Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2577
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: 44105
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Found at i:2132 original size:3 final size:3
Alignment explanation
Indices: 2111--2175 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
2101 GGACTTTCCT
* * * * * * * *
2111 CCA CCA CCG CCA CCT CCA CCA CCT CCA CCA CCT CCG CCC CCG CCG CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
2159 CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CC
2176 TCCTCCACCG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.20, C:0.69, G:0.06, T:0.05
Consensus pattern (3 bp):
CCA
Found at i:2132 original size:9 final size:9
Alignment explanation
Indices: 2120--2184 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
2110 TCCACCACCG
2120 CCACCTCCA
1 CCACCTCCA
2129 CCACCTCCA
1 CCACCTCCA
*
2138 CCACCTCCG
1 CCACCTCCA
* * *
2147 CCCCCGCCG
1 CCACCTCCA
*
2156 CCACCACCA
1 CCACCTCCA
*
2165 CCACCACCA
1 CCACCTCCA
*
2174 CCTCCTCCA
1 CCACCTCCA
2183 CC
1 CC
2185 GGCAGCCATC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.18, C:0.69, G:0.05, T:0.08
Consensus pattern (9 bp):
CCACCTCCA
Found at i:2740 original size:32 final size:32
Alignment explanation
Indices: 2668--2742 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
2658 TAGATATTTG
* *
2668 TATTAAATTATATAAATTTTAATATATTAATA
1 TATTATATTATATAAATTTTAATATACTAATA
*
2700 -ATTAATATTATATAAATTTT-ATGATACTGATA
1 TATT-ATATTATATAAATTTTAAT-ATACTAATA
2732 TATTATATTAT
1 TATTATATTAT
2743 TTGTTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 5 0.14
32 29 0.78
33 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
TATTATATTATATAAATTTTAATATACTAATA
Found at i:3314 original size:15 final size:15
Alignment explanation
Indices: 3228--3323 Score: 56
Period size: 15 Copynumber: 6.1 Consensus size: 15
3218 TATATTATAA
* *
3228 TTATA-TTTAAAATA
1 TTATATTTTAATATT
3242 TTATATATTTATATATT
1 TTATAT-TTTA-ATATT
*
3259 TTA-ATTTATTAATA-A
1 TTATA-TT-TTAATATT
3274 TTA-ATTTTATATAAATT
1 TTATATTTTA-AT--ATT
3291 TTAATATTTTAATATT
1 TT-ATATTTTAATATT
*
3307 TTATATTTTTATATT
1 TTATATTTTAATATT
3322 TT
1 TT
3324 TTTATATTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
13 3 0.05
14 9 0.14
15 18 0.27
16 15 0.23
17 12 0.18
18 3 0.05
19 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTTAATATT
Found at i:4655 original size:13 final size:12
Alignment explanation
Indices: 4629--4664 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
4619 TTATAAAAAT
4629 ATATAAATATTA
1 ATATAAATATTA
4641 ATATAAATAATTA
1 ATATAAAT-ATTA
4654 ATATAAA-ATTA
1 ATATAAATATTA
4665 TTTTTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:5681 original size:24 final size:24
Alignment explanation
Indices: 5654--5704 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
5644 TATCAACCTC
* *
5654 TTTTTTATCTTTAAATTATAATTA
1 TTTTTTATATTTAAATTACAATTA
5678 TTTTTTATATTTAAATTACAATTA
1 TTTTTTATATTTAAATTACAATTA
5702 TTT
1 TTT
5705 AATATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTTTATATTTAAATTACAATTA
Found at i:6155 original size:22 final size:23
Alignment explanation
Indices: 6118--6164 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
6108 TAATTTAAAT
6118 AATTTAATTTATTAA-TAATAAA
1 AATTTAATTTATTAATTAATAAA
6140 AATTTAA-TTATATAATTTAATAAA
