Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 139 of 221
Found at i:42723553 original size:41 final size:40
Alignment explanation
Indices: 42723471--42723612 Score: 180
Period size: 40 Copynumber: 3.5 Consensus size: 40
42723461 TTTTATTGTT
* * * *
42723471 ATCCTTTTCGACCTTTTCATTGATAT-CTTTTTCAGACAAC
1 ATCCTTTTCAACCTTTTCATTTATATCCTTTTT-TGATAAC
42723511 ATCCTTTTCAACCTTTTCATTTTATATCCTTTTTTGATAAC
1 ATCCTTTTCAACCTTTTCA-TTTATATCCTTTTTTGATAAC
*
42723552 ATCATTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
1 ATCCTTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
* *
42723592 -GCCATTTTCAACCTGTTCATT
1 ATCC-TTTTCAACCTTTTCATT
42723613 GATTCAGAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
39 1 0.01
40 55 0.60
41 29 0.32
42 6 0.07
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (40 bp):
ATCCTTTTCAACCTTTTCATTTATATCCTTTTTTGATAAC
Found at i:42726681 original size:24 final size:24
Alignment explanation
Indices: 42726648--42726698 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
42726638 TTTAAGGTGT
42726648 ACACGACCTGGGACACGGGCTGTC
1 ACACGACCTGGGACACGGGCTGTC
* *
42726672 ACACGGCCTGGGACATGGGCTGTC
1 ACACGACCTGGGACACGGGCTGTC
42726696 ACA
1 ACA
42726699 TAGCCTGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.31, G:0.33, T:0.14
Consensus pattern (24 bp):
ACACGACCTGGGACACGGGCTGTC
Found at i:42726704 original size:24 final size:24
Alignment explanation
Indices: 42726654--42726706 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
42726644 GTGTACACGA
*
42726654 CCTGGGACACGGGCTGTCACACGG
1 CCTGGGACACGGGCTGTCACACAG
* *
42726678 CCTGGGACATGGGCTGTCACATAG
1 CCTGGGACACGGGCTGTCACACAG
42726702 CCTGG
1 CCTGG
42726707 CCACACGGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.17, C:0.30, G:0.36, T:0.17
Consensus pattern (24 bp):
CCTGGGACACGGGCTGTCACACAG
Found at i:42728886 original size:52 final size:52
Alignment explanation
Indices: 42728824--42728929 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
42728814 CATTGTAAAT
42728824 AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
1 AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
42728876 AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
1 AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
42728928 AA
1 AA
42728930 ATAATGTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.26
Consensus pattern (52 bp):
AAGTATACGTTTCAGATGTAAAACAAAGTATATAAAAAATTACAAAATTACA
Found at i:42731425 original size:25 final size:25
Alignment explanation
Indices: 42731377--42731468 Score: 78
Period size: 25 Copynumber: 3.7 Consensus size: 25
42731367 TCCTATACAT
** * *
42731377 GTATGCTCATACGAGCTCTGAATCA
1 GTATGCTCGCACGAGCTGTAAATCA
*
42731402 GTATGCTCGCTCGAGCTGTAAATCTA
1 GTATGCTCGCACGAGCTGTAAATC-A
* *
42731428 -TATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCGCACGAGCTGTAAATCA
* **
42731452 GTAAGCTCATACGAGCT
1 GTATGCTCGCACGAGCT
42731469 ATGGTGTGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
25 53 0.98
26 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (25 bp):
GTATGCTCGCACGAGCTGTAAATCA
Found at i:42734091 original size:7 final size:7
Alignment explanation
Indices: 42734079--42734140 Score: 63
Period size: 7 Copynumber: 8.9 Consensus size: 7
42734069 CTAAGGATTG
42734079 AAAATTT
1 AAAATTT
42734086 AAAATTT
1 AAAATTT
42734093 AAAA-TT
1 AAAATTT
42734099 AAAATTT
1 AAAATTT
42734106 AAAATTT
1 AAAATTT
* *
42734113 GAAGATTA
1 -AAAATTT
*
42734121 AAAATAT
1 AAAATTT
*
42734128 AAAGTTT
1 AAAATTT
*
42734135 GAAATT
1 AAAATT
42734141 GGGGATTGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 6 0.14
7 33 0.75
8 5 0.11
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (7 bp):
AAAATTT
Found at i:42734102 original size:13 final size:13
Alignment explanation
Indices: 42734079--42734111 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
42734069 CTAAGGATTG
42734079 AAAATTTAAAATTT
1 AAAA-TTAAAATTT
42734093 AAAATTAAAATTT
1 AAAATTAAAATTT
42734106 AAAATT
1 AAAATT
42734112 TGAAGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:42734104 original size:20 final size:21
Alignment explanation
Indices: 42734079--42734138 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
42734069 CTAAGGATTG
42734079 AAAATTTAAAATTT-AAAATT
1 AAAATTTAAAATTTGAAAATT
*
42734099 AAAATTTAAAATTTGAAGATT
1 AAAATTTAAAATTTGAAAATT
* *
42734120 AAAAATATAAAGTTTGAAA
1 -AAAATTTAAAATTTGAAA
42734139 TTGGGGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 14 0.41
21 5 0.15
22 15 0.44
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAATTTAAAATTTGAAAATT
Found at i:42734154 original size:7 final size:7
Alignment explanation
Indices: 42734144--42734177 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
42734134 TGAAATTGGG
42734144 GATTGAA
1 GATTGAA
*
42734151 GATTGAG
1 GATTGAA
42734158 GATTGAA
1 GATTGAA
*
42734165 GATTGAT
1 GATTGAA
42734172 GATTGA
1 GATTGA
42734178 GAATTTAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (7 bp):
GATTGAA
Found at i:42734155 original size:14 final size:14
Alignment explanation
Indices: 42734133--42734177 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
42734123 AATATAAAGT
*
42734133 TTGAA-ATTGGGGA
1 TTGAAGATTGAGGA
42734146 TTGAAGATTGAGGA
1 TTGAAGATTGAGGA
*
42734160 TTGAAGATTGATGA
1 TTGAAGATTGAGGA
42734174 TTGA
1 TTGA
42734178 GAATTTAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 5 0.17
14 24 0.83
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (14 bp):
TTGAAGATTGAGGA
Found at i:42735880 original size:27 final size:28
Alignment explanation
Indices: 42735844--42735896 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
42735834 AGTTAATAAA
42735844 TTCTCTTTGAGTTTTTCTTTTA-AAGAAT
1 TTCTCTTTGAGTTTTT-TTTTAGAAGAAT
42735872 TTCTC-TTGAGTTTTTTTTTAGAAGA
1 TTCTCTTTGAGTTTTTTTTTAGAAGA
42735897 GTTTTAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 5 0.21
27 14 0.58
28 5 0.21
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.57
Consensus pattern (28 bp):
TTCTCTTTGAGTTTTTTTTTAGAAGAAT
Found at i:42736589 original size:19 final size:19
Alignment explanation
Indices: 42736548--42736590 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
42736538 ATATTATGTA
**
42736548 TAATTTTAAGATTTATTTC
1 TAATTTTAAGATTTAAGTC
* *
42736567 TAATTTTAAGTTTTAAGTG
1 TAATTTTAAGATTTAAGTC
42736586 TAATT
1 TAATT
42736591 AATATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (19 bp):
TAATTTTAAGATTTAAGTC
Found at i:42740744 original size:10 final size:10
Alignment explanation
Indices: 42740729--42740764 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
42740719 TGAGTAGTTT
42740729 AATTTTTTTA
1 AATTTTTTTA
42740739 AATTTTTTTTA
1 AA-TTTTTTTA
*
42740750 AATTTTTTTT
1 AATTTTTTTA
42740760 AATTT
1 AATTT
42740765 CTCATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:42740784 original size:10 final size:11
Alignment explanation
Indices: 42740731--42740761 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
42740721 AGTAGTTTAA
42740731 TTTTTTTAAAT
1 TTTTTTTAAAT
42740742 TTTTTTTAAAT
1 TTTTTTTAAAT
42740753 TTTTTTTAA
1 TTTTTTTAA
42740762 TTTCTCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:42744984 original size:40 final size:40
Alignment explanation
Indices: 42744935--42745032 Score: 178
Period size: 40 Copynumber: 2.5 Consensus size: 40
42744925 TTCCGTACAT
*
42744935 CGGCATTAAGCCTGCTAGACGTATAGTCTGAATATTTCAC
1 CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
42744975 CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
1 CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
*
42745015 CGGTATTAAGCCTGCTAG
1 CGGCATTAAGCCTGCTAG
42745033 GCAAAAGCCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (40 bp):
CGGCATTAAGCCTGCTAGACGTATAGTCTAAATATTTCAC
Found at i:42747194 original size:24 final size:23
Alignment explanation
Indices: 42747159--42747218 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
42747149 CTTTTAAAGT
*
42747159 ACCCTAATCCTAAAAAAACCAAAA
1 ACCCTAACCCTAAAAAAA-CAAAA
* *
42747183 ACCCTAACCCTACAAAAATAAAA
1 ACCCTAACCCTAAAAAAACAAAA
*
42747206 AGCTCTAACCCTA
1 A-CCCTAACCCTA
42747219 GAGAGAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.16
24 26 0.84
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (23 bp):
ACCCTAACCCTAAAAAAACAAAA
Found at i:42757591 original size:16 final size:16
Alignment explanation
Indices: 42757557--42757592 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42757547 TTTTACATAA
**
42757557 ATATAAATATTTGTTT
1 ATATAAATATTTGCAT
42757573 ATATAAATATTTGCAT
1 ATATAAATATTTGCAT
42757589 ATAT
1 ATAT
42757593 TAATTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
ATATAAATATTTGCAT
Found at i:42760979 original size:30 final size:30
Alignment explanation
Indices: 42760943--42761002 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
42760933 ACTTAATAAG
42760943 CAAATGCCTCTAAAACAATAACAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
* *
42760973 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAACAATAACAAAATTAA
42761003 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (30 bp):
CAAATGCCTCTAAAACAATAACAAAATTAA
Found at i:42762197 original size:22 final size:21
Alignment explanation
Indices: 42762149--42762198 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
42762139 AAAAATTATG
*
42762149 AAAAAAATTAAAATTTTAAAA
1 AAAAAAATAAAAATTTTAAAA
**
42762170 ATAAAAAATAAAAATATTTTTAA
1 A-AAAAAATAAAAAT-TTTAAAA
42762193 AAAAAA
1 AAAAAA
42762199 TCTAAACTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAATAAAAATTTTAAAA
Found at i:42762675 original size:23 final size:23
Alignment explanation
Indices: 42762639--42762706 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
42762629 CCACAATAAT
42762639 AATCGCA-CAGAAGTGCTAGTATA-
1 AATCGCACCA-AAGTGCTAGTA-AC
* *
42762662 AATCGCACCAAAGT-ATCAATAAC
1 AATCGCACCAAAGTGCT-AGTAAC
*
42762685 AATCGCACCAAAGTGCCAGTAA
1 AATCGCACCAAAGTGCTAGTAA
42762707 GTTCCCACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (23 bp):
AATCGCACCAAAGTGCTAGTAAC
Found at i:42766816 original size:29 final size:30
Alignment explanation
Indices: 42766774--42766832 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42766764 ATTCTACTTG
42766774 GGAGGGTAAGCCTT-AACTTTTAACCCATA
1 GGAGGGTAAGCCTTGAACTTTTAACCCATA
42766803 GGAGGGTAAGCCTTGAACTTTTAACCCATA
1 GGAGGGTAAGCCTTGAACTTTTAACCCATA
42766833 CATTGTTGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (30 bp):
GGAGGGTAAGCCTTGAACTTTTAACCCATA
Found at i:42767710 original size:12 final size:12
Alignment explanation
