Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1360
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: 64588
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5456 original size:34 final size:34
Alignment explanation
Indices: 5417--5485 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5407 ATGGCCTTTC
5417 ACTTTTTTTGTTAATTAAGTTAATTAATTTAATT
1 ACTTTTTTTGTTAATTAAGTTAATTAATTTAATT
5451 ACTTTTTTTGTTAATTAAGTTAATTAATTTAATT
1 ACTTTTTTTGTTAATTAAGTTAATTAATTTAATT
5485 A
1 A
5486 ATCTCATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (34 bp):
ACTTTTTTTGTTAATTAAGTTAATTAATTTAATT
Found at i:5487 original size:9 final size:9
Alignment explanation
Indices: 5427--5487 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
5417 ACTTTTTTTG
*
5427 TTAATTAAG
1 TTAATTAAT
5436 TTAATTAAT
1 TTAATTAAT
*
5445 TTAATTACT
1 TTAATTAAT
*
5454 TT--TT-TT
1 TTAATTAAT
*
5460 GTTAATTAAG
1 -TTAATTAAT
5470 TTAATTAAT
1 TTAATTAAT
5479 TTAATTAAT
1 TTAATTAAT
5488 CTCATGTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 1 0.02
7 4 0.10
9 37 0.88
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (9 bp):
TTAATTAAT
Found at i:11824 original size:43 final size:44
Alignment explanation
Indices: 11776--11868 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
11766 AGGAATGTTC
*
11776 AATAATGAAGGAG-TTAGAAATTTTAGATTCTATGGAATGGGAA
1 AATAATGAAGGAGAATAGAAATTTTAGATTCTATGGAATGGGAA
*** *
11819 AATAATTTTGTAGAATAGAAATTTTAGATTCTATGGAATGGGAA
1 AATAATGAAGGAGAATAGAAATTTTAGATTCTATGGAATGGGAA
11863 AATAAT
1 AATAAT
11869 TTTTTAGAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 9 0.20
44 35 0.80
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (44 bp):
AATAATGAAGGAGAATAGAAATTTTAGATTCTATGGAATGGGAA
Found at i:11834 original size:21 final size:21
Alignment explanation
Indices: 11810--11878 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
11800 AGATTCTATG
*
11810 GAATGGGAAAATAATTTTGTA
1 GAATGGGAAAATAATTTTATA
* * * *
11831 GAAT-AGAAATTTTAGATTCTATG
1 GAATGGGAAA--ATA-ATTTTATA
*
11854 GAATGGGAAAATAATTTTTTA
1 GAATGGGAAAATAATTTTATA
11875 GAAT
1 GAAT
11879 ACCAATTAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
20 4 0.12
21 13 0.38
22 4 0.12
23 9 0.26
24 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.20, T:0.36
Consensus pattern (21 bp):
GAATGGGAAAATAATTTTATA
Found at i:11839 original size:44 final size:44
Alignment explanation
Indices: 11790--11879 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
11780 ATGAAGGAGT
11790 TAGAAATTTTAGATTCTATGGAATGGGAAAATAATTTTGTAGAA
1 TAGAAATTTTAGATTCTATGGAATGGGAAAATAATTTTGTAGAA
*
11834 TAGAAATTTTAGATTCTATGGAATGGGAAAATAATTTTTTAGAA
1 TAGAAATTTTAGATTCTATGGAATGGGAAAATAATTTTGTAGAA
11878 TA
1 TA
11880 CCAATTAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (44 bp):
TAGAAATTTTAGATTCTATGGAATGGGAAAATAATTTTGTAGAA
Found at i:20885 original size:15 final size:15
Alignment explanation
Indices: 20848--20889 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
20838 TTATGATATG
20848 GTATCTTGGATTTCT
1 GTATCTTGGATTTCT
*
20863 GTACCTTGGATATT-T
1 GTATCTTGGAT-TTCT
*
20878 TTATCTTGGATT
1 GTATCTTGGATT
20890 CCTCTGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 20 0.87
16 2 0.09
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (15 bp):
GTATCTTGGATTTCT
Found at i:30271 original size:39 final size:39
Alignment explanation
Indices: 30215--30304 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
30205 GACTTTAGGC
* *
30215 CCGGATAT-ATTCCAGCACGTAGCCTGCAGACCTCAAGT
1 CCGGATATGTTTCTAGCACGTAGCCTGCAGACCTCAAGT
* *
30253 CTGGATATGTTTCTAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATGTTTCTAGCACGTAGCCTGCAGACCTCAAGT
30292 CCGGATATGTTTC
1 CCGGATATGTTTC
30305 CAAATATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 7 0.15
39 39 0.85
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (39 bp):
CCGGATATGTTTCTAGCACGTAGCCTGCAGACCTCAAGT
Found at i:30978 original size:21 final size:21
Alignment explanation
Indices: 30952--30991 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
30942 TGCATATTCT
30952 AATTTCATAAACTAATTTACG
1 AATTTCATAAACTAATTTACG
30973 AATTTCATAAACTAATTTA
1 AATTTCATAAACTAATTTA
30992 GCAAATCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (21 bp):
AATTTCATAAACTAATTTACG
Found at i:32818 original size:5 final size:5
Alignment explanation
Indices: 32808--32832 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
32798 GATGTTTTAG
32808 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
32833 GTGCAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:36695 original size:40 final size:40
Alignment explanation
Indices: 36644--36833 Score: 278
Period size: 40 Copynumber: 4.8 Consensus size: 40
36634 GGATATAGCT
* *
36644 ACTCGCTCAAATGCCTTCGAGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
** *
36684 GTTCGTACAAATGCCTTCGGGACTTAGCCC-G-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
36723 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
36763 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
36803 ACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCG
36834 TTATCATCCG
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
39 36 0.26
40 100 0.72
41 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:36773 original size:79 final size:79
Alignment explanation
