Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold974
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: 53706
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5180 original size:50 final size:50
Alignment explanation
Indices: 5094--5487 Score: 348
Period size: 50 Copynumber: 7.9 Consensus size: 50
5084 ACTAAAGCTC
* *
5094 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
** * * * *
5144 TCTGATACATGTAGTAGCCTGTACTTAGTACTACACATGTGACTTAACCA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * *** *
5194 TTTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATAGAAGTTAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * * *
5246 -CGGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
** * * *
5295 TCT-AGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCA
1 TCTGA-TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-ATCAA
* * ** *
5345 TCTGATACACATAG-AGCTTACACTTAGTACTACACATGTGATCAAAGTTAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * * * * *
5396 -CAGGTACGCATAGTATCCTGCACTTAGTATTACACATGCGACCTATCAA
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* *
5445 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGAC
5488 TCACAACGAA
Statistics
Matches: 264, Mismatches: 69, Indels: 22
0.74 0.19 0.06
Matches are distributed among these distances:
49 32 0.12
50 174 0.66
51 57 0.22
52 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (50 bp):
TCTGATACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:5283 original size:101 final size:100
Alignment explanation
Indices: 5105--5487 Score: 309
Period size: 101 Copynumber: 3.8 Consensus size: 100
5095 CTGGTACGCA
* * * ** **
5105 TAGTAGCCTGCACTTAGTACTACACATGTGACCT--ATCAATCTGATACATGTAGTAGCCTGTAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCAA-CGGATACACATAGTAGCCTACAC
* * *
5168 TTAGTACTACACATGTGACTTAACCATTTAATACACG
64 TTAGTACTACACATGTGACCTAACAATCTAATACACG
** * *
5205 TAGTAGCCTGCACTTAGTACTACACACGTGA-TAGAAGTTAACGGGTACGCATAGTAGCCTACAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTA-AA-CCAACGGATACACATAGTAGCCTACAC
* * * *
5269 TTAGTACTACACATGCGACCTATCAATCTAGTACATG
64 TTAGTACTACACATGTGACCTAACAATCTAATACACG
* * *
5306 TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCATCTGATACACATAG-AGCTTACACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCAACGGATACACATAGTAGCCTACACTT
* * * *
5370 AGTACTACACATGTGATC-AA-AGT-TAACAGGTACGCA
66 AGTACTACACATGTGACCTAACAATCT-A-A--TACACG
* * * * * *
5406 TAGTATCCTGCACTTAGTATTACACATGCGACCT--ATCAATCTGG-TACACATAGTAGCCTGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CTAAACCAA-C-GGATACACATAGTAGCCTACA
*
5468 CTTAGTACTACACACGTGAC
63 CTTAGTACTACACATGTGAC
5488 TCACAACGAA
Statistics
Matches: 228, Mismatches: 42, Indels: 25
0.77 0.14 0.08
Matches are distributed among these distances:
96 1 0.00
97 3 0.01
98 2 0.01
99 29 0.13
100 81 0.36
101 107 0.47
102 5 0.02
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (100 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACTAAACCAACGGATACACATAGTAGCCTACACTT
AGTACTACACATGTGACCTAACAATCTAATACACG
Found at i:5436 original size:150 final size:150
Alignment explanation
Indices: 5097--5488 Score: 590
Period size: 150 Copynumber: 2.6 Consensus size: 150
5087 AAAGCTCTCT
*
5097 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGATACATGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTG-TACATGTAGTAGC
* * * * * *
5162 CTGTACTTAGTACTACACATGTGACTTAACCATTTAATACACGTAGTAGCCTGCACTTAGTACTA
65 CTGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTA
*
5227 CACACGTGATAGAAGTTAACG
130 CACACGTGATAGAAGTTAACA
*
5248 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTATCAATCTAGTACATGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-GTACATGTAGTAGC
* *
5313 CTGCACTTAGTACTACACACGTGACTAAACCATCTGATACACATAG-AGCTTACACTTAGTACTA
65 CTGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTA
*
5377 CACATGTGATCA-AAGTTAACA
130 CACACGTGAT-AGAAGTTAACA
* * **
5398 GGTACGCATAGTATCCTGCACTTAGTATTACACATGCGACCTATCAATCTGGTACACATAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-GTACATGTAGTAGC
5463 CTGCACTTAGTACTACACACGTGACT
65 CTGCACTTAGTACTACACACGTGACT
5489 CACAACGAAT
Statistics
Matches: 221, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
150 118 0.53
151 102 0.46
