Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 1 of 182
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 1--192 Score: 280
Period size: 7 Copynumber: 27.6 Consensus size: 7
1 AACCCGA
1 AACCCGA
8 AACCCGA
1 AACCCGA
15 AACCCGA
1 AACCCGA
22 AACCCGA
1 AACCCGA
29 AACCCGA
1 AACCCGA
*
36 AACCCCA
1 AACCCGA
*
43 AACCCCA
1 AACCCGA
*
50 AACCCCA
1 AACCCGA
*
57 AACCCCA
1 AACCCGA
*
64 AACCCCA
1 AACCCGA
71 AACCCGA
1 AACCCGA
78 AACCCGA
1 AACCCGA
85 AACCCGA
1 AACCCGA
92 AACCCGA
1 AACCCGA
99 AACCCGA
1 AACCCGA
106 AACCCG-
1 AACCCGA
112 AACCCGA
1 AACCCGA
119 AACCCGA
1 AACCCGA
126 AACCCGA
1 AACCCGA
133 AACCCGA
1 AACCCGA
140 AACCCGA
1 AACCCGA
147 AACCCCG-
1 AA-CCCGA
*
154 AACCCCA
1 AACCCGA
*
161 AACCCTA
1 AACCCGA
168 AACCCGA
1 AACCCGA
*
175 ACCCCGA
1 AACCCGA
*
182 ACCCCGA
1 AACCCGA
189 AACC
1 AACC
193 TAACCCTAAC
Statistics
Matches: 175, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
6 9 0.05
7 162 0.93
8 4 0.02
ACGTcount: A:0.41, C:0.48, G:0.10, T:0.01
Consensus pattern (7 bp):
AACCCGA
Found at i:208 original size:12 final size:12
Alignment explanation
Indices: 191--237 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
181 AACCCCGAAA
191 CCTAACCCTAAC
1 CCTAACCCTAAC
203 CCTAACCCTAAC
1 CCTAACCCTAAC
215 CCTAACCCTAAC
1 CCTAACCCTAAC
227 CCTAACCCTAA
1 CCTAACCCTAA
238 ACCCGAGCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (12 bp):
CCTAACCCTAAC
Found at i:214 original size:18 final size:18
Alignment explanation
Indices: 191--237 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
181 AACCCCGAAA
191 CCTAACCCTAACCCTAAC
1 CCTAACCCTAACCCTAAC
209 CCTAACCCTAACCCTAAC
1 CCTAACCCTAACCCTAAC
227 CCTAACCCTAA
1 CCTAACCCTAA
238 ACCCGAGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (18 bp):
CCTAACCCTAACCCTAAC
Found at i:249 original size:7 final size:7
Alignment explanation
Indices: 239--334 Score: 104
Period size: 7 Copynumber: 13.4 Consensus size: 7
229 TAACCCTAAA
239 CCCGAGC
1 CCCGAGC
246 CCCGAGC
1 CCCGAGC
253 CCCGAGC
1 CCCGAGC
260 CCCGAGC
1 CCCGAGC
267 CCCGAGC
1 CCCGAGC
274 CCCGAGC
1 CCCGAGC
*
281 CCCTAAAG-
1 CCC--GAGC
*
289 CCCGAGA
1 CCCGAGC
*
296 CCCGAGA
1 CCCGAGC
*
303 CCCGAGA
1 CCCGAGC
*
310 CCCGAGA
1 CCCGAGC
*
317 CCCGAGA
1 CCCGAGC
324 CCCGAGAC
1 CCCGAG-C
332 CCC
1 CCC
335 TAACCCTAAC
Statistics
Matches: 82, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
6 2 0.02
7 72 0.88
8 6 0.07
9 2 0.02
ACGTcount: A:0.22, C:0.51, G:0.26, T:0.01
Consensus pattern (7 bp):
CCCGAGC
Found at i:340 original size:7 final size:7
Alignment explanation
Indices: 330--517 Score: 74
Period size: 7 Copynumber: 27.1 Consensus size: 7
320 GAGACCCGAG
330 ACCCCTA
1 ACCCCTA
337 A-CCCTA
1 ACCCCTA
343 A-CCCTA
1 ACCCCTA
*
349 ACCCCGA
1 ACCCCTA
*
356 ACCCCGA
1 ACCCCTA
*
363 ACCCCAA
1 ACCCCTA
*
370 AACCCTA
1 ACCCCTA
*
377 AACCCTA
1 ACCCCTA
*
384 AACCCTAA
1 ACCCCT-A
* *
392 ACCTCAA
1 ACCCCTA
*
399 ACCCCAA
1 ACCCCTA
406 ACCCC-A
1 ACCCCTA
412 GACCCC-A
1 -ACCCCTA
*
419 GACCCCGAA
1 -ACCCC-TA
*
428 ACCCCCAA
1 A-CCCCTA
436 ACCCC-A
1 ACCCCTA
442 AGCCCC-A
1 A-CCCCTA
449 AGCCCC-A
1 A-CCCCTA
456 AGCCCC-A
1 A-CCCCTA
463 AGCCCC-A
1 A-CCCCTA
*
470 ACCCCCA
1 ACCCCTA
*
477 ACCCCCA
1 ACCCCTA
484 ACCCC-A
1 ACCCCTA
*
490 ACCCCCA
1 ACCCCTA
497 A-CCCTA
1 ACCCCTA
*
503 AACCCTA
1 ACCCCTA
*
510 AACCCTA
1 ACCCCTA
517 A
1 A
518 ACCTTAAACC
Statistics
Matches: 162, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
6 30 0.19
7 119 0.73
8 8 0.05
9 5 0.03
ACGTcount: A:0.35, C:0.55, G:0.05, T:0.05
Consensus pattern (7 bp):
ACCCCTA
Found at i:340 original size:21 final size:21
Alignment explanation
Indices: 2--333 Score: 121
Period size: 21 Copynumber: 16.2 Consensus size: 21
1 A
* * *
2 ACCCGAAACCCGAAACCCGAA
1 ACCCGAGACCCGAGACCCGAG
* * * *
23 ACCCGAAACCCGAAACCCCAA
1 ACCCGAGACCCGAGACCCGAG
* * * * * *
44 ACCCCAAACCCCAAACCCCAA
1 ACCCGAGACCCGAGACCCGAG
* * * *
65 ACCCCAAACCCGAAACCCGAA
1 ACCCGAGACCCGAGACCCGAG
* * *
86 ACCCGAAACCCGAAACCCGAA
1 ACCCGAGACCCGAGACCCGAG
* *
107 ACCCGA-ACCCGAAACCCGAA
1 ACCCGAGACCCGAGACCCGAG
* * *
127 ACCCGAAACCCGAAACCCGAA
1 ACCCGAGACCCGAGACCCGAG
* * * *
148 ACCCCGA-ACCCCAAACCCTAA
1 A-CCCGAGACCCGAGACCCGAG
169 ACCCGA-ACCCCGA-ACCCCGA-
1 ACCCGAGA-CCCGAGA-CCCGAG
* * * *
189 AACCTA-ACCCTA-ACCCTA-
1 ACCCGAGACCCGAGACCCGAG
* * *
207 ACCCTA-ACCCTA-ACCCTA-
1 ACCCGAGACCCGAGACCCGAG
* * *
225 ACCCTA-ACCCTAAACCCGAG
1 ACCCGAGACCCGAGACCCGAG
* * *
245 CCCCGAGCCCCGAGCCCCGAG
1 ACCCGAGACCCGAGACCCGAG
* * * * *
266 CCCCGAGCCCCGAGCCCCTAA
1 ACCCGAGACCCGAGACCCGAG
287 AGCCCGAGACCCGAGACCCGAG
1 A-CCCGAGACCCGAGACCCGAG
309 ACCCGAGACCCGAGACCCGAG
1 ACCCGAGACCCGAGACCCGAG
330 ACCC
1 ACCC
334 CTAACCCTAA
Statistics
Matches: 274, Mismatches: 29, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
18 33 0.12
19 10 0.04
20 36 0.13
21 173 0.63
22 22 0.08
ACGTcount: A:0.35, C:0.48, G:0.14, T:0.03
Consensus pattern (21 bp):
ACCCGAGACCCGAGACCCGAG
Found at i:400 original size:21 final size:21
Alignment explanation
Indices: 342--706 Score: 186
Period size: 21 Copynumber: 17.2 Consensus size: 21
332 CCCTAACCCT
*
342 AACCCT-AACCCCGAACCCCGA
1 AACCCTAAACCCCAAACCCC-A
* * * *
363 ACCCCAAAACCCTAAACCCTA
1 AACCCTAAACCCCAAACCCCA
*
384 AACCCTAAACCTCAAACCCCA
1 AACCCTAAACCCCAAACCCCA
* * *
405 AACCCCAGACCCCAGACCCCGA
1 AACCCTAAACCCCAAACCCC-A
* *
427 AACCCCCAAACCCCAAGCCCCA
1 AA-CCCTAAACCCCAAACCCCA
* * * *
449 AGCCCCAAGCCCCAAGCCCC-
1 AACCCTAAACCCCAAACCCCA
** *
469 AACCCCCAACCCCCAACCCC-
1 AACCCTAAACCCCAAACCCCA
** * *
489 AACCCCCAACCCTAAACCCTA
1 AACCCTAAACCCCAAACCCCA
** **
510 AACCCTAAACCTTAAACCTTA
1 AACCCTAAACCCCAAACCCCA
* **
531 AACCTTAAACCTTAAACCCCGA
1 AACCCTAAACCCCAAACCCC-A
* * * *
553 ACCCCTAAAACCTAAACCTCA
1 AACCCTAAACCCCAAACCCCA
*
574 AACCCCAAACCCCAAACCCCA
1 AACCCTAAACCCCAAACCCCA
* *
595 AATCCC-AAATCCCAAAACTCCA
1 AA-CCCTAAA-CCCCAAACCCCA
* * *
617 AACCCCAAACCCCAAATCCTA
1 AACCCTAAACCCCAAACCCCA
*
638 AA-CCTAAGCCCCTAAACCCCA
1 AACCCTAAACCCC-AAACCCCA
* * *
659 AGCTCC-AAGCTCCAAA-CCCA
1 AAC-CCTAAACCCCAAACCCCA
* *
679 AGACCCGAAACCCTCAAACCCTA
1 A-ACCCTAAACCC-CAAACCCCA
702 AACCC
1 AACCC
707 CCAAACCCAA
Statistics
Matches: 269, Mismatches: 60, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
20 47 0.17
21 138 0.51
22 63 0.23
23 21 0.08
ACGTcount: A:0.38, C:0.49, G:0.04, T:0.08
Consensus pattern (21 bp):
AACCCTAAACCCCAAACCCCA
Found at i:518 original size:7 final size:7
Alignment explanation
Indices: 496--706 Score: 112
Period size: 7 Copynumber: 29.7 Consensus size: 7
486 CCCAACCCCC
496 AACCCTA
1 AACCCTA
503 AACCCTA
1 AACCCTA
510 AACCCTA
1 AACCCTA
*
517 AACCTTA
1 AACCCTA
*
524 AACCTTA
1 AACCCTA
*
531 AACCTTA
1 AACCCTA
*
538 AACCTTA
1 AACCCTA
*
545 AACCCCGA
1 AA-CCCTA
*
553 ACCCCTA
1 AACCCTA
*
560 AAACCTA
1 AACCCTA
567 AA-CCTCA
1 AACCCT-A
*
574 AACCCCA
1 AACCCTA
*
581 AACCCCA
1 AACCCTA
*
588 AACCCCA
1 AACCCTA
595 AATCCC-A
1 AA-CCCTA
*
602 AATCCCAA
1 AA-CCCTA
610 AACTCC-A
1 AAC-CCTA
*
617 AACCCCA
1 AACCCTA
*
624 AACCCCA
1 AACCCTA
*
631 AATCCTA
1 AACCCTA
638 AA-CCTA
1 AACCCTA
*
644 AGCCCCTA
1 A-ACCCTA
*
652 AACCCCA
1 AACCCTA
*
659 AGCTCC-A
1 AAC-CCTA
*
666 AGCTCC-A
1 AAC-CCTA
673 AACCC-A
1 AACCCTA
*
679 AGACCCGA
1 A-ACCCTA
687 AACCCTCA
1 AACCCT-A
695 AACCCTA
1 AACCCTA
702 AACCC
1 AACCC
707 CCAAACCCAA
Statistics
Matches: 175, Mismatches: 16, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
6 14 0.08
7 131 0.75
8 30 0.17
ACGTcount: A:0.41, C:0.44, G:0.03, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:570 original size:29 final size:30
Alignment explanation
Indices: 530--586 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
520 CTTAAACCTT
* *
530 AAACCTTAAACCTTAAACCCCGAACCCCTA
1 AAACCTTAAACCTCAAACCCCAAACCCCTA
560 AAACC-TAAACCTCAAACCCCAAACCCC
1 AAACCTTAAACCTCAAACCCCAAACCCC
587 AAACCCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (30 bp):
AAACCTTAAACCTCAAACCCCAAACCCCTA
Found at i:640 original size:14 final size:14
Alignment explanation
Indices: 1--714 Score: 319
Period size: 14 Copynumber: 51.4 Consensus size: 14
* *
1 AACCCGAAACCCGA
1 AACCCCAAACCCCA
* *
15 AACCCGAAACCCGA
1 AACCCCAAACCCCA
*
29 AACCCGAAACCCCA
1 AACCCCAAACCCCA
43 AACCCCAAACCCCA
1 AACCCCAAACCCCA
57 AACCCCAAACCCCA
1 AACCCCAAACCCCA
* *
71 AACCCGAAACCCGA
1 AACCCCAAACCCCA
* *
85 AACCCGAAACCCGA
1 AACCCCAAACCCCA
* *
99 AACCCGAAA-CCCG
1 AACCCCAAACCCCA
* *
112 AACCCGAAACCCGA
1 AACCCCAAACCCCA
* *
126 AACCCGAAACCCGA
1 AACCCCAAACCCCA
* *
140 AACCCGAAACCCCG
1 AACCCCAAACCCCA
*
154 AACCCCAAACCCTA
1 AACCCCAAACCCCA
* *
168 AA-CCCGAACCCCG
1 AACCCCAAACCCCA
*
181 AACCCCGAAA--CCT
1 AACCCC-AAACCCCA
* *
194 AA-CCCTAA-CCCT
1 AACCCCAAACCCCA
* *
206 AA-CCCTAA-CCCT
1 AACCCCAAACCCCA
* *
218 AA-CCCTAA-CCCT
1 AACCCCAAACCCCA
* *
230 AACCCTAAA-CCCG
1 AACCCCAAACCCCA
* * * *
243 AGCCCCGAGCCCCG
1 AACCCCAAACCCCA
* * * *
257 AGCCCCGAGCCCCG
1 AACCCCAAACCCCA
* * *
271 AGCCCCGAGCCCCTA
1 AACCCCAAACCCC-A
* * *
286 AAGCCCGAGACCCGA
1 AA-CCCCAAACCCCA
* * * *
301 GACCCGAGACCCGA
1 AACCCCAAACCCCA
* * * *
315 GACCCGAGACCCGA
1 AACCCCAAACCCCA
* * *
329 GACCCCTAA-CCCT
1 AACCCCAAACCCCA
* *
342 AA-CCCTAACCCCG
1 AACCCCAAACCCCA
*
355 AACCCCGAACCCCAA
1 AACCCCAAACCCC-A
* *
370 AACCCTAAACCCTA
1 AACCCCAAACCCCA
* *
384 AACCCTAAACCTCA
1 AACCCCAAACCCCA
398 AACCCCAAACCCCA
1 AACCCCAAACCCCA
* *
412 GACCCCAGACCCCGA
1 AACCCCAAACCCC-A
427 AACCCCCAAACCCCA
1 AA-CCCCAAACCCCA
* *
442 AGCCCCAAGCCCCA
1 AACCCCAAACCCCA
* *
456 AGCCCCAAGCCCC-
1 AACCCCAAACCCCA
* *
469 AACCCCCAACCCCC
1 AACCCCAAACCCCA
*
483 AACCCC-AACCCCC
1 AACCCCAAACCCCA
* *
496 AACCCTAAACCCTA
1 AACCCCAAACCCCA
* **
510 AACCCTAAACCTTA
1 AACCCCAAACCCCA
** **
524 AACCTTAAACCTTA
1 AACCCCAAACCCCA
** *
538 AACCTTAAACCCCG
1 AACCCCAAACCCCA
* *
552 AACCCCTAAAACCTA
1 AACCCC-AAACCCCA
*
567 AACCTCAAACCCCA
1 AACCCCAAACCCCA
581 AACCCCAAACCCCA
1 AACCCCAAACCCCA
* *
595 AATCCCAAATCCCAA
1 AACCCCAAA-CCCCA
*
610 AACTCCAAACCCCA
1 AACCCCAAACCCCA
* *
624 AACCCCAAATCCTA
1 AACCCCAAACCCCA
* *
638 AA-CCTAAGCCCCTA
1 AACCCCAAACCCC-A
* *
652 AACCCCAAGCTCCA
1 AACCCCAAACCCCA
* *
666 AGCTCCAAA-CCCA
1 AACCCCAAACCCCA
*
679 AGACCCGAAACCCTCA
1 A-ACCCCAAACCC-CA
*
695 AACCCTAAACCCCCA
1 AACCCCAAA-CCCCA
710 AACCC
1 AACCC
715 AAAAAGCTTT
Statistics
Matches: 579, Mismatches: 98, Indels: 45
0.80 0.14 0.06
Matches are distributed among these distances:
11 2 0.00
12 38 0.07
13 77 0.13
14 376 0.65
15 64 0.11
16 22 0.04
ACGTcount: A:0.37, C:0.49, G:0.08, T:0.06
Consensus pattern (14 bp):
AACCCCAAACCCCA
Found at i:1552 original size:10 final size:10
Alignment explanation
Indices: 1537--1561 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1527 TACATATATT
1537 AAATATTTTA
1 AAATATTTTA
1547 AAATATTTTA
1 AAATATTTTA
1557 AAATA
1 AAATA
1562 ACTGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATATTTTA
Found at i:3002 original size:20 final size:19
Alignment explanation
Indices: 2977--3023 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
2967 TAATGAAACC
2977 GTCATTTCTTTAGTGCAACG
1 GTCATTT-TTTAGTGCAACG
2997 GTCA--TTTTAGTGCAACG
1 GTCATTTTTTAGTGCAACG
*
3014 GTTATTTTTT
1 GTCATTTTTT
3024 TTAGGGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 15 0.62
