Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008110.1 Hibiscus syriacus cultivar Beakdansim tig00110646_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 844371
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 5
Found at i:423232 original size:6 final size:6
Alignment explanation
Indices: 423221--423921 Score: 1123
Period size: 6 Copynumber: 120.8 Consensus size: 6
423211 TAATATTGTT
423221 TATATC TATATC TATATC TATATC TATA-- TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423267 --TATC TATATC TATATC TATATC --TATC TATATC --TATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
423309 TATATC TATATC TATA-- TATATC TATATC TATATC TATATC TATATA
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
423355 TCTATC TATATC TATATC --TATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423401 TATA-- TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423447 TATATC TATATC --TATC TATATC TATATC TATATC --TATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423491 TATATC TATATC TATATC TATATC TATATC TATA-- TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423537 TATATC --TATC -ATATC TATA-- TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
* *
423580 TCTATC TATATC TATATC TATATC TATATC TATATC TATATC TATATA
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423628 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423676 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423724 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC --TATATC
* *
423774 TATATC TATATC TCTATC TATATC TATATC TCTATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
*
423822 TATATC TATATC TATATC TATATC TATATC TATATC TCTATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423870 TATATC --TATC TATATC TATATC TATATC TATATC TATATC TATATC
1 TATATC TATATC TATATC TATATC TATATC TATATC TATATC TATATC
423916 TCATAT
1 T-ATAT
423922 AGGTTGAGTT
Statistics
Matches: 652, Mismatches: 14, Indels: 57
0.90 0.02 0.08
Matches are distributed among these distances:
4 52 0.08
5 4 0.01
6 586 0.90
7 4 0.01
8 6 0.01
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:427598 original size:2 final size:2
Alignment explanation
Indices: 427591--427630 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
427581 TGTTGTACAT
427591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
427631 AATCATCCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:428273 original size:45 final size:44
Alignment explanation
Indices: 428221--428461 Score: 286
Period size: 45 Copynumber: 5.4 Consensus size: 44
428211 AATACATCAT
* *
428221 TATGCATTTTAAACTCTAACATCTTTTCTGTTGATAATGCACCCA
1 TATGCA-TTTCAACTCTAGCATCTTTTCTGTTGATAATGCACCCA
* * * *
428266 TATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTCAACTCTAGCAT-CTTTTCTGTTGATAATGCACCCA
* * * *
428311 TATACATCTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCA
1 TATGCATTTCAACTC-TAGCAT-CTTTTCTGTTGATAATGCACCCA
* *
428356 TATACATTTCAACTCTAGCAAACTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTCTAGC-ATCTTTTCTGTTGATAATGCACCCA
* * *
428401 TATGCATTTCAACTCTAGTATATTATTCTGTTGATAATACACCCA
1 TATGCATTTCAACTCTAGCATCTT-TTCTGTTGATAATGCACCCA
428446 TATGCATTTCAACTCT
1 TATGCATTTCAACTCT
428462 GACATCCTTT
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
44 14 0.08
45 156 0.91
46 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (44 bp):
TATGCATTTCAACTCTAGCATCTTTTCTGTTGATAATGCACCCA
Found at i:428460 original size:90 final size:90
Alignment explanation
Indices: 428243--428461 Score: 316
Period size: 90 Copynumber: 2.4 Consensus size: 90
428233 ACTCTAACAT
* * * *
428243 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAAACTTTTATGTTGATAATGCAC
428308 CCATATACATCTCAACCATAGTATA
66 CCATATACATCTCAACCATAGTATA
* * *
428333 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCAAACTTTTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAAACTTTTATGTTGATAATGCAC
* *
428398 CCATATGCATTTCAACTC-TAGTATA
66 CCATATACATCTCAAC-CATAGTATA
*
428423 -TTATTCTGTTGATAATACACCCATATGCATTTCAACTCT
1 CTT-TTCTGTTGATAATGCACCCATATGCATTTCAACTCT
428462 GACATCCTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
89 2 0.02
90 112 0.97
91 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (90 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCAAACTTTTATGTTGATAATGCAC
CCATATACATCTCAACCATAGTATA
Found at i:428483 original size:90 final size:90
Alignment explanation
Indices: 428243--428498 Score: 304
Period size: 90 Copynumber: 2.8 Consensus size: 90
428233 ACTCTAACAT
* * * * *
428243 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAC
*
428308 CCATATACATCTCAACCATAGTATA
66 CCATATACATTTCAACCATAGTATA
* * * *
428333 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCAAACTTTTC-TGTTGATAATGCA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGC-ATCCTTTCATGTTGATAATGCA
*
428397 CCCATATGCATTTCAACTC-TAGTATA
65 CCCATATACATTTCAAC-CATAGTATA
* ***
428423 -TTATTCTGTTGATAATACACCCATATGCATTTCAACTCT-GACATCCTTTCATGCCAATAATGC
1 CTT-TTCTGTTGATAATGCACCCATATGCATTTCAACTCTAG-CATCCTTTCATGTTGATAATGC
*
428486 ACCTATATACATT
64 ACCCATATACATT
428499 ATTTTGTTAT
Statistics
Matches: 140, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
89 9 0.06
90 126 0.90
91 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (90 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATCCTTTCATGTTGATAATGCAC
CCATATACATTTCAACCATAGTATA
Found at i:428483 original size:135 final size:135
Alignment explanation
Indices: 428243--428498 Score: 331
Period size: 135 Copynumber: 1.9 Consensus size: 135
428233 ACTCTAACAT
**
428243 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATACAC
* * *** *
428308 CCATATACATCTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTA
66 CCATATACATCTCAACCATAGCATACCTTTCTGCCAATAATGCACCCATATACATTTCAACTCTA
428373 GCAAA
131 GCAAA
* *
428378 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA-TTATTCTGTTGATAATACA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTT-TTATGTTGATAATACA
* * *
428442 CCCATATGCATTTCAACTC-T-GACAT-CCTTTCATGCCAATAATGCACCTATATACATT
65 CCCATATACATCTCAAC-CATAG-CATACCTTTC-TGCCAATAATGCACCCATATACATT
428499 ATTTTGTTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
134 8 0.08
135 95 0.91
136 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (135 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATACAC
CCATATACATCTCAACCATAGCATACCTTTCTGCCAATAATGCACCCATATACATTTCAACTCTA
GCAAA
Found at i:428999 original size:22 final size:21
Alignment explanation
Indices: 428949--429007 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
428939 CTGGCCCTCT
*
428949 GGTATCGATACCCCTACTTAT
1 GGTATCGATACCCCTACTTAG
*
428970 AGTATCGATACTACCCTA-TTAG
1 GGTATCGATAC--CCCTACTTAG
428992 GGTATCGATATCCCCT
1 GGTATCGATA-CCCCT
429008 TCATGTATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 14 0.44
22 12 0.38
23 6 0.19
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCCCTACTTAG
Found at i:432170 original size:17 final size:17
Alignment explanation
Indices: 432145--432178 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
432135 AATGAAATAA
*
432145 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
432162 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
432179 TGAGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:437925 original size:35 final size:35
Alignment explanation
Indices: 437864--437932 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
437854 GTTTCAAAGA
** *
437864 TGGTATCGATACTATCTTTATGGTATCGGTACTCT
1 TGGTATCGATACTATCTACATGGTATCGATACTCT
*
437899 TGGTATCGATATTATTCTACAT-GTATCGATACTC
1 TGGTATCGATACTA-TCTACATGGTATCGATACTC
437933 ATGAATGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (35 bp):
TGGTATCGATACTATCTACATGGTATCGATACTCT
Found at i:439115 original size:18 final size:18
Alignment explanation
Indices: 439092--439127 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
439082 ACATGAGTCA
*
439092 TATATATTCTTTCATACT
1 TATATACTCTTTCATACT
*
439110 TATATACTCTTTTATACT
1 TATATACTCTTTCATACT
439128 CATCTCTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATACTCTTTCATACT
Found at i:444551 original size:11 final size:10
Alignment explanation
Indices: 444535--444595 Score: 88
Period size: 11 Copynumber: 6.0 Consensus size: 10
444525 AAGTTTGTTA
444535 AAAATAAAAT
1 AAAATAAAAT
444545 GAAAATAAAAT
1 -AAAATAAAAT
444556 AAAATAAAAT
1 AAAATAAAAT
444566 AAAAATAAAAT
1 -AAAATAAAAT
444577 -AAATAAAAT
1 AAAATAAAAT
*
444586 AAAACAAAAT
1 AAAATAAAAT
444596 GAGTTGCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
9 9 0.19
10 18 0.38
11 20 0.43
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:444554 original size:5 final size:5
Alignment explanation
Indices: 444535--444595 Score: 88
Period size: 5 Copynumber: 12.0 Consensus size: 5
444525 AAGTTTGTTA
444535 AAAAT AAAAT GAAAAT AAAAT AAAAT AAAAT AAAAAT AAAAT -AAAT AAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
*
444586 AAAAC AAAAT
1 AAAAT AAAAT
444596 GAGTTGCCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
4 4 0.08
5 37 0.73
6 10 0.20
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:444554 original size:16 final size:15
Alignment explanation
