Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011008.1 Kokia drynarioides strain JFW-HI SEQ_125978, whole genome shotgun sequence
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: 320535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 89 characters in sequence are not A, C, G, or T
Found at i:1667 original size:33 final size:32
Alignment explanation
Indices: 1630--1765 Score: 123
Period size: 33 Copynumber: 4.2 Consensus size: 32
1620 TGACGGTTAA
1630 GGAGGGTGATGTTGAAGGGGTAGAAGTTGATGG
1 GGAGGGTGAT-TTGAAGGGGTAGAAGTTGATGG
*
1663 GGAGGGTGACTATGAAGGGGTAGAA-TCTGATGG
1 GGAGGGTGA-TTTGAAGGGGTAGAAGT-TGATGG
* * * * *
1696 TGAAGGTGATTTGGAAAGGGTAAAAGTTG-TTG
1 GGAGGGTGATTT-GAAGGGGTAGAAGTTGATGG
* * * *
1728 GGAGGGTGATGTAGGAGGGGTACAAGCTGATGG
1 GGAGGGTGAT-TTGAAGGGGTAGAAGTTGATGG
1761 GGAGG
1 GGAGG
1766 TTGTGTCTGC
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
32 25 0.30
33 55 0.67
34 2 0.02
ACGTcount: A:0.26, C:0.03, G:0.48, T:0.23
Consensus pattern (32 bp):
GGAGGGTGATTTGAAGGGGTAGAAGTTGATGG
Found at i:1749 original size:65 final size:66
Alignment explanation
Indices: 1634--1760 Score: 152
Period size: 65 Copynumber: 1.9 Consensus size: 66
1624 GGTTAAGGAG
* * * *
1634 GGTGATGTTGAAGGGGTAGAAGTTGATGGGGAGGGTGACTATGAAGGGGTAGAATCTGATGGTGA
1 GGTGATGTTGAAAGGGTAAAAGTTGATGGGGAGGGTGACTATGAAGGGGTACAAGCTGATGGTGA
1699 A
66 A
* * *
1700 GGTGAT-TTGGAAAGGGTAAAAGTTG-TTGGGAGGGTGA-TGTAGGAGGGGTACAAGCTGATGG
1 GGTGATGTT-GAAAGGGTAAAAGTTGATGGGGAGGGTGACTAT-GAAGGGGTACAAGCTGATGG
1761 GGAGGTTGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.04
65 30 0.58
66 20 0.38
ACGTcount: A:0.27, C:0.03, G:0.46, T:0.24
Consensus pattern (66 bp):
GGTGATGTTGAAAGGGTAAAAGTTGATGGGGAGGGTGACTATGAAGGGGTACAAGCTGATGGTGA
A
Found at i:5090 original size:17 final size:18
Alignment explanation
Indices: 5063--5096 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5053 ACTTATTACT
5063 TTTATTACTTGAACATTG
1 TTTATTACTTGAACATTG
*
5081 TTTA-TACTTGCACATT
1 TTTATTACTTGAACATT
5097 TGCTACAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTATTACTTGAACATTG
Found at i:9633 original size:10 final size:10
Alignment explanation
Indices: 9602--9635 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
9592 TGACAATATA
9602 TTTCTTTTCTT
1 TTTC-TTTCTT
*
9613 CTTCTTTCTT
1 TTTCTTTCTT
9623 TTTCTTTCTT
1 TTTCTTTCTT
9633 TTT
1 TTT
9636 GTGAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:10249 original size:17 final size:18
Alignment explanation
Indices: 10229--10265 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10219 ATGTACTAAG
*
10229 AAATG-AAATGCAGTGAC
1 AAATGAAAATGCAATGAC
10246 AAATGAAAATGCAATGAC
1 AAATGAAAATGCAATGAC
10264 AA
1 AA
10266 TTAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.54, C:0.11, G:0.19, T:0.16
Consensus pattern (18 bp):
AAATGAAAATGCAATGAC
Found at i:10277 original size:21 final size:20
Alignment explanation
Indices: 10246--10288 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
10236 ATGCAGTGAC
10246 AAATGAAAATGCAATGACAATT
1 AAATGAAAATGC-ATG-CAATT
10268 AAAT-AAAATGCATGCAATT
1 AAATGAAAATGCATGCAATT
10287 AA
1 AA
10289 TTACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 3 0.14
21 7 0.33
22 4 0.19
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (20 bp):
AAATGAAAATGCATGCAATT
Found at i:10403 original size:21 final size:21
Alignment explanation
Indices: 10377--10417 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10367 CTCGCCTTCT
*
10377 TCTTTATGC-TTCTTCTTCTTA
1 TCTTTACGCTTTC-TCTTCTTA
10398 TCTTTACGCTTTCTCTTCTT
1 TCTTTACGCTTTCTCTTCTT
10418 GTCCTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.07, C:0.27, G:0.05, T:0.61
Consensus pattern (21 bp):
TCTTTACGCTTTCTCTTCTTA
Found at i:13300 original size:27 final size:26
Alignment explanation
Indices: 13232--13309 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
13222 AATTTAGTAC
*
13232 TTATCTTGAT-AGTATTTTATTAATT
1 TTATCTTGATAAGTATTATATTAATT
* * *
13257 TAATATT-A-AAGTGATTATCTTAATAT
1 TTATCTTGATAAGT-ATTATATTAAT-T
13283 TTATCTTGATAAGTATTATATTAATT
1 TTATCTTGATAAGTATTATATTAATT
13309 T
1 T
13310 AGTATTAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 4 0.10
25 14 0.34
26 8 0.20
27 11 0.27
28 4 0.10
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (26 bp):
TTATCTTGATAAGTATTATATTAATT
Found at i:14164 original size:13 final size:11
Alignment explanation
Indices: 14132--14179 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
14122 TAATTAATTA
*
14132 ATTATTATTTT
1 ATTAATATTTT
14143 ATTAATATTTT
1 ATTAATATTTT
14154 ACTTAA-ATATTT
1 A-TTAATAT-TTT
*
14166 ATTATTATTTT
1 ATTAATATTTT
14177 ATT
1 ATT
14180 TAGAAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:15929 original size:4 final size:4
Alignment explanation
Indices: 15920--15946 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
15910 TTAGGTAATG
15920 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
15947 AAGTGTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:17581 original size:26 final size:26
Alignment explanation
Indices: 17552--17610 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
17542 CTAGTCATGC
*
17552 ATGACTCTAAGTGATAATGTCCCAAG
1 ATGACTCTAAGTGAGAATGTCCCAAG
*
17578 ATGACTTTAAGTGAGAATGTCCCAAG
1 ATGACTCTAAGTGAGAATGTCCCAAG
17604 ATGACTC
1 ATGACTC
17611 ATAAAGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (26 bp):
ATGACTCTAAGTGAGAATGTCCCAAG
Found at i:20536 original size:78 final size:78
Alignment explanation
Indices: 20407--20597 Score: 235
Period size: 78 Copynumber: 2.4 Consensus size: 78
20397 AGATTCTGAA
* * * * *
20407 GAATTACTGTATTGGCTCGTGAGAGCGA-ATTATTGTACTGGCTCGTAAGAGCGATATACTGAAT
1 GAATTACTGTATTGGCTCGTAAGAGCGATA-TACTGAACTAGCTCGTAAGAGCGATATACTGAAC
**
20471 TGGCTCGTG-AGAGC
65 TAACTCG-GAAGAGC
* *
20485 GAATTACTGTATTGGCTCGTAAGAGCTATATACTGAACTAGCTCGTAAGAGCGATATACTGCACT
1 GAATTACTGTATTGGCTCGTAAGAGCGATATACTGAACTAGCTCGTAAGAGCGATATACTGAACT
20550 AACTCGGAAGAGC
66 AACTCGGAAGAGC
* *
20563 G-ATATACTGTACTGGCTTGTAAGAGCGATATACTG
1 GAAT-TACTGTATTGGCTCGTAAGAGCGATATACTG
20598 CATTGGCTCA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
77 3 0.03
78 94 0.96
79 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (78 bp):
GAATTACTGTATTGGCTCGTAAGAGCGATATACTGAACTAGCTCGTAAGAGCGATATACTGAACT
AACTCGGAAGAGC
Found at i:20612 original size:26 final size:26
Alignment explanation
Indices: 20419--20640 Score: 198
Period size: 26 Copynumber: 8.5 Consensus size: 26
20409 ATTACTGTAT
* * *
20419 TGGCTCGTGAGAGCGA-ATTATTGTAC
1 TGGCTCGTAAGAGCGATA-TACTGAAC
*
20445 TGGCTCGTAAGAGCGATATACTGAAT
1 TGGCTCGTAAGAGCGATATACTGAAC
* * *
20471 TGGCTCGTGAGAGCGA-ATTACTGTAT
1 TGGCTCGTAAGAGCGATA-TACTGAAC
*
20497 TGGCTCGTAAGAGCTATATACTGAAC
1 TGGCTCGTAAGAGCGATATACTGAAC
* *
20523 TAGCTCGTAAGAGCGATATACTGCAC
1 TGGCTCGTAAGAGCGATATACTGAAC
** * *
20549 TAACTCGGAAGAGCGATATACTGTAC
1 TGGCTCGTAAGAGCGATATACTGAAC
* * *
20575 TGGCTTGTAAGAGCGATATACTGCAT
1 TGGCTCGTAAGAGCGATATACTGAAC
** *
20601 TGGCTCAG-AAGAGTTATATACTGTAC
1 TGGCTC-GTAAGAGCGATATACTGAAC
* *
20627 TAGCTTGTAAGAGC
1 TGGCTCGTAAGAGC
20641 AATTTTTTGA
Statistics
Matches: 161, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.01
26 156 0.97
27 3 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (26 bp):
TGGCTCGTAAGAGCGATATACTGAAC
Found at i:20613 original size:78 final size:78
Alignment explanation
Indices: 20407--20628 Score: 227
Period size: 78 Copynumber: 2.8 Consensus size: 78
20397 AGATTCTGAA
* * * * *
20407 GAATTACTGTATTGGCTCGTGAGAGCGA-ATTATTGTACTGGCTCGTAAGAGCGATATACTGAAT
1 GAATTACTGTACTGGCTCGTAAGAGCGATA-TACTGAACTGGCTCGTAAGAGCGATATACTGAAC
**
20471 TGGCTCGTGAGAGC
65 TAACTCGTGAGAGC
* * * *
20485 GAATTACTGTATTGGCTCGTAAGAGCTATATACTGAACTAGCTCGTAAGAGCGATATACTGCACT
1 GAATTACTGTACTGGCTCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATACTGAACT
20550 AACTCG-GAAGAGC
66 AACTCGTG-AGAGC
* * * ** *
20563 G-ATATACTGTACTGGCTTGTAAGAGCGATATACTGCATTGGCTCAG-AAGAGTTATATACTGTA
1 GAAT-TACTGTACTGGCTCGTAAGAGCGATATACTGAACTGGCTC-GTAAGAGCGATATACTGAA
20626 CTA
64 CTA
20629 GCTTGTAAGA
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
77 3 0.02
78 117 0.96
79 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (78 bp):
GAATTACTGTACTGGCTCGTAAGAGCGATATACTGAACTGGCTCGTAAGAGCGATATACTGAACT
AACTCGTGAGAGC
Found at i:21451 original size:55 final size:55
Alignment explanation
Indices: 21376--21483 Score: 123
Period size: 55 Copynumber: 2.0 Consensus size: 55
21366 CGGATGTGCG
* * **
21376 GGGTATTTCGCATGTTCACACG-GCTTGTCACACGATTTGTGACACGATCGTGTAA
1 GGGTATTTCGCATGTTCACACGATC-TGGCACACGATTTAAGACACGATCGTGTAA
*
21431 GGGTATTTCG-A-GTATACACACGATCTGGCACACGATTTAAGGCACGATCGTGT
1 GGGTATTTCGCATGT-T-CACACGATCTGGCACACGATTTAAGACACGATCGTGT
21484 GACCCCTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 40 0.89
56 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (55 bp):
GGGTATTTCGCATGTTCACACGATCTGGCACACGATTTAAGACACGATCGTGTAA
Found at i:23002 original size:19 final size:19
Alignment explanation
Indices: 22980--23035 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
22970 TTAACTGTTG
22980 ACTTGATCGTTGACCGTCA
1 ACTTGATCGTTGACCGTCA
* * * **
22999 ACTTGACCGTTTATCGTTG
1 ACTTGATCGTTGACCGTCA
23018 ACTTTGATCGTTGACCGT
1 AC-TTGATCGTTGACCGT
23036 TGATCGTTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (19 bp):
ACTTGATCGTTGACCGTCA
Found at i:29401 original size:52 final size:52
Alignment explanation
Indices: 29339--29529 Score: 249
Period size: 52 Copynumber: 3.7 Consensus size: 52
29329 ATATTCTGAA
*
29339 GAATTATTGTACTGGCTCATAAAAGCGATATACTGAACTGGCTCATGAGAGC
1 GAATTATTGTACTGGCTCGTAAAAGCGATATACTGAACTGGCTCATGAGAGC
* * *
29391 GAATTATTGTACTGGCTCGTAAGAGAGATATACTGAACTGGCTCGTGAGAGC
1 GAATTATTGTACTGGCTCGTAAAAGCGATATACTGAACTGGCTCATGAGAGC
* * * *
29443 GAATTACTGTACTAGCTCGTAAAAGCTATATACTGAACTGGCTCATAAGAGC
1 GAATTATTGTACTGGCTCGTAAAAGCGATATACTGAACTGGCTCATGAGAGC
* * * * *
29495 G-ATATACTGCAGTGGCTCGGAAGAGCGATATACTG
1 GAAT-TATTGTACTGGCTCGTAAAAGCGATATACTG
29530 TACTAGCTTG
Statistics
Matches: 121, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
51 2 0.02
52 119 0.98
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (52 bp):
GAATTATTGTACTGGCTCGTAAAAGCGATATACTGAACTGGCTCATGAGAGC
Found at i:29519 original size:104 final size:104
Alignment explanation
Indices: 29339--29529 Score: 276
Period size: 104 Copynumber: 1.8 Consensus size: 104
29329 ATATTCTGAA
* * * * *
29339 GAATTATTGTACTGGCTCATAAAAGCGATATACTGAACTGGCTCATGAGAGCGAATTATTGTACT
1 GAATTACTGTACTAGCTCATAAAAGCGATATACTGAACTGGCTCATAAGAGCGAATTACTGCACT
*
29404 GGCTCGTAAGAGAGATATACTGAACTGGCTCGTGAGAGC
66 GGCTCGGAAGAGAGATATACTGAACTGGCTCGTGAGAGC
* * *
29443 GAATTACTGTACTAGCTCGTAAAAGCTATATACTGAACTGGCTCATAAGAGCG-ATATACTGCAG
1 GAATTACTGTACTAGCTCATAAAAGCGATATACTGAACTGGCTCATAAGAGCGAAT-TACTGCAC
*
29507 TGGCTCGGAAGAGCGATATACTG
65 TGGCTCGGAAGAGAGATATACTG
29530 TACTAGCTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
103 2 0.03
104 74 0.97
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (104 bp):
