Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1639
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: 20343
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2071 original size:39 final size:39
Alignment explanation
Indices: 1950--2120 Score: 209
Period size: 39 Copynumber: 4.3 Consensus size: 39
1940 GCTACTCGTT
* * *
1950 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
* * * *
1990 CAATTGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGGCTTAGCCCGGAATTAGTAACTCGCA
* *
2030 CAAATGCCTTCGGGCTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
* *
2069 CAAATGTCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
2108 CAAATGCCTTCGG
1 CAAATGCCTTCGG
2121 ATCGCACAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
39 72 0.63
40 39 0.34
41 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCA
Found at i:2127 original size:19 final size:19
Alignment explanation
Indices: 2103--2139 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2093 AATTAGTATC
2103 TCGCACAAATGCCTTCGGA
1 TCGCACAAATGCCTTCGGA
2122 TCGCACAAATGCCTTCGG
1 TCGCACAAATGCCTTCGG
2140 GCTTAGCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCACAAATGCCTTCGGA
Found at i:2154 original size:58 final size:58
Alignment explanation
Indices: 2064--2181 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
2054 AATTAGTATC
*
2064 TCGCACAAATGTCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA
1 TCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA
2122 TCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA
1 TCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA
2180 TC
1 TC
2182 TTAGTCCGGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (58 bp):
TCGCACAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGA
Found at i:2176 original size:39 final size:41
Alignment explanation
Indices: 2122--2231 Score: 122
Period size: 40 Copynumber: 2.7 Consensus size: 41
2112 TGCCTTCGGA
2122 TCGCACAAATGCCTTCGGGCTTAGCCCGGAAT-TAGT-A-T
1 TCGCACAAATGCCTTCGGGCTTAGCCCGGAATATAGTCACT
* * *
2160 CTCGCACAAATGCCTTCGGATCTTAGTCCGG-ATATGGTCACT
1 -TCGCACAAATGCCTTCGG-GCTTAGCCCGGAATATAGTCACT
*
2202 TAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
2232 CATCATTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
39 20 0.34
40 29 0.49
41 9 0.15
42 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (41 bp):
TCGCACAAATGCCTTCGGGCTTAGCCCGGAATATAGTCACT
Found at i:7900 original size:26 final size:26
Alignment explanation
Indices: 7829--7977 Score: 212
Period size: 26 Copynumber: 5.8 Consensus size: 26
7819 CCTCTTTAAT
*
7829 AACTGGGGCA-AATCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
7854 AACTGGGGCA-AAGCCTTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
7879 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
7905 AATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
7931 AACTGGGGCATAAGCCATTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
7957 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
7978 GCACTTCCTC
Statistics
Matches: 108, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 31 0.29
26 77 0.71
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:7937 original size:52 final size:52
Alignment explanation
Indices: 7829--7977 Score: 248
Period size: 52 Copynumber: 2.9 Consensus size: 52
7819 CCTCTTTAAT
* *
7829 AACTGGGGCA-AATCCCTTTTCGGTAAACTGGGGCA-AAGCCTTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
*
7879 AACTGGGGCATAAGCCCTTTTCGGTAAATTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
*
7931 AACTGGGGCATAAGCCATTTTCGGTAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
7978 GCACTTCCTC
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 10 0.11
51 23 0.25
52 59 0.64
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (52 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
Found at i:10869 original size:40 final size:40
Alignment explanation
Indices: 10814--10926 Score: 176
Period size: 40 Copynumber: 2.9 Consensus size: 40
10804 CATGTTAATG
10814 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
10854 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * *
10894 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
10927 GTGCTAATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
39 17 0.25
40 52 0.75
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:20207 original size:27 final size:26
Alignment explanation
Indices: 20166--20291 Score: 130
Period size: 27 Copynumber: 4.7 Consensus size: 26
20156 TAGAAAGTCA
**
20166 AGGGTATTTCT-GTAATTTTGTAAATC
1 AGGGTATTT-TGGTAATTTTACAAATC
*
20192 AGGTGTATTTTGGTAATTTTACAAATTA
1 AGG-GTATTTTGGTAATTTTACAAA-TC
* * *
20220 AGGGTATTTCGGTAATTTCACAAACC
1 AGGGTATTTTGGTAATTTTACAAATC
20246 AGTGGTATTTTGGTAATTTTACAAA-C
1 AG-GGTATTTTGGTAATTTTACAAATC
20272 TAGGGGTATTTTGGTAATTT
1 -A-GGGTATTTTGGTAATTT
20292 GTAAACCAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
26 7 0.08
27 73 0.86
28 5 0.06
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAATC
Found at i:20224 original size:54 final size:54
Alignment explanation
Indices: 20165--20317 Score: 172
Period size: 54 Copynumber: 2.9 Consensus size: 54
20155 TTAGAAAGTC
* *
20165 AAGGGTATTTCTGTAATTTTGTAAATCAGGTGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTCTGTAATTTTGTAAACCAGGTGTATTTTGGTAATTTTACAAACT
* ***
20219 AAGGGTATTTCGGTAATTTCACAAACCA-GTGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTCTGTAATTTTGTAAACCAGGT-GTATTTTGGTAATTTTACAAACT
* *
20273 AGGGGTATTT-TGGTAA-TTTGTAAACCAAGG-GTA-TTTAGTAATTTT
1 AAGGGTATTTCT-GTAATTTTGTAAACC-AGGTGTATTTTGGTAATTTT
20318 GTAAATCGAG
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
52 11 0.13
53 12 0.14
54 59 0.71
55 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (54 bp):
AAGGGTATTTCTGTAATTTTGTAAACCAGGTGTATTTTGGTAATTTTACAAACT
Found at i:20304 original size:26 final size:26
Alignment explanation
Indices: 20164--20331 Score: 105
Period size: 27 Copynumber: 6.3 Consensus size: 26
20154 TTTAGAAAGT
*
20164 CAAGGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAA-TTTGTAAAC
*
20191 C-AGGTGTATTTTGGTAATTT-TACAAAT
1 CAAGG-GTATTTTGGTAATTTGT--AAAC
* * **
20218 TAAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTT-GTAAAC
20245 C-AGTGGTATTTTGGTAATTT-TACAAAC
1 CAAG-GGTATTTTGGTAATTTGT--AAAC
* *
20272 TAGGGGTATTTTGGTAATTTGTAAAC
1 CAAGGGTATTTTGGTAATTTGTAAAC
* *
20298 CAAGGGTA-TTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAA-TTTGTAAAC
*
20324 CGAGGGTA
1 CAAGGGTA
20332 AATGGTAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
25 8 0.07
26 34 0.30
27 67 0.59
28 5 0.04
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (26 bp):
CAAGGGTATTTTGGTAATTTGTAAAC
Found at i:20339 original size:26 final size:26
Alignment explanation
Indices: 20283--20341 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
20273 AGGGGTATTT
**
20283 TGGTAA-TTTGTAAACCAAGGGTATT
1 TGGTAATTTTGTAAACCAAGGGTAAA
* * *
20308 TAGTAATTTTGTAAATCGAGGGTAAA
1 TGGTAATTTTGTAAACCAAGGGTAAA
20334 TGGTAATT
1 TGGTAATT
20342 CT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGGTAATTTTGTAAACCAAGGGTAAA
Done.