Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2292
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: 332330
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 3 of 3
Found at i:260344 original size:21 final size:21
Alignment explanation
Indices: 260318--260357 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
260308 CTTTTATTGA
*
260318 TTTTTTTTCTTTT-CTTTTTT
1 TTTTTTTTTTTTTGCTTTTTT
260338 TTTTTTTTTTTTTGCTTTTT
1 TTTTTTTTTTTTTGCTTTTT
260358 GCAATTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (21 bp):
TTTTTTTTTTTTTGCTTTTTT
Found at i:262943 original size:25 final size:26
Alignment explanation
Indices: 262887--262962 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 26
262877 ATTTTTTTTT
** *
262887 AATATTTAAATAATAATATTTTATATT
1 AATATTTAAA-AATAATATTAAATATA
*
262914 TATATTTAAAAAT-ATATTAAATATA
1 AATATTTAAAAATAATATTAAATATA
**
262939 AATA-TTAAAAA-AATAAAAAATATA
1 AATATTTAAAAATAATATTAAATATA
262963 TAACTCTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
24 17 0.41
25 12 0.29
26 3 0.07
27 9 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATTTAAAAATAATATTAAATATA
Found at i:262963 original size:33 final size:33
Alignment explanation
Indices: 262921--262985 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
262911 ATTTATATTT
262921 AAAAATATATTAAATATAAATAT-TAAAAAAATA
1 AAAAATATA-TAAATATAAATATATAAAAAAATA
* *
262954 AAAAATATATAACTCTAAATATATAAAAAAAT
1 AAAAATATATAAATATAAATATATAAAAAAAT
262986 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (33 bp):
AAAAATATATAAATATAAATATATAAAAAAATA
Found at i:263206 original size:11 final size:10
Alignment explanation
Indices: 263190--263348 Score: 52
Period size: 9 Copynumber: 17.0 Consensus size: 10
263180 AATAAATTTA
263190 ATATTTATAT
1 ATATTTATAT
263200 CATATTTATAT
1 -ATATTTATAT
*
263211 AT-TATAT-T
1 ATATTTATAT
263219 ATA-TTATAATT
1 ATATTTAT-A-T
*
263230 ATATTTAAAT
1 ATATTTATAT
263240 AT-TTTATAT
1 ATATTTATAT
*
263249 -TA-ATAT-T
1 ATATTTATAT
263256 A-ATTT-TA-
1 ATATTTATAT
263263 ATATATTA-AT
1 ATAT-TTATAT
263273 A-ATTTATAT
1 ATATTTATAT
263282 -TATATTA-AT
1 ATAT-TTATAT
* *
263291 -T-TTGAAAT
1 ATATTTATAT
263299 ATATTTATAT
1 ATATTTATAT
263309 CATA-TTATATT
1 -ATATTTATA-T
263320 ATATTT-TA-
1 ATATTTATAT
263328 ATTATTTA-AT
1 A-TATTTATAT
263338 ATATATTATAT
1 ATAT-TTATAT
263349 TTAAATAATC
Statistics
Matches: 112, Mismatches: 9, Indels: 54
0.64 0.05 0.31
Matches are distributed among these distances:
7 6 0.05
8 20 0.18
9 32 0.29
10 28 0.25
11 23 0.21
12 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (10 bp):
ATATTTATAT
Found at i:263215 original size:18 final size:18
Alignment explanation
Indices: 263185--263233 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
263175 AATTTAATAA
263185 ATTTA-ATATTTATATCAT
1 ATTTATATA-TTATATCAT
*
263203 ATTTATATATTATATTAT
1 ATTTATATATTATATCAT
263221 A-TTATA-ATTATAT
1 ATTTATATATTATAT
263234 TTAAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 7 0.24
17 5 0.17
18 14 0.48
19 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATATTATATCAT
Found at i:263216 original size:5 final size:5
Alignment explanation
Indices: 263194--263349 Score: 87
Period size: 5 Copynumber: 31.4 Consensus size: 5
263184 AATTTAATAT
* * *
263194 TTATA TCATA TT-TA -TATA TTATA TTATA TTATAA TTATA TT-TAA ATATT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTAT-A TTATA
* * *
263243 TTATA TTAATA TTA-A TTTTA ATATA TTA-A TAAT- TTATA TTATA TTA-A
1 TTATA TT-ATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * *
263290 TTTTGAA ATATA TTTATA TCATA TTATA TTATA TTTTAA TTAT- TTA-A
1 TTAT--A TTATA -TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA
263337 TATATA TTATA TT
1 T-TATA TTATA TT
263350 TAAATAATCA
Statistics
Matches: 114, Mismatches: 20, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
3 1 0.01
4 21 0.18
5 68 0.60
6 21 0.18
7 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:263285 original size:18 final size:17
Alignment explanation
Indices: 263187--263349 Score: 113
Period size: 16 Copynumber: 10.1 Consensus size: 17
263177 TTTAATAAAT
*
263187 TTAATATTTATATCATA
1 TTAATATTTATATTATA
*
263204 TTTATATATTATATTATA
1 TTAATAT-TTATATTATA
*
263222 TT-ATAATTATATT-TA
1 TTAATATTTATATTATA
263237 --AATATTTTATATTAATA
1 TTAATA-TTTATATT-ATA
263254 TTAAT-TTTA-A-TATA
1 TTAATATTTATATTATA
263268 TTAATAATTTATATTATA
1 TTAAT-ATTTATATTATA
*
263286 TTAAT-TTTGA-AATATA
1 TTAATATTT-ATATTATA
* *
263302 TTTATA-TCATATTATA
1 TTAATATTTATATTATA
263318 TT-ATATTT-TAATTAT-
1 TTAATATTTAT-ATTATA
263333 TTAATA--TATATTATA
1 TTAATATTTATATTATA
263348 TT
1 TT
263350 TAAATAATCA
Statistics
Matches: 118, Mismatches: 9, Indels: 40
0.71 0.05 0.24
Matches are distributed among these distances:
14 17 0.14
15 20 0.17
16 41 0.35
