Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1822
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: 1013428
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
File 4 of 7
Found at i:430359 original size:53 final size:53
Alignment explanation
Indices: 430279--430385 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
430269 GCTGCAATTG
430279 ATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTA
1 ATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTA
430332 ATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTA
1 ATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTA
430385 A
1 A
430386 CAATAAACAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (53 bp):
ATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTA
Found at i:435360 original size:42 final size:42
Alignment explanation
Indices: 435305--435423 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
435295 TTCTTCTCTC
* *
435305 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
435347 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
435389 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
435424 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:435364 original size:12 final size:11
Alignment explanation
Indices: 435338--435413 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
435328 TCTATTATCT
*
435338 CTCCTGTCTCTC
1 CTCCTATCTC-C
435350 CTCCTATCATCC
1 CTCCTATC-TCC
435362 CTCCTATCT--
1 CTCCTATCTCC
*
435371 CTACTATCT--
1 CTCCTATCTCC
*
435380 CTCCTGTCTCTC
1 CTCCTATCTC-C
435392 CTCCTATCATCC
1 CTCCTATC-TCC
*
435404 CTCCTCTCTC
1 CTCCTATCTC
435414 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:435365 original size:24 final size:24
Alignment explanation
Indices: 435329--435414 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
435319 CCTCCTCTCT
* *
435329 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
435353 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
435374 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
435395 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
435415 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:435389 original size:18 final size:18
Alignment explanation
Indices: 435320--435390 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
435310 CCTGTCATCC
* *
435320 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
435338 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
435360 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
435380 CTCCTGTCTCT
1 CTCCTGTCTCT
435391 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:437683 original size:647 final size:645
Alignment explanation
Indices: 436395--437688 Score: 2428
Period size: 647 Copynumber: 2.0 Consensus size: 645
436385 CTTGAGATGG
*
436395 ATTTCTAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGACGCAGAAAAAAATAAC
1 ATTTCTAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAATAAC
* *
436460 AAAATGGAATAGATTAGAGATGGAGGATGGCGCCATAATCACAAGATTGATAAGACAAAAGGAAT
66 AAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGACAAAAGGAAT
436525 GATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAG
131 GATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAG
*
436590 AATCACACTCTCACACAAAATGTGTTTTCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTT
196 AAT-ACACTCTCACAAAAAATGTGTTTTCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTT
*
436655 ACAAGAGCTTATATATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATTATGCTA
260 ACAAGAGCTTATATATGCCCTCATAAGCCATAGATAACACAAACCCTAAGGGGCTTATTATGCTA
*
436720 ACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGT
325 ACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGAAAGT
*
436785 CACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTGAATCCATTGGAGCCCATAT
390 CACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATAT
*
436850 CTTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAGATTGGGTCTACTTTCAAAT
455 CTTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAAT
*
436915 AGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCC
520 AGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCATTATTGGTCC
436980 TTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
585 TTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
*
437041 ATTTCTAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAG
1 ATTTCTAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAG-AAAAAAATAA
*
437106 CAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAA
65 CAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGACAAAAGGAA
437171 TGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAA
130 TGATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAA
437236 GAAT-CACTCTCACAAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGT
195 GAATACACTCTCACAAAAAATGTGTTT--TCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGT
*
437300 TTACAAGAGCTTATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGC
258 TTACAAGAGCTTATATATGCCCTCATAAGCCATAGATAACACAAACCCTAAGGGGCTTATTATGC
437365 TAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGAAA
323 TAACAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGAAA
437430 GTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCAT
388 GTCACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCAT
437495 ATCTTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAA
453 ATCTTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAA
*
437560 ATAGGCCAGCAACCATCTTCTTTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCATTATTGGT
518 ATAGGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCATTATTGGT
437625 CCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
583 CCTTGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
437688 A
1 A
437689 CCCCTCCTTC
Statistics
Matches: 632, Mismatches: 13, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
645 21 0.03
646 53 0.08
647 558 0.88
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (645 bp):
ATTTCTAACAATAAACAGAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAATAAC
AAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGACAAAAGGAAT
GATCGCCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAG
AATACACTCTCACAAAAAATGTGTTTTCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTA
CAAGAGCTTATATATGCCCTCATAAGCCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAA
CAAGCCCAACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGAAAGTC
ACAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATC
TTCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATA
GGCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCATTATTGGTCCT
TGAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
Found at i:441980 original size:42 final size:42
Alignment explanation
Indices: 441925--442027 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
441915 TTCTTCTCTC
* * *
441925 CTCCTCCTGTCATCCCTCCGCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCGATCTCTACTATCTCTCCTGTCT
* *
441967 CTCCTCCTATCATCCTTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCGATCTCTACTATCTCTCCTGTCT
442009 CTCCTCCTATCATCCCTCC
1 CTCCTCCTATCATCCCTCC
442028 TCCTTCTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.10, C:0.47, G:0.04, T:0.40
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCGATCTCTACTATCTCTCCTGTCT
Found at i:446938 original size:16 final size:16
Alignment explanation
Indices: 446919--446949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
446909 TCTTTTTTTA
446919 TTTTTTTGTACTCTTT
1 TTTTTTTGTACTCTTT
*
446935 TTTTTTTGTATTCTT
1 TTTTTTTGTACTCTT
446950 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTTTGTACTCTTT
Found at i:448057 original size:106 final size:107
Alignment explanation
Indices: 447867--448079 Score: 322
Period size: 106 Copynumber: 2.0 Consensus size: 107
447857 ACCATCTTCT
* * *
447867 CTAGGTCTTCCTTTATCCTCTTTGCTTTTGCCCTCGTTATTGGTACTTGAAACCTTTCCAACGCC
1 CTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTACTGGAAACCTTTCCAACGCC
* * *
447932 TTCAGGTCTTTGTCCTCAATGGACTTTCCTT-GTTCTCATCA
66 TTCAGGCCTATGTCCTCAATGGACCTTCCTTGGTTCTCATCA
* *
447973 CTAGGTC-TCTCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTGGAAACCTTTCCAATGC
1 CTAGGTCTTC-CTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTACTGGAAACCTTTCCAACGC
*
448037 CTTCAGGCCTATGTCTTCAATGGACCTTCCTTGGTTCTCATCA
65 CTTCAGGCCTATGTCCTCAATGGACCTTCCTTGGTTCTCATCA
448080 ACCCCTCCTT
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
105 2 0.02
106 84 0.88
107 10 0.10
ACGTcount: A:0.14, C:0.31, G:0.15, T:0.40
Consensus pattern (107 bp):
CTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTACTGGAAACCTTTCCAACGCC
TTCAGGCCTATGTCCTCAATGGACCTTCCTTGGTTCTCATCA
Found at i:450710 original size:12 final size:11
Alignment explanation
Indices: 450682--450756 Score: 50
Period size: 12 Copynumber: 6.8 Consensus size: 11
450672 AAGAAAGAAA
450682 AGATAGGAGGG
1 AGATAGGAGGG
*
450693 ATGATATGAGGAG
1 A-GATAGGAGG-G
450706 AGATAGGA--G
1 AGATAGGAGGG
*
450715 AGATAGTA--G
1 AGATAGGAGGG
*
450724 AGATAGAAGGG
1 AGATAGGAGGG
*
450735 ATGATAGAAGGAG
1 A-GATAGGAGG-G
450748 AGATAGGAG
1 AGATAGGAG
450757 AGATAATAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 16 0.30
11 3 0.06
12 30 0.57
13 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.15
Consensus pattern (11 bp):
AGATAGGAGGG
Found at i:450715 original size:9 final size:9
Alignment explanation
Indices: 450701--450761 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
450691 GGATGATATG
450701 AGGAGAGAT
1 AGGAGAGAT
450710 AGGAGAGAT
1 AGGAGAGAT
*
450719 AGTAGAGAT
1 AGGAGAGAT
* *
450728 AGAAGGGAT
1 AGGAGAGAT
*
450737 --GATAGA-
1 AGGAGAGAT
450743 AGGAGAGAT
1 AGGAGAGAT
450752 AGGAGAGAT
1 AGGAGAGAT
450761 A
1 A
450762 ATAGAGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 3 0.07
8 5 0.12
9 34 0.81
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:450747 original size:42 final size:42
Alignment explanation
Indices: 450682--450789 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
450672 AAGAAAGAAA
*
450682 AGATAGGAGGGATGATATGAGGAGAGATAGGAGAGATAGTAG
1 AGATAGGAGGGATGATATGAGGAGAGATAGGAGAGATAATAG
*
450724 AGATAGAAGGGATGATA-GAAGGAGAGATAGGAGAGATAATAG
1 AGATAGGAGGGATGATATG-AGGAGAGATAGGAGAGATAATAG
* * *
450766 AGAGAGGAGGAATGATAAGAGGAG
1 AGATAGGAGGGATGATATGAGGAG
450790 GAGAGAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 1 0.02
42 57 0.97
43 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (42 bp):
AGATAGGAGGGATGATATGAGGAGAGATAGGAGAGATAATAG
Found at i:450765 original size:24 final size:23
Alignment explanation
Indices: 450682--450771 Score: 75
Period size: 24 Copynumber: 4.1 Consensus size: 23
450672 AAGAAAGAAA
* *
450682 AGATAGGAGGGATGATATGAGGAG
1 AGATAGGAGAGATAATA-GAGGAG
* *
450706 AGATAGGAGAGATAGTAGA-GAT
1 AGATAGGAGAGATAATAGAGGAG
*
450728 AGA-A-G-G-GATGATAGAAGGAG
1 AGATAGGAGAGATAATAG-AGGAG
450748 AGATAGGAGAGATAATAGA-GAG
1 AGATAGGAGAGATAATAGAGGAG
450770 AG
1 AG
450772 GAGGAATGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
18 6 0.12
19 2 0.04
20 6 0.12
21 2 0.04
22 11 0.21
23 4 0.08
24 21 0.40
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.14
Consensus pattern (23 bp):
AGATAGGAGAGATAATAGAGGAG
Found at i:450773 original size:18 final size:18
Alignment explanation
Indices: 450746--450795 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
450736 TGATAGAAGG
*
450746 AGAGATAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
*
450764 AGAGAGAGGAG-GAATGAT
1 AGAGAGAGGAGAG-ATAAT
450782 A-AGAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
450796 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.42, T:0.10
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:462630 original size:42 final size:42
Alignment explanation
Indices: 462575--462693 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
462565 TTCTTCTCTC
* *
462575 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
462617 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
462659 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
462694 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:462634 original size:12 final size:11
Alignment explanation
Indices: 462608--462683 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