Indices: 444535--444595 Score: 88
Period size: 16 Copynumber: 4.0 Consensus size: 15
444525 AAGTTTGTTA
444535 AAAATAAAATGAAAAT
1 AAAATAAAAT-AAAAT
444551 AAAATAAAATAAAAT
1 AAAATAAAATAAAAT
444566 AAAAATAAAAT-AAAT
1 -AAAATAAAATAAAAT
*
444581 AAAATAAAACAAAAT
1 AAAATAAAATAAAAT
444596 GAGTTGCCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
14 9 0.21
15 13 0.31
16 20 0.48
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:444559 original size:21 final size:20
Alignment explanation
Indices: 444535--444595 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
444525 AAGTTTGTTA
444535 AAAATAAAATGAAAATAAAAT
1 AAAATAAAAT-AAAATAAAAT
444556 AAAATAAAATAAAAATAAAAT
1 AAAATAAAAT-AAAATAAAAT
*
444577 -AAATAAAATAAAACAAAAT
1 AAAATAAAATAAAATAAAAT
444596 GAGTTGCCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.24
20 9 0.24
21 20 0.53
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAAATAAAAT
Found at i:446731 original size:20 final size:22
Alignment explanation
Indices: 446686--446743 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
446676 GCATGGGTAG
446686 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
446710 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
446730 TGTATCGATGCACT
1 TGCATCGATGCACT
446744 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:451501 original size:13 final size:13
Alignment explanation
Indices: 451483--451523 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
451473 GATATGTTAC
451483 ATATGTGTTAATG
1 ATATGTGTTAATG
*
451496 ATATGTGTGAAT-
1 ATATGTGTTAATG
451508 ATATGT-TTATATG
1 ATATGTGTTA-ATG
451521 ATA
1 ATA
451524 CATGTTCAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 14 0.58
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (13 bp):
ATATGTGTTAATG
Found at i:454490 original size:17 final size:16
Alignment explanation
Indices: 454468--454508 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
454458 CCGAAGCGTA
454468 GGTGCCCACCTGATAGG
1 GGTGCCCACCTGAT-GG
454485 GGTGCCCACCTGATGG
1 GGTGCCCACCTGATGG
454501 GAGTGCCC
1 G-GTGCCC
454509 TCAGGTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.15, C:0.32, G:0.37, T:0.17
Consensus pattern (16 bp):
GGTGCCCACCTGATGG
Found at i:454685 original size:35 final size:34
Alignment explanation
Indices: 454639--454755 Score: 137
Period size: 35 Copynumber: 3.3 Consensus size: 34
454629 CTTAGATCCG
*
454639 TAAGGAATTACCATCTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAT-TCGATCAGTCTGAACCTATA
* ***
454674 TAAGGAATTACCAATTTGATCAAGT-TGAACCTGCCG
1 TAAGGAATTACC-ATTCGATC-AGTCTGAACCT-ATA
454710 TAAGGAATTACCAGTTCGATCAGTCTGAACCTATA
1 TAAGGAATTACCA-TTCGATCAGTCTGAACCTATA
454745 TAAGGAATTAC
1 TAAGGAATTAC
454756 AAGTTTGATC
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (34 bp):
TAAGGAATTACCATTCGATCAGTCTGAACCTATA
Found at i:454773 original size:35 final size:34
Alignment explanation
Indices: 454663--454774 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 34
454653 CTCGATCGGT
454663 CTGAACCTATATAAGGAATTACCAA-TTTGATCAA
1 CTGAACCTATATAAGGAATTA-CAAGTTTGATCAA
* *** * * *
454697 GTTGAACCTGCCGTAAGGAATTACCAGTTCGATCAGT
1 -CTGAACCT-ATATAAGGAATTACAAGTTTGATCA-A
454734 CTGAACCTATATAAGGAATTACAAGTTTGATCGAA
1 CTGAACCTATATAAGGAATTACAAGTTTGATC-AA
454769 CTGAAC
1 CTGAAC
454775 TGTAGAGACT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
35 34 0.58
36 25 0.42
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (34 bp):
CTGAACCTATATAAGGAATTACAAGTTTGATCAA
Found at i:454774 original size:71 final size:71
Alignment explanation
Indices: 454636--454774 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 71
454626 CATCTTAGAT
* *
454636 CCGTAAGGAATTACCATCTCGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGTTG
1 CCGTAAGGAATTACCATCTCGATCAGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
454701 AACCTG
66 AACCTG
454707 CCGTAAGGAATTACCAGT-TCGATCAGTCTGAACCTATATAAGGAATTA-CAAGTTTGATCGAA-
1 CCGTAAGGAATTACCA-TCTCGATCAGTCTGAACCTATATAAGGAATTACCAA-TTTGATC-AAG
454769 CTGAAC
63 CTGAAC
454775 TGTAGAGACT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
70 3 0.05
71 57 0.90
72 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (71 bp):
CCGTAAGGAATTACCATCTCGATCAGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
AACCTG
Found at i:455885 original size:27 final size:27
Alignment explanation
Indices: 455855--455906 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
455845 TCTTTTTACA
*
455855 ACATAAGGGTATTTTCGTAATTTTATC
1 ACATAAGGGAATTTTCGTAATTTTATC
*
455882 ACATAAGGGAATTTTTGTAATTTTA
1 ACATAAGGGAATTTTCGTAATTTTA
455907 CCTAACTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (27 bp):
ACATAAGGGAATTTTCGTAATTTTATC
Found at i:456544 original size:19 final size:19
Alignment explanation
Indices: 456520--456568 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
456510 AGTTAAACTG
456520 GTCAACGGGTCAAGCCAAA
1 GTCAACGGGTCAAGCCAAA
** *
456539 GTCAACGGGTCGGGTCAAA
1 GTCAACGGGTCAAGCCAAA
*
456558 GTTAACGGGTC
1 GTCAACGGGTC
456569 GTGTTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (19 bp):
GTCAACGGGTCAAGCCAAA
Found at i:457930 original size:29 final size:29
Alignment explanation
Indices: 457888--457946 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
457878 CAGACTCCTC
457888 TATCCCCGAAATTAGAGAATGAAAATATA
1 TATCCCCGAAATTAGAGAATGAAAATATA
*
457917 TATCCCCGAAATTAGGGAATGAAAATATA
1 TATCCCCGAAATTAGAGAATGAAAATATA
457946 T
1 T
457947 CTTCTTTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (29 bp):
TATCCCCGAAATTAGAGAATGAAAATATA
Found at i:461621 original size:20 final size:21
Alignment explanation
Indices: 461596--461644 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
461586 AATTCCTTTG
461596 TTGCATTTACATTTTGCAT-T
1 TTGCATTTACATTTTGCATCT
**
461616 TTGCATTCCCATTTTGCATCT
1 TTGCATTTACATTTTGCATCT
*
461637 TTCCATTT
1 TTGCATTT
461645 GCATGAGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.16, C:0.22, G:0.08, T:0.53
Consensus pattern (21 bp):
TTGCATTTACATTTTGCATCT
Found at i:461644 original size:28 final size:29
Alignment explanation
Indices: 461612--461671 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
461602 TTACATTTTG
**
461612 CATTTTGCATTCCCAT-TTTGCATCTTTC
1 CATTTTGCATGACCATATTTGCATCTTTC
* *
461640 CA-TTTGCATGAGCATATTTGCATCTTTG
1 CATTTTGCATGACCATATTTGCATCTTTC
461668 CATT
1 CATT
461672 AGCATCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 10 0.38
28 15 0.58
29 1 0.04
ACGTcount: A:0.18, C:0.23, G:0.12, T:0.47
Consensus pattern (29 bp):
CATTTTGCATGACCATATTTGCATCTTTC
Found at i:462974 original size:30 final size:28
Alignment explanation
Indices: 462932--463012 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 28
462922 CAACACAGAG
*
462932 AAAAAAGAAGAAATATAGAA-AAACACACAA
1 AAAAAAG-AGAAAAATAGAAGAAA-A-ACAA
*
462962 AAAGAAAGAGAAAAATAGAAGAAAAAGAA
1 AAA-AAAGAGAAAAATAGAAGAAAAACAA
462991 AAAAAAGAGAAAAA-AGAAGAAA
1 AAAAAAGAGAAAAATAGAAGAAA
463013 TAATAAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
27 8 0.17
28 11 0.23
29 6 0.13
30 15 0.32
31 7 0.15
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.04
Consensus pattern (28 bp):
AAAAAAGAGAAAAATAGAAGAAAAACAA
Found at i:462975 original size:11 final size:9
Alignment explanation
Indices: 462960--463008 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
462950 AAAAACACAC
462960 AAAAAGAAAG
1 AAAAA-AAAG
*
462970 AGAAAAATAG
1 A-AAAAAAAG
*
462980 AAGAAAAAG
1 AAAAAAAAG
462989 AAAAAAAAG
1 AAAAAAAAG
*
462998 AGAAAAAAG
1 AAAAAAAAG
463007 AA
1 AA
463009 GAAATAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 23 0.72
10 5 0.16
11 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:463001 original size:17 final size:19
Alignment explanation
Indices: 462928--463008 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
462918 TTAACAACAC
*
462928 AGAG-AAAAAAGAAGAAAT
1 AGAGAAAAAAAGAAGAAAA
* * *
462946 ATAGAAAAACACACAAAAAGAA
1 AGAGAAAAA-A-AGAAGAA-AA
*
462968 AGAGAAAAATAGAAGAAAA
1 AGAGAAAAAAAGAAGAAAA
462987 AGA-AAAAAAAG-AGAAAA
1 AGAGAAAAAAAGAAGAAAA
463004 A-AGAA
1 AGAGAA
463009 GAAATAATAA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
16 1 0.02
17 9 0.18
18 10 0.20
19 9 0.18
20 6 0.12
21 5 0.10
22 9 0.18
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (19 bp):
AGAGAAAAAAAGAAGAAAA
Found at i:465550 original size:136 final size:135
Alignment explanation
Indices: 465261--466012 Score: 680
Period size: 136 Copynumber: 5.5 Consensus size: 135
465251 CATTTCCAAT
* * ** *
465261 GAGAGTTTATAATGAGAAGAACTTATCCG-ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTCG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
465325 TTCAACCT-T-AGCTCGATTCATCG-CATATGGAGTTGAATCAGAAACACCTCACTCGAGGG-AT
66 TTCGACCTATCA-CTCGATTCA-CGACAT-T----TCGAATCAGTAACACCTCACTTGAGGGAAT
*
465386 CAATATTTCCAGTG
124 -AACATTT-CAGTG
* *
465400 GAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAAAAGTTCATAATGAGAAGAACTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * ** * * *
465465 CTCTACCTATCACTTGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTAAGGGAATGACATTT
66 TTCGACCTATCACTCGATTCACGACATTTCGAATCAGTAACACCTCACTTGAGGGAATAACATTT
465530 CAGATG
131 CAG-TG
* **
