Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001177.1 Hibiscus syriacus cultivar Beakdansim tig00002343_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: 103201
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:831 original size:21 final size:23
Alignment explanation
Indices: 793--835 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
783 GGAAGAGTAA
793 TATTATTTATCTTATTTTTTAAT
1 TATTATTTATCTTATTTTTTAAT
816 TATT-TTTATC-TATTTTTTAA
1 TATTATTTATCTTATTTTTTAA
836 AAATTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
22 6 0.30
23 4 0.20
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTATTTATCTTATTTTTTAAT
Found at i:4086 original size:17 final size:17
Alignment explanation
Indices: 4044--4079 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4034 ATTATACCAA
4044 CTGATTATTAGTATTTT
1 CTGATTATTAGTATTTT
4061 CTGATTATTAGTATTTT
1 CTGATTATTAGTATTTT
4078 CT
1 CT
4080 TTGTATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (17 bp):
CTGATTATTAGTATTTT
Found at i:5597 original size:18 final size:18
Alignment explanation
Indices: 5576--5618 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
5566 ACACTTCTCA
5576 AACAATTATACTATTTGC
1 AACAATTATACTATTTGC
5594 AACAATTATACTATTTGC
1 AACAATTATACTATTTGC
5612 AACAATT
1 AACAATT
5619 CTCCCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (18 bp):
AACAATTATACTATTTGC
Found at i:7371 original size:22 final size:22
Alignment explanation
Indices: 7343--7387 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
7333 CCAGAAGTCT
7343 GTATCCCCGATCACATAGGCAC
1 GTATCCCCGATCACATAGGCAC
7365 GTATCCCCGATCACATAGGCAC
1 GTATCCCCGATCACATAGGCAC
7387 G
1 G
7388 CATCTAGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.18
Consensus pattern (22 bp):
GTATCCCCGATCACATAGGCAC
Found at i:10703 original size:62 final size:62
Alignment explanation
Indices: 10633--10756 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
10623 TACAGATCCC
10633 AAAGCATTCAAAGTCTCACCCTCAGAAGCAGCTTGATCAGACCCTTTGACTCTCCAGATCTT
1 AAAGCATTCAAAGTCTCACCCTCAGAAGCAGCTTGATCAGACCCTTTGACTCTCCAGATCTT
*
10695 AAAGCATTCAAAGTCTCACCCTCAGAAGCAGCTTGATCAGGCCCTTTGACTCTCCAGATCTT
1 AAAGCATTCAAAGTCTCACCCTCAGAAGCAGCTTGATCAGACCCTTTGACTCTCCAGATCTT
10757 CTCAACTTTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (62 bp):
AAAGCATTCAAAGTCTCACCCTCAGAAGCAGCTTGATCAGACCCTTTGACTCTCCAGATCTT
Found at i:12116 original size:120 final size:120
Alignment explanation
Indices: 11946--12232 Score: 470
Period size: 120 Copynumber: 2.4 Consensus size: 120
11936 AGATGTCATT
* * * * *
11946 CATTAAGTTAAATTTTAAGATAAAT-TGTTAAAAT-TGATCAAATCATATTAAACTTTAAATAGA
1 CATTAACTTAAATTTTACGAGAATTCTTTTAAAATCT-ATCAAATCATATTAAACTTTAAATAGA
*
12009 CGATTGTTTTATTTATCTGATTAAACTCATGAATAGATTTAAATAGAGACAACACC
65 CGATTGTTTTATTTATCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACC
12065 CATTAACTTAAATTTTACGAGAATTCTTTTAAAATCTATCAAATCATATTAAACTTTAAATAGAC
1 CATTAACTTAAATTTTACGAGAATTCTTTTAAAATCTATCAAATCATATTAAACTTTAAATAGAC
*
12130 GATTGTTTTATTTATCTAATTAAACTCATGAATAGATTTAAATAGAGACAACGCC
66 GATTGTTTTATTTATCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACC
* *
12185 CATTAACTTAAATTTTACGAGGATTCTTTTAAAATCCATCAAATCATA
1 CATTAACTTAAATTTTACGAGAATTCTTTTAAAATCTATCAAATCATA
12233 CCAAATTCTA
Statistics
Matches: 157, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
119 21 0.13
120 135 0.86
121 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (120 bp):
CATTAACTTAAATTTTACGAGAATTCTTTTAAAATCTATCAAATCATATTAAACTTTAAATAGAC
GATTGTTTTATTTATCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACC
Found at i:12276 original size:120 final size:120
Alignment explanation
Indices: 11832--12296 Score: 419
Period size: 120 Copynumber: 3.9 Consensus size: 120
11822 CAACGTTCAC
* * ** * *
11832 TAACTTAAATTTTACGATAA-ACTTTTAAAATTGATCAAATTATACCAAACTTTAAATAGATGAT
1 TAACTTAAATTTTACGAGAATTCTTTTAAAATCCATCAAATCATACCAAACTTTAAATAGACGAT
* * * *** **
11896 TACTTTATTTACC-AGA-TACAACTTATAGACA-A-ATCTAAA-A-AGATGTCATTCAT
66 TACTTTACTTACCTA-ATTA-AACTCAT-GA-ATAGATTTAAATAGAGACAACACCCAT
* * * * * ** **
11949 TAAGTTAAATTTTAAGATAAAT-TGTTAAAATTGATCAAATCATATTAAACTTTAAATAGACGAT
1 TAACTTAAATTTTACGAGAATTCTTTTAAAATCCATCAAATCATACCAAACTTTAAATAGACGAT
** * * *
12013 TGTTTTATTTATCTGATTAAACTCATGAATAGATTTAAATAGAGACAACACCCAT
66 TACTTTACTTACCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACCCAT
* **
12068 TAACTTAAATTTTACGAGAATTCTTTTAAAATCTATCAAATCATATTAAACTTTAAATAGACGAT
1 TAACTTAAATTTTACGAGAATTCTTTTAAAATCCATCAAATCATACCAAACTTTAAATAGACGAT
** * * *
12133 TGTTTTATTTATCTAATTAAACTCATGAATAGATTTAAATAGAGACAACGCCCAT
66 TACTTTACTTACCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACCCAT
* *
12188 TAACTTAAATTTTACGAGGATTCTTTTAAAATCCATCAAATCATACCAAA-TTCTAAATAGATGA
1 TAACTTAAATTTTACGAGAATTCTTTTAAAATCCATCAAATCATACCAAACTT-TAAATAGACGA
* * * * *
12252 TTACTTTCCTTACCTCATTCAACTCATTG-ATAGATCTGAATAGAG
65 TTACTTTACTTACCTAATTAAACTCA-TGAATAGATTTAAATAGAG
12297 GTATCGTTTA
Statistics
Matches: 296, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
115 1 0.00
116 3 0.01
117 78 0.26
118 3 0.01
119 28 0.09
120 181 0.61
121 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (120 bp):
TAACTTAAATTTTACGAGAATTCTTTTAAAATCCATCAAATCATACCAAACTTTAAATAGACGAT
TACTTTACTTACCTAATTAAACTCATGAATAGATTTAAATAGAGACAACACCCAT
Found at i:12774 original size:5 final size:5
Alignment explanation
Indices: 12764--12790 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12754 TTGAAGAAAA
12764 GGAGG GGAGG GGAGG GGAGG GGAGG GG
1 GGAGG GGAGG GGAGG GGAGG GGAGG GG
12791 GGCCTGGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:13192 original size:27 final size:27
Alignment explanation
Indices: 13146--13207 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
13136 GTCAAATTCG
* *
13146 AGTCGGGTGTAAGGTGTAT-ATTTTTC
1 AGTCGGGTGGAAGATGTATAATTTTTC
* *
13172 AGGTCGGGTGGAAGATTTATAATTTTTT
1 A-GTCGGGTGGAAGATGTATAATTTTTC
13200 AGTCGGGT
1 AGTCGGGT
13208 CAATTAGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 22 0.73
28 7 0.23
ACGTcount: A:0.21, C:0.06, G:0.32, T:0.40
Consensus pattern (27 bp):
AGTCGGGTGGAAGATGTATAATTTTTC
Found at i:13328 original size:26 final size:26
Alignment explanation
Indices: 13295--13350 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
13285 TTTTTTATAA
13295 ATTTAT-C-CTACTATAAAATTTTATT
1 ATTTATCCTCTACTATAAAATTTTA-T
*
13320 ATTTCATCCTCTAGTATAAAATTTTAT
1 ATTT-ATCCTCTACTATAAAATTTTAT
13347 ATTT
1 ATTT
13351 GTCTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 4 0.15
26 2 0.07
27 6 0.22
28 15 0.56
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATCCTCTACTATAAAATTTTAT
Found at i:16493 original size:5 final size:6
Alignment explanation
Indices: 16477--16557 Score: 56
Period size: 6 Copynumber: 12.8 Consensus size: 6
16467 GAGACAACCC
* * *
16477 ATTTTT ATTTTT ATTTTT CATTTGTT CAAATTTT ATTTTT ATTTTC AATTTT
1 ATTTTT ATTTTT ATTTTT -ATTT-TT --ATTTTT ATTTTT ATTTTT ATTTTT
* * *
16529 ATTTTT CTAATTT A-TTTT GTTTTT ATTTT
1 ATTTTT AT-TTTT ATTTTT ATTTTT ATTTT
16558 CTTAGAATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
5 3 0.05
6 40 0.70
7 7 0.12
8 4 0.07
9 3 0.05
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:16528 original size:18 final size:22
Alignment explanation
Indices: 16485--16535 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 22
16475 CCATTTTTAT
16485 TTTTATTTTTCATTTGTTCAAA
1 TTTTATTTTTCATTTGTTCAAA
16507 TTTTATTTTT-A-TT-TTC-AA
1 TTTTATTTTTCATTTGTTCAAA
16525 TTTTATTTTTC
1 TTTTATTTTTC
16536 TAATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.43
19 3 0.11
20 2 0.07
21 1 0.04
22 10 0.36
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTTTTCATTTGTTCAAA
Found at i:21019 original size:17 final size:18
Alignment explanation
Indices: 20960--21022 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
20950 CAATTTAAAC
* *
20960 TATAATAAAAATATAAAAA
1 TATAAT-AAAATATATAAT
*
20979 TAGAAATAAAATATATAAT
1 TA-TAATAAAATATATAAT
*
20998 TATAATAAAATATAT-TT
1 TATAATAAAATATATAAT
21015 TATAATAA
1 TATAATAA
21023 CTCGCTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 9 0.24
18 12 0.32
19 14 0.37
20 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TATAATAAAATATATAAT
Found at i:30959 original size:24 final size:24
Alignment explanation
Indices: 30863--30971 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
30853 AAATATTTTA
* * *
30863 TCTGATTTCTGATTTGAATTCTAT
1 TCTGATATCTGATTTGAATTTTGT
* * * * *
30887 TTTGACATCTGATCTAAAATTTGT
1 TCTGATATCTGATTTGAATTTTGT
* * * *
30911 TCTGAT-TCCTAACTTGGATTATGT
1 TCTGATAT-CTGATTTGAATTTTGT
30935 TCTGATATCTGATTTGAATTTTGT
1 TCTGATATCTGATTTGAATTTTGT
* *
30959 TTTGATTTCTGAT
1 TCTGATATCTGAT
30972 ATCTCCATTT
Statistics
Matches: 60, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
23 1 0.02
24 58 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (24 bp):
TCTGATATCTGATTTGAATTTTGT
Found at i:36270 original size:23 final size:23
Alignment explanation
Indices: 36240--36284 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
36230 ATTAACCCCT
36240 TCTTCTTCTCC-TCTCTTTATTCG
1 TCTTCTTCTCCTTCT-TTTATTCG
*
36263 TCTTCTTCTTCTTCTTTTATTC
1 TCTTCTTCTCCTTCTTTTATTC
36285 CTAAAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62
Consensus pattern (23 bp):
TCTTCTTCTCCTTCTTTTATTCG
Found at i:38486 original size:36 final size:36
