Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 42 of 75
Found at i:13408387 original size:47 final size:47
Alignment explanation
Indices: 13408332--13408429 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
13408322 GCATACAAAA
13408332 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGT
1 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGT
*
13408379 ACATTGAATGATTTATGGGATGGGATGGTGAAATATGAGGAAAGGGT
1 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGT
13408426 ACAT
1 ACAT
13408430 CACATTTAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.36, C:0.03, G:0.34, T:0.28
Consensus pattern (47 bp):
ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGT
Found at i:13419214 original size:16 final size:18
Alignment explanation
Indices: 13419187--13419221 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13419177 CACTACCTCA
13419187 AAATTAACAAGATT-TGG
1 AAATTAACAAGATTATGG
13419204 AAATT-ACAAGATTATGG
1 AAATTAACAAGATTATGG
13419221 A
1 A
13419222 TATCACGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (18 bp):
AAATTAACAAGATTATGG
Found at i:13422849 original size:7 final size:7
Alignment explanation
Indices: 13422837--13422861 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13422827 ACACCACCAG
13422837 GAATTTT
1 GAATTTT
13422844 GAATTTT
1 GAATTTT
13422851 GAATTTT
1 GAATTTT
13422858 GAAT
1 GAAT
13422862 ACCTCAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (7 bp):
GAATTTT
Found at i:13431006 original size:12 final size:12
Alignment explanation
Indices: 13430989--13431022 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
13430979 TGGCCTACCC
13430989 ATATTAATTTTT
1 ATATTAATTTTT
*
13431001 ATATTATTTTTT
1 ATATTAATTTTT
13431013 ATA-TAATTTT
1 ATATTAATTTT
13431023 AAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:13431045 original size:17 final size:17
Alignment explanation
Indices: 13431025--13431071 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
13431015 ATAATTTTAA
13431025 AAAATATATAATACATC
1 AAAATATATAATACATC
*
13431042 AAAA-ATACTAAAAACATC
1 AAAATATA-T-AATACATC
*
13431060 AAAATAAATAAT
1 AAAATATATAAT
13431072 TCCCAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.12
17 7 0.29
18 12 0.50
19 2 0.08
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATATATAATACATC
Found at i:13431047 original size:18 final size:18
Alignment explanation
Indices: 13431024--13431063 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
13431014 TATAATTTTA
*
13431024 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
13431042 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
13431060 AAAA
1 AAAA
13431064 TAAATAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:13433179 original size:2 final size:2
Alignment explanation
Indices: 13433172--13433207 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13433162 AAACTACATA
13433172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13433208 AATTCTTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13433335 original size:18 final size:18
Alignment explanation
Indices: 13433312--13433348 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13433302 GAATTATTGT
13433312 CGCGGCAATAGTCGTGCC
1 CGCGGCAATAGTCGTGCC
13433330 CGCGGCAATAGTCGTGCC
1 CGCGGCAATAGTCGTGCC
13433348 C
1 C
13433349 ACAACATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (18 bp):
CGCGGCAATAGTCGTGCC
Found at i:13441006 original size:22 final size:22
Alignment explanation
Indices: 13440963--13441006 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
13440953 TGAACTTATA
**
13440963 ATTTTTATAATTTTCATTTTTT
1 ATTTTTATAATTTTCAAATTTT
* *
13440985 ATTTTTATACTTTTTAAATTTT
1 ATTTTTATAATTTTCAAATTTT
13441007 TTTCTTAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTTTTATAATTTTCAAATTTT
Found at i:13445981 original size:42 final size:42
Alignment explanation
Indices: 13445931--13446032 Score: 154
Period size: 40 Copynumber: 2.5 Consensus size: 42
13445921 TGATTCTGTA
*
13445931 CACCGGCATTAAGCCTGCTATAGATGTATAGTATGAAAATTT
1 CACCGGCATTAAGCCTGCTATAGACGTATAGTATGAAAATTT
* *
13445973 CACCGGCATTAAGCCTGC--TAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCTATAGACGTATAGTATGAAAATTT
*
13446013 CACTGGCATTAAGCCTGCTA
1 CACCGGCATTAAGCCTGCTA
13446033 GGCACAAGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
40 36 0.67
42 18 0.33
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTATAGACGTATAGTATGAAAATTT
Found at i:13447515 original size:13 final size:13
Alignment explanation
Indices: 13447497--13447521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13447487 TCAAACGATC
13447497 AAATTTTTATACG
1 AAATTTTTATACG
13447510 AAATTTTTATAC
1 AAATTTTTATAC
13447522 ATATTAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATTTTTATACG
Found at i:13449119 original size:21 final size:22
Alignment explanation
Indices: 13449095--13449141 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
13449085 AGTAGAGGAG
* *
13449095 ACACGGT-CGTGTGGTTGAGAT
1 ACACGGTCCGTGTGGCTAAGAT
13449116 ACAC-GTCCGTGTGGCTAAGAT
1 ACACGGTCCGTGTGGCTAAGAT
13449137 ACACG
1 ACACG
13449142 ACCGTGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.23
Consensus pattern (22 bp):
ACACGGTCCGTGTGGCTAAGAT
Found at i:13449146 original size:21 final size:21
Alignment explanation
Indices: 13449102--13449148 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
13449092 GAGACACGGT
* * *
13449102 CGTGTGGTTGAGATACACGTC
1 CGTGTGGCTAAGATACACGAC
13449123 CGTGTGGCTAAGATACACGAC
1 CGTGTGGCTAAGATACACGAC
13449144 CGTGT
1 CGTGT
13449149 ATACAGGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (21 bp):
CGTGTGGCTAAGATACACGAC
Found at i:13453290 original size:50 final size:50
Alignment explanation
Indices: 13453175--13453367 Score: 287
Period size: 50 Copynumber: 3.8 Consensus size: 50
13453165 GATAATAACA
* * ** *
13453175 TGCCAAAGTCATGTCCTAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
*
13453226 TGCCCATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
13453276 TACCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
13453326 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCT
13453368 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:13456335 original size:14 final size:13
Alignment explanation
Indices: 13456306--13456331 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13456296 CCTTTGTTTT
13456306 TTTTTTCAAACTG
1 TTTTTTCAAACTG
13456319 TTTTTTCAAACTG
1 TTTTTTCAAACTG
13456332 GTTTGATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTTTCAAACTG
Found at i:13461079 original size:20 final size:20
Alignment explanation
Indices: 13461054--13461093 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13461044 AATATTTTCT
*
13461054 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
13461074 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
13461094 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:13461096 original size:34 final size:35
Alignment explanation
Indices: 13461042--13461108 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
13461032 CAAACACCAA
* *
13461042 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
13461077 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
13461109 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:13461100 original size:14 final size:14
Alignment explanation
Indices: 13461077--13461116 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13461067 ACAGAAAAGT
*
13461077 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
13461091 AAATCATTTTACGG
1 AAAACATTTTACAG
13461105 AAAACATTTTAC
1 AAAACATTTTAC
13461117 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:13461488 original size:5 final size:5
Alignment explanation
Indices: 13461478--13461519 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
13461468 ATGTTGGATG
13461478 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TA
1 TATAC TATAC TATAC TATAC TATAC TATAC TATAC TATAC TA
13461520 ATTTGTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAC
Found at i:13466851 original size:13 final size:13
Alignment explanation
Indices: 13466833--13466857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13466823 TGAATATAGA
13466833 AGATGGTTAATGC
1 AGATGGTTAATGC
13466846 AGATGGTTAATG
1 AGATGGTTAATG
13466858 TAGAAATGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (13 bp):
AGATGGTTAATGC
Found at i:13468658 original size:11 final size:12
Alignment explanation
Indices: 13468595--13468660 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 12
13468585 AACTAATCCT
*
13468595 CTCTCAAATTTC
1 CTCTCAAATTTG
*
13468607 CTTTC-AATTTG
1 CTCTCAAATTTG
*
13468618 CTCT-TAATTTG
1 CTCTCAAATTTG
*
13468629 CTCTCAAA-TTC
1 CTCTCAAATTTG
13468640 CT-TCCAAATTT-
1 CTCT-CAAATTTG
13468651 CTCTCAAATT
1 CTCTCAAATT
13468661 CATATTTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
10 1 0.02
11 34 0.77
12 9 0.20
ACGTcount: A:0.24, C:0.27, G:0.03, T:0.45
Consensus pattern (12 bp):
CTCTCAAATTTG
Found at i:13468729 original size:51 final size:50
Alignment explanation
Indices: 13468622--13468730 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 50
13468612 AATTTGCTCT
* * **
13468622 TAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATTCATATTTAATC
