Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold284
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: 883815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 12436 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2958 original size:20 final size:21
Alignment explanation
Indices: 2909--2958 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2899 ATGATTTTCT
2909 TATATTATTAATAAAATATATA
1 TATATTA-TAATAAAATATATA
* **
2931 TATGTTATAATAAGGTATA-A
1 TATATTATAATAAAATATATA
2951 TATATTAT
1 TATATTAT
2959 TATGTTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 10 0.42
22 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATTATAATAAAATATATA
Found at i:4543 original size:41 final size:41
Alignment explanation
Indices: 4518--4713 Score: 286
Period size: 41 Copynumber: 4.8 Consensus size: 41
4508 TTTATTGCTA
4518 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
* * * * *
4559 GTGAAACATTTCAAACTTTACATCTAGTAGGCTTGACGTCG
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
* * *
4600 GTAAAACATTTCAGACTTTGCGTCTAGTAGGCTTGATGCCG
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
* *
4641 GTGAAACA-TTCAGACTTTATGTCTAGCAGGCTTGACGCCG
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
*
4681 GTGAAACATTTCAGACTTTATGTCTAGCAGGCT
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCT
4714 AAGTGCCAGT
Statistics
Matches: 138, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 36 0.26
41 102 0.74
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCG
Found at i:4706 original size:81 final size:82
Alignment explanation
Indices: 4518--4713 Score: 304
Period size: 81 Copynumber: 2.4 Consensus size: 82
4508 TTTATTGCTA
4518 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAACATTTCAAACTTTACATC
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAACATTTCAAACTTTACATC
* *
4583 TAGTAGGCTTGACGTCG
66 TAGCAGGCTTGACGCCG
* * * * **
4600 GTAAAACATTTCAGACTTTGCGTCTAGTAGGCTTGATGCCGGTGAAACA-TTCAGACTTTATGTC
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAACATTTCAAACTTTACATC
4664 TAGCAGGCTTGACGCCG
66 TAGCAGGCTTGACGCCG
*
4681 GTGAAACATTTCAGACTTTATGTCTAGCAGGCT
1 GTGAAACATTTCAGACTTTACGTCTAGCAGGCT
4714 AAGTGCCAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 56 0.55
82 46 0.45
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (82 bp):
GTGAAACATTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAACATTTCAAACTTTACATC
TAGCAGGCTTGACGCCG
Found at i:16174 original size:7 final size:7
Alignment explanation
Indices: 16162--16229 Score: 84
Period size: 7 Copynumber: 9.9 Consensus size: 7
16152 TTCTAAAATA
16162 CATTTCC
1 CATTTCC
16169 CATTTCC
1 CATTTCC
16176 CATTTCC
1 CATTTCC
*
16183 CACTTCC
1 CATTTCC
*
16190 CACTTCC
1 CATTTCC
16197 CATTTCC
1 CATTTCC
* *
16204 C-CTCCC
1 CATTTCC
16210 CATTTCC
1 CATTTCC
*
16217 TATTTCC
1 CATTTCC
16224 CATTTC
1 CATTTC
16230 TCCGTGCATC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
6 4 0.08
7 48 0.92
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (7 bp):
CATTTCC
Found at i:16484 original size:6 final size:6
Alignment explanation
Indices: 16475--16510 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
16465 TCTTTTTGCT
*
16475 TTTTGA TTTTGA TTTTAA TTTTGA TTTTGAA TTTTG
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTG-A TTTTG
16511 CTGTTAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:16810 original size:128 final size:128
Alignment explanation
Indices: 16582--16836 Score: 465
Period size: 128 Copynumber: 2.0 Consensus size: 128
16572 AGAATTTTGG
16582 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
1 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
*
16647 GCAGTCAAAGATTGTATTGACATTTTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
66 GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
* * *
16710 TTTTGATTTTAATTTTTGCTGTTAACCCTATTTCCTGTTCGAATAATTAGACTAATAGGTTTAAA
1 TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
*
16775 GCAGTCAAAGATTGTGTTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATG
66 GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATG
16837 CTTAAAATGA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 122 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (128 bp):
TTTTGATTTTAATTTTTACTATTAACCCTATTTCCTGTTCGAACAATTAGACTAATAGGTTTAAA
GCAGTCAAAGATTGTATTGACATATTTAACCTTTAAATGTTGCGTGTTTTAATCTTGTTATGA
Found at i:17189 original size:28 final size:28
Alignment explanation
Indices: 17156--17210 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
17146 TATTTGATTT
17156 AACTGACAGTGAGAGTGTCCTTTTGAAG
1 AACTGACAGTGAGAGTGTCCTTTTGAAG
*
17184 AACTGATAGTGAGAGTGTCCTTTTGAA
1 AACTGACAGTGAGAGTGTCCTTTTGAA
17211 CCCTTGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AACTGACAGTGAGAGTGTCCTTTTGAAG
Found at i:19229 original size:26 final size:26
Alignment explanation
Indices: 19196--19250 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
19186 GATGGGAAAG
*
19196 AAAAAACTAAGTTAGGAATTTGGGGA
1 AAAAAACTAAGTCAGGAATTTGGGGA
* *
19222 AAAAAACTCAGTCAGGGATTTGGGGA
1 AAAAAACTAAGTCAGGAATTTGGGGA
19248 AAA
1 AAA
19251 CAATTTGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (26 bp):
AAAAAACTAAGTCAGGAATTTGGGGA
Found at i:20345 original size:2 final size:2
Alignment explanation
Indices: 20291--20326 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20281 CACTCACATA
20291 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
20327 TCTCCATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23191 original size:19 final size:19
Alignment explanation
Indices: 23167--23208 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
23157 AAAATTGAAG
23167 GGAGACTTGGTCAGAAATT
1 GGAGACTTGGTCAGAAATT
*
23186 GGAGACTTGGTCAGCAATT
1 GGAGACTTGGTCAGAAATT
23205 GGAG
1 GGAG
23209 TTTTGACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.24
Consensus pattern (19 bp):
GGAGACTTGGTCAGAAATT
Found at i:27179 original size:3 final size:3
Alignment explanation
Indices: 27171--27197 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27161 TCCTCTTGCA
27171 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
27198 AGTATTGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:29507 original size:72 final size:73
Alignment explanation
Indices: 29378--29518 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 73
29368 ACTGCTTACA
* * *
29378 TCATCATTGTTTTGATGATAGCTTCCACGTTGCAAGACTTTTTTGTCTGCATCTGGATTTC-TTC
1 TCATCATGGATTTGATGATAGCTTCCACGTTGCAAGACTTTGTTGTCTGCATCTGGATTTCTTTC
29442 TTTTGTCT
66 TTTTGTCT
* * *
29450 TCATCATGGATTTGATGAT-GACTTCCACGTTGCCAATA-TTTGTTG-CTGGTATGTGGATTTCT
1 TCATCATGGATTTGATGATAG-CTTCCACGTTG-CAAGACTTTGTTGTCT-GCATCTGGATTTCT
29512 TTCTTTT
63 TTCTTTT
29519 CAGGTTACTA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
71 3 0.05
72 45 0.76
73 11 0.19
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (73 bp):
TCATCATGGATTTGATGATAGCTTCCACGTTGCAAGACTTTGTTGTCTGCATCTGGATTTCTTTC
TTTTGTCT
Found at i:30305 original size:10 final size:10
Alignment explanation
Indices: 30290--30320 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
30280 ATTACAAATC
30290 ATTTTCTATT
1 ATTTTCTATT
30300 ATTTTCTATT
1 ATTTTCTATT
30310 ATTTTCATATT
1 ATTTTC-TATT
30321 GAAATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTCTATT
Found at i:30918 original size:24 final size:25
Alignment explanation
Indices: 30878--30924 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
30868 AGTTATCATC
30878 AAATCCATGATGAAGACAAAAAAAG
1 AAATCCATGATGAAGACAAAAAAAG
*
30903 AAATCCA-GATGCAGACAAAAAA
1 AAATCCATGATGAAGACAAAAAA
30925 GTCTTGCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.60, C:0.15, G:0.15, T:0.11
Consensus pattern (25 bp):
AAATCCATGATGAAGACAAAAAAAG
Found at i:32772 original size:14 final size:14
Alignment explanation
Indices: 32750--32782 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
32740 ATTTTCTAAA
32750 AAAAGAAAAGAAGTT
1 AAAAGAAAAGAA-TT
32765 AAAA-AAAAGAATT
1 AAAAGAAAAGAATT
32778 AAAAG
1 AAAAG
32783 TCTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 7 0.41
15 4 0.24
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAGAAAAGAATT
Found at i:34112 original size:34 final size:32
Alignment explanation
Indices: 34073--34146 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 32
34063 AATTAATAAC
34073 AAAACCTATAAAAATAATAGGTATAGATGGTAAT
1 AAAACC-ATAAAAATAAT-GGTATAGATGGTAAT
*
34107 AAAACCAT--AATTAATGGTATAGATGGTAAT
1 AAAACCATAAAAATAATGGTATAGATGGTAAT
34137 AAAACCATAA
1 AAAACCATAA
34147 TTAATTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 23 0.62
31 6 0.16
33 2 0.05
34 6 0.16
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.26
Consensus pattern (32 bp):
AAAACCATAAAAATAATGGTATAGATGGTAAT
Found at i:34126 original size:30 final size:31
Alignment explanation
Indices: 34087--34151 Score: 123
Period size: 30 Copynumber: 2.1 Consensus size: 31
34077 CCTATAAAAA
34087 TAATAGGTATAGATGGTAATAAAACCATAAT
1 TAATAGGTATAGATGGTAATAAAACCATAAT
34118 TAAT-GGTATAGATGGTAATAAAACCATAAT
1 TAATAGGTATAGATGGTAATAAAACCATAAT
34148 TAAT
1 TAAT
34152 TATAAAGCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (31 bp):
TAATAGGTATAGATGGTAATAAAACCATAAT
Found at i:41552 original size:72 final size:72
