Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 39
Found at i:1003119 original size:110 final size:108
Alignment explanation
Indices: 1002967--1003492 Score: 470
Period size: 107 Copynumber: 4.8 Consensus size: 108
1002957 ATTTTTTAAG
* * *
1002967 AACTACGTCTGATTTTCATAAGTTTCTTGATGATTTTCAAATGAGTTTTTCAAGAAACTAAGTCT
1 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATGAG-TTTTCAAGAAACTAAGTCT
* * * *
1003032 AATTTTTGGAAGTTTCTAGATTATTTTTAATCGAGCTTTCAAAGA
65 GATTTTTAGAAGTTTCTTGATGATTTTTAAT-GAGCTTTCAAAGA
* * * * * * *
1003077 GACTACGTCTAATTTTTAGAAGTTTATTGATGATTTTTAAATGAGCTTTCAACGAGACTAAGTCT
1 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAA-GAAACTAAGTCT
* * * * *
1003142 GATTTTTCAGAAGTTTCTTGACGATTTTCAAATTAGTTTTTAAAGA
65 GATTTTT-AGAAGTTTCTTGATGATTTT-TAATGAGCTTTCAAAGA
* * * *
1003188 AACTAAGTCTGATTTTCAGAAGTTTCTTAATGATTTTCAAATGAATTTTAAAGAAACTAAGTCTG
1 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAGAAACTAAGTCTG
* * *
1003253 ATTTTCAGAAGTTTCTTGATGATTTTTAAAAGAACTTTCAAAGA
66 ATTTTTAGAAGTTTCTTGATGATTTTT-AATGAGCTTTCAAAGA
* * * ** * * ** * *
1003297 AATTAAGCCTAATTTTTAGGGGTTTCTT-ATG-TTTTCAAATAAATTTGAAAGAAATTAAGCCTG
1 AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAGAAACTAAGTCTG
* * * * *
1003360 ATTTTCAGGAGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
66 ATTTTTAGAAGTTTCTTGATGATTTT-TAATGAGCTTTCAAAGA
* * * * ** * * *
1003402 AGCTAAGCCTGATTTTTTAGGGGTTTCTTGAT-ATTTTCAAATGA-TTTTTATAGAAAGTAAGTT
1 AACTAAGTCT-AATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCA-AGAAACTAAGTC
1003465 TGATTTTTAGAAGTTTCTTGATGATTTT
64 TGATTTTTAGAAGTTTCTTGATGATTTT
1003493 CAGGAGTTTC
Statistics
Matches: 344, Mismatches: 62, Indels: 22
0.80 0.14 0.05
Matches are distributed among these distances:
105 16 0.05
106 29 0.08
107 90 0.26
108 7 0.02
109 58 0.17
110 73 0.21
111 68 0.20
112 3 0.01
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (108 bp):
AACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAGAAACTAAGTCTG
ATTTTTAGAAGTTTCTTGATGATTTTTAATGAGCTTTCAAAGA
Found at i:1003489 original size:21 final size:21
Alignment explanation
Indices: 1003465--1003514 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1003455 AAAGTAAGTT
*
1003465 TGATTTTTAGAAGTTTCTTGA
1 TGATTTTCAGAAGTTTCTTGA
*
1003486 TGATTTTCAGGAGTTTCTTGA
1 TGATTTTCAGAAGTTTCTTGA
1003507 TG-TTTTCA
1 TGATTTTCA
1003515 AATAAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (21 bp):
TGATTTTCAGAAGTTTCTTGA
Found at i:1003565 original size:55 final size:55
Alignment explanation
Indices: 1003486--1003635 Score: 191
Period size: 53 Copynumber: 2.8 Consensus size: 55
1003476 AGTTTCTTGA
* * *
1003486 TGATTTTCAGGAGTTTCTTGATGTTTTCAAATAAATTTGAAAAAAAAACTAA-AC
1 TGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAAAAAAACTAAGAC
* * * * *
1003540 TTACTTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTG--AAAGAAGCTAAGCC
1 TGA-TTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAAAAAAACTAAGAC
1003594 TGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTT-AAAA
1 TGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAA
1003636 GGTGTTAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
53 43 0.52
54 7 0.09
55 32 0.39
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (55 bp):
TGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAAAAAAACTAAGAC
Found at i:1003645 original size:53 final size:53
Alignment explanation
Indices: 1003488--1003658 Score: 189
Period size: 53 Copynumber: 3.2 Consensus size: 53
1003478 TTTCTTGATG
* * * * * * * *
1003488 ATTTTCAGGAGTTTCTTGATGTTTTCAAATAAATTTGAAAAAAAAACTAAACTTA
1 ATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTT--AAAAGAAGCTAAGCCTA
* * *
1003543 CTTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTG
1 ATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTAAAAGAAGCTAAGCCTA
* ** *
1003596 ATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTAAAAGGTGTTAAGCCTA
1 ATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTAAAAGAAGCTAAGCCTA
1003649 ATTTTTAGGG
1 ATTTTTAGGG
1003659 TTCCTTGACA
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 66 0.68
55 31 0.32
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (53 bp):
ATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTAAAAGAAGCTAAGCCTA
Found at i:1003982 original size:85 final size:84
Alignment explanation
Indices: 1003710--1004048 Score: 430
Period size: 85 Copynumber: 4.0 Consensus size: 84
1003700 TCTTGATGAG
* *
1003710 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTATTGCTCAAT
1 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCT-TTGCTCGAT
1003775 TCATAACACTT-TGAATCAGCT
65 TCAT-ACACTTCT-AATCAGCT
* * * * * * *
1003796 TAAGTCCTTTGGGCCATCCACAAGACCTTCAGGTATGATGTTTTCAGCATTTCCTTTACTTGATT
1 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTTTGCTCGATT
* *
1003861 CACACACTTCAAATCAGCT
66 CATACACTTCTAATCAGCT
* *
1003880 TAAGTCCTTCGAGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTATTGCTCGAT
1 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCT-TTGCTCGAT
*
1003945 TCATACACTTCTAATCAACT
65 TCATACACTTCTAATCAGCT
* * * *
1003965 TAAGTCCTTTGGGCCATCCATAAGACCTTCGGG-AAGGATGTTTTCAACACTTCCTTTGCTTGAT
1 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAA-GATGTTTTCAACATTTCCTTTGCTCGAT
* *
1004029 TCACAACACTTCGAATCAGC
65 TCA-TACACTTCTAATCAGC
1004049 AATTCCCCAC
Statistics
Matches: 220, Mismatches: 29, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
84 75 0.34
85 95 0.43
86 50 0.23
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (84 bp):
TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTTTGCTCGATT
CATACACTTCTAATCAGCT
Found at i:1004040 original size:170 final size:170
Alignment explanation
Indices: 1003710--1004048 Score: 529
Period size: 170 Copynumber: 2.0 Consensus size: 170
1003700 TCTTGATGAG
* *
1003710 TAAGTCCTTCGGGCCATCCACAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTATTGCTCAAT
1 TAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTATTGCTCAAT
* * *
1003775 TCATAACACTTTGAATCAGCTTAAGTCCTTTGGGCCATCCACAAGACCTTCAGGTATGATGTTTT
66 TCATAACACTTTGAATCAACTTAAGTCCTTTGGGCCATCCACAAGACCTTCAGGAAGGATGTTTT
* *
1003840 CAGCATTTCCTTTACTTGATTCACACACTTCAAATCAGCT
131 CAACACTTCCTTTACTTGATTCACACACTTCAAATCAGCT
* *
1003880 TAAGTCCTTCGAGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTATTGCTCGAT
1 TAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTATTGCTCAAT
* *
1003945 TCAT-ACACTTCT-AATCAACTTAAGTCCTTTGGGCCATCCATAAGACCTTCGGGAAGGATGTTT
66 TCATAACACTT-TGAATCAACTTAAGTCCTTTGGGCCATCCACAAGACCTTCAGGAAGGATGTTT
* *
1004008 TCAACACTTCCTTTGCTTGATTCACAACACTTCGAATCAGC
130 TCAACACTTCCTTTACTTGATTCAC-ACACTTCAAATCAGC
1004049 AATTCCCCAC
Statistics
Matches: 154, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
169 74 0.48
170 80 0.52
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (170 bp):
TAAGTCCTTCGAGCCATCCACAAGACCTTCGGGCAAGATGTTTTCAACATTTCCTATTGCTCAAT
TCATAACACTTTGAATCAACTTAAGTCCTTTGGGCCATCCACAAGACCTTCAGGAAGGATGTTTT
CAACACTTCCTTTACTTGATTCACACACTTCAAATCAGCT
Found at i:1005342 original size:138 final size:133
Alignment explanation
Indices: 1005041--1005400 Score: 485
Period size: 138 Copynumber: 2.6 Consensus size: 133
1005031 AATATGAACC
*
1005041 GATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAT-AAGGAGAAGAAGTTCA
* * **
1005106 TAATGAGAAGAGCTTGTTCGACCTATCGCTCGATTCACGACATTTCAAATCAGTAACACCTCACT
65 TAATGAGAAGAACTTGTTC-AACTATAACTCGATTCACGACATTTCAAATCAGTAACACCTCACT
1005171 CTAGG
129 CTAGG
* *
1005176 GATCAACATTT-ATAGTGGAGAGTTCATAATGAAAAGAACTCATCCGATAAAGGAGAAGAAGTTC
1 GATCAACATTTCA-AGTGGAGAGTTCATAATGAGAAGAACTCATCTGAT-AAGGAGAAGAAGTTC
* * *
1005240 ATAATGAGAAGAACTTCTTCAACTTTAACTCGATTCATCG-CATATGGAGTCGAATCA-TAACAC
64 ATAATGAGAAGAACTTGTTCAACTATAACTCGATTCA-CGACAT-T----TCAAATCAGTAACAC
1005303 CTCACT-TGAGG
123 CTCACTCT-AGG
*
1005314 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAGGAAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAGG-AGAAGAAGTTCA
1005379 TAATGAGAAGAACTTGTTCAAC
65 TAATGAGAAGAACTTGTTCAAC
1005401 CATAGCTTGT
Statistics
Matches: 200, Mismatches: 15, Indels: 17
0.86 0.06 0.07
Matches are distributed among these distances:
134 17 0.09
135 79 0.40
137 5 0.03
138 92 0.46
139 7 0.04
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (133 bp):
GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTATAACTCGATTCACGACATTTCAAATCAGTAACACCTCACTCT
AGG
Found at i:1005397 original size:20 final size:19
Alignment explanation
Indices: 1005335--1005398 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
1005325 CCAGTGGAGA
1005335 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
1005354 CATCTGATAAGGAAGAAGAA--
1 -GT-TCATAATG-AGAAGAACT
1005374 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
1005394 GTTCA
1 GTTCA
1005399 ACCATAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 7 0.21
18 6 0.18
19 1 0.03
20 6 0.18
21 6 0.18
22 7 0.21
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:1005448 original size:138 final size:137
Alignment explanation
Indices: 1005041--1005448 Score: 408
Period size: 138 Copynumber: 3.0 Consensus size: 137
1005031 AATATGAACC
* *
1005041 GATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAAGGAGAAGAAGTTCA
* * * * ** ** * *
1005106 TAATGAGAAGAGCTTGTTCGACCTATCGCTCGATTCACGACATTTCA-AATCAGT-AACACCTC-
66 TAATGAGAAGAACTTGTTCAACC-ATAGCTCGA-TCTC--CATCACATAAGGAGTGAACAACACA
1005168 ACT-C-T-AGG
127 ACTACTTGAGG
* *
1005176 GATCAACATTT-ATAGTGGAGAGTTCATAATGAAAAGAACTCATCCGATAAAGGAGAAGAAGTTC
1 GATCAACATTTCA-AGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAAGGAGAAGAAGTTC
* ** * * *
1005240 ATAATGAGAAGAACTTCTTCAACTTTAACTCGAT-T-CATCGCATATGGAGTCGAATCATA-ACA
65 ATAATGAGAAGAACTTGTTCAACCATAGCTCGATCTCCATCACATAAGGAGT-GAA-CA-ACACA
*
1005302 CCTCACTTGAGG
127 ACT-ACTTGAGG
*
1005314 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAT-AAGGAAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAAGG-AGAAGAAGTTC
*
1005378 ATAATGAGAAGAACTTGTTCAACCATAGCTTG-TCTCCATCACATAAGGAGTTGGAACAACACAA
65 ATAATGAGAAGAACTTGTTCAACCATAGCTCGATCTCCATCACATAAGGAG-T-GAACAACACAA
*
1005442 ATACTTG
128 CTACTTG
1005449 GCTCATCCAT
Statistics
Matches: 223, Mismatches: 33, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
129 5 0.02
130 4 0.02
132 2 0.01
133 4 0.02
134 9 0.04
135 78 0.35
136 1 0.00
137 6 0.03
138 92 0.41
139 18 0.08
140 4 0.02
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (137 bp):
GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGATAAAGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCATAGCTCGATCTCCATCACATAAGGAGTGAACAACACAACTA
CTTGAGG
Found at i:1007336 original size:21 final size:21
Alignment explanation
Indices: 1007300--1007347 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1007290 ATTATTTCTA
1007300 TTAA-TTGCCTTTAATTTA-T
1 TTAATTTGCCTTTAATTTAGT
*
1007319 TTGATTTGCCTGTTAATTTAGT
1 TTAATTTGCCT-TTAATTTAGT
1007341 TTAATTT
1 TTAATTT
1007348 CAATCCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 6 0.25
21 8 0.33
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.58
Consensus pattern (21 bp):
TTAATTTGCCTTTAATTTAGT
Found at i:1020104 original size:21 final size:22
Alignment explanation
Indices: 1020071--1020111 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1020061 GTTCCTGGCA
1020071 CGGGGACGATACT-GGGACGGC
1 CGGGGACGATACTAGGGACGGC
1020092 CGGGGTACG-TACTAGGGACG
1 CGGGG-ACGATACTAGGGACG
1020112 TGCCACGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.20, C:0.22, G:0.46, T:0.12
Consensus pattern (22 bp):
CGGGGACGATACTAGGGACGGC
Found at i:1021340 original size:75 final size:75
Alignment explanation
Indices: 1021221--1021387 Score: 196
Period size: 75 Copynumber: 2.2 Consensus size: 75
1021211 ATGATTTCAG
* *
1021221 TCTTAAGATTTGACACTTTAATATTATAGTTTGATTATAGATTTTATTATTCTAAAGTTAATATT
1 TCTTGAGATTTGACATTTTAATATTATAGTTTGATTATAGATTTTATTATTCTAAAGTTAATATT
* *
1021286 GTGGGTTGAA
66 ATAGGTTGAA
* * * *
1021296 TCTTGAGATTTGACATTTTAATATTGTTA-TTTGTTTAT-GAATTTTATTGTTCTAAATTTAATA
1 TCTTGAGATTTGACATTTTAATATT-ATAGTTTGATTATAG-ATTTTATTATTCTAAAGTTAATA
* *
1021359 TTATAGTTTGAG
64 TTATAGGTTGAA
*
1021371 TCTTGATATTTGA-ATTT
1 TCTTGAGATTTGACATTT
1021388 ATTTATAATT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
74 5 0.06
75 72 0.91
76 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (75 bp):
TCTTGAGATTTGACATTTTAATATTATAGTTTGATTATAGATTTTATTATTCTAAAGTTAATATT
ATAGGTTGAA
Found at i:1021403 original size:11 final size:11
Alignment explanation
Indices: 1021383--1021419 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1021373 TTGATATTTG
1021383 AATTTATTTAT
1 AATTTATTTAT
1021394 AATTT-TTT-T
1 AATTTATTTAT
1021403 ACATTTATTTAT
1 A-ATTTATTTAT
1021415 AATTT
1 AATTT
1021420 TAAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
AATTTATTTAT
Found at i:1021508 original size:12 final size:12
Alignment explanation
Indices: 1021491--1021518 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1021481 GTTTCTTGTC
1021491 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1021503 CCGTCCCCGTAT
1 CCGTCCCCGTAT
1021515 CCGT
1 CCGT
1021519 ATCAGTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.50, G:0.18, T:0.25
Consensus pattern (12 bp):
CCGTCCCCGTAT
Found at i:1022739 original size:23 final size:23
Alignment explanation
Indices: 1022712--1022763 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1022702 CTTGTACTAA
* *
1022712 TACCTCTATAGTGCATCTTCCAT
1 TACCTATAAAGTGCATCTTCCAT
*
1022735 TACCTATAAAGTGCATTTTCC-T
1 TACCTATAAAGTGCATCTTCCAT
*
1022757 TATCTAT
1 TACCTAT
1022764 TGGATTTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (23 bp):
TACCTATAAAGTGCATCTTCCAT
Found at i:1024442 original size:20 final size:19
Alignment explanation
Indices: 1024413--1024465 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1024403 GAACCGGCTG
1024413 AAAACCGGAAAAAATCAAA
1 AAAACCGGAAAAAATCAAA
*
1024432 AAAACCCGGAAAAAATTAAA
1 AAAA-CCGGAAAAAATCAAA
**
1024452 AAAAAGGGAAAAAA
1 AAAACCGGAAAAAA
1024466 CCACCAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.70, C:0.11, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAACCGGAAAAAATCAAA
Found at i:1031978 original size:3 final size:3
Alignment explanation
Indices: 1031970--1032010 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1031960 AGGGAAAACA
1031970 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1032011 AGAGAAACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1033565 original size:18 final size:18
Alignment explanation
Indices: 1033542--1033591 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1033532 AGAGAAAGGA
1033542 ATTAGGGATTGAAGGGGG
1 ATTAGGGATTGAAGGGGG
1033560 ATTAGGGATTGAAGGGGG
1 ATTAGGGATTGAAGGGGG
1033578 ATTAGGGATTGAAG
1 ATTAGGGATTGAAG
1033592 TGTTATCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (18 bp):
ATTAGGGATTGAAGGGGG
Found at i:1034268 original size:11 final size:12
Alignment explanation
Indices: 1034238--1034283 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
1034228 TTGGTGCTGG
1034238 AAACAAGATAAA
1 AAACAAGATAAA
* *
1034250 AAATAAGAT-TA
1 AAACAAGATAAA
1034261 AAACAAGATAAA
1 AAACAAGATAAA
*
1034273 GAA-AAGATAAA
1 AAACAAGATAAA
1034284 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:1034268 original size:23 final size:22
Alignment explanation
Indices: 1034238--1034280 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1034228 TTGGTGCTGG
1034238 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
1034261 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
1034281 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:1038599 original size:17 final size:16
Alignment explanation
Indices: 1038579--1038627 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1038569 TTTTTTGAAA
1038579 TTTTGGCTTTTTTGTTT
1 TTTTGGCTTTTTT-TTT
* *
1038596 TTTTGCCTTTTTTTTG
1 TTTTGGCTTTTTTTTT
1038612 TTTT-G-TTTTTTTTT
1 TTTTGGCTTTTTTTTT
1038626 TT
1 TT
1038628 GAAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 10 0.36
16 6 0.21
17 12 0.43
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (16 bp):
TTTTGGCTTTTTTTTT
Found at i:1038986 original size:11 final size:12
Alignment explanation
Indices: 1038956--1039001 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
1038946 TTGGTGCTGG
1038956 AAACAAGATAAA
1 AAACAAGATAAA
* *
1038968 AAATAAGAT-TA
1 AAACAAGATAAA
1038979 AAACAAGATAAA
1 AAACAAGATAAA
*
1038991 GAA-AAGATAAA
1 AAACAAGATAAA
1039002 GGAATTGCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:1038986 original size:23 final size:22
Alignment explanation
Indices: 1038956--1038998 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1038946 TTGGTGCTGG
1038956 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
1038979 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
1038999 AAAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:1040983 original size:32 final size:34
Alignment explanation
Indices: 1040947--1041016 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1040937 ACCTTACAAC
* *
1040947 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
*
1040979 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
1041013 TCCC
1 TCCC
1041017 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:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:1041360 original size:21 final size:21
Alignment explanation
Indices: 1041336--1041419 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
1041326 CTAGCCGTTG
*
1041336 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
**
1041357 CAG-CAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
*
1041377 CAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
1041398 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
1041419 C
1 C
1041420 TAATTGCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.02
20 14 0.26
21 39 0.72
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:1041487 original size:22 final size:23
Alignment explanation
Indices: 1041454--1041496 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1041444 ATGGATGCAC
1041454 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
1041477 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
1041497 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:1041509 original size:21 final size:20
Alignment explanation
Indices: 1041440--1041538 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
1041430 CGGTGTTTGA
*
1041440 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
1041460 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1041482 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
1041502 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
1041524 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1041539 TTGACACCCT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.21
21 31 0.44
22 17 0.24
23 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1041639 original size:29 final size:29
Alignment explanation
Indices: 1041618--1041675 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1041608 AAACTTTGAA
1041618 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1041647 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1041676 TTCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1041665 original size:30 final size:30
Alignment explanation
Indices: 1041618--1041676 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
1041608 AAACTTTGAA
1041618 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1041647 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
1041677 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1042996 original size:19 final size:20
Alignment explanation
Indices: 1042953--1043000 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1042943 TCTAAATCCT
*
1042953 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1042973 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1042992 TTTTCAAAA
1 TTTTCAAAA
1043001 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1044407 original size:22 final size:20
Alignment explanation
Indices: 1044360--1044437 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 20
1044350 CGGTGTTTGA
1044360 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCATG
1044380 GTGCATGGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCATG
* *
1044402 GTGCATGGATGCATTGCAGGG
1 GTGCATGGATGCACTGCA-TG
*
1044423 GTGCATGAATGCACT
1 GTGCATGGATGCACT
1044438 TTGACACCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
19 4 0.08
20 14 0.28
21 14 0.28
22 14 0.28
23 4 0.08
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (20 bp):
GTGCATGGATGCACTGCATG
Found at i:1044538 original size:29 final size:29
Alignment explanation
Indices: 1044517--1044574 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1044507 AAACTTTGAA
1044517 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1044546 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1044575 TCCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1044564 original size:30 final size:30
Alignment explanation
