Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 38 of 38
Found at i:5783388 original size:29 final size:28
Alignment explanation
Indices: 5783356--5783446 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 28
5783346 AAGATGGTCC
5783356 TAAATCATGAAAAATTACTAAGATAACCT
1 TAAATCATGAAAAATTACTAA-ATAACCT
* * * *
5783385 TAAA--ATGTATGAAATTGCATAAATGATCT
1 TAAATCATG-A-AAAATTAC-TAAATAACCT
* *
5783414 TAAATCATTAAAAATTACTAAAATAACCC
1 TAAATCATGAAAAATTACT-AAATAACCT
5783443 TAAA
1 TAAA
5783447 ATACATAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
27 3 0.07
28 2 0.04
29 35 0.76
30 4 0.09
31 2 0.04
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.30
Consensus pattern (28 bp):
TAAATCATGAAAAATTACTAAATAACCT
Found at i:5783476 original size:58 final size:56
Alignment explanation
Indices: 5783349--5783529 Score: 157
Period size: 58 Copynumber: 3.1 Consensus size: 56
5783339 AAATGTAAAG
* * * ** *
5783349 ATGGTCCTAAATCATGAAAAATTACTAAGATAACCTTAAAATGTATGAAATTGCATAA
1 ATGGTCCTAAATCATAAAAAATTACTAAAATAACCCTAAAATACAT-AAATTACAT-A
* * *
5783407 ATGATCTTAAATCATTAAAAATTACTAAAATAACCCTAAAATACATAAATTTACATA
1 ATGGTCCTAAATCATAAAAAATTACTAAAATAACCCTAAAATACATAAA-TTACATA
* * * ***
5783464 ATGGTCCCTAAATTATAAAAAATGATTAAAAT-GGTCTAAAAATACATAAAATTACATA
1 ATGGT-CCTAAATCATAAAAAATTACTAAAATAACCCT-AAAATACAT-AAATTACATA
*
5783522 ATAGTCCT
1 ATGGTCCT
5783530 TAACTAATAG
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
57 13 0.13
58 85 0.84
59 3 0.03
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (56 bp):
ATGGTCCTAAATCATAAAAAATTACTAAAATAACCCTAAAATACATAAATTACATA
Found at i:5783544 original size:58 final size:58
Alignment explanation
Indices: 5783412--5783588 Score: 167
Period size: 58 Copynumber: 3.1 Consensus size: 58
5783402 CATAAATGAT
* * * * * *
5783412 CTTAAATCATTAAAAATTACTAAAATAACCCT-AAAATACATAAATTTACATAATGGTC
1 CTTAAATAATAAAAAATGACTAAAATAA-TCTAAAAATACATAAAATTACATAATAGTC
* * * **
5783470 CCTAAATTATAAAAAATGATTAAAATGGTCTAAAAATACATAAAATTACATAATAGTC
1 CTTAAATAATAAAAAATGACTAAAATAATCTAAAAATACATAAAATTACATAATAGTC
* * * * * * * *
5783528 CTTAACTAATAGAAAATGACTAAAGTAATCTTAAATTGCTTGAAATTACATAATAGTC
1 CTTAAATAATAAAAAATGACTAAAATAATCTAAAAATACATAAAATTACATAATAGTC
5783586 CTT
1 CTT
5783589 GTTGCAACAT
Statistics
Matches: 95, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
57 2 0.02
58 93 0.98
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.32
Consensus pattern (58 bp):
CTTAAATAATAAAAAATGACTAAAATAATCTAAAAATACATAAAATTACATAATAGTC
Found at i:5784491 original size:78 final size:78
Alignment explanation
Indices: 5784409--5784560 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 78
5784399 ACCTTCGACA
* * * *
5784409 TAAAAGTATACTAATGACCCT-AAAGGCTCGTCTCTAAGGTAAAATTACTAAAAT-ATCCTTTAA
1 TAAAAATATACT-ATGACCCTAAAAGACTCGGCTCTAAGGTAAAATTACTAAAATGCT-CTTTAA
5784472 AGTATACTTTCAATG
64 AGTATACTTTCAATG
* * * * *
5784487 TAAAAATATCCTATGACCCTAAAATACTTGGCTCTAAGGTAAAATTATTAAAATGCTTTTTAAAG
1 TAAAAATATACTATGACCCTAAAAGACTCGGCTCTAAGGTAAAATTACTAAAATGCTCTTTAAAG
5784552 TATACTTTC
66 TATACTTTC
5784561 GACATGAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 8 0.13
78 54 0.86
79 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (78 bp):
TAAAAATATACTATGACCCTAAAAGACTCGGCTCTAAGGTAAAATTACTAAAATGCTCTTTAAAG
TATACTTTCAATG
Found at i:5786224 original size:11 final size:11
Alignment explanation
Indices: 5786208--5786232 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5786198 TTTGGCCAAA
5786208 TTTCTCTTTAT
1 TTTCTCTTTAT
5786219 TTTCTCTTTAT
1 TTTCTCTTTAT
5786230 TTT
1 TTT
5786233 TTTACCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTCTTTAT
Found at i:5786771 original size:1 final size:1
Alignment explanation
Indices: 5786765--5786831 Score: 89
Period size: 1 Copynumber: 67.0 Consensus size: 1
5786755 AAAGTGTTTG
*** * *
5786765 AAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5786830 AA
1 AA
5786832 TTTAAATGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.93, C:0.00, G:0.01, T:0.06
Consensus pattern (1 bp):
A
Found at i:5786794 original size:24 final size:24
Alignment explanation
Indices: 5786762--5786833 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
5786752 GATAAAGTGT
5786762 TTGAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAA
5786786 TTGAAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAAA
*
5786810 ---AAAAAAAAAATAAAAATAAAAA
1 TTGAAAAAAAAAA-AAAAAAAAAAA
5786832 TT
1 TT
5786834 TAAATGTATC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 10 0.23
22 10 0.23
24 24 0.55
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (24 bp):
TTGAAAAAAAAAAAAAAAAAAAAA
Found at i:5786831 original size:34 final size:33
Alignment explanation
Indices: 5786765--5786831 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
5786755 AAAGTGTTTG
* *
5786765 AAAAAAAAAAAAAAAAAAAAATTGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
*
5786798 AAAAAAAAAAAAAAAAAAAAAATAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
5786831 A
1 A
5786832 TTTAAATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.93, C:0.00, G:0.01, T:0.06
Consensus pattern (33 bp):
AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
Found at i:5786860 original size:21 final size:21
Alignment explanation
Indices: 5786836--5786892 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
5786826 TAAAAATTTA
5786836 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
5786857 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
5786878 AATGTATCGATACAT
1 AATGTATCGATACAT
5786893 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:5786972 original size:19 final size:19
Alignment explanation
Indices: 5786948--5787015 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
5786938 AATTCAACAA
5786948 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
5786967 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
5786982 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
5786999 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
5787016 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:5786987 original size:13 final size:13
Alignment explanation
Indices: 5786969--5786993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5786959 ACATAAGTTT
5786969 TGTATCGATACAA
1 TGTATCGATACAA
5786982 TGTATCGATACA
1 TGTATCGATACA
5786994 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5786991 original size:32 final size:32
Alignment explanation
Indices: 5786950--5787012 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5786940 TTCAACAATT
*
5786950 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
5786982 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
5787013 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:5787073 original size:13 final size:13
Alignment explanation
Indices: 5787055--5787080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5787045 CATTTTTCTG
5787055 TGTATCGATACAT
1 TGTATCGATACAT
5787068 TGTATCGATACAT
1 TGTATCGATACAT
5787081 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5787077 original size:33 final size:33
Alignment explanation
Indices: 5787035--5787101 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5787025 GCCAAGGAAA
***
5787035 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
5787068 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
