Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2426
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: 29627
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:5503 original size:19 final size:20
Alignment explanation
Indices: 5455--5499 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 20
5445 ACATCTATAA
*
5455 TAAAGATTATATTATTTAAT
1 TAAATATTATATTATTTAAT
5475 TAAATA-TATATT-TTT-AT
1 TAAATATTATATTATTTAAT
5492 TAAATATT
1 TAAATATT
5500 TATAACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 6 0.26
20 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAATATTATATTATTTAAT
Found at i:5534 original size:16 final size:18
Alignment explanation
Indices: 5504--5536 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5494 AATATTTATA
5504 ACATGTAATACTTATTTG
1 ACATGTAATACTTATTTG
5522 ACAT-TAATA-TTATTT
1 ACATGTAATACTTATTT
5537 ATTTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (18 bp):
ACATGTAATACTTATTTG
Found at i:6831 original size:31 final size:30
Alignment explanation
Indices: 6791--6861 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
6781 ATATTAGTTT
* **
6791 TTTATTTTTTTATTTTTAAATATATTTTTAA
1 TTTAATTTTTTATAATTAAATATATTTTT-A
*
6822 TTTAATTTTTAATAATTAAATATATTTTTA
1 TTTAATTTTTTATAATTAAATATATTTTTA
6852 -TTAATTTTTT
1 TTTAATTTTTT
6862 TATTAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 9 0.26
30 1 0.03
31 25 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTAATTTTTTATAATTAAATATATTTTTA
Found at i:6984 original size:16 final size:17
Alignment explanation
Indices: 6955--6986 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6945 TAACTATCAT
6955 TATTAAATATATAATTG
1 TATTAAATATATAATTG
6972 TATTAAA-ATATAATT
1 TATTAAATATATAATT
6987 TCAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TATTAAATATATAATTG
Found at i:7248 original size:19 final size:20
Alignment explanation
Indices: 7226--7264 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
7216 AAATTTAAAA
*
7226 TTTAAAATTATTAT-TATTT
1 TTTAAAATAATTATATATTT
7245 TTTAAAATAATTATATATTT
1 TTTAAAATAATTATATATTT
7265 CAACTGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAATAATTATATATTT
Found at i:8234 original size:34 final size:34
Alignment explanation
Indices: 8184--8268 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
8174 ATTAGTTGTA
* *
8184 ATTAATTTATATAATAAGATTTAGACTTTTAACCT
1 ATTAAATT-TATAATAAGATTTAAACTTTTAACCT
*
8219 ATTAAATTTATAATAAGATTTAAATTTTTAACCT
1 ATTAAATTTATAATAAGATTTAAACTTTTAACCT
8253 ATTAAATTTATAATAA
1 ATTAAATTTATAATAA
8269 AAATTATATC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 40 0.85
35 7 0.15
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (34 bp):
ATTAAATTTATAATAAGATTTAAACTTTTAACCT
Found at i:10914 original size:1 final size:1
Alignment explanation
Indices: 10908--10933 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10898 TTACTGCCCC
10908 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
10934 CAATCATCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:12371 original size:5 final size:5
Alignment explanation
Indices: 12358--12450 Score: 53
Period size: 5 Copynumber: 17.4 Consensus size: 5
12348 TTACATAGGA
* * *
12358 AATAA AATAT AATAT AAATTT AATAT AATAATT AATTAA AATAT AATAT
1 AATAT AATAT AATAT -AATAT AATAT AAT-A-T AA-TAT AATAT AATAT
* * * *
12407 AAAAAT AATAT AAATAT AA-AT ATTTT AAAATT AATAT AATAT AA
1 -AATAT AATAT -AATAT AATAT AATAT AATA-T AATAT AATAT AA