1 AATTTAATTTAT-TAA-TTAATAAA
6164 A
1 A
6165 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
24 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAATTTATTAATTAATAAA
Found at i:6158 original size:30 final size:32
Alignment explanation
Indices: 6122--6186 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
6112 TTAAATAATT
*
6122 TAATTTATTAATAA-TAAAAATT-TAA-TTATA
1 TAATTTAATAA-AATTAAAAATTATAATTTATA
6152 TAATTTAATAAAATTAAAAATTATAATTTATA
1 TAATTTAATAAAATTAAAAATTATAATTTATA
6184 TAA
1 TAA
6187 AAGTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 3 0.10
32 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
TAATTTAATAAAATTAAAAATTATAATTTATA
Found at i:6198 original size:24 final size:23
Alignment explanation
Indices: 6150--6206 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
6140 AATTTAATTA
6150 TATAATTTAATAAAATTAAAAAT
1 TATAATTTAATAAAATTAAAAAT
*
6173 TATAATTTATATAAAAGTT-AATAT
1 TATAATTTA-ATAAAA-TTAAAAAT
6197 TA-AATTTAAT
1 TATAATTTAAT
6207 TACTCAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 2 0.06
23 15 0.48
24 12 0.39
25 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TATAATTTAATAAAATTAAAAAT
Found at i:6202 original size:36 final size:32
Alignment explanation
Indices: 6127--6202 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 32
6117 TAATTTAATT
* *
6127 TATTAATAATAAAAATTTAATTATATAATTTAA
1 TATTAA-ATTAAAAATTTAATTATATAAGTTAA
6160 TA--AAATTAAAAATTATAATTTATATAAAAGTTAA
1 TATTAAATTAAAAATT-TAA-TTATAT--AAGTTAA
6194 TATTAAATT
1 TATTAAATT
6203 TAATTACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 9 0.26
31 5 0.14
32 6 0.17
33 2 0.06
34 8 0.23
36 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
TATTAAATTAAAAATTTAATTATATAAGTTAA
Found at i:9037 original size:4 final size:4
Alignment explanation
Indices: 9028--9053 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9018 ATCCAGTTGC
9028 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
9054 GTGGTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:11356 original size:17 final size:19
Alignment explanation
Indices: 11334--11376 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
11324 TTATATTTAA
*
11334 ATTTAAATAA-AAATA-TT
1 ATTTAAATAATAAATAGTG
*
11351 ATTTAATTAATAAATAGTG
1 ATTTAAATAATAAATAGTG
11370 ATTTAAA
1 ATTTAAA
11377 CTGAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 7 0.33
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTTAAATAATAAATAGTG
Found at i:11590 original size:8 final size:8
Alignment explanation
Indices: 11577--11601 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11567 ACCTCCCCAT
11577 CTCTGCAA
1 CTCTGCAA
11585 CTCTGCAA
1 CTCTGCAA
11593 CTCTGCAA
1 CTCTGCAA
11601 C
1 C
11602 AATAAGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (8 bp):
CTCTGCAA
Found at i:12966 original size:15 final size:15
Alignment explanation
Indices: 12948--12986 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12938 ATTAAAATAA
12948 AAATAATTTAATATT
1 AAATAATTTAATATT
*
12963 AAATATCTTTAATATT
1 AAATA-ATTTAATATT
12979 AATATAAT
1 AA-ATAAT
12987 AATTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.25
16 12 0.60
17 3 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATAATTTAATATT
Found at i:13034 original size:6 final size:6
Alignment explanation
Indices: 13025--13088 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
