1037522 CAGGGGGGTATGCATACCCCTG
1 CAGGGGAGTATGCATACCCCTG
1037544 CA-GGGAGTATGCATACCCCTG
1 CAGGGGAGTATGCATACCCCTG
1037565 CAGGGGAGTA
1 CAGGGGAGTA
1037575 GGTACCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.23, C:0.25, G:0.36, T:0.17
Consensus pattern (22 bp):
CAGGGGAGTATGCATACCCCTG
Found at i:1037684 original size:29 final size:30
Alignment explanation
Indices: 1037651--1037707 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1037641 AAACTTTGAA
1037651 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACATTTTG
* *
1037680 TAAATTCAATTCAAGTCTAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
1037708 GCCTTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAAACATTTTG
Found at i:1039088 original size:113 final size:114
Alignment explanation
Indices: 1038890--1039117 Score: 449
Period size: 113 Copynumber: 2.0 Consensus size: 114
1038880 ATAAATCATC
1038890 GATTCGGGGAAGTGGATACTTGTTCTTGATGGTCACTTTATTGAGTTGTCTGTAATCGATACAAA
1 GATTCGGGGAAGTGGATACTTGTTCTTGATGGTCACTTTATTGAGTTGTCTGTAATCGATACAAA
1038955 GACGCATTGATCCATCTTTCTTCTTAACAAATAGAACTGGAGC-CCCAA
66 GACGCATTGATCCATCTTTCTTCTTAACAAATAGAACTGGAGCTCCCAA
1039003 GATTCGGGGAAGTGGATACTTGTTCTTGATGGTCACTTTATTGAGTTGTCTGTAATCGATACAAA
1 GATTCGGGGAAGTGGATACTTGTTCTTGATGGTCACTTTATTGAGTTGTCTGTAATCGATACAAA
1039068 GACGCATTGATCCATCTTTCTTCTTAACAAATAGAACTGGAGCTCCCAA
66 GACGCATTGATCCATCTTTCTTCTTAACAAATAGAACTGGAGCTCCCAA
1039117 G
1 G
1039118 GTGATACACT
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 108 0.95
114 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (114 bp):
GATTCGGGGAAGTGGATACTTGTTCTTGATGGTCACTTTATTGAGTTGTCTGTAATCGATACAAA
GACGCATTGATCCATCTTTCTTCTTAACAAATAGAACTGGAGCTCCCAA
Found at i:1041966 original size:27 final size:25
Alignment explanation
Indices: 1041908--1041976 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 25
1041898 ATTCATATGT
1041908 TCATGTACTCATGTCATTCTTGTGA
1 TCATGTACTCATGTCATTCTTGTGA
1041933 TCATGTAGCTCATGTCATTCTCTGTGA
1 TCATGTA-CTCATGTCATTCT-TGTGA
*
1041960 TCATGTAACTCACGTCA
1 TCATGT-ACTCATGTCA
1041977 CTTCATATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 7 0.17
26 13 0.32
27 19 0.47
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (25 bp):
TCATGTACTCATGTCATTCTTGTGA
Found at i:1042007 original size:10 final size:10
Alignment explanation
Indices: 1041992--1042022 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1041982 TATCATGTTC
1041992 TCATATCACA
1 TCATATCACA
*
1042002 TCATATCATA
1 TCATATCACA
1042012 TCATATCACA
1 TCATATCACA
1042022 T
1 T
1042023 GAACATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (10 bp):
TCATATCACA
Found at i:1042437 original size:64 final size:64
Alignment explanation
Indices: 1042329--1042505 Score: 212
Period size: 64 Copynumber: 2.8 Consensus size: 64
1042319 TAATGAAGGT
* ** * **
1042329 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCGGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAAGGGG
* * ** * *
1042393 ATGCATCGATGCACTCCTTATGCATCGATGAACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAAGGGG
* *
1042457 ATACATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT
1042506 CTTTATTTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 1 0.01
64 94 0.99
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAAGGGG
Found at i:1042528 original size:64 final size:64
Alignment explanation
Indices: 1042329--1042553 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
1042319 TAATGAAGGT
* ** ** * * *** *
1042329 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTCGATGTAGT-ATTATTGCGGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * * *
1042393 ATGCATCGATGCACTCCTTATGCATCGATGAACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
* ** *
1042457 ATACATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
1042520 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
1042554 ATTCAAACAA
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
63 3 0.02
