Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009381.1 Hibiscus syriacus cultivar Beakdansim tig00113264_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: 70482
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:726 original size:13 final size:13
Alignment explanation
Indices: 708--748 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
698 GTTATATAAA
708 TAAATATTTATTT
1 TAAATATTTATTT
**
721 TAAATAAATATTT
1 TAAATATTTATTT
734 T-AATATTTATTT
1 TAAATATTTATTT
746 TAA
1 TAA
749 TATCGAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:744 original size:12 final size:12
Alignment explanation
Indices: 710--751 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
700 TATATAAATA
710 AATATTTATTTT
1 AATATTTATTTT
**
722 AAATAAATATTTT
1 -AATATTTATTTT
735 AATATTTATTTT
1 AATATTTATTTT
747 AATAT
1 AATAT
752 CGAAGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATATTTATTTT
Found at i:1448 original size:26 final size:26
Alignment explanation
Indices: 1402--1462 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
1392 TCAAATTTTT
* *
1402 TTTATTATTATTTATAATATTATA-TG
1 TTTATT-TTATTTACAATATTATATTA
* *
1428 TTTATTTTATTTGCAAGTATTTTATTA
1 TTTATTTTATTTACAA-TATTATATTA
1455 TTTATTTT
1 TTTATTTT
1463 TTGTCAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 8 0.28
26 12 0.41
27 9 0.31
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (26 bp):
TTTATTTTATTTACAATATTATATTA
Found at i:8530 original size:17 final size:18
Alignment explanation
Indices: 8493--8530 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
8483 TGGCAATCAT
* *
8493 TTTTTACATTTTATTACA
1 TTTTTACATTTCATTAAA
8511 TTTTTACATTTCA-TAAA
1 TTTTTACATTTCATTAAA
8528 TTT
1 TTT
8531 ACTATATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTACATTTCATTAAA
Found at i:12053 original size:1 final size:1
Alignment explanation
Indices: 12049--12115 Score: 80
Period size: 1 Copynumber: 67.0 Consensus size: 1
12039 AAGGAAAAGG
* * * * * *
12049 AAAAAAGAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12114 AA
1 AA
12116 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.91, C:0.00, G:0.07, T:0.01
Consensus pattern (1 bp):
A
Found at i:12053 original size:13 final size:13
Alignment explanation
Indices: 12027--12086 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
12017 ATGCTTGAAG
12027 AAAAG-AAA-GAA
1 AAAAGAAAAGGAA
*
12038 AAAGGAAAAGGAA
1 AAAAGAAAAGGAA
**
12051 AAAAGAAAAAAAA
1 AAAAGAAAAGGAA
* *
12064 AAAAAAAAAGAAAA
1 AAAAGAAAAG-GAA
12078 AAAAGAAAA
1 AAAAGAAAA
12087 AAAAAGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
11 4 0.10
12 3 0.08
13 21 0.54
14 11 0.28
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGGAA
Found at i:12055 original size:14 final size:14
Alignment explanation
Indices: 12024--12116 Score: 93
Period size: 14 Copynumber: 6.6 Consensus size: 14
12014 ATTATGCTTG
12024 AAGAAAAGAAAGAAA
1 AAGAAAAGAAA-AAA
*
12039 AAGGAAAAG-GAAAA
1 AA-GAAAAGAAAAAA
12053 AAGAAAA-AAAAAA
1 AAGAAAAGAAAAAA
*
12066 AAAAAAAGAAAAAA
1 AAGAAAAGAAAAAA
*
12080 AAGAAAAAAAAAGAA
1 AAGAAAAGAAAA-AA
*
12095 AAAAAAAGAAAAATA
1 AAGAAAAGAAAAA-A
12110 AA-AAAAG
1 AAGAAAAG
12117 GGGGTCAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
13 15 0.23
14 27 0.41
15 18 0.27
16 6 0.09
ACGTcount: A:0.85, C:0.00, G:0.14, T:0.01
Consensus pattern (14 bp):
AAGAAAAGAAAAAA
Found at i:12059 original size:6 final size:6
Alignment explanation
Indices: 12032--12113 Score: 69
Period size: 6 Copynumber: 13.5 Consensus size: 6
12022 TGAAGAAAAG
* * * *
12032 AAAGAA AAAGGAA AAGGAAA AAAGAA AAAAAA AAAAAA AAAGAA AAAAAA
1 AAAGAA AAA-GAA AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* *
12082 GAAAAAA AAAG-A AAA-AA AAAGAA AAATAA AAA
1 -AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
12114 AAGGGGGTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
5 8 0.12
6 40 0.62
7 16 0.25
ACGTcount: A:0.87, C:0.00, G:0.12, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:12064 original size:10 final size:10
Alignment explanation
Indices: 12049--12112 Score: 98
Period size: 10 Copynumber: 6.6 Consensus size: 10
12039 AAGGAAAAGG
12049 AAAAAAG-AA
1 AAAAAAGAAA
12058 AAAAAA-AAA
1 AAAAAAGAAA
12067 AAAAAAG-AA
1 AAAAAAGAAA
12076 AAAAAAGAAA
1 AAAAAAGAAA
12086 AAAAAAGAAA
1 AAAAAAGAAA
12096 AAAAAAGAAA
1 AAAAAAGAAA
12106 AATAAAA
1 AA-AAAA
12113 AAAGGGGGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 23 0.45
10 24 0.47
11 4 0.08
ACGTcount: A:0.91, C:0.00, G:0.08, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:12115 original size:9 final size:9
Alignment explanation
Indices: 12049--12107 Score: 91
Period size: 9 Copynumber: 6.3 Consensus size: 9
12039 AAGGAAAAGG
12049 AAAAAAGAA
1 AAAAAAGAA
*
12058 AAAAAAAAA
1 AAAAAAGAA
12067 AAAAAAGAA
1 AAAAAAGAA
12076 AAAAAAGAAA
1 AAAAAAG-AA
12086 AAAAAAGAAA
1 AAAAAAG-AA
12096 AAAAAAGAA
1 AAAAAAGAA
12105 AAA
1 AAA
12108 TAAAAAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
