Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001339.1 Hibiscus syriacus cultivar Beakdansim tig00002613_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: 92581
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4577 original size:25 final size:26
Alignment explanation
Indices: 4522--4591 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 26
4512 CCAATTATTT
* *
4522 AAATATAAAATATTT-TTTATAATAA
1 AAATTTAATATATTTATTTATAATAA
** *
4547 TTATTTTATATATTTATTTAT-ATAA
1 AAATTTAATATATTTATTTATAATAA
* *
4572 AAATTTAATTTATTAATTTA
1 AAATTTAATATATTTATTTA
4592 GATTAAATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
25 29 0.85
26 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATTTAATATATTTATTTATAATAA
Found at i:5313 original size:36 final size:36
Alignment explanation
Indices: 5242--5314 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
5232 GTTGAAAAAT
* * *
5242 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTGTCTTTAAAAATTGAAAATCATAAA
5278 ATTTATATAATTGT-TTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTGTCTTTA-AAAATTGAAAATCATAAA
5314 A
1 A
5315 AGGTTTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (36 bp):
ATTTATATATTGTCTTTAAAAATTGAAAATCATAAA
Found at i:6017 original size:16 final size:17
Alignment explanation
Indices: 5992--6026 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5982 CATTACAAGT
5992 TATAACAATA-TAGTTA
1 TATAACAATATTAGTTA
*
6008 TATAATAATATTAGTTA
1 TATAACAATATTAGTTA
6025 TA
1 TA
6027 AAATTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
TATAACAATATTAGTTA
Found at i:9321 original size:19 final size:19
Alignment explanation
Indices: 9297--9369 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
9287 AATCTAATTT
9297 GGGTATCGATACCTAGAGG
1 GGGTATCGATACCTAGAGG
9316 GGGTATC-AGTACCTAGAGG
1 GGGTATCGA-TACCTAGAGG
* *
9335 GGGTATCGGTACCATAGCAAAG
1 GGGTATCGATACC-TAG--AGG
9357 GGGTATCGATACC
1 GGGTATCGATACC
9370 ATGGTGAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.02
19 28 0.61
20 3 0.07
22 14 0.30
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.21
Consensus pattern (19 bp):
GGGTATCGATACCTAGAGG
Found at i:10235 original size:135 final size:135
Alignment explanation
Indices: 9993--10550 Score: 748
Period size: 135 Copynumber: 4.1 Consensus size: 135
9983 TATACAAGAA
*** * * * *
9993 AAATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCATAGTTGAAATGTATATGGGTACATT
1 AAATGCATATGGGTGCATTATCAACA-GAAAAGTATACTATGGTTGAAATGTATATGGGTACATT
* * * *
10057 ATCAACAGAAAAACATACTTTAATTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTA
65 ATCAACAGAAAAACATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGCTA
10122 GAGTTG
130 GAGTTG
*
10128 AAATGCATATGGGTGCATTATCAACAGAAAAGTAAACTATGGTTGAAATGTATATGGGTACATTA
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTA
* * *
10193 TCAACAGAAAAACATACTATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTACGCTAG
66 TCAACAGAAAAACATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGCTAG
*
10258 AGTTT
131 AGTTG
*
10263 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGAACATTA
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTA
* * * * *
10328 TCAACA-AAAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTA
66 TCAACAGAAAAA-CATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGCTA
10392 TG-GTTG
130 -GAGTTG
* *
10398 AAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTA
1 AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTA
* ** * * * *
10463 TCAAAAGAAAAGTATACTATAGTTGAAATGCATACGGGTGCATTATCAACAGAAAAG-ATGTTAT
66 TCAACAGAAAAACATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGCTAG
*
10527 AGTTTA
131 AG-TTG
10533 AAATGCATAAT-GGTGCAT
1 AAATGCAT-ATGGGTGCAT
10551 GATAAACATG
Statistics
Matches: 377, Mismatches: 39, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
134 11 0.03
135 359 0.95
136 7 0.02
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (135 bp):
AAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATGGTTGAAATGTATATGGGTACATTA
TCAACAGAAAAACATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATGCTAG
AGTTG
Found at i:10541 original size:45 final size:45
Alignment explanation
Indices: 10034--10519 Score: 681
Period size: 45 Copynumber: 10.8 Consensus size: 45
10024 GGATGCCATA
** * *
10034 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTTTA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
10079 ATTGAAATGTATATGGGTACATTATCAACATAAAAGTATGCTA-G
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
10123 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAAACTATG
1 -GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
**
10169 GTTGAAATGTATATGGGTACATTATCAACAGAAAAACATACTATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
**
10214 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTACGCTA-G
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
10258 AGTTTAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATG
1 -GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
10304 GTTGAAATGTATATGGGAACATTATCAACAAAAAAGTATGCTA-G
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
10348 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTATG
1 -GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
10394 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* *
10439 GTTGAAATGTATATGGGTACATTATCAAAAGAAAAGTATACTATA
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
* * *
10484 GTTGAAATGCATACGGGTGCATTATCAACAGAAAAG
1 GTTGAAATGTATATGGGTACATTATCAACAGAAAAG
10520 ATGTTATAGT
Statistics
Matches: 389, Mismatches: 46, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
44 2 0.01
45 384 0.99
46 3 0.01
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (45 bp):
GTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATG
Found at i:15011 original size:12 final size:12
Alignment explanation
Indices: 14991--15024 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14981 AATGGGTAAT
*
14991 TTTTTAAAACAA
1 TTTTGAAAACAA
15003 TTTTGAAAACAA
1 TTTTGAAAACAA
15015 TGTTTGAAAA
1 T-TTTGAAAA
15025 ATTAATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACAA
Found at i:23121 original size:3 final size:3
Alignment explanation
Indices: 23113--23147 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23103 AATAGTAAAT
23113 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23148 TAATCTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28601 original size:21 final size:22
Alignment explanation
Indices: 28557--28601 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28547 TATAATTTAT
*
28557 TATATTTTTAATAATTAAATAA
1 TATATTTTTAATAATTAAAAAA
28579 TATA-TTTTAAT-ATTATAAAAA
1 TATATTTTTAATAATTA-AAAAA
28600 TA
1 TA
28602 AAATATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATTTTTAATAATTAAAAAA
Found at i:28720 original size:18 final size:19
Alignment explanation
Indices: 28681--28721 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
28671 TCTAACTATT
28681 ATAAAAGATTACCAGTGGGA
1 ATAAAAGATTACCAG-GGGA
28701 ATAAAAGATTACCA-GGGA
1 ATAAAAGATTACCAGGGGA
28719 ATA
1 ATA
28722 GGATTACTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.20
Consensus pattern (19 bp):
ATAAAAGATTACCAGGGGA
Found at i:28893 original size:15 final size:15
