Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold417
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: 511691
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 1 of 6
Found at i:2918 original size:22 final size:23
Alignment explanation
Indices: 2881--2936 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
2871 TGGACATGTT
2881 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
2904 AAAAATGCATG-AACATAATAAA
1 AAAAATGCATGAAACATAATAAA
2926 AAAAATGCATG
1 AAAAATGCATG
2937 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:3897 original size:20 final size:20
Alignment explanation
Indices: 3850--3924 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3840 AAAAAGACAT
*
3850 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3869 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3890 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
3910 AATGCATCGATACAT
1 AATGTATCGATACAT
3925 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3919 original size:40 final size:39
Alignment explanation
Indices: 3847--3924 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3837 GGTAAAAAGA
* * *
3847 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
3886 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
3925 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:4756 original size:29 final size:28
Alignment explanation
Indices: 4400--5916 Score: 2110
Period size: 28 Copynumber: 53.4 Consensus size: 28
4390 ACAGTGGTGA
*
4400 TTTGAAAAGGGTTGCCATTGACTTGCATGGGC
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGC
* *
4432 TTTAAAAGGGTGCCACTGACGTGCGTGGGC
1 TTTGAAAGGGTGCCACTGAC-T-TGTGGGC
** * *
4462 TTTGAAAGAATGCCACTAACTCGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
4490 TTTGAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
4518 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
4546 TTTGAAAAGGTACCACTGACTTGCGTGAGC
1 TTTGAAAGGGTGCCACTGACTT--GTGGGC
*
4576 TTTAAAAGGAGTGCCACTGACTTGTGTGAGC
1 TTTGAAAGG-GTGCCACTGACTTGTG-G-GC
*
4607 TTTAAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
4635 TTTGAAA-GGTGCCACTGAATTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
4662 TTCGCAATGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
4690 TTCGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
4718 TCTGAAAGGGTGCCACTAACTTGTGGGGC
1 TTTGAAAGGGTGCCACTGACTTGT-GGGC
4747 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
4775 TTTGAAAAGAGCGCCACTGATTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
*
4804 TTTGAAAAGAGTGCCACTGACTT-TGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
*
4832 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
4860 TTTGAAAGGGTGCCATTGACTTGTGGTC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
4888 TTTGAAAAGAGTGCCACTGATTTGTGGGGC
1 TTTG-AAAGGGTGCCACTGACTTGT-GGGC
*
4918 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
4947 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
*
4976 TTTGAAAGGGTGCCA-TAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
5003 TCTGAAAGGGGTGCCACTGAGTTGTGGGC
1 TTTGAAA-GGGTGCCACTGACTTGTGGGC
*
5032 TTTGAAAGGGTGCCACTGAGTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5060 TTTGAAAGAGTAGGTG-CACTGACTTGTGGTGC
1 TTTG-AA-AG--GGTGCCACTGACTTGTGG-GC
*
5092 TTTGAAAGGAGTGCCACTAACTT-TGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
5120 TTTGAAAGGAGTGCCACTGACCTTGTGGGC
1 TTTGAAAGG-GTGCCACTGA-CTTGTGGGC
*
5150 TTTGAAAGGGTGCCACTGAATTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
5178 TTCGCAATGGTGCTACTGACTATGTGCTGC
1 TTTGAAAGGGTGCCACTGACT-TGTG-GGC
5208 TTCTGAAAGGGTGCCACTGACTTGTGGGC
1 TT-TGAAAGGGTGCCACTGACTTGTGGGC
* *
5237 TCTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5265 TTTGAAAGGGTGCCACT---TTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
5290 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
5318 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5346 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5374 TTTGAAA-GGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
5401 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
*
5429 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
5458 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
5487 TTTGAAA-GGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5514 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5542 TTTGAAA-GGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5569 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
5598 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
*
5627 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5655 TTTGAAAGGAGTGCCACTGA-TTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
5683 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5711 TTTGAAAGGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGG-GTGCCACTGACTTGTGGGC
*
5740 TTTGAAAGAGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5768 TTTG-AA-GGTGCCACTGACTTGT-GGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5793 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
5821 TTTGAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAGGGTGCCACTGACTTGTGGGC
* *
5849 TTTGAAAAGAGTGCCACTGATTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
*
5878 TTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TTTG-AAAGGGTGCCACTGACTTGTGGGC
5907 TTTGAAAGGG
1 TTTGAAAGGG
5917 ATGAACATTC
Statistics
Matches: 1360, Mismatches: 81, Indels: 92
0.89 0.05 0.06
Matches are distributed among these distances:
25 31 0.02
26 17 0.01
27 167 0.12
28 582 0.43
29 371 0.27
30 119 0.09
31 59 0.04
32 14 0.01
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (28 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:4771 original size:113 final size:112
Alignment explanation
Indices: 4400--5916 Score: 2110
Period size: 113 Copynumber: 13.3 Consensus size: 112
4390 ACAGTGGTGA
* * *
4400 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTGACGTGCGTGGGCTTT
1 TTTG-AAAGGG-TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGAC-T-TGTGGGCTTT
** * * *
4465 GAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
60 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
4518 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTTAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAA
*
4583 GGAGTGCCACTGACTTGTGTGAGCTTTAAAAGGGTGCCACTGACTTGTGGGC
64 GG-GTGCCACTGACTTGTG-G-GCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
4635 TTTGAAA-GGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAGG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
4699 GTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGGC
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT-GGGC
* * *
4747 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGCGCCACTGATTTGTGGGCTTTGAAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAA
* *
4812 GAGTGCCACTGACTT-TGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
64 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * *
4860 TTTGAAAGGGTGCCATTGACTTGTGGTCTTTGAAAAGAGTGCCACTGATTTGTGGGGCTTTGAAA
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGT-GGGCTTTG-AA
*
4925 AGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGC
63 AGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGC
* * *
4976 TTTGAAAGGGTGCCA-TAACTTGTGGGCTCTGAAAGGGGTGCCACTGAGTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAG
*
5040 GGTGCCACTGAGTTGTGGGCTTTGAAAGAGTAGGTG-CACTGACTTGTGGTGC
65 GGTGCCACTGACTTGTGGGCTTTG-AA-AG--GGTGCCACTGACTTGTGG-GC
*
5092 TTTGAAAGGAGTGCCACTAACTT-TGGGCTTTGAAAGGAGTGCCACTGACCTTGTGGGCTTTGAA
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGA-CTTGTGGGCTTTGAA
* * * * * *
5156 AGGGTGCCACTGAATTGTGGGCTTCGCAATGGTGCTACTGACTATGTGCTGC
63 AGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT-TGTG-GGC
* *
5208 TTCTGAAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAG
1 TT-TGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
*
5273 GGTGCCACT---TTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
65 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
5318 TTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA-G
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
*
5382 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
66 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
5429 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAA
5494 -GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
