Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold361
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: 439703
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 26097 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:408171 original size:3 final size:3
Alignment explanation
Indices: 408163--408212 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
408153 GTTACACCTC
* * * * *
408163 CAT CAT CAT CAT CAT CCT CAT CAT AAT CAT AAC CAT CAT CAC CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
408211 CA
1 CA
408213 ACTATGGTGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (3 bp):
CAT
Found at i:414125 original size:3 final size:3
Alignment explanation
Indices: 414117--414162 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
414107 TAAAGTATGT
* *
414117 TTA TTA TTA CTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
414163 AGACAATCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:419034 original size:306 final size:306
Alignment explanation
Indices: 418481--419096 Score: 1153
Period size: 306 Copynumber: 2.0 Consensus size: 306
418471 TCTCGGTTTA
418481 CTGGCACAACACTTCGTGGTTGTGAATCATCAATTATATGAATACAATCGACAAAAGGAAAAAGA
1 CTGGCACAACACTTCGTGGTTGTGAATCATCAATTATATGAATACAATCGACAAAAGGAAAAAGA
*
418546 CACACTTTAATCCTGTCAAGAAAATTCAAGCTAAGAACAAGGCCGTAATCATCTAAGTGGATTAC
66 CACACTTTAATCCTGTCAAGAAAATTCAAGCTAAGAACAAAGCCGTAATCATCTAAGTGGATTAC
*
418611 CTCAAAATATTTCTTGCCCTTCCACACTCTGATTTGTAGCTCCACTCATCGTGTTATTCTCACAG
131 CTCAAAATATTTCTTGCCCTTCCACACTCCGATTTGTAGCTCCACTCATCGTGTTATTCTCACAG
* *
418676 TTGGGACCTTTTCAGGATTTATCGTCTTGATCTTCTTATTCGATTTTCTAACTGAGAGACCAAGT
196 TTGGGACCTTTTCAGGATTTATCGTCTTGATCTTCTTATTCGATTTTCTAACTAAGAGACAAAGT
*
418741 TTGTCTGCGGCTTTTTTTGGAATTTATCGACAAGAGCATTCATTCT
261 TTGCCTGCGGCTTTTTTTGGAATTTATCGACAAGAGCATTCATTCT
418787 CTGGCACAACACTTCGTGGTTGTGAATCATCAATTATATGAATACAATCGACAAAAGGAAAAAGA
1 CTGGCACAACACTTCGTGGTTGTGAATCATCAATTATATGAATACAATCGACAAAAGGAAAAAGA
*
418852 CACATTTTAATCCTGTCAAGAAAATTCAAGCTAAGAACAAAGCCGTAATCATCTAAGTGGATTAC
66 CACACTTTAATCCTGTCAAGAAAATTCAAGCTAAGAACAAAGCCGTAATCATCTAAGTGGATTAC
*
418917 CTCAAAATATTTCTTGCCCTTCCACACTCCGATTTGTAGCTCCACTCGTCGTGTTATTCTCACAG
131 CTCAAAATATTTCTTGCCCTTCCACACTCCGATTTGTAGCTCCACTCATCGTGTTATTCTCACAG
418982 TTGGGACCTTTTC-GGAATTTATCGTCTTGATCTTCTTATTCGATTTTCTAACTAAGAGACAAAG
196 TTGGGACCTTTTCAGG-ATTTATCGTCTTGATCTTCTTATTCGATTTTCTAACTAAGAGACAAAG
419046 TTTGCCTGCGGCTTTTTTTGGAATTTATCGACAAGAGCATTCATTCT
260 TTTGCCTGCGGCTTTTTTTGGAATTTATCGACAAGAGCATTCATTCT
419093 CTGG
1 CTGG
419097 TCTACGATGT
Statistics
Matches: 302, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
305 2 0.01
306 300 0.99
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (306 bp):
CTGGCACAACACTTCGTGGTTGTGAATCATCAATTATATGAATACAATCGACAAAAGGAAAAAGA
CACACTTTAATCCTGTCAAGAAAATTCAAGCTAAGAACAAAGCCGTAATCATCTAAGTGGATTAC
CTCAAAATATTTCTTGCCCTTCCACACTCCGATTTGTAGCTCCACTCATCGTGTTATTCTCACAG
TTGGGACCTTTTCAGGATTTATCGTCTTGATCTTCTTATTCGATTTTCTAACTAAGAGACAAAGT
TTGCCTGCGGCTTTTTTTGGAATTTATCGACAAGAGCATTCATTCT
Found at i:420305 original size:33 final size:33
Alignment explanation
Indices: 420260--420332 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
420250 ATGCCATTAA
* ** *
420260 CAACCACTACTTACTA-CACCATCTTCTTCAACC
1 CAACCACCACTTA-TAGCACCATCAACTCCAACC
420293 CAACCACCACTTATAGCACCATCAACTCCAACC
1 CAACCACCACTTATAGCACCATCAACTCCAACC
420326 CAACCAC
1 CAACCAC
