Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3865
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: 16877
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Found at i:3236 original size:29 final size:28
Alignment explanation
Indices: 3171--3267 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 28
3161 TAAAAAATAA
* * *
3171 AATTGCATTTTGACACCTAAACTTTTCCTA
1 AATTTCATTTTGAC-CCTAAAC-TTTCATT
*
3201 AATTTCATTTTGACCCTTAAACTTTCTTT
1 AATTTCATTTTGACCC-TAAACTTTCATT
* *
3230 AATTTCACTTAGACCCT-AACTTTCATT
1 AATTTCATTTTGACCCTAAACTTTCATT
3257 AATTTCATTTT
1 AATTTCATTTT
3268 AATCCTAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.31
28 1 0.02
29 21 0.36
30 18 0.31
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTCATTTTGACCCTAAACTTTCATT
Found at i:3258 original size:27 final size:29
Alignment explanation
Indices: 3201--3263 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
3191 ACTTTTCCTA
* * *
3201 AATTTCATTTTGACCCTTAAACTTTCTTT
1 AATTTCACTTAGACCCTTAAACTTTCATT
3230 AATTTCACTTAGACCC-T-AACTTTCATT
1 AATTTCACTTAGACCCTTAAACTTTCATT
3257 AATTTCA
1 AATTTCA
3264 TTTTAATCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 16 0.52
28 1 0.03
29 14 0.45
ACGTcount: A:0.29, C:0.22, G:0.03, T:0.46
Consensus pattern (29 bp):
AATTTCACTTAGACCCTTAAACTTTCATT
Found at i:3274 original size:27 final size:27
Alignment explanation
Indices: 3201--3280 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
3191 ACTTTTCCTA
* *
3201 AATTTCATTTTGACCCTTAAACTTTCTTT
1 AATTTCATTTTAACCC-T-AACTTTCATT
*
3230 AATTTCA-CTTAGACCCTAACTTTCATT
1 AATTTCATTTTA-ACCCTAACTTTCATT
* *
3257 AATTTCATTTTAATCCTAATTTTC
1 AATTTCATTTTAACCCTAACTTTC
3281 TAAAATTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
27 26 0.60
28 6 0.14
29 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.49
Consensus pattern (27 bp):
AATTTCATTTTAACCCTAACTTTCATT
Found at i:3623 original size:25 final size:24
Alignment explanation
Indices: 3589--3636 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3579 AGACTTTGAA
* *
3589 GAAGAAGAAAAGAAGAAAAGAAAAG
1 GAAGAAG-AAAGAAAAAAAAAAAAG
3614 GAAGAAGAAAGAAAAAAAAAAAA
1 GAAGAAGAAAGAAAAAAAAAAAA
3637 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAGAAAAAAAAAAAAG
Found at i:3635 original size:28 final size:28
Alignment explanation
Indices: 3586--3640 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3576 GCTAGACTTT
* *
3586 GAAGAAGAAGAAAAGAAGAAAAGAAAAG
1 GAAGAAGAAGAAAAGAAAAAAAAAAAAG
3614 GAAGAAGAAAGAAAA-AAAAAAAAAAAA
1 GAAGAAG-AAGAAAAGAAAAAAAAAAAA
3641 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (28 bp):
GAAGAAGAAGAAAAGAAAAAAAAAAAAG
Found at i:3740 original size:17 final size:16
Alignment explanation
Indices: 3718--3772 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
3708 AAGAAAAACA
3718 AAAAAAAAAAC-AAGCCC
1 AAAAAAAAAACAAAG--C
*
3735 AAAAAAAAATCAAAGC
1 AAAAAAAAAACAAAGC
3751 AAAAAAAAAA-AAA--
1 AAAAAAAAAACAAAGC
3764 AAAAAAAAA
1 AAAAAAAAA
3773 GCGCACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 9 0.26
15 3 0.09
16 10 0.29
17 10 0.29
18 3 0.09
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAACAAAGC
Found at i:3760 original size:18 final size:16
Alignment explanation
Indices: 3716--3772 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
3706 CCAAGAAAAA
3716 CAAAAAAAAAAACAAG
1 CAAAAAAAAAAACAAG
* *
3732 CCCAAAAAAAAATCAAAG
1 -CAAAAAAAAAAAC-AAG
3750 CAAAAAAAAAAA-AA-
1 CAAAAAAAAAAACAAG
3764 -AAAAAAAAA
1 CAAAAAAAAA
3773 GCGCACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