64 125 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:1044615 original size:19 final size:19
Alignment explanation
Indices: 1044568--1044615 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1044558 ACCCCCCAAA
*
1044568 CCGATACGAGTGACCTGAT
1 CCGATATGAGTGACCTGAT
1044587 CCGATATGAGTGACCTGAT
1 CCGATATGAGTGACCTGAT
* *
1044606 TCGATTTGAG
1 CCGATATGAG
1044616 GTGTCACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (19 bp):
CCGATATGAGTGACCTGAT
Found at i:1046086 original size:34 final size:32
Alignment explanation
Indices: 1046026--1046095 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1046016 CCTTACAAAC
*
1046026 TCCCTAGTTTTTCCGGGATAAACTAGAACATT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* *
1046058 TCCCTAGCTTTTACACGGGATTAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
1046092 TCCC
1 TCCC
1046096 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:1046402 original size:21 final size:21
Alignment explanation
Indices: 1046377--1046434 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1046367 TCTCATACAG
1046377 GGGGTATCGGTACCTCTTCAA
1 GGGGTATCGGTACCTCTTCAA
1046398 GGGGTATCGGTACCTCTTCAA
1 GGGGTATCGGTACCTCTTCAA
*
1046419 GGGGTATCAGTACCTC
1 GGGGTATCGGTACCTC
1046435 CTTTGTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (21 bp):
GGGGTATCGGTACCTCTTCAA
Found at i:1046647 original size:29 final size:29
Alignment explanation
Indices: 1046626--1046683 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1046616 AAACTTTGAA
1046626 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
1046655 TAAATTCAATTCAAGTCTAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1046684 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1046677 original size:30 final size:30
Alignment explanation
Indices: 1046626--1046685 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1046616 AAACTTTGAA
1046626 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
1046655 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1046686 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1051002 original size:16 final size:16
Alignment explanation
Indices: 1050981--1051013 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1050971 TAATAAATAG
1050981 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1050997 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1051013 A
1 A
1051014 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1051133 original size:20 final size:16
Alignment explanation
Indices: 1051082--1051144 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1051072 TAATAAATAA
1051082 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1051098 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1051114 ACGAACATAAATG--C
1 ACGAACATAAACGAAC
1051128 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1051144 A
1 A
1051145 AACGTTGGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.30
16 30 0.70
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1051139 original size:30 final size:31
Alignment explanation
Indices: 1051082--1051144 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 31
1051072 TAATAAATAA
1051082 ACGAACATAAACGAACACGAACATAAACGAAC
1 ACGAACATAAACG-ACACGAACATAAACGAAC
*
1051114 ACGAACATAAATG-CACGAACATAAACGAAC
1 ACGAACATAAACGACACGAACATAAACGAAC
1051144 A
1 A
1051145 AACGTTGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 18 0.60
32 12 0.40
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.08
Consensus pattern (31 bp):
ACGAACATAAACGACACGAACATAAACGAAC
Found at i:1051881 original size:14 final size:14
Alignment explanation
Indices: 1051864--1051914 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
1051854 GGTTGGGTTA
1051864 AACATAATCGAACG
1 AACATAATCGAACG
1051878 AACAT-A---AACG
1 AACATAATCGAACG
1051888 AACATAATCGAACG
1 AACATAATCGAACG
*
1051902 AACATAAACGAAC
1 AACATAATCGAAC
1051915 ATAACCGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 9 0.28
11 1 0.03
13 1 0.03
14 21 0.66
