Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold507
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: 914714
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
File 8 of 8
Found at i:899464 original size:26 final size:28
Alignment explanation
Indices: 899416--899467 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
899406 AAATGTAATA
*
899416 AAAATAATATATTAAATATAATTTTTTT
1 AAAATAATATATAAAATATAATTTTTTT
899444 AAAATAATA-ATAAAATA-AATTTTT
1 AAAATAATATATAAAATATAATTTTT
899468 ATAATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAAATAATATATAAAATATAATTTTTTT
Found at i:899704 original size:2 final size:2
Alignment explanation
Indices: 899697--899721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
899687 CTTTTTCCAT
899697 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
899722 GGATAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:899879 original size:27 final size:27
Alignment explanation
Indices: 899847--899901 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
899837 TGAAAATTTT
899847 TTATTTTATCATA-AATATATAA-AATAA
1 TTATTTTAT-ATATAATA-ATAATAATAA
*
899874 TTATTTTGTATATAATAATAATAATAA
1 TTATTTTATATATAATAATAATAATAA
899901 T
1 T
899902 AATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
TTATTTTATATATAATAATAATAATAA
Found at i:899893 original size:3 final size:3
Alignment explanation
Indices: 899885--899919 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
899875 TATTTTGTAT
899885 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
899920 GAAATTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:900298 original size:19 final size:20
Alignment explanation
Indices: 900274--900329 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
900264 ATCAAAGATT
900274 TATTAAATTGATAAAAA-TA
1 TATTAAATTGATAAAAATTA
900293 TATT-AATTGATTAAAAAATTA
1 TATTAAATTGA-T-AAAAATTA
*
900314 AATTAAATT-ATAAAAA
1 TATTAAATTGATAAAAA
900330 AATTATATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 6 0.19
19 10 0.31
20 6 0.19
21 6 0.19
22 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TATTAAATTGATAAAAATTA
Found at i:900318 original size:21 final size:21
Alignment explanation
Indices: 900274--900343 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
900264 ATCAAAGATT
900274 TATTAAATTGA-T-AAAAA-TA
1 TATT-AATTGATTAAAAAATTA
900293 TATTAATTGATTAAAAAATTA
1 TATTAATTGATTAAAAAATTA
* *
900314 AATTAAATT-ATAAAAAAATTA
1 TATT-AATTGATTAAAAAATTA
900335 TATGTAATT
1 TAT-TAATT
900344 ATATGCTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 6 0.14
19 5 0.12
20 5 0.12
21 22 0.51
22 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TATTAATTGATTAAAAAATTA
Found at i:900344 original size:21 final size:20
Alignment explanation
Indices: 900286--900346 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
900276 TTAAATTGAT
*
900286 AAAAA-TATATTAATTGATTA
1 AAAAATTATATTAATT-ATAA
*
900306 AAAAATTAAATTAAATTATAA
1 AAAAATTATATT-AATTATAA
900327 AAAAATTATATGTAATTATA
1 AAAAATTATAT-TAATTATA
900347 TGCTAAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAATTATATTAATTATAA
Found at i:901186 original size:36 final size:39
Alignment explanation
Indices: 901145--901227 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 39
901135 ACCTTTAAAA
* *
901145 TTTATATTATTATTTA-AAATAATATT-AA-AAAATTAT
1 TTTATATTAATATTTATAAATAATATTAAATAAAAATAT
* *
901181 TTTATATTAATATTTATAATTAATTTTAAATAAAAATAT
1 TTTATATTAATATTTATAAATAATATTAAATAAAAATAT
901220 TTT-TATTA
1 TTTATATTA
901228 CTTAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.38
37 8 0.20
38 7 0.17
39 10 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (39 bp):
TTTATATTAATATTTATAAATAATATTAAATAAAAATAT
Found at i:901517 original size:36 final size:32
Alignment explanation
Indices: 901429--901518 Score: 99
Period size: 36 Copynumber: 2.7 Consensus size: 32
901419 TATTTCTCAA
**
901429 AAAATATATATAATATAAATTATTAATATATT
1 AAAATATATATAATATAAAAAATTAATATATT
*
901461 AAAATTTATATAAATATAAAAAATTTAAATATAATT
1 AAAATATATAT-AATATAAAAAA-TT-AATAT-ATT
*
901497 ATAATATAATATAATATAAAAA
1 AAAATAT-ATATAATATAAAAA
901519 TATACAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
32 10 0.21
33 9 0.19
34 2 0.04
35 5 0.10
36 18 0.38
37 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAATATATATAATATAAAAAATTAATATATT
Found at i:902529 original size:18 final size:18
Alignment explanation
Indices: 902495--902532 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
902485 TTTTTAATTT
902495 AATAAAAATAATATATTA
1 AATAAAAATAATATATTA
*
902513 AATATAAAA-AATTTATTA
1 AATA-AAAATAATATATTA
902531 AA
1 AA
902533 AAATAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAAAATAATATATTA
Found at i:907086 original size:2 final size:2
Alignment explanation
Indices: 907081--907124 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
907071 ATATAGAATT
*
907081 TA TA TA TA TA TA TA TA TA CTA -A AA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
907122 TA T
1 TA T
907125 TTTAAAGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:907507 original size:11 final size:11
Alignment explanation
Indices: 907486--907522 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
907476 AAAAAAATTA
907486 TCATA-TATAT