465536 GAGAGTTCATAATGAGAAGAACTAATCC-AATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
465600 TTCAACCT-T-AGCTCGATTCACCG-CATATGGAGTTGAATCAGCAACACCTTACTCGAGGG-AT
66 TTCGACCTATCA-CTCGATTCA-CGACAT-T----TCGAATCAGTAACACCTCACTTGAGGGAAT
465661 CAACATTTCCAGTG
124 -AACATTT-CAGTG
* * * * *
465675 GAAAGTTCATAATGAGAAGAACTCATCTGACAAAGGGGGAAGAAGTTCATAATGAGAAGAGCTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
** * * * *
465740 TTCGACCTATCACTTAATTCACGACATTTTGAATCAGTGACGCCTCACTTGAGGGAATGACATTT
66 TTCGACCTATCACTCGATTCACGACATTTCGAATCAGTAACACCTCACTTGAGGGAATAACATTT
465805 CAGATG
131 CAG-TG
* * * * * *
465811 GAGAGTTCATAATGAGAAGAACTCATCTGACAGATGGAGAATAAGTTCATAATGAGAAGAGCTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
** * * * ** * *
465876 TTCGACCTATTGCTCGATTCACAACAATTCGAGTCAGTAACACCTTGCTTGAGGGATTAACTTTT
66 TTCGACCTATCACTCGATTCACGACATTTCGAATCAGTAACACCTCACTTGAGGGAATAACATTT
465941 CTAGTG
131 C-AGTG
* * * * * *
465947 GAGAGTTCGTAATGAGAATAACTCATCCGATAAA-GGAGAAGAAGTTTATAATAAGAATAACTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
466011 TT
66 TT
466013 AAACCTTAGC
Statistics
Matches: 506, Mismatches: 85, Indels: 48
0.79 0.13 0.08
Matches are distributed among these distances:
133 1 0.00
134 12 0.02
135 75 0.15
136 224 0.44
137 6 0.01
138 2 0.00
139 77 0.15
140 84 0.17
141 23 0.05
142 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (135 bp):
GAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
TTCGACCTATCACTCGATTCACGACATTTCGAATCAGTAACACCTCACTTGAGGGAATAACATTT
CAGTG
Found at i:465752 original size:275 final size:275
Alignment explanation
Indices: 465261--466012 Score: 1023
Period size: 275 Copynumber: 2.7 Consensus size: 275
465251 CATTTCCAAT
* * * *
465261 GAGAGTTTATAATGAGAAGAACTTATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTCGT
1 GAGAGTTCATAATGAGAAGAACTAATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
465326 TCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGAAACACCTCACTCGAGGGATCAATA
66 TCAACCTTAGCTCGATTCACCGCATATGGAGTTGAATCAGAAACACCTTACTCGAGGGATCAACA
*
465391 TTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAAAAGTTCATAATGAG
131 TTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAG
* * * * * *
465456 AAGAACTTGCTCTACCTATCACTTGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTAAGGGA
196 AAGAACTTGTTCGACCTATCACTTAATTCACGACATTTCGAATCAGTGACGCCTCACTTAAGGGA
465521 ATGACATTTCAGATG
261 ATGACATTTCAGATG
465536 GAGAGTTCATAATGAGAAGAACTAATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTAATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
465601 TCAACCTTAGCTCGATTCACCGCATATGGAGTTGAATCAGCAACACCTTACTCGAGGGATCAACA
66 TCAACCTTAGCTCGATTCACCGCATATGGAGTTGAATCAGAAACACCTTACTCGAGGGATCAACA
* * *
465666 TTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCTGACAAAGGGGGAAGAAGTTCATAATGAG
131 TTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAG
* * *
465731 AAGAGCTTGTTCGACCTATCACTTAATTCACGACATTTTGAATCAGTGACGCCTCACTTGAGGGA
196 AAGAACTTGTTCGACCTATCACTTAATTCACGACATTTCGAATCAGTGACGCCTCACTTAAGGGA
465796 ATGACATTTCAGATG
261 ATGACATTTCAGATG
* * * * *
465811 GAGAGTTCATAATGAGAAGAACTCATCTGACA-GATGGAGAATAAGTTCATAATGAGAAGAGCTT
1 GAGAGTTCATAATGAGAAGAACTAATC-CA-ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* * ** * * * * * *
465875 GTTCGACCTATTGCTCGATTCACAACA-AT----TCGAGTCAGTAACACCTTGCTTGAGGGATTA
64 GTTCAACCT-TAGCTCGATTCACCGCATATGGAGTTGAATCAGAAACACCTTACTCGAGGGATCA
* * * * * * *
465935 ACTTTTCTAGTGGAGAGTTCGTAATGAGAATAACTCATCCGATAAA-GGAGAAGAAGTTTATAAT
128 ACATTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAAT
* *
465999 AAGAATAACTTGTT
193 GAGAAGAACTTGTT
466013 AAACCTTAGC
Statistics
Matches: 426, Mismatches: 48, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
271 27 0.06
272 64 0.15
275 280 0.66
276 40 0.09
277 15 0.04
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (275 bp):
GAGAGTTCATAATGAGAAGAACTAATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTAGCTCGATTCACCGCATATGGAGTTGAATCAGAAACACCTTACTCGAGGGATCAACA
TTTCCAGTGGAAAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCGACCTATCACTTAATTCACGACATTTCGAATCAGTGACGCCTCACTTAAGGGA
ATGACATTTCAGATG
Found at i:467533 original size:15 final size:14
Alignment explanation
Indices: 467513--467592 Score: 51
Period size: 15 Copynumber: 5.6 Consensus size: 14
467503 TTTATTTACA
467513 TTTGTAATGTTCATT
1 TTTGTAAT-TTCATT
467528 TTTGT-ATTT-ATT
1 TTTGTAATTTCATT
* *
467540 ATT-TAATTTTATT
1 TTTGTAATTTCATT
*
467553 ATTTAG-AACTTTAATT
1 -TTT-GTAA-TTTCATT
467569 TTTGTAATGTTCATT
1 TTTGTAAT-TTCATT
*
467584 TTAGTAATT
1 TTTGTAATT
467593 ATATTTTGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
11 1 0.02
12 9 0.17
13 5 0.10
14 7 0.13
15 24 0.46
16 6 0.12
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTGTAATTTCATT
Found at i:470702 original size:17 final size:17
Alignment explanation
Indices: 470682--470714 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
470672 ATATTTGTTT
470682 ATATA-AAATATAATATA
1 ATATACAAA-ATAATATA
470699 ATATACAAAATAATAT
1 ATATACAAAATAATAT
470715 TTTGGTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATACAAAATAATATA
Found at i:472054 original size:2 final size:2
Alignment explanation
Indices: 472049--472193 Score: 74
Period size: 2 Copynumber: 74.0 Consensus size: 2
472039 AAATTAAAAA
* *
472049 AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * * * *
472090 AT -T AT -T AT A- AG CT AT AT AT AT AA AT -T AT GT TT AT AT GA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * *
472128 ACT AT AT AT AT AA ACT AT AT AT GT AT AA ACT AT A- AT TT AT AT
1 A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT
472170 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
472194 TATTCAAAGT
Statistics
Matches: 108, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
1 9 0.08
2 94 0.87
3 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:472521 original size:2 final size:2
Alignment explanation
Indices: 472514--472630 Score: 73
Period size: 2 Copynumber: 59.0 Consensus size: 2
472504 TTTAATTTTC
* * **
472514 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA GG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
472556 AA CTA TA TA -A AA TA TA TA AA CTA TA TA GTT TA TA AA T- TA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
*
472597 AA T- TA TA T- TA -A TA TA GTA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
472631 AACACTATGC
Statistics
Matches: 87, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
1 5 0.06
2 77 0.89
3 5 0.06
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:472564 original size:9 final size:8
Alignment explanation
Indices: 472550--472632 Score: 62
Period size: 9 Copynumber: 10.0 Consensus size: 8
472540 TGTATGTAGG
472550 TATATAAA
1 TATATAAA
472558 CTATATAAAA
1 -TATAT-AAA
472568 TATATAAA
1 TATATAAA
*
472576 CTATAT-AG
1 -TATATAAA
*
472584 TTTATAAA
1 TATATAAA
472592 T-TATAAA
1 TATATAAA
*
472599 TTATATTAA
1 -TATATAAA
*
472608 TATAGTATA
1 TATA-TAAA
*
472617 TATATATA
1 TATATAAA
472625 TATATAAA
1 TATATAAA
472633 CACTATGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
7 10 0.16
8 22 0.36
9 26 0.43
10 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
TATATAAA
Found at i:473226 original size:25 final size:25
Alignment explanation
Indices: 473198--473258 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
473188 ACACCCAATG
*
473198 TAACATGCAATGCAACATGAATTAA
1 TAACATGCAATACAACATGAATTAA
* *
473223 TAACATGCAATACCACATGAATTAG
1 TAACATGCAATACAACATGAATTAA
473248 TAACATGCAAT
1 TAACATGCAAT
473259 TATTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (25 bp):
TAACATGCAATACAACATGAATTAA
Found at i:475059 original size:23 final size:24
Alignment explanation
Indices: 475028--475078 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
475018 TTATTTTTTC
475028 TTTAAATAAATTAAACTATA-TAA
1 TTTAAATAAATTAAACTATATTAA
*
475051 TTTACATAAATTAAACTATATTAA
1 TTTAAATAAATTAAACTATATTAA
475075 TTTA
1 TTTA
475079 TATTTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATAAATTAAACTATATTAA
Found at i:475134 original size:13 final size:13
Alignment explanation
Indices: 475118--475161 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
475108 TTATTAATCA
*
475118 TTTCTTATATAAT
1 TTTCTTAAATAAT
475131 TTTCATTTAAATAAT
1 TTTC--TTAAATAAT
*
475146 TTTATTAAATAAT
1 TTTCTTAAATAAT
475159 TTT
1 TTT
475162 ATATAATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCTTAAATAAT
Found at i:475162 original size:13 final size:13
Alignment explanation
Indices: 475126--475163 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
475116 CATTTCTTAT
475126 ATAATTTTCATTTAA
1 ATAATTTT-A-TTAA
475141 ATAATTTTATTAA
1 ATAATTTTATTAA
475154 ATAATTTTAT
1 ATAATTTTAT
475164 ATAATAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.61
14 1 0.04
15 8 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:475169 original size:13 final size:12
Alignment explanation
Indices: 475101--475169 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 12
475091 GTTCAATGCC
*
475101 AATATTTTTATT
1 AATAATTTTATT
* *
475113 AATCA-TTTCTT
1 AATAATTTTATT
475124 ATATAATTTTCATTT
1 A-ATAATTTT-A-TT
475139 AAATAATTTTATT
1 -AATAATTTTATT
