Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold916
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: 15307
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:286 original size:52 final size:51
Alignment explanation
Indices: 125--297 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 51
115 GAAATAACGA
* *
125 GGTTGGAGTATCCTCGATTGTG-AAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-TGAAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * *
177 AATTGGAGTATCCCCGATTTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTTGAA--A-AAATTGGTATTTTGAAAATAAAATCGG
* * *
231 GGTTGGAGTATCCCCGATTATGAAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATT-TGAAAAAATTGGTATTTTGAAAATAAAATCGG
283 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
298 TCAGAAATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
51 1 0.01
52 53 0.54
53 1 0.01
54 33 0.33
55 11 0.11
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTTGAAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:343 original size:27 final size:28
Alignment explanation
Indices: 280--355 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
270 AAAATAAAGT
*
280 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
308 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
335 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
356 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2843 original size:13 final size:13
Alignment explanation
Indices: 2825--2850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2815 ACAAAGATCC
2825 ATGTATCGATACA
1 ATGTATCGATACA
2838 ATGTATCGATACA
1 ATGTATCGATACA
2851 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2846 original size:33 final size:33
Alignment explanation
Indices: 2804--2870 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2794 AAAATTTCCA
***
2804 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2837 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2870 A
1 A
2871 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2930 original size:13 final size:13
Alignment explanation
Indices: 2912--2936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2902 ACAATACTTA
2912 TGTATCGATACAT
1 TGTATCGATACAT
2925 TGTATCGATACA
1 TGTATCGATACA
2937 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2935 original size:32 final size:32
Alignment explanation
Indices: 2893--2955 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2883 TAGCTAATTA
* *
2893 TGTATTGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2925 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2956 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2949 original size:19 final size:19
Alignment explanation
Indices: 2890--2957 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2880 CAGTAGCTAA
* *
2890 TTATGTATTGATACAATAC
1 TTATGTATCGATACAAAAC
2909 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
2924 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
2941 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2958 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 27 0.64
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:3037 original size:21 final size:21
Alignment explanation
Indices: 3013--3069 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3003 CATTTGTAGG
3013 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3034 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3055 ATGTATCGATACATT
1 ATGTATCGATACATT
3070 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3079 original size:1 final size:1
Alignment explanation
Indices: 3073--3112 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
3063 ATACATTTAA
***
3073 TTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3113 CAAACACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.05, C:0.03, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:3097 original size:21 final size:21
Alignment explanation
Indices: 3071--3111 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3061 CGATACATTT
3071 AATTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTC
3092 AATTTTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTTTT
3112 TCAAACACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.02, G:0.00, T:0.88
Consensus pattern (21 bp):
AATTTTTTTTTTTTTTTTTTC
Found at i:3101 original size:22 final size:22
Alignment explanation
Indices: 3073--3115 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3063 ATACATTTAA
3073 TTTTTTTTTTTTTTTTTTCAAT
1 TTTTTTTTTTTTTTTTTTCAAT
3095 TTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTCAA
3116 ACACTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTTTTTTTTTTTTTTCAAT
Found at i:4402 original size:27 final size:27
Alignment explanation
Indices: 4345--4400 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
4335 CGAAACTCTT
*
4345 AAATAATCTATAGGGTTATTTAATAAA
1 AAATAATCTATAGGCTTATTTAATAAA
*
4372 AAATAATTTATA-GCTTATTTAATAAA
1 AAATAATCTATAGGCTTATTTAATAAA
4398 AAA
1 AAA
4401 ATCAACTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (27 bp):
AAATAATCTATAGGCTTATTTAATAAA
Found at i:9840 original size:21 final size:21
Alignment explanation
Indices: 9808--9867 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 21
9798 TGATTAAAAT
9808 TCAAATTC-AATTTAATAATGA
1 TCAAA-TCAAATTTAATAATGA
* **
9829 TCAAATCAAATTCGAAT-ATTT
1 TCAAATCAAATT-TAATAATGA
9850 TCAAATCAAATTTGAATA
1 TCAAATCAAATTT-AATA
9868 GTTTACAAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (21 bp):
TCAAATCAAATTTAATAATGA
Found at i:14925 original size:21 final size:22
Alignment explanation
Indices: 14882--14925 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
14872 ATTTTTACTA
*
14882 AAAAATATTTAAATACTAATTAT
1 AAAAATA-TTAAATAATAATTAT
*
14905 AAAAATA-TAAATAATATTTAT
1 AAAAATATTAAATAATAATTAT
14926 GAGTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATTAAATAATAATTAT
Found at i:15017 original size:15 final size:15
Alignment explanation
Indices: 14993--15022 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14983 TTTTTATTTA
14993 ATTTACTTAATTTTT
1 ATTTACTTAATTTTT
*
15008 ATTTATTTAATTTTT
1 ATTTACTTAATTTTT
15023 TGGATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTACTTAATTTTT
Done.