Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2569
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: 60491
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:2426 original size:27 final size:27
Alignment explanation
Indices: 2396--2572 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
2386 ATATTGAGCC
* * *
2396 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
2423 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
2450 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
** * *
2478 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
2505 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
2532 CGCACACTTAGTGCAACATAGTCAA-T
1 CGCACACTTAGTGCTACATAGTCAACT
2558 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
2573 GTACAATTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
26 15 0.12
27 89 0.70
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:2535 original size:82 final size:80
Alignment explanation
Indices: 2417--2571 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 80
2407 TGCTATATAA
* * *
2417 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCA-A-TCGCA
2482 CACTTAGTGCCGCATGG
64 CACTTAGTGCCGCATGG
* * **
2499 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAATCGCAC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAATCGCAC
2563 ACTTAGTGC
65 ACTTAGTGC
2572 TGTACAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 15 0.23
81 2 0.03
82 48 0.74
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAATCGCACA
CTTAGTGCCGCATGG
Found at i:10513 original size:27 final size:27
Alignment explanation
Indices: 10483--10658 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
10473 ATATTGAGCC
* *
10483 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
10510 CGCACACTTAGTGC-ACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
10536 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
** ** *
10563 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
10590 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
10617 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
10644 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10659 GTACAATTTA
Statistics
Matches: 127, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.18
27 102 0.80
28 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:10648 original size:81 final size:80
Alignment explanation
Indices: 10504--10657 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 80
10494 TGCTATATAA
* *
10504 TCAACTCGCACACTTAGTGCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCACA
1 TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCAACATAGTCAACTCGCACA
10569 CTTAGTGCCGCATGG
66 CTTAGTGCCGCATGG
* * **
10584 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAA-TCGCA
1 TCAACTCGCACACTTAGTGCA-CATAATCAAATCGCACACTTAGTGCAACATAGTC-AACTCGCA
10648 CACTTAGTGC
64 CACTTAGTGC
10658 TGTACAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 20 0.30
81 44 0.67
82 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCAACATAGTCAACTCGCACA
CTTAGTGCCGCATGG
Found at i:13579 original size:46 final size:46
Alignment explanation
Indices: 13512--13729 Score: 228
Period size: 46 Copynumber: 4.7 Consensus size: 46
13502 AACCCGCCCC
* *
13512 TAAGTGAACTCGGGCTCAACTCAATGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGGCATTCGCATCCA
* *
13558 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGGCATTCGCATCCA
** *
13604 TAAGTGAACTCGGACTCAACTCAACAAGTTC-GG-ATTC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGGCATTCGC-A--TCCA
* * * ** *
13650 TCTCA-CGAACTCGGACTCAACTGAATGAGTTCGAACATTCGCATCCG
1 --TAAGTGAACTCGGACTCAACTCAATGAGTTCGGGCATTCGCATCCA
* *
13697 TAAGTGAACTCGGACTCATCTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAATGAGTTCGG
13730 ATGTCAACCA
Statistics
Matches: 141, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.03
45 4 0.03
46 99 0.70
47 25 0.18
48 2 0.01
49 5 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAATGAGTTCGGGCATTCGCATCCA
Found at i:13691 original size:93 final size:93
Alignment explanation
Indices: 13563--13731 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
13553 ATCCATAAGT
** *
13563 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
