Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold805
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: 32318
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2099 original size:40 final size:40
Alignment explanation
Indices: 2005--2147 Score: 161
Period size: 40 Copynumber: 3.6 Consensus size: 40
1995 TGAATGATGT
* * * *
2005 CCGGGCTAAGT-CCGAAGGC--TTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
2043 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2082 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2123 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
2148 AACGAGGAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
38 9 0.10
39 11 0.12
40 62 0.69
41 8 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:2161 original size:40 final size:40
Alignment explanation
Indices: 2032--2166 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 40
2022 GCTTGTGCTA
* * * **
2032 AGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 AGTGACTATAACCGGGCTAAG-TCCCGAAGGCATTTGAACG
* * **
2072 AGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTTGTGCG
1 AGTGACTATAA-CCGGGCTAAGTCCCGAAGGCATTTGAACG
* *
2112 AGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACG
1 AGTGACTATAACCGGGCTAAGTCCCGAAGGCATTTGAACG
*
2152 AG-GAGCTATATCCGG
1 AGTGA-CTATAACCGG
2167 TTAAATTCCG
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
39 3 0.04
40 75 0.94
41 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (40 bp):
AGTGACTATAACCGGGCTAAGTCCCGAAGGCATTTGAACG
Found at i:6125 original size:68 final size:68
Alignment explanation
Indices: 5958--6133 Score: 184
Period size: 68 Copynumber: 2.6 Consensus size: 68
5948 TAGTACCACC
* * * *
5958 CATGTGACCTAGC--CA-ATTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGTGACCTAGCTACACATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
6020 CACA
65 CACA
** * *
6024 CATGTGACCTAGCTACATTTATCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGTGACCTAGCTACACATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
6086 ATCACA
63 ATCACA
6092 CATGTGACCTAGCTACTACATAGTATCTCGTAGCTCTCTTGT
1 CATGTGACCTAGCTAC-ACATA-TATCTCGTAGCTCTCTTGT
6134 ACACATGATG
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
68 39 0.42
69 8 0.09
70 6 0.07
71 26 0.28
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (68 bp):
CATGTGACCTAGCTACACATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:10621 original size:44 final size:44
Alignment explanation
Indices: 10558--10649 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
10548 AATTTTGATA
10558 TAAAGTTAGTATTTTACCATTTGAAATATGTATGTGGTTTAGAC
1 TAAAGTTAGTATTTTACCATTTGAAATATGTATGTGGTTTAGAC
10602 TAAAGTTAGTATTTTACCATTTGAAATATGTATGTGGTTTAGAC
1 TAAAGTTAGTATTTTACCATTTGAAATATGTATGTGGTTTAGAC
10646 TAAA
1 TAAA
10650 TCTCATATGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (44 bp):
TAAAGTTAGTATTTTACCATTTGAAATATGTATGTGGTTTAGAC
Found at i:12865 original size:52 final size:52
Alignment explanation
Indices: 12800--12923 Score: 196
Period size: 52 Copynumber: 2.4 Consensus size: 52
12790 CATGAGAGCT
12800 AATCCAACCGATAACACGCCCCGGCACTAAGTGCCTAACCCATAGGCTATAC
1 AATCCAACCGATAACACGCCCCGGCACTAAGTGCCTAACCCATAGGCTATAC
**
12852 AATCCAATTGATAACACGCCCCGGCACTAAGTGCCTAACCCATAGGCTATAC
1 AATCCAACCGATAACACGCCCCGGCACTAAGTGCCTAACCCATAGGCTATAC
* *
12904 -ATCCACCCCCATAACACGCC
1 AATCCA-ACCGATAACACGCC
12924 AGAACAGGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 5 0.08
52 60 0.92
ACGTcount: A:0.32, C:0.38, G:0.14, T:0.16
Consensus pattern (52 bp):
AATCCAACCGATAACACGCCCCGGCACTAAGTGCCTAACCCATAGGCTATAC
Found at i:14848 original size:17 final size:17
Alignment explanation
Indices: 14826--14860 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14816 TACGGTTTAG
14826 TCGATTATAGGAATAAA
1 TCGATTATAGGAATAAA
14843 TCGATTATAGGAATAAA
1 TCGATTATAGGAATAAA
14860 T
1 T
14861 GTAGTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (17 bp):
TCGATTATAGGAATAAA
Found at i:19341 original size:16 final size:16
Alignment explanation
Indices: 19320--19350 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19310 ATTTGTTTTC
*
19320 ATTTGCATCATATATA
1 ATTTGCATCAAATATA
19336 ATTTGCATCAAATAT
1 ATTTGCATCAAATAT
19351 CAAATAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATCAAATATA
Found at i:19758 original size:56 final size:56
Alignment explanation
Indices: 19567--19758 Score: 287
Period size: 56 Copynumber: 3.4 Consensus size: 56
19557 GCCAGACAGC
* * * * * *
19567 GTCTTACTTGCACACACATATCGGAGTCACATATCGATGCCAATGTATTAAATGTG
1 GTCTTACTCGCACACATATATCGAAGTCACATATCGCTGCCAACGTATTAAAAGTG
19623 GTCTTACTCGCACACATATATC-AGAGTCACATATCGCTGCCAACGTATTAAAAGTG
1 GTCTTACTCGCACACATATATCGA-AGTCACATATCGCTGCCAACGTATTAAAAGTG
* *
19679 GTCTTACTCGCACACATATATCGAAGTCACATATCGCTACCAACGTATTAAACGTG
1 GTCTTACTCGCACACATATATCGAAGTCACATATCGCTGCCAACGTATTAAAAGTG
*
19735 GTCTTACTCACACACATATATCGA
1 GTCTTACTCGCACACATATATCGA
19759 TGCCATGGTC
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
56 124 0.99
57 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (56 bp):
GTCTTACTCGCACACATATATCGAAGTCACATATCGCTGCCAACGTATTAAAAGTG
Found at i:22148 original size:3 final size:3
Alignment explanation
Indices: 22140--22171 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
22130 GCTTTATGTT
*
22140 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22172 TTGAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25367 original size:29 final size:29
Alignment explanation
Indices: 25304--25371 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
25294 TAATCAACCA
*
25304 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
25333 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
25362 CGCACACTTA
1 CGCACACTTA
25372 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:25483 original size:174 final size:174
Alignment explanation
Indices: 25193--25520 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
25183 AACTCAAGGT
* * *
25193 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
25258 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
25323 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
25367 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
25432 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
25497 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
25521 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGATAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:25514 original size:29 final size:30
Alignment explanation
Indices: 25480--25551 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
25470 ATCAACCACG
*
25480 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTGCCATGTACATTTAAACCCA
*
25509 CACACTTAGTG-C-TGTACAATTTAAACCCG
1 CACACTTAGTGCCATGTAC-ATTTAAACCCA
25538 CACACTTAGTGCCA
1 CACACTTAGTGCCA
25552 ATCTCATGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.81
30 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (30 bp):
CACACTTAGTGCCATGTACATTTAAACCCA
Done.