1 TAATTTTCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAAAA
* * *
13468672 TCAATTTTCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCATATTTTAAAA
1 T-AATTTTCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATA-TTTAAAA
13468724 TAATTTT
1 TAATTTT
13468731 TAAAAAAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
50 3 0.06
51 40 0.82
52 6 0.12
ACGTcount: A:0.30, C:0.21, G:0.01, T:0.48
Consensus pattern (50 bp):
TAATTTTCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAAAA
Found at i:13471205 original size:22 final size:22
Alignment explanation
Indices: 13471137--13471304 Score: 161
Period size: 21 Copynumber: 7.6 Consensus size: 22
13471127 CCTAAACCCT
*
13471137 AAACCCT-AACCTTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
*
13471157 AAACCCTAAACCCTTGACTT-A
1 AAACCCTAAACCCTTAACTTAA
*
13471178 AAACCCTAAACCCTTGACTTAA
1 AAACCCTAAACCCTTAACTTAA
13471200 AAACCCTAAACCCATAACTTAACTTAA
1 AAACCCTAAA-CC----CTTAACTTAA
* * *
13471227 AAACTCTTTAACCCTAAACCTT--
1 AAAC-CCTAAACCCTTAA-CTTAA
13471249 AAACCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
13471270 AACCCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
13471292 AAACCCT-AACCCT
1 AAACCCTAAACCCT
13471305 AACCATAACC
Statistics
Matches: 126, Mismatches: 10, Indels: 23
0.79 0.06 0.14
Matches are distributed among these distances:
19 3 0.02
20 15 0.12
21 45 0.36
22 35 0.28
23 6 0.05
24 3 0.02
27 15 0.12
28 4 0.03
ACGTcount: A:0.41, C:0.33, G:0.01, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:13471207 original size:43 final size:41
Alignment explanation
Indices: 13471137--13471304 Score: 151
Period size: 43 Copynumber: 3.8 Consensus size: 41
13471127 CCTAAACCCT
* *
13471137 AAACCCT-AACCTTTAACTTAAAACCCTAAACCCTTGACTTA
1 AAACCCTAAACCCTTAACTTAAAACCCT-AACCCTTAACTTA
*
13471178 AAACCCTAAACCCTTGACTTAAAAACCCTAAACCCATAACTTAACTTAA
1 AAACCCTAAACCCTTAACTT-AAAACCCT-AA-CC----CTTAACTT-A
* * *
13471227 AAACTCTTTAACCCTAAACCTT-AAACCCTAACCCTTAACTTA
1 AAAC-CCTAAACCCTTAA-CTTAAAACCCTAACCCTTAACTTA
13471269 AAACCCCTAAACCCTTAACTTAAAAACCCTAACCCT
1 AAA-CCCTAAACCCTTAACTT-AAAACCCTAACCCT
13471305 AACCATAACC
Statistics
Matches: 104, Mismatches: 10, Indels: 24
0.75 0.07 0.17
Matches are distributed among these distances:
41 10 0.10
42 24 0.23
43 33 0.32
44 2 0.02
47 2 0.02
48 9 0.09
49 12 0.12
50 9 0.09
51 3 0.03
ACGTcount: A:0.41, C:0.33, G:0.01, T:0.24
Consensus pattern (41 bp):
AAACCCTAAACCCTTAACTTAAAACCCTAACCCTTAACTTA
Found at i:13471210 original size:70 final size:69
Alignment explanation
Indices: 13471130--13471291 Score: 195
Period size: 70 Copynumber: 2.3 Consensus size: 69
13471120 GACAAATCCT
**
13471130 AAACCCTAAACCCTAACCTTTAACTT-AAAAC-CCTAAACCCTTGA-CTTAAAACCCTAAACCCT
1 AAACCCTAAACCCTAA-C-TTAACTTAAAAACTCCTAAACCCTAAACCTT-AAACCCT-AACCCT
*
13471192 TGACTTAA
62 TAACTTAA
* *
13471200 AAACCCTAAACCCATAACTTAACTTAAAAACTCTTTAACCCTAAACCTTAAACCCTAACCCTTAA
1 AAACCCTAAACCC-TAACTTAACTTAAAAACTCCTAAACCCTAAACCTTAAACCCTAACCCTTAA
13471265 CTTAA
65 CTTAA
*
13471270 AACCCCTAAACCCTTAACTTAA
1 AAACCCTAAACCC-TAACTTAA
13471292 AAACCCTAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
69 7 0.09
70 52 0.64
71 19 0.23
72 3 0.04
ACGTcount: A:0.41, C:0.33, G:0.01, T:0.25
Consensus pattern (69 bp):
AAACCCTAAACCCTAACTTAACTTAAAAACTCCTAAACCCTAAACCTTAAACCCTAACCCTTAAC
TTAA
Found at i:13474672 original size:127 final size:126
Alignment explanation
Indices: 13474406--13474972 Score: 798
Period size: 127 Copynumber: 4.5 Consensus size: 126
13474396 CCCAAACATG
* * *
13474406 CTACTGTAGCAAAAGCACGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
13474471 TTGAAGC-GTTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTTTT-TCAGGAC
66 TTGAAGCATTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCT-AGGAC
* * *
13474531 CTACTGTAACAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATACTGT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
13474596 TTAAAGCATTTTTTAAAACTATTTGCTCAAAAACATCAAGTCGAAATTATTTTTTCTAGGAC
66 TTGAAGCATTTTTT-AAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCTAGGAC
*
13474658 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
13474723 TTGAAGCATTTTTTTAAATTATTTGCTTAGAAATGTCAAGTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCA-TTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCTAGGAC
* *
13474785 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
13474850 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTGC-AGGAC
66 TTGAAGCATTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCTAGGAC
* * * * * * *
13474910 CTACTGTAGCAAAAGCGCGTACACGTGGGCGTGACTTCAGAAATTATTCTGATAAAGCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
13474973 ACTTTGATTT
Statistics
Matches: 395, Mismatches: 43, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
125 126 0.32
126 44 0.11
127 218 0.55
128 7 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCATTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCTAGGAC
Found at i:13474921 original size:252 final size:252
Alignment explanation
Indices: 13474406--13474972 Score: 850
Period size: 252 Copynumber: 2.2 Consensus size: 252
13474396 CCCAAACATG
*
13474406 CTACTGTAGCAAAAGCACGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* * *
13474471 TTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTTTTTCAGGACCTACT
66 TTGAAGCGTTTTTAAACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTACT
* *
13474536 GTAACAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATACTGTTTAAA
131 GTAACAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAACATACTGCTTAAA
* * *
13474601 GCATTTTTTAAAACTATTTGCTCAAAAACATCAAGTCGAAATTATTTTTTCTAGGAC
196 GCATTTTTTAAAACTATTTGCTCAAAAACATCAACTCAAAATTATTTTTGCTAGGAC
* * *
13474658 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* * *
13474723 TTGAAGCATTTTTTTAAATTATTTGCTTAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTA
66 TTGAAGC--GTTTTTAAACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTA
* * * *
13474788 CTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAACATCCTGCTTG
129 CTGTAACAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAACATACTGCTTA
* * * *
13474853 AAGCGTTTTTT-ATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTGC-AGGAC
194 AAGCATTTTTTAAAACTATTTGCTCAAAAACATCAACTCAAAATTATTTTTGCTAGGAC
* * * * *
13474910 CTACTGTAGCAAAAGCGCGTACACGTGGGCGTGACTTCAGAAATTATTCTGATAAAGCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCT
13474973 ACTTTGATTT
Statistics
Matches: 282, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
252 128 0.45
253 35 0.12
254 119 0.42
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (252 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGTTTTTAAACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGACCTACT
GTAACAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAACATACTGCTTAAA
GCATTTTTTAAAACTATTTGCTCAAAAACATCAACTCAAAATTATTTTTGCTAGGAC
Found at i:13486490 original size:24 final size:27
Alignment explanation
Indices: 13486463--13486528 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 27
13486453 CTCTTTAACA
13486463 GCCACCTCCTCCTCCT-C-CC-CCACC
1 GCCACCTCCTCCTCCTCCACCACCACC
* *
13486487 GCCACTATCACAACCTCCTCCACCACCACC
1 GCCAC-CTC-C-TCCTCCTCCACCACCACC
13486517 GCCACCTCCTCC
1 GCCACCTCCTCC
13486529 CCAACTGCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 1 0.03
27 8 0.25
28 2 0.06
29 4 0.12
30 10 0.31
ACGTcount: A:0.17, C:0.64, G:0.05, T:0.15
Consensus pattern (27 bp):
GCCACCTCCTCCTCCTCCACCACCACC
Found at i:13488454 original size:2 final size:2
Alignment explanation
Indices: 13488447--13488479 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13488437 CGTAGACATC
*
13488447 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13488480 AATTAGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13501275 original size:113 final size:111
Alignment explanation
Indices: 13501108--13501644 Score: 586
Period size: 113 Copynumber: 4.8 Consensus size: 111
13501098 AAAATAAGAA
* * ** *
13501108 TTAGCGGCGTTTTAT-AGAAAGCGCCGCAAAAAACCTAAGCCGAACAACGTCGTTTACCGAGCTT
1 TTAGCGGCGTTTT-TGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACACCGTTT-CTGAGCTT
13501172 TCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGTTCAGGGCT
64 TCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGTT-AGGGCT
* *
13501221 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACACCG-TTTCTGAGCTTT
** *
13501286 CGAGTCA-TTAGTGGCGTTTTTAATAACA-CGCCGCTAATGCTTAGGGCT
65 CG-GGGATTTAGCGGCGTTTTTAATAA-AGCGCCGCTAATG-TTAGGGCT
* * * *
13501334 TTAGCGGCATTTTTGAAAAAGCGCCGCAAGAAAACCAAAGCACAACGACACCGTTTCTGAGCTTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAA-AAAACCTAAGCCCAACGACACCGTTTCTGAGC-TT
* * *
13501399 TCGGGGATTTAGCGGAGTTTCTAA-AGAAGCGCCGCTAATG-TAGGGAT
64 TCGGGGATTTAGCGGCGTTTTTAATA-AAGCGCCGCTAATGTTAGGGCT
* * * *
13501446 TTAGCGGCGTTTTTG-GAATAGCGCCGCAAAAAAAACTAAGCCCAATGGCACCGTTTTCTGTGCT
1 TTAGCGGCGTTTTTGAGAA-AGCGCCGC-AAAAAACCTAAGCCCAACGACACCG-TTTCTGAGCT
* * * * *
13501510 TTC-AGGATTTTGCGGCGTTTTT-TTAAAAGCGCCGCTAATGCTCAGCGCT
63 TTCGGGGATTTAGCGGCGTTTTTAAT-AAAGCGCCGCTAATG-TTAGGGCT
* * * * *
