Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008694.1 Hibiscus syriacus cultivar Beakdansim tig00111723_pilon, 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: 1352611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:458731 original size:19 final size:19
Alignment explanation
Indices: 458709--458749 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
458699 TTTTAAAGGG
458709 TTTTCAAAATGAGTGAACAT
1 TTTTCAAAATGAGTG-ACAT
* *
458729 TTTTTAAAGTGAGTGACAT
1 TTTTCAAAATGAGTGACAT
458748 TT
1 TT
458750 GTATTCGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (19 bp):
TTTTCAAAATGAGTGACAT
Found at i:463086 original size:44 final size:44
Alignment explanation
Indices: 463031--463123 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
463021 ATTTTCTTTT
* * *
463031 GTGGCGTTTGTTCCAAAAAATGCCGCTAAATGTTCTAACATATA
1 GTGGTGTTTGTTCCAAAAAATGCAGCTAAATATTCTAACATATA
* *
463075 GTGGTGTTTGTTCCTAAAAATGCAGCTAAATATTCTGACATATA
1 GTGGTGTTTGTTCCAAAAAATGCAGCTAAATATTCTAACATATA
463119 GTGGT
1 GTGGT
463124 ATTTTTTTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (44 bp):
GTGGTGTTTGTTCCAAAAAATGCAGCTAAATATTCTAACATATA
Found at i:463335 original size:21 final size:21
Alignment explanation
Indices: 463311--463350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
463301 TTATTCAATA
* *
463311 AACTTGACATTCATAACAACG
1 AACTTGAAATCCATAACAACG
463332 AACTTGAAATCCATAACAA
1 AACTTGAAATCCATAACAA
463351 TAAATCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.07, T:0.23
Consensus pattern (21 bp):
AACTTGAAATCCATAACAACG
Found at i:470460 original size:123 final size:123
Alignment explanation
Indices: 470333--470611 Score: 362
Period size: 123 Copynumber: 2.3 Consensus size: 123
470323 ACGTTTTGAA
* * * * *
470333 CTATTGTGGCATTTGTTTGAAAACGCTACTAGAGAA-GAATTCTTTTGCAGAGTTTGTTTAGAAA
1 CTATTGCGGCATTTGTTTAAAAACGCCACTAAACAATG-ATTCTTTTGCAGAGTTTGTTTAGAAA
* * ** ** *
470397 CGCCACTAATGTACTAGGTTTTAGTTGCGTTTGTTTAAAAACGCCACAATATATGTACC
65 CGCCACTAAAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACC
* * *
470456 CTATTGCGGCTTTTGTTTAAAAACGCCACTAAACAATGATTCTTTTGCAGCGTTTGTTTAGAAAT
1 CTATTGCGGCATTTGTTTAAAAACGCCACTAAACAATGATTCTTTTGCAGAGTTTGTTTAGAAAC
* * *
470521 GGCACTAAAGTACAAGGTTTTAGCGGCACTTGTCTAAAAATGCCACAATATGTGTACC
66 GCCACTAAAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACC
* *
470579 CTATTACGGCATTTATTTAAAAACGCCACTAAA
1 CTATTGCGGCATTTGTTTAAAAACGCCACTAAA
470612 ATACTTATAT
Statistics
Matches: 134, Mismatches: 21, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
123 133 0.99
124 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (123 bp):
CTATTGCGGCATTTGTTTAAAAACGCCACTAAACAATGATTCTTTTGCAGAGTTTGTTTAGAAAC
GCCACTAAAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACC
Found at i:470512 original size:41 final size:41
Alignment explanation
Indices: 470423--470529 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 41
470413 GGTTTTAGTT
* *
470423 GCGTTTGTTTAAAAACGCCAC-AATATATGTACCCTATTGCG
1 GCGTTTGTTTAAAAACGCCACTAA-AAATGTACCCTATTGCA
* ** *
470464 GCTTTTGTTTAAAAACGCCACTAAACAATG-ATTCTTTTGCA
1 GCGTTTGTTTAAAAACGCCACTAAA-AATGTACCCTATTGCA
* * *
470505 GCGTTTGTTTAGAAATGGCACTAAA
1 GCGTTTGTTTAAAAACGCCACTAAA
470530 GTACAAGGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 49 0.91
42 5 0.09
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (41 bp):
GCGTTTGTTTAAAAACGCCACTAAAAATGTACCCTATTGCA
Found at i:470664 original size:123 final size:123
Alignment explanation
Indices: 470340--470671 Score: 300
Period size: 123 Copynumber: 2.7 Consensus size: 123
470330 GAACTATTGT
* * * * * * * * *
470340 GGCATTTGTTTGAAAACGCTACTAGAGAA-GAATTCTTTTGCAGAGTTTGTT-TAGAAACGCCAC
1 GGCATTTATTTAAAAACGCCACTAAACAATG-ATTATTTTGCAGCGTTTGTTGAAAAAACG-CAC
* * ** ** * *
470403 TAATGTACTAGGTTTTAGTTGCGTTTGTTTAAAAACGCCACAATATATGTACCCTATTGC
64 TAAAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACCCTATTAC
* * * * * **
470463 GGCTTTTGTTTAAAAACGCCACTAAACAATGATTCTTTTGCAGCGTTTGTTTAGAAATGGCACTA
1 GGCATTTATTTAAAAACGCCACTAAACAATGATTATTTTGCAGCGTTTGTTGAAAAAACGCACTA
* *
470528 AAGTACAAGGTTTTAGCGGCACTTGTCTAAAAATGCCACAATATGTGTACCCTATTAC
66 AAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACCCTATTAC
* *
470586 GGCATTTATTTAAAAACGCCACT-AA-AAT-ACTTATATGTTGCGGTGTTTG-TGAAATAAACGC
1 GGCATTTATTTAAAAACGCCACTAAACAATGA-TTAT-T-TTGCAGCGTTTGTTGAAA-AAACGC
470647 TACTAAAGTACAA-GTTTTAGCGGCA
62 -ACTAAAGTACAAGGTTTTAGCGGCA
470672 TTTATGAAAA
Statistics
Matches: 172, Mismatches: 30, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
120 1 0.01
121 6 0.03
122 6 0.03
123 143 0.83
124 16 0.09
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (123 bp):
GGCATTTATTTAAAAACGCCACTAAACAATGATTATTTTGCAGCGTTTGTTGAAAAAACGCACTA
AAGTACAAGGTTTTAGCGGCACTTGTCTAAAAACGCCACAATATATGTACCCTATTAC
Found at i:471106 original size:18 final size:18
Alignment explanation
Indices: 471083--471118 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
471073 ACTTAATTTG
471083 CATACTATATACTATATA
1 CATACTATATACTATATA
*
471101 CATACTATATATTATATA
1 CATACTATATACTATATA
471119 TGCCCATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (18 bp):
CATACTATATACTATATA
Found at i:471854 original size:16 final size:15
Alignment explanation
Indices: 471828--471865 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
471818 TGCGTTCTTG
471828 CTTTTTTGTTTGTTGT
1 CTTTTTTGTTT-TTGT
471844 -TTTTCTTGTTTTTGT
1 CTTTT-TTGTTTTTGT
471859 CTTTTTT
1 CTTTTTT
471866 TCTCTCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.00, C:0.08, G:0.13, T:0.79
Consensus pattern (15 bp):
CTTTTTTGTTTTTGT
Found at i:473688 original size:20 final size:20
Alignment explanation
Indices: 473640--474007 Score: 355
Period size: 20 Copynumber: 18.2 Consensus size: 20
473630 AAATGACCAA
*
473640 CAAATTCGCAACGCGAT-CT
1 CAAATTCGCAACGCGATAGT
*
473659 CAAATTCGCAACGCGA-ACT
1 CAAATTCGCAACGCGATAGT
* * *
473678 GCAATTTCGCAAC-CCAGT-TT
1 -CAAATTCGCAACGCGA-TAGT
*
473698 CCAATTTCGCAACGCGA-A-T
1 -CAAATTCGCAACGCGATAGT
* *
473717 CTGAAAATCGCAACGCGAATTTGT
1 C--AAATTCGCAACGCG-A-TAGT
473741 -AAA-TCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
473759 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
473779 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
473799 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
473819 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
473839 CAAATTCGCAACACGATAGT
1 CAAATTCGCAACGCGATAGT
* *
473859 TAAATTCACAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
473879 CAAATTCGCAATGTGATAGT
1 CAAATTCGCAACGCGATAGT
*
473899 CAAATTCGCAACACAATGCGAATTTGT
1 CAAATTCGC-A-AC---GCG-A-TAGT
*
473926 -AAA-TCGCAACACAGA-AGT
1 CAAATTCGCAACGC-GATAGT
473944 C-AATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
473963 CAAATTCGCAACACGATAGT
1 CAAATTCGCAACGCGATAGT
* *
473983 CAAATTCACAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
474003 CAAAT
1 CAAAT
474008 GTTTTTACGC
Statistics
Matches: 296, Mismatches: 27, Indels: 51
0.79 0.07 0.14
Matches are distributed among these distances:
18 10 0.03
19 37 0.12
20 223 0.75
21 8 0.03
22 1 0.00
23 2 0.01
24 2 0.01
25 6 0.02
26 4 0.01
27 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:474560 original size:20 final size:20
Alignment explanation
Indices: 474501--474548 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
474491 TTTAGTTTTG
474501 CGTTGCGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCA
*
474521 CGTTGTGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCA
474541 CGTTGCGA
1 CGTTGCGA
474549 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:476405 original size:21 final size:21
Alignment explanation
Indices: 476375--476473 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
476365 TGCACCTATA
* *
476375 TCATCATTCAAGAGGCGCCT-
1 TCATCGTTCAAGAGGCCCCTC
476395 TCTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
476417 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* *
476438 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
476459 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
476474 TCATGCCCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.06
21 58 0.88
22 4 0.06
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:478403 original size:39 final size:39
Alignment explanation
Indices: 478347--478432 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
478337 TCAAGTTGTA
478347 GATTTTGA-TTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
478385 GATTTTGATTTCCTTTTGCTTGGTACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
478424 AATTTTGAT
1 GATTTTGAT
478433 GAGTATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 8 0.18
39 36 0.82
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:478799 original size:24 final size:24
Alignment explanation
Indices: 478736--478788 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
478726 AGTGGAGCCG
*
478736 AAATTTATATTGAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
478760 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
478784 CAATT
1 AAATT
478789 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTTAAATTGAAATTCAAACTC
Found at i:479294 original size:20 final size:20
Alignment explanation
Indices: 479202--479295 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
479192 AAATAATGTA
* *
479202 CAACGCGATAGTCAAATTTG
1 CAACGCGAAAGTCAAATTCG
*
479222 CAACGCGAAAGGT-AAATTCA
1 CAACGCGAAA-GTCAAATTCG
*
479242 CAATGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
** *
479256 CATTGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
479276 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
479296 GTTTGCGATT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
14 8 0.14
15 1 0.02
17 4 0.07
18 1 0.02
20 41 0.72
21 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:479705 original size:17 final size:18
Alignment explanation
Indices: 479685--479733 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
479675 GAGCTTTGGA
479685 TTTTGAT-GAGGATCCAT
1 TTTTGATAGAGGATCCAT
*
479702 TTTTGGTAGAGGATCCATT
1 TTTTGATAGAGGATCCA-T
*
479721 TTTTGGTAGAGGA
1 TTTTGATAGAGGA
479734 AAAGATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 14 0.48
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.41
Consensus pattern (18 bp):
TTTTGATAGAGGATCCAT
Found at i:479715 original size:18 final size:19
Alignment explanation
Indices: 479692--479733 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
479682 GGATTTTGAT
479692 GAGGATCCA-TTTTTGGTA
1 GAGGATCCATTTTTTGGTA
479710 GAGGATCCATTTTTTGGTA
1 GAGGATCCATTTTTTGGTA
479729 GAGGA
1 GAGGA
479734 AAAGATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (19 bp):
GAGGATCCATTTTTTGGTA
Found at i:481961 original size:24 final size:24