Indices: 42767695--42767794 Score: 54
Period size: 12 Copynumber: 8.6 Consensus size: 12
42767685 TTCATATAAG
42767695 AATAATTATATT
1 AATAATTATATT
*
42767707 AATAATTTTATT
1 AATAATTATATT
*
42767719 AAATTATATT-TAAT
1 -AA-TA-ATTATATT
*
42767733 AATAATTATGTT
1 AATAATTATATT
42767745 AA-AA-TATGATT
1 AATAATTAT-ATT
42767756 -A-AATTAT-TT
1 AATAATTATATT
* *
42767765 ATTATTTATATT
1 AATAATTATATT
42767777 AATAATCT-TATT
1 AATAAT-TATATT
42767789 AA-AATT
1 AATAATT
42767795 TAATAAAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
9 2 0.03
10 7 0.10
11 18 0.26
12 29 0.42
13 5 0.07
14 5 0.07
15 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (12 bp):
AATAATTATATT
Found at i:42767722 original size:37 final size:37
Alignment explanation
Indices: 42767665--42767791 Score: 106
Period size: 37 Copynumber: 3.6 Consensus size: 37
42767655 TATATTATTA
* *
42767665 TATATT-ATGATTTTAGTAAATTCATA-TAAGAATAAT
1 TATATTAATAATTTTATTAAATT-ATATTAAGAATAAT
*
42767701 TATATTAATAATTTTATTAAATTATATTTAATAATAAT
1 TATATTAATAATTTTATTAAATTATA-TTAAGAATAAT
* * * * *
42767739 TATGTTAA-AATATGATTAAATTAT-TT---ATTATT
1 TATATTAATAATTTTATTAAATTATATTAAGAATAAT
*
42767771 TATATTAATAATCTTATTAAA
1 TATATTAATAATTTTATTAAA
42767792 ATTTAATAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
32 11 0.14
33 10 0.13
35 2 0.03
36 9 0.12
37 28 0.37
38 16 0.21
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (37 bp):
TATATTAATAATTTTATTAAATTATATTAAGAATAAT
Found at i:42767977 original size:45 final size:44
Alignment explanation
Indices: 42767885--42767977 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
42767875 ATTACAACAT
* *
42767885 CATTCCATTCAACCAAACACAAGAATATTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAATTCTATTC
*
42767929 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAATTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAATTCTATTC
42767974 CATT
1 CATT
42767978 ACAACGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAATTCTATTC
Found at i:42788482 original size:17 final size:18
Alignment explanation
Indices: 42788460--42788495 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42788450 TTTTAATGTC
*
42788460 ATTA-TTTTTCTTTTGTA
1 ATTATTTTTTATTTTGTA
42788477 ATTATTTTTTATTTTGTA
1 ATTATTTTTTATTTTGTA
42788495 A
1 A
42788496 AATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (18 bp):
ATTATTTTTTATTTTGTA
Found at i:42789410 original size:29 final size:30
Alignment explanation
Indices: 42789356--42789412 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42789346 TCCGAGCCTT
*
42789356 GGGGCAGAAATGTAATTATGTAAAAGTTTA
1 GGGGCAGAAATGTAATTATGAAAAAGTTTA
42789386 GGGGCA-AAATTGTAATT-TGAAAAAGTT
1 GGGGCAGAAA-TGTAATTATGAAAAAGTT
42789413 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (30 bp):
GGGGCAGAAATGTAATTATGAAAAAGTTTA
Found at i:42789642 original size:13 final size:13
Alignment explanation
Indices: 42789624--42789655 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
42789614 TTTCCAGCAA
42789624 TTATGAATTTATT
1 TTATGAATTTATT
42789637 TTATGAATTTATT
1 TTATGAATTTATT
*
42789650 TGATGA
1 TTATGA
42789656 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:42789863 original size:50 final size:50
Alignment explanation
Indices: 42789750--42789991 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
42789740 ATTTGGGTAA
* * *
42789750 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
42789806 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42789856 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
42789906 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
42789956 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42789992 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:42789939 original size:100 final size:103
Alignment explanation
Indices: 42789750--42789999 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
42789740 ATTTGGGTAA
42789750 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
42789815 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
42789856 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
42789918 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
42789956 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42790000 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:42795869 original size:159 final size:159
Alignment explanation
Indices: 42795580--42795899 Score: 577
Period size: 159 Copynumber: 2.0 Consensus size: 159
42795570 ATAGGGAGAG
* *
42795580 TTTAAAGAGTTCAACTATGATTAAACTTAATCACTTTAATATTAAATTGATTGTCTCGAGGACCT
1 TTTAAAGAGTTCAACTATGATTAAACCTAATCACTTTAATATGAAATTGATTGTCTCGAGGACCT
* * * *
42795645 GAGGATGGAAGTTGTAATGTGATAGTTGTAATTTGGAAATTGAAATTGAAATTTGAAATAGTGTT
66 AAGGATGGAAGTTGTAATGTGATAGTCGCAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
42795710 TAATTAAAATTTTTGAAAAGGAAAATAAC
131 TAATTAAAATTTTTGAAAAGGAAAATAAC
*
42795739 TTTAAAGAGTTCAACTATGATTAAACCTAATCACTTTAATATGAAATTGATTGTCTCGAGGATCT
1 TTTAAAGAGTTCAACTATGATTAAACCTAATCACTTTAATATGAAATTGATTGTCTCGAGGACCT
42795804 AAGGATGGAAGTTGTAATGTGATAGTCGCAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
66 AAGGATGGAAGTTGTAATGTGATAGTCGCAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
42795869 TAATTAAAATTTTTGAAAAGGAAAATAAC
131 TAATTAAAATTTTTGAAAAGGAAAATAAC
42795898 TT
1 TT
42795900 GAAAACTTAA
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
159 154 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (159 bp):
TTTAAAGAGTTCAACTATGATTAAACCTAATCACTTTAATATGAAATTGATTGTCTCGAGGACCT
AAGGATGGAAGTTGTAATGTGATAGTCGCAATTTGGAAATTGAAATTGAAATTTGAAAGAGTGTT
TAATTAAAATTTTTGAAAAGGAAAATAAC
Found at i:42796862 original size:17 final size:16
Alignment explanation
Indices: 42796827--42796865 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
42796817 AAATAACTTT
*
42796827 AAATAAAATAATTTAA
1 AAATAAAAAAATTTAA
*
42796843 AAATAAACAAAATTTTA
1 AAATAAA-AAAATTTAA
42796860 AAATAA
1 AAATAA
42796866 CATATGTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATAAAAAAATTTAA
Found at i:42798906 original size:44 final size:44
Alignment explanation
Indices: 42798856--42799019 Score: 143
Period size: 43 Copynumber: 3.8 Consensus size: 44
42798846 CGATGCAGGA
* *
42798856 AGGCAAGACCTGCTATCTTCAACCTGCTCCATTACAACCAAGGG
1 AGGCAAGACCTGCTATCTTCGACCTGCTCCACTACAACCAAGGG
* * * * * *** **
42798900 AGGCAAGGCTTG-TATCTTCGATCTACCCCACTATTGCTTAGGG
1 AGGCAAGACCTGCTATCTTCGACCTGCTCCACTACAACCAAGGG
* * * *
42798943 AGGCAAGATCTGCTATCTTTGACCTGCTCCACTGCAACCGAGGG
1 AGGCAAGACCTGCTATCTTCGACCTGCTCCACTACAACCAAGGG
* * *
42798987 AGGCAAG-GCTGGTATCTTCGATCTGCTCCACTA
1 AGGCAAGACCTGCTATCTTCGACCTGCTCCACTA
42799020 TTGCTTAGGG
Statistics
Matches: 89, Mismatches: 30, Indels: 3
0.73 0.25 0.02
Matches are distributed among these distances:
43 51 0.57
44 38 0.43
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.25
Consensus pattern (44 bp):
AGGCAAGACCTGCTATCTTCGACCTGCTCCACTACAACCAAGGG
Found at i:42798960 original size:87 final size:87
Alignment explanation
Indices: 42798856--42799266 Score: 325
Period size: 87 Copynumber: 4.7 Consensus size: 87
42798846 CGATGCAGGA
* * * *
42798856 AGGCAAGACCTGCTATCTTCAACCTGCTCCATTACAACCAAGGGAGGCAAGGCTTGTATCTTCGA
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATCTTCGA
42798921 TCTACCCCACTATTGCTTAGGG
66 TCTACCCCACTATTGCTTAGGG
* * *
42798943 AGGCAAGATCTGCTATCTTTGACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTATCTTCGA
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATCTTCGA
* *
42799008 TCTGCTCCACTATTGCTTAGGG
66 TCTACCCCACTATTGCTTAGGG
* * * * * * ** * *
42799030 AGACAAGATTTGCTATCTTTAACCCGCTCTACTGCAACCGATAGAGGCAAGGCTTTGT-T-TTCA
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGC-TGGTATCTTCG
**** * * *
42799093 ATCTACTTCGTTGTCAATGC--AAGA
65 ATCTAC--CCCACT-ATTGCTTAGGG
* * * * *
42799117 AGGCATGATCTGCTATCTTTAACCTGCTCCACTACAACCGATGGAGGCAAGGCT-TTA-CTTTCA
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATC-TTCG
* * ** * *
42799180 ATCTGCTTCGCTGTCAATGC--AGGA
65 ATCTAC--CCCACT-ATTGCTTAGGG
* * * *
42799204 AGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTGGTATCTTC
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATCTTC
42799267 ACTGATCTGT
Statistics
Matches: 273, Mismatches: 42, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
85 1 0.00
86 9 0.03
87 249 0.91
88 9 0.03
89 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (87 bp):
AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATCTTCGA
TCTACCCCACTATTGCTTAGGG
Found at i:42799030 original size:43 final size:43
Alignment explanation
Indices: 42798896--42799036 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 43
42798886 ATTACAACCA
* * *
42798896 AGGGAGGCAAGGCTTGTATCTTCGATCTACCCCACTATTGCTT
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTCCACTATTGCTT
* * * * **** **
42798939 AGGGAGGCAAGATCTGCTATCTTTGACCTGCTCCACTGCAACCG
1 AGGGAGGCAAG-GCTGGTATCTTCGATCTGCTCCACTATTGCTT
42798983 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTCCACTATTGCTT
1 AGGGAGGCAAGGCTGGTATCTTCGATCTGCTCCACTATTGCTT
*
42799026 AGGGAGACAAG
1 AGGGAGGCAAG
42799037 ATTTGCTATC
Statistics
Matches: 73, Mismatches: 24, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
43 43 0.59
44 30 0.41
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.26
Consensus pattern (43 bp):
AGGGAGGCAAGGCTGGTATCTTCGATCTGCTCCACTATTGCTT
Found at i:42799129 original size:174 final size:174
Alignment explanation
Indices: 42798943--42799257 Score: 431
Period size: 174 Copynumber: 1.8 Consensus size: 174
42798933 TTGCTTAGGG
* * *
42798943 AGGCAAGATCTGCTATCTTTGACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTGGTA-TCTTCG
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCGAGGGAGGCAAGGCT-GTACT-TTCA
* * * * *
42799007 ATCTGC-TC-CACT-ATTGCTTAGGGAGACAAGATTTGCTATCTTTAACCCGCTCTACTGCAACC
64 ATCTGCTTCGCACTCAATGC--AGGAAGACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACC
42799069 GATAGAGGCAAGGCTTTGTTTTCAATCTACTTCGTTGTCAATGCAAGA
127 GATAGAGGCAAGGCTTTGTTTTCAATCTACTTCGTTGTCAATGCAAGA
* * *
42799117 AGGCATGATCTGCTATCTTTAACCTGCTCCACTACAACCGATGGAGGCAAGGCTTTACTTTCAAT
1 AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGTACTTTCAAT
** * *
42799182 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATG
66 CTGCTTCGCACTCAATGCAGGAAGACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATA
42799247 GAGGCAAGGCT
131 GAGGCAAGGCT
42799258 GGTATCTTCA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
173 11 0.09
174 105 0.86
175 2 0.02
176 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (174 bp):
AGGCAAGATCTGCTATCTTTAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTGTACTTTCAAT
CTGCTTCGCACTCAATGCAGGAAGACAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATA
GAGGCAAGGCTTTGTTTTCAATCTACTTCGTTGTCAATGCAAGA
Found at i:42801407 original size:29 final size:29
Alignment explanation
Indices: 42801375--42801438 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
42801365 CTTTTTCATA
42801375 TTTTTTA-ATTTGACTTTAATTGATTTCT
1 TTTTTTACATTTGACTTTAATTGATTTCT
* * **
42801403 CTTTTTTACTTTTGACTTTGATTTTTTTCT
1 -TTTTTTACATTTGACTTTAATTGATTTCT
42801433 TTTTTT
1 TTTTTT
42801439 GTTTTGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.14, C:0.09, G:0.06, T:0.70
Consensus pattern (29 bp):
TTTTTTACATTTGACTTTAATTGATTTCT
Found at i:42801433 original size:28 final size:27
Alignment explanation
Indices: 42801366--42801455 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
42801356 CTTTTTTCTC
* * *
42801366 TTTTTCATATTTTTTAATTTGACTTTAA
1 TTTTTC-TCTTTTTTATTTTGACTTTGA
42801394 TTGATTTCTCTTTTTTACTTTTGACTTTGA
1 TT--TTTCTCTTTTTTA-TTTTGACTTTGA
* * *
42801424 TTTTTTTCTTTTTTTGTTTTGATTTTGA
1 TTTTTCTC-TTTTTTATTTTGACTTTGA
42801452 TTTT
1 TTTT
42801456 GATTTTTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
28 22 0.42
29 14 0.27
30 16 0.31
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.70
Consensus pattern (27 bp):
TTTTTCTCTTTTTTATTTTGACTTTGA
Found at i:42806336 original size:16 final size:16
Alignment explanation
Indices: 42806302--42806339 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
42806292 AAATAACTTT
42806302 AAATAAAAAAATTTGA
1 AAATAAAAAAATTTGA
*
42806318 AAATAAAAAAATTTTA
1 AAATAAAAAAATTTGA
42806334 AAATAA
1 AAATAA
42806340 CATATGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAAAAAAATTTGA
Found at i:42807917 original size:23 final size:23
Alignment explanation
Indices: 42807886--42807940 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
42807876 CAGAGATTTC
* *
42807886 TACTATTCATACTAGAAAATATT
1 TACTGTTCACACTAGAAAATATT
* *
42807909 TACTGTTCACGCTAGAGAATATT
1 TACTGTTCACACTAGAAAATATT
42807932 T-CTTGTTCA
1 TAC-TGTTCA
42807941 ATCATGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (23 bp):
TACTGTTCACACTAGAAAATATT
Found at i:42811568 original size:26 final size:26
Alignment explanation
Indices: 42811539--42811615 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
42811529 ATACCAATAT
*
42811539 CGCAGCAAAGCTGTCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
42811565 CGCAGCAAAGCTGCCAGTAATAGTAA
1 CGCAGCAAAGCTGCCAGTAATAGTAA
* * *
42811591 CGTAGCAAAGCTGCTAGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAATAGTA
42811616 TATGTGGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAATAGTAA
Found at i:42811786 original size:27 final size:27
Alignment explanation
Indices: 42811756--42811814 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
42811746 ATCTCCTAGA
42811756 GGTATAACAATCATTTTACCCTATGGG
1 GGTATAACAATCATTTTACCCTATGGG
** **
42811783 GGTATTCCGGTCATTTTACCCTATGGG
1 GGTATAACAATCATTTTACCCTATGGG
*
42811810 AGTAT
1 GGTAT
42811815 TTCGGTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (27 bp):
GGTATAACAATCATTTTACCCTATGGG
Found at i:42811815 original size:27 final size:27
Alignment explanation
Indices: 42811766--42811825 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
42811756 GGTATAACAA
*
42811766 TCATTTTACCCTATGGGGGTATTCCGG
1 TCATTTTACCCTATGGGAGTATTCCGG
*
42811793 TCATTTTACCCTATGGGAGTATTTCGG
1 TCATTTTACCCTATGGGAGTATTCCGG
*
42811820 TTATTT
1 TCATTT
42811826 ATTGATCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGAGTATTCCGG
Found at i:42814277 original size:20 final size:20
Alignment explanation
Indices: 42814252--42814289 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42814242 AAAGGTTAAC
42814252 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
42814272 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
42814290 AATAAAACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:42816443 original size:23 final size:24
Alignment explanation
Indices: 42816415--42816460 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
42816405 TATATATGTG
42816415 AAAATATTC-ATTTAAAAAAAAGA
1 AAAATATTCGATTTAAAAAAAAGA
*
42816438 AAAATATTCGTTTTTAAAAAAAA
1 AAAATATTCG-ATTTAAAAAAAA
42816461 TATATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAATATTCGATTTAAAAAAAAGA
Found at i:42817078 original size:19 final size:19
Alignment explanation
Indices: 42817051--42817163 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
42817041 AATCATATAT
42817051 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
42817070 TCCAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
42817089 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42817108 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
42817129 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42817148 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
42817164 CTCAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
19 63 0.79
21 17 0.21
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42817138 original size:40 final size:40
Alignment explanation
Indices: 42817051--42817162 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
42817041 AATCATATAT
* *
42817051 TCTAAGATTGCATATCATATCCAAGATT--ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
42817089 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
42817129 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
42817163 CCTCAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.40
40 41 0.60
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:42817144 original size:59 final size:56
Alignment explanation
Indices: 42817044--42817163 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 56
42817034 ATTACAAAAT
* *
42817044 CATAT-ATTCTAAGATTGCATATCATATCCAAGATTATATATCATCTCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCCAAGATTACATATCATATCTAAGATTG
*** *
42817099 CATATCATATCTAAGATTGCATATATCATATCTTGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCCAAGATTACATATCATATCTAAGATTG
42817158 CATATC
1 CATATC
42817164 CTCAAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.20
59 37 0.67
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCCAAGATTACATATCATATCTAAGATTG
Found at i:42817447 original size:45 final size:44
Alignment explanation
Indices: 42817373--42817494 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 44
42817363 AGTGCTTCAA
* * *
42817373 TCTACTCCATTGCAACTTGAGG-GAGATAAGACTTGCCTT-CTTCAG
1 TCTACTCCACTGCAAATTAAGGAGA-ATAAGACTTG-CTTCCTT-AG
*
42817418 TCTGC-CTCACTGCAAATTAAGGAGAATAAGACTTGCTTCCTTAG
1 TCTACTC-CACTGCAAATTAAGGAGAATAAGACTTGCTTCCTTAG
* *
42817462 TCTACTCCACTGCAACTTCAGG-GAGATAAGACT
1 TCTACTCCACTGCAAATTAAGGAGA-ATAAGACT
42817495 AGATGCGATC
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
43 2 0.03
44 31 0.48
45 30 0.46
46 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
TCTACTCCACTGCAAATTAAGGAGAATAAGACTTGCTTCCTTAG
Found at i:42817473 original size:44 final size:45
Alignment explanation
Indices: 42817367--42817494 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
42817357 GAACTTAGTG
* * *
42817367 CTTCAATCTACTCCATTGCAACTTGAGGGAGATAAGACTTGCCTT
1 CTTCAGTCTACTCCACTGCAACTTAAGGGAGATAAGACTTGCCTT
* *
42817412 CTTCAGTCTGC-CTCACTGCAAATTAA-GGAGAATAAGACTTG-CTT
1 CTTCAGTCTACTC-CACTGCAACTTAAGGGAG-ATAAGACTTGCCTT
*
42817456 CCTT-AGTCTACTCCACTGCAACTTCAGGGAGATAAGACT
1 -CTTCAGTCTACTCCACTGCAACTTAAGGGAGATAAGACT
42817495 AGATGCGATC
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
44 33 0.47
45 37 0.53
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
CTTCAGTCTACTCCACTGCAACTTAAGGGAGATAAGACTTGCCTT
Found at i:42817652 original size:45 final size:44
Alignment explanation
Indices: 42817596--42817711 Score: 130
Period size: 45 Copynumber: 2.6 Consensus size: 44
42817586 TTAATCTGCT
* *
42817596 CCACTGCAACTTTAGGGAGATAAGATTTGC-TATCTTCAGTC-TGC
1 CCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGTCTTGC
* *
42817640 CTCACTGTAACTTCA-GGAGGATAAGACTTGCTTACTTAGTCTTGT
1 C-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGTCTTGC
*
42817685 CCACCGCAACTTCAGGGAGATAAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
42817712 AGATGCGATC
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
44 28 0.46
45 31 0.51
46 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTCTTGC
Found at i:42817760 original size:217 final size:217
Alignment explanation
Indices: 42817366--42818238 Score: 1289
Period size: 217 Copynumber: 4.1 Consensus size: 217
42817356 AGAACTTAGT
* * * * * * * *
42817366 GCTTCAATCTACTCCATTGCAACTTGAGGGAGATAAGACTTGCCTTCTTCAGTCTGCCTCACTGC
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* * * * ** *
42817431 AAATTAAGGAGAATAAGACTTGCTTCCTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAACTTCAGGGAGATAAGACTA
* *
42817496 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCTACTACAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
42817561 CTTCAGGGAGATAGGATTATCG
196 CTTCAGGGAGATAGGATTATCG
* * *
42817583 GCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCTATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
42817648 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAACTTCAGGGAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAACTTCAGGGAGATAAGACTA
* * *
42817713 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTATAATTTTAATCCACTCCATTGCAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
*
42817778 CTTTA-GG-G--A-G---ATCG
196 CTTCAGGGAGATAGGATTATCG
42817792 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* * *
42817857 AACTTCAGGAGGATAAGACTTGATTACTTAGTCTTGTCCACCGCAACTTCTGGTAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAACTTCAGGGAGATAAGACTA
42817922 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
* * *
42817987 CTTCAGGAAGACAGGATTGTCG
196 CTTCAGGGAGATAGGATTATCG
*
42818009 GCTTTAATCTGCTCCACTGTAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
* * * *
42818074 AAC-TCTAGAAGGATAAGACTTGCTTACTTAGTC-TGCTCCACTGTAACTTTAGGGAGATAAGAC
66 AACTTC-AGGAGGATAAGACTTGCTTACTTAGTCTTG-TCCACCGCAACTTCAGGGAGATAAGAC
* * *
42818137 TAGATGCGATCTTCTCTCTGTAACTTCAGAGGGATAAGATCTGTGATTTTAATCCGCTCCACTGC
129 TAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGC
*
42818202 AACTTCAGGGAGATAGGATTGTCG
194 AACTTCAGGGAGATAGGATTATCG
**
42818226 AATTTAATCTGCT
1 GCTTTAATCTGCT
42818239 TCCCGCTATC
Statistics
Matches: 598, Mismatches: 48, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
