Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2373
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: 110604
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:4833 original size:56 final size:55
Alignment explanation
Indices: 4717--4834 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
4707 TGCATGCTTT
* * * *
4717 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
4771 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
4827 CATTAAAT
1 CATTAAAT
4835 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:5485 original size:20 final size:20
Alignment explanation
Indices: 5460--5514 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
5450 ACGAGTTAAA
* *
5460 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
5480 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
5500 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
5515 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:6860 original size:14 final size:14
Alignment explanation
Indices: 6841--6868 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6831 GGTAAGCAAT
6841 GGTAAGTTGGAAGA
1 GGTAAGTTGGAAGA
6855 GGTAAGTTGGAAGA
1 GGTAAGTTGGAAGA
6869 TAAAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GGTAAGTTGGAAGA
Found at i:8599 original size:30 final size:30
Alignment explanation
Indices: 8565--8661 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
8555 AGCTCACTCC
8565 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * *
8595 TAGCTCAACTTCAGCTTAGGAGTTTAACCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
8625 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
8655 TAGCTCA
1 TAGCTCA
8662 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:11477 original size:23 final size:22
Alignment explanation
Indices: 11426--11477 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
11416 CCTCGTCTTT
*
11426 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
11448 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
11471 TTCTTTT
1 TTCTTTT
11478 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:11486 original size:12 final size:12
Alignment explanation
Indices: 11435--11490 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
11425 TTTCTTTTGT
11435 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
11448 -TCATTTTC-TC
1 TTCTTTTTCAAC
11458 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
11471 TTCTTTTTCAAT
1 TTCTTTTTCAAC
11483 TTCTTTTT
1 TTCTTTTT
11491 GTTTCACATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.11
12 23 0.66
13 7 0.20
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:14057 original size:12 final size:12
Alignment explanation
Indices: 14040--14078 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
14030 TTAAACTAAG
*
14040 TAAATAAATAAA
1 TAAATAAAAAAA
14052 TAAATAAAAAAA
1 TAAATAAAAAAA
*
14064 TAAA-ATAAAAA
1 TAAATAAAAAAA
14075 TAAA
1 TAAA
14079 ACTTTACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAATAAAAAAA
Found at i:15278 original size:10 final size:10
Alignment explanation
Indices: 15263--15347 Score: 66
Period size: 10 Copynumber: 8.5 Consensus size: 10
15253 AGTTTTTCCC
15263 AGCTCAATTT
1 AGCTCAATTT
*
15273 AGCTCACA-TG
1 AGCTCA-ATTT
*
15283 AGCTTAATTT
1 AGCTCAATTT
** *
15293 AGCTCGCTTG
1 AGCTCAATTT
15303 AGCTCAATTT
1 AGCTCAATTT
*
15313 AGCTC-GTTT
1 AGCTCAATTT
15322 GAGCTCAATTT
1 -AGCTCAATTT
* *
15333 AGCTTACTTT
1 AGCTCAATTT
15343 AGCTC
1 AGCTC
15348 GTTTGAGCTT
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
9 4 0.07
10 48 0.86
11 4 0.07
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:15327 original size:30 final size:30
Alignment explanation
Indices: 15300--15356 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
15290 TTTAGCTCGC
15300 TTGAGCTCAATTTAGCTCGTTTGAGCTCAA
1 TTGAGCTCAATTTAGCTCGTTTGAGCTCAA
* * *
15330 TTTAGCTTACTTTAGCTCGTTTGAGCT
1 TTGAGCTCAATTTAGCTCGTTTGAGCT
15357 TGGCTTAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (30 bp):
TTGAGCTCAATTTAGCTCGTTTGAGCTCAA
Found at i:15346 original size:20 final size:20
Alignment explanation
Indices: 15263--15347 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
15253 AGTTTTTCCC
*
15263 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACTTG
* *
15283 AGCTTAATTTAGCTCGCTTG
1 AGCTCAATTTAGCTCACTTG
**
15303 AGCTCAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACTTG
* *
15323 AGCTCAATTTAGCTTACTTT
1 AGCTCAATTTAGCTCACTTG
15343 AGCTC
1 AGCTC
15348 GTTTGAGCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACTTG
Found at i:15356 original size:20 final size:20
Alignment explanation
Indices: 15263--15336 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
15253 AGTTTTTCCC
* *
15263 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCGCTTG
*
15283 AGCTTAATTTAGCTCGCTTG
1 AGCTCAATTTAGCTCGCTTG
*
15303 AGCTCAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCGCTTG
15323 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
15337 TACTTTAGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (20 bp):
AGCTCAATTTAGCTCGCTTG
Found at i:19775 original size:22 final size:23
Alignment explanation
Indices: 19744--19786 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
