Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_186 ID=scaffold_186-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: 9743
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:459 original size:19 final size:19
Alignment explanation
Indices: 420--526 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
410 AAATTAAATC
420 TCTAAGA-T-CATATC-T-
1 TCTAAGATTGCATATCATA
435 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
454 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
473 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
492 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
511 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
527 CTTGAATATT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.09
16 1 0.01
17 6 0.07
18 1 0.01
19 67 0.82
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:481 original size:38 final size:38
Alignment explanation
Indices: 435--526 Score: 175
Period size: 38 Copynumber: 2.4 Consensus size: 38
425 GATCATATCT
435 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
*
473 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTACATATCATA
511 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
527 CTTGAATATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTACATATCATA
Found at i:1526 original size:128 final size:128
Alignment explanation
Indices: 1375--1661 Score: 405
Period size: 128 Copynumber: 2.2 Consensus size: 128
1365 GCTTACTTAG
* *
1375 TCTGCTCCAATGCAACTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAGAAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGAAAG
* ** * *
1440 ATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA-GAATTATTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATATG-ATTAGTGGCTTTAA
* * * * * * *
1503 TCTGCTCCACTGCAATTTTAGGGAGATAAGACTCGATGCGATTTGCTCTCTGTAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGAAAG
*
1568 ATAAGATCTGTGATTTTAATTCACTCCACTGCAACTTCAGGGAGATATGATTAGTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATATGATTAGTGGCTTTAA
* *
1631 TCTACTCCACTGTAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1662 TTCGCCATCT
Statistics
Matches: 139, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
128 138 0.99
129 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGAAAG
ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATATGATTAGTGGCTTTAA
Found at i:1630 original size:44 final size:43
Alignment explanation
Indices: 1158--2570 Score: 448
Period size: 44 Copynumber: 32.8 Consensus size: 43
1148 CTTTCTTGCG
** ***
1158 TCTACTCCACTGCAACTTCAGGGAGATAAGA-CCTGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * * *
1199 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* * * * * *
1242 TCCACTTCACTACAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGACTTTAA
* * ** * *
1286 TCTGCTCCACTCCAACTTCAGGGAGATAAGATTCGCCATCTTCAG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGA-CTTTAA
* * * * *
1331 TCTGC-CTCACTACAACTTCA-GGAGGATAAAGCTTGCTTAC-TTAG
1 TCTACTC-CACTGCAACTTCAGGGA-GAT-AAGATTG-TGACTTTAA
* * * * * *
1375 TCTGCTCCAATGCAACTTCAGGGAGATAAGACT-AGA-TGTGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* ** *
1416 TCTACT-CTCTGCAACTTCAGAAAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
** ** * * *
1459 TCCGCTCCACTGTGACTTTAGGGAGAT-AGAATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAG-ATT-GTGACTTTAA
* * * * * ***
1503 TCTGCTCCACTGCAATTTTAGGGAGATAAGACT-CGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * * * * *
1544 TTTGCT-CTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* *
1587 T-TCACTCCACTGCAACTTCAGGGAGATATGATTAGTGGCTTTAA
1 TCT-ACTCCACTGCAACTTCAGGGAGATAAGATT-GTGACTTTAA
* ** * *
1631 TCTACTCCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGA-CTTTAA
* * * * *
1676 TCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTAC-TTAG
1 TCTACTC-CACTGCAACTTCAGGGA-GATAA-GATTG-TGACTTTAA
* * * ***
1720 TCTGCTCCACTGCAACTTCAGGGAGATAAGACT-AGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * * *
1761 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* * * *
1804 TC-AGCTCAACTGCGACTTCAGGGAGAT-AGAATTATTGGCTTTAA
1 TCTA-CTCCACTGCAACTTCAGGGAGATAAG-ATT-GTGACTTTAA
* * * * *** ***
1848 TTTGCTCCACTGCAATTTTAGGGAGATAAGA-CCCGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * * *
1889 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* * * *
1932 TCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGACTTTAA
* * * ** *
1976 TCTGCTCCACTGTAACTTCGGGGAGATAAGATTCGCCATCTTTAG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGA-CTTTAA
* * * * *
2021 TCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTAC-TTAG
1 TCTACTC-CACTGCAACTTCAGGGA-GATAA-GATTG-TGACTTTAA
* * * * * ***
2065 TCTGCTCCACTGCAACTTCAGAGAGATAATACT-AGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * ** *
