Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_7238
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: 3756
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Found at i:743 original size:284 final size:295
Alignment explanation
Indices: 177--2991 Score: 3895
Period size: 284 Copynumber: 10.1 Consensus size: 295
167 AGTTAGGGTG
*
177 TCATACCAGCACTAATGCACCGGATCCCATCAG-ACTCCCCAG-TAAGCGTGCTTGGCGA-AGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
* *
239 GTACTAGGATGG-GTACCT--GGGAAGTCCTCG-G-TGCA-CCCTCCCTTTTTTC--ATAATG-T
66 GTACTAGGATGGTG-ACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCATTTTTTCATATAATGTT
295 TTTTTTAGTTGCGTTTTCTCCA-GTGGTGTAACTCATTCGTTATTTGCGTTTGTG-AAT-AATAA
130 TTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAATAA
357 TTTGGAACGATATTTGGTCGAATTTGCATTT-AATTCGAGGCGCAAGTGCGATAAGGGCAGCCTT
195 TTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCCTT
421 TATATGAATAGATTGCGCAAGAGTTG-C-GGTGC-A
260 TATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
454 TCATACCAGCACTAATGCACCGGAT-CCATCAGAACT-CGCAGTTAAGCGTGCTTGGCGAGAGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
517 GTACTA-GATGGT-ACCTCCTGGGAAGTCCT-GTGTTGCACCCCTCCATTTATTTCATATAATGT
66 GTACTAGGATGGTGACCTCCT-GGAAGTCCTCGTGTTGCACCCCTCCATTT-TTTCATATAATGT
579 TTTTTTTAGTTGCGTTTTCTCCA-GTGGTGT-ACTCATTC-TTATTTGCGTTTTGTGAAATAAAT
129 TTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCG-TTTGTGAAATAAAT
641 AATTT-GAACGATATTT-GTCGAATTTGCA-TT-AATTCGA-GCGCAAGTGCGATAAGGG-AGCC
193 AATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCC
700 TTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
258 TTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
738 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGCGAGAGT
*
803 AGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCTTTTATTTCATATAA
65 AGTACTAGGAT-GGTGACCTCCT-GGAAGTCCTCGTGTTGCACCCCT-CCATTT-TTTCATATAA
868 TGTTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTG-GAAATAA
126 TGTTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAA
932 AT-ATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGT-C-ATAAGGGCAG
191 ATAATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAG
994 CCTTTATATG-ATAGATTGCGCAAGA-TTGACGGGTGCGA
256 CCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
1032 TCATA-CAGCACTAATG-ACC-GAT-CCATCAGAACTCCGCA-TTAA--G-GCTT-GCGAGA-TA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
*
1087 -TACTA-G--GGTGACCTCCTGGAAGT-CTC-TGTTGCA-CCCTCCCATTTTTTTATATAA--TT
66 GTACTAGGATGGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCT-CCATTTTTTCATATAATGTT
*
1143 TTTTTTAGTTGCATTTTCTCCACGTGGT-TAA-TCATTC-TTATTTGCGTTTTGTGAAATAAAT-
130 TTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCG-TTTGTGAAATAAATA
1204 ATTT--AACGATA-TTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCCT
194 ATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCCT
1266 TTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
259 TTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
1303 TCATACCAGCACTAATGCACCGGATCCCATCA-AACTCCGCAG-TAAGCGTGCTTGGC-AGAGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
1365 GTACTAGGATGGTGACCT-CTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTTTTCATATAATG
66 GTACTAGGATGGTGACCTCCT-GGAAGTCCTCGTGTTGCACCCCT-CCA-TTTTTTCATATAATG
1429 --TTTTTTAGTT--GTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTT-TGAAATAAAT
128 TTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAAT
1489 AA-TTGGAACGATA-TTGGTCGAA-TTG-ATTTAAA-TCGAGGCGCAAGTGCGATAA-GGCAGCC
193 AATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCC
1548 -TT-TATGAATAGATTGCGCAAGAG-TGACGGGTGCGA
258 TTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
1583 TCATACCAGCACTAATGCACC-GATCCCATCA-AACTCCGCAGTTAAGC-TGCTTGGC--GAGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
1643 -TACTAGGATGGTGACCT-CTGGAAGTCCTC-TGTTGCA-CCCTCCATTTTTTCATATAA---TT
66 GTACTAGGATGGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCATTTTTTCATATAATGTTT
*
1701 TTTTTAGTTGC-TTTTCTCCACGT-GTGTAACTCATTCGTTATTTGCGTTTTTGAAATAAATAAT
131 TTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAATAAT
1764 TTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTT
196 TTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAA-GGGCAGCCTT