GAATTACTGTACTAGCTCATAAAAGCGATATACTGAACTGGCTCATAAGAGCGAATTACTGCACT
GGCTCGGAAGAGAGATATACTGAACTGGCTCGTGAGAGC
Found at i:29544 original size:26 final size:26
Alignment explanation
Indices: 29349--29546 Score: 193
Period size: 26 Copynumber: 7.6 Consensus size: 26
29339 GAATTATTGT
* *
29349 ACTGGCTCATAAAAGCGATATACTGA
1 ACTGGCTCGTAAGAGCGATATACTGA
* * * *
29375 ACTGGCTCATGAGAGCGA-ATTATTGT
1 ACTGGCTCGTAAGAGCGATA-TACTGA
*
29401 ACTGGCTCGTAAGAGAGATATACTGA
1 ACTGGCTCGTAAGAGCGATATACTGA
* *
29427 ACTGGCTCGTGAGAGCGA-ATTACTGT
1 ACTGGCTCGTAAGAGCGATA-TACTGA
* * *
29453 ACTAGCTCGTAAAAGCTATATACTGA
1 ACTGGCTCGTAAGAGCGATATACTGA
* *
29479 ACTGGCTCATAAGAGCGATATACTGC
1 ACTGGCTCGTAAGAGCGATATACTGA
* * *
29505 AGTGGCTCGGAAGAGCGATATACTGT
1 ACTGGCTCGTAAGAGCGATATACTGA
* *
29531 ACTAGCTTGTAAGAGC
1 ACTGGCTCGTAAGAGC
29547 AATTTTCTGA
Statistics
Matches: 138, Mismatches: 30, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
25 2 0.01
26 134 0.97
27 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (26 bp):
ACTGGCTCGTAAGAGCGATATACTGA
Found at i:31172 original size:18 final size:18
Alignment explanation
Indices: 31149--31185 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31139 TTTGTGATCA
31149 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
31167 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
31185 A
1 A
31186 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:36392 original size:17 final size:17
Alignment explanation
Indices: 36348--36386 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
36338 CTCCACCTTG
* *
36348 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
36365 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
36382 ACAAG
1 ACAAG
36387 TTCTCTATCT
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:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:57480 original size:19 final size:19
Alignment explanation
Indices: 57456--57494 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
57446 ATACTTTAAT
57456 TTGT-AAATAAATTAAGTTA
1 TTGTAAAAT-AATTAAGTTA
*
57475 TTGTAAAATAATTAATTTA
1 TTGTAAAATAATTAAGTTA
57494 T
1 T
57495 CATAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TTGTAAAATAATTAAGTTA
Found at i:64318 original size:2 final size:2
Alignment explanation
Indices: 64311--64339 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64301 TAAGTAAAGC
64311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64340 ATTCATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70299 original size:14 final size:16
Alignment explanation
Indices: 70280--70311 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
70270 AAAGTGAATA
70280 TTGCAAA-TA-ATTGT
1 TTGCAAATTATATTGT
70294 TTGCAAATTATATTGT
1 TTGCAAATTATATTGT
70310 TT
1 TT
70312 TATTGAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TTGCAAATTATATTGT
Found at i:72166 original size:18 final size:18
Alignment explanation
Indices: 72143--72194 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
72133 AATTTATATG
72143 AAAATCCCTGAAGGATTT
1 AAAATCCCTGAAGGATTT
**
72161 AAAATCCCAAAAGGATTT
1 AAAATCCCTGAAGGATTT
*
72179 AAAATCCTTGAAGGAT
1 AAAATCCCTGAAGGAT
72195 AAAGAGTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (18 bp):
AAAATCCCTGAAGGATTT
Found at i:98956 original size:19 final size:19
Alignment explanation
Indices: 98932--98969 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
98922 TCATTGTTAT
98932 TATTCCCGGAAATTTGATG
1 TATTCCCGGAAATTTGATG
98951 TATTCCCGGAAATTTGATG
1 TATTCCCGGAAATTTGATG
98970 ATTGATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
TATTCCCGGAAATTTGATG
Found at i:104941 original size:17 final size:17
Alignment explanation
Indices: 104919--104954 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
104909 AGGTGGAGAA
* *
104919 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
104936 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
104953 CT
1 CT
104955 AGTCAAGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.44
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:110119 original size:18 final size:19
Alignment explanation
Indices: 110087--110123 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
110077 GAAATTTTAA
110087 TAATATTTTTCTAAAAAAT
1 TAATATTTTTCTAAAAAAT
*
110106 TAAT-TTTTTTTAAAAAAT
1 TAATATTTTTCTAAAAAAT
110124 ATTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTTTTCTAAAAAAT
Found at i:110131 original size:17 final size:19
Alignment explanation
Indices: 110087--110123 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
110077 GAAATTTTAA
*
110087 TAATATTTTTCTAAAAAAT
1 TAATTTTTTTCTAAAAAAT
110106 TAATTTTTTT-TAAAAAAT
1 TAATTTTTTTCTAAAAAAT
110124 ATTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATTTTTTTCTAAAAAAT
Found at i:112965 original size:27 final size:27
Alignment explanation
Indices: 112920--113066 Score: 122
Period size: 27 Copynumber: 5.6 Consensus size: 27
112910 GAAGATATTC
* **
112920 TGATTTTGGCTCACAAGAGCGTAATTT
1 TGATTCTGGCTCGTAAGAGCGTAATTT
* * * *
112947 TGATTCTGGCTTGTTAGAGCGTAACTC
1 TGATTCTGGCTCGTAAGAGCGTAATTT
* *
112974 TGATTTTGGCTCGTAAGAGCATAATTT
1 TGATTCTGGCTCGTAAGAGCGTAATTT
* * * * *
113001 TGATTTTAGCTCGTATGAGTGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTT
* *
113028 TG--TCTGGCTCGTAAGAGTGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTT
113053 T-A-TCTGGCTCGTAA
1 TGATTCTGGCTCGTAA
113067 AAGTGATATT
Statistics
Matches: 98, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
25 33 0.34
27 65 0.66
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (27 bp):
TGATTCTGGCTCGTAAGAGCGTAATTT
Found at i:113045 original size:25 final size:25
Alignment explanation
Indices: 113009--113095 Score: 104
Period size: 25 Copynumber: 3.4 Consensus size: 25
112999 TTTGATTTTA
*
113009 GCTCGTATGAGTGTAATTCTGTCTG
1 GCTCGTAAGAGTGTAATTCTGTCTG
*
113034 GCTCGTAAGAGTGTAATTCTATCTG
1 GCTCGTAAGAGTGTAATTCTGTCTG
* *
113059 GCTCGTAAAAGTG-ATATTCTGTTTGG
1 GCTCGTAAGAGTGTA-ATTCTGTCT-G
*
113085 GCTCATAAGAG
1 GCTCGTAAGAG
113096 CTAAGCTCTG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 1 0.02
25 42 0.79
26 10 0.19
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (25 bp):
GCTCGTAAGAGTGTAATTCTGTCTG
Found at i:115977 original size:3 final size:3
Alignment explanation
Indices: 115969--116016 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
115959 AAAGGCCCAA
115969 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
116017 TTTAAGGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:116647 original size:140 final size:143
Alignment explanation
Indices: 116433--117118 Score: 697
Period size: 140 Copynumber: 4.7 Consensus size: 143
116423 GATTTTGGGA
* * * *
116433 AAAGTTTTGTTTTTTTTAAACAATTTCGAAATAAAAGCTTT-GATTTTTAACTAAAATAGTGATT
1 AAAGTTTTGTTTTTTTTTAACTATTTCGAAATAAAAG-TTTAGATTTTTAA-GAAAGTAGTGATT
* * *
116497 TTCTTTAAAAAAGAGAAAGTTTAGATTTTTAAAGATAAAAAT-TTGTT-TT-TTTT-AG-AAAAG
64 TTCATTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATTTTTATTATTTTAAGAAAAAG
116557 TTTAAATTTTTAAAC
129 TTTAAATTTTTAAAC
116572 AAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTT
1 AAAGTTTTG-TTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTT
*
116637 TCATTAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTAGTTATTTTAAAGAA
65 TCATTAAAAAAG-AGAAAGTTTAGATTTTTAAAAATAAAAA--TATTTTTA-TTATTTT-AAGAA
*
116702 AAAGTTTAAATTTTTAAAT
125 AAAGTTTAAATTTTTAAAC
* *
116721 AAAGTTTTGATTTTTTTTTAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATT
1 AAAGTTTTG-TTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATT
* * * *
116786 TTCATTAAAAAAGAAAGAAAGTTTATATTTTAAAAAATATAATATGTTTTTTAGTTATTTTAAAG
64 TTCATTAAAAAAG--AGAAAGTTTAGATTTTTAAAAATA-AAAAT-ATTTTTA-TTATTTT-AAG
* *
116851 AAATAA-TTTAAAATTTTAAAT
123 AAA-AAGTTTAAATTTTTAAAC
* * *
116872 AAAG-TTT-TTATTTTTTAATTATTTCGAAATAAAAATTTAGATTTTTAAGAAAAGTAGTGATTT
1 AAAGTTTTGTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATTT
*
116935 TCATT---AAA-A-AAA--TTAGATTTTTAAAAAATAAAAATCTATTTTTAGTGATTTTAAAGAA
65 TCATTAAAAAAGAGAAAGTTTAGATTTTT-AAAAATAAAAA--TATTTTTA-TTATTTT-AAG-A
*
116993 AAAAGCTTAAATTTTTAAAC
124 AAAAGTTTAAATTTTTAAAC
* * * * * *
117013 AAAATTTT-TATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAATAAAATAGTGATTT
1 AAAGTTTTGTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTT-TAAGAAAGTAGTGATTT
** * * *
117077 TGTTTTAATCAAAAGA-AAACTTTTGATTTTTAAAAAAAAAAA
65 T-CATTAA--AAAAGAGAAAGTTTAGATTTTTAAAAATAAAAA
117119 AAGAAAATTT
Statistics
Matches: 472, Mismatches: 42, Indels: 55
0.83 0.07 0.10
Matches are distributed among these distances:
139 46 0.10
140 87 0.18
141 22 0.05
142 51 0.11
143 8 0.02
145 5 0.01
146 4 0.01
148 60 0.13
149 73 0.15
150 39 0.08
151 72 0.15
152 5 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (143 bp):
AAAGTTTTGTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
CATTAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATATTTTTATTATTTTAAGAAAAAGTT
TAAATTTTTAAAC
Found at i:116719 original size:149 final size:148
Alignment explanation
Indices: 116552--117077 Score: 691
Period size: 149 Copynumber: 3.6 Consensus size: 148
116542 TTTTTTTTAG
116552 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGTTTAGAT
1 AAAAGTTTAAATTTTTAAACAAAGTTTT--TTTTTTTTTAACTATTTCGAAATAAAAGTTTAGAT
116617 TTTTAAG-AAAGTAGTGATTTTCATTAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATCT
64 TTTTAAGAAAAGTAGTGATTTTCATTAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATCT
116681 ATTTTTAGTTATTTTAAAGA
129 ATTTTTAGTTATTTTAAAGA
* * *
116701 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTAACTATTTCAAAATAAAAGTTTGGAT
1 AAAAGTTTAAATTTTTAAACAAAGTTTT--TTTTTTTTTAACTATTTCGAAATAAAAGTTTAGAT
* * *
116766 TTTTAAGTAAAGTAGTGATTTTCATTAAAAAAGAAAGAAAGTTTATATTTTAAAAAATATAATAT
64 TTTTAAGAAAAGTAGTGATTTTCATTAAAAAAG-AAGAAAGTTTATATTTTTAAAAATA-AAAAT
*
116831 GT-TTTTTAGTTATTTTAAAGA
127 CTATTTTTAGTTATTTTAAAGA
* * * * *
116852 AATAA-TTTAAAATTTTAAATAAAG-TTTTTATTTTTTAATTATTTCGAAATAAAAATTTAGATT
1 AA-AAGTTTAAATTTTTAAACAAAGTTTTTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
*
116915 TTTAAGAAAAGTAGTGATTTTCATT----AA-AA-AAA--TTAGATTTTTAAAAAATAAAAATCT
65 TTTAAGAAAAGTAGTGATTTTCATTAAAAAAGAAGAAAGTTTATATTTTT-AAAAATAAAAATCT
*
116972 ATTTTTAGTGATTTTAAAGAA
129 ATTTTTAGTTATTTTAAAG-A
* * * *
116993 AAAAGCTTAAATTTTTAAACAAAATTTTTATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTT
1 AAAAGTTTAAATTTTTAAACAAAGTTTTTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
* *
117058 TGAA-ATAAAATAGTGATTTT
66 TTAAGA-AAAGTAGTGATTTT
117078 GTTTTAATCA
Statistics
Matches: 338, Mismatches: 29, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
139 13 0.04
140 26 0.08
141 22 0.07
142 53 0.16
144 2 0.01
148 55 0.16
149 69 0.20
150 28 0.08
151 63 0.19
152 7 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (148 bp):
AAAAGTTTAAATTTTTAAACAAAGTTTTTTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
TTAAGAAAAGTAGTGATTTTCATTAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATCTAT
TTTTAGTTATTTTAAAGA
Found at i:116759 original size:53 final size:51
