Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2752
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: 47084
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Found at i:1735 original size:156 final size:156
Alignment explanation
Indices: 1451--1738 Score: 513
Period size: 156 Copynumber: 1.8 Consensus size: 156
1441 TCTTATCCCA
* * *
1451 TTAAATTTTGCTACTTTGGTCGATTGGTCTAAGAACATGGCTGATCATAGGAACTAATCTAAACT
1 TTAAATTTTGCTACTTTGGCCGATTGGTCTAAGAACATGGCTGATCATAGGAAATAATATAAACT
* *
1516 CCCCAGGTCAGTGATGGCTTCAAATCATGTTTGCATCCTCGAATTGTACTAAACTGTGTAAGTAT
66 CCCCAGGTCAATGATGGCTTCAAATCATGTTTGCATCATCGAATTGTACTAAACTGTGTAAGTAT
1581 TGCTTACCGATAGTGGATATGTTGTG
131 TGCTTACCGATAGTGGATATGTTGTG
1607 TTAAATTTTGCTACTTTGGCCGATTGGTCTAAGAACATGGCTGATCATAGGAAATAATATAAACT
1 TTAAATTTTGCTACTTTGGCCGATTGGTCTAAGAACATGGCTGATCATAGGAAATAATATAAACT
* *
1672 CCCTAGGTCAATGATGGCTTCAAATCGTGTTTGCATCATCGAATTGTACTAAACTGTGTAAGTAT
66 CCCCAGGTCAATGATGGCTTCAAATCATGTTTGCATCATCGAATTGTACTAAACTGTGTAAGTAT
1737 TG
131 TG
1739 TAATATCCTG
Statistics
Matches: 125, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 125 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (156 bp):
TTAAATTTTGCTACTTTGGCCGATTGGTCTAAGAACATGGCTGATCATAGGAAATAATATAAACT
CCCCAGGTCAATGATGGCTTCAAATCATGTTTGCATCATCGAATTGTACTAAACTGTGTAAGTAT
TGCTTACCGATAGTGGATATGTTGTG
Found at i:3139 original size:47 final size:46
Alignment explanation
Indices: 3022--3194 Score: 187
Period size: 45 Copynumber: 3.8 Consensus size: 46
3012 GGATGGTTGA
*
3022 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAT
* *
3069 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA-T
* * *
3112 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGC-AAT
*
3162 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
3195 TAGGGGCGGG
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 30 0.28
46 29 0.27
47 30 0.28
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAT
Found at i:3190 original size:46 final size:45
Alignment explanation
Indices: 3026--3196 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 45
3016 GGTTGAGCAT
* *
3026 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
* * *
3071 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAC---GC
*
3116 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
3164 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3197 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
42 6 0.06
44 2 0.02
45 29 0.27
46 31 0.29
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:3457 original size:19 final size:20
Alignment explanation
Indices: 3420--3457 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3410 ATAAGGTGGT
3420 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3440 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3458 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:10635 original size:46 final size:46
Alignment explanation
Indices: 10585--10756 Score: 208
Period size: 45 Copynumber: 3.7 Consensus size: 46
10575 TGGTTGAGCA
*
10585 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
10631 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
10678 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
10724 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
10757 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
45 34 0.32
46 30 0.28
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:11018 original size:19 final size:20
Alignment explanation
Indices: 10981--11018 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
10971 ATAAGGTGGT
10981 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
11001 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
11019 TGGTGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:14248 original size:46 final size:49
Alignment explanation
Indices: 14133--14248 Score: 159
Period size: 49 Copynumber: 2.4 Consensus size: 49
14123 GTCGATGCCA
14133 TGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGTAG
1 TGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGTAG
* * *
14182 TGTCCCAGACAGGTCTTACACTGGCTCTT-ATA-AT-GTGGCCGATG-CG
1 TGTCCCAGACAGGTCTTACACTGACT-TTCATATATCGAGGCCGATGTAG
*
14228 TGTCCCAGACATGTCTTACAC
1 TGTCCCAGACAGGTCTTACAC
14249 AATCACACAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
46 21 0.34
47 9 0.15
48 2 0.03
49 28 0.45
50 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (49 bp):
TGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGTAG
Found at i:17844 original size:3 final size:3
Alignment explanation
Indices: 17836--17874 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
17826 CACACTAAGC
17836 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17875 CACATATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:18483 original size:25 final size:26
Alignment explanation