17 17 0.14
18 20 0.17
19 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTAATATTTATATTATA
Found at i:263287 original size:32 final size:33
Alignment explanation
Indices: 263208--263349 Score: 136
Period size: 32 Copynumber: 4.3 Consensus size: 33
263198 ATCATATTTA
* *
263208 TATATTATATTATATTATAATTATATTTAAATATTT
1 TATATTATATTATATTTTAA-TATA-TT-AATAATT
263244 TATATTAATATTA-ATTTTAATATATTAATAATT
1 TATATT-ATATTATATTTTAATATATTAATAATT
*
263277 TATATTATATTA-ATTTTGAAATATATTTAT-A-T
1 TATATTATATTATATTTT--AATATATTAATAATT
* *
263309 CATATTATATTATATTTTAAT-TATT--TAATA
1 TATATTATATTATATTTTAATATATTAATAATT
263339 TATATTATATT
1 TATATTATATT
263350 TAAATAATCA
Statistics
Matches: 94, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 14 0.15
31 3 0.03
32 23 0.24
33 18 0.19
34 12 0.13
35 4 0.04
36 12 0.13
37 6 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
TATATTATATTATATTTTAATATATTAATAATT
Found at i:263302 original size:69 final size:73
Alignment explanation
Indices: 263208--263341 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 73
263198 ATCATATTTA
* *
263208 TATATTATATTATATTATAATTATATTTAAAT-ATTTTATATTA-ATATTAA-T-TTTAATATAT
1 TATATTATATTATATTATAAATATATTTAAATCATATTATATTATATATTAATTATTTAATATAT
263269 TAATAATT
66 TAATAATT
* * *
263277 TATATTATATTA-ATTTTGAAATATATTTATATCATATTATATTATATTTTAATTATTTAATATA
1 TATATTATATTATATTAT-AAATATATTTAAATCATATTATATTATATATTAATTATTTAATATA
263341 T
65 T
263342 ATTATATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
68 4 0.07
69 24 0.44
70 10 0.18
71 6 0.11
72 1 0.02
73 10 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (73 bp):
TATATTATATTATATTATAAATATATTTAAATCATATTATATTATATATTAATTATTTAATATAT
TAATAATT
Found at i:263304 original size:27 final size:26
Alignment explanation
Indices: 263213--263315 Score: 86
Period size: 27 Copynumber: 3.7 Consensus size: 26
263203 ATTTATATAT
263213 TATA-TTATATTATAATT-ATATTTAAA
1 TATATTTATATTAT-ATTAAT-TTTAAA
263239 TAT-TTTATATTAATATTAATTTTAATATA
1 TATATTTATATT-ATATTAATTTT-A-A-A
263268 TTAATAATTTATATTATATTAATTTTGAAA
1 -T-AT-ATTTATATTATATTAATTTT-AAA
*
263298 TATATTTATATCATATTA
1 TATATTTATATTATATTA
263316 TATTATATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
26 16 0.25
27 19 0.29
28 3 0.05
29 2 0.03
30 2 0.03
31 3 0.05
32 12 0.18
33 8 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
TATATTTATATTATATTAATTTTAAA
Found at i:263362 original size:23 final size:25
Alignment explanation
Indices: 263304--263369 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
263294 GAAATATATT
*
263304 TATATCATATTATATTATATTTTAAT
1 TATATCATA-TATATTATATTTTAAA
* *
263330 TATTTAATATATATTATA-TTTAAA
1 TATATCATATATATTATATTTTAAA
*
263354 TA-ATCATATTTATTAT
1 TATATCATATATATTAT
263370 TATTAGATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 11 0.32
24 7 0.21
25 9 0.26
26 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATCATATATATTATATTTTAAA
Found at i:263519 original size:15 final size:15
Alignment explanation
Indices: 263496--263525 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
263486 TTATATTTAA
263496 TAAAATTTTAATTTT
1 TAAAATTTTAATTTT
*
263511 TAAATTTTTAATTTT
1 TAAAATTTTAATTTT
263526 ATATTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TAAAATTTTAATTTT
Found at i:263643 original size:13 final size:12
Alignment explanation
Indices: 263615--263641 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
263605 TATATTAAAA
263615 TTTATTTAATTT
1 TTTATTTAATTT
263627 TTTATTTAATTT
1 TTTATTTAATTT
263639 TTT
1 TTT
263642 TAATCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTAATTT
Found at i:264164 original size:28 final size:26
Alignment explanation
Indices: 264132--264183 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
264122 TAATCATTTT
*
264132 TTAAATTAATATTTAATAAATTTTAAAC
1 TTAAATTAATATAT-AT-AATTTTAAAC
*
264160 TTAAATTATTATATATAATTTTAA
1 TTAAATTAATATATATAATTTTAA
264184 TGTTATCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 2 0.09
28 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTAAATTAATATATATAATTTTAAAC
Found at i:264359 original size:323 final size:320
Alignment explanation
Indices: 263772--264385 Score: 878
Period size: 323 Copynumber: 1.9 Consensus size: 320
263762 CATTTCCCCC
*
263772 CTCATCTTCTTTCGGTGGGTAATAAATGTAATATTTTTTAAAATTAATATTTAATAAATTTAAAA
1 CTCATCTTCTTTCGGTGGGCAATAAATGTAATATTTTTTAAAATTAATATTTAATAAATTTAAAA
* * * *
263837 ATTAAATTTTATTATATGTAATTTTAATTTTATCTCAAAATTATAGTTAAAATTATTCATAATTA
66 ATTAAA-TTTATTATATATAATTTTAATGTTATCTCAAAATTACAGTTAAAAGTATTCATAATTA
* * *
263902 AGTTATTATTTAATTTTTTATTTTTTTCTTTAAGTTCGAGTGAGAATAATTTAAAAACTCATTTT
130 AATTATTATTTAATTTTTTATTCTTTTCTTAAAGTTCGAGTGAGAATAATTTAAAAACTCATTTT
* * *
263967 ATTATTAAAAATAATATTAAAAAATTTAAAAATTATTTTTATATTAATATTTTATAATTAAATTT
