Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3002
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: 28689
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Found at i:1148 original size:3 final size:3
Alignment explanation
Indices: 1142--1188 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
1132 TTTAGCCACT
*
1142 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1187 TT
1 TT
1189 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1742 original size:16 final size:16
Alignment explanation
Indices: 1723--1753 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1713 TACACCCATA
*
1723 TATATGTACATATTTT
1 TATATATACATATTTT
1739 TATATATACATATTT
1 TATATATACATATTT
1754 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:4461 original size:28 final size:29
Alignment explanation
Indices: 4430--4485 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
4420 TATTATTATT
*
4430 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
4458 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
4486 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:5253 original size:3 final size:3
Alignment explanation
Indices: 5245--5274 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5235 GTGAGGTAAG
5245 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5275 GAGTGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5458 original size:24 final size:25
Alignment explanation
Indices: 5426--5484 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
5416 CGGATTAATT
5426 ATTG-ATTGAAAG-GTGGAAAA-ATG
1 ATTGAATTGAAAGTGT-GAAAAGATG
*
5449 ATTGAATTGAAAGTGTGAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAG-ATG
5475 ATTGAATTGA
1 ATTGAATTGA
5485 GAATATATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 4 0.13
24 13 0.42
25 2 0.06
26 12 0.39
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.31
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAGATG
Found at i:5687 original size:37 final size:39
Alignment explanation
Indices: 5628--5723 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
5618 CGGATAGATT
* * * *
5628 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
5665 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
5704 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
5724 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:16543 original size:46 final size:44
Alignment explanation
Indices: 16476--16772 Score: 206
Period size: 44 Copynumber: 6.9 Consensus size: 44
16466 ATTATACAGG
*
16476 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
16522 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
16566 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
16605 TC-TATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
16645 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
16691 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * *
16735 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
16773 CACTATCCTA
Statistics
Matches: 199, Mismatches: 36, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 20 0.10
39 3 0.02
40 4 0.02
41 24 0.12
42 3 0.02
43 2 0.01
44 70 0.35
45 1 0.01
46 70 0.35
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:16593 original size:44 final size:46
Alignment explanation
Indices: 16479--16772 Score: 187
Period size: 46 Copynumber: 6.8 Consensus size: 46
16469 ATACAGGTCT
* * * *
16479 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
*
16525 TATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAAT-GTCAGATCC
* * * *
16569 TATCTCCTTGAGATTACAATGGAGCGGAT--TA-AA-G---GAT-C
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
* * * * * *
16607 TATCTCTCTGA-AGTTACAGTAGAGAAGATC--A-CA--TCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAATGTCAGATCC
* * * *
16648 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
* ** * *
16694 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-G--AGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-AATGTCAGATCC
* *
16738 TATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGA
16773 CACTATCCTA
Statistics
Matches: 195, Mismatches: 37, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