420333 TTTTTCCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.34, C:0.45, G:0.01, T:0.19
Consensus pattern (33 bp):
CAACCACCACTTATAGCACCATCAACTCCAACC
Found at i:422878 original size:6 final size:6
Alignment explanation
Indices: 422867--422891 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
422857 AATCAAAATT
422867 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
422892 AAATAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:426033 original size:212 final size:213
Alignment explanation
Indices: 425653--426079 Score: 847
Period size: 212 Copynumber: 2.0 Consensus size: 213
425643 CAATTGACAC
425653 TGTTCGTAGAAGAATGATGATGACTTCTGGTGAAGCTGTCAAATACAAGAGCTCGCTCGATGCTT
1 TGTTCGTAGAAGAATGATGATGACTTCTGGTGAAGCTGTCAAATACAAGAGCTCGCTCGATGCTT
425718 TCTCTCAGATCTTGAAAAACGAAGGTGCCAAGTCTCTATTCAAGGGTGCTGGAGCTAACATCCTT
66 TCTCTCAGATCTTGAAAAACGAAGGTGCCAAGTCTCTATTCAAGGGTGCTGGAGCTAACATCCTT
425783 CGTGCCATTGCCGGTGCTGGTGTGCTCGCTGGATACGACAAGTTGCAGCTCATTGTTTTCGGAAA
131 CGTGCCATTGCCGGTGCTGGTGTGCTCGCTGGATACGACAAGTTGCAGCTCATTGTTTTCGGAAA
425848 GAAGTACGGATCTGGTGG
196 GAAGTACGGATCTGGTGG
425866 TGTTCGTAGAAG-ATGATGATGACTTCTGGTGAAGCTGTCAAATACAAGAGCTCGCTCGATGCTT
1 TGTTCGTAGAAGAATGATGATGACTTCTGGTGAAGCTGTCAAATACAAGAGCTCGCTCGATGCTT
425930 TCTCTCAGATCTTGAAAAACGAAGGTGCCAAGTCTCTATTCAAGGGTGCTGGAGCTAACATCCTT
66 TCTCTCAGATCTTGAAAAACGAAGGTGCCAAGTCTCTATTCAAGGGTGCTGGAGCTAACATCCTT
425995 CGTGCCATTGCCGGTGCTGGTGTGCTCGCTGGATACGACAAGTTGCAGCTCATTGTTTTCGGAAA
131 CGTGCCATTGCCGGTGCTGGTGTGCTCGCTGGATACGACAAGTTGCAGCTCATTGTTTTCGGAAA
426060 GAAGTACGGATCTGGTGG
196 GAAGTACGGATCTGGTGG
426078 TG
1 TG
426080 CTTAAATTTA
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
212 202 0.94
213 12 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (213 bp):
TGTTCGTAGAAGAATGATGATGACTTCTGGTGAAGCTGTCAAATACAAGAGCTCGCTCGATGCTT
TCTCTCAGATCTTGAAAAACGAAGGTGCCAAGTCTCTATTCAAGGGTGCTGGAGCTAACATCCTT
CGTGCCATTGCCGGTGCTGGTGTGCTCGCTGGATACGACAAGTTGCAGCTCATTGTTTTCGGAAA
GAAGTACGGATCTGGTGG
Found at i:429031 original size:14 final size:14
Alignment explanation
Indices: 429014--429043 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
429004 GATTCACGCA
429014 ATTCTAACATTAAT
1 ATTCTAACATTAAT
*
429028 ATTCTAACGTTAAT
1 ATTCTAACATTAAT
429042 AT
1 AT
429044 ATATAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTCTAACATTAAT
Found at i:430742 original size:41 final size:41
Alignment explanation
Indices: 430679--430952 Score: 372
Period size: 41 Copynumber: 6.7 Consensus size: 41
430669 GTTTTCGGGG
* ** * *
430679 CTTTAGTGGCGTTTTTCAAAAAGCGCCGCTAAAGATCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
430720 CTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
430761 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* * **
430802 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGTTCTATT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
430843 CTTTAGCGGCGCTTTTGTGAAAA-CGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTG-GAAAAGCGCCGCTAATGCTCTGGT
* * * * *
430884 CTTTAGCGGCGTTTTTGTACAAGTGCCGCTATTACTCT-GT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
430924 CTTTAGCGGCGTTTTTGGGAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGC
430953 AAAATGTATT
Statistics
Matches: 205, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
40 30 0.15
41 171 0.83
42 4 0.02
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Done.