12451 ATTATTAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
4 3 0.04
5 39 0.58
6 20 0.30
7 4 0.06
8 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:12381 original size:11 final size:11
Alignment explanation
Indices: 12358--12481 Score: 80
Period size: 11 Copynumber: 11.2 Consensus size: 11
12348 TTACATAGGA
12358 AATA-AAATAT
1 AATATAAATAT
*
12368 AATATAAATTT
1 AATATAAATAT
12379 AATAT-AATAATT
1 AATATAAAT-A-T
12391 AAT-TAAAATAT
1 AATAT-AAATAT
*
12402 AATATAAAAAT
1 AATATAAATAT
12413 AATATAAATAT
1 AATATAAATAT
* *
12424 AA-AT-ATTTT
1 AATATAAATAT
* *
12433 AAAATTAATAT
1 AATATAAATAT
12444 AATATAAATTATT
1 AATATAAA-TA-T
*
12457 AAT-TAAATAA
1 AATATAAATAT
12467 AATATTTAAATAT
1 AATA--TAAATAT
12480 AA
1 AA
12482 AATATATTAT
Statistics
Matches: 89, Mismatches: 12, Indels: 23
0.72 0.10 0.19
Matches are distributed among these distances:
9 5 0.06
10 14 0.16
11 43 0.48
12 12 0.13
13 15 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAAATAT
Found at i:12382 original size:16 final size:16
Alignment explanation
Indices: 12363--12453 Score: 68
Period size: 16 Copynumber: 5.9 Consensus size: 16
12353 TAGGAAATAA
12363 AATATAATATAAATTT
1 AATATAATATAAATTT
* *
12379 AATATAATAATTAATTAA
1 AATATAAT-ATAAATT-T
12397 AATATAATAT-AA---
1 AATATAATATAAATTT
*
12409 AA-ATAATATAAATAT
1 AATATAATATAAATTT
* * *
12424 AA-ATATTTTAAAATT
1 AATATAATATAAATTT
12439 AATATAATATAAATT
1 AATATAATATAAATT
12454 ATTAATTAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 7 0.12
12 4 0.07
15 13 0.22
16 19 0.32
17 8 0.14
18 8 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAATATAAATTT
Found at i:12402 original size:18 final size:18
Alignment explanation
Indices: 12360--12409 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
12350 ACATAGGAAA
12360 TAAAATATAAT-ATAAAT
1 TAAAATATAATAATAAAT
* *
12377 T-TAATATAATAATTAAT
1 TAAAATATAATAATAAAT
12394 TAAAATATAAT-ATAAA
1 TAAAATATAATAATAAA
12410 AATAATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATATAATAATAAAT
Found at i:13019 original size:19 final size:18
Alignment explanation
Indices: 12997--13042 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
12987 AAAATATTAT
12997 ATATTTATATAAATTTTAA
1 ATATTTATAT-AATTTTAA
* *
13016 ATATTTATATTATTTTAT
1 ATATTTATATAATTTTAA
13034 AT-TTTATAT
1 ATATTTATAT
13043 TTTATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 8 0.32
19 10 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATATAATTTTAA
Found at i:13019 original size:26 final size:25
Alignment explanation
Indices: 12983--13065 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 25
12973 TTATAATTAT
*
12983 ATTTAAAATATTATATATTTATATAA
1 ATTTTAAATATTATATATTTATAT-A
13009 ATTTTAAATATTTATATTATTT-TAT-
1 ATTTTAAATA-TTATA-TATTTATATA
* *
13034 ATTTTATATTTTATAT-TTTATATTA
1 ATTTTAAATATTATATATTTATA-TA
13059 TATTTTA
1 -ATTTTA
13066 TTTATTTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
22 3 0.06
23 3 0.06
24 6 0.12
25 8 0.17
26 15 0.31
27 8 0.17
28 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTTAAATATTATATATTTATATA
Found at i:13054 original size:7 final size:7
Alignment explanation
Indices: 13016--13066 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
13006 TAAATTTTAA
13016 ATATTTAT
1 ATATTT-T
13024 ATTATTTT
1 A-TATTTT
13032 ATATTTT
1 ATATTTT
13039 ATATTTT
1 ATATTTT
13046 ATATTTT
1 ATATTTT
13053 ATA--TT
1 ATATTTT
13058 ATATTTT
1 ATATTTT
13065 AT
1 AT
13067 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.12