475152 AAATAATTTTATAT
1 -AATAATTTTAT-T
475166 AATA
1 AATA
475170 GATATATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 6 0.13
12 6 0.13
13 21 0.46
14 2 0.04
15 10 0.22
16 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (12 bp):
AATAATTTTATT
Found at i:476610 original size:2 final size:2
Alignment explanation
Indices: 476605--476664 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
476595 AAATTAGAAA
*
476605 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
476645 AT AT AT AA ACT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT A
476665 AACTATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 3 0.06
2 45 0.92
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:476621 original size:11 final size:11
Alignment explanation
Indices: 476605--476733 Score: 64
Period size: 11 Copynumber: 11.5 Consensus size: 11
476595 AAATTAGAAA
476605 ATATATAATAT
1 ATATATAATAT
476616 ATATATATATAT
1 ATATATA-ATAT
476628 ATATATAATAT
1 ATATATAATAT
476639 A-AGT-T--TAT
1 ATA-TATAATAT
476647 ATATA-AACTAT
1 ATATATAA-TAT
476658 ATATATAA-ACT
1 ATATATAATA-T
476669 ATA-A-AAT-T
1 ATATATAATAT
476677 AT-TATAAGCTAT
1 ATATATAA--TAT
476689 ATATATAAATTAT
1 ATATAT-AA-TAT
476702 ATTTATATCAACTAT
1 A--TATAT-AA-TAT
476717 ATATATAA-ACT
1 ATATATAATA-T
476728 ATATAT
1 ATATAT
476734 GTAAACTATA
Statistics
Matches: 95, Mismatches: 3, Indels: 40
0.69 0.02 0.29
Matches are distributed among these distances:
8 9 0.09
9 5 0.05
10 5 0.05
11 33 0.35
12 18 0.19
13 12 0.13
14 2 0.02
15 11 0.12
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (11 bp):
ATATATAATAT
Found at i:476623 original size:13 final size:14
Alignment explanation
Indices: 476605--476743 Score: 112
Period size: 13 Copynumber: 9.9 Consensus size: 14
476595 AAATTAGAAA
476605 ATATATAA-TATAT
1 ATATATAACTATAT
476618 ATATATATA-TATAT
1 ATATATA-ACTATAT
* *
476632 ATAATATAAGTTTAT
1 AT-ATATAACTATAT
476647 ATATA-AACTATAT
1 ATATATAACTATAT
*
476660 ATATA-AACTATAAA
1 ATATATAACTAT-AT
476674 ATTATTATAAGCTATAT
1 A-TA-TATAA-CTATAT
*
476691 ATATA-AATTATAT
1 ATATATAACTATAT
*
476704 TTATATCAACTATAT
1 ATATAT-AACTATAT
476719 ATATA-AACTATAT
1 ATATATAACTATAT
*
476732 ATGTA-AACTATA
1 ATATATAACTATA
476744 AAAAGTATAT
Statistics
Matches: 106, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
13 52 0.49
14 16 0.15
15 26 0.25
16 4 0.04
17 4 0.04
18 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (14 bp):
ATATATAACTATAT
Found at i:476625 original size:15 final size:15
Alignment explanation
Indices: 476605--476723 Score: 76
Period size: 15 Copynumber: 8.2 Consensus size: 15
476595 AAATTAGAAA
476605 ATATATAATATATAT
1 ATATATAATATATAT
476620 ATATAT-ATATATAT
1 ATATATAATATATAT
*
476634 A-ATATAAGTTTATAT
1 ATATATAA-TATATAT
*
476649 ATAAACT-ATATATAT
1 ATATA-TAATATATAT
*
476664 AAACTATAA-A-AT-T
1 ATA-TATAATATATAT
**
476677 AT-TATAAGCTATAT
1 ATATATAATATATAT
476691 ATATA-AAT-TATAT
1 ATATATAATATATAT
*
476704 TTATATCAACTATATAT
1 ATATAT-AA-TATATAT
476721 ATA
1 ATA
476724 AACTATATAT
Statistics
Matches: 80, Mismatches: 10, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
11 5 0.06
13 17 0.21
14 17 0.21
15 27 0.34
16 6 0.08
17 8 0.10
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATATAATATATAT
Found at i:476634 original size:23 final size:24
Alignment explanation
Indices: 476605--476664 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
476595 AAATTAGAAA
476605 ATATATAATATATA-TATATATAT
1 ATATATAATATATAGTATATATAT
*
476628 ATATATAATATA-AGTTTATATAT
1 ATATATAATATATAGTATATATAT
*
476651 AAACTAT-ATATATA
1 ATA-TATAATATATA
476665 AACTATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 27 0.84
24 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
ATATATAATATATAGTATATATAT
Found at i:477165 original size:24 final size:25
Alignment explanation
Indices: 477138--477190 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
477128 TATATGTATG
477138 TATATAAACTATATA-TGTATAAAC
1 TATATAAACTATATAGTGTATAAAC
* *
477162 TATATAAACTATATAGTTTATAAAT
1 TATATAAACTATATAGTGTATAAAC
477187 TATA
1 TATA
477191 ATTTATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (25 bp):
TATATAAACTATATAGTGTATAAAC
Found at i:477407 original size:23 final size:23
Alignment explanation
Indices: 477373--477425 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
477363 TACATGTATG
*
477373 TATA-ATATATATATAAGCTATA
1 TATATATATATATATAACCTATA
477395 TATATATATATATATAACCTATA
1 TATATATATATATATAACCTATA
477418 TATATATA
1 TATATATA
477426 ACCTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (23 bp):
TATATATATATATATAACCTATA
Found at i:477417 original size:15 final size:15
Alignment explanation
Indices: 477399--477434 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
477389 GCTATATATA
477399 TATATATATATAACC
1 TATATATATATAACC
477414 TATATATATATAACC
1 TATATATATATAACC
477429 TATATA
1 TATATA
477435 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATATATATAACC
Found at i:477546 original size:21 final size:21
Alignment explanation
Indices: 477513--477552 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
477503 TTATAAAACC
477513 CTAAATCATAAACCCTAAATA
1 CTAAATCATAAACCCTAAATA
477534 CTAAA-CATGAAACCCTAAA
1 CTAAATCAT-AAACCCTAAA
477553 CTATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (21 bp):
CTAAATCATAAACCCTAAATA
Found at i:477790 original size:24 final size:21
Alignment explanation
Indices: 477722--477811 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 21
477712 ATATGTAACT
* * *
477722 TATAGTACATGTGTGTATAAAA
1 TATAGTATATGT-TATATAAAC
*
477744 TAT-GTATA-GTATATATAACC
1 TATAGTATATGT-TATATAAAC
477764 TATAGTATATGTATATATACAATC
1 TATAGTATATGT-TATATA-AA-C
*
477788 TAT-TTATATGTTATATAAAC
1 TATAGTATATGTTATATAAAC
477808 TATA
1 TATA
477812 TATGTAACAT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
20 15 0.27
21 11 0.20
22 18 0.32
23 8 0.14
24 4 0.07
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
TATAGTATATGTTATATAAAC
Found at i:477810 original size:20 final size:21
Alignment explanation
Indices: 477737--477817 Score: 80
Period size: 22 Copynumber: 3.9 Consensus size: 21
477727 TACATGTGTG
*
477737 TATAAAATATGTATA-GTATA
1 TATAAACTATGTATATGTATA
*
477757 TATAACCTATAGTATATGTATA
1 TATAAACTAT-GTATATGTATA
*
477779 TATACAATCTATTTATATGT-TA
1 TATA-AA-CTATGTATATGTATA
477801 TATAAACTA--TATATGTA
1 TATAAACTATGTATATGTA
477818 ACATATAGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
18 7 0.13
20 11 0.21
21 7 0.13
22 15 0.29
23 8 0.15
24 4 0.08
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (21 bp):
TATAAACTATGTATATGTATA
Found at i:477841 original size:14 final size:15
Alignment explanation
Indices: 477817--477845 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
477807 CTATATATGT
477817 AACATATAGTTTATA
1 AACATATAGTTTATA
477832 AACA-ATAGTTTATA
1 AACATATAGTTTATA
477846 TTAGTGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AACATATAGTTTATA
Found at i:477946 original size:22 final size:22
Alignment explanation
Indices: 477899--477947 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
477889 ATTTATAAAC
* *
477899 TATAGTTTATATTAATGTACTA
1 TATAGTATATATTAATGTAATA
477921 TATAGTATATATTAATGTTAATTA
1 TATAGTATATATTAATG-TAA-TA
477945 TAT
1 TAT
477948 TAACTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 2 0.09
24 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (22 bp):
TATAGTATATATTAATGTAATA
Found at i:478019 original size:21 final size:21
Alignment explanation
Indices: 477952--478019 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
477942 TTATATTAAC
**
477952 TATAATTTATATTGATATAGTA
1 TATAATTTATA-AAATATAGTA
* * * *
477974 TATAGTTTATAAACTACACTA
1 TATAATTTATAAAATATAGTA
*
477995 TATAATTTATAAAATATAGTT
1 TATAATTTATAAAATATAGTA
478016 TATA
1 TATA
478020 TTAATATTAA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (21 bp):
TATAATTTATAAAATATAGTA
Found at i:478074 original size:67 final size:64
Alignment explanation
Indices: 478001--478127 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
477991 ACTATATAAT
* *
478001 TTATAAAATAT-AGTTTATATTAATATTAATTTCATAGACT-ATATTTTATATTAATATTAATTA
1 TTATAAAATATAAG-TTATATTAATA-TAAGTT-A-AGACTAATA-TTAATATTAATATTAATTA
478064 CAAA
61 CAAA
* *
478068 TTATAAACTATAAGTTATATTAATATAAGTTAATACTAATATTAATATTAATATTAATTA
1 TTATAAAATATAAGTTATATTAATATAAGTTAAGACTAATATTAATATTAATATTAATTA
478128 TATTAACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
64 22 0.41
65 4 0.07
66 5 0.09
67 21 0.39
68 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (64 bp):
TTATAAAATATAAGTTATATTAATATAAGTTAAGACTAATATTAATATTAATATTAATTACAAA
Found at i:478096 original size:15 final size:14
Alignment explanation
Indices: 478076--478173 Score: 76
Period size: 15 Copynumber: 6.7 Consensus size: 14
478066 AATTATAAAC
478076 TATAAGTTATATTAA
1 TATAA-TTATATTAA
*
478091 TATAAGTTAATACTAA
1 TATAA-TT-ATATTAA
*
478107 TAT--TAATATTAA
1 TATAATTATATTAA
478119 TATTAATTATATTAA
1 TA-TAATTATATTAA
* *
478134 CATTAATTATAAT-A
1 TA-TAATTATATTAA
478148 TATAATTTATATTAA
1 TATAA-TTATATTAA
478163 TATTAATTATA
1 TA-TAATTATA
478174 AATAGTTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
12 8 0.12
13 5 0.07
14 8 0.12
15 35 0.51