209 194 0.32
210 1 0.00
211 1 0.00
212 1 0.00
213 2 0.00
214 1 0.00
215 1 0.00
216 6 0.01
217 391 0.65
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (217 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
AACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
CTTCAGGGAGATAGGATTATCG
Found at i:42818133 original size:44 final size:45
Alignment explanation
Indices: 42817799--42818137 Score: 160
Period size: 44 Copynumber: 7.7 Consensus size: 45
42817789 TCGGCTTTAA
* * *
42817799 TCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGTAACTTTAGGAAGATAAGACTTGCCATCTTCAG
* *
42817844 TCTGC-CTCACTGTAACTTCAGGAGGATAAGACTTG--ATTACTT-AG
1 TCTGCTC-CACTGTAACTTTAGGAAGATAAGACTTGCCA-T-CTTCAG
* * * * *
42817888 TCTTG-TCCACCGCAACTTCT-GGTAGATAAGACTAG--A--TGC-G
1 TC-TGCTCCACTGTAACTT-TAGGAAGATAAGACTTGCCATCTTCAG
* * ** * *
42817928 ATCTGCT-CTCTGTAACTTCA-GAGAGATAAGA-TCTGTAAT-TTTAA
1 -TCTGCTCCACTGTAACTTTAGGA-AGATAAGACT-TGCCATCTTCAG
* * * * * * ** * *
42817972 TCCGCTCCACTGCAACTTCAGGAAGACAGGA-TTGTCGGCTTTAA
1 TCTGCTCCACTGTAACTTTAGGAAGATAAGACTTGCCATCTTCAG
* *
42818016 TCTGCTCCACTGTAACTTCAGGAAGATAAGATTTGCCATCTTCAG
1 TCTGCTCCACTGTAACTTTAGGAAGATAAGACTTGCCATCTTCAG
* *
42818061 TCTGC-CTCACTGTAACTCTA-GAAGGATAAGACTTG-CTTACTT-AG
1 TCTGCTC-CACTGTAACTTTAGGAA-GATAAGACTTGCCAT-CTTCAG
*
42818105 TCTGCTCCACTGTAACTTTAGGGAGATAAGACT
1 TCTGCTCCACTGTAACTTTAGGAAGATAAGACT
42818138 AGATGCGATC
Statistics
Matches: 227, Mismatches: 42, Indels: 51
0.71 0.13 0.16
Matches are distributed among these distances:
39 2 0.01
40 21 0.09
41 3 0.01
42 1 0.00
43 10 0.04
44 112 0.49
45 78 0.34
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGTAACTTTAGGAAGATAAGACTTGCCATCTTCAG
Found at i:42818176 original size:426 final size:426
Alignment explanation
Indices: 42817366--42818215 Score: 1326
Period size: 426 Copynumber: 2.0 Consensus size: 426
42817356 AGAACTTAGT
* * * *
42817366 GCTTCAATCTACTCCATTGCAACTTGAGGGAGATAAGACTTGCCTTCTTCAGTCTGCCTCACTGC
1 GCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGC
* * *
42817431 AAATTAAGGAGAATAAGACTTGCTTCCTTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTA
66 AAATTAAGGAGAATAAGACTTGATTACTTAGTCTACTCCACCGCAACTTCAGGGAGATAAGACTA
*
42817496 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCTACTACAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTACAA
* * * *
42817561 CTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGC
196 CTTCAGGAAGACAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGC
* *
42817626 TATCTTCAGTCTGCCTCACTGTAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTTGTCCACCG
261 CATCTTCAGTCTGCCTCACTGTAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTTGTCCACCG
42817691 CAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTATA
326 CAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTATA
* *
42817756 ATTTTAATCCACTCCATTGCAACTTTAGGGAGATCG
391 ATTTTAATCCACTCCACTGCAACTTCAGGGAGATCG
* * * *
42817792 GCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGC
* * * ** * *
42817857 AACTTCAGGAGGATAAGACTTGATTACTTAGTCTTGTCCACCGCAACTTCTGGTAGATAAGACTA
66 AAATTAAGGAGAATAAGACTTGATTACTTAGTCTACTCCACCGCAACTTCAGGGAGATAAGACTA
*
42817922 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTGCAA
131 GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTACAA
* *
42817987 CTTCAGGAAGACAGGATTGTCGGCTTTAATCTGCTCCACTGTAACTTCAGGAAGATAAGATTTGC
196 CTTCAGGAAGACAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGC
42818052 CATCTTCAGTCTGCCTCACTGTAAC-TCTAGAAGGATAAGACTTGCTTACTTAGTC-TGCTCCAC
261 CATCTTCAGTCTGCCTCACTGTAACTTC-AGAAGGATAAGACTTGCTTACTTAGTCTTG-TCCAC
* * * * * *
42818115 TGTAACTTTAGGGAGATAAGACTAGATGCGATCTTCTCTCTGTAACTTCAGAGGGATAAGATCTG
324 CGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTA
* *
42818180 TGATTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
389 TAATTTTAATCCACTCCACTGCAACTTCAGGGAGAT
42818216 AGGATTGTCG
Statistics
Matches: 384, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
425 4 0.01
426 380 0.99
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (426 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGACTTGCCATCTTCAGTCTGCCTCACTGC
AAATTAAGGAGAATAAGACTTGATTACTTAGTCTACTCCACCGCAACTTCAGGGAGATAAGACTA
GATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTAATTTTAATCCGCTCCACTACAA
CTTCAGGAAGACAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGC
CATCTTCAGTCTGCCTCACTGTAACTTCAGAAGGATAAGACTTGCTTACTTAGTCTTGTCCACCG
CAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTATA
ATTTTAATCCACTCCACTGCAACTTCAGGGAGATCG
Found at i:42818504 original size:132 final size:131
Alignment explanation
Indices: 42818231--42818712 Score: 788
Period size: 132 Copynumber: 3.7 Consensus size: 131
42818221 TGTCGAATTT
* * * *
42818231 AATCTGCTTCCCGCTATCTTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCG-CGTCTTCGATCTGCTCCACTACTGATTA
*
42818296 GGGAGATAAGAT-TACAATTTTCAACCTTCACCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
65 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
42818360 TA
130 TA
* *
42818362 AATCTGCTTCCCACTATCTTGGAAATATAAGATTCGCAGTCTTCGATCTGCTCCACTATTGATTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGC-GTCTTCGATCTGCTCCACTACTGATTA
42818427 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
65 GGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
42818492 TA
130 TA
* *
42818494 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACTGTCTTCAATCTGCTCCACTACT-ACTT
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGC-GTCTTCGATCTGCTCCACTACTGA-TT
* * *
42818558 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTGCTGCTCAAGGAGACAAGGCTTGGTGGC
64 AGGGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGC
42818623 TTA
129 TTA
*
42818626 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCG-CGTCTTCGATCTGCTCCACTACTGATTA
42818691 GGGAGATAAGATCTACAATTTT
65 GGGAGATAAGATCTACAATTTT
42818713 TACTGATCTG
Statistics
Matches: 327, Mismatches: 19, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
130 1 0.00
131 70 0.21
132 255 0.78
133 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (131 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCGTCTTCGATCTGCTCCACTACTGATTAG
GGAGATAAGATCTACAATTTTCAACCTTCTCCGCTGCTGCTCAGGGAGACAAGGCTTGGTGGCTT
A
Found at i:42818566 original size:44 final size:44
Alignment explanation
Indices: 42818518--42818702 Score: 110
Period size: 44 Copynumber: 4.2 Consensus size: 44
42818508 TATCTTGGAA
42818518 AGATAAGATTCACTGTCTTCAATCTGCTCCACTACTACTTAGGG
1 AGATAAGATTCACTGTCTTCAATCTGCTCCACTACTACTTAGGG
** * * * * * *
42818562 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTGCTGCTCAAGG
1 AGATAAGATTC-ACTGTCTTCAATCTGCTCCACTACTACTTAGGG
* * ** * * *
42818606 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCC-C-ACTATCTT-GGAA
1 AGATAA-GATTCACTGTCTTCAATCTGC-TCCACTACTA-CTTAGG-G
* * * **
42818650 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGTTTAGGG
1 AGATAAGATTCACTGTCTTCAATCTGCTCCACTACTACTTAGGG
42818694 AGATAAGAT
1 AGATAAGAT
42818703 CTACAATTTT
Statistics
Matches: 98, Mismatches: 33, Indels: 20
0.65 0.22 0.13
Matches are distributed among these distances:
43 11 0.11
44 77 0.79
45 9 0.09
46 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCACTGTCTTCAATCTGCTCCACTACTACTTAGGG
Found at i:42819945 original size:5 final size:6
Alignment explanation
Indices: 42819923--42819967 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
42819913 TTGGCCTCTC
* *
42819923 CTTTTA CTTTTT CTTTTT CTTTTTT CCTTTTT CCTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT C-TTTTT -CTTTTT CTTTTT CTTTTT C
42819968 CTCTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 23 0.68
7 10 0.29
8 1 0.03
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (6 bp):
CTTTTT
Found at i:42819952 original size:20 final size:19
Alignment explanation
Indices: 42819924--42819979 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
42819914 TGGCCTCTCC
*
42819924 TTTTACTTTTTCTTTTTCTT
1 TTTTCCTTTTTCTTTTTC-T
*
42819944 TTTTCCTTTTTCCTTTTCT
1 TTTTCCTTTTTCTTTTTCT
42819963 TTTTCCTCTTTT-TTTTT
1 TTTTCCT-TTTTCTTTTT
42819980 GAAATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTCCTTTTTCTTTTTCT
Found at i:42819968 original size:12 final size:12
Alignment explanation
Indices: 42819931--42819978 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
42819921 TCCTTTTACT
*
42819931 TTTTCTTTTTCTT
1 TTTTCTTTTTC-C
42819944 TTTTCCTTTTTCC
1 TTTT-CTTTTTCC
42819957 TTTTCTTTTTCC
1 TTTTCTTTTTCC
42819969 TCTTT-TTTTT
1 T-TTTCTTTTT
42819979 TGAAATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.44
13 11 0.34
14 7 0.22
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTCC
Found at i:42819973 original size:14 final size:13
Alignment explanation
Indices: 42819931--42819979 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
42819921 TCCTTTTACT
*
42819931 TTTTCTTTTTCTT
1 TTTTCTTTTTCTC
42819944 TTTTCCTTTTTC-C
1 TTTT-CTTTTTCTC
42819957 TTTTCTTTTTCCTC
1 TTTTCTTTTT-CTC
42819971 TTTT-TTTTT
1 TTTTCTTTTT
42819980 GAAATATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.19
13 14 0.44
14 12 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTCTC
Found at i:42824907 original size:23 final size:24
Alignment explanation
Indices: 42824879--42824925 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
42824869 ATATATATGT
42824879 GAAAATATTC-ATTTAAAAAAAAG
1 GAAAATATTCGATTTAAAAAAAAG
*
42824902 GAAAATATTCGTTTTTAAAAAAAA
1 GAAAATATTCG-ATTTAAAAAAAA
42824926 TATATATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (24 bp):
GAAAATATTCGATTTAAAAAAAAG
Found at i:42825582 original size:19 final size:19
Alignment explanation
Indices: 42825555--42825667 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
42825545 AATCATATAT
42825555 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
42825574 TCCAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
42825593 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42825612 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
42825633 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
42825652 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
42825668 CTCAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
19 63 0.79
21 17 0.21
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:42825642 original size:40 final size:40
Alignment explanation
Indices: 42825555--42825666 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
42825545 AATCATATAT
* *
42825555 TCTAAGATTGCATATCATATCCAAGATT--ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
