Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3323
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: 19193
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:1212 original size:60 final size:60
Alignment explanation
Indices: 1106--1219 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
1096 AGTAGCCTTC
*
1106 ACATAGTACTAACACGTAATCAGTTTTACAGTTCACGTAGTAGCCTT-CATAGTGTGTAA
1 ACATAGTACTAACACGTAATCAGTTTTACAGCTCACGTAGTAGCCTTACATAGTGTGTAA
* * *
1165 ACATAGTACTACACACGTGATCAAGTTTTACGGCTCACTTAGT-GCCTTACATAGT
1 ACATAGTACTA-ACACGTAATC-AGTTTTACAGCTCACGTAGTAGCCTTACATAGT
1220 ACTACATACG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 11 0.23
60 14 0.29
61 23 0.48
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (60 bp):
ACATAGTACTAACACGTAATCAGTTTTACAGCTCACGTAGTAGCCTTACATAGTGTGTAA
Found at i:1274 original size:49 final size:48
Alignment explanation
Indices: 1165--1425 Score: 183
Period size: 49 Copynumber: 5.3 Consensus size: 48
1155 TAGTGTGTAA
* *
1165 ACATAGTACTACACACGTGATCAAG-TTTTACGGCT-CACTTAGT-GCCTT-
1 ACATAGTACTACACACGTG-CCAAGCTTTT-C-G-TACACATAGTAGCCTTC
* *
1213 ACATAGTACTACATACGTGGCCAAGCTTTTCGGTAC-CATTGTAGCCTTC
1 ACATAGTACTACACACGT-GCCAAGCTTTTC-GTACACATAGTAGCCTTC
* * ** * * * *
1262 ACTTAGTACTACACATGTAACATG-TTTACCGTACACGTAGTAGCATTC
1 ACATAGTACTACACACGTGCCAAGCTTT-TCGTACACATAGTAGCCTTC
*
1310 ACACAGTACTACACACGTGCTCAAGCTTTTCGTACACATAGTAGCCTTC
1 ACATAGTACTACACACGTGC-CAAGCTTTTCGTACACATAGTAGCCTTC
* * *** **
1359 ACTTAGTACTACACATGTGACCATTATTTATCGATACATGTAGTAGCCTTC
1 ACATAGTACTACACACGTG-CCAAGCTTT-TCG-TACACATAGTAGCCTTC
*
1410 ACACAGTTACTACACA
1 ACATAG-TACTACACA
1426 TGTGTTCATC
Statistics
Matches: 167, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
47 12 0.07
48 59 0.35
49 61 0.37
50 7 0.04
51 19 0.11
52 9 0.05
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (48 bp):
ACATAGTACTACACACGTGCCAAGCTTTTCGTACACATAGTAGCCTTC
Found at i:1336 original size:97 final size:100
Alignment explanation
Indices: 1217--1425 Score: 293
Period size: 97 Copynumber: 2.1 Consensus size: 100
1207 TGCCTTACAT
* *
1217 AGTACTACATACGTGGCCAAGCTTTTCGGTAC-CATTGTAGCCTTCACTTAGTACTACACATGT-
1 AGTACTACACACGTGGCCAAGCTTTTC-GTACACATAGTAGCCTTCACTTAGTACTACACATGTG
*
1280 AACA-TGTTTACCG-TACACGTAGTAGCATTCACAC
65 AACATTATTTACCGATACACGTAGTAGCATTCACAC
1314 AGTACTACACACGT-GCTCAAGCTTTTCGTACACATAGTAGCCTTCACTTAGTACTACACATGTG
1 AGTACTACACACGTGGC-CAAGCTTTTCGTACACATAGTAGCCTTCACTTAGTACTACACATGTG
* * * *
1378 ACCATTATTTATCGATACATGTAGTAGCCTTCACAC
65 AACATTATTTACCGATACACGTAGTAGCATTCACAC
1414 AGTTACTACACA
1 AG-TACTACACA
1426 TGTGTTCATC
Statistics
Matches: 99, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
96 6 0.06
97 53 0.54
98 3 0.03
99 7 0.07
100 21 0.21
101 9 0.09
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (100 bp):
AGTACTACACACGTGGCCAAGCTTTTCGTACACATAGTAGCCTTCACTTAGTACTACACATGTGA
ACATTATTTACCGATACACGTAGTAGCATTCACAC
Found at i:4665 original size:26 final size:26
Alignment explanation
Indices: 4586--4668 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
4576 GACGCCATCA
* *
4586 ATAAATATAGATAAATTTAATATAAA
1 ATAAATATAAATAAATTTAATATAAG
** * *
4612 ATCTATAAATAATAAA-TT-ATCTGCAAG
1 ATAAATATA-AATAAATTTAATAT--AAG
4639 ATAAATATAAATAAATTTAATATAAG
1 ATAAATATAAATAAATTTAATATAAG
4665 ATAA
1 ATAA
4669 TCATTTAATA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
25 3 0.07
26 21 0.50
27 15 0.36
28 3 0.07
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.34
Consensus pattern (26 bp):
ATAAATATAAATAAATTTAATATAAG
Found at i:4676 original size:18 final size:15
Alignment explanation
Indices: 4642--4682 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
4632 CTGCAAGATA
4642 AATATAAATAAATTT
1 AATATAAATAAATTT
4657 AATATAAGATAATCATTT
1 AATATAA-ATAA--ATTT
4675 AATATAAA
1 AATATAAA
4683 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 1 0.04
18 11 0.48
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATAAATAAATTT
Found at i:9531 original size:46 final size:46
Alignment explanation
Indices: 9474--9700 Score: 174
Period size: 49 Copynumber: 4.7 Consensus size: 46
9464 GATAATAACA
* * *
9474 TGCCAAAGCCATGTCCTAGACATGGTCTACATGGGATGT-TCTTTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTACATGGGA-GTCTC-ATACG
* *
9520 TGCCAATGCCATATCCCAGATATGGTCTACATGGGAGTCTCATACGG
1 TGCCAATGCCATGTCCCAGACATGGTCTACATGGGAGTCTCATAC-G
* * ** * *
9567 TGCCCATGCCATGTCCCAGACATGATCTACGGGGGACCTCTCATCCCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTACATGGGA-GTCTCAT-AC-G
* * * *
9616 TACCCACGCCATGTCCCAGACATGGTCTACATGGGACCTCTCATAACCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTACATGGGA-GTCTCAT-A-C---G
9668 ATGCCAATGCCA-G-CCCAGACATGGTCTACATGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTACATGG
9701 ATCTCTTACC
Statistics
Matches: 148, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
45 5 0.03
46 34 0.23
47 30 0.20
48 6 0.04
49 42 0.28
50 1 0.01
51 20 0.14
52 2 0.01
53 8 0.05
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.23
Consensus pattern (46 bp):
TGCCAATGCCATGTCCCAGACATGGTCTACATGGGAGTCTCATACG
Found at i:19043 original size:24 final size:25
Alignment explanation
Indices: 19006--19055 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
18996 TTTAGGCAGT
19006 AGAAAAAGAAGAGAA-AA-AGAAAA
1 AGAAAAAGAAGAGAAGAAGAGAAAA
*
19029 AGAAAAAGGAGGAGAAGAAGAGAAAA
1 AGAAAAA-GAAGAGAAGAAGAGAAAA
19055 A
1 A
19056 AATGGAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 7 0.30
25 2 0.09
26 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (25 bp):
AGAAAAAGAAGAGAAGAAGAGAAAA
Done.