19734 ACCTTTTTGA
19744 ACCATTACCAATTCGTACCAACT
1 ACCATTACCAATTCGTACCAACT
*
19767 ACCA-TACCATTTCGTACCAA
1 ACCATTACCAATTCGTACCAA
19787 TCCCTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCGTACCAACT
Found at i:20111 original size:12 final size:12
Alignment explanation
Indices: 20094--20122 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20084 TAGACTCGTG
20094 AAAAAAATTGAA
1 AAAAAAATTGAA
20106 AAAAAAATTGAA
1 AAAAAAATTGAA
20118 AAAAA
1 AAAAA
20123 TAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:20120 original size:22 final size:21
Alignment explanation
Indices: 20092--20153 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
20082 AGTAGACTCG
20092 TGAAAAAAATTGAAAAAAAAAT
1 TGAAAAAAA-TGAAAAAAAAAT
*
20114 TGAAAAAAAT-AAATAAATAATT
1 TGAAAAAAATGAAA-AAA-AAAT
*
20136 TGAAAAAAAAGAAAAAAA
1 TGAAAAAAATGAAAAAAA
20154 TTGTATAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 3 0.09
21 5 0.14
22 24 0.69
23 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
TGAAAAAAATGAAAAAAAAAT
Found at i:22381 original size:20 final size:20
Alignment explanation
Indices: 22356--22400 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
22346 GCGAAAATAC
*
22356 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
22376 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
22395 AAAAGA
1 AAAAGA
22401 GAATGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:28907 original size:17 final size:18
Alignment explanation
Indices: 28885--28925 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28875 TCATTTTTTT
28885 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
28902 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
28920 T-TTTTG
1 TCTTTTG
28926 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:36819 original size:22 final size:23
Alignment explanation
Indices: 36788--36830 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
36778 ACCTTTTTGA
36788 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCGTACCAAAT
*
36811 ACCA-TACCATTTCGTACCAA
1 ACCATTACCAATTCGTACCAA
36831 TCCCTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.33, G:0.05, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCGTACCAAAT
Found at i:42340 original size:30 final size:30
Alignment explanation
Indices: 42306--42402 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
42296 TAAACTAAAA
42306 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
42336 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
42366 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
42395 ATGAGCTA
1 -TGAGCTA
42403 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:44596 original size:12 final size:12
Alignment explanation
Indices: 44581--44611 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
44571 TTCTTTTTGC
44581 TTTTCAAAGGCT
1 TTTTCAAAGGCT
44593 TTTTCAAAGGCT
1 TTTTCAAAGGCT
44605 TTTTCAA
1 TTTTCAA
44612 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:44688 original size:6 final size:6
Alignment explanation
Indices: 44672--44721 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
44662 TTTCTTTTTA
*
44672 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
44721 T
1 T
44722 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:44704 original size:37 final size:37
Alignment explanation
Indices: 44661--44731 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
44651 CTTGCCTCTC
44661 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
44698 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
44732 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:44732 original size:16 final size:16
Alignment explanation
Indices: 44657--44717 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
44647 GCCTCTTGCC
*
44657 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
44673 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
44689 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
44705 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
44718 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:45628 original size:12 final size:12
Alignment explanation
Indices: 45612--45656 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
45602 TTCACTTTTT
45612 TTTTTTCTTCAAA
1 TTTTTTCTTC-AA
*
45625 TTTTTT-TTGAA
1 TTTTTTCTTCAA
*
45636 TTTTTTTTTCAA
1 TTTTTTCTTCAA
45648 TTTTTTCTT
1 TTTTTTCTT
45657 TTTTTTGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 8 0.29
12 14 0.50
13 6 0.21
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTTCTTCAA
Found at i:45637 original size:11 final size:11
Alignment explanation
Indices: 45612--45677 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 11
45602 TTCACTTTTT
45612 TTTTTTCTTCAAA
1 TTTTTT-TTC-AA
*
45625 TTTTTTTTGAA
1 TTTTTTTTCAA
45636 TTTTTTTTTCAA
1 -TTTTTTTTCAA
45648 --TTTTTTC--
1 TTTTTTTTCAA
*
45655 TTTTTTTT-GA
1 TTTTTTTTCAA
45665 TTTTTTTTCAA
1 TTTTTTTTCAA
45676 TT
1 TT
45678 ACAATATGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
9 13 0.30
10 8 0.18
11 5 0.11
12 12 0.27
13 6 0.14
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:47373 original size:30 final size:30
Alignment explanation
