Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1743
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: 41163
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2663 original size:19 final size:19
Alignment explanation
Indices: 2639--2675 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2629 TATTTGAATG
2639 CTATGTGAATAATTTGATA
1 CTATGTGAATAATTTGATA
* *
2658 CTATGTGATTATTTTGAT
1 CTATGTGAATAATTTGAT
2676 GATATAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (19 bp):
CTATGTGAATAATTTGATA
Found at i:3110 original size:50 final size:50
Alignment explanation
Indices: 3029--3421 Score: 364
Period size: 50 Copynumber: 7.9 Consensus size: 50
3019 TTCGTTGTGA
*
3029 GTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
* * * * *
3079 GTCGCATGTGTAATACTAAGTGCAGGCTACTATGCGTACCTG-TTAACTTTG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGA--TAG
* * * * * * *
3130 ATCACATGTGTAGTACTAAGTGTAAGCT-CTATGTGTATCAGATGGTTTA-
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG-ATAG
* *** *
3179 GTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
* * * * **
3229 GTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCG-TTAACTTCT
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGA--TAG
* * * * ** * * *
3280 ATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATGGTTAA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
* ***
3330 GTCACATGTGTAGTACTAAGTGCAGGCTATTACATGTA-CAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
*
3379 GTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
3422 GAGCTTTAGT
Statistics
Matches: 267, Mismatches: 66, Indels: 20
0.76 0.19 0.06
Matches are distributed among these distances:
49 72 0.27
50 134 0.50
51 60 0.22
52 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
GTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAG
Found at i:3299 original size:150 final size:150
Alignment explanation
Indices: 3028--3418 Score: 615
Period size: 150 Copynumber: 2.6 Consensus size: 150
3018 ATTCGTTGTG
*** *
3028 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGATAGGTCGCATGTGTAAT
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTA-CAGATTGATAGGTCGCATGTGTAGT
* *
3093 ACTAAGTGCAGGCTACTATGCGTACCTGTTAACTTTGATCACATGTGTAGTACTAAGTGTAAGCT
65 ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTTGATCACATGTGTAGTACTAAGTGCAAGCT
* *
3158 -CTATGTGTATCAGATGGTTT
130 ACTACGTGTATCAGATGGTTA
3178 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTAGATTGATAGGTCGCATGTGTAGT
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTAC-AGATTGATAGGTCGCATGTGTAGT
* * *
3243 ACTAAGTGTAGGCTACTATGCGTACCCGTTAACTTCT-ATCACGTGTGTAGTACTAAGTGCAGGC
65 ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTT-TGATCACATGTGTAGTACTAAGTGCAAGC
*
3307 TACTACGTGTATTAGATGGTTA
129 TACTACGTGTATCAGATGGTTA
* *
3329 AGTCACATGTGTAGTACTAAGTGCAGGCTATTACATGTACAGATTGATAGGTCGCATGTGTAGTA
1 AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGATTGATAGGTCGCATGTGTAGTA
3394 CTAAGTGCAGGCTACTATGCGTACC
66 CTAAGTGCAGGCTACTATGCGTACC
3419 AGAGAGCTTT
Statistics
Matches: 223, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
149 1 0.00
150 166 0.74
151 56 0.25
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (150 bp):
AGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACAGATTGATAGGTCGCATGTGTAGTA
CTAAGTGCAGGCTACTATGCGTACCCGTTAACTTTGATCACATGTGTAGTACTAAGTGCAAGCTA
CTACGTGTATCAGATGGTTA
Found at i:4866 original size:21 final size:21
Alignment explanation
Indices: 4840--4882 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4830 TAAGGACAAC
4840 ATAAGGCTTGGAAAATAGCCT
1 ATAAGGCTTGGAAAATAGCCT
4861 ATAAGGCTTGGAAAATAGCCT
1 ATAAGGCTTGGAAAATAGCCT
4882 A
1 A
4883 AGTGTTGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
ATAAGGCTTGGAAAATAGCCT
Found at i:20477 original size:50 final size:51
Alignment explanation
Indices: 20354--20562 Score: 199
Period size: 50 Copynumber: 4.3 Consensus size: 51
20344 GCTAAATGAC
* * * * * *
20354 CTTGTATATTTGGCCACATAGGTATGTACATATGTGATGTTGTA-TTGGAT
1 CTTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAAT
* * *
20404 CTTGAATATTCGGCCATGA-AGGTATGCAGAAATGTGATATTATATTTGAAT
1 CTTGTATATTCGGCCAT-ATAGGTATGCACATATGTGATATTATATTTGAAT
* *
20455 -TTGTATATTCGGCCATATAGGTAAGCACATATGTGATATTAAATTT-AAT
1 CTTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAAT
* *
20504 CTTG-------GGCCATATAGGTAAGCACATATGTGCTATTATATTTG-AT
1 CTTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAAT
*
20547 CTTGTATATTTGGCCA
1 CTTGTATATTCGGCCA
20563 AATGAGTGAT
Statistics
Matches: 131, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
43 40 0.31
49 4 0.03
50 81 0.62
51 6 0.05
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (51 bp):
CTTGTATATTCGGCCATATAGGTATGCACATATGTGATATTATATTTGAAT
Found at i:20512 original size:43 final size:43
Alignment explanation
Indices: 20465--20550 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
20455 TTGTATATTC
20465 GGCCATATAGGTAAGCACATATGTGATATTAAATTTAATCTTG
1 GGCCATATAGGTAAGCACATATGTGATATTAAATTTAATCTTG
* * *
20508 GGCCATATAGGTAAGCACATATGTGCTATTATATTTGATCTTG
1 GGCCATATAGGTAAGCACATATGTGATATTAAATTTAATCTTG
20551 TATATTTGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (43 bp):
GGCCATATAGGTAAGCACATATGTGATATTAAATTTAATCTTG
Found at i:25882 original size:68 final size:64
Alignment explanation
Indices: 25766--26024 Score: 233
Period size: 68 Copynumber: 3.9 Consensus size: 64
25756 TGGATGATAC
** * * *
25766 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCACATGGGTGGTACTGAGTGTACACCATGTAG-ACAAGAGAGCTAC
25830 AAG
64 --G
* *
25833 ACATTATGATGTAGCTAGGTCACATGGGTGATACT-ATGTGTACACCATGTAGACAAGAGAGCTA
1 AGA-TAT-ATGTAGCTAGGTCACATGGGTGGTACTGA-GTGTACACCATGTAGACAAGAGAGCTA
25897 CG
63 CG
* * * *
25899 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAG-G-ACACCATGTAGACAAGAGAGC
1 AGATATATGTAGCTAGGTCACATGGGTGG-T--A-CTG-AGTGTACACCATGTAGACAAGAGAGC
25962 TACG
61 TACG
* * *
25966 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTGAGTGTTCACCATGT-GTACAAGAGAGC
1 AGATATATGTAGCTAGGTCACATGGGTGGTACTGAGTGTACACCATGTAG-ACAAGAGAGC
26025 CAAACTATAT
Statistics
Matches: 159, Mismatches: 20, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
61 2 0.01
62 4 0.03
63 19 0.12
64 20 0.13
65 5 0.03
66 19 0.12
67 36 0.23
68 51 0.32
69 2 0.01
70 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.24
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCACATGGGTGGTACTGAGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:30020 original size:40 final size:40
Alignment explanation
Indices: 29976--30161 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
29966 GCTACTCATT
*
29976 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
30016 CAAATTCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
**
30056 CAAATGCCTTCGGGACTTAAACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
30096 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
30137 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30162 CATCATTCAA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 112 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Done.