Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 194 of 214
Found at i:56874400 original size:19 final size:20
Alignment explanation
Indices: 56874363--56874403 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
56874353 ATACTAAAAA
*
56874363 TATTAAAATTGATATAAACT
1 TATTAAAATTGATAAAAACT
56874383 TATTAAAA-TGATAAAAACT
1 TATTAAAATTGATAAAAACT
56874402 TA
1 TA
56874404 AAAGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
TATTAAAATTGATAAAAACT
Found at i:56875157 original size:19 final size:17
Alignment explanation
Indices: 56875133--56875171 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
56875123 TTTATATCAA
56875133 TTTTAATATTTGTAATATT
1 TTTTAATATTTG-AA-ATT
56875152 TTTTAATATTTGAAATT
1 TTTTAATATTTGAAATT
56875169 TTT
1 TTT
56875172 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 2 0.10
19 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTAATATTTGAAATT
Found at i:56879987 original size:127 final size:128
Alignment explanation
Indices: 56879829--56880087 Score: 475
Period size: 127 Copynumber: 2.0 Consensus size: 128
56879819 TCTTTTGTCA
56879829 TTCATCTTCCTCGACATTAAAGCTAAAGCTTGTGATAGAATAGATACCAACAAAACATTAAAGAG
1 TTCATCTTCCTCGACATTAAAGCTAAAGCTTGTGATAGAATAGATACCAACAAAACATTAAAGAG
*
56879894 AGCT-AAAAAAAGAATGCCAAAGTAATCATGAAACTAATCTATCCATTGTTTATACTAACATG
66 AGCTAAAAAAAAGAAAGCCAAAGTAATCATGAAACTAATCTATCCATTGTTTATACTAACATG
*
56879956 TTCATCTTCCTCGACATTAAAGTTAAAGCTTGTGATAGAATAGATACCAACAAAACATTAAAGAG
1 TTCATCTTCCTCGACATTAAAGCTAAAGCTTGTGATAGAATAGATACCAACAAAACATTAAAGAG
* *
56880021 AGCTAAAAAAAAGAAAGCCAAAGTAATCATGAAACTAATTTGTCCATTGTTTATACTAACATG
66 AGCTAAAAAAAAGAAAGCCAAAGTAATCATGAAACTAATCTATCCATTGTTTATACTAACATG
56880084 TTCA
1 TTCA
56880088 GTAAAGTATG
Statistics
Matches: 127, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
127 68 0.54
128 59 0.46
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (128 bp):
TTCATCTTCCTCGACATTAAAGCTAAAGCTTGTGATAGAATAGATACCAACAAAACATTAAAGAG
AGCTAAAAAAAAGAAAGCCAAAGTAATCATGAAACTAATCTATCCATTGTTTATACTAACATG
Found at i:56882223 original size:29 final size:30
Alignment explanation
Indices: 56882191--56882272 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
56882181 CCATTGTACT
* *
56882191 TTTTGAAATTTC-TATTTTGACCCCAAACC
1 TTTTGAAAATTCACATTTTGACCCCAAACC
* *
56882220 TTTTTAAAATTCACATTTTGACCCCAAA-A
1 TTTTGAAAATTCACATTTTGACCCCAAACC
* *
56882249 TTTTCTAAAATT-ATATTTTGACCC
1 TTTT-GAAAATTCACATTTTGACCC
56882273 TTAAATTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTGAAAATTCACATTTTGACCCCAAACC
Found at i:56882223 original size:30 final size:28
Alignment explanation
Indices: 56882188--56882290 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
56882178 TAACCATTGT
*
56882188 ACTTTTTGAAATTTCTATTTTGACCCCAA
1 ACTTTTT-AAAATTCTATTTTGACCCCAA
*
56882217 ACCTTTTTAAAATTCACATTTTGACCCCAA
1 A-CTTTTTAAAATTC-TATTTTGACCCCAA
* * *
56882247 AATTTTCTAAAATTATATTTTGACCCTTAA
1 ACTTTT-TAAAATTCTATTTTGACCC-CAA
*
56882277 ATTTTCTTAAAATT
1 ACTTT-TTAAAATT
56882291 TCACTTTAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
29 21 0.34
30 40 0.65
31 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (28 bp):
ACTTTTTAAAATTCTATTTTGACCCCAA
Found at i:56882869 original size:14 final size:14
Alignment explanation
Indices: 56882846--56882911 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
56882836 GTACGGCCCG
*
56882846 AAGAAGAAGAAGAA
1 AAGAAAAAGAAGAA
56882860 AAGAAAAAGAA-AGA
1 AAGAAAAAGAAGA-A
* *
56882874 AGGAAAAAG-AGAG
1 AAGAAAAAGAAGAA
56882887 AAG-AAAAG-AG-A
1 AAGAAAAAGAAGAA
56882898 AAGAAAAA-AAGAA
1 AAGAAAAAGAAGAA
56882911 A
1 A
56882912 TATATCACAG
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.07
12 13 0.31
13 6 0.14
14 20 0.48
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAAGAA
Found at i:56882874 original size:21 final size:21
Alignment explanation
Indices: 56882849--56882892 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
56882839 CGGCCCGAAG
56882849 AAGAAGAAGAAAAGA-AAAAGA
1 AAGAAGAA-AAAAGAGAAAAGA
* *
56882870 AAGAAGGAAAAAGAGAGAAGA
1 AAGAAGAAAAAAGAGAAAAGA
56882891 AA
1 AA
56882893 AGAGAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
AAGAAGAAAAAAGAGAAAAGA
Found at i:56883052 original size:28 final size:26
Alignment explanation
Indices: 56883016--56883081 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 26
56883006 AAACCAAAAC
56883016 AGAA-AAAGAAGCAGCAGAAAAAAG-
1 AGAAGAAAGAAGCAGCAGAAAAAAGA
*
56883040 A-AAGAAAGAAAGAAGCAGAAAAAAGA
1 AGAAGAAAG-AAGCAGCAGAAAAAAGA
56883066 AGAAGAAAGAAGCAGC
1 AGAAGAAAGAAGCAGC
56883082 CCAAATGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 2 0.06
24 5 0.14
25 15 0.42
26 7 0.19
27 7 0.19
ACGTcount: A:0.67, C:0.08, G:0.26, T:0.00
Consensus pattern (26 bp):
AGAAGAAAGAAGCAGCAGAAAAAAGA
Found at i:56883071 original size:23 final size:23
Alignment explanation
Indices: 56883011--56883080 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
56883001 AAAAAAAACC
* * *
56883011 AAAACAGAAAAAG-AAGCAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
56883033 AAAAAAGAAAGAAAGAAAGAAGCAG
1 AAAAAAG-AAG-AAGAAAGAAGCAG
56883058 AAAAAAGAAGAAGAAAGAAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
56883081 CCCAAATGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.14
23 15 0.36
24 6 0.14
25 15 0.36
ACGTcount: A:0.69, C:0.07, G:0.24, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAGAAGAAAGAAGCAG
Found at i:56883158 original size:22 final size:24
Alignment explanation
Indices: 56883112--56883162 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56883102 GCAGCAGGCC
56883112 CAGCAGGCCCCCAGGCCCAGTGCAG
1 CAGCAGGCCCCCAGGCCCAG-GCAG
*
56883137 CAGCA-GCCCCCAGGCCTA-GCAG
1 CAGCAGGCCCCCAGGCCCAGGCAG
56883159 CAGC
1 CAGC
56883163 CCAACAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
24 12 0.48
25 5 0.20
ACGTcount: A:0.22, C:0.45, G:0.29, T:0.04
Consensus pattern (24 bp):
CAGCAGGCCCCCAGGCCCAGGCAG
Found at i:56883172 original size:20 final size:19
Alignment explanation
Indices: 56883135--56883172 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
56883125 GGCCCAGTGC
*
56883135 AGCAGCAGCCCCCAGGCCT
1 AGCAGCAGCCCACAGGCCT
56883154 AGCAGCAGCCCAACAGGCC
1 AGCAGCAGCCC-ACAGGCC
56883173 AGCCCAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.45, G:0.26, T:0.03
Consensus pattern (19 bp):
AGCAGCAGCCCACAGGCCT
Found at i:56883196 original size:10 final size:10
Alignment explanation
Indices: 56883183--56883242 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
56883173 AGCCCAGTCC
56883183 AGAAAAAAAA
1 AGAAAAAAAA
*
56883193 AGAAAAAAAG
1 AGAAAAAAAA
**
56883203 AGAGGAAAAA
1 AGAAAAAAAA
* *
56883213 AGAAGATAAA
1 AGAAAAAAAA
*
56883223 AGAAGAAAAA
1 AGAAAAAAAA
56883233 AGAAAAAAAA
1 AGAAAAAAAA
56883243 GGGTTTTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 42 1.00
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:56883213 original size:20 final size:18
Alignment explanation
Indices: 56883183--56883241 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 18
56883173 AGCCCAGTCC
*
56883183 AGAAAAAAAAAGAAAAAA
1 AGAAGAAAAAAGAAAAAA
56883201 AGAGAGGAAAAAAGAAGATAAA
1 AGA-A-GAAAAAAGAA-A-AAA
56883223 AGAAGAAAAAAGAAAAAA
1 AGAAGAAAAAAGAAAAAA
56883241 A
1 A
56883242 AGGGTTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.19
19 2 0.06
20 19 0.53
21 2 0.06
22 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AGAAGAAAAAAGAAAAAA
Found at i:56883605 original size:18 final size:18
Alignment explanation
Indices: 56883548--56883812 Score: 120
Period size: 17 Copynumber: 14.7 Consensus size: 18
56883538 TAAATATTCA
56883548 AAAAATTTT-GTGTTTTTC
1 AAAAATTTTCGTG-TTTTC
**
56883566 GAAAAAATTCCCGTG-TTT-
1 --AAAAATTTTCGTGTTTTC
*
56883584 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
56883602 -AAAATTTTCGTGTTTT-
1 AAAAATTTTCGTGTTTTC
**
56883618 AAAAATACTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
****
56883636 AAAAATCCAGGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
56883653 AAAAATTTTCGTGTTCTC
1 AAAAATTTTCGTGTTTTC
* ****
56883671 AAAAA-TTCCGATGATCAAAAAA
1 AAAAATTTTCG-TG-T---TTTC
*
56883693 AAAAATTTCTCGTTTTTTC
1 AAAAATTT-TCGTGTTTTC
* *
56883712 TAAAAAATTCCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
*
56883730 AAAAATTTTCGCG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
56883747 AAAAAAATAT--TGTTTTC
1 -AAAAATTTTCGTGTTTTC
*
56883764 AAAAAATTGTCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
* *
56883783 AAAAATATTCGTGTTTTT
1 AAAAATTTTCGTGTTTTC
*
56883801 AAGAATTTTCGT
1 AAAAATTTTCGT
56883813 CTCTAAAATT
Statistics
Matches: 184, Mismatches: 43, Indels: 38
0.69 0.16 0.14
Matches are distributed among these distances:
16 11 0.06
17 75 0.41
18 56 0.30
19 14 0.08
20 14 0.08
21 3 0.02
22 6 0.03
23 3 0.02
24 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:56883800 original size:19 final size:19
Alignment explanation
Indices: 56883692--56883799 Score: 70
Period size: 18 Copynumber: 5.9 Consensus size: 19
56883682 TGATCAAAAA
* *
56883692 AAAAAATTTCTCGTTTTTTC
1 AAAAAA-TTGTCGTGTTTTC
*
56883712 TAAAAAATT-CCGTG-TTTC
1 -AAAAAATTGTCGTGTTTTC
* *
56883730 -AAAAATTTTCGCG-TTTC
1 AAAAAATTGTCGTGTTTTC
* *
56883747 AAAAAAATAT--TGTTTTC
1 AAAAAATTGTCGTGTTTTC
56883764 AAAAAATTGTCGTGTTTTC
1 AAAAAATTGTCGTGTTTTC
56883783 -AAAAATAT-TCGTGTTTT
1 AAAAAAT-TGTCGTGTTTT
56883800 TAAGAATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.11
17 19 0.26
18 26 0.36
19 11 0.15
20 2 0.03
21 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (19 bp):
AAAAAATTGTCGTGTTTTC
Found at i:56883854 original size:16 final size:17
Alignment explanation
Indices: 56883824--56883856 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56883814 TCTAAAATTC
56883824 TCGTATTTTAAAAAAAA
1 TCGTATTTTAAAAAAAA
*
56883841 TCGTATTTTCAAAAAA
1 TCGTATTTTAAAAAAA
56883857 TTGTTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (17 bp):
TCGTATTTTAAAAAAAA
Found at i:56890759 original size:12 final size:12
Alignment explanation
Indices: 56890742--56890767 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56890732 GAACTGAACC
56890742 AGGAGAAGCTGA
1 AGGAGAAGCTGA
56890754 AGGAGAAGCTGA
1 AGGAGAAGCTGA
56890766 AG
1 AG
56890768 AAAAATCAGG
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:0.42, C:0.08, G:0.42, T:0.08
Consensus pattern (12 bp):
AGGAGAAGCTGA
Found at i:56891500 original size:5 final size:5
Alignment explanation
Indices: 56891492--56891519 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
56891482 AATTAAATGC
56891492 AATCA AATCA AATCA AATCA AATCA AAT
1 AATCA AATCA AATCA AATCA AATCA AAT
56891520 TGATCATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:56893651 original size:15 final size:13
Alignment explanation
Indices: 56893619--56893643 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56893609 TATTTCTCTA
56893619 ATTTTAAAAAATT
1 ATTTTAAAAAATT
56893632 ATTTTAAAAAAT
1 ATTTTAAAAAAT
56893644 AATATTTTTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAAAAATT
Found at i:56894307 original size:126 final size:126
Alignment explanation
Indices: 56894152--56894448 Score: 402
Period size: 126 Copynumber: 2.4 Consensus size: 126
56894142 AGTGTTAATT
* * * * * *
56894152 TAAAA-AAGCTCCCACGTGGACGCTCTTTTGTTACAGTAGCTCTTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCTCACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGAAG
* * **
56894216 ACATTTCTGAGTAAATAGTGTCAAAAACACTTTAAG-TGTGATGCTTTGTCAGCAAAAGTAC
66 ACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAG-GATGCTTTAACAGCAAAAGTAC
* *