Indices: 47339--47435 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
47329 TAAACTAAAA
*
47339 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
47369 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
47399 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
47428 ATGAGCTA
1 -TGAGCTA
47436 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:48561 original size:23 final size:22
Alignment explanation
Indices: 48509--48561 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
48499 TCCATGTCTT
*
48509 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
48531 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
48554 TTTCTTTT
1 TTTCTTTT
48562 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:50457 original size:22 final size:22
Alignment explanation
Indices: 50429--50472 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
50419 TTTTGAACCA
50429 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
50451 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
50473 AAATACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:50830 original size:15 final size:16
Alignment explanation
Indices: 50792--50832 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
50782 AAAATTTTTT
50792 AAAAAAATTGAAAGAA
1 AAAAAAATTGAAAGAA
50808 AAAAAAATT-AAA-AA
1 AAAAAAATTGAAAGAA
50822 GAAAAAAATTG
1 -AAAAAAATTG
50833 TATACGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 9 0.39
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (16 bp):
AAAAAAATTGAAAGAA
Found at i:53997 original size:11 final size:12
Alignment explanation
Indices: 53981--54032 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
53971 TTATACTTCG
53981 ATTTTTTTTT-A
1 ATTTTTTTTTCA
*
53992 ATTTTTTTTTCG
1 ATTTTTTTTTCA
54004 ATTTTTTTTTCA
1 ATTTTTTTTTCA
*
54016 AATTTTTTTTCGA
1 ATTTTTTTTTC-A
54029 ATTT
1 ATTT
54033 CCTCTTCTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 10 0.29
12 21 0.60
13 4 0.11
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:53999 original size:12 final size:12
Alignment explanation
Indices: 53981--54025 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
53971 TTATACTTCG
53981 ATTTTTTTTT-A
1 ATTTTTTTTTAA
**
53992 ATTTTTTTTTCG
1 ATTTTTTTTTAA
54004 ATTTTTTTTTCAA
1 ATTTTTTTTT-AA
54017 ATTTTTTTT
1 ATTTTTTTT
54026 CGAATTTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.34
12 10 0.34
13 9 0.31
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (12 bp):
ATTTTTTTTTAA
Found at i:54003 original size:23 final size:24
Alignment explanation
Indices: 53977--54028 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
53967 TTTTTTATAC
*
53977 TTCGATTTTTTTTT-AATTTTTTT
1 TTCGATTTTTTTTTCAAATTTTTT
54000 TTCGATTTTTTTTTCAAATTTTTT
1 TTCGATTTTTTTTTCAAATTTTTT
54024 TTCGA
1 TTCGA
54029 ATTTCCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (24 bp):
TTCGATTTTTTTTTCAAATTTTTT
Found at i:54009 original size:24 final size:23
Alignment explanation
Indices: 53977--54063 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
53967 TTTTTTATAC
* *
53977 TTCGATTTTTTTTTAATTTTTTT
1 TTCGATTTTTTTTCAAATTTTTT
54000 TTCGATTTTTTTTTCAAATTTTTT
1 TTCGA-TTTTTTTTCAAATTTTTT
* * **
54024 TTCGAATTTCCTCTTC-TCTTTTTT
1 TTCG-ATTT-TTTTTCAAATTTTTT
*
54048 TTTGATTTTTTTTCAA
1 TTCGATTTTTTTTCAA
54064 TTACAATATG
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
22 4 0.08
23 9 0.18
24 32 0.64
25 5 0.10
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (23 bp):
TTCGATTTTTTTTCAAATTTTTT
Found at i:64819 original size:30 final size:30
Alignment explanation
Indices: 64783--64879 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
64773 AGCTCACTCC
64783 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
64813 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
*
64843 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
64873 TAGCTCA
1 TAGCTCA
64880 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:70756 original size:21 final size:23
Alignment explanation
Indices: 70711--70757 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
70701 TCACCTGCAA
* *
70711 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
70734 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
70755 TAA
1 TAA
70758 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:75560 original size:20 final size:19
Alignment explanation
Indices: 75537--75601 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
75527 AAGCTCAAAC
75537 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
75557 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
75577 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
75597 GAGCT
1 GAGCT
75602 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:77629 original size:14 final size:14
Alignment explanation
Indices: 77610--77660 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
77600 TAGCTTCTTC
77610 TTTTTTCACGAAAATT
1 TTTTTTCACG-AAA-T
77626 TTTTTTCACG-AAT
1 TTTTTTCACGAAAT
*
77639 TTTTTTCACGAATT
1 TTTTTTCACGAAAT
77653 TTTTTTCA
1 TTTTTTCA
77661 ACTTGATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 11 0.33
14 12 0.36
16 10 0.30
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTTTCACGAAAT
Found at i:77641 original size:13 final size:13
Alignment explanation
Indices: 77610--77657 Score: 69
Period size: 13 Copynumber: 3.5 Consensus size: 13
77600 TAGCTTCTTC
77610 TTTTTTCACGAAAATT
1 TTTTTTCACG--AA-T
77626 TTTTTTCACGAAT
1 TTTTTTCACGAAT
77639 TTTTTTCACGAAT
1 TTTTTTCACGAAT
77652 TTTTTT
1 TTTTTT
77658 TCAACTTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 20 0.62
14 2 0.06
16 10 0.31
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (13 bp):
TTTTTTCACGAAT
Found at i:77743 original size:10 final size:11
Alignment explanation
Indices: 77701--77740 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
77691 GAAACCAATT
77701 TTTTTTTTGAA
1 TTTTTTTTGAA
77712 TTTTTTTTGAA
1 TTTTTTTTGAA
77723 TTTTTTTTGAA
1 TTTTTTTTGAA
77734 TTTTTTT
1 TTTTTTT
77741 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:79702 original size:11 final size:10
Alignment explanation
Indices: 79677--79737 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
79667 ACCAATAAAA
79677 TAAA-TGAGC
1 TAAATTGAGC
*
79686 TGAATTGTAGC
1 TAAATTG-AGC
79697 TAAATTGAGC
1 TAAATTGAGC
**
79707 TCGATTGAGC
1 TAAATTGAGC
79717 TGAAA-TGAGC
1 T-AAATTGAGC
*
79727 TCAATTGAGC
1 TAAATTGAGC
79737 T
1 T
79738 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:79738 original size:20 final size:20
Alignment explanation
Indices: 79678--79738 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
79668 CCAATAAAAT
*
79678 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
79698 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
79719 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
79739 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:81825 original size:18 final size:18
Alignment explanation
Indices: 81804--81838 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
81794 TTTTTCTTTT
81804 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
81822 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
81839 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:81835 original size:6 final size:6
Alignment explanation
Indices: 81826--81930 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
81816 TCAATCTCAA
* * * ** **
81826 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
81878 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
81924 TTTCTT T
1 TTTCTT T
81931 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:81943 original size:6 final size:6
Alignment explanation
Indices: 81877--81930 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
81867 ACTATTTTGA
* ** * *
81877 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
81924 TTTCTT T
1 TTTCTT T
81931 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:84410 original size:11 final size:10
Alignment explanation
Indices: 84385--84445 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
84375 ACCAATAAAA
84385 TAAA-TGAGC
1 TAAATTGAGC
*
84394 TGAATTGTAGC
1 TAAATTG-AGC
84405 TAAATTGAGC
1 TAAATTGAGC
**
84415 TCGATTGAGC
1 TAAATTGAGC
84425 TGAAA-TGAGC
1 T-AAATTGAGC
*
84435 TCAATTGAGC
1 TAAATTGAGC
84445 T
1 T
84446 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:84446 original size:20 final size:20
Alignment explanation
Indices: 84386--84446 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
84376 CCAATAAAAT
*
84386 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
84406 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
84427 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
84447 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:85003 original size:21 final size:23
Alignment explanation
Indices: 84958--85004 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
84948 TCACCTACAA
* *
84958 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
84981 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
85002 TAA
1 TAA
85005 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:92544 original size:15 final size:15
Alignment explanation
Indices: 92524--92578 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
92514 ACTCTCCTCA
*
92524 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
92539 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
92554 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
92568 TTCTTTT-TCTC
1 TTCTTTTCTCTC
92579 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:94772 original size:13 final size:13
Alignment explanation
Indices: 94756--94815 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 13
94746 CAAAAAAATC
94756 AAAAAAAATTCGA
1 AAAAAAAATTCGA
*
94769 AAAAAAAATTTGA
1 AAAAAAAATTCGA
94782 TTGAAAAAAAATTC-A
1 ---AAAAAAAATTCGA
*
94797 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
94809 AAAAAAA
1 AAAAAAA
94816 TCGAGCAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 17 0.43
13 12 0.30
15 1 0.03
16 10 0.25
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:94857 original size:16 final size:16
Alignment explanation
Indices: 94818--94860 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
94808 AAAAAAAATC
94818 GAGCAAAAAAAAAGAA
1 GAGCAAAAAAAAAGAA
* * **
94834 AAGAAAAAAAAAAGGT
1 GAGCAAAAAAAAAGAA
94850 GAGCAAAAAAA
1 GAGCAAAAAAA
