Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 221 of 221
Found at i:64845046 original size:178 final size:178
Alignment explanation
Indices: 64844741--64845092 Score: 596
Period size: 178 Copynumber: 2.0 Consensus size: 178
64844731 ATTCTTAGGT
* * * * *
64844741 CTTATTTAGCCTTTTATCGTGAGAATTAAACTTCTTTTTATAAACATGCATGAAGGTTTAAGTTC
1 CTTATATAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
* * * *
64844806 TTAGATTTGACTTAGTAACTTTTTTGAGGCGAAATCTTAGGAGGCATAAGAATCTAAACATGATT
66 TTAGAATTAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
*
64844871 TAGGCATATTTTATTTGGACCATTTGAGCCTTTCAAGCCCACCCTAAG
131 TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCCACCCTAAG
64844919 CTTATATAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
1 CTTATATAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
64844984 TTAGAATTAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
66 TTAGAATTAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
* *
64845049 TAGGCACATTTTATTTGGATCATTTGAGCCTTTCAAGCCTACCC
131 TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCCACCC
64845093 CATATAAATT
Statistics
Matches: 162, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
178 162 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (178 bp):
CTTATATAGCCTTTTACCATGAAAATTAAACTTCTTTTTATAAACATGCATGAAGATTTAAGTTC
TTAGAATTAACTTAGTAACTTTCTTGAGGCGAAATCTTAGGAGGCATAAGAACCTAAACATGATT
TAGGCACATTTTATTTGGACCATTTGAGCCTTTCAAGCCCACCCTAAG
Found at i:64848959 original size:15 final size:15
Alignment explanation
Indices: 64848939--64848968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64848929 TTAAATGTAT
64848939 TCATTAACAATTTCA
1 TCATTAACAATTTCA
*
64848954 TCATTAATAATTTCA
1 TCATTAACAATTTCA
64848969 CGTGGGTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATTAACAATTTCA
Found at i:64856355 original size:19 final size:19
Alignment explanation
Indices: 64856318--64856357 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64856308 CTTTAAATCA
* * *
64856318 AATTTAACTCCTTATTTTC
1 AATTAAACTCCTAAATTTC
64856337 AATTAAACTCCTAAATTTC
1 AATTAAACTCCTAAATTTC
64856356 AA
1 AA
64856358 AATTTTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAAACTCCTAAATTTC
Found at i:64856659 original size:19 final size:20
Alignment explanation
Indices: 64856632--64856669 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
64856622 TAGCCATGCG
64856632 TTCTCTCATTT-CTTTCTTT
1 TTCTCTCATTTCCTTTCTTT
*
64856651 TTCTTTCATTTCCTTTCTT
1 TTCTCTCATTTCCTTTCTT
64856670 AGTTTGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTCTCATTTCCTTTCTTT
Found at i:64864386 original size:24 final size:25
Alignment explanation
Indices: 64864356--64864468 Score: 99
Period size: 25 Copynumber: 4.6 Consensus size: 25
64864346 AAATATCGAA
*
64864356 AAGCTCATACGAGCCATAAAT-GGG
1 AAGCTCATAAGAGCCATAAATCGGG
* *
64864380 AAGCTCA-AGAGAGCCATTAATCAGG
1 AAGCTCATA-AGAGCCATAAATCGGG
*
64864405 AAGCTCATAAGAGTCA-AATATCGGG
1 AAGCTCATAAGAGCCATAA-ATCGGG
* *
64864430 AAGCTCAAAAGAGTCATATAA-CGGG
1 AAGCTCATAAGAGCCATA-AATCGGG
**
64864455 GTGCTCATAAGAGC
1 AAGCTCATAAGAGC
64864469 TAAATAGCGG
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
23 1 0.01
24 18 0.25
25 49 0.68
26 3 0.04
27 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.18
Consensus pattern (25 bp):
AAGCTCATAAGAGCCATAAATCGGG
Found at i:64864417 original size:25 final size:24
Alignment explanation
Indices: 64864356--64864417 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
64864346 AAATATCGAA
* *
64864356 AAGCTCATACGAGCCATAAATGGG
1 AAGCTCATAAGAGCCATAAATAGG
*
64864380 AAGCTCA-AGAGAGCCATTAATCAGG
1 AAGCTCATA-AGAGCCATAAAT-AGG
64864405 AAGCTCATAAGAG
1 AAGCTCATAAGAG
64864418 TCAAATATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 1 0.03
24 17 0.53
25 13 0.41
26 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.16
Consensus pattern (24 bp):
AAGCTCATAAGAGCCATAAATAGG
Found at i:64864431 original size:25 final size:25
Alignment explanation
Indices: 64864403--64864485 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
64864393 CCATTAATCA
*
64864403 GGAAGCTCATAAGAGTCAAATATCG
1 GGAAGCTCATAAGAGTCAAATAACG
* *
64864428 GGAAGCTCAAAAGAGTCATATAACG
1 GGAAGCTCATAAGAGTCAAATAACG
** *
64864453 GGGTGCTCATAAGAG-CTAAATAGCG
1 GGAAGCTCATAAGAGTC-AAATAACG
*
64864478 GGACGCTC
1 GGAAGCTC
64864486 TTACGAGCTG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 46 0.98
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (25 bp):
GGAAGCTCATAAGAGTCAAATAACG
Found at i:64866442 original size:50 final size:50
Alignment explanation
Indices: 64866332--64866630 Score: 264