56894277 TAAAAGAAGCT-TCAATGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGTA
1 TAAAAGAAGCTCTC-ACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGAA
* *
56894341 GACTTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTAACAGCAAAAGTAC
65 GACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTAACAGCAAAAGTAC
* * *
56894403 TGAAAGAAGCTCTCACGTGGACGTGCTTTTGCTACAATAGATCCTG
1 TAAAAGAAGCTCTCACGTGGACGCGCTTTTGCTACAATAGCTCCTG
56894449 TTTGGCCTGA
Statistics
Matches: 150, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
125 6 0.04
126 141 0.94
127 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (126 bp):
TAAAAGAAGCTCTCACGTGGACGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTCGAGAAG
ACATTTCTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTAACAGCAAAAGTAC
Found at i:56898163 original size:18 final size:18
Alignment explanation
Indices: 56898137--56898175 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
56898127 AACTAGAAAA
* *
56898137 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
56898155 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
56898173 AGG
1 AGG
56898176 GTACGCACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.18
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:56900030 original size:11 final size:11
Alignment explanation
Indices: 56900016--56900085 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
56900006 AAAAATTTTA
56900016 AGAGGAATTTG
1 AGAGGAATTTG
*
56900027 AGAGGAAATTG
1 AGAGGAATTTG
* *
56900038 AAAAGAATTTG
1 AGAGGAATTTG
56900049 AGAGGAATTTG
1 AGAGGAATTTG
56900060 AGA-GAATATTG
1 AGAGGAAT-TTG
*
56900071 -GAGAGAAATTG
1 AGAG-GAATTTG
56900082 AGAG
1 AGAG
56900086 AAACGATTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
10 6 0.12
11 36 0.75
12 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:56900053 original size:33 final size:33
Alignment explanation
Indices: 56900016--56900085 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
56900006 AAAAATTTTA
*
56900016 AGAGGAATTTGAGAGGAA-ATTGAAAAGAATTTG
1 AGAGGAATTTGAGA-GAATATTGAAAAGAAATTG
* *
56900049 AGAGGAATTTGAGAGAATATTGGAGAGAAATTG
1 AGAGGAATTTGAGAGAATATTGAAAAGAAATTG
56900082 AGAG
1 AGAG
56900086 AAACGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (33 bp):
AGAGGAATTTGAGAGAATATTGAAAAGAAATTG
Found at i:56900085 original size:22 final size:21
Alignment explanation
Indices: 56900020--56900087 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
56900010 ATTTTAAGAG
*
56900020 GAATTTGAGAGGAAATTGAAAA
1 GAATTTGAGAGGAAATTG-AGA
*
56900042 GAATTTGAGAGGAATTTGAGA
1 GAATTTGAGAGGAAATTGAGA
56900063 GAATATTG-GAGAGAAATTGAGA
1 GAAT-TTGAGAG-GAAATTGAGA
56900085 GAA
1 GAA
56900088 ACGATTTAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
21 9 0.22
22 32 0.78
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.24
Consensus pattern (21 bp):
GAATTTGAGAGGAAATTGAGA
Found at i:56901208 original size:15 final size:15
Alignment explanation
Indices: 56901184--56901214 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56901174 CTTACATACA
56901184 TGTTTATTTATTGTT
1 TGTTTATTTATTGTT
*
56901199 TGTTTGTTTATTGTT
1 TGTTTATTTATTGTT
56901214 T
1 T
56901215 ACGGACATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (15 bp):
TGTTTATTTATTGTT
Found at i:56904856 original size:4 final size:4
Alignment explanation
Indices: 56904847--56904872 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
56904837 TCACACAACC
56904847 AGGG AGGG AGGG AGGG AGGG AGGG AG
1 AGGG AGGG AGGG AGGG AGGG AGGG AG
56904873 AGACCTGAGC
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:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (4 bp):
AGGG
Found at i:56911059 original size:47 final size:50
Alignment explanation
Indices: 56910994--56911102 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 50
56910984 CATGGCAATA
*
56910994 TGTGATATGTGATTTCCGTATAACACCATAGCTGGGCTATGACATT-G-G
1 TGTGATATGTGACTTCCGTATAACACCATAGCTGGGCTATGACATTGGTG
* * * * * *
56911042 TGTGATATGTG-CTTCCGTGTAAGACCATGGCTGGGTTATGGCTTTGGTG
1 TGTGATATGTGACTTCCGTATAACACCATAGCTGGGCTATGACATTGGTG
56911091 TGTGATATGTGA
1 TGTGATATGTGA
56911103 TTATGCGCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
47 27 0.53
48 12 0.24
49 12 0.24
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (50 bp):
TGTGATATGTGACTTCCGTATAACACCATAGCTGGGCTATGACATTGGTG
Found at i:56911679 original size:25 final size:25
Alignment explanation
Indices: 56911650--56911726 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
56911640 ACCTTAGTGC
56911650 GCTCTTTGATTATTAGCACATCAGT
1 GCTCTTTGATTATTAGCACATCAGT
* * *
56911675 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTTTGATTATTAGCACATCAGT
* *
56911700 GCTCTTCG---ATTAGCACATCTGT
1 GCTCTTTGATTATTAGCACATCAGT
56911722 GCTCT
1 GCTCT
56911727 CTGTTCATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 16 0.36
25 28 0.64
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.39
Consensus pattern (25 bp):
GCTCTTTGATTATTAGCACATCAGT
Found at i:56914439 original size:25 final size:24
Alignment explanation
Indices: 56914397--56914444 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
56914387 CTGATTAATT
56914397 GCTCTTTGGAGCTACCCGTTATAG
1 GCTCTTTGGAGCTACCCGTTATAG
*
56914421 GCTCTTTGTGAGCTTCCCGTTATA
1 GCTCTTTG-GAGCTACCCGTTATA
56914445 TTACCTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTGGAGCTACCCGTTATAG
Found at i:56918152 original size:11 final size:11
Alignment explanation
Indices: 56918136--56918160 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
56918126 CATATAAGGG
56918136 AATATATGATT
1 AATATATGATT
56918147 AATATATGATT
1 AATATATGATT
56918158 AAT
1 AAT
56918161 TTCTGACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
AATATATGATT
Found at i:56930063 original size:33 final size:35
Alignment explanation
Indices: 56930000--56930074 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 35
56929990 TATAATGGGA
*
56930000 TTTACATTTTTAAAAGTAAATTTTAAATAAATA-T
1 TTTATATTTTTAAAAGTAAATTTTAAATAAATATT
* *
56930034 TTTATATTTTTATAATTAAA-TTTAAATAAATATT
1 TTTATATTTTTAAAAGTAAATTTTAAATAAATATT
56930068 TTTATAT
1 TTTATAT
56930075 ATTACAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 12 0.32
34 25 0.68
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (35 bp):
TTTATATTTTTAAAAGTAAATTTTAAATAAATATT
Found at i:56946292 original size:3 final size:3
Alignment explanation
Indices: 56946278--56946327 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
56946268 AAATGACATT
* * *
56946278 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56946324 TTA T
1 TTA T
56946328 GAAATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:56946313 original size:18 final size:18
Alignment explanation
Indices: 56946281--56946322 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
56946271 TGACATTTTA
*
56946281 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
56946298 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
56946316 TTATTAT
1 TTATTAT
56946323 ATTATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:56954588 original size:28 final size:27
Alignment explanation
Indices: 56954541--56954600 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
56954531 ATACACAATT
56954541 AAAAATATAATGAAAAATAAATTTA-TAA
1 AAAAATATAATGAAAAAT-AA-TTACTAA
56954569 AAAAATAT-AT-AAATATATAATTACTAA
1 AAAAATATAATGAAA-A-ATAATTACTAA
56954596 AAAAA
1 AAAAA
56954601 ACCACACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.21
27 13 0.45
28 10 0.34
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAATATAATGAAAAATAATTACTAA
Found at i:56957313 original size:17 final size:17
Alignment explanation
Indices: 56957282--56957332 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
56957272 TATGGGAAGT
*
56957282 AATCTTTAGAGGATTTGC
1 AATC-TTAGAAGATTTGC
*
56957300 AATCTTAGAAGATTTGT
1 AATCTTAGAAGATTTGC
*
56957317 AATCTTAGAAAATTTG
1 AATCTTAGAAGATTTG
56957333 ATTCTGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (17 bp):
AATCTTAGAAGATTTGC
Found at i:56961872 original size:39 final size:39
Alignment explanation
Indices: 56961818--56961910 Score: 168
Period size: 39 Copynumber: 2.4 Consensus size: 39
56961808 ATATTCCGAC
56961818 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
* *
56961857 TACTGTTACTGTTACCGATTTGGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
56961896 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
56961911 TATTACCGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (39 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
Found at i:56961906 original size:45 final size:45
Alignment explanation
Indices: 56961818--56962017 Score: 196
Period size: 45 Copynumber: 4.4 Consensus size: 45
56961808 ATATTCCGAC
56961818 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCG-A-A----
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* *
56961857 TACTGTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
56961902 TACTGTTACTATTACCGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTAC---T---GTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * ** ** *
56961953 TACCGTTGCTGTTACAAATTTAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
56961998 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACCGATT
56962018 ACTGTTTAGG
Statistics
Matches: 132, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
39 35 0.27
40 1 0.01
41 1 0.01
45 53 0.40
48 2 0.02
51 40 0.30
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:56961996 original size:90 final size:87
Alignment explanation
Indices: 56961818--56962017 Score: 235
Period size: 90 Copynumber: 2.2 Consensus size: 87
56961808 ATATTCCGAC
* ** *
56961818 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACCGATTTGGCAC
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACAAATTTAGCAC
56961883 TTTGTGTGTTGAATACTGTTACTGT
66 TTTGTGTGTTGAATA---TTACTGT
*
56961908 TACTATTACCGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTGCTGTTACAAATT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTA------CTGTTACAAATT
56961973 TAGCACTTTGTGTGTTG-A-A-TACTGT
60 TAGCACTTTGTGTGTTGAATATTACTGT
* *
56961998 TACTGCTACCGTTACTGATT
1 TACTGTTACCGTTACCGATT
56962018 ACTGTTTAGG
Statistics
Matches: 96, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
90 68 0.71
94 1 0.01
95 1 0.01
96 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (87 bp):
TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACAAATTTAGCAC
TTTGTGTGTTGAATATTACTGT
Found at i:56962002 original size:51 final size:51
Alignment explanation
Indices: 56961861--56962019 Score: 177
Period size: 51 Copynumber: 3.2 Consensus size: 51
56961851 GTCGAATACT
*
56961861 GTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGTTACTGTTACT
1 GTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGTTACTGTTACC
* * * *
56961912 ATTACCGTTACCGATTCGGCACTTTGTGTGTCG-A-A----TACTGTTACC
1 GTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGTTACTGTTACC
* ** * *
56961957 GTTGCTGTTACAAATTTAGCACTTTGTGTGTTGAATACTGTTACTGCTACC
1 GTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGTTACTGTTACC
56962008 GTTACTGATTAC
1 GTTACTG-TTAC
56962020 TGTTTAGGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 13
0.75 0.13 0.11
Matches are distributed among these distances:
45 34 0.40
46 1 0.01
47 1 0.01
49 1 0.01
50 1 0.01
51 44 0.51
52 4 0.05
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (51 bp):
GTTACTGTTACCGATTTGGCACTTTGTGTGTTGAATACTGTTACTGTTACC
Found at i:56986361 original size:21 final size:21
Alignment explanation
Indices: 56986299--56986361 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
