Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007834.1 Hibiscus syriacus cultivar Beakdansim tig00110183_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: 925658
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:807798 original size:29 final size:29
Alignment explanation
Indices: 807764--807822 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
807754 CTTAAATTAA
807764 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
807793 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
807822 T
1 T
807823 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:812479 original size:29 final size:29
Alignment explanation
Indices: 812445--812503 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
812435 CTTAAATTAA
812445 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
812474 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
812503 T
1 T
812504 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:815325 original size:25 final size:26
Alignment explanation
Indices: 815297--815349 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
815287 AATCATTCAA
815297 TTATTACCAAAG-ATTATAAAAT-ATT
1 TTATTACCAAAGCATTA-AAAATCATT
* *
815322 TTATTTCCATAGCATTAAAAATCATT
1 TTATTACCAAAGCATTAAAAATCATT
815348 TT
1 TT
815350 CACTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (26 bp):
TTATTACCAAAGCATTAAAAATCATT
Found at i:816387 original size:48 final size:47
Alignment explanation
Indices: 816257--816388 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 47
816247 CCTGGTACTT
* *
816257 TAGCACCACTGTCACACAGACGTTAGACGCGTGCTAAGTACCATATAG
1 TAGCACCAC-GTCACACAGACGTCAGACGCGTACTAAGTACCATATAG
* * *** **
816305 TAGCACCACCGTCACACAGATGTCGGATATGTACTAAGTTTCATATAG
1 TAGCACCA-CGTCACACAGACGTCAGACGCGTACTAAGTACCATATAG
*
816353 TAGCACCATCGTCACACATACGTCAGACGCGTACTA
1 TAGCACCA-CGTCACACAGACGTCAGACGCGTACTA
816389 TAAGTATAAT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
48 66 0.99
49 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (47 bp):
TAGCACCACGTCACACAGACGTCAGACGCGTACTAAGTACCATATAG
Found at i:816495 original size:25 final size:25
Alignment explanation
Indices: 816461--816517 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
816451 AATGCTCCAA
816461 ACATATGGCATGCCAATTATATTAT
1 ACATATGGCATGCCAATTATATTAT
816486 ACATATGGCATGCCAATTATATTAT
1 ACATATGGCATGCCAATTATATTAT
*
816511 ACCTATG
1 ACATATG
816518 ACTCTCAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (25 bp):
ACATATGGCATGCCAATTATATTAT
Found at i:819083 original size:23 final size:23
Alignment explanation
Indices: 819057--819148 Score: 58
Period size: 24 Copynumber: 3.6 Consensus size: 23
819047 ATATTTATTT
819057 ATTTATTTTTAAAATAATTTAAA
1 ATTTATTTTTAAAATAATTTAAA
*
819080 ATTTGTATTCTATTATAAATAAATATCATAA
1 A-TT-TATT-T-TTA-AAAT-AAT-TTA-AA
* *
819111 ATTTAATTTTTAAAATAAATTAAT
1 ATTT-ATTTTTAAAATAATTTAAA
*
819135 ATTAATTTTATAAA
1 ATTTATTTT-TAAA
819149 TTATATAACT
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
23 6 0.11
24 10 0.19
25 6 0.11
26 3 0.06
27 7 0.13
28 7 0.13
29 5 0.09
30 7 0.13
31 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (23 bp):
ATTTATTTTTAAAATAATTTAAA
Found at i:819654 original size:64 final size:64
Alignment explanation
Indices: 819585--819735 Score: 169
Period size: 64 Copynumber: 2.4 Consensus size: 64
819575 CCACATAGAT
* * * **
819585 AAATAATATCTCACCTCTAAGGTCATATGTATAAATAATC-TCTCAACATTAAGGCAGCATAAAC
1 AAATAATATCTCACCACTAAGGTCACATGGATAAATAA-CATCTCAACATTAAAACAGCATAAAC
* * * ** * *
819649 AAATAATATATCGCCACTAAGGTCGCATGGATAAATAACATCTCGCCATTAAAACCGCATAAAT
1 AAATAATATCTCACCACTAAGGTCACATGGATAAATAACATCTCAACATTAAAACAGCATAAAC
*
819713 AAATAATATCTCACCAATAAGGT
1 AAATAATATCTCACCACTAAGGT
819736 TGTTGAATAA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 1 0.01
64 70 0.99
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.26
Consensus pattern (64 bp):
AAATAATATCTCACCACTAAGGTCACATGGATAAATAACATCTCAACATTAAAACAGCATAAAC
Found at i:819685 original size:32 final size:32
Alignment explanation
Indices: 819631--819765 Score: 112
Period size: 32 Copynumber: 4.2 Consensus size: 32
819621 AATCTCTCAA
* *
819631 CATTAAGG-CAGCATAAACAAATAATATATCGC
1 CATTAAGGTC-GCATGAATAAATAATATATCGC
* * * *
819663 CACTAAGGTCGCATGGATAAATAACATCTCGC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
*** * * *
819695 CATTAAAACCGCATAAATAAATAATATCTCAC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
* * *
819727 CAATAAGGTTG-TTGAATAAATAATATATCGC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
819758 CATTAAGG
1 CATTAAGG
819766 CCGTATATAT
Statistics
Matches: 78, Mismatches: 24, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
31 23 0.29
32 54 0.69
33 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (32 bp):
CATTAAGGTCGCATGAATAAATAATATATCGC
Found at i:822573 original size:15 final size:12
Alignment explanation
Indices: 822541--822571 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
822531 ACCATGCTTC
822541 CATCATCCCTTA
1 CATCATCCCTTA
822553 CATCATCCCTTA
1 CATCATCCCTTA
822565 CATCATC
1 CATCATC
822572 ATGAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.00, T:0.32
Consensus pattern (12 bp):
CATCATCCCTTA
Found at i:822983 original size:29 final size:31
Alignment explanation
Indices: 822904--822983 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 31
822894 ATAACTTTTT
822904 AAAA-TTAAACTTTGGTC-CTAAATCTTTCC
1 AAAATTTAAACTTTGGTCACTAAATCTTTCC
* * *
822933 CAAGTTTATACTTTGG-CTACTAAA-CTTT-C
1 AAAATTTAAACTTTGGTC-ACTAAATCTTTCC
*
822962 AAAATTTAAATTTTGGTCACTA
1 AAAATTTAAACTTTGGTCACTA
822984 GATGAAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
29 20 0.50
30 15 0.38
31 5 0.12
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (31 bp):
AAAATTTAAACTTTGGTCACTAAATCTTTCC
Found at i:824457 original size:18 final size:18