Period size: 50 Copynumber: 5.9 Consensus size: 50
64866322 ACATTAAGAG
* *
64866332 GATGAGA--TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
* *
64866383 GATTATGAGAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* *
64866436 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * * *
64866486 GATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * ** * * * *
64866536 TATGTGAACTCCCATGTAATACCATATCTGGGATATGACATTGGCA--GTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* * * ** * * *
64866585 CAAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
64866631 TGTTATATTC
Statistics
Matches: 203, Mismatches: 39, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
49 34 0.17
50 124 0.61
51 1 0.00
53 3 0.01
54 6 0.03
55 1 0.00
56 34 0.17
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:64866853 original size:12 final size:12
Alignment explanation
Indices: 64866838--64866869 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
64866828 TAAGTAAACG
64866838 AGTAAAGAAGAA
1 AGTAAAGAAGAA
64866850 AGTAAAGAAGAA
1 AGTAAAGAAGAA
64866862 AGTAAAGA
1 AGTAAAGA
64866870 TCTTAATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (12 bp):
AGTAAAGAAGAA
Found at i:64877499 original size:44 final size:44
Alignment explanation
Indices: 64877436--64877650 Score: 268
Period size: 51 Copynumber: 4.6 Consensus size: 44
64877426 TTTGAGTACT
64877436 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
64877480 TCTGATCAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
64877524 TCTGATCAGTGACAAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTG---A-T-A--AGTGGTAGCTTTAGCTACACTTA
*
64877575 TCTGATCAGTGACAAGTGACAAGTGATGAGGTGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAA--G-T---G-GTAGCTTTAGCTACACTTA
* *
64877626 TCTGATCAGGGACAAGTGACAAGTG
1 TCTGATCAGTGACAAGTGATAAGTG
64877651 ATAAATGTGA
Statistics
Matches: 153, Mismatches: 4, Indels: 27
0.83 0.02 0.15
Matches are distributed among these distances:
44 62 0.41
45 1 0.01
46 2 0.01
47 2 0.01
48 3 0.02
49 2 0.01
50 1 0.01
51 80 0.52
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:64877542 original size:51 final size:50
Alignment explanation
Indices: 64877487--64877654 Score: 282
Period size: 51 Copynumber: 3.3 Consensus size: 50
64877477 TTATCTGATC
64877487 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAGTGACA
*
64877538 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
64877589 AGTGACAAGTGATGAGGTGTAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGAT-AAGTGTAGCTTTAGCTACACTTATCTGATCAGTGACA
64877640 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
64877655 ATGTGATCCG
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.01
51 106 0.96
52 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:64877592 original size:95 final size:98
Alignment explanation
Indices: 64877443--64877654 Score: 340
Period size: 95 Copynumber: 2.2 Consensus size: 98
64877433 ACTTCTGATC
*
64877443 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATAA-G-TGA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGGATGA
*
64877506 -TAGCTTTAGCTACACTTATCTGATCAGTGACA
66 GTAGCTTTAGCTACACTTATCTGATCAGGGACA
*
64877538 AGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATG
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAG-GATG
64877603 AGGTGTAGCTTTAGCTACACTTATCTGATCAGGGACA
65 A---GTAGCTTTAGCTACACTTATCTGATCAGGGACA
64877640 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
64877655 ATGTGATCCG
Statistics
Matches: 106, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
95 57 0.54
97 1 0.01
98 3 0.03
102 45 0.42
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (98 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGGATGA
GTAGCTTTAGCTACACTTATCTGATCAGGGACA
Found at i:64889650 original size:111 final size:111
Alignment explanation
Indices: 64889530--64889751 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
64889520 ATATCCGAAA
64889530 TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
1 TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
64889595 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
66 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
64889641 TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
1 TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
*
64889706 TCATAGACGCCGAATGCTTCCCACAAAATGATAACAGGGTGCTCTC
66 TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
64889752 GAATTTCTAC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.24
Consensus pattern (111 bp):
TCCATTCAGGCAAGAAAAAAAAAGGATTAACCCCAGATAAAATGTTTTGATTCATATGCTCCAAT
TCATAGACGCCGAATGCTTCCCACAAAATGATAAAAGGGTGCTCTC
Done.