462598 TCTATTATCT
*
462608 CTCCTGTCTCTC
1 CTCCTATCTC-C
462620 CTCCTATCATCC
1 CTCCTATC-TCC
462632 CTCCTATCT--
1 CTCCTATCTCC
*
462641 CTACTATCT--
1 CTCCTATCTCC
*
462650 CTCCTGTCTCTC
1 CTCCTATCTC-C
462662 CTCCTATCATCC
1 CTCCTATC-TCC
*
462674 CTCCTCTCTC
1 CTCCTATCTC
462684 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:462635 original size:24 final size:24
Alignment explanation
Indices: 462599--462684 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
462589 CCTCCTCTCT
* *
462599 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
462623 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
462644 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
462665 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
462685 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:462659 original size:18 final size:18
Alignment explanation
Indices: 462590--462660 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
462580 CCTGTCATCC
* *
462590 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
462608 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
462630 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
462650 CTCCTGTCTCT
1 CTCCTGTCTCT
462661 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:468016 original size:42 final size:42
Alignment explanation
Indices: 467961--468079 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
467951 TTCTTCTCTC
* * *
467961 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
*
468003 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* *
468045 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
468080 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
Found at i:468020 original size:12 final size:11
Alignment explanation
Indices: 467994--468069 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
467984 TCTATTATCT
*
467994 CTCCTGTCTCTC
1 CTCCTATCTC-C
468006 CTCCTATCATCC
1 CTCCTATC-TCC
468018 CTCCTATCT--
1 CTCCTATCTCC
*
468027 CTACTATCT--
1 CTCCTATCTCC
468036 CTCCTATCTCTC
1 CTCCTATCTC-C
468048 CTCCTATCATCC
1 CTCCTATC-TCC
*
468060 CTCCTCTCTC
1 CTCCTATCTC
468070 TTCTTTCTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
9 16 0.29
11 3 0.05
12 32 0.58
13 4 0.07
ACGTcount: A:0.11, C:0.49, G:0.01, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:468047 original size:9 final size:9
Alignment explanation
Indices: 467989--468049 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
467979 CTCTCTCTAT
467989 TATCTCTCC
1 TATCTCTCC
*
467998 TGTCTCTCC
1 TATCTCTCC
* *
468007 T-CCTAT-C
1 TATCTCTCC
*
468014 -ATCCCTCC
1 TATCTCTCC
*
468022 TATCTCTAC
1 TATCTCTCC
468031 TATCTCTCC
1 TATCTCTCC
468040 TATCTCTCC
1 TATCTCTCC
468049 T
1 T
468050 CCTATCATCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:472246 original size:38 final size:38
Alignment explanation
Indices: 472195--472283 Score: 169
Period size: 38 Copynumber: 2.3 Consensus size: 38
472185 ATCATACAGC
*
472195 TGCTGTTAGTTTTGAATCTTGAACGCATTTGATCTTGT
1 TGCTGTTAGTTTTGAATCTTGAACACATTTGATCTTGT
472233 TGCTGTTAGTTTTGAATCTTGAACACATTTGATCTTGT
1 TGCTGTTAGTTTTGAATCTTGAACACATTTGATCTTGT
472271 TGCTGTTAGTTTT
1 TGCTGTTAGTTTT
472284 TTTTCAAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.49
Consensus pattern (38 bp):
TGCTGTTAGTTTTGAATCTTGAACACATTTGATCTTGT
Found at i:481403 original size:42 final size:42
Alignment explanation
Indices: 481342--481422 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
481332 CTCACTCTTC
* * * *
481342 TATCTTCTTCTCTCCTCCTCCTGTTATCCCTCCTCTCTCTAT
1 TATCTTCTTCTATCCTCCTCCTATCATCCCTCCTATCTCTAT
481384 TATC-TCTTCTATCTCTCCTCCTATCATCCCTCCTATCTC
1 TATCTTCTTCTATC-CTCCTCCTATCATCCCTCCTATCTC
481423 CTCTTCTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 8 0.24
42 26 0.76
ACGTcount: A:0.10, C:0.43, G:0.01, T:0.46
Consensus pattern (42 bp):
TATCTTCTTCTATCCTCCTCCTATCATCCCTCCTATCTCTAT
Found at i:483763 original size:31 final size:31
Alignment explanation
Indices: 483687--483763 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
483677 GACTCATGGG
** *
483687 CTAACTTGTG-AG-CTTTGAAAAGGTTGTCA
1 CTAACTTGTGTAGACTTCAAAAAGGTTATCA
* * * *
483716 CCAACTCGTTTGGACTTCAAAAAGGTTATCA
1 CTAACTTGTGTAGACTTCAAAAAGGTTATCA
483747 CTAACTTGTGTAGACTT
1 CTAACTTGTGTAGACTT
483764 TGACTGGGGT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
29 7 0.20
30 1 0.03
31 27 0.77
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (31 bp):
CTAACTTGTGTAGACTTCAAAAAGGTTATCA
Found at i:483829 original size:65 final size:65
Alignment explanation
Indices: 483745--483929 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 65
483735 AAAAGGTTAT
* * ** * *
483745 CACTAACTTGTGTAGACTTTGACTGGGGTGTTACTAGCT-TGTGTGACTTTAAAAAGGTTTGGTT
1 CACTAACTTGTGTGGACTTTGAATGGGGTGCCACCAACTATGTG-GACTTTAAAAAGGTTTGGTT
483809 G
65 G
* * * *
483810 CACTGACTTGTGTGGACTTTTATTGGGGTGCCACCAACTCATGTGGACTTTGAAAAGGTTTGGTT
1 CACTAACTTGTGTGGACTTTGAATGGGGTGCCACCAACT-ATGTGGACTTTAAAAAGGTTTGGTT
483875 G
65 G
* * * *
483876 CTACCAAATTGTGTGAACTTTGAATGGGGTGGCACCAACT-TGCGTGGACTTTAA
1 C-ACTAACTTGTGTGGACTTTGAATGGGGTGCCACCAACTAT--GTGGACTTTAA
483930 CTATGGTGCC
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
65 32 0.33
66 21 0.21
67 45 0.46
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (65 bp):
CACTAACTTGTGTGGACTTTGAATGGGGTGCCACCAACTATGTGGACTTTAAAAAGGTTTGGTTG
Found at i:483857 original size:31 final size:31
Alignment explanation
Indices: 483815--484114 Score: 253
Period size: 31 Copynumber: 9.5 Consensus size: 31
483805 GGTTGCACTG
* * *
483815 ACTTGTGTGGACTTTTATTGGGGTGCCACCA
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
** * *
483846 ACTCATGTGGACTTTGAAAAGGTTTGGTTGCTACCA
1 ACTTGTGTGGACTTTGAATA-G---GG-TGCCACCA
* * * *
483882 AATTGTGTGAACTTTGAATGGGGTGGCACCA
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
* * *
483913 ACTTGCGTGGACTTT-AACTATGGTGCCAACA
1 ACTTGTGTGGACTTTGAA-TAGGGTGCCACCA
* * *
483944 ACTCGTGTGGACTTTGGAA-AGGTTACCACCA
1 ACTTGTGTGGACTTT-GAATAGGGTGCCACCA
* *
483975 ACTTGTGTGGACTTTGATTGGGGTGCCACCA
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
* * * * *
484006 ACTCGGGTAGACTTTGAAAAGGTTGCCACCA
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
* * *
484037 ACTTATGTGGACTTTGACTGGGGTGCCACCA
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
* *
484068 ACGTGTGTGGACTTTGAATAGGGTGCCACCG
1 ACTTGTGTGGACTTTGAATAGGGTGCCACCA
*
484099 ACTTGTGTGGGCTTTG
1 ACTTGTGTGGACTTTG
484115 GAAAAGGTTT
Statistics
Matches: 205, Mismatches: 55, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
30 4 0.02
31 172 0.84
32 3 0.01
33 2 0.01
35 3 0.01
36 21 0.10
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (31 bp):
ACTTGTGTGGACTTTGAATAGGGTGCCACCA
Found at i:484132 original size:37 final size:38
Alignment explanation
Indices: 484091--484198 Score: 118
Period size: 37 Copynumber: 2.9 Consensus size: 38
484081 TTGAATAGGG
* * *
484091 TGCCACCGACTTGTGTGG-GCTTTGGAAAA-GGTTTGGT
1 TGCCACCGACTTGTGTGGCACTTT-AAAAATGATTTGGT
* *
484128 TGCCATCGA-TT-TGTAGGCACTTTAAAAATGATTTTGT
1 TGCCACCGACTTGTGT-GGCACTTTAAAAATGATTTGGT
484165 TGCCACCGACTTGTGT-GCACTTTAAAAATGATTT
1 TGCCACCGACTTGTGTGGCACTTTAAAAATGATTT
484199 ACTTTGTGTG
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
35 3 0.05
36 8 0.13
37 44 0.73
38 2 0.03
39 3 0.05
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (38 bp):
TGCCACCGACTTGTGTGGCACTTTAAAAATGATTTGGT
Found at i:484426 original size:55 final size:55
Alignment explanation
Indices: 484355--484458 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
484345 TTGACACGGG
* * * *
484355 TGTCAATGTGCTAATTCAAGGCTAGCA-ACATTGGACTTAAAGACTTTGACAAAGA
1 TGTCAATATGCTAATTCAAGGCCAG-AGACACTAGACTTAAAGACTTTGACAAAGA
* *
484410 TGTCAATATGTTAATTCAAGGCCAGAGACACTAGACTTAAAGATTTTGA
1 TGTCAATATGCTAATTCAAGGCCAGAGACACTAGACTTAAAGACTTTGA
484459 AAAATTTTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 1 0.02
55 41 0.98
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (55 bp):
TGTCAATATGCTAATTCAAGGCCAGAGACACTAGACTTAAAGACTTTGACAAAGA
Found at i:484497 original size:26 final size:26
Alignment explanation
Indices: 484448--484533 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 26
484438 CACTAGACTT
*
484448 AAAGATTTTGA-AAA-ATT-TTGACA
1 AAAGTTTTTGACAAAGATTCTTGACA
484471 AAAGTTTTTGACACAAG-TTCTTGAC-
1 AAAGTTTTTGACA-AAGATTCTTGACA
* * *
484496 AAAGATTTTGATAAAGATTCTTGGCA
1 AAAGTTTTTGACAAAGATTCTTGACA
*
484522 AAGGTTTTTGAC
1 AAAGTTTTTGAC
484534 GATTTCTTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
23 10 0.20
24 4 0.08
25 22 0.44
26 14 0.28
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (26 bp):
AAAGTTTTTGACAAAGATTCTTGACA
Found at i:484504 original size:25 final size:23
Alignment explanation
Indices: 484448--484548 Score: 78
Period size: 25 Copynumber: 4.2 Consensus size: 23
484438 CACTAGACTT
*
484448 AAAGATTTTGAAAAATT-TTGAC
1 AAAGATTTTGAAAAGTTCTTGAC
*
484470 AAAAGTTTTTGACACAAGTTCTTGAC
1 -AAAGATTTTGA-A-AAGTTCTTGAC
*
484496 AAAGATTTTGATAAAGATTCTTGGC
1 AAAGATTTTGA-AAAG-TTCTTGAC
* ** *
484521 AAAGGTTTTTGACGATTTCTTGAC
1 AAA-GATTTTGAAAAGTTCTTGAC
484545 AAAG
1 AAAG
484549 GAAAGGATGC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
23 11 0.17
24 14 0.22
25 26 0.41
26 12 0.19
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (23 bp):
AAAGATTTTGAAAAGTTCTTGAC
Found at i:484511 original size:12 final size:12
Alignment explanation
Indices: 484448--484529 Score: 71
Period size: 13 Copynumber: 6.8 Consensus size: 12
484438 CACTAGACTT
484448 AAAGATTTTGA-
1 AAAGATTTTGAC
484459 AAA-ATTTTGAC
1 AAAGATTTTGAC
*
484470 AAAAGTTTTTGAC
1 -AAAGATTTTGAC
484483 ACAAG-TTCTTGAC
1 A-AAGATT-TTGAC
*
484496 AAAGATTTTGAT
1 AAAGATTTTGAC
*
484508 AAAGATTCTTGGC
1 AAAGATT-TTGAC
*
484521 AAAGGTTTT
1 AAAGATTTT
484530 TGACGATTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
10 7 0.12
11 3 0.05
12 22 0.37
13 27 0.46
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (12 bp):
AAAGATTTTGAC
Found at i:485918 original size:34 final size:34
Alignment explanation
Indices: 485880--485948 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
485870 TTTTGAAAGG
*
485880 AACTTTGTACATTT-TCGATTTGCCACTTGTTGTT
1 AACTTTGTACATTTCT-AATTTGCCACTTGTTGTT
485914 AACTTTGTACATTTCTAATTTGCCACTTGTTGTT
1 AACTTTGTACATTTCTAATTTGCCACTTGTTGTT
485948 A
1 A
485949 GGCATTCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 32 0.97
35 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (34 bp):
AACTTTGTACATTTCTAATTTGCCACTTGTTGTT
Found at i:487461 original size:683 final size:690
Alignment explanation
Indices: 486092--487468 Score: 2491
Period size: 683 Copynumber: 2.0 Consensus size: 690
486082 GGTGGCAAGG
* * *
486092 TGATGAAAACCAAGCAAGGTCCATTGAATACAATGACCTGAAGGCATTGGAAGGGTTTCAAGGAC
1 TGATGAAAACCAAGCAAGGTCCATTGAAGACAATGACCTGAAGGCACTGGAAGGATTTCAAGGAC
*
486157 CAATGACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCTTTGAA
66 CAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCTTTGAA
486222 AGTAGACCCAATTTGGAGTTAAAGCAGCCCAAGCTAGTTAATTGCATATATTTGGAAGATATGGG
131 AGTAGACCCAATTTGGAGTTAAAGCAGCCCAAGCTAGTTAATTGCATATATTTGGAAGATATGGG
486287 CTCCAATGGATTGAATTAGGACTTGGGTAATTTTGTAATAAAGGGCCTGCTGGTTGTGACTTGCT
196 CTCCAATGGATTGAATTAGGACTTGGGTAATTTTGTAATAAAGGGCCTGCTGGTTGTGACTTGCT
486352 TTGGGCTTTATTTAGCATAAAAACTTGTTATTTGGGTTTAACTAAGAGTTGAGCTTGTTAGCATA
261 TTGGGCTTTATTTAGCATAAAAACTTGTTATTTGGGTTT-A-TAAGAGTTGAGCTTGTTAGCATA
*
486417 ATAAGCCCCTTAGGGTTTGTGTTAACTATGGCTTATGAGAGCATATATAAGCTCTTGTAAACAGA
324 ATAAGCCCCTTAGGGTTTGTGTTAACTATGACTTATGAGAGCATATATAAGCTCTTGTAAACAGA
*
486482 TTTGGAGGGGGGCAGACATTGATATTTGCAGATTAAACACATTTTGTGTGAGAGTGTGATTCTTA
389 TTTGGA-GGGGGCAGACATTCATATTTGCAGA-TAAACACATTTTGTGTGAGAGTGTGATTCTTA
486547 GGTTCTTGAGTGAGCCAATTTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATAATTC
452 GGTTCTTGAGTGAGCCAATTTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATAATTC
486612 CTTTTGGCTTATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTA
517 CTTTTGGCTTATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTA
*
486677 TTTTTTTCTGCTTCTTTCAATTTCTGTTCTTGCATCAATAATTCTGTTTATTGTTAGAAATCCAT
582 TTTTTTTCTGCTTCTTTCAATTTCTGTTCTTGCATCAATAATTCTGTTTAATGTTAGAAATCCAT