Alignment explanation
Indices: 824434--824472 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
824424 TAGAGACAAA
*
824434 AGAAAAGTAAACATTGTT
1 AGAAAAATAAACATTGTT
824452 AGAAAAATAAACATTGTT
1 AGAAAAATAAACATTGTT
824470 AGA
1 AGA
824473 GTTTGGCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (18 bp):
AGAAAAATAAACATTGTT
Found at i:824610 original size:21 final size:21
Alignment explanation
Indices: 824585--824625 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
824575 TTTAGGGGTC
*
824585 AAAATTATAAGTTTTAGAAAA
1 AAAATAATAAGTTTTAGAAAA
* *
824606 AAAATAATCATTTTTAGAAA
1 AAAATAATAAGTTTTAGAAA
824626 GTTGTAGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAATAATAAGTTTTAGAAAA
Found at i:825392 original size:30 final size:30
Alignment explanation
Indices: 825347--825421 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
825337 TGACCGGGTC
* * *
825347 AACTCGTTAACTTTGATCGAGTCAAACCGTT
1 AACT-GTTGACTTTGACCGAGTCAAACCATT
*
825378 AACTGTTGACTTTGACCGAGTCAACCCATT
1 AACTGTTGACTTTGACCGAGTCAAACCATT
* *
825408 GACCGTTGACTTTG
1 AACTGTTGACTTTG
825422 TCTGAAAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (30 bp):
AACTGTTGACTTTGACCGAGTCAAACCATT
Found at i:826419 original size:27 final size:28
Alignment explanation
Indices: 826381--826439 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
826371 ATTATAGAAT
*
826381 TACCCCTGAAGTGTAAAATGA-CTAAAA
1 TACCCCTAAAGTGTAAAATGACCTAAAA
* *
826408 TACCCCTAAAGTGTATAATGACCTAAAG
1 TACCCCTAAAGTGTAAAATGACCTAAAA
826436 TACC
1 TACC
826440 TCTGAACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (28 bp):
TACCCCTAAAGTGTAAAATGACCTAAAA
Found at i:830080 original size:270 final size:270
Alignment explanation
Indices: 829591--830134 Score: 964
Period size: 270 Copynumber: 2.0 Consensus size: 270
829581 CTTGTGCTGC
* *
829591 ATGAATCAACTAGCTTAAACTGTGTAAGAAAATGCAAGGGTTCTTCTAATAATATTAGAAGGGGT
1 ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
* *
829656 AGATAAAAATCTTCCAATCGTGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
66 AGATAAAAATCTTCCAATCATAGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
829721 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
131 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
** *
829786 GTGAGGTTGATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGGCGATAACTTT
196 GTGAGGTCAATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTTT
829851 ATAACAAGTG
261 ATAACAAGTG
* * *
829861 ATGAATCGACTTGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTGATAATATTAGAAGGGGT
1 ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
*
829926 AGATAATAATCTTCCAATCATAGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
66 AGATAAAAATCTTCCAATCATAGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
*
829991 GGAGTATTACAAGTTACATAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
131 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
830056 GTGAGGTCAATGTAG-AAGAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTT
196 GTGAGGTCAATGTAGCAA-AGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTT
830120 TATAACAAGTG
260 TATAACAAGTG
830131 ATGA
1 ATGA
830135 GTGGATACCT
Statistics
Matches: 261, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
269 2 0.01
270 259 0.99
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (270 bp):
ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
AGATAAAAATCTTCCAATCATAGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
GTGAGGTCAATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTTT
ATAACAAGTG
Found at i:831944 original size:21 final size:21
Alignment explanation
Indices: 831918--831959 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
831908 GTAAGTTTTA
831918 CGAACCATCTATAAATCATCC
1 CGAACCATCTATAAATCATCC
831939 CGAACCATCTATAAATCATCC
1 CGAACCATCTATAAATCATCC
831960 AACCATGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (21 bp):
CGAACCATCTATAAATCATCC
Found at i:832574 original size:36 final size:35
Alignment explanation
Indices: 832527--832603 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
832517 AGAGTAGGTA
* *
832527 TTTTTTTATTGATGTCAAGTTTAGAGTGGATTAAT
1 TTTTTTTATTGAAGTCAAGATTAGAGTGGATTAAT
*
832562 TTTTTTTAATTGAAGTCTAGATTAGAGTGGATTAAT
1 TTTTTTT-ATTGAAGTCAAGATTAGAGTGGATTAAT
832598 TTTTTT
1 TTTTTT
832604 ACTATTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 7 0.18
36 31 0.82
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (35 bp):
TTTTTTTATTGAAGTCAAGATTAGAGTGGATTAAT
Found at i:832601 original size:35 final size:35
Alignment explanation
Indices: 832511--832604 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 35
832501 ATGGTATTTA
*
832511 AAGATTAGAGTAGG--T-ATTTTTTT-ATTGATGTC
1 AAGATTAGAGT-GGATTAATTTTTTTAATTGAAGTC
*
832543 AAGTTTAGAGTGGATTAATTTTTTTTAATTGAAGTC
1 AAGATTAGAGTGGATTAA-TTTTTTTAATTGAAGTC
*
832579 TAGATTAGAGTGGATTAATTTTTTTA
1 AAGATTAGAGTGGATTAATTTTTTTA
832605 CTATTAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
31 2 0.04
32 10 0.19
33 1 0.02
34 1 0.02
35 15 0.28
36 24 0.45
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (35 bp):
AAGATTAGAGTGGATTAATTTTTTTAATTGAAGTC
Found at i:835030 original size:53 final size:53
Alignment explanation
Indices: 834961--835151 Score: 375
Period size: 53 Copynumber: 3.6 Consensus size: 53
834951 ACTTGAGGAA
834961 GCTACT-TTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
835013 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
835066 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
835119 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAAT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAAT
835152 TCTTGTTTTA
Statistics
Matches: 138, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 6 0.04
53 132 0.96
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (53 bp):
GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
Found at i:835635 original size:12 final size:12
Alignment explanation
Indices: 835600--835636 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
835590 ATTAGTATAT
835600 ATTTTT-ATTTG
1 ATTTTTCATTTG
835611 -TATTTTCATTTG
1 AT-TTTTCATTTG
835623 ATTTTTCATTTG
1 ATTTTTCATTTG
835635 AT
1 AT
835637 AATCTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 4 0.17
12 17 0.74
13 1 0.04
ACGTcount: A:0.19, C:0.05, G:0.08, T:0.68
Consensus pattern (12 bp):
ATTTTTCATTTG
Found at i:835999 original size:16 final size:16
Alignment explanation
Indices: 835941--836003 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
835931 GATACAAAAT
*
835941 ATATCCAAAGAATTTTCG
1 ATATCC-AA-AATTTTAG
*
835959 ATATCTAAAATTTTAG
1 ATATCCAAAATTTTAG
* *
835975 -TGATACAAATTTTTAG
1 AT-ATCCAAAATTTTAG
835991 ATATCCAAAATTT
1 ATATCCAAAATTT
836004 CGGATCAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 27 0.75
17 3 0.08
18 5 0.14
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (16 bp):
ATATCCAAAATTTTAG
Found at i:837256 original size:60 final size:59
Alignment explanation
Indices: 837098--837260 Score: 150
Period size: 60 Copynumber: 2.7 Consensus size: 59
837088 GCATAATGTG
* * * * *
837098 TCCTTAAAGTATGATCTTCATTTTAAATTAG-CCCTAAACTTTTAAATATTCTGACTTCA
1 TCCTTAAACTATGACCTT-ATTCTAAATTAGTCCCCAAACTTTTAAATATTCTAACTTCA
* * * * * * * *
837157 T-CTCTAAATTATGACAATTATTCTAAACTAATCCTCAAACTTTTGAATATTTTAATTTCA
1 TCCT-TAAACTATGAC-CTTATTCTAAATTAGTCCCCAAACTTTTAAATATTCTAACTTCA
*
837217 TCCTTAAACTATGACCTTAATTCTAAATTGGTCCCCAAACTTTT
1 TCCTTAAACTATGACCTT-ATTCTAAATTAGTCCCCAAACTTTT
837261 TGAACATTCC
Statistics
Matches: 81, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
58 2 0.02
59 21 0.26
60 56 0.69
61 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.42
Consensus pattern (59 bp):
TCCTTAAACTATGACCTTATTCTAAATTAGTCCCCAAACTTTTAAATATTCTAACTTCA
Found at i:837596 original size:60 final size:60
Alignment explanation
Indices: 837411--837573 Score: 170
Period size: 60 Copynumber: 2.8 Consensus size: 60
837401 CTTGGATGAA
* * * * * * * **
837411 TTTGGGGATTAAATTGGAATATTCAAAAGTTT-GGGGCCAATATAGAA-AGAGGTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTATAATGGAATTCATAG
* * * *
837469 TGTAGGGATGAAATTAGAATATTCAAAATTTTAAGGACTAATTTATAATGGAATTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTATAATGGAATTCATAG
*
837529 TTTGGGGATGCAATT-GAAATATTCAAAAGTTTAAGGACCAATTTA
1 TTTGGGGATGAAATTAG-AATATTCAAAAGTTTAAGGACCAATTTA
837574 AATAAGGGTT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
58 27 0.32
59 11 0.13
60 46 0.55
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (60 bp):
TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTATAATGGAATTCATAG
Found at i:841019 original size:19 final size:20
Alignment explanation
Indices: 840967--841025 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
840957 TAAAATCAAT
840967 CCTAGAACCCCTAACCCAAC
1 CCTAGAACCCCTAACCCAAC
840987 CCTAGAACCCCTAACCCAAC
1 CCTAGAACCCCTAACCCAAC
841007 CCTAGAA-CCCTAACCCAAC
1 CCTAGAACCCCTAACCCAAC
841026 TTACCATCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.36, C:0.49, G:0.05, T:0.10
Consensus pattern (20 bp):
CCTAGAACCCCTAACCCAAC
Found at i:845893 original size:30 final size:30
Alignment explanation
Indices: 845853--845930 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
845843 TATTTAGTGT
*
845853 CCAAATTATAAATTTGTTAAAGTTT-GGTGA
1 CCAAAATATAAATTTGTTAAAGTTTAGG-GA
*
845883 CCAAAGTATAAACTTTG--AAAGTTTAGGGA
1 CCAAAATATAAA-TTTGTTAAAGTTTAGGGA
845912 CCAAAATAT-AATTT-TTAAA
1 CCAAAATATAAATTTGTTAAA
845931 AAATTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
27 3 0.07
28 5 0.12
29 17 0.40
30 13 0.31
31 4 0.10
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (30 bp):
CCAAAATATAAATTTGTTAAAGTTTAGGGA
Found at i:846149 original size:14 final size:14
Alignment explanation
Indices: 846130--846165 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
846120 GACTATTGGA
846130 AGATGATAATACTG
1 AGATGATAATACTG
846144 AGATGATAATACTG
1 AGATGATAATACTG
846158 AGATGATA
1 AGATGATA
846166 TGATTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (14 bp):
AGATGATAATACTG
Found at i:848049 original size:24 final size:23
Alignment explanation
Indices: 847971--848053 Score: 91
Period size: 23 Copynumber: 3.6 Consensus size: 23
847961 ACATATTATA
*
847971 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
847994 TGGCACTTCGGTGC-ATCTCTACG
1 TGGCACTTCGGTGCAAT-TCTACG
*
848017 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
848041 TGGCACTTCGGTG
1 TGGCACTTCGGTG
848054 TAAATTTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
22 3 0.06
23 29 0.58
24 15 0.30
25 3 0.06
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:848550 original size:6 final size:6
Alignment explanation
Indices: 848539--848585 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
848529 GAACGTATTT
848539 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
848586 TAGTAATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTAA
Found at i:848690 original size:21 final size:22
Alignment explanation
Indices: 848649--848693 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
848639 TGTAGCAGTA
*
848649 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
*
848671 CTGTAGCA-GGGTACCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
848692 CT
1 CT
848694 ATTTGGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.20, C:0.27, G:0.29, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGAACCGATTCC
Found at i:849360 original size:31 final size:31
Alignment explanation
Indices: 849290--849360 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
849280 TGTAATTTTT
* * *
849290 GAAAAGTTAGGGTACTAATTCGACAACTTTG
1 GAAAAGTTGGGGGACCAATTCGACAACTTTG
849321 GAAAAGTTGGGGGACCAATTCGACAACTTTG