195 ATTATTAAAAATAATATTAAAAAATTAAAAAATTATTTTTATATTAATATTATATAAATAAATTT
264032 AATTAAAAATAAAATTTCTTATCATTTAAATATTTAATAAATTTTATTATATGTAATTTTTT
260 AATTAAAAAT-AAATTTCTTATCATTTAAATATTTAATAAATTTTATTATATGTAATTTTTT
* *
264094 CTCATCTTCTTTCTGTGGGCAATAAATGTAATCATTTTTT-AAATTAATATTTAATAAATTTTAA
1 CTCATCTTCTTTCGGTGGGCAATAAATGTAAT-ATTTTTTAAAATTAATATTTAATAAATTTAAA
* * * * *
264158 ACTTAAA-TTATTATATATAATTTTAATGTTATCTCGAGATTACAGTTAAAAGTATTTATGATTA
65 AATTAAATTTATTATATATAATTTTAATGTTATCTCAAAATTACAGTTAAAAGTATTCATAATTA
* * *
264222 AATTATTATTTAAAATTTTTTTATTCCCTTTT-TTAAATTTGGA-TGAG-ATCAATTTAAAAATT
130 AATTATTATTT--AA-TTTTTTATT--CTTTTCTTAAAGTTCGAGTGAGAAT-AATTTAAAAACT
* * *
264284 TATTTTATTATTAAAAATAATATTTAAGAATTAAAAAATTATTTTTATATTAATATTATATAAAT
189 CATTTTATTATTAAAAATAATATTAAAAAATTAAAAAATTATTTTTATATTAATATTATATAAAT
* *
264349 AAATTTAATTAAAAATAAATTTTTTATTATTTAAATA
254 AAATTTAATTAAAAATAAATTTCTTATCATTTAAATA
264386 ATAATTTGAA
Statistics
Matches: 259, Mismatches: 26, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
320 59 0.23
322 82 0.32
323 106 0.41
324 8 0.03
325 4 0.02
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (320 bp):
CTCATCTTCTTTCGGTGGGCAATAAATGTAATATTTTTTAAAATTAATATTTAATAAATTTAAAA
ATTAAATTTATTATATATAATTTTAATGTTATCTCAAAATTACAGTTAAAAGTATTCATAATTAA
ATTATTATTTAATTTTTTATTCTTTTCTTAAAGTTCGAGTGAGAATAATTTAAAAACTCATTTTA
TTATTAAAAATAATATTAAAAAATTAAAAAATTATTTTTATATTAATATTATATAAATAAATTTA
ATTAAAAATAAATTTCTTATCATTTAAATATTTAATAAATTTTATTATATGTAATTTTTT
Found at i:265710 original size:6 final size:6
Alignment explanation
Indices: 265699--265724 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
265689 CTAGTCATCT
265699 GAACTA GAACTA GAACTA GAACTA GA
1 GAACTA GAACTA GAACTA GAACTA GA
265725 TTCATCCATC
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:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
GAACTA
Found at i:265799 original size:27 final size:28
Alignment explanation
Indices: 265768--265831 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
265758 AAGCTTCCGG
* *
265768 CGAGGATCAGG-AGAAGGTGGTGCAAGA
1 CGAGGCTCAGGCAGAAGGTGGTGCAACA
* *
265795 CGAGGCTC-GGCGGAAGGTGGTTCAACA
1 CGAGGCTCAGGCAGAAGGTGGTGCAACA
265822 CGAGGCTCAG
1 CGAGGCTCAG
265832 AGGAAGACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 28 0.90
28 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.42, T:0.12
Consensus pattern (28 bp):
CGAGGCTCAGGCAGAAGGTGGTGCAACA
Found at i:265836 original size:27 final size:27
Alignment explanation
Indices: 265780--265837 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
265770 AGGATCAGGA
* * *
265780 GAAGGTGGTGCAAGACGAGGCTCGGCG
1 GAAGGTGGTGCAACACGAGGCTCAGAG
*
265807 GAAGGTGGTTCAACACGAGGCTCAGAG
1 GAAGGTGGTGCAACACGAGGCTCAGAG
265834 GAAG
1 GAAG
265838 ACGGTGCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.17, G:0.43, T:0.12
Consensus pattern (27 bp):
GAAGGTGGTGCAACACGAGGCTCAGAG
Found at i:275537 original size:18 final size:19
Alignment explanation
Indices: 275500--275546 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
275490 TAGCCTCAAA
275500 TTAATATTTTTATTAATAAAT
1 TTAAT-TTTTTATT-ATAAAT
*
275521 TTTATTTTTTATT-TAAAT
1 TTAATTTTTTATTATAAAT
275539 TTAATTTT
1 TTAATTTT
275547 AAATTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAATTTTTTATTATAAAT
Found at i:275546 original size:17 final size:19
Alignment explanation
Indices: 275505--275546 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
275495 TCAAATTAAT
275505 ATTTTTATTAATAAATTTTA
1 ATTTTTATT-ATAAATTTTA
*
275525 TTTTTTATT-TAAA-TTTA
1 ATTTTTATTATAAATTTTA
275542 ATTTT
1 ATTTT
275547 AAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
20 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTATTATAAATTTTA
Found at i:275885 original size:20 final size:20
Alignment explanation
Indices: 275860--275900 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
275850 TTGAAGATTT
*
275860 TTAAATTAATAAAAAATTAA
1 TTAAATCAATAAAAAATTAA
* *
275880 TTAAATCGATAAAAATTTAA
1 TTAAATCAATAAAAAATTAA
275900 T
1 T
275901 AAAAATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TTAAATCAATAAAAAATTAA
Found at i:276220 original size:20 final size:20
Alignment explanation
Indices: 276195--276233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
276185 CAATCAATTT
* *
276195 ACTTAAACAAAGTTTTAAAA
1 ACTTAAAAAAAGATTTAAAA
276215 ACTTAAAAAAAGATTTAAA
1 ACTTAAAAAAAGATTTAAA
276234 TATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (20 bp):
ACTTAAAAAAAGATTTAAAA
Found at i:291297 original size:1 final size:1
Alignment explanation
Indices: 291291--291367 Score: 55
Period size: 1 Copynumber: 77.0 Consensus size: 1
291281 CTTTACACCC
* * * * ** * * **
291291 AAAAAAAATAAAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAACCAAGAAAAAATAGCAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
