Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 185 of 226
Found at i:58988247 original size:7 final size:7
Alignment explanation
Indices: 58988237--58988347 Score: 73
Period size: 7 Copynumber: 15.7 Consensus size: 7
58988227 CCACAGCCTT
58988237 TAAACCA
1 TAAACCA
58988244 TAAACCA
1 TAAACCA
*
58988251 TAAATCA
1 TAAACCA
58988258 TAAACCA
1 TAAACCA
*
58988265 TAACCCA
1 TAAACCA
*
58988272 TAATCCA
1 TAAACCA
*
58988279 TAAACCT
1 TAAACCA
***
58988286 TAAAATGG
1 T-AAACCA
58988294 TAACACC-
1 TAA-ACCA
*
58988301 TAAACCT
1 TAAACCA
58988308 TAAACTC-
1 TAAAC-CA
58988315 TAAACCA
1 TAAACCA
* *
58988322 TATACCC
1 TAAACCA
58988329 TAAACCA
1 TAAACCA
* *
58988336 AAAACCC
1 TAAACCA
58988343 TAAAC
1 TAAAC
58988348 TATAGTGATA
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
6 4 0.05
7 71 0.88
8 6 0.07
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:58988612 original size:28 final size:29
Alignment explanation
Indices: 58988567--58988631 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 29
58988557 TTTTCTGAAT
*
58988567 ATTTTAAATATTCAATTAAAAATAAGTTGA
1 ATTTT-AATATTCAATTAAAAATAAATTGA
58988597 ATTTTAATA-TCAATTAAAAATAAATTGA
1 ATTTTAATATTCAATTAAAAATAAATTGA
58988625 ATTTTAA
1 ATTTTAA
58988632 CTAATATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 25 0.74
29 4 0.12
30 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.42
Consensus pattern (29 bp):
ATTTTAATATTCAATTAAAAATAAATTGA
Found at i:58988918 original size:40 final size:40
Alignment explanation
Indices: 58988874--58988980 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 40
58988864 GGAAACGCCG
*
58988874 CTAATGCTCTATTTTTAGCGGCGTTTTTAAAAAAGCACCT
1 CTAATGCTCTATTTTTAGCGGCGTTTTTAAAAAAGCACCA
* *** * *
58988914 CTAATGCTCTA-TTTTAGCGGCATTTTCCTAAGAGCGCCA
1 CTAATGCTCTATTTTTAGCGGCGTTTTTAAAAAAGCACCA
* *
58988953 CTAATGCTCGATTTATAGCGGCGTTTTT
1 CTAATGCTCTATTTTTAGCGGCGTTTTT
58988981 TTGTCCAAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 31 0.56
40 24 0.44
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (40 bp):
CTAATGCTCTATTTTTAGCGGCGTTTTTAAAAAAGCACCA
Found at i:58995125 original size:9 final size:9
Alignment explanation
Indices: 58995111--58995563 Score: 163
Period size: 9 Copynumber: 52.6 Consensus size: 9
58995101 TAACTATAAA
58995111 TAAGTTATG
1 TAAGTTATG
58995120 TAAGTTATG
1 TAAGTTATG
* * *
58995129 ATATGATATA
1 -TAAGTTATG
*
58995139 T-ATTTATG
1 TAAGTTATG
*
58995147 T-A-TTAGG
1 TAAGTTATG
*
58995154 TAAATTATG
1 TAAGTTATG
58995163 TAAGTTATG
1 TAAGTTATG
*
58995172 T-A-TTATA
1 TAAGTTATG
58995179 TAAGTTATG
1 TAAGTTATG
58995188 TAAGTTATG
1 TAAGTTATG
58995197 T-A-TTATG
1 TAAGTTATG
*
58995204 TAAGCTATG
1 TAAGTTATG
* *
58995213 TAACTTATT
1 TAAGTTATG
*
58995222 TAAGTTACG
1 TAAGTTATG
*
58995231 TAAGTTGTG
1 TAAGTTATG
58995240 T-A-TTATG
1 TAAGTTATG
*
58995247 TTAGTTATG
1 TAAGTTATG
*
58995256 T-A-CTATG
1 TAAGTTATG
58995263 TAAGTTATG
1 TAAGTTATG
*
58995272 TGTA-TTATG
1 T-AAGTTATG
58995281 T-A-TTATG
1 TAAGTTATG
58995288 T-A-TTATG
1 TAAGTTATG
*
58995295 TATGTTATG
1 TAAGTTATG
*
58995304 TATAATATTAAT-
1 --TAA-GTT-ATG
*
58995316 TAAGTTGTG
1 TAAGTTATG
58995325 T-A-TTATG
1 TAAGTTATG
58995332 T-A-TTATG
1 TAAGTTATG
58995339 T-A-TTATG
1 TAAGTTATG
58995346 T-A-TTATG
1 TAAGTTATG
58995353 T-A-TTATG
1 TAAGTTATG
*
58995360 TATGTTATG
1 TAAGTTATG
*
58995369 TATAATATTAAT-
1 --TAA-GTT-ATG
*
58995381 TAAGTTGTG
1 TAAGTTATG
58995390 T-A-TTATG
1 TAAGTTATG
58995397 TAAGTTATG
1 TAAGTTATG
58995406 TAAGTTATG
1 TAAGTTATG
*
58995415 T-ATTTAAGTG
1 TAAGTT-A-TG
*
58995425 TATGTTATG
1 TAAGTTATG
* *
58995434 TAACTTGTG
1 TAAGTTATG
*
58995443 T-A-TAATG
1 TAAGTTATG
* *
58995450 TTAGTTATC
1 TAAGTTATG
*
58995459 AAAGTTATG
1 TAAGTTATG
*
58995468 T-A-CTATG
1 TAAGTTATG
*
58995475 TAAGTTATT
1 TAAGTTATG
58995484 TAAGTTATG
1 TAAGTTATG
*
58995493 TAAGTTGTG
1 TAAGTTATG
58995502 T-A-TTATG
1 TAAGTTATG
58995509 TAAGTTAT-
1 TAAGTTATG
*
58995517 TATGTTATTATG
1 TAAG---TTATG
58995529 TAAGTTATG
1 TAAGTTATG
* *
58995538 CAAGTTTATATA
1 TAAG--T-TATG
58995550 TAAGTTATG
1 TAAGTTATG
58995559 TAAGT
1 TAAGT
58995564 ATATCACTTT
Statistics
Matches: 337, Mismatches: 63, Indels: 88
0.69 0.13 0.18
Matches are distributed among these distances:
7 92 0.27
8 31 0.09
9 168 0.50
10 18 0.05
11 11 0.03
12 13 0.04
13 4 0.01
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.49
Consensus pattern (9 bp):
TAAGTTATG
Found at i:58995173 original size:25 final size:25
Alignment explanation
Indices: 58995142--58995563 Score: 230
Period size: 25 Copynumber: 17.0 Consensus size: 25
58995132 TGATATATAT
* *
58995142 TTATGTATTAGGTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
58995167 TTATGTATTATATAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
58995192 TTATGTATTATGTAAGCTATGTAAC
1 TTATGTATTATGTAAGTTATGTAAG
* * *
58995217 TTATTTAAGTTACGTAAGTTGTGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
58995242 TTATGTTAGTTATGT-A-CTATGTAAG
1 TTATG-TA-TTATGTAAGTTATGTAAG
58995267 TTATGTGTATTATGT-A-TTATGT-A-
1 TTA--TGTATTATGTAAGTTATGTAAG
*
58995290 TTATGTATGTTATGTATAATATTAAT-TAAG
1 TTATGTA--TTATG--TAA-GTT-ATGTAAG
*
58995320 TTGTGTATTATGT-A-TTATGT-A-
1 TTATGTATTATGTAAGTTATGTAAG
*
58995341 TTATGTATTATGT-A-TTATGTATG
1 TTATGTATTATGTAAGTTATGTAAG
*
58995364 TTATGTA-TA-AT-A-TTAAT-TAAG
1 TTATGTATTATGTAAGTT-ATGTAAG
*
58995385 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
58995410 TTATGTATTTAAGTGTATGTTATGTAAC
1 TTATGTA-TT-A-TGTAAGTTATGTAAG
* * * **
58995438 TTGTGTATAATGTTAGTTATCAAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
58995463 TTATGTACTATGTAAGTTATTTAAG
1 TTATGTATTATGTAAGTTATGTAAG
*
58995488 TTATGTAAGTTGTGT-A-TTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
*
58995513 TTATTATGTTATTATGTAAGTTATGCAAG
1 ---TTATG-TATTATGTAAGTTATGTAAG
*
58995542 -T-T-TA-TATATAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
58995563 T
1 T
58995564 ATATCACTTT
Statistics
Matches: 314, Mismatches: 45, Indels: 79
0.72 0.10 0.18
Matches are distributed among these distances:
21 51 0.16
22 11 0.04
23 23 0.07
24 7 0.02
25 133 0.42
26 12 0.04
27 25 0.08
28 34 0.11
29 12 0.04
30 6 0.02
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:58995176 original size:16 final size:16
Alignment explanation
Indices: 58995157--58995537 Score: 182
Period size: 16 Copynumber: 22.9 Consensus size: 16
58995147 TATTAGGTAA
58995157 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
58995173 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
58995189 AAGTTATGT-A-TTATGT
1 -A-TTATGTAAGTTATGT
* * *
58995205 AAGCTATGTAACTTATTT
1 -A-TTATGTAAGTTATGT
* *
58995223 AAGTTACGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
*
58995241 ATTATGTTAGTTATGT
1 ATTATGTAAGTTATGT
*
58995257 ACTATGTAAGTTATGTGT
1 ATTATGTAAGTTA--TGT
58995275 ATTATGT-A-TTATGT
1 ATTATGTAAGTTATGT
*
58995289 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
* *
58995305 ATAATATTAATTAAGTTGTGT
1 AT--TA-T--GTAAGTTATGT
58995326 ATTATGT-A-TTATGT
1 ATTATGTAAGTTATGT
58995340 ATTATGT-A-TTATGT
1 ATTATGTAAGTTATGT
*
58995354 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
*
58995370 ATAATAT-TAA-TTAAG-
1 AT--TATGTAAGTTATGT
*
58995385 -TTGTGT-A-TTATGT
1 ATTATGTAAGTTATGT
58995398 AAGTTATGTAAGTTATGT
1 -A-TTATGTAAGTTATGT
*
58995416 ATTTAAGTGTATGTTATGT
1 A-TT-A-TGTAAGTTATGT
* *
58995435 AACTTGTGT-A-TAATGTT
1 -A-TTATGTAAGTTATG-T
**
58995452 AGTTATCAAAGTTATGT
1 A-TTATGTAAGTTATGT
* *
58995469 ACTATGTAAGTTATTT
1 ATTATGTAAGTTATGT
*
58995485 AAGTTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
58995503 ATTATGTAAGTTATTATGTT
1 ATTATGTAAG---TTATG-T
58995523 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
58995538 CAAGTTTATA
Statistics
Matches: 283, Mismatches: 46, Indels: 71
0.71 0.12 0.18
Matches are distributed among these distances:
12 7 0.02
13 1 0.00
14 37 0.13
15 1 0.00
16 109 0.39
17 22 0.08
18 64 0.23
19 18 0.06
20 14 0.05
21 10 0.04
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.50
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:58995282 original size:7 final size:7
Alignment explanation
Indices: 58995238--58995362 Score: 103
Period size: 7 Copynumber: 16.7 Consensus size: 7
58995228 ACGTAAGTTG
58995238 TGTATTA
1 TGTATTA
58995245 TGTTAGTTA
1 TG-TA-TTA
*
58995254 TGTACTA
1 TGTATTA
58995261 TGTAAGTTA
1 TGT-A-TTA
58995270 TGTGTATTA
1 --TGTATTA
58995279 TGTATTA
1 TGTATTA
58995286 TGTATTA
1 TGTATTA
58995293 TGTATGTTA
1 TGTA--TTA
58995302 TGTA-TA
1 TGTATTA
*
58995308 -ATATTAA
1 TGTATT-A
*
58995315 T-TAAGTTG
1 TGT-A-TTA
58995323 TGTATTA
1 TGTATTA
58995330 TGTATTA
1 TGTATTA
58995337 TGTATTA
1 TGTATTA
58995344 TGTATTA
1 TGTATTA
58995351 TGTATTA
1 TGTATTA
58995358 TGTAT
1 TGTAT
58995363 GTTATGTATA
Statistics
Matches: 99, Mismatches: 5, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
5 2 0.02
6 3 0.03
7 62 0.63
8 8 0.08
9 20 0.20
10 1 0.01
11 3 0.03
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.54
Consensus pattern (7 bp):
TGTATTA
Found at i:58995312 original size:21 final size:23
Alignment explanation
Indices: 58995272--58995418 Score: 81
Period size: 21 Copynumber: 6.3 Consensus size: 23
58995262 GTAAGTTATG
* *
58995272 TGTATTATGTATTATGTATTATGTA
1 TGTATTATATATTATGTA-TGT-TA
* *
58995297 TGTTATGTATAATATTAAT-TAAGTTG
1 TG-TAT-TAT-ATATTA-TGTATGTTA
*
58995323 TGTATTATGTATTATGTA--TTA
1 TGTATTATATATTATGTATGTTA
*
58995344 TGTATTATGTATTATGTATGTTA
1 TGTATTATATATTATGTATGTTA
* *
58995367 TGTA-TA-ATATTAAT-TAAGTTG
1 TGTATTATATATT-ATGTATGTTA
* *
58995388 TGTATTATGTAAGTTATGTAAGTTA
1 TGTATTATAT-A-TTATGTATGTTA
58995413 TGTATT
1 TGTATT
58995419 TAAGTGTATG
Statistics
Matches: 98, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
21 33 0.34
22 7 0.07
23 15 0.15
24 6 0.06
25 19 0.19
26 6 0.06
27 4 0.04
28 7 0.07
29 1 0.01
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (23 bp):
TGTATTATATATTATGTATGTTA
Found at i:58995329 original size:37 final size:37
Alignment explanation
Indices: 58995286--58995407 Score: 156
Period size: 37 Copynumber: 3.5 Consensus size: 37
58995276 TTATGTATTA
58995286 TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