13501559 TTAGCGGCGTTTTTAAAAAAGCACCGCAAGAAAACCTAAGCCCAATGACACCGTTTCTTAGCCTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCAA-AAAACCTAAGCCCAACGACACCGTTTCTGAG-CTT
13501624 TCGGGGATTTAGCGGCGTTTT
64 TCGGGGATTTAGCGGCGTTTT
13501645 AGGTGTAGCG
Statistics
Matches: 358, Mismatches: 45, Indels: 41
0.81 0.10 0.09
Matches are distributed among these distances:
111 31 0.09
112 60 0.17
113 192 0.54
114 75 0.21
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (111 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCCAACGACACCGTTTCTGAGCTTTC
GGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGTTAGGGCT
Found at i:13501658 original size:225 final size:226
Alignment explanation
Indices: 13501108--13501645 Score: 662
Period size: 225 Copynumber: 2.4 Consensus size: 226
13501098 AAAATAAGAA
* * * ** *
13501108 TTAGCGGCG-TTTTATAGAAAGCGCCGCAA-AAAACCTAAGCCGAACAACGTCGTTTACCGAG-C
1 TTAGCGGCGTTTTTA-AAAAAGCGCCGCAAGAAAACCTAAGCCCAACGACACCGTTT-CTGAGCC
* *
13501170 TTTCGGGGATTTAGCGGCGTTTTTAATAAAGCGCCGCTAATGTTCAGGGCTTTAGCGGCGTTTTT
64 TTTCGGGGATTTAGCGGCG-TTTTAATGAAGCGCCGCTAATGTTCAGGGATTTAGCGGCGTTTTT
* * * *
13501235 GAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTTCTGAGCTTTCGAGTCATTAGTGG
128 GAGAAAGCGCCGCAAAAAAACTAAGCCCAACGACACCGTTTTCTGAGCTTTCGAGTCATTAGCGG
* * *
13501300 CGTTTTTAATAACACGCCGCTAATGCTTAGGGCT
193 CGTTTTTAATAAAACGCCGCTAATGCTCAGCGCT
* * * * *
13501334 TTAGCGGCATTTTTGAAAAAGCGCCGCAAGAAAACCAAAGCACAACGACACCGTTTCTGAGCTTT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCAAGAAAACCTAAGCCCAACGACACCGTTTCTGAGCCTT
* *
13501399 TCGGGGATTTAGCGGAGTTTCTAAAGAAGCGCCGCTAATG-T-AGGGATTTAGCGGCGTTTTTG-
66 TCGGGGATTTAGCGGCGTTT-TAATGAAGCGCCGCTAATGTTCAGGGATTTAGCGGCGTTTTTGA
* * * * *
13501461 GAATAGCGCCGCAAAAAAAACTAAGCCCAATGGCACCGTTTTCTGTGCTTTC-AG-GATTTTGCG
130 GAA-AGCGCCGC-AAAAAAACTAAGCCCAACGACACCGTTTTCTGAGCTTTCGAGTCA-TTAGCG
*
13501524 GCGTTTTT-TTAAAAGCGCCGCTAATGCTCAGCGCT
192 GCGTTTTTAATAAAA-CGCCGCTAATGCTCAGCGCT
* * *
13501559 TTAGCGGCGTTTTTAAAAAAGCACCGCAAGAAAACCTAAGCCCAATGACACCGTTTCTTAGCCTT
1 TTAGCGGCGTTTTTAAAAAAGCGCCGCAAGAAAACCTAAGCCCAACGACACCGTTTCTGAGCCTT
13501624 TCGGGGATTTAGCGGCGTTTTA
66 TCGGGGATTTAGCGGCGTTTTA
13501646 GGTGTAGCGC
Statistics
Matches: 267, Mismatches: 37, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
224 10 0.04
225 136 0.51
226 62 0.23
227 59 0.22
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.27
Consensus pattern (226 bp):
TTAGCGGCGTTTTTAAAAAAGCGCCGCAAGAAAACCTAAGCCCAACGACACCGTTTCTGAGCCTT
TCGGGGATTTAGCGGCGTTTTAATGAAGCGCCGCTAATGTTCAGGGATTTAGCGGCGTTTTTGAG
AAAGCGCCGCAAAAAAACTAAGCCCAACGACACCGTTTTCTGAGCTTTCGAGTCATTAGCGGCGT
TTTTAATAAAACGCCGCTAATGCTCAGCGCT
Found at i:13501727 original size:72 final size:73
Alignment explanation
Indices: 13501558--13501730 Score: 210
Period size: 72 Copynumber: 2.4 Consensus size: 73
13501548 TGCTCAGCGC
** * * *
13501558 TTTAGCGGCGTTTTTAAAAAAGCACCGCAAGAAAACCTAAGCCCAATGACACCGTTTCTTAGCCT
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAGAAAAACTAAGCCCAACGACACCGTTTCTTAGCCT
13501623 TTCGGGGA
66 TTCGGGGA
** **
13501631 TTTAGCGGCG-TTTTAGGTGTAGCGCCGCAA-AAAAACTAAGCCCAACGATGCCGTTTTCTGT-G
1 TTTAGCGGCGTTTTTAGG-AAAGCGCCGCAAGAAAAACTAAGCCCAACGACACCG-TTTCT-TAG
13501693 -CTTTCGGGGA
63 CCTTTCGGGGA
13501703 TTTAGCGGCGTTTTTAGGAAAGCGCCGC
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGC
13501731 TAATGCTCAG
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
72 52 0.61
73 32 0.38
74 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTAGGAAAGCGCCGCAAGAAAAACTAAGCCCAACGACACCGTTTCTTAGCCT
TTCGGGGA
Found at i:13502083 original size:16 final size:16
Alignment explanation
Indices: 13502062--13502131 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
13502052 TTTGGTTCGC
* *
13502062 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
13502078 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
13502094 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
*
13502110 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAGG
13502126 TGTAAT
1 TGTAAT
13502132 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:13502161 original size:45 final size:44
Alignment explanation
Indices: 13502110--13502200 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
13502100 GGAATAGATG
*
13502110 TGTAATGGAATAGAAGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
13502155 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
13502199 TG
1 TG
13502201 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.45
45 22 0.55
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:13502386 original size:18 final size:17
Alignment explanation
Indices: 13502365--13502399 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13502355 TTATTATTAA
*
13502365 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
13502383 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13502400 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:13502619 original size:18 final size:19
Alignment explanation
Indices: 13502596--13502632 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
13502586 TAAAATAATT
13502596 ATTATTACATAT-AATTTA
1 ATTATTACATATAAATTTA
13502614 ATTATTACATATAAATTTA
1 ATTATTACATATAAATTTA
13502633 GTTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTACATATAAATTTA
Found at i:13508968 original size:16 final size:16
Alignment explanation
Indices: 13508944--13508980 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
13508934 TAAGAAATCA
*
13508944 CAGCCATGTACTCCTG
1 CAGCTATGTACTCCTG
13508960 CAGCTATGTACTCCTG
1 CAGCTATGTACTCCTG
13508976 CAGCT
1 CAGCT
13508981 CCTGAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (16 bp):
CAGCTATGTACTCCTG
Found at i:13512569 original size:31 final size:32
Alignment explanation
Indices: 13512526--13512600 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
13512516 AATAAATTTT
* *
13512526 TTTAGGGGTTATGGTTTAGGGGTTAAAGGAG-
1 TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
* *
13512557 TTTAGGGTTTATGCTTTAAGGGTTAAAGGGGA
1 TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
13512589 TTTAGGGGTTAT
1 TTTAGGGGTTAT
13512601 ATATGGGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.23, C:0.01, G:0.37, T:0.39
Consensus pattern (32 bp):
TTTAGGGGTTATGCTTTAAGGGTTAAAGGAGA
Found at i:13514993 original size:44 final size:44
Alignment explanation
Indices: 13514943--13515026 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
13514933 AGCAAAATAA
* *
13514943 AAGTTGTGATAATTATACATTTAAAAACAATTATATTTTAGTAG
1 AAGTTGTGATAATTACACATTTAAAAACAATTATAATTTAGTAG
* *
13514987 AAGTTGTGATAATTACATATTTAAAAATAATTATAATTTA
1 AAGTTGTGATAATTACACATTTAAAAACAATTATAATTTA
13515027 ATTTACAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (44 bp):
AAGTTGTGATAATTACACATTTAAAAACAATTATAATTTAGTAG
Found at i:13515003 original size:256 final size:254
Alignment explanation
Indices: 13514640--13515107 Score: 599
Period size: 256 Copynumber: 1.8 Consensus size: 254
13514630 TATTTTTTTT
*
13514640 ATATTACTAAATTCACATTTAAAAAATTTAAAGTAAAATAAAAGCTGCGATAATTATACATTTAA
1 ATATTACTAAATTCACATTTAAAAAATTTAAAGCAAAATAAAAGCTGCGATAATTATACATTTAA
*
13514705 AATAATCATAATTTATTAAAAGTTGAAATTGAGACCAATTACACATTTAAAAATAATTATAATTT
66 AATAATCA-AATTTATTAAAAGTAGAAATTGAGACCAATTACACATTTAAAAATAATTATAATTT
* * * *
13514770 AATTTACAATTATTAATTAAAAAATGTTGTGCTAA-TTCTAAAATAAATTTATTACTTAAATAAA
130 AATTTACAATTATTAACTAAAAAA-ATTCTGCTAACTT-TAAAATAAAGTTATTACTTAAATAAA
*
13514834 AATCTAAGCTTAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
193 AATCTAAGCATAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
* * *
13514896 ATATTACTAAATTCACATTTAAAAATTAAATAGTTGAAGCAAAATAAAAGTTGTGATAATTATAC
1 ATATTACTAAATTCACATTT--AAA--AAAT--TTAAAGCAAAATAAAAGCTGCGATAATTATAC
** * * * *
13514961 ATTT-AAA-AA-C-AATTATATT-TTAGTAGAAGTTGTGA-TAATTACATATTTAAAAATAATTA
60 ATTTAAAATAATCAAATT-TATTAAAAGTAGAAATTGAGACCAATTACACATTTAAAAATAATTA
* * *
13515020 TAATTTAATTTACAATTATTAGCTAAAAAAATTCTGCTAACTTTAAAATAGAGTTATTACTTGAA
124 TAATTTAATTTACAATTATTAACTAAAAAAATTCTGCTAACTTTAAAATAAAGTTATTACTTAAA
* * *
13515085 TAGAACTCTAAGCATAGAATATA
189 TAAAAATCTAAGCATAAAATATA
13515108 AGAAAAAGTT
Statistics
Matches: 182, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
255 46 0.25
256 72 0.40
257 15 0.08
258 7 0.04
259 1 0.01
260 6 0.03
261 3 0.02
262 32 0.18
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (254 bp):
ATATTACTAAATTCACATTTAAAAAATTTAAAGCAAAATAAAAGCTGCGATAATTATACATTTAA
AATAATCAAATTTATTAAAAGTAGAAATTGAGACCAATTACACATTTAAAAATAATTATAATTTA
ATTTACAATTATTAACTAAAAAAATTCTGCTAACTTTAAAATAAAGTTATTACTTAAATAAAAAT
CTAAGCATAAAATATAGGGAAAACGTTAAATATAATTATAATTATAATTATTTTCAATC
Found at i:13534234 original size:21 final size:21
Alignment explanation
Indices: 13534208--13534247 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13534198 AATGGGACCA
13534208 CTGATGTGGCAAGTTAACTAG
1 CTGATGTGGCAAGTTAACTAG
*
13534229 CTGATGTGGCCAGTTAACT
1 CTGATGTGGCAAGTTAACT
13534248 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
CTGATGTGGCAAGTTAACTAG
Found at i:13535804 original size:58 final size:58
Alignment explanation
Indices: 13535740--13535857 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
13535730 ATTACTAATT