486742 CTCAAGATCATTATTTAGGCAACCTTGGTTCATGGTTGTCATCA
647 CTCAAGATCATTATTTAGGCAACCTTGGTTCATGGTTGTCATCA
* *
486786 TGATGAAAACCAAGGAAGGTCCATTGAAGAC-A-GACCTGAAGGCGCTGGAAGGATTTCAAGGAC
1 TGATGAAAACCAAGCAAGGTCCATTGAAGACAATGACCTGAAGGCACTGGAAGGATTTCAAGGAC
486849 CAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCTTTGAA
66 CAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCTTTGAA
486914 AGTAGACCCAATTTGGAGTTAAAGCAGCCCAAGCTAGTTAATTGCATATATTTGG-AGATATGGG
131 AGTAGACCCAATTTGGAGTTAAAGCAGCCCAAGCTAGTTAATTGCATATATTTGGAAGATATGGG
*
486978 CTCCAATGGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGCCTGCTGGTTGTGACTTGCT
196 CTCCAATGGATTGAATTAGGACTTGGGTAATTTTGTAATAAAGGGCCTGCTGGTTGTGACTTGCT
*
487043 TTGGGCTTTATTTAGCATAAAAACTTGTTATTTGGG-TT-TAAGAGTTGGGCTTGTTAGCATAAT
261 TTGGGCTTTATTTAGCATAAAAACTTGTTATTTGGGTTTATAAGAGTTGAGCTTGTTAGCATAAT
* *
487106 AAGCCCCTTAGGGTTTGTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAACAGATT
326 AAGCCCCTTAGGGTTTGTGTTAACTATGACTTATGAGAGCATATATAAGCTCTTGTAAACAGATT
487171 TGGA-GGGGCAGACATTCATATTTGCAGA-AAACACATTTTGTGTGAGAGTGTGATTCTTAGGTT
391 TGGAGGGGGCAGACATTCATATTTGCAGATAAACACATTTTGTGTGAGAGTGTGATTCTTAGGTT
* *
487234 CTTGAGTGAGCCAA-TTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGTGATCATTCCTTT
456 CTTGAGTGAGCCAATTTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATAATTCCTTT
487298 TGGCTTATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTT
521 TGGCTTATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTA-TTT
* * *
487363 TTTTCTGCTTCTTTCACTTTTTGTTCTTGCATTAATAATTCTGTTTAATGTTAGAAATCCATCTC
585 TTTTCTGCTTCTTTCAATTTCTGTTCTTGCATCAATAATTCTGTTTAATGTTAGAAATCCATCTC
487428 AAGATCATTATTTAGGCAACCTTGGTTCATGGTTGTCATCA
650 AAGATCATTATTTAGGCAACCTTGGTTCATGGTTGTCATCA
487469 ATTGGTATCA
Statistics
Matches: 664, Mismatches: 18, Indels: 13
0.96 0.03 0.02
Matches are distributed among these distances:
682 109 0.16
683 154 0.23
685 23 0.03
687 90 0.14
690 2 0.00
691 109 0.16
692 147 0.22
693 1 0.00
694 29 0.04
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.34
Consensus pattern (690 bp):
TGATGAAAACCAAGCAAGGTCCATTGAAGACAATGACCTGAAGGCACTGGAAGGATTTCAAGGAC
CAATAACGAGGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCTTTGAA
AGTAGACCCAATTTGGAGTTAAAGCAGCCCAAGCTAGTTAATTGCATATATTTGGAAGATATGGG
CTCCAATGGATTGAATTAGGACTTGGGTAATTTTGTAATAAAGGGCCTGCTGGTTGTGACTTGCT
TTGGGCTTTATTTAGCATAAAAACTTGTTATTTGGGTTTATAAGAGTTGAGCTTGTTAGCATAAT
AAGCCCCTTAGGGTTTGTGTTAACTATGACTTATGAGAGCATATATAAGCTCTTGTAAACAGATT
TGGAGGGGGCAGACATTCATATTTGCAGATAAACACATTTTGTGTGAGAGTGTGATTCTTAGGTT
CTTGAGTGAGCCAATTTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATAATTCCTTT
TGGCTTATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTT
TTTCTGCTTCTTTCAATTTCTGTTCTTGCATCAATAATTCTGTTTAATGTTAGAAATCCATCTCA
AGATCATTATTTAGGCAACCTTGGTTCATGGTTGTCATCA
Found at i:488448 original size:42 final size:42
Alignment explanation
Indices: 488401--488546 Score: 238
Period size: 42 Copynumber: 3.5 Consensus size: 42
488391 AAGAAGAGAG
488401 AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
1 AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
488443 AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
1 AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
** * * *
488485 AAAAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGAGAG
1 AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
*
488527 AGGAGGGATGACAGGAGGAG
1 AGGAGGGATGATAGGAGGAG
488547 GAGAGAAGAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.43, C:0.03, G:0.44, T:0.10
Consensus pattern (42 bp):
AGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAAAGAT
Found at i:493862 original size:12 final size:11
Alignment explanation
Indices: 493843--493914 Score: 71
Period size: 12 Copynumber: 6.5 Consensus size: 11
493833 AGAGAAAGAA
493843 GAGATAGGAGG
1 GAGATAGGAGG
493854 GATGATAGGAGG
1 GA-GATAGGAGG
493866 AGAGATAGGA--
1 -GAGATAGGAGG
*
493876 GAGATAGTA--
1 GAGATAGGAGG
493885 GAGATAGGAGG
1 GAGATAGGAGG
493896 GATGATAGGAGG
1 GA-GATAGGAGG
493908 AGAGATA
1 -GAGATA
493915 ATAGAGAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
9 16 0.30
11 4 0.08
12 29 0.55
13 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.46, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:493877 original size:9 final size:9
Alignment explanation
Indices: 493863--493894 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
493853 GGATGATAGG
493863 AGGAGAGAT
1 AGGAGAGAT
493872 AGGAGAGAT
1 AGGAGAGAT
*
493881 AGTAGAGAT
1 AGGAGAGAT
493890 AGGAG
1 AGGAG
493895 GGATGATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:493889 original size:18 final size:18
Alignment explanation
Indices: 493866--493927 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
493856 TGATAGGAGG
493866 AGAGATAGGAGAGATAGT
1 AGAGATAGGAGAGATAGT
*
493884 AGAGATAGGAGGGAT-GAT
1 AGAGATAGGAGAGATAG-T
*
493902 AG-G--AGGAGAGATAAT
1 AGAGATAGGAGAGATAGT
*
493917 AGAGAAAGGAG
1 AGAGATAGGAG
493928 GGATGACAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 2 0.06
18 22 0.61
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (18 bp):
AGAGATAGGAGAGATAGT
Found at i:493892 original size:42 final size:42
Alignment explanation
Indices: 493833--493924 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
493823 TAGCCCTCAA
493833 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* * **
493875 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAAT
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
493917 AGAGAAAG
1 AGAGAAAG
493925 GAGGGATGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (42 bp):
AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:493909 original size:33 final size:33
Alignment explanation
Indices: 493872--493942 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
493862 GAGGAGAGAT
* * *
493872 AGGAGAGATAGTAGAGATAGGAGGGATGATAGG
1 AGGAGAGATAATAGAGAAAGGAGGGATGACAGG
493905 AGGAGAGATAATAGAGAAAGGAGGGATGACAGG
1 AGGAGAGATAATAGAGAAAGGAGGGATGACAGG
493938 AGGAG
1 AGGAG
493943 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.01, G:0.45, T:0.11
Consensus pattern (33 bp):
AGGAGAGATAATAGAGAAAGGAGGGATGACAGG
Found at i:493943 original size:15 final size:15
Alignment explanation
Indices: 493890--493943 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
493880 TAGTAGAGAT
493890 AGGAGGGATGATAGG
1 AGGAGGGATGATAGG
* *
493905 AGGAGAGATAATAGAG
1 AGGAGGGATGATAG-G
*
493921 AAAGGAGGGATGACAGG
1 --AGGAGGGATGATAGG
493938 AGGAGG
1 AGGAGG
493944 AGAGAAGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 18 0.58
16 1 0.03
17 1 0.03
18 11 0.35
ACGTcount: A:0.41, C:0.02, G:0.48, T:0.09
Consensus pattern (15 bp):
AGGAGGGATGATAGG
Found at i:501873 original size:42 final size:42
Alignment explanation
Indices: 501818--501936 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
501808 TTCTTCTCTC
* *
501818 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
501860 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
501902 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
501937 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:501877 original size:12 final size:11
Alignment explanation
Indices: 501851--501926 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
501841 TCTATTATCT
*
501851 CTCCTGTCTCTC
1 CTCCTATCTC-C
501863 CTCCTATCATCC
1 CTCCTATC-TCC
501875 CTCCTATCT--
1 CTCCTATCTCC
*
501884 CTACTATCT--
1 CTCCTATCTCC
*
501893 CTCCTGTCTCTC
1 CTCCTATCTC-C
501905 CTCCTATCATCC
1 CTCCTATC-TCC
*
501917 CTCCTCTCTC
1 CTCCTATCTC
501927 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:501878 original size:24 final size:24
Alignment explanation
Indices: 501842--501927 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
501832 CCTCCTCTCT
* *
501842 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
501866 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
501887 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
501908 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
501928 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:501902 original size:18 final size:18
Alignment explanation
Indices: 501833--501903 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
501823 CCTGTCATCC
* *
501833 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
501851 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
501873 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
501893 CTCCTGTCTCT
1 CTCCTGTCTCT
501904 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:503268 original size:212 final size:212
Alignment explanation
Indices: 502901--503323 Score: 819
Period size: 212 Copynumber: 2.0 Consensus size: 212
502891 ATGATCTTGA
* *
502901 GATGGATTTCTAACATTAAACAGAATTATTAATGCAAGAACAGAAATGGAAAGAAGTAAAAAAAA
1 GATGGATTTCTAACATTAAACAGAATTATTAATGCAAGAACAGAAATGAAAAGAAGCAAAAAAAA
502966 ATTACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAA
66 ATTACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAA
503031 GGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAATTGGCTCACTCAAGAACC
131 GGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAATTGGCTCACTCAAGAACC
503096 TAAGAATCACACTCTCT
196 TAAGAATCACACTCTCT
*
503113 GATGGATTTCTAACATTAAACAGAATTATTAATGCAAGAACAGAAATGAAAAGAAGCAGAAAAAA
1 GATGGATTTCTAACATTAAACAGAATTATTAATGCAAGAACAGAAATGAAAAGAAGCAAAAAAAA
503178 ATTACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAA
66 ATTACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAA
503243 GGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAATTGGCTCACTCAAGAACC
131 GGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAATTGGCTCACTCAAGAACC
503308 TAAGAATCACACTCTC
196 TAAGAATCACACTCTC
503324 ACACAAAATG
Statistics
Matches: 208, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 208 1.00
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (212 bp):
GATGGATTTCTAACATTAAACAGAATTATTAATGCAAGAACAGAAATGAAAAGAAGCAAAAAAAA
ATTACAAAATGGAATAGATTAGAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAA
GGAATGATCACCACAAGAGTCTTGGCCTCTTGATAAGATCCAGAAAATTGGCTCACTCAAGAACC
TAAGAATCACACTCTCT
Found at i:510803 original size:26 final size:27
Alignment explanation
Indices: 510773--510826 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
510763 TTTTGATGAT
*
510773 TTTGAA-AAGCGGGGTTAGGGTATCCC
1 TTTGAAGAAGCGGGGTTAGAGTATCCC
* *
510799 TTTGAAGATGTGGGGTTAGAGTATCCC
1 TTTGAAGAAGCGGGGTTAGAGTATCCC
510826 T
1 T
510827 AAAAGTGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.31
Consensus pattern (27 bp):
TTTGAAGAAGCGGGGTTAGAGTATCCC
Found at i:511497 original size:23 final size:23
Alignment explanation
Indices: 511458--511532 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
511448 ATTGTTCCCA
* *
511458 TGGCATCAACCATTTTCAGCTAC
1 TGGCAGCAACCACTTTCAGCTAC
* *
511481 TGGTAGCAACCACTTTCATCTAC
1 TGGCAGCAACCACTTTCAGCTAC
*
511504 TGGCAGCAACCACTTTCAGTTAC
1 TGGCAGCAACCACTTTCAGCTAC
511527 TGGCAG
1 TGGCAG
511533 TAGCTAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (23 bp):
TGGCAGCAACCACTTTCAGCTAC
Found at i:511675 original size:82 final size:82
Alignment explanation
Indices: 511529--511695 Score: 289
Period size: 82 Copynumber: 2.0 Consensus size: 82
511519 TCAGTTACTG
* *
511529 GCAGTAGCTAATCACCCTACTCCTCCCTTTCCTGTTGACAAAAATCACCATTAGCCACCCTACTT
1 GCAGCAGCTAATCACCCTACTCCTCCCTTGCCTGTTGACAAAAATCACCATTAGCCACCCTACTT
511594 GCTGGTATATCAATTCA
66 GCTGGTATATCAATTCA
* * *
511611 GCAGCAGCTAATCACCTTACTCCTCCCTTGCTTGTTGACAAAAATCACCATTAGCCACCTTACTT
1 GCAGCAGCTAATCACCCTACTCCTCCCTTGCCTGTTGACAAAAATCACCATTAGCCACCCTACTT
511676 GCTGGTATATCAATTCA
66 GCTGGTATATCAATTCA
511693 GCA
1 GCA
511696 TTTAAACCAG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (82 bp):
GCAGCAGCTAATCACCCTACTCCTCCCTTGCCTGTTGACAAAAATCACCATTAGCCACCCTACTT
GCTGGTATATCAATTCA
Found at i:518705 original size:80 final size:77
Alignment explanation
Indices: 518561--518753 Score: 219
Period size: 80 Copynumber: 2.5 Consensus size: 77
518551 TGACTAGGTA
* * * * *
518561 CCAATGTGTTGATTCAAGTCAACGACATTGAGCTTTGACTAGAATTACACGAAAAGTGCATTTTG
1 CCAATGTGCTGATTCAAGGCAGCGACATTGAGCTTGGACTAGAACTACACGAAAAGTGCATTTTG
*
518626 GCATAGGTGGGGTG
66 ACATAGG-GGGG-G
* * *
518640 CCAATGTGCTGATTCAAGGCTAGCGACATT-AGGCTTGGACTAGAACTATATGACAAGTGTC-TT