56986289 TCAGCACTTT
*
56986299 TGAGCTTCAGTTTAACCCTTA
1 TGAGCTTCTGTTTAACCCTTA
* * *
56986320 TGGGTTTCTG-TTAAGCTCTTA
1 TGAGCTTCTGTTTAA-CCCTTA
56986341 TGAGCTTCTGTTTAACCCTTA
1 TGAGCTTCTGTTTAACCCTTA
56986362 CGGGTTCCCG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (21 bp):
TGAGCTTCTGTTTAACCCTTA
Found at i:56986367 original size:42 final size:42
Alignment explanation
Indices: 56986242--56986367 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 42
56986232 TCTCGTGAGC
* * *
56986242 TTCAATTAA-CTCATATGAGTTTCAGTTTAACCCTT-CTAGGT
1 TTCAATTAAGCTCTTATGAGCTTCAGTTTAACCCTTAC-GGGT
* * * *
56986283 TTCAATTCAGCACTTTTGAGCTTCAGTTTAACCCTTATGGGT
1 TTCAATTAAGCTCTTATGAGCTTCAGTTTAACCCTTACGGGT
** *
56986325 TTCTGTTAAGCTCTTATGAGCTTCTGTTTAACCCTTACGGGT
1 TTCAATTAAGCTCTTATGAGCTTCAGTTTAACCCTTACGGGT
56986367 T
1 T
56986368 CCCGTTTAGC
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
41 8 0.12
42 61 0.88
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCAATTAAGCTCTTATGAGCTTCAGTTTAACCCTTACGGGT
Found at i:56986383 original size:42 final size:42
Alignment explanation
Indices: 56986255--56986389 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 42
56986245 AATTAACTCA
* * * ** *
56986255 TATGAGTTTCAGTTTAACCCTT-CTAGGTTTCAATTCAGCACT
1 TATGAGCTTCAGTTTAACCCTTAC-GGGTTCCCGTTAAGCACT
* * * * *
56986297 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCTGTTAAGCTCT
1 TATGAGCTTCAGTTTAACCCTTACGGGTTCCCGTTAAGCACT
* *
56986339 TATGAGCTTCTGTTTAACCCTTACGGGTTCCCGTTTAGCACT
1 TATGAGCTTCAGTTTAACCCTTACGGGTTCCCGTTAAGCACT
*
56986381 TATGTGCTT
1 TATGAGCTT
56986390 TTGTGCAGCT
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTACGGGTTCCCGTTAAGCACT
Found at i:56988164 original size:21 final size:22
Alignment explanation
Indices: 56988132--56988172 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
56988122 TTAGTGGTAA
56988132 ATGTGATGCATTTAGGATATTG
1 ATGTGATGCATTTAGGATATTG
*
56988154 ATGTGAT-CATTTATGATAT
1 ATGTGATGCATTTAGGATAT
56988173 CCAACAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (22 bp):
ATGTGATGCATTTAGGATATTG
Found at i:56989018 original size:16 final size:16
Alignment explanation
Indices: 56988993--56989023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56988983 GATATACGAA
*
56988993 AAAAATGAAAAAAAAG
1 AAAAACGAAAAAAAAG
56989009 AAAAACGAAAAAAAA
1 AAAAACGAAAAAAAA
56989024 ATTTGGGTGC
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:0.84, C:0.03, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAACGAAAAAAAAG
Found at i:56989378 original size:206 final size:201
Alignment explanation
Indices: 56989017--56989737 Score: 780
Period size: 205 Copynumber: 3.5 Consensus size: 201
56989007 AGAAAAACGA
* * * **
56989017 AAAAAAAATTTGGGTGCTGGCTTGTCAATGGCTGGCACCCAGTACAAATTTTAAAAAAAAAATTC
1 AAAAAAAATTTGGGTGCTTGCCTGTCAATGGCCGGCACCCAGTACAAA--TTAAAAAAAATCTT-
56989082 TTTTTTTCGTGTCAAAATCAGATATAAATATACG-AAAAAAAA-TTGGTGCTGTCCTGTCAATGG
63 TTTTTTTCGTGTCAAAATCAGATATAAATATACGAAAAAAAAATTTGGTGCTGT-CTGTCAATGG
* *
56989145 CTAGAACCCAGTAC-AAATTTAAAAAAAATTATTTTTTTTCGTGTCAGAATCAAATATAAATATA
127 CTGGCACCCAGTACAAAATTTAAAAAAAATTATTTTTTTTCGTGTCAGAATCAAATATAAATATA
56989209 CGAAAAAAAT
192 CGAAAAAAAT
* * *
56989219 AAAAAAAAAAAGTTT-GGTGGTTGCCTGTCAATGGCCGGCAACCAGTAGAAATTAAAAAAAATTC
1 ---AAAAAAAA-TTTGGGTGCTTGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAA-TC
* * *
56989283 TTTTTTTTTTCATGTCAGAATCATATATAAATATACGAAAAAAAAATTTGGTGCTGGTCTGTCAA
61 -TTTTTTTTTCGTGTCAAAATCAGATATAAATATACGAAAAAAAAATTTGGTGCT-GTCTGTCAA
** *
56989348 TGG-TCGGCACTTAGTACAAAATTTAAAAAAAATTCTTTTTTTTTCGTGTCAGAATCAAATATAA
124 TGGCT-GGCACCCAGTACAAAATTTAAAAAAAATT-ATTTTTTTTCGTGTCAGAATCAAATATAA
56989412 ATATACGAAAAAAAT
187 ATATACGAAAAAAAT
** * *
56989427 AAAAAAAATTTCGGGTG-TTGGCCTGTCAATGGCAAGCACCCAGTACGAATTTAAAAAAAA---A
1 AAAAAAAATTT-GGGTGCTT-GCCTGTCAATGGCCGGCACCCAGTAC-AAATTAAAAAAAATCTT
* * ** * * * * ** * * *
56989488 TTATTGTCAGAATCATATAT-AAATATACGAAAAAAATAAAAAAAAATTTGGGTGCAAGCCTATC
63 TTTTTTTC-GTGTCA-AAATCAGATATA--AATATACGAAAAAAAAATTT-GGTGC-TGTCTGTC
* *
56989552 AATGGCTGGCACCCAGTACAAATTTTTAAAAAAAATTA-TTTTTTTCGTGTCAGAATCAGATATA
122 AATGGCTGGCACCCAGTACAAA-ATTTAAAAAAAATTATTTTTTTTCGTGTCAGAATCAAATATA
56989616 AATATACGAAAAAAAT
186 AATATACGAAAAAAAT
** *
56989632 AAAAAAAATTTTGGGTGCTAACCTGACAATGGCCGGCACCCAGTACAAATTAAAAAAAAATCTTA
1 AAAAAAAA-TTTGGGTGCTTGCCTGTCAATGGCCGGCACCCAGTACAAATT-AAAAAAAATCTT-
*
56989697 TTTTTTTCGTGTCAAAATCAGATATACATATACGAAAAAAA
63 TTTTTTTCGTGTCAAAATCAGATATAAATATACGAAAAAAA
56989738 TAAAAAAATT
Statistics
Matches: 427, Mismatches: 60, Indels: 57
0.78 0.11 0.10
Matches are distributed among these distances:
202 6 0.01
203 19 0.04
204 40 0.09
205 159 0.37
206 97 0.23
207 47 0.11
208 53 0.12
209 6 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (201 bp):
AAAAAAAATTTGGGTGCTTGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAATCTTTTT
TTTTCGTGTCAAAATCAGATATAAATATACGAAAAAAAAATTTGGTGCTGTCTGTCAATGGCTGG
CACCCAGTACAAAATTTAAAAAAAATTATTTTTTTTCGTGTCAGAATCAAATATAAATATACGAA
AAAAAT
Found at i:56989508 original size:98 final size:97
Alignment explanation
Indices: 56989394--56989793 Score: 361
Period size: 107 Copynumber: 3.9 Consensus size: 97
56989384 TTTTTTTTCG
* *
56989394 TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTCGGGTGTTGGCCTGTCAATGG
1 TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTT-GGGTGCTAGCCTGTCAATGG
*
56989459 CAAGCACCCAGTACGAATTTAAAAAAAAATTAT-
65 CAGGCACCCAGTAC-AATTTAAAAAAAAATTATC
* * *
56989492 TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCAAGCCTATCAATGG
1 TGTCAGAATCAAATATAAATATACGAAAAAAAT-AAAAAAAATTTGGGTGCTAGCCTGTCAATGG
* *
56989557 CTGGCACCCAGTACAAATTTTTAAAAAAAATTATTTTTTTC
65 CAGGCACCCAGTAC-AA--TTTAAAAAAAA--A---TTATC
* * *
56989598 GTGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTAACCTGACAATG
1 -TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAA-TTTGGGTGCTAGCCTGTCAATG
* *
56989663 GCCGGCACCCAGTACAAATTAAAAAAAAATCTTATTTTTTTC
64 GCAGGCACCCAGTACAATTTAAAAAAAAA--TTA------TC
* * * * * ** *
56989705 GTGTCAAAATCAGATATACATATACGAAAAAAATAAAAAAATTTTTGAGTGCCGGCTTGTCAATG
1 -TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAA-ATTTGGGTGCTAGCCTGTCAATG
* **
56989770 GCCGGCTTCCAGTACAAATTTAAA
64 GCAGGCACCCAGTAC-AATTTAAA
56989794 TTTTTTTTCG
Statistics
Matches: 253, Mismatches: 30, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
98 62 0.25
99 11 0.04
100 11 0.04
101 3 0.01
102 2 0.01
104 10 0.04
105 3 0.01
106 10 0.04
107 134 0.53
108 7 0.03
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.27
Consensus pattern (97 bp):
TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAATTTGGGTGCTAGCCTGTCAATGGC
AGGCACCCAGTACAATTTAAAAAAAAATTATC
Found at i:56989615 original size:107 final size:106
Alignment explanation
Indices: 56989492--56989793 Score: 381
Period size: 107 Copynumber: 2.8 Consensus size: 106
56989482 AAAAAATTAT
* ** *
56989492 TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCAAGCCTATCAATGG
1 TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGG
*
56989557 CTGGCACCCAGTACAAATTTTTAAAAAAAA-TTATTTTTTTCG
66 CCGGCACCCAGTACAAA--TTTAAAAAAAATTTATTTTTTTCG
* * ** *
56989599 TGTCAGAATCAGATATAAATATACGAAAAAAATAAAAAAAATTTTGGGTGCTAACCTGACAATGG
1 TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGG
*
56989664 CCGGCACCCAGTACAAATTAAAAAAAAATCTTATTTTTTTCG
66 CCGGCACCCAGTACAAATTTAAAAAAAAT-TTATTTTTTTCG
* * * ** * * *
56989706 TGTCAAAATCAGATATACATATACGAAAAAAATAAAAAAATTTTTGAGTGCCGGCTTGTCAATGG
1 TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGG
**
56989771 CCGGCTTCCAGTACAAATTTAAA
66 CCGGCACCCAGTACAAATTTAAA
56989794 TTTTTTTTCG
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
105 10 0.06
107 163 0.94
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (106 bp):
TGTCAGAATCAAATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGG
CCGGCACCCAGTACAAATTTAAAAAAAATTTATTTTTTTCG
Found at i:56989801 original size:205 final size:203
Alignment explanation
Indices: 56989016--56989827 Score: 640
Period size: 205 Copynumber: 4.0 Consensus size: 203
56989006 AAGAAAAACG
* * * * *
56989016 AAAAAAAAATTTGGGTGCTGGCTTGTCAATGGCTGGCACCCAGTACAAATTTTAAAAAAAAA-AT
1 AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAA--TTAAAAAAAAATCT
* * * * * *
56989080 TCTTTTTTTCGTGTCAAAATCAGATATAAATATACG------A-AAAAAAA-TTGGTGCTGTCCT
64 TATTTTTTTC-TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAATTTGGTGCAGGCTT
** ***
56989137 GTCAATGGCTAGAACCCAGTACAAATTTAAAAAAAATTATTTTTTTTCGTGTCAGAATCAAATAT
128 GTCAATGGCCGGCTTCCAGTACAAATTT----AAAA-T-TTTTTTTTCGTGTCAGAATCAAATAT
56989202 AAATATACGAAAAAAAT
187 AAATATACGAAAAAAAT
* * * * * *
56989219 AAAAAAAAAAAGTTT-GGTGGTTGCCTGTCAATGGCCGGCAACCAGTAGAAATTAAAAAAAATTC
1 ---AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAAATC
* *
56989283 TTTTTTTTTTCATGTCAGAATCATATATAAATATACG-----AA-AAAAAAATTTGGTGCTGG-T
63 TTATTTTTTTC-TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAATTTGGTGCAGGCT
*
56989341 CTGTCAATGGTCGGCACTT--AGTACAAAATTTAAAAAAAATTCTTTTTTTTTCGTGTCAGAATC
127 -TGTCAATGGCCGG--CTTCCAGTAC-AAATTT----AAAA---TTTTTTTTTCGTGTCAGAATC
56989404 AAATATAAATATACGAAAAAAAT
181 AAATATAAATATACGAAAAAAAT
* * * ** *
56989427 AAAAAAAATTTCGGGTGTTGGCCTGTCAATGGCAAGCACCCAGTACGAATTTAAAAAAAAA--TT
1 AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTAC-AAATTAAAAAAAAATCTT
* *
56989490 A------T-TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAAAATTTGGGTGCAAGCC
65 ATTTTTTTCTGTCAGAATCATATATAAATATACGAAAAAAAT--AAAAAAATTT-GGTGCAGGCT
* * ** *
56989548 TATCAATGGCTGGCACCCAGTACAAATTTTTAAAAAAAATTATTTTTTTCGTGTCAGAATCAGAT
127 TGTCAATGGCCGGCTTCCAGTACAAA--TTT----AAAATT-TTTTTTTCGTGTCAGAATCAAAT
56989613 ATAAATATACGAAAAAAAT
185 ATAAATATACGAAAAAAAT
* *
56989632 AAAAAAAATTTTGGGTGCTAACCTGACAATGGCCGGCACCCAGTACAAATTAAAAAAAAATCTTA
1 AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAAATCTTA
* * * *
56989697 TTTTTTTCGTGTCAAAATCAGATATACATATACGAAAAAAATAAAAAAATTTTTGAGTGCCGGCT
66 TTTTTTTC-TGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAA--TTTG-GTGCAGGCT
* * *
56989762 TGTCAATGGCCGGCTTCCAGTACAAATTT-AAA-TTTTTTTTCGTGTAAGAATCATATACAAATA
127 TGTCAATGGCCGGCTTCCAGTACAAATTTAAAATTTTTTTTTCGTGTCAGAATCAAATATAAATA
56989825 TAC
192 TAC
56989828 AAAGTCATAT
Statistics
Matches: 504, Mismatches: 63, Indels: 79
0.78 0.10 0.12
Matches are distributed among these distances:
197 25 0.05
199 1 0.00
202 2 0.00
203 10 0.02
204 49 0.10
205 173 0.34
206 87 0.17
207 40 0.08
208 43 0.09
209 1 0.00
212 11 0.02
213 1 0.00
214 61 0.12
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (203 bp):
AAAAAAAATTTTGGGTGCTAGCCTGTCAATGGCCGGCACCCAGTACAAATTAAAAAAAAATCTTA
TTTTTTTCTGTCAGAATCATATATAAATATACGAAAAAAATAAAAAAATTTGGTGCAGGCTTGTC
AATGGCCGGCTTCCAGTACAAATTTAAAATTTTTTTTTCGTGTCAGAATCAAATATAAATATACG
AAAAAAAT
Found at i:56994972 original size:112 final size:109
Alignment explanation
Indices: 56994772--56995421 Score: 780
Period size: 112 Copynumber: 5.8 Consensus size: 109
56994762 TTTTTTAAAA
*
56994772 ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAAAAATTTTTTTAAATTTGTAC
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACG--AAAAAAAAGAATTTTTTTAAATTTGTAC
56994837 TGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATATATTTTTTTT
64 TGGGTGCCGGCCATTGACAGGCCAGCACCC--AAAATATATTTTTTTT
*
56994885 AATTTTTTTCGTATATTTATATTTGATTCTGACACGAAAAAAAAGAATTTTTTTAAATTTGTACT
1 -ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTAAATTTGTACT
* * *
56994950 GGGTACCGGCTATTGACAGGCCAGCACCCAAAA-ATTATTTTTTTAA