152 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (150 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGTACATGTAGTAGCC
TGCACTTAGTACTACACACGTGACTAAACCATCTAATACACATAGTAGCCTACACTTAGTACTAC
ACACGTGATAGAAGTTAACA
Found at i:22336 original size:27 final size:26
Alignment explanation
Indices: 22298--22379 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 26
22288 GAAGTATTCC
22298 GGTGGCTCTGCCACAAATATCTGTTCT
1 GGTGGCTCTGCCAC-AATATCTGTTCT
*
22325 GGTGGCTCTGCCACAATATCTGTATTT
1 GGTGGCTCTGCCACAATATCTGT-TCT
* * * *
22352 GGTGACGCTGTCACAATATTTGTTCT
1 GGTGGCTCTGCCACAATATCTGTTCT
22378 GG
1 GG
22380 CAGCCATGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 13 0.27
27 35 0.73
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (26 bp):
GGTGGCTCTGCCACAATATCTGTTCT
Found at i:36292 original size:40 final size:40
Alignment explanation
Indices: 36259--36491 Score: 319
Period size: 40 Copynumber: 5.8 Consensus size: 40
36249 CGGATATAGC
* *
36259 CACTCGCTCAAATGCCTTCGAGACTTAGCCCGG-ATATAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
36299 -AGTTCGCACAAATGCCTTCGGGACTTAGCCCAG-ATATAGT
1 CA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
*
36339 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* * * *
36379 AACTCGCACAAATGCCTTCGGTACTTAGCTCGGAATTTGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
*
36419 CACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
*
36459 CACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGG
36492 TTATCATCCG
Statistics
Matches: 176, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.01
40 172 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
Found at i:39126 original size:60 final size:60
Alignment explanation
Indices: 39057--39177 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
39047 CATACAAAGT
39057 AAGCTTTCAAAAGCTTAGTAAGCCATATACAAACAAACTTATCATTTTAAGCACATAAGC
1 AAGCTTTCAAAAGCTTAGTAAGCCATATACAAACAAACTTATCATTTTAAGCACATAAGC
* *
39117 AAGCTTTCAAAAGCTTAGTAAGCCATATACAAACAAACTTTTCATTTTAAGCATATAAGC
1 AAGCTTTCAAAAGCTTAGTAAGCCATATACAAACAAACTTATCATTTTAAGCACATAAGC
39177 A
1 A
39178 TCATAAAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (60 bp):
AAGCTTTCAAAAGCTTAGTAAGCCATATACAAACAAACTTATCATTTTAAGCACATAAGC
Found at i:43168 original size:20 final size:20
Alignment explanation
Indices: 43135--43229 Score: 124
Period size: 20 Copynumber: 4.8 Consensus size: 20
43125 ATACATGGGA
43135 TATGATAT--ACATGAT-TGG
1 TATGATATGCACATGATAT-G
43153 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
* *
43173 TATAAAATGCACATGATATG
1 TATGATATGCACATGATATG
43193 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
* *
43213 TATGAAATGCACGTGAT
1 TATGATATGCACATGAT
43230 GTATTCATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
18 8 0.12
20 59 0.87
21 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:43170 original size:11 final size:11
Alignment explanation
Indices: 43154--43212 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
43144 CATGATTGGT
43154 ATGATATGCAC
1 ATGATATGCAC
*
43165 ATGATATG--T
1 ATGATATGCAC
* *
43174 ATAAAATGCAC
1 ATGATATGCAC
*
43185 ATGATATG--T
1 ATGATATGCAC
43194 ATGATATGCAC
1 ATGATATGCAC
43205 ATGATATG
1 ATGATATG
43213 TATGAAATGC
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
9 14 0.39
11 22 0.61
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:43187 original size:40 final size:40
Alignment explanation
Indices: 43143--43229 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
43133 GATATGATAT
43143 ACATGAT-TGGTATGATATGCACATGATATGTATAAAATGC
1 ACATGATAT-GTATGATATGCACATGATATGTATAAAATGC
*
43183 ACATGATATGTATGATATGCACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGCACATGATATGTATAAAATGC
*
43223 ACGTGAT
1 ACATGAT
43230 GTATTCATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (40 bp):
ACATGATATGTATGATATGCACATGATATGTATAAAATGC
Found at i:43309 original size:26 final size:25
Alignment explanation
Indices: 43278--43350 Score: 119
Period size: 26 Copynumber: 2.9 Consensus size: 25
43268 GGAGGAAGTG
43278 CAAAAGGGCTTATGCCCCAGTTTAC
1 CAAAAGGGCTTATGCCCCAGTTTAC
43303 CAAAAAGGGCTTATGCCCCAGTTTAC
1 C-AAAAGGGCTTATGCCCCAGTTTAC
* *
43329 CAAAAGGGATTTTGCCCCAGTT
1 CAAAAGGGCTTATGCCCCAGTT
43351 ATTAAAAGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 20 0.44
26 25 0.56
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.25
Consensus pattern (25 bp):