7 27 0.68
8 3 0.08
9 5 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATATTTT
Found at i:13071 original size:14 final size:14
Alignment explanation
Indices: 12961--13071 Score: 56
Period size: 14 Copynumber: 8.0 Consensus size: 14
12951 TTGTATTTTC
12961 ATATTTT-TTATATT
1 ATATTTTATT-TATT
* **
12975 ATAATTATATTTAAA
1 AT-ATTTTATTTATT
12990 ATATTATATATTTATAT
1 ATATT-T-TATTTAT-T
* **
13007 AAATTTTAAATATT
1 ATATTTTATTTATT
*
13021 -TATATTA-TT-TT
1 ATATTTTATTTATT
13032 ATATTTTATATT-TT
1 ATATTTTAT-TTATT
13046 ATATTTTA--TATT
1 ATATTTTATTTATT
13058 ATATTTTATTTATT
1 ATATTTTATTTATT
13072 TTTAATATCA
Statistics
Matches: 73, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
11 3 0.04
12 17 0.23
13 5 0.07
14 22 0.30
15 13 0.18
16 9 0.12
17 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTTATTTATT
Found at i:13072 original size:51 final size:52
Alignment explanation
Indices: 12962--13072 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 52
12952 TGTATTTTCA
12962 TATTT-TTTATATTATAATTATATTTAAAATATTATATATTTATATAAATTT
1 TATTTATTTATATTATAATTATATTTAAAATATTATATATTTATATAAATTT
** * * * * *
13013 TAAATATTTATATTAT-TTTATATTTTATATTTTATAT-TTTATATTATATTT
1 TATTTATTTATATTATAATTATATTTAAAATATTATATATTTATA-TAAATTT
13064 TATTTATTT
1 TATTTATTT
13073 TTAATATCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
50 6 0.12
51 33 0.67
52 10 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (52 bp):
TATTTATTTATATTATAATTATATTTAAAATATTATATATTTATATAAATTT
Found at i:13235 original size:21 final size:18
Alignment explanation
Indices: 13211--13257 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 18
13201 TAAAATTAAG
13211 AAAGAAAATAAATCCAAAAAA
1 AAAGAAAATAAA---AAAAAA
*
13232 AAAGGAAATAAAAAAAAA
1 AAAGAAAATAAAAAAAAA
13250 AAA-AAAAT
1 AAAGAAAAT
13258 TGAGAGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
21 11 0.46
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAGAAAATAAAAAAAAA
Found at i:14925 original size:10 final size:10
Alignment explanation
Indices: 14903--14940 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
14893 GAATTTCGTG
*
14903 TATATGTAAA
1 TATATATAAA
*
14913 TATATATACA
1 TATATATAAA
14923 TATATATAAA
1 TATATATAAA
14933 TATATATA
1 TATATATA
14941 TTTCAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (10 bp):
TATATATAAA
Found at i:14932 original size:20 final size:20
Alignment explanation
Indices: 14903--14940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14893 GAATTTCGTG
*
14903 TATATGTAAATATATATACA
1 TATATATAAATATATATACA
14923 TATATATAAATATATATA
1 TATATATAAATATATATA
14941 TTTCAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATATAAATATATATACA
Found at i:16967 original size:17 final size:17
Alignment explanation
Indices: 16945--16995 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
16935 TAAATGTTTT
16945 TTTATATTTTTATTATA
1 TTTATATTTTTATTATA
16962 TTTATATTATTT-TTAT-
1 TTTATATT-TTTATTATA
*
16978 TTT-TATTTTTATTTTA
1 TTTATATTTTTATTATA
16994 TT
1 TT
16996 ATTTGCCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 7 0.23
16 5 0.17
17 12 0.40
18 3 0.10
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATATTTTTATTATA
Found at i:16985 original size:12 final size:12
Alignment explanation
Indices: 16968--16992 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16958 TATATTTATA
16968 TTATTTTTATTT
1 TTATTTTTATTT
16980 TTATTTTTATTT
1 TTATTTTTATTT
16992 T
1 T
