Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009597.1 Hibiscus syriacus cultivar Beakdansim tig00116976_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: 1557931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 7
Found at i:420938 original size:41 final size:41
Alignment explanation
Indices: 420893--420985 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
420883 TTTTCCCAAT
*
420893 TCGCAATGCGAATAAGTAAATCGCAAAGCAAATTGGGGAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCAAATTGGGAAAA
* *
420934 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCAAATTGGGAAAA
420975 TCGCAATGCGA
1 TCGCAATGCGA
420986 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAAAGCAAATTGGGAAAA
Found at i:420998 original size:41 final size:41
Alignment explanation
Indices: 420912--421046 Score: 105
Period size: 41 Copynumber: 3.3 Consensus size: 41
420902 GAATAAGTAA
* * * * *
420912 ATCGCAAAGCAAATTGGGGAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
420953 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
420994 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
421035 TTCGCAACGCGA
1 ATCGCAACGCGA
421047 TACTGACTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
40 4 0.05
41 71 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:420999 original size:20 final size:20
Alignment explanation
Indices: 420974--421088 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
420964 AATTGGGAAA
*
420974 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
420994 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
421015 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
421035 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
421055 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
421075 TTCGCAACGCGATA
1 ATCGCAACGCGATA
421089 ATACATAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:421047 original size:41 final size:41
Alignment explanation
Indices: 420971--421102 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
420961 GCGAATTGGG
* * *
420971 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* * * *
421012 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACT-G
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
*** * *
421052 ACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
*
421093 ATAATCGCAA
1 AAAATCGCAA
421103 TACGATTTTC
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.44
41 40 0.56
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:421304 original size:22 final size:22
Alignment explanation
Indices: 421276--421319 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
421266 CACTCTCTCA
421276 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
421298 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
421320 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:421621 original size:20 final size:20
Alignment explanation
Indices: 421598--421640 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
421588 GATAGTCGAA
421598 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
421618 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
421638 TTC
1 TTC
421641 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:422981 original size:18 final size:18
Alignment explanation
Indices: 422960--422995 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
422950 TCCACTTTGG
*
422960 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
422978 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
422996 CGTCACATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.47, G:0.14, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:423442 original size:20 final size:20
Alignment explanation
Indices: 423393--423458 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
423383 AGTTTACTTC
*
423393 CGCAACACGAAAATGACTAT
1 CGCAACGCGAAAATGACTAT
*
423413 CGCAACGCGAAAATGGCTAT
1 CGCAACGCGAAAATGACTAT
* **
423433 CGCAATGCG-AAATGAAAAT
1 CGCAACGCGAAAATGACTAT
423452 CGCAACG
1 CGCAACG
423459 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
CGCAACGCGAAAATGACTAT
Found at i:423466 original size:14 final size:14
Alignment explanation
Indices: 423447--423504 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
423437 ATGCGAAATG
423447 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
423461 AAAATCGCAACGTGAA
1 AAAATCGCAAC--GAC
423477 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
423493 AAAATCGCAACG
1 AAAATCGCAACG
423505 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.58
16 6 0.16
18 10 0.26
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:423489 original size:32 final size:33
Alignment explanation
Indices: 423431--423521 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
423421 GAAAATGGCT
*
423431 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
423464 ATCGCAACGTGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
423496 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
423522 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:423567 original size:19 final size:19
Alignment explanation
Indices: 423552--423674 Score: 131
Period size: 19 Copynumber: 6.4 Consensus size: 19
423542 GCGATTTTGT
423552 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
423570 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
423589 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
423609 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
423628 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
423647 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
423667 TGTTGCGA
1 CGTTGCGA
423675 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.09
19 55 0.60
20 29 0.32
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:423666 original size:39 final size:38
Alignment explanation
Indices: 423552--423674 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 38
423542 GCGATTTTGT
*
423552 CGTTGCGAT-TTCATTTCGCGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCGCGTTGCGATTTTCATTTCG
* * **
423589 CATTGCGATAGCCATTTCCGCGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTTTCATTTCG
*
423628 CGTTGCGATAGTCATTTCGCGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTCATTTCGCGTTGCGATTTTCA-TTTCG
*
423667 TGTTGCGA
1 CGTTGCGA
423675 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
37 8 0.11
38 18 0.25
39 46 0.64
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (38 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTTTCATTTCG
Found at i:425543 original size:14 final size:14
Alignment explanation
Indices: 425524--425559 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
425514 ATTGTTTAAT
425524 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
425538 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
425552 TGATTTGT
1 TGATTTGT
425560 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:425685 original size:14 final size:16
Alignment explanation
Indices: 425666--425738 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 16
425656 CGAAATGGCT
425666 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
425680 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG-AATGAAA
425699 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATGAAA
425718 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
425732 ATCGCAA
1 ATCGCAA
425739 TGCGATTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.31
15 2 0.04
16 3 0.06
17 3 0.06
18 2 0.04
19 26 0.50
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ATCGCAACGAATGAAA
Found at i:425698 original size:19 final size:19
Alignment explanation
Indices: 425676--425724 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
425666 ATCGCAACGA
425676 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATACGAAAT
*
425695 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATACGAAAT
425714 GAAAATCGCAA
1 GAAAATCGCAA
425725 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:425731 original size:19 final size:18
Alignment explanation
Indices: 425676--425731 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
425666 ATCGCAACGA
*
425676 GAAAATCGCAATACGAAAT
1 GAAAATCGCAAGA-GAAAT
*
425695 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GAGAAAT
425714 GAAAATCGCAACGAGAAA
1 GAAAATCGCAA-GAGAAA
425732 ATCGCAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (18 bp):
GAAAATCGCAAGAGAAAT
Found at i:425787 original size:20 final size:20
Alignment explanation
Indices: 425770--425819 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
425760 CGATTTTCTA
*
425770 GTTGCGATAGCTATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
425790 TTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
425810 GTTGCGATAG
1 GTTGCGATAG
425820 TCAAATGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:426903 original size:24 final size:24
Alignment explanation
Indices: 426876--426929 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
426866 GTATTCAAAA
* *
426876 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
426900 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
426924 TTTGAT
1 TTTGAT
426930 GATGTTTCAG
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:429460 original size:33 final size:33
