Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1307
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: 60358
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:107 original size:22 final size:23
Alignment explanation
Indices: 82--127 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
72 AAAATAATGT
*
82 ATTAAATA-TAAAAAAATTTTAA
1 ATTAAAAACTAAAAAAATTTTAA
* *
104 ATTAAAAACTAAATAATTTTTAA
1 ATTAAAAACTAAAAAAATTTTAA
127 A
1 A
128 CTTATACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTAAAAACTAAAAAAATTTTAA
Found at i:443 original size:2 final size:2
Alignment explanation
Indices: 436--466 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
426 GATCAAACCA
436 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 A
467 ATTGTGGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:559 original size:2 final size:2
Alignment explanation
Indices: 512--540 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
502 TCACAAACCA
512 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 A
541 ATTGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1073 original size:28 final size:29
Alignment explanation
Indices: 1002--1087 Score: 129
Period size: 30 Copynumber: 3.0 Consensus size: 29
992 TTATATATAT
* *
1002 TTTATAGATTATAGATAACAATAGTAATA
1 TTTATAGATTATAGATGATAATAGTAATA
1031 TTTTATAGATTATAGATGATAATAGTAATA
1 -TTTATAGATTATAGATGATAATAGTAATA
*
1061 -TTATAGATTATAGATGATAATACTAAT
1 TTTATAGATTATAGATGATAATAGTAAT
1088 TACAGCTCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
28 26 0.49
30 27 0.51
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTATAGATTATAGATGATAATAGTAATA
Found at i:1330 original size:10 final size:9
Alignment explanation
Indices: 1315--1428 Score: 74
Period size: 10 Copynumber: 11.8 Consensus size: 9
1305 TGAATACATG
1315 ATATAATAA
1 ATATAATAA
1324 TATATAA-AA
1 -ATATAATAA
1333 ATATAATTAA
1 ATATAA-TAA
1343 ATATAATAGCAA
1 ATATAAT---AA
1355 ATATAATAA
1 ATATAATAA
1364 TATATAA-AA
1 -ATATAATAA
1373 A-ATAATACGA
1 ATATAATA--A
1383 ATATAATATA
1 ATATAATA-A
1393 A-ATATATAA
1 ATATA-ATAA
*
1402 ATATATTAA
1 ATATAATAA
*
1411 ATATTTATATA
1 ATA-TAATA-A
1422 ATATAAT
1 ATATAAT
1429 TATTAATATA
Statistics
Matches: 85, Mismatches: 5, Indels: 28
0.72 0.04 0.24
Matches are distributed among these distances:
7 4 0.05
8 8 0.09
9 18 0.21
10 36 0.42
11 10 0.12
12 9 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (9 bp):
ATATAATAA
Found at i:1360 original size:40 final size:38
Alignment explanation
Indices: 1300--1407 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 38
1290 ACTTTAAATG
*
1300 CAATATGAATACATGATATAATAATATATAAAAATATAATTA
1 CAATAT-AATACA-AATATAATAATATATAAAAA-ATAA-TA
1342 -AATATAATAGCAAATATAATAATATATAAAAAATAATA
1 CAATATAATA-CAAATATAATAATATATAAAAAATAATA
*
1380 CGAATATAATATAAATAT-ATAAATATAT
1 C-AATATAATACAAATATAAT-AATATAT
1408 TAAATATTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
38 4 0.07
39 17 0.28
40 32 0.53
41 7 0.12
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (38 bp):
CAATATAATACAAATATAATAATATATAAAAAATAATA
Found at i:1401 original size:8 final size:8
Alignment explanation
Indices: 1388--1487 Score: 62
Period size: 8 Copynumber: 11.9 Consensus size: 8
1378 TACGAATATA
1388 ATATAAAT
1 ATATAAAT
1396 ATATAAAT
1 ATATAAAT
1404 ATATTAAAT
1 ATA-TAAAT
* *
1413 ATTTATAT
1 ATATAAAT
1421 A-ATATAAT
1 ATATA-AAT
*
1429 -TATTAAT
1 ATATAAAT
1436 ATATTAAATTT
1 ATA-TAAA--T
1447 ATATAAAT
1 ATATAAAT
*
1455 AGAT-AAT
1 ATATAAAT
1462 ATATTAAAT
1 ATA-TAAAT
*
1471 ACGTAAAAAT
1 A--TATAAAT
1481 ATATAAA
1 ATATAAA
1488 AAAAATACAC
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
7 10 0.14
8 32 0.45
9 14 0.20
10 9 0.13
11 6 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:1411 original size:17 final size:17
Alignment explanation
Indices: 1391--1471 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 17
1381 GAATATAATA
1391 TAAATATATAAATATAT
1 TAAATATATAAATATAT
1408 TAAATATTTATATAATATAAT
1 TAAATA--TATA-AATAT-AT
*
1429 TATTAATATATTAAATTTAT
1 TA--AATATA-TAAATATAT
*
1449 ATAAATAGAT-AATATAT
1 -TAAATATATAAATATAT
1466 TAAATA
1 TAAATA
1472 CGTAAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 6 0.11
17 12 0.23
18 1 0.02
19 9 0.17
20 7 0.13
21 12 0.23
22 2 0.04
23 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATATATAAATATAT
Found at i:1426 original size:34 final size:32
Alignment explanation
Indices: 1383--1471 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 32
1373 AATAATACGA
1383 ATATAATATAAATATATAAATATATTAAATATTT
1 ATATAATATAAATATATAAATATATT-AA-ATTT
*
1417 ATATAATAT-AAT-TATTAATATATTAAATTT
1 ATATAATATAAATATATAAATATATTAAATTT
*
1447 ATATAAATAGATAATATATTAAATA
1 ATAT-AATATA-AATATA-TAAATA
1472 CGTAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 8 0.17
31 6 0.13
32 11 0.23
33 6 0.13
34 11 0.23
35 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATATATAAATATATTAAATTT
Found at i:1430 original size:21 final size:18
Alignment explanation
Indices: 1382--1471 Score: 62
Period size: 19 Copynumber: 4.8 Consensus size: 18
1372 AAATAATACG
1382 AATATAATATAAATATATA
1 AATATAAT-TAAATATATA
1401 AATAT-ATTAAATATTTATA
1 AATATAATTAAATA--TATA
1420 TAATATAATTATTAATATATTA
1 -AATATAATTA--AATATA-TA
* *
1442 AAT-TTATATAAATAGAT-
1 AATATAAT-TAAATATATA
1459 AATAT-ATTAAATA
1 AATATAATTAAATA
1472 CGTAAAAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 21
0.72 0.02 0.25
Matches are distributed among these distances:
16 6 0.10
17 11 0.18
18 4 0.07
19 14 0.23
20 8 0.13
21 11 0.18
22 2 0.03
23 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
AATATAATTAAATATATA
Found at i:1465 original size:26 final size:26
Alignment explanation
Indices: 1388--1470 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 26
1378 TACGAATATA
1388 ATATAAATATATAAATATATTAAATATTT
1 ATATAAATATAT-AATATATT-AA-ATTT
1417 ATATAATATAATTATTAATATATTAAATTT
1 ATATAA-AT-A-TA-TAATATATTAAATTT
*
1447 ATATAAATAGATAATATATTAAAT
1 ATATAAATATATAATATATTAAAT
1471 ACGTAAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
26 13 0.27
27 1 0.02
28 1 0.02
29 8 0.16
30 12 0.24
31 3 0.06
32 10 0.20
33 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATAAATATATAATATATTAAATTT
Found at i:1480 original size:26 final size:26
Alignment explanation