Alignment explanation
Indices: 28875--28905 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28865 AAATTCTAAA
28875 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
28890 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
28905 T
1 T
28906 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:34590 original size:22 final size:21
Alignment explanation
Indices: 34542--34592 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
34532 TAATCTTTTA
*
34542 AAATTTATTAATTAGTGATTT
1 AAATTTATAAATTAGTGATTT
** *
34563 CGATTTATAAATTAATTGATTT
1 AAATTTATAAATT-AGTGATTT
34585 AAATTTAT
1 AAATTTAT
34593 TTTACGAGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (21 bp):
AAATTTATAAATTAGTGATTT
Found at i:41297 original size:20 final size:20
Alignment explanation
Indices: 41218--41297 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
41208 CAGAACCCCA
* **
41218 GGGGGTATCGATTCCCTGTG
1 GGGGGAATCGATTCCCTCAG
* *
41238 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCC-TCAG
* *
41260 AGGGGAATCGGTTCCCTCAG
1 GGGGGAATCGATTCCCTCAG
41280 GGGGGAATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
41298 TGCACCAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 30 0.61
21 6 0.12
22 13 0.27
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAG
Found at i:47758 original size:16 final size:17
Alignment explanation
Indices: 47737--47783 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
47727 AAAAAGTGCT
*
47737 AAAAATGTTAAAA-GAA
1 AAAAATGTTAAAATAAA
*
47753 AAAAATGTAACAAAATAAA
1 AAAAATGT--TAAAATAAA
47772 AAAAATGTTAAA
1 AAAAATGTTAAA
47784 TTTTAGAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
18 4 0.16
19 10 0.40
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (17 bp):
AAAAATGTTAAAATAAA
Found at i:47835 original size:35 final size:34
Alignment explanation
Indices: 47737--47836 Score: 89
Period size: 35 Copynumber: 2.9 Consensus size: 34
47727 AAAAAGTGCT
*
47737 AAAAATGTTAAAAGA-AAAAAATGTAACAAAATAAA
1 AAAAATGTTAAAAGAGAAAAAA-ATAA-AAAATAAA
** **
47772 AAAAATGTTAAATTTTAG-AAGGAA-AAAAAATAATA
1 AAAAATGTTAAA--AGAGAAAAAAATAAAAAATAA-A
47807 AAAAATGTTAAAAGAGAAAAAAATAAAAAA
1 AAAAATGTTAAAAGAGAAAAAAATAAAAAA
47837 ATGGAAATGA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
33 2 0.04
34 11 0.22
35 33 0.66
37 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.10, T:0.19
Consensus pattern (34 bp):
AAAAATGTTAAAAGAGAAAAAAATAAAAAATAAA
Found at i:47887 original size:14 final size:14
Alignment explanation
Indices: 47846--47888 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 14
47836 AATGGAAATG
47846 AAATAAAA-AAGTT
1 AAATAAAATAAGTT
47859 AAA-AAAATAA--T
1 AAATAAAATAAGTT
47870 -AATAAAATAAGTT
1 AAATAAAATAAGTT
47883 AAATAA
1 AAATAA
47889 TAATTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
12 4 0.16
13 6 0.24
14 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
AAATAAAATAAGTT
Found at i:49054 original size:3 final size:3
Alignment explanation
Indices: 49022--49072 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
49012 AAATATTAAA
*
49022 AAT AA- AAT AA- AAT GAAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
49067 AA- AAT A
1 AAT AAT A
49073 TTTTAAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 6 0.15
3 29 0.71
4 6 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:49148 original size:36 final size:35
Alignment explanation
Indices: 49067--49339 Score: 151
Period size: 36 Copynumber: 7.4 Consensus size: 35
49057 TAATAATAAT
* * *
49067 AAAATATTTT-AAAACTATACATTACATATATTTTTA
1 AAAATGTTTTCAAAACTATATATT--ATATATTTTTC
*