65 GGGTGCCGGCCATTGACAGGCCAGCACCCAAAATA-TATTTTTTT-T
*
56994996 AATTTTTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAGAAATTTTTTTTTAAATTTGTA
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAG-AA--TTTTTTTAAATTTGTA
* *
56995060 CTGGGTGCCGGCCATTGACAGACCAGCACCCAAAATA-AATTTTTTT
63 CTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATATATTTTTTTT
* **
56995106 ATTTTTTTCGTATATTTATATCTGATTCTGACACG-----GAA-TTTTTTTTTAAAAAAAATTTG
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTT-----AAATTTG
* * *
56995165 TACTAGGTGCCGGCCATTGATAGGCTAGCACCCAAAATAT-TTTTTTTT
61 TACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATATATTTTTTTT
*
56995213 ATATTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAAGAAATTTTTTTTCTAGAATTT
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACG-AAAAAAAAG-AA--TTTTTT-TA-AATTT
* *
56995278 GTACTGGGTGCCGGCCATTGACAGGCCAACACCCAAAATAAATTTTTTTT
60 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATATATTTTTTTT
* * * * ******
56995328 CTTTTTTCCATATATTTATATATGATTCTGACACGAAAAATTTTTTTTTTTTTAAAAATTTGTAC
1 ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTT--AAATTTGTAC
56995393 TGGGTGCCGGCCATTGACAGGCCAGCACC
64 TGGGTGCCGGCCATTGACAGGCCAGCACC
56995422 TAAATTTTTT
Statistics
Matches: 467, Mismatches: 42, Indels: 57
0.83 0.07 0.10
Matches are distributed among these distances:
102 7 0.01
106 2 0.00
107 83 0.18
109 9 0.02
110 83 0.18
111 50 0.11
112 104 0.22
113 4 0.01
114 80 0.17
115 38 0.08
117 6 0.01
118 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (109 bp):
ATTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAAGAATTTTTTTAAATTTGTACTG
GGTGCCGGCCATTGACAGGCCAGCACCCAAAATATATTTTTTTT
Found at i:56996398 original size:27 final size:30
Alignment explanation
Indices: 56996368--56996437 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 30
56996358 ATCTCTATAC
*
56996368 ACTTTTTATATTT-GGAATTTAGT-C-TCT
1 ACTTTTTATATTTAGGAATTTAATCCTTCT
*
56996395 AC-TTTTATTTTTAGGAATTTAATCCTTCT
1 ACTTTTTATATTTAGGAATTTAATCCTTCT
*
56996424 ACTTTTTAAATTTA
1 ACTTTTTATATTTA
56996438 AAAATTTAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.26
27 11 0.31
28 1 0.03
29 5 0.14
30 9 0.26
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (30 bp):
ACTTTTTATATTTAGGAATTTAATCCTTCT
Found at i:56996402 original size:26 final size:29
Alignment explanation
Indices: 56996371--56996429 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 29
56996361 TCTATACACT
*
56996371 TTTTATATTT-GGAATTTAGT-C-TCTAC
1 TTTTATATTTAGGAATTTAATCCTTCTAC
*
56996397 TTTTATTTTTAGGAATTTAATCCTTCTAC
1 TTTTATATTTAGGAATTTAATCCTTCTAC
56996426 TTTT
1 TTTT
56996430 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
27 9 0.32
28 1 0.04
29 9 0.32
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (29 bp):
TTTTATATTTAGGAATTTAATCCTTCTAC
Found at i:56997507 original size:31 final size:32
Alignment explanation
Indices: 56997452--56997511 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
56997442 ACATAAACAA
*
56997452 AATATTTTAAAATTTTAAATATAATGATAAAC
1 AATATTTTAAAATATTAAATATAATGATAAAC
56997484 AATATTTTAACAA-ATT-AATATAATGATA
1 AATATTTTAA-AATATTAAATATAATGATA
56997512 TTTTAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 12 0.46
32 12 0.46
33 2 0.08
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
AATATTTTAAAATATTAAATATAATGATAAAC
Found at i:56999069 original size:8 final size:8
Alignment explanation
Indices: 56999008--56999073 Score: 80
Period size: 8 Copynumber: 8.0 Consensus size: 8
56998998 CGCCTTCTCA
56999008 AAAAGAAAG
1 AAAA-AAAG
56999017 -AAAAAAG
1 AAAAAAAG
*
56999024 AAGAAAAG
1 AAAAAAAG
56999032 AAAAAAAG
1 AAAAAAAG
56999040 AAAAAAAG
1 AAAAAAAG
56999048 AAAAAAGAG
1 AAAAAA-AG
56999057 AAATAAAAG
1 AAA-AAAAG
*
56999066 AATAAAAG
1 AAAAAAAG
56999074 TGAATGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
7 4 0.08
8 35 0.69
9 9 0.18
10 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:57011004 original size:4 final size:4
Alignment explanation
Indices: 57010995--57011024 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
57010985 GGTGGACAGG
57010995 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GA
57011025 TAGTGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:57013118 original size:28 final size:27
Alignment explanation
Indices: 57013087--57013152 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
57013077 TAAAATTCAA
* *
57013087 AAAATATTTAAAAAAATCTAAAATTATT
1 AAAATATTTAAAAAAATATAAAAATA-T
*
57013115 AAAAT-TACTAAAAAAATATAAAAATAT
1 AAAATAT-TTAAAAAAATATAAAAATAT
*
57013142 AAAAAATTTAA
1 AAAATATTTAA
57013153 TCAATTGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATATTTAAAAAAATATAAAAATAT
Found at i:57014303 original size:21 final size:18
Alignment explanation
Indices: 57014270--57014308 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 18
57014260 AACAATGTTT
57014270 TAATTAATATTTTTTAAAA
1 TAATTAATA-TTTTTAAAA
57014289 TAATTAAATTATTTTTAAAA
1 TAATT-AA-TATTTTTAAAA
57014309 GATTAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 11 0.61
21 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATATTTTTAAAA
Found at i:57014315 original size:23 final size:20
Alignment explanation
Indices: 57014269--57014315 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
57014259 TAACAATGTT
*
57014269 TTAATTAATATTTTTTAAAA
1 TTAATTAATATTTTTAAAAA
57014289 -TAATTAAATTATTTTTAAAAGA
1 TTAATT-AA-TATTTTTAAAA-A
57014311 TTAAT
1 TTAAT
57014316 GGAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 10 0.45
22 1 0.05
23 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAATTAATATTTTTAAAAA
Found at i:57023367 original size:24 final size:25
Alignment explanation
Indices: 57023340--57023387 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
57023330 TTACTGCTAC
57023340 TCTTTTCCT-TCTTTT-TTCCTTTCT
1 TCTTTT-CTATCTTTTCTTCCTTTCT
57023364 TCTTTTCTATCTTTTCCTTCCTTT
1 TCTTTTCTATCTTTT-CTTCCTTT
57023388 TTTTCATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 2 0.10
24 12 0.57
26 7 0.33
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (25 bp):
TCTTTTCTATCTTTTCTTCCTTTCT
Found at i:57033506 original size:2 final size:2
Alignment explanation
Indices: 57033499--57033525 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57033489 TTACACATCT
57033499 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57033526 GTAAAACTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57039843 original size:12 final size:12
Alignment explanation
Indices: 57039826--57039859 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57039816 TTAGAGCAAT
57039826 TGCAAGAACAGA
1 TGCAAGAACAGA
**
57039838 TGCAAGCCCAGA
1 TGCAAGAACAGA
57039850 TGCAAGAACA
1 TGCAAGAACA
57039860 ACTAGAAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (12 bp):
TGCAAGAACAGA
Found at i:57041460 original size:23 final size:23
Alignment explanation
Indices: 57041418--57041461 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
57041408 AAGAGATCCC
* * *
57041418 TGTAGTATTTAGAGCTTACTTAG
1 TGTAATATTTAGAACATACTTAG
57041441 TGTAATATTTAGAACATACTT
1 TGTAATATTTAGAACATACTT
57041462 GTTGCTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (23 bp):
TGTAATATTTAGAACATACTTAG
Found at i:57042556 original size:25 final size:22
Alignment explanation
Indices: 57042511--57042562 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
57042501 AAAATATTTA
*
57042511 AAGAAAAAAGAATAAAGAAAAG
1 AAGAAAAAAGAACAAAGAAAAG
57042533 AAGAAAGAAAGAACATAAG-AAA-
1 AAGAAA-AAAGAACA-AAGAAAAG
57042555 AAGAAAAA
1 AAGAAAAA
57042563 TGAGAGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 2 0.07
22 12 0.44
23 10 0.37
24 3 0.11
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (22 bp):
AAGAAAAAAGAACAAAGAAAAG
Found at i:57044145 original size:132 final size:132
Alignment explanation
Indices: 57043782--57044149 Score: 515
Period size: 132 Copynumber: 2.8 Consensus size: 132
57043772 CAGATCGGTG
* ** * *
57043782 AAACCACCAGTCCTATCTCCCTGAGCAACAGTGGAGTAGGTC-AAAGATTTTAGATCCTGTCTCC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAA-ATTGTAAATCCTGTCTCC
* *
57043846 CTAAGTAGTAGTGGAGCAAATCGAAGATGGTGAATCTTATCTTCTCAATGTAGTAGGGAAGCAGA
65 CTAAGTAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCTCAATGTAGTAGGGAAGCAGA
57043911 TTT
130 TTT
* * * **
57043914 AAACCACTAGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTTTC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAAATTGTAAATCCTGTCTCCC
* * *
57043979 TAAGCAGTAGTGGAGCAGATCAAAAACGGTGAATCTTATCTTC-CAAATGTAGTAGGGAAGCAGA
66 TAAGTAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCTC-AATGTAGTAGGGAAGCAGA
57044043 TTT
130 TTT
* * *
57044046 AAACCACCAGTTCTATCTCACTAAGCAGTAGTGGAGTAGGTCGAAAATTGTAAATCATGTCTCCC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAAATTGTAAATCCTGTCTCCC
* * *
57044111 TAAGTAGTAGTGGAGCAGATCGAAGGCAGCGAATCTTAT
66 TAAGTAGTAGTGGAGCAGATCGAAGACGGTGAATCTTAT
57044150 TTCACTGGCG
Statistics
Matches: 205, Mismatches: 29, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
131 1 0.00
132 202 0.99
133 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (132 bp):
AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAAATTGTAAATCCTGTCTCCC
TAAGTAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATCTTCTCAATGTAGTAGGGAAGCAGAT
TT
Found at i:57044274 original size:100 final size:100
Alignment explanation
Indices: 57044137--57044956 Score: 1034
Period size: 100 Copynumber: 8.2 Consensus size: 100
57044127 AGATCGAAGG
* * * * * *
57044137 CAGCGAATCTTATTTCACTGGCGGTGCAGTGGAACAGATTAAAGCTGCAACGGCAAATCTTGCTT
1 CAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTT
* *
57044202 CCCCGACATTGCAATT-AAAATATTGAAGCTACAA
66 CCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* *
57044236 CAGCGAATCTCACTTTTCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
1 CAGCGAATCTTAC-TTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
* * * * *
57044301 TCCTCGATATTGCAGTTGAAAAGATTGAAGCTACAA
65 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* ** * *
57044337 CAGTGAATCTTACTTCCCCAGATGGTGCAGTGGAACAGATTGATGCTACAACGGTGAATCTTGCT
1 CAGCGAATCTTACTT-CCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
*
57044402 TCCCCGATATTGCAATTAAAAAGATTGAAGCCACAA
65 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
** * * *
57044438 TGGCGAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACAACGGTGAATCTTGCTT
1 CAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTT
*
57044503 CCACGACATTGCAATTAAAAAGATTGAAGCCACAA
66 CCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * * *
57044538 CGGCGAATCATACTTCCCTAGGTGGTGTAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACT
1 CAGCGAATCTTACTTCCC-AGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
* * * *
57044603 TTCCCAACATTGCATTTAAAAAGATTGAAGCTACAA
65 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * *
57044639 C-GATGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCT
1 CAG-CGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
* * * * *
57044703 TTCCTGACATTGAAATTAAAACGATTGAAGCCTCAA
65 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * ** *
57044739 CGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACTTATTGAAGCTACAATGGCGAATCTTGCTT
1 CAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTT
* *
57044804 CCCCGACATTACAATTAAAAATATTGAAGCCACAA
66 CCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
* * * **
57044839 CAGCGAATCTTACTTCCTTA-GCGGTGTAGTGGAACAGATTGAAGCTATAATAGCGAATCTTGCT
1 CAGCGAATCTTACTTCC-CAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCT
* *
57044903 TCCCCGACAATGCAGTTAAAAAGATTGAAGCCACAA