13015 ATGTATACTT
* * * *
13025 ATAAAA ATAAAA ATATACAC ATAATA ATTAAA A-AGAA A-AAAA ATAAAA
1 ATAAAA ATAAAA ATA-A-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
*
13073 ATAAAA ATAGAA ATAA
1 ATAAAA ATAAAA ATAA
13089 TTATGTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 7 0.16
6 32 0.71
7 2 0.04
8 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:13273 original size:234 final size:225
Alignment explanation
Indices: 12926--13382 Score: 763
Period size: 234 Copynumber: 2.0 Consensus size: 225
12916 TTATCCGACT
12926 TAAAAGAAAAAAATTAAAATAAAAATAATTTAATATTAAATATCTTTAATATTAATATAATAATT
1 TAAAAGAAAAAAATTAAAATAAAAATAATTTAATATTAAATATCTTTAATATTAATATAATAATT
*
12991 TTATGTTAAATATAAATATTAAATATGTATACTTATAAAAATAAAAATATACACATAATAATTAA
66 TTATGTTAAATATAAATATTAAATATGTATACTTATAAAAACAAAAATATACACATAATAATTAA
13056 AAAGAAAAAAAATAAAAATAAAAATAGAAATAATTATGTTTTTTATTTTTAAATAAATAAATAAC
131 AAAG--AAAAAATAAAAAT----AT--AAATAATTATGTTTTTTATTTTTAAATAAATAAATAAC
13121 AAAAAAAAAGAATTGATTAG-TTTTTTTAACTACAAAACC
188 --AAAAAAAGAATTGATTAGTTTTTTTTAACTACAAAACC
*
13160 TAAAAGAAAAAAATTAAAATAAAAATAATTTAGTATTAAATATCTTTAATATTAATATAATAATT
1 TAAAAGAAAAAAATTAAAATAAAAATAATTTAATATTAAATATCTTTAATATTAATATAATAATT
* *
13225 TTATGTTAAATGTAAATATTAAATATGTATACTTATAAAAACAAAAATATACACATAATAATTAG
66 TTATGTTAAATATAAATATTAAATATGTATACTTATAAAAACAAAAATATACACATAATAATTAA
* *
13290 AAAGAAAAAATACAAATATAAATAGTTATGTTTTTTATTTTTAAATAAATAAATAACAAAAAAAG
131 AAAGAAAAAATAAAAATATAAATAATTATGTTTTTTATTTTTAAATAAATAAATAACAAAAAAAG
13355 AATTGATTAGTTTTTTTTAACTACAAAA
196 AATTGATTAGTTTTTTTTAACTACAAAA
13383 ATAATGAAAA
Statistics
Matches: 216, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
224 18 0.08
225 17 0.08
226 37 0.17
228 2 0.01
232 12 0.06
234 130 0.60
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (225 bp):
TAAAAGAAAAAAATTAAAATAAAAATAATTTAATATTAAATATCTTTAATATTAATATAATAATT
TTATGTTAAATATAAATATTAAATATGTATACTTATAAAAACAAAAATATACACATAATAATTAA
AAAGAAAAAATAAAAATATAAATAATTATGTTTTTTATTTTTAAATAAATAAATAACAAAAAAAG
AATTGATTAGTTTTTTTTAACTACAAAACC
Found at i:15287 original size:23 final size:23
Alignment explanation
Indices: 15249--15316 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
15239 ATTACATTTA
15249 ATAATTAAATAATTAATATTTATT
1 ATAA-TAAATAATTAATATTTATT
* * * *
15273 TTAATAATTTATTAATAATTATT
1 ATAATAAATAATTAATATTTATT
*
15296 ATAATAAATAATTAATCTTTA
1 ATAATAAATAATTAATATTTA
15317 AAAATTTAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 32 0.91
24 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATAAATAATTAATATTTATT
Found at i:17298 original size:15 final size:15
Alignment explanation
Indices: 17280--17314 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17270 TAAGGATGCT
**
17280 TATCCCCCGCCGGGA
1 TATCCCCCGCAAGGA
17295 TATCCCCCGCAAGGA
1 TATCCCCCGCAAGGA
17310 TATCC
1 TATCC
17315 TCAGGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.17
Consensus pattern (15 bp):
TATCCCCCGCAAGGA
Found at i:17809 original size:15 final size:15
Alignment explanation
Indices: 17781--17821 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
17771 TAAAAAAATT
* *
17781 TATATAATATTTTTA
1 TATATTATAATTTTA
17796 TATATTATAATTTTA
1 TATATTATAATTTTA
17811 TA-ATTA-AATTT
1 TATATTATAATTT
17822 AAATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.21
14 4 0.17
