Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 20
Found at i:400143 original size:37 final size:39
Alignment explanation
Indices: 400059--400143 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 39
400049 TGAGATAGAA
*
400059 TTTGTTTTTAAGAGAAAGTTGTCTCCAACGAGACAAAAT
1 TTTGTTTTTAAGAGAAAGTTGTCTCCAACGAGACAAAAC
* * * * *
400098 TTTATTTTTAAGA-AAA-TTGTCTCTAGCGAGACGACAC
1 TTTGTTTTTAAGAGAAAGTTGTCTCCAACGAGACAAAAC
400135 TTTGTTTTT
1 TTTGTTTTT
400144 TTAAGAAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 24 0.62
38 3 0.08
39 12 0.31
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (39 bp):
TTTGTTTTTAAGAGAAAGTTGTCTCCAACGAGACAAAAC
Found at i:400492 original size:14 final size:14
Alignment explanation
Indices: 400473--400508 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
400463 TTCATGTGTC
400473 ATGTATGTATATGT
1 ATGTATGTATATGT
400487 ATGTATGTATATGT
1 ATGTATGTATATGT
400501 -TG-ATGTAT
1 ATGTATGTAT
400509 GTTTTCTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.27
13 2 0.09
14 14 0.64
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (14 bp):
ATGTATGTATATGT
Found at i:401537 original size:2 final size:2
Alignment explanation
Indices: 401530--401559 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
401520 TATTGTGTAC
401530 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
401560 GGTTATACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404661 original size:5 final size:5
Alignment explanation
Indices: 404651--404686 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
404641 TTTTGCAATG
404651 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
404687 GTGAAAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:406658 original size:3 final size:3
Alignment explanation
Indices: 406650--406695 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
406640 ATTTAGTTAT
406650 TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
406694 TA
1 TA
406696 TTTTTGATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:407519 original size:26 final size:26
Alignment explanation
Indices: 407485--407537 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
407475 GAAAAAATTT
407485 GTTGCAAGGAGGAAGAAGAAGAAGAA
1 GTTGCAAGGAGGAAGAAGAAGAAGAA
* *
407511 GTTGTAAGGAGGAGGAAGAAGAAGAA
1 GTTGCAAGGAGGAAGAAGAAGAAGAA
407537 G
1 G
407538 AAAAGGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.42, T:0.09
Consensus pattern (26 bp):
GTTGCAAGGAGGAAGAAGAAGAAGAA
Found at i:409762 original size:19 final size:19
Alignment explanation
Indices: 409735--409772 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
409725 TGGTGACTCC
*
409735 AATTCAAAATTTTCAAATT
1 AATTCAAAATTGTCAAATT
*
409754 AATTTAAAATTGTCAAATT
1 AATTCAAAATTGTCAAATT
409773 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (19 bp):
AATTCAAAATTGTCAAATT
Found at i:415530 original size:21 final size:21
Alignment explanation
Indices: 415506--415569 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
415496 GCAAATTCCT
415506 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** *
415527 GTTGAAAATCGTGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
415547 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
415568 GT
1 GT
415570 CTACAGTTGT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:415586 original size:22 final size:22
Alignment explanation
Indices: 415558--415610 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
415548 TTCCATTTCG
415558 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
415580 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
415602 CGTTGCGAT
1 CGTTGCGAT
415611 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:415720 original size:6 final size:6
Alignment explanation
Indices: 415709--415746 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
415699 GACACGTATT
415709 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
415747 CGAGACAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:416419 original size:41 final size:41
Alignment explanation
Indices: 416362--416508 Score: 231
Period size: 41 Copynumber: 3.6 Consensus size: 41
416352 GCAACGCGAA
*
416362 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATTGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
* ***
416403 GCGAACTGGAAAATCGCTTTGCGATTTTCAACTATCGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
*
416444 GCGAAATGGAAAATCGTAACGCGATTTTCAACTATCGCAAC
1 GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
*
416485 GCGAACTGGAAAATCGCAACGCGA
1 GCGAAATGGAAAATCGCAACGCGA
416509 AATGCAACGC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (41 bp):
GCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
Found at i:416447 original size:21 final size:21
Alignment explanation
Indices: 416374--416488 Score: 81
Period size: 21 Copynumber: 5.6 Consensus size: 21
416364 GAAATGGAAA
416374 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
416395 ATTGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
***
416415 ATCGCTTTGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
416436 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
416456 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
416477 ATCGCAACGCGA
1 ATCGCAACGCGA
416489 ACTGGAAAAT
Statistics
Matches: 62, Mismatches: 30, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
20 25 0.40
21 37 0.60
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:416464 original size:20 final size:20
Alignment explanation
Indices: 416436--416512 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
416426 ATTTTCAACT
416436 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
416456 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
416477 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
416497 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
416513 CAACGCGAAT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:420155 original size:40 final size:40
Alignment explanation
Indices: 420111--420197 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
420101 GGTTCCAAAT
* *
420111 TCGCAACTCGAATAGGTAAATCACAAC-TATAATATGTAAA
1 TCGCAACGCGAATAGGTAAATCACAACGT-GAATATGTAAA
** * *
420151 TCGCAACGCGAATTTGTAAATCGCAACGTGAATTTGTAAA
1 TCGCAACGCGAATAGGTAAATCACAACGTGAATATGTAAA
420191 TCGCAAC
1 TCGCAAC
420198 ACAGAAGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (40 bp):
TCGCAACGCGAATAGGTAAATCACAACGTGAATATGTAAA
Found at i:420168 original size:20 final size:20
Alignment explanation
Indices: 420145--420197 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
420135 AACTATAATA
420145 TGTAAATCGCAACGCGAATT
1 TGTAAATCGCAACGCGAATT
*
420165 TGTAAATCGCAACGTGAATT
1 TGTAAATCGCAACGCGAATT
420185 TGTAAATCGCAAC
1 TGTAAATCGCAAC
420198 ACAGAAGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (20 bp):
TGTAAATCGCAACGCGAATT
Found at i:422403 original size:20 final size:21
Alignment explanation
Indices: 422378--422429 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
422368 TTTTCTCTAT
*
422378 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
422398 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
422419 TCGCAATGCGA
1 TCGCAATGCGA
422430 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:422442 original size:41 final size:41
Alignment explanation
Indices: 422415--422492 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
422405 GCGAATTGGG
* * *
422415 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
422456 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
422493 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:422443 original size:20 final size:20
Alignment explanation
Indices: 422418--422512 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
422408 AATTGGGAAA
*
422418 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
422438 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
422459 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
422479 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
422499 TTCGCAACGCGATA
1 ATCGCAACGCGATA
422513 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:422728 original size:22 final size:22
Alignment explanation
Indices: 422700--422765 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
422690 CACTCTCTCA
**
422700 CCCATCTCCAACGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
*
422722 CCCATCTCCGGCGAAATTCGTC
1 CCCATCTCCGGCGAAATCCGTC
422744 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
422766 TATCTAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.44, G:0.15, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:423035 original size:20 final size:20
Alignment explanation
Indices: 423010--423047 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
423000 CGATTCTCTC
423010 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