16 12 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
TATAATTATATTAA
Found at i:478107 original size:6 final size:6
Alignment explanation
Indices: 478084--478169 Score: 71
Period size: 6 Copynumber: 15.3 Consensus size: 6
478074 ACTATAAGTT
* *
478084 ATATTA ATA-TA A-GTTA ATACTA ATATTA ATATTA ATATT- A-ATT-
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
478127 ATATTA ACATTA AT-TATA ATATATA AT-TT- ATATTA ATATTA AT
1 ATATTA ATATTA ATAT-TA ATAT-TA ATATTA ATATTA ATATTA AT
478170 TATAAATAGT
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
4 6 0.09
5 14 0.21
6 40 0.61
7 6 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:478109 original size:16 final size:15
Alignment explanation
Indices: 478076--478109 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
478066 AATTATAAAC
*
478076 TATAAGTTATATTAA
1 TATAAGTTATACTAA
478091 TATAAGTTAATACTAA
1 TATAAGTT-ATACTAA
478107 TAT
1 TAT
478110 TAATATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
TATAAGTTATACTAA
Found at i:478167 original size:29 final size:29
Alignment explanation
Indices: 478090--478174 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
478080 AGTTATATTA
* *
478090 ATATAAGTTAATACTAATATTAA-TATTAAT
1 ATATAA-TTTATATTAATATTAATTA-TAAT
*
478120 AT-TAA-TTATATTAACATTAATTATAAT
1 ATATAATTTATATTAATATTAATTATAAT
478147 ATATAATTTATATTAATATTAATTATAA
1 ATATAATTTATATTAATATTAATTATAA
478175 ATAGTTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 18 0.38
28 5 0.10
29 23 0.48
30 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATAATTTATATTAATATTAATTATAAT
Found at i:478911 original size:13 final size:13
Alignment explanation
Indices: 478893--478919 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
478883 TTTAAATAAT
478893 TTAAATAATTTTA
1 TTAAATAATTTTA
478906 TTAAATAATTTTA
1 TTAAATAATTTTA
478919 T
1 T
478920 ATAGTAAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:480378 original size:24 final size:23
Alignment explanation
Indices: 480351--480400 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
480341 AAATATATGT
480351 TTTTGAAAAATC-AATATTAAAATA
1 TTTT-AAAAATCAAAT-TTAAAATA
*
480375 TTTTAAAAATTAAATTTAAAATA
1 TTTTAAAAATCAAATTTAAAATA
480398 TTT
1 TTT
480401 ATTTATGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTTAAAAATCAAATTTAAAATA
Found at i:480484 original size:28 final size:27
Alignment explanation
Indices: 480430--480502 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
480420 AAATATAAAT
** *
480430 TAAATAAATATTAAAAAATTATTTTTATCA
1 TAAAT-AAT-TTAAAATTTTATATTTAT-A
*
480460 TAAATAATTTAAAATTTTATATTTATT
1 TAAATAATTTAAAATTTTATATTTATA
*
480487 TAAATAATTTTAAATT
1 TAAATAATTTAAAATT
480503 AATAGATGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
27 15 0.39
28 15 0.39
29 3 0.08
30 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
TAAATAATTTAAAATTTTATATTTATA
Found at i:502329 original size:37 final size:37
Alignment explanation
Indices: 502283--502360 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
502273 GTTATAGCTA
*
502283 AAAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
502320 AAAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
502357 AAAA
1 AAAA
502361 TCCCGAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (37 bp):
AAAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:503582 original size:15 final size:15
Alignment explanation
Indices: 503561--503599 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
503551 ATCTTAATTT
503561 ATCTTTATTATCTTA
1 ATCTTTATTATCTTA
* *
503576 TTCTTTATTGTCTTA
1 ATCTTTATTATCTTA
503591 ATCTTTATT
1 ATCTTTATT
503600 CTTGATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.64
Consensus pattern (15 bp):
ATCTTTATTATCTTA
Found at i:507782 original size:20 final size:20
Alignment explanation
Indices: 507757--507801 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
507747 TCTTAAGGCA
** *
507757 TATTTAGGTTCATATAGATG
1 TATTTAGGAGCATATAAATG
507777 TATTTAGGAGCATATAAATG
1 TATTTAGGAGCATATAAATG
507797 TATTT
1 TATTT
507802 GGTGGATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (20 bp):
TATTTAGGAGCATATAAATG
Found at i:512832 original size:18 final size:18
Alignment explanation
Indices: 512806--513164 Score: 459
Period size: 18 Copynumber: 19.9 Consensus size: 18
512796 ATTTGTAATT
* *
512806 ATCTAATAACTGTAAATC
1 ATCTGATAACTGAAAATC
*
512824 ATCTGATAACTGTAAATC
1 ATCTGATAACTGAAAATC
*
512842 ATATGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
* *
512860 ATATGATAACTGAAAATA
1 ATCTGATAACTGAAAATC
* * * *
512878 ATTTGATAATTGTAAATG
1 ATCTGATAACTGAAAATC
* * * *
512896 ATTTGATAATTGTAAATA
1 ATCTGATAACTGAAAATC
512914 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
512932 ATCTGATAACT-ATAAATC
1 ATCTGATAACTGA-AAATC
*
512950 ATCTGATAACTGTAAATC
1 ATCTGATAACTGAAAATC
*
512968 ATCTGATAACCGAAAATC
1 ATCTGATAACTGAAAATC
*
512986 ATCTGATAACTAAAAATC
1 ATCTGATAACTGAAAATC
*
513004 ATCTGATAACTGTAAATC
1 ATCTGATAACTGAAAATC
*
513022 ATCTGATAATTGAAAATC
1 ATCTGATAACTGAAAATC
* *
513040 ATTTGATAACTAAAAATC
1 ATCTGATAACTGAAAATC
* *
513058 ACCTGATAACTAAAAATC
1 ATCTGATAACTGAAAATC
* * *
513076 ATCTAATAATTGTAAATC
1 ATCTGATAACTGAAAATC
513094 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
513112 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
513130 ATCTGATAACTGAAAATC
1 ATCTGATAACTGAAAATC
*
513148 ATCTGATAACTGTAAAT
1 ATCTGATAACTGAAAAT
513165 ATTTAGAATT
Statistics
Matches: 303, Mismatches: 36, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
17 1 0.00
18 302 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (18 bp):
ATCTGATAACTGAAAATC
Found at i:515083 original size:18 final size:18
Alignment explanation
Indices: 515060--515104 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
515050 AAACTTTTTC
*
515060 ATTCAATTTCAAGCATGA
1 ATTCAACTTCAAGCATGA
515078 ATTCAACTTCAAGCATGA
1 ATTCAACTTCAAGCATGA
515096 ATTCAACTT
1 ATTCAACTT
515105 TATATTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (18 bp):
ATTCAACTTCAAGCATGA
Found at i:519260 original size:30 final size:30
Alignment explanation
Indices: 519221--519283 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
519211 CTAAATCTGA
*
519221 ACTTTCCATTGCATTTTTCTTTTACTGACC
1 ACTTGCCATTGCATTTTTCTTTTACTGACC
*
519251 ACTTGCCATTGCATTTTTCTTTTGCTGACC
1 ACTTGCCATTGCATTTTTCTTTTACTGACC
519281 ACT
1 ACT
519284 ATCCTTTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.10, T:0.48
Consensus pattern (30 bp):
ACTTGCCATTGCATTTTTCTTTTACTGACC
Found at i:526486 original size:54 final size:56
Alignment explanation
Indices: 526421--526592 Score: 253
Period size: 62 Copynumber: 3.0 Consensus size: 56
526411 TATCGATACT
526421 CGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAG-TTTTTACTGTTGG-
1 CGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAGTTTTTTACTGTTGGA
526475 CGAGCTTGAAGTA-TGATATCACACTAAT-AAATCTAGTAGTTTTTTTACTGTTGGAGATA
1 CGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAG-TTTTTTACTGTT-G-G--A
526534 CTCGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAGTTTTTTACTGTTGGA
1 --CGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAGTTTTTTACTGTTGGA
526592 C
1 C
526593 AGGGAGTATC
Statistics
Matches: 107, Mismatches: 0, Indels: 20
0.84 0.00 0.16
Matches are distributed among these distances:
52 11 0.10
53 15 0.14
54 24 0.22
55 1 0.01
56 2 0.02
58 1 0.01
60 1 0.01
61 14 0.13
62 27 0.25
63 11 0.10
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.37
Consensus pattern (56 bp):
CGAGCTTGAAGTATTGATATCACACTAATAAAATCTAGTAGTTTTTTACTGTTGGA
Found at i:528588 original size:20 final size:20
Alignment explanation
Indices: 528560--528602 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
528550 ATGATTCTCA
* *
528560 TCTCATTTTTTTCTTTTTCT
1 TCTCATTTTCTTCTTCTTCT
*
528580 TCTCTTTTTCTTCTTCTTCT
1 TCTCATTTTCTTCTTCTTCT
528600 TCT
1 TCT
528603 TTTGGAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTCATTTTCTTCTTCTTCT
Found at i:528589 original size:17 final size:18
Alignment explanation
Indices: 528567--528605 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
528557 TCATCTCATT
*
528567 TTTTTCTTTTTCTTC-TC
1 TTTTTCTTCTTCTTCTTC
528584 TTTTTCTTCTTCTTCTTC
1 TTTTTCTTCTTCTTCTTC
528602 TTTT
1 TTTT
528606 GGAGTTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTCTTCTTCTTCTTC
Found at i:529641 original size:87 final size:88
Alignment explanation
Indices: 529534--529708 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 88
529524 AAGCTCAACA
529534 GTAACCTTTTACAACTCCCTAGTTTTCAATGGCTAAACTTGAACCAAACCCCTTTGACAAAAGTA
1 GTAACCTTTTACAACTCCCTAGTTTTCAATGGCTAAACTTGAACCAAACCCCTTTGACAAAAGTA
529599 TAAAAAGAATATAATCAAGAAAC
66 TAAAAAGAATATAATCAAGAAAC
529622 GTAACC-TTTACAACTCCCTAGTTTTCAATGGCTAAACTTGAACCAAACCCCTTTGACAAAAGTA
1 GTAACCTTTTACAACTCCCTAGTTTTCAATGGCTAAACTTGAACCAAACCCCTTTGACAAAAGTA
529686 TAAAAAGAATATAATCAAGAAAC
66 TAAAAAGAATATAATCAAGAAAC
529709 CTCTCAAAGG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 81 0.93
88 6 0.07
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (88 bp):
GTAACCTTTTACAACTCCCTAGTTTTCAATGGCTAAACTTGAACCAAACCCCTTTGACAAAAGTA
TAAAAAGAATATAATCAAGAAAC
Found at i:534414 original size:19 final size:18
Alignment explanation
