Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1686
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: 48101
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:14516 original size:39 final size:40
Alignment explanation
Indices: 14413--14597 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
14403 TTGAATGATG
* * *
14413 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* * *
14452 ATCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
14493 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
14532 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
14571 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
14598 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 77 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:14549 original size:79 final size:81
Alignment explanation
Indices: 14413--14597 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
14403 TTGAATGATG
*
14413 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCTGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCTGAAGGCATT
14477 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
14492 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCTGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CTGAAGGCA
*
14554 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
14572 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
14598 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCTGAAGGCATT
TGTGCGAGATACTATA
Found at i:14630 original size:79 final size:79
Alignment explanation
Indices: 14466--14620 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
14456 GGACTAAGAT
* **
14466 CTGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CTGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
14531 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
14545 CTGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CTGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
14608 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
14621 ATTCCGAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.60
80 25 0.37
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CTGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:15958 original size:21 final size:21
Alignment explanation
Indices: 15932--15977 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
15922 GGGTGTTACA
15932 GCCTCCGCCTCCCGCGCTGCT
1 GCCTCCGCCTCCCGCGCTGCT
*
15953 GCCTCCGCCTCCCGCGTTGCT
1 GCCTCCGCCTCCCGCGCTGCT
15974 GCCT
1 GCCT
15978 TCGCTCTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.24, T:0.22
Consensus pattern (21 bp):
GCCTCCGCCTCCCGCGCTGCT
Found at i:21656 original size:39 final size:39
Alignment explanation
Indices: 21537--21657 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
21527 ATGCAAGACA
21537 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
21576 CTAGAAATGTATCCGGGCTAAAGTCCCGTAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
21615 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
21654 CTGG
1 CTGG
21658 TAATATAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.25
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:25312 original size:27 final size:27
Alignment explanation
Indices: 25274--25326 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
25264 ATGTACGTTG
*
25274 TTATGTACGTTATGTGAGTTATGTAAA
1 TTATGTAAGTTATGTGAGTTATGTAAA
25301 TTATGTAAGTTATGTGAGTTATGTAA
1 TTATGTAAGTTATGTGAGTTATGTAA
25327 GTTGTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (27 bp):
TTATGTAAGTTATGTGAGTTATGTAAA
Found at i:25329 original size:9 final size:9
Alignment explanation
Indices: 25273--25376 Score: 84
Period size: 9 Copynumber: 11.2 Consensus size: 9
25263 TATGTACGTT
*
25273 GTTATGTAC