CAAAAGGGCTTATGCCCCAGTTTAC
Found at i:51669 original size:46 final size:47
Alignment explanation
Indices: 51551--51719 Score: 216
Period size: 48 Copynumber: 3.6 Consensus size: 47
51541 TGATATGTGT
* *
51551 GCTAGTGTAAGACATGTCTGGGACATGCATCTGCTTCAAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTT-GAGATATACAA
* * ** *
51599 GCCAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGA-CGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGC-TTGAGATATACAA
*
51645 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTTGAGATATACAA
*
51693 GCTAGTGTAAGACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
51720 GCGTCAACTT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
46 37 0.36
47 3 0.03
48 61 0.59
49 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCTTGAGATATACAA
Found at i:51712 original size:94 final size:93
Alignment explanation
Indices: 51551--51817 Score: 294
Period size: 94 Copynumber: 2.9 Consensus size: 93
51541 TGATATGTGT
* * * *
51551 GCTAGTGTAAGACATGTCTGGGACATGCATCTG-CTTCAAGATATACAAGCCAGTGTAAGACATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTT-GAGATATACAAGCTAGTGTAAGACCTG
51615 TCTGGGACAT-GCATCAACATTG-AGACGAG
65 TCTGGGACATGGCATCAAC-TTGTAGAC-AG
51644 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCTG
1 -GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCTG
* * * *
51709 TCTGGGACATGGCGTCAACTTGTTGTCTG
65 TCTGGGACATGGCATCAACTTGTAGACAG
* * * * * * *
51738 TC-AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGA-GAGCCT-GTGTAAGACC
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGATAT-ACAAG-CTAGTGTAAGACC
51800 TGTCTGGGACATGGCATC
63 TGTCTGGGACATGGCATC
51818 GGCCTTGATA
Statistics
Matches: 151, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
92 21 0.14
93 45 0.30
94 73 0.48
95 12 0.08
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCTGT
CTGGGACATGGCATCAACTTGTAGACAG
Found at i:51799 original size:49 final size:48
Alignment explanation
Indices: 51602--51871 Score: 184
Period size: 49 Copynumber: 5.7 Consensus size: 48
51592 TATACAAGCC
* * ** * *
51602 AGTGTAAGACATGTCTGGGACAT-GCATCAACATTG--AGACGAGAGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAAAG-T
* * * * *
51648 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGATAT-ACAAGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGA-AAG-T
* * ** ***
51696 AGTGTAAGACCTGTCTGGGACATGGCGTCAAC-TTG-T---TGTCTGT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAAAGT
*
51739 CAGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAGAGCCT
1 -AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAAAG--T
* * *
51790 -GTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGATATATGAAAGT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAAAGT
* *
51837 AGTGTAAGACCATGTTTAGGACATGGCGTCGGCAT
1 AGTGTAAGACC-TGTCTAGGACATGGCATCGGCAT
51872 CTTATCCCAT
Statistics
Matches: 180, Mismatches: 29, Indels: 27
0.76 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 30 0.17
45 3 0.02
46 33 0.18
47 2 0.01
48 41 0.23
49 69 0.38
51 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAAAGT
Found at i:51846 original size:141 final size:139
Alignment explanation
Indices: 51601--51866 Score: 369
Period size: 141 Copynumber: 1.9 Consensus size: 139
51591 ATATACAAGC
*
51601 CAGTGTAAGACATGTCTGGGACATGCATCAACATTGAGACGAGAGCTAGTGTAAGACATGTCTGG
1 CAGTGTAAGACATGTCTAGGACATGCATCAACATTGAGACGAGAGCTAGTGTAAGACATGTCTGG
*
51666 GACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACC-TGTCTGGGACATGGCGTCAACTT
66 GACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCATGTCTAGGACATGGCGTCAACTT
51730 GTTGTCTGT
131 GTTGTCTGT
* ** * *
51739 CAGTGTAAGACCTGTCTAGGACATGGCATCGGCATTGATAGATGAGAGCCT-GTGTAAGACCTGT
1 CAGTGTAAGACATGTCTAGGACAT-GCATCAACATTG--AGACGAGAG-CTAGTGTAAGACATGT
* *
51803 CTGGGACATGGCATCGGCCTTGATATATGA-AAG-TAGTGTAAGACCATGTTTAGGACATGGCGT
62 CTGGGACAT-GCATCGGCCTTGAGATAT-ACAAGCTAGTGTAAGACCATGTCTAGGACATGGCGT
51866 C
125 C
51867 GGCATCTTAT
Statistics
Matches: 112, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
138 22 0.20
139 10 0.09
141 41 0.37
142 38 0.34
143 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (139 bp):
CAGTGTAAGACATGTCTAGGACATGCATCAACATTGAGACGAGAGCTAGTGTAAGACATGTCTGG
GACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCATGTCTAGGACATGGCGTCAACTT
GTTGTCTGT
Done.