Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1754
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: 49127
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Found at i:232 original size:17 final size:17
Alignment explanation
Indices: 212--247 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
202 ATGCACTTTT
*
212 TTTTAATATAAAATTAA
1 TTTTAATATAAAAATAA
*
229 TTTTAATTTAAAAATAA
1 TTTTAATATAAAAATAA
246 TT
1 TT
248 AATAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTAATATAAAAATAA
Found at i:256 original size:22 final size:21
Alignment explanation
Indices: 223--271 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
213 TTTAATATAA
* *
223 AATTAATTTTAATTTAAAA-AT
1 AATTAATATTAA-TAAAAATAT
244 AATTAATAATTAATAAAAATAT
1 AATTAAT-ATTAATAAAAATAT
266 AATTAA
1 AATTAA
272 CTTATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTAATATTAATAAAAATAT
Found at i:290 original size:12 final size:12
Alignment explanation
Indices: 263--295 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
253 TTAATAAAAA
263 TATAAT-TAACT
1 TATAATATAACT
*
274 TATAATATAATT
1 TATAATATAACT
286 TATAATATAA
1 TATAATATAA
296 AATTAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAATATAACT
Found at i:3848 original size:2 final size:2
Alignment explanation
Indices: 3836--3877 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3826 CATTAACTGA
3836 AT AT A- AT AT 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 AT AT AT AT AT
3877 A
1 A
3878 AAGATTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4861 original size:31 final size:31
Alignment explanation
Indices: 4826--4884 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4816 TTTTTAATTA
*
4826 TATTTA-AAATATATATAATATTT-ATTAACAT
1 TATTTATAAA-ATATA-AAAATTTCATTAACAT
4857 TATTTATAAAATATAAAAATTTCATTAA
1 TATTTATAAAATATAAAAATTTCATTAA
4885 TAATATATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 6 0.24
31 16 0.64
32 3 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTTATAAAATATAAAAATTTCATTAACAT
Found at i:5437 original size:3 final size:3
Alignment explanation
Indices: 5429--5454 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5419 TCCCAATTTA
5429 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5455 AAGTTAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5646 original size:26 final size:28
Alignment explanation
Indices: 5581--5646 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 28
5571 AAAGAAATTT
5581 AATAA-AAAAGTATATATATGTAATAATA
1 AATAATAAAA-TATATATATGTAATAATA
** * *
5609 AATAATTTAATAT-TATAT-TTATATTA
1 AATAATAAAATATATATATGTAATAATA
5635 AATAATAAAATA
1 AATAATAAAATA
5647 AAAATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
26 16 0.52
27 5 0.16
28 8 0.26
29 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (28 bp):
AATAATAAAATATATATATGTAATAATA
Found at i:5662 original size:17 final size:18
Alignment explanation
Indices: 5640--5676 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5630 TATTAAATAA
5640 TAAAATA-AAAATTATTT
1 TAAAATATAAAATTATTT
*
5657 TAAAATATTAAATTATTT
1 TAAAATATAAAATTATTT
5675 TA
1 TA
5677 TATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATATAAAATTATTT
Found at i:6179 original size:2 final size:2
Alignment explanation
Indices: 6172--6222 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
6162 TATGAGTATG
* *
6172 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT A- AT AT ACG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
6213 AT AA AT AT AT
1 AT AT AT AT AT