423030 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
423048 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:424387 original size:18 final size:18
Alignment explanation
Indices: 424366--424410 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
424356 TCCACTTCGG
*
424366 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
424384 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
424402 GAGCCATCA
1 GAGCCATCA
424411 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:424908 original size:20 final size:20
Alignment explanation
Indices: 424883--424937 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
424873 TAGTTTACTT
424883 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
424903 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
424923 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
424938 AAAATCGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:424957 original size:14 final size:14
Alignment explanation
Indices: 424938--424995 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
424928 ATGCGAAATG
424938 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
424952 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
424968 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
424984 AAAATCGCAACG
1 AAAATCGCAACG
424996 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:424980 original size:32 final size:32
Alignment explanation
Indices: 424922--425005 Score: 150
Period size: 32 Copynumber: 2.6 Consensus size: 32
424912 GGAAATGGCT
*
424922 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
424955 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
424987 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
425006 ATCGTTTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 35 0.70
33 15 0.30
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:426935 original size:14 final size:15
Alignment explanation
Indices: 426900--426937 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
426890 GATTGTTTAA
426900 TTGATTTGTAAAAAG
1 TTGATTTGTAAAAAG
* *
426915 ATGATTTGT-AAATG
1 TTGATTTGTAAAAAG
426929 TTGATTTGT
1 TTGATTTGT
426938 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (15 bp):
TTGATTTGTAAAAAG
Found at i:428424 original size:12 final size:12
Alignment explanation
Indices: 428407--428431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
428397 ATATAATCCT
428407 GAAGAAGAAAAA
1 GAAGAAGAAAAA
428419 GAAGAAGAAAAA
1 GAAGAAGAAAAA
428431 G
1 G
428432 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:430720 original size:19 final size:19
Alignment explanation
Indices: 430698--430795 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
430688 GGAAATTACT
430698 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
430717 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
430731 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
430750 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
430764 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
430783 ATCGCAACGCGAA
1 ATCGCAATGCGAA
430796 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:430735 original size:33 final size:33
Alignment explanation
Indices: 430698--430791 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
430688 GGAAATTACT
430698 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
430731 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
430764 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
430792 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:430964 original size:13 final size:14
Alignment explanation
Indices: 430948--430983 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
430938 CATCAATTAA
430948 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
430961 ACAAATCACCTTTT
1 ACAAATCAACTTTT
430975 ACAAATCAA
1 ACAAATCAA
430984 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:432380 original size:21 final size:21
Alignment explanation
Indices: 432314--432380 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
432304 GTGAATCGGG
*
432314 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
432334 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
432356 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
432377 CTCT
1 CTCT
432381 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:432399 original size:42 final size:41
Alignment explanation
Indices: 432314--432436 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
432304 GTGAATCGGG
* * * * *
432314 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
432356 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
432398 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
432437 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:434426 original size:19 final size:19
Alignment explanation
Indices: 434376--434470 Score: 145
Period size: 19 Copynumber: 4.9 Consensus size: 19
434366 TCTTTTGGTT
* *
434376 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAATGC
*
434395 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAATGC
*
434415 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAATGC
434434 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
434453 GAAATGAAAATCGCAATG
1 GAAATGAAAATCGCAATG
434471 TGATTTTGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
19 53 0.77
20 16 0.23
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:434449 original size:38 final size:39
Alignment explanation
Indices: 434376--434468 Score: 161
Period size: 38 Copynumber: 2.4 Consensus size: 39
434366 TCTTTTGGTT
*
434376 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAATGC
*
434415 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGATAATGAAAATCGCAATGC
434453 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
434469 TGTGATTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 32 0.62
39 20 0.38
ACGTcount: A:0.48, C:0.16, G:0.22, T:0.14
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGATAATGAAAATCGCAATGC
Found at i:434502 original size:19 final size:19
Alignment explanation
Indices: 434469--434513 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
434459 AAAATCGCAA
*
434469 TGTGATTTTGGTTTCGCGT
1 TGTGATTTTGATTTCGCGT
*
434488 TGTGATTTTTATTTCGCGT
1 TGTGATTTTGATTTCGCGT
*
434507 TGCGATT
1 TGTGATT
434514 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.11, G:0.27, T:0.53
Consensus pattern (19 bp):
TGTGATTTTGATTTCGCGT
Found at i:435092 original size:20 final size:20
Alignment explanation
Indices: 435067--435118 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
435057 CGCTAAGTAA
*
435067 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
435087 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
435107 ATCTCGTTGCGA
1 ATCGCGTTGCGA
435119 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:435155 original size:20 final size:20
Alignment explanation
Indices: 435067--435160 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
435057 CGCTAAGTAA
*
435067 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
435087 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
435107 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
* *
435128 ATCACATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
435148 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
435161 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:435179 original size:41 final size:41
Alignment explanation
Indices: 435149--435244 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
435139 ATAGTCAGTA
* * *
435149 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
435190 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
435231 TCGCATTGCGAATT
1 TCGCATTGCGAATT
435245 GGTAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:435193 original size:20 final size:20
Alignment explanation
Indices: 435149--435241 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
435139 ATAGTCAGTA
* **
435149 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
435170 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
435190 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
435211 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
435231 TCGCATTGCGA
1 TCGCATTGCGA
435242 ATTGGTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:436066 original size:296 final size:298
Alignment explanation
Indices: 435508--436106 Score: 950
Period size: 296 Copynumber: 2.0 Consensus size: 298
435498 GTATAGTTAC
*
435508 AATGATCATGCCTTAGAGATCGTTGGCGTGGGAACCATCAAATTGAAGATGTATGATGGAACAAT
1 AATGATCATGCCTTAGAGATCGTTGGCGTGAGAACCATCAAATTGAAGATGTATGATGGAACAAT
* * *
435573 TAAAGTTGTTCGAGATGTGCGGCACGTAAAAGGCCTGAAGAAAAATTTATTATCATACGGATTGT
66 TAAAGTTGTTCGAGATGT-CGGCACGTAAAAGGCCTGAAGAAAAAATTATTATCATACGAAATGT
* *
435638 TGAATAATAATGCAAGCAAGATTGAAACACAGAAATGAATCATAAAAGTGTTTCGTGGAGCGCTT