65 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
*
57044939 CAGTGAATCTTACTTCCC
1 CAGCGAATCTTACTTCCC
57044957 CGACGAACAG
Statistics
Matches: 628, Mismatches: 86, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
99 11 0.02
100 415 0.66
101 202 0.32
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (100 bp):
CAGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTT
CCCCGACATTGCAATTAAAAAGATTGAAGCCACAA
Found at i:57044504 original size:201 final size:201
Alignment explanation
Indices: 57044159--57044957 Score: 1066
Period size: 201 Copynumber: 4.0 Consensus size: 201
57044149 TTTCACTGGC
* * * *
57044159 GGTGCAGTGGAACAGATTAAAGCTGCAACGGCAAATCTTGCTTCCCCGACATTGCAATT-AAAAT
1 GGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
* * * *
57044223 ATTGAAGCTACAACAGCGAATCTCACTTTTCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
66 ATTGAAGCCACAACAGCGAATCTTAC-TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
* * * *
57044288 GGCGAATCTTGCTTCCTCGATATTGCAGTTGAAAAGATTGAAGCTACAACAGTGAATCTTACTTC
130 GGCGAATCTTGCTTCCTCGACATTGCAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTC
*
57044353 CCCAGAT
195 CCCAGGT
* * *
57044360 GGTGCAGTGGAACAGATTGATGCTACAACGGTGAATCTTGCTTCCCCGATATTGCAATTAAAAAG
1 GGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
** *
57044425 ATTGAAGCCACAATGGCGAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTGAAGCTACAACG
66 ATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACG
* * * * *
57044490 GTGAATCTTGCTTCCACGACATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCATACTTCC
131 GCGAATCTTGCTTCCTCGACATTGCAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCC
*
57044555 CTAGGT
196 CCAGGT
* * * * *
57044561 GGTGTAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTTCCCAACATTGCATTTAAAAAG
1 GGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
* *
57044626 ATTGAAGCTACAAC-GATGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
66 ATTGAAGCCACAACAG-CGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAAC
* * * * *
57044690 GGTGAATCTTGCTTTCCT-GACATTGAAATTAAAACGATTGAAGCCTCAACGGTGAATCTTACTT
130 GGCGAATCTTGC-TTCCTCGACATTGCAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTT
* *
57044754 -CCCTGGC
194 CCCCAGGT
** * * *
57044761 GGTGCAGTGGAACTTATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAT
1 GGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
* * * * **
57044826 ATTGAAGCCACAACAGCGAATCTTACTTCCTTAGCGGTGTAGTGGAACAGATTGAAGCTATAATA
66 ATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACG
* * *
57044891 GCGAATCTTGCTTCCCCGACAATGCAGTTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCC
131 GCGAATCTTGCTTCCTCGACATTGCAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCC
57044956 CC
196 CC
57044958 GACGAACAGA
Statistics
Matches: 520, Mismatches: 72, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
199 4 0.01
200 165 0.32
201 321 0.62
202 30 0.06
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (201 bp):
GGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAG
ATTGAAGCCACAACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACG
GCGAATCTTGCTTCCTCGACATTGCAATTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCC
CCAGGT
Found at i:57044957 original size:50 final size:50
Alignment explanation
Indices: 57044160--57044960 Score: 548
Period size: 50 Copynumber: 16.0 Consensus size: 50
57044150 TTCACTGGCG
* * * * * *
57044160 GTGCAGTGGAACAGATTAAAGCTGCAACGGCAAATCTTGCTTCCCCGACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * * * * *
57044210 TTGCAATT-AAAATATTGAAGCTACAACAGCGAATCTCACTTTTCCAGGCG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTAC-TTCCCCGACA
* * * * *
57044260 GTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCTCGATA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * **
57044310 TTGCAGTTGAAAAGATTGAAGCTACAACAGTGAATCTTACTTCCCCAGATG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCC-GACA
* * * * * *
57044361 GTGCAGTGGAACAGATTGATGCTACAACGGTGAATCTTGCTTCCCCGATA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * * * *
57044411 TTGCAATTAAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCTGGCG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * *
57044461 GTGCAATGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCACGACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * * ***
57044511 TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCATACTTCCCTAGGTG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-CGACA
* * * * *
57044562 GTGTAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTTCCCAACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * ** * * *
57044612 TTGCATTTAAAAAGATTGAAGCTACAACGATGAATCTTACTTCCCTGGCG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * *
57044662 GTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTTCCTGACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * * *
57044712 TTGAAATT-AAAACGATTGAAGCCT-CAACGGTGAATCTTACTTCCCTGGCG
1 GTGCAGTTGAAAA-GATTGAAG-CTACAACGGCGAATCTTACTTCCCCGACA
* *** * *
57044762 GTGCAGTGGAACTTATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * * * * ** *
57044812 TTACAATTAAAAATATTGAAGCCACAACAGCGAATCTTACTT-CCTTAGCG
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGA-CA
* * * * ** *
57044862 GTGTAGTGGAACAGATTGAAGCTATAATAGCGAATCTTGCTTCCCCGACA
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
* * * * *
57044912 ATGCAGTTAAAAAGATTGAAGCCACAACAGTGAATCTTACTTCCCCGAC
1 GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGAC
57044961 GAACAGATTG
Statistics
Matches: 560, Mismatches: 181, Indels: 20
0.74 0.24 0.03
Matches are distributed among these distances:
49 31 0.06
50 416 0.74
51 113 0.20
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
GTGCAGTTGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCCGACA
Found at i:57045803 original size:17 final size:18
Alignment explanation
Indices: 57045771--57045805 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57045761 GGGAAATAAT
*
57045771 AAAAGAAAACGGTTCAAA
1 AAAAGAAAACGATTCAAA
57045789 AAAAGAAAA-GATTCAAA
1 AAAAGAAAACGATTCAAA
57045806 GGTTGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAGAAAACGATTCAAA
Found at i:57052050 original size:25 final size:24
Alignment explanation
Indices: 57052022--57052072 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
57052012 TATAATAGGA
*
57052022 AGCTCACAAAGAGCCTAT-AACGGGT
1 AGCTC-CAAAGAG-CAATCAACGGGT
*
57052047 AGCTCCGAAGAGCAATCAACGGGT
1 AGCTCCAAAGAGCAATCAACGGGT
57052071 AG
1 AG
57052073 AAAGAGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.13
24 15 0.65
25 5 0.22
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATCAACGGGT
Found at i:57060082 original size:32 final size:32
Alignment explanation
Indices: 57060041--57060131 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
57060031 ATACTTCAGT
**
57060041 TGACCAGTCTTACTAACAATGAAAATCCTAAA
1 TGACCAGTCTTACTAACAGCGAAAATCCTAAA
57060073 TGACCAGTCTTACTAACAGCGAAAATCCTAAA
1 TGACCAGTCTTACTAACAGCGAAAATCCTAAA
57060105 TGACCAGTCTTACTAACAGCGAAAATC
1 TGACCAGTCTTACTAACAGCGAAAATC
57060132 TTTTGATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.23
Consensus pattern (32 bp):
TGACCAGTCTTACTAACAGCGAAAATCCTAAA
Found at i:57060409 original size:37 final size:37
Alignment explanation
Indices: 57060368--57060441 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
57060358 TATCCAATAA
57060368 CATGACCCAAAAATGAGATTGATCAGCTATGCAAAAT
1 CATGACCCAAAAATGAGATTGATCAGCTATGCAAAAT
*
57060405 CATGACCCAAGAATGAGATTGATCAGCTATGCAAAAT
1 CATGACCCAAAAATGAGATTGATCAGCTATGCAAAAT
57060442 AATAGCCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (37 bp):
CATGACCCAAAAATGAGATTGATCAGCTATGCAAAAT
Found at i:57070312 original size:45 final size:45
Alignment explanation
Indices: 57070248--57070362 Score: 198
Period size: 45 Copynumber: 2.6 Consensus size: 45
57070238 TTTGAGTACT
57070248 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
57070293 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
* *
57070338 TCTGAT-TAGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
57070363 ATCATACGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
43 12 0.18
44 5 0.07
45 51 0.75
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
Found at i:57073746 original size:16 final size:15
Alignment explanation
Indices: 57073703--57073749 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
57073693 ATTTAAAAAT
* *
57073703 AATAGAAATGTAT-A
1 AATATAAATATATAA
*
57073717 AATATATATATATAA
1 AATATAAATATATAA
57073732 AATATAAAGTATATAA
1 AATATAAA-TATATAA
57073748 AA
1 AA
57073750 GTTTAAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (15 bp):
AATATAAATATATAA
Found at i:57073960 original size:3 final size:3
Alignment explanation
Indices: 57073939--57073987 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
57073929 TGTACATGAA
* * *
57073939 AAT AAT GAAT AAT ATT AAT AAT AAT AAT AGAC AAT AAT AGT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
57073986 AA
1 AA
57073988 ACAAGTAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57073976 original size:19 final size:20
Alignment explanation
Indices: 57073954--57073997 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
57073944 TGAATAATAT
*
57073954 TAATAATAATAATAGACAA-
1 TAATAATAATAATAAACAAG
*
57073973 TAATAGTAATAATAAACAAG
1 TAATAATAATAATAAACAAG
57073993 TAATA
1 TAATA
57073998 GTACCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (20 bp):
TAATAATAATAATAAACAAG
Found at i:57074925 original size:22 final size:22
Alignment explanation
Indices: 57074874--57074930 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
57074864 TGTTGAGTGC
* *
57074874 GCGCGATGCGTGGGAGCGACAA
1 GCGCGATGTGCGGGAGCGACAA
* **
57074896 GCGTGATGTGCGGGAGCGACGG
1 GCGCGATGTGCGGGAGCGACAA
57074918 GCGCGATGTGCGG
1 GCGCGATGTGCGG
57074931 TGCTTGCGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.21, G:0.51, T:0.12
Consensus pattern (22 bp):
GCGCGATGTGCGGGAGCGACAA
Found at i:57078116 original size:15 final size:15
Alignment explanation
Indices: 57078082--57078116 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57078072 AATTAAGTTT
*
57078082 AAAAAAAGATAACAG
1 AAAAAAAGATAACAA
*
57078097 CAAAAAAGATAACAA
1 AAAAAAAGATAACAA
57078112 AAAAA
1 AAAAA
57078117 TATAAAGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAAAAAGATAACAA
Found at i:57083262 original size:42 final size:42
Alignment explanation
Indices: 57083183--57083263 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
57083173 TGAATTTTCG
***
57083183 TTTAACCCTAATGGGTTTCCATTTAGCTATTTTGAGCTTCAA
1 TTTAACCCTAATGGGTTTCCATTTAGCTATCACGAGCTTCAA
* * *
57083225 TTTAACCCTTATGGGTTTCCGTTTAGCTCTCACGAGCTT
1 TTTAACCCTAATGGGTTTCCATTTAGCTATCACGAGCTT
57083264 TTGTCCAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (42 bp):
TTTAACCCTAATGGGTTTCCATTTAGCTATCACGAGCTTCAA
Found at i:57084964 original size:28 final size:27
Alignment explanation
Indices: 57084932--57084990 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
57084922 TTAAATTTTT
57084932 TTAAAAAA-AAATTCAATTCAATTAATAA
1 TTAAAAAATAAATT-AATTCAATTAAT-A
* *
57084960 TTAAAAAATTAATTAATTCGATTAATA
1 TTAAAAAATAAATTAATTCAATTAATA
57084987 TTAA
1 TTAA
57084991 TTCAGTATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (27 bp):
TTAAAAAATAAATTAATTCAATTAATA
Found at i:57093330 original size:21 final size:21
Alignment explanation
Indices: 57093304--57093344 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57093294 ATCTGCTCAA
* *
57093304 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
