Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 26
Found at i:423520 original size:18 final size:19
Alignment explanation
Indices: 423497--423542 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
423487 GAAACTTAAA
*
423497 ATCGCAACATG-AATGACT
1 ATCGCAACACGAAATGACT
*
423515 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
423535 ATCGCAAC
1 ATCGCAAC
423543 GAGAGAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:423630 original size:20 final size:20
Alignment explanation
Indices: 423586--423653 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
423576 GCGATTCTTT
* ** *
423586 CGTTGCAATAGTCAAATTCA
1 CGTTGCGATAGTCATTTTCG
*
423606 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
423626 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
423646 CGTTGCGA
1 CGTTGCGA
423654 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:425587 original size:20 final size:20
Alignment explanation
Indices: 425559--425634 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
425549 TCTAAAACTT
425559 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
425579 AAAACCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
425599 ACTATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
*
425618 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
425635 CTAAATCGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:426280 original size:40 final size:40
Alignment explanation
Indices: 426225--426401 Score: 149
Period size: 40 Copynumber: 4.3 Consensus size: 40
426215 GCGCTTTGAA
*
426225 AATCGCATTGCGATAGTCAGCATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
* *
426265 AATCGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
* ** * * * * *
426305 ACTCGCATTGTAAT-TTACATATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGT-CAGAATCGCGTTGCGATAGTC--AG
* * ** *
426347 AATCGCAATGCGATAGTCGGAAAATCGCAATGCGTTAGTCAG
1 AATCGCATTGCGATAGTC--AGAATCGCGTTGCGATAGTCAG
*
426389 AATCGCGTTGCGA
1 AATCGCATTGCGA
426402 ATCTGGAAAC
Statistics
Matches: 107, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
39 1 0.01
40 65 0.61
42 24 0.22
43 1 0.01
44 16 0.15
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
Found at i:426310 original size:20 final size:20
Alignment explanation
Indices: 426225--426303 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
426215 GCGCTTTGAA
*
426225 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
426245 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
426265 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
426285 AATCGCGTTGCGATAGTCA
1 AATCGCGTTGCGATAGTCA
426304 TACTCGCATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:426358 original size:22 final size:22
Alignment explanation
Indices: 426327--426386 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
426317 ATTTACATAT
*
426327 TCGCATTGCGATAGTCGGAAAA
1 TCGCAATGCGATAGTCGGAAAA
426349 TCGCAATGCGATAGTCGGAAAA
1 TCGCAATGCGATAGTCGGAAAA
*
426371 TCGCAATGCGTTAGTC
1 TCGCAATGCGATAGTC
426387 AGAATCGCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (22 bp):
TCGCAATGCGATAGTCGGAAAA
Found at i:426394 original size:20 final size:21
Alignment explanation
Indices: 426327--426394 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
426317 ATTTACATAT
*
426327 TCGCATTGCGATAGTCGGAAAA
1 TCGCAATGCGATAGTC-GAAAA
426349 TCGCAATGCGATAGTCGGAAAA
1 TCGCAATGCGATAGTC-GAAAA
* *
426371 TCGCAATGCGTTAGTC-AGAA
1 TCGCAATGCGATAGTCGAAAA
426391 TCGC
1 TCGC
426395 GTTGCGAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 7 0.16
22 36 0.84
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGAAAA
Found at i:429860 original size:184 final size:184
Alignment explanation
Indices: 429551--429921 Score: 733
Period size: 184 Copynumber: 2.0 Consensus size: 184
429541 CGTTCTCTCA
429551 AAATAGCATCCTCCTTTATTTCCTTTATGCAACCCAATAAACCTTAGTTTTATGAGAAACTCAAA
1 AAATAGCATCCTCCTTTATTTCCTTTATGCAACCCAATAAACCTTAGTTTTATGAGAAACTCAAA
429616 TAACAAAGACCTAGATTGTGAACATAAAGTGTGGAATGAATTTGCTATCATATCCAAATATGAAA
66 TAACAAAGACCTAGATTGTGAACATAAAGTGTGGAATGAATTTGCTATCATATCCAAATATGAAA
429681 TGTAATCTTATATATCACATTTCAAACGTAATGTAAGCTTGGTTTCAGACAAGG
131 TGTAATCTTATATATCACATTTCAAACGTAATGTAAGCTTGGTTTCAGACAAGG
429735 AAATAGCATCCTCCTTTATTTCCTTTATGCAACCCAATAAACCTTAGTTTTATGAGAAACTCAAA
1 AAATAGCATCCTCCTTTATTTCCTTTATGCAACCCAATAAACCTTAGTTTTATGAGAAACTCAAA
*
429800 TAACAAAGACCTAGATTGTGAACATAAAGTGTGGAATGAATTTGTTATCATATCCAAATATGAAA
66 TAACAAAGACCTAGATTGTGAACATAAAGTGTGGAATGAATTTGCTATCATATCCAAATATGAAA
429865 TGTAATCTTATATATCACATTTCAAACGTAATGTAAGCTTGGTTTCAGACAAGG
131 TGTAATCTTATATATCACATTTCAAACGTAATGTAAGCTTGGTTTCAGACAAGG
429919 AAA
1 AAA
429922 ACTTTAGTAT
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 186 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.32
Consensus pattern (184 bp):
AAATAGCATCCTCCTTTATTTCCTTTATGCAACCCAATAAACCTTAGTTTTATGAGAAACTCAAA
TAACAAAGACCTAGATTGTGAACATAAAGTGTGGAATGAATTTGCTATCATATCCAAATATGAAA
TGTAATCTTATATATCACATTTCAAACGTAATGTAAGCTTGGTTTCAGACAAGG
Found at i:434247 original size:12 final size:12
Alignment explanation
Indices: 434219--434248 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
434209 ACATGCTCAA
*
434219 ATACATACATAC
1 ATACGTACATAC
434231 ATACGTACATAC
1 ATACGTACATAC
434243 ATACGT
1 ATACGT
434249 TATTCATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (12 bp):
ATACGTACATAC
Found at i:445619 original size:16 final size:16
Alignment explanation
Indices: 445586--445624 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
445576 GTTTACTTCA
* *
445586 GAATGA-TTAAGTGCT
1 GAATGATTTAAATGAT
445601 GAATGATTTAAATGAT
1 GAATGATTTAAATGAT
445617 GAATGATT
1 GAATGATT
445625 CAGAGACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (16 bp):
GAATGATTTAAATGAT
Found at i:447702 original size:24 final size:23
Alignment explanation
Indices: 447670--447715 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
447660 AGCAGTTGCT
*
447670 TCTCTATCATCATACTC-ATTATCC
1 TCTCAATCA-CAT-CTCTATTATCC
447694 TCTCAATCACATCTCTATTATC
1 TCTCAATCACATCTCTATTATC
447716 ATATTTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (23 bp):
TCTCAATCACATCTCTATTATCC
Found at i:450192 original size:32 final size:31
Alignment explanation
Indices: 450156--450232 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 31
450146 TCATTCCCAC
450156 AAAGAATGCAACCAGCATCCA-TAACCAGACTA
1 AAAGAAT-CAACCAGCAT-CAGTAACCAGACTA
450188 AAAGAAATCAACCAGCATCAGTAACCAGACTA
1 AAAG-AATCAACCAGCATCAGTAACCAGACTA
450220 AAAGAAATCAACC
1 AAAG-AATCAACC
450233 TATCCCTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
31 2 0.05
32 38 0.88
33 3 0.07
ACGTcount: A:0.51, C:0.26, G:0.12, T:0.12
Consensus pattern (31 bp):
AAAGAATCAACCAGCATCAGTAACCAGACTA
Found at i:450702 original size:31 final size:31
Alignment explanation
Indices: 450642--450707 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
450632 TTAATGCAAT
*
450642 TATATACATAAAATTTTAATTGTGGTTTAAA
1 TATATACATAAAATTTTAATTGTGATTTAAA
* *
450673 TATATACATAAAATTTTGA-TGTTGATTTAAC
1 TATATACATAAAATTTTAATTG-TGATTTAAA
450704 TATA
1 TATA
450708 CTCATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (31 bp):
TATATACATAAAATTTTAATTGTGATTTAAA
Found at i:456529 original size:12 final size:13
Alignment explanation
Indices: 456507--456535 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
456497 CTTAGTTGCG
456507 TAAAGTTAAAATT
1 TAAAGTTAAAATT
456520 TAAA-TTAAAATT
1 TAAAGTTAAAATT
456532 TAAA
1 TAAA
456536 ACGTTCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
TAAAGTTAAAATT
Found at i:456762 original size:8 final size:8
Alignment explanation
Indices: 456749--456810 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
456739 AAAATATGAT
456749 AAAAATAA
1 AAAAATAA
456757 AAAAATAA
1 AAAAATAA
*
456765 AAACAT-A
1 AAAAATAA
456772 AAAAATGAA
1 AAAAAT-AA
* *
456781 GAAAATGA
1 AAAAATAA
*
456789 AGAAATAA
1 AAAAATAA
456797 TAATAAATAA
1 -AA-AAATAA
456807 AAAA
1 AAAA
456811 GTTAAATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
7 6 0.14
8 21 0.50
9 9 0.21
10 6 0.14
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (8 bp):
AAAAATAA
Found at i:457938 original size:4 final size:4
Alignment explanation
Indices: 457920--457971 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
457910 CTAAAACGAG
*
457920 ATAA A-AA AT-A ATAA ATAA ATAA ATAA AT-A ACAA AT-A AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
457963 ATAA ATAA A
1 ATAA ATAA A
457972 ATATTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 14 0.33
4 28 0.67
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:457974 original size:26 final size:26
Alignment explanation
Indices: 457920--457971 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
457910 CTAAAACGAG
457920 ATAAAAAATAATAAATAAATAAATAA
1 ATAAAAAATAATAAATAAATAAATAA
*
457946 ATAACAAATAAT-AATAAATAAATAA
1 ATAAAAAATAATAAATAAATAAATAA
457971 A
1 A
457972 ATATTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (26 bp):
ATAAAAAATAATAAATAAATAAATAA
Found at i:458066 original size:15 final size:15
Alignment explanation
Indices: 458046--458094 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
458036 ATTTTCAAAA
458046 ATATTTTAAAACTAT
1 ATATTTTAAAACTAT
*
458061 ATATTTTCAAAC-AT
1 ATATTTTAAAACTAT
* *
458075 GTTTTTTTAAAACTAT
1 -ATATTTTAAAACTAT
458091 ATAT
1 ATAT
458095 ATATAATTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATTTTAAAACTAT
Found at i:458092 original size:102 final size:102
Alignment explanation
Indices: 457975--458168 Score: 243
Period size: 102 Copynumber: 1.9 Consensus size: 102
457965 AAATAAAATA
* *
457975 TTTTTTAAAATTATAT-TTTAT-ATATGATTTAAAAATGATTTTCAAAACCATATA-ATATAATA
1 TTTTTTAAAACTATATATATATAAT-TGATTTAAAAATG-TTTTCAAAACCATATATATATAAT-
458037 TTTTCAAAAATATTTT-AAAACTATATATTTTCAAACATGT
63 TTTT-AAAAATATTTTAAAAACTATATATTTTCAAACATGT
* * ** *
458077 TTTTTTAAAACTATATATATATAATTGTTTTCAAAATGTTTTTTAAACTATATATTATATAATTT
1 TTTTTTAAAACTATATATATATAATTGATTTAAAAATGTTTTCAAAACCATATA-TATATAATTT
*
458142 TTAAAAATGTTTTAAAAACTATATATT