17 21 0.60
18 3 0.09
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (16 bp):
CAAAAAAAAAAACAAG
Found at i:3893 original size:6 final size:6
Alignment explanation
Indices: 3877--3928 Score: 70
Period size: 6 Copynumber: 8.3 Consensus size: 6
3867 GCCAGCAGAA
3877 AAAAAG AAAAAAG AAAAAG AAAAAG AAAAAAGG AAAAAG AAAAA- AAAAAG
1 AAAAAG -AAAAAG AAAAAG AAAAAG -AAAAA-G AAAAAG AAAAAG AAAAAG
3927 AA
1 AA
3929 GAAAAAGGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.12
6 20 0.48
7 16 0.38
8 1 0.02
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3900 original size:14 final size:14
Alignment explanation
Indices: 3873--3934 Score: 83
Period size: 14 Copynumber: 4.5 Consensus size: 14
3863 GGCAGCCAGC
3873 AGAAAAAAAGAAAA
1 AGAAAAAAAGAAAA
*
3887 A-AGAAAAAGAAAA
1 AGAAAAAAAGAAAA
*
3900 AGAAAAAAGGAAAA
1 AGAAAAAAAGAAAA
3914 AGAAAAAAA-AAAGA
1 AGAAAAAAAGAAA-A
3928 AGAAAAA
1 AGAAAAA
3935 GGGGGTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 15 0.36
14 27 0.64
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAA
Found at i:3906 original size:20 final size:20
Alignment explanation
Indices: 3877--3935 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
3867 GCCAGCAGAA
3877 AAAAAG-AAAAAAGAAAAAG
1 AAAAAGAAAAAAAGAAAAAG
*
3896 AAAAAGAAAAAAGGAAAAAG
1 AAAAAGAAAAAAAGAAAAAG
3916 AAAAA-AAAAAGAAGAAAAAG
1 AAAAAGAAAAA-AAGAAAAAG
3936 GGGGTTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 11 0.31
20 25 0.69
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAAGAAAAAG
Found at i:3934 original size:27 final size:27
Alignment explanation
Indices: 3873--3936 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
3863 GGCAGCCAGC
*
3873 AGAAAAAAAGAAAAAAGAAAAAGAAAA
1 AGAAAAAAAGGAAAAAGAAAAAGAAAA
3900 AG-AAAAAAGGAAAAAGAAAAA-AAAA
1 AGAAAAAAAGGAAAAAGAAAAAGAAAA
3925 AGAAGAAAAAGG
1 AGAA-AAAAAGG
3937 GGGTTCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.18
26 19 0.56
27 9 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (27 bp):
AGAAAAAAAGGAAAAAGAAAAAGAAAA
Found at i:4542 original size:18 final size:17
Alignment explanation
Indices: 4471--4734 Score: 95
Period size: 18 Copynumber: 14.9 Consensus size: 17
4461 GAAATTTTCG
* *
4471 AATTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTAAAA
*
4489 AGTTTTCGTGTTTGAAAA
1 AATTTTCGTGTTT-AAAA
*
4507 AATTTTCGCGTTTAAAA
1 AATTTTCGTGTTTAAAA
* *
4524 AATTTCTCGTATTTCAAA
1 AATTT-TCGTGTTTAAAA
* * * *
4542 AATTGTCGTTTTTTATA
1 AATTTTCGTGTTTAAAA
* * *
4559 AATCTTCGTGCTTTCAAT
1 AATTTTCGTG-TTTAAAA
** *
4577 AATCCTCGTGCTTT-TAA
1 AATTTTCGTG-TTTAAAA
* * *
4594 AATTCTCATGTTT-CAA
1 AATTTTCGTGTTTAAAA
* **
4610 AATCTTCGTGTTT-TCA
1 AATTTTCGTGTTTAAAA
* * *
4626 AATTCTAGTGTTTCAAA
1 AATTTTCGTGTTTAAAA
*
4643 AATTTTCTTGTTTTCAAAAA
1 AATTTTCGTG-TTT--AAAA
*
4663 AAATTTCGTGTTTTAAAAAAA
1 AATTTTCGTG-TTT---AAAA
*
4684 AATATTTCCGTGTTTTAAA
1 AAT-TTT-CGTGTTTAAAA
*
4703 AATTTTCGTGTTT-TAA
1 AATTTTCGTGTTTAAAA
* *
4719 AATTCTCGTATTTAAA
1 AATTTTCGTGTTTAAA
4735 TTTTTTTTTA
Statistics
Matches: 188, Mismatches: 47, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
16 39 0.21
17 53 0.28
18 58 0.31
19 6 0.03
20 15 0.08
21 7 0.04
22 6 0.03
23 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (17 bp):
AATTTTCGTGTTTAAAA
Found at i:4645 original size:33 final size:33
Alignment explanation
Indices: 4570--4660 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 33
4560 ATCTTCGTGC
* * *
4570 TTTCAATAATCCTCGTGCTTTTAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAATTCTCATG
4604 TTTC-AAAATCTTCGTGTTTTCAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAATTCTCA-TG
* *
4636 TTTCAAAAATTTTCTTGTTTTCAAA
1 TTTCAAAAATCTTCGTGTTTTCAAA
4661 AAAAATTTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
31 1 0.02
32 17 0.34
33 28 0.56
34 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (33 bp):
TTTCAAAAATCTTCGTGTTTTCAAATTCTCATG
Found at i:4666 original size:21 final size:20
Alignment explanation
Indices: 4640--4720 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 20
4630 CTAGTGTTTC
*
4640 AAAAATTTTCTTGTTTTCAAA
1 AAAAATTTTCGTGTTTT-AAA
4661 AAAAA-TTTCGTGTTTTAAAA
1 AAAAATTTTCGTGTTTT-AAA
4681 AAAAATATTTCCGTGTTTT---
1 AAAAAT-TTT-CGTGTTTTAAA
4700 AAAAATTTTCGTGTTTTAAA
1 AAAAATTTTCGTGTTTTAAA
4720 A
1 A
4721 TTCTCGTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
17 8 0.15
18 3 0.06
19 6 0.12
20 19 0.37
21 5 0.10
22 3 0.06
23 8 0.15
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (20 bp):
AAAAATTTTCGTGTTTTAAA
Found at i:4683 original size:22 final size:23
Alignment explanation
Indices: 4658--4704 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4648 TCTTGTTTTC
4658 AAAAAAAATTT-CGTGTTTTAAA
1 AAAAAAAATTTCCGTGTTTTAAA
*
4680 AAAAAATATTTCCGTGTTTTAAA
1 AAAAAAAATTTCCGTGTTTTAAA
4703 AA
1 AA
4705 TTTTCGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (23 bp):
AAAAAAAATTTCCGTGTTTTAAA
Found at i:4827 original size:18 final size:17
Alignment explanation
Indices: 4492--4906 Score: 88
Period size: 17 Copynumber: 24.0 Consensus size: 17
4482 TTTCAAAAGT
*
4492 TTTCGTGTTTGAAAAAA
1 TTTCGTGTTTTAAAAAA
*
4509 TTTTCGCG-TTTAAAAAA
1 -TTTCGTGTTTTAAAAAA
*
4526 TTTC-TCGTATTTCAAAAA
1 TTTCGT-GT-TTTAAAAAA
* *
4544 TTGTCGT-TTTTTATAAA
1 TT-TCGTGTTTTAAAAAA
* * *
4561 TCTTCGTGCTTTCAATAA
1 T-TTCGTGTTTTAAAAAA
*
4579 TCCTCGTGCTTTT--AAAA
1 T-TTCGTG-TTTTAAAAAA
* *
4596 TTCTCATG-TTT-CAAAA
1 TT-TCGTGTTTTAAAAAA
*
4612 TCTTCGTGTTTT--CAAA
1 T-TTCGTGTTTTAAAAAA
* * *
4628 TTCTAGTGTTTCAAAAAT
1 TT-TCGTGTTTTAAAAAA
*
4646 TTTCTTGTTTTCAAAAAAAA
1 TTTCGTGTTTT---AAAAAA
4666 TTTCGTGTTTTAAAAAAAAATA
1 TTTCGTGTTTT----AAAAA-A
*
4688 TTTCCGTGTTTTAAAAAT
1 TTT-CGTGTTTTAAAAAA
4706 TTTCGTGTTTT--AAAA
1 TTTCGTGTTTTAAAAAA
*
4721 TTCTCGT-ATTT---AAA
1 TT-TCGTGTTTTAAAAAA
*
4735 TTT--TTTTTTAAGAAAAAA
1 TTTCGTGTTTT---AAAAAA
*
4753 TTT--TGTTTCAAAAAA
1 TTTCGTGTTTTAAAAAA
* *
4768 TGTCTTGTTTT-AAAAA
1 TTTCGTGTTTTAAAAAA
* *
4784 TTCCCGTGTTTCAAAAAAAA
1 TT-TCGTGTTT--TAAAAAA
*
4804 TGTCGTGTTTTAAGAAAA
1 TTTCGTGTTTTAA-AAAA
* *
4822 TTTCGTTTTTTTCCAAAAA
1 TTTCG-TGTTTT-AAAAAA
*
4841 TTTCGTGTTTCTAAAATA
1 TTTCGTGTTT-TAAAAAA
*
4859 -TTCGTG-TTT--ACAA
1 TTTCGTGTTTTAAAAAA
*
4872 TTCTCGTGTTTT-CAAAA
1 TT-TCGTGTTTTAAAAAA
*
4889 TTCTCGTATTTTAAAAAA
1 TT-TCGTGTTTTAAAAAA
4907 AAAACTTTCG
Statistics
Matches: 300, Mismatches: 53, Indels: 88
0.68 0.12 0.20
Matches are distributed among these distances:
11 1 0.00
12 3 0.01
13 3 0.01
14 6 0.02
15 26 0.09
16 40 0.13
17 79 0.26
18 68 0.23
19 32 0.11
20 23 0.08
21 7 0.02
22 4 0.01
23 8 0.03
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTCGTGTTTTAAAAAA
Found at i:13463 original size:72 final size:72
Alignment explanation
Indices: 13121--14135 Score: 1643
Period size: 72 Copynumber: 14.1 Consensus size: 72
13111 TAAGCCTTTT
* * * * ** * *
13121 AATTTATGTTTTTCAAAA-TCAATTCAAATTGCTAGAGGTGAGTTGAG-CTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
*
13184 GTAATTTT
65 GTAATTTC
* * * *
13192 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
13257 GGTAATTTC
64 GGTAATTTC
* * *
13266 AATTTCTG-TTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