1 GAAAAGTTGGGGGACCAATTCGACAACTTTG
849352 GAAAAGTTG
1 GAAAAGTTG
849361 TGAATGATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (31 bp):
GAAAAGTTGGGGGACCAATTCGACAACTTTG
Found at i:850471 original size:45 final size:45
Alignment explanation
Indices: 850363--850500 Score: 219
Period size: 45 Copynumber: 3.1 Consensus size: 45
850353 GATAAACTAG
850363 AAAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
850407 -AAATAAGCTTACGAGCTTATGAAATAAATGGTAAGAATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
850451 AAAATAAGATTATGAGCTTATGGAATAAATGGTAAGTATA-TGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
850495 AAAATA
1 AAAATA
850501 TTGGATATGC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
43 24 0.28
44 27 0.31
45 35 0.41
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:851433 original size:24 final size:21
Alignment explanation
Indices: 851401--851452 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 21
851391 ACACCATTTA
851401 AACCAAAATCAAACAAAAAATAT
1 AACCAAAATCAAA-AAAAAAT-T
*
851424 CAACCAAAATCGAAAAAAAATT
1 -AACCAAAATCAAAAAAAAATT
851446 AACCAAA
1 AACCAAA
851453 CTATAAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 7 0.26
24 12 0.44
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (21 bp):
AACCAAAATCAAAAAAAAATT
Found at i:852719 original size:2 final size:2
Alignment explanation
Indices: 852712--852799 Score: 133
Period size: 2 Copynumber: 44.5 Consensus size: 2
852702 TAACTATACC
852712 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
* * * *
852754 AT AT AT AT AT AT AT AT AT AT AT -T AC AT GT AT AT AA AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
852795 AT AT A
1 AT AT A
852800 GCCATGGCCC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:853693 original size:2 final size:2
Alignment explanation
Indices: 853686--853722 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
853676 AAATATCTAA
853686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
853723 ATCTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:857222 original size:4 final size:4
Alignment explanation
Indices: 857213--857290 Score: 56
Period size: 4 Copynumber: 19.5 Consensus size: 4
857203 GGACCTGAAA
* *
857213 AAAT AAAT AAAT -AAT AATAT ATAT AAAT ATAAT -AAT -AAT -AAT AAAG
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* *
857259 AAAG AAAG AAAT AATAT AAAT AATAT AAAT AA
1 AAAT AAAT AAAT AA-AT AAAT AA-AT AAAT AA
857291 TATTAATATA
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
3 12 0.19
4 38 0.59
5 14 0.22
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:857256 original size:18 final size:19
Alignment explanation
Indices: 857214--857292 Score: 68
Period size: 21 Copynumber: 3.8 Consensus size: 19
857204 GACCTGAAAA
857214 AATAAATAAATAATAATAT
1 AATAAATAAATAATAATAT
857233 ATATAAATATAATAATAATAAT
1 A-ATAAATA-AATAATAAT-AT
* * *
857255 AAAGAAAGAAAGAAATAATAT
1 -AATAAATAAA-TAATAATAT
857276 AAATAATATAAATAATA
1 -AATAA-ATAAATAATA
857293 TTAATATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.02
20 7 0.15
21 22 0.46
22 17 0.35
23 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
AATAAATAAATAATAATAT
Found at i:857281 original size:9 final size:9
Alignment explanation
Indices: 857215--857305 Score: 68
Period size: 9 Copynumber: 10.3 Consensus size: 9
857205 ACCTGAAAAA
857215 ATAAATAA-
1 ATAAATAAT
857223 AT-AATAAT
1 ATAAATAAT
*
857231 ATATATAA-
1 ATAAATAAT
857239 ATATAATAAT
1 ATA-AATAAT
857249 A-ATAATAA-
1 ATA-AATAAT
* *
857257 AGAAAGAA-
1 ATAAATAAT
*
857265 AGAAATAAT
1 ATAAATAAT
857274 ATAAATAAT
1 ATAAATAAT
857283 ATAAATAAT
1 ATAAATAAT
857292 ATTAATATAAT
1 A-TAA-ATAAT
857303 ATA
1 ATA
857306 TAAGGTAATG
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
7 5 0.07
8 19 0.27
9 34 0.49
10 6 0.09
11 6 0.09
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
ATAAATAAT
Found at i:857363 original size:18 final size:18
Alignment explanation
Indices: 857334--857376 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
857324 TGAACATATA
857334 ATATATAAGTATATTAACT
1 ATATA-AAGTATATTAACT
857353 ATATAAAGTATATTAACT
1 ATATAAAGTATATTAACT
857371 ATATAA
1 ATATAA
857377 TATATTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
ATATAAAGTATATTAACT
Found at i:857442 original size:16 final size:16
Alignment explanation
Indices: 857421--857474 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
857411 TATTATATAC
857421 GTTTTCAAAACCATAT
1 GTTTTCAAAACCATAT
857437 GTTTTC-AAA--A-AT
1 GTTTTCAAAACCATAT
* *
857449 GTTTTCAAACCCATAC
1 GTTTTCAAAACCATAT
*
857465 GTTTTTAAAA
1 GTTTTCAAAA
857475 ATGTTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
15 4 0.13
16 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (16 bp):
GTTTTCAAAACCATAT
Found at i:857452 original size:12 final size:12
Alignment explanation
Indices: 857435--857486 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
857425 TCAAAACCAT
857435 ATGTTTTCAAAA
1 ATGTTTTCAAAA
857447 ATGTTTTCAAACCCA
1 ATGTTTTCAAA---A
* *
857462 TACGTTTTTAAAA
1 -ATGTTTTCAAAA
857475 ATGTTTTCAAAA
1 ATGTTTTCAAAA
857487 CTATATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 21 0.66
13 1 0.03
15 1 0.03
16 9 0.28
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:857462 original size:28 final size:28
Alignment explanation
Indices: 857421--857487 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
857411 TATTATATAC
*
857421 GTTTTCAAAACCATATGTTTTCAAAAAT
1 GTTTTCAAAACCATACGTTTTCAAAAAT
* *
857449 GTTTTCAAACCCATACGTTTTTAAAAAT
1 GTTTTCAAAACCATACGTTTTCAAAAAT
857477 GTTTTCAAAAC
1 GTTTTCAAAAC
857488 TATATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (28 bp):
GTTTTCAAAACCATACGTTTTCAAAAAT
Found at i:862197 original size:18 final size:18
Alignment explanation
Indices: 862174--862226 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