42825593 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
42825633 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
42825667 CCTCAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.40
40 41 0.60
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:42825648 original size:59 final size:56
Alignment explanation
Indices: 42825548--42825667 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 56
42825538 ATTACAAAAT
* *
42825548 CATAT-ATTCTAAGATTGCATATCATATCCAAGATTATATATCATCTCTAAGATTG
1 CATATCATTCTAAGATTGCATATCATATCCAAGATTACATATCATATCTAAGATTG
*** *
42825603 CATATCATATCTAAGATTGCATATATCATATCTTGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCCAAGATTACATATCATATCTAAGATTG
42825662 CATATC
1 CATATC
42825668 CTCAAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.20
59 37 0.67
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCCAAGATTACATATCATATCTAAGATTG
Found at i:42826648 original size:23 final size:23
Alignment explanation
Indices: 42826631--42826797 Score: 199
Period size: 23 Copynumber: 7.1 Consensus size: 23
42826621 TGGTGTAAAA
42826631 ATGCTGCCCAATTTGGTGTCTAT
1 ATGCTGCCCAATTTGGTGTCTAT
42826654 ATGCTGCCCAATTTGGTGTCTAT
1 ATGCTGCCCAATTTGGTGTCTAT
* ** *
42826677 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTGGTGTCTAT
42826701 ATGCTGCCCAATTTGGTGTCTAT
1 ATGCTGCCCAATTTGGTGTCTAT
* **
42826724 ATGTTGTTCAATTTGGTGTCTAT
1 ATGCTGCCCAATTTGGTGTCTAT
* ** *
42826747 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCCAA--TTTGGTGTCTAT
*
42826772 ATTCTGCCCAATTTGGTGTCTAT
1 ATGCTGCCCAATTTGGTGTCTAT
42826795 ATG
1 ATG
42826798 GTCTATATGC
Statistics
Matches: 119, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
23 82 0.69
24 19 0.16
25 18 0.15
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (23 bp):
ATGCTGCCCAATTTGGTGTCTAT
Found at i:42826694 original size:47 final size:46
Alignment explanation
Indices: 42826612--42827086 Score: 239
Period size: 47 Copynumber: 9.8 Consensus size: 46
42826602 TTCGATTCAA
** * * ** *
42826612 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCT
1 GTCCAA-TTTGGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
*
42826659 GCCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCT
1 GTCCAATTTGGTGTCTATATGCTGTCCAA-TTTGGTGTAAAAATGCT
* * * ** *
42826706 GCCCAATTTGGTGTCTATATGTTGTTCAATTTGGTGTCTATATGCT
1 GTCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
** * * * *
42826752 GTCCAATTTTTGGTGTAAAAATTCTGCCCAATTTGGTGTCTATATGGTCTATATGCT
1 GTCCAA--TTTGGTGTCTATATGCTGTCCAATTTGGTG--TA-A------AAATGCT
** * ** *
42826809 GTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTATATGCT
1 GTCCAATTT-GGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
** * ** *
42826856 GTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTATATGCT
1 GTCCAA-TTTGGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
** * * * * *
42826903 GTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATATATGCT
1 GTCCAA-TTTGGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
* * * * *
42826950 GCCCAATTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAAAAAAATGTT
1 GTCCAATTTGGTGTCTATATGCTGTCCAA-TTTGGTGT---AAAAATGCT
* * * * * * * * *
42827000 GTTCAATTTGATATATATATATGCTGCCCAAATTAGTGTATAAATGTT
1 GTCCAATTTG--GTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
* * *
42827048 GTCCAATTTTGGTGTATAAATGCTGTCCAATTTGATGTA
1 GTCCAA-TTTGGTGTCTATATGCTGTCCAATTTGGTGTA
42827087 TAAGAGCTGT
Statistics
Matches: 349, Mismatches: 58, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
46 57 0.16
47 172 0.49
48 39 0.11
49 4 0.01
50 15 0.04
51 6 0.02
52 14 0.04
54 1 0.00
55 3 0.01
56 25 0.07
57 13 0.04
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (46 bp):
GTCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTAAAAATGCT
Found at i:42826725 original size:70 final size:70
Alignment explanation
Indices: 42826612--42826964 Score: 369
Period size: 70 Copynumber: 5.2 Consensus size: 70
42826602 TTCGATTCAA
*
42826612 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGCCCAATTTGGTGTCTAT
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTCTAT
42826677 ATGCT
66 ATGCT
* *
42826682 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGTTGTTCAATTTGGTGTCTAT
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTCTAT
42826747 ATGCT
66 ATGCT
* * * *
42826752 GTCCAATTTTTGGTGTAAAAATTCTGCCCAATTTGGTGTCTATATG--GT-CTATATGCTGTC--
1 GTCCAA-TTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTCTA
42826812 ----C-
65 TATGCT
* **
42826813 ----AATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAA-TTTGGTGTCTA
*
42826874 AATGCT
65 TATGCT
** * * ** * * * *
42826880 GTCCAA-TTTGGTGTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATA
1 GTCCAATTTTGGTGTAAAAATGCTGCCCAA-TTTGGTGTCTATATGCTGTCCAATTTGGTGTCTA
42826944 TATGCT
65 TATGCT
*
42826950 GCCCAA-TTTGGTGTA
1 GTCCAATTTTGGTGTA
42826965 TATTTGCTGT
Statistics
Matches: 241, Mismatches: 25, Indels: 34
0.80 0.08 0.11
Matches are distributed among these distances:
56 37 0.15
57 2 0.01
58 2 0.01
59 2 0.01
60 6 0.02
62 1 0.00
66 1 0.00
68 9 0.04
69 2 0.01
70 119 0.49
71 60 0.25
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (70 bp):
GTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAATTTGGTGTCTAT
ATGCT
Found at i:42826914 original size:127 final size:126
Alignment explanation
Indices: 42826671--42826917 Score: 361
Period size: 127 Copynumber: 1.9 Consensus size: 126
42826661 CCAATTTGGT
* *
42826671 GTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGTTGTTCAAT
1 GTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAAT
** * *
42826736 TTGGTGTCTATATGCTGTCCAATTTTTGGTGTAAAAATTCTGCCCAATTTGGTGTCTATATG
66 TTGGTGTAAAAATGCTGTCCAA-TTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATG
*
42826798 GTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTATATGCTGTCCAAT
1 GTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAA-
** * *
42826863 TTTGGTGTAAAAATGCTGTCCAA-TTTGGTGTCTATATGCTGTCCAATTTTGGTGT
65 TTTGGTGTAAAAATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAA-TTTGGTGT
42826918 AAAAATGCTG
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
126 18 0.17
127 69 0.64
128 20 0.19
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (126 bp):
GTCTATATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATGCTGTCCAAT
TTGGTGTAAAAATGCTGTCCAATTTTGGTGTAAAAATGCTGCCCAATTTGGTGTCTATATG
Found at i:42827039 original size:75 final size:71
Alignment explanation
Indices: 42826801--42827088 Score: 296
Period size: 70 Copynumber: 4.0 Consensus size: 71
42826791 CTATATGGTC
* * * ** *
42826801 TATATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAA-TTTGGTGT-CTATATGCTGTCCAATT
1 TATATGCTGCCCAA-TTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAAATGCTGTCCAA-T
* *
42826864 TTGGTGTA
64 TTGATATA
* * * *
42826872 AAAATGCTGTCCAATTTGGTGTCTATATGCTGTCCAATTTTGGTGT-AAAAATGCTGTCCAATTT
1 TATATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAAATGCTGTCCAATTT
42826936 GATATA
66 GATATA
* * * *
42826942 TATATGCTGCCCAATTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAAAAAAATGTTGTTCAAT
1 TATATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGT--AAAAAATGCTGTCCAAT
42827007 TTGATATATA
64 TTG--ATATA
* * * * *
42827017 TATATGCTGCCCAAATTAGTGTATAAATGTTGTCCAATTTTGGTGT-ATAAATGCTGTCCAATTT
1 TATATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAAATGCTGTCCAATTT
*
42827081 GATGTA
66 GATATA
42827087 TA
1 TA
42827089 AGAGCTGTAC
Statistics
Matches: 183, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
70 73 0.40
71 32 0.17
72 16 0.09
73 17 0.09
75 45 0.25
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (71 bp):
TATATGCTGCCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAAATGCTGTCCAATTT
GATATA
Found at i:42827089 original size:47 final size:47
Alignment explanation
Indices: 42826804--42827089 Score: 272
Period size: 47 Copynumber: 6.0 Consensus size: 47
42826794 TATGGTCTAT
* * *
42826804 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTAT
1 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATGTATAA
* * *
42826851 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGGTGTCTAT
1 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATGTATAA
* *
42826898 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATATATAT
1 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATGTATAA
* * ** * * *
42826945 ATGCTGCCCAA-TTTGGTGTATATTTGCTGTCAAATTTTGGTGTAAAAAAA
1 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAA-TTTGATGT---ATAA
* * * * * * *
42826995 ATGTTGTTCAA-TTTGATATATATATATGCTGCCCAAATT-AGTGTATAA
1 ATGCTGTCCAATTTTGGTGTA-A-AAATGCTGTCCAATTTGA-TGTATAA
* *
42827043 ATGTTGTCCAATTTTGGTGTATAAATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATGTATAA
42827090 GAGCTGTACA
Statistics
Matches: 199, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
46 19 0.10
47 127 0.64
48 14 0.07
49 7 0.04
50 17 0.09
51 5 0.03
52 10 0.05
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (47 bp):
ATGCTGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTGATGTATAA
Found at i:42827096 original size:23 final size:23
Alignment explanation
Indices: 42826804--42827089 Score: 266
Period size: 23 Copynumber: 12.0 Consensus size: 23
42826794 TATGGTCTAT
*
42826804 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAA
* *
42826828 ATGCTGTCCAATTTGGTGTCTAT
1 ATGCTGTCCAATTTGGTGTATAA
*
42826851 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAA
* *
42826875 ATGCTGTCCAATTTGGTGTCTAT
1 ATGCTGTCCAATTTGGTGTATAA
*
42826898 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAA
* * *
42826922 ATGCTGTCCAATTTGATATATAT
1 ATGCTGTCCAATTTGGTGTATAA
* *
42826945 ATGCTGCCCAATTTGGTGTATAT
1 ATGCTGTCCAATTTGGTGTATAA
* * *
42826968 TTGCTGTCAAATTTTGGTGTAAAAAAA
1 ATGCTGTCCAA-TTTGGTGT---ATAA
* * * *
42826995 ATGTTGTTCAATTTGATATATATA
1 ATGCTGTCCAATTTGGTGTATA-A
* * *
42827019 TATGCTGCCCAAATTAGTGTATAA
1 -ATGCTGTCCAATTTGGTGTATAA
*
42827043 ATGTTGTCCAATTTTGGTGTATAA
1 ATGCTGTCCAA-TTTGGTGTATAA
*
42827067 ATGCTGTCCAATTTGATGTATAA
1 ATGCTGTCCAATTTGGTGTATAA
42827090 GAGCTGTACA
Statistics
Matches: 209, Mismatches: 44, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
23 98 0.47
24 81 0.39
25 15 0.07
26 6 0.03
27 9 0.04
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (23 bp):
ATGCTGTCCAATTTGGTGTATAA
Found at i:42829391 original size:15 final size:12
Alignment explanation
Indices: 42829360--42829385 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42829350 TGTTTTCAGC