ACGTcount: A:0.55, C:0.22, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAATCGAACG
Found at i:1051889 original size:10 final size:10
Alignment explanation
Indices: 1051874--1051924 Score: 57
Period size: 10 Copynumber: 4.7 Consensus size: 10
1051864 AACATAATCG
1051874 AACGAACATA
1 AACGAACATA
1051884 AACGAACATAA
1 AACGAACAT-A
1051895 TCGAACGAACATA
1 ---AACGAACATA
1051908 AACGAACATA
1 AACGAACATA
*
1051918 ACCGAAC
1 AACGAAC
1051925 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 25 0.69
11 1 0.03
13 1 0.03
14 9 0.25
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
AACGAACATA
Found at i:1051896 original size:24 final size:24
Alignment explanation
Indices: 1051864--1051925 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1051854 GGTTGGGTTA
1051864 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
1051888 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
1051912 AACATAACCGAACG
1 AACATAATCGAACG
1051926 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1051925 original size:14 final size:13
Alignment explanation
Indices: 1051864--1051925 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 13
1051854 GGTTGGGTTA
1051864 AACATAATCGAACG
1 AACATAA-CGAACG
1051878 AACAT-A--AACG
1 AACATAACGAACG
1051888 AACATAATCGAACG
1 AACATAA-CGAACG
1051902 AACAT-A--AACG
1 AACATAACGAACG
1051912 AACATAACCGAACG
1 AACATAA-CGAACG
1051926 TTCACGAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
10 18 0.45
11 2 0.05
13 2 0.05
14 18 0.45
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (13 bp):
AACATAACGAACG
Found at i:1051934 original size:34 final size:34
Alignment explanation
Indices: 1051874--1051948 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
1051864 AACATAATCG
1051874 AACGAACATAAACGAACATAATCGAACG-AACATA
1 AACGAACATAAACGAACATAATCGAACGTAA-ATA
* * * *
1051908 AACGAACATAACCGAACGTTCA-CGAACGTAAATG
1 AACGAACATAAACGAAC-ATAATCGAACGTAAATA
1051942 AACGAAC
1 AACGAAC
1051949 GAGACCTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 31 0.89
35 4 0.11
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.12
Consensus pattern (34 bp):
AACGAACATAAACGAACATAATCGAACGTAAATA
Found at i:1060017 original size:24 final size:24
Alignment explanation
Indices: 1059982--1060041 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
1059972 TATAGATCAA
* *
1059982 TCTAGT-TTAGTGTATTTGTACAC
1 TCTAGTATTAGTGCATTCGTACAC
*
1060005 TCTAGTATTAGTGCATTCGTGCAC
1 TCTAGTATTAGTGCATTCGTACAC
*
1060029 TCCAG-ATTAGTGC
1 TCTAGTATTAGTGC
1060042 TTTATGCACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (24 bp):
TCTAGTATTAGTGCATTCGTACAC
Found at i:1061150 original size:32 final size:32
Alignment explanation
Indices: 1061065--1061142 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
1061055 CTGATTTTGG
1061065 TACCAAATTGGAATTGGGATGGGATTGAAAAA
1 TACCAAATTGGAATTGGGATGGGATTGAAAAA
*
1061097 TACCAAATTGGAATTGGGATGGGATTGGAAAA
1 TACCAAATTGGAATTGGGATGGGATTGAAAAA
*
1061129 TACCAAATTAGAAT
1 TACCAAATTGGAAT
1061143 AAGGATGGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (32 bp):
TACCAAATTGGAATTGGGATGGGATTGAAAAA
Found at i:1074287 original size:24 final size:24
Alignment explanation
Indices: 1074260--1074332 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1074250 CGTTCATTTA
1074260 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1074284 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
1074308 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1074332 C
1 C
1074333 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1074289 original size:14 final size:14
Alignment explanation
Indices: 1074270--1074325 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
1074260 CGTTCGTGAA
1074270 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1074284 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1074298 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1074308 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1074322 CGTT