49103 AAAAAGTTTTCAAAACTATATATTATATAGTTTTTC
1 AAAATGTTTTCAAAACTATATATTATATA-TTTTTC
* ** * * *
49139 AAAACGTTTTTTTTAAATTAAATGCTATATATATTTTT-
1 AAAA--TGTTTTCAAAACTATAT-AT-TATATATTTTTC
* * **
49177 AAAATGTTTTTTAAAAAAC-A-ATATAATATATAATTC
1 AAAATG--TTTT-CAAAACTATATATTATATATTTTTC
* *
49213 AAAATGATTTCTAAACTATATATTATATAAGTTTTT-
1 AAAATGTTTTCAAAACTATATATTATAT-A-TTTTTC
* * *
49249 GACATGATTTCAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCAAAACTATATATTATATAT-TTTTC
* * *
49285 AAAATGTTTTAAAAAACTATATAATATATACATTTTC
1 AAAATGTTTT-CAAAACTATATATTATATA-TTTTTC
49322 AAAAATCGTTTTCTAAAA
1 -AAAAT-GTTTTC-AAAA
49340 AAAATATTTT
Statistics
Matches: 181, Mismatches: 35, Indels: 39
0.71 0.14 0.15
Matches are distributed among these distances:
33 4 0.02
34 5 0.03
35 26 0.14
36 58 0.32
37 39 0.22
38 25 0.14
39 18 0.10
40 6 0.03
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAATGTTTTCAAAACTATATATTATATATTTTTC
Found at i:50274 original size:85 final size:85
Alignment explanation
Indices: 50144--50660 Score: 670
Period size: 85 Copynumber: 6.1 Consensus size: 85
50134 CAACTTAAGT
* * * * * *
50144 TATGCTGTAAATTTAACATGCCATTGAGCTGAATGGAACCGAACTCGAAGGTATTTGTTGACAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGA
*
50209 TAACCCTTCTCGCCTTGAGT
66 TAACCCTTCTCGCCTTGAGC
* *
50229 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCAAACTCGAAGGTCTTGGTTGACAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGA
* ** *
50294 TAGCCCTTCTCTTCATGAGC
66 TAACCCTTCTCGCCTTGAGC
* * *
50314 TATGCTGTAAATTTGATATGTCCTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGA
* *
50379 TAACCCTTCTTGCCTTAAGC
66 TAACCCTTCTCGCCTTGAGC
* *
50399 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATCGAACTCGAAGGTCTTGGTTGACAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGA
* * *
50464 TAGCCCTTATCGCCTTTAGC
66 TAACCCTTCTCGCCTTGAGC
* ** * *
50484 TATGTTGTAAATTTGATATATCCTTGAGCTGAGTGTAATCGAACAT-GAAGGTCTTTGCTGACAG
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAAC-TCGAAGGTCTTTGTTGACAG
50548 ATAACCCTTCTCGCCTTGAGC
65 ATAACCCTTCTCGCCTTGAGC
* *
50569 TATGCTGTAAATTTG--A---CCTTGAGCTGAGTGTAATCGAACTCGAAGGT-TTTGGTTGATAG
1 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTT-GTTGACAG
* *
50628 ATAGCCATTCTCGCCTTGAGC
65 ATAACCCTTCTCGCCTTGAGC
*
50649 TATGCTGCAAAT
1 TATGCTGTAAAT
50661 AGTTCCTTTA
Statistics
Matches: 380, Mismatches: 49, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
79 4 0.01
80 65 0.17
83 1 0.00
85 309 0.81
86 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (85 bp):
TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGA
TAACCCTTCTCGCCTTGAGC
Found at i:50359 original size:170 final size:170
Alignment explanation
Indices: 50144--50660 Score: 742
Period size: 170 Copynumber: 3.1 Consensus size: 170
50134 CAACTTAAGT
* * * * * *
50144 TATGCTGTAAATTTAACATG-CCATTGAGCTGAATGGAACCGAACTCGAAGGTATTTGTTGACAG
1 TATGCTGTAAATTTGATATGTCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAG
* *
50208 ATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCAAAC
65 ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAAC
** *
50273 TCGAAGGTCTTGGTTGACAGATAGCCCTTCTCTTCATGAGC
130 TCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGC
*
50314 TATGCTGTAAATTTGATATGTCCTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGA
1 TATGCTGTAAATTTGATATGTCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGA
* * *
50379 TAACCCTTCTTGCCTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATATAATCGAACT
66 TAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACT
* *
50444 CGAAGGTCTTGGTTGACAGATAGCCCTTATCGCCTTTAGC