Alignment explanation
Indices: 429418--429544 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
429408 GGAAATTACT
429418 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
*
429451 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
* **
429483 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGATAGA
429517 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
429545 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATAGA
Found at i:429525 original size:66 final size:66
Alignment explanation
Indices: 429419--429551 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
429409 GAAATTACTA
* *
429419 TCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
429484 T
66 T
*
429485 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
429550 T
66 T
429551 T
1 T
429552 AGTTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:429566 original size:19 final size:20
Alignment explanation
Indices: 429544--429586 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
429534 AAATCGCAAC
429544 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCAGTTTCGCGTT
* *
429563 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAGTTTCGCGTT
429583 GCGA
1 GCGA
429587 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAGTTTCGCGTT
Found at i:429571 original size:14 final size:14
Alignment explanation
Indices: 429572--429605 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
429562 TGCGATTTTC
429572 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
429586 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
429600 ATTTTC
1 ATTTTC
429606 ATTTTGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:429746 original size:14 final size:14
Alignment explanation
Indices: 429727--429763 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
429717 CATCAATTAA
429727 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
429741 ACAAATCACCTTTT
1 ACAAATCAACTTTT
429755 ACAAATCAA
1 ACAAATCAA
429764 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:431207 original size:42 final size:42
Alignment explanation
Indices: 431161--431244 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
431151 CGATGACAGT
* * *
431161 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
431203 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
431245 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:433277 original size:20 final size:19
Alignment explanation
Indices: 433246--433419 Score: 109
Period size: 20 Copynumber: 9.6 Consensus size: 19
433236 TCTTTTGGTT
433246 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
433265 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
433286 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
433305 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
433319 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
433335 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
433352 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
433372 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
433391 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
433410 GAAAT-AAAAT
1 GAAATGAAAAT
433420 TCACAATGCG
Statistics
Matches: 124, Mismatches: 18, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
14 17 0.14
15 1 0.01
16 4 0.03
17 4 0.03
18 6 0.05
19 43 0.35
20 47 0.38
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:433328 original size:33 final size:33
Alignment explanation
Indices: 433271--433369 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
433261 ACGAGATAAT
*
433271 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
433305 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
433338 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
433370 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:433363 original size:19 final size:19
Alignment explanation
Indices: 433246--433419 Score: 154
Period size: 19 Copynumber: 9.6 Consensus size: 19
433236 TCTTTTGGTT
*
433246 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
433265 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
433285 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
433303 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
433319 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
433337 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
433352 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
433372 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
433391 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
433410 GAAAT-AAAAT
1 GAAATGAAAAT
433420 TCACAATGCG
Statistics
Matches: 128, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.15
15 3 0.02
16 2 0.02
17 1 0.01
18 9 0.07
19 47 0.37
20 45 0.35
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:433384 original size:39 final size:38
Alignment explanation
Indices: 433341--433418 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 38
433331 GCGACCAGAC
433341 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
433380 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
433418 A
1 A
433419 TTCACAATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 12 0.31
39 27 0.69
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:433448 original size:19 final size:19
Alignment explanation
Indices: 433426--433492 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
433416 AAATTCACAA
*
433426 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
433445 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
433464 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
433484 TGCGATTTT
1 TGCGATTTT
433493 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:434033 original size:20 final size:20
Alignment explanation
Indices: 434008--434060 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
433998 GCGCTATGTA
434008 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
434028 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
434048 TATCTCGTTGCGA
1 AATCGCGTTGCGA
434061 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:434094 original size:20 final size:20
Alignment explanation
Indices: 434069--434122 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
434059 GATTTTGTAT
434069 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
434089 TATCGCATTGTGATAGTCAG
1 TATCGCATTGCGATAGTAAG
434109 TATCGCATTGCGAT
1 TATCGCATTGCGAT
434123 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:434107 original size:61 final size:61
Alignment explanation
Indices: 434009--434125 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
433999 CGCTATGTAA
* * * * *
434009 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
434070 ATCGCATTGCGATAGTAAGTATCGCATTGTGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
434126 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:434141 original size:61 final size:61
Alignment explanation
Indices: 434009--434143 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
433999 CGCTATGTAA
* * * * * ** *
434009 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
434070 ATCGCATTGCGATAGTAAGTATCGCATTGTGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
434132 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
434144 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:434233 original size:21 final size:21
Alignment explanation
Indices: 434193--434233 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
434183 ATTGTATACC
**
434193 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
434214 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
434234 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:434810 original size:13 final size:13
Alignment explanation
Indices: 434792--434816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
434782 ACTCATCTCT
434792 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
434805 TTTTTCTTTTTT
1 TTTTTCTTTTTT
434817 GGCAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:434844 original size:2 final size:2
Alignment explanation
Indices: 434837--434872 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
434827 CCCTCTTTTC
434837 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
434873 TAACTCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435827 original size:2 final size:2
Alignment explanation
Indices: 435816--435857 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
435806 AATTTATGAA
435816 AT AT -T 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
435857 A
1 A
435858 ATCCGTCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:439198 original size:42 final size:42
Alignment explanation
Indices: 439139--439237 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
439129 ACCCCCACTT
* *
439139 CGAGAGCCATCACCTGATCGATCCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGATCCGATTATACACCTCGACAC
* **
439181 CGAGAGTCATCACCTGATCGATCCGATTATACACCTCGGGAC
1 CGAGAGCCATCACCTGATCGATCCGATTATACACCTCGACAC
**
439223 TTAGAGCCATCACCT
1 CGAGAGCCATCACCT
439238 ATTCCATCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.21
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGATCCGATTATACACCTCGACAC
Found at i:439829 original size:21 final size:21