1 CCAATGTGCTGATTCAAGGC-AGCGACATTGA-GCTTGGACTAGAACTACACGAAAAGTG-CATT
518703 TTGACATAGGGGGGG
63 TTGACATAGGGGGGG
* *
518718 CCAATGTGCTAATTCAAGGCCAGCAACATTGAGCTT
1 CCAATGTGCTGATTCAAGG-CAGCGACATTGAGCTT
518754 AGGAAGAAGA
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
78 31 0.32
79 25 0.26
80 41 0.42
81 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (77 bp):
CCAATGTGCTGATTCAAGGCAGCGACATTGAGCTTGGACTAGAACTACACGAAAAGTGCATTTTG
ACATAGGGGGGG
Found at i:518931 original size:80 final size:79
Alignment explanation
Indices: 518636--518933 Score: 232
Period size: 80 Copynumber: 3.7 Consensus size: 79
518626 GCATAGGTGG
* * * * *
518636 GGTGCCAATGTGCTGATTCAAGGCTAGCGACATTAGGCTTG-GACTAGAACTATATGACAAGTG-
1 GGTGCCAATGTGCTGATTCAAGGCTAGCAACATTAGCCTTGAGA-AAGAAGT-TTTGACAAGTGC
*
518699 TCTTTTGACATAGG--G
64 T-TTTTGACATAGGCAA
* * * * * *
518714 GGGGCCAATGTGCTAATTCAAGGCCAGCAACATTGAG-CTT-AGGAAGAAGATTTAGAC-AGATA
1 GGTGCCAATGTGCTGATTCAAGGCTAGCAACATT-AGCCTTGAGAAAGAAG-TTTTGACAAG-TG
*** *
518776 CTACATGACTTAGGGCAA
63 CTTTTTGACATA-GGCAA
* * * * * * * *
518794 AGTACCAATGTGTTGATTTAAGGCTAGCAACATTGGCCTTTAGTGAAGAAGATTTGACAAGTGCT
1 GGTGCCAATGTGCTGATTCAAGGCTAGCAACATTAGCCTTGAG-AAAGAAGTTTTGACAAGTGCT
*
518859 TTTTGACATAGGCAT
65 TTTTGACATAGGCAA
*
518874 GGTGCCAATGTGCTGATTCAAGGCTATCAACATTAGCCTTGAGAAAGAAGGTTTTGACAA
1 GGTGCCAATGTGCTGATTCAAGGCTAGCAACATTAGCCTTGAGAAAGAA-GTTTTGACAA
518934 ATGCCGCATG
Statistics
Matches: 167, Mismatches: 40, Indels: 24
0.72 0.17 0.10
Matches are distributed among these distances:
76 2 0.01
77 15 0.09
78 38 0.23
79 8 0.05
80 79 0.47
81 16 0.10
82 9 0.05
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTGCCAATGTGCTGATTCAAGGCTAGCAACATTAGCCTTGAGAAAGAAGTTTTGACAAGTGCTT
TTTGACATAGGCAA
Found at i:518989 original size:160 final size:158
Alignment explanation
Indices: 518690--518989 Score: 338
Period size: 160 Copynumber: 1.9 Consensus size: 158
518680 TAGAACTATA
518690 TGACAAGTGTCTTTTGACATAGGGGGGGCCAATGTGCTAATTCAAGGCCAGCAACATTGAGCTTA
1 TGACAAGTGTCTTTTGACATAGGGGGGGCCAATGTGCTAATTCAAGGCCAGCAACATTGAGCTTA
* * * ** * *
518755 GGAAGAAGATTTAGACAGATACTACATGACTTAGGGCAAAGTACCAATGTGTTGATTTAAGGCTA
66 GAAAGAAGATTTAGACAAATACCACATGACTTAGGGCAAAGTACCAATGTACTGATTCAAGGCCA
518820 GCAACATTGGCCTTTAGTGAAGAAGATT
131 GCAACATTGGCCTTTAGTGAAGAAGATT
* * * * *
518848 TGACAAGTG-CTTTTTGACATAGGCATGGTGCCAATGTGCTGATTCAAGGCTATCAACATT-AGC
1 TGACAAGTGTC-TTTTGACATAGG--GGGGGCCAATGTGCTAATTCAAGGCCAGCAACATTGAG-
* * * * * *
518911 CTTGAGAAAGAAGGTTTTGACAAATGCCGCATGA-TTAGGGCAGAA-TGCTAATGTACTGATTCA
62 CTT-AGAAAGAAGATTTAGACAAATACCACATGACTTAGGGCA-AAGTACCAATGTACTGATTCA
**
518974 AGGCCAGTGACATTGG
125 AGGCCAGCAACATTGG
518990 GCTTAGAAAG
Statistics
Matches: 116, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
157 1 0.01
158 21 0.18
159 2 0.02
160 67 0.58
161 25 0.22
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (158 bp):
TGACAAGTGTCTTTTGACATAGGGGGGGCCAATGTGCTAATTCAAGGCCAGCAACATTGAGCTTA
GAAAGAAGATTTAGACAAATACCACATGACTTAGGGCAAAGTACCAATGTACTGATTCAAGGCCA
GCAACATTGGCCTTTAGTGAAGAAGATT
Found at i:519021 original size:79 final size:79
Alignment explanation
Indices: 518876--519226 Score: 400
Period size: 79 Copynumber: 4.4 Consensus size: 79
518866 ATAGGCATGG
* * * * * *
518876 TGCCAATGTGCTGATTCAAGGCTA-TCAACATTAGCCTTGAGAAAGAAGGTTTTGACAAATGCCG
1 TGCCAATGTGCTGATTCAAGGCCAGT-AACATTGGGCTT-AGAAAAAAGGTTTTGATAGATGCCG
*
518940 CATGATTAGGGCAGAA
64 CATGACTAGGGCAGAA
* * * * * *
518956 TGCTAATGTACTGATTCAAGGCCAGTGACATTGGGCTTAGAAAGAAGGTTTTGATAGTTACCGCA
1 TGCCAATGTGCTGATTCAAGGCCAGTAACATTGGGCTTAGAAAAAAGGTTTTGATAGATGCCGCA
519021 TGACTAGGGCAGAA
66 TGACTAGGGCAGAA
** * * *
519035 TGCCAATGTATTGATTCAAGGCCAGTGACATTGGGCCTAGAAAAAAGGTTTTGATAGATGCTGCA
1 TGCCAATGTGCTGATTCAAGGCCAGTAACATTGGGCTTAGAAAAAAGGTTTTGATAGATGCCGCA
*
519100 TGACTAGGGTAGAA
66 TGACTAGGGCAGAA
* * * * * ** *
519114 TGCCAATGTGTTGATTCAAGTCCAGCAACATTAGGC-TAAAAAAATAGGTTTTGATAGATGTTGT
1 TGCCAATGTGCTGATTCAAGGCCAGTAACATTGGGCTTAGAAAAA-AGGTTTTGATAGATGCCGC
*
519178 ATGACTAGGGTAGAA
65 ATGACTAGGGCAGAA
*
519193 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGG
1 TGCCAATGTGCTGATTCAAGGCCAGTAACATTGG
519227 TTCAAAAGGA
Statistics
Matches: 239, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
78 7 0.03
79 201 0.84
80 30 0.13
81 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
TGCCAATGTGCTGATTCAAGGCCAGTAACATTGGGCTTAGAAAAAAGGTTTTGATAGATGCCGCA
TGACTAGGGCAGAA
Found at i:519776 original size:31 final size:31
Alignment explanation
Indices: 519740--519808 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
519730 AGCTCGTATG
* * * *
519740 GGCTTTGATTTAGGTGTCGCCAGCTCGTGC-
1 GGCTTTGACTTAGGTGGCACCAACTCGTGCA
*
519770 GAGCTTTAACTTAGGTGGCACCAACTCGTGCA
1 G-GCTTTGACTTAGGTGGCACCAACTCGTGCA
519802 GGCTTTG
1 GGCTTTG
519809 GTGTCTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
30 1 0.03
31 29 0.94
32 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.30
Consensus pattern (31 bp):
GGCTTTGACTTAGGTGGCACCAACTCGTGCA
Found at i:521043 original size:168 final size:164
Alignment explanation
Indices: 520799--521151 Score: 403
Period size: 168 Copynumber: 2.1 Consensus size: 164
520789 TTTCATTAGT
* * * *
520799 TTTTGAATTTTTTCCTTGAAA-TTTTTTTTTTCGAAATTCGGAGTTTTCTACTCTGAAATTTTTT
1 TTTTGAATTTTTTCCTTGAAATTTTTTTTTTTCAAAATACGGAATTTTCTACTCTGAAATTTTTG
** * * *
520863 CAAAGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATT-
66 CAAAGAGATTTTTCTCAGTTTTTAATTTTTAAAAGTAATCAAATATTATCATTTATTTCATATTA
* *
520927 ATTTCAGTTTTCAAAAATTCA-TTCATTTCCATGAA
131 ATTT-AGTTTT-AAAAAATAATTTCATTTCCATGAA
520962 TTTTGAATTTTTTCCTTGAAATCTCTTTTTTTTTCTAAAATAC-GATATTTTCTACT-TCGTAAA
1 TTTTGAATTTTTTCCTTGAAAT-T-TTTTTTTTTC-AAAATACGGA-ATTTTCTACTCT-G-AAA
* *
521025 TTTTTGC-GAGCAGATTTTTCTCAGTTTTTGATTTTTAAAAGTAATCAAATATTATCATTTATTT
60 TTTTTGCAAAG-AGATTTTTCTCAGTTTTTAATTTTTAAAAGTAATCAAATATTATCATTTATTT
* * * * * *
521089 CATGTTAATTTGGTTTTAAAAAATAATTTCGTTTTCGTGAG
124 CATATTAATTTAGTTTTAAAAAATAATTTCATTTCCATGAA
*
521130 TTTTGGATTTTTTCCTTGAAAT
1 TTTTGAATTTTTTCCTTGAAAT
521152 ACCCCTTTTC
Statistics
Matches: 160, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
163 21 0.13
165 1 0.01
166 13 0.08
167 24 0.15
168 97 0.61
169 4 0.03
ACGTcount: A:0.27, C:0.11, G:0.10, T:0.52
Consensus pattern (164 bp):
TTTTGAATTTTTTCCTTGAAATTTTTTTTTTTCAAAATACGGAATTTTCTACTCTGAAATTTTTG
CAAAGAGATTTTTCTCAGTTTTTAATTTTTAAAAGTAATCAAATATTATCATTTATTTCATATTA
ATTTAGTTTTAAAAAATAATTTCATTTCCATGAA
Found at i:521947 original size:11 final size:11
Alignment explanation
Indices: 521931--521970 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
521921 GGCTCCAGCT
*
521931 AAAAAGAGAGA
1 AAAAAGAAAGA
521942 AAAAAGAAAAGA
1 AAAAAG-AAAGA
521954 AAAAGAGAAAGA
1 AAAA-AGAAAGA
521966 AAAAA
1 AAAAA
521971 TAGGGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 7 0.27
12 17 0.65
13 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:521954 original size:12 final size:13
Alignment explanation
Indices: 521931--521970 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 13
521921 GGCTCCAGCT
521931 AAAAAGAG--AGA
1 AAAAAGAGAAAGA
521942 AAAAAGA-AAAG-
1 AAAAAGAGAAAGA
521953 AAAAAGAGAAAGA
1 AAAAAGAGAAAGA
521966 AAAAA
1 AAAAA
521971 TAGGGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 14 0.56
12 6 0.24
13 5 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAGA
Found at i:534829 original size:21 final size:21
Alignment explanation
Indices: 534801--534862 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
534791 AAAAAAAAAT
534801 TTTC-CAAATGTATCGATACA
1 TTTCACAAATGTATCGATACA
534821 TTTCACAAATGTATCGATACA
1 TTTCACAAATGTATCGATACA
534842 -TTCTACAAATGTATCGATACA
1 TTTC-ACAAATGTATCGATACA
534863 GGGTCCCAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.17
21 33 0.82
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (21 bp):
TTTCACAAATGTATCGATACA
Found at i:534974 original size:13 final size:13
Alignment explanation
Indices: 534956--534981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534946 CATTTTTCTG
534956 TGTATCGATACAT
1 TGTATCGATACAT
534969 TGTATCGATACAT
1 TGTATCGATACAT
534982 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:534978 original size:33 final size:33
Alignment explanation
Indices: 534936--535002 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
534926 GCCAAGGAAA
***
534936 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
534969 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
535002 T
1 T
535003 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:535533 original size:20 final size:17
Alignment explanation
Indices: 535496--535529 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
535486 ATCCTTTAGC
535496 AAAAAAAAAAAAAAACT
1 AAAAAAAAAAAAAAACT
*
535513 AAAAAACAAAGAAAAAC
1 AAAAAA-AAAAAAAAAC
535530 ACTATTCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAAAAACT
Found at i:537393 original size:51 final size:53
Alignment explanation
Indices: 537329--537671 Score: 173
Period size: 52 Copynumber: 6.5 Consensus size: 53
537319 AGTTTCTCAA
* * * *
537329 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * *
537380 TT-TTCTATAATCGGGGATACTCTAACTCTGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * * *
537434 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGAGGATACTCCAAC-CCCAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTCCA--A-A----AACACCAAT
* * * *
537492 TAT-TTC-CGA--GGGGATACTCCAAC-CTCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTC-CGATTTTATTTC-CAAAAACACCAAT
* * * * *
537541 TTTTTCCACAATCGGGGATGCTCCAA-TCCCGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAA-T
* * *
537595 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
537647 TT-TTCACAATTGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
537672 CTCGTTATTT
Statistics
Matches: 221, Mismatches: 37, Indels: 67
0.68 0.11 0.21
Matches are distributed among these distances:
48 4 0.02
49 6 0.03
50 5 0.02
51 34 0.15
52 52 0.24
53 49 0.22
54 31 0.14
55 23 0.10
57 5 0.02
58 8 0.04
59 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:537515 original size:28 final size:28
Alignment explanation
Indices: 537446--537515 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
537436 CTTCACAATC
*
537446 GGGGATACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCATTAATCA-CGA
*
537475 --GGATACTCCAACCCCATTATTTC-CGA
1 GGGGATACTCCAACCCCATTA-ATCACGA
537501 GGGGATACTCCAACC
1 GGGGATACTCCAACC
537516 TCGGTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTAATCACGA
Found at i:537699 original size:213 final size:213
Alignment explanation
Indices: 537332--537726 Score: 562
Period size: 213 Copynumber: 1.9 Consensus size: 213
537322 TTCTCAATTC
* *
537332 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
537397 TACTCTAACTCTGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
537462 CGTTAATCATCGAGGATACTCCAACCCCATTATTTCCGAGGGGATACTCCAACCTCGGTTTTATC
131 CGTTAATCATCGAGGATACTCCAACCCCATTACTTCCGAGAGGATACTCCAACCTCGGTTTTATC
537527 GCTAAAACACTAATTTTT
196 GCTAAAACACTAATTTTT
* * * *
537545 TCCACAATCGGGGATGCTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* * *
537609 GATACTCCAACTCCGATTTTATTT-CTAAAAATACCAATTT-TTCACAATTGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * * * *
537672 CTCGTTATTTCATCGGGGATCCTCCAACCCCGTTACTTCTGAGAGGATACTCCAA
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCATTACTTCCGAGAGGATACTCCAA
537727 TCCCGATTTT
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
212 28 0.18
213 99 0.62
214 32 0.20
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (213 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCATTACTTCCGAGAGGATACTCCAACCTCGGTTTTATC
GCTAAAACACTAATTTTT
Found at i:537719 original size:28 final size:29
Alignment explanation
Indices: 537658--537731 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
537648 TTTCACAATT
* *
537658 GAGGATACTCCAACCTCGTTATTTCATCG
1 GAGGATACTCCAACCCCGTTACTTCATCG
*
537687 G-GGATCCTCCAACCCCGTTACTTC-T-G
1 GAGGATACTCCAACCCCGTTACTTCATCG
*
537713 AGAGGATACTCCAATCCCG
1 -GAGGATACTCCAACCCCG
537732 ATTTTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 2 0.05
28 34 0.89
29 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (29 bp):
GAGGATACTCCAACCCCGTTACTTCATCG