1 GTTATGTAA
*
25282 GTTATGTGA
1 GTTATGTAA
25291 GTTATGTAA
1 GTTATGTAA
*
25300 ATTATGTAA
1 GTTATGTAA
*
25309 GTTATGTGA
1 GTTATGTAA
25318 GTTATGTAA
1 GTTATGTAA
25327 GTTGTTATGTAA
1 ---GTTATGTAA
* *
25339 ATTGT-TCAA
1 GTTATGT-AA
* *
25348 GTTATATGA
1 GTTATGTAA
25357 GTTATGTAA
1 GTTATGTAA
*
25366 GTTATTTAA
1 GTTATGTAA
25375 GT
1 GT
25377 AATGATCAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
8 1 0.01
9 64 0.85
10 1 0.01
12 9 0.12
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:25334 original size:39 final size:39
Alignment explanation
Indices: 25291--25368 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
25281 CGTTATGTGA
*
25291 GTTATGTAAATTATGT-AAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTAT-TCAAGTTATATGAGTTATGTAAGTT
*
25330 GTTATGTAAATTGTTCAAGTTATATGAGTTATGTAAGTT
1 GTTATGTAAATTATTCAAGTTATATGAGTTATGTAAGTT
25369 ATTTAAGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (39 bp):
GTTATGTAAATTATTCAAGTTATATGAGTTATGTAAGTT
Found at i:25351 original size:57 final size:57
Alignment explanation
Indices: 25256--25370 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 57
25246 ATGACAAGAC
* ** * *
25256 TGTGAGTTATGTACGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTA
1 TGTGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTA
* * *
25313 TGTGAGTTATGTAAGTTGTTATGTAAATTGT-TCAAGTTATATGAGTTATGTAAGTTA
1 TGTGAGTTATGTAAGTTGTTATGTAAATTATGT-AAGTTATATAAATTATGTAAGTTA
25370 T
1 T
25371 TTAAGTAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 1 0.02
57 48 0.98
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (57 bp):
TGTGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTA
Found at i:26813 original size:14 final size:14
Alignment explanation
Indices: 26796--26824 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26786 GTGATTATAT
26796 TGAATCTAAGAGAC
1 TGAATCTAAGAGAC
26810 TGAATCTAAGAGAC
1 TGAATCTAAGAGAC
26824 T
1 T
26825 ATGTTAGTTA
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:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
TGAATCTAAGAGAC
Found at i:27878 original size:39 final size:39
Alignment explanation
Indices: 27824--27991 Score: 228
Period size: 39 Copynumber: 4.3 Consensus size: 39
27814 ATGAGATTGA
*
27824 AAATATATCCGGACATGAGGTCTGCAGGCTATATGCTAG
1 AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAG
*
27863 AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTGG
1 AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAG
* * * * *
27902 AAAAATTTCCGGACATGAGATCTGCAAGCTATATGCTAG
1 AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAG
* ** *
27941 AAATATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGG
1 AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAG
*
27980 AAAAATATCCGG
1 AAATATATCCGG
27992 GTTAAAGACC
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (39 bp):
AAATATATCCGGACATGAGGTCCGCAGGCTATATGCTAG
Found at i:27926 original size:78 final size:78
Alignment explanation
Indices: 27822--27991 Score: 277
Period size: 78 Copynumber: 2.2 Consensus size: 78
27812 GTATGAGATT
* *
27822 GAAAATATATCCGGACATGAGGTCTGCAGGCTATATGCTAGAAATATATCCGGACATGAGGTCCG
1 GAAAA-ATATCCGGACATGAGATCTGCAAGCTATATGCTAGAAATATATCCGGACATGAGGTCCG
*
27887 CAGGCTATATGCTG
65 CAGGCTACATGCTG
* *
27901 GAAAAATTTCCGGACATGAGATCTGCAAGCTATATGCTAGAAATATATCCGGACTTGAGGTCCGC
1 GAAAAATATCCGGACATGAGATCTGCAAGCTATATGCTAGAAATATATCCGGACATGAGGTCCGC
*
27966 AGGCTACGTGCTG
66 AGGCTACATGCTG
27979 GAAAAATATCCGG
1 GAAAAATATCCGG
27992 GTTAAAGACC
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 79 0.94
79 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (78 bp):
GAAAAATATCCGGACATGAGATCTGCAAGCTATATGCTAGAAATATATCCGGACATGAGGTCCGC
AGGCTACATGCTG
