Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2933
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: 21011
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:5251 original size:22 final size:20
Alignment explanation
Indices: 5219--5259 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
5209 TTTAATATGT
5219 TTATATGATATGATGCTTTA
1 TTATATGATATGATGCTTTA
*
5239 TTATCATGAATATTATGCTTT
1 TTAT-ATG-ATATGATGCTTT
5260 GTGGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.51
Consensus pattern (20 bp):
TTATATGATATGATGCTTTA
Found at i:5581 original size:45 final size:44
Alignment explanation
Indices: 5437--5600 Score: 140
Period size: 46 Copynumber: 3.6 Consensus size: 44
5427 TGAGCATCGA
* * *
5437 ACTCGTTGAGTTGAGTCCAGTTCACTTATGGATGCGAATGTCCG
1 ACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCG
* * * * *
5481 AATCGTTGA-TTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCCG
1 ACTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGAAC---GC--CCG
5526 AACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCG
1 -ACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCG
5571 AGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 A-CTCGTTGAGTTGAGTC-GAGTTCACTTA
5601 GGGCGGGTAC
Statistics
Matches: 93, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
40 2 0.02
41 3 0.03
43 9 0.10
44 15 0.16
45 22 0.24
46 26 0.28
47 10 0.11
49 3 0.03
50 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (44 bp):
ACTCGTTGAGTTGAGTCGAGTTCACTTATGGATGCGAACGCCCG
Found at i:10919 original size:55 final size:57
Alignment explanation
Indices: 10859--10964 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 57
10849 AAATTCACAT
* *
10859 ACCTGTATCTGGCCCATTAAGCCC-AATCATATTCATAT-GCCCTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTAGGCCCAAATC
* * *
10914 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCGTTAGGCC
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTAGGCC
10965 AGCCACATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 22 0.50
56 12 0.27
57 10 0.23
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (57 bp):
ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTAGGCCCAAATC
Found at i:10939 original size:29 final size:29
Alignment explanation
Indices: 10862--10964 Score: 108
Period size: 29 Copynumber: 3.7 Consensus size: 29
10852 TTCACATACC
* * *
10862 TGTATCTGGCCCATTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
10890 T-TCATAT-GCCC-TTAGGCCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
10917 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
10946 TTTATATGG-CCGTTAGGCC
1 TGTATATGGCCCATTAGGCC
10965 AGCCACATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.11
27 15 0.24
28 18 0.29
29 23 0.37
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:12739 original size:40 final size:40
Alignment explanation
Indices: 12684--12858 Score: 305
Period size: 40 Copynumber: 4.4 Consensus size: 40
12674 TATGTGCATA
*
12684 GCATTCGTGCGGGTTATTACAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
12724 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
12764 GCATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
12804 GCATTCGTGTGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
12844 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
12859 GTTACATCCG
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 127 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:13448 original size:50 final size:50
Alignment explanation
Indices: 13394--13617 Score: 172
Period size: 50 Copynumber: 4.5 Consensus size: 50
13384 TTAGGCCAAG
*
13394 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTAATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTAATAGGTCACA
* * ** * * *
13444 TGTGTAGTACTAAGTGTAGCCTACT--ATGCATACC-CGTTAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATG--TACCAAATTAA--TAGGTCACA
* * ** * *
13495 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATATGGATAAGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTAATAGGTCACA
* * * ** * * *
13545 TGTGTAGTATTGAGTGCAGGGTACTATGTGTACCAGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTAATAGGTCACA
13595 --TGT-GTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
13618 TGCGTACCAG
Statistics
Matches: 137, Mismatches: 30, Indels: 17
0.74 0.16 0.09
Matches are distributed among these distances:
47 17 0.12
48 6 0.04
49 4 0.03
50 74 0.54
51 32 0.23
52 2 0.01
53 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTAATAGGTCACA
Found at i:13520 original size:151 final size:151
Alignment explanation
Indices: 13284--13625 Score: 429
Period size: 151 Copynumber: 2.3 Consensus size: 151
13274 AAGATAGTTT
* * * * **
13284 TAGGTCACGTGTGTAGTACTAAGTGCAGGCAACTATGCGTACCTGATAGTTTCGATCACGTGTGT
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGT
* * * *
13349 AGTACTAAATGTAGGCTACTACGTATATCAGATGGTTAGGCCAAGTGTGTAGTACTAAGTGCAGG
66 AGTACTAAATGCAGGCTACTACGTATACCAGATGGATAAGCCAAGTGTGTAGTACTAAGTGCAGG
13414 CTACTACATGTACCAAATTAA
131 CTACTACATGTACCAAATTAA
* * * *
13435 TAGGTCGCATGTGTAGTACTAAGTGTAGCCTACTATGCATACCCGTTAACTTCGATCACGTGTGT
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGT
* * * * * * *
13500 AGTACTAAGTGCAGGCTACTACGTGTACCATATGGATAAGTCACGTGTGTAGTATTGAGTGCAGG