Alignment explanation
Indices: 38421--38489 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
38411 AATATCTTTT
* *
38421 AATATCTTTTTAATATTTAAATTTTAAAAAATAGTA
1 AATATCTTTTTAATATTAAAATTTAAAAAAATAGTA
38457 AATATC-TTTTAAT-TTAAAATATTCAAAAAAATA
1 AATATCTTTTTAATATTAAAAT-TT-AAAAAAATA
38490 TTGACATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.21
35 9 0.31
36 14 0.48
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (36 bp):
AATATCTTTTTAATATTAAAATTTAAAAAAATAGTA
Found at i:38543 original size:81 final size:82
Alignment explanation
Indices: 38416--38565 Score: 214
Period size: 81 Copynumber: 1.8 Consensus size: 82
38406 TATATAATAT
* *
38416 CTTTTAATATCTTTTTAATATTTAAATTTTAAAAAATAGTAAATATCTTTTAATTTAAAATATTC
1 CTTTTAATATCTTTTTAATATTCAAATTTTAAAAAATAATAAATATCTTTTAATTTAAAATATTC
38481 AAAAAAATATTGACATC
66 AAAAAAATATTGACATC
* * * *
38498 CTTTTAATATC-TTTTAATATTCAAA-TTTAAAAGGATAATATATATCTTTTACTTTAAGATATT
1 CTTTTAATATCTTTTTAATATTCAAATTTTAAAA-AATAATAAATATCTTTTAATTTAAAATATT
*
38561 TAAAA
65 CAAAA
38566 GGATATAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
80 7 0.12
81 42 0.70
82 11 0.18
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (82 bp):
CTTTTAATATCTTTTTAATATTCAAATTTTAAAAAATAATAAATATCTTTTAATTTAAAATATTC
AAAAAAATATTGACATC
Found at i:38548 original size:35 final size:34
Alignment explanation
Indices: 38502--38621 Score: 111
Period size: 35 Copynumber: 3.4 Consensus size: 34
38492 GACATCCTTT
38502 TAATATCTTTTAATATTCAAATTTAAAAGGATAA
1 TAATATCTTTTAATATTCAAATTTAAAAGGATAA
* *
38536 TATATATCTTTTACT-TTAAGATATTTAAAAGGAT-A
1 TA-ATATCTTTTAATATTCA-A-ATTTAAAAGGATAA
* *
38571 TAATTATCCTGTTAATATTCAAATAT-AAAGAGATAA
1 TAA-TAT-CTTTTAATATTCAAATTTAAAAG-GATAA
*
38607 TAAATATATTTTAAT
1 T-AATATCTTTTAAT
38622 TTAGAATATT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
34 10 0.14
35 30 0.43
36 24 0.35
37 5 0.07
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (34 bp):
TAATATCTTTTAATATTCAAATTTAAAAGGATAA
Found at i:38580 original size:81 final size:81
Alignment explanation
Indices: 38407--38588 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 81
38397 AAAAGATAAT
* *
38407 ATATAATAT-CTTTTAATATCTTTTTAATATTTAAATTTTAAAAAATAGTAAATATCTTTTAATT
1 ATATAATATCCTTTTAATATCTTTTTAATATTCAAATTTTAAAAAATAATAAATATCTTTTAATT
38471 TAAAATATTCAAAAAA
66 TAAAATATTCAAAAAA
* * * * *
38487 ATATTGACATCCTTTTAATATC-TTTTAATATTCAAA-TTTAAAAGGATAATATATATCTTTTAC
1 ATA-TAATATCCTTTTAATATCTTTTTAATATTCAAATTTTAAAA-AATAATAAATATCTTTTAA
* * **
38550 TTTAAGATATTTAAAAGG
64 TTTAAAATATTCAAAAAA
*
38568 ATATAATTATCCTGTTAATAT
1 ATATAA-TATCCTTTTAATAT
38589 TCAAATATAA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
80 12 0.14
81 61 0.73
82 11 0.13
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (81 bp):
ATATAATATCCTTTTAATATCTTTTTAATATTCAAATTTTAAAAAATAATAAATATCTTTTAATT
TAAAATATTCAAAAAA
Found at i:43705 original size:3 final size:3
Alignment explanation
Indices: 43697--43739 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
43687 AGCTTGCATA
43697 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
43740 TCAAAACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44743 original size:26 final size:26
Alignment explanation
Indices: 44710--44767 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
44700 TTATTTATTA
44710 TATT-TTATTATTACTATAAT-AATTT
1 TATTATTATTATTACTA-AATAAATTT
*
44735 TATTATTATTATTATTAAATAAATTT
1 TATTATTATTATTACTAAATAAATTT
44761 TATTATT
1 TATTATT
44768 TCAGATCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTATTATTATTACTAAATAAATTT
Found at i:46232 original size:2 final size:2
Alignment explanation
Indices: 46219--46254 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
46209 TTATTTAGTC
*
46219 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46255 GTAATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46471 original size:22 final size:22
Alignment explanation
Indices: 46441--46492 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
46431 TATATATATA
46441 TATATATATATTTATT-TATAAAAT
1 TATA-ATATATTT-TTCT-TAAAAT
46465 T-TAATATATTTTTCTTAAAAT
1 TATAATATATTTTTCTTAAAAT
46486 TATAATA
1 TATAATA
46493 ATAAATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 9 0.35
22 14 0.54
23 2 0.08
24 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATAATATATTTTTCTTAAAAT
Found at i:46992 original size:42 final size:41
Alignment explanation
Indices: 46891--46997 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
46881 CGACAAAGGT
* ** *
46891 CTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACGGATGGCCTGAAGGACTTAGAATCATGCTCGAAAGA
* * *
46932 CTTACGGATGACAC-GAAGGATTTAAGAATCATGCTTGAAAGA
