Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1446
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: 45332
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:2837 original size:40 final size:40
Alignment explanation
Indices: 2773--2882 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
2763 CGGATATCAC
* * *
2773 TAGCACGAATGCTCTTCGAACTTAGCCCGGATTTAGTAAC-
1 TAGCACCAATGC-CTTCGGACTTAGCCCGGATATAGTAACT
* * * *
2813 TCGCACCAATGCCTTCGGATCTTAGTCCGGATATGGTCACT
1 TAGCACCAATGCCTTCGGA-CTTAGCCCGGATATAGTAACT
*
2854 TAGCA-CAAAGCCTTCGGACTTAGCCCGGA
1 TAGCACCAATGCCTTCGGACTTAGCCCGGA
2883 CATCATTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 16 0.28
40 38 0.66
41 4 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TAGCACCAATGCCTTCGGACTTAGCCCGGATATAGTAACT
Found at i:3216 original size:29 final size:29
Alignment explanation
Indices: 3182--3255 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
3172 ATAATCACCA
* *
3182 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACC
*
3211 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAACC
3240 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
3256 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 3 0.07
29 38 0.93
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACC
Found at i:3298 original size:43 final size:42
Alignment explanation
Indices: 3237--3373 Score: 207
Period size: 43 Copynumber: 3.4 Consensus size: 42
3227 TGCATTTCAA
3237 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTT-GTGCCAATCTCACAACCGTGAACACTTATT
3280 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTT-GTGCCAATCTCACAACCGTGAACACTTATT
3323 GCCCG--CACTTGTG-C-ATCTCACAA-CGTGAAC-CTTATT
1 GCCCGCACACTTGTGCCAATCTCACAACCGTGAACACTTATT
3359 G-CCGCACACTTGTGC
1 GCCCGCACACTTGTGC
3374 TGAAAACCAA
Statistics
Matches: 91, Mismatches: 0, Indels: 11
0.89 0.00 0.11
Matches are distributed among these distances:
35 3 0.03
36 7 0.08
37 15 0.16
38 9 0.10
39 1 0.01
40 3 0.03
41 5 0.05
43 48 0.53
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.24
Consensus pattern (42 bp):
GCCCGCACACTTGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:5515 original size:47 final size:47
Alignment explanation
Indices: 5365--5931 Score: 902
Period size: 47 Copynumber: 12.1 Consensus size: 47
5355 CCCTTCGGGA
* * * * * * *
5365 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5412 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5458 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5505 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5552 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5599 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5646 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
5693 CTTATCACACATATACACTTTCACATTCATCACATCGACCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5740 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
5787 CTTATCACACATATACACTTTCACATTCATCACGTCGTCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5834 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5881 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5928 CTTA
1 CTTA
5932 CTATCATTTC
Statistics
Matches: 490, Mismatches: 29, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
46 40 0.08
47 450 0.92
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:13764 original size:13 final size:13
Alignment explanation
Indices: 13746--13771 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13736 GCTCAGCATG
13746 GACACGCCCGTGT
1 GACACGCCCGTGT
13759 GACACGCCCGTGT
1 GACACGCCCGTGT
13772 TCGATTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:23868 original size:47 final size:47
Alignment explanation
Indices: 23799--23892 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
23789 GATCATGCTA
23799 CTCAAGATTCTTTTCAGGAAATCGTACACAAGGACACGATGGAACTG
1 CTCAAGATTCTTTTCAGGAAATCGTACACAAGGACACGATGGAACTG
23846 CTCAAGATTCTTTTCAGGAAATCGTACACAAGGACACGATGGAACTG
1 CTCAAGATTCTTTTCAGGAAATCGTACACAAGGACACGATGGAACTG
23893 TGCCTCGTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (47 bp):
CTCAAGATTCTTTTCAGGAAATCGTACACAAGGACACGATGGAACTG
Found at i:31773 original size:56 final size:56
Alignment explanation
Indices: 31702--31862 Score: 180
Period size: 56 Copynumber: 2.9 Consensus size: 56
31692 CATGGCATCA
* *
31702 ATATGTGTACGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGAGTTCGAT
1 ATATGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGACTTCGAT
* * * * * *
31758 ATATATGTGCGAGTAAGACTACGTTTAATACGTTGGTATC-ACTATGTGCCTTCGAT
1 ATATGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGA-TATGTGACTTCGAT
* * * ** *
31814 ATATGTGTGTGAGTAAGACCCTGTCTAGGACAGTGGCATCGATATGTGA
1 ATATGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGA
31863 TTACATGTAA