Indices: 1432--1486 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1422 ATATAATTAT
** *
1432 TAATATATTAAATTTATATAAATAGA
1 TAATATATTAAATACATAAAAATAGA
* *
1458 TAATATATTAAATACGTAAAAATATA
1 TAATATATTAAATACATAAAAATAGA
1484 TAA
1 TAA
1487 AAAAAATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
TAATATATTAAATACATAAAAATAGA
Found at i:2313 original size:15 final size:16
Alignment explanation
Indices: 2293--2329 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
2283 ATTTATGCAC
2293 ATATATGTATATACA-
1 ATATATGTATATACAT
2308 ATATATGTATATACAT
1 ATATATGTATATACAT
2324 ATATAT
1 ATATAT
2330 ATAATCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (16 bp):
ATATATGTATATACAT
Found at i:3245 original size:21 final size:20
Alignment explanation
Indices: 3211--3253 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3201 ATTTTTTATT
3211 TAAATTTAATTATAAAATTAA
1 TAAATTTAATTATAAAA-TAA
3232 TAAATATTAA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
3252 TA
1 TA
3254 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 12 0.57
22 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTAATTATAAAATAA
Found at i:3271 original size:35 final size:36
Alignment explanation
Indices: 3231--3335 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 36
3221 TATAAAATTA
3231 ATAAATATTAATATAAAATAATATTTTATTAAAT-T
1 ATAAATATTAATATAAAATAATATTTTATTAAATAT
* * * * * * *
3266 TTAAATAATAATTTAAATTACTATAATTATAAAATAT
1 ATAAATATTAATATAAAATAATAT-TTTATTAAATAT
*
3303 AAAAATATTAATATAAAAATAATATTTT-TTAAA
1 ATAAATATTAATAT-AAAATAATATTTTATTAAA
3336 ATAGTAATTT
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
35 19 0.37
36 12 0.23
37 13 0.25
38 8 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
ATAAATATTAATATAAAATAATATTTTATTAAATAT
Found at i:6565 original size:17 final size:16
Alignment explanation
Indices: 6533--6581 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
6523 AATGACAGAT
* *
6533 TTTTAAAATAAGATTA
1 TTTTAAATTAAAATTA
6549 CTTTTAAATTAAAATTA
1 -TTTTAAATTAAAATTA
*
6566 TTTGAAATT-AAATTA
1 TTTTAAATTAAAATTA
6581 T
1 T
6582 GGTACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (16 bp):
TTTTAAATTAAAATTA
Found at i:7146 original size:10 final size:10
Alignment explanation
Indices: 7111--7264 Score: 51
Period size: 10 Copynumber: 16.1 Consensus size: 10
7101 TAGATCTAAT
7111 TATTTTTATA
1 TATTTTTATA
* *
7121 AATTTGTATCA
1 TATTTTTAT-A
7132 -A-TTTTATA
1 TATTTTTATA
*
7140 TATTTTTAAA
1 TATTTTTATA
* *
7150 TATTATAAT-
1 TATTTTTATA
*
7159 TATATTTA-A
1 TATTTTTATA
* *
7168 -AATATTATA
1 TATTTTTATA
7177 TA--TTTATA
1 TATTTTTATA
*
7185 TATTTTAATA
1 TATTTTTATA
**
7195 TATTAATA-A
1 TATTTTTATA
* *
7204 TTAATATTATA
1 -TATTTTTATA
*
7215 TAAATTTTA-A
1 T-ATTTTTATA
*
7225 TATATTTATA
1 TATTTTTATA
7235 TATTTTTATCA
1 TATTTTTAT-A
7246 TA--TTTATA
1 TATTTTTATA
*
7254 TTTTTTTATA
1 TATTTTTATA
7264 T
1 T
7265 TATGTCATAT
Statistics
Matches: 104, Mismatches: 25, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
8 14 0.13
9 23 0.22
10 56 0.54
11 11 0.11
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TATTTTTATA
Found at i:7172 original size:20 final size:20
Alignment explanation
Indices: 7147--7232 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
7137 ATATATTTTT
7147 AAATATTATAATTATATTTA
1 AAATATTATAATTATATTTA
7167 AAATATTATATATTTATATATTTTA
1 AAATATTATA-A--T-TATA-TTTA
*
7192 ATATATTAATAATTAATATTATA
1 AAATATT-ATAATT-ATATT-TA
7215 TAAAT-TT-TAA-TATATTTA
1 -AAATATTATAATTATATTTA
7233 TATATTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 11 0.20
21 4 0.07
22 3 0.05
23 9 0.16
24 7 0.13
25 11 0.20
26 3 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTATAATTATATTTA
Found at i:7185 original size:8 final size:8
Alignment explanation
Indices: 7134--7265 Score: 62
Period size: 8 Copynumber: 16.2 Consensus size: 8
7124 TTGTATCAAT
7134 TTTATATA
1 TTTATATA
* *
7142 TTTTTAAA
1 TTTATATA
7150 TATTATA-A
1 T-TTATATA
7158 -TTATAT-
1 TTTATATA
* *
7164 TTAAAATA
1 TTTATATA
7172 -TTATATA
1 TTTATATA
7179 TTTATATA
1 TTTATATA
7187 TTT-TAATA
1 TTTAT-ATA
7195 TATTA-ATA
1 T-TTATATA
*
7203 ATTA-ATA
1 TTTATATA
*
7210 TTATATAAA
1 TT-TATATA
7219 TTTTAATATA
1 -TTT-ATATA
7229 TTTATATA
1 TTTATATA
7237 TTTTTATCATA
1 --TTTAT-ATA
*
7248 TTTATATT
1 TTTATATA
*
7256 TTTTTATA
1 TTTATATA
7264 TT
1 TT
7266 ATGTCATATT
Statistics
Matches: 95, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.05
7 17 0.18
8 42 0.44
9 17 0.18
10 11 0.12
11 3 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:7233 original size:20 final size:18
Alignment explanation
Indices: 7114--7264 Score: 88
Period size: 19 Copynumber: 8.4 Consensus size: 18
7104 ATCTAATTAT
* *
7114 TTTTATAAATTTGTATCAA
1 TTTTATATATTTATAT-AA
*
7133 TTTTATATATTTTTA-AA
1 TTTTATATATTTATATAA
7150 TATTATAATTATATTTA-A-AA
1 T-TT-T-A-TATATTTATATAA
*
7170 TATTATATATTTATAT-A
1 TTTTATATATTTATATAA
7187 TTTTA-ATATATTA-ATAA
1 TTTTATATAT-TTATATAA
7204 --TTA-ATA-TTATATAAA
1 TTTTATATATTTATAT-AA
*
7219 TTTTAATATATTTATATAT
1 TTTT-ATATATTTATATAA
**
7238 TTTTATCATATTTATATTT
1 TTTTAT-ATATTTATATAA
7257 TTTTATAT
1 TTTTATAT
7265 TATGTCATAT
Statistics
Matches: 109, Mismatches: 7, Indels: 33
0.73 0.05 0.22
Matches are distributed among these distances:
13 3 0.03
14 2 0.02
15 8 0.07
16 14 0.13
17 16 0.15
18 8 0.07
19 40 0.37
20 11 0.10
21 7 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (18 bp):
TTTTATATATTTATATAA
Found at i:7286 original size:26 final size:26
Alignment explanation
Indices: 7243--7293 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
7233 TATATTTTTA
7243 TCATATTTATATTTTTTTATATTATG
1 TCATATTTATATTTTTTTATATTATG
*
7269 TCATATTT-TATTTATTTTTTATTAT
1 TCATATTTATATTT-TTTTATATTAT
7294 ATTTATATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (26 bp):
TCATATTTATATTTTTTTATATTATG
Found at i:7295 original size:21 final size:21
Alignment explanation
Indices: 7219--7297 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
7209 ATTATATAAA
* *
7219 TTTTAATATA-TTTATATA-T
1 TTTTATTATATTTTATTTATT
* *
7238 TTTTATCATATTTATATTTTTT
1 TTTTATTATATTT-TATTTATT
7260 TATATTATGTCATATTTTATTTATT
1 T-T-TTAT-T-ATATTTTATTTATT
7285 TTTTATTATATTT
1 TTTTATTATATTT
7298 ATATCATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
19 8 0.17
20 2 0.04
21 10 0.21
22 3 0.06
23 5 0.11
24 5 0.11
25 8 0.17
26 6 0.13