291356 AAAAAAAGAAAA
1 AAAAAAAAAAAA
291368 GGGTCTAGAT
Statistics
Matches: 57, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.03
Consensus pattern (1 bp):
A
Found at i:291314 original size:11 final size:11
Alignment explanation
Indices: 291291--291335 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
291281 CTTTACACCC
*
291291 AAAAAA-AATA
1 AAAAAACAAAA
291301 AAAAAAC-AAA
1 AAAAAACAAAA
291311 AAAAAACAAAA
1 AAAAAACAAAA
291322 AAAAAACAAAA
1 AAAAAACAAAA
291333 AAA
1 AAA
291336 CCAAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:291344 original size:11 final size:10
Alignment explanation
Indices: 291291--291359 Score: 70
Period size: 10 Copynumber: 6.7 Consensus size: 10
291281 CTTTACACCC
*
291291 AAAAAAA-AT
1 AAAAAAACAA
291300 AAAAAAACAA
1 AAAAAAACAA
291310 AAAAAAACAA
1 AAAAAAACAA
291320 AAAAAAA-ACA
1 AAAAAAACA-A
*
291330 AAAAAACCAA
1 AAAAAAACAA
291340 GAAAAAATAGCAA
1 -AAAAAA-A-CAA
291353 AAAAAAA
1 AAAAAAA
291360 AAAGAAAAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
9 8 0.16
10 26 0.51
11 8 0.16
12 6 0.12
13 3 0.06
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:291361 original size:29 final size:29
Alignment explanation
Indices: 291290--291362 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
291280 CCTTTACACC
291290 CAAAAAAAATAAAAAAACAAAAAAAAACAA
1 CAAAAAAAA-AAAAAAACAAAAAAAAACAA
* * *
291320 -AAAAAAAACAAAAAAACCAAGAAAAAATAG
1 CAAAAAAAA-AAAAAAA-CAAAAAAAAACAA
291350 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
291363 GAAAAGGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 15 0.41
30 14 0.38
31 8 0.22
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (29 bp):
CAAAAAAAAAAAAAAACAAAAAAAAACAA
Found at i:292744 original size:28 final size:28
Alignment explanation
Indices: 292549--293622 Score: 1090
Period size: 28 Copynumber: 37.5 Consensus size: 28
292539 TGTTCATCCC
*
292549 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-CT
* *
292580 TTTCAAAGCCCACACAAGTCGGTGGCAACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CT
292612 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
* *
292641 TTTCAAAGCCCACGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
292669 TTTC-AAGCCCACGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
292696 TTTC-AAGCCCACGAGTTAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
292723 TTTCAAAGCCCACGAGTCAGTGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
292750 CTTTCAAAGCCCACAAGTCAGTGGCATCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACCT
*
292779 TTTCAAAGCCCACGCAAGTCAGTGGTACCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCT
* *
292809 TTTCAAAGCCCACGAGTTAGTGGCACCTT
1 TTTCAAAGCCCACAAGTCAGTGGCACC-T
*
292838 TTTCAAAGCCCACGAGTCAGTGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
292865 CTTTCAAAGCCCACAAATCAGTGGCATCC-
1 -TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
292894 TTTCAAAGCCCACGTATGTCAGTGGCACCCT
1 TTTCAAAGCCCAC--AAGTCAGTGGCA-CCT
*
292925 TTT-AAAGCCCACACAAGTCAGTGGCACCA
1 TTTCAAAG-CC-CACAAGTCAGTGGCACCT
* *
292954 TTTCAAAGCCCACGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
292982 TTTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCA-CCT
*
293013 TTT-AAAGCCCACGCAAGTTAGTGGCACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCA-CCT
* *
293043 TTT-AAAGCCCATGTAAGTCAGTGGCACAT
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCT
* *
293072 TTTC-AAGCCCACGAGTCAATGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
293098 CTTTCAAAGCCCACAAGTCAGTGGCATCC-
1 -TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
293127 TTTCAAAGCCCACGCAAGTCAGTGGTACCCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCA-CCT
293158 TTT-AAAGCCCACGCAAGTCAGTGGCACTCT
1 TTTCAAAGCCCA--CAAGTCAGTGGCAC-CT
*
293188 TTTCAAAGCCCATGCAAGTCAGTGGCACTCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCAC-CT
* ** *
293219 TTTCAAAGCCTATGAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
** *
293247 TTTCAAAGCCCATGAGTCAGTGGTACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
293275 TTTC-AAGCCCACAAGTCAGTGGTA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
293301 TTT-TAAGCCCACAAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
293328 TTTCAAAGCCCACAAGTTAGTGGCA-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*** *
293355 TTTTTTAGCCCACAAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* *
293383 TTTCAAAGCCCACAATTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
293411 TTTCAAAGCCCACAAGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
*
293439 TTTCAAAGCCCACAAGTCAATGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
293467 TTTC-AAGCCCACAAGTCAGTGGCACTT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