18 1 0.04
19 4 0.17
20 4 0.17
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (19 bp):
GTCATTTTTTAGTGCAACG
Found at i:3007 original size:17 final size:17
Alignment explanation
Indices: 2985--3021 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2975 CCGTCATTTC
2985 TTTAGTGCAACGGTCAT
1 TTTAGTGCAACGGTCAT
*
3002 TTTAGTGCAACGGTTAT
1 TTTAGTGCAACGGTCAT
3019 TTT
1 TTT
3022 TTTTAGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (17 bp):
TTTAGTGCAACGGTCAT
Found at i:3892 original size:21 final size:21
Alignment explanation
Indices: 3866--3931 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
3856 TCATTTGCCG
3866 TTTCTTCTTCTGCTTTTATCT
1 TTTCTTCTTCTGCTTTTATCT
* * *
3887 TTTCTT-GTGTG--GTTAT-T
1 TTTCTTCTTCTGCTTTTATCT
*
3904 ATTTCTTCTTCTGCTTTTAGCT
1 -TTTCTTCTTCTGCTTTTATCT
3926 TTTCTT
1 TTTCTT
3932 GTGTGGCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
17 1 0.03
18 10 0.30
19 3 0.09
20 3 0.09
21 15 0.45
22 1 0.03
ACGTcount: A:0.06, C:0.18, G:0.11, T:0.65
Consensus pattern (21 bp):
TTTCTTCTTCTGCTTTTATCT
Found at i:3920 original size:39 final size:39
Alignment explanation
Indices: 3866--3960 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
3856 TCATTTGCCG
* *
3866 TTTCTTCTTCTGCTTTTATCTTTTCTTGTGTGGTTATTA
1 TTTCTTCTTCTGCTTTTAGCTTTTCTTGTGTGGCTATTA
3905 TTTCTTCTTCTGCTTTTAGCTTTTCTTGTGTGGCTATTA
1 TTTCTTCTTCTGCTTTTAGCTTTTCTTGTGTGGCTATTA
3944 TTTCTTCTTCTGCTTTT
1 TTTCTTCTTCTGCTTTT
3961 TAGATAAGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.06, C:0.18, G:0.13, T:0.63
Consensus pattern (39 bp):
TTTCTTCTTCTGCTTTTAGCTTTTCTTGTGTGGCTATTA
Found at i:3951 original size:21 final size:21
Alignment explanation
Indices: 3888--3952 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3878 CTTTTATCTT
*
3888 TTCTTGTGTGGTTATTATTTC
1 TTCTTGTGTGGCTATTATTTC
* * *
3909 TTC-T-TCT-GCTTTTAGCTT-
1 TTCTTGTGTGGCTATTA-TTTC
3927 TTCTTGTGTGGCTATTATTTC
1 TTCTTGTGTGGCTATTATTTC
3948 TTCTT
1 TTCTT
3953 CTGCTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
18 8 0.25
19 5 0.16
20 5 0.16
21 14 0.44
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (21 bp):
TTCTTGTGTGGCTATTATTTC
Found at i:5018 original size:140 final size:135
Alignment explanation
Indices: 4787--5043 Score: 354
Period size: 140 Copynumber: 1.9 Consensus size: 135
4777 AAGGGTTAAA
* * *
4787 TTGCCTTAAGTAAGTTTATCGGTAATCGCATTACTGTTTTCTTTTGCAATTGTGATGTGTTGGGA
1 TTGCCTTAAGTAAGTTTATCGATAATAGCATTACTGTTTTCTTTTGCAATTATGATGTGTTGGGA
* * * * *
4852 AGTGTTTCTATTTGACTGACATTTATACATCTTCATGGGGATAAGGTTGTGGTGAGTTGTTACTG
66 AATATTTCTATTTGACTGACATTTATACACCTTCATGAGGATAAGATTGTGGTGAGTTGTTACTG
4917 CTGAT
131 CTGAT
* *
4922 TTGCCTTAAGTAAGTTTATCGATAATAGCATTACTGTTTTTTTTTTTTTTAG-AATTATGATGTT
1 TTGCCTTAAGTAAGTTTATCGATAATAGCATTACTG-----TTTTCTTTT-GCAATTATGATGTG
*
4986 TTGTGAAATATTTCTATTTGACTGACATTTATACACCTTCATGAGGATAAGATTGTGG
60 TTGGGAAATATTTCTATTTGACTGACATTTATACACCTTCATGAGGATAAGATTGTGG
5044 ATAATTGTTA
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
135 34 0.32
140 70 0.67
141 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (135 bp):
TTGCCTTAAGTAAGTTTATCGATAATAGCATTACTGTTTTCTTTTGCAATTATGATGTGTTGGGA
AATATTTCTATTTGACTGACATTTATACACCTTCATGAGGATAAGATTGTGGTGAGTTGTTACTG
CTGAT
Found at i:6033 original size:129 final size:128
Alignment explanation
Indices: 5867--6124 Score: 385
Period size: 129 Copynumber: 2.0 Consensus size: 128
5857 CCAAGGAAAA
* *
5867 AACCAGCTCTAATCCCATCGTAGCCTTTACTTGCTCCGCTCTTTCATATTCTATACATATATTAG
1 AACCAGCTCCAATCCCATCGCAGCCTTTACTTGCTCCGCTCTTTCATATTCTAT--ATATATTAG
* *
5932 TATTTGTCCATCCCTGAAAATACTCCTCCATTCCATA-T-TATATACATGCCACGTGCTAGGTGG
64 TATTTGTCCATCCCTGAAAATAC-CCTCCATTCCAGATTATATATACATGCCACATGCTAGGTGG
5995 C
128 C
* * * *
5996 AACCAGCTCCAATCCCATCGCATCCTTTGCTTGCTCCGCTCTTTCGTTTTCTATATATATTAGTA
1 AACCAGCTCCAATCCCATCGCAGCCTTTACTTGCTCCGCTCTTTCATATTCTATATATATTAGTA
* *
6061 TTTGTCTATCCCTGAAAATACCCTCCATTTCAGATTATATATACATGCCACATGCTAGGTGGC
66 TTTGTCCATCCCTGAAAATACCCTCCATTCCAGATTATATATACATGCCACATGCTAGGTGGC
6124 A
1 A
6125 TCATCAAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
126 11 0.09
127 32 0.27
128 26 0.22
129 48 0.41
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.35
Consensus pattern (128 bp):
AACCAGCTCCAATCCCATCGCAGCCTTTACTTGCTCCGCTCTTTCATATTCTATATATATTAGTA
TTTGTCCATCCCTGAAAATACCCTCCATTCCAGATTATATATACATGCCACATGCTAGGTGGC
Found at i:12219 original size:28 final size:27
Alignment explanation
Indices: 12142--12233 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
12132 AATGAAAACC
* *
12142 AAAATCTAATATAAATAGTGAAACCTTA
1 AAAATCTAGTAAAAATAGTGAAACC-TA
* *
12170 AAAAGTCTAGTAGAAAGAGTGAAATCCTA
1 AAAA-TCTAGTAAAAATAGTGAAA-CCTA
*
12199 AAAATCTGGTAAAAATAGTGAAAACCTA
1 AAAATCTAGTAAAAATAGTG-AAACCTA
12227 AAAATCT
1 AAAATCT
12234 TGATTTTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 28 0.51
29 25 0.45
30 2 0.04
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (27 bp):
AAAATCTAGTAAAAATAGTGAAACCTA
Found at i:14874 original size:23 final size:23
Alignment explanation
Indices: 14783--14922 Score: 142
Period size: 23 Copynumber: 6.1 Consensus size: 23
14773 CTCTCTATTA
* * *
14783 TTAGCACTGTGTGTACTCTCTGA
1 TTAGCACTTTGTGTGCTCTCTGT
* *
14806 TTAGCACTTTATGTGCTCTCTGA
1 TTAGCACTTTGTGTGCTCTCTGT
14829 TTAGCACTTTGTGTGCTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
* *
14852 TTAGAACTGTGTGTGCTCTCTGTT
1 TTAGCACTTTGTGTGCTCTCTG-T
*
14876 GTCTAGCAC-TTATGTGCTCTCTG-
1 -T-TAGCACTTTGTGTGCTCTCTGT
* *
14899 TTAGTACTTTG-GTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
14921 TT
1 TT
14923 GTTCCGTATA
Statistics
Matches: 99, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.14
22 5 0.05
23 61 0.62
24 1 0.01
25 13 0.13
26 5 0.05
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (23 bp):
TTAGCACTTTGTGTGCTCTCTGT
Found at i:14920 original size:69 final size:69
Alignment explanation
Indices: 14783--14922 Score: 187
Period size: 69 Copynumber: 2.0 Consensus size: 69
14773 CTCTCTATTA
* *
14783 TTAGCACTGTGTGTACTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTTGTGTGCTCT
1 TTAGAACTGTGTGTACTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTTGTGTACTCT
14848 CTGT
66 CTGT
* * *
14852 TTAGAACTGTGTGTGCTCTCTGTTGTCTAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTAC
1 TTAGAACTGTGTGTACTCTCTG--AT-TAGCACTTTATGTGCTCTCTGATTAGCACTTTGTGTAC
14914 TCTCTGT
63 TCTCTGT
14921 TT
1 TT
14923 GTTCCGTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
69 32 0.51
70 10 0.16
71 15 0.24
72 6 0.10
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (69 bp):
TTAGAACTGTGTGTACTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGCACTTTGTGTACTCT
CTGT
Found at i:15929 original size:149 final size:149
Alignment explanation
Indices: 15659--15952 Score: 516
Period size: 149 Copynumber: 2.0 Consensus size: 149
15649 CCACATGATT
15659 GCATAACTAGTCATATAACAACATGACCAAGAAAATATGTTAGACATGTTCCCAAATCATAAGTA
1 GCATAACTAGTCATATAACAACATGACCAAGAAAATATGTTAGACATGTTCCCAAATCATAAGTA
* * *
15724 ATATCAATATCCTAATGGAATCACATACCAATTATAATTCAAACATCAACATATACCATATCATT
66 ATATCAATAACCTAATAGAATCACATACCAATTACAATTCAAACATCAACATATACCATATCATT
15789 TCCAAATCACATTTTTATG
131 TCCAAATCACATTTTTATG
* *
15808 GCATAACTAGTCATATGACAACATGACCAAGAAAATGTGTTAGACATGTTCCCAAATCATAAGTA
1 GCATAACTAGTCATATAACAACATGACCAAGAAAATATGTTAGACATGTTCCCAAATCATAAGTA
* * *
15873 ATATCAATAACTTAATAGAATCACATGCCAATTACAATTTAAACATCAACATATACCATATCATT
66 ATATCAATAACCTAATAGAATCACATACCAATTACAATTCAAACATCAACATATACCATATCATT
15938 TCCAAATCACATTTT
131 TCCAAATCACATTTT
15953 AGTTTCCATT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 137 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (149 bp):
GCATAACTAGTCATATAACAACATGACCAAGAAAATATGTTAGACATGTTCCCAAATCATAAGTA
ATATCAATAACCTAATAGAATCACATACCAATTACAATTCAAACATCAACATATACCATATCATT
TCCAAATCACATTTTTATG
Found at i:16061 original size:30 final size:30
Alignment explanation
Indices: 16027--16085 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
16017 CGAGAATAAG
*
16027 TTGCTCACACAAGTTGACAATATATCAAGT
1 TTGCTCACACAAGCTGACAATATATCAAGT
* *
16057 TTGCTTACACAAGCTGACACTATATCAAG
1 TTGCTCACACAAGCTGACAATATATCAAG
16086 GTTACCCGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (30 bp):
TTGCTCACACAAGCTGACAATATATCAAGT
Found at i:16290 original size:24 final size:24
Alignment explanation
Indices: 16262--16312 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
16252 TTGGTAATTA
16262 ACATTCAATATAAACATAATTCAT
1 ACATTCAATATAAACATAATTCAT
*
16286 ACATTCAATATAAGCATAATTCAT
1 ACATTCAATATAAACATAATTCAT
16310 ACA
1 ACA
16313 ATCATTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (24 bp):
ACATTCAATATAAACATAATTCAT
Found at i:18262 original size:14 final size:14
Alignment explanation
Indices: 18243--18283 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
18233 TTAAATCGTT
18243 TTTAATTATTTTAA
1 TTTAATTATTTTAA
*
18257 TTTAATTATTTAAAA
1 TTTAATTATTT-TAA
*
18272 TTTAGTTATTTT
1 TTTAATTATTTT
18284 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTAATTATTTTAA
Found at i:18435 original size:53 final size:52
Alignment explanation
Indices: 18338--18444 Score: 117
Period size: 53 Copynumber: 2.0 Consensus size: 52
18328 AAAAAAATAT
** **
18338 ATTTAAATTTAGAAAAAGTGATGTAGGTCATTGAATGATTAACACTCAAAAAA
1 ATTTAAATTTAGAAAAAGTGATGTAAATCATTGAATGACAAACAC-CAAAAAA
* * * *
18391 ATTTAAATTT-GAAAAAAGTGGTGTAAATTATTGGATGACAAACACCTAAAAA
1 ATTTAAATTTAG-AAAAAGTGATGTAAATCATTGAATGACAAACACCAAAAAA
18443 AT
1 AT
18445 ATTTTTTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
52 9 0.20
53 36 0.80
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (52 bp):
ATTTAAATTTAGAAAAAGTGATGTAAATCATTGAATGACAAACACCAAAAAA
Found at i:25316 original size:16 final size:17
Alignment explanation
Indices: 25287--25320 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25277 TATTCAATGG
25287 TTTTATAAATTTAAAAT
1 TTTTATAAATTTAAAAT
* *
25304 TTTTATTAATTAAAAAT
1 TTTTATAAATTTAAAAT
25321 ATATTATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTATAAATTTAAAAT
Found at i:36193 original size:23 final size:22
Alignment explanation
Indices: 36162--36215 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
36152 CATAAATATG
36162 TTTAAATTAAATT-TTACAAATAA
1 TTTAAATT-AATTATTACAAA-AA
*
36185 TTTATATTAATTACTTACAAAAA
1 TTTAAATTAATTA-TTACAAAAA
36208 TTTAAATT
1 TTTAAATT
36216 TGATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 16 0.59
24 7 0.26
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAAATTAATTATTACAAAAA
Found at i:36688 original size:12 final size:12
Alignment explanation
Indices: 36671--36695 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36661 TCCGTAGGTT
36671 TCTCTCTTTCTC
1 TCTCTCTTTCTC
36683 TCTCTCTTTCTC
1 TCTCTCTTTCTC
36695 T
1 T
36696 GTGTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
TCTCTCTTTCTC
Found at i:41201 original size:96 final size:96
Alignment explanation
Indices: 41037--41233 Score: 394
Period size: 96 Copynumber: 2.1 Consensus size: 96
41027 GTCTTCAGGA