Alignment explanation
Indices: 439765--439836 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
439755 TGTTATTACG
439765 TCTCATCGTTCAAGAGGCCCC
1 TCTCATCGTTCAAGAGGCCCC
* *
439786 TATTATCGTTCAAGAGGCCCC
1 TCTCATCGTTCAAGAGGCCCC
* *
439807 TCTCATCATTTAAGAGGCCCC
1 TCTCATCGTTCAAGAGGCCCC
*
439828 TCCCATCGT
1 TCTCATCGT
439837 ACATGATCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.28
Consensus pattern (21 bp):
TCTCATCGTTCAAGAGGCCCC
Found at i:439850 original size:21 final size:21
Alignment explanation
Indices: 439826--439889 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
439816 TTAAGAGGCC
* * *
439826 CCTCCCATCGTACATGATCCA
1 CCTCCCACCGTTCAGGATCCA
*
439847 CCTCACACCGTTCAGGATCCA
1 CCTCCCACCGTTCAGGATCCA
439868 CCTCCCACCGTTCAGGATCCA
1 CCTCCCACCGTTCAGGATCCA
439889 C
1 C
439890 ATGGCTTACT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.45, G:0.12, T:0.20
Consensus pattern (21 bp):
CCTCCCACCGTTCAGGATCCA
Found at i:447618 original size:7 final size:8
Alignment explanation
Indices: 447587--447625 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
447577 CACGTGAGGA
*
447587 TTATTTTC
1 TTATTTTT
*
447595 TTCTTTTT
1 TTATTTTT
447603 TTAATTTTT
1 TT-ATTTTT
447612 TTATTTTT
1 TTATTTTT
447620 TTATTT
1 TTATTT
447626 ACTGTCTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (8 bp):
TTATTTTT
Found at i:448779 original size:45 final size:45
Alignment explanation
Indices: 448728--448830 Score: 206
Period size: 45 Copynumber: 2.3 Consensus size: 45
448718 AGACAAAAAA
448728 GTTAATATAAAAAGTAACATTCTTATCAAAATGGTAAAATCTAAT
1 GTTAATATAAAAAGTAACATTCTTATCAAAATGGTAAAATCTAAT
448773 GTTAATATAAAAAGTAACATTCTTATCAAAATGGTAAAATCTAAT
1 GTTAATATAAAAAGTAACATTCTTATCAAAATGGTAAAATCTAAT
448818 GTTAATATAAAAA
1 GTTAATATAAAAA
448831 AGTTTTTGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (45 bp):
GTTAATATAAAAAGTAACATTCTTATCAAAATGGTAAAATCTAAT
Found at i:448785 original size:27 final size:27
Alignment explanation
Indices: 448755--448830 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
448745 CATTCTTATC
448755 AAAATGGTAAAATCTAATGTTAATATA
1 AAAATGGTAAAATCTAATGTTAATATA
*
448782 AAAA--GT--AA-C--AT-TCT--TATC
1 AAAATGGTAAAATCTAATGT-TAATATA
448800 AAAATGGTAAAATCTAATGTTAATATA
1 AAAATGGTAAAATCTAATGTTAATATA
448827 AAAA
1 AAAA
448831 AGTTTTTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 22
0.60 0.03 0.37
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 5 0.14
22 3 0.08
23 3 0.08
25 5 0.14
26 1 0.03
27 11 0.31
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATGGTAAAATCTAATGTTAATATA
Found at i:460117 original size:169 final size:169
Alignment explanation
Indices: 459838--460173 Score: 647
Period size: 169 Copynumber: 2.0 Consensus size: 169
459828 TCATTTTCAA
459838 AAGATCAAAATGCCTTTGAAGCCAAAAGTTCAGAAATCAAAGCTTTTGTGTTGATTGATAAATAT
1 AAGATCAAAATGCCTTTGAAGCCAAAAGTTCAGAAATCAAAGCTTTTGTGTTGATTGATAAATAT
459903 CATGCTTGTAATATGTAACTGTTGCGACTGTTTCATTCCATATACTTGTCATGTGTAAC-TTTTT
66 CATGCTTGTAATATGTAACTGTTGCGACTGTTTCATTCCATATACTTGTCATGTGTAACTTTTTT
459967 CTTTCTGTTGCATTCGATTGCTTTATTTTAAATATTTAAT
131 CTTTCTGTTGCATTCGATTGCTTTATTTT-AATATTTAAT
460007 AAGATCAAAATGCCTTTGAAGCCAAAAGTTCAGAAATCAAAGCTTTTGTGTTGATTGATAAATAT
1 AAGATCAAAATGCCTTTGAAGCCAAAAGTTCAGAAATCAAAGCTTTTGTGTTGATTGATAAATAT
460072 CATGCTTGTAATATGTAACTGTTGCGACTGTTTCATTCCATATACTTGTCATGTGTAACTTTTTT
66 CATGCTTGTAATATGTAACTGTTGCGACTGTTTCATTCCATATACTTGTCATGTGTAAC-TTTTT
460137 TCTTTCTGTTGCATTCGATTGCTTTATTTTAATATTT
130 TCTTTCTGTTGCATTCGATTGCTTTATTTTAATATTT
460174 TAATTAATGG
Statistics
Matches: 165, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
169 124 0.75
170 7 0.04
171 34 0.21
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (169 bp):
AAGATCAAAATGCCTTTGAAGCCAAAAGTTCAGAAATCAAAGCTTTTGTGTTGATTGATAAATAT
CATGCTTGTAATATGTAACTGTTGCGACTGTTTCATTCCATATACTTGTCATGTGTAACTTTTTT
CTTTCTGTTGCATTCGATTGCTTTATTTTAATATTTAAT
Found at i:463060 original size:26 final size:27
Alignment explanation
Indices: 463017--463070 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
463007 AGATTATCAG
463017 TTAAAAATACAAAGAAAACATTTAAAA
1 TTAAAAATACAAAGAAAACATTTAAAA
* *
463044 TTAAAAA-ACAAATAAAATATTTAAAA
1 TTAAAAATACAAAGAAAACATTTAAAA
463070 T
1 T
463071 ATATGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.26
Consensus pattern (27 bp):
TTAAAAATACAAAGAAAACATTTAAAA
Found at i:464628 original size:13 final size:13
Alignment explanation
Indices: 464598--464632 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
464588 AACCGGTTCG
*
464598 ACCCGACCCGTTG
1 ACCCGACCCGTTA
464611 A-CCGACCCGTTA
1 ACCCGACCCGTTA
464623 ACCCGACCCG
1 ACCCGACCCG
464633 ATGATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.20, C:0.49, G:0.20, T:0.11
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:464690 original size:28 final size:28
Alignment explanation
Indices: 464642--464774 Score: 106
Period size: 28 Copynumber: 4.6 Consensus size: 28
464632 GATGATATTC
* * *
464642 TGGG-ATTTTTTTTAAATAGTGATATTT
1 TGGGAATTTTTTTAAAACAGTGACATTT
*
464669 TGGGAATTTTTTTAAAACAGTGACATTC
1 TGGGAATTTTTTTAAAACAGTGACATTT
* * * *
464697 AGGTAATTATTGTTAAAACGGTGACATTT
1 TGGGAATT-TTTTTAAAACAGTGACATTT
* *
464726 TGAGATTTTTTTTGTGTAAAACAGTGACATTT
1 TGGGA--ATTTTT-T-TAAAACAGTGACATTT
* *
464758 TGGTAATTATTTTAAAA
1 TGGGAATTTTTTTAAAA
464775 AAAAGTGATA
Statistics
Matches: 81, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
27 4 0.05
28 30 0.37
29 20 0.25
30 6 0.07
31 3 0.04
32 18 0.22
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (28 bp):
TGGGAATTTTTTTAAAACAGTGACATTT
Found at i:465750 original size:32 final size:31
Alignment explanation
Indices: 465674--465750 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
465664 ATAATATGAC
** *
465674 TCTTAGGTAGGCTGTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** **
465705 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
465737 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
465751 CACGATCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.32, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:465866 original size:25 final size:25
Alignment explanation
Indices: 465814--465866 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
465804 ATGGTAACTC
*
465814 TTTTATGAGATTTACTGCAGTATAA
1 TTTTATGAGATTTACTGCACTATAA
* *
465839 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTGCACTATAA
465864 TTT
1 TTT
465867 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (25 bp):
TTTTATGAGATTTACTGCACTATAA
Found at i:466705 original size:3 final size:3
Alignment explanation
Indices: 466695--466736 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
466685 TATTATAGTA
466695 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
466737 TATTTTTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:471168 original size:109 final size:110
Alignment explanation
Indices: 470755--471222 Score: 712
Period size: 110 Copynumber: 4.3 Consensus size: 110
470745 TACAGCTTTT
* *
470755 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGATCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
470820 TGAAGGGGCGACTGGCTGTCAATAAATAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTC
* * * *
470865 AGAGTCAATTTCAACTTTACAGCGAAGGATATTGGACTAGAGACAACACAAGCTCAACTTCATAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
470930 CGAAGGGGCGATTGGCTGTCAATAAACAACTTTTCAATTTCATTC
66 CGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTC
470975 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* *
471040 CGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTC
* * *
471085 AGAGTCAATATCAACTTCACAACG-ATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
471149 CGAAGGTGTGGCTGGCTGTCAACAAACAACTTTTCAG--T--TTC
66 CGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTC
*
471190 AGAGTCAATTTCAACTTCACAGCGAATGATATT
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATT
471223 GGCCTCGAAA
Statistics
Matches: 328, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
105 25 0.08
106 8 0.02
107 1 0.00
109 71 0.22
110 223 0.68
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:471636 original size:84 final size:84
Alignment explanation
Indices: 471342--471629 Score: 332
Period size: 84 Copynumber: 3.5 Consensus size: 84
471332 AAGGGAATCG
* * * * *
471342 TGCCAACCAAAGTCATTCGAGTTCTACTACGCTCAGCTCCAAGGAACATCATTTGCAACATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCT
* *
471407 TAAGTCGAGAAGGGCTATC
66 TAAGTCAAGAAGGGTTATC
* * * * * * * *
471426 TG----TCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGTATCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAACATAGC
* * *
471487 TCAAGGCTAGAAGGGTTATC
65 TTAAGTCAAGAAGGGTTATC
* * *
471507 TGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCT
471572 TAAGTCAAGAAGGGTTATC
66 TAAGTCAAGAAGGGTTATC
* *
471591 TGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTC
471630 AGAGGCAAAC
Statistics
Matches: 165, Mismatches: 34, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
80 24 0.15
81 39 0.24
84 76 0.46
85 26 0.16
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCT
TAAGTCAAGAAGGGTTATC
Found at i:472364 original size:33 final size:33
Alignment explanation