13330 TATTTTC
66 TAATTTC
13337 AATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
13402 GTAATTTC
65 GTAATTTC
13410 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
13475 TAATTTC
66 TAATTTC
13482 AA-TTCTGTTTTCAAAATTCAACTCATA-TGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
13545 TATTTTC
66 TAATTTC
*
13552 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
13617 GTAATTTC
65 GTAATTTC
13625 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
13690 T-ATTTC
66 TAATTTC
*
13696 AATTTCTGCTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
13761 TATTTTC
66 TAATTTC
13768 AATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
13832 TAATTTC
66 TAATTTC
13839 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
13904 T-ATTTC
66 TAATTTC
*
13910 AATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
13975 GTAATTTC
65 GTAATTTC
*
13983 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
14048 TATTTTC
66 TAATTTC
* * *
14055 AATTTCTGCTTTTCAAAACTT-AACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACGCTGA
1 AATTTCTG-TTTTCAAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGA
*
14119 GGTATTTTC
64 GGTAATTTC
14128 AATTTCTG
1 AATTTCTG
14136 CTTTACTAAT
Statistics
Matches: 898, Mismatches: 31, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
70 46 0.05
71 256 0.29
72 343 0.38
73 220 0.24
74 33 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TAATTTC
Found at i:13584 original size:215 final size:216
Alignment explanation
Indices: 13117--14135 Score: 1662
Period size: 215 Copynumber: 4.7 Consensus size: 216
13107 GAGTTAAGCC
* * * * ** *
13117 TTTT-AATTTATGTTTTTCAAAA-TCAATTCAAATTGCTAGAGGTGAGTTGAG-CTCAGGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
* * * *
13179 CTGAGGTAATTTTAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
65 TTGAGGTAATTTCAATTTCTGTT-TT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCT
* * *
13244 CAGGACACGCTGAGGTAATTTCAATTTCTG-TTTCAAAATTCAACTTATATTGCGAGAAATGAGT
128 CAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
* *
13308 TGAGCCTCAGGACACGCTGAGGTA
193 TGAGCCTCAAGACACGTTGAGGTA
13332 TTTTCAATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
13397 TTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 TTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
13462 AGACACGTTGAGGTAATTTCAA-TTCTGTTTTCAAAATTCAACTCATA-TGCGAGAAATGAGTTG
130 AGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
13525 AGCCTCAAGACACGTTGAGGTA
195 AGCCTCAAGACACGTTGAGGTA
*
13547 TTTTCAATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 TTTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
13612 TTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
65 TTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
*
13677 AGACACGTTGAGGT-ATTTCAATTTCTGCTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
130 AGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
13741 AGCCTCAAGACACGTTGAGGTA
195 AGCCTCAAGACACGTTGAGGTA
13763 TTTTCAATTTCTG-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
13827 TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
66 TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
*
13892 GACACGTTGAGGT-ATTTCAATTTCTGCTTCTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
131 GACACGTTGAGGTAATTTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTG
13956 AGCCTCAAGACACGTTGAGGTA
195 AGCCTCAAGACACGTTGAGGTA
* *
13978 ATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACAT
1 TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
* *
14043 TGAGGTATTTTCAATTTCTGCTTTTCAAAACTT-AACTCATATTGCGAGAGATGAGTTGAGCCTC
66 TGAGGTAATTTCAATTTCTG-TTTTCAAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTC
* * *
14107 AAGGCACGCTGAGGTATTTTCAATTTCTG
129 AAGACACGTTGAGGTAATTTCAATTTCTG
14136 CTTTACTAAT
Statistics
Matches: 764, Mismatches: 29, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
214 148 0.19
215 281 0.37
216 212 0.28
217 78 0.10
218 45 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (216 bp):
TTTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
TGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAA
GACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGA
GCCTCAAGACACGTTGAGGTA
Found at i:14241 original size:14 final size:14
Alignment explanation
Indices: 14219--14251 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14209 TCTTTTCAAA
14219 TTCTG-TTTTTAAT
1 TTCTGTTTTTTAAT
14232 TTCTGTTTTTTAAT
1 TTCTGTTTTTTAAT
14246 TTCTGT
1 TTCTGT
14252 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.70
Consensus pattern (14 bp):
TTCTGTTTTTTAAT
Found at i:14241 original size:86 final size:87
Alignment explanation
Indices: 14050--14241 Score: 214
Period size: 86 Copynumber: 2.2 Consensus size: 87
14040 CATTGAGGTA
* * * *
14050 TTTTCAATTTCTGCTTTTCAAAACTTAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGGCACG
1 TTTTTAATTTCTGTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGGCACG
*
14115 CTGAGGTATTTTCAATTTCTGC
66 CTGAGGTATTTTCAAATTCTGC
* * * *
14137 TTTACTAA-TTCTACTTTTTC-AAA-TCAACTCATATTGCAAGAGGTGAGTTGAGTCTC-AGGCC
1 TTT-TTAATTTCT-GTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGG--
*
14198 ACACGCTGAGGTCTTTTCAAATTCTG-
62 -CACGCTGAGGTATTTTCAAATTCTGC
14224 TTTTTAATTTCTGTTTTT
1 TTTTTAATTTCTGTTTTT
14242 TAATTTCTGT
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
85 3 0.03
86 37 0.43
87 17 0.20
88 30 0.34
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (87 bp):
TTTTTAATTTCTGTTTTTCAAAACTCAACTCATATTGCAAGAGATGAGTTGAGCCTCAAGGCACG
CTGAGGTATTTTCAAATTCTGC
Found at i:14355 original size:53 final size:54
Alignment explanation
Indices: 14262--14507 Score: 350
Period size: 54 Copynumber: 4.7 Consensus size: 54
14252 GTTTCAAAAA
*
14262 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAG-CTTTTAATTTCTGTTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
*
14315 AAAAATCAA-TCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTATTTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
* *
14368 AAAAACCAACTCATATTGCGAGA-GTGAGTTGAGCC--TT--TTTCT-ATTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
*
14416 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCTG-TTTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT--AATTTCTGTTTTTC
*
14471 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
14508 GGCTCACGTG
Statistics
Matches: 176, Mismatches: 7, Indels: 19
0.87 0.03 0.09
Matches are distributed among these distances:
48 27 0.15
49 17 0.10
51 4 0.02
52 23 0.13
53 47 0.27
54 49 0.28
55 9 0.05
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (54 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTC
Found at i:14443 original size:102 final size:103
Alignment explanation
Indices: 14262--14507 Score: 347
Period size: 102 Copynumber: 2.4 Consensus size: 103
14252 GTTTCAAAAA
* * *
14262 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCTTTTAATTTCTGTTTTTCAAAAATCAATCA
1 AAAAATCAACTCATATTGCGAGA-GTGAGTTGAGC-CTT-ATTTCTGATTTTCAAAAATCAATCA
* *
