Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2001
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: 49441
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:6911 original size:27 final size:27
Alignment explanation
Indices: 6876--6927 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6866 CCACTGAATC
* *
6876 GGGGAATCATCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
6903 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
6928 TTCATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:6997 original size:69 final size:70
Alignment explanation
Indices: 6886--7034 Score: 230
Period size: 71 Copynumber: 2.1 Consensus size: 70
6876 GGGGAATCAT
*
6886 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTT-CATTTCAAATATACAATGGA
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTACATTTCAAAGATACAATGGA
6950 TATCG
66 TATCG
***
6955 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTT-ACATTTCAAAGATACAATG
7019 GATATCG
64 GATATCG
7026 CACTTAGCA
1 CACTTAGCA
7035 CCACCAATGA
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
68 20 0.27
69 23 0.32
71 30 0.41
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (70 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTACATTTCAAAGATACAATGGA
TATCG
Found at i:7138 original size:104 final size:103
Alignment explanation
Indices: 6954--7176 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
6944 AATGGATATC
6954 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
7019 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
7057 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
7122 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
7161 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
7177 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:7538 original size:29 final size:29
Alignment explanation
Indices: 7505--7568 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
7495 TAATCCACCA
7505 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
7534 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
7564 CCCAA
1 CCCAA
7569 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:7542 original size:30 final size:30
Alignment explanation
Indices: 7512--7568 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
7502 CCACCCAACT
7512 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
7541 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
7569 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:23620 original size:27 final size:27
Alignment explanation
Indices: 23584--23672 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
23574 CCCCCAATTG
* *
23584 TAAAATTA-CCAAAGTACCCTCGGTTTA
1 TAAAACTACCCAAA-TACCCTCGATTTA
*
23611 TAAAACTACCCAAATATCCTCGATTTA
1 TAAAACTACCCAAATACCCTCGATTTA
* * ****
23638 TAGAATTACCGTTTTACCCTCGATTTA
1 TAAAACTACCCAAATACCCTCGATTTA
*
23665 TAGAACTA
1 TAAAACTA
23673 TCGTTTTACC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
27 45 0.90
28 5 0.10
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (27 bp):
TAAAACTACCCAAATACCCTCGATTTA
Found at i:23656 original size:54 final size:54
Alignment explanation
Indices: 23598--23790 Score: 251
Period size: 54 Copynumber: 3.6 Consensus size: 54
23588 ATTACCAAAG
* **** * *
23598 TACCCTCGGTTTATAAAACTACCCAAATATCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAAAACTACCGTTTTACCCTCGATTTATAGAATTACCATTT
* *
23652 TACCCTCGATTTATAGAACTATCGTTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAACTACCGTTTTACCCTCGATTTATAGAATTACCATTT
* * *
23706 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAAAACTACCGTTTTACCCTCGATTTATAGAATTACCATTT
* * *
23760 TACCCCCGATTTACAAAATTACCGTTTTACC
1 TACCCTCGATTTATAAAACTACCGTTTTACC
23791 ATTGTTTACA
Statistics
Matches: 123, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 123 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (54 bp):
TACCCTCGATTTATAAAACTACCGTTTTACCCTCGATTTATAGAATTACCATTT
Found at i:23677 original size:27 final size:27
Alignment explanation
Indices: 23628--23790 Score: 254
Period size: 27 Copynumber: 6.0 Consensus size: 27
23618 ACCCAAATAT
23628 CCTCGATTTATAGAATTACCGTTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
* *
23655 CCTCGATTTATAGAACTATCGTTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
*
23682 CCTCGATTTATAGAATTACCATTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
*
23709 CCTCGATTTATAGAATTACTGTTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
*
23736 CCTCGATTTATAGAATTACCATTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
