Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013698.1 Kokia drynarioides strain JFW-HI SEQ_128726, 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: 206427
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 299 characters in sequence are not A, C, G, or T
Found at i:4071 original size:29 final size:28
Alignment explanation
Indices: 3984--4251 Score: 196
Period size: 29 Copynumber: 9.1 Consensus size: 28
3974 TGCCCAAGCA
* * *
3984 ACCCCAAACTTTCCTAAAATCATATTTTG
1 ACCCTAAACTTTCC-AAAATTACATTTTG
* * *
4013 TCACCTAAACTTCTCTAAAATTATATTTTG
1 AC-CCTAAACTT-TCCAAAATTACATTTTG
4043 ACCCTTAAACTTTCCAAAATTACATTTTG
1 ACCC-TAAACTTTCCAAAATTACATTTTG
** * *
4072 ACCCTTAATTTTTCCAAAAGTGCATTTTG
1 ACCC-TAAACTTTCCAAAATTACATTTTG
* * *
4101 AGGCCTCAACTTTTCTAAAATTACATTTTG
1 A-CCCTAAAC-TTTCCAAAATTACATTTTG
* *
4131 GCCCATAAACTTTCCAAAATTACACTTTG
1 ACCC-TAAACTTTCCAAAATTACATTTTG
* *
4160 ACCCCTAAACCTTTCTAAAATCACATTTT-
1 A-CCCTAAA-CTTTCCAAAATTACATTTTG
* * * *
4189 AGCCCTAAACTCCTCAAAAATCACATTTTT
1 A-CCCTAAACT-TTCCAAAATTACATTTTG
* *
4219 ACCCTCAAAATTTTCTAAAATTACATTTTG
1 ACCCT--AAACTTTCCAAAATTACATTTTG
4249 ACC
1 ACC
4252 TCGTATTCTT
Statistics
Matches: 192, Mismatches: 35, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 96 0.50
30 88 0.46
31 6 0.03
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (28 bp):
ACCCTAAACTTTCCAAAATTACATTTTG
Found at i:4123 original size:59 final size:59
Alignment explanation
Indices: 4039--4251 Score: 175
Period size: 59 Copynumber: 3.6 Consensus size: 59
4029 AAAATTATAT
* * * ** * *
4039 TTTGACCCTTAAA-CTTTCCAAAATTACATTTTGACCCTTAATTTTTCCAAAAGTGCAT
1 TTTGACCCCTAAACCTTTCTAAAATTACATTTTGACCCATAAACTTTCCAAAAGTACAC
** * * * *
4097 TTTGAGGCCTCAACTTTTCTAAAATTACATTTTGGCCCATAAACTTTCCAAAATTACAC
1 TTTGACCCCTAAACCTTTCTAAAATTACATTTTGACCCATAAACTTTCCAAAAGTACAC
* * * *
4156 TTTGACCCCTAAACCTTTCTAAAATCACATTTT-AGCCC-TAAAC-TCCTCAAAAATCACAT
1 TTTGACCCCTAAACCTTTCTAAAATTACATTTTGA-CCCATAAACTTTC-CAAAAGT-ACAC
* **
4215 TTTTA-CCCTCAAAATTTTCTAAAATTACATTTTGACC
1 TTTGACCCCT-AAACCTTTCTAAAATTACATTTTGACC
4252 TCGTATTCTT
Statistics
Matches: 123, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
57 2 0.02
58 24 0.20
59 96 0.78
60 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (59 bp):
TTTGACCCCTAAACCTTTCTAAAATTACATTTTGACCCATAAACTTTCCAAAAGTACAC
Found at i:4209 original size:88 final size:87
Alignment explanation
Indices: 3984--4251 Score: 256
Period size: 88 Copynumber: 3.0 Consensus size: 87
3974 TGCCCAAGCA
* *
3984 ACCCC-AAACTTTCCTAAAATCATATTTT-GTCACCTAAACTTCTCTAAAATTATATTTTGACCC
1 ACCCCTAAACTTT-CTAAAATCACATTTTAG-C-CCTAAACTTCTCTAAAATTACATTTTGACCC
* *
4047 TTAAACTTTCCAAAATTACATTTTG
63 ATAAACTTTCCAAAATTACACTTTG
* ** * * * * * *
4072 ACCCTTAATTTTTCCAAAAGT-GCATTTTGAGGCCTCAACTTTTCTAAAATTACATTTTGGCCCA
1 ACCCCTAAACTTTCTAAAA-TCACATTTT-AGCCCTAAACTTCTCTAAAATTACATTTTGACCCA
4136 TAAACTTTCCAAAATTACACTTTG
64 TAAACTTTCCAAAATTACACTTTG
* * * *
4160 ACCCCTAAACCTTTCTAAAATCACATTTTAGCCCTAAACTCCTCAAAAATCACATTTTTACCC-T
1 ACCCCTAAA-CTTTCTAAAATCACATTTTAGCCCTAAACTTCTCTAAAATTACATTTTGACCCAT
* * *
4224 CAAAATTTTCTAAAATTACATTTTG
65 --AAACTTTCCAAAATTACACTTTG
4249 ACC
1 ACC
4252 TCGTATTCTT
Statistics
Matches: 143, Mismatches: 29, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
87 1 0.01
88 98 0.69
89 43 0.30
90 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (87 bp):
ACCCCTAAACTTTCTAAAATCACATTTTAGCCCTAAACTTCTCTAAAATTACATTTTGACCCATA
AACTTTCCAAAATTACACTTTG
Found at i:15626 original size:3 final size:3
Alignment explanation
Indices: 15614--15657 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
15604 AAAATATAAG
15614 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15658 ATAAGTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16650 original size:16 final size:18
Alignment explanation
Indices: 16625--16661 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16615 AAATGAAACT
*
16625 AAAATGAGAA-TGATATG
1 AAAATGAGAATTGAGATG
16642 AAAAT-AGAATTGAGATG
1 AAAATGAGAATTGAGATG
16659 AAA
1 AAA
16662 CGGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAATGAGAATTGAGATG
Found at i:16659 original size:22 final size:22
Alignment explanation