1 CGTT
1074326 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1074345 original size:24 final size:24
Alignment explanation
Indices: 1074271--1074332 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1074261 GTTCGTGAAC
*
1074271 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1074295 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1074319 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1074333 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:1075383 original size:16 final size:16
Alignment explanation
Indices: 1075362--1075428 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1075352 GTCTCCAACG
1075362 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1075378 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
**
1075394 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
1075410 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1075424 TTTAT
1 TTTAT
1075429 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1075401 original size:32 final size:32
Alignment explanation
Indices: 1075360--1075420 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1075350 GGGTCTCCAA
1075360 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
**
1075392 CGTTTATGTTCGTGTTTGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
1075421 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:1075751 original size:6 final size:6
Alignment explanation
Indices: 1075733--1075763 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1075723 TGTACTAAAT
*
1075733 ATCGGA ATTGGA ATCGGA ATCGGA ATCGGA A
1 ATCGGA ATCGGA ATCGGA ATCGGA ATCGGA A
1075764 GTGAAGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.19
Consensus pattern (6 bp):
ATCGGA
Found at i:1085905 original size:35 final size:36
Alignment explanation
Indices: 1085859--1085929 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
1085849 AAGCACTAGG
1085859 AAACTGTTGATAAAGGTAATCGGCAAAAAGATGAAT
1 AAACTGTTGATAAAGGTAATCGGCAAAAAGATGAAT
*
1085895 AAAC-GTTGATAAAGGTAATTGGCAAAAAGATGAAT
1 AAACTGTTGATAAAGGTAATCGGCAAAAAGATGAAT
1085930 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (36 bp):
AAACTGTTGATAAAGGTAATCGGCAAAAAGATGAAT
Found at i:1090720 original size:20 final size:20
Alignment explanation
Indices: 1090695--1090780 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
1090685 AAATCTCAAT
1090695 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
1090715 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
* *
1090736 GCGATACTGCCTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* * *
1090756 GTGATACTGACTTTCGCAAT
1 GCGATACTGACTATCGCAAC
1090776 GCGAT
1 GCGAT
1090781 TTACATAGCG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.04
20 35 0.66
21 15 0.28
22 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1090729 original size:41 final size:41
Alignment explanation
Indices: 1090684--1090761 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1090674 GCGAATTGGG
* *
1090684 AAAATCTCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1090725 AAAATCGCAACGCGATACTGCCTTTCGCAACGTGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
1090762 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1091370 original size:19 final size:19
Alignment explanation
Indices: 1091335--1091371 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1091325 CGAGAGAATC
*
1091335 GCAACGCGAAATAAAAATT
1 GCAACGCGAAACAAAAATT
*
1091354 GCAACGCGAAACCAAAAT
1 GCAACGCGAAACAAAAAT
1091372 CGCATTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.22, G:0.16, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAACAAAAATT
Found at i:1091413 original size:19 final size:19
Alignment explanation
Indices: 1091371--1091516 Score: 87
Period size: 19 Copynumber: 8.1 Consensus size: 19
1091361 GAAACCAAAA
*