Indices: 472322--472388 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
472312 GAAAATAAAT
*
472322 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1 CAACGTATTTAAGTCATATTGAAACACTAAAAC
*
472355 CAACGTATTTAAGTTATATTGAAACACTAAAAC
1 CAACGTATTTAAGTCATATTGAAACACTAAAAC
472388 C
1 C
472389 GAAGCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (33 bp):
CAACGTATTTAAGTCATATTGAAACACTAAAAC
Found at i:472826 original size:14 final size:14
Alignment explanation
Indices: 472780--472819 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
472770 TATATATTTC
472780 ATTTTTTTATTAAT
1 ATTTTTTTATTAAT
* *
472794 ATTATTATATTAAT
1 ATTTTTTTATTAAT
472808 ATTTTTTTATTA
1 ATTTTTTTATTA
472820 TTCTTTTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTTTTATTAAT
Found at i:476873 original size:35 final size:35
Alignment explanation
Indices: 476826--476937 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
476816 AAAACAGTCC
*
476826 TCAATTTCATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
476861 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * *
476896 TCAATTACATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
476931 TCAATTT
1 TCAATTT
476938 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:478051 original size:35 final size:35
Alignment explanation
Indices: 477996--478107 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
477986 AAAAAGACAT
* *
477996 AAATTAAAGTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
* * *
478031 TAATTGAATTATTTTAGAATTTACGGTTTTGAATG
1 AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
* * *
478066 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
478101 AAATTGA
1 AAATTGA
478108 GGACTGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
Found at i:483159 original size:29 final size:29
Alignment explanation
Indices: 483114--483172 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
483104 AAAAAGAAGT
*
483114 AAGAGAATTTCTGGGGAGGTTATATTGCC
1 AAGAGAATTTCTAGGGAGGTTATATTGCC
483143 AAGAGAATTTCTAGGGAGGTTATATTGCC
1 AAGAGAATTTCTAGGGAGGTTATATTGCC
483172 A
1 A
483173 GATTCATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31
Consensus pattern (29 bp):
AAGAGAATTTCTAGGGAGGTTATATTGCC
Found at i:486354 original size:85 final size:84
Alignment explanation
Indices: 486242--486461 Score: 257
Period size: 83 Copynumber: 2.6 Consensus size: 84
486232 GGAACTATTC
* * *
486242 ACAGCATAACTCAAGG-TAAGAAAGGTTATCTGTCAACCAAGACCTTCGAGTTCGACTATACTCA
1 ACAGCATAACTCAAGGCGAA-AAGGGTTATCTGTCAACCAA-ACCTTCGAGTTCGACTACACTCA
*
486306 TCTCAAAGG-CATATCAAATTT
64 GCTC-AAGGACATATCAAATTT
* * * * *
486327 ACAGCATAACTAAAGGCGAAAAGGGTTATCTGTCAACC-ATCCTTCGAGTTTGATTACATTCAGC
1 ACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAACCTTCGAGTTCGACTACACTCAGC
*
486391 TCAAGGACATGTCAAATTT
66 TCAAGGACATATCAAATTT
* * * *
486410 ATAGCATAACTCAAGGCGAGAAGGGTTATATGTCAACAAACACCTTCGAGTT
1 ACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAA-ACCTTCGAGTT
486462 TGATTCCATT
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
82 4 0.03
83 65 0.57
84 2 0.02
85 42 0.37
86 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (84 bp):
ACAGCATAACTCAAGGCGAAAAGGGTTATCTGTCAACCAAACCTTCGAGTTCGACTACACTCAGC
TCAAGGACATATCAAATTT
Found at i:487321 original size:197 final size:198
Alignment explanation
Indices: 486957--488131 Score: 1489
Period size: 197 Copynumber: 6.1 Consensus size: 198
486947 CCCCAAATTA
** * * *
486957 ACCCGA-TTTCCTCAACATGAAGG---AACGTCATAATTTATCGAAAATGACCTGATCTCTTTAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* * *
487018 CACGAATGAGCAATGTCATCTTCAACATCAAATTGACCTGATCTCCTCAACGCGAAGGAGCAGTG
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
* * * *
487083 TCATCATCAGACAATCAGACTTTCTCATCACGAAAGAACCGTATTTTCCCCAAATTATCTCCTGA
131 TCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGA
487148 TTG
196 TTG
* * *
487151 ACCC-ATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATTGAAAACGACCTGATCTCTTTAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* * * * * *
487215 CACGGATGATCAGTGTCGTCTTCAACATCAAATTGACCCAATCTTCTTAACACGAAGGAGCAGTG
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
* *
487280 TCATCTTCAAACAATCAGACTTCCTCGT-ATCGAAGGAACCGTATTGTCCCC-AA--A-----T-
131 TCATCTTCAGACAATCAGACTTCCTCATCA-CGAAGGAACCGTATTGTCCCCAAATTATCTCCTG
487335 A---
195 ATTG
* * * *
487336 ACCC-AATTTCCTTAACGCGAAGGAACATCGTCATAATTTATCGAAAATGACCCGATCTCTTCAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* ** *
487400 CACGGATGAGCAGTGTCGTCTTCAACATCAAATTGACCTC-ATC-GAT--A--CGAAAGAGCAGT
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACC-CGATCTCCTCAACGCGAAGGAGCAGT
* *
487459 GTCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTACTATCCCC-AA--A--T--T-
130 GTCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTG
487516 A---
195 ATTG
* * *
487517 ACCAGA-TTTCCTCAACACGAAGGAACATCGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* *
487581 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGTGAAGGAGTAGTG
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
* *
487646 TCATCCTT-AGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCTCCAAATTATCTTCTG
131 TCAT-CTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTG
487710 ATTG
195 ATTG
*
487714 ACCCGA-TTTCCTCAATGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* *
487778 CACGGATGAGTAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCA-TG
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
* * *
487842 TCATCCTCAGAAAATCAGACTTCCTCATCACGAAAGAACCGTATTGTCCCCAAATTATCTCCTGA
131 TCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGA
487907 TTG
196 TTG
* * *
487910 ACCCGATTTT-CTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGATCTGATCTCTTCAA
1 ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
* * * *
487974 CACGGATGAGCAGTGTTATCTTCAACATTAAATTTACCCGATCTCCTCAACGCGAATGAGCAGTG
66 CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
* * * *
488039 TCATTTTCAGACAATCAGACTTCCTCATCATGAAGGAACCATATTTGTCCCCAAATTATCTCTTG
131 TCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTA-TTGTCCCCAAATTATCTCCTG
*
488104 ATTT
195 ATTG
*
488108 ACCCGATCTT-CTCAACGCGAAGGA
1 ACCCGATTTTCCTCAACGCGAAGGA
488132 GAAGTGTCAC
Statistics
Matches: 872, Mismatches: 78, Indels: 58
0.87 0.08 0.06
Matches are distributed among these distances:
180 61 0.07
181 101 0.12
182 3 0.00
184 2 0.00
185 97 0.11
186 55 0.06
187 5 0.01
188 1 0.00
189 2 0.00
191 1 0.00
193 2 0.00
194 21 0.02
195 2 0.00
196 178 0.20
197 295 0.34
198 46 0.05
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (198 bp):
ACCCGATTTTCCTCAACGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAA
CACGGATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAGGAGCAGTG
TCATCTTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGA
TTG
Found at i:487978 original size:196 final size:197
Alignment explanation
Indices: 487521--488131 Score: 949
Period size: 196 Copynumber: 3.1 Consensus size: 197
487511 AAATTAACCA
*
487521 GATTTCCTCAACACGAAGGAAC-ATCGTCATAATTTATCGAAAACGACCCGATCTCTTCAACACG
1 GATTTCCTCAACGCGAAGGAACAAT-GTCATAATTTATCGAAAACGACCCGATCTCTTCAACACG
* * *
487585 GATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGTGAAGGAGTAGTGTCAT
65 GATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCAGTGTCAT
* * *
487650 CCTTAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCTCCAAATTATCTTCTGATTGA
130 CCTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGATTGA
487715 CCC
195 CCC
* *
487718 GATTTCCTCAATGCGAAGGAACAACGTCATAATTTATCGAAAACGACCCGATCTCTTCAACACGG
1 GATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTTCAACACGG
*
487783 ATGAGTAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCA-TGTCATC
66 ATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCAGTGTCATC
* *
487847 CTCAGAAAATCAGACTTCCTCATCACGAAAGAACCGTATTGTCCCCAAATTATCTCCTGATTGAC
131 CTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGATTGAC
487912 CC
196 CC
* * *
487914 GATTTTCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGATCTGATCTCTTCAACACGG
1 GATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTTCAACACGG
* * * * *
487979 ATGAGCAGTGTTATCTTCAACATTAAATTTACCCGATCTCCTCAACGCGAATGAGCAGTGTCATT
66 ATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCAGTGTCATC
* * * * *
488044 TTCAGACAATCAGACTTCCTCATCATGAAGGAACCATATTTGTCCCCAAATTATCTCTTGATTTA
131 CTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTA-TTGTCCCCAAATTATCTCCTGATTGA
488109 CCC
195 CCC
488112 GATCTT-CTCAACGCGAAGGA
1 GAT-TTCCTCAACGCGAAGGA
488132 GAAGTGTCAC
Statistics
Matches: 380, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
196 181 0.48
197 152 0.40
198 45 0.12
199 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (197 bp):
GATTTCCTCAACGCGAAGGAACAATGTCATAATTTATCGAAAACGACCCGATCTCTTCAACACGG
ATGAGCAGTGTCATCTTCAACATCAAATTGACCCGATCTCCTCAACGCGAAAGAGCAGTGTCATC
CTCAGACAATCAGACTTCCTCATCACGAAGGAACCGTATTGTCCCCAAATTATCTCCTGATTGAC
CC
Found at i:488782 original size:20 final size:21
Alignment explanation
Indices: 488757--488800 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
488747 GTAAAGGGGG
*
488757 GATTTTTTCAGCAA-AAAAAA
1 GATTTTATCAGCAATAAAAAA
488777 GATTTTATCAGCAATTAAAAAA
