Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003345.1 Hibiscus syriacus cultivar Beakdansim tig00007043_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: 605145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:460954 original size:17 final size:15
Alignment explanation
Indices: 460915--460970 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
460905 ATCTGGAATA
*
460915 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
460930 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
460945 TTAAAAAACCGGTTTTT
1 TT--AAAACCGGTTTTT
*
460962 TTTAAACCG
1 TTAAAACCG
460971 AAACCGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 21 0.60
17 14 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:460967 original size:18 final size:17
Alignment explanation
Indices: 460917--460963 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
460907 CTGGAATATT
*
460917 AAAATCGGTTTTTTT--
1 AAAACCGGTTTTTTTAA
*
460932 ATAACCGGTTTTTTTAA
1 AAAACCGGTTTTTTTAA
460949 AAAACCGGTTTTTTT
1 AAAACCGGTTTTTTT
460964 TAAACCGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.49
Consensus pattern (17 bp):
AAAACCGGTTTTTTTAA
Found at i:460968 original size:15 final size:15
Alignment explanation
Indices: 460925--460970 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
460915 TTAAAATCGG
460925 TTTTTTTATAACCGGT
1 TTTTTTTA-AACCGGT
*
460941 TTTTTTAAAAAACCGGT
1 TTTTTT--TAAACCGGT
460958 TTTTTTTAAACCG
1 TTTTTTTAAACCG
460971 AAACCGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 6 0.23
17 13 0.50
18 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (15 bp):
TTTTTTTAAACCGGT
Found at i:460979 original size:21 final size:18
Alignment explanation
Indices: 460934--460967 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
460924 GTTTTTTTAT
460934 AACCGG-TTTTTTTAAAA
1 AACCGGTTTTTTTTAAAA
460951 AACCGGTTTTTTTTAAA
1 AACCGGTTTTTTTTAAA
460968 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (18 bp):
AACCGGTTTTTTTTAAAA
Found at i:461087 original size:15 final size:17
Alignment explanation
Indices: 461061--461092 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
461051 TTCTATGAGA
461061 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
461077 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
461093 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:461190 original size:55 final size:55
Alignment explanation
Indices: 461124--461274 Score: 196
Period size: 55 Copynumber: 2.7 Consensus size: 55
461114 TTCATCTCTA
461124 GTGGTGTCGGACACACGTATCAAACACGAGTAACAAAGCATTCCTCAAACTCG-G
1 GTGGTGTCGGACACACGTATCAAACACGAGTAACAAAGCATTCCTCAAACTCGAG
* * * * *
461178 CGTGGTGTCGGACACACATATCAAACATGAGTAACAAAGCAGTCCTCGAACTTGAG
1 -GTGGTGTCGGACACACGTATCAAACACGAGTAACAAAGCATTCCTCAAACTCGAG
* ** * *
461234 GTGGTGTCGAACATTCGTATCAAACACAAGTAGCAAAGCAT
1 GTGGTGTCGGACACACGTATCAAACACGAGTAACAAAGCAT
461275 CCGATAAATA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 81 0.99
56 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (55 bp):
GTGGTGTCGGACACACGTATCAAACACGAGTAACAAAGCATTCCTCAAACTCGAG
Found at i:466455 original size:23 final size:23
Alignment explanation
Indices: 466429--466479 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
466419 TGTGATATGG
*
466429 AATCTGCTTTTCTTAAT-AAAAAT
1 AATCTGCTTTTATT-ATCAAAAAT
* *
466452 AATCTTCTTTTATTATCAATAAT
1 AATCTGCTTTTATTATCAAAAAT
466475 AATCT
1 AATCT
466480 AATACGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (23 bp):
AATCTGCTTTTATTATCAAAAAT
Found at i:466878 original size:19 final size:20
Alignment explanation
Indices: 466853--466943 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
466843 TTTATTTTGG
466853 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
466873 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
466893 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
* *
466917 A-TTTTAACTACCGCAACAC
1 ATTTTTCACTATCGCAACAC
466936 ATTTTTCA
1 ATTTTTCA
466944 AAATCGCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 29 0.49
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:466915 original size:44 final size:41
Alignment explanation
Indices: 466864--466945 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
466854 TTTTTCACTA
* * *
466864 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTACCGCAAC-ACA--TTTTTCAAACTC
466908 TCGCAACACATTTTAACTACCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTACCGCAACACATTTTTCAAA
466946 ATCGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 3 0.09
44 23 0.66
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.30
Consensus pattern (41 bp):
TCGCAACACATTTTAACTACCGCAACACATTTTTCAAACTC
Found at i:467530 original size:26 final size:26
Alignment explanation
Indices: 467479--467530 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
467469 AATTTGGTCC
* *
467479 TAATTTTAATAAATTTGATCATAATT
1 TAATTTTAATAAATTAGATCAAAATT
467505 TAATTTTAATAAATTAGAAT-AAAATT
1 TAATTTTAATAAATTAG-ATCAAAATT
467531 AACCCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
TAATTTTAATAAATTAGATCAAAATT
Found at i:468511 original size:20 final size:21
Alignment explanation
Indices: 468486--468537 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
468476 TTTTCCCAAT
*
468486 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
468506 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
468527 TCGCAATGCGA
1 TCGCAATGCGA
468538 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:468551 original size:20 final size:20
Alignment explanation
Indices: 468526--468660 Score: 128
Period size: 20 Copynumber: 6.7 Consensus size: 20
468516 AATTGGGAAA
468526 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
468546 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* **
468566 ATCGCAATGCGATAATAGAAA
1 ATCGCAATGCGATACT-GACT
* *
468587 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
468607 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
468627 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
468647 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
468661 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
19 2 0.02
20 68 0.72
21 25 0.26
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:468570 original size:61 final size:61
Alignment explanation
Indices: 468505--468654 Score: 176
Period size: 61 Copynumber: 2.5 Consensus size: 61
468495 GAATAAGTAA
* * * * * *
468505 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGATAAT-AGAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
468566 ATCGCAATGCGATAATAGAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATAGAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
468627 TTCGCAACGCGATAATACATAATCGCAA
1 ATCGCAACGCGATAATAGAAAATCGCAA
468655 TGCGATTTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
61 73 0.97
62 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (61 bp):
ATCGCAACGCGATAATAGAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:468591 original size:41 final size:40
Alignment explanation
Indices: 468526--468619 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 40
468516 AATTGGGAAA
* ** * * *
468526 ATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAATGCGATAATGAAAATCGCAACGAGATACTGACT
468566 ATCGCAATGCGATAATAGAAAATCGCAACGAGATACTGACT
1 ATCGCAATGCGATAAT-GAAAATCGCAACGAGATACTGACT
* *
468607 TTCGCAACGCGAT
1 ATCGCAATGCGAT
468620 TCTGACTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 15 0.33
41 30 0.67
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (40 bp):
ATCGCAATGCGATAATGAAAATCGCAACGAGATACTGACT
Found at i:468861 original size:22 final size:22
Alignment explanation
Indices: 468836--468879 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
468826 CACTCTCTCA
468836 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
468858 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
468880 TATCTCAATC
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:469166 original size:20 final size:20
Alignment explanation
Indices: 469141--469178 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
469131 CGATTCTCTC
469141 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
469161 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
469179 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:469369 original size:25 final size:24
Alignment explanation
Indices: 469315--469369 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
469305 TGTTTATTAT
* *
469315 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