14327 TATTGCGAGAGGTGAGTTGAGCCTTTT-AATTTCTATTTTTC
63 TATTGCGAGAGGTGAGTTGAGCCTTTTCAAATTCT-GTTTTC
*
14368 AAAAACCAACTCATATTGCGAGAGTGAGTTGAGCCTT-TTTCT-ATTTTCAAAAATCAACTCATA
1 AAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTTATTTCTGATTTTCAAAAATCAA-TCATA
14431 TTGCGAGAGGTGAGTTGAGCCTTTTGCAAATTCTGTTTTC
65 TTGCGAGAGGTGAGTTGAGCCTTTT-CAAATTCTGTTTTC
14471 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTT
1 AAAAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTT
14508 GGCTCACGTG
Statistics
Matches: 129, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
101 14 0.11
102 55 0.43
103 20 0.16
104 8 0.06
105 11 0.09
106 21 0.16
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (103 bp):
AAAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTTATTTCTGATTTTCAAAAATCAATCATAT
TGCGAGAGGTGAGTTGAGCCTTTTCAAATTCTGTTTTC
Found at i:14811 original size:28 final size:29
Alignment explanation
Indices: 14774--14873 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 29
14764 TTTAAAAATA
* *
14774 AAATTGCATTTTGACACCTAAACTTTC-CT
1 AAATTTCATTTTGAC-CCTAAACTTTCATT
*
14803 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCATT
* *
14832 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTCATT
14862 AAATTTCATTTT
1 AAATTTCATTTT
14874 AATCCTAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 22 0.37
29 1 0.02
30 32 0.53
31 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCATT
Found at i:14839 original size:30 final size:28
Alignment explanation
Indices: 14774--14898 Score: 112
Period size: 30 Copynumber: 4.4 Consensus size: 28
14764 TTTAAAAATA
* *
14774 AAATTGCATTTTGACACCTAAACTTTCCT
1 AAATTTCATTTTGAC-CCTAAACTTTCTT
14803 -AATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTC-TT
* *
14832 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGA-CCCTAAACTTTC-TT
* * *
14862 AAATTTCATTTTAATCCT-AA-TTTCTA
1 AAATTTCATTTTGACCCTAAACTTTCTT
*
14888 AAATTACATTT
1 AAATTTCATTT
14899 AGCCCCAGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
26 11 0.14
27 6 0.07
28 24 0.30
29 4 0.05
30 33 0.41
31 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.44
Consensus pattern (28 bp):
AAATTTCATTTTGACCCTAAACTTTCTT
Found at i:15147 original size:18 final size:18
Alignment explanation
Indices: 15120--15161 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
15110 TTTTTTCGAG
*
15120 GAAAAAAGAAAAAGAGAA
1 GAAAAGAGAAAAAGAGAA
* *
15138 GAAAAGAGAAGAGGAGAA
1 GAAAAGAGAAAAAGAGAA
15156 -AAAAGA
1 GAAAAGA
15162 AAGAGTACCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
GAAAAGAGAAAAAGAGAA
Found at i:15218 original size:3 final size:3
Alignment explanation
Indices: 15212--15252 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
15202 GGCTAGACTT
*
15212 GAA GAA GAA GAA GAA GAA GAAA GAA GAA -AA GAG GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA
15253 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15248 original size:8 final size:8
Alignment explanation
Indices: 15216--15256 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
15206 AGACTTGAAG
15216 AAGAAGAA
1 AAGAAGAA
15224 GAAGAAG-A
1 -AAGAAGAA
15232 AAGAAGAA
1 AAGAAGAA
*
15240 AAGAGGAA
1 AAGAAGAA
15248 AAGAA-AA
1 AAGAAGAA
15255 AA
1 AA
15257 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 10 0.34
8 13 0.45
9 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:15380 original size:19 final size:18
Alignment explanation
Indices: 15344--15396 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
15334 CCAAGAAAAA
15344 CAAAAAAAAGAAAC-AAGCC
1 CAAAAAAAA-AAACAAAG-C
*
