Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.009G254600.2-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: 3147
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--1526 Score: 1004
Period size: 117 Copynumber: 7.9 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 GGAGAAAAGTGTTGAGCAAATGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGG
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * *
962 CTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
** * * *
1027 GAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGG
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * ** * * *
1079 CTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
* *
1144 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTTGCTC---AA--AG-
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
** ** * * * *
1190 CTGAAGAAGAGAAGGTACCGCAATTGATA-TTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAA
1 CTGAAGCTGAGAAGGTACCAAAACTGA-AGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
****
1254 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGACGCTGA-A
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * * * *
1306 GCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAACC--
1 -CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAA
** * * * *
1369 -GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGG
65 GGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
* * * * * *
1421 CTGAACCTGAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAG
1 CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
1486 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
66 GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
1527 TGAGAAGAAG
Statistics
Matches: 671, Mismatches: 114, Indels: 40
0.81 0.14 0.05
Matches are distributed among these distances:
111 90 0.13
112 2 0.00
114 95 0.14
116 2 0.00
117 371 0.55
118 3 0.00
119 1 0.00
120 8 0.01
121 1 0.00
122 4 0.01
123 94 0.14
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (117 bp):
CTGAAGCTGAGAAGGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAG
GAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCGAAAAGGAGA
Found at i:1028 original size:240 final size:237
Alignment explanation
Indices: 600--1526 Score: 1044
Period size: 240 Copynumber: 4.0 Consensus size: 237
590 AAACTGCAGC
* * * * *
600 TGAAGCTGAAGCTGCA-AAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTA
1 TGAAGCTGAAGCTG-AGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTA
* ** * ** * *
664 CCCAAGGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGACTGAAGC
65 ACCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGC
** *
729 TGAGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA
130 TGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA
* * *
794 GTGTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGA
195 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT-C-AAA-GAGGA
* ** * *
840 TGAAGCTGAACCTGAGAATTTACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTAC
1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA
* *
905 CCAAGGAGAAAAGTGTTGAGCAAATGGTGCCAAAACCAAAGTTAGTCGTAAAGGAGGCTGAAGCT
66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT
* * *
970 GAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAACCAAGGAGGAAAG
131 GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
** * *
1035 CATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAA-AGGA
196 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC-AAAGAGGA
* * * * ** * *
1077 -G--GCTGAAGCTGAGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAA
1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA
* * *
1139 CCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCACAGTT-GCTC---AA--A-GCTGAAGA
66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAG-TCGAAAAGGAGGCTGAAGC
* ** * * * * *
1197 AGAGAAGGTACCGCAATTGATATTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAA
130 TGAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAA
* *
1262 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTC---GACGC
195 GTGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAAGAGGA
* * * *
1302 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGTAA
1 TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA
* ** * * * * *
1367 CC---GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAACCT
66 CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT
* * * *
1429 GAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
131 GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
1494 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
196 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGT
1527 TGAGAAGAAG
Statistics
Matches: 583, Mismatches: 91, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
225 36 0.06
226 2 0.00
228 147 0.25
229 1 0.00
230 1 0.00
231 95 0.16
233 1 0.00
234 91 0.16
236 1 0.00
237 4 0.01
239 5 0.01
240 199 0.34
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (237 bp):
TGAAGCTGAAGCTGAGAAAGTACCAAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAA
CCAAGGAGAAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTTAGTCGAAAAGGAGGCTGAAGCT
GAGAAGGTACCAAAACTGATGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
TGTTGAGCAAAAGGTGCCAAAACCAAAGTTGGTCAAAGAGGA
Found at i:1499 original size:342 final size:347
Alignment explanation
Indices: 601--1524 Score: 1067
Period size: 357 Copynumber: 2.6 Consensus size: 347
591 AACTGCAGCT
* * * * * * ** *
601 GAAGCTGAAGCTGCAAAGGCATCAAAACTGAAGTTGGCTGAAGAGAAGAAACCCGAAGAGGTACC
1 GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC
* ** * ** * * * *** * *
666 CAAGGAGAAAAGTGTTGAGCAAGTGGTGCCAAAACCAATGCCAGTTGAAAAGGAGACTGAAGCTG
66 C-A-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTG
** * * *
731 AGAAGGTACTGAAACTGAAGTTGGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT
129 AGAAGGTACCAAAACAGATGATGGCTG-AAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT
* * * * **
796 GTTAAGCAAAAGGTGCAAAAACCAAAGCTGGTCCAAAAGGAGGATGAAGCTGAACCTGAGAATTT
193 GTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCC-AAA-GAGGATGAA-C-GAA-C-GAGAAGGT
* * * *
861 ACCAAAACTGAAGTTTGCTGAAAAGAAGAAACCTGAAGAGGTACCCAAGGAGAAAAGTGTTGAGC
252 ACCAAAACTGAAGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGC
*
926 AAATGGTGCCAAAACCAAAGTTAGTCGTAAAG
317 AAAAGGTGCCAAAACCAAAGTTAGTCG-AAAG
* * *
958 GAGGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCTGAAAAGAAGAAACCTGAAGAGGTAAC
1 GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC
* * *
1023 CAAGGAGGAAAGCATTGAGCAAAAGGTGCCCAAACCAAATTTGGTCGAAAAGGAGGCTGAAGCTG
66 C-A-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTG
* * * *
1088 AGAAGGTACCAAAACAGATGATGGCTGAACTGAAGAAACTTGAAGAGATAACCAAGGAGGAAAGT
129 AGAAGGTACCAAAACAGATGATGGCTGAA-AGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGT
* * **
1153 GTTGAGCAAAAGGTGCCAAAACCACAGTTGCT-C-AA-A-GCTGAA-GAA-GAGAAGGTACCGCA
193 GTTGAGCAAAAGGTGCCAAAACCAAAGTTGCTCCAAAGAGGATGAACGAACGAGAAGGTACCAAA
* *
1212 ATTGATA-TTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGGAAAGTGTTGAGCAAAAG
258 ACTGA-AGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGCAAAAG
* *
1276 GTGCCAAAACCAAAGTTGGTCG-ACG
322 GTGCCAAAACCAAAGTTAGTCGAAAG
* *
1301 CTGAAGCTGAAGCTGAGAAA-GTACCAAAACTGATGTTGTCCGAAAAGAAGAAACCTAAAGAGGT
1 --GAAGCTGAAGCTGA-AAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGT
*
1365 AACC-GAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAACCT
63 AACCAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCT
*
1429 GAGAAGGTGCCAAAACAGATGATGGCTGCAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
128 GAGAAGGTACCAAAACAGATGATGGCTG-AAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAG
1494 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTG
192 TGTTGAGCAAAAGGTGCCAAAACCAAAGTTG
1525 GTTGAGAAGA
Statistics
Matches: 497, Mismatches: 64, Indels: 27
0.85 0.11 0.05
Matches are distributed among these distances:
342 143 0.29
343 4 0.01
345 143 0.29
346 4 0.01
348 3 0.01
351 5 0.01
352 1 0.00
354 2 0.00
356 3 0.01
357 189 0.38
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.15
Consensus pattern (347 bp):
GAAGCTGAAGCTGAAAAGGTACCAAAACTGACGTTGGCCGAAAAGAAGAAACCTAAAGAGGTAAC
CAGAGGAAAGCATTCAGCAAAAGATGCCCAAACCAAAGTTGGTCGAAAAGGAGGCTGAAGCTGAG
AAGGTACCAAAACAGATGATGGCTGAAAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTT
GAGCAAAAGGTGCCAAAACCAAAGTTGCTCCAAAGAGGATGAACGAACGAGAAGGTACCAAAACT
GAAGTTGGCAGAAAAGAAGAAACCTAAAGAGATACCCAAGGAGAAAAGTGTTGAGCAAAAGGTGC
CAAAACCAAAGTTAGTCGAAAG
Found at i:1510 original size:72 final size:72
Alignment explanation
Indices: 1459--2206 Score: 671
Period size: 72 Copynumber: 10.4 Consensus size: 72
1449 GATGGCTGCA
* * * * * *
1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
1524 GGTTGAG
66 GGTTGAG
* * *
1531 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
1596 GGTTGAG
66 GGTTGAG
* * *
1603 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
1668 GGTTGAG
66 GGTTGAG
* * * * * ** *
1675 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAACCAAAGT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAA-AAGGTACCAAAACCAAAGT
*
1739 TGATTGAG
65 TGGTTGAG
* * * ** * *
1747 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
1812 GGTTGAG
66 GGTTGAG
* * * * * ** * * *