469339 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
469365 TGTTT
1 TGTTT
469370 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:470519 original size:18 final size:18
Alignment explanation
Indices: 470498--470539 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
470488 TCCACTTCGG
*
470498 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
470516 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
470534 GAGCCA
1 GAGCCA
470540 CCATCTGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.45, G:0.17, T:0.12
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:471062 original size:19 final size:20
Alignment explanation
Indices: 471008--471074 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
470998 TAGTTTACTT
* *
471008 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
471028 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
471048 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
471067 TCGCAACG
1 TCGCAACG
471075 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:471082 original size:14 final size:14
Alignment explanation
Indices: 471063--471120 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
471053 ATGCGAAATG
471063 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
471077 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
471093 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
471109 AAAATCGCAACG
1 AAAATCGCAACG
471121 CGAAACAGAA
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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:471105 original size:32 final size:32
Alignment explanation
Indices: 471047--471136 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
471037 GGAAATGGCT
471047 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
471080 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
* *
471112 ATCGCAACGCGAAACAGAAATCGCA
1 ATCGCAATGCGAAA-TGAAATCGCA
471137 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:471132 original size:19 final size:18
Alignment explanation
Indices: 471078--471136 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
471068 CGCAACGACA
*
471078 AAATCGCAATGCGAAA-TG
1 AAATCGCAA-GCGAAACAG
471096 AAATCGCAA-CG--ACA-
1 AAATCGCAAGCGAAACAG
471110 AAATCGCAACGCGAAACAG
1 AAATCGCAA-GCGAAACAG
471129 AAATCGCA
1 AAATCGCA
471137 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 10 0.29
16 4 0.12
18 12 0.35
19 8 0.24
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (18 bp):
AAATCGCAAGCGAAACAG
Found at i:471154 original size:19 final size:19
Alignment explanation
Indices: 471132--471195 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
471122 GAAACAGAAA
471132 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
471151 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
471167 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
471184 TCGCATTGCGAT
1 TCGCATTGCGAT
471196 AGCCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.46
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:471214 original size:20 final size:19
Alignment explanation
Indices: 471180--471234 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
471170 TTGCGATTTT
*
471180 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
471199 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
471219 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
471235 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:473034 original size:8 final size:8
Alignment explanation
Indices: 473021--473046 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
473011 CACAAAGTTG
473021 TTGATTCA
1 TTGATTCA
473029 TTGATTCA
1 TTGATTCA
473037 TTGATTCA
1 TTGATTCA
473045 TT
1 TT
473047 AATTGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTGATTCA
Found at i:473112 original size:14 final size:14
Alignment explanation
Indices: 473093--473128 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
473083 ATTGTTTAAT
473093 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
473107 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
473121 TGATTTGT
1 TGATTTGT
473129 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:473236 original size:20 final size:20
Alignment explanation
Indices: 473211--473249 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
473201 ATGTTGAAGG
473211 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
473231 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
473250 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:473279 original size:19 final size:19
Alignment explanation
Indices: 473255--473319 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
473245 GCAACGAGAG
473255 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
473274 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
473293 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
473307 AATCGCAATGCGA
1 AATCGCAATGCGA
473320 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:473369 original size:19 final size:20
Alignment explanation
Indices: 473345--473394 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
473335 GCGATTTTGT
473345 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
473364 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
473384 CGTTGCGATAG
1 CGTTGCGATAG
473395 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:473632 original size:20 final size:20
Alignment explanation
Indices: 473607--473657 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
473597 AAATGATTGC
473607 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
473627 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
473647 CTTTCGCAACG
1 CTTTCGCAACG
473658 AGATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:474429 original size:24 final size:24
Alignment explanation
Indices: 474402--474455 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
474392 GTATTCGAAA
*
474402 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
474426 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
474450 TTTGAT
1 TTTGAT
474456 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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:476949 original size:19 final size:19
Alignment explanation
Indices: 476927--477057 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
476917 GGAAATTACT
476927 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
476946 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
476960 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
476979 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
476993 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
477012 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
477026 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
477045 ATCGCAACGCGAA
1 ATCGCAATGCGAA
477058 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:476969 original size:33 final size:33
Alignment explanation
Indices: 476927--477053 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
476917 GGAAATTACT
476927 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
476960 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
476992 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
477026 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
477054 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:477034 original size:66 final size:66
Alignment explanation
Indices: 476928--477060 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
476918 GAAATTACTA
*
476928 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
476993 T
66 T
*
476994 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
477059 T
66 T
477060 T
1 T
477061 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:477085 original size:14 final size:14
Alignment explanation
Indices: 477068--477124 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
477058 TTTAATTTCG
477068 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
477082 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
477100 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
477115 CGTTGCGATT
1 CGTTGCGATT
477125 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 2 0.06
16 3 0.08
17 3 0.08
18 2 0.06
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:477106 original size:19 final size:19
Alignment explanation
Indices: 477082--477142 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
477072 GCGATTCTCT
477082 CGTTGCGATTTTCATTTTG
1 CGTTGCGATTTTCATTTTG
*
477101 CGTTGCGA--TTC--TCT-
1 CGTTGCGATTTTCATTTTG
*
477115 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTTG
*
477134 CATTGCGAT
1 CGTTGCGAT
477143 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 3 0.09
17 3 0.09
18 1 0.03
19 16 0.48
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTTG
Found at i:477109 original size:33 final size:33
Alignment explanation
Indices: 477053--477142 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
477043 AAATCGCAAC
* *
477053 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
477086 GCGATTTTCATTTTGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
477119 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
477143 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:477268 original size:14 final size:14
Alignment explanation
Indices: 477249--477285 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
477239 CATCAATTAA
477249 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
477263 ACAAATCACCTTTT
1 ACAAATCAACTTTT
477277 ACAAATCAA
1 ACAAATCAA
477286 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:478684 original size:21 final size:21
Alignment explanation
Indices: 478660--478770 Score: 55
Period size: 21 Copynumber: 5.3 Consensus size: 21
478650 GTGGGAGGGA
*
478660 CCTCTTCAATGATGACAGTGG
1 CCTCTTCAAGGATGACAGTGG
* * ** *
478681 CCTCTTGAACGATGGGAGGGG
1 CCTCTTCAAGGATGACAGTGG
* * * *
478702 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAAGG-ATGACAGTGG
* *
478723 CCTCTTCAATGAT-AGGAGTGG
1 CCTCTTCAAGGATGA-CAGTGG
* * *
478744 ACTCTTGAGGGATGACAGTGG
1 CCTCTTCAAGGATGACAGTGG
478765 CCTCTT
1 CCTCTT
478771 GAACGGTGGG
Statistics
Matches: 64, Mismatches: 22, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
20 4 0.06
21 55 0.86
22 5 0.08
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (21 bp):
CCTCTTCAAGGATGACAGTGG
Found at i:478699 original size:42 final size:41
Alignment explanation
Indices: 478640--478845 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
478630 GTGAATCGAG
* * *
478640 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGATGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
478682 CTCTTGAACGATGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGATGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
478724 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGATGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
478766 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGATGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * *
478808 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGATGGGAG-GGACTCTTCAAGGATGACAG
478846 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGATGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:478781 original size:84 final size:84
Alignment explanation
Indices: 478670--478845 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
478660 CCTCTTCAAT
*
478670 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
478735 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
478754 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
478819 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
478838 GATGACAG
1 GATGACAG
478846 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGATGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:479238 original size:90 final size:90
Alignment explanation
Indices: 479062--479247 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
479052 ATATTTCAAA
*
479062 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
479127 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
479155 ACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGC
1 ACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGC
*
479219 AGTATTGGCAGCAACCGAATAAATTT
65 AGAATTGGCAGCAACCGAATAAATTT
479245 ACT
1 ACT
479248 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
90 42 0.47
93 21 0.23
94 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:479450 original size:63 final size:62
Alignment explanation
Indices: 479414--479607 Score: 343
Period size: 63 Copynumber: 3.1 Consensus size: 62
479404 TAAAGTAGAC
*
479414 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCTTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTC-CCACGCAAGGCATTG
*
479477 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCC-CACGCAAGGCATTG
479540 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCC-CACGCAAGGCATTG
479603 ACCTC
1 ACCTC
479608 ATCACGTAAC
Statistics
Matches: 127, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 127 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.22
Consensus pattern (62 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCCACGCAAGGCATTG
Found at i:481097 original size:19 final size:19
Alignment explanation
Indices: 481068--481190 Score: 122
Period size: 19 Copynumber: 7.0 Consensus size: 19
481058 TTGAAATGAT
*
481068 AATGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
481087 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
481103 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
481120 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
481139 AATGAAAATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
481155 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
*
481172 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
481191 TTTTGGTTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 55 0.64
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:481113 original size:33 final size:33
Alignment explanation
Indices: 481071--481135 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
481061 AAATGATAAT
**
481071 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
481104 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
481136 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:481131 original size:52 final size:52
Alignment explanation
Indices: 481068--481190 Score: 210
Period size: 52 Copynumber: 2.4 Consensus size: 52
481058 TTGAAATGAT
* **
481068 AATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
481120 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
*
481172 AATGAAAATCGCAATGCGA
1 AATGAAAATCGCAACGCGA
481191 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (52 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:481831 original size:20 final size:20
Alignment explanation
Indices: 481806--481859 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
481796 GAATTTGTAT
481806 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
481826 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
481846 TATCGCATTGCGAT
1 TATCGCATTGCGAT
481860 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:482871 original size:27 final size:29
Alignment explanation
Indices: 482796--482864 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
482786 GACTCTGTAT
*
482796 GATATATATATATCACATATGAACAAAAA
1 GATATATGTATATCACATATGAACAAAAA
482825 GATATATGTATATCACATATGAACAAAAA
1 GATATATGTATATCACATATGAACAAAAA
482854 GATATATGTAT
1 GATATATGTAT
482865 TGTATATAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (29 bp):
GATATATGTATATCACATATGAACAAAAA
Found at i:507266 original size:2 final size:2
Alignment explanation
Indices: 507259--507286 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
507249 CCTGTAAATA
507259 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
507287 TCCATGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:511081 original size:20 final size:20
Alignment explanation
Indices: 511041--511081 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
511031 TAGATTTTCA
* *
511041 AAATATATTTTTGAAATTAT
1 AAATATATTTTTAAAAATAT
511061 AAATATATTTTTAAAAATAT
1 AAATATATTTTTAAAAATAT
511081 A
1 A
511082 TTTAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATATATTTTTAAAAATAT
Found at i:511851 original size:29 final size:30
Alignment explanation
Indices: 511818--511876 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
511808 AGTATCATTT
511818 TGATCATTAAACTTTT-AAAAGTTATAAAA
1 TGATCATTAAACTTTTGAAAAGTTATAAAA
** *
511847 TGATCATTAATTTTTTGAACAGTTATAAAA
1 TGATCATTAAACTTTTGAAAAGTTATAAAA
511877 CGATATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (30 bp):
TGATCATTAAACTTTTGAAAAGTTATAAAA
Found at i:513182 original size:31 final size:31
Alignment explanation
Indices: 513146--513212 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
513136 TACAAAACAA
*
513146 TCCCCCAATATTTAGT-TCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCT-GTTTGCAATATGG
513177 TCCCCCAACATTTAGTCTGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTGTTTGCAATATGG
513208 TCCCC