65 TTAAAAATATTTTAAAAACTATATATT
458169 ATATAATTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
102 38 0.48
103 32 0.41
104 9 0.11
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (102 bp):
TTTTTTAAAACTATATATATATAATTGATTTAAAAATGTTTTCAAAACCATATATATATAATTTT
TAAAAATATTTTAAAAACTATATATTTTCAAACATGT
Found at i:458136 original size:38 final size:37
Alignment explanation
Indices: 458064--458178 Score: 153
Period size: 36 Copynumber: 3.1 Consensus size: 37
458054 AAACTATATA
458064 TTTTCAAACATGTTTTTTTAAAACTATATA-TATATAATT
1 TTTTCAAA-ATG-TTTTTT-AAACTATATATTATATAATT
458103 GTTTTCAAAATGTTTTTTAAACTATATATTATATAA-T
1 -TTTTCAAAATGTTTTTTAAACTATATATTATATAATT
* **
458140 TTTTAAAAATGTTTTAAAAACTATATATTATATAATT
1 TTTTCAAAATGTTTTTTAAACTATATATTATATAATT
458177 TT
1 TT
458179 CAAAAAAATG
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
36 32 0.46
37 14 0.20
38 13 0.19
39 3 0.04
40 8 0.11
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.51
Consensus pattern (37 bp):
TTTTCAAAATGTTTTTTAAACTATATATTATATAATT
Found at i:458186 original size:38 final size:36
Alignment explanation
Indices: 458078--458213 Score: 166
Period size: 36 Copynumber: 3.6 Consensus size: 36
458068 CAAACATGTT
* *
458078 TTTTTAAAACTATATA-TATATAATTGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATAA-T-TTTTAAAAATG
**
458115 TTTTTTAAACTATATATTATATAATTTTTAAAAATG
1 TTTTAAAAACTATATATTATATAATTTTTAAAAATG
*
458151 TTTTAAAAACTATATATTATATAATTTTCAAAAAAATG
1 TTTTAAAAACTATATATTATATAATTTT--TAAAAATG
458189 TTTTAAAAACTATAATATATATATA
1 TTTTAAAAACTAT-ATAT-TATATA
458214 TATATATATA
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
36 36 0.40
37 16 0.18
38 27 0.30
39 4 0.04
40 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATAATTTTTAAAAATG
Found at i:458210 original size:2 final size:2
Alignment explanation
Indices: 458199--458246 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
458189 TTTTAAAAAC
458199 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
458240 TA TA TA T
1 TA TA TA T
458247 GTATGTATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:458251 original size:4 final size:4
Alignment explanation
Indices: 458244--458284 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
458234 TATATATATA
458244 TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
458285 AAAAAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:458273 original size:18 final size:18
Alignment explanation
Indices: 458250--458284 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
458240 TATATATGTA
458250 TGTATGTATGTATGTATG
1 TGTATGTATGTATGTATG
458268 TGTATGTATGTATGTAT
1 TGTATGTATGTATGTAT
458285 AAAAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (18 bp):
TGTATGTATGTATGTATG
Found at i:458968 original size:84 final size:84
Alignment explanation
Indices: 458888--459845 Score: 733
Period size: 84 Copynumber: 11.6 Consensus size: 84
458878 TTGAACTCGG
* * * * * * * *
458888 AGGTCTTCGGTTGGCAGATATCCCTTCTCGACTGAAGCTATACTGCAAATAATGTGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
*
458953 TGAGCGTAGTCGAACTCGA
66 TGAGCGTAGTCGAACTCAA
* ** * * * * * * *
458972 AGATCTTTGG-TAACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGACG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGA-G
* * *
459036 CTGAGTGTAATCGAACTC-G
65 CTGAGCGTAGTCGAACTCAA
* * * * * * * * *
459055 AGGTC-CT--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGTAGATGATGTGTCGTT-GAG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAG
*
459116 CTGAGCGTATTCGAACTCAA
65 CTGAGCGTAGTCGAACTCAA
* * * *
459136 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
*
459201 TGAGCGTAGTCGAATTCAA
66 TGAGCGTAGTCGAACTCAA
* * * * * *
459220 AGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAG
* **
459284 CTGAGTGT-GATCGAACTTGA
65 CTGAGCGTAG-TCGAACTCAA
* * * * * * *
459304 GGGTC--T--TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTT-GAG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAG
*
459364 CTGAGCGTAGTAGAACTCAA
65 CTGAGCGTAGTCGAACTCAA
* * * * *
459384 AAGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
* * **
459449 AGAGCGTAGTCAAACTTGA
66 TGAGCGTAGTCGAACTCAA
* * * ** * * *
459468 AGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAA
1 AGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGA
* * * **
459532 GCTGAGTGTAATAGAACT-TG
64 GCTGAGCGTAGTCGAACTCAA
* * * * * *
459552 AGTGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATACCTTAGAG
1 AG-GTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
* *
459613 CTGAGCGTAGTCAAACTCGA
65 CTGAGCGTAGTCGAACTCAA
* * * * * * * * * *
459633 AGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATTTCCCTCGAAGA
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
* * *
459697 TGAGTGTAATCGAACTTAA
66 TGAGCGTAGTCGAACTCAA
* * * * *
459716 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTTGGAGC
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
459777 TGAGCGTAGTCGAACTCAA
66 TGAGCGTAGTCGAACTCAA
* *
459796 AGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1 AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
459846 TTGTCTTTTA
Statistics
Matches: 667, Mismatches: 177, Indels: 61
0.74 0.20 0.07
Matches are distributed among these distances:
80 117 0.18
81 118 0.18
82 9 0.01
83 179 0.27
84 219 0.33
85 25 0.04
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGC
TGAGCGTAGTCGAACTCAA
Found at i:459092 original size:164 final size:163
Alignment explanation
Indices: 458813--459845 Score: 968
Period size: 164 Copynumber: 6.2 Consensus size: 163
458803 ACGATTTTAT
* * * * * *
458813 TGACAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATTTGGTTTG-CCTCTGAGTTGAATGTA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAA--TGATGTGCCCTC-GAGCTGAGTGTA
* ** * * * *
458877 ATTGAACTCGGAGGTCTTCGGTTGGCAGATATCCCTTCTCGACTGAAGCTATACTGCAAATAATG
63 ATCGAACTCAAAGGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATA
*
458942 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGG
124 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
458982 TAACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGACGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGA-GCTGAGTGTAAT
* * * * *
459047 CGAACTC-GAGGTCCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGTAGATGATGTGTCG
65 CGAACTCAAAGGT-CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATG-CC
* * *
459111 TT-GAGCTGAGCGTATTCGAACTCAAAGGTCTTTTGT
128 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
* * * * * * * * * * * *
459147 TGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAGCTGAGTGTAATC
* * * * * * * *
459212 GAATTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCC
66 GAACTCAAAGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATG-C
* * * * *
459277 CTCGAAGCTGAGTGT-GATCGAACTTGAGGGTCTTT-G
127 CTTGGAGCTGAGCGTAG-TCGAACTCGAAGGTCTTTGG
* * * * * ** * * * * * *
459313 -G-CAGATATCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGCGTAGTA
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAGCTGAGTGTAATC
* * * * * * * *
459376 GAACTCAAAAGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGC
66 GAACTCAAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGC
* * *
459441 CTTGGAGCAGAGCGTAGTCAAACTTGAAGGTCTTTTGG
127 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
*
459479 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG-AGCTGAGTGTAAT
* ** * *
459544 AGAACT-TGAGTGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATACCT
65 CGAACTCAAAG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCT
* *
459608 TAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
129 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * *
459643 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAAT-TTCCCTCGAAGATGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG-AGCTGAGTGTAAT
* * *
459707 CGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTT
65 CGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTT
* *
459772 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGT
130 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
459806 TGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
459846 TTGTCTTTTA
Statistics
Matches: 721, Mismatches: 120, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
163 145 0.20
164 218 0.30
165 161 0.22
166 4 0.01
167 55 0.08
168 84 0.12
169 54 0.07
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (163 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAGCTGAGTGTAATC
GAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGCCTTG
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:459327 original size:248 final size:248
Alignment explanation
Indices: 458888--459670 Score: 1097
Period size: 248 Copynumber: 3.2 Consensus size: 248
458878 TTGAACTCGG
** * * * * * * * *
458888 AGGTCTTCGGTTGGCAGATATCCCTTCTCGACTGAAGCTATACTGCAAATAATGTGCCTTGGAGC
1 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
* * * *
458953 TGAGCGTAGTCGAACTCGAAGATCTTTGGTAACATATAACCCTTCTAGCCTTGAGTTATGCTGTA
66 TGAGCGTAGTCGAATTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
* *
459018 AATGATGTGCCCTCGACGCTGAGTGTAATCGAACTCGA-GGTCCTTTGGCAGATAGCCCTTCTCG
131 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGT-CTTTGGCAGATAGCCCTTCTCG
* * *
459082 ACTTAAGCTATACTGTAGATGATGTGTCGTTGAGCTGAGCGTATTCGAACTCAA
195 ACTTAAGCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAA
459136 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
1 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
*
459201 TGAGCGTAGTCGAATTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
66 TGAGCGTAGTCGAATTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
* * *
459266 AATGATATGCCCTCGAAGCTGAGTGTGATCGAACTTGAGGGTCTTTGGCAGATATCCCTTCTCGA
131 AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGA
* * *
459331 CTTAAGCTATGCTACAAATGATGTGTCGTTGAGCTGAGCGTAGTAGAACTCAA
196 CTTAAGCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAA
* * *
