Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold381
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: 370863
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.31
Warning! 21801 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1039 original size:16 final size:16
Alignment explanation
Indices: 1017--1055 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1007 GTTTGGTTCA
*
1017 CTGTAATGGAATAGAG
1 CTGTAATGGAATAAAG
*
1033 TTGTAATGGAATAAAG
1 CTGTAATGGAATAAAG
1049 CTGTAAT
1 CTGTAAT
1056 TAGTAATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:5819 original size:27 final size:27
Alignment explanation
Indices: 5542--5817 Score: 313
Period size: 27 Copynumber: 10.2 Consensus size: 27
5532 GTAATGGGCC
* **
5542 TAAAATAACCGAAATACCTTTGAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
*
5569 TAAAATAACCGAAATACCCTCAAAAGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* *
5596 TAAAATAACCGAAATACCCCCGAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
*
5623 TAAAATAACCGAAATACCCTCGAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* * *
5650 TAAAATGACCGAAATATCCTTAAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
5677 TAAAATAACCGAAATACCCTCAAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* * *
5704 TAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* **
5731 TAAAATAACTGAAATACCCTCGCAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
* * *
5758 TAGAATGACTGAAATACCCT-AGCAA-GG
1 TAAAATAACCGAAATACCCTCA--AAGGG
* ** *
5785 TAAAATGACTAAAATACCCCCAAAGGG
1 TAAAATAACCGAAATACCCTCAAAGGG
5812 TAAAAT
1 TAAAAT
5818 GATTGTTATA
Statistics
Matches: 214, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 210 0.98
28 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
TAAAATAACCGAAATACCCTCAAAGGG
Found at i:6030 original size:26 final size:26
Alignment explanation
Indices: 5994--6070 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
5984 TTGCCACATA
* *
5994 TACTGTTACTGGCAACTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
6020 TACTGTTACTGGTAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGCTGCGT
* *
6046 CACTATTACTGGCAGCTTTGCTGCG
1 TACTGTTACTGGCAGCTTTGCTGCG
6071 ATATTGGTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGCTGCGT
Found at i:6216 original size:28 final size:28
Alignment explanation
Indices: 6176--6243 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
6166 ACTGCATTAT
* *
6176 ACTGTTATTGTATTGGGCTAAGGGCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
6204 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* *
6232 GCTGTTGCTGTA
1 ACTGTTACTGTA
6244 AAGAGCTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:7814 original size:23 final size:23
Alignment explanation
Indices: 7758--8018 Score: 207
Period size: 23 Copynumber: 11.6 Consensus size: 23
7748 TGCAGCACTC
* *
7758 AAACACTTCGATTTACATCATTT
1 AAACACTTCAATTTACAACATTT
* * * *
7781 CAGCACCTCAATTTACAACAATT
1 AAACACTTCAATTTACAACATTT
*
7804 AAACACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
* **
7827 AAACACCTCACCTTACAACACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
7851 -AACA-TCCCAATTAACAACATTT
1 AAACACT-TCAATTTACAACATTT
* * * *
7873 ATACACCTC-A-GT---AC-TTA
1 AAACACTTCAATTTACAACATTT
7890 AAACACTTCAATTTACAACATTT
1 AAACACTTCAATTTACAACATTT
* *
7913 AAACACTTCAATTTGCAGCACTTT
1 AAACACTTCAATTTACAACA-TTT
* *
7937 -AACACTTCAATTCACAGCATTT
1 AAACACTTCAATTTACAACATTT
* * *
7959 AAATACTTCAATTTGCTACATTT
1 AAACACTTCAATTTACAACATTT
* *
7982 TAACACTTCAATTTACAGCATTT
1 AAACACTTCAATTTACAACATTT
8005 AAACACTTCAATTT
1 AAACACTTCAATTT
8019 GCAGCACTTT
Statistics
Matches: 181, Mismatches: 45, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
17 9 0.05
18 3 0.02
19 1 0.01
22 9 0.05
23 153 0.85
24 6 0.03
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.33
Consensus pattern (23 bp):
AAACACTTCAATTTACAACATTT
Found at i:7826 original size:46 final size:46
Alignment explanation
Indices: 7753--8063 Score: 217
Period size: 46 Copynumber: 6.9 Consensus size: 46
7743 TCATTTGCAG
* * * * *
7753 CACTCAAACACTTCGATTTACATCATTTCAGCACCTCAATTTACAA
1 CACTTAAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
* * **
7799 CAATTAAACACTTCAATTTACAGCATTTAAACACCTCACCTTACAA
1 CACTTAAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
* * * * *
7845 CACTTTAACA-TCCCAATTAACAACATTTATACACCTC-A-GT----
1 CACTTAAACACT-TCAATTTACAACATTTAAACACCTCAATTTACAA
* * *
7885 -ACTTAAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAG
1 CACTT-AAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
* * * * * * *
7931 CACTTTAACACTTCAATTCACAGCATTTAAATACTTCAATTTGCTA
1 CACTTAAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
* * * * * *
7977 CATTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAG
1 CACTTAAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
* * * **
8023 CACTTTAACA-TCTCTATTAACAACATTTATGCACCTCAATT
1 CACTTAAACACT-TCAATTTACAACATTTAAACACCTCAATT
8064 ACAGCAATAA
Statistics
Matches: 214, Mismatches: 40, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
39 4 0.02
40 25 0.12
41 2 0.01
42 1 0.00
44 1 0.00
45 2 0.01
46 175 0.82
47 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (46 bp):
CACTTAAACACTTCAATTTACAACATTTAAACACCTCAATTTACAA
Found at i:8004 original size:132 final size:132
Alignment explanation
Indices: 7758--8010 Score: 301
Period size: 132 Copynumber: 1.9 Consensus size: 132
7748 TGCAGCACTC
* * * * *
7758 AAACACTTCGATTTACATCATTTCAGCACCTCAATTTACAACAATTAAACACTTCAATTTACAGC
1 AAACACTTCAATTTACAACATTTAAACACCTCAATTTACAACAATTAAACACTTCAATTCACAGC
* *
7823 ATTTAAACACCTCACCTTACAACACTTTAACATCCCAATTAACAACATTTATACACCTCAGTACT
66 ATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTTAAACACCTCAGTACT
7888 TA
131 TA
* * * * *
7890 AAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACACTTCAATTCACAGC
1 AAACACTTCAATTTACAACATTTAAACACCTCAATTTACAACAATTAAACACTTCAATTCACAGC
* * * * * * * * *
7955 ATTTAAATACTTCAATTTGCTACATTTTAACA-CTTCAATTTACAGCATTTAAACAC
66 ATTTAAACACCTCAACTTACAACACTTTAACATC-CCAATTAACAACATTTAAACAC
8011 TTCAATTTGC
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
131 1 0.01
132 98 0.99
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (132 bp):
AAACACTTCAATTTACAACATTTAAACACCTCAATTTACAACAATTAAACACTTCAATTCACAGC
ATTTAAACACCTCAACTTACAACACTTTAACATCCCAATTAACAACATTTAAACACCTCAGTACT
TA
Found at i:10980 original size:18 final size:20
Alignment explanation
Indices: 10947--10985 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
10937 ATAAATTTTG
10947 ATAATTATACATTTAA-AAA
1 ATAATTATACATTTAATAAA
10966 ATAATTATA-ATTTAATAAA
1 ATAATTATACATTTAATAAA
10985 A
1 A
10986 ATGGTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATTATACATTTAATAAA
Found at i:11637 original size:6 final size:6
Alignment explanation
Indices: 11626--11654 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11616 TAAACCCTTT
11626 TCAGTA TCAGTA TCAGTA TCAGTA TCAGT
1 TCAGTA TCAGTA TCAGTA TCAGTA TCAGT
11655 CCTGTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
TCAGTA
Found at i:14444 original size:898 final size:899
Alignment explanation
Indices: 12699--14496 Score: 3589
Period size: 898 Copynumber: 2.0 Consensus size: 899
12689 AATATCTCAT
12699 AATATGAAATTCTTTTGCTTACTTAGTTTCTTCTATGAGAAACTAGACTCAAATTTATTTAATCC
1 AATATGAAATTCTTTTGCTTACTTAGTTTCTTCTATGAGAAACTAGACTCAAATTTATTTAATCC
12764 CATACTTTTTTCTTCCTCTAATTCGATTTCCATAATTTATGGTGATTTTTCAAATTTAGCCTACT
66 CATACTTTTTTCTTCCTCTAATTCGATTTCCATAATTTATGGTGATTTTTCAAATTTAGCCTACT
12829 GCTGCTGTCCAAACAGCAAGCAATTTTAGCTTTTCGTCGAATCCCTTATTTTTGTGTTTCAGGCA
131 GCTGCTGTCCAAACAGCAAGCAATTTTAGCTTTTCGTCGAATCCCTTATTTTTGTGTTTCAGGCA
12894 CACACCTGGTTTTGTTTCGTTGCAAAAACATTCCCGAGAACTCCAATACCTAAAATTGACCAAAC
196 CACACCTGGTTTTGTTTCGTTGCAAAAACATTCCCGAGAACTCCAATACCTAAAATTGACCAAAC
12959 GAACCCAGAATTAAACACTTAGAATGACATTAAATCGAACCAAAAGTGATAGACAACCCACTTAA
261 GAACCCAGAATTAAACACTTAGAATGACATTAAATCGAACCAAAAGTGATAGACAACCCACTTAA
13024 ATCGACTAAAATCTTACCTTCGGTCGAGCAACGTTCATCCGCATGTTTAAAGCGCCGACTGGGAA
326 ATCGACTAAAATCTTACCTTCGGTCGAGCAACGTTCATCCGCATGTTTAAAGCGCCGACTGGGAA
13089 ACCCCAGCACCTTGATCTTCTCATAAACACAGGATACATCGATTAACTACAATAAACTGACGTTG
391 ACCCCAGCACCTTGATCTTCTCATAAACACAGGATACATCGATTAACTACAATAAACTGACGTTG
13154 CTAGACCCCAAATCAAAGGAAGAAGGCCAAAAGAGATCACTTAGCAGATGAAAAATGGCCACGAA
456 CTAGACCCCAAATCAAAGGAAGAAGGCCAAAAGAGATCACTTAGCAGATGAAAAATGGCCACGAA
13219 CGCAAGAGCAATGATTGACTGCGAAAAATCCAACAGGAAGCCGCGAAAAATTGAAGAAGAAAAGT
521 CGCAAGAGCAATGATTGACTGCGAAAAATCCAACAGGAAGCCGCGAAAAATTGAAGAAGAAAAGT
13284 GAAGAAGAAAGTCGACGTCAAAATTTTGGAGAGATAGAAAGAGAAATGAATTTTGAAAAGAATAA
586 GAAGAAGAAAGTCGACGTCAAAATTTTGGAGAGATAGAAAGAGAAATGAATTTTGAAAAGAATAA
13349 AATAATAATGATAAAAAACAAAAATAATCCTGATAACTCTCATATCTTCTCTCAATTAACTACCC
651 AATAATAATGATAAAAAACAAAAATAATCCTGATAACTCTCATATCTTCTCTCAATTAACTACCC
13414 ACTAACAATCCACTACTCAGAATCCATCTTCTACACAACTCTTCCAGGAAACAGAGTAAAAAGAT
716 ACTAACAATCCACTACTCAGAATCCATCTTCTACACAACTCTTCCAGGAAACAGAGTAAAAAGAT
13479 TAACATTCTTACTCACGCAAAGATTCGAACACAAAACCTCCAACACTCCAACTCGTAAACTTAAG
781 TAACATTCTTACTCACGCAAAGATTCGAACACAAAACCTCCAACACTCCAACTCGTAAACTTAAG
13544 CCAACTGAACAAGGATAAGGCTTTAATCAGAAAATATTTTCAAAATTTCGCCGA
846 CCAACTGAACAAGGATAAGGCTTTAATCAGAAAATATTTTCAAAATTTCGCCGA
13598 AATATGAAA-TCTTTTGCTTACTTAGTTTCTTCTATGAGAAACTAGACTCAAATTTATTTAATCC