1 TCCCC
513213 GACCGTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCTGTTTGCAATATGG
Found at i:516789 original size:17 final size:17
Alignment explanation
Indices: 516769--516801 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
516759 TTGAATTTCA
516769 TTAGTTGCAA-TCAACTG
1 TTAGTT-CAACTCAACTG
516786 TTAGTTCAACTCAACT
1 TTAGTTCAACTCAACT
516802 AGATCCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (17 bp):
TTAGTTCAACTCAACTG
Found at i:521098 original size:23 final size:23
Alignment explanation
Indices: 521068--521143 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
521058 CGAACGGATG
*
521068 TAAACGAACACAAAAAATGAACC
1 TAAACGAACACAAAAAATGAACA
521091 TAAACGAACACAAAAAATGAACA
1 TAAACGAACACAAAAAATGAACA
* *
521114 TAAAC-AA-ACATAAAA-GAATA
1 TAAACGAACACAAAAAATGAACA
*
521134 TAAATGAACA
1 TAAACGAACA
521144 TAAACCACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 8 0.17
21 9 0.19
22 3 0.06
23 27 0.57
ACGTcount: A:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (23 bp):
TAAACGAACACAAAAAATGAACA
Found at i:530381 original size:26 final size:27
Alignment explanation
Indices: 530352--530404 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
530342 CTTTCATGTC
530352 TTTTTTTTCGAACAG-ATTTTTTTTCT
1 TTTTTTTTCGAACAGTATTTTTTTTCT
*
530378 TTTTTTTTCGAACTGTTATTTTTTTTC
1 TTTTTTTTCGAACAG-TATTTTTTTTC
530405 AACATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
28 10 0.42
ACGTcount: A:0.13, C:0.11, G:0.08, T:0.68
Consensus pattern (27 bp):
TTTTTTTTCGAACAGTATTTTTTTTCT
Found at i:538525 original size:22 final size:22
Alignment explanation
Indices: 538474--538527 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
538464 ATCGATTCCC
*
538474 TCAAGGAGGGAATCGGTTTCCAT
1 TCAAGG-GGGAATCGGTTCCCAT
*
538497 TCAAAGGGGGAATCGGTTCCCCT
1 TC-AAGGGGGAATCGGTTCCCAT
538520 TCAAGGGG
1 TCAAGGGG
538528 ATATCGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 6 0.21
23 18 0.64
24 4 0.14
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTCCCAT
Found at i:538540 original size:21 final size:21
Alignment explanation
Indices: 538464--538540 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 21
538454 CGTAGGAGGT
538464 ATCGATTCCC-TCAAGGAGGGA
1 ATCGATTCCCTTCAAGG-GGGA
* *
538485 ATCGGTTTCCATTCAAAGGGGGA
1 ATC-GATTCCCTTC-AAGGGGGA
*
538508 ATCGGTTCCCCTTCAA-GGGGA
1 ATCGATT-CCCTTCAAGGGGGA
538529 TATCGATTCCCT
1 -ATCGATTCCCT
538541 CTGCACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
21 12 0.26
22 16 0.35
23 14 0.30
24 4 0.09
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (21 bp):
ATCGATTCCCTTCAAGGGGGA
Found at i:547837 original size:30 final size:30
Alignment explanation
Indices: 547801--547864 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
547791 TCCTATTTTG
547801 TATTCAATTTAGCCACTAACCTTAGTTTAA
1 TATTCAATTTAGCCACTAACCTTAGTTTAA
* *
547831 TATTCAATTTAGCCATTAACCTTAGTTTAG
1 TATTCAATTTAGCCACTAACCTTAGTTTAA
547861 TATT
1 TATT
547865 TGGTTAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (30 bp):
TATTCAATTTAGCCACTAACCTTAGTTTAA
Found at i:547952 original size:6 final size:6
Alignment explanation
Indices: 547941--547976 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
547931 GATTCCTTAG
* *
547941 AATTAT AATTAT AATTGT AATTGT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT
547977 TATGTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:549142 original size:40 final size:40
Alignment explanation
Indices: 549077--549266 Score: 183
Period size: 40 Copynumber: 4.8 Consensus size: 40
549067 AGTTTCCAAT
*
549077 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAATGCG-ATA-GTCAAATTCGCAACACAGAAGTCAAA
*
549117 TTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGAAGTCAAA
* * *
549157 TTCGCAACGCGATAGTCAAATTCGCAACGC-GATAATCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGA-AGTCAAA
* * * * * *
549197 TTCGCAATACAAAAGTCAAATTCGCAACGCGGAATTTCAAA
1 TTCGCAATGCGATAGTCAAATTCGCAACACAGAA-GTCAAA
* *
549238 TTCGCAACTG-AAT-TTCAAATTCGCAACAC
1 TTCGCAA-TGCGATAGTCAAATTCGCAACAC
549267 GAATTTAATT
Statistics
Matches: 129, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 7 0.05
40 103 0.80
41 16 0.12
42 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (40 bp):
TTCGCAATGCGATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:549174 original size:60 final size:60
Alignment explanation
Indices: 549098--549266 Score: 218
Period size: 60 Copynumber: 2.8 Consensus size: 60
549088 AATATGTAAA
* * *
549098 TCGCAACACAGAAGTCAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGGAAGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
* *
549158 TCGCAACGC-GATAGTCAAATTCGCAACGCGATAATCAAATTCGCAATACAAAAGTCAAAT
1 TCGCAACGCGGA-AGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
* * *
549218 TCGCAACGCGGAATTTCAAATTCGCAACTG-AAT-TTCAAATTCGCAACAC
1 TCGCAACGCGGAA-GTCAAATTCGCAA-TGCGATAATCAAATTCGCAACAC
549267 GAATTTAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
59 2 0.02
60 77 0.80
61 16 0.17
62 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (60 bp):
TCGCAACGCGGAAGTCAAATTCGCAATGCGATAATCAAATTCGCAACACAAAAGTCAAAT
Found at i:549252 original size:19 final size:19
Alignment explanation
Indices: 549212--549264 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
549202 AATACAAAAG
549212 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CGGAATT
*
549233 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGGAATT
549252 TCAAATTCGCAAC
1 TCAAATTCGCAAC
549265 ACGAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 19 0.61
21 12 0.39
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (19 bp):
TCAAATTCGCAACGGAATT
Found at i:549272 original size:20 final size:20
Alignment explanation
Indices: 549077--549270 Score: 150
Period size: 20 Copynumber: 9.7 Consensus size: 20
549067 AGTTTCCAAT
549077 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCG-A-ATGTCAAA
*
549098 -TCGCAACACAGAA-GTCAAA
1 TTCGCAACGC-GAATGTCAAA
*
549117 TTCGCAATGCG-ATAGTCAAA
1 TTCGCAACGCGAAT-GTCAAA
* * *
549137 TTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATGTCAAA
549157 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAAT-GTCAAA
*
549177 TTCGCAACGCG-ATAATCAAA
1 TTCGCAACGCGAAT-GTCAAA
** * *
549197 TTCGCAATACAAAAGTCAAA
1 TTCGCAACGCGAATGTCAAA
*
549217 TTCGCAACGCGGAATTTCAAA
1 TTCGCAACGC-GAATGTCAAA
* *
549238 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACGCGAATGTCAAA
*
549257 TTCGCAACACGAAT
1 TTCGCAACGCGAAT
549271 TTAATTTCAC
Statistics
Matches: 140, Mismatches: 23, Indels: 21
0.76 0.12 0.11
Matches are distributed among these distances:
18 3 0.02
19 24 0.17
20 95 0.68
21 18 0.13
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
TTCGCAACGCGAATGTCAAA
Found at i:549283 original size:19 final size:20
Alignment explanation
Indices: 549212--549284 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 20
549202 AATACAAAAG
* *
549212 TCAAATTCGCAACGCGGAATT
1 TCAAATTCACAACAC-GAATT
* *
549233 TCAAATTCGCAAC-TGAATT
1 TCAAATTCACAACACGAATT
*
549252 TCAAATTCGCAACACGAATT
1 TCAAATTCACAACACGAATT
*
549272 T-AATTTCACAACA
1 TCAAATTCACAACA
549285 GGTTTTAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 28 0.60
20 6 0.13
21 13 0.28
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.27
Consensus pattern (20 bp):
TCAAATTCACAACACGAATT
Found at i:549459 original size:14 final size:16
Alignment explanation
Indices: 549440--549476 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
549430 TCCCCATCTC
549440 TAATTTT-TTT-TACA
1 TAATTTTATTTCTACA
*
549454 TAATTTTATTTCTATA
1 TAATTTTATTTCTACA
549470 TAATTTT
1 TAATTTT
549477 CCAATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTTATTTCTACA
Found at i:550285 original size:24 final size:24
Alignment explanation
Indices: 550218--550296 Score: 106
Period size: 24 Copynumber: 3.3 Consensus size: 24
550208 AGTATTCGAA
* * *
550218 ATTTT-ATATTGGTCAATACCCAG
1 ATTTTGATCTTGGTCAATACTCGG
* *
550241 ACTTTGATCTTGGTTAATACTCGG
1 ATTTTGATCTTGGTCAATACTCGG
550265 ATTTTGATCTTGGTCAATACTCGG
1 ATTTTGATCTTGGTCAATACTCGG
550289 ATTTTGAT
1 ATTTTGAT
550297 GATGTGATGG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 4 0.08
24 44 0.92
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (24 bp):
ATTTTGATCTTGGTCAATACTCGG
Found at i:552577 original size:18 final size:18
Alignment explanation
Indices: 552554--552589 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
552544 AAGCAAAAGG
*
552554 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
552572 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