13535740 TAAAACTTTATAAATTATAAATGGCCTAAATAAAACAATTTCATTTTAGGGAATACAA
1 TAAAACTTTATAAATTATAAATGGCCTAAATAAAACAATTTCATTTTAGGGAATACAA
*
13535798 TAAAACTTTATAAATTATAAATGGCCTAAATAAAACAATTTCATTTTAGGGAATATAA
1 TAAAACTTTATAAATTATAAATGGCCTAAATAAAACAATTTCATTTTAGGGAATACAA
13535856 TA
1 TA
13535858 TTATAATTGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (58 bp):
TAAAACTTTATAAATTATAAATGGCCTAAATAAAACAATTTCATTTTAGGGAATACAA
Found at i:13536130 original size:19 final size:20
Alignment explanation
Indices: 13536108--13536158 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
13536098 TCACACAAAG
13536108 TAAAAAAAAATTTAAAAAA-
1 TAAAAAAAAATTTAAAAAAT
13536127 T--AAAAAAA--TAAAAAAT
1 TAAAAAAAAATTTAAAAAAT
13536143 TAATAAAAAAATTTAA
1 TAA-AAAAAAATTTAA
13536159 TAGAAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
15 7 0.27
16 1 0.04
17 7 0.27
19 8 0.31
21 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAAAAAATTTAAAAAAT
Found at i:13536581 original size:144 final size:145
Alignment explanation
Indices: 13536321--13536607 Score: 461
Period size: 144 Copynumber: 2.0 Consensus size: 145
13536311 GTAAAAATAT
* * * *
13536321 AATTTCATCATTTTAATAGTCTCTATCTTTATACTTTTTAAAGGATTAAATTAAAATTTTATCAT
1 AATTTCACCATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
* *
13536386 TTTTAGGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTCAAAGGGCC
66 TTTTAGGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAAGTTTAAAAATTTCAAAGGGCA
13536451 TAAAT-GAAAATTAC
131 TAAATAGAAAATTAC
13536465 AATTTCACCATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
1 AATTTCACCATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
* * * *
13536530 TTTTAAGGGGGG-CAAAGTGTAATTTTATCTTTATTAATTTAAAAGTTTAAAAATTTCAAAGGGC
66 TTTT-AGGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAAGTTTAAAAATTTCAAAGGGC
13536594 ATAAATAGAAAATT
130 ATAAATAGAAAATT
13536608 TTCCATTTTA
Statistics
Matches: 131, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
144 117 0.89
145 14 0.11
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40
Consensus pattern (145 bp):
AATTTCACCATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
TTTTAGGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAAGTTTAAAAATTTCAAAGGGCA
TAAATAGAAAATTAC
Found at i:13537247 original size:3 final size:3
Alignment explanation
Indices: 13537235--13537283 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
13537225 AACATAGTTG
13537235 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13537281 TAT
1 TAT
13537284 AACATACATG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:13542275 original size:13 final size:13
Alignment explanation
Indices: 13542257--13542286 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13542247 GCACTAAAAG
*
13542257 ACAACAGAAGCAA
1 ACAACAGAAACAA
13542270 ACAACAGAAACAA
1 ACAACAGAAACAA
13542283 ACAA
1 ACAA
13542287 AAACAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.23, G:0.10, T:0.00
Consensus pattern (13 bp):
ACAACAGAAACAA
Found at i:13543241 original size:12 final size:12
Alignment explanation
Indices: 13543221--13543253 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13543211 ATAAAAAAAC
13543221 ATTTTATTTAAT
1 ATTTTATTTAAT
*
13543233 ATTTCATTTAAT
1 ATTTTATTTAAT
13543245 -TTTTATTTA
1 ATTTTATTTA
13543254 TTTACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTATTTAAT
Found at i:13549625 original size:34 final size:34
Alignment explanation
Indices: 13549581--13549664 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
13549571 TTTAGCTTTT
* * *
13549581 ATATATTTTATATTTTATAGATATATACATATTC
1 ATATTTTTTATATTTTAAAGATATATACATATAC
** * *
13549615 AT-TTCTTTTATGCTGTAAATATATATACATATAC
1 ATATT-TTTTATATTTTAAAGATATATACATATAC
13549649 ATATTTTTTATATTTT
1 ATATTTTTTATATTTT
13549665 CATTTTACTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
33 1 0.03
34 35 0.92
35 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.55
Consensus pattern (34 bp):
ATATTTTTTATATTTTAAAGATATATACATATAC
Found at i:13551293 original size:13 final size:13
Alignment explanation
Indices: 13551275--13551300 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13551265 AAAGAGATTT
13551275 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
13551288 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
13551301 AAAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:13551371 original size:19 final size:20
Alignment explanation
Indices: 13551331--13551374 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
13551321 GTCTCTTTTC
* *
13551331 GCATT-CATTTCATGCATTT
1 GCATTACATTACATGCATAT
13551350 GCATTACATTACAT-CATAT
1 GCATTACATTACATGCATAT
13551369 GCATTA
1 GCATTA
13551375 AAGATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (20 bp):
GCATTACATTACATGCATAT
Found at i:13553250 original size:19 final size:19
Alignment explanation
Indices: 13553226--13553265 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13553216 GCAAATATTC
*
13553226 TTTCATT-CTTTACGATTTT
1 TTTCATTCCTTCA-GATTTT
13553245 TTTCATTCCTTCAGATTTT
1 TTTCATTCCTTCAGATTTT
13553264 TT
1 TT
13553266 CTGCCAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTCATTCCTTCAGATTTT
Found at i:13554214 original size:21 final size:21
Alignment explanation
Indices: 13554190--13554233 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13554180 AAAAGTGATG
*
13554190 TGAAAAAT-AAAAAGATGAAAA
1 TGAAAAATGAAAAAG-TAAAAA
13554211 TGAAAAATGAAAAAGTAAAAA
1 TGAAAAATGAAAAAGTAAAAA
13554232 TG
1 TG
13554234 TAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (21 bp):
TGAAAAATGAAAAAGTAAAAA
Found at i:13557029 original size:46 final size:45
Alignment explanation
Indices: 13556947--13557036 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 45
13556937 AAGTTGCAAT
* *
13556947 GGGGCAGACTAAGGAAGCAAGTCTTATCCTCTTGAAGTTACAGTA
1 GGGGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTA
** *
13556992 GGGGCAGACTGAAGGTTGCAAATCTTAT-CTCCCTGAAGTTGCAGT
1 GGGGCAGACT-AAGGAAGCAAATCTTATCCT-CCTGAAGTTACAGT
13557037 GGAGCGGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
45 12 0.32
46 26 0.68
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (45 bp):
GGGGCAGACTAAGGAAGCAAATCTTATCCTCCTGAAGTTACAGTA
Found at i:13558940 original size:34 final size:34
Alignment explanation
Indices: 13558896--13558979 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
13558886 TTTAGCTTTT
* * *
13558896 ATATATTTTATATTTTATA-GATATATACATATTC
1 ATATTTTTTATATTTTAAATG-TATATACATATAC
** *
13558930 AT-TTCTTTTATGCTGTAAATGTATATACATATAC
1 ATATT-TTTTATATTTTAAATGTATATACATATAC
13558964 ATATTTTTTATATTTT
1 ATATTTTTTATATTTT
13558980 CATTTTANNN
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
33 1 0.03
34 34 0.89
35 3 0.08
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (34 bp):
ATATTTTTTATATTTTAAATGTATATACATATAC
Found at i:13565589 original size:42 final size:43
Alignment explanation
Indices: 13565541--13565663 Score: 160
Period size: 42 Copynumber: 2.9 Consensus size: 43
13565531 TAGGATTCCG
* *
13565541 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCGT-T
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
* * *
13565583 GTATATGATTTCGTGTAAGA-CACTGTCTGGGACAGTGGCATCA
1 ATATATGATTACGTGTAAGACCA-TGTCTGGGACATTGGCATCA
* *
13565626 ATATTTGATTACATGTAAGACCATGTCTGGGACATTGG
1 ATATATGATTACGTGTAAGACCATGTCTGGGACATTGG
13565664 AATTGTACGA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 34 0.50
43 30 0.44
44 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (43 bp):
ATATATGATTACGTGTAAGACCATGTCTGGGACATTGGCATCA
Found at i:13570945 original size:17 final size:19
Alignment explanation
Indices: 13570906--13570957 Score: 81
Period size: 18 Copynumber: 2.8 Consensus size: 19
13570896 AGCAAGAAAC
13570906 TTGAGTTGAGCTCGCATCTT
1 TTGA-TTGAGCTCGCATCTT
13570926 TTGA-TGAGCTCGCA-CTT
1 TTGATTGAGCTCGCATCTT
13570943 TTGATTGAGCTCGCA
1 TTGATTGAGCTCGCA
13570958 AATGTAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.23
18 20 0.65
20 4 0.13
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (19 bp):
TTGATTGAGCTCGCATCTT
Found at i:13573730 original size:44 final size:43
Alignment explanation
Indices: 13573651--13573993 Score: 179
Period size: 43 Copynumber: 7.9 Consensus size: 43
13573641 AAAAGCATGT
* * * * * *
13573651 TTTTAGCGACGTTTGT-GAAAAATCGTCGCTAAAAGTCATTTC
1 TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCATATC
* ** *
13573693 TTTATAGCGGCATTTGTAATAGAAGCGCCGCTAAAAGTCACGAT-
1 TTT-TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCA-TATC
* * * *
13573737 TTTTAGCGGCGTTTGTGGCAAAAGCGCAGCTAAAGGTCATGATC
1 TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCAT-ATC
*
13573781 -TTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATC
1 TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCAT-ATC
* * * *
13573824 -TTTAGCGGCGTTT-TTGCACATAAACGCCGCCTTTTTTAAAAGT--TATG
1 TTTTAGCGGCGTTTGTAG--CAGAAGCGCCG-C-----TAAAAGTCATATC
* * *
13573871 TTTTAGCGGCGTTTGTA-AAAAAGCGTCGCTAAAAGTCA-ATC
1 TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCATATC
* * ** * * *
13573912 TTCTAGCTGCGTTTGTAATAGAAGTGCTGCTAAATGTCATGA-C
1 TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCAT-ATC
* * * *