459384 AAGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGC
1 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
* * *
459449 AGAGCGTAGTCAAACTT-GAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTA
66 TGAGCGTAGTCGAA-TTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* *
459513 TAAATGATGTGCCCTCGAAGCTGAGTGTAATAGAACTTGAGTGTCTTTGGCAGATAGCCCTTCTC
129 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTC
* * * * * *
459578 GACTTAAGCTATTCTGCAAATGATAT-ACCTTAGAGCTGAGCGTAGTCAAACTCGA
194 GACTTAAGCTATACTGCAAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAA
* * * * *
459633 AGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
1 AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
459671 ATGCTGTAAA
Statistics
Matches: 479, Mismatches: 52, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
248 329 0.69
249 150 0.31
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
AGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGC
TGAGCGTAGTCGAATTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
AATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGA
CTTAAGCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAA
Found at i:465123 original size:14 final size:13
Alignment explanation
Indices: 465104--465158 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
465094 AAAAAATATG
465104 ATAAAAATAAAAA
1 ATAAAAATAAAAA
465117 CATAAAACATAAAAA
1 -ATAAAA-ATAAAAA
* *
465132 ATGAAGA-AAAAA
1 ATAAAAATAAAAA
465144 ATAATAAATAAAAA
1 ATAA-AAATAAAAA
465158 A
1 A
465159 GTTAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 16 0.47
15 7 0.21
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.15
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:465143 original size:33 final size:33
Alignment explanation
Indices: 465093--465156 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
465083 GTGAAGCTAG
*
465093 TAAAAAATATG-ATAAAAATAAAAACATAAAACA
1 TAAAAAATAAGAATAAAAATAAAAA-ATAAAACA
*
465126 TAAAAAATGAAGAA-AAAAATAATAAATAAAA
1 TAAAAAAT-AAGAATAAAAATAAAAAATAAAA
465157 AAGTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 14 0.52
34 12 0.44
35 1 0.04
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (33 bp):
TAAAAAATAAGAATAAAAATAAAAAATAAAACA
Found at i:466387 original size:37 final size:36
Alignment explanation
Indices: 466343--466619 Score: 376
Period size: 37 Copynumber: 7.5 Consensus size: 36
466333 ATTTTAAAAC
* ** *
466343 TATATATATTTTCAAACATGTTTTTTTTAAACTATATAA
1 TATATA-ATTTTCAAAAATG--TTTTAAAAACTATATAT
*
466382 TATATAATTGTTTTC-AAAATGTTTTTAAAACTATATAT
1 TATATAA---TTTTCAAAAATGTTTTAAAAACTATATAT
* *
466420 TATATAATTTTTAAAATTGTTTTCAAAAACTATATAT
1 TATATAATTTTCAAAAATGTTTT-AAAAACTATATAT
*
466457 TATATAATTTTCTAAAATGTTTTAAAAACTATATAT
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATAT
466493 TATATAATTTTCAAAAAATGTTTTAAAAACTATATAT
1 TATATAATTTTC-AAAAATGTTTTAAAAACTATATAT
*
466530 TATATAATTTTCTAAAATGTTTTAAAAACTATATAT
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATAT
466566 TATATAATTTTCAAAAAATGTTTTAAAAACTATATAT
1 TATATAATTTTC-AAAAATGTTTTAAAAACTATATAT
*
466603 TATATAATTTCCAAAAA
1 TATATAATTTTCAAAAA
466620 CTATATATAT
Statistics
Matches: 218, Mismatches: 13, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
35 4 0.02
36 74 0.34
37 101 0.46
38 23 0.11
39 6 0.03
40 5 0.02
41 5 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATAATTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:466491 original size:36 final size:36
Alignment explanation
Indices: 466371--466612 Score: 378
Period size: 37 Copynumber: 6.6 Consensus size: 36
466361 TGTTTTTTTT
* * *
466371 AAACTATATAATATATAATTGTTTTCAAAATGTTTTTA
1 AAACTATATATTATATAATT-TTCT-AAAATGTTTTAA
466409 AAACTATATATTATATAATTTT-TAAAATTGTTTTCAA
1 AAACTATATATTATATAATTTTCTAAAA-TGTTTT-AA
466446 AAACTATATATTATATAATTTTCTAAAATGTTTTAA
1 AAACTATATATTATATAATTTTCTAAAATGTTTTAA
*
466482 AAACTATATATTATATAATTTTCAAAAAATGTTTTAA
1 AAACTATATATTATATAATTTTC-TAAAATGTTTTAA
466519 AAACTATATATTATATAATTTTCTAAAATGTTTTAA
1 AAACTATATATTATATAATTTTCTAAAATGTTTTAA
*
466555 AAACTATATATTATATAATTTTCAAAAAATGTTTTAA
1 AAACTATATATTATATAATTTTC-TAAAATGTTTTAA
466592 AAACTATATATTATATAATTT
1 AAACTATATATTATATAATTT
466613 CCAAAAACTA
Statistics
Matches: 194, Mismatches: 5, Indels: 11
0.92 0.02 0.05
Matches are distributed among these distances:
35 4 0.02
36 67 0.35
37 99 0.51
38 24 0.12
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (36 bp):
AAACTATATATTATATAATTTTCTAAAATGTTTTAA
Found at i:466626 original size:2 final size:2
Alignment explanation
Indices: 466621--466678 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
466611 TTCCAAAAAC
466621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
466663 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
466679 AGTATGGACG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:466644 original size:73 final size:73
Alignment explanation
Indices: 466371--466612 Score: 405
Period size: 73 Copynumber: 3.3 Consensus size: 73
466361 TGTTTTTTTT
* * * *
466371 AAACTATATAATATATAATTGTTTTCAAAATGTTTTTAAAACTATATATTATATAATTTT-TAAA
1 AAACTATATATTATATAATT-TTCT-AAAATGTTTTAAAAACTATATATTATATAATTTTCAAAA
*
466435 ATTGTTTTCAA
64 AATGTTTT-AA
466446 AAACTATATATTATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAA
1 AAACTATATATTATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAA
466511 TGTTTTAA
66 TGTTTTAA
466519 AAACTATATATTATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAA
1 AAACTATATATTATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAA
466584 TGTTTTAA
66 TGTTTTAA
466592 AAACTATATATTATATAATTT
1 AAACTATATATTATATAATTT
466613 CCAAAAACTA
Statistics
Matches: 161, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
73 129 0.80
74 13 0.08
75 19 0.12
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (73 bp):
AAACTATATATTATATAATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAAAA
TGTTTTAA
Found at i:466984 original size:2 final size:2
Alignment explanation
Indices: 466977--467002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
466967 TAATTCACAA
466977 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
467003 TAATAAAAAA
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:472944 original size:15 final size:15
Alignment explanation
Indices: 472924--472953 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
472914 AGTCACATTT
472924 AAGAGAAAAAAAACA
1 AAGAGAAAAAAAACA
*
472939 AAGAGAAAAGAAACA
1 AAGAGAAAAAAAACA
472954 GAAACCTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAGAAAAAAAACA
Found at i:481146 original size:58 final size:58
Alignment explanation
Indices: 481051--481162 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
481041 CCTCTCCATG
* * * * *
481051 TTCTGCAGCAAGATTTTTACATACGATCAATCCTCAACCATCGGATCTTCCTAGTTCA
1 TTCTCCAGCAAGACTTCTACATACAATCAATCCTCAACCACCGGATCTTCCTAGTTCA
* *
481109 TTCTCCAGCAAGACTTCTACATATAATCAATCTTCAACCACCGGATCTTCCTAG
1 TTCTCCAGCAAGACTTCTACATACAATCAATCCTCAACCACCGGATCTTCCTAG
481163 CTCAGAGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (58 bp):
TTCTCCAGCAAGACTTCTACATACAATCAATCCTCAACCACCGGATCTTCCTAGTTCA
Found at i:484567 original size:28 final size:28
Alignment explanation
Indices: 484535--484593 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
484525 ACATATTTAA
*
484535 AAGTAATCAATAAAACAAATATAGTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
* * *
484563 AAGTAAACATTAAAACATATATATTAGC
1 AAGTAAACAATAAAACAAATATAGTAGC
484591 AAG
1 AAG
484594 GAAAGATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (28 bp):
AAGTAAACAATAAAACAAATATAGTAGC
Found at i:484830 original size:78 final size:78
Alignment explanation
Indices: 484730--485064 Score: 425
Period size: 78 Copynumber: 4.5 Consensus size: 78
484720 CTTGAACGAA
* *
484730 AATATTTAGTCACTGTTTTTTTTTCATCAAACTAAATTTGCCACTACACAATCAAAATTCAAACA
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
484795 AGCCCATAAACTC
66 AGCCCATAAACTC
* * *
484808 AATATTTGGCCACTGTTTTTTTTTCATTAAACTAAGTTTGCCACTACACAATGAAAATTCAAACA
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
*
484873 AGCACATAAACTC
66 AGCCCATAAACTC
* *
484886 AATATTTAACCACTG-----CTTTCATCAAACTAAGTTTGCCACT--AC-A-C--AA-TCAAACA
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
* *
484939 AGTCCAGAAACTC
66 AGCCCATAAACTC
* *
484952 AATATTTAGCCACTG-TTTTTTTTCATGAAACTAAGTTTGCCACTACACAATCAAAATGCAAACA
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
*
485016 AGCCAATAAACTC
66 AGCCCATAAACTC
*
485029 AATATTTAGCCAC----TATTTTTCATCAAACTAAGTTTG
1 AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTG
485065 TCACAGTGTG
Statistics
Matches: 223, Mismatches: 23, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
66 31 0.14
67 2 0.01
70 24 0.11
71 2 0.01
72 2 0.01
73 24 0.11
74 22 0.10
76 2 0.01
77 29 0.13
78 85 0.38
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (78 bp):
AATATTTAGCCACTGTTTTTTTTTCATCAAACTAAGTTTGCCACTACACAATCAAAATTCAAACA
AGCCCATAAACTC
Found at i:485001 original size:70 final size:66
Alignment explanation
Indices: 484866--485006 Score: 194
Period size: 70 Copynumber: 2.1 Consensus size: 66
484856 CAATGAAAAT
*
484866 TCAAACAAGCACATAAACTCAATATTTAACCACTGCTTTCATCAAACTAAGTTTGCCACTACACA
1 TCAAACAAGCACAGAAACTCAATATTTAACCACTGCTTTCATCAAACTAAGTTTGCCACTACACA
484931 A
66 A
* * *
484932 TCAAACAAGTC-CAGAAACTCAATATTTAGCCACTGTTTTTTTTCATGAAACTAAGTTTGCCACT
1 TCAAACAAG-CACAGAAACTCAATATTTAACCACTG----CTTTCATCAAACTAAGTTTGCCACT
484996 ACACAA
61 ACACAA
485002 TCAAA
1 TCAAA
485007 ATGCAAACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
66 31 0.47
67 1 0.02
70 34 0.52
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (66 bp):
TCAAACAAGCACAGAAACTCAATATTTAACCACTGCTTTCATCAAACTAAGTTTGCCACTACACA
A
Found at i:485017 original size:143 final size:150
Alignment explanation
Indices: 484751--485064 Score: 455
Period size: 143 Copynumber: 2.1 Consensus size: 150
484741 ACTGTTTTTT
* * *
484751 TTTCATCAAACTAAATTTGCCACTACACAATCAAAATTCAAACAAGCCCATAAACTCAATATTTG