Found at i:540063 original size:78 final size:78
Alignment explanation
Indices: 539853--540066 Score: 195
Period size: 78 Copynumber: 2.7 Consensus size: 78
539843 TTTTAGCCGA
* * * * * * ** *
539853 CCACACATTCCTAATCATATCCTT-TTTACCCAAATACCAGATGATATT-AGTGCATCCCAAGGC
1 CCACACATTCCCAATTATATCCTTACTTA-CCAACTACTAAATGATATTGA-TGCATCATAAAGC
539916 CAAAAAGGGCACTTC
64 CAAAAAGGGCACTTC
* * * * * *
539931 CCATACATTCCCAATTATATCCTTCCTTATCAACTACTAGATGATGTTGGTGCATCATAAAGCCA
1 CCACACATTCCCAATTATATCCTTACTTACCAACTACTAAATGATATTGATGCATCATAAAGCCA
539996 AAAAGGGCACTTC
66 AAAAGGGCACTTC
* *
540009 CCACACATTCCCAATTGCATA-CC-TACTTCCCAAAC-ACTAAATGGTATTGATGCATCAT
1 CCACACATTCCCAATT--ATATCCTTACTTACC-AACTACTAAATGATATTGATGCATCAT
540067 GTGGCTATAA
Statistics
Matches: 111, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
78 100 0.90
79 8 0.07
80 3 0.03
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.28
Consensus pattern (78 bp):
CCACACATTCCCAATTATATCCTTACTTACCAACTACTAAATGATATTGATGCATCATAAAGCCA
AAAAGGGCACTTC
Found at i:540600 original size:43 final size:43
Alignment explanation
Indices: 540538--540664 Score: 146
Period size: 43 Copynumber: 3.0 Consensus size: 43
540528 TATCTGCCCA
* * * * *
540538 TCGGCTTAGACCCGGGAGACTTCCTTTGTCAATCATCTACCCG
1 TCGGCTCAAACCCAGGAGACTTCCTTTATCAATCGTCTACCCG
* **
540581 TCGGCTCAAACCCATGAGACTTCCTTTATCAATCGTCTACTTG
1 TCGGCTCAAACCCAGGAGACTTCCTTTATCAATCGTCTACCCG
* * * *
540624 TCGGCTTAGACCCGGGAGATTTCCTTTATCAATCGTCTACC
1 TCGGCTCAAACCCAGGAGACTTCCTTTATCAATCGTCTACC
540665 TGAGAGACTT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (43 bp):
TCGGCTCAAACCCAGGAGACTTCCTTTATCAATCGTCTACCCG
Found at i:540729 original size:43 final size:41
Alignment explanation
Indices: 540676--541705 Score: 443
Period size: 42 Copynumber: 24.0 Consensus size: 41
540666 GAGAGACTTA
* * *
540676 TTTTGTCAATCGTCTGCCCGTTGGCTCAGACCCGGGAGACT
1 TTTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * ** *
540717 TCCTTTATCAATCATCTGCCCGTCGACTCAGACCTAGGAAACT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * *
540760 TCCTTTATCAATCCTCTACCCGTCAGCTTAGACCTGGGAG-CT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
** * * **
540802 TTTTCCATCAATTATCTACCCGTCGACTTAGACCCAAGAGA-T
1 TTTT--ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * *
540844 TTTTCCATCAATTGTCTACCCATCAGCTTAGACCCGGGAGACT
1 TTTT--ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * *
540887 TTTCCATCAATTGTCTGCACGTCGGCTTAGACCCGGGAGA-T
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * * * *
540928 TTTTCCATCAATCATCTACCCGTCGACTTAGACTCAGAAGACT
1 TTTT--ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* *
540971 TTTTCATCAATCGTCTGCCCGTCGACTTAGACTCGGGAGACT
1 TTTT-ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * ** * *
541013 TTTTCATCAATCATCTGCCAGTCAACTTAGACCCGAGAGATT
1 TTTT-ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * * * * * *
541055 TCCTTTGTTAATTGTCTGTCGGTTGGCTTAGACTCGGGAGATT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * ** * * *
541098 TCCTTTGTAAATTATCT-ACCGATCGACTTAGACTCGGGAGACT
1 T--TTTATCAATCGTCTGCCCG-TCGGCTTAGACCCGGGAGACT
* * ** **
541141 TTTCTATCAATCGTTTACCCGTTAGCTTAGACCTAGGAGACT
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
** * **
541183 TTTTCATCAATCGTCTGCCCGTTAGCTTAAACTAGGGAGACT
1 TTTT-ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * * * ** * *
541225 TTTCCATCAATCGTCTACCCGTCGACTCAAAATCAGAAGACTT
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGAC-T
* * * * *
541268 TCTTTATCAATCATTTGCCTGTCGGCTTAGACCCAGGAGATT
1 T-TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* ** * * * *
541310 TCCTTTGTC-ATTTTCTACCCATCGACTTAGACCCGAGAGACT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * **
541352 TTTCCATCAATCGTCTACCCGTCAGCTTAGACTTGGGAGACT
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
** * * **
541394 CTTCCATCAATCGTCTGCTCATCGGCTTAGACTTGGGAGACT
1 -TTTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * *
541436 TTTCCATCAATCGTCTACCCATCGGCTTAGACCCCGTCGGCTTAGACTT
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGA-CCCG--GG---AGAC-T
* * *
541485 GGAGGACTTTTCCATCAATCATCTCCCCGTCGGCTTAGACTCGGGAGACT
1 -------TTTT--ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * *
541535 TTTTCATTAATCATTTGCCCGTCGGCTTAGACCCGGGAGACT
1 TTTT-ATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * * * ***
541577 TCCTTTGTCAATCATCTGCCCGTCAGCTCAGACTTAGGAGACT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
* * ** *
541620 TCCTTTATCAATCATTTGCCCGTCAACTTAGA-CCGAGAAGACT
1 T--TTTATCAATCGTCTGCCCGTCGGCTTAGACCCG-GGAGACT
* * * * *
541663 TTTCCATCAATCTTCTACCCGTCGGCTCAGACCCGAGAGACT
1 TTT-TATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
541705 T
1 T
541706 CCTTCTTCAT
Statistics
Matches: 770, Mismatches: 174, Indels: 89
0.75 0.17 0.09
Matches are distributed among these distances:
40 5 0.01
41 14 0.02
42 454 0.59
43 246 0.32
44 8 0.01
45 2 0.00
48 4 0.01
49 1 0.00
50 1 0.00
51 4 0.01
54 2 0.00
56 6 0.01
57 23 0.03
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.31
Consensus pattern (41 bp):
TTTTATCAATCGTCTGCCCGTCGGCTTAGACCCGGGAGACT
Found at i:540763 original size:115 final size:115
Alignment explanation
Indices: 540553--540779 Score: 283
Period size: 115 Copynumber: 2.0 Consensus size: 115
540543 TTAGACCCGG
* * *
540553 GAGACTTCCTTTGTCAATCATCTACCCGTCGGCTCAAACCCATGAGACTTCCTTTATCAATCGTC
1 GAGACTTACTTTGTCAATCATCTACCCGTCGGCTCAAACCCAGGAGACTTCCTTTATCAATCATC
** * * * * * *
540618 TACTTGTCGGCTTAGACCCGGGAGATTTCCTTTATCAATCGTCTACCTGA
66 TACCCGTCGACTCAGACCCAGGAAACTTCCTTTATCAATCCTCTACCTGA
* * * * * *
540668 GAGACTTATTTTGTCAATCGTCTGCCCGTTGGCTCAGACCCGGGAGACTTCCTTTATCAATCATC
1 GAGACTTACTTTGTCAATCATCTACCCGTCGGCTCAAACCCAGGAGACTTCCTTTATCAATCATC
* *
540733 TGCCCGTCGACTCAGACCTAGGAAACTTCCTTTATCAATCCTCTACC
66 TACCCGTCGACTCAGACCCAGGAAACTTCCTTTATCAATCCTCTACC
540780 CGTCAGCTTA
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (115 bp):
GAGACTTACTTTGTCAATCATCTACCCGTCGGCTCAAACCCAGGAGACTTCCTTTATCAATCATC
TACCCGTCGACTCAGACCCAGGAAACTTCCTTTATCAATCCTCTACCTGA
Found at i:541184 original size:212 final size:211
Alignment explanation
Indices: 540912--541454 Score: 610
Period size: 212 Copynumber: 2.6 Consensus size: 211
540902 TGCACGTCGG
* * * *
540912 CTTAGACCCGGGAGATTTTTCCATCAATCATCTACCCG-TCGACTTAGA-CTCAGAAGACTTTTT
1 CTTAGACCCGGGAGACTTTTCCATCAATCGTCTACCCGTTAG-CTTAGACCT-AGGAGACTTTTT
* * *
540975 CATCAATCGTCTGCCCGTCGACTTAGACTCGGGAGACTTTTTCATCAATCATCTGCCAGTCAACT
64 CATCAATCGTCTGCCCGTCGACTTAGACTAGGGAGACTTTTCCATCAATCATCTACCAGTCAACT
* * * * * ** * * * *
541040 -TAGACCCGAGAGA-TTTCCTTTGTTAATTGTCTGTCGGTTGGCTTAGACTCGGGAGATTTCCTT
129 CAAAACCAGA-AGACTTT-CTTTATCAATCATCTGCCGGTCGGCTTAGACCCAGGAGATTTCCTT
*
541103 TGTAAATTATCTACCGATCGA
192 TGT-AATTATCTACCCATCGA
* * *
541124 CTTAGACTCGGGAGACTTTTCTATCAATCGTTTACCCGTTAGCTTAGACCTAGGAGACTTTTTCA
1 CTTAGACCCGGGAGACTTTTCCATCAATCGTCTACCCGTTAGCTTAGACCTAGGAGACTTTTTCA
* * * * *
541189 TCAATCGTCTGCCCGT-TAGCTTAAACTAGGGAGACTTTTCCATCAATCGTCTACCCGTCGACTC
66 TCAATCGTCTGCCCGTCGA-CTTAGACTAGGGAGACTTTTCCATCAATCATCTACCAGTCAACTC
* * *
541253 AAAATCAGAAGACTTTCTTTATCAATCATTTGCCTGTCGGCTTAGACCCAGGAGATTTCCTTTGT
130 AAAACCAGAAGACTTTCTTTATCAATCATCTGCCGGTCGGCTTAGACCCAGGAGATTTCCTTTGT
* *
541318 CATTTTCTACCCATCGA
195 AATTATCTACCCATCGA
* * * * * *
541335 CTTAGACCCGAGAGACTTTTCCATCAATCGTCTACCCGTCAGCTTAGACTTGGGAGACTCTTCCA
1 CTTAGACCCGGGAGACTTTTCCATCAATCGTCTACCCGTTAGCTTAGACCTAGGAGACTTTTTCA
* * * * *
541400 TCAATCGTCTGCTCATCGGCTTAGACTTGGGAGACTTTTCCATCAATCGTCTACC
66 TCAATCGTCTGCCCGTCGACTTAGACTAGGGAGACTTTTCCATCAATCATCTACC
541455 CATCGGCTTA
Statistics
Matches: 278, Mismatches: 47, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
211 119 0.43
212 147 0.53
213 12 0.04
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (211 bp):
CTTAGACCCGGGAGACTTTTCCATCAATCGTCTACCCGTTAGCTTAGACCTAGGAGACTTTTTCA
TCAATCGTCTGCCCGTCGACTTAGACTAGGGAGACTTTTCCATCAATCATCTACCAGTCAACTCA
AAACCAGAAGACTTTCTTTATCAATCATCTGCCGGTCGGCTTAGACCCAGGAGATTTCCTTTGTA
ATTATCTACCCATCGA
Found at i:541485 original size:57 final size:57
Alignment explanation
Indices: 541415--541524 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
541405 CGTCTGCTCA
*
541415 TCGGCTTAGACTTGG-GAGACTTTTCCATCAATCGTCTACCCATCGGCTTAGACCCCG
1 TCGGCTTAGACTTGGAG-GACTTTTCCATCAATCATCTACCCATCGGCTTAGACCCCG
* *
541472 TCGGCTTAGACTTGGAGGACTTTTCCATCAATCATCTCCCCGTCGGCTTAGAC
1 TCGGCTTAGACTTGGAGGACTTTTCCATCAATCATCTACCCATCGGCTTAGAC
541525 TCGGGAGACT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 48 0.98
58 1 0.02
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (57 bp):
TCGGCTTAGACTTGGAGGACTTTTCCATCAATCATCTACCCATCGGCTTAGACCCCG
Found at i:541504 original size:99 final size:99
Alignment explanation
Indices: 541369--541568 Score: 267
Period size: 99 Copynumber: 2.0 Consensus size: 99
541359 CAATCGTCTA
* * * *
541369 CCCGTCAGCTTAGACTTGGGAGACTCTTCCATCAATCGTCTGCTCATCGGCTTAGACTTGGGAGA
1 CCCGTCAGCTTAGACTTGGGAGACTCTTCCATCAATCATCTCCCCATCGGCTTAGACTCGGGAGA
*
541434 CTTTTCCATCAATCGTCTACCCATCGGCTTAGAC
66 CTTTTCCATCAATCATCTACCCATCGGCTTAGAC
* * *
541468 CCCGTCGGCTTAGACTT-GGAGGACTTTTCCATCAATCATCTCCCCGTCGGCTTAGACTCGGGAG
1 CCCGTCAGCTTAGACTTGGGA-GACTCTTCCATCAATCATCTCCCCATCGGCTTAGACTCGGGAG
* * * * *
541532 ACTTTTTCATTAATCATTTGCCCGTCGGCTTAGAC
65 ACTTTTCCATCAATCATCTACCCATCGGCTTAGAC
541567 CC
1 CC
541569 GGGAGACTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
98 3 0.03
99 84 0.97
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.30
Consensus pattern (99 bp):
CCCGTCAGCTTAGACTTGGGAGACTCTTCCATCAATCATCTCCCCATCGGCTTAGACTCGGGAGA
CTTTTCCATCAATCATCTACCCATCGGCTTAGAC
Found at i:541703 original size:85 final size:86
Alignment explanation
Indices: 541489--541709 Score: 229
Period size: 85 Copynumber: 2.6 Consensus size: 86
541479 AGACTTGGAG
* * * * *
541489 GACTTTTCCATCAATCATCTCCCCGTCGGCTTAGACTCGGGAGACTT--TTTCATTAATCATTTG
1 GACTTTTCCATCAATCATCTACCCGTCGGCTCAGACCCGAGAGACTTCCTTTCATCAATCATTTG
** *
541552 CCCGTCGGCTTAGACCCGGGA
66 CCCGTCAACTTAGACCCGGAA
** * * **
541573 GACTTCCTT-TGTCAATCATCTGCCCGTCAGCTCAGA-CTTAGGAGACTTCCTTT-ATCAATCAT
1 GACTT--TTCCATCAATCATCTACCCGTCGGCTCAGACCCGA-GAGACTTCCTTTCATCAATCAT
541635 TTGCCCGTCAACTTAGA-CCGAGAA
63 TTGCCCGTCAACTTAGACCCG-GAA
*
541659 GACTTTTCCATCAATCTTCTACCCGTCGGCTCAGACCCGAGAGACTTCCTT
1 GACTTTTCCATCAATCATCTACCCGTCGGCTCAGACCCGAGAGACTTCCTT
541710 CTTCATCTTT
Statistics
Matches: 109, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
84 7 0.06
85 65 0.60
86 34 0.31
87 3 0.03
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.30
Consensus pattern (86 bp):
GACTTTTCCATCAATCATCTACCCGTCGGCTCAGACCCGAGAGACTTCCTTTCATCAATCATTTG
CCCGTCAACTTAGACCCGGAA
Found at i:542980 original size:48 final size:49
Alignment explanation
Indices: 542902--543002 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 49
542892 TCTACTCCGT
* ** *
542902 AAATTTTTTCGAGGAGATTTTTCTCAGTTTTTGATTTTTAAAAGTAATC
1 AAATTTTTTCGAGGAGATTTTTATCAGTTTTCAATTTCTAAAAGTAATC
* ** *
542951 AAATTTTTT-GAGGGGATTTTTATTGGTTTTCAATTTCTAAAAGTCATC
1 AAATTTTTTCGAGGAGATTTTTATCAGTTTTCAATTTCTAAAAGTAATC
542999 AAAT
1 AAAT
543003 ACTATCATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 35 0.80
49 9 0.20
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.48
Consensus pattern (49 bp):
AAATTTTTTCGAGGAGATTTTTATCAGTTTTCAATTTCTAAAAGTAATC
Found at i:544709 original size:131 final size:132
Alignment explanation
Indices: 544553--544801 Score: 401
Period size: 131 Copynumber: 1.9 Consensus size: 132
544543 ATATATATTT
* * *
544553 TAAATATTAATCATTTTTAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTGTAAAAGATTTC
1 TAAATATCAATCATTTTCAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTC
* * *
544618 -AAAAACTTTTTGTATCTTTTCGGGTATCCATTAAGGTACGAAATGATTTTTTTTTCCAAATATA
66 AAAAAACTCTTCGTATCTTTTCAGGTATCCATTAAGGTACGAAATGATTTTTTTTTCCAAATATA
544682 AA
131 AA
* * *
544684 TAAATATCAATTATTTTCAAGTCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAATATTTC
1 TAAATATCAATCATTTTCAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTC
*
544749 AAAAAACTCTTCGTATCTTTTCAGGTATCCATTAAGGTATGAAATGATTTTTT
66 AAAAAACTCTTCGTATCTTTTCAGGTATCCATTAAGGTACGAAATGATTTTTT
544802 GGAAATAATT
Statistics
Matches: 107, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