13628 CAAGTTCGGATTCCTAGTTACATCTCAC
66 CAAGTTCGGATTCCTAGTTACATCTCAC
* * * *
13656 GAACTCGGACTCAACTGAATGAGTTCGAACATTCGCATCCGTAAGTGAACTCGGACTCATCTCAA
1 GAACTCGGACTCAACTCAATGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
13721 CGAGTTCGGAT
66 CAAGTTCGGAT
13732 GTCAACCATC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAATGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGTTCGGATTCCTAGTTACATCTCAC
Found at i:21184 original size:46 final size:45
Alignment explanation
Indices: 21115--21288 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
21105 GTAACCCGCC
* *
21115 CCTAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
21160 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACG--T
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTT-CGCAT
* * * ** *
21210 -CTCA-CGAACTCGGACTCAACTCAACGAGTTTGAACATTCGCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
21253 CCGTAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
21289 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 1 0.01
44 2 0.02
45 4 0.04
46 57 0.54
47 26 0.25
48 3 0.03
49 2 0.02
50 1 0.01
51 3 0.03
52 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:21230 original size:93 final size:93
Alignment explanation
Indices: 21122--21292 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
21112 GCCCCTAAGT
** *
21122 GAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
21187 CGAGTTCGGATGCCTAGTTACGTCTCAC
66 CGAGTTCGGATGCCTAGTTACGTCTCAC
* * * *
21215 GAACTCGGACTCAACTCAACGAGTTTGAACATTCGCATCCGTAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
21280 CGAGTTCGGATGC
66 CGAGTTCGGATGC
21293 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACGTCTCAC
Found at i:27916 original size:15 final size:15
Alignment explanation
Indices: 27896--27949 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
27886 GGTCGTGAAT
*
27896 CACACATGGCCTAGA
1 CACACACGGCCTAGA
27911 CACACACGGCCTAGACA
1 CACACACGGCCTAG--A
27928 CACACACGGCCTAGA
1 CACACACGGCCTAGA
27943 CACACAC
1 CACACAC
27950 CTGTGTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
15 21 0.58
17 15 0.42
ACGTcount: A:0.35, C:0.41, G:0.17, T:0.07
Consensus pattern (15 bp):
CACACACGGCCTAGA
Found at i:27930 original size:17 final size:17
Alignment explanation
Indices: 27896--27949 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
27886 GGTCGTGAAT
*
27896 CACACATGGCCTAG--A
1 CACACACGGCCTAGACA
27911 CACACACGGCCTAGACA
1 CACACACGGCCTAGACA
27928 CACACACGGCCTAGACA
1 CACACACGGCCTAGACA
27945 CACAC
1 CACAC
27950 CTGTGTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
15 13 0.36
17 23 0.64
ACGTcount: A:0.35, C:0.41, G:0.17, T:0.07
Consensus pattern (17 bp):
CACACACGGCCTAGACA
Found at i:33041 original size:48 final size:48
Alignment explanation
Indices: 32975--33186 Score: 186
Period size: 46 Copynumber: 4.5 Consensus size: 48
32965 AAGCTGACGC
* *
32975 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCAAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCTGATG
** * ** * *
33023 CATGTCTGAGACATGTCTTACACTAGC-TCT-CGTCTGAAAG-TCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCT-GATG
* * * *
33069 CATGTCCCAGACATGTCTTACACTGGCTAGTATATCTCAAGGCCGATT
1 CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCTGATG
* * *
33117 CATGTCCCAGATATGTCTTACACTAGCTCTCGTA-ATGT---GGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-T-GTATATCTCAAGGCTGATG
* *
33163 CATGTCCCAGACATATCTTCCACT
1 CATGTCCCAGACATGTCTTACACT
33187 GGCATACGTA
Statistics
Matches: 130, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
45 1 0.01
46 61 0.47
47 3 0.02
48 59 0.45
49 3 0.02
50 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGACATGTCTTACACTAGCTTGTATATCTCAAGGCTGATG
Found at i:33187 original size:94 final size:94
Alignment explanation
Indices: 32975--33189 Score: 279
Period size: 94 Copynumber: 2.3 Consensus size: 94
32965 AAGCTGACGC
* * * * **
32975 CATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCAAGGCTAATGCATGTCTGAGACATGTC
1 CATGTCCCAGACATGTCTTACACTGGCTAGTATATCTCAAGGCCAATGCATGTCCCAGACATGTC
* *
33040 TTACACTAGCTCTCGTCTGAAAGTCGATG
66 TTACACTAGCTCTCGTATGAAAGCCGATG
* * *
33069 CATGTCCCAGACATGTCTTACACTGGCTAGTATATCTCAAGGCCGATTCATGTCCCAGATATGTC