1 TTTCATCAAACTAAGTTTGCCACTA-ACAATC-AAATTCAAACAAGCCCAGAAACTCAATATTTA
* * *
484816 GCCACTGTTTTTTTTTCATTAAACTAAGTTTGCCACTACACAATGAAAATTCAAACAAG-CACAT
64 GCCACTGTTTTTTTTTCATGAAACTAAGTTTGCCACTACACAATCAAAATGCAAACAAGCCA-AT
484880 AAACTCAATATTTAACCACT-GC
128 AAACTCAATATTTAACCACTAGC
*
484902 TTTCATCAAACTAAGTTTGCCACT-AC-A-C-AA-TCAAACAAGTCCAGAAACTCAATATTTAGC
1 TTTCATCAAACTAAGTTTGCCACTAACAATCAAATTCAAACAAGCCCAGAAACTCAATATTTAGC
484962 CACTG-TTTTTTTTCATGAAACTAAGTTTGCCACTACACAATCAAAATGCAAACAAGCCAATAAA
66 CACTGTTTTTTTTTCATGAAACTAAGTTTGCCACTACACAATCAAAATGCAAACAAGCCAATAAA
* **
485026 CTCAATATTTAGCCACTATT
131 CTCAATATTTAACCACTAGC
485046 TTTCATCAAACTAAGTTTG
1 TTTCATCAAACTAAGTTTG
485065 TCACAGTGTG
Statistics
Matches: 151, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
143 69 0.46
144 53 0.35
145 2 0.01
147 1 0.01
148 1 0.01
149 2 0.01
151 23 0.15
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (150 bp):
TTTCATCAAACTAAGTTTGCCACTAACAATCAAATTCAAACAAGCCCAGAAACTCAATATTTAGC
CACTGTTTTTTTTTCATGAAACTAAGTTTGCCACTACACAATCAAAATGCAAACAAGCCAATAAA
CTCAATATTTAACCACTAGC
Found at i:488732 original size:77 final size:78
Alignment explanation
Indices: 488613--488902 Score: 341
Period size: 85 Copynumber: 3.6 Consensus size: 78
488603 CTGTCATACT
*
488613 GTGGCAAACTTAGTTTGATG-AAAAAAACAATGGCTAAATATTGAGTTTATGGGC-TTGTTTGAA
1 GTGGCAAACTTAGTTTGATGAAAAAAAACAGTGGCTAAATATTGAGTTTATGGGCTTTGTTTGAA
488676 TTTTGATTGTGTA
66 TTTTGATTGTGTA
***
488689 GTGGCAAACTTAGTTTGATGGGGAAAAACAGTGGCTAAATATTGAGTTTATGGGCTTGTTTGATT
1 GTGGCAAACTTAGTTTGATGAAAAAAAACAGTGGCTAAATATTGAGTTTATGGGC-----T--TT
488754 GTTTGAATTTTGATTGTGTA
59 GTTTGAATTTTGATTGTGTA
* * *
488774 GTCGAAAACTTAGTTTGATGAAAAAAAACAGTGGTTAAATATTGAGTTTATGGGCTTGTTTGATT
1 GTGGCAAACTTAGTTTGATGAAAAAAAACAGTGGCTAAATATTGAGTTTATGGGC-----T--TT
488839 GTTTGAATTTTGATTGTGTA
59 GTTTGAATTTTGATTGTGTA
* * *
488859 CTGGCAAACTTAGTTTGATAGAGAAAAAACAGTGGTTAAATATT
1 GTGGCAAACTTAGTTTGAT-GAAAAAAAACAGTGGCTAAATATT
488903 TTCGTTCAAG
Statistics
Matches: 191, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
76 20 0.10
77 31 0.16
85 117 0.61
86 23 0.12
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.38
Consensus pattern (78 bp):
GTGGCAAACTTAGTTTGATGAAAAAAAACAGTGGCTAAATATTGAGTTTATGGGCTTTGTTTGAA
TTTTGATTGTGTA
Found at i:488813 original size:85 final size:85
Alignment explanation
Indices: 488667--488902 Score: 400
Period size: 85 Copynumber: 2.8 Consensus size: 85
488657 GTTTATGGGC
* * *
488667 TTGTTTGAATTTTGATTGTGTAGTGGCAAACTTAGTTTGATGGGGAAAAACAGTGGCTAAATATT
1 TTGTTTGAATTTTGATTGTGTAGTGGCAAACTTAGTTTGATGAGAAAAAACAGTGGTTAAATATT
488732 GAGTTTATGGGCTTGTTTGA
66 GAGTTTATGGGCTTGTTTGA
* * *
488752 TTGTTTGAATTTTGATTGTGTAGTCGAAAACTTAGTTTGATGAAAAAAAACAGTGGTTAAATATT
1 TTGTTTGAATTTTGATTGTGTAGTGGCAAACTTAGTTTGATGAGAAAAAACAGTGGTTAAATATT
488817 GAGTTTATGGGCTTGTTTGA
66 GAGTTTATGGGCTTGTTTGA
*
488837 TTGTTTGAATTTTGATTGTGTACTGGCAAACTTAGTTTGATAGAGAAAAAACAGTGGTTAAATAT
1 TTGTTTGAATTTTGATTGTGTAGTGGCAAACTTAGTTTGAT-GAGAAAAAACAGTGGTTAAATAT
488902 T
65 T
488903 TTCGTTCAAG
Statistics
Matches: 140, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
85 117 0.84
86 23 0.16
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (85 bp):
TTGTTTGAATTTTGATTGTGTAGTGGCAAACTTAGTTTGATGAGAAAAAACAGTGGTTAAATATT
GAGTTTATGGGCTTGTTTGA
Found at i:489085 original size:21 final size:21
Alignment explanation
Indices: 489059--489113 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
489049 TGTTTTATTG
489059 TTTATTTG-CTACTATATTTGT
1 TTTA-TTGACTACTATATTTGT
*
489080 TTTATTGATTACTATATTTGT
1 TTTATTGACTACTATATTTGT
* *
489101 TTTGTTGATTACT
1 TTTATTGACTACT
489114 TTTAAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 3 0.10
21 28 0.90
ACGTcount: A:0.20, C:0.07, G:0.11, T:0.62
Consensus pattern (21 bp):
TTTATTGACTACTATATTTGT
Found at i:499887 original size:147 final size:147
Alignment explanation
Indices: 499620--499914 Score: 581
Period size: 147 Copynumber: 2.0 Consensus size: 147
499610 AATAAAACAG
499620 AAAGGTGCATAAAAGACCTAAAAATAGTTGAGGGAGTACAGAAGTAGTAGTCATCATGAAAAATC
1 AAAGGTGCATAAAAGACCTAAAAATAGTTGAGGGAGTACAGAAGTAGTAGTCATCATGAAAAATC
499685 TGACATAACCATACAATGGCAAGTTTAAAATAAGACTCAACAACCCGAATTAAGAAGTTATCGAA
66 TGACATAACCATACAATGGCAAGTTTAAAATAAGACTCAACAACCCGAATTAAGAAGTTATCGAA
499750 CTCATTTAAACACTTGA
131 CTCATTTAAACACTTGA
499767 AAAGGTGCATAAAAGACCTAAAAATAGTTGAGGGAGTACAGAAGTAGTAGTCATCATGAAAAATC
1 AAAGGTGCATAAAAGACCTAAAAATAGTTGAGGGAGTACAGAAGTAGTAGTCATCATGAAAAATC
*
499832 TGACATAACCATACAATGGCAAGTTTAAAATAAGACTCAACAACCCGAATTAAGAAGTTGTCGAA
66 TGACATAACCATACAATGGCAAGTTTAAAATAAGACTCAACAACCCGAATTAAGAAGTTATCGAA
499897 CTCATTTAAACACTTGA
131 CTCATTTAAACACTTGA
499914 A
1 A
499915 GCTTTTTTTT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (147 bp):
AAAGGTGCATAAAAGACCTAAAAATAGTTGAGGGAGTACAGAAGTAGTAGTCATCATGAAAAATC
TGACATAACCATACAATGGCAAGTTTAAAATAAGACTCAACAACCCGAATTAAGAAGTTATCGAA
CTCATTTAAACACTTGA
Found at i:500774 original size:22 final size:25
Alignment explanation
Indices: 500727--500780 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 25
500717 TATAATTATG
*
500727 AGAAAAAAATAATTTATATATATTT
1 AGAAATAAATAATTTATATATATTT
*
500752 ATAAATAAAT-ATTTAT-T-TATTT
1 AGAAATAAATAATTTATATATATTT
500774 AGAAATA
1 AGAAATA
500781 TCAGAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 11 0.42
23 1 0.04
24 6 0.23
25 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AGAAATAAATAATTTATATATATTT
Found at i:502997 original size:101 final size:99
Alignment explanation
Indices: 502762--503009 Score: 322
Period size: 101 Copynumber: 2.5 Consensus size: 99
502752 CCCTCTCCTT
* * *
502762 TTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGATGCTGATATATCTCTTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGA---TGATATATCTCCTTATG
* *
502827 TGATAGAATCACGCAAAATGTTGAACAAGTTCTTCTC
63 TGATAGAATCACGCAAAAGGTTAAACAAGTTCTTCTC
* * *
502864 TTCAGATGAATTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATGATCTATCTCCTTATGTGA
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGATATATCTCCTTATGTGA
**
502928 TAGCGTCGA-GCAAAAGGTTAAACAAGTTCTTCTCTTC
66 TAGAATC-ACGCAAAAGGTTAAACAAGTTC-T-TC-TC
502965 TTCAGATGAGTTCTT-TCATTATGAACTCCTTCTGGAAATGTTGAT
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGAT
503010 CTTCAAAAGA
Statistics
Matches: 129, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
98 40 0.31
99 2 0.02
100 13 0.10
101 48 0.37
102 26 0.20
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (99 bp):
TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATGATATATCTCCTTATGTGA
TAGAATCACGCAAAAGGTTAAACAAGTTCTTCTC
Found at i:503010 original size:98 final size:96
Alignment explanation
Indices: 502762--503011 Score: 281
Period size: 98 Copynumber: 2.5 Consensus size: 96
502752 CCCTCTCCTT
* * *
502762 TTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGATGCTGATATATCTCTTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGAT-C-----TATCTCCTTATG
* *
502827 TGATAGAATCACGCAAAATGTTGAACAAGTTCTTCTC
60 TGATAGAATCACGCAAAAGGTTAAACAAGTTCTTCTC
* *
502864 TTCAGATGAATTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGATGATCTATCTCCTTATGTGA
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATG-T--TGATCTATCTCCTTATGTGA
**
502928 TAGCGTCGA-GCAAAAGGTTAAACAAGTTCTTCTCTTC
63 TAGAATC-ACGCAAAAGGTTAAACAAGTTC-T-TC-TC
502965 TTCAGATGAGTTCTT-TCATTATGAACTCCTTCTGGAAATGTTGATCT
1 TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATCT
503012 TCAAAAGAGG
Statistics
Matches: 129, Mismatches: 11, Indels: 20
0.81 0.07 0.12
Matches are distributed among these distances:
98 42 0.33
99 2 0.02
100 14 0.11
101 39 0.30
102 27 0.21
103 1 0.01
104 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (96 bp):
TTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGATCTATCTCCTTATGTGATAG
AATCACGCAAAAGGTTAAACAAGTTCTTCTC
Found at i:503362 original size:112 final size:112
Alignment explanation
Indices: 503178--503607 Score: 510
Period size: 112 Copynumber: 3.8 Consensus size: 112
503168 ATAGAGTCAT
* *
503178 GCAAAAGGCTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
* * *
503243 TTATGAACTTTCT-TCGAAAAAGTTAATTCATCAAGTGATGAATTCAG
66 TTATGAACTTTCTCT-GGAAATGTTGATTCATCAAGTGATGAATTCAG
* * * * *
503290 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTGTCG
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
503355 TTATGAACTTTCTCTGGAAATGTTGA-TCTATCAAGTGATGAATT-AG
66 TTATGAACTTTCTCTGGAAATGTTGATTC-ATCAAGTGATGAATTCAG
* * * *
503401 AGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACCTCTTCTTCTTTCTTCAGATGAGTTCTTCT
1 -GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCT
* ** * * * * * * *
503466 TATTATGAACTCGCCCTGGCAATGCTGGTCCATCGAA-TGATAAATTCAA
64 CATTATGAACTTTCTCTGGAAATGTTGATTCATC-AAGTGATGAATTCAG
* *
503515 GCGAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCT
* *
503580 CATTATGAACTCT-TCTAGAAATGTTGAT
64 CATTATGAACTTTCTCTGGAAATGTTGAT
503608 CCATTGAATG
Statistics
Matches: 271, Mismatches: 38, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
111 4 0.01
112 134 0.49
113 61 0.23
114 72 0.27
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGTTGATTCATCAAGTGATGAATTCAG
Found at i:504053 original size:21 final size:22
Alignment explanation
Indices: 504014--504067 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
504004 GATAAAGCTT
*
504014 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
504036 TCATCTTT-AAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
504057 TCATCTTTGAA
1 TCATCTTTGAA
504068 GAGTTGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:506274 original size:114 final size:114
Alignment explanation
Indices: 506077--506621 Score: 849
Period size: 114 Copynumber: 4.8 Consensus size: 114
506067 CATGCAGTTC
* * * * * *
506077 ATCTTTCAACTTCAATGATTGGTTCTGAGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* * * * **
506142 CTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAATTC
66 CCTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCACATGG
* *
506191 ATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