Found at i:29675 original size:26 final size:25
Alignment explanation
Indices: 29621--29692 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 25
29611 GGATATCTGT
* *
29621 GAAATCAATTGAAACGGTGCGTGGTG
1 GAAA-CAATTGAAATGGTGAGTGGTG
29647 GAAACAATTGAAATGGTGAGTGGTG
1 GAAACAATTGAAATGGTGAGTGGTG
*
29672 GGAACAATTGAAATGGTGAGT
1 GAAACAATTGAAATGGTGAGT
29693 TTTGAATTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
25 39 0.91
26 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.24
Consensus pattern (25 bp):
GAAACAATTGAAATGGTGAGTGGTG
Found at i:30646 original size:11 final size:11
Alignment explanation
Indices: 30630--30654 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30620 ATGGGCCATG
30630 AAACATCAGTA
1 AAACATCAGTA
30641 AAACATCAGTA
1 AAACATCAGTA
30652 AAA
1 AAA
30655 AGTAAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (11 bp):
AAACATCAGTA
Found at i:30798 original size:24 final size:24
Alignment explanation
Indices: 30766--30811 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
30756 TTGTATTTGT
30766 AAACAGAGACTTAGAAATTAAAAG
1 AAACAGAGACTTAGAAATTAAAAG
30790 AAACAGAGACTTAGAAATTAAA
1 AAACAGAGACTTAGAAATTAAA
30812 GTTACCTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.17
Consensus pattern (24 bp):
AAACAGAGACTTAGAAATTAAAAG
Found at i:31736 original size:14 final size:14
Alignment explanation
Indices: 31713--31803 Score: 85
Period size: 14 Copynumber: 6.5 Consensus size: 14
31703 ATTCCAAAAT
*
31713 TAAACCCCAAACTC
1 TAAACCCCAAACCC
*
31727 TAAACTCCAAACCC
1 TAAACCCCAAACCC
* *
31741 CAAACACCAAACCC
1 TAAACCCCAAACCC
*
31755 TAAACCCCAAACCA
1 TAAACCCCAAACCC
*
31769 TAAACCACAAAACCC
1 TAAACC-CCAAACCC
* * *
31784 -AATCCACAAACTC
1 TAAACCCCAAACCC
31797 TAAACCC
1 TAAACCC
31804 TAAAATCCTA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
13 5 0.08
14 49 0.82
15 6 0.10
ACGTcount: A:0.47, C:0.43, G:0.00, T:0.10
Consensus pattern (14 bp):
TAAACCCCAAACCC
Found at i:31740 original size:21 final size:21
Alignment explanation
Indices: 31713--31766 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
31703 ATTCCAAAAT
* *
31713 TAAACCCCAAACTCTAAACTCC
1 TAAACCCCAAACACCAAAC-CC
31735 -AAACCCCAAACACCAAACCC
1 TAAACCCCAAACACCAAACCC
31755 TAAACCCCAAAC
1 TAAACCCCAAAC
31767 CATAAACCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.46, C:0.44, G:0.00, T:0.09
Consensus pattern (21 bp):
TAAACCCCAAACACCAAACCC
Found at i:31767 original size:7 final size:7
Alignment explanation
Indices: 31714--31767 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
31704 TTCCAAAATT
31714 AAACCCC
1 AAACCCC
* *
31721 AAACTCT
1 AAACCCC
*
31728 AAACTCC
1 AAACCCC
31735 AAACCCC
1 AAACCCC
*
31742 AAACACC
1 AAACCCC
*
31749 AAACCCT
1 AAACCCC
31756 AAACCCC
1 AAACCCC
31763 AAACC
1 AAACC
31768 ATAAACCACA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.07
Consensus pattern (7 bp):
AAACCCC
Found at i:31773 original size:21 final size:21
Alignment explanation
Indices: 31713--31803 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
31703 ATTCCAAAAT
*
31713 TAAACCCCAAACTC-TAAACTCC
1 TAAACCCCAAAC-CACAAAC-CC
31735 -AAACCCCAAA-CACCAAACCC
1 TAAACCCCAAACCA-CAAACCC
*
31755 TAAACCCCAAACCATAAACCAC
1 TAAACCCCAAACCACAAACC-C
* * *
31777 -AAAACCCAATCCACAAACTC
1 TAAACCCCAAACCACAAACCC
31797 TAAACCC
1 TAAACCC
31804 TAAAATCCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 49 0.88
22 3 0.05
ACGTcount: A:0.47, C:0.43, G:0.00, T:0.10
Consensus pattern (21 bp):
TAAACCCCAAACCACAAACCC
Found at i:31806 original size:7 final size:7
Alignment explanation
Indices: 31713--31807 Score: 54
Period size: 7 Copynumber: 13.6 Consensus size: 7
31703 ATTCCAAAAT
31713 TAAACCC
1 TAAACCC
* *
31720 CAAACTC
1 TAAACCC
31727 TAAACTCC