Alignment explanation
Indices: 116552--116787 Score: 143
Period size: 53 Copynumber: 4.7 Consensus size: 51
116542 TTTTTTTTAG
* * *
116552 AAAAGTTTAAATTTTTAAACAAAGTTTTGATTTTTTTTTAACTATTTCGAAA-T
1 AAAAGTTTAAATTTTTAAATAAAGTTGTGATTTTTTTTTAA-TATTT--AAAGA
* * * **
116605 AAAAGTTTAGATTTTT-AAGAAAGTAGTGA-TTTTCATTAA-A---AAAGA
1 AAAAGTTTAAATTTTTAAATAAAGTTGTGATTTTTTTTTAATATTTAAAGA
* ** * **
116650 AGAAAGTTTATATTTTTAAAAATAAAAATCT-ATTTTTAGTT-AT-TTTAAAGA
1 A-AAAGTTTAAATTTTT--AAATAAAGTTGTGATTTTTTTTTAATATTTAAAGA
*
116701 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTAACTATTTCAAA-A
1 AAAAGTTTAAATTTTTAAATAAAGTTGTGATTTTTTTTTAA-TATTT-AAAGA
** * *
116753 TAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
1 -AAAAGTTTAAATTTTTAAATAAAGTTGTGATTTT
116788 CATTAAAAAA
Statistics
Matches: 141, Mismatches: 26, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
44 3 0.02
45 1 0.01
46 14 0.10
48 11 0.08
49 21 0.15
50 15 0.11
51 15 0.11
52 14 0.10
53 47 0.33
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (51 bp):
AAAAGTTTAAATTTTTAAATAAAGTTGTGATTTTTTTTTAATATTTAAAGA
Found at i:117051 original size:290 final size:282
Alignment explanation
Indices: 116443--117077 Score: 789
Period size: 290 Copynumber: 2.2 Consensus size: 282
116433 AAAGTTTTGT
* * *
116443 TTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTAACTAAAATAGTGATTTTCTTTAAAAA
1 TTTTTTT-AACTATTTCGAAATAAAAG-TTTGATTTTTAAATAAAATAGTGATTTTCATTAAAAA
* * * *
116508 AGAGAAAGTTTAGATTTTTAAAGATAAAAATTTGTTTTTTTTAGAAAAGTTTAAATTTTTAAACA
64 AGAGAAAGTTTAGATTTTAAAAAATAAAAATTTGTTTTTTTTAGAAAAATTTAAAATTTTAAACA
* *
116573 AAGTTTTGATTTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTT
129 AAGTTTT-ATTATTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGAAAGTAGTGATTTT
* *
116638 CATTAAAAAAGAAGAAAGTTTATATTTTTAAAAATAAAAATCTATTTTTAGTTATTTTAAAGAAA
193 CATT---AAAGAAGAAAG-TTAGATTTTTAAAAATAAAAATCTATTTTTAGTGATTTTAAAGAAA
* * * *
116703 AAGTTTAAATTTTTAAATAAAGTTTTGATT
254 AAGCTTAAATTTTTAAACAAAATTTT-ATA
* * *
116733 TTTTTTTAACTATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTT-GATTTTTAAATAAAATAGTGATTTTCATTAAAAAA
* * *
116798 GAAAGAAAGTTTATATTTTAAAAAATATAATATGTTTTTTAGTTATTTTAAAGAAATAATTTAAA
65 G--AGAAAGTTTAGATTTTAAAAAATA-AA-A-ATTTGTT--TT-TTTT--AGAAA-AATTTAAA
* *
116863 ATTTTAAATAAAG-TTT-TTATTTTTTAATTATTTCGAAATAAAAATTTAGATTTTTAAGAAAAG
119 ATTTTAAACAAAGTTTTATTATTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAG-AAAG
116926 TAGTGATTTTCATT-AA-AA-AAA-TTAGATTTTTAAAAAATAAAAATCTATTTTTAGTGATTTT
183 TAGTGATTTTCATTAAAGAAGAAAGTTAGATTTTT-AAAAATAAAAATCTATTTTTAGTGATTTT
116987 AAAGAAAAAAGCTTAAATTTTTAAACAAAATTTT-TA
247 AAAG-AAAAAGCTTAAATTTTTAAACAAAATTTTATA
*
117023 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAATAAAATAGTGATTTT
1 TTTTTTTAACTATTTCGAAATAAAAG-TTTGATTTTTAAATAAAATAGTGATTTT
117078 GTTTTAATCA
Statistics
Matches: 303, Mismatches: 26, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
288 3 0.01
289 50 0.17
290 64 0.21
291 56 0.18
292 31 0.10
293 3 0.01
294 7 0.02
296 2 0.01
297 43 0.14
298 18 0.06
299 8 0.03
300 18 0.06
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.45
Consensus pattern (282 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAATAAAATAGTGATTTTCATTAAAAAAG
AGAAAGTTTAGATTTTAAAAAATAAAAATTTGTTTTTTTTAGAAAAATTTAAAATTTTAAACAAA
GTTTTATTATTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGAAAGTAGTGATTTTCAT
TAAAGAAGAAAGTTAGATTTTTAAAAATAAAAATCTATTTTTAGTGATTTTAAAGAAAAAGCTTA
AATTTTTAAACAAAATTTTATA
Found at i:134055 original size:20 final size:20
Alignment explanation
Indices: 134030--134073 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
134020 TGTCAATGCA
134030 TTTTTACATTTACTT-TTATC
1 TTTTTACATTTACTTGTT-TC
*
134050 TTTTTACTTTTACTTGTTTC
1 TTTTTACATTTACTTGTTTC
134070 TTTT
1 TTTT
134074 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACTTGTTTC
Found at i:134074 original size:13 final size:14
Alignment explanation
Indices: 134038--134074 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
134028 CATTTTTACA
134038 TTTACTTTTATCTT
1 TTTACTTTTATCTT
134052 TTTACTTTTA-CTT
1 TTTACTTTTATCTT
134065 GTTT-CTTTTA
1 -TTTACTTTTA
134075 AATCTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.14, C:0.14, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTACTTTTATCTT
Found at i:140792 original size:10 final size:10
Alignment explanation
Indices: 140764--140797 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
140754 TAAATCAAGA
*
140764 AAAAAAATACA
1 AAAAAAATA-G
140775 AAAAAAATAG
1 AAAAAAATAG
140785 AAAAAAATAG
1 AAAAAAATAG
140795 AAA
1 AAA
140798 GAGAGCAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:141259 original size:42 final size:42
Alignment explanation
Indices: 141197--141448 Score: 337
Period size: 42 Copynumber: 6.0 Consensus size: 42
141187 AAGGAAAGCA
* * *
141197 TTCATTGCATTTAAATGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
141239 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGACTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
141281 TTCATTGAATTTAGAGGTCCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **
141323 TTCATTGCATTTAGAGGCCCAGGTGTGGAAGTTTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
141365 TTCATTGCATTTAGAGGTCCAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * *
141407 TTTATTGCATTTAGAGGCCTAGGCGTAGAGGTCCATTT-CTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
141448 T
1 T
141449 ATTTTTTCAT
Statistics
Matches: 185, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
41 4 0.02
42 179 0.97
43 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:142642 original size:20 final size:20
Alignment explanation
Indices: 142598--142636 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
142588 TTCTATAGTT
142598 ATTTTAAAGAAAAGTTTGAA
1 ATTTTAAAGAAAAGTTTGAA
* *
142618 ATTTTAAATAAAATTTTGA
1 ATTTTAAAGAAAAGTTTGA
142637 TTTTTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTTTAAAGAAAAGTTTGAA
Found at i:142714 original size:150 final size:149
Alignment explanation
Indices: 142341--143148 Score: 913
Period size: 150 Copynumber: 5.4 Consensus size: 149
142331 TTGGGAAAAA
* * * * *
142341 TTTTGGTTTTTTTAAACAATTTCGAAATAAAAGCTTT-GATTTTTAAGTAAAATAGTGATTTTCC
1 TTTTGATTTTTTTTAACTATTTCGAAATAAAAG-TTTAGATTTTTAAGTAAAGTAGTGATTTTCA
* *
142405 TTAAAAAAG--AGAAAGTTTAGATTTTTAAAAATAAAAATC-------TA-TT-TTTT-TAGAAA
65 TTAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAA
*
142458 AGTTTAAATTTTTAAACAAAG
130 AGTTTAAA-TTTTAAATAAAG
* *
142479 TTTTGATTTTTTTTTAAAACTATTTCGAAATAAAAGTTTAGATTTGTAAG-AAAATAGTGATTTT
1 TTTTGA-TTTTTTTT--AACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
* * *
142543 CATTAAAAAA-AGGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTCTATAGTTATTTTAAAG
63 CATTAAAAAAGA-AAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG
*
142607 AAAAGTTTGAAATTTTAAATAAAA
127 AAAAGTTT-AAATTTTAAATAAAG
* * *
142631 TTTTGATTTTTTTTAGCTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAATGATTTTCAT
1 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCAT
**
142696 TAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCCATTTTTTAGTTATTTTAAAGAAAA
66 TAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG-AAA
* *
142761 AGTTTAAATTTTTAATTAATG
130 AGTTTAAA-TTTTAAATAAAG
*
142782 TTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCAT
1 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCAT
*
142846 T---AAA-AAATAAAGTTTATATTTTTAAAAATAAAAATAAAATCTGTTTTTTAGTTATTTTAAA
66 TAAAAAAGAAAGAAAGTTTATATTTTTAAAAAT----A-AAAATCTGTTTTTTAGTTATTTTAAA
*
142907 GAAATAGTTTAAGTTTTTAAATAAAG
126 GAAA-AGTTTAA-ATTTTAAATAAAG
* * *
142933 TTATGA-TTTTTTTAACTATTTC-AAATAAAAGTTTAAATTTTTAATTAAAGTAGTGATTTTCAT
1 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCAT
* ** * *
142996 TAAAAAAAGAAGAAGAAAGTTTAGATTTCAAAAAAATAAAAATTTGTTTTTTAGTGATTTTAAAG
66 T-AAAAAAG-A-AAGAAAGTTTATATTT-TTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAG
** * *
143061 AAAAAAACTTAACTTTTTAAACAAAG
127 --AAAAGTTTAA-ATTTTAAATAAAG
* *
143087 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTT
1 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
143149 GTTTTAATCA
Statistics
Matches: 580, Mismatches: 49, Indels: 64
0.84 0.07 0.09
Matches are distributed among these distances:
138 5 0.01
139 7 0.01
140 26 0.04
141 27 0.05
142 29 0.05
146 24 0.04
147 3 0.01
149 32 0.06
150 174 0.30
151 99 0.17
152 26 0.04
153 28 0.05
154 26 0.04
155 19 0.03
156 35 0.06
157 14 0.02
158 6 0.01
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (149 bp):
TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCAT
TAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAA
GTTTAAATTTTAAATAAAG
Found at i:142967 original size:50 final size:51
Alignment explanation
Indices: 142889--142992 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 51
142879 ATAAAATCTG
** * *
142889 TTTTTTAGTTATTTTAAAGAAATAGTTTAAGTTTTTAAATAAAGTTA-TGAT
1 TTTTTTAACTATTTCAAAGAAATAGTTTAAATTTTTAAATAAAG-TAGTGAT
* *
142940 TTTTTTAACTATTTCAAATAAA-AGTTTAAATTTTTAATTAAAGTAGTGAT
1 TTTTTTAACTATTTCAAAGAAATAGTTTAAATTTTTAAATAAAGTAGTGAT
142990 TTT
1 TTT
142993 CATTAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 2 0.04
50 26 0.57
51 18 0.39
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (51 bp):
TTTTTTAACTATTTCAAAGAAATAGTTTAAATTTTTAAATAAAGTAGTGAT
Found at i:149137 original size:25 final size:25
Alignment explanation
Indices: 149051--149240 Score: 173
Period size: 25 Copynumber: 7.5 Consensus size: 25
149041 TATGATTCTT
149051 GCTCGTAAGAGCATAATTCTGATTCTG
1 GCTCGTAAGAGCATAATTCT-A-TCTG
* * * * * * *
149078 GTTTGTAAAAGCGTATTTTGTTTCTG
1 GCTCGTAAGAGCATA-ATTCTATCTG
* * *
149104 GCTCATAAGAGCGTAATTCTATCCG
1 GCTCGTAAGAGCATAATTCTATCTG
** * *
149129 GCTCGTAAGAGTGTAATTTTGTCTG
1 GCTCGTAAGAGCATAATTCTATCTG
*
149154 GCTCGTAAGAGCATAATTCTAGCTG
1 GCTCGTAAGAGCATAATTCTATCTG
* *
149179 GCTCGTAAGAGCATAATTTTAGCTG
1 GCTCGTAAGAGCATAATTCTATCTG
*
149204 GCTCGTAAGAGCATAATTCTGTCTG
1 GCTCGTAAGAGCATAATTCTATCTG
**
149229 GCTTATAAGAGC
1 GCTCGTAAGAGC
149241 GATATTATGT
Statistics
Matches: 131, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
25 102 0.78
26 15 0.11
27 11 0.08
28 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (25 bp):
GCTCGTAAGAGCATAATTCTATCTG
Found at i:149164 original size:50 final size:50
Alignment explanation
Indices: 149051--149265 Score: 220
Period size: 50 Copynumber: 4.2 Consensus size: 50
149041 TATGATTCTT
* * *
149051 GCTCGTAAGAGCATAATTCTGATTCTGGTTTGTAAAAGCGT-ATTTTGTTTCTG
1 GCTCGTAAGAGCATAATTCT-A-TCTGGCTCGTAAGAGCGTAATTTTG--TCTG
* * * *
149104 GCTCATAAGAGCGTAATTCTATCCGGCTCGTAAGAGTGTAATTTTGTCTG
1 GCTCGTAAGAGCATAATTCTATCTGGCTCGTAAGAGCGTAATTTTGTCTG
* *
149154 GCTCGTAAGAGCATAATTCTAGCTGGCTCGTAAGAGCATAATTTTAG-CTG
1 GCTCGTAAGAGCATAATTCTATCTGGCTCGTAAGAGCGTAATTTT-GTCTG
* ** * *
149204 GCTCGTAAGAGCATAATTCTGTCTGGCTTATAAGAGCG-ATATTATGTTTGG
1 GCTCGTAAGAGCATAATTCTATCTGGCTCGTAAGAGCGTA-ATTTTGTCT-G
149255 GCTCGTAAGAG
1 GCTCGTAAGAG
149266 GTAAACTCTG
Statistics