* * *
293494 TTTCAAAACCCACATGTTAGTGGCATCC-
1 TTTCAAAGCCCACAAGTCAGTGGCA-CCT
* *
293522 TTTCAAAGCCCACAAGTCAATGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCACCT
*
293550 TTTCAAAGCCCACAAGTCAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CT
* * * *
293579 TTTCAAAGCCCACAAGCCACTAGCAACTAT
1 TTTCAAAGCCCACAAGTCAGTGGC-AC-CT
293609 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
293623 CGTGTCGGTG
Statistics
Matches: 913, Mismatches: 90, Indels: 81
0.84 0.08 0.07
Matches are distributed among these distances:
26 25 0.03
27 139 0.15
28 354 0.39
29 111 0.12
30 192 0.21
31 76 0.08
32 16 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCT
Found at i:294280 original size:20 final size:19
Alignment explanation
Indices: 294257--294307 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
294247 TCAATATGTT
294257 GATACATGTATGAATGTATC
1 GATACAT-TATGAATGTATC
* * *
294277 GATATATTCTACAATGTATC
1 GATACATTAT-GAATGTATC
294297 GATACATTATG
1 GATACATTATG
294308 TCTTTTCACC
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
GATACATTATGAATGTATC
Found at i:294301 original size:40 final size:39
Alignment explanation
Indices: 294230--294307 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 39
294220 TTTTACCCAG
* * * *
294230 ATGTATCGATACATTTTTCAATATGTTGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
294270 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
294308 TCTTTTCACC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:297775 original size:22 final size:22
Alignment explanation
Indices: 297749--297791 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
297739 AGGAAAAATA
297749 AATT-TTTAAAA-T-TTTTATT
1 AATTATTTAAAATTATTTTATT
297768 AATTATTTAAAATTATTTTATT
1 AATTATTTAAAATTATTTTATT
297790 AA
1 AA
297792 AAATTGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 1 0.05
22 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTTAAAATTATTTTATT
Found at i:299933 original size:51 final size:51
Alignment explanation
Indices: 299877--300114 Score: 266
Period size: 51 Copynumber: 4.6 Consensus size: 51
299867 TTAAGTTTCT
* *
299877 CAATTTTTCATAATCAGGGG-TACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCACAATC-GGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* * * ** *
299928 TAATTTTCCACAATCGGGGATATTCCAACTTCGATTTTACTTTC-GAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACAC
* *
299979 CAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACAC
* * * * * *
300030 CAATTTTTTATAATCGGGGATACTTCAACTCCAATTTTATTTCCAAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACAC
300082 CAATTTTTTCACAATCGGGGATACTCCAACCCC
1 CAA-TTTTTCACAATCGGGGATACTCCAACCCC
300115 ATTAATCATT
Statistics
Matches: 154, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
50 7 0.05
51 108 0.70
52 14 0.09
53 25 0.16
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
Found at i:300059 original size:102 final size:103
Alignment explanation
Indices: 299877--300114 Score: 315
Period size: 102 Copynumber: 2.3 Consensus size: 103
299867 TTAAGTTTCT
* *
299877 CAATTTTTCATAATCAGGGG-TACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCACAA
1 CAATTTTTCACAATC-GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACAA
* * *
299941 TCGGGGATATTCCAACTTCGATTTTACTTT-C-GAAACAC
65 TCGGGGATATTCCAACTCCAATTTTA-TTTCCAAAAACAC
* ** *
299979 CAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTTTATAA
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTCCACAA
300043 TCGGGGATACTT-CAACTCCAATTTTATTTCCAAAAACAC
65 TCGGGGATA-TTCCAACTCCAATTTTATTTCCAAAAACAC
300082 CAATTTTTTCACAATCGGGGATACTCCAACCCC
1 CAA-TTTTTCACAATCGGGGATACTCCAACCCC
300115 ATTAATCATT
Statistics
Matches: 120, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
101 8 0.07
102 73 0.61
103 11 0.09
104 28 0.23
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (103 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTCCACAAT
CGGGGATATTCCAACTCCAATTTTATTTCCAAAAACAC
Found at i:300164 original size:28 final size:27
Alignment explanation
Indices: 300098--300170 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
300088 TTTCACAATC
* *
300098 GGGGATACTCCAACCCCATTAATCATT
1 GGGGATACTCCAACCCCGTTAATCATA
* *
300125 GGGGATAATCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
300153 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
300171 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:300225 original size:79 final size:79
Alignment explanation
Indices: 300125--300392 Score: 317
Period size: 79 Copynumber: 3.4 Consensus size: 79
300115 ATTAATCATT
* * * *
300125 GGGGATAATCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCCGGCTTTATTCTTAAAATATT
300190 GATTTCTCATAATC
66 GATTTCTCATAATC
* *