94861 TCAAGTTTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (16 bp):
GAGCAAAAAAAAAGAA
Found at i:95892 original size:12 final size:12
Alignment explanation
Indices: 95880--95997 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
95870 GAAAGAGATT
*
95880 GAAAAAGAAATT
1 GAAAAAGAAATA
95892 G--AAAGAAA-A
1 GAAAAAGAAATA
*
95901 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
95912 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
95925 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
95937 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
95949 GAAAAAGTGAGA
1 GAAAAAGAAATA
95961 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
95972 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
95988 GAAAAAGAAA
1 GAAAAAGAAA
95998 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:95923 original size:18 final size:18
Alignment explanation
Indices: 95897--96000 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
95887 AAATTGAAAG
*
95897 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
95915 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
95933 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
95951 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
95969 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
95990 AAAAGAAAAAG
1 AAAAGAAAAAG
96001 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:95925 original size:6 final size:6
Alignment explanation
Indices: 95893--96000 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
95883 AAAGAAATTG
* * ** *
95893 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
95940 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
95991 AAAGAA AAAG
1 AAAGAA AAAG
96001 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:95982 original size:14 final size:13
Alignment explanation
Indices: 95961--95998 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
95951 AAAAGTGAGA
95961 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
95973 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
95988 GAAAAAGAAAA
1 GAAAAAGAAAA
95999 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:96012 original size:21 final size:21
Alignment explanation
Indices: 95962--96012 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
95952 AAAGTGAGAG
*
95962 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
95983 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
96004 AAAAAGAAA
1 AAAAAGAAA
96013 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:96052 original size:33 final size:33
Alignment explanation
Indices: 96015--96077 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
96005 AAAAGAAATT
96015 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
96048 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
96078 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:97876 original size:20 final size:20
Alignment explanation
Indices: 97853--97906 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
97843 AGTTTTTCCC
*
97853 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
97873 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
97893 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
97907 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:97888 original size:30 final size:30
Alignment explanation
Indices: 97853--97926 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
97843 AGTTTTTCCC
97853 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
97883 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
97913 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
97927 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:97916 original size:20 final size:20
Alignment explanation
Indices: 97853--97917 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
97843 AGTTTTTCCC
* * * *
97853 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
97873 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
97892 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
97913 AGCTC
1 AGCTC
97918 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:101465 original size:22 final size:22
Alignment explanation
Indices: 101437--101480 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101427 TTTTGAACCA
101437 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
101459 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
101481 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:104044 original size:18 final size:18
Alignment explanation
Indices: 104006--104047 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
103996 GCGAAAATAC
* *
104006 AAAAGAAAAGAAAAATGA
1 AAAAAAAAAGAAAAATCA
*
104024 AAAAAAAAAGAAAATTCA
1 AAAAAAAAAGAAAAATCA
104042 AAAAAA
1 AAAAAA
104048 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAGAAAAATCA
Found at i:109836 original size:22 final size:22
Alignment explanation
Indices: 109806--109849 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
109796 TTTGGTATTT
109806 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
109828 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
109850 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Done.