862164 AGGGATTATC
*
862174 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
862192 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
862210 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
862227 AATACTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:862678 original size:212 final size:213
Alignment explanation
Indices: 862310--862709 Score: 757
Period size: 212 Copynumber: 1.9 Consensus size: 213
862300 ATACCTTCTA
*
862310 TTCTCAATAATGTATATGGGCATTCAAACATAAATTAAAGGAAAACTCTTATGAAACATAATTGT
1 TTCTCAATAATGTACATGGGCATTCAAACATAAATTAAAGGAAAACTCTTATGAAACATAATTGT
862375 TCATTCATGCATATCATACTTATATGTCATAATGTGATATCTACAGGTGCATTGCAATGTCTTAG
66 TCATTCATGCATATCATACTTATATGTCATAATGTGATATCTACAGGTGCATTGCAATGTCTTAG
862440 TGGATTAATAGTAGTGTGTATTCATGATATTATTGTTGTATGTTTATTTTATGCCTCACCTCACT
131 TGGATTAATAGTAGTGTGTATTCATGATATTATTGTTGTATGTTTATTTTATGCCTCACCTCACT
862505 GTACTCACGTACTTTTTG
196 GTACTCACGTACTTTTTG
* *
862523 TTCTCAATAATGTGCATGGGCATTCAAAGATAAATTAAA-GAAAACTCTTATGAAACATAATTGT
1 TTCTCAATAATGTACATGGGCATTCAAACATAAATTAAAGGAAAACTCTTATGAAACATAATTGT
*
862587 TCATTCATGCATATCATACTTATATGTCATAGTGTGATATCTACAGGTGCATTGCAATGTCTTAG
66 TCATTCATGCATATCATACTTATATGTCATAATGTGATATCTACAGGTGCATTGCAATGTCTTAG
862652 TGGATTAATAGTAGTGTGTATTCATGATATTATTGTTGTATGTTTATTTTATGCCTCA
131 TGGATTAATAGTAGTGTGTATTCATGATATTATTGTTGTATGTTTATTTTATGCCTCA
862710 ATAAGTTTGT
Statistics
Matches: 183, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
212 147 0.80
213 36 0.20
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (213 bp):
TTCTCAATAATGTACATGGGCATTCAAACATAAATTAAAGGAAAACTCTTATGAAACATAATTGT
TCATTCATGCATATCATACTTATATGTCATAATGTGATATCTACAGGTGCATTGCAATGTCTTAG
TGGATTAATAGTAGTGTGTATTCATGATATTATTGTTGTATGTTTATTTTATGCCTCACCTCACT
GTACTCACGTACTTTTTG
Found at i:868274 original size:18 final size:18
Alignment explanation
Indices: 868249--868301 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
868239 AGGGATTATC
868249 AGTGGTCCTAT-GGGACAT
1 AGTGGTCCT-TCGGGACAT
*
868267 ATTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
868285 AGTGGTTCTTCGAGACA
1 AGTGGTCCTTCGGGACA
868302 AATACTTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:870203 original size:25 final size:23
Alignment explanation
Indices: 870146--870206 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
870136 CCCCCCATAC
*
870146 TTTAACACTTTTCCCATTTAAAA
1 TTTAACACTTCTCCCATTTAAAA
870169 --TAACACTTCTCCCATTTAAAACA
1 TTTAACACTTCTCCCATTT-AAA-A
870192 TTTAACACTTCTCCC
1 TTTAACACTTCTCCC
870207 CCTTTTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 16 0.48
22 3 0.09
23 1 0.03
25 13 0.39
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAACACTTCTCCCATTTAAAA
Found at i:871542 original size:21 final size:21
Alignment explanation
Indices: 871510--871591 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 21
871500 CCAGAACCCT
871510 AGGGGGATATCGATTCCCCTAA
1 AGGGGGA-ATCGATTCCCCTAA
* *
871532 AGGGGGAATCGGTTCCTCTTCAA
1 AGGGGGAATCGATTCC-CCT-AA
* * *
871555 AGGGGGGATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCTAA
* *
871575 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
871592 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 12 0.24
21 12 0.24
22 10 0.20
23 15 0.31
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTAA
Found at i:871585 original size:20 final size:21
Alignment explanation
Indices: 871510--871593 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 21
871500 CCAGAACCCT
*
871510 AGGGGGATATCGATTCCC-CTAA
1 AGGGGGA-ATCGGTTCCCTC-AA
871532 AGGGGGAATCGGTTCCTCTTCAA
1 AGGGGGAATCGGTTCC-C-TCAA
*
871555 AGGGGGGATCGGTTCCCTC-A
1 AGGGGGAATCGGTTCCCTCAA
* * *
871575 TGGGGGTATCGATTCCCTC
1 AGGGGGAATCGGTTCCCTC
871594 TGCACCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 17 0.31
21 10 0.19
22 9 0.17
23 17 0.31
24 1 0.02
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:872793 original size:20 final size:20
Alignment explanation
Indices: 872732--872793 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
872722 ACCAGAACCC
*
872732 CAGGGGGATATCGATTCCCCT
1 CAGGGGGGTATCGATT-CCCT
* * *
872753 AAGGGGGGAATCGGTTCCCT
1 CAGGGGGGTATCGATTCCCT
*
872773 CATGGGGGTATCGATTCCCT
1 CAGGGGGGTATCGATTCCCT
872793 C
1 C
872794 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (20 bp):
CAGGGGGGTATCGATTCCCT
Found at i:873965 original size:20 final size:21
Alignment explanation
Indices: 873934--874014 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 21
873924 CCAGAACCCC
873934 AGGGGGATATCGATTCCCCT-A
1 AGGGGGA-ATCGATTCCCCTCA
*
873955 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-TC-A
*
873978 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGATTCCCCTCA
* *
873998 TGGGGGTATCGATTCCC
1 AGGGGGAATCGATTCCC
874015 TCTGCACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
20 22 0.42
21 12 0.23
22 3 0.06
23 15 0.29
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTCA
Found at i:873984 original size:23 final size:20
Alignment explanation
Indices: 873934--873994 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
873924 CCAGAACCCC
*
873934 AGGGGGATATCGATTCCCCTA
1 AGGGGGA-ATCGGTTCCCCTA
873955 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCC-T--A
873978 AGGGGGAATCGGTTCCC
1 AGGGGGAATCGGTTCCC
873995 TCATGGGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 10 0.28
21 8 0.22
23 18 0.50
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (20 bp):
AGGGGGAATCGGTTCCCCTA
Found at i:889498 original size:22 final size:23
Alignment explanation
Indices: 889472--889517 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
889462 TTTGTTTTTC
889472 TTCA-CTTTCGGTTTCGAAAGTT
1 TTCACCTTTCGGTTTCGAAAGTT
* *
889494 TTCACCTTTGGGTTTCGAATGTT
1 TTCACCTTTCGGTTTCGAAAGTT
889517 T
1 T
889518 ATCGAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (23 bp):