1 CTTACGGATGGC-CTGAAGGACTT-AGAATCATGCTCGAAAGA
*
46974 CTTACTGATGGCCTGAAGGACTTA
1 CTTACGGATGGCCTGAAGGACTTA
46998 CCAATTTTGG
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (41 bp):
CTTACGGATGGCCTGAAGGACTTAGAATCATGCTCGAAAGA
Found at i:47174 original size:41 final size:42
Alignment explanation
Indices: 47139--47225 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
47129 GGATGGCTTG
* * *
47139 AAGGATTT-ATCATCTTGCTCGAAAGACTTACGGATGACCCA
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACGGATGGCCCA
* *
47180 AAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGA
1 AAGGATTTAAGCATCATGCTCGAAAGACTTACGGATGGCCC-A
47223 AAG
1 AAG
47226 ACTTACTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 8 0.21
42 27 0.69
43 4 0.10
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (42 bp):
AAGGATTTAAGCATCATGCTCGAAAGACTTACGGATGGCCCA
Found at i:47279 original size:233 final size:232
Alignment explanation
Indices: 46886--47635 Score: 1137
Period size: 233 Copynumber: 3.2 Consensus size: 232
46876 ATCCTCGACA
* *
46886 AAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGACTTACGGATGACACGAAGG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGGATGACCCGAAGG
* * * *
46951 ATTTAAGAATCATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTT
66 ATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAATT
47016 TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTCAAATTTAAATGAGAAACTTT
131 TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTCAAATTTAAATGAGAAA-TTT
47081 TCTCATTTTTTGAAAAACATGTGAAAACATCATGC-CTG
195 TCTCATTTTTTGAAAAACATGTGAAAACATCATGCTC-G
** * *
47119 AAGGTCTTATGGATGGCTTGAAGGATTTATCATCTTGCTCGAAAGACTTACGGATGACCCAAAGG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGGATGACCCGAAGG
*
47184 ATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAAGACTTACTAATTTTGGAAATAATT
66 ATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAATT
* * * *
47249 TATTAGGTAAGAAATTTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAATTTT
131 TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTCAAATTTAAATGAGAAA-TTT
* * * *
47314 TCTCATTTCTCGAAAAACAAGTGAAAACATAATGCTCG
195 TCTCATTTTTTGAAAAACATGTGAAAACATCATGCTCG
* * *
47352 AAGGTCTTATGGATGGTCCGAAGGACTTATCATCTTGCTCGAAAGCCTTACGGATGACCCGAAGA
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGGATGACCCGAAGG
* * * * *
47417 ATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCC-AAATGACTTGCCAACTTTGGAAATATT
66 ATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAA-GACTTACCAATTTTGGAAATAAT
*
47481 TTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAAATTTT-AGATTTAAATGAGAAATA
130 TTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTT-AAATTTTCAAATTTAAATGAGAAAT-
* *
47545 TTTCTCATTTTTTGAAAAACATGCGAAAACATCTTGCTCG
193 TTTCTCATTTTTTGAAAAACATGTGAAAACATCATGCTCG
* *
47585 AAGGTCTTATGGATGGCCCGAATGACTTATTATCTTGCTCGAAAGACTTAC
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
47636 TGATTGCTCG
Statistics
Matches: 468, Mismatches: 45, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
232 4 0.01
233 457 0.98
234 7 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (232 bp):
AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACGGATGACCCGAAGG
ATTTAAGCATCATGCTTGAAAGACTTACTGATGGCCCGAAAGACTTACCAATTTTGGAAATAATT
TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTAAATTTTCAAATTTAAATGAGAAATTTT
CTCATTTTTTGAAAAACATGTGAAAACATCATGCTCG
Found at i:47407 original size:41 final size:42
Alignment explanation
Indices: 47345--47443 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 42
47335 TGAAAACATA
* * * ** * *
47345 ATGCTCGAAGGTCTTATGGATGGTCCGAAGGACTT-ATCATC
1 ATGCTCGAAAGACTTACGGATGACCCGAAGAACTTAAGCATC
* * *
47386 TTGCTCGAAAGCCTTACGGATGACCCGAAGAATTTAAGCATC
1 ATGCTCGAAAGACTTACGGATGACCCGAAGAACTTAAGCATC
47428 ATGCTCGAAAGACTTA
1 ATGCTCGAAAGACTTA
47444 TTGATGGCCC
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 27 0.59
42 19 0.41
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (42 bp):
ATGCTCGAAAGACTTACGGATGACCCGAAGAACTTAAGCATC
Found at i:47653 original size:41 final size:41
Alignment explanation
Indices: 47575--47654 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
47565 ATGCGAAAAC
* * *
47575 ATCTTGCTCGAAGGTCTTATGGATGGCCCGAATGACTTATT
1 ATCTTGCTCGAAAGACTTATGGATGGCCCGAAGGACTTATT
* *
47616 ATCTTGCTCGAAAGACTTACT-GATTGCTCGAAGGACTTA
1 ATCTTGCTCGAAAGACTTA-TGGATGGCCCGAAGGACTTA
47655 CCAAATTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
41 32 0.97
42 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
ATCTTGCTCGAAAGACTTATGGATGGCCCGAAGGACTTATT
Found at i:47755 original size:190 final size:191
Alignment explanation