1 TAAAC-CC
31735 -AAACCC
1 TAAACCC
*
31741 CAAACACC
1 TAAAC-CC
31749 -AAACCC
1 TAAACCC
31755 TAAACCC
1 TAAACCC
* *
31762 CAAACCA
1 TAAACCC
31769 TAAACCAC
1 TAAACC-C
*
31777 AAAACCC
1 TAAACCC
*
31784 -AATCCAC
1 TAAACC-C
*
31791 -AAACTC
1 TAAACCC
31797 TAAACCC
1 TAAACCC
31804 TAAA
1 TAAA
31808 ATCCTAAATC
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
6 9 0.13
7 51 0.75
8 8 0.12
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (7 bp):
TAAACCC
Found at i:31911 original size:14 final size:14
Alignment explanation
Indices: 31892--31927 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31882 CACTAAATAT
*
31892 AACCCTAAACTTTA
1 AACCCTAAACCTTA
31906 AACCCTAAACCTTA
1 AACCCTAAACCTTA
31920 AACCCTAA
1 AACCCTAA
31928 CACCCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAACCTTA
Found at i:31934 original size:8 final size:7
Alignment explanation
Indices: 31892--31936 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
31882 CACTAAATAT
31892 AACCCTA
1 AACCCTA
**
31899 AACTTTA
1 AACCCTA
31906 AACCCTA
1 AACCCTA
*
31913 AACCTTA
1 AACCCTA
31920 AACCCTA
1 AACCCTA
31927 ACACCCTA
1 A-ACCCTA
31935 AA
1 AA
31937 ACGCTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (7 bp):
AACCCTA
Found at i:32049 original size:14 final size:14
Alignment explanation
Indices: 32038--32080 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
32028 TGACCCTATT
32038 CCATAAACCCTAAA
1 CCATAAACCCTAAA
32052 CCATAAACTCC-AAA
1 CCATAAAC-CCTAAA
* *
32066 CCTTAAACCCCAAA
1 CCATAAACCCTAAA
32080 C
1 C
32081 ACTAGACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.14
Consensus pattern (14 bp):
CCATAAACCCTAAA
Found at i:32080 original size:21 final size:21
Alignment explanation
Indices: 32042--32096 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
32032 CCTATTCCAT
* ** *
32042 AAACCCTAAACCATAAACTCC
1 AAACCTTAAACCCCAAACACC
*
32063 AAACCTTAAACCCCAAACACT
1 AAACCTTAAACCCCAAACACC
*
32084 AGACCTTAAACCC
1 AAACCTTAAACCC
32097 TAATTAACCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.15
Consensus pattern (21 bp):
AAACCTTAAACCCCAAACACC
Found at i:32506 original size:14 final size:13
Alignment explanation
Indices: 32456--32521 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 13
32446 ATAAACCTCA
32456 AACCCTAAATCAT
1 AACCCTAAATCAT
* *
32469 AAAACATAAATCAT
1 -AACCCTAAATCAT
32483 CAACCCTAAATCAT
1 -AACCCTAAATCAT
*
32497 AACCCTTAAACCCAT
1 AACCC-TAAA-TCAT
32512 AACCCCTAAA
1 AA-CCCTAAA
32522 CCTATAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
13 5 0.12
14 26 0.60
15 9 0.21
16 3 0.07
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (13 bp):
AACCCTAAATCAT
Found at i:32514 original size:15 final size:15
Alignment explanation
Indices: 32494--32528 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
32484 AACCCTAAAT
*
32494 CATAACCCTTAAACC
1 CATAACCCCTAAACC
32509 CATAACCCCTAAACC
1 CATAACCCCTAAACC
*
32524 TATAA
1 CATAA
32529 AAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAACCCCTAAACC
Found at i:32515 original size:28 final size:28
Alignment explanation
Indices: 32446--32530 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 28
32436 ATTCTAAATT
32446 ATAAACCTCA-AACCCTAAATCATAAAAC
1 ATAAACC-CATAACCCTAAATCATAAAAC
* **
32474 ATAAA-TCATCAACCCTAAATCATAACCC
1 ATAAACCCAT-AACCCTAAATCATAAAAC
* *
32502 TTAAACCCATAACCCCTAAACCTATAAAA
1 ATAAACCCATAA-CCCTAAATC-ATAAAA
32531 ATATTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
26 2 0.05
28 27 0.61
29 11 0.25
30 4 0.09
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (28 bp):
ATAAACCCATAACCCTAAATCATAAAAC
Found at i:33491 original size:74 final size:73
Alignment explanation
Indices: 33384--33523 Score: 181