58995323 TGTATTATGTA--TTATGTAT--TATGT-ATT-A----
1 TGTATTATGTATGTTATGTATAATAT-TAATTAAGTTG
58995351 TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
1 TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
*
58995388 TGTATTATGTAAGTTATGTA
1 TGTATTATGTATGTTATGTA
58995408 AGTTATGTAT
Statistics
Matches: 73, Mismatches: 1, Indels: 22
0.76 0.01 0.23
Matches are distributed among these distances:
28 11 0.15
30 8 0.11
31 1 0.01
32 7 0.10
33 7 0.10
34 1 0.01
35 8 0.11
37 30 0.41
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.52
Consensus pattern (37 bp):
TGTATTATGTATGTTATGTATAATATTAATTAAGTTG
Found at i:58995347 original size:65 final size:67
Alignment explanation
Indices: 58995249--58995418 Score: 272
Period size: 65 Copynumber: 2.5 Consensus size: 67
58995239 GTATTATGTT
* *
58995249 AGTTATGTACTATGTAAGTTATGTGTATTATGTATTATGTATTATGTATGTTATGTATAATATTA
1 AGTTGTGTATTATGTAAGTTA--TGTATTATGTATTATGTATTATGTATGTTATGTATAATATTA
58995314 ATTA
64 ATTA
58995318 AGTTGTGTATTATGT-A-TTATGTATTATGTATTATGTATTATGTATGTTATGTATAATATTAAT
1 AGTTGTGTATTATGTAAGTTATGTATTATGTATTATGTATTATGTATGTTATGTATAATATTAAT
58995381 TA
66 TA
58995383 AGTTGTGTATTATGTAAGTTATGTAAGTTATGTATT
1 AGTTGTGTATTATGTAAGTTATGT-A-TTATGTATT
58995419 TAAGTGTATG
Statistics
Matches: 95, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
65 61 0.64
66 1 0.01
67 9 0.09
68 2 0.02
69 22 0.23
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.52
Consensus pattern (67 bp):
AGTTGTGTATTATGTAAGTTATGTATTATGTATTATGTATTATGTATGTTATGTATAATATTAAT
TA
Found at i:58995797 original size:17 final size:17
Alignment explanation
Indices: 58995777--58995810 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58995767 TATCCATACC
58995777 ATATATAAAAATTTTAA
1 ATATATAAAAATTTTAA
*
58995794 ATATATATAAATTTTAA
1 ATATATAAAAATTTTAA
58995811 GTAATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAAAAATTTTAA
Found at i:58995829 original size:18 final size:18
Alignment explanation
Indices: 58995806--58995894 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
58995796 ATATATAAAT
58995806 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
58995824 TTTAAGTAATGTAAATTATAAA
1 TTTAAGTAATGT-AA-TAT--A
*
58995846 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
*
58995863 TTTAAGTAATGTAACATA
1 TTTAAGTAATGTAATATA
*
58995881 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
58995895 GTAAGTAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 27 0.44
19 5 0.08
20 5 0.08
21 2 0.03
22 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:58995865 original size:39 final size:41
Alignment explanation
Indices: 58995799--58995876 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 41
58995789 TTTAAATATA
58995799 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
1 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
58995840 TATAAATTTT-AGTAA-GTAATATATTTAAGTAATGTAA
1 TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAA
58995877 CATATTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 22 0.59
40 5 0.14
41 10 0.27
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (41 bp):
TATAAATTTTAAGTAATGTAATATATTTAAGTAATGTAAAT
Found at i:58995876 original size:22 final size:22
Alignment explanation
Indices: 58995811--58995903 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
58995801 TAAATTTTAA
58995811 GTAATGTAATATATTTAAGTAAT
1 GTAA-GTAATATATTTAAGTAAT
* * *
58995834 GTAAATTATAAATTT---T-A-
1 GTAAGTAATATATTTAAGTAAT
58995851 GTAAGTAATATATTTAAGTAAT
1 GTAAGTAATATATTTAAGTAAT
* *
58995873 GTAA--CATATTTTAGTAAGTAAT
1 GTAAGTAATATATT--TAAGTAAT
58995895 GTAAGTAAT
1 GTAAGTAAT
58995904 GTAATATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 17
0.67 0.12 0.22
Matches are distributed among these distances:
17 12 0.23
18 1 0.02
19 1 0.02
20 7 0.13
21 1 0.02
22 24 0.46
23 4 0.08
24 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.13, T:0.42
Consensus pattern (22 bp):
GTAAGTAATATATTTAAGTAAT
Found at i:58995893 original size:39 final size:39
Alignment explanation
Indices: 58995804--58995898 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 39
58995794 ATATATATAA
58995804 ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
1 ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
58995843 AAATTTT-AGTAA-GTAATATATTTAAGTAATGTAACA-TAT
1 --ATTTTAAGTAATGTAATATATTTAAGTAATGTAA-ATTAT
58995882 -TTTAGTAAGTAATGTAA
1 ATTT--TAAGTAATGTAA
58995899 GTAATGTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
36 3 0.06
38 1 0.02
39 30 0.61
40 10 0.20
41 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (39 bp):
ATTTTAAGTAATGTAATATATTTAAGTAATGTAAATTAT
Found at i:58995937 original size:47 final size:47
Alignment explanation
Indices: 58995886--58996059 Score: 218
Period size: 47 Copynumber: 3.8 Consensus size: 47
58995876 ACATATTTTA
*
58995886 GTAAGTAATGTAAGTAATGTAATATATACTTAAAAATATATATTTCG
1 GTAAGTAATGTAAGTAATGTAATATATACTTAAGAATATATATTTCG
58995933 GTAAGTAATGTAAGTAATGTAATATATACTTAAGAATATATA-TT--
1 GTAAGTAATGTAAGTAATGTAATATATACTTAAGAATATATATTTCG
* * * * * *
58995977 -TAAGTAATGTAAATAAAGTAA-ACT-GAGTTATGTA-ATATATTTCG
1 GTAAGTAATGTAAGTAATGTAATA-TATACTTAAGAATATATATTTCG
*
58996021 GTAAGTAATGTAAGTAATGTAATATATGCTTAAGAATAT
1 GTAAGTAATGTAAGTAATGTAATATATACTTAAGAATAT
58996060 TGCGTTTTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.05
42 9 0.09
43 20 0.19
45 20 0.19
46 8 0.08
47 43 0.41
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.37
Consensus pattern (47 bp):
GTAAGTAATGTAAGTAATGTAATATATACTTAAGAATATATATTTCG
Found at i:58998634 original size:17 final size:18
Alignment explanation
Indices: 58998597--58998634 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
58998587 TAAAGCATAA
58998597 CCCCTAAACCCTAAATCC
1 CCCCTAAACCCTAAATCC
*
58998615 CCCCTAAACCTTAAATCC
1 CCCCTAAACCCTAAATCC
58998633 CC
1 CC
58998635 TTACCCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (18 bp):
CCCCTAAACCCTAAATCC
Found at i:58998902 original size:14 final size:14
Alignment explanation
Indices: 58998883--58998909 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58998873 GAAACGGATG
58998883 AAATTTGGTATAAT
1 AAATTTGGTATAAT
58998897 AAATTTGGTATAA
1 AAATTTGGTATAA
58998910 AAAAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
AAATTTGGTATAAT
Found at i:58998933 original size:32 final size:31
Alignment explanation
Indices: 58998897--58998958 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
58998887 TTGGTATAAT
58998897 AAATTTGGTATAAAAAAAAT-TATTTTTTTATA
1 AAATTTGGTAT--AAAAAATGTATTTTTTTATA
58998929 AAATTTGGTATAAAAAATGTATTTTTTTAT
1 AAATTTGGTATAAAAAATGTATTTTTTTAT
58998959 CCAATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 7 0.24
31 11 0.38
32 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (31 bp):
AAATTTGGTATAAAAAATGTATTTTTTTATA
Found at i:59000232 original size:114 final size:112
Alignment explanation
Indices: 58999995--59000431 Score: 434
Period size: 114 Copynumber: 3.8 Consensus size: 112
58999985 ATTTTCAAAT
* * **
58999995 CCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAACGACG
1 CCCTGAGCATTAGCGGCGC-TT-CTAAAAACGCCGCTAAAT-CCCCAAAAGCTCAGAAAACGGTG
* *** * * *
59000060 CCGTTGGGCTTA-GTTTTTCTTGCGGCGCTACCCCAAAAACGCCGTTAAAT
63 TCGTTGGGCTTAGGTTTTT-TTGCGGCGCTTTTCCAAAAATGCCGCTAAAG
* * * *
59000110 CCCCGAGCACTAGCGGCGCTTCTAGAGAAACGCCGCTAGATCCCCAAAATCTCAGAAAACAGG-G
1 CCCTGAGCATTAGCGGCGCTTCTA-A-AAACGCCGCTAAATCCCCAAAAGCTCAGAAAAC-GGTG
* *
59000174 TCGTTGGGCTTAGGTTATTTTGCGGCGCTTTTCCAAAAGTGCCGCTAAAG
63 TCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAATGCCGCTAAAG
* * * *
59000224 CCATGAGCATTAGCGGCGCTCCCTTAAAAACGCCGCTAAATCCCTGAAAAGCTTAG-AAACGGTG
1 CCCTGAGCATTAGCGGCGCT-TC-TAAAAACGCCGCTAAATCCC-CAAAAGCTCAGAAAACGGTG
*
59000288 TCGTTGGGCTTAGGTTTTTTTACGGCGCTTCTT-CAAAAATGCCGCTAAAG
63 TCGTTGGGCTTAGGTTTTTTTGCGGCGCTT-TTCCAAAAATGCCGCTAAAG
* * * * * * * * *
59000338 CCCTAAGTATTAGCGGCACTTTAATAAAAATGCCGCTAAACCCCCGAATGCTAAGAAAACGGTGT
1 CCCTGAGCATTAGCGGCGC-TT-CTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGTGT
*
59000403 CGTTGGGCTTAGG-TTTTTTGCGACGCTTT
64 CGTTGGGCTTAGGTTTTTTTGCGGCGCTTT
59000432 CTGGAAAACG
Statistics
Matches: 269, Mismatches: 41, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
112 1 0.00
113 25 0.09
114 192 0.71
115 49 0.18
116 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (112 bp):
CCCTGAGCATTAGCGGCGCTTCTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGTGTCG
TTGGGCTTAGGTTTTTTTGCGGCGCTTTTCCAAAAATGCCGCTAAAG
Found at i:59000397 original size:228 final size:228
Alignment explanation
Indices: 58999998--59000431 Score: 513
Period size: 228 Copynumber: 1.9 Consensus size: 228
58999988 TTCAAATCCC
*
58999998 TGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAACGACGCCG
1 TGAGCATTAGCGGCGCTTCCCTAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAACGACGCCG
* * * * *
59000063 TTGGGCTTAGTTTTTCTTGCGGCGCTACCCCAAAAACGCCGTTAAATCCCCGAGCACTAGCGGCG
66 TTGGGCTTAGTTTTTCTTACGGCGCTACCCCAAAAACGCCGCTAAAGCCCCAAGCACTAGCGGCA
* * *
59000128 CTTCTAGAGAAACGCCGCTAGATCCCCAAAATCTCAGAAAACAGG-GTCGTTGGGCTTAGGTTAT
131 CTTCTAGAAAAACGCCGCTAGAACCCCAAAATCTAAGAAAAC-GGTGTCGTTGGGCTTAGGTT-T
*
59000192 TTTGCGGCGCTTTTCCAAAAGTGCCGCTAAAGCCA
194 TTTGCGACGCTTTTCCAAAAGTGCCGCTAAAGCCA
* ** ** *
59000227 TGAGCATTAGCGGCGC-TCCCTTAAAAACGCCGCTAAAT-CCCTGAAAAGCTTAG-AAACGGTGT
1 TGAGCATTAGCGGCGCTTCCC-TAAAAACGCCGCTAAATCCCCCG-AAAGCACAGAAAACGACGC
* ** * * * *
59000289 CGTTGGGCTTAGGTTTTT-TTACGGCGCTTCTTCAAAAATGCCGCTAAAGCCCTAAGTATTAGCG
64 CGTTGGGCTTA-GTTTTTCTTACGGCGCTACCCCAAAAACGCCGCTAAAGCCCCAAGCACTAGCG
* * **
59000353 GCACTT-TAATAAAAATGCCGCTA-AACCCCCGAATGCTAAGAAAACGGTGTCGTTGGGCTTAGG
128 GCACTTCT-AGAAAAACGCCGCTAGAACCCCAAAAT-CTAAGAAAACGGTGTCGTTGGGCTTAGG
59000416 TTTTTTGCGACGCTTT
191 TTTTTTGCGACGCTTT
59000432 CTGGAAAACG
Statistics
Matches: 172, Mismatches: 27, Indels: 14
0.81 0.13 0.07
Matches are distributed among these distances:
227 24 0.14
228 102 0.59
229 46 0.27
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (228 bp):
TGAGCATTAGCGGCGCTTCCCTAAAAACGCCGCTAAATCCCCCGAAAGCACAGAAAACGACGCCG
TTGGGCTTAGTTTTTCTTACGGCGCTACCCCAAAAACGCCGCTAAAGCCCCAAGCACTAGCGGCA