506256 CCTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCACATGG
66 CCTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCACATGG
* *
506305 ATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* *
506370 CCTCCAGAAGATACTATTGGGCCTCCTTATTTCTACCATGAGCACATGG
66 CCTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCACATGG
* *
506419 ATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
* * *
506484 CTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACATGG
66 CCTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCACATGG
506533 ATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
*
506598 A-CTTCAGAAGATGCTATTGGGTCT
65 ACCTCCAGAAGATGCTATTGGGTCT
506622 TCTACTATGA
Statistics
Matches: 401, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
114 359 0.90
115 42 0.10
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CCTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACCATGAGCACATGG
Found at i:508731 original size:37 final size:36
Alignment explanation
Indices: 508682--508756 Score: 141
Period size: 37 Copynumber: 2.1 Consensus size: 36
508672 ATTTCTTGCT
508682 CTTCTGTTCGTACTTTATCAACCTTGTAACTTGAGG
1 CTTCTGTTCGTACTTTATCAACCTTGTAACTTGAGG
508718 CTTCTTGTTCGTACTTTATCAACCTTGTAACTTGAGG
1 CTTC-TGTTCGTACTTTATCAACCTTGTAACTTGAGG
508755 CT
1 CT
508757 CAATAAGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 4 0.11
37 34 0.89
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.43
Consensus pattern (36 bp):
CTTCTGTTCGTACTTTATCAACCTTGTAACTTGAGG
Found at i:513969 original size:22 final size:25
Alignment explanation
Indices: 513922--513975 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 25
513912 TATAATTATG
*
513922 AGAAAAAAATAATTTATATATATTT
1 AGAAATAAATAATTTATATATATTT
*
513947 ATAAATAAAT-ATTTAT-T-TATTT
1 AGAAATAAATAATTTATATATATTT
513969 AGAAATA
1 AGAAATA
513976 TCAGAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 11 0.42
23 1 0.04
24 6 0.23
25 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AGAAATAAATAATTTATATATATTT
Found at i:519158 original size:151 final size:155
Alignment explanation
Indices: 518922--519278 Score: 476
Period size: 151 Copynumber: 2.3 Consensus size: 155
518912 TATTTTAGTA
* * * *
518922 TATGAGCATGTGGTTCAAATTT-AGTAAAAGACGAACTTAAAATAAATGATGAATTGAAGACATA
1 TATGAGCATGTGGTTCAAATTTGAGTAAAAGACGAACTTAAAATAAAGGATAAATTGAAGAAAAA
* * * *
518986 AGGAAAATATGAAATATTAAGGGACTAAATTG-A-AAAAAATTTGTTAT-AAAAAGAGGAATTGA
66 AGGAAAATATGAAAAATTAAGGAACTAAATTGAAGAAAAAAATTGTTATCAAAAAGAGAAATTGA
*
519048 AAGTACATATGTATTCTACGATGGTT
131 AAGTACATATGTATTCTAAGATGG-T
* * *
519074 TATGAGTATGTGGTTCAAATTTGA-TAGAAG-CGGACTTAAAATAAAGGATAAATTGAAGAAAAA
1 TATGAGCATGTGGTTCAAATTTGAGTAAAAGACGAACTTAAAATAAAGGATAAATTGAAGAAAAA
519137 AGGAAAATATGAAAAATTAAGGAACTAAATTGAAAAGTAAAAAAATTGTTATCAAAAAGAGAAAT
66 AGGAAAATATGAAAAATTAAGGAACTAAATTG--AAG-AAAAAAATTGTTATCAAAAAGAGAAAT
519202 TGAAAGTACATATGTATTCTAAGATGGT
128 TGAAAGTACATATGTATTCTAAGATGGT
* * *
519230 TATGAGCATTTGGTTCAAATTTG-GTAAAAAAATGAACTTAAAATGAAAG
1 TATGAGCATGTGGTTCAAATTTGAGT-AAAAGACGAACTTAAAAT-AAAG
519279 AGGAATTGAA
Statistics
Matches: 176, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
151 58 0.33
152 26 0.15
153 1 0.01
154 1 0.01
156 36 0.20
157 40 0.23
158 10 0.06
159 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (155 bp):
TATGAGCATGTGGTTCAAATTTGAGTAAAAGACGAACTTAAAATAAAGGATAAATTGAAGAAAAA
AGGAAAATATGAAAAATTAAGGAACTAAATTGAAGAAAAAAATTGTTATCAAAAAGAGAAATTGA
AAGTACATATGTATTCTAAGATGGT
Found at i:524385 original size:30 final size:31
Alignment explanation
Indices: 524302--524382 Score: 74
Period size: 36 Copynumber: 2.5 Consensus size: 31
524292 TTGTATAATA
**
524302 TTACAAATTGTAAAATATTTATATATTTTCT
1 TTACAAATTAAAAAATATTTATATATTTTCT
*
524333 TTAAAAAATTAAATTCATAATATTTATATAATTTT-T
1 TT-ACAAATTAAA---A-AATATTTATAT-ATTTTCT
524369 TTACAAATTAAAAA
1 TTACAAATTAAAAA
524383 TATAAAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
31 3 0.08
32 8 0.20
35 10 0.25
36 14 0.35
37 5 0.12
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (31 bp):
TTACAAATTAAAAAATATTTATATATTTTCT
Found at i:525043 original size:21 final size:22
Alignment explanation
Indices: 525019--525067 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
525009 ATTTATCTTT
* *
525019 TAAATTTTGTAAA-AAAATCTA
1 TAAATTTTATAAAGAAAATATA
525040 TAAATTTTATAAAGAAAATATA
1 TAAATTTTATAAAGAAAATATA
525062 TAAATT
1 TAAATT
525068 AAAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (22 bp):
TAAATTTTATAAAGAAAATATA
Found at i:526499 original size:17 final size:17
Alignment explanation
Indices: 526477--526513 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
526467 GGTATCTTAC
*
526477 TTTTTAATTATTTTCTT
1 TTTTTAATTATTTTATT
526494 TTTTTAATTATTTTATT
1 TTTTTAATTATTTTATT
526511 TTT
1 TTT
526514 ATTTGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTAATTATTTTATT
Found at i:539732 original size:19 final size:20
Alignment explanation
Indices: 539704--539752 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
539694 AGTAATCTCG
*
539704 GTATCGATACCACCCCTG-A
1 GTATCGATACCAACCCTGTA
*
539723 GTATCAATACCAACCCTGTA
1 GTATCGATACCAACCCTGTA
539743 GTATCGATAC
1 GTATCGATAC
539753 TCTTATGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAACCCTGTA
Found at i:542510 original size:15 final size:15
Alignment explanation
Indices: 542484--542520 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
542474 CTTATGCCAC
542484 AACCAGTAATTATTGG
1 AACCA-TAATTATTGG
542500 AACCATAATTATTGG
1 AACCATAATTATTGG
542515 AACCAT
1 AACCAT
542521 CAATGTGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (15 bp):
AACCATAATTATTGG
Found at i:552227 original size:16 final size:16
Alignment explanation
Indices: 552208--552249 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
552198 AAAAAATGTT
552208 GAAAAAAAAGCAGTTC
1 GAAAAAAAAGCAGTTC
* *
552224 GAAAAAAAAACTGTTC
1 GAAAAAAAAGCAGTTC
552240 GAAAAAAAAG
1 GAAAAAAAAG
552250 ACATGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.17, T:0.12
Consensus pattern (16 bp):
GAAAAAAAAGCAGTTC
Found at i:558094 original size:10 final size:11
Alignment explanation
Indices: 558069--558093 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
558059 TTTAATTAGT
558069 AAAATAAATAA
1 AAAATAAATAA
558080 AAAATAAATAA
1 AAAATAAATAA
558091 AAA
1 AAA
558094 TTCCCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:567311 original size:2 final size:2
Alignment explanation
Indices: 567304--567346 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
567294 TAAAACAACC
567304 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
567346 A
1 A
567347 GTTTAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:573273 original size:17 final size:18
Alignment explanation
Indices: 573230--573270 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
573220 AAATTATATT
573230 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
573247 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
573265 ATTAAA
1 AGTAAA
573271 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:574447 original size:17 final size:18
Alignment explanation
Indices: 574425--574465 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
574415 AAAATATATT
574425 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
574442 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
574460 ATTAAA
1 AGTAAA
574466 TATAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:574488 original size:22 final size:22
Alignment explanation
Indices: 574447--574493 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
574437 AATAAAGTAA
574447 AATACTTAAATAAATTAAATAT
1 AATACTTAAATAAATTAAATAT
574469 AATA-TTAAA-AATATTAAAATAT
1 AATACTTAAATAA-ATT-AAATAT
574491 AAT
1 AAT
574494 TAAACAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 8 0.35
22 13 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AATACTTAAATAAATTAAATAT
Found at i:575805 original size:33 final size:32
Alignment explanation
Indices: 575743--575844 Score: 96
Period size: 39 Copynumber: 2.9 Consensus size: 32
575733 ATACAACCAT
*
575743 AATATCATACTTAAAAAAACCCGACCGACCCG
1 AATATCACACTTAAAAAAACCCGACCGACCCG
* *
575775 AATATCACACTTTAAAAAACCTGTCTCGACCCCGACCTG
1 AATATCACAC-TTAAAAAAAC---C-CGA--CCGACCCG
*
575814 AATATCAAACTTAAAAAAACCCGACCAGACC
1 AATATCACACTTAAAAAAACCCGACC-GACC
575845 TGAACCCGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
32 11 0.19
33 13 0.23
34 3 0.05
35 1 0.02
36 1 0.02
37 3 0.05
38 9 0.16
39 16 0.28
ACGTcount: A:0.42, C:0.31, G:0.09, T:0.18
Consensus pattern (32 bp):
AATATCACACTTAAAAAAACCCGACCGACCCG
Found at i:575848 original size:33 final size:32
Alignment explanation
Indices: 575743--575848 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 32
575733 ATACAACCAT
* *
575743 AATATCATACTTAAAAAAACCCGACCGACCCG
1 AATATCAAACTTAAAAAAACCCGACCGACCTG
* *
575775 AATATCACACTTTAAAAAACCTGTCTCGACCCCGACCTG
1 AATATCAAAC-TTAAAAAAAC---C-CGA--CCGACCTG
575814 AATATCAAACTTAAAAAAACCCGACCAGACCTG
1 AATATCAAACTTAAAAAAACCCGACC-GACCTG
575847 AA
1 AA
575849 CCCGATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
32 11 0.18
33 17 0.28
34 3 0.05
35 1 0.02
36 1 0.02
37 3 0.05
38 9 0.15
39 16 0.26
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (32 bp):
AATATCAAACTTAAAAAAACCCGACCGACCTG
Found at i:578342 original size:2 final size:2
Alignment explanation
Indices: 578335--578367 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
578325 TGAATGGTTA
578335 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
578368 ATTCAAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:581678 original size:40 final size:36
Alignment explanation
Indices: 581615--581701 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
581605 AAACAATCAC
*
581615 GTGTCCTGAAACATGAAAAAGGTAAAGGAAGTACTATAAT
1 GTGTCATGAAACATGAAAAAGGTAAA-GAA--AC-ATAAT
*** *
581655 GTGTCATGAAACATGACTTAGGTAAAGTAACATAAT
1 GTGTCATGAAACATGAAAAAGGTAAAGAAACATAAT
581691 GTGTCATGAAA
1 GTGTCATGAAA