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (21 bp):
TTTTATTATATTTTATTTATT
Found at i:8108 original size:31 final size:31
Alignment explanation
Indices: 8073--8134 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
8063 TTTACATAGT
8073 CGAATATTCGCCTTTTTTTGTACTAAAAACC
1 CGAATATTCGCCTTTTTTTGTACTAAAAACC
*
8104 CGAATATTCTCCTTTTTTTGTACTAAAAACC
1 CGAATATTCGCCTTTTTTTGTACTAAAAACC
8135 TAAAATTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (31 bp):
CGAATATTCGCCTTTTTTTGTACTAAAAACC
Found at i:8620 original size:6 final size:6
Alignment explanation
Indices: 8609--8646 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
8599 TGAAAGTTAT
*
8609 TTGTAA TTGTAA TTGTAAA TTTTAA TTGTAA TTGTAA T
1 TTGTAA TTGTAA TTGT-AA TTGTAA TTGTAA TTGTAA T
8647 AATTACATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (6 bp):
TTGTAA
Found at i:8636 original size:19 final size:20
Alignment explanation
Indices: 8607--8645 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
8597 TTTGAAAGTT
8607 ATTTGTAATTGTAATTGTAA
1 ATTTGTAATTGTAATTGTAA
8627 ATTT-TAATTGTAATTGTAA
1 ATTTGTAATTGTAATTGTAA
8646 TAATTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTTGTAATTGTAATTGTAA
Found at i:9347 original size:17 final size:16
Alignment explanation
Indices: 9317--9362 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
9307 TAATTTCATG
9317 ATTATAAA-TATATTT
1 ATTATAAATTATATTT
*
9332 TTTATTAAATTATATTT
1 ATTA-TAAATTATATTT
9349 ATTAT-AATTATATT
1 ATTATAAATTATATT
9363 ATTTCGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 5 0.19
17 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATAAATTATATTT
Found at i:9892 original size:11 final size:11
Alignment explanation
Indices: 9876--9924 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
9866 AATTATGATT
9876 ATATAAATATA
1 ATATAAATATA
*
9887 ATATAAAAATA
1 ATATAAATATA
9898 AT-TAAAATATA
1 ATAT-AAATATA
9909 ATAT-AATATTA
1 ATATAAATA-TA
9920 ATATA
1 ATATA
9925 TAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.16
11 26 0.81
12 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:9921 original size:22 final size:24
Alignment explanation
Indices: 9875--9931 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 24
9865 TAATTATGAT
9875 TATATAAATATAATATAAAAATAA
1 TATATAAATATAATATAAAAATAA
* *
9899 T-TA-AAATATAATATAATATTAA
1 TATATAAATATAATATAAAAATAA
9921 TATATAAATAT
1 TATATAAATAT
9932 TTTAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.62
23 4 0.14
24 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TATATAAATATAATATAAAAATAA
Found at i:9969 original size:32 final size:33
Alignment explanation
Indices: 9874--9979 Score: 119
Period size: 33 Copynumber: 3.2 Consensus size: 33
9864 TTAATTATGA
*
9874 TTATATAA-ATATAATATAAAAATA-ATTAAAAT
1 TTATATAATAT-TAATATATAAATATATTAAAAT
* *
9906 ATAATATAATATTAATATATAAATATTTTAAAAT
1 -TTATATAATATTAATATATAAATATATTAAAAT
* * *
9940 TTATATAATA-TATTTTATTAATATATTAAAAT
1 TTATATAATATTAATATATAAATATATTAAAAT
9972 TTATATAA
1 TTATATAA
9980 AAATATAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
32 26 0.41
33 28 0.44
34 9 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TTATATAATATTAATATATAAATATATTAAAAT
Found at i:9974 original size:18 final size:18
Alignment explanation
Indices: 9887--10001 Score: 58
Period size: 18 Copynumber: 6.1 Consensus size: 18
9877 TATAAATATA
* *
9887 ATATAAAAATAATTAAA-
1 ATATAAAATTTATTAAAT
* *
9904 ATATAATATAATATT-AAT
1 ATATAAAAT-TTATTAAAT
*
9922 ATATAAATATTT-TAAAATTT
1 ATATAAA-ATTTATTAAA--T
9942 ATATAATATATTTTATT-AAT
1 ATATAA-A-A-TTTATTAAAT
*
9962 ATATTAAAATTTATATAAAA
1 ATA-TAAAATTTAT-TAAAT
*
9982 ATATAAAATTTTTTAAAT
1 ATATAAAATTTATTAAAT
10000 AT
1 AT
10002 GATTATGATA
Statistics
Matches: 75, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
17 10 0.13
18 23 0.31
19 13 0.17
20 17 0.23
21 6 0.08
22 5 0.07
23 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAAAATTTATTAAAT
Found at i:9986 original size:40 final size:39
Alignment explanation
Indices: 9901--10001 Score: 92
Period size: 40 Copynumber: 2.7 Consensus size: 39
9891 AAAAATAATT
*
9901 AAAATATAATATA--ATATTAATATA-TAAATATTTTAA
1 AAAATATAATATATTTTATTAATATATTAAATATTTTAA
*
9937 AATTTATATAATATATTTTATTAATATATTAAA-ATTTATATA
1 AA--AATATAATATATTTTATTAATATATTAAATATTT-TA-A
9979 AAAATATAA-A-ATTTT-TTAA-ATAT
1 AAAATATAATATATTTTATTAATATAT
10002 GATTATGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
36 6 0.11
37 4 0.07
38 15 0.27
39 1 0.02
40 20 0.36
41 6 0.11
42 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (39 bp):
AAAATATAATATATTTTATTAATATATTAAATATTTTAA
Found at i:10660 original size:21 final size:21
Alignment explanation
Indices: 10634--10674 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10624 ATTATTTTTA
10634 ATAAAT-TTAATTATAAAATAT
1 ATAAATCTTAA-TATAAAATAT
10655 ATAAATCTTAATATAAAATA
1 ATAAATCTTAATATAAAATA
10675 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAATCTTAATATAAAATAT
Found at i:10686 original size:19 final size:20
Alignment explanation
Indices: 10634--10687 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
10624 ATTATTTTTA
10634 ATAAATTTAATTATAAAATAT
1 ATAAATTTAA-TATAAAATAT
10655 ATAAATCTTAATATAAAATA-
1 ATAAAT-TTAATATAAAATAT
**
10675 ATTTATTTAATAT
1 ATAAATTTAATAT
10688 TTTAATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 15 0.50
22 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTTAATATAAAATAT
Found at i:10893 original size:11 final size:12
Alignment explanation
Indices: 10873--10906 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10863 TAAAATAAAT
10873 ATAATATAAAAA
1 ATAATATAAAAA
10885 ATAAT-TAAAAA
1 ATAATATAAAAA
*
10896 ATTATATAAAA
1 ATAATATAAAA
10907 CTTGACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATATAAAAA
Found at i:12103 original size:11 final size:11
Alignment explanation
Indices: 12087--12123 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
12077 TTATTACTTT
12087 TTATTTATAAA
1 TTATTTATAAA
* *
12098 TTATTTTTAAT
1 TTATTTATAAA
12109 TTATTTATAAA
1 TTATTTATAAA
12120 TTAT
1 TTAT
12124 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:12521 original size:298 final size:299
Alignment explanation
Indices: 12059--12617 Score: 924
Period size: 298 Copynumber: 1.9 Consensus size: 299
12049 TATTATTTTT
12059 ATTAATATTATACATGTATTATTACTTTTTATTTATAAATTATTTTTAATTTATTTATAAATTAT