131 CGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGC
* * *
50484 TATGTTGTAAATTTGATATATCCTTGAGCTGAGTGTAATCGAACAT-GAAGGTCTTTGCTGACAG
1 TATGCTGTAAATTTGATATGTCCTTGAGCTGAGTGTAATCGAAC-TCGAAGGTCTTTGTTGACAG
*
50548 ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG--A---CCTTGAGCTGAGTGTAATCGAAC
65 ATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAAC
* * *
50608 TCGAAGGTTTTGGTTGATAGATAGCCATTCTCGCCTTGAGC
130 TCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGC
*
50649 TATGCTGCAAAT
1 TATGCTGTAAAT
50661 AGTTCCTTTA
Statistics
Matches: 313, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
165 67 0.21
168 1 0.00
170 242 0.77
171 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (170 bp):
TATGCTGTAAATTTGATATGTCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGA
TAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACT
CGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGC
Found at i:51117 original size:65 final size:64
Alignment explanation
Indices: 51046--51199 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 64
51036 TGCACCATTG
* *
51046 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG
51109 AA
64 -A
* * * * *
51111 AACATCGAATACATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGA
*
51175 AACATCGAATGCACTTGATGCATCG
1 AACATCGAATGCATTTGATGCATCG
51200 CACTCTTAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 24 0.31
65 49 0.63
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:60177 original size:17 final size:19
Alignment explanation
Indices: 60149--60197 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
60139 TATTTTGAAA
60149 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
60167 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
60186 CACCGATGCACT
1 CATCGATGCACT
60198 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:62313 original size:84 final size:83
Alignment explanation
Indices: 62192--62419 Score: 242
Period size: 94 Copynumber: 2.6 Consensus size: 83
62182 GGCTAGCTGA
* * *
62192 ATCCATAAAGCCGAGGCATTTAACCAATTGCTCTAGAGGGATATCTCAATATTATAATCACCTTT
1 ATCCATAAAGCCG-GGCATTTAACCAATTGCTATAGAGGGAAATCTCAATATTATAATCACATTT
*
62257 ATCAGGCTAGCTGAATTTT
65 ATCAGGCTAGCTGAATCTT
* * *
62276 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGATTATTGTATATTAT
1 ATCCATAAAGCC-GGGCATTTAACCAATTGCTATAGAGGGA-AA-TC----TCA----ATATTAT
62341 AATCACATTTATCAGGCTAGCTGAATCTT
55 AATCACATTTATCAGGCTAGCTGAATCTT
* *
62370 ATCCATAAAGCGGGGGCATTTAACCAATTTCTATAGAGGGACAA-CTCAAT
1 ATCCATAAAGC-CGGGCATTTAACCAATTGCTATAGAGGGA-AATCTCAAT
62420 GCAGATCCAA
Statistics
Matches: 121, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
84 39 0.32
85 2 0.02
86 2 0.02
88 2 0.02
90 2 0.02
92 1 0.01
94 73 0.60
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (83 bp):
ATCCATAAAGCCGGGCATTTAACCAATTGCTATAGAGGGAAATCTCAATATTATAATCACATTTA
TCAGGCTAGCTGAATCTT
Found at i:62407 original size:94 final size:94
Alignment explanation
Indices: 62240--62418 Score: 295
Period size: 94 Copynumber: 1.9 Consensus size: 94
62230 GGATATCTCA
* * *
62240 ATATTATAATCACCTTTATCAGGCTAGCTGAATTTTATCCATAAAGCCAGGGCGTTTAACCAATT
1 ATATTATAATCACATTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATT
*
62305 GCTTTAGAGGGACAACTCAAGATTATTGT
66 GCTATAGAGGGACAACTCAAGATTATTGT
**
62334 ATATTATAATCACATTTATCAGGCTAGCTGAATCTTATCCATAAAGCGGGGGCATTTAACCAATT
1 ATATTATAATCACATTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATT
*
62399 TCTATAGAGGGACAACTCAA
66 GCTATAGAGGGACAACTCAA
62419 TGCAGATCCA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (94 bp):
ATATTATAATCACATTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATT
GCTATAGAGGGACAACTCAAGATTATTGT
Found at i:66062 original size:4 final size:4
Alignment explanation
Indices: 66055--66090 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
66045 ACTTAAATAA
* *
66055 AAAT AAAT AAAT AAAT AACT AAAT AAAT AACT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
66091 CAAAGAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:66072 original size:12 final size:12
Alignment explanation
Indices: 66055--66090 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
66045 ACTTAAATAA
*
66055 AAATAAATAAAT
1 AAATAACTAAAT
66067 AAATAACTAAAT
1 AAATAACTAAAT
66079 AAATAACTAAAT
1 AAATAACTAAAT
66091 CAAAGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (12 bp):
AAATAACTAAAT
Found at i:66258 original size:5 final size:5
Alignment explanation
Indices: 66229--66290 Score: 56
Period size: 5 Copynumber: 12.4 Consensus size: 5
66219 AACAAAACGG
* * * *
66229 AAATG AAATG AAATG AAATA AAATA AAATA AAA-A AAGTTA AAA-A AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA
66278 ATAATA AAATA AA
1 A-AATA AAATA AA
66291 GGTTGGGGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 7 0.14
5 35 0.70
6 8 0.16
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:67486 original size:16 final size:15
Alignment explanation
Indices: 67465--67508 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
67455 TGGACTTGGA
*
67465 AAAAATAATAAAATTT
1 AAAAATAATAAAA-TG
67481 AAAAATATATAAAATG
1 AAAAATA-ATAAAATG
67497 AATAAATAATAA
1 AA-AAATAATAA
67509 TAATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATAATAAAATG
Found at i:67574 original size:37 final size:36
Alignment explanation
Indices: 67533--67603 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
67523 AAATATTTTG
67533 AAACTATACATTATATATATTTTTAAAAAAGTTTTCA
1 AAACTATACATTATATA-ATTTTTAAAAAAGTTTTCA
* * *
67570 AAACTATATATTATATAATTTTTCAAAATGTTTT
1 AAACTATACATTATATAATTTTTAAAAAAGTTTT
67604 TTTAATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 15 0.48
37 16 0.52
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
AAACTATACATTATATAATTTTTAAAAAAGTTTTCA
Found at i:67605 original size:49 final size:49
Alignment explanation
Indices: 67552--67694 Score: 126
Period size: 49 Copynumber: 3.1 Consensus size: 49
67542 ATTATATATA
*
67552 TTTTTAAAAAAGTTTTCAAAACTATATATTATATA-ATTTTTCAAAATGT
1 TTTTTAAAAAAGTTTTCAAAACTATATACTATATATA-TTTTCAAAATGT
* **** * *
67601 TTTTTTAATGTTTTTTTAAAATTATATACTATATATATTTTCAAAATG-
1 TTTTTAAAAAAGTTTTCAAAACTATATACTATATATATTTTCAAAATGT
*
67649 TTTTT-AAAAA------AAATC-ATATACTATATATATTTTCAAAATGT
1 TTTTTAAAAAAGTTTTCAAAACTATATACTATATATATTTTCAAAATGT
67690 TTTTT
1 TTTTT
67695 TTAAAAACCA
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
40 25 0.32
41 8 0.10
47 2 0.03
48 5 0.06
49 38 0.48
50 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (49 bp):
TTTTTAAAAAAGTTTTCAAAACTATATACTATATATATTTTCAAAATGT
Found at i:67652 original size:38 final size:38
Alignment explanation
Indices: 67607--67766 Score: 187
Period size: 40 Copynumber: 4.1 Consensus size: 38
67597 ATGTTTTTTT
**
67607 AATGTTTTTTTAAAATTATATACTATATATATTTTCAA
1 AATGTTTTTTTAAAACCATATACTATATATATTTTCAA
** *
67645 AATGTTTTTAAAAAAAATCATATACTATATATATTTTCAA
1 AATGTTTTT--TTAAAACCATATACTATATATATTTTCAA
*
67685 AATGTTTTTTTTAAAAACCATATATTATATATATTTTCAA
1 AATG-TTTTTTT-AAAACCATATACTATATATATTTTCAA
* * *
67725 AATGTTTTTTGAAAACAATATAATATATA-AGTTTTCAA
1 AATGTTTTTTTAAAACCATATACTATATATA-TTTTCAA
67763 AATG
1 AATG
67767 ATTTCAAAAC
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.01
38 36 0.34
39 6 0.06
40 59 0.55
