Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 137 of 343
Found at i:45854139 original size:30 final size:29
Alignment explanation
Indices: 45854044--45854140 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
45854034 AGCTCACTCC
*
45854044 TAGCTC-ACTTTCAACTCACGAGCTAAACTT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAC-T
* * * * *
45854074 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAG-CTAAACT
* *
45854104 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAA-CT
45854134 TAGCTCA
1 TAGCTCA
45854141 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 3 0.06
30 39 0.78
31 8 0.16
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (29 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACT
Found at i:45856645 original size:10 final size:11
Alignment explanation
Indices: 45856600--45856644 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
45856590 TCAAGTAAGT
45856600 TTCAAAAAAAA
1 TTCAAAAAAAA
*
45856611 GTCGAAAAAAAA
1 TTC-AAAAAAAA
45856623 TTCAAAAAAAAA
1 TTC-AAAAAAAA
45856635 TTCAAAAAAA
1 TTCAAAAAAA
45856645 TAACAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:45862846 original size:20 final size:20
Alignment explanation
Indices: 45862799--45862846 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
45862789 AGTAAGCTCG
45862799 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
45862819 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
45862839 GTTGAGCT
1 GTTGAGCT
45862847 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:45863608 original size:42 final size:42
Alignment explanation
Indices: 45863560--45863665 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
45863550 CATTTAAGCC
*
45863560 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTACTGGTCATTAATACAACTCA
45863602 TCTTAGTTTAATAAATGAGTTACTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTACTGGTCATTAATACAACTCA
45863644 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
45863666 TATTTAATGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 52 0.84
43 10 0.16
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTACTGGTCATTAATACAACTCA
Found at i:45863667 original size:14 final size:14
Alignment explanation
Indices: 45863648--45863692 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
45863638 AACTCATCTT
*
45863648 AGTTTAATTAAATG
1 AGTTTAATTTAATG
45863662 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
45863675 AATTTAATTTAATG
1 AGTTTAATTTAATG
45863689 AGTT
1 AGTT
45863693 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:45867174 original size:14 final size:14
Alignment explanation
Indices: 45867157--45867191 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
45867147 AATTTGATCA
*
45867157 TACCATTTTGTTCC
1 TACCATTTCGTTCC
*
45867171 TACCCTTTCGTTCC
1 TACCATTTCGTTCC
45867185 TACCATT
1 TACCATT
45867192 CCATTCGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (14 bp):
TACCATTTCGTTCC
Found at i:45874128 original size:14 final size:14
Alignment explanation
Indices: 45874111--45874145 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
45874101 AATTTGATCA
*
45874111 TACCATTTTGTTCC
1 TACCATTTCGTTCC
*
45874125 TACCCTTTCGTTCC
1 TACCATTTCGTTCC
45874139 TACCATT
1 TACCATT
45874146 CCATTCGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (14 bp):
TACCATTTCGTTCC
Found at i:45884281 original size:30 final size:31
Alignment explanation
Indices: 45884247--45884343 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 31
45884237 AGCTCACTCC
*
45884247 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
45884277 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
*
45884307 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
45884337 TAGCTCA
1 TAGCTCA
45884344 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 49 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:45887796 original size:23 final size:22
Alignment explanation
Indices: 45887744--45887796 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
45887734 TCCACGTCTT
*
45887744 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
45887766 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
45887789 TTTCTTTT
1 TTTCTTTT
45887797 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:45894074 original size:30 final size:30
Alignment explanation
Indices: 45894040--45894136 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
45894030 TAAACTAAAA
45894040 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
45894070 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTGAGCTAAAGT
* *
45894100 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
45894130 TGAGCTA
1 TGAGCTA
45894137 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.88
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:45900845 original size:13 final size:12
Alignment explanation
Indices: 45900813--45900846 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
45900803 TTGGAGTAAC
45900813 AAAAAAAA-TCA
1 AAAAAAAATTCA
45900824 AAAAAAAATTCGA
1 AAAAAAAATTC-A
45900837 AAAAAAAATT
1 AAAAAAAATT
45900847 TGATTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 11 0.52
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:45901966 original size:6 final size:6
Alignment explanation
Indices: 45901934--45902047 Score: 88
Period size: 6 Copynumber: 18.7 Consensus size: 6
45901924 AAAGAAATTG
* * ** *
45901934 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
45901981 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
45902032 AAAGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAG
45902048 CGAAAAAAGA
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
5 4 0.05
6 67 0.81
7 8 0.10
8 4 0.05
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:45901982 original size:57 final size:57
Alignment explanation
Indices: 45901921--45902044 Score: 137
Period size: 57 Copynumber: 2.2 Consensus size: 57
45901911 GAAAGAGATT
* *
45901921 GAAAAAGAAATTGAAAGAAAACAAAAAGAAAACGAAAAAG-A-AAAAG-AAATTGCAAAA
1 GAAAAAGAAA-T-AAA-AAAACAAAAAGAAAAAGAAAAAGAAGAAAAGAAAATTGAAAAA
* *** *
45901978 GAAAAAGAAATCAAAAAAGTGAAAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAAATAAAAAAACAAAAAGAAAAAGAAAAAGAAGAAAAGAAAATTGAAAAA
45902035 GAAAAAGAAA
1 GAAAAAGAAA
45902045 AAGCGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
54 18 0.32
55 3 0.05
56 6 0.11
57 30 0.53
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (57 bp):
GAAAAAGAAATAAAAAAACAAAAAGAAAAAGAAAAAGAAGAAAAGAAAATTGAAAAA
Found at i:45902021 original size:14 final size:13
Alignment explanation
Indices: 45902002--45902039 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
45901992 AAAAGTGAAA
45902002 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
45902014 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
45902029 GAAAAAGAAAA
1 GAAAAAGAAAA