6223 TTCAAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.93
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:7099 original size:25 final size:27
Alignment explanation
Indices: 7070--7128 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
7060 TTTTTAAATA
7070 TAAATTA-TTAATATTAAAATAATT-T
1 TAAATTATTTAATATTAAAATAATTAT
* *
7095 TAAA-TATTTAATTTTTAAATAATTAAT
1 TAAATTATTTAATATTAAAATAATT-AT
7122 TAAATTA
1 TAAATTA
7129 AACTTGATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 19 0.68
27 5 0.18
28 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAATTATTTAATATTAAAATAATTAT
Found at i:7112 original size:15 final size:15
Alignment explanation
Indices: 7092--7122 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7082 ATTAAAATAA
*
7092 TTTTAAATATTTAAT
1 TTTTAAATAATTAAT
7107 TTTTAAATAATTAAT
1 TTTTAAATAATTAAT
7122 T
1 T
7123 AAATTAAACT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAAATAATTAAT
Found at i:7407 original size:8 final size:9
Alignment explanation
Indices: 7368--7443 Score: 52
Period size: 8 Copynumber: 8.3 Consensus size: 9
7358 TATTTTAAAC
7368 ATATATTAA
1 ATATATTAA
7377 ATATGATTATA
1 ATAT-ATTA-A
*
7388 ATATAATAA
1 ATATATTAA
7397 A-ATATATAA
1 ATATAT-TAA
7406 ATATAATATAA
1 ATAT-AT-TAA
*
7417 ATATA-TGA
1 ATATATTAA
7425 AT-TATTAA
1 ATATATTAA
*
7433 ATCT-TTAA
1 ATATATTAA
7441 ATA
1 ATA
7444 AAGTTTTTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
7 2 0.04
8 17 0.31
9 11 0.20
10 10 0.18
11 15 0.27
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (9 bp):
ATATATTAA
Found at i:8392 original size:15 final size:18
Alignment explanation
Indices: 8359--8407 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
8349 AATTTTTAGT
8359 TATTATTTAATATTAATA
1 TATTATTTAATATTAATA
*
8377 TATT-TTTAAT-TTATATTT
1 TATTATTTAATATTA-A-TA
8395 TATTATTTAATAT
1 TATTATTTAATAT
8408 ACATATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.12
17 7 0.27
18 9 0.35
19 6 0.23
20 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTATTTAATATTAATA
Found at i:8393 original size:28 final size:30
Alignment explanation
Indices: 8316--8408 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 30
8306 ATTAATTTTA
* * *
8316 TTAATTTATTTTTAATATA-AGTATAA-AT
1 TTAATATATTTTTAATTTATAGTTTAATAT
*
8344 TTAATA-ATTTTT-AGTTATTA-TTTAATA-
1 TTAATATATTTTTAATTTA-TAGTTTAATAT
* *
8371 TTAATATATTTTTAATTTATATTTTATTAT
1 TTAATATATTTTTAATTTATAGTTTAATAT
8401 TTAATATA
1 TTAATATA
8409 CATATGATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 3 0.06
27 16 0.31
28 15 0.29
29 10 0.19
30 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TTAATATATTTTTAATTTATAGTTTAATAT
Found at i:8427 original size:73 final size:72
Alignment explanation
Indices: 8320--8461 Score: 175
Period size: 73 Copynumber: 2.0 Consensus size: 72
8310 ATTTTATTAA
*
8320 TTTATTTTTAATATAAGTATAAATTTAATAATTTTTAGTTATTATTTAATATTA-ATATAT-TTT
1 TTTATTTTTAATATAAGTATAAATTTAATAATTTTTA---ATTATTTAATATTATATAAATATTT
8383 TAATTTATAT
63 TAATTTATAT
* * *
8393 TTTATTATTTAATATACA-TAT-GATTTAATGATTTTTAATTATTTATTATTATATAAATATTTT
1 TTTATT-TTTAATATA-AGTATAAATTTAATAATTTTTAATTATTTAATATTATATAAATATTTT
8456 AATTTA
64 AATTTA
8462 ATGTCCTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
70 13 0.21
71 5 0.08
72 10 0.16
73 20 0.33
74 12 0.20
75 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (72 bp):
TTTATTTTTAATATAAGTATAAATTTAATAATTTTTAATTATTTAATATTATATAAATATTTTAA
TTTATAT
Found at i:9094 original size:21 final size:20
Alignment explanation
