Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold942
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: 4000
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.25
Warning! 243 characters in sequence are not A, C, G, or T
Found at i:694 original size:10 final size:10
Alignment explanation
Indices: 679--713 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
669 TTTAGACTAG
679 AAAAAAAAT-
1 AAAAAAAATA
688 AAAAAAAATA
1 AAAAAAAATA
698 AAAAAAAATA
1 AAAAAAAATA
708 AAAAAA
1 AAAAAA
714 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:727 original size:9 final size:9
Alignment explanation
Indices: 679--723 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
669 TTTAGACTAG
679 AAAAAAAAT
1 AAAAAAAAT
688 AAAAAAAAT
1 AAAAAAAAT
697 AAAAAAAA-
1 AAAAAAAAT
705 ATAAAAAAAT
1 A-AAAAAAAT
*
715 CAAAAAAAT
1 AAAAAAAAT
724 CAAAGTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 1 0.03
9 32 0.97
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:749 original size:6 final size:6
Alignment explanation
Indices: 740--782 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
730 CAAAATAGAA
*
740 AAAAAG AAAAAG AAAAA- AAGAGAAG AAAACG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AA-A-AAG AAAAAG AAAAAG AAAAAG
783 GAGGGGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 25 0.78
7 3 0.09
8 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:758 original size:24 final size:25
Alignment explanation
Indices: 731--781 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
721 AATCAAAGTC
*
731 AAAATAGAA-AAAAAGAAAAAGAAA
1 AAAAGAGAAGAAAAAGAAAAAGAAA
*
755 AAAAGAGAAGAAAACGAAAAAGAAA
1 AAAAGAGAAGAAAAAGAAAAAGAAA
780 AA
1 AA
782 GGAGGGGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAGAAGAAAAAGAAAAAGAAA
Found at i:1171 original size:14 final size:14
Alignment explanation
Indices: 1117--1161 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1107 TCAAAAAAGA
*
1117 AAAAGATGAAGAATG
1 AAAA-ATGAAAAATG
*
1132 -AAAATGGAAAATG
1 AAAAATGAAAAATG
1145 AAAAATGAAAAATG
1 AAAAATGAAAAATG
1159 AAA
1 AAA
1162 GAGTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:2740 original size:88 final size:88
Alignment explanation
Indices: 2591--3186 Score: 921
Period size: 88 Copynumber: 6.8 Consensus size: 88
2581 NNNNNNNNNN
* *
2591 TGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCAAAGCAGAG-CGAAGACACAAACCT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAG-GTCGAAGACACAAACCT
2655 TGCCTCTCTCGGTTGTGATGGAGC
65 TGCCTCTCTCGGTTGTGATGGAGC
*
2679 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
*
2744 GCCTCTCTCAGTTGT-AGTGGAGC
66 GCCTCTCTCGGTTGTGA-TGGAGC
* * * * *
2767 TGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGTCAGCGAAGCAGGTCAAAAACAAAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
**
2832 GCCTCTCTTAGTTGTGATGGAGC
66 GCCTCTCTCGGTTGTGATGGAGC
2855 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
* *
2920 GCCTCTCTTGGTGGTGATGGAGC
66 GCCTCTCTCGGTTGTGATGGAGC
*
2943 TGGTTGAAAACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
3008 GCCTCTCTCGGTTGTGATGGAGC
66 GCCTCTCTCGGTTGTGATGGAGC
3031 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
*
3096 GCCTCTCTC-GTTGT-AGTGGAGA
66 GCCTCTCTCGGTTGTGA-TGGAGC
* * * * * * * * *
3118 TGGTTGAAGACAACAGATCTTGCCTTCTTGCCTTGATAGGGAAACAGATCGAAGACACCAGCCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
3183 GCCT
66 GCCT
3187 TCCTGTACTG
Statistics
Matches: 474, Mismatches: 30, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
86 1 0.00
87 72 0.15
88 400 0.84
89 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
GCCTCTCTCGGTTGTGATGGAGC
Found at i:3227 original size:264 final size:264
Alignment explanation
Indices: 2591--3261 Score: 843
Period size: 264 Copynumber: 2.5 Consensus size: 264
2581 NNNNNNNNNN
* *
2591 TGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGC-AAAGCAGAGCGAAGACACAAACCT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAA-CAGATCGAAGACACAAACCT
** * * ** *
2655 TGCCTCT-CTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