45902040 AGAAAAAGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:45902053 original size:27 final size:27
Alignment explanation
Indices: 45901918--45902043 Score: 75
Period size: 27 Copynumber: 4.7 Consensus size: 27
45901908 GGAGAAAGAG
** *
45901918 ATTGAAAAAGAAATTGAAAGAAAACAAA
1 ATTGAAAAAGAAAAAG-AAGAAAAGAAA
* *
45901946 A-AGAAAACGAAAAAG-A-AAAAG-AA
1 ATTGAAAAAGAAAAAGAAGAAAAGAAA
*
45901969 ATTGCAAAAGAAAAAGAA-ATCAAA-AAA
1 ATTGAAAAAGAAAAAGAAGA--AAAGAAA
** *
45901996 GTGAAAGAAAAAGAAAATGAAGAAAAGAAA
1 ---ATTGAAAAAGAAAAAGAAGAAAAGAAA
45902026 ATTGAAAAAGAAAAAGAA
1 ATTGAAAAAGAAAAAGAA
45902044 AAAGCGAAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
23 3 0.04
24 15 0.21
25 3 0.04
27 30 0.41
28 1 0.01
29 3 0.04
30 17 0.23
31 1 0.01
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (27 bp):
ATTGAAAAAGAAAAAGAAGAAAAGAAA
Found at i:45902064 original size:33 final size:33
Alignment explanation
Indices: 45901999--45902069 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
45901989 CAAAAAAGTG
*
45901999 AAAGAAAAAGAAAATGAAGAAAAGAAAATTGAA
1 AAAGAAAAAGAAAACGAAGAAAAGAAAATTGAA
*
45902032 AAAGAAAAAGAAAAAGCGAA-AAAAG-AATTTGAA
1 AAAGAAAAAG-AAAA-CGAAGAAAAGAAAATTGAA
45902065 AAAGA
1 AAAGA
45902070 GTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 22 0.65
34 9 0.26
35 3 0.09
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.08
Consensus pattern (33 bp):
AAAGAAAAAGAAAACGAAGAAAAGAAAATTGAA
Found at i:45902082 original size:12 final size:12
Alignment explanation
Indices: 45902051--45902082 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
45902041 GAAAAAGCGA
*
45902051 AAAAAGAATTTG
1 AAAAAGAGTTTG
45902063 AAAAAGAGTTTG
1 AAAAAGAGTTTG
45902075 AAAAAGAG
1 AAAAAGAG
45902083 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:45905643 original size:20 final size:20
Alignment explanation
Indices: 45905620--45905680 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
45905610 CAACTCCGAC
45905620 CAGCTCAATTGAGCTTATTT
1 CAGCTCAATTGAGCTTATTT
* *
45905640 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCT-TATTT
*
45905661 -AGCTACAATTCAGCTTATTT
1 CAGCT-CAATTGAGCTTATTT
45905681 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (20 bp):
CAGCTCAATTGAGCTTATTT
Found at i:45905675 original size:11 final size:10
Alignment explanation
Indices: 45905620--45905675 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
45905610 CAACTCCGAC
45905620 CAGCTCAATT
1 CAGCTCAATT
* * *
45905630 GAGCTTATTT
1 CAGCTCAATT
45905640 CAGCTCAA-T
1 CAGCTCAATT
45905649 CGAGCTCAATT
1 C-AGCTCAATT
*
45905660 TAGCTACAATT
1 CAGCT-CAATT
45905671 CAGCT
1 CAGCT
45905676 TATTTATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
9 2 0.06
10 23 0.66
11 10 0.29
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:45918288 original size:14 final size:14
Alignment explanation
Indices: 45918241--45918288 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
45918231 GTACGAATAG
*
45918241 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
45918255 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
45918269 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
45918283 ATTGGT
1 AATGGT
45918289 CGTTTAGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:45920134 original size:29 final size:29
Alignment explanation
Indices: 45920092--45920160 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
45920082 CCATCTCAAT
45920092 GACATATTAAAACCTTGTTTTTTAGCTAA
1 GACATATTAAAACCTTGTTTTTTAGCTAA
45920121 GACATATTAAAACCTTGTTTTTTAGCTAA
1 GACATATTAAAACCTTGTTTTTTAGCTAA
*
45920150 GACACATTAAA
1 GACATATTAAA
45920161 CATGTAAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (29 bp):
GACATATTAAAACCTTGTTTTTTAGCTAA
Found at i:45921972 original size:30 final size:30
Alignment explanation
Indices: 45921938--45922034 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
45921928 AGCTCACTCC
*
45921938 TAGCTCATA-TTCAGCTCATGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
45921968 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
45921998 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
45922028 TAGCTCA
1 TAGCTCA
45922035 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:45924587 original size:15 final size:14
Alignment explanation
Indices: 45924567--45924612 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
45924557 AATAAAAGAA
45924567 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
45924582 AAGAAAAAGAAAATG
1 AAGAAAAAGAAAA-G
*
45924597 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
45924612 A
1 A
45924613 GAGGCAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:45924713 original size:12 final size:12
Alignment explanation
Indices: 45924698--45924731 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
45924688 AAATTAAAAA
*
45924698 GAAAATGAGATT
1 GAAAAAGAGATT
45924710 GAAAAAGAGATT
1 GAAAAAGAGATT
45924722 GAAAAAGAGA
1 GAAAAAGAGA
45924732 ACGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:45924768 original size:30 final size:31
Alignment explanation
Indices: 45924716--45924775 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
45924706 GATTGAAAAA
*
45924716 GAGATTGAAAAAGAGAACG-AAAAGAAATTT
1 GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
*
45924746 GAGAGTGAAAAAGA-AGATGAAAAAGAAATT
1 GAGAGTGAAAAAGAGA-ACGAAAAAGAAATT
45924776 GAAACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.58
31 10 0.38
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (31 bp):
GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
Found at i:45926105 original size:14 final size:14
Alignment explanation
Indices: 45926086--45926130 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
45926076 AACTCATCTT
*
45926086 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
45926100 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
45926113 AATTTAATTTAATG
1 AGTTTAATTTAATG
45926127 AGTT
1 AGTT
45926131 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:45927141 original size:29 final size:29
Alignment explanation
Indices: 45927108--45927167 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
45927098 ATAACCAAAC
*
45927108 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
45927137 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
45927166 CT
1 CT
45927168 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:45927160 original size:15 final size:15
Alignment explanation
Indices: 45927114--45927161 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
45927104 AAACCTACAA
*
45927114 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
45927129 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
45927143 AAACTTCATATCCAT
1 AAACTTCATATCCAT
45927158 AAAC
1 AAAC
45927162 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:45928491 original size:30 final size:30
Alignment explanation
Indices: 45928457--45928553 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