Alignment explanation
Indices: 41476--41610 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
41466 CCTGTAAGGA
* * *
41476 AAGAAATCCAGATACCA-ACAACAAAGAT-TGGCAACGTGGAAG-TCATCATCAAATCCATGATG
1 AAGAAATCCAGAT-CCAGACAAAAAAG-TCTGGCAACGTGGAAGCT-ATCATCAAAACAATGATG
41538 AAGACAAAAG
63 AAGACAAAAG
* * *
41548 AAGAAATCTAGATGCAGACAAAAAAGTCTTGCAACGTGGAAGCTATCATCAAAACAATGATGA
1 AAGAAATCCAGATCCAGACAAAAAAGTCTGGCAACGTGGAAGCTATCATCAAAACAATGATGA
41611 TGTAAGCAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
71 3 0.06
72 50 0.93
73 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.17
Consensus pattern (72 bp):
AAGAAATCCAGATCCAGACAAAAAAGTCTGGCAACGTGGAAGCTATCATCAAAACAATGATGAAG
ACAAAAG
Found at i:42952 original size:19 final size:21
Alignment explanation
Indices: 42928--42975 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 21
42918 CGAATATGCC
*
42928 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTA
42947 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
42968 AACAGAAG
1 AACAGAAG
42976 TTCATTAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 12 0.46
20 2 0.08
21 12 0.46
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:42992 original size:21 final size:21
Alignment explanation
Indices: 42928--42992 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
42918 CGAATATGCC
*
42928 AACAGAAGCTC-GAA-AGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
42947 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* * *
42968 AACAGAAGTTCATTAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
42989 AACA
1 AACA
42993 AAAAGTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
19 11 0.30
20 2 0.05
21 24 0.65
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:48524 original size:26 final size:26
Alignment explanation
Indices: 48495--48577 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
48485 AAAGTAGTTA
48495 AGTAATACAATTTAATTGTGACATTC
1 AGTAATACAATTTAATTGTGACATTC
* * * ** * *
48521 AGTACCTAGAAGTTAGAAAAGT-A-GTTA
1 AGTA-ATACAA-TT-TAATTGTGACATTC
48548 AGTAATACAATTTAATTGTGACATTC
1 AGTAATACAATTTAATTGTGACATTC
48574 AGTA
1 AGTA
48578 CCTAGACCCG
Statistics
Matches: 38, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
24 4 0.11
25 3 0.08
26 14 0.37
27 10 0.26
28 3 0.08
29 4 0.11
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (26 bp):
AGTAATACAATTTAATTGTGACATTC
Found at i:48535 original size:53 final size:53
Alignment explanation
Indices: 48475--48583 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
48465 TGTAAATAAA
48475 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
1 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
48528 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
1 AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
48581 AGA
1 AGA
48584 CCCGACGATC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (53 bp):
AGAAGTTAGAAAAGTAGTTAAGTAATACAATTTAATTGTGACATTCAGTACCT
Found at i:63699 original size:25 final size:25
Alignment explanation
Indices: 63638--63699 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
63628 AACACAGATT
* * *
63638 ATTTGAAAAGCATTTGTGGTGTATC
1 ATTTGGAAAGCCTTTGTGATGTATC
63663 ATTTGGAAAGCCTTTGTGATGTATC
1 ATTTGGAAAGCCTTTGTGATGTATC
63688 ATTTGGAAAGCC
1 ATTTGGAAAGCC
63700 ATCATGGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (25 bp):
ATTTGGAAAGCCTTTGTGATGTATC
Found at i:66712 original size:20 final size:18
Alignment explanation
Indices: 66687--66723 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
66677 ACCTAACATG
66687 AATTAAATTGAAACCATATT
1 AATTAAATT-AAA-CATATT
66707 AATTAAATTAAACATAT
1 AATTAAATTAAACATAT
66724 CAACATCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTAAATTAAACATATT
Found at i:69725 original size:32 final size:32
Alignment explanation
Indices: 69689--69754 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
69679 CATTTGAGGT
* *
69689 ATGCTTACTTGGGAGATAATAGCACATTGCCA
1 ATGCTTACTTAGGAGATAATAACACATTGCCA
69721 ATGCTTACTTAGGAGATAATAACACATTGCCA
1 ATGCTTACTTAGGAGATAATAACACATTGCCA
69753 AT
1 AT
69755 AGTTATCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (32 bp):
ATGCTTACTTAGGAGATAATAACACATTGCCA
Found at i:72467 original size:35 final size:35
Alignment explanation
Indices: 72419--72486 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
72409 GAATCTCTCT
* *
72419 TTTTAATTCTATTTTAGTTTTTCTCTTT-TTTTAGG
1 TTTTAATTCTATTTCAATTTTT-TCTTTGTTTTAGG
72454 TTTTAGATT-TATTTCAATTTTTTCTTTGTTTTA
1 TTTTA-ATTCTATTTCAATTTTTTCTTTGTTTTA
72487 TCTTAGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 21 0.72
36 3 0.10
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.69
Consensus pattern (35 bp):
TTTTAATTCTATTTCAATTTTTTCTTTGTTTTAGG
Found at i:74526 original size:22 final size:23
Alignment explanation
Indices: 74469--74541 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
74459 AAGAATATAG
* *
74469 AATGGAAAAAATAAAAACCAAAAAA
1 AATGGACAAAATAAAAA-C-ACAAA
74494 AATGTGGAC-AAATAAAAACACAAA
1 AA--TGGACAAAATAAAAACACAAA
*
74518 AATGGACAAAATAAAACCACAAA
1 AATGGACAAAATAAAAACACAAA
74541 A
1 A
74542 TCGTGAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.12
23 15 0.36
24 6 0.14
25 3 0.07
26 9 0.21
27 4 0.10
ACGTcount: A:0.68, C:0.12, G:0.10, T:0.10
Consensus pattern (23 bp):
AATGGACAAAATAAAAACACAAA
Found at i:81501 original size:31 final size:31
Alignment explanation
Indices: 81466--81561 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
81456 TGCACAGAGA
* * *
81466 CTTATCACAGAAAGCTCGCATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
81497 CTTATCATAGAGAGCTCACATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
81528 CTTATCATAGAGAGCTCACATAGGGAGCTTG
1 CTTATCATAGAGAGCTCACATAGGGAGCTTG
81559 CTT
1 CTT
81562 GCAAACACTT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (31 bp):
CTTATCATAGAGAGCTCACATAGGGAGCTTG
Found at i:81511 original size:18 final size:18
Alignment explanation
Indices: 81484--81543 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
81474 AGAAAGCTCG
*
81484 CATAGGGAGCTTGCTTAT
1 CATAGAGAGCTTGCTTAT
81502 CATAGAGAGC-T-C--A-
1 CATAGAGAGCTTGCTTAT
*
81515 CATAGGGAGCTTGCTTAT
1 CATAGAGAGCTTGCTTAT
81533 CATAGAGAGCT
1 CATAGAGAGCT
81544 CACATAGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 1 0.03
16 1 0.03
17 2 0.06
18 19 0.56
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (18 bp):
CATAGAGAGCTTGCTTAT
Found at i:81701 original size:27 final size:26
Alignment explanation
Indices: 81671--81726 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
81661 GCACACATAA
* *
81671 AACATATCTTTAAAATCATAGCTTAAG
1 AACATATCTTGAAAAT-AGAGCTTAAG
*
81698 AACATATCTTGAAAATAGAGTTTAAG
1 AACATATCTTGAAAATAGAGCTTAAG
81724 AAC
1 AAC
81727 TTGAAAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (26 bp):
AACATATCTTGAAAATAGAGCTTAAG
Found at i:81729 original size:21 final size:22
Alignment explanation
Indices: 81705--81747 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
81695 AAGAACATAT
*
81705 CTTGAAAATAGAGTTT-AAGAA
1 CTTGAAAACAGAGTTTGAAGAA
81726 CTTGAAAACAGAGTTTGAAGAA
1 CTTGAAAACAGAGTTTGAAGAA
81748 AACTTACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (22 bp):
CTTGAAAACAGAGTTTGAAGAA
Found at i:82303 original size:27 final size:27
Alignment explanation
Indices: 82272--82326 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
82262 ACTGGCGAAT
* *
82272 CCTAGTTTGAAACTTAAGTAGCAAACC
1 CCTAGTTCGAAACTTAACTAGCAAACC
* *
82299 CCTAGTTCGCAACTTACCTAGCAAACC
1 CCTAGTTCGAAACTTAACTAGCAAACC
82326 C
1 C
82327 TAGCTCGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.24
Consensus pattern (27 bp):
CCTAGTTCGAAACTTAACTAGCAAACC
Found at i:82346 original size:27 final size:26
Alignment explanation
Indices: 82290--82365 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
82280 GAAACTTAAG
* *
82290 TAGCAAACCCCTAGTTCG-CAACTTACC
1 TAGCAAA-CCCTAGCTCGCCAA-ATACC
82317 TAGCAAACCCTAGCTCGCCAAATACAC
1 TAGCAAACCCTAGCTCGCCAAATAC-C
** *
82344 TAGTGAACCCTAGCTCACCAAA
1 TAGCAAACCCTAGCTCGCCAAA
82366 CATACTGGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 12 0.29
27 30 0.71
ACGTcount: A:0.34, C:0.36, G:0.12, T:0.18
Consensus pattern (26 bp):
TAGCAAACCCTAGCTCGCCAAATACC
Found at i:82378 original size:27 final size:27
Alignment explanation
Indices: 82316--82379 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
82306 CGCAACTTAC
* * *
82316 CTAGCAAACCCTAGCTCGCCAAATACA
1 CTAGCGAACCCTAGCTCACCAAACACA
* *
82343 CTAGTGAACCCTAGCTCACCAAACATA
1 CTAGCGAACCCTAGCTCACCAAACACA
*
82370 CTGGCGAACC
1 CTAGCGAACC
82380 TACATGTAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (27 bp):
CTAGCGAACCCTAGCTCACCAAACACA
Found at i:84382 original size:21 final size:21
Alignment explanation
Indices: 84358--84398 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
84348 TATATTTATC
84358 ATGTTGATAATTTATTGAATG
1 ATGTTGATAATTTATTGAATG
*
84379 ATGTTTATAATTTATTGAAT
1 ATGTTGATAATTTATTGAAT
84399 AATATTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
ATGTTGATAATTTATTGAATG
Found at i:84406 original size:21 final size:21
Alignment explanation
Indices: 84364--84407 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
84354 TATCATGTTG
* *
84364 ATAATTTATTGAATGATGTTT
1 ATAATTTATTGAATAATATTT
