Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2262
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: 37295
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Found at i:2071 original size:13 final size:13
Alignment explanation
Indices: 2053--2078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2043 ATATTATAAT
2053 TATTTTATGTTAA
1 TATTTTATGTTAA
2066 TATTTTATGTTAA
1 TATTTTATGTTAA
2079 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:3463 original size:40 final size:40
Alignment explanation
Indices: 3415--3620 Score: 362
Period size: 40 Copynumber: 5.2 Consensus size: 40
3405 GGACTAAGAT
3415 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
*
3455 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
3495 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
3535 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
3575 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
3614 CCGAAGG
1 CCGAAGG
3621 TACTTGGGTT
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 15 0.09
40 144 0.89
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:10116 original size:13 final size:13
Alignment explanation
Indices: 10098--10123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10088 ATATTATAAT
10098 TATTTTATGTTAA
1 TATTTTATGTTAA
10111 TATTTTATGTTAA
1 TATTTTATGTTAA
10124 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:11514 original size:40 final size:40
Alignment explanation
Indices: 11466--11671 Score: 317
Period size: 40 Copynumber: 5.2 Consensus size: 40
11456 GGACTAAGAT
11466 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
11506 CCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGGC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
11546 CCGAAGACATTTGTGCTAGTGACCATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
11586 CCGAAGGAATTTGTGCTAGTGATTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
* *
11626 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
11665 CCGAAGG
1 CCGAAGG
11672 TACTTGGGTT
Statistics
Matches: 151, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 15 0.10
40 134 0.89
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:19194 original size:25 final size:26
Alignment explanation
Indices: 19152--19202 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
19142 CCCTTTATCC
*
19152 ATTTTAAAATTATTTATA-ACTTATTT
1 ATTTTAAAATTATATATATA-TTATTT
*
19178 ATTTT-AAATTGTATATATATTATTT
1 ATTTTAAAATTATATATATATTATTT
19203 TATATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTAAAATTATATATATATTATTT
Found at i:19230 original size:5 final size:5
Alignment explanation
Indices: 19189--19260 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
19179 TTTTAAATTG
* * * *
19189 TATA- TATAT TATTT TATAT ATGTAT TGTA- TATTT TATAT TATTAT T-TACT
1 TATAT TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TA-TAT TATA-T
*
19239 TATAT TTTAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TA
19261 CTTCATATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
4 8 0.15
5 36 0.67
6 10 0.19
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:19242 original size:23 final size:24
Alignment explanation
Indices: 19216--19335 Score: 88
Period size: 24 Copynumber: 4.9 Consensus size: 24
19206 ATATGTATTG
19216 TATATTTTA-TATTATTAT-TTACT
1 TATATTTTATTA-TATTATATTACT
19239 TATATTTTATTATATTATATTACT
1 TATATTTTATTATATTATATTACT
* * *
19263 TCATATTTT-TCTATTATCAAATTAAT
1 T-ATATTTTAT-TA-TATTATATTACT
** *
19289 ATATATTTTAACATA-TACCATTACT
1 -TATATTTTATTATATTA-TATTACT
19314 TAT-TATTTATTATATTATATTA
1 TATAT-TTTATTATATTATATTA
19336 TATTTTTATC
Statistics
Matches: 76, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
23 16 0.21
24 24 0.32
25 18 0.24
26 17 0.22
27 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTTTATTATATTATATTACT
Found at i:19364 original size:86 final size:87
Alignment explanation
Indices: 19227--19428 Score: 214
Period size: 86 Copynumber: 2.3 Consensus size: 87
19217 ATATTTTATA
* * * * * *
19227 TTATTATTTACTTATATTTTATTATA-TTATATTACTTCATATTTTTCTATTATCAAATTAATAT
1 TTATTATTTA-TTATATTATATTATATTTTTATCACATAATATTTTTATATTATCAAATTAATAT
*
19291 ATATTTTAAC-ATATACCATTAC
65 ACATTTTAACAATATACCATTAC
* * * *
19313 TTATTATTTATTATATTATATTATATTTTTATCACATAATATTTTTATATTATTATATTATTTTA
1 TTATTATTTATTATATTATATTATATTTTTATCACATAATATTTTTATATTATCAAATTAATATA
** *
19378 CATTTTAACAATATATTATTTC
66 CATTTTAACAATATACCATTAC
*