Indices: 1044517--1044575 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
1044507 AAACTTTGAA
1044517 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1044546 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
1044576 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1048667 original size:22 final size:22
Alignment explanation
Indices: 1048639--1048682 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1048629 ACTGTCGTTA
1048639 GATTTTTAATA-GATTATTGACT
1 GATTTTT-ATAGGATTATTGACT
1048661 GATTTTTATAGGATTATTGACT
1 GATTTTTATAGGATTATTGACT
1048683 TTATACGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (22 bp):
GATTTTTATAGGATTATTGACT
Found at i:1052829 original size:13 final size:13
Alignment explanation
Indices: 1052796--1052831 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1052786 ATAATAATAA
*
1052796 TTCAAAAATACTT
1 TTCAAAATTACTT
*
1052809 CTCAAAATTACTT
1 TTCAAAATTACTT
1052822 TTCAAAATTA
1 TTCAAAATTA
1052832 TATTTTCACG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (13 bp):
TTCAAAATTACTT
Found at i:1055989 original size:29 final size:29
Alignment explanation
Indices: 1055956--1056011 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1055946 AATTTGATGT
*
1055956 TTCAGGGAGAGTCTTTGGTTGTTCATAAC
1 TTCAGGGAGAGTCTTAGGTTGTTCATAAC
*
1055985 TTCAGGGAGATTCTTAGGTTGTTCATA
1 TTCAGGGAGAGTCTTAGGTTGTTCATA
1056012 GAGTGATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.39
Consensus pattern (29 bp):
TTCAGGGAGAGTCTTAGGTTGTTCATAAC
Found at i:1059031 original size:3 final size:3
Alignment explanation
Indices: 1059023--1059110 Score: 81
Period size: 3 Copynumber: 28.3 Consensus size: 3
1059013 CTCCCCCAGG
* *
1059023 TCT TCT TCT TCT TCT TCT TCT TCAT TCT TCAT TCT TCCT TCT TCC TAT
1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TC-T TCT T-CT TCT TCT TCT
* *
1059071 T-T CCT TCT TCTT TCTT TCT T-T TTT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TC-T TC-T TCT TCT TCT TCT TCT TCT TCT TCT T
1059111 GCACAGTGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.04
3 54 0.74
4 16 0.22
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1063352 original size:24 final size:23
Alignment explanation
Indices: 1063311--1063388 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 23
1063301 ATACCTTACT
* *
1063311 TGGATTCTGATCGGATACTTAACC
1 TGGATTCTGAT-TGATACTTGACC
*
1063335 TGGATTCTGATTGAATACTTGATC
1 TGGATTCTGATTG-ATACTTGACC
*
1063359 TGGATTTTGATATGATACTTGACC
1 TGGATTCTGAT-TGATACTTGACC
1063383 TGGATT
1 TGGATT
1063389 ATGTTATGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.02
24 44 0.94
25 2 0.04
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (23 bp):
TGGATTCTGATTGATACTTGACC
Found at i:1063404 original size:24 final size:24
Alignment explanation
Indices: 1063324--1063398 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1063314 ATTCTGATCG
* *
1063324 GATACTTAACCTGGATTCTGAT-T
1 GATACTTGACCTGGATTATGATAT
* *
1063347 GAATACTTGATCTGGATTTTGATAT
1 G-ATACTTGACCTGGATTATGATAT
*
1063372 GATACTTGACCTGGATTATGTTAT
1 GATACTTGACCTGGATTATGATAT
1063396 GAT
1 GAT
1063399 TTTTGATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 41 0.93
25 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
GATACTTGACCTGGATTATGATAT
Found at i:1065526 original size:12 final size:13
Alignment explanation
Indices: 1065488--1065528 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1065478 AACCCCACCC
*
1065488 GACCTGACCCGTT
1 GACCCGACCCGTT
1065501 GACCCGACCCGTT
1 GACCCGACCCGTT
1065514 GACCCGA-CCGTT
1 GACCCGACCCGTT
1065526 GAC
1 GAC
1065529 TGTTGACCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1068033 original size:24 final size:24
Alignment explanation
Indices: 1068005--1068092 Score: 142
Period size: 24 Copynumber: 3.7 Consensus size: 24
1067995 TTCTATTATA
1068005 ATACTTGACCTGGATTTTGATTGG
1 ATACTTGACCTGGATTTTGATTGG
* *
1068029 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTTTGATTGG
1068053 ATACTTGACCTGGATTTTGATCT-G
1 ATACTTGACCTGGATTTTGAT-TGG
1068077 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1068093 ATGTTATGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 58 0.98
25 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.40
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATTGG
Found at i:1068108 original size:24 final size:24
Alignment explanation
Indices: 1068005--1068102 Score: 119
Period size: 24 Copynumber: 4.1 Consensus size: 24
1067995 TTCTATTATA
*
1068005 ATACTTGACCTGGATTTTGAT-TGG
1 ATACTTGACCTGGATTATGATAT-G
*
1068029 ATACTTGACCTGGATTCTGAT-TG
1 ATACTTGACCTGGATTATGATATG
* *
1068052 AATACTTGACCTGGATTTTGATCTG
1 -ATACTTGACCTGGATTATGATATG
*
1068077 ATACTTGACCTGGATTATGTTATG
1 ATACTTGACCTGGATTATGATATG
1068101 AT
1 AT
1068103 TTTTGATATA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.01
24 64 0.96
25 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (24 bp):
ATACTTGACCTGGATTATGATATG
Found at i:1075741 original size:3 final size:3
Alignment explanation
Indices: 1075733--1075764 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1075723 ATATGAGAAT
1075733 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1075765 GTTCCCAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1078208 original size:3 final size:3
Alignment explanation
Indices: 1078200--1078795 Score: 964
Period size: 3 Copynumber: 203.3 Consensus size: 3
1078190 ACTGTAGATA
1078200 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AA- AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078246 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078293 AAG AAG AAG AAAG AAG AAG AAG -AG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
1078338 AAT AA- AAG AAAG AAG AAG AAG AA- AAG AAG AAG AAG AAG AAG AAAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
1078383 AAG AAG AAG AAG AAG -AG AAAG AA- AAG AA- AA- AAG AAAG AAG AAG
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG AAG
*
1078426 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG ACG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078473 AAG AAG AAG AAG AA- AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078519 AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078565 AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078612 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA- AAG -AG AAG -AG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078656 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078704 -AG AAG AAG AAAG AAG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1078750 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1078796 CTATATTGGG
Statistics
Matches: 563, Mismatches: 3, Indels: 54
0.91 0.00 0.09
Matches are distributed among these distances:
2 42 0.07
3 501 0.89
4 20 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1079942 original size:26 final size:27
Alignment explanation
Indices: 1079890--1079948 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1079880 CCATATTACT
** *
1079890 TTTTACTCTTTAAGGGTATTTTTGTAA
1 TTTTACTCCATAAGGGTATTTTCGTAA
1079917 TTTTACTCCATAA-GGTATTTTCGTAA
1 TTTTACTCCATAAGGGTATTTTCGTAA
1079943 TTTTAC
1 TTTTAC
1079949 CTAACTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (27 bp):
TTTTACTCCATAAGGGTATTTTCGTAA
Found at i:1083910 original size:2 final size:2
Alignment explanation
Indices: 1083903--1083934 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1083893 GTTAACTTGC
1083903 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
1083935 TAATGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1088038 original size:15 final size:13
Alignment explanation
Indices: 1088004--1088030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1087994 ATCATATATA
1088004 ATTATAAAAAAAT
1 ATTATAAAAAAAT
1088017 ATTATAAAAAAAT
1 ATTATAAAAAAAT
1088030 A
1 A
1088031 CCTTATAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATTATAAAAAAAT
Found at i:1088273 original size:13 final size:13
Alignment explanation
Indices: 1088255--1088279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1088245 TGCATTATGC
1088255 ATGTGATAATTGA
1 ATGTGATAATTGA
1088268 ATGTGATAATTG
1 ATGTGATAATTG
1088280 CAAGACGCGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (13 bp):
ATGTGATAATTGA
Found at i:1092091 original size:21 final size:21
Alignment explanation
Indices: 1092067--1092108 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1092057 CTACCTAACT
1092067 ATGTTTTTCTTTTCTTGCAAA
1 ATGTTTTTCTTTTCTTGCAAA
1092088 ATGTTTTTCTTTTCTTGCAAA
1 ATGTTTTTCTTTTCTTGCAAA
1092109 GTAAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (21 bp):
ATGTTTTTCTTTTCTTGCAAA
Found at i:1096140 original size:16 final size:16
Alignment explanation
Indices: 1096119--1096165 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
1096109 ATGATTAAGC
1096119 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
1096135 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
1096151 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
1096166 GAATCTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:1100267 original size:34 final size:34
Alignment explanation
Indices: 1100227--1100314 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
1100217 AATGATAATA
* * *
1100227 AACAAAATTATCAAAATATATTA-ACAAAAAGTCC
1 AACAAAATTAACAAAATAAATTATA-AAAAAATCC
*
1100261 AACAAAATAAACAAAATAAATTATAAAAAAATCC
1 AACAAAATTAACAAAATAAATTATAAAAAAATCC
*
1100295 AACCAAATTAACAAAATAAA
1 AACAAAATTAACAAAATAAA
1100315 GCAAGTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 46 0.98
35 1 0.02
ACGTcount: A:0.66, C:0.14, G:0.01, T:0.19
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTATAAAAAAATCC
Found at i:1100970 original size:23 final size:23
Alignment explanation
Indices: 1100940--1100998 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
1100930 ATAATTGGTT
1100940 CAATAATTGAGTGAGTAGACCAG
1 CAATAATTGAGTGAGTAGACCAG
1100963 CAATAATTGAGTGAGTAGACCAG
1 CAATAATTGAGTGAGTAGACCAG
*
1100986 CAATAACTGAGTG
1 CAATAATTGAGTG
1100999 TGCGGTGCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (23 bp):
CAATAATTGAGTGAGTAGACCAG
Found at i:1103530 original size:30 final size:30
Alignment explanation
Indices: 1103494--1103789 Score: 164
Period size: 30 Copynumber: 10.1 Consensus size: 30
1103484 TCTTTCACAA
* *
1103494 TAACTAAAAAAATGTGTTTTATTTTTATCT
1 TAACTAAAAAAATATATTTTATTTTTATCT
* *
1103524 TAACT--AAAAATATATTTTAATCTTATCT
1 TAACTAAAAAAATATATTTTATTTTTATCT
*
1103552 TAACTTAAAAATATATATTTTATTTTTATCT