Indices: 9064--9102 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9054 TACATTTTTA
9064 TCTAAATGTATCAATACATT
1 TCTAAATGTATCAATACATT
*
9084 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCAATACA
9103 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCAATACATT
Found at i:12547 original size:14 final size:15
Alignment explanation
Indices: 12528--12560 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12518 CATATTCATA
12528 AAATAAA-AAAAATC
1 AAATAAATAAAAATC
*
12542 AAATAAATGAAAATC
1 AAATAAATAAAAATC
12557 AAAT
1 AAAT
12561 TGAGTACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAATAAAAATC
Found at i:12815 original size:22 final size:21
Alignment explanation
Indices: 12787--12906 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 21
12777 TTTGGAATAA
12787 ATGTACATATCATTTTTACTAT
1 ATGTACATAT-ATTTTTACTAT
* *
12809 ATGTACATATGA--TATATTAT
1 ATGTACATAT-ATTTTTACTAT
* *
12829 ATGTACGTA-ATATTTTAATAT
1 ATGTACATATAT-TTTTACTAT
* * *
12850 ATGTACATATAATTATGCTAT
1 ATGTACATATATTTTTACTAT
* *
12871 ATGTATAT-TATTTTTATTAT
1 ATGTACATATATTTTTACTAT
* *
12891 ATATGCATATTATTTT
1 ATGTACATA-TATTTT
12907 AGTTAAAAGA
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
18 1 0.01
20 27 0.37
21 27 0.37
22 18 0.25
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (21 bp):
ATGTACATATATTTTTACTAT
Found at i:12871 original size:21 final size:21
Alignment explanation
Indices: 12787--12875 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
12777 TTTGGAATAA
* *
12787 ATGTACATATCATTTTTACTAT
1 ATGTACATAT-AATTATACTAT
* *
12809 ATGTACATATGA-TATATTAT
1 ATGTACATATAATTATACTAT
* * *
12829 ATGTACGTA-ATATTTTAATAT
1 ATGTACATATA-ATTATACTAT
*
12850 ATGTACATATAATTATGCTAT
1 ATGTACATATAATTATACTAT
12871 ATGTA
1 ATGTA
12876 TATTATTTTT
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
20 15 0.29
21 26 0.50
22 11 0.21
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (21 bp):
ATGTACATATAATTATACTAT
Found at i:12886 original size:41 final size:40
Alignment explanation
Indices: 12793--12892 Score: 105
Period size: 41 Copynumber: 2.5 Consensus size: 40
12783 ATAAATGTAC
* * *
12793 ATATCATTTTTACTATATGTACATATGATATATTATATGT
1 ATATTATTTTTAATATATGTACATATAATATATTATATGT
*
12833 ACGTAATA-TTTTAATATATGTACATATAAT-TATGCTATATGT
1 A--TATTATTTTTAATATATGTACATATAATATAT--TATATGT
*
12875 ATATTATTTTTATTATAT
1 ATATTATTTTTAATATAT
12893 ATGCATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
40 8 0.16
41 30 0.61
42 11 0.22
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (40 bp):
ATATTATTTTTAATATATGTACATATAATATATTATATGT
Found at i:15469 original size:21 final size:18
Alignment explanation
Indices: 15440--15485 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
15430 TATTATTAAA
15440 TTTAAATAAAAATATATTAT
1 TTTAAAT-AAAAT-TATTAT
15460 TTTAATATAAAATTATTAT
1 TTTAA-ATAAAATTATTAT
15479 TTTAAAT
1 TTTAAAT
15486 TGATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 11 0.44
20 10 0.40
21 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAAATTATTAT
Found at i:18461 original size:2 final size:2
Alignment explanation
Indices: 18448--18477 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18438 TTTAGTGAAA
*
18448 AT AT AC 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
18478 TGCAAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19185 original size:21 final size:21
Alignment explanation
Indices: 19155--19196 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19145 TTCATAAATT
**
19155 TATTAAAATTTTTTAATAAAA