37 1 0.01
38 24 0.12
39 2 0.01
40 3 0.02
41 23 0.12
42 3 0.02
43 1 0.01
44 66 0.34
45 3 0.02
46 68 0.35
47 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (46 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATCAAAGAATGTCAGATCC
Found at i:16799 original size:43 final size:44
Alignment explanation
Indices: 16519--16804 Score: 138
Period size: 44 Copynumber: 6.7 Consensus size: 44
16509 AAAGAATTTC
* * * *
16519 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGATAG
1 AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACAG
* * * *
16563 TA-ATCCTATCTCCTTG-AGATTACAATGGAGCGGAT--TA-A-AG
1 -AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACAG
* * * *
16603 -GAT-CTATCTCTCTGAAGTTACAGTAGAGAAGATC-ACA-TCAG
1 AGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATCGA-AGACAG
* * * * *
16644 -G-TCTTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGA-ATTTC
1 AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACA---G
* * * *
16688 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACAG
* *
16732 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATCGAAGACAG
** *
16775 CTATCCTATCTCCCCGAAGTTACAGTGGAG
1 AGATCCTATCTCCCTGAAGTTACAGTGGAG
16805 TGGATTAAAA
Statistics
Matches: 185, Mismatches: 38, Indels: 38
0.71 0.15 0.15
Matches are distributed among these distances:
38 21 0.11
39 4 0.02
40 6 0.03
41 28 0.15
42 2 0.01
43 23 0.12
44 67 0.36
45 2 0.01
46 30 0.16
47 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
AGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATCGAAGACAG
Found at i:16962 original size:218 final size:213
Alignment explanation
Indices: 16519--16974 Score: 451
Period size: 218 Copynumber: 2.1 Consensus size: 213
16509 AAAGAATTTC
* * * **
16519 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCCTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCCGAGATT
* *
16584 ACAATGGAGCGGATTAAAGGATCTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTT
66 ACAATGGAGCGGATTAAAGGATCTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCTT
*** * *
16649 ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAGT
131 ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAACAACAGATCTTATCTCCCTAAAGTTACAGT
* *
16714 GGAGCAGATTGAAGCCAG
196 GGAACAGATTGAAGCAAG
* *
16732 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCCGA-AGT
1 AGATCCTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCCGAGA-T
* * * * * *
16795 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATC-TATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
* * * ***
16860 AAGTCTTATTTCCCTGAAGA-TGCAGTGGAATAGATTGAA-AACAAC-GAATCTTAT-TCCCTAA
124 AAGTCTTATCTCCCTG-AGATTACAGTGGAACAGACCAAAGAACAACAG-ATCTTATCTCCCTAA
** *
16921 AGTTGTAGTGGAATAGA-TGAAGCGAAG
187 AGTTACAGTGGAACAGATTGAAGC-AAG
*
16948 TCATATCCTATCTCCCTGA-AGTTACAG
1 --AGATCCTATCTCCCTGAGA-TTACAG
16975 TGGAACGGAT
Statistics
Matches: 199, Mismatches: 31, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
211 1 0.01
212 26 0.13
213 43 0.22
215 6 0.03
216 21 0.11
217 20 0.10
218 79 0.40
219 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (213 bp):
AGATCCTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCCGAGATT
ACAATGGAGCGGATTAAAGGATCTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCTT
ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAACAACAGATCTTATCTCCCTAAAGTTACAGT
GGAACAGATTGAAGCAAG
Found at i:16973 original size:175 final size:172
Alignment explanation
Indices: 16732--17184 Score: 524
Period size: 175 Copynumber: 2.6 Consensus size: 172
16722 TTGAAGCCAG
* * *
16732 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGAT--CGAAGACACTATCCTATCTCCCCGAAGT
1 AGATCTTATCTCCCTAAG-TTACAGCGGAACAGATAACGAAGACA-TATCCTATCTCCCTGAAGT
* * * *
16795 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGTCGCATC
64 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCATC
* * **
16860 AAGTCTTATTTCCCTGAAGATGCAGTGGAATAGATTGAAAACAACG-
129 AAGTCTTATTT-CCTG-AGATACAGCGGAATAGACCGAAAA-AACGC
** * * *
16906 A-ATCTTAT-TCCCTAAAGTTGTAGTGGAATAGATGAAGCGAAGTCATATCCTATCTCCCTGAAG
1 AGATCTTATCTCCCT-AAGTTACAGCGGAACAGAT-AA-CGAAGACATATCCTATCTCCCTGAAG
* *