TTCACCTTTCGGTTTCGAAAGTT
Found at i:890063 original size:8 final size:7
Alignment explanation
Indices: 890035--890080 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 7
890025 AGGTAATGAA
890035 AATATAT
1 AATATAT
*
890042 GAACATAT
1 -AATATAT
890050 AATATAT
1 AATATAT
890057 AAGTATAT
1 AA-TATAT
890065 AACTATAT
1 AA-TATAT
890073 AATATAT
1 AATATAT
890080 A
1 A
890081 TTATGTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
7 14 0.41
8 20 0.59
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (7 bp):
AATATAT
Found at i:890063 original size:23 final size:23
Alignment explanation
Indices: 890037--890080 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
890027 GTAATGAAAA
890037 TATATGAAC-ATATAATATATAAG
1 TATAT-AACTATATAATATATAAG
890060 TATATAACTATATAATATATA
1 TATATAACTATATAATATATA
890081 TTATGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (23 bp):
TATATAACTATATAATATATAAG
Found at i:890101 original size:11 final size:11
Alignment explanation
Indices: 890085--890132 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 11
890075 TATATATTAT
890085 GTTTTCAAAAC
1 GTTTTCAAAAC
890096 GTTTTCAAAATC
1 GTTTTCAAAA-C
890108 ATATGTTTTCAAAAC
1 ----GTTTTCAAAAC
890123 GTTTTCAAAA
1 GTTTTCAAAA
890133 TCATATGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 20 0.62
12 1 0.03
15 1 0.03
16 10 0.31
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (11 bp):
GTTTTCAAAAC
Found at i:890117 original size:16 final size:16
Alignment explanation
Indices: 890096--890148 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
890086 TTTTCAAAAC
890096 GTTTTCAAAATCATAT
1 GTTTTCAAAATCATAT
890112 GTTTTCAAAA-C----
1 GTTTTCAAAATCATAT
890123 GTTTTCAAAATCATAT
1 GTTTTCAAAATCATAT
890139 GTTTTCAAAA
1 GTTTTCAAAA
890149 ACTATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 10 0.31
12 1 0.03
15 1 0.03
16 20 0.62
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (16 bp):
GTTTTCAAAATCATAT
Found at i:890120 original size:27 final size:27
Alignment explanation
Indices: 890082--890201 Score: 138
Period size: 27 Copynumber: 4.4 Consensus size: 27
890072 TAATATATAT
890082 TATGTTTTCAAAACGTTTTCAAAATCA
1 TATGTTTTCAAAACGTTTTCAAAATCA
890109 TATGTTTTCAAAACGTTTTCAAAATCA
1 TATGTTTTCAAAACGTTTTCAAAATCA
* **
890136 TATGTTTTCAAAAAC-TATAT-ATTAT-A
1 TATGTTTTC-AAAACGT-TTTCAAAATCA
* * *
890162 TACGTTTTCAAAGATGTTTTCAAAACCA
1 TATGTTTTCAAA-ACGTTTTCAAAATCA
890190 TATGTTTTCAAA
1 TATGTTTTCAAA
890202 TATATTTTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
25 3 0.04
26 12 0.16
27 43 0.56
28 19 0.25
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (27 bp):
TATGTTTTCAAAACGTTTTCAAAATCA
Found at i:890155 original size:17 final size:16
Alignment explanation
Indices: 890096--890155 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
890086 TTTTCAAAAC
*
890096 GTTTTCAAAATCATAT
1 GTTTTCAAAAACATAT
890112 GTTTTC-AAAAC----
1 GTTTTCAAAAACATAT
*
890123 GTTTTCAAAATCATAT
1 GTTTTCAAAAACATAT
890139 GTTTTCAAAAACTATAT
1 GTTTTCAAAAAC-ATAT
890156 ATTATATACG
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
15 4 0.11
16 17 0.49
17 4 0.11
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (16 bp):
GTTTTCAAAAACATAT
Found at i:890204 original size:12 final size:12
Alignment explanation
Indices: 890165--890278 Score: 68
Period size: 12 Copynumber: 8.8 Consensus size: 12
890155 TATTATATAC
*
890165 GTTTTCAAAGAT
1 GTTTTCAAATAT
890177 GTTTTCAAAACCATAT
1 GTTTTC--AA--ATAT
890193 GTTTTCAAATAT
1 GTTTTCAAATAT
*
890205 ATTTTCAAAACTAT
1 GTTTTC-AAA-TAT
* * *
890219 ATATT-ATATAT
1 GTTTTCAAATAT
*
890230 GTTTTCAAAGAT
1 GTTTTCAAATAT
890242 GTTTTCAAAACCATAT
1 GTTTTC--AA--ATAT
*
890258 GTTTTCAAAAAT
1 GTTTTCAAATAT
890270 GTTTTCAAA
1 GTTTTCAAA
890279 ACCATATATT
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.07
12 39 0.48
13 3 0.04
14 15 0.19
16 18 0.22
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (12 bp):
GTTTTCAAATAT
Found at i:890209 original size:28 final size:27
Alignment explanation
Indices: 890082--890220 Score: 120
Period size: 27 Copynumber: 5.1 Consensus size: 27
890072 TAATATATAT
* *
890082 TATGTTTTCAAAACGTTTTCAAAATCA
1 TATGTTTTCAAAATGTTTTCAAAACCA
* *
890109 TATGTTTTCAAAACGTTTTCAAAATCA
1 TATGTTTTCAAAATGTTTTCAAAACCA
** * ** *
890136 TATGTTTTCAAAAACTATAT-ATTA-TA
1 TATGTTTTCAAAATGT-TTTCAAAACCA
*
890162 TACGTTTTCAAAGATGTTTTCAAAACCA
1 TATGTTTTCAAA-ATGTTTTCAAAACCA
* *
890190 TATGTTTTCAAATATATTTTCAAAACTA
1 TATGTTTTCAAA-ATGTTTTCAAAACCA
890218 TAT
1 TAT
890221 ATTATATATG
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.15
27 47 0.52
28 30 0.33
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (27 bp):
TATGTTTTCAAAATGTTTTCAAAACCA
Found at i:890215 original size:65 final size:65
Alignment explanation
Indices: 890135--890320 Score: 304
Period size: 65 Copynumber: 2.9 Consensus size: 65
890125 TTTCAAAATC
890135 ATATGTTTTCAAAAACTATATATTATATACGTTTTCAAAGATGTTTTCAAAACCATATGTTTTCA
1 ATATGTTTTC-AAAACTATATATTATATACGTTTTCAAAGATGTTTTCAAAACCATATGTTTTCA
890200 A
65 A
* *
890201 ATATATTTTCAAAACTATATATTATATATGTTTTCAAAGATGTTTTCAAAACCATATGTTTTCAA
1 ATATGTTTTCAAAACTATATATTATATACGTTTTCAAAGATGTTTTCAAAACCATATGTTTTCAA
* * *
890266 AAATGTTTTCAAAACCATATA-T-TATACGTTTTCAAACATGTTTTCAAAACCATAT
1 ATATGTTTTCAAAACTATATATTATATACGTTTTCAAAGATGTTTTCAAAACCATAT
890321 AATATACATT
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
63 31 0.27
64 1 0.01
65 72 0.64
66 9 0.08
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (65 bp):
ATATGTTTTCAAAACTATATATTATATACGTTTTCAAAGATGTTTTCAAAACCATATGTTTTCAA
Found at i:890261 original size:16 final size:16
Alignment explanation
Indices: 890240--890285 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
890230 GTTTTCAAAG
890240 ATGTTTTCAAAACCAT
1 ATGTTTTCAAAACCAT
890256 ATGTTTTC-AAA--A-
1 ATGTTTTCAAAACCAT
890268 ATGTTTTCAAAACCAT
1 ATGTTTTCAAAACCAT