Indices: 36632--36833 Score: 284
Period size: 79 Copynumber: 2.5 Consensus size: 79
36622 TGGGATTTAA
* * ** *
36632 CCGGATATAGCTACTCGCTCAAATGCCTTCGAGACTTAGCCCGGATATAGTAGTTCGTACAAATG
1 CCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
36697 CCTTCGGGACTTAGC
65 CCTTCGGGACTTAGC
36712 CC-GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAAT
1 CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAAT
36775 GCCTTCGGGACTTAGC
64 GCCTTCGGGACTTAGC
*
36791 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCG
36834 TTATCATCCG
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
78 2 0.02
79 71 0.64
80 38 0.34
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
CTTCGGGACTTAGC
Found at i:44696 original size:40 final size:40
Alignment explanation
Indices: 44634--44848 Score: 269
Period size: 40 Copynumber: 5.4 Consensus size: 40
44624 AAACCAAGTA
* * *
44634 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
** *
44673 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
44713 CCTTCGGGACTTACCCCGGATATAGTGACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
44753 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
44793 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
44832 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
44849 CGTTATCATC
Statistics
Matches: 155, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 50 0.32
40 105 0.68
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:50207 original size:7 final size:7
Alignment explanation
Indices: 50191--50219 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
50181 TTCCTAGAGC
50191 AAAAAA-
1 AAAAAAG
50197 AAAAAAG
1 AAAAAAG
50204 AAAAAAG
1 AAAAAAG
50211 AAAAAAG
1 AAAAAAG
50218 AA
1 AA
50220 TAGATATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:54457 original size:104 final size:105
Alignment explanation
Indices: 54277--54544 Score: 443
Period size: 104 Copynumber: 2.6 Consensus size: 105
54267 TAACCGTTAT
* **
54277 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
54342 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
54381 TGGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGG
54445 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
54486 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
54545 TTATATACAA
Statistics
Matches: 154, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
103 1 0.01
104 81 0.53
105 70 0.45
106 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:54905 original size:29 final size:29
Alignment explanation
Indices: 54872--54935 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
54862 TAATCCACCA
54872 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
54901 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
54931 CCCAA
1 CCCAA
54936 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:54909 original size:30 final size:30
Alignment explanation
Indices: 54879--54935 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54869 CCACCCAACT
54879 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
54908 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
54936 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:57943 original size:39 final size:40
Alignment explanation
Indices: 57843--58066 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
57833 TTGAATGATG
*
57843 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
57882 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
57923 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
57962 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
58001 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
58040 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
58067 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
39 74 0.46
40 74 0.46
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:58018 original size:79 final size:81
Alignment explanation
Indices: 57843--58066 Score: 273
Period size: 79 Copynumber: 2.8 Consensus size: 81
57833 TTGAATGATG
* * *
57843 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
57906 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
*
57923 TTCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
57984 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * * *
58001 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
58065 TG
66 TG
58067 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
78 36 0.29
79 53 0.42
80 36 0.29
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:58088 original size:79 final size:79
Alignment explanation
Indices: 57843--58099 Score: 208
Period size: 79 Copynumber: 3.3 Consensus size: 79
57833 TTGAATGATG
* * * *
57843 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
57905 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* * *
57923 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
57987 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
58001 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
58064 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
58081 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
58100 TACGTGATTT
Statistics
Matches: 151, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
77 1 0.01
78 36 0.24
79 66 0.44
80 47 0.31
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Done.