Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold836
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: 30672
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:13556 original size:13 final size:13
Alignment explanation
Indices: 13538--13569 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13528 CTTTCGTACC
13538 AAAAAAACAAACA
1 AAAAAAACAAACA
*
13551 AAAAAAATAAACA
1 AAAAAAACAAACA
13564 AAAAAA
1 AAAAAA
13570 GAGGTCCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAACA
Found at i:14447 original size:26 final size:27
Alignment explanation
Indices: 14409--14459 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
14399 CAGAAAAGTC
*
14409 TGAATAGCCTACAA-CCCTAGTGGAGT
1 TGAATAGCCTACAATCCCTAATGGAGT
**
14435 TGAATAGTTTACAATCCCTAATGGA
1 TGAATAGCCTACAATCCCTAATGGA
14460 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (27 bp):
TGAATAGCCTACAATCCCTAATGGAGT
Found at i:15183 original size:179 final size:178
Alignment explanation
Indices: 14862--15361 Score: 594
Period size: 179 Copynumber: 2.8 Consensus size: 178
14852 TTTCAAAGCT
* * * * * * *
14862 CACAAGTCAGTGGCATCCTTCTCAAAGCCAACAAGTCAAT-AGCATCTTTTCAAAGCCCACAAGT
1 CACAAATCAATGGCA-CCTTTTCAAAGCCCACAAGTCAATGA-CACCCTTTCAAAGCCTACAAGT
* * * * *
14926 CAATGGCAT--CCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTTTAAAGCCCACAAGTCAGTGG
64 TAGTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCCTACAAGTCAGTGG
***
14989 TAACTCTTTTCAAAGTCCACACAAGTTGGTGGCAACTCTATTCAAAGCCCA
128 TAACTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
* *
15040 CACAAATCAATGGTACCTTTTCAAAGCCCACAAGTTAATGACACCCTTTCAAAGCCTACAAGTTA
1 CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCTACAAGTTA
15105 GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCGTTTTCAAAGCCTACAAGTCAGTGGTA
66 GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACC-TTTTCAAAGCCTACAAGTCAGTGGTA
* * *
15170 ACTCTTATCAAAGTCCACACAAGTCAATGGCAACTGTGTTCAAAGCCCA
130 ACTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
* * * * * ** *
15219 CATAAATCGATGGCACCCTTCCAAAGCCCACAAGTCAGTGGTACCCTCTCAAAG-CTCACAAGTT
1 CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCT-ACAAGTT
* * * ** * *
15283 AGCGACACACCCTTTCAAAGCCCACAAGTCGGTGGCACCCTTTCAAAGCCTACACAAGTCGGTGG
65 AGTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCT--ACAAGTCAGTGG
15348 TAACTCTTTTCAAA
128 TAACTCTTTTCAAA
15362 TCACCACTTT
Statistics
Matches: 277, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
177 47 0.17
178 28 0.10
179 178 0.64
180 24 0.09
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (178 bp):
CACAAATCAATGGCACCTTTTCAAAGCCCACAAGTCAATGACACCCTTTCAAAGCCTACAAGTTA
GTGGCATACCCTTTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCTACAAGTCAGTGGTAA
CTCTTTTCAAAGTCCACACAAGTCAATGGCAACTCTATTCAAAGCCCA
Found at i:15212 original size:149 final size:144
Alignment explanation
Indices: 14851--15342 Score: 519
Period size: 149 Copynumber: 3.3 Consensus size: 144
14841 AATACTACCT
* * * * *
14851 TTTTCAAAGCTCACAAGTCAGTGGCATC-CTTCTCAAAGCCA-ACAAGTCAATAGCATCTTTTCA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCCACACAAGTCAATGGCAACTTTTCA
* *
14914 AAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTTTAAAGCCCAC
66 AAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCC-TTTCAAAGCCCAC
* * *
14979 AAGTCAGTGGTAACTC
130 AAGTTAGTGG-CACAC
** * * *
14995 TTTTCAAAGTCCACACAAGTTGGTGGCAACTC-TATTCAAAGCCCACACAAATCAATGGTACCTT
1 TTTTCAAAG-CC-CACAAGTCAGTGGCAACTCTTA-TCAAAG-CCACACAAGTCAATGGCAACTT
* * *
15059 TTCAAAGCCCACAAGTTAATGACACCCTTTCAAAGCCTACAAGTTAGTGGCATACCCTTTCAAAG
62 TTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGG--TACCCTTTCAAAG
15124 CCCACAAGTTAGTGGCAC-C
125 CCCACAAGTTAGTGGCACAC
* *