1829 TATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
260 TATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
1865 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGCGAGAGT
1930 AGTACTAGGATGGGTGACCT-CTGGGAAGTCCTCGTGTTGCACCCCTCCATTTTATTTCATA-AA
65 AGTACTAGGAT-GGTGACCTCCT-GGAAGTCCTCGTGTTGCACCCCTCCA-TTT-TTTCATATAA
1993 TGTTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAA
126 TGTTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAA
2058 ATAATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAG
191 ATAATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAG
2123 CCTTTATATGAATAGATTGCGCAAGAGTTGAC-GGTGCGA
256 CCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
2162 TCATACCAGCACTAATGCACC-GATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGT
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGCGAGAGT
2226 AGTACTAGGATGG-GTACCT-CTGGAAGTCCTCGTGTTGCACCCCTCCATTTTATTTCATATAAT
65 AGTACTAGGATGGTG-ACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCA-TTT-TTTCATATAAT
*
2289 G-TTTTTTTAGTT--GATTTCTCCACGTGGTGTAACTCATTCG-TATTTGCGTTTGTG-AATAAA
127 GTTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAA
2349 TAATTTGGAACGATATTTGGTCGAATTT-CA-TTAAATTCGAGGCGCAAGTGCGATAAGGGCAGC
192 TAATTTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGC
2412 CTTTATATGAATAGATTGCGCAAGAGTTGACGGGT--G-
257 CTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
2448 -CATACCAG-ACTAATG--CCGGAT-CCATCAGAAC-CCGCAGTTAAGCGT-CTTGG-GAGAGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
2505 -TACTAGGATGGTGA-CTCCTGGAAGT-CTCGTGTTGCA-CCCTCC-TTTTTT--T-T-A--TTT
66 GTACTAGGATGGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCATTTTTTCATATAATGTTT
2559 TTTTT-G-T---TTTTCTCCACGT-GTGT-A-TC-TTC-TTA-TTGCGTTT-TG-AAT-AAT-AT
131 TTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAATAAT
2609 TTGGAA--ATA-TT-GTC-AATTT--A-TT---TT-GA-GC-CAA-T-C--TAA-GG-AG-C-TT
196 TTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCCTTT
2652 -TAT-AATAGATTGCGCAAGAG-T-AC-GGTGCG-
261 ATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
2681 TC--A-CAG--C-AAT-C-CC--AT-CCATCAGAACTCCGCAGTT-AGCGTGCTTGGCGAGAGTA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
2734 G--CTTAGGATGGGTGA-CTCCTGGAA-T-CTCGTG-TGCA-CCC-CCATTTATTTCATATAATG
66 GTAC-TAGGAT-GGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCATTT-TTTCATATAATG
2791 --TTTTTTAGTTGCGTTTTCT-CACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAA
128 TTTTTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCG-TTTGTGAAATAAA
2853 TAATTTGGAACGATATTTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGGCA
192 TAATTTGGAACGATA-TTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAA-GGGCA
2918 GCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
255 GCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
2959 TCATACCAGCACTAATGCA-CGGATCCCATCAGA
1 TCATACCAGCACTAATGCACCGGATCCCATCAGA
2992 CCGCAGTAAC
Statistics
Matches: 2340, Mismatches: 12, Indels: 361
0.86 0.00 0.13
Matches are distributed among these distances:
227 19 0.01
228 24 0.01
229 28 0.01
230 15 0.01
231 7 0.00
232 4 0.00
233 9 0.00
234 19 0.01
235 4 0.00
236 2 0.00
237 6 0.00
238 12 0.01
239 3 0.00
240 5 0.00
241 3 0.00
242 4 0.00
243 6 0.00
244 6 0.00
245 4 0.00
246 5 0.00
247 5 0.00
248 8 0.00
250 6 0.00
251 5 0.00
252 5 0.00
253 5 0.00
254 8 0.00
256 9 0.00
257 5 0.00
258 5 0.00
259 8 0.00
260 7 0.00
261 4 0.00
262 3 0.00
263 7 0.00
264 12 0.01
265 2 0.00
266 1 0.00
267 45 0.02
268 18 0.01
269 33 0.01
270 34 0.01
271 84 0.04
272 53 0.02
273 32 0.01
274 55 0.02
275 30 0.01
276 51 0.02
277 127 0.05
278 41 0.02
279 52 0.02
280 49 0.02
281 103 0.04
282 89 0.04
283 49 0.02
284 132 0.06
285 100 0.04
286 67 0.03
287 45 0.02
288 80 0.03
289 21 0.01
290 77 0.03
291 40 0.02
292 83 0.04
293 45 0.02
294 97 0.04
295 52 0.02
296 74 0.03
297 49 0.02
298 50 0.02
299 93 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (295 bp):
TCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGCGAGAGTA
GTACTAGGATGGTGACCTCCTGGAAGTCCTCGTGTTGCACCCCTCCATTTTTTCATATAATGTTT
TTTTTAGTTGCGTTTTCTCCACGTGGTGTAACTCATTCGTTATTTGCGTTTGTGAAATAAATAAT
TTGGAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAAGTGCGATAAGGGCAGCCTTT
ATATGAATAGATTGCGCAAGAGTTGACGGGTGCGA
Done.