84385 ATAATTTATTGAATAATATTT
1 ATAATTTATTGAATAATATTT
84406 AT
1 AT
84408 GAGTAGAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (21 bp):
ATAATTTATTGAATAATATTT
Found at i:87377 original size:30 final size:30
Alignment explanation
Indices: 87343--87405 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
87333 GCTAGAAAAC
*
87343 TAAACCTATAAAATATCATGAGGACCACAA
1 TAAACCCATAAAATATCATGAGGACCACAA
87373 TAAACCCATAAAATATCATGAGGACCACAA
1 TAAACCCATAAAATATCATGAGGACCACAA
87403 TAA
1 TAA
87406 TAATCAATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.51, C:0.21, G:0.10, T:0.19
Consensus pattern (30 bp):
TAAACCCATAAAATATCATGAGGACCACAA
Found at i:90408 original size:140 final size:140
Alignment explanation
Indices: 90235--91188 Score: 1169
Period size: 140 Copynumber: 7.0 Consensus size: 140
90225 TATAACAAAA
* ** * * *
90235 GTTGGCATAGTGTTGGACAAAGCTGACTCTTATTTAATTGCTGCATTAGGCATACATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * * *
90300 CCTTATACAAAGAGTTGGCCAAAGCGTATATCAGTAAGTCTATCCCAACAATTAGGAAAGTGCCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
90365 GCCCAAAAGT
131 GCCCAAAAGT
* * *
90375 GTTGGCATAGTGTTGCACAAAGCCGACTCTTATTTAAGTGTTGCCTTAGGAAAT-CATATCCCAA
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGG-CATGCATATCCCAA
* * * * *
90439 CCCTTATATAAAGAGTTGGCCAAAGTGTATGTTGGCAAGTTTATCCCAACACTTAGGAAAGTTTC
65 CCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTC
90504 GGCCCAAAAGT
130 GGCCCAAAAGT
* * * ** * *
90515 GTCGGCATAGCT-TTGGACAAAGTCGACTCTTATTTAAGTGTTATCTTAAGTATGCATATCCCAA
1 GTTGGCATAG-TGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAA
* * * *
90579 CCCTTATACAAAGAGTTGGCTAAAGCATATGTCTGCAAGTCTATCCCAACATTTAGGAAAGTGTC
65 CCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTC
90644 GGCCCAAAAGT
130 GGCCCAAAAGT
* * *
90655 GTTGTCATAGTGTTGGTCAAAGCCCACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* *
90720 CCTTATATAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAAGAAAGTGTCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
90785 GCCCAAAAGT
131 GCCCAAAAGT
* * *
90795 GTTGGCATAGTGTTGGACAAAGCTGACCCTTATTTAAGCGTTGCCTTAGGCATGAATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * * *
90860 CCTTATAGAAAGAGTTGGCCAACGTGTCTGTCAAG-AAGTCTATCCCAACACTTAGGAAAGTGT-
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTC-GGCAAGTCTATCCCAACACTTAGGAAAGTGTC
90923 ----C------
130 GGCCCAAAAGT
* *
90924 ---GGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * *
90986 CCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGGAAAGTGT--
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
91049 ---C------
131 GCCCAAAAGT
* *
91050 ---GGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATCCCAAC
1 GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
* * * *
91112 CCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGAAAAGTGTCG
66 CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
*
91177 TCCCAAAAGT
131 GCCCAAAAGT
91187 GT
1 GT
91189 CGTCTTAGGA
Statistics
Matches: 721, Mismatches: 74, Indels: 39
0.86 0.09 0.05
Matches are distributed among these distances:
125 1 0.00
126 235 0.33
131 1 0.00
135 1 0.00
139 3 0.00
140 476 0.66
141 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (140 bp):
GTTGGCATAGTGTTGGACAAAGCCGACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAAC
CCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCG
GCCCAAAAGT
Found at i:91025 original size:126 final size:126
Alignment explanation
Indices: 90790--91176 Score: 625
Period size: 126 Copynumber: 3.1 Consensus size: 126
90780 TGTCGGCCCA
* * * * * *
90790 AAAGTGTTGGCATAGTGTTGGACAAAGCTGACCCTTATTTAAGCGTTGCCTTAGGCATGAATATC
1 AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
* * * * **
90855 CCAACCCTTATAGAAAGAGTTGGCCAACGT-GTCTGTCAAG-AAGTCTATCCCAACACTTAGG
66 CCAACCCTTATACAAAGAGTTGGCCAA-ATCATATGT-TGGCAAGTCTATCCCAACACTTAGG
90916 AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
90981 CCAACCCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGG
66 CCAACCCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGG
91042 AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
*
91107 CCAACCCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGA
66 CCAACCCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGG
91168 AAAGTGTCG
1 AAAGTGTCG
91177 TCCCAAAAGT
Statistics
Matches: 246, Mismatches: 13, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
125 2 0.01
126 244 0.99
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (126 bp):
AAAGTGTCGGCATAGTATTGGACAAAGCCGACTCTTATTTAACCGTTGCCTTAGGCATGCATATC
CCAACCCTTATACAAAGAGTTGGCCAAATCATATGTTGGCAAGTCTATCCCAACACTTAGG
Found at i:97761 original size:20 final size:19
Alignment explanation
Indices: 97718--97761 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
97708 AAAAACTTAG
* *
97718 ATTTTCTAGAAGATATCAT
1 ATTTTCTAGAAAATAACAT
*
97737 ATTTTCTAGAAAATCAACCT
1 ATTTTCTAGAAAAT-AACAT
97757 ATTTT
1 ATTTT
97762 TCGTTAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (19 bp):
ATTTTCTAGAAAATAACAT
Found at i:99240 original size:41 final size:41
Alignment explanation
Indices: 99144--99265 Score: 154
Period size: 41 Copynumber: 2.9 Consensus size: 41
99134 AATACACCGG
* * *
99144 TTTGTGGACAAACCACCAGTAATTGTAGATATACTGCCAAAAA
1 TTTGTGGACAAGCCACCAGT-ATTGTAGATAAATTGCC-AAAA
* * *
99187 TATGTGGACAAGCCACCAGTATTGTATACAAATTGCCAAAA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
* *
99228 TTTGTGGACAAGCCATCAATATTGTAGATAAATTGCCA
1 TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCA
99266 GTACTTCCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.54
42 13 0.19
43 18 0.26
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
TTTGTGGACAAGCCACCAGTATTGTAGATAAATTGCCAAAA
Found at i:99478 original size:6 final size:6
Alignment explanation
Indices: 99469--99551 Score: 112
Period size: 6 Copynumber: 13.8 Consensus size: 6
99459 AATGTAGAAT
* * * * *
99469 AGTGAT AGTGAC AGTGAT AGTGAC AGTGAC AGTGAT AGTGAC GGTGAT
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
*
99517 AGTGAC AGTGAC AGTGAT AGTGAC AGTGAC AGTGA
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGA
99552 TAGTATCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.33, C:0.10, G:0.35, T:0.23
Consensus pattern (6 bp):
AGTGAC
Found at i:99490 original size:18 final size:18
Alignment explanation
Indices: 99467--99555 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
99457 TAAATGTAGA
* *
99467 ATAGTGATAGTGACAGTG
1 ATAGTGACAGTGATAGTG
*
99485 ATAGTGACAGTGACAGTG
1 ATAGTGACAGTGATAGTG
*
99503 ATAGTGACGGTGATAGTG
1 ATAGTGACAGTGATAGTG
*
99521 ACAGTGACAGTGATAGTG
1 ATAGTGACAGTGATAGTG
*
99539 ACAGTGACAGTGATAGT
1 ATAGTGACAGTGATAGT
99556 ATCAATAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.33, C:0.09, G:0.34, T:0.25
Consensus pattern (18 bp):
ATAGTGACAGTGATAGTG
Found at i:116103 original size:29 final size:29
Alignment explanation
Indices: 116069--116130 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
116059 ATGTGGTTAT
116069 GTTTGGGTTATTACCGACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
116098 GTTTGGGTTATTACCGACTTTGTTACTTA
1 GTTTGGGTTATTACCGACTTTGTTACTTA
116127 GTTT
1 GTTT
116131 TTTTGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (29 bp):
GTTTGGGTTATTACCGACTTTGTTACTTA
Found at i:128560 original size:17 final size:18
Alignment explanation
Indices: 128518--128561 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
128508 GCCCAATATT
128518 CCCACACGCCCGTATGGGG
1 CCCACACGCCCG-ATGGGG
* *
128537 CCAACACGCCCG-TGTGG
1 CCCACACGCCCGATGGGG
128554 CCCACACG
1 CCCACACG
128562 GCCCAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
19 11 0.50
ACGTcount: A:0.18, C:0.45, G:0.27, T:0.09
Consensus pattern (18 bp):
CCCACACGCCCGATGGGG
Found at i:130722 original size:138 final size:138
Alignment explanation
Indices: 130568--130851 Score: 514
Period size: 138 Copynumber: 2.1 Consensus size: 138
130558 GTGAACATAG
*
130568 ATATAATTAATCTATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
* *
130633 AATATCAACAATTATATTAATTAATTTCAATTAAAATATAAAAGACATGGAAATTAATATTCTTT
66 AATATCAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTT
130698 TGGAAAGA
131 TGGAAAGA
130706 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
* * *
130771 AATATCAACAATTATATTAATTAATTTCGATCAAAATATAAAGGACATGAAAATTAATGTTCTTT
66 AATATCAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTT
130836 TGGAAAGA
131 TGGAAAGA
130844 ATATAATT
1 ATATAATT
130852 TATTTTTCTA
Statistics
Matches: 140, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.41
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTATT
AATATCAACAATTATATTAATTAATTTCAATCAAAATATAAAAGACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:130958 original size:75 final size:75
Alignment explanation
Indices: 130830--130974 Score: 245
Period size: 75 Copynumber: 1.9 Consensus size: 75
130820 AAAATTAATG
* * * * *
130830 TTCTTTTGGAAAGAATATAATTTATTTTTCTAACTTTTCATTTGTCTTTTCTATTATTAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
130895 TAATCCTATA
66 TAATCCTATA
130905 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
1 TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
130970 TAATC
66 TAATC