300204 GGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTCTTAAAATATT
1 GGGGATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCCGGCTTTATTCTTAAAATATT
*
300269 GATTTCTCATAATT
66 GATTTCTCATAATC
* * * * * * *
300283 GGGGATACTCCAACCTTATTATTT-TCACGGGGATACTCCAATCCCGACTTTATTTTTGAAATAT
1 GGGGATACTCCAACCCTGTTATTTCT-AAGGGGATACTCCAACCCCGGCTTTATTCTTAAAATAT
300347 CT-ATTT-TCTATAATC
65 -TGATTTCTC-ATAATC
* *
300362 GGGGACACTTCAACCCTTGTCTTATTTCTAA
1 GGGGATACTCCAACCC-TG--TTATTTCTAA
300393 ATCATCGATT
Statistics
Matches: 160, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.01
79 148 0.93
80 2 0.01
82 7 0.04
83 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (79 bp):
GGGGATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCCGGCTTTATTCTTAAAATATT
GATTTCTCATAATC
Found at i:312563 original size:21 final size:21
Alignment explanation
Indices: 312537--312578 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
312527 AGCTACTGCC
312537 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
312558 AAGGAAGTGTATCGATACATT
1 AAGGAAATGTATCGATACATT
312579 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:312583 original size:13 final size:13
Alignment explanation
Indices: 312565--312590 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312555 ATTAAGGAAG
312565 TGTATCGATACAT
1 TGTATCGATACAT
312578 TGTATCGATACAT
1 TGTATCGATACAT
312591 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:314999 original size:51 final size:51
Alignment explanation
Indices: 314943--315181 Score: 268
Period size: 51 Copynumber: 4.6 Consensus size: 51
314933 TTAAGTTTCT
* *
314943 CAATTTTTCATAATCGGGGGTACTCCAACCCCGATTTTATTTCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* * ** *
314994 TAATTTTCCACAATCGGGGATACTCCAACTTCGATTTTACTTTC-GAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACAC
* * *
315045 CAATTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACAC
* * * * *
315096 CAA-TTTTCTATAATCGAGGATACTCCAACTCCAATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACAC
*
315148 CAATTTTTTTACAATCGGGGATACTCCAACCCCG
1 CAA-TTTTTCACAATCGGGGATACTCCAACCCCG
315182 TTAATCATCG
Statistics
Matches: 156, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
50 7 0.04
51 111 0.71
52 14 0.09
53 20 0.13
54 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
Found at i:315119 original size:102 final size:103
Alignment explanation
Indices: 314943--315181 Score: 313
Period size: 102 Copynumber: 2.3 Consensus size: 103
314933 TTAAGTTTCT
* * *
314943 CAATTTTTCATAATCGGGGGTACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAAT
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAAT
* * * *
315008 CGGGGATACTCCAACTTCGATTTTACTTT-C-GAAACAC
66 CGAGGATACTCCAACTCCAATTTTA-TTTCCAAAAACAC
* * * * *
315045 CAATTTTCCACAATCGAGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTATAA
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTCCACAA
315109 TCGAGGATACTCCAACTCCAATTTTATTTCCAAAAACAC
65 TCGAGGATACTCCAACTCCAATTTTATTTCCAAAAACAC
*
315148 CAATTTTTTTACAATCGGGGATACTCCAACCCCG
1 CAA-TTTTTCACAATCGGGGATACTCCAACCCCG
315182 TTAATCATCG
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
101 4 0.03
102 78 0.66
103 9 0.08
104 27 0.23
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (103 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAAT
CGAGGATACTCCAACTCCAATTTTATTTCCAAAAACAC
Found at i:315231 original size:28 final size:27
Alignment explanation
Indices: 315164--315236 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
315154 TTTTACAATC
**
315164 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
315191 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
*
315219 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
315237 GATTTATTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.23, C:0.36, G:0.22, T:0.19
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:315426 original size:79 final size:80
Alignment explanation
Indices: 315188--315444 Score: 310
Period size: 79 Copynumber: 3.2 Consensus size: 80
315178 CCCGTTAATC
* * * *
315188 ATCGGGGATACTCCAACCC-CGTTATTTCCGAGGGGACACTCCAACCCCGGA-TTTATTCCTAAA
1 ATCGGGGATACTCCAACCCTCATTATTTCCAAGGGGATACTCCAACCCC-GACTTTATTCTTAAA
315251 ATATTGATTTCTCATA
65 ATATTGATTTCTCATA
* *
315267 ATCGGGGATACTCCAA-CCTCGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTCTTAAAA
1 ATCGGGGATACTCCAACCCTCATTATTTCCAAGGGGATACTCCAACCCCGACTTTATTCTTAAAA
315331 TATTGATTTCTCATA
66 TATTGATTTCTCATA
* * * * *
315346 ATTGGGGATACTCCAACCCT-ATTATTTTCACGGGGATACTCCAATCCCGACTTTATTTTTGAAA
1 ATCGGGGATACTCCAACCCTCATTATTTCCAAGGGGATACTCCAACCCCGACTTTATTCTT-AAA
* *
315410 CATCTT-TTTTCT-ATA
65 -ATATTGATTTCTCATA
* *
315425 ATCGGGGACACTTCAACCCT
1 ATCGGGGATACTCCAACCCT
315445 TGTCTTATTT
Statistics
Matches: 158, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