15143 GTTTTCAAAGCCTACAAGTCAGTGGTAACTCTTATCAAAGTCCACACAAGTCAATGGCAACTGTG
1 -TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAG-CCACACAAGTCAATGGCAACT-T-
* * * * *
15208 TTCAAAGCCCACATAAATCGATGGCACCCTTCCAAAGCCCACAAGTCAGTGGTACCCTCTCAAAG
62 TTCAAAGCCCAC--AAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAG
* * *
15273 CTCACAAGTTAGCGACACACC
125 CCCACAAGTTAGTGGCACA-C
* * *
15294 CTTTCAAAGCCCACAAGTCGGTGGC-ACCCTT-TCAAAGCCTACACAAGTC
1 TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCC-ACACAAGTC
15343 GGTGGTAACT
Statistics
Matches: 291, Mismatches: 40, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
144 9 0.03
145 1 0.00
146 15 0.05
147 48 0.16
148 24 0.08
149 115 0.40
150 42 0.14
151 37 0.13
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (144 bp):
TTTTCAAAGCCCACAAGTCAGTGGCAACTCTTATCAAAGCCACACAAGTCAATGGCAACTTTTCA
AAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTTAGTGGTACCCTTTCAAAGCCCACA
AGTTAGTGGCACAC
Found at i:15339 original size:30 final size:28
Alignment explanation
Indices: 14852--15347 Score: 355
Period size: 28 Copynumber: 16.8 Consensus size: 28
14842 ATACTACCTT
* *
14852 TTTCAAAGCTCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
14880 TTCTCAAAGCCAACAAGTCAATAGCATCT
1 TT-TCAAAGCCCACAAGTCAGTGGCACCC
* *
14909 TTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
14937 TTTCAAAGCCCACAAGTTAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
14965 TTTTTAAAGCCCACAAGTCAGTGGTAACTCT
1 -TTTCAAAGCCCACAAGTCAGTGG-CAC-CC
** *
14996 TTTCAAAGTCCACACAAGTTGGTGGCAACTC
1 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC
* * * *
15027 TATTCAAAGCCCACACAAATCAATGGTACCT
1 T-TTCAAAG-CC-CACAAGTCAGTGGCACCC
* * *
15058 TTTCAAAGCCCACAAGTTAATGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
15086 TTTCAAAGCCTACAAGTTAGTGGCATACCC
1 TTTCAAAGCCCACAAGTCAGTGGC--ACCC
* *
15116 TTTCAAAGCCCACAAGTTAGTGGCACCGT
1 TTTCAAAGCCCACAAGTCAGTGGCACC-C
* * *
15145 TTTCAAAGCCTACAAGTCAGTGGTAACTC
1 TTTCAAAGCCCACAAGTCAGTGG-CACCC
* **
15174 TTATCAAAGTCCACACAAGTCAATGGCAACTG
1 TT-TCAAAG-CC-CACAAGTCAGTGGC-ACCC
*
15206 TGTTCAAAGCCCACATAAATC-GATGGCACCC
1 T-TTCAAAGCCCAC--AAGTCAG-TGGCACCC
* *
15237 TTCCAAAGCCCACAAGTCAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
15265 TCTCAAAGCTCACAAGTTAGCGACACACCC
1 TTTCAAAGCCCACAAGTCAGTG--GCACCC
*
15295 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
15323 TTTCAAAGCCTACACAAGTCGGTGG
1 TTTCAAAGCC--CACAAGTCAGTGG
15348 TAACTCTTTT
Statistics
Matches: 374, Mismatches: 69, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
28 129 0.34
29 70 0.19
30 99 0.26
31 14 0.04
32 61 0.16
33 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:15495 original size:49 final size:49
Alignment explanation
Indices: 15435--15560 Score: 173
Period size: 49 Copynumber: 2.6 Consensus size: 49
15425 TTAACCTAAT
*
15435 GTCGCTGGCCTTGAATTAGAACATTGGTCCACTTTTCCCT-TAGCCCAAC
1 GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATA-CCCAAC
* * * * *
15484 GTCTCTGGCCTTGAATGAGCACATTAGTCTACTTTTCCCTATACCCAAT
1 GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATACCCAAC
*
15533 GTCGCTGGCCCTGAATTAGCACATTGGT
1 GTCGCTGGCCTTGAATTAGCACATTGGT
15561 TATCTTCTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
49 64 0.97
50 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.32
Consensus pattern (49 bp):
GTCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTATACCCAAC
Found at i:16226 original size:20 final size:20
Alignment explanation
Indices: 16194--16359 Score: 127
Period size: 20 Copynumber: 7.8 Consensus size: 20
16184 TTTTACCCAG
*
16194 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
16214 ATTTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
16234 ATGTATCGATACATTATTCA
1 ATGTATCGATACATTCTTCA
