Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011132.1 Kokia drynarioides strain JFW-HI SEQ_126105, whole genome shotgun sequence
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: 4802
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.25
Warning! 367 characters in sequence are not A, C, G, or T
Found at i:896 original size:62 final size:62
Alignment explanation
Indices: 804--986 Score: 222
Period size: 62 Copynumber: 3.0 Consensus size: 62
794 TAAGTTTGAA
* * * *
804 AAGTTCAGAAGTTCACCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTGAC
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
* * * * * * *
866 AAGTTTGGAAGTTCGTCCAAGAATCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCAT
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
* ** * *
928 ATGTTCGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCATGTAACTAAGTTTTT
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
987 AATCAACAGT
Statistics
Matches: 99, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 99 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (62 bp):
AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
Found at i:1236 original size:62 final size:62
Alignment explanation
Indices: 1138--1323 Score: 246
Period size: 62 Copynumber: 3.0 Consensus size: 62
1128 CTCATGAAAG
* * * * *
1138 TTTGACAAGTTCGAAACTTCATCCAAGAATCAAGAGAGAAATAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * * *
1200 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGAT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * ** *
1262 TTTCATAAGTTCGGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
1324 ATTAATCAAC
Statistics
Matches: 106, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 106 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (62 bp):
TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:1256 original size:340 final size:340
Alignment explanation
Indices: 739--1540 Score: 1390
Period size: 340 Copynumber: 2.4 Consensus size: 340
729 AAAATTCTCT
* * * ** * * ** *
739 AAGGAATGGATCGTCATGAATTCTGTAAGGTGCCGAAGTTATAAAAGAACTCGTTTAAGTTTGAA
1 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
* *
804 AAGTTC-AGAAGTTCACCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTGACAA
66 AAGTTCGA-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAA
* *
868 GTTTGGAAGTTCGTCCAAGAATCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATATGTT
130 GTTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTT
* *
933 CGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCATGTAACTAAGTTTTTAATCAACAGTC
195 CGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTC
*
998 CAAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTATTGAGCACGGAATG
260 CAAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTATCGAGCACGGAATG
1063 TTTGGAAATTTGCTCA
325 TTTGGAAATTTGCTCA
1079 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
1 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
* * *
1144 AAGTTCGAAACTTCATCCAAGAATCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTGACAAG
66 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAG
1209 TTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTTC
131 TTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTTC
*
1274 GGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCC
196 GGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCC
*
1339 AAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTCGAGCACGGAATGT
261 AAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTATCGAGCACGGAATGT
1404 TTGGAAATTTGCTCA
326 TTGGAAATTTGCTCA
1419 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
1 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
1484 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
66 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT
1541 CTAATTCAAA
Statistics
Matches: 436, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
340 435 1.00
341 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (340 bp):
AAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTGAC
AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAG
TTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTTC
GGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCC
AAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTATCGAGCACGGAATGT
TTGGAAATTTGCTCA
Found at i:1740 original size:215 final size:214
Alignment explanation
Indices: 1268--1971 Score: 835
Period size: 215 Copynumber: 3.3 Consensus size: 214
1258 AGATTTTCAT
* ** *
1268 AAGTTCGGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAA-TC-
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT-TTAATTCA
* * * *
1331 AACAGTCCAAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTG-ATATTTCTCGAGC
65 AACA--CCAAAACTTGTTTAC-AAATGACAAACTATTTAGACCAAATGATGCA-ATTTCACGAGC
* * * * * *
1395 ACGGAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTA
126 ATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTA
* * *