9 28 0.60
10 19 0.40
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:12115 original size:19 final size:18
Alignment explanation
Indices: 12049--12107 Score: 100
Period size: 19 Copynumber: 3.2 Consensus size: 18
12039 AAGGAAAAGG
12049 AAAAAAGAAAAAAAAAAA
1 AAAAAAGAAAAAAAAAAA
12067 AAAAAAGAAAAAAAAGAAA
1 AAAAAAGAAAAAAAA-AAA
12086 AAAAAAGAAAAAAAAAGAA
1 AAAAAAGAAAAAAAAA-AA
12105 AAA
1 AAA
12108 TAAAAAAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 16 0.41
19 23 0.59
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAA
Found at i:12451 original size:16 final size:16
Alignment explanation
Indices: 12425--12469 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12415 TTTGAATACA
*
12425 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
12442 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
12457 ATTCAATTTATTT
1 ATTCAATTTATTT
12470 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:13177 original size:82 final size:82
Alignment explanation
Indices: 13077--13625 Score: 901
Period size: 82 Copynumber: 6.7 Consensus size: 82
13067 AATTAAATGA
*
13077 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
*
13141 TACAATCATTGAGTTTAG
65 AACAATCATTGAGTTTAG
*
13159 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
13223 AACAATCATTGAGTTTAG
65 AACAATCATTGAGTTTAG
*
13241 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
13306 ACAATCATTGAGTTTAG
66 ACAATCATTGAGTTTAG
13323 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
13388 ACAATCATTGAGTTTAG
66 ACAATCATTGAGTTTAG
*
13405 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
13469 AACCAATCATTGAGTTTAG
65 AA-CAATCATTGAGTTTAG
* *
13488 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-GAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
* **
13552 AACCAATCATTGAATTCGG
65 AA-CAATCATTGAGTTTAG
*
13571 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
13626 ATTCAGTAGG
Statistics
Matches: 452, Mismatches: 11, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
81 1 0.00
82 300 0.66
83 150 0.33
84 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (82 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACAATCATTGAGTTTAG
Found at i:14635 original size:93 final size:95
Alignment explanation
Indices: 14558--14728 Score: 229
Period size: 94 Copynumber: 1.8 Consensus size: 95
14548 TTCATAATGA
* * * * **
14558 GAAGAATTTGTTC-AACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAG
1 GAAGAATTTGTTCAAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAG
**
14621 TTCATAATGAGAAGAACTCATCTAAAGAAG
66 TTCATAATGAGAAGAACGAATCTAAAGAAG
* * *
14651 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAAG
1 GAAGAATTTGTTCAAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAG
14716 TTCATAATGAGAA
66 TTCATAATGAGAA
14729 TAACTTGTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
93 13 0.19
94 36 0.54
95 18 0.27
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (95 bp):
GAAGAATTTGTTCAAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAG
TTCATAATGAGAAGAACGAATCTAAAGAAG
Found at i:14664 original size:113 final size:113
Alignment explanation
Indices: 14368--14656 Score: 535
Period size: 113 Copynumber: 2.6 Consensus size: 113
14358 TCGAATCCAC
14368 TTGATGGATCA-TTTCTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAGTTT-TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
14432 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
65 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
14481 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
*
14546 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCAT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
* *
14594 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
14657 TTTGTTCAAA
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
113 169 0.98
114 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Found at i:14912 original size:114 final size:114
Alignment explanation
Indices: 14712--15094 Score: 477
Period size: 114 Copynumber: 3.3 Consensus size: 114
14702 TCCCCAGCGG
* * **
14712 AAAGTTCATAATGAGAATAACTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACA
1 AAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACA
* *
14777 TTGCCAGGTAGAGTTCATAATGAGAAGAAATCATCATCTGAAGAAGGAA
66 TTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAA
14826 AAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACA
1 AAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACA
* *
14891 TTGCCAGGAAGAGTTAATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
66 TTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGG-A-A
* * * * * * *
14942 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATT
1 A-AAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA--
* * *
15006 TC-TT-CCAGAGAA-AGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAA
63 ACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAG---GAA
* *
15059 GAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTG
1 AAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
15095 CATAATTCTA
Statistics
Matches: 236, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
114 104 0.44
115 1 0.00
116 90 0.38
117 38 0.16
118 2 0.01
119 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (114 bp):
AAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACA
TTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAA
Found at i:15334 original size:3 final size:3
Alignment explanation
Indices: 15321--15374 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
15311 TTTTTATCCA
* *
15321 TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
15367 TAT TAT TA
1 TAT TAT TA
15375 AATATATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15401 original size:14 final size:15
Alignment explanation
Indices: 15373--15407 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
15363 TTATTATTAT
15373 TAAATATATATTAAA
1 TAAATATATATTAAA
15388 TAAATATATA-TAAA
1 TAAATATATATTAAA
15402 TAAATA
1 TAAATA
15408 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:15839 original size:19 final size:19
Alignment explanation
Indices: 15815--15855 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
15805 ACCCCAACCT
15815 GAAAAAAAAAACG-GAGACA
1 GAAAAAAAAAA-GAGAGACA
*
15834 GAAAAAAAAGAGAGAGACA
1 GAAAAAAAAAAGAGAGACA
15853 GAA
1 GAA
15856 CCGGAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.68, C:0.07, G:0.24, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAAAGAGAGACA
Found at i:15840 original size:16 final size:16
Alignment explanation
Indices: 15815--15888 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 16
15805 ACCCCAACCT
*
15815 GAAA-AAAAAAACGGA
1 GAAAGAAAAAAACAGA
*
15830 GACAGAAAAAAA-AGA
1 GAAAGAAAAAAACAGA
* * * * *
15845 GAGAGACAGAACCGGA
1 GAAAGAAAAAAACAGA
15861 GAAAGAAAAAAACAGA
1 GAAAGAAAAAAACAGA
15877 GAAAGAAAAAAA
1 GAAAGAAAAAAA
15889 ACTACTAAAC
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
15 13 0.29
16 32 0.71
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAACAGA
Found at i:16615 original size:14 final size:14
Alignment explanation
Indices: 16588--16634 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
16578 TAATATCCGA
16588 ATTTTAGATAATTTT
1 ATTTTAG-TAATTTT
16603 ATTTTAGTAA-TTT
1 ATTTTAGTAATTTT
16616 ATTTTAAGT-ATTTT
1 ATTTT-AGTAATTTT
16630 -TTTTA
1 ATTTTA
16635 TTTGCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 13 0.43
14 9 0.30
15 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (14 bp):
ATTTTAGTAATTTT
Found at i:16722 original size:13 final size:13
Alignment explanation
Indices: 16706--16751 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
16696 ATATAATAAA
16706 TAAATATTTATTT
1 TAAATATTTATTT
*
16719 TAAATAAATTATTT
1 TAAAT-ATTTATTT
16733 T-AATATTTATTT
1 TAAATATTTATTT
*
16745 TTAATAT
1 TAAATAT
16752 CGAAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:18502 original size:18 final size:18
Alignment explanation
Indices: 18475--18509 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18465 CACTTAAACT
18475 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
18493 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
18510 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:36177 original size:14 final size:15
Alignment explanation
Indices: 36158--36191 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
36148 GTCTGTAATT
36158 ATTTATTT-ATATAG
1 ATTTATTTAATATAG
*
36172 ATTTATTTAATATAT
1 ATTTATTTAATATAG
36187 ATTTA
1 ATTTA
36192 ATAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTATTTAATATAG
Found at i:36198 original size:3 final size:3
Alignment explanation
Indices: 36190--36260 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
36180 AATATATATT
*
36190 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36238 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
36261 TGGGTAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:36888 original size:229 final size:227
Alignment explanation
Indices: 36395--37262 Score: 1280
Period size: 229 Copynumber: 3.8 Consensus size: 227
36385 ATTGAATAAA
* ** * *
36395 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATAATCCATC
* * *
36459 AAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
65 AAATGATGAATTCAGA-TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
* * * *
36523 CAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATT
129 CAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATGATCCATCAAATGATGAATT
* * *
36587 CA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
190 CAGAGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
36624 TTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
* * *
36689 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCACTATGAACTTCTTCTTCCTTCTTC
66 A-ATGATGAATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * *
36754 AGATGGGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGA
130 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAGA
*
36819 AAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
194 GAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
36853 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
* *
36918 ATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
66 A-ATGATGAATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
* * *
36983 AGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG-G
130 AGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGAG
*
37047 TAAAAGGTTGAACAAATTCTTCTCATTATGAAC
195 AAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
37080 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
* *
37145 AATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AATGATGAATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* **
37210 GATGAGTTCTTCTCATTATGAA-CTTCTCTGGAAAAGCTGATCTTTCAAATGAT
131 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCAAATGAT
37263 AGATTTGAAT
Statistics
Matches: 590, Mismatches: 43, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
225 28 0.05
226 87 0.15
227 132 0.22
228 22 0.04
229 225 0.38
230 95 0.16
231 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (227 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
AATGATGAATTCAGATAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGAGA
AAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:37119 original size:113 final size:113
Alignment explanation
Indices: 36395--37262 Score: 1292
Period size: 113 Copynumber: 7.6 Consensus size: 113
36385 ATTGAATAAA
* ** *
36395 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-CTGGAAAAGATGATCCATC
* * * *
36459 AAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * *
36508 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCC
* * * *
36572 ATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
36624 TTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
* ** *
36689 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCACTATGAAC
66 A-ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
36738 TTCTTCTTCCTTCTTCAGATGGGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
* **
36803 ATTTGATGAATTCAGAAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAG-GTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
36853 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
*
36918 ATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
36967 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
*
37032 AATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
37080 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
*
37145 AATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 AATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* **
37193 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCTGATCTTTCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
37257 AATGAT
66 AATGAT
37263 AGATTTGAAT
Statistics
Matches: 715, Mismatches: 32, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
112 30 0.04
113 241 0.34
114 226 0.32
115 111 0.16
116 84 0.12
117 21 0.03
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
AATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:38002 original size:83 final size:83
Alignment explanation
Indices: 37895--38610 Score: 1135
Period size: 83 Copynumber: 8.7 Consensus size: 83
37885 CCTACTGAAT
* * ** *
37895 CAGATCAGATAACT-AAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
37958 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* *
37977 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
*
38042 TGATTGGTTTTGCCAAAC
66 TGATTGGTTCTGCCAAAC
* * * *
38060 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATTTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
38124 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* *
38143 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTT-TCAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCT-AAACTC
38206 AATGATTGGTTCTGCCAAAC
64 AATGATTGGTTCTGCCAAAC
38226 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
38291 TGATT-GTTCTGTCC-AAC
66 TGATTGGTTCTG-CCAAAC
* * *
38308 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
38373 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
*
38391 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
38456 TGATT-GTTCTGTCC-AAC
66 TGATTGGTTCTG-CCAAAC
* *
38473 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
38538 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCCAAAC
38556 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
38611 TCATTTAATT
Statistics
Matches: 596, Mismatches: 26, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
82 174 0.29
83 417 0.70
84 5 0.01
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
TGATTGGTTCTGCCAAAC
Found at i:38380 original size:165 final size:166