45928447 AGCTCACTCC
45928457 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
45928487 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
45928517 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
45928547 TAGCTCA
1 TAGCTCA
45928554 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:45931039 original size:22 final size:20
Alignment explanation
Indices: 45931007--45931055 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
45930997 GCCAAATTTA
45931007 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
45931030 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
45931050 TGAACA
1 TGAACA
45931056 CCTAGATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:45934739 original size:14 final size:14
Alignment explanation
Indices: 45934720--45934764 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
45934710 AACTCATCTT
*
45934720 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
45934734 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
45934747 AATTTAATTTAATG
1 AGTTTAATTTAATG
45934761 AGTT
1 AGTT
45934765 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:45935951 original size:12 final size:12
Alignment explanation
Indices: 45935934--45935982 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
45935924 AGTAAGTTTC
45935934 AAAAAAAAATTG
1 AAAAAAAAATTG
*
45935946 AAAAAAAAATTCAA
1 AAAAAAAAATT--G
45935960 ATTAAAAAAAATTG
1 A--AAAAAAAATTG
45935974 AAAAAAAAA
1 AAAAAAAAA
45935983 ACAAAATCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:45935996 original size:28 final size:28
Alignment explanation
Indices: 45935935--45935987 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
45935925 GTAAGTTTCA
*
45935935 AAAAAAAATTGAAAAAAAAATTCAAATT
1 AAAAAAAATTGAAAAAAAAATACAAATT
45935963 AAAAAAAATTGAAAAAAAAA-ACAAA
1 AAAAAAAATTGAAAAAAAAATACAAA
45935988 ATCTGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (28 bp):
AAAAAAAATTGAAAAAAAAATACAAATT
Found at i:45939266 original size:10 final size:10
Alignment explanation
Indices: 45939251--45939312 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
45939241 TTTGAACCGT
*
45939251 TACCAATTCG
1 TACCAATTCA
*
45939261 TACCAAATACCA
1 TACC-AAT-TCA
*
45939273 TACCATTTCA
1 TACCAATTCA
45939283 TACCAATTCCA
1 TACCAATT-CA
* *
45939294 TACCATTTCG
1 TACCAATTCA
45939304 TACCAATTC
1 TACCAATTC
45939313 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:45939296 original size:21 final size:21
Alignment explanation
Indices: 45939251--45939313 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
45939241 TTTGAACCGT
* *
45939251 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
45939273 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
45939294 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
45939314 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:45942891 original size:11 final size:10
Alignment explanation
Indices: 45942866--45942926 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
45942856 ACCAATAAAA
45942866 TAAA-TGAGC
1 TAAATTGAGC
*
45942875 TGAATTGTAGC
1 TAAATTG-AGC
45942886 TAAATTGAGC
1 TAAATTGAGC
**
45942896 TCGATTGAGC
1 TAAATTGAGC
45942906 TGAAA-TGAGC
1 T-AAATTGAGC
*
45942916 TCAATTGAGC
1 TAAATTGAGC
45942926 T
1 T
45942927 GGTCGAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:45942927 original size:20 final size:20
Alignment explanation
Indices: 45942867--45942927 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
45942857 CCAATAAAAT
*
45942867 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
45942887 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
45942908 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
45942928 GTCGAAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:45945017 original size:18 final size:18
Alignment explanation
Indices: 45944996--45945030 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45944986 TTTTTCTTTT
45944996 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
45945014 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
45945031 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:45945980 original size:28 final size:27
Alignment explanation
Indices: 45945903--45945982 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 27
45945893 GCAAGACTTT
**
45945903 TCACTTTTTTTTAACTTGATTTTTTTTGC
1 TCAC-TTTTTTT-ACTTTTTTTTTTTTGC
*
45945932 TCACTTTTTTTTCTTTCTTTTTTTTTGC
1 TCACTTTTTTTACTTT-TTTTTTTTTGC
45945960 TCGA-TTTTTTTCACTTTTTTTTT
1 TC-ACTTTTTTT-ACTTTTTTTTT
45945983 GAATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.07
28 32 0.73
29 9 0.20
ACGTcount: A:0.09, C:0.15, G:0.05, T:0.71
Consensus pattern (27 bp):
TCACTTTTTTTACTTTTTTTTTTTTGC
Found at i:45945989 original size:11 final size:11
Alignment explanation
Indices: 45945975--45946000 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45945965 TTTTTTCACT
45945975 TTTTTTTTGAA
1 TTTTTTTTGAA
45945986 TTTTTTTTGAA
1 TTTTTTTTGAA
45945997 TTTT
1 TTTT
45946001 GATTTTTTTG
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:45947386 original size:20 final size:20
Alignment explanation
Indices: 45947328--45947388 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
45947318 CCAATAAAAT
* *
45947328 AAATGAGCTGAATTGTAGAT-
1 AAATGAGCTCAATTG-AGCTG
*
45947348 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
45947369 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
45947389 GTCCGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:45958530 original size:23 final size:22
Alignment explanation
Indices: 45958478--45958530 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
45958468 TCCACGTCTT
*
45958478 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
45958500 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
45958523 TTTCTTTT
1 TTTCTTTT
45958531 TCACTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:45960075 original size:72 final size:73
Alignment explanation
Indices: 45959962--45960109 Score: 174
Period size: 72 Copynumber: 2.0 Consensus size: 73
45959952 TTTAATGCTA
* * *
45959962 TCCCAAGTCCCATGCACACACTAAATTCGACTGGTTGGG-AAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTT-GCTT
45960025 TAAATGCCG
65 TAAATGCCG
* * * * * * * *
45960034 TCCCAAGTCCCATGCACTCAATAAATTTGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
45960099 AAATGCCG
66 AAATGCCG
45960107 TCC
1 TCC
45960110 ATGTACCTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
72 32 0.51
73 25 0.40
74 6 0.10
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:45960317 original size:16 final size:16
Alignment explanation
Indices: 45960296--45960327 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45960286 CATTCTGCAT
45960296 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45960312 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45960328 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:45962381 original size:18 final size:18