1 TAAC-TAAAAAAATATATTTTATTTTTATCT
* **
1103583 TAAATTTAAAAATATATTTTATTTTTATCT
1 TAACTAAAAAAATATATTTTATTTTTATCT
* ** * * *
1103613 TAACTTATTACATATATTATATTATTGAT-T
1 TAACTAAAAAAATATATTTTATT-TTTATCT
* * ** * * *
1103643 TAAATTATTAAATATATTCTATTCTTACCT
1 TAACTAAAAAAATATATTTTATTTTTATCT
* * ** * * *
1103673 TAAATTATTAAGTAT-TATTTATTATTATTT
1 TAACTAAAAAAATATAT-TTTATTTTTATCT
* * * *
1103703 TAACTTAAAATATATA-TTTATTCTTATTT
1 TAACTAAAAAAATATATTTTATTTTTATCT
**
1103732 TAA-T-TTAAAA-ATA--TT-TTTTTATCT
1 TAACTAAAAAAATATATTTTATTTTTATCT
*
1103756 TAATTAAAAAAGATATATTTTATTTTTATCT
1 TAACTAAAAAA-ATATATTTTATTTTTATCT
1103787 TAA
1 TAA
1103790 TTTTAAAATA
Statistics
Matches: 210, Mismatches: 42, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
24 10 0.05
25 3 0.01
26 6 0.03
27 4 0.02
28 27 0.13
29 19 0.09
30 102 0.49
31 39 0.19
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (30 bp):
TAACTAAAAAAATATATTTTATTTTTATCT
Found at i:1103657 original size:60 final size:56
Alignment explanation
Indices: 1103531--1103801 Score: 189
Period size: 60 Copynumber: 4.7 Consensus size: 56
1103521 TCTTAACTAA
* ** * *
1103531 AAATATATTTTAATCTTATCTTAACTTAAAAATATATATTTTATTTTTATCTTAAATTTAA
1 AAATATATTTTATTCTTATCTTAACTT-ATTA-ATATA-TTTATTATTAT-TTAAA-TTAT
*
1103592 AAATATATTTTATTTTTATCTTAACTTATTACATATATTATATTATTGATTTAAATTATT
1 AAATATATTTTATTCTTATCTTAACTTATTA-ATATATT-TATTATT-ATTTAAATTA-T
* * * *
1103652 AAATATATTCTATTCTTACCTTAAATTATTAAGTATTATTTATTATTATTTTAACTTA-
1 AAATATATTTTATTCTTATCTTAACTTATTAA-TA-TATTTATTATTA-TTTAAATTAT
* * * *
1103710 AAATATATATTTATTCTTATTTTAA-TT-TAAAAATATTT-TT-TTATCTT-AATTAAAA
1 AAATATAT-TTTATTCTTATCTTAACTTATTAATATATTTATTATTAT-TTAAATT--AT
* *
1103765 AAGATATATTTTATTTTTATCTTAA-TT-TTAAAATATT
1 AA-ATATATTTTATTCTTATCTTAACTTATTAATATATT
1103802 ATAAGAATAA
Statistics
Matches: 177, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
52 4 0.02
53 5 0.03
54 3 0.02
55 32 0.18
56 7 0.04
57 3 0.02
58 10 0.06
59 20 0.11
60 62 0.35
61 31 0.18
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.55
Consensus pattern (56 bp):
AAATATATTTTATTCTTATCTTAACTTATTAATATATTTATTATTATTTAAATTAT
Found at i:1103753 original size:24 final size:26
Alignment explanation
Indices: 1103688--1103781 Score: 95
Period size: 24 Copynumber: 3.6 Consensus size: 26
1103678 TATTAAGTAT
1103688 TATTTATTATTATTTTAACTTAAAATATA
1 TATTTATTATTATTTTAA-TTAAAA-A-A
* *
1103717 TATTTATTCTTATTTTAATTTAAAAA
1 TATTTATTATTATTTTAATTAAAAAA
*
1103743 TATTT-TT-TTATCTTAATTAAAAAA
1 TATTTATTATTATTTTAATTAAAAAA
* *
1103767 GATATATT-TTATTTT
1 TATTTATTATTATTTT
1103782 TATCTTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
24 18 0.32
25 10 0.18
26 6 0.11
27 1 0.02
28 5 0.09
29 17 0.30
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
TATTTATTATTATTTTAATTAAAAAA
Found at i:1104022 original size:40 final size:41
Alignment explanation
Indices: 1103846--1104162 Score: 345
Period size: 41 Copynumber: 7.7 Consensus size: 41
1103836 TAGCGTCGTT
*
1103846 TACAAACGCCGCTATAGACTCTTACTTTAGTGGTGTTTTTA
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
* * * * * * *
1103887 TACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTT
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
* * *
1103928 TAGCAAACGCCG-TAATAGAGTAGTACTTTAGCGGTGTTATTT-
1 TA-CAAACGCCGCT-ATAGACTCGTACTTTAGTGGTGTT-TTTA
* *
1103970 TACAAATGCCGCTATAGACTCTTACTTTAGTGG-GTTTTTA
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
* *
1104010 TACAAATGCCGCTATAGACTCTTACTTTAGTGG-GTTTTTA
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
* *
1104050 CACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTA
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
* * *
1104091 TAAAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTTTTGTT
1 TACAAACGCCGCTATAGACTCGTACTTTAGTGGTG-TTTT-TA
* * * *
1104134 TATAAACGCCGTTAAAGACTCTTACTTTA
1 TACAAACGCCGCTATAGACTCGTACTTTA
1104163 CAAATTTGTA
Statistics
Matches: 241, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.01
40 73 0.30
41 97 0.40
42 38 0.16
43 30 0.12
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (41 bp):
TACAAACGCCGCTATAGACTCGTACTTTAGTGGTGTTTTTA
Found at i:1105047 original size:14 final size:14
Alignment explanation
Indices: 1105011--1105038 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1105001 ATGTATAAAT
1105011 AAATAAATCCCTGC
1 AAATAAATCCCTGC
1105025 AAATAAATCCCTGC
1 AAATAAATCCCTGC
1105039 GTAAAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATAAATCCCTGC
Found at i:1112627 original size:24 final size:26
Alignment explanation
Indices: 1112569--1112650 Score: 92
Period size: 29 Copynumber: 2.9 Consensus size: 26
1112559 AATATTTTAA
1112569 AATTAAGATAAAAATAAAATATATCTTTT
1 AATTAAGATAAAAATAAAATATA---TTT
1112598 AATTAAGATAAAAATAAAATATATTGTT
1 AATTAAGATAAAAATAAAATATA-T-TT
* *
1112626 AAATTAAAATAAGAATAAAATATAT
1 -AATTAAGATAAAAATAAAATATAT
1112651 ATTTTAAGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
29 44 0.90
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (26 bp):
AATTAAGATAAAAATAAAATATATTT
Found at i:1112665 original size:30 final size:29
Alignment explanation
Indices: 1112560--1112922 Score: 329
Period size: 30 Copynumber: 12.2 Consensus size: 29
1112550 TATTCTTATA
* *
1112560 ATATTTTAAAATTAAGATAAAAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
1112589 ATATCTTTTAA-TTAAGATAAAAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
* * * *
1112618 ATATTGTTAAATTAAAATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
1112647 ATATATTTTAAGTTAAAATAATAATAAAGA-
1 ATAT-TTTTAAGTTAAGATAAAAATAAA-AT
** * * * *
1112677 ATACTTAATAATTTAAGGTAAGAATAGAAT
1 ATA-TTTTTAAGTTAAGATAAAAATAAAAT
* * * *
1112707 ATATTTAATAATTTAA-ATTAATAATATAAT
1 ATATTT-TTAAGTTAAGA-TAAAAATAAAAT
**
1112737 ATATGTAATAAGTTAAGATAAAAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
1112767 ATATTTTTAAAAGTTAAGATAAAAATAAAATAT
1 ATATTTTT--AAGTTAAGATAAAAAT-AAA-AT
*** *
1112800 ATATTTTTAAGTTAAGATTTGATTAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
1112829 ATATTTTT-AGTTAAGATAAAAATAAAAC
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* * *
1112857 ACATTTTTTAGTTAAGATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
1112886 ATATTTAATAAGTTAAGATAAAAATAAAAT
1 ATATTT-TTAAGTTAAGATAAAAATAAAAT
1112916 ATATTTT
1 ATATTTT
1112923 AAAATAATTC
Statistics
Matches: 277, Mismatches: 41, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
28 27 0.10
29 84 0.30
30 121 0.44
31 32 0.12
32 3 0.01
33 10 0.04
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAGTTAAGATAAAAATAAAAT
Found at i:1112887 original size:149 final size:150
Alignment explanation
Indices: 1112564--1112927 Score: 390
Period size: 149 Copynumber: 2.5 Consensus size: 150
1112554 CTTATAATAT
** *
1112564 TTTAA-AA-TTAAGATAAAAATAAAATATATCTTTTAA-TTAAGATAAAAATAAAATATATTGTT
1 TTTAATAAGTTAAGATAAAAATAAAATATATCTAATAAGTTAAGATAAAAATAAAATATATTTTT
* *
1112626 -AAATTAAAATAAGAATAAAATATATATTTTAAGTTAAAATAATAATAAAGAATACTTAATAATT
66 AAAATTAAAATAAAAATAAAATATATATTTTAAGTTAAAATAATAATAAAGAATACTTAATAAGT
* * * * *
1112690 TAAGGTAAGAATAGAATATA
131 TAAGATAAAAATAAAACACA
* * * *
1112710 TTTAATAATTTAA-ATTAATAATATAATATATGTAATAAGTTAAGATAAAAATAAAATATATTTT
1 TTTAATAAGTTAAGA-TAAAAATAAAATATATCTAATAAGTTAAGATAAAAATAAAATATATTTT
* * * * *
1112774 TAAAAGTTAAGATAAAAATAAAATATATATTTTTAAGTTAAGAT-TTGATTAAA-ATATA-TT-T
65 TAAAA-TTAAAATAAAAATAAAATATATA-TTTTAAGTTAAAATAAT-AATAAAGA-ATACTTAA
*
1112835 TTAGTTAAGATAAAAATAAAACACA
126 TAAGTTAAGATAAAAATAAAACACA
* * * *
1112860 TTT-TTTAGTTAAGATAAGAATAAAATATATTTAATAAGTTAAGATAAAAATAAAATATA-TTTT
1 TTTAATAAGTTAAGATAAAAATAAAATATATCTAATAAGTTAAGATAAAAATAAAATATATTTTT
1112923 AAAAT
66 AAAAT
1112928 AATTCAAAAA
Statistics
Matches: 183, Mismatches: 25, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
146 5 0.03
147 4 0.02
148 30 0.16
149 73 0.40
150 25 0.14
151 25 0.14
152 21 0.11
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (150 bp):
TTTAATAAGTTAAGATAAAAATAAAATATATCTAATAAGTTAAGATAAAAATAAAATATATTTTT
AAAATTAAAATAAAAATAAAATATATATTTTAAGTTAAAATAATAATAAAGAATACTTAATAAGT
TAAGATAAAAATAAAACACA
Found at i:1117077 original size:34 final size:35
Alignment explanation
Indices: 1117036--1117120 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1117026 AATGGTAATA
* * * * *
1117036 AACAAAATTATCAAAATATATTA-ACAAAAAGTCC
1 AACAAAATTAACAAAAAAAATTATAAAAAAAATCC
*
1117070 AACAAAATAAACAAAAAAAATTATAAAAAAAATCC
1 AACAAAATTAACAAAAAAAATTATAAAAAAAATCC
*
1117105 AACCAAATTAACAAAA
1 AACAAAATTAACAAAA
1117121 CAAAGTAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 19 0.45
35 23 0.55
ACGTcount: A:0.67, C:0.14, G:0.01, T:0.18
Consensus pattern (35 bp):
AACAAAATTAACAAAAAAAATTATAAAAAAAATCC
Found at i:1117173 original size:26 final size:23
Alignment explanation
Indices: 1117143--1117200 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 23
1117133 TTAATGATAA
1117143 AAAAAATTACA-ACAATAAAATATCT
1 AAAAAATTA-ATA-AATAAAATAT-T
1117168 ACAAAAATTAATTAAATAAAATATT
1 A-AAAAATTAA-TAAATAAAATATT
1117193 AAAAAATT
1 AAAAAATT
1117201 TAAATACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 7 0.23
25 4 0.13
26 18 0.60
27 1 0.03
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAAATTAATAAATAAAATATT
Found at i:1117211 original size:17 final size:17
Alignment explanation
Indices: 1117186--1117218 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1117176 TAATTAAATA
1117186 AAATATTAAA-AAATTT
1 AAATATTAAATAAATTT
1117202 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
1117219 ACAAACAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTAAATAAATTT
Found at i:1117212 original size:25 final size:26
Alignment explanation
Indices: 1117156--1117206 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1117146 AAATTACAAC
*
1117156 AATAAAATATCTACAAAAATTAATTA
1 AATAAAATATCTACAAAAATTAAATA
1117182 AATAAAATAT-TA-AAAAATTTAAATA
1 AATAAAATATCTACAAAAA-TTAAATA
1117207 CTTAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 8 0.35
26 10 0.43
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AATAAAATATCTACAAAAATTAAATA
Found at i:1121750 original size:23 final size:23
Alignment explanation
Indices: 1121724--1121778 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
1121714 TAAATACACA
1121724 GAAGTGCCACGTAGAATTGCACC
1 GAAGTGCCACGTAGAATTGCACC
*
1121747 GAAGTGCCGCGTAGAATTGCACC
1 GAAGTGCCACGTAGAATTGCACC
*
1121770 GTAGTGCCA
1 GAAGTGCCA
1121779 TATAAAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.18
Consensus pattern (23 bp):
GAAGTGCCACGTAGAATTGCACC