1 CATGTCCCAGACATGTCTTACACTGGCTAGTATATCTCAAGGCCAATGCATGTCCCAGACATGTC
**
33134 TTACACTAGCTCTCGTAATG-TGGCCGATG
66 TTACACTAGCTCTCGT-ATGAAAGCCGATG
* *
33163 CATGTCCCAGACATATCTTCCACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
33190 ATACGTATCA
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
94 103 0.98
95 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (94 bp):
CATGTCCCAGACATGTCTTACACTGGCTAGTATATCTCAAGGCCAATGCATGTCCCAGACATGTC
TTACACTAGCTCTCGTATGAAAGCCGATG
Found at i:38728 original size:27 final size:27
Alignment explanation
Indices: 38698--38780 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 27
38688 ATCTCATATC
* *
38698 TGTAGGCTAGTATTACTGAAATACCCT
1 TGTAGGATAGAATTACTGAAATACCCT
* * *
38725 TGTAGGGTAGAATTACTGAAATGCCCA
1 TGTAGGATAGAATTACTGAAATACCCT
* *
38752 TGTAGGATAGAATTACTAAAATATCCT
1 TGTAGGATAGAATTACTGAAATACCCT
38779 TG
1 TG
38781 GGTTACAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (27 bp):
TGTAGGATAGAATTACTGAAATACCCT
Found at i:38798 original size:26 final size:27
Alignment explanation
Indices: 38762--38832 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
38752 TGTAGGATAG
* * *
38762 AATTACTAAAATA-TCCTTGGGT-TACA
1 AATTACCAAAATACCCCTAGGGTGTA-A
*
38788 AATTACCAAAATACCCCTAGGTTGTAA
1 AATTACCAAAATACCCCTAGGGTGTAA
38815 AATTACCAAAATACCCCT
1 AATTACCAAAATACCCCT
38833 GATTTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 12 0.31
27 25 0.64
28 2 0.05
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGGGTGTAA
Found at i:38823 original size:27 final size:27
Alignment explanation
Indices: 38787--38884 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
38777 CTTGGGTTAC
*
38787 AAATTACCAAAATACCCCT-AGGTTGTA
1 AAATTACCAAAATACCCCTGA-CTTGTA
* *
38814 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGACTTGTA
***
38841 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GACTTGTA
*
38868 AAATTACAAAAATACCC
1 AAATTACCAAAATACCC
38885 TCAACTTGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
26 4 0.07
27 51 0.88
28 3 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGACTTGTA
Found at i:38938 original size:27 final size:25
Alignment explanation
Indices: 38908--39024 Score: 85
Period size: 27 Copynumber: 4.4 Consensus size: 25
38898 AAATACCTTC
38908 GATTTCTAAAATTACCAAAATAACCCT
1 GATTTC-AAAATTA-CAAAATAACCCT
* *
38935 GATTTAGAAAATTACAAAATACCCCT
1 GATTT-CAAAATTACAAAATAACCCT
* *
38961 -ATTTACAAAATTATAGAAATACCCCT
1 GATTT-CAAAATTACA-AAATAACCCT
* *
38987 AATTTACAAAATTATAGAAAT-ACCCTT
1 GATTT-CAAAATTACA-AAATAACCC-T
39014 GACTTTCAAAA
1 GA-TTTCAAAA
39025 ATTATAGAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
25 13 0.16
26 24 0.30
27 39 0.49
28 3 0.04
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (25 bp):
GATTTCAAAATTACAAAATAACCCT
Found at i:38960 original size:26 final size:27
Alignment explanation
Indices: 38925--39038 Score: 144
Period size: 27 Copynumber: 4.3 Consensus size: 27
38915 AAAATTACCA
* * *
38925 AAATAACCCTGATTTAGAAAATTACA-
1 AAATACCCCTGATTTACAAAATTATAG
38951 AAATACCCCT-ATTTACAAAATTATAG
1 AAATACCCCTGATTTACAAAATTATAG
*
38977 AAATACCCCTAATTTACAAAATTATAG
1 AAATACCCCTGATTTACAAAATTATAG
*
39004 AAATACCCTTGACTTT-CAAAAATTATAG
1 AAATACCCCTGA-TTTAC-AAAATTATAG
39032 AAATACC
1 AAATACC
39039 ATTGGTTTGC
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
25 13 0.16
26 19 0.24
27 27 0.34
28 20 0.25
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (27 bp):
AAATACCCCTGATTTACAAAATTATAG
Found at i:38981 original size:52 final size:55
Alignment explanation
Indices: 38925--39036 Score: 142
Period size: 52 Copynumber: 2.1 Consensus size: 55
38915 AAAATTACCA
* *
38925 AAATAACCCTGATTTAGAAAATTACA-AAATACCCCT-A-TTT-ACAAAATTATAG
1 AAATAACCCTAATTTACAAAATTACAGAAATACCCCTGACTTTCA-AAAATTATAG
* * *
38977 AAATACCCCTAATTTACAAAATTATAGAAATACCCTTGACTTTCAAAAATTATAG
1 AAATAACCCTAATTTACAAAATTACAGAAATACCCCTGACTTTCAAAAATTATAG
39032 AAATA
1 AAATA
39037 CCATTGGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
52 22 0.43
53 9 0.18
54 1 0.02
55 18 0.35
56 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.29
Consensus pattern (55 bp):
AAATAACCCTAATTTACAAAATTACAGAAATACCCCTGACTTTCAAAAATTATAG
Found at i:39062 original size:27 final size:27
Alignment explanation