41 5 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (38 bp):
AATGTTTTTTTAAAACCATATACTATATATATTTTCAA
Found at i:67820 original size:2 final size:2
Alignment explanation
Indices: 67813--67873 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
67803 ATTTCAAAAC
67813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67855 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
67874 TTTAAATGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67897 original size:32 final size:32
Alignment explanation
Indices: 67861--67937 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
67851 TATATATATA
** *
67861 TATATATATATATTTTAAATGTTTTTAAAAAC
1 TATATATATATATTCAAAATGTTTTCAAAAAC
*
67893 TATATATATATCTTCAAAATGTTTTCAAAAAC
1 TATATATATATATTCAAAATGTTTTCAAAAAC
67925 TATATAATATATA
1 TATAT-ATATATA
67938 CATTTTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (32 bp):
TATATATATATATTCAAAATGTTTTCAAAAAC
Found at i:67897 original size:38 final size:39
Alignment explanation
Indices: 67623--67903 Score: 169
Period size: 36 Copynumber: 7.2 Consensus size: 39
67613 TTTTTAAAAT
*
67623 TATATACTATATATATTTTCAAAATGTTTTTAAAAA--AAA
1 TATATA-TATATATATTTT-AAAATGTTTTTAAAAACTATA
*
67662 TCATATACTATATATATTTTCAAAATGTTTTTTTTAAAAACCATA
1 T-ATATA-TATATATATTTT-AAAATG---TTTTTAAAAACTATA
* *
67707 TAT-TATATATAT-TTTCAAAATGTTTTTTGAAAAC-A-A
1 TATATATATATATATTTTAAAATG-TTTTTAAAAACTATA
* *
67743 TATA-ATATATA-AGTTTTCAAAATG-ATTTCAAAACTATA
1 TATATATATATATA-TTTT-AAAATGTTTTTAAAAACTATA
* * * *
67781 TAT-TATATA-AGT-TTTTGACATG-ATTTCAAAACTATA
1 TATATATATATA-TATTTTAAAATGTTTTTAAAAACTATA
* * * * * *
67817 TATATATATATATATATATATATATATATATATATATA-TATA
1 TATATATATATATAT-T-T-TA-AAATGTTTTTAAAAACTATA
67859 TATATATATATATATTTT-AAATGTTTTTAAAAACTATA
1 TATATATATATATATTTTAAAATGTTTTTAAAAACTATA
67897 TATATAT
1 TATATAT
67904 CTTCAAAATG
Statistics
Matches: 197, Mismatches: 21, Indels: 49
0.74 0.08 0.18
Matches are distributed among these distances:
36 40 0.20
37 26 0.13
38 39 0.20
39 3 0.02
40 33 0.17
41 5 0.03
42 29 0.15
43 17 0.09
44 2 0.01
45 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (39 bp):
TATATATATATATATTTTAAAATGTTTTTAAAAACTATA
Found at i:67897 original size:40 final size:40
Alignment explanation
Indices: 67623--67903 Score: 132
Period size: 40 Copynumber: 7.1 Consensus size: 40
67613 TTTTTAAAAT
67623 TATATACTATATATATTTTCAAAATGTTTTTAAAAA--A-A-A
1 TATATA-TATATATATTTT--AAATGTTTTTAAAAACTATATA
*
67662 TCATATACTATATATATTTTCAAAATGTTTTTTTTAAAAACCATATA
1 T-ATATA-TATATATATTTT--AAATG---TTTTTAAAAACTATATA
** *
67709 T-TATATATAT-T-TTCAAAATGTTTTTTGAAAAC-A-ATA
1 TATATATATATATATTTTAAATG-TTTTTAAAAACTATATA
* * *
67745 TA-ATATATA-AGT-TTTCAAAATG-ATTTCAAAACTATATA
1 TATATATATATA-TATTT-TAAATGTTTTTAAAAACTATATA
* * * *
67783 T-TATATA-AGT-T-TTTGACATG-ATTTCAAAACTATATA
1 TATATATATA-TATATTTTAAATGTTTTTAAAAACTATATA
* * * * * * *
67819 TATATATATATATATATATATATATATATATATA-TATATA
1 TATATATATATATAT-TTTAAATGTTTTTAAAAACTATATA
67859 TATATATATATATATTTTAAATGTTTTTAAAAACTATATA
1 TATATATATATATATTTTAAATGTTTTTAAAAACTATATA
67899 TATAT
1 TATAT
67904 CTTCAAAATG
Statistics
Matches: 195, Mismatches: 23, Indels: 47
0.74 0.09 0.18
Matches are distributed among these distances:
36 40 0.21
37 17 0.09
38 28 0.14
39 13 0.07
40 66 0.34
41 5 0.03
42 2 0.01
43 11 0.06
44 5 0.03
45 5 0.03
46 1 0.01
47 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (40 bp):
TATATATATATATATTTTAAATGTTTTTAAAAACTATATA
Found at i:68037 original size:16 final size:16
Alignment explanation
Indices: 68001--68049 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
67991 ATATATATAT
68001 ATAAAA-AAAATACATAA
1 ATAAAATAAAA-ACA-AA