Period size: 74 Copynumber: 1.9 Consensus size: 73
33374 CTAATATCAC
**** *
33384 TGAAGCTCATATAAAACGACGTTGTTTTGCTTAACATTTTAGCGACTTTTTTGGGAAAACGCCAC
1 TGAAGCTCATATAAAACGACACCATTTTGCTTAACATTTTAGCGAC-GTTTTGGGAAAACGCCAC
33449 TACTGCCAA
65 TACTGCCAA
* * * * *
33458 TGAAGCTCATGTAAAACGACACCATTTTTCTTAACCTTTTAGCGGCGTTTTGGTAAAACGCCACT
1 TGAAGCTCATATAAAACGACACCATTTTGCTTAACATTTTAGCGACGTTTTGGGAAAACGCCACT
33523 A
66 A
33524 AAGGTCGACT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
73 18 0.32
74 38 0.68
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (73 bp):
TGAAGCTCATATAAAACGACACCATTTTGCTTAACATTTTAGCGACGTTTTGGGAAAACGCCACT
ACTGCCAA
Found at i:33589 original size:40 final size:40
Alignment explanation
Indices: 33512--33589 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
33502 GCGTTTTGGT
* *
33512 AAAACGCCACTAAAGGTCGACTTATAGTGGCGCTTTTTCA
1 AAAACGCCACTAAAGCTCGACTTATAGCGGCGCTTTTTCA
* * *
33552 AAAACGCCGCTAAAGCTCGA-TCTATTGCGGCGTTTTTT
1 AAAACGCCACTAAAGCTCGACT-TATAGCGGCGCTTTTT
33590 TTTATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.03
40 31 0.97
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (40 bp):
AAAACGCCACTAAAGCTCGACTTATAGCGGCGCTTTTTCA
Found at i:37456 original size:48 final size:48
Alignment explanation
Indices: 37383--37748 Score: 399
Period size: 48 Copynumber: 7.6 Consensus size: 48
37373 TGTGTGCTAA
37383 TGTAAGACCATGTC-GGGACATGGCATCGGCCACATCATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACATCATGAGAGCCAG
* * * ** * * *
37430 TGTAAGATCATGTTTGGGACATGGCATCAG-CATTTAGACGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACAT-CATGAGAGCCAG
* ** * *
37478 TGTATGACCATGTCTGGGACATGGCATCGGCCTTGA-CGTGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCC-ACATCATGAGAGCCAG
* * *
37526 TGTAAGACCATGTCTGGGACATGGCATTGG-CA-TTGACATGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACAT--CATGAGAGCCAG
* *
37574 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATCATGAGAGCCAG
* *
37622 TGTAAGACCATGTCTGGGACATGGCATCGG-CA-TTGACATGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACAT--CATGAGAGCCAG
* *
37670 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATCATGAGAGCCAG
37718 TGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTCTGGGACATGGCATCGGC
37749 AAGTTTCCCT
Statistics
Matches: 263, Mismatches: 40, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
47 17 0.06
48 243 0.92
49 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCACATCATGAGAGCCAG
Found at i:37569 original size:96 final size:96
Alignment explanation
Indices: 37378--37749 Score: 604
Period size: 96 Copynumber: 3.9 Consensus size: 96
37368 TCATATGTGT
* * * *
37378 GCTAATGTAAGACCATGTC-GGGACATGGCATCGGCCAC-ATCATGAGAGCCAGTGTAAGATCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-CATGTGAGCCAGTGTAAGACCAT
* * * * *
37441 GTTTGGGACATGGCATCAGCATTTAGACGAGA
65 GTCTGGGACATGGCATCGGCATTGACATGAGA
* * *
37473 GCTAGTGTATGACCATGTCTGGGACATGGCATCGGCCTTGACGTGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
*
37538 TCTGGGACATGGCATTGGCATTGACATGAGA
66 TCTGGGACATGGCATCGGCATTGACATGAGA
37569 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
37634 TCTGGGACATGGCATCGGCATTGACATGAGA
66 TCTGGGACATGGCATCGGCATTGACATGAGA
37665 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
37730 TCTGGGACATGGCATCGGCA
66 TCTGGGACATGGCATCGGCA
37750 AGTTTCCCTT
Statistics
Matches: 258, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
95 17 0.07
96 240 0.93
97 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGGCATTGACATGAGA
Found at i:37658 original size:144 final size:143
Alignment explanation
Indices: 37383--37749 Score: 504
Period size: 144 Copynumber: 2.6 Consensus size: 143
37373 TGTGTGCTAA
* * *
