Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold296
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: 679504
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.24
Warning! 166439 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:498983 original size:33 final size:33
Alignment explanation
Indices: 498936--499124 Score: 174
Period size: 33 Copynumber: 5.7 Consensus size: 33
498926 TCCATTGCCC
* **
498936 CCATAACTCTGTGGCACTTTTTTTCCCTTAAGT
1 CCATAACTCAGTGGCACCCTTTTTCCCTTAAGT
* *
498969 CCACAACTCAGTGGCACCCTTTTTCCTTTTAAGT
1 CCATAACTCAGTGGCACCCTTTTTCC-CTTAAGT
499003 CCATAACTTC-GTGGCA-CCTTTTTCCCTTTAAGT
1 CCATAAC-TCAGTGGCACCCTTTTTCCC-TTAAGT
* * * *
499036 CCATAACTCAATGGCACCTTTTTTCCTTTTAAAT
1 CCATAACTCAGTGGCACCCTTTTTCC-CTTAAGT
* * *
499070 CCATAATTCTGTGGCA-CC-TTTTCCTTTCAAGT
1 CCATAACTCAGTGGCACCCTTTTTCCCTT-AAGT
499102 CCATAACTCTA-TGGCA-CCTTTTT
1 CCATAACTC-AGTGGCACCCTTTTT
499125 AAATCCACAA
Statistics
Matches: 129, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
31 3 0.02
32 26 0.20
33 54 0.42
34 44 0.34
35 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.40
Consensus pattern (33 bp):
CCATAACTCAGTGGCACCCTTTTTCCCTTAAGT
Found at i:499001 original size:34 final size:34
Alignment explanation
Indices: 498936--499253 Score: 222
Period size: 34 Copynumber: 9.7 Consensus size: 34
498926 TCCATTGCCC
* ** *
498936 CCATAACTCTGTGGCACTTTTTTTCC-CTTAAGT
1 CCATAACTCAGTGGCACCCTTTTTCCTTTTAAGT
*
498969 CCACAACTCAGTGGCACCCTTTTTCCTTTTAAGT
1 CCATAACTCAGTGGCACCCTTTTTCCTTTTAAGT
*
499003 CCATAACTTC-GTGGCA-CCTTTTTCCCTTTAAGT
1 CCATAAC-TCAGTGGCACCCTTTTTCCTTTTAAGT
* * *
499036 CCATAACTCAATGGCACCTTTTTTCCTTTTAAAT
1 CCATAACTCAGTGGCACCCTTTTTCCTTTTAAGT
* * *
499070 CCATAATTCTGTGGCA-CC-TTTTCCTTTCAAGT
1 CCATAACTCAGTGGCACCCTTTTTCCTTTTAAGT
*
499102 CCATAACTCTA-TGGCA-CC----T--TTTTAAAT
1 CCATAACTC-AGTGGCACCCTTTTTCCTTTTAAGT
* * *
499129 CCACAAATCCA-TGGCA-CCTTTTT-CTTTTCAAAGC
1 CCATAACT-CAGTGGCACCCTTTTTCCTTTT--AAGT
** * **
499163 CCATAACTTC-GTAACACTCTTTCACCTTTTAAGT
1 CCATAAC-TCAGTGGCACCCTTTTTCCTTTTAAGT
* *
499197 CCACAACTCTA-TGGCACCCTTTTTGCTTTTAAGT
1 CCATAACTC-AGTGGCACCCTTTTTCCTTTTAAGT
* *
499231 CCACAACTCTGTGGCACCCTTTT
1 CCATAACTCAGTGGCACCCTTTT
499254 ATGTCTACAA
Statistics
Matches: 224, Mismatches: 41, Indels: 39
0.74 0.13 0.13
Matches are distributed among these distances:
27 20 0.09
28 1 0.00
29 1 0.00
31 1 0.00
32 33 0.15
33 53 0.24
34 103 0.46
35 7 0.03
36 5 0.02
ACGTcount: A:0.22, C:0.30, G:0.10, T:0.38
Consensus pattern (34 bp):
CCATAACTCAGTGGCACCCTTTTTCCTTTTAAGT
Found at i:499044 original size:67 final size:67
Alignment explanation
Indices: 498936--499124 Score: 248
Period size: 67 Copynumber: 2.9 Consensus size: 67
498926 TCCATTGCCC
* *
498936 CCATAAC-TCTGTGGCACTTTTTTTCCC-TTAAGTCCACAACTCAGTGGCACCCTTTTTCCTTTT
1 CCATAACTTCTGTGGCAC-CTTTTTCCCTTTAAGTCCATAACTCA-TGGCACCCTTTTTCCTTTT
*
498999 AAGT
64 AAAT
*
499003 CCATAACTTC-GTGGCACCTTTTTCCCTTTAAGTCCATAACTCAATGGCACCTTTTTTCCTTTTA
1 CCATAACTTCTGTGGCACCTTTTTCCCTTTAAGTCCATAACTC-ATGGCACCCTTTTTCCTTTTA
499067 AAT
65 AAT
499070 CCATAA-TTCTGTGGCACC-TTTT-CCTTTCAAGTCCATAACTCTATGGCA-CCTTTTT
1 CCATAACTTCTGTGGCACCTTTTTCCCTTT-AAGTCCATAACTC-ATGGCACCCTTTTT
499125 AAATCCACAA
Statistics
Matches: 111, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
65 11 0.10
66 34 0.31
67 63 0.57
68 3 0.03
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.40
Consensus pattern (67 bp):
CCATAACTTCTGTGGCACCTTTTTCCCTTTAAGTCCATAACTCATGGCACCCTTTTTCCTTTTAA
AT
Found at i:499218 original size:27 final size:27
Alignment explanation
Indices: 499187--499339 Score: 110
Period size: 27 Copynumber: 5.2 Consensus size: 27
499177 CACTCTTTCA
499187 CCTTTTAAGTCCACAACTCTATGGCACC
1 CCTTTTAAGTCCACAACTCTATGGCA-C
*
499215 CTTTTTGCTTTTAAGTCCACAACTCTGTGGCAC
1 C------CTTTTAAGTCCACAACTCTATGGCAC
* *
499248 CCTTTTATGTCTACAACT-TCATGGCAC
1 CCTTTTAAGTCCACAACTCT-ATGGCAC
* * *
499275 ATTTTCCTTCTAAGTCCACATCTCCATGGCAC
1 -----CCTTTTAAGTCCACAACTCTATGGCAC
*
499307 CCTTTTAAGTCCACAACTCTATGCCAC
1 CCTTTTAAGTCCACAACTCTATGGCAC
*
499334 CATTTT
1 CCTTTT
499340 CCCTTTAACA
Statistics
Matches: 98, Mismatches: 14, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
26 1 0.01
27 49 0.50
28 1 0.01
32 21 0.21
33 2 0.02
34 24 0.24
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.35
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCTATGGCAC
Found at i:499370 original size:59 final size:59
Alignment explanation
Indices: 499187--499372 Score: 207
Period size: 59 Copynumber: 3.1 Consensus size: 59
499177 CACTCTTTCA
* *
499187 CCTTTTAAGTCCACAACTCTATGGCACCCTTTTTGCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTATGGCA-CCATTTT-CCTTTAAGTCCACAACTCTGTGGCAC
* * * **
499248 CCTTTTATGTCTACAACT-TCATGGCA-CATTTTCCTTCTAAGTCCACATCTCCATGGCAC
1 CCTTTTAAGTCCACAACTCT-ATGGCACCATTTTCCTT-TAAGTCCACAACTCTGTGGCAC
* *
499307 CCTTTTAAGTCCACAACTCTATGCCACCATTTTCCCTTTAACAT-CACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTATGGCACCATTTT-CCTTTAA-GTCCACAACTCTGTGGCAC
*
499367 CTTTTT
1 CCTTTT
499373 TTTTAAACTC
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
58 3 0.03
59 45 0.43
60 29 0.28
61 27 0.26
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.35
Consensus pattern (59 bp):
CCTTTTAAGTCCACAACTCTATGGCACCATTTTCCTTTAAGTCCACAACTCTGTGGCAC
Found at i:499496 original size:33 final size:32
Alignment explanation
Indices: 499411--499513 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
499401 CATCCCTTCA
* *
499411 AAAGCCCACACAAGTTGATGGCAACCCTACTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTTCTT
*
499443 AAAGCCCACATAAGTTGGTGGCAACCCTTCTCT
1 AAAGCCCACACAAGTTGGTGGCAACCCTTCT-T
* * *
499476 AAAGCTCACACAAGTCGGTGGCAACTCTTC-T
1 AAAGCCCACACAAGTTGGTGGCAACCCTTCTT
499507 AAA-CCCA
1 AAAGCCCA
499514 ATGTCGCTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.05
31 4 0.06
32 28 0.45
33 27 0.44
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (32 bp):
AAAGCCCACACAAGTTGGTGGCAACCCTTCTT
Found at i:499580 original size:49 final size:48
Alignment explanation
Indices: 499511--499888 Score: 258
Period size: 49 Copynumber: 7.7 Consensus size: 48
499501 TCTTCTAAAC
499511 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTCGATCTTTATGT
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTC-ATCTTTATGT
* * * * * *
499560 CCAATGCCGCTAGCCCTAAATTAGCATA-TGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC-TCATCTTTATGT
* * * *
499608 CCAAGGTCACTGGCCTTGAATCAG-ACATTAGCACCTCTATCTTTATGT
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTC-ATCTTTATGT
* * * * **
499656 CTAATGTCGCTGGCCTTGAAA-CAACACATTAGCACTTTCATCTTTAAAT
1 CCAATGTCGCTGGCCTT-AAATCAGCACATTGGCAC-CTCATCTTTATGT
* * * * ** * *
499705 CCAATGTTGCTGGCCTTGAATTAACATGTTGGCACCTTCACCTTTAAGT
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC-TCATCTTTATGT
** * *
499754 CCAATGTCATTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC-TCATCTTTATGT
* * * * * ** * * * * *
499803 TCGATATGGCTAGCCTGGAATCAGCATATTGGCACCTTTAACATTCCTAAGG
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACC-TCATC-TT--TATGT
* *
499855 CCAATGTCGCTAGCCTTAAATTAGCACATTGGCA
1 CCAATGTCGCTGGCCTTAAATCAGCACATTGGCA
499889 TTCTTCTCAT
Statistics
Matches: 256, Mismatches: 62, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
47 4 0.02
48 66 0.26
49 152 0.59
50 4 0.02
52 30 0.12
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (48 bp):
CCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTCATCTTTATGT
Found at i:499913 original size:52 final size:52
Alignment explanation
Indices: 499856--499992 Score: 148