Alignment explanation
Indices: 45962360--45962419 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
45962350 GACCTCACTC
45962360 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
45962378 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
45962396 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
45962417 TCT
1 TCT
45962420 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:45963372 original size:12 final size:13
Alignment explanation
Indices: 45963349--45963377 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
45963339 CAAAAAAAAA
45963349 TTTTGAATTTTTT
1 TTTTGAATTTTTT
45963362 TTTTGAATTTTTT
1 TTTTGAATTTTTT
45963375 TTT
1 TTT
45963378 CAAATTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTGAATTTTTT
Found at i:45964873 original size:16 final size:16
Alignment explanation
Indices: 45964852--45964883 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45964842 CATTCTGCAT
45964852 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45964868 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
45964884 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:45970460 original size:14 final size:14
Alignment explanation
Indices: 45970436--45970480 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
45970426 AAATCATCTT
* *
45970436 AGTTTCATTAAATG
1 AGTTTAATTTAATG
45970450 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
45970463 AATTTAATTTAATG
1 AGTTTAATTTAATG
45970477 AGTT
1 AGTT
45970481 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:45973394 original size:20 final size:20
Alignment explanation
Indices: 45973371--45973417 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
45973361 GGGTTAAGAT
*
45973371 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
45973391 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
45973411 TGAGCTG
1 TGAGCTG
45973418 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:45983960 original size:20 final size:20
Alignment explanation
Indices: 45983935--45983993 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
45983925 GTGTGGGTTC
45983935 CTCATTCAGCTCAAGTTAAG
1 CTCATTCAGCTCAAGTTAAG
* * *
45983955 CTCATTCGTGCTCACG-TCAG
1 CTCATTC-AGCTCAAGTTAAG
*
45983975 CTCATTCAGCTCAATTTAA
1 CTCATTCAGCTCAAGTTAA
45983994 CTCGTTAAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 5 0.17
20 19 0.63
21 6 0.20
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (20 bp):
CTCATTCAGCTCAAGTTAAG
Found at i:46000596 original size:20 final size:20
Alignment explanation
Indices: 46000550--46000596 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46000540 AGCTCGTTTC
*
46000550 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46000570 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46000590 CAGCTCA
1 CAGCTCA
46000597 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46003156 original size:20 final size:19
Alignment explanation
Indices: 46003105--46003158 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
46003095 TGTGGTTCAA
*
46003105 CTCATTCAGCTCAAGTTAG
1 CTCATTCAGCTCAAGTCAG
*
46003124 CTCATTCGTGCTCAAGTCAG
1 CTCATTC-AGCTCAAGTCAG
46003144 CTCATTCAAGCTCAA
1 CTCATTC-AGCTCAA
46003159 TTTAACTCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (19 bp):
CTCATTCAGCTCAAGTCAG
Found at i:46011525 original size:11 final size:11
Alignment explanation
Indices: 46011495--46011530 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
46011485 CTTTTTTTCC
46011495 TTTTTTTTCG-A
1 TTTTTTTT-GAA
46011506 TTTTTTTTGAA
1 TTTTTTTTGAA
46011517 TTTTTTTTGAA
1 TTTTTTTTGAA
46011528 TTT
1 TTT
46011531 CTTCTCTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 23 0.96
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:46014921 original size:12 final size:12
Alignment explanation
Indices: 46014906--46014931 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46014896 TTTTTTTTTG
46014906 TTTTTTTTGAAT
1 TTTTTTTTGAAT
46014918 TTTTTTTTGAAT
1 TTTTTTTTGAAT
46014930 TT
1 TT
46014932 CTTCTCTCTC
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:46020288 original size:23 final size:22
Alignment explanation
Indices: 46020236--46020288 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
46020226 TCCACGTCTT
*
46020236 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
46020258 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
46020281 TTTCTTTT
1 TTTCTTTT
46020289 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:46023959 original size:18 final size:18
Alignment explanation
Indices: 46023938--46023972 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46023928 TTTTTCTTTT
46023938 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
46023956 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
46023973 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:46024922 original size:14 final size:14
Alignment explanation
Indices: 46024905--46024933 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46024895 TTTTTTTTCC
46024905 TTTTTTTT-TGAAT
1 TTTTTTTTCTGAAT
46024918 TTTTTTTTCTGAAT
1 TTTTTTTTCTGAAT
46024932 TT
1 TT
46024934 CTTCTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (14 bp):
TTTTTTTTCTGAAT
Found at i:46030705 original size:62 final size:61
Alignment explanation
Indices: 46030608--46030726 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 61
46030598 GGGACTTTGC
* *
46030608 CTATGAGAGCTACGTTCCTTATAAGTTGTCTTGGTAATCCCTCGTTTATGTTACGTTTCAGA
1 CTATGAGAGCTACGTTCCTTACAAGTTGTCTTGGTAAACCCTCGTTTATGTTA-GTTTCAGA
* *
46030670 CTATGAGAGCTACGTTCCTTACAGGTTGTCTTGGTAAACCCTTGTTTATGTTAGTTT
1 CTATGAGAGCTACGTTCCTTACAAGTTGTCTTGGTAAACCCTCGTTTATGTTAGTTT
46030727 TGGACTTCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 4 0.08
62 49 0.92
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (61 bp):
CTATGAGAGCTACGTTCCTTACAAGTTGTCTTGGTAAACCCTCGTTTATGTTAGTTTCAGA
Found at i:46032687 original size:30 final size:30
Alignment explanation
Indices: 46032637--46032719 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
46032627 GCTAAGTTTG
**
46032637 AGCTC-TGAGCTGGAAG-TGAGCTGAGTCCA
1 AGCTCATGAGCT-GAAGTTGAGCTGAGAACA
46032666 AGCTCGA-GAGCTGAAGTTGAGCTGAGAACA
1 AGCTC-ATGAGCTGAAGTTGAGCTGAGAACA
46032696 AGCTCATGAGCTGAAGTTGAGCTG
1 AGCTCATGAGCTGAAGTTGAGCTG
46032720 GATGTGAACA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
29 10 0.21
30 38 0.79
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (30 bp):
AGCTCATGAGCTGAAGTTGAGCTGAGAACA
Found at i:46040033 original size:42 final size:42
Alignment explanation
Indices: 46039971--46040067 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
46039961 AGATTATGAG
* * * *
46039971 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAA
46040013 AGAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAA
*
46040055 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