16993 ATTATTTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:17143 original size:17 final size:17
Alignment explanation
Indices: 17117--17155 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17107 TTTAATTTAA
*
17117 AAATTTAAAAACAGTTT
1 AAATTAAAAAACAGTTT
* *
17134 AAATTAAAAAATATTTT
1 AAATTAAAAAACAGTTT
17151 AAATT
1 AAATT
17156 TAAATCACTT
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:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTAAAAAACAGTTT
Found at i:17641 original size:19 final size:19
Alignment explanation
Indices: 17619--17664 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
17609 TAATTTTTTA
17619 TATTTAATTTAAAATTAAT
1 TATTTAATTTAAAATTAAT
*
17638 TATTTTAA-TTAAATTTAAT
1 TA-TTTAATTTAAAATTAAT
*
17657 TAATTAAT
1 TATTTAAT
17665 AAATATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 14 0.61
20 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTAATTTAAAATTAAT
Found at i:17652 original size:25 final size:26
Alignment explanation
Indices: 17608--17664 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
17598 TAAAAGTAAT
*
17608 TTAATTTTTTATATTTAATTTAA-AA
1 TTAATTTTTTATATTAAATTTAATAA
17633 TTAATTATTTTA-ATTAAATTTAATTAA
1 TTAATT-TTTTATATTAAATTTAA-TAA
17660 TTAAT
1 TTAAT
17665 AAATATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 16 0.57
26 5 0.18
27 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTAATTTTTTATATTAAATTTAATAA
Found at i:17752 original size:21 final size:22
Alignment explanation
Indices: 17710--17754 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
17700 ACTTTATTCA
*
17710 ATAATTAAAATTTTACTCAAAT
1 ATAATTAAAATTATACTCAAAT
* *
17732 ATAATT-AAATTATATTTAAAT
1 ATAATTAAAATTATACTCAAAT
17753 AT
1 AT
17755 TTCTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATTAAAATTATACTCAAAT
Found at i:18387 original size:14 final size:13
Alignment explanation
Indices: 18363--18393 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
18353 GAAAGAGATG
18363 TATTTTATATTTA
1 TATTTTATATTTA
18376 TATTTATATATTTA
1 TATTT-TATATTTA
18390 TATT
1 TATT
18394 ATGTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATATTTA
Found at i:19131 original size:13 final size:13
Alignment explanation
Indices: 19113--19137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19103 TTTTATGGTA
19113 AAAAAATAAAAAT
1 AAAAAATAAAAAT
19126 AAAAAATAAAAA
1 AAAAAATAAAAA
19138 GATGCAAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:19966 original size:16 final size:17
Alignment explanation
Indices: 19932--19975 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
19922 AATTTATATC
19932 ATATATAAATATAATAA
1 ATATATAAATATAATAA
19949 ATATAT-AATATTAA-AA
1 ATATATAAATA-TAATAA
19965 ATATATTAAAT
1 ATATA-TAAAT
19976 TATTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.46
17 10 0.42
18 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATAAATATAATAA
Found at i:19977 original size:16 final size:16
Alignment explanation
Indices: 19932--19977 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
19922 AATTTATATC
19932 ATATATAAATATAATAA
1 ATATATAAAT-TAATAA
19949 ATATATAATATTAA-AA
1 ATATATAA-ATTAATAA
19965 ATATATTAAATTA
1 ATATA-TAAATTA
19978 TTTATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.41
17 14 0.52
18 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATAAATTAATAA
Found at i:20016 original size:14 final size:15
Alignment explanation
Indices: 19985--20020 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
