Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold677
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: 13197
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:241 original size:44 final size:40
Alignment explanation
Indices: 153--252 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 40
143 GCTACTCGTT
*
153 CAAATGCCTTC-GGACAT-ACCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCA
191 CAAATGCCTTCGGGACTTAACCGCGGATT-TAGTAACTCGGTGCA
1 CAAATGCCTTCGGGACTTAACC-CGG-TTATAGTAACTC---GCA
235 CAAATG-CTTCGGGACTTA
1 CAAATGCCTTCGGGACTTA
253 CTCTACGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
38 11 0.20
39 5 0.09
40 3 0.06
41 12 0.22
42 2 0.04
43 12 0.22
44 9 0.17
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGTTATAGTAACTCGCA
Found at i:2100 original size:38 final size:38
Alignment explanation
Indices: 2031--2145 Score: 221
Period size: 38 Copynumber: 3.0 Consensus size: 38
2021 TTCAACCTTT
2031 TTCATTTCTTTTGGCCGAAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCG-AAAATTCTAAGGAAGGAGGAA
2070 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
2108 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
2146 GGAGTTCTTG
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
38 59 0.78
39 17 0.22
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.31
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:3433 original size:40 final size:40
Alignment explanation
Indices: 3328--3472 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 40
3318 TACTCGAATG
* *
3328 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
3369 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAG-GACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
3408 ATATCCGGGCTAATGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTGTGCTAGCGACT
* *
3449 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
3473 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
39 15 0.17
40 31 0.34
41 43 0.48
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:3491 original size:80 final size:80
Alignment explanation
Indices: 3328--3507 Score: 188
Period size: 80 Copynumber: 2.3 Consensus size: 80
3318 TACTCGAATG
* * ** *
3328 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGATTACATCCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGACCCGAAGGC
* *
3393 ATTTGTGCTAGGACT
66 ACTTGTGCGAGGACT
* * **
3408 ATATCCGGGCTAATGTCCCGAAGGCATTTATGCT-AGTGACCATATCCGGGTTAAGACCCGAAGG
1 ATATCCGGGCTAA-GTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGACCCGAAGG
**
3472 C-CTTGTGCGAGTGGTT
65 CACTTGTGCGAG-GACT
*
3488 ATATCC-GGCTAA-ACCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
3508 ATGCTTGATT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
77 7 0.08
79 14 0.17
80 45 0.54
81 18 0.21
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAAGCGACCACATCCGGACTAAGACCCGAAGGC
ACTTGTGCGAGGACT
Found at i:10158 original size:37 final size:38
Alignment explanation
Indices: 10116--10190 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
10106 TTCATCCTTT
10116 TTCATTTCTTTTGGCCGAAAATTCTAAGGAA-GAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
10153 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
10191 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 31 0.84
38 6 0.16
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:10199 original size:37 final size:37
Alignment explanation
Indices: 10121--10199 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
10111 CCTTTTTCAT
* *
10121 TTCTTTTGGCCGAAAATTCTAAGGAAGAGGAATTCAT
1 TTCTTTTGGCCGAAAATTCTAAGGAAGAGGAATGCAG
*
10158 TTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA-GGAG
1 TTCTTTTGGCCGAAAATTCTAAGGAA-GAGGAATGCAG
10195 TTCTT
1 TTCTT
10200 GCTTCATGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (37 bp):
TTCTTTTGGCCGAAAATTCTAAGGAAGAGGAATGCAG
Done.