Indices: 16612--16661 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
16602 TGATTTGATT
*
16612 ATGAAATGAAACTAAAATGAGA
1 ATGAAATGAAAATAAAATGAGA
* *
16634 ATGATATGAAAATAGAATTGAG-
1 ATGAAATGAAAATA-AAATGAGA
16656 ATGAAA
1 ATGAAA
16662 CGGATTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (22 bp):
ATGAAATGAAAATAAAATGAGA
Found at i:20064 original size:6 final size:6
Alignment explanation
Indices: 20053--20080 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20043 AAACACTTTT
20053 CAACCA CAACCA CAACCA CAACCA CAAC
1 CAACCA CAACCA CAACCA CAACCA CAAC
20081 AATGCTAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACCA
Found at i:25188 original size:7 final size:7
Alignment explanation
Indices: 25178--25207 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
25168 TATTTTTTTT
25178 ATTTTGA
1 ATTTTGA
25185 ATTTTGA
1 ATTTTGA
25192 ATTTTGA
1 ATTTTGA
25199 ATTTTGA
1 ATTTTGA
25206 AT
1 AT
25208 AATCAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (7 bp):
ATTTTGA
Found at i:31802 original size:37 final size:37
Alignment explanation
Indices: 31742--31895 Score: 263
Period size: 37 Copynumber: 4.2 Consensus size: 37
31732 GAGAAAGTAA
* * *
31742 AAGGAAATAAAAAGGCATTAGTGAATGAAAAATATAT
1 AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
31779 AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
1 AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
*
31816 AAGGTAATAAACAGGCATCAGTGAATGAAAAATATAC
1 AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
*
31853 AAGGTAATAAAAAGGCATTAGTGAATGAAAAATATAC
1 AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
31890 AAGGTA
1 AAGGTA
31896 CATGATGAGC
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 111 1.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.20
Consensus pattern (37 bp):
AAGGTAATAAAAAGGCATCAGTGAATGAAAAATATAC
Found at i:34686 original size:17 final size:17
Alignment explanation
Indices: 34660--34697 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
34650 ATAATAAAAA
*
34660 AATATTTCATAATAA-TT
1 AATATATCAT-ATAACTT
34677 AATATATCATATAACTT
1 AATATATCATATAACTT
34694 AATA
1 AATA
34698 ATAAATAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATCATATAACTT
Found at i:35795 original size:13 final size:13
Alignment explanation
Indices: 35777--35802 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35767 TGGCCCCCCA
35777 AATTTAATTTTTT
1 AATTTAATTTTTT
35790 AATTTAATTTTTT
1 AATTTAATTTTTT
35803 TGTAAATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTAATTTTTT
Found at i:36572 original size:2 final size:2
Alignment explanation
Indices: 36565--36596 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36555 AATATAACTA
36565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36597 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54245 original size:29 final size:29
Alignment explanation
Indices: 54188--54245 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
54178 TTACTTTATA
* * *
54188 AAATTATTTAAAAATATATGATGATTTTT
1 AAATTATTTAAAAACATATGATAAATTTT
*
54217 AAATTATTTAAAAACATTTGATAAATTTT
1 AAATTATTTAAAAACATATGATAAATTTT
54246 CTTTGTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
AAATTATTTAAAAACATATGATAAATTTT
Found at i:65236 original size:11 final size:11
Alignment explanation
Indices: 65213--65241 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
65203 TATAATTATT
65213 AATATAT-ACA
1 AATATATAACA
65223 AATATATAACA
1 AATATATAACA
65234 AATATATA
1 AATATATA
65242 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (11 bp):
AATATATAACA
Found at i:66507 original size:24 final size:24
Alignment explanation
Indices: 66456--66507 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
66446 TTCGTAAGCC
* *
66456 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
66480 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
66504 AAAT
1 AAAT
66508 CTTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:69929 original size:19 final size:18
Alignment explanation
Indices: 69905--69943 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
69895 AGTAAAATTA
69905 TTATTCCAAAAAATAGAAT
1 TTATTCCAAAAAATA-AAT
* *
69924 TTATTCTAGAAAATAAAT
1 TTATTCCAAAAAATAAAT
69942 TT
1 TT