Found at i:1125318 original size:21 final size:21
Alignment explanation
Indices: 1125292--1125331 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1125282 CAGAACTCCA
*
1125292 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
1125313 GGGGGGAATCGATTCCCCT
1 GGGGGGAATCGATTCCCCT
1125332 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1136064 original size:15 final size:14
Alignment explanation
Indices: 1136031--1136084 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 14
1136021 TTATATGACT
1136031 AAAT-AATA-ATAA
1 AAATAAATATATAA
*
1136043 TAATAAATATATTAA
1 AAATAAATATA-TAA
*
1136058 AAATAAACATATAA
1 AAATAAATATATAA
*
1136072 AATTAAATA-ATAA
1 AAATAAATATATAA
1136085 TTAAATAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 3 0.09
13 8 0.24
14 11 0.32
15 12 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAATATATAA
Found at i:1137397 original size:3 final size:3
Alignment explanation
Indices: 1137391--1137475 Score: 93
Period size: 3 Copynumber: 29.0 Consensus size: 3
1137381 ATTTATTATT
* * * *
1137391 TAA TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAT TAT TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1137437 TAA TAA TAT TAA TAA TAA TAA AAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1137476 AAATGATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
2 3 0.04
3 67 0.96
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1138092 original size:123 final size:120
Alignment explanation
Indices: 1137837--1138405 Score: 567
Period size: 123 Copynumber: 4.7 Consensus size: 120
1137827 GAATTAAGGC
* * * * *
1137837 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTTAAATGAGTT-TTTCTTATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTT-TCATT
* * * * * * **
1137900 ATGAACACTTCT-GGAAATTTTGATACTGATTTATCTCCTTATGTGATAAAGTCATAAAA
64 ATGAAC-TTTCTCTGAAA-ATTGATA-TGATCTATCTCCTTCTGTGATAGAGTCATGCAA
*
1137959 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTTTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCATTAT
*
1138024 GAACTTTCTCTGAAAGAGTTGATGATGATCTATCTTCTTCTGTGATAGAGTCATGCAA
66 GAACTTTCTCTGAAA-A-TTGAT-ATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
*
1138082 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCATTAT
* ** *
1138147 GAACTTTCTCTGGAAAA--G-T-TG----ATC-CATTGAGTGAT-GAATTCGA-GCAA
66 GAACTTTCTCT-GAAAATTGATATGATCTATCTCCTTCTGTGATAG-AGTC-ATGCAA
* * *
1138194 AAGGTTAAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTTCTCATT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTT-TCATT
* * * * * *
1138258 ATGAACTCCTTCT-GGAAATATTAATGTTGATCTATCTCCTTCTGCGATAGCGTTATGCAA
64 ATGAACT--TTCTCTGAAA-ATTGAT-ATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* * *
1138318 AAGGTTGAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTCTTCTGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCATTAT
1138383 GAACTTTCTCTGGAAAAGTTGAT
66 GAACTTTCTCT-GAAAA-TTGAT
1138406 CCATCGAATG
Statistics
Matches: 374, Mismatches: 44, Indels: 57
0.79 0.09 0.12
Matches are distributed among these distances:
111 1 0.00
112 54 0.14
113 33 0.09
114 1 0.00
115 4 0.01
117 3 0.01
119 3 0.01
120 1 0.00
121 8 0.02
122 60 0.16
123 149 0.40
124 56 0.15
125 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (120 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCATTAT
GAACTTTCTCTGAAAATTGATATGATCTATCTCCTTCTGTGATAGAGTCATGCAA
Found at i:1138332 original size:236 final size:235
Alignment explanation
Indices: 1137957--1138418 Score: 723
Period size: 236 Copynumber: 2.0 Consensus size: 235
1137947 AAAGTCATAA
*
1137957 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTTTCATT
1 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTTTCATT
* * * *
1138022 ATGAACTTTCTCTGAAAGAGTTGATGATGATCTATCTTCTTCTGTGATAGAGTCATGCAAAAGGT
66 ATGAACTTTCTCGGAAAGAGTTAATGATGATCTATCTCCTTCTGCGATAGAGTCATGCAAAAGGT
*
1138087 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
131 TGAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
* *
1138152 TTCTCTGGAAAAGTTGATCCATTGAGTGATGAATTCGAGC
196 TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGC
* * *
1138192 AAAAGGTTAAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTTCTCA
1 AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAATTCTTT-TCA
* * * *
1138256 TTATGAACTCCTTCT-GGAAATA-TTAATGTTGATCTATCTCCTTCTGCGATAGCGTTATGCAAA
64 TTATGAACT--TTCTCGGAAAGAGTTAATGATGATCTATCTCCTTCTGCGATAGAGTCATGCAAA
*
1138319 AGGTTGAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTCTTCTGATAAGTTCTTCTCATTATG
127 AGGTTGAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
1138384 AACTTTCTCTGGAAAAGTTGATCCATCGAATGATG
192 AACTTTCTCTGGAAAAGTTGATCCATCGAATGATG
1138419 GATTTGAATC
Statistics
Matches: 207, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
235 43 0.21
236 155 0.75
237 5 0.02
238 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (235 bp):
AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAATTCTTTTCATT
ATGAACTTTCTCGGAAAGAGTTAATGATGATCTATCTCCTTCTGCGATAGAGTCATGCAAAAGGT
TGAACAAGTTCTTCCCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCGAGC
Found at i:1138731 original size:22 final size:22
Alignment explanation
Indices: 1138706--1138788 Score: 112
Period size: 22 Copynumber: 3.8 Consensus size: 22
1138696 AAATCTTTCT
* *
1138706 TCTTTGAAAATAGAATATATTA
1 TCTTTGAAAAGAGAATCTATTA
1138728 TCTTTGAAAAGAGAATCTATTA
1 TCTTTGAAAAGAGAATCTATTA
* *
1138750 TCTTTGAAGAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATTA
**
1138772 TCTTTGAGGAGAGAATC
1 TCTTTGAAAAGAGAATC
1138789 GATAATATGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATTA
Found at i:1139229 original size:54 final size:54
Alignment explanation
Indices: 1139147--1139254 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1139137 ATAATTACTG
* * *
1139147 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGACTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTATAACTTCTGCACAGAT
* *
1139201 GTTCGTAAAATATTTGACAACACATTCATCTTTTCCTATAACTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTATAACTTCTGCACAGAT
1139255 TTCTGGTCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTATAACTTCTGCACAGAT
Found at i:1140262 original size:75 final size:75
Alignment explanation
Indices: 1140129--1140377 Score: 347
Period size: 75 Copynumber: 3.3 Consensus size: 75
1140119 AAGATGATAT
* * *** * *
1140129 GGGTCTTCAGCATGCCCCAACATTGGCTAATATAAATGTTCAAAATACATCAACATTCCTGATTC
1 GGGTTTTCAGCATGCCCCAACATTGGCTAATATAAACGTTCAAAATGTGTCAATATTCCTGATTA
*
1140194 TGATTGAAAA
66 TAATTGAAAA
* *
1140204 GGGTTTTCAGCATGCCCCAGCATTGGCTAATATAAACGTTCAAAACGTGTCAATATTCCTGATTA
1 GGGTTTTCAGCATGCCCCAACATTGGCTAATATAAACGTTCAAAATGTGTCAATATTCCTGATTA
1140269 TAATTGAAAA
66 TAATTGAAAA
*
1140279 GGGCTTTT-AGCATGGCCCAACATTGGCTAATATAAACGTTCAAAATGTGTCAATATTCCTGATT
1 GGG-TTTTCAGCATGCCCCAACATTGGCTAATATAAACGTTCAAAATGTGTCAATATTCCTGATT
*
1140343 ATAATTGAAAT
65 ATAATTGAAAA
* * *
1140354 GGGCTTTCAGCATGCTCCATCATT
1 GGGTTTTCAGCATGCCCCAACATT
1140378 TGCTTCTTGT
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
74 3 0.02
75 147 0.95
76 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (75 bp):
GGGTTTTCAGCATGCCCCAACATTGGCTAATATAAACGTTCAAAATGTGTCAATATTCCTGATTA
TAATTGAAAA
Found at i:1140442 original size:36 final size:36
Alignment explanation
Indices: 1140397--1140516 Score: 128
Period size: 36 Copynumber: 3.4 Consensus size: 36
1140387 TTAATCTGAG
*
1140397 CCTTCAAAATGCCCCACATGGATCTGTCTGAAGTAA
1 CCTTTAAAATGCCCCACATGGATCTGTCTGAAGTAA
*
1140433 CCTTTAAAATGCCCCAACAT---T-TAT-TG-A-TACA
1 CCTTTAAAATGCCCC-ACATGGATCTGTCTGAAGTA-A
**
1140464 AATGTTAAAATGCCCCACATGGATCTGTCTGAAGTAA
1 CCT-TTAAAATGCCCCACATGGATCTGTCTGAAGTAA
1140501 CCTTTAAAATGCCCCA
1 CCTTTAAAATGCCCCA
1140517 ACATTTATTG
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
30 2 0.03
31 7 0.10
32 14 0.21
33 2 0.03
34 2 0.03
35 2 0.03
36 29 0.43
37 7 0.10
38 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (36 bp):
CCTTTAAAATGCCCCACATGGATCTGTCTGAAGTAA
Found at i:1140477 original size:32 final size:32
Alignment explanation
Indices: 1140436--1140552 Score: 107
Period size: 32 Copynumber: 3.6 Consensus size: 32
1140426 GAAGTAACCT
1140436 TTAAAATGCCCCAACATTTATTGATACAAATG
1 TTAAAATGCCCCAACATTTATTGATACAAATG
* **
1140468 TTAAAATGCCCC-ACATGGATCTGTCTGAAGTA-ACCT-
1 TTAAAATGCCCCAACAT---T-TAT-TG-A-TACAAATG
1140504 TTAAAATGCCCCAACATTTATTGATACAAATG
1 TTAAAATGCCCCAACATTTATTGATACAAATG
*
1140536 TTAAAATG-CTCAACATT
1 TTAAAATGCCCCAACATT
1140553 ACTTCTTCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 21
0.71 0.07 0.22
Matches are distributed among these distances:
30 2 0.03
31 15 0.22
32 22 0.32
33 2 0.03
34 2 0.03
35 2 0.03
36 14 0.21
37 7 0.10
38 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (32 bp):
TTAAAATGCCCCAACATTTATTGATACAAATG
Found at i:1140511 original size:68 final size:68
Alignment explanation
Indices: 1140402--1140544 Score: 286
Period size: 68 Copynumber: 2.1 Consensus size: 68
1140392 CTGAGCCTTC
1140402 AAAATGCCCCACATGGATCTGTCTGAAGTAACCTTTAAAATGCCCCAACATTTATTGATACAAAT
1 AAAATGCCCCACATGGATCTGTCTGAAGTAACCTTTAAAATGCCCCAACATTTATTGATACAAAT
1140467 GTT
66 GTT
1140470 AAAATGCCCCACATGGATCTGTCTGAAGTAACCTTTAAAATGCCCCAACATTTATTGATACAAAT
1 AAAATGCCCCACATGGATCTGTCTGAAGTAACCTTTAAAATGCCCCAACATTTATTGATACAAAT
1140535 GTT
66 GTT
1140538 AAAATGC
1 AAAATGC
1140545 TCAACATTAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 75 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (68 bp):
AAAATGCCCCACATGGATCTGTCTGAAGTAACCTTTAAAATGCCCCAACATTTATTGATACAAAT
GTT
Found at i:1141935 original size:7 final size:7
Alignment explanation
Indices: 1141906--1141947 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1141896 AAATGTAATT
1141906 ATGCAAA
1 ATGCAAA
1141913 GATG-AAA
1 -ATGCAAA
1141920 ATGCAAAA
1 ATGC-AAA
1141928 ATGCAAA
1 ATGCAAA
1141935 ATGC-AA
1 ATGCAAA
1141941 ATGCAAA
1 ATGCAAA
1141948 TGTAAATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 9 0.29
7 12 0.39
8 10 0.32
ACGTcount: A:0.57, C:0.12, G:0.17, T:0.14
Consensus pattern (7 bp):
ATGCAAA
Found at i:1142204 original size:43 final size:44
Alignment explanation
Indices: 1142121--1142207 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
1142111 TCGTGCATCA
* *
1142121 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * *
1142165 AACAAAAC-TTTACATATAGGGGATAACTTTCCCTTCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
1142208 TCTAAAGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 30 0.79
44 8 0.21