581702 GATTGAGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 16 0.38
37 2 0.05
39 2 0.05
40 22 0.52
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
GTGTCATGAAACATGAAAAAGGTAAAGAAACATAAT
Found at i:585219 original size:20 final size:22
Alignment explanation
Indices: 585186--585229 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
585176 CACCCGCAGC
585186 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
* *
585206 ATCCATCTATCCATATATATAT
1 ATCCATCCACCCATATATATAT
585228 AT
1 AT
585230 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.36
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:585223 original size:2 final size:2
Alignment explanation
Indices: 585218--585277 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
585208 CCATCTATCC
*
585218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
585259 AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
585278 TAAAAAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:590648 original size:103 final size:102
Alignment explanation
Indices: 590424--590640 Score: 371
Period size: 103 Copynumber: 2.1 Consensus size: 102
590414 GTCGAGGGTT
*
590424 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAAACT
1 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACAAACT
** *
590489 TGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
590526 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACAAAC
*
590591 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
590629 TATGTGGTCCTT
1 TATGTGGTCCTT
590641 ATGGACATTA
Statistics
Matches: 108, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 13 0.12
103 95 0.88
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACAAACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:590690 original size:23 final size:23
Alignment explanation
Indices: 590656--590724 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
590646 CATTATTATA
590656 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
590679 CT-GCACTCCGGTACAATTCTACG
1 -TGGCACTACGGTGCAATTCTACG
* *
590702 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
590725 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:590772 original size:16 final size:17
Alignment explanation
Indices: 590753--590786 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
590743 GTGCACAACC
590753 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
590769 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
590786 T
1 T
590787 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:595759 original size:103 final size:103
Alignment explanation
Indices: 595534--595751 Score: 393
Period size: 103 Copynumber: 2.1 Consensus size: 103
595524 GTCGAGGGTC
595534 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
595599 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
*
595637 TATGTGGTCCTTCGGGACATATATGTATTCTTTTGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
595702 TTGATACC-TAGTATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTTAGCATATGTATATGATTCTTAAGGAATGA
595740 TATGTGGTCCTT
1 TATGTGGTCCTT
595752 ATGGACATTA
Statistics
Matches: 111, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 109 0.98
104 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:595805 original size:23 final size:23
Alignment explanation
Indices: 595768--595835 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
595758 ATTATTATAT
*
595768 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
595791 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
595814 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
595836 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:596028 original size:22 final size:20
Alignment explanation
Indices: 596001--596040 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
595991 AAATGCTATG
596001 TGATATGTATATGATGTGTGCA
1 TGATATG-ATAT-ATGTGTGCA
596023 TGATATGATATATGTGTG
1 TGATATGATATATGTGTG
596041 ATAGGGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.42
Consensus pattern (20 bp):
TGATATGATATATGTGTGCA
Found at i:598490 original size:64 final size:64
Alignment explanation
Indices: 598411--598550 Score: 183
Period size: 64 Copynumber: 2.2 Consensus size: 64
598401 CGGATCTTGG
* * *
598411 CAGGTCGGGTAAAATCGGGTACAGGTCA-ATTCAGGTTGATTTGACACCAGATTCAGATCGGGTT
1 CAGGTCAGGTAAAATC-AGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
* * * * *
598475 CAGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
1 CAGGTCAGGTAAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
*
598539 CAGGTCGGGTAA
1 CAGGTCAGGTAA
598551 TTTTCAGTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 7 0.11
64 58 0.89
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (64 bp):
CAGGTCAGGTAAAATCAGTACAGGTCATATTCAGGTTGATTTGACACCAGATCCAGATCGGGTT
Found at i:598879 original size:29 final size:32
Alignment explanation
Indices: 598823--598881 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
598813 AAAATAAGAG
* *
598823 AAAAATAAATATTCATGGATCAATTTTGAAAA
1 AAAAATAAATATTAATGGATCAAATTTGAAAA
598855 AAAAATAAAT-TTAAT-GA-CAAATTTGAA
1 AAAAATAAATATTAATGGATCAAATTTGAA
598882 GAATGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 2 0.08
31 4 0.16
32 10 0.40
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (32 bp):
AAAAATAAATATTAATGGATCAAATTTGAAAA
Found at i:599235 original size:17 final size:17
Alignment explanation
Indices: 599207--599274 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
599197 ATTGAAAAAA
599207 ATATAA-TATATATAAT
1 ATATAATTATATATAAT
* *
599223 ATAAAATTATATATAAA
1 ATATAATTATATATAAT
*
599240 ATATATTTATATTATAAACT
1 ATATAATTATA-TAT-AA-T
599260 ATATAATTAT-TATAA
1 ATATAATTATATATAA
599275 ACTATATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 5 0.12
17 20 0.48
18 6 0.14
19 2 0.05
20 9 0.21
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTATATATAAT
Found at i:599257 original size:18 final size:18
Alignment explanation
Indices: 599229--599384 Score: 77
Period size: 18 Copynumber: 8.3 Consensus size: 18
599219 TAATATAAAA
*
599229 TTATA-TATAAAATATAT
1 TTATATTATAAACTATAT
599246 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
*
599263 TAATTATTATAAACTATAT
1 TTA-TATTATAAACTATAT
* ** * *
599282 ATATAAATTAT-ATTTTTGT
1 -T-TATATTATAAACTATAT
*
599301 GCACTATATATATAAACTATGTAT
1 ---TTATAT-TATAAACTA--TAT
* *
599325 ATAAAATTATAAACTATAT
1 -TTATATTATAAACTATAT
599344 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
*
599361 TTATTATTATAAGCTATAT
1 TTA-TATTATAAACTATAT
*
599380 ATATA
1 TTATA
599385 AATTATGTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 25
0.70 0.14 0.17
Matches are distributed among these distances:
17 10 0.10
18 54 0.51
19 9 0.09
20 10 0.10
21 14 0.13
22 6 0.06
24 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TTATATTATAAACTATAT
Found at i:599347 original size:98 final size:98
Alignment explanation
Indices: 599234--599418 Score: 316
Period size: 98 Copynumber: 1.9 Consensus size: 98
599224 TAAAATTATA
*
599234 TATAAAATATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTTT
1 TATAAAATATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
*
599299 GTGCACTATATATATAAACTATGTATATAAAAT
66 GTGAACTATATATATAAACTATGTATATAAAAT
* * * *
599332 TATAAACTATATTTATATTATAAACTATATTATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAAATATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
599397 GTGAACTATATATATAAACTAT
66 GTGAACTATATATATAAACTAT
599419 ATATGTATAA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 81 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (98 bp):
TATAAAATATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTGAACTATATATATAAACTATGTATATAAAAT
Found at i:599410 original size:2 final size:2
Alignment explanation
Indices: 599403--599514 Score: 67
Period size: 2 Copynumber: 57.5 Consensus size: 2
599393 TTATGTGAAC
* * * * *
599403 TA TA TA TA TA AA CTA TA TA TG TA TA AA CTA TA TA -A TT TA TA TG
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
599446 T- TA TA -A TT TA TA T- TA -A TA TA GTA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
599485 -A CTA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
599515 TAAAAAACAC
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
1 7 0.08
2 72 0.86
3 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:599431 original size:28 final size:27
Alignment explanation
Indices: 599303--599436 Score: 87
Period size: 28 Copynumber: 4.8 Consensus size: 27
599293 ATTTTTGTGC
*
599303 ACTATATA-TATAAACTATGTATATAAA
1 ACTATATATTATAAACTATATATAT-AA
* * * **
599330 ATTATAAACTAT-ATTTATAT-TATAA
1 ACTATATATTATAAACTATATATATAA
599355 ACTATATTATTATTATAAGCTATATATATAA
1 ACTATA-TATTA-TA-AA-CTATATATATAA
* * *
599386 ATTATGT-TTATGTGAACTATATATATAA
1 ACTATATATTA--TAAACTATATATATAA
599414 ACTATATATGTATAAACTATATA
1 ACTATATAT-TATAAACTATATA
599437 ATTTATATGT
Statistics
Matches: 80, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
25 7 0.09
26 6 0.08
27 12 0.15
28 30 0.38
29 7 0.09
30 9 0.11
31 9 0.11
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (27 bp):
ACTATATATTATAAACTATATATATAA
Found at i:599434 original size:22 final size:23
Alignment explanation
Indices: 599407--599465 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
599397 GTGAACTATA
599407 TATATAAACTATATATG-TATAAAC
1 TATAT-AA-TATATATGTTATAAAC
* **
599431 TATATAATTTATATGTTATAATT
1 TATATAATATATATGTTATAAAC
599454 TATATTAATATA
1 TATA-TAATATA
599466 GTATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 7 0.24
23 11 0.38
24 11 0.38
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (23 bp):
TATATAATATATATGTTATAAAC
Found at i:599436 original size:15 final size:13
Alignment explanation
Indices: 599270--599436 Score: 77
Period size: 13 Copynumber: 12.0 Consensus size: 13
599260 ATATAATTAT
599270 TATAAACTATATA
1 TATAAACTATATA
* *
599283 TATAAATTATATTTT
1 TATAAACTATA--TA
* **
599298 TGTGCACTATATA
1 TATAAACTATATA
*
599311 TATAAACTATGTA
1 TATAAACTATATA
*
599324 TATAAAAT-TATA
1 TATAAACTATATA
* * *