15 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTATAATTTTA
Found at i:19419 original size:10 final size:10
Alignment explanation
Indices: 19391--19431 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
19381 TCGATCGGTT
19391 AATTTTAATA
1 AATTTTAATA
*
19401 GAATTTTAATT
1 -AATTTTAATA
*
19412 ATTTTTAATA
1 AATTTTAATA
19422 AATTTTAATA
1 AATTTTAATA
19432 TTAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
AATTTTAATA
Found at i:19459 original size:22 final size:22
Alignment explanation
Indices: 19420--19461 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
19410 TTATTTTTAA
*
19420 TAAATTTTAATATTAAATATAT
1 TAAATTTTAATATAAAATATAT
19442 TAAATTATTAATA-AAAATAT
1 TAAATT-TTAATATAAAATAT
19462 GTATTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTAATATAAAATATAT
Found at i:20327 original size:42 final size:42
Alignment explanation
Indices: 20268--20355 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
20258 ATTTTTACAT
20268 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
1 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
*
20310 AATTTATTTACTGTAAACTACATAAAATTTTACATGTATTCG
1 AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
20352 AATT
1 AATT
20356 CAATTACATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (42 bp):
AATTTATTTACTATAAACTACATAAAATTTTACATGTATTCG
Found at i:20360 original size:22 final size:21
Alignment explanation
Indices: 20293--20360 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
20283 AACTACATAA
20293 AATTTTACATGTATTCGAATT
1 AATTTTACATGTATTCGAATT
* ** * *
20314 TA-TTTAC-TGTAAACTACATAA
1 AATTTTACATGTATTCGA-AT-T
20335 AATTTTACATGTATTCGAATT
1 AATTTTACATGTATTCGAATT
20356 CAATT
1 -AATT
20361 ACATTGCGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 9
0.63 0.20 0.18
Matches are distributed among these distances:
19 6 0.19
20 7 0.22
21 2 0.06
22 11 0.34
23 6 0.19
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTTTACATGTATTCGAATT
Found at i:21413 original size:18 final size:18
Alignment explanation
Indices: 21345--21411 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
21335 TGTTTTTGTA
* *
21345 TAATTGAAATAAAA-TCT
1 TAATTAAAATAAAATTTT
* *
21362 TAATATAAATTAATA-TTT
1 TAAT-TAAAATAAAATTTT
*
21380 TATTTAAAATAAAATTTT
1 TAATTAAAATAAAATTTT
21398 TAATTAAATATAAA
1 TAATTAAA-ATAAA
21412 TTAAATAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 12 0.31
18 22 0.56
19 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (18 bp):
TAATTAAAATAAAATTTT
Found at i:25576 original size:2 final size:2
Alignment explanation
Indices: 25569--25600 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25559 GCTTATTTGT
25569 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
25601 GCATTTATGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:26511 original size:22 final size:22
Alignment explanation
Indices: 26467--26511 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
26457 TTACTTATAA
*
26467 ATTTGATAAATTAAATATAATT
1 ATTTGATAAATTAAATAAAATT
*
26489 ATTT-ATAAATTTAATAAATATT
1 ATTTGATAAATTAAATAAA-ATT
26511 A
1 A
26512 AATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTGATAAATTAAATAAAATT
Found at i:26521 original size:32 final size:32
Alignment explanation
Indices: 26436--26544 Score: 125
Period size: 32 Copynumber: 3.5 Consensus size: 32
26426 GCATAAACTT