Alignment explanation
Indices: 481934--481987 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
481924 CCATCACATC
481934 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * *
481958 ATCAAAGTCTGGGTATTGAGCAAG
1 ATCAAAATCTGAGTATTGACCAAG
481982 ATCAAA
1 ATCAAA
481988 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:482924 original size:20 final size:19
Alignment explanation
Indices: 482899--482952 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
482889 TTAAATTCTT
*
482899 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAAATC-A
*
482919 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAAATCA
*
482938 GTTACGAATTTGAAA
1 GTTGCGAATTTGAAA
482953 TTTCGCGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAAAATCA
Found at i:482940 original size:19 final size:20
Alignment explanation
Indices: 482880--482954 Score: 91
Period size: 19 Copynumber: 3.9 Consensus size: 20
482870 ACTAAAACCT
* *
482880 GTTGCGAAATT-AAATTCTT
1 GTTGCGAATTTGAAATTCTA
* *
482899 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCTA
482919 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCTA
*
482938 GTTACGAATTTGAAATT
1 GTTGCGAATTTGAAATT
482955 TCGCGTTACG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 26 0.54
20 22 0.46
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCTA
Found at i:482964 original size:21 final size:19
Alignment explanation
Indices: 482903--482971 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
482893 ATTCTTGTTG
* * *
482903 CGAATTCGAAAATCTAGTTG
1 CGAATTTGAAATTC-AGTTA
482923 CGAATTTGAAATTCAGTTA
1 CGAATTTGAAATTCAGTTA
*
482942 CGAATTTGAAATTTCGCGTTA
1 CGAATTTGAAA-TTC-AGTTA
482963 CGAATTTGA
1 CGAATTTGA
482972 CTATCGCGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 15 0.35
20 15 0.35
21 13 0.30
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
CGAATTTGAAATTCAGTTA
Found at i:482980 original size:20 final size:20
Alignment explanation
Indices: 482955--483146 Score: 171
Period size: 20 Copynumber: 9.6 Consensus size: 20
482945 ATTTGAAATT
*
482955 TCGCGTTACGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
482975 TCGCGTTGTGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
482994 TCTGTGTTGCG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
483014 TTCGTGTTGCGAATTTGACTA
1 -TCGCGTTGCGAATTTGACTA
*
483035 TCGCGTTGCAAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
483054 TCTGTGTTGCGAATTTGACTT
1 TC-GCGTTGCGAATTTGACTA
* *
483075 TTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
483095 TCGCGTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
483115 TCGCATTGCG-ATTT-ACATA
1 TCGCGTTGCGAATTTGAC-TA
*
483134 TTCGTGTTGCGAA
1 -TCGCGTTGCGAA
483147 ATTGGAAACT
Statistics
Matches: 142, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.03
19 14 0.10
20 113 0.80
21 9 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:482988 original size:60 final size:60
Alignment explanation
Indices: 482879--483146 Score: 237
Period size: 60 Copynumber: 4.5 Consensus size: 60
482869 AACTAAAACC
* * * ** ** *
482879 TGTTGCGAAATT-AAA-TTCTTGTTGCGAATTCGAAAATCTAGTTGCGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTG-ACTTCG
* * * * *
482937 AGTTACGAATTTGAAATTTCGCGTTACGAATTTGACTATCGCGTTGTGAATTTGACTTCTG
1 TGTTGCGAATTTGAAATTTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTC-G
* *
482998 TGTTGCG-ATTT-ACAAATTCGTGTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTG
1 TGTTGCGAATTTGA-AATTTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTC-G
* * *
483058 TGTTGCGAATTTG-ACTTTTGTGTTGCGAATTTGACTATCGCGTTGTGAATTTGACTATCG
1 TGTTGCGAATTTGAAATTTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCG
** *
483118 CATTGCG-ATTT-ACATATTCGTGTTGCGAA
1 TGTTGCGAATTTGAAAT-TTCGTGTTGCGAA
483147 ATTGGAAACT
Statistics
Matches: 170, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
58 9 0.05
59 13 0.08
60 137 0.81
61 11 0.06
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (60 bp):
TGTTGCGAATTTGAAATTTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCG
Found at i:486316 original size:13 final size:13
Alignment explanation
Indices: 486276--486318 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
486266 TTTTTTTTCC
486276 TTTCTTTTCATTT
1 TTTCTTTTCATTT
* * *
486289 TTTATTTCCCTTTT
1 TTTCTTT-TCATTT
486303 TTTCTTTTCATTT
1 TTTCTTTTCATTT
486316 TTT
1 TTT
486319 TTCTTTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTTCATTT
Found at i:486325 original size:5 final size:5
Alignment explanation
Indices: 486256--486335 Score: 58
Period size: 5 Copynumber: 15.6 Consensus size: 5
486246 TTCAATTCTA
* * * *
486256 TTTTC TTTTA TTTT- TTTTC CTTTC TTTTC ATTTTT TATTTCC CTTT-
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC T-TTT-C TTTTC
486302 TTTTC TTTTC ATTTT- TTTTC TTTTTC TTTTC TTT
1 TTTTC TTTTC -TTTTC TTTTC -TTTTC TTTTC TTT
486336 AAATGTAGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
4 11 0.18
5 30 0.50
6 19 0.32
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:491127 original size:19 final size:19
Alignment explanation
Indices: 491103--491144 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
491093 TTGCAAAAAT
*
491103 AGTATCAATACTATAGTAG
1 AGTATCAATACCATAGTAG
* *
491122 AGTATCGATACCATAGTAT
1 AGTATCAATACCATAGTAG
491141 AGTA
1 AGTA
491145 GTATCGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (19 bp):
AGTATCAATACCATAGTAG
Found at i:491150 original size:22 final size:20
Alignment explanation
Indices: 491102--491162 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
491092 ATTGCAAAAA
* *
491102 TAGTATCAATACTATAGTAG
1 TAGTATCGATACCATAGTAG
491122 -AGTATCGATACCATAGTATAG
1 TAGTATCGATACCATAG--TAG
*
491143 TAGTATCGATACCATGGTAG
1 TAGTATCGATACCATAGTAG
491163 GGGTATTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 14 0.40
20 3 0.09
21 3 0.09
22 15 0.43
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (20 bp):
TAGTATCGATACCATAGTAG
Found at i:491809 original size:68 final size:68
Alignment explanation
Indices: 491725--492205 Score: 685
Period size: 68 Copynumber: 7.1 Consensus size: 68
491715 AAATAAAAAA
*
491725 TTTGAGGCCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
*
491790 GCT
66 GCC
* * * * *
491793 TTTGAGGCCTAACTGTGCA-TTAAGAGAAAGGTGTCAATTATACCAATTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
491857 GCC
66 GCC
* * * *
491860 TTTGAGGCATAGCTGTGCATTTGACAGAAAAGTGCCAATTATGCCAATTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
491925 GCC
66 GCC
* * * * *
491928 TTTGAGTCCTAGCTGTGCATTCGACAGAAAGATGTCAATTATGTCAGTTAGATCAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
491993 GCC
66 GCC
*
491996 TTTGAGTCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
*
492061 ACC
66 GCC
* * * *
492064 TTTGAGTCCTAGGTGTGCATTTGACAGAAAGGTGTTAATTATGACAGTTAGATGAAAGGCTAAGT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
492129 GCC
66 GCC
* * * * * * * *
492132 TTTGAGACCTAGCGGTGCATTTGACAAAAAGGTGTTAGTCATGCCAGTTAGATGAAAGGTTAAAT
1 TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
492197 GCC
66 GCC
492200 TTTGAG
1 TTTGAG
492206 TAAAAGACTA
Statistics
Matches: 371, Mismatches: 41, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
67 59 0.16
68 312 0.84
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (68 bp):
TTTGAGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGT
GCC
Found at i:492403 original size:91 final size:90
Alignment explanation
Indices: 492238--492448 Score: 325
Period size: 91 Copynumber: 2.3 Consensus size: 90
492228 TGCATAACGT
* * *
492238 TGTATAAAATGGAATGAAAGGATGCAATAAAGGAAATGTATAATAGTGTAAAAAAGGCATGAAAG
1 TGTATAAAA-GGCATGAAATGATGCCATAAAGGAAATGTATAATAGTGTAAAAAAGGCATGAAAG
492303 GATGCCAT-AAATGAAATGTATAATAG
65 GATGCCATAAAAT-AAATGTATAATAG
*
492329 TGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTGTATAAAAAGGCATGAAAG
1 TGTATAAAAGGCATGAAATGATGCCATAAAGGAAATGTATAATAGTGTA-AAAAAGGCATGAAAG
*
492394 GATGCCATAAAATAAATGTATACTAG
65 GATGCCATAAAATAAATGTATAATAG
* *
492420 AGTATAAAAGGCTTGAAATGATGCCATAA
1 TGTATAAAAGGCATGAAATGATGCCATAA
492449 TTAAAATGCA
Statistics
Matches: 111, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
90 36 0.32
91 71 0.64
92 4 0.04
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (90 bp):
TGTATAAAAGGCATGAAATGATGCCATAAAGGAAATGTATAATAGTGTAAAAAAGGCATGAAAGG
ATGCCATAAAATAAATGTATAATAG
Found at i:492456 original size:45 final size:45
Alignment explanation
Indices: 492238--492806 Score: 312
Period size: 45 Copynumber: 12.6 Consensus size: 45
492228 TGCATAACGT
* * **
492238 TGTATAAAATGGAATGAAAGGATGCAATAAAGGAAATGTATAATAG
1 TGTATAAAA-GGCATGAAAGGATGCCATAAATAAAATGTATAATAG
* *
492284 TGTAAAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAG
* *
492329 TGTATAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAG
*
492374 TGTATAAAAAGGCATGAAAGGATGCCATAAA-ATAAATGTATACTAG
1 TGTAT-AAAAGGCATGAAAGGATGCCATAAATA-AAATGTATAATAG
* * * * * *
492420 AGTATAAAAGGCTTGAAATGATGCCATAATTAAAATGCAT-ATGGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAAT-AG
* * ** * * *
492465 TGCATTATTGGCATGAAAGGATGCCATAATTAAAATGCAT-ATGGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAAT-AG
* ** * * * *
492510 TGTATTATCGGCATGAAAGGATGTCATAATTGAAATGCAT-AT-G
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAG
* * ** ** * * * * *
492553 TGCATTATCGGCATGAAATTATGTCATAATTAAAATGCAT-GTGGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAAT-AG
* * ** * * * *
492598 TGCATTATTGGCATGAAATGATGCAATAATTAAAATGCAT-ATAGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATA-G
* ** * * * *
492643 TGTATTATCGGCATGAAAGGATGCCATAATTGAAATGCAT-ATGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAG
* * ** * * *
492687 TTGCATTATTGGCATGAAAGGATGCCATAAGTAAAATGCAT-ATGGG
1 -TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAAT-AG
* ** * * * * *
492733 TGTATTATCGTCATGAAAGGATGACATAACTAAAATGCAT-ATCGG
1 TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAAT-AG
* ** *
492778 TGTATTATCGGCACGAAAGGATGCCATAA
1 TGTATAAAAGGCATGAAAGGATGCCATAA
492807 TTGAAATGCA
Statistics
Matches: 457, Mismatches: 57, Indels: 19
0.86 0.11 0.04
Matches are distributed among these distances:
43 38 0.08
44 2 0.00
45 366 0.80
46 51 0.11
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.28
Consensus pattern (45 bp):
TGTATAAAAGGCATGAAAGGATGCCATAAATAAAATGTATAATAG
Found at i:492527 original size:90 final size:89
Alignment explanation
Indices: 492293--492919 Score: 641
Period size: 90 Copynumber: 7.0 Consensus size: 89
492283 GTGTAAAAAA
* * * * * ** *
492293 GGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATAAAAGGCATGAAATGATGCCATA
1 GGCATGAAAGGATGCCATAATTAAAATGCAT-ATGGGTGTATTATCGGCATGAAAGGATGCCATA
* * * * * **
492357 AATGAAATGTATAATAGTGTATAAAAA
65 ATTGAAATGCAT-ATGGTGCAT-TATC