1 AATATGAAATTCTTTTGCTTACTTAGTTTCTTCTATGAGAAACTAGACTCAAATTTATTTAATCC
13662 CATACTTTTTTCTTCCTCTAATTCGATTTCCATAATTTATGGTGATTTTTCAAATTTAGCCTACT
66 CATACTTTTTTCTTCCTCTAATTCGATTTCCATAATTTATGGTGATTTTTCAAATTTAGCCTACT
13727 GCTGCTGTCCAAACAGCAAGCAATTTTAGCTTTTCGTCGAATCCCTTATTTTTGTGTTTCAGGCA
131 GCTGCTGTCCAAACAGCAAGCAATTTTAGCTTTTCGTCGAATCCCTTATTTTTGTGTTTCAGGCA
13792 CACACCTGGTTTTGTTTCGTTGCAAAAACATTCCCGAGAACTCCAATACCTAAAATTGACCAAAC
196 CACACCTGGTTTTGTTTCGTTGCAAAAACATTCCCGAGAACTCCAATACCTAAAATTGACCAAAC
13857 GAACCCAGAATTAAACACTTAGAATGACATTAAATCGAACCAAAAGTGATAGACAACCCACTTAA
261 GAACCCAGAATTAAACACTTAGAATGACATTAAATCGAACCAAAAGTGATAGACAACCCACTTAA
13922 ATCGACTAAAATCTTACCTTCGGTCGAGCAACGTTCATCCGCATGTTTAAAGCGCCGACTGGGAA
326 ATCGACTAAAATCTTACCTTCGGTCGAGCAACGTTCATCCGCATGTTTAAAGCGCCGACTGGGAA
13987 ACCCCAGCACCTTGATCTTCTCATAAACACAGGATACATCGATTAACTACAATAAACTGACGTTG
391 ACCCCAGCACCTTGATCTTCTCATAAACACAGGATACATCGATTAACTACAATAAACTGACGTTG
14052 CTAGACCCCAAATCAAAGGAAGAAGGCCAAAAGAGATCACTTAGCAGATGAAAAATGGCCACGAA
456 CTAGACCCCAAATCAAAGGAAGAAGGCCAAAAGAGATCACTTAGCAGATGAAAAATGGCCACGAA
14117 CGCAAGAGCAATGATTGACTGCGAAAAATCCAACAGGAAGCCGCGAAAAATTGAAGAAGAAAAGT
521 CGCAAGAGCAATGATTGACTGCGAAAAATCCAACAGGAAGCCGCGAAAAATTGAAGAAGAAAAGT
14182 GAAGAAGAAAGTCGACGTCAAAATTTTGGAGAGATAGAAAGAGAAATGAATTTTGAAAAGAATAA
586 GAAGAAGAAAGTCGACGTCAAAATTTTGGAGAGATAGAAAGAGAAATGAATTTTGAAAAGAATAA
14247 AATAATAATGATAAAAAACAAAAATAATCCTGATAACTCTCATATCTTCTCTCAATTAACTACCC
651 AATAATAATGATAAAAAACAAAAATAATCCTGATAACTCTCATATCTTCTCTCAATTAACTACCC
14312 ACTAACAATCCACTACTCAGAATCCATCTTCTACACAACTCTTCCAGGAAACAGAGTAAAAAGAT
716 ACTAACAATCCACTACTCAGAATCCATCTTCTACACAACTCTTCCAGGAAACAGAGTAAAAAGAT
14377 TAACATTCTTACTCACGCAAAGATTCGAACACAAAACCTCCAACACTCCAACTCGTAAACTTAAG
781 TAACATTCTTACTCACGCAAAGATTCGAACACAAAACCTCCAACACTCCAACTCGTAAACTTAAG
14442 CCAACTGAACAAGGATAAGGCTTTAATCAGAAAATATTTTCAAAATTTCGCCGA
846 CCAACTGAACAAGGATAAGGCTTTAATCAGAAAATATTTTCAAAATTTCGCCGA
14496 A
1 A
14497 GGCATGGCTT
Statistics
Matches: 899, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
898 890 0.99
899 9 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (899 bp):
AATATGAAATTCTTTTGCTTACTTAGTTTCTTCTATGAGAAACTAGACTCAAATTTATTTAATCC
CATACTTTTTTCTTCCTCTAATTCGATTTCCATAATTTATGGTGATTTTTCAAATTTAGCCTACT
GCTGCTGTCCAAACAGCAAGCAATTTTAGCTTTTCGTCGAATCCCTTATTTTTGTGTTTCAGGCA
CACACCTGGTTTTGTTTCGTTGCAAAAACATTCCCGAGAACTCCAATACCTAAAATTGACCAAAC
GAACCCAGAATTAAACACTTAGAATGACATTAAATCGAACCAAAAGTGATAGACAACCCACTTAA
ATCGACTAAAATCTTACCTTCGGTCGAGCAACGTTCATCCGCATGTTTAAAGCGCCGACTGGGAA
ACCCCAGCACCTTGATCTTCTCATAAACACAGGATACATCGATTAACTACAATAAACTGACGTTG
CTAGACCCCAAATCAAAGGAAGAAGGCCAAAAGAGATCACTTAGCAGATGAAAAATGGCCACGAA
CGCAAGAGCAATGATTGACTGCGAAAAATCCAACAGGAAGCCGCGAAAAATTGAAGAAGAAAAGT
GAAGAAGAAAGTCGACGTCAAAATTTTGGAGAGATAGAAAGAGAAATGAATTTTGAAAAGAATAA
AATAATAATGATAAAAAACAAAAATAATCCTGATAACTCTCATATCTTCTCTCAATTAACTACCC
ACTAACAATCCACTACTCAGAATCCATCTTCTACACAACTCTTCCAGGAAACAGAGTAAAAAGAT
TAACATTCTTACTCACGCAAAGATTCGAACACAAAACCTCCAACACTCCAACTCGTAAACTTAAG
CCAACTGAACAAGGATAAGGCTTTAATCAGAAAATATTTTCAAAATTTCGCCGA
Found at i:21600 original size:52 final size:51
Alignment explanation
Indices: 21507--21606 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 51
21497 ACTTATATAT
21507 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
1 ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
* * * *
21558 ATATAAAATATATTCATGCATTTACT-AAAA-AATGAAATATATAAGTATA
1 ATATAAAATACA-TAATGCATTTA-TGAAAACAAGGAAA-ATATAAATATA
21607 ATATAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
51 17 0.40
52 24 0.57
53 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (51 bp):
ATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATATACAC
Found at i:21882 original size:3 final size:3
Alignment explanation
Indices: 21874--21913 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
21864 ATATGTAGGT
*
21874 ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21914 CAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21897 original size:15 final size:12
Alignment explanation
Indices: 21876--21927 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
21866 ATGTAGGTAT
21876 AATAATAATATATA
1 AATAATAATA-A-A
21890 ATATAATAATAAA
1 A-ATAATAATAAA
21903 AATAATAATAACA
1 AATAATAATAA-A
*
21916 AA-ATTAATAAA
1 AATAATAATAAA
21927 A
1 A
21928 TAGACTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 5 0.14
14 2 0.06
15 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:22174 original size:19 final size:21
Alignment explanation
Indices: 22136--22174 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
22126 CCTTTTTTAA
*
22136 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
22157 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
22175 AGAAAACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:22370 original size:22 final size:21
Alignment explanation
Indices: 22335--22393 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
22325 AAAGGGTATC
* * *
22335 TACAAATTAAATCTATGAGAT
1 TACAAATCATATCTATAAGAT
*
22356 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TATAAGAT
*
22379 TACATATCATATCTA
1 TACAAATCATATCTA
22394 AGATTGCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTATAAGAT
Found at i:22386 original size:17 final size:17
Alignment explanation
Indices: 22364--22416 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
22354 ATTACAAAAT
22364 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
22381 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
* *
22400 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
22417 TGTTTCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:23505 original size:21 final size:21
Alignment explanation
Indices: 23488--23527 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23478 ACCGTTATAG
23488 TAACTAATATTACTGTTACAA
1 TAACTAATATTACTGTTACAA
* *
23509 TAATTAATATTACTATTAC
1 TAACTAATATTACTGTTAC
23528 TGTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (21 bp):
TAACTAATATTACTGTTACAA
Found at i:26481 original size:36 final size:36
Alignment explanation
Indices: 26441--26511 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
26431 TTCAGATTAA
26441 TCCATCCTCCCTAGATTCTATTTGATTTATGTTATT
1 TCCATCCTCCCTAGATTCTATTTGATTTATGTTATT
* *
26477 TCCATCCTCTCTAGATTCTCTTTGATTTATGTTAT
1 TCCATCCTCCCTAGATTCTATTTGATTTATGTTAT
26512 CAACACCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (36 bp):
TCCATCCTCCCTAGATTCTATTTGATTTATGTTATT
Found at i:29014 original size:30 final size:30
Alignment explanation
Indices: 28949--29029 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
28939 AAATTTTAAA
* *
28949 TTAATAATAATAAAAATTT-ATTTTGGTCC
1 TTAAAAATAATAAAAATTTAATTTTAGTCC
* * *
28978 TCAAAAATAATAAAAATTTAATTTTATTCT
1 TTAAAAATAATAAAAATTTAATTTTAGTCC
*
29008 TTAAAAATTATAAAAATATTAA
1 TTAAAAATAATAAAAAT-TTAA
29030 CTATTATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 17 0.40
30 22 0.51
31 4 0.09
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAAAATAATAAAAATTTAATTTTAGTCC
Found at i:29870 original size:28 final size:29
Alignment explanation
Indices: 29794--29878 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 29
29784 ACTGTTATTT
* * * *
29794 TGTTTCTT-TATGTAGATTTAAATTTAAA
1 TGTTTATTATATGTAAATTTAATTTTTAA
* * * *
29822 TGTTTATTTTATATGATTTTAATTTTTAA
1 TGTTTATTATATGTAAATTTAATTTTTAA
*
29851 TG-TTATTATATGTAAATTT-ATTTATAA
1 TGTTTATTATATGTAAATTTAATTTTTAA
29878 T
1 T
29879 TAATAGTTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
27 8 0.18
28 20 0.45
29 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.59
Consensus pattern (29 bp):
TGTTTATTATATGTAAATTTAATTTTTAA
Found at i:30478 original size:333 final size:334
Alignment explanation
Indices: 29862--30528 Score: 1327
Period size: 333 Copynumber: 2.0 Consensus size: 334
29852 GTTATTATAT
29862 GTAAATTTATTTATAATTAATAGTTATTTAATATAATTATAAAGTAAATATATAATACATGTAAA
1 GTAAATTTATTTATAATTAATAGTTATTTAATATAATTATAAAGTAAATATATAATACATGTAAA
29927 TTTATTTACAAATTATATAAAAGATAGTTTTTATACCATGTCTATAACTCCTCATAGTTTATTTA
66 TTTATTTACAAATTATATAAAAGATAGTTTTTATACCATGTCTATAACTCCTCATAGTTTATTTA
29992 CATCTTTCAAGTTATTTTTAATAATAATAGACAATATTGTTTTTGACACAATTCTTAGAACTATT
131 CATCTTTCAAGTTATTTTTAATAATAATAGACAATATTGTTTTTGACACAATTCTTAGAACTATT
30057 AATAGCTGCACTTAAACCTACATCCTCTTGCATTGACAACCATGCTCATACCAATCGAAATAAGA
196 AATAGCTGCACTTAAACCTACATCCTCTTGCATTGACAACCATGCTCATACCAATCGAAATAAGA
30122 TTCGACAAAGTTGATTTTAAAAATAAGATATTGTATTCTTTAATTTAATTTGAAAACCTCTTTTT
261 TTCGACAAAGTTGATTTTAAAAATAAGATATTGTATTCTTTAATTTAATTTGAAAACCTCTTTTT
30187 GCAAAAATA
326 GCAAAAATA
30196 GTAAATTTA-TTATAATTAATAGTTATTTAATATAATTATAAAGTAAATATATAATACATGTAAA
1 GTAAATTTATTTATAATTAATAGTTATTTAATATAATTATAAAGTAAATATATAATACATGTAAA
30260 TTTATTTACAAATTATATAAAAGATAGTTTTTATACCATGTCTATAACTCCTCATAGTTTATTTA
66 TTTATTTACAAATTATATAAAAGATAGTTTTTATACCATGTCTATAACTCCTCATAGTTTATTTA
30325 CATCTTTCAAGTTATTTTTAATAATAATAGACAATATTGTTTTTGACACAATTCTTAGAACTATT
131 CATCTTTCAAGTTATTTTTAATAATAATAGACAATATTGTTTTTGACACAATTCTTAGAACTATT
30390 AATAGCTGCACTTAAACCTACATCCTCTTGCATTGACAACCATGCTCATACCAATCGAAATAAGA
196 AATAGCTGCACTTAAACCTACATCCTCTTGCATTGACAACCATGCTCATACCAATCGAAATAAGA
30455 TTCGACAAAGTTGATTTTAAAAATAAGATATTGTATTCTTTAATTTAATTTGAAAACCTCTTTTT
261 TTCGACAAAGTTGATTTTAAAAATAAGATATTGTATTCTTTAATTTAATTTGAAAACCTCTTTTT