41037 CTTAGCACACTAGCATTCAAGAAGGGAGGCTGTTTTGGGGAGGGAATCACACAACGTCTATCAGT
1 CTTAGCACACTAGCATTCAAGAAGGGAGGCTGTTTTGGGGAGGGAATCACACAACGTCTATCAGT
41102 TAACATTTGAGCTACTTCAGACATGGTTGGT
66 TAACATTTGAGCTACTTCAGACATGGTTGGT
41133 CTTAGCACACTAGCATTCAAGAAGGGAGGCTGTTTTGGGGAGGGAATCACACAACGTCTATCAGT
1 CTTAGCACACTAGCATTCAAGAAGGGAGGCTGTTTTGGGGAGGGAATCACACAACGTCTATCAGT
41198 TAACATTTGAGCTACTTCAGACATGGTTGGT
66 TAACATTTGAGCTACTTCAGACATGGTTGGT
41229 CTTAG
1 CTTAG
41234 TGCAACTGAG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 101 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (96 bp):
CTTAGCACACTAGCATTCAAGAAGGGAGGCTGTTTTGGGGAGGGAATCACACAACGTCTATCAGT
TAACATTTGAGCTACTTCAGACATGGTTGGT
Found at i:45784 original size:17 final size:17
Alignment explanation
Indices: 45762--45800 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
45752 AGGTGCAGAA
* *
45762 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
45779 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
45796 CTTGT
1 CTTGT
45801 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:59204 original size:20 final size:20
Alignment explanation
Indices: 59160--59197 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59150 ATTTTTATAA
59160 TTTTTACAAATATTTTGAAT
1 TTTTTACAAATATTTTGAAT
59180 TTTTTA-AAATTATTTTGA
1 TTTTTACAAA-TATTTTGA
59198 TTATTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTACAAATATTTTGAAT
Found at i:59680 original size:6 final size:6
Alignment explanation
Indices: 59669--59699 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
59659 ATACTAATGG
*
59669 AGGGAT AGGGAT AGGGAT AGGGAC AGGGAT A
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT A
59700 CGTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.03, G:0.48, T:0.13
Consensus pattern (6 bp):
AGGGAT
Found at i:86676 original size:2 final size:2
Alignment explanation
Indices: 86669--86694 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
86659 GCAATTTCAA
86669 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
86695 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90759 original size:2 final size:2
Alignment explanation
Indices: 90754--90779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
90744 ACATTTGACT
90754 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
90780 GACTGATAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94260 original size:26 final size:26
Alignment explanation
Indices: 94231--94294 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
94221 AGCTTGCAAG
* *
94231 AGGAGAGCTCACCGATAGGGCCCGCA
1 AGGAGAGCTCACCGATAGGACCCACA
94257 AGGAGAGCTCACCGATAGGACCCACA
1 AGGAGAGCTCACCGATAGGACCCACA
*
94283 AGGAGAGTTCAC
1 AGGAGAGCTCAC
94295 AGGCTCTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.31, T:0.09
Consensus pattern (26 bp):
AGGAGAGCTCACCGATAGGACCCACA
Found at i:98183 original size:2 final size:2
Alignment explanation
Indices: 98176--98201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98166 CTTAAGAGGA
98176 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
98202 GGACACACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124225 original size:44 final size:44
Alignment explanation
Indices: 124162--124250 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
124152 CCACCTCACA
124162 TAACAAGCACCACCATTTTCCCCACAATAATTACATGCACGCTT
1 TAACAAGCACCACCATTTTCCCCACAATAATTACATGCACGCTT
124206 TAACAAGCACCACCATTTTCCCCACAATAATTACATGCACGCTT
1 TAACAAGCACCACCATTTTCCCCACAATAATTACATGCACGCTT
124250 T
1 T
124251 CCCTCCTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.26
Consensus pattern (44 bp):
TAACAAGCACCACCATTTTCCCCACAATAATTACATGCACGCTT
Found at i:125649 original size:21 final size:22
Alignment explanation
Indices: 125624--125675 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
125614 TATATTGAAA
* *
125624 ATTATTTACT-TAATGTTTTAT
1 ATTATTTAATATAATATTTTAT
125645 ATTA-TTAATATAATATTTTAT
1 ATTATTTAATATAATATTTTAT
125666 ATTAATTTAA
1 ATT-ATTTAA
125676 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 17 0.65
22 1 0.04
23 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTATTTAATATAATATTTTAT
Found at i:128328 original size:7 final size:7
Alignment explanation
Indices: 128316--128354 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
128306 GTGTTGAGGG
128316 TGGCGAC
1 TGGCGAC
128323 TGGCGAC
1 TGGCGAC
128330 TGGCGAC
1 TGGCGAC
128337 TGGCGAC
1 TGGCGAC
128344 TGGCGAC
1 TGGCGAC
128351 TGGC
1 TGGC
128355 AAACGATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.28, G:0.44, T:0.15
Consensus pattern (7 bp):
TGGCGAC
Found at i:137714 original size:84 final size:88
Alignment explanation
Indices: 137618--137820 Score: 209
Period size: 88 Copynumber: 2.3 Consensus size: 88
137608 AAAAGCTCTA
* * * * * *
137618 AAATCTTTTCAAAAATAGCAATTAAG-CCC-C-TTTTTTTCCACTCATTTG-GATATTTGAACTG
1 AAATATTTTCAAAAAAAGAAATTAAGTCCCACATTTCTTTCCACTCAATTGAG-TACTTGAACTG
137679 TCAAAATGCATCAAAAAGA-CCTC
65 TCAAAATGCATCAAAAAGATCCTC
* * *
137702 AAATATTTTCAAAAAAAGAAATTAAGTCCCTACATTTCTTTGCACTCAATTGAGTGCTTGAACTT
1 AAATATTTTCAAAAAAAGAAATTAAGTCCC-ACATTTCTTTCCACTCAATTGAGTACTTGAACTG
*
137767 TCAAAATGTATCAAAAAGATCCTC
65 TCAAAATGCATCAAAAAGATCCTC
* * * *
137791 AATCTTTTTTTAAAAAAAAGCAATTAAGTC
1 AA--ATATTTTCAAAAAAAGAAATTAAGTC
137821 AAAAAAAATA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
84 23 0.24
85 3 0.03
87 1 0.01
88 41 0.42
89 7 0.07
91 22 0.23
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (88 bp):
AAATATTTTCAAAAAAAGAAATTAAGTCCCACATTTCTTTCCACTCAATTGAGTACTTGAACTGT
CAAAATGCATCAAAAAGATCCTC
Found at i:138088 original size:19 final size:19
Alignment explanation
Indices: 138026--138089 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
138016 TACGATAATG
138026 TTATAATTTTTTTATGAATT
1 TTATAATTTTTTTATG-ATT
* *
138046 TTAT-ATTTCTTTA-CATTT
1 TTATAATTTTTTTATGA-TT
*
138064 TATATAATTTTTTTATGGTT
1 T-TATAATTTTTTTATGATT
138084 TTATAA
1 TTATAA
138090 AATTTCATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
17 1 0.03
18 3 0.09
19 16 0.46
20 15 0.43
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTATAATTTTTTTATGATT
Found at i:138114 original size:29 final size:28
Alignment explanation
Indices: 138066--138158 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 28
138056 TTACATTTTA
**
138066 TATAATTTTTTTATGGTTTTATAAAATT
1 TATAATTTTTTTATATTTTTATAAAATT
* *
138094 TCATAATTTTTTTATATTTTTAATCAAAGT
1 T-ATAATTTTTTTATATTTTT-ATAAAATT
* *
138124 TATATATTTTATTATAGTTTTTATTAAATT
1 TATA-ATTTTTTTATA-TTTTTATAAAATT
138154 T-TAAT
1 TATAAT
138159 AAATTTTATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.06
29 22 0.41
30 24 0.44
31 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
TATAATTTTTTTATATTTTTATAAAATT
Found at i:139596 original size:37 final size:37
Alignment explanation
Indices: 139555--139660 Score: 90
Period size: 37 Copynumber: 3.1 Consensus size: 37
139545 TTAAATTTAC
139555 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAG
1 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAG
* * * *
139592 -AAA-AGTATA--GA-CA-A--AG--TTGAA-GATCTG
1 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCA-CAG
139619 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAG
1 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAG
139656 AAAAG
1 AAAAG
139661 TATAGACAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 24
0.60 0.10 0.30
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 3 0.06
29 8 0.16
31 3 0.06
32 2 0.04
33 3 0.06
35 8 0.16
36 3 0.06
37 11 0.22
38 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.21
Consensus pattern (37 bp):
AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAG
Found at i:139630 original size:64 final size:64
Alignment explanation
Indices: 139555--139682 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
139545 TTAAATTTAC
139555 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAGAAAAGTATAGACAAAGTTGAAGATCTG
1 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAGAAAAGTATAGACAAAGTTGAAGATCTG
139619 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAGAAAAGTATAGACAAAGTTGAAGATCTG
1 AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAGAAAAGTATAGACAAAGTTGAAGATCTG
139683 GCCCAACATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.22
Consensus pattern (64 bp):
AAAAGAGTATAGGGAGTATAGCAGATTTTAACCACAGAAAAGTATAGACAAAGTTGAAGATCTG
Found at i:140460 original size:2 final size:2
Alignment explanation
Indices: 140453--140483 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
140443 CTCAAGATTC
140453 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
140484 GTGCTTTGTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:147111 original size:3 final size:3
Alignment explanation
Indices: 147103--147135 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
147093 GATAAAATTT
147103 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
147136 AAGATAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:153016 original size:6 final size:6
Alignment explanation
Indices: 153005--153029 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
152995 TTTGATGTAG
153005 TCCTAC TCCTAC TCCTAC TCCTAC T
1 TCCTAC TCCTAC TCCTAC TCCTAC T
153030 ACAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCTAC
Found at i:161166 original size:23 final size:23
Alignment explanation
Indices: 161042--161168 Score: 116
Period size: 23 Copynumber: 5.4 Consensus size: 23
161032 CGAAGTACTT
161042 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
* *
161068 AACAGTAAACACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * *
161090 ATTCAGTAGGCACACACAGTGC-A
1 A-ACAGTAAGCACACAAAGTGCGA
* * *
161113 ATCAGTAGGCACACAAGGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
161136 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
161159 AACAGTAAGC
1 AACAGTAAGC
161169 GCACTAGCGT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
22 20 0.23
23 50 0.57
26 13 0.15
27 5 0.06
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:163277 original size:25 final size:23
Alignment explanation
Indices: 163228--163278 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
163218 ATATGTATAT
*
163228 GAAATAAAAGAATAAAGAAGAAA
1 GAAAAAAAAGAATAAAGAAGAAA
*
163251 GAAAAAAAAGAAATAAAAGAAGGAA
1 GAAAAAAAAG-AAT-AAAGAAGAAA
163276 GAA
1 GAA
163279 CAGAGAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 3 0.12
25 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.06
Consensus pattern (23 bp):
GAAAAAAAAGAATAAAGAAGAAA
Found at i:176110 original size:2 final size:2
Alignment explanation
Indices: 176103--176134 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
176093 CACCACTTAA
176103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176135 TAAAACAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:207372 original size:25 final size:25
Alignment explanation
Indices: 207344--207395 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
207334 ATTTTATTTC
* *
207344 AATATTTATATTCATATCAAATAAA
1 AATAATTATATTAATATCAAATAAA
*
207369 AATAATTATATTAATATTAAATAAA
1 AATAATTATATTAATATCAAATAAA