66 AGTACTAAATGCAGGCTACTACGTATACCAGATGGATAAGCCAAGTGTGTAGTACTAAGTGCAGG
* ** * *
13565 GTACTATGTGTACCAGATTGA
131 CTACTACATGTACCAAATTAA
13586 TAGGTCGCA--TGT-GTACTAAGTGCAGGCTACTATGCGTACC
1 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
13626 AGAGAGCTTC
Statistics
Matches: 162, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
148 25 0.15
149 3 0.02
151 134 0.83
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (151 bp):
TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGT
AGTACTAAATGCAGGCTACTACGTATACCAGATGGATAAGCCAAGTGTGTAGTACTAAGTGCAGG
CTACTACATGTACCAAATTAA
Found at i:14485 original size:180 final size:176
Alignment explanation
Indices: 14181--14539 Score: 513
Period size: 180 Copynumber: 2.0 Consensus size: 176
14171 TCTTATATCT
* *
14181 GTACCATGGGATAAATATTTTTTAGTGAAGAAAGATCGGAACTGTCGGACAGTGAAACAAGGGTA
1 GTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCGGAACTGTCGGACAGTGAAACAAGGGTA
* * *
14246 TCTTTAATGAATAAATTGTACTAATTGGCTAAACCAAAAATTTTGAAAATTTTATGGTAAGAGTA
66 ACTTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTTTGAAAATTTGATGGTAAGA--A
* * *
14311 TATGTGAGTTTAGTTTCTGGGAAAATTAATGGTTCTTAATTTGGAGTACC
129 TA--TGAGTATAGTTTCTGAGAAAATTAATGGATCTTAATTTGGAGTACC
* * * * *
14361 GTACCATGAGATAAATAATTTTTAGTGAAGAGAGGAT-GGAACTGTTGGATAGTGAAATAGGGGT
1 GTACCATGAGATAAATAATTTTTAGTGAAGA-AAGATCGGAACTGTCGGACAGTGAAACAAGGGT
* *
14425 AACTTTAATGAATAAAATGTAGTAATTGGCTGAACCAAAAATTTTGAAAATTTGATGGTAAGAAT
65 AACTTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTTTGAAAATTTGATGGTAAGAAT
* *
14490 ATGAGTATAGTTTTTGAGAAAATTAATGGATCTTAATTTGGAGTTCC
130 ATGAGTATAGTTTCTGAGAAAATTAATGGATCTTAATTTGGAGTACC
14537 GTA
1 GTA
14540 ACTCTAGCAA
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
176 44 0.27
178 3 0.02
180 110 0.68
181 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (176 bp):
GTACCATGAGATAAATAATTTTTAGTGAAGAAAGATCGGAACTGTCGGACAGTGAAACAAGGGTA
ACTTTAATGAATAAAATGTACTAATTGGCTAAACCAAAAATTTTGAAAATTTGATGGTAAGAATA
TGAGTATAGTTTCTGAGAAAATTAATGGATCTTAATTTGGAGTACC
Found at i:16901 original size:43 final size:42
Alignment explanation
Indices: 16847--17016 Score: 216
Period size: 43 Copynumber: 4.0 Consensus size: 42
16837 ATATCGTACA
* *
16847 ATGCCAATGTCCCATACATGGTCTTACATGCCATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AATCACATATCG
* * * *
16890 ATGCCACTGTCCCAGACAGGGTCTTACACGAATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAATCACATATCG
*
16931 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCCCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AATCACATATCG
** *
16974 ATGCCAAAATCCCAGACATGGTCTTACATGAGAACACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGA-ATCACATATCG
17017 GAAATCCTAT
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
41 29 0.27
42 15 0.14
43 65 0.60
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAATCACATATCG
Found at i:16988 original size:84 final size:84
Alignment explanation
Indices: 16847--17001 Score: 238
Period size: 84 Copynumber: 1.8 Consensus size: 84
16837 ATATCGTACA
* * ***
16847 ATGCCAATGTCCCATACATGGTCTTACATGCCATCACATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCGATGCCAAAATCCCAGACAGGGT
16912 CTTACACGAATCAAATACG
66 CTTACACGAATCAAATACG
* * *
16931 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCCCATATCGATGCCAAAATCCCAGACATGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCGATGCCAAAATCCCAGACAGGGT
16996 CTTACA
66 CTTACA
17002 TGAGAACACA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 63 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (84 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCGATGCCAAAATCCCAGACAGGGT
CTTACACGAATCAAATACG
Found at i:17618 original size:15 final size:15
Alignment explanation
Indices: 17595--17625 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17585 TCAAAAATTC
17595 TAATACAAAACATAT
1 TAATACAAAACATAT
*
17610 TAATCCAAAACATAT
1 TAATACAAAACATAT
17625 T
1 T
17626 TTCATAATTC
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:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATACAAAACATAT
Found at i:19395 original size:43 final size:43
Alignment explanation
Indices: 19282--19433 Score: 143
Period size: 43 Copynumber: 3.5 Consensus size: 43
19272 ACAATGCCAG
* *
19282 CATCCCAGACGTGGTCTTACATGT-AATCAAATATAGATGCC-A
1 CATCCCAGACGTGGTCTTACATGTAAATCAAGTA-AGATACCAA
* *
19324 CTATCCCAGACAG-GGTCTTACACG-AAATCAAGTACGATACCAA
1 C-ATCCCAGAC-GTGGTCTTACATGTAAATCAAGTAAGATACCAA
* **
19367 CATCCCAGACGTGGTCTTACATGTAAATCATAAGT-TGATATGAA
1 CATCCCAGACGTGGTCTTACATGTAAATC--AAGTAAGATACCAA
* *
19411 CGTCCCGGACGTGGTCTTACATG
1 CATCCCAGACGTGGTCTTACATG
19434 ATAACACATA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 25 0.27
43 34 0.37
44 28 0.30
45 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (43 bp):
CATCCCAGACGTGGTCTTACATGTAAATCAAGTAAGATACCAA
Found at i:20060 original size:20 final size:20
Alignment explanation
Indices: 20022--20060 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20012 AACTTAGTAA
20022 TCTAACACATATCTTTCATTT
1 TCTAACACATA-CTTTCATTT
20043 TCTAACATCATA-TTTCAT
1 TCTAACA-CATACTTTCAT
20061 AAAGTTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (20 bp):
TCTAACACATACTTTCATTT
Done.