Indices: 47429--47796 Score: 571
Period size: 190 Copynumber: 1.9 Consensus size: 191
47419 TTAAGCATCA
* * * * *
47429 TGCTCGAAAGACTTATTGATGGCCCAAATGACTTGCCAACTTTGGAAATATTTTACTAGGTAAGA
1 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAAATTTGGAAATAGTTTACTAGGTAAGA
**
47494 AACTTTTCTTACTTTTCAAAAATTTCAAATTTTAGATTTAAATGAGAAATATTTCTCATTTTTTG
66 AACTTTTCTTACTTTTCAAAAATTTCAAATTTTAGATTTAAATGAGAAATATTTCTCATTTTTCA
*
47559 AAAAACATGCGAAAACATCTTGCTCGAAGGTCTTATGGATGGCCCGAATGACTTATTATCT
131 AAAAACATGCGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAATGACTTATTATCT
* * *
47620 TGCTCGAAAGACTTACTGATTGCTCGAAGGACTTACCAAATTTGGAAATAGTTTACTAGGTAAGA
1 TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAAATTTGGAAATAGTTTACTAGGTAAGA
*
47685 AAC-TTTCTTACTTTTCAAAAATTT-TAATTTTCAGATTTAAATGAGAAACT-TTTCTCATTTTT
66 AACTTTTCTTACTTTTCAAAAATTTCAAATTTT-AGATTTAAATGAGAAA-TATTTCTCATTTTT
* *
47747 CAAAAAACATGTGAAAACTTCTTGCCCGAAGGTCTTATGGATGGCCCGAA
129 CAAAAAACATGCGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAA
47797 GGTCTTACGG
Statistics
Matches: 161, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
189 6 0.04
190 94 0.58
191 61 0.38
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (191 bp):
TGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAAATTTGGAAATAGTTTACTAGGTAAGA
AACTTTTCTTACTTTTCAAAAATTTCAAATTTTAGATTTAAATGAGAAATATTTCTCATTTTTCA
AAAAACATGCGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAATGACTTATTATCT
Found at i:47795 original size:20 final size:20
Alignment explanation
Indices: 47770--47808 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
47760 AAAACTTCTT
*
47770 GCCCGAAGGTCTTATGGATG
1 GCCCGAAGGTCTTACGGATG
47790 GCCCGAAGGTCTTACGGAT
1 GCCCGAAGGTCTTACGGAT
47809 TGCCTGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (20 bp):
GCCCGAAGGTCTTACGGATG
Found at i:48134 original size:42 final size:41
Alignment explanation
Indices: 48033--48139 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
48023 GCCCGAAGGT
* * *
48033 CTTACGGATGGCCAGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACTGATGGCCAGAAGGACTTAGCATCATGCTCGAAAGA
** * *
48074 CTTA-TGGATGATCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTACT-GATGGCCAGAAGGACTT-AGCATCATGCTCGAAAGA
*
48116 CTTACTGATGGCCCGAAGGACTTA
1 CTTACTGATGGCCAGAAGGACTTA
48140 CCAATCTTGG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
41 18 0.35
42 33 0.63
43 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTACTGATGGCCAGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:48259 original size:234 final size:232
Alignment explanation
Indices: 47574--48607 Score: 1246
Period size: 234 Copynumber: 4.4 Consensus size: 232
47564 CATGCGAAAA
* * * * * * ** *
47574 CATCTTGCTCGAAGGTCTTATGGATGGCCCGAATGACTT-ATTATCTTGCTCGAAAGACTTACTG
1 CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
* *
47638 ATTGCTCGAAGGACTTACCAAATTTGGAAATAGTTTACTAGGTAAGAAAC-TTTCTTACTTTTCA
66 ATGGCCCGAAGGACTTACC-AATTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCA
* * * *
47702 AAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCAAAAAACATGTGAAAACTT
130 AAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACAT
* **
47767 CTTGCCCGAAGGTCTTATGGATGGCCCGAAGGTCTTACGGATTGCCTGAGGACTT
195 CCTGCCCGAAGGTCTTACAGATGGCCCGAAGG----AC----T---T----A--T
* * * * *
47822 ACCATCTTGCTCGAAAGAATTACGGGTGACCCGAAGGATTTAAACATCATACTCAAAAGACTTAC
1 --CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* *
47887 TGATGGCCCAAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTT
64 TGATGGCCCGAAGGACTTACCAA-TTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTT
* *
47952 CAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTATCATTTTTCGAAAAAGCATGTGACAA
128 CAAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAA-CATGTGAAAA
* * *
48017 CGTCCTGCCCGAAGGTCTTACGGATGGCCAGAAGGACTTAT
192 CATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTAT
* * *
48058 CATCTTGCTCGAAAGACTTATGGATGATCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
1 CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
* *
48123 ATGGCCCGAAGGACTTACCAATCTTGGAAATAGTTTACAAGGTAAGAAACTTTTCTTACTTTTAA
66 ATGGCCCGAAGGACTTACCAAT-TTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTT-C
* * * * * *
48188 AAAAAATTCAATTTTCATATTTGAATGAGAAACTTTTCTCATTTTTCGAACAACGTGTGAAAACA
129 AAAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACA
* *
48253 TCCTGCCCGAAGTTCTTATAGATGGCCCGAAGGACTTAT
194 TCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTAT
* * * * * * * *
48292 TATCTTTCTCGAAAGACTCACAGATGACACGAAGGATTTACGCATCATGCTCGAAAGAATTACTA
1 CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
*
