Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1252
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: 33838
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2046 original size:3 final size:3
Alignment explanation
Indices: 2038--2062 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2028 AATATTATCT
2038 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2063 CATAGTGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4048 original size:21 final size:17
Alignment explanation
Indices: 4010--4044 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4000 CTTCAAGAAA
4010 AAGTTAGTGAGACTGAC
1 AAGTTAGTGAGACTGAC
4027 AAGTTAGTGAGACTGAC
1 AAGTTAGTGAGACTGAC
4044 A
1 A
4045 GACATGACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (17 bp):
AAGTTAGTGAGACTGAC
Found at i:13942 original size:69 final size:69
Alignment explanation
Indices: 13822--13995 Score: 183
Period size: 69 Copynumber: 2.5 Consensus size: 69
13812 CTTTCCAAGG
* * **
13822 AAAATCAACTCATATTGTGAG-AGATGAATTGAGCCTCAAGACACGTTGAGGTATTTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
13885 T-TTT
65 TGTTT
** * *
13889 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTT
1 --AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTT
13954 ATGTTT
64 ATGTTT
* ** * *
13960 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
13996 TTTAATTTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 83 0.93
70 3 0.03
71 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTT
Found at i:14136 original size:75 final size:74
Alignment explanation
Indices: 14013--14258 Score: 343
Period size: 72 Copynumber: 3.3 Consensus size: 74
14003 TTTGTTTTTC
* **
14013 AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
14078 TTGTTAAAAA
66 TT-TTAAAAA
*
14088 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTA
1 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
*
14153 TTTT--CAA
66 TTTTAAAAA
* * * * *
14160 AATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTG
1 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
14225 TTTTCAAAAAAAA
66 TTTT----AAAAA
14238 AAATCAACTCATATTGCGAGA
1 AAATCAACTCATATTGCGAGA
14259 GGTGGGTTGA
Statistics
Matches: 151, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
72 65 0.43
74 2 0.01
75 63 0.42
78 21 0.14
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (74 bp):
AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG
TTTTAAAAA
Found at i:14571 original size:88 final size:87
Alignment explanation
Indices: 14367--14613 Score: 282
Period size: 88 Copynumber: 2.8 Consensus size: 87
14357 TGTTTTAATT
* *
14367 TCAACTCATATTGCGAGAGGTGAATTGAGCCTCAGGACACACGCCGAGGTATTTTCAATTAAGC-
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCAATT--TCT
* * *
14431 CTTTTGATTTCTGTTTTTCAAAAAAAA
62 GTTTTCATTTATGTTTTT-AAAAAAAA
* *
14458 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
* *
14523 TCATTATTATGTTTTT-GAAAGAA
66 TCA-T-TTATGTTTTTAAAAAAAA
** * ** *
14546 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
14611 TCA
66 TCA
14614 AAATTCAACT
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
87 1 0.01
88 70 0.51
89 17 0.12
90 9 0.07
91 39 0.29
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (87 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCAATTTCTGTTT
TCATTTATGTTTTTAAAAAAAA
Found at i:14730 original size:73 final size:72
Alignment explanation
Indices: 14546--14798 Score: 409
Period size: 73 Copynumber: 3.5 Consensus size: 72
14536 TTTGAAAGAA
*
14546 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
14611 TCAAAAT
66 TCAAAAT
*
14618 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTG-TT
14683 TTCAAAAT
65 TTCAAAAT
* * *
14691 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
*
14756 TCAAAAAA
66 TC-AAAAT
*
14764 TCAACTCATATTGC-AAAAAGTGAGTTGAGCCTCAA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAA
14799 TTCACATGTT
Statistics
Matches: 169, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
72 68 0.40
73 101 0.60
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:19969 original size:12 final size:12
Alignment explanation
Indices: 19952--19982 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
19942 ATTCCAGCAA
19952 TTATGAATTTAT
1 TTATGAATTTAT
19964 TTATGAATTTAT
1 TTATGAATTTAT
19976 TTGATGA
1 TT-ATGA
19983 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (12 bp):
TTATGAATTTAT
Found at i:20190 original size:50 final size:50
Alignment explanation
Indices: 20077--20317 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
20067 ATTTGGGTAA
* * *
20077 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
20133 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
20183 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