Period size: 52 Copynumber: 2.6 Consensus size: 52
499846 TTCCTAAGGC
* * * * *
499856 CAATGTCGCTAGCCTTAAATTAGCACATTGGCATTCTTCTCATCTTTAAGTA
1 CAATGTCGCTGGCCTTGAATTAGCACATTAGCATTCTTCGCATCTTTAAGCA
* * * * * * *
499908 TAATGTCGTTGGTCGTGAATCAACACATTAGCATTCTTCGCATCTTTAAGCC
1 CAATGTCGCTGGCCTTGAATTAGCACATTAGCATTCTTCGCATCTTTAAGCA
* *
499960 CAATATCGCTGGCCTTGAATTAGCATATTAGCA
1 CAATGTCGCTGGCCTTGAATTAGCACATTAGCA
499993 CTTTTATCAT
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (52 bp):
CAATGTCGCTGGCCTTGAATTAGCACATTAGCATTCTTCGCATCTTTAAGCA
Found at i:500075 original size:18 final size:17
Alignment explanation
Indices: 500052--500085 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
500042 AGCATACTGG
*
500052 CATCTTTATCACTCTTCT
1 CATCTTCATCA-TCTTCT
500070 CATCTTCATCATCTTC
1 CATCTTCATCATCTTC
500086 AAGTCCAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (17 bp):
CATCTTCATCATCTTCT
Found at i:500075 original size:61 final size:61
Alignment explanation
Indices: 499942--500075 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 61
499932 ACATTAGCAT
* ** * * *
499942 TCTTCGCATCTTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTAGCACTTTTATCAT
1 TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACTTTTATCAC
* * *
500003 TTTTCTTATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTGGCA-TCTTTATCAC
1 TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACT-TTTATCAC
500064 TCTTCTCATCTT
1 TCTTCTCATCTT
500076 CATCATCTTC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 60 0.98
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (61 bp):
TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACTTTTATCAC
Found at i:500790 original size:19 final size:21
Alignment explanation
Indices: 500742--500794 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
500732 AATTTCTATA
500742 ATTTGTATCGATACAAATAGT
1 ATTTGTATCGATACAAATAGT
** *
500763 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAATAGT
500783 -TTTGTATCGATA
1 ATTTGTATCGATA
500795 TAATGTATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACAAATAGT
Found at i:500859 original size:20 final size:20
Alignment explanation
Indices: 500834--500889 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
500824 ACTACCAAGG
*
500834 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATTAAC
*
500854 AAATGTATCGATACATTTAC
1 AAATGTATCGATACATTAAC
* *
500874 CATTGTATCGATACAT
1 AAATGTATCGATACAT
500890 CTGGGTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (20 bp):
AAATGTATCGATACATTAAC
Found at i:502743 original size:11 final size:11
Alignment explanation
Indices: 502713--502769 Score: 62
Period size: 11 Copynumber: 5.3 Consensus size: 11
502703 ATTTCAAGAA
502713 TTTGGAATATT
1 TTTGGAATATT
***
502724 TTAAAAATATT
1 TTTGGAATATT
502735 TTTGGAATATT
1 TTTGGAATATT
* *
502746 TTT-TAAGATT
1 TTTGGAATATT
502756 TTTGGAATATT
1 TTTGGAATATT
502767 TTT
1 TTT
502770 AGATCGACCT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
10 8 0.23
11 27 0.77
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
TTTGGAATATT
Found at i:502769 original size:22 final size:22
Alignment explanation
Indices: 502713--502770 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
502703 ATTTCAAGAA
* *
502713 TTTGGAATATTTTAAAAATATT
1 TTTGGAATATTTTTAAAAGATT
*
502735 TTTGGAATATTTTT-TAAGATT
1 TTTGGAATATTTTTAAAAGATT
502756 TTTGGAATATTTTTA
1 TTTGGAATATTTTTA
502771 GATCGACCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (22 bp):
TTTGGAATATTTTTAAAAGATT
Found at i:506221 original size:13 final size:13
Alignment explanation
Indices: 506203--506232 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
506193 ACATTTTACT
506203 ATGTATCGATACA
1 ATGTATCGATACA
*
506216 ATGTATCGATATA
1 ATGTATCGATACA
506229 ATGT
1 ATGT
506233 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:506223 original size:33 final size:33
Alignment explanation
Indices: 506180--506249 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
506170 GCTGTTGGGC
* * *
506180 ACAATATATCGATACATTTTACTATGTATCGAT
1 ACAATATATCGATACAATGTACCATGTATCGAT
* * *
506213 ACAATGTATCGATATAATGTCCCATGTATCGAT
1 ACAATATATCGATACAATGTACCATGTATCGAT
506246 ACAA
1 ACAA
506250 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (33 bp):
ACAATATATCGATACAATGTACCATGTATCGAT
Found at i:506362 original size:20 final size:21
Alignment explanation
Indices: 506339--506377 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
506329 CAAAGCAATA
506339 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
506359 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
506378 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:508927 original size:19 final size:18
Alignment explanation
Indices: 508903--508947 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
508893 TCAATGTATC
508903 ATTCAAACAAACAAACATA
1 ATTCAAACAAAC-AACATA
**
508922 ATTCAATTAAACAACATA
1 ATTCAAACAAACAACATA
508940 ATT-AAACA
1 ATTCAAACA
508948 TCAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (18 bp):
ATTCAAACAAACAACATA
Found at i:510986 original size:79 final size:79
Alignment explanation
Indices: 510850--511258 Score: 497
Period size: 79 Copynumber: 5.2 Consensus size: 79
510840 GAGATAATAA
* * ** * * *
510850 CGGGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
510915 TTTAGAAATAAAAC
66 TTTAGAAATAAAAC
* * * *
510929 CGGGATTGGAATATCCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGACTATGAAAAATTGATG
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
510993 TTTTAGAAATAAAAC
65 TTTTAGAAATAAAAC
* * * * *
511008 CGGGGTTGGAGTATTCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTATGAGAAATTAATA
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
*
511072 TTTTAGAAATAAAGC
65 TTTTAGAAATAAAAC
* *
511087 CGGGGTTGGGGTAT-CCCTCGAAAATAACAGGGTTGGAGTATCCCCG---ATGAAAAATTGATGT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
511148 TTTAGAAATAAAAC
66 TTTAGAAATAAAAC
* * * * * *
511162 CAGGGTTGGAGTGTCCCCTCGAAAATAACGTGGTTGGAGTATCCCCGATTATGGAAAATGGGTGT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
*
511227 TTTAGAAATAAAAT
66 TTTAGAAATAAAAC
* * *
511241 CAGAGTTTGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
511259 GATTAAGAAA
Statistics
Matches: 286, Mismatches: 38, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
75 36 0.13
76 30 0.10
78 29 0.10
79 191 0.67
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGT
TTTAGAAATAAAAC
Found at i:511230 original size:154 final size:155
Alignment explanation
Indices: 510852--511239 Score: 489
Period size: 154 Copynumber: 2.5 Consensus size: 155
510842 GATAATAACG
** * * *
510852 GGGTTGGAGTATTCCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTGTGAAAAATCGATGATT
1 GGGTTGGAGTATTCCCTCGAAAATAAC-GGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTT
**
510917 TAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGACTATG
65 TAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGA--ATG
*
510982 AAAAATTGATGTTTTAGAAATAAAACCG
128 AAAAATTGATGTTTTAGAAATAAAACCA
* ** *
511010 GGGTTGGAGTATTCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTAT-GAGAAATTAATAT
1 GGGTTGGAGTATTCCCTCGA-AAATAA-CGGGTTGGAGTATCCCCGATTATGGA-AAATCGATGT
* * **
511073 TTTAGAAATAAAGCCGGGGTTGGGGTAT-CCCTC-GAAAATAACAGGGTTGGAGTATCCCCG-AT
63 TTTAGAAATAAAACCGGGATTGGAATATCCCCTCAG-AAATAACAGGGTTGGAGTATCCCCGAAT
511135 GAAAAATTGATGTTTTAGAAATAAAACCA
127 GAAAAATTGATGTTTTAGAAATAAAACCA
* * * *
511164 GGGTTGGAGTGTCCCCTCGAAAATAACGTGGTTGGAGTATCCCCGATTATGGAAAATGGGTGTTT
1 GGGTTGGAGTATTCCCTCGAAAATAACG-GGTTGGAGTATCCCCGATTATGGAAAATCGATGTTT
511229 TAGAAATAAAA
65 TAGAAATAAAA
511240 TCAGAGTTTG