64 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
5542 TTTGAAA-GGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAG
*
5606 GAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
65 G-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
5655 TTTGAAAGGAGTGCCACTGA-TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
1 TTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
*
5719 GAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
65 G-GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
5768 TTTG-AA-GGTGCCACTGACTTGT-GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
1 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
* *
5830 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
66 GTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
*
5878 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGG
5917 ATGAACATTC
Statistics
Matches: 1283, Mismatches: 74, Indels: 88
0.89 0.05 0.06
Matches are distributed among these distances:
108 9 0.01
109 81 0.06
110 81 0.06
111 127 0.10
112 77 0.06
113 344 0.27
114 169 0.13
115 129 0.10
116 129 0.10
117 89 0.07
118 48 0.04
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (112 bp):
TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG
GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
Found at i:7151 original size:1 final size:1
Alignment explanation
Indices: 7147--7207 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
7137 TTTTTTGCTA
* * * * * * *
7147 TTTTTTCTTTTTTTGTTTTTTGTTTTGTTTTTTTTTTGTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7208 GGGTGTAAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:7160 original size:23 final size:21
Alignment explanation
Indices: 7134--7208 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 21
7124 GACCCTTCTA
*
7134 TTTTTTTTTGCTATTTTTTCTTT
1 TTTTTTTTTG-T-TTTTTTGTTT
* *
7157 TTTTGTTTT-TTGTTTTGTTT
1 TTTTTTTTTGTTTTTTTGTTT
* *
7177 TTTTTTTGTGTTTTTTTTTGTT
1 TTTTTTTTTGTTTTTTTGT-TT
7199 TTTTTTTTTG
1 TTTTTTTTTG
7209 GGTGTAAAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 15 0.36
21 8 0.19
22 11 0.26
23 8 0.19
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTGTTTTTTTGTTT
Found at i:7165 original size:25 final size:25
Alignment explanation
Indices: 7137--7206 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 25
7127 CCTTCTATTT
7137 TTTTTTGCTATTT-TTTCTTTTTT-TG
1 TTTTTTG-T-TTTGTTTCTTTTTTGTG
*
7162 TTTTTTGTTTTGTTTTTTTTTTGTG
1 TTTTTTGTTTTGTTTCTTTTTTGTG
*
7187 -TTTTT-TTTTGTTTTTTTTTT
1 TTTTTTGTTTTGTTTCTTTTTT
7207 TGGGTGTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 18 0.43
24 15 0.36
25 9 0.21
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (25 bp):
TTTTTTGTTTTGTTTCTTTTTTGTG
Found at i:7174 original size:12 final size:11
Alignment explanation
Indices: 7154--7206 Score: 88
Period size: 12 Copynumber: 4.6 Consensus size: 11
7144 CTATTTTTTC
7154 TTTTTTTGTTT
1 TTTTTTTGTTT
7165 TTTGTTTTGTTT
1 TTT-TTTTGTTT
7177 TTTTTTTGTGTT
1 TTTTTTTGT-TT
7189 TTTTTTTGTTT
1 TTTTTTTGTTT
7200 TTTTTTT
1 TTTTTTT
7207 TGGGTGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.45
12 22 0.55
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:7207 original size:12 final size:12
Alignment explanation
Indices: 7149--7208 Score: 86
Period size: 12 Copynumber: 5.0 Consensus size: 12
7139 TTTTGCTATT
7149 TTTTCTTTTTTTG
1 TTTT-TTTTTTTG
*
7162 TTTTTTGTTTTG
1 TTTTTTTTTTTG
7174 -TTTTTTTTTTG
1 TTTTTTTTTTTG
*
7185 TGTTTTTTTTTG
1 TTTTTTTTTTTG
7197 TTTTTTTTTTTG
1 TTTTTTTTTTTG
7209 GGTGTAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
11 10 0.24
12 28 0.67
13 4 0.10
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.87
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:20301 original size:22 final size:23
Alignment explanation
Indices: 20273--20328 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
20263 TGGACATGTT
20273 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
20295 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
20318 AAAAATGCATG
1 AAAAATGCATG
20329 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:21286 original size:20 final size:20
Alignment explanation
Indices: 21239--21313 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
21229 AAAAAGACAT
*
21239 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
21258 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
21279 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
21299 AATGCATCGATACAT
1 AATGTATCGATACAT
21314 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:21308 original size:40 final size:39
Alignment explanation
Indices: 21236--21313 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
21226 GGTAAAAAGA
* * *
21236 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATACATCGATACATT
* *
21275 CATACATGTATCGATATATTGAAAAATGCATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATACATCGATACAT
21314 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATACATCGATACATT
Found at i:21594 original size:17 final size:17
Alignment explanation
Indices: 21572--21606 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21562 TTAGATTAAC
21572 TTTTAAAAAAATAAATA
1 TTTTAAAAAAATAAATA
*
21589 TTTTAAAAATATAAATA
1 TTTTAAAAAAATAAATA
21606 T
1 T
21607 CCTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTTAAAAAAATAAATA
Found at i:21789 original size:2 final size:2
Alignment explanation
Indices: 21782--21868 Score: 140
Period size: 2 Copynumber: 44.0 Consensus size: 2
21772 GTAAAGTTTA
*
21782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
21824 AT AT GT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21865 AT AT
1 AT AT
21869 CATAATAAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22223 original size:15 final size:15
Alignment explanation
Indices: 22164--22223 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
22154 TATTAATTAT
*
22164 ATAAATATAAATATAAC
1 ATAAATAT-TATAT-AC
* *
22181 ATTAATATTA-ATAT
1 ATAAATATTATATAC
* *
22195 ATAAAAATTTTATAC
1 ATAAATATTATATAC
22210 ATAAATATTATATA
1 ATAAATATTATATA
22224 TGTATGAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
14 8 0.24
15 17 0.52
16 1 0.03
17 7 0.21
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATATTATATAC
Found at i:22813 original size:63 final size:64
Alignment explanation
Indices: 22713--22839 Score: 193
Period size: 63 Copynumber: 2.0 Consensus size: 64
22703 ATTTCATATC
*
22713 TTAAGAATATTAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAGGAGTTATGTAA
1 TTAAGAATATTAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTAA
* * ***
22777 TTAAGAATATT-CAAAAAAAATCATTTGTCCTTATAAATAAACTCTTTTATAAGAGTTATGTAA
1 TTAAGAATATTAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTAA
22840 AATTTATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 46 0.81
64 11 0.19
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (64 bp):
TTAAGAATATTAAAAAAAAAACCATTTGTCCTTATAAATAAACTCCCATATAAGAGTTATGTAA
Found at i:27415 original size:24 final size:24
Alignment explanation
Indices: 27383--27433 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
27373 AATGTTTGAT
27383 AAAAAAGGGGGGA-GTCGAGAAAA
1 AAAAAAGGGGGGAGGTCGAGAAAA
*
27406 AAAAAGAGGGGGGAGGTTGAGAAAA
1 AAAAA-AGGGGGGAGGTCGAGAAAA
27431 AAA
1 AAA
27434 TCAAAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 12 0.48
ACGTcount: A:0.53, C:0.02, G:0.39, T:0.06
Consensus pattern (24 bp):
AAAAAAGGGGGGAGGTCGAGAAAA
Found at i:27822 original size:14 final size:14
Alignment explanation
Indices: 27803--27845 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
27793 TCCTAGTTAG
27803 ATAAGAAAGAAAGA
1 ATAAGAAAGAAAGA
27817 ATAAGAAAGAAAGA
1 ATAAGAAAGAAAGA
*
27831 AGATAGAGAAGAAAG
1 ATA-AGA-AAGAAAG
27846 GAAGAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 16 0.62
15 3 0.12
16 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.26, T:0.07
Consensus pattern (14 bp):
ATAAGAAAGAAAGA
Found at i:31177 original size:16 final size:17
Alignment explanation
Indices: 31134--31182 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
31124 TTAATTAAAA
31134 ATTTAATATTTAATTATT
1 ATTTAATATTT-ATTATT
31152 -TTTAATATTTATT-TT
1 ATTTAATATTTATTATT
*
31167 ATTTTATATTTATTAT
1 ATTTAATATTTATTAT
31183 CACAATATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 15 0.54
17 11 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTAATATTTATTATT
Found at i:31610 original size:18 final size:15
Alignment explanation