* * *
26436 TTTAA-AAAAATTAAATTAATATTACTTATAAA
1 TTTAATAAATATTAAA-TAAAATTATTTATAAA
* *
26468 TTTGAT-AA-ATTAAATATAATTATTTATAAA
1 TTTAATAAATATTAAATAAAATTATTTATAAA
**
26498 TTTAATAAATATTAAATAAAATTATTCGTAAA
1 TTTAATAAATATTAAATAAAATTATTTATAAA
26530 TTTAATAAATATTAA
1 TTTAATAAATATTAA
26545 CACTTAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 18 0.27
31 8 0.12
32 40 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (32 bp):
TTTAATAAATATTAAATAAAATTATTTATAAA
Found at i:28165 original size:24 final size:23
Alignment explanation
Indices: 28131--28186 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 23
28121 AATTAAAATA
28131 AATTTATTTATATATTAATATTT-AT
1 AATTT-TTTATA-ATTAA-ATTTAAT
28156 AATTTTTTATAATTAAATTTAAAT
1 AATTTTTTATAATTAAATTT-AAT
28180 AATTTTT
1 AATTTTT
28187 ATTTATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 15 0.52
25 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTTTTATAATTAAATTTAAT
Found at i:28806 original size:2 final size:2
Alignment explanation
Indices: 28794--28829 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28784 CTGCAAATCG
*
28794 AT AT CT 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
28830 CTAAAGTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37950 original size:24 final size:25
Alignment explanation
Indices: 37923--37970 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
37913 TGTAGAGGCG
*
37923 ATTTT-TTTTTCTTTTGTAAAATTA
1 ATTTTGTTTTTATTTTGTAAAATTA
*
37947 ATTTTGTTTTTATTTTTTAAAATT
1 ATTTTGTTTTTATTTTGTAAAATT
37971 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (25 bp):
ATTTTGTTTTTATTTTGTAAAATTA
Found at i:38155 original size:17 final size:19
Alignment explanation
Indices: 38121--38157 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
38111 TATTCATATG
*
38121 TAAAAAAATTAATTATTTT
1 TAAAAAAATTAATCATTTT
38140 TAAAAAAA-T-ATCATTTT
1 TAAAAAAATTAATCATTTT
38157 T
1 T
38158 TGTCGCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAAATTAATCATTTT
Found at i:38461 original size:30 final size:29
Alignment explanation
Indices: 38401--38462 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
38391 TAAGATAAAT
* **
38401 TTTAATATTTATTTAATTTGATAATCATA
1 TTTAATATTTATTTAAATAAATAATCATA
* *
38430 TTTAATATTTTATTTAAATAAATTATTATA
1 TTTAATA-TTTATTTAAATAAATAATCATA
38460 TTT
1 TTT
38463 TGAATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTAATATTTATTTAAATAAATAATCATA
Found at i:40271 original size:23 final size:23
Alignment explanation
Indices: 40243--40306 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
40233 ATTTTAATTA
**
40243 AGCTTTTAATTTAAATTTTGATG
1 AGCTTTTAATTTAAATTTAAATG
40266 AGCTTTTAATTTAAATTTAAATG
1 AGCTTTTAATTTAAATTTAAATG
40289 AG--TTTAAGTTTAAATTTA
1 AGCTTTTAA-TTTAAATTTA
40307 TATTTTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 5 0.13
22 10 0.26
23 23 0.61
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (23 bp):
AGCTTTTAATTTAAATTTAAATG
Found at i:40332 original size:21 final size:22
Alignment explanation
Indices: 40306--40346 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40296 GTTTAAATTT
*
40306 ATATTTTATT-AAATATTTTAA
1 ATATTTAATTCAAATATTTTAA
*
40327 ATATTTAATTCAATTATTTT
1 ATATTTAATTCAAATATTTT
40347 GATTTATTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATTTAATTCAAATATTTTAA
Found at i:41739 original size:51 final size:49
Alignment explanation
Indices: 41664--41790 Score: 127
Period size: 51 Copynumber: 2.6 Consensus size: 49
41654 ATATTAAATA
* * *
41664 TAAATAAATTTATTTA-AAAATTAAATTACATATTTGATTTAATTTA-TATTT
1 TAAATAAA-ATATTTATAAATTTAAATTA-ATA--TGATTTAAATTATTATTT
*
41715 TAAATAAAGTATTTATAAATTTAAATTAATATGATTTAAATTATTATTT
1 TAAATAAAATATTTATAAATTTAAATTAATATGATTTAAATTATTATTT
*
41764 AATAATAAAAATATTTAT--ATTTAAATT
1 TA-AAT-AAAATATTTATAAATTTAAATT
41791 TAATTATAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
48 11 0.16
49 15 0.22
50 12 0.18
51 29 0.43
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (49 bp):
TAAATAAAATATTTATAAATTTAAATTAATATGATTTAAATTATTATTT
Found at i:41779 original size:28 final size:28
Alignment explanation
Indices: 41748--41829 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 28
41738 AATTAATATG
41748 ATTTAAATTATTATTTAATAATAAAAAT
1 ATTTAAATTATTATTTAATAATAAAAAT
* * *
41776 ATTTATATT-TAAATTTAATTATAAAATAT
1 ATTTAAATTAT-TATTTAATAATAAAA-AT
*
41805 ATATAAA--ATTA-TTAA-AATAAAAAT
1 ATTTAAATTATTATTTAATAATAAAAAT
41829 A
1 A
41830 AATTTTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
24 3 0.07
25 6 0.14
26 4 0.09
27 2 0.05
28 22 0.50
29 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTAAATTATTATTTAATAATAAAAAT
Found at i:41833 original size:19 final size:20
Alignment explanation
Indices: 41792--41831 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41782 ATTTAAATTT
* *
41792 AATTA-TAAAATATATATAA
1 AATTATTAAAATAAAAATAA
41811 AATTATTAAAATAAAAATAA
1 AATTATTAAAATAAAAATAA
41831 A
1 A
41832 TTTTTAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTATTAAAATAAAAATAA
Found at i:42015 original size:2 final size:2
Alignment explanation
Indices: 42008--42033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41998 AAATATTATT
42008 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42034 GAAGATAGTA
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):
TA
Found at i:42831 original size:26 final size:24
Alignment explanation
Indices: 42801--42856 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
42791 AAATTTAATT
*
42801 TTTATACTATTAATAAATTAAATGA
1 TTTATACTATTAA-AAATAAAATGA
** *
42826 TGTTATTTTATTAAAAATAAAATTA
1 T-TTATACTATTAAAAATAAAATGA
42851 TTTATA
1 TTTATA
42857 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (24 bp):
TTTATACTATTAAAAATAAAATGA
Found at i:42860 original size:25 final size:26
Alignment explanation
Indices: 42808--42862 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
42798 ATTTTTATAC
*
42808 TATTAATAAATTAAATGATGTTATTT
1 TATTAATAAATAAAATGATGTTATTT
*
42834 TATTAA-AAATAAAATTAT-TTATATT
1 TATTAATAAATAAAATGATGTTAT-TT
42859 TATT
1 TATT
42863 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 16 0.62
26 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTAATAAATAAAATGATGTTATTT
Found at i:43210 original size:22 final size:19
Alignment explanation
Indices: 43183--43234 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 19
43173 AATTACCAAC
*
43183 TTTTAAAAAATTAATTGTATT
1 TTTTAAAAAATT-ACT-TATT
*
43204 TTATTAAAAAAATACTTATT
1 TT-TTAAAAAATTACTTATT
43224 TTTTAAAAAAT
1 TTTTAAAAAAT
43235 ATATTCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 6 0.22
21 4 0.15
22 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTTAAAAAATTACTTATT
Done.