19975 TTATTTATAT
19985 TTAAATTTTAATAAAA
1 TTAAA-TTTAATAAAA
20001 TTAAATTTAA-AAAA
1 TTAAATTTAATAAAA
20015 TTAAAT
1 TTAAAT
20021 AAAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAATTTAATAAAA
Found at i:20464 original size:16 final size:15
Alignment explanation
Indices: 20437--20497 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 15
20427 TAAAATTTTA
20437 TAAATTTAATTTATT
1 TAAATTTAATTTATT
20452 TAAATTATAATTTATT
1 TAAATT-TAATTTATT
* *
20468 AATAAAATATATTTTTATT
1 --T-AAATTTA-ATTTATT
20487 TAAATTTAATT
1 TAAATTTAATT
20498 AAAAATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
15 8 0.22
16 15 0.41
17 1 0.03
18 3 0.08
19 10 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAATTTAATTTATT
Found at i:20515 original size:21 final size:23
Alignment explanation
Indices: 20486--20531 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
20476 ATATTTTTAT
20486 TTAAATTTAAT-TAAAAAT-ATA
1 TTAAATTTAATATAAAAATAATA
*
20507 TTAATTTTAATATAAAAATAATA
1 TTAAATTTAATATAAAAATAATA
20530 TT
1 TT
20532 TTTATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAATTTAATATAAAAATAATA
Found at i:21253 original size:28 final size:29
Alignment explanation
Indices: 21222--21290 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
21212 TTTTACAATC
*
21222 AAATGAATATAAAAAT-AATTTAATTATA
1 AAATAAATATAAAAATAAATTTAATTATA
***
21250 AAATAAATATGTTAATAAATTTAATTATA
1 AAATAAATATAAAAATAAATTTAATTATA
*
21279 AAA-ATATATAAA
1 AAATAAATATAAA
21291 TATTAATATA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
AAATAAATATAAAAATAAATTTAATTATA
Found at i:21300 original size:22 final size:22
Alignment explanation
Indices: 21264--21306 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21254 AAATATGTTA
21264 ATAAATTTAATTATAAAAATAT
1 ATAAATTTAATTATAAAAATAT
21286 ATAAATATTAA-TATAAAAATA
1 ATAAAT-TTAATTATAAAAATA
21307 AATTTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAATTTAATTATAAAAATAT
Found at i:21779 original size:27 final size:28
Alignment explanation
Indices: 21700--21797 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 28
21690 AGATCTAATA
*
21700 ATTTATATATTTATATCAAA-TTT-ATAT
1 ATTTATATATTTATAT-AAATTTTAAAAT
*
21727 ATTT-TAT-TATATCATAATTATATTTAAAAT
1 ATTTATATATTTAT-ATAA--AT-TTTAAAAT
21757 ATTT-TATATTTATATAAATTTTAAAAT
1 ATTTATATATTTATATAAATTTTAAAAT
*
21784 ATTTATGTATTTAT
1 ATTTATATATTTAT
21798 TAATTAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
25 6 0.10
26 5 0.08
27 17 0.29
28 10 0.17
29 3 0.05
30 14 0.24
31 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (28 bp):
ATTTATATATTTATATAAATTTTAAAAT
Found at i:22305 original size:6 final size:6
Alignment explanation
Indices: 22294--22319 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
22284 ATAATAAAAA
22294 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
22320 AAATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:23564 original size:15 final size:15
Alignment explanation
Indices: 23544--23577 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23534 AAATATTTGA
**
23544 TTAATTTATTTAAAT
1 TTAATTTATAAAAAT
23559 TTAATTTATAAAAAT
1 TTAATTTATAAAAAT
23574 TTAA
1 TTAA
23578 AATGATCTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATTTATAAAAAT
Found at i:25106 original size:2 final size:2
Alignment explanation
Indices: 25099--25137 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25089 TAGAAATTAA
25099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25138 AACTGACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25967 original size:2 final size:2
Alignment explanation
Indices: 25960--26000 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
25950 GGCACGTCCC
25960 AT AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26001 TTCTTTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26211 original size:89 final size:89
Alignment explanation
Indices: 26118--26388 Score: 418
Period size: 89 Copynumber: 3.0 Consensus size: 89
26108 TAAATCGAAT
* * * *
26118 ATAAACTATAATTTTTTAAATATATCAAAAAGTTTAAAAAA-ATAAGATATTTATATTAAACTTT
1 ATAAACTATAATTATTCAAATATATCAAAAATTTTAAAAAATA-AATATATTTATATTAAACTTT
*
26182 AATATTCAATCCAAATTCAAATAAC
65 AACATTCAATCCAAATTCAAATAAC
* *
26207 ATAAACTATAATTCTTCAAATATATCAAAATTTTTAAAAAATAAATATATTTATATTAAACTTTA
1 ATAAACTATAATTATTCAAATATATCAAAAATTTTAAAAAATAAATATATTTATATTAAACTTTA
* *
26272 ACATTCATTCCAAATTCGAATAAC
66 ACATTCAATCCAAATTCAAATAAC
*
26296 ATAAATTATAATTATTCAAATATATCAAAAATTTTAAAAAATAAATATATTTATATTAAACTTTA
1 ATAAACTATAATTATTCAAATATATCAAAAATTTTAAAAAATAAATATATTTATATTAAACTTTA
* *
26361 ACATTCAACCCAAATTCAAAAAAC
66 ACATTCAATCCAAATTCAAATAAC
26385 ATAA
1 ATAA
26389 TATTTTATGT
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
89 165 0.99
90 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.01, T:0.37
Consensus pattern (89 bp):
ATAAACTATAATTATTCAAATATATCAAAAATTTTAAAAAATAAATATATTTATATTAAACTTTA
ACATTCAATCCAAATTCAAATAAC
Found at i:27669 original size:25 final size:24
Alignment explanation
Indices: 27648--27692 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
27638 TACAAAAAGG
27648 TTAT-AAT-TTAAAATTTTAAAAAA
1 TTATAAATATTAAAA-TTTAAAAAA
27671 TTATAAATATTAAAATTTAAAA
1 TTATAAATATTAAAATTTAAAA
27693 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TTATAAATATTAAAATTTAAAAAA
Found at i:27690 original size:7 final size:7
Alignment explanation
Indices: 27652--27702 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
27642 AAAAGGTTAT
27652 AATTTAA
1 AATTTAA
27659 AATTTTAAA
1 AA-TTT-AA
*
27668 AAATTATA
1 AATTTA-A
27676 AATATTAA
1 AAT-TTAA
27684 AATTTAA
1 AATTTAA
27691 AATTT-A
1 AATTTAA
27697 AATTTA
1 AATTTA
27703 TTAGATATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 6 0.16
7 12 0.32
8 12 0.32
9 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTTAA
Found at i:29354 original size:26 final size:26
Alignment explanation
Indices: 29280--29358 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
29270 TTTTATTCGT
29280 TTTTA-ATTATATAATATAATATATAA
1 TTTTATATTATATAA-ATAATATATAA
* ** *
29306 TATTTATATT-TATATATGTTATATAC
1 T-TTTATATTATATAAATAATATATAA
*
29332 TTTTATATTATATAAAAAATATATAA
1 TTTTATATTATATAAATAATATATAA
29358 T
1 T
29359 ATTAAAGTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 8 0.20
26 22 0.54
27 8 0.20
28 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TTTTATATTATATAAATAATATATAA
Found at i:29449 original size:14 final size:15
Alignment explanation
Indices: 29424--29487 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
29414 AAAAAACATA
29424 AAATTATTAAAAAT-T
1 AAATT-TTAAAAATAT
29439 AAATTTTAAAAATAT
1 AAATTTTAAAAATAT
** *
29454 ATTTTTTAAAAATAA
1 AAATTTTAAAAATAT
* *
29469 AAATATATAAAAAGAT
1 AAAT-TTTAAAAATAT
29485 AAA
1 AAA
29488 CTTAAATGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 8 0.21
15 20 0.51
16 11 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AAATTTTAAAAATAT
Done.