Indices: 31575--31603 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31565 ATTTTTATGA
31575 TTTAATATATATATC
1 TTTAATATATATATC
31590 TTTAAT-TATATATC
1 TTTAATATATATATC
31604 ATTCTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATATATATATC
Found at i:32624 original size:32 final size:32
Alignment explanation
Indices: 32599--32659 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
32589 TCAGGTTCTT
*
32599 TCGAGTTCGAGCTTTTTCGGATTCAGACTTTC
1 TCGAGTTCGAGCTTTCTCGGATTCAGACTTTC
* *
32631 TCGGGTTCGAGCTTTCTCGGATTCGGACT
1 TCGAGTTCGAGCTTTCTCGGATTCAGACT
32660 ATTTCAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (32 bp):
TCGAGTTCGAGCTTTCTCGGATTCAGACTTTC
Found at i:33606 original size:21 final size:20
Alignment explanation
Indices: 33568--33608 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
33558 TCGAATTGAT
33568 TTAAAATATTTATTTATTTA
1 TTAAAATATTTATTTATTTA
33588 TTAAAATAATATT-TTTATTTA
1 TTAAAAT-AT-TTATTTATTTA
33609 AATTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 10 0.53
22 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAAAATATTTATTTATTTA
Found at i:33625 original size:27 final size:25
Alignment explanation
Indices: 33576--33626 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
33566 ATTTAAAATA
33576 TTTATTTATTTATTAAAATAATATT
1 TTTATTTATTTATTAAAATAATATT
33601 TTTATTTAAATTTAATTAAAA-AATAT
1 TTTATTT--ATTT-ATTAAAATAATAT
33627 AAATATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.30
27 9 0.39
28 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTATTTATTTATTAAAATAATATT
Found at i:37412 original size:201 final size:201
Alignment explanation
Indices: 37029--38169 Score: 1392
Period size: 201 Copynumber: 5.7 Consensus size: 201
37019 AACTTCAATG
* * * *
37029 GCATCAAAGATGTAATAAACAATGACTTCA-TTTTATTTAATATCAAAATAAACATATACAAGCA
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
* * * * * ** * * *
37093 AACAAGATTCATAAATATGAACATTTCTAAGAGGT--T-TGATGCAAGAATCAAAACCTTTACAA
66 CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATC--AACCTTCACGA
* * *
37155 ACT--TTCACTTACACATTAGAATAAATGATCAACTGATTAAAGGCTTTCATTTCGAGCACAAAA
129 ACTCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAA
* **
37218 CTTTGACA
194 CCTCAACA
* * * * * *
37226 GCATCAAAGATATAACGAACAATGACTTCAATTTTATTTTATATCAAAATAAACATATACAACCA
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
* * * * *
37291 CACAAAATTCATAAATATAAACATTTCTAGGAGGTCCTACAATGCAAGAATCAACCTTCATGAAC
66 CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAAC
** *
37356 TC-TTCAACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTTGTTTCGAGCAAAAAAC
131 TCATTC-ACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAAC
37420 CTCAACA
195 CTCAACA
* * *
37427 GCATCAAAGATGCAATGAAGAATGACTTCACTTTTAGTTAATATCAAAATGAACATATACAA-C-
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
* * * ** *
37490 CAC-AAATTCATTAATATTAGCATTTCTATGAGGTCCTATGACACAAGAATCAACCTTCACGAAC
66 CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAAC
* * *
37554 TCTTTCACTTACAAATTAGAATAAATGATTAACTGACTAAATGCTTTTATTTCGAGCA-AAAATC
131 TCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAA-C
37618 CTCAACA
195 CTCAACA
* * * **
37625 GCATCAAAAATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACAAATACAATGG
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
* * * *
37690 CACGAAATTCATGAATATGAGCA-TT-TAGGAGGTCCTAAAACGCAAGAATCAACCTTTATGAAC
66 CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAAC
*
37753 TCATTCACTTACAAATTAGAATAAATAATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAACC
131 TCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAACC
37818 TCAACA
196 TCAACA
* * ** * * * *
37824 GCATTAACGATGTAATGAACCCTGACTTCACTTTTAATTAATATCAAAA-AGAGCACATACAACT
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATA-AACATATACAACC
* * * * *
37888 GTACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATCAACCTTTACGAG
65 GCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAA
* * * *
37953 CTCATTCACTTACAAATTAAAATAAATAATTAACTGACTAAAGGCTTTAATTTCGAGCAGAAAAC
130 CTCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAAC
38018 CTCAACA
195 CTCAACA
*** * *
38025 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAACGGAAGATATACAACTG
1 GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
* * * * *
38090 CATAAGATTCATGAATATGAGCATTTCTAGGAGGTCTTACAATGCAAGAATCAACCTTCACGAAT
66 CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAAC
38155 TCATTCACTTACAAA
131 TCATTCACTTACAAA
38170 CCTCAACAGC
Statistics
Matches: 828, Mismatches: 100, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
197 31 0.04
198 233 0.28
199 185 0.22
200 16 0.02
201 363 0.44
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (201 bp):
GCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATAAACATATACAACCG
CACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAACGCAAGAATCAACCTTCACGAAC
TCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTCATTTCGAGCACAAAACC
TCAACA
Found at i:38059 original size:400 final size:397
Alignment explanation
Indices: 37029--38169 Score: 1429
Period size: 400 Copynumber: 2.9 Consensus size: 397
37019 AACTTCAATG
* * * *
37029 GCATCAAAGATGTAATAAACAATGACTTCA-TTTTATTTAATATCAAAATA-AACATATACAAGC
1 GCATCAAAGATGCAATGAACAATGACTTCACTTTTAATTAATATCAAAA-AGAACACATACAA-C
* * * * * ** * *
37092 AAACAAGATTCATAAATATGAACATTTCTAAGAGGT--T-TGATGCAAGAATCAAAACCTTTACA
64 -CACAA-ATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATC--AACCTTCACG
* * * *
37154 AACT--TTCACTTACACATTAGAATAAATGATCAACTGATTAAAGGCTTTCATTTCGAGCACAAA
125 AACTCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTAATTTCGAGCA-AAA
* ** * * * * * *
37217 ACTTTGACAGCATCAAAGATATAACGAACAATGACTTCAATTTTATTTTATATCAAAATAAACAT
189 ACCTCAACAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACAT
** * * *
37282 ATACAACCACACAAAATTCATAAATATAAACATTTCTAGGAGGTCCTACAATGCAAGAATCAACC
254 ATACAA-TGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAACC
* **
37347 TTCATGAACTC-TTCAACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTTGTTTCGA
318 TTCATGAACTCATTC-ACTTACAAATTAGAATAAATAATTAACTGACTAAAGGCTTTCATTTCGA
37411 GCAAAAAACCTCAACA
382 GCAAAAAACCTCAACA
* * * *
37427 GCATCAAAGATGCAATGAAGAATGACTTCACTTTTAGTTAATATCAAAATGAACATATACAACCA
1 GCATCAAAGATGCAATGAACAATGACTTCACTTTTAATTAATATCAAAAAGAACACATACAACCA
* * * * *
37492 CAAATTCATTAATATTAGCATTTCTATGAGGTCCTATGACACAAGAATCAACCTTCACGAACTCT
66 CAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATCAACCTTCACGAACTCA
* *
37557 TTCACTTACAAATTAGAATAAATGATTAACTGACTAAATGCTTTTATTTCGAGCAAAAATCCTCA
131 TTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTAATTTCGAGCAAAAA-CCTCA
* *
37622 ACAGCATCAAAAATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACAAATACAA
195 ACAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACATATACAA
* * * *
37687 TGGCACGAAATTCATGAATATGAGCA-TT-TAGGAGGTCCTAAAACGCAAGAATCAACCTTTATG
260 T-GCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAACCTTCATG
*
37750 AACTCATTCACTTACAAATTAGAATAAATAATTAACTGACTAAAGGCTTTCATTTCGAGCACAAA
324 AACTCATTCACTTACAAATTAGAATAAATAATTAACTGACTAAAGGCTTTCATTTCGAGCAAAAA
37815 ACCTCAACA
389 ACCTCAACA
* * * ** *
37824 GCATTAACGATGTAATGAACCCTGACTTCACTTTTAATTAATATCAAAAAGAGCACATACAACTG
1 GCATCAAAGATGCAATGAACAATGACTTCACTTTTAATTAATATCAAAAAGAACACATACAAC--
* * *
37889 TACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATCAACCTTTACGAGC
64 CAC-AAATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATCAACCTTCACGAAC
* *
37954 TCATTCACTTACAAATTAAAATAAATAATTAACTGACTAAAGGCTTTAATTTCGAGCAGAAAACC
128 TCATTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTAATTTCGAGCA-AAAACC
** *
38019 TCAACAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAACGGAAGATATA
192 TCAACAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACATATA
* * *
38084 CAACTGCATAAGATTCATGAATATGAGCATTTCTAGGAGGTCTTACAATGCAAGAATCAACCTTC
257 CAA-TGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAACCTTC
* *
38149 ACGAATTCATTCACTTACAAA
321 ATGAACTCATTCACTTACAAA
38170 CCTCAACAGC
Statistics
Matches: 647, Mismatches: 79, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
396 25 0.04
397 167 0.26
398 38 0.06
399 169 0.26
400 194 0.30
401 7 0.01
402 47 0.07
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (397 bp):
GCATCAAAGATGCAATGAACAATGACTTCACTTTTAATTAATATCAAAAAGAACACATACAACCA
CAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACGACACAAGAATCAACCTTCACGAACTCA