130975 ATGGTTTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.48
Consensus pattern (75 bp):
TTCTTTTGGAAAGAATATAACTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAA
TAATCCTATA
Found at i:141921 original size:10 final size:11
Alignment explanation
Indices: 141908--141956 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
141898 TAAATAAAGC
141908 TAATAATA-AT
1 TAATAATATAT
141918 TAAT-ATATAT
1 TAATAATATAT
*
141928 T-ATAATAGAT
1 TAATAATATAT
*
141938 ATAATTATATAT
1 -TAATAATATAT
141950 TAATAAT
1 TAATAAT
141957 TATCATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 5 0.16
10 12 0.39
11 7 0.23
12 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATAATATAT
Found at i:141946 original size:22 final size:20
Alignment explanation
Indices: 141908--141956 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
141898 TAAATAAAGC
141908 TAATAATAATTAATATATAT
1 TAATAATAATTAATATATAT
141928 T-ATAATAGATATAATTATATAT
1 TAATAATA-AT-TAA-TATATAT
141950 TAATAAT
1 TAATAAT
141957 TATCATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 3 0.12
21 3 0.12
22 8 0.32
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAATAATTAATATATAT
Found at i:142085 original size:30 final size:30
Alignment explanation
Indices: 142028--142089 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
142018 TCTTTTTGAA
***
142028 AATATTTACAAAAAGAGGCATTTAATTTTT
1 AATATTTACAAAAAGAGGCACAAAATTTTT
142058 AATATTTACAAAAAGA-GCAACAAAATTTTT
1 AATATTTACAAAAAGAGGC-ACAAAATTTTT
142088 AA
1 AA
142090 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACAAAATTTTT
Found at i:162342 original size:26 final size:26
Alignment explanation
Indices: 162296--162345 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
162286 AGCCCAAGAA
*
162296 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAACT
* *
162322 GTTAAGATAGGGCTATTTACACAA
1 GTTAAGATAGGGATATCTACACAA
162346 ATTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAACT
Found at i:162352 original size:26 final size:26
Alignment explanation
Indices: 162296--162352 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
162286 AGCCCAAGAA
* *
162296 GTTAAGATAGGGATGTCTACACAACT
1 GTTAAGATAGGGATATCTACACAAAT
* *
162322 GTTAAGATAGGGCTATTTACACAAAT
1 GTTAAGATAGGGATATCTACACAAAT
*
162348 TTTAA
1 GTTAA
162353 TATATTGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (26 bp):
GTTAAGATAGGGATATCTACACAAAT
Found at i:163545 original size:27 final size:29
Alignment explanation
Indices: 163515--163587 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 29
163505 GAATAGTATA
163515 TGTGGCAAAGCCACCAGTAACAGTA-AT-
1 TGTGGCAAAGCCACCAGTAACAGTATATG
* * *
163542 TGTGGCAAAGCCACTAGTATCAGTATGTG
1 TGTGGCAAAGCCACCAGTAACAGTATATG
*
163571 TGTGGCAGAGCCACCAG
1 TGTGGCAAAGCCACCAG
163588 AAATAGTACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.59
28 1 0.03
29 15 0.38
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (29 bp):
TGTGGCAAAGCCACCAGTAACAGTATATG
Found at i:163595 original size:29 final size:25
Alignment explanation
Indices: 163501--163595 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 25
163491 CAGCAGAGCT
163501 ACCAGAATAGTATATGTGGCAAAGCC
1 ACCAGAATAGTAT-TGTGGCAAAGCC
*
163527 ACCAGTAACAGTAATTGTGGCAAAGCC
1 ACCAG-AATAGT-ATTGTGGCAAAGCC
* * *
163554 ACTAGTATCAGTATGTGTGTGGCAGAGCC
1 ACCAGAAT-AGTA--T-TGTGGCAAAGCC
163583 ACCAGAAATAGTA
1 ACCAG-AATAGTA
163596 CTTCCTCTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 7 0.13
27 24 0.44
28 3 0.05
29 19 0.35
30 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
ACCAGAATAGTATTGTGGCAAAGCC
Found at i:163759 original size:27 final size:27
Alignment explanation
Indices: 163711--163983 Score: 347
Period size: 27 Copynumber: 10.2 Consensus size: 27
163701 CCTAGAAGTC
* * *
163711 ATTTTGCCCTATCGAGAGTATTTCGATA
1 ATTTTACCC-ATCGAGGGTATTTCGGTA
* * *
163739 ACTTTACCCATCGGGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
163766 ATTTTACCCATC-AGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
163792 ATTTTACCCATAGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
163819 ATTTTACCCATTGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
163846 ATTTTACCCAT-TAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
163872 ATTTTACCCATTGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
163899 ATTTTACCCATCGGGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
* *
163926 ATTTCACTCATCGA-GGTA-TTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
163951 ATTTTACCCATCGAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGGTA
*
163978 GTTTTA
1 ATTTTA
163984 GGCCGATAAC
Statistics
Matches: 214, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.08
26 55 0.26
27 134 0.63
28 7 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGGTA
Found at i:163798 original size:53 final size:54
Alignment explanation
Indices: 163728--163983 Score: 324
Period size: 53 Copynumber: 4.8 Consensus size: 54
163718 CCTATCGAGA
* * * *
163728 GTATTTCGATAACTTTACCCATCGGGGGTATTTTGGTAATTTTACCCA-TCAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * *
163781 GTATTTCGGTAATTTTACCCATAGAGGGTATTTTGGTAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * *
163835 GTATTTCGGTAATTTTACCCAT-TAGGGTATTTCGATAATTTTACCCATTGAGG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
* * * * *
163888 GTATTTCGATAATTTTACCCATCGGGGGTATTTCAGTAATTTCACTCA-TC-GAG
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAG-G
*
163941 GTA-TTCGGTAATTTTACCCATCGAGGGTATTTCGGTAGTTTTA
1 GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTA
163984 GGCCGATAAC
Statistics
Matches: 179, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
52 36 0.20
53 98 0.55
54 45 0.25
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (54 bp):
GTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCATTCAGG
Found at i:163862 original size:80 final size:80
Alignment explanation
Indices: 163728--163983 Score: 345
Period size: 80 Copynumber: 3.2 Consensus size: 80
163718 CCTATCGAGA
* * * *
163728 GTATTTCGATAACTTTACCCATCGGGGGTATTTTGGTAATTTTACCCATCAGGGTATTTCGGTAA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
163793 TTTTACCCATAGAGG
66 TTTTACCCATAGAGG
* * * *
163808 GTATTTTGGTAATTTTACCCATTGAGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGATAA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
*
163873 TTTTACCCATTGAGG
66 TTTTACCCATAGAGG
* * * * *
163888 GTATTTCGATAATTTTACCCATCGGGGGTATTTCAGTAATTTCACTCA-TCGAGGTA-TTCGGTA
1 GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAG-GGTATTTCGGTA
*
163951 ATTTTACCCATCGAGG
65 ATTTTACCCATAGAGG
*
163967 GTATTTCGGTAGTTTTA
1 GTATTTCGGTAATTTTA
163984 GGCCGATAAC
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
79 38 0.25
80 116 0.75
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (80 bp):
GTATTTCGGTAATTTTACCCATCGGGGGTATTTCGGTAATTTTACCCATTAGGGTATTTCGGTAA
TTTTACCCATAGAGG
Found at i:174978 original size:56 final size:57
Alignment explanation
Indices: 174917--175043 Score: 157
Period size: 56 Copynumber: 2.2 Consensus size: 57
174907 GGTTTTCTCC
* * *
174917 AAAAATGAAAATGGAGAAATGAAATCAACTGGAAATGATTATGG-TTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
* * *** *
174973 AAAAATTAAAATGAAGAAATGGAATCCTTTGGAAATGAATGTGGTTTTCTCCAAAAT
1 AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
*
175030 GAAAATAAAAATGA
1 AAAAATAAAAATGA
175044 TCTGGAAATG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 36 0.60
57 24 0.40
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.26
Consensus pattern (57 bp):
AAAAATAAAAATGAAGAAATGAAATCAACTGGAAATGAATATGGTTTTCTCCAAAAT
Found at i:176501 original size:20 final size:19
Alignment explanation
Indices: 176465--176503 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
176455 TTTTTCTAAA
* *
176465 ATTTAAAATTATTAAAATT
1 ATTTAAAACTATAAAAATT
176484 ATTTAAAAACTATAAAAATT
1 ATTT-AAAACTATAAAAATT
176504 TATATATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAACTATAAAAATT
Found at i:180308 original size:42 final size:42
Alignment explanation
Indices: 180248--180595 Score: 378
Period size: 42 Copynumber: 8.3 Consensus size: 42
180238 AAGGAAATCA
* *
180248 TTCATTACATTTAAAGGCCCAGATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * ** * * *
180290 TTCATTACATTTAGAGGCCTAGGCGTGTAAGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
*
180332 TTCATTGCATTTAGAGGCCC-GAGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
* *
180374 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAG-A-TGTGGAGGTCCATTTACTT
* * ** *
180417 TTCATTGCATTTAGAGGCTCAGGTGTGGAAATTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * * * **
180459 TTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* **
180501 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTT
1 TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
* * *
180543 TACATTGCATTTAAAGGCCCA-AGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGA-TGTGGAGGTCCATTTACTT
180585 TTCATTGCATT
1 TTCATTGCATT
180596 GTATAATAAG
Statistics
Matches: 264, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 222 0.84
43 39 0.15
44 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTT
Found at i:180429 original size:127 final size:126
Alignment explanation