1 ATTAATATTATACATGTATTATTACTTTTTATTTATAAATTATTTTTAATTTATTTATAAATTAT
* *
12124 ACAAATTTATTTTTATTAAAAAAATTAATTAATATTGTATATGTATTATTTTTATAATTGATAGA
66 ACAAATTTATTTTTATT--AAAAATTAATTAATATTATACATGTATTATTTTTATAATTGATAGA
* * * **
12189 ACTTAAATTTATGTTAGCCAATAATATTTTACTTTTTTCGATAATGACTTATTTCGGA-TTACAA
129 ACTTAAATTTATGTTAACCAATAATATATTACTTTTTTCGATAACGACTTATTTCAAATTTACAA
* * * * *
12253 CCGCACACATTTTATTTTTCGGTAACGACTTAAATATGAGCTTTCTTTTATTTGTAAAGTGACCA
194 ACGCACACATTTTATTTTTCGGTAACAACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACCA
12318 AGAGAAAATTTATTATACATGTATTATTTTTATTAAAATTA
259 AGAGAAAATTTATTATACATGTATTATTTTTATTAAAATTA
* * *
12359 ATTAATATTGTGCATGTATTATTATTTTTTATTTATAAATTATTTTTAATTTTATTTATAAATTA
1 ATTAATATTATACATGTATTATTACTTTTTATTTATAAATTATTTTTAA-TTTATTTATAAATTA
12424 TACAAATTTATTTTTATT-AAAATTAATTAATATTATACATGTATTATTTTTATAATTGATAGAA
65 TACAAATTTATTTTTATTAAAAATTAATTAATATTATACATGTATTATTTTTATAATTGATAGAA
12488 CTTAAATTTATGTTAACCAATAATATATTACTTTTTTCGATAACGACTTATTTCAAATTTACAAA
130 CTTAAATTTATGTTAACCAATAATATATTACTTTTTTCGATAACGACTTATTTCAAATTTACAAA
* *
12553 CGCACACATTTTATTTTTTGGTAATAACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACCAA
195 CGCACACATTTTATTTTTCGGTAACAACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACCAA
12618 AATGAAGTAA
Statistics
Matches: 240, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
298 96 0.40
299 65 0.27
300 46 0.19
301 33 0.14
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.48
Consensus pattern (299 bp):
ATTAATATTATACATGTATTATTACTTTTTATTTATAAATTATTTTTAATTTATTTATAAATTAT
ACAAATTTATTTTTATTAAAAATTAATTAATATTATACATGTATTATTTTTATAATTGATAGAAC
TTAAATTTATGTTAACCAATAATATATTACTTTTTTCGATAACGACTTATTTCAAATTTACAAAC
GCACACATTTTATTTTTCGGTAACAACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACCAAG
AGAAAATTTATTATACATGTATTATTTTTATTAAAATTA
Found at i:12698 original size:16 final size:17
Alignment explanation
Indices: 12661--12698 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
12651 ATTAAATACG
12661 TAATATTTATTAAAAAT
1 TAATATTTATTAAAAAT
* *
12678 AAATATTT-TTAATAAT
1 TAATATTTATTAAAAAT
12694 TAATA
1 TAATA
12699 AAATTTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTATTAAAAAT
Found at i:13724 original size:22 final size:22
Alignment explanation
Indices: 13694--13740 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
13684 GTTAACAAAT
*
13694 AAAAATAAAAA-TTTATTTTTC
1 AAAAATAAAAACATTATTTTTC
13715 AAAAACTAAAAACATTATTTTTC
1 AAAAA-TAAAAACATTATTTTTC
13738 AAA
1 AAA
13741 TAGAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 6 0.26
23 12 0.52
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATAAAAACATTATTTTTC
Found at i:14417 original size:20 final size:22
Alignment explanation
Indices: 14371--14418 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
14361 AATACGGTTA
14371 AAAATGATTTTAAAATCAATAG
1 AAAATGATTTTAAAATCAATAG
14393 AAAATGA-TTTAAAAT-AATAG
1 AAAATGATTTTAAAATCAATAG
*
14413 TAAATG
1 AAAATG
14419 TACTTTAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.40
21 8 0.32
22 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAATGATTTTAAAATCAATAG
Found at i:18461 original size:44 final size:44
Alignment explanation
Indices: 18411--18501 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
18401 TACTCCATCT
18411 GATAGCAAGGATACCACATTCAAGACATGGGAGGCTGAAAACTC
1 GATAGCAAGGATACCACATTCAAGACATGGGAGGCTGAAAACTC
*
18455 GATAGCAAGGATACCACATTCAAGATATGGGAGGCTGAAAACTC
1 GATAGCAAGGATACCACATTCAAGACATGGGAGGCTGAAAACTC
18499 GAT
1 GAT
18502 CGTTATATCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (44 bp):
GATAGCAAGGATACCACATTCAAGACATGGGAGGCTGAAAACTC
Found at i:24789 original size:16 final size:17
Alignment explanation
Indices: 24738--24792 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
24728 TATTTAATCT
* *
24738 AAATTCAAAAATAATTT
1 AAATTCAAATATAATTA
* *
24755 GAATTCAAATATGATTA
1 AAATTCAAATATAATTA
24772 AAATTCAAATA-AATTA
1 AAATTCAAATATAATTA
24788 AAATT
1 AAATT
24793 AATAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (17 bp):
AAATTCAAATATAATTA
Found at i:24829 original size:13 final size:15
Alignment explanation
Indices: 24797--24827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24787 AAAATTAATA
24797 ATAAAATATATATTT
1 ATAAAATATATATTT
*
24812 ATAAAATATGTATTT
1 ATAAAATATATATTT
24827 A
1 A
24828 AATATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATAAAATATATATTT
Found at i:24988 original size:25 final size:24
Alignment explanation
Indices: 24960--25012 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
24950 ATTATTGAAA
24960 TTAAAATAAATAAAATAAAATATAT
1 TTAAAATAAATAAAATAAAA-ATAT
* ***
24985 TTAAACTTCTTAAAATAAAAATAT
1 TTAAAATAAATAAAATAAAAATAT
25009 TTAA
1 TTAA
25013 TATTTTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAATAAATAAAATAAAAATAT
Found at i:25093 original size:17 final size:18
Alignment explanation
Indices: 25071--25104 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25061 TAAACATATC
*
25071 AAATATATATA-TATAAA
1 AAATATAGATACTATAAA
25088 AAATATAGATACTATAA
1 AAATATAGATACTATAA
25105 GGATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
AAATATAGATACTATAAA
Found at i:25291 original size:2 final size:2
Alignment explanation
Indices: 25282--25476 Score: 106
Period size: 2 Copynumber: 106.5 Consensus size: 2
25272 AATTTTTTTA
*
25282 AT AT -T AT AT AT AT AT AT GT -T AT AT -T AT AT AT -T AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
25318 AT AT AA AT AT AT AT AA AC A- ACT AC AT AT A- AT A- AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
25358 AA AT AT AT AA AT AC CT AT AT AT A- AT A- AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
25396 AT A- AT AT AT A- AT AT A- AT A- AT AT AT AT AGT GT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
25435 AT A- AT AT A- AT AT AT AC AT A- AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25474 AT A
1 AT A
25477 AAATTTTGTT
Statistics
Matches: 148, Mismatches: 23, Indels: 44
0.69 0.11 0.20
Matches are distributed among these distances:
1 20 0.14
2 126 0.85
3 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:25411 original size:27 final size:26
Alignment explanation
Indices: 25373--25476 Score: 74
Period size: 27 Copynumber: 3.9 Consensus size: 26