890284 AT
1 AT
890286 ATTATACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
15 4 0.15
16 10 0.38
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (16 bp):
ATGTTTTCAAAACCAT
Found at i:890261 original size:28 final size:28
Alignment explanation
Indices: 890226--890285 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
890216 TATATATTAT
*
890226 ATATGTTTTCAAAGATGTTTTCAAAACC
1 ATATGTTTTCAAAAATGTTTTCAAAACC
890254 ATATGTTTTCAAAAATGTTTTCAAAACC
1 ATATGTTTTCAAAAATGTTTTCAAAACC
890282 ATAT
1 ATAT
890286 ATTATACGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (28 bp):
ATATGTTTTCAAAAATGTTTTCAAAACC
Found at i:890307 original size:35 final size:35
Alignment explanation
Indices: 890258--890403 Score: 171
Period size: 35 Copynumber: 4.3 Consensus size: 35
890248 AAAACCATAT
*
890258 GTTTTCAAAAATGTTTTCAAAACCATATATTATAC
1 GTTTTCAAAAATGTTTTCAAAACCATATAATATAC
*
890293 GTTTTCAAACATGTTTTCAAAACCATATAATATAC
1 GTTTTCAAAAATGTTTTCAAAACCATATAATATAC
*
890328 ATTTTCAAAAATGTTTTCAAAACC-----ATAT--
1 GTTTTCAAAAATGTTTTCAAAACCATATAATATAC
* * *
890356 GTTTTTAAAAATGTTTTCAAAACTATATATTATATAT
1 GTTTTCAAAAATGTTTTCAAAACCATATA--ATATAC
890393 GTTTTCAAAAA
1 GTTTTCAAAAA
890404 CCGTTTTTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
28 21 0.22
30 4 0.04
35 59 0.63
37 10 0.11
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (35 bp):
GTTTTCAAAAATGTTTTCAAAACCATATAATATAC
Found at i:890310 original size:12 final size:12
Alignment explanation
Indices: 890165--890313 Score: 54
Period size: 12 Copynumber: 11.8 Consensus size: 12
890155 TATTATATAC
*
890165 GTTTTCAAAGAT
1 GTTTTCAAACAT
890177 GTTTTCAAAACCATAT
1 GTTTTC-AAA-C--AT
*
890193 GTTTTCAAATAT
1 GTTTTCAAACAT
*
890205 ATTTTCAAAACTAT
1 GTTTTC-AAAC-AT
* * * *
890219 ATATT-ATATAT
1 GTTTTCAAACAT
*
890230 GTTTTCAAAGAT
1 GTTTTCAAACAT
890242 GTTTTCAAAACCATAT
1 GTTTTC-AAA-C--AT
*
890258 GTTTTCAAAAAT
1 GTTTTCAAACAT
890270 GTTTTCAAAACCAT
1 GTTTTC-AAA-CAT
* * *
890284 ATATT-ATAC--
1 GTTTTCAAACAT
890293 GTTTTCAAACAT
1 GTTTTCAAACAT
890305 GTTTTCAAA
1 GTTTTCAAA
890314 ACCATATAAT
Statistics
Matches: 101, Mismatches: 20, Indels: 32
0.66 0.13 0.21
Matches are distributed among these distances:
9 3 0.03
10 3 0.03
11 6 0.06
12 44 0.44
13 12 0.12
14 11 0.11
15 6 0.06
16 16 0.16
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (12 bp):
GTTTTCAAACAT
Found at i:890346 original size:12 final size:12
Alignment explanation
Indices: 890329--890377 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
890319 ATAATATACA
890329 TTTTCAAAAATG
1 TTTTCAAAAATG
890341 TTTTCAAAACCATATG
1 TTTTC-AAA--A-ATG
*
890357 TTTTTAAAAATG
1 TTTTCAAAAATG
890369 TTTTCAAAA
1 TTTTCAAAA
890378 CTATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 16 0.52
13 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTTCAAAAATG
Found at i:890356 original size:98 final size:99
Alignment explanation
Indices: 890193--890389 Score: 306
Period size: 98 Copynumber: 2.0 Consensus size: 99
890183 AAAACCATAT
* * ** *
890193 GTTTTCAAATATATTTTCAAAACTATATATTATATATGTTTTCAAAGATGTTTTCAAAACCATAT
1 GTTTTCAAACATATTTTCAAAACCATATA-TATATACATTTTCAAAAATGTTTTCAAAACCATAT
890258 GTTTTCAAAAATGTTTTCAAAACCATATATTATAC
65 GTTTTCAAAAATGTTTTCAAAACCATATATTATAC
*
890293 GTTTTCAAACATGTTTTCAAAACCATATA-ATATACATTTTCAAAAATGTTTTCAAAACCATATG
1 GTTTTCAAACATATTTTCAAAACCATATATATATACATTTTCAAAAATGTTTTCAAAACCATATG
* *
890357 TTTTTAAAAATGTTTTCAAAACTATATATTATA
66 TTTTCAAAAATGTTTTCAAAACCATATATTATA
890390 TATGTTTTCA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 63 0.71
100 26 0.29
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (99 bp):
GTTTTCAAACATATTTTCAAAACCATATATATATACATTTTCAAAAATGTTTTCAAAACCATATG
TTTTCAAAAATGTTTTCAAAACCATATATTATAC
Found at i:890369 original size:28 final size:28
Alignment explanation
Indices: 890329--890383 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
890319 ATAATATACA
890329 TTTTCAAAAATGTTTTCAAAACCATATG
1 TTTTCAAAAATGTTTTCAAAACCATATG
* *
890357 TTTTTAAAAATGTTTTCAAAACTATAT
1 TTTTCAAAAATGTTTTCAAAACCATAT
890384 ATTATATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (28 bp):
TTTTCAAAAATGTTTTCAAAACCATATG
Found at i:893585 original size:2 final size:2
Alignment explanation
Indices: 893576--893608 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
893566 ATGTTTAAAC
893576 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
893609 AAAGATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:895352 original size:20 final size:20
Alignment explanation
Indices: 895315--895352 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
895305 ACTTAACTTC
*
895315 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
895335 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
895353 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:895596 original size:31 final size:32
Alignment explanation
Indices: 895560--895652 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 32
895550 ACCTCGGCAA
*
895560 CTGTCCATATGTTCCTTAGAACATAGGT-ATAT
1 CTGTCCATATGTTCCCTAGAACATAGGTAAT-T
* *
895592 -TGTCCATATG-TCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCCTAGA-ACATAGGTAATT
* *
895623 CTATCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTTCCCTAGAACATAGGTAA
895653 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
30 5 0.10
31 19 0.38
32 21 0.42
33 5 0.10
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (32 bp):
CTGTCCATATGTTCCCTAGAACATAGGTAATT
Found at i:898722 original size:13 final size:15
Alignment explanation
Indices: 898704--898735 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
898694 ATGCATGAAC
898704 ATATCATA-AAAT-A
1 ATATCATACAAATCA
898717 ATATCATACAAATCA
1 ATATCATACAAATCA
898732 ATAT
1 ATAT
898736 AACATTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATCATACAAATCA
Found at i:898897 original size:20 final size:20