207394 AA
1 AA
207396 AAAATTACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAATTATATTAATATCAAATAAA
Found at i:209532 original size:23 final size:23
Alignment explanation
Indices: 209506--209671 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
209496 AGTGCTGGGC
209506 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
209529 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
209548 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
209568 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
209591 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
209615 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
209639 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
209662 ATCAGAGAGC
1 AACAGAGAGC
209672 GTGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:209566 original size:39 final size:39
Alignment explanation
Indices: 209512--209586 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
209502 GGGCAACAGA
*
209512 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
209551 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
209587 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:209625 original size:48 final size:46
Alignment explanation
Indices: 209551--209671 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
209541 ACAAAGTACT
* * *
209551 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
209597 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
209645 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
209672 GTGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:222267 original size:29 final size:29
Alignment explanation
Indices: 222226--222294 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
222216 TAGGGACCTT
222226 ATCAAATTAGTCCCTCTATTATTAAATAG
1 ATCAAATTAGTCCCTCTATTATTAAATAG
* * *
222255 ATCAATTTGGTCCCTGTATTATTAAATAAG
1 ATCAAATTAGTCCCTCTATTATTAAAT-AG
*
222285 GTCAAATTAG
1 ATCAAATTAG
222295 AATAGAGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 24 0.73
30 9 0.27
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (29 bp):
ATCAAATTAGTCCCTCTATTATTAAATAG
Found at i:233000 original size:2 final size:2
Alignment explanation
Indices: 232993--233020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
232983 CTAAATACAA
232993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233021 TCGTATAATT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234551 original size:61 final size:57
Alignment explanation
Indices: 234439--234605 Score: 152
Period size: 52 Copynumber: 2.9 Consensus size: 57
234429 TTTGCATTTG
* * * *
234439 ATACTCACGATGACACAGAGTCATCGGATCT-TTAATC-TAAAATGGATTTCATTTCATTCAT
1 ATACTCACGATGACACATAGCCATCGGACCTCATAATCGT-AAA-GGA-TTCA--T-ATTCAT
*
234500 ATACTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAGG------ATTCAT
1 ATACTCACGATGACACATAGCCATCGGACCTCATAAT-CGTAAAGGATTCATATTCAT
*
234552 ATACTCACGATGACACATAGCCATCGAACCTCATAATTCGTAAAGGATTCATAT
1 ATACTCACGATGACACATAGCCATCGGACCTCATAA-TCGTAAAGGATTCATAT
234606 ACTCACGATG
Statistics
Matches: 89, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
52 48 0.54
53 1 0.01
58 2 0.02
61 27 0.30
62 6 0.07
63 4 0.04
64 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (57 bp):
ATACTCACGATGACACATAGCCATCGGACCTCATAATCGTAAAGGATTCATATTCAT
Found at i:234572 original size:52 final size:52
Alignment explanation
Indices: 234494--234633 Score: 235
Period size: 52 Copynumber: 2.7 Consensus size: 52
234484 ATTTCATTTC
*
234494 ATTCATATACTCACGATGACACATAGCCACCGGACCTCATAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
234546 ATTCATATACTCACGATGACACATAGCCATCGAACCTCATAATTCGTAAAGG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
* *
234598 ATTCATATACTCACGATGACACTTAGTCATCGGACC
1 ATTCATATACTCACGATGACACATAGCCATCGGACC
234634 CTTTTTCATT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.24
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAGG
Found at i:236175 original size:14 final size:14
Alignment explanation
Indices: 236158--236185 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
236148 TAATCATTTT
236158 CATTTAATTAACTA
1 CATTTAATTAACTA
236172 CATTTAATTAACTA
1 CATTTAATTAACTA
236186 TTTAAGCGAT
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:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
CATTTAATTAACTA
Found at i:237172 original size:17 final size:16
Alignment explanation
Indices: 237150--237192 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
237140 AAGCCGAAAT
*
237150 ATATTATGTTAGAATAA
1 ATATTATATTA-AATAA
237167 ATATTATATTAAATAA
1 ATATTATATTAAATAA
*
237183 TTATTTATAT
1 ATA-TTATAT
237193 GTATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
ATATTATATTAAATAA
Found at i:237207 original size:6 final size:6
Alignment explanation
Indices: 237184--237217 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
237174 ATTAAATAAT
* *
237184 TATTTA TATGTA TATTTA TTTTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
237218 AAATCACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:237789 original size:64 final size:64
Alignment explanation
Indices: 237688--237816 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
237678 TGCACAATTT
237688 AAAATGATTTAATAGTTTAATTGCTTTTAGATTTGAACTATTATTATCGTTTTATTCATATTAC
1 AAAATGATTTAATAGTTTAATTGCTTTTAGATTTGAACTATTATTATCGTTTTATTCATATTAC
237752 AAAATGATTTAATAGTTTAATTGCTTTTAGATTTGAACTATTATTATCGTTTTATTCATATTAC
1 AAAATGATTTAATAGTTTAATTGCTTTTAGATTTGAACTATTATTATCGTTTTATTCATATTAC
237816 A
1 A
237817 GATTGAATTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (64 bp):
AAAATGATTTAATAGTTTAATTGCTTTTAGATTTGAACTATTATTATCGTTTTATTCATATTAC
Found at i:241997 original size:14 final size:14
Alignment explanation
Indices: 241970--242013 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
241960 TGTACTCTTC
*
241970 TAAAATTTAAATTT
1 TAAACTTTAAATTT
* *
241984 TAATCTTTATATTT
1 TAAACTTTAAATTT
241998 TAAACTTTAAAATTT
1 TAAACTTT-AAATTT
242013 T
1 T
242014 GATTTTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAACTTTAAATTT
Found at i:249321 original size:15 final size:16
Alignment explanation
Indices: 249301--249331 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
249291 TACATTTATA
249301 TAAAATTAA-AAAAAT
1 TAAAATTAATAAAAAT
249316 TAAAATTAATAAAAAT
1 TAAAATTAATAAAAAT
249332 CCACACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATTAATAAAAAT
Found at i:262567 original size:7 final size:7
Alignment explanation
Indices: 262555--262590 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
262545 GTATGAAATT
262555 TTAAAAA
1 TTAAAAA
262562 TTAAAAA
1 TTAAAAA
262569 TTAAAAA
1 TTAAAAA
262576 TTAAAAA
1 TTAAAAA
262583 TTAAAAA
1 TTAAAAA
262590 T
1 T
262591 GGGGTAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:265356 original size:144 final size:144
Alignment explanation
Indices: 265092--265388 Score: 522
Period size: 144 Copynumber: 2.1 Consensus size: 144
265082 GTAAGTTCTT
* *
265092 TTGGTCTTCTATATATTAGGCTTTTCATCTTTATATTCTTGTTTCTAGTTGCTGAGATTGCTCAA
1 TTGGTCTTCTATATATTAGGCTTTTCATCTTCATATTCTTGTTTCCAGTTGCTGAGATTGCTCAA
* *
265157 AAAGTAGGAGGTATATTTCTGTTTCTATTACCTAATCATTATATATATTGCTTTGATTTCTCTAA
66 AAAGTAGGAGATATATTTCTGTTTCTATTACCTAATCATCATATATATTGCTTTGATTTCTCTAA
265222 ACATTTTCGTCCCA
131 ACATTTTCGTCCCA
*
265236 TTGGTCTTCTGTATATTAGGCTTTTCATCTTCATATTCTTGTTTCCAGTTGCTGAGATTGCTCAA
1 TTGGTCTTCTATATATTAGGCTTTTCATCTTCATATTCTTGTTTCCAGTTGCTGAGATTGCTCAA
* *
265301 AAAGTAGGAGATATATTTCTGTTTCTATTACCTAGTCATCATATATATTGGTTTGATTTCTCTAA
66 AAAGTAGGAGATATATTTCTGTTTCTATTACCTAATCATCATATATATTGCTTTGATTTCTCTAA
*
265366 ACATTTTTGTCCCA
131 ACATTTTCGTCCCA
265380 TTGGTCTTC
1 TTGGTCTTC
265389 CCCTTCTACT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (144 bp):
TTGGTCTTCTATATATTAGGCTTTTCATCTTCATATTCTTGTTTCCAGTTGCTGAGATTGCTCAA
AAAGTAGGAGATATATTTCTGTTTCTATTACCTAATCATCATATATATTGCTTTGATTTCTCTAA
ACATTTTCGTCCCA
Found at i:268289 original size:200 final size:198
Alignment explanation
Indices: 267948--268333 Score: 700
Period size: 200 Copynumber: 1.9 Consensus size: 198
267938 TTTGACAGTT
267948 TTGGGTTTCTTCTTATTGAAGTTGTGATTAATCCCAAACCGAAAACAGAGTACTTGTGTTTGGTC
1 TTGGGTTTCTTCTTATTGAAGTTGTGATTAATCCCAAACCGAAAACAGAGTACTTGTGTTTGGTC
*
268013 AGACCAGACACGAACCAAAAAAAAACACTGGTATCCATGATTACTCTCCTTCAGTATCATTTCTT
66 AGACCAGACACGAACCAAAAAAAAACACTGGTATCCATGAGTACTCTCCTTCAGTATCATTTCTT
*
268078 CCTTGTAAACCTTACAACTCTTTGGTGCTCTTAACTTTTGTTGCTTAATATGATGCAACACGGAG
131 CCTTGTAAACCTTACAACTCTTTGCTGCTCTTAACTTTTGTTGCTTAATATGATGCAACACGGAG
268143 TAC
196 TAC
268146 TTGGGTTTCTTCTTATTGAAGTTGTGATTAATCCCAAACCGAAAACACAGAGTACTTGTGTTTGG
1 TTGGGTTTCTTCTTATTGAAGTTGTGATTAATCCCAAACCG-AAA-ACAGAGTACTTGTGTTTGG
* * * *
268211 TCATACCAGACACGAACCAAACAAAAACATTGGTATCCATGAGTACTCTCCTTTAGTATCATTTC
64 TCAGACCAGACACGAACCAAAAAAAAACACTGGTATCCATGAGTACTCTCCTTCAGTATCATTTC
268276 TTCCTTGTAAACCTTACAACTCTTTGCTGCTCTTAACTTTTGTTGCTTAATATGATGC
129 TTCCTTGTAAACCTTACAACTCTTTGCTGCTCTTAACTTTTGTTGCTTAATATGATGC
268334 TCAAGGTTGT
Statistics
Matches: 180, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
198 41 0.23
199 3 0.02
200 136 0.76
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (198 bp):
TTGGGTTTCTTCTTATTGAAGTTGTGATTAATCCCAAACCGAAAACAGAGTACTTGTGTTTGGTC
AGACCAGACACGAACCAAAAAAAAACACTGGTATCCATGAGTACTCTCCTTCAGTATCATTTCTT
CCTTGTAAACCTTACAACTCTTTGCTGCTCTTAACTTTTGTTGCTTAATATGATGCAACACGGAG
TAC
Found at i:289700 original size:5 final size:5
Alignment explanation
Indices: 289690--289715 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
289680 TGAGATGGGT
289690 GTATA GTATA GTATA GTATA GTATA G
1 GTATA GTATA GTATA GTATA GTATA G
289716 CATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
GTATA
Found at i:293781 original size:17 final size:18
Alignment explanation
Indices: 293761--293798 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
293751 AGTATATAAA
293761 AAATATAAAAAT-AATTT
1 AAATATAAAAATAAATTT
* *
293778 AAATTTAATAATAAATTT
1 AAATATAAAAATAAATTT
293796 AAA
1 AAA
293799 AAAATAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATAAAAATAAATTT
Found at i:306263 original size:78 final size:78
Alignment explanation
Indices: 306129--306283 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
306119 AACATGATAC
*
306129 ATTTAAAACATAAATTAAATATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAATG
1 ATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAATG
306194 CATAATAGAAAAT
66 CATAATAGAAAAT
* *
306207 ATTTTAAACATAAATTAAACATAGTTTGAAACATACTTCAAACAAACACAACAACAAACAAAATG
1 ATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAATG
306272 CATAATAGAAAA
66 CATAATAGAAAA
306284 CAACAACAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.22
Consensus pattern (78 bp):
ATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAATG
CATAATAGAAAAT
Found at i:307080 original size:17 final size:17
Alignment explanation
Indices: 307036--307105 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
307026 TCATTTTAAG
307036 TTTAAATTTA-TTGTAAA
1 TTTAAATTTATTTG-AAA
** * *
307053 TTTAAGCTTATTTGGAG
1 TTTAAATTTATTTGAAA