69944 CCACTACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (18 bp):
TTATTCCAAAAAATAAAT
Found at i:70662 original size:21 final size:21
Alignment explanation
Indices: 70638--70690 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
70628 TTGTGCTAGC
70638 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
70657 TTTCTACCGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
70680 TCTACCGATAC
1 TCTACCGATAC
70691 GAAAAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 26 0.87
22 3 0.10
23 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:76251 original size:6 final size:6
Alignment explanation
Indices: 76240--76266 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
76230 ATACATAAGA
76240 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
76267 CCATTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:76582 original size:32 final size:32
Alignment explanation
Indices: 76539--76601 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
76529 TGGAGAAAAC
* *
76539 CAAGAATATGATGAACTAGAAGACTTTCCTCG
1 CAAGAAAATGATGAACCAGAAGACTTTCCTCG
76571 CAAGAAAATGATGAACCAGAAGACTTTCCTC
1 CAAGAAAATGATGAACCAGAAGACTTTCCTC
76602 TCCCCAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (32 bp):
CAAGAAAATGATGAACCAGAAGACTTTCCTCG
Found at i:78270 original size:13 final size:12
Alignment explanation
Indices: 78237--78294 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
78227 ATTTAAAGTT
*
78237 TTAAAAAATATAA
1 TTAAAAAA-AAAA
*
78250 TTATAAAAAAAA
1 TTAAAAAAAAAA
*
78262 TTAAGAAAAAAAC
1 TTAA-AAAAAAAA
*
78275 TTAAAATAAAATA
1 TTAAAA-AAAAAA
78288 TTAAAAA
1 TTAAAAA
78295 GATTCAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
13 28 0.76
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (12 bp):
TTAAAAAAAAAA
Found at i:79061 original size:23 final size:23
Alignment explanation
Indices: 79035--79115 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
79025 TAATGTTTAC
*
79035 GAACATGTTCATTTAAC-TTAATT
1 GAACATGTTCA-TAAACATTAATT
** * *
79058 GAACATGTTCACGAACTTTAAAT
1 GAACATGTTCATAAACATTAATT
79081 GAACATGTTCATAAACATATAATT
1 GAACATGTTCATAAACAT-TAATT
79105 GAACATGTTCA
1 GAACATGTTCA
79116 CGAACAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.63
24 15 0.31
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (23 bp):
GAACATGTTCATAAACATTAATT
Found at i:79121 original size:24 final size:24
Alignment explanation
Indices: 79053--79121 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
79043 TCATTTAACT
*
79053 TAATTGAACATGTTCACGAAC-TT
1 TAATTGAACATGTTCACGAACATA
* **
79076 TAAATGAACATGTTCATAAACATA
1 TAATTGAACATGTTCACGAACATA
79100 TAATTGAACATGTTCACGAACA
1 TAATTGAACATGTTCACGAACA
79122 ATGTTAATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (24 bp):
TAATTGAACATGTTCACGAACATA
Found at i:79244 original size:24 final size:24
Alignment explanation
Indices: 79212--79259 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
79202 TCATTAATAA
* *
79212 ATAAACAAGTCAGTAAACGAGCTT
1 ATAAACAAGCCAATAAACGAGCTT
79236 ATAAACAAGCCAATAAACGAGCTT
1 ATAAACAAGCCAATAAACGAGCTT
79260 GTTCGTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (24 bp):
ATAAACAAGCCAATAAACGAGCTT
Found at i:92441 original size:22 final size:22
Alignment explanation
Indices: 92413--92458 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
92403 AATGATGGGC
92413 ACCAATTTAAAGTGAATGACCA
1 ACCAATTTAAAGTGAATGACCA
92435 ACCAATTTAAAGTGAATGACCA
1 ACCAATTTAAAGTGAATGACCA
92457 AC
1 AC
92459 GATTAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (22 bp):
ACCAATTTAAAGTGAATGACCA
Found at i:112870 original size:5 final size:5
Alignment explanation
Indices: 112860--112907 Score: 78
Period size: 5 Copynumber: 9.2 Consensus size: 5
112850 TAAGAAAAAG
112860 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAAA AGAAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AG-AAA AG-AAA AGAAA A
112908 AGATATATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 31 0.74
6 11 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:112898 original size:6 final size:6
Alignment explanation
Indices: 112851--112910 Score: 76
Period size: 5 Copynumber: 10.7 Consensus size: 6
112841 ACATATGTAT
112851 AAGAAA AAGAGAA AAG-AA AAG-AA AAG-AA AAG-AA AAG-AA AAGAAA