Statistics
Matches: 199, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
153 1 0.01
154 91 0.46
155 3 0.02
156 1 0.01
157 30 0.15
158 73 0.37
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (155 bp):
GGGTTGGAGTATTCCCTCGAAAATAACGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTT
AGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGAATGAAA
AATTGATGTTTTAGAAATAAAACCA
Found at i:511304 original size:51 final size:51
Alignment explanation
Indices: 511194--511307 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
511184 AAATAACGTG
* * * * *
511194 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTATAGAAATAAAACCAGA
* * * *
511245 GTTTGAGTATCCCCGATTAAGAAAAATTGATGTTATGGAAATGAAACCAG-
1 GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTATAGAAATAAAACCAGA
511295 GATTGGAGTATCC
1 G-TTGGAGTATCC
511308 ACGAGATGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATGGATGTTATAGAAATAAAACCAGA
Found at i:513625 original size:20 final size:20
Alignment explanation
Indices: 513600--513653 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
513590 AAAATGCCTG
*
513600 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGCA-A
513620 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
513640 AATGTATCGATACA
1 AATGTATCGATACA
513654 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:516256 original size:13 final size:13
Alignment explanation
Indices: 516238--516268 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
516228 ACAATTCATC
516238 ATGTATCGATACA
1 ATGTATCGATACA
*
516251 ATGTATTGATACA
1 ATGTATCGATACA
516264 ATGTA
1 ATGTA
516269 CCCTGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:516262 original size:33 final size:33
Alignment explanation
Indices: 516216--516284 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
516206 CCGTTAAAAG
* *
516216 CAATGTGTCGATACAAT-TCATCATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
* *
516249 CAATGTATTGATACAATGTACCCTGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
516282 CAA
1 CAA
516285 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:518856 original size:13 final size:13
Alignment explanation
Indices: 518838--518862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518828 TAGTAACCTA
518838 TGTATCGATACAT
1 TGTATCGATACAT
518851 TGTATCGATACA
1 TGTATCGATACA
518863 AGGAATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:523381 original size:9 final size:9
Alignment explanation
Indices: 523367--523400 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
523357 TCCGAGTCAC
523367 CATCATTAT
1 CATCATTAT
523376 CATCATTAT
1 CATCATTAT
523385 CATC-TTCAT
1 CATCATT-AT
523394 CATCATT
1 CATCATT
523401 GATGGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:525002 original size:13 final size:13
Alignment explanation
Indices: 524986--525016 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
524976 ACAATTCATC
*
524986 ATGTATCGATACA
1 ATGTATCAATACA
524999 ATGTATCAATACA
1 ATGTATCAATACA
525012 ATGTA
1 ATGTA
525017 CTGTGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:525105 original size:19 final size:19
Alignment explanation
Indices: 525061--525116 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
525051 CTGCCAGTTT
* **
525061 CATGTATCAATACAATTGTC
1 CATGTATCGATACAA-TGAA
525081 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
525100 CATGTATCGATACAATG
1 CATGTATCGATACAATG
525117 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:525119 original size:13 final size:13
Alignment explanation
Indices: 525101--525127 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
525091 TACAATGAAC
525101 ATGTATCGATACA
1 ATGTATCGATACA
525114 ATGTATCGATACA
1 ATGTATCGATACA
525127 A
1 A
525128 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:531103 original size:155 final size:155
Alignment explanation
Indices: 530845--531493 Score: 631
Period size: 155 Copynumber: 4.2 Consensus size: 155
530835 TACCTTAGAT
* * * *
530845 ATGAAAGTAT-TACGGTAACCC-AAAAGGACTCGAAAATGATCCT-AGAGGAAAGAACCTATCCT
1 ATGAAAGTATCTA-AGTAACCCTAAAA-GACTCGAAAATGATCATAAAAGGATA-AACCTATCCT
* * * * * * *
530907 -AATGCATACATTTGGCATAAAAGCATCCTAGTGACTACATCGGACTTGATTTTAAATAACTTAC
63 AAATGCACACCTTTGGCATAAAAGCAACCTAGTGACTACATCGGACTCGATTCTAAAAAAATTAC
* * *
530971 CAAAATACCTTTGGGGTATACCTTCCAC
128 CAAAATACCTTTAGAGTATACCTTCAAC
* * * * *
530999 CTGAAGGTATTCT-GGTCACCCTAAAAGACTTGAAAATGATCATAAAAGGATAAACCTATCCTAA
1 ATGAAAGTA-TCTAAGTAACCCTAAAAGACTCGAAAATGATCATAAAAGGATAAACCTATCCTAA
* * *
531063 ATGCACACCTTTGGCATAAAAGTAACCTAGTGACTACATCGGACTCAATTCT-AAAAAATTATCA
65 ATGCACACCTTTGGCATAAAAGCAACCTAGTGACTACATCGGACTCGATTCTAAAAAAATTACCA
* * * *
531127 AAATGCCATTAAAGTATACCTTCGAC
130 AAATACCTTTAGAGTATACCTTCAAC
* * **
531153 ATAAAAGTATCTCAA-TAACTCTAAAAGACTCGAAAATGATTGTCAAAA-GATAAACCTATCCTA
1 ATGAAAGTATCT-AAGTAACCCTAAAAGACTCGAAAATGATCAT-AAAAGGATAAACCTATCCTA
* **
531216 AATGCACACCTTTGGCATGAAAA-CATCCTAGTGACTACATCAAACTC-AGTTCTAAAAAAATTA
64 AATGCACACCTTTGGCAT-AAAAGCAACCTAGTGACTACATCGGACTCGA-TTCTAAAAAAATTA
* * *
531279 CTAAAATGCCTTTAGAGTATACCTTTAAC
127 CCAAAATACCTTTAGAGTATACCTTCAAC
* * * * * * * * *
531308 ATGAAAGTGTCTAAGTAACCCTAAAGGACTTGAAAATGATCATAGAAGAATGAACATGTCCTAGA
1 ATGAAAGTATCTAAGTAACCCTAAAAGACTCGAAAATGATCATAAAAGGATAAACCTATCCTAAA
* * *
531373 TGCACACCTTTGGCATAAAAGC-ACCTCGGTGACTATATC-GAGCTCGATTTTAAAAAAATTACC
66 TGCACACCTTTGGCATAAAAGCAACCT-AGTGACTACATCGGA-CTCGATTCTAAAAAAATTACC
* * * *
531436 AAATTACCCTTAGAATGTACCTTCAAC
129 AAAATACCTTTAGAGTATACCTTCAAC
*
531463 ATGAAAGTATCT-CGATAACCCTAAAAGACTC
1 ATGAAAGTATCTAAG-TAACCCTAAAAGACTC
531494 TAAATAATAT
Statistics
Matches: 406, Mismatches: 71, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
153 4 0.01
154 168 0.41
155 232 0.57
156 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (155 bp):
ATGAAAGTATCTAAGTAACCCTAAAAGACTCGAAAATGATCATAAAAGGATAAACCTATCCTAAA
TGCACACCTTTGGCATAAAAGCAACCTAGTGACTACATCGGACTCGATTCTAAAAAAATTACCAA
AATACCTTTAGAGTATACCTTCAAC
Found at i:531378 original size:309 final size:309
Alignment explanation
Indices: 530897--531493 Score: 722
Period size: 309 Copynumber: 1.9 Consensus size: 309
530887 TAGAGGAAAG
* ** * *
530897 AACCTATCCTAATGCATACATTTGGCATAAAAGCATCCTAGTGACTACATCGGACTTGATTTTAA
1 AACCTATCCTAATGCACACATTTGGCATAAAAGCATCCTAGTGACTACATCAAACTAGATTCTAA
* * * * * * * * * *
530962 ATAACTTACCAAAATACCTTTGGGGTATACCTTCCACCTGAAGGTATTCTGGTCACCCTAAAAGA
66 AAAAATTACCAAAATACCTTTAGAGTATACCTTCAACATGAAAGTAGTCTAGTAACCCTAAAAGA
* *
531027 CTTGAAAATGATCATAAAAGGATAAACCTATCCTAAATGCACACCTTTGGCATAAAAGTAACCT-
131 CTTGAAAATGATCATAAAAGAATAAACATATCCTAAATGCACACCTTTGGCATAAAAG-AACCTC
* * *
531091 AGTGACTACATCG-GACTCAATTCT-AAAAAATTATCAAAATGCCATTA-AAGTATACCTTCGAC
195 AGTGACTACATCGAG-CTCAATTCTAAAAAAATTACCAAAATACCATTAGAA-TATACCTTCAAC
*
531153 ATAAAAGTATCTCAATAACTCTAAAAGACTCGAAAATGATTGTCAAAAGATA
258 ATAAAAGTATCTCAATAACCCTAAAAGACTCGAAAATGATTGTCAAAAGATA
*
531205 AACCTATCCTAAATGCACACCTTTGGCATGAAAA-CATCCTAGTGACTACATCAAACTCAG-TTC
1 AACCTATCCT-AATGCACACATTTGGCAT-AAAAGCATCCTAGTGACTACATCAAACT-AGATTC
* * *
531268 TAAAAAAATTACTAAAATGCCTTTAGAGTATACCTTTAACATGAAAGT-GTCTAAGTAACCCTAA
63 TAAAAAAATTACCAAAATACCTTTAGAGTATACCTTCAACATGAAAGTAGTCT-AGTAACCCTAA
* * * * * *
531332 AGGACTTGAAAATGATCATAGAAGAATGAACATGTCCTAGATGCACACCTTTGGCATAAAAGCAC
127 AAGACTTGAAAATGATCATAAAAGAATAAACATATCCTAAATGCACACCTTTGGCATAAAAGAAC
* * * * * * *
531397 CTCGGTGACTATATCGAGCTCGATTTTAAAAAAATTACCAAATTACCCTTAGAATGTACCTTCAA
192 CTCAGTGACTACATCGAGCTCAATTCTAAAAAAATTACCAAAATACCATTAGAATATACCTTCAA
* *
531462 CATGAAAGTATCTCGATAACCCTAAAAGACTC
257 CATAAAAGTATCTCAATAACCCTAAAAGACTC
531494 TAAATAATAT