5787101 T
1 T
5787102 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:5789701 original size:102 final size:102
Alignment explanation
Indices: 5789441--5789722 Score: 365
Period size: 102 Copynumber: 2.8 Consensus size: 102
5789431 CAAGTTTTCT
* * * * *
5789441 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
* * *
5789506 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACAC
66 CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
**
5789543 CAATTTTCCA-CAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTATA
1 CAATTTTCCATC-ATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACATTAATTTTCTATA
*
5789606 ATCGGGGATACTCCAACTCCGATTGTATT-TCCAAAATAC
64 ATCGGGGATACTCCAACTCCGATTGTATTCT-CAAAACAC
* * * *
5789645 TAATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATTAA-TTTCTCATAA
1 CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCT-ATAA
5789709 TCGGGGATACTCCA
65 TCGGGGATACTCCA
5789723 TCCCCGTTAT
Statistics
Matches: 157, Mismatches: 17, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
101 7 0.04
102 148 0.94
103 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
CAATTTTCCATCATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTCTATAAT
CGGGGATACTCCAACTCCGATTGTATTCTCAAAACAC
Found at i:5789719 original size:153 final size:153
Alignment explanation
Indices: 5789441--5789728 Score: 359
Period size: 153 Copynumber: 1.9 Consensus size: 153
5789431 CAAGTTTTCT
* * * *
5789441 CAATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATTAATTTTCCACAAT
1 CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
* *
5789506 CGGGGACACTCCAACTCCGATTTTATTCTCAGAACACCAATTTTCCACAATCGGGGATACTCCAA
66 CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
5789571 CCCCGGTTTTATTTTCAAAACAC
131 CCCCGGTTTTATTTTCAAAACAC
* * * *
5789594 CAATTTT-CTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACTAATTTTTCATC-
1 CAATTTTGC-ATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCA-CA
* * * ** *
5789657 ATCGGGGATACTCCAACCCCGTTTTTATT-TCTAAAATATTAA-TTTCTCATAATCGGGGATACT
64 ATCGGGGACACTCCAACCCCGATTTTATTCTC-AAAACACCAATTTTC-CACAATCGGGGATACT
*
5789720 CCATCCCCG
127 CCAACCCCG
5789729 TTATTTTCGA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
152 7 0.06
153 106 0.93
154 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (153 bp):
CAATTTTGCATAATCGGGGATACTCCAACCCCGATTGTACTTCCAAAACACTAATTTTCCACAAT
CGGGGACACTCCAACCCCGATTTTATTCTCAAAACACCAATTTTCCACAATCGGGGATACTCCAA
CCCCGGTTTTATTTTCAAAACAC
Found at i:5789730 original size:51 final size:50
Alignment explanation
Indices: 5789442--5789728 Score: 308
Period size: 51 Copynumber: 5.6 Consensus size: 50
5789432 AAGTTTTCTC
* * *
5789442 AATTTTGCATAATCGGGGATACTCCAACCCCGGTTTTACTTCTAAAACATT
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * * *
5789493 AATTTTCCACAATCGGGGACACTCCAACTCCGATTTTA-TTCTCAGAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * *
5789544 AATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACACC
1 AATTTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACT
* * * *
5789595 AATTTTCTATAATCGGGGATACTCCAACTCCGATTGTATTTCCAAAATACT
1 AATTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
* * * *
5789646 AATTTTTCATCATCGGGGATACTCCAACCCCGTTTTTATTTCTAAAATATT
1 AA-TTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
*
5789697 AATTTCTCATAATCGGGGATACTCCATCCCCG
1 AATTT-TCATAATCGGGGATACTCCAACCCCG
5789729 TTATTTTCGA
Statistics
Matches: 203, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
50 8 0.04
51 188 0.93
52 7 0.03
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
AATTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACT
Done.