Alignment explanation
Indices: 37895--38610 Score: 1171
Period size: 165 Copynumber: 4.3 Consensus size: 166
37885 CCTACTGAAT
* * * *
37895 CAGATCAGATAACT-AAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTCCGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAACTCA
37958 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
65 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
*
38023 ATTCATCTTCTAAACTCACTGATTGGTTTTGCCAAAC
130 ATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAAC
* * *
38060 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATTTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAACTCA
*
38124 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACA
65 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCA
* * *
38188 CATTCATCTT-TCAAATTCAATGATTGGTTCTGCCAAAC
129 AATTCATCTTCT-AAACTCACTGATTGGTTCTGCCAAAC
*
38226 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAA
38291 TGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
66 TGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
*
38354 ATTCATCTTCTAAATTCACTGATTGGTTCTGCCAAAC
130 ATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAAC
* *
38391 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCTAAACTCAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAA
38456 TGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
66 TGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAA
38519 ATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAAC
130 ATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAAC
38556 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
38611 TCATTTAATT
Statistics
Matches: 528, Mismatches: 16, Indels: 14
0.95 0.03 0.03
Matches are distributed among these distances:
165 319 0.60
166 207 0.39
167 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAACTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
TTCATCTTCTAAACTCACTGATTGGTTCTGCCAAAC
Found at i:38384 original size:248 final size:249
Alignment explanation
Indices: 37895--38610 Score: 1205
Period size: 248 Copynumber: 2.9 Consensus size: 249
37885 CCTACTGAAT
* * *
37895 CAGATCAGATAACT-AAAGAACACTTCCAGAAGATGCTATGAACACATTCATGTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTCAAATTCAA
37959 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
*
38024 TTCATCTTCTAAACTCACTGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCTAAACTCACTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
* *
38089 GAAGATGCTA-TGAACACATTCATTTTCCAAATTCAATGATTGGTTCTGCCAAAC
196 GAAGATGCTATTG-ACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
38143 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTCAAATTCAA
*
38208 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
*
38273 TTCATCTTCTAAACTCAATGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCC
131 TTCATCTTCTAAACTCACTGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCC
* * *
38336 AGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGCCAAAC
195 AGAAGATGCTATTGACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
* *
38391 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATC-TTCTAAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTC-AAATTC
*
38454 ACTGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
64 AATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGC
38517 AAATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTT
128 AAATTCATCTTCTAAACTCACTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTT
38582 CCAGAAGATGCTATTGACAAATTCATCTT
193 CCAGAAGATGCTATTGACAAATTCATCTT
38611 TCATTTAATT
Statistics
Matches: 443, Mismatches: 17, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
247 82 0.19
248 222 0.50
249 139 0.31
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (249 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTTCAAATTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
TTCATCTTCTAAACTCACTGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
Found at i:39413 original size:16 final size:16
Alignment explanation
Indices: 39394--39433 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
39384 AATTTCCAAA
39394 AAATAAATTG-ACTCTC
1 AAATAAATTGAACT-TC
*
39410 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
39426 AAATAAAT
1 AAATAAAT
39434 AGAATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:39417 original size:20 final size:20
Alignment explanation
Indices: 39370--39409 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39360 AATTCAATAG
*
39370 AAAAGAATAAATTGAATTTCC
1 AAAA-AATAAATTGAATCTCC
*
39391 AAAAAATAAATTGACTCTC
1 AAAAAATAAATTGAATCTC
39410 AAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAAATAAATTGAATCTCC
Found at i:52578 original size:14 final size:15
Alignment explanation
Indices: 52559--52592 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
52549 GTCTGTAATT
52559 ATTTATTT-ATATAG
1 ATTTATTTAATATAG
*
52573 ATTTATTTAATATAT