65 TGCCTCTCCT-GGTACTGACGGAGCAGAATGAAAACAAAAGATCTTGCCTTCCTGCATTGACAGC
* *
2719 GAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCAGTTGTAGTGGAGCTGGTTGAAGACAACAGA
129 GAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTAGTGGAGCTGGTTGAAGACAAAAGA
*
2784 TCTTGCCTTCCTGCATTGTCAGCGAAGCAGGTCAAAAACAAAAACCTTGCCTCTCTTAGTTGTGA
194 TCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAAACAAAAACCTTGCCTCTCTTAGTTGTGA
*
2849 TGGAGC
259 TGGAGA
* *
2855 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAGACACAAACCTT
* ** * * **
2920 GCCTCTCTTGGTGGTGATGGAGCTGGTTGAAAACAAAAGATCTTGCCTTCCTGCATTGACAGCGA
66 GCCTCTCCTGGTACTGACGGAGCAGAATGAAAACAAAAGATCTTGCCTTCCTGCATTGACAGCGA
*
2985 AGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGAT
131 AGCAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTAG-TGGAGCTGGTTGAAGACAAAAGAT
* * * *
3049 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC-TCGTTGT-AG
195 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAAACAAAAACCTTGCCTCTCTTAGTTGTGA-
3112 TGGAGA
259 TGGAGA
* * * * * * *
3118 TGGTTGAAGACAACAGATCTTGCCTTCTTGCCTTGATAGGGAAACAGATCGAAGACACCAGCCTT
1 TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAGACACAAACCTT
* * ** * * * *
3183 GCCT-TCCT-GTACTGACAGCGGAGCAGAATGAAGATAGCAGATCTTGCCTTCTTGTACTAACAG
66 GCCTCTCCTGGTACTG--A-CGGAGCAGAATGAAAACAAAAGATCTTGCCTTCCTGCATTGACAG
*
3246 CGAAGCAGATCGAAGA
128 CGAAGCAGGTCGAAGA
3262 AACCACAGTT
Statistics
Matches: 359, Mismatches: 41, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
261 4 0.01
262 4 0.01
263 73 0.20
264 275 0.77
265 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (264 bp):
TGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAACAGATCGAAGACACAAACCTT
GCCTCTCCTGGTACTGACGGAGCAGAATGAAAACAAAAGATCTTGCCTTCCTGCATTGACAGCGA
AGCAGGTCGAAGACACAAACCTTGCCTCTCTCAGTTGTAGTGGAGCTGGTTGAAGACAAAAGATC
TTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAAACAAAAACCTTGCCTCTCTTAGTTGTGATG
GAGA
Found at i:3453 original size:98 final size:99
Alignment explanation
Indices: 3281--3467 Score: 261
Period size: 98 Copynumber: 1.9 Consensus size: 99
3271 TTTCAATTCA
* * * *
3281 AAAGATTGAAGCTACAACAGCGGATCTTACATTCTAAGCGGTGCAGCGTAACAGATTGAAGCTAC
1 AAAGATTGAAGCCACAACAGCGAATCTTACATTCCAAGCGGTGCAGCGGAACAGATTGAAGCTAC
3346 AACGACGGATCTCACTTCCCTGACATTGCAATCC
66 AACGACGGATCTCACTTCCCTGACATTGCAATCC
* * * * *
3380 AAAGATTGAGGCCACAACGGCGAATCTTA-TTTCCAGGCGGTGCAGTGGAACAGATTGAAGCTAC
1 AAAGATTGAAGCCACAACAGCGAATCTTACATTCCAAGCGGTGCAGCGGAACAGATTGAAGCTAC
*
3444 AAC-AGCGGATCTTACTTCCCTGAC
66 AACGA-CGGATCTCACTTCCCTGAC
3468 GAATCTTGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
97 1 0.01
98 51 0.66
99 25 0.32
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (99 bp):
AAAGATTGAAGCCACAACAGCGAATCTTACATTCCAAGCGGTGCAGCGGAACAGATTGAAGCTAC
AACGACGGATCTCACTTCCCTGACATTGCAATCC
Found at i:3688 original size:124 final size:124
Alignment explanation
Indices: 3468--3835 Score: 630
Period size: 124 Copynumber: 3.0 Consensus size: 124
3458 CTTCCCTGAC
3468 GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
1 GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
3533 CACATCGGTGAATCTTGCTTCCCTTACATTGCAGTTAAAAAGATTAAAGCCACATCGGT
66 CACATCGGTGAATCTTGCTTCCCTTACATTGCAGTTAAAAAGATTAAAGCCACATCGGT
3592 GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
1 GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
3657 CACATCGGTGAATCTTGCTTCCCTTACATTGCAGTTAAAAAGATTAAAGCCACATCGGT
66 CACATCGGTGAATCTTGCTTCCCTTACATTGCAGTTAAAAAGATTAAAGCCACATCGGT
* *
3716 GAATCTTGATTAAAGCTATAATAGCGAATCTTATGCCCCAAGCGATGCAGTGGAACAGATTAAAG
1 GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
* * * * * * *
3781 CCAAATTGGCGAATCTTGTTTCTCC-GATATTGTAGTTAAAAAGATTAAAGCCACA
66 -CACATCGGTGAATCTTGCTTC-CCTTACATTGCAGTTAAAAAGATTAAAGCCACA
3836 ATGACGAATC
Statistics
Matches: 233, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
124 187 0.80
125 44 0.19
126 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (124 bp):
GAATCTTGATTAAAGCTACAATAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAG
CACATCGGTGAATCTTGCTTCCCTTACATTGCAGTTAAAAAGATTAAAGCCACATCGGT
Done.