Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold477
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: 32493
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Found at i:1274 original size:27 final size:26
Alignment explanation
Indices: 1244--1297 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1234 AGGACTACCG
*
1244 ATTTACCCCTAGAGGGTAAAATGACTA
1 ATTTACCCCTAGAGCGT-AAATGACTA
* * *
1271 ATTTGCCCCTCGTGCGTAAATGACTA
1 ATTTACCCCTAGAGCGTAAATGACTA
1297 A
1 A
1298 CTTGTGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (26 bp):
ATTTACCCCTAGAGCGTAAATGACTA
Found at i:8712 original size:27 final size:26
Alignment explanation
Indices: 8682--8735 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
8672 AGGACTACTG
* *
8682 ATTTACCCCTGGAGGGTAAAATGACTA
1 ATTTACCCCTCGAGCGT-AAATGACTA
* *
8709 ATTTGCCCCTCGTGCGTAAATGACTA
1 ATTTACCCCTCGAGCGTAAATGACTA
8735 A
1 A
8736 CTTGTGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (26 bp):
ATTTACCCCTCGAGCGTAAATGACTA
Found at i:12376 original size:19 final size:19
Alignment explanation
Indices: 12352--12391 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12342 TGTGTCATAA
*
12352 TAAATTCGTAGGCATAACT
1 TAAATTCGTAGACATAACT
* *
12371 TAAATTTGTATACATAACT
1 TAAATTCGTAGACATAACT
12390 TA
1 TA
12392 CAAATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (19 bp):
TAAATTCGTAGACATAACT
Found at i:15540 original size:16 final size:16
Alignment explanation
Indices: 15516--15552 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
15506 AAATATTGAC
*
15516 AAAGAAAGGAAAAGAG
1 AAAGTAAGGAAAAGAG
15532 AAAGTAAGGAAAAGAG
1 AAAGTAAGGAAAAGAG
15548 AAAGT
1 AAAGT
15553 GGGCGAAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (16 bp):
AAAGTAAGGAAAAGAG
Found at i:18132 original size:27 final size:26
Alignment explanation
Indices: 18102--18181 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
18092 ATCTCATATC
18102 TGTAGGCTAGTATTACTGAAATACCCA
1 TGTAGG-TAGTATTACTGAAATACCCA
* * * *
18129 TGTATGATAGAATTACTGAAATGCCCC
1 TGTA-GGTAGTATTACTGAAATACCCA
18156 TGTAAGGTA-TAATTACTGAAATACCC
1 TGT-AGGTAGT-ATTACTGAAATACCC
18182 TTGATTTACA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (26 bp):
TGTAGGTAGTATTACTGAAATACCCA
Found at i:18196 original size:27 final size:27
Alignment explanation
Indices: 18166--18462 Score: 171
Period size: 27 Copynumber: 11.1 Consensus size: 27
18156 TGTAAGGTAT
*
18166 AATTACTGAAATACCCTTGATTTACAA
1 AATTACTGAAATACCCTTGATTTATAA
* *
18193 AATTACTG-AATA-CCTTGGTTTACAA
1 AATTACTGAAATACCCTTGATTTATAA
* * ** * * *
18218 AACTCCCAAAATACCCCTGATTTGTGA
1 AATTACTGAAATACCCTTGATTTATAA
* **
18245 AATTACCGAAAT-CCCTTGACCTATAA
1 AATTACTGAAATACCCTTGATTTATAA
* * * *
18271 AATTACCGAAAATACCCTCGACTTGTAA
1 AATTACTG-AAATACCCTTGATTTATAA
* * *
18299 AATTA-TCGAAATACCCTCGATCTGTAA
1 AATTACT-GAAATACCCTTGATTTATAA
** * *
18326 AATTA-TCGAAATACCCTCCACTTGTAA
1 AATTACT-GAAATACCCTTGATTTATAA
* * **
18353 AATTA-TCAAAATATCCTTGATTTGGAA
1 AATTACT-GAAATACCCTTGATTTATAA
*
18380 AATTACCGAAATACCCTTGATTTGA-AA
1 AATTACTGAAATACCCTTGATTT-ATAA
* * *
18407 AATTACAGAAATACCCCTGATTTACAA
1 AATTACTGAAATACCCTTGATTTATAA
*
18434 AATTA-TAGAAATACCTTTGACTTT-TAA
1 AATTACT-GAAATACCCTTGA-TTTATAA
18461 AA
1 AA
18463 AAGTAGAAAA
Statistics
Matches: 217, Mismatches: 43, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
25 16 0.07
26 26 0.12
27 155 0.71
28 20 0.09
