Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold519
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: 11477
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Found at i:783 original size:363 final size:362
Alignment explanation
Indices: 80--817 Score: 1254
Period size: 363 Copynumber: 2.0 Consensus size: 362
70 CATGAGATAT
* *
80 AATAGATTT-GTGAGATAATATCAGAATAATTTTGGGTTCCCCTGTTCTGACTTTTGAAAATCAT
1 AATA-ATTTAGTGAGACAATATCAGAATAATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCAT
*
144 AAAAAAATTGGAGAAAAATAATTAGGGCTTAAATTTATATTTTTTAAAATACTTAATGAGTCTAT
65 AAAAAAATTGGAGAAAAATAATTAGGGCTTAAATTTATATTTTTTAAAATACTTAATGAATCTAT
209 TTTCAAATAGAAATAAACATGGACATCATCCGAATTCTGTACGAAGAGATAATTAATTTTAGTGA
130 TTTCAAATAGAAATAAACATGGACATCATCCGAATTCTGTACGAAGAGATAATTAATTTTAGTGA
*
274 AGAAGGGTTTGGAATTGTCAGACAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTATTA
195 AGAAGGGTTCGGAATTGTCAGACAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTATTA
* *
339 GATAAAACCAAAAATTCTAAAAATTTTATGATAGAGGACATATGAATCTAGTTTTCAGGGAAAAT
260 GATAAAACCAAAAATTCTAAAAATTTTATGATAGAAGAAATATGAATCTAGTTTTCAGGGAAAAT
404 TAGCGGATCCAATTTGGAGCTCTTTAGCTAAAGATAAA
325 TAGCGGATCCAATTTGGAGCTCTTTAGCTAAAGATAAA
* *
442 AATAATTTAGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTTCTGACTTTTTGAAAATCA
1 AATAATTTAGTGAGACAATATCAGAATAATTTCGGGTTCCCCTG-TTCTGAC-TTTTGAAAATCA
*
507 TAAAAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATA-TTTTTAAAATCCTTAATGAATCT
64 TAAAAAAATTGGAGAAAAATAATTA-GGGCTTAAATTTATATTTTTTAAAATACTTAATGAATCT
*
571 ATTTTC-AATAGAAATAAACATGGACATTATCCGAATTCTGTACGAAGAGATAATTAATTTTTAG
128 ATTTTCAAATAGAAATAAACATGGACATCATCCGAATTCTGTACGAAGAGATAATTAA-TTTTAG
*
635 TGAAGAAGGG-TCGGAATTGTCAGATAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTA
192 TGAAGAAGGGTTCGGAATTGTCAGACAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTA
*
699 TTAGAT-AAACCAAAAATTCTAAAAATTTTATGATTAGAAGAAATATGAATGTAG-TTTCAGGGA
257 TTAGATAAAACCAAAAATTCTAAAAATTTTATGA-TAGAAGAAATATGAATCTAGTTTTCAGGGA
*
762 AAATTAGCGGATCCTAATTTGGAGTTCTTTAGCTAAAGATAAA
321 AAATTAGCGGATCC-AATTTGGAGCTCTTTAGCTAAAGATAAA
805 AATAATTTAGTGA
1 AATAATTTAGTGA
818 CTATGGCATT
Statistics
Matches: 356, Mismatches: 13, Indels: 13
0.93 0.03 0.03
Matches are distributed among these distances:
361 4 0.01
362 85 0.24
363 172 0.48
364 80 0.22
365 15 0.04
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (362 bp):
AATAATTTAGTGAGACAATATCAGAATAATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCATA
AAAAAATTGGAGAAAAATAATTAGGGCTTAAATTTATATTTTTTAAAATACTTAATGAATCTATT
TTCAAATAGAAATAAACATGGACATCATCCGAATTCTGTACGAAGAGATAATTAATTTTAGTGAA
GAAGGGTTCGGAATTGTCAGACAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTATTAG
ATAAAACCAAAAATTCTAAAAATTTTATGATAGAAGAAATATGAATCTAGTTTTCAGGGAAAATT
AGCGGATCCAATTTGGAGCTCTTTAGCTAAAGATAAA
Found at i:1252 original size:7 final size:7
Alignment explanation
Indices: 1242--1268 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1232 AGTGATAAGT
1242 GACAAGC
1 GACAAGC
1249 GACAAGC
1 GACAAGC
1256 GACAAGC
1 GACAAGC
1263 GACAAG
1 GACAAG
1269 TGATAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.30, T:0.00
Consensus pattern (7 bp):
GACAAGC
Found at i:1332 original size:51 final size:51
Alignment explanation
Indices: 1256--1369 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
1246 AGCGACAAGC
* *
1256 GACAAGCGACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGT
* *
1307 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGT
1358 GACAAGTGATAA
1 GACAAGTGATAA
1370 ATGTGATCAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:9017 original size:50 final size:51
Alignment explanation
Indices: 8937--9045 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 51
8927 ACTTCTGATC
*
8937 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTAT-TGATCAGTGACA
1 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACA
* * * *
8987 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGGCA
1 AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACA
9038 AGTGATAA
1 AGTGATAA
9046 ATGTGATCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 35 0.66
51 18 0.34
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTGATAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACA
Done.