1460 TAAAAGAACTCATGAAAGTTTGAC
191 TAAAAGAACTCGTAAAAGTTTAAC
*
1484 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCA
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT-TAATTCA
* * * *
1549 AACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTATGCGATTTCCCGAGCATG
65 AACACCAAAACTTGTTTACAAA-TGACAAACTATTTAGACCAAATGATGCAATTTCACGAGCATG
* * * *
1614 GAATGTTCGAAAAATTGCTCGAAGGAATAGAT-GTCTTGAATACTATCAGGAACCGAAGATATAA
129 GAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAA
* *
1678 AAGAAATCGCAAAAGTTTAAC
194 AAGAACTCGTAAAAGTTTAAC
* * * *
1699 AAGTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCA
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCA
* * * * * * * *
1764 AAAACCAAAACATGGTTACGAAATGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATG
65 AACACCAAAACTTGTTTAC-AAATGACAAACTATTTAGACCAAATGATGCAATTTCACGAGCATG
* * * * **
1829 GAGTGTTCGAAAAATT-CTCTAAGGAATGGATCGTCTTGAATTCTGTAAGGTGCCGAAGTTATAA
129 GAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAA
*
1893 AAGAACTCGTATAAGTTTGAA-
194 AAGAACTCGTAAAAGTTT-AAC
* *
1914 AAGTTCAGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
1972 TGACAAGTTT
Statistics
Matches: 418, Mismatches: 61, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
214 17 0.04
215 258 0.62
216 137 0.33
217 2 0.00
218 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (214 bp):
AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAA
ACACCAAAACTTGTTTACAAATGACAAACTATTTAGACCAAATGATGCAATTTCACGAGCATGGA
ATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAAA
GAACTCGTAAAAGTTTAAC
Found at i:1998 original size:62 final size:62
Alignment explanation
Indices: 1914--2093 Score: 243
Period size: 62 Copynumber: 2.9 Consensus size: 62
1904 TAAGTTTGAA
* * *
1914 AAGTTCAGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGAC
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
* * * * * *
1976 AAGTTTGGAAGTTCATCCAAGAATCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCAT
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
* ** *
2038 ATGTTCGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTT
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
2094 ATTAATCAAC
Statistics
Matches: 100, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 100 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (62 bp):
AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCAC
Found at i:2509 original size:215 final size:214
Alignment explanation
Indices: 2040--2648 Score: 701
Period size: 215 Copynumber: 2.8 Consensus size: 214
2030 ATTTTCATAT
* ** *
2040 GTTCGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAA-TC-AA
1 GTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT-TTAATTCAAA
* * **
2103 CAGTCCAAAACTTGTTTACAAAATGACAAACTATTTT-GACCACATGGTG-ATATTTCTTGAGCA
65 CA--CCAAAACTTGTTTAC-AAATGACAAACT-TTTTAGACCAAATCGTGCA-ATTTCACGAGCA
* * * * * * *
2166 CGGAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTAT
125 TGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGATAT
* **
2231 AAAAGAACTCATGAAAGTTTGACAA
190 AAAAGAAATCACAAAAGTTTGACAA
2256 GTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCAAA
1 GTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT-TAATTCAAA
* * *
2321 CACCAAAACTTGTTTACAAACTGACAAACTTTTTAGACCAAATTGTGCGATTTCCCGAGCATGGA
65 CACCAAAACTTGTTTACAAA-TGACAAACTTTTTAGACCAAATCGTGCAATTTCACGAGCATGGA
* * *
2386 ATGTTCGAAAAATTGCTCGAAGGAATAGAT-GTCTTGAATACTATCAGGAACCGAAGATATAAAA
129 ATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGATATAAAA
*
2450 GAAATCGCAAAAGTTTGACAA
194 GAAATCACAAAAGTTTGACAA
* * * * *
2471 GTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAA
1 GTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCAAA
* * * * * *
2536 AACCAAAACATGGTTACGAAATGACAAACTTTTTAGAGCATA-CGATGCAATTTTACGAGCATGG
65 CACCAAAACTTGTTTAC-AAATGACAAACTTTTTAGACCAAATCG-TGCAATTTCACGAGCATGG
* * * * *
2600 AGTGTTCAAAAAATT-CTCTAAGGAATGGATCGTCTTGAATCCTGTAAGG
128 AATGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGG
2649 TGCGGAAGTT
Statistics
Matches: 339, Mismatches: 44, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
214 14 0.04
215 188 0.55
216 131 0.39
217 2 0.01
218 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (214 bp):
GTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAAAC
ACCAAAACTTGTTTACAAATGACAAACTTTTTAGACCAAATCGTGCAATTTCACGAGCATGGAAT
GTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGATATAAAAGA
AATCACAAAAGTTTGACAA
Found at i:2558 original size:770 final size:770
Alignment explanation
Indices: 951--2658 Score: 2942
Period size: 770 Copynumber: 2.2 Consensus size: 770
941 CATCCTGGAA
* * * ** * * *
951 CCAAGAGAGAAACAATTCTCATGTAACTAAGTTTTTAA-TCAACAGTCCAAAACTTGTTTACAAA
1 CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAA-AAACCAAAACATGGTTACGAA
* * * * * * * * * *
1015 ATGACAAACTATTTT-GACCACATGGTG--ATATTTATTGAGCACGGAATGTTTGGAAATTTGCT
65 ATGACAAACT-TTTTAGAGCATACGATGCAAT-TTTA-CGAGCATGGAGTGTTCGAAAAATT-CT
* * ** *