CTTCTAGAAAAACGCCGCTAGAACCCCAAAATCTAAGAAAACGGTGTCGTTGGGCTTAGGTTTTT
TGCGACGCTTTTCCAAAAGTGCCGCTAAAGCCA
Found at i:59002045 original size:18 final size:18
Alignment explanation
Indices: 59002003--59002046 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
59001993 AAAGGAGGAT
* *
59002003 TAGATGAACCAATTGAAT
1 TAGAAGAACCAATTGAAG
* *
59002021 TAAAAGAACCAATTGGAG
1 TAGAAGAACCAATTGAAG
59002039 TAGAAGAA
1 TAGAAGAA
59002047 ACACTAAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (18 bp):
TAGAAGAACCAATTGAAG
Found at i:59002728 original size:41 final size:40
Alignment explanation
Indices: 59002600--59002823 Score: 187
Period size: 41 Copynumber: 5.5 Consensus size: 40
59002590 TTCAGCGGCA
* *
59002600 TTTTTAAAAAAAGCGCCGCTAATGCTCAGATCTTTAGCTGCG
1 TTTTT-AAAAAAGCGCCGCTAATGCTCAGAGCTTTAGC-GGG
* * * ** **
59002642 TTTTTGAAAAAGTGTCGCTAATGCTCAGATATTTAGCGACA
1 TTTTTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCG-GG
*
59002683 TTTTTAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCAGGG
1 TTTTTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGC-GGG
* * * * * *
59002724 TTTTTCAAGAAGCGCTGCTAATGCTCCGGGCTTTAGTGGTG
1 TTTTTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGG-G
** * * * *
59002765 TTTTCCAAGAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCA
1 TTTTTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGG-G
*
59002806 TTTTTGAAAAAGCGCCGC
1 TTTTTAAAAAAGCGCCGC
59002824 AAAAACATTT
Statistics
Matches: 152, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
40 3 0.02
41 143 0.94
42 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (40 bp):
TTTTTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGG
Found at i:59002744 original size:82 final size:83
Alignment explanation
Indices: 59002593--59002749 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 83
59002583 TCGGGGCTTC
* ** * * *
59002593 AGCGGCATTTTTAAAAAAAGCGCCGCTAATGCTCAGATCTTTAGCTGCGTTTTTGAAAAAGTGTC
1 AGCGACATTTTTAAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCAGCGTTTTTCAAAAAGCGTC
59002658 GCTAATGCTCAGATATTT
66 GCTAATGCTCAGATATTT
* *
59002676 AGCGACATTTTT-AAAAAAGCGCCGCTAATGCTCAGAGATTTAGCAGGGTTTTTCAAGAAGCG-C
1 AGCGACATTTTTAAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCAGCGTTTTTCAAAAAGCGTC
59002739 TGCTAATGCTC
66 -GCTAATGCTC
59002750 CGGGCTTTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 1 0.02
82 53 0.82
83 11 0.17
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (83 bp):
AGCGACATTTTTAAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCAGCGTTTTTCAAAAAGCGTC
GCTAATGCTCAGATATTT
Found at i:59002858 original size:20 final size:19
Alignment explanation
Indices: 59002830--59002875 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
59002820 CCGCAAAAAC
*
59002830 ATTTTATTTGTCTATTTACT
1 ATTTAATTTGTCTATTTA-T
*
59002850 ATTTAATTTGTTTATTTAT
1 ATTTAATTTGTCTATTTAT
59002869 A-TTAATT
1 ATTTAATT
59002876 AAAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
ATTTAATTTGTCTATTTAT
Found at i:59003259 original size:14 final size:15
Alignment explanation
Indices: 59003231--59003263 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
59003221 AAGGTTTATA
59003231 GATTATGGAATTAGG
1 GATTATGGAATTAGG
59003246 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
59003260 GATT
1 GATT
59003264 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:59003534 original size:21 final size:21
Alignment explanation
Indices: 59003510--59003552 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59003500 AGGTTTAGGG
* *
59003510 GTTAGTGGTTTGGGGTTAAGA
1 GTTAGTGATTTAGGGTTAAGA
*
59003531 GTTAGTGATTTAGGGTTTAGA
1 GTTAGTGATTTAGGGTTAAGA
59003552 G
1 G
59003553 ATTCAGGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
GTTAGTGATTTAGGGTTAAGA
Found at i:59003928 original size:4 final size:4
Alignment explanation
Indices: 59003914--59003946 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
59003904 ATATTAGATT
*
59003914 TAAA AAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
59003947 GTAACAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:59004571 original size:23 final size:23
Alignment explanation
Indices: 59004536--59004585 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
59004526 ATAAATTTCT
* *
59004536 CCCCCTCTGAAATCCCCAACTTC
1 CCCCCCCTAAAATCCCCAACTTC
* *
59004559 CCCCCCCTAAAATCCCTAATTTC
1 CCCCCCCTAAAATCCCCAACTTC
59004582 CCCC
1 CCCC
59004586 TTGAAACCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.54, G:0.02, T:0.22
Consensus pattern (23 bp):
CCCCCCCTAAAATCCCCAACTTC
Found at i:59004817 original size:24 final size:23
Alignment explanation
Indices: 59004785--59004834 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
59004775 GTCGAAAGTT
59004785 ACAACCAAAAAACATAAAATATGA
1 ACAACC-AAAAACATAAAATATGA
* *
59004809 ACAATCAAAAACCTAAAATATGA
1 ACAACCAAAAACATAAAATATGA
59004832 ACA
1 ACA
59004835 CTAATCGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.64, C:0.18, G:0.04, T:0.14
Consensus pattern (23 bp):
ACAACCAAAAACATAAAATATGA
Found at i:59008493 original size:42 final size:42
Alignment explanation
Indices: 59008447--59008527 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
59008437 ATAGTGGCGT
* * * *
59008447 TTGTGGTATAAGCGTCGCTAAAAGTTATTATCTTTAGCGACA
1 TTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCGACA
*
59008489 TTGTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGCG
1 TTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCG
59008528 GCGTTTTCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (42 bp):
TTGTGGTAGAAGCGCCGCTAAAAGTCATGATCTTTAGCGACA
Found at i:59010561 original size:30 final size:29
Alignment explanation
Indices: 59010507--59010619 Score: 140
Period size: 27 Copynumber: 3.8 Consensus size: 29
59010497 GGGTTTATGG
*
59010507 TTTATTTTTTATATATTATTTTTTTATAGTT
1 TTTATTATTTATATATTA--TTTTTATAGTT
59010538 TTTAATTATTTATATATTATTTTTATAG-T
1 TTT-ATTATTTATATATTATTTTTATAGTT
*
59010567 TTT-TTATTTTTATATTATTTTTATAGTTT
1 TTTATTATTTATATATTATTTTTATAG-TT
*
59010596 TTTATTTTTTATATATTAATTTTT
1 TTTATTATTTATATATT-ATTTTT
59010620 TAAAAAGTAT
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
27 22 0.30
29 8 0.11
30 20 0.27
31 9 0.12
32 14 0.19
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.73
Consensus pattern (29 bp):
TTTATTATTTATATATTATTTTTATAGTT
Found at i:59010563 original size:59 final size:58
Alignment explanation
Indices: 59010500--59010619 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
59010490 GATTTTAGGG
*
59010500 TTTATGGTTTATTT-TTTATATATTATTTTTTTATAGTTTTTAATTATTTATATATT-ATT
1 TTTATAGTTT-TTTATTTATATATTA--TTTTTATAGTTTTTAATTATTTATATATTAATT
* * *
59010559 TTTATAGTTTTTTATTTTTATATTATTTTTATAGTTTTTTATTTTTTATATATTAATT
1 TTTATAGTTTTTTATTTATATATTATTTTTATAGTTTTTAATTATTTATATATTAATT
59010617 TTT
1 TTT
59010620 TAAAAAGTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
57 27 0.49
58 9 0.16
59 19 0.35
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (58 bp):
TTTATAGTTTTTTATTTATATATTATTTTTATAGTTTTTAATTATTTATATATTAATT
Found at i:59010598 original size:11 final size:11
Alignment explanation
Indices: 59010509--59010619 Score: 72
Period size: 11 Copynumber: 9.9 Consensus size: 11
59010499 GTTTATGGTT
59010509 TATT-TTTTATA
1 TATTATTTT-TA
*
59010520 TATTATTTTTT
1 TATTATTTTTA
59010531 TA-TAGTTTTTA
1 TATTA-TTTTTA
*
59010542 -ATTATTTATA
1 TATTATTTTTA
59010552 TATTATTTTTA
1 TATTATTTTTA
59010563 TAGTTTTTTATTTTTA
1 TA-----TTATTTTTA
59010579 TATTATTTTTA
1 TATTATTTTTA
*
59010590 TAGT-TTTTTA
1 TATTATTTTTA
*
59010600 T-TT-TTTATA
1 TATTATTTTTA
59010609 TATTAATTTTT
1 TATT-ATTTTT
59010620 TAAAAAGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
9 7 0.09
10 17 0.21
11 37 0.46
12 8 0.10
16 11 0.14
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TATTATTTTTA
Found at i:59010607 original size:57 final size:59
Alignment explanation
Indices: 59010500--59010648 Score: 169
Period size: 59 Copynumber: 2.5 Consensus size: 59
59010490 GATTTTAGGG
*
59010500 TTTATGGTTTATTTTTTATATATTATTTTTTTATAGTTTTTAATTATTTATATATT-ATT
1 TTTATAGTTTATTTTTTATATATTA-TTTTTTATAGTTTTTAATTATTTATATATTAATT
* * *
59010559 TTTATAGTTT-TTTATTTTTATATTA-TTTTTATAGTTTTTTATTTTTTATATATTAATTT
1 TTTATAGTTTATTT-TTTATATATTATTTTTTATAGTTTTTAATTATTTATATATTAA-TT
* *** *
59010618 TTTAAAAAGTATTTTTTATATATAATTTTTT
1 TTTATAGTTTATTTTTTATATATTATTTTTT
59010649 TTATAATTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
57 27 0.36
58 4 0.05
59 36 0.48
60 8 0.11
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (59 bp):
TTTATAGTTTATTTTTTATATATTATTTTTTATAGTTTTTAATTATTTATATATTAATT
Found at i:59010659 original size:12 final size:14
Alignment explanation
Indices: 59010599--59010660 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
59010589 ATAGTTTTTT
59010599 ATTTTTTATATATTA
1 ATTTTTTATATA-TA
* *
59010614 ATTTTTTAAAAAGT-
1 ATTTTTTATATA-TA
59010628 ATTTTTTATATATA
1 ATTTTTTATATATA
59010642 ATTTTTT-T-TATA
1 ATTTTTTATATATA
59010654 ATTTTTT
1 ATTTTTT
59010661 GAGATGTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.27
13 2 0.05
14 17 0.41
15 11 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
ATTTTTTATATATA
Found at i:59018800 original size:14 final size:14
Alignment explanation
Indices: 59018781--59018808 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59018771 ACTTCGAAAG
59018781 TCTGCTCTAAAATA
1 TCTGCTCTAAAATA
59018795 TCTGCTCTAAAATA
1 TCTGCTCTAAAATA
59018809 GGAGAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TCTGCTCTAAAATA
Found at i:59018974 original size:18 final size:19
Alignment explanation
Indices: 59018951--59019002 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
59018941 GTTATAAAAA
59018951 ATATTATATTAAT-TATAT
1 ATATTATATTAATATATAT
* *
59018969 ATATTA-AATAATATTTAT
1 ATATTATATTAATATATAT
*
59018987 ATATTTATATTTATAT
1 ATA-TTATATTAATAT
59019003 TAAATCACCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 5 0.19
18 13 0.48
19 3 0.11
20 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATATTAATATATAT
Found at i:59018994 original size:28 final size:29
Alignment explanation
Indices: 59018945--59019007 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
