Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.009G254600.1-JGI_221_v2.1
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: 3861
ACGTcount: A:0.41, C:0.15, G:0.27, T:0.17
Found at i:756 original size:117 final size:117
Alignment explanation
Indices: 605--2240 Score: 1531
Period size: 117 Copynumber: 13.9 Consensus size: 117
595 GCAGCTGAAG
* * * *
605 CTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTACCCAA
1 CTGAAGCTG-AGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
* ** * *** *
669 GGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGA
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
**
722 CTGAAGCTGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
* * * *
787 GAGGAAAGTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGATGAA
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-CGAAA--AGGA-G-A
* ** *
844 GCTGAACCTGAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
* * * * *
909 GGAGAAAAGTGTTGAGCAAATGGTGCCAGAACCAAGGATGGTTC-AAAAGGAGA
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGG-TCGAAAAGGAGA
* * * *
962 CTGAAGCTGAGAAGGTAACAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGATGTAACCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
** * *
1027 GAGGAAAGCATTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGGCTGAA
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCG-AAA--AGG-AG-A
** * * *
1084 GCTGAAGCTGAGAAGGTACCAAAACTGATTTTGGCCGAAAAGAAGAAACTTGAAGAGGTGCCCAA
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
* * * *
1149 GGAGGAAAGTGTTGAGCAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGA-A
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * *
1201 GCT-AAG--AAGAAAGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAA
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
* *
1263 GGACGAAAGTGTTGAGCAAAAGGTGCCAAAA-CAGAAGTTGGTCGAAAAGGAGG
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCA-AAGTTGGTCGAAAAGGAGA
* *
1316 CTGAAGTCGCAGCTGAAGATGAAAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAA
1 CTG-A-----AGCT---GA-G--AAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAA
**** ** *
1381 GAGGTACAGGTGGAGGAAAACGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-----AGAAG-
54 GAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * *
1439 CTGAATCTGAGAAAGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
* * *
1504 GAGGAAAGTGTTGAGCAAAAGGCGCCAAAACAAAAGTTGGTTGAAAAGGAGGCTGAA
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGA----G-A
* *
1561 GTTGAAGCAGAAGATGAGAAGGTACCAAAACT--A----GCCGAAAAGAAGAAACCTGAAGAGGT
1 -CTGAAGC------TGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGT
*** * * ****
1620 A--C-AGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGA-A
59 ACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* *
1675 GCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAA
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
** * * *
1740 GGAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGG
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * ** * * *
1793 CTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
* *
1858 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTC---AA--AG-
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
** ** * * * *
1904 CTGAAGAAGAGAAGGTACCGCAATTGATA-TTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAA
1 CTGAAGCTGAGAAGGTACCAAAACTGA-AGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
****
1968 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGACGCTGA-A
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * * * *
2020 GCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAACC--
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
** * * * *
2083 -GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGG
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * * * *
2135 CTGAACCTGAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
2200 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
2241 TGAGAAGAAG
Statistics
Matches: 1245, Mismatches: 200, Indels: 148
0.78 0.13 0.09
Matches are distributed among these distances:
108 18 0.01
111 172 0.14
112 2 0.00
113 2 0.00
114 226 0.18
116 12 0.01
117 409 0.33
118 7 0.01
119 1 0.00
120 55 0.04
121 5 0.00
122 8 0.01
123 222 0.18
124 5 0.00
126 1 0.00
127 1 0.00
129 97 0.08
130 2 0.00
ACGTcount: A:0.42, C:0.15, G:0.28, T:0.14
Consensus pattern (117 bp):
CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
Found at i:1028 original size:240 final size:237
Alignment explanation
Indices: 600--2240 Score: 1673
Period size: 240 Copynumber: 6.9 Consensus size: 237
590 AAACTGCAGC
* * * *
600 TGAAGCTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTA
1 TGAAGCTGAAGCTG-AGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTA
* ** **
664 CCCAAGGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTT-GAAAAGGAGACTGAAG
65 CCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAA----AGTTGGTCAAGGAGACTGAAG
** * *
728 CTGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAA
126 CTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAA
* * *
793 AGTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGA
191 AGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGAGGA
* ** *
840 TGAAGCTGAACCTGAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTAC
1 TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAC
* * * * *
905 CCAAGGAGAAAAGTGTTGAGCAAATGGTGCCAGAACCAAGGATGGTTCAAAAGGAGACTGAAGCT
66 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGG-TC--AAGGAGACTGAAGCT
* *
970 GAGAAGGTAACAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGATGTAACCAAGGAGGAAAG
128 GAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG
** * ** *
1035 CATTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGGC
193 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGAGGA
** * * *
1080 TGAAGCTGAAGCTGAGAAGGTACCAAAACTGATTTTGGCCGAAAAGAAGAAACTTGAAGAGGTGC
1 TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAC
* * *
1145 CCAAGGAGGAAAGTGTTGAGCAAAATGTGCCAAAACAAAAGTTGGTC--GAAGA-TGAAGCTAAG
66 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAGGAGACTGAAGCT--G
* * *
1207 AAGAAAGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGACGAAAG
129 -AGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG
*
1272 TGTTGAGCAAAAGGTGCCAAAA-CAGAAGTTGGTCGAAAAGGAGGCTGAA
193 TGTTGAGCAAAAGGTGCCAAAACCA-AAGTTGGTCCAAAAGGA-G--G-A
* * * * *
1321 GTCGCAGCTGAAGATGAAAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGT
1 -T-GAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGT
**** ** * *
1386 ACAGGTGGAGGAAAACGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT--AGAAG-CTGAATCTG
64 ACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAGGAGACTGAAGCTG
*
1448 AGAAAGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGT
129 AGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGT
* * **
1513 GTTGAGCAAAAGGCGCCAAAACAAAAGTTGGTTGAAAAGGAGGCTGAA
194 GTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGA-G--G-A
* * *
1561 GTTGAAGCAGAAGATGAGAAGGTACCAAAACT--A----GCCGAAAAGAAGAAACCTGAAGAGGT
1 --TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGT
*** * * *
1620 A--C-AGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGA-AGCTGAA
64 ACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC-AAG--GAGA-CTGAA
1681 GCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGA
125 GCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGA
** * * *
1746 AAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGT-CGAAA--AGGA
190 AAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGAGGA
* * * ** * * *
1791 -G--GCTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAA
1 TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAC
* * **
1853 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTCAA--AG-CTGAAGAAGAG
66 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAGGAGACTGAAGCTGAG
** * ** * * * *
1915 AAGGTACCGCAATTGATATTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAAGTGT
131 AAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGT
* *
1980 TGAGCAAAAGGTGCCAAAACCAAAGTTGGT-C-----GACGC
196 TGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGAGGA
* * * * * *
2016 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAA
1 TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAC
** * * * * *
2081 CC---GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAACCT
66 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC---AAGGAGACTGAAGCT
* * * * * *
2143 GAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
128 GAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG
2208 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
193 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
2241 TGAGAAGAAG
Statistics
Matches: 1188, Mismatches: 167, Indels: 101
0.82 0.11 0.07
Matches are distributed among these distances:
225 60 0.05
226 1 0.00
227 1 0.00
228 147 0.12
229 1 0.00
230 3 0.00
231 153 0.13
233 3 0.00
234 71 0.06
235 4 0.00
236 9 0.01
237 193 0.16
238 2 0.00
239 3 0.00
240 429 0.36
241 3 0.00
242 1 0.00
243 104 0.09
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.15
Consensus pattern (237 bp):
TGAAGCTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAC
CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAGGAGACTGAAGCTGAG
AAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGT
TGAGCAAAAGGTGCCAAAACCAAAGTTGGTCCAAAAGGAGGA
Found at i:1501 original size:477 final size:468
Alignment explanation
Indices: 598--2240 Score: 1669
Period size: 477 Copynumber: 3.5 Consensus size: 468
588 CGAAACTGCA
* * * * * *
598 GCTGAAGCTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGG
1 GCTGAAGCTGAAGCTG-AGAAGGTACCAAAACTGATGTTGGCCGAAAAGAAGAAACCTGAAGAGG
* ** * * * *** * * *
662 TACCCAAGGAGAAAAGTGTTGAGC-AAGTGGTGCCAAAACCAATGCCAGTTGAA-AAGGAGACTG
65 TACCC-AGGAGGAAAGCATTGAGCAAAAT-GTGCCAAAACAAAAGTTGGTCGAAGATGAAG-CTG
** * *
725 AAGCTGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAG
127 AA---GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAG
* * * * * **
790 GAAAGTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGATGA--AGCTGAACCT
189 GAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGGCTGATGAGCTGAAGAT
** * * *
853 GAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGA-GAAAA
254 GA-AAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTA--CAAGGAGGAAAA
* * * * * *
917 GTGTTGAGCAAATGGTGCCAGAACCAAGGATGGTTCAAAAGGAGACTGAAGCTGAGAAGGTAACA
316 -TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGG-T---AAGAAG-CTGAAGCTGAGAAGGTACCA
* **
982 AAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGATGTAACCAAGGAGGAAAGCATTGAGCAAAA
375 AAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGTTGAGCAAAA
1047 GGTGCCAAAACCAAAGTTAGTCGTAAAGGAG
440 GGTGCCAAAACCAAAGTT-GT-GTAAAGGAG
* *
1078 GCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGATTTTGGCCGAAAAGAAGAAACTTGAAGAGGT
1 GCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCCGAAAAGAAGAAACCTGAAGAGGT
* **
1143 GCCCAAGGAGGAAAGTGTTGAGCAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGCT-AAG
66 ACCC-AGGAGGAAAGCATTGAGCAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGCTGAAG
* *
1207 AAGAAAGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGACGAAAG
130 -AGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG
1272 TGTTGAGCAAAAGGTGCCAAAA-CAGAAGTTGGTCGAAAAGGAGGCTGAAGTCGCAGCTGAAGAT
194 TGTTGAGCAAAAGGTGCCAAAACCA-AAGTTGGTCGAAAAGGAGGCTG-A-T-G-AGCTGAAGAT
*
1336 GAAAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTACAGGTGGAGGAAAA
254 G-AAAGGTACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTACA--AGGAGGAAAA
* * *
1401 CGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-AGAAGCTGAATCTGAGAAAGTACCAAAACTG
316 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGAAGCTGAAGCTGAGAAGGTACCAAAACTG
*
1465 ACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGTTGAGCAAAAGGCGCC
381 ACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGTTGAGCAAAAGGTGCC
* *
1530 AAAACAAAAGTTGGTTGAAAAGGAG
446 AAAACCAAAGTT-G-TGTAAAGGAG
*
1555 GCTGAAGTTGAAGCAGAAGATGAGAAGGTACCAAAACT-A-----GCCGAAAAGAAGAAACCTGA
1 GCTGAAGCTGAAGC------TGAGAAGGTACCAAAACTGATGTTGGCCGAAAAGAAGAAACCTGA
* * * * * * *
1614 AGAGGTA--CAGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCTGGTCGATGCTGAAGC
60 AGAGGTACCCAGGAGGAAAGCATTGAGCAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGC
*
1677 TGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGG
125 TGAA---GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGG
** * *
1742 AGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGGCTGA--AGCT---G
187 AGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGGCTGATGAGCTGAAG
* * ** * *
1802 A-G-AAGGTACCAAAACAGATGA-TGGCTGAACTGAAGAAACTTGAAGAGATAACCAAGGAGGAA
252 ATGAAAGGTACCAAAACTGA-AATTGGCTGAAAAGAAGAAACATGAAGAGGT-A-CAAGGAGGAA
* * * * ** ** *
1864 AGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTCA-AAGCTGAAGAAGAGAAGGTACCGCAAT
314 AATGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTAAGAAGCTGAAGCTGAGAAGGTACCAAAAC
** * * * *
1928 TGATATTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAAGTGTTGAGCAAAAGGTG
379 TGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGTTGAGCAAAAGGTG
* *
1993 CCAAAACCAAAGTTG-GT---CGAC
444 CCAAAACCAAAGTTGTGTAAAGGAG
* * *
2014 GCTGAAGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGT
1 GCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCCGAAAAGAAGAAACCTGAAGAGGT
* * * * * * *
2079 AACC--GAGGAAAGCATTCAGCAAAA-GATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAC
66 ACCCAGGAGGAAAGCATTGAGCAAAATG-TGCCAAAACAAAAGTTGGTCGAAGATGAAGCTGAA-
* * * * *
2141 CTGAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAA
129 --GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAA
2206 AGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
192 AGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
2241 TGAGAAGAAG
Statistics
Matches: 996, Mismatches: 127, Indels: 101
0.81 0.10 0.08
Matches are distributed among these distances:
453 17 0.02
454 1 0.00
458 1 0.00
459 175 0.18