599336 AACTATA-TTTATA
1 TA-TAAACTATATA
599349 TTATAAACTATATTA
1 -TATAAACTATA-TA
599364 TTATTATAAGCTATATA
1 -TA-TA-AA-CTATATA
* *
599381 TATAAATTATGTTTA
1 TATAAACTA--TATA
* *
599396 TGTGAACTATATA
1 TATAAACTATATA
599409 TATAAACTATATA
1 TATAAACTATATA
599422 TGTATAAACTATATA
1 --TATAAACTATATA
599437 ATTTATATGT
Statistics
Matches: 114, Mismatches: 26, Indels: 26
0.69 0.16 0.16
Matches are distributed among these distances:
12 5 0.04
13 53 0.46
14 6 0.05
15 37 0.32
16 4 0.04
17 4 0.04
18 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:599787 original size:42 final size:42
Alignment explanation
Indices: 599729--599838 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
599719 ACAATAGTTA
*
599729 ATATATGTAACTTATAGTATGTGTATACATGCAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
599771 ATATATGTAACTTATAGTATATGTATACATGTAATGTAAACT
1 ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
*
599813 ATATATGTAACTTATAGTACATGTAT
1 ATATATGTAACTTATAGTATATGTAT
599839 GTATAAACTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (42 bp):
ATATATGTAACTTATAGTATATGTATACATGCAATGTAAACT
Found at i:599797 original size:24 final size:22
Alignment explanation
Indices: 599770--599884 Score: 55
Period size: 24 Copynumber: 5.3 Consensus size: 22
599760 CAATGTAAAC
599770 TATATATGTAACTTATAGTATATG
1 TATATATGTAAC-TAT-GTATATG
* **
599794 TATACATGT-A--ATGTA-AAC
1 TATATATGTAACTATGTATATG
*
599812 TATATATGTAACTTATAGTACATG
1 TATATATGTAAC-TAT-GTATATG
* *
599836 TATGTAT-AAACTATGTATA-G
1 TATATATGTAACTATGTATATG
* * *
599856 TATATATATATA-TATATATATA
1 TATATATGTA-ACTATGTATATG
599878 TATATAT
1 TATATAT
599885 ATCATATAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 20
0.68 0.13 0.20
Matches are distributed among these distances:
18 9 0.13
19 4 0.06
20 9 0.13
21 12 0.17
22 13 0.19
23 7 0.10
24 15 0.22
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (22 bp):
TATATATGTAACTATGTATATG
Found at i:599863 original size:2 final size:2
Alignment explanation
Indices: 599851--599892 Score: 66
Period size: 2 Copynumber: 20.0 Consensus size: 2
599841 ATAAACTATG
599851 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
599893 AAGTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.89
3 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:600136 original size:55 final size:57
Alignment explanation
Indices: 600077--600212 Score: 170
Period size: 57 Copynumber: 2.4 Consensus size: 57
600067 TGTATACATG
* * *
600077 TAAACTATATATGTAACTTATAGTATATGTATGTATA-AA-CTATGTAT-AGCATATA
1 TAAACTATATATGTAACCTATAGTATATGTATATAAACAATCTATGTATAAG-ATATA
* * * * *
600132 TAAACTATATATATAACCTATAATATATTTATATAAACAATCTATTTATAAGTTATA
1 TAAACTATATATGTAACCTATAGTATATGTATATAAACAATCTATGTATAAGATATA
600189 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
600213 TTATAGGCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
55 31 0.46
56 2 0.03
57 33 0.49
58 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (57 bp):
TAAACTATATATGTAACCTATAGTATATGTATATAAACAATCTATGTATAAGATATA
Found at i:600295 original size:21 final size:21
Alignment explanation
Indices: 600243--600295 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
600233 TTGTGTACTA
* *
600243 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
600264 TATTGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
600285 TATAGTTTATA
1 TATAGTTTATA
600296 TTAATGCTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:600347 original size:88 final size:88
Alignment explanation
Indices: 600242--600421 Score: 231
Period size: 88 Copynumber: 2.0 Consensus size: 88
600232 TTTGTGTACT
* * *** *
600242 ATATAGTTTATACTTTATAACCTATTGTATATAATTTATAA-ACTATAGTTTATATTAATGCTAA
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACA-TATAGTTTATATTAATACTAA
600306 TTATCT-TA-ACTATAATTTATATTA
65 TT-T-TATAGACTATAATTTATATTA
* *
600330 ATATAGTATATAGTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATATTAAT
1 ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATACTAAT
*
600395 TTTATAGACTATATTTTATATTA
66 TTTATAGACTATAATTTATATTA
600418 ATAT
1 ATAT
600422 TAATTACAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
86 1 0.01
87 3 0.04
88 75 0.94
89 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.48
Consensus pattern (88 bp):
ATATAGTATATACTTTATAAACTATACAATATAATTTATAACATATAGTTTATATTAATACTAAT
TTTATAGACTATAATTTATATTA
Found at i:600383 original size:21 final size:21
Alignment explanation
Indices: 600316--600383 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
600306 TTATCTTAAC
600316 TATAATTTATATTA-ATATAGTA
1 TATAATTTATA--ACATATAGTA
* **
600338 TATAGTTTATAA-ACTATACAA
1 TATAATTTATAACA-TATAGTA
*
600359 TATAATTTATAACATATAGTT
1 TATAATTTATAACATATAGTA
600380 TATA
1 TATA
600384 TTAATATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.05
21 24 0.65
22 11 0.30
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (21 bp):
TATAATTTATAACATATAGTA
Found at i:600413 original size:31 final size:31
Alignment explanation
Indices: 600357--600426 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
600347 TAAACTATAC
600357 AATA-TAA-TTTATAACATATAGTTTATATT
1 AATATTAATTTTATAACATATAGTTTATATT
*
600386 AATATTAATTTTATAGAC-TATATTTTATATT
1 AATATTAATTTTATA-ACATATAGTTTATATT
600417 AATATTAATT
1 AATATTAATT
600427 ACAAATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 4 0.11
30 3 0.08
31 28 0.76
32 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (31 bp):
AATATTAATTTTATAACATATAGTTTATATT
Found at i:600436 original size:88 final size:88
Alignment explanation
Indices: 600270--600443 Score: 221
Period size: 88 Copynumber: 2.0 Consensus size: 88
600260 AACCTATTGT
*
600270 ATATAATTTATAAACTATAGTTTATATTAATGCTAATTATCTTAACTATAATTTATATTAATATA
1 ATATAATTTATAAACTATAGTTTATATTAATACTAATTATCTTAACTATAATTTATATTAATATA
* * **
600335 GTATATAGTTTATAAACTATACA
66 ATATACAAATTATAAACTATACA
* *
600358 ATATAATTTAT-AACATATAGTTTATATTAATATTAATT-T-TATAGACTATATTTTATATTAAT
1 ATATAATTTATAAAC-TATAGTTTATATTAATACTAATTATCT-TA-ACTATAATTTATATTAAT
600420 ATTAAT-TACAAATTATAAACTATA
63 A-TAATATACAAATTATAAACTATA
600444 TTATATTAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
86 1 0.01
87 6 0.08
88 65 0.87
89 3 0.04
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (88 bp):
ATATAATTTATAAACTATAGTTTATATTAATACTAATTATCTTAACTATAATTTATATTAATATA
ATATACAAATTATAAACTATACA
Found at i:600477 original size:12 final size:12
Alignment explanation
Indices: 600460--600502 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 12
600450 TAATATAAGT
600460 TAATATTAATTA
1 TAATATTAATTA
600472 TAATATATAATTA
1 TAATAT-TAATTA
600485 TTTTAATATTAATTA
1 ---TAATATTAATTA
600500 TAA
1 TAA
600503 ATATCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
15 6 0.22
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATTAATTA
Found at i:600477 original size:28 final size:28
Alignment explanation
Indices: 600440--600506 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
600430 AATTATAAAC
*
600440 TATATTATATTAATATAAGTTAATATTAAT
1 TATAATATA-TAAT-TAAGTTAATATTAAT
**
600470 TATAATATATAATTATTTTAATATTAAT
1 TATAATATATAATTAAGTTAATATTAAT
600498 TATAA-ATAT
1 TATAATATAT
600507 CATTTTCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 18 0.53
29 4 0.12
30 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TATAATATATAATTAAGTTAATATTAAT
Found at i:600497 original size:22 final size:23
Alignment explanation
Indices: 600441--600502 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
600431 ATTATAAACT
*
600441 ATATT-ATATTAATATA-AGTTA
1 ATATTAATATTAATATATAATTA
600462 ATATTAAT-TATAATATATAATT-
1 ATATTAATAT-TAATATATAATTA
*
600484 ATTTTAATATTAAT-TATAA
1 ATATTAATATTAATATATAA
600503 ATATCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 11 0.31
22 20 0.57
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTAATATTAATATATAATTA
Found at i:601964 original size:33 final size:33
Alignment explanation
Indices: 601924--601992 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
601914 TTAATATTTT
601924 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
1 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
601957 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
1 ATATTTATTATGTTTATTTAATAAAAGTTTCAA
601990 ATA
1 ATA
601993 GTTCATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (33 bp):
ATATTTATTATGTTTATTTAATAAAAGTTTCAA
Found at i:602256 original size:23 final size:23
Alignment explanation
Indices: 602206--602259 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
602196 CTTCATGCAG
* *
602206 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGATGAATTGATACAAT
* * *
602229 AATGCTTGATGAATTGGTACATT
1 GATGCTTGATGAATTGATACAAT
602252 GATGCTTG
1 GATGCTTG
602260 CCGGTTGCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
GATGCTTGATGAATTGATACAAT
Found at i:602862 original size:15 final size:15
Alignment explanation
Indices: 602800--602865 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
602790 AATATTCAGC
602800 TATTATCAATTTAAT
1 TATTATCAATTTAAT
*
602815 TATTAATCATGTTTAA-
1 TATT-ATCA-ATTTAAT
* *
602831 TATTAAC-ATTTAGT
1 TATTATCAATTTAAT
602845 TATTATCAATTTAAT
1 TATTATCAATTTAAT
602860 TATTAT
1 TATTAT
602866 TTTATTGCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 4 0.10
14 6 0.15
15 18 0.44
16 8 0.20
17 5 0.12
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (15 bp):
TATTATCAATTTAAT
Found at i:602981 original size:23 final size:24
Alignment explanation
Indices: 602954--603003 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
602944 TTGTTTTTTC
602954 TTTATATAAATTAAAATATA-TAA
1 TTTATATAAATTAAAATATATTAA
*
602977 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAAATATATTAA
603001 TTT
1 TTT
603004 TCCTTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAAATATATTAA
Found at i:603043 original size:25 final size:23
Alignment explanation
Indices: 603014--603076 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
603004 TCCTTTTGCA
603014 TTATT-AATAATGTTTTATCTAATT
1 TTATTAAATAAT-TTTTAT-TAATT