1077 CAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCATGAAAGTTTG
126 CTAAGGAATGGATCGTCTTGAATACTGTAAGGTGCCGAAGTTATAAAAGAACTCATGAAAGTTTG
* * * *
1142 ACAAGTTCGAAACTTCATCCAAGAATCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTGACA
191 AAAAGTTCGAAACTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACA
*
1207 AGTTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGT
256 AGTTTGGAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGT
*
1272 TCGGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGT
321 TCGGAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGT
1337 CCAAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTCGAGCACGGAAT
386 CCAAAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTCGAGCACGGAAT
1402 GTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGA
451 GTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGA
1467 ACTCATGAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTA
516 ACTCATGAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTA
1532 AATAAGTTTCTAATTCAAACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTAT
581 AATAAGTTTCTAATTCAAACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTAT
1597 GCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATAGATGTCTTGAATACTATCA
646 GCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATAGATGTCTTGAATACTATCA
1662 GGAACCGAAGATATAAAAGAAATCGCAAAAGTTTAACAAGTTCGGATGTTCGTCCAAGAG
711 GGAACCGAAGATATAAAAGAAATCGCAAAAGTTTAACAAGTTCGGATGTTCGTCCAAGAG
1722 CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAA
1 CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAA
1787 TGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATGGAGTGTTCGAAAAATTCTCTAAG
66 TGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATGGAGTGTTCGAAAAATTCTCTAAG
* *
1852 GAATGGATCGTCTTGAATTCTGTAAGGTGCCGAAGTTATAAAAGAACTCGT-ATAAGTTTGAAAA
131 GAATGGATCGTCTTGAATACTGTAAGGTGCCGAAGTTATAAAAGAACTCATGA-AAGTTTGAAAA
*
1916 GTTC-AGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGT
195 GTTCGA-AACTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGT
* *
1980 TTGGAAGTTCATCCAAGAATCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATATGTTCG
259 TTGGAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTTCG
2045 GAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCCA
324 GAAGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCCA
*
2110 AAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTTGAGCACGGAATGTT
389 AAACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTCGAGCACGGAATGTT
2175 TGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACT
454 TGGAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACT
2240 CATGAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
519 CATGAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* *
2305 AAGTTTCTAATTCAAACACCAAAACTTGTTTACAAACTGACAAACTTTTTAGACCAAATTGTGCG
584 AAGTTTCTAATTCAAACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTATGCG
2370 ATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATAGATGTCTTGAATACTATCAGGA
649 ATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATAGATGTCTTGAATACTATCAGGA
*
2435 ACCGAAGATATAAAAGAAATCGCAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAG
714 ACCGAAGATATAAAAGAAATCGCAAAAGTTTAACAAGTTCGGATGTTCGTCCAAGAG
2492 CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAA
1 CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAA
*
2557 TGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATGGAGTGTTCAAAAAATTCTCTAAG
66 TGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATGGAGTGTTCGAAAAATTCTCTAAG
* *
2622 GAATGGATCGTCTTGAATCCTGTAAGGTGCGGAAGTT
131 GAATGGATCGTCTTGAATACTGTAAGGTGCCGAAGTT
2659 CAGAAGTTCA
Statistics
Matches: 890, Mismatches: 41, Indels: 13
0.94 0.04 0.01
Matches are distributed among these distances:
769 2 0.00
770 791 0.89
771 87 0.10
772 8 0.01
773 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (770 bp):
CCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAAACCAAAACATGGTTACGAAA
TGACAAACTTTTTAGAGCATACGATGCAATTTTACGAGCATGGAGTGTTCGAAAAATTCTCTAAG
GAATGGATCGTCTTGAATACTGTAAGGTGCCGAAGTTATAAAAGAACTCATGAAAGTTTGAAAAG
TTCGAAACTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTT
GGAAGTTCATCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAGTTCGGA
AGTTCATCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAATCAACAGTCCAAA
ACTTGTTTACAAAATGACAAACTATTTTGACCACATGGTGATATTTCTCGAGCACGGAATGTTTG
GAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCA
TGAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
GTTTCTAATTCAAACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTATGCGAT
TTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATAGATGTCTTGAATACTATCAGGAAC
CGAAGATATAAAAGAAATCGCAAAAGTTTAACAAGTTCGGATGTTCGTCCAAGAG
Found at i:3125 original size:216 final size:216
Alignment explanation
Indices: 2654--3144 Score: 655
Period size: 216 Copynumber: 2.3 Consensus size: 216
2644 TAAGGTGCGG
* *
2654 AAGTTC-AGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTG
1 AAGTTCGA-AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA-GTTTTAATTC
* * * * *
2718 AAAGACCAAATCCTGTTTGCAAAATGACAAACTATTCAGACCAAATGATGCGATTTCTCGAGCAT
64 AAACACCAAAACCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCAC
* * * *
2783 GGAAATCTTCGAAAAACTGCCCGAAAGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTAT
129 GGAAATCTTCGAAAAACTGCCCGAAAGAACGGATCCTCCTGAATACTTTAAGGAACCAAAGTTAT
* * *
2848 AAAAGAACTCATGAAAGTTTGAC
194 AAAAGAAATCATAAAAGTTTGAA
2871 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCA
1 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT-TAATTCA
* * * * *
2936 AACACCAAAACTTGTTTACAAACTGACAAACTGTTTAGACCAAATTATGCGATTTCCCGAGCACG
65 AACACCAAAACCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCACG
* * * * * *
3001 G-AATGTTCGAAAAATTGCTCGAAGGAACGGATCCTCCTGAATACTTT-CGAGAATCAAAGTTAT
130 GAAATCTTCGAAAAACTGCCCGAAAGAACGGATCCTCCTGAATACTTTAAG-GAACCAAAGTTAT
*
3064 AAAAGAAATCGTAAAAGTTTGAA
194 AAAAGAAATCATAAAAGTTTGAA
* * * *
3087 AATTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
1 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
3145 TGACAAGTTT
Statistics
Matches: 241, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
215 2 0.01
216 126 0.52
217 112 0.46
218 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (216 bp):
AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAA
ACACCAAAACCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCCCGAGCACGG
AAATCTTCGAAAAACTGCCCGAAAGAACGGATCCTCCTGAATACTTTAAGGAACCAAAGTTATAA
AAGAAATCATAAAAGTTTGAA
Found at i:3166 original size:62 final size:62
Alignment explanation
Indices: 3090--3266 Score: 264
Period size: 62 Copynumber: 2.9 Consensus size: 62
3080 GTTTGAAAAT
* *
3090 TTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAG
1 TTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCACAAG
* * * * *
3152 TTTGGAAGTTCGTCCAAGAACCGAGAGAGAAACAATTCTCACGTGAATAAGATTTTCATAAG
1 TTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCACAAG
** *
3214 TTCGGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTT
1 TTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
3267 ATTAATCAAC
Statistics
Matches: 101, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 101 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (62 bp):
TTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTCACAAG
Found at i:4170 original size:215 final size:215
Alignment explanation
Indices: 3710--4523 Score: 902
Period size: 215 Copynumber: 3.8 Consensus size: 215
3700 AGATTTTCAT
* ** *
3710 AAGTTCGGAAGTTCGTCCTGGAACCAAGAGAGAAACAATTCTCACGTAACTAAGTTATTAA-TC-
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT-TTAATTCA
* * * * * **
3773 AACAGTCCAATACTTGTTTACAAAATGACAAATTATTTTGACCACATGGTGATATTTCTCGAGCA
65 AACA--CCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCA
* * * *
3838 CGGAATGTTTGAAAATTTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTAT
128 TGGAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTAT
* * *
3903 AAAAGAACTCATGAAAGTTTGAC
193 AAAAGAAATCGTAAAAGTTTGAC
*
3926 AAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTCTAATTCA
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTT-TAATTCA
* * * * *
3991 AACACCAAAACTTGTTCACAAACTGACAAACTGTTTAGACCAAATTATGCGATTTCCCGAGCATG
65 AACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATG
* * * * *
4056 GAATTTTTGAAAAATTGCTCGAAGGAATAGAT-GTCTTGAATACTATCAGGAACCGAAGATATAA
130 GAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAA
*
4120 AAGAAATCGCAAAAGTTTGAC
195 AAGAAATCGTAAAAGTTTGAC
* * * *
4141 AAGTTCGGATGTTCGTCCAAGAGCCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCA
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG-TTTTAATTCA
* * * * * * * *
4206 AAAACCAAAACATGGTTACTAAATGACAAACTTTTTAGACCATACGATGCAATTT-TACGAGCAT
65 AACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCT-CGAGCAT
* ** * * * * * **
4270 GGAGTGTTCAAAAAATT-CTCTAAGGAATGGATCATCTTGAATTCTGTAAAGTTCCGAAGTTATA
129 GGAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATA
* * *
4334 AAAGAAGTCGTACAAGTTTGAA
194 AAAGAAATCGTAAAAGTTTGAC
* * * *
4356 AAGTTCAGAAGTTCACCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAACTAA
1 AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA-GTTTTAATTCA
* * * *
4421 AAGACCAAATCCTGTTTACAAAATGACAAACTATTCAGACCAAATGATGCGATTTCTCGAGCATG
65 AACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATG
* * * *
4486 GAAATCTTCGAAAAACTGCCCGAAA-GAATGGATCGTCT
130 G-AATGTTTGAAAAATTGCTC-AAAGGAATGGATCGTCT
4524 NNNNNNNNNN
Statistics
Matches: 497, Mismatches: 90, Indels: 21
0.82 0.15 0.03
Matches are distributed among these distances:
214 13 0.03
215 316 0.64
216 146 0.29
217 16 0.03
218 6 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (215 bp):
AAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTAATTCAA
ACACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGG
AATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTATAAGGAACCGAAGTTATAAA
AGAAATCGTAAAAGTTTGAC
Done.