* * * * * ** * *
492384 GGCATGAAAGGATGCCATAA-AATAAATGTATACT-AGAGTATAAAAGGCTTGAAATGATGCCAT
1 GGCATGAAAGGATGCCATAATTA-AAATGCATA-TGGGTGTATTATCGGCATGAAAGGATGCCAT
* *
492447 AATTAAAATGCATATGGGTGCATTATT
64 AATTGAAATGCATAT-GGTGCATTATC
*
492474 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGTCATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
492539 TTGAAATGCATAT-GTGCATTATC
66 TTGAAATGCATATGGTGCATTATC
** * * * * * *
492562 GGCATGAAATTATGTCATAATTAAAATGCATGTGGGTGCATTATTGGCATGAAATGATGCAATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
* *
492627 TTAAAATGCATATAGGTGTATTATC
66 TTGAAATGCATAT-GGTGCATTATC
* * * *
492652 GGCATGAAAGGATGCCATAATTGAAATGCATATGGTTGCATTATTGGCATGAAAGGATGCCATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
* * *
492717 GTAAAATGCATATGGGTGTATTATC
66 TTGAAATGCATAT-GGTGCATTATC
* * * * *
492742 GTCATGAAAGGATGACATAACTAAAATGCATATCGGTGTATTATCGGCACGAAAGGATGCCATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
492807 TTGAAATGCATATGGGTGCATTATC
66 TTGAAATGCATAT-GGTGCATTATC
* * * * * *
492832 AGCATGAAAGGATGCCATAGTTGAAATACATATGGGTGCATTATCGACATGAAAGGATGCCATAA
1 GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
*
492897 TTGAAATGTATATGGTGCATTAT
66 TTGAAATGCATATGGTGCATTAT
492920 AAGTATGAAG
Statistics
Matches: 460, Mismatches: 69, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
88 77 0.17
89 11 0.02
90 300 0.65
91 72 0.16
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (89 bp):
GGCATGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCATAA
TTGAAATGCATATGGTGCATTATC
Found at i:492814 original size:45 final size:45
Alignment explanation
Indices: 492433--492919 Score: 656
Period size: 45 Copynumber: 10.9 Consensus size: 45
492423 ATAAAAGGCT
* *
492433 TGAAATGATGCCATAATTAAAATGCATATGGGTGCATTATTGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
*
492478 TGAAAGGATGCCATAATTAAAATGCATATGGGTGTATTATCGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* *
492523 TGAAAGGATGTCATAATTGAAATGCATAT--GTGCATTATCGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
** * * *
492566 TGAAATTATGTCATAATTAAAATGCATGTGGGTGCATTATTGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * * *
492611 TGAAATGATGCAATAATTAAAATGCATATAGGTGTATTATCGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * *
492656 TGAAAGGATGCCATAATTGAAATGCATATGGTTGCATTATTGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * *
492701 TGAAAGGATGCCATAAGTAAAATGCATATGGGTGTATTATCGTCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * * *
492746 TGAAAGGATGACATAACTAAAATGCATATCGGTGTATTATCGGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * *
492791 CGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCAGCA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* * * *
492836 TGAAAGGATGCCATAGTTGAAATACATATGGGTGCATTATCGACA
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
* *
492881 TGAAAGGATGCCATAATTGAAATGTATAT-GGTGCATTAT
1 TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTAT
492920 AAGTATGAAG
Statistics
Matches: 390, Mismatches: 50, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
43 38 0.10
44 10 0.03
45 342 0.88
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (45 bp):
TGAAAGGATGCCATAATTAAAATGCATATGGGTGCATTATCGGCA
Found at i:496031 original size:21 final size:21
Alignment explanation
Indices: 495981--496019 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
495971 TGCTTCCATT
495981 AATG-AATGAGCT-AGATAAC
1 AATGAAATGAGCTAAGATAAC
496000 AATGAAATGAGCTAAGATAA
1 AATGAAATGAGCTAAGATAA
496020 TCATAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (21 bp):
AATGAAATGAGCTAAGATAAC
Found at i:496589 original size:14 final size:15
Alignment explanation
Indices: 496572--496626 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
496562 GATATAATAA
496572 AATTAATAATAAAA-
1 AATTAATAATAAAAT
* *
496586 AATTATTTAACAGAAAT
1 AATTA-ATAATA-AAAT
*
496603 AATTTA-AATAAAAT
1 AATTAATAATAAAAT
496617 AATTAATAAT
1 AATTAATAAT
496627 TTAAAGTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
14 14 0.45
15 10 0.32
16 3 0.10
17 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
AATTAATAATAAAAT
Found at i:497311 original size:11 final size:11
Alignment explanation
Indices: 497290--497362 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
497280 TTCGGACACT
497290 TAAATTATATAA
1 TAAA-TATATAA
497302 TAAATATATAA
1 TAAATATATAA
*
497313 TAAATTATTTACA
1 TAAA-TATATA-A
497326 -AAATAT-T-A
1 TAAATATATAA
497334 -AAA-ATA-AA
1 TAAATATATAA
497342 TAAATATATGAA
1 TAAATATAT-AA
*
497354 TAAAAATAT
1 TAAATATAT
497363 TACCATATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 3 0.06
10 4 0.08
11 14 0.27
12 22 0.43
13 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (11 bp):
TAAATATATAA
Found at i:497329 original size:23 final size:22
Alignment explanation
Indices: 497290--497338 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
497280 TTCGGACACT
497290 TAAATTATATAATAAATATATAA
1 TAAATTATATAATAAATAT-TAA
*
497313 TAAATTATTTACA-AAATATTAA
1 TAAATTATATA-ATAAATATTAA
497335 -AAAT
1 TAAAT
497339 AAATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.17
22 3 0.12
23 16 0.67
24 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTATATAATAAATATTAA
Found at i:498078 original size:24 final size:24
Alignment explanation
Indices: 498051--498101 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
498041 GTGAACCAGT
498051 AGCGACGACAACAGCCCATCTAGC
1 AGCGACGACAACAGCCCATCTAGC
498075 AGCGACGACAACAGCCCATCTAGC
1 AGCGACGACAACAGCCCATCTAGC
498099 AGC
1 AGC
498102 AATAACGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.37, G:0.22, T:0.08
Consensus pattern (24 bp):
AGCGACGACAACAGCCCATCTAGC
Found at i:504285 original size:38 final size:38
Alignment explanation
Indices: 504229--504347 Score: 184
Period size: 38 Copynumber: 3.1 Consensus size: 38
504219 TTAATCGTTA
* *
504229 TAACGGTTATTATTATTTTTTAATTATAACATAACTAT
1 TAACAGTTATTATTATTTTTTAATCATAACATAACTAT
*
504267 TAACAGTTATTGTTATTTTTTAATCATAACATAACTAT
1 TAACAGTTATTATTATTTTTTAATCATAACATAACTAT
*
504305 TAAAACAGTTATTATTACTTTTTAATCATAACATAACTAT
1 T--AACAGTTATTATTATTTTTTAATCATAACATAACTAT
504345 TAA
1 TAA
504348 GAAATTGATA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 38 0.51
40 36 0.49
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (38 bp):
TAACAGTTATTATTATTTTTTAATCATAACATAACTAT
Found at i:504327 original size:40 final size:40
Alignment explanation
Indices: 504234--504347 Score: 187
Period size: 40 Copynumber: 2.9 Consensus size: 40
504224 CGTTATAACG
*
504234 GTTATTATTATTTTTTAATTATAACATAACTATT--AACA
1 GTTATTATTATTTTTTAATCATAACATAACTATTAAAACA
*
504272 GTTATTGTTATTTTTTAATCATAACATAACTATTAAAACA
1 GTTATTATTATTTTTTAATCATAACATAACTATTAAAACA
*
504312 GTTATTATTACTTTTTAATCATAACATAACTATTAA
1 GTTATTATTATTTTTTAATCATAACATAACTATTAA
504348 GAAATTGATA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 32 0.46
40 38 0.54
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.47
Consensus pattern (40 bp):
GTTATTATTATTTTTTAATCATAACATAACTATTAAAACA
Found at i:505917 original size:21 final size:20
Alignment explanation
Indices: 505881--505919 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
505871 CTTCCATATA
505881 AAAGATAGGATTTTGAGTTT
1 AAAGATAGGATTTTGAGTTT
505901 AAAGA-AGTGATTATTGAGT
1 AAAGATAG-GATT-TTGAGT
505920 AGAAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (20 bp):
AAAGATAGGATTTTGAGTTT
Found at i:506808 original size:18 final size:18
Alignment explanation
Indices: 506785--506873 Score: 142
Period size: 18 Copynumber: 4.9 Consensus size: 18
506775 AGGGATTATC
*
506785 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
506803 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
506821 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
506839 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
506857 AGTAGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
506874 AATATTTAGT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:513731 original size:18 final size:18
Alignment explanation
Indices: 513683--513731 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
513673 AGGGATTATC
*
513683 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
513701 AATGGTCCCTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
513719 AGTGGTCATTCGG
1 AGTGGTCCTTCGG
513732 TACAAATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:521489 original size:5 final size:5
Alignment explanation
Indices: 521479--521523 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
521469 TATAAAGTTC
*
521479 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCAAT TTTCT TTTAT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC--T TTTCT TTTCT TTT
521524 AAGTTTTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 32 0.86
7 5 0.14
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:522797 original size:18 final size:18
Alignment explanation
Indices: 522774--522816 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
522764 TATTCATCTT
*
522774 CTTCCCACTTTCCATGGC
1 CTTCCCACTCTCCATGGC
522792 CTTCCCACTCTCCATGGC
1 CTTCCCACTCTCCATGGC
522810 CTTCCCA
1 CTTCCCA
522817 ATGAAAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.49, G:0.09, T:0.30
Consensus pattern (18 bp):
CTTCCCACTCTCCATGGC
Found at i:535419 original size:44 final size:43
Alignment explanation
Indices: 535357--535448 Score: 132
Period size: 44 Copynumber: 2.1 Consensus size: 43
535347 AGTTTTAATT
** *
535357 GTGAATTTGTGATTACTTTATGCTTTTC-TATCCCATTTTGTAA
1 GTGAATTTGTGAACACTTTATGC-TTCCGTATCCCATTTTGTAA
535400 GTGAATTTTGTGAACACTTTATGCTTCCGTATCCCATTTTGTAA
1 GTGAA-TTTGTGAACACTTTATGCTTCCGTATCCCATTTTGTAA
535444 GTGAA
1 GTGAA
535449 AGTCTGACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 8 0.18
44 36 0.82
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (43 bp):
GTGAATTTGTGAACACTTTATGCTTCCGTATCCCATTTTGTAA
Found at i:538093 original size:23 final size:21
Alignment explanation
Indices: 538049--538095 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
538039 CATTTCTAAG
538049 AAACAAATGAATAATCGAATT
1 AAACAAATGAATAATCGAATT
* *
538070 AAACAAGATTAATATATTGAATT
1 AAACAA-ATGAATA-ATCGAATT
538093 AAA
1 AAA
538096 AGGACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (21 bp):
AAACAAATGAATAATCGAATT
Found at i:542505 original size:20 final size:20
Alignment explanation
Indices: 542480--542551 Score: 144
Period size: 20 Copynumber: 3.6 Consensus size: 20
542470 ATGGAGCCAT
542480 GAGTGTATCGGTACACTGGG
1 GAGTGTATCGGTACACTGGG
542500 GAGTGTATCGGTACACTGGG
1 GAGTGTATCGGTACACTGGG
542520 GAGTGTATCGGTACACTGGG
1 GAGTGTATCGGTACACTGGG
542540 GAGTGTATCGGT
1 GAGTGTATCGGT
542552 TCCGAAATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.19, C:0.14, G:0.40, T:0.26
