Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold427
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: 25419
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Found at i:696 original size:110 final size:106
Alignment explanation
Indices: 540--853 Score: 306
Period size: 110 Copynumber: 2.8 Consensus size: 106
530 GGAAATCGTG
* * *
540 ATTTTATCAACATAAGGGGAAAAATCATCAATTTACCACATAAGGGAAAAATCATCATTTATCAC
1 ATTTTATC-ACATAA-GGGCAAAATC-TCATTTTATCACATAAGGGAAAAATCATCATTTATCAC
* *
605 -TAAGGGCAAAATCGTTATTTTATCAGCATAAGGGAAAAAATCGTCA
63 ATAAGGG-AAAATCGTAATTTTATCA-CATAAGGG-AAAAATCATCA
* * *
651 ATTTTCCTCACTTAAGGGCAAAATCGTCATTTTATCACCTAAGGGAAAAATCATCATTTTATCAC
1 ATTTT-ATCACATAAGGGCAAAATC-TCATTTTATCACATAAGGGAAAAATCATCA-TTTATCAC
* * * * * * * *
716 ATGAGGGAAAATAGTCCACTTGATGCACATGAGGGCAAAATCATCC
63 ATAAGGGAAAATCGT-AATTTTAT-CACATAAGGGAAAAATCATCA
* * *
762 ATTTTATCACATGAGGGCAAAATCACATTTGATCACATAAGGGAAAAATCAATCATTTATCACAT
1 ATTTTATCACATAAGGGCAAAATCTCATTTTATCACATAAGGGAAAAATC-ATCATTTATCACAT
* *
827 ATGGGAAAAAATCATAATTTTATCACA
65 AAGGG--AAAATCGTAATTTTATCACA
854 AATGAGGGTT
Statistics
Matches: 166, Mismatches: 29, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
109 40 0.24
110 61 0.37
111 44 0.27
112 19 0.11
113 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (106 bp):
ATTTTATCACATAAGGGCAAAATCTCATTTTATCACATAAGGGAAAAATCATCATTTATCACATA
AGGGAAAATCGTAATTTTATCACATAAGGGAAAAATCATCA
Found at i:836 original size:28 final size:27
Alignment explanation
Indices: 485--853 Score: 308
Period size: 27 Copynumber: 13.5 Consensus size: 27
475 GGTATTTCGG
* *
485 TCATTTTAATCA-ACTAAGGCAAAAATCT
1 TCATTTT-ATCACA-TAAGGGAAAAATCA
*
513 TCATTTTATTCAC-TAAGGG--AAATCG
1 TCATTTTA-TCACATAAGGGAAAAATCA
*
538 TGATTTTATCAACATAAGGGGAAAAATCA
1 TCATTTTATC-ACATAA-GGGAAAAATCA
* *
567 TCAATTTACCACATAAGGGAAAAATCA
1 TCATTTTATCACATAAGGGAAAAATCA
* *
594 TCA-TTTATCAC-TAAGGGCAAAATCG
1 TCATTTTATCACATAAGGGAAAAATCA
* *
619 TTATTTTATCAGCATAAGGGAAAAAATCG
1 TCATTTTATCA-CATAAGGG-AAAAATCA
* * * *
648 TCAATTTTCCTCACTTAAGGGCAAAATCG
1 TC-ATTTT-ATCACATAAGGGAAAAATCA
*
677 TCATTTTATCACCTAAGGGAAAAATCA
1 TCATTTTATCACATAAGGGAAAAATCA
*
704 TCATTTTATCACATGAGGG-AAAAT-A
1 TCATTTTATCACATAAGGGAAAAATCA
* * * *
729 GTCCACTTGATGCACATGAGGGCAAAATCA
1 -T-CATTTTAT-CACATAAGGGAAAAATCA
* *
759 TCCATTTTATCACATGAGGGCAAAATCA
1 T-CATTTTATCACATAAGGGAAAAATCA
*
787 -CATTTGATCACATAAGGGAAAAATCAA
1 TCATTTTATCACATAAGGGAAAAATC-A
*
814 TCA-TTTATCACATATGGGAAAAAATCA
1 TCATTTTATCACATAAGGG-AAAAATCA
*
841 TAATTTTATCACA
1 TCATTTTATCACA
854 AATGAGGGTT
Statistics
Matches: 287, Mismatches: 32, Indels: 44
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.01
25 29 0.10
26 45 0.16
27 80 0.28
28 73 0.25
29 42 0.15
30 13 0.05
31 3 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (27 bp):
TCATTTTATCACATAAGGGAAAAATCA
Found at i:12248 original size:47 final size:47
Alignment explanation
Indices: 12188--12372 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
12178 GATAATTGTG
** *
12188 ATGTGAATGTGCATATATGTGACAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
*
12235 ATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* *
12282 ATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * * *
12329 ATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAATGTGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGA
12373 AATATATGTA
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:12643 original size:36 final size:37
Alignment explanation
Indices: 12579--12722 Score: 240
Period size: 37 Copynumber: 4.0 Consensus size: 37
12569 AATATATTCT
12579 GGGTAAGA-CCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
12615 GGGTAAGACCCGATGACTACGTGT-GAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
*
12651 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
12688 GGGTAAGACCCGATAACTTCGTGTGGAGATT-TGTC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
12723 TGAGCTAAAG
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
36 48 0.47
37 55 0.53
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:12697 original size:73 final size:72
Alignment explanation
Indices: 12579--12722 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 72
12569 AATATATTCT
*
12579 GGGTAAGACCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGACTACGTGT-GAGA
1 GGGTAAGACCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTACGTGTGGAGA
12643 TTATGTCC
66 TT-TGTCC
* *
12651 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTAAGACCCGATAACTTCGTGTGGAG