1 GATTTTATCAGCAA-TAAAAAA
488799 GA
1 GA
488801 GGAACCGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
22 8 0.38
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (21 bp):
GATTTTATCAGCAATAAAAAA
Found at i:489751 original size:14 final size:14
Alignment explanation
Indices: 489732--489759 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
489722 TATTTATGCA
489732 ATTTATTTATTTTT
1 ATTTATTTATTTTT
489746 ATTTATTTATTTTT
1 ATTTATTTATTTTT
489760 CAGCACCTTA
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTATTTATTTTT
Found at i:489799 original size:29 final size:31
Alignment explanation
Indices: 489751--489817 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 31
489741 TTTTTATTTA
* *
489751 TTTATTTTTCAGCACCTTAA-TTT-TAGTAT
1 TTTATTTTTCAGCACCTTAACTTTCCAGCAT
489780 TTTATTTTTCTA-C-CCTTTAACTTTCCAGCAT
1 TTTATTTTTC-AGCACC-TTAACTTTCCAGCAT
489811 TTTATTT
1 TTTATTT
489818 CAGTCCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 2 0.06
29 15 0.47
30 4 0.12
31 11 0.34
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (31 bp):
TTTATTTTTCAGCACCTTAACTTTCCAGCAT
Found at i:489816 original size:31 final size:30
Alignment explanation
Indices: 489778--489850 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
489768 TAATTTTAGT
489778 ATTTTATTTTTCTACC-CTTTAACTTTCCAGC
1 ATTTTATTTTTCT-CCTCTTTAA-TTTCCAGC
***
489809 ATTTTATTTCAGTCCTCTTTAATTTCCAGC
1 ATTTTATTTTTCTCCTCTTTAATTTCCAGC
489839 A-TTTAGTTTTTC
1 ATTTTA-TTTTTC
489851 AGTATTTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.12
30 14 0.41
31 16 0.47
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.53
Consensus pattern (30 bp):
ATTTTATTTTTCTCCTCTTTAATTTCCAGC
Found at i:493054 original size:12 final size:12
Alignment explanation
Indices: 493022--493066 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
493012 ATATAACTAG
493022 ATTA-TATTTAA
1 ATTATTATTTAA
*
493033 ATT-TAAATTTAA
1 ATTAT-TATTTAA
493045 ATTATTATTTAA
1 ATTATTATTTAA
493057 ATTATTATTT
1 ATTATTATTT
493067 GTCTTCACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 3 0.10
12 25 0.86
13 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTTAA
Found at i:493963 original size:21 final size:22
Alignment explanation
Indices: 493939--493984 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
493929 AAGGGATCGG
*
493939 AAATGTT-AATCGAGAAATAAT
1 AAATGTTAAATAGAGAAATAAT
*
493960 AAATGTTAAATATAGAAATAAT
1 AAATGTTAAATAGAGAAATAAT
493982 AAA
1 AAA
493985 CTAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
AAATGTTAAATAGAGAAATAAT
Found at i:494059 original size:69 final size:69
Alignment explanation
Indices: 493975--494121 Score: 162
Period size: 69 Copynumber: 2.1 Consensus size: 69
493965 TTAAATATAG
493975 AAATAATAAACTAAAAA-ATAATC-ATAAAATCAAAA-GAGAGAAAATAAATAA-ATAAATAAAA
1 AAATAATAAACTAAAAATA-AATCGATAAAAT-AAAATGAGAGAAAATAAA-AATA-AAATAAAA
494036 ATAGAGGA
62 ATAGAGGA
* *
494044 AAATAAATAAA-TAAAAATAAATCGATGAAATAAAATGAGATAAAATAAAAATAAAAT-AAAATA
1 AAAT-AATAAACTAAAAATAAATCGATAAAATAAAATGAGAGAAAATAAAAATAAAATAAAAATA
* *
494107 AATGA
65 GAGGA
494112 ATAATAATAA
1 A-AATAATAA
494122 TAATAATGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
68 15 0.22
69 27 0.40
70 26 0.38
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (69 bp):
AAATAATAAACTAAAAATAAATCGATAAAATAAAATGAGAGAAAATAAAAATAAAATAAAAATAG
AGGA
Found at i:494065 original size:28 final size:29
Alignment explanation
Indices: 494000--494065 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
493990 AAATAATCAT
494000 AAAATCAAA-AGAGAGAAAATAAATAAATA
1 AAAAT-AAATAGAGAGAAAATAAATAAATA
494029 AATAA-AAATAGAG-GAAAATAAATAAATA
1 AA-AATAAATAGAGAGAAAATAAATAAATA
494057 AAAATAAAT
1 AAAATAAAT
494066 CGATGAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
27 2 0.06
28 24 0.71
29 6 0.18
30 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.17
Consensus pattern (29 bp):
AAAATAAATAGAGAGAAAATAAATAAATA
Found at i:494073 original size:28 final size:28
Alignment explanation
Indices: 494009--494123 Score: 92
Period size: 28 Copynumber: 4.0 Consensus size: 28
493999 TAAAATCAAA
494009 AGAGAGAAAATAAATAAATAAATAAAAAT
1 AGAG-GAAAATAAATAAATAAATAAAAAT
494038 AGAGGAAAATAAATAAATAAA-AATAAAT
1 AGAGGAAAATAAATAAATAAATAA-AAAT
* * *
494066 CGATG-AAATAAAATGAGATAAAATAAAAAT
1 AGAGGAAAAT-AAAT-AAAT-AAATAAAAAT
* ** * *
494096 AAAATAAAATAAATGAAT-AATAATAAT
1 AGAGGAAAATAAATAAATAAATAAAAAT
494123 A
1 A
494124 ATAATGCTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
27 15 0.21
28 28 0.40
29 9 0.13
30 12 0.17
31 6 0.09
ACGTcount: A:0.70, C:0.01, G:0.10, T:0.20
Consensus pattern (28 bp):
AGAGGAAAATAAATAAATAAATAAAAAT
Found at i:495261 original size:3 final size:3
Alignment explanation
Indices: 495255--495305 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
495245 TACTGAAATA
*
495255 AAT AAT AAT AA- AAT -AT AAT AAT AAT AAT AAAG AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
495298 AAA AAT AA
1 AAT AAT AA
495306 CATAAAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 6 0.15
3 32 0.80
4 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:495310 original size:14 final size:15
Alignment explanation
Indices: 495271--495310 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
495261 AATAAAATAT
495271 AATAATAATAATAAAG
1 AATAA-AATAATAAAG
495287 AATAAAATAATAAA-
1 AATAAAATAATAAAG
*
495301 AATAACATAA
1 AATAAAATAA
495311 AAATGTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAAAATAATAAAG
Found at i:495310 original size:19 final size:19
Alignment explanation
Indices: 495250--495312 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
495240 AAAAATACTG
495250 AAATAAATAATAATAAAATA
1 AAAT-AATAATAATAAAATA
*
495270 TAATAATAATAATAAAGAATA
1 AAATAATAATAAT-AA-AATA
* *
495291 AAATAATAAAAATAACATA
1 AAATAATAATAATAAAATA
495310 AAA
1 AAA
495313 ATGTTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.41
20 7 0.19
21 15 0.41
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAATAATAATAAAATA
Found at i:495383 original size:16 final size:15
Alignment explanation
Indices: 495330--495383 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 15
495320 CAAAACCTTA
*
495330 TTTC-AAAAAATGTT
1 TTTCAAAAAAATATT
*
495344 TTTCAAAATAATATAT
1 TTTCAAAAAAATAT-T
495360 TTTCAAAAAAATATT
1 TTTCAAAAAAATATT
495375 TTT-AAAAAA
1 TTTCAAAAAA
495384 CTATATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.29
15 11 0.31
16 14 0.40
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (15 bp):
TTTCAAAAAAATATT
Found at i:495389 original size:16 final size:15
Alignment explanation
Indices: 495334--495389 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 15
495324 ACCTTATTTC
* *
495334 AAAAAATGT-TTTTC
1 AAAAAATATATTTTT
*
495348 AAAATAATATATTTTC
1 AAAA-AATATATTTTT
495364 AAAAAA-ATATTTTT
1 AAAAAATATATTTTT
495378 AAAAAACTATAT
1 AAAAAA-TATAT
495390 ATTATATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
14 17 0.47
15 6 0.17
16 13 0.36
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (15 bp):
AAAAAATATATTTTT
Found at i:495389 original size:30 final size:30
Alignment explanation
Indices: 495330--495389 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
495320 CAAAACCTTA
*
495330 TTTCAAAAAATGTTTTTCAAAATAATATAT
1 TTTCAAAAAATATTTTTCAAAATAATATAT
495360 TTTCAAAAAAATATTTTT-AAAA-AACTATAT
1 TTTC-AAAAAATATTTTTCAAAATAA-TATAT
495390 ATTATATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 13 0.48
31 12 0.44
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
TTTCAAAAAATATTTTTCAAAATAATATAT
Found at i:495463 original size:36 final size:37
Alignment explanation
Indices: 495374--495616 Score: 250
Period size: 36 Copynumber: 6.6 Consensus size: 37
495364 AAAAAAATAT
* *
495374 TTTTAAAAAACTATATATTATATATGTTTTCAAAAATG
1 TTTTCAAAAACTATATA-TATATATGTTTTTAAAAATG
495412 TTTT-AAAAACTATATA-ATATATGTTTTTAAAAATG
1 TTTTCAAAAACTATATATATATATGTTTTTAAAAATG
495447 TTTTCAAAAACTATATAATATATAT-TTTTT-AAAATG
1 TTTTCAAAAACTATAT-ATATATATGTTTTTAAAAATG
* * * *
495483 TTATCAAAAGCTATATATTATATATATATATTAAAAATG
1 TTTTCAAAAACTATATA-TATATATGT-TTTTAAAAATG
* **
495522 TTTTCAAAAACTATATATTATAAATGTTTCCAAAAA--
1 TTTTCAAAAACTATATA-TATATATGTTTTTAAAAATG
* ** *
495558 ATTTC-AAAACTATATAATATATATAGTTTTTCGAAATA
1 TTTTCAAAAACTATAT-ATATATAT-GTTTTTAAAAATG
495596 TTTTC-AAAACTATATATATAT
1 TTTTCAAAAACTATATATATAT
495617 TTTCGAAAAC
Statistics
Matches: 176, Mismatches: 18, Indels: 23
0.81 0.08 0.11
Matches are distributed among these distances:
35 39 0.22
36 50 0.28
37 25 0.14
38 33 0.19
39 29 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACTATATATATATATGTTTTTAAAAATG
Found at i:495536 original size:28 final size:26
Alignment explanation
Indices: 495507--495557 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
495497 ATATTATATA
*
495507 TATATATTAAAAATGTTTTCAAAAAC
1 TATATATTAAAAATGTTTCCAAAAAC
*
495533 TATATATTATAAATGTTTCCAAAAA
1 TATATATTAAAAATGTTTCCAAAAA
495558 ATTTCAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (26 bp):
TATATATTAAAAATGTTTCCAAAAAC
Found at i:495665 original size:29 final size:31
Alignment explanation
Indices: 495610--495667 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
495600 CAAAACTATA
* * *
495610 TATATATTTTCGAAAACCGTTTTCAAAAAAT