*
307070 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTGAAA
307087 TTTAAATTTATTTTGAAA
1 TTTAAATTTA-TTTGAAA
307105 T
1 T
307106 AAAAATTTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
17 31 0.76
18 10 0.24
ACGTcount: A:0.36, C:0.01, G:0.09, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTGAAA
Found at i:307098 original size:34 final size:34
Alignment explanation
Indices: 307011--307099 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 34
307001 CCGATTTTAG
** * *
307011 ATTTTAAATTTTCATTCATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
* ** *
307045 ATTGTAAATTTAAGCTTATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
307079 ATTTTAAATTTAAATTTATTT
1 ATTTTAAATTTAAATTTATTT
307100 TGAAATAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTGAAGTTTAAATTT
Found at i:307111 original size:18 final size:17
Alignment explanation
Indices: 307073--307114 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
307063 TTTGGAGTTT
**
307073 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATAA
307090 AAATTTATTTTGAAATAA
1 AAATTTATTTT-AAATAA
307108 AAATTTA
1 AAATTTA
307115 AAGTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATAA
Found at i:308097 original size:78 final size:78
Alignment explanation
Indices: 308002--308160 Score: 246
Period size: 78 Copynumber: 2.0 Consensus size: 78
307992 CAAACACGAT
* *
308002 ACATTTAAAATATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAATAACAAACAAAA
1 ACATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAA
308067 TGCATAATAGAAA
66 TGCATAATAGAAA
* * * * *
308080 ACATTTAAAACATAAATTAAACATAGTTTGAAACATACTTTAAATAAACATAACAACAGACAAAA
1 ACATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAA
*
308145 TGCATGATAGAAA
66 TGCATAATAGAAA
308158 ACA
1 ACA
308161 ACAGATAGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.23
Consensus pattern (78 bp):
ACATTTAAAACATAAATTAAACATAGTTCGAAACATACTTCAAACAAACACAACAACAAACAAAA
TGCATAATAGAAA
Found at i:311172 original size:973 final size:971
Alignment explanation
Indices: 310035--313413 Score: 5794
Period size: 973 Copynumber: 3.5 Consensus size: 971
310025 TTAAGAATAA
*
310035 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCACACTAATTGAAACC
1 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
* * * * *
310100 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATATCGCTACGTCGCTGATATGACATGAAGGACCA
66 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTACGTCGCTGTTATGAGATGAAGGAACA
* *
310165 GTTCTACAATCTCGAAAAACAACACTTTGAGTACCTTTCTTCACATTGTAACCCAAAGATTTCGT
131 GTTCTACAATCTCGAAAAACAACACTTCGAGTACCTTTCTTCACATTGTAACCCAAAAATTTCGT
* *
310230 TACCTGTTTTTGGAATG-GGGTGTTACAAGTTACAAGGATCC-AT-A-TG-GACACCCCATTCCA
196 TACCTCTTTTTGGAATGAGGG-G-T-CAA--T--AAGGATCCTATAACTGTAACACCCCATTCCA
310290 AAAACAGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGAG
254 AAAACAGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGAG
*
310355 ATTGTAGAACTGGTCCTTCATCTCATAACAGTC-ACGTAGTGAGATATTGACTCCAATCCAAGCA
319 ATTGTAGAACTGGTCCTTCATGTCATAACAG-CGACGTAGTGAGATATTGACTCCAATCCAAGCA
* * *
310419 ACAAAAAAGCTGGTTTCAATTAGTTTGCAATTTATTTCTTCTTTTTTCCCCTATTTTTGAAAGTT
383 ACAGAAAAGCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTT
310484 AAATACATTATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTA
448 AAATACATTATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTA
*
310549 AAATTTTCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCTA
513 AAATTTTCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCCA
310614 CAAGCATTATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAAGATAC
578 CAAGCATTATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAAGATAC
*
310679 GAATTGACTGTTATAGCTGAACTCCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTAGGA
643 GAATTGACTGTTATAGCTGAACTCCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTGGGA
*
310744 GGATCTAGGACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGC
708 GGATCTAGGACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGG
* * *
310809 TGTGAGCGAGCATCTGGGTTAATAAGATTAATTTTTTGCTGCTTGGACTGGAGTCAATATCTCAC
773 TGTGAGCGAGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCAC
* *
310874 TACGTCGCTGTTATGACATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTT
838 TACGTCGTTGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTT
310939 TCTTCACATTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGG
903 TCTTCACATTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGG
311004 ATTC
968 ATTC
311008 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
1 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
*
311073 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTATGTCGCTGTTATGAGATGAAGGAACA
66 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTACGTCGCTGTTATGAGATGAAGGAACA
* *
311138 GTTCTACAATCTCGAAAAACAACCCTTCGAGTACCTTTCTTCACATTGTAACCTAAAAATTTCGT
131 GTTCTACAATCTCGAAAAACAACACTTCGAGTACCTTTCTTCACATTGTAACCCAAAAATTTCGT
* * * *
311203 TACCTCTTTTTGGAATGAGGGGTCCATATGGATCCTTTTAACTTGTAACACCTCATTCCAAAAAC
196 TACCTCTTTTTGGAATGAGGGGTCAATAAGGATCC-TATAAC-TGTAACACCCCATTCCAAAAAC
*
311268 AGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGATACTCGAAGTGTTGCTTTTCGAGATTGT
259 AGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGAGATTGT
* *
311333 AGAACTGGTCCTTCATGTCATATCAGCGACGTAGTGAGATATTGACTCCAGTCCAAGCAACAGAA
324 AGAACTGGTCCTTCATGTCATAACAGCGACGTAGTGAGATATTGACTCCAATCCAAGCAACAGAA
* *
311398 AAGCTGATTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTTCCCTAATTTTGAAAGTTAAATAC
389 AAGCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTTAAATAC
* * * *
311463 CTTATTTTTTCTTAATTTTCATTAATCTTATTAACCCAGCAACCCATTTTATTAGGTTAAAATTT
454 ATTATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTAAAATTT
* *
311528 TCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAGTCACTTCTCCCACAAACA
519 TCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCCACAAGCA
*
311593 TTATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAATATACGAATTG
584 TTATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAAGATACGAATTG
* *
311658 ACTGTTATAGCTGAACTACC-CGATTGTTTGATATCTGTAGGGCACGAGGAAAGTTGGGAGGATC
649 ACTGTTATAGCTGAACT-CCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTGGGAGGATC
* *
311722 TAGGAGCGCATGTTATTGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGGTGTGA
713 TAGGACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGGTGTGA
311787 GCGAGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCACTACGT
778 GCGAGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCACTACGT
311852 CGTTGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTTTCTTC
843 CGTTGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTTTCTTC
* *
311917 ACATTGTAACCCAAAGATTTCGTTATCTGTTTTTGGAATGAGGTGTTACAAGTTAAAAGGA-TC
908 ACATTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGGATTC
311980 TATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAAC
1 -ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAAC
* * *
312045 CAGCTTTTCTGTTGCTTGGACTGGAGTTAATATCTCACTACCTCGCTGTTATGAGATGAAGGACC
65 CAGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTACGTCGCTGTTATGAGATGAAGGAAC
** * *
312110 AGTTCTACAATCTCGAAAAGTAACACTTTGAGTACCTTTCTTCACATTGTAACCCAAAGATTTCG
130 AGTTCTACAATCTCGAAAAACAACACTTCGAGTACCTTTCTTCACATTGTAACCCAAAAATTTCG
* * *
312175 TTACCTATTTTTGAAATG-GGGTGTTACAAGTTAAAAGGATCC-AT-A-TG-GACACCCCATTCC
195 TTACCTCTTTTTGGAATGAGGG-G-T-CAA--T--AAGGATCCTATAACTGTAACACCCCATTCC
*
312235 AAAAACAGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTTGA
253 AAAAACAGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGA
*
312300 GATTGTAGAACTGGTCCTTCATGTCATATCAGCGACGTAGTGAGATATTGACTCCAATCCAAGCA
318 GATTGTAGAACTGGTCCTTCATGTCATAACAGCGACGTAGTGAGATATTGACTCCAATCCAAGCA
312365 ACAGAAAAGCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTT
383 ACAGAAAAGCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTT
312430 AAATACATTATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTA
448 AAATACATTATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTA
312495 AAATTTTCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCCA
513 AAATTTTCAACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCCA
*
312560 CAAGCATTATATATATTGCACACTGCATTCTACTTTACTTCGCCTTCACCATGGAACAAAGATAC
578 CAAGCATTATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAAGATAC
312625 GAATTGACTGTTATAGCTGAACTCCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTGGGA
643 GAATTGACTGTTATAGCTGAACTCCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTGGGA
312690 GGATCTAGGACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGG
708 GGATCTAGGACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGG
312755 TGTGAGCGAGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCAC
773 TGTGAGCGAGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCAC
312820 TACGTCGTTGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTT
838 TACGTCGTTGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTT
*
312885 TCTTCACTTTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGG
903 TCTTCACATTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGG
312950 ATTC
968 ATTC
312954 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
1 ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
* *
313019 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTATGTCGCTATTATGAGATGAAGGAACA
66 AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTACGTCGCTGTTATGAGATGAAGGAACA
* * *
313084 GTTCTACAATCTCGAAAAGCAACCCTTCGAGTACCTTTCTTCACATTGTAACCTAAAAATTTCGT
131 GTTCTACAATCTCGAAAAACAACACTTCGAGTACCTTTCTTCACATTGTAACCCAAAAATTTCGT
* * *
313149 TACCTCTTTTTGGAATGAGGGGTCCATATGGATCCTTTTAACTTGTAACACCCCATTCCAAAAAC
196 TACCTCTTTTTGGAATGAGGGGTCAATAAGGATCC-TATAAC-TGTAACACCCCATTCCAAAAAC
* * *
313214 AGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTAATCAAAGTGTTACTTTTCGAGATTGT
259 AGGTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGAGATTGT
* *
313279 AAAACTAGTCCTTCATGTCATAACAGCGACGTAGTGAGATATTGACTCCAATCCAAGCAACAGAA
324 AGAACTGGTCCTTCATGTCATAACAGCGACGTAGTGAGATATTGACTCCAATCCAAGCAACAGAA
*
313344 AAGCTGGTTTCAATTAGTTTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTTAAATAC
389 AAGCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTTAAATAC
*
313409 CTTAT
454 ATTAT
313414 GGATCTTTTC
Statistics
Matches: 2271, Mismatches: 109, Indels: 52
0.93 0.04 0.02
Matches are distributed among these distances:
967 14 0.01
969 4 0.00
970 2 0.00
971 4 0.00
972 14 0.01
973 2208 0.97
974 13 0.01
975 2 0.00
976 1 0.00
977 2 0.00
979 7 0.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (971 bp):
ATAAGGTATTTAACTTTCAAAATTAGGGGAAAAAAGAAGAAATAAATTGCAAACTAATTGAAACC
AGCTTTTCTGTTGCTTGGACTGGAGTCAATATCTCACTACGTCGCTGTTATGAGATGAAGGAACA
GTTCTACAATCTCGAAAAACAACACTTCGAGTACCTTTCTTCACATTGTAACCCAAAAATTTCGT
TACCTCTTTTTGGAATGAGGGGTCAATAAGGATCCTATAACTGTAACACCCCATTCCAAAAACAG
GTAACGAAATCTTTGGGTTACAATGTGAAGAAAGGTACTCGAAGTGTTGCTTTTCGAGATTGTAG
AACTGGTCCTTCATGTCATAACAGCGACGTAGTGAGATATTGACTCCAATCCAAGCAACAGAAAA
