Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2439
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: 34248
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Found at i:1786 original size:39 final size:40
Alignment explanation
Indices: 1609--1759 Score: 256
Period size: 39 Copynumber: 3.9 Consensus size: 40
1599 ATTCGGATTG
1609 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
1648 AT-TCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
1686 ATAACCGGGC-AAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1725 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1760 AAGCTATATC
Statistics
Matches: 105, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
38 40 0.38
39 42 0.40
40 23 0.22
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:9763 original size:40 final size:40
Alignment explanation
Indices: 9602--9755 Score: 238
Period size: 40 Copynumber: 3.9 Consensus size: 40
9592 ATTCGGATTG
*
9602 ATAACCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
9641 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
9681 ATAACCGGGCTAAGTCCCGAATGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* * *
9721 ATAACCGGGCTAAGTCCCAAAGGCATTTGAGCGAG
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAG
9756 AAGCTATATC
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 13 0.12
40 91 0.88
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:9763 original size:80 final size:79
Alignment explanation
Indices: 9602--9782 Score: 231
Period size: 80 Copynumber: 2.3 Consensus size: 79
9592 ATTCGGATTG
* * *
9602 ATAACCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAA
1 ATAACCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCAA
* * *
9667 TTGTGTGAGTTACT
66 TTGAGCGAGTAACT
*
9681 ATAACCGGGCTAAGTCCCGAATGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCA
1 ATAACCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCA
*
9746 TTTGAGCGAG-AAGCT
65 ATTGAGCGAGTAA-CT
* *
9761 ATATCC-GGCTAAACACCGAAGG
1 ATAACCGGGCTAAGC-CCGAAGG
9783 TACTTGGTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 27 0.31
80 60 0.68
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.22
Consensus pattern (79 bp):
ATAACCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACTATAACCGGGCTAAGTCCCAAAGGCAA
TTGAGCGAGTAACT
Found at i:12472 original size:24 final size:24
Alignment explanation
Indices: 12445--12492 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
12435 ATACGGAGTG
12445 TATAGAGACTTAAAGCATATTTTA
1 TATAGAGACTTAAAGCATATTTTA
* *
12469 TATAGGGACTTAGAGCATATTTTA
1 TATAGAGACTTAAAGCATATTTTA
12493 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
TATAGAGACTTAAAGCATATTTTA
Found at i:13101 original size:34 final size:34
Alignment explanation
Indices: 13032--13101 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
13022 TATCAAGTAA
*
13032 TTTTTTTAATTTCAAAATATCACATTAGGATAAT
1 TTTTTTTAATTTCAAAATATCACATTAGGAAAAT
13066 TTTTTTTAAATTTCAAAATATCACATTA-GAAAAT
1 TTTTTTT-AATTTCAAAATATCACATTAGGAAAAT
13100 TT
1 TT
13102 AATAAAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (34 bp):
TTTTTTTAATTTCAAAATATCACATTAGGAAAAT
Found at i:21655 original size:85 final size:84
Alignment explanation
Indices: 21512--21689 Score: 329
Period size: 85 Copynumber: 2.1 Consensus size: 84
21502 GGCCAGCCAT
*
21512 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCAGTAT
21577 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAAT-AAATAAA
21597 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCAGTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCAGTAT
21662 GTAAGGATTAATAAATAAA
66 GTAAGGATTAATAAATAAA
*
21681 GGGCATGGG
1 GAGCATGGG
21690 CAATAAAATA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 15 0.16
85 76 0.84
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (84 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCAGTAT
GTAAGGATTAATAAATAAA
Found at i:23000 original size:47 final size:47
Alignment explanation
Indices: 22947--23635 Score: 987
Period size: 47 Copynumber: 14.6 Consensus size: 47
22937 TATTTGAATA
* *
22947 AATGTGAA-AGTGTATATATGTTATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
22994 AATGTGAA-AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23043 AATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
23090 AATGTGAA-AGTGTACATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
23137 AATGTGAA-AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23186 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23233 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23280 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23327 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23374 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23421 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23468 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
23515 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
23562 AATGTGAA-AGTGTATATATGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
23609 GATGTGGAA-GTGTATAAATGTGATAAG
1 AATGT-GAACATGTATATATGTGATAAG
23636 CCCCGAAGGG
Statistics
Matches: 601, Mismatches: 34, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 507 0.84
48 3 0.00
49 89 0.15
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:26250 original size:40 final size:40
Alignment explanation
Indices: 26195--26512 Score: 433
Period size: 40 Copynumber: 7.8 Consensus size: 40
26185 AACGATGATT
26195 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