15363 CAAAAAAAAAATCAAAG-
1 CAAAAAAAAAAACAAAGC
15380 CAAAAAAAAAAAGCAAA
1 CAAAAAAAAAAA-CAAA
15397 AAAAAAGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 11 0.37
18 7 0.23
19 12 0.40
ACGTcount: A:0.75, C:0.15, G:0.08, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAAACAAAGC
Found at i:15397 original size:12 final size:13
Alignment explanation
Indices: 15366--15402 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
15356 ACAAGCCCAA
15366 AAAAAAAATCAAAGC
1 AAAAAAAA--AAAGC
15381 AAAAAAAAAAAGC
1 AAAAAAAAAAAGC
15394 AAAAAAAAA
1 AAAAAAAAA
15403 GAGGGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
15 8 0.36
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAGC
Found at i:15402 original size:18 final size:18
Alignment explanation
Indices: 15364--15402 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
15354 AAACAAGCCC
* **
15364 AAAAAAAAAATCAAAGCA
1 AAAAAAAAAAGCAAAAAA
15382 AAAAAAAAAAGCAAAAAA
1 AAAAAAAAAAGCAAAAAA
15400 AAA
1 AAA
15403 GAGGGAAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAGCAAAAAA
Found at i:15531 original size:9 final size:9
Alignment explanation
Indices: 15517--15580 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
15507 GCAGCCCAGC
15517 AGAAAAAAA
1 AGAAAAAAA
15526 AG--AAAAA
1 AGAAAAAAA
15533 AGAAAAAAGA
1 AGAAAAAA-A
15543 A-AAAAAGGAA
1 AGAAAAA--AA
*
15553 A-AAGAAAA
1 AGAAAAAAA
15561 AGAAAAAAA
1 AGAAAAAAA
*
15570 AGAAGAAAA
1 AGAAAAAAA
15579 AG
1 AG
15581 GGGTTCAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
7 7 0.15
8 3 0.07
9 27 0.59
10 8 0.17
11 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:15533 original size:7 final size:7
Alignment explanation
Indices: 15521--15568 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
15511 CCCAGCAGAA
15521 AAAAAAG
1 AAAAAAG
15528 AAAAAAG
1 AAAAAAG
15535 AAAAAAG
1 AAAAAAG
15542 AAAAAAAG
1 -AAAAAAG
*
15550 GAAAAAG
1 AAAAAAG
15557 -AAAAAG
1 AAAAAAG
15563 AAAAAA
1 AAAAAA
15569 AAGAAGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
6 6 0.16
7 25 0.66
8 7 0.18
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:15540 original size:15 final size:15
Alignment explanation
Indices: 15521--15580 Score: 79
Period size: 15 Copynumber: 4.0 Consensus size: 15
15511 CCCAGCAGAA
15521 AAAAAAG-AAAAAAG
1 AAAAAAGAAAAAAAG
15535 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
15550 GAAAAAGAAAAAGAA-
1 AAAAAAGAAAAA-AAG
15565 AAAAAAGAAGAAAAAG
1 AAAAAAGAA-AAAAAG
15581 GGGTTCAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.17
15 28 0.70
16 5 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:15548 original size:22 final size:22
Alignment explanation
Indices: 15517--15578 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
15507 GCAGCCCAGC
15517 AGAAAAAAAAGAAAAAAGAAAA
1 AGAAAAAAAAGAAAAAAGAAAA
*
15539 A-AGAAAAAAAGGAAAAAGAAAA
1 AGA-AAAAAAAGAAAAAAGAAAA
15561 AGAAAAAAAAGAAGAAAA
1 AGAAAAAAAAGAA-AAAA
15579 AGGGGTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 29 0.83
23 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAGAAAAAAGAAAA
Found at i:16170 original size:18 final size:17
Alignment explanation
Indices: 16100--16287 Score: 109
Period size: 18 Copynumber: 11.1 Consensus size: 17
16090 AGAATTTTCG
*
16100 AATTTTCGCGTTTTCAAA
1 AATTTTCGTG-TTTCAAA
* *
16118 AGTTTTCGTGTTTGAAAA
1 AATTTTCGTGTTT-CAAA
*
16136 AATTTTCGCGTTT-AAA
1 AATTTTCGTGTTTCAAA
*
16152 AATTTCTCGTATTTCAAA
1 AATTT-TCGTGTTTCAAA
* ***
16170 AATTGTCGT-TTTTTTA
1 AATTTTCGTGTTTCAAA
* *
16186 AATCTTCGTGCTTTCAAT
1 AATTTTCGTG-TTTCAAA