130 TGAATAATAATGCAAGCAAGATTGAAACACAGAAAGGAATCATAAAAGTGTTCCGTGGAGCGCTT
* * *
435703 GTGGTGATGAAAGGCGAAAAGATAGCAACAAACTTATACATGCTAAAGGGAAAGACTTTGTTAGA
195 GTGGTGATGAAAGGCGAAAAGATAACAACAAACTTATACATACTAAAGGGAAAGACTTTGCTAGA
* *
435768 AGCAGAAGCCTCTGTTGTCTCATATAGTTCAGATTCTGT
260 AGCAGAAGCCTCTGTTGCCTCATATAGTTCAGATTCTAT
* *
435807 AATGATTATGTCTTAGAGATCGTTGGCGTGAGAACCATCAAATTGAAGATGTATGATGGAACAAT
1 AATGATCATGCCTTAGAGATCGTTGGCGTGAGAACCATCAAATTGAAGATGTATGATGGAACAAT
* *
435872 TAAAGTTGTTCGAGATGT-GGCATGTTAAAGGCCTGAA-AAAAAATTATTATCATACGAAATGTT
66 TAAAGTTGTTCGAGATGTCGGCACGTAAAAGGCCTGAAGAAAAAATTATTATCATACGAAATGTT
* * * *
435935 GGATAATAATGCAAGCAAGATTGAAACACGGAAAGGAATCATGAAGGTGTTCCGTGGAGCGCTTG
131 GAATAATAATGCAAGCAAGATTGAAACACAGAAAGGAATCATAAAAGTGTTCCGTGGAGCGCTTG
* * * * *
436000 TGGTGATGAAAGGTGAAAAGATAACAACAAACTTGTACATACTGAAGGGAGAGATTTTGCTAGAA
196 TGGTGATGAAAGGCGAAAAGATAACAACAAACTTATACATACTAAAGGGAAAGACTTTGCTAGAA
*
436065 GCAGAAGCCTCTGTTGCCTCATGTAGTTCAGATTCTAT
261 GCAGAAGCCTCTGTTGCCTCATATAGTTCAGATTCTAT
436103 AATG
1 AATG
436107 CTATGGCATC
Statistics
Matches: 275, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
296 178 0.65
297 17 0.06
299 80 0.29
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (298 bp):
AATGATCATGCCTTAGAGATCGTTGGCGTGAGAACCATCAAATTGAAGATGTATGATGGAACAAT
TAAAGTTGTTCGAGATGTCGGCACGTAAAAGGCCTGAAGAAAAAATTATTATCATACGAAATGTT
GAATAATAATGCAAGCAAGATTGAAACACAGAAAGGAATCATAAAAGTGTTCCGTGGAGCGCTTG
TGGTGATGAAAGGCGAAAAGATAACAACAAACTTATACATACTAAAGGGAAAGACTTTGCTAGAA
GCAGAAGCCTCTGTTGCCTCATATAGTTCAGATTCTAT
Found at i:437073 original size:21 final size:21
Alignment explanation
Indices: 437049--437104 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
437039 GAGAATCTTC
437049 TGAAGCAGAACCAGCACATGA
1 TGAAGCAGAACCAGCACATGA
*
437070 TGAAGCAGAACTAGCACATGA
1 TGAAGCAGAACCAGCACATGA
437091 TGAA-CAAGAACCAG
1 TGAAGC-AGAACCAG
437105 AGAGTTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (21 bp):
TGAAGCAGAACCAGCACATGA
Found at i:438927 original size:23 final size:23
Alignment explanation
Indices: 438900--438954 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
438890 ATACTTTAGG
438900 TGGTTGAAAGTTGGCAACC-ATAA
1 TGGTTGAAAGTTGGC-ACCAATAA
* *
438923 TGGTTTATAGTTGGCACCAATAA
1 TGGTTGAAAGTTGGCACCAATAA
438946 TGGTTGAAA
1 TGGTTGAAA
438955 AGTGACATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGTTGAAAGTTGGCACCAATAA
Found at i:441429 original size:25 final size:25
Alignment explanation
Indices: 441400--441449 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
441390 CCCTAGGGGA
441400 TTCATGTTTCCCTCACAACAAATCG
1 TTCATGTTTCCCTCACAACAAATCG
441425 TTCATGTTTCCCTCACAACAAATCG
1 TTCATGTTTCCCTCACAACAAATCG
441450 ATTTTCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (25 bp):
TTCATGTTTCCCTCACAACAAATCG
Found at i:442448 original size:2 final size:2
Alignment explanation
Indices: 442441--442483 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
442431 ATCTCCTTTT
* *
442441 TA TA TA TA TA GA TA TA TA TA TA -A TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
442482 TA
1 TA
442484 AGGTATTCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:442466 original size:21 final size:21
Alignment explanation
Indices: 442442--442484 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
442432 TCTCCTTTTT
*
442442 ATATATATAGATATATATATA
1 ATATATATAGATATACATATA
*
442463 ATATATATATATATACATATA
1 ATATATATAGATATACATATA
442484 A
1 A
442485 GGTATTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATATATAGATATACATATA
Found at i:446131 original size:11 final size:11
Alignment explanation
Indices: 446115--446170 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
446105 ATTTTATATG
446115 AATAATAATAA
1 AATAATAATAA
*
446126 AATAATTATGAA
1 AATAATAAT-AA
446138 AAT-ATAATAA
1 AATAATAATAA
*
446148 ACATATAAAATTAA
1 A-ATA-ATAA-TAA
446162 AATAATAAT
1 AATAATAAT
446171 GAGTAAGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.08
11 15 0.42
12 8 0.22
13 6 0.17
14 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAATAATAA
Found at i:446169 original size:25 final size:23
Alignment explanation
Indices: 446115--446170 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
446105 ATTTTATATG
**
446115 AATAATAATAAAATAATTATGAA
1 AATAATAATAAAATAAAAATGAA
*
446138 AAT-ATAATAAACATATAAAATTAA
1 AATAATAATAAA-ATA-AAAATGAA
446162 AATAATAAT
1 AATAATAAT
446171 GAGTAAGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 6 0.22
24 8 0.30
25 5 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AATAATAATAAAATAAAAATGAA
Found at i:447884 original size:3 final size:3
Alignment explanation
Indices: 447878--447926 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
447868 ATAATATATT
* * **
447878 TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
447926 T
1 T
447927 TTAAGTAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:447889 original size:18 final size:19
Alignment explanation
Indices: 447866--447926 Score: 90
Period size: 18 Copynumber: 3.2 Consensus size: 19
447856 CTTGGGCTTG
447866 TAATAAT-ATATTTAATAA
1 TAATAATAATATTTAATAA
447884 TAATAATAATATTT-ATAA
1 TAATAATAATATTTAATAA
447902 TAATAATAATAATTTTAATAA
1 TAATAATAAT-A-TTTAATAA
447923 TAAT
1 TAAT
447927 TTAAGTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
18 21 0.54
19 7 0.18
20 3 0.08
21 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAATAATATTTAATAA
Found at i:447892 original size:21 final size:21
Alignment explanation
Indices: 447866--447926 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
447856 CTTGGGCTTG
447866 TAATAATATATTTAATAATAA
1 TAATAATATATTTAATAATAA
447887 TAAT-A-ATATTT-ATAATAA
1 TAATAATATATTTAATAATAA
447905 TAATAATA-ATTTTAATAATAA
1 TAATAATATA-TTTAATAATAA
447926 T
1 T
447927 TTAAGTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 11 0.31
19 8 0.22
20 5 0.14
21 12 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATATATTTAATAATAA
Found at i:448180 original size:76 final size:76
Alignment explanation
Indices: 448080--448563 Score: 814
Period size: 76 Copynumber: 6.4 Consensus size: 76
448070 GAGGTCTTAA
* *
448080 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAA-CTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA-AAAAGCTCCCG
448144 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
448156 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
448221 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
448232 AAATATCATGCATTGCAGGACTTACAGATGACCCTAAAGCTTTTGAAAACATCAAAAAG--CCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTTGAAAACATCAAAAAGCTCCCG
448295 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
448307 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTGAAACCATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
448371 AGGCTTTTTGG
66 AGGCTTTTTGG
*
448382 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
448447 AGGCTTTTTGG
66 AGGCTTTTTGG
**
448458 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATATCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
448523 AGGATTTTTGG
66 AGGCTTTTTGG
448534 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
448564 TGGGAAATAG
Statistics
Matches: 385, Mismatches: 18, Indels: 10
0.93 0.04 0.02
Matches are distributed among these distances:
73 16 0.04
75 111 0.29
76 240 0.62
77 18 0.05
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:448477 original size:226 final size:228
Alignment explanation
Indices: 448080--448563 Score: 823
Period size: 226 Copynumber: 2.1 Consensus size: 228
448070 GAGGTCTTAA
* *
448080 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAACTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAACTCCCGA
*
448145 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
* *
448210 AAAGCTCCCGAAGGCTTTTTGGAAATATCATGCATTGCAGGACTTACAGATGACCCTAAAGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAAGC-TT
*
448275 TGAAAACATC-AAAA-AGCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAATAGCCCGAAGGATTTTTGG
* *
448307 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTGAAACCATCA-AAAAGCTCCTG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAA-CTCCCG
*
448370 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
*
448435 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAAGCTT
*
448500 TGAAAACATCAAAAATATCCCGAAGGATTTTTGG
195 TGAAAACATCAAAAATAGCCCGAAGGATTTTTGG
448534 AAACATCATGCACTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
448564 TGGGAAATAG
Statistics
Matches: 243, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
225 16 0.07
226 143 0.59
227 84 0.35
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (228 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAACTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAAGCTTT
GAAAACATCAAAAATAGCCCGAAGGATTTTTGG