30520 GCAAAAATA
326 GCAAAAATA
30529 TATTTAATTT
Statistics
Matches: 333, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
333 324 0.97
334 9 0.03
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (334 bp):
GTAAATTTATTTATAATTAATAGTTATTTAATATAATTATAAAGTAAATATATAATACATGTAAA
TTTATTTACAAATTATATAAAAGATAGTTTTTATACCATGTCTATAACTCCTCATAGTTTATTTA
CATCTTTCAAGTTATTTTTAATAATAATAGACAATATTGTTTTTGACACAATTCTTAGAACTATT
AATAGCTGCACTTAAACCTACATCCTCTTGCATTGACAACCATGCTCATACCAATCGAAATAAGA
TTCGACAAAGTTGATTTTAAAAATAAGATATTGTATTCTTTAATTTAATTTGAAAACCTCTTTTT
GCAAAAATA
Found at i:34517 original size:36 final size:36
Alignment explanation
Indices: 34468--34536 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
34458 ATTCTCTGTC
34468 TATAGATTAATTTAAGTAACAGAAAGTGATCATGTT
1 TATAGATTAATTTAAGTAACAGAAAGTGATCATGTT
* *
34504 TATAGATTGATTTAAGTATCAGAAAGTGATCAT
1 TATAGATTAATTTAAGTAACAGAAAGTGATCAT
34537 AATATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (36 bp):
TATAGATTAATTTAAGTAACAGAAAGTGATCATGTT
Found at i:35287 original size:20 final size:20
Alignment explanation
Indices: 35262--35302 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35252 AGAAAAATAC
35262 ATGCATCCGCCCAAATTTTA
1 ATGCATCCGCCCAAATTTTA
35282 ATGCATCCGCCCAAATTTTA
1 ATGCATCCGCCCAAATTTTA
35302 A
1 A
35303 AAACAACGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
ATGCATCCGCCCAAATTTTA
Found at i:35473 original size:26 final size:25
Alignment explanation
Indices: 35406--35474 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
35396 ATTATACATT
*
35406 TAAT-TTACTTTTTATCTCATTTTA
1 TAATATTACTTTTTATCTAATTTTA
*
35430 TAATATTA-TTATAATATCTAATTTTA
1 TAATATTACTT-T-TTATCTAATTTTA
35456 TTAA-ACTTACTTTTTATCT
1 -TAATA-TTACTTTTTATCT
35475 CACATTATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
24 6 0.17
25 4 0.11
26 17 0.47
27 7 0.19
28 2 0.06
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATATTACTTTTTATCTAATTTTA
Found at i:35489 original size:52 final size:52
Alignment explanation
Indices: 35410--35510 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
35400 TACATTTAAT
** * *
35410 TTACTTTTTATCTCATTTTATAATATTATTATAATATCTAATTTTATTAAAC
1 TTACTTTTTATCTCACATTATAATATTATCATAATATCTAATTTCATTAAAC
*
35462 TTACTTTTTATCTCACATTATACTATTATCATAATATCTAATTTCATTA
1 TTACTTTTTATCTCACATTATAATATTATCATAATATCTAATTTCATTA
35511 TCGCCATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (52 bp):
TTACTTTTTATCTCACATTATAATATTATCATAATATCTAATTTCATTAAAC
Found at i:39994 original size:6 final size:6
Alignment explanation
Indices: 39983--40077 Score: 190
Period size: 6 Copynumber: 15.8 Consensus size: 6
39973 ATTATATAGT
39983 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
40031 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATAT
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATAT
40078 TGTGCCTTCA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
CATATA
Found at i:43859 original size:18 final size:18
Alignment explanation
Indices: 43802--43864 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
43792 TTTTTATTTA
43802 ATTTTTTAAATAATT-ATGT
1 ATTTTTT-AA-AATTAATGT
*
43821 -TTTTTT-AAATTAAAAGTT
1 ATTTTTTAAAATT-AATG-T
43839 ATTTTTTAAAATTAATGT
1 ATTTTTTAAAATTAATGT
*
43857 ATTGTTTA
1 ATTTTTTA
43865 TTTATTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.11
16 1 0.03
17 2 0.06
18 15 0.42
19 9 0.25
20 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
ATTTTTTAAAATTAATGT
Found at i:43917 original size:29 final size:30
Alignment explanation
Indices: 43885--43951 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 30
43875 TATTTTCTAC
43885 ATGTAATTATTTTATTGGGTTACTTAAGT-
1 ATGTAATTATTTTATTGGGTTACTTAAGTA
43914 ATGTAATTATTTTATTGGGTTACTTAAGTA
1 ATGTAATTATTTTATTGGGTTACTTAAGTA
43944 ATG-AATTA
1 ATGTAATTA
43952 CATCTAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 34 0.92
30 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.49
Consensus pattern (30 bp):
ATGTAATTATTTTATTGGGTTACTTAAGTA
Found at i:44465 original size:20 final size:20
Alignment explanation
Indices: 44431--44472 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44421 AACTATTTAA
** *
44431 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
44451 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
44471 AT
1 AT
44473 GGGTTTATTT
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:49497 original size:110 final size:110
Alignment explanation
Indices: 49304--49508 Score: 383
Period size: 110 Copynumber: 1.9 Consensus size: 110
49294 GTAAGACACC
49304 AATATTAAATGAATAATTATGTGTTTATTTTAAAGACATTATTATTCATAAAGACACTTATTGAA
1 AATATTAAATGAATAATTATGTGTTTATTTTAAAGACATTATTATTCATAAAGACACTTATTGAA
* * *
49369 AGATGTCTTTATGGAGAGACATGAAAATTCTATTTAAATAGTTAT
66 AAATGTCTCTATGAAGAGACATGAAAATTCTATTTAAATAGTTAT
49414 AATATTAAATGAATAATTATGTGTTTATTTTAAAGACATTATTATTCATAAAGACACTTATTGAA
1 AATATTAAATGAATAATTATGTGTTTATTTTAAAGACATTATTATTCATAAAGACACTTATTGAA
49479 AAATGTCTCTATGAAGAGACATGAAAATTC
66 AAATGTCTCTATGAAGAGACATGAAAATTC
49509 CTATAGATAG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 92 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (110 bp):
AATATTAAATGAATAATTATGTGTTTATTTTAAAGACATTATTATTCATAAAGACACTTATTGAA
AAATGTCTCTATGAAGAGACATGAAAATTCTATTTAAATAGTTAT
Found at i:56137 original size:16 final size:16
Alignment explanation
Indices: 56118--56148 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56108 ATATCTTGGC
*
56118 ATATATATTTTTATTA
1 ATATATATCTTTATTA
56134 ATATATATCTTTATT
1 ATATATATCTTTATT
56149 TTGCATAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATATCTTTATTA
Found at i:60375 original size:16 final size:16
Alignment explanation
Indices: 60337--60374 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
60327 AGCAATTTAA
60337 TTTTTTTAATTTTATG
1 TTTTTTTAATTTTATG
* *
60353 TTATTTTAATTTTCT-
1 TTTTTTTAATTTTATG
60368 TTTTTTT
1 TTTTTTT
60375 TCTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTTTAATTTTATG
Found at i:65765 original size:25 final size:26
Alignment explanation
Indices: 65726--65774 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
65716 CAATAAATGA
65726 AAAGAAATGAAAGAAAAACAAAACAG
1 AAAGAAATGAAAGAAAAACAAAACAG
* *
65752 AAAGAAA-GAAAGAAGAAGAAAAC
1 AAAGAAATGAAAGAAAAACAAAAC
65775 GTTAGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.73, C:0.06, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAGAAATGAAAGAAAAACAAAACAG
Found at i:69390 original size:33 final size:32
Alignment explanation
Indices: 69348--69409 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
69338 ACATGACGAA
*
69348 TATTAGCTGTATAACACAGCCACGTTGCAAGCC
1 TATTAGCTGTATAACACAG-CACGTCGCAAGCC
* *
69381 TATTAGCTGTATGATACAGCACGTCGCAA
1 TATTAGCTGTATAACACAGCACGTCGCAA
69410 ATCTATTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 9 0.35
33 17 0.65
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (32 bp):
TATTAGCTGTATAACACAGCACGTCGCAAGCC
Found at i:69416 original size:32 final size:33
Alignment explanation
Indices: 69348--69416 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
69338 ACATGACGAA
* *
69348 TATTAGCTGTATAACACAGCCACGTTGCAAGCC
1 TATTAGCTGTATAACACAGCCACGTCGCAAACC
* * *
69381 TATTAGCTGTATGATACAG-CACGTCGCAAATC
1 TATTAGCTGTATAACACAGCCACGTCGCAAACC
69413 TATT
1 TATT
69417 GCATCGTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (33 bp):
TATTAGCTGTATAACACAGCCACGTCGCAAACC
Found at i:71366 original size:21 final size:21
Alignment explanation
Indices: 71340--71402 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
71330 TTGGTATTTG
71340 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
71361 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
71382 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
71403 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:72338 original size:10 final size:10
Alignment explanation
Indices: 72323--72364 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
72313 TTTGCAAGTT
72323 TTGAGCTAAA
1 TTGAGCTAAA
* *
72333 TTGAGCTGAT
1 TTGAGCTAAA
*
72343 TTGAGCT-CA
1 TTGAGCTAAA
72352 TTGAGCTAAA
1 TTGAGCTAAA
72362 TTG
1 TTG
72365 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:77109 original size:30 final size:30
Alignment explanation
Indices: 76981--77110 Score: 140
Period size: 30 Copynumber: 4.4 Consensus size: 30
76971 AAAAAATTGT
* *
76981 ATTTTGACCCCTAAACTTTTTCAAAATTAC
1 ATTTCGACCCCTAAACTTTCTCAAAATTAC
**
77011 ATTTAAACCCCTAAACATTT-TC-AAATTAC
1 ATTTCGACCCCTAAAC-TTTCTCAAAATTAC
* * *
77040 ATTTCAACCCTTAAAATTTCTCAAAATTAC
1 ATTTCGACCCCTAAACTTTCTCAAAATTAC
*
77070 AATTT-GACCCCTAAACTTTCTAAAAATTAC
1 -ATTTCGACCCCTAAACTTTCTCAAAATTAC
*
77100 GTTTCGACCCC
1 ATTTCGACCCC
77111 AAAAGTTTTG
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.04
29 25 0.29
30 50 0.59
31 7 0.08
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTCGACCCCTAAACTTTCTCAAAATTAC
Found at i:77437 original size:20 final size:21
Alignment explanation
Indices: 77412--77451 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
77402 AACAAAAAAC
*
77412 AAAAGAGAAAGAGAA-AGAAA
1 AAAAGAAAAAGAGAAGAGAAA
77432 AAAAGAAAAAGAGAAGAGAA
1 AAAAGAAAAAGAGAAGAGAA
77452 GAGGAGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAGAAGAGAAA
Found at i:77557 original size:4 final size:4