Matches: 137, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
49 2 0.01
50 84 0.61
51 26 0.19
52 7 0.05
53 18 0.13
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (50 bp):
GCTCGTAAGAGCATAATTCTATCTGGCTCGTAAGAGCGTAATTTTGTCTG
Found at i:149263 original size:26 final size:25
Alignment explanation
Indices: 149051--149265 Score: 150
Period size: 25 Copynumber: 8.4 Consensus size: 25
149041 TATGATTCTT
*
149051 GCTCGTAAGAGCATAATTCTGATTCTG
1 GCTCGTAAGAGCATAATTATG--TCTG
* * * * *
149078 GTTTGTAAAAGCGT-ATTTTGTTTCTG
1 GCTCGTAAGAGCATAATTATG--TCTG
* * * * *
149104 GCTCATAAGAGCGTAATTCTATCCG
1 GCTCGTAAGAGCATAATTATGTCTG
** *
149129 GCTCGTAAGAGTGTAATTTTGTCTG
1 GCTCGTAAGAGCATAATTATGTCTG
*
149154 GCTCGTAAGAGCATAATTCTAG-CTG
1 GCTCGTAAGAGCATAATTAT-GTCTG
*
149179 GCTCGTAAGAGCATAATTTTAG-CTG
1 GCTCGTAAGAGCATAATTAT-GTCTG
*
149204 GCTCGTAAGAGCATAATTCTGTCTG
1 GCTCGTAAGAGCATAATTATGTCTG
** *
149229 GCTTATAAGAGCGAT-ATTATGTTTGG
1 GCTCGTAAGAGC-ATAATTATGTCT-G
149255 GCTCGTAAGAG
1 GCTCGTAAGAG
149266 GTAAACTCTG
Statistics
Matches: 154, Mismatches: 29, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.01
25 106 0.69
26 33 0.21
27 14 0.09
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (25 bp):
GCTCGTAAGAGCATAATTATGTCTG
Found at i:150869 original size:20 final size:20
Alignment explanation
Indices: 150844--150881 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
150834 AACCCGACCC
*
150844 GTTGACCGTTAACTTTTTGG
1 GTTGACCGCTAACTTTTTGG
150864 GTTGACCGCTAACTTTTT
1 GTTGACCGCTAACTTTTT
150882 TTGAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (20 bp):
GTTGACCGCTAACTTTTTGG
Found at i:151800 original size:17 final size:16
Alignment explanation
Indices: 151778--151811 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
151768 ACTATAGACC
151778 TATTTTATTTTATCTTT
1 TATTTTATTTTAT-TTT
*
151795 TATTTTGTTTTATTTT
1 TATTTTATTTTATTTT
151811 T
1 T
151812 GGGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TATTTTATTTTATTTT
Found at i:156230 original size:26 final size:26
Alignment explanation
Indices: 156185--156235 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
156175 TTAAAAGATT
*
156185 TTTCCTTATGCTCTCCGGTAACATTG
1 TTTCCTTATGCTCTCAGGTAACATTG
* *
156211 TTTCCTTATGCTCTTAGGTAGCATT
1 TTTCCTTATGCTCTCAGGTAACATT
156236 TTTTTCCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.45
Consensus pattern (26 bp):
TTTCCTTATGCTCTCAGGTAACATTG
Found at i:161956 original size:68 final size:66
Alignment explanation
Indices: 161916--162060 Score: 200
Period size: 68 Copynumber: 2.1 Consensus size: 66
161906 TTCCTTATTT
* *
161916 TTCCCCTTTTCACCCCATGTGTTTCCCTTTTTCCTTTCTTCTTCCTTATTTTCTTCACATTCCTT
1 TTCCCCTTTTCACCCCATGTGTTTCCCTTTTGCCTTTCTTC-TCCATATTTTCTT-ACATTCCTT
161981 CTC
64 CTC
* * *
161984 TTCTCCTTTTCACCCCATGTGTTTCCCTTTTGCCTTTCTTCTTCCTTATTTCCTTCACATTCCTT
1 TTCCCCTTTTCACCCCATGTGTTTCCCTTTTGCCTTTCTTC-TCCATATTTTCTT-ACATTCCTT
162049 CTC
64 CTC
*
162052 TTCTCCTTT
1 TTCCCCTTT
162061 GACTATTTAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 74 1.00
ACGTcount: A:0.07, C:0.37, G:0.03, T:0.53
Consensus pattern (66 bp):
TTCCCCTTTTCACCCCATGTGTTTCCCTTTTGCCTTTCTTCTCCATATTTTCTTACATTCCTTCT
C
Found at i:163035 original size:23 final size:23
Alignment explanation
Indices: 163007--163097 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
162997 ACCAAGATTG
* * *
163007 TTATTGTACTAATTTGGATACTA
1 TTATTGAACTGATTTTGATACTA
*
163030 TTATTGTACTGA-TTTGATA-TAA
1 TTATTGAACTGATTTTGATACT-A
* *
163052 TTATCGAACTGATTTTGACACTA
1 TTATTGAACTGATTTTGATACTA
163075 TTATTGAACTGATTTTGATACTA
1 TTATTGAACTGATTTTGATACTA
163098 AAATGCAGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.02
22 17 0.29
23 39 0.67
24 1 0.02
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (23 bp):
TTATTGAACTGATTTTGATACTA
Found at i:170438 original size:18 final size:17
Alignment explanation
Indices: 170415--170448 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
170405 GGATATTAAT
170415 TATTATCATTGTTATTAG
1 TATTATCA-TGTTATTAG
170433 TATTATCATGTTATTA
1 TATTATCATGTTATTA
170449 TTGTCATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (17 bp):
TATTATCATGTTATTAG
Found at i:170544 original size:3 final size:3
Alignment explanation
Indices: 170536--170571 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
170526 AAATTGATCC
* *
170536 TAT TAT TAT TGT TAT TAT TAT TCT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
170572 CATCATCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:170576 original size:3 final size:3
Alignment explanation
Indices: 170570--170607 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
170560 TATTATTATT
170570 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
170608 ATTATTCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:186053 original size:13 final size:13
Alignment explanation
Indices: 186035--186059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186025 CCCATTTAAT
186035 CATTTTTAGCATG
1 CATTTTTAGCATG
186048 CATTTTTAGCAT
1 CATTTTTAGCAT
186060 TTTTAACTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:186081 original size:20 final size:21
Alignment explanation
Indices: 186056--186095 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
186046 TGCATTTTTA
186056 GCATTTT-TAACTCAGTGATT
1 GCATTTTCTAACTCAGTGATT
186076 GCATTTTCTAACTCAGTGAT
1 GCATTTTCTAACTCAGTGAT
186096 GCTCGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGATT
Found at i:193582 original size:16 final size:16
Alignment explanation
Indices: 193561--193602 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
193551 TATATCTATT
193561 TTTTCTTTTTATTAAC
1 TTTTCTTTTTATTAAC
* *
193577 TTTTCTTTCT-TTATC
1 TTTTCTTTTTATTAAC
193592 TTTT-TTTTTAT
1 TTTTCTTTTTAT
193603 GTGACTAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 9 0.41
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTTATTAAC
Found at i:193657 original size:12 final size:12
Alignment explanation
Indices: 193640--193664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
193630 ATACTCTTGT
193640 TTTGGGCAATAA
1 TTTGGGCAATAA
193652 TTTGGGCAATAA
1 TTTGGGCAATAA
193664 T
1 T
193665 GATAGGGTGC
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:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (12 bp):
TTTGGGCAATAA
Found at i:194219 original size:17 final size:17
Alignment explanation
Indices: 194199--194238 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
194189 AAATGTGAGA
194199 ACAATTAAAATGCAAAG
1 ACAATTAAAATGCAAAG
* *
194216 ACAA-TAAAATGTAACG
1 ACAATTAAAATGCAAAG
194232 ACAATTA
1 ACAATTA
194239 GATGAAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (17 bp):
ACAATTAAAATGCAAAG
Found at i:194648 original size:3 final size:3
Alignment explanation
Indices: 194640--194697 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
194630 CAGGTCAATG
* *
194640 TCT TCT TCT TCT TCT TCCT TC- TCT TCT TTT TAT TCT TCT T-T TC-
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
194683 TCT TC- TCT TTT TCT T
1 TCT TCT TCT TCT TCT T
194698 TTCCTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
2 8 0.18
3 34 0.76
4 3 0.07
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:194675 original size:24 final size:23
Alignment explanation
Indices: 194643--194704 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
194633 GTCAATGTCT
*
194643 TCTTCTTCTTCTTCCTTCTCTTC
1 TCTTTTTCTTCTTCCTTCTCTTC
*
194666 TTTTTATTCTTCTT--TTCTCTTC
1 TCTTT-TTCTTCTTCCTTCTCTTC
194688 TCTTTTTCTT-TTCCTTC
1 TCTTTTTCTTCTTCCTTC
194705 AATACCCTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 15 0.45
23 3 0.09
24 8 0.24
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (23 bp):
TCTTTTTCTTCTTCCTTCTCTTC
Found at i:207102 original size:19 final size:19
Alignment explanation
Indices: 207078--207115 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
207068 TTCTCAGCAT
207078 GCTGTGGATGATCCTCATA
1 GCTGTGGATGATCCTCATA
207097 GCTGTGGATGATCCTCATA
1 GCTGTGGATGATCCTCATA
207116 AATTTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (19 bp):
GCTGTGGATGATCCTCATA
Found at i:217491 original size:71 final size:72
Alignment explanation
Indices: 217370--217573 Score: 286
Period size: 71 Copynumber: 2.9 Consensus size: 72
217360 ATGTGATTAG
* *
217370 TGACTCACGATGCTATAGAGAATCCGCAACAAATGCAAAATCTCAACCATCGGACCAG-TTTCAC
1 TGACTCACGATGCTATAGAGAATCCGCAAAAAATGCAAGATCTCAACCATCGGACCAGTTTTCAC
*
217434 TTTACAT
66 TTTACAA
* * * *
217441 TGACTCACAATGCTATAGAGAATCCACAAAAAAAGCAAGATCTCAGCCATCGGACC-GTTTTCAC
1 TGACTCACGATGCTATAGAGAATCCGCAAAAAATGCAAGATCTCAACCATCGGACCAGTTTTCAC
217505 TTTACAA
66 TTTACAA
* * * * *
217512 TGACTCACGATGCTGTAAAGAATCTGCAATAAATGCAAGATCTCAACCATCGGACCATTTTT
1 TGACTCACGATGCTATAGAGAATCCGCAAAAAATGCAAGATCTCAACCATCGGACCAGTTTT
217574 TATCTTTGGC
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
70 1 0.01
71 110 0.96
72 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (72 bp):
TGACTCACGATGCTATAGAGAATCCGCAAAAAATGCAAGATCTCAACCATCGGACCAGTTTTCAC
TTTACAA
Found at i:218059 original size:16 final size:16
Alignment explanation
Indices: 218035--218066 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
218025 TCCTTACAAA
*
218035 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
218051 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
218067 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:222369 original size:71 final size:70
Alignment explanation
Indices: 222248--222508 Score: 324
Period size: 71 Copynumber: 3.7 Consensus size: 70
222238 TTTCACATAT
* * * * * * * *
222248 AGTGACTGAAGATGTTGTAGAGAATCTGCAATAAATGTAGGATCTCAGCCATTAGACTAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAGCCATTAGAC-AGTTTCA
*
222313 CTTTAC
65 CTTTAA
* *
222319 AGTGACTCATGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAGCCATTGGACCAGTTTCA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAGCCATTAGA-CAGTTTCA
*
222384 CTTTAT
65 CTTTAA
* * * * * *
222390 AGTAACTCACGATACTGTAGAGAATCCGCAACAAATGCAATATCTTAGCCATCAGACCGTTTTAA
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAGCCATTAGACAG-TTTCA
222455 CTTTAA
65 CTTTAA
*
222461 AGTGACTTACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAG
1 AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAG
222509 ACATCAAACT
Statistics
Matches: 165, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
70 2 0.01
71 162 0.98
72 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (70 bp):
AGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTTAGCCATTAGACAGTTTCAC
TTTAA
Found at i:227741 original size:130 final size:130
Alignment explanation
Indices: 227503--227763 Score: 450
Period size: 130 Copynumber: 2.0 Consensus size: 130
227493 TTGGGAAACC
*
227503 AAAGGCATATCCAGATTCACATACACAGCTAACCGTGCAAAGCGAACCCTTGTTCTATTATCTGT
1 AAAGGCATATCCAGATTCACATACACAGCTAACCGTGCAAAGCGAACCCTTGTTCTATTATCCGT
227568 ACTGAGATCTAATTTTGCAAATTTGCCCACCAAACTGCCTATTTCGCGTAGGATTTTTTGTCTAT
66 ACTGAGATCTAATTTTGCAAATTTGCCCACCAAACTGCCTATTTCGCGTAGGATTTTTTGTCTAT
* *