48357 ATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTTCTTTCTTTTCA
66 ATGGCCCGAAGGACTTACCAATTT-GGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCA
*
48422 AAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTCAAAACAT
130 AAAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACAT
* * * *
48487 CTTGTCCAAAGGTCTTACAGATGGCCCGAAGGACTTGT
195 CCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTAT
* * ** * *
48525 CATCTTGCTCGAAAGACTTAAGAAAAACCTGAAGGATTTAAGCATCATGCTCGAAAGACTTACCG
1 CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
48590 ATGGCCCG-AGAGACTTAC
66 ATGGCCCGAAG-GACTTAC
48608 TAAGTAAGAA
Statistics
Matches: 684, Mismatches: 92, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
232 2 0.00
233 160 0.23
234 271 0.40
235 47 0.07
236 1 0.00
238 1 0.00
242 1 0.00
245 1 0.00
249 2 0.00
250 33 0.05
251 63 0.09
252 62 0.09
253 40 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (232 bp):
CATCTTGCTCGAAAGACTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTG
ATGGCCCGAAGGACTTACCAATTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAA
AAATTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTCGAAAAACATGTGAAAACATC
CTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTAT
Found at i:48914 original size:17 final size:17
Alignment explanation
Indices: 48888--48928 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
48878 ATGCATTTTC
48888 TTTT-ATGCAAATGATG
1 TTTTCATGCAAATGATG
48904 TTTTCATGCAAATGATG
1 TTTTCATGCAAATGATG
48921 TTTTCATG
1 TTTTCATG
48929 TATGCATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (17 bp):
TTTTCATGCAAATGATG
Found at i:66757 original size:19 final size:19
Alignment explanation
Indices: 66733--66769 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
66723 AAAGGTAAGA
*
66733 TTTTTCTCCTTTTTTCCTC
1 TTTTTCTCCATTTTTCCTC
*
66752 TTTTTCTCGATTTTTCCT
1 TTTTTCTCCATTTTTCCT
66770 TCTCTCTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.27, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTCTCCATTTTTCCTC
Found at i:67499 original size:3 final size:3
Alignment explanation
Indices: 67479--67527 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
67469 CATAAAGAAA
67479 AAT AAT AGA- AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
67525 AAT
1 AAT
67528 CAAAGCATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:67851 original size:10 final size:10
Alignment explanation
Indices: 67822--67851 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
67812 ATTTAAATGA
*
67822 TAAACGAACA
1 TAAACGAACG
67832 TAAACGAACG
1 TAAACGAACG
67842 TAAACGAACG
1 TAAACGAACG
67852 AACATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.17, T:0.10
Consensus pattern (10 bp):
TAAACGAACG
Found at i:67869 original size:24 final size:24
Alignment explanation
Indices: 67824--67870 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
67814 TTAAATGATA
** *
67824 AACGAACATAAACGAACGTAAACG
1 AACGAACATAAAAAAACATAAACG
*
67848 AACGAACATAAAAAAATATAAAC
1 AACGAACATAAAAAAACATAAAC
67871 AAACACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.17, G:0.11, T:0.11
Consensus pattern (24 bp):
AACGAACATAAAAAAACATAAACG
Found at i:72886 original size:9 final size:9
Alignment explanation
Indices: 72872--72909 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
72862 TGCTCAAGAC
72872 GACGACGAT
1 GACGACGAT
72881 GACGACGAT
1 GACGACGAT
72890 GACGACGAT
1 GACGACGAT
72899 GACGACGAT
1 GACGACGAT
72908 GA
1 GA
72910 TGATGGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:73097 original size:12 final size:12
Alignment explanation
Indices: 73055--73097 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
73045 ATTTAGTACT
*
73055 TTTTTATTGTAG
1 TTTTTATTGTAA
*
73067 TTGTTTATTGGACA
1 TT-TTTATTGTA-A
73081 TTTTTATTGTAA
1 TTTTTATTGTAA
73093 TTTTT
1 TTTTT
73098 TTTATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 8 0.31
13 16 0.62
14 2 0.08
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.65
Consensus pattern (12 bp):
TTTTTATTGTAA
Found at i:88172 original size:32 final size:31
Alignment explanation
Indices: 88131--88260 Score: 118
Period size: 32 Copynumber: 4.1 Consensus size: 31
88121 AGGTGACCCA
*
88131 TGGGTAGGCTCTTAGGCCCCAAGATGTTCCCT
1 TGGGTAGGCTCTCAGGCCCCAAGATGTT-CCT
* * * *
88163 TGGGTAGGCTCTCAAGCCCCAAAATACTTCTT
1 TGGGTAGGCTCTCAGGCCCCAAGAT-GTTCCT
* *
88195 TTGGCAGGCTCTCAGGCCCCAATG-TGCTTCCT
1 TGGGTAGGCTCTCAGGCCCCAA-GATG-TTCCT
* * * *
88227 TGGGTAGGCTTTGAGGCCCCAAGGTTTTCCT
1 TGGGTAGGCTCTCAGGCCCCAAGATGTTCCT
88258 TGG
1 TGG
88261 TTGGCCCTAT
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
31 9 0.12
32 67 0.86
33 2 0.03
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (31 bp):