1 GGGTAAGA-CCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTACGTGTGGAG
12716 ATTTGTC
65 ATTTGTC
12723 TGAGCTAAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
72 8 0.12
73 53 0.79
74 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (72 bp):
GGGTAAGACCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTACGTGTGGAGA
TTTGTCC
Found at i:12764 original size:25 final size:25
Alignment explanation
Indices: 12734--12784 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12724 GAGCTAAAGG
12734 TCTCACCGATAATCCGAGTAGAGGT
1 TCTCACCGATAATCCGAGTAGAGGT
12759 TCTCACCGATAATCCGAGTAGAGGT
1 TCTCACCGATAATCCGAGTAGAGGT
12784 T
1 T
12785 AAAGCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (25 bp):
TCTCACCGATAATCCGAGTAGAGGT
Found at i:15950 original size:27 final size:27
Alignment explanation
Indices: 15919--16096 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15909 TGAATTGTAC
15919 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
15946 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
15972 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
16000 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
16028 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
16055 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
16082 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
16097 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:16033 original size:82 final size:81
Alignment explanation
Indices: 15920--16075 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
15910 GAATTGTACA
* *
15920 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
15984 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
16001 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
16066 TGCGAGTTGA
65 TGCGAATTGA
16076 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:16087 original size:82 final size:81
Alignment explanation
Indices: 15916--16096 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
15906 GATTGAATTG
* *
15916 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
15981 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
15997 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
16061 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
16079 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
16097 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:24009 original size:27 final size:27
Alignment explanation
Indices: 23961--24129 Score: 171
Period size: 27 Copynumber: 6.3 Consensus size: 27
23951 GTACAGCACT
* *
23961 GTGTGCG-ATTTACTATGTTGCACTAA
1 GTGTGCGAATTGACTATGTAGCACTAA
* *
23987 GTGTGCGAAATGAATATG-ATGCACTAA
1 GTGTGCGAATTGACTATGTA-GCACTAA
* **
24014 GTGTGCGAATTGACCATGCGGCACTAA
1 GTGTGCGAATTGACTATGTAGCACTAA
*
24041 GTGTGCGAGTTTGACTATGTAGCACTAA
1 GTGTGCGA-ATTGACTATGTAGCACTAA
* * *
24069 GTGTGCGATTTGATTACGTAGCACTAA
1 GTGTGCGAATTGACTATGTAGCACTAA
* * * *
24096 GTGTGCGAGTTGATTATATAGCACTGA
1 GTGTGCGAATTGACTATGTAGCACTAA
24123 GTGTGCG
1 GTGTGCG
24130 GACTCAAATA
Statistics
Matches: 121, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.06
27 91 0.75
28 23 0.19
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GTGTGCGAATTGACTATGTAGCACTAA
Found at i:24076 original size:55 final size:54
Alignment explanation
Indices: 23980--24129 Score: 167
Period size: 55 Copynumber: 2.8 Consensus size: 54
23970 TTACTATGTT
** * *
23980 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACGCA
* * ** *
24034 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
* * *
24089 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
24130 GACTCAAATA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 37 0.45
55 44 0.54
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
Found at i:24120 original size:82 final size:80
Alignment explanation
Indices: 23952--24129 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 80
23942 GATTAAATTG
* *
23952 TACAGCACT--GTGTGCGATTTACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
24015 TGTGCGAATTGACCA
66 TGTGCGAATTGACCA
* * ** *
24030 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
24094 AAGTGTGCGAGTTGATTA
63 AAGTGTGCGAATTGACCA
* *
24112 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
24130 GACTCAAATA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 7 0.09
80 8 0.10
81 4 0.05
82 62 0.77
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGATTTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGAATTGACCA
Done.