131 59 0.55
132 48 0.45
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (132 bp):
TAAATATCAATCATTTTCAAATCTTTTATATTCCTATGGGTATCCGTAGGGGTATAAAAGATTTC
AAAAAACTCTTCGTATCTTTTCAGGTATCCATTAAGGTACGAAATGATTTTTTTTTCCAAATATA
AA
Found at i:544871 original size:149 final size:148
Alignment explanation
Indices: 544681--544949 Score: 400
Period size: 149 Copynumber: 1.8 Consensus size: 148
544671 TTCCAAATAT
* * *
544681 AAATAAATATCAATTATTTTCAAGTCTTTTATATTCCTATGGGTATCCGTAGGGGTA-TAAAATA
1 AAATAAATATCAATCATTTTCAAGTCTTTTATATTCCTATGGGTATCCATAGGGGTATTAAAAGA
* *
544745 TTTCAAAAAACTCTTCGTATCTTT-TCAGGTATCCATTAAGGTATGAAATGATTTTTTGGAAATA
66 TTTC-AAAAACT-TTCGTAT-TTTGT-AGGTATCCATCAAGGTACGAAATGATTTTTTGGAAATA
544809 ATTAAATTAACCCTCCTCACTA
127 ATTAAATTAACCCTCCTCACTA
*
544831 AAATAAATATTAATCATTTTCAA-TCTTTTATATTCCTATGGGTATCCATAGGGGTATTAAAAGA
1 AAATAAATATCAATCATTTTCAAGTCTTTTATATTCCTATGGGTATCCATAGGGGTATTAAAAGA
* *
544895 TTTCAAAAACTTTCGTATTTTGGTGGGTTTCCATCAAGGTACGAAATGATTTTTT
66 TTTCAAAAACTTTCGTATTTT-GTAGGTATCCATCAAGGTACGAAATGATTTTTT
544950 TTAAAGAAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
147 3 0.03
148 34 0.31
149 40 0.37
150 31 0.29
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (148 bp):
AAATAAATATCAATCATTTTCAAGTCTTTTATATTCCTATGGGTATCCATAGGGGTATTAAAAGA
TTTCAAAAACTTTCGTATTTTGTAGGTATCCATCAAGGTACGAAATGATTTTTTGGAAATAATTA
AATTAACCCTCCTCACTA
Found at i:546294 original size:166 final size:165
Alignment explanation
Indices: 546088--546487 Score: 450
Period size: 166 Copynumber: 2.4 Consensus size: 165
546078 AATTCTCCAT
* * * * * *
546088 ATATTATTATTTAA-TCACCATGAAGCCAATTTTGAAAAATTCTTTTTAT-TTCATGAGTTATT-
1 ATATTATTATTTAATTCA-TATTAAACCAATTTTCAAAAATT-TATTCATCTTCATGAGTT-TTG
* * * *
546150 AATTTTTTT-TTGGAAATCCCCTTGTTTTCAAAAGATGGAGTTTTCTTCTCCGTAAATTTTTTTG
63 AATTTTTTTCTT-CAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCCGTAAATATTTTTG
* * *
546214 GGAGGATTTTTAAGGGTTTTTAATTTTTAAAATGCATCAA
127 GG-GGATTTTTAACGATTTTTAATTTATAAAATGCATCAA
*
546254 ATATTATTATTTAATTCATATTAAACCAGTTTTCAAAAATTTATTCATCTTCATGAGTTTTGAAT
1 ATATTATTATTTAATTCATATTAAACCAATTTTCAAAAATTTATTCATCTTCATGAGTTTTGAAT
** * *
546319 TTTTTTCTTCAAATTGCCTTATTTTCGAAATATGGAGTTTTCTACTCCGTAAATATTTTTGGGGG
66 TTTTTTCTTCAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCCGTAAATATTTTTGGGGG
** *
546384 ATTTTTCTCGATTTTTAATTTATAAAATTCATCAA
131 ATTTTTAACGATTTTTAATTTATAAAATGCATCAA
* ** * * * * *
546419 ATATCATTATTTAATTCATATTAAATTATTTTTGAAAAA-TTAATCTATTTTCATGAGTTTTAAA
1 ATATTATTATTTAATTCATATTAAACCAATTTTCAAAAATTTATTC-ATCTTCATGAGTTTTGAA
546483 TTTTT
65 TTTTT
546488 CTTTGAAGTT
Statistics
Matches: 200, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
164 5 0.03
165 93 0.47
166 97 0.49
167 5 0.03
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.49
Consensus pattern (165 bp):
ATATTATTATTTAATTCATATTAAACCAATTTTCAAAAATTTATTCATCTTCATGAGTTTTGAAT
TTTTTTCTTCAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCCGTAAATATTTTTGGGGG
ATTTTTAACGATTTTTAATTTATAAAATGCATCAA
Found at i:546432 original size:165 final size:165
Alignment explanation
Indices: 546137--546492 Score: 448
Period size: 165 Copynumber: 2.1 Consensus size: 165
546127 TTCTTTTTAT
* * *
546137 TTCATGAGTTATTAATTTTTTTTTGGAAATCCCCTTGTTTTCAAAAGATGGAGTTTTCTTCTCCG
1 TTCATGAGTT-TTAATTTTTTTTTGCAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCCG
* * * * *
546202 TAAATTTTTTTGGGAGGATTTTTAAGGGTTTTTAATTTTTAAAATGCATCAAATATTATTATTTA
65 TAAATATTTTTGGGAGGATTTTTAACGATTTTTAATTTATAAAATGCATCAAATATCATTATTTA
*
546267 ATTCATATTAAACCAGTTTTCAAAAATTTAT-TCATC
130 ATTCATATTAAACCAGTTTTCAAAAATTAATCT-ATC
** * *
546303 TTCATGAGTTTTGAATTTTTTTCTT-CAAATTGCCTTATTTTCGAAATATGGAGTTTTCTACTCC
1 TTCATGAGTTTT-AATTTTTTT-TTGCAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCC
** *
546367 GTAAATATTTTTGGG-GGATTTTTCTCGATTTTTAATTTATAAAATTCATCAAATATCATTATTT
64 GTAAATATTTTTGGGAGGATTTTTAACGATTTTTAATTTATAAAATGCATCAAATATCATTATTT
** * * *
546431 AATTCATATTAAATTATTTTTGAAAAATTAATCTATT
129 AATTCATATTAAACCAGTTTTCAAAAATTAATCTATC
*
546468 TTCATGAGTTTTAAATTTTTCTTTG
1 TTCATGAGTTTT-AATTTTTTTTTG
546493 AAGTTCCCTT
Statistics
Matches: 163, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
164 2 0.01
165 93 0.57
166 66 0.40
167 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.49
Consensus pattern (165 bp):
TTCATGAGTTTTAATTTTTTTTTGCAAATCCCCTTATTTTCAAAAGATGGAGTTTTCTACTCCGT
AAATATTTTTGGGAGGATTTTTAACGATTTTTAATTTATAAAATGCATCAAATATCATTATTTAA
TTCATATTAAACCAGTTTTCAAAAATTAATCTATC
Found at i:546525 original size:165 final size:164
Alignment explanation
Indices: 546137--546556 Score: 415
Period size: 165 Copynumber: 2.5 Consensus size: 164
546127 TTCTTTTTAT
* * * * * * *
546137 TTCATGAGTTATT-AATTTTT-TTTTGGAAATCCCCTTGTTTTCAAAAGATGGAGTTTTCTTCTC
1 TTCATGAGTT-TTAAATTTTTCTCTT-CAAATTCCCTTATTTTCGAAATATGAAGTTTTCTTCTC
*** * * *
546200 CGTAAATTTTTTTGGGAGGATTTTTAAGGGTTTTTAATTTTTAAAATGCATCAAATATTATTATT
64 CGTAAA-TTTTTTGGG-GGATTTTTCTCGATTTTTAATTTATAAAATGCATCAAATATCATTATT
*
546265 TAATTCATATTAAACCAGTTTTCAAAAATTTATTCATC
127 TAATTCATATTAAACCAGTTTTCAAAAATTAATTCATC
* * * * *
546303 TTCATGAGTTTTGAATTTTTTTCTTCAAATTGCCTTATTTTCGAAATATGGAGTTTTCTACTCCG
1 TTCATGAGTTTTAAATTTTTCTCTTCAAATTCCCTTATTTTCGAAATATGAAGTTTTCTTCTCCG
*
546368 TAAATATTTTTGGGGGATTTTTCTCGATTTTTAATTTATAAAATTCATCAAATATCATTATTTAA
66 TAAAT-TTTTTGGGGGATTTTTCTCGATTTTTAATTTATAAAATGCATCAAATATCATTATTTAA
** * * *
546433 TTCATATTAAATTATTTTTGAAAAATTAA-TCTATT
130 TTCATATTAAACCAGTTTTCAAAAATTAATTC-ATC
* *
546468 TTCATGAGTTTTAAATTTTTCT-TTGAAGTTCCCTT-TTTTCTAGAGAA-ACT-AAGTTTTCTTC
1 TTCATGAGTTTTAAATTTTTCTCTTCAAATTCCCTTATTTTC--GA-AATA-TGAAGTTTTCTTC
** *
546529 TTTGTAAATTTTTTGAGGG-TCTTTTCTC
62 TCCGTAAATTTTTTGGGGGAT-TTTTCTC
546557 TAGTTTAAAA
Statistics
Matches: 214, Mismatches: 31, Indels: 20
0.81 0.12 0.08
Matches are distributed among these distances:
163 6 0.03
164 28 0.13
165 112 0.52
166 65 0.30
167 3 0.01
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (164 bp):
TTCATGAGTTTTAAATTTTTCTCTTCAAATTCCCTTATTTTCGAAATATGAAGTTTTCTTCTCCG
TAAATTTTTTGGGGGATTTTTCTCGATTTTTAATTTATAAAATGCATCAAATATCATTATTTAAT
TCATATTAAACCAGTTTTCAAAAATTAATTCATC
Found at i:547874 original size:79 final size:77
Alignment explanation
Indices: 547783--548031 Score: 222
Period size: 79 Copynumber: 3.2 Consensus size: 77
547773 AGATAAAAAT
* * *
547783 GAGGTTGGAGTATCCCTTCGAAAATAATGGGGTTAGAGTATCCTCGATTGTGAAAAATCGGTGTT
1 GAGGTTGAAGTATCCCTTCGAAAATAATGGGGTT-GAGTATCCCCGATTGTGGAAAATCGGTGTT
**
547848 TTAGAAATAAAATT
65 TT-GAAATAAAACC
* * * * * *
547862 G-GGATTGAAGTAT--C-TCGAAAATAATAGGATTGGGTATCCCCGATGGTGGCAAATCGATGTT
1 GAGG-TTGAAGTATCCCTTCGAAAATAATGGGGTTGAGTATCCCCGATTGTGGAAAATCGGTGTT
547923 TTGAAAATAAAACC
65 TTG-AAATAAAACC
* * * * * *
547937 GATGTTGGAGTATCCTTTC-AGAAATAATGGGGTTGGAGTATCCCCAATTATGGAAAATTGGTGT
1 GAGGTTGAAGTATCCCTTCGA-AAATAATGGGGTT-GAGTATCCCCGATTGTGGAAAATCGGTGT
548001 TTTGGAAATAAAACC
64 TTT-GAAATAAAACC
*
548016 -AGGGTTGGAGTATCCC
1 GA-GGTTGAAGTATCCC
548032 CGATTATGGA
Statistics
Matches: 135, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
74 1 0.01
75 43 0.32
76 16 0.12
77 2 0.01
78 16 0.12
79 56 0.41
80 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (77 bp):
GAGGTTGAAGTATCCCTTCGAAAATAATGGGGTTGAGTATCCCCGATTGTGGAAAATCGGTGTTT
TGAAATAAAACC
Found at i:548030 original size:51 final size:51
Alignment explanation
Indices: 547966--548082 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
547956 AGAAATAATG
* **
547966 GGGTTGGAGTATCCCCAATTATGGAAAATTGGTGTTTTGGAAATAAAACCA
1 GGGTTGGAGTATCCCCAATTATGGAAAATTGGTATTTTAAAAATAAAACCA
* *
548017 GGGTTGGAGTATCCCCGATTATGGAAAATTGGTATTTTAAAAATAAAATCA
1 GGGTTGGAGTATCCCCAATTATGGAAAATTGGTATTTTAAAAATAAAACCA
* *
548068 AGGTTGGAATATCCC
1 GGGTTGGAGTATCCC
548083 TTCGGAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCAATTATGGAAAATTGGTATTTTAAAAATAAAACCA
Found at i:552761 original size:24 final size:24
Alignment explanation
Indices: 552733--552779 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
552723 TCTAGTAGCC
* *
552733 AGGAGAGACAGGAGGGATGATAGG
1 AGGAGAGACAGGAGAGATAATAGG
552757 AGGAGAGACAGGAGAGATAATAG
1 AGGAGAGACAGGAGAGATAATAG
552780 AGAGAGGAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.45, T:0.09
Consensus pattern (24 bp):
AGGAGAGACAGGAGAGATAATAGG
Found at i:552769 original size:12 final size:12
Alignment explanation
Indices: 552733--552770 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
552723 TCTAGTAGCC
552733 AGGAGAGACAGG
1 AGGAGAGACAGG
*
552745 AGG-GATGATAGG
1 AGGAGA-GACAGG
552757 AGGAGAGACAGG
1 AGGAGAGACAGG
552769 AG
1 AG
552771 AGATAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.39, C:0.05, G:0.50, T:0.05
Consensus pattern (12 bp):
AGGAGAGACAGG
Found at i:558131 original size:423 final size:414
Alignment explanation
Indices: 557354--558191 Score: 1527
Period size: 423 Copynumber: 2.0 Consensus size: 414
557344 TTTGGGCTTT
557354 ATTTAGCATAAAAACTTGTTATTTGGGTTTAAGTAAGAGTTGGGCTTGTTAGCCCCTTAGGGTTT
1 ATTTAGCATAAAAACTTGTTATTTGGGTTTAAGTAAGAGTTGGGCTTGTTAGCCCCTTAGGGTTT
557419 GTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAAAAGATTTGGAGGGGGCAGACAT
66 GTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAAAAGATTTGGAGGGGGCAGACAT
557484 TCATATTTGCAGATTAAACACATTTTTGTGTGAGAGTGATTCTTAGGTTCTTGAGTGAGCCAATT
131 TCATATTTGCAGATTAAACACATTTTTGTGTGAGAGTGATTCTTAGGTTCTTGAGTGAGCCAATT
557549 TTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATCATTCCTTTTGGCTTATCAATCTTG
196 TTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATCATTCCTTTTGGCTTATCAATCTTG
557614 TGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTTCTGCTTCTTTCA
261 TGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTTCTGCTTCTTTCA
557679 ATTTCTGTTCTTGCATCAATAATTCTGTTTATTGTTAGAAATCCATCTCAAGATCATTATTTAGG
326 ATTTCTGTTCTTGCATCAATAATTCTGTTTATTGTTAGAAATCCATCTCAAGATCATTATTTAGG
557744 CAACCTTGGTTCATGGTTGTCATC
391 CAACCTTGGTTCATGGTTGTCATC
557768 ATTTAGCATAAAAACTTGTTATTTGGGTTTAAGTAAGAGTTGGGCTTGTTAGCATAATAAGCCCC
1 ATTTAGCATAAAAACTTGTTATTTGGGTTTAAGTAAGAGTTGGGC---TT-G--T--T-AGCCCC
557833 TTAGGGTTTGTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAAAAGATTTGGAGGG
57 TTAGGGTTTGTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAAAAGATTTGGAGGG
*
557898 GGCAGACATTCATATTTTCAGATTAAACACATTTTTGTGTGAGAGTGTGATTCTTAGGTTCTTGA
122 GGCAGACATTCATATTTGCAGATTAAACACATTTTTGTGTGAGA--GTGATTCTTAGGTTCTTGA
*
557963 GTGAGCCAA-TTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGTGATCATTCCTTTTGGCT
185 GTGAGCCAATTTTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATCATTCCTTTTGGCT
*
558027 TATTAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTT-
250 TATCAATCTTGTGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTTC
*
558091 TGCTTCTTTCAATTTCTGTTTTTGCATCAATAATTCTGTTTATTGTTAGAAATCCATCTCAAGAT
315 TGCTTCTTTCAATTTCTGTTCTTGCATCAATAATTCTGTTTATTGTTAGAAATCCATCTCAAGAT
558156 CATTATTTAGGCAACCTTGGTTCATGGTTGTCATC
380 CATTATTTAGGCAACCTTGGTTCATGGTTGTCATC
558191 A
1 A
558192 ATTGGTATCA
Statistics
Matches: 409, Mismatches: 4, Indels: 13
0.96 0.01 0.03
Matches are distributed among these distances:
414 45 0.11
417 2 0.00
418 1 0.00
420 1 0.00
422 1 0.00
423 214 0.52
424 117 0.29
425 28 0.07
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (414 bp):
ATTTAGCATAAAAACTTGTTATTTGGGTTTAAGTAAGAGTTGGGCTTGTTAGCCCCTTAGGGTTT
GTGTTATCTATGACTTATGAGGGCATATATAAGCTCTTGTAAAAAGATTTGGAGGGGGCAGACAT
TCATATTTGCAGATTAAACACATTTTTGTGTGAGAGTGATTCTTAGGTTCTTGAGTGAGCCAATT
TTTCTGGATCTTATCAAGAGGCCAAGACTCTTGTGGCGATCATTCCTTTTGGCTTATCAATCTTG
TGATTGTGGCGCCATCCTTCATCTCTAATCTATTCCATTTTGTTATTTTTTTTCTGCTTCTTTCA
ATTTCTGTTCTTGCATCAATAATTCTGTTTATTGTTAGAAATCCATCTCAAGATCATTATTTAGG
CAACCTTGGTTCATGGTTGTCATC
Found at i:559167 original size:42 final size:42
Alignment explanation
Indices: 559112--559230 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
559102 CAGCCCTCAA
* * *
559112 AGAGAAAGAAGAGAGAGGATGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
559154 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
559196 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
559231 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:559197 original size:24 final size:24