1 TATTAAAATTTTAAAATAAAA
*
19176 TATTATAATTTTAAAATAAAA
1 TATTAAAATTTTAAAATAAAA
19197 AAATTACAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTAAAATTTTAAAATAAAA
Found at i:20213 original size:25 final size:25
Alignment explanation
Indices: 20173--20242 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 25
20163 AATAATTTAT
20173 TTTTAT-ATTAATATTTATATATATA
1 TTTTATAATTAA-ATTTATATATATA
*
20198 TTTTATAATTAAATTTA-A-ATAAA
1 TTTTATAATTAAATTTATATATATA
20221 TTTT-TAATT--ATTTAGTATATAT
1 TTTTATAATTAAATTTA-TATATAT
20243 TTGGGTTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 5 0.13
22 6 0.15
23 11 0.28
24 1 0.03
25 11 0.28
26 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TTTTATAATTAAATTTATATATATA
Found at i:21192 original size:13 final size:12
Alignment explanation
Indices: 21173--21217 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
21163 ATTTTTTTAT
21173 TAATATTTATAA
1 TAATATTTATAA
*
21185 TCAATATTTATTA
1 T-AATATTTATAA
*
21198 TAATTAATTATAA
1 TAA-TATTTATAA
21211 TAATATT
1 TAATATT
21218 CATTATGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:24946 original size:116 final size:114
Alignment explanation
Indices: 24737--25151 Score: 321
Period size: 102 Copynumber: 3.7 Consensus size: 114
24727 CTTTACTTTC
** *
24737 TAGTGATATGAAGA-AAGATTTGGTTTAAAACAATGCTATGACACGGTCATAGTGTCA----CAT
1 TAGTGATATGAAGAGAAG-TTTGGTTTAAAACTTTGCTATGCCAC-GTCATAGTGTCATGTGCAT
* * *** * * * *
24797 -GGAATTTAAGCCAAGCAAGGCGTTTAGGGTCATCATCTGCTTGGAACGTCT
64 AGG-ACTTAAGCCGAGCAACATGCTTAGGATCATCATCTACTTGGAACCTCT
* *
24848 TAGTGATATGAAGCGAAGCTTGGTTTAAAACTTTGCTATGCCACTGTCATTAGTGTCATGTGCAT
1 TAGTGATATGAAGAGAAGTTTGGTTTAAAACTTTGCTATGCCAC-GTCA-TAGTGTCATGTGCAT
* * * * *
24913 AGGACTTAAGCCGAGCAATATGCTTAGGATCATCATCCACTTGTAACTTCC
64 AGGACTTAAGCCGAGCAACATGCTTAGGATCATCATCTACTTGGAACCTCT
* * * *
24964 TAGTGATTTGAA-AG-A-TTTGATTTAAAACTTTGCTATTCCAC-TC-------C-TGTGCGTAG
1 TAGTGATATGAAGAGAAGTTTGGTTTAAAACTTTGCTATGCCACGTCATAGTGTCATGTGCATAG
* *
25017 GAATTAAGCCGAGCAACATGCTTA-GATTCATCATTTACTTGGAACCT-T
66 GACTTAAGCCGAGCAACATGCTTAGGA-TCATCATCTACTTGGAACCTCT
* * * ** *
25065 CTAGTGATCTGAAGAGAGGTTTGGTTTAAAACTCTGCTATGCCACGGTCATAGTGTCACATACAT
1 -TAGTGATATGAAGAGAAGTTTGGTTTAAAACTTTGCTATGCCAC-GTCATAGTGTCATGTGCAT
* *
25130 AGGACCTAAGCCAAGCAACATG
64 AGGACTTAAGCCGAGCAACATG
25152 AGTGTATTCT
Statistics
Matches: 239, Mismatches: 43, Indels: 40
0.74 0.13 0.12
Matches are distributed among these distances:
101 2 0.01
102 57 0.24
103 3 0.01
105 23 0.10
107 2 0.01
111 41 0.17
112 11 0.05
113 23 0.10
114 2 0.01
115 23 0.10
116 50 0.21
117 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTGATATGAAGAGAAGTTTGGTTTAAAACTTTGCTATGCCACGTCATAGTGTCATGTGCATAG
GACTTAAGCCGAGCAACATGCTTAGGATCATCATCTACTTGGAACCTCT
Found at i:28434 original size:2 final size:2
Alignment explanation
Indices: 28427--28452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28417 TTTAACAAGA
28427 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
28453 GTAAGGGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30313 original size:2 final size:2
Alignment explanation
Indices: 30306--30332 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30296 TTTTTACATA
30306 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
30333 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31400 original size:11 final size:13
Alignment explanation
Indices: 31375--31411 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
31365 ATCGATATAA
31375 TAAAATATAATTT
1 TAAAATATAATTT