GCTGGTTTCAATTAGTGTGCAATTTATTTCTTCTTTTTTCCCCTAATTTTGAAAGTTAAATACAT
TATTTATTCTTAATTTTTATTAATCTTATTAACCCAACAACCCATTTTATTAGGTTAAAATTTTC
AACCAAATATCTCCCACAAGCATTATATATATGCGGGTGCTCCAATCACTTCTCCCACAAGCATT
ATATATATTGCACACTGCATTCTACTCTACTTCGCCTTCACCATGGAACAAAGATACGAATTGAC
TGTTATAGCTGAACTCCTCGATTATTTGATATCTGTAGGGCTCGAGGAAAGTTGGGAGGATCTAG
GACCGCATGTTATGGTAAAATATATAAGTTAAAAGGATCCATATGGACACAAAATGGTGTGAGCG
AGCATCTGGGTTAATAAGATTAATTTTCTGTTGCTTGGACTTGAGTCAATATCTCACTACGTCGT
TGTTATGATATGAAGGACCAGTTCTACAATCTCGAAAAGCAACACTTCGAGTACCTTTCTTCACA
TTGTAACCCAAAGATTTCGTTATATGTTTTTGGAATGGGGTGTTACAAGTTAAAAGGATTC
Found at i:318322 original size:18 final size:18
Alignment explanation
Indices: 318299--318341 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
318289 AGAATAATTT
318299 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
318317 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
318335 TTAATTA
1 TTAATTA
318342 TACCTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:325887 original size:3 final size:3
Alignment explanation
Indices: 325879--325903 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
325869 TTTTGCACAC
325879 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
325904 AGCAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:328769 original size:30 final size:30
Alignment explanation
Indices: 328733--328793 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
328723 AAACTCAGGG
328733 AGAAGATGAAACTTGTCAACAACCGATTTT
1 AGAAGATGAAACTTGTCAACAACCGATTTT
328763 AGAAGATGAAACTTGTCAACAACCGATTTT
1 AGAAGATGAAACTTGTCAACAACCGATTTT
328793 A
1 A
328794 TTGGAGCAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (30 bp):
AGAAGATGAAACTTGTCAACAACCGATTTT
Found at i:330203 original size:12 final size:12
Alignment explanation
Indices: 330188--330217 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
330178 CCTTTTCTTA
330188 ATTTTTTTATTT
1 ATTTTTTTATTT
*
330200 ATTTATTTATTT
1 ATTTTTTTATTT
330212 ATTTTT
1 ATTTTT
330218 AGTACTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:330215 original size:24 final size:23
Alignment explanation
Indices: 330188--330301 Score: 59
Period size: 24 Copynumber: 4.5 Consensus size: 23
330178 CCTTTTCTTA
330188 ATTTTTTTATTTATTTATTTATTT
1 ATTTTTTTATTTATTTATTT-TTT
* *
330212 ATTTTTAGTACTTGTATTTA-TTTGT
1 ATTTTT-TTA-TT-TATTTATTTTTT
* **
330237 ATTTTGTCCTTTAAATTTCAATTTATTT
1 ATTTTTTTATTT--ATTT--ATTT-TTT
*
330265 ATTTTTATTATTTTTTTATTTTTT
1 ATTTTT-TTATTTATTTATTTTTT
*
330289 ATTTCTATTATTT
1 ATTT-TTTTATTT
330302 CCAATATTTT
Statistics
Matches: 67, Mismatches: 12, Indels: 22
0.66 0.12 0.22
Matches are distributed among these distances:
22 1 0.01
23 2 0.03
24 23 0.34
25 14 0.21
26 5 0.07
27 11 0.16
28 7 0.10
29 4 0.06
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (23 bp):
ATTTTTTTATTTATTTATTTTTT
Found at i:330291 original size:18 final size:17
Alignment explanation
Indices: 330188--330287 Score: 55
Period size: 17 Copynumber: 5.8 Consensus size: 17
330178 CCTTTTCTTA
* *
330188 ATTTTTTTATTTAT-TT
1 ATTTATTTATTTTTATT
*
330204 ATTTATTTATTTTTAGT
1 ATTTATTTATTTTTATT
*
330221 ACTTGTATTTATTTGTATT
1 A-TT-TATTTATTTTTATT
* * *
330240 -TTGTCCTTTAAATTTCA--
1 ATT-T-ATTT-ATTTTTATT
330257 ATTTATTTATTTTTATT
1 ATTTATTTATTTTTATT
*
330274 ATTTTTTTATTTTT
1 ATTTATTTATTTTT
330288 TATTTCTATT
Statistics
Matches: 63, Mismatches: 13, Indels: 15
0.69 0.14 0.16
Matches are distributed among these distances:
15 5 0.08
16 15 0.24
17 20 0.32
18 7 0.11
19 16 0.25
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (17 bp):
ATTTATTTATTTTTATT
Found at i:330429 original size:20 final size:18
Alignment explanation
Indices: 330397--330480 Score: 75
Period size: 20 Copynumber: 4.6 Consensus size: 18
330387 TATTCTTTTA
*
330397 TTATTTGTATTTATTCAT
1 TTATTTTTATTTATTCAT
330415 TTATTTTGATATTTATTCAT
1 TTATTTT--TATTTATTCAT
*
330435 CTATTTTAGTATTTAATT--T
1 TTATTTT--TATTT-ATTCAT
*
330454 TTATTTTT-TTTATTTAT
1 TTATTTTTATTTATTCAT
330471 TTATTTTTAT
1 TTATTTTTAT
330481 GTCATTTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
15 3 0.05
16 3 0.05
17 10 0.18
18 7 0.13
19 7 0.13
20 22 0.40
21 3 0.05
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (18 bp):
TTATTTTTATTTATTCAT
Found at i:330469 original size:13 final size:14
Alignment explanation
Indices: 330453--330495 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
330443 GTATTTAATT
330453 TTTATTT-TTTTTA
1 TTTATTTATTTTTA
330466 TTTATTTATTTTTA
1 TTTATTTATTTTTA
* *
330480 TGTCATTTATATTTA
1 T-TTATTTATTTTTA
330495 T
1 T
330496 GCTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 12 0.46
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTATTTATTTTTA
Found at i:330488 original size:23 final size:24
Alignment explanation
Indices: 330444--330489 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
330434 TCTATTTTAG
* **
330444 TATTTAATTTTTATTTTTTTTATT
1 TATTTAATTTTTATGTCATTTATT
330468 TATTT-ATTTTTATGTCATTTAT
1 TATTTAATTTTTATGTCATTTAT
330490 ATTTATGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (24 bp):
TATTTAATTTTTATGTCATTTATT
Found at i:330502 original size:15 final size:14
Alignment explanation
Indices: 330402--330509 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 14
330392 TTTTATTATT
330402 TGTATTTATTCATTTA
1 TGTATTTA-T-ATTTA
*
330418 T-T-TTGATATTTA
1 TGTATTTATATTTA
*
330430 T-TCATCTAT-TTTA
1 TGT-ATTTATATTTA
330443 -GTATTTA-ATTT-
1 TGTATTTATATTTA
*
330454 T-TATTT-TTTTTA
1 TGTATTTATATTTA
* *
330466 TTTATTTATTTTTA
1 TGTATTTATATTTA
330480 TGTCATTTATATTTA
1 TGT-ATTTATATTTA
330495 TGCTATTTTATATTT
1 TG-TA-TTTATATTT
330510 TTATTTTGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
11 8 0.11
12 15 0.21
13 11 0.15
14 14 0.19
15 14 0.19
16 11 0.15
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (14 bp):
TGTATTTATATTTA
Found at i:333247 original size:27 final size:27
Alignment explanation
Indices: 333216--333285 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
333206 TGAAGAGTAA
333216 TCTGATTCTGGCTCGAAAGAGCGTTAT
1 TCTGATTCTGGCTCGAAAGAGCGTTAT
*
333243 TCTGATTCTAGCTCGAAAGAGCGTTAT
1 TCTGATTCTGGCTCGAAAGAGCGTTAT
333270 TCTGATTCTGGACTCG
1 TCTGATTCTGG-CTCG
333286 TGAGAGCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (27 bp):
TCTGATTCTGGCTCGAAAGAGCGTTAT
Found at i:334067 original size:3 final size:3
Alignment explanation
Indices: 334059--334097 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
334049 TACATCTCAA
334059 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
334098 GAATAGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:335143 original size:7 final size:7
Alignment explanation
Indices: 335131--335223 Score: 93
Period size: 7 Copynumber: 13.7 Consensus size: 7
335121 TTTCGAAAAA
335131 GTCAACG
1 GTCAACG
335138 GTCAACG
1 GTCAACG
335145 GTCAACG
1 GTCAACG
* *
335152 ATCAA-A
1 GTCAACG
*
335158 GTCAATG
1 GTCAACG
*
335165 GTCAAAG
1 GTCAACG
*
335172 GTCAA-A
1 GTCAACG
*
335178 GTCAATG
1 GTCAACG
*
335185 GTCAATG
1 GTCAACG
*
335192 GTCAA-A
1 GTCAACG
335198 GTCAACG
1 GTCAACG
335205 GTCAACG
1 GTCAACG
335212 GTCAACG
1 GTCAACG
335219 GTCAA
1 GTCAA
335224 TCAACATCGA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
6 14 0.19
7 60 0.81
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:335167 original size:20 final size:20
Alignment explanation
Indices: 335138--335216 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
335128 AAAGTCAACG
*
335138 GTCAACGGTCAACGATCAAA
1 GTCAACGGTCAACGGTCAAA
* *
335158 GTCAATGGTCAAAGGTCAAA
1 GTCAACGGTCAACGGTCAAA
* *
335178 GTCAATGGTCAATGGTCAAA
1 GTCAACGGTCAACGGTCAAA
335198 GTCAACGGTCAACGGTCAA
1 GTCAACGGTCAACGGTCAA
335217 CGGTCAATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCAAA
Found at i:335167 original size:27 final size:26
Alignment explanation
Indices: 335130--335223 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 26
335120 TTTTCGAAAA
335130 AGTCAACGGTCAACGGTCAACGATCAA-
1 AGTCAACGGTCAA-GGTCAACG-TCAAC
* * *
335157 AGTCAATGGTCAAAGGTCAAAGTCAAT
1 AGTCAACGGTC-AAGGTCAACGTCAAC
* * *
335184 GGTCAATGGTCAAAGTCAACGGTCAAC
1 AGTCAACGGTCAAGGTCAAC-GTCAAC
*
335211 GGTCAACGGTCAA
1 AGTCAACGGTCAA
335224 TCAACATCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
26 11 0.19
27 44 0.77
28 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.18
Consensus pattern (26 bp):
AGTCAACGGTCAAGGTCAACGTCAAC
Found at i:335286 original size:21 final size:21
Alignment explanation
Indices: 335248--335289 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
335238 CGCCGATAAT
*
335248 CGGTCGGTCAACATCGGTCAA
1 CGGTCGGTCAACACCGGTCAA
**
335269 CGGTCGGTCAATGCCGGTCAA
1 CGGTCGGTCAACACCGGTCAA
335290 TGGTTTGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (21 bp):
CGGTCGGTCAACACCGGTCAA
Found at i:335334 original size:14 final size:15
Alignment explanation
Indices: 335315--335349 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
335305 TGGGTTGGAC
*
335315 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
335329 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
335344 TTGGTT
1 TTGGTT
335350 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:335347 original size:20 final size:20
Alignment explanation
Indices: 335324--335393 Score: 95
Period size: 20 Copynumber: 3.4 Consensus size: 20
335314 CTTGGTTCAA
335324 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
* *
335344 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
*
335364 TTGGTTTGGTTGAAATGGGAT
1 TTGGTTTGGTTCAAATGGG-T
335385 TTGGGTTTG
1 TT-GGTTTG
335394 ATGGGTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 35 0.80
21 3 0.07
22 6 0.14
ACGTcount: A:0.16, C:0.01, G:0.37, T:0.46
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:340656 original size:31 final size:30
Alignment explanation
Indices: 340621--340875 Score: 117
Period size: 30 Copynumber: 8.5 Consensus size: 30
340611 TGAAAATGAA
340621 ATTTTA-AAGAAGTTCGAGGGTCGAAAATATG
1 ATTTTAGAA-AAGTTCGAGGGT-GAAAATATG
* * *
340652 ATTTTAGAAAAGTTTGAGGGTTAAAATGTG
1 ATTTTAGAAAAGTTCGAGGGTGAAAATATG
* ** * * *
340682 ATTTTGGAAACA-TTTAAGGGGTTAAAATGTA
1 ATTTTAGAAA-AGTTCGA-GGGTGAAAATATG
* *
340713 ATTTT-GAAAAGTT-TAGAGGTTAAAATATG
1 ATTTTAGAAAAGTTCGAG-GGTGAAAATATG
* * * * *
340742 ATTTTGGAAAAGTT-TAGGGGTTAAAATGTA
1 ATTTTAGAAAAGTTCGA-GGGTGAAAATATG
** * * * *
340772 ATTTTAGAAAAGTTTAAAGGTCAAAATGTA
1 ATTTTAGAAAAGTTCGAGGGTGAAAATATG
* * * * *
340802 ATTTTGGAAAAGTTTGAGGGTCAAAATGTA
1 ATTTTAGAAAAGTTCGAGGGTGAAAATATG
* * * *
340832 ATTTTGGAAAAGTTTGAGGGTCAAAATGT-
1 ATTTTAGAAAAGTTCGAGGGTGAAAATATG
*
340861 AGTTTTGGAAAAGTT
1 A-TTTTAGAAAAGTT
340876 TAGGTTTTAA
Statistics
Matches: 197, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.01
29 18 0.09
30 139 0.71
31 37 0.19
32 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
ATTTTAGAAAAGTTCGAGGGTGAAAATATG
Found at i:340684 original size:30 final size:29
Alignment explanation
Indices: 340652--340940 Score: 332
Period size: 30 Copynumber: 9.7 Consensus size: 29
340642 CGAAAATATG
* *
340652 ATTTTAGAAAAGTTTGAGGGTTAAAATGTG
1 ATTTTGGAAAAGTTT-AGGGTTAAAATGTA
