Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2091
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: 23063
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Found at i:2248 original size:15 final size:16
Alignment explanation
Indices: 2228--2264 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2218 GTTATGTATA
2228 TATTTAA-ATT-AGATT
1 TATTTAAGATTCAG-TT
2243 TATTTAAGATTCAGTT
1 TATTTAAGATTCAGTT
2259 TATTTA
1 TATTTA
2265 TTTGATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 11 0.55
17 2 0.10
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (16 bp):
TATTTAAGATTCAGTT
Found at i:2301 original size:29 final size:31
Alignment explanation
Indices: 2269--2346 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 31
2259 TATTTATTTG
* *
2269 ATTCGATATTTAAATTA-ATTACTTA-TCAA
1 ATTCAATATTCAAATTAGATTACTTACTCAA
* *
2298 ATTCAATGTTCGAATTAGATTACTTACTC-A
1 ATTCAATATTCAAATTAGATTACTTACTCAA
* * *
2328 ATTCCACATCCAAATTAGA
1 ATTCAATATTCAAATTAGA
2347 CTTAAGATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 13 0.34
30 23 0.61
31 2 0.05
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (31 bp):
ATTCAATATTCAAATTAGATTACTTACTCAA
Found at i:4787 original size:22 final size:21
Alignment explanation
Indices: 4762--4805 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
4752 TATTTTTATT
4762 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TAT-AAAATATA
*
4784 TAAATATTCATATAAAATATA
1 TAAATATTAATATAAAATATA
4805 T
1 T
4806 TCTAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 8 0.40
23 3 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:6644 original size:18 final size:18
Alignment explanation
Indices: 6612--6741 Score: 59
Period size: 18 Copynumber: 7.6 Consensus size: 18
6602 ATATTGTAAT
6612 TATATTTA-A-AATTTTA
1 TATATTTATATAATTTTA
6628 TATATTTATATAATTTT-
1 TATATTTATATAATTTTA
6645 TGATATATTA-ATAA-TTTA
1 T-ATAT-TTATATAATTTTA
* * *
6663 TTTA-ATATA-AATTTAA
1 TATATTTATATAATTTTA
* *
6679 TATTTTTTATATTAATATTA
1 TA-TATTTATA-TAATTTTA
* *
6699 CATATATAT-TAATTTT-
1 TATATTTATATAATTTTA
*
6715 TATATTATATTTAA--TTA
1 TATATT-TATATAATTTTA
6732 TAT-TTTATAT
1 TATATTTATAT
6742 TATATTTAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 29
0.66 0.12 0.22
Matches are distributed among these distances:
15 8 0.09
16 21 0.25
17 20 0.24
18 22 0.26
19 8 0.09
20 6 0.07
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
TATATTTATATAATTTTA
Found at i:6652 original size:20 final size:18
Alignment explanation
Indices: 6612--6690 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 18
6602 ATATTGTAAT
6612 TATATTTAA-AA-TTTTA
1 TATATTTAATAATTTTTA
6628 TATATTTATATAATTTTTGA
1 TATATTTA-ATAATTTTT-A
6648 TATA-TTAATAATTTATTTAA
1 TATATTTAATAA-TT-TTT-A
*
6668 TATAAATTTAATATTTTTTA
1 TAT--ATTTAATAATTTTTA
6688 TAT
1 TAT
6691 TAATATTACA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 8 0.15
17 1 0.02
18 6 0.12
19 9 0.17
20 16 0.31
21 3 0.06
22 3 0.06
23 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (18 bp):
TATATTTAATAATTTTTA
Found at i:6720 original size:12 final size:11
Alignment explanation
Indices: 6703--6749 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
6693 ATATTACATA
6703 TATATTAATTTT
1 TATATT-ATTTT
*
6715 TATATTATATT
1 TATATTATTTT
6726 TA-ATTATATTT
1 TATATTAT-TTT
*
6737 TATATTATATT
1 TATATTATTTT
6748 TA
1 TA
6750 AAATTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
12 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATTTT
Found at i:6723 original size:17 final size:16
Alignment explanation
Indices: 6685--6748 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
6675 TTAATATTTT
* *
6685 TTATATTAATATTACA
1 TTATATTAATTTTATA
6701 TATATATTAATTTTTATA
1 T-TATATTAA-TTTTATA
* *
6719 TTATATTTAATTATATT
1 TTATA-TTAATTTTATA
6736 TTATATTATATTT
1 TTATATTA-ATTT
6749 AAAATTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.10
17 25 0.64
18 10 0.26
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTAATTTTATA
Found at i:6758 original size:27 final size:27
Alignment explanation
Indices: 6594--6758 Score: 84
Period size: 27 Copynumber: 6.3 Consensus size: 27
6584 TAAAGAATCT
*
6594 AATTATTTATATTGTA-ATTATATTTAA
1 AATTA-TTATATTTTATATTATATTTAA
* * *
6621 AATT-TTATATATTTATATAATTTTTGA
1 AATTATTATAT-TTTATATTATATTTAA
* * *
6648 TA-TATTAATAATTTAT-TTA-ATATAA
1 AATTATT-ATATTTTATATTATATTTAA
* * *
6673 ATTTAATATTTTTTATATTA-ATATTACA
1 AATTATTATATTTTATATTATAT-TTA-A
*
6701 TATATATTA-ATTTTTATATTATATTT--
1 AAT-TATTATA-TTTTATATTATATTTAA
6727 -A--ATTATATTTTATATTATATTTAA
1 AATTATTATATTTTATATTATATTTAA
6751 AATTATTA
1 AATTATTA
6759 AATTAAAATA
Statistics
Matches: 101, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
22 19 0.19
23 1 0.01
25 18 0.18
26 14 0.14
27 26 0.26
28 5 0.05
29 16 0.16
30 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
AATTATTATATTTTATATTATATTTAA
Found at i:7139 original size:19 final size:19
Alignment explanation
Indices: 7115--7168 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
7105 GGATTTATTT
7115 TTATTTTTAATTTAAATTA
1 TTATTTTTAATTTAAATTA
*
7134 TTATTTATTAA-TTAAAATA
1 TTATTT-TTAATTTAAATTA
*
7153 ATA-TTTT-ATTTAAATT
1 TTATTTTTAATTTAAATT
7169 TAATTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 8 0.27
18 2 0.07
19 15 0.50
20 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTTAATTTAAATTA
Found at i:7249 original size:20 final size:19
Alignment explanation
Indices: 7221--7268 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
7211 TTTTTATTAT
7221 ATTTTAAAT-AATAATTTAA
1 ATTTTAAATCAA-AATTTAA
7240 ATTATTAAATCAAAATTTAA
1 ATT-TTAAATCAAAATTTAA
7260 ATTTTAAAT
1 ATTTTAAAT
7269 TTTGATCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.33
20 16 0.59
21 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTAAATCAAAATTTAA
Found at i:7944 original size:13 final size:11
Alignment explanation
Indices: 7920--8004 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
7910 TATAAAAAAA
7920 TAATATAAATT
1 TAATATAAATT
7931 TAATATAAATAT
1 TAATATAAAT-T
*
7943 T-TTA-AAATT
1 TAATATAAATT
*
7952 T-ATATAAATA
1 TAATATAAATT
7962 T-ATA-AAATTTT
1 TAATATAAA--TT
7973 TAATAT-AATT
1 TAATATAAATT
*
7983 TATTATATAAATA
1 TA--ATATAAATT
7996 TAATATAAA
1 TAATATAAA
8005 ATATAATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
9 7 0.12
10 16 0.27
11 21 0.35
12 11 0.18
13 5 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATATAAATT
Found at i:7948 original size:20 final size:20
Alignment explanation
Indices: 7925--8004 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
7915 AAAAATAATA
7925 TAAATTTAATATAAATATTT
1 TAAATTTAATATAAATATTT
*
7945 TAAAATTT-ATATAAATATAT
1 T-AAATTTAATATAAATATTT
* *
7965 AAAATTTTTAATATAATTTATTAT
1 TAAA--TTTAATATAA-ATATT-T
*
7989 ATAAATATAATATAAA
1 -TAAATTTAATATAAA
8005 ATATAATACA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.07
20 12 0.26
21 9 0.20
22 6 0.13
23 12 0.26
24 1 0.02
25 3 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATTTAATATAAATATTT
Found at i:8568 original size:2 final size:2
Alignment explanation
Indices: 8563--8587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8553 AAAAAGAAGA
8563 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 A
8588 ATCAATTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8665 original size:3 final size:3
Alignment explanation
Indices: 8657--8684 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8647 TACAGATTAT
8657 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
8685 CTCTGACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9221 original size:15 final size:14
Alignment explanation
Indices: 9186--9249 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 14
9176 TATTATAATA
9186 TATAAAATTTG-AT
1 TATAAAATTTGTAT
9199 ATATTAAAATTTTGTAT
1 -TA-TAAAA-TTTGTAT
9216 TATAAAAATTT-TAT
1 TAT-AAAATTTGTAT
**
9230 T-TAGTATTTGTAT
1 TATAAAATTTGTAT
9243 TATAAAA
1 TATAAAA
9250 ATAATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