* * *
23763 CCCCGATTTACAAAATTACCGTTTTAC
1 CCTCGATTTATAGAATTACCGTTTTAC
23790 C
1 C
23791 ATTGTTTACA
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CCTCGATTTATAGAATTACCGTTTTAC
Found at i:23832 original size:27 final size:27
Alignment explanation
Indices: 23794--23951 Score: 185
Period size: 27 Copynumber: 5.9 Consensus size: 27
23784 TTTTACCATT
* * *
23794 GTTTACAAAATTACTAAAATACCCTTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
23821 GTTTAAAAAATTACCAAAATA-CCCTC
1 GTTTATAAAATTACCAAAATACCCCTG
* *
23847 GATCAGTAAAATTACCAAAATACCCCTG
1 GTTTA-TAAAATTACCAAAATACCCCTG
* *
23875 GTTTGTAAAATTACTAAAATACCCCTG
1 GTTTATAAAATTACCAAAATACCCCTG
* *
23902 GTTTGTAAAATTACCAAAATACCCCTA
1 GTTTATAAAATTACCAAAATACCCCTG
*
23929 ATTTATAAAA-TACCAAAATACCC
1 GTTTATAAAATTACCAAAATACCC
23952 TTATAGGGTA
Statistics
Matches: 113, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 19 0.17
27 88 0.78
28 6 0.05
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
GTTTATAAAATTACCAAAATACCCCTG
Found at i:23938 original size:81 final size:80
Alignment explanation
Indices: 23800--23951 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 80
23790 CATTGTTTAC
* *
23800 AAAATTACTAAAATACCCTTGGTTTAAAAAATTACCAAAATACCCTCGATCAGTAAAATTACCAA
1 AAAATTACTAAAATACCCCTGGTTTAAAAAATTACCAAAATACCCTCAATCAGTAAAA-TACCAA
23865 AATACCCCTGGTTTGT
65 AATACCCCTGGTTTGT
** *
23881 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC-CTAATTTA-TAAAATACCA
1 AAAATTACTAAAATACCCCTGGTTTAAAAAATTACCAAAATACCCTC-AA-TCAGTAAAATACCA
23944 AAATACCC
64 AAATACCC
23952 TTATAGGGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 14 0.22
81 48 0.75
82 2 0.03
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.28
Consensus pattern (80 bp):
AAAATTACTAAAATACCCCTGGTTTAAAAAATTACCAAAATACCCTCAATCAGTAAAATACCAAA
ATACCCCTGGTTTGT
Found at i:23988 original size:27 final size:27
Alignment explanation
Indices: 23936--24046 Score: 107
Period size: 27 Copynumber: 4.1 Consensus size: 27
23926 CTAATTTATA
* *
23936 AAATACCAAAATACCCTTATAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
** ** *
23963 ATTTATTGAAATACCCTTGTACGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
*
23990 AAATACCGAAATACCCCTGTAGGGTAG
1 AAATACCGAAATACCCTTGTAGGGTAG
* * * *
24017 AATTACCGAGATACCCATGTGGGGTA-
1 AAATACCGAAATACCCTTGTAGGGTAG
24043 AAAT
1 AAAT
24047 TATCATTTTG
Statistics
Matches: 66, Mismatches: 18, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
26 3 0.05
27 63 0.95
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
AAATACCGAAATACCCTTGTAGGGTAG
Found at i:24296 original size:25 final size:25
Alignment explanation
Indices: 24256--24350 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
24246 AGGAAGTGCT
24256 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* * *
24281 AAGAGGGCTTTCCCCCAGTTTACAG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
24306 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
24331 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
24351 ATTAAAAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:26774 original size:27 final size:26
Alignment explanation
Indices: 26744--26807 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
26734 CCCCCAGTTG
*
26744 TAAAATTACCAAAGTATCCCCGGTTTA
1 TAAAATTACCAAA-TATCCCCGATTTA
* *
26771 TAAAACTACCCAAATATCCTCGATTTA
1 TAAAATTA-CCAAATATCCCCGATTTA
*
26798 TAGAATTACC
1 TAAAATTACC
26808 GTTTTACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.06
27 24 0.77
28 5 0.16
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (26 bp):
TAAAATTACCAAATATCCCCGATTTA
Found at i:26818 original size:27 final size:27
Alignment explanation
Indices: 26788--26912 Score: 178
Period size: 27 Copynumber: 4.6 Consensus size: 27
26778 ACCCAAATAT
*
26788 CCTCGATTTATAGAATTACCGTTTTAC
1 CCTCGATTTACAGAATTACCGTTTTAC
*
26815 CCTCGATTTACAGAATTACTGTTTTAC
1 CCTCGATTTACAGAATTACCGTTTTAC
* * *
26842 CCTCGTTTTATAGAATTACCATTTTAC
1 CCTCGATTTACAGAATTACCGTTTTAC
*
26869 CCTCGATTTACAGAATTATCGTTTTAC
1 CCTCGATTTACAGAATTACCGTTTTAC
* *
26896 CCTTGATTTACAAAATT
1 CCTCGATTTACAGAATT
26913 GCTAAAATAC
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (27 bp):
CCTCGATTTACAGAATTACCGTTTTAC
Found at i:26923 original size:27 final size:27
Alignment explanation
Indices: 26893--27058 Score: 156
Period size: 27 Copynumber: 6.2 Consensus size: 27
26883 ATTATCGTTT
* * *
26893 TACCCTTGATTTACAAAATTGCTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