31388 TAAAATA-AA-TT
1 TAAAATATAATTT
*
31399 TAAAATTTAATTT
1 TAAAATATAATTT
31412 AATTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 8 0.38
12 4 0.19
13 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAAATATAATTT
Found at i:31986 original size:7 final size:7
Alignment explanation
Indices: 31974--32004 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31964 GATAATAATC
31974 ATATTTA
1 ATATTTA
31981 ATATTTA
1 ATATTTA
31988 ATATTT-
1 ATATTTA
31994 ATATTTA
1 ATATTTA
32001 ATAT
1 ATAT
32005 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTTA
Found at i:31997 original size:13 final size:13
Alignment explanation
Indices: 31974--32012 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
31964 GATAATAATC
31974 ATATTTAATATTTA
1 ATATTT-ATATTTA
31988 ATATTTATATTTA
1 ATATTTATATTTA
32001 ATA--TATATTTA
1 ATATTTATATTTA
32012 A
1 A
32013 ATATATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.36
13 10 0.40
14 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:32009 original size:11 final size:11
Alignment explanation
Indices: 31981--32018 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
31971 ATCATATTTA
31981 ATATTTAATATTT
1 ATATTTAATA--T
31994 ATATTTAATAT
1 ATATTTAATAT
32005 ATATTTAA-AT
1 ATATTTAATAT
32015 ATAT
1 ATAT
32019 GAATATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.24
11 9 0.36
13 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:32261 original size:9 final size:9
Alignment explanation
Indices: 32249--32273 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
32239 TAATCGAATT
32249 AATATTTAA
1 AATATTTAA
32258 AATATTTAA
1 AATATTTAA
32267 AATATTT
1 AATATTT
32274 TAATAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATATTTAA
Found at i:32304 original size:14 final size:13
Alignment explanation
Indices: 32285--32337 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
32275 AATAAACTAT
32285 AAATATATTTAACA
1 AAATATATTTAA-A
32299 AAATATA-TT-AA
1 AAATATATTTAAA
32310 AAATATATTTAATA
1 AAATATATTTAA-A
32324 AAATATATTTAAA
1 AAATATATTTAAA
32337 A
1 A
32338 CCGAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.22
12 3 0.08
13 5 0.14
14 20 0.56
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATATTTAAA
Found at i:32305 original size:20 final size:19
Alignment explanation
Indices: 32266--32305 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
32256 AAAATATTTA
* *
32266 AAATATTTTAATAAACTAT
1 AAATATTTTAACAAAATAT
32285 AAATATATTTAACAAAATAT
1 AAATAT-TTTAACAAAATAT
32305 A
1 A
32306 TTAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATTTTAACAAAATAT
Found at i:32313 original size:25 final size:25
Alignment explanation
Indices: 32285--32337 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
32275 AATAAACTAT
32285 AAATATATTTAACAAAATATATTAA
1 AAATATATTTAACAAAATATATTAA
* *
32310 AAATATATTTAATAAAATATATTTA
1 AAATATATTTAACAAAATATATTAA
32335 AAA
1 AAA
32338 CCGAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATATTTAACAAAATATATTAA
Found at i:32314 original size:11 final size:12
Alignment explanation
Indices: 32285--32337 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 12
32275 AATAAACTAT
32285 AAATATATTTAA
1 AAATATATTTAA
32297 CAAA-ATATATTAA
1 -AAATATAT-TTAA
32310 AAATATATTTAATA
1 AAATATATTT-A-A
32324 AAATATATTTAA
1 AAATATATTTAA
32336 AA
1 AA
32338 CCGAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.33
13 13 0.36
14 11 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATTTAA
Found at i:32323 original size:20 final size:20