13573955 CTTTAGCGGCGTTT-TCAG-AAAAGCGCCACTAAAGGTCAT
1 TTTTAGCGGCGTTTGT-AGCAGAAGCGCCGCTAAAAGTCAT
13573994 GGTCTATAGC
Statistics
Matches: 232, Mismatches: 48, Indels: 42
0.72 0.15 0.13
Matches are distributed among these distances:
40 7 0.03
41 17 0.07
42 37 0.16
43 108 0.47
44 30 0.13
45 3 0.01
46 7 0.03
47 2 0.01
48 14 0.06
49 1 0.00
50 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
TTTTAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAAGTCATATC
Found at i:13573745 original size:43 final size:43
Alignment explanation
Indices: 13573697--13574094 Score: 262
Period size: 43 Copynumber: 9.3 Consensus size: 43
13573687 CATTTCTTTA
* ** * * *
13573697 TAGCGGCATTTGTAATAGAAGCGCCGCTAAAAGTCACGATTTT
1 TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
* * *
13573740 TAGCGGCGTTTGTGGCAAAAGCGCAGCTAAAGGTCATGATCTT
1 TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
13573783 TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
1 TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
* * * * *
13573826 TAGCGGCGTTT-TTGCACATAAACGCCGCCTTTTTTAAAAGTTATG-T-TT
1 TAGCGGCGTTTGTAG--CAGAAGCGCCG-C-----TAAAGGTCATGATCTT
* * * *
13573874 TAGCGGCGTTTGTA-AAAAAGCGTCGCTAAAAGTCA--ATCTT
1 TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
* ** * * * *
13573914 CTAGCTGCGTTTGTAATAGAAGTGCTGCTAAATGTCATGACCTT
1 -TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
* * * *
13573958 TAGCGGCGTTT-TCAG-AAAAGCGCCACTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGT-AGCAGAAGCGCCGCTAAAGGTCATGATCTT
* * * * * *
13574000 TAGCAGCGTCTTTTGGGAG-A-CGTCGCTAAAGGTCATGACCTT
1 TAGCGGCGT-TTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
* * *
13574042 TAGCGGCG-TTGTGGC-GAAATCGCCGCTAAAGGTCATGACCTT
1 TAGCGGCGTTTGTAGCAG-AAGCGCCGCTAAAGGTCATGATCTT
13574084 TAGCGGCGTTT
1 TAGCGGCGTTT
13574095 ATTTTAAAAA
Statistics
Matches: 279, Mismatches: 53, Indels: 46
0.74 0.14 0.12
Matches are distributed among these distances:
39 2 0.01
40 15 0.05
41 14 0.05
42 98 0.35
43 102 0.37
44 15 0.05
45 2 0.01
46 7 0.03
48 13 0.05
49 2 0.01
50 9 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTAGCAGAAGCGCCGCTAAAGGTCATGATCTT
Found at i:13573795 original size:86 final size:86
Alignment explanation
Indices: 13573650--13573836 Score: 227
Period size: 86 Copynumber: 2.2 Consensus size: 86
13573640 TAAAAGCATG
* * * *
13573650 TTTTTAGCGACGTTTGTGAAAAATCGTCGCTAAAAGTCATTTCTTTATAGCGGCATTTGTAATAG
1 TTTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAAGTCATATCTTTATAGCGGCATTTGTAACAG
13573715 AAGCGCCGCTAAAAGTCACGA
66 AAGCGCCGCTAAAAGTCACGA
* * * *
13573736 TTTTTAGCGGCGTTTGTGGCAAAAGCG-CAGCTAAAGGTCATGATC-TT-TAGCGGCGTTTGTAG
1 TTTTTAGCGGCGTTTGT-GAAAAAGCGTC-GCTAAAAGTCAT-ATCTTTATAGCGGCATTTGTAA
* *
13573798 CAGAAGCGCCGCTAAAGGTCATGA
63 CAGAAGCGCCGCTAAAAGTCACGA
*
13573822 TCTTTAGCGGCGTTT
1 TTTTTAGCGGCGTTT
13573837 TTGCACATAA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
86 65 0.75
87 20 0.23
88 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (86 bp):
TTTTTAGCGGCGTTTGTGAAAAAGCGTCGCTAAAAGTCATATCTTTATAGCGGCATTTGTAACAG
AAGCGCCGCTAAAAGTCACGA
Found at i:13574069 original size:42 final size:40
Alignment explanation
Indices: 13573940--13574094 Score: 143
Period size: 42 Copynumber: 3.7 Consensus size: 40
13573930 TAGAAGTGCT
* *
13573940 GCTAAATGTCATGACCTTTAGCGGCGTTT-TCAGAAAAGCGCC
1 GCTAAAGGTCATGACCTTTAGCGGCGTTTGGC-G-AAA-CGCC
* ** * * * *
13573982 ACTAAAGGTCATGGTCTATAGCAGCGTCTTTTGG-GAGACGTC
1 GCTAAAGGTCATGACCTTTAGC-G-G-CGTTTGGCGAAACGCC
13574024 GCTAAAGGTCATGACCTTTAGCGGCGTTGTGGCGAAATCGCC
1 GCTAAAGGTCATGACCTTTAGCGGCGTT-TGGCGAAA-CGCC
13574066 GCTAAAGGTCATGACCTTTAGCGGCGTTT
1 GCTAAAGGTCATGACCTTTAGCGGCGTTT
13574095 ATTTTAAAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
39 3 0.03
40 4 0.04
41 5 0.06
42 69 0.77
43 3 0.03
44 2 0.02
45 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GCTAAAGGTCATGACCTTTAGCGGCGTTTGGCGAAACGCC
Found at i:13576354 original size:40 final size:40
Alignment explanation
Indices: 13576299--13576383 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
13576289 CCTCCTACTA
13576299 AAAATTTGGTAAATCGGTCCTTATACGTTAGACAAAGAGC
1 AAAATTTGGTAAATCGGTCCTTATACGTTAGACAAAGAGC
13576339 AAAATTTGGTAAATCGGTCCTTATACGTTAGACAAAGAGC
1 AAAATTTGGTAAATCGGTCCTTATACGTTAGACAAAGAGC
13576379 AAAAT
1 AAAAT
13576384 AGTCATTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (40 bp):
AAAATTTGGTAAATCGGTCCTTATACGTTAGACAAAGAGC
Found at i:13581584 original size:17 final size:17
Alignment explanation
Indices: 13581562--13581595 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13581552 TCTGTTCTGA
13581562 TGAATTTAATAAACTGT
1 TGAATTTAATAAACTGT
13581579 TGAATTTAATAAACTGT
1 TGAATTTAATAAACTGT
13581596 GCAAGTCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TGAATTTAATAAACTGT
Found at i:13587814 original size:10 final size:10
Alignment explanation
Indices: 13587801--13587828 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
13587791 TACTATTATT
13587801 TTTTATTTGG
1 TTTTATTTGG
13587811 TTTTATTTGG
1 TTTTATTTGG
13587821 TTTTATTT
1 TTTTATTT
13587829 TTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.75
Consensus pattern (10 bp):
TTTTATTTGG
Found at i:13596023 original size:23 final size:23
Alignment explanation
Indices: 13595993--13596056 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
13595983 ATTTCTTCCA
*
13595993 GCATGGCCACCTTTGCATGTCGT
1 GCATGGCCACCTTTGCATATCGT
*
13596016 GCATGGCCACCTTTTCATATCGT
1 GCATGGCCACCTTTGCATATCGT
13596039 GCATGGCCACCTTTGCAT
1 GCATGGCCACCTTTGCAT
13596057 TGGAACTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (23 bp):
GCATGGCCACCTTTGCATATCGT
Found at i:13612348 original size:29 final size:29
Alignment explanation
Indices: 13612308--13612366 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13612298 GAATAAAAAC
*
13612308 TATATTTTTTATTTTTAAAATATACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
13612337 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
13612366 T
1 T
13612367 TTAAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:13613698 original size:5 final size:5
Alignment explanation
Indices: 13613690--13613737 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
13613680 CGAACAAATA
* *
13613690 ATTCG ATTCG ATTCG ATTCG ATCTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG AT-TCG AT-TCG ATTCG ATTCG ATTCG AT
13613738 AAAACTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 2 0.05
5 29 0.76
6 7 0.18
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:13613810 original size:5 final size:5
Alignment explanation
Indices: 13613800--13613825 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13613790 CTCGAAAATT
13613800 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
13613826 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:13618409 original size:36 final size:36
Alignment explanation
Indices: 13618362--13618451 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
13618352 GGGTCAGAGG
13618362 TCAAAACGGCGTCTTTTTGGCCTCTAAACCTAAAAA
1 TCAAAACGGCGTCTTTTTGGCCTCTAAACCTAAAAA
* *
13618398 TCAAAGCGGCGT-TGTTTTGGCCTCTGAACCTAAAAA
1 TCAAAACGGCGTCT-TTTTGGCCTCTAAACCTAAAAA
*
13618434 TCAAAACGGCGTCATTTT
1 TCAAAACGGCGTCTTTTT
13618452 ATTTATGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.02
36 47 0.98
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (36 bp):
TCAAAACGGCGTCTTTTTGGCCTCTAAACCTAAAAA
Found at i:13620882 original size:16 final size:16
Alignment explanation
Indices: 13620861--13620893 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13620851 ACAAATTTAC
13620861 TGAGTTTTTGAGGTTA
1 TGAGTTTTTGAGGTTA
*
13620877 TGAGTTTTTGAGTTTA
1 TGAGTTTTTGAGGTTA
13620893 T
1 T
13620894 CAAAATCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (16 bp):
TGAGTTTTTGAGGTTA
Found at i:13629024 original size:12 final size:11
Alignment explanation
Indices: 13629007--13629041 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
13628997 AACAAATCCT
13629007 CTCTCATATTTC
1 CTCTCA-ATTTC
13629019 CTCTCAA-TTC
1 CTCTCAATTTC
13629029 CTCTCAATTTC
1 CTCTCAATTTC
13629040 CT
1 CT
13629042 TCCAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:13629145 original size:22 final size:22
Alignment explanation
Indices: 13629032--13629138 Score: 214
Period size: 22 Copynumber: 4.9 Consensus size: 22
13629022 TCAATTCCTC
13629032 TCAATTTCCTTCCAAAATTATT
1 TCAATTTCCTTCCAAAATTATT
13629054 TCAATTTCCTTCCAAAATTATT
1 TCAATTTCCTTCCAAAATTATT
13629076 TCAATTTCCTTCCAAAATTATT
1 TCAATTTCCTTCCAAAATTATT
13629098 TCAATTTCCTTCCAAAATTATT
1 TCAATTTCCTTCCAAAATTATT
13629120 TCAATTTCCTTCCAAAATT
1 TCAATTTCCTTCCAAAATT
13629139 CTCTCAAATC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 85 1.00
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTATT
Found at i:13629171 original size:29 final size:29
Alignment explanation
Indices: 13629139--13629225 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
13629129 TTCCAAAATT
*
13629139 CTCTCAAATCCATATTTAATTTTAATTTC
1 CTCTCAAATCCATATTTAATTTAAATTTC
* *
13629168 CTCTCAATTTCC----TTAA---AAAATT-
1 CTCTCAA-ATCCATATTTAATTTAAATTTC
*
13629190 CTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAAATCCATATTTAATTTAAATTTC
13629219 CTCTCAA