Indices: 180248--180595 Score: 434
Period size: 127 Copynumber: 2.8 Consensus size: 126
180238 AAGGAAATCA
* * * *
180248 TTCATTACATTTAAAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGCCTAGG
1 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
* * ** *
180313 CGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTGTGGAGGTTCATTTACTT
66 AGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
*
180374 TTCATTGCATTTAGAGGCTC-GAAGTGTGGAGGTCCATTTATTTTTCATTGCATTTAGAGG-CTC
1 TTCATTGCATTTAGAGGCTCAG-A-TGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCT-
* * * * *
180437 AGGTGTGGAAATTCATTTACTTTTCATTGCATTTAGAGGCTCGGGTATGGAAATCCATTTACTT
63 AGGAGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
** * * *
180501 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTTAATTTACTTTACATTGCATTTAAAGGCCCA--
1 TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
*
180564 AGTGTAGAGGTCCATTTACTTTTCATTGCATT
66 AGTGTA-A-GTTCATTTACTTTTCATTGCATT
180596 GTATAATAAG
Statistics
Matches: 191, Mismatches: 24, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
124 4 0.02
125 2 0.01
126 73 0.38
127 111 0.58
128 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCTCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGG
AGTGTAAGTTCATTTACTTTTCATTGCATTTAGAGGCCCGAGTATGGAAATCCATTTACTT
Found at i:181837 original size:21 final size:22
Alignment explanation
Indices: 181811--181855 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
181801 AAAGCTTTGA
*
181811 TTTTTAAGA-AAAA-TTGTGATT
1 TTTTTAAAACAAAACTT-TGATT
181832 TTTTTAAAACAAAACTTTGATT
1 TTTTTAAAACAAAACTTTGATT
181854 TT
1 TT
181856 GCAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 11 0.52
23 2 0.10
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (22 bp):
TTTTTAAAACAAAACTTTGATT
Found at i:181864 original size:140 final size:141
Alignment explanation
Indices: 181597--181854 Score: 373
Period size: 140 Copynumber: 1.9 Consensus size: 141
181587 GTTTTTAGTC
* * *
181597 ATTTTAAAGTAAAAGTTTAAATTTTTTAAAATAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
1 ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* * *
181662 AAGTTTTGATTTTTAAGAAAAATGGTGATTTTTTTTTAAAAGAGAAAGGTTAGATTTAAAAAA-A
66 AAGCTTTGATTTTTAAGAAAAATGGTGA-TTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAGA
181726 AAACATTTAGCT
130 AAACATTTAGCT
* * *
181738 ATTTTAAAGGAAAAGTTTAAA-ATTTTAGAACAATGTTTTGATCTTTTTCAACTGTTTCAAAATA
1 ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
* *
181802 AAGCTTTGATTTTTAAGAAAAATTGTGA-TTTTTTTAAAACA-AAA-CTTTGATTT
66 AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTT
181855 TGCAAAAAAA
Statistics
Matches: 106, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
136 7 0.07
137 3 0.03
138 12 0.11
140 64 0.60
141 20 0.19
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (141 bp):
ATTTTAAAGGAAAAGTTTAAATATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTCAAAATA
AAGCTTTGATTTTTAAGAAAAATGGTGATTTTTTTTAAAACAGAAAGCTTAGATTTAAAAAAGAA
AACATTTAGCT
Found at i:182434 original size:16 final size:17
Alignment explanation
Indices: 182405--182450 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
182395 ATAATTTTTA
*
182405 TTTATTTTTATTTCATC
1 TTTATTTATATTTCATC
*
182422 TTTATTTAT-TTTCATG
1 TTTATTTATATTTCATC
*
182438 TCTATTTATATTT
1 TTTATTTATATTT
182451 ATGGTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTATTTATATTTCATC
Found at i:184544 original size:17 final size:18
Alignment explanation
Indices: 184524--184557 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
184514 TTTTTTCATT
184524 TGACTTTATTT-TTTTAC
1 TGACTTTATTTGTTTTAC
*
184541 TGACTTTGTTTGTTTTA
1 TGACTTTATTTGTTTTA
184558 TGTCTGTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.09, G:0.12, T:0.65
Consensus pattern (18 bp):
TGACTTTATTTGTTTTAC
Found at i:193644 original size:24 final size:24
Alignment explanation
Indices: 193616--193663 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
193606 ATGAAGAATG
193616 AATGCAAAATTATGAATTCTTGAT
1 AATGCAAAATTATGAATTCTTGAT
193640 AATGCAAAATTATGAATTCTTGAT
1 AATGCAAAATTATGAATTCTTGAT
193664 CTCATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
AATGCAAAATTATGAATTCTTGAT
Found at i:194255 original size:10 final size:10
Alignment explanation
Indices: 194240--194284 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
194230 GCCTACACAA
194240 AAAAAAAACT
1 AAAAAAAACT
194250 AAAAAAAACT
1 AAAAAAAACT
194260 AAAAAATAA--
1 AAAAAA-AACT
*
194269 AAAATAAACT
1 AAAAAAAACT
194279 AAAAAA
1 AAAAAA
194285 GATAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 2 0.07
9 5 0.17
10 21 0.70
11 2 0.07
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:194265 original size:19 final size:20
Alignment explanation
Indices: 194241--194284 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
194231 CCTACACAAA
194241 AAAAAAACT-AAAAA-AAACT
1 AAAAAAA-TAAAAAATAAACT
194260 -AAAAAATAAAAAATAAACT
1 AAAAAAATAAAAAATAAACT
194279 AAAAAA
1 AAAAAA
194285 GATAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 5 0.23
20 5 0.23
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAATAAAAAATAAACT
Found at i:194755 original size:42 final size:42
Alignment explanation
Indices: 194691--194953 Score: 343
Period size: 42 Copynumber: 6.3 Consensus size: 42
194681 AAGGAAAGCA
*
194691 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
194733 TTCACTGCATTTAGAGGCCCAGGCGTAGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* **
194775 TTCATTGCATTTAGAAG-CTTGGTTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGG-TGTGGAGGTCCATTTACTT
* *
194817 TACATTGCATTTAGAGGCCC-GAGTGTGGAGGTCAATTTACTT
1 TTCATTGCATTTAGAGGCCCAG-GTGTGGAGGTCCATTTACTT
** * *
194859 TTCATTGCATTTAGAATCGCAAGTGTGGAGG-CTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
*
194901 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
194943 TTCATTGCATT
1 TTCATTGCATT
194954 GTATATGAAG
Statistics
Matches: 192, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.02
42 185 0.96
43 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:196732 original size:69 final size:69
Alignment explanation
Indices: 196621--196891 Score: 234
Period size: 69 Copynumber: 3.9 Consensus size: 69
196611 TATTCACACT
* * *
196621 TATAAGATCAAGGCTTGCAAGCG-AAAAG-CTACAACCCCCAAAACAGTTAGCAATAGCAAAGCT
1 TATAAGATCAAGGCTCGC-AGCGAAAAAGTC-GCAACCCCCAAAACAGTTAGCAAGAGCAAAGCT
196684 CCTAGC
64 CCTAGC
* * * *
196690 TATAAGATCAAGGCTTGCAG-GAAAAGAGTCGCAACCCCCAAAATAGTTAACAAAAGCAAAGCTC
1 TATAAGATCAAGGCTCGCAGCGAAAA-AGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
* *
196754 CCAAC
65 CTAGC
* * * * * * *
196759 TATCAGATCAAGGCTCACAG-GTGAAAAG-C-C-ACTGCTCTAGAATAGTTAGCAAGAGCAAAGC
1 TATAAGATCAAGGCTCGCAGCG-AAAAAGTCGCAAC--CCCCAAAACAGTTAGCAAGAGCAAAGC
196820 TCCTAGC
63 TCCTAGC
* * * * *
196827 TGTAAGGTCAAGGCTCGTAAGCG-AAAAGTCGCAGCTCCCAAAACAGTTAGCAAGAGCAAAGCTC
1 TATAAGATCAAGGCTCG-CAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTC
196891 C
65 C
196892 CAGTTGTAAT
Statistics
Matches: 163, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
66 2 0.01
67 2 0.01
68 51 0.31
69 101 0.62
70 6 0.04
71 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (69 bp):
TATAAGATCAAGGCTCGCAGCGAAAAAGTCGCAACCCCCAAAACAGTTAGCAAGAGCAAAGCTCC
TAGC
Found at i:196946 original size:69 final size:69
Alignment explanation
Indices: 196797--196970 Score: 170
Period size: 69 Copynumber: 2.5 Consensus size: 69
196787 CCACTGCTCT
* * * * *
196797 AGAATAGTTAGCAAGAGCAAAGCTCCTAGCTGTAAGGTCAAGGCTCGTAAGCGAAAAGTCGCAGC
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
196862 TCCC
66 TCCC
* * * * * * **
196866 AAAACAGTTAGCAAGAGCAAAGCTCCCAGTTGTAATCTAAAGACTCATAGGCGAAGAGTCGTGGC
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
196931 -CTCC
66 TC-CC
* ** * *
196935 AGAATAATTAGCGCGAACAAAGCTCCCAGCAGTAAG
1 AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAG
196971 ATCAAGGCTC
Statistics
Matches: 82, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
68 1 0.01
69 81 0.99
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (69 bp):
AGAATAGTTAGCAAGAGCAAAGCTCCCAGCTGTAAGCTAAAGACTCATAAGCGAAAAGTCGCAGC
TCCC
Found at i:197196 original size:58 final size:58
Alignment explanation
Indices: 197070--197246 Score: 275
Period size: 58 Copynumber: 3.1 Consensus size: 58
197060 CTGTAGTATC
* * * *
197070 AGTATAAAACAGACCGCAAATTCATATTCCTAGCTTATAA-TTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
* *
197127 TGTAAAAAATAGATCGCGAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
* *
197185 AGTAGAAAATAGATCGCAAATTCATGTTCCCAGCTTATAATTTTGAGAAAAATCTCTA
1 AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
197243 AGTA
1 AGTA
197247 TCAGACGGCT
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
57 34 0.31
58 75 0.69
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (58 bp):
AGTAAAAAATAGATCGCAAATTCATATTCCCAGCTTATAATTTTGAGAAAAATCTCTA
Found at i:212706 original size:33 final size:33
Alignment explanation
Indices: 212664--212729 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
212654 TTGCGAGGGT
212664 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
1 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
212697 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
