Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1799
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: 10849
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:1540 original size:79 final size:78
Alignment explanation
Indices: 1282--1621 Score: 380
Period size: 79 Copynumber: 4.3 Consensus size: 78
1272 AAAAATGGGA
* * * * * *
1282 TTGGAGTATCCCCGATGGTGAAAAGTCGATATTTTGAAAATAAAATCGAAGTTGGGGTATCCCTC
1 TTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCTC
* **
1347 GGAAATAATGGGG
66 GAAAATAACAGGG
* * *
1360 TTGGAGTAT-CCCGATGGTGAAAAATTGGTGTTTTAGAAATAAAACCG-GAGTTGGAGTATCCCT
1 TTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTAAAAATAAAATCGAG-GTTGGAGTATCCCT
1423 CGAAAATAACAGGG
65 CGAAAATAACAGGG
* * * * *
1437 TTGGAATATCCTCGTTGGTGAAAAATTGATGTTTTAAAAATAAAATTGAGGTTGGAATATCCCCT
1 TTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTGGAGTAT-CCCT
*
1502 CGAAAATAACGGGG
65 CGAAAATAACAGGG
* * * * *
1516 TTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTAGAAATAAAATCGGGGTTAGAGTATCCCCT
1 TTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTGGAGTAT-CCCT
* *
1581 CAGAAAAAAACAAGG
65 C-GAAAATAACAGGG
*
1596 -TGGAGCATCCCCGATGGTAGAAAAAT
1 TTGGAGTATCCCCGATGGT-GAAAAAT
1622 GGAGTATCCC
Statistics
Matches: 222, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
77 63 0.28
78 50 0.23
79 92 0.41
80 17 0.08
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (78 bp):
TTGGAGTATCCCCGATGGTGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCTC
GAAAATAACAGGG
Found at i:1658 original size:132 final size:131
Alignment explanation
Indices: 1489--1752 Score: 368
Period size: 132 Copynumber: 2.0 Consensus size: 131
1479 AAATTGAGGT
** * * * *
1489 TGGAATATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTAGA
1 TGGAATATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATCGGTATTTTAGA
*
1554 AATAAAATCGGGGTTAGAGTATCCCCTCAGAAAAAAACAAGG-TGGAGCATCCCCGATGGTAGAA
66 AATAAAATCGAGGTTAGAGTATCCCCTCAG-AAAAAACAAGGTTGGAGCATCCCCGATGG-AGAA
1618 AAA
129 AAA
* *
1621 TGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTAGA
1 TGGAATATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATCGGTATTTTAGA
* * * * * *
1686 AATAAAATCGAGGTTGGAGTATCCCTTCAGAAATAACAAGGTTGGAGTATCCCTGATGGAGGAAA
66 AATAAAATCGAGGTTAGAGTATCCCCTCAGAAAAAACAAGGTTGGAGCATCCCCGATGGAGAAAA
1751 A
131 A
1752 T
1 T
1753 CGATATTTAG
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
131 17 0.15
132 99 0.85
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (131 bp):
TGGAATATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATGATGAAAAATCGGTATTTTAGA
AATAAAATCGAGGTTAGAGTATCCCCTCAGAAAAAACAAGGTTGGAGCATCCCCGATGGAGAAAA
A
Found at i:1752 original size:79 final size:77
Alignment explanation
Indices: 1621--1769 Score: 183
Period size: 79 Copynumber: 1.9 Consensus size: 77
1611 GGTAGAAAAA
** * *
1621 TGGAGTATCCCCTAAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCGGTATTTTAGA
1 TGGAGTATCCCCTAAAAAATAACAAGGTTGGAGTATCCCCGATGATGAAAAATCGATA-TTTAG-
1686 AATAAAATCGAGGT
64 AATAAAATCGAGGT
* * * * *
1700 TGGAGTATCCCTTCAGAAATAACAAGGTTGGAGTATCCCTGATGGA-GGAAAATCGATATTTAGA
1 TGGAGTATCCCCTAAAAAATAACAAGGTTGGAGTATCCCCGAT-GATGAAAAATCGATATTTAGA
1764 ATAAAA
65 ATAAAA
1770 ACATAAATGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 7 0.12
78 5 0.08
79 47 0.78
80 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (77 bp):
TGGAGTATCCCCTAAAAAATAACAAGGTTGGAGTATCCCCGATGATGAAAAATCGATATTTAGAA
TAAAATCGAGGT
Found at i:4192 original size:20 final size:21
Alignment explanation
Indices: 4166--4223 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
4156 GTCAAAACCC
4166 AAAATGTATCGATACAATGAT
1 AAAATGTATCGATACAATGAT
* * *
4187 -AAATGTATCAATATAATTAT
1 AAAATGTATCGATACAATGAT
4207 AAATATGTATCGATACA
1 AAA-ATGTATCGATACA
4224 TTTACTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 17 0.57
21 2 0.07
22 11 0.37
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAATGTATCGATACAATGAT
Found at i:4314 original size:13 final size:13
Alignment explanation
Indices: 4292--4329 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
4282 ATTTTAGGCA
*
4292 TGTATTGATACAT
1 TGTATCGATACAT
4305 TGTATCGATACA-
1 TGTATCGATACAT
4317 T-TATCGATACAT
1 TGTATCGATACAT
4329 T
1 T
4330 TACTGTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 2 0.09
13 11 0.48
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:7080 original size:16 final size:17
Alignment explanation
Indices: 7047--7082 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7037 TCTAGATTTA
7047 ATTTTCTTAATGGTGAT
1 ATTTTCTTAATGGTGAT
*
7064 ATTTTTTTAAT-GTGAT
1 ATTTTCTTAATGGTGAT
7080 ATT
1 ATT
7083 ATTTAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (17 bp):
ATTTTCTTAATGGTGAT
Found at i:10520 original size:32 final size:32
Alignment explanation
Indices: 10484--10561 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
10474 AGGGTAGCTT
10484 TGTATCGATACATTGTATCAATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
*
10516 TGTATCGATACATTGTATCTATACAACACTTA
1 TGTATCGATACATTGTATCAATACAACACTTA
*
10548 TGTATCAATACATT
1 TGTATCGATACATT
10562 TACTGTTTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATTGTATCAATACAACACTTA
Found at i:10521 original size:19 final size:19
Alignment explanation
Indices: 10497--10559 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
10487 ATCGATACAT
10497 TGTATCAATACAACACTTA
1 TGTATCAATACAACACTTA
*
10516 TGTATCGAT---ACA--T-
1 TGTATCAATACAACACTTA
*
10529 TGTATCTATACAACACTTA
1 TGTATCAATACAACACTTA
10548 TGTATCAATACA
1 TGTATCAATACA
10560 TTTACTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.54
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (19 bp):
TGTATCAATACAACACTTA
Done.