20233 AGAGGTCCC-TATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
20282 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
20318 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.21
50 61 0.37
51 24 0.14
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:20283 original size:99 final size:103
Alignment explanation
Indices: 20077--20325 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
20067 ATTTGGGTAA
20077 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
20142 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
* * *
20183 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGT-CCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
20244 TAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGA-CACG
* *
20282 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
20326 GTTATTATCA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
98 1 0.01
99 41 0.31
100 46 0.35
101 2 0.02
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCGACACG
Found at i:22980 original size:17 final size:17
Alignment explanation
Indices: 22960--22995 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
22950 ATTTTTAAAA
22960 TAATATTA-ATATTATAT
1 TAATATTATATATT-TAT
22977 TAATATTATATATTTAT
1 TAATATTATATATTTAT
22994 TA
1 TA
22996 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATTATATATTTAT
Found at i:22990 original size:13 final size:11
Alignment explanation
Indices: 22962--22987 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22952 TTTTAAAATA
22962 ATATTAATATT
1 ATATTAATATT
22973 ATATTAATATT
1 ATATTAATATT
22984 ATAT
1 ATAT
22988 ATTTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATTAATATT
Found at i:24618 original size:17 final size:18
Alignment explanation
Indices: 24587--24626 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
24577 AATTATATAC
24587 ATAAAAAATAAATAATTG
1 ATAAAAAATAAATAATTG
*
24605 ATAAAAAA-AGATAATTG
1 ATAAAAAATAAATAATTG
24622 -TAAAA
1 ATAAAA
24627 TTTATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
ATAAAAAATAAATAATTG
Found at i:29237 original size:16 final size:15
Alignment explanation
Indices: 29189--29239 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
29179 AAAAAATAAA
*
29189 AAAATATTAATAATAG
1 AAAATATTAA-AATAT
*
29205 AAAA-ATTAAATTAT
1 AAAATATTAAAATAT
29219 AAAATATTAAAAGTAT
1 AAAATATTAAAA-TAT
29235 AAAAT
1 AAAAT
29240 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (15 bp):
AAAATATTAAAATAT
Found at i:33095 original size:19 final size:20
Alignment explanation
Indices: 33067--33104 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33057 TAGTAAGAGG
33067 ATTGTC-AAAAAAAATTCTA
1 ATTGTCAAAAAAAAATTCTA
*
33086 ATTGTTAAAAAAAAATTCT
1 ATTGTCAAAAAAAAATTCT
33105 TTAAAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTGTCAAAAAAAAATTCTA
Found at i:33692 original size:31 final size:31
Alignment explanation
Indices: 33652--33755 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 31
33642 TTAAAACAGG
*
33652 TGAGTTAATAATATTTTCATCATTATCTAAT
1 TGAGTTAATAATATTTTCATCATTATCCAAT
* ** * * *
33683 TAAGTTAAT-ATCCGTTTAACTCATGA-CACAAG
1 TGAGTTAATAAT-ATTTTCA-TCATTATC-CAAT
33715 TGAGTTAATAATATTTTCATCATTATCCAAT
1 TGAGTTAATAATATTTTCATCATTATCCAAT
33746 TGAGTTAATA
1 TGAGTTAATA
33756 TCCGTTTAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
30 2 0.04
31 31 0.56
32 20 0.36
33 2 0.04
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (31 bp):
TGAGTTAATAATATTTTCATCATTATCCAAT
Found at i:33723 original size:32 final size:32
Alignment explanation
Indices: 33685--33780 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
33675 TATCTAATTA
*
33685 AGTTAATATCCGTTTAACTCATGACACAAGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
** * * *
33717 AGTTAATAAT-ATTTTCA-TCATTATC-CAATTG
1 AGTTAAT-ATCCGTTTAACTCATCA-CACAAGTG
*
33748 AGTTAATATCCGTTTAACTCATCACACAGGTG
1 AGTTAATATCCGTTTAACTCATCACACAAGTG
33780 A
1 A
33781 TTATCTCCCA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
30 2 0.04
31 22 0.46
32 22 0.46
33 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
AGTTAATATCCGTTTAACTCATCACACAAGTG
Found at i:33724 original size:63 final size:63
Alignment explanation
Indices: 33651--33780 Score: 224
Period size: 63 Copynumber: 2.1 Consensus size: 63
33641 CTTAAAACAG
* *
33651 GTGAGTTAATAATATTTTCATCATTATCTAATTAAGTTAATATCCGTTTAACTCATGACACAA
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
* *
33714 GTGAGTTAATAATATTTTCATCATTATCCAATTGAGTTAATATCCGTTTAACTCATCACACAG
1 GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
33777 GTGA
1 GTGA
33781 TTATCTCCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (63 bp):
GTGAGTTAATAATATTTTCATCATTATCCAATTAAGTTAATATCCGTTTAACTCATCACACAA
Done.