42829360 TAGTTCTTTTTT
1 TAGTTCTTTTTT
42829372 TAGTTCTTTTTT
1 TAGTTCTTTTTT
42829384 TA
1 TA
42829386 TCAGTTGACT
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:0.12, C:0.08, G:0.08, T:0.73
Consensus pattern (12 bp):
TAGTTCTTTTTT
Found at i:42831422 original size:20 final size:18
Alignment explanation
Indices: 42831372--42831423 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
42831362 CTACAATATA
42831372 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
42831389 AATATTAAGA-TAATCATTTT
1 AATATTAA-ATTAAT-A-TTT
42831409 AATATTAAATTAATA
1 AATATTAAATTAATA
42831424 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:42834727 original size:21 final size:23
Alignment explanation
Indices: 42834703--42834745 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42834693 CATATCATTT
42834703 TGAATT-TTT-TTATTATTTATA
1 TGAATTGTTTGTTATTATTTATA
*
42834724 TGAATTGTTTGTTATTTTTTAT
1 TGAATTGTTTGTTATTATTTAT
42834746 TTAATGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (23 bp):
TGAATTGTTTGTTATTATTTATA
Found at i:42842469 original size:10 final size:9
Alignment explanation
Indices: 42842439--42842503 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
42842429 TAAAATATAT
42842439 ATTA-TAAA
1 ATTATTAAA
* *
42842447 AATAATAAA
1 ATTATTAAA
42842456 ATTATTAGAA
1 ATTATTA-AA
42842466 ATTATTAATAA
1 ATTATT-A-AA
*
42842477 ATTATAAAA
1 ATTATTAAA
*
42842486 ACTATTAAA
1 ATTATTAAA
42842495 ATTTATTAA
1 A-TTATTAA
42842504 TTTTAATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 3 0.07
9 19 0.42
10 15 0.33
11 8 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
ATTATTAAA
Found at i:42844205 original size:18 final size:17
Alignment explanation
Indices: 42844178--42844211 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42844168 TCAACAAGTC
*
42844178 ATTTTAAAAAACATAAA
1 ATTTTAAAAAAAATAAA
42844195 ATTTATAAAAAAAATAA
1 ATTT-TAAAAAAAATAA
42844212 TTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTTAAAAAAAATAAA
Found at i:42845688 original size:19 final size:19
Alignment explanation
Indices: 42845653--42845694 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42845643 TAATTCATGA
42845653 TATTAATATCAAATAATAT
1 TATTAATATCAAATAATAT
*
42845672 TATTGAATAT-AATTAATA-
1 TATT-AATATCAAATAATAT
42845690 TATTA
1 TATTA
42845695 TATTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 11 0.52
20 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAATATCAAATAATAT
Found at i:42852722 original size:68 final size:67
Alignment explanation
Indices: 42852483--42852724 Score: 216
Period size: 68 Copynumber: 3.6 Consensus size: 67
42852473 TGTCTTGGTG
* * ** *
42852483 GACTTTATATGTTAACATAACCCAACTATGGTCTTACACTACGTGGTGCCATGTTTACTGTCCTG
1 GACTTTATATGTTACCATAACCCAACTATGGTCTTACATTATATGGTGCCATGTTTACTGTCTTG
*
42852548 GC
66 AC
* * ** * * *
42852550 GGACTTTGTATGTTGCCATTGCCCAACAATGGCCTTAC-TCTATATGGTGTCATGTTTACTGTCC
1 -GACTTTATATGTTACCATAACCCAACTATGGTCTTACAT-TATATGGTGCCATGTTTACTGT-C
* **
42852614 TAGTG
63 TTGAC
* * * * * *
42852619 GACTTTATATGTTGCCATAGCCTAGCTACGGTCTTACATTATATGGTGCCATGTTTATTGTCTTG
1 GACTTTATATGTTACCATAACCCAACTATGGTCTTACATTATATGGTGCCATGTTTACTGTCTTG
42852684 AC
66 AC
* * *
42852686 AAATTTCATATGTTACCATAACCCAACTATGATCTTACA
1 GACTTT-ATATGTTACCATAACCCAACTATGGTCTTACA
42852725 CTCTTATAAG
Statistics
Matches: 135, Mismatches: 35, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
67 7 0.05
68 125 0.93
69 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (67 bp):
GACTTTATATGTTACCATAACCCAACTATGGTCTTACATTATATGGTGCCATGTTTACTGTCTTG
AC
Found at i:42852723 original size:136 final size:136
Alignment explanation
Indices: 42852471--42852723 Score: 283
Period size: 136 Copynumber: 1.9 Consensus size: 136
42852461 TTTTTGGCCC
* * * *
42852471 ACTGTCTTGGTGGACTTTATATGTTAACATAACCCAACTATGGTCTTACACTACGTGGTGCCATG
1 ACTGTCCTAGTGGACTTTATATGTTAACATAACCCAACTACGGTCTTACACTACATGGTGCCATG
* * * * * ** *
42852536 TTTACTGTCCTGGCGGACTTTGTATGTTGCCATTGCCCAACAATGGCCTTACTCTATATGGTGTC
66 TTTACTGTCCTGACGAAATTTATATGTTACCATAACCCAACAATGACCTTACTCTATATGGTGTC
42852601 ATGTTT
131 ATGTTT
** * * * * *
42852607 ACTGTCCTAGTGGACTTTATATGTTGCCATAGCCTAGCTACGGTCTTACATTATATGGTGCCATG
1 ACTGTCCTAGTGGACTTTATATGTTAACATAACCCAACTACGGTCTTACACTACATGGTGCCATG
* * * *
42852672 TTTATTGTCTTGAC-AAATTTCATATGTTACCATAACCCAACTATGATCTTAC
66 TTTACTGTCCTGACGAAATTT-ATATGTTACCATAACCCAACAATGACCTTAC
42852724 ACTCTTATAA
Statistics
Matches: 93, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
135 4 0.04
136 89 0.96
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (136 bp):
ACTGTCCTAGTGGACTTTATATGTTAACATAACCCAACTACGGTCTTACACTACATGGTGCCATG
TTTACTGTCCTGACGAAATTTATATGTTACCATAACCCAACAATGACCTTACTCTATATGGTGTC
ATGTTT
Found at i:42852854 original size:122 final size:122
Alignment explanation
Indices: 42852648--42852901 Score: 384
Period size: 122 Copynumber: 2.1 Consensus size: 122
42852638 GCCTAGCTAC
* * *
42852648 GGTCTTACATTATATGGTGCCATGTTTATTGTCTTGACAAATTTCATATGTTACCATAACCCAAC
1 GGTCTTACACTATATGGTGCCATGTTTATTGTCATGACAAACTTCATATGTTACCATAACCCAAC
*
42852713 TATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGGTGCCATGGCCCAACTAT
66 TATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGGTGCCATGACCCAACTAT
* * *
42852770 GGTCTTACACTATATGGTGCCATGTTTATTGTCATGA-AGGACTTCATATGTTACCATAGCCCAG
1 GGTCTTACACTATATGGTGCCATGTTTATTGTCATGACA-AACTTCATATGTTACCATAACCCAA
* * * **
42852834 CTATGATCTTACATTTTTATAGGCTTAGAGCCTCCAATTGGTGCCATGACCCAACTAT
65 CTATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGGTGCCATGACCCAACTAT
42852892 GGTCTTACAC
1 GGTCTTACAC
42852902 ATCATTCCCG
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 1 0.01
122 118 0.99
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (122 bp):
GGTCTTACACTATATGGTGCCATGTTTATTGTCATGACAAACTTCATATGTTACCATAACCCAAC
TATGATCTTACACTCTTATAAGCTTAGAGCCTCCAACCGGTGCCATGACCCAACTAT
Found at i:42853374 original size:38 final size:38
Alignment explanation
Indices: 42853323--42853403 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
42853313 ACCATTTCAT
42853323 ACACAACAGCAGGTTCTGACAACTTAGAACAAACACTA
1 ACACAACAGCAGGTTCTGACAACTTAGAACAAACACTA
*
42853361 ACACAATAGCAGGTTCTGACAACTTAGAACAAACACTA
1 ACACAACAGCAGGTTCTGACAACTTAGAACAAACACTA
42853399 ACACA
1 ACACA
42853404 GACCATTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.46, C:0.26, G:0.12, T:0.16
Consensus pattern (38 bp):
ACACAACAGCAGGTTCTGACAACTTAGAACAAACACTA
Found at i:42856418 original size:14 final size:14
Alignment explanation
Indices: 42856399--42856427 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42856389 TCATTCATGT
42856399 AACAGCTAAACACA
1 AACAGCTAAACACA
42856413 AACAGCTAAACACA
1 AACAGCTAAACACA
42856427 A
1 A
42856428 TACCAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.07, T:0.07
Consensus pattern (14 bp):
AACAGCTAAACACA
Found at i:42858222 original size:10 final size:10
Alignment explanation
Indices: 42858191--42858223 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42858181 AATTTAAAAT
42858191 TTTTATCGAA
1 TTTTATCGAA
42858201 TTTT-TCGAA
1 TTTTATCGAA
*
42858210 TTTTATCGGA
1 TTTTATCGAA
42858220 TTTT
1 TTTT
42858224 GCTCACCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.21, C:0.09, G:0.12, T:0.58
Consensus pattern (10 bp):
TTTTATCGAA
Found at i:42859142 original size:12 final size:12
Alignment explanation
Indices: 42859125--42859149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42859115 AAAGCATATG
42859125 TGATTTTAGTTT
1 TGATTTTAGTTT
42859137 TGATTTTAGTTT
1 TGATTTTAGTTT
42859149 T
1 T
42859150 TAGTTTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TGATTTTAGTTT
Found at i:42861456 original size:3 final size:3
Alignment explanation
Indices: 42861448--42861480 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
42861438 AACTTCATGT
42861448 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42861481 GAAGAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42881346 original size:24 final size:25
Alignment explanation
Indices: 42881319--42881365 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
42881309 TAATATATAA
*
42881319 AATTAATTTTAAATATTT-TTAAGT
1 AATTAATATTAAATATTTATTAAGT
*
42881343 AATTAATATTAATTATTTATTAA
1 AATTAATATTAAATATTTATTAA
42881366 ATTTAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTAATATTAAATATTTATTAAGT
Found at i:42883109 original size:165 final size:160
Alignment explanation
Indices: 42882832--42883157 Score: 426
Period size: 165 Copynumber: 2.0 Consensus size: 160
42882822 TCAAGTCAAG
** * *
42882832 TCAAGCATATGATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCTCATAATTCTT
1 TCAAGCATACAATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
* *
42882897 ATCTATAATTTTTATAGTCTTAGGAAATAAAGAGATTTGGCCTTTCAAATGAGTAGTGCAGAAAA
66 ATCTATAATTTTTATAGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
*
42882962 TTTACAGATTCAGATTTTG-AAGCGTTGAAA
131 TTTACACATTCA-ATTTTGTAAGCGTTGAAA
* * *
42882992 TCAAGCATACAATTTTCAAAT-TGCAAATTCTAAGAATATTTTTCATTGCAAAAACTCACATAAT
1 TCAAGCATACAATTGTCAAATCT-CAAAATCTAA-AATA-TCTTCATTGC-AAAACTCACATAAT
* *
42883056 TCATA-CTTATAATTTTCGTGA-AGTCATATGAAATAAAGAGAATTGGCCTTTCAAATGATTAGT
62 TCATATC-TATAATTTT--T-ATAGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGT
*
42883119 GCAGAAAATTTACACATTCAATTTTGTAAGTGTTGAAA
123 GCAGAAAATTTACACATTCAATTTTGTAAGCGTTGAAA
42883157 T
1 T
42883158 TAAATGAATG
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
159 1 0.01
160 27 0.19
161 4 0.03
162 10 0.07
163 26 0.18
164 6 0.04
165 69 0.48
166 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (160 bp):
TCAAGCATACAATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
ATCTATAATTTTTATAGTCATAGGAAATAAAGAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
TTTACACATTCAATTTTGTAAGCGTTGAAA
Found at i:42884656 original size:20 final size:21
Alignment explanation
Indices: 42884618--42884673 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
42884608 TGAGGGCAAA
42884618 GAACCAGCGTAGCAGCAGAGG
1 GAACCAGCGTAGCAGCAGAGG
42884639 GAACCAGCAG-AG-AGCAGA--
1 GAACCAGC-GTAGCAGCAGAGG
*
42884657 G-AGCAGCGTAGCAGCAG
1 GAACCAGCGTAGCAGCAG
42884674 GTACTGGGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
16 1 0.03
17 7 0.23
18 6 0.19
20 6 0.19
21 10 0.32
22 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.38, T:0.04
Consensus pattern (21 bp):
GAACCAGCGTAGCAGCAGAGG
Found at i:42885440 original size:98 final size:96
Alignment explanation
Indices: 42885311--42885505 Score: 320