Alignment explanation
Indices: 32250--32323 Score: 51
Period size: 25 Copynumber: 3.5 Consensus size: 20
32240 AATCGAATTA
* *
32250 ATATTTAAAATATTTAAAAT
1 ATATTTAATATATTAAAAAT
* * *
32270 AT-TTTAATAAACTATAAAT
1 ATATTTAATATATTAAAAAT
32289 ATATTTAACAAAATATATTAAAAAT
1 ATATTT-----AATATATTAAAAAT
32314 ATATTTAATA
1 ATATTTAATA
32324 AAATATATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
19 14 0.35
20 9 0.22
25 17 0.43
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATTTAATATATTAAAAAT
Found at i:33408 original size:4 final size:4
Alignment explanation
Indices: 33399--33427 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
33389 ATCATTTATA
33399 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
33428 TATTAGCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:33719 original size:21 final size:21
Alignment explanation
Indices: 33680--33719 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33670 ATTAAAATAT
*
33680 TATTTTATATTAATTTTTATA
1 TATTTTATATTAATATTTATA
33701 TATTTTATAATTAA-ATTTA
1 TATTTTAT-ATTAATATTTA
33720 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATATTAATATTTATA
Found at i:35363 original size:2 final size:2
Alignment explanation
Indices: 35356--35403 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
35346 TAACAAGTGC
35356 AT AT AT AT AT 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 AT AT AT AT AT
35398 AT AT AT
1 AT AT AT
35404 GAGTGTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39338 original size:103 final size:103
Alignment explanation
Indices: 39211--39420 Score: 343
Period size: 103 Copynumber: 2.0 Consensus size: 103
39201 TGAAATTATC
39211 AAAAACCCAAAATTGAAATAATAACAAAAAAAAAAGAAAAC-GTATTTATATCTTTTAAAATTTA
1 AAAAACCCAAAATTGAAATAATAAC-AAAAAAAAAGAAAACGGTATTTATATCTTTTAAAATTTA
39275 GTATTTAAAAAATTAT-AAAAACTACCCAATTTTATAATA
65 GTATTT-AAAAATTATGAAAAACTACCCAATTTTATAATA
* * ** *
39314 AAAAACTCAAAATTGAAATTATAACAAAAAAACTGAAAACGGTATTTATATCTTTTAAAATTTAT
1 AAAAACCCAAAATTGAAATAATAACAAAAAAAAAGAAAACGGTATTTATATCTTTTAAAATTTAG
39379 TATTTAAAAATTATGAAAAACTACCCAATTTTATAATA
66 TATTTAAAAATTATGAAAAACTACCCAATTTTATAATA
39417 AAAA
1 AAAA
39421 CTAATTGAAT
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
102 22 0.22
103 78 0.78
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (103 bp):
AAAAACCCAAAATTGAAATAATAACAAAAAAAAAGAAAACGGTATTTATATCTTTTAAAATTTAG
TATTTAAAAATTATGAAAAACTACCCAATTTTATAATA
Found at i:41407 original size:37 final size:36
Alignment explanation
Indices: 41366--41460 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 36
41356 TTTTTCGTGA
**
41366 ATTGGCGCTGCCACCCAAATTTTAACAATCATAGTGG
1 ATTGGC-CTGCCACCCAAATACTAACAATCATAGTGG
*
41403 ATTGGCACTACCACCCAAATACTAACAATCATAGTGG
1 ATTGGC-CTGCCACCCAAATACTAACAATCATAGTGG
*
41440 ATTGGCCAAGCCACCCAAATA
1 ATTGGCC-TGCCACCCAAATA
41461 TTACTTGTCG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
36 1 0.02
37 50 0.98
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (36 bp):
ATTGGCCTGCCACCCAAATACTAACAATCATAGTGG
Found at i:45820 original size:37 final size:37
Alignment explanation
Indices: 45779--45859 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
45769 ATAGCTTTGT
* *
45779 CAATCCACTATGATTGTTAGTATTTAAGTAGCAGTGC
1 CAATCCACTATGATTGTTAGAATTTAAGTAGCAGCGC
** *
45816 CAATCCACTATGATTGTTAGAATTTGGGTGGCAGCGC
1 CAATCCACTATGATTGTTAGAATTTAAGTAGCAGCGC
45853 CAATCCA
1 CAATCCA
45860 TGAAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (37 bp):
CAATCCACTATGATTGTTAGAATTTAAGTAGCAGCGC
Done.