1 TCATATTATAT
907496 TCATATTATAT
1 TCATATTATAT
907507 TCATATTATAT
1 TCATATTATAT
907518 TCATA
1 TCATA
907523 AATTTTTACG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.19
11 21 0.81
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (11 bp):
TCATATTATAT
Found at i:910596 original size:28 final size:28
Alignment explanation
Indices: 910557--910666 Score: 84
Period size: 28 Copynumber: 3.9 Consensus size: 28
910547 AATGCTGAGA
910557 AAAATAATTATAATATAATATAAATATATT
1 AAAAT-ATTATAATATAATA-AAATATATT
* *
910587 AAAAT-TTAT-ATAATTATAAAAATATTTT
1 AAAATATTATAAT-ATAAT-AAAATATATT
* *
910615 AAAATAATTATAAAATATTAAAATATA-T
1 AAAAT-ATTATAATATAATAAAATATATT
* * *
910643 AAATTAATATAA-ATATTAAAATAT
1 AAAATATTATAATATAATAAAATAT
910667 GAATCACATT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 12 0.18
27 8 0.12
28 26 0.39
29 8 0.12
30 12 0.18
31 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAAATATTATAATATAATAAAATATATT
Found at i:910636 original size:47 final size:47
Alignment explanation
Indices: 910556--910660 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 47
910546 TAATGCTGAG
* *
910556 AAAAATAATTATAATATAATATAAATATATTAAAATTTATATAATT-AT
1 AAAAAT-ATTATAAAATAATATAAATATATTAAAATATATA-AATTAAT
*
910604 AAAAATATTTTAAAATAATTATAAA-ATATTAAAATATATAAATTAAT
1 AAAAATATTATAAAATAA-TATAAATATATTAAAATATATAAATTAAT
*
910651 ATAAATATTA
1 AAAAATATTA
910661 AAATATGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 4 0.08
47 34 0.68
48 12 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (47 bp):
AAAAATATTATAAAATAATATAAATATATTAAAATATATAAATTAAT
Found at i:910653 original size:55 final size:58
Alignment explanation
Indices: 910557--910666 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 58
910547 AATGCTGAGA
* * *
910557 AAAATAATTATAATATAATATAAATATATTAAAATTTATATAATTATAAAAATATTTT
1 AAAATAATTATAAAATAATATAAATATATTAAAATTAATATAAATATAAAAATATTTT
* *
910615 AAAATAATTATAAAATATTA-AAATATA-T-AAATTAATATAAATATTAAAATAT
1 AAAATAATTATAAAATAATATAAATATATTAAAATTAATATAAATATAAAAATAT
910667 GAATCACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
55 21 0.45
56 1 0.02
57 7 0.15
58 18 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (58 bp):
AAAATAATTATAAAATAATATAAATATATTAAAATTAATATAAATATAAAAATATTTT
Found at i:910868 original size:5 final size:5
Alignment explanation
Indices: 910858--910900 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
910848 TTTTTGTATA
*
910858 AATAT AATAT AATAT AAATAT AAAAAT AATAT AATA- AATAT AA
1 AATAT AATAT AATAT -AATAT -AATAT AATAT AATAT AATAT AA
910901 ATGTATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 20 0.59
6 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:910877 original size:6 final size:6
Alignment explanation
Indices: 910854--910902 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
910844 AAATTTTTTG
*
910854 TATAAA TAT-AA TAT-AA TATAAA TATAAA AATAATA TAATAAA TATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAA-A T-ATAAA TATAAA
910902 T
1 T
910903 GTATTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 10 0.26
6 21 0.55
7 3 0.08
8 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:910877 original size:11 final size:11
Alignment explanation
Indices: 910854--910902 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
910844 AAATTTTTTG
910854 TATAAATATAA
1 TATAAATATAA
910865 TAT-AATATAAA
1 TATAAATAT-AA
*
910876 TATAAAAATAA
1 TATAAATATAA
910887 TAT-AATA-AA
1 TATAAATATAA
910896 TATAAAT
1 TATAAAT
910903 GTATTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 5 0.15
10 11 0.33
11 13 0.39
12 4 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAAATATAA
Found at i:910886 original size:22 final size:20
Alignment explanation
Indices: 910854--910901 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 20
910844 AAATTTTTTG
*
910854 TATAAATATAATATAATATAAA
1 TATAAAAATAATAT-A-ATAAA
910876 TATAAAAATAATATAATAAA
1 TATAAAAATAATATAATAAA
910896 TATAAA
1 TATAAA
910902 TGTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATAATATAATAAA
Found at i:910964 original size:17 final size:17
Alignment explanation
Indices: 910942--910974 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
910932 TATTTAATAT
910942 TATATTTAAAATTTTAA
1 TATATTTAAAATTTTAA
*
910959 TATATTTAATATTTTA
1 TATATTTAAAATTTTA
910975 TATTATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTAAAATTTTAA
Found at i:912250 original size:20 final size:20
Alignment explanation
Indices: 912222--912261 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
912212 TGAGCGTTTT
912222 TTCTAAACCAGTATAGTTCA
1 TTCTAAACCAGTATAGTTCA
*
912242 TTCTGAACCAGTATAGTTCA
1 TTCTAAACCAGTATAGTTCA
912262 GCCCCCTGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCTAAACCAGTATAGTTCA
Found at i:914189 original size:18 final size:19
Alignment explanation
Indices: 914163--914203 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
914153 ATAGAGACAT
*
914163 AAAAGAAAG-TTAAAGGAA
1 AAAACAAAGCTTAAAGGAA
*
914181 AAAACAAAGCTTAAGGGAA
1 AAAACAAAGCTTAAAGGAA
914200 AAAA
1 AAAA
914204 AAAATACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.66, C:0.05, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAACAAAGCTTAAAGGAA
Done.