1 AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
112895 AAGAAA AAGAAA AAGA
1 AAGAAA AAGAAA AAGA
112911 TATATGTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 25 0.48
6 22 0.42
7 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:113431 original size:26 final size:26
Alignment explanation
Indices: 113393--113466 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
113383 CCTAGAATTG
* * *
113393 TCGCTGTAGGAACTTGTTCAGAGTTA
1 TCGCTGCAGGAACATGTCCAGAGTTA
* *
113419 TCGCTGCATGAACATGTCCAGAGTTG
1 TCGCTGCAGGAACATGTCCAGAGTTA
*
113445 TCGCTGTAGGAGA-ATGTCCAGA
1 TCGCTGCAGGA-ACATGTCCAGA
113467 ATTGCGCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (26 bp):
TCGCTGCAGGAACATGTCCAGAGTTA
Found at i:117533 original size:24 final size:24
Alignment explanation
Indices: 117503--117585 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
117493 TAGGCTAATA
117503 AGAGTTTAACTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* ** *
117527 AAAGTTTATTTGAGACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
117551 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
117575 AGAGTTTAACT
1 AGAGTTTAACT
117586 CGAAGATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:125723 original size:17 final size:18
Alignment explanation
Indices: 125701--125742 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
125691 CTTCTCCAGG
*
125701 TAATAAATATAT-ATGAA
1 TAATAAATATATAATAAA
125718 TAATAAATATATAATAAA
1 TAATAAATATATAATAAA
125736 TAATAAA
1 TAATAAA
125743 ATACAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATAAATATATAATAAA
Found at i:126646 original size:29 final size:30
Alignment explanation
Indices: 126611--126683 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
126601 TGCTTTACTT
126611 AAAAATTACATTTTGACCC-TAAACTTTTC
1 AAAAATTACATTTTGACCCTTAAACTTTTC
* *
126640 CAAAATTACATTTTGACCCTTGAACTTTTC
1 AAAAATTACATTTTGACCCTTAAACTTTTC
126670 AAAAATTACATTTT
1 AAAAATTACATTTT
126684 TTCCTCGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTTAAACTTTTC
Found at i:126668 original size:30 final size:30
Alignment explanation
Indices: 126611--126761 Score: 143
Period size: 29 Copynumber: 5.2 Consensus size: 30
126601 TGCTTTACTT
*
126611 AAAAATTACATTTTGACCC-TAAACTTTTC
1 AAAAATTACATTTTGACCCTTGAACTTTTC
*
126640 CAAAATTACATTTTGACCCTTGAACTTTTC
1 AAAAATTACATTTTGACCCTTGAACTTTTC
** * *
126670 AAAAATTACATTTT-TTCCTCGAA-TCATTC
1 AAAAATTACATTTTGACCCTTGAACT-TTTC
*
126699 AAAAATTACAATTTTG-CCCTTGAAC-TTCC
1 AAAAATTAC-ATTTTGACCCTTGAACTTTTC
* * * *
126728 AAAAGTCACATTTT-TCCCTCGAACTTTTC
1 AAAAATTACATTTTGACCCTTGAACTTTTC
126757 AAAAA
1 AAAAA
126762 AGTTCGAATT
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
28 14 0.14
29 52 0.53
30 33 0.33
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTTGAACTTTTC
Found at i:126762 original size:59 final size:59
Alignment explanation
Indices: 126632--126761 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 59
126622 TTTGACCCTA
* * * *
126632 AACTTTTCCAAAATTACATTTTGACCCTTGAACTTTTCAAAAATTACATTTTTTCCTCG
1 AACTTTTCAAAAATTACATTTTGACCCTTGAACTTTCCAAAAATCACATTTTTCCCTCG
* *
126691 AA-TCATTCAAAAATTACAATTTTG-CCCTTGAAC-TTCCAAAAGTCACATTTTTCCCTCG
1 AACT-TTTCAAAAATTAC-ATTTTGACCCTTGAACTTTCCAAAAATCACATTTTTCCCTCG
126749 AACTTTTCAAAAA
1 AACTTTTCAAAAA
126762 AGTTCGAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
58 32 0.52
59 23 0.38
60 6 0.10
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (59 bp):
AACTTTTCAAAAATTACATTTTGACCCTTGAACTTTCCAAAAATCACATTTTTCCCTCG
Found at i:131846 original size:21 final size:23
Alignment explanation
Indices: 131821--131874 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
131811 CGGAATCAAT
*
131821 GAAGAAAAAATAAA-TAAAAAA-
1 GAAGAAAAAAAAAATTAAAAAAG
131842 GAAGAAAAATAAAAATTAAAAAAG
1 GAAGAAAAA-AAAAATTAAAAAAG
131866 GAA-AAAAAA
1 GAAGAAAAAA
131875 GGGAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.31
22 5 0.17
23 12 0.41
24 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
GAAGAAAAAAAAAATTAAAAAAG
Found at i:132909 original size:99 final size:99
Alignment explanation
Indices: 132788--133000 Score: 245
Period size: 99 Copynumber: 2.2 Consensus size: 99
132778 ATGGAAATGA