1 CTCTCAA
13629226 TTTCCTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 18
0.64 0.09 0.27
Matches are distributed among these distances:
21 3 0.07
22 7 0.16
23 4 0.09
25 4 0.09
26 4 0.09
28 4 0.09
29 14 0.33
30 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (29 bp):
CTCTCAAATCCATATTTAATTTAAATTTC
Found at i:13629175 original size:51 final size:51
Alignment explanation
Indices: 13629120--13629232 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
13629110 CAAAATTATT
** *
13629120 TCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTTAATTTCCTC
1 TCAATTTCCTTAAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTC
13629171 TCAATTTCCTTAAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTC
1 TCAATTTCCTTAAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTC
13629222 TCAATTTCCTT
1 TCAATTTCCTT
13629233 TTTTAAAATA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (51 bp):
TCAATTTCCTTAAAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCTC
Found at i:13630139 original size:7 final size:7
Alignment explanation
Indices: 13630129--13630153 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13630119 ATTCGATTGA
13630129 TATTTAG
1 TATTTAG
13630136 TATTTAG
1 TATTTAG
13630143 TATTTAG
1 TATTTAG
13630150 TATT
1 TATT
13630154 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:13635491 original size:125 final size:126
Alignment explanation
Indices: 13635269--13635621 Score: 530
Period size: 126 Copynumber: 2.8 Consensus size: 126
13635259 CCCAAACATG
* * * *
13635269 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
13635334 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-ATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * * *
13635394 CTACTGTAGCAAAAGAGCG-CTGACGATGCCGCGATTTCACAAATTTTTCTCAACTAGCATCCTG
1 CTACTGTAGCAAAAGAGCGTC-CACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
13635458 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * * *
13635520 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
13635585 TAGAAGCGATTTTATATTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAA
13635622 CTCGAAATTA
Statistics
Matches: 203, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
124 1 0.00
125 96 0.47
126 105 0.52
127 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGAGCGTCCACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
Found at i:13635571 original size:126 final size:125
Alignment explanation
Indices: 13635269--13635647 Score: 553
Period size: 125 Copynumber: 3.0 Consensus size: 125
13635259 CCCAAACATG
* *
13635269 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
13635334 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
* * * * * *
13635394 CTACTGTAGCAAAAGAGCG-CTGACGATGCCGCGATTTCACAAATTTTTCTCAACTAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
13635458 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
65 CTAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTCCATGAC
* *
13635520 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** **** *
13635585 TAGAAGCGATTTTATATTATTTTATCAGAAACGTCAACTCGAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
13635645 CTA
1 CTA
13635648 AAAACCCTTA
Statistics
Matches: 224, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
124 1 0.00
125 116 0.52
126 106 0.47
127 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATATTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTCCATGAC
Found at i:13637330 original size:26 final size:26
Alignment explanation
Indices: 13637269--13637330 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 26
13637259 ATGCTTTGGG
* *
13637269 ATTAATAAGATTATTATTAAATATATT
1 ATTAATAA-AATACTATTAAATATATT
13637296 -TTAAT--AATACTATT-AATATATTT
1 ATTAATAAAATACTATTAAATATA-TT
13637319 ATTAATAAAATA
1 ATTAATAAAATA
13637331 TGAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 5 0.17
26 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTAATAAAATACTATTAAATATATT
Found at i:13647443 original size:26 final size:26
Alignment explanation
Indices: 13647382--13647443 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 26
13647372 ATGCTTTGGG
* *
13647382 ATTAATAAGATTATTATTAAATATATT
1 ATTAATAA-AATACTATTAAATATATT
13647409 -TTAAT--AATACTATT-AATATATTT
1 ATTAATAAAATACTATTAAATATA-TT
13647432 ATTAATAAAATA
1 ATTAATAAAATA
13647444 TGAATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 6 0.21
23 9 0.31
24 5 0.17
26 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTAATAAAATACTATTAAATATATT
Found at i:13660584 original size:25 final size:26
Alignment explanation
Indices: 13660546--13660597 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
13660536 AGTTGTAAAT
13660546 TGGAAAAATATCTTCAG-AAATTTTC
1 TGGAAAAATATCTTCAGAAAATTTTC
* * *
13660571 TGGAACAATCTCTTTAGAAAATTTTC
1 TGGAAAAATATCTTCAGAAAATTTTC
13660597 T
1 T
13660598 CTCTATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (26 bp):
TGGAAAAATATCTTCAGAAAATTTTC
Found at i:13663410 original size:20 final size:21
Alignment explanation
Indices: 13663365--13663417 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
13663355 ATGTCAAATA
*
13663365 TATTTTTATTTATGAAAAGTG
1 TATTTTTATTTATAAAAAGTG
*
13663386 AATTTTT-TTTATAAAAGAGT-
1 TATTTTTATTTATAAAA-AGTG
*
13663406 TATTTTGATTTA
1 TATTTTTATTTA
13663418 ACAATCAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (21 bp):
TATTTTTATTTATAAAAAGTG
Found at i:13675547 original size:19 final size:19
Alignment explanation
Indices: 13675520--13675560 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
13675510 TGATTTATTT
*
13675520 TAAGCTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
13675539 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
13675558 TAA
1 TAA
13675561 CTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:13676312 original size:17 final size:17
Alignment explanation
Indices: 13676272--13676313 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
13676262 ATATGCAAAC
*
13676272 AAAAACCTCGACTCATA
1 AAAAACTTCGACTCATA
13676289 AAAAACTTCGACTCATA
1 AAAAACTTCGACTCATA
13676306 AAAAACTT
1 AAAAACTT
13676314 GTTAAGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAAACTTCGACTCATA
Found at i:13678042 original size:20 final size:20
Alignment explanation
Indices: 13678017--13678056 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13678007 TATTCAAACA
* *
13678017 ATATTACTTGAATAGTTATG
1 ATATTACATGAATAATTATG
*
13678037 ATATTAGATGAATAATTATG
1 ATATTACATGAATAATTATG
13678057 CCTATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.15, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATG
Found at i:13678135 original size:22 final size:24
Alignment explanation
Indices: 13678096--13678144 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
13678086 AGACACCTAT
*
13678096 TGAAAATGTCTCTATAAAGAGACA
1 TGAAAATGTCTCTATAAAGAGAAA
*
13678120 TGAAAAT-TC-CTATAAATAGAAA
1 TGAAAATGTCTCTATAAAGAGAAA
13678142 TGA
1 TGA
13678145 GATTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 2 0.09
24 7 0.30
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
TGAAAATGTCTCTATAAAGAGAAA
Found at i:13680438 original size:12 final size:11
Alignment explanation
Indices: 13680421--13680456 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
13680411 AACAAATCCT
13680421 CTCTCATATTTC
1 CTCTCA-ATTTC
*
13680433 CTCTCAATTTT
1 CTCTCAATTTC
13680444 CTCTCAATTTC
1 CTCTCAATTTC
13680455 CT
1 CT
13680457 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:13680467 original size:22 final size:23
Alignment explanation
Indices: 13680420--13680468 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
13680410 AAACAAATCC
**
13680420 TCTCTCATATTTCCTCTCAATTT
1 TCTCTCATATTTCCTCTCAAAAT
13680443 TCTCTCA-ATTTCCT-TCCAAAAT
1 TCTCTCATATTTCCTCT-CAAAAT
13680465 TCTC
1 TCTC
13680469 ATAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCTCATATTTCCTCTCAAAAT
Found at i:13680501 original size:51 final size:51
Alignment explanation
Indices: 13680436--13680559 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
13680426 ATATTTCCTC
* * *
13680436 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAATT
*
13680487 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
*
13680538 TCAATTTGCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
13680560 TTTTAAAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.30, C:0.26, G:0.01, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
Found at i:13680587 original size:11 final size:12
Alignment explanation
Indices: 13680560--13680589 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
13680550 CAATTTCCTT
13680560 TTTTAAAATAGG
1 TTTTAAAATAGG
13680572 TTTTAAAATA-G
1 TTTTAAAATAGG
13680583 TTTTAAA
1 TTTTAAA
13680590 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (12 bp):
TTTTAAAATAGG
Found at i:13683283 original size:25 final size:25
Alignment explanation
Indices: 13683254--13683367 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
13683244 TTTAAATTTG
13683254 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
13683279 TTATTTGATGTAATACACATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
* ** *
13683306 TT-TTCGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