Indices: 18445--18496 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18435 ATATTAGATA
*
18445 TTTATATTAGA-TTTAGAATTTTTAT
1 TTTATATTAAATTTTAGAATTTTTAT
* *
18470 TTTATTTTAAATTTTAGGATTTTTAT
1 TTTATATTAAATTTTAGAATTTTTAT
18496 T
1 T
18497 ATTTCAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (26 bp):
TTTATATTAAATTTTAGAATTTTTAT
Found at i:19452 original size:24 final size:25
Alignment explanation
Indices: 19402--19466 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
19392 TCTATAATAA
*
19402 ATAATTTAAAATT-ATAATTATAATT
1 ATAATTT-AAATTAAAAATTATAATT
*
19427 AT-ATTTATATTAAAAATTA-AATTT
1 ATAATTTAAATTAAAAATTATAA-TT
19451 ATGAATTTAAATTAAA
1 AT-AATTTAAATTAAA
19467 TTTATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 6 0.18
24 14 0.42
25 2 0.06
26 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
ATAATTTAAATTAAAAATTATAATT
Found at i:19464 original size:37 final size:36
Alignment explanation
Indices: 19407--19477 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
19397 AATAAATAAT
*
19407 TTAAAATTATAATTATAATTATATTTATATTAAAAA
1 TTAAAATTATAATTATAATTAAATTTATATTAAAAA
*
19443 TTAAATTTATGAATT-TAAATTAAATTTATATTAAA
1 TTAAAATTAT-AATTAT-AATTAAATTTATATTAAA
19478 TAATAATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 10 0.32
37 21 0.68
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (36 bp):
TTAAAATTATAATTATAATTAAATTTATATTAAAAA
Found at i:23292 original size:18 final size:17
Alignment explanation
Indices: 23265--23344 Score: 77
Period size: 18 Copynumber: 5.0 Consensus size: 17
23255 TTTAAAAGTT
23265 AAAA-AAATATTATATAA
1 AAAATAAATATTA-ATAA
23282 AAAATAAATA-TAAT--
1 AAAATAAATATTAATAA
23296 --AATAACATA-TAATAA
1 AAAATAA-ATATTAATAA
23311 AAAATAAATATTATATAA
1 AAAATAAATATTA-ATAA
23329 AAAATAAATA-TAATAA
1 AAAATAAATATTAATAA
23345 CAACATATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.09
13 7 0.13
16 9 0.16
17 15 0.27
18 19 0.35
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAATATTAATAA
Found at i:23330 original size:47 final size:46
Alignment explanation
Indices: 23265--23355 Score: 164
Period size: 47 Copynumber: 2.0 Consensus size: 46
23255 TTTAAAAGTT
*
23265 AAAAAAATATTATATAAAAAATAAATATAATAATAACATATAATAA
1 AAAAAAATATTATATAAAAAATAAATATAATAACAACATATAATAA
23311 AAAATAAATATTATATAAAAAATAAATATAATAACAACATATAAT
1 AAAA-AAATATTATATAAAAAATAAATATAATAACAACATATAAT
23356 GAAGTTAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 4 0.09
47 39 0.91
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (46 bp):
AAAAAAATATTATATAAAAAATAAATATAATAACAACATATAATAA
Found at i:23338 original size:29 final size:29
Alignment explanation
Indices: 23268--23335 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
23258 AAAAGTTAAA
23268 AAAATATTATATAAAAAATAAATATAATAAT
1 AAAATA-TA-ATAAAAAATAAATATAATAAT
* *
23299 AACATATAATAAAAAATAAATATTAT-AT
1 AAAATATAATAAAAAATAAATATAATAAT
*
23327 AAAAAATAA
1 AAAATATAA
23336 ATATAATAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 9 0.27
29 17 0.52
30 2 0.06
31 5 0.15
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (29 bp):
AAAATATAATAAAAAATAAATATAATAAT
Found at i:27909 original size:40 final size:40
Alignment explanation
Indices: 27849--28068 Score: 227
Period size: 40 Copynumber: 5.5 Consensus size: 40
27839 TATTCGAATG
*
27849 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
27889 ATATCCGGACTAAGATCCGAAGGCATTTGTGCAAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
27929 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
27969 ATATCCGGGATAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * * * *
28009 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
28048 ATAT-CGGGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGAT-CCGAAG
28069 ATACTTGGGT
Statistics
Matches: 151, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
37 1 0.01
38 14 0.09
39 15 0.10
40 118 0.78
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:27989 original size:80 final size:79
Alignment explanation
Indices: 27849--28068 Score: 268
Period size: 80 Copynumber: 2.8 Consensus size: 79
27839 TATTCGAATG
* * *
27849 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCC-GGACTAAGAT-CCGAAGG
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGA-TAAG-TCCCGAAGG
* *
27912 CATTTGTGCAAGTTG-CT
63 CATTTATGCAAG-TGACC
*
27929 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGATAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGATAAGTCCCGAAGGCA
*
27994 TTTATGCTAGTGACC
65 TTTATGCAAGTGACC
* * * *
28009 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGATTATAT-CGGGCTAAATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGATAAGTCCCGAAG
28069 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
78 15 0.12
79 19 0.15
80 87 0.70
81 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGATAAGTCCCGAAGGCAT
TTATGCAAGTGACC
Done.