Alignment explanation
Indices: 559121--559206 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
559111 AAGAGAAAGA
* *
559121 AGAGAGAGGATGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
559145 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
559163 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
559187 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
559207 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:564408 original size:61 final size:61
Alignment explanation
Indices: 564218--564717 Score: 637
Period size: 61 Copynumber: 8.2 Consensus size: 61
564208 AAGAGCCCTA
* * * * * *
564218 CTCTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGGAAAG-TGTCCTA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
* *
564277 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTAGGGCTTTAAAAGGAAAAGACATCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGT-GGGCTTTAAAAAGAAAAGACGTCCTG
* * * * * *
564339 CTCTTTGAGGATTGAAAGGTGCCACCAGCTTATGTGGGCTTTAAAAACAAAAAATGTCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
* * ** *
564400 CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGTGTCCTA
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AAAAGACGTCCTG
* * * * * **
564462 CTCTTTGAGGATTGGAAGGTGCCACTAACTTGTGTGGACTTTAAAAGGAAAAGATATCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
* * * * * *
564523 CTTTTTGAGAACTGAAAGGTGCCACCAACTTCTGTGGGCTTTAAAAGGAAAAGGCATCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
* *
564584 CTCTTTGAGGACAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAA-AAAAGGCGTCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
* *
564644 CTCTTTAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
1 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
564705 CTCTTTGAGGACT
1 CTCTTTGAGGACT
564718 AAAAAGGATA
Statistics
Matches: 387, Mismatches: 49, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
59 33 0.09
60 63 0.16
61 200 0.52
62 91 0.24
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (61 bp):
CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
Found at i:564453 original size:123 final size:121
Alignment explanation
Indices: 564218--564715 Score: 665
Period size: 123 Copynumber: 4.1 Consensus size: 121
564208 AAGAGCCCTA
* * ** * *
564218 CTCTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTT-GAAAGGAAAGTGTCCTACTCTT
1 CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAATGTCCTGCTCTT
564282 TGAGGACTGAAAGGTGCCACCAACTTGTGTAGGGCTTTAAAAGGAAAAGACATCCTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGT-GGGCTTTAAAAGGAAAAGACATCCTG
* *
564339 CTCTTTGAGGATTGAAAGGTGCCACCAGCTTATGTGGGCTTTAAAAACAAAAAATGTCCTGCTCT
1 CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAA-AAAAAATGTCCTGCTCT
* *** *
564404 TTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGTGTCCTA
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAAGACATCCTG
* * * * * * *
564462 CTCTTTGAGGATTGGAAGGTGCCACTAACTTGTGTGGACTTTAAAAGGAAAAGATATCCTGCTTT
1 CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AAAAAAATGTCCTGCTCT
* * *
564527 TTGAGAACTGAAAGGTGCCACCAACTTCTGTGGGCTTTAAAAGGAAAAGGCATCCTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTG
** ***
564584 CTCTTTGAGGACAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAGGCGTCCTGCTCTT
1 CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAATGTCCTGCTCTT
* * * *
564649 TAAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGACGTCCTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTG
564705 CTCTTTGAGGA
1 CTCTTTGAGGA
564716 CTAAAAAGGA
Statistics
Matches: 328, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
121 113 0.34
122 67 0.20
123 148 0.45
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (121 bp):
CTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAAAAATGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTG
Found at i:573805 original size:18 final size:19
Alignment explanation
Indices: 573782--573818 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
573772 TTGACCTGAC
573782 GCTGAGACTTACCA-CGAT
1 GCTGAGACTTACCATCGAT
573800 GCTGAGACTTACCATCGAT
1 GCTGAGACTTACCATCGAT
573819 TCTCAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (19 bp):
GCTGAGACTTACCATCGAT
Found at i:574941 original size:26 final size:27
Alignment explanation
Indices: 574911--574963 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
574901 TAACTTTTGA
574911 TTGAA-AAA-CGGAGTTGGAGTATCCCC
1 TTGAAGAAATCGG-GTTGGAGTATCCCC
*
574937 TTGAAGAAATCGGGTTGGAGTGTCCCC
1 TTGAAGAAATCGGGTTGGAGTATCCCC
574964 GATGATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 16 0.67
28 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (27 bp):
TTGAAGAAATCGGGTTGGAGTATCCCC
Found at i:577235 original size:20 final size:20
Alignment explanation
Indices: 577210--577336 Score: 110
Period size: 20 Copynumber: 5.7 Consensus size: 20
577200 TTTTAACTAG
577210 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
577230 ATGTATCAATACATCTGTGTAAAAA
1 ATGTATCGATACA--T-TG--AAAA
*
577255 GATAGAATATATCGATACATTGAAGA
1 -AT-G--T--ATCGATACATTGAAAA
*
577281 ATGTATCGATACATTCATATAA
1 ATGTATCGATACATTGA-A-AA
577303 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
577323 ATGTATCGATACAT
1 ATGTATCGATACAT
577337 CTGGGTACTT
Statistics
Matches: 88, Mismatches: 6, Indels: 26
0.73 0.05 0.22
Matches are distributed among these distances:
20 40 0.45
21 2 0.02
22 19 0.22
23 2 0.02
24 1 0.01
25 6 0.07
26 5 0.06
27 1 0.01
28 2 0.02
29 2 0.02
31 8 0.09
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:578098 original size:48 final size:48
Alignment explanation
Indices: 578037--578214 Score: 234
Period size: 48 Copynumber: 3.8 Consensus size: 48
578027 AGAGGAGTGT
* * *
578037 CAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTAATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
578085 CAATGTGCTAATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAATGGA
1 CAATGTGCTAATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* * * * *
578133 CAATGTGCTGATTCAAGGCCGGTGACATTGAGCTAA--TAAAGGTGGA
1 CAATGTGCTAATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
* *
578179 CAATGTGCTGATTTAAGGCCAGCGACATTGAGCTAA
1 CAATGTGCTAATTCAAGGCCAGCGACATTGAGCTAA
578215 TAAAGGTGCC
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 40 0.35
48 75 0.65
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (48 bp):
CAATGTGCTAATTCAAGGCCAGCGACATTGAGCTAAGGGAAAAGTGGA
Found at i:578180 original size:21 final size:22
Alignment explanation
Indices: 578156--578223 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 22
578146 CAAGGCCGGT
578156 GACATTGAGCTAATAAAGGTG-
1 GACATTGAGCTAATAAAGGTGC
* * * * *
578177 GACAATGTGCTGATTTAAGGCCAGC
1 GACATTGAGCT-AATAAAGG--TGC
578202 GACATTGAGCTAATAAAGGTGC
1 GACATTGAGCTAATAAAGGTGC
578224 CAAGATGCTG
Statistics
Matches: 33, Mismatches: 10, Indels: 7
0.66 0.20 0.14
Matches are distributed among these distances:
21 9 0.27
22 8 0.24
24 7 0.21
25 9 0.27
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.24
Consensus pattern (22 bp):
GACATTGAGCTAATAAAGGTGC
Found at i:578248 original size:45 final size:46
Alignment explanation
Indices: 578037--578248 Score: 221
Period size: 48 Copynumber: 4.5 Consensus size: 46
578027 AGAGGAGTGT
** * * * *
578037 CAATGTGCCAATTCAAGGCCAACGACATCGAGCTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA--TAAAGGTGGA
* * * **
578085 CAATGTGCTAATTCAAGGCCAGCAACATTGAGCTAAGGGAAAAATGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAA--TAAAGGTGGA
* *
578133 CAATGTGCTGATTCAAGGCCGGTGACATTGAGCTAATAAAGGTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATAAAGGTGGA
* *
578179 CAATGTGCTGATTTAAGGCCAGCGACATTGAGCTAATAAAGGT-GC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATAAAGGTGGA
*
578224 CAA-GATGCTGATTCAATGCCAGCGA
1 CAATG-TGCTGATTCAAGGCCAGCGA
578249 TATCGGACTT
Statistics
Matches: 145, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 22 0.15
46 47 0.32
48 75 0.52
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (46 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGAGCTAATAAAGGTGGA
Found at i:578521 original size:29 final size:29
Alignment explanation
Indices: 578371--578653 Score: 258
Period size: 28 Copynumber: 9.8 Consensus size: 29
578361 CCGACTTGTG
* * *
578371 TGGGCTTTG-GAAGGGTGCCACTGATTTGTG
1 TGGGCTTTGAGAAGGATGCCACTGA-CT-TA
* * * *
578401 TGGGCTTTTAAAAGG-TGCCACTGACCTG
1 TGGGCTTTGAGAAGGATGCCACTGACTTA
*
578429 TGGGCTTTGA-ACAGG-TGCCACTGACTTG
1 TGGGCTTTGAGA-AGGATGCCACTGACTTA
* * *
578457 TGGGCTTCGA-AAGGGTGCCACTGATTTA
1 TGGGCTTTGAGAAGGATGCCACTGACTTA
* * *
578485 CGGTCTTTTGAGGA-GATGCCACTGACTTA
1 TGGGC-TTTGAGAAGGATGCCACTGACTTA
* *
578514 TGGGCTTTGA-AAGGATGCCACTAACTTG
1 TGGGCTTTGAGAAGGATGCCACTGACTTA
* *
578542 TGGGCTTTGA-AATGATGCCACTGATTTGTA
1 TGGGCTTTGAGAAGGATGCCACTGA-CT-TA
*
578572 TGGGCTTTGAGAAGGATGCCACTGACTTG
1 TGGGCTTTGAGAAGGATGCCACTGACTTA
* *
578601 TGGGCTTTGAGAAGGATGACATTGACTTA
1 TGGGCTTTGAGAAGGATGCCACTGACTTA
*
578630 TGGGCTTTGAAAAGGATGCCACTG
1 TGGGCTTTGAGAAGGATGCCACTG
578654 GGTTGCCACC
Statistics
Matches: 211, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
27 5 0.02
28 90 0.43
29 69 0.33
30 30 0.14
31 17 0.08
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (29 bp):
TGGGCTTTGAGAAGGATGCCACTGACTTA
Found at i:578533 original size:85 final size:87
Alignment explanation
Indices: 578369--578653 Score: 337
Period size: 85 Copynumber: 3.3 Consensus size: 87
578359 CACCGACTTG
* * ** * * *
578369 TGTGGGCTTTGGAAGGGTGCCACTGATTTGTGTGGGCTTTTAAAAGG-TGCCACTGACCTGTGGG
1 TGTGGGCTTTGAAAGGATGCCACTGATTTGTACGGGCTTTGAGAAGGATGCCACTGACTTGTGGG
578433 CTTTGAACAGG-TGCCACTGACT
66 CTTTGAA-AGGATGCCACTGACT
* * * * *
578455 TGTGGGCTTCGAAAGGGTGCCACTGA-TT-TACGGTCTTTTGAGGA-GATGCCACTGACTTATGG
1 TGTGGGCTTTGAAAGGATGCCACTGATTTGTACGGGC-TTTGAGAAGGATGCCACTGACTTGTGG
*
578517 GCTTTGAAAGGATGCCACTAACT
65 GCTTTGAAAGGATGCCACTGACT
* *
578540 TGTGGGCTTTGAAATGATGCCACTGATTTGTATGGGCTTTGAGAAGGATGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGATGCCACTGATTTGTACGGGCTTTGAGAAGGATGCCACTGACTTGTGGG
* *
578605 CTTTGAGAAGGATGACATTGACT
66 CTTTGA-AAGGATGCCACTGACT
*
578628 TATGGGCTTTGAAAAGGATGCCACTG
1 TGTGGGCTTTG-AAAGGATGCCACTG
578654 GGTTGCCACC
Statistics
Matches: 168, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
84 8 0.05
85 62 0.37
86 33 0.20
87 29 0.17
88 23 0.14
89 13 0.08
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (87 bp):
TGTGGGCTTTGAAAGGATGCCACTGATTTGTACGGGCTTTGAGAAGGATGCCACTGACTTGTGGG
CTTTGAAAGGATGCCACTGACT
Found at i:578693 original size:32 final size:32
Alignment explanation
Indices: 578655--578838 Score: 271
Period size: 32 Copynumber: 5.8 Consensus size: 32
578645 ATGCCACTGG
* * *
578655 GTTGCCACCGACTTGTGTAGGCTTTGAAATGG
1 GTTGCCATCGACTTGTGTGGGCTTTGAAATGA
*
578687 GTTGCCATCGACTTGTGTGGGCTTTCAAATGA
1 GTTGCCATCGACTTGTGTGGGCTTTGAAATGA
578719 GTTGCCA-CTGACTTGTGTGGGCTTTGAAATGA
1 GTTGCCATC-GACTTGTGTGGGCTTTGAAATGA
* *
578751 GTTGCCATCGACTTGTGTGAGCTTTGAAATGG
1 GTTGCCATCGACTTGTGTGGGCTTTGAAATGA
** *
578783 GTTTTCATCGACTTGTGTGGGCTTTCAAATGA
1 GTTGCCATCGACTTGTGTGGGCTTTGAAATGA
578815 GTTGCCATCGACTTGTGTGGGCTT
1 GTTGCCATCGACTTGTGTGGGCTT
578839 AAAAGGTTGC
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 1 0.01
32 134 0.99
33 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (32 bp):
GTTGCCATCGACTTGTGTGGGCTTTGAAATGA
Found at i:578764 original size:96 final size:96
Alignment explanation
Indices: 578655--578838 Score: 309
Period size: 96 Copynumber: 1.9 Consensus size: 96
578645 ATGCCACTGG
578655 GTTGCCACCGACTTGTGT-AGGCTTTGAAATGGGTTGCCATCGACTTGTGTGGGCTTTCAAATGA
1 GTTGCCACCGACTTGTGTGA-GCTTTGAAATGGGTTGCCATCGACTTGTGTGGGCTTTCAAATGA
578719 GTTGCCA-CTGACTTGTGTGGGCTTTGAAATGA
65 GTTGCCATC-GACTTGTGTGGGCTTTGAAATGA
* **
578751 GTTGCCATCGACTTGTGTGAGCTTTGAAATGGGTTTTCATCGACTTGTGTGGGCTTTCAAATGAG
1 GTTGCCACCGACTTGTGTGAGCTTTGAAATGGGTTGCCATCGACTTGTGTGGGCTTTCAAATGAG
578816 TTGCCATCGACTTGTGTGGGCTT
66 TTGCCATCGACTTGTGTGGGCTT
578839 AAAAGGTTGC
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
96 81 0.98
97 2 0.02
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (96 bp):
GTTGCCACCGACTTGTGTGAGCTTTGAAATGGGTTGCCATCGACTTGTGTGGGCTTTCAAATGAG
TTGCCATCGACTTGTGTGGGCTTTGAAATGA