227633 AAAGGCATATCCAGATTCACATACACAGCTAACCGTGCAAAGCGACCCCTTGTTCTGTTATCCGT
1 AAAGGCATATCCAGATTCACATACACAGCTAACCGTGCAAAGCGAACCCTTGTTCTATTATCCGT
* * * * *
227698 ATTGGGATCTAATTTTGTAAATTTGCCCACCAGACTGCTTATTTCGCGTAGGATTTTTTGTCTAT
66 ACTGAGATCTAATTTTGCAAATTTGCCCACCAAACTGCCTATTTCGCGTAGGATTTTTTGTCTAT
227763 A
1 A
227764 CATATAGCCA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 123 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (130 bp):
AAAGGCATATCCAGATTCACATACACAGCTAACCGTGCAAAGCGAACCCTTGTTCTATTATCCGT
ACTGAGATCTAATTTTGCAAATTTGCCCACCAAACTGCCTATTTCGCGTAGGATTTTTTGTCTAT
Found at i:229670 original size:21 final size:21
Alignment explanation
Indices: 229631--229671 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
229621 CTAGCAGCCC
* *
229631 TCGCCACAGCCCCCGCCGGCA
1 TCGCCACAACCACCGCCGGCA
*
229652 TCGCCACAACCACCTCCGGC
1 TCGCCACAACCACCGCCGGC
229672 GTCACTATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.56, G:0.20, T:0.07
Consensus pattern (21 bp):
TCGCCACAACCACCGCCGGCA
Found at i:230564 original size:15 final size:16
Alignment explanation
Indices: 230544--230577 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
230534 TAATTTAATT
*
230544 AAATAAATTA-TTAAA
1 AAATAAAATATTTAAA
230559 AAATAAAATATTTAAA
1 AAATAAAATATTTAAA
230575 AAA
1 AAA
230578 ATATTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAAAATATTTAAA
Found at i:230903 original size:17 final size:18
Alignment explanation
Indices: 230867--230903 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
230857 TTTACTGGTG
230867 TATTTATTTATGTCTTGA
1 TATTTATTTATGTCTTGA
230885 TATTT-TTTAT-TCTTAGA
1 TATTTATTTATGTCTT-GA
230902 TA
1 TA
230904 AAACAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (18 bp):
TATTTATTTATGTCTTGA
Found at i:230981 original size:27 final size:25
Alignment explanation
Indices: 230943--231029 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 25
230933 AAAAATTGAA
230943 AAAAAAAATTAGATCTCTTAAAAGTTT
1 AAAAAAAATTAGATCT-TTAAAA-TTT
230970 AAAAAAAATTAGGATCTTTAAAAATTGAT
1 AAAAAAAATTA-GATCTTT-AAAATT--T
* * *
230999 AAAAAAAATTTGACCTTTAAAAATT
1 AAAAAAAATTAGATCTTTAAAATTT
231024 AAAAAA
1 AAAAAA
231030 TAATATTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
25 7 0.13
27 20 0.38
28 15 0.28
29 11 0.21
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (25 bp):
AAAAAAAATTAGATCTTTAAAATTT
Found at i:231157 original size:24 final size:22
Alignment explanation
Indices: 231129--231190 Score: 61
Period size: 26 Copynumber: 2.6 Consensus size: 22
231119 TTTTTAATTT
*
231129 TTAAATATAAATGAATACAAAAAA
1 TTAAATATAAATCAAT--AAAAAA
*
231153 TTAAAAATATATATCAATAAAAAA
1 TT--AAATATAAATCAATAAAAAA
231177 TTAAATATATAATC
1 TTAAATATA-AATC
231191 TTTCTCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 7 0.22
23 3 0.09
24 10 0.31
26 12 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAATATAAATCAATAAAAAA
Found at i:231161 original size:26 final size:24
Alignment explanation
Indices: 231131--231188 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
231121 TTTAATTTTT
*
231131 AAATATAAATGAATACAAAAAATTAA
1 AAATATAAATCAAT--AAAAAATTAA
*
231157 AAATATATATCAATAAAAAATTAA
1 AAATATAAATCAATAAAAAATTAA
*
231181 ATATATAA
1 AAATATAA
231189 TCTTTCTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 16 0.57
26 12 0.43
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATATAAATCAATAAAAAATTAA
Found at i:231704 original size:156 final size:157
Alignment explanation
Indices: 231535--231848 Score: 558
Period size: 156 Copynumber: 2.0 Consensus size: 157
231525 ATAATATTTT
* *
231535 TTTAGATAAGTGTATTATAAATTAGGATAAACTATATAAATGGCCAAGGAACTATTAGTGTCTTC
1 TTTAAATAAGTGTATTATAAATTAGGATAAACTATATAAATGGCCAAGCAACTATTAGTGTCTTC
* *
231600 TATTTTGGTCACTCAATTATAAATTTTTTTAATTTAAATATTAATGTTTTCAGTT-TTTTTTTTG
66 TATTTTGGTCACTCAATTATAAATTTTTTTAATTTAAATATTAATATTTTCAATTGTTTTTTTTG
*
231664 TCACCTTCCGTTAAATTGTTAGTGTTG
131 TCACCCTCCGTTAAATTGTTAGTGTTG
*
231691 TTTAAATAAGTGTATTATAAATTAGGATAAACTATATAAATGGCCAAGCAACTATTATTGTCTTC
1 TTTAAATAAGTGTATTATAAATTAGGATAAACTATATAAATGGCCAAGCAACTATTAGTGTCTTC
*
231756 TATTTTGGTCACTCAATTATAAATTTTTTTAATTTAAGTATTAATATTTTCAATTGTTTTTTTTG
66 TATTTTGGTCACTCAATTATAAATTTTTTTAATTTAAATATTAATATTTTCAATTGTTTTTTTTG
231821 TCACCCTCCGTTAAATTGTTAGTGTTG
131 TCACCCTCCGTTAAATTGTTAGTGTTG
231848 T
1 T
231849 CATGGTCTTT
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
156 114 0.76
157 36 0.24
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (157 bp):
TTTAAATAAGTGTATTATAAATTAGGATAAACTATATAAATGGCCAAGCAACTATTAGTGTCTTC
TATTTTGGTCACTCAATTATAAATTTTTTTAATTTAAATATTAATATTTTCAATTGTTTTTTTTG
TCACCCTCCGTTAAATTGTTAGTGTTG
Found at i:233108 original size:5 final size:5
Alignment explanation
Indices: 233098--233125 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
233088 GTGTAGTCAG
233098 GTGAA GTGAA GTGAA GTGAA GTGAA GTG
1 GTGAA GTGAA GTGAA GTGAA GTGAA GTG
233126 TATGGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (5 bp):
GTGAA
Found at i:234230 original size:20 final size:18
Alignment explanation
Indices: 234183--234270 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 18
234173 CAAGATAAAC
234183 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
234200 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
** *
234220 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
234239 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
234256 ATTAAATTTAATATT
1 ATTAAA-TTAATATT
234271 AAAATAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 17
0.70 0.09 0.22
Matches are distributed among these distances:
17 16 0.29
18 7 0.13
19 16 0.29
20 16 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:241606 original size:11 final size:11
Alignment explanation
Indices: 241592--241667 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
241582 GATAATCACT
241592 TTAATATTAAA
1 TTAATATTAAA
241603 TTAATA--AAA
1 TTAATATTAAA
*
241612 -TACTATTAAA
1 TTAATATTAAA
*
241622 ATAAGTATTAAA
1 TTAA-TATTAAA
241634 TTAA-ATTTAATA
1 TTAATA-TTAA-A
241646 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
241659 ATAATATTA
1 TTAATATTA
241668 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:241607 original size:20 final size:18
Alignment explanation
Indices: 241560--241666 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 18
241550 CAATATAAAC
241560 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
241577 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
241597 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
241616 ATTAAAATAAGTA-TTAA-
1 ATTAAATTAA-TATTTAAT
*
241633 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
241653 ATTAAAATAATATT
1 ATTAAATTAATATT
241667 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
17 16 0.23
18 9 0.13
19 22 0.31
20 23 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:241654 original size:37 final size:36
Alignment explanation
Indices: 241592--241667 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
241582 GATAATCACT
241592 TTAATATTAAATTAATAAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAAATACTATTAAAATAA-TA
*
241629 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
241665 TTA
1 TTA
241668 TTTTTGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
37 23 0.64
38 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:242615 original size:11 final size:12
Alignment explanation
Indices: 242583--242616 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
242573 CGTTACAAGT
242583 AAATTAATTCAC
1 AAATTAATTCAC
*
242595 AAATTGATTCA-
1 AAATTAATTCAC
242606 AAATTAATTCA
1 AAATTAATTCA
242617 TCTTGGGTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (12 bp):
AAATTAATTCAC
Found at i:243645 original size:45 final size:45
Alignment explanation
Indices: 243585--243686 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
243575 AACCATCAAT
* * *
243585 AAAT-TGTCCATCAAAATACAACCATCAGAATGATTCAACAAAAT-
1 AAATCTGTCAATCAAAATACAACCATCAAAATGATCCAA-AAAATA
* *
243629 TAATCTGTCAATCAAAATACAGCCATCAAAATGATCCAAAAAATA
1 AAATCTGTCAATCAAAATACAACCATCAAAATGATCCAAAAAATA
243674 AAATC-GTCAATCA
1 AAATCTGTCAATCA
243687 TATGTTAACA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 16 0.32
45 34 0.68
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.23
Consensus pattern (45 bp):
AAATCTGTCAATCAAAATACAACCATCAAAATGATCCAAAAAATA
Found at i:246235 original size:2 final size:2
Alignment explanation
Indices: 246228--246253 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
246218 TAATTGAGTT
246228 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
246254 CTAAATAAGT
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:246513 original size:20 final size:20
Alignment explanation
Indices: 246462--246513 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
246452 TACTTTTGTA
* *
246462 CTCTTGTTAACACTATAGTG
1 CTCTTGATAGCACTATAGTG
* * *
246482 CTCCTGACAGCACTATGGTG
1 CTCTTGATAGCACTATAGTG
246502 CTCTTGATAGCA
1 CTCTTGATAGCA
246514 TATTTATGCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (20 bp):
CTCTTGATAGCACTATAGTG
Found at i:261466 original size:152 final size:148
Alignment explanation
Indices: 261245--261714 Score: 622
Period size: 152 Copynumber: 3.2 Consensus size: 148
261235 TGATTAAACA
* * * * *
261245 AAAATTACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAAATCATAACA
1 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTT-AAAAAAAATCAAAACT
*
261310 TTGTTAAAAATTTAAACTTTTTATTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAAATC
65 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TTTTT-AAAAATC
*
261375 TTAACTTTCTCTTTTTTTAAAG
128 TAAACTTTCTC-TTTTTTAAAG
* *
261397 AAAATCACTATTTTGCTTAAAAATCTAAACTTTTATTTCGGAATAGTTAGAAAAAAATCAAAACT
1 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTA-AAAAAAATCAAAACT
* * *
261462 TTGTTAAAAATTTAAATTTTTTCCTTAAAATAACTAAAAATATAGATTTTTATTTTTAAAAATAT
65 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAA-ATAGATTTTTATTTTTAAAAATCT
* *
261527 AAACATTCTCTTCTTTAAAG
129 AAACTTTCTCTTTTTTAAAG
* * * * *
261547 AACATCAGTATTTTACCT-AAAATCTAAACTTTTATTTCAAAATAGTT--AAAAAATCAGAACTT
1 AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* * * * * *
261609 TATTAAAAATTTAAACTTTTTCTTGAAAATAAATAAAAAACAGATTTTCAATTTTAAAAATCTAA
66 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATCTAA
261674 ACTTTCTCTTTTTTAAAG
131 ACTTTCTCTTTTTTAAAG
* *
261692 AAAATCACTATTTTGCTAAAAAA
1 AAAATCACTATTTTACTTAAAAA
261715 AAAAAATCAA
Statistics
Matches: 278, Mismatches: 37, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
145 51 0.18
146 52 0.19
149 27 0.10
150 23 0.08
151 16 0.06
152 98 0.35
153 11 0.04
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (148 bp):
AAAATCACTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATCTAA
ACTTTCTCTTTTTTAAAG
Found at i:262281 original size:11 final size:11
Alignment explanation
Indices: 262267--262291 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
262257 CCCAAAAAAG
262267 AAAGAAAAATA
1 AAAGAAAAATA
262278 AAAGAAAAATA
1 AAAGAAAAATA
262289 AAA
1 AAA
