Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_840 ID=scaffold_840-JGI_221_v2.0
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: 3239
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Found at i:184 original size:43 final size:45
Alignment explanation
Indices: 105--223 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 45
95 GATTGTGAAC
* * * * *
105 CTTATCTCCTTGAGGTT-GCAGCGGAGTAGATAGAAGA-AGTAGAT
1 CTTATCTCCCT-AAGTTAGCAGTGGAGTAGATAGAAGATAGCAAAT
* * *
149 CTTATCTCCCTAAG-TAGTAGTGGAGTAGATCGAAGATGGCAAAT
1 CTTATCTCCCTAAGTTAGCAGTGGAGTAGATAGAAGATAGCAAAT
* *
193 CTTATCTCCCTGAGTTTGCAGTGGAGTAGAT
1 CTTATCTCCCTAAGTTAGCAGTGGAGTAGAT
224 TAAAGCCGGT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
42 1 0.02
43 19 0.31
44 27 0.44
45 14 0.23
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (45 bp):
CTTATCTCCCTAAGTTAGCAGTGGAGTAGATAGAAGATAGCAAAT
Found at i:570 original size:218 final size:218
Alignment explanation
Indices: 105--3233 Score: 4096
Period size: 218 Copynumber: 14.4 Consensus size: 218
95 GATTGTGAAC
* * * * *
105 CTTATCTCCTTGAGGTTGCAGCGGAGTAGA-T-AGAAGAAG-TAGATCTTATCTCCCT-AAGTAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAG-A-AAGCAAG-TCTTATCCCCCTGAAGTTG
* * * **
166 TAGTGGAGTAGA-TCGAAGATGGCAAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGC
63 AAGTGGGGCAGACT-GAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGC
* * * * * * * * * *
230 CGGTGAGCCCGTCTCCCTGAAGTTGCAGTGGAGCGAATTCAAATAATAGATCGTATCTCTCTAAA
127 CAGTAATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAA
* *
295 GTTTCAATAGAGTAGATCGCATCAGGT
192 GTTGCAGTAGAGTAGATCGCATCAGGT
* * * * * * ** *
322 CTTATCTCCCTAAGGTTACTGCGAAGCAGACTGAAAAAGCAAGTCTTATCCCCTTGAAGCAGTAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*** ** * *
387 TTTAGCAGA-TCGAAGATGGAAAATCTTATCTCCCTAAGTTTGCAGTGGGGTAGATTAAAGCCAG
66 TGGGGCAGACT-GAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAG
*
451 TAATC-CAATCTCCCTGAAGTTGTAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGT
130 TAATCTC-ATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGT
515 TGCAGTAGAGTAGATCGCATCAGGT
194 TGCAGTAGAGTAGATCGCATCAGGT
* * ** *
540 CTTATCTCCCTGATGTTGCAGCGGAGCAGACTTAGAAATAAAGTCTTATCCCCTTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * *
605 TGGGGCAGACTAAAGATGGTGAATCTTATCTCCCTGAGTTTGCTGTGGGGTAAATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
670 AATCCCATCTCCCTGAAGTTGCAATGGAGCTGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
*
735 CAGTAGAGTAGATTGCATCAGGT
196 CAGTAGAGTAGATCGCATCAGGT
* * ** *
758 CTTATCTCCCTAAGGTTGAAAAGGAGCAGACTGAGAAAGCAAGTCTAATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * *
823 TGCGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTGCAGTGGAGTAGAATAAAGTCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * * * * *
888 AATCTCATCTCTCTGAAGTTACAGTGTAGCGGATTCAAATAACAAATCCTATCTCACTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
*
953 CAGTAGAGTAGATCGCATCAAGT
196 CAGTAGAGTAGATCGCATCAGGT
* * * ** *
976 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATACCCTTCAAGCAGTAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
** * * ** * * * *
1041 TGAAGCAGA-TCAAATATGGCAAATCTTATCTTCTTGAGTTTGTAGTAGAGTAGATTAAAGCCAG
66 TGGGGCAGACT-GAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAG
* * * *
1105 TAATCTCTTCTCCCTGAAGTTGCAGTGGAGCGGATTCAAATAATAGATCCTATCTCTCTGAAGTT
130 TAATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTT
*
1170 GCAGTAAAGTAGATCGCATCAGGT
195 GCAGTAGAGTAGATCGCATCAGGT
* * *
1194 CTTATCTCCCTGAGGTCGCAGCGGAGCAGACTGAGAAAGCAAGTCATATCCTCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* ** *
1259 T-GGGCATAAAGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTAGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * * *** *
1323 AATCCCATCTCCCTGAAGTAGTAATGGAGCGAATTTGGATAACAGATCTTATCTCTCTAAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
** * * *
1388 TTGTAGAGTGGATTGCATCAAGT
196 CAGTAGAGTAGATCGCATCAGGT
* * * *
1411 CTTATATCCCTAAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTAATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * ** * *
