Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold650
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: 43389
ACGTcount: A:0.10, C:0.08, G:0.08, T:0.11
Warning! 27365 characters in sequence are not A, C, G, or T
Found at i:6417 original size:1 final size:1
Alignment explanation
Indices: 6413--6457 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
6403 TATTTTTTCA
* * * *
6413 TTTTTTTTTTTTTTTTTTTATTTATTTATTTTATTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6458 CAAACATTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:6419 original size:9 final size:8
Alignment explanation
Indices: 6401--6457 Score: 64
Period size: 8 Copynumber: 7.1 Consensus size: 8
6391 AAATAACATG
6401 TTTATTTT
1 TTTATTTT
*
6409 TTCATTTT
1 TTTATTTT
6417 TTT-TTTT
1 TTTATTTT
*
6424 TTTTTTTT
1 TTTATTTT
6432 ATTTATTTAT
1 -TTTATTT-T
6442 TTTATTTT
1 TTTATTTT
6450 TTT-TTTT
1 TTTATTTT
6457 T
1 T
6458 CAAACATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
7 12 0.28
8 17 0.40
9 13 0.30
10 1 0.02
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTATTTT
Found at i:6443 original size:28 final size:28
Alignment explanation
Indices: 6401--6457 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
6391 AAATAACATG
*
6401 TTTATTTTTTCATTTTTTTTTTTTTTTT
1 TTTATTTTTTCATTTTATTTTTTTTTTT
6429 TTTATTTATTT-ATTTTATTTTTTTTTTT
1 TTTATTT-TTTCATTTTATTTTTTTTTTT
6457 T
1 T
6458 CAAACATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.88
Consensus pattern (28 bp):
TTTATTTTTTCATTTTATTTTTTTTTTT
Found at i:7064 original size:63 final size:63
Alignment explanation
Indices: 6965--7084 Score: 231
Period size: 63 Copynumber: 1.9 Consensus size: 63
6955 GGTTGATTCG
6965 ACAATTTGTCTGCTATATTAAGCACGGATGATTTCACTTTTCATCCGCAATATTTCGAGTGAA
1 ACAATTTGTCTGCTATATTAAGCACGGATGATTTCACTTTTCATCCGCAATATTTCGAGTGAA
*
7028 ACAATTTGTCTGCTATATTAAGCACGGATGATTTCACTTTTCGTCCGCAATATTTCG
1 ACAATTTGTCTGCTATATTAAGCACGGATGATTTCACTTTTCATCCGCAATATTTCG
7085 GTTCGTTCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (63 bp):
ACAATTTGTCTGCTATATTAAGCACGGATGATTTCACTTTTCATCCGCAATATTTCGAGTGAA
Found at i:11435 original size:117 final size:117
Alignment explanation
Indices: 11252--11602 Score: 639
Period size: 117 Copynumber: 3.0 Consensus size: 117
11242 AGCGCGTTGT
* * * *
11252 GCTCCTGTTTAATGTGCGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGCTCGGCACCATGT
1 GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCATGT
*
11317 TCGTGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
66 TCATGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
*
11369 GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCGTGT
1 GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCATGT
11434 TCATGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
66 TCATGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
11486 GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCATGT
1 GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCATGT
*
11551 TCATGCTTTTCACCTTGTTTATAAAATTCATCACAAATATCACATTGGATGA
66 TCATGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
11603 AAGTTTCAAC
Statistics
Matches: 226, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 226 1.00
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (117 bp):
GCTCCTGTTTAATATACGTTTCATCGTTGATACCCTCCTCCTTCTTAATTTGTTCCGCACCATGT
TCATGCTTTTCACCTTGTCTATAAAATTCATCACAAATATCACATTGGATGA
Found at i:12377 original size:48 final size:48
Alignment explanation
Indices: 12306--12446 Score: 282
Period size: 48 Copynumber: 2.9 Consensus size: 48
12296 GCGCTTGACT
12306 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCACCC
1 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCACCC
12354 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCACCC
1 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCACCC
12402 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCA
1 AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCA
12447 TTGTTATCCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.19
Consensus pattern (48 bp):
AGAGTGGTTCGAGTAGCTGATGCAAGAGGCGAGAAAGTTGCATCACCC
Found at i:41089 original size:31 final size:32
Alignment explanation
Indices: 41048--41280 Score: 111
Period size: 31 Copynumber: 7.4 Consensus size: 32
41038 TCCATGTCCT
*
41048 TCGACATGGAAATCATAACGTTTCCATGAAAC
1 TCGACATGGAAATCATAACATTTCCATGAAAC
* * * *
41080 TC-ACATGGAAACCA-AGTCATTTCCATCAAGC
1 TCGACATGGAAATCATA-ACATTTCCATGAAAC
* * * * * *
41111 -CGTCATGGAAATGAAAACATTTCCTTGTGAGC
1 TCGACATGGAAATCATAACATTTCCATG-AAAC
* *
41143 TCGACATGGAAATCATAACGTTTCCATGCAAC
1 TCGACATGGAAATCATAACATTTCCATGAAAC
* * * * *
41175 TC-ACACGGAAACCA-AGTCATTTCCAT-CAAG
1 TCGACATGGAAATCATA-ACATTTCCATGAAAC
** * * * * * *
41205 TCTTCATGGAAATGAAAATATTTCCTTGTGAGC
1 TCGACATGGAAATCATAACATTTCCATG-AAAC
* * *
41238 TCGACATGGAACTCATAACACTTCCATGCAAC
1 TCGACATGGAAATCATAACATTTCCATGAAAC
*
41270 TC-ACACGGAAA
1 TCGACATGGAAA
41281 CCAAGTCATT
Statistics
Matches: 145, Mismatches: 46, Indels: 21
0.68 0.22 0.10
Matches are distributed among these distances:
30 8 0.06
31 79 0.54
32 15 0.10
33 43 0.30
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (32 bp):
TCGACATGGAAATCATAACATTTCCATGAAAC
Found at i:41318 original size:95 final size:95
Alignment explanation
Indices: 41048--41318 Score: 461
Period size: 95 Copynumber: 2.9 Consensus size: 95
41038 TCCATGTCCT
* * *
41048 TCGACATGGAAATCATAACGTTTCCATGAAACTCACATGGAAACCAAGTCATTTCCATCAAGCCG
1 TCGACATGGAAATCATAACGTTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGCCT
*
41113 TCATGGAAATGAAAACATTTCCTTGTGAGC
66 TCATGGAAATGAAAATATTTCCTTGTGAGC
*
41143 TCGACATGGAAATCATAACGTTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGTCT
1 TCGACATGGAAATCATAACGTTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGCCT
41208 TCATGGAAATGAAAATATTTCCTTGTGAGC
66 TCATGGAAATGAAAATATTTCCTTGTGAGC
* **
41238 TCGACATGGAACTCATAACACTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGCCT
1 TCGACATGGAAATCATAACGTTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGCCT
*
41303 TCATGGAATTGAAAAT
66 TCATGGAAATGAAAAT
41319 CCCCTTCTCA
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 166 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (95 bp):
TCGACATGGAAATCATAACGTTTCCATGCAACTCACACGGAAACCAAGTCATTTCCATCAAGCCT
TCATGGAAATGAAAATATTTCCTTGTGAGC
Done.