Indices: 534378--534439 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
534368 CCTAAATCAT
*
534378 TTTTCAAAATTTAATTTTA
1 TTTTCAAAA-TCAATTTTA
*
534397 TTTTCAAAATCAACTTTTG
1 TTTTCAAAATCAA-TTTTA
* *
534416 CTTTCAAAATCGA-TTTA
1 TTTTCAAAATCAATTTTA
534433 TTTTCAA
1 TTTTCAA
534440 TTTTGAGTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 9 0.25
18 3 0.08
19 24 0.67
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTCAAAATCAATTTTA
Found at i:536434 original size:22 final size:22
Alignment explanation
Indices: 536401--536479 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
536391 AATTTGAGCC
*
536401 TTCATA-GGGTATTGATACCCT
1 TTCATAGGGGTATTGATACCCA
* *
536422 TTCATATGGGTATCGATACCCA
1 TTCATAGGGGTATTGATACCCA
*
536444 TTAATAGGGGGTATTGATACCCA
1 TTCATA-GGGGTATTGATACCCA
536467 TTCATAGGGGTAT
1 TTCATAGGGGTAT
536480 CGGTACCTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.12
22 25 0.50
23 19 0.38
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (22 bp):
TTCATAGGGGTATTGATACCCA
Found at i:536457 original size:45 final size:45
Alignment explanation
Indices: 536407--536494 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
536397 AGCCTTCATA
* *
536407 GGGTATTGATACCCTTTCATATGGGTATCGATACC-CATTAATAGG
1 GGGTATTGATACCCATTCATAGGGGTATCGATACCTC-TTAATAGG
*
536452 GGGTATTGATACCCATTCATAGGGGTATCGGTACCTCTTAATA
1 GGGTATTGATACCCATTCATAGGGGTATCGATACCTCTTAATA
536495 TATTTTCTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 38 0.97
46 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (45 bp):
GGGTATTGATACCCATTCATAGGGGTATCGATACCTCTTAATAGG
Found at i:536462 original size:23 final size:23
Alignment explanation
Indices: 536407--536476 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
536397 AGCCTTCATA
* *
536407 GGGTATTGATACCCTTTCATA-T
1 GGGTATTGATACCCATTCATAGG
* *
536429 GGGTATCGATACCCATTAATAGG
1 GGGTATTGATACCCATTCATAGG
536452 GGGTATTGATACCCATTCATAGG
1 GGGTATTGATACCCATTCATAGG
536475 GG
1 GG
536477 TATCGGTACC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 18 0.44
23 23 0.56
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (23 bp):
GGGTATTGATACCCATTCATAGG
Found at i:544417 original size:21 final size:21
Alignment explanation
Indices: 544370--544418 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
544360 TGACTATCGT
544370 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCGC
**
544391 GTTGCGATTTTCCCAA-TTCGC
1 AATGCGATTTT-CCAATTTCGC
544412 AATGCGA
1 AATGCGA
544419 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCGC
Found at i:544451 original size:21 final size:21
Alignment explanation
Indices: 544408--544522 Score: 142
Period size: 21 Copynumber: 5.5 Consensus size: 21
544398 TTTTCCCAAT
** *
544408 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
* *
544428 TCGCAATGCGGATTTTGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
544449 TCGCAATGTGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
544470 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
544491 TCGCAATGCAAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* *
544512 TTGCAACGCGA
1 TCGCAATGCGA
544523 TACTGACTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
20 11 0.13
21 71 0.87
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:544539 original size:20 final size:20
Alignment explanation
Indices: 544514--544619 Score: 106
Period size: 20 Copynumber: 5.2 Consensus size: 20
544504 TTGGAAAATT
*
544514 GCAACGCGATACTGACTATC
1 GCAACGCGATACTGACTTTC
* **
544534 GCAACGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TTTC
*
544555 ACAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTTTC
* * *
544575 GCAACTCGATACTTAATTTC
1 GCAACGCGATACTGACTTTC
*
544595 GCAACGCAATACTGACTTTC
1 GCAACGCGATACTGACTTTC
544615 GCAAC
1 GCAAC
544620 TAGATAATAC
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
19 2 0.03
20 51 0.74
21 14 0.20
22 2 0.03
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTTTC
Found at i:544611 original size:40 final size:41
Alignment explanation
Indices: 544508--544645 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
544498 GCAAATTTGG
* * *
544508 AAAATTGCAACGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATAATAC
* * *
544549 AAAATCACAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATAATAC
** * *
544589 AATTTCGCAACGCAATACTGACTTTCGCAACTAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATAATAC
* *
544630 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
544646 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 33 0.42
41 45 0.58
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACTCGATAATAC
Found at i:545286 original size:25 final size:24
Alignment explanation
Indices: 545232--545288 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
545222 TGTTTATTAT
* *
545232 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
545256 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
545282 TGTTTTT
1 TGTTTTT
545289 TTTTGTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.19, C:0.09, G:0.18, T:0.54
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:546431 original size:18 final size:18
Alignment explanation
Indices: 546410--546457 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
546400 TCCACTTCGG
546410 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
546428 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
546446 GAGCCATCACCT
1 GAGCCATCACCT
546458 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:547016 original size:19 final size:18
Alignment explanation
Indices: 546992--547087 Score: 64
Period size: 19 Copynumber: 5.6 Consensus size: 18
546982 TAGTTTACTT
546992 TCGCAACGCGAAATGAAAA
1 TCGCAA-GCGAAATGAAAA
*
547011 TCGCAA-CG--A-CAAAA
1 TCGCAAGCGAAATGAAAA
*
547025 TCGCAATGCAAAATGAAAA
1 TCGCAA-GCGAAATGAAAA
*
547044 TCGCAA-CG--A-CAAAA
1 TCGCAAGCGAAATGAAAA
*
547058 TCGAAACGCGAAATGAAAA
1 TCGCAA-GCGAAATGAAAA
547077 TCGCAATGCGA
1 TCGCAA-GCGA
547088 TTTGTGTTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 29 0.50
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (18 bp):
TCGCAAGCGAAATGAAAA
Found at i:547039 original size:33 final size:33
Alignment explanation
Indices: 546992--547082 Score: 155
Period size: 33 Copynumber: 2.8 Consensus size: 33
546982 TAGTTTACTT
546992 TCGCAACGCGAAATGAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGACAAAA
* *
547025 TCGCAATGCAAAATGAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGACAAAA
*
547058 TCGAAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
547083 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGACAAAA
Found at i:547099 original size:19 final size:19
Alignment explanation
Indices: 547094--547218 Score: 80
Period size: 20 Copynumber: 6.7 Consensus size: 19
547084 GCGATTTGTG
*
547094 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
547113 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
547129 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
***
547146 TTTCGCATTGCGATAGCCA
1 TTTCGCATTGCGATTTTCA
* **
547165 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
* **
547185 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCATTGCGATTTTCA
*
547205 TTTTCGCGTTGCGA
1 -TTTCGCATTGCGA
547219 AAGTAAGTTT
Statistics
Matches: 91, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
14 6 0.07
15 3 0.03
16 4 0.04
17 4 0.04
18 3 0.03
19 24 0.26
20 44 0.48
21 3 0.03
ACGTcount: A:0.14, C:0.22, G:0.23, T:0.41
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:547178 original size:20 final size:20
Alignment explanation
Indices: 547132--547218 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
547122 GCGATTTTGT
**
547132 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
547151 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
547171 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
547191 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
547211 CGTTGCGA
1 CGTTGCGA
547219 AAGTAAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:547229 original size:20 final size:19
Alignment explanation
Indices: 547143--547240 Score: 97
Period size: 20 Copynumber: 4.9 Consensus size: 19
547133 GTTGCGATTT
* *
547143 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGAAAG
* *
547162 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGAAAG
*
547182 TCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGAAAG
547202 TCATTTTCGCGTTGCGAAAG
1 TCA-TTTCGCGTTGCGAAAG
* *
547222 TAAGTTTCGTGTTGCGAAA
1 TCA-TTTCGCGTTGCGAAA
547241 TTAAACTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
19 5 0.07
20 62 0.89
21 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (19 bp):
TCATTTCGCGTTGCGAAAG
Found at i:547236 original size:40 final size:40
Alignment explanation
Indices: 547145--547238 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
547135 TGCGATTTTC
* * *
547145 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
547184 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
547224 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
547239 AATTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:547619 original size:21 final size:20
Alignment explanation