Period size: 98 Copynumber: 2.0 Consensus size: 96
42885301 CCTTACTTAT
* *
42885311 CTAAATATCTTCCTCAAGTAAACTATGAAATATATTGAATAATATCCTTTAAGAAAGTGCACAAA
1 CTAAATATCCTCCTCAAGTAAACTATGAAATATATTGAATAATATCCCTTAA-AAA-TGCACAAA
42885376 AATAATCACAATAATCAAATCAAAATATGCCAA
64 AATAATCACAATAATCAAATCAAAATATGCCAA
*
42885409 CTAAATATCCTCCTCATGTAAA-TAATGAAATATATTGAATAATATCCCTTAAAAATGCACAAAA
1 CTAAATATCCTCCTCAAGTAAACT-ATGAAATATATTGAATAATATCCCTTAAAAATGCACAAAA
*
42885473 ATAGTCACAATAATCAAATCAAAATATGCCAA
65 ATAATCACAATAATCAAATCAAAATATGCCAA
42885505 C
1 C
42885506 AAAACAAGCA
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
96 41 0.45
97 4 0.04
98 47 0.51
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (96 bp):
CTAAATATCCTCCTCAAGTAAACTATGAAATATATTGAATAATATCCCTTAAAAATGCACAAAAA
TAATCACAATAATCAAATCAAAATATGCCAA
Found at i:42886050 original size:6 final size:6
Alignment explanation
Indices: 42886039--42886074 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
42886029 AAGACTTTTC
*
42886039 TTTTGT TTTTGT TTTTGTT TTTTTT TTTTGT TTTTG
1 TTTTGT TTTTGT TTTTG-T TTTTGT TTTTGT TTTTG
42886075 CATTTGGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:42890304 original size:25 final size:25
Alignment explanation
Indices: 42890276--42890335 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
42890266 AAGTATTATG
*
42890276 CAGAGAACATAAATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
* **
42890301 CAGAGAGCACCGATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
42890326 CAGAGAACAC
1 CAGAGAACAC
42890336 GCTAAAATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (25 bp):
CAGAGAACACAAATGTGCTAATAAT
Found at i:42891359 original size:50 final size:50
Alignment explanation
Indices: 42891235--42891478 Score: 267
Period size: 50 Copynumber: 4.9 Consensus size: 50
42891225 GATAATAACA
* ** * * *
42891235 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
42891284 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
42891334 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
42891384 TGCCAACGCCATGTCCCAAACATGATCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42891434 TGCCAACGCCATGTCCTAAACATGGTCTTACATGAGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
42891479 AATTTCAATA
Statistics
Matches: 166, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
48 1 0.01
49 38 0.23
50 127 0.77
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42898710 original size:22 final size:22
Alignment explanation
Indices: 42898667--42898723 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
42898657 TGTAGTTTTT
42898667 TAGGTGAAA-AGTTGGATGTGA
1 TAGGTGAAAGAGTTGGATGTGA
*
42898688 TAGGTGAAAGA-TTAGGATTTGA
1 TAGGTGAAAGAGTT-GGATGTGA
42898710 TAGGTGAAAG-GTTG
1 TAGGTGAAAGAGTTG
42898724 ATAGGTGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (22 bp):
TAGGTGAAAGAGTTGGATGTGA
Found at i:42899056 original size:10 final size:10
Alignment explanation
Indices: 42899041--42899094 Score: 56
Period size: 10 Copynumber: 5.0 Consensus size: 10
42899031 TTTCCCTACA
42899041 AAAATAAAAT
1 AAAATAAAAT
42899051 AAAATAAAAT
1 AAAATAAAAT
42899061 AATAAT-AAAT
1 AA-AATAAAAT
42899071 AATAATAATAAAT
1 AA-AAT-A-AAAT
42899084 AAAATTAAAAT
1 AAAA-TAAAAT
42899095 GTGTATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 22 0.56
11 7 0.18
12 3 0.08
13 7 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:42899074 original size:13 final size:13
Alignment explanation
Indices: 42899058--42899085 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42899048 AATAAAATAA
42899058 AATAATAATAAAT
1 AATAATAATAAAT
42899071 AATAATAATAAAT
1 AATAATAATAAAT
42899084 AA
1 AA
42899086 AATTAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:42908211 original size:38 final size:38
Alignment explanation
Indices: 42908169--42908273 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 38
42908159 AGGTATTATT
* *
42908169 CAGGCTTAGTGTCGGTGTTTTTCAGG-TTTAGTGGCTAG
1 CAGGCTTAGTGCCGGTGTTATTCAGGCTTT-GTGGCTAG
42908207 CAGGCTTAGTGCCGGTGTTATTCAGGCTTTGTGGCTAG
1 CAGGCTTAGTGCCGGTGTTATTCAGGCTTTGTGGCTAG
* * ** *
42908245 CAAGCTTAATGCTTGTGTTATGCAGGCTT
1 CAGGCTTAGTGCCGGTGTTATTCAGGCTT
42908274 AATGTCGGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 56 0.95
39 3 0.05
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.37
Consensus pattern (38 bp):
CAGGCTTAGTGCCGGTGTTATTCAGGCTTTGTGGCTAG
Found at i:42908273 original size:22 final size:23
Alignment explanation
Indices: 42908248--42908300 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
42908238 TGGCTAGCAA
*
42908248 GCTTAATGCT-TGTGTT-ATGCAG
1 GCTTAATGCTCGGTGTTAAT-CAG
42908270 GCTTAATG-TCGGTGTTAATCAG
1 GCTTAATGCTCGGTGTTAATCAG
42908292 GCTTAATGC
1 GCTTAATGC
42908301 CTAGCAGGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (23 bp):
GCTTAATGCTCGGTGTTAATCAG
Found at i:42913981 original size:50 final size:50
Alignment explanation
Indices: 42913927--42914054 Score: 157
Period size: 50 Copynumber: 2.6 Consensus size: 50
42913917 ATGAACAAAT
* * * * *
42913927 GAGTTACTTAATGCAAGACTTACTTAAAGATGCACACTTAACTATAATGG
1 GAGTTACATAATGCAAGACATAATTAAAGATGCAAACTTAACTATAATGA
* * * * *
42913977 GAGTTACATAATGCATGTCATAATTTAATATGCAAACTTAACTATCATGA
1 GAGTTACATAATGCAAGACATAATTAAAGATGCAAACTTAACTATAATGA
*
42914027 GAGTTACATAATGCATGACATAATTAAA
1 GAGTTACATAATGCAAGACATAATTAAA
42914055 TCATGGACTT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (50 bp):
GAGTTACATAATGCAAGACATAATTAAAGATGCAAACTTAACTATAATGA
Found at i:42919410 original size:50 final size:50
Alignment explanation
Indices: 42919355--42919583 Score: 278
Period size: 50 Copynumber: 4.6 Consensus size: 50
42919345 CATTGAGATT
*
42919355 ATGAGAGGTCCCATGTAAGAACATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * *
42919405 ATGAGAGGTTCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * *
42919455 ATGAGAGGTCCCATGTAAGACCATGTCTGGGCCATGGCGTTGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * * * * * * *
42919505 ATGAGAGGTCCCCCGTAAGATCATGTTTGGGACATGGCATGGGCATCTAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** * *
42919555 ATGAGAACTCTCATGTAAGACCATATCTG
1 ATGAGAGGTCCCATGTAAGACCATGTCTG
42919584 AGATATGACA
Statistics
Matches: 152, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 152 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:42922905 original size:176 final size:175
Alignment explanation
Indices: 42922584--42922906 Score: 533
Period size: 176 Copynumber: 1.8 Consensus size: 175
42922574 AGGAGTTTGG
*
42922584 GAGAGTTTTACGGTTTTTTGGAGAGGATTGTCAGTGAAAACAAAAGAGAATAGAGTAAGCAATGA
1 GAGAGTTTTACGGTTTTTTGGAGAGGATTGTCAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
* *
42922649 ATTATTTATAAGAAGGGACCTCAACATCCATGGGTTTTGAAGTCTTTGGTATTAAATGGGTTGGT
66 ATTATTTATAAGAAGGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
*
42922714 TGGTCCTATGAGCAATAGAAATTTAGAGGTTCTTTTGCTAGATGA
131 TGGTCCTACGAGCAATAGAAATTTAGAGGTTCTTTTGCTAGATGA
*
42922759 GAGAGTTTTA-GGTTTTTTTTGGAGAGGATTTTCAGTGAAAACAAAAGAGAATAAAGTAAGCAAT
1 GAGAGTTTTACGG--TTTTTTGGAGAGGATTGTCAGTGAAAACAAAAGAGAATAAAGTAAGCAAT
* *
42922823 GAGTTATTTATAAGAAGGGACCTGAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTG
64 GAATTATTTATAAGAAGGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTG
*
42922888 GTTAGG-CTTACGAGCAATA
129 GTT-GGTCCTACGAGCAATA
42922907 AATTCATGAT
Statistics
Matches: 137, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
174 2 0.01
175 10 0.07
176 123 0.90
177 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.32
Consensus pattern (175 bp):
GAGAGTTTTACGGTTTTTTGGAGAGGATTGTCAGTGAAAACAAAAGAGAATAAAGTAAGCAATGA
ATTATTTATAAGAAGGGACCTCAACATCCATGGGTGTTGAAGTCTCTGGTATTAAATGGGTTGGT
TGGTCCTACGAGCAATAGAAATTTAGAGGTTCTTTTGCTAGATGA
Found at i:42923193 original size:194 final size:194
Alignment explanation
Indices: 42922873--42923236 Score: 466
Period size: 194 Copynumber: 1.9 Consensus size: 194
42922863 GAAGTCTCTG
** * ** * *
42922873 GTATTAAATGGGTTGGTTAGGCTTACGAGCAATAAATTCATGATTCAATGTTGATCGGCTAAGCC
1 GTATTAAATAAGTTGGTTAGGCTTACAAGCAATAAATTCATGAGCCAATATAGATCGGCTAAGCC
* * ** * *
42922938 TTGATAACCATGGATGTTGAGGTCCTTGGATTTTACTTCATTAGTACTTCTCTTGATAGTTAGGA
66 TTGATAACCATAGATGTTGAGGTCCTTGGATTATACACCATTAGTACTTCTCCTAATAGTTAGGA
*
42923003 GCACAAATTTCATGAAAAATTTT-TATCTCACGAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
131 GCACAAATTTCATG-AAAATTTTATATCTCACAAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
* * *
42923067 GTATTAAATAAGTTGGTTGGGCTTATAAGCAATAAATTCCTGAGCCAATATAGA-CTGGCTGAA-
1 GTATTAAATAAGTTGGTTAGGCTTACAAGCAATAAATTCATGAGCCAATATAGATC-GGCT-AAG
* *
42923130 CCTTGATAGCCATAGATGTTGAGGTTCTTAGG-TTATACACCATTAGTACTTCTCCTAATAGTTA
64 CCTTGATAACCATAGATGTTGAGGTCCTT-GGATTATACACCATTAGTACTTCTCCTAATAGTTA
* **
42923194 GGAGCACGAATTTTGTGAAAATTTTATATCTCACAAACCTTGA
128 GGAGCACAAATTTCATGAAAATTTTATATCTCACAAACCTTGA
42923237 TACCCATAGG
Statistics
Matches: 144, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
193 9 0.06
194 131 0.91
195 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (194 bp):
GTATTAAATAAGTTGGTTAGGCTTACAAGCAATAAATTCATGAGCCAATATAGATCGGCTAAGCC
TTGATAACCATAGATGTTGAGGTCCTTGGATTATACACCATTAGTACTTCTCCTAATAGTTAGGA
GCACAAATTTCATGAAAATTTTATATCTCACAAACCTTGAAATTCGTGAGTGTTGAGGTTTTTA
Found at i:42925042 original size:19 final size:18
Alignment explanation
Indices: 42925013--42925062 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
42925003 AAAAAAGATT
42925013 ATAAAAAAATAAATTTTA
1 ATAAAAAAATAAATTTTA
42925031 GA-AAAAATAATAAATTTTA
1 -ATAAAAA-AATAAATTTTA
42925050 ATAAAAAAATAAA
1 ATAAAAAAATAAA
42925063 AAATTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
ATAAAAAAATAAATTTTA
Found at i:42925058 original size:21 final size:19
Alignment explanation
Indices: 42925015--42925068 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
42925005 AAAAGATTAT
*
42925015 AAAAA-AATAAATTTTAGA
1 AAAAATAATAAATTTTAAA
42925033 AAAAATAATAAATTTTAATAA
1 AAAAATAATAAATTTT-A-AA
*
42925054 AAAAATAAAAAATTT
1 AAAAATAATAAATTT
42925069 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 5 0.16
19 10 0.32
20 1 0.03
21 15 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATAATAAATTTTAAA
Found at i:42925082 original size:17 final size:19
Alignment explanation
Indices: 42925062--42925101 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
42925052 AAAAAAATAA
42925062 AAAATTTA-AATTTTTT-T
1 AAAATTTAGAATTTTTTAT
42925079 AAAATTTAGAATTTTTTAT
1 AAAATTTAGAATTTTTTAT
42925098 AAAA
1 AAAA
42925102 ATAGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 8 0.38