Alignment explanation
Indices: 77548--77617 Score: 50
Period size: 4 Copynumber: 19.8 Consensus size: 4
77538 AAGGGAAGAT
* * *
77548 GAAA GAAA GAAA G-AA G-AA G-AA GGAA -AAA GAAA GAAA -AAG GGAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
77591 -AAA -AAA GAAA -AAA GAAA -AAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
77618 CTTTTTTTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
3 24 0.44
4 31 0.56
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:77564 original size:7 final size:7
Alignment explanation
Indices: 77543--77617 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
77533 AGAAAAAGGG
*
77543 AAGATGA
1 AAGAAGA
77550 AAGAAAGA
1 AAG-AAGA
77558 AAGAAG-
1 AAGAAGA
77564 AAGAAGGA
1 AAGAA-GA
77572 AA-AAGA
1 AAGAAGA
77578 AAGAA-A
1 AAGAAGA
77584 AAGGGAA-A
1 AA--GAAGA
*
77592 AAAAAGA
1 AAGAAGA
*
77599 AAAAAGA
1 AAGAAGA
*
77606 AAAAAGA
1 AAGAAGA
77613 AAGAA
1 AAGAA
77618 CTTTTTTTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
6 14 0.24
7 30 0.52
8 14 0.24
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (7 bp):
AAGAAGA
Found at i:77587 original size:17 final size:17
Alignment explanation
Indices: 77557--77617 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
77547 TGAAAGAAAG
*
77557 AAAG-AAGAAGAAGGAA
1 AAAGAAAGAAAAAGGAA
77573 AAAGAAAGAAAAAGGGAA
1 AAAGAAAGAAAAA-GGAA
*
77591 AAA-AAAGAAAAAAGAAA
1 AAAGAAAG-AAAAAGGAA
77608 AAAGAAAGAA
1 AAAGAAAGAA
77618 CTTTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.10
17 19 0.49
18 16 0.41
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAGGAA
Found at i:77615 original size:11 final size:11
Alignment explanation
Indices: 77525--77617 Score: 60
Period size: 11 Copynumber: 8.1 Consensus size: 11
77515 GGGCTGAACG
*
77525 AAAAAGGAAGA
1 AAAAAGAAAGA
* *
77536 AAAAGGGAAGA
1 AAAAAGAAAGA
**
77547 TGAAAGAAAGA
1 AAAAAGAAAGA
* *
77558 AAGAAGAAGAAGG
1 AAAAAG-A-AAGA
77571 AAAAAGAAAGA
1 AAAAAGAAAGA
* *
77582 AAAAGGGAAAAA
1 AAAA-AGAAAGA
*
77594 AAAGAAAAAAGA
1 AAA-AAGAAAGA
77606 AAAAAGAAAGA
1 AAAAAGAAAGA
77617 A
1 A
77618 CTTTTTTTAA
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 35 0.57
12 17 0.28
13 9 0.15
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:77709 original size:27 final size:28
Alignment explanation
Indices: 77673--77733 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
77663 CGACCCACAT
*
77673 CAGCCTAGCAGCCCAAAT-AAAAAACAG
1 CAGCCCAGCAGCCCAAATAAAAAAACAG
77700 CAGCCCAGCAGCCCAAATAAAAAAACAG
1 CAGCCCAGCAGCCCAAATAAAAAAACAG
77728 CAGCCC
1 CAGCCC
77734 CCTAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (28 bp):
CAGCCCAGCAGCCCAAATAAAAAAACAG
Found at i:77730 original size:20 final size:19
Alignment explanation
Indices: 77705--77748 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
77695 AACAGCAGCC
77705 CAGCAGCCCAAATAAAAAAA
1 CAGCAGCCC-AATAAAAAAA
**
77725 CAGCAGCCCCCTAAAAAAA
1 CAGCAGCCCAATAAAAAAA
77744 CAGCA
1 CAGCA
77749 AACAGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.52, C:0.32, G:0.11, T:0.05
Consensus pattern (19 bp):
CAGCAGCCCAATAAAAAAA
Found at i:77936 original size:8 final size:8
Alignment explanation
Indices: 77914--77951 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
77904 AGCAGCAGAA
77914 AAAAAAAG
1 AAAAAAAG
77922 AAGAAAAAAG
1 -A-AAAAAAG
77932 AAAAAAAG
1 AAAAAAAG
77940 AAAAAAAG
1 AAAAAAAG
77948 AAAA
1 AAAA
77952 GGGTTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 19 0.68
9 2 0.07
10 7 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:87710 original size:18 final size:17
Alignment explanation
Indices: 87689--87748 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
87679 TTATGCCTAA
87689 AAAAACAAAAAAAAAAGG
1 AAAAA-AAAAAAAAAAGG
*
87707 AAAAAAGCAAAAAAAAGG
1 AAAAAA-AAAAAAAAAGG
*
87725 AAAAAAAGAAAAAAGAAAG
1 AAAAAAA-AAAAAA-AAGG
87744 AAAAA
1 AAAAA
87749 TCAAGATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.75
19 8 0.22
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAGG
Found at i:87710 original size:19 final size:19
Alignment explanation
Indices: 87688--87748 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
87678 ATTATGCCTA
87688 AAAAAACAAAAAAAAAAGG
1 AAAAAACAAAAAAAAAAGG
87707 AAAAAAGC--AAAAAAAAGG
1 AAAAAA-CAAAAAAAAAAGG
87725 AAAAAA-AGAAAAAAGAAA-G
1 AAAAAACA-AAAAAA-AAAGG
87744 AAAAA
1 AAAAA
87749 TCAAGATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 16 0.43
19 17 0.46
20 4 0.11
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAAGG
Found at i:87743 original size:11 final size:10
Alignment explanation
Indices: 87687--87748 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
87677 TATTATGCCT
*
87687 AAAAAAACAA
1 AAAAAAAGAA
*
87697 AAAAAAA-AG
1 AAAAAAAGAA
* *
87706 GAAAAAAGCA
1 AAAAAAAGAA
*
87716 AAAAAAAG-G
1 AAAAAAAGAA
87725 AAAAAAAGAA
1 AAAAAAAGAA
87735 AAAAGAAAGAA
1 AAAA-AAAGAA
87746 AAA
1 AAA
87749 TCAAGATGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
9 15 0.36
10 18 0.43
11 9 0.21
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:87747 original size:26 final size:27
Alignment explanation
Indices: 87698--87748 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
87688 AAAAAACAAA
87698 AAAAAAAGGAAAAAAGCAAAAAAAAGG
1 AAAAAAAGGAAAAAAGCAAAAAAAAGG
87725 AAAAAAA-GAAAAAAG-AAAGAAAAA
1 AAAAAAAGGAAAAAAGCAAA-AAAAA
87749 TCAAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 13 0.57
27 7 0.30
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (27 bp):
AAAAAAAGGAAAAAAGCAAAAAAAAGG
Found at i:89041 original size:78 final size:75
Alignment explanation
Indices: 88599--89626 Score: 1101
Period size: 77 Copynumber: 13.3 Consensus size: 75
88589 AGAATTATAT
* * *
88599 TTTTCAATTTCTGGTTTTTCAAAAAAAAAAATCAACTCATAATACGAGAGGTAAGTTGAGCCTTG
1 TTTTCAATTTCT-GTTTTTC----AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* * *
88664 GGCCGCACACTGAGGTA
61 GG--TCACGCCGAGGTA
*
88681 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
*
88746 TATGCCGAGGTA
65 -ACGCCGAGGTA
*
88758 TTTTCAATTTCTATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
*
88823 TATGCCGAGGTA
65 -ACGCCGAGGTA
* * * *
88835 TTTTCAATTTCTATTTTTCAAAAAAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
1 TTTTCAATTTCTGTTTTTC---AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
88900 CCATGCCGAGGTA
63 TCACGCCGAGGTA
** *
88913 -TTTCTTTTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
88977 CGCTGAGGTA
66 CGCCGAGGTA
* * *
88987 TTTTCAATTTTTGTTTTTCAAAAAAAAAATCAACTCATAATGCGAGAAGCGAGTTGAGCCTCGGG
1 TTTTCAATTTCTGTTTTTC---AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
*
89052 TCACGCTGAGGTA
63 TCACGCCGAGGTA
* **
89065 TTTTCAATTTCTGTTTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAC
1 TTTTCAATTTCTGTTTTTC--AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
* *
89130 CATGCCGATGTA
64 CACGCCGAGGTA
** * * *
89142 -TTTCTTTTTCTGTTTTTC-AAAAAATCAACTCATAATGTGAGAAGTGAGTTGAGCTTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
89205 CGCTGAGGTA
66 CGCCGAGGTA
*
89215 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
89280 CAAGCTGAGGTA
66 C--GCCGAGGTA
* * * *
89292 TTTTTCAATTACTGTTTTT--TAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTC
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
89355 ATACGCCGAGGTA
65 --ACGCCGAGGTA
* * *
89368 TTTTTCAATTGT-TATTTTTC--AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGT
1 -TTTTCAATT-TCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
89430 CACATGCCGAGGTA
64 CAC--GCCGAGGTA
* * *
89444 TTTCTTTTAAATTTCT-TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG
1 ----TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
* *
89506 GTCGCATGCCGATGTA
62 GT--CACGCCGAGGTA
* *
89522 TTCTTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG
1 ---TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* *
89585 TCGCACGCTGAGCTA
63 T--CACGCCGAGGTA
* * *
89600 TTATCGATTTCTGATTTTCAAATAAAA
1 TTTTCAATTTCTGTTTTTCAAA-AAAA
89627 AGAAAATTTT
Statistics
Matches: 840, Mismatches: 76, Indels: 64
0.86 0.08 0.07
Matches are distributed among these distances:
73 46 0.05
74 67 0.08
75 74 0.09
76 130 0.15
77 233 0.28
78 220 0.26
79 9 0.01
80 43 0.05
81 6 0.01
82 12 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
CGCCGAGGTA
Found at i:89798 original size:30 final size:30
Alignment explanation
Indices: 89757--89924 Score: 223
Period size: 30 Copynumber: 5.6 Consensus size: 30
89747 GTGTTTTAAA
* * *
89757 AAAATTGCATTTTGACCCCTAAACTTTTTC
1 AAAATTACATTTTAACCCCTAAACTTTCTC
*
89787 AAAATTACATTTAAACCCCTAAACATTT-T-
1 AAAATTACATTTTAACCCCTAAAC-TTTCTC
* * *
89816 GAAATTGCATTTCAACCCCTAAACTTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTCTC
*
89846 AAAATTACATTTTAACCTCTAAACTTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTCTC
*
89876 AAAATTACATTTTAACCTCTAAACTTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTCTC
*
89906 AAAATTACATTTCAACCCC
1 AAAATTACATTTTAACCCC
89925 AAAAGTTTTG
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.02
29 22 0.18
30 95 0.77
31 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTCTC
Found at i:89850 original size:59 final size:60
Alignment explanation
Indices: 89757--89924 Score: 232
Period size: 59 Copynumber: 2.8 Consensus size: 60
89747 GTGTTTTAAA
* *
89757 AAAATTGCATTTTGACCCCTAAACTTTTTCAAAATTACATTTAAACCCCTAAACATTT-T-