26235 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
26275 CGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* *
26314 CGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
26354 GGGCTAAGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
1 ---C---GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * * *
26400 CGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * * * * *
26440 CGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATATC
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
* * *
26479 CGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
26513 CGTGTATTCG
Statistics
Matches: 251, Mismatches: 19, Indels: 16
0.88 0.07 0.06
Matches are distributed among these distances:
39 71 0.28
40 141 0.56
43 2 0.01
46 37 0.15
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATC
Found at i:26329 original size:79 final size:80
Alignment explanation
Indices: 26195--26512 Score: 433
Period size: 79 Copynumber: 3.9 Consensus size: 80
26185 AACGATGATT
26195 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCA
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCA
26260 TGCTAGTGATGTATC
66 TGCTAGTGATGTATC
* *
26275 CGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCA
26339 TGCTAGTGATGTATC
66 TGCTAGTGATGTATC
* *
26354 GGGCTAAGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCAAAGAG
1 ---C---GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAG
* *
26419 CATTCGTGCTAGTGATATATC
60 CATTCATGCTAGTGATGTATC
* * * * * * * *
26440 CGTGCTAA-ACCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCA
1 CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCA
*
26504 TGCTGGTGA
66 TGCTAGTGA
26513 CGTGTATTCG
Statistics
Matches: 215, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
79 121 0.56
80 16 0.07
82 1 0.00
83 1 0.00
85 9 0.04
86 67 0.31
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCA
TGCTAGTGATGTATC
Found at i:26481 original size:165 final size:165
Alignment explanation
Indices: 26196--26499 Score: 491
Period size: 165 Copynumber: 1.8 Consensus size: 165
26186 ACGATGATTC
*
26196 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCAT
1 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCAAAGAGCATTCAT
* ** * *
26261 GCTAGTGATGTATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTC
66 GCTAGTGATATATCCGGGCTAAACCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCC
26326 CGAAGAGCATTCGTGCTAGTGATGTATCGGGCTAA
131 CGAAGAGCATTCGTGCTAGTGATGTATCGGGCTAA
* *
26361 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCAAAGAGCATTCGT
1 GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCAAAGAGCATTCAT
* * * * *
26426 GCTAGTGATATATCCGTGCTAAACCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCC
66 GCTAGTGATATATCCGGGCTAAACCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCC
26491 CGAAGAGCA
131 CGAAGAGCA
26500 ATCATGCTGG
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
165 126 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (165 bp):
GGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTCCCAAAGAGCATTCAT
GCTAGTGATATATCCGGGCTAAACCCGAAGAGCATTCATGCTAGTGATATATCCGGGCTAAGTCC
CGAAGAGCATTCGTGCTAGTGATGTATCGGGCTAA
Found at i:26716 original size:25 final size:25
Alignment explanation
Indices: 26675--26726 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
26665 TGTGTAATAA
26675 TGAATGAATAAGAGCACTATGTGTG
1 TGAATGAATAAGAGCACTATGTGTG
* *
26700 TGAATG-ATTAGAGGCACTGTGTGTG
1 TGAATGAATAAGA-GCACTATGTGTG
26725 TG
1 TG
26727 CGAATTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.29, C:0.08, G:0.33, T:0.31
Consensus pattern (25 bp):
TGAATGAATAAGAGCACTATGTGTG
Found at i:27906 original size:85 final size:85
Alignment explanation
Indices: 27763--27939 Score: 345
Period size: 85 Copynumber: 2.1 Consensus size: 85
27753 TGGCGGCCAT
27763 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
27828 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
27848 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
27913 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
27933 GGGCATG
1 GAGCATG
27940 AGCAATAAAA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:29305 original size:47 final size:47
Alignment explanation
Indices: 29195--29783 Score: 847
Period size: 47 Copynumber: 12.6 Consensus size: 47
29185 TATTTGAATA
*
29195 AATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29241 AATGTGAAAGTGTTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG-TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29289 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
29336 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
29383 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29430 AATGTGAACA-TG-GTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29476 AATGTGAACA-TGCATATAT-AGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29522 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29569 AATATGAACATGTGT-T-TGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-A-GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29616 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29663 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
29710 AATGTGAAAGTGTATATATCTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
29757 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
29784 TCCCGAAGGG
Statistics
Matches: 508, Mismatches: 25, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
45 3 0.01
46 100 0.20
47 364 0.72
48 38 0.07
49 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Done.