Found at i:448589 original size:151 final size:151
Alignment explanation
Indices: 448080--448564 Score: 771
Period size: 151 Copynumber: 3.2 Consensus size: 151
448070 GAGGTCTTAA
* * * *
448080 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAGAAAA-CTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATG-TCCTAAAGCTTTGAAAACATCA-AAAAGCTCCCG
*
448144 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
64 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
448209 AAAAGCTCCCGAAGGCTTTTTGG
129 AAAAGCTCCCGAAGGCTTTTTGG
* * *
448232 AAATATCATGCATTGCAGGACTTACAGATGACCCTAAAGCTTTTGAAAACATCAAAAAG--CCCG
1 AAACATCATGCACTGCAGGACTTACAGATG-TCCTAAAGC-TTTGAAAACATCAAAAAGCTCCCG
*
448295 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTGAAACCATCA
64 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
*
448359 AAAAGCTCCTGAAGGCTTTTTGG
129 AAAAGCTCCCGAAGGCTTTTTGG
*
448382 AAACATCATGCACTGCAGGACTTACAGATGATCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATG-TCCTAAAGCTTTGAAAACATCAAAAAGCTCCCGA
448447 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
** *
448512 AAATATCCCGAAGGATTTTTGG
130 AAAGCTCCCGAAGGCTTTTTGG
448534 AAACATCATGCACTGCAGGACTTACAGATGT
1 AAACATCATGCACTGCAGGACTTACAGATGT
448565 GGGAAATAGT
Statistics
Matches: 311, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
149 18 0.06
150 69 0.22
151 112 0.36
152 99 0.32
153 13 0.04
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (151 bp):
AAACATCATGCACTGCAGGACTTACAGATGTCCTAAAGCTTTGAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
AAGCTCCCGAAGGCTTTTTGG
Found at i:449360 original size:22 final size:22
Alignment explanation
Indices: 449332--449386 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
449322 GATAAAGCTT
*
449332 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
449354 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
449376 TCATCTTTGAA
1 TCATCTTTGAA
449387 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:449860 original size:53 final size:53
Alignment explanation
Indices: 449745--449899 Score: 229
Period size: 54 Copynumber: 2.9 Consensus size: 53
449735 AGAATAGCAG
* *
449745 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTT-CTGTGGCTTCTGCTCAGAT
* *
449799 GTTCGTAAAACATTTGATAACACATTCATCCTTTCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTGTGGCTTCTGCTCAGAT
* * *
449852 GTTCGTAAAGCGTTTGACAACACATTCGTCCTTTTCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCC-TTTCTGTGGCTTCTGC
449900 CAAGATTCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 45 0.49
54 46 0.51
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (53 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTGTGGCTTCTGCTCAGAT
Found at i:452207 original size:114 final size:112
Alignment explanation
Indices: 451990--452313 Score: 484
Period size: 114 Copynumber: 2.9 Consensus size: 112
451980 ATACAGTTCT
* * * *
451990 TCTTTCAATTCCAATGA-TGGTTCTGGGTTC-TACCGAACCA-ATCAGATAACTCAAAG-A-ACT
1 TCTTTCAAATCCAATGATTGGTTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAGAATACT
*
452050 TCCAGAAGATGCTA-TGGGGCTCCTTATTTCTACTATGAACAAATTCA
66 TCCAGAAGATG-TATTGGGGCTCCTTATTTCTACTATGAGCAAATTCA
452097 TCTTTCAAATCCAATGATTGGTTTTGGGATTCATACCAAATCAGATCAGATAACTCAAAGAATAC
1 TCTTTCAAATCCAATGATTGGTTTTGGG-TTCATACCAAATCAGATCAGATAACTCAAAGAATAC
* * *
452162 TTCCAGAAGATGGTATTGGGTCTTCTTATTTCTATTATGAGCAAATTCA
65 TTCCAGAAGAT-GTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCA
452211 TCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAATAC
1 TCTTTCAAATCCAATGATTGGTTTT-GGGTTCATACCAAATCAGATCAGATAACTCAAAGAATAC
452276 TTCCAGAAGA--TATTGGGGCTCCTTATTTCTACTATGAG
65 TTCCAGAAGATGTATTGGGGCTCCTTATTTCTACTATGAG
452314 AACATGACAC
Statistics
Matches: 197, Mismatches: 11, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
107 16 0.08
108 9 0.05
109 3 0.02
110 8 0.04
111 41 0.21
112 1 0.01
113 15 0.08
114 101 0.51
115 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (112 bp):
TCTTTCAAATCCAATGATTGGTTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAGAATACT
TCCAGAAGATGTATTGGGGCTCCTTATTTCTACTATGAGCAAATTCA
Found at i:454431 original size:7 final size:7
Alignment explanation
Indices: 454414--454471 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
454404 CAATTTCTCC
454414 CCTTTTT
1 CCTTTTT
454421 -CTTTTT
1 CCTTTTT
454427 CCTTTTT
1 CCTTTTT
454434 CCTTTTTT
1 CC-TTTTT
* *
454442 TCATTTT
1 CCTTTTT
454449 CCTTTTT
1 CCTTTTT
454456 CATCTTTTTT
1 C--C-TTTTT
454466 CCTTTT
1 CCTTTT
454472 CTCATTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 6 0.14
7 22 0.52
8 7 0.17
9 1 0.02
10 6 0.14
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (7 bp):
CCTTTTT
Found at i:454448 original size:22 final size:23
Alignment explanation
Indices: 454416--454472 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
454406 ATTTCTCCCC
* *
454416 TTTTTCTTTTTCCTTTTTCCT-T
1 TTTTTCATTTTCCTTTTTCATCT
454438 TTTTTCATTTTCCTTTTTCATCT
1 TTTTTCATTTTCCTTTTTCATCT
*
454461 TTTTTCCTTTTC
1 TTTTTCATTTTC
454473 TCATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTCATTTTCCTTTTTCATCT
Found at i:454479 original size:15 final size:16
Alignment explanation
Indices: 454416--454480 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 16
454406 ATTTCTCCCC
454416 TTTTT-CTTTTTC-C-
1 TTTTTCCTTTTTCTCA
*
454429 TTTTTCCTTTTTTTCA
1 TTTTTCCTTTTTCTCA
*
454445 -TTTTCCTTTTTCATCT
1 TTTTTCCTTTTTC-TCA
454461 TTTTTCC-TTTTCTCA
1 TTTTTCCTTTTTCTCA
454476 TTTTT
1 TTTTT
454481 TTATTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 19 0.44
16 7 0.16
17 6 0.14
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCCTTTTTCTCA
Found at i:454480 original size:17 final size:17
Alignment explanation
Indices: 454445--454482 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
454435 CTTTTTTTCA
454445 TTTTCCTTTTTCATCTT
1 TTTTCCTTTTTCATCTT
454462 TTTTCCTTTTCTCAT-TT
1 TTTTCCTTTT-TCATCTT
454479 TTTT
1 TTTT
454483 ATTCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTCCTTTTTCATCTT
Found at i:454494 original size:15 final size:15
Alignment explanation
Indices: 454416--454504 Score: 58
Period size: 15 Copynumber: 6.0 Consensus size: 15
454406 ATTTCTCCCC
*
454416 TTTTTCTTTTTC-CT
1 TTTTTCTTTTTCTTT
* *
454430 TTTTCCTTTTT-TTCA
1 TTTTTCTTTTTCTT-T
* *
454445 TTTTCCTTTTTCATCT
1 TTTTTCTTTTTC-TTT
* **
454461 TTTTTCCTTTTCTCA
1 TTTTTCTTTTTCTTT
*
454476 TTTTT-TTATTCTTT
1 TTTTTCTTTTTCTTT
454490 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
454505 CTTTGCGGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
14 20 0.35
15 26 0.46
16 10 0.18
17 1 0.02
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:455917 original size:32 final size:31
Alignment explanation
Indices: 455861--455925 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
455851 CCTTACAACT
* *
455861 CCTAGTTTTTCGGGTTAAACTAGAACCTTTC
1 CCTAGTTTTACGGGCTAAACTAGAACCTTTC
*
455892 CCTAGATTTTACGGGCTAAGCTAGAACCTTTC
1 CCTAG-TTTTACGGGCTAAACTAGAACCTTTC
455924 CC
1 CC
455926 CTTTACAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (31 bp):
CCTAGTTTTACGGGCTAAACTAGAACCTTTC
Found at i:456346 original size:19 final size:19
Alignment explanation
Indices: 456322--456380 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
456312 AAAACCTGCA
456322 GGGGGTATCTGTACCCCTG
1 GGGGGTATCTGTACCCCTG
*
456341 GGGGGTATCTGT-TCCC--
1 GGGGGTATCTGTACCCCTG
456357 -GGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTA-CCCCTG
456376 GGGGG
1 GGGGG
456381 AAATCTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 11 0.33
17 3 0.09
18 3 0.09
19 12 0.36
20 4 0.12
ACGTcount: A:0.08, C:0.25, G:0.41, T:0.25
Consensus pattern (19 bp):
GGGGGTATCTGTACCCCTG
Found at i:456516 original size:29 final size:31
Alignment explanation
Indices: 456483--456541 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
456473 TAAAACTTAA
*
456483 TAAATTCAATT-AAGTTCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
456512 TAAATTCAATTCAAGTCCAAAAATCATTTT
1 TAAATTCAATTCAAGTCCAAAAATCATTTT
456542 CCTTAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:458678 original size:32 final size:34
Alignment explanation
Indices: 458642--458711 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
458632 AACCTACAAC
* *
458642 TCCCTAG-TTTT-TCCGGGTTAAACTAGAACCTT
1 TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
*
458674 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
458708 TCCC
1 TCCC
458712 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (34 bp):
TCCCTAGCTTTTATACGGGCTAAACTAGAACCTT
Found at i:459023 original size:20 final size:21
Alignment explanation
Indices: 458983--459026 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
458973 GTTGCCCAGA
*
458983 ATAGGGAATCGGTACCCCTTC
1 ATAGGGAATCGATACCCCTTC
459004 ATAGGGAATCGATA-CCCTTC
1 ATAGGGAATCGATACCCCTTC
459024 ATA
1 ATA