46040068 AAAGAAAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.58, C:0.05, G:0.23, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCAAGAAAAGAAACAA
Found at i:46040103 original size:18 final size:18
Alignment explanation
Indices: 46040082--46040120 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
46040072 AAAATGAGAG
46040082 TGAGAGTGAAAAAGAAAA
1 TGAGAGTGAAAAAGAAAA
* *
46040100 TGAGATTGAAAAAGAGAA
1 TGAGAGTGAAAAAGAAAA
46040118 TGA
1 TGA
46040121 AAAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (18 bp):
TGAGAGTGAAAAAGAAAA
Found at i:46040171 original size:18 final size:19
Alignment explanation
Indices: 46040135--46040173 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
46040125 TTTGAGAGAG
*
46040135 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
46040154 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
46040172 AA
1 AA
46040174 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:46041775 original size:20 final size:21
Alignment explanation
Indices: 46041752--46041799 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
46041742 AGCTCCGTCC
46041752 AGCTCAAC-TCAGCTCATTTG
1 AGCTCAACTTCAGCTCATTTG
* *
46041772 AGCTC-GCTTCAGCTCGTTTG
1 AGCTCAACTTCAGCTCATTTG
46041792 AGCTCAAC
1 AGCTCAAC
46041800 CGAGCTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (21 bp):
AGCTCAACTTCAGCTCATTTG
Found at i:46044235 original size:19 final size:19
Alignment explanation
Indices: 46044211--46044250 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
46044201 AGCTCCCATG
46044211 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
46044230 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
46044249 TA
1 TA
46044251 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:46045025 original size:4 final size:4
Alignment explanation
Indices: 46045016--46045043 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
46045006 AAGTTTTATT
46045016 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
46045044 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:46048178 original size:23 final size:22
Alignment explanation
Indices: 46048126--46048178 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
46048116 TCCACGTCTT
*
46048126 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
46048148 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
46048171 TTTCTTTT
1 TTTCTTTT
46048179 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:46056712 original size:11 final size:10
Alignment explanation
Indices: 46056687--46056747 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
46056677 ACCAATAAAA
46056687 TAAA-TGAGC
1 TAAATTGAGC
*
46056696 TGAATTGTAGC
1 TAAATTG-AGC
46056707 TAAATTGAGC
1 TAAATTGAGC
**
46056717 TCGATTGAGC
1 TAAATTGAGC
46056727 TGAAA-TGAGC
1 T-AAATTGAGC
*
46056737 TCAATTGAGC
1 TAAATTGAGC
46056747 T
1 T
46056748 GGTCGAAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:46056748 original size:20 final size:20
Alignment explanation
Indices: 46056688--46056748 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
46056678 CCAATAAAAT
*
46056688 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
46056708 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
46056729 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
46056749 GTCGAAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:46063012 original size:13 final size:13
Alignment explanation
Indices: 46062994--46063024 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
46062984 GGACACTCCA
46062994 GATTTAATTTCGT
1 GATTTAATTTCGT
46063007 GATTTAATTTCGT
1 GATTTAATTTCGT
46063020 GATTT
1 GATTT
46063025 TTGAGATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (13 bp):
GATTTAATTTCGT
Found at i:46065593 original size:12 final size:13
Alignment explanation
Indices: 46065571--46065599 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
46065561 GTTGTAAAGT
46065571 TTTATTTTATTTA
1 TTTATTTTATTTA
46065584 TTTA-TTTATTTA
1 TTTATTTTATTTA
46065596 TTTA
1 TTTA
46065600 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:46069334 original size:29 final size:29
Alignment explanation
Indices: 46069301--46069360 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
46069291 ATAACCAAAC
*
46069301 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
46069330 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
46069359 CT
1 CT
46069361 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:46069353 original size:15 final size:15
Alignment explanation
Indices: 46069307--46069354 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46069297 AAACCTACAA
*
46069307 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
46069322 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
46069336 AAACTTCATATCCAT
1 AAACTTCATATCCAT
46069351 AAAC
1 AAAC
46069355 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:46070124 original size:20 final size:20
Alignment explanation
Indices: 46070099--46070138 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46070089 ATAACTTCTT
46070099 TTTTTTAC-GAATTTTTTTTA
1 TTTTTTACAG-ATTTTTTTTA
*
46070119 TTTTTTTCAGATTTTTTTTA
1 TTTTTTACAGATTTTTTTTA
46070139 ACTTGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTACAGATTTTTTTTA
Found at i:46077051 original size:30 final size:30
Alignment explanation
Indices: 46077017--46077104 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
46077007 CTAGCTTATA
46077017 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * *
46077047 TTCAGCTTAGGAGTTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* *
46077077 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
46077105 TTTTAGTTTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:46079720 original size:9 final size:10
Alignment explanation
Indices: 46079713--46079769 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
46079703 AAGAGAAAAC
46079713 AAAGAAAAGA
1 AAAGAAAAGA
46079723 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
46079735 AAAGAAGA-A
1 AAAGAAAAGA
46079744 AAAGAAAATGA
1 AAAGAAAA-GA
46079755 AATA-AAAAGA
1 AA-AGAAAAGA
46079765 AAAGA
1 AAAGA
46079770 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:46079736 original size:21 final size:20
Alignment explanation
Indices: 46079702--46079769 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
46079692 ACATTCTTGT
46079702 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
46079723 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
46079744 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
46079765 AAAGA
1 AAAGA
46079770 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:46079737 original size:6 final size:5
Alignment explanation
Indices: 46079713--46079769 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
46079703 AAGAGAAAAC
*
46079713 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
46079760 AAAGA AAAGA