461 1 0.00
462 1 0.00
464 1 0.00
465 168 0.17
466 3 0.00
467 3 0.00
468 2 0.00
471 4 0.00
474 47 0.05
475 3 0.00
476 4 0.00
477 340 0.34
478 9 0.01
479 3 0.00
480 96 0.10
481 9 0.01
482 2 0.00
483 100 0.10
484 6 0.01
ACGTcount: A:0.42, C:0.15, G:0.29, T:0.14
Consensus pattern (468 bp):
GCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGATGTTGGCCGAAAAGAAGAAACCTGAAGAGGT
ACCCAGGAGGAAAGCATTGAGCAAAATGTGCCAAAACAAAAGTTGGTCGAAGATGAAGCTGAAGA
GAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTG
TTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGGCTGATGAGCTGAAGATGAAAGGT
ACCAAAACTGAAATTGGCTGAAAAGAAGAAACATGAAGAGGTACAAGGAGGAAAATGTTGAGCAA
AAGGTGCCAAAACCAAAGTTGGTAAGAAGCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTG
AAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAG
TTGTGTAAAGGAG
Found at i:2181 original size:342 final size:340
Alignment explanation
Indices: 1597--2238 Score: 1009
Period size: 342 Copynumber: 1.9 Consensus size: 340
1587 AAAACTAGCC
* *
1597 GAAAAGAAGAAACCTGAAGAGGTACAGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCT
1 GAAAAGAAGAAACCTAAAGAGATACAGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCT
* * * *
1662 GGTCGATGCTGAAGCTGAAGCTGAGAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTG
66 GGTCGACGCTGAAGCTGAAGCTGAGAAAGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTA
* * *
1727 AAGAGGTAACCAAGGAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAG
131 AAGAGGTAACC-A-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAG
* * *
1792 GCTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAA
194 GCTGAACCTGAGAAGGTACCAAAACAGATGATGGCTGAACAGAAGAAACCTGAAGAGATAACCAA
*
1857 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTCAAAGCTGAAGAAGAGAAGGTAC
259 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCAAAGCTGAAGAAGAGAAGGTAC
1922 CGCAATTGATATTGGCA
324 CGCAATTGATATTGGCA
*** *
1939 GAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAA
1 GAAAAGAAGAAACCTAAAGAGATA--C-AGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAA
* * *
2004 GTTGGTCGACGCTGAAGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAAC
63 GCTGGTCGACGCTGAAGCTGAAGCTGAGAAAGTACCAAAACTGACGTTGGCCGAAAAGAAGAAAC
2069 CTAAAGAGGTAACC-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGA
128 CTAAAGAGGTAACCAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGA
* * *
2133 GGCTGAACCTGAGAAGGTGCCAAAACAGATGATGGCTGCAA-AGAAGAAACCTGAAGAGGTACCC
193 GGCTGAACCTGAGAAGGTACCAAAACAGATGATGGCTG-AACAGAAGAAACCTGAAGAGATAACC
2197 AAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTG
257 AAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTG
2239 GTTGAGAAGA
Statistics
Matches: 273, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
342 165 0.60
343 2 0.01
344 1 0.00
345 105 0.38
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.14
Consensus pattern (340 bp):
GAAAAGAAGAAACCTAAAGAGATACAGGAGGAAACCATTGAGCAAAAGGGGCCAAAACCAAAGCT
GGTCGACGCTGAAGCTGAAGCTGAGAAAGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTA
AAGAGGTAACCAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGC
TGAACCTGAGAAGGTACCAAAACAGATGATGGCTGAACAGAAGAAACCTGAAGAGATAACCAAGG
AGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCAAAGCTGAAGAAGAGAAGGTACCG
CAATTGATATTGGCA
Found at i:2224 original size:72 final size:72
Alignment explanation
Indices: 2173--2920 Score: 671
Period size: 72 Copynumber: 10.4 Consensus size: 72
2163 GATGGCTGCA
* * * * * *
2173 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
2238 GGTTGAG
66 GGTTGAG
* * *
2245 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
2310 GGTTGAG
66 GGTTGAG
* * *
2317 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
2382 GGTTGAG
66 GGTTGAG
* * * * * ** *
2389 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAACCAAAGT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAA-AAGGTACCAAAACCAAAGT
*
2453 TGATTGAG
65 TGGTTGAG
* * * ** * *
2461 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
2526 GGTTGAG
66 GGTTGAG
* * * * * ** * * *
2533 AAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAA-GCACCAAAATCAAAGT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGA-GAAAAAGGTACCAAAACCAAAGT
2597 TGGTTGAG
65 TGGTTGAG
* ** * * * * * * ***
2605 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* *
2670 GATCGAG
66 GGTTGAG
* *** * * * * * *
2677 AAGAAGGAACCTGAAGACACACCCAAGAAGGG-GAGTGTTGAGGAAAATGTACCAAAATCAAGGC
1 AAGAAGGAACCTAAAGAGGTACCCAAG-GGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT
2741 TGGTTGA-
65 TGGTTGAG
* * * * * * *
2748 AACTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGGTACCAAAACTAAAGT
1 AA-GAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT
2813 TGGTTGAG