459027 ATATCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
ATAGGGAATCGATACCCCTTC
Found at i:459156 original size:20 final size:21
Alignment explanation
Indices: 459131--459207 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
459121 AAAACCTGCA
459131 GGGGGTATCTGTA-CCCCTGG
1 GGGGGTATCTGTACCCCCTGG
459151 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
459167 --GGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
459186 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
459207 G
1 G
459208 CAATCTTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
19 3 0.06
20 13 0.27
21 18 0.38
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:459171 original size:34 final size:35
Alignment explanation
Indices: 459133--459201 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
459123 AACCTGCAGG
* *
459133 GGGTATCTGTA-CCCCTGGGGGGGTATCTGTACCC
1 GGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
459167 GGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
459202 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (35 bp):
GGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:459172 original size:14 final size:14
Alignment explanation
Indices: 459153--459180 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
459143 ACCCCTGGGG
459153 GGGTATCTGTACCC
1 GGGTATCTGTACCC
459167 GGGTATCTGTACCC
1 GGGTATCTGTACCC
459181 CCTGGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (14 bp):
GGGTATCTGTACCC
Found at i:459535 original size:21 final size:21
Alignment explanation
Indices: 459505--459550 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
459495 AAGCTCCCCC
459505 TTTTTCATTAAGAAATTGAAT
1 TTTTTCATTAAGAAATTGAAT
*
459526 TTTTTTATTAAGAAATTGAAT
1 TTTTTCATTAAGAAATTGAAT
459547 TTTT
1 TTTT
459551 CAAACAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (21 bp):
TTTTTCATTAAGAAATTGAAT
Found at i:461552 original size:34 final size:32
Alignment explanation
Indices: 461490--461559 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
461480 ACCTTACAAC
* *
461490 TCCCTAGTTTTTCCGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
*
461522 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACCTT
461556 TCCC
1 TCCC
461560 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
Found at i:461800 original size:20 final size:22
Alignment explanation
Indices: 461775--461814 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
461765 AGTCGTATAT
461775 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
461795 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
461815 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:461866 original size:21 final size:21
Alignment explanation
Indices: 461842--461884 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
461832 CCCAGAATAG
*
461842 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
461863 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
461884 A
1 A
461885 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:462000 original size:21 final size:21
Alignment explanation
Indices: 461975--462053 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
461965 AAAACCTGCA
461975 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
461996 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
462012 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
462032 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
462053 G
1 G
462054 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:462017 original size:15 final size:15
Alignment explanation
Indices: 461997--462026 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
461987 ACCCCCTGGG
461997 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
462012 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
462027 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:462023 original size:36 final size:36
Alignment explanation
Indices: 461976--462047 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
461966 AAACCTGCAG
* *
461976 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
462012 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
462048 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:462175 original size:29 final size:31
Alignment explanation
Indices: 462143--462202 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
462133 AAACTTTGAA
*
462143 TAAATTCAATT-AAGTTCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
462172 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
462203 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:465332 original size:14 final size:15
Alignment explanation
Indices: 465301--465342 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
465291 AGACAAATAA
465301 AATAAAAAAATACCTT
1 AATAAAAAAATA-CTT
465317 AATAAAAAAATA-TT
1 AATAAAAAAATACTT
*
465331 AATAAAATAATA
1 AATAAAAAAATA
465343 AAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
16 12 0.48
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAAAATACTT
Found at i:466005 original size:21 final size:22
Alignment explanation
Indices: 465981--466024 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
465971 AAACATTTTC
465981 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
466002 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
466024 T
1 T
466025 ATTGAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:466915 original size:9 final size:9
Alignment explanation
Indices: 466901--466934 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
466891 CAGCGTTTCA
466901 TTTCTCTTC
1 TTTCTCTTC
466910 TTTCTCTTC
1 TTTCTCTTC
466919 TTTCTCTTC
1 TTTCTCTTC
*
466928 TCTCTCT
1 TTTCTCT
466935 AACTGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTCTCTTC
Found at i:467303 original size:18 final size:19
Alignment explanation
Indices: 467270--467307 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
467260 TTTTTGTTTT
467270 TGTGGTTTGCTGCTTGTTG
1 TGTGGTTTGCTGCTTGTTG
*
467289 TGTGG-TTGTTGCTTGTTG
1 TGTGGTTTGCTGCTTGTTG
467307 T
1 T
467308 TTTTTTTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.00, C:0.08, G:0.37, T:0.55
Consensus pattern (19 bp):
TGTGGTTTGCTGCTTGTTG
Found at i:467863 original size:12 final size:11
Alignment explanation
Indices: 467846--467928 Score: 80
Period size: 12 Copynumber: 7.3 Consensus size: 11
467836 CTTGGGCTTG
467846 TAATAATATATT
1 TAATAATA-ATT
*
467858 TAATAATAATAA
1 TAATAATAAT-T
*
467870 TAATAATAATAA
1 TAATAATAAT-T
467882 TAATAATAATAT
1 TAATAATAAT-T
*
467894 TTATAATAA--
1 TAATAATAATT
467903 TAATAATAATTT
1 TAATAATAA-TT
467915 TAATAATAATT
1 TAATAATAATT
467926 TAA
1 TAA
467929 GTAAAATGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.13
11 7 0.11
12 48 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATT
Found at i:467864 original size:3 final size:3
Alignment explanation
Indices: 467858--467924 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
467848 ATAATATATT
* *
467858 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
467906 TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
467925 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:467869 original size:18 final size:19
Alignment explanation
Indices: 467846--467924 Score: 110
Period size: 18 Copynumber: 4.2 Consensus size: 19
467836 CTTGGGCTTG
467846 TAATAAT-ATATTTAATAA
1 TAATAATAATATTTAATAA
*
467864 TAATAATAATA-ATAATAA
1 TAATAATAATATTTAATAA
467882 TAATAATAATATTT-ATAA
1 TAATAATAATATTTAATAA
467900 TAATAATAATAATTTTAATAA
1 TAATAATAAT-A-TTTAATAA
467921 TAAT
1 TAAT
467925 TTAAGTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
18 38 0.70
19 5 0.09
20 3 0.06
21 8 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAATAATATTTAATAA
Found at i:468557 original size:23 final size:23
Alignment explanation
Indices: 468514--468558 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
468504 ACATATTAAG
**
468514 TAACGCTTATATAATGTAATAGA
1 TAACGCTTATATAATAAAATAGA
468537 TAACGCTTATATAATAAAATAG
1 TAACGCTTATATAATAAAATAG
468559 GTATTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
TAACGCTTATATAATAAAATAGA
Found at i:469094 original size:182 final size:182
Alignment explanation
Indices: 468770--469303 Score: 942
Period size: 182 Copynumber: 2.9 Consensus size: 182
468760 TGCGTTCACC
* * * * * *
468770 TTTTATCATTTATAGACCGGTTTTATCATATTTTTACATATTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCTAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* *
468835 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTATTCTCTTTTAAATTCCAAAAGTATCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
468900 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
*
468952 TTTTGTCATTTCTAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCTAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* *
469017 TTTATAAAGTATCGATACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