Consensus pattern (20 bp):
GAGTGTATCGGTACACTGGG
Found at i:552489 original size:17 final size:17
Alignment explanation
Indices: 552469--552502 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
552459 GACCTAACTT
*
552469 GTTGACCAGTGTTGACC
1 GTTGACCAGCGTTGACC
*
552486 GTTGACCGGCGTTGACC
1 GTTGACCAGCGTTGACC
552503 ACCGTTGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (17 bp):
GTTGACCAGCGTTGACC
Found at i:554630 original size:21 final size:21
Alignment explanation
Indices: 554601--554653 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
554591 TGTCAGTTAA
554601 TAAACTCTTCCAATAGTGATTC
1 TAAA-TCTTCCAATAGTGATTC
554623 TAAATCTTCCAATAGTGATTC
1 TAAATCTTCCAATAGTGATTC
554644 T-AA-CTTCCAA
1 TAAATCTTCCAA
554654 CATTCTATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.23
20 2 0.06
21 18 0.58
22 4 0.13
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (21 bp):
TAAATCTTCCAATAGTGATTC
Found at i:554834 original size:12 final size:12
Alignment explanation
Indices: 554764--554909 Score: 71
Period size: 12 Copynumber: 12.2 Consensus size: 12
554754 AGAATGTTTT
* *
554764 ATCTGATTTTTG
1 ATCTGAATTCTG
*
554776 ATTTGAATTCTG
1 ATCTGAATTCTG
* *
554788 TTCTG-ATTTTCG
1 ATCTGAATTCT-G
* *
554800 ATTTGAATTATG
1 ATCTGAATTCTG
* *
554812 TTCTGATTTCTG
1 ATCTGAATTCTG
554824 ATCTGAATTCTG
1 ATCTGAATTCTG
* * *
554836 CTATGATTTCTG
1 ATCTGAATTCTG
*
554848 ATCTGGATTCTG
1 ATCTGAATTCTG
* * *
554860 TTCTGGATTTTG
1 ATCTGAATTCTG
* *
554872 TTCTG-ATATCTT
1 ATCTGAAT-TCTG
554884 ATCTGAATTCTG
1 ATCTGAATTCTG
* * *
554896 TTTTGATTTCTG
1 ATCTGAATTCTG
554908 AT
1 AT
554910 ATCTCCGTTT
Statistics
Matches: 98, Mismatches: 32, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
11 6 0.06
12 86 0.88
13 6 0.06
ACGTcount: A:0.18, C:0.12, G:0.17, T:0.53
Consensus pattern (12 bp):
ATCTGAATTCTG
Found at i:554876 original size:24 final size:24
Alignment explanation
Indices: 554765--554877 Score: 122
Period size: 24 Copynumber: 4.7 Consensus size: 24
554755 GAATGTTTTA
* *
554765 TCTGATTTTTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
554789 TCTGATTT-TCGATTTGAATTATGT
1 TCTGATTTCT-GATCTGAATTCTGT
*
554813 TCTGATTTCTGATCTGAATTCTGC
1 TCTGATTTCTGATCTGAATTCTGT
* *
554837 TATGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
554861 TCTGGATTT-TGTTCTGA
1 TCT-GATTTCTGATCTGA
554878 TATCTTATCT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
23 1 0.01
24 69 0.91
25 6 0.08
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:555023 original size:19 final size:19
Alignment explanation
Indices: 554995--555039 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
554985 GCTTTGTGCT
*
554995 CAGGGCTTAACTATTGTTA
1 CAGGGTTTAACTATTGTTA
* * *
555014 CAGGGTTTAATTGTTGTTC
1 CAGGGTTTAACTATTGTTA
555033 CAGGGTT
1 CAGGGTT
555040 GTATGGTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (19 bp):
CAGGGTTTAACTATTGTTA
Found at i:556020 original size:14 final size:15
Alignment explanation
Indices: 555989--556022 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
555979 TGAATATTGG
555989 TTATTTGACTTGTGT
1 TTATTTGACTTGTGT
*
556004 TTATTTGA-TTTTGT
1 TTATTTGACTTGTGT
556018 TTATT
1 TTATT
556023 AAATATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (15 bp):
TTATTTGACTTGTGT
Found at i:557415 original size:31 final size:31
Alignment explanation
Indices: 557373--557468 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
557363 TCTTTTTCAA
* *
557373 TTTAAATTGTTTTCCACTTTGGTGCCCAACC
1 TTTAAAATGTTTTCCACTTTTGTGCCCAACC
557404 TTTAAAATGTTTTCCACTTTTGTGCCCAACC
1 TTTAAAATGTTTTCCACTTTTGTGCCCAACC
557435 TTTAAAATGTTTTCCACTTTTGTGCCCAACC
1 TTTAAAATGTTTTCCACTTTTGTGCCCAACC
557466 TTT
1 TTT
557469 GTCTCCGTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTAAAATGTTTTCCACTTTTGTGCCCAACC
Found at i:565643 original size:23 final size:23
Alignment explanation
Indices: 565592--565636 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
565582 CGCTAGGTGT
*
565592 TGATACCCCCTTTGAATGGGTAC
1 TGATACCCCCTTTGAATAGGTAC
*
565615 TGATACCCTCTTTGAATAGGTA
1 TGATACCCCCTTTGAATAGGTA
565637 TCGATACACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (23 bp):
TGATACCCCCTTTGAATAGGTAC
Found at i:568744 original size:14 final size:14
Alignment explanation
Indices: 568725--568752 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
568715 TTCATGATTC
568725 TCTTGAATCTTTTG
1 TCTTGAATCTTTTG
568739 TCTTGAATCTTTTG
1 TCTTGAATCTTTTG
568753 GAAAACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TCTTGAATCTTTTG
Found at i:570229 original size:16 final size:17
Alignment explanation
Indices: 570208--570243 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
570198 CCGATGTGTC
570208 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
570224 ACATTGACTTTTACAAA
1 ACATTGACTTTTACAAA
570241 ACA
1 ACA
570244 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:571032 original size:23 final size:23
Alignment explanation
Indices: 571003--571051 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
570993 GGAGGACCAT
571003 ATAGGTTTGCACCGAAGTGCCAC
1 ATAGGTTTGCACCGAAGTGCCAC
571026 ATAGGTTTGCACCGAAGTGCCAC
1 ATAGGTTTGCACCGAAGTGCCAC
571049 ATA
1 ATA
571052 AGTGTCCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (23 bp):
ATAGGTTTGCACCGAAGTGCCAC
Found at i:574506 original size:16 final size:16
Alignment explanation
Indices: 574487--574529 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
574477 TTATTTATTA
*
574487 AAATTATTTTAAAATT
1 AAATTAATTTAAAATT
*
574503 AAATTAATTTAAATTT
1 AAATTAATTTAAAATT
574519 AAATTGAATTT
1 AAATT-AATTT
574530 TTCTCATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATTAATTTAAAATT
Found at i:575032 original size:20 final size:20
Alignment explanation
Indices: 575007--575047 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
574997 TTTTAATAAT
*
575007 TTTTTATCTACAAAATTAAA
1 TTTTTATCTACAAAATAAAA
* *
575027 TTTTTATTTTCAAAATAAAA
1 TTTTTATCTACAAAATAAAA
575047 T
1 T
575048 ATTAAAAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTATCTACAAAATAAAA
Found at i:575045 original size:19 final size:19
Alignment explanation
Indices: 575001--575045 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
574991 TATTTTTTTT
*
575001 AATAATTTTTTATCTACAA
1 AATAAATTTTTATCTACAA
* *
575020 AATTAAATTTTTATTTTCAA
1 AA-TAAATTTTTATCTACAA
575040 AATAAA
1 AATAAA
575046 ATATTAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAAATTTTTATCTACAA
Found at i:579665 original size:42 final size:41
Alignment explanation
Indices: 579618--579764 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 41
579608 TGTATTTTAG
* *
579618 TTTAAATATGTTTTAGTATTTCAATTAGGATTTAGGATATTA
1 TTTAAATATATTTTA-TATTTCAATTATGATTTAGGATATTA
* * *
579660 TTTAAATAATATTTTAT-TTT--ATCTTTGTTTTAGGTATTTTA
1 TTTAAAT-ATATTTTATATTTCAAT-TATGATTTAGG-ATATTA
**
579701 GTTTAAATAGGTTTTAGTATTTCAATTATGATTTAGGATATTA
1 -TTTAAATATATTTTA-TATTTCAATTATGATTTAGGATATTA
579744 TTTAAATAGTATTTTATATTT
1 TTTAAATA-TATTTTATATTT
579765 TATCTTTTAG
Statistics
Matches: 84, Mismatches: 12, Indels: 18
0.74 0.11 0.16
Matches are distributed among these distances:
39 2 0.02
40 8 0.10
41 14 0.17
42 29 0.35
43 20 0.24
44 9 0.11
45 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (41 bp):
TTTAAATATATTTTATATTTCAATTATGATTTAGGATATTA
Found at i:579816 original size:82 final size:82
Alignment explanation
Indices: 579594--579828 Score: 309
Period size: 84 Copynumber: 2.9 Consensus size: 82
579584 ATTTTAAACA
* *
579594 TTATATTTAATC-TTT--GTATTTTAGTTTAAATATGTTTTAGTATTTCAATTAGGATTTAGGAT
1 TTATATTTTATCTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGGAT
579656 ATTATTTAAATAATATT
66 ATTATTTAAATAATATT
* * * *
579673 TTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTATGATTTAGG
1 TTATATT-T-TATCTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGG
*
579738 ATATTATTTAAATAGTATT
64 ATATTATTTAAATAATATT
* *
579757 TTATATTTTATCTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTAT-AATTAGGATTTAAG
1 TTATATTTTATCTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATT-TCAATTAGGATTTAGG
*
579820 ATGTTATTT
64 ATATTATTT
579829 TCTTTAGCTT
Statistics
Matches: 135, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
79 6 0.04
80 1 0.01
81 6 0.04
82 53 0.39
83 2 0.01
84 67 0.50
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.55
Consensus pattern (82 bp):
TTATATTTTATCTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGGAT
ATTATTTAAATAATATT
Found at i:584739 original size:5 final size:5
Alignment explanation
Indices: 584729--584768 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
584719 TTGTTCTATT
*
584729 TTTTA TTTTA TTTTA TTTTA TTTCA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
584769 TTAGCAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:586863 original size:75 final size:80
Alignment explanation
Indices: 586669--586881 Score: 267
Period size: 84 Copynumber: 2.7 Consensus size: 80
586659 ATTTATCTTT
* *
586669 GTATTTTAGTTTAAATAGGTTTTAGTATTTCAAGTAGGATTTAGGATATTATTTAAATAATATTT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGGATATTATTT-AATAATA-TG
*
586734 TATTTTATCTTTGTTTTA
64 TATTTTATC-TTGTTTAA
*
586752 GATATTTTAGTTTAAATAGGTTTTAGTATTTCAATTATGATTTAGGATATTATTT-A-AATA-GT
1 G-TATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGGATATTATTTAATAATATGT
586814 ATTTTATC-T-TTTAA
65 ATTTTATCTTGTTTAA
* * * *
586828 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAAGATGTTATTT
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTCAATTAGGATTTAGGATATTATTT
586882 TCTTTAGCTT
Statistics
Matches: 119, Mismatches: 9, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
74 5 0.04
75 42 0.35
76 5 0.04
77 1 0.01
79 9 0.08
81 4 0.03
82 1 0.01
83 1 0.01
84 51 0.43
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (80 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAGGATTTAGGATATTATTTAATAATATGTA
TTTTATCTTGTTTAA
Found at i:587578 original size:20 final size:20
Alignment explanation
Indices: 587553--587602 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
587543 TTACTATTTA
587553 TTATTTTATTATT-TCCCT-TT
1 TTATTTTATTATTAT--CTATT
587573 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCTATT
587592 TTATTTTATTA
1 TTATTTTATTA
587603 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 14 0.52
20 11 0.41
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTATTATTATCTATT
Found at i:588944 original size:109 final size:108
Alignment explanation
Indices: 588801--589017 Score: 353
Period size: 109 Copynumber: 2.0 Consensus size: 108
588791 GGACCTAGAG
* *
588801 GGGGTGGGTGGGGGTAGTCGCCCTCATAAAAATTTCAATTTCCTATATATTTTAGATATTTTCTT
1 GGGGCGGGTGGGGGTAGTCGCCCTCAAAAAAATTTCAATTTCCTATATATTTTAGATATTTTCTT
*