57093325 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
57093345 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:57095720 original size:176 final size:176
Alignment explanation
Indices: 57095426--57095779 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 176
57095416 ATGGTCCGTG
57095426 CCATCAAAGATCTCCACGGCCAATCTTGCATTTGCAATTGTCGGTCTTGTCCACATGGACGATGT
1 CCATCAAAGATCTCCACGGCCAATCTTGCATTTGCAATTGTCGGTCTTGTCCACATGGACGATGT
57095491 TGAAGCTCCTACACCGACCGTTTTCTCCATAATCTTTCAATATACCTAAGGAAATCTTTTCTGAT
66 TGAAGCTCCTACACCGACCGTTTTCTCCATAATCTTTCAATATACCTAAGGAAATCTTTTCTGAT
57095556 GTGGAAGATCAATTTAAACTGCAACCACAGAGCATACTACGATTAA
131 GTGGAAGATCAATTTAAACTGCAACCACAGAGCATACTACGATTAA
57095602 CCATCAAAGATCTCCACGGCCAATCTTGCATTTGCAATTGTCGGTCTTGTCCACATGGACGATGT
1 CCATCAAAGATCTCCACGGCCAATCTTGCATTTGCAATTGTCGGTCTTGTCCACATGGACGATGT
57095667 TGAAGCTCCTACACCGACCGTTTTCTCCATAATCTTTCAATATACCTAAGGAAATCTTTTCTGAT
66 TGAAGCTCCTACACCGACCGTTTTCTCCATAATCTTTCAATATACCTAAGGAAATCTTTTCTGAT
*
57095732 GTGGAAGATCAGTTTAAACTGCAACCACAGAGCATACTACGATTAA
131 GTGGAAGATCAATTTAAACTGCAACCACAGAGCATACTACGATTAA
57095778 CC
1 CC
57095780 TTCGGCTCTG
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (176 bp):
CCATCAAAGATCTCCACGGCCAATCTTGCATTTGCAATTGTCGGTCTTGTCCACATGGACGATGT
TGAAGCTCCTACACCGACCGTTTTCTCCATAATCTTTCAATATACCTAAGGAAATCTTTTCTGAT
GTGGAAGATCAATTTAAACTGCAACCACAGAGCATACTACGATTAA
Found at i:57103980 original size:47 final size:47
Alignment explanation
Indices: 57103908--57104022 Score: 124
Period size: 47 Copynumber: 2.4 Consensus size: 47
57103898 ATCTAAACAA
* *
57103908 TACTATAGGATTTGAGATGAACATTTCCCGA-ACTACAGCATAAAAAG
1 TACTATAAGATTTCAGATGAACATTTCCC-ACACTACAGCATAAAAAG
* * * * ** *
57103955 TACTATAAGATTACAGATGAGCATTTTCCACACTATAGTGTAAACAG
1 TACTATAAGATTTCAGATGAACATTTCCCACACTACAGCATAAAAAG
*
57104002 AACTATAAGATTTCAGATGAA
1 TACTATAAGATTTCAGATGAA
57104023 TATCTTCCAA
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
46 1 0.02
47 54 0.98
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (47 bp):
TACTATAAGATTTCAGATGAACATTTCCCACACTACAGCATAAAAAG
Found at i:57114325 original size:15 final size:16
Alignment explanation
Indices: 57114298--57114333 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
57114288 CTGAACAATT
57114298 ATTTTATTTTTTAAAC
1 ATTTTATTTTTTAAAC
57114314 ATTTTA-TTTTTAAAC
1 ATTTTATTTTTTAAAC
57114329 -TTTTA
1 ATTTTA
57114334 ACAACGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 6 0.30
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTATTTTTTAAAC
Found at i:57118811 original size:43 final size:43
Alignment explanation
Indices: 57118696--57118835 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 43
57118686 AGACTAAGAC
* * *
57118696 CTTTAGTGGCGTTTGT-GGTCG-AAGCGCCGCTATAGATCAGGAT
1 CTTTAGCGGCGTTTGTAGG--GAAAGAGCCGCTATAGATCAGGGT
* * *
57118739 TTTTTGCGGCGTTTGTAGGGAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTAGGGAAAGAGCCGCTATAGATCAGGGT
* * * *
57118782 CTTTAGCGGCGTTT-TTGCGGCAAGAGCCGCTAAAGATTAGGGT
1 CTTTAGCGGCGTTTGTAG-GGAAAGAGCCGCTATAGATCAGGGT
57118825 CTTTAGCGGCG
1 CTTTAGCGGCG
57118836 CTTCTCCCTA
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
42 3 0.04
43 78 0.94
44 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTAGGGAAAGAGCCGCTATAGATCAGGGT
Found at i:57118966 original size:86 final size:85
Alignment explanation
Indices: 57118824--57119011 Score: 225
Period size: 86 Copynumber: 2.2 Consensus size: 85
57118814 AAGATTAGGG
* *
57118824 TCTTTAGCGGCGCTTCTCCCTAAAATGCCGCAAAAGACCCTGATCTATAGCAGCGCTTCGACCAC
1 TCTTTAGCGGCGCTT-TCCCCAAAATGCCGCAAAAGACCATGATCTATAGCAGCGCTTCGACCAC
57118889 AAACGCCACTAAAAAACCTAA
65 AAACGCCACTAAAAAACCTAA
* * ** ***
57118910 TCTTTAGCGGCGCTTTCCCCACAAACT-CCGCGAAAGACCATGATCTTTAGGGGCGCTTTTTCCA
1 TCTTTAGCGGCGCTTTCCCCA-AAA-TGCCGCAAAAGACCATGATCTATAGCAGCGCTTCGACCA
* * *
57118974 CAAACGCCGCTAAAGAACCTTA
64 CAAACGCCACTAAAAAACCTAA
*
57118996 TCTTTAGCGACGCTTT
1 TCTTTAGCGGCGCTTT
57119012 TACCAAAAAC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 5 0.06
86 81 0.93
87 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCCCAAAATGCCGCAAAAGACCATGATCTATAGCAGCGCTTCGACCACA
AACGCCACTAAAAAACCTAA
Found at i:57119031 original size:43 final size:43
Alignment explanation
Indices: 57118824--57119031 Score: 168
Period size: 43 Copynumber: 4.8 Consensus size: 43
57118814 AAGATTAGGG
* * * * * * *
57118824 TCTTTAGCGGCGCTTCTCCCTA-AAATGCCGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTACC-ACAAACGCCACTAAAGAACCTAA
* * ** *
57118867 TCTATAGCAGCGCTTCGACCACAAACGCCACTAAAAAACCTAA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGAACCTAA
** * * * *
57118910 TCTTTAGCGGCGCTTTCCCCACAAACTCCGCGAAAG-ACCATGA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGAACC-TAA
* * * *
57118953 TCTTTAGGGGCGCTTTTTCCACAAACGCCGCTAAAGAACCTTA
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGAACCTAA
* *
57118996 TCTTTAGCGACGCTTTTACCAAAAACGCCACTAAAG
1 TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAG
57119032 GCCAACACCT
Statistics
Matches: 131, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
42 4 0.03
43 124 0.95
44 3 0.02
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTACCACAAACGCCACTAAAGAACCTAA
Found at i:57119044 original size:86 final size:86
Alignment explanation
Indices: 57118885--57119056 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 86
57118875 AGCGCTTCGA
* * * * *
57118885 CCACAAACGCCACTAAAAAACCTAATCTTTAGCGGCGCTTTCCCCACAAACTCCGCGAAAGACCA
1 CCACAAACGCCACTAAAAAACCTAATCTTTAGCGACGCTTTCACCAAAAACGCCACGAAAGACCA
** *
57118950 TGATCTTTAGGGGCGCTTTTT
66 ACACCTTTAGGGGCGCTTTTT
* * * * * *
57118971 CCACAAACGCCGCTAAAGAACCTTATCTTTAGCGACGCTTTTACCAAAAACGCCACTAAAGGCCA
1 CCACAAACGCCACTAAAAAACCTAATCTTTAGCGACGCTTTCACCAAAAACGCCACGAAAGACCA
* *
57119036 ACACCTTTAGTGGCGTTTTTT
66 ACACCTTTAGGGGCGCTTTTT
57119057 TGAAAAACGA
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
86 70 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (86 bp):
CCACAAACGCCACTAAAAAACCTAATCTTTAGCGACGCTTTCACCAAAAACGCCACGAAAGACCA
ACACCTTTAGGGGCGCTTTTT
Found at i:57119475 original size:21 final size:21
Alignment explanation
Indices: 57119382--57119477 Score: 111
Period size: 21 Copynumber: 4.6 Consensus size: 21
57119372 TTTGACGCTG
*
57119382 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCTCTCGCTGTAGC
* *
57119403 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCTCTCGCTGTAGC
* *
57119424 CTCTACTTCTCTCGCTATAGC
1 CTCTGCTTCTCTCGCTGTAGC
* * **
57119445 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCTCTCGCTGTAGC
57119466 CTCTGCTTCTCT
1 CTCTGCTTCTCT
57119478 TACTGCCGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.06, C:0.42, G:0.15, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGTAGC
Found at i:57119483 original size:21 final size:21
Alignment explanation
Indices: 57119450--57119494 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57119440 ATAGCCTGTA
* *
57119450 CTTCTCTCGCTGCCGCCTCTG
1 CTTCTCTCACTGCCGCATCTG
*
57119471 CTTCTCTTACTGCCGCATCTG
1 CTTCTCTCACTGCCGCATCTG
57119492 CTT
1 CTT
57119495 TAAGCTGCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.04, C:0.42, G:0.16, T:0.38
Consensus pattern (21 bp):
CTTCTCTCACTGCCGCATCTG
Found at i:57119559 original size:66 final size:66
Alignment explanation
Indices: 57119465--57119611 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
57119455 CTCGCTGCCG
* **
57119465 CCTCTGCTTCTCTTACTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
57119528 GAA
64 GAA
* * * * *
57119531 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGTTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
57119596 A
66 A
57119597 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
57119612 ATGTTGCCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:57119633 original size:66 final size:66
Alignment explanation
Indices: 57119506--57119634 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
57119496 AAGCTGCTGC
* ** *
57119506 TGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAG
1 TGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGTAG
57119571 T
66 T
* * *
57119572 TGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCACTTTAAGTTGT
1 TGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGT
57119635 GTAATTTGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 51 0.93
67 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.43
Consensus pattern (66 bp):
TGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGTAG
T
Found at i:57121786 original size:13 final size:15
Alignment explanation
Indices: 57121768--57121807 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 15
57121758 ATATAAGTTC
57121768 ATGTAAGTTATG-A-
1 ATGTAAGTTATGTAT
57121781 ATGTAAGTTATGTATT
1 ATGTAAGTTATGTA-T
57121797 ATGTAAGTTAT
1 ATGTAAGTTAT
57121808 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (15 bp):
ATGTAAGTTATGTAT
Found at i:57121802 original size:16 final size:16
Alignment explanation
Indices: 57121768--57121844 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
57121758 ATATAAGTTC
57121768 ATGTAAGTTATG-A--
1 ATGTAAGTTATGTATT
57121781 ATGTAAGTTATGTATT
1 ATGTAAGTTATGTATT
*
57121797 ATGTAAGTTATTTAAATT
1 ATGTAAGTTATGT--ATT
* *
57121815 ATTTAAGTTGTGTATT
1 ATGTAAGTTATGTATT
* *
57121831 ATATAAGTCATGTA
1 ATGTAAGTTATGTA
57121845 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
13 12 0.23
14 1 0.02
16 26 0.50
18 13 0.25
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (16 bp):
ATGTAAGTTATGTATT
Found at i:57123315 original size:15 final size:15
Alignment explanation
Indices: 57123295--57123328 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
57123285 CATCAATTGC
*
57123295 AAGACAGCTAGAAAA
1 AAGACAACTAGAAAA
57123310 AAGACAACTAGAAAA
1 AAGACAACTAGAAAA
57123325 AAGA
1 AAGA
57123329 GGTATATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06
Consensus pattern (15 bp):
AAGACAACTAGAAAA
Found at i:57123565 original size:11 final size:11
Alignment explanation
Indices: 57123551--57123587 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
57123541 TTGATACTAC
57123551 ATTATAATGAA
1 ATTATAATGAA
57123562 ATTATAATGAA
1 ATTATAATGAA
*
57123573 ATTATAATCAA
1 ATTATAATGAA
57123584 ATTA
1 ATTA
57123588 GAAAAGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (11 bp):
ATTATAATGAA
Found at i:57124804 original size:27 final size:27
Alignment explanation
Indices: 57124772--57124823 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
57124762 TCTTACTTTT
* *
57124772 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
57124799 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
57124824 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:57124914 original size:8 final size:10
Alignment explanation
Indices: 57124891--57124927 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
57124881 TAATAACTAT
57124891 ATATATATCC
1 ATATATATCC
*
57124901 ATATATATTC
1 ATATATATCC
57124911 ATATATATCC
1 ATATATATCC
57124921 ATATATA
1 ATATATA
57124928 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:57126795 original size:15 final size:14
Alignment explanation
Indices: 57126775--57126842 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
57126765 ATGACCGTTG
57126775 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
57126789 AAAACCCTAAACCTC
1 -AAACCCTAAATCTC
*
57126804 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
*
57126817 -AACCTTAAATCTC
1 AAACCCTAAATCTC
*
57126830 AAACCTTAAATCT
1 AAACCCTAAATCT