132788 AAGGG-AAGGTTGAGGTCATAACGGCGAACCCGA-TACCTTAAAAGACA-TGATGAGAAAGGTTG
1 AAGGGAAAGGTTGAGGTCATAACGGCGAA-CCGAGTACCTTAAAAGA-AGTGATGAGAAAGGTTG
* * ** *
132850 AGGCTGCAATGATGAACCCAGTACAACGAAGGTATG
64 AGGCCGCAACGACAAACCCAGTACAACGAAGATATG
* * * *
132886 AAGGGAAAGGTTGACGG-CATAACGGCGAATCTAGTACCTTAGAAGAAGTGATGGGAAAGGTTGA
1 AAGGGAAAGGTTGA-GGTCATAACGGCGAACCGAGTACCTTAAAAGAAGTGATGAGAAAGGTTGA
* * * *
132950 GGCCGCAACGGCAAACCTAGTACCACGAAGATGTG
65 GGCCGCAACGACAAACCCAGTACAACGAAGATATG
*
132985 AAGGAAAAGGTTGAGG
1 AAGGGAAAGGTTGAGG
133001 CCACAATTGC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
98 10 0.10
99 85 0.88
100 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.32, T:0.16
Consensus pattern (99 bp):
AAGGGAAAGGTTGAGGTCATAACGGCGAACCGAGTACCTTAAAAGAAGTGATGAGAAAGGTTGAG
GCCGCAACGACAAACCCAGTACAACGAAGATATG
Found at i:132999 original size:49 final size:49
Alignment explanation
Indices: 132864--133022 Score: 151
Period size: 49 Copynumber: 3.2 Consensus size: 49
132854 TGCAATGATG
* * * * * *
132864 AACCCAGTACAACGAAGGTATGAAGGGAAAGGTTGACGG-CATAACGGCG
1 AACCTAGTACCACGAAGATGTGAAGGGAAAGGTTGA-GGCCACAACGGCA
* * * *
132913 AATCTAGTACCTTA-GAAGAAGTGATGGGAAAGGTTGAGGCCGCAACGGCA
1 AACCTAGTACC--ACGAAGATGTGAAGGGAAAGGTTGAGGCCACAACGGCA
* **
132963 AACCTAGTACCACGAAGATGTGAAGGAAAAGGTTGAGGCCACAATTGCA
1 AACCTAGTACCACGAAGATGTGAAGGGAAAGGTTGAGGCCACAACGGCA
*
133012 AACCTTGTACC
1 AACCTAGTACC
133023 TTAAAAGATG
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 1 0.01
49 50 0.57
50 36 0.41
51 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (49 bp):
AACCTAGTACCACGAAGATGTGAAGGGAAAGGTTGAGGCCACAACGGCA
Found at i:133022 original size:99 final size:99
Alignment explanation
Indices: 132821--133030 Score: 226
Period size: 99 Copynumber: 2.1 Consensus size: 99
132811 GCGAACCCGA
* * ** *
132821 TACCTTAAAAGACATGATGAGAAAGGTTGAGGCTGCAATGATGAACCCAGTACAACGAAGGTATG
1 TACCTTAAAAGACATGATGAGAAAGGTTGAGGCCGCAACGACAAACCCAGTACAACGAAGATATG
* * * *
132886 AAGGGAAAGGTTGACGGCATAACGGCGAATCTAG
66 AAGGAAAAGGTTGACGGCACAACGGCAAACCTAG
* * * * * *
132920 TACCTTAGAAGA-AGTGATGGGAAAGGTTGAGGCCGCAACGGCAAACCTAGTACCACGAAGATGT
1 TACCTTAAAAGACA-TGATGAGAAAGGTTGAGGCCGCAACGACAAACCCAGTACAACGAAGATAT
** *
132984 GAAGGAAAAGGTTGA-GGCCACAATTGCAAACCTTG
65 GAAGGAAAAGGTTGACGG-CACAACGGCAAACCTAG
133019 TACCTTAAAAGA
1 TACCTTAAAAGA
133031 TGAGAGGGAC
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
98 3 0.03
99 87 0.97
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (99 bp):
TACCTTAAAAGACATGATGAGAAAGGTTGAGGCCGCAACGACAAACCCAGTACAACGAAGATATG
AAGGAAAAGGTTGACGGCACAACGGCAAACCTAG
Found at i:133094 original size:46 final size:46
Alignment explanation
Indices: 133033--133397 Score: 426
Period size: 46 Copynumber: 7.9 Consensus size: 46
133023 TTAAAAGATG
* * *
133033 AGAGGGACATATTGAAGCCATCATCCAATCTCAGACCCTTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
* * * * * * * *
133079 ATAAGGGAAAATTGAAGTCATTATCCAATCCCATACCCCTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
*
133125 AGAGGGGCAGATTGAAGCCATCATCCAAACTCATACCCTTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
* * * * * *
133171 AGAAGGGCAGATTGAAGTCATTATCAAATCTTA-ACCCCTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
* **
133216 AGAGGGGTAGATTGAAGTTATCATCCAATCTCATACCCTTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
133262 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTT--AAGTCA
* * *
133310 AGAGGGGTAGATTGAAGCCACCATCACAATCTCATACCCCTAAGTCA
1 AGAGGGGCAGATTGAAGCCATCATC-CAATCTCATACCCTTAAGTCA
* * ** * *
133357 AAAGGGGCAAATTGAAGTTATCATCCGATCTCATATCCTTA
1 AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTA
133398 GGTTATGGGC
Statistics
Matches: 267, Mismatches: 48, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
45 38 0.14
46 161 0.60
47 25 0.09
48 29 0.11
49 14 0.05
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (46 bp):
AGAGGGGCAGATTGAAGCCATCATCCAATCTCATACCCTTAAGTCA
Found at i:133249 original size:91 final size:92
Alignment explanation
Indices: 133043--133391 Score: 459
Period size: 91 Copynumber: 3.8 Consensus size: 92
133033 AGAGGGACAT
* * *
133043 ATTGAAGCCATCATCCAATCTCAGACCCTTAAGTCAATAAGGGAAAATTGAAGTCATTATCCAAT