588866 TTTATTTTCAATCGAAACTATGTTTTTGCTATCCTAAAATTTTA
66 TTTATTTT-AATCGAAACTATGTTTTCGCTATCCTAAAATTTTA
* * * *
588910 GGGGCGGGTGGGGGTAGTCTCCCTCAAAAAAATTTTAATTTTCTGTATATTTTAGATATTTTCTT
1 GGGGCGGGTGGGGGTAGTCGCCCTCAAAAAAATTTCAATTTCCTATATATTTTAGATATTTTCTT
*
588975 TTTATTTTAATCGAAACTATGTTTTCGCTATCTTAAAATTTTA
66 TTTATTTTAATCGAAACTATGTTTTCGCTATCCTAAAATTTTA
589018 TAAGTTTACC
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 33 0.33
109 67 0.67
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (108 bp):
GGGGCGGGTGGGGGTAGTCGCCCTCAAAAAAATTTCAATTTCCTATATATTTTAGATATTTTCTT
TTTATTTTAATCGAAACTATGTTTTCGCTATCCTAAAATTTTA
Found at i:589259 original size:12 final size:12
Alignment explanation
Indices: 589205--589273 Score: 61
Period size: 12 Copynumber: 5.6 Consensus size: 12
589195 TTATTATTTT
589205 TATTATTAA-AA
1 TATTATTAATAA
* *
589216 TTATTATTATTAT
1 -TATTATTAATAA
*
589229 TAATATTATATATA
1 TATTATTA-ATA-A
589243 TATTATTAATAA
1 TATTATTAATAA
589255 TATTATTAA-ATA
1 TATTATTAATA-A
589267 TATTATT
1 TATTATT
589274 TAAAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
11 1 0.02
12 33 0.70
13 6 0.13
14 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATTAATAA
Found at i:589270 original size:9 final size:10
Alignment explanation
Indices: 589205--589271 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 10
589195 TTATTATTTT
589205 TATTATTAAA
1 TATTATTAAA
*
589215 -ATTATT-AT
1 TATTATTAAA
589223 TATTATT-AA
1 TATTATTAAA
*
589232 TATTATATATA
1 TATTAT-TAAA
589243 TATTATTAATAA
1 TATTATT-A-AA
589255 TATTATTAAA
1 TATTATTAAA
589265 TA-TATTA
1 TATTATTA
589272 TTTAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
8 1 0.02
9 24 0.50
10 6 0.12
11 9 0.19
12 8 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTATTAAA
Found at i:589273 original size:3 final size:3
Alignment explanation
Indices: 589195--589262 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
589185 TCATTTCGTT
* ** *
589195 TTA TTA TTT TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
589241 TATA TTA TTA ATA ATA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA
589263 AATATATTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 47 0.87
4 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:589280 original size:24 final size:23
Alignment explanation
Indices: 589220--589273 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
589210 TTAAAATTAT
* *
589220 TATTATTATTAATATTATATATA
1 TATTATTAATAATATTATAAATA
589243 TATTATTAATAATATTATTAAATA
1 TATTATTAATAATATTA-TAAATA
589267 TATTATT
1 TATTATT
589274 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATTAATAATATTATAAATA
Found at i:589745 original size:13 final size:13
Alignment explanation
Indices: 589723--589760 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
589713 GAAGAGATAC
589723 ACAGAGACGAGCA
1 ACAGAGACGAGCA
*
589736 ACATAGACGAGCA
1 ACAGAGACGAGCA
589749 ACAGAGACGAGC
1 ACAGAGACGAGC
589761 CACGAACCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.24, G:0.29, T:0.03
Consensus pattern (13 bp):
ACAGAGACGAGCA
Found at i:590613 original size:17 final size:18
Alignment explanation
Indices: 590593--590628 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
590583 TTAATCATTG
590593 TTTAAAT-ATATTTTAAT
1 TTTAAATAATATTTTAAT
*
590610 TTTATATAATATTTTAAT
1 TTTAAATAATATTTTAAT
590628 T
1 T
590629 AGTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATAATATTTTAAT
Found at i:590623 original size:18 final size:18
Alignment explanation
Indices: 590600--590657 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
590590 TTGTTTAAAT
590600 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
590618 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
*
590636 TTATTTT-ATTTTA-ATA
1 ATATTTTAATTTTATATA
590652 TATATT
1 -ATATT
590658 ATTTGATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 19 0.58
19 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:596010 original size:17 final size:16
Alignment explanation
Indices: 595983--596015 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
595973 CTTATCCAAC
595983 AAAGAAAGAAGAAAAA
1 AAAGAAAGAAGAAAAA
595999 AAAGAGAAGAAGAAAAA
1 AAAGA-AAGAAGAAAAA
596016 GGAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAGAAAAA
Found at i:598270 original size:93 final size:93
Alignment explanation
Indices: 598106--598377 Score: 440
Period size: 93 Copynumber: 2.9 Consensus size: 93
598096 AGAAGACCCA
* *
598106 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
598171 TCATTGAATTTGGAAGATGAATATGCTC
66 TCATTGAATTTGGAAGATGAATATGCTC
* *
598199 ATAGCATCTTTTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
598264 TCATTGAATTTGGAAGATGAATATGCTC
66 TCATTGAATTTGGAAGATGAATATGCTC
* * *
598292 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAATCA
* *
598355 ATCATTGGATTTGAAAGATGAAT
65 ATCATTGAATTTGGAAGATGAAT
598378 TTTCTCATGG
Statistics
Matches: 167, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
92 31 0.19
93 136 0.81
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
TCATTGAATTTGGAAGATGAATATGCTC
Found at i:598693 original size:115 final size:115
Alignment explanation
Indices: 598288--598719 Score: 717
Period size: 114 Copynumber: 3.8 Consensus size: 115
598278 AGATGAATAT
*
598288 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
598352 TCAATCATTGGATTTGAAAGATGAATTTT-CTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTTGCTCATGGTAGAAATAAGGAG
*
598401 GCTCAATAGCATCTTCTGGAATTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
598466 TCAATCATTGGATTTGAAAGATGAA-TTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTTGCTCATGGTAGAAATAAGGAG
598515 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* * *
598580 TCAATCATTGGATTTGAAAGATGAATTTTGCTTATAGTAGAAATAAAGAG
66 TCAATCATTGGATTTGAAAGATGAATTTTGCTCATGGTAGAAATAAGGAG
* * * * *
598630 ACACAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTCGGTAGGAACCCCAAAA
1 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* * * *
598695 CCGATCATTGGAATTAAAAGATGAA
66 TCAATCATTGGATTTGAAAGATGAA
598720 CTGCATGATC
Statistics
Matches: 301, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
113 7 0.02
114 192 0.64
115 102 0.34
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (115 bp):
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
TCAATCATTGGATTTGAAAGATGAATTTTGCTCATGGTAGAAATAAGGAG
Found at i:601353 original size:22 final size:22
Alignment explanation
Indices: 601324--601378 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
601314 ATCTACACTC
* *
601324 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
*
601346 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
601368 TTCAAAGATGA
1 TTCAAAGATGA
601379 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:602183 original size:76 final size:74
Alignment explanation
Indices: 602057--602249 Score: 275
Period size: 76 Copynumber: 2.6 Consensus size: 74
602047 ATTTCCCACG
*
602057 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCT-TAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
602122 CC-TCAGGGTCA
64 CCTTC-GGGTCA
*
602133 TCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCT-TAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
602198 CTTCGGGTCA
65 CTTCGGGTCA
* * *
602208 TATGTAAGCCCTTCAGTGCATGATGTTTTC--AAAGCCTTCGGG
1 TCTGTAAGTCCTT-AGTGCATGATGTTTCCAAAAAGCCTTCGGG
602250 TCATCCGTAA
Statistics
Matches: 108, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
73 11 0.10
74 1 0.01
75 33 0.31
76 63 0.58
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (74 bp):
TCTGTAAGTCCTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACC
TTCGGGTCA
Found at i:602234 original size:44 final size:45
Alignment explanation
Indices: 602184--602285 Score: 170
Period size: 45 Copynumber: 2.3 Consensus size: 45
602174 GGGAGCTTTT
* *
602184 TGATGTTTTCAAA-CCTTCGGGTCATATGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATACGTAAGCCCTGCAGTGCA
*
602228 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATACGTAAGCCCTGCAGTGCA
602273 TGATGTTTTCAAA
1 TGATGTTTTCAAA
602286 AAGCCTTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 13 0.24
45 41 0.76
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATACGTAAGCCCTGCAGTGCA
Found at i:602398 original size:76 final size:77
Alignment explanation
Indices: 602228--602598 Score: 612
Period size: 76 Copynumber: 4.9 Consensus size: 77
602218 CTTCAGTGCA
* * *
602228 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTT-CAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
**
602292 TCAAGAGCTTTT
66 TCGGGAGCTTTT
*
602304 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
602369 TCGGGAGCTTTT
66 TCGGGAGCTTTT
* *
602381 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
602445 TCGGGAGCTTTT
66 TCGGGAGCTTTT
*
602457 TGATATTTT-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
602521 TCGGGAGCTTTT
66 TCGGGAGCTTTT
602533 TGATGTTTTC-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT-C--AAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
602594 TCGGG
66 TCGGG
602599 TCATCCGTAA
Statistics
Matches: 280, Mismatches: 13, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
73 12 0.04
75 1 0.00
76 239 0.85
77 28 0.10
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (77 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
TCGGGAGCTTTT
Found at i:602581 original size:44 final size:45
Alignment explanation
Indices: 602533--602635 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
602523 GGGAGCTTTT
* *
602533 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
602577 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
*
602622 TGATTTTTTTCAAA
1 TGA-TGTTTTCAAA
602636 AAGCCTTCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 13 0.24
45 32 0.59
46 9 0.17
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
Found at i:602588 original size:273 final size:272
Alignment explanation
Indices: 602057--602866 Score: 996
Period size: 273 Copynumber: 3.0 Consensus size: 272
602047 ATTTCCCACG
*
602057 TCTGTAAGTCCTACAGTGCATGATG-TTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 TCTGTAAGCCCTACAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
602121 GCC-TCAGGGTCATCTGTAAGTCCTGT-AGTGCATGATG-TTTCCAAAAAGCCTTTGGGAGCTTT
66 GCCTTC-GGGTCATCTGTAAGTCCT-TCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTT
*
602183 TTGATGTTTTCAAACCTTCGGGTCATATGTAAGCCCTTCAGTGCATGATGTTTT-C--AAAGCCT
129 TTGATGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
* * ** * ** * ** * * ** *** * *
602245 TCGGG-TC-ATCCGTAAGCCCTGCAGTGCAT-GATGTTTTCAAAAAGCCTTCAAGAGCTTTTTGA
194 TCGGGAGCTTTTTG-ATG-TTTTCA-AACCTCG-GGTCATCTGTAAGCCTTC-AGTGC---ATGA
*
602307 TATTTTCAAAACCTTCGGGTCA
251 TGTTTTCAAAACCTTCGGGTCA
*