65 TGGTTGAG
* * * * * * *
2821 AAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCAAAACCAAAG
1 AAGAAGGAACCT-AAAGAGGTACCCAAGGGGGAGAGTG-TTGAGAAAAAGGTACCAAAACCAAAG
*
2884 TTGGTTGAA
64 TTGGTTGAG
* * * *
2893 AATAAGGAACTTGAAGAGGTACCTAAGG
1 AAGAAGGAACCTAAAGAGGTACCCAAGG
2921 AGAAGACTGT
Statistics
Matches: 547, Mismatches: 118, Indels: 22
0.80 0.17 0.03
Matches are distributed among these distances:
71 16 0.03
72 517 0.95
73 14 0.03
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (72 bp):
AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
GGTTGAG
Found at i:2406 original size:144 final size:144
Alignment explanation
Indices: 2173--2940 Score: 763
Period size: 144 Copynumber: 5.3 Consensus size: 144
2163 GATGGCTGCA
* * * * *
2173 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * * * * *
2238 GGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAAC
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
2303 CAAAGTTGGTTGAG
131 CAAAGTTGGTTGAG
* * * *
2317 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* ** * * * * *
2382 GGTTGAGAAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAA
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAA-AAAGTACCAAAA
*
2446 CCAAAGTTGATTGAG
130 CCAAAGTTGGTTGAG
* * * * * * *
2461 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * * * * * *
2526 GGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGCACCAAAAT
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
2591 CAAAGTTGGTTGAG
131 CAAAGTTGGTTGAG
* * * * * * * * * ***
2605 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * ** * * * *
2670 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
* *
2735 CAAGGCTGGTTGA-
131 CAAAGTTGGTTGAG
* * * * * *
2748 AACTAAGGAACCTGAAGAGGAACCCAAAGG-GGAGAGTATTGAGGAAAAGGTACCAAAACTAAAG
1 AA-GAAGGAACCTGAAGAGGTACCC-AAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAG
* * * *
2812 TTGGTTGAGAAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCA
64 TTGGTTGAGAAGAAGGAACCT-GAAGAGGCACCCAAGGAGGAGAGTG-TTGAGGAAAAAGTACCA
*
2875 AAACCAAAGTTGGTTGAA
127 AAACCAAAGTTGGTTGAG
* * * * * *
2893 AATAAGGAACTTGAAGAGGTACCTAAGGAGAAGACTGTCGAGAGAAAG
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAG
2941 ATTCAAAGTA
Statistics
Matches: 505, Mismatches: 111, Indels: 16
0.80 0.18 0.03
Matches are distributed among these distances:
143 9 0.02
144 485 0.96
145 11 0.02
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (144 bp):
AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
CAAAGTTGGTTGAG
Found at i:2559 original size:216 final size:216
Alignment explanation
Indices: 2173--2833 Score: 747
Period size: 216 Copynumber: 3.1 Consensus size: 216
2163 GATGGCTGCA
* * * * * * * * *
2173 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAA-AAGGTGCCAAAACCAAAGT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAG-AAGAAAGTACCGAAACCAAAGT
* * * * *
2237 TGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAA
65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA
* * * * *
2302 CCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGT
130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT
2367 ACCAAAATCAAAGTTGGTTGAG
195 ACCAAAATCAAAGTTGGTTGAG
* * * *
2389 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGAA-AAGAAATTACCGAAACCAAAGT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATT-AAGAAGAAAGTACCGAAACCAAAGT
* * * ** *
2453 TGATTGAGAATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAA
65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA
* * * ** * *
2518 CCAAAGTTGGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGC
130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT
2583 ACCAAAATCAAAGTTGGTTGAG
195 ACCAAAATCAAAGTTGGTTGAG
* * * * **
2605 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAGAAGAAAGTACCGAAACCAAAGTT
* * * * * * * *
2670 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT
66 GATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAAC
* * * * *
2735 CAAGGCTGGTTGA-AA-CTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGG
131 CAAAGTTGGTTGAGAAGC--AGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAG
2798 TACCAAAA-CTAAAGTTGGTTGAG
194 TACCAAAATC-AAAGTTGGTTGAG
2821 AAGAAGGAACCTG
1 AAGAAGGAACCTG
2834 GAAAGGCAAC
Statistics
Matches: 371, Mismatches: 68, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
214 1 0.00
215 7 0.02
216 362 0.98
217 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.30, T:0.15
Consensus pattern (216 bp):
AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAGAAGAAAGTACCGAAACCAAAGTT
GATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAAC
CAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGTA
CCAAAATCAAAGTTGGTTGAG
Done.