1 ATTGAAGCCATCATCCAATCTCATACCCTTAAGTCAAGAAGGGCAAATTGAAGTCATTATCCAAT
* *
133108 CCCATACCCCTAAGTCAAGAGGGGCAG
66 CTCATACCCCTAAGTCAAGAGGGGTAG
* * *
133135 ATTGAAGCCATCATCCAAACTCATACCCTTAAGTCAAGAAGGGCAGATTGAAGTCATTATCAAAT
1 ATTGAAGCCATCATCCAATCTCATACCCTTAAGTCAAGAAGGGCAAATTGAAGTCATTATCCAAT
*
133200 CTTA-ACCCCTAAGTCAAGAGGGGTAG
66 CTCATACCCCTAAGTCAAGAGGGGTAG
** * * * *
133226 ATTGAAGTTATCATCCAATCTCATACCCTTAAGTCAAGAGGGGCAGATTGAAGCCATCATCCAAT
1 ATTGAAGCCATCATCCAATCTCATACCCTTAAGTCAAGAAGGGCAAATTGAAGTCATTATCCAAT
*
133291 CTCATACCCTTAAAAGTCAAGAGGGGTAG
66 CTCATACCCCT--AAGTCAAGAGGGGTAG
* * * * *
133320 ATTGAAGCCACCATCACAATCTCATACCCCTAAGTCAA-AAGGGGCAAATTGAAGTTATCATCCG
1 ATTGAAGCCATCATC-CAATCTCATACCCTTAAGTCAAGAA-GGGCAAATTGAAGTCATTATCCA
133384 ATCTCATA
64 ATCTCATA
133392 TCCTTAGGTT
Statistics
Matches: 225, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
91 82 0.36
92 66 0.29
94 29 0.13
95 48 0.21
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (92 bp):
ATTGAAGCCATCATCCAATCTCATACCCTTAAGTCAAGAAGGGCAAATTGAAGTCATTATCCAAT
CTCATACCCCTAAGTCAAGAGGGGTAG
Found at i:133908 original size:207 final size:208
Alignment explanation
Indices: 133457--134257 Score: 1045
Period size: 207 Copynumber: 3.8 Consensus size: 208
133447 GAGAGGCATA
* * * *
133457 TCAAACTCCCATCTTCTTGATGAGATACTGAGAAGTGGGTCAAAGTAATAAAGCGTTCATCTTCC
1 TCAAAC-CCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
* *
133522 TGATGAGATATAGAGAAGTAGACCAAATCCGTT-TTCCTGGTGAGATACAGAGAAGTGGATTAAA
65 TGATGAGATACAGAGAAGTAGACCAAATCC-TTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
* * * * *
133586 ATAATGAGGTA-GTAATCTTCTTGATAAGATACAGAGAAGTAGACCAAATCGATGAAGCCAAGCT
129 ACAATGAGG-AGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCAAAGCT
133650 CAATGTGAGTGAAACT
193 CAATGTGAGTGAAACT
* * * * *
133666 TCAAACCCTATCTTCTTGATGAGATATAAAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTCTT
1 TCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCT
* * *
133731 GACGAGATACAAAGAAGTAGACCAAATCCTTCTTCCCGATGAGATACAGAGAAGTGGATT-AAAC
66 GATGAGATACAGAGAAGTAGACCAAATCCTTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAC
* * *
133795 AGTGAGGAGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAA
131 AATGAGGAGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAA
133860 TGTGAGTGAAACT
196 TGTGAGTGAAACT
* *
133873 TCATACCCCATCTTCTTGTTGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCT
1 TCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCT
* * *
133938 AATGAGATACAGAGAAGTAGACCAAATCCTTCTTCCTGACGAGATACATAGAAGTGGATTAAAAC
66 GATGAGATACAGAGAAGTAGACCAAATCCTTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAC
* * * ** **
134003 AATGAGGCGGCCATCTTCCTGATGAGGA-ACAGAGAAGTAGACCAAATCGATAAAGTGAAGCTTG
131 AATGAGGAGGTCATCTTCCTGATGA-GATACAGAGAAGTAGACCAAATCGATGAAGCAAAGCTCA
* *
134067 ATATGAGTAAAAACT
195 ATGTGAGT-GAAACT
* * * *
134082 TCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGTGTCAAAGCAATAAAGCGGTCATCTTCT
1 TCAAA-CCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCC
* * * * * * *
134147 TGATGAGATACAGAGAAGTGGACTAAATTCATCTTCCTGATGAGATACGGAGGAGTGGATTAAGA
65 TGATGAGATACAGAGAAGTAGACCAAATCCTTCTTCCTGATGAGATACAGAGAAGTGGATTAAAA
* * * *
134212 CAATGA-AATAGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAA
130 CAATGAGGA-GGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAA
134258 GAGATGAAGC
Statistics
Matches: 516, Mismatches: 68, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
206 1 0.00
207 186 0.36
208 165 0.32
209 19 0.04
210 145 0.28
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (208 bp):
TCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCT
GATGAGATACAGAGAAGTAGACCAAATCCTTCTTCCTGATGAGATACAGAGAAGTGGATTAAAAC
AATGAGGAGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCAAAGCTCAA
TGTGAGTGAAACT
Found at i:134028 original size:85 final size:85
Alignment explanation
Indices: 133893--134050 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
133883 TCTTCTTGTT
* * *
133893 GAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGA-GATACAGAGAAGTA
1 GAGATACAGAGAAGTGGATCAAAACAATAAAGAGGCCATCTTCCTAATGAGGA-ACAGAGAAGTA
133957 GACCAAATCCTTCTTCCTGAC
65 GACCAAATCCTTCTTCCTGAC
* * * * * *