57126843 ATACCCCGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
11 8 0.18
12 1 0.02
14 13 0.30
15 22 0.50
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:57127451 original size:41 final size:43
Alignment explanation
Indices: 57127384--57127644 Score: 258
Period size: 41 Copynumber: 6.3 Consensus size: 43
57127374 GCTTACCTAT
*
57127384 AAAACGCCGCTAAA-AGA-CAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
* * * * *
57127425 AAAACGCCACTAAAGATACTA-A-CATTAGCGGCGCTTAGAAA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
* *
57127466 AAAACGCCGCTAAAG--GCCAGAGAATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
* * * *
57127507 AAAACGCCACTAAAGATA-C-GAGCATTAGCGGCGCTTAGAGA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
*
57127548 AAAACGCCGCTAAAG--GCCAGAGCATTAGTGGCGCTCAGATA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
* * ** * *
57127589 AAAACGCCGCTAAAGAT--CGGACCATTAGCAGCGCTAAAATA
1 AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
*
57127630 AAAATGCCGCTAAAG
1 AAAACGCCGCTAAAG
57127645 GTTTAAAAAT
Statistics
Matches: 179, Mismatches: 31, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 170 0.95
42 4 0.02
43 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (43 bp):
AAAACGCCGCTAAAGATACCAGAGCATTAGTGGCGCTCAGATA
Found at i:57127499 original size:82 final size:82
Alignment explanation
Indices: 57127384--57127645 Score: 393
Period size: 82 Copynumber: 3.2 Consensus size: 82
57127374 GCTTACCTAT
* * *
57127384 AAAACGCCGCTAAAAGACAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACTAACA
1 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACGAACA
57127449 TTAGCGGCGCTTAGAAA
66 TTAGCGGCGCTTAGAAA
* *
57127466 AAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACGAGCA
1 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACGAACA
*
57127531 TTAGCGGCGCTTAGAGA
66 TTAGCGGCGCTTAGAAA
* *
57127548 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGAT-CGGACC
1 AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATAC-GAAC
* *
57127612 ATTAGCAGCGC-TAAAATA
65 ATTAGCGGCGCTTAGAA-A
*
57127630 AAAATGCCGCTAAAGG
1 AAAACGCCGCTAAAGG
57127646 TTTAAAAATC
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
81 4 0.02
82 161 0.98
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (82 bp):
AAAACGCCGCTAAAGGCCAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACGAACA
TTAGCGGCGCTTAGAAA
Found at i:57127616 original size:123 final size:123
Alignment explanation
Indices: 57127384--57127644 Score: 285
Period size: 123 Copynumber: 2.1 Consensus size: 123
57127374 GCTTACCTAT
* * *
57127384 AAAACGCCGCTAAA-AGACAGAGCATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATACTAAC
1 AAAACGCCGCTAAAGAGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGA-ACCAAC
* * * ** * *
57127448 ATTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGGCCAGAGAATTAGTGGCGCTCAGATA
65 ATTAGCGGCGCTCAGAAAAAAACGCCGCTAAAGACCAGACAATTAGCAGCGCTAAAATA
* * * * *
57127507 AAAACGCCACTAAAGATAC-GAGCATTAGCGGCGCTTAGAGAAAAACGCCGCTAAAG-GCCAGAG
1 AAAACGCCGCTAAAGAGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGAACCA-A-
* * * * *
57127570 CATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGATCGGACCATTAGCAGCGCTAAAATA
64 CATTAGCGGCGCTCAGAAAAAAACGCCGCTAAAGACCAGACAATTAGCAGCGCTAAAATA
*
57127630 AAAATGCCGCTAAAG
1 AAAACGCCGCTAAAG
57127645 GTTTAAAAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
121 2 0.02
122 1 0.01
123 107 0.95
124 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (123 bp):
AAAACGCCGCTAAAGAGACAGAGCATTAGCGGCGCTCAGAGAAAAACGCCACTAAAGAACCAACA
TTAGCGGCGCTCAGAAAAAAACGCCGCTAAAGACCAGACAATTAGCAGCGCTAAAATA
Found at i:57128036 original size:18 final size:19
Alignment explanation
Indices: 57128015--57128051 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
57128005 TTTAGTTGGA
57128015 TTTGAA-TTTTTTCAAGAG
1 TTTGAATTTTTTTCAAGAG
57128033 TTTGAATTTTTTTCAAGAG
1 TTTGAATTTTTTTCAAGAG
57128052 AAAAAAGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (19 bp):
TTTGAATTTTTTTCAAGAG
Found at i:57133128 original size:15 final size:16
Alignment explanation
Indices: 57133108--57133140 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
57133098 TTCTATTTTG
*
57133108 ATAAAAAT-TTAAAAT
1 ATAAAAATGGTAAAAT
57133123 ATAAAAATGGTAAAAT
1 ATAAAAATGGTAAAAT
57133139 AT
1 AT
57133141 CGTGTTATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATAAAAATGGTAAAAT
Found at i:57143003 original size:113 final size:114
Alignment explanation
Indices: 57142867--57143355 Score: 603
Period size: 113 Copynumber: 4.3 Consensus size: 114
57142857 AACAACGCTA
* * * *
57142867 TTTTCTGAGCTTTCGGTGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGCTTTCG
1 TTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAG
* *
57142932 CGGCG-TTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACACCG
66 CAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACACCG
* * *
57142980 TTTTTTGAGCTTTAGGGGATTTAGTGGTGTTTTTAAGTAAA-CGCCGCTAATGCTCAGGGCTTTA
1 TTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAG-AAAGCGCCGCTAATGCTCAGGGCTTTA
* * * * *
57143044 GCAGCGTTTTTGGGAAAGCGCTGA-AAAAATACCTAAGCCCAACGACGCCG
65 GCAGCGTTTTTGAGAAAGCGC-CACAAAAAAACCAAAGCCCAACGACACCG
* * * * *
57143094 TTTTCTGAGCTTTCGGGAATTTAGTTGCGTTTTTAAGTAAGCGCCACTAATGTTCAGGGCTTTAG
1 TTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAG
* *
57143159 CAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCCAATGACGCCG
66 CAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACACCG
** * *
57143208 TTTT-TGAGCTTTCAAGGATTTAGTGGTGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAG
1 TTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAG
* * * *
57143272 CGGCGTTTTTGAGAAAGCGCCGCAACAAAAA-CTAAGCCCAACTACACCG
66 CAGCGTTTTTGAGAAAGCGCCACAA-AAAAACCAAAGCCCAACGACACCG
* * *
57143321 TTTTCTGA-CAATTCGTGGGCTTTAGCGGCGTTTTT
1 TTTTCTGAGC-TTTCG-GGGATTTAGTGGCGTTTTT
57143356 GTTGAAGCGC
Statistics
Matches: 321, Mismatches: 46, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
113 156 0.49
114 149 0.46
115 16 0.05
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (114 bp):
TTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAG
CAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCCCAACGACACCG
Found at i:57143237 original size:227 final size:229
Alignment explanation
Indices: 57142841--57143355 Score: 704
Period size: 227 Copynumber: 2.3 Consensus size: 229
57142831 TAAAGTGCCG
* **
57142841 CAAAATACCTAAACCCAACAACGCTATTTTCTGAGCTTTCGGTGATTTAGCGGCGTTTTTAAGAA
1 CAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGTGATTTAGCGGCGTTTTTAAGAA
* * *
57142906 AGCGCCGCTAATGCTCAAGGCTTTCGCGGCGTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCA
66 AGCGCCACTAATGCTCAAGGCTTTAGCAGCGTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCA
*
57142971 ACGACACCGTTTTTTGAGCTTTAGGGGATTTAGTGGTGTTTTTAAGTAAACGCCGCTAATGCTCA
131 ACGACACCGTTTTTTGAGCTTTAGAGGATTTAGTGGTGTTTTTAAGTAAACGCCGCTAATGCTCA
* *
57143036 GGGCTTTAGCAGCGTTTTTGGGAAAGCGCTG-AA
196 GGGCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
* ** *
57143069 -AAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGG-GAATTTAGTTGCGTTTTTAAGT
1 CAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGTG-ATTTAGCGGCGTTTTTAAGA
* * *
57143132 AAGCGCCACTAATGTTCAGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCACAAAAAAACCAAAGCC
65 AAGCGCCACTAATGCTCAAGGCTTTAGCAGCG-TTTCGAGAAAGCGCCACAAAAAAACCAAAGCC
* * *
57143197 CAATGACGCCG-TTTTTGAGCTTTCA-AGGATTTAGTGGTGTTTTTAAGTAAGCGCCGCTAATGC
129 CAACGACACCGTTTTTTGAGCTTT-AGAGGATTTAGTGGTGTTTTTAAGTAAACGCCGCTAATGC
*
57143260 TCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
193 TCAGGGCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
* * * * *
57143297 CAAAA-A-CTAAGCCCAACTACACCGTTTTCTGA-CAATTCGTGGGCTTTAGCGGCGTTTTT
1 CAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGC-TTTCG-GTGATTTAGCGGCGTTTTT
57143356 GTTGAAGCGC
Statistics
Matches: 253, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
226 2 0.01
227 188 0.74
228 58 0.23
229 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (229 bp):
CAAAATACCTAAGCCCAACAACGCCGTTTTCTGAGCTTTCGGTGATTTAGCGGCGTTTTTAAGAA
AGCGCCACTAATGCTCAAGGCTTTAGCAGCGTTTCGAGAAAGCGCCACAAAAAAACCAAAGCCCA
ACGACACCGTTTTTTGAGCTTTAGAGGATTTAGTGGTGTTTTTAAGTAAACGCCGCTAATGCTCA
GGGCTTTAGCAGCGTTTTTGAGAAAGCGCCGCAA
Found at i:57143428 original size:73 final size:75
Alignment explanation
Indices: 57143262--57143442 Score: 223
Period size: 74 Copynumber: 2.5 Consensus size: 75
57143252 GCTAATGCTC
*
57143262 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAACAAAAACTAAGCCCAACTACACCGTTTTCT
1 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAACAAAAACTAAGCCCAACGACACCGTTTTCT
57143327 GACAATTCGT
66 GACAATTCGT
* * **
57143337 -GGGCTTTAGCGGCGTTTTTGTTG-AAGCGCCGCAA-AAAAACCTAAGCCCAACGGCGTCGTTTT
1 AGGGCTTTAGCGGCGTTTTTG-AGAAAGCGCCGCAACAAAAA-CTAAGCCCAACGACACCGTTTT
*
57143399 CT-A-AACTT-TT
64 CTGACAA-TTCGT
*
57143409 AGGGCTTTAGCGGCGTTTTT-AAAAAGCGCCGCAA
1 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAA
57143443 AAGCCTTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
72 14 0.15
73 27 0.29
74 51 0.55
75 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (75 bp):
AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAACAAAAACTAAGCCCAACGACACCGTTTTCT
GACAATTCGT
Found at i:57143795 original size:14 final size:15
Alignment explanation
Indices: 57143769--57143801 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
57143759 AACGTTTATA
57143769 GATTATGGAATTAGG
1 GATTATGGAATTAGG
57143784 GATTAT-GAATTAGG
1 GATTATGGAATTAGG
57143798 GATT
1 GATT
57143802 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:57144460 original size:21 final size:20
Alignment explanation
Indices: 57144436--57144486 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
57144426 GGTTTTGACT
* *
57144436 TTTAGGGTTTGGGATTTGGGG
1 TTTAAGGTTT-GGATTTAGGG
*
57144457 TTTAAGGTTTGGTTTTAGGG
1 TTTAAGGTTTGGATTTAGGG
57144477 TTTAAGGTTT
1 TTTAAGGTTT
57144487 AGAATTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.14, C:0.00, G:0.37, T:0.49
Consensus pattern (20 bp):
TTTAAGGTTTGGATTTAGGG
Found at i:57145559 original size:147 final size:146
Alignment explanation
Indices: 57145366--57145817 Score: 365
Period size: 147 Copynumber: 3.1 Consensus size: 146
57145356 TACGTTGCTA
* * * ** * * *
57145366 TTAGTGACGCTTTACATCAAACGCCGCAAAATTGTAATTATGTTTATTGAAATGTTATCGTTTTG
1 TTAGTGGCGCTTTAC-TCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGCTACCGTTTTG
** * *
57145431 TCTATGATATTAGTGGCGTTTTTAT-GAAAACGCCACAAGCTTGAGTTAACTGTTGGGGAAACGA
65 TAAATGATATTAGTGGCGTTTTT-TCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGA
*
57145495 CTTCG-TTTGAGCTTATAG
129 CTGCGTTTTGA-CTTATAG
* * * *
57145513 TTGGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTCTAACATTTATAGAAACGCTGCCGTTTTG
1 TTAGTGGCGCTTTACTC-AAACGCCGCAAAATTGTTATAACATTTATTGAAACGCTACCGTTTTG
* * ** * * * *
57145578 TAAATGTTATTAGTGGCGTTTTTTCGAAAATGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGAC
65 TAAATGATATTAGTGGCGTTTTTTCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGAC
*
57145643 TGCGTTTTGATTTATAG
130 TGCGTTTTGACTTATAG
* *** * * ** ***
57145660 TTAGTGGTGCTTCGGTTCAAACGCCGCAAAAATGTTTTAACATTTATTGGTACGAGGCCGTTTTG
1 TTAGTGGCGCTT-TACTCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGCTACCGTTTTG
** * * * * * ** *
57145725 CTGTAT--TATTAGTGGCATTTATTCAAAAACGCCAC-AGGTGTGAGCTATTTGTTGATGAAACG
65 -TAAATGATATTAGTGGCGTTTTTTCGAAAACGCCACAAGCT-TGAGGTAACTGTTGAGGAAACG
* *
57145787 GCTTCGTTTTGACTTATAG
