Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1781
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: 23550
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:8601 original size:20 final size:20
Alignment explanation
Indices: 8572--8646 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
8562 AAAAAGGCAT
*
8572 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGTAA
*
8592 AATATATCGATACATT-TATA
1 AATGTATCGATACATTGTA-A
* * *
8612 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGTAA
8632 AATGTATCGATACAT
1 AATGTATCGATACAT
8647 CAAGGTATGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGTAA
Found at i:10094 original size:2 final size:2
Alignment explanation
Indices: 10087--10126 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
10077 TTGAAGTTGT
* * *
10087 TA TA TA TA TA TG TA TA TA TG TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10127 CTCGCTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11520 original size:2 final size:2
Alignment explanation
Indices: 11513--11537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11503 TACATCATGT
11513 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
11538 TATATATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:17668 original size:170 final size:166
Alignment explanation
Indices: 17390--17725 Score: 469
Period size: 170 Copynumber: 2.0 Consensus size: 166
17380 TTTTTATATT
* * * *
17390 AGACACTAGATAATCTTAGTAAATAGATTTTTTTTAATTTGAGTTTTATTTTTTATAAGGTATAT
1 AGACACTAAATAATCCTAGTAAATAGATTTTTTTTAATTTGAGTTTGATTATTTATAAGGTATAT
* * * *
17455 ATATTTTAAAAATAAAATTATTAATATATAATAAATAAATGTAAGGAGA-TGTCTTCATAAAATT
66 ATATTTCAAAAATAAAATTATTAATATATAATAAATAAATGTAAAGAAACTATCTTCATAAAATT
* *
17519 AT-TTAAGAAAAAAATTTAAATTATTCAAATAAAATC
131 ATATGAA-AAAAAAATTTAAATTATTCAAACAAAATC
17555 AGACACTAAATAATCCTAGTAAATAGAGTTTTCTTTTCTCAATTTGAGTTTGATTATTTATAAGG
1 AGACACTAAATAATCCTAGTAAATAGA--TTT-TTTT-T-AATTTGAGTTTGATTATTTATAAGG
* * *
17620 TATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACTATCTTCATA
61 TATATATATTTCAAAAATAAAATTATTAATATATAATAAATAAATGTAAAGAAACTATCTTCATA
* *
17685 AAATTATATGAAAAAAAGATTTAAGTTATTCAAACAAAATC
126 AAATTATATGAAAAAAAAATTTAAATTATTCAAACAAAATC
17726 TAAAAAGTAA
Statistics
Matches: 149, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
165 25 0.17
167 3 0.02
168 4 0.03
169 1 0.01
170 71 0.48
171 42 0.28
172 3 0.02
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (166 bp):
AGACACTAAATAATCCTAGTAAATAGATTTTTTTTAATTTGAGTTTGATTATTTATAAGGTATAT
ATATTTCAAAAATAAAATTATTAATATATAATAAATAAATGTAAAGAAACTATCTTCATAAAATT
ATATGAAAAAAAAATTTAAATTATTCAAACAAAATC
Found at i:17974 original size:219 final size:219
Alignment explanation
Indices: 17552--18388 Score: 1167
Period size: 219 Copynumber: 3.9 Consensus size: 219
17542 TTCAAATAAA
* * *
17552 ATCAGACACTAAATAATCCTAGTAAAT-AGAGTTTTCTTTTCTCAATTTGAGTTTGATTATTTAT
1 ATCAAACACTAGATAATCCTAGTAAATAAGAGTTTTCTTTTCTCAATTTGGGTTTGATTATTTAT
17616 AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACTATCTT
66 AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAAC-ATCTT
* * * *
17681 CATAAAATTATATGAAAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAGTAATCTTAAACAT
130 CATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAATAT
17746 ATATTTTTTATAAGATTTAAGTTAT
195 ATATTTTTTATAAGATTTAAGTTAT
* *
17771 ATCATACACTAGATAATCCTAGTAAATAAG-GTTTTCTTTTCTCAATTTGGGTTTGATTTTTTAT
1 ATCAAACACTAGATAATCCTAGTAAATAAGAGTTTTCTTTTCTCAATTTGGGTTTGATTATTTAT
* *