Statistics
Matches: 241, Mismatches: 40, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
308 17 0.07
309 159 0.66
310 63 0.26
311 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (309 bp):
AACCTATCCTAATGCACACATTTGGCATAAAAGCATCCTAGTGACTACATCAAACTAGATTCTAA
AAAAATTACCAAAATACCTTTAGAGTATACCTTCAACATGAAAGTAGTCTAGTAACCCTAAAAGA
CTTGAAAATGATCATAAAAGAATAAACATATCCTAAATGCACACCTTTGGCATAAAAGAACCTCA
GTGACTACATCGAGCTCAATTCTAAAAAAATTACCAAAATACCATTAGAATATACCTTCAACATA
AAAGTATCTCAATAACCCTAAAAGACTCGAAAATGATTGTCAAAAGATA
Found at i:535043 original size:50 final size:51
Alignment explanation
Indices: 534926--535047 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
534916 TGAAAATTTT
* * *
534926 CCTACATGTATCGATACATTGAATAATGTATCGATACATCTAGGTAAAATA
1 CCTAGATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAAAA
* *
534977 CCTAGATGTACCGATACAATG-ATCAATGTATCGATACAT-TTGGTAAAAAA
1 CCTAGATGTATCGATACAATGAAT-AATGTATCGATACATCTAGGTAAAAAA
*
535027 TCTAGATGTATCGATACAATG
1 CCTAGATGTATCGATACAATG
535048 TATCGATACA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 30 0.48
51 33 0.52
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (51 bp):
CCTAGATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAAAA
Found at i:535050 original size:13 final size:13
Alignment explanation
Indices: 535032--535057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535022 AAAAATCTAG
535032 ATGTATCGATACA
1 ATGTATCGATACA
535045 ATGTATCGATACA
1 ATGTATCGATACA
535058 TTTCCTTGGC
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:538314 original size:66 final size:66
Alignment explanation
Indices: 538077--538354 Score: 265
Period size: 66 Copynumber: 4.2 Consensus size: 66
538067 GATGAAATCA
* * *
538077 ATAAAGTCAACTAAAGGTGACCAAG--GTAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA
1 ATAAAGTCAACTAAGGGTGACCAAGACG-A-AACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAA
538140 -TCG
64 CT-G
* * * * ** **
538143 ATAGAGTCAACTAAGGGTGGCCAAGGCAAAACCTAAGTCGAAAAAGGGGTTGACTAGGAAAAAAA
1 ATAAAGTCAACTAAGGGTGACCAAGACGAAACCTAAGTC-AAAAAAAGGTTGACTAGG-GCAAAA
**
538208 CCA
64 CTG
* * *
538211 ATAAAGTCAACTAAGGGTGACCATGATGGAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAACT
1 ATAAAGTCAACTAAGGGTGACCAAGACGAAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAACT
538276 G
66 G
* * ** * * * * *
538277 ATGATGTCAACTAAGGGTGACCAAGACGAAATTTAAGTCGATAAAGGGTTAACTAGGGCAAAATT
1 ATAAAGTCAACTAAGGGTGACCAAGACGAAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAACT
538342 G
66 G
538343 ATAAAGTCAACT
1 ATAAAGTCAACT
538355 GAAGATGACA
Statistics
Matches: 168, Mismatches: 39, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
66 101 0.60
67 31 0.18
68 36 0.21
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.18
Consensus pattern (66 bp):
ATAAAGTCAACTAAGGGTGACCAAGACGAAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAACT
G
Found at i:538315 original size:134 final size:133
Alignment explanation
Indices: 538075--538333 Score: 360
Period size: 134 Copynumber: 1.9 Consensus size: 133
538065 AAGATGAAAT
*
538075 CAATAAAGTCAACTAAAGGTGACCAAGGTAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA
1 CAATAAAGTCAACTAAAGGTGACCAAGATAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA
* * *
538140 TCGATAGAGTCAACTAAGGGTGGCCAAGGCAAAACCTAAGTCGAAAAAGGGGTTGACTAGGAAAA
66 TCGATAGAGTCAACTAAGGGTGACCAAGACAAAACCTAAGTCGAAAAA-GGGTTAACTAGGAAAA
538205 AAAC
130 AAAC
* * * * *
538209 CAATAAAGTCAACTAAGGGTGACCATGATGGAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAA
1 CAATAAAGTCAACTAAAGGTGACCAAGATAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA
* ** *
538274 -CTGAT-GATGTCAACTAAGGGTGACCAAGACGAAATTTAAGTCGATAAAGGGTTAACTAGG
66 TC-GATAGA-GTCAACTAAGGGTGACCAAGACAAAACCTAAGTCGAAAAAGGGTTAACTAGG
538334 GCAAAATTGA
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 14 0.13
134 96 0.87
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.17
Consensus pattern (133 bp):
CAATAAAGTCAACTAAAGGTGACCAAGATAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA
TCGATAGAGTCAACTAAGGGTGACCAAGACAAAACCTAAGTCGAAAAAGGGTTAACTAGGAAAAA
AAC
Found at i:538380 original size:66 final size:64
Alignment explanation
Indices: 538077--538495 Score: 229
Period size: 66 Copynumber: 6.3 Consensus size: 64
538067 GATGAAATCA
* * * * * * * *
538077 ATAAAGTCAACTAAAGGTGACCAAGGTAGAACCTAAGTCAAAAAAAGGTTGACCAAGGCAAAA-T
1 ATAAAGTCAACTAAGGGTGA-CAAGATGGAACCTAAGTC-GAAAAGGGTTAACTAGGGCAAAACT
538141 CG
64 -G
* * **** * **
538143 ATAGAGTCAACTAAGGGTGGCCAAGGCAAAACCTAAGTCGAAAAAGGGGTTGACTAGGAAAAAAA
1 ATAAAGTCAACTAAGGGT-GACAAGATGGAACCTAAGTCG-AAAA-GGGTTAACTAGG-GCAAAA
**
538208 CCA
62 CTG
* * * *
538211 ATAAAGTCAACTAAGGGTGACCATGATGGAACCTAAGTCAAAAAAAGGTTGACTAGGGCAAAACT
1 ATAAAGTCAACTAAGGGTGA-CAAGATGGAACCTAAGTC-GAAAAGGGTTAACTAGGGCAAAACT
538276 G
64 G
* * * * ** *
538277 ATGATGTCAACTAAGGGTGACCAAGACGAAATTTAAGTCGATAAAGGGTTAACTAGGGCAAAATT
1 ATAAAGTCAACTAAGGGTGA-CAAGATGGAACCTAAGTCGA-AAAGGGTTAACTAGGGCAAAACT
538342 G
64 G
* * * *
538343 ATAAAGTCAACTGAA-GATGACAAGGATGGAACCTAAGTTGAAAAGGTATTAA-TGAGGGAAAAA
1 ATAAAGTCAACT-AAGGGTGACAA-GATGGAACCTAAGTCGAAAAGG-GTTAACT-AGGGCAAAA
538406 CTG
62 CTG
* * * * * * *
538409 ATAAAGTTAACTAAAGTTGACCAG--GGCAAAACCTAGGTCGAAAAGGGGTTAA-TCAAGGTAAA
1 ATAAAGTCAACTAAGGGTGACAAGATGG---AACCTAAGTCGAAAA-GGGTTAACT-AGGGCAAA
*
538471 ACCG
61 ACTG
*
538475 ATAAAGTCAAGTAAGGGTGAC
1 ATAAAGTCAACTAAGGGTGAC
538496 TAGGGCATAA
Statistics
Matches: 274, Mismatches: 62, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
63 2 0.01
65 13 0.05
66 195 0.71
67 26 0.09
68 38 0.14
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.18
Consensus pattern (64 bp):
ATAAAGTCAACTAAGGGTGACAAGATGGAACCTAAGTCGAAAAGGGTTAACTAGGGCAAAACTG
Found at i:538644 original size:66 final size:65
Alignment explanation
Indices: 538403--538713 Score: 180
Period size: 66 Copynumber: 4.7 Consensus size: 65
538393 AATGAGGGAA
* * * * * * * *
538403 AAACTGATAAAGTTAACTAAAGTTGACCAGGGCAAAACCTAGGTCGAAAAGG-GGTTAATCAAGG
1 AAACCGATAAAGTCAACTAAAGGTGACTAGGGCAAAACCTAAGTC--AAAGGAGATTGACCAAGG
*
538467 TA
64 TG
* * * * * * ***
538469 AAACCGATAAAGTCAAGTAAGGGTGACTAGGGCATAACCTAAGTTGAAAAGAGTTTGACCAATAC
1 AAACCGATAAAGTCAACTAAAGGTGACTAGGGCAAAACCTAAG-TCAAAGGAGATTGACCAAGGT
538534 G
65 G
** * * **
538535 AAATTGATAAAGTCAACTAAAGGTGA-TTGTGGCAGAATTTAAGTCAAACGGAGATTGACCAAGG
1 AAACCGATAAAGTCAACTAAAGGTGACTAG-GGCAAAACCTAAGTCAAA-GGAGATTGACCAAGG
538599 TG
64 TG
* * * * * * *
538601 AAACCAATAAAGTTAATTAAAGGTGACAAGGGCAAAACCTAAGTTGAAAAGG-GGTTGAGC-AGG
1 AAACCGATAAAGTCAACTAAAGGTGACTAGGGCAAAACCTAAG-T-CAAAGGAGATTGACCAAGG
**
538664 ACA
64 -TG
* * * * *
538667 AAACTGGTAAAGTCAACTAAGGGTGACAAAGGCAAAACCTAAGTCAA
1 AAACCGATAAAGTCAACTAAAGGTGACTAGGGCAAAACCTAAGTCAA
538714 TAGATTTAAA
Statistics
Matches: 183, Mismatches: 54, Indels: 18
0.72 0.21 0.07
Matches are distributed among these distances:
64 2 0.01
65 14 0.08
66 159 0.87
67 5 0.03
68 3 0.02
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (65 bp):
AAACCGATAAAGTCAACTAAAGGTGACTAGGGCAAAACCTAAGTCAAAGGAGATTGACCAAGGTG
Found at i:538710 original size:132 final size:131
Alignment explanation
Indices: 538372--538713 Score: 319
Period size: 132 Copynumber: 2.6 Consensus size: 131
538362 ACAAGGATGG
* * * * * *
538372 AACCTAAGTTGAAAAGGTATTAATG-AGGGA-AAAACTGATAAAGTTAACTAAAGTTGACCAGGG
1 AACCTAAGTTGAAAAGGGATTGA-GCA-GGACAAAACTGATAAAGTCAACTAAAGGTGACAAAGG
* * * * * *
538435 CAAAACCTAGGTCGAAAAGGGGTTAATCAAGGTAAAACCGATAAAGTCAAGTAAGGGTGACTAGG
64 CAAAACCTAAGTC-AAAAGGGATTAACCAAGGTAAAACCAATAAAGTCAAGTAAAGGTGACAAGG
*
538500 GCAT
128 GCAA
* * * ** * * ****