469082 TACTTATAATAAATTATTGACACTTTCAACATATCCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
*
469134 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCTAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
469199 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
469264 TACTTATAATAAATTATCGACACTTTCAACATATCAGGTA
131 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTA
469304 ACATTATGAT
Statistics
Matches: 334, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
182 334 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (182 bp):
TTTTGTCATTTCTAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGACGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
Found at i:470439 original size:257 final size:257
Alignment explanation
Indices: 469977--470619 Score: 1196
Period size: 257 Copynumber: 2.5 Consensus size: 257
469967 GTGTTTCATG
*
469977 TTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
1 TTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
470042 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTA
66 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTA
*
470107 ATATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTA
131 ATATATATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTA
* *
470172 GACGCATATAATTACTAAATTGATATCTTAAAACTCACTCAAAACATAACCTTAAATTAATA
196 AACGCATATAATAACTAAATTGATATCTTAAAACTCACTCAAAACATAACCTTAAATTAATA
*
470234 TTTTTCACCTACAATATTAATTTAATAATTTCATTTACAAAAAAAATTATTTGATTGTTTTGATA
1 TTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
470299 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTA
66 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTA
*
470364 ATATATATGTTTATTATTTTTAATTTAATAGTAATATATACCGTAACATAAAAAATAAATCATTA
131 ATATATATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTA
* * *
470429 AACTCATATAATAACTAAATTGATATCTTAAAACTCACTCAAAACATAATCTTAAATTAATG
196 AACGCATATAATAACTAAATTGATATCTTAAAACTCACTCAAAACATAACCTTAAATTAATA
*
470491 TTTTTAACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
1 TTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
470556 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
66 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGT
470620 TTTCCACAGT
Statistics
Matches: 375, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
257 375 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (257 bp):
TTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTA
ATATATATGTTTATTATTTTTAATTTAATAATAATATATACCGTAACATAAAAAATAAATCATTA
AACGCATATAATAACTAAATTGATATCTTAAAACTCACTCAAAACATAACCTTAAATTAATA
Found at i:472716 original size:19 final size:19
Alignment explanation
Indices: 472694--472736 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
472684 GAAAAAATTT
472694 AAAAATGTAAA-AAAAAAA
1 AAAAATGTAAAGAAAAAAA
* *
472712 GAAAAATTTAAAGAGAAAAA
1 -AAAAATGTAAAGAAAAAAA
472732 AAAAA
1 AAAAA
472737 GCAAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (19 bp):
AAAAATGTAAAGAAAAAAA
Found at i:472731 original size:26 final size:26
Alignment explanation
Indices: 472686--472749 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 26
472676 AAATAAGAGA
472686 AAAAATTTAAAAATGTAAAAAAAAAAG
1 AAAAATTTAAAAATG-AAAAAAAAAAG
*
472713 AAAAATTTAAAGA-GAAAAAAAAAAG
1 AAAAATTTAAAAATGAAAAAAAAAAG
*
472738 CAAAATGTTAAA
1 AAAAAT-TTAAA
472750 TGGGAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 16 0.47
26 6 0.18
27 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (26 bp):
AAAAATTTAAAAATGAAAAAAAAAAG
Found at i:476287 original size:12 final size:11
Alignment explanation
Indices: 476250--476278 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
476240 TTAAAATGTA
476250 AAAAAAAAAAG
1 AAAAAAAAAAG
476261 AAAAAAAAAAG
1 AAAAAAAAAAG
476272 AAAAAAA
1 AAAAAAA
476279 CAAGCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:477617 original size:34 final size:35
Alignment explanation
Indices: 477574--477743 Score: 125
Period size: 39 Copynumber: 4.7 Consensus size: 35
477564 TAAATTTTTG
* *
477574 AAAATGTTTTTGAAACTATAGTA-TATATATTTC-A
1 AAAAAGTTTTTAAAACTATA-TATTATATATTTCGA
*
477608 AAAACG-TTTTAAAACTATATATTTATATATTTCGA
1 AAAAAGTTTTTAAAACTATATA-TTATATATTTCGA
* *
477643 AAAAAGTTTTCAAAATTATATATTATATATATTTTTTC-A
1 AAAAAGTTTTTAAAACTATATA-T-TATATA---TTTCGA
* * *
477682 AAAATGTCTTCAAAACTATATACTATATATATTTTC-A
1 AAAAAGTTTTTAAAACTATATA-T-TATATA-TTTCGA
*
477719 AAAAATGTTTTCAAAACTATATATT
1 AAAAA-GTTTTTAAAACTATATATT
477744 CAAAAATATT
Statistics
Matches: 116, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.02
33 12 0.10
34 15 0.13
35 6 0.05
36 16 0.14
37 17 0.15
38 16 0.14
39 28 0.24
40 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAAAGTTTTTAAAACTATATATTATATATTTCGA
Found at i:477665 original size:38 final size:38
Alignment explanation
Indices: 477595--477741 Score: 178
Period size: 39 Copynumber: 3.9 Consensus size: 38
477585 GAAACTATAG
*
477595 TATATATATTTCAAAAACGTTTT-AAAACTATATA-T-
1 TATATATATTTCAAAAAAGTTTTCAAAACTATATACTA
* *
477630 T-TATATATTTCGAAAAAAGTTTTCAAAATTATATATTA
1 TATATATATTTC-AAAAAAGTTTTCAAAACTATATACTA
* * *
477668 TATATATTTTTTCAAAAATGTCTTCAAAACTATATACTA
1 TATATA-TATTTCAAAAAAGTTTTCAAAACTATATACTA
477707 TATATAT-TTTCAAAAAATGTTTTCAAAACTATATA
1 TATATATATTTCAAAAAA-GTTTTCAAAACTATATA
477742 TTCAAAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
34 10 0.10
35 11 0.11
36 10 0.10
37 10 0.10
38 18 0.19
39 32 0.33
40 5 0.05
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (38 bp):
TATATATATTTCAAAAAAGTTTTCAAAACTATATACTA
Found at i:477685 original size:39 final size:37
Alignment explanation
Indices: 477590--477887 Score: 290
Period size: 37 Copynumber: 8.3 Consensus size: 37
477580 TTTTTGAAAC
* *
477590 TATAGTATATATA-TTTCAAAAACGTTTT-AAAACTA
1 TATATTATATATATTTTCAAAAAAGTTTTCAAAACTA
*
477625 TATATT-TATATA-TTTCGAAAAAAGTTTTCAAAATTA
1 TATATTATATATATTTTC-AAAAAAGTTTTCAAAACTA
* *
477661 TATATTATATATATTTTTTCAAAAATGTCTTCAAAACTA
1 TATATTATATATA--TTTTCAAAAAAGTTTTCAAAACTA
*
477700 TATACTATATATATTTTCAAAAAATGTTTTCAAAAC--
1 TATATTATATATATTTTCAAAAAA-GTTTTCAAAACTA
477736 -------TATATA--TTCAAAAATA-TTTTCAAAACTA
1 TATATTATATATATTTTCAAAAA-AGTTTTCAAAACTA
* *
477764 TATACTATATATATTTTCAAAAATGTTTTCAAAACTA
1 TATATTATATATATTTTCAAAAAAGTTTTCAAAACTA
477801 TATATTATATATATTTTC-AAAAA-TTTCTCAAAACTA
1 TATATTATATATATTTTCAAAAAAGTTT-TCAAAACTA
* * *
477837 TATATTATATATATTTTTGAAAAAAATGCTTTCAACACTA
1 TATATTATATATA-TTTT-CAAAAAA-GTTTTCAAAACTA
477877 TATATTATATA
1 TATATTATATA
477888 CACTATACGT
Statistics
Matches: 222, Mismatches: 15, Indels: 47
0.78 0.05 0.17
Matches are distributed among these distances:
26 10 0.05
27 8 0.04
28 1 0.00
29 6 0.03
34 10 0.05
35 24 0.11
36 38 0.17
37 57 0.26
38 10 0.05
39 33 0.15
40 23 0.10
41 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAAAAGTTTTCAAAACTA
Found at i:477717 original size:64 final size:64
Alignment explanation
Indices: 477649--477853 Score: 182
Period size: 64 Copynumber: 3.1 Consensus size: 64
477639 TCGAAAAAAG
* *
477649 TTTTCAAAATTATATATTATATATATTTTTTCAAAAATGTCTTCAAAACTATATACTATATATA
1 TTTTCAAAATTATATATTATATATATATTTTCAAAAATATCTTCAAAACTATATACTATATATA
* * * * * *
477713 TTTTCAAAA-AATGTTTTCA-AAACTATATATTCAAAAATATTTTCAAAACTATATACTATATAT
1 TTTTCAAAATTATATATT-ATATA-TATATTTTCAAAAATATCTTCAAAACTATATACTATATAT
477776 A
64 A
* *
477777 TTTTCAAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATTTC-TCAAAACTATATA
1 TTTTC-AAAA----TT--ATA-TAT-TA-TATATATATTTTCAAAAATATCTTCAAAACTATATA
*
477841 TTATATATA
56 CTATATATA
477850 TTTT
1 TTTT
477854 TGAAAAAAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
63 7 0.06
64 52 0.47
65 4 0.04
72 1 0.01
73 28 0.25
74 16 0.15
75 2 0.02
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.45
Consensus pattern (64 bp):
TTTTCAAAATTATATATTATATATATATTTTCAAAAATATCTTCAAAACTATATACTATATATA
Found at i:477747 original size:14 final size:14
Alignment explanation
Indices: 477728--477767 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
477718 AAAAAATGTT
477728 TTCAAAACTATATA
1 TTCAAAACTATATA
*
477742 TTCAAAA--ATATT
1 TTCAAAACTATATA
477754 TTCAAAACTATATA
1 TTCAAAACTATATA
477768 CTATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
TTCAAAACTATATA
Found at i:477783 original size:25 final size:26
Alignment explanation
Indices: 477719--477785 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
477709 TATATTTTCA
* *
477719 AAAAATGTTTTCAAAACTATATATTC
1 AAAAATATTTTCAAAACTATATACTC
477745 AAAAATATTTTCAAAACTATATACT-
1 AAAAATATTTTCAAAACTATATACTC
* *
477770 ATATATATTTTCAAAA
1 AAAAATATTTTCAAAA
477786 ATGTTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 14 0.38
26 23 0.62
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (26 bp):
AAAAATATTTTCAAAACTATATACTC
Found at i:477798 original size:101 final size:101