1 ATTTATTTAATATAG
52588 ATTTA
1 ATTTA
52593 ATAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTATTTAATATAG
Found at i:52599 original size:3 final size:3
Alignment explanation
Indices: 52591--52653 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
52581 AATATATATT
*
52591 TAA TAA TAA T-A TAA TGA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52637 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
52654 TGGGTAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 4 0.07
3 52 0.93
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52600 original size:17 final size:15
Alignment explanation
Indices: 52591--52653 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 15
52581 AATATATATT
52591 TAATAATAATAT-AA
1 TAATAATAATATAAA
*
52605 TGATAATAATA-ATAA
1 TAATAATAATATA-AA
52620 TAATAATAATAT-AA
1 TAATAATAATATAAA
52634 TAATAATAATA-ATAA
1 TAATAATAATATA-AA
52649 TAATA
1 TAATA
52654 TGGGTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.55
15 19 0.45
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TAATAATAATATAAA
Found at i:52621 original size:23 final size:23
Alignment explanation
Indices: 52592--52654 Score: 110
Period size: 23 Copynumber: 2.7 Consensus size: 23
52582 ATATATATTT
52592 AATAATAAT-ATAATGATAATAAT
1 AATAATAATAATAAT-ATAATAAT
52615 AATAATAATAATAATATAATAAT
1 AATAATAATAATAATATAATAAT
52638 AATAATAATAATAATAT
1 AATAATAATAATAATAT
52655 GGGTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 34 0.87
24 5 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AATAATAATAATAATATAATAAT
Found at i:55723 original size:35 final size:35
Alignment explanation
Indices: 55684--55792 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 35
55674 ACATTCCTCG
55684 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
*
55719 ATTTCATTCTAAACCCTAAATTCCAAAATAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
* * *
55754 ATTAT-ATTCTAAAACCCAAATTCTAAAATATTTCA
1 ATT-TCATTCTAAACCCCAAATTCCAAAATAATTCA
55789 ATTT
1 ATTT
55793 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.01
35 66 0.97
36 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (35 bp):
ATTTCATTCTAAACCCCAAATTCCAAAATAATTCA
Found at i:56568 original size:19 final size:20
Alignment explanation
Indices: 56544--56583 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
56534 TAATTAACAT
56544 AACTCATATAT-AAATTTTG
1 AACTCATATATAAAATTTTG
56563 AACTCATATATAAAATTTTG
1 AACTCATATATAAAATTTTG
56583 A
1 A
56584 CTCTGCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (20 bp):
AACTCATATATAAAATTTTG
Found at i:56877 original size:35 final size:35
Alignment explanation
Indices: 56828--56940 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 35
56818 AAAAAAGACA
* * *
56828 GAAATTGAAGTATTTTAGAATTTGAGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
*
56863 GTAATTGAATTATTTTGGAATTT-AGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGA-GGTTTAGAAT
* *
56898 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
56933 GAAATTGA
1 GAAATTGA
56941 GGATTGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 68 0.99
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
Found at i:59723 original size:18 final size:18
Alignment explanation
Indices: 59700--59751 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
59690 TTTCGTTCTG
59700 GAATGATCAAAGAATTAA
1 GAATGATCAAAGAATTAA
59718 GAATGATCAAAGAATTAA
1 GAATGATCAAAGAATTAA
*
59736 GAACGATC-AAGAATTA
1 GAATGATCAAAGAATTA
59752 GGATCACTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 8 0.24
18 25 0.76
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (18 bp):
GAATGATCAAAGAATTAA
Found at i:60394 original size:19 final size:19
Alignment explanation
Indices: 60370--60474 Score: 115
Period size: 19 Copynumber: 5.6 Consensus size: 19
60360 ACTGTTCACG
60370 GTACTATTCATACCATATA
1 GTACTATTCATACCATATA
* *
60389 GTACTATTTAAACCATATA
1 GTACTATTCATACCATATA
*
60408 GTACTATTTATA-CA-ATA
1 GTACTATTCATACCATATA
* * * *
60425 ATACTATTTAAACCGTATA
1 GTACTATTCATACCATATA
*
60444 GTACTATTCATACAATATA
1 GTACTATTCATACCATATA
*
60463 GTATTATTCATA
1 GTACTATTCATA
60475 AAAACGTTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
17 13 0.18
18 3 0.04
19 56 0.78
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (19 bp):
GTACTATTCATACCATATA
Found at i:60433 original size:36 final size:36
Alignment explanation
Indices: 60370--60460 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
60360 ACTGTTCACG
*
60370 GTACTATTCATACCATATAGTACTATTTAAACCATATA
1 GTACTATTCATA-CA-ATAATACTATTTAAACCATATA
* *
60408 GTACTATTTATACAATAATACTATTTAAACCGTATA
1 GTACTATTCATACAATAATACTATTTAAACCATATA
60444 GTACTATTCATACAATA
1 GTACTATTCATACAATA
60461 TAGTATTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 36 0.73
37 2 0.04
38 11 0.22
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.37
Consensus pattern (36 bp):
GTACTATTCATACAATAATACTATTTAAACCATATA
Done.