1476 T-GGTCATACTAAAGATGGCAAATCTTATCTCCCTAAGTTTACAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * *
1540 AATCTCATCTCCCTGAAGTTGGAGTGGAGCGGATTCAAATAATAGATCGTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* *
1605 TAGTAGAGTAAATCGCATCAGGT
196 CAGTAGAGTAGATCGCATCAGGT
* *
1628 CTTATTTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTATTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*
1693 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGTAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * *
1758 AATCTCATCTCCCTAAAGTTGCAGTGGAGCGGATTCAAATAATAGATCCTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* *** *
1823 CAATAGAGTAGATAATAACAGGT
196 CAGTAGAGTAGATCGCATCAGGT
* *
1846 CTTATTTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCTTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * ** *
1911 TGGGGTAGACTGAAGATGGTGAATCTTATCTCCCCGAGTTTACAGTGGAGTAGATTAGGGCTAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * **** ** *
1976 AATCTCATCTCCCTAAAGTTGTAGA-GGAATATAACCAAATAACATATCTTATCTCTCTGAAGTT
131 AATCTCATCTCCCTGAAGTTGCA-ATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTT
* *
2040 GCAGTAGAGTAGATCGTATCAAGT
195 GCAGTAGAGTAGATCGCATCAGGT
* * * * *
2064 CTTATCTCCCTAAGTTTACAGCGGAGCAGACTGAAAAAGGAAGTCTTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*
2129 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCTTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * * *
2194 AATCTCATCTCCCTAAAGTTGCAATAGAGCGGATTCAAATAATAGATCCTATCTCTCTTAAG-TG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* *
2258 TCAGTAGAGTAGATCGAATCAAGT
196 -CAGTAGAGTAGATCGCATCAGGT
2282 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* *
2347 T-GGGCAGACTGAAGGTGGTGAATCTTATCTCCCTCAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
2411 AATCTCATCTCCCTGAAGTTACAATGGAGCGGATTCGAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
*
2476 CAGTAG-GCTAGATCGCATTAGGT
196 CAGTAGAG-TAGATCGCATCAGGT
* * * *
2499 CTTATCTCCCTGAGGTTACAACGGGGCAGACTGAGAAAGCAAGTCTTATCCCCCTAAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*
2564 TGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * * * * *
2629 AATCCCATCTCCCTAAAGTTACAGTGGAGTGAATTCAAATAACAGATCTTATCTCTCTTAAG-TG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
*
2693 TCAGTAGAGTAGATCGTATCAGGT
196 -CAGTAGAGTAGATCGCATCAGGT
* * *
2717 CTTATCTCCCTGAGCTTGTAGCGGAGCAGATTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* *
2782 T-GGGCAGACTGAAGGTGGTGAATCTTATCTCCTTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
2846 AATCTCATCTCCCTGAAGTTGCAATGGAGCAGATTCGAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
*
2911 CAGTAGAGTAGATCGCATCAGTT
196 CAGTAGAGTAGATCGCATCAGGT
*
2934 CTTATCTCCCTGAGGTTGCAGCAGG-GCAGGCTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAA
1 CTTATCTCCCTGAGGTTGCAGC-GGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAA
* *
2998 GTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTGCAGTAGAGTAGATTAAAGCCAG
65 GTGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAG
* * * *
3063 TAATCCCATCTCCCTGAAGTTGTAATAGAGCGGATTCAAATAATAGATCTTATCTCTCTGAAGTT
130 TAATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTT
* * *
3128 GTAATAGAGTAGATCGCATCAAGT
195 GCAGTAGAGTAGATCGCATCAGGT
* * * * * * * *
3152 CTTATATCCCTAAGGTTGCAGCAGAGAAGACTAAGAAAGCAAGTCTTATCCCACTAAAGTTAAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*
3217 TGGGGTAGACTGAAGAT
66 TGGGGCAGACTGAAGAT
3234 TATGAA
Statistics
Matches: 2549, Mismatches: 341, Indels: 43
0.87 0.12 0.01
Matches are distributed among these distances:
216 1 0.00
217 800 0.31
218 1744 0.68
219 4 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (218 bp):
CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGTAGATCGCATCAGGT
Found at i:996 original size:436 final size:436
Alignment explanation
Indices: 105--3233 Score: 4066
Period size: 435 Copynumber: 7.2 Consensus size: 436
95 GATTGTGAAC
* * * * *
105 CTTATCTCCTTGAGGTTGCAGCGGAGTAGA-T-AGAAGAAG-TAGATCTTATCTCCCT-AAGTAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAG-A-AAGCAAG-TCTTATCCCCCTGAAGTTG
* * * **