TTCACTTACAAATTAGAATAAATGATTAACTGACTAAAGGCTTTAATTTCGAGCAAAAACCTCAA
CAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAAATGAACATATACAAT
GCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAACCTTCATGAA
CTCATTCACTTACAAATTAGAATAAATAATTAACTGACTAAAGGCTTTCATTTCGAGCAAAAAAC
CTCAACA
Found at i:38292 original size:153 final size:152
Alignment explanation
Indices: 38014--38321 Score: 465
Period size: 153 Copynumber: 2.0 Consensus size: 152
38004 TTCGAGCAGA
* * * *
38014 AAACCTCAACAGCATCAAAGATGTAATGAACAATGACTTCACTTTTAGTTAATATCAAACGGAAG
1 AAACCTCAACAGCACCAAAGATGTAATGAACAATGACTTCAATTTTAGTTAATATCAAAAGGAAC
* * * *
38079 ATATACAACTGCATAAGATTCATGAATATGAGCATTTCTAGGAGGTCTTACAATGCAAGAATCAA
66 ATATACAACAGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAA
*
38144 CCTTCACGAATTCATTCACTTAC
131 -CTTCACGAACTCATTCACTTAC
* *
38167 AAACCTCAACAGCACCAAAGATGTAATGAACAATGACTTCAATTTTAGTTAATGTCAAAATGAAC
1 AAACCTCAACAGCACCAAAGATGTAATGAACAATGACTTCAATTTTAGTTAATATCAAAAGGAAC
* *
38232 ATATACAACAGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTATGACT-CAAGAATCA
66 ATATACAACAGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTA-CAATGCAAGAATCA
*
38296 ACTTTACGAACTCATTCACTTAC
130 ACTTCACGAACTCATTCACTTAC
38319 AAA
1 AAA
38322 TTAGAATATA
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
152 23 0.16
153 115 0.82
154 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (152 bp):
AAACCTCAACAGCACCAAAGATGTAATGAACAATGACTTCAATTTTAGTTAATATCAAAAGGAAC
ATATACAACAGCACAAAATTCATGAATATGAGCATTTCTAGGAGGTCCTACAATGCAAGAATCAA
CTTCACGAACTCATTCACTTAC
Found at i:39760 original size:22 final size:23
Alignment explanation
Indices: 39735--39796 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
39725 ATTATTAACA
39735 ATAAAAATATTTAATAT-TTAAT
1 ATAAAAATATTTAATATATTAAT
*
39757 ATAAAAA-ATATTAAAATATTAAT
1 ATAAAAATAT-TTAATATATTAAT
*
39780 ATAAAATTATTTTAATA
1 ATAAAAATA-TTTAATA
39797 ATATCAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 13 0.39
23 11 0.33
24 6 0.18
25 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAAATATTTAATATATTAAT
Found at i:39763 original size:23 final size:23
Alignment explanation
Indices: 39737--39785 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
39727 TATTAACAAT
*
39737 AAAAATATT-TAATATTTAATATA
1 AAAAATATTAAAATA-TTAATATA
39760 AAAAATATTAAAATATTAATATA
1 AAAAATATTAAAATATTAATATA
39783 AAA
1 AAA
39786 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAATATTAAAATATTAATATA
Found at i:39808 original size:15 final size:14
Alignment explanation
Indices: 39788--39867 Score: 54
Period size: 15 Copynumber: 5.5 Consensus size: 14
39778 ATATAAAATT
39788 ATTTTAATAATATCA
1 ATTTTAATAATAT-A
* * *
39803 ATTTTAATATTTTT
1 ATTTTAATAATATA
* *
39817 ATTTTAAATATTATT
1 ATTTT-AATAATATA
39832 ATTTTAATAATA-A
1 ATTTTAATAATATA
* *
39845 ATTATAATACTATCA
1 ATTTTAATAATAT-A
39860 TATTTTAA
1 -ATTTTAA
39868 ATTTAAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
13 10 0.19
14 11 0.21
15 25 0.48
16 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:39864 original size:44 final size:43
Alignment explanation
Indices: 39785--39869 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 43
39775 TTAATATAAA
* **
39785 ATTATTTTAATAATATCAATTTTAATATTTTTATTTTAAATATT
1 ATTATTTTAATAATA-CAATTATAATATTCATATTTTAAATATT
39829 ATTATTTTAATAATA-AATTATAATACTATCATATTTTAAAT
1 ATTATTTTAATAATACAATTATAATA-T-TCATATTTTAAAT
39870 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 9 0.25
43 1 0.03
44 26 0.72
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (43 bp):
ATTATTTTAATAATACAATTATAATATTCATATTTTAAATATT
Found at i:40030 original size:17 final size:17
Alignment explanation
Indices: 39990--40032 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39980 AAAAATTAAT
*
39990 ATTTTAATAGTATATAA
1 ATTTTAATAGTAGATAA
*
40007 ATATTAATAG-AGATAA
1 ATTTTAATAGTAGATAA
40023 CATTTTAATA
1 -ATTTTAATA
40033 ATTATTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (17 bp):
ATTTTAATAGTAGATAA
Found at i:40065 original size:16 final size:19
Alignment explanation
Indices: 40027--40066 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
40017 AGATAACATT
*
40027 TTAATAATTATTACTATAT
1 TTAATAATTATTACTATAA
40046 TTAA-AATT-TTA-TATAA
1 TTAATAATTATTACTATAA
40062 TTAAT
1 TTAAT
40067 TTTTTAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 4 0.21
19 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTAATAATTATTACTATAA
Found at i:40174 original size:21 final size:22
Alignment explanation
Indices: 40135--40176 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40125 ATGTTAAATA
* *
40135 TTAAAATATTACTATTTTAATT
1 TTAAAATATTAATAATTTAATT
40157 TTAAAA-ATTAATAATTTAAT
1 TTAAAATATTAATAATTTAAT
40177 GAAAAATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATATTAATAATTTAATT
Found at i:40263 original size:15 final size:15
Alignment explanation
Indices: 40243--40289 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
40233 TATTTAAAAA
*
40243 TAATAAAATCATATT
1 TAATAAAATAATATT
*
40258 TAATAATAATTATA-T
1 TAATAA-AATAATATT
40273 TAATATAAATAATATT
1 TAATA-AAATAATATT
40289 T
1 T
40290 TAATCATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAAAATAATATT
Found at i:40292 original size:32 final size:30
Alignment explanation
Indices: 40243--40303 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
40233 TATTTAAAAA
*
40243 TAATAAAATCATATTTAATAATAATTATAT
1 TAATAAAATAATATTTAATAATAATTATAT
* *
40273 TAATATAAATAATATTTTAATCATTATTATA
1 TAATA-AAATAATA-TTTAATAATAATTATA
40304 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.19
31 7 0.27
32 14 0.54
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATAAAATAATATTTAATAATAATTATAT
Found at i:40298 original size:24 final size:23
Alignment explanation
Indices: 40271--40390 Score: 83
Period size: 21 Copynumber: 5.2 Consensus size: 23
40261 TAATAATTAT
40271 ATTAATATAAATAATATTTTAATC
1 ATTAATAT-AATAATATTTTAATC
*
40295 ATT-AT-T-ATAATATTTTAAAAC
1 ATTAATATAATAATATTTT-AATC
* *
40316 ATTTATATAATCAATGTTTTAAT-
1 ATTAATATAAT-AATATTTTAATC
* *
40339 AATAA-ATAATATTATTTTAA-C
1 ATTAATATAATAATATTTTAATC
40360 TATTTAATATAATATAATATTTTAAT-
1 -A-TTAATAT-A-ATAATATTTTAATC
40386 ATTAA
1 ATTAA
40391 ATATTCTGAT
Statistics
Matches: 75, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
20 10 0.13
21 14 0.19
22 9 0.12
23 9 0.12
24 13 0.17
25 9 0.12
26 11 0.15
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (23 bp):
ATTAATATAATAATATTTTAATC
Found at i:40325 original size:45 final size:46
Alignment explanation
Indices: 40272--40393 Score: 135
Period size: 45 Copynumber: 2.7 Consensus size: 46
40262 AATAATTATA
*
40272 TTAATATAAATAATATTTTAATCATTATTATAATATT-TTAAAAC-AT
1 TTAATATAAATAATATTTTAAT-ATTA-AATAATATTATTAAAACTAT
* * **
40318 TT-ATAT-AATCAATGTTTTAATAATAAATAATATTATTTTAACTAT
1 TTAATATAAAT-AATATTTTAATATTAAATAATATTATTAAAACTAT
40363 TTAATATAATATAATATTTTAATATTAAATA
1 TTAATATAA-ATAATATTTTAATATTAAATA
40394 TTCTGATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
43 8 0.13
44 11 0.17
45 18 0.29
46 6 0.10
47 18 0.29
48 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (46 bp):
TTAATATAAATAATATTTTAATATTAAATAATATTATTAAAACTAT
Found at i:40380 original size:26 final size:26
Alignment explanation
Indices: 40338--40394 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
40328 AATGTTTTAA
*
40338 TAATA-AATAATATTATTTTAACTATT
1 TAATATAATAATAATATTTTAA-TATT
40364 TAATATAAT-ATAATATTTTAATATT
1 TAATATAATAATAATATTTTAATATT
*
40389 AAATAT
1 TAATAT
40395 TCTGATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 16 0.57
27 3 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATATAATAATAATATTTTAATATT
Found at i:40408 original size:14 final size:15
Alignment explanation
Indices: 40389--40436 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
40379 TTTTAATATT
*
40389 AAATATTCTGA-TTA
1 AAATATTATGATTTA
*
40403 AAATATTATTATTTA
1 AAATATTATGATTTA
*
40418 AAATATTAATGTTTTA
1 AAATATT-ATGATTTA
40434 AAA
1 AAA
40437 ATAAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 9 0.32
15 10 0.36
16 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
AAATATTATGATTTA
Found at i:40451 original size:25 final size:25
Alignment explanation
Indices: 40423--40479 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
40413 ATTTAAAATA
*
40423 TTAATGTTTTAAAAATAAATAATTT
1 TTAATATTTTAAAAATAAATAATTT
* *
40448 TTAATATTTTAATAATTAATAA--T
1 TTAATATTTTAAAAATAAATAATTT
40471 TTAATATTT
1 TTAATATTT