25363 TATAAATACC
25373 TATAT-ATAATAATATAATAATATATAA
1 TATATAAT-ATAATAT-ATAATATATAA
*
25400 TATATAATATAATA-AT-ATATATAG
1 TATATAATATAATATATAATATATAA
* *
25424 TGTGT-ATATATATAATATAATATATACA
1 TATATAATATA-AT-ATATAATATATA-A
25452 TA-ATATATATATATATATACATATA
1 TATATA-ATATA-ATATATA-ATATA
25477 AAATTTTGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
23 5 0.08
24 12 0.19
25 3 0.05
26 2 0.03
27 19 0.31
28 8 0.13
29 13 0.21
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (26 bp):
TATATAATATAATATATAATATATAA
Found at i:25545 original size:10 final size:9
Alignment explanation
Indices: 25528--25570 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
25518 ATTTTATATG
*
25528 TTAAAAATT
1 TTAAAAAAT
25537 TTAAAAAA-
1 TTAAAAAAT
25545 TTAAAAAAT
1 TTAAAAAAT
25554 TTAAATAAA-
1 TTAAA-AAAT
25563 TTAAAAAA
1 TTAAAAAA
25571 ACTCGCCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 11 0.35
9 17 0.55
10 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:25553 original size:18 final size:18
Alignment explanation
Indices: 25528--25570 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
25518 ATTTTATATG
*
25528 TTAAAAATTTTAAA-AAA
1 TTAAAAAATTTAAATAAA
25545 TTAAAAAATTTAAATAAA
1 TTAAAAAATTTAAATAAA
25563 TTAAAAAA
1 TTAAAAAA
25571 ACTCGCCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAATTTAAATAAA
Found at i:25557 original size:9 final size:8
Alignment explanation
Indices: 25537--25570 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
25527 GTTAAAAATT
25537 TTAAAAAA
1 TTAAAAAA
25545 TTAAAAAA
1 TTAAAAAA
25553 TTTAAATAAA
1 -TTAAA-AAA
25563 TTAAAAAA
1 TTAAAAAA
25571 ACTCGCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 11 0.46
9 10 0.42
10 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:25644 original size:2 final size:2
Alignment explanation
Indices: 25637--25676 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
25627 TTCTCAATCG
* * *
25637 AT AT AT AT AG AT AA AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25677 TTTATTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:25710 original size:11 final size:11
Alignment explanation
Indices: 25656--25728 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
25646 GATAAATATA
*
25656 TATATATATATG
1 TATATATAT-TT
25668 TATATATATTT
1 TATATATATTT
* *
25679 TATTTATTTTT
1 TATATATATTT
*
25690 TAGAGT-TATTT
1 TATA-TATATTT
25701 TATATATATTT
1 TATATATATTT
25712 T-TA-ATATTAT
1 TATATATATT-T
25722 T-TATATA
1 TATATATA
25729 AAAGTTTTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
9 5 0.10
10 7 0.14
11 28 0.56
12 10 0.20
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (11 bp):
TATATATATTT
Found at i:25821 original size:21 final size:21
Alignment explanation
Indices: 25795--25840 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
25785 TTTATACATT
25795 AAAATTTTGAAAAAAATT-AAA
1 AAAATTTT-AAAAAAATTGAAA
*
25816 AAAATTTTAAATAAATTGAAA
1 AAAATTTTAAAAAAATTGAAA
25837 AAAA
1 AAAA
25841 AAAAAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATTTTAAAAAAATTGAAA
Found at i:26351 original size:2 final size:2
Alignment explanation
Indices: 26344--26509 Score: 62
Period size: 2 Copynumber: 91.0 Consensus size: 2
26334 TATTATATGT
* * *
26344 TA TA TA TA -A TA TG TA TA TA T- TA TA T- TA TA AA TA TA CA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
** * * *
26384 TA TA TA -A T- TA T- TA TA TA GC TG TT TA TA TA TA TT TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
26424 -A TA TA -A TA TA -A TA TA TA TA -A AA TA TA -A CA TA TA -A CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
26460 TA -A TA TA TA TA TA -A TC TA TA -A CA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
26497 -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA
26510 ATAAAAAATA
Statistics
Matches: 122, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
1 18 0.15
2 101 0.83
3 3 0.02
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:26398 original size:13 final size:12
Alignment explanation
Indices: 26343--26504 Score: 72
Period size: 12 Copynumber: 13.8 Consensus size: 12
26333 ATATTATATG
26343 TTATATATAATA
1 TTATATATAATA
*
26355 TGTATATATTATA
1 T-TATATATAATA
* *
26368 TTATAAATATACA
1 TTATATATA-ATA
*
26381 CTATATATAATTA
1 TTATATATAA-TA
** *
26394 TTATATA-GCTG
1 TTATATATAATA
26405 TT-TATAT-ATA
1 TTATATATAATA
26415 TT-TATAGTAATA
1 TTATATA-TAATA
26427 -TA-ATATAATA
1 TTATATATAATA
*
26437 -TATATAAAATA
1 TTATATATAATA
* * *
26448 TAACATATAACA
1 TTATATATAATA
*
26460 TAATATAT-ATA
1 TTATATATAATA
* * *
26471 TAATCTATAACA
1 TTATATATAATA
26483 -TATAATATAATA
1 TTAT-ATATAATA
*
26495 TAATATATAA
1 TTATATATAA
26505 ATATAATAAA
Statistics
Matches: 112, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
10 18 0.16
11 26 0.23
12 39 0.35
13 29 0.26
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (12 bp):
TTATATATAATA
Found at i:26432 original size:5 final size:5
Alignment explanation
Indices: 26422--26512 Score: 82
Period size: 5 Copynumber: 18.0 Consensus size: 5
26412 ATATTTATAG
* *
26422 TAATA TAATA TAATA TATATA AAATA TAACATA TAACA TAATA TATATA
1 TAATA TAATA TAATA TA-ATA TAATA T-A-ATA TAATA TAATA TA-ATA
*
26471 TAATC T-ATA -ACATA TAATA TAATA TAATA T-ATA -AATA TAATA
1 TAATA TAATA TA-ATA TAATA TAATA TAATA TAATA TAATA TAATA
26513 AAAAATAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
4 8 0.11
5 47 0.66
6 12 0.17
7 4 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:26438 original size:28 final size:28
Alignment explanation
Indices: 26407--26502 Score: 90
Period size: 28 Copynumber: 3.3 Consensus size: 28
26397 TATAGCTGTT
26407 TATATATATTTATAGTA-ATATAATATAA
1 TATATATATTTATA-TACATATAATATAA
** *
26435 TATATATA-AAATATAACATATAACATAA
1 TATATATATTTATAT-ACATATAATATAA
26463 TATATATATAATCTATA-ACATATAATATAA
1 TATATATAT--T-TATATACATATAATATAA
26493 TATAATATAT
1 TAT-ATATAT
26503 AAATATAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 4 0.07
28 26 0.47
30 15 0.27
31 6 0.11
32 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (28 bp):
TATATATATTTATATACATATAATATAA
Found at i:26468 original size:30 final size:30
Alignment explanation
Indices: 26434--26510 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
26424 ATATAATATA
26434 ATATATATAAAATATAACATATAACATAAT
1 ATATATATAAAATATAACATATAACATAAT