552590 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:552952 original size:20 final size:20
Alignment explanation
Indices: 552929--552982 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
552919 TCGCAACTCG
552929 AATTTGACTTTCGCGTTACA
1 AATTTGACTTTCGCGTTACA
* * *
552949 AATTTGAGTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTACA
*
552969 AATTTGACTATCGC
1 AATTTGACTTTCGC
552983 AACGCTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTACA
Found at i:553016 original size:20 final size:22
Alignment explanation
Indices: 552991--553034 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
552981 GCAACGCTTA
552991 TTTCGCGTTGC-AAA-TTTACC
1 TTTCGCGTTGCGAAAGTTTACC
553011 TTTCGCGTTGCGAAAGTTTACC
1 TTTCGCGTTGCGAAAGTTTACC
553033 TT
1 TT
553035 CAACAGTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
TTTCGCGTTGCGAAAGTTTACC
Found at i:553132 original size:25 final size:25
Alignment explanation
Indices: 553094--553143 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
553084 AAATCAATTA
*
553094 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
553119 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
553144 GAAAATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:553550 original size:18 final size:18
Alignment explanation
Indices: 553529--553565 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
553519 GTAATTGGAG
553529 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
553547 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
553565 T
1 T
553566 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:553572 original size:24 final size:24
Alignment explanation
Indices: 553521--553573 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
553511 TTTCATATGT
* * *
553521 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
553545 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
553569 AATTT
1 AATTT
553574 CGATTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:554437 original size:13 final size:13
Alignment explanation
Indices: 554419--554451 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
554409 CAAGTGTCAT
554419 TAGCTTGTATTTA
1 TAGCTTGTATTTA
554432 TAGCTTGTATTTA
1 TAGCTTGTATTTA
554445 TAGCTTG
1 TAGCTTG
554452 GAATGTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (13 bp):
TAGCTTGTATTTA
Found at i:554773 original size:51 final size:51
Alignment explanation
Indices: 554677--554787 Score: 188
Period size: 51 Copynumber: 2.2 Consensus size: 51
554667 ATCAACTTTT
554677 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAA
1 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAA
* *
554729 ACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
554779 ACAAATCAA
1 ACAAATCAA
554788 CTTTCAATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
50 15 0.26
51 23 0.40
52 19 0.33
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (51 bp):
ACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAA
Found at i:556194 original size:21 final size:21
Alignment explanation
Indices: 556170--556268 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
556160 GCGGGTGGGA
*
556170 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
556191 CCTCTTGAACGGTGGGATGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
556212 CTTCTTCG-ATGATGAAAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
556233 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
*
556254 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
556269 TAGGTGCATC
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:556226 original size:42 final size:42
Alignment explanation
Indices: 556150--556243 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
556140 ATGAATCAGG
*
556150 CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGAAAGGGGC
* * *
556192 CTCTTGAACGGTGGGATGGG-CTTCTTCG-ATGATGAAAGGGGC
1 CTCTTGAACGGCGGG-TGGGACCTCTT-GAACGATGAAAGGGGC
556234 CTCTTGAACG
1 CTCTTGAACG
556244 ATAGGAGGCG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 41 0.89
43 5 0.11
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGCGGGTGGGACCTCTTGAACGATGAAAGGGGC
Found at i:556266 original size:42 final size:42
Alignment explanation
Indices: 556165--556268 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
556155 GAACGGCGGG
* * * *
556165 TGGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGA
1 TGGG-CCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGA
*
556208 TGGGCTTCTTCG-ATGATGAAAGGGGCCTCTTGAACGATAGGA
1 TGGGCCTCTT-GAATGATGAAAGGGGCCTCTTGAACGATAGGA
556250 -GGCGCCTCTTGAATGATGA
1 TGG-GCCTCTTGAATGATGA
556269 TAGGTGCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 3 0.06
42 44 0.85
43 5 0.10
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
TGGGCCTCTTGAATGATGAAAGGGGCCTCTTGAACGATAGGA
Found at i:558530 original size:20 final size:20
Alignment explanation
Indices: 558491--558530 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
558481 TGCAATTTTG
* * *
558491 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
558511 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
558531 AAAAACTATT
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:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:559045 original size:40 final size:40
Alignment explanation
Indices: 559001--559172 Score: 185
Period size: 40 Copynumber: 4.3 Consensus size: 40
558991 ATATTGTGTT
559001 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
*
559041 TCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
** * *
559080 TCTATGTTGCG-ATTT-ACAAATTAGCGTTGCGAATTTGACTA
1 TC-GCGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTA
* *
559121 TCGCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAAA
1 TCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-TA
559160 TTCGCGTTGCGAA
1 -TCGCGTTGCGAA
559173 ATTGGAAACT
Statistics
Matches: 112, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
38 4 0.04
39 13 0.12
40 87 0.78
41 6 0.05
42 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTA
Found at i:559069 original size:60 final size:60
Alignment explanation
Indices: 559001--559172 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 60
558991 ATATTGTGTT
* * * *
559001 TCGCGTTGCGAATTTGACTATC-GCGTTGCGAATTTGAC-TA-TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACT-TCTACGTTGCG-ATTT-ACAAATTAGCGTTGCGAATTTGACTA
*
559061 TCGCGTTGCGAATTTGACTTCTATGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
** *
559121 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAA
1 TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAA
559173 ATTGGAAACT
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
58 2 0.02
59 7 0.07
60 93 0.91
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTCTACGTTGCGATTTACAAATTAGCGTTGCGAATTTGACTA
Found at i:559151 original size:20 final size:20
Alignment explanation
Indices: 559001--559139 Score: 185
Period size: 20 Copynumber: 7.0 Consensus size: 20
558991 ATATTGTGTT
559001 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
559021 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
559041 TCGCGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
559061 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
** *
559080 TCTATGTTGCG-ATTT-ACAAA
1 TC-GCGTTGCGAATTTGAC-TA
*
559100 TTAGCGTTGCGAATTTGACTA
1 -TCGCGTTGCGAATTTGACTA
559121 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
559140 TCTGTGTTGC
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
18 2 0.02
19 6 0.06
20 87 0.84
21 6 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:559168 original size:20 final size:20
Alignment explanation
Indices: 559000--559171 Score: 112
Period size: 20 Copynumber: 8.6 Consensus size: 20
558990 AATATTGTGT
*
559000 TTCGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
*
559021 -TCGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
*
559041 -TCGCGTTGCGGATTTGACTA
1 TTCGCGTTGC-GATTTGACAA
559061 -TCGCGTTGCGAATTTGAC--
1 TTCGCGTTGCG-ATTTGACAA
**
559079 TTCTATGTTGCGATTT-ACAAA
1 TTC-GCGTTGCGATTTGAC-AA
* *
559100 TTAGCGTTGCGAATTTGACTA
1 TTCGCGTTGCG-ATTTGACAA
559121 -TCGCGTTGCGAATTTGAC--
1 TTCGCGTTGCG-ATTTGACAA
*
559139 TTCTGTGTTGCGATTT-ACAAA
1 TTC-GCGTTGCGATTTGAC-AA
559160 TTCGCGTTGCGA
1 TTCGCGTTGCGA
559172 AATTGGAAAC
Statistics
Matches: 128, Mismatches: 9, Indels: 29
0.77 0.05 0.17
Matches are distributed among these distances:
18 4 0.03
19 13 0.10
20 98 0.77
21 11 0.09
22 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATTTGACAA
Found at i:563837 original size:20 final size:19
Alignment explanation
Indices: 563789--563837 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
563779 AAAATTTATC
563789 TTTTATATTTAAACTTTTTT
1 TTTTA-ATTTAAACTTTTTT
* *
563809 TTGTCAATTTAATCTTTATTT
1 TT-TTAATTTAAACTTT-TTT
563830 TTTTAATT
1 TTTTAATT
563838 ACTTTGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTAAACTTTTTT
Found at i:564227 original size:20 final size:20
Alignment explanation
Indices: 564202--564275 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
564192 GCGAAATAAA
564202 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCTCCAG
** *
564222 AATCGCAAATCAGTTC-CCAG
1 AATCGCAACGC-GATCTCCAG
* **
564242 AATCGCAACGCGATTATTAAG
1 AATCGCAACGCGA-TCTCCAG
564263 AATCGCAACGCGA
1 AATCGCAACGCGA
564276 ATATGAAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 23 0.55
21 18 0.43
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGATCTCCAG
Found at i:564288 original size:20 final size:20
Alignment explanation
Indices: 564242--564497 Score: 180
Period size: 20 Copynumber: 12.7 Consensus size: 20
564232 CAGTTCCCAG
* **
564242 AATCGCAACGCGATTATTAA
1 AATCGCAACGCGAATACGAA
*
564262 GAATCGCAACGCGAATATGAA
1 -AATCGCAACGCGAATACGAA
* *
564283 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
564303 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
564323 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
564344 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
564364 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
564384 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
564404 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
564424 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
564444 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
564465 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
564485 AATCGCAGCGCGA
1 AATCGCAACGCGA
564498 TTTTTAAAGC
Statistics
Matches: 192, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.01
20 137 0.71
21 52 0.27
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:564326 original size:40 final size:40
Alignment explanation
Indices: 564263--564497 Score: 240
Period size: 40 Copynumber: 5.8 Consensus size: 40
564253 GATTATTAAG
* ** *
564263 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * *
564303 AATCGCAACGCGTATCCATAAATCGCAACGACAATACGTA-A
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATA
* * **
564344 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * * **
564384 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
* * *
564424 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA-A
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATA
*
564465 AATCGCAACGCGTATCCGTAAATCGCAGCGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
564498 TTTTTAAAGC
Statistics
Matches: 164, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 96 0.59
41 62 0.38
42 5 0.03
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATA
Found at i:564327 original size:81 final size:81
Alignment explanation
Indices: 564242--564497 Score: 295
Period size: 81 Copynumber: 3.2 Consensus size: 81
564232 CAGTTCCCAG
* * * ** *
564242 AATCGCAACGCGATTA-TTAAGAATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAAT
1 AATCGCAACGCGAATACGTAA-AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAAT
*
564306 CGCAACGCGTATCCATA
65 CGCAACGCGTATCCGTA
* * **
564323 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAAT
1 AATCGCAACG-CGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAAT
*
564387 CGCAACGCGTATCTGTA
65 CGCAACGCGTATCCGTA
* * * *
564404 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA-AAA
1 AATCGCAACGCGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATAAA
564467 TCGCAACGCGTATCCGTA
64 TCGCAACGCGTATCCGTA
*
564485 AATCGCAGCGCGA
1 AATCGCAACGCGA
564498 TTTTTAAAGC
Statistics
Matches: 147, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
80 30 0.20
81 112 0.76
82 5 0.03
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.18
Consensus pattern (81 bp):
AATCGCAACGCGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATC
GCAACGCGTATCCGTA
Found at i:564395 original size:121 final size:121
Alignment explanation
Indices: 564263--564491 Score: 377
Period size: 121 Copynumber: 1.9 Consensus size: 121
564253 GATTATTAAG
* *
564263 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCATAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
564328 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * * * *
564384 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
564449 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
66 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCA
564492 GCGCGATTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 99 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (121 bp):
AATCGCAACGCGAATATGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCATAAATCG
CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:565089 original size:20 final size:19
Alignment explanation
Indices: 565058--565135 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 19
565048 TTCTAAACTT
*
565058 AAAATCGAAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
565078 AAAACCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
565098 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
565119 AAAATCGCAACGAGAAA
1 AAAATCGCAAC-AGAAA
565136 CCAAAATCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 29 0.60
21 19 0.40
ACGTcount: A:0.54, C:0.18, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:565119 original size:21 final size:21
Alignment explanation
Indices: 565073--565133 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
565063 CGAAACATGA
*
565073 AAATGAAAACCGCAAC-ACGA-
1 AAATGAAAATCGCAACGA-GAG
**
565093 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
565114 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
565134 AACCAAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:565189 original size:33 final size:33
Alignment explanation
Indices: 565147--565268 Score: 127
Period size: 33 Copynumber: 3.5 Consensus size: 33
565137 CAAAATCGCA
565147 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * * *
565180 TTGCGATTTTAATTTTGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
565213 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
565253 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
565269 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
33 41 0.59
34 7 0.10
39 1 0.01
40 21 0.30
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:565245 original size:20 final size:21
Alignment explanation
Indices: 565213--565268 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
565203 GATTCTCTCA
**
565213 TTGCGATAGTCATTTC-CGCG
1 TTGCGATTTTCATTTCTCGCG
*
565233 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTCTCGCG
565253 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
565269 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.46
Consensus pattern (21 bp):
TTGCGATTTTCATTTCTCGCG
Found at i:567314 original size:21 final size:21
Alignment explanation
Indices: 567290--567356 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
567280 TCATTCCTCG
567290 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
567311 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
567332 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
567353 AGAG
1 AGAG
567357 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:567314 original size:42 final size:42
Alignment explanation
Indices: 567238--567356 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
567228 GACTCGCCTG
* * * * * * *
567238 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
567280 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
567322 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
567357 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:568748 original size:13 final size:13
Alignment explanation
Indices: 568701--568753 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
568691 TTGATTGTTT
568701 AATTGATTTGTAA
1 AATTGATTTGTAA
*
568714 AAGATGATTTGTAA
1 AA-TTGATTTGTAA
**
568728 ATATTGATTTGTTT
1 A-ATTGATTTGTAA
*
568742 AATTGATGTGTA
1 AATTGATTTGTA
568754 CATAATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:568876 original size:19 final size:20
Alignment explanation
Indices: 568841--568885 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
568831 AAAACAGACT
568841 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGCGGAAATGAAA
*
568861 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGAAA
568880 ATCGCA
1 ATCGCA
568886 TTTAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGAAA
Found at i:571200 original size:24 final size:24
Alignment explanation
Indices: 571166--571219 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
571156 CTGAAAAATC
571166 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
571190 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
571214 ATCAAA
1 ATCAAA
571220 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:571233 original size:24 final size:24
Alignment explanation
Indices: 571166--571233 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
571156 CTGAAAAATC
* * *
571166 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
571190 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
571214 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
571234 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:572104 original size:20 final size:19
Alignment explanation
Indices: 572079--572270 Score: 161
Period size: 20 Copynumber: 9.6 Consensus size: 19
572069 GTAAGAATCT
572079 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTAC-GATTCG
*
572099 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACG-ATTCG
* * * *
572119 CATTGCAATTTACGGATACA
1 CGTTGCGATTTAC-GATTCG
* *
572139 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
572159 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTAC-GATTCG
*
572179 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACG-ATTCG
*
572199 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GATTCG
* *
572219 CATTGTGATTTTACGTATT-G
1 CGTTGCGA-TTTACG-ATTCG
*
572239 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTAC-GATTCG
572260 CGTTGCGATTT
1 CGTTGCGATTT
572271 TACGGGTACT
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
19 3 0.02
20 120 0.85
21 18 0.13
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTACGATTCG
Found at i:572107 original size:40 final size:40
Alignment explanation
Indices: 572076--572289 Score: 284
Period size: 40 Copynumber: 5.3 Consensus size: 40
572066 ATAGTAAGAA
* *
572076 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
* * * *
572116 TCGCATTGCAATTTACGGATACACATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
* *
572156 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
*
572196 TCTCGTTGCGATTTACGGATACGCATTGTGATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
* * **
572237 TGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGGT
1 TCTCGTTGCGATTTACGGATACGCATTGCGA-TTTACGTAT
*
572278 ACTCGTTGCGAT
1 TCTCGTTGCGAT
572290 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 96 0.64
41 55 0.36
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
TCTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
Found at i:574144 original size:199 final size:198
Alignment explanation
Indices: 573717--574394 Score: 839
Period size: 200 Copynumber: 3.4 Consensus size: 198
573707 TACACCATGA
*
573717 ACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGGATTGATACAATTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATAC-ATTT
* * ** *
573782 T--AAATGTATCGACACTTTATACGTGCACCTTGTGGGGCATTCATTCTGGA-AAAAAGTATCGA
65 TAAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAAA-TATCGA
* * * *
573844 CACAAACTTAAAAAGTGTCGATACATTATGTAGAACTATTTTCTCATAAAATCGGTATATTTCTA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTG-ACTATTTTCTCATAAAACCGGTATATTTATA
** *
573909 TTGGGT
193 CCGGTT
* * *
573915 ACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATAGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
*
573979 AATAAATGTATCGACACTTTATGCGTGCACCCCGTTTGACATTCATTCTGGACAAAATATATCGA
66 AA-AAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAA-ATATCGA
*
574044 CACAAATTTAAAAAGTGTCGATACATTATGTTGACTTATTCTCTCATAAAACCGGTATATTTATA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTGAC-TATTTTCTCATAAAACCGGTATATTTATA
574109 CCGGTT
193 CCGGTT
* * * * * * * * * *
574115 ATATTG-AAAATTACATATTACATTGTAATTATAGGTTTGGATGTTTTTGAGATCGATACTTTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
* * *
574179 AAAAATGTATCTACACTTTATGCGTGCACCTCGTTTTGACATTCATTTTGGACAATAAGTATCGA
66 AAAAATGTATCGACACTTTATGCGTGCACCTCG-TTTGACATTCATTCTGGACAA-AAATATCGA
** * * * * *
574244 CACAAATTCCACAAGTGTCGATACATTATGTTGAAATGTTTTCTAAT-TAACCGGTATATTTATA
129 CACAAATTTAAAAAGTGTCGATACATTATGTTG-ACTATTTTCTCATAAAACCGGTATATTTATA
574308 CCGGTT
193 CCGGTT
* * *
574314 ACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTTGGGGTTGATAC-TTTT
1 ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
*
574378 AGAAAATGTATCTACAC
66 A-AAAATGTATCGACAC
574395 ATATTTAGGT
Statistics
Matches: 420, Mismatches: 48, Indels: 22
0.86 0.10 0.04
Matches are distributed among these distances:
196 4 0.01
198 56 0.13
199 153 0.36
200 203 0.48
201 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (198 bp):
ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATTGATACATTTT
AAAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAAATATCGACA
CAAATTTAAAAAGTGTCGATACATTATGTTGACTATTTTCTCATAAAACCGGTATATTTATACCG
GTT
Found at i:577866 original size:2 final size:2
Alignment explanation
Indices: 577859--577884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
577849 TCTTTTTGAA
577859 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
577885 GCATAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:579071 original size:15 final size:15
Alignment explanation
Indices: 579051--579085 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
579041 GTTCGACCGG
**
579051 ATAAAATTTTAAAAA
1 ATAAAATTAAAAAAA
579066 ATAAAATTAAAAAAA
1 ATAAAATTAAAAAAA
579081 ATAAA
1 ATAAA
579086 TTTATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAATTAAAAAAA
Found at i:579719 original size:25 final size:25
Alignment explanation
Indices: 579691--579745 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
579681 TATTATTAAC
* *
579691 AAAAAATAGTTAAATTAATCAAATT
1 AAAAAAGAGTTAAATAAATCAAATT
* * *
579716 AAAAAAGGGTTAAATAAATGAAGTT
1 AAAAAAGAGTTAAATAAATCAAATT
579741 AAAAA
1 AAAAA
579746 TTATCTTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (25 bp):
AAAAAAGAGTTAAATAAATCAAATT
Found at i:582333 original size:48 final size:48
Alignment explanation
Indices: 582216--582341 Score: 155
Period size: 48 Copynumber: 2.6 Consensus size: 48
582206 CCGGAACTGA
*** * *
582216 TGCTGATCT-CTATATAAATCTCCCGGATTGTCCCATTGAAACTGCTGC
1 TGCTGATCTGC-ATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
582264 TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
1 TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
* * * *
582312 TGCTGATTTGTATATGAATCTTGAAGATTT
1 TGCTGATCTGCATATAAATCTTGAGGATTT
582342 CCCCATCCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 67 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (48 bp):
TGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTGAAACTGCTGC
Found at i:582354 original size:48 final size:48
Alignment explanation
Indices: 582254--582355 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 48
582244 TGTCCCATTG
* * **
582254 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAGGATTTTCCAATTG
1 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
* * * *
582302 AAACTGCTGCTGCTGATTTGTATATGAATCTTGAAGATTTCCCCATCC
1 AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
582350 AAACTG
1 AAACTG
582356 AGCTGCAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (48 bp):
AAACTGCTGCTGCTGATCTGCATATAAATCTTGAAGATTTCCCAATCC
Found at i:582507 original size:114 final size:114
Alignment explanation
Indices: 582296--582541 Score: 429
Period size: 114 Copynumber: 2.1 Consensus size: 114
582286 GAGGATTTTC
*
582296 CAATTGAAACTGCTGCTGCTGATTTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTG
1 CAATT-AAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTG
*
582361 CAGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGTTACCA
65 CAGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
* *
582411 CAATTAAACTGCTGCTGTTGATGTGTATATGAATCTTGAGGATTTCCCCATCCAAACTGAGCTGC
1 CAATTAAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTGC
*
582476 AGGTGGTATCTCTAACATTGGTGGCATTGCTGTTGATCCAACGCTACCA
66 AGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
*
582525 CAATTAAATTGCTGCTG
1 CAATTAAACTGCTGCTG
582542 ATTTACCCAT
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
114 120 0.96
115 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (114 bp):
