Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2749
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: 44667
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Found at i:7124 original size:47 final size:47
Alignment explanation
Indices: 7058--7482 Score: 692
Period size: 47 Copynumber: 9.1 Consensus size: 47
7048 GAAATGATAG
7058 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
7105 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
7152 TAAGGCCTAATAGCCGATGTGATGAATATGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
7199 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
7246 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
7293 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
7339 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
7386 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
7432 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
7479 TAAG
1 TAAG
7483 TCCCGAAGGG
Statistics
Matches: 359, Mismatches: 17, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
46 85 0.24
47 274 0.76
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:7657 original size:37 final size:37
Alignment explanation
Indices: 7601--7679 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
7591 CCGAGCTCTA
* *
7601 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
7638 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
7675 AAGAC
1 AAGAC
7680 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:9154 original size:40 final size:40
Alignment explanation
Indices: 9030--9154 Score: 180
Period size: 40 Copynumber: 3.1 Consensus size: 40
9020 GGGTGTTACA
9030 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
1 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
* * * * * *
9070 GTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGCAATT
1 GTGCTAG-TGATTTTATCCGGGCTAAGACCCGAAGGCATTT
9110 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
1 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
9150 GTGCT
1 GTGCT
9155 TGTAGTTATA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
39 2 0.03
40 67 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (40 bp):
GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
Found at i:9167 original size:40 final size:39
Alignment explanation
Indices: 9030--9173 Score: 173
Period size: 40 Copynumber: 3.6 Consensus size: 39
9020 GGGTGTTACA
*
9030 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
1 GTGCTAGTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
* * * * *
9070 GTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCAATT
1 GTGCTAG-TGTTATATCCGGGCTAAGACCCGAAGGCATTT
*
9110 GTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTT
1 GTGCTAGTG-TTATATCCGGGCTAAGACCCGAAGGCATTT
*
9150 GTGCTTGTAGTTATATCC-GGCTAA
1 GTGCTAGT-GTTATATCCGGGCTAA
9174 ATTCCGAAGA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 8 0.09
40 76 0.87
41 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCTAGTGTTATATCCGGGCTAAGACCCGAAGGCATTT
Found at i:15444 original size:40 final size:40
Alignment explanation
Indices: 15398--15641 Score: 339
Period size: 40 Copynumber: 6.1 Consensus size: 40
15388 CGGGATTTCA
* * *
15398 CCGGATATAGCT-ACTCGCTCGAATGCATTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACGAATGCCTTCGGGACTTAGC
15438 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
* *
15478 CCAGATATAGTAACTCGCACGAATGCCTTCCGGACTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
15518 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
* * *
15558 CCGGATATAGTAACTCACACAAATGGCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
* * * * *
15598 CC-GAAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACGAATGCCTTCGGGACTTAGC
15638 CCGG
1 CCGG
15642 TTATCATCCA
Statistics
Matches: 185, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 4 0.02
40 180 0.97
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGC
Found at i:26139 original size:19 final size:19
Alignment explanation
Indices: 26103--26141 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
26093 TTTTCATCAT
* *
26103 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
26122 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
26141 A
1 A
26142 AATAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:26654 original size:28 final size:29
Alignment explanation
Indices: 26581--26668 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
26571 AGCATGGCTG
* * * *
26581 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
26608 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
26637 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
26665 CCAG
1 CCAG
26669 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:26830 original size:27 final size:28
Alignment explanation
Indices: 26774--26837 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
26764 AAATTAACCC
*
26774 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTCAATTTGCATACA
*
26802 TAGGGGTATAATGGT-AATTTGCATACA
1 TAGGGGTATAAAGGTCAATTTGCATACA
26829 TAGGGGTAT
1 TAGGGGTAT
26838 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAAAGGTCAATTTGCATACA
Found at i:33972 original size:19 final size:19
Alignment explanation
Indices: 33936--33974 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
33926 TTTTCATCAT
* *
33936 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
33955 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
33974 A
1 A
33975 AATAATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:34678 original size:28 final size:28
Alignment explanation
Indices: 34631--34695 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
34621 AAATTAACCC
*
34631 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
34659 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
34687 TAGGGGTAT
1 TAGGGGTAT
34696 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Done.