** *
26464 ATATATATAATCTATAACATATAATATAAT
1 ATATATATAAAATATAACATATAACATAAT
26494 ATA-ATATATAAATATAA
1 ATATATATA-AAATATAA
26511 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (30 bp):
ATATATATAAAATATAACATATAACATAAT
Found at i:27218 original size:121 final size:117
Alignment explanation
Indices: 27036--27384 Score: 390
Period size: 121 Copynumber: 2.9 Consensus size: 117
27026 AAAATATTAC
* * *
27036 TATAATAAAAAA--ATTTAATTTAAAATTTTTTATTTTAAAAAACATAATAATTAATAGTTTAAT
1 TATAATAAAAAACCTTTTATTTTAAAATTTTTTATTTT-AAAAA-ATAATAATTAA-ATTTTAAT
*
27099 TT-TCTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAATAT
63 TTGT-TAATGTAAATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAA-AA
27155 TATAATAAAAAACCTTTTATTTTAAAATTTTTTATTGTTATAAAATATAATAATTAAATTTTAAT
1 TATAATAAAAAACCTTTTATTTTAAAATTTTTTATT-TTA-AAAA-ATAATAATTAAATTTTAAT
* *
27220 TTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAA
63 TTGTTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
* * * *
27275 TAAAATAATAAACCCTTTTTATTTTTATTTAATTTTTTTATTTTAAAAAAT--TAATT---TTTA
1 TATAATAA-AAAACC-TTTTA-TTTTA---AAATTTTTTATTTTAAAAAATAATAATTAAATTTT
* *
27335 AATTTGTTAATATAAATTTCTTTAAAGTTAATTAAATATTATTTTTTATT
60 AATTTGTTAATGTAAA-TT-TTTAAACTTAATTAAATATTATTTTTTATT
27385 AAAAACAATA
Statistics
Matches: 202, Mismatches: 15, Indels: 25
0.83 0.06 0.10
Matches are distributed among these distances:
118 17 0.08
119 14 0.07
120 36 0.18
121 87 0.43
122 23 0.11
123 7 0.03
124 4 0.02
125 3 0.01
126 11 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (117 bp):
TATAATAAAAAACCTTTTATTTTAAAATTTTTTATTTTAAAAAATAATAATTAAATTTTAATTTG
TTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTTATTTTATTAAAAA
Found at i:27422 original size:117 final size:114
Alignment explanation
Indices: 27084--27424 Score: 255
Period size: 121 Copynumber: 2.9 Consensus size: 114
27074 AAAACATAAT
* * *
27084 AATTAATAGTTTAATTT-TCTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTTATTTTAT
1 AATTAA-ATTTTAATTTGT-TAATATAATTTTTTAAACTTAATTAAATATTA---TTTATTTTAT
** * * ** *
27148 TAAATATTATAATAAAAAACC-TT-TTATTTTAAAATTT--TTTATTGTTATAAAATATAAT
61 TAAA-AACAAAATAATAAACCATTATTA-TTT-AAATTTAATTT-TT-TTAT--TTTA-AAA
*
27206 AATTAAATTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTA
1 AATTAAATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATTA--TTT-ATTTTATTA
* * * **
27271 AAAATAAAATAATAAACCCTTTTTATTTTTATTTAATTTTTTTATTTTAAAA
63 AAAACAAAATAATAAACCATTATTATTTAAATTTAATTTTTTTATTTTAAAA
* *
27323 AATTAATTTTTAAATTTGTTAATATAAATTTCTTTAAAGTTAATTAAATATTA-TT-TTTTATTA
1 AATTAAATTTT-AATTTGTTAATAT-AATTT-TTTAAACTTAATTAAATATTATTTATTTTATTA
* **
27386 AAAACAATAATTAATATATTATTATTATTTAAATTTAAT
63 AAAACAA-AA-TAATAAACCATTATTATTTAAATTTAAT
27425 AAATTTATAA
Statistics
Matches: 187, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
115 14 0.07
116 2 0.01
117 35 0.19
118 14 0.07
119 5 0.03
120 46 0.25
121 58 0.31
122 13 0.07
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (114 bp):
AATTAAATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATTATTTATTTTATTAAAA
ACAAAATAATAAACCATTATTATTTAAATTTAATTTTTTTATTTTAAAA
Found at i:27432 original size:117 final size:114
Alignment explanation
Indices: 27206--27432 Score: 242
Period size: 117 Copynumber: 1.9 Consensus size: 114
27196 AAAATATAAT
*
27206 AATTAAATTTTAATTTGTTAATGTAATTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTA
1 AATTAAATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATTA--TTT-ATTTTATTA
* * * ** ***
27271 AAAATAAAATAATAAACCCTTTTTATTTTTATTTAATTTTTTTATTTTAAAA
63 AAAACAAAATAATAAACCATTATTATTTAAATTTAATAAATTTATTTTAAAA
* *
27323 AATTAATTTTTAAATTTGTTAATATAAATTTCTTTAAAGTTAATTAAATATTA-TT-TTTTATTA
1 AATTAAATTTT-AATTTGTTAATAT-AATTT-TTTAAACTTAATTAAATATTATTTATTTTATTA
* **
27386 AAAACAATAATTAATATATTATTATTATTTAAATTTAATAAATTTAT
63 AAAACAA-AA-TAATAAACCATTATTATTTAAATTTAATAAATTTAT
27433 AAAAAAACTG
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
115 14 0.15
116 2 0.02
117 38 0.42
118 12 0.13
119 5 0.05
120 20 0.22
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (114 bp):
AATTAAATTTTAATTTGTTAATATAATTTTTTAAACTTAATTAAATATTATTTATTTTATTAAAA
ACAAAATAATAAACCATTATTATTTAAATTTAATAAATTTATTTTAAAA
Found at i:28224 original size:92 final size:92
Alignment explanation
Indices: 27939--28334 Score: 507
Period size: 91 Copynumber: 4.3 Consensus size: 92
27929 TCTTAAGATT
* * * *
27939 GGATTCTTTTTTATGGAAAAAAAGAAA-AGTTGATTGATTGTAAATATCAGGCTGCAAGGATTAG
1 GGATTCTTTTTTATAGAAAAAAAGAAAGA-CTGATTGATTGTAAATGTCAGACTGCAAGGATTAG
* *
28003 ACTAATATATGAATTATATGTGAGAATC
65 ACTAATACATGAATTATATCTGAGAATC
* * * *
28031 -AATTCTTTTTTATAGAAAAAAAGAATAG-TTGATTGATTATAAATGTCAAACTGCAAGGATTAG
1 GGATTCTTTTTTATAGAAAAAAAGAA-AGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAG
28094 ACTAATACATGAATTATATCTGAGAATC
65 ACTAATACATGAATTATATCTGAGAATC
* * * *
28122 GAATTCTTTTTTATAGAAAAAAAGAAAGACTAATTGATTGTAAATGTCAGACTGTAA-TATTAGA
1 GGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGA
** *
28186 CTAACGCATGAATTATATCTGAAAATC
66 CTAATACATGAATTATATCTGAGAATC
*
28213 GGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTTA-AGCTGCAAGGATT-G
1 GGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGA-CTGCAAGGATTAG
* *
28276 AACTAATGCATGAATTATATCTGAGAATT
65 -ACTAATACATGAATTATATCTGAGAATC
* *
28305 AGATTCTTTTTTATAGGAAAAAGAGAAAGA
1 GGATTCTTTTTTATA-GAAAAAAAGAAAGA
28335 TTGCAGCGAT
Statistics
Matches: 269, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.00
91 164 0.61
92 91 0.34
93 13 0.05
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.33
Consensus pattern (92 bp):
GGATTCTTTTTTATAGAAAAAAAGAAAGACTGATTGATTGTAAATGTCAGACTGCAAGGATTAGA
CTAATACATGAATTATATCTGAGAATC
Found at i:28231 original size:183 final size:184
Alignment explanation
Indices: 27923--28334 Score: 523
Period size: 183 Copynumber: 2.2 Consensus size: 184
27913 AAAAAATGTG
* * * * *
27923 ATTATATCTTAAGATTG-GATTCTTTTTTATGGAAAAAAAGAAA-AGTTGATTGATTGTAAATAT
1 ATTATATC-TGAGAATGAGATTCTTTTTTATAGAAAAAAAGAAAGAGCTAATTGATTGTAAATAT
* * * * *
27986 CAGGCTGCAAGGATTAGACTAATATATGAATTATATGTGAGAATCAATTCTTTTTTATAGAAAAA
65 CAGACTGCAAGGATTAGACTAACACATGAATTATATCTGAAAATCAATTCTTTTTTATAGAAAAA
*
28051 AAGAATAG-TTGATTGATTATAAATGTCAAACTGCAAGGATT-AGACTAATACATGA
130 AAGAA-AGACTGATTGATTATAAATGTCAAACTGCAAGGATTGA-ACTAATACATGA
*