** *
16204 AATCCTCGTGCTTTCAAT
1 AATTTTCGTG-TTTCAAA
** *
16222 AATCCTCATGTTTC-AA
1 AATTTTCGTGTTTCAAA
*
16238 AATCTTCGTGTTTC-AA
1 AATTTTCGTGTTTCAAA
*
16254 AATTCT-GTGTTTCAAA
1 AATTTTCGTGTTTCAAA
*
16270 AATTTTC-TGTTTTAAA
1 AATTTTCGTGTTTCAAA
16286 AA
1 AA
16288 AAAAAATTTC
Statistics
Matches: 137, Mismatches: 26, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
15 7 0.05
16 55 0.40
17 17 0.12
18 58 0.42
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.45
Consensus pattern (17 bp):
AATTTTCGTGTTTCAAA
Found at i:16286 original size:15 final size:15
Alignment explanation
Indices: 16230--16286 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
16220 ATAATCCTCA
*
16230 TGTTTCAAAATCTTC
1 TGTTTCAAAATTTTC
* *
16245 GTGTTTCAAAATTCTG
1 -TGTTTCAAAATTTTC
16261 TGTTTCAAAAATTTTC
1 TGTTTC-AAAATTTTC
*
16277 TGTTTTAAAA
1 TGTTTCAAAA
16287 AAAAAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.29
16 24 0.71
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (15 bp):
TGTTTCAAAATTTTC
Found at i:16293 original size:22 final size:22
Alignment explanation
Indices: 16267--16330 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
16257 TCTGTGTTTC
*
16267 AAAAATTTTC-TGTTTTAAAAA
1 AAAAAATTTCGTGTTTTAAAAA
16288 AAAAAATTTCGTGTTTT-AAAA
1 AAAAAATTTCGTGTTTTAAAAA
*
16309 AAAATATTTCCGTG-TTTAAAAA
1 AAAAAATTT-CGTGTTTTAAAAA
16331 TTTCGTGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (22 bp):
AAAAAATTTCGTGTTTTAAAAA
Found at i:16310 original size:17 final size:17
Alignment explanation
Indices: 16288--16483 Score: 63
Period size: 17 Copynumber: 11.2 Consensus size: 17
16278 GTTTTAAAAA
16288 AAAAAATTTCGTGTTTT
1 AAAAAATTTCGTGTTTT
16305 AAAAAAAATATTTCCGTG-TTT
1 ---AAAAA-ATTT-CGTGTTTT
16326 -AAAAATTTCGTGTTTT
1 AAAAAATTTCGTGTTTT
*
16342 -AAAAATTCTCGT-ATTT
1 AAAAAATT-TCGTGTTTT
*
16358 --AAAATTT--TTTTTT
1 AAAAAATTTCGTGTTTT
*
16371 AAGAAAAAATTT--TGTTTC
1 ---AAAAAATTTCGTGTTTT
* *
16389 AAAAAATGTCTTGTTTT
1 AAAAAATTTCGTGTTTT
* **
16406 -AAAAATTCCCGTGTTCAAA
1 AAAAAATT-TCGTGTT--TT
*
16425 AAAAAATGTCGTGTTTT
1 AAAAAATTTCGTGTTTT
*
16442 AAGAAAATTTCGTTTTTTTT
1 AA-AAAATTTCG--TGTTTT
**
16462 CCAAAATTTCGTGTTTCT
1 AAAAAATTTCGTGTTT-T
16480 AAAA
1 AAAA
16484 TATTCGTTTA
Statistics
Matches: 134, Mismatches: 22, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
12 1 0.01
13 3 0.02
14 1 0.01
15 18 0.13
16 23 0.17
17 24 0.18
18 22 0.16
19 15 0.11
20 16 0.12
21 7 0.05
22 4 0.03
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTT
Found at i:16339 original size:15 final size:15
Alignment explanation
Indices: 16309--16361 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
16299 TGTTTTAAAA
16309 AAAATATTTCCGTGTTT
1 AAAA-ATTT-CGTGTTT
16326 AAAAATTTCGTGTTTT
1 AAAAATTTCGTG-TTT
*
16342 AAAAATTCTCGTATTT
1 AAAAATT-TCGTGTTT
16358 AAAA
1 AAAA
16362 TTTTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 4 0.12
16 21 0.64
17 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.43
Consensus pattern (15 bp):
AAAAATTTCGTGTTT
Found at i:16342 original size:16 final size:16
Alignment explanation
Indices: 16289--16353 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 16
16279 TTTTAAAAAA
16289 AAAAATTTCGTGTTTT
1 AAAAATTTCGTGTTTT
16305 AAAAAAAATATTTCCGTG-TTT
1 ----AAAA-ATTT-CGTGTTTT
16326 AAAAATTTCGTGTTTT
1 AAAAATTTCGTGTTTT
16342 AAAAATTCTCGT
1 AAAAATT-TCGT
16354 ATTTAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.10
16 14 0.34
17 8 0.20
20 4 0.10
21 7 0.17
22 4 0.10
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTT
Done.