1 GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
212730 AACTCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.27
Consensus pattern (33 bp):
GGCGGTTGTTGAGCAGCTAGATTCGTTCGAACA
Found at i:214110 original size:13 final size:13
Alignment explanation
Indices: 214092--214119 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
214082 ATCTTAACCT
214092 TTTCTATTTGAAC
1 TTTCTATTTGAAC
214105 TTTCTATTTGAAC
1 TTTCTATTTGAAC
214118 TT
1 TT
214120 CCTACTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTCTATTTGAAC
Found at i:214931 original size:16 final size:15
Alignment explanation
Indices: 214906--214936 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
214896 TTTCACCATA
214906 CAACACAAAAAGCTT
1 CAACACAAAAAGCTT
214921 CAACAACAAAAAGCTT
1 CAAC-ACAAAAAGCTT
214937 GAATATTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.55, C:0.26, G:0.06, T:0.13
Consensus pattern (15 bp):
CAACACAAAAAGCTT
Found at i:219826 original size:42 final size:42
Alignment explanation
Indices: 219764--219932 Score: 196
Period size: 42 Copynumber: 4.0 Consensus size: 42
219754 GTTTTTACTA
* * **
219764 AAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTT-TGGCG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGG-G
* * *
219806 ACAGCGTCGCTAAAGGACATGTCTTTTAGTGGCGTTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
* *
219848 AAAGCGCCGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
* * * * *
219890 AAAGCGCCGCTAAAGGTCATGTTCTATAGTGACGTTTATGGG
1 AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
219932 A
1 A
219933 GGTGTCGCTA
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 106 0.97
43 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGGACATGTCCTTTAGTGGCGTTTGTGGG
Found at i:219901 original size:84 final size:84
Alignment explanation
Indices: 219764--219952 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 84
219754 GTTTTTACTA
** * * * *
219764 AAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTTGGCGACAGCGTCGCTAAAGGACATG-T
1 AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTTTGGCGAAAGCGCCGCTAAAGGACATGTT
* * *
219828 CTTTTAGTGGCGTTTGTGGG
66 C-TATAGTGACGTTTATGGG
** *
219848 AAAGCGCCGCTAAAGGTCATGTCCTTTAGTGGCATTTGTGG-GAAAGCGCCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTT-TGGCGAAAGCGCCGCTAAAGGACATGT
219912 TCTATAGTGACGTTTATGGG
65 TCTATAGTGACGTTTATGGG
* * *
219932 -AGGTGTCGCTAAAGGTCATGT
1 AAAGCGCCGCTAAAGGTCATGT
219953 TCTATAGCTG
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 18 0.20
84 65 0.74
85 5 0.06
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (84 bp):
AAAGCGCCGCTAAAGGTCATGTCCTTTAACGGCATTTTGGCGAAAGCGCCGCTAAAGGACATGTT
CTATAGTGACGTTTATGGG
Found at i:219953 original size:41 final size:42
Alignment explanation
Indices: 219794--219959 Score: 185
Period size: 42 Copynumber: 4.0 Consensus size: 42
219784 GACCTTTAAC
* * * *
219794 GGCGTTT-TGGCGACAGCGTCGCTAAAGGACATG-TCTTTTAGT
1 GGCGTTTGTGG-GAAAGCGCCGCTAAAGGTCATGTTC-TATAGT
* *
219836 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTCCTTTAGT
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
*
219878 GGCATTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
* * * * *
219920 GACGTTTATGGG-AGGTGTCGCTAAAGGTCATGTTCTATAG
1 GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAG
219960 CTGCATTTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
41 25 0.23
42 80 0.73
43 4 0.04
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (42 bp):
GGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGTTCTATAGT
Found at i:220216 original size:29 final size:30
Alignment explanation
Indices: 220175--220233 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
220165 TTTTGTTCAA
220175 TGTGCAATATTATATA-TAAAT-TTCAATTT
1 TGTGCAATATTATATATTAAATGTT-AATTT
* *
220204 TGTGTAATTTTATATATTAAATGTTAATTT
1 TGTGCAATATTATATATTAAATGTTAATTT
220234 GATCTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 10 0.38
31 2 0.08
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (30 bp):
TGTGCAATATTATATATTAAATGTTAATTT
Found at i:220242 original size:30 final size:29
Alignment explanation
Indices: 220184--220244 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
220174 ATGTGCAATA
*
220184 TTATATATAAATTTCAATTTTGTGTAATT
1 TTATATATAAATTTCAATTTTGTCTAATT
220213 TTATATATTAAATGTT-AA-TTTGATCTAATT
1 TTATATA-TAAAT-TTCAATTTTG-TCTAATT
220243 TT
1 TT
220245 CAAAAATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 11 0.39
30 15 0.54
31 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (29 bp):
TTATATATAAATTTCAATTTTGTCTAATT
Found at i:222056 original size:22 final size:22
Alignment explanation
Indices: 222031--222072 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
222021 CAATTTAATC
* *
222031 TAATTTAATATATATTTCATTT
1 TAATATAATACATATTTCATTT
*
222053 TAATATCATACATATTTCAT
1 TAATATAATACATATTTCAT
222073 GTGTTATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATAATACATATTTCATTT
Found at i:222936 original size:18 final size:19
Alignment explanation
Indices: 222908--222957 Score: 84
Period size: 18 Copynumber: 2.7 Consensus size: 19
222898 AGAATTTCTG
*
222908 AAAATTCAAAAAATACATA
1 AAAATTCAAAAAACACATA
222927 AAAATT-AAAAAACACATA
1 AAAATTCAAAAAACACATA
222945 AAAATTCAAAAAA
1 AAAATTCAAAAAA
222958 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAATTCAAAAAACACATA
Found at i:231504 original size:20 final size:19
Alignment explanation
Indices: 231476--231527 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
231466 AATTACGGTT
*
231476 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
231497 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
231517 TTAATGAGAAA
1 TTAATGAGAAA
231528 AATGGTCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:231930 original size:20 final size:20
Alignment explanation
Indices: 231905--231946 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
231895 TTAAAATTCA
* *
231905 AATTACTGATTATATGATTG
1 AATTACTGATTACATGAATG
*
231925 AATTACTGTTTACATGAATG
1 AATTACTGATTACATGAATG
231945 AA
1 AA
231947 AGTGAAATGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.40
Consensus pattern (20 bp):
AATTACTGATTACATGAATG
Found at i:232263 original size:23 final size:23
Alignment explanation
Indices: 232237--232296 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
232227 CTCATTGGAA
232237 CTTACCATTTCAGCTAGT-ATGAG
1 CTTACCATTTCAGCTAGTCA-GAG
*
232260 CTTA-C-TGTTCAGCTCGTCAGAG
1 CTTACCAT-TTCAGCTAGTCAGAG
*
232282 CTTACCATTTTAGCT
1 CTTACCATTTCAGCT
232297 TAATAGAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 17 0.55
23 12 0.39
24 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (23 bp):
CTTACCATTTCAGCTAGTCAGAG
Found at i:232506 original size:20 final size:21
Alignment explanation
Indices: 232476--232516 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
232466 TATGAATAAG
232476 ATATGTGTTTATACAGATGAA
1 ATATGTGTTTATACAGATGAA
*
232497 ATAT-TGTTTATACGGATGAA
1 ATATGTGTTTATACAGATGAA
232517 CCACTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (21 bp):
ATATGTGTTTATACAGATGAA
Found at i:232524 original size:20 final size:20
Alignment explanation
Indices: 232481--232528 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
232471 ATAAGATATG
* *
232481 TGTTTATACAGATGAAATAT
1 TGTTTATACAGATGAAACAC
* *
232501 TGTTTATACGGATGAACCAC
1 TGTTTATACAGATGAAACAC
232521 TGTTTATA
1 TGTTTATA
232529 TGAATGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTTTATACAGATGAAACAC
Found at i:233481 original size:13 final size:13
Alignment explanation
Indices: 233463--233487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233453 ATATGTTTGG
233463 ATATGAAATTGAT
1 ATATGAAATTGAT
233476 ATATGAAATTGA
1 ATATGAAATTGA
233488 GATTGAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:238957 original size:20 final size:19
Alignment explanation
Indices: 238929--238980 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
238919 AATTACGGTT
*
238929 TTAATTGAGAAATTTGTAAAA
1 TTAA-TGAGAAATGTGT-AAA
* *
238950 TTCATGAGTAAATGTGTGAA
1 TTAATGAG-AAATGTGTAAA
238970 TTAATGAGAAA
1 TTAATGAGAAA
238981 AATAGGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (19 bp):
TTAATGAGAAATGTGTAAA
Found at i:239768 original size:22 final size:22
Alignment explanation
Indices: 239694--239781 Score: 83
Period size: 22 Copynumber: 3.9 Consensus size: 22
239684 TATCGATATA
*
239694 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCGTATGAGCTTACTG--T
*
239718 TCAGCTCAT-TGGAGCTTACCAT-T
1 TCAGCTCGTAT-GAGCTTA-C-TGT
239741 TCAGCTCGTATGAGCTTACTGT
1 TCAGCTCGTATGAGCTTACTGT
239763 TCAGCTCGTCA-GAGCTTAC
1 TCAGCTCGT-ATGAGCTTAC
239782 CATTTTAGCT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
21 1 0.02
22 19 0.35
23 17 0.31
24 16 0.29
25 1 0.02
26 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (22 bp):
TCAGCTCGTATGAGCTTACTGT
Found at i:239781 original size:45 final size:46
Alignment explanation
Indices: 239694--239792 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 46
239684 TATCGATATA
**
239694 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCATT
1 TCAGCTCGTAAGAGCTTACTG-TTTCAGCTCATCAGAGCTTACCATT
* *
239741 TCAGCTCGTATGAGCTTACTG-TTCAGCTCGTCAGAGCTTACCATT