128 ACTGCGTTTTGACTTATAG
57145806 TTAGTGGCGCTT
1 TTAGTGGCGCTT
57145818 ATTTATAAAC
Statistics
Matches: 245, Mismatches: 54, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
145 2 0.01
146 73 0.30
147 160 0.65
148 10 0.04
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (146 bp):
TTAGTGGCGCTTTACTCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGCTACCGTTTTGT
AAATGATATTAGTGGCGTTTTTTCGAAAACGCCACAAGCTTGAGGTAACTGTTGAGGAAACGACT
GCGTTTTGACTTATAG
Found at i:57145805 original size:146 final size:146
Alignment explanation
Indices: 57145457--57145835 Score: 363
Period size: 146 Copynumber: 2.6 Consensus size: 146
57145447 CGTTTTTATG
* * * ** *
57145457 AAAACGCCACAAGCT-TGAGTTAACTGTTGGGGAAACGACTTCG-TTTGAGCTTATAGTTGGTGG
1 AAAACGCCAC-AGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGA-CTTATAGTTAGTGG
* * ** *
57145520 CGCTTTACTCAAAACGCCGCAAAATTGTTCTAACATTTATAGAAACGCTGCCGTTTTGTAAATGT
64 CGCTTGACTCAAAACGCCGCAAAAATGTTCTAACATTTATAGAAACGAGGCCGTTTTGT-AATAT
* * *
57145585 TATTAGTGGCGTTTTTTCG
128 TATTAGTGGCATTTATTCA
* * * * * * * *
57145604 AAAATGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGACTGCGTTTTGATTTATAGTTAGTGGTG
1 AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCG
** * * ** *
57145669 CTTCGGTTC-AAACGCCGCAAAAATGTTTTAACATTTATTGGTACGAGGCCGTTTTGCT-GTATT
66 CTT-GACTCAAAACGCCGCAAAAATGTTCTAACATTTATAGAAACGAGGCCGTTTTG-TAATATT
57145732 ATTAGTGGCATTTATTCA
129 ATTAGTGGCATTTATTCA
** *
57145750 AAAACGCCACAGGTGTGAGCTATTTGTTGATGAAACGGCTTCGTTTTGACTTATAGTTAGTGGCG
1 AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCG
* *
57145815 CTT-ATTTATAAACGCCGCAAA
66 CTTGACTCA-AAACGCCGCAAA
57145836 TGGTTAATTT
Statistics
Matches: 186, Mismatches: 40, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
144 2 0.01
146 89 0.48
147 87 0.47
148 8 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (146 bp):
AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCG
CTTGACTCAAAACGCCGCAAAAATGTTCTAACATTTATAGAAACGAGGCCGTTTTGTAATATTAT
TAGTGGCATTTATTCA
Found at i:57147683 original size:7 final size:7
Alignment explanation
Indices: 57147671--57147696 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57147661 CAAGTTATTG
57147671 ATTTTCA
1 ATTTTCA
57147678 ATTTTCA
1 ATTTTCA
57147685 ATTTTCA
1 ATTTTCA
57147692 ATTTT
1 ATTTT
57147697 ATGTCAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCA
Found at i:57147962 original size:20 final size:19
Alignment explanation
Indices: 57147920--57147972 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
57147910 ACTTATTAAT
*
57147920 ATATATATTTTAA-AGTTA
1 ATATATATTTTAATATTTA
57147938 ATATATATTTTCAATATTTA
1 ATATATATTTT-AATATTTA
*
57147958 TTATAT-TTTTAATAT
1 ATATATATTTTAATAT
57147973 ATTTTTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 6 0.19
20 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATATATTTTAATATTTA
Found at i:57148139 original size:13 final size:13
Alignment explanation
Indices: 57148123--57148287 Score: 127
Period size: 13 Copynumber: 12.5 Consensus size: 13
57148113 TTACTAAAAT
*
57148123 TTACTTTAATATA
1 TTACTTAAATATA
*
57148136 TTACTTGAATATA
1 TTACTTAAATATA
*
57148149 TTACTTAAATAAA
1 TTACTTAAATATA
*
57148162 TTACTTAAATACA
1 TTACTTAAATATA
*
57148175 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
57148189 TTGGTTAAATTTA
1 TTACTTAAATATA
* *
57148202 TTACGTAAATATG
1 TTACTTAAATATA
*
57148215 TTACTTAAATACA
1 TTACTTAAATATA
*
57148228 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
57148242 TTGTTTAAATTTA
1 TTACTTAAATATA
*
57148255 TTACTTAAATATG
1 TTACTTAAATATA
*
57148268 TTACTTAAATACA
1 TTACTTAAATATA
57148281 TTACTTA
1 TTACTTA
57148288 CTAAAATTTA
Statistics
Matches: 116, Mismatches: 30, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
12 6 0.05
13 94 0.81
14 10 0.09
15 6 0.05
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:57148204 original size:53 final size:53
Alignment explanation
Indices: 57148147--57148296 Score: 264
Period size: 53 Copynumber: 2.8 Consensus size: 53
57148137 TACTTGAATA
**
57148147 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
* *
57148200 TATTACGTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
57148253 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
57148297 AAGTATATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:57148512 original size:16 final size:16
Alignment explanation
Indices: 57148491--57148540 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
57148481 CTTATATGTA
57148491 AACTTACATAATACAT
1 AACTTACATAATACAT
*
57148507 AACTTACAT-GT---T
1 AACTTACATAATACAT
57148519 AACTTACATAATACAT
1 AACTTACATAATACAT
57148535 AACTTA
1 AACTTA
57148541 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:57148517 original size:28 final size:28
Alignment explanation
Indices: 57148456--57148540 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 28
57148446 AATATTTATA
*
57148456 TAAACTTACATAACTATCACATAAGCTTATATG
1 TAAACTTACAT-A--AT-ACATAA-CTTACATG
57148489 TAAACTTACATAATACATAACTTACATG
1 TAAACTTACATAATACATAACTTACATG
*
57148517 TTAACTTACATAATACATAACTTA
1 TAAACTTACATAATACATAACTTA
57148541 TAAATTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
28 30 0.60
29 6 0.12
30 2 0.04
32 1 0.02
33 11 0.22
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAACTTACATAATACATAACTTACATG
Found at i:57148579 original size:67 final size:67
Alignment explanation
Indices: 57148489--57148725 Score: 260
Period size: 67 Copynumber: 3.6 Consensus size: 67
57148479 AGCTTATATG
*
57148489 TAAACTTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAAATTTTTTTTA
1 TAAACTTACATAATACATAACTTACATATTAACTTACATAATACATAACTTATAAATTTTTTTTA
57148554 TA
66 TA
* * * *
57148556 TAAACTTACATAATGCATTACTTACATATT-A---AC-T--TACATAACTTATTAA---TATTTA
1 TAAACTTACATAATACATAACTTACATATTAACTTACATAATACATAACTTATAAATTTTTTTTA
57148611 TA
66 TA
* * *
57148613 TAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATAAATTTT
1 TAAACTTACAT-A--AT-ACAT-AACTTACATATTAACTTACATAATACATAACTTATAAATTTT
57148678 TTTTATA
61 TTTTATA
* * *
57148685 TAAACTTACATAACACATTACTTACATATGAACTTACATAA
1 TAAACTTACATAATACATAACTTACATATTAACTTACATAA
57148726 GTTATCTACA
Statistics
Matches: 138, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
57 18 0.13
58 1 0.01
60 16 0.12
61 3 0.02
62 9 0.07
63 3 0.02
66 3 0.02
67 47 0.34
68 4 0.03
69 15 0.11
71 1 0.01
72 18 0.13
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.40
Consensus pattern (67 bp):
TAAACTTACATAATACATAACTTACATATTAACTTACATAATACATAACTTATAAATTTTTTTTA
TA
Found at i:57148603 original size:28 final size:30
Alignment explanation
Indices: 57148553--57148627 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
57148543 AATTTTTTTT
*
57148553 ATATAAACTTACATAA-TGCATTACT-TAC
1 ATATAAACTTACATAACTGCATTAATATAC
* * **
57148581 ATATTAACTTACATAACT-TATTAATATTT
1 ATATAAACTTACATAACTGCATTAATATAC
57148610 ATATAAACTTACATAACT
1 ATATAAACTTACATAACT
57148628 ATCACATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 20 0.51
29 19 0.49
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (30 bp):
ATATAAACTTACATAACTGCATTAATATAC
Found at i:57148657 original size:129 final size:124
Alignment explanation
Indices: 57148489--57148730 Score: 385
Period size: 129 Copynumber: 1.9 Consensus size: 124
57148479 AGCTTATATG
*
57148489 TAAACTTACATAATACATAACTTACATGTTAACTTACATAATACATAACTTATAAATTTTTTTTA
1 TAAACTTACATAATACATAACTTACATGTAAACTTACATAATACATAACTTATAAATTTTTTTTA
** *
57148554 TATAAACTTACATAATGCATTACTTACATATTAACTTACATAACTTATTAATATTTATA
66 TATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTATTAATATTTATA
*
57148613 TAAACTTACATAACTATCACATAAACTTATATGTAAACTTACATAATACATAACTTATAAATTTT
1 TAAACTTACAT-A--AT-ACAT-AACTTACATGTAAACTTACATAATACATAACTTATAAATTTT
*
57148678 TTTTATATAAACTTACATAACACATTACTTACATATGAACTTACATAAGTTAT
61 TTTTATATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTAT
57148731 CTACAAGCTT
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
124 11 0.10
125 1 0.01
127 2 0.02
128 4 0.04
129 89 0.83
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (124 bp):
TAAACTTACATAATACATAACTTACATGTAAACTTACATAATACATAACTTATAAATTTTTTTTA
TATAAACTTACATAACACATTACTTACATATGAACTTACATAACTTATTAATATTTATA
Found at i:57148781 original size:129 final size:129
Alignment explanation
Indices: 57148519--57148793 Score: 373
Period size: 129 Copynumber: 2.1 Consensus size: 129
57148509 CTTACATGTT
**
57148519 AACTTACATAATACATAACTTATAAATTTTTTTTATATAAACTTACATAATGCATTACTTACATA
1 AACTTACATAATACATAACTTATAAATTTTTTTTATATAAACTTACATAACACATTACTTACATA
* * * *
57148584 TTAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTTATATGTA
66 TGAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAA
57148648 AACTTACATAATACATAACTTATAAATTTTTTTTATATAAACTTACATAACACATTACTTACATA
1 AACTTACATAATACATAACTTATAAATTTTTTTTATATAAACTTACATAACACATTACTTACATA
* * *
57148713 TGAACTTACATAAGTTATCTACA-AGCTTATATATAAACTTGCATAACT-T-ACGT-AA-TAACA
66 TGAACTTACATAACTTAT-TA-ATA--TT-TATATAAACTTACATAACTATCACATAAACTAACA
57148773 T-AA
126 TGAA
57148776 CAACTTACATAATACATA
1 -AACTTACATAATACATA
57148794 GCATACATAA
Statistics
Matches: 131, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
128 1 0.01
129 100 0.76
130 5 0.04
131 4 0.03
132 3 0.02
133 18 0.14
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (129 bp):
AACTTACATAATACATAACTTATAAATTTTTTTTATATAAACTTACATAACACATTACTTACATA
TGAACTTACATAACTTATTAATATTTATATAAACTTACATAACTATCACATAAACTAACATGAA
Found at i:57148809 original size:9 final size:9
Alignment explanation
Indices: 57148777--57149217 Score: 329
Period size: 9 Copynumber: 50.8 Consensus size: 9
57148767 ATAACATAAC
57148777 AACTTACAT
1 AACTTACAT
57148786 AA--TACAT
1 AACTTACAT
* *
57148793 AGCATACAT
1 AACTTACAT
57148802 AACTTACAT
1 AACTTACAT
57148811 AACTTACAT
1 AACTTACAT
*
57148820 AA--TACAA
1 AACTTACAT
57148827 AACTTACAT
1 AACTTACAT
*
57148836 AACTTAAAT
1 AACTTACAT
* *
57148845 ATCTTACAC
1 AACTTACAT
57148854 AACTTACAT
1 AACTTACAT
*
57148863 AACCTACAT
1 AACTTACAT
57148872 AA--TACATTT
1 AACTTACA--T
57148881 AACTTACAT
1 AACTTACAT
57148890 AACTTACAT
1 AACTTACAT
*
57148899 AA--TACAA
1 AACTTACAT
57148906 AACTTACAT
1 AACTTACAT
*
57148915 AACTTAAAT
1 AACTTACAT
* *
57148924 ATCTTACAC
1 AACTTACAT
57148933 AACTTACAT
1 AACTTACAT
*
57148942 AACCTACAT
1 AACTTACAT
57148951 AA--TACATTT
1 AACTTACA--T
57148960 AACTTACAT
1 AACTTACAT
57148969 AACTTACAT
1 AACTTACAT
* *
57148978 -A-GTACAA
1 AACTTACAT
*
57148985 AATTTACAT
1 AACTTACAT
*
57148994 AACTTAAAT
1 AACTTACAT
* * *
57149003 ATCTCACAC
1 AACTTACAT
57149012 AACTTACAT
1 AACTTACAT
*
57149021 AACCTACAT
1 AACTTACAT
57149030 AA--TACATTT
1 AACTTACA--T
57149039 AACTTACAT
1 AACTTACAT
57149048 AACTTACAT
1 AACTTACAT
57149057 AACTTACAT
1 AACTTACAT
57149066 AA--TACAT
1 AACTTACAT
57149073 AACTTACAT
1 AACTTACAT
*
57149082 AATACATA-AT
1 -A-ACTTACAT
57149092 AACTTAC--
1 AACTTACAT
*
57149099 AACTTAAAT
1 AACTTACAT
*
57149108 AACATACAT
1 AACTTACAT
* **
57149117 TACTTTGAT
1 AACTTACAT
*
57149126 AACTTACCT
1 AACTTACAT
57149135 AACTTACAT
1 AACTTACAT
*
57149144 AA--TACAC
1 AACTTACAT
57149151 AACTTACAT
1 AACTTACAT
* *
57149160 AGCTTACTT
1 AACTTACAT
57149169 AA--TACAT
1 AACTTACAT
*
57149176 AACTTACGT
1 AACTTACAT
57149185 AACTT--AT
1 AACTTACAT
*
57149192 ACACGTACAT
1 A-ACTTACAT
57149202 AACTTACAT
1 AACTTACAT
*
57149211 AATTTAC
1 AACTTAC
57149218 TTAATACATA
Statistics
Matches: 338, Mismatches: 60, Indels: 68
0.73 0.13 0.15
Matches are distributed among these distances:
7 61 0.18
8 9 0.03
9 246 0.73
10 6 0.02
11 16 0.05
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Done.