13683324 ATTATTTGATATAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
13683350 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
13683368 ACCCTAACCT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 4 0.06
21 4 0.06
23 2 0.03
24 3 0.04
25 35 0.51
26 10 0.15
27 6 0.09
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:13683450 original size:29 final size:29
Alignment explanation
Indices: 13683367--13683723 Score: 560
Period size: 29 Copynumber: 12.4 Consensus size: 29
13683357 ATGTAATAAA
* ** *
13683367 AACCCTAACCTAATTTAGTTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * * *
13683396 AA-CCT-A-A-ACCCCAATTAAGAATCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
13683421 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
13683450 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
13683479 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
13683508 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
13683537 AACCCTAACATAACCTAATTAAAAGCCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
13683566 AACCCTAACATAACTTAATTAAAAGCCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
13683595 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
13683624 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
13683653 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
13683682 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
13683711 AACCCTAACATAA
1 AACCCTAACATAA
13683724 TAATTTTACA
Statistics
Matches: 303, Mismatches: 21, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
25 13 0.04
26 3 0.01
27 2 0.01
28 3 0.01
29 282 0.93
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:13683783 original size:37 final size:37
Alignment explanation
Indices: 13683741--13683824 Score: 168
Period size: 37 Copynumber: 2.3 Consensus size: 37
13683731 ACATAATTTG
13683741 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
13683778 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
1 ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
13683815 ATAATTTTAC
1 ATAATTTTAC
13683825 ATAATTTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (37 bp):
ATAATTTTACTAACAATTAACACAATTTTTGGACTTA
Found at i:13686743 original size:124 final size:125
Alignment explanation
Indices: 13686523--13686872 Score: 607
Period size: 124 Copynumber: 2.8 Consensus size: 125
13686513 CCCAAACTTG
13686523 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
13686588 TAGAAGCGATTTTATACTTTTTGCTCAGAAACGTCAAAAAAAAA-TATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
*
13686647 CTACTGTAGCAAAATAGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
13686712 TAGAAGCGATTTTATACAATTTGCTTAGAAACGT-AAAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * *
13686771 CTACTGTGGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
13686836 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
13686873 CTCGAAATAA
Statistics
Matches: 213, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
123 9 0.04
124 201 0.94
125 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:13697096 original size:42 final size:42
Alignment explanation
Indices: 13697050--13697180 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
13697040 GCCTGAAGGC
* * *
13697050 TGAACAGAAGCTCATGAGAGCTAAATGGAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
* ** * *
13697092 TGAACGGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
* * * * *
13697134 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
13697176 TGAAC
1 TGAAC
13697181 GAAAACTCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAATGGAAACCCATAAGGGT
Found at i:13697186 original size:21 final size:21
Alignment explanation
Indices: 13697113--13697191 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
13697103 TTGTAAGAGC
13697113 TGAACGAAAACCCATAAGGGT
1 TGAACGAAAACCCATAAGGGT
* * * * *
13697134 TTAACTG-AAGCTCAAAAGAGT
1 TGAAC-GAAAACCCATAAGGGT
* * *
13697155 TGAATGGAAACCCATTAGGGT
1 TGAACGAAAACCCATAAGGGT
*
13697176 TGAACGAAAACTCATA
1 TGAACGAAAACCCATA
13697192 TGAGTTAACA
Statistics
Matches: 40, Mismatches: 16, Indels: 4
0.67 0.27 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
TGAACGAAAACCCATAAGGGT
Found at i:13697197 original size:42 final size:41
Alignment explanation
Indices: 13697050--13697197 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 41
13697040 GCCTGAAGGC
* * * *
13697050 TGAACAGAAGCTCATGAGAGCTAAATGGAAACCTATAAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
** * * *
13697092 TGAACGGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
* * *
13697134 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAAC-GAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
* *
13697176 TGAACGAAAACTCATATGAGTT
1 TGAACG-AAGCTCATAAGAGTT
13697198 AACAGAAGCT
Statistics
Matches: 84, Mismatches: 21, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
41 1 0.01
42 83 0.99
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (41 bp):
TGAACGAAGCTCATAAGAGTTGAATGGAAACCCATAAGGGT
Found at i:13697342 original size:25 final size:24
Alignment explanation
Indices: 13697282--13697373 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
13697272 GGTACATTTG
13697282 CCGTCAATTCATCCTTTGCATATA
1 CCGTCAATTCATCCTTTGCATATA
* *
13697306 CCGTCAATTCATCCTTTGTATTTTA
1 CCGTCAATTCATCCTTTGCA-TATA
*
13697331 CTGTCAATTCATCCTTTGCATATA
1 CCGTCAATTCATCCTTTGCATATA
*
13697355 CCGTCAATTCATCATTTGC
1 CCGTCAATTCATCCTTTGC
13697374 CAGAGAACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 39 0.65
25 21 0.35
ACGTcount: A:0.23, C:0.27, G:0.09, T:0.41
Consensus pattern (24 bp):
CCGTCAATTCATCCTTTGCATATA
Found at i:13701194 original size:13 final size:13
Alignment explanation
Indices: 13701176--13701201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13701166 TTGATTTATA
13701176 TGTGTGAAAATTT
1 TGTGTGAAAATTT
13701189 TGTGTGAAAATTT
1 TGTGTGAAAATTT
13701202 CATCGTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:13702411 original size:42 final size:43
Alignment explanation
Indices: 13702358--13702469 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
13702348 TTCGATTTGA
*
13702358 GATTTACGTGTAAGACCATGTTTGGGAC-ATCGGCATCG-TATAC
1 GATTT-CGTGTAAGACCATGTCTGGGACAAT-GGCATCGATATAC
* **
13702401 GATTTCGTGTAAGACCTTGTCTGGGACAATGGCATCGATATTT
1 GATTTCGTGTAAGACCATGTCTGGGACAATGGCATCGATATAC
* * *
13702444 GATTACATGCAAGACCATGTCTGGGA
1 GATTTCGTGTAAGACCATGTCTGGGA
13702470 TGTTGGCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGGGACAATGGCATCGATATAC
Found at i:13707171 original size:24 final size:24
Alignment explanation
Indices: 13707140--13707186 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
13707130 AAAGGGTAAC
* *
13707140 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
13707164 AAGAAGATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
13707187 GAACATCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:13711142 original size:3 final size:3
Alignment explanation
Indices: 13711134--13711172 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
13711124 ATTAATTTGG
13711134 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13711173 ATTTATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:13711178 original size:12 final size:12
Alignment explanation
Indices: 13711139--13711253 Score: 58
Period size: 12 Copynumber: 9.0 Consensus size: 12
13711129 TTTGGTATTA
13711139 TTATTATTAT-T
1 TTATTATTATAT
13711150 ATTATTATTAT-T
1 -TTATTATTATAT
13711162 ATTATTATTATAT
1 -TTATTATTATAT
13711175 TTA-TATTTATAT
1 TTATTA-TTATAT
*
13711187 TTACTTATTTAAAT
1 TTA-TTA-TTATAT
* *
13711201 TT-TAAATATATT
1 TTATTATTATA-T
*
13711213 TGTCTTATTATAT
1 T-TATTATTATAT
*
13711226 ATTAATATTATTAT
1 -TTATTATTA-TAT
13711240 TTACTTATTTATAT
1 TTA-TTA-TTATAT
13711254 CTTTTTTATT
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
11 5 0.06
12 38 0.46
13 12 0.14
14 25 0.30
15 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:13711210 original size:25 final size:27
Alignment explanation
Indices: 13711171--13711250 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 27
13711161 TATTATTATT
*
13711171 ATATTTATATTTATATTTACTTATTTAA
1 ATATTAATA-TTATATTTACTTATTTAA
* * *
13711199 ATTTTAA-A-TATATTTGTCTTA-TTAT
1 ATATTAATATTATATTT-ACTTATTTAA
13711224 ATATTAATATTATTATTTACTTATTTA
1 ATATTAATATTA-TATTTACTTATTTA
13711251 TATCTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
25 16 0.39
26 5 0.12
27 7 0.17
28 13 0.32
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (27 bp):
ATATTAATATTATATTTACTTATTTAA
Found at i:13718251 original size:24 final size:24
Alignment explanation
Indices: 13718206--13718269 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
13718196 GGGTTACAAG
* *
13718206 AAGATGAAAGGTTAAAGGTTAAAA
1 AAGATGAAAGGTGAAAGCTTAAAA
* **
13718230 AAGATGAAAGGTGGAAGCTTAAGG
1 AAGATGAAAGGTGAAAGCTTAAAA
*
13718254 GAGATGAAAGGTGAAA
1 AAGATGAAAGGTGAAA
13718270 AGTTGATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGATGAAAGGTGAAAGCTTAAAA
Found at i:13722285 original size:9 final size:9
Alignment explanation
Indices: 13722268--13722304 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13722258 TGAGTTTTCG
13722268 AATTCGAAT
1 AATTCGAAT