12 5 0.12
13 5 0.12
14 9 0.22
15 9 0.22
16 10 0.25
17 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
TATAAAATTTGTAT
Found at i:9272 original size:28 final size:27
Alignment explanation
Indices: 9200--9275 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
9190 AAATTTGATA
*
9200 TATTAAAATTTTGTATTATAAAAATTT
1 TATTAAGATTTTGTATTATAAAAATTT
*
9227 TATTTAG-TATTTGTATTATAAAAATAATT
1 TATTAAGAT-TTTGTATTATAAAAAT--TT
*
9256 TA-TAAGATTTTATATTATAA
1 TATTAAGATTTTGTATTATAA
9276 TATTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.02
27 21 0.51
28 14 0.34
29 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
TATTAAGATTTTGTATTATAAAAATTT
Found at i:9284 original size:15 final size:15
Alignment explanation
Indices: 9255--9327 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 15
9245 TAAAAATAAT
* *
9255 TTATAAGATTTTATA
1 TTATAATATTATATA
9270 TTATAATATTATATA
1 TTATAATATTATATA
*
9285 --A-AATTTTATATA
1 TTATAATATTATATA
*
9297 -T-TAATATTAT-TT
1 TTATAATATTATATA
* *
9309 TTATTATATTATATT
1 TTATAATATTATATA
9324 TTAT
1 TTAT
9328 GTTATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
12 11 0.23
13 9 0.19
14 8 0.17
15 19 0.40
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (15 bp):
TTATAATATTATATA
Found at i:9301 original size:25 final size:25
Alignment explanation
Indices: 9256--9306 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
9246 AAAAATAATT
*
9256 TATAAGATTTTATATTATAATATTA
1 TATAAAATTTTATATTATAATATTA
9281 TATAAAATTTTATA-TATTAATATTA
1 TATAAAATTTTATATTA-TAATATTA
9306 T
1 T
9307 TTTTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATAAAATTTTATATTATAATATTA
Found at i:9316 original size:20 final size:18
Alignment explanation
Indices: 9288--9347 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
9278 TTATATAAAA
9288 TTTTATATATTAATATTAT
1 TTTTATATATT-ATATTAT
9307 TTTTATTATATTATATT-T
1 TTTTA-TATATTATATTAT
*
9325 TATGTTATATTTTAT-TTAT
1 T-T-TTATATATTATATTAT
9344 TTTT
1 TTTT
9348 TCTGTTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 20 0.56
20 9 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATATATTATATTAT
Found at i:9320 original size:27 final size:26
Alignment explanation
Indices: 9265--9344 Score: 67
Period size: 25 Copynumber: 3.1 Consensus size: 26
9255 TTATAAGATT
** *
9265 TTATATTATAATATTATA-TAAAATT-
1 TTATATT-TAATATTATATTTTATTTA
9290 TTATATATTAATATTAT-TTTTATTATA
1 TTATAT-TTAATATTATATTTTATT-TA
* *
9317 TTATATTTTATGTTATATTTTATTTA
1 TTATATTTAATATTATATTTTATTTA
9343 TT
1 TT
9345 TTTTCTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
25 18 0.40
26 14 0.31
27 13 0.29
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (26 bp):
TTATATTTAATATTATATTTTATTTA
Found at i:9332 original size:12 final size:12
Alignment explanation
Indices: 9312--9353 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9302 ATTATTTTTA
*
9312 TTATATTATATT
1 TTATGTTATATT
9324 TTATGTTATATT
1 TTATGTTATATT
*
9336 TTAT-TTATTTT
1 TTATGTTATATT
*
9347 TTCTGTT
1 TTATGTT
9354 TGTTATGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (12 bp):
TTATGTTATATT
Found at i:9334 original size:17 final size:15
Alignment explanation
Indices: 9295--9341 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
9285 AAATTTTATA
9295 TATTAATATTAT-TTT
1 TATT-ATATTATATTT
9310 TATTATATTATATTT
1 TATTATATTATATTT
*
9325 TATGTTATATTTTATTT
1 TA--TTATATTATATTT
9342 ATTTTTTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
17 12 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTATATTATATTT
Found at i:9721 original size:18 final size:22
Alignment explanation
Indices: 9684--9727 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
9674 TTATGAATGG
9684 AAAATAATTTATATGAAAAA-T
1 AAAATAATTTATATGAAAAATT
9705 AAAAT-ATTT-TA-GAAAAATT
1 AAAATAATTTATATGAAAAATT
9724 AAAA
1 AAAA
9728 AGTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 4 0.18
21 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
AAAATAATTTATATGAAAAATT
Found at i:10318 original size:22 final size:21