340682 ATTTTGGAAACA-TTTAAGGGGTTAAAATGTA
1 ATTTTGGAAA-AGTTT-A-GGGTTAAAATGTA
* *
340713 ATTTT-GAAAAGTTTAGAGGTTAAAATATG
1 ATTTTGGAAAAGTTTAG-GGTTAAAATGTA
340742 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTA-GGGTTAAAATGTA
* * *
340772 ATTTTAGAAAAGTTTAAAGGTCAAAATGTA
1 ATTTTGGAAAAGTTT-AGGGTTAAAATGTA
*
340802 ATTTTGGAAAAGTTTGAGGGTCAAAATGTA
1 ATTTTGGAAAAGTTT-AGGGTTAAAATGTA
*
340832 ATTTTGGAAAAGTTTGAGGGTCAAAATGTA
1 ATTTTGGAAAAGTTT-AGGGTTAAAATGTA
* * *
340862 GTTTTGGAAAAGTTTAGGTTTTAAAATATA
1 ATTTTGGAAAAGTTTAGG-GTTAAAATGTA
*
340892 ATTTTCGAAAAGTTTAGTGGTTAAAATGTA
1 ATTTTGGAAAAGTTTAG-GGTTAAAATGTA
340922 ATTTTTGG-AAAGTTTAGGG
1 A-TTTTGGAAAAGTTTAGGG
340941 ACTTTCTGGG
Statistics
Matches: 227, Mismatches: 22, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.00
29 22 0.10
30 178 0.78
31 26 0.11
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
ATTTTGGAAAAGTTTAGGGTTAAAATGTA
Found at i:341801 original size:78 final size:78
Alignment explanation
Indices: 341681--341863 Score: 197
Period size: 78 Copynumber: 2.4 Consensus size: 78
341671 AATGATAGCC
* * * * * * *
341681 ATCTGCCCCATGATC-GGGTAAGAGATTAATTGATAATGATCTGCCTCAGGCTTGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTAACTGATAATGATCTGCCACAAGCTCGAGGTAAAAGA
* * *
341745 CCGAATGGTTGCA
66 CCAAATGGCTACA
* ** * * *
341758 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTGTCACAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTAACTGATAATGATCTGCCACAAGCTCGAGGTAAAAGA
*
341823 TCAAATGGCTACA
66 CCAAATGGCTACA
*
341836 ATTTGCCCCAAGCTCGGGGTAAGAGATT
1 ATCTGCCCCAAGCTCGGGGTAAGAGATT
341864 GGTTTATGAT
Statistics
Matches: 87, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
77 13 0.15
78 74 0.85
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (78 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTAACTGATAATGATCTGCCACAAGCTCGAGGTAAAAGA
CCAAATGGCTACA
Found at i:342199 original size:52 final size:51
Alignment explanation
Indices: 342136--342390 Score: 198
Period size: 52 Copynumber: 5.4 Consensus size: 51
342126 CTATCCAACT
*
342136 TTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTC
1 TTACTACAACTTCAAGAGGATAGGAATTGATGTTT-AAGCTTCATCTTGCTC
* ***
342188 TTACTACAACTTC-AGAGAGATA--AA--GA--CTT--GC-T-ATCCAACT-
1 TTACTACAACTTCAAGAG-GATAGGAATTGATGTTTAAGCTTCATCTTGCTC
*
342228 TTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTC
1 TTACTACAACTTCAAGAGGATAGGAATTGATGTTT-AAGCTTCATCTTGCTC
* **
342280 TTACTACAACTTC-AGAGAGATA--AA--GA--CTT--G-TT-ATCTAACT-
1 TTACTACAACTTCAAGAG-GATAGGAATTGATGTTTAAGCTTCATCTTGCTC
342320 TTACTACAACTTCAAGAGGATAGGAATTGATGTTTCAAGCTTCATCTTGCTC
1 TTACTACAACTTCAAGAGGATAGGAATTGATGTTT-AAGCTTCATCTTGCTC
*
342372 TTACTAGAACTTCAGAGAG
1 TTACTACAACTTCA-AGAG
342391 ATAAAGACTT
Statistics
Matches: 156, Mismatches: 18, Indels: 57
0.68 0.08 0.25
Matches are distributed among these distances:
40 33 0.21
41 19 0.12
42 7 0.04
43 3 0.02
44 4 0.03
46 8 0.05
48 4 0.03
49 3 0.02
50 7 0.04
51 19 0.12
52 45 0.29
53 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (51 bp):
TTACTACAACTTCAAGAGGATAGGAATTGATGTTTAAGCTTCATCTTGCTC
Found at i:342201 original size:92 final size:92
Alignment explanation
Indices: 342040--342405 Score: 651
Period size: 92 Copynumber: 4.0 Consensus size: 92
342030 TTTTTAATCT
* *
342040 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTCACTACAT
1 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
*
342105 CTTCAGAGAGATAAAGATTTGCTATCC
66 CTTCAGAGAGATAAAGACTTGCTATCC
*
342132 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAA
1 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
342197 CTTCAGAGAGATAAAGACTTGCTATCC
66 CTTCAGAGAGATAAAGACTTGCTATCC
342224 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
1 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
* *
342289 CTTCAGAGAGATAAAGACTTGTTATCT
66 CTTCAGAGAGATAAAGACTTGCTATCC
* * *
342316 AACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTCAAGCTTCATCTTGCTCTTACTAGAA
1 AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
342381 CTTCAGAGAGATAAAGACTTGCTAT
66 CTTCAGAGAGATAAAGACTTGCTAT
342406 TATTTTTGAT
Statistics
Matches: 263, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 263 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (92 bp):
AACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAA
CTTCAGAGAGATAAAGACTTGCTATCC
Found at i:342232 original size:40 final size:39
Alignment explanation
Indices: 342188--342337 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
342178 CATCTTGCTC
*
342188 TTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACT
1 TTACTACAACTTCA-AGAGATAAAGACTTGCTATCTAACT
* * **
342228 TTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCT
1 TTACTACAACTTCAAGA-GATA--AA--GA--CTT---GC-T-ATCTAACT
*
342279 CTTACTACAACTTCAGAGAGATAAAGACTTGTTATCTAACT
1 -TTACTACAACTTCA-AGAGATAAAGACTTGCTATCTAACT
342320 TTACTACAACTTCAAGAG
1 TTACTACAACTTCAAGAG
342338 GATAGGAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 29
0.69 0.08 0.23
Matches are distributed among these distances:
39 7 0.08
40 31 0.36
41 6 0.07
42 3 0.03
43 1 0.01
44 2 0.02
46 4 0.05
48 2 0.02
49 2 0.02
50 3 0.03
51 5 0.06
52 17 0.20
53 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31
Consensus pattern (39 bp):
TTACTACAACTTCAAGAGATAAAGACTTGCTATCTAACT
Found at i:342546 original size:49 final size:49
Alignment explanation
Indices: 342493--342598 Score: 113
Period size: 49 Copynumber: 2.2 Consensus size: 49
342483 TACAGGGTTT
*
342493 GCCGTTGCAACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGATCC
1 GCCGTTGCAACTTAAACCTTTCCCTTCAAATCTTCGCGGTACTAGATCC
* *** * * ** *
342542 GCCGTCGTGGCTTAGATCTTTCCCTTCATGTCTTCGCGGTACTGGATCC
1 GCCGTTGCAACTTAAACCTTTCCCTTCAAATCTTCGCGGTACTAGATCC
*
342591 ACCGTTGC
1 GCCGTTGC
342599 GGTCTTAGAT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (49 bp):
GCCGTTGCAACTTAAACCTTTCCCTTCAAATCTTCGCGGTACTAGATCC
Found at i:342633 original size:50 final size:49
Alignment explanation
Indices: 342525--342822 Score: 328
Period size: 50 Copynumber: 6.0 Consensus size: 49
342515 CCTTCAAATC
* * * * * * *
342525 TTCGTGGTACTAGATCCGCCGTCGTGGCTTAGATCTTTCCCTTCATGTC
1 TTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
* *
342574 TTCGCGGTACTGGATCCACCGTTGCGGTCTTAGATCTTTCTCGTCGTGTT
1 TTCGTGGTACTGGATCCACCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
** * ** *
342624 TTCGTGGTACTGGATCCGTCGTCGCGGCTTAGATCTTTCCC-TTATGTC
1 TTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
* *
342672 TTCGTGGTACTGGATCCACCGTTACGGTCTTAGATATTTCCCGTCGTGTT
1 TTCGTGGTACTGGATCCACCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
* * * *
342722 TTTGTGGTACTGGATCCGCCGTTGTGGCCTTAGATCTTTCCCATCGTGTT
1 TTCGTGGTACTGGATCCACCGTTGCGG-CTTAGATCTTTCCCGTCGTGTT
* * * *
342772 TCCGTGGTACTGGATCTACCGTTGCGACTTTAGATCTTTCCCGTTGTGTT
1 TTCGTGGTACTGGATCCACCGTTGCGGC-TTAGATCTTTCCCGTCGTGTT
342822 T
1 T
342823 CATGGTGCTG
Statistics
Matches: 205, Mismatches: 40, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
48 27 0.13
49 49 0.24
50 129 0.63
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (49 bp):
TTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCGTCGTGTT
Found at i:342717 original size:98 final size:98
Alignment explanation
Indices: 342525--342822 Score: 411
Period size: 98 Copynumber: 3.0 Consensus size: 98
342515 CCTTCAAATC
* *
342525 TTCGTGGTACTAGATCCGCCGTCGTGGCTTAGATCTTTCCCTTCATGTCTTCGCGGTACTGGATC
1 TTCGTGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTT-ATGTCTTCGTGGTACTGGATC
*
342590 CACCGTTGCGGTCTTAGATCTTTCTCGTCGTGTT
65 CACCGTTGCGGTCTTAGATCTTTCCCGTCGTGTT
* *
342624 TTCGTGGTACTGGATCCGTCGTCGCGGCTTAGATCTTTCCCTTATGTCTTCGTGGTACTGGATCC
1 TTCGTGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTATGTCTTCGTGGTACTGGATCC
* *
342689 ACCGTTACGGTCTTAGATATTTCCCGTCGTGTT
66 ACCGTTGCGGTCTTAGATCTTTCCCGTCGTGTT
* * **
342722 TTTGTGGTACTGGATCCGCCGTTGTGGCCTTAGATCTTTCCCATCGTGT-TTCCGTGGTACTGGA
1 TTCGTGGTACTGGATCCGCCGTCGTGG-CTTAGATCTTTCCC-TTATGTCTT-CGTGGTACTGGA
* * *
342786 TCTACCGTTGC-GACTTTAGATCTTTCCCGTTGTGTT
63 TCCACCGTTGCGGTC-TTAGATCTTTCCCGTCGTGTT
342822 T
1 T
342823 CATGGTGCTG
Statistics
Matches: 177, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
98 74 0.42
99 58 0.33
100 45 0.25
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (98 bp):
TTCGTGGTACTGGATCCGCCGTCGTGGCTTAGATCTTTCCCTTATGTCTTCGTGGTACTGGATCC
ACCGTTGCGGTCTTAGATCTTTCCCGTCGTGTT
Found at i:343231 original size:30 final size:30
Alignment explanation
Indices: 343181--343517 Score: 348
Period size: 30 Copynumber: 11.2 Consensus size: 30
343171 AATTTTAAAG
* * *
343181 AAGTTCGAGGGTCAAAAATATGATTTTGGAA
1 AAGTTTGAGGGT-TAAAATATAATTTTGGAA
*
343212 AAGTTCGAGGGTTAAAATATAATTTTGGAA
1 AAGTTTGAGGGTTAAAATATAATTTTGGAA
* * *
343242 ACA-TTTGAGGGGTCAAGATGTAATTTT-GAA
1 A-AGTTTGA-GGGTTAAAATATAATTTTGGAA
*
343272 AAGTTT-AGAGGTTAAAATATGATTTTGGAA
1 AAGTTTGAG-GGTTAAAATATAATTTTGGAA
* * *
343302 AAGTTT-AGGGGTCAAGATGTAATTTT-GAA
1 AAGTTTGA-GGGTTAAAATATAATTTTGGAA
* *
343331 AAGTTTAAGGGTTAAAATATAATTTTGGCA
1 AAGTTTGAGGGTTAAAATATAATTTTGGAA
*
343361 AAGTTTAAGGGTTAAAATATAATTTTGGAA
1 AAGTTTGAGGGTTAAAATATAATTTTGGAA
*
343391 AAGTTTGAGGGTTAAAATGTAATTTTGGAA
1 AAGTTTGAGGGTTAAAATATAATTTTGGAA
* * *
343421 AAGTTT-AGGGGTCAAAATGTAATTTTAGAA
1 AAGTTTGA-GGGTTAAAATATAATTTTGGAA
* *
343451 AAGTTTAAGGGTTAAAATGTAATTTTGGAA
1 AAGTTTGAGGGTTAAAATATAATTTTGGAA
* *
343481 AAGTTT-AGTGGATAAAATGTAATTTTTGG-A
1 AAGTTTGAG-GGTTAAAATATAA-TTTTGGAA
343511 AAGTTTG
1 AAGTTTG
343518 GGGACCTTTT
Statistics
Matches: 267, Mismatches: 26, Indels: 26
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.00
29 42 0.16
30 188 0.70
31 36 0.13
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AAGTTTGAGGGTTAAAATATAATTTTGGAA
Found at i:343290 original size:60 final size:61
Alignment explanation
Indices: 343189--343516 Score: 415
Period size: 60 Copynumber: 5.5 Consensus size: 61
343179 AGAAGTTCGA
* * *
343189 GGGTCAAAAATATGATTTTGGAAAAG-TTCGAGGGTTAAAATATAATTTTGGAAACA-TTTGAG
1 GGGTC-AAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAA-AGTTT-AG
* *
343251 GGGTCAAGATGTAATTTT-GAAAAGTTTAGA-GGTTAAAATATGATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAAAGTTTAG
* * *
343310 GGGTCAAGATGTAATTTT-GAAAAGTTTA-AGGGTTAAAATATAATTTTGGCAAAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAAAGTTTAG
* * *
343369 GGGTTAAAATATAATTTTGGAAAAGTTT-GAGGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAAAGTTTAG
* *
343429 GGGTCAAAATGTAATTTTAGAAAAGTTTA-AGGGTTAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAAAGTTTAG
*
343489 TGGAT-AAAATGTAATTTTTGG-AAAGTTT
1 -GGGTCAAAATGTAA-TTTTGGAAAAGTTT
343517 GGGGACCTTT
Statistics
Matches: 239, Mismatches: 19, Indels: 18
0.87 0.07 0.07
Matches are distributed among these distances:
58 1 0.00
59 72 0.30
60 139 0.58
61 22 0.09
62 5 0.02
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (61 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGGTTAAAATATAATTTTGGAAAAGTTTAG
Found at i:343464 original size:90 final size:89
Alignment explanation