133978 GAGATACATAGAAGTGGATTAAAACAATGAGGCGGCCATCTTCCTGATGAGGAACAGAGAAGTAG
1 GAGATACAGAGAAGTGGATCAAAACAATAAAGAGGCCATCTTCCTAATGAGGAACAGAGAAGTAG
134043 ACCAAATC
66 ACCAAATC
134051 GATAAAGTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 61 0.97
86 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (85 bp):
GAGATACAGAGAAGTGGATCAAAACAATAAAGAGGCCATCTTCCTAATGAGGAACAGAGAAGTAG
ACCAAATCCTTCTTCCTGAC
Found at i:135124 original size:11 final size:10
Alignment explanation
Indices: 135108--135147 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
135098 TGGAACGTTT
135108 TAATAAATGAA
1 TAATAAAT-AA
135119 TAATAAATATA
1 TAATAAATA-A
135130 TAATAAATAA
1 TAATAAATAA
135140 TAA-AAATA
1 TAATAAATA
135148 CGAAAGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.18
10 5 0.18
11 18 0.64
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
TAATAAATAA
Found at i:136070 original size:30 final size:31
Alignment explanation
Indices: 136036--136208 Score: 109
Period size: 29 Copynumber: 5.8 Consensus size: 31
136026 TAAAAATTGT
*
136036 ATTTTGACCCCTAAAATTTTCCTAAATTAC-
1 ATTTTGACCCCTAAAATTTTCCAAAATTACA
* *
136066 ATTTT-AGCCCCT-AAACTTTCAAAAATTACA
1 ATTTTGA-CCCCTAAAATTTTCCAAAATTACA
* * *
136096 ATTTT-A-CCCTCAAATCTTCTAAAAATTACA
1 ATTTTGACCCCTAAAATTTTC-CAAAATTACA
* **
136126 ATTTTG-CCCCTAAACTTTTCCAAAAGTT-TG
1 ATTTTGACCCCTAAAATTTTCCAAAA-TTACA
*
136156 ATTTTGA--CCTCAAATTTTCCAAAAGTT-CA
1 ATTTTGACCCCTAAAATTTTCCAAAA-TTACA
* * *
136185 CTTTT-AACCCGAAAA-TTTCCAAAA
1 ATTTTGACCCCTAAAATTTTCCAAAA
136209 AGCCTGATTT
Statistics
Matches: 115, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
28 5 0.04
29 52 0.45
30 46 0.40
31 12 0.10
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (31 bp):
ATTTTGACCCCTAAAATTTTCCAAAATTACA
Found at i:136095 original size:29 final size:31
Alignment explanation
Indices: 136059--136143 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 31
136049 AAATTTTCCT
136059 AAATTAC-ATTTTAGCCCCTAAACTTTC-AA
1 AAATTACAATTTTAGCCCCTAAACTTTCTAA
136088 AAATTACAATTTTA--CCCTCAAA-TCTTCTAA
1 AAATTACAATTTTAGCCCCT-AAACT-TTCTAA
136118 AAATTACAATTTT-GCCCCTAAACTTT
1 AAATTACAATTTTAGCCCCTAAACTTT
136144 TCCAAAAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
28 5 0.10
29 13 0.27
30 26 0.53
31 5 0.10
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (31 bp):
AAATTACAATTTTAGCCCCTAAACTTTCTAA
Found at i:156763 original size:41 final size:41
Alignment explanation
Indices: 156706--156801 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
156696 GAATTTTATT
156706 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
156747 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
156788 TTGACAAGAATTCT
1 TTAACAAGAATTCT
156802 CTACGAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:156813 original size:17 final size:17
Alignment explanation
Indices: 156791--156829 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
156781 CTTCACCTTG
* *
156791 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
*
156808 ACAAGAACTCTCAATGA
1 ACAAGAACTCTCAACGA
156825 ACAAG
1 ACAAG
156830 TTCTCCTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:164479 original size:23 final size:20
Alignment explanation
Indices: 164442--164482 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
164432 GTGCAACCAG
164442 ATGTGAAAAACATGGATCCA
1 ATGTGAAAAACATGGATCCA
164462 ATGTAGAAACAACAATGGATC
1 ATGT-GAAA-AAC-ATGGATC
164483 TGGAACTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 3 0.17
23 7 0.39
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (20 bp):
ATGTGAAAAACATGGATCCA
Found at i:165790 original size:135 final size:135
Alignment explanation
Indices: 165545--165813 Score: 450
Period size: 135 Copynumber: 2.0 Consensus size: 135
165535 GAAGTGATAC
* *
165545 CCTAGCTGAATTAGTAGTATGCATTTAATTCCTATTTAACAAAAAAACAGTCCCTTAGTTGAACT
1 CCTAGCTGAATTAGTAGAATGCATTTAATGCCTATTTAACAAAAAAACAGTCCCTTAGTTGAACT
* *
165610 AGGAGGGTGAGGGACTAATAGGGTGTGCTTCCTCTCATATGTATTATGATAGAGATTCCAACCTC
66 AGGAGGGTGAGGGACTAATAGGGTATGCTTCCTCTCATATGTATTATGACAGAGATTCCAACCTC
165675 TCATT
131 TCATT
* *
165680 CCTAGTTGAATTAGTAGAATGCATTTAATGCCTATTTAACAAAAAAATAGTCCCTTAGTTGAACT
1 CCTAGCTGAATTAGTAGAATGCATTTAATGCCTATTTAACAAAAAAACAGTCCCTTAGTTGAACT
