Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2398
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: 33670
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:2198 original size:13 final size:13
Alignment explanation
Indices: 2176--2217 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2166 GATACTATTC
2176 ACAATGTATCGAT
1 ACAATGTATCGAT
*
2189 ACACTGTATCGAT
1 ACAATGTATCGAT
*
2202 ACAATGTATAGAT
1 ACAATGTATCGAT
2215 ACA
1 ACA
2218 TGAACAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:2568 original size:13 final size:13
Alignment explanation
Indices: 2550--2574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2540 CATAAAGTGT
2550 TGTATCGATACAA
1 TGTATCGATACAA
2563 TGTATCGATACA
1 TGTATCGATACA
2575 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2590 original size:32 final size:33
Alignment explanation
Indices: 2530--2595 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2520 TTCAACGATT
2530 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
2563 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2595 T
1 T
2596 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2654 original size:13 final size:13
Alignment explanation
Indices: 2636--2660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2626 ATTGCTCAAA
2636 TGTATCGATACAT
1 TGTATCGATACAT
2649 TGTATCGATACA
1 TGTATCGATACA
2661 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2714 original size:52 final size:52
Alignment explanation
Indices: 2669--2797 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
2659 CACTGATCTT
*
2669 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2721 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2773 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2798 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:8492 original size:13 final size:13
Alignment explanation
Indices: 8474--8499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8464 CAATTTTTGG
8474 TGTATCGATACAT
1 TGTATCGATACAT
8487 TGTATCGATACAT
1 TGTATCGATACAT
8500 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8511 original size:32 final size:33
Alignment explanation
Indices: 8454--8517 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
8444 TACAAGCCAA
** *
8454 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCCATACAT
8487 TGTATCGATAC-ATACTTGGTGTATCCATACA
1 TGTATCGATACAATACTTGGTGTATCCATACA
8518 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCCATACAT
Found at i:11062 original size:13 final size:13
Alignment explanation
Indices: 11044--11082 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
11034 ATAATCACCC
11044 TGTATCGATACAA
1 TGTATCGATACAA
11057 TGTATCGATACAA
1 TGTATCGATACAA
11070 TGTATCGATACAA
1 TGTATCGATACAA
11083 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14546 original size:19 final size:18
Alignment explanation
Indices: 14511--14548 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
14501 CTTTTAACTA
14511 ATAAAAAATAAAATTTTT
1 ATAAAAAATAAAATTTTT
*
14529 ATAATAAAAT-TAATTTTT
1 ATAA-AAAATAAAATTTTT
14547 AT
1 AT
14549 TAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAAAATAAAATTTTT
Found at i:14572 original size:20 final size:19
Alignment explanation
Indices: 14517--14574 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
14507 ACTAATAAAA
* *
14517 AATAAAATTTTTATAATAA
1 AATATAATTTTTATAATAT
14536 AAT-TAATTTTTATTAATAT
1 AATATAATTTTTA-TAATAT
*
14555 AATATAATTATTACTAATAT
1 AATATAATTTTTA-TAATAT
14575 TAAAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.24
19 11 0.33
20 14 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATAATTTTTATAATAT
Found at i:16158 original size:165 final size:164
Alignment explanation
Indices: 15878--16310 Score: 408
Period size: 165 Copynumber: 2.6 Consensus size: 164
15868 TTTTCCTGAG
* * * * *
15878 TTTATAAATT-TTAAAATTCATCAGAGATTATTATTTAACTCATAATAAATCAGTTTTAAAAAAT
1 TTTA-AAATTATTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAA-
* ** * * * * *
15942 TTCTTTTA-TTAAATTAATTTTC-TTTTCTTCTTAAAATTTTCCTTGTTTTCGAAATAT-GAGAT
64 TTCATTTATTTTCATTATTTTTCATTTT-TTCTTGAAA-TTTCATTATTTTCGAAAAATCGAG-T
* ** * *
16004 TTTCTATTCTATAATTATTTTTGGAGGGATTTTTCTTAA
126 TTTCTATTCCATAAAGATTTTTGCAGGGATTTTTCTCAA
** * * *
16043 TTTTTAATTATTAGAATTAATTAAATATTATTATTTAATTCATATTAAATCAATTTTAAAAAATT
1 TTTAAAATTATTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAATT
*
16108 CATTCATTTTCATTCATTTTTCATTTTTTCCTTGAAATTT-ATTATTTTCGAAAAATCGAGTTTT
66 CATTTATTTTCATT-ATTTTTCATTTTTT-CTTGAAATTTCATTATTTTCGAAAAATCGAGTTTT
* * *
16172 CTATTCCATAAAGGTTTTTGCAGGGGTTTTTCTCAG
129 CTATTCCATAAAGATTTTTGCAGGGATTTTTCTCAA
* * * * * * * **
16208 TTTAAAATTTTTAAAATTCATCAAATGTAATCATTTGATTCATATTAAATCAGTTTTGAAATTTT
1 TTTAAAATTATTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAATT
* *
16273 CATTTATTTTCATGAGTTTTTAATTTTTTTCTTGAAAT
66 CATTTATTTTCATTA-TTTTTCA-TTTTTTCTTGAAAT
16311 GCCCCTCTTT
Statistics
Matches: 216, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
164 11 0.05
165 175 0.81
166 20 0.09
167 10 0.05
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.51
Consensus pattern (164 bp):
TTTAAAATTATTAAAATTAATCAAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAATT
CATTTATTTTCATTATTTTTCATTTTTTCTTGAAATTTCATTATTTTCGAAAAATCGAGTTTTCT
ATTCCATAAAGATTTTTGCAGGGATTTTTCTCAA
Found at i:16965 original size:9 final size:9
Alignment explanation
Indices: 16949--17000 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
16939 TTGGCAAGTG
16949 AGAAAGAAAA
1 AGAAA-AAAA
*
16959 A-AAAGAAA
1 AGAAAAAAA
*
16967 GGAAAAAAA
1 AGAAAAAAA
16976 AGAAAAAAGA
1 AGAAAAAA-A
16986 GAGAAAAAAA
1 -AGAAAAAAA
16996 AGAAA
1 AGAAA