Alignment explanation
Indices: 477631--477842 Score: 313
Period size: 101 Copynumber: 2.1 Consensus size: 101
477621 ACTATATATT
* *
477631 TATATATTTCGAAAAAAGTTTTCAAAATTATATATTATATATATTTTTTCAAAAATGTCTTCAAA
1 TATATA-TTCGAAAAAAGTTTTCAAAACTATATACTATATATA-TTTTTCAAAAATGTCTTCAAA
*
477696 ACTATATACTATATATATTTTCAAAAAATGTTTTCAAAAC
64 ACTATATACTATATATATTTTC-AAAAAT-TTCTCAAAAC
*
477736 TATATATTC-AAAAATA-TTTTCAAAACTATATACTATATATA-TTTTCAAAAATGTTTTCAAAA
1 TATATATTCGAAAAA-AGTTTTCAAAACTATATACTATATATATTTTTCAAAAATGTCTTCAAAA
*
477798 CTATATATTATATATATTTTCAAAAATTTCTCAAAAC
65 CTATATACTATATATATTTTCAAAAATTTCTCAAAAC
477835 TATATATT
1 TATATATT
477843 ATATATATTT
Statistics
Matches: 101, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
99 17 0.17
100 6 0.06
101 40 0.40
103 28 0.28
104 4 0.04
105 6 0.06
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.43
Consensus pattern (101 bp):
TATATATTCGAAAAAAGTTTTCAAAACTATATACTATATATATTTTTCAAAAATGTCTTCAAAAC
TATATACTATATATATTTTCAAAAATTTCTCAAAAC
Found at i:483136 original size:14 final size:14
Alignment explanation
Indices: 483102--483136 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
483092 AACTGTAATT
*
483102 TATTTTACAAAAAA
1 TATTTTCCAAAAAA
483116 TATTTTCCAAAAAA
1 TATTTTCCAAAAAA
483130 TATTTTC
1 TATTTTC
483137 AGTGAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTTTCCAAAAAA
Found at i:486838 original size:30 final size:29
Alignment explanation
Indices: 486779--486860 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
486769 TTTTTTATTT
* * *
486779 TTTCTAAAAAATTAATTAAGTCCTTAAAC
1 TTTCTAAAAAATCAATTAAGCCCTCAAAC
486808 TTTCTAAAATAATCAATT-AGACCCTCAAAC
1 TTTCTAAAA-AATCAATTAAG-CCCTCAAAC
* *
486838 TTAGC-CAAAAATCAATTAAGCCC
1 TT-TCTAAAAAATCAATTAAGCCC
486861 ATCTACCACA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
29 22 0.50
30 21 0.48
31 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (29 bp):
TTTCTAAAAAATCAATTAAGCCCTCAAAC
Found at i:491578 original size:39 final size:39
Alignment explanation
Indices: 491534--491825 Score: 340
Period size: 39 Copynumber: 7.5 Consensus size: 39
491524 AAATGAAACA
* *
491534 ATTTATTTTCTTTTACAAAATAAGAAATTAAATCCAAC-
1 ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
* *
491572 AGTTTATTTCCTTTTACAAAATAGAAAAATAAATCCAACG
1 A-TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
* ** * ** *
491612 ATTTATTTTCTTTTACCAACCAGGAAAAT-TATTGAATG
1 ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
491650 ATTTA-TTTCATTTTACAAAATAGGAAAATAAATCCAACG
1 ATTTATTTTC-TTTTACAAAATAGGAAAATAAATCCAACG
* *
491689 ATTTATTTCCTTTTACGAAATAGGAAAATAAATCCAACG
1 ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
* * * *
491728 ATTT-TTTTCCTTCTACAAAACAGGAAAATAAATCTAATG
1 ATTTATTTT-CTTTTACAAAATAGGAAAATAAATCCAACG
* *
491767 ATTTATTTTTCTTTTACAAACTAGGAAAATAAATCCACCG
1 ATTTA-TTTTCTTTTACAAAATAGGAAAATAAATCCAACG
*
491807 ATTTATTTCCTTTTACAAA
1 ATTTATTTTCTTTTACAAA
491826 CCAAAATCAT
Statistics
Matches: 211, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
37 4 0.02
38 30 0.14
39 140 0.66
40 33 0.16
41 4 0.02
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (39 bp):
ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACG
Found at i:491752 original size:116 final size:117
Alignment explanation
Indices: 491534--491825 Score: 414
Period size: 116 Copynumber: 2.5 Consensus size: 117
491524 AAATGAAACA
* *
491534 ATTTATTTTCTTTTACAAAATAAGAAATTAAATCCAAC-AGTTTATTTCCTTTTACAAAATAGAA
1 ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACGA-TTTATTTCCTTTTACAAAATAGAA
* * * *
491598 AAATAAATCCAACGATTTATTTTCTTTTACCAACCAGGAAAAT-TAT-TGAATG
65 AAATAAATCCAACGATTTATTTTCTTCTACAAAACAGGAAAATAAATCT-AATG
* *
491650 ATTTA-TTTCATTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACGAAATAGGA
1 ATTTATTTTC-TTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGAA
491714 AAATAAATCCAACGATTT-TTTTCCTTCTACAAAACAGGAAAATAAATCTAATG
65 AAATAAATCCAACGATTTATTTT-CTTCTACAAAACAGGAAAATAAATCTAATG
* *
491767 ATTTATTTTTCTTTTACAAACTAGGAAAATAAATCCACCGATTTATTTCCTTTTACAAA
1 ATTTA-TTTTCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAA
491826 CCAAAATCAT
Statistics
Matches: 158, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
115 8 0.05
116 88 0.56
117 12 0.08
118 46 0.29
119 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (117 bp):
ATTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGAAA
AATAAATCCAACGATTTATTTTCTTCTACAAAACAGGAAAATAAATCTAATG
Found at i:491912 original size:58 final size:57
Alignment explanation
Indices: 491791--492051 Score: 197
Period size: 58 Copynumber: 4.5 Consensus size: 57
491781 TACAAACTAG
* * ** *
491791 GAAAATAAATCCACCGATTTATTTCCTTTTACAAACCAAAATCATCTAAGATTCT-TA
1 GAAAATAAATTCAACGATTTATTTCCTTTTA-AAAATAAAATCATCTAAGATTCTCAA
* * * * *
491848 GAAAAATAAATTCAACGATTAATTTCCGTTTAGAAAATAGAATCATTTAAGATTATCAA
1 G-AAAATAAATTCAACGATTTATTTCCTTTTA-AAAATAAAATCATCTAAGATTCTCAA
* * * *
491907 GAAAATGAATTAAAC-AGTTTATTTCCTTTTAAAATATAAAATCATCCACGATTCTCAA
1 GAAAATAAATTCAACGA-TTTATTTCCTTTTAAAA-ATAAAATCATCTAAGATTCTCAA
* * * ** ** *
491965 GAAAATAATTTCAATGATTTATTTTCCTTATAAAGTTGGAATCGT-TCAAGATTCTCAA
1 GAAAATAAATTCAACGATTTA-TTTCCTTTTAAAAATAAAATCATCT-AAGATTCTCAA
* *
492023 -AGAAATAGATTCAATGATTTATTTTCCTT
1 GA-AAATAAATTCAACGATTTA-TTTCCTT
492052 ACAAAGTTTG
Statistics
Matches: 162, Mismatches: 34, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
57 6 0.04
58 142 0.88
59 14 0.09
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (57 bp):
GAAAATAAATTCAACGATTTATTTCCTTTTAAAAATAAAATCATCTAAGATTCTCAA
Found at i:492052 original size:58 final size:58
Alignment explanation
Indices: 491956--492065 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
491946 AATCATCCAC
*
491956 GATTCTCAAGAAAATAATTTCAATGATTTATTTTCCTTATAAAGTTGGAATCGTTCAA
1 GATTCTCAAGAAAATAATTTCAATGATTTATTTTCCTTACAAAGTTGGAATCGTTCAA
*
492014 GATTCTCAA-AGAAATAGA-TTCAATGATTTATTTTCCTTACAAAGTTTGAATC
1 GATTCTCAAGA-AAATA-ATTTCAATGATTTATTTTCCTTACAAAGTTGGAATC
492066 AACTCAAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
57 1 0.02
58 46 0.96
59 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (58 bp):
GATTCTCAAGAAAATAATTTCAATGATTTATTTTCCTTACAAAGTTGGAATCGTTCAA
Found at i:492215 original size:45 final size:45
Alignment explanation
Indices: 492118--492215 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
492108 CAACTAAGTC
* * * *
492118 ATCAAAAGGAACTAATCATTTGATTTTAATTTTGGCAACTCAATT
1 ATCAAAAAGAACTAATCATTTGATTTTAATTTCGGAAACTCAATA
* *
492163 ATCAAAAAGAACTAATCCTTTGATTTTACTTTCGGAAACAT-AATA
1 ATCAAAAAGAACTAATCATTTGATTTTAATTTCGGAAAC-TCAATA
*
492208 ATGAAAAA
1 ATCAAAAA
492216 TATTTAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (45 bp):
ATCAAAAAGAACTAATCATTTGATTTTAATTTCGGAAACTCAATA
Found at i:492330 original size:45 final size:45
Alignment explanation
Indices: 492238--492371 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
492228 TGATTAAACT
* **
492238 GAACTAATCCTTTGGTTTTACTTTTAACAA-TCAATAATCAAAAG
1 GAACTAATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
**
492282 GAACTAATATTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
1 GAACTAATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
* * *
492327 GAACAAATCCTTTGATTTTACTTTTGGGAACCCAATAATCAAAAG
1 GAACTAATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
492372 CTTTGGATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 25 0.32
45 54 0.68
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (45 bp):
GAACTAATCCTTTGATTTTACTTTTGGCAACTCAATAATCAAAAG
Found at i:497083 original size:20 final size:20
Alignment explanation
Indices: 497055--497094 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
497045 CACCATAGTA
*
497055 TAGAAGTATTGATACCATGG
1 TAGAAGTATCGATACCATGG
* *
497075 TAGAGGTATCGATACTATGG
1 TAGAAGTATCGATACCATGG
497095 AGCCTGGAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (20 bp):
TAGAAGTATCGATACCATGG
Found at i:497483 original size:46 final size:47
Alignment explanation
Indices: 497430--497631 Score: 201
Period size: 55 Copynumber: 4.0 Consensus size: 47
497420 TGTGCAAAAT
497430 CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTG-
1 CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGA
*
497476 CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
1 CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCAC--T-T-TG----A
497531 CTAAGAAATTCATAATGAGTTTATGAATTT-CGTATGGGCACTTTATGTGCAAAA
1 CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCAC--T-T-TG----A
* * *
497585 GCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGAGTACTTTG
1 -CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTG
497632 TGTGCAAAAC
Statistics
Matches: 140, Mismatches: 5, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
46 41 0.29
48 1 0.01
49 1 0.01
50 2 0.01
52 2 0.01
53 1 0.01
54 24 0.17