78 4 0.03
79 139 0.88
80 11 0.07
81 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCTCATTATTTCCAAGGGGATACTCCAACCCCGACTTTATTCTTAAAA
TATTGATTTCTCATA
Found at i:316944 original size:2 final size:2
Alignment explanation
Indices: 316937--316981 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
316927 CAAAATGACA
316937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316978 AT AT
1 AT AT
316982 TGGAGCAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:317259 original size:13 final size:14
Alignment explanation
Indices: 317243--317276 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
317233 TCTTGTAAAC
*
317243 TTATTTTAAT-TTT
1 TTATATTAATATTT
317256 TTATATTAATATTT
1 TTATATTAATATTT
317270 TTATATT
1 TTATATT
317277 TTTATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATATTAATATTT
Found at i:317278 original size:22 final size:22
Alignment explanation
Indices: 317244--317291 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
317234 CTTGTAAACT
317244 TATTTTAATTTTTTAT-ATTAA
1 TATTTTAATTTTTTATAATTAA
*
317265 TATTTTTATATTTTTATAATTAA
1 TATTTTAAT-TTTTTATAATTAA
317288 -ATTT
1 TATTT
317292 AAATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTAATTTTTTATAATTAA
Found at i:320066 original size:19 final size:18
Alignment explanation
Indices: 320042--320131 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 18
320032 GAAAAAAATA
320042 AAATATTATATAAATATAT
1 AAATATTATA-AAATATAT
*
320061 AAATATTTTAAAATTTATAT
1 AAATATTATAAAA--TATAT
*
320081 AATATAAATTATTAAAAAAT-T
1 AA-AT--ATTA-TAAAATATAT
320102 AAA-ATTTATAAAATATA-
1 AAATA-TTATAAAATATAT
*
320119 AAATATTTTAAAA
1 AAATATTATAAAA
320132 ATTATATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
17 18 0.32
18 7 0.12
19 9 0.16
20 8 0.14
21 5 0.09
22 2 0.04
23 3 0.05
24 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATTATAAAATATAT
Found at i:320080 original size:60 final size:59
Alignment explanation
Indices: 320016--320148 Score: 166
Period size: 58 Copynumber: 2.3 Consensus size: 59
320006 TAATAATATA
* *
320016 TATATAAATAT-GATT-TGAAAAAAATAAAATATTATATAAATATATAAATATTTTAAAATT
1 TATATAAATATAAATTATGAAAAAAATAAAAT-TTATA-AAATATA-AAATATTTTAAAAAT
* *
320076 TATAT-AATATAAATTATTAAAAAATTAAAATTTATAAAATATAAAATATTTTAAAAAT
1 TATATAAATATAAATTATGAAAAAAATAAAATTTATAAAATATAAAATATTTTAAAAAT
*
320134 TATAT-AATAAAAATT
1 TATATAAATATAAATT
320149 TTATATAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
58 28 0.42
59 12 0.18
60 13 0.20
61 13 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (59 bp):
TATATAAATATAAATTATGAAAAAAATAAAATTTATAAAATATAAAATATTTTAAAAAT
Found at i:320089 original size:25 final size:25
Alignment explanation
Indices: 320057--320151 Score: 86
Period size: 32 Copynumber: 3.6 Consensus size: 25
320047 TTATATAAAT
320057 ATATAAATATTTTAAAATTTATATA
1 ATATAAATATTTTAAAATTTATATA
*
320082 ATATAAATTATTAAAAAATTAAAATTTATAAA
1 ATATAAA-TATT------TTAAAATTTATATA
*
320114 ATATAAAATATTTTAAAAATTATATA
1 ATAT-AAATATTTTAAAATTTATATA
320140 ATA-AAA-ATTTTA
1 ATATAAATATTTTA
320152 TATAAATAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
23 6 0.10
24 3 0.05
25 7 0.12
26 19 0.32
32 21 0.36
33 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATAAATATTTTAAAATTTATATA
Found at i:320107 original size:32 final size:33
Alignment explanation
Indices: 320068--320135 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
320058 TATAAATATT
* *
320068 TTAAAATTTATATAATATAAATTA-TTAAAAAA
1 TTAAAATTTATAAAATATAAAATATTTAAAAAA
*
320100 TTAAAATTTATAAAATATAAAATATTTTAAAAA
1 TTAAAATTTATAAAATATAAAATATTTAAAAAA
320133 TTA
1 TTA
320136 TATAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TTAAAATTTATAAAATATAAAATATTTAAAAAA
Found at i:320131 original size:58 final size:61
Alignment explanation
Indices: 320033--320148 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 61
320023 ATATGATTTG
* *
320033 AAAAAAATAAAATATTATATAAATATATAAATATTTTAAAATTTATATAATATAAATTATT
1 AAAAAAATAAAATATTATATAAATATATAAATATTTTAAAAATTATATAATAAAAATTATT
*
320094 AAAAAATTAAAAT-TTATA-AAATATA-AAATATTTTAAAAATTATATAATAAAAATT
1 AAAAAAATAAAATATTATATAAATATATAAATATTTTAAAAATTATATAATAAAAATT
320149 TTATATAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 28 0.54
59 7 0.13
60 5 0.10
61 12 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (61 bp):
AAAAAAATAAAATATTATATAAATATATAAATATTTTAAAAATTATATAATAAAAATTATT
Found at i:320760 original size:2 final size:2
Alignment explanation
Indices: 320753--320778 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
320743 CAATAATGAC
320753 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
320779 GCTTGGATTC
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:320860 original size:22 final size:22
Alignment explanation
