Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold865
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: 19460
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:15942 original size:7 final size:8
Alignment explanation
Indices: 15873--15954 Score: 51
Period size: 8 Copynumber: 9.8 Consensus size: 8
15863 AAAAATAAAA
15873 ATTTATAT
1 ATTTATAT
15881 ATTTATATT
1 ATTTATA-T
15890 ATGTTAGTATT
1 AT-TTA-TA-T
*
15901 ATTTTTAT
1 ATTTATAT
* *
15909 GTTTACA-
1 ATTTATAT
*
15916 ATATTATAA
1 AT-TTATAT
15925 ATTTATAT
1 ATTTATAT
15933 ATTT-TAT
1 ATTTATAT
*
15940 ATTTAAAT
1 ATTTATAT
15948 AATTTAT
1 -ATTTAT
15955 TTAATATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
7 8 0.14
8 27 0.47
9 12 0.21
10 5 0.09
11 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:17192 original size:34 final size:34
Alignment explanation
Indices: 17146--17363 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
17136 GTAAAAACCA
*
17146 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
17180 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * *
17214 CCATTTAATCAACAATGGTAAGCTATCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
17248 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
17281 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
17315 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
17348 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
17364 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
33 45 0.28
34 113 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:17322 original size:67 final size:67
Alignment explanation
Indices: 17144--17363 Score: 307
Period size: 67 Copynumber: 3.3 Consensus size: 67
17134 TGGTAAAAAC
* *
17144 CACCATTTAATCAACAATGGC-AACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCA
1 CACCATTTAATCAACAATGGCAAACC-ACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
17208 AAT
65 AAT
* * * * *
17211 CACCCATTTAATCAACAATGGTAAGCTATCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
17276 AAT
65 AAT
* * * * *
17279 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
17344 AT
66 AT
17346 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
17364 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 74 0.56
68 56 0.42
69 2 0.02
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACCACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:17322 original size:101 final size:101
Alignment explanation
Indices: 17144--17363 Score: 347
Period size: 101 Copynumber: 2.2 Consensus size: 101
17134 TGGTAAAAAC
* *
17144 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
*
17209 ATCACCCATTTAATCAACAATGGTAAGCTA-TCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACT-AAA--T
* *
17247 C-CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
17310 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
17346 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
17364 TCTCCCACTT
Statistics
Matches: 110, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
99 2 0.02
100 16 0.15
101 59 0.54
102 32 0.29
103 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
Done.