166 TAGTGGAGTAGA-TCGAAGATGGCAAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGC
63 AAGTGGGGCAGACT-GAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGC
* * * * * * * * * *
230 CGGTGAGCCCGTCTCCCTGAAGTTGCAGTGGAGCGAATTCAAATAATAGATCGTATCTCTCTAAA
127 CAGTAATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAA
* * * * * *
295 GTTTCAATAGAGTAGATCGCATCAGGTCTTATCTCCCTAAGGTT-ACTGCGAAGCAGACTGAAAA
192 GTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGA-AGCGGAGCAGACTGAGAA
* ** * *** ** * *
359 AGCAAGTCTTATCCCCTTGAAGCAGTAGTTTAGCAGA-TCGAAGATGGAAAATCTTATCTCCCTA
256 AGCAAGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACT-GAAGATGGTGAATCTTATCTTCCTG
* * *
423 AGTTTGCAGTGGGGTAGATTAAAGCCAGTAATCCAATCTCCCTGAAGTTGTAATGGAGCGGATTC
320 AGTTTGCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTC
*
488 AAATAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGT
385 AAATAACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
* * ** *
540 CTTATCTCCCTGATGTTGCAGCGGAGCAGACTTAGAAATAAAGTCTTATCCCCTTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * *
605 TGGGGCAGACTAAAGATGGTGAATCTTATCTCCCTGAGTTTGCTGTGGGGTAAATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
670 AATCCCATCTCCCTGAAGTTGCAATGGAGCTGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* * **
735 CAGTAGAGTAGATTGCATCAGGTCTTATCTCCCTAAGGTTGAAAAGGAGCAGACTGAGAAAGCAA
196 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGAAGCGGAGCAGACTGAGAAAGCAA
* *
800 GTCTAATCCCCCTGAAGTTGAAGTGCGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTG
261 GTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTG
* * * * * * *
865 CAGTGGAGTAGAATAAAGTCAGTAATCTCATCTCTCTGAAGTTACAGTGTAGCGGATTCAAATAA
326 CAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAA
* * *
930 CAAATCCTATCTCACTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
391 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
* * * ** *
976 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATACCCTTCAAGCAGTAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
** * * ** * * * *
1041 TGAAGCAGA-TCAAATATGGCAAATCTTATCTTCTTGAGTTTGTAGTAGAGTAGATTAAAGCCAG
66 TGGGGCAGACT-GAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAG
* * * *
1105 TAATCTCTTCTCCCTGAAGTTGCAGTGGAGCGGATTCAAATAATAGATCCTATCTCTCTGAAGTT
130 TAATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTT
* * *
1170 GCAGTAAAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTCGCAGCGGAGCAGACTGAGAAAGCA
195 GCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGAAGCGGAGCAGACTGAGAAAGCA
* * * ** *
1235 AGTCATATCCTCCTGAAGTTGAAGT-GGGCATAAAGAAGATGGTGAATCTTATCTCCCTGAGTTT
260 AGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTT
* * * * ***
1299 GCAGTAGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTAGTAATGGAGCGAATTTGGATA
325 GCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATA
* ** * *
1364 ACAGATCTTATCTCTCTAAAGTTGTTGTAGAGTGGATTGCATCAAGT
390 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
* * * *
1411 CTTATATCCCTAAGGTTGCAGCGGAGCAGACTAAGAAAGCAAGTCTAATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * ** * *
1476 T-GGTCATACTAAAGATGGCAAATCTTATCTCCCTAAGTTTACAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * * *
1540 AATCTCATCTCCCTGAAGTTGGAGTGGAGCGGATTCAAATAATAGATCGTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* * * *
1605 TAGTAGAGTAAATCGCATCAGGTCTTATTTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAA
196 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGAAGCGGAGCAGACTGAGAAAGCAA
* *
1670 GTATTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTG
261 GTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTG
* * * *
1735 TAGTGGAGTAGATTAAAGCCAGTAATCTCATCTCCCTAAAGTTGCAGTGGAGCGGATTCAAATAA
326 CAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAA
* * * *** * *
1800 TAGATCCTATCTCTCTGAAGTTGCAATAGAGTAGATAATAACAGGT
391 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
* *
1846 CTTATTTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCTTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* * * ** *
1911 TGGGGTAGACTGAAGATGGTGAATCTTATCTCCCCGAGTTTACAGTGGAGTAGATTAGGGCTAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* * **** ** *
