Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2483
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: 23155
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:5681 original size:16 final size:15
Alignment explanation
Indices: 5660--5707 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
5650 AATGGGAATA
5660 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
5676 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
5691 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
5707 A
1 A
5708 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:5690 original size:8 final size:8
Alignment explanation
Indices: 5656--5707 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
5646 CAATAATGGG
*
5656 AATAATAA
1 AATATTAA
5664 AATATATAA
1 AATAT-TAA
5673 AATA-TAA
1 AATATTAA
5680 AATATTAA
1 AATATTAA
*
5688 AATATCAA
1 AATATTAA
*
5696 AATATTAG
1 AATATTAA
5704 AATA
1 AATA
5708 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:5707 original size:24 final size:24
Alignment explanation
Indices: 5655--5711 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
5645 ACAATAATGG
*
5655 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
5679 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
5703 GAATAATAA
1 GAATAATAA
5712 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:5873 original size:23 final size:22
Alignment explanation
Indices: 5822--5875 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
5812 ATACTACATC
5822 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
5841 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
5864 AATATGTACATA
1 AATATGTACATA
5876 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:5922 original size:22 final size:24
Alignment explanation
Indices: 5838--5923 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
5828 TACATATATA
* *
5838 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
5861 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
5886 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
5909 -AAGATATATACATAA
1 AAAAATATATACATAA
5924 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:5977 original size:25 final size:25
Alignment explanation
Indices: 5943--6075 Score: 93
Period size: 25 Copynumber: 5.6 Consensus size: 25
5933 TAGAAAAAAT
5943 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
5968 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
5993 ATATATATACGTAATATAA-ATTTAA-
1 ATATATA-A-ATAATATAATATTAAAG
** *
6018 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
6040 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
6063 AAATAT-AATAATA
1 ATATATAAATAATA
6076 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
21 4 0.05
22 18 0.21
23 12 0.14
24 10 0.12
25 29 0.35
26 5 0.06
27 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:6009 original size:52 final size:46
Alignment explanation
Indices: 5936--6070 Score: 114
Period size: 52 Copynumber: 2.8 Consensus size: 46
5926 TAACATGTAG
5936 AAAAAATATATATAAATAATATAATATTAAAGATATATAAATAAAATAGTAT
1 AAAAAATATATAT--ATAATATAATATT-AAGA-ATATAAATAAAATA-T-T
* ** *
5988 AAAATATATATATACGTAATATAA-ATTTAA-AATATACCTAATATATT
1 AAAAAATATATATA--TAATATAATA-TTAAGAATATAAATAAAATATT
*
6035 AAAAGA-ATATATATAATATAATATTAAGAAATATAA
1 AAAAAATATATATATAATATAATATTAAG-AATATAA
6071 TAATAACAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
44 12 0.17
45 1 0.01
46 13 0.18
47 6 0.08
48 1 0.01
49 11 0.15
50 2 0.03
51 3 0.04
52 22 0.31
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (46 bp):
AAAAAATATATATATAATATAATATTAAGAATATAAATAAAATATT
Found at i:6068 original size:22 final size:22
Alignment explanation
Indices: 6004--6075 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
5994 TATATATACG
*
6004 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
6024 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
6048 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
6071 TAATA
1 TAATA
6076 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:6597 original size:30 final size:30
Alignment explanation
Indices: 6561--6675 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
6551 TAGGTACAAG
* *
6561 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
6591 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
6621 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
*
6651 TGGTGGTGGAAAATGAGTGGCTAGT
1 TGGTGGTGGAAAAGGAGTGGCTAGT
6676 TGAGAAAAGT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
Found at i:6654 original size:60 final size:60
Alignment explanation
Indices: 6561--6675 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
6551 TAGGTACAAG
*
6561 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
*
6621 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAATGAGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGT
6676 TGAGAAAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.26
Consensus pattern (60 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGTTGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
Found at i:7783 original size:6 final size:6
Alignment explanation
Indices: 7774--7805 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
7764 TTTTAATTAC
7774 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA AT
7806 ATAATCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTTA
Found at i:13676 original size:24 final size:24
Alignment explanation
Indices: 13649--13719 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 24
13639 ATGTTTTACA
13649 TAGGGTGGTAAATTAATTGTTATG
1 TAGGGTGGTAAATTAATTGTTATG
**
13673 TAGGGACG--AA-T-ATTGTTA-G
1 TAGGGTGGTAAATTAATTGTTATG
*
13692 CTGAGGGTGGTAAATTAAGTGTTATG
1 -T-AGGGTGGTAAATTAATTGTTATG
13718 TA
1 TA
13720 CTGACGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
19 1 0.03
20 8 0.23
21 6 0.17
22 2 0.06
23 2 0.06
24 8 0.23
25 7 0.20
26 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.37
Consensus pattern (24 bp):
TAGGGTGGTAAATTAATTGTTATG
Found at i:13701 original size:45 final size:45
Alignment explanation
Indices: 13650--13741 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
13640 TGTTTTACAT
* *
13650 AGGGTGGTAAATTAATTGTTATGTAGGGACGAATATTGTTAGCTG
1 AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
*
13695 AGGGTGGTAAATTAAGTGTTATGTACTGACGAATATTGTTAGCTG
1 AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
13740 AG
1 AG
13742 TCCGCACCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.35
Consensus pattern (45 bp):
AGGGTGGTAAATTAAGTGTTATGTACGGACGAATATTGTTAGCTG
Found at i:16063 original size:28 final size:29
Alignment explanation
Indices: 16022--16078 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
16012 AAAAATAAGT
16022 AATTAAACTCTAAAAATA-AAAATATAAA
1 AATTAAACTCTAAAAATACAAAATATAAA
* * *
16050 AATTAAATTTTAAATATACGAAAATATAA
1 AATTAAACTCTAAAAATAC-AAAATATAA
16079 TAACATCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.62
30 9 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (29 bp):
AATTAAACTCTAAAAATACAAAATATAAA
Found at i:18982 original size:37 final size:36
Alignment explanation
Indices: 18932--19003 Score: 135
Period size: 37 Copynumber: 2.0 Consensus size: 36
18922 CAAAAATTTC
18932 TGTTTTGTTATGATGTGAATTTTCAATTGGTACTAGT
1 TGTTTTGTTATGATGTGAATTTTCAATT-GTACTAGT
18969 TGTTTTGTTATGATGTGAATTTTCAATTGTACTAG
1 TGTTTTGTTATGATGTGAATTTTCAATTGTACTAG
19004 CTGTACCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.22, C:0.06, G:0.21, T:0.51
Consensus pattern (36 bp):
TGTTTTGTTATGATGTGAATTTTCAATTGTACTAGT
Done.