28106 ATTATATCTGAGAATCGA-ATTCTTTTTTATAGAAAAAAAGAAAGA-CTAATTGATTGTAAATGT
1 ATTATATCTGAGAAT-GAGATTCTTTTTTATAGAAAAAAAGAAAGAGCTAATTGATTGTAAATAT
* * * *
28169 CAGACTGTAA-TATTAGACTAACGCATGAATTATATCTGAAAATCGGATTCTTTTTTATAGAAAA
65 CAGACTGCAAGGATTAGACTAACACATGAATTATATCTGAAAATC-AATTCTTTTTTATAGAAAA
* * * *
28233 AAAGAAAGACTGATTGATTGTAAATGTTAAGCTGCAAGGATTGAACTAATGCATGA
129 AAAGAAAGACTGATTGATTATAAATGTCAAACTGCAAGGATTGAACTAATACATGA
* *
28289 ATTATATCTGAGAATTAGATTCTTTTTTATAGGAAAAAGAGAAAGA
1 ATTATATCTGAGAATGAGATTCTTTTTTATA-GAAAAAAAGAAAGA
28335 TTGCAGCGAT
Statistics
Matches: 199, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
182 36 0.18
183 148 0.74
184 15 0.08
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (184 bp):
ATTATATCTGAGAATGAGATTCTTTTTTATAGAAAAAAAGAAAGAGCTAATTGATTGTAAATATC
AGACTGCAAGGATTAGACTAACACATGAATTATATCTGAAAATCAATTCTTTTTTATAGAAAAAA
AGAAAGACTGATTGATTATAAATGTCAAACTGCAAGGATTGAACTAATACATGA
Found at i:29279 original size:74 final size:74
Alignment explanation
Indices: 29190--29339 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 74
29180 ATGCATAGCC
29190 AGAAATAATTAATTTCTACGAGTCATTTCATTATTCATCTGTGTCACCGATAATTTCTAACACTG
1 AGAAATAATTAATTTCTACGAGTCATTTCATTATTCATCTGTGTCACCGATAATTTCTAACACTG
29255 AAGATGATG
66 AAGATGATG
*
29264 AGAAATAATTAATTTCTACGAGTCATTTCATTATTCATCTGTGTCACCTATAATTTCTAACACTG
1 AGAAATAATTAATTTCTACGAGTCATTTCATTATTCATCTGTGTCACCGATAATTTCTAACACTG
29329 AAGATGATG
66 AAGATGATG
29338 AG
1 AG
29340 CCACACAACT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (74 bp):
AGAAATAATTAATTTCTACGAGTCATTTCATTATTCATCTGTGTCACCGATAATTTCTAACACTG
AAGATGATG
Found at i:31836 original size:12 final size:11
Alignment explanation
Indices: 31799--31837 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
31789 AAATTATATA
31799 TAAATTTAATT
1 TAAATTTAATT
*
31810 TAATATTGAATT
1 TAA-ATTTAATT
31822 TAAATTTAATGT
1 TAAATTTAAT-T
31834 TAAA
1 TAAA
31838 AAAAAAGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:32514 original size:2 final size:2
Alignment explanation
Indices: 32502--32536 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32492 TTACAAAAAG
*
32502 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32537 GATACCTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32995 original size:22 final size:24
Alignment explanation
Indices: 32961--33011 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
32951 AAATTATTAA
* *
32961 ATTATATTTTTAATTT-A-TTTTT
1 ATTATAATATTAATTTAATTTTTT
32983 ATTATAATATTAATTTAATTTTTT
1 ATTATAATATTAATTTAATTTTTT
33007 ATTAT
1 ATTAT
33012 TTTAATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.56
23 1 0.04
24 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTATAATATTAATTTAATTTTTT
Found at i:32999 original size:27 final size:29
Alignment explanation
Indices: 32969--33026 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
32959 AAATTATATT
32969 TTTAATTTATTT-TTATTATAAT-A-TTAA
1 TTTAATTT-TTTATTATTATAATGATTTAA
*
32996 TTTAATTTTTTATTATTTTAATGATTTAA
1 TTTAATTTTTTATTATTATAATGATTTAA
33025 TT
1 TT
33027 AATATTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 17 0.63
28 1 0.04
29 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTAATTTTTTATTATTATAATGATTTAA
Found at i:33322 original size:16 final size:16
Alignment explanation
Indices: 33303--33333 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33293 TTTATAATTT
*
33303 AAAAATTAATTTTTGA
1 AAAAATAAATTTTTGA
33319 AAAAATAAATTTTTG
1 AAAAATAAATTTTTG
33334 TATTTACGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AAAAATAAATTTTTGA
Found at i:33434 original size:19 final size:20
Alignment explanation
Indices: 33412--33451 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
33402 TTAAATATTT
* *
33412 AAAA-TTTTTGAGTTAAAAA
1 AAAAGTTTTTAAGTCAAAAA
33431 AAAAGTTTTTAAGTCAAAAA
1 AAAAGTTTTTAAGTCAAAAA
33451 A
1 A
33452 GGCGTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAAGTTTTTAAGTCAAAAA
Found at i:35565 original size:2 final size:2
Alignment explanation
Indices: 35558--35585 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35548 ATTAGAGAAC
35558 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35586 TTTTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35565 original size:19 final size:19
Alignment explanation
Indices: 35529--35566 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35519 AGAAATAAGG
*
35529 ATTAGAGGAAGAGCAGAGA
1 ATTAGAGAAAGAGCAGAGA
35548 ATTAGAGAACAGAG-AGAGA
1 ATTAGAGAA-AGAGCAGAGA
35567 GAGAGAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.05, G:0.34, T:0.11
Consensus pattern (19 bp):
ATTAGAGAAAGAGCAGAGA
Found at i:36637 original size:2 final size:2
Alignment explanation
Indices: 36630--36660 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36620 AGAAAATGAA
36630 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 A
36661 ACAACATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37843 original size:14 final size:14
Alignment explanation
Indices: 37795--37844 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
37785 ATATCGAATT
*
37795 TTAAATTTATTAAA
1 TTAAATTAATTAAA
* *
37809 TATCAATTAATTATA
1 T-TAAATTAATTAAA
*
37824 TAAAATTAATTAAA
1 TTAAATTAATTAAA
37838 TTAAATT
1 TTAAATT
37845 TTAAATTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATTAATTAAA
Found at i:39863 original size:19 final size:19
Alignment explanation
Indices: 39825--39863 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39815 TAAAAATTTT
*
39825 ATAAAATTAGTAAAACAAA
1 ATAAAATTAGTAAAAAAAA
39844 ATAAAATTA-TAAAATAAAA
1 ATAAAATTAGTAAAA-AAAA
39863 A
1 A
39864 ATAATTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (19 bp):
ATAAAATTAGTAAAAAAAA
Found at i:39870 original size:18 final size:19
Alignment explanation
Indices: 39825--39862 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39815 TAAAAATTTT
39825 ATAAAATTAGTAAAACAAA
1 ATAAAATTAGTAAAACAAA
*
39844 ATAAAATTA-TAAAATAAA
1 ATAAAATTAGTAAAACAAA
39862 A
1 A
39863 AATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAAAATTAGTAAAACAAA
Found at i:40110 original size:2 final size:2
Alignment explanation
Indices: 40103--40127 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40093 TTGCTACATT
40103 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40128 TCTATCATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40539 original size:49 final size:48