40480 ATATTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.34
25 19 0.66
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTAATATTTTAAAAATAAATAATTT
Found at i:40494 original size:23 final size:23
Alignment explanation
Indices: 40415--40479 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 23
40405 ATATTATTAT
* *
40415 TTAA-AATATTAATGTTTTAAAAA
1 TTAATAAT-TTAATATTTTAATAA
*
40438 TAAATAATTTTTAATATTTTAATAA
1 TTAATAA--TTTAATATTTTAATAA
40463 TTAATAATTTAATATTT
1 TTAATAATTTAATATTT
40480 ATATTAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 13 0.37
24 2 0.06
25 19 0.54
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAATAATTTAATATTTTAATAA
Found at i:40873 original size:19 final size:18
Alignment explanation
Indices: 40849--40889 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
40839 AAATTTTAAT
40849 TATTTATATATTTGTATTA
1 TATTTATATATTT-TATTA
*
40868 TATTTATGTATTTTATTA
1 TATTTATATATTTTATTA
40886 TATT
1 TATT
40890 ATAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TATTTATATATTTTATTA
Found at i:41233 original size:16 final size:17
Alignment explanation
Indices: 41212--41244 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41202 AAAATTACAT
41212 AAAATTGT-AATAATAA
1 AAAATTGTAAATAATAA
*
41228 AAAATTTTAAATAATAA
1 AAAATTGTAAATAATAA
41245 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTGTAAATAATAA
Found at i:41427 original size:6 final size:6
Alignment explanation
Indices: 41400--41445 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
41390 ATTTACGTTA
*
41400 TTAAATT TTAAAA TTAAA- TTAAAT TT-AAT TT-AAT TTAAAT TTAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
41446 AGTTAACTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
5 15 0.42
6 16 0.44
7 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:41427 original size:11 final size:11
Alignment explanation
Indices: 41399--41445 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
41389 AATTTACGTT
41399 ATTAAATTTTAAA
1 ATTAAA-TTT-AA
41412 ATTAAA-TTAA
1 ATTAAATTTAA
*
41422 ATTTAATTTAA
1 ATTAAATTTAA
*
41433 TTTAAATTTAA
1 ATTAAATTTAA
41444 AT
1 AT
41446 AGTTAACTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 7 0.24
11 16 0.55
13 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:41437 original size:16 final size:16
Alignment explanation
Indices: 41399--41443 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
41389 AATTTACGTT
*
41399 ATTAAATTTTAAAATTAA
1 ATTAAA-TTT-AATTTAA
41417 ATTAAATTTAATTTAA
1 ATTAAATTTAATTTAA
*
41433 TTTAAATTTAA
1 ATTAAATTTAA
41444 ATAGTTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.64
17 3 0.12
18 6 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAAATTTAATTTAA
Found at i:42116 original size:16 final size:16
Alignment explanation
Indices: 42097--42167 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
42087 TCTGAATTCG
42097 AAATAATTCTAAATTA
1 AAATAATTCTAAATTA
42113 AAATAATT-TAAATCTA
1 AAATAATTCTAAAT-TA
* * *
42129 AAGTGATCCCT-AATTA
1 AAATAAT-TCTAAATTA
*
42145 AAATAA-TATAAATTTA
1 AAATAATTCTAAA-TTA
42161 AAATAAT
1 AAATAAT
42168 CAATTCAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.02
15 7 0.17
16 30 0.71
17 3 0.07
18 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATAATTCTAAATTA
Found at i:43048 original size:12 final size:12
Alignment explanation
Indices: 43033--43057 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43023 TATTATATCA
43033 ATATTGATTGGT
1 ATATTGATTGGT
43045 ATATTGATTGGT
1 ATATTGATTGGT
43057 A
1 A
43058 CATATCAGTT
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (12 bp):
ATATTGATTGGT
Found at i:43184 original size:14 final size:15
Alignment explanation
Indices: 43156--43189 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43146 TGAGAATATG
*
43156 ATTTTGATTTTTTTA
1 ATTTTGATTTATTTA
43171 ATTTT-ATTTATTTA
1 ATTTTGATTTATTTA
43185 ATTTT
1 ATTTT
43190 TAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTGATTTATTTA
Found at i:43196 original size:11 final size:11
Alignment explanation
Indices: 43165--43205 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
43155 GATTTTGATT
43165 TTTTTAATT--
1 TTTTTAATTAA
*
43174 TTATTTATTTAA
1 TT-TTTAATTAA
43186 TTTTTAATTAA
1 TTTTTAATTAA
43197 TTTTTAATT
1 TTTTTAATT
43206 TTTTTATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 2 0.07
10 6 0.22
11 17 0.63
12 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTAATTAA
Found at i:43838 original size:20 final size:21
Alignment explanation
Indices: 43784--43838 Score: 51
Period size: 24 Copynumber: 2.5 Consensus size: 21
43774 CTGACCAGTA
*
43784 AATTAAT-ACTTATATTTTTT
1 AATTAATAAATTATATTTTTT
43804 AATTAAATTTAAAATTATA-TTTTT
1 AATT-AA--T-AAATTATATTTTTT
43828 AATTAATAAAT
1 AATTAATAAAT
43839 AATAATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
20 8 0.28
21 3 0.10
23 3 0.10
24 9 0.31
25 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AATTAATAAATTATATTTTTT
Found at i:44105 original size:2 final size:2
Alignment explanation
Indices: 44098--44145 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
44088 AAAAACAATG
44098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44140 AT AT AT
1 AT AT AT
44146 CCCCTCAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44629 original size:20 final size:21
Alignment explanation
Indices: 44595--44639 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
44585 AAACTTTTAA
*
44595 TTTTATATTTATTTTA-ATAAT
1 TTTTAAATTTATTTTATA-AAT
44616 TTTTAAATTT-TTTTATAAAT
1 TTTTAAATTTATTTTATAAAT
44636 TTTT
1 TTTT
44640 TTATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAAATTTATTTTATAAAT
Found at i:44649 original size:13 final size:12
Alignment explanation
Indices: 44615--44646 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
44605 ATTTTAATAA
44615 TTTT-TAAATTT
1 TTTTATAAATTT
44626 TTTTATAAATTT
1 TTTTATAAATTT
44638 TTTTATAAA
1 TTTTATAAA
44647 ATTAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTATAAATTT
Found at i:46606 original size:13 final size:13
Alignment explanation
Indices: 46577--46611 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
46567 TCTGATTATG
46577 ATTTAAATTTTTT
1 ATTTAAATTTTTT
46590 -TTTAAATTTTTT
1 ATTTAAATTTTTT
46602 ATTTAAATTT
1 ATTTAAATTT
46612 GAATTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTAAATTTTTT
Found at i:50077 original size:2 final size:2
Alignment explanation
Indices: 50070--50094 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50060 CATCTATCTA
50070 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
50095 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:50099 original size:2 final size:2
Alignment explanation
Indices: 50094--50120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50084 TCTCTCTCTC
50094 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
50121 GAATGGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51227 original size:2 final size:2
Alignment explanation
Indices: 51220--51249 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51210 TAAGGTGATT
51220 TA TA 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 TA TA
51250 AGTAACAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51439 original size:22 final size:22
Alignment explanation
Indices: 51395--51440 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
51385 AAAATTTAAA
* *
51395 AATATTTTTATATTTTTATATT
1 AATATTTATATATTTATATATT
51417 AATATTTATATAGTTTATA-ATT
1 AATATTTATATA-TTTATATATT
51439 AA
1 AA
51441 AATTAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AATATTTATATATTTATATATT
Found at i:52180 original size:2 final size:2
Alignment explanation
Indices: 52173--52209 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
52163 TCACTACCAG
52173 AT AT AT AT 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 AT AT AT AT A
52210 GGATTCTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52426 original size:3 final size:3
Alignment explanation
Indices: 52418--52450 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
52408 AACAAAACCC
52418 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52451 GTCACAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:53309 original size:31 final size:31
Alignment explanation
Indices: 53244--53305 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
53234 TTGTCAAATT
53244 ATTAAGGATTATAATTGTCTAATTATTTTAA
1 ATTAAGGATTATAATTGTCTAATTATTTTAA
* *
53275 ATTAAGGGTTGTAATTGTC-AATTATTTTAA
1 ATTAAGGATTATAATTGTCTAATTATTTTAA
53305 A
1 A