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGATTTATAA
Found at i:18302 original size:54 final size:54
Alignment explanation
Indices: 18226--18427 Score: 210
Period size: 54 Copynumber: 3.7 Consensus size: 54
18216 AAAACTCCCA
* * * *
18226 AAATACCC-CTGATTTGTGAAATTACCGAAAT-CCCTTGACCTATAAAATTACCG
1 AAATACCCTC-GACTTGTAAAATTACCGAAATACCCTTGATCTGTAAAATTACCG
* * *
18279 AAAATACCCTCGACTTGTAAAATTATCGAAATACCCTCGATCTGTAAAATTATCG
1 -AAATACCCTCGACTTGTAAAATTACCGAAATACCCTTGATCTGTAAAATTACCG
* * * * * *
18334 AAATACCCTCCACTTGTAAAATTATCAAAATATCCTTGATTTGGAAAATTACCG
1 AAATACCCTCGACTTGTAAAATTACCGAAATACCCTTGATCTGTAAAATTACCG
* * * * *
18388 AAATACCCTTGATTTGAAAAATTACAGAAATACCCCTGAT
1 AAATACCCTCGACTTGTAAAATTACCGAAATACCCTTGAT
18428 TTACAAAATT
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
54 104 0.85
55 19 0.15
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (54 bp):
AAATACCCTCGACTTGTAAAATTACCGAAATACCCTTGATCTGTAAAATTACCG
Found at i:18428 original size:54 final size:53
Alignment explanation
Indices: 18166--18463 Score: 199
Period size: 54 Copynumber: 5.5 Consensus size: 53
18156 TGTAAGGTAT
* * *
18166 AATTACTGAAATACCCTTGATTT-ACAAAATTACTG-AATACCTTGGTTTACAA
1 AATTACCGAAATACCCTTGATTTGA-AAAATTACAGAAATACCTTGATTTACAA
* * * * ** * * ** *
18218 AACTCCCAAAATACCCCTGATTTGTGAAATTACCGAAATCCCTTGACCTATAA
1 AATTACCGAAATACCCTTGATTTGAAAAATTACAGAAATACCTTGATTTACAA
* * * * * **
18271 AATTACCGAAAATACCCTCGACTTGTAAAATTATC-GAAATACCCTCGATCTGTAA
1 AATTACCG-AAATACCCTTGATTTGAAAAATTA-CAGAAATA-CCTTGATTTACAA
* ** * * **
18326 AATTATCGAAATACCCTCCACTTGTAAAATTATCA-AAATATCCTTGATTTGGAA
1 AATTACCGAAATACCCTTGATTTGAAAAATTA-CAGAAATA-CCTTGATTTACAA
*
18380 AATTACCGAAATACCCTTGATTTGAAAAATTACAGAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTTGATTTGAAAAATTACAGAAATA-CCTTGATTTACAA
** * *
18434 AATTATAGAAATACCTTTGACTTTTAAAAA
1 AATTACCGAAATACCCTTGA-TTTGAAAAA
18464 AGTAGAAAAA
Statistics
Matches: 195, Mismatches: 43, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
52 26 0.13
53 19 0.10
54 124 0.64
55 26 0.13
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (53 bp):
AATTACCGAAATACCCTTGATTTGAAAAATTACAGAAATACCTTGATTTACAA
Found at i:18436 original size:81 final size:79
Alignment explanation
Indices: 18166--18450 Score: 218
Period size: 81 Copynumber: 3.5 Consensus size: 79
18156 TGTAAGGTAT
* * ** * * * * *
18166 AATTACTGAAATACCCTTGATTTACAAAATTA-CTGAATACCTTGGTTTACAAAACTCCCAAAAT
1 AATTAC-GAAATACCCCTGACTTACAAAATTATCAAAATACCTTGATTTGCAAAATTACCGAAAT
* *
18230 ACCCCTGATTTGTGA
65 ACCCTTGATTTGTAA
* * * * * * * *
18245 AATTACCGAAAT-CCCTTGACCTATAAAATTACCGAAAATACCCTCGACTTGTAAAATTATCGAA
1 AATTA-CGAAATACCCCTGACTTACAAAATTATC-AAAATA-CCTTGATTTGCAAAATTACCGAA
* *
18309 ATACCCTCGATCTGTAA
63 ATACCCTTGATTTGTAA
* ** *
18326 AATTATCGAAATA-CCCTCCACTTGTAAAATTATCAAAATATCCTTGATTTGGAAAATTACCGAA
1 AATTA-CGAAATACCCCT-GACTTACAAAATTATCAAAATA-CCTTGATTTGCAAAATTACCGAA
*
18390 ATACCCTTGATTTGAAA
63 ATACCCTTGATTTGTAA
*
18407 AATTACAGAAATACCCCTGATTTACAAAATTAT-AGAAATACCTT
1 AATTAC-GAAATACCCCTGACTTACAAAATTATCA-AAATACCTT
18451 TGACTTTTAA
Statistics
Matches: 161, Mismatches: 36, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
78 16 0.10
79 11 0.07
80 11 0.07
81 107 0.66
82 16 0.10
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (79 bp):
AATTACGAAATACCCCTGACTTACAAAATTATCAAAATACCTTGATTTGCAAAATTACCGAAATA
CCCTTGATTTGTAA