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:1142653 original size:36 final size:36
Alignment explanation
Indices: 1142593--1142664 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1142583 TCTTACCGTA
* *
1142593 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
** *
1142629 GAATACTTTTGGTATTGATATAACAGTATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
1142665 TGCATAGCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:1144471 original size:13 final size:14
Alignment explanation
Indices: 1144416--1144471 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 14
1144406 TTTATATGAC
1144416 TAAATAATAGTAATAAT
1 TAAAT-ATA-TAA-AAT
*
1144433 TAAATATATTAAAAA
1 TAAATATA-TAAAAT
*
1144448 TAAACATATAAAAT
1 TAAATATATAAAAT
1144462 TAAATA-ATAA
1 TAAATATATAA
1144472 TTAACATTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.12
14 10 0.29
15 9 0.26
16 6 0.18
17 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAATATATAAAAT
Found at i:1145780 original size:3 final size:3
Alignment explanation
Indices: 1145774--1145891 Score: 123
Period size: 3 Copynumber: 40.0 Consensus size: 3
1145764 ATTTATTATT
* * * *
1145774 TAA TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAT TAT TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1145820 TAA TAA TAT TAA TAA TAA TAA AAA TAT TAT TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1145868 TAA TAA AAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1145892 AAATGATATA
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
2 3 0.03
3 94 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1145840 original size:33 final size:33
Alignment explanation
Indices: 1145783--1145878 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
1145773 TTAATAATAA
* * *
1145783 TAATAATAATATAACATAATAATAATATTATTAT
1 TAATAATAATATTA-ATAATAATAAAAATATTAT
1145817 TAATAATAATATTAATAATAATAAAAATATTAT
1 TAATAATAATATTAATAATAATAAAAATATTAT
1145850 TAATAATAATATTAATAATAATAAAAATA
1 TAATAATAATATTAATAATAATAAAAATA
1145879 ATAATACTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATAATAATATTAATAATAATAAAAATATTAT
Found at i:1150586 original size:24 final size:26
Alignment explanation
Indices: 1150529--1150631 Score: 93
Period size: 29 Copynumber: 3.8 Consensus size: 26
1150519 ATATTTTAAA
1150529 ATTAAGATAAAAATAAAATATATCTTTT
1 ATTAAGATAAAAATAAAATATA--TTTT
1150557 AATTAAGATAAAAATAAAATATATTTTT
1 -ATTAAGATAAAAATAAAATATA-TTTT
* * *
1150585 AAATTAAAATAAGAATAAAATATATATT
1 --ATTAAGATAAAAATAAAATATATTTT
*
1150613 -TTAAG-TTAAAATAATAATA
1 ATTAAGATAAAAATAA-AATA
1150632 AAGAATACTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
24 7 0.11
25 8 0.12
28 7 0.11
29 43 0.66
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (26 bp):
ATTAAGATAAAAATAAAATATATTTT
Found at i:1150622 original size:30 final size:29
Alignment explanation
Indices: 1150519--1150879 Score: 329
Period size: 30 Copynumber: 12.2 Consensus size: 29
1150509 TATTCTTATA
* *
1150519 ATATTTTAAAATTAAGATAAAAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
1150548 ATATCTTTTAA-TTAAGATAAAAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
* * *
1150577 ATATTTTTAAATTAAAATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* *
1150606 ATATATTTTAAGTTAAAATAATAATAAAGA-
1 ATAT-TTTTAAGTTAAGATAAAAATAAA-AT
** * * * *
1150636 ATACTTAATAATTTAAGGTAAGAATAGAAT
1 ATA-TTTTTAAGTTAAGATAAAAATAAAAT
* * * *
1150666 ATATTTAATAATTTAA-ATTAATAATATAAT
1 ATATTT-TTAAGTTAAGA-TAAAAATAAAAT
**
1150696 ATATGTAATAAGTTAAGATAAAAATAAAAT
1 ATAT-TTTTAAGTTAAGATAAAAATAAAAT
*
1150726 ATATTTTTAAAAATTAAGAT-AAAATAAAAT
1 ATATTTTT--AAGTTAAGATAAAAATAAAAT
* *
1150756 ATATTTTTTTAAGTTAAGATAAGATTAAAAT
1 ATA--TTTTTAAGTTAAGATAAAAATAAAAT
*
1150787 ATATTTTT-AGTT-AGATAAAAATAAAAC
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
* * *
1150814 ACATTTTTTAGTTAAGATAAGAATAAAAT
1 ATATTTTTAAGTTAAGATAAAAATAAAAT
*
1150843 ATATTTAATAAGTTAAGATAAAAATAAAAT
1 ATATTT-TTAAGTTAAGATAAAAATAAAAT
1150873 ATATTTT
1 ATATTTT
1150880 AAAATAATTC
Statistics
Matches: 277, Mismatches: 37, Indels: 36
0.79 0.11 0.10
Matches are distributed among these distances:
27 19 0.07
28 14 0.05
29 74 0.27
30 141 0.51
31 24 0.09
32 5 0.02
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
ATATTTTTAAGTTAAGATAAAAATAAAAT
Found at i:1154875 original size:22 final size:22
Alignment explanation
Indices: 1154847--1154891 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1154837 AATGATACAA
1154847 GATAACGAGATTAGACGTTGGC
1 GATAACGAGATTAGACGTTGGC
*
1154869 GATAACGAGATTGGACGTTGGC
1 GATAACGAGATTAGACGTTGGC
1154891 G
1 G
1154892 TTATATGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (22 bp):
GATAACGAGATTAGACGTTGGC
Found at i:1155158 original size:34 final size:35
Alignment explanation
Indices: 1155088--1155176 Score: 126
Period size: 35 Copynumber: 2.6 Consensus size: 35
1155078 AATGGTAATA
* *
1155088 AACAAAATTATCAAAATATATTAAAAAAAAAGTCC
1 AACAAAATTAACAAAATAAATTAAAAAAAAAGTCC
* *
1155123 AACAAAATAAACAAAATAAATTATAAAAAAA-TCC
1 AACAAAATTAACAAAATAAATTAAAAAAAAAGTCC
*
1155157 AACCAAATTAACAAAATAAA
1 AACAAAATTAACAAAATAAA
1155177 GTAAGTATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 21 0.44
35 27 0.56
ACGTcount: A:0.67, C:0.12, G:0.01, T:0.19
Consensus pattern (35 bp):
AACAAAATTAACAAAATAAATTAAAAAAAAAGTCC
Found at i:1155479 original size:15 final size:13
Alignment explanation
Indices: 1155447--1155479 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1155437 TTAAACCCAA
1155447 GGCGCGCTACAGG
1 GGCGCGCTACAGG
1155460 GGCGCGCTACAGG
1 GGCGCGCTACAGG
1155473 GGCGCGC
1 GGCGCGC
1155480 CTTTCTGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.33, G:0.48, T:0.06
Consensus pattern (13 bp):
GGCGCGCTACAGG
Found at i:1160686 original size:17 final size:17
Alignment explanation
Indices: 1160666--1160701 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1160656 AATAAATAAA
*
1160666 TAAATAATATTTAATTT
1 TAAATAATAATTAATTT
1160683 TAAATAATAATTAATTT
1 TAAATAATAATTAATTT
1160700 TA
1 TA
1160702 CGTGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATAATAATTAATTT
Found at i:1165221 original size:18 final size:19
Alignment explanation
Indices: 1165188--1165231 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1165178 TAATCCTAAG
*
1165188 TATAAATATCAATTAATCA
1 TATAAAAATCAATTAATCA
*
1165207 TATAAAAAT-AATTAATGA
1 TATAAAAATCAATTAATCA
1165225 T-TAAAAA
1 TATAAAAA
1165232 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAAAAATCAATTAATCA
Found at i:1166320 original size:11 final size:11
Alignment explanation
Indices: 1166300--1166330 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1166290 ACTGTTAAGA
1166300 ATAATAATAAT
1 ATAATAATAAT
*
1166311 ATAATTATAAT
1 ATAATAATAAT
1166322 ATAATAATA
1 ATAATAATA
1166331 TTTATAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:1166322 original size:17 final size:17
Alignment explanation
Indices: 1166300--1166337 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1166290 ACTGTTAAGA
1166300 ATAATAATAAT-ATAATT
1 ATAAT-ATAATAATAATT
*
1166317 ATAATATAATAATATTT
1 ATAATATAATAATAATT
1166334 ATAA
1 ATAA
1166338 CATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATAATAATAATT
Found at i:1166343 original size:19 final size:18
Alignment explanation
Indices: 1166303--1166337 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1166293 GTTAAGAATA
1166303 ATAATAATATAATTATAAT
1 ATAATAATAT-ATTATAAT
1166322 ATAATAATAT-TTATAA
1 ATAATAATATATTATAA
1166338 CATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAATAATATATTATAAT
Found at i:1166576 original size:37 final size:37
Alignment explanation
Indices: 1166521--1166617 Score: 142
Period size: 37 Copynumber: 2.6 Consensus size: 37
1166511 TGATCTGATC
* * * *
1166521 TTGCTTCACTAATTTTTTTGTGAAAGTTGAATTTGTA
1 TTGCTTCACTACTCTTTTTGTGAAAGCTGAATTTGCA
*
1166558 TTGCTTCACTACTCTTTTTGTGAAGGCTGAATTTGCA
1 TTGCTTCACTACTCTTTTTGTGAAAGCTGAATTTGCA
1166595 TTGCTTCACTACTC-TTTTGTGAA
1 TTGCTTCACTACTCTTTTTGTGAA
1166618 GGCTTCGTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 9 0.16
37 46 0.84
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.47
Consensus pattern (37 bp):
TTGCTTCACTACTCTTTTTGTGAAAGCTGAATTTGCA
Found at i:1177588 original size:3 final size:3
Alignment explanation
Indices: 1177582--1177638 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
1177572 TCGAAAAAAA
1177582 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1177628 TAT TAT TAT TA
1 TAT TAT TAT TA
1177639 CCCAAGCACT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1177694 original size:12 final size:12
Alignment explanation
Indices: 1177679--1177715 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1177669 TTTCCACCAC
1177679 TCCATGTTTTAT
1 TCCATGTTTTAT
*
1177691 TCCATGTTTTCT
1 TCCATGTTTTAT
1177703 TCCATGTTTTAT
1 TCCATGTTTTAT
1177715 T
1 T
1177716 ATTCCACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.08, T:0.59
Consensus pattern (12 bp):
TCCATGTTTTAT
Found at i:1178168 original size:146 final size:146
Alignment explanation
Indices: 1177896--1178273 Score: 517
Period size: 146 Copynumber: 2.6 Consensus size: 146
1177886 AGAGATCGGG
*
1177896 ATCTTCGATCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAA
1 ATCTTCGATCAATATTCCGAACGGTCAAAAGTTGCGAAAGGCCATCACGAACAACATATTGAAAA
* * * * **
1177961 ATC-AGAACAATCAGACGGTGGACGGTGACGGATCGGATAAAACAAATCCGGGCGGTGTTTAGCC
66 ATCAAG-ACAATCGGACGGTGGACGGTGACGGATCGAAGAAAACAAATCCGGACAATGTTTAGCC
1178025 TCTTGCCGGTGATCAGA
130 TCTTGCCGGTGATCAGA
* *
1178042 ATCTTTGATCAATATTCCGAATGGTCAAAAGTTGCGAAAGGCCATCACGAACAACATATTGAAAA
1 ATCTTCGATCAATATTCCGAACGGTCAAAAGTTGCGAAAGGCCATCACGAACAACATATTGAAAA
* * *
1178107 ATCAAGACGATCGGACGGTGGACGGTGACGGATCGAAGAAAACAAATCTGGACAATTTTTAGCCT
66 ATCAAGACAATCGGACGGTGGACGGTGACGGATCGAAGAAAACAAATCCGGACAATGTTTAGCCT
* **
1178172 CTTGTCGGTGATTGGA
131 CTTGCCGGTGATCAGA
** * ** * * * *
1178188 AT-TTCGATCAATATTCCGAACCCTGAAAAGTTGCGCGATGCCAACACAAACAACCTATTGAAAA
1 ATCTTCGATCAATATTCCGAACGGTCAAAAGTTGCGAAAGGCCATCACGAACAACATATTGAAAA
1178252 ATCAAGACAATCGGACGGTGGA
66 ATCAAGACAATCGGACGGTGGA
1178274 TGACGGCAGA
Statistics
Matches: 204, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
145 72 0.35
146 130 0.64
147 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (146 bp):
ATCTTCGATCAATATTCCGAACGGTCAAAAGTTGCGAAAGGCCATCACGAACAACATATTGAAAA
ATCAAGACAATCGGACGGTGGACGGTGACGGATCGAAGAAAACAAATCCGGACAATGTTTAGCCT
CTTGCCGGTGATCAGA
Found at i:1178397 original size:28 final size:28
Alignment explanation
