Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2468
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: 34254
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:759 original size:40 final size:40
Alignment explanation
Indices: 704--789 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
694 TAAGCATATT
* * *
704 GAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCC
1 GAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACCC
* *
744 GAAGGCATTTATGCTAGTGACCATATCCGGGTTAAGACCC
1 GAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACCC
784 GAAGGC
1 GAAGGC
790 CTTGTGCGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
GAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACCC
Found at i:2457 original size:27 final size:27
Alignment explanation
Indices: 2418--2568 Score: 196
Period size: 27 Copynumber: 5.6 Consensus size: 27
2408 CAAATTAATT
*
2418 AAATGACTATTTTGCCTTTATGTGGTA
1 AAATGACTGTTTTGCCTTTATGTGGTA
* *
2445 AAGTGACAGTTTTGCCTTTATGTGGTA
1 AAATGACTGTTTTGCCTTTATGTGGTA
* *
2472 AAATAACTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCTTTATGTGGTA
*
2499 AAATGATTGTTTTGCCTTTATGTGGTA
1 AAATGACTGTTTTGCCTTTATGTGGTA
* * *
2526 AAATAACTATTTTGCCCTTATAG-GGTA
1 AAATGACTGTTTTGCCTTTAT-GTGGTA
*
2553 AGATGACTGTTTTGCC
1 AAATGACTGTTTTGCC
2569 CTTAATTGGT
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
27 105 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.42
Consensus pattern (27 bp):
AAATGACTGTTTTGCCTTTATGTGGTA
Found at i:2493 original size:54 final size:54
Alignment explanation
Indices: 2418--2568 Score: 216
Period size: 54 Copynumber: 2.8 Consensus size: 54
2408 CAAATTAATT
* * *
2418 AAATGACTATTTTGCCTTTATGTGGTAAAGTGACAGTTTTGCCTTTATGTGGTA
1 AAATAACTATTTTGCCCTTATGTGGTAAAGTGACTGTTTTGCCTTTATGTGGTA
* * *
2472 AAATAACTGTTTTGCCCTTATGTGGTAAAATGATTGTTTTGCCTTTATGTGGTA
1 AAATAACTATTTTGCCCTTATGTGGTAAAGTGACTGTTTTGCCTTTATGTGGTA
2526 AAATAACTATTTTGCCCTTATAG-GGT-AAGATGACTGTTTTGCC
1 AAATAACTATTTTGCCCTTAT-GTGGTAAAG-TGACTGTTTTGCC
2569 CTTAATTGGT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 2 0.02
54 83 0.97
55 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.42
Consensus pattern (54 bp):
AAATAACTATTTTGCCCTTATGTGGTAAAGTGACTGTTTTGCCTTTATGTGGTA
Found at i:2917 original size:18 final size:18
Alignment explanation
Indices: 2891--2930 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2881 AGGACTTGTA
* * *
2891 TACTGTTACTGGACTGAT
1 TACTATTACTGCACTAAT
2909 TACTATTACTGCACTAAT
1 TACTATTACTGCACTAAT
2927 TACT
1 TACT
2931 GTTTTCGCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (18 bp):
TACTATTACTGCACTAAT
Found at i:8549 original size:25 final size:25
Alignment explanation
Indices: 8521--8582 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
8511 ATGCTTATAT
*
8521 GAGCTGTAATTCGGTATGCTCACTC
1 GAGCTGTAATTCGGTATGCTCACAC
* *
8546 GAGCTATAGATT-GGTATGCTCTCAC
1 GAGCTGTA-ATTCGGTATGCTCACAC
*
8571 AAGCTGTAATTC
1 GAGCTGTAATTC
8583 TGTAACAGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 3 0.10
25 24 0.80
26 3 0.10
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTGTAATTCGGTATGCTCACAC
Found at i:8709 original size:13 final size:13
Alignment explanation
Indices: 8691--8717 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8681 ATATGTGATA
8691 TGTGTGAAAATTT
1 TGTGTGAAAATTT
8704 TGTGTGAAAATTT
1 TGTGTGAAAATTT
8717 T
1 T
8718 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:9865 original size:43 final size:42
Alignment explanation
Indices: 9818--9991 Score: 174
Period size: 43 Copynumber: 4.1 Consensus size: 42
9808 ACATAGGATT
9818 TTGATATGTGTTATCATGTAAGACCATGTCTGGGACATTGGCA
1 TTGATATGTGTT-TCATGTAAGACCATGTCTGGGACATTGGCA
** *
9861 TTGATTCATGAT-TCACATGTAAGACCATGTTTGGGACATTGGCA
1 TTGA-T-ATG-TGTTTCATGTAAGACCATGTCTGGGACATTGGCA
* * * *
9905 TCT-ATATG-ATTTCGTGTAAGACCCTGTCTGGGACAGTGGCA
1 T-TGATATGTGTTTCATGTAAGACCATGTCTGGGACATTGGCA
* * * *
9946 TCGATATCTGATTTTATGTAAGACCACGTCTGGGACATTGGCA
1 TTGATATGTG-TTTCATGTAAGACCATGTCTGGGACATTGGCA
9989 TTG
1 TTG
9992 TACGAGCTTT
Statistics
Matches: 105, Mismatches: 18, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
41 31 0.30
42 3 0.03
43 34 0.32
44 31 0.30
45 5 0.05
46 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (42 bp):
TTGATATGTGTTTCATGTAAGACCATGTCTGGGACATTGGCA
Found at i:9933 original size:85 final size:84
Alignment explanation
Indices: 9834--9989 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 84
9824 TGTGTTATCA
* * * *
9834 TGTAAGACCATGTCTGGGACATTGGCATTGAT-TCATGATTCACATGTAAGACCATGTTTGGGAC
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATC-TGATT-ACATGTAAGACCACGTCTGGGAC
9898 ATTGGCATCTATATGATTTCG
64 ATTGGCATCTATATGATTTCG
* **
9919 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATCTGATTTTATGTAAGACCACGTCTGGGACAT
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATCTGATTACATGTAAGACCACGTCTGGGACAT
9984 TGGCAT
66 TGGCAT
9990 TGTACGAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 27 0.43
