Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2239
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: 24604
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1015 original size:17 final size:16
Alignment explanation
Indices: 990--1024 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
980 GTACATATGC
990 TCTTCTCTTTTTTCTTT
1 TCTTCTCTTTTTT-TTT
*
1007 TCTTTTCTTTTTTTTT
1 TCTTCTCTTTTTTTTT
1023 TC
1 TC
1025 ACGAGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTCTCTTTTTTTTT
Found at i:1836 original size:16 final size:16
Alignment explanation
Indices: 1817--1849 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1807 AAAAACTAAA
*
1817 AATCCTAAAATATCCT
1 AATCCTAAAATAACCT
1833 AATCCTAAAATAACCT
1 AATCCTAAAATAACCT
1849 A
1 A
1850 GGAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (16 bp):
AATCCTAAAATAACCT
Found at i:5178 original size:10 final size:11
Alignment explanation
Indices: 5155--5183 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5145 GTCCGCGAAG
5155 GAGAAAAATAA
1 GAGAAAAATAA
5166 GAGAAAAAT-A
1 GAGAAAAATAA
5176 GAGAAAAA
1 GAGAAAAA
5184 GGCTGCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (11 bp):
GAGAAAAATAA
Found at i:7749 original size:21 final size:19
Alignment explanation
Indices: 7710--7760 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
7700 TGAAATTTAG
*
7710 TTTATATTTTATTTTAAAA
1 TTTAAATTTTATTTTAAAA
7729 TTTAAATTTTATTTCTTAAAA
1 TTTAAATTTTA-TT-TTAAAA
*
7750 TTTAAAATTTA
1 TTTAAATTTTA
7761 AGTTTAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 16 0.57
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAATTTTATTTTAAAA
Found at i:19693 original size:16 final size:17
Alignment explanation
Indices: 19658--19694 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
19648 ACCCAAATGT
*
19658 TAAAGAAGGAAAAATCA
1 TAAAGAAGGAAAAATAA
19675 TAAAGAAGGAAAAA-AA
1 TAAAGAAGGAAAAATAA
19691 TAAA
1 TAAA
19695 TTACCTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.70, C:0.03, G:0.16, T:0.11
Consensus pattern (17 bp):
TAAAGAAGGAAAAATAA
Found at i:23383 original size:131 final size:136
Alignment explanation
Indices: 23207--23516 Score: 425
Period size: 131 Copynumber: 2.3 Consensus size: 136
23197 TAGAGAACAT
* *
23207 AGATATAATCAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTAT-AAATTTA
1 AGATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTA
* * * ** * *
23271 TTAATATAAATAGTTATATTAATTAA-TTCGGT-CAAATAT-AAAGATATGAAATTAATATT-TT
66 TTAAGATAAAAAATTATATTAATTAATTTCAATAAAAATATAAAAGACATGAAATTAATATTCTT
*
23332 TTGGAA
131 TTAGAA
*
23338 AGATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTA
1 AGATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTA
*
23403 TTAAGATAAAAAATTATATTAATTAATTTCAATAAAAATATAAAAGACATGAAATTAATCTTCTT
66 TTAAGATAAAAAATTATATTAATTAATTTCAATAAAAATATAAAAGACATGAAATTAATATTCTT
23468 TTAGAA
131 TTAGAA
* * *
23474 ATAATATAATTAATATATTACTTTGATTCATATC-AAATATTAA
1 A-GATATAATTAATATATGAATTTGATTCATA-CAAAATATTAA
23517 GGTCAAAATA
Statistics
Matches: 157, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
131 55 0.35
132 29 0.18
133 4 0.03
134 6 0.04
135 18 0.11
136 8 0.05
137 36 0.23
138 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (136 bp):
AGATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATCAAATTTA
TTAAGATAAAAAATTATATTAATTAATTTCAATAAAAATATAAAAGACATGAAATTAATATTCTT
TTAGAA
Found at i:23565 original size:85 final size:83
Alignment explanation
Indices: 23437--23600 Score: 258
Period size: 85 Copynumber: 2.0 Consensus size: 83
23427 AATTTCAATA
* * *
23437 AAAATATAAAAGACATGAAATTAATCTTCTTTTAGAAATAATATAATTAATATATTACTTTGATT
1 AAAATATAAAAGACATGAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGACTTTGATT
23502 CATATC-AAATATTAAGGTC
66 -ATA-CAAAATATTAAGGTC
*
23521 AAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGACTTTGAT
1 AAAATATAAAAGACAT-GAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGACTTTGAT
23586 TATACAAAATATTAA
65 TATACAAAATATTAA
23601 TTGTATATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
83 1 0.01
84 28 0.38
85 45 0.61
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (83 bp):
AAAATATAAAAGACATGAAATTAATATTCTTTTAGAAAGAATATAATTAATATATGACTTTGATT
ATACAAAATATTAAGGTC
Found at i:23688 original size:219 final size:216
Alignment explanation
Indices: 23300--23703 Score: 627
Period size: 219 Copynumber: 1.9 Consensus size: 216
23290 TAATTAATTC
*
23300 GGTCAAATATAAAGATATGAAATTAATATTTTTTGGAAAGATATAATTAATATATGAATTTGATT
1 GGTCAAATATAAAGACATGAAATTAATATTTTTTGGAAAGATATAATTAATATATGAATTTGATT
23365 CATACAAAATATTAATTGTATATATTTTATCGAATTTATTAAGATAAAAAATTATATTAATTAAT
66 CATACAAAATATTAATTG-ATATATTTTATCGAATTTATTAAGATAAAAAATTATATTAATTAAT
23430 TTCAATAAAAATATAAAAGACATGAAATTAATCTTCTTTTAGAAATAATATAATTAATATATTAC
130 TTCAATAAAAATATAAAAGACATGAAATTAATCTTCTTTTAGAAATAATATAATTAATATATTAC
23495 TTTGATTCATATCAAATATTAA
195 TTTGATTCATATCAAATATTAA
*
23517 GGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATATATGACTT
1 GGTC-AAATAT-AAAGACAT-GAAATTAATATT-TTTTGGAAAG-ATATAATTAATATATGAATT
* * *
23582 TGATT-ATACAAAATATTAATTG-TATATTTTATGGAATTTATTAATATAAATAATTATATTAAT
61 TGATTCATACAAAATATTAATTGATATATTTTATCGAATTTATTAAGATAAAAAATTATATTAAT
* * * *
23645 TAA-TTCGATCAATATATAAAAGACATTGAAATTAA-CATTCTTTTGGAAATAATATAATT
126 TAATTTCAATAAAAATATAAAAGACA-TGAAATTAATC-TTCTTTTAGAAATAATATAATT
23704 CATTTTTTTA
Statistics
Matches: 171, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
217 4 0.02
218 26 0.15
219 78 0.46
220 12 0.07
221 27 0.16
222 24 0.14
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (216 bp):
GGTCAAATATAAAGACATGAAATTAATATTTTTTGGAAAGATATAATTAATATATGAATTTGATT
CATACAAAATATTAATTGATATATTTTATCGAATTTATTAAGATAAAAAATTATATTAATTAATT
TCAATAAAAATATAAAAGACATGAAATTAATCTTCTTTTAGAAATAATATAATTAATATATTACT
TTGATTCATATCAAATATTAA
Done.