Alignment explanation
Indices: 40443--40540 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 48
40433 TGAAATGAAA
*
40443 TTTTTATGAAAATAAAAACTTAAAAAAAATAAAAACTGTTTGATCATT
1 TTTTTATGAAAATAAAAACTTAAAAAAAATAAAAACTATTTGATCATT
40491 TTTTTATGAAAA-AAAAA-TTAAAAAACGAAGTAAAAACTATTTGATCATT
1 TTTTTATGAAAATAAAAACTTAAAAAA--AA-TAAAAACTATTTGATCATT
40540 T
1 T
40541 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 8 0.17
47 5 0.11
48 14 0.30
49 19 0.41
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (48 bp):
TTTTTATGAAAATAAAAACTTAAAAAAAATAAAAACTATTTGATCATT
Found at i:40615 original size:13 final size:13
Alignment explanation
Indices: 40599--40624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40589 TAAAGGATAA
40599 AAATTTTTTTTTT
1 AAATTTTTTTTTT
40612 AAATTTTTTTTTT
1 AAATTTTTTTTTT
40625 CTCTTTCTAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
AAATTTTTTTTTT
Found at i:41732 original size:21 final size:22
Alignment explanation
Indices: 41706--41746 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
41696 TAACTTGGTT
41706 CGGACTTCTAATG-CAGTCGTG
1 CGGACTTCTAATGCCAGTCGTG
41727 CGGACTTCTAATGCCAGTCG
1 CGGACTTCTAATGCCAGTCG
41747 CCGTCCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
CGGACTTCTAATGCCAGTCGTG
Found at i:42164 original size:6 final size:6
Alignment explanation
Indices: 42153--42192 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
42143 TACAAAAAGT
* *
42153 ATATAA ATATAA ATATAA ATATAA ATATAT ATATAT ATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATAT
42193 GATGCCCGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:44418 original size:2 final size:2
Alignment explanation
Indices: 44413--44443 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44403 AGGAAAAAAC
44413 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
44444 TTCCTCAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45363 original size:8 final size:8
Alignment explanation
Indices: 45344--45394 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
45334 ATATAATAAC
45344 ATAAATTT
1 ATAAATTT
45352 -TAAATTT
1 ATAAATTT
*
45359 ATAAATAAAT
1 ATAAAT--TT
*
45369 ATGAATTT
1 ATAAATTT
45377 AATAAATTT
1 -ATAAATTT
45386 ATAAATTT
1 ATAAATTT
45394 A
1 A
45395 AAAAATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
7 7 0.20
8 15 0.43
9 7 0.20
10 6 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (8 bp):
ATAAATTT
Found at i:46459 original size:16 final size:16
Alignment explanation
Indices: 46434--46518 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
46424 CTCAAAATCC
*
46434 AAAATAATCCGAACCT
1 AAAATGATCCGAACCT
** *
46450 AAAATGATCCTCACTT
1 AAAATGATCCGAACCT
* *
46466 AAAATGA-CTTGAACCC
1 AAAATGATC-CGAACCT
* *
46482 GAAATGACCCGAA-CT
1 AAAATGATCCGAACCT
*
46497 CGAAATGATCCGAACCT
1 -AAAATGATCCGAACCT
46514 AAAAT
1 AAAAT
46519 AATCTGAACA
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
15 2 0.04
16 46 0.90
17 3 0.06
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.20
Consensus pattern (16 bp):
AAAATGATCCGAACCT
Found at i:47326 original size:22 final size:24
Alignment explanation
Indices: 47284--47327 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
47274 TGACCTAAAT
47284 TCAAAATGATCTAAACTCGATTAA
1 TCAAAATGATCTAAACTCGATTAA
*
47308 TCAAAAT-AT-TACACTCGATT
1 TCAAAATGATCTAAACTCGATT
47328 GACCCAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (24 bp):
TCAAAATGATCTAAACTCGATTAA
Found at i:47399 original size:16 final size:16
Alignment explanation
Indices: 47380--47428 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
47370 GAGATGATCT
47380 GAACTTGAAATAA-CTC
1 GAACTTGAAATAATC-C
**
47396 GAACCCGAAATAATCC
1 GAACTTGAAATAATCC
47412 GAACTTGAAAATAATCC
1 GAACTTG-AAATAATCC
47429 AAAAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.20
Consensus pattern (16 bp):
GAACTTGAAATAATCC
Found at i:52589 original size:10 final size:10
Alignment explanation
Indices: 52574--52603 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
52564 AAAGTCATGT
52574 AGAAAGACAA
1 AGAAAGACAA
52584 AGAAAGACAA
1 AGAAAGACAA
*
52594 AGAAAAACAA
1 AGAAAGACAA
52604 GGGACTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAAAGACAA
Found at i:55961 original size:23 final size:25
Alignment explanation
Indices: 55910--55964 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 25
55900 TATTTAAACT
55910 TAAAAAT-ATTTTGAATAAAATAAG
1 TAAAAATAATTTTGAATAAAATAAG
*
55934 T-AAAATAATTTT-ATTAAAATAA-
1 TAAAAATAATTTTGAATAAAATAAG
55956 TAAAAATAA
1 TAAAAATAA
55965 CCCTTAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 1 0.04
23 21 0.75
24 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAAATAATTTTGAATAAAATAAG
Found at i:56110 original size:30 final size:30
Alignment explanation
Indices: 56038--56142 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 30
56028 TTATAACATC
* * *
56038 TAAATAAATTGTTAA-C-TTTAATTTACAT
1 TAAATAAGTTTTTAATCTTTTAATTTATAT
56066 TAAAATTAA-TTTTTAAT-TTTTAATTTATAT
1 T-AAA-TAAGTTTTTAATCTTTTAATTTATAT
* * *
56096 TCAAATAAGATTTTAGTCTTTAAATTT-TACT
1 T-AAATAAGTTTTTAATCTTTTAATTTATA-T
56127 TAAATAAGTTTTTAAT
1 TAAATAAGTTTTTAAT
56143 AGAAATCAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
28 1 0.02
29 12 0.19
30 39 0.63
31 10 0.16
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (30 bp):
TAAATAAGTTTTTAATCTTTTAATTTATAT
Found at i:57675 original size:16 final size:16
Alignment explanation
Indices: 57641--57684 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
57631 AAATACGAAT
57641 AATTATAAAAT-ATACA
1 AATT-TAAAATAATACA
*
57657 AATTTAAAATAATATA
1 AATTTAAAATAATACA
*
57673 AATATAAAATAA
1 AATTTAAAATAA
57685 CTTAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTTAAAATAATACA
Found at i:58005 original size:17 final size:17
Alignment explanation
Indices: 57978--58041 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
57968 GCGTCAATTA
57978 TTTTA-TTATTAAAAAT
1 TTTTATTTATTAAAAAT
57994 TTTTATTTATT-AAAAT
1 TTTTATTTATTAAAAAT
* *
58010 TTCTT-TCATATTAAAGAT
1 TT-TTAT-TTATTAAAAAT
*
58028 ATTTATTTATTAAA
1 TTTTATTTATTAAA
58042 TAAATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 13 0.33
17 20 0.51
18 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTATTTATTAAAAAT
Done.