26920 TACCCTTGGTTTACAAAATTACCAATA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
26947 TACCCTCGA-TCAGTAAAATTACGAAAA
1 TACCCTTGATTTA-TAAAATTACCAAAA
* * *
26974 TACCCTTGGTTTGTAAAATTACTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
27001 TACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
27028 TACCCCTGATTTATAAAA-TACCGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
27054 TACCC
1 TACCC
27059 CTGTAGGGTA
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
26 14 0.12
27 102 0.87
28 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
TACCCTTGATTTATAAAATTACCAAAA
Found at i:26924 original size:54 final size:54
Alignment explanation
Indices: 26812--26941 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
26802 ATTACCGTTT
* * * ***
26812 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGTTTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCAAAA
* * *
26866 TACCCTCGATTTACAGAATTA-TCGTTTTACCCTTGATTTACAAAATTGCTAAAA
1 TACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTACAAAATTACCAAAA
* * *
26920 TACCCTTGGTTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
26942 CAATATACCC
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
53 1 0.02
54 61 0.98
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACCAAAA
Found at i:26924 original size:81 final size:81
Alignment explanation
Indices: 26745--26956 Score: 212
Period size: 81 Copynumber: 2.6 Consensus size: 81
26735 CCCCAGTTGT
* * * * * *
26745 AAAATTACCAAAGTATCCC-CGGTTTATAAAACTACCCAA-ATATCCTCGATTTATAGAATTACC
1 AAAATTACTAAAATA-CCCTCGGTTTACAAAATTA-CCAATATACCCTCGATTTACAGAATTACC
26808 GTTTTACCCTCGATTTAC
64 GTTTTACCCTCGATTTAC
* **** * * * * * *
26826 AGAATTACTGTTTTACCCTCGTTTTATAGAATTACCATTTTACCCTCGATTTACAGAATTATCGT
1 AAAATTACTAAAATACCCTCGGTTTACAAAATTACCAATATACCCTCGATTTACAGAATTACCGT
*
26891 TTTACCCTTGATTTAC
66 TTTACCCTCGATTTAC
* *
26907 AAAATTGCTAAAATACCCTTGGTTTACAAAATTACCAATATACCCTCGAT
1 AAAATTACTAAAATACCCTCGGTTTACAAAATTACCAATATACCCTCGAT
26957 CAGTAAAATT
Statistics
Matches: 102, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
80 6 0.06
81 96 0.94
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTCGGTTTACAAAATTACCAATATACCCTCGATTTACAGAATTACCGT
TTTACCCTCGATTTAC
Found at i:27045 original size:81 final size:80
Alignment explanation
Indices: 26893--27058 Score: 194
Period size: 81 Copynumber: 2.1 Consensus size: 80
26883 ATTATCGTTT
* * *
26893 TACCCTTGATTTACAAAATTGCTAAAATACCCTTGGTTTACAAAATTACCAATATACCCTCGATC
1 TACCCTTGATTTACAAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCGATC
26958 AGTAAAATTA-CGAAAA
66 AGTAAAA-TACCG-AAA
* ** **
26974 TACCCTTGGTTTGTAAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC-CTGAT
1 TACCCTTGATTTACAAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTC-GA-
*
27038 TTA-TAAAATACCGAAA
64 TCAGTAAAATACCGAAA
27054 TACCC
1 TACCC
27059 CTGTAGGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
80 11 0.15
81 60 0.82
82 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (80 bp):
TACCCTTGATTTACAAAATTACTAAAATACCCCTGGTTTACAAAATTACCAAAATACCCTCGATC
AGTAAAATACCGAAA
Found at i:27090 original size:27 final size:27
Alignment explanation
Indices: 27046--27236 Score: 256
Period size: 27 Copynumber: 7.1 Consensus size: 27
27036 ATTTATAAAA
27046 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
27073 TACTGAAATACCCTTGTAAGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
*
27100 TACCGAAATACCCCAGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
*
27127 TACTGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
27154 TATCGAAATATCCTTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
27181 TACCGAAATATCCCTGTAGAGTTGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * *
27208 TACCGAGATACCCATGTAGGGTAAAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
27235 TA
1 TA
27237 TCATTTTGCC
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 141 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAT
Found at i:27162 original size:81 final size:82
Alignment explanation
Indices: 27046--27238 Score: 282
Period size: 81 Copynumber: 2.4 Consensus size: 82
27036 ATTTATAAAA
27046 TACCGAAATACCCCTGTAGGGTAGAATTA-CTGAAATACCCTTGTAAGGTAGAATTACCGAAATA
1 TACCGAAATACCCCTGTAGGGTAGAATTATCTGAAATACCCTTGTAAGGTAGAATTACCGAAATA
*
27110 CCCCAGTAGGGTAGAAT
66 CCCCAGTAGAGTAGAAT
* * *
27127 TACTGAAATACCCCTGTAGGGTAGAATTATC-GAAATATCCTTGTAGGGTAGAATTACCGAAATA
1 TACCGAAATACCCCTGTAGGGTAGAATTATCTGAAATACCCTTGTAAGGTAGAATTACCGAAATA
* * *
27191 TCCCTGTAGAGTTGAAT
66 CCCCAGTAGAGTAGAAT