*
68018 ATAATATAAAAACAAA
1 ATAAAATAAAAACAAA
68034 ATAAAATAAAAACAAA
1 ATAAAATAAAAACAAA
68050 TCCGGACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 17 0.59
17 8 0.28
18 4 0.14
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAAATAAAAACAAA
Found at i:69885 original size:60 final size:60
Alignment explanation
Indices: 69811--69998 Score: 222
Period size: 60 Copynumber: 3.1 Consensus size: 60
69801 CCATCATATG
*
69811 TCCCCAAACTATGACTCTCATTTCAAATTAATCCTTAAACTTTTAAACATTCCAATTTCA
1 TCCCCAAACTATGACTCTCATTTCAAATTAATCCCTAAACTTTTAAACATTCCAATTTCA
* * * * * *
69871 TTCTCAAACAATGACTCTCATTAT-AAATTAATCCCTACACTTTTGAACATTCCAATTTTA
1 TCCCCAAACTATGACTCTCATT-TCAAATTAATCCCTAAACTTTTAAACATTCCAATTTCA
** *
69931 TCCCCAAACTATGAAC-CTCA-TTCTAAATTGTTCCCTAAACTTTTATATC-TTCCAATTTCA
1 TCCCCAAACTATG-ACTCTCATTTC-AAATTAATCCCTAAACTTTTA-AACATTCCAATTTCA
69991 TCCCCAAA
1 TCCCCAAA
69999 TTCATCCAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 100 0.93
61 5 0.05
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTTCAAATTAATCCCTAAACTTTTAAACATTCCAATTTCA
Found at i:70226 original size:60 final size:60
Alignment explanation
Indices: 70162--70307 Score: 163
Period size: 60 Copynumber: 2.4 Consensus size: 60
70152 TGAGGACTGG
* * *
70162 TTTAGAATAAAGATCATAGTTTGAGGATGAAAATGAAATGTTTAAAAGTTTAAGGACT-AA
1 TTTAGAATAAAGATCATAGTTTGAGAATGAAAATGAAATATTTAAAAGTTT-AGGAATCAA
* * * *
70222 TTTAGAATGATAG-TCATAATTTAAGAATGAAATTGAAATATTTAAAAGTTTAGGAATCAA
1 TTTAGAAT-AAAGATCATAGTTTGAGAATGAAAATGAAATATTTAAAAGTTTAGGAATCAA
* *
70282 TTT-GAAATGAAGATCATAGATTGAGA
1 TTTAG-AATAAAGATCATAGTTTGAGA
70308 TTGAGGACGC
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 8 0.11
60 59 0.84
61 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (60 bp):
TTTAGAATAAAGATCATAGTTTGAGAATGAAAATGAAATATTTAAAAGTTTAGGAATCAA
Found at i:79378 original size:2 final size:2
Alignment explanation
Indices: 79371--79397 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79361 ACATGAACAA
79371 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
79398 AAGGGATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82141 original size:4 final size:4
Alignment explanation
Indices: 82134--82981 Score: 1628
Period size: 4 Copynumber: 212.5 Consensus size: 4
82124 TGATACGTAA
82134 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82182 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82230 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82278 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82326 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82374 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82422 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82468 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82516 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82564 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82612 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82660 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82708 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82756 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82804 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82852 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
82900 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * * * *
82948 GCAT GCAT GCAT GCAT ACAT GCAT ACAT GCAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
82982 TTCAAATAAT
Statistics
Matches: 836, Mismatches: 6, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
2 2 0.00
4 834 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ACAT
Done.