Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1364
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: 34350
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Found at i:2826 original size:28 final size:28
Alignment explanation
Indices: 2764--2860 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
2754 TATTAAGTCT
*
2764 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
2791 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * *
2819 GCACACTTAGTGCTGA-ACAATTTAAACCC
1 GCACACTTAGTGCT-ATATAA-TCAAACTC
2848 GCACACTTAGTGC
1 GCACACTTAGTGC
2861 CAATCTCATG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 21 0.33
28 22 0.35
29 20 0.32
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:7634 original size:20 final size:20
Alignment explanation
Indices: 7605--7651 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
7595 ATTTTGATAA
*
7605 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
7625 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
7645 ACATGAT
1 ACATGAT
7652 GTATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:7770 original size:23 final size:24
Alignment explanation
Indices: 7700--7795 Score: 142
Period size: 24 Copynumber: 4.0 Consensus size: 24
7690 GGAGGAAGTG
7700 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
7724 TAAAAGGGCTTATGCCCCAATTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
7748 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
7771 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
7796 ATGAAAAAGC
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.27
24 40 0.61
25 8 0.12
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:8044 original size:31 final size:31
Alignment explanation
Indices: 7990--8050 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
7980 CGTTTACAGT
*
7990 AAAGGCTTCGGCCCAGTAATATGAGATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
* * **
8021 AAAGGTTTCGGCCTAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
8051 AAATATTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:15659 original size:31 final size:31
Alignment explanation
Indices: 15622--15692 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
15612 TTACTAGGCT
15622 GAAGCCTTTTCATAAATCATATCACTGGGCC
1 GAAGCCTTTTCATAAATCATATCACTGGGCC
*
15653 GAAGCCTTTTCATAAATCATATCATTGGGCC
1 GAAGCCTTTTCATAAATCATATCACTGGGCC
15684 GAAGCCTTT
1 GAAGCCTTT
15693 ACTGTAAGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (31 bp):
GAAGCCTTTTCATAAATCATATCACTGGGCC
Found at i:15982 original size:26 final size:26
Alignment explanation
Indices: 15898--16033 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
15888 CTAGAGGCCT
15898 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
15922 AGCCCTTTTTGATAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
*
15947 AGCCCTTTTCAATAAATTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
** *
15973 AGCCCTTTTCGGTAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
15999 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
16025 AGCCCTTTT
1 AGCCCTTTT
16034 GCACTTCCTC
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
23 5 0.05
24 6 0.06
25 32 0.33
26 55 0.56
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:16934 original size:27 final size:27
Alignment explanation
Indices: 16839--16925 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
16829 CATTCGTCAT
* *
16839 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
16866 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
*
16893 TTTACCCTACAGGGGCTTTACGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
16920 TTTACC
1 TTTACC
16926 TAATAGGGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:17158 original size:81 final size:80
Alignment explanation
Indices: 17070--17273 Score: 302
Period size: 81 Copynumber: 2.5 Consensus size: 80
17060 TGTAAATTAG
*
17070 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTTTA
*
17134 GTAATTTTACAAACTA
65 GCAATTTTACAAACTA
*
17150 GGGATATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTA
1 GGG-TATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTA
* *
17215 GCAATTTTATAGACTA
65 GCAATTTTACAAACTA
** * *
17231 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATT
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATT
17274 CTGTAAACCG
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
80 39 0.35
81 72 0.64
82 2 0.02
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG
CAATTTTACAAACTA
Found at i:17239 original size:26 final size:27
Alignment explanation
Indices: 17204--17266 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
17194 TTACAAACCA
*
17204 AGGGTATTTTAGCAATTTTA-TAGA-CT
1 AGGGTATTTTAGCAATTTTACT-GATCG
* *
17230 AGGGTATTTTGGTAATTTTACTGATCG
1 AGGGTATTTTAGCAATTTTACTGATCG
17257 AGGGTATTTT
1 AGGGTATTTT
17267 GGTAATTCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.44
Consensus pattern (27 bp):
AGGGTATTTTAGCAATTTTACTGATCG
Found at i:17316 original size:27 final size:27
Alignment explanation
Indices: 16956--17384 Score: 213
Period size: 27 Copynumber: 15.8 Consensus size: 27
16946 TTTCATCCTA
* * * * *
16956 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * *
16983 CAAGGGTATTTCAGTAATTTTGTTAAAC
1 CAAGGGTATTTTGGTAATTTT-ATAAAT
* *** *
17011 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTATAAA-T
* * *
17040 CAAGGGTATTTCT-ATAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTATAAAT
* * *
17067 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
** * * *
17094 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
17120 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTATAAAT
* *
17147 CTAGGGATATTTTGGTAATTTTACAAAT
1 CAAGGG-TATTTTGGTAATTTTATAAAT
** * * *
17175 TGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* * *
17202 CAAGGGTATTTTAGCAATTTTATAGA-
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
17228 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTA-TAAAT
* * * *
17255 CGAGGGTATTTTGGTAATTCTGTAAAC
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
17282 CGAA-GGTATTTTAGTAATTTTGTAAAT
1 C-AAGGGTATTTTGGTAATTTTATAAAT
***** * *
17309 CAAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
*** * *
17336 CAAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTGGTAATTTTATAAAT
* *
17363 CGAGGGTACTTTGGTAATTTTA
1 CAAGGGTATTTTGGTAATTTTA
17385 CAATTTGAAG
Statistics
Matches: 320, Mismatches: 69, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
26 29 0.09
27 241 0.75
28 32 0.10
29 18 0.06
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTATAAAT
Found at i:25566 original size:93 final size:93
Alignment explanation
Indices: 25454--25625 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
25444 CGCCCATAAG
*
25454 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
25518 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
25547 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
25612 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
25626 TCAACATCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:25620 original size:46 final size:46
Alignment explanation
Indices: 25447--25622 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
25437 TGTAACCCGC
* *
25447 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
25493 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
25543 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
25586 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
25623 TGCTCAACAT
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Done.