Indices: 320835--320900 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
320825 GATCATTAAA
320835 GATATTTAATTAAAATATATAT
1 GATATTTAATTAAAATATATAT
**
320857 GATAAATAATTAAAA-ATATAT
1 GATATTTAATTAAAATATATAT
* *
320878 TATATTAAATAATAAAAT-TATAT
1 GATATTTAAT--TAAAATATATAT
320901 TTATGTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 12 0.34
22 13 0.37
23 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
GATATTTAATTAAAATATATAT
Found at i:320876 original size:23 final size:23
Alignment explanation
Indices: 320841--320900 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
320831 TAAAGATATT
320841 TAATT-AAAATATATATGA-TAAA
1 TAATTAAAAATATATAT-ATTAAA
320863 TAATTAAAAATATATTATATTAAA
1 TAATTAAAAATATA-TATATTAAA
*
320887 TAA-TAAAATTATAT
1 TAATTAAAAATATAT
320901 TTATGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 6 0.18
23 18 0.53
24 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATTAAAAATATATATATTAAA
Found at i:320923 original size:28 final size:27
Alignment explanation
Indices: 320850--320940 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
320840 TTAATTAAAA
*
320850 TATATATGATAAATAATTAAAAATATA-T
1 TATAT-TGA-AAATAATTAAAATTATATT
320878 TATATT--AAATAA-TAAAATTATATT
1 TATATTGAAAATAATTAAAATTATATT
* *
320902 TATGTTGAATAATAATTAAAATTATGTT
1 TATATTGAA-AATAATTAAAATTATATT
320930 TATATTGAAAA
1 TATATTGAAAA
320941 AACATAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.17
24 12 0.22
26 1 0.02
27 8 0.15
28 24 0.44
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
TATATTGAAAATAATTAAAATTATATT
Found at i:320926 original size:22 final size:21
Alignment explanation
Indices: 320888--320929 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
320878 TATATTAAAT
* *
320888 AATAAAATTATATTTATGTTG
1 AATAAAATTAAAATTATGTTG
320909 AATAATAATTAAAATTATGTT
1 AATAA-AATTAAAATTATGTT
320930 TATATTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
AATAAAATTAAAATTATGTTG
Found at i:322639 original size:23 final size:25
Alignment explanation
Indices: 322593--322650 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
322583 TTTAAATAAA
* *
322593 ATATTATATTATATATTTTTTATT-
1 ATATTATATTATAAATTTTGTATTC
322617 A-ATTATATT-TAAATTATTGTATTC
1 ATATTATATTATAAATT-TTGTATTC
322641 ATATTATATT
1 ATATTATATT
322651 CAAAATTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 2 0.07
25 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
ATATTATATTATAAATTTTGTATTC
Found at i:323322 original size:17 final size:18
Alignment explanation
Indices: 323286--323332 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
323276 TTTAAGATTT
* *
323286 TTTTATCAATTAAATTAA
1 TTTTATCAATTTAATCAA
323304 TTTTAT-AATTTAATCAA
1 TTTTATCAATTTAATCAA
*
323321 TTTTATGAATTT
1 TTTTATCAATTT
323333 TAAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTATCAATTTAATCAA
Found at i:325345 original size:26 final size:26
Alignment explanation
Indices: 325316--325368 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
325306 TCTTTTTCTT
325316 TTTGTTTTTTAGCAATGGCATGATAA
1 TTTGTTTTTTAGCAATGGCATGATAA
325342 TTTGTTTTTTAGCAATGGCATGATAA
1 TTTGTTTTTTAGCAATGGCATGATAA
325368 T
1 T
325369 CTATAGCTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (26 bp):
TTTGTTTTTTAGCAATGGCATGATAA
Found at i:329709 original size:4 final size:4
Alignment explanation
Indices: 329700--329732 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
329690 AAATAACAGC
329700 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
329733 AATTTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:330749 original size:107 final size:107
Alignment explanation
Indices: 330557--330750 Score: 282
Period size: 107 Copynumber: 1.8 Consensus size: 107
330547 CAACCAATGG
* *
330557 GACCTTATCTAATCACCTTATTTCTTTTCCATTTTAAAGAGCAAACTAGGAAATTTTATTTTTAA
1 GACCTTATCTAATCACCTTATTCCTTTTCCATTTTAAAGAGCAAACTAGGAAATTTTAGTTTTAA
* *
330622 ACTTCAATAAATATTTTTTTTTTGAAAAAAATGCTATTATGA
66 ACTTAAATAAATATTATTTTTTTGAAAAAAATGCTATTATGA
* * * * * *
330664 GACCTTATTTAGTCACCTTATTCCTTTTCCATTTTAAGGAGTAAAGTAGGAAATTTTCGTTTTAA
1 GACCTTATCTAATCACCTTATTCCTTTTCCATTTTAAAGAGCAAACTAGGAAATTTTAGTTTTAA
330729 ACCTTAAATAAATA-TATTTTTT
66 A-CTTAAATAAATATTATTTTTT
330751 AAAAAATATA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
107 65 0.86
108 11 0.14
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (107 bp):
GACCTTATCTAATCACCTTATTCCTTTTCCATTTTAAAGAGCAAACTAGGAAATTTTAGTTTTAA
ACTTAAATAAATATTATTTTTTTGAAAAAAATGCTATTATGA
Found at i:331283 original size:3 final size:3
Alignment explanation
Indices: 331275--331304 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
331265 TTTACCCATA
331275 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
331305 GAATTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.