37383 TGTAAGACCATGTC-GGGACATGGCATCGGCCA-CATCATGAGAGCCAGTGTAAGATCATGTTTG
1 TGTAAGACCATGTCTGGGACATGGCATCGG-CATGA-CATGAGAGCCAGTGTAAGACCATGTCTG
* ** * * * *
37446 GGACATGGCATCAGCATTTAGACGAGAGCTAGTGTATGACCATGTCTGGGACATGGCATCGGCCT
64 GGACATGGCATCGGCATCGACACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
* *
37511 TGACGTGTGAGCCAG
129 TGACATGAGAGCCAG
* *
37526 TGTAAGACCATGTCTGGGACATGGCATTGGCATTGACATGAGAGCTAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCA-TGACATGAGAGCCAGTGTAAGACCATGTCTGG
* * *
37591 GACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
65 GACATGGCATCGGCATCGACACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
*
37656 GACATGAGAGCTAG
130 GACATGAGAGCCAG
* *
37670 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACATGTGAGCCAGTGTAAGACCATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAT-GACATGAGAGCCAGTGTAAGACCATGTCTGG
37735 GACATGGCATCGGCA
65 GACATGGCATCGGCA
37750 AGTTTCCCTT
Statistics
Matches: 197, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
143 17 0.09
144 179 0.91
145 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (143 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCATGACATGAGAGCCAGTGTAAGACCATGTCTGGG
ACATGGCATCGGCATCGACACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG
ACATGAGAGCCAG
Found at i:40781 original size:16 final size:16
Alignment explanation
Indices: 40762--40792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40752 CTTCTTCACT
40762 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
40778 TACTTACTTACTTAA
1 TACTCACTTACTTAA
40793 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:40798 original size:20 final size:20
Alignment explanation
Indices: 40759--40798 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40749 AAACTTCTTC
* *
40759 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
40779 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
40799 TTATGAACAT
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:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:41177 original size:55 final size:52
Alignment explanation
Indices: 41038--41183 Score: 166
Period size: 55 Copynumber: 2.7 Consensus size: 52
41028 ATCCTTTTGA
* * * *
41038 AACTTACCATTGCTATGTCTTGACATGGTCTTTACATGGTATCATTGCCTTATG
1 AACTTA-CAATGCCATGTCTTGACATGGTC-TTACATGGGACCATTGCCTTATG
* * * *
41092 AACTCACTAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAG
1 AACTTAC-AATGCCATGTCTTGACATGGTCTTACATGGGACCATTGCCTTAT-G
41146 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATG
1 -AACTTA-CAATGCCATGTCTTGACATGGTCTTACATG
41184 ATTTCCTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
53 20 0.26
54 24 0.31
55 32 0.42
56 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (52 bp):
AACTTACAATGCCATGTCTTGACATGGTCTTACATGGGACCATTGCCTTATG
Found at i:41194 original size:55 final size:51
Alignment explanation
Indices: 41038--41246 Score: 154
Period size: 55 Copynumber: 3.8 Consensus size: 51
41028 ATCCTTTTGA
* * *
41038 AACTTACCATTGCTATGTCTTGACATGGTCTTTACATGGTATCATTGCCTTATG
1 AACTTA-CAATGCCATGTCTTGACATGGTC-TTACAT-GTATCCTTGCCTTATG
* * * *
41092 AACTCACTAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTTAC-AATGCCATGTCTTGACATGGTCTTACAT-GTATCC-TTGCCTTAT-G
*
41146 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-G
1 -AACTTA-CAATGCCATGTCTTGACATGGTCTTACATG-TATCCTTGCCTTATG
** *
41199 AAACCTTACCAATTGCCATACCTT-AGCATGGTCTTACACGGTATCCTT
1 -AA-CTTA-CAA-TGCCATGTCTTGA-CATGGTCTTACA-TGTATCCTT
41247 AAACCCTAAT
Statistics
Matches: 126, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
52 1 0.01
53 22 0.17
54 33 0.26
55 66 0.52
56 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (51 bp):
AACTTACAATGCCATGTCTTGACATGGTCTTACATGTATCCTTGCCTTATG
Done.