1 AAAGA AAAGA
46079770 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:46079744 original size:15 final size:14
Alignment explanation
Indices: 46079713--46079769 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
46079703 AAGAGAAAAC
46079713 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
46079729 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
46079744 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
46079760 AAAGAAAAGA
1 AAAGAAAAGA
46079770 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:46079856 original size:12 final size:12
Alignment explanation
Indices: 46079824--46079856 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
46079814 TTGAGGGAAC
*
46079824 TTGAAAAAGCCT
1 TTGAAAAATCCT
46079836 TTGAAAAATCCT
1 TTGAAAAATCCT
46079848 TTGAAAAAT
1 TTGAAAAAT
46079857 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (12 bp):
TTGAAAAATCCT
Found at i:46082159 original size:15 final size:15
Alignment explanation
Indices: 46082139--46082186 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46082129 TCAAATATGG
46082139 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
46082154 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
46082168 GTTTATGGATATAAA
1 GTTTATGGATATGAA
46082183 GTTT
1 GTTT
46082187 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:46082202 original size:29 final size:29
Alignment explanation
Indices: 46082135--46082192 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
46082125 TGATTCAAAT
*
46082135 ATGGGTTTATGGATATGAAGTTTATGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
*
46082164 ATGGGTTTATGGATATAAAGTTTTTGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
46082193 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (29 bp):
ATGGGTTTATGGATATAAAGTTTATGTAG
Found at i:46083652 original size:30 final size:30
Alignment explanation
Indices: 46083616--46083703 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
46083606 TCGCATCATA
46083616 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * * * * * *
46083646 TTCAGCTTAGGAGTTTAGCCTCAACTCAAC
1 TTCAGCTCACGAGCTAAACCTTAGCTCAAC
* * *
46083676 TTTAGCTCACAAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAACCTTAGCTCA
46083704 TTTTAGTTTA
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAACCTTAGCTCAAC
Found at i:46088135 original size:30 final size:30
Alignment explanation
Indices: 46088039--46088123 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
46088029 TAAACTAAAA
*
46088039 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
46088069 TGAGCTGAGATTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
46088099 TGAGCTAAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
46088124 GAATATGAGC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:46088856 original size:42 final size:42
Alignment explanation
Indices: 46088741--46088860 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 42
46088731 GTCTGAGACA
* * * *
46088741 TCGTGTAAGACCGTGTCTGGAATACAGGCCTCGATTGAGATT
1 TCGTGTAAGACCATGTCTGGGATACAGGCATCGATTCAGATT
* *
46088783 TACGTATAAGACCATGTCTGGGACATC-GGCATCG-TATCAGATT
1 T-CGTGTAAGACCATGTCTGGGATA-CAGGCATCGAT-TCAGATT
* *
46088826 TCGTGTAAGACCCTGTCTGGGATAGAGGCATCGAT
1 TCGTGTAAGACCATGTCTGGGATACAGGCATCGAT
46088861 ATTGAATTAC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
42 29 0.46
43 33 0.52
44 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGATACAGGCATCGATTCAGATT
Found at i:46088897 original size:85 final size:85
Alignment explanation
Indices: 46088741--46088904 Score: 188
Period size: 85 Copynumber: 1.9 Consensus size: 85
46088731 GTCTGAGACA
* * * * * *
46088741 TCGTGTAAGACCGTGTCTGGAATACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGA
1 TCGTGTAAGACCCTGTCTGGAATACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGAGA
46088806 CATCGGCATCGTATCAGATT
66 CATCGGCATCGTATCAGATT
* * *
46088826 TCGTGTAAGACCCTGTCTGGGATAGAGGCATCGATATTGA-A-TTACATGTAAGACCACGTCCGA
1 TCGTGTAAGACCCTGTCTGGAATACAGGCATCG--ATTGAGATTTACATATAAGACCACGTCCGA
** *
46088889 GATGTCGGCATTGTAT
64 GACATCGGCATCGTAT
46088905 TTTTTTATGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 59 0.91
86 1 0.02
87 5 0.08
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (85 bp):
TCGTGTAAGACCCTGTCTGGAATACAGGCATCGATTGAGATTTACATATAAGACCACGTCCGAGA
CATCGGCATCGTATCAGATT
Found at i:46090661 original size:49 final size:49
Alignment explanation
Indices: 46090589--46090732 Score: 200
Period size: 49 Copynumber: 2.9 Consensus size: 49
46090579 GCCGAAGCTA
46090589 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG-
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-ACAGT
* * * * *
46090638 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTT
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAG-T
*
46090688 TTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 TCT-GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
46090733 TCACAATAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
48 4 0.05
49 39 0.48
50 2 0.02
51 36 0.44
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (49 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCACAGT
Found at i:46092857 original size:65 final size:65
Alignment explanation
Indices: 46092727--46092854 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 65
46092717 TGGGTTAAAT
*
46092727 TCAGTAGCTAGCTAAGTATCACACGGCCATAGTACACGAGCGTGCCTATTGGCTGTGTGAAAAAG
1 TCAGTAGCTAGCTAAGTATCACACGGCCATAGTACACGAGCGTGCCTATTGGCCGTGTGAAAAAG
46092792 TCAGTAGCTAGCTAAGTATCACA-GGCCATAGTACACGAGCGTGCCTATTGGCCGTGTGAAAAA
1 TCAGTAGCTAGCTAAGTATCACACGGCCATAGTACACGAGCGTGCCTATTGGCCGTGTGAAAAA
46092855 AGTTAGTATA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 39 0.63
65 23 0.37
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (65 bp):
TCAGTAGCTAGCTAAGTATCACACGGCCATAGTACACGAGCGTGCCTATTGGCCGTGTGAAAAAG
Found at i:46094436 original size:30 final size:31
Alignment explanation
Indices: 46094402--46094498 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
46094392 AGCTCACTCC
*
46094402 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
46094432 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
46094462 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
46094492 TAGCTCA
1 TAGCTCA
46094499 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:46094635 original size:36 final size:36
Alignment explanation
Indices: 46094591--46094663 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
46094581 TTAATATTTG
46094591 TTATTAATATGCCATAGTCATTACATAAATTGATTA
1 TTATTAATATGCCATAGTCATTACATAAATTGATTA
46094627 TTATTAATATGCCATAGTCATTACATAAATTGATTA
1 TTATTAATATGCCATAGTCATTACATAAATTGATTA
46094663 T
1 T
46094664 GTTCAAATAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (36 bp):
TTATTAATATGCCATAGTCATTACATAAATTGATTA
Found at i:46095441 original size:6 final size:6
Alignment explanation