262292 ACCTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:262642 original size:42 final size:42
Alignment explanation
Indices: 262606--263215 Score: 740
Period size: 42 Copynumber: 14.5 Consensus size: 42
262596 ACCTCTATGT
*
262606 CTAGGCCTCTAATTGCAATGAAAAGTAAATGGACCTCCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
** *
262648 CTAGGCCTCCGAATGCAATGAAAAATAAATGGACCTCCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* *
262690 CT-GGTCCTCTAAATACAA-GAAAAAGTAAATGGGCCTCCACAC
1 CTAGG-CCTCTAAATGCAATG-AAAAGTAAATGGACCTCCACAC
* *
262732 CTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCTACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * * *
262774 CTGGGCCTTTGAATGCAATGAAAAATAAATGGACCTCCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * * * *
262816 CTGGGCCTCTAAATGCGATGAAAAGTAAGTGAAACTCCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* ** * *
262858 CTGGGCCTCTAAATGCAATGAAAAGTAAATGGGTCTTCAAAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* *
262900 CTAGGCCTCTAAATGCAATGAAAAGTAAATGAACCTCTACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * * *
262942 CTAGGCCTTTGAATGCAATGAAAAATAAATGGACCTCTACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * * ** * *
262984 CTGGGCCTTTAAATGAAATGAAAAAAAAAATGGAGCTCCACTC
1 CTAGGCCTCTAAATGCAATG-AAAAGTAAATGGACCTCCACAC
* *
263027 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCAACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* **
263069 CTAGGCCTTTAAATGTGATGAAAAGTAAATGGACCTCCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * *
263111 CTGGGCCTCTAAATGCGATGAAAAGTAAATGGGCC-CCACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* * *
263152 CTAGGCCTCTGAATGCAATGAAGAGTAAATGGACCTCTACAC
1 CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
* *
263194 TTAGGCCTCTAAATGAAATGAA
1 CTAGGCCTCTAAATGCAATGAA
263216 TGCTTTCTTT
Statistics
Matches: 484, Mismatches: 78, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
41 39 0.08
42 407 0.84
43 38 0.08
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
CTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
Found at i:275727 original size:20 final size:20
Alignment explanation
Indices: 275690--275728 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
275680 GGGTTTATGA
* *
275690 TTTATCTTACTTTAAAATTT
1 TTTATCTAAATTTAAAATTT
*
275710 TTTATCTAAATTTTAAATT
1 TTTATCTAAATTTAAAATT
275729 AATCAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATCTAAATTTAAAATTT
Found at i:276068 original size:15 final size:16
Alignment explanation
Indices: 276024--276065 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
276014 TAAAAAAAAA
276024 AAACAT-AAATATAAAC
1 AAACATGAAA-ATAAAC
*
276040 AGACATGAAAATAAAC
1 AAACATGAAAATAAAC
*
276056 AAATATGAAA
1 AAACATGAAA
276066 TAAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (16 bp):
AAACATGAAAATAAAC
Found at i:276991 original size:148 final size:147
Alignment explanation
Indices: 276649--277113 Score: 684
Period size: 149 Copynumber: 3.2 Consensus size: 147
276639 TGATTAAACA
* * * *
276649 AAAATCATTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACATT
1 AAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *
276714 GTCAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTTAAAAATCTTA
66 GTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAATAGATTTTTA-TTTTTAAAAATCTAA
276779 ACTTTCTCTTTTTTTAAAG
130 ACTTTCTC-TTTTTTAAAG
* *
276798 AAAATCACTATTTTGCTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
1 AAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
276863 GTTAAAAATTTAAATTTTTTCCTTAAAATAACTAAAAAAATAGATTTTTATTTTTAAAAATATAA
66 GTTAAAAATTTAAACTTTTTCCTTAAAATAACT-AAAAAATAGATTTTTATTTTTAAAAATCTAA
*
276928 ACTTTCTCTTCTTTAAAG
130 ACTTTCTCTTTTTTAAAG
* * * * *
276946 AACATCACTATTTTACCTAAAAATCTAAATTTTTATTTCAAAATAGTT-AAAAAA-CATAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
277009 GTTAAAAATTTAAACTTTTT-CTTGAAAATAACTAAAAAATAGATTTTTAATTTTAAAAATCTAA
66 GTTAAAAATTTAAACTTTTTCCTT-AAAATAACTAAAAAATAGATTTTTATTTTTAAAAATCTAA
277073 ACTTTCTCTTTTTTAAAG
130 ACTTTCTCTTTTTTAAAG
* *
277091 AAAATCATTATTTTGCTTAAAAA
1 AAAATCACTATTTTACTTAAAAA
277114 AATCAAAGCT
Statistics
Matches: 286, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
145 68 0.24
146 35 0.12
147 6 0.02
148 52 0.18
149 109 0.38
150 16 0.06
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (147 bp):
AAAATCACTATTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATCTAAA
CTTTCTCTTTTTTAAAG
Found at i:278210 original size:221 final size:221
Alignment explanation
Indices: 277760--278292 Score: 516
Period size: 221 Copynumber: 2.4 Consensus size: 221
277750 ATAACAGTAG
* * *
277760 AATAATTATTTCTTTCCTT-CACTGCCACCTTTAATGTCCTTATA-AATAAACAGAAACTGAAGT
1 AATAATTATTTATTT-CTTCCACTGCCACCATTAATGTCCTTATATAA-AAACAGAAATTGAAGT
* * * * *
277823 AGAAAAAAAAGGGAAAATCTTTTTAACAAAAAAAACCTTTGGTAATAATCATGATTAACTAGCTG
64 AGAAAAAAAAGGGAAAATCTCTTTAACAAAAAAAACCTTGGGTAACAATCATCATTAACTAGCTC
* * * * * * * **
277888 AGGAAAATGTTCTTTTTTAAACCCATAGTAGAGTAATTATTTATTTCATCATTAACTTGCATTGG
129 AGGAAAATGTACCTTTTAAAACCCATAGTAGAGTAATTAGTTATTTAACCATCAACTTGCATAAG
* * *
277953 AAAACTTGCCTTCTTAAACCTATAGTGG
194 AAAACTTGCCTTCTTAAACCCACAGTGA
* * *
277981 AGTAATTATTTATTTCTTCCTA-TGCCACCATTAATGTCCTTATATAAAAACAAAAATTGGAGTA
1 AATAATTATTTATTTCTTCC-ACTGCCACCATTAATGTCCTTATATAAAAACAGAAATTGAAGTA
* * *
278045 GAAAAAAAGGGAGGAAAATCTCTTT-A-ATAAAAAACCTTGGGTAACAATCATCATTAACTATCT
65 GAAAAAAA-AG-GGAAAATCTCTTTAACAAAAAAAACCTTGGGTAACAATCATCATTAACTAGCT
* * *
278108 CAGGAAAACT-TACCTTTTAAAACCTATAGTGGAGTACTTAGTTATTTAACCATCAA-TTAGC-T
128 CAGGAAAA-TGTACCTTTTAAAACCCATAGTAGAGTAATTAGTTATTTAACCATCAACTT-GCAT
* *
278170 AAAGAAAACTTGTCCTT-TTCATCCCACAGTGA
191 -AAGAAAACTTG-CCTTCTTAAACCCACAGTGA
* * * ** * *
278202 AATAATTATTTATTT-TCTCCATTGTCGCTGTTAATGTCCTTATATATAAATAGAAATTGAAGTA
1 AATAATTATTTATTTCT-TCCACTGCCACCATTAATGTCCTTATATAAAAACAGAAATTGAAGTA
*
278266 GAAGGAAACAA---AAAATCTCTTTAACAA
65 GAA--AAAAAAGGGAAAATCTCTTTAACAA
278293 TGAAAACCAT
Statistics
Matches: 254, Mismatches: 43, Indels: 31
0.77 0.13 0.09
Matches are distributed among these distances:
218 11 0.04
219 1 0.00
220 9 0.04
221 207 0.81
222 10 0.04
223 16 0.06
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (221 bp):
AATAATTATTTATTTCTTCCACTGCCACCATTAATGTCCTTATATAAAAACAGAAATTGAAGTAG
AAAAAAAAGGGAAAATCTCTTTAACAAAAAAAACCTTGGGTAACAATCATCATTAACTAGCTCAG
GAAAATGTACCTTTTAAAACCCATAGTAGAGTAATTAGTTATTTAACCATCAACTTGCATAAGAA
AACTTGCCTTCTTAAACCCACAGTGA
Found at i:278518 original size:159 final size:158
Alignment explanation
Indices: 278174--278525 Score: 390
Period size: 158 Copynumber: 2.2 Consensus size: 158
278164 TTAGCTAAAG
* * * * * * *
278174 AAAACTTGTCC-TTTTCATCCCACAGTGAAATAATTATTTATTTTC-TCCATTGTCGCTGTTAAT
1 AAAACTTG-CCTTTTTAAACCCACAGTGGAGTAATTATATA-TGTCATCCATTGTCCCTGTTAAT
* * * * *
278237 GTCCTTATATATAAATAGAAATTGAAGTAGAAGGAAACAAAAAATCTCTTTAACAATGAAAACCA
64 GTCCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAAAAAATCTCTTTAACAAAGAAAACCA
** * *
278302 TAAGTAATTATCGTCATTAAAAACTTGAGT
129 TAAGTAACAATCATCATTAAAAACTTGAGA
278332 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATATATGTCATCCATTGTCACCT-TTAATG
1 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATATATGTCATCCATTGTC-CCTGTTAATG
278396 TCCTTATATATAAACAAAAATTGAAGTAGAA-AAAAAAAGGAAAATCTCTTTAACAAAGAAAACC
65 TCCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAA--AAAATCTCTTTAACAAAGAAAACC
* ** * * *
278460 TTGGGTAACAATCATGATTAACTAGC-TGAGA
128 ATAAGTAACAATCATCATTAA-AAACTTGAGA
* * *
278491 AAAACTTGCCTTTTTAAGCCTATAGTGGAGTAATT
1 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATT
278526 GTTTATTTCA
Statistics
Matches: 163, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
157 10 0.06
158 76 0.47
159 75 0.46
160 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (158 bp):
AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATATATGTCATCCATTGTCCCTGTTAATGT
CCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAAAAAATCTCTTTAACAAAGAAAACCATA
AGTAACAATCATCATTAAAAACTTGAGA
Found at i:278537 original size:159 final size:158
Alignment explanation
Indices: 278174--278537 Score: 405
Period size: 159 Copynumber: 2.3 Consensus size: 158
278164 TTAGCTAAAG
* * * * *
278174 AAAACTTGTCC-TTTTCATCCCACAGTGAAATAATTATTTATTTTC-TCCATTGTCGCTGTTAAT
1 AAAACTTG-CCTTTTTAAACCCACAGTGGAGTAATTATTTA-TTTCATCCATTGTCCCTGTTAAT
* * * * *
278237 GTCCTTATATATAAATAGAAATTGAAGTAGAAGGAAACAAAAAATCTCTTTAACAATGAAAACCA
64 GTCCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAAAAAATCTCTTTAACAAAGAAAACCA
** * *
278302 TAAGTAATTATCGTCATTAAAAACTTGAGT
129 TAAGTAACAATCATCATTAAAAACTTGAGA
* *
278332 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATATATGTCATCCATTGTCACCT-TTAATG
1 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATTTATTTCATCCATTGTC-CCTGTTAATG
278396 TCCTTATATATAAACAAAAATTGAAGTAGAA-AAAAAAAGGAAAATCTCTTTAACAAAGAAAACC
65 TCCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAA--AAAATCTCTTTAACAAAGAAAACC
* ** * * *
278460 TTGGGTAACAATCATGATTAACTAGC-TGAGA
128 ATAAGTAACAATCATCATTAA-AAACTTGAGA
* * * *
278491 AAAACTTGCCTTTTTAAGCCTATAGTGGAGTAATTGTTTATTTCATC
1 AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATTTATTTCATC
278538 ATTAATAAGT
Statistics
Matches: 172, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
157 10 0.06
158 76 0.44
159 84 0.49
160 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (158 bp):
AAAACTTGCCTTTTTAAACCCACAGTGGAGTAATTATTTATTTCATCCATTGTCCCTGTTAATGT
CCTTATATATAAACAAAAATTGAAGTAGAAGAAAAAAAAAAATCTCTTTAACAAAGAAAACCATA
AGTAACAATCATCATTAAAAACTTGAGA
Found at i:279373 original size:14 final size:14
Alignment explanation
Indices: 279350--279424 Score: 80
Period size: 14 Copynumber: 5.3 Consensus size: 14
279340 ACAACTAACA
279350 CATA-AATAGTTCG
1 CATACAATAGTTCG
*
279363 CATACAATAGTTCA
1 CATACAATAGTTCG
* *
279377 CATACGATCAGTTCA
1 CATACAAT-AGTTCG
* *
279392 CATACAACAGTTTG
1 CATACAATAGTTCG
279406 CATACAATAAGTTCG
1 CATACAAT-AGTTCG
279421 CATA
1 CATA
279425 TAACCAGTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
13 4 0.08
14 26 0.51
15 21 0.41
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (14 bp):
CATACAATAGTTCG
Found at i:279391 original size:15 final size:14
Alignment explanation
Indices: 279348--279439 Score: 78
Period size: 15 Copynumber: 6.4 Consensus size: 14
279338 AAACAACTAA
279348 CACATA-AATAGTT
1 CACATACAATAGTT
*
279361 CGCATACAATAGTT
1 CACATACAATAGTT
*
279375 CACATACGATCAGTT
1 CACATACAAT-AGTT
*
279390 CACATACAACAGTT
1 CACATACAATAGTT
**
279404 TGCATACAATAAGTT
1 CACATACAAT-AGTT
* * *
279419 CGCATATAACCAGTT
1 CACATACAA-TAGTT
279434 CACATA
1 CACATA
279440 TAAGCATTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
13 5 0.08
14 26 0.41
15 32 0.51
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (14 bp):
CACATACAATAGTT
Found at i:279395 original size:29 final size:29
Alignment explanation
Indices: 279348--279439 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
279338 AAACAACTAA
*
279348 CACATA-AAT-AGTTCGCATACAATAGTT