Indices: 1178327--1178395 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1178317 ATCTTTCCTG
* * *
1178327 ATTTTGACACTTTAATTTCTGTTATTTT
1 ATTTTAACCCTTTAATTTCTGTTATTTC
1178355 ATTTTAACCCTTTAATTTCTGTT-TTTACC
1 ATTTTAACCCTTTAATTTCTGTTATTT--C
*
1178384 ATTTTAATCCTT
1 ATTTTAACCCTT
1178396 AAGGTTCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.09
28 21 0.60
29 11 0.31
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTAACCCTTTAATTTCTGTTATTTC
Found at i:1180388 original size:47 final size:46
Alignment explanation
Indices: 1180315--1180434 Score: 186
Period size: 47 Copynumber: 2.6 Consensus size: 46
1180305 GAATAAATGT
*
1180315 ATGCGAACTAGAAATCATGCGATTAGGTTTATTTTCTCGAACAAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAAC-AAGC
1180362 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAGC
* * **
1180408 ATGAGAATTAGTTATCATGCGGTTAGG
1 ATGCGAACTAGAAATCATGCGGTTAGG
1180435 ACTTTTTGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (46 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCGAACAAGC
Found at i:1186659 original size:36 final size:35
Alignment explanation
Indices: 1186545--1186717 Score: 168
Period size: 36 Copynumber: 4.8 Consensus size: 35
1186535 GGCAAGTCAG
*
1186545 TCTTAAGCCTTTACCAAAGAGA-AGTGAAGCAACTCAA
1 TCTTAAGCCTTCACCAAAGA-ATAGTGAAGCAAC-C-A
* *
1186582 TCTGAAGCCTTCACCGAAGAATAGTGAAGCAACCA
1 TCTTAAGCCTTCACCAAAGAATAGTGAAGCAACCA
** * *
1186617 TCTTAAGCCTTCACTGAAGAGTAGTGAAACAAACCA
1 TCTTAAGCCTTCACCAAAGAATAGTGAAGC-AACCA
* *
1186653 TCTTAAGCCTTCACCAAAGAATGGTGAAGTAAACCA
1 TCTTAAGCCTTCACCAAAGAATAGTGAAG-CAACCA
* * * * *
1186689 TCTTATGTCTTCATCAAAGAGTCGTGAAG
1 TCTTAAGCCTTCACCAAAGAATAGTGAAG
1186718 GAAATTCATT
Statistics
Matches: 115, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
35 27 0.23
36 60 0.52
37 28 0.24
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (35 bp):
TCTTAAGCCTTCACCAAAGAATAGTGAAGCAACCA
Found at i:1186688 original size:72 final size:72
Alignment explanation
Indices: 1186545--1186709 Score: 190
Period size: 72 Copynumber: 2.3 Consensus size: 72
1186535 GGCAAGTCAG
* * *
1186545 TCTTAAGCCTTTACCAAAGAGAAGTGAAGCAACTCAATCTGAAGCCTTCACCGAAGAATAGTGAA
1 TCTTAAGCCTTCACCAAAGAGAAGTGAAACAACTCAATCTGAAGCCTTCACCAAAGAATAGTGAA
*
1186610 GCAACCA
66 GAAACCA
** * * *
1186617 TCTTAAGCCTTCACTGAAGAGTAGTGAAACAAAC-C-ATCTTAAGCCTTCACCAAAGAATGGTGA
1 TCTTAAGCCTTCACCAAAGAGAAGTGAAAC-AACTCAATCTGAAGCCTTCACCAAAGAATAGTGA
1186680 AGTAAACCA
65 AG-AAACCA
* * *
1186689 TCTTATGTCTTCATCAAAGAG
1 TCTTAAGCCTTCACCAAAGAG
1186710 TCGTGAAGGA
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
71 27 0.35
72 47 0.61
73 3 0.04
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (72 bp):
TCTTAAGCCTTCACCAAAGAGAAGTGAAACAACTCAATCTGAAGCCTTCACCAAAGAATAGTGAA
GAAACCA
Found at i:1187219 original size:54 final size:54
Alignment explanation
Indices: 1187105--1188551 Score: 1421
Period size: 54 Copynumber: 27.0 Consensus size: 54
1187095 AGTGAAGCAA
* * * * **
1187105 AAGAAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGAAGCGAA--CGTTTG
1 AAGAAGA-TGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAG
1187159 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
*
1187213 AAGAAGATGTTCGAGTTCTATACTCCCT-GAAGAAAGATGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* * * * **
1187267 AAGAAGATATTCGAGTTCTATACTTCCTAGAAGAAAGAGGAAGTGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
** * * **
1187322 TTGAAGATGTCCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGTGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* *
1187376 AAGAAGAT-TTCTGAGTTCTATACTCCCT-GAAGAAAGAGGGAGTGAACCCGTCAG
1 AAGAAGATGTTC-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* * **
1187430 TAGAAGATTATTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
** * * **
1187485 TTGAAGATG-TCTGAATTCTATACTCCCT-GAAGAAAGAGAGAGCGAACCCGTTTG
1 AAGAAGATGTTC-GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* *
1187539 AAGAAGATGTCCGAGTTCTATACTCCCT-GAAGAAAGAGGAAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* * * **
1187593 AAGAAGATGTTCGAGTTCCATACTCCATAGAGAAAGAGGGAACGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * *
1187647 AAG--G-TGTCCAAGTTTTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * * * * **
1187698 AATAAGATATTCGAGTTCTATACTTCCTGAAAGAAAGAGGAAGCGAACCCATTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAG
* * * * *
1187753 CAGAAGATTATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAACGAACCCG-ATTG
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA-AG
* ** *
1187808 AAGAAGATTTTTTAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT--T
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
*
1187860 TA-AAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGT---
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
** * * ** **
1187910 TTGAAGATATTCGAGTTCCATACTCCCTAGAGAAAGAGGGAAAGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * * **
1187964 AAG-A-TTGTTCGAGTTCCATACT-CCTTGAAGAAAGAGGGAGGGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* * * * **
1188016 AAGAAGAGGTACGAGTTCTATACTCCTTAAAGAAAGAGGGAGCGAACCCGTTGG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
*
1188070 AAGAAGATGTTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCC---AT
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
** * *
1188121 TTGAAGATTTTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCTGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAG
* * * * * * **
1188175 AAAAAGATATTCGAGTTCTATACTTCCTGAAAGAAAGAGGAAGTGAACCCGTTTG
1 AAGAAGATGTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAG
* *
1188230 CAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* *
1188284 AAGAAGATTGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGA-TGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * * **
1188338 CAGAAGATCGTTCAAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCAAAAG
1 AAGAAGAT-GTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * *
1188392 CAGAAGATCGTTCGAGTTC-CTACTGCCTAAAGAAAGAGGGAGCGAACCCGTAAG
1 AAGAAGAT-GTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * *
1188446 CAGAAGATCGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAG
1 AAGAAGAT-GTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
* * * *
1188500 CAGAAGATCGTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGTGAACCCGTA
1 AAGAAGAT-GTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1188552 GGCAAAAGAT
Statistics
Matches: 1205, Mismatches: 155, Indels: 66
0.85 0.11 0.05
Matches are distributed among these distances:
50 1 0.00
51 179 0.15
52 59 0.05
53 28 0.02
54 717 0.60
55 199 0.17
56 22 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTAAG
Found at i:1187381 original size:163 final size:163
Alignment explanation
Indices: 1187105--1188551 Score: 1514
Period size: 163 Copynumber: 9.0 Consensus size: 163
1187095 AGTGAAGCAA
* * **
1187105 AAGAAGATTATTCGAGTTCTATACTTCCT-GAAAGAAAGAGGAAGCGAA--CGTTTGAAGAAGAT
1 AAGAAGA-TATTCGAGTTCCATACTCCCTAG-AAGAAAGAGGAAGCGAACCCGTTTGTTGAAGAT
1187167 GTTCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTC
64 GTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTC
*
1187231 TATACTCCCTGAAGAAAGATGGAGCGAACCCGTAAG
128 TATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * *
1187267 AAGAAGATATTCGAGTTCTATACTTCCTAGAAGAAAGAGGAAGTGAACCCGTTTGTTGAAGATGT
1 AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGATGT
* * **
1187332 CCGAGTTCTATACTCCCTGAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGAT-TTCTGAGTTCTA
66 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTC-GAGTTCTA
* *
1187396 TACTCCCTGAAGAAAGAGGGAGTGAACCCGTCAG
130 TACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * *
1187430 TAGAAGATTATTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTGTTGAAGATG
1 AAGAAGA-TATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGATG
* * ** *
1187494 -TCTGAATTCTATACTCCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCT
65 TTC-GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
*
1187558 ATACTCCCTGAAGAAAGAGGAAGCGAACCCGTAAG
129 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * *
1187593 AAGAAGATGTTCGAGTTCCATACTCCATAG-AGAAAGAGGGAA-CGAACCCG--T-TTGAAGGTG
1 AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGA-GGAAGCGAACCCGTTTGTTGAAGATG
* * * * *
1187653 TCCAAGTTTTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTAAGAATAAGATATTCGAGTTCT
65 TTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
* * * **
1187717 ATACTTCCTGAAAGAAAGAGGAAGCGAACCCATTTG
129 ATACTCCCTG-AAGAAAGAGGGAGCGAACCCGTAAG
* * **
1187753 CAGAAGATTATTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAA-CGAACCCGATTGAAGAAGAT
1 AAGAAGA-TATTCGAGTTCCATACTCCCTAGAAGAAAGA-GGAAGCGAACCCGTTTGTTGAAGAT
* ** **
1187816 TTTTTAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGT--TTA-AAGATGTTCGAGTTC
64 GTTCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTC
1187877 TATACTCCCT-AGAGAAAGAGGGAGCGAACCCGT---
128 TATACTCCCTGA-AGAAAGAGGGAGCGAACCCGTAAG
** *
1187910 TTGAAGATATTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAA-AGAACCCG--T-TTGAAGATT
1 AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGA-GGAAGCGAACCCGTTTGTTGAAGA-T
* * * ** * *
1187970 GTTCGAGTTCCATACTCCTTGAAGAAAGAGGGAGGGAACCCGTTTGAAGAAGAGGTACGAGTTCT
64 GTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCT
* * **
1188035 ATACTCCTTAAAGAAAGAGGGAGCGAACCCGTTGG
129 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * *
1188070 AAGAAGATGTTCGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCC--AT-TTGAAGATTT
1 AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGATGT
* * *
1188131 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCTGTAAGAAAAAGATATTCGAGTTCTAT
66 TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCTAT
* * * **
1188196 ACTTCCTGAAAGAAAGAGGAAGTGAACCCGTTTG
131 ACTCCCTG-AAGAAAGAGGGAGCGAACCCGTAAG
* * * ** **
1188230 CAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTG
1 AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGA-TG
* * * *
1188294 TTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGCAGAAGATCGTTCAAGTTC-
65 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGAT-GTTCGAGTTCT
* * **
1188357 CTACTCCCTAAAGAAAGAGGGAGCGAACCCAAAAG
129 ATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * ** **
1188392 CAGAAGATCGTTCGAGTTCC-TACTGCCTA-AAGAAAGAGGGAGCGAACCCGTAAGCAGAAGATC
1 AAGAAGAT-ATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGAT-
* * * *
1188455 GTTCGAGTTC-CTACTCCCTAAAGAAAGAGGGAGCGAACCCGAAAGCAGAAGATCGTTCGAGTTC