602329 TCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AAA
1 TCTGTAAGCCCTACAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
602393 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
602458 GATATTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTC
131 GATGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTC
602523 GGGAGCTTTTTGATGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCA
196 GGGAGCTTTTTGATGTTTTCAAACC-TCGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCA
*
602588 AAGCCTTCGGGTCA
259 AAACCTTCGGGTCA
* * * * ** *
602602 TCCGTAAGCCCTGCAGTGCATGATTTTTTTCAAAAAGCCTTCAAGAGCTTTTTGGATATTTTCAA
1 TCTGTAAGCCCTACAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTT-GATGTTTTCAA
* * *
602667 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAGAAGCCTTCGGGAGCTTTT
65 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTT
* * *
602732 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATG-TTTCCAAAAAGCCT
130 TGATGTTTTCAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
* *
602796 TCGGGAGCTTTTTGATGTTTTCAAAACCTCAGGGCCATCTGTAAGTCCTGCAGTGCATGATGTTT
194 TCGGGAGCTTTTTGATGTTTTC-AAACCTC-GGGTCATCTGTAAG-CCTTCAGTGCATGATGTTT
*
602861 CCAAAA
256 TCAAAA
602867 AGCCTTTGGG
Statistics
Matches: 474, Mismatches: 47, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
271 1 0.00
272 58 0.12
273 182 0.38
274 8 0.02
275 118 0.25
276 96 0.20
277 9 0.02
278 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (272 bp):
TCTGTAAGCCCTACAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAACCTCGGGTCATCTGTAAGCCTTCAGTGCATGATGTTTTCAAA
ACCTTCGGGTCA
Found at i:602613 original size:121 final size:123
Alignment explanation
Indices: 602457--602724 Score: 407
Period size: 121 Copynumber: 2.2 Consensus size: 123
602447 GGGAGCTTTT
* * * *
602457 TGATATTTT-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
** *
602521 TCGGGAGCTTTTT-GATGTTTTC-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 TCAAGAGCTTTTTGGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
602577 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATTTTTTTCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
602642 TCAAGAGCTTTTTGGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 TCAAGAGCTTTTTGGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
602700 TGATGTTTTCCAAGAAGCCTTCGGG
1 TGATGTTTT-C-A-AAGCCTTCGGG
602725 AGCTTTTTGA
Statistics
Matches: 133, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
120 8 0.06
121 61 0.46
122 8 0.06
123 43 0.32
124 1 0.01
125 1 0.01
126 11 0.08
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (123 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
TCAAGAGCTTTTTGGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:602728 original size:199 final size:198
Alignment explanation
Indices: 602381--602800 Score: 682
Period size: 199 Copynumber: 2.1 Consensus size: 198
602371 GGGAGCTTTT
* * *
602381 TGATGTTTT-AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
**
602445 TCGGGAGCTTTTTGATATTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
66 TCAAGAGCTTTTTGATATTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
* *
602510 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCTTC-GGGTCATCTGTAAGCCCTTCAGT
131 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGT
602574 GCA
196 GCA
* *
602577 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATTTTTTTCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
602642 TCAAGAGCTTTTTGGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTT
66 TCAAGAGCTTTTT-GATATTTT-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTT
* *
602707 TTCCAAGAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCA
129 TTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCA
602772 GTGCA
194 GTGCA
*
602777 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
602801 AGCTTTTTGA
Statistics
Matches: 206, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
196 9 0.04
197 61 0.30
198 8 0.04
199 83 0.40
200 33 0.16
202 12 0.06
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (198 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
TCAAGAGCTTTTTGATATTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGT
GCA
Found at i:602764 original size:77 final size:77
Alignment explanation
Indices: 602577--602938 Score: 498
Period size: 76 Copynumber: 4.7 Consensus size: 77
602567 CTTCAGTGCA
* * * *
602577 TGATGTTTTCAAAGCCTTC-GGGTCATCCGTAAGCCCTGCAGTGCATGATTTTTTTCAAAAAGCC
1 TGATGTTTTCAAA-CCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCC
**
602641 TTCAAGAGCTTTT
65 TTCGGGAGCTTTT
* * * *
602654 TGGATATTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCCAAGAAGC
1 T-GATGTTTTC-AAACCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGC
602718 CTTCGGGAGCTTTT
64 CTTCGGGAGCTTTT
*
602732 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATG-TTTCCAAAAAGCCT
1 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
602796 TCGGGAGCTTTT
66 TCGGGAGCTTTT
* * *
602808 TGATGTTTTCAAAACCTCAGGGCCATCTGTAAGTCCTGCAGTGCATGATG-TTTCCAAAAAGCCT
1 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
* *
602872 TTGGGAGTTTTT
66 TCGGGAGCTTTT
* * *
602884 TGATGTTTTCAAACCCTCAGGATCATCTGTAAGACCTACAGTGCATGATGTTTTC
1 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTC
602939 AATATTTCCA
Statistics
Matches: 259, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
76 149 0.58
77 42 0.16
78 65 0.25
79 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (77 bp):
TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGCCCTGCAGTGCATGATGTTTTCCAAAAAGCCT
TCGGGAGCTTTT
Found at i:603082 original size:3 final size:3
Alignment explanation
Indices: 603067--603147 Score: 74
Period size: 3 Copynumber: 26.7 Consensus size: 3
603057 TCATTTCATT
* ** *
603067 TTA TTA TTT TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
603115 TTA TTA TTA ATA ATA TTA TTAA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
603148 TAAAATAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.89
4 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:604468 original size:18 final size:18
Alignment explanation
Indices: 604447--604482 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
604437 TTATATAATA
*
604447 TTTTTAGTAT-TATTATT
1 TTTTTAATATATATTATT
604464 TTTTTAATATATATTATT
1 TTTTTAATATATATTATT
604482 T
1 T
604483 GATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTAATATATATTATT
Found at i:612947 original size:26 final size:26
Alignment explanation
Indices: 612918--613005 Score: 141
Period size: 26 Copynumber: 3.6 Consensus size: 26
612908 CTAATTCATA
612918 TATTCGGGTCGGGTCGGATGAAACTT
1 TATTCGGGTCGGGTCGGATGAAACTT
612944 TATTCGGGTCGGGTCGGATGAAACTT
1 TATTCGGGTCGGGTCGGATGAAACTT
612970 TATTCGGGTC--G--GG-TGAAACTT
1 TATTCGGGTCGGGTCGGATGAAACTT
612991 TATTCGGGTCGGGTC
1 TATTCGGGTCGGGTC
613006 AGGTTCGGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
21 18 0.31
22 2 0.03
23 1 0.02
24 1 0.02
26 36 0.62
ACGTcount: A:0.17, C:0.16, G:0.35, T:0.32
Consensus pattern (26 bp):
TATTCGGGTCGGGTCGGATGAAACTT
Found at i:613003 original size:21 final size:21
Alignment explanation
Indices: 612926--613004 Score: 104
Period size: 21 Copynumber: 3.5 Consensus size: 21
612916 TATATTCGGG
*
612926 TCGGGTCGGATGAAACTTTAT
1 TCGGGTCGGGTGAAACTTTAT
612947 TCGGGTCGGGTCGGATGAAACTTTAT
1 TCGGGTC--G--GG-TGAAACTTTAT
612973 TCGGGTCGGGTGAAACTTTAT
1 TCGGGTCGGGTGAAACTTTAT
612994 TCGGGTCGGGT
1 TCGGGTCGGGT
613005 CAGGTTCGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
21 29 0.56
22 2 0.04
23 1 0.02
24 1 0.02
25 1 0.02
26 18 0.35
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.32
Consensus pattern (21 bp):
TCGGGTCGGGTGAAACTTTAT
Found at i:614327 original size:17 final size:17
Alignment explanation
Indices: 614300--614340 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
614290 GGATCTTGAT
*
614300 TAAAAAATTTTGGAGTG
1 TAAAAATTTTTGGAGTG
*
614317 TCAAAATTTTTGGAGTG
1 TAAAAATTTTTGGAGTG
614334 TAAAAAT
1 TAAAAAT
614341 GAATGATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (17 bp):
TAAAAATTTTTGGAGTG
Found at i:616792 original size:19 final size:19
Alignment explanation
Indices: 616741--616792 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
616731 ACAGTCGGAC
*
616741 CTATGATTTCTGTTGTGAA
1 CTATGATTTCTGTTATGAA
* * *
616760 CTTTGATATCTGTTATGAT
1 CTATGATTTCTGTTATGAA
*
616779 CTATGATTTATGTT
1 CTATGATTTCTGTT
616793 CTAAACTCGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (19 bp):
CTATGATTTCTGTTATGAA
Found at i:618357 original size:24 final size:24
Alignment explanation
Indices: 618325--618378 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
618315 GTATTCGAAA
618325 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
618349 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
618373 TTTGAT
1 TTTGAT
618379 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:620933 original size:14 final size:14
Alignment explanation
Indices: 620914--620948 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
620904 GGAAATTACT
620914 ATCGCAACGAGGGA
1 ATCGCAACGAGGGA
620928 ATCGCAACGAGGGA
1 ATCGCAACGAGGGA
620942 ATCGCAA
1 ATCGCAA
620949 AGCGAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.31, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGGGA
Found at i:620996 original size:19 final size:19
Alignment explanation
Indices: 620974--621014 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
620964 GCAACGTGAA
620974 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
620993 TTTAGTTTCGTGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
621012 TTT
1 TTT
621015 GTCGTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.54
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:621028 original size:33 final size:33
Alignment explanation
Indices: 620984--621077 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
620974 TTTAGTTTCG
** * *
620984 CGTTGCGATTTT-AGTTTCGTGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
621017 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
621050 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
621078 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 53 0.98
34 1 0.02
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:621076 original size:19 final size:19
Alignment explanation
Indices: 621019--621077 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
621009 GATTTTGTCG
*
621019 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
621038 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
621052 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
621071 TTGCGAT
1 TTGCGAT
621078 AGTCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 6 0.19
16 7 0.22