1 AAAATTGCATTTTAACCCCTAAACTTTCTCAAAATTACATTTAAACCCCTAAAC-TTTCTC
* * * *
89816 GAAATTGCATTTCAACCCCTAAACTTTCTCAAAATTACATTTTAACCTCTAAACTTTCTC
1 AAAATTGCATTTTAACCCCTAAACTTTCTCAAAATTACATTTAAACCCCTAAACTTTCTC
* * *
89876 AAAATTACATTTTAACCTCTAAACTTTCTCAAAATTACATTTCAACCCC
1 AAAATTGCATTTTAACCCCTAAACTTTCTCAAAATTACATTTAAACCCC
89925 AAAAGTTTTG
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
58 3 0.03
59 49 0.52
60 43 0.45
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (60 bp):
AAAATTGCATTTTAACCCCTAAACTTTCTCAAAATTACATTTAAACCCCTAAACTTTCTC
Found at i:90412 original size:7 final size:7
Alignment explanation
Indices: 90391--90465 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 7
90381 AGAAAAAGGG
90391 AAGAAGA
1 AAGAAGA
90398 AAGAAAGA
1 AAG-AAGA
90406 AAGAAGA
1 AAGAAGA
* *
90413 AGGAGGA
1 AAGAAGA
90420 AA-AAGA
1 AAGAAGA
90426 AAGAA-A
1 AAGAAGA
*
90432 AAGGGAAAA
1 AA--GAAGA
*
90441 AAAAAGA
1 AAGAAGA
90448 AA-AAGA
1 AAGAAGA
*
90454 AAAAAGA
1 AAGAAGA
90461 AAGAA
1 AAGAA
90466 ATTTTTTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
6 14 0.25
7 28 0.51
8 10 0.18
9 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:90429 original size:28 final size:28
Alignment explanation
Indices: 90383--90466 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
90373 GAAAAGGAAG
* *
90383 AAAAAGGGAAGAAGAAAGAAAGAAAGAA
1 AAAAAAGGAAAAAGAAAGAAAGAAAGAA
* ** *
90411 GAAGGAGGAAAAAGAAAGAAA-AAGGGAA
1 AAAAAAGGAAAAAGAAAGAAAGAA-AGAA
*
90439 AAAAAAAGAAAAAGAAA-AAAGAAAGAA
1 AAAAAAGGAAAAAGAAAGAAAGAAAGAA
90466 A
1 A
90467 TTTTTTTAAC
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
27 9 0.21
28 34 0.79
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (28 bp):
AAAAAAGGAAAAAGAAAGAAAGAAAGAA
Found at i:90557 original size:27 final size:28
Alignment explanation
Indices: 90521--90581 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
90511 CGACCCACAT
*
90521 CAGCCTAGCAGCCCAAAT-AAAAAACAG
1 CAGCCCAGCAGCCCAAATAAAAAAACAG
*
90548 CAGCCCAGCAGCCCAAATAAAAAAATAG
1 CAGCCCAGCAGCCCAAATAAAAAAACAG
90576 CAGCCC
1 CAGCCC
90582 CCTAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.46, C:0.33, G:0.15, T:0.07
Consensus pattern (28 bp):
CAGCCCAGCAGCCCAAATAAAAAAACAG
Found at i:90767 original size:10 final size:9
Alignment explanation
Indices: 90748--90782 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
90738 GCCCAGCAGT
90748 AGAAAAAAA
1 AGAAAAAAA
90757 AGAAGAAAAA
1 AGAA-AAAAA
90767 AGAAAAAAAA
1 AG-AAAAAAA
90777 AGAAAA
1 AGAAAA
90783 GGGTTCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.33
10 14 0.58
11 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:95274 original size:69 final size:69
Alignment explanation
Indices: 95174--95336 Score: 213
Period size: 69 Copynumber: 2.4 Consensus size: 69
95164 ATTTAAAATT
*
95174 AACGTAAAAGAACACAGTTTT-AAGACAACAAATCAGCCCTACACAACAACACATTAAGAACTTA
1 AACGTAAATGAACACA-TTTTAAAGACAACAAATCAGCCCTACACAACAACACATTAAGAACTTA
*
95238 AATGG
65 AATCG
* *** * * *
95243 AATGTAAATGAACACATTTTAAAGA-ATACAAATCAGCCCTTTGCAACAGCACATTAAGCATTTA
1 AACGTAAATGAACACATTTTAAAGACA-ACAAATCAGCCCTACACAACAACACATTAAGAACTTA
95307 AATCG
65 AATCG
95312 AACGTAAATGAACACATTTTAAAGA
1 AACGTAAATGAACACATTTTAAAGA
95337 TGCTGAGTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
68 5 0.06
69 77 0.94
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (69 bp):
AACGTAAATGAACACATTTTAAAGACAACAAATCAGCCCTACACAACAACACATTAAGAACTTAA
ATCG
Found at i:95373 original size:20 final size:20
Alignment explanation
Indices: 95344--95382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
95334 AGATGCTGAG
95344 TCTTCCTTGTCAAAGTTGTA
1 TCTTCCTTGTCAAAGTTGTA
* *
95364 TCTTCGTTGTCAAATTTGT
1 TCTTCCTTGTCAAAGTTGT
95383 TCATTTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (20 bp):
TCTTCCTTGTCAAAGTTGTA
Found at i:99899 original size:6 final size:6
Alignment explanation
Indices: 99888--99922 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
99878 AGGATTACAA
*
99888 ATTTCC ATTTCC ATTTTC ATTTCC ATTTCC ATTTC
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTTC
99923 TAGAAACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTCC
Found at i:101628 original size:20 final size:20
Alignment explanation
Indices: 101586--101629 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
101576 ATAAATACAA
* *
101586 ATGTATTTAAAATTTGATTC
1 ATGTATTTAAAATTTAATCC
*
101606 ATGTATTTTAAATTTAATCC
1 ATGTATTTAAAATTTAATCC
101626 ATGT
1 ATGT
101630 CAAATTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (20 bp):
ATGTATTTAAAATTTAATCC
Found at i:106740 original size:30 final size:30
Alignment explanation
Indices: 106701--106763 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
106691 ACTTATTTTA
*
106701 TTGTCAATTTTGTTATTTTTTTAAAAACAT
1 TTGTCAATTTTGTTATTATTTTAAAAACAT
* * *
106731 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTCAATTTTGTTATTATTTTAAAAACAT
106761 TTG
1 TTG
106764 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTCAATTTTGTTATTATTTTAAAAACAT
Found at i:110936 original size:22 final size:22
Alignment explanation
Indices: 110911--110953 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
110901 GTTGACATGT
110911 GAGATGATGTTATGATATGGAA
1 GAGATGATGTTATGATATGGAA
*
110933 GAGATGATGTTATGATGTGGA
1 GAGATGATGTTATGATATGGA
110954 GAAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (22 bp):
GAGATGATGTTATGATATGGAA
Found at i:111121 original size:27 final size:27
Alignment explanation
Indices: 111083--111150 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
111073 TGGAGGGTAG
*
111083 CCCATGGGCGGCACCAAATGTGCCTTT
1 CCCATGGGCGGCACCAAATGTGCCATT
* ***
111110 CCCATAGGCGGCACCGGTTGTGCCATT
1 CCCATGGGCGGCACCAAATGTGCCATT
111137 CCCATGGGCGGCAC
1 CCCATGGGCGGCAC
111151 TGCCCATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.19
Consensus pattern (27 bp):
CCCATGGGCGGCACCAAATGTGCCATT
Found at i:111219 original size:10 final size:10
Alignment explanation
Indices: 111204--111291 Score: 63
Period size: 10 Copynumber: 8.7 Consensus size: 10
111194 AAGGAGAGGG
111204 AAAGAAAGAA
1 AAAGAAAGAA
111214 AAAGAAAGAA
1 AAAGAAAGAA
* *
111224 AAGGAAAGGA
1 AAAGAAAGAA
* *
111234 GAGGAAAGAA
1 AAAGAAAGAA
*
111244 AAGGAAAGGAGA
1 AAAGAAA-GA-A
*
111256 AGAAGAAAAAA
1 A-AAGAAAGAA
*
111267 AAAG-AAGGA
1 AAAGAAAGAA
*
111276 AAGGAAAG-A
1 AAAGAAAGAA
111285 AAAGAAA
1 AAAGAAA
111292 AGGAGAAGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
9 13 0.21
10 38 0.60
11 4 0.06
12 3 0.05
13 5 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:111228 original size:30 final size:30
Alignment explanation
Indices: 111205--111312 Score: 85
Period size: 30 Copynumber: 3.5 Consensus size: 30
111195 AGGAGAGGGA
111205 AAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
* * * * *
111235 AGGAAAGAAAAGGAAAGGAGAA-G-AAGAAA
1 AAGAAAGAAAAAGAAA-GAAAAGGAAAGGAG
* *
111264 AAAAAAGAAGGAAAGGAAAGAAAAGAAAAGGAG
1 AAGAAAGAA--AAA-GAAAGAAAAGGAAAGGAG
*
111297 AAGAGAAGAAGAAGAA
1 AAGA-AAGAAAAAGAA
111313 GAGGGGAGGG
Statistics
Matches: 57, Mismatches: 14, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
29 11 0.19
30 15 0.26
31 13 0.23
32 6 0.11
33 7 0.12
34 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (30 bp):
AAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
Found at i:111231 original size:5 final size:5
Alignment explanation
Indices: 111202--111295 Score: 57
Period size: 5 Copynumber: 18.6 Consensus size: 5
111192 AGAAGGAGAG
* * * * *
111202 GGAAA -GAAA GAAAA AGAAA GAAAA GGAAA GGAGA GGAAA GAAAA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
** * * *
111251 GGAGAA GAAGAAA AAAAA AG-AA GGAAA GGAAA GAAAA GAAAA GGA
1 GGA-AA G--GAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA
111296 GAAGAGAAGA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
4 7 0.10
5 54 0.79
6 3 0.04
7 2 0.03
8 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:111241 original size:15 final size:15
Alignment explanation
Indices: 111202--111300 Score: 75
Period size: 15 Copynumber: 6.8 Consensus size: 15
111192 AGAAGGAGAG
111202 GGAAA-GAAAGAAAA
1 GGAAAGGAAAGAAAA
* * *
111216 AGAAAGAAAAGGAAA
1 GGAAAGGAAAGAAAA
*
111231 GGAGAGGAAAGAAAA
1 GGAAAGGAAAGAAAA
111246 GGAAAGGAGAAGAAGAA
1 GGAAAGGA-AAGAA-AA
*
111263 --AAA--AAA-AGAA
1 GGAAAGGAAAGAAAA
111273 GGAAAGGAAAGAAAA
1 GGAAAGGAAAGAAAA
*
111288 GAAAAGGAGAAGA
1 GGAAAGGA-AAGA
111301 GAAGAAGAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
10 2 0.03
11 1 0.02
12 5 0.08
13 1 0.02
14 7 0.11
15 38 0.58
16 9 0.14
17 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GGAAAGGAAAGAAAA
Found at i:111282 original size:42 final size:43
Alignment explanation
Indices: 111210--111300 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 43
111200 AGGGAAAGAA
* * * * *
111210 AGAAAAAGAAAGAAAAGGAAAGGAGAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAAAAAGAAAGGAAAGGAAAGAAAAGAAAAGG
111253 AGAAGAAGAAAAAAAAAG-AAGGAAAGGAAAGAAAAGAAAAGG
1 AGAAGAAGAAAAAAAAAGAAAGGAAAGGAAAGAAAAGAAAAGG
111295 AGAAGA
1 AGAAGA
111301 GAAGAAGAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.65
43 15 0.35
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (43 bp):
AGAAGAAGAAAAAAAAAGAAAGGAAAGGAAAGAAAAGAAAAGG
Found at i:111289 original size:47 final size:49