59018935 TATTATGTTA
*
59018945 TAAAAAATATTATATTAATTATA-TATAT
1 TAAATAATATTATATTAATTATATTATAT
*
59018973 TAAATAATATT-TATATATTTATATTTATAT
1 TAAATAATATTATAT-TAATTATA-TTATAT
59019003 TAAAT
1 TAAAT
59019008 CACCAACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 17 0.57
30 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TAAATAATATTATATTAATTATATTATAT
Found at i:59021088 original size:50 final size:50
Alignment explanation
Indices: 59020971--59021093 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
59020961 ACATTAAGAG
** * *
59020971 GATGAG-A-TCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGAGACATAACATGGGCACCGA
** **
59021019 GATGAGAGGTCCCCCGTAAGACCATGTCTGAGACATAACATGGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGAGACATAACATGGGCACCGA
* *
59021069 TATTAGAACTCCCATGTAAGACCAT
1 GATGAGAACTCCCATGTAAGACCAT
59021094 ATTTGGGATA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 6 0.10
50 54 0.90
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.20
Consensus pattern (50 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGAGACATAACATGGGCACCGA
Found at i:59021390 original size:20 final size:20
Alignment explanation
Indices: 59021365--59021403 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
59021355 TGAATTATTT
59021365 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
59021385 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
59021404 GAAGAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:59025414 original size:20 final size:20
Alignment explanation
Indices: 59025379--59025427 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
59025369 ATCATGGTCT
*
59025379 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
59025398 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
59025418 TTGCTTACTT
1 TTGCTTACTT
59025428 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:59025756 original size:50 final size:50
Alignment explanation
Indices: 59025637--59025814 Score: 155
Period size: 50 Copynumber: 3.6 Consensus size: 50
59025627 CATGCGAAAA
** * * * **
59025637 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--TGTAAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAATG
* * * * **
59025686 TCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATCGGTGCCCAA-G
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAATG
* ** *
59025736 CCATGTCCCATACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
*
59025786 CCATGTCCTAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
59025815 TCTCATCCTC
Statistics
Matches: 100, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 1 0.01
49 34 0.34
50 63 0.63
51 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATG
Found at i:59032989 original size:20 final size:20
Alignment explanation
Indices: 59032966--59033011 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
59032956 TGTTAATATT
*
59032966 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
59032986 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
59033006 TTGTTA
1 TTGTTA
59033012 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:59036279 original size:20 final size:21
Alignment explanation
Indices: 59036256--59036301 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
59036246 TGTTAATATT
59036256 TTGTTAT-TTATTCAAATAGG
1 TTGTTATCTTATTCAAATAGG
*
59036276 TTGTT-TCTTATTTAAATAGG
1 TTGTTATCTTATTCAAATAGG
59036296 TTGTTA
1 TTGTTA
59036302 AGCTTTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (21 bp):
TTGTTATCTTATTCAAATAGG
Found at i:59036691 original size:27 final size:27
Alignment explanation
Indices: 59036661--59036808 Score: 167
Period size: 27 Copynumber: 5.5 Consensus size: 27
59036651 TACGATTCGT
59036661 GGTAAAATTACTGAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
59036688 GGTAAAATTA-TCGAAATACCCCCGAAG
1 GGTAAAATTACT-GAAATACCCTCGAAG
*
59036715 GAG-AAAATTA-TCAAAATACCCTCGAAG
1 G-GTAAAATTACT-GAAATACCCTCGAAG
* **
59036742 GGCAAAATTACCAAAATACCCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
* * *
59036769 GGTAAAACTACCGAAATACTCTCGAAG
1 GGTAAAATTACTGAAATACCCTCGAAG
*
59036796 GGTAAAATGACTG
1 GGTAAAATTACTG
59036809 TTATACCCCT
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.02
27 103 0.97
28 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
GGTAAAATTACTGAAATACCCTCGAAG
Found at i:59037026 original size:26 final size:27
Alignment explanation
Indices: 59036951--59037026 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 27
59036941 ATAGGGGAAG
** * *
59036951 TATACTG-TACTGGTGGTTTTGCCACA
1 TATACTGTTACTGGCAGCTTTGCTACA
* * **
59036977 TATATTGTTATTGGCAGCCCTGCTACA
1 TATACTGTTACTGGCAGCTTTGCTACA
59037004 T-TACTGTTACTGGCAGCTTTGCT
1 TATACTGTTACTGGCAGCTTTGCT
59037027 GCGTCATTAT
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
26 24 0.65
27 13 0.35
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (27 bp):
TATACTGTTACTGGCAGCTTTGCTACA
Found at i:59037695 original size:20 final size:20
Alignment explanation
Indices: 59037670--59037712 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
59037660 TTCCAAACTT
59037670 AAGAAACGAGTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
59037690 AAGAAACGAGTTTTATCAAC
1 AAGAAACGAGTTTTATCAAC
59037710 AAG
1 AAG
59037713 TCTAAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (20 bp):
AAGAAACGAGTTTTATCAAC
Found at i:59038973 original size:24 final size:24
Alignment explanation
Indices: 59038939--59038993 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
59038929 AGTCGTTTTC
* * *
59038939 TTTTTTAGTCACCCAATTATGGAT
1 TTTTTTAGTCAACCAACTATGAAT
* *
59038963 TTTTTTTGTCAATCAACTATGAAT
1 TTTTTTAGTCAACCAACTATGAAT
59038987 TTTTTTA
1 TTTTTTA
59038994 AAATTTGTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTTTTAGTCAACCAACTATGAAT
Found at i:59042565 original size:25 final size:23
Alignment explanation
Indices: 59042499--59042591 Score: 66
Period size: 25 Copynumber: 3.9 Consensus size: 23
59042489 ATATAATTTC
*
59042499 TTTAAAATAAAAA-AAGATATA-AT
1 TTTAAAATAAAAATAA-A-AAAGAT
* *
59042522 TTTAAAA-AAATATGAAAAAAAACT
1 TTTAAAATAAAAAT-AAAAAAGA-T
59042546 CTTTAAAATAAAAAATAAAAAATGAT
1 -TTTAAAAT-AAAAATAAAAAA-GAT
*
59042572 TTTAAAATATAAATAAAAAA
1 TTTAAAATAAAAATAAAAAA
59042592 TTCTAAAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
22 6 0.11
23 9 0.16
24 14 0.25
25 15 0.26
26 7 0.12
27 6 0.11
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (23 bp):
TTTAAAATAAAAATAAAAAAGAT
Found at i:59042839 original size:15 final size:16
Alignment explanation
Indices: 59042819--59042854 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
59042809 TAAATTATTG
*
59042819 AAAATTGAAAATTA-A
1 AAAATTAAAAATTATA
59042834 AAAATTAAAAATTATA
1 AAAATTAAAAATTATA
59042850 AAAAT
1 AAAAT
59042855 CGATTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAATTAAAAATTATA
Found at i:59047762 original size:16 final size:17
Alignment explanation
Indices: 59047726--59047762 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
59047716 TAGTTTGCAT
59047726 ATTTA-GGATAATTGGC
1 ATTTAGGGATAATTGGC
59047742 A-TTAGGGATAATT-GC
1 ATTTAGGGATAATTGGC
59047757 ATTTAG
1 ATTTAG
59047763 TTTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (17 bp):
ATTTAGGGATAATTGGC
Found at i:59058560 original size:19 final size:19
Alignment explanation
Indices: 59058492--59058564 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
59058482 TAACGATTTT
*
59058492 CATTAGAAATATTGGTATC
1 CATTAGAAATTTTGGTATC
* *
59058511 GCATTAAAAATTTTGGTATTT
1 -CATTAGAAATTTTGGTA-TC
** *
59058532 GGTGAGAAATTTTGGTATC
1 CATTAGAAATTTTGGTATC
59058551 CATTAGAAATTTTG
1 CATTAGAAATTTTG
59058565 ATATGCCAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 12 0.29
20 28 0.68
21 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (19 bp):
CATTAGAAATTTTGGTATC
Found at i:59059101 original size:9 final size:9
Alignment explanation
Indices: 59059087--59059161 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
59059077 ATTTTTTCTA
59059087 TAAAAATAT
1 TAAAAATAT
59059096 TAAAAAT-T
1 TAAAAATAT
*
59059104 AGAAAAATAT
1 -TAAAAATAT
59059114 TAAAAAATAT
1 T-AAAAATAT
59059124 TAAAAAATAT
1 T-AAAAATAT
59059134 TAAAAA-A-
1 TAAAAATAT
59059141 T-AAAATAT
1 TAAAAATAT
*
59059149 TTAAAATAT
1 TAAAAATAT
59059158 TAAA
1 TAAA
59059162 TTTGATATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
6 4 0.07
7 2 0.04
8 3 0.05
9 28 0.49
10 20 0.35
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:59059110 original size:10 final size:10
Alignment explanation
Indices: 59059088--59059142 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
59059078 TTTTTTCTAT
59059088 AAAAATATT-
1 AAAAATATTA
59059097 -AAAA-ATTA
1 AAAAATATTA
59059105 GAAAAATATTA
1 -AAAAATATTA
59059116 AAAAATATTA
1 AAAAATATTA
59059126 AAAAATATTA
1 AAAAATATTA
59059136 AAAAATA
1 AAAAATA
59059143 AAATATTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
10 31 0.74
11 4 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATATTA
Found at i:59059111 original size:18 final size:17
Alignment explanation
Indices: 59059088--59059161 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 17
59059078 TTTTTTCTAT
59059088 AAAAATATTAAAAATTA
1 AAAAATATTAAAAATTA
59059105 GAAAAATATTAAAAAATATTA
1 -AAAAATATT--AAAA-ATTA
*
59059126 AAAAATATTAAAAAATA
1 AAAAATATTAAAAATTA
*
59059143 AAATAT-TTAAAATATTA
1 AAAAATATTAAAA-ATTA
59059160 AA
1 AA
59059162 TTTGATATAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.12
17 13 0.27
18 13 0.27
20 13 0.27
21 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAAATATTAAAAATTA
Found at i:59059189 original size:19 final size:17
Alignment explanation
Indices: 59059085--59059228 Score: 73
Period size: 18 Copynumber: 8.1 Consensus size: 17
59059075 ATATTTTTTC
*
59059085 TATAAAAATATTAAAAAT
1 TATAAAAAT-TTATAAAT
* * *
59059103 TAGAAAAATATTAAAAAA
1 TATAAAAAT-TTATAAAT
59059121 TATTAAAAAATATTA-AAA-
1 TA-T-AAAAAT-TTATAAAT
*
59059139 AATAAAATATTTA-AAA-
1 TATAAAA-ATTTATAAAT
* *
59059155 TATTAAATTTGATATAAACT
1 TATAAAAATT--TATAAA-T
59059175 TATAAAAATATTATAAA-
1 TATAAAAAT-TTATAAAT
*
59059192 TATAATAAATCTAATAAAT