* *
165745 AGGAGGGTGAGGGAC-AGATAGGGTATGCTTCCTCTCATATTTATTATGACAGAGATTCCAGCCT
66 AGGAGGGTGAGGGACTA-ATAGGGTATGCTTCCTCTCATATGTATTATGACAGAGATTCCAACCT
165809 CTCAT
130 CTCAT
165814 GTGTTAGGTC
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 1 0.01
135 124 0.99
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (135 bp):
CCTAGCTGAATTAGTAGAATGCATTTAATGCCTATTTAACAAAAAAACAGTCCCTTAGTTGAACT
AGGAGGGTGAGGGACTAATAGGGTATGCTTCCTCTCATATGTATTATGACAGAGATTCCAACCTC
TCATT
Found at i:169742 original size:17 final size:17
Alignment explanation
Indices: 169722--169776 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
169712 AACTACAATG
* *
169722 AAAATGTACTAACAACT
1 AAAATGTAATGACAACT
* * *
169739 AAAATGCAGTGACAATT
1 AAAATGTAATGACAACT
169756 AAAAATGTAATGACAACT
1 -AAAATGTAATGACAACT
169774 AAA
1 AAA
169777 TGCTATGCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAATGTAATGACAACT
Found at i:169762 original size:18 final size:18
Alignment explanation
Indices: 169733--169776 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
169723 AAATGTACTA
*
169733 ACAACT-AAAATGCAGTG
1 ACAACTAAAAATGCAATG
* *
169750 ACAATTAAAAATGTAATG
1 ACAACTAAAAATGCAATG
169768 ACAACTAAA
1 ACAACTAAA
169777 TGCTATGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (18 bp):
ACAACTAAAAATGCAATG
Found at i:172089 original size:21 final size:21
Alignment explanation
Indices: 172060--172102 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
172050 AGAAACAGAT
172060 AAAAGAATAAAAATAAA-GTA
1 AAAAGAATAAAAATAAATGTA
*
172080 AAAAGAAATAAACATAAATGTA
1 AAAAG-AATAAAAATAAATGTA
172102 A
1 A
172103 GAATGCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAAGAATAAAAATAAATGTA
Found at i:189242 original size:5 final size:5
Alignment explanation
Indices: 189232--189304 Score: 65
Period size: 5 Copynumber: 14.2 Consensus size: 5
189222 TATTTTATAA
* * * * *
189232 CATAT CATAT CGTAT CAGGTTT CATAT CAAAT CATAT CTTAT CATAT CATAA
1 CATAT CATAT CATAT CA--TAT CATAT CATAT CATAT CATAT CATAT CATAT
* *
189284 CGTAT AATAT CATAT CATAT C
1 CATAT CATAT CATAT CATAT C
189305 CTACCCCCAT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
5 48 0.92
7 4 0.08
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:189268 original size:44 final size:42
Alignment explanation
Indices: 189200--189288 Score: 115
Period size: 44 Copynumber: 2.1 Consensus size: 42
189190 TGTTATAGCA
* *
189200 TATCAGATTTCAAATCAAAACATATTTTATAACATATCATATCG
1 TATCAGATTTCAAATCAAAACATATCTTAT--CATATCATAACG
* * *
189244 TATCAGGTTTCATATCAAATCATATCTTATCATATCATAACG
1 TATCAGATTTCAAATCAAAACATATCTTATCATATCATAACG
189286 TAT
1 TAT
189289 AATATCATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 14 0.35
44 26 0.65
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (42 bp):
TATCAGATTTCAAATCAAAACATATCTTATCATATCATAACG
Found at i:196876 original size:13 final size:13
Alignment explanation
Indices: 196858--196888 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
196848 ATAAGATTTA
196858 ACTTAGATTTTTC
1 ACTTAGATTTTTC
196871 ACTTAGATTTTTC
1 ACTTAGATTTTTC
196884 ACTTA
1 ACTTA
196889 ATAAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (13 bp):
ACTTAGATTTTTC
Found at i:196986 original size:50 final size:50
Alignment explanation
Indices: 196927--197027 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
196917 TTTGTTTTAT
196927 TATCTTTAAGTCCAATTGAGGCCTAAAGGTTAGCTAACATACTTCATGAG
1 TATCTTTAAGTCCAATTGAGGCCTAAAGGTTAGCTAACATACTTCATGAG
*
196977 TATCTTTAAGTCCAATTGAGGCCTAAAGGTTAGCTAACATGCTTCATGAG
1 TATCTTTAAGTCCAATTGAGGCCTAAAGGTTAGCTAACATACTTCATGAG
197027 T
1 T
197028 CTGCAGGAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Consensus pattern (50 bp):
TATCTTTAAGTCCAATTGAGGCCTAAAGGTTAGCTAACATACTTCATGAG
Found at i:203754 original size:25 final size:25
Alignment explanation
Indices: 203721--203787 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
203711 AGTTTGGCTT
* * *
203721 ATACGAGCCTAGATAGGGTTAGGTC
1 ATACGAGCCCAGATAGAGTTAGCTC
* * *
203746 TTACGAGCCCAAATAAAGTTAGCTC
1 ATACGAGCCCAGATAGAGTTAGCTC
203771 ATACGAGCCCAGATAGA
1 ATACGAGCCCAGATAGA
203788 CTTTAACCAG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (25 bp):
ATACGAGCCCAGATAGAGTTAGCTC
Done.