19 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAAATTTAGAATTTTTTAT
Found at i:42925111 original size:10 final size:9
Alignment explanation
Indices: 42925098--42925139 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
42925088 AATTTTTTAT
42925098 AAAAATAGTA
1 AAAAATA-TA
*
42925108 AAAAATAAA
1 AAAAATATA
42925117 AAAAATAT-
1 AAAAATATA
42925125 AAAAATCATA
1 AAAAAT-ATA
42925135 AAAAA
1 AAAAA
42925140 ATTAACGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 6 0.21
9 10 0.36
10 12 0.43
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATATA
Found at i:42925141 original size:19 final size:19
Alignment explanation
Indices: 42925098--42925140 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
42925088 AATTTTTTAT
42925098 AAAAATAGTAAAAAATAAA
1 AAAAATAGTAAAAAATAAA
42925117 AAAAATA-TAAAAATCATAAA
1 AAAAATAGTAAAAA--ATAAA
42925137 AAAA
1 AAAA
42925141 TTAACGATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAATAGTAAAAAATAAA
Found at i:42925351 original size:29 final size:26
Alignment explanation
Indices: 42925318--42925420 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 26
42925308 TTACATTTTG
42925318 TATAATTTTCTTATGACTTTATAAAATTT
1 TATAATTTT-TTAT-A-TTTATAAAATTT
* *
42925347 TATAATTTTTTTATATTTCTATATATTT
1 TATAA-TTTTTTATATTTATA-AAATTT
42925375 TATAATTTTTTACTATTTTTATAAAATTT
1 TATAATTTTTTA-TA--TTTATAAAATTT
42925404 TATAATTTTTTATATTT
1 TATAATTTTTTATATTT
42925421 TTTATGATTT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.05
27 12 0.18
28 15 0.23
29 26 0.40
30 9 0.14
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (26 bp):
TATAATTTTTTATATTTATAAAATTT
Found at i:42925375 original size:19 final size:18
Alignment explanation
Indices: 42925343--42925445 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 18
42925333 ACTTTATAAA
42925343 ATTTTATA-ATTTTTTTAT
1 ATTTTATATA-TTTTTTAT
*
42925361 ATTTCTATATATTTTATA-
1 ATTT-TATATATTTTTTAT
* *
42925379 ATTTTTTACTATTTTTATAAA
1 ATTTTATA-TATTTTT-T-AT
42925400 ATTTTATA-ATTTTTTAT
1 ATTTTATATATTTTTTAT
*
42925417 ATTTTTTATGATTTTTATAT
1 ATTTTATAT-ATTTTT-TAT
42925437 ATTTT-TATA
1 ATTTTATATA
42925446 AAATTTAATA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
17 11 0.16
18 16 0.23
19 26 0.37
20 10 0.14
21 7 0.10
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (18 bp):
ATTTTATATATTTTTTAT
Found at i:42925386 original size:38 final size:35
Alignment explanation
Indices: 42925335--42925469 Score: 99
Period size: 38 Copynumber: 3.5 Consensus size: 35
42925325 TTCTTATGAC
*
42925335 TTTATAAAATTTTATAATTTTTTTATATTTCTATATAT
1 TTTATAAATTTTTAT-ATTTTTTTATATTT-TATA-AT
* * *
42925373 TTTATAATTTTTTACTATTTTTATAAAATTTTATAAT
1 TTTATAAATTTTTA-TATTTTT-TTATATTTTATAAT
* * *
42925410 TTTTTATATTTTTTATGATTTTTATATATTTTTATAAAAT
1 TTTATA-AATTTTTAT-ATTTTTTTATA-TTTTAT--AAT
*
42925450 TTAATAAATTTTTAATATTT
1 TTTATAAATTTTT-ATATTT
42925470 GAATTTTTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
37 10 0.13
38 42 0.54
39 17 0.22
40 9 0.12
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (35 bp):
TTTATAAATTTTTATATTTTTTTATATTTTATAAT
Found at i:42925440 original size:48 final size:49
Alignment explanation
Indices: 42925366--42925469 Score: 149
Period size: 48 Copynumber: 2.1 Consensus size: 49
42925356 TTTATATTTC
* *
42925366 TATATATTTTATAATTTTTTACTATTTTTATAAAATTTTAT-AATTTTT
1 TATATTTTTTATAATTTTTTACTATTTTTATAAAATTTAATAAATTTTT
*
42925414 TATATTTTTTATGATTTTTATA-TATTTTTATAAAATTTAATAAATTTTT
1 TATATTTTTTATAATTTTT-TACTATTTTTATAAAATTTAATAAATTTTT
*
42925463 AATATTT
1 TATATTT
42925470 GAATTTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 35 0.70
49 15 0.30
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (49 bp):
TATATTTTTTATAATTTTTTACTATTTTTATAAAATTTAATAAATTTTT
Found at i:42925443 original size:28 final size:27
Alignment explanation
Indices: 42925344--42925445 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 27
42925334 CTTTATAAAA
* *
42925344 TTTTATAATTTTTTTATATTTCTATAT
1 TTTTATAATTTTTATATATTTTTATAT
*
42925371 ATTTTATAATTTTT-TACTATTTTTATAAAA
1 -TTTTATAATTTTTATA-TATTTTTAT--AT
42925401 TTTTATAATTTTT-TATATTTTTTATGAT
1 TTTTATAATTTTTATATA-TTTTTAT-AT
42925429 TTTTATATATTTTTATA
1 TTTTATA-ATTTTTATA
42925446 AAATTTAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
27 2 0.03
28 31 0.48
29 28 0.44
30 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (27 bp):
TTTTATAATTTTTATATATTTTTATAT
Found at i:42925466 original size:11 final size:10
Alignment explanation
Indices: 42925335--42925463 Score: 90
Period size: 10 Copynumber: 13.4 Consensus size: 10
42925325 TTCTTATGAC
*
42925335 TTTATAAAAT
1 TTTATAAATT
42925345 TTTAT-AATT
1 TTTATAAATT
* *
42925354 TTTTTATATT
1 TTTATAAATT
* *
42925364 TCTATATA-T
1 TTTATAAATT
42925373 TTTAT-AATT
1 TTTATAAATT
*
42925382 TTT-TACTATT
1 TTTATA-AATT
*
42925392 TTTATAAAAT
1 TTTATAAATT
*
42925402 TTTATAATTT
1 TTTATAAATT
*
42925412 TTTAT-ATTT
1 TTTATAAATT
*
42925421 TTTAT-GATT
1 TTTATAAATT
*
42925430 TTTATATATT
1 TTTATAAATT
*
42925440 TTTATAAAAT
1 TTTATAAATT
*
42925450 TTAATAAATT
1 TTTATAAATT
42925460 TTTA
1 TTTA
42925464 ATATTTGAAT
Statistics
Matches: 93, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
8 2 0.02
9 32 0.34
10 57 0.61
11 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTATAAATT
Found at i:42925719 original size:88 final size:87
Alignment explanation
Indices: 42925546--42925742 Score: 219
Period size: 88 Copynumber: 2.3 Consensus size: 87
42925536 AATAAAAGCA
* * * *
42925546 AGGG-CTTAATTGCTTTTTTTTTGAAAAAGTTTGAGAGTCTTTTTTGATGCATTTTGAAAGGTAA
1 AGGGACTTAATTGC--TTTTTTT-AAAAAGATTGAGAGTCCTTTTTGATACATTTTAAAAGGTAA
* *
42925610 GTACTCAATTGAGTGCAAAAAAAAG
63 ATACTCAAATGAGTGCAAAAAAAAG
*
42925635 TAGGGACTTAATTGCTTTTTTTAAAAAGGATTGAGAG-CCTTTTTGATACATTTTAAAAGTTTAA
1 -AGGGACTTAATTGCTTTTTTTAAAAA-GATTGAGAGTCCTTTTTGATACATTTTAAAAG-GTAA
42925699 ATA-TCTAAATGAGTGC-AAAAAAAG
63 ATACTC-AAATGAGTGCAAAAAAAAG
42925723 A--GA-TTAATTGCTTTTTTTAA
1 AGGGACTTAATTGCTTTTTTTAA
42925743 CAAAAACTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
84 17 0.18
85 2 0.02
87 1 0.01
88 34 0.35
89 29 0.30
90 4 0.04
91 9 0.09
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (87 bp):
AGGGACTTAATTGCTTTTTTTAAAAAGATTGAGAGTCCTTTTTGATACATTTTAAAAGGTAAATA
CTCAAATGAGTGCAAAAAAAAG
Found at i:42928235 original size:21 final size:20
Alignment explanation
Indices: 42928201--42928239 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
42928191 TCTTTTAATC
*
42928201 TTTTAAAAGTTATTAAAAGT
1 TTTTAAAAGCTATTAAAAGT
42928221 TTTTAGAAAGCTATTAAAA
1 TTTTA-AAAGCTATTAAAA
42928240 TTGAGTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTAAAAGCTATTAAAAGT
Found at i:42929485 original size:2 final size:2
Alignment explanation
Indices: 42929480--42929514 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
42929470 CTCTCTCTCT
*
42929480 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC GC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
42929515 TACATACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:42935699 original size:55 final size:52
Alignment explanation
Indices: 42935541--42935699 Score: 180
Period size: 51 Copynumber: 3.0 Consensus size: 52
42935531 CCCTCAAGCC
* * * *
42935541 CTTTTACTTTCCCCCAAAAAATTGTACTCCCCCCAAACCCTCAAAAC-TTT-TT
1 CTTTTACTTTCCTCC-AAAACTTTTACTTCCCCCAAACCC-CAAAACTTTTATT
*
42935593 -TTTTACTTTCCTCTCAAAACTTTTACTTCCTCCAAACCCCTAAAACTTTTTATT
1 CTTTTACTTTCCTC-CAAAACTTTTACTTCCCCCAAACCCC-AAAAC-TTTTATT
42935647 CTTTTACTTTCTCTCCAAAACTTTTACTTCCCCCAAATCCCGCAAAACTTTTA
1 CTTTTACTTTC-CTCCAAAACTTTTACTTCCCCCAAA-CCC-CAAAACTTTTA
42935700 CTTTCTCCCA
Statistics
Matches: 92, Mismatches: 6, Indels: 15
0.81 0.05 0.13
Matches are distributed among these distances:
50 1 0.01
51 37 0.40
52 1 0.01
53 3 0.03
54 2 0.02
55 36 0.39
56 11 0.12
57 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.01, T:0.38
Consensus pattern (52 bp):
CTTTTACTTTCCTCCAAAACTTTTACTTCCCCCAAACCCCAAAACTTTTATT
Found at i:42935726 original size:28 final size:27
Alignment explanation
Indices: 42935662--42935725 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
42935652 ACTTTCTCTC
42935662 CAAAACTTTTACTTCCCCCAAATCCCG
1 CAAAACTTTTACTTCCCCCAAATCCCG
*
42935689 CAAAACTTTTACTTTCTCCCAAA-CCC-
1 CAAAACTTTTAC-TTCCCCCAAATCCCG
42935715 CAAAAACTTTT
1 C-AAAACTTTT
42935726 TTTTTCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 1 0.03
27 24 0.71
28 9 0.26
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.30
Consensus pattern (27 bp):
CAAAACTTTTACTTCCCCCAAATCCCG
Found at i:42936102 original size:19 final size:19
Alignment explanation
Indices: 42936078--42936115 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42936068 AAGTTAATAA
*
42936078 CAAATTTGATTATGGTGGG
1 CAAATTTGATTACGGTGGG
42936097 CAAATTTGATTACGGTGGG
1 CAAATTTGATTACGGTGGG
42936116 TGGCAGTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGG
Found at i:42937025 original size:9 final size:9
Alignment explanation
Indices: 42937008--42937044 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42936998 TGAATTTTCG
42937008 AATTCGAAT
1 AATTCGAAT
*
42937017 AACTCGAAT
1 AATTCGAAT
42937026 AATTCGAAT
1 AATTCGAAT
42937035 AATTCGAAT
1 AATTCGAAT
42937044 A
1 A
42937045 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42937463 original size:20 final size:18
Alignment explanation
Indices: 42937403--42937463 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
42937393 TATTTACTTT
42937403 CCCTCAAACTTTTATTC-C
1 CCCT-AAACTTTTATTCTC
* * *
42937421 CCCAAAATTTTTATTTTCC
1 CCCTAAACTTTTATTCT-C
42937440 CCCTAAACTTTTACTTCTC
1 CCCTAAACTTTTA-TTCTC
42937459 ACCCT
1 -CCCT
42937464 TTACTCTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 10 0.30
18 3 0.09
19 13 0.39
20 7 0.21
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (18 bp):
CCCTAAACTTTTATTCTC
Found at i:42942426 original size:29 final size:30
Alignment explanation
Indices: 42942337--42942451 Score: 99
Period size: 31 Copynumber: 3.8 Consensus size: 30
42942327 TAAGGTATCC
* *
42942337 AACACTGGTACATAGTACCTGATAAGATAAA
1 AACACCGGTACATAGTACCTGATAA-ATATA
** *
42942368 AACACCGACACATAGTGCCTGATACAATATA
1 AACACCGGTACATAGTACCTGATA-AATATA
* *
42942399 CACACCGGTACAAAGTACCTGAT-AATATA
1 AACACCGGTACATAGTACCTGATAAATATA
** *
42942428 GTCACCGGT-CTATAATACCTGATA
1 AACACCGGTAC-ATAGTACCTGATA
42942452 CTTTAAACCC
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.01
29 23 0.34
31 42 0.63
32 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (30 bp):
AACACCGGTACATAGTACCTGATAAATATA
Done.