1 TATAA-AAAT-TTATAAAT
59059211 TATAAAAATTTATAAAT
1 TATAAAAATTTATAAAT
59059228 T
1 T
59059229 TAATAAAAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 23
0.75 0.09 0.17
Matches are distributed among these distances:
15 2 0.02
16 15 0.15
17 18 0.17
18 36 0.35
19 14 0.14
20 17 0.17
21 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (17 bp):
TATAAAAATTTATAAAT
Found at i:59059193 original size:37 final size:34
Alignment explanation
Indices: 59059142--59059231 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 34
59059132 ATTAAAAAAT
*
59059142 AAAATATT-TAAAATATTAAATTTGATATAAACTTATA
1 AAAATATTAT-AAATATTAAATCT-A-ATAAA-TTATA
59059179 AAAATATTATAAATATAATAAATCTAATAAATTATA
1 AAAATATTATAAATAT--TAAATCTAATAAATTATA
59059215 AAAAT-TTATAAAT-TTAA
1 AAAATATTATAAATATTAA
59059232 TAAAAACATA
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
32 3 0.06
34 1 0.02
35 8 0.16
36 10 0.20
37 19 0.39
38 2 0.04
39 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (34 bp):
AAAATATTATAAATATTAAATCTAATAAATTATA
Found at i:59059234 original size:9 final size:9
Alignment explanation
Indices: 59059187--59059235 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
59059177 TAAAAATATT
*
59059187 ATAAATATA
1 ATAAATTTA
*
59059196 ATAAATCTA
1 ATAAATTTA
59059205 ATAAATTATA
1 ATAAATT-TA
59059215 A-AAATTT-
1 ATAAATTTA
59059222 ATAAATTTA
1 ATAAATTTA
59059231 ATAAA
1 ATAAA
59059236 AACATATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 1 0.03
8 7 0.20
9 24 0.69
10 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAAATTTA
Found at i:59059236 original size:18 final size:19
Alignment explanation
Indices: 59059179--59059236 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
59059169 TAAACTTATA
*
59059179 AAAATATTATAAATATAAT
1 AAAATATTATAAATTTAAT
* *
59059198 -AAATCTAATAAA-TT-AT
1 AAAATATTATAAATTTAAT
59059214 AAAA-ATTTATAAATTTAAT
1 AAAATA-TTATAAATTTAAT
59059233 AAAA
1 AAAA
59059237 ACATATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.07
17 10 0.33
18 12 0.40
19 6 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATATTATAAATTTAAT
Found at i:59059265 original size:21 final size:21
Alignment explanation
Indices: 59059214--59059269 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
59059204 AATAAATTAT
59059214 AAAAATTTATAAATTTAATAA
1 AAAAATTTATAAATTTAATAA
59059235 AAACATATTTA-AAATATTCAA-AA
1 AAA-A-ATTTATAAAT-TT-AATAA
59059258 AAAAATTT-TAAA
1 AAAAATTTATAAA
59059270 CCTATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
21 10 0.33
22 6 0.20
23 12 0.40
24 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATTTATAAATTTAATAA
Found at i:59059326 original size:19 final size:20
Alignment explanation
Indices: 59059304--59059356 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
59059294 TAAAAATTCA
*
59059304 TAAAAATT-TTAAAAAATAT
1 TAAAAATTGATAAAAAATAT
*
59059323 T-AAAATTGATATAAAATAT
1 TAAAAATTGATAAAAAATAT
*
59059342 TAAAAAAT-ATAAAAA
1 TAAAAATTGATAAAAA
59059357 GAATCATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 17 0.61
20 5 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAATTGATAAAAAATAT
Found at i:59059326 original size:29 final size:29
Alignment explanation
Indices: 59059294--59059371 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
59059284 TAACAACTTA
59059294 TAAAAATTCATAAAAATTTTAAAAAATAT
1 TAAAAATTCATAAAAATTTTAAAAAATAT
* *
59059323 T-AAAATTGATATAAAATATTAAAAAATAT
1 TAAAAATTCATA-AAAATTTTAAAAAATAT
* *
59059352 AAAAAGAATCATAAAAATTT
1 TAAAA-ATTCATAAAAATTT
59059372 GAACTGGACC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 9 0.22
29 17 0.43
30 9 0.22
31 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAAAATTCATAAAAATTTTAAAAAATAT
Found at i:59059984 original size:27 final size:29
Alignment explanation
Indices: 59059954--59060012 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
59059944 ATAATTTTTA
59059954 ATATT-TTAATAATT-TATTA-GAATATTT
1 ATATTATTAATAATTAT-TTATGAATATTT
* *
59059981 ATATTATTTATAATTATTTATGAATTTTT
1 ATATTATTAATAATTATTTATGAATATTT
59060010 ATA
1 ATA
59060013 AGTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
ATATTATTAATAATTATTTATGAATATTT
Found at i:59059998 original size:10 final size:10
Alignment explanation
Indices: 59059976--59060028 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
59059966 TTTATTAGAA
59059976 TATTTAT-AT
1 TATTTATAAT
59059985 TATTTATAAT
1 TATTTATAAT
59059995 TATTTATGAAT
1 TATTTAT-AAT
59060006 T-TTTATAAGT
1 TATTTATAA-T
59060016 T-TTTATAA-
1 TATTTATAAT
59060024 TATTT
1 TATTT
59060029 TAAATATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 12 0.30
10 23 0.57
11 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
TATTTATAAT
Found at i:59060034 original size:9 final size:10
Alignment explanation
Indices: 59059947--59060035 Score: 59
Period size: 10 Copynumber: 9.2 Consensus size: 10
59059937 TTTCTATATA
59059947 ATTTT-TAAT
1 ATTTTATAAT
59059956 ATTTTAATAAT
1 ATTTT-ATAAT
*
59059967 -TTATTAGAAT
1 ATT-TTATAAT
*
59059977 A-TTTATATT
1 ATTTTATAAT
59059986 A-TTTATAAT
1 ATTTTATAAT
59059995 -TATTTATGAAT
1 AT-TTTAT-AAT
59060006 -TTTTATAAGT
1 ATTTTATAA-T
59060016 -TTTTATAAT
1 ATTTTATAAT
59060025 ATTTTA-AAT
1 ATTTTATAAT
59060034 AT
1 AT
59060036 ATCTTATTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
9 26 0.39
10 31 0.46
11 10 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTTTATAAT
Found at i:59060058 original size:28 final size:25
Alignment explanation
Indices: 59060018--59060070 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
59060008 TTATAAGTTT
59060018 TTATAATATTTTAAATATATCTTATTAA
1 TTATAATATTTT-AATA-AT-TTATTAA
59060046 TTAT-ATATTTTTAATAATTTATTAA
1 TTATAATA-TTTTAATAATTTATTAA
59060071 AATTTATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 7 0.29
28 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTATAATATTTTAATAATTTATTAA
Found at i:59060067 original size:25 final size:28
Alignment explanation
Indices: 59060018--59060070 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
59060008 TTATAAGTTT
59060018 TTATAATATTTTAAATATATCTTATTAA
1 TTATAATATTTTAAATATATCTTATTAA
*
59060046 TTAT-ATATTTTTAATA-AT-TTATTAA
1 TTATAATATTTTAAATATATCTTATTAA
59060071 AATTTATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 7 0.29
26 2 0.08
27 11 0.46
28 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
TTATAATATTTTAAATATATCTTATTAA
Found at i:59060077 original size:28 final size:27
Alignment explanation
Indices: 59060017--59060146 Score: 72
Period size: 29 Copynumber: 4.6 Consensus size: 27
59060007 TTTATAAGTT
*
59060017 TTTATAATATTTTAAATATATCTTATTAA
1 TTTAT-ATATTTTTAATA-ATCTTATTAA
59060046 -TTATATATTTTTAATAAT-TTATTAAAA
1 TTTATATATTTTTAATAATCTTATT--AA
* * *
59060073 TTTATTAGATTTTTTATAATCTT-TACAA
1 TTTA-TATATTTTTAATAATCTTAT-TAA
* *
59060101 GTTTTTATGATTTTTTAAT-AT-TTAATAA
1 -TTTATAT-A-TTTTTAATAATCTTATTAA
*
59060129 TTTATATTATTTCTAATA
1 TTTATA-TATTTTTAATA
59060147 TTTTTTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
25 5 0.06
26 9 0.12
27 19 0.24
28 16 0.21
29 20 0.26
30 9 0.12
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTATATATTTTTAATAATCTTATTAA
Found at i:59060091 original size:29 final size:29
Alignment explanation
Indices: 59060052--59060117 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
59060042 TTAATTATAT
* *
59060052 ATTTTTAATAATTTATTA-AAATTTATTA-G
1 ATTTTTTATAATCT-TTACAAATTT-TTATG
*
59060081 ATTTTTTATAATCTTTACAAGTTTTTATG
1 ATTTTTTATAATCTTTACAAATTTTTATG
59060110 ATTTTTTA
1 ATTTTTTA
59060118 ATATTTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (29 bp):
ATTTTTTATAATCTTTACAAATTTTTATG
Found at i:59063344 original size:2 final size:2
Alignment explanation
Indices: 59063337--59063361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59063327 GCATTGAAAT
59063337 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
59063362 TGTTTTGAAT
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:59068584 original size:22 final size:20
Alignment explanation
Indices: 59068522--59068586 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
59068512 ACATATGTAC
*
59068522 ATTAAAAAATATACATGT-AA
1 ATTAAAAAAT-TACATATAAA
*
59068542 A-T-AATAATTACATATAAA
1 ATTAAAAAATTACATATAAA
59068560 ATTAAAAAATTACATTATTAAA
1 ATTAAAAAATTACA-TA-TAAA
59068582 ATTAA
1 ATTAA
59068587 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 6 0.16
18 8 0.22
19 2 0.05
20 10 0.27
21 2 0.05
22 9 0.24
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (20 bp):
ATTAAAAAATTACATATAAA
Found at i:59068592 original size:22 final size:20
Alignment explanation
Indices: 59068544--59068592 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
59068534 ACATGTAAAT
59068544 AATAATTACATATAAAATTA
1 AATAATTACATATAAAATTA
*
59068564 AAAAATTACATTATTAAAATTA
1 AATAATTACA-TA-TAAAATTA
*
59068586 ATTAATT
1 AATAATT
59068593 TTAAGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 13 0.54
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATTACATATAAAATTA
Found at i:59070291 original size:44 final size:42
Alignment explanation
Indices: 59070243--59070470 Score: 145
Period size: 44 Copynumber: 5.2 Consensus size: 42
59070233 CAACTTCAGA
*
59070243 GAGATAAGATTTACCATCCTCGATCTACTCCACTACTGCTTAGG
1 GAGATAAGATTTA--ATCTTCGATCTACTCCACTACTGCTTAGG
* * * *
59070287 GAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCTTAAG
1 GAGATAAGAT-T-TAATCTTCGATCTACTCCACTACTGCTTAGG
* * *** *
59070331 GAGACAAGGCTGGGGA-CTTCGATCTGCTCCACTACTGCTTAGG
1 GAGATAA-GAT-TTAATCTTCGATCTACTCCACTACTGCTTAGG
* * * * *
59070374 GAGATAAGATCTGTAATTTTCAACCTACTCCACTACTACTCAGG
1 GAGATAAGAT-T-TAATCTTCGATCTACTCCACTACTGCTTAGG
* * *** * *
59070418 GAGACAAGGCTGGGGA-CTTTGATCTGCTCCACTACTGCTTAGG
1 GAGATAA-GAT-TTAATCTTCGATCTACTCCACTACTGCTTAGG
59070461 GAGATAAGAT
1 GAGATAAGAT
59070471 CTGCAATTTT
Statistics
Matches: 135, Mismatches: 43, Indels: 14
0.70 0.22 0.07
Matches are distributed among these distances:
42 4 0.03
43 55 0.41
44 69 0.51
45 5 0.04
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (42 bp):
GAGATAAGATTTAATCTTCGATCTACTCCACTACTGCTTAGG
Found at i:59070366 original size:87 final size:87