1 TCAGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATT
*
239786 TTAGCTC
1 TCAGCTC
239793 AATAGAGCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 27 0.57
47 20 0.43
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (46 bp):
TCAGCTCGTAAGAGCTTACTGTTTCAGCTCATCAGAGCTTACCATT
Found at i:239800 original size:23 final size:22
Alignment explanation
Indices: 239694--239792 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 22
239684 TATCGATATA
**
239694 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCGT-AGAGCTTAC-CATT
* *
239718 TCAGCTCATTGGAGCTTACCATT
1 TCAGCTC-GTAGAGCTTACCATT
239741 TCAGCTCGTATGAGCTTA-C-TGT
1 TCAGCTCGTA-GAGCTTACCAT-T
239763 TCAGCTCGTCAGAGCTTACCATT
1 TCAGCTCGT-AGAGCTTACCATT
*
239786 TTAGCTC
1 TCAGCTC
239793 AATAGAGCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 19 0.31
23 25 0.40
24 16 0.26
25 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (22 bp):
TCAGCTCGTAGAGCTTACCATT
Found at i:240001 original size:20 final size:20
Alignment explanation
Indices: 239977--240048 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
239967 TAAAATATGT
*
239977 GTTTATACGAATGAATTATT
1 GTTTATACGAATGAATTATA
* **
239997 GTTTATACGGATGAACCACTA
1 GTTTATACGAATGAATTA-TA
* *
240018 G-TTATATGAATGAATTACA
1 GTTTATACGAATGAATTATA
240037 GTTTATACGAAT
1 GTTTATACGAAT
240049 AGAAATGAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
GTTTATACGAATGAATTATA
Found at i:251097 original size:37 final size:37
Alignment explanation
Indices: 251047--251119 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
251037 AAGTCCTTTC
251047 TATCGCCGTAGCAATATCATTGCAAGAGTAGCCTTGA
1 TATCGCCGTAGCAATATCATTGCAAGAGTAGCCTTGA
251084 TATCGCCGTAGCAATATCATTGCAAGAGTAGCCTTG
1 TATCGCCGTAGCAATATCATTGCAAGAGTAGCCTTG
251120 TCGCTGCCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (37 bp):
TATCGCCGTAGCAATATCATTGCAAGAGTAGCCTTGA
Found at i:254130 original size:2 final size:2
Alignment explanation
Indices: 254123--254167 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
254113 TTTCTCATGA
254123 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
254165 AT A
1 AT A
254168 CACATGTACC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:261507 original size:45 final size:45
Alignment explanation
Indices: 261439--261541 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
261429 TTGGACTATC
* * * * *
261439 CACCATGTTTGTTTGCCATTTGGATTGTTCATCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
* *
261484 CTCCATGTGTGTTTGCCAATTGGACTATTCGCCATTTATGTTGTT
1 CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
261529 CACCATGTGTGTT
1 CACCATGTGTGTT
261542 CACCATTGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (45 bp):
CACCATGTGTGTTTGCCAATTGGACTATTCACCATTTATGTTGTT
Found at i:265256 original size:25 final size:25
Alignment explanation
Indices: 265196--265266 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
265186 TGTACTTTAG
265196 CTTGTGAGAGCTTACCGATTCTCAA
1 CTTGTGAGAGCTTACCGATTCTCAA
* *
265221 CTCGT-ATGAGCTTACCGATT-TACAG
1 CTTGTGA-GAGCTTACCGATTCT-CAA
* *
265246 GTTGTGAGAGCATACCGATTC
1 CTTGTGAGAGCTTACCGATTC
265267 ATAGCTCGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.05
25 34 0.92
26 1 0.03
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (25 bp):
CTTGTGAGAGCTTACCGATTCTCAA
Found at i:279644 original size:140 final size:142
Alignment explanation
Indices: 279392--279674 Score: 527
Period size: 140 Copynumber: 2.0 Consensus size: 142
279382 CGTCATTGGA
*
279392 CCAATATCACCGAAGGCTTCTAATGGACATCGTTTCATTTTTTGTGGTTTGTGACTGCTTTACTA
1 CCAATATCACCGAAGGCTTCTAATGGACATCGTTTCATTTTTTGTGGTATGTGACTGCTTTACTA
279457 AGTGGGTAGAGGCAGCCTCATATGCTAATGTCACGAAGTCAGCAGTCAGCAAGTTTTTGAAGAA-
66 AGTGGGTAGAGGCAGCCTCATATGCTAATGTCACGAAGTCAGCAGTCAGCAAGTTTTTGAAGAAG
279521 G-GATTGTATGT
131 GAGATTGTATGT
279532 CCAATATCACCGAAGGCTTCTAATGGACATCGTTTCATTTTTTGTGGTGAT-TGACTGCTTTACT
1 CCAATATCACCGAAGGCTTCTAATGGACATCGTTTCATTTTTTGTGGT-ATGTGACTGCTTTACT
279596 AAGTGGGTAGAGGCAGCCTCATATGCTAATGTCACGAAGTCAGCAGTCAGCAAGTTTTTGAAGAA
65 AAGTGGGTAGAGGCAGCCTCATATGCTAATGTCACGAAGTCAGCAGTCAGCAAGTTTTTGAAGAA
279661 GGAGATTGTATGT
130 GGAGATTGTATGT
279674 C
1 C
279675 GATATGAAAT
Statistics
Matches: 139, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
140 126 0.91
141 2 0.01
142 11 0.08
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (142 bp):
CCAATATCACCGAAGGCTTCTAATGGACATCGTTTCATTTTTTGTGGTATGTGACTGCTTTACTA
AGTGGGTAGAGGCAGCCTCATATGCTAATGTCACGAAGTCAGCAGTCAGCAAGTTTTTGAAGAAG
GAGATTGTATGT
Found at i:286174 original size:132 final size:132
Alignment explanation
Indices: 285937--286321 Score: 655
Period size: 132 Copynumber: 2.9 Consensus size: 132
285927 GTGAAACACC
* *
285937 AGATCATATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* *
286002 GTGGGAAGCACATTTAAGCCACCAAACCTTATCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
286067 GT
131 GT
286069 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
*
286134 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCGGTGGAGAAGGTTGAAGATT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
286199 GT
131 GT
* * *
286201 AGATATTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCTTATCTTTCCAAGATA
1 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
* * * *
286266 GTGGGAAGCAGATTT-AGCCACCAAGCCTTGTCTCCCTAAGCAGTAGTGGAGCAGGT
66 GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTGGAGAAGGT
286322 CGTACCCAAT
Statistics
Matches: 240, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
131 36 0.15
132 204 0.85
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATA
GTGGGAAGCAGATTTAAGCCACCAAACCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATT
GT
Found at i:286254 original size:44 final size:44
Alignment explanation
Indices: 285943--286255 Score: 147
Period size: 44 Copynumber: 7.1 Consensus size: 44
285933 CACCAGATCA
** * *
285943 TATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGACGGCGAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAAATTGAAGACGGCAAATCT
* * * * ** *
285987 TATCTTTCC-AAG-A-TAGTGGGAAGCACATTTAAGCCACCAAACCT
1 TATC-TCCCTAAGCAGTAGT-GG-AGCAAATTGAAGACGGCAAATCT
* * * ** * *
286031 TATCTCCCTGAGCAGCAGTGGAG-AAGGTTGAAGATTGTAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAA-ATTGAAGACGGCAAATCT
* * *
286075 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAAATTGAAGACGGCAAATCT
* * * * ** *
286119 TATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAACCT
1 TATC-TCCCTAAGCAGTAGT-GG-AGCAAATTGAAGACGGCAAATCT
* * ** * ** * * *
286163 TGTCTCCCTGAGCAGCGGTGGAG-AAGGTTGAAGATTGTAGATAT
1 TATCTCCCTAAGCAGTAGTGGAGCAA-ATTGAAGACGGCAAATCT
*
286207 TATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGACGGCAAATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAAATTGAAGACGGCAAATCT
286251 TATCT
1 TATCT
286256 TTCCAAGATA
Statistics
Matches: 185, Mismatches: 68, Indels: 32
0.65 0.24 0.11
Matches are distributed among these distances:
42 8 0.04
43 14 0.08
44 143 0.77
45 15 0.08
46 5 0.03
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
TATCTCCCTAAGCAGTAGTGGAGCAAATTGAAGACGGCAAATCT
Found at i:287775 original size:33 final size:31
Alignment explanation
Indices: 287713--287775 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
287703 AGTCCTTTTT
* ** *
287713 TATATATTTCTCTTAAAATCAATATTTTATG
1 TATATATTTCTCTAAAAAAAAATAATTTATG
287744 TATATATTTCTACTAAAAAAAACATAATTTAT
1 TATATATTTCT-CTAAAAAAAA-ATAATTTAT
287776 ATTCACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 11 0.42
32 7 0.27
33 8 0.31
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (31 bp):
TATATATTTCTCTAAAAAAAAATAATTTATG
Found at i:306892 original size:111 final size:110
Alignment explanation
Indices: 306698--306920 Score: 392
Period size: 111 Copynumber: 2.0 Consensus size: 110
306688 AAATTGTACC
* *
306698 TTTCCAATTCGTCTAGGATAAACGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCATAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
306763 CTACCGAGTGTGGGCTCACTTTGAACCAAAAAAATTTTCACAAAAA
66 CTACCGAGTGTGGGCTCACTTTGAACC-AAAAAATTTTCACAAAAA
*
306809 TTTCCAATTTGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
1 TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
**
306874 CTGTCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
66 CTACCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
306919 TT
1 TT
306921 ACTAGTGGCA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 20 0.19
111 87 0.81
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (110 bp):
TTTCCAATTCGTCTAGGATAAAAGCTTCGACCAAGTAGTCTTCTCCATTATCCTCAAGCTCACAT
CTACCGAGTGTGGGCTCACTTTGAACCAAAAAATTTTCACAAAAA
Found at i:307236 original size:61 final size:58
Alignment explanation
Indices: 307128--307239 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 58
307118 ATCACTTTAA
* * *
307128 TATTCAATTAATATAATACTTTCCAAGATAAATATTAGATTAAATTTAATACTAAATC
1 TATTAAATTAATAGAATACTTTCCAAGATAAATATTAAATTAAATTTAATACTAAATC
* *
307186 TATTAAATTAATAGAATACTTATCTACAATATAAATATTAAATTAGATTTAATA
1 TATTAAATTAATAGAATACTT-TC--CAAGATAAATATTAAATTAAATTTAATA
307240 TTAAGATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
58 19 0.41
59 2 0.04
61 25 0.54
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTTCCAAGATAAATATTAAATTAAATTTAATACTAAATC