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
55 1 0.01
56 81 0.98
57 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (56 bp):
ATATGTGTGCGAGTAAGACCATGTTTAATACATTGGCATCGATATGTGACTTCGAT
Found at i:34350 original size:48 final size:46
Alignment explanation
Indices: 34244--34615 Score: 199
Period size: 48 Copynumber: 7.9 Consensus size: 46
34234 TTATTTGTGT
* * *
34244 GCCAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCACATTA-TGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-G--GCATTAGAGAGA
34290 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT-AGA-GAGA
* * * * *
34338 GCTAGTGAAAGA-CATGTTTGGGACAT-GCATCGGC-TAAGAGATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAGAGA-GA
* * * *
34382 GTCAGTGTAAGACCATGTCTGCGACATGGCATTGGCACATATAGA-AGT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG--CAT-TAGAGAGA
* * * *
34430 GCCAGTGTAAGATCATGTCTGGGACATGGCAGCGGCACGAATATGTGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG--C-ATTA-GAGAGA
** * ** * *
34480 GTTAGTGTAAGACCATGTCTAGGACATGGTGTCGGCCTCGATTTTGATAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGG---C-A-TTAGAGAGA
* **
34531 --CAGTGTAAGACCATGTCTAGGACATGGCATCAAC-TT-GATGGATGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAGA--GA-GA
* * * * *
34576 GCTAGTGTATGACAAAGTCTGGGACATGGCATCTGCATTA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTA
34616 TACCCTATGT
Statistics
Matches: 254, Mismatches: 48, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 14 0.06
45 19 0.07
46 28 0.11
47 54 0.21
48 59 0.23
49 32 0.13
50 33 0.13
51 8 0.03
52 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAGAGAGA
Found at i:40600 original size:47 final size:47
Alignment explanation
Indices: 40549--41100 Score: 935
Period size: 47 Copynumber: 11.7 Consensus size: 47
40539 TTAGGATTCT
* * *
40549 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
40596 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
40643 ATGTGATGAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
40690 ATGTGATGAATGTAAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40737 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40784 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40831 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
40878 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40925 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40972 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * * *
41019 ATGTGATTAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
41066 ACGTGATGGATGTGAAAGTGTATAAATATGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41101 TCCCAAAGGG
Statistics
Matches: 480, Mismatches: 24, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 1 0.00
47 479 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:41269 original size:37 final size:37
Alignment explanation
Indices: 41219--41297 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
41209 CCGAGCTCTA
* *
41219 AAGACCCGATAACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
41256 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41293 AAGAC
1 AAGAC
41298 TTCGTAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42831 original size:40 final size:40
Alignment explanation
Indices: 42508--42819 Score: 462
Period size: 40 Copynumber: 7.8 Consensus size: 40
42498 GAGAATTGAG
42508 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
42548 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
42588 AGTGATATATCTGGGCTAAGTCCCGAAGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
42628 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
42668 AGTGATATATCCAGGTTAAATCCCGAAGAACATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
42708 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* ** *
42748 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
42788 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
42820 ATCATGCTGG
Statistics
Matches: 240, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 240 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:44615 original size:85 final size:85
Alignment explanation
Indices: 44452--44622 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 85
44442 GGCCGGCCAT
*
44452 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATCAT
* **
44517 GTAAGGATTAATAAAATAAA
66 GGAAGGAACAATAAAATAAA
* * * *
44537 GAGCATGGGTGGACAAGATGTTATGGCT-AAAACATGTCATAGACATGTTGTGTTGGTGCATCAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATCAT
*
44601 GGGAGGAAACAATAAAATAAA
66 GGAAGG-AACAATAAAATAAA
44622 G
1 G
44623 TTAGTAATAA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
84 35 0.46
85 41 0.54
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATCAT
GGAAGGAACAATAAAATAAA
Done.