TGGGTAGGCTCTCAGGCCCCAAGATGTTCCT
Found at i:90766 original size:3 final size:3
Alignment explanation
Indices: 90751--90827 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
90741 AATTTTAATT
*
90751 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTAA TGT- TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA
90796 TTA TT- TGT- TTA TTA TTTA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TTA TTA
90828 ATTACATATT
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
2 7 0.11
3 51 0.80
4 5 0.08
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:90807 original size:11 final size:11
Alignment explanation
Indices: 90750--90823 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
90740 TAATTTTAAT
90750 TTTATTATTGT-
1 TTTATTATT-TA
90761 TATTATTA-TTA
1 T-TTATTATTTA
*
90772 -TTATTATTAA
1 TTTATTATTTA
*
90782 TGT-TTATATTA
1 TTTATTAT-TTA
*
90793 -TTATTATTTG
1 TTTATTATTTA
90803 TTTATTATTTA
1 TTTATTATTTA
90814 TTATATTATT
1 TT-TATTATT
90824 ATTAATTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
9 6 0.12
10 10 0.20
11 20 0.41
12 13 0.27
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:90831 original size:15 final size:15
Alignment explanation
Indices: 90745--90831 Score: 68
Period size: 18 Copynumber: 5.5 Consensus size: 15
90735 CTAGTTAATT
* *
90745 TTAATTTTATTATTG
1 TTAATTATATTATTA
90760 TTATTATTATTATTATTA
1 TTA--ATTA-TATTATTA
90778 TTAATGTTTATATTATTA
1 TTAA---TTATATTATTA
* *
90796 TTATTTGT-TTATTA
1 TTAATTATATTATTA
*
90810 TTTATTATATTATTA
1 TTAATTATATTATTA
90825 TTAATTA
1 TTAATTA
90832 CATATTACAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
14 11 0.19
15 18 0.32
16 1 0.02
17 3 0.05
18 21 0.37
19 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTAATTATATTATTA
Found at i:94295 original size:31 final size:32
Alignment explanation
Indices: 94260--94320 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
94250 TTTTACATGT
*
94260 ACTAACTTGTTT-TTCTCTTTTGTTTGTGTAC
1 ACTAACTTATTTCTTCTCTTTTGTTTGTGTAC
94291 ACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 ACTAACTTATTTCTTCTCTTTTGTTTGTGT
94321 CATTTTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.59
Consensus pattern (32 bp):
ACTAACTTATTTCTTCTCTTTTGTTTGTGTAC
Found at i:96353 original size:11 final size:11
Alignment explanation
Indices: 96308--96355 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
96298 TGCAGAGTAC
**
96308 AAAGAAAAATC
1 AAAGAAAAAGA
96319 AAAGAAAAATAGCA
1 AAAG-AAAA-AG-A
96333 AAAGAAAAAGA
1 AAAGAAAAAGA
96344 AAAGAAAAAGA
1 AAAGAAAAAGA
96355 A
1 A
96356 GACAAAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 17 0.53
12 6 0.19
13 5 0.16
14 4 0.12
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:97248 original size:24 final size:23
Alignment explanation
Indices: 97193--97250 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
97183 TGAAAGGAGC
*
97193 AATATTTTCAAAACTTTTGATTA
1 AATATTTTCAAAACTTTTAATTA
97216 AATATTTTTCAAAACTCTTTTAATT-
1 AATA-TTTTCAAAA--CTTTTAATTA
*
97241 GATATTTTCA
1 AATATTTTCA
97251 TACTTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.13
24 15 0.50
25 3 0.10
26 8 0.27
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.50
Consensus pattern (23 bp):
AATATTTTCAAAACTTTTAATTA
Found at i:97526 original size:4 final size:4
Alignment explanation
Indices: 97519--97555 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
97509 TAGATAGAAA
97519 ATAC ATAC AT-- ATAC AATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC -ATAC ATAC ATAC ATAC ATAC AT
97556 GTTACATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.07
4 24 0.80
5 4 0.13
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:98189 original size:33 final size:34
Alignment explanation
Indices: 98106--98196 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 34
98096 CAAAACAAAC
98106 TTTGTCTCGCTTGAGACAATTTATCTAAAAACAATT
1 TTTGTCTCGCTTGAGACAATTTATCT--AAACAATT
* * *
98142 TTCGTCTCGTTTGAGACAATTTCTCT-AA-AATT
1 TTTGTCTCGCTTGAGACAATTTATCTAAACAATT
*
98174 TATTGTCTCACTTGAGACAATTT
1 T-TTGTCTCGCTTGAGACAATTT
98197 TCCAAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
32 5 0.10
33 20 0.42
36 23 0.48
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (34 bp):
TTTGTCTCGCTTGAGACAATTTATCTAAACAATT
Found at i:98659 original size:36 final size:35
Alignment explanation
Indices: 98608--98704 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 35
98598 TTTAAGAAAA
* **
98608 ATCTTTGAGTCTGTTT-CTTTGGAAACAAAATTAAT
1 ATCTTTGAGTCTGTTTCCCTT-GAAACAAAACAAAT
*
98643 CATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAAT
1 -ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
*
98679 ATCTTTGAGATC-ATTTCCCTTGAAAC