53306 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (31 bp):
ATTAAGGATTATAATTGTCTAATTATTTTAA
Found at i:53310 original size:11 final size:11
Alignment explanation
Indices: 53294--53319 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53284 TGTAATTGTC
53294 AATTATTTTAA
1 AATTATTTTAA
53305 AATTATTTTAA
1 AATTATTTTAA
53316 AATT
1 AATT
53320 TTAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:54658 original size:22 final size:22
Alignment explanation
Indices: 54623--54664 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54613 ATATTTATAT
54623 ATTTTATAATTAAAT-TCAAAA
1 ATTTTATAATTAAATATCAAAA
*
54644 ATTTTAATTATTAAATATCAA
1 ATTTT-ATAATTAAATATCAA
54665 TTCAAGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTATAATTAAATATCAAAA
Found at i:56494 original size:36 final size:36
Alignment explanation
Indices: 56416--56490 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
56406 ATTAAATTCG
56416 ATTTAAATTTAATTTGATAATTATAAAATTTAAGCAA
1 ATTTAAATTTAATTTGATAATTATAAAATTTAA-CAA
*
56453 A-TTAAATTTAAATATT-ATAA-TATTAAATTTAA-AA
1 ATTTAAATTT-AAT-TTGATAATTATAAAATTTAACAA
56487 ATTT
1 ATTT
56491 TAAAAGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
34 3 0.09
35 2 0.06
36 19 0.56
37 8 0.24
38 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (36 bp):
ATTTAAATTTAATTTGATAATTATAAAATTTAACAA
Found at i:56524 original size:19 final size:20
Alignment explanation
Indices: 56502--56548 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
56492 AAAAGTTTAG
*
56502 TTAAATTTTTTAA-TTAATA
1 TTAAATTTTTTAATTTAAAA
*
56521 TTAAATATTTTAATTTAAAA
1 TTAAATTTTTTAATTTAAAA
56541 TTAAATTT
1 TTAAATTT
56549 AAATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAATTTTTTAATTTAAAA
Found at i:58203 original size:2 final size:2
Alignment explanation
Indices: 58196--58240 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
58186 GTACGGTACT
58196 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
58238 TA T
1 TA T
58241 TCTCATGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59025 original size:29 final size:27
Alignment explanation
Indices: 58978--59038 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
58968 TACTCAAATC
58978 ATTTTTTTATCATATTTTATATTATTA
1 ATTTTTTTATCATATTTTATATTATTA
* *
59005 ATTTTTTTCAT-ATTATATTTATTTTATTT
1 ATTTTTTT-ATCA-TAT-TTTATATTATTA
59034 ATTTT
1 ATTTT
59039 ATATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.31
28 5 0.17
29 15 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (27 bp):
ATTTTTTTATCATATTTTATATTATTA
Found at i:59028 original size:20 final size:20
Alignment explanation
Indices: 59000--59046 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
58990 TATTTTATAT
59000 TATTAATTTT-TTTCATATTA
1 TATTAATTTTATTT-ATATTA
* *
59020 TATTTATTTTATTTATTTTA
1 TATTAATTTTATTTATATTA
59040 TA-TAATT
1 TATTAATT
59047 ACATCGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTAATTTTATTTATATTA
Found at i:59033 original size:25 final size:25
Alignment explanation
Indices: 58980--59027 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
58970 CTCAAATCAT
*
58980 TTTTTTATCATATTTTATATTATTAA
1 TTTTTT-TCATATTATATATTATTAA
59006 TTTTTTTCATATTATAT-TTATT
1 TTTTTTTCATATTATATATTATT
59028 TTATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 10 0.48
26 6 0.29
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTTCATATTATATATTATTAA
Found at i:59286 original size:34 final size:35
Alignment explanation
Indices: 59241--59315 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
59231 ATTTTATATT
*
59241 AATA-TTTTATTTTTATAATTA-AATTTAAA-TAAA
1 AATATTTTTATTTTTA-AATAATAATTTAAATTAAA
59274 AATATTTTTATTTTTAAATAATAATTTAAATTAAA
1 AATATTTTTATTTTTAAATAATAATTTAAATTAAA
*
59309 AAAATTT
1 AATATTT
59316 ATATCCGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 8 0.22
34 19 0.51
35 10 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AATATTTTTATTTTTAAATAATAATTTAAATTAAA
Found at i:59535 original size:15 final size:14
Alignment explanation
Indices: 59517--59552 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
59507 TTAATTTTAT
59517 TTTAAATATATAGTA
1 TTTAAATATATA-TA
*
59532 TTTATATATATATA
1 TTTAAATATATATA
59546 TTTAAAT
1 TTTAAAT
59553 TTTCAAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTTAAATATATATA
Found at i:60070 original size:34 final size:32
Alignment explanation
Indices: 59974--60072 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 32
59964 AATATAATAA
*
59974 AATAAATTT-AGATATAATAATTTATGTATTTTT
1 AATAAATTTAATATATAATAATTT-T-TATTTTT
60007 AATAAATTATAATTATATTTAA-AATTTTTATTTTT
1 AATAAATT-TAA-TATA--TAATAATTTTTATTTTT
60042 ATATAAATTTAATATGATAATAATTTTTATT
1 A-ATAAATTTAATAT-ATAATAATTTTTATT
60073 ATATAAATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 15
0.78 0.01 0.21
Matches are distributed among these distances:
33 11 0.19
34 14 0.25
35 13 0.23
36 11 0.19
37 5 0.09
38 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (32 bp):
AATAAATTTAATATATAATAATTTTTATTTTT
Found at i:62233 original size:16 final size:15
Alignment explanation
Indices: 62208--62258 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
62198 TTTATATAAT
*
62208 TATTTTTAAATTTAA
1 TATTTATAAATTTAA
62223 TATTTAATAAATTTAA
1 TATTT-ATAAATTTAA
62239 -ATTT-TAAATTTTAA
1 TATTTATAAA-TTTAA
62253 TATTTA
1 TATTTA
62259 CAATTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 13 0.42
16 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATAAATTTAA
Found at i:62244 original size:23 final size:22
Alignment explanation
Indices: 62212--62254 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
62202 TATAATTATT
62212 TTTAAATTT-AATATTTAATAAA
1 TTTAAATTTAAAT-TTTAATAAA
62234 TTTAAATTTTAAATTTTAATA
1 TTTAAA-TTTAAATTTTAATA
62255 TTTACAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 10 0.53
24 3 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAATTTAAATTTTAATAAA
Found at i:62597 original size:3 final size:3
Alignment explanation
Indices: 62589--62613 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
62579 GTGTCATAAC
62589 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
62614 CGATGTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63088 original size:38 final size:37
Alignment explanation
Indices: 63002--63104 Score: 93
Period size: 38 Copynumber: 2.6 Consensus size: 37
62992 TATTCATATT
63002 GTATTAGTATATTTTATAATATTATAATTATATTTAAA
1 GTATT-GTATATTTTATAATATTATAATTATATTTAAA
* * * *
63040 GTATTTTATATTTATATAA-ATTGTAGTATATTTTTAAA
1 GTATTGTATATTT-TATAATATTATAAT-TATATTTAAA
63078 -TATTCGTATATTTGTATGTAATATTAT
1 GTATT-GTATATTT-TA--TAATATTAT
63105 TTTTTAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
37 17 0.33
38 28 0.54
40 3 0.06
41 4 0.08
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54
Consensus pattern (37 bp):
GTATTGTATATTTTATAATATTATAATTATATTTAAA
Found at i:63972 original size:14 final size:14
Alignment explanation
Indices: 63953--63979 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
63943 AGAATTTATA
63953 TAGATTATAATATG
1 TAGATTATAATATG
63967 TAGATTATAATAT
1 TAGATTATAATAT
63980 ATAGGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAGATTATAATATG
Found at i:65120 original size:2 final size:2
Alignment explanation
Indices: 65109--65150 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
65099 GAAATTCTTA
* *
65109 AT AT -T AT AT AT AT AT AT AT AT AT AA AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65150 A
1 A
65151 AATACATAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67414 original size:2 final size:2
Alignment explanation
Indices: 67407--67438 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
67397 TTCAATCTTC
*
67407 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67439 CATGCTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:68737 original size:50 final size:51
Alignment explanation
Indices: 68638--68738 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
68628 ATGAATCCTG
*
68638 AAAAACAGCTAAAAGAATCCTAGTTAATCACTAAAAAATCGATGTCTTAGA
1 AAAAACAGCTAAAAGAATCCTAGTTAATCACTAAAAAATCCATGTCTTAGA
* * *
68689 AAAAACAGCTAAAGGAATCCTAGTTAATTAC-AAAGAATCCATGTCTTAGA
1 AAAAACAGCTAAAAGAATCCTAGTTAATCACTAAAAAATCCATGTCTTAGA
68739 TTTAGCTGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 17 0.37
51 29 0.63
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (51 bp):
AAAAACAGCTAAAAGAATCCTAGTTAATCACTAAAAAATCCATGTCTTAGA
Found at i:69056 original size:21 final size:21
Alignment explanation