19400 ATATTA-TTATTATCTATTATA-TATATTTT
1 TTATTATTTATTA--TATTATATTATATTTT
19429 CATGTATATT
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
85 14 0.14
86 54 0.56
87 22 0.23
88 7 0.07
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (87 bp):
TTATTATTTATTATATTATATTATATTTTTATCACATAATATTTTTATATTATCAAATTAATATA
CATTTTAACAATATACCATTAC
Found at i:19370 original size:16 final size:16
Alignment explanation
Indices: 19313--19371 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
19303 ATACCATTAC
*
19313 TTATTAT-TTATTATA
1 TTATTATATTTTTATA
19328 TTATATTATATTTTTATCA
1 -T-TATTATATTTTTAT-A
* *
19347 -CATAATATTTTTATA
1 TTATTATATTTTTATA
19362 TTATTATATT
1 TTATTATATT
19372 ATTTTACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.03
16 20 0.59
17 6 0.18
18 6 0.18
19 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATATTTTTATA
Found at i:19410 original size:16 final size:16
Alignment explanation
Indices: 19391--19465 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
19381 TTTAACAATA
19391 TATTATTTCATATTAT
1 TATTATTTCATATTAT
19407 TATTA--TC-TATTA-
1 TATTATTTCATATTAT
*
19419 TATATATTTTCATGTATAT
1 TAT-TA-TTTCATAT-TAT
*
19438 TATTA-TTCACATTAT
1 TATTATTTCATATTAT
19453 TA-T-TTTCATATTA
1 TATTATTTCATATTA
19466 AATTGATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
12 3 0.06
13 7 0.15
14 11 0.23
15 5 0.11
16 12 0.26
17 2 0.04
18 4 0.09
19 3 0.06
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (16 bp):
TATTATTTCATATTAT
Found at i:19613 original size:21 final size:22
Alignment explanation
Indices: 19579--19622 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19569 TATTTCAAAA
*
19579 TTCATTATTAATT-ACTATGTT
1 TTCATTATTAATTAAATATGTT
19600 TTCATGTATT-ATTAAATATGTT
1 TTCAT-TATTAATTAAATATGTT
19622 T
1 T
19623 ATTATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTCATTATTAATTAAATATGTT
Found at i:26526 original size:38 final size:38
Alignment explanation
Indices: 26483--26558 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
26473 TTCATCCTTT
26483 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
26521 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
26559 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:27840 original size:40 final size:40
Alignment explanation
Indices: 27746--27890 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
27736 TACTCGAATG
*
27746 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
27787 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
27827 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
27867 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
27891 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:34567 original size:37 final size:37
Alignment explanation
Indices: 34526--34599 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
34516 GTTCATCCTT
34526 TTCATTTCTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTGGCCGAAAATTCTAAGGAAGGAGGAA
34563 TTCATTTCTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTGGCCGAAAATTCTAAGGAAGGAGGAA
34600 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (37 bp):
TTCATTTCTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:35842 original size:41 final size:40
Alignment explanation
Indices: 35783--35894 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 40
35773 CTCGAATGAT
*
35783 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACTAC
1 ATCCGGGCTAAGT-CCGAAGGCATTTGTGCTAAGCGACTAC
* *
35824 ATCCGGACTAAGATCCGAAGGCATTTGTGCT-AGCGACTAT
1 ATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAAGCGACTAC
*
35864 ATCCGGGCTAAGTCCGAAGGCATTTATGCTA
1 ATCCGGGCTAAGTCCGAAGGCATTTGTGCTA
35895 GTGACCATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
39 17 0.27
40 19 0.30
41 27 0.42
42 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCGAAGGCATTTGTGCTAAGCGACTAC
Found at i:35894 original size:39 final size:40
Alignment explanation
Indices: 35781--35924 Score: 184
Period size: 39 Copynumber: 3.6 Consensus size: 40
35771 TACTCGAATG
*
35781 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCT-AGCGACT
* *
35822 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * *
35862 ATATCCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* *
35901 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
35925 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 35 0.38
40 27 0.30
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Done.