538504 AACCTAAGTTGAAAAGAGTTTGACCAATACGAAATTGATAAAGTCAACTAAAGGTGATTGTGGCA
1 AACCTAAGTTGAAAAGGGATTGAGCAGGACAAAACTGATAAAGTCAACTAAAGGTGACAAAGGCA
* ** * * * * *
538569 GAATTTAAGTCAAACGGAGATTGACCAAGGTGAAACCAATAAAGTTAATTAAAGGTGACAAGGGC
66 AAACCTAAGTCAAAAGG-GATTAACCAAGGTAAAACCAATAAAGTCAAGTAAAGGTGACAAGGGC
538634 AA
130 AA
* * *
538636 AACCTAAGTTGAAAAGGGGTTGAGCAGGACAAAACTGGTAAAGTCAACTAAGGGTGACAAAGGCA
1 AACCTAAGTTGAAAAGGGATTGAGCAGGACAAAACTGATAAAGTCAACTAAAGGTGACAAAGGCA
538701 AAACCTAAGTCAA
66 AAACCTAAGTCAA
538714 TAGATTTAAA
Statistics
Matches: 161, Mismatches: 46, Indels: 6
0.76 0.22 0.03
Matches are distributed among these distances:
131 6 0.04
132 155 0.96
ACGTcount: A:0.43, C:0.13, G:0.25, T:0.20
Consensus pattern (131 bp):
AACCTAAGTTGAAAAGGGATTGAGCAGGACAAAACTGATAAAGTCAACTAAAGGTGACAAAGGCA
AAACCTAAGTCAAAAGGGATTAACCAAGGTAAAACCAATAAAGTCAAGTAAAGGTGACAAGGGCA
A
Found at i:539344 original size:59 final size:60
Alignment explanation
Indices: 539268--539424 Score: 183
Period size: 60 Copynumber: 2.6 Consensus size: 60
539258 AATCTCCCAT
* * * *
539268 CCAAGACTCAAAAAAATGG-TCTGGATAAAACCATAAACCT-AAAAATGACTTAAGCGAAA
1 CCAAGACTCAAATAAATGGCT-TGGATAAAACCAAAAACCTAAAAAATGACTGAAGCAAAA
* * * * *
539327 CTAAGACTCAAGTAAATGGCTTGGATGAAACTAAAAACCTAAAAAATGACTGGAGCAAAA
1 CCAAGACTCAAATAAATGGCTTGGATAAAACCAAAAACCTAAAAAATGACTGAAGCAAAA
* * *
539387 CCAAGACTTAACTAAATGGCTTGGACAAAACCAAAAAC
1 CCAAGACTCAAATAAATGGCTTGGATAAAACCAAAAAC
539425 TTGAACAATA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 32 0.40
60 49 0.60
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.17
Consensus pattern (60 bp):
CCAAGACTCAAATAAATGGCTTGGATAAAACCAAAAACCTAAAAAATGACTGAAGCAAAA
Found at i:541125 original size:33 final size:32
Alignment explanation
Indices: 541085--541153 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
541075 CCGTTACAAG
*
541085 CAATGTATCGATACAATTCAT-CATGTATTGATA
1 CAATGTATCGATAC-ATT-ATACATGTATCGATA
541118 CAATGTATCGATACATTATACCATGTATCGATA
1 CAATGTATCGATACATTATA-CATGTATCGATA
541151 CAA
1 CAA
541154 ATAGTGGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 2 0.06
32 3 0.09
33 28 0.85
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CAATGTATCGATACATTATACATGTATCGATA
Found at i:541138 original size:20 final size:20
Alignment explanation
Indices: 541115--541152 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
541105 TCATGTATTG
541115 ATACAATGTATCGATACATT
1 ATACAATGTATCGATACATT
*
541135 ATACCATGTATCGATACA
1 ATACAATGTATCGATACA
541153 AATAGTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCGATACATT
Found at i:541205 original size:43 final size:43
Alignment explanation
Indices: 541139--541239 Score: 193
Period size: 43 Copynumber: 2.3 Consensus size: 43
541129 TACATTATAC
*
541139 CATGTATCGATACAAATAGTGGAAGGTTAGCTACTGCCAATTT
1 CATGTATCGATACAAATAATGGAAGGTTAGCTACTGCCAATTT
541182 CATGTATCGATACAAATAATGGAAGGTTAGCTACTGCCAATTT
1 CATGTATCGATACAAATAATGGAAGGTTAGCTACTGCCAATTT
541225 CATGTATCGATACAA
1 CATGTATCGATACAA
541240 TTGTCCATGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (43 bp):
CATGTATCGATACAAATAATGGAAGGTTAGCTACTGCCAATTT
Found at i:541269 original size:19 final size:19
Alignment explanation
Indices: 541225--541280 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
541215 CTGCCAATTT
**
541225 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
541245 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
541264 CATGTATCAATACAATG
1 CATGTATCGATACAATG
541281 TATCGATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:542399 original size:19 final size:20
Alignment explanation
Indices: 542375--542427 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
542365 ACATTATGCT
**
542375 TTGTATCGATACATGCTC-A
1 TTGTATCGATACACACTCAA
542394 TTGTATCGATACACACTCAA
1 TTGTATCGATACACACTCAA
542414 TTGTATCGATACAC
1 TTGTATCGATACAC
542428 GAAACTAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACACACTCAA
Found at i:542502 original size:33 final size:33
Alignment explanation
Indices: 542458--542522 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
542448 TATCACTGTT
* * *
542458 TGTATCGATACATGGGACATTGTATCGATACAA
1 TGTATCGATACATAGGAAAATGTATCGATACAA
* *
542491 TGTATCTATACATAGTAAAATGTATCGATACA
1 TGTATCGATACATAGGAAAATGTATCGATACA
542523 TTGTGCCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGAAAATGTATCGATACAA
Found at i:542818 original size:23 final size:25
Alignment explanation
Indices: 542783--542834 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
542773 TTTTCAAGAG
* *
542783 CTTTTAAACTCATTGT-TG-TTATT
1 CTTTGAAAATCATTGTCTGCTTATT
*
542806 CTTTGAAAATCATTTTCTGCTTATT
1 CTTTGAAAATCATTGTCTGCTTATT
542831 CTTT
1 CTTT
542835 CACAAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 13 0.54
24 2 0.08
25 9 0.38
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (25 bp):
CTTTGAAAATCATTGTCTGCTTATT
Found at i:552616 original size:20 final size:20
Alignment explanation
Indices: 552591--552735 Score: 110
Period size: 20 Copynumber: 6.8 Consensus size: 20
552581 TTTTACCTAG
*
552591 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
552611 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
552631 ATGTATCAATACATTCTGCCTTTTACCTA
1 ATGTATCGATACA---T---TTTT--C-A
* *
552660 GATGTATTGACACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
552681 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
552701 AAGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
552721 ATGTATGGATACATT
1 ATGTATCGATACATT
552736 CTGTCTTTTC
Statistics
Matches: 98, Mismatches: 17, Indels: 20
0.73 0.13 0.15
Matches are distributed among these distances:
20 74 0.76
21 1 0.01
22 1 0.01
23 1 0.01
24 4 0.04
26 4 0.04
27 1 0.01
28 1 0.01
29 1 0.01
30 10 0.10
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:552694 original size:70 final size:70
Alignment explanation
Indices: 552581--552717 Score: 220
Period size: 70 Copynumber: 2.0 Consensus size: 70
552571 AAAGTCACAT
* * * *
552581 TTTTACCTAGATGTATTGATACATTTTTCAATGTATCGATACATTTTTCAATGTATCAATACATT
1 TTTTACCTAGATGTATTGACACATTTTTCAATGTATCGATACATGTATCAAAGTATCAATACATT
552646 CTGCC
66 CTGCC
* *
552651 TTTTACCTAGATGTATTGACACATTTTTCAATGTATCGATACATGTATGAAAGTATCGATACATT
1 TTTTACCTAGATGTATTGACACATTTTTCAATGTATCGATACATGTATCAAAGTATCAATACATT
552716 CT
66 CT
552718 TCAATGTATG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (70 bp):
TTTTACCTAGATGTATTGACACATTTTTCAATGTATCGATACATGTATCAAAGTATCAATACATT
CTGCC
Found at i:552744 original size:90 final size:91
Alignment explanation
Indices: 552613--552785 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 91
552603 ATTTTTCAAT
* *
552613 GTATCGATACATTTTTCAATGTATCAATACATTCTGCCTTTT-ACCTAGATGTATTGACACATTT
1 GTATCGATACATTCTTCAATGTATCAATACATTCTGCCTTTTCACCTAGATGTATCGACACATTT
552677 TTCAATGTATCGATACATGTATGAAA
66 TTCAATGTATCGATACATGTATGAAA
** * *
552703 GTATCGATACATTCTTCAATGTATGGATACATTCTGTCTTTTCACCTAGATGTATCGATACATTT
1 GTATCGATACATTCTTCAATGTATCAATACATTCTGCCTTTTCACCTAGATGTATCGACACATTT
*
552768 TTCATTGTATCGATACAT
66 TTCAATGTATCGATACAT
552786 CTAGTTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
90 38 0.51
91 37 0.49
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (91 bp):
GTATCGATACATTCTTCAATGTATCAATACATTCTGCCTTTTCACCTAGATGTATCGACACATTT
TTCAATGTATCGATACATGTATGAAA
Found at i:555104 original size:98 final size:97
Alignment explanation
Indices: 554939--555262 Score: 488
Period size: 98 Copynumber: 3.3 Consensus size: 97
554929 CATTGAGGAT
* * * *
554939 ACTCCAACCTCATTCCTCTGAGGGAATACTCCAACTCGTTTTTAAAACTTGTTGAGATTTGAAAC
1 ACTCCAACCCCATTCCTCCGAGGGGATACTCCAACTCGTTTTTAAAACTTGTCGAGATTTGAAAC