17 7 0.22
19 12 0.38
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:621085 original size:19 final size:17
Alignment explanation
Indices: 621027--621077 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
621017 CGTTGCAATT
621027 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
621044 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
621058 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
621077 T
1 T
621078 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:624520 original size:20 final size:20
Alignment explanation
Indices: 624497--624552 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
624487 TGAAATGAAA
624497 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
624517 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
624537 ATCGTAACGAGAGAAT
1 ATCGCAACGAGAGAAT
624553 TGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:624579 original size:33 final size:33
Alignment explanation
Indices: 624488--624642 Score: 184
Period size: 33 Copynumber: 4.5 Consensus size: 33
624478 TCTTTTGGTT
624488 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGAGAG-A--A-T-T-GCAACGC
** *
624527 GGAAATGACTATCGTAACGAGAGAATTGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATTGCAACGC
624561 GAAATGAAAATCGCAACGAGAGAATTGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATTGCAACGC
* * *
624594 GAAATGAAAATCGCAATGAGAGAATCGAAACGC
1 GAAATGAAAATCGCAACGAGAGAATTGCAACGC
*
624627 GAAATTAAAATCGCAA
1 GAAATGAAAATCGCAA
624643 TGCGATTTTG
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
33 75 0.71
34 7 0.07
35 1 0.01
36 1 0.01
37 1 0.01
39 1 0.01
40 19 0.18
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATTGCAACGC
Found at i:624714 original size:40 final size:40
Alignment explanation
Indices: 624670--624764 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
624660 GTTGCGATTA
624670 TCTCGTTGCAATTTTCA-TTTCGCGTTGCAATTTTCATTT
1 TCTCGTTGCAATTTTCATTTTCGCGTTGCAATTTTCATTT
* ** * *
624709 CTCTCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
1 -TCTCGTTGCAATTTTCATTTTCGCGTTGCAATTTTCATTT
624750 TCAT-GTTGCAATTTT
1 TC-TCGTTGCAATTTT
624765 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 24 0.53
41 21 0.47
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.51
Consensus pattern (40 bp):
TCTCGTTGCAATTTTCATTTTCGCGTTGCAATTTTCATTT
Found at i:624763 original size:20 final size:20
Alignment explanation
Indices: 624674--624764 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
624664 CGATTATCTC
*
624674 GTTGCAATTTTCA-TTTCGC
1 GTTGCAATTTTCATTTTCGT
624693 GTTGCAATTTTCATTTCTC-T
1 GTTGCAATTTTCATTT-TCGT
* **
624713 CGTTGCGATAGTCATTTTCGT
1 -GTTGCAATTTTCATTTTCGT
* *
624734 GTTGCGATTTTCATTTTCAT
1 GTTGCAATTTTCATTTTCGT
624754 GTTGCAATTTT
1 GTTGCAATTTT
624765 AAGTTTAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.22
20 31 0.52
21 16 0.27
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.51
Consensus pattern (20 bp):
GTTGCAATTTTCATTTTCGT
Found at i:625350 original size:20 final size:20
Alignment explanation
Indices: 625323--625555 Score: 164
Period size: 20 Copynumber: 11.5 Consensus size: 20
625313 TTTAAAAATT
625323 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* * *
625343 GAGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
**
625363 GTCGTTGCGATTTATAGATAC
1 G-CGTTGCGATTTACGGATAC
* **
625384 GCATTGCGATTTACATATAC
1 GCGTTGCGATTTACGGATAC
* * * *
625404 ACATTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* * *
625424 TCGTTGCGATTGACAGATAC
1 GCGTTGCGATTTACGGATAC
* * *
625444 GCGTTGCGATTAACGTATTC
1 GCGTTGCGATTTACGGATAC
*
625464 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
** * *
625484 GCGTTGTAATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
* *
625504 GTCGTTGTGATTTACAGATAC
1 G-CGTTGCGATTTACGGATAC
625525 GCGTTGCGATTTTACGGATAC
1 GCGTTGCGA-TTTACGGATAC
**
625546 TTGTTGCGAT
1 GCGTTGCGAT
625556 AGTCAGAATC
Statistics
Matches: 164, Mismatches: 42, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
20 115 0.70
21 49 0.30
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:625516 original size:41 final size:41
Alignment explanation
Indices: 625387--625555 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 41
625377 TAGATACGCA
* * *
625387 TTGCGATTTACATATACACATTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
* *
625427 TTGCGATTGACAGATACGCGTTGCGA-TTAACGTATTCTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
* ** *
625467 TTGCGATTTACGGATACGCGTTGTAATTTTACGTATTGTCG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
* * * *
625508 TTGTGATTTACAGATACGCGTTGCGATTTTACGGATACTTG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
625549 TTGCGAT
1 TTGCGAT
625556 AGTCAGAATC
Statistics
Matches: 108, Mismatches: 20, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
40 57 0.53
41 51 0.47
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCG
Found at i:625669 original size:21 final size:22
Alignment explanation
Indices: 625584--625683 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 22
625574 ATTTATATGT
* *
625584 TCGCGTTGCGATT-T-TCATAT
1 TCGCGTTGCGATTCTGTAATAA
*
625604 TCGCGTTGCGATTCTGGAA-AA
1 TCGCGTTGCGATTCTGTAATAA
** *
625625 TCGCAATGCGAATT-TGTACT-A
1 TCGCGTTGCG-ATTCTGTAATAA
*
625646 TCGCATTGCGATTCT-TAATAA
1 TCGCGTTGCGATTCTGTAATAA
625667 TCGCGTTGCGATTCTGT
1 TCGCGTTGCGATTCTGT
625684 GAACTGATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 19 0.30
21 39 0.62
22 5 0.08
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (22 bp):
TCGCGTTGCGATTCTGTAATAA
Found at i:625677 original size:42 final size:42
Alignment explanation
Indices: 625584--625738 Score: 98
Period size: 42 Copynumber: 3.8 Consensus size: 42
625574 ATTTATATGT
*
625584 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGGAAAA
** *
625625 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCT-TAATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGGAA-AA
* * *
625667 TCGCGTTGCG-ATTCTGTGA-ACT-G-ATTTGCGATTCTGG-AGA
1 TCGCGTTGCGAATT-T-TCATATTCGCA-TTGCGATTCTGGAAAA
* *
625707 TCGCGTTACG-ATTTTTAT-TTCGCATTGCGATT
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATT
625739 TTGTTGGTCA
Statistics
Matches: 91, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
38 3 0.03
39 10 0.11
40 15 0.16
41 26 0.29
42 33 0.36
43 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGGAAAA
Found at i:626893 original size:23 final size:24
Alignment explanation
Indices: 626853--626899 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
626843 TTTTAGCACC
* *
626853 AAATATTATAATTTTCAAGGTGAA
1 AAATATCATAATTGTCAAGGTGAA
626877 AAATATCA-AATTGTCAAGGTGAA
1 AAATATCATAATTGTCAAGGTGAA
626900 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (24 bp):
AAATATCATAATTGTCAAGGTGAA
Found at i:628975 original size:2 final size:2
Alignment explanation
Indices: 628968--628995 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
628958 CTAATTTGTA
628968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
628996 TTAGTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:629133 original size:22 final size:22
Alignment explanation
Indices: 629093--629157 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
629083 AACACTATTA
* * *
629093 AATTATAAAGTACTAAAAATAT
1 AATTATAAATTAATTAAAATAT
* *
629115 AATTATAAATTAGTTAAAATTT
1 AATTATAAATTAATTAAAATAT
* * *
629137 AAATGTAATTTAATTAAAATA
1 AATTATAAATTAATTAAAATA
629158 CAATATTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTATAAATTAATTAAAATAT
Found at i:630102 original size:46 final size:46
Alignment explanation
Indices: 630052--630210 Score: 191
Period size: 46 Copynumber: 3.5 Consensus size: 46
630042 TTAATTTATA
*
630052 GCATCCTTTCATGCATATTATTTATGGCATCCTTTCATACCTTAAT
1 GCATCCTTTCATGCATATTAATTATGGCATCCTTTCATACCTTAAT
* * * * *
630098 GCATCCCTTCATGC--CTTAATTATGACATCCTTTAATGCCTTAAT
1 GCATCCTTTCATGCATATTAATTATGGCATCCTTTCATACCTTAAT
* *
630142 GCATCCTTTCATGCATTTTAATTATGGCATCATTTCATGA-CTTAAT
1 GCATCCTTTCATGCATATTAATTATGGCATCCTTTCAT-ACCTTAAT
*
630188 GCATCC-TTCAATGCATTTTAATT
1 GCATCCTTTC-ATGCATATTAATT
630211 TTAATTATGC
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
44 38 0.39
45 3 0.03
46 56 0.58
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.42
Consensus pattern (46 bp):
GCATCCTTTCATGCATATTAATTATGGCATCCTTTCATACCTTAAT
Found at i:630103 original size:20 final size:20
Alignment explanation
Indices: 630078--630155 Score: 93
Period size: 20 Copynumber: 3.7 Consensus size: 20
630068 ATTATTTATG
*
630078 GCATCCTTTCATACCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
630098 GCATCCCTTCATGCCTTAATTAT
1 GCATCCTTTCATGCCTT-A--AT
*
630121 GACATCCTTTAATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
630142 GCATCCTTTCATGC
1 GCATCCTTTCATGC
630156 ATTTTAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
20 27 0.55
21 4 0.08
23 4 0.08
24 14 0.29
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.38
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:630240 original size:2 final size:2
Alignment explanation
Indices: 630233--630273 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
630223 TTTTGAACAT
630233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
630274 CATCCCTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:630625 original size:68 final size:68
Alignment explanation
Indices: 630440--632904 Score: 2846
Period size: 68 Copynumber: 36.5 Consensus size: 68
630430 TGTTTAACCG
* * *
630440 TTCATCTAACTGACATAAATGACA-TCTTTCTATCATTTGCACAGTTAGGCCTTAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
630504 GCCT
65 GCCT
* * * * *
630508 TTCATCTAA-TTGCATAAATGAGACCTTTATGTCATTTGCACAGTTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
630572 CCT
66 CCT
* * * * *
630575 TTCATCTAACTGGCATAAATAACACTTTTCTATCATTTGTACAGTTAGGCCTCAGAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
630640 CCT
66 CCT
** * * *
630643 TTCATCTAACTAACATAAATGACACATTTCTTTCATTTGCACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
630708 CCT
66 CCT
* * * * *
630711 TTCATCTACCTGACATAAATGACACATTTATGTCATTTGCATAGTTAGGCCTCAAAGG-ACCTTA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA-CTTA
630775 GCCT
65 GCCT
630779 TTCATCTAACTGGCATAAATGACA-TCTTTCTGTCATTTGCACA-TATAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGT-TAGGCCTCAAAGGCACTT
*
630842 ATCCT
64 AGCCT
* * * * * * *
630847 TTCATCTAACTAGCATAAATAACA-TATTTATGTCATTTACACAGTTAGGCTTCAAAGCCACTAA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
630911 GCCA
65 GCCT
* * * * * *
630915 TTCATCTAACTGGCATGAATGACACATTTCTTTCATTTGCACAGTTAGGCCACAAAGACACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
630980 CCT
66 CCT
* * * * * *
630983 TTCATCTAACTGACATGAATGA-ACCTTTCTGTCATTTCCACTGTTATGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