1 TATATATTTTCGAAAAACATTTGCAAAAAAT
495641 TATAT-TTTTC-AAAAACATTTGCAAAAA
1 TATATATTTTCGAAAAACATTTGCAAAAA
495668 TTAAACTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
30 5 0.21
31 5 0.21
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (31 bp):
TATATATTTTCGAAAAACATTTGCAAAAAAT
Found at i:495957 original size:15 final size:15
Alignment explanation
Indices: 495933--495968 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
495923 TCACTATTAA
*
495933 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
495948 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
495963 ACTAAA
1 ATTAAA
495969 CATATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:496590 original size:2 final size:2
Alignment explanation
Indices: 496573--496607 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
496563 TAATTGAACA
* *
496573 AT AT AA AT AA 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 A
496608 AACAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:498561 original size:15 final size:15
Alignment explanation
Indices: 498538--498604 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
498528 CACTATTAAA
*
498538 TTAATTTATAAAATT
1 TTAAATTATAAAATT
*
498553 TTAAATTATAAAATA
1 TTAAATTATAAAATT
* *
498568 TTAAA-CATATAATT
1 TTAAATTATAAAATT
* *
498582 ATAAATTAATTAAAAAT
1 TTAAATT-A-TAAAATT
498599 TTAAAT
1 TTAAAT
498605 GTAATTTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 10 0.26
15 18 0.46
16 1 0.03
17 10 0.26
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATTATAAAATT
Found at i:498593 original size:23 final size:23
Alignment explanation
Indices: 498556--498619 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
498546 TAAAATTTTA
* *
498556 AATTATAAAAT-ATTAAACATAT
1 AATTATAAATTAATTAAAAATAT
*
498578 AATTATAAATTAATTAAAAATTT
1 AATTATAAATTAATTAAAAATAT
* * *
498601 AAATGTAATTTAATTAAAA
1 AATTATAAATTAATTAAAA
498620 TACAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 10 0.29
23 25 0.71
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTATAAATTAATTAAAAATAT
Found at i:499201 original size:27 final size:27
Alignment explanation
Indices: 499171--499235 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
499161 CTTAGCAATC
*
499171 TCATCATCTTCATCTGCACCATCGTCG
1 TCATCATCTTCATCCGCACCATCGTCG
* * * *
499198 TCATCATCTTTATCCGCATCGTTGTCG
1 TCATCATCTTCATCCGCACCATCGTCG
*
499225 TCATTATCTTC
1 TCATCATCTTC
499236 TTCTTAACTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.32, G:0.11, T:0.40
Consensus pattern (27 bp):
TCATCATCTTCATCCGCACCATCGTCG
Found at i:501935 original size:26 final size:27
Alignment explanation
Indices: 501906--501959 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
501896 TCACATGCAA
501906 TTTTATACAG-TTGTCTACTGCTGTTTT
1 TTTTATA-AGATTGTCTACTGCTGTTTT
501933 TTTTATAAGAATTTGTCTACTGCTGTT
1 TTTTATAAG-A-TTGTCTACTGCTGTT
501960 GCTGATGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.08
27 7 0.29
29 15 0.62
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.54
Consensus pattern (27 bp):
TTTTATAAGATTGTCTACTGCTGTTTT
Found at i:512862 original size:2 final size:2
Alignment explanation
Indices: 512855--512905 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
512845 TCATAAACTC
* *
512855 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TCC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
512898 TA TA TA TA
1 TA TA TA TA
512906 CCATTTCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 44 0.98
3 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:513364 original size:23 final size:23
Alignment explanation
Indices: 513346--513429 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
513336 CTCGTATAAT
*
513346 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAA
* *
513369 TGCACCGTAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
* *
513392 TGCACCGAAGTGCCGCCTAGAAA
1 TGCACCGAAGTGCCACGTAGAAA
*
513415 TGCACCAAAGTGCCA
1 TGCACCGAAGTGCCA
513430 TATAAGATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.15
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Found at i:515674 original size:2 final size:2
Alignment explanation
Indices: 515667--515701 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
515657 TTGGGATATT
515667 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
515702 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:515768 original size:2 final size:2
Alignment explanation
Indices: 515701--515751 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
515691 ACACACACAC
515701 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
515743 AT AT AT AT A
1 AT AT AT AT A
515752 AAGTACATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:518471 original size:13 final size:13
Alignment explanation
Indices: 518453--518480 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
518443 GCTATTTTTT
518453 AAAAAAAACAAAA
1 AAAAAAAACAAAA
518466 AAAAAAAACAAAA
1 AAAAAAAACAAAA
518479 AA
1 AA
518481 TCCAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:525754 original size:5 final size:5
Alignment explanation
Indices: 525741--525779 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
525731 ACCACGACCA
* * *
525741 CGAGC CGAGT CGAGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
525780 ACGGACGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.41, T:0.08
Consensus pattern (5 bp):
CGAGC
Found at i:537689 original size:18 final size:18
Alignment explanation
Indices: 537666--537748 Score: 87
Period size: 18 Copynumber: 4.6 Consensus size: 18
537656 CAAAAGAAAG
* *
537666 AAAAAATGAATGAAATAA
1 AAAAAATAAAAGAAATAA
*
537684 AAAAAATAAAAGAAGTAA
1 AAAAAATAAAAGAAATAA
537702 AAAAAATTAAAA-AAATAA
1 AAAAAA-TAAAAGAAATAA
* * * *
537720 AAGAAGTAAAAAAAATTA
1 AAAAAATAAAAGAAATAA
537738 AAAAAATAAAA
1 AAAAAATAAAA
537749 AGTTAAATCT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
17 5 0.09
18 44 0.81
19 5 0.09
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAAGAAATAA
Found at i:537690 original size:9 final size:9
Alignment explanation
Indices: 537678--537749 Score: 90
Period size: 9 Copynumber: 8.0 Consensus size: 9
537668 AAAATGAATG
537678 AAATAAAAA
1 AAATAAAAA
*
537687 AAATAAAAG
1 AAATAAAAA
*
537696 AAGTAAAAA
1 AAATAAAAA
*
537705 AAATTAAAA
1 AAATAAAAA
*
537714 AAATAAAAG
1 AAATAAAAA
*
537723 AAGTAAAAA
1 AAATAAAAA
*
537732 AAATTAAAA
1 AAATAAAAA
537741 AAATAAAAA
1 AAATAAAAA
537750 GTTAAATCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (9 bp):
AAATAAAAA
Found at i:537708 original size:27 final size:27
Alignment explanation
Indices: 537678--537748 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
537668 AAAATGAATG
*
537678 AAATAAAAAAAATAAAAGAAGTAAAAA
1 AAATTAAAAAAATAAAAGAAGTAAAAA
537705 AAATTAAAAAAATAAAAGAAGTAAAAA
1 AAATTAAAAAAATAAAAGAAGTAAAAA
537732 AAATTAAAAAAATAAAA
1 AAATTAAAAAAATAAAA
537749 AGTTAAATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (27 bp):
AAATTAAAAAAATAAAAGAAGTAAAAA
Found at i:539029 original size:85 final size:85
Alignment explanation
Indices: 538922--539513 Score: 642
Period size: 85 Copynumber: 7.0 Consensus size: 85
538912 ATTTTATTGA
* * * * * * *
538922 CAGATATCCCTTCTTGCCTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
*
538987 ACTCGAAGGTCTTCGGTTGG
66 ACTCGAAGGTCTTTGGTTGG
* * * *
539007 CAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
*
539071 ACTCGAAGGTCTTTTGG-TGA
66 ACTCGAAGGTC-TTTGGTTGG
* * * * * * * * *
539091 CAAATAACCCTTCTAGGCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
* *
539156 ACTCGAGGGTCTTTGGCTGG
66 ACTCGAAGGTCTTTGGTTGG
* * * * * * *
539176 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAA-CCGAACGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
* *
539240 ACTCAAAGGTCTTTTGTTGG
66 ACTCGAAGGTCTTTGGTTGG
* * * * *
539260 CAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATG-CCATGGAGCTGAGCGTAGTCAA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
539324 ACTCGAAGGTCTTT-GTTGG
66 ACTCGAAGGTCTTTGGTTGG
* * * * * * *
539343 CAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTTAGCGTCGTCGA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
539407 ACTCGAAGGTCTTTTGGTTGG
66 ACTCGAAGGTC-TTTGGTTGG
* * * *
539428 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGT-ACCTT-AGAGTTGAGCGTAGTCA
1 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGA-AGCTGAGCGTAGTCG
* *
539491 AACTCGAAGGCCTTTGGTGGG
65 AACTCGAAGGTCTTTGGTTGG
539512 CA
1 CA
539514 CAATTCCCTT
Statistics
Matches: 419, Mismatches: 80, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
83 74 0.18
84 171 0.41
85 174 0.42
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (85 bp):
CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTTGG
Found at i:539210 original size:169 final size:169
Alignment explanation
Indices: 538919--539513 Score: 703
Period size: 169 Copynumber: 3.5 Consensus size: 169
538909 ACAATTTTAT
* * *
538919 TGACAGATATCCCTTCTTGCCTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* *
538984 CGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
539049 CCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * *
539088 TGACAAATAACCCTTCTAGGCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * *
539153 CGAACTCGAGGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * * * *
539218 TCGTT-GAACCGAACGTAGTCGAACTCAAAGGTCTTTTGT
131 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* ** * * * * *
539257 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCAT-GGAGCTGAGCGTAGT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* * * * * *
539321 CAAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
539385 CCTTGGAGCTTAGCGTCGTCGAACTCGAAGGTCTTTTGG
131 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
* * * * * * * * *
539424 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGTACCTTAG-AGTTGAGCGTAG
1 -TGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * *
539488 TCAAACTCGAAGGCCTTTGGTGGGCA
65 TCGAACTCGAAGGTCTTTGGTTGGCA
539514 CAATTCCCTT
Statistics
Matches: 363, Mismatches: 58, Indels: 10
0.84 0.13 0.02
Matches are distributed among these distances:
166 3 0.01
167 66 0.18
168 99 0.27
169 192 0.53
170 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (169 bp):
TGACAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
Found at i:539276 original size:253 final size:252
Alignment explanation
Indices: 538983--539463 Score: 712
Period size: 253 Copynumber: 1.9 Consensus size: 252
538973 CTGAGTGTAA
* * *
538983 TCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAATGATAT
* * *
539048 GCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGGCTTGA
66 GCCATGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTTGGTGACAAATAACCCTTATAGCCTTGA
* * * *
539113 GTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGCTGGC
130 GTTATGCTGCAAATGATGTG-CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCTGGC
*
539177 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAACGTAG
194 AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAACGTAG
** * *
539236 TCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATAT
1 TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAATGATAT
* * *
539301 GCCATGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGTTGGCAGATAACCCTTATAGCCTTGAG
66 GCCATGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAAATAACCCTTATAGCCTTGAG
* * * ** *
539366 TTATGCTGCAAATGATGTGCCTTGGAGCTTAGCGTCGTCGAACTCGAAGGTCTTTTGGTTGGCAG
131 TTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCTGGCAG
*
539431 ATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
196 ATAACCCTTCTCGACTTAAGCTATGCTGCAAAT
539464 AATGTACCTT
Statistics
Matches: 202, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
251 26 0.13
252 85 0.42
253 91 0.45
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (252 bp):
TCGAACTCAAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATACTACAAATGATAT
GCCATGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAAATAACCCTTATAGCCTTGAG
TTATGCTGCAAATGATGTGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCTGGCAG
ATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCGTTGAACCGAACGTAG
Found at i:539906 original size:110 final size:110
Alignment explanation
Indices: 539626--540098 Score: 713
Period size: 110 Copynumber: 4.3 Consensus size: 110
539616 TATTGTTTCA
* ** *
539626 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAGTCGTTTGTTGA
1 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
* * * * *
539687 CAGCCAGCCGCCCCTTCGCTGTAAAGTTGAGCTTGTGTTGTCTCG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCG
*
539732 AGTCTAATAT-CATCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
1 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
*
539796 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTTG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCG
* *
539841 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTTGTTTGTTGA
1 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
* * *
539906 CAGTCAGTCACCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTTG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCG
* * * *
539951 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTTTTGA
1 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
* *
540016 CAGTCAGTCGCCTCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCG
66 CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCG
540061 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
540099 AAAGCTGCAA
Statistics
Matches: 335, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
105 24 0.07
106 10 0.03
109 69 0.21
110 232 0.69
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.36
Consensus pattern (110 bp):
AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA
CAGTCAGTCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCG
Found at i:543867 original size:16 final size:16
Alignment explanation
Indices: 543845--543924 Score: 72
Period size: 16 Copynumber: 4.7 Consensus size: 16
543835 CAAAAGAAAG
*
543845 AAAAAAATGAATGAAAT
1 AAAAAAATAAAT-AAAT
543862 AAAAAAAATAAAAATAAA-
1 -AAAAAAAT--AAATAAAT
543880 AGTAAAAAATAAATAAAT
1 A--AAAAAATAAATAAAT
* *
543898 CAAAAAATGAATAAAT
1 AAAAAAATAAATAAAT
543914 AAAAAAATAAA
1 AAAAAAATAAA
543925 AGTTAAATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
16 23 0.44
17 8 0.15
18 8 0.15
19 10 0.19
20 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.05, T:0.16
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:543887 original size:37 final size:37
Alignment explanation
Indices: 543813--543925 Score: 101
Period size: 37 Copynumber: 3.1 Consensus size: 37
543803 GACAGTAAAT
**
543813 AATAAATAAAT-ATTAAATGAATCAAA-AGAAAGAAAAA
1 AATAAATAAATAAAAAAATGAAT-AAATA-AAAGAAAAA
* *
543850 AATGAATGAAATAAAAAAAAT-AA-AAATAAAAGTAAAA
1 AATAAAT-AAAT-AAAAAAATGAATAAATAAAAGAAAAA
*
543887 AATAAATAAATCAAAAAATGAATAAATAAAA-AAATAA
1 AATAAATAAATAAAAAAATGAATAAATAAAAGAAA-AA
543924 AA
1 AA
543926 GTTAAATCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
35 7 0.11
36 8 0.13
37 35 0.56
38 5 0.08
39 2 0.03
40 5 0.08
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (37 bp):
AATAAATAAATAAAAAAATGAATAAATAAAAGAAAAA
Found at i:543925 original size:8 final size:8
Alignment explanation
Indices: 543858--543925 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
543848 AAAATGAATG
543858 AAATAAAAA
1 AAAT-AAAA
543867 AAATAAAA
1 AAATAAAA
*
543875 ATAAAAGTAAA
1 A-AATA--AAA
*
543886 AAATAAAT
1 AAATAAAA
*
543894 AAATCAAA
1 AAATAAAA
* *
543902 AAATGAAT
1 AAATAAAA
543910 AAATAAAA
1 AAATAAAA
543918 AAATAAAA
1 AAATAAAA
543926 GTTAAATCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
8 33 0.70
9 7 0.15
10 3 0.06
11 4 0.09
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:543954 original size:51 final size:53
Alignment explanation
Indices: 543846--543947 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 53
543836 AAAAGAAAGA
*
543846 AAAAAATGAATGAAATAAAAAAAATAAAAATAAAAGTAAAAAATAAATAAATC
1 AAAAAATGAATGAAATAAAAAAAATAAAAATAAAACTAAAAAATAAATAAATC
* * *
543899 AAAAAATGAAT-AAAT-AAAAAAATAAAAGTTAAATCTTAAAAAT-AATAAA
1 AAAAAATGAATGAAATAAAAAAAATAAAA-ATAAAACTAAAAAATAAATAAA
543948 ATAAAAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 18 0.41
52 15 0.34
53 11 0.25
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (53 bp):
AAAAAATGAATGAAATAAAAAAAATAAAAATAAAACTAAAAAATAAATAAATC
Found at i:543993 original size:13 final size:13
Alignment explanation
Indices: 543972--544021 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
543962 AAGATAAACA
*
543972 TAAATAATACTGAT
1 TAAA-AATAATGAT
543986 TAAAAATAATGAT
1 TAAAAATAATGAT
543999 TAAAAATAATGAT
1 TAAAAATAATGAT
*
544012 AAAAAATAAT
1 TAAAAATAAT
544022 AAAGTGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
13 30 0.88
14 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (13 bp):
TAAAAATAATGAT
Found at i:546290 original size:20 final size:20
Alignment explanation
Indices: 546265--546302 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
546255 GGTAAACACA
546265 TCGCAACGCGAATTTCGTTT
1 TCGCAACGCGAATTTCGTTT
546285 TCGCAACGCGAATTTCGT
1 TCGCAACGCGAATTTCGT
546303 AAATCGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (20 bp):
TCGCAACGCGAATTTCGTTT
Found at i:552136 original size:16 final size:14
Alignment explanation
Indices: 552100--552134 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
552090 ATATATATAC
*
552100 AATATAATTTTAAT
1 AATATATTTTTAAT
552114 AATATATTTTTAAT
1 AATATATTTTTAAT
*
552128 ATTATAT
1 AATATAT
552135 ATATACTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATATTTTTAAT
Found at i:552137 original size:43 final size:44
Alignment explanation
Indices: 552064--552163 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 44
552054 TTTAACATAG
*
552064 TTTTAATAA-AAATATTCAATATTCAAATATATA-TACAA-TATAA
1 TTTTAATAATATATATTCAATATTCAAATATATACT-CAATTAT-A
* * *
552107 TTTTAATAATATATTTTTAATATT-ATATATATACTCAATTATA
1 TTTTAATAATATATATTCAATATTCAAATATATACTCAATTATA
*
552150 TTATAATAATATAT
1 TTTTAATAATATAT
552164 GATATTATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 34 0.69
44 15 0.31
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (44 bp):
TTTTAATAATATATATTCAATATTCAAATATATACTCAATTATA
Found at i:552597 original size:18 final size:16
Alignment explanation
Indices: 552574--552623 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