17835 AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATTTAAGGAAACATCTTC
66 AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACATCTTC
*
17900 ATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAATGTA
131 ATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAATATA
*
17965 TATTTTTTTATAAGATTTCAGTTAT
196 TA-TTTTTTATAAGATTTAAGTTAT
* *
17990 ATTAAACATTAGATAATCCTAGTAAATAA-AGTTTTCTTTTCTCAATTTGGGTTTGATTATTTAT
1 ATCAAACACTAGATAATCCTAGTAAATAAGAGTTTTCTTTTCTCAATTTGGGTTTGATTATTTAT
* * *
18054 AAGGTACATATATTTCAAAAATAAAATTATTAATATATGACAAGTGAA--T--ATAAA-A-----
66 AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACATCTTC
* * *
18109 A-AAAGTC-T-TGAGAAAAATATTTAAGTTATTCAAATAAAATCTAAAAAATAATCTTAAATATA
131 ATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAATATA
*
18171 TATTTTTTATAAAATTTAAGTTAT
196 TATTTTTTATAAGATTTAAGTTAT
* * *
18195 AT-AACATACTAGAGAATCCTAATAAA-ATAGAGTTTTCTTTTCTCAATTTGGGTTTGATT-TTT
1 ATCAA-ACACTAGATAATCCTAGTAAATA-AGAGTTTTCTTTTCTCAATTTGGGTTTGATTATTT
* * **
18257 ATAAGGTCATATA-A-TTCAAAAATAAAACTATTAATATATAATAAGTGAATGTAAAGAAGTATC
64 ATAAGGT-ATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACATC
* * * * * *
18320 TTCATAAATTTATCTGAGAAAAAAATTTAAGTTATTTAAACAAAATCTAAAAAATAATCTTAAAC
128 TTCATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAAT
18385 ATAT
193 ATAT
18389 TACCAATAAA
Statistics
Matches: 556, Mismatches: 42, Indels: 42
0.87 0.07 0.07
Matches are distributed among these distances:
204 35 0.06
205 51 0.09
206 87 0.16
207 1 0.00
208 8 0.01
209 2 0.00
214 2 0.00
215 7 0.01
216 1 0.00
217 52 0.09
218 68 0.12
219 240 0.43
220 2 0.00
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (219 bp):
ATCAAACACTAGATAATCCTAGTAAATAAGAGTTTTCTTTTCTCAATTTGGGTTTGATTATTTAT
AAGGTATATATATTTCAAAAATAAAATTATTAATATATGATAAGTGAATGTAAAGAAACATCTTC
ATAAAATCATATGAGAAAAAGATTTAAGTTATTCAAACAAAATCTAAAAAATAATCTTAAATATA
TATTTTTTATAAGATTTAAGTTAT
Found at i:19295 original size:13 final size:14
Alignment explanation
Indices: 19272--19300 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19262 TTTATTTTGC
19272 TTTATATTTTATTT
1 TTTATATTTTATTT
19286 TTTA-ATTTTATTT
1 TTTATATTTTATTT
19299 TT
1 TT
19301 CTAAATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATATTTTATTT
Found at i:19380 original size:26 final size:24
Alignment explanation
Indices: 19349--19429 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 24
19339 TAAATATAAA
19349 ATATTTCAATATTTTATAATTTTATT
1 ATATTT-AATATTTTATAATTTT-TT
** *
19375 ATATTTAAATATGCTATAA-ATTTT
1 ATATTT-AATATTTTATAATTTTTT
19399 A-ATTTAATATTTTTATAATTATTTT
1 ATATTTAATA-TTTTATAATT-TTTT
19424 ATATTT
1 ATATTT
19430 TTCATTGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
22 4 0.09
23 10 0.23
24 3 0.07
25 7 0.16
26 20 0.45
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (24 bp):
ATATTTAATATTTTATAATTTTTT
Found at i:20815 original size:4 final size:4
Alignment explanation
Indices: 20806--20831 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20796 ATGTTTTTGG
20806 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
20832 TCCTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:22318 original size:17 final size:17
Alignment explanation
Indices: 22296--22329 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
22286 ATACTTTATT
22296 AATTTTT-GATAAATTAA
1 AATTTTTAGA-AAATTAA
22313 AATTTTTAGAAAATTAA
1 AATTTTTAGAAAATTAA
22330 GGTAATGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AATTTTTAGAAAATTAA
Done.