1976 AATCTCATCTCCCTAAAGTTGTAGA-GGAATATAACCAAATAACATATCTTATCTCTCTGAAGTT
131 AATCTCATCTCCCTGAAGTTGCA-ATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTT
* * * * * *
2040 GCAGTAGAGTAGATCGTATCAAGTCTTATCTCCCT-AAGTTTACAGCGGAGCAGACTGAAAAAGG
195 GCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGA-AGCGGAGCAGACTGAGAAAGC
2104 AAGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATC-TCCTTGAGT
259 AAGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCC-TGAGT
* * *
2168 TTGCAGTGGAGTAGATTAAAGCCAGTAATCTCATCTCCCTAAAGTTGCAATAGAGCGGATTCAAA
323 TTGCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAA
* * * *
2233 TAATAGATCCTATCTCTCTTAAG-TGTCAGTAGAGTAGATCGAATCAAGT
388 TAACAGATCTTATCTCTCTGAAGTTG-CAGTAGAGTAGATCGCATCAAGT
2282 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* *
2347 T-GGGCAGACTGAAGGTGGTGAATCTTATCTCCCTCAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
2411 AATCTCATCTCCCTGAAGTTACAATGGAGCGGATTCGAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* * *
2476 CAGTAG-GCTAGATCGCATTAGGTCTTATCTCCCTGAGGTT-ACAACGGGGCAGACTGAGAAAGC
196 CAGTAGAG-TAGATCGCATCAGGTCTTATCTCCCTGAGGTTGA-AGCGGAGCAGACTGAGAAAGC
*
2539 AAGTCTTATCCCCCTAAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTT
259 AAGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTT
* * * * *
2604 TGCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTAAAGTTACAGTGGAGTGAATTCAAAT
324 TGCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAAT
* * *
2669 AACAGATCTTATCTCTCTTAAG-TGTCAGTAGAGTAGATCGTATCAGGT
389 AACAGATCTTATCTCTCTGAAGTTG-CAGTAGAGTAGATCGCATCAAGT
* * *
2717 CTTATCTCCCTGAGCTTGTAGCGGAGCAGATTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
* *
2782 T-GGGCAGACTGAAGGTGGTGAATCTTATCTCCTTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
66 TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
* *
2846 AATCTCATCTCCCTGAAGTTGCAATGGAGCAGATTCGAATAACAGATCTTATCTCTCTGAAGTTG
131 AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
* * *
2911 CAGTAGAGTAGATCGCATCAGTTCTTATCTCCCTGAGGTTGCAGCAGG-GCAGGCTGAGAAAGCA
196 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGAAGC-GGAGCAGACTGAGAAAGCA
2975 AGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTT
260 AGTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTT
* * *
3040 GCAGTAGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGTAATAGAGCGGATTCAAATA
325 GCAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATA
* * *
3105 ATAGATCTTATCTCTCTGAAGTTGTAATAGAGTAGATCGCATCAAGT
390 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
* * * * * * * *
3152 CTTATATCCCTAAGGTTGCAGCAGAGAAGACTAAGAAAGCAAGTCTTATCCCACTAAAGTTAAAG
1 CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
*
3217 TGGGGTAGACTGAAGAT
66 TGGGGCAGACTGAAGAT
3234 TATGAA
Statistics
Matches: 2357, Mismatches: 313, Indels: 47
0.87 0.12 0.02
Matches are distributed among these distances:
434 195 0.08
435 1187 0.50
436 970 0.41
437 5 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (436 bp):
CTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGAAAGCAAGTCTTATCCCCCTGAAGTTGAAG
TGGGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAGTTTGCAGTGGAGTAGATTAAAGCCAGT
AATCTCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGAAGCGGAGCAGACTGAGAAAGCAA
GTCTTATCCCCCTGAAGTTGAAGTGGGGCAGACTGAAGATGGTGAATCTTATCTTCCTGAGTTTG
CAGTGGAGTAGATTAAAGCCAGTAATCCCATCTCCCTGAAGTTGCAATGGAGCGGATTCAAATAA
CAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAAGT
Found at i:2900 original size:44 final size:41
Alignment explanation
Indices: 2847--2953 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 41
2837 AAAGCCAGTA
* *
2847 ATCTCATCTCCCTGAAGTTGCAATGGAGCAGATTCGAATAACAG
1 ATCTTATCTCCCTGAAGTTGCAATAGAGCAGA-TCGAAT--CAG
* * * *
2891 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAG
1 ATCTTATCTCCCTGAAGTTGCAATAGAGCAGATCGAATCAG
* *
2932 TTCTTATCTCCCTGAGGTTGCA
1 ATCTTATCTCCCTGAAGTTGCA
2954 GCAGGGCAGG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
41 22 0.41
43 5 0.09
44 27 0.50
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
ATCTTATCTCCCTGAAGTTGCAATAGAGCAGATCGAATCAG
Done.