Indices: 39031--39084 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
39021 AAAAATTATA
39031 GAAATACCATTGGTTTGCAGAATTACC
1 GAAATACCATTGGTTTGCAGAATTACC
* * *
39058 GAAATACCCTTGGTTTGTAGATTTACC
1 GAAATACCATTGGTTTGCAGAATTACC
39085 AAAACACCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GAAATACCATTGGTTTGCAGAATTACC
Found at i:39093 original size:27 final size:27
Alignment explanation
Indices: 39040--39096 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39030 AGAAATACCA
* *
39040 TTGGTTTGCAGAATTACCGAAATACCC
1 TTGGTTTGCAGAATTACCAAAACACCC
* *
39067 TTGGTTTGTAGATTTACCAAAACACCC
1 TTGGTTTGCAGAATTACCAAAACACCC
39094 TTG
1 TTG
39097 TAGGGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (27 bp):
TTGGTTTGCAGAATTACCAAAACACCC
Found at i:40891 original size:15 final size:16
Alignment explanation
Indices: 40871--40902 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40861 ATTATATGAA
40871 TAATTATG-TTTTATT
1 TAATTATGTTTTTATT
40886 TAATTATGTTTTTATT
1 TAATTATGTTTTTATT
40902 T
1 T
40903 CTTTGTAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TAATTATGTTTTTATT
Found at i:43259 original size:6 final size:6
Alignment explanation
Indices: 43234--43308 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
43224 AGTGTGAAAG
** * **
43234 AAAGTAA AAAGAGA ATAAGAA AAAGAAA AAAGAA ATTGAA AAGGAA AGTGAA
1 AAAG-AA AAAGA-A A-AAGAA AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA
* *
43286 AAAGAA AAAGAG AAGGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGA
43309 GATCGAAATC
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
6 35 0.66
7 14 0.26
8 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:51485 original size:40 final size:39
Alignment explanation
Indices: 51441--51664 Score: 236
Period size: 40 Copynumber: 5.7 Consensus size: 39
51431 GCCACTAGCT
*
51441 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
** * *
51481 CAAATGCCTTCAAGACTTCGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
51520 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
51560 CAAACGCCTT-TGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * * ** * *
51599 CGAATGCCTTCGGGACTTAGCCCAGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
51639 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
51665 TATCATCCGA
Statistics
Matches: 155, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
39 72 0.46
40 83 0.54
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:51597 original size:79 final size:79
Alignment explanation
Indices: 51441--51621 Score: 247
Period size: 79 Copynumber: 2.3 Consensus size: 79
51431 GCCACTAGCT
* * * * *
51441 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCAAGACTTCGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCAAGACTTAGCCCGG
51506 TATAATAACTCGCA
66 TATAATAACTCGCA
* **
51520 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCACAAACGCCTT-TGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCAAGACTTAGCCCGG
* *
51584 ATATAGTAGCTCGCA
66 -TATAATAACTCGCA
*
51599 CGAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
51622 AGAATTAGCC
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 11 0.12
79 79 0.88
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAACGCCTTCAAGACTTAGCCCGG
TATAATAACTCGCA
Found at i:58586 original size:39 final size:40
Alignment explanation
Indices: 58542--58785 Score: 266
Period size: 39 Copynumber: 6.2 Consensus size: 40
58532 CCTTCGGAGT
* * *
58542 TTAG-CCGGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
* * *
58581 TTAGCCCGGTTATAGTAACTTGCACAAATGCCTTC-GGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
**
58620 TTAGCCCGG-TATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
** * *
58659 TTAGCCCGGATATAATAGCTCGCACAAACGCCTTC-GGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
* * *
58698 TTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
* * * *
58738 TTAGCCCGAAT-TAGCCACTAGCTCAAATG-CTCTCGGGAC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCT-TCGGGAC
58777 TTAGCCCGG
1 TTAGCCCGG
58786 TTATCATCCG
Statistics
Matches: 180, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
38 25 0.14
39 93 0.52
40 62 0.34
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGAC
Done.