64 GTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGAT-GTTCGAGTTC
* * *
1188519 -CTACTCCCTAAAGAAAGAGGGAGTGAACCCGTA
128 TATACTCCCTGAAGAAAGAGGGAGCGAACCCGTA
1188552 GGCAAAAGAT
Statistics
Matches: 1118, Mismatches: 127, Indels: 80
0.84 0.10 0.06
Matches are distributed among these distances:
153 5 0.00
154 37 0.03
155 1 0.00
156 43 0.04
157 48 0.04
158 2 0.00
159 134 0.12
160 161 0.14
161 103 0.09
162 204 0.18
163 296 0.26
164 84 0.08
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (163 bp):
AAGAAGATATTCGAGTTCCATACTCCCTAGAAGAAAGAGGAAGCGAACCCGTTTGTTGAAGATGT
TCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATGTTCGAGTTCTAT
ACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:1188798 original size:3 final size:3
Alignment explanation
Indices: 1188792--1188878 Score: 165
Period size: 3 Copynumber: 28.7 Consensus size: 3
1188782 TTGAAAATAA
1188792 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1188838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1188879 CCCAAGCACT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 80 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1188934 original size:12 final size:12
Alignment explanation
Indices: 1188919--1188955 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1188909 TTTCCACCAC
*
1188919 TCCATGTTTTCT
1 TCCATGTTTTAT
1188931 TCCATGTTTTAT
1 TCCATGTTTTAT
1188943 TCCATGTTTTAT
1 TCCATGTTTTAT
1188955 T
1 T
1188956 ATTCCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.14, C:0.19, G:0.08, T:0.59
Consensus pattern (12 bp):
TCCATGTTTTAT
Found at i:1189481 original size:146 final size:146
Alignment explanation
Indices: 1189143--1189461 Score: 512
Period size: 146 Copynumber: 2.2 Consensus size: 146
1189133 GGATCTCGGT
* *
1189143 TCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATTAGGAC
1 TCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAAGAC
*** * *
1189208 GATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGGTGGTTTTTAGCCTCTTGTCGG
66 GATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACAGTTTTTAGCCTCTTGCCGA
*
1189273 TAATCGGAATCTTTGA
131 TAATCGGAATCTTCGA
* *
1189289 TCAATATTCCGAATGGTCAAAAGTTGTGGAAGGCCATCACGAACAACATATTGAAAAATCAAGAC
1 TCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAAGAC
*
1189354 GATCGGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACAGTTTTTAGCCTCTTGCCGA
66 GATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACAGTTTTTAGCCTCTTGCCGA
*
1189419 TGATCGGAATCTTCGA
131 TAATCGGAATCTTCGA
* *
1189435 TCAATATTCCGAACGATGAAAAGTTGC
1 TCAATATTCCGAACGGTCAAAAGTTGC
1189462 ACGATGCCAA
Statistics
Matches: 157, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
146 157 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (146 bp):
TCAATATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAAGAC
GATCAGACGGTGGACGGTGACGGATCAGAGAAAACAAATCCGGACAGTTTTTAGCCTCTTGCCGA
TAATCGGAATCTTCGA
Found at i:1189598 original size:28 final size:28
Alignment explanation
Indices: 1189528--1189596 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1189518 ATCTTTCCTT
* * *
1189528 ATTTTGACACTTTAATTTCTGTTATTTT
1 ATTTTAACCCTTTAATTTCTGTTATTTC
1189556 ATTTTAACCCTTTAATTTCTGTT-TTTACC
1 ATTTTAACCCTTTAATTTCTGTTATTT--C
*
1189585 ATTTTAATCCTT
1 ATTTTAACCCTT
1189597 AAGGTTCATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.09
28 21 0.60
29 11 0.31
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTAACCCTTTAATTTCTGTTATTTC
Found at i:1191119 original size:22 final size:21
Alignment explanation
Indices: 1191090--1191136 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 21
1191080 TTTAATATAA
1191090 ATATTATTAATCTTAGTATAAGATT
1 ATATTA-TAA-CTTA-TATAA-ATT
1191115 ATATTATAACTTATATAAATT
1 ATATTATAACTTATATAAATT
1191136 A
1 A
1191137 ACTTAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 5 0.23
23 4 0.18
24 3 0.14
25 6 0.27
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
ATATTATAACTTATATAAATT
Found at i:1191202 original size:18 final size:19
Alignment explanation
Indices: 1191169--1191222 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
1191159 TAATCCTAAG
* *
1191169 TATAAATATCAATTAATCA
1 TATAAAAATAAATTAATCA
*
1191188 TATAAAAAT-AATTAATGA
1 TATAAAAATAAATTAATCA
1191206 T-TAAAAAATAAATTAAT
1 TAT-AAAAATAAATTAAT
1191223 AAAATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 15 0.48
19 15 0.48
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAAATAAATTAATCA
Found at i:1191362 original size:2 final size:2
Alignment explanation
Indices: 1191355--1191383 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1191345 TTTAACCTAA
1191355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1191384 GCAATGACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1193680 original size:20 final size:20
Alignment explanation
Indices: 1193655--1193789 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
1193645 AATTTGGAAA
*
1193655 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
1193675 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
1193695 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1193716 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1193736 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1193756 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1193776 TTCGCAATGCGATA
1 ATCGCAACGCGATA
1193790 ATACATAATC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.02
20 79 0.83
21 12 0.13
22 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1194006 original size:22 final size:22
Alignment explanation
Indices: 1193978--1194021 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1193968 CACTCTCTCA
*
1193978 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
1194000 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
1194022 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:1194324 original size:20 final size:20
Alignment explanation
Indices: 1194299--1194336 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1194289 CGATTCTCTC
1194299 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1194319 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1194337 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1195671 original size:18 final size:18
Alignment explanation
Indices: 1195650--1195697 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1195640 TCCACTTCGG
1195650 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1195668 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1195686 GAGTCATCACCT
1 GAGCCATCACCT
1195698 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1196286 original size:19 final size:20
Alignment explanation
Indices: 1196232--1196298 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1196222 TAGTTTACTT
* *
1196232 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1196252 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1196272 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1196291 TCGCAACG
1 TCGCAACG
1196299 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1196306 original size:14 final size:14
Alignment explanation
Indices: 1196287--1196345 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1196277 ATGCGAAATG
1196287 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1196301 AAAATCGCAATGTGAAATG
1 AAAATCGCAA--CG--A-C
1196320 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1196334 AAAATCGCAACG
1 AAAATCGCAACG
1196346 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1196318 original size:33 final size:33
Alignment explanation
Indices: 1196271--1196362 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
1196261 GGAAATGGCT
1196271 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1196304 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1196337 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1196363 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1196358 original size:19 final size:19
Alignment explanation
Indices: 1196232--1196367 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
1196222 TAGTTTACTT
* **
1196232 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1196252 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1196272 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1196291 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
* *
1196305 TCGCAATGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1196324 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1196338 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1196357 TCGCAATGCGA
1 TCGCAACGCGA
1196368 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 37 0.40
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1196398 original size:14 final size:14
Alignment explanation
Indices: 1196379--1196469 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
1196369 TTGTGTTTCG
1196379 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1196393 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1196409 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1196425 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
1196442 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1196458 CATTGCGATTTT
1 CGTTGCGATTTT
1196470 CATTTCGCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 27 0.43
15 3 0.05
16 11 0.17
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1196443 original size:33 final size:33
Alignment explanation
Indices: 1196374--1196485 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
1196364 GCGATTTGTG
*
1196374 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1196406 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1196439 TTTCGCATTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1196472 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1196486 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1196451 original size:19 final size:18
Alignment explanation
Indices: 1196395--1196485 Score: 90
Period size: 14 Copynumber: 5.4 Consensus size: 18
1196385 GATTTTGTCG
1196395 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
1196413 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
1196427 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
1196446 TTGCGATTT--TGT--CA
1 TTGCGATTTCATTTCGCA
1196460 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
1196479 TTGCGAT
1 TTGCGAT
1196486 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 14 0.24
15 6 0.10
16 6 0.10
17 6 0.10
18 13 0.22
19 14 0.24
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Done.