Indices: 46095430--46095454 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
46095420 TAATTAGAAC
46095430 ACTAAA ACTAAA ACTAAA ACTAAA A
1 ACTAAA ACTAAA ACTAAA ACTAAA A
46095455 AAAAACTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTAAA
Found at i:46104731 original size:6 final size:5
Alignment explanation
Indices: 46104707--46104769 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
46104697 AAGAGAAAAC
*
46104707 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
46104755 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
46104770 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:46104737 original size:12 final size:10
Alignment explanation
Indices: 46104707--46104769 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
46104697 AAGAGAAAAC
46104707 AAAGAAAAGA
1 AAAGAAAAGA
46104717 AAAGAAAAAGCA
1 AAAG-AAAAG-A
46104729 AAAGCAAAAGA
1 AAAG-AAAAGA
*
46104740 AGA-AAAAGA
1 AAAGAAAAGA
46104749 AAATGAAATA-A
1 AAA-GAAA-AGA
46104760 AAAGAAAAGA
1 AAAGAAAAGA
46104770 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:46104881 original size:18 final size:18
Alignment explanation
Indices: 46104844--46104899 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
46104834 AAAAGCTTTG
46104844 AAAAGCAAAATGAAAATGA
1 AAAAG-AAAATGAAAATGA
* *
46104863 AAAAGAAAATGAGATTGA
1 AAAAGAAAATGAAAATGA
* *
46104881 AAAAGAGAACGAAAA-GA
1 AAAAGAAAATGAAAATGA
46104898 AA
1 AA
46104900 TTTGAGAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.68, C:0.04, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAGAAAATGAAAATGA
Found at i:46104895 original size:30 final size:31
Alignment explanation
Indices: 46104850--46104931 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
46104840 TTTGAAAAGC
* * *
46104850 AAAATGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAACTGAAAAAGAAATATGAGAGTG
*
46104880 AAAAAGAGAAC-G-AAAAGAAATTTGAGAGTG
1 AAAAAGA-AACTGAAAAAGAAATATGAGAGTG
*
46104910 AAAAAGAAGCTGAAAAAGAAAT
1 AAAAAGAAACTGAAAAAGAAAT
46104932 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 10 0.23
30 22 0.51
31 11 0.26
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.13
Consensus pattern (31 bp):
AAAAAGAAACTGAAAAAGAAATATGAGAGTG
Found at i:46107087 original size:30 final size:30
Alignment explanation
Indices: 46107034--46107130 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
46107024 AGCTCACTCC
*
46107034 TAGCTC-ACTCTCAACTCACGAGTTAAACCT
1 TAGCTCAACT-TCAGCTCACGAGTTAAACCT
* * * *
46107064 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGTTAAACCT
* * * *
46107094 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGTTAAACCT
46107124 TAGCTCA
1 TAGCTCA
46107131 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGTTAAACCT
Found at i:46132973 original size:14 final size:14
Alignment explanation
Indices: 46132956--46133005 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
46132946 TTTTTTTCAC
46132956 TTTTTTTTGAATTT
1 TTTTTTTTGAATTT
* *
46132970 TTTTTTCAATCAATTT
1 TTTTTT--TTGAATTT
*
46132986 TTTTTTTCGAATTT
1 TTTTTTTTGAATTT
46133000 TTTTTT
1 TTTTTT
46133006 GATTTTTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGAATTT
Found at i:46133010 original size:11 final size:13
Alignment explanation
Indices: 46132956--46133014 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 13
46132946 TTTTTTTCAC
46132956 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
*
46132968 TTTTTTTTCAATCAATT
1 TTTTTTTTC---GAA-T
46132985 TTTTTTTTCGAAT
1 TTTTTTTTCGAAT
46132998 TTTTTTTT-G-AT
1 TTTTTTTTCGAAT
46133009 TTTTTT
1 TTTTTT
46133015 GTTACTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 8 0.20
12 9 0.22
13 9 0.22
14 2 0.05
16 2 0.05
17 10 0.25
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:46143996 original size:30 final size:30
Alignment explanation
Indices: 46143911--46144007 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
46143901 TAAACTAAAA
* *
46143911 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
46143941 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
46143971 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
46144000 ATGAGCTA
1 -TGAGCTA
46144008 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:46144716 original size:21 final size:20
Alignment explanation
Indices: 46144680--46144728 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
46144670 ATCAGCTCAC
*
46144680 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGATTTAGCTTGT
46144700 TTGAGCTCGAATTTAGCTTGT
1 TTGAGCTCG-ATTTAGCTTGT
*
46144721 TTCAGCTC
1 TTGAGCTC
46144729 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTTGT
Found at i:46144969 original size:13 final size:13
Alignment explanation
Indices: 46144951--46144975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46144941 TGAATAGTTG
46144951 TGTTATTTAATTA
1 TGTTATTTAATTA
46144964 TGTTATTTAATT
1 TGTTATTTAATT
46144976 TTGTAGGTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:46145729 original size:22 final size:22
Alignment explanation
Indices: 46145699--46145742 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46145689 TTTGGTATTT
46145699 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
46145721 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
46145743 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:46149329 original size:20 final size:20
Alignment explanation
Indices: 46149283--46149329 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
46149273 AGCTCGTTTC
*
46149283 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
46149303 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
46149323 CAGCTCA
1 CAGCTCA
46149330 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:46152125 original size:42 final size:42
Alignment explanation
Indices: 46152063--46152159 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
46152053 AGATTATGAG
* * *
46152063 AGAAAATGAAAGGATTTTGAATGAAATAGAGAGAAGAAACAA
1 AGAAAATGAAAGAATCTTGAATGAAATAGAGAAAAGAAACAA
*
46152105 AGAAAATGAGAGAATCTTGAATGAAATAGAGAAAAGAAACAA
1 AGAAAATGAAAGAATCTTGAATGAAATAGAGAAAAGAAACAA
46152147 AG-AAATGAAAGAA
1 AGAAAATGAAAGAA
46152160 AAAGAAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 10 0.20
42 40 0.80
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.14
Consensus pattern (42 bp):
AGAAAATGAAAGAATCTTGAATGAAATAGAGAAAAGAAACAA
Found at i:46152186 original size:18 final size:18
Alignment explanation
Indices: 46152163--46152215 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
46152153 GAAAGAAAAA
46152163 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGATTGAGAGT
* ** *
46152181 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAGATTGAGAGT
*
46152199 GAAAAAGAGTTTGAGAG
1 GAAAAAGAGATTGAGAG
46152216 ACAAAAAGAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.13
Consensus pattern (18 bp):
GAAAAAGAGATTGAGAGT
Found at i:46152194 original size:36 final size:36