* * *
27208 TACCGAGATACCCATGTAGGGTAAAATTATC
1 TACCGAAATACCCCTGTAGGGTAGAATTATC
27239 ATTTTGCCTC
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 99 0.99
82 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (82 bp):
TACCGAAATACCCCTGTAGGGTAGAATTATCTGAAATACCCTTGTAAGGTAGAATTACCGAAATA
CCCCAGTAGAGTAGAAT
Found at i:27477 original size:25 final size:25
Alignment explanation
Indices: 27443--27534 Score: 141
Period size: 25 Copynumber: 3.7 Consensus size: 25
27433 AGGAAGTGCT
*
27443 AAAAGGGCTTTGCTCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
27468 AAAAGGGCTTTGCCCCAGTTTACTG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
27493 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTACCG
27517 AAAGAGGGCTTTGCCCCA
1 AAA-AGGGCTTTGCCCCA
27535 ATTATTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 3 0.05
25 59 0.95
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:27545 original size:25 final size:25
Alignment explanation
Indices: 27471--27548 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
27461 TTTACCGAAA
* * *
27471 AGGGCTTTGCCCCAGTTTACTGAAA-
1 AGGGCTTTGCCCCA-ATTATTAAAAG
* *
27496 AGGGCTTTGCCCCAGTT-TATCAAAG
1 AGGGCTTTGCCCCAATTAT-TAAAAG
27521 AGGGCTTTGCCCCAATTATTAAAAG
1 AGGGCTTTGCCCCAATTATTAAAAG
27546 AGG
1 AGG
27549 TTAGGCCTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.13
25 38 0.84
26 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (25 bp):
AGGGCTTTGCCCCAATTATTAAAAG
Found at i:27561 original size:50 final size:51
Alignment explanation
Indices: 27443--27562 Score: 126
Period size: 50 Copynumber: 2.4 Consensus size: 51
27433 AGGAAGTGCT
* *
27443 AAAAGGGCTTTG-CTCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTACTG
1 AAAAGGGCTTGGCCTCCAGTTTACCGAAAAGGGCTTTGCCCCAGATTACTG
* * *
27493 AAAAGGGCTTTGCC-CCAGTTTATC-AAAGAGGGCTTTGCCCCA-ATTA-TT
1 AAAAGGGCTTGGCCTCCAGTTTACCGAAA-AGGGCTTTGCCCCAGATTACTG
27541 AAAAGAGG-TTAGGCCTCCAGTT
1 AAAAG-GGCTT-GGCCTCCAGTT
27563 ATATTATAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
48 8 0.13
49 11 0.18
50 41 0.67
51 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTGGCCTCCAGTTTACCGAAAAGGGCTTTGCCCCAGATTACTG
Found at i:29459 original size:29 final size:29
Alignment explanation
Indices: 29396--29463 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
29386 TAATCAACCA
29396 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
29425 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
29454 CGCACACTTA
1 CGCACACTTA
29464 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:29604 original size:29 final size:30
Alignment explanation
Indices: 29565--29643 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
29555 CTTAATAATC
29565 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
29595 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
29624 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
29644 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:37450 original size:29 final size:29
Alignment explanation
Indices: 37388--37454 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
37378 GTAATCACCA
37388 CGCAC-CTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
37416 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
37445 CGCACACTTA
1 CGCACACTTA
37455 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:37598 original size:29 final size:31
Alignment explanation
Indices: 37560--37633 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
37550 TAATCAACCG
*
37560 CGCA-ACTTAGTGCCATGTAC-TTTAAAC-T
1 CGCACACTTAGTGCCATGTACATTTAAACAC
37588 CGCACACTTAGTG-C-TGTACAATTTAAACAC
1 CGCACACTTAGTGCCATGTAC-ATTTAAACAC
37618 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
37634 ATCTCATGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 5 0.13
28 5 0.13
29 15 0.38
30 13 0.33
31 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (31 bp):
CGCACACTTAGTGCCATGTACATTTAAACAC
Found at i:39224 original size:31 final size:30
Alignment explanation
Indices: 39181--39262 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 30
39171 CATGAGATTT
39181 GGCACTAAGTGTGCG-GGTTTTAAAGTGGACA
1 GGCACTAAGTGTGCGAGGTTTTAAAGT--ACA
39212 -GCACGTAAGTGTGCGAGGTTTTAAAGTACA
1 GGCAC-TAAGTGTGCGAGGTTTTAAAGTACA
*
39242 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCGAGGTT
39263 GTATTATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
30 7 0.15
31 24 0.52
32 15 0.33
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (30 bp):
GGCACTAAGTGTGCGAGGTTTTAAAGTACA
Done.