Alignment explanation
Indices: 111209--111314 Score: 146
Period size: 47 Copynumber: 2.2 Consensus size: 49
111199 GAGGGAAAGA
* *
111209 AAGAAAAAGAAAGAAAAGGAAAGGAGAGGAAAGAAAAGGA-AAGGAGAAG
1 AAGAAAAAGAAAGAAAAGGAAAGGAAAGAAAAGAAAAGGAGAA-GAGAAG
*
111258 AAGAAAAA-AAA-AGAAGGAAAGGAAAGAAAAGAAAAGGAGAAGAGAAG
1 AAGAAAAAGAAAGAAAAGGAAAGGAAAGAAAAGAAAAGGAGAAGAGAAG
*
111305 AAGAAGAAGA
1 AAGAAAAAGA
111315 GGGGAGGGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
47 37 0.73
48 6 0.12
49 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (49 bp):
AAGAAAAAGAAAGAAAAGGAAAGGAAAGAAAAGAAAAGGAGAAGAGAAG
Found at i:111294 original size:20 final size:20
Alignment explanation
Indices: 111204--111295 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 20
111194 AAGGAGAGGG
* *
111204 AAAG-AAAGAAAAAGAAAGA
1 AAAGAAAAGGAAAGGAAAGA
* *
111223 AAAGGAAAGGAGAGGAAAGA
1 AAAGAAAAGGAAAGGAAAGA
*
111243 AAAGGAAAGGAGAAGAAGAAA-A
1 AAAGAAAAGGA-AAG--GAAAGA
111265 AAA-AAGAAGGAAAGGAAAGA
1 AAAGAA-AAGGAAAGGAAAGA
111285 AAAGAAAAGGA
1 AAAGAAAAGGA
111296 GAAGAGAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
19 8 0.13
20 32 0.52
21 8 0.13
22 9 0.15
23 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
AAAGAAAAGGAAAGGAAAGA
Found at i:112237 original size:286 final size:285
Alignment explanation
Indices: 111709--112286 Score: 1021
Period size: 286 Copynumber: 2.0 Consensus size: 285
111699 TGAAATAAAG
*
111709 TAAAATTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGAAGAGAAAAAAATACGA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGAAGAGAAAAAAATACGA
*
111774 AGAAATGGCCGAAATAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
66 AGAAATAGCCGAAATAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
*
111839 ATTTCAAACAAAATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATTTTTTATTGA
131 ATTTCAAACAAAATGTACTAAAATAATATAAAACAATAAAATACGAAAATAATATTTTTTATTGA
* * *
111904 AAGTAATAAAATTCGGGAAAATAATACGAGCAAAGGGCAGGAATAAGGGTTTTTTTTACACTAAA
196 AAATAATAAAATTCGGGAAAATAATACGAGCAAAGGACAGAAATAAGGG-TTTTTTTACACTAAA
**
111969 ATAATTTAAAAAACGGACCAAATTAA
260 ATAATTTAAAAAACACACCAAATTAA
*
111995 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCAGAGAAAAAAATACGA
1 TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGAAGAGAAAAAAATACGA
*
112060 AGAAATAGCCGAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
66 AGAAATAGCCGAAATAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
*
112125 ATTTCAAACAAAATGTACTGAAATAATATAAAACAATAAAATACGAAAATAATATTTTTTATTGA
131 ATTTCAAACAAAATGTACTAAAATAATATAAAACAATAAAATACGAAAATAATATTTTTTATTGA
* *
112190 AAATAATAAAATTCGGGAAAATAATACGAGCAAAGGACAGAAATAAGGGTTTTTTTCCACTAAAT
196 AAATAATAAAATTCGGGAAAATAATACGAGCAAAGGACAGAAATAAGGGTTTTTTTACACTAAAA
*
112255 TAATTTAAAAAACACACTAAATTAA
261 TAATTTAAAAAACACACCAAATTAA
112280 TAAATTT
1 TAAATTT
112287 CAAACATAAT
Statistics
Matches: 278, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
285 43 0.15
286 235 0.85
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (285 bp):
TAAATTTATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGAAGAGAAAAAAATACGA
AGAAATAGCCGAAATAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAAT
ATTTCAAACAAAATGTACTAAAATAATATAAAACAATAAAATACGAAAATAATATTTTTTATTGA
AAATAATAAAATTCGGGAAAATAATACGAGCAAAGGACAGAAATAAGGGTTTTTTTACACTAAAA
TAATTTAAAAAACACACCAAATTAA
Found at i:120851 original size:35 final size:35
Alignment explanation
Indices: 120800--120870 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
120790 GTAATTTCGC
*
120800 AACCTTTTTCATCCCAATTCGTTCCTCACACATGG
1 AACCTTTTTCACCCCAATTCGTTCCTCACACATGG
120835 AACCTTTTTCACCCCAATTCGTTCCTCACACATGG
1 AACCTTTTTCACCCCAATTCGTTCCTCACACATGG
120870 A
1 A
120871 TTCCTTGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.35, G:0.08, T:0.32
Consensus pattern (35 bp):
AACCTTTTTCACCCCAATTCGTTCCTCACACATGG
Found at i:121969 original size:43 final size:42
Alignment explanation
Indices: 121863--121998 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 42
121853 CCACTAACCC
* * *
121863 TAATAACTAACACAATAGCAATAATAATAGTTTTATACTCAAAA
1 TAATAACTAAC-C-ATAACAATAATAATAGGTTTATACTAAAAA
121907 TAAT-ACTAA-CA-AACAATAATAATTAGGGTTT-TACTAAAAA
1 TAATAACTAACCATAACAATAATAA-TA-GGTTTATACTAAAAA
* * * * *
121947 TAATAACTAACCATAATAATAATACTAGTTTTTTTACTAACAA
1 TAATAACTAACCATAACAATAATAATAG-GTTTATACTAAAAA
121990 TAAT-ACTAA
1 TAATAACTAA
121999 GTAACATCTA
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
39 10 0.13
40 15 0.19
41 11 0.14
42 12 0.15
43 26 0.33
44 4 0.05
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.32
Consensus pattern (42 bp):
TAATAACTAACCATAACAATAATAATAGGTTTATACTAAAAA
Found at i:122312 original size:27 final size:27
Alignment explanation
Indices: 122274--122370 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
122264 TGACACAAGT
122274 GGTGCCGCCTATGGGAAAGGCACCTTC
1 GGTGCCGCCTATGGGAAAGGCACCTTC
* * *
122301 GGTGTCGCCTATGGGAATGGCACCATC
1 GGTGCCGCCTATGGGAAAGGCACCTTC
*
122328 GGTGCCGCCTATGGGAAAGGCACCTTT
1 GGTGCCGCCTATGGGAAAGGCACCTTC
*
122355 GGTGCCGCCCATGGGA
1 GGTGCCGCCTATGGGA
122371 TACCCTCCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.18, C:0.28, G:0.35, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAAAGGCACCTTC
Found at i:122731 original size:21 final size:20
Alignment explanation
Indices: 122699--122737 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
122689 TATAATTATT
*
122699 TTGGGAATAAATATAACAAC
1 TTGGGAAAAAATATAACAAC
*
122719 TTGGGCAAAAAATGTAACA
1 TTGGG-AAAAAATATAACA
122738 TACATCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.23
Consensus pattern (20 bp):
TTGGGAAAAAATATAACAAC
Found at i:127496 original size:20 final size:20
Alignment explanation
Indices: 127451--127501 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
127441 TATATTATTT
* *
127451 TTAAAATATATA-TAACATA
1 TTAAAATAAATATTAAAATA
127470 -T-AAATAAATATTAAAATA
1 TTAAAATAAATATTAAAATA
127488 TTAAAATAAATATT
1 TTAAAATAAATATT
127502 TCTTAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 1 0.04
20 11 0.41
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAAATAAATATTAAAATA
Found at i:127617 original size:17 final size:19
Alignment explanation
Indices: 127595--127639 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
127585 CTAAAATAGT
127595 AACAAAATGA-ACAATAA-
1 AACAAAATGATACAATAAC
*
127612 AACAAAAGTTATACAATAAC
1 AACAAAA-TGATACAATAAC
127632 AACAAAAT
1 AACAAAAT
127640 AATAGCAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 2 0.08
19 8 0.33
20 7 0.29
ACGTcount: A:0.67, C:0.13, G:0.04, T:0.16
Consensus pattern (19 bp):
AACAAAATGATACAATAAC
Found at i:129206 original size:41 final size:42
Alignment explanation
Indices: 129150--129237 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 42
129140 CAATTAAGTA
*
129150 TTTTTTAAAATTTAAAA-ATTCAAAAAAAT-TAAAAATATATT
1 TTTTTTAAAAATTAAAAGATT-AAAAAAATATAAAAATATATT
*
129191 TTTTTTAAAAATTAAAATGATTAAAAAAGTATAAAAATATATT
1 TTTTTTAAAAATTAAAA-GATTAAAAAAATATAAAAATATATT
129234 TTTT
1 TTTT
129238 AATATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 16 0.38
42 7 0.17
43 19 0.45
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (42 bp):
TTTTTTAAAAATTAAAAGATTAAAAAAATATAAAAATATATT
Found at i:129238 original size:41 final size:39
Alignment explanation
Indices: 129148--129239 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 39
129138 AGCAATTAAG
*
129148 TATTTTTTAAAATTTAAAAATTCAAAAAAATTAAAAATA
1 TATTTTTTAAAAATTAAAAATTCAAAAAAATTAAAAATA
*
129187 TATTTTTTTTAAAAATTAAAATGATT-AAAAAAGTATAAAAATA
1 TA--TTTTTTAAAAATTAAAA--ATTCAAAAAAAT-TAAAAATA
129230 TATTTTTTAA
1 TATTTTTTAA
129240 TATTTTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
39 2 0.04
41 24 0.52
42 7 0.15
43 13 0.28
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (39 bp):
TATTTTTTAAAAATTAAAAATTCAAAAAAATTAAAAATA
Found at i:129723 original size:31 final size:31
Alignment explanation
Indices: 129656--129738 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
129646 TTGAGAAGCT
* * * *
129656 CTTATTTGAGCCCTTTCAAAAAAGATTTGATT
1 CTTATTTGAGCACTTT-GAAAAAGATTCGATC
* *
129688 CTTATTTGAGCACTTTGAAAAAGCTTCGGTC
1 CTTATTTGAGCACTTTGAAAAAGATTCGATC
*
129719 CTTATTTGAGAACTTTGAAA
1 CTTATTTGAGCACTTTGAAA
129739 TGTTTGTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 29 0.66
32 15 0.34
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (31 bp):
CTTATTTGAGCACTTTGAAAAAGATTCGATC
Found at i:134731 original size:22 final size:21
Alignment explanation
Indices: 134703--134746 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
134693 GTACAACAAG
134703 GGAAGAGGT-AGGAAGGAGATAT
1 GGAAGAGGTAAGG-AGGAG-TAT
134725 GGAAGAGGTAAGGAGGAGTAT
1 GGAAGAGGTAAGGAGGAGTAT
134746 G
1 G
134747 AGGTGGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.48, T:0.14
Consensus pattern (21 bp):
GGAAGAGGTAAGGAGGAGTAT
Found at i:159396 original size:44 final size:45
Alignment explanation
Indices: 159304--159517 Score: 236
Period size: 44 Copynumber: 4.8 Consensus size: 45
159294 GAGTAGCAGT
* * * * * *
159304 AGATCTTATATTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAAAGC
**
159349 AGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAAAGATAA-C
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGA-AAGC
* * *
159393 AGATCTTGTCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAAAGC
** * * *
159438 AGATCTTGTCTTCATGTATTGGT-GTGAATTAGATCAAAGATAGC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAAAGC
* *
159482 AGATCTTGTCTTCCCATACTGGTGGGGAAGTAGATC
1 AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC
159518 TTGTCTTCAT
Statistics
Matches: 138, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
44 74 0.54
45 64 0.46
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (45 bp):
AGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAAAGC
Found at i:159455 original size:89 final size:89
Alignment explanation
Indices: 159304--159517 Score: 347
Period size: 89 Copynumber: 2.4 Consensus size: 89
159294 GAGTAGCAGT
* * *
159304 AGATCTTATATTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
159369 GGTGTGAAGTAGATCAAAGATAAC
66 GGTGTGAAGTAGATCAAAGATAAC
* * *
159393 AGATCTTGTCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
* *
159458 GGTGTGAATTAGATCAAAGATAGC
66 GGTGTGAAGTAGATCAAAGATAAC
*
159482 AGATCTTGTCTTCCCATACTGGTGGGGAAGTAGATC
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
159518 TTGTCTTCAT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 115 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACT
GGTGTGAAGTAGATCAAAGATAAC
Found at i:159576 original size:44 final size:44
Alignment explanation
Indices: 159513--159598 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
159503 GTGGGGAAGT
* *
159513 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATTGAAGATAGC
1 AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGC
159557 AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATA
1 AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATA
159599 TAAATCTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGC
Found at i:159683 original size:44 final size:44
Alignment explanation
Indices: 159584--159704 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 44
159574 ATTAGCGTGA
* **
159584 AGTAGATCGAAGA-TATAAATCTTATCTCCCTGAAGTTGTAGGG
1 AGTAGATCGAAGATTATAGATCTTATCTCCCTGAAGCAGTAGGG
* * * * *
159627 GGCAAATTGAAGATTATAGATCTTATCTCCCT-AGGCAGTAGTGG
1 AGTAGATCGAAGATTATAGATCTTATCTCCCTGAAGCAGTAG-GG
* * * *
159671 AGTAGATCGAAGATGACAGATTTTACCTCCCTGA
1 AGTAGATCGAAGATTATAGATCTTATCTCCCTGA
159705 GGTTACAGTG
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
43 15 0.25
44 43 0.73
45 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTAGATCGAAGATTATAGATCTTATCTCCCTGAAGCAGTAGGG
Found at i:160565 original size:13 final size:13
Alignment explanation
Indices: 160547--160572 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160537 ACTGAGAGTA
160547 CAAAGTTTCTAAG
1 CAAAGTTTCTAAG
160560 CAAAGTTTCTAAG
1 CAAAGTTTCTAAG
160573 GTGAACCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAAAGTTTCTAAG
Found at i:161237 original size:3 final size:3
Alignment explanation
Indices: 161229--161271 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
161219 TTATACTTTT
161229 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
161272 CATACTTGCG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:169219 original size:17 final size:19
Alignment explanation
Indices: 169199--169234 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
169189 ATATAAATCT
169199 TAAAAAAT-TAT-TAAAAA
1 TAAAAAATATATATAAAAA
169216 TAAAAAATATATATAAAAA
1 TAAAAAATATATATAAAAA
169235 ATTCAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATATATATAAAAA
Found at i:172690 original size:10 final size:10
Alignment explanation
Indices: 172675--172699 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
172665 AATTTTAGCT
172675 TTTATATTTA
1 TTTATATTTA
172685 TTTATATTTA
1 TTTATATTTA
172695 TTTAT
1 TTTAT
172700 CTTTTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATATTTA
Found at i:176388 original size:7 final size:7
Alignment explanation
Indices: 176378--176428 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
176368 TTATTTTTCT
176378 TTATTTA
1 TTATTTA
176385 TTATTTA
1 TTATTTA
176392 TTATTTA
1 TTATTTA
176399 TTA-TT-
1 TTATTTA
176404 TTATTTTA
1 TTA-TTTA
176412 TTATTTA
1 TTATTTA
176419 TTACTTTA
1 TTA-TTTA
176427 TT
1 TT
176429 TTGTTTGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.08
6 2 0.05
7 26 0.65
8 9 0.22
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:176413 original size:20 final size:20
Alignment explanation
Indices: 176388--176430 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
176378 TTATTTATTA
*
176388 TTTATTATTTATTATTTTAT
1 TTTATTATTTATTACTTTAT
176408 TTTATTATTTATTACTTTAT
1 TTTATTATTTATTACTTTAT
176428 TTT
1 TTT
176431 GTTTGGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATTTATTACTTTAT
Found at i:178454 original size:10 final size:10
Alignment explanation
Indices: 178439--178467 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
178429 AATTTTAGCT
178439 TTTATCTTTA
1 TTTATCTTTA
178449 TTTATCTTTA
1 TTTATCTTTA
178459 TTTATCTTT
1 TTTATCTTT
178468 TAAGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:192205 original size:26 final size:26
Alignment explanation
Indices: 192169--192219 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
192159 GAAATCACAA
192169 TGACACAACGTTTTTCATATTTTTCG
1 TGACACAACGTTTTTCATATTTTTCG
192195 TGACACAACGTTTTTCATATTTTTC
1 TGACACAACGTTTTTCATATTTTTC
192220 AATGTCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.47
Consensus pattern (26 bp):
TGACACAACGTTTTTCATATTTTTCG
Found at i:195134 original size:27 final size:27
Alignment explanation
Indices: 195095--195164 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
195085 GGGTGTGGTG
195095 CCTATCTGATAGGCGGCACCAGTGACC
1 CCTATCTGATAGGCGGCACCAGTGACC
* **
195122 CCTATCTGGTAGGCAACACCAGTGACC
1 CCTATCTGATAGGCGGCACCAGTGACC
195149 CCTATCTGATAGGCGG
1 CCTATCTGATAGGCGG
195165 TATACCTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (27 bp):
CCTATCTGATAGGCGGCACCAGTGACC
Found at i:199477 original size:13 final size:13
Alignment explanation
Indices: 199459--199491 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
199449 CCTTCCCTCG
199459 CTCTTTTTCTCTT
1 CTCTTTTTCTCTT
*
199472 CTCTTTTTTTCTT
1 CTCTTTTTCTCTT
199485 -TCTTTTT
1 CTCTTTTT
199492 TACCTTCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTCTTTTTCTCTT
Found at i:199534 original size:15 final size:14
Alignment explanation
Indices: 199514--199566 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
199504 CCGCCCTCTC
*
199514 CTTCTCCTTCTCCTT
1 CTTCTCCTTCT-TTT
199529 CTTCT-CTTCTTTT
1 CTTCTCCTTCTTTT
199542 CTTCTCCTTCTATTT
1 CTTCTCCTTCT-TTT
199557 CTTCTCCTTC
1 CTTCTCCTTC
199567 ACTCACCGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 7 0.20
14 10 0.29
15 18 0.51
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (14 bp):
CTTCTCCTTCTTTT
Found at i:200195 original size:23 final size:22
Alignment explanation
Indices: 200163--200205 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
200153 AGTCTCTATA
200163 TTTTTATTTTAATAATTTAATT
1 TTTTTATTTTAATAATTTAATT
* *
200185 TTTTTACTTTTCATAGTTTAA
1 TTTTTA-TTTTAATAATTTAA
200206 AATTTAGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTATTTTAATAATTTAATT
Found at i:209543 original size:11 final size:11
Alignment explanation
Indices: 209527--209552 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
209517 GGCCCGNNNA
209527 TTTTAAAATAC
1 TTTTAAAATAC
209538 TTTTAAAATAC
1 TTTTAAAATAC
209549 TTTT
1 TTTT
209553 TTTAAATTTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:209564 original size:10 final size:10
Alignment explanation
Indices: 209549--209611 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
209539 TTTAAAATAC
209549 TTTTTTTAAA
1 TTTTTTTAAA
209559 -TTTTTTAAA
1 TTTTTTTAAA
*
209568 --TTTTAAAA
1 TTTTTTTAAA
209576 TTTTTTTAAAA
1 TTTTTTT-AAA
209587 TACTTTTTT-AA
1 T--TTTTTTAAA
*
209598 TTTTTTTTAA
1 TTTTTTTAAA
209608 TTTT
1 TTTT
209612 AAAATACTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
8 7 0.16
9 15 0.33
10 10 0.22
11 7 0.16
13 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:209572 original size:30 final size:29
Alignment explanation
Indices: 209538--209601 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
209528 TTTAAAATAC
*
209538 TTTTAAAATACTTTTTTTAAAT-TTTTTAAA
1 TTTTAAAAT--TTTTTTAAAATATTTTTAAA
*
209568 TTTTAAAATTTTTTTAAAATACTTTTTTAA
1 TTTTAAAATTTTTTTAAAATA-TTTTTAAA
209598 TTTT
1 TTTT
209602 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
30 20 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAAAATTTTTTTAAAATATTTTTAAA
Found at i:209610 original size:40 final size:41
Alignment explanation
Indices: 209526--209622 Score: 151
Period size: 40 Copynumber: 2.4 Consensus size: 41
209516 CGGCCCGNNN
209526 ATTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTAA
1 ATTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTAA
** * *
209567 ATTTTAAAATTTTTTTAAAATAC-TTTTTTAATTTTTTTTA
1 ATTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTAA
209607 ATTTTAAAATACTTTT
1 ATTTTAAAATACTTTT
209623 TTTAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 29 0.58
41 21 0.42
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (41 bp):
ATTTTAAAATACTTTTAAAATACTTTTTTTAAATTTTTTAA
Found at i:209612 original size:29 final size:33
Alignment explanation
Indices: 209578--209650 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 33
209568 TTTTAAAATT