Indices: 547593--547661 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
547583 CTGTCATCCC
547593 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
547614 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
547635 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
547655 TCAAGAG
1 TCAAGAG
547662 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:547673 original size:41 final size:42
Alignment explanation
Indices: 547583--547673 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
547573 GCCGAATCAC
* *
547583 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
547625 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
547666 CTGTCATC
1 CTGTCATC
547674 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:547682 original size:41 final size:41
Alignment explanation
Indices: 547586--547691 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 41
547576 GAATCACCTG
* *
547586 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCAACCGTTCAAGAGGCCACTA
* *
547628 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCAACCGTTCAAGAGGCCACTA
** *
547669 TCATCGTTGAAGAGGTCCCCCCA
1 TCATCCCTCAAGA-GTCCCCCCA
547692 CCATTCCAGA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 28 0.51
42 27 0.49
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.20
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:548512 original size:19 final size:18
Alignment explanation
Indices: 548490--548620 Score: 88
Period size: 19 Copynumber: 7.7 Consensus size: 18
548480 GGAAATTACT
548490 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
548509 ATCGCAA-CG--A-GATA
1 ATCGCAAGCGAAATGAAA
548523 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
548542 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
548556 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
548575 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
548589 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
548608 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
548621 TTTAGTTTCG
Statistics
Matches: 86, Mismatches: 10, Indels: 32
0.67 0.08 0.25
Matches are distributed among these distances:
14 26 0.30
15 5 0.06
16 6 0.07
17 6 0.07
18 5 0.06
19 38 0.44
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:548532 original size:33 final size:33
Alignment explanation
Indices: 548490--548616 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
548480 GGAAATTACT
**
548490 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
548523 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
548556 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
*
548589 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
548617 CGAATTTAGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:548651 original size:19 final size:19
Alignment explanation
Indices: 548616--548678 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
548606 AAATCGCAAC
*
548616 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
548635 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
548654 GCAATTTTTA-TTTCGCATT
1 GCGA-TTTTAGTTTCGCGTT
548673 GCGATT
1 GCGATT
548679 CTCTAGTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 2 0.05
19 32 0.82
20 5 0.13
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:548688 original size:33 final size:33
Alignment explanation
Indices: 548650--548776 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
548640 TTTAGTTTCG
* * *
548650 CGTTGCAATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
*
548683 AGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
548716 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
548749 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
548777 AGTAATTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:548709 original size:19 final size:19
Alignment explanation
Indices: 548626--548776 Score: 109
Period size: 19 Copynumber: 8.7 Consensus size: 19
548616 GCGAATTTAG
*
548626 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
* * *
548644 GTTTCGCGTTGCAATTTTTA
1 -TTTCGCATTGCGATTTTCA
548664 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
* *
548680 TCTAG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
548697 TTTCGCATTGCGA--TT-A
1 TTTCGCATTGCGATTTTCA
*
548713 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
548730 TTTCGCATTGCGA--TT-A
1 TTTCGCATTGCGATTTTCA
*
548746 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
548763 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
548777 AGTAATTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
14 18 0.17
16 20 0.19
17 19 0.18
19 46 0.44
20 1 0.01
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:548723 original size:14 final size:14
Alignment explanation
Indices: 548704--548758 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
548694 TCATTTCGCA
548704 TTGCGATTATCTCG
1 TTGCGATTATCTCG
*
548718 TTGCGATTTTCATTTCG
1 TTGCGA--TT-ATCTCG
548735 CATTGCGATTATCTCG
1 --TTGCGATTATCTCG
548751 TTGCGATT
1 TTGCGATT
548759 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTATCTCG
Found at i:548902 original size:14 final size:13
Alignment explanation
Indices: 548883--548921 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
548873 CATCAATTAA
548883 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
548897 ACAAATCATATTTT
1 ACAAATCA-ATTTT
548911 ACAAATCAATT
1 ACAAATCAATT
548922 AAACAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:550352 original size:42 final size:42
Alignment explanation
Indices: 550306--550385 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
550296 CGATGACAGT
* * *
550306 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
550348 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
550386 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:550788 original size:91 final size:90
Alignment explanation
Indices: 550607--550791 Score: 273
Period size: 91 Copynumber: 2.0 Consensus size: 90
550597 ATTTCAAACT
*
550607 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAATTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAATTTAGC
*
550672 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAACAACCGAATAAATTTAC
*
550700 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCA
**
550764 TTATTGGCAACAACCGAATAAATTTAC
64 GAATTGGCAACAACCGAATAAATTTAC
550791 T
1 T
550792 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
91 39 0.46
93 19 0.22
95 27 0.32
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCAGA
ATTGGCAACAACCGAATAAATTTAC
Found at i:551604 original size:30 final size:30
Alignment explanation
Indices: 551533--551592 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
551523 ACAACTTAAG
551533 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
551563 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
551593 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:551733 original size:21 final size:21
Alignment explanation
Indices: 551676--551733 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
551666 AGGGTGTCAA
*
551676 AGTGCATCCATGCATACCTGC
1 AGTGCATCCATGCATCCCTGC
551697 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
551718 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
551734 TGCACTACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:551809 original size:8 final size:8
Alignment explanation
Indices: 551796--551858 Score: 50
Period size: 8 Copynumber: 8.8 Consensus size: 8
551786 ATGCAATTAG
*
551796 TGCATCGA
1 TGCATCCA
*
551804 TGCATCCT
1 TGCATCCA
551812 TGC--C-A
1 TGCATCCA
551817 TGCATCCA
1 TGCATCCA
*
551825 TGCATCGA
1 TGCATCCA
551833 TGCATCC-
1 TGCATCCA
551840 TG---CCA
1 TGCATCCA
551845 TGCATCCA
1 TGCATCCA
551853 TGCATC
1 TGCATC
551859 AAGGTTGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
4 2 0.05
5 5 0.12
6 1 0.02
7 3 0.07
8 32 0.74
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (8 bp):
TGCATCCA
Found at i:551849 original size:12 final size:13
Alignment explanation
Indices: 551803--551855 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
551793 TAGTGCATCG
*
551803 ATGCATCCTTGCC
1 ATGCATCCATGCC
551816 ATGCATCCATGCATC
1 ATGCATCCATGC--C
551831 GATGCATCC-TGCC
1 -ATGCATCCATGCC
551844 ATGCATCCATGC
1 ATGCATCCATGC
551856 ATCAAGGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 8 0.23
13 15 0.43
15 4 0.11
16 8 0.23
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (13 bp):
ATGCATCCATGCC
Found at i:551852 original size:28 final size:29
Alignment explanation
Indices: 551796--551858 Score: 119
Period size: 28 Copynumber: 2.2 Consensus size: 29
551786 ATGCAATTAG
551796 TGCATCGATGCATCCTTGCCATGCATCCA
1 TGCATCGATGCATCCTTGCCATGCATCCA
551825 TGCATCGATGCATCC-TGCCATGCATCCA
1 TGCATCGATGCATCCTTGCCATGCATCCA
551853 TGCATC
1 TGCATC
551859 AAGGTTGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.56
29 15 0.44
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (29 bp):
TGCATCGATGCATCCTTGCCATGCATCCA
Found at i:555161 original size:30 final size:30
Alignment explanation
Indices: 555090--555149 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
555080 ACAACTTAAG
555090 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