Alignment explanation
Indices: 898860--898897 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
898850 ACTTAACTTC
*
898860 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
898880 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
898898 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:899141 original size:31 final size:31
Alignment explanation
Indices: 899106--899196 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
899096 CCTCGACAAT
*
899106 TGTCCATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATATGTTCCGTAGAACATAGGTATAC
* * * **
899137 TGTCCATATGTCCCGAAAAACATAGGTAATTT
1 TGTCCATATGTTCCGTAGAACATAGGT-ATAC
* *
899169 TGTCCATATGTTCAGTAGAATATAGGTA
1 TGTCCATATGTTCCGTAGAACATAGGTA
899197 AACCCTCGAC
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (31 bp):
TGTCCATATGTTCCGTAGAACATAGGTATAC
Found at i:899194 original size:32 final size:32
Alignment explanation
Indices: 899104--899197 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 32
899094 AACCTCGACA
*
899104 ATTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ATTGTCCATATGTTCCGTAGAACATAGGTAAT
* * * *
899135 ACTGTCCATATGTCCCGAAAAACATAGGTAAT
1 ATTGTCCATATGTTCCGTAGAACATAGGTAAT
* * *
899167 TTTGTCCATATGTTCAGTAGAATATAGGTAA
1 ATTGTCCATATGTTCCGTAGAACATAGGTAA
899198 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (32 bp):
ATTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:903047 original size:20 final size:20
Alignment explanation
Indices: 903010--903047 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
903000 ACTTAACTTC
*
903010 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
903030 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
903048 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:905610 original size:22 final size:22
Alignment explanation
Indices: 905585--905626 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
905575 GTTTCAAGCC
905585 CTAGGTGTTTA-GCTCTGTTGGG
1 CTAGG-GTTTAGGCTCTGTTGGG
*
905607 CTAGGGTTTAGGCTTTGTTG
1 CTAGGGTTTAGGCTCTGTTG
905627 TTGGGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.10, C:0.12, G:0.36, T:0.43
Consensus pattern (22 bp):
CTAGGGTTTAGGCTCTGTTGGG
Found at i:909210 original size:3 final size:3
Alignment explanation
Indices: 909202--909275 Score: 125
Period size: 3 Copynumber: 25.0 Consensus size: 3
909192 TTGTCTCGAC
909202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT -TT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
909246 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
909276 TTGTGCAGGC
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 62 0.90
4 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:911477 original size:131 final size:130
Alignment explanation
Indices: 911259--911591 Score: 515
Period size: 131 Copynumber: 2.5 Consensus size: 130
911249 ATTTCGGTTG
** *
911259 GAGTAATAAATGACCGCTTTAAGGCATAAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAAT-ATTAGATAT
* * * *
911324 TATCGTTTTCTCTCGAATCAATATTGA-TTTTCAAGACGGAATAGTGATATCTCTTCATTTCTAT
65 TATCGTTTTCACTCGAAGCAATATTGACTTTT-AAGACGAAATAGTGATATCTCTTCATTTCGAT
*
911388 TA
129 CA
*
911390 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTAGAAATCATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAAT-ATTAGATAT
* *
911455 TATCGTTTTCACTCGAAGCAATATTGACTTTTAAGATGAAATAGTGATATCTCTTCTTTTCGATC
65 TATCGTTTTCACTCGAAGCAATATTGACTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATC
*
911520 G
130 A
911521 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATACTTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATA-TTAGATAT
911586 TATCGT
65 TATCGT
911592 GTTTTAAAAA
Statistics
Matches: 186, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
130 1 0.01
131 181 0.97
132 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (130 bp):
GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATATTAGATATT
ATCGTTTTCACTCGAAGCAATATTGACTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATCA
Found at i:914372 original size:27 final size:27
Alignment explanation
Indices: 914340--914408 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
914330 TATGGGGTTG
* *
914340 TGCATCATCTCGAAAGATGGAATACTA
1 TGCATCACCTCGAAAGATGAAATACTA
* *
914367 TGCATCACCTCGAAGGATGAAATATTA
1 TGCATCACCTCGAAAGATGAAATACTA
*
914394 TGCATCACCTTGAAA
1 TGCATCACCTCGAAA
914409 TGTGGAACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (27 bp):
TGCATCACCTCGAAAGATGAAATACTA
Found at i:914550 original size:17 final size:17
Alignment explanation
Indices: 914524--914576 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
914514 TACAAACCTC
* *
914524 TATAATATTTAATAGCA
1 TATAACATTTAATAACA
* *
914541 TGTAACATTTAATAACT
1 TATAACATTTAATAACA
914558 TATAACATTTAAT-ACA
1 TATAACATTTAATAACA
914574 TAT
1 TAT
914577 GATCATGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (17 bp):
TATAACATTTAATAACA
Found at i:921674 original size:29 final size:29
Alignment explanation
Indices: 921637--921696 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
921627 CATTTAATTT
*
921637 TGGATCTACGAAAATTGCAATAATCCTCA
1 TGGAGCTACGAAAATTGCAATAATCCTCA
*
921666 TGGAGCTACGACAATTGCAATAATCCTCA
1 TGGAGCTACGAAAATTGCAATAATCCTCA
921695 TG
1 TG
921697 AAACTCGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
TGGAGCTACGAAAATTGCAATAATCCTCA
Found at i:924026 original size:27 final size:26
Alignment explanation
Indices: 923979--924030 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
923969 GAAATGATTG
* *
923979 AAATACCTTGGATATGTAAAATGACCA
1 AAATACCCTGGATATGCAAAA-GACCA
924006 AAATAACCCTGGA-ATGCAAAAGACC
1 AAAT-ACCCTGGATATGCAAAAGACC
924031 CAAGAATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 7 0.32
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.19
Consensus pattern (26 bp):
AAATACCCTGGATATGCAAAAGACCA
Done.