Found at i:18500 original size:27 final size:27
Alignment explanation
Indices: 18166--18513 Score: 144
Period size: 27 Copynumber: 12.9 Consensus size: 27
18156 TGTAAGGTAT
*
18166 AATTACTGAAATACCCTTGATTT-ACAA
1 AATTACTAAAATACCCTTGATTTGA-AA
* *
18193 AATTACT-GAATA-CCTTGGTTT-ACAA
1 AATTACTAAAATACCCTTGATTTGA-AA
* * * * **
18218 AACTCCCAAAATACCCCTGATTTGTGA
1 AATTACTAAAATACCCTTGATTTGAAA
** **
18245 AATTACCGAAAT-CCCTTGACCT-ATAA
1 AATTACTAAAATACCCTTGATTTGA-AA
* * * *
18271 AATTACCGAAAATACCCTCGACTTGTAA
1 AATTA-CTAAAATACCCTTGATTTGAAA
* * * *
18299 AATTA-TCGAAATACCCTCGATCTGTAA
1 AATTACT-AAAATACCCTTGATTTGAAA
* ** * *
18326 AATTA-TCGAAATACCCTCCACTTGTAA
1 AATTACT-AAAATACCCTTGATTTGAAA
* *
18353 AATTA-TCAAAATATCCTTGATTTGGAA
1 AATTACT-AAAATACCCTTGATTTGAAA
**
18380 AATTACCGAAATACCCTTGATTTGAAA
1 AATTACTAAAATACCCTTGATTTGAAA
*
18407 AATTAC-AGAAATACCCCTGATTT-ACAA
1 AATTACTA-AAATACCCTTGATTTGA-AA
* *
18434 AATTA-TAGAAATACCTTTGACTTTTAAAA
1 AATTACTA-AAATACCCTTGA--TTTGAAA
* ** * *
18463 AAGTAGAAAAATACCATTAATTTGAAA
1 AATTACTAAAATACCCTTGATTTGAAA
* *
18490 AATTACTAAAATGCCCTTGGTTTG
1 AATTACTAAAATACCCTTGATTTG
18514 TAGATTTACC
Statistics
Matches: 249, Mismatches: 56, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
25 16 0.06
26 22 0.09
27 175 0.70
28 15 0.06
29 19 0.08
30 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
AATTACTAAAATACCCTTGATTTGAAA
Found at i:18818 original size:41 final size:41
Alignment explanation
Indices: 18773--18895 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 41
18763 GGAAGAAGAA
* * *
18773 ATTGAGGATTGCATGGTTGCTTGACGATCGTGGATCCACTG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* *
18814 ATTGAGGGTCGCATGGTTTCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
* * *
18855 ATTAAGGATGGCATGGTTGCTTGACGACCATGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
18896 GTGGCTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:23078 original size:40 final size:40
Alignment explanation
Indices: 22878--23083 Score: 235
Period size: 40 Copynumber: 5.2 Consensus size: 40
22868 TATTCGAATG
* * *
22878 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
*
22919 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
* *
22959 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
22998 AAAT-CGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
23036 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
23076 ATATCCGG
1 ATATCCGG
23084 TTAAATTCCA
Statistics
Matches: 141, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
38 32 0.23
39 35 0.25
40 45 0.32
41 28 0.20
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:31129 original size:39 final size:39
Alignment explanation
Indices: 31025--31230 Score: 245
Period size: 39 Copynumber: 5.2 Consensus size: 39
31015 TATTCGAATG
* * *
31025 ATATCCGGGCTAAGTCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACT
*
31065 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACT
* * *
31105 A-ATTCCGGGCTAAGCCCGAAGGCATTGGAGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
* *
31144 AAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
* * *
31183 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTA-CT
31223 ATATCCGG
1 ATATCCGG
31231 TTAAATTCTG
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
39 69 0.48
40 58 0.41
41 16 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACT
Done.