17001 TATCATGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 3 0.09
9 21 0.60
10 3 0.09
11 8 0.23
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:16967 original size:13 final size:14
Alignment explanation
Indices: 16949--16980 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
16939 TTGGCAAGTG
16949 AGAAA-GAAAAAAA
1 AGAAAGGAAAAAAA
16962 AGAAAGGAAAAAAA
1 AGAAAGGAAAAAAA
16976 AGAAA
1 AGAAA
16981 AAAGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAGGAAAAAAA
Found at i:16991 original size:20 final size:21
Alignment explanation
Indices: 16957--17000 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
16947 TGAGAAAGAA
16957 AAAAAAGAAAGGAAAAAAAAG
1 AAAAAAGAAAGGAAAAAAAAG
*
16978 AAAAAAGAGA-GAAAAAAAAG
1 AAAAAAGAAAGGAAAAAAAAG
16998 AAA
1 AAA
17001 TATCATGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAGGAAAAAAAAG
Found at i:17828 original size:17 final size:17
Alignment explanation
Indices: 17806--17842 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17796 AAACTTTTAA
17806 AAAATAAAA-AATAAAAT
1 AAAATAAAATAAT-AAAT
17823 AAAATAAAATAATAAAT
1 AAAATAAAATAATAAAT
17840 AAA
1 AAA
17843 TATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAATAAAT
Found at i:18044 original size:142 final size:143
Alignment explanation
Indices: 17856--18114 Score: 321
Period size: 142 Copynumber: 1.8 Consensus size: 143
17846 TATTTTATTC
* * * * *
17856 AATAAAAATTATCACCTCAATTTTTTTAAATTTTTAATATTTCTATGGGTATCCGT-GGGCGTAT
1 AATAAAAATTATCACCTCAATTTTTTCAAATTTCTAATATTCCTATGAGTATCCATAGGG-GTAT
* * * *
17920 GAG-AATTTTTAAAA-ATTTTTGTATCTTTTCGATTCTCTATTAAGGTATGAAATGAATTTTTTT
65 -AGCAATCTTCAAAACA-TTTTGTATCTTTTCGATTCTCCATTAAGGTACGAAATGAATTTTTTT
17983 AAAAAATTAAAAATTA
128 AAAAAATTAAAAATTA
* * * * *
17999 AATAAAAATTATTATCTTAA-TTTTTCAAGATTTCT-ATATTCCTATGATTTTCCATAGGGGTAT
1 AATAAAAATTATCACCTCAATTTTTTCAA-ATTTCTAATATTCCTATGAGTATCCATAGGGGTAT
18062 AGCAATCTTCAAAACATTTTGTATCTTTTCGATTCTCCATTAAGGTACGAAAT
65 AGCAATCTTCAAAACATTTTGTATCTTTTCGATTCTCCATTAAGGTACGAAAT
18115 AAGATTTTCT
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
141 2 0.02
142 70 0.71
143 26 0.27
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (143 bp):
AATAAAAATTATCACCTCAATTTTTTCAAATTTCTAATATTCCTATGAGTATCCATAGGGGTATA
GCAATCTTCAAAACATTTTGTATCTTTTCGATTCTCCATTAAGGTACGAAATGAATTTTTTTAAA
AAATTAAAAATTA
Found at i:18961 original size:13 final size:13
Alignment explanation
Indices: 18943--18968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18933 GATAAAGTGT
18943 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
18956 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
18969 AAAAAATTTA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:19003 original size:21 final size:21
Alignment explanation
Indices: 18979--19035 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
18969 AAAAAATTTA
18979 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
19000 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
19021 AATGTATCGATACAT
1 AATGTATCGATACAT
19036 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:19115 original size:19 final size:19
Alignment explanation
Indices: 19091--19158 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
19081 AATTCAACAA
19091 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
19110 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
19125 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
19142 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
19159 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:19130 original size:13 final size:13
Alignment explanation
Indices: 19112--19136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19102 ACATAAGTTT
19112 TGTATCGATACAA
1 TGTATCGATACAA
19125 TGTATCGATACA
1 TGTATCGATACA
19137 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:19134 original size:32 final size:32
Alignment explanation
Indices: 19093--19155 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
19083 TTCAACAATT
*
19093 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
19125 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
19156 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:19216 original size:13 final size:13
Alignment explanation
Indices: 19198--19223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19188 CATTTTTCTG
19198 TGTATCGATACAT
1 TGTATCGATACAT
19211 TGTATCGATACAT
1 TGTATCGATACAT
19224 GGATCTTTGT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19220 original size:33 final size:33
Alignment explanation
Indices: 19178--19244 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
19168 GCCAAGGAAA
***
19178 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
19211 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
19244 T
1 T
19245 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:21800 original size:51 final size:51
Alignment explanation
Indices: 21738--21908 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
21728 TTATTTCTGA
* * *
21738 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
21789 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
21842 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
21894 GAGGATACTCCAACC
1 GGGGATACTCCAACC
21909 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:21927 original size:28 final size:28
Alignment explanation
Indices: 21891--21972 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
21881 ATTTTTCACA
*
21891 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
21919 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
21947 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
21973 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Done.