2106 TCTGCT-CTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
*** ** * * *
2149 TCCGTTCCACTGTGACTTTAGGGAGAT-AGAATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAG-ATT-GTGACTTTAA
* * * *** ***
2193 TCTGCTCCACTGCAATTTTAGGGAGATAAGA-CCCG-CTGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* * * * *
2234 TCTGCT-CTCTGCAACTTCAGAGAGATAATATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* * * * *
2277 TCCACTCCAGTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-GTGACTTTAA
* * * * *
2321 TCTGCTCCACTGTAACTTCGGGGAGATAAGATTCGCT-ATCTTCAG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATT-G-TGA-CTTTAA
* * * * *
2366 TCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTAC-TTAG
1 TCTACTC-CACTGCAACTTCAGGGA-GATAA-GATTG-TGACTTTAA
* * * * ***
2410 TCTTCTCCACTGCAACTTTAGGGAGATAAGACT-AGA-TGCGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
* ** * *
2451 TCTGCT-CTTTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TGTGACTTTAA
* ** * * * *
2494 T-TCGCTCCACTGTGACTTTAGGGAGATAGGATTATTGGCTTTAA
1 TCT-ACTCCACTGCAACTTCAGGGAGATAAGATT-GTGACTTTAA
*
2538 TCTACTCCACTAG-AACTTTAGGGAGATAAGATT
1 TCTACTCCACT-GCAACTTCAGGGAGATAAGATT
2571 CACCGTCGTG
Statistics
Matches: 994, Mismatches: 292, Indels: 169
0.68 0.20 0.12
Matches are distributed among these distances:
40 163 0.16
41 60 0.06
42 21 0.02
43 71 0.07
44 529 0.53
45 132 0.13
46 18 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
TCTACTCCACTGCAACTTCAGGGAGATAAGATTGTGACTTTAA
Found at i:1793 original size:345 final size:345
Alignment explanation
Indices: 1162--2568 Score: 2420
Period size: 345 Copynumber: 4.1 Consensus size: 345
1152 CTTGCGTCTA
* * *
1162 CTCCACTGCAACTTCAGGGAGATAAGACCTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* *
1227 GATCTGTGATTTTAATCCACTTCACTACAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
66 GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
**
1292 CCACTCCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
131 CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
* * * *
1357 TAAAGCTTGCTTACTTAGTCTGCTCCAATGCAACTTCAGGGAGATAAGACTAGATGTGATCTACT
196 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
*
1422 CTCTGCAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
261 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
1487 GAATTATTGGCTTTAATCTG
326 GAATTATTGGCTTTAATCTG
* * *
1507 CTCCACTGCAATTTTAGGGAGATAAGACTCGATGCGATTTGCTCTCTGTAACTTCAGAGAGATAA
1 CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* * * *
1572 GATCTGTGATTTTAATTCACTCCACTGCAACTTCAGGGAGATATGATTAGTGGCTTTAATCTACT
66 GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
1637 CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
131 CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
1702 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
196 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
* * * *
1767 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCAGCTCAACTGCGACTTCAGGGAGATA
261 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
*
1832 GAATTATTGGCTTTAATTTG
326 GAATTATTGGCTTTAATCTG
1852 CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1917 GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
66 GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
* *
1982 CCACTGTAACTTCGGGGAGATAAGATTCGCCATCTTTAGTCTGCCTCACTACAACTTCAGGAGGA
131 CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
* *
2047 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGAGAGATAATACTAGATGCGATCTGCT
196 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
* *
2112 CTCTGCAACTTCAAAGAGATAAGATCTGTGATTTTAATCCGTTCCACTGTGACTTTAGGGAGATA
261 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
2177 GAATTATTGGCTTTAATCTG
326 GAATTATTGGCTTTAATCTG
*
2197 CTCCACTGCAATTTTAGGGAGATAAGACCCGCTGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
* *
2262 TATCTGTGATTTTAATCCACTCCAGTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
66 GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
* *
2327 CCACTGTAACTTCGGGGAGATAAGATTCGCTATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
131 CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
* *
2392 TAAGGCTTGCTTACTTAGTCTTCTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCT
196 TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
* *
2457 CTTTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATTCGCTCCACTGTGACTTTAGGGAGATA
261 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
* *
2522 GGATTATTGGCTTTAATCTA
326 GAATTATTGGCTTTAATCTG
*
2542 CTCCACTAG-AACTTTAGGGAGATAAGA
1 CTCCACT-GCAATTTTAGGGAGATAAGA
2569 TTCACCGTCG
Statistics
Matches: 1003, Mismatches: 58, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
345 1002 1.00
346 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (345 bp):
CTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
GATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCT
CCACTGTAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGA
TAAGGCTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTGACTTTAGGGAGATA
GAATTATTGGCTTTAATCTG
Found at i:1871 original size:128 final size:128
Alignment explanation
Indices: 1720--2006 Score: 468
Period size: 128 Copynumber: 2.2 Consensus size: 128
1710 GCTTACTTAG
*
1720 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
*
1785 ATAAGATCTGTGATTTTAAT-CAGCTCAACTGCGACTTCAGGGAGATAGAATTATTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCA-CTCAACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
* * * *
1848 TTTGCTCCACTGCAATTTTAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
* *
1913 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCACTCAACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
* *
1976 TCTGCTCCACTGTAACTTCGGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
2007 TTCGCCATCT
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
128 143 0.99
129 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
ATAAGATCTGTGATTTTAATCCACTCAACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
Found at i:2219 original size:128 final size:128
Alignment explanation
Indices: 2065--2351 Score: 403
Period size: 128 Copynumber: 2.2 Consensus size: 128
2055 GCTTACTTAG
* *
2065 TCTGCTCCACTGCAACTTCAGAGAGATAATACTAGATGCGATCTGCTCTCTGCAACTTCAAAGAG
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAAAGAG
** ** *
2130 ATAAGATCTGTGATTTTAATCCGTTCCACTGTGACTTTAGGGAGATAGAATTATTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
* * * * * *
2193 TCTGCTCCACTGCAATTTTAGGGAGATAAGACCCGCTGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAAAGAG
* * *
2258 ATAATATCTGTGATTTTAATCCACTCCAGTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
66 ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
* * *
2321 TCTGCTCCACTGTAACTTCGGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGA
2352 TTCGCTATCT
Statistics
Matches: 139, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
128 139 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACCAGATGCGATCTGCTCTCTGCAACTTCAAAGAG
ATAAGATCTGTGATTTTAATCCACTCCACTGCAACTTCAGGGAGATAGAATTATTGGCTTTAA
Found at i:2610 original size:50 final size:50
Alignment explanation
Indices: 2529--2640 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
2519 ATAGGATTAT
* * ** * *
2529 TGGCTTTAATCTACTCCACTAGAACTTTAGGGAGATAAGATTCACCGTCG
1 TGGCTTCAATCTACTCCACTACAACACTAGGGAAAAAAGATTCACCGTCG
* * * *
2579 TGGCTTCAATCTACTCCGCTACAACACTAGGGAAAAAATATTCGCCGTTG
1 TGGCTTCAATCTACTCCACTACAACACTAGGGAAAAAAGATTCACCGTCG
*
2629 TGGTTTCAATCT
1 TGGCTTCAATCT
2641 TTTCCATTGC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
TGGCTTCAATCTACTCCACTACAACACTAGGGAAAAAAGATTCACCGTCG
Found at i:2772 original size:44 final size:44
Alignment explanation
Indices: 2722--2843 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
2712 ATTTGCTATT
*
2722 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGTTGCTCAGGGAGATAGGACTT-ACAATC
*
2766 TTCAACCTATTCCACTGTTGAC-CAGGGAGATATGACTTACAATC
1 TTCAACCTATTCCACTGTTG-CTCAGGGAGATAGGACTTACAATC
*
2810 TTCAACCTATTCCACTGCTG-TCCAGGGAGATAGG
1 TTCAACCTATTCCACTGTTGCT-CAGGGAGATAGG
2844 GTTGGGGTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
44 67 0.96
45 3 0.04
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTGTTGCTCAGGGAGATAGGACTTACAATC
Found at i:2905 original size:88 final size:88
Alignment explanation
Indices: 2843--3331 Score: 800
Period size: 88 Copynumber: 5.6 Consensus size: 88
2833 AGGGAGATAG
* * *
2843 GGTTGGGGTCATCGATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
2908 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * * *
2931 AGCTGGTGTCTTCGATCTTCTTCGCTGTCGGTGCAGGAAGGAAAGATCTACTATTTTTAACCTGC
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
2996 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
3019 GGTTGGTGTCTTCGATCTACTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
3084 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
3107 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGC
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3172 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
3195 GGTTAGTGTCTTCGATCTGC-TCGCTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACCTGC
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
3259 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
3282 GGTTGGTGTCTTCGATCTGCTTCACTGTCGGTGTAGGAAGGCAATATCTG
1 GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
3332 TTATCTTCAC
Statistics
Matches: 374, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
87 86 0.23
88 288 0.77
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
GGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAA
Done.