16969 TTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGATCGCAT
63 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCAT
* * * * **
17034 CAGGTCTTATTTCCTGAGTTACAGCGGAGTAGACCGAAGAATTGC
128 CAAGTCTTATTTCCTGAGATACAGCGGAATAGACCGAAAAAACGC
* * *
17079 AGATCTTATCTCCCTGAGTTACAGCGGAGCAGATTA--AAGACATAATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCTAAGTTACAGCGGAACAGATAACGAAGACAT-ATCCTATCTCCCTGAAGTT
*
17142 ACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGT
65 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGT
17185 GGCAGTAGAG
Statistics
Matches: 236, Mismatches: 34, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
170 6 0.03
171 60 0.25
172 18 0.08
173 28 0.12
174 25 0.11
175 92 0.39
176 7 0.03
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (172 bp):
AGATCTTATCTCCCTAAGTTACAGCGGAACAGATAACGAAGACATATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGATCGCATCAA
GTCTTATTTCCTGAGATACAGCGGAATAGACCGAAAAAACGC
Found at i:17028 original size:90 final size:88
Alignment explanation
Indices: 16733--17199 Score: 266
Period size: 85 Copynumber: 5.4 Consensus size: 88
16723 TGAAGCCAGA
* ** * * *
16733 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGAT--CGAAGACACTATCCTATCTCCCCGAAGT
1 GATCTTATCTCTCTGAAG-TTACAGTAGAGTAGATGGCGAAGTCA-TATCCTATCTCCCTGAAGT
*
16795 TACAGTGGAGTGGATTAAAATAAAG
64 TACAGTGGAATGGATTAAAATAAAG
* * * * * * *
16820 GATCTTATCTCTCTGAGGTTACAGCAGAGTAG--GTCGCA-TCA-AGTCTTATTTCCCTGAAGAT
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATGGCGAAGTCATA-TCCTATCTCCCTGAAGTT
* * * *
16881 GCAGTGGAATAGATTGAAAACAACG
65 ACAGTGGAATGGATT-AAAATAAAG
* * * ** * *
16906 AATCTTAT-TCCCTAAAGTTGTAGTGGAATAGATGAAGCGAAGTCATATCCTATCTCCCTGAAGT
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATG--GCGAAGTCATATCCTATCTCCCTGAAGT
*
16970 TACAGTGGAACGGATTAAAATAAAG
64 TACAGTGGAATGGATTAAAATAAAG
* * ** * *
16995 GATCTTATCTCTCTGAAGTTACAATAGAGTAGAT--CGCA-TCAGGTCTTAT-TTCCTG-AGTTA
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATGGCGAAGTCATATCCTATCTCCCTGAAGTTA
* * * ** **
17055 CAGCGGAGTAGACCGAAGAATTGCA-
66 CAGTGGAATGGA-TTAA-AA-TAAAG
* ** * ** *
17080 GATCTTATCTCCCTG-AGTTACAGCGGAGCAGAT--TAAAGACATAATCCTATCTCCCTGAAGTT
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATGGCGAAGTCAT-ATCCTATCTCCCTGAAGTT
**
17142 ACAGTGGAGCGGATTAAAATAAAG
65 ACAGTGGAATGGATTAAAATAAAG
* **
17166 AATCTTATCTCTCTGAAGTGGCAGTAGAGTAGAT
1 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
17200 TACATCCAAG
Statistics
Matches: 277, Mismatches: 82, Indels: 42
0.69 0.20 0.10
Matches are distributed among these distances:
83 13 0.05
84 23 0.08
85 69 0.25
86 41 0.15
87 50 0.18
88 15 0.05
89 17 0.06
90 48 0.17
91 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (88 bp):
GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATGGCGAAGTCATATCCTATCTCCCTGAAGTTA
CAGTGGAATGGATTAAAATAAAG
Found at i:17510 original size:27 final size:27
Alignment explanation
Indices: 17480--17548 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
17470 TCAGAACCAC
17480 TAGCCCAATAACCCAATAGCCTACCCT
1 TAGCCCAATAACCCAATAGCCTACCCT
17507 TAGCCCAATAACCCAATAGCCTACCCT
1 TAGCCCAATAACCCAATAGCCTACCCT
*
17534 CAGCCCAA-AACCCAA
1 TAGCCCAATAACCCAA
17549 AACAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.36, C:0.42, G:0.07, T:0.14
Consensus pattern (27 bp):
TAGCCCAATAACCCAATAGCCTACCCT
Found at i:18679 original size:3 final size:3
Alignment explanation
Indices: 18673--18702 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
18663 TGTTTATTCT
18673 TTA TTA TTA TTA TTA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
18703 TGTTTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18688 original size:19 final size:20
Alignment explanation
Indices: 18652--18702 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
18642 TTTTTAGCCA
*
18652 CTTTATTATT-TTGTTTATT
1 CTTTATTATTATTGATTATT
18671 CTTTATTATTATT-ATTATT
1 CTTTATTATTATTGATTATT
*
18690 -ATTATTACTTATT
1 CTTTATTA-TTATT
18703 TGTTTATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.21
19 20 0.71
20 2 0.07
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (20 bp):
CTTTATTATTATTGATTATT
Done.