1091371 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1091390 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1091409 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1091423 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1091442 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1091456 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1091475 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
1091495 ATCTCGTTGCAATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1091515 TC
1 TC
1091517 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
14 17 0.18
16 4 0.04
17 5 0.05
19 40 0.42
20 29 0.30
21 1 0.01
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1091441 original size:33 final size:33
Alignment explanation
Indices: 1091404--1091491 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1091394 GTTGCGATTT
* *
1091404 TCATTTCGCGTTACGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
1091437 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
1091470 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1091492 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:1091493 original size:20 final size:20
Alignment explanation
Indices: 1091470--1091516 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1091460 ATTGCGATAG
*
1091470 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCAATTC
* *
1091490 TCATTAT-CTCGTTGCAATTT
1 TCATT-TCCGCGTTGCAATTC
1091510 TCATTTC
1 TCATTTC
1091517 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:1093672 original size:21 final size:21
Alignment explanation
Indices: 1093648--1093714 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1093638 TCATTCCTCG
1093648 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1093669 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1093690 AGAAGT-CCCTCCCACCATTCA
1 AG-AGTCCCCTCCCACCGTTCA
1093711 AGAG
1 AGAG
1093715 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1093672 original size:42 final size:42
Alignment explanation
Indices: 1093621--1093714 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1093611 CTACTCCTAT
* *
1093621 CATTGAAGAGGCCCCTATCATTCCTCG-AG-AGTCCCCTCCCAC
1 CATTCAAGAGGCCACTATCA-TCCTCGAAGAAGT-CCCTCCCAC
* * * *
1093663 CGTTCAAGAGGCCACTGTCATCGTTGAAGAAGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCCTCGAAGAAGTCCCTCCCAC
1093705 CATTCAAGAG
1 CATTCAAGAG
1093715 CCCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.09
42 36 0.84
43 3 0.07
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCCTCGAAGAAGTCCCTCCCAC
Found at i:1095294 original size:19 final size:19
Alignment explanation
Indices: 1095231--1095359 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1095221 CGAAATTAAA
* *
1095231 TTCGCGTTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1095250 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1095266 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1095283 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
*
1095297 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1095316 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
1095331 -TCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1095347 TTCGCATTGCGAT
1 TTCGCATTGCGAT
1095360 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 10, Indels: 34
0.65 0.08 0.27
Matches are distributed among these distances:
12 6 0.07
14 24 0.29
16 6 0.07
17 12 0.14
19 35 0.42
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1095312 original size:66 final size:64
Alignment explanation
Indices: 1095228--1095358 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 64
1095218 ACGCGAAATT
1095228 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATT--CTCGTTGCGATTTTCATTTCGCATTGC
1095293 G
64 G
*
1095294 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
1095358 A
1 A
1095359 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 29 0.45
66 35 0.55
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (64 bp):
AAATTCGCGTTGCAATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:1095339 original size:31 final size:31
Alignment explanation
Indices: 1095230--1095359 Score: 197