55 60 0.43
56 8 0.06
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (47 bp):
CTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGA
Found at i:497693 original size:55 final size:55
Alignment explanation
Indices: 497476--497676 Score: 341
Period size: 55 Copynumber: 3.7 Consensus size: 55
497466 GGGCACTTTG
497476 CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
1 CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
497531 CTAAGAAATTCATAATGAGTTTATGAATTTC-GTATGGGCACTTTATGTGCAAAA
1 CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
* * *
497585 GCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGAGTACTTTGTGTGCAAAA
1 -CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
* *
497641 CTAAGAAATTCATAATAAGTTTATGAATTTATGTAT
1 CTAAGAAATTCATAATGAGTTTATGAATTTCTGTAT
497677 TGGTAGTGGG
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
54 23 0.17
55 96 0.69
56 20 0.14
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (55 bp):
CTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAA
Found at i:497747 original size:165 final size:156
Alignment explanation
Indices: 497416--497748 Score: 346
Period size: 165 Copynumber: 2.1 Consensus size: 156
497406 AATGGCACTA
* *
497416 TATGTGTGCAAAATCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTTTGCTAAG
1 TATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCACTTTGCTAAG
* * ** *
497481 AAATTCATAATGAGTTTATGAATTTCTGTATGGGCACTTTATGTGCAAAACTAAGAAATTCATAA
66 AAATTCATAATAAGTTTATGAATTTATGTATGGGCACTGGATGTGCAAAACCAAGAAATTCATAA
* *
497546 TGAGTTTATGAATTTCGTATGGGCAC
131 TAAGTTTATGAATTACGTATGGGCAC
* * * *
497572 TTTATGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCTGTATGAGTACTTTGTGTGC
1 TATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCAC--T-T-TG-
* * * * * *
497637 AAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGTAGTGGGTGTGC-AACCCACGT
61 ----CTAAGAAATTCATAATAAGTTTATGAATTTATGTATGGGCACTGGATGTGCAAAACCAAG-
* * * *
497701 AAATT-ATAGTAAGTTTGTGACTTACAGTATTGGCAC
121 AAATTCATAATAAGTTTATGAATTAC-GTATGGGCAC
497737 TATGTGTGCAAA
1 TATGTGTGCAAA
497749 CTATAGTGTT
Statistics
Matches: 141, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
156 50 0.35
158 1 0.01
159 1 0.01
160 2 0.01
164 20 0.14
165 67 0.48
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (156 bp):
TATGTGTGCAAAAGCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGAGCACTTTGCTAAG
AAATTCATAATAAGTTTATGAATTTATGTATGGGCACTGGATGTGCAAAACCAAGAAATTCATAA
TAAGTTTATGAATTACGTATGGGCAC
Found at i:498226 original size:13 final size:13
Alignment explanation
Indices: 498208--498235 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
498198 ATATACAGAA
498208 GGATAGGTATGCT
1 GGATAGGTATGCT
498221 GGATAGGTATGCT
1 GGATAGGTATGCT
498234 GG
1 GG
498236 GACTACTAAG
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:0.21, C:0.07, G:0.43, T:0.29
Consensus pattern (13 bp):
GGATAGGTATGCT
Found at i:499151 original size:64 final size:63
Alignment explanation
Indices: 499062--499216 Score: 197
Period size: 64 Copynumber: 2.4 Consensus size: 63
499052 TAGTTGACCT
* * * * *
499062 AGTGCATCGGTACACTAATTACATTCGATGTTTCAA-AAGAGA-CAGGAGTGTATCGATGCATGG
1 AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-A-ATCAGGAGTGCATCGATGCAT-A
499125 C
63 C
* **
499126 TGTGCATCGGTACTTAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATAC
1 AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATAC
499189 AGTGCATCGGTACACAAAATGCATTCGA
1 AGTGCATCGGTACACAAAATGCATTCGA
499217 ATTAGGGTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 27 0.35
64 49 0.63
65 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (63 bp):
AGTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAATCAGGAGTGCATCGATGCATAC
Found at i:499924 original size:2 final size:2
Alignment explanation
Indices: 499917--499965 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
499907 AAAACCAAAC
499917 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
499959 AT AT AT A
1 AT AT AT A
499966 AACATTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:501408 original size:12 final size:13
Alignment explanation
Indices: 501391--501423 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
501381 ATGGGCAAAG
*
501391 TTTGAAAACTAT-
1 TTTGAAAACAATA
501403 TTTGAAAACAATA
1 TTTGAAAACAATA
501416 TTTGAAAA
1 TTTGAAAA
501424 ATCATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATA
Found at i:505992 original size:116 final size:117
Alignment explanation
Indices: 505752--505971 Score: 293
Period size: 117 Copynumber: 1.9 Consensus size: 117
505742 CTTTCAAATA
*
505752 AAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAATATTT
1 AAAA-TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * * *
505817 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAGAAGAAGTTTGTTTAATTCG
65 CATTTTGATTTTCAAAATCCATTTTAGCTTCTAAAAAAAGTTTGTTTAATGCG
* * * *
505870 AAAATTTCTTTTTCAA-AGTTTTCATATTTTATTTTTGAAAGCTCTAACTCCTT-TTCAACATTT
1 AAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* * *
505933 CATTTTGTTTTTCCAAATCTATTTTAGCTT-TAAAAAAAG
65 CATTTTGATTTTCAAAATCCATTTTAGCTTCTAAAAAAAG
505972 ATCATTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
115 7 0.08
116 36 0.40
117 43 0.48
118 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.49
Consensus pattern (117 bp):
AAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTC
ATTTTGATTTTCAAAATCCATTTTAGCTTCTAAAAAAAGTTTGTTTAATGCG
Found at i:507280 original size:14 final size:14
Alignment explanation
Indices: 507257--507298 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
507247 AGTTGACCTA
507257 GTGCATCGGTACAC
1 GTGCATCGGTACAC
*
507271 GTGTATCGGTACAC
1 GTGCATCGGTACAC
507285 GTGCATCGGTACAC
1 GTGCATCGGTACAC
507299 TTGGGGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (14 bp):
GTGCATCGGTACAC
Found at i:507415 original size:64 final size:64
Alignment explanation
Indices: 507324--507458 Score: 175
Period size: 64 Copynumber: 2.1 Consensus size: 64
507314 ACACTAATTA
* * * *
507324 CATTTGATGTTTCAAAAGAGCTAGGAGTGTATCGATAG-ATGGCTGTGCATCGATATATAAAATG
1 CATTCGATGTTTCAAAAAAGCTAGGAGTGCATCGAT-GCATGGCTGTGCATCGATACATAAAATG
* * *
507388 CATTCGATGTTTCAATAAAATC-AGGAGTGCATCGATGCATGGTTGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAA-AAAAGCTAGGAGTGCATCGATGCATGGCTGTGCATCGATACATAAAATG
507452 CATTCGA
1 CATTCGA
507459 ATTAGGGTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.02
64 57 0.92
65 4 0.06
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (64 bp):
CATTCGATGTTTCAAAAAAGCTAGGAGTGCATCGATGCATGGCTGTGCATCGATACATAAAATG
Found at i:511440 original size:20 final size:20
Alignment explanation
Indices: 511417--511480 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
511407 CAAAGTATTG
511417 AAACTTTAGGGAAAGTTTCA
1 AAACTTTAGGGAAAGTTTCA
* * *
511437 AAACTCTT--GAAAAGTATCG
1 AAACT-TTAGGGAAAGTTTCA
511456 AAACTTTAGGGAAAGTTTCA
1 AAACTTTAGGGAAAGTTTCA
511476 AAACT
1 AAACT
511481 CTTGAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 18 0.51
21 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (20 bp):
AAACTTTAGGGAAAGTTTCA
Found at i:511451 original size:39 final size:39
Alignment explanation
Indices: 511408--511501 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
511398 CGTTGAACCC
*
511408 AAAGTATTGAAACTTTAGGGAAAGTTTCAAAACTCTTGA
1 AAAGTATCGAAACTTTAGGGAAAGTTTCAAAACTCTTGA
511447 AAAGTATCGAAACTTTAGGGAAAGTTTCAAAACTCTTGA
1 AAAGTATCGAAACTTTAGGGAAAGTTTCAAAACTCTTGA
*
511486 AAAATATCGAAACTTT
1 AAAGTATCGAAACTTT
511502 TTGGGAAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (39 bp):
AAAGTATCGAAACTTTAGGGAAAGTTTCAAAACTCTTGA
Found at i:512668 original size:21 final size:22
Alignment explanation
Indices: 512644--512689 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
512634 CTTAACTTTC
* *
512644 AAATCAA-AGTTTTCTTTTTTA
1 AAATCAATAATTTTCATTTTTA
*
512665 AAATCAATAATTTTGATTTTTA
1 AAATCAATAATTTTCATTTTTA
512687 AAA
1 AAA
512690 GATCTAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATCAATAATTTTCATTTTTA
Found at i:514555 original size:19 final size:19
Alignment explanation
Indices: 514515--514556 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
514505 TTCTGCACAC
* *
514515 AAAGTTTTGAAACTCTGGG
1 AAAGTTTCGAAACTCTGCG
*
514534 AAAGTTTCGAAACTCTTCG
1 AAAGTTTCGAAACTCTGCG
514553 AAAG
1 AAAG
514557 AGCCGTTGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (19 bp):
AAAGTTTCGAAACTCTGCG
Found at i:514631 original size:20 final size:20
Alignment explanation
Indices: 514608--514655 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
514598 ACTTTAGGGA
514608 AAGTTTCGAAACTCTTGTAG
1 AAGTTTCGAAACTCTTGTAG
*
514628 AAGTTTTGAAACTCTTGTAG
1 AAGTTTCGAAACTCTTGTAG
514648 AAGTTTCG
1 AAGTTTCG
514656 GAATTTCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
AAGTTTCGAAACTCTTGTAG
Done.