209578 TTTTTAAAATAC-TTTTTTAA-TTTT-TTTTAA
1 TTTTTAAAATACTTTTTTTAATTTTTGTTTTAA
209608 -TTTTAAAATACTTTTTTTAATTTTTGTTTTAA
1 TTTTTAAAATACTTTTTTTAATTTTTGTTTTAA
209640 TTTTTAAAATA
1 TTTTTAAAATA
209651 AATTTTTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 11 0.28
30 8 0.21
31 4 0.10
32 6 0.15
33 10 0.26
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (33 bp):
TTTTTAAAATACTTTTTTTAATTTTTGTTTTAA
Found at i:209623 original size:41 final size:42
Alignment explanation
Indices: 209526--209623 Score: 148
Period size: 41 Copynumber: 2.4 Consensus size: 42
209516 CGGCCCGNNN
209526 ATTTTAAAATAC-TTTTAAAATACTTTTTTTAAATTTTTTAA
1 ATTTTAAAATACTTTTTAAAATACTTTTTTTAAATTTTTTAA
* * *
209567 ATTTTAAAAT-TTTTTTAAAATAC-TTTTTTAATTTTTTTTA
1 ATTTTAAAATACTTTTTAAAATACTTTTTTTAAATTTTTTAA
209607 ATTTTAAAATACTTTTT
1 ATTTTAAAATACTTTTT
209624 TTAATTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 25 0.49
41 26 0.51
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (42 bp):
ATTTTAAAATACTTTTTAAAATACTTTTTTTAAATTTTTTAA
Found at i:209644 original size:41 final size:41
Alignment explanation
Indices: 209526--209649 Score: 130
Period size: 40 Copynumber: 3.0 Consensus size: 41
209516 CGGCCCGNNN
*
209526 ATTTTAAAATAC-TTTTAAAATACTTTTTTTAAATTTTTTAA
1 ATTTTAAAATACTTTTTTAAATA-TTTTTTTAAATTTTTTAA
* * *
209567 ATTTTAAAAT--TTTTTTAAAATACTTTTTTAATTTTTTTTA
1 ATTTTAAAATACTTTTTT-AAATATTTTTTTAAATTTTTTAA
* * *
209607 ATTTTAAAATACTTTTTTTAAT-TTTTGTTTTAATTTTTAAA
1 ATTTTAAAATACTTTTTTAAATATTTT-TTTAAATTTTTTAA
209648 AT
1 AT
209650 AAATTTTTGG
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
40 32 0.47
41 30 0.44
42 6 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (41 bp):
ATTTTAAAATACTTTTTTAAATATTTTTTTAAATTTTTTAA
Found at i:218084 original size:38 final size:37
Alignment explanation
Indices: 217999--218085 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 37
217989 TGGGGTTGAT
* * *
217999 TTGTGATTTTTGTTCTGACACAATGTCACTAGGTTAA
1 TTGTGATTTTTGTTCCGACACAATGCCACTAGGCTAA
* *
218036 TTGTTG-TTTTTGTTCCGAC-CAATTGCCATTGGGGCTAA
1 TTG-TGATTTTTGTTCCGACACAA-TGCCACT-AGGCTAA
218074 TTGTGATTTTTG
1 TTGTGATTTTTG
218086 ATCTTTGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
36 3 0.07
37 22 0.54
38 16 0.39
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (37 bp):
TTGTGATTTTTGTTCCGACACAATGCCACTAGGCTAA
Found at i:224982 original size:20 final size:20
Alignment explanation
Indices: 224946--224983 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
224936 ATTTTTACCA
*
224946 CTAAATTAAAAGGTTATTGG
1 CTAAATTAAAAGATTATTGG
*
224966 CTAAATTAAAATATTATT
1 CTAAATTAAAAGATTATT
224984 ATTCATTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (20 bp):
CTAAATTAAAAGATTATTGG
Found at i:233196 original size:3 final size:3
Alignment explanation
Indices: 233188--233212 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
233178 TATCACCCTT
233188 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
233213 CTTTTCTTGG
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:236142 original size:30 final size:30
Alignment explanation
Indices: 236106--236164 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
236096 ACAAAAAAAT
236106 AGTAATATAATGTAGTATATTTCGGTTATC
1 AGTAATATAATGTAGTATATTTCGGTTATC
236136 AGTAATATAATGTAGTATATTTCGGTTAT
1 AGTAATATAATGTAGTATATTTCGGTTAT
236165 AAAATTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AGTAATATAATGTAGTATATTTCGGTTATC
Found at i:237151 original size:12 final size:12
Alignment explanation
Indices: 237136--237161 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
237126 TTTTTTATCG
237136 TTATTTTATTAT
1 TTATTTTATTAT
237148 TTATTTTATTAT
1 TTATTTTATTAT
237160 TT
1 TT
237162 TTGATACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:244220 original size:2 final size:2
Alignment explanation
Indices: 244215--244240 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
244205 AGAAAAAAAA
244215 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
244241 TATGAGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250653 original size:19 final size:19
Alignment explanation
Indices: 250631--250676 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
250621 ATTAAATTAC
* *
250631 ATTATTG-CCCTTAATTTA
1 ATTATTGACCCTAAACTTA
250649 TATTATTGACCCTAAACTTA
1 -ATTATTGACCCTAAACTTA
250669 ATTATTGA
1 ATTATTGA
250677 TTCTAGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (19 bp):
ATTATTGACCCTAAACTTA
Found at i:266233 original size:23 final size:25
Alignment explanation
Indices: 266185--266233 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
266175 GTTATGTGCA
*
266185 TATTAAGTGCTTTTGTTGAGTGTTT
1 TATTAAGTGCTTTTGTTGAGTATTT
*
266210 TATTAA-T-CTTTTGTTGGGTATTT
1 TATTAAGTGCTTTTGTTGAGTATTT
266233 T
1 T
266234 GGAGAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 1 0.05
25 6 0.27
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.59
Consensus pattern (25 bp):
TATTAAGTGCTTTTGTTGAGTATTT
Found at i:268980 original size:85 final size:86
Alignment explanation
Indices: 268870--269043 Score: 341
Period size: 85 Copynumber: 2.0 Consensus size: 86
268860 CAATTAAGCA
268870 TTTATATTGTTAAAAGAAAATCAAATAAATCCAAATTGTAATGGAATTAATATTTATAATATAAA
1 TTTATATTGTTAAAAGAAAATCAAATAAATCCAAATTGTAATGGAATTAATATTTATAATATAAA
268935 AAAACATTTTGAAAAATATTT
66 AAAACATTTTGAAAAATATTT
268956 TTTATATTGTT-AAAGAAAATCAAATAAATCCAAATTGTAATGGAATTAATATTTATAATATAAA
1 TTTATATTGTTAAAAGAAAATCAAATAAATCCAAATTGTAATGGAATTAATATTTATAATATAAA
269020 AAAACATTTTGAAAAATATTT
66 AAAACATTTTGAAAAATATTT
269041 TTT
1 TTT
269044 TCAATTATAG
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 77 0.88
86 11 0.12
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (86 bp):
TTTATATTGTTAAAAGAAAATCAAATAAATCCAAATTGTAATGGAATTAATATTTATAATATAAA
AAAACATTTTGAAAAATATTT
Found at i:270154 original size:4 final size:4
Alignment explanation
Indices: 270145--270170 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
270135 CAAAAAATCT
270145 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
270171 TTTCTTCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:271228 original size:42 final size:41
Alignment explanation
Indices: 271165--271292 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 41
271155 ATTCGACGTT
* * *
271165 TTGGTTGATACATCCAATGATTTAACGAGCTTGGTTTGGTTC
1 TTGGTCGATACATTC-ATGATTTAACAAGCTTGGTTTGGTTC
*
271207 TTGGTCGATACATTCACTGATTTAACCAGCTTGGTTTGGTTC
1 TTGGTCGATACATTCA-TGATTTAACAAGCTTGGTTTGGTTC
* * *
271249 TTGGTGGATACATTTGATGGTTTAACAAGCTTGGTTTGGTTC
1 TTGGTCGATACA-TTCATGATTTAACAAGCTTGGTTTGGTTC
271291 TT
1 TT
271293 CTTGTTGGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 73 0.95
43 3 0.04
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (41 bp):
TTGGTCGATACATTCATGATTTAACAAGCTTGGTTTGGTTC
Found at i:275780 original size:19 final size:20
Alignment explanation
Indices: 275743--275783 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
275733 TACAACACAA
*
275743 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
275763 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
275782 TT
1 TT
275784 GCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:276213 original size:16 final size:15
Alignment explanation
Indices: 276192--276251 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
276182 CTGTATGTTC
276192 TTCTTTCTTTCTCTTT
1 TTCTTTCTTT-TCTTT
*
276208 TTCTTTTTCTTTCTTT
1 TTCTTTCT-TTTCTTT
*
276224 TTGTTTCGTTTTGCTTT
1 TTCTTTC-TTTT-CTTT
276241 TGTCTTTCTTT
1 T-TCTTTCTTT
276252 ATTTCTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 20 0.56
17 11 0.31
18 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75
Consensus pattern (15 bp):
TTCTTTCTTTTCTTT
Found at i:279641 original size:24 final size:24
Alignment explanation
Indices: 279612--279657 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
279602 ACCCTAAAAC
279612 TTGAATTAAATCAAATTAATCAGG
1 TTGAATTAAATCAAATTAATCAGG
279636 TTGAATTAAATCAAATTAATCA
1 TTGAATTAAATCAAATTAATCA
279658 AGCTGCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (24 bp):
TTGAATTAAATCAAATTAATCAGG
Found at i:287757 original size:26 final size:26
Alignment explanation
Indices: 287705--287965 Score: 85
Period size: 25 Copynumber: 10.6 Consensus size: 26
287695 CACACCACAA
*
287705 CTCTT-ATGAGCGTCCCGA-TATATGG
1 CTCTTCATGAGCTTCCCGATTA-ATGG
*
287730 CTCTTCATGAGCTTCCCGATTAAAGG
1 CTCTTCATGAGCTTCCCGATTAATGG
** ** *
287756 CTCTTTGTGAGCTTCTTGATTGATGG
1 CTCTTCATGAGCTTCCCGATTAATGG
* *
287782 CTCTCCA-GAGCTTCCTGA-T-ATGG
1 CTCTTCATGAGCTTCCCGATTAATGG
* * * *
287805 CTC-GCTTGAACTTCCCGA-TATATAG
1 CTCTTCATGAGCTTCCCGATTA-ATGG
* *
287830 CTATTC--GAAGCTTCTCG-TTAATGG
1 CTCTTCATG-AGCTTCCCGATTAATGG
* *
287854 CTCTT--TGGAGCTACCCG-TTATTGG
1 CTCTTCAT-GAGCTTCCCGATTAATGG
* ** * *
287878 CTC-GCATGAGCTTCTTGGTT-ATGA
1 CTCTTCATGAGCTTCCCGATTAATGG
*
287902 CTCTT-ATGAGCTTCCCGTATT-ATAG
1 CTCTTCATGAGCTTCCCG-ATTAATGG
** *
287927 C-CTGGATAAGCTTCCCGA-TATATGG
1 CTCTTCATGAGCTTCCCGATTA-ATGG
*
287952 CTC-ACATGAGCTTC
1 CTCTTCATGAGCTTC
287966 TCGTTCTATG
Statistics
Matches: 173, Mismatches: 44, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
22 1 0.01
23 18 0.10
24 50 0.29
25 61 0.35
26 41 0.24
27 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
CTCTTCATGAGCTTCCCGATTAATGG
Done.