Found at i:318038 original size:130 final size:130
Alignment explanation
Indices: 317772--318027 Score: 404
Period size: 130 Copynumber: 2.0 Consensus size: 130
317762 CCTTAGCTAA
* * * * *
317772 ATTTTTAAGGATTTTTTATAAATGAGTAGTCTGTTTAGAAATTTAAATTGCAAAAAACCAAACAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
*
317837 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAGTTCACTTTTTTAGAAAATAC
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
* * *
317902 ATTTTTAAGGATTTCTTGTAAATGAGTAGTCTGCTCAGAAATTTGAACTGCGAAAAACCAAAAAA
1 ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
* * *
317967 TTAGTGACTTAAGGCCCTTGTTGTAAGAGTGATTAAATTTTAAAATTCAGTTTTTTAGAAA
66 TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAA
318028 GTTTTATTTT
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 114 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (130 bp):
ATTTTTAAGGATTTCTTATAAATGAGTAGTCTGCTCAGAAATTTAAACTGCAAAAAACCAAAAAA
TTAGTGACTTAAGGCCCTTGCTGTAAGAATGATTAAATTTTAAAATTCACTTTTTTAGAAAATAC
Found at i:319381 original size:28 final size:28
Alignment explanation
Indices: 319342--319399 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
319332 ATAAAAAAAA
319342 TTCATTACATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
*
319370 TTCATTATATTAATATACTTTGTATAAT
1 TTCATTACATTAATATACTTTGTATAAT
319398 TT
1 TT
319400 TTGTCATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (28 bp):
TTCATTACATTAATATACTTTGTATAAT
Found at i:322981 original size:54 final size:54
Alignment explanation
Indices: 322892--323078 Score: 198
Period size: 54 Copynumber: 3.5 Consensus size: 54
322882 ACATGCCAGA
*
322892 AAAAGGAAGCCTTTGTAGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
* * * * * *
322946 AAAAGAAAGCCTTTGTGGCGATCTAACAAATGAAAGTCTTTATGGATTT-T-AATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGT-G-TTTATCTATG
* * * * **
323000 AAAAGGAAGCCTTTATGGCTATCTATGAAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
* * *
323054 ACAAGGAAGCCTTCGTGGTGATCTA
1 AAAAGGAAGCCTTTGTGGCGATCTA
323079 TGAAGGGAAT
Statistics
Matches: 105, Mismatches: 24, Indels: 8
0.77 0.18 0.06
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 97 0.92
55 2 0.02
56 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (54 bp):
AAAAGGAAGCCTTTGTGGCGATCTAAGAAAAGAAAGCCTTTGTGTTTATCTATG
Found at i:323079 original size:27 final size:27
Alignment explanation
Indices: 322892--323082 Score: 161
Period size: 27 Copynumber: 7.1 Consensus size: 27
322882 ACATGCCAGA
* * *
322892 AAAAGGAAGCCTTTGTAGCGATCTAAG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* **
322919 AAAAGAAAGCCTTTGTGTTTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * **
322946 AAAAGAAAGCCTTTGTGGCGATCTAAC
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* * * * * *
322973 AAATGAAAGTCTTTATGGAT-TTTAATG
1 AAAAGGAAGCCTTTGTGGCTATCT-ATG
*
323000 AAAAGGAAGCCTTTATGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
323027 AAAAGAAAACCTTTGTGGCTATCTATG
1 AAAAGGAAGCCTTTGTGGCTATCTATG
* *
323054 ACAAGGAAGCCTTCGTGG-TGATCTATG
1 AAAAGGAAGCCTTTGTGGCT-ATCTATG
323081 AA
1 AA
323083 GGGAATGCCC
Statistics
Matches: 129, Mismatches: 32, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
26 3 0.02
27 124 0.96
28 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (27 bp):
AAAAGGAAGCCTTTGTGGCTATCTATG
Found at i:338763 original size:23 final size:22
Alignment explanation
Indices: 338719--338763 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
338709 TAAAGAATTT
*
338719 TTTTAGGGCTGAAAATATTATA
1 TTTTAGGGCTGAAAATAATATA
338741 TTTTA-GGCTTGAAAATCAATATA
1 TTTTAGGGC-TGAAAAT-AATATA
338764 AATCAAGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 12 0.60
23 5 0.25
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (22 bp):
TTTTAGGGCTGAAAATAATATA
Found at i:353119 original size:85 final size:84
Alignment explanation
Indices: 352977--353149 Score: 337
Period size: 85 Copynumber: 2.0 Consensus size: 84
352967 AGCCCAGCAC
352977 TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
1 TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
353042 TGTAATGTTGCTACTAAGA
66 TGTAATGTTGCTACTAAGA
353061 TCCACCAACATTGTTTATTTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGAT
1 TCCACCAACATTGTTTA-TTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGAT
353126 TTGTAATGTTGCTACTAAGA
65 TTGTAATGTTGCTACTAAGA
353146 TCCA
1 TCCA
353150 TCATGCATTG
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 17 0.19
85 71 0.81
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (84 bp):
TCCACCAACATTGTTTATTTAGCATTCCAGCGTTTCGTGCTCACAAGCATTTACCAGAAATGATT
TGTAATGTTGCTACTAAGA
Found at i:353328 original size:34 final size:34
Alignment explanation
Indices: 353285--353351 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
353275 CCATGTTCTG
353285 CACCAATCAACTCAACAGTACATTATACAAATTT
1 CACCAATCAACTCAACAGTACATTATACAAATTT
*
353319 CACCAATCAACTCAACAGTACATTATGCAAATT
1 CACCAATCAACTCAACAGTACATTATACAAATT
353352 CCAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.43, C:0.27, G:0.04, T:0.25
Consensus pattern (34 bp):
CACCAATCAACTCAACAGTACATTATACAAATTT
Found at i:360817 original size:24 final size:24
Alignment explanation
Indices: 360790--360840 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
360780 ATAGATAGGA
360790 TACAAATGACATGTCATTAGGGGT
1 TACAAATGACATGTCATTAGGGGT
360814 TACAAATGACATGTCATTAGGGGT
1 TACAAATGACATGTCATTAGGGGT
360838 TAC
1 TAC
360841 CATGATTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (24 bp):
TACAAATGACATGTCATTAGGGGT
Found at i:364079 original size:9 final size:9
Alignment explanation
Indices: 364067--364128 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
364057 TATTAAAAAC
364067 GAGAGACTT
1 GAGAGACTT
*
364076 GAGAAACTT
1 GAGAGACTT
**
364085 GAGAAGGTTT
1 GAG-AGACTT
*
364095 GAGAGATTTT
1 GAGAGA-CTT
*
364105 GAGAGAATT
1 GAGAGACTT
*
364114 GAGAGAGTT
1 GAGAGACTT
364123 GAGAGA
1 GAGAGA
364129 ATGATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 29 0.66
10 15 0.34
ACGTcount: A:0.37, C:0.03, G:0.35, T:0.24
Consensus pattern (9 bp):
GAGAGACTT
Found at i:364126 original size:18 final size:19
Alignment explanation
Indices: 364093--364130 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
364083 TTGAGAAGGT
*
364093 TTGAGAGATTTTGAGAGAA
1 TTGAGAGATGTTGAGAGAA
364112 TTGAGAGA-GTTGAGAGAA
1 TTGAGAGATGTTGAGAGAA
364130 T
1 T
364131 GATATGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (19 bp):
TTGAGAGATGTTGAGAGAA
Found at i:376912 original size:25 final size:26
Alignment explanation
Indices: 376878--376928 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
376868 AAGTTGTAAA
376878 TAAAAAAATATC-TCTAGA-AATTTTC
1 TAAAAAAATATCTTC-AGAGAATTTTC
*
376903 TAAAATAATATCTTCAGAGAATTTTC
1 TAAAAAAATATCTTCAGAGAATTTTC
376929 CCTCTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (26 bp):
TAAAAAAATATCTTCAGAGAATTTTC
Found at i:377043 original size:21 final size:22
Alignment explanation
Indices: 377017--377070 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
377007 ATTCAACTAT
*
377017 TATTAAACTTAAT-CACTTTAA
1 TATTAAACTTAATACAATTTAA
*
377038 TATTAAA-TTAATATAATTTAA
1 TATTAAACTTAATACAATTTAA
377059 TATTAAATCTTA
1 TATTAAA-CTTA
377071 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.18
21 20 0.71
23 3 0.11
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAACTTAATACAATTTAA
Found at i:377050 original size:11 final size:11
Alignment explanation
Indices: 377034--377066 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
377024 CTTAATCACT
377034 TTAATATTAAA
1 TTAATATTAAA
*
377045 TTAATA-TAAT
1 TTAATATTAAA
377055 TTAATATTAAA
1 TTAATATTAAA
377066 T
1 T
377067 CTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:377337 original size:18 final size:18
Alignment explanation
Indices: 377311--377345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
377301 CCGCTGTTGA
*
377311 CCATCGGGATGTCATCGG
1 CCATCGGGATGCCATCGG
*
377329 CCATTGGGATGCCATCG
1 CCATCGGGATGCCATCG
377346 TCGCAGCCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (18 bp):
CCATCGGGATGCCATCGG
Found at i:383928 original size:13 final size:12
Alignment explanation
Indices: 383910--383943 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
383900 TACATAATAT
383910 AAATATTATAAAC
1 AAATA-TATAAAC
383923 AAATATA-AAAC
1 AAATATATAAAC
383934 AAATATATAA
1 AAATATATAA
383944 GGAGATAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 4 0.20
13 5 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATATAAAC
Found at i:387667 original size:5 final size:5
Alignment explanation
Indices: 387657--387693 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
387647 TTTTTAGAGT
*
387657 AATAA AATAA AATAA CATAA AATAA AAT-A AATAA AAT
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT
387694 TCAAGAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:387678 original size:15 final size:14
Alignment explanation
Indices: 387657--387693 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
387647 TTTTTAGAGT
387657 AATAAAATAAAATA
1 AATAAAATAAAATA
387671 ACATAAAATAAAATA
1 A-ATAAAATAAAATA
387686 AATAAAAT
1 AATAAAAT
387694 TCAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAATA
Done.