1 CACATACAATAAGTTCGCATACAACAGTT
* * *
279375 CACATACGATCAGTTCACATACAACAGTT
1 CACATACAATAAGTTCGCATACAACAGTT
** *
279404 TGCATACAATAAGTTCGCATATAACCAGTT
1 CACATACAATAAGTTCGCATACAA-CAGTT
279434 CACATA
1 CACATA
279440 TAAGCATTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 6 0.12
28 2 0.04
29 34 0.67
30 9 0.18
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (29 bp):
CACATACAATAAGTTCGCATACAACAGTT
Found at i:279692 original size:31 final size:31
Alignment explanation
Indices: 279654--279748 Score: 127
Period size: 31 Copynumber: 3.1 Consensus size: 31
279644 AATTTGTCAT
* *
279654 CCCGAATTGCTCGACAAAGATGACCTACCAC
1 CCCGAATTGCTCGGCAAAGATGGCCTACCAC
* * *
279685 CTCGAATTGCTCGGTAACGATGGCCTACCAC
1 CCCGAATTGCTCGGCAAAGATGGCCTACCAC
* *
279716 CCCGAATTGATCGGCAATGATGGCCTACCAC
1 CCCGAATTGCTCGGCAAAGATGGCCTACCAC
279747 CC
1 CC
279749 TGGATTGATC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.19
Consensus pattern (31 bp):
CCCGAATTGCTCGGCAAAGATGGCCTACCAC
Found at i:279756 original size:31 final size:31
Alignment explanation
Indices: 279657--279769 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
279647 TTGTCATCCC
* * * *
279657 GAATTGCTCGACAAAGATGACCTACCA-CCT
1 GAATTGATCGGCAATGATGGCCTACCACCCT
* * * *
279687 CGAATTGCTCGGTAACGATGGCCTACCACCCC
1 -GAATTGATCGGCAATGATGGCCTACCACCCT
279719 GAATTGATCGGCAATGATGGCCTACCACCCT
1 GAATTGATCGGCAATGATGGCCTACCACCCT
* * *
279750 GGATTGATCGACAATAATGG
1 GAATTGATCGGCAATGATGG
279770 TTTATCGAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
31 67 0.97
32 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (31 bp):
GAATTGATCGGCAATGATGGCCTACCACCCT
Found at i:280420 original size:21 final size:21
Alignment explanation
Indices: 280350--280433 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
280340 TACCATACAT
* * * *
280350 AAGAGCTCACACAACATGTGA
1 AAGAGTTCACATAACATATAA
*
280371 AAGAGTTTGCACAT--CATGTAA
1 AAGAG-TT-CACATAACATATAA
280392 AAGAGTTCACATAACATATAA
1 AAGAGTTCACATAACATATAA
*
280413 AAGAGTTCCCATAACATATAA
1 AAGAGTTCACATAACATATAA
280434 CTAGCTTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
19 5 0.09
20 2 0.04
21 42 0.78
22 1 0.02
23 4 0.07
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (21 bp):
AAGAGTTCACATAACATATAA
Found at i:282941 original size:380 final size:377
Alignment explanation
Indices: 282091--282945 Score: 876
Period size: 379 Copynumber: 2.3 Consensus size: 377
282081 TTTTTATTTT
* * ** * * * *
282091 ATCATTAACTAGTTTAGAAACACTTGCCTTTTAAAACCCACAATGGAGTAATTATTTATTTCCTC
1 ATCATTAACTAGTTGAGAAAAACTTTTCTTTTTAAACCCATAGTGGAGTAAATATTTATTTCCTC
* * * * ***
282156 CATTGTCACTTTTAATATCC-AAATATATAAATAGAAACTAAAGAAGTTAAAAACGAAAATCACT
66 CATTGTCAC-TTTAATGTCCTATATATATAAATAAAAACTAAACAAAAAAAAAACGAAAATCACT
* * * *
282220 TTAACAAAGAAAACCTTGAGTAATAATCATAATTTATTAATCGAGGAAAATTTATCTTTTTAAAC
130 TTAACAAAAAAAACCTTGAGTAATAACCATAATTTACTAATCGAGGAAAATTTATCCTTTTAAAC
* * * * * **
282285 ACACAATGGAGTAATTATTTATTTTGTCATTAACTAGTTGAGAAAAACTTGTCTTTTTAAACCGA
195 ACACAATGAAATAATTATTTACTTTATCATTAACTAGTTGAGAAAAACTTGTCTATAGAAACCGA
* * *
282350 CAGTGAAATTATTTATTTTCTCCATTGCCACATTTAATATCCTTATATATAAACTGAAACTGAAG
260 CAGTGAAATTATTTAATTTCTCCATTGCCACAATTAATATCCTTATATATAAACTAAAACTGAA-
* * **
282415 CACAAAAAAAAAAAAAGGAAAACCTCTTTAATAACGAAAACATTTGATATAATC
324 CACAAAAAAAAAAAAAGGAAAACCTATTTAACAAAAAAAACATTTGATATAATC
* * * * * * *
282469 CTCATCAATTAGTTGAGGAAAATTTATTTTTTTTAAACACATAGTGGAG-AAATTATTTATTTCC
1 ATCATTAACTAGTTGAGAAAAACTT-TTCTTTTTAAACCCATAGTGGAGTAAA-TATTTATTTCC
* *
282533 TCCATTGTCATCTTTAATGTTC-ATATATATAAA-AAAAACTGAAACAAAAAAATAAAGGAAAAT
64 TCCATTGTCA-CTTTAATGTCCTATATATATAAATAAAAACT-AAACAAAAAAA-AAACGAAAAT
* * *
282596 -ATCTTTAACAAAAAAAAAATCTTGGGTAATAACCATCATTTACTATAT-GA-GAAAATTTA-CC
126 CA-CTTTAAC--AAAAAAAACCTTGAGTAATAACCATAATTTACTA-ATCGAGGAAAATTTATCC
*
282657 TTTTAAA-ATCACAATGAAATAATTATTTACTTTATCATTAACTAGTTGAGGAAAACTTGTCTAT
187 TTTTAAACA-CACAATGAAATAATTATTTACTTTATCATTAACTAGTTGAGAAAAACTTGTCTAT
* * ** *
282721 AGAAATCGATAGTGGAGTAATTATTTAATTTCTCCATTGTTA-AATTAATGTCCTTATATATAAA
251 AGAAACCGACAGT-GA--AATTATTTAATTTCTCCATTGCCACAATTAATATCCTTATATATAAA
* * * * *
282785 -TAAAAATTG-A-ACTAGAAAAAAAAAA-GAAAATCTATTTAACAAAAAAAATATTGTG-TAATA
313 CT-AAAACTGAACACAAAAAAAAAAAAAGGAAAACCTATTTAACAAAAAAAACATT-TGAT-ATA
282845 ATC
375 ATC
** * *
282848 ATCATTAACTACCTGAGAAAAACTTTTCTTTTTAAACCCATAGTGGAGTAAATATTTAGTTGCTC
1 ATCATTAACTAGTTGAGAAAAACTTTTCTTTTTAAACCCATAGTGGAGTAAATATTTATTTCCTC
*
282913 CATTGCCACTGTTAATGTCCTTATATATATAAA
66 CATTGTCACT-TTAATGTCC-TATATATATAAA
282946 CAGAAATTAA
Statistics
Matches: 388, Mismatches: 69, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
377 2 0.01
378 95 0.24
379 106 0.27
380 94 0.24
381 13 0.03
382 55 0.14
383 23 0.06
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (377 bp):
ATCATTAACTAGTTGAGAAAAACTTTTCTTTTTAAACCCATAGTGGAGTAAATATTTATTTCCTC
CATTGTCACTTTAATGTCCTATATATATAAATAAAAACTAAACAAAAAAAAAACGAAAATCACTT
TAACAAAAAAAACCTTGAGTAATAACCATAATTTACTAATCGAGGAAAATTTATCCTTTTAAACA
CACAATGAAATAATTATTTACTTTATCATTAACTAGTTGAGAAAAACTTGTCTATAGAAACCGAC
AGTGAAATTATTTAATTTCTCCATTGCCACAATTAATATCCTTATATATAAACTAAAACTGAACA
CAAAAAAAAAAAAAGGAAAACCTATTTAACAAAAAAAACATTTGATATAATC
Found at i:283078 original size:62 final size:61
Alignment explanation
Indices: 283012--283132 Score: 163
Period size: 62 Copynumber: 2.0 Consensus size: 61
283002 AGTAATCATC
* *
283012 ATTAACTAGATAAGAAAAACTTGTCTTTTTAAACTCACAGTAGAA-TAATTATTTAATTTCTT
1 ATTAACTAGATAAGAAAAACTTGCCTTTTTAAACTCAAAGT-GAAGTAATTATTT-ATTTCTT
* * * *
283074 ATTAATTAGCTGAGAAAAATTTGCCTTTTTAAACTCAAAGTGAAGTAATTATTTATTTC
1 ATTAACTAGATAAGAAAAACTTGCCTTTTTAAACTCAAAGTGAAGTAATTATTTATTTC
283133 CTCCATTTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 8 0.15
62 44 0.85
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (61 bp):
ATTAACTAGATAAGAAAAACTTGCCTTTTTAAACTCAAAGTGAAGTAATTATTTATTTCTT
Found at i:283481 original size:158 final size:156
Alignment explanation
Indices: 283207--283618 Score: 421
Period size: 158 Copynumber: 2.6 Consensus size: 156
283197 TTGAAACAGA
* * *
283207 AAAAGATCTCTTTAATAAAGAAAATTTTGG--ATAATAATCAATAACTAGTCGAGGAAAACTTGC
1 AAAA-ATCTCTTTAATAAAGAAAATTTTGGTAATAATAATTATTAACTAGT-GAGGAAAACTTAC
* * **
283270 CTTTTTAAACCAATAGTGGAGTAATTATTTATTT-CTACTATTGCCACCTTTAATGTCTTTATAT
64 CTTTTTAAACCAATAGTGGAGTAATTATTTATTTCCTACCATTACCACCTTTAATGTCCCTATAT
*
283334 AGAAA-A-AAGATTGAAGCAAAAAAGAAAAG
129 AGAAATAGAA-ACTGAAGC-AAAAA-AAAAG
* *
283363 AAAAATCTTTTTAATATAGAAAATTTTGGGTAATAATAATTATTAACTAGGTGAGGAAAAC-TAT
1 AAAAATCTCTTTAATAAAGAAAATTTT-GGTAATAATAATTATTAACTA-GTGAGGAAAACTTA-
* * *
283427 CCTTTTTAAACCAATAGTGGAGTAATTATTTATTTCCT-CCATTATC-GCTGTTAATTTCCCTAT
63 CCTTTTTAAACCAATAGTGGAGTAATTATTTATTTCCTACCATTACCACCT-TTAATGTCCCTAT
* *
283490 ATATAAATAGAAACTGAAGCAAAAAAAATG
127 ATAGAAATAGAAACTGAAGCAAAAAAAAAG
* * * ** * * *
283520 -AAAATCTCTTTAACAAATAAAATCTTAGGTAATAATCGTTGTTATCTACCG-GAGAAAAACTTA
1 AAAAATCTCTTTAATAAAGAAAAT-TTTGGTAATAATAATTATTAACTA--GTGAGGAAAACTTA
* *
283583 CCTTTTTAAACCCACAGTGGAGTAATTATTTATTTC
63 CCTTTTTAAACCAATAGTGGAGTAATTATTTATTTC
283619 ATCATTAACT
Statistics
Matches: 216, Mismatches: 28, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
155 21 0.10
156 84 0.39
157 12 0.06
158 85 0.39
159 12 0.06
160 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (156 bp):
AAAAATCTCTTTAATAAAGAAAATTTTGGTAATAATAATTATTAACTAGTGAGGAAAACTTACCT
TTTTAAACCAATAGTGGAGTAATTATTTATTTCCTACCATTACCACCTTTAATGTCCCTATATAG
AAATAGAAACTGAAGCAAAAAAAAAG
Found at i:284251 original size:159 final size:161
Alignment explanation
Indices: 284010--284386 Score: 422
Period size: 159 Copynumber: 2.4 Consensus size: 161
284000 ATTTATTTCA
*
284010 TAACTAATTGAGGAAAACTTGTCCTTTTAAACCCGCAATGGAGTAATTATTTATTTTCTCCATTT
1 TAACTAATTGAGGAAAACTTGTCCTTTTAAACCCGCAATGGAGTAATTATTTAGTTTCTCCATTT
* * * * * **
284075 CCACCTTTAATATCCTTATATATAAACAGAAATTGAAGTAGAAAA-AAAAAAGAAAATCTCTTTA
66 CCACCATTAATACCCTTATATATAAACAAAAACTAAAACAGAAAATAAAAAAGAAAATCTCTTTA
* *
284139 AC-AAAGAAAACCTTGGGTAATAATCATCAT
131 ACAAAAAAAAACCTTGGGTAATAATCAACAT
* * * * * * *
284169 TAACTAGTTGAGGAAAACTTGTCTTTTTAAACCTGTAGTGGAGTTATTATTT-GTTTCT-TATTT
1 TAACTAATTGAGGAAAACTTGTCCTTTTAAACCCGCAATGGAGTAATTATTTAGTTTCTCCA-TT
* * * * * *
284232 TGTCATCATTAATGCCCTTATATATAAACAAAAACTAAAACAGAAAATGAAAATGAAACTCTCTT
65 T-CCACCATTAATACCCTTATATATAAACAAAAACTAAAACAGAAAATAAAAAAGAAAATCTCTT
*
284297 TAACAAAAAAAAACCTTGGGTAATAATTAACAT
129 TAACAAAAAAAAACCTTGGGTAATAATCAACAT
** * * * * *
284330 TAACTAACGGAGGAAAACTTGTTCTTGTAAACCCACAGTGGGGTAATTATTTA-TTTC
1 TAACTAATTGAGGAAAACTTGTCCTTTTAAACCCGCAATGGAGTAATTATTTAGTTTC
284387 ATCAATAATT
Statistics
Matches: 178, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
157 1 0.01
158 8 0.04
159 81 0.46
160 18 0.10
161 70 0.39
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (161 bp):
TAACTAATTGAGGAAAACTTGTCCTTTTAAACCCGCAATGGAGTAATTATTTAGTTTCTCCATTT
CCACCATTAATACCCTTATATATAAACAAAAACTAAAACAGAAAATAAAAAAGAAAATCTCTTTA
ACAAAAAAAAACCTTGGGTAATAATCAACAT
Found at i:284600 original size:220 final size:220
Alignment explanation
Indices: 284374--284786 Score: 521
Period size: 220 Copynumber: 1.9 Consensus size: 220
284364 ACAGTGGGGT
* * * * *
284374 AATTATTTATTTCATCAA-TAATTAGTTGAGGAAAACTTGCCTTTTTAAACCCACAATGGAGT-A
1 AATTATTTATTTCAT-AATTAACTAGCTAAGAAAAACTTGCATTTTTAAACCCACAATGGAGTAA
* * * *
284437 TCTATTTATTTCCTCAATTTCTACCTTTAATG-TCTTATATATCAACACAAAGTGAA-CTTGAAG
65 T-TATTTATTTCCTCAATTGCAACCTTTAATGTTCTTATATATAAACACAAAGTGAAGC-AGAA-
* * *
284500 AAAAAAGGTAAATCTCTTCAACAAAGAAAACCTT-AGTTAATAATCATCATTAACTAGATAAGAA
127 AAAAAAAGAAAATCTCTTCAACAAAGAAAACCTTAAG-TAATAATAATCATTAACTAGATAAGAA
284564 AAAATTCTCTTTTCAAGCTTACAATGATGC
191 AAAATTCTCTTTTCAAGCTTACAATGATGC
* *
284594 AATTATTTATTTCATAATTAACTAGCTAAGAAAAACTTGCATTTTTAAACCCACAGTGGGGTAAT
1 AATTATTTATTTCATAATTAACTAGCTAAGAAAAACTTGCATTTTTAAACCCACAATGGAGTAAT
* * * * * *
284659 TATTTATTTCCTCCATTGCAACCTTTAATGTTCTTATATTTAAATAGATATTGAAGCAGAAAAAA
66 TATTTATTTCCTCAATTGCAACCTTTAATGTTCTTATATATAAACACAAAGTGAAGCAGAAAAAA
* * * * *
284724 AAAGAAAATCTCTTTAACAAATAAAATCTTAAGTAATAATAATCATTAACTAGTTGAGAAAAA
131 AAAGAAAATCTCTTCAACAAAGAAAACCTTAAGTAATAATAATCATTAACTAGATAAGAAAAA
284787 CATGCCTTTT
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
219 2 0.01
220 135 0.83
221 25 0.15
222 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (220 bp):
AATTATTTATTTCATAATTAACTAGCTAAGAAAAACTTGCATTTTTAAACCCACAATGGAGTAAT
TATTTATTTCCTCAATTGCAACCTTTAATGTTCTTATATATAAACACAAAGTGAAGCAGAAAAAA
AAAGAAAATCTCTTCAACAAAGAAAACCTTAAGTAATAATAATCATTAACTAGATAAGAAAAAAT
TCTCTTTTCAAGCTTACAATGATGC
Found at i:287229 original size:26 final size:26
Alignment explanation
Indices: 287185--287302 Score: 182
Period size: 26 Copynumber: 4.5 Consensus size: 26
287175 AGCTCTTTTT
* *
287185 GAGCCTAGAATAAAGTTTAGCTCATGC
1 GAGCCTAG-ATAGAGTTTAGCTCATAC
*
287212 GAGCCCAGATAGAGTTTAGCTCATAC
1 GAGCCTAGATAGAGTTTAGCTCATAC
287238 GAGCCTAGATAGAGTTTAGCTCATAC
1 GAGCCTAGATAGAGTTTAGCTCATAC
* *
287264 GAGCCTAGACAGAGATTAGCTCATAC