* * *
555004 TTATTCGTGCCTAAATTATCATTATCGAAGG-C
66 TTATTCTTGCCTAAATTATCATTGTCG-GGGAC
* * * *
555036 ATTCCAACCTCATTCCTCTGAGGGGATACTCCAACTCTGTTTTTAAACCTTGTCGAGATTTGAAA
1 ACTCCAACCCCATTCCTCCGAGGGGATACTCCAACTC-GTTTTTAAAACTTGTCGAGATTTGAAA
555101 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
65 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
* *
555134 ACTCCAACCCCATTTCTCCGAGGGGATACTCCAACTCCGTTTTTAAAACTTGTCAAGATTTGAAA
1 ACTCCAACCCCATTCCTCCGAGGGGATACTCCAACT-CGTTTTTAAAACTTGTCGAGATTTGAAA
*
555199 CTTATTCTTGCCCAAATTATCATTGTCGGGGAC
65 CTTATTCTTGCCTAAATTATCATTGTCGGGGAC
555232 ACTCCAACCCCATTCCTCCGAGGGGATACTC
1 ACTCCAACCCCATTCCTCCGAGGGGATACTC
555263 TAACCCCATT
Statistics
Matches: 209, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
97 37 0.18
98 171 0.82
99 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (97 bp):
ACTCCAACCCCATTCCTCCGAGGGGATACTCCAACTCGTTTTTAAAACTTGTCGAGATTTGAAAC
TTATTCTTGCCTAAATTATCATTGTCGGGGAC
Found at i:562655 original size:15 final size:15
Alignment explanation
Indices: 562635--562679 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
562625 ATTCTACCAA
562635 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
562650 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
562665 ACCCACCACAAAATC
1 ATCCACCACAAAATC
562680 GTCGATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:567031 original size:13 final size:13
Alignment explanation
Indices: 567013--567071 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
567003 CATTATTCAA
567013 TGTATCGATACAT
1 TGTATCGATACAT
567026 TGTATCGATACAT
1 TGTATCGATACAT
567039 TG-ATC--T---T
1 TGTATCGATACAT
567046 TGTATCGATACAT
1 TGTATCGATACAT
567059 TGTATCGATACAT
1 TGTATCGATACAT
567072 GCAGGCAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
10 2 0.05
12 3 0.08
13 29 0.73
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:567035 original size:33 final size:33
Alignment explanation
Indices: 566993--567071 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
566983 GCCAAGGAAA
566993 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
567026 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
567059 TGTATCGATACAT
1 TGTATCGATACAT
567072 GCAGGCAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
33 42 0.98
34 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:574040 original size:11 final size:11
Alignment explanation
Indices: 574024--574074 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
574014 AAAGGAGAAC
574024 AAAAAACAAAA
1 AAAAAACAAAA
574035 AAAAAACAAAA
1 AAAAAACAAAA
*
574046 CAAAAAC-AAA
1 AAAAAACAAAA
*
574056 TAAAAACATGAAA
1 AAAAAACA--AAA
574069 AAAAAA
1 AAAAAA
574075 GAGTGCAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.26
11 17 0.50
13 8 0.24
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:574045 original size:16 final size:15
Alignment explanation
Indices: 574024--574074 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
574014 AAAGGAGAAC
574024 AAAAAACAAAAAAAA
1 AAAAAACAAAAAAAA
574039 AACAAAACAAAAACAAA
1 AA-AAAACAAAAA-AAA
*
574056 TAAAAACATGAAAAAAA
1 AAAAAACA--AAAAAAA
574073 AA
1 AA
574075 GAGTGCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 16 0.53
17 8 0.27
18 4 0.13
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (15 bp):
AAAAAACAAAAAAAA
Found at i:575383 original size:30 final size:30
Alignment explanation
Indices: 575347--575620 Score: 280
Period size: 30 Copynumber: 9.0 Consensus size: 30
575337 TCTTCAAATC
* *
575347 TCTCTTCTCAAAGTCTACGACTCAGTGGCG
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
575377 TCTCTTCCCAAAGTCTACGACTCAGTGGCG
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* *
575407 TCTTTTCTCAAAGTCCACGATTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* **
575437 TCTTTTCTTCAAAGTCCATAACTCAGTGGCA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
* *
575468 TCTCTTTTCTAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
575498 TCCTTTTCTTCCAAGTCCATGACTCAGTGGCA
1 T-CTCTTC-TCAAAGTCCACGACTCAGTGGCA
* *
575530 TCT-TGTCCCAAAGTCTACGACTCAGTGGCA
1 TCTCT-TCTCAAAGTCCACGACTCAGTGGCA
* * * *
575560 TCTTTTTTTCAAAGTCCACAACTTAGTGGCA
1 TC-TCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
575591 TCTCTTTTCAAAGTCCACAACTCTGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
575621 CCCTTTTAAG
Statistics
Matches: 208, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
30 129 0.62
31 56 0.27
32 23 0.11
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.32
Consensus pattern (30 bp):
TCTCTTCTCAAAGTCCACGACTCAGTGGCA
Found at i:575482 original size:61 final size:61
Alignment explanation
Indices: 575347--575748 Score: 333
Period size: 61 Copynumber: 6.6 Consensus size: 61
575337 TCTTCAAATC
* * * * * * * *
575347 TCTCTTCTCAAAGTCTACGACTCAGTGGCGTCTCTTC-CCAAAGTCTACGACTCAGTGGCG
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* *
575407 TCT-TTTCTCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCATAACTCAGTGGCA
1 TCTCTTT-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* * **
575468 TCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCCAAGTCCATGACTCAGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCAT-CTTTTCTTCAAAGTCCACAACTCAGTGGCA
** * * *
575530 TCT-TGTCCCAAAGTCTACGACTCAGTGGCATCTTTTTTTCAAAGTCCACAACTTAGTGGCA
1 TCTCT-TTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* * ** *
575591 TCTCTTTTCAAAGTCCACAACTCTGTGGCA-CCCTT-TT--AAGTCCACAACTCCGTGGCA
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* ** * * *
575648 CCTTTTTCTTTTCAAAGTCCATAACTCTGTGG-A-CCTTT-TT--AAGTCCACAACTCCGTGGCA
1 ----TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* * *
575708 TTTTTTTCTTCAAAGTCCACGACTCCGTGGCACTCTTTTCT
1 -TCTCTT-TTCAAAGTCCACGACTCAGTGGCA-TCTTTTCT
575749 CTTTTAAGCC
Statistics
Matches: 287, Mismatches: 40, Indels: 28
0.81 0.11 0.08
Matches are distributed among these distances:
57 24 0.08
58 19 0.07
59 5 0.02
60 59 0.21
61 122 0.43
62 58 0.20
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (61 bp):
TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
Found at i:575563 original size:123 final size:122
Alignment explanation
Indices: 575347--575627 Score: 368
Period size: 123 Copynumber: 2.3 Consensus size: 122
575337 TCTTCAAATC
* * * * * *
575347 TCTCTTCTCAAAGTCTACGACTCAGTGGCGT-CTCTTCCCAAAGTCTACGACTCAGTGGCGTCTT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTTTTCCCAAAGTCCACGACTCAGTGGCATCTT
* * * *
575411 TTCTCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCATAACTCAGTGGCA
66 GTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* *
575468 TCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTTCTTCC-AAGTCCATGACTCAGTGGCATC
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTTTTC--CCAAAGTCCACGACTCAGTGGCATC
* * *
575532 TTGTCCCAAAGTCTACGACTCAGTGGCATCTTTTTTTCAAAGTCCACAACTTAGTGGCA
64 TTGTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
* * *
575591 TCTCTTTTCAAAGTCCACAACTCTGTGGCACCCTTTT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTTTT
575628 AAGTCCACAA
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
121 27 0.20
122 5 0.04
123 104 0.75
124 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (122 bp):
TCTCTTTTCAAAGTCCACGACTCAGTGGCATCCTTTTCCCAAAGTCCACGACTCAGTGGCATCTT
GTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCA
Found at i:575787 original size:180 final size:173
Alignment explanation
Indices: 575601--575952 Score: 406
Period size: 180 Copynumber: 2.0 Consensus size: 173
575591 TCTCTTTTCA
** * * * *
575601 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGT
1 AAGTCCACAACTCCATGGCACCCCTGTAACTCCACAACTCCGTGGCACC-----CTTTT--AAGC
* * *
575666 CCATAACTCTGTGG-A-C-CTTTTTAAGTCCACAACTCCGTGGCA-TTTTTTTCTTCAAAGTCCA
59 CCACAACTCTGTGGCATCTCCTTTTAAGTCCACAACTCCGTGGCACTTTTCTT-TTC-AAGTCCA
* * * *
575727 CGACTCCGTGGCACTCTTTTCTCTTTTAAGCCCACAACTTTGTGGCACCCCTGT
122 CAACTCCGTGGAAC-CTTTTC-CTTTTAAACCCACAACTCTGTGGCACCCCTGT
575781 AAGTCCACAACTCCATGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
1 AAGTCCACAACTCCATGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
575846 TCTGTGGCATCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTCAAGTCCACAAC
66 TCTGTGGCATC----TCCTTTTAAGTCCACAACTCCGTGGCA-CTTTTCTTTTCAAGTCCACAAC
*
575911 TCCGTGGAACCTTTTCCTTTTAAATCCACAACTCTGTGGCAC
126 TCCGTGGAACCTTTTCCTTTTAAACCCACAACTCTGTGGCAC
575953 TTTTCCCTTT
Statistics
Matches: 149, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
173 16 0.11
174 1 0.01
175 6 0.04
178 23 0.15
179 6 0.04
180 88 0.59
181 3 0.02
182 6 0.04
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.32
Consensus pattern (173 bp):
AAGTCCACAACTCCATGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAAC
TCTGTGGCATCTCCTTTTAAGTCCACAACTCCGTGGCACTTTTCTTTTCAAGTCCACAACTCCGT
GGAACCTTTTCCTTTTAAACCCACAACTCTGTGGCACCCCTGT
Found at i:575909 original size:32 final size:31
Alignment explanation
Indices: 575417--576162 Score: 362
Period size: 27 Copynumber: 24.7 Consensus size: 31
575407 TCTTTTCTCA
* * * * **
575417 AAGTCCACGATTCAGTGGCATCTTTTCTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * * * *
575448 AAGTCCATAACTCAGTGGCATCTCTT-TTCT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * **
575478 AAGTCCACGACTCAGTGGCATCCTTTTCTTCC
1 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTT
** * * * ***
575510 AAGTCCATGACTCAGTGGCATCTTGTC-CCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * * * *
575540 AAGTCTACGACTCAGTGGCATCTTTT-TTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTTT-T
** * * **
575571 AAGTCCACAACTTAGTGGCATCTCTT-TTCA
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
*
575601 AAGTCCACAACTCTGTGGCACC----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
575628 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACC-TTTTCTTTT
* *
575660 CAAAGTCCATAACTCTGTGG-ACC---T-TTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTCTTTT
** **
575688 AAGTCCACAACTCCGTGGCATTTTTTTCTTCA
1 AAGTCCACAACTCCGTGGCA-CCTTTTCTTTT
*
575720 AAGTCCACGACTCCGTGGCACTCTTTTCTCTTTT
1 AAGTCCACAACTCCGTGGCAC-C-TTT-TCTTTT
* ** * *
575754 AAGCCCACAACTTTGTGGCACC----CCTGT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * *
575781 AAGTCCACAACTCCATGGCACC----CCTGT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
*
575808 AACTCCACAACTCCGTGGCACC----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* * *
575835 AAGCCCACAACTCTGTGGCATCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTT-TT-CTTTT
575868 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
*
575899 CAAGTCCACAACTCCGTGGAACCTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCACCTTTT-CTTTT
* * *
575932 AAATCCACAACTCTGTGGCA-CTTTTCCCTTTC
1 AAGTCCACAACTCCGTGGCACCTTTT--CTTTT
* *
575964 AAGCCCACAACTTCGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTC-TTTT
* ** * *
575996 AAGTCCACGACTCTATGGCACATTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACCTTTT-CTTTT
* * *
576028 AAGCCCACAACTTCATGGCACC----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
*
576055 AAGTCCACAACTCCATGGCACC----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
* *
576082 TAGTCCACAACTCTGTGGCACC----CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTT
** *
576109 AAGTCCACAACTTTGTGGCATCTTTCTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTT-T-CTTTT
* * *
576142 AAGCCCACAAGTCAGTGGCAC
1 AAGTCCACAACTCCGTGGCAC
576163 TCATTTCAAA
Statistics
Matches: 575, Mismatches: 101, Indels: 76
0.76 0.13 0.10
Matches are distributed among these distances:
26 16 0.03
27 163 0.28
28 4 0.01
29 1 0.00
30 65 0.11
31 68 0.12
32 156 0.27
33 65 0.11
34 37 0.06
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (31 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTT
Found at i:575939 original size:64 final size:64
Alignment explanation
Indices: 575593--576162 Score: 350
Period size: 64 Copynumber: 9.4 Consensus size: 64
575583 TAGTGGCATC
*
575593 TCTTTTCAAAGTCCACAACTCTGTGGCA-C----CCTTTTAAGTCCACAACTCCGTGGCACCTTT
1 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACC-TT
575653 T
64 T
* *
575654 TCTTTTCAAAGTCCATAACTCTGTGG-ACC---T--TTTTAAGTCCACAACTCCGTGGCA--TTT
1 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * * **
575711 TTTTCTTCAAAGTCCACGACTCCGTGGCACTCTTTTCTCTTTTAAGCCCACAACTTTGTGGCACC
1 TCTT-TTC-AAGTCCACAACTCCGTGGCAC-CTTTTC-CTTTTAAGTCCACAACTCCGTGGCACC
575776 ---
62 TTT
* * * * *
575776 -CCTGT-AAGTCCACAACTCCATGGCACC----CC-TGTAACTCCACAACTCCGTGGCACC---
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * *
575830 -CTTTT-AAGCCCACAACTCTGTGGCATCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTT-TTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * *
575893 TCTTTTCAAGTCCACAACTCCGTGGAACCTTTTCCTTTTAAATCCACAACTCTGTGGCA-CTTT
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * * * * ** *
575956 TCCCTTTCAAGCCCACAACTTCGTGGCACCTTTTCTTTTTAAGTCCACGACTCTATGGCACATTT
1 T-CTTTTCAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * * * *
576021 TC-CTTCTAAGCCCACAACTTCATGGCA-C----CCTTTTAAGTCCACAACTCCATGGCACC---
1 TCTTTTC-AAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * ** *
576077 -CTTTT-TAGTCCACAACTCTGTGGCA-C----CCTTTTAAGTCCACAACTTTGTGGCATCTTT
1 TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
* * *
576134 CTCCTTTT-AAGCCCACAAGTCAGTGGCAC
1 -T-CTTTTCAAGTCCACAACTCCGTGGCAC
576163 TCATTTCAAA
Statistics
Matches: 413, Mismatches: 61, Indels: 70
0.76 0.11 0.13
Matches are distributed among these distances:
54 81 0.20
55 2 0.00
56 3 0.01
57 6 0.01
58 19 0.05
59 28 0.07
60 71 0.17
61 45 0.11
63 11 0.03
64 102 0.25
65 24 0.06
66 21 0.05
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.32
Consensus pattern (64 bp):
TCTTTTCAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTT
Found at i:576022 original size:96 final size:97
Alignment explanation
Indices: 575829--576039 Score: 291
Period size: 96 Copynumber: 2.2 Consensus size: 97
575819 TCCGTGGCAC
* *
575829 CCTTTTAAGCCCACAACTCTGTGGCATCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTT
1 CCTTTTAAGCCCACAACTCTGTGGCATCTTGTTCCTTTCAAGCCCACAACTCCGTGGCACCTTTT
* *
575894 CTTTTCAAGTCCACAACTCCGTGGAACCTTTT
66 CTTTTCAAGTCCACAACTCCATGGAACATTTT
** *
575926 CCTTTTAAATCCACAACTCTGTGGCA-CTT-TTCCCTTTCAAGCCCACAACTTCGTGGCACCTTT
1 CCTTTTAAGCCCACAACTCTGTGGCATCTTGTT-CCTTTCAAGCCCACAACTCCGTGGCACCTTT
* * * *
575989 TCTTTTTAAGTCCACGACTCTATGGCACATTTT
65 TCTTTTCAAGTCCACAACTCCATGGAACATTTT
*
576022 CCTTCTAAGCCCACAACT
1 CCTTTTAAGCCCACAACT
576040 TCATGGCACC
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 2 0.02
96 73 0.74
97 24 0.24
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.35
Consensus pattern (97 bp):
CCTTTTAAGCCCACAACTCTGTGGCATCTTGTTCCTTTCAAGCCCACAACTCCGTGGCACCTTTT
CTTTTCAAGTCCACAACTCCATGGAACATTTT
Found at i:576060 original size:274 final size:266
Alignment explanation
Indices: 575601--576162 Score: 706
Period size: 274 Copynumber: 2.1 Consensus size: 266
575591 TCTCTTTTCA
* * *
575601 AAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGT
1 AAGTCCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGAACCTTTTCCTTTTCAAAGT
* *
575666 CCATAACTCTGTGGACCTTTTTAAGTCCACAACTCCGTGGCATTTTTTTCTTCAAAGTCCACGAC
66 CCACAACTCTGTGGACCTTTTTAAGCCCACAACTCCGTGGCATTTTTTTCTT-AAAGTCCACGAC