16254 ATGTATCGATACATTCTGTCTTTTTACCTA
1 ATGTATCGATACA---T-TC---TT--C-A
*
16284 GATGTATCGATACATTCTACA
1 -ATGTATCGATACATTCTTCA
* * * *
16305 ATGCATCGATACATGCATAA
1 ATGTATCGATACATTCTTCA
16325 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
16345 ATGTATCGATACATT
1 ATGTATCGATACATT
16360 TTGTCTTTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 26
0.72 0.11 0.16
Matches are distributed among these distances:
19 1 0.01
20 88 0.77
21 2 0.02
22 1 0.01
23 1 0.01
24 2 0.02
27 4 0.03
28 1 0.01
29 1 0.01
30 1 0.01
31 13 0.11
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:16313 original size:51 final size:50
Alignment explanation
Indices: 16234--16397 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 50
16224 ACATGTATGA
*
16234 ATGTATCGATACATTATTCAATGTATCGATACATTCTGTCTTTTTACCTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATT-TGTCTTTTTACCTAG
* * *
16285 ATGTATCGATACATTCTACAATGCATCGATACA--TG-C-----A--TAA
1 ATGTATCGATACATTCTTCAATGTATCGATACATTTGTCTTTTTACCTAG
16325 ATGTATCGATACATTCTTCAATGTATCGATACATTTTGTCTTTTTACCTAG
1 ATGTATCGATACATTCTTCAATGTATCGATACA-TTTGTCTTTTTACCTAG
* *
16376 ATGTATCAATACATTATTCAAT
1 ATGTATCGATACATTCTTCAAT
16398 ATATGAATAC
Statistics
Matches: 93, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
40 33 0.35
42 1 0.01
43 2 0.02
44 1 0.01
47 1 0.01
48 2 0.02
49 1 0.01
51 52 0.56
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (50 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTTGTCTTTTTACCTAG
Found at i:16408 original size:91 final size:91
Alignment explanation
Indices: 16183--16409 Score: 330
Period size: 91 Copynumber: 2.5 Consensus size: 91
16173 AAAAATCACA
* * * * *
16183 TTTTTACCCAGATGTATTGATACATTCTTCAATTTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
16248 TATTCAATGTATCGATACATTCTGTC
66 TATTCAATGTATCGATACATTCTGTC
* **
16274 TTTTTACCTAGATGTATCGATACATTCTACAATGCATCGATACATGCATAAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
* *
16339 TCTTCAATGTATCGATACATTTTGTC
66 TATTCAATGTATCGATACATTCTGTC
* *
16365 TTTTTACCTAGATGTATCAATACATTATTCAATATAT-GAATACAT
1 TTTTTACCTAGATGTATCGATACATTCTTCAATATATCG-ATACAT
16410 CTAGTTAAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
90 1 0.01
91 120 0.99
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (91 bp):
TTTTTACCTAGATGTATCGATACATTCTTCAATATATCGATACATGCATAAATGTATCGATACAT
TATTCAATGTATCGATACATTCTGTC
Found at i:21154 original size:13 final size:13
Alignment explanation
Indices: 21136--21161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21126 CAATTTTTTG
21136 TGTATCGATACAT
1 TGTATCGATACAT
21149 TGTATCGATACAT
1 TGTATCGATACAT
21162 ACTTGTGTAT
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:23743 original size:13 final size:13
Alignment explanation
Indices: 23725--23749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23715 ATAATCCCCC
23725 TGTATCGATACAT
1 TGTATCGATACAT
23738 TGTATCGATACA
1 TGTATCGATACA
23750 AAGAAAAATG
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:25842 original size:15 final size:15
Alignment explanation
Indices: 25822--25852 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25812 ATTTCGTTTG
*
25822 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
25837 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
25852 G
1 G
25853 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:27914 original size:20 final size:20
Alignment explanation
Indices: 27886--27926 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27876 GTCTGAAAAA
27886 TGCTCAGAACCAA-CCCCTTT
1 TGCTCAGAA-CAATCCCCTTT
*
27906 TGCTGAGAACAATCCCCTTT
1 TGCTCAGAACAATCCCCTTT
27926 T
1 T
27927 ATAGGGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.29
Consensus pattern (20 bp):
TGCTCAGAACAATCCCCTTT
Done.