552564 ATAATATTTT
*
552574 AATAATAATCTTTACATA
1 AATAATAATATTTA-A-A
552592 AATAATCTAATATTTAAA
1 AATAA--TAATATTTAAA
552610 AATAATAATATTTA
1 AATAATAATATTTA
552624 TTATATTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 9 0.31
18 11 0.38
19 1 0.03
20 8 0.28
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAATATTTAAA
Found at i:554329 original size:384 final size:384
Alignment explanation
Indices: 553620--554387 Score: 1518
Period size: 384 Copynumber: 2.0 Consensus size: 384
553610 ACAAATCATC
553620 TGGCTATTCATATATTACAAACTCGTCCTTTTTTGAAAAATTAAAGGCAGTCTAAGCTACACGTT
1 TGGCTATTCATATATTACAAACTCGTCCTTTTTTGAAAAATTAAAGGCAGTCTAAGCTACACGTT
553685 AACTTACTCACTGTGATATGATAAAATTTGATCATAAAATCTCAAACGACTATCATATCTAAGTC
66 AACTTACTCACTGTGATATGATAAAATTTGATCATAAAATCTCAAACGACTATCATATCTAAGTC
553750 AATAGATTAACTTTAAGATTAAATTGTCACAATTTCTAACAAAAAATGATGAGTTTGAATTATAT
131 AATAGATTAACTTTAAGATTAAATTGTCACAATTTCTAACAAAAAATGATGAGTTTGAATTATAT
*
553815 GGATAGTTAGGTGACTATTTTATAATTTTTAGTTGTTAAGTGACTCAGCAAAACAACACCTTATA
196 GGATAGTTAGGTGACTATTTTATAATTTTTAATTGTTAAGTGACTCAGCAAAACAACACCTTATA
553880 ATCTAAGGATATTCTGTAATTTTTAATAATCGAATGACTCAATAAAACAATGCCTAGTAGCCGAA
261 ATCTAAGGATATTCTGTAATTTTTAATAATCGAATGACTCAATAAAACAATGCCTAGTAGCCGAA
553945 TACCATTTGTATATTTTACTCTAATATTTTTATACACTTGAAAAGTTAATTAAATTTTA
326 TACCATTTGTATATTTTACTCTAATATTTTTATACACTTGAAAAGTTAATTAAATTTTA
554004 TGGCTATTCATATATTACAAACTCGTCCTTTTTTGAAAAATTAAAGGCAGTCTAAGCTACACGTT
1 TGGCTATTCATATATTACAAACTCGTCCTTTTTTGAAAAATTAAAGGCAGTCTAAGCTACACGTT
554069 AACTTACTCACTGTGATATGATAAAATTTGATCATAAAATCTCAAACGACTATCATATCTAAGTC
66 AACTTACTCACTGTGATATGATAAAATTTGATCATAAAATCTCAAACGACTATCATATCTAAGTC
554134 AATAGATTAACTTTAAGATTAAATTGTCACAATTTCTAACAAAAAATGATGAGTTTGAATTATAT
131 AATAGATTAACTTTAAGATTAAATTGTCACAATTTCTAACAAAAAATGATGAGTTTGAATTATAT
554199 GGATAGTTAGGTGACTATTTTATAATTTTTAATTGTTAAGTGACTCAGCAAAACAACACCTTATA
196 GGATAGTTAGGTGACTATTTTATAATTTTTAATTGTTAAGTGACTCAGCAAAACAACACCTTATA
554264 ATCTAAGGATATTCTGTAATTTTTAATAATCGAATGACTCAATAAAACAATGCCTAGTAGCCGAA
261 ATCTAAGGATATTCTGTAATTTTTAATAATCGAATGACTCAATAAAACAATGCCTAGTAGCCGAA
*
554329 TATCATTTGTATATTTTACTCTAATATTTTTATACACTTGAAAAGTTAATTAAATTTTA
326 TACCATTTGTATATTTTACTCTAATATTTTTATACACTTGAAAAGTTAATTAAATTTTA
554388 GTGATTATAT
Statistics
Matches: 382, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
384 382 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.37
Consensus pattern (384 bp):
TGGCTATTCATATATTACAAACTCGTCCTTTTTTGAAAAATTAAAGGCAGTCTAAGCTACACGTT
AACTTACTCACTGTGATATGATAAAATTTGATCATAAAATCTCAAACGACTATCATATCTAAGTC
AATAGATTAACTTTAAGATTAAATTGTCACAATTTCTAACAAAAAATGATGAGTTTGAATTATAT
GGATAGTTAGGTGACTATTTTATAATTTTTAATTGTTAAGTGACTCAGCAAAACAACACCTTATA
ATCTAAGGATATTCTGTAATTTTTAATAATCGAATGACTCAATAAAACAATGCCTAGTAGCCGAA
TACCATTTGTATATTTTACTCTAATATTTTTATACACTTGAAAAGTTAATTAAATTTTA
Found at i:557959 original size:6 final size:6
Alignment explanation
Indices: 557931--558012 Score: 67
Period size: 6 Copynumber: 13.0 Consensus size: 6
557921 TAATTATTTT
* * * *
557931 ATTATT ATTATA GATATATTA ATTATA ATTATA ATTTTA TTTATA TATCAT-
1 ATTATA ATTATA -AT-TA-TA ATTATA ATTATA ATTATA ATTATA -ATTATA
*
557982 ATTATAA ATTATG ATTATA ATTATA ATTATA
1 ATTAT-A ATTATA ATTATA ATTATA ATTATA
558013 TGAGTATACT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.07
6 39 0.64
7 12 0.20
8 4 0.07
9 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:557970 original size:29 final size:30
Alignment explanation
Indices: 557921--557999 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 30
557911 CATGTATTAA
* *
557921 TAATTAT-TTTATTATTATTATAGATATAT
1 TAATTATAATTATAATTATTATAGATATAT
**
557950 TAATTATAATTATAATT-TTATTTATATAT
1 TAATTATAATTATAATTATTATAGATATAT
* *
557979 CATATTATAAATTATGATTAT
1 TA-ATTAT-AATTATAATTAT
558000 AATTATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 18 0.45
30 12 0.30
31 9 0.22
32 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (30 bp):
TAATTATAATTATAATTATTATAGATATAT
Found at i:558020 original size:20 final size:19
Alignment explanation
Indices: 557982--558020 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
557972 TATATATCAT
*
557982 ATTATAAATTATGATTATA
1 ATTATAAATTATGAGTATA
*
558001 ATTATAATTATATGAGTATA
1 ATTATAAAT-TATGAGTATA
558021 CTAACAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTATAAATTATGAGTATA
Found at i:558422 original size:20 final size:20
Alignment explanation
Indices: 558397--558464 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
558387 ATAATACATA
*
558397 ATCGCAACTCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
558417 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
558437 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
558457 GTCGCAAC
1 ATCGCAAC
558465 ACTGAATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:559375 original size:24 final size:23
Alignment explanation
Indices: 559317--559371 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
559307 TAGTCAGTAT
* *
559317 TCGAATTTGATCTTGGTCAATAC
1 TCGAATTTGATATTGATCAATAC
* *
559340 CCGGACTTTGATATTGATCAATAC
1 TC-GAATTTGATATTGATCAATAC
559364 TCGAATTT
1 TCGAATTT
559372 TGATGATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (23 bp):
TCGAATTTGATATTGATCAATAC
Found at i:560199 original size:23 final size:23
Alignment explanation
Indices: 560130--560298 Score: 279
Period size: 23 Copynumber: 7.4 Consensus size: 23
560120 TTGATATTTA
*
560130 TCCCGAAGGACCACATG-ATATG
1 TCCCGAAGGACCACTTGAATATG
560152 TCCCGAAGGACCACTTG-ATATG
1 TCCCGAAGGACCACTTGAATATG
* *
560174 TCCCGTATGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
560197 TCCCGAAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
* *
560220 TCCCGTATGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
560243 TCCCGAAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
560266 TCCCGAAGGACCACTTGAATATG
1 TCCCGAAGGACCACTTGAATATG
560289 TCCCGAAGGA
1 TCCCGAAGGA
560299 TATGTCCCGA
Statistics
Matches: 137, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
22 36 0.26
23 101 0.74
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (23 bp):
TCCCGAAGGACCACTTGAATATG
Found at i:560303 original size:14 final size:14
Alignment explanation
Indices: 560284--560312 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
560274 GACCACTTGA
560284 ATATGTCCCGAAGG
1 ATATGTCCCGAAGG
560298 ATATGTCCCGAAGG
1 ATATGTCCCGAAGG
560312 A
1 A
560313 CCACTTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (14 bp):
ATATGTCCCGAAGG
Found at i:563420 original size:24 final size:24
Alignment explanation
Indices: 563358--563426 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
563348 AAGTACAAAA
* *
563358 CAGAGTCCATGTCAAGTATCATAT
1 CAGAATCCATGTCAAATATCATAT
* * *
563382 AAAAATTCA-GATCAAATATCATAT
1 CAGAATCCATG-TCAAATATCATAT
*
563406 CAGAATCCATGTCAAAAATCA
1 CAGAATCCATGTCAAATATCA
563427 GATAAACTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
23 1 0.03
24 32 0.94
25 1 0.03
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (24 bp):
CAGAATCCATGTCAAATATCATAT
Found at i:564154 original size:29 final size:29
Alignment explanation
Indices: 564135--564216 Score: 155
Period size: 29 Copynumber: 2.8 Consensus size: 29
564125 GCACCATTTT
564135 CGAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
*
564164 CAAATTAATTCCCAGAATAGCACCAAAAC
1 CGAATTAATTCCCAGAATAGCACCAAAAC
564193 CGAATTAATTCCCAGAATAGCACC
1 CGAATTAATTCCCAGAATAGCACC
564217 GGTCAACGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.44, C:0.28, G:0.10, T:0.18
Consensus pattern (29 bp):
CGAATTAATTCCCAGAATAGCACCAAAAC
Found at i:564256 original size:13 final size:12
Alignment explanation
Indices: 564224--564266 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
564214 ACCGGTCAAC
*
564224 GGTCAACGGTCAAC
1 GGTCAACGGTC--G
564238 GGTCAACGGGTCG
1 GGTCAAC-GGTCG
564251 GGTCAACGGTCG
1 GGTCAACGGTCG
564263 GGTC
1 GGTC
564267 GGGTAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 7 0.26
15 4 0.15
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:564261 original size:7 final size:7
Alignment explanation
Indices: 564216--564246 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
564206 AGAATAGCAC
564216 CGGTCAA
1 CGGTCAA
564223 CGGTCAA
1 CGGTCAA
564230 CGGTCAA
1 CGGTCAA
564237 CGGTCAA
1 CGGTCAA
564244 CGG
1 CGG
564247 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:564281 original size:18 final size:17
Alignment explanation
Indices: 564244--564294 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
564234 CAACGGTCAA
*
564244 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTAAACGGT
564261 CGGGTCGGGTAAACTGGT
1 CGGGTCGGGTAAAC-GGT
564279 CGGGTCGGGTAAACGG
1 CGGGTCGGGTAAACGG
564295 GTAAACGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTAAACGGT
Found at i:564339 original size:11 final size:10
Alignment explanation
Indices: 564309--564360 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
564299 ACGGGTCGTG
564309 ACCGGTC-AA
1 ACCGGTCAAA
564318 ACCGGTCAAA
1 ACCGGTCAAA
564328 ACCGGTTCAAA
1 ACCGG-TCAAA
*
564339 ACCGGT-TAA
1 ACCGGTCAAA
564348 ACCGGTCAAA
1 ACCGGTCAAA
564358 ACC
1 ACC
564361 AGTTTCCAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Done.