Found at i:578868 original size:27 final size:27
Alignment explanation
Indices: 578830--578950 Score: 179
Period size: 27 Copynumber: 4.5 Consensus size: 27
578820 CATCGACTTG
* * *
578830 TGTGGGCTTAAAAGGTTGCCACGGAAT
1 TGTGGACTTAAAAGGGTGCCACGGAGT
*
578857 TGTGGGCTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTAAAAGGGTGCCACGGAGT
* *
578884 TGTGGACTTAAAAGGTTGCCACGGACT
1 TGTGGACTTAAAAGGGTGCCACGGAGT
*
578911 TGTGGACTTAAAAGGGTGCCACAGAGT
1 TGTGGACTTAAAAGGGTGCCACGGAGT
578938 TGTGGACTTAAAA
1 TGTGGACTTAAAA
578951 AGGAATGCCA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (27 bp):
TGTGGACTTAAAAGGGTGCCACGGAGT
Found at i:578894 original size:54 final size:54
Alignment explanation
Indices: 578830--578950 Score: 206
Period size: 54 Copynumber: 2.2 Consensus size: 54
578820 CATCGACTTG
* * *
578830 TGTGGGCTTAAAAGGTTGCCACGGAATTGTGGGCTTAAAAGGGTGCCACGGAGT
1 TGTGGACTTAAAAGGTTGCCACGGAATTGTGGACTTAAAAGGGTGCCACAGAGT
*
578884 TGTGGACTTAAAAGGTTGCCACGGACTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGTGGACTTAAAAGGTTGCCACGGAATTGTGGACTTAAAAGGGTGCCACAGAGT
578938 TGTGGACTTAAAA
1 TGTGGACTTAAAA
578951 AGGAATGCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (54 bp):
TGTGGACTTAAAAGGTTGCCACGGAATTGTGGACTTAAAAGGGTGCCACAGAGT
Found at i:589458 original size:4 final size:4
Alignment explanation
Indices: 589449--589486 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
589439 AAACAAATCA
* *
589449 AAAT AAAT AAAT AAAT GAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
589487 GCACCTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:591900 original size:79 final size:79
Alignment explanation
Indices: 591531--591901 Score: 261
Period size: 79 Copynumber: 4.7 Consensus size: 79
591521 ATAAAAATGG
** * * * * * * * **
591531 GGTTGGAGTATCCCCTAAAAAATAATAGGGTTGGAGTATCCCCAATTATGG-AAATTAGTGTTTT
1 GGTTGGAGTATCCTTTCAGAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATCAACGTTTT
591595 -AGAAATAAAATC-A
66 GA-AAATAAAATCGA
** * * * * * * ** *
591608 GGATTGGAGTATCCCCTCAAAAATAACAGGATTGAAGTA-CCCCGATGGT-GAAATATCGATATC
1 GG-TTGGAGTATCCTTTCAGAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAA-ATCAACGTT
*
591671 TTGGAAATAAAATCGA
64 TTGAAAATAAAATCGA
* * * *
591687 GGTTGGAGTATCTTTTTCAAAAATAACAGGGTTAGAGTATCCCCGATTGTGGAAAATCAACGTTT
1 GGTTGGAGTATC-CTTTCAGAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATCAACGTTT
* *
591752 TGGAAATAAAACCGA
65 TGAAAATAAAATCGA
* * * * * **
591767 GGTTAGAGTAT-CTTCTCAGAAATAACAGGGTTGGAGTATCTTTGATTATAGAAAATCAGTGTTT
1 GGTTGGAGTATCCTT-TCAGAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATCAACGTTT
* *
591831 TGAAAATAAAATGGG
65 TGAAAATAAAATCGA
* * * *
591846 GGTTGGAGTATCCCTTCGGAAATAAC-GAGGTTGGAGGATCCTCGATGGTGGAAAAT
1 GGTTGGAGTATCCTTTCAGAAATAACAG-GGTTGGAGTATCCTCGATTGTGGAAAAT
591902 TGATATTTTA
Statistics
Matches: 234, Mismatches: 49, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
76 1 0.00
77 11 0.05
78 61 0.26
79 116 0.50
80 41 0.18
81 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCTTTCAGAAATAACAGGGTTGGAGTATCCTCGATTGTGGAAAATCAACGTTTT
GAAAATAAAATCGA
Found at i:595126 original size:11 final size:11
Alignment explanation
Indices: 595110--595134 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
595100 TTGTTTCATG
595110 CTTGATTTAGC
1 CTTGATTTAGC
595121 CTTGATTTAGC
1 CTTGATTTAGC
595132 CTT
1 CTT
595135 CATGATCCAT
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:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (11 bp):
CTTGATTTAGC
Found at i:595881 original size:174 final size:173
Alignment explanation
Indices: 595579--595895 Score: 544
Period size: 174 Copynumber: 1.8 Consensus size: 173
595569 AGATATTTCC
*
595579 ATATTAATCATTTTTTAATCTTTTATATTCTTATGGGGGTCTGTAGGGGTATAAAAGATTTCAAA
1 ATATTAATCATTTTTTAATCTTTTATATTCTTATGGGGGTCCGTAGGGGTATAAAAGATTTCAAA
* * * *
595644 AACTTTTCGTATCTTTTTGAGTTTCCATTAAGGTACAAAATGGTATTTTTTAAAAATAAATAAAT
66 AACTTTTCGTATCTTTTTGAGTTTCCATTAAAGTACAAAAAGGTATTTTCTAAAAACAAATAAAT
*
595709 TAAATTAAATTAAATTAAAGTAACACTTTCATAATTGAAATAA
131 AAAATTAAATTAAATTAAAGTAACACTTTCATAATTGAAATAA
595752 ATATTAATCATTTTTTTAATCTTTTATATTCTTATGGGGGTCCGTAGGGGTATAAAAGATTTCAA
1 ATATTAATCA-TTTTTTAATCTTTTATATTCTTATGGGGGTCCGTAGGGGTATAAAAGATTTCAA
* * *
595817 AAACTTTTCGTATCTTTTTGGGTTTCTATTAAAGTACAAAAAGGTATTTTCTGAAAACAAATAAA
65 AAACTTTTCGTATCTTTTTGAGTTTCCATTAAAGTACAAAAAGGTATTTTCTAAAAACAAATAAA
595882 TAAAATTAAATTAA
130 TAAAATTAAATTAA
595896 TACTTTCATA
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
173 10 0.07
174 124 0.93
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (173 bp):
ATATTAATCATTTTTTAATCTTTTATATTCTTATGGGGGTCCGTAGGGGTATAAAAGATTTCAAA
AACTTTTCGTATCTTTTTGAGTTTCCATTAAAGTACAAAAAGGTATTTTCTAAAAACAAATAAAT
AAAATTAAATTAAATTAAAGTAACACTTTCATAATTGAAATAA
Found at i:596233 original size:3 final size:3
Alignment explanation
Indices: 596225--596276 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
596215 GAAATATCCT
596225 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
596273 ATA A
1 ATA A
596277 AGATTTTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:599183 original size:22 final size:22
Alignment explanation
Indices: 599156--599200 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
599146 CAAATGCTGG
599156 TTTTTCCTTTTTTTTTTTGTAT
1 TTTTTCCTTTTTTTTTTTGTAT
*
599178 TTTTTCTTTTTTTTTTTTGTAT
1 TTTTTCCTTTTTTTTTTTGTAT
599200 T
1 T
599201 CTTGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.04, C:0.07, G:0.04, T:0.84
Consensus pattern (22 bp):
TTTTTCCTTTTTTTTTTTGTAT
Found at i:604964 original size:12 final size:12
Alignment explanation
Indices: 604947--604993 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
604937 AAGAGAAAGA
604947 AGAGATAGGAGG
1 AGAGATAGGAGG
604959 AGAGATAGGAGG
1 AGAGATAGGAGG
*
604971 -GATGACAGGAGG
1 AGA-GATAGGAGG
604983 AGAGATAGGAG
1 AGAGATAGGAG
604994 AGATAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.49, T:0.09
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:605010 original size:18 final size:18
Alignment explanation
Indices: 604983--605032 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
604973 TGACAGGAGG
*
604983 AGAGATAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
605001 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
605019 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
605033 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:611562 original size:42 final size:42
Alignment explanation
Indices: 611507--611625 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
611497 TTCTTCTCTC
* *
611507 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
611549 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
611591 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
611626 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:611566 original size:12 final size:11
Alignment explanation
Indices: 611540--611615 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
611530 TCTATTATCT
*
611540 CTCCTGTCTCTC
1 CTCCTATCTC-C
611552 CTCCTATCATCC
1 CTCCTATC-TCC
611564 CTCCTATCT--
1 CTCCTATCTCC
*
611573 CTACTATCT--
1 CTCCTATCTCC
*
611582 CTCCTGTCTCTC
1 CTCCTATCTC-C
611594 CTCCTATCATCC
1 CTCCTATC-TCC
*
611606 CTCCTCTCTC
1 CTCCTATCTC
611616 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:611567 original size:24 final size:24
Alignment explanation
Indices: 611531--611616 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
611521 CCTCCTCTCT
* *
611531 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
611555 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
611576 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
611597 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
611617 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:611591 original size:18 final size:18
Alignment explanation
Indices: 611522--611592 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
611512 CCTGTCATCC
* *
611522 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
611540 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
611562 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
611582 CTCCTGTCTCT
1 CTCCTGTCTCT
611593 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:614718 original size:42 final size:42
Alignment explanation
Indices: 614657--614775 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
614647 TAGCCCTCAA
* *
614657 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
614699 AGAGATAGTAGAGATAGGAGGGATGATTGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
614741 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
614776 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:615901 original size:15 final size:14
Alignment explanation
Indices: 615864--615902 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
615854 AGAATACAAA
615864 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
615878 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
615894 AAAAAAAAA
1 AAAAAAAAA
615903 CCAGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:616671 original size:12 final size:11
Alignment explanation
Indices: 616649--616724 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
616639 AGAGAAAGAA
*
616649 GAGAGAGGAGG
1 GAGATAGGAGG
616660 GATGATAGGAGG
1 GA-GATAGGAGG
*
616672 AGAGACAGGA--
1 -GAGATAGGAGG
*
616682 GAGATAGTA--
1 GAGATAGGAGG
616691 GAGATAGGAGG
1 GAGATAGGAGG
616702 GATGATAGGAGG
1 GA-GATAGGAGG
*
616714 AGAGACAGGAG
1 -GAGATAGGAG
616725 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:616700 original size:42 final size:42
Alignment explanation
Indices: 616639--616757 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
616629 TAGCCCTCAA
* *
616639 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
616681 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
616723 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
616758 GAGAGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:616741 original size:18 final size:18
Alignment explanation
Indices: 616714--616763 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
616704 TGATAGGAGG
*
616714 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
616732 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
616750 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
616764 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:623171 original size:22 final size:24
Alignment explanation
Indices: 623143--623186 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
623133 TTTTTTTTTC
623143 AAGAATACAAAAA-A-AAAAAAGA
1 AAGAATACAAAAAGAGAAAAAAGA
623165 AAGAATACAAAAAGAGAAAAAA
1 AAGAATACAAAAAGAGAAAAAA
623187 AAAAACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 1 0.05
24 6 0.30
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (24 bp):
AAGAATACAAAAAGAGAAAAAAGA
Found at i:623960 original size:12 final size:11
Alignment explanation
Indices: 623938--624013 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
623928 AGAGAAAGAA
*
623938 GAGAGAGGAGG
1 GAGATAGGAGG
623949 GATGATAGGAGG
1 GA-GATAGGAGG
*
623961 AGAGACAGGA--
1 -GAGATAGGAGG
*
623971 GAGATAGTA--
1 GAGATAGGAGG
623980 GAGATAGGAGG
1 GAGATAGGAGG
623991 GATGATAGGAGG
1 GA-GATAGGAGG
*
624003 AGAGACAGGAG
1 -GAGATAGGAG
624014 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:623970 original size:24 final size:24
Alignment explanation
Indices: 623937--624022 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
623927 AAGAGAAAGA
*
623937 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
623961 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
623979 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
624003 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
624023 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:623989 original size:42 final size:42
Alignment explanation
Indices: 623928--624046 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
623918 TAGCCCTCAA
* *
623928 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
623970 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
624012 AGAGATAATAGAGAGAGGAGGGATGACAGAAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
624047 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Done.