Indices: 69032--69072 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
69022 TTAATTATAA
* *
69032 TAAATTTTAATAATAAAAATT
1 TAAAATTTAAAAATAAAAATT
69053 TAAAATTTAAAAATAAAAAT
1 TAAAATTTAAAAATAAAAAT
69073 AATAACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATTTAAAAATAAAAATT
Found at i:72127 original size:35 final size:35
Alignment explanation
Indices: 72088--72154 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
72078 ACGTAGCATG
*
72088 AAATATA-ATAAGA-TATCAAAAATTAAATGAATCAT
1 AAATATATA-AAGACTATC-AAAATTAAAAGAATCAT
*
72123 AAATATATAAATACTATCAAAATTAAAAGAAT
1 AAATATATAAAGACTATCAAAATTAAAAGAAT
72155 TGGTCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
35 23 0.82
36 5 0.18
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.28
Consensus pattern (35 bp):
AAATATATAAAGACTATCAAAATTAAAAGAATCAT
Found at i:72631 original size:25 final size:25
Alignment explanation
Indices: 72597--72658 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
72587 TATATTATTT
*
72597 TTATTATAAT-TATATATAATAAATA
1 TTATTATAATAAATA-ATAATAAATA
*
72622 TTATTTTAATAAATAATAATAAATA
1 TTATTATAATAAATAATAATAAATA
* *
72647 TTTTTATTATAA
1 TTATTATAATAA
72659 TTAGTTGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 28 0.90
26 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATTATAATAAATAATAATAAATA
Found at i:73820 original size:17 final size:17
Alignment explanation
Indices: 73786--73868 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 17
73776 CAGTTTATAT
73786 ATTTTATTATATCATAA
1 ATTTTATTATATCATAA
* *
73803 ATTTTGATTATATTTAAAA
1 ATTTT-ATTATA-TCATAA
73822 CATCTTTATT-TAT-ATAA
1 -AT-TTTATTATATCATAA
* *
73839 ATTTTAATATATTAATAA
1 ATTTTATTATA-TCATAA
*
73857 ATTATATTATAT
1 ATTTTATTATAT
73869 AATTTTTAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.09
16 4 0.08
17 10 0.19
18 20 0.38
19 6 0.11
20 5 0.09
21 3 0.06
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTTTATTATATCATAA
Found at i:74653 original size:19 final size:17
Alignment explanation
Indices: 74629--74663 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
74619 ATAATATAAT
74629 ATTTAATTATTATTTTATG
1 ATTTAATT-TT-TTTTATG
74648 ATTTAATTTTTTTTAT
1 ATTTAATTTTTTTTAT
74664 TATTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
ATTTAATTTTTTTTATG
Found at i:75511 original size:3 final size:3
Alignment explanation
Indices: 75503--75533 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
75493 CCTTCAGCTT
*
75503 CTG CTG CTG CCG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
75534 CCTTTCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.32, T:0.29
Consensus pattern (3 bp):
CTG
Found at i:76055 original size:22 final size:22
Alignment explanation
Indices: 76027--76069 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
76017 ATTTAATAAT
*
76027 AAAATATATAAATATTATTATA
1 AAAATATATAAATAATATTATA
* *
76049 AAAATATTTTAATAATATTAT
1 AAAATATATAAATAATATTAT
76070 GAATAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATATATAAATAATATTATA
Found at i:77467 original size:16 final size:16
Alignment explanation
Indices: 77446--77479 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
77436 AATATTCATG
77446 TTATA-TTTATATTATT
1 TTATATTTTA-ATTATT
77462 TTATATTTTAATTATT
1 TTATATTTTAATTATT
77478 TT
1 TT
77480 TATAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTTTAATTATT
Found at i:79848 original size:20 final size:20
Alignment explanation
Indices: 79819--79879 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
79809 TTATATTAAA
*
79819 AATTTTAATAAATATAAAAT
1 AATTTAAATAAATATAAAAT
*
79839 AATTTAAATATAAT-TATAAT
1 AATTTAAATA-AATATAAAAT
* *
79859 AA-ATAAA-ATATATAAAAT
1 AATTTAAATAAATATAAAAT
79877 AAT
1 AAT
79880 GCCTATACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 2 0.06
18 8 0.24
19 4 0.12
20 16 0.48
21 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTAAATAAATATAAAAT
Found at i:79928 original size:2 final size:2
Alignment explanation
Indices: 79921--79955 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
79911 ATCCTAGTTA
*
79921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79956 AAAAAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:81662 original size:34 final size:33
Alignment explanation
Indices: 81581--81662 Score: 78
Period size: 33 Copynumber: 2.4 Consensus size: 33
81571 CAGAGTTCAA
* **
81581 ATAAAATATTATTTTATTTTTTAAAATTCAATTT
1 ATAAAA-ATTATTTTATTTTTTAAAATTAAAAAT
*
81615 ACTTAAAAA--ATTTTATTTTTTTAAATATAAAAAT
1 A--TAAAAATTATTTTATTTTTTAAAAT-TAAAAAT
81649 ATAAAAATTATTTT
1 ATAAAAATTATTTT
81663 TATAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
32 6 0.15
33 16 0.41
34 11 0.28
35 1 0.03
36 5 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (33 bp):
ATAAAAATTATTTTATTTTTTAAAATTAAAAAT
Found at i:81963 original size:16 final size:16
Alignment explanation
Indices: 81937--82005 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
81927 TAAAATATTA
*
81937 AATACATAATTTTAAT
1 AATAAATAATTTTAAT
*
81953 ACTAAATAATTATTAA-
1 AATAAATAATT-TTAAT
*
81969 AATAAAAAATATTTAAT
1 AATAAATAAT-TTTAAT
*
81986 AAAAATATACATTTTAAT
1 AATAA-ATA-ATTTTAAT
82004 AA
1 AA
82006 ATTATGTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 21 0.50
17 9 0.21
18 10 0.24
19 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAATAATTTTAAT
Found at i:83810 original size:4 final size:4
Alignment explanation
Indices: 83801--83830 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
83791 TCCTAATAAT
*
83801 TTTA TTTA TTTA TCTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
83831 ATGTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:83897 original size:91 final size:91
Alignment explanation
Indices: 83742--84004 Score: 438
Period size: 91 Copynumber: 2.9 Consensus size: 91
83732 ATATATATAA
* *
83742 GTAATTTTCAAAAAGATAAATTAGCAGACAAAGAAATCATAGCTATAGTTCCTAATAATTTTATT
1 GTAATTTTCAAAAAGATAAATTACCAGACAAAGAAATCATAGCTATAGTTCCAAATAATTTTATT
83807 TATTTATCTATTTATTTATTTATTAT
66 TATTTATCTATTTATTTATTTATTAT
83833 GTAATTTTCAAAAAGATAAATTACCAGACAAAGAAATCATAGCTATAGTTCCAAATAATTTTATT
1 GTAATTTTCAAAAAGATAAATTACCAGACAAAGAAATCATAGCTATAGTTCCAAATAATTTTATT
83898 TATTTATCTATTTATTTATTTATTAT
66 TATTTATCTATTTATTTATTTATTAT
* * * *
83924 ATAATTTTCAAAAAGATACATTACCAGACAAAGAACTCCATAGCTATAGTT-CATAACAATTTTA
1 GTAATTTTCAAAAAGATAAATTACCAGACAAAGAAAT-CATAGCTATAGTTCCA-AATAATTTTA
*
83988 TTTATTTATTTATTTAT
64 TTTATTTATCTATTTAT
84005 CATTGAGTTA
Statistics
Matches: 163, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
91 125 0.77
92 38 0.23
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (91 bp):
GTAATTTTCAAAAAGATAAATTACCAGACAAAGAAATCATAGCTATAGTTCCAAATAATTTTATT
TATTTATCTATTTATTTATTTATTAT
Found at i:83901 original size:4 final size:4
Alignment explanation
Indices: 83892--83921 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
83882 TCCAAATAAT
*
83892 TTTA TTTA TTTA TCTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
83922 ATATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:85301 original size:15 final size:16
Alignment explanation
Indices: 85272--85302 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
85262 AATAAGTACC
85272 GAATAAAATATATATT
1 GAATAAAATATATATT
85288 GAATAAAA-ATATATT
1 GAATAAAATATATATT
85303 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
GAATAAAATATATATT
Found at i:85416 original size:15 final size:15
Alignment explanation
Indices: 85380--85419 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
85370 ATATAAATAT
* *
85380 TTTAAAAAATTTAAA
1 TTTAAATAATATAAA
*
85395 TTTAAATAATATAAC
1 TTTAAATAATATAAA
85410 TTTAAATAAT
1 TTTAAATAAT
85420 GTCTCTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAATAATATAAA
Found at i:85853 original size:5 final size:5
Alignment explanation
Indices: 85833--85926 Score: 82
Period size: 5 Copynumber: 17.8 Consensus size: 5
85823 TTCATATAAA
* * * *
85833 ATATAT ATATT TTATT ATATT ATAATT ATATTT AAAAT ATATTT ATATC
1 ATAT-T ATATT ATATT ATATT AT-ATT ATA-TT ATATT ATA-TT ATATT
*
85882 ATATT ATATT ATATT ATAATT ATTTT AT-TT ATATT ATAGTT ATAT
1 ATATT ATATT ATATT AT-ATT ATATT ATATT ATATT ATA-TT ATAT
85927 AATTACATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
4 4 0.05
5 42 0.58
6 27 0.37
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:85860 original size:11 final size:11
Alignment explanation
Indices: 85846--85926 Score: 73
Period size: 11 Copynumber: 7.6 Consensus size: 11
85836 TATATATTTT
85846 ATTATATTATA
