Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1606
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: 34041
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:752 original size:3 final size:3
Alignment explanation
Indices: 744--786 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
734 GGCTAGTTGT
744 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
787 GCCAAACACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1306 original size:20 final size:20
Alignment explanation
Indices: 1283--1320 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1273 AGAGTGTGTC
*
1283 GAAAACAAGAACAAGAAATG
1 GAAAACAACAACAAGAAATG
*
1303 GAAAGCAACAACAAGAAA
1 GAAAACAACAACAAGAAA
1321 GGTCTGCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.13, G:0.18, T:0.03
Consensus pattern (20 bp):
GAAAACAACAACAAGAAATG
Found at i:2074 original size:3 final size:3
Alignment explanation
Indices: 2068--2104 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2058 TGACTACTAT
2068 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2105 TGGGGTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2786 original size:62 final size:62
Alignment explanation
Indices: 2717--2844 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
2707 AAGAATGCAT
2717 ATAAGTAATTAGGACATCTGAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAG
1 ATAAGTAATTAGGACATCTGAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAG
2779 ATAAGTAATTAGGACATCTGAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAG
1 ATAAGTAATTAGGACATCTGAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAG
2841 ATAA
1 ATAA
2845 AAGGAAAAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (62 bp):
ATAAGTAATTAGGACATCTGAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAG
Found at i:2859 original size:57 final size:60
Alignment explanation
Indices: 2736--2860 Score: 175
Period size: 62 Copynumber: 2.1 Consensus size: 60
2726 TAGGACATCT
* * *
2736 GAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAGATAAGTAATTAGGACATCT
1 GAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAGATAAG-AA-TAGGAAAACA
*
2798 GAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAGAT-A-AA-AGGAAAAGA
1 GAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAGATAAGAATAGGAAAACA
2855 GAAAAA
1 GAAAAA
2861 GTTAAAAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
57 11 0.19
59 2 0.03
61 1 0.02
62 45 0.76
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.25
Consensus pattern (60 bp):
GAAAAACCAAAGGAAATTAGATAAAATAAATTTATTTTATAAGATAAGAATAGGAAAACA
Found at i:2932 original size:16 final size:15
Alignment explanation
Indices: 2905--2973 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 15
2895 GCAAATTTTT
*
2905 AAATATTATTAAATTC
1 AAATATT-TTAATTTC
*
2921 AAATCATTTTAATTTT
1 AAAT-ATTTTAATTTC
2937 AAATTATTTTAATTTTC
1 AAA-TATTTTAA-TTTC
*
2954 AAATATTTTTTATTTC
1 AAATA-TTTTAATTTC
2970 AAAT
1 AAAT
2974 CAATTAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 30 0.67
17 15 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATATTTTAATTTC
Found at i:2940 original size:32 final size:32
Alignment explanation
Indices: 2901--2962 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
2891 ATTAGCAAAT
2901 TTTTAAA-TATTATTAA-ATTCAAATCATTTTAA
1 TTTTAAATTATT-TTAATATTCAAAT-ATTTTAA
*
2933 TTTTAAATTATTTTAATTTTCAAATATTTT
1 TTTTAAATTATTTTAATATTCAAATATTTT
2963 TTATTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTTAAATTATTTTAATATTCAAATATTTTAA
Found at i:2994 original size:21 final size:19
Alignment explanation
Indices: 2970--3010 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2960 TTTTTATTTC
2970 AAATCAATTAAATTTAATATT
1 AAATCAA-TAAATTTAA-ATT
*
2991 AAATTAATAAATTTAAATT
1 AAATCAATAAATTTAAATT
3010 A
1 A
3011 TTTATCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATCAATAAATTTAAATT
Found at i:2998 original size:49 final size:49
Alignment explanation
Indices: 2898--2998 Score: 114
Period size: 49 Copynumber: 2.1 Consensus size: 49
2888 TGGATTAGCA
* * * **
2898 AATTTTTAAATATTATTAAATTCAAATCATTTTAATTTTAAATTATTTT
1 AATTTTCAAATATTATTAAATTCAAATCATATTAAATTTAAATTAAATT
* * *
2947 AATTTTCAAATATTTTTTATTTCAAATCA-ATTAAATTTAATATTAAATT
1 AATTTTCAAATATTATTAAATTCAAATCATATTAAATTTAA-ATTAAATT
2996 AAT
1 AAT
2999 AAATTTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 9 0.21
49 34 0.79
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (49 bp):
AATTTTCAAATATTATTAAATTCAAATCATATTAAATTTAAATTAAATT
Found at i:3120 original size:24 final size:24
Alignment explanation
Indices: 3084--3162 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
3074 ACTATTTAAA
* *
3084 TTTATATTTATTAAATTTAATCAT
1 TTTAAATTAATTAAATTTAATCAT
3108 TTTAAATTAATT--ATTTAAATCAT
1 TTTAAATTAATTAAATTT-AATCAT
* * *
3131 TTTAACTATAA-AAAATTCAATCAT
1 TTTAAAT-TAATTAAATTTAATCAT
*
3155 TTCAAATT
1 TTTAAATT
3163 TAAATCATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.09
23 13 0.30
24 24 0.55
25 3 0.07
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAAATTAATTAAATTTAATCAT
Found at i:3173 original size:15 final size:16
Alignment explanation
Indices: 3149--3207 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
3139 TAAAAAATTC
3149 AATCATTTCAAATTTA
1 AATCATTTCAAATTTA
3165 AATCA-TTCAAAATTTA
1 AATCATTTC-AAATTTA
* * *
3181 AAACATTTCAACTCTA
1 AATCATTTCAAATTTA
3197 AATCATTTCAA
1 AATCATTTCAA
3208 CTCAGCGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 31 0.84
17 3 0.08
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (16 bp):
AATCATTTCAAATTTA
Found at i:14663 original size:18 final size:18
Alignment explanation
Indices: 14640--14697 Score: 116
Period size: 18 Copynumber: 3.2 Consensus size: 18
14630 CATTGCTGCC
14640 TCAGATTTGGGTACAAAT
1 TCAGATTTGGGTACAAAT
14658 TCAGATTTGGGTACAAAT
1 TCAGATTTGGGTACAAAT
14676 TCAGATTTGGGTACAAAT
1 TCAGATTTGGGTACAAAT
14694 TCAG
1 TCAG
14698 GAAATGCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (18 bp):
TCAGATTTGGGTACAAAT
Found at i:26687 original size:15 final size:17
Alignment explanation
Indices: 26657--26692 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
26647 AATAAAAAAC
26657 TTAAAAAAACTAAATAT
1 TTAAAAAAACTAAATAT
26674 TTAAAAAAA-T-AATAT
1 TTAAAAAAACTAAATAT
26689 TTAA
1 TTAA
26693 CGAAAATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAAAAACTAAATAT
Found at i:31321 original size:27 final size:27
Alignment explanation
Indices: 31291--31344 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
31281 AAAATTTAAC
*
31291 AAAA-TAATAAAATGGAAAAAATACTTA
1 AAAATTAATAAAATAG-AAAAATACTTA
**
31318 AAAATTAATATGATAGAAAAATACTTA
1 AAAATTAATAAAATAGAAAAATACTTA
31345 TTAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATTAATAAAATAGAAAAATACTTA
Done.