Alignment explanation
Indices: 46152154--46152240 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
46152144 CAAAGAAATG
**
46152154 AAAGAAAAAGAAAAAGAGATTGAGAGTGAAAAAGAA
1 AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
* * *
46152190 AAAGAGAATGAAAAAGAGTTTGAGAGACAAAAAGAA
1 AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
* * *
46152226 TATGAACAAGAAAAA
1 AAAGAAAAAGAAAAA
46152241 AGAGTGGAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.64, C:0.02, G:0.23, T:0.10
Consensus pattern (36 bp):
AAAGAAAAAGAAAAAGAGATTGAGAGACAAAAAGAA
Found at i:46161942 original size:10 final size:10
Alignment explanation
Indices: 46161910--46161954 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
46161900 AAATGAAATG
* *
46161910 AGCTGAAACG
1 AGCTAAAACA
46161920 AGCTAAAATCA
1 AGCTAAAA-CA
*
46161931 AGCTCAAACA
1 AGCTAAAACA
46161941 AGCTAAAACA
1 AGCTAAAACA
46161951 AGCT
1 AGCT
46161955 CAAGTGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (10 bp):
AGCTAAAACA
Found at i:46161964 original size:20 final size:21
Alignment explanation
Indices: 46161910--46161957 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
46161900 AAATGAAATG
*
46161910 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAATCA
*
46161931 AGCTCAAACAAGCTAAAA-CA
1 AGCTCAAACGAGCTAAAATCA
46161951 AGCTCAA
1 AGCTCAA
46161958 GTGAGCTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAAATCA
Found at i:46162540 original size:10 final size:10
Alignment explanation
Indices: 46162525--46162589 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
46162515 AGTTTTTCCC
46162525 AGCTCAATTT
1 AGCTCAATTT
*
46162535 AGCTCACA-TG
1 AGCTCA-ATTT
*
46162545 AGCTTAATTT
1 AGCTCAATTT
*
46162555 AGCTC-GTTT
1 AGCTCAATTT
46162564 GAGCTCAATTT
1 -AGCTCAATTT
* *
46162575 AGCTTACTTT
1 AGCTCAATTT
46162585 AGCTC
1 AGCTC
46162590 GTTTGAGCTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 4 0.10
10 34 0.81
11 4 0.10
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:46162548 original size:20 final size:20
Alignment explanation
Indices: 46162525--46162578 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
46162515 AGTTTTTCCC
46162525 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
46162545 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
46162565 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
46162579 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:46162559 original size:30 final size:30
Alignment explanation
Indices: 46162525--46162598 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
46162515 AGTTTTTCCC
46162525 AGCTCAATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTC-ATTTGAGCTCA-ATTGAGCTTAATTT
* * *
46162555 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCATTTGAGCTCAATTGAGCTTAATTT
*
46162585 AGCTCGTTTGAGCT
1 AGCTCATTTGAGCT
46162599 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCATTTGAGCTCAATTGAGCTTAATTT
Found at i:46162588 original size:20 final size:20
Alignment explanation
Indices: 46162525--46162589 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
46162515 AGTTTTTCCC
* * *
46162525 AGCTCAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
46162545 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
46162564 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
46162585 AGCTC
1 AGCTC
46162590 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:46164782 original size:17 final size:16
Alignment explanation
Indices: 46164760--46164802 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
46164750 TGGACTGAAT
*
46164760 ATAAAAATTTAAACTAA
1 ATAAAAATATAAA-TAA
*
46164777 ATAAAATAAATAAATAA
1 ATAAAA-ATATAAATAA
46164794 ATAAAAATA
1 ATAAAAATA
46164803 AAACTTTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.68
18 5 0.23
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAATATAAATAA
Found at i:46164800 original size:18 final size:18
Alignment explanation
Indices: 46164769--46164804 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
46164759 TATAAAAATT
46164769 TAAACTAAATAAAATAAA
1 TAAACTAAATAAAATAAA
46164787 TAAA-TAAATAAAAATAAA
1 TAAACTAAAT-AAAATAAA
46164805 ACTTTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACTAAATAAAATAAA
Found at i:46171243 original size:22 final size:23
Alignment explanation
Indices: 46171218--46171277 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
46171208 TGGACTGAAT
46171218 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
46171240 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
46171262 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
46171278 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:46171245 original size:4 final size:4
Alignment explanation
Indices: 46171227--46171260 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
46171217 TATAAAAATT
46171227 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
46171261 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:46175467 original size:22 final size:22
Alignment explanation
Indices: 46175439--46175482 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46175429 TTTTGAACCA
46175439 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
46175461 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
46175483 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:46177701 original size:30 final size:28
Alignment explanation
Indices: 46177648--46177703 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
46177638 TTCTTCCACG
* *
46177648 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
46177676 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
46177704 TTTTTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:46178781 original size:10 final size:10
Alignment explanation
Indices: 46178768--46178793 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
46178758 TTTATTTATT
46178768 TTTTTTAGAA
1 TTTTTTAGAA
46178778 TTTTTTAGAA
1 TTTTTTAGAA
46178788 TTTTTT
1 TTTTTT
46178794 TATTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (10 bp):
TTTTTTAGAA
Found at i:46178781 original size:11 final size:11
Alignment explanation
Indices: 46178767--46178795 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
46178757 TTTTATTTAT
46178767 TTTTTTTAGAA
1 TTTTTTTAGAA
46178778 -TTTTTTAGAA
1 TTTTTTTAGAA
46178788 TTTTTTTA
1 TTTTTTTA
46178796 TTTTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTTTTTAGAA
Found at i:46181801 original size:31 final size:31
Alignment explanation
Indices: 46181766--46181829 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
46181756 GATGAAGGAT
46181766 AGAAGCGAACCTTGACCCAATACCTATATAG
1 AGAAGCGAACCTTGACCCAATACCTATATAG
46181797 AGAAGCGAACCTTGACCCAATACCTATATAG
1 AGAAGCGAACCTTGACCCAATACCTATATAG
46181828 AG
1 AG
46181830 GTAAGAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAAGCGAACCTTGACCCAATACCTATATAG
Done.