Period size: 33 Copynumber: 4.1 Consensus size: 31
1095220 GCGAAATTAA
*
1095230 ATTCGCGTTGCAATTTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
1095261 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CGCGTTGCGATTTTCATTTCGCATTGCG
1095294 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
1095327 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1095358 AT
1 AT
1095360 AGTAATTTCC
Statistics
Matches: 91, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 35 0.38
33 53 0.58
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (31 bp):
ATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:1097564 original size:12 final size:12
Alignment explanation
Indices: 1097547--1097571 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1097537 TCTTTGGGGA
1097547 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1097559 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1097571 C
1 C
1097572 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1097780 original size:24 final size:24
Alignment explanation
Indices: 1097746--1097799 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1097736 CTGAAACATC
*
1097746 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1097770 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1097794 ATCAAA
1 ATCAAA
1097800 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1098662 original size:41 final size:42
Alignment explanation
Indices: 1098561--1098677 Score: 141
Period size: 41 Copynumber: 2.9 Consensus size: 42
1098551 GAAAGTCAAA
* **
1098561 ATCGCGTTGCGAAATTCAGTATCGCGTTGCGA--AAGTCAGT
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTCAGT
* *
1098601 ATCGCGTTGCGAAAGGCAGTATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTCAGT
* * *
1098642 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTT
1098678 ACCAATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
40 30 0.45
41 34 0.52
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTCAGT
Found at i:1098665 original size:61 final size:60
Alignment explanation
Indices: 1098540--1098673 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
1098530 GATTCTGTAT
* * *
1098540 TATCTCGTTGCGAAAGTCAAAATCGCGTTGCGAAATTCAGTATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGGCAAAATCGCGTTGCGAAATTCAGTATCGCATTGCGAAAGTCAG
** ** * * *
1098600 TATCGCGTTGCGAAAGGCAGTATCGCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGGCAAAATCGCGTTGCGAAATT-CAGTATCGCATTGCGAAAGTCAG
*
1098661 TATCGCATTGCGA
1 TATCGCGTTGCGA
1098674 TTTTACCAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 31 0.50
61 31 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (60 bp):
TATCGCGTTGCGAAAGGCAAAATCGCGTTGCGAAATTCAGTATCGCATTGCGAAAGTCAG
Found at i:1098674 original size:20 final size:20
Alignment explanation
Indices: 1098540--1098673 Score: 144
Period size: 20 Copynumber: 6.7 Consensus size: 20
1098530 GATTCTGTAT
* *
1098540 TATCTCGTTGCGAAAGTCAA
1 TATCGCGTTGCGAAAGTCAG
* *
1098560 AATCGCGTTGCGAAATTCAG
1 TATCGCGTTGCGAAAGTCAG
1098580 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1098600 TATCGCGTTGCGAAAGGCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1098620 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
1098641 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1098661 TATCGCATTGCGA
1 TATCGCGTTGCGA
1098674 TTTTACCAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 80 0.82
21 13 0.13
22 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1098688 original size:41 final size:41
Alignment explanation
Indices: 1098600--1098695 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
1098590 CGAAAGTCAG
* * * ** *
1098600 TATCGCGTTGCGAAAGGCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCATTGCGATAGGCAGTATCGCATTGCGATTTTCCAA
*
1098641 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTACCAA
1 TATCGCATTGCGATAGGCAGTATCGCATTGCGATTTT-CCAA
1098683 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