Indices: 343164--343520 Score: 413
Period size: 90 Copynumber: 4.0 Consensus size: 89
343154 ACTCGGGATG
* ** * * *
343164 AAAATGAAATTTTA-AAGAAGTTCGAGGGTCAAAAATATGATTTTGGAAAAGTTCGAGGGTTAAA
1 AAAATGTAATTTTAGAA-AAGTTTAAGGGT-TAAAATATAATTTTGGAAAAGTT-TAGGGTTAAA
*
343228 ATATAATTTTGGAAACA-TTTGAGGGGTC
63 ATGTAATTTTGGAAA-AGTTT-AGGGGTC
* * * *
343256 AAGATGTAATTTT-GAAAAGTTT-AGAGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAGA
1 AAAATGTAATTTTAGAAAAGTTTAAG-GGTTAAAATATAATTTTGGAAAAGTTTA-GGGTTAAAA
* *
343319 TGTAATTTT-GAAAAGTTTAAGGGTT
64 TGTAATTTTGGAAAAGTTTAGGGGTC
* * *
343344 AAAATATAATTTTGGCAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTGAGGGTTAAAAT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTT-AGGGTTAAAAT
343409 GTAATTTTGGAAAAGTTTAGGGGTC
65 GTAATTTTGGAAAAGTTTAGGGGTC
* *
343434 AAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGTGGATAAAAT
1 AAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTAG-GGTTAAAAT
343499 GTAATTTTTGG-AAAGTTT-GGGG
65 GTAA-TTTTGGAAAAGTTTAGGGG
343521 ACCTTTTGGG
Statistics
Matches: 232, Mismatches: 23, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
88 17 0.07
89 64 0.28
90 124 0.53
91 14 0.06
92 13 0.06
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (89 bp):
AAAATGTAATTTTAGAAAAGTTTAAGGGTTAAAATATAATTTTGGAAAAGTTTAGGGTTAAAATG
TAATTTTGGAAAAGTTTAGGGGTC
Found at i:345050 original size:17 final size:17
Alignment explanation
Indices: 345023--345117 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
345013 TTAAATTTTT
345023 ATTTCAAAATAAATTTAA
1 ATTT-AAAATAAATTTAA
345041 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** **
345058 ACTCCAAATAAGCTTAA
1 ATTTAAAATAAATTTAA
*
345075 ATTTACAATAAATTTAA
1 ATTTAAAATAAATTTAA
* * **
345092 ACTTAAAATGAATGAAA
1 ATTTAAAATAAATTTAA
345109 ATTTAAAAT
1 ATTTAAAAT
345118 CTAAAATCGG
Statistics
Matches: 60, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
17 56 0.93
18 4 0.07
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:345981 original size:78 final size:78
Alignment explanation
Indices: 345848--346002 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
345838 TTTGTTGTTG
*
345848 TTTTCTATTATGCATTTTGTTTGTTGTTGTGTTTGTTTGAAGTATGTTTCAAACTATGTTTAATT
1 TTTTCTATTATGCATTTTGTTTGTTGTTGTGTTTGTTTGAAGTATGTTTCAAACTATATTTAATT
345913 TATGTTTAAAATA
66 TATGTTTAAAATA
*
345926 TTTTCTATTATGCATTTTGTTTGTTGTTGTGTTTGTTTGAAGTATGTTTCGAACTATATTTAATT
1 TTTTCTATTATGCATTTTGTTTGTTGTTGTGTTTGTTTGAAGTATGTTTCAAACTATATTTAATT
*
345991 TATGTTTTAAAT
66 TATGTTTAAAAT
346003 GTATCATGTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.22, C:0.05, G:0.15, T:0.57
Consensus pattern (78 bp):
TTTTCTATTATGCATTTTGTTTGTTGTTGTGTTTGTTTGAAGTATGTTTCAAACTATATTTAATT
TATGTTTAAAATA
Found at i:352908 original size:33 final size:33
Alignment explanation
Indices: 352869--352937 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
352859 AACTGCTATT
352869 ATCATAATAAACACGATTATTCAATTCAATCCC
1 ATCATAATAAACACGATTATTCAATTCAATCCC
*
352902 ATCATAATAAACACGGTTATTCAATTCAATCCC
1 ATCATAATAAACACGATTATTCAATTCAATCCC
352935 ATC
1 ATC
352938 TTACAACTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (33 bp):
ATCATAATAAACACGATTATTCAATTCAATCCC
Found at i:353120 original size:2 final size:2
Alignment explanation
Indices: 353113--354779 Score: 3057
Period size: 2 Copynumber: 852.0 Consensus size: 2
353103 TTTAAGTATT
353113 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353155 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353197 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
353239 GA GA GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353281 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353323 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353363 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353405 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353447 GA GA GA GA GA GA GA GA GA GA -A GA GA GA -A GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353487 GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353528 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353568 GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353609 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353650 GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353691 -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353732 GA GA GA GA G- GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353772 GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353813 GA GA -A GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353853 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353894 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353936 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
353978 GA GA GA -A GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354018 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354060 GA GA GA GA -A GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354099 GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354140 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354182 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354224 GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354264 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354306 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
354347 G- GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA G- GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354387 GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354428 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354470 GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354510 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354552 GA -A GA -A GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354591 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354633 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354675 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354715 GA GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
354756 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
354780 TTGACTATCT
Statistics
Matches: 1624, Mismatches: 4, Indels: 74
0.95 0.00 0.04
Matches are distributed among these distances:
1 37 0.02
2 1587 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:361807 original size:24 final size:24
Alignment explanation
Indices: 361746--361808 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
361736 TAGAGTAATA
* * *
361746 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
361770 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
361794 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
361809 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:363770 original size:24 final size:24
Alignment explanation
Indices: 363742--363806 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
363732 TAGAGTAATA
* *
363742 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
* *
363766 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
363790 AGAGTTTAACTGAAATA
1 AGAGTTTAACTGAAATA
363807 TTATTTCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTGAAATAAATAAAC
Found at i:368081 original size:20 final size:20
Alignment explanation
Indices: 368051--368095 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
368041 ATTACTTCTC
368051 AAAAG-TACTTTTGAGAAAT
1 AAAAGCTACTTTTGAGAAAT
368070 AAAAGCTACTTTTGAGAAAT
1 AAAAGCTACTTTTGAGAAAT
368090 AAAAGC
1 AAAAGC
368096 ATTACTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.27
Consensus pattern (20 bp):
AAAAGCTACTTTTGAGAAAT
Found at i:374116 original size:16 final size:16
Alignment explanation
Indices: 374095--374125 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
374085 TCAAGTAAAT
374095 AAATAAAAAAAAAACA
1 AAATAAAAAAAAAACA
*
374111 AAATAAAATAAAAAC
1 AAATAAAAAAAAAAC
374126 TTAACAAAAC
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:0.84, C:0.06, G:0.00, T:0.10
Consensus pattern (16 bp):
AAATAAAAAAAAAACA
Found at i:377089 original size:7 final size:7
Alignment explanation
Indices: 377077--377101 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
377067 TTAACAAATG
377077 ATAATAA
1 ATAATAA
377084 ATAATAA
1 ATAATAA
377091 ATAATAA
1 ATAATAA
377098 ATAA
1 ATAA
377102 AAAGACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:379968 original size:25 final size:26
Alignment explanation
Indices: 379932--379980 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
379922 TAATATTTAT
379932 TATTAAATTTTATTT-TACAAACACC
1 TATTAAATTTTATTTATACAAACACC
*
379957 TATT-AATATTTATTTATATAAACA
1 TATTAAAT-TTTATTTATACAAACA
379981 AATTTATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 11 0.52
26 7 0.33
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTAAATTTTATTTATACAAACACC
Found at i:387072 original size:29 final size:28
Alignment explanation
Indices: 387013--387074 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
387003 CAATATGTAT
*
387013 TTTTATATATAAACTTTAATTTTATGCAA
1 TTTTATATATAAACTTTAATTTAAT-CAA
*
387042 TTTTATATATAAAATTTTAATTTAAAT-AA
1 TTTTATATAT-AAACTTTAATTT-AATCAA
387071 TTTT
1 TTTT
387075 TTACAAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.55
30 11 0.38
31 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTTATATATAAACTTTAATTTAATCAA
Found at i:391999 original size:120 final size:120
Alignment explanation
Indices: 391786--392026 Score: 482
Period size: 120 Copynumber: 2.0 Consensus size: 120
391776 AGCAGTCTAG
391786 TGCATTCTTTGTTTCCTGACCTCATCTTTCTACTATATCAGAAAATTTTACAGCATACAGATTTG
1 TGCATTCTTTGTTTCCTGACCTCATCTTTCTACTATATCAGAAAATTTTACAGCATACAGATTTG
391851 AAATGCAGGTTATTTTTCCAGCCCTTGATATACGTGTAAAAAATGTGGCAAAAAC
66 AAATGCAGGTTATTTTTCCAGCCCTTGATATACGTGTAAAAAATGTGGCAAAAAC
391906 TGCATTCTTTGTTTCCTGACCTCATCTTTCTACTATATCAGAAAATTTTACAGCATACAGATTTG
1 TGCATTCTTTGTTTCCTGACCTCATCTTTCTACTATATCAGAAAATTTTACAGCATACAGATTTG
391971 AAATGCAGGTTATTTTTCCAGCCCTTGATATACGTGTAAAAAATGTGGCAAAAAC
66 AAATGCAGGTTATTTTTCCAGCCCTTGATATACGTGTAAAAAATGTGGCAAAAAC
392026 T
1 T
392027 TACTCCCTTG
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (120 bp):
TGCATTCTTTGTTTCCTGACCTCATCTTTCTACTATATCAGAAAATTTTACAGCATACAGATTTG
AAATGCAGGTTATTTTTCCAGCCCTTGATATACGTGTAAAAAATGTGGCAAAAAC
Found at i:399637 original size:32 final size:32
Alignment explanation
Indices: 399601--399662 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
399591 CAACTCATAG
* *
399601 TTTCCGAGTCAATTGCCTACCTTTCAACTAAC
1 TTTCCAAGTCAATTGCCTACCCTTCAACTAAC
399633 TTTCCAAGTCAATTGCCTACCCTTCAACTA
1 TTTCCAAGTCAATTGCCTACCCTTCAACTA
399663 TATGGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (32 bp):
TTTCCAAGTCAATTGCCTACCCTTCAACTAAC
Found at i:409724 original size:16 final size:17
Alignment explanation
Indices: 409691--409729 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
409681 TTTGAAAGGA
*
409691 TTAAAATTATTATTAAT
1 TTAAAATTATTATAAAT
409708 TTAAAATT-TTATAAAT
1 TTAAAATTATTATAAAT
409724 TATAAA
1 T-TAAA
409730 GAGTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAAATTATTATAAAT
Done.