Alignment explanation
Indices: 59070262--59070535 Score: 476
Period size: 87 Copynumber: 3.1 Consensus size: 87
59070252 TTTACCATCC
*
59070262 TCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCT
* *
59070327 TAAGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
*
59070349 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTACT
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCT
59070414 CAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
* * * *
59070436 TTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCCACTGCTGCC
1 TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCT
59070501 CAGGGAGACAAGGCTGGGGACT
66 CAGGGAGACAAGGCTGGGGACT
59070523 TCGATCTGCTCCA
1 TCGATCTGCTCCA
59070536 TTATCGGTGC
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 177 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (87 bp):
TCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTACTGCT
CAGGGAGACAAGGCTGGGGACT
Found at i:59070377 original size:43 final size:43
Alignment explanation
Indices: 59070314--59070535 Score: 187
Period size: 43 Copynumber: 5.1 Consensus size: 43
59070304 TTTCAACCTA
*
59070314 CTCCACTACTGCTTAAGGAGACAAGGCTGGGGACTTCGATCTG
1 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGACTTCGATCTG
* * ** * * * *
59070357 CTCCACTACTGCTTAGGGAGATAAGATCT-GTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAAG-GCTGGGGA-CTTCGATCTG
* * *
59070401 CTCCACTACTACTCAGGGAGACAAGGCTGGGGACTTTGATCTG
1 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGACTTCGATCTG
* * ** * * * *
59070444 CTCCACTACTGCTTAGGGAGATAAGATCT-GCAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAAG-GCTGGGGA-CTTCGATCTG
* **
59070488 CTCCACTGCTGCCCAGGGAGACAAGGCTGGGGACTTCGATCTG
1 CTCCACTACTGCTTAGGGAGACAAGGCTGGGGACTTCGATCTG
59070531 CTCCA
1 CTCCA
59070536 TTATCGGTGC
Statistics
Matches: 131, Mismatches: 42, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
43 69 0.53
44 62 0.47
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGACAAGGCTGGGGACTTCGATCTG
Found at i:59070506 original size:44 final size:44
Alignment explanation
Indices: 59070267--59070508 Score: 231
Period size: 44 Copynumber: 5.5 Consensus size: 44
59070257 CATCCTCGAT
*
59070267 CTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGATCTGGAATTTTCAAC
* * * * * * *
59070311 CTACTCCACTACTGCTTAAGGAGACAAG-GCTGGGGA-CTTCGAT
1 CTACTCCACTACTGCTTAGGGAGATAAGATCT-GGAATTTTCAAC
* *
59070354 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGATCTGGAATTTTCAAC
* * * * * * * *
59070398 CTACTCCACTACTACTCAGGGAGACAAG-GCTGGGGACTTT-GAT
1 CTACTCCACTACTGCTTAGGGAGATAAGATCT-GGAATTTTCAAC
* *
59070441 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAAC
1 CTACTCCACTACTGCTTAGGGAGATAAGATCTGGAATTTTCAAC
* **
59070485 CTACTCCACTGCTGCCCAGGGAGA
1 CTACTCCACTACTGCTTAGGGAGA
59070509 CAAGGCTGGG
Statistics
Matches: 151, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
43 65 0.43
44 86 0.57
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CTACTCCACTACTGCTTAGGGAGATAAGATCTGGAATTTTCAAC
Found at i:59070617 original size:88 final size:88
Alignment explanation
Indices: 59070466--59071002 Score: 716
Period size: 88 Copynumber: 6.1 Consensus size: 88
59070456 TTAGGGAGAT
* * * ** * * * * *
59070466 AAGATCTGCAATTTTCAACCTACTCCACTGCTGCCCAGGGAGACAAGGCTGGGGACTTCGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
* ** * *
59070531 CTCCATTATCGGTGCAGGAAGGC
66 CTTCGCTGTCGGCGCAGGAAGGC
* * *
59070554 AAGATCTGCTATTTTTAACCTGTTCCGCTGCAACCAAGGGAGGCAAGGTTGGTGTCTTTGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
59070619 CTTCGCTGTCGGCGCAGGAAGGC
66 CTTCGCTGTCGGCGCAGGAAGGC
* * * *
59070642 AAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGTGAGGTAAGGCTGGTGT-TTTCGATCT
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTT-GATCT
*
59070706 GCTTCACTGTCGGCGCAGGAAGGC
65 GCTTCGCTGTCGGCGCAGGAAGGC
59070730 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
* * *
59070795 TTTCGTTGTTGGCGCAGGAAGGC
66 CTTCGCTGTCGGCGCAGGAAGGC
** * * *
59070818 AAGATCTGCTATTTTTAAACCTGCTCTGCTGCAACCCCGGGAGGCAAGGTTAGTGTCTTTAATCT
1 AAGATCTGCTATTTTT-AACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCT
*
59070883 GCTTCGCTGTCGGCGCAAGAAGGC
65 GCTTCGCTGTCGGCGCAGGAAGGC
* *
59070907 AAGATCTGCTATTTTTAACCTGCTCCACTACAACCCAGGGAGGCAAGGTTGGTGTCTTCGATCTG
1 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
***
59070972 CTTCGCTGTCAATGCAGGAAGGC
66 CTTCGCTGTCGGCGCAGGAAGGC
59070995 AAGATCTG
1 AAGATCTG
59071003 TTATCTTCAC
Statistics
Matches: 394, Mismatches: 52, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
87 3 0.01
88 309 0.78
89 82 0.21
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (88 bp):
AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
CTTCGCTGTCGGCGCAGGAAGGC
Found at i:59070907 original size:265 final size:264
Alignment explanation
Indices: 59070466--59071002 Score: 768
Period size: 265 Copynumber: 2.0 Consensus size: 264
59070456 TTAGGGAGAT
**
59070466 AAGATCTGCAATTTTCAACCTACTCCACTGCTGCCCAGGGAGACAAGGCTGGGGACTTCGATCTG
1 AAGATCTGCAATTTTCAACCTACTCCACTGCAACCCAGGGAGACAAGGCTGGGGACTTCGATCTG
* *
59070531 CTCCATTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGTTCCGCTGCAACCAAGGGAG
66 CTCCATTATCGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCAAGGGAG
* * *
59070596 GCAAGGTTGGTGTCTTTGATCTGCTTCGCTGTCGGCGCAGGAAGGCAAGATCTGCTATTTTTAAC
131 GCAAGGTTAGTGTCTTTAATCTGCTTCGCTGTCGGCGCAAGAAGGCAAGATCTGCTATTTTTAAC
* * * * * **
59070661 CTGCTCCGCTGCAACCCAGTGAGGTAAGGCTGGTGTTTTCGATCTGCTTCACTGTCGGCGCAGGA
196 CTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCAACGCAGGA
59070726 AGGC
261 AGGC
* * * * * * * *
59070730 AAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCAGGGAGGCAAGGTTGGTGTCTTTGATCTG
1 AAGATCTGCAATTTTCAACCTACTCCACTGCAACCCAGGGAGACAAGGCTGGGGACTTCGATCTG
* * * * * * **
59070795 TTTCGTTGTTGGCGCAGGAAGGCAAGATCTGCTATTTTTAAACCTGCTCTGCTGCAACCCCGGGA
66 CTCCATTATCGGCGCAGGAAGGCAAGATCTGCTATTTTT-AACCTGCTCCGCTGCAACCAAGGGA
59070860 GGCAAGGTTAGTGTCTTTAATCTGCTTCGCTGTCGGCGCAAGAAGGCAAGATCTGCTATTTTTAA
130 GGCAAGGTTAGTGTCTTTAATCTGCTTCGCTGTCGGCGCAAGAAGGCAAGATCTGCTATTTTTAA
* * *
59070925 CCTGCTCCACTACAACCCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCAATGCAGG
195 CCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCAACGCAGG
59070990 AAGGC
260 AAGGC
59070995 AAGATCTG
1 AAGATCTG
59071003 TTATCTTCAC
Statistics
Matches: 239, Mismatches: 33, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
264 88 0.37
265 151 0.63
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (264 bp):
AAGATCTGCAATTTTCAACCTACTCCACTGCAACCCAGGGAGACAAGGCTGGGGACTTCGATCTG
CTCCATTATCGGCGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCAAGGGAG
GCAAGGTTAGTGTCTTTAATCTGCTTCGCTGTCGGCGCAAGAAGGCAAGATCTGCTATTTTTAAC
CTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCACTGTCAACGCAGGA
AGGC
Found at i:59077205 original size:12 final size:11
Alignment explanation
Indices: 59077188--59077221 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
59077178 AATACACATG
59077188 AATTTATATATA
1 AATTTATATA-A
59077200 AATTTATA-AA
1 AATTTATATAA
59077210 AATTTATATAA
1 AATTTATATAA
59077221 A
1 A
59077222 CAAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 4 0.19
12 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTATATAA
Found at i:59077557 original size:22 final size:20
Alignment explanation
Indices: 59077508--59077557 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
59077498 TACATGTAAA
59077508 TAATAATTATATATAAAAAT
1 TAATAATTATATATAAAAAT
* *
59077528 TAAAAATTATATTATTAAAAT
1 TAATAATTATA-TATAAAAAT
59077549 TAATTAATT
1 TAA-TAATT
59077558 TTAAGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 11 0.44
22 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATAATTATATATAAAAAT
Found at i:59088632 original size:27 final size:27
Alignment explanation
Indices: 59088566--59088632 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
59088556 TATTACAAAA
* *
59088566 TATGCCACAAAGACAATTCATATAGAG
1 TATGCCACAAAGGCAATTCATACAGAG
* *
59088593 TATGCCAAAAAGGCGATTCATACAGAG
1 TATGCCACAAAGGCAATTCATACAGAG
59088620 TATGCCACAAAGG
1 TATGCCACAAAGG
59088633 TTGACAGGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
TATGCCACAAAGGCAATTCATACAGAG
Found at i:59092105 original size:2 final size:2
Alignment explanation
Indices: 59092098--59092140 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
59092088 NNNNNNCAAC
*
59092098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59092140 A
1 A
59092141 AACGTGATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59099641 original size:43 final size:43
Alignment explanation
Indices: 59099580--59099666 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
59099570 TCTACCTGGC
* *
59099580 AAAGTTGTTTTATCTTAACCGGCTCTTCTTACAATGCTTAGCT
1 AAAGTTGTTTTATCTTAACCGGCTATTCTTACAATCCTTAGCT
* *
59099623 AAAGTTGTTTTATCTTAACTGGTTATTCTTACAATCCTTAGCT
1 AAAGTTGTTTTATCTTAACCGGCTATTCTTACAATCCTTAGCT
59099666 A
1 A
59099667 CTTCATGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (43 bp):
AAAGTTGTTTTATCTTAACCGGCTATTCTTACAATCCTTAGCT
Found at i:59101911 original size:30 final size:30
Alignment explanation
Indices: 59101871--59101932 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
59101861 TCACTGTTCA
59101871 CTTGAATCACTGTTACTAAATTATTTATAT
1 CTTGAATCACTGTTACTAAATTATTTATAT
* *
59101901 CTTGAGTCACTGTTCCTAAATTATTTATAT
1 CTTGAATCACTGTTACTAAATTATTTATAT
59101931 CT
1 CT
59101933 GGAGCTACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (30 bp):
CTTGAATCACTGTTACTAAATTATTTATAT
Found at i:59108382 original size:144 final size:144
Alignment explanation
Indices: 59108115--59108406 Score: 494
Period size: 144 Copynumber: 2.0 Consensus size: 144
59108105 CTGGGCCCAT
*
59108115 CACAGAATTAGTTTGGGCCTTAGCCTGTTCAGATACAGTCTCAGAATGACATTAGGGCCTTGGCC
1 CACAGAATTAGTTTGGGCCTTAGCCTGTTAAGATACAGTCTCAGAATGACATTAGGGCCTTGGCC
59108180 CATATCAGATACAAAATGGAGATACAGAAAATCAGAATCCTACCCACCAACCTATACACACCATC
66 CATATCAGATACAAAATGGAGATACAGAAAATCAGAATCCTACCCACCAACCTATACACACCATC
*
59108245 TCGGTCCAATCCTA
131 TCCGTCCAATCCTA
* * *
59108259 CACAGAATTAGTTTGGGCCTTAGCTTGTTAAGATACAGTCTCAGAGTGACATTAGGGCCTTGGGC