* * * **
575731 TCCGTGGCACTCTTTTCTCTTTTAAGCCCACAACTTTGTGGCACCCCTGTAAGTCCACAACTCCA
130 TCCATGGCACTATTTTCTCTTCTAAGCCCACAACTTCATGGCACCCCTGTAAGTCCACAACTCCA
575796 TGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATCTTGT
195 TGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATCTT-T
575861 -TCCTTTT
259 CTCCTTTT
*
575868 AAGTCCACAACTCCGTGGCACCTTTTCTTTTCAAGTCCACAACTCCGTGGAACCTTTTCCTTTT-
1 AAGTCCACAACTCAGTGGCACC----CTTTT-AAGTCCACAACTCCGTGGAACCTTTTCCTTTTC
* *
575932 AAA-TCCACAACTCTGTGGCACTTTTCCCTTTCAAGCCCACAACTTCGTGGCACCTTTTCTTT-T
61 AAAGTCCACAACTCTGTGG-AC-CTT---TTT-AAGCCCACAACTCCGTGGCA--TTTT-TTTCT
* * *
575995 T-AAGTCCACGACTCTATGGCAC-ATTTTC-CTTCTAAGCCCACAACTTCATGGCACCCTTTTAA
117 TAAAGTCCACGACTCCATGGCACTATTTTCTCTTCTAAGCCCACAACTTCATGGCACCCCTGTAA
* * * * * * *
576057 GTCCACAACTCCATGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTT
182 GTCCACAACTCCATGGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTC
576122 TGTGGCATCTTTCTCCTTTT
247 TGTGGCATCTTTCTCCTTTT
* *
576142 AAGCCCACAAGTCAGTGGCAC
1 AAGTCCACAACTCAGTGGCAC
576163 TCATTTCAAA
Statistics
Matches: 255, Mismatches: 25, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
267 21 0.08
270 14 0.05
271 10 0.04
272 32 0.13
273 1 0.00
274 123 0.48
275 8 0.03
276 37 0.15
278 6 0.02
279 3 0.01
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.32
Consensus pattern (266 bp):
AAGTCCACAACTCAGTGGCACCCTTTTAAGTCCACAACTCCGTGGAACCTTTTCCTTTTCAAAGT
CCACAACTCTGTGGACCTTTTTAAGCCCACAACTCCGTGGCATTTTTTTCTTAAAGTCCACGACT
CCATGGCACTATTTTCTCTTCTAAGCCCACAACTTCATGGCACCCCTGTAAGTCCACAACTCCAT
GGCACCCCTGTAACTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCATCTTTCT
CCTTTT
Found at i:576178 original size:30 final size:30
Alignment explanation
Indices: 576142--576325 Score: 193
Period size: 29 Copynumber: 6.3 Consensus size: 30
576132 TTCTCCTTTT
* *
576142 AAGCCCACAAGTCAGTGGCACTCATTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
576172 AAGCCCACAAGTC-GATGGCACCCCTTTC-A
1 AAGCCCACAAGTCAG-TGGCACCCCTTTCAA
* *
576201 AAGCCCACAAGTCAATGGCACCCATTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* *
576231 AAGCCCATAAGT-TGATGGCACCCCTTTC-A
1 AAGCCCACAAGTCAG-TGGCACCCCTTTCAA
* *
576260 AAGCCCACAAGTTAGTGGCA-ACC-TTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
* ** *
576288 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCCTTTCAA
576317 AAGCCCACA
1 AAGCCCACA
576326 CAAGTTGGTG
Statistics
Matches: 131, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
27 6 0.05
28 19 0.15
29 57 0.44
30 49 0.37
ACGTcount: A:0.33, C:0.32, G:0.16, T:0.18
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCCTTTCAA
Found at i:576211 original size:59 final size:58
Alignment explanation
Indices: 576142--576325 Score: 248
Period size: 59 Copynumber: 3.2 Consensus size: 58
576132 TTCTCCTTTT
*
576142 AAGCCCACAAGTCAGTGGCACTCATTTCAAAAGCCCACAAGTCGATGGCACCCCTTTCA
1 AAGCCCACAAGTCAGTGGCAC-CATTTCAAAAGCCCACAAGTTGATGGCACCCCTTTCA
* *
576201 AAGCCCACAAGTCAATGGCACCCATTTCAAAAGCCCATAAGTTGATGGCACCCCTTTCA
1 AAGCCCACAAGTCAGTGGCA-CCATTTCAAAAGCCCACAAGTTGATGGCACCCCTTTCA
* * * *
576260 AAGCCCACAAGTTAGTGGCAACC--TTCAAAAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGC-ACCATTTCAAAAGCCCACAAGTTGATGGCACCCCTTTC-A
576317 AAGCCCACA
1 AAGCCCACA
576326 CAAGTTGGTG
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
56 10 0.09
57 28 0.25
59 73 0.65
60 2 0.02
ACGTcount: A:0.33, C:0.32, G:0.16, T:0.18
Consensus pattern (58 bp):
AAGCCCACAAGTCAGTGGCACCATTTCAAAAGCCCACAAGTTGATGGCACCCCTTTCA
Found at i:576583 original size:49 final size:49
Alignment explanation
Indices: 576442--576952 Score: 431
Period size: 49 Copynumber: 10.6 Consensus size: 49
576432 CGCAAGTCTG
* *
576442 ATATCGCTGGCCTTGAATCTA-CATATTGGCACCTTCATCTTTAAAACCA
1 ATATCGCTGGCCTTGAATC-AGCATATTGGCACCTTCACCTTTAAGACCA
* * * * * * *
576491 ATGTCGCT-ACCTTGAACCAGTATATTGGCATCTTCATCC-TTAAGTCCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA-CCTTTAAGACCA
*
576539 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
* * ** * * * * * *
576588 ATGTCGCCGATCTTGAATCAGTACATTGGCATCTTCATCC-TTCAGTCCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA-CCTTTAAGACCA
*
576637 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
* * * * * * * **
576686 ATGTCACCGGCCTTGAATCAGGACATTGGCATCTTCATCC-TTAAGTCTG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA-CCTTTAAGACCA
* *
576735 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
* * * * * *
576784 ATGTTGTTAGCCTTGAATCAGCACATTGG------CA----TAAGCCCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
* * *
576823 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTCTTTAAGACTA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCA-CCTTTAAGACCA
* * * * * * *
576873 ATGTCGCTAGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGCCCG
1 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
*
576922 ATATCGTTGGCCTTGAATCAGCATATTGGCA
1 ATATCGCTGGCCTTGAATCAGCATATTGGCA
576953 TTTTTAACAT
Statistics
Matches: 356, Mismatches: 87, Indels: 38
0.74 0.18 0.08
Matches are distributed among these distances:
39 31 0.09
43 1 0.00
45 1 0.00
47 1 0.00
48 41 0.12
49 239 0.67
50 42 0.12
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGACCA
Found at i:576652 original size:98 final size:97
Alignment explanation
Indices: 576435--576952 Score: 671
Period size: 98 Copynumber: 5.4 Consensus size: 97
576425 ACATTAGCGC
* * * *
576435 AAGTCTGATATCGCTGGCCTTGAATCTA-CATATTGGCACCTTCATCTTTAAAACCAATGTCGCT
1 AAGTCCGATATCGCTGGCCTTGAATC-AGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCT
* *
576499 ACCTTGAACCAGTATATTGGCATCTTCATCCTT
65 ACCTTGAATCAGTACATTGGCATCTTCATCCTT
*
576532 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCCG
1 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCG-CT
*
576597 ATCTTGAATCAGTACATTGGCATCTTCATCCTT
65 ACCTTGAATCAGTACATTGGCATCTTCATCCTT
* * *
576630 CAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCACCG
1 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTC-GCT
* *
576695 GCCTTGAATCAGGACATTGGCATCTTCATCCTT
65 ACCTTGAATCAGTACATTGGCATCTTCATCCTT
* * * *
576728 AAGTCTGATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTTGTTA
1 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCTA
*
576793 GCCTTGAATCAGCACATTGG------CA----T
66 -CCTTGAATCAGTACATTGGCATCTTCATCCTT
* * * *
576816 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTCTTTAAGACTAATGTCGCT
1 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CCTTTAAGACCAATGTCGCT
* *
576881 AGCCTTGAATCAGTACATTGGCACCTTCATCTTT
65 A-CCTTGAATCAGTACATTGGCATCTTCATCCTT
* *
576915 AAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCA
1 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCA
576953 TTTTTAACAT
Statistics
Matches: 373, Mismatches: 33, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
88 41 0.11
89 36 0.10
92 2 0.01
95 2 0.01
96 1 0.00
97 56 0.15
98 198 0.53
99 37 0.10
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (97 bp):
AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCTA
CCTTGAATCAGTACATTGGCATCTTCATCCTT
Found at i:576774 original size:196 final size:185
Alignment explanation
Indices: 576334--576952 Score: 741
Period size: 196 Copynumber: 3.3 Consensus size: 185
576324 CACAAGTTGG
* * *
576334 TGGCATCTTC-TTC-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGT--CTC
1 TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TACCTT
* * ** *
576395 TAAGACCAATGTTGCTG-GCCTTGAATCAGCACATTAGCGCAAGTCTGATATCGCTGGCCTTGAA
65 TAAGACCAATGTCGC-GAGCCTTGAATCAGCACATTGGCATAAGTCCGATATCGCTGGCCTTGAA
* * * * *