555120 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
555150 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:555258 original size:21 final size:21
Alignment explanation
Indices: 555232--555289 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
555222 AGGGTGTCAA
*
555232 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
555253 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
555274 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
555290 TGCACTAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:555266 original size:8 final size:8
Alignment explanation
Indices: 555255--555414 Score: 51
Period size: 8 Copynumber: 20.8 Consensus size: 8
555245 ATCCCTGTAG
555255 TGCATCCA
1 TGCATCCA
*
555263 TGCATCCC
1 TGCATCCA
*
555271 TGCA---G
1 TGCATCCA
555276 TGCATCCA
1 TGCATCCA
555284 TGCAT-C-
1 TGCATCCA
*
555290 TGCA-CTAA
1 TGCATC-CA
*
555298 TGCATCGA
1 TGCATCCA
555306 TGCATCAGGCAA
1 TGCATC---C-A
555318 TGCATCCA
1 TGCATCCA
555326 TGCATCCA
1 TGCATCCA
** *
555334 AACATCGAA
1 TGCATC-CA
*
555343 TGCAAT-TA
1 TGC-ATCCA
*
555351 GTGCATCGA
1 -TGCATCCA
*
555360 TGCATCCT
1 TGCATCCA
555368 TGC--C-A
1 TGCATCCA
555373 TGCATCCA
1 TGCATCCA
*
555381 TGCATCGA
1 TGCATCCA
555389 TGCAT-CA
1 TGCATCCA
555396 TG---CCA
1 TGCATCCA
555401 TGCATCCA
1 TGCATCCA
555409 TGCATC
1 TGCATC
555415 AAGGCTACAA
Statistics
Matches: 112, Mismatches: 18, Indels: 44
0.64 0.10 0.25
Matches are distributed among these distances:
5 11 0.10
6 5 0.04
7 5 0.04
8 74 0.66
9 8 0.07
10 2 0.02
12 7 0.06
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:555403 original size:20 final size:20
Alignment explanation
Indices: 555359--555415 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
555349 TAGTGCATCG
*
555359 ATGCATCCTTGCCATGCAT-CC
1 ATGCATCCATG-CAT-CATGCC
*
555380 ATGCATCGATGCATCATGCC
1 ATGCATCCATGCATCATGCC
555400 ATGCATCCATGCATCA
1 ATGCATCCATGCATCA
555416 AGGCTACAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 20 0.62
21 9 0.28
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (20 bp):
ATGCATCCATGCATCATGCC
Found at i:555814 original size:34 final size:33
Alignment explanation
Indices: 555768--555838 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
555758 CCTTTTGTAA
*
555768 AGGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
555803 AGGGG-AAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
555835 AGGG
1 AGGG
555839 AGTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 10 0.29
33 1 0.03
34 18 0.53
35 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (33 bp):
AGGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:556479 original size:20 final size:20
Alignment explanation
Indices: 556454--556565 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
556444 TCTATGTAAA
556454 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
556474 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
556494 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* * ** *
556515 CCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
556535 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
556555 TCGCATTGCGA
1 TCGCATTGCGA
556566 ATTATGAAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:556578 original size:41 final size:41
Alignment explanation
Indices: 556451--556703 Score: 149
Period size: 41 Copynumber: 6.2 Consensus size: 41
556441 GGCTCTATGT
* * * *
556451 AAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTACG-
1 AAATCGCATTGCGAT-TTACGTATTCGCATTGCGAATTAGGA
* * * * * * **
556491 TATTCGCATTGCGATTTTCCTAATCCGCATTGCGATTTA-CT
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * *
556532 TAATCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
* ** * *
556573 AAATCGCAATGC-AAATACGTAAATCGCAATGCGAATTAGGA
1 AAATCGCATTGCGATTTACGT-ATTCGCATTGCGAATTAGGA
* * * ***
556614 AAATTGCATTGCGATAGT-CAGTA-TCGCATTGCGATTTTCCA
1 AAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAATTAGGA
* * * *
556655 AATTTGCATTGCGATTTACTTATTCGCATTGCGAATTGGGA
1 AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
556696 AAATCGCA
1 AAATCGCA
556704 ACGCGAAATT
Statistics
Matches: 161, Mismatches: 42, Indels: 19
0.73 0.19 0.09
Matches are distributed among these distances:
39 1 0.01
40 37 0.23
41 117 0.73
42 3 0.02
43 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
AAATCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGA
Found at i:556598 original size:61 final size:61
Alignment explanation
Indices: 556474--556606 Score: 144
Period size: 61 Copynumber: 2.2 Consensus size: 61
556464 ATAGTAAGAT
* ** * ** *
556474 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATCCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTATCAAAATCCGCAATGCGAAATACTAAA
* *
556535 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAAT-CGCAATGC-AAATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCAAAATCCGCAATGCGAAATAC-TAAA
*
556596 TCGCAATGCGA
1 TCGCATTGCGA
556607 ATTAGGAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 4 0.07
61 48 0.81
62 7 0.12
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (61 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCAAAATCCGCAATGCGAAATACTAAA
Found at i:556626 original size:21 final size:21
Alignment explanation
Indices: 556555--556627 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
556545 ATTTACGTAT
* *
556555 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
556576 TCGCAATGC-AAATACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
556596 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
556617 TTGCATTGCGA
1 TCGCAATGCGA
556628 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:556685 original size:20 final size:21
Alignment explanation
Indices: 556637--556688 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
556627 ATAGTCAGTA
*
556637 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
556658 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
556678 TCGCATTGCGA
1 TCGCATTGCGA
556689 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:561735 original size:17 final size:17
Alignment explanation
Indices: 561713--561772 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
561703 AATAAATATT
561713 AAATAAATCAAAGGGAA
1 AAATAAATCAAAGGGAA
*** *
561730 AAATAAAAAT-AAAAATATT
1 AAAT--AAATCAAAGGGA-A
561749 AAATAAATCAAAGGGAA
1 AAATAAATCAAAGGGAA
561766 AAATAAA
1 AAATAAA
561773 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 15 0.48
18 8 0.26
19 8 0.26
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (17 bp):
AAATAAATCAAAGGGAA
Found at i:561747 original size:36 final size:35
Alignment explanation
Indices: 561701--561778 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 35
561691 AAAATGTTAG
561701 ATAATAAATATTAAATAAATCAAAGGGAAAAATAAAA
1 ATAA-AAATATTAAATAAATCAAAGGGAAAAAT-AAA
561738 ATAAAAATATTAAATAAATCAAAGGGAAAAATAAA
1 ATAAAAATATTAAATAAATCAAAGGGAAAAATAAA
561773 ATAAAA
1 ATAAAA
561779 TAAATAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 9 0.22
36 28 0.68
37 4 0.10
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (35 bp):
ATAAAAATATTAAATAAATCAAAGGGAAAAATAAA
Found at i:562429 original size:21 final size:21
Alignment explanation
Indices: 562391--562431 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
562381 AAAGGCTTCG
562391 ACTTTTACCTTTTCTGATGCA
1 ACTTTTACCTTTTCTGATGCA
562412 ACTTCTTACCTTTT-TGATGC
1 ACTT-TTACCTTTTCTGATGC
562432 TCATTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.49
Consensus pattern (21 bp):
ACTTTTACCTTTTCTGATGCA
Found at i:563065 original size:25 final size:24
Alignment explanation
Indices: 563010--563066 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 24
563000 AAATAAAAAA
*
563010 ATAAGTAAATAATAAATATATATAT
1 ATAA-TAAAAAATAAATATATATAT
563035 ATTAATAAAAAATAAATA-ATATTAAT
1 A-TAATAAAAAATAAATATATA-T-AT
563061 ATAATA
1 ATAATA
563067 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 3 0.11
25 19 0.68
26 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAATAAAAAATAAATATATATAT
Found at i:563122 original size:38 final size:38
Alignment explanation
Indices: 563079--563373 Score: 402
Period size: 38 Copynumber: 7.8 Consensus size: 38
563069 AATTTTTTTG
*
563079 AAACTATATATTATATACA-TTTTCAAAAATATTTTCAA
1 AAACTATATATTATATATATTTTTC-AAAATATTTTCAA
*
563117 AAACTATATATTATATATATGTTTTCAAAATGTTTT-AA
1 AAACTATATATTATATATAT-TTTTCAAAATATTTTCAA
* *
563155 AAAATATATATTATATATATGTTTTCAAATTATTTTC-A
1 AAACTATATATTATATATAT-TTTTCAAAATATTTTCAA
* *
563193 AAACTATAAATTATATATATTTTTTCAAAATGTTTTTCAA
1 AAACTATATATTATATATA-TTTTTCAAAAT-ATTTTCAA
* *
563233 AAATTATATTTTATATATATTTTTCAAAATATTTTCAA
1 AAACTATATATTATATATATTTTTCAAAATATTTTCAA
* *
563271 AAACTATATATTATATATAATTTTCAAAATGTTTTCAA
1 AAACTATATATTATATATATTTTTCAAAATATTTTCAA
*
563309 AAACTATATATTATATATA-TTTTCAAAATGTTTTCAA
1 AAACTATATATTATATATATTTTTCAAAATATTTTCAA
*
563346 AAACTATATAATATATAT-TTTTTCAAAA
1 AAACTATATATTATATATATTTTTCAAAA
563374 AACCGATTTT
Statistics
Matches: 232, Mismatches: 18, Indels: 15
0.88 0.07 0.06
Matches are distributed among these distances:
37 44 0.19
38 140 0.60
39 26 0.11
40 22 0.09
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (38 bp):
AAACTATATATTATATATATTTTTCAAAATATTTTCAA
Done.