1 ATTATATTATA
85857 ATTATATT-TAA
1 ATTATATTAT-A
*
85868 AATATATT-TA
1 ATTATATTATA
*
85878 TATCATATTAT-
1 -ATTATATTATA
85889 ATTATATTATA
1 ATTATATTATA
85900 ATTAT-TT-TA
1 ATTATATTATA
*
85909 TTTATATTATA
1 ATTATATTATA
*
85920 GTTATAT
1 ATTATAT
85927 AATTACATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 6 0.10
10 15 0.26
11 36 0.62
12 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTATATTATA
Found at i:85887 original size:38 final size:35
Alignment explanation
Indices: 85829--85899 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 35
85819 GCAGTTCATA
**
85829 TAAAATATATATATTTTATTATATTATAATTATATT
1 TAAAATATATATATCATATTATATTAT-ATTATATT
85865 TAAAATATATTTATATCATATTATATTATATTATA
1 TAAAATATA--TATATCATATTATATTATATTATA
85900 ATTATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 9 0.29
37 6 0.19
38 16 0.52
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (35 bp):
TAAAATATATATATCATATTATATTATATTATATT
Found at i:85936 original size:25 final size:25
Alignment explanation
Indices: 85885--85944 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
85875 TTATATCATA
* **
85885 TTATATTATATTATAATTATTTTAT
1 TTATATTATATTATAATAATTACAT
85910 TTATATTATAGTTAT-ATAATTACAT
1 TTATATTATA-TTATAATAATTACAT
85935 TTAATATTAT
1 TT-ATATTAT
85945 CAGATTTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATATTATATTATAATAATTACAT
Found at i:87250 original size:28 final size:28
Alignment explanation
Indices: 87206--87262 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
87196 CACGACACGA
* *
87206 AAAAAATAACTAAAATATAATAAGATAC
1 AAAAAATAACTAAAATATAAAAAAATAC
*
87234 AAAAAATAA-TACGAATATAAAAAAATAC
1 AAAAAATAACTA-AAATATAAAAAAATAC
87262 A
1 A
87263 TAAATATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.19
Consensus pattern (28 bp):
AAAAAATAACTAAAATATAAAAAAATAC
Found at i:87962 original size:20 final size:17
Alignment explanation
Indices: 87937--87988 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
87927 TTAAAAATTT
87937 ATTTAATATAAAATATTAAA
1 ATTTAA-AT-AAATA-TAAA
87957 ATTTAAATAAATATAAA
1 ATTTAAATAAATATAAA
* *
87974 ATAT-ATTAAATATAA
1 ATTTAAATAAATATAA
87989 TTATTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.33
17 7 0.23
18 5 0.17
19 2 0.07
20 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATAAATATAAA
Found at i:87985 original size:16 final size:16
Alignment explanation
Indices: 87964--88015 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
87954 AAAATTTAAA
87964 TAAATATAAAATATAT
1 TAAATATAAAATATAT
87980 TAAATAT--AAT-TAT
1 TAAATATAAAATATAT
*
87993 TATATAATAAAATATA-
1 TAAAT-ATAAAATATAT
88009 TAAATAT
1 TAAATAT
88016 TTATTAACGC
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.23
14 5 0.17
15 2 0.07
16 14 0.47
17 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATATAAAATATAT
Found at i:90768 original size:18 final size:19
Alignment explanation
Indices: 90733--90779 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
90723 ATTAATTTAA
* *
90733 TAAAAAATATATTAAATAT
1 TAAAAAATAAAATAAATAT
90752 TAAAAAATAAAAT-AATAT
1 TAAAAAATAAAATAAATAT
90770 TAAAATAATA
1 TAAAA-AATA
90780 CTTAACCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAATAAAATAAATAT
Found at i:91302 original size:6 final size:6
Alignment explanation
Indices: 91291--91317 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
91281 TACATACTGC
91291 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
91318 CTCAATCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:92024 original size:11 final size:12
Alignment explanation
Indices: 91993--92025 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
91983 AAGAAAATGA
91993 AAAATTATTTTT
1 AAAATTATTTTT
92005 AAAATTATTTTT
1 AAAATTATTTTT
*
92017 TAAA-TATTT
1 AAAATTATTT
92026 ATATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AAAATTATTTTT
Found at i:92420 original size:18 final size:20
Alignment explanation
Indices: 92399--92441 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
92389 TATTTTAAAA
92399 TGTATATTTTTA-ATTCA-T
1 TGTATATTTTTATATTCATT
*
92417 TGTAT-TTTTTATTTTCATT
1 TGTATATTTTTATATTCATT
92436 TGTATA
1 TGTATA
92442 GTGATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TGTATATTTTTATATTCATT
Found at i:92956 original size:3 final size:3
Alignment explanation
Indices: 92948--92988 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
92938 TTCATCTTTA
92948 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
92989 ATTGATGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93801 original size:5 final size:5
Alignment explanation
Indices: 93793--93865 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
93783 CAATTCAATA
* * *
93793 AATTT AATTT AATTT AATTT AAATTG ATTTT AATAT AATATT --TTAT
1 AATTT AATTT AATTT AATTT -AATTT AATTT AATTT AAT-TT AATT-T
* * *
93839 TATTT AAATT AATAT AATTT AATTT AA
1 AATTT AATTT AATTT AATTT AATTT AA
93866 ATTATTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 42 0.81
6 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:93851 original size:20 final size:18
Alignment explanation
Indices: 93828--93875 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
93818 GATTTTAATA
93828 TAATATTTTATTATTTAAAT
1 TAATATTTTA--ATTTAAAT
93848 TAATATAATTTAATTTAAAT
1 TAATAT--TTTAATTTAAAT
*
93868 TATTATTT
1 TAATATTT
93876 ATATAGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 19 0.76
22 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATATTTTAATTTAAAT
Found at i:93908 original size:51 final size:47
Alignment explanation
Indices: 93794--93908 Score: 110
Period size: 51 Copynumber: 2.3 Consensus size: 47
93784 AATTCAATAA
*
93794 ATTT-AATTTAATTTAATTTAAATTGATTTTAATATAATATTTTATT
1 ATTTAAATTTAATTTAATTTAAATTGATTTTAATATAAAATTTTATT
93840 ATTTAAATTAATATAATTTAATTTAAATT-ATTATTTATATAGTAAAAATATTT-TT
1 ATTTAAA-T--T-TAATTTAATTTAAATTGA-T-TTTA-ATA-T-AAAAT-TTTATT
93895 ATTTAAATTTAATT
1 ATTTAAATTTAATT
93909 ATAAAAATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
46 4 0.07
47 2 0.04
48 1 0.02
50 2 0.04
51 22 0.39
52 5 0.09
53 3 0.05
54 2 0.04
55 13 0.23
56 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (47 bp):
ATTTAAATTTAATTTAATTTAAATTGATTTTAATATAAAATTTTATT
Found at i:93916 original size:14 final size:14
Alignment explanation
Indices: 93899--93946 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
93889 ATTTTTATTT
93899 AAATTTAATTATAA
1 AAATTTAATTATAA
93913 AAATATTAA-TATAA
1 AAAT-TTAATTATAA
* * *
93927 AAATATATTTTTAA
1 AAATTTAATTATAA
93941 AAATTT
1 AAATTT
93947 TAATATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 22 0.79
15 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTAATTATAA
Found at i:93930 original size:28 final size:28
Alignment explanation
Indices: 93899--93953 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
93889 ATTTTTATTT
*
93899 AAATTTAATTATAAAAATATTAATATAA
1 AAATATAATTATAAAAATATTAATATAA
* * *
93927 AAATATATTTTTAAAAATTTTAATATA
1 AAATATAATTATAAAAATATTAATATA
93954 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATAATTATAAAAATATTAATATAA
Found at i:93978 original size:23 final size:22
Alignment explanation
Indices: 93941--93991 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
93931 ATATTTTTAA
* *
93941 AAATTTTAATATATTTAAATAAT
1 AAATTTAAATATATTCAAAT-AT
* *
93964 AAATTTAAATTTATTCAAATTT
1 AAATTTAAATATATTCAAATAT
93986 AAATTT
1 AAATTT
93992 GAGTTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTAAATATATTCAAATAT
Found at i:94494 original size:2 final size:2
Alignment explanation
Indices: 94478--94513 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
94468 ATAATTATTC
94478 AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94514 GCCTACTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94945 original size:19 final size:18
Alignment explanation
Indices: 94905--94949 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
94895 ATAATTTATA
* *
94905 TATTTATATTATATTTATT
1 TATTT-TATCATATTTAAT
94924 TATTTTATCATATTATAAT
1 TATTTTATCATATT-TAAT
94943 TATTTTA
1 TATTTTA
94950 AAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATCATATTTAAT
Found at i:95054 original size:22 final size:21
Alignment explanation
Indices: 95029--95071 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
95019 TATGTCGTGT
*
95029 TATATATTTTATACTTTATATA
1 TATATATATTATA-TTTATATA
95051 TATATATATTATATTTATATA
1 TATATATATTATATTTATATA
95072 ATTGTATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATATATATTATATTTATATA
Done.