*
631047 TCT
66 CCT
* * * *
631050 TTCATCTAACTGGCATAAAT-ATCA-TATTTTTATCATTTACACATTTAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCATAAATGA-CACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTT
631113 AGCCT
64 AGCCT
* * * * *
631118 CTCATCTACCTAGCATAAATGACACCTTTC--T-A--T-CA-A--TAGGCCTC-TAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631173 CCT
66 CCT
* * * *
631176 TTCATCTAACTGGCATAAATGACACCTTTATATCATTTGCACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631241 CCT
66 CCT
** * * *
631244 TTCATCTAACTAACATAATTGACACCTTTCTGTCATTT-CACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631308 CCT
66 CCT
* * *
631311 TTCATCT-ACTTGACATAAATGACACCTTTCTGCCATTTGCACAGTTAGGCCTCAAAGG-ACCTT
1 TTCATCTAAC-TGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCA-CTT
631374 AGCCT
64 AGCCT
* **
631379 TTCATCTAACTGGCATAAATGACA-TCTTTCTG-CATTTGCATAGTTATACCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
631442 GCCT
65 GCCT
* *
631446 TTCATCTAACTGGCATAAATGACA-TCTTTCTATCATTTGCATAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
631510 GCCT
65 GCCT
* * * * * * *
631514 TTCATATAACTGGCATGAATGAAACCTTTCTTTTATTTGCACAGTTAGGCTTCAAAGGCACTTTA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCAC-TTA
631579 -CCT
65 GCCT
* * * *
631582 TTCATCTAACTGACATAAATGACACCTTTCCGCCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631647 CCT
66 CCT
*
631650 TTCATCTAACTGGCATAAATGACA-TCTTTATGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
631714 GCCT
65 GCCT
* * * * *
631718 TTCATCTAACTGGCATAAATGACACCTTTT-TATCGTTTGCACTGTTAGACCTCAAAGGCATTTA
1 TTCATCTAACTGGCATAAATGACA-CTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
631782 GCCT
65 GCCT
* * * * * *
631786 TTCATCTAACTGGCATAAATGAAACCTTTCTATCATATGCACAATTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631851 CCT
66 CCT
** * * * *
631854 TTCATCTAACTGATATAAATGACACATTTCTATCATTTGCATAGTTAGGCCTCAAAGGCACTTTG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
631919 CCT
66 CCT
* *
631922 TTCATCAAACTGGCATAAATGACA-TCTTTCTGTCATTTGCATAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
631986 GCCT
65 GCCT
* * * * *
631990 TCCATCTAATTGGCATAAATGACACATGTT-TGTTATTTGCACAGTTAGGCCTCAAAGGCACTTG
1 TTCATCTAACTGGCATAAATGACAC-TTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
632054 GCCT
65 GCCT
* * *
632058 TTCATCTAACTGGCATAAATGACACCTTTT-TGTCATTTGCATAGTTATGCCTAAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACA-CTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
632122 GCCT
65 GCCT
* ** ** * *
632126 TTCATCTAATTGAAATAAATGACAGC-TTTAGGTCATTTGGACAGTTAGGCCTCAAAGGCCCTTA
1 TTCATCTAACTGGCATAAATGACA-CTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
632190 ACCT
65 GCCT
* ** *
632194 TTAATCTAACTGAAATAAATGACA-TCTTTCTGTCATTTGCACAGTTAGGCGTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
632258 ACCT
65 GCCT
* * * * * * * *
632262 TTCATCTAACTGACATAAATGACACATTTATGTCATTTGCACATTTAGGCCTCAAATGTACGTAA
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
632327 CCT
66 CCT
* ** * * *
632330 TTCATCTATCTGATATAAATGACACATTTT-TTTCATTTGCATAGTTAGGCCTCAAAGGAACTTA
1 TTCATCTAACTGGCATAAATGACAC-TTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
632394 ACCT
65 GCCT
* * * * *
632398 TTCATCTAACTGACATAAATGACACCTTTCTATTATTTGAACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
632463 CCT
66 CCT
* * * * *
632466 TTCTTCTAACTGGCATAAATGACA-TCTTTATGTCATTTGCACAGTTAGGCCTTAAAGGTAGTTA
1 TTCATCTAACTGGCATAAATGACACT-TTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
632530 GCCT
65 GCCT
*
632534 TTCATCTAACTGGCATAAATGACACGTTTT-TGTCATTTGCACAGTTAGGCCTCAAAGGCCCTTA
1 TTCATCTAACTGGCATAAATGACAC-TTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
* *
632598 ACTT
65 GCCT
** * * *
632602 TTCATCTAACTAACATAAATGACACATTTATGTCATTTGCACATTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
*
632667 CAT
66 CCT
* * * * * *
632670 TTGATCTAACTGACATAAGTGATATCTTTT-TGTCATTTGCATAGTTAGGCCTCAAAGGTACTTA
1 TTCATCTAACTGGCATAAATGACA-CTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
632734 GCCT
65 GCCT
* * * * * *
632738 TTCATATAACTGGAAAAAATGGA-ACCTTTCTATCATTTGCACAGTTAGGCCACAAAGGCACTTA
1 TTCATCTAACTGGCATAAAT-GACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
632802 TCCT
65 GCCT
* * * *
632806 TTCATCTAACTGGCATAAATGACACCTTTCAGTCGTTTGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
632871 CCT
66 CCT
* * * *
632874 TTAATCTAACTGTCATAAATGAAACATTTCT
1 TTCATCTAACTGGCATAAATGACACTTTTCT
632905 TGTATTTTCA
Statistics
Matches: 2063, Mismatches: 279, Indels: 110
0.84 0.11 0.04
Matches are distributed among these distances:
58 39 0.02
59 8 0.00
60 1 0.00
61 2 0.00
62 2 0.00
63 2 0.00
64 2 0.00
65 2 0.00
66 4 0.00
67 267 0.13
68 1705 0.83
69 26 0.01
70 3 0.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACTTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:633292 original size:55 final size:54
Alignment explanation
Indices: 633135--633293 Score: 194
Period size: 55 Copynumber: 2.9 Consensus size: 54
633125 ACATCTATTT
* * * * * * ** *
633135 CCCATACAGAAATTCATACATTTAGTATGAATTTCTCAGTTCCCACCCATGGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTATTTTCTACACAAAGTC
633189 CCCATACTA-AAATTCATACACTTAGTATGAATTTCTTATTTTCGTACACAAAGTC
1 CCCATAC-AGAAATTCATACACTTAGTATGAATTTCTTATTTTC-TACACAAAGTC
*
633244 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTAATTTTTTACACA
1 CCCATACAGAAATTCATACACTTAGTATGAATTTCTT-ATTTTCTACACA
633294 CCTAGTTCCA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
54 38 0.42
55 48 0.53
56 5 0.05
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (54 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTCTTATTTTCTACACAAAGTC
Found at i:633724 original size:95 final size:94
Alignment explanation
Indices: 633624--633847 Score: 324
Period size: 95 Copynumber: 2.4 Consensus size: 94
633614 TATGGCTCTA
*
633624 TAGTATCAATACCCCTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCCT-A
1 TAGTAT-AATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTT-CTGA
* *
633688 TATCGATACCAATTTTTGATTCGATGTTGCC
64 TATCGATACCAATTTTAGATTCGATGTTACC
* * *
633719 TAGTATAGATACCCTTACCATGGTATCGATACTACTATATTATGGTACTGATACCCCCTTCTGGT
1 TAGTATA-ATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGAT
*
633784 ATCGATACCCATTTTAGATTCGATGTTACC
65 ATCGATACCAATTTTAGATTCGATGTTACC
* *
633814 TAGTATTGATAACCTTACCATGGTATCGATACTA
1 TAGTA-TAATACCCTTACCATGGTATCGATACTA
633848 TCTCATTGGT
Statistics
Matches: 117, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
94 3 0.03
95 113 0.97
96 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (94 bp):
TAGTATAATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGATA
TCGATACCAATTTTAGATTCGATGTTACC
Found at i:633857 original size:20 final size:21
Alignment explanation
Indices: 633834--633892 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
633824 AACCTTACCA
633834 TGGTATCGATACTATCTCAT-
1 TGGTATCGATACTATCTCATC
633854 TGGTATCGATACTGAT-TCAATC
1 TGGTATCGATACT-ATCTC-ATC
633876 T-GTATCGATACTA-CTCA
1 TGGTATCGATACTATCTCA
633893 GCTATTTCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.03
20 18 0.51
21 15 0.43
22 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.37
Consensus pattern (21 bp):
TGGTATCGATACTATCTCATC
Found at i:633881 original size:95 final size:93
Alignment explanation
Indices: 633639--633886 Score: 243
Period size: 95 Copynumber: 2.6 Consensus size: 93
633629 TCAATACCCC
* * * ** *
633639 TACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCCT-ATATCGATACCAATTT
1 TACCATGGTATCGATACTACTATATTATGATACTGAT--CCCAAT-CTGGTATCGATACCAATTT
* * *
633703 TTGATTCGATGTTGCCTAGTATAGATACCCT
63 TAGATTCGATGTTACCTAGTATAGATAACCT
* ** *
633734 TACCATGGTATCGATACTACTATATTATGGTACTGATACCCCCTTCTGGTATCGATACCCATTTT
1 TACCATGGTATCGATACTACTATATTATGATACTGAT--CCCAATCTGGTATCGATACCAATTTT
*
633799 AGATTCGATGTTACCTAGTATTGATAACCT
64 AGATTCGATGTTACCTAGTATAGATAACCT
*
633829 TACCATGGTATCGATACTATCTCAT-TGGTATCGATACTGAT-TCAATCT-GTATCGATAC
1 TACCATGGTATCGATACTA-CT-ATAT--TAT-GATACTGATCCCAATCTGGTATCGATAC
633887 TACTCAGCTA
Statistics
Matches: 135, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
94 2 0.01
95 113 0.84
96 7 0.05
97 2 0.01
98 3 0.02
99 8 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (93 bp):
TACCATGGTATCGATACTACTATATTATGATACTGATCCCAATCTGGTATCGATACCAATTTTAG
ATTCGATGTTACCTAGTATAGATAACCT
Found at i:643409 original size:18 final size:18
Alignment explanation
Indices: 643386--643448 Score: 90
Period size: 18 Copynumber: 3.5 Consensus size: 18
643376 GTCACAACCC
643386 GACCCGACCCGACCTGTT
1 GACCCGACCCGACCTGTT
*
643404 GACCCGACCCGACCCGTT
1 GACCCGACCCGACCTGTT
* *
643422 GACTCGACCCGATCTGTT
1 GACCCGACCCGACCTGTT
*
643440 AACCCGACC
1 GACCCGACC
643449 AATTGACCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.19, C:0.44, G:0.21, T:0.16
Consensus pattern (18 bp):
GACCCGACCCGACCTGTT
Found at i:645793 original size:72 final size:72
Alignment explanation
Indices: 645665--645799 Score: 168
Period size: 72 Copynumber: 1.9 Consensus size: 72
645655 GGACCTAATG
** * * *
645665 TGACTCTTAGGTAGGCTCTGAGGCCCTGAGATCATTCTCGTGTATGCCCTGCGGCCCTAAGATGT
1 TGACTCTTAGGTAGGCTCTGAGGCCCCAAAATCATTCTCGGGTAGGCCCTGCGGCCCTAAGATGT
645730 GTTCTTA
66 GTTCTTA
*
645737 TGACTCTTAGGTAGGCTCTGAGGCCCCAAAATCTATAT-T-GGGTAGGCTCT-CAGGCCCTAAGA
1 TGACTCTTAGGTAGGCTCTGAGGCCCCAAAATC-AT-TCTCGGGTAGGCCCTGC-GGCCCTAAGA
645799 T
63 T
645800 ATTCCCTTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
71 1 0.02
72 49 0.91
73 3 0.06
74 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (72 bp):
TGACTCTTAGGTAGGCTCTGAGGCCCCAAAATCATTCTCGGGTAGGCCCTGCGGCCCTAAGATGT
GTTCTTA
Found at i:646541 original size:35 final size:35
Alignment explanation
Indices: 646492--646560 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
646482 TTATTAACAG
* *
646492 GAATTATGCGTGGAAGAAGAACGGAAATAAGAAAT
1 GAATTAGGCATGGAAGAAGAACGGAAATAAGAAAT
*
646527 GAATTAGGCATGGAAGAAGAAGGGAAATAAGAAA
1 GAATTAGGCATGGAAGAAGAACGGAAATAAGAAA
646561 AGTGTGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.30, T:0.14
Consensus pattern (35 bp):
GAATTAGGCATGGAAGAAGAACGGAAATAAGAAAT
Found at i:651508 original size:32 final size:34
Alignment explanation
Indices: 651463--651530 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
651453 GATTATTAAC
*
651463 AGGAATTATGCGT-G-GAAGAAGGGAAATAAGAA
1 AGGAATTAGGCGTGGAGAAGAAGGGAAATAAGAA
651495 AGGAATTAGGCGTGGAAGAAGAAGGGAAATAAGAA
1 AGGAATTAGGCGTGG-AGAAGAAGGGAAATAAGAA
651530 A
1 A
651531 AGTGTGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 12 0.38
33 1 0.03
35 19 0.59
ACGTcount: A:0.49, C:0.03, G:0.35, T:0.13
Consensus pattern (34 bp):
AGGAATTAGGCGTGGAGAAGAAGGGAAATAAGAA
Done.