1 CACAGAATTAGTTTGGGCCTTAGCCTGTTAAGATACAGTCTCAGAATGACATTAGGGCCTTGGCC
* * * * *
59108324 CATATCAGATACAGAATGGAGATACAGTAAATCAGAATCCTACCCACCAGCCTCTACACACTATC
66 CATATCAGATACAAAATGGAGATACAGAAAATCAGAATCCTACCCACCAACCTATACACACCATC
59108389 TCCGTCCAATCCTA
131 TCCGTCCAATCCTA
59108403 CACA
1 CACA
59108407 CCATAAGTGG
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 138 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (144 bp):
CACAGAATTAGTTTGGGCCTTAGCCTGTTAAGATACAGTCTCAGAATGACATTAGGGCCTTGGCC
CATATCAGATACAAAATGGAGATACAGAAAATCAGAATCCTACCCACCAACCTATACACACCATC
TCCGTCCAATCCTA
Found at i:59119354 original size:20 final size:20
Alignment explanation
Indices: 59119329--59119376 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
59119319 ATATTTATTT
* *
59119329 TTTATTTTTAATCATATATA
1 TTTATTTTTAATCAAACATA
59119349 TTTATTTTTAATCAAACATA
1 TTTATTTTTAATCAAACATA
*
59119369 TATATTTT
1 TTTATTTT
59119377 ATATATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATTTTTAATCAAACATA
Found at i:59127461 original size:4 final size:4
Alignment explanation
Indices: 59127452--59127505 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
59127442 AATTATTCCC
*
59127452 TAAA TAAA T-AA TAAA T-AA TAAA TAATA GTAAA TAATA TAAT TAAA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAA-A TAAA TAAA TAAA
59127500 TAAA TA
1 TAAA TA
59127506 GCATAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 9 0.21
4 24 0.57
5 6 0.14
6 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (4 bp):
TAAA
Found at i:59127466 original size:7 final size:7
Alignment explanation
Indices: 59127454--59127505 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
59127444 TTATTCCCTA
59127454 AATAAAT
1 AATAAAT
59127461 AATAAAT
1 AATAAAT
59127468 AATAAAT
1 AATAAAT
*
59127475 AAT-AGT
1 AATAAAT
59127481 AAATAATAT
1 -AATAA-AT
*
59127490 AATTAAAA
1 AA-TAAAT
59127498 AATAAAT
1 AATAAAT
59127505 A
1 A
59127506 GCATAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 2 0.05
7 25 0.68
8 6 0.16
9 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:59129747 original size:16 final size:15
Alignment explanation
Indices: 59129728--59129776 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
59129718 AATAATAAAC
59129728 AAAAATCAAAAATTAA
1 AAAAAT-AAAAATTAA
*
59129744 AAAAATTAAAATTAAA
1 AAAAATAAAAATT-AA
59129760 AAAAATAATAAA-TAA
1 AAAAATAA-AAATTAA
59129775 AA
1 AA
59129777 TTAAAGGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 10 0.34
16 16 0.55
17 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAATAAAAATTAA
Found at i:59135936 original size:17 final size:17
Alignment explanation
Indices: 59135904--59135960 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
59135894 CCTATGAGCC
*
59135904 CAAAAAAAATCAAAAAT
1 CAAAAAAAATAAAAAAT
* *
59135921 CAAAATAAATAAAAAAA
1 CAAAAAAAATAAAAAAT
* * *
59135938 GAAGAAAAAGAGAAAAAT
1 CAAAAAAAATA-AAAAAT
59135956 CAAAA
1 CAAAA
59135961 TCAGGGTCAA
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (17 bp):
CAAAAAAAATAAAAAAT
Found at i:59138462 original size:131 final size:131
Alignment explanation
Indices: 59138210--59138528 Score: 460
Period size: 131 Copynumber: 2.4 Consensus size: 131
59138200 GTGAATATTA
* * *
59138210 CAGATCTTATCTCCC-AAACAATAGCAGAGCAGATCGAAGACGGTGAATCTTATCTTCCCCAAGA
1 CAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCCAAGA
*
59138274 GTAGGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTAGAAATT
66 GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTAGAAATT
59138339 G
131 G
** * *
59138340 CAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCAAAGACGGTGAATCTTATCTTCCCCAGGA
1 CAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCCAAGA
* * *
59138405 GTAGGGAAACAGATTTAAGCCACAAGTCCTATTTCCCTGACCAGCAGTGGAATAGGTTGGAAATT
66 GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTAGAAATT
59138470 G
131 G
* * * ** * * *
59138471 CAGATCTTGTCTCCCTAAGCAGTAGCGGATCAGATTGAAGACAGCGAATCCTATCTTC
1 CAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGGTGAATCTTATCTTC
59138529 AAGTGTAAGG
Statistics
Matches: 168, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
130 14 0.08
131 154 0.92
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (131 bp):
CAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCCAAGA
GTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTAGAAATT
G
Found at i:59138755 original size:216 final size:216
Alignment explanation
Indices: 59138514--59138934 Score: 707
Period size: 216 Copynumber: 1.9 Consensus size: 216
59138504 ATTGAAGACA
* *
59138514 GCGAATCCTATCTTCAAGTGTAAGGAAGCAGATTGAAGTCGATAATCTTATCTCCCTGAAGTTGT
1 GCGAATCCTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGT
* *
59138579 AGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGG
66 AGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAGG
* * *
59138644 TCTTATCTCCCTGAGGTTGCAGTGGAGCAAACTGAGAAAACAAGTCTTATGCCCCTGAAGTCACA
131 TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACA
59138709 GTGGGGCAGACTGAAGAAGCG
196 GTGGGGCAGACTGAAGAAGCG
*
59138730 GCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGT
1 GCGAATCCTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGT
*
59138795 AGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAGG
66 AGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAGG
* * * * **
59138860 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCA
131 TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACA
59138925 GTGGGGCAGA
196 GTGGGGCAGA
59138935 TCGAAGATGA
Statistics
Matches: 190, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
216 190 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (216 bp):
GCGAATCCTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGT
AGTGGAGCAGATTAAAGTAATAGATCTTATCTCTCTAAAGTTGCAGCAGAGTGGATCGCATCAGG
TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTGAGAAAACAAGTCTTATCCCCCTGAAGTCACA
GTGGGGCAGACTGAAGAAGCG
Found at i:59138909 original size:44 final size:43
Alignment explanation
Indices: 59138856--59139004 Score: 156
Period size: 44 Copynumber: 3.4 Consensus size: 43
59138846 TGGATCGCAT
* * *
59138856 CAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAG
1 CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAG-AAG
*
59138900 CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGA-TCGAAGATG
1 CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT-G-AGAAG
* ** *
59138944 ACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTAAGGAAG
1 -CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGA-GAAG
* *
59138989 CAGATCTTATCTCCCT
1 CAGGTCTTATCCCCCT
59139005 AAGCACAAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.01
44 49 0.56
45 37 0.42
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.23
Consensus pattern (43 bp):
CAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAGAAG
Found at i:59139601 original size:15 final size:16
Alignment explanation
Indices: 59139581--59139613 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
59139571 TAATAATAAT
59139581 AAATT-AAAAAAATTA
1 AAATTAAAAAAAATTA
59139596 AAATTAAAAAAAATTA
1 AAATTAAAAAAAATTA
59139612 AA
1 AA
59139614 GGCCCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTAAAAAAAATTA
Found at i:59162176 original size:195 final size:197
Alignment explanation
Indices: 59161862--59162240 Score: 505
Period size: 195 Copynumber: 1.9 Consensus size: 197
59161852 TCTCTGAAAT
* * * * *
59161862 AAGGAGATTGGATCAAGATTGCATTGAAAACTTATCTGTAAGATCTTCACATTATCTTGGTATTT
1 AAGGAGATTAGACCAAGATTGCATTGAAAACTTATCTCTAAGATATCCACATTATCTTGGTATTT
* * * * *
59161927 ATTATTATATTGTATATGTTATTTTAGCTGCAATTTCATATGTGATAGGATTGTAATTGATCTAG
66 ATTATTATATTATATATGTTATTTTAGATACAATTTCATATGGGATAGGATTGTAATTGATCTAA
*** * *
59161992 TATGTTAGCAAGTCTTGATCTCTTAGATATTTAGAGAGACTTGTATAGGTTTTGTATAGAAGGTT
131 TATGTTAGCAAGTCACAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTGTATAGAAGGTT
59162057 AC
196 AC
* * *
59162059 AAGGAGATTAGACCAGGATTGCATTGAAGACTTA-CTCTAAGATATCCACATTATCTTGGTCTTT
1 AAGGAGATTAGACCAAGATTGCATTGAAAACTTATCTCTAAGATATCCACATTATCTTGGTATTT
* **
59162123 A-TATTATATTATATAT-TCTATTTTAGATACAATTTTATA-GAGGATTTGATTGTAATTGATCT
66 ATTATTATATTATATATGT-TATTTTAGATACAATTTCATATG-GGATAGGATTGTAATTGATCT
* *
59162185 AATATGTTAGCAAGTCACAATCTCTTATATATTTGGAGAGACTTGCATAGATTTTG
129 AATATGTTAGCAAGTCACAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTG
59162241 CATAAGCACT
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
194 2 0.01
195 98 0.62
196 27 0.17
197 30 0.19
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (197 bp):
AAGGAGATTAGACCAAGATTGCATTGAAAACTTATCTCTAAGATATCCACATTATCTTGGTATTT
ATTATTATATTATATATGTTATTTTAGATACAATTTCATATGGGATAGGATTGTAATTGATCTAA
TATGTTAGCAAGTCACAATCTCTTAGATATTTAGAGAGACTTGCATAGATTTTGTATAGAAGGTT
AC
Found at i:59165900 original size:37 final size:37
Alignment explanation
Indices: 59165850--59165940 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 37
59165840 TTCCAAAAAT
*
59165850 AATATTATTTTAATAGT-TTAATATTAAATTAA-ATTA
1 AATATTATCTTAATAGTATT-ATATTAAATTAATATTA
* *
59165886 AATACTTATCTTAATAGTATTTTATTAATTTAATATTA
1 AATA-TTATCTTAATAGTATTATATTAAATTAATATTA
59165924 AAGTAATTATCTTAATA
1 AA-T-ATTATCTTAATA
59165941 TTAAATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 4 0.09
37 22 0.47
38 8 0.17
39 12 0.26
40 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (37 bp):
AATATTATCTTAATAGTATTATATTAAATTAATATTA
Found at i:59166017 original size:17 final size:17
Alignment explanation
Indices: 59165995--59166027 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59165985 TAATAAGATT
*
59165995 TAATATTAATTTTAATC
1 TAATATTAAATTTAATC
59166012 TAATATTAAATTTAAT
1 TAATATTAAATTTAAT
59166028 ATTAAAGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:59166317 original size:110 final size:110
Alignment explanation
Indices: 59166116--59166341 Score: 416
Period size: 110 Copynumber: 2.0 Consensus size: 110
59166106 CACACACTTG
*
59166116 AATTCAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAGAGAT
1 AATT-AAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGAT
59166181 ATTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
65 ATTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
*
59166227 AATTAAGAGAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGATA
1 AATTAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGATA
*
59166292 TTTTTTTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
66 TTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
59166337 AATTA
1 AATTA
59166342 CTTCACTTGT
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
110 108 0.96
111 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (110 bp):
AATTAAGAAAAAGTTGTAGAGAGAAAATTCACTGAAGAGATTATTTCAGAAAATTTTTAAAGATA
TTTTTCTGATTTACAACTTGACCCAAAAGTTTAGAGAAATTGCGA
Found at i:59166731 original size:20 final size:19
Alignment explanation
Indices: 59166700--59166755 Score: 103
Period size: 20 Copynumber: 2.9 Consensus size: 19
59166690 ATTAGGTTAG
59166700 ATAATTAAATTAAATATGA
1 ATAATTAAATTAAATATGA
59166719 ATAATTAAAATTAAATATGA
1 ATAATT-AAATTAAATATGA
59166739 ATAATTAAATTAAATAT
1 ATAATTAAATTAAATAT
59166756 TAAAACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
ATAATTAAATTAAATATGA
Found at i:59173184 original size:25 final size:25
Alignment explanation
Indices: 59173131--59173186 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
59173121 CAACTCTTAT
* *
59173131 GAGCTTACTGTTACTCAGCTCGTAT
1 GAGCTTACTGTTACTCAGCTCGAAA
* **
59173156 GAGCTTACTGTTATTTTGCTCGAAA
1 GAGCTTACTGTTACTCAGCTCGAAA
59173181 GAGCTT
1 GAGCTT
59173187 GCCGTTTATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTACTGTTACTCAGCTCGAAA
Found at i:59176566 original size:11 final size:11
Alignment explanation
Indices: 59176536--59176571 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
59176526 AGTTTTAGAC
*
59176536 TTAGTTTTTAA
1 TTAGATTTTAA
59176547 TTAGAATTTTAA
1 TTAG-ATTTTAA
59176559 TTAGATTTTAA
1 TTAGATTTTAA
59176570 TT
1 TT
59176572 TTCTTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTAGATTTTAA
Found at i:59180233 original size:53 final size:54
Alignment explanation
Indices: 59180170--59180277 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
59180160 TTTTGAGGTG
* *
59180170 ACCAAATTAATC-AAAAAAATTTGGGATGACCATAATAAGAAGGTCCCATGAGT
1 ACCAAATTAATCAAAAAAAATTTAGGATGACCATAATAAGAAAGTCCCATGAGT
59180223 ACCAAATTAATCAAAAAAAATTTAGGATGACCATAATAAGAAAGTCCCATGAGT
1 ACCAAATTAATCAAAAAAAATTTAGGATGACCATAATAAGAAAGTCCCATGAGT
59180277 A
1 A
59180278 ACAATATAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
53 12 0.23
54 40 0.77
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (54 bp):
ACCAAATTAATCAAAAAAAATTTAGGATGACCATAATAAGAAAGTCCCATGAGT
Found at i:59181019 original size:13 final size:15
Alignment explanation
Indices: 59180997--59181028 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59180987 GTTATGTCTT
59180997 TTTTTAAATAA-TTA
1 TTTTTAAATAATTTA
59181011 TTTTT-AATAATTTA
1 TTTTTAAATAATTTA
59181025 TTTT
1 TTTT
59181029 ACCTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAAATAATTTA
Found at i:59183867 original size:15 final size:16
Alignment explanation
Indices: 59183847--59183877 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59183837 TGACGGTTGG
59183847 ATTGTT-AAAATATTA
1 ATTGTTGAAAATATTA
59183862 ATTGTTGAAAATATTA
1 ATTGTTGAAAATATTA
59183878 TGAAATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (16 bp):
ATTGTTGAAAATATTA
Found at i:59189160 original size:26 final size:27
Alignment explanation
Indices: 59189115--59189166 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
59189105 AAACCCCAAA
*
59189115 TTTTCTTTCTTTCCTTCCCT-TTTTCT
1 TTTTCTTTCTTTCCTCCCCTGTTTTCT
59189141 TTTTCTTTCCTTT-CTCCCCTGTTTTC
1 TTTTCTTT-CTTTCCTCCCCTGTTTTC
59189167 GTTTGCCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCTTTCTTTCCTCCCCTGTTTTCT
Found at i:59189394 original size:14 final size:13
Alignment explanation
Indices: 59189368--59189418 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
59189358 ATTTATTTGG
59189368 AATATAATAATAT
1 AATATAATAATAT
59189381 AATATAATTAATAT
1 AATATAA-TAATAT
* *
59189395 AAT-TTACAATAT
1 AATATAATAATAT
*
59189407 AATACAATAATA
1 AATATAATAATA
59189419 ATATACTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:59193766 original size:18 final size:20
Alignment explanation
Indices: 59193723--59193771 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
59193713 AAATAATTAT
*
59193723 TAAAAATAAAAAAATTAATC
1 TAAAATTAAAAAAATTAATC
*
59193743 TTAAATTAAAAAAA-TAA-C
1 TAAAATTAAAAAAATTAATC
59193761 TAAAATTAAAA
1 TAAAATTAAAA
59193772 TAACCATCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 12 0.46
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAATTAAAAAAATTAATC
Found at i:59194058 original size:13 final size:12
Alignment explanation
Indices: 59194028--59194065 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
59194018 TACTAGTTAT
59194028 TATAA-TTTTTA
1 TATAATTTTTTA
*
59194039 AATAATTTTTTA
1 TATAATTTTTTA
59194051 TATCAATTTTTTA
1 TAT-AATTTTTTA
59194064 TA
1 TA
59194066 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 11 0.48
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
TATAATTTTTTA
Found at i:59194072 original size:13 final size:13
Alignment explanation
Indices: 59194024--59194072 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
59194014 TTTTTACTAG
*
59194024 TTATTATAA-TTT
1 TTATAATAATTTT
59194036 TTA-AATAATTTT
1 TTATAATAATTTT
59194048 TTAT-ATCAATTTT
1 TTATAAT-AATTTT
*
59194061 TTATAATTATTT
1 TTATAATAATTT
59194073 AAAAAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 4 0.13
12 11 0.35
13 14 0.45
14 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATAATAATTTT
Found at i:59195798 original size:6 final size:6
Alignment explanation
Indices: 59195787--59195814 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
59195777 GTCTTTTAAT
59195787 CTTTAG CTTTAG CTTTAG CTTTAG CTTT
1 CTTTAG CTTTAG CTTTAG CTTTAG CTTT
59195815 GGCTCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.54
Consensus pattern (6 bp):
CTTTAG
Found at i:59201268 original size:18 final size:18
Alignment explanation
Indices: 59201245--59201282 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
59201235 TATATTAAAA
59201245 TATAAAT-TTTAGAATTTT
1 TATAAATATTT-GAATTTT
59201263 TATAAATACTTTGAATTTT
1 TATAAATA-TTTGAATTTT
59201282 T
1 T
59201283 TTGTAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:59201948 original size:26 final size:26
Alignment explanation
Indices: 59201891--59201954 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
59201881 AGTATAAATT
* * *
59201891 AAATATCAAATAATAATAAAAGTATC
1 AAATATCAAATAACAATAAAAGCATA
*
59201917 AAATATCAAATAACGATAAAAGCA-A
1 AAATATCAAATAACAATAAAAGCATA
*
59201942 AACATATAAAATA
1 AA-ATATCAAATA
59201955 TTATATAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.22
Consensus pattern (26 bp):
AAATATCAAATAACAATAAAAGCATA
Found at i:59206046 original size:24 final size:25
Alignment explanation
Indices: 59205995--59206047 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
59205985 ATGAAGCAAA
*
59205995 TAACGTCCATGAATTAATGAGCCAT
1 TAACGTCCATGAATTAAAGAGCCAT
*
59206020 TAACGT-C-TGAATTAAAGAAGCCCT
1 TAACGTCCATGAATTAAAG-AGCCAT
59206044 TAAC
1 TAAC
59206048 CTCAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.36
24 10 0.40
25 6 0.24
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (25 bp):
TAACGTCCATGAATTAAAGAGCCAT
Found at i:59215536 original size:19 final size:19
Alignment explanation
Indices: 59215501--59215540 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
59215491 TCTTATTCTT
*
59215501 AAAAAAAAACAGCAAAAAG
1 AAAAAAAAACAGAAAAAAG
59215520 AAAAAGAAAA-AGAAAAAAG
1 AAAAA-AAAACAGAAAAAAG
59215539 AA
1 AA
59215541 GAAGCTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAGAAAAAAG
Found at i:59215567 original size:13 final size:13
Alignment explanation
Indices: 59215549--59215587 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
59215539 AAGAAGCTTT
59215549 GCGCAAAAAAAAA
1 GCGCAAAAAAAAA
59215562 GCGC-AAAAAAAA
1 GCGCAAAAAAAAA
* *
59215574 TCGTAAAAAAAAA
1 GCGCAAAAAAAAA
59215587 G
1 G
59215588 TTGCCTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.67, C:0.13, G:0.15, T:0.05
Consensus pattern (13 bp):
GCGCAAAAAAAAA
Found at i:59222513 original size:4 final size:4
Alignment explanation
Indices: 59222499--59222556 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
59222489 AATTTTTATT
* *
59222499 TTTA TTTTA TTTA TTTTA TTTA CTTTA TTTA TTTC TTTA TTT- TGT- TTTA
1 TTTA -TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA
59222548 -TTA TTTA TT
1 TTTA TTTA TT
59222557 ACTTATTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
3 7 0.16
4 26 0.58
5 12 0.27
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:59222513 original size:9 final size:9
Alignment explanation
Indices: 59222499--59222556 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
59222489 AATTTTTATT
59222499 TTTATTTTA
1 TTTATTTTA
59222508 TTTATTTTA
1 TTTATTTTA
*
59222517 TTTACTTTA
1 TTTATTTTA
*
59222526 TTTA-TTTC
1 TTTATTTTA
*
59222534 TTTATTTTG
1 TTTATTTTA
*
59222543 TTT-TATTA
1 TTTATTTTA
59222551 TTTATT
1 TTTATT
59222557 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 13 0.32
9 28 0.68
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:59223899 original size:16 final size:16
Alignment explanation
Indices: 59223880--59223925 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
59223870 TTCCTAAAGC
59223880 ATAAA-AAATATAAATA
1 ATAAATAAATA-AAATA
59223896 ATAAATAAATAAAAATA
1 ATAAATAAAT-AAAATA
59223913 A-AAATAAATAAAA
1 ATAAATAAATAAAA
59223926 AAGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.14
16 13 0.46
17 10 0.36
18 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAATAAATAAAATA
Found at i:59223903 original size:20 final size:19
Alignment explanation
Indices: 59223880--59223927 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
59223870 TTCCTAAAGC
*
59223880 ATAAAAAATATAAATAATAA
1 ATAAAAAAAATAAA-AATAA
59223900 ATAAATAAAAATAAAAATAA
1 ATAAA-AAAAATAAAAATAA
59223920 ATAAAAAA
1 ATAAAAAA
59223928 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
ATAAAAAAAATAAAAATAA
Done.