1 ATCTTTGAG-TCTGTTTCCCTTGAAAC
98705 GAATTTTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 22 0.42
36 28 0.53
37 3 0.06
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (35 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAACAAAT
Found at i:98696 original size:35 final size:36
Alignment explanation
Indices: 98629--98704 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
98619 TGTTTCTTTG
** * **
98629 GAAACAAAATTAATCATCTTTGAGTTTGTTTCCCTT
1 GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
98665 GAAACAAAACAAAT-ATCTTTGAGATCATTTCCCTT
1 GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
98700 GAAAC
1 GAAAC
98705 GAATTTTGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (36 bp):
GAAACAAAACAAATCATCTTTGAGATCATTTCCCTT
Found at i:99088 original size:130 final size:128
Alignment explanation
Indices: 98797--99158 Score: 369
Period size: 130 Copynumber: 2.8 Consensus size: 128
98787 CCAGTCATCC
* * * * * *
98797 TCATCACGTAGGAACTGTGTCATC-CCCTGGCCATATCTCCTCATCACGTAGGAGTCGTGTCAAC
1 TCATCACGTATGAGCTGTGTCATCACTC-GACCAAATCTCCTCATCACGTAGGAGCCGTGTCAAC
* * * * *
98861 CTTAGATAACCA-ATCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGTCAGAACTC
65 CTTAGATAA-CAGAAC-TCTTCATCACGTATGAGCCGTGTTATCACCTTTAGATGGCCAGAACTC
98925 T
128 T
** *
98926 TCATCACGTATGAGCCTGTGTCATCACTCGACCTGATCTCCTCATCACGTGGGAGCCGTGTCAAC
1 TCATCACGTATGAG-CTGTGTCATCACTCGACCAAATCTCCTCATCACGTAGGAGCCGTGTCAAC
* * *
98991 CTTTGATAACAGAACTCTTCATCATGTATGAGTCGTGTTATCACCTTTGTAAAGATGGCCAAGAA
65 CTTAGATAACAGAACTCTTCATCACGTATGAGCCGTGTTATCACC-TT-T--AGATGGCC-AGAA
99056 CTC-
125 CTCT
* *
99059 TCATCACGTATGAG-TAGTGTCATC-C-CGACCAAATCTCCTCATCACGTAGGA-CCGAGTCACC
1 TCATCACGTATGAGCT-GTGTCATCACTCGACCAAATCTCCTCATCACGTAGGAGCCGTGTCAAC
* * * *
99120 CTTAGACGACCCGAACTCTTCATCACGTATGAGCAGTGT
65 CTTAGA-TAACAGAACTCTTCATCACGTATGAGCCGTGT
99159 CGTCCCCAAC
Statistics
Matches: 195, Mismatches: 28, Indels: 19
0.81 0.12 0.08
Matches are distributed among these distances:
129 52 0.27
130 102 0.52
131 5 0.03
132 8 0.04
133 21 0.11
134 7 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (128 bp):
TCATCACGTATGAGCTGTGTCATCACTCGACCAAATCTCCTCATCACGTAGGAGCCGTGTCAACC
TTAGATAACAGAACTCTTCATCACGTATGAGCCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:99333 original size:3 final size:3
Alignment explanation
Indices: 99318--99392 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
99308 AATTTTAATT
* *
99318 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA -TG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
99365 TTA TT- TT- TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
99393 ATTACATATT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 5 0.08
3 61 0.92
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:99882 original size:20 final size:22
Alignment explanation
Indices: 99845--99887 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
99835 GGGGAAAGAA
99845 AAAAAATATCAAGAGGC-TCAGG
1 AAAAAATA-CAAGAGGCTTCAGG
*
99867 AAAAAATA-AAGGGGCTTCAGG
1 AAAAAATACAAGAGGCTTCAGG
99888 GAGAACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 8 0.42
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.14
Consensus pattern (22 bp):
AAAAAATACAAGAGGCTTCAGG
Found at i:102208 original size:31 final size:31
Alignment explanation
Indices: 102140--102248 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 31
102130 TTAAGAATAT
* *
102140 AAAACATTTAAATTTTAGAATTATCTCTTAAG
1 AAAACATTTAAA-TTTGGAATTATCTCCTAAG
*
102172 -GAACA-TTAAATTTGGAATTATCTCCTAACG
1 AAAACATTTAAATTTGGAATTATCTCCTAA-G
* * *
102202 AAAACATTTAAGGTTTGAAATTATCTTCTAAG
1 AAAACATTTAA-ATTTGGAATTATCTCCTAAG
102234 AAAACATTTAAATTT
1 AAAACATTTAAATTT
102249 TGAGAATATC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
29 16 0.25
30 6 0.09
31 11 0.17
32 16 0.25
33 16 0.25
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (31 bp):
AAAACATTTAAATTTGGAATTATCTCCTAAG
Found at i:102240 original size:32 final size:33
Alignment explanation
Indices: 102140--102262 Score: 109
Period size: 32 Copynumber: 3.9 Consensus size: 33
102130 TTAAGAATAT
*
102140 AAAACATTTAAA-TTTTAGAATTATC-TCTTAA-G
1 AAAACATTTAAAGTTTGA-AATTATCTTC-TAACG
* * *
102172 -GAACA-TTAAA-TTTGGAATTATCTCCTAACG
1 AAAACATTTAAAGTTTGAAATTATCTTCTAACG
*
102202 AAAACATTTAAGGTTTGAAATTATCTTCTAA-G
1 AAAACATTTAAAGTTTGAAATTATCTTCTAACG
*
102234 AAAACATTTAAATTTTGAGAA-TATCTTCT
1 AAAACATTTAAAGTTTGA-AATTATCTTCT
102263 CTTCAAAAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
29 10 0.13
30 10 0.13
31 8 0.11
32 29 0.39
33 18 0.24
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (33 bp):
AAAACATTTAAAGTTTGAAATTATCTTCTAACG
Done.