CAATTAAACTGCTGCTGCTGATGTGTATATGAATCTTGAAGATTTCCCCATCCAAACTGAGCTGC
AGGTGGTATCTCTAACATTGGTGGCACTGCTGTTGATCCAACGCTACCA
Found at i:586673 original size:35 final size:35
Alignment explanation
Indices: 586627--586694 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
586617 TTGCAAGAAC
* *
586627 GGTACGGATACT-TCTACATTGGTATCGATACCCAT
1 GGTACAGATACTATC-ACATTAGTATCGATACCCAT
*
586662 GGTACAGATACTATCACTTTAGTATCGATACCC
1 GGTACAGATACTATCACATTAGTATCGATACCC
586695 CATGAAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (35 bp):
GGTACAGATACTATCACATTAGTATCGATACCCAT
Found at i:589616 original size:19 final size:18
Alignment explanation
Indices: 589579--589634 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
589569 GGGCCTGTAA
*
589579 TTATATT-TTTTAT-TAT
1 TTATATTATTTAATATAT
589595 TTAT-TTATTTTAATAATAT
1 TTATATTA-TTTAAT-ATAT
589614 TTATATTATTTAATATAT
1 TTATATTATTTAATATAT
589632 TTA
1 TTA
589635 ATAATAATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.06
16 4 0.12
17 5 0.15
18 7 0.21
19 13 0.38
20 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATATTATTTAATATAT
Found at i:589639 original size:3 final size:3
Alignment explanation
Indices: 589633--589736 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
589623 TTAATATATT
*
589633 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
589681 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
589729 TAA TAA TA
1 TAA TAA TA
589737 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:590972 original size:113 final size:113
Alignment explanation
Indices: 589990--590986 Score: 1631
Period size: 113 Copynumber: 8.8 Consensus size: 113
589980 TCTTGATGAG
*
589990 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * *
590054 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
590103 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * *
590167 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
590216 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
590281 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
* *
590329 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
590394 GAAAAGCTGTTCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
590442 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
590507 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
590555 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
590620 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
590668 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * * * *
590732 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
590781 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
590846 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
*
590894 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
590959 CAAAAAATAATCCATCAATTGATAGATT
66 GAAAAGATGATCCATCAAATGATGGATT
590987 TGAATCTTTG
Statistics
Matches: 838, Mismatches: 43, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
112 2 0.00
113 835 1.00
114 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:591868 original size:82 final size:82
Alignment explanation
Indices: 591604--592029 Score: 694
Period size: 82 Copynumber: 5.2 Consensus size: 82
591594 TACTATGAGC
* *
591604 AAATTCATCTTCCAAATTCAATGATTGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCT-AAACCAGGTCAGATAACTCAAAGAACACTT
*
591668 CCAGAAGATGCTATTGGC
65 CCAGAAGATGCTATTGGT
* * * * *
591686 AAATTCATCTTCCAAATTCAATGCTTGATTCT-ATATAATCAGATCAAATAACTCAAAGAACACT
1 AAATTCATCTTCCAAATTCAATGATTG-TTCTGCTA-AACCAGGTCAGATAACTCAAAGAACACT
*
591750 TCCAGAAGATGCTATTGGC
64 TCCAGAAGATGCTATTGGT
*
591769 AAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
591834 CAGAAGATGCTATTGGT
66 CAGAAGATGCTATTGGT
*
591851 AAATTCATCTTCCAAATTCAATGACTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
591916 CAGAAGATGCTATTGGT
66 CAGAAGATGCTATTGGT
*
591933 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATT-GTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTT
591998 CCAGAAGATGCTATTGGT
65 CCAGAAGATGCTATTGGT
592016 AAATTCATCTTCCA
1 AAATTCATCTTCCA
592030 TTTAATGTTT
Statistics
Matches: 324, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
82 178 0.55
83 146 0.45
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (82 bp):
AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGT
Found at i:591973 original size:165 final size:165
Alignment explanation
Indices: 591602--592029 Score: 709
Period size: 165 Copynumber: 2.6 Consensus size: 165
591592 TTTACTATGA
** *
591602 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACT
* *
591667 TCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGATTCTATATAATCAGATCA
66 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGCTTGATTCTATATAACCAGATCA
591732 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
131 AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* *
591767 GCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACT
* *
591832 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGAC-TG-TTCTGCTA-AACCAGGT
66 TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATG-CTTGATTCT-ATATAACCAGAT
*
591894 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
129 CAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG
*
591931 GTAAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGTTAAACCAGGTCAGATAACTCAAAGAACAC
591996 TTCCAGAAGATGCTATTGGTAAATTCATCTTCCA
65 TTCCAGAAGATGCTATTGGTAAATTCATCTTCCA
592030 TTTAATGTTT
Statistics
Matches: 247, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
164 72 0.29
165 174 0.70
166 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (165 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGGTAAATTCATCTTCCAAATTCAATGCTTGATTCTATATAACCAGATCA
AATAACTCAAAGAACACTTCCAGAAGATGCTATTG
Found at i:593170 original size:17 final size:16
Alignment explanation
Indices: 593150--593216 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 16
593140 CTTGACCCCC
*
593150 TTTTTCTTTTTTTCCTT
1 TTTTTCTTTTTTT-TTT
593167 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
593183 CTTTTTCTATTTTTTTTCT
1 -TTTTTCT-TTTTTTTT-T
593202 TTTTTCTTCTTTTTT
1 TTTTTCTT-TTTTTT
593217 CTCTTCAAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
16 2 0.04
17 21 0.47
18 21 0.47
19 1 0.02
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:593196 original size:28 final size:27
Alignment explanation
Indices: 593150--593215 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
593140 CTTGACCCCC
* *
593150 TTTTTCTTTTTTTCCTTTTTTTCTTTTT
1 TTTTTCTTTTTCTACTTTTTTTC-TTTT
*
593178 TTTTTCTTTTTCTATTTTTTTTCTTTT
1 TTTTTCTTTTTCTACTTTTTTTCTTTT
*
593205 TTCTTCTTTTT
1 TTTTTCTTTTT
593216 TCTCTTCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.85
Consensus pattern (27 bp):
TTTTTCTTTTTCTACTTTTTTTCTTTT
Found at i:593217 original size:10 final size:10
Alignment explanation
Indices: 593157--593218 Score: 64
Period size: 9 Copynumber: 6.8 Consensus size: 10
593147 CCCTTTTTCT
*
593157 TTTTTTCCT-
1 TTTTTTCTTC
593166 TTTTTTCTT-
1 TTTTTTCTTC
593175 TTTTTT-TTC
1 TTTTTTCTTC
*
593184 -TTTTTC-TA
1 TTTTTTCTTC
593192 TTTTTT-TTC
1 TTTTTTCTTC
593201 TTTTTTCTTC
1 TTTTTTCTTC
593211 TTTTTTCT
1 TTTTTTCT
593219 CTTCAAGCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 8 0.18
9 26 0.58
10 11 0.24
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:596752 original size:11 final size:11
Alignment explanation
Indices: 596728--596759 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
596718 TGAAATAAAT
596728 AAATGT-AA-A
1 AAATGTAAAGA
596737 AAATGTAAAGA
1 AAATGTAAAGA
596748 AAATGTAAAGA
1 AAATGTAAAGA
596759 A
1 A
596760 TGATTGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.29
10 2 0.10
11 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (11 bp):
AAATGTAAAGA
Found at i:604522 original size:17 final size:17
Alignment explanation
Indices: 604500--604548 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
604490 TATATATTTG
*
604500 AATATATAAAAATTAAA
1 AATATATAAAAAATAAA
604517 AATATAATAAAAAAATAAA
1 AATAT-AT-AAAAAATAAA
604536 AATATACTAAAAA
1 AATATA-TAAAAA
604549 CAATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AATATATAAAAAATAAA
Found at i:604535 original size:19 final size:19
Alignment explanation
Indices: 604507--604553 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
604497 TTGAATATAT
*
604507 AAAAATTAAAAATATAATA
1 AAAAAATAAAAATATAATA
*
604526 AAAAAATAAAAATATACTA
1 AAAAAATAAAAATATAATA
604545 AAAACAATA
1 AAAA-AATA
604554 TATTTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATAAAAATATAATA
Done.