*
13722277 AACTCGAAT
1 AATTCGAAT
13722286 AATTCGAAT
1 AATTCGAAT
13722295 AATTCGAAT
1 AATTCGAAT
13722304 A
1 A
13722305 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:13722500 original size:14 final size:14
Alignment explanation
Indices: 13722481--13722514 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
13722471 TTATTTTTTT
13722481 TCAAAATTTTACTC
1 TCAAAATTTTACTC
13722495 TCAAAATTTTACTC
1 TCAAAATTTTACTC
*
13722509 CCAAAA
1 TCAAAA
13722515 CCTTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (14 bp):
TCAAAATTTTACTC
Found at i:13723035 original size:5 final size:5
Alignment explanation
Indices: 13723025--13723050 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13723015 CTCAAAAATT
13723025 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
13723051 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:13723564 original size:51 final size:51
Alignment explanation
Indices: 13723488--13723590 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
13723478 TGAATTGCAT
*
13723488 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAGAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
* *
13723539 CGAGTGTAGGCTTGAGCATCACGAACCAAGTCACAAGAAAAAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
13723590 C
1 C
13723591 TTACTTTCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (51 bp):
CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
Found at i:13727908 original size:12 final size:12
Alignment explanation
Indices: 13727891--13727964 Score: 66
Period size: 12 Copynumber: 6.2 Consensus size: 12
13727881 ATATCCAAAC
*
13727891 AAAATAAAGTAA
1 AAAATAAAATAA
13727903 AAAATAATAA-AA
1 AAAATAA-AATAA
13727915 TAAAATAAAATAA
1 -AAAATAAAATAA
*
13727928 ATAATAAAAT-A
1 AAAATAAAATAA
13727939 AAAATAAAA-ATA
1 AAAATAAAATA-A
*
13727951 AAGA-AAAATAA
1 AAAATAAAATAA
13727962 AAA
1 AAA
13727965 CTGGGTTGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 16 0.31
12 25 0.49
13 10 0.20
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:13727916 original size:5 final size:5
Alignment explanation
Indices: 13727891--13727963 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
13727881 ATATCCAAAC
*
13727891 AAAAT AAAGT AAAA- AATAAT AAAAT AAAAT AAAAT AAATAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT -AA-AAT AAAAT
13727938 AAAAAT AAAAAT AAAGA- AAAAT AAAA
1 -AAAAT -AAAAT AAA-AT AAAAT AAAA
13727964 ACTGGGTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 3 0.05
5 35 0.59
6 18 0.31
7 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:13727949 original size:34 final size:37
Alignment explanation
Indices: 13727893--13727962 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 37
13727883 ATCCAAACAA
*
13727893 AATAAAGTAAAAAATAATAAAATAAA-ATAAAATAAAT
1 AATAAAATAAAAAATAATAAAATAAAGA-AAAATAAAT
13727930 AATAAAAT-AAAAAT-A-AAAATAAAGAAAAATAAA
1 AATAAAATAAAAAATAATAAAATAAAGAAAAATAAA
13727963 AACTGGGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 16 0.52
35 2 0.06
36 6 0.19
37 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (37 bp):
AATAAAATAAAAAATAATAAAATAAAGAAAAATAAAT
Found at i:13727958 original size:22 final size:23
Alignment explanation
Indices: 13727904--13727964 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
13727894 ATAAAGTAAA
13727904 AAATAATAAAAT-AAAATAAAAT
1 AAATAATAAAATAAAAATAAAAT
13727926 AAATAATAAAATAAAAATAAAAAT
1 AAATAATAAAATAAAAAT-AAAAT
*
13727950 AAA-GA-AAAATAAAAA
1 AAATAATAAAATAAAAA
13727965 CTGGGTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 22 0.61
23 6 0.17
24 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AAATAATAAAATAAAAATAAAAT
Found at i:13728086 original size:12 final size:12
Alignment explanation
Indices: 13728069--13728142 Score: 66
Period size: 12 Copynumber: 6.2 Consensus size: 12
13728059 ATATCCAAAC
*
13728069 AAAATAAAGTAA
1 AAAATAAAATAA
13728081 AAAATAATAA-AA
1 AAAATAA-AATAA
13728093 TAAAATAAAATAA
1 -AAAATAAAATAA
*
13728106 ATAATAAAAT-A
1 AAAATAAAATAA
13728117 AAAATAAAA-ATA
1 AAAATAAAATA-A
*
13728129 AAGA-AAAATAA
1 AAAATAAAATAA
13728140 AAA
1 AAA
13728143 CTGGGTTGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
11 16 0.31
12 25 0.49
13 10 0.20
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:13728094 original size:5 final size:5
Alignment explanation
Indices: 13728069--13728141 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
13728059 ATATCCAAAC
*
13728069 AAAAT AAAGT AAAA- AATAAT AAAAT AAAAT AAAAT AAATAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT -AA-AAT AAAAT
13728116 AAAAAT AAAAAT AAAGA- AAAAT AAAA
1 -AAAAT -AAAAT AAA-AT AAAAT AAAA
13728142 ACTGGGTTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
4 3 0.05
5 35 0.59
6 18 0.31
7 3 0.05
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:13728127 original size:34 final size:37
Alignment explanation
Indices: 13728071--13728140 Score: 94
Period size: 34 Copynumber: 2.0 Consensus size: 37
13728061 ATCCAAACAA
*
13728071 AATAAAGTAAAAAATAATAAAATAAA-ATAAAATAAAT
1 AATAAAATAAAAAATAATAAAATAAAGA-AAAATAAAT
13728108 AATAAAAT-AAAAAT-A-AAAATAAAGAAAAATAAA
1 AATAAAATAAAAAATAATAAAATAAAGAAAAATAAA
13728141 AACTGGGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 16 0.52
35 2 0.06
36 6 0.19
37 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.19
Consensus pattern (37 bp):
AATAAAATAAAAAATAATAAAATAAAGAAAAATAAAT
Found at i:13728136 original size:22 final size:23
Alignment explanation
Indices: 13728082--13728142 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
13728072 ATAAAGTAAA
13728082 AAATAATAAAAT-AAAATAAAAT
1 AAATAATAAAATAAAAATAAAAT
13728104 AAATAATAAAATAAAAATAAAAAT
1 AAATAATAAAATAAAAAT-AAAAT
*
13728128 AAA-GA-AAAATAAAAA
1 AAATAATAAAATAAAAA
13728143 CTGGGTTGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 22 0.61
23 6 0.17
24 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AAATAATAAAATAAAAATAAAAT
Found at i:13728160 original size:178 final size:179
Alignment explanation
Indices: 13727850--13728206 Score: 707
Period size: 178 Copynumber: 2.0 Consensus size: 179
13727840 TCCTCGCCGA
13727850 TTTACCTAGACAGAAGAAGAGAAATTTATTAATATCCAAACAAAATAAAGTAAAAAATAATAAAA
1 TTTACCTAGACAGAAGAAGAGAAATTTATTAATATCCAAACAAAATAAAGTAAAAAATAATAAAA
13727915 TAAAATAAAATAAATAATAAAATAAAAATAAAAATAAAGAAAAATAAAAACTGGGTTGTCTCCCA
66 TAAAATAAAATAAATAATAAAATAAAAATAAAAATAAAGAAAAATAAAAACTGGGTTGTCTCCCA
13727980 ACAAGCACTTGTTTAACACCGATAGCTTGATGCCCCCAACTAGTATTGG
131 ACAAGCACTTGTTTAACACCGATAGCTTGATGCCCCCAACTAGTATTGG
13728029 TTTACCTAGA-AGAAGAAGAGAAATTTATTAATATCCAAACAAAATAAAGTAAAAAATAATAAAA
1 TTTACCTAGACAGAAGAAGAGAAATTTATTAATATCCAAACAAAATAAAGTAAAAAATAATAAAA
13728093 TAAAATAAAATAAATAATAAAATAAAAATAAAAATAAAGAAAAATAAAAACTGGGTTGTCTCCCA
66 TAAAATAAAATAAATAATAAAATAAAAATAAAAATAAAGAAAAATAAAAACTGGGTTGTCTCCCA
13728158 ACAAGCACTTGTTTAACACCGATAGCTTGATGCCCCCAACTAGTATTGG
131 ACAAGCACTTGTTTAACACCGATAGCTTGATGCCCCCAACTAGTATTGG
13728207 GGCTGTTCCA
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 168 0.94
179 10 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (179 bp):
TTTACCTAGACAGAAGAAGAGAAATTTATTAATATCCAAACAAAATAAAGTAAAAAATAATAAAA
TAAAATAAAATAAATAATAAAATAAAAATAAAAATAAAGAAAAATAAAAACTGGGTTGTCTCCCA
ACAAGCACTTGTTTAACACCGATAGCTTGATGCCCCCAACTAGTATTGG
Found at i:13732101 original size:20 final size:17
Alignment explanation
Indices: 13732076--13732114 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
13732066 TTCTTAGAAT
13732076 TTTAATCCAATATTTTATAA
1 TTTAAT-CAAT-TTTT-TAA
13732096 TTTAATCAATTTTTTAA
1 TTTAATCAATTTTTTAA
13732113 TT
1 TT
13732115 GATTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 4 0.21
20 6 0.32
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATCAATTTTTTAA
Found at i:13736854 original size:18 final size:17
Alignment explanation
Indices: 13736815--13736874 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
13736805 ATGTTATTTT
13736815 TTAATATTATTTAAATA
1 TTAATATTATTTAAATA
13736832 TTAATATTAATTT--ATA
1 TTAATATT-ATTTAAATA
*
13736848 CT-ATAATTATTTAAAATA
1 TTAAT-ATTATTT-AAATA
13736866 TTAAT-TTAT
1 TTAATATTAT
13736875 AGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 6 0.17
16 7 0.20
17 12 0.34
18 8 0.23
19 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTATTTAAATA
Found at i:13742801 original size:25 final size:25
Alignment explanation
Indices: 13742766--13742822 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
13742756 ACATAAACGC
13742766 AGCTCTTTATGAGCGTCCTGAT-AT
1 AGCTCTTTATGAGCGTCCTGATAAT
*
13742790 AGGCTCTTTATGAGCTTCCTGATAAT
1 A-GCTCTTTATGAGCGTCCTGATAAT
13742816 AGCTCTT
1 AGCTCTT
13742823 CGGAGTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 26 0.87
26 3 0.10
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (25 bp):
AGCTCTTTATGAGCGTCCTGATAAT
Found at i:13744270 original size:12 final size:13
Alignment explanation
Indices: 13744253--13744282 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13744243 TATTTTAGTC
13744253 AACAC-AGGCAGA
1 AACACAAGGCAGA
13744265 AACACAAGGCAGA
1 AACACAAGGCAGA
13744278 AACAC
1 AACAC
13744283 GGTCGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.27, G:0.20, T:0.00
Consensus pattern (13 bp):
AACACAAGGCAGA
Done.