1098696 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (41 bp):
TATCGCATTGCGATAGGCAGTATCGCATTGCGATTTTCCAA
Found at i:1098705 original size:20 final size:21
Alignment explanation
Indices: 1098663--1098714 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1098653 ATAGTCAGTA
1098663 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
**
1098684 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
1098704 TCGCATTGCGA
1 TCGCATTGCGA
1098715 ATTGGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:1099966 original size:332 final size:332
Alignment explanation
Indices: 1099349--1100016 Score: 848
Period size: 332 Copynumber: 2.0 Consensus size: 332
1099339 TTAAACTTTA
* * * * * * *
1099349 GGGTAAACTATACCATTGACCACTCGATTATTTAGCCTTTTTACTTTTATCATCGATCTTTCAAT
1 GGGTAAACTATACCATTAACCACTCAACTATTTAACCATTTTACTTTTACCATCAATCTTTCAAT
* * * * *
1099414 TTTGTCAATTAGACTACTTATCTATTTAATTGTATTCAATCAAACAACTAGCCGTTAACATTTAA
66 TTTGTCAATCAAACTACTTAACTATTTAATTGTATTCAATCAAACAACTAACCATTAACATTTAA
** * *
1099479 TGAACATGTGATGTGGCAGTTAAAACATTTGGTATAATTACACATCTAGTCACTGATACTTACAT
131 TGAACATGTGACATGGCAGTTAAAACATTTGGTATAATTACACATCTAGTCACTGAAAATTACAT
* ** *
1099544 ATTATATTAATTTGGTCCTAATTTTAATTACTTAAAATAAATTTAATAATTGAATGAAACCATGT
196 ATTATATTAATTTGGTCCTAATTTTAATTAATTAAAATAAATCCAATAA-TGAATGAAACCATGC
* * * *
1099609 GTCATCATCCAATTGGAGGATTAATTATATTTTAATTTATTTTTAATTC-ATACTTTCCACCAAT
260 ATCATCAACCAATTAGAGAATTAATTATATTTTAATTTATTTTTAATTCAATACTTTCCACCAAT
*
1099673 CATAGGGT
325 CATAAGGT
* *
1099681 GGGTAAACTATACCATTAACCACTCAACTATTTAATCATTTTACTTTTACCATTAATCTTTCAAT
1 GGGTAAACTATACCATTAACCACTCAACTATTTAACCATTTTACTTTTACCATCAATCTTTCAAT
* *
1099746 TTTGTCAATCAAA-TCACTTAACTATTTAATTGTATTCAATCAAACCACTAACCATTAATATTTA
66 TTTGTCAATCAAACT-ACTTAACTATTTAATTGTATTCAATCAAACAACTAACCATTAACATTTA
*
1099810 AT-AGACATGGTGACATGGCAGTTAAAACATTTTGTATAATTACACATCTAG-CTACT-AAAATT
130 ATGA-ACAT-GTGACATGGCAGTTAAAACATTTGGTATAATTACACATCTAGTC-ACTGAAAATT
* **
1099872 ACATATTATATTAATTAT-TTTTTAATTTTAATTAATTAAAATAAATCACCCAATAA-G-ATGAA
192 ACATATTATATTAATT-TGGTCCTAATTTTAATTAATTAAAATAAAT---CCAATAATGAATGAA
* * *
1099934 GCCATGCATCATCAACCAATTAGATAATTAATTATATTTTATTTTATTTTTAATTCAATATACTT
253 ACCATGCATCATCAACCAATTAGAGAATTAATTATATTTTAATTTATTTTTAATTC-A-ATACTT
*
1099999 TCCACTAATCATAAGGT
316 TCCACCAATCATAAGGT
1100016 G
1 G
1100017 ACATATGTAG
Statistics
Matches: 288, Mismatches: 37, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
331 2 0.01
332 215 0.75
333 44 0.15
335 27 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (332 bp):
GGGTAAACTATACCATTAACCACTCAACTATTTAACCATTTTACTTTTACCATCAATCTTTCAAT
TTTGTCAATCAAACTACTTAACTATTTAATTGTATTCAATCAAACAACTAACCATTAACATTTAA
TGAACATGTGACATGGCAGTTAAAACATTTGGTATAATTACACATCTAGTCACTGAAAATTACAT
ATTATATTAATTTGGTCCTAATTTTAATTAATTAAAATAAATCCAATAATGAATGAAACCATGCA
TCATCAACCAATTAGAGAATTAATTATATTTTAATTTATTTTTAATTCAATACTTTCCACCAATC
ATAAGGT
Found at i:1100288 original size:19 final size:19
Alignment explanation
Indices: 1100264--1100311 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
1100254 TATTTTTATC
1100264 TTAATTTATTAAATATATT
1 TTAATTTATTAAATATATT
*
1100283 TTAATTTA-AAAATATATT
1 TTAATTTATTAAATATATT
1100301 TTAATCTTATT
1 TTAAT-TTATT
1100312 TTATCTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATTTATTAAATATATT
Found at i:1100337 original size:29 final size:29
Alignment explanation
Indices: 1100279--1100380 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
1100269 TTATTAAATA
*
1100279 TATTTTAATTTAAAAATATATTTTAATCT
1 TATTTTAATTTAAAAATATATCTTAATCT
*
1100308 TATTTT-ATCTTAAAAATATATCTTATTCT
1 TATTTTAAT-TTAAAAATATATCTTAATCT
** * * * *
1100337 TATACTAACTTTTACAAATATATTTTACTTT
1 TATTTTAA--TTTAAAAATATATCTTAATCT
1100368 TATTTTAATTTAA
1 TATTTTAATTTAA
1100381 GATATATTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
28 2 0.03
29 32 0.55
30 1 0.02
31 22 0.38
32 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (29 bp):
TATTTTAATTTAAAAATATATCTTAATCT
Done.