603038 TATATTTAAATAA-TTTTATTAATT
1 T-TA-TTAAATAATTTTTATTAATT
603062 TTATTAAATAATTTT
1 TTATTAAATAATTTT
603077 ATATAATAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 8 0.23
23 5 0.14
24 7 0.20
25 8 0.23
26 2 0.06
27 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTAAATAATTTTTATTAATT
Found at i:603281 original size:16 final size:16
Alignment explanation
Indices: 603260--603346 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
603250 CGGATTATTT
*
603260 ACAGGTCATGTTAAAA
1 ACAGGTCAAGTTAAAA
*
603276 ACAGGTCAGGTTAAAA
1 ACAGGTCAAGTTAAAA
*
603292 ACAAGTCAAGTTAAAA
1 ACAGGTCAAGTTAAAA
* *
603308 ACATGTCAAGTTGAAA
1 ACAGGTCAAGTTAAAA
* * *
603324 ACAAGTCAGGTTGAAA
1 ACAGGTCAAGTTAAAA
603340 ACAGGTC
1 ACAGGTC
603347 GGGTAATACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (16 bp):
ACAGGTCAAGTTAAAA
Found at i:619261 original size:22 final size:21
Alignment explanation
Indices: 619219--619258 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
619209 AAGTCTATTT
619219 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
619240 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
619259 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:626253 original size:24 final size:25
Alignment explanation
Indices: 626200--626250 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
626190 TATAAACATC
* *
626200 AAATACAATAAATAATATTATTTAT
1 AAATAAAATAAATAATAATATTTAT
*
626225 TAATAAAAT-AATAATAATATTT-T
1 AAATAAAATAAATAATAATATTTAT
626248 AAA
1 AAA
626251 ATATTATAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 3 0.14
24 12 0.55
25 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
AAATAAAATAAATAATAATATTTAT
Found at i:626392 original size:42 final size:45
Alignment explanation
Indices: 626346--626440 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
626336 CATATTTTAT
* *
626346 TAAAATAAAAT-TA-A-TATAAATTAGATTAATTATTTATTAAAA
1 TAAAATAAAATATATATTATAAACTAGATTAATTACTTATTAAAA
* *
626388 TAAAA-AAAATAATATATTATCAACTATATTAATTACTTATTAAAA
1 TAAAATAAAAT-ATATATTATAAACTAGATTAATTACTTATTAAAA
626433 TAATAATA
1 TAA-AATA
626441 TTATTAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
41 5 0.12
42 5 0.12
43 2 0.05
44 1 0.02
45 27 0.63
46 2 0.05
47 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (45 bp):
TAAAATAAAATATATATTATAAACTAGATTAATTACTTATTAAAA
Found at i:626446 original size:17 final size:17
Alignment explanation
Indices: 626393--626451 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
626383 TAAAATAAAA
*
626393 AAAATAAT-ATATTATC
1 AAAATAATAATATTATT
* *
626409 AACTATATTAATTACTTATT
1 AA-AATAATAA-TA-TTATT
626429 AAAATAATAATATTATT
1 AAAATAATAATATTATT
626446 AAAATA
1 AAAATA
626452 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.44
18 3 0.09
19 8 0.24
20 6 0.18
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATAATATTATT
Found at i:626455 original size:8 final size:8
Alignment explanation
Indices: 626425--626475 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
626415 ATTAATTACT
626425 TATTAAAA
1 TATTAAAA
* *
626433 TAATAATAT
1 TATTAA-AA
626442 TATTAAAA
1 TATTAAAA
626450 TATTAAAA
1 TATTAAAA
* *
626458 -AATATAA
1 TATTAAAA
626465 TATTAAAA
1 TATTAAAA
626473 TAT
1 TAT
626476 CAATATTATA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
7 5 0.15
8 22 0.67
9 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TATTAAAA
Found at i:626472 original size:23 final size:25
Alignment explanation
Indices: 626425--626475 Score: 79
Period size: 23 Copynumber: 2.1 Consensus size: 25
626415 ATTAATTACT
*
626425 TATTAAAATAATAATATTATTAAAA
1 TATTAAAATAATAATAATATTAAAA
626450 TATTAAAA-AAT-ATAATATTAAAA
1 TATTAAAATAATAATAATATTAAAA
626473 TAT
1 TAT
626476 CAATATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 14 0.56
24 3 0.12
25 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
TATTAAAATAATAATAATATTAAAA
Found at i:626480 original size:14 final size:13
Alignment explanation
Indices: 626425--626483 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
626415 ATTAATTACT
626425 TATTAAAATAATAA
1 TATTAAAAT-ATAA
*
626439 TATTATTAAA-ATAT
1 TATTA--AAATATAA
*
626453 TA-AAAAATATAA
1 TATTAAAATATAA
626465 TATTAAAATATCAA
1 TATTAAAATAT-AA
626479 TATTA
1 TATTA
626484 TAGTATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
11 3 0.08
12 5 0.14
13 8 0.22
14 17 0.47
16 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAAAATATAA
Found at i:638839 original size:34 final size:32
Alignment explanation
Indices: 638779--638850 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
638769 CCTTACAAAC
* * *
638779 TCCCTAGTTTTTTCAGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACAGGCTAAACTAGAACATT
*
638811 TCCCTAGCTTTTACACGAGCTAAGCTAGAACATT
1 TCCCTAGCTTTTACA-G-GCTAAACTAGAACATT
638845 TACCCT
1 T-CCCT
638851 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 13 0.39
33 1 0.03
34 15 0.45
35 4 0.12
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.33
Consensus pattern (32 bp):
TCCCTAGCTTTTACAGGCTAAACTAGAACATT
Found at i:639250 original size:19 final size:19
Alignment explanation
Indices: 639226--639265 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
639216 AAAACATGCA
639226 GGGGGAATC-AGTACCCCCT
1 GGGGGAATCTA-TACCCCCT
639245 GGGGGAATCTATACCCCCT
1 GGGGGAATCTATACCCCCT
639264 GG
1 GG
639266 TCATTCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (19 bp):
GGGGGAATCTATACCCCCT
Found at i:646484 original size:19 final size:20
Alignment explanation
Indices: 646430--646484 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
646420 CAAAATTAGT
*
646430 ACATTTGTTTATTAATTAACG
1 ACATTTGTAT-TTAATTAACG
* * *
646451 TC-TTTGTAATAAATTAAC-
1 ACATTTGTATTTAATTAACG
646469 ACATTTGTATTTAATT
1 ACATTTGTATTTAATT
646485 TCAATTTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
18 1 0.04
19 19 0.73
20 5 0.19
21 1 0.04
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
ACATTTGTATTTAATTAACG
Found at i:646856 original size:117 final size:119
Alignment explanation
Indices: 646685--646937 Score: 293
Period size: 118 Copynumber: 2.1 Consensus size: 119
646675 TTAATATGCA
* * ** *
646685 AAGTACT-ATAATAGTAAATAATTCTAAAAATAATATTTAAAATTATTATTTTAAAACTAAAG-G
1 AAGTACTAATAGT-GTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACT-AAGTG
* *
646748 ATTAAAATTGT-AAAATATCA-AAATTAAAAATC-TAATTCTAAATATCATGAAATCT
64 ATT-AAATTGTAAAAATAT-ATAAATTAAAAATCTTAATTCAAAATATCATGAAATAT
* * * * * *
646803 AGGTATTATTAGTGTAAATAATCCT-AAAATATTATTTAAAATTAAAATATTAAACCTTAGTGAT
1 AAGTACTAATAGTGTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACTAAGTGAT
**
646867 TAAATTGTAAAAATATATAAATTAAAGGTCTTAATTCAAAATATCATGAAATAT
66 TAAATTGTAAAAATATATAAATTAAAAATCTTAATTCAAAATATCATGAAATAT
646921 AAGTACTAATAGTGTAA
1 AAGTACTAATAGTGTAA
646938 TTTAACCCTA
Statistics
Matches: 112, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
116 10 0.09
117 48 0.43
118 51 0.46
119 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (119 bp):
AAGTACTAATAGTGTAAATAATCCTAAAAATAATATTTAAAATTAAAATATTAAAACTAAGTGAT
TAAATTGTAAAAATATATAAATTAAAAATCTTAATTCAAAATATCATGAAATAT
Found at i:647703 original size:5 final size:5
Alignment explanation
Indices: 647693--647718 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
647683 TGACTTAGAA
647693 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
647719 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:648430 original size:3 final size:3
Alignment explanation
Indices: 648422--648465 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
648412 ATATTACTTG
648422 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
648466 CGAGACGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:649794 original size:16 final size:15
Alignment explanation
Indices: 649762--649799 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
649752 AGTTTAAGAA
649762 AAAAATAAATTTTAT
1 AAAAATAAATTTTAT
649777 AAAAA-AAATTATTAAT
1 AAAAATAAATT-TT-AT
649793 AAAAATA
1 AAAAATA
649800 TATAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 7 0.35
16 7 0.35
17 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATAAATTTTAT
Found at i:650546 original size:25 final size:25
Alignment explanation
Indices: 650495--650543 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
650485 TTAATAAAAA
650495 AATATTTATCTAATGACAAATATTT
1 AATATTTATCTAATGACAAATATTT
*
650520 AATATATT-TCTAATGA-TAATATTT
1 AATAT-TTATCTAATGACAAATATTT
650544 TAAATAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 13 0.59
26 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTATCTAATGACAAATATTT
Found at i:652135 original size:13 final size:13
Alignment explanation
Indices: 652117--652199 Score: 68
Period size: 13 Copynumber: 6.8 Consensus size: 13
652107 TCGAGCTTAA
* *
652117 AATCGAGCTTTTT
1 AATCGAGCTTCTC
652130 AATCGAGCTTCTC
1 AATCGAGCTTCTC
*
652143 AATCGAGCTT-GC
1 AATCGAGCTTCTC
* *
652155 -ATCGAGTTTTTC
1 AATCGAGCTTCTC
**
652167 AATCGAGC-TCAA
1 AATCGAGCTTCTC
652179 AATCGAGCTT-T-
1 AATCGAGCTTCTC
652190 AATCGAGCTT
1 AATCGAGCTT
652200 GAGTCTCGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
11 18 0.32
12 11 0.19
13 28 0.49
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (13 bp):
AATCGAGCTTCTC
Found at i:652160 original size:11 final size:11
Alignment explanation
Indices: 652085--652222 Score: 87
Period size: 11 Copynumber: 11.6 Consensus size: 11
652075 TAACCCGTTT
652085 TCGAGCTTGAA
1 TCGAGCTTGAA
*
652096 ACGAGCTTGAA
1 TCGAGCTTGAA
*
652107 TCGAGCTTAAAA
1 TCGAGCTT-GAA
*
652119 TCGAGCTTTTTAA
1 TCGAGC--TTGAA
*
652132 TCGAGCTTCTCAA
1 TCGAGC-T-TGAA
*
652145 TCGAGCTTGCA
1 TCGAGCTTGAA
* *
652156 TCGAGTTTTTCAA
1 TCGAG--CTTGAA
**
652169 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
652181 TCGAGCTTTAA
1 TCGAGCTTGAA
*
652192 TCGAGCTTGAGTC
1 TCGAGCTTGA--A
652205 TCGAGCTTGAA
1 TCGAGCTTGAA
652216 TCGAGCT
1 TCGAGCT
652223 CTTAAATTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
11 43 0.43
12 20 0.20
13 35 0.35
14 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Done.