1819 AAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAA-GCACCAAAATCAAAGT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGA-GAAAAAGGTACCAAAACCAAAGT
1883 TGGTTGAG
65 TGGTTGAG
* ** * * * * * * ***
1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* *
1956 GATCGAG
66 GGTTGAG
* *** * * * * * *
1963 AAGAAGGAACCTGAAGACACACCCAAGAAGGG-GAGTGTTGAGGAAAATGTACCAAAATCAAGGC
1 AAGAAGGAACCTAAAGAGGTACCCAAG-GGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT
2027 TGGTTGA-
65 TGGTTGAG
* * * * * * *
2034 AACTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGGTACCAAAACTAAAGT
1 AA-GAAGGAACCTAAAGAGGTACCCAAGGGGGAGAGTGTTGAGAAAAAGGTACCAAAACCAAAGT
2099 TGGTTGAG
65 TGGTTGAG
* * * * * * *
2107 AAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCAAAACCAAAG
1 AAGAAGGAACCT-AAAGAGGTACCCAAGGGGGAGAGTG-TTGAGAAAAAGGTACCAAAACCAAAG
*
2170 TTGGTTGAA
64 TTGGTTGAG
* * * *
2179 AATAAGGAACTTGAAGAGGTACCTAAGG
1 AAGAAGGAACCTAAAGAGGTACCCAAGG
2207 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:1692 original size:144 final size:144
Alignment explanation
Indices: 1459--2226 Score: 763
Period size: 144 Copynumber: 5.3 Consensus size: 144
1449 GATGGCTGCA
* * * * *
1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAAAAGGTGCCAAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * * * * *
1524 GGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAAC
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
1589 CAAAGTTGGTTGAG
131 CAAAGTTGGTTGAG
* * * *
1603 AAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGTACCAAAATCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* ** * * * * *
1668 GGTTGAGAAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGA-AAAGAAATTACCGAAA
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAA-AAAGTACCAAAA
*
1732 CCAAAGTTGATTGAG
130 CCAAAGTTGGTTGAG
* * * * * * *
1747 AATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * * * * * *
1812 GGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGCACCAAAAT
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
1877 CAAAGTTGGTTGAG
131 CAAAGTTGGTTGAG
* * * * * * * * * ***
1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAGTT
* * ** * * * *
1956 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT
66 GGTTGAGAAGAAGGAACCTGAAGAGGCACCCAAGGAGGAGAGTGTTGAGGAAAAAGTACCAAAAC
* *
2021 CAAGGCTGGTTGA-
131 CAAAGTTGGTTGAG
* * * * * *
2034 AACTAAGGAACCTGAAGAGGAACCCAAAGG-GGAGAGTATTGAGGAAAAGGTACCAAAACTAAAG
1 AA-GAAGGAACCTGAAGAGGTACCC-AAGGAGGAGACTGTTGAGAAAAAGGTACCAAAACCAAAG
* * * *
2098 TTGGTTGAGAAGAAGGAACCTGGAA-AGGCAACCAAAGAGGAAAG-GCTTGAGGAAAAGGTACCA
64 TTGGTTGAGAAGAAGGAACCT-GAAGAGGCACCCAAGGAGGAGAGTG-TTGAGGAAAAAGTACCA
*
2161 AAACCAAAGTTGGTTGAA
127 AAACCAAAGTTGGTTGAG
* * * * * *
2179 AATAAGGAACTTGAAGAGGTACCTAAGGAGAAGACTGTCGAGAGAAAG
1 AAGAAGGAACCTGAAGAGGTACCCAAGGAGGAGACTGTTGAGAAAAAG
2227 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:1845 original size:216 final size:216
Alignment explanation
Indices: 1459--2119 Score: 747
Period size: 216 Copynumber: 3.1 Consensus size: 216
1449 GATGGCTGCA
* * * * * * * * *
1459 AAGAAGAAACCTGAAGAGGTACCCAAGGAGGAAAGTGTTGAGCAA-AAGGTGCCAAAACCAAAGT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAG-AAGAAAGTACCGAAACCAAAGT
* * * * *
1523 TGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGTGAGTGTTGAGGAAAAGGTATCAAAA
65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA
* * * * *
1588 CCAAAGTTGGTTGAGAAGAAGGAACCTAAAGAGGTACCCAAGGGGGAGACTGTTGAGAAAAAAGT
130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT
1653 ACCAAAATCAAAGTTGGTTGAG
195 ACCAAAATCAAAGTTGGTTGAG
* * * *
1675 AAAAAGGAACCTGAAGAGATACCCAAGGTGGAGGGTGTTGAA-AAGAAATTACCGAAACCAAAGT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATT-AAGAAGAAAGTACCGAAACCAAAGT
* * * ** *
1739 TGATTGAGAATAAGGAACCTAAAGAGTTACCCAAGGTGGAGACCGATGAGGAAAAGGTACCAAAA
65 TGATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAA
* * * ** * *
1804 CCAAAGTTGGTTGAGAAGCAGAAACCTGATGAGGCACCCAAGGAAGAGAGGGTTGAGGAAAAAGC
130 CCAAAGTTGGTTGAGAAGCAGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAGT
1869 ACCAAAATCAAAGTTGGTTGAG
195 ACCAAAATCAAAGTTGGTTGAG
* * * * **
1891 AAGAAGGAACTTGGAGAGATACCTAAGGTGGAGAGTATTAAGAAGAAGGTATGGAAACCAAAGTT
1 AAGAAGGAACCTGAAGAGATACCCAAGGTGGAGAGTATTAAGAAGAAAGTACCGAAACCAAAGTT
* * * * * * * *
1956 GATCGAGAAGAAGGAACCTGAAGACACACCCAAGAAGGGGAGTGTTGAGGAAAATGTACCAAAAT
66 GATTGAGAAGAAGGAACCTAAAGAGATACCCAAGGAGGAGAGTGTTGAGGAAAAGGTACCAAAAC
* * * * *
2021 CAAGGCTGGTTGA-AA-CTAAGGAACCTGAAGAGGAACCCAAAGGGGAGAGTATTGAGGAAAAGG
131 CAAAGTTGGTTGAGAAGC--AGGAACCTGAAGAGGAACCCAAGGGGGAGAGTGTTGAGGAAAAAG
2084 TACCAAAA-CTAAAGTTGGTTGAG
194 TACCAAAATC-AAAGTTGGTTGAG
2107 AAGAAGGAACCTG
1 AAGAAGGAACCTG
2120 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.