85 34 0.54
86 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (84 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATCTGATTACATGTAAGACCACGTCTGGGACAT
TGGCATCTATATGATTTCG
Found at i:11864 original size:27 final size:26
Alignment explanation
Indices: 11810--11920 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
11800 AGCATTGCTG
* * *
11810 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGAAAATGTGGCAGAGCCA
11836 CCAGAACAGAAAATTGTGGCAGAGCCA
1 CCAGAACAGAAAA-TGTGGCAGAGCCA
*
11863 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
* * *
11890 CCAGATCAGATAAATATGGCATAGCCA
1 CCAGAACAGA-AAATGTGGCAGAGCCA
11917 CCAG
1 CCAG
11921 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
26 12 0.16
27 61 0.81
28 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (26 bp):
CCAGAACAGAAAATGTGGCAGAGCCA
Found at i:11910 original size:54 final size:53
Alignment explanation
Indices: 11810--11920 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 53
11800 AGCATTGCTG
* *
11810 CCAGAACAGATAATGTGACAGAGTCACCAGAACAGAAAATTGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGAACAGAAAATTATGGCAGAGCCA
* * *
11863 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAAA-TATGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGAACAGA-AAATTATGGCAGAGCCA
11917 CCAG
1 CCAG
11921 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
53 12 0.24
54 36 0.71
55 3 0.06
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGAACAGAAAATTATGGCAGAGCCA
Found at i:19595 original size:27 final size:27
Alignment explanation
Indices: 19541--19649 Score: 150
Period size: 27 Copynumber: 4.1 Consensus size: 27
19531 AGCATTGCTG
* * *
19541 CCAGAACAGATGA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
19567 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
19594 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
19621 CCAGAACAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
19648 CC
1 CC
19650 TGGACGCTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.19
27 60 0.80
28 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:24762 original size:24 final size:24
Alignment explanation
Indices: 24735--24788 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
24725 TAACATATAT
24735 ATAAAA-ACAATAAATAATATGAAA
1 ATAAAACACAATAAATAATAT-AAA
* * *
24759 ATAAAACATAATAAATATTATATA
1 ATAAAACACAATAAATAATATAAA
24783 ATAAAA
1 ATAAAA
24789 TGTAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
ATAAAACACAATAAATAATATAAA
Found at i:24769 original size:18 final size:19
Alignment explanation
Indices: 24724--24771 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
24714 CATGATATAC
24724 ATAACATATATATAAAAACA
1 ATAACATA-ATATAAAAACA
* *
24744 ATAA-ATAATATGAAAATA
1 ATAACATAATATAAAAACA
24762 A-AACATAATA
1 ATAACATAATA
24772 AATATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 3 0.12
20 4 0.16
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAACATAATATAAAAACA
Found at i:26720 original size:83 final size:83
Alignment explanation
Indices: 26590--27425 Score: 1420
Period size: 83 Copynumber: 10.1 Consensus size: 83
26580 ATGTCAAATT
* *
26590 ATCTTGAGTCTGCTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
26655 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
* * *
26673 ATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTATTCCTTATAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
26738 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
** *
26756 ATCTTGAGTCTGTTTGAGGGCATTTGAGAGTCATGTCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
26821 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
* * *
26839 ATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTACAACATCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
26904 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
*
26922 ATCTTGAGTCTGTTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
26987 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
* * *
27005 ATCTTGAGTCTGTTTGAGAACGTTTGAGAGTCATATCTGCTATGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
27070 GCACAAGGATGCCAAACT
66 GCACAAGGATGCCAAACC
*
27088 ATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
27153 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
*
27171 ATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
27236 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
*
27254 ATCTTGAGTCTGTTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
27319 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
* * * *
27337 ATCTTGAGTCTATTTGAGAACGTTTGAGAGTCATATCTGCTATGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
27402 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
27420 ATCTTG
1 ATCTTG
27426 GATCTGCTTT
Statistics
Matches: 716, Mismatches: 37, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 716 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (83 bp):
ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
GCACAAGGATGCCAAACC
Done.