1 GAGCCTAGATAGAGTTTAGCTCATAC
287290 GAGCCTAGATAGA
1 GAGCCTAGATAGA
287303 ATAGCGCTCT
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
26 77 0.92
27 7 0.08
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (26 bp):
GAGCCTAGATAGAGTTTAGCTCATAC
Found at i:291477 original size:154 final size:146
Alignment explanation
Indices: 291144--291515 Score: 485
Period size: 154 Copynumber: 2.5 Consensus size: 146
291134 TGATTTTGGG
* * * *
291144 AAAAA-TTTTGATTTTTTTAAATAATTCCAAAATAAAAGTTTTATTTTTAAGTAAAATAGTGATT
1 AAAAAGTTTTGA-TTTTTTAACT-ATTTCGAAATAAAAGTTTGATTTTTAAGTAAAATAGTGATT
* * *
291208 TTCTTTAAAAAGAAATAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAG
64 TTCTTAAAAAAGAAAGAAAGTTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAG
291273 AAAAAGTTTAAAATTAAA
129 AAAAAGTTTAAAATTAAA
* *
291291 AAAAAGTTTTGATTTTTTACCTATTTCGAAATAAAAGTTTGAATTTTTAAGTAAAGTAGTGATTT
1 AAAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTG-ATTTTTAAGTAAAATAGTGATTT
*
291356 TCATTAAAAAAAAGAAAGAAATTTTAGATTTTAAAAAAATAAAAATCTGTTTTTTTAGTGATTTT
65 TC-TT--AAAAAAGAAAGAAAGTTTAGATTTT-AAAAAATAAAAATCTG-TTTTTTAGTGATTTT
*
291421 AAAGAAAAAAGTTTAAAATTTTAA
125 AAAG-AAAAAGTTTAAAA-TTAAA
** * * *
291445 ACTAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTAAAGTAAATTAGTTATTT
1 AAAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAG-TTTGATTTTTAAGTAAAATAGTGATTT
291510 TGCTTA
65 T-CTTA
291516 GATCAAAAGA
Statistics
Matches: 197, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
146 16 0.08
147 37 0.19
148 8 0.04
150 22 0.11
151 15 0.08
152 20 0.10
153 13 0.07
154 61 0.31
155 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (146 bp):
AAAAAGTTTTGATTTTTTAACTATTTCGAAATAAAAGTTTGATTTTTAAGTAAAATAGTGATTTT
CTTAAAAAAGAAAGAAAGTTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTAAAGAA
AAAGTTTAAAATTAAA
Found at i:295118 original size:4 final size:4
Alignment explanation
Indices: 295111--295155 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
295101 AATCAATCAA
* * * *
295111 TCAT TCAT TCAT TCAT TCAT CCAT TCCT TCAC TCAT TCAC TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
295156 TGTTTATTCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (4 bp):
TCAT
Found at i:299090 original size:30 final size:29
Alignment explanation
Indices: 299033--299088 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
299023 ATTTAAATAA
299033 AAAAAACATAAAAAATAAAAAAAGAGAGG
1 AAAAAACATAAAAAATAAAAAAAGAGAGG
*
299062 AAAAAACA-AAAAAATAAAAAAATAGAG
1 AAAAAACATAAAAAATAAAAAAAGAGAG
299089 AGAGCAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.79, C:0.04, G:0.11, T:0.07
Consensus pattern (29 bp):
AAAAAACATAAAAAATAAAAAAAGAGAGG
Found at i:299555 original size:42 final size:42
Alignment explanation
Indices: 299487--300026 Score: 626
Period size: 42 Copynumber: 12.9 Consensus size: 42
299477 AAGGAAAGCA
* * *
299487 TTCATTGCATTTAAAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **
299529 TTCA-CTGTATTTAGAGGCCCAGGTGTGGAGG-CCCGTTACTT
1 TTCATC-GCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
299570 TTCATCGCATCTAGAGGTCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
299612 TTCATAGTATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
299654 TCCATCGCATTTAGAGGCCTACGTGTGGGGGTCTATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
299696 TTCATTGCATTCAGAAGCCCAAGTGTAGAGG-CCTATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* *
299738 TTCATCGCATTTAGAGGCCCAGATGTGGAGGTCCGTTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
299780 TTCATCACATTTAGAGGCCCATGTGTGGAGTTCCATTTATTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
299822 TTCATCGCATTTTA-AGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCA-TTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
299864 TTTATCGCATTTAGAGGCCCAAGTGTGGAGGTTCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
299906 TTCATCGTATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
299948 TTCATTC-CATTTAGAGGCCTACGTGTGG-GGGCCTATTTACTT
1 TTCA-TCGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * *
299990 TTCATTGCATTTAGAGACCCAAGTGT-GAGGTCTATTT
1 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTT
300027 GCATTCCTTC
Statistics
Matches: 416, Mismatches: 71, Indels: 23
0.82 0.14 0.05
Matches are distributed among these distances:
41 49 0.12
42 359 0.86
43 8 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:301286 original size:22 final size:24
Alignment explanation
Indices: 301234--301286 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
301224 AAAATAGTGT
*
301234 TTTTCTTTAAAAAAAAAAAAGTTTA
1 TTTT-TTTAAAAAAAAAAAAGTCTA
* *
301259 TATTTTT-AAAAATAAAAA-TCTA
1 TTTTTTTAAAAAAAAAAAAGTCTA
301281 TTTTTT
1 TTTTTT
301287 AGTTATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 8 0.33
23 10 0.42
24 3 0.12
25 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTTTTAAAAAAAAAAAAGTCTA
Found at i:301693 original size:153 final size:150
Alignment explanation
Indices: 300877--301685 Score: 1009
Period size: 151 Copynumber: 5.4 Consensus size: 150
300867 GATTTTGGGA
* * * ** **
300877 AAAGTTTTG-GTTTTTTAAATAATTTCTAAATAAATTTTTTTATTTTTAAGTAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTAACT-ATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
* * * *
300941 TCTT-----TAAAAAGAGAGTTTATATTTTTAAAAGTAAAAATCTATTTTTTAGAT-ATTTTAAA
65 TCTTAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAG-TGATTTTAAA
*
301000 GAAAAAGTTTAAAATTTTAAAC
129 GAAAAAGTTTAAATTTTTAAAC
301022 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
* * * *
301087 CTTTAAAAAAAACAGAAAGTTTATAATTTTTTAAAAATAAAAATCTA-TTTTTAGTTATTTTAAA
66 CTTAAAAAAAAAAAGAAAGTTTA-GA-TTTTTAAAAATAAAAATCTATTTTTTAGTGATTTTAAA
301151 GAAAAAGTTTAAATTTTTAAAC
129 GAAAAAGTTTAAATTTTTAAAC
* * *
301173 AAAGTTTTTG-TTTTTTTAACTATTTCGAAATAAAAGTTTAGTTTTTTAAGTAAAATAGTGTTTT
1 AAAG-TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
* * * *
301237 TCTT-TAAAAAAAAA-AAAGTTTATATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAT
65 TCTTAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTGATTTTAAAG
301300 AAAAAGGTTTAAATTTTTAAAC
130 AAAAA-GTTTAAATTTTTAAAC
* * *
301322 AAAATTTTGA-TTTTTTAACTATTTCGAAAAAAAAGTTT--ATATTTTACGTAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGAT-TTTTAAGTAAAATAGTGATTT
* *
301384 TCATTAAAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAAAAATAAAAATATGTTTTTTAGTGATT
65 TC-TT--AAAAAAAAAAAGAAAGTTTAGATTTTT---AAAAATAAAAATCTATTTTTTAGTGATT
* *
301449 TTAAAGAAAAAATTTTAATTTTT-AAC
124 TTAAAGAAAAAGTTTAAATTTTTAAAC
* * * *
301475 AAAGTTTTAATTTTTTTTAACTATTTCAAAATAAAAGTTTGGATTTTTAAATAAAGTAGTGATTT
1 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
* *
301540 TCATTAAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTGTTTTTTAGTGATTTTT
65 TC-TT-AAAAAAAAAAAGAAAGTTTAGATTTTT-AAAAATAAAAATCTATTTTTTAGTGATTTTA
*
301605 AAGAAAAAATTTAAATTTTTAAAC
127 AAGAAAAAGTTTAAATTTTTAAAC
* *
301629 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAATA
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATA
301686 ATTATTTTAT
Statistics
Matches: 588, Mismatches: 49, Indels: 46
0.86 0.07 0.07
Matches are distributed among these distances:
145 51 0.09
146 10 0.02
147 41 0.07
148 57 0.10
149 27 0.05
150 21 0.04
151 105 0.18
152 38 0.06
153 102 0.17
154 22 0.04
155 89 0.15
156 23 0.04
157 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (150 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
CTTAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTGATTTTAAAGA
AAAAGTTTAAATTTTTAAAC
Found at i:302318 original size:16 final size:16
Alignment explanation
Indices: 302279--302320 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
302269 CTTATTCTTA
* *
302279 TTTCATATTTGTTTAT
1 TTTCATGTTTATTTAT
302295 TTTCATGTTTATTTAT
1 TTTCATGTTTATTTAT
302311 ATTT-ATGTTT
1 -TTTCATGTTT
302321 TTTTTTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (16 bp):
TTTCATGTTTATTTAT
Found at i:303558 original size:14 final size:14
Alignment explanation
Indices: 303539--303568 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
303529 ATACAACTGC
303539 CTTTCCTGCAAAAT
1 CTTTCCTGCAAAAT
*
303553 CTTTCCTGGAAAAT
1 CTTTCCTGCAAAAT
303567 CT
1 CT
303569 ACAATACCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (14 bp):
CTTTCCTGCAAAAT
Found at i:306417 original size:21 final size:21
Alignment explanation
Indices: 306381--306433 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
306371 AACTATTAAT
* *
306381 TTCTATCGGTAGAAGTGATAG-
1 TTCTATCGATACAAGT-ATAGA
306402 TTCTATCGATACAAGTATAGA
1 TTCTATCGATACAAGTATAGA
*
306423 TACTATCGATA
1 TTCTATCGATA
306434 TGATCCACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (21 bp):
TTCTATCGATACAAGTATAGA
Found at i:308192 original size:24 final size:24
Alignment explanation
Indices: 308165--308217 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
308155 ACATACACAT
*
308165 TTAGCCCACATGAGCCCAGAATGG
1 TTAGCCCACACGAGCCCAGAATGG
* **
308189 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCCCACACGAGCCCAGAATGG
308213 TTAGC
1 TTAGC
308218 TCTTACGAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (24 bp):
TTAGCCCACACGAGCCCAGAATGG
Found at i:308218 original size:24 final size:24
Alignment explanation
Indices: 308176--308230 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
308166 TAGCCCACAT
308176 GAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
308200 GAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGGTTAGCTCTTAC
308224 GAGCCCA
1 GAGCCCA
308231 AACAAAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (24 bp):
GAGCCCAGAATGGTTAGCTCTTAC
Found at i:313355 original size:26 final size:26
Alignment explanation
Indices: 313317--313423 Score: 124
Period size: 26 Copynumber: 4.1 Consensus size: 26
313307 TTTTCAACAT
*
313317 AGAGTTTAGCTCATGCGAGCCCAGAC
1 AGAGTTTAGCTCATACGAGCCCAGAC
* **
313343 AGAGTTTATCTCATGTGAGCCCAGAC
1 AGAGTTTAGCTCATACGAGCCCAGAC
* * * *
313369 AAAGTTTAGCTTATACGAGCCTAGAT
1 AGAGTTTAGCTCATACGAGCCCAGAC
* *
313395 AGAGTTTAGCTCATACAAGCCTAGAC
1 AGAGTTTAGCTCATACGAGCCCAGAC
313421 AGA
1 AGA
313424 ATAATGCTCT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 68 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (26 bp):
AGAGTTTAGCTCATACGAGCCCAGAC
Found at i:314389 original size:17 final size:17
Alignment explanation
Indices: 314367--314400 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
314357 ATTGGCCCTT
314367 ATACTTAGCTTCCCTAA
1 ATACTTAGCTTCCCTAA
314384 ATACTTAGCTTCCCTAA
1 ATACTTAGCTTCCCTAA
314401 GCTATTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
ATACTTAGCTTCCCTAA
Found at i:315597 original size:22 final size:22
Alignment explanation
Indices: 315569--315610 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
315559 ACCTTCCATG
*
315569 AATCAAACAAAACTCAAGCATA
1 AATCAAACAAAAATCAAGCATA
315591 AATCAAACAAAAATCAAGCA
1 AATCAAACAAAAATCAAGCA
315611 ACCACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.21, G:0.05, T:0.12
Consensus pattern (22 bp):
AATCAAACAAAAATCAAGCATA
Done.