Alignment explanation
Indices: 10283--10330 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
10273 AGTTACTTAT
*
10283 TAAAATTGTCATTAT-TTTAA
1 TAAAATTGTCATTATCTCTAA
10303 TAAATATTGTGCATTATCTCTAA
1 TAAA-ATTGT-CATTATCTCTAA
10326 TAAAA
1 TAAAA
10331 ATAGACTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 5 0.21
22 7 0.29
23 8 0.33
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (21 bp):
TAAAATTGTCATTATCTCTAA
Found at i:10812 original size:49 final size:50
Alignment explanation
Indices: 10730--10824 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 50
10720 TCAAAATTAA
*
10730 AAAAAAAAAAGAAAGGAAGAGAAATTTGAGTTTTAAACTGTTAATTTTTT
1 AAAAAAAAAAGAAAGGAAGAGAAATTTGAGTTTTAAACTGATAATTTTTT
* * * *
10780 AAAAGAAAAAGAAA-GATA-AGGAATTTGTGTTTTAAATTGATAATT
1 AAAAAAAAAAGAAAGGA-AGAGAAATTTGAGTTTTAAACTGATAATT
10825 AAAAAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 25 0.64
50 14 0.36
ACGTcount: A:0.51, C:0.01, G:0.17, T:0.32
Consensus pattern (50 bp):
AAAAAAAAAAGAAAGGAAGAGAAATTTGAGTTTTAAACTGATAATTTTTT
Found at i:12061 original size:18 final size:18
Alignment explanation
Indices: 12043--12077 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12033 TATTTATATA
12043 AATTT-TAATATATTAAT
1 AATTTATAATATATTAAT
*
12060 AATTTATATTATATTAAT
1 AATTTATAATATATTAAT
12078 TTATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTATAATATATTAAT
Found at i:12089 original size:18 final size:16
Alignment explanation
Indices: 12036--12110 Score: 54
Period size: 14 Copynumber: 4.8 Consensus size: 16
12026 TAATACATAT
*
12036 TTATATAAATTTTA-A
1 TTATATTAATTTTATA
12051 -TATATTAATAATTTATA
1 TTATATTAAT--TTTATA
12068 TTATATTAA-TTTATA
1 TTATATTAATTTTATA
12083 -TAT-TTATATCTTTATA
1 TTATATTA-AT-TTTATA
*
12099 TCATA-TAATTTT
1 TTATATTAATTTT
12111 TATCACATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
13 3 0.06
14 12 0.24
15 9 0.18
16 12 0.24
17 5 0.10
18 8 0.16
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTAATTTTATA
Found at i:12468 original size:29 final size:28
Alignment explanation
Indices: 12432--12486 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
12422 ATTTACAATC
12432 AAATAAATTTTTAAT-TTTTAATTTATTA
1 AAATAAA-TTTTAATATTTTAATTTATTA
12460 AAATAAAATTTTAATATTTTAATTTAT
1 AAAT-AAATTTTAATATTTTAATTTAT
12487 ATTTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATAAATTTTAATATTTTAATTTATTA
Found at i:12498 original size:31 final size:31
Alignment explanation
Indices: 12411--12505 Score: 106
Period size: 31 Copynumber: 3.2 Consensus size: 31
12401 ATCAAATAAG
* * * * *
12411 TTAAAATTTTAATTTACAATCAAATAAATTT
1 TTAATATTTTAATTTATATTAAAATAAAATT
12442 TTAAT-TTTTAA-TT-TATTAAAATAAAATT
1 TTAATATTTTAATTTATATTAAAATAAAATT
* *
12470 TTAATATTTTAATTTATATTTAAATAAAATC
1 TTAATATTTTAATTTATATTAAAATAAAATT
12501 TTAAT
1 TTAAT
12506 GTAAATTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 16 0.30
29 8 0.15
30 8 0.15
31 22 0.41
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATATTTTAATTTATATTAAAATAAAATT
Found at i:19408 original size:20 final size:21
Alignment explanation
Indices: 19383--19427 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
19373 GTTGGACATT
*
19383 ATATGAAAAAGAA-AATTGTA
1 ATATGAAAAAGAATAAGTGTA
*
19403 ATATGAAAAATAATAAGTGTA
1 ATATGAAAAAGAATAAGTGTA
19424 ATAT
1 ATAT
19428 TAATATAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (21 bp):
ATATGAAAAAGAATAAGTGTA
Found at i:21132 original size:27 final size:26
Alignment explanation
Indices: 21067--21132 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
21057 TTAAAAATAA
* *
21067 ATTTTTAAA-AAATTATAATACTAAT
1 ATTTTAAAATAAATTATAACACTAAT
**
21092 A-TAAAAAATCAAATTATAAACACTAAT
1 ATTTTAAAAT-AAATTAT-AACACTAAT
21119 ATTTTAAAATAAAT
1 ATTTTAAAATAAAT
21133 GATATTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
24 4 0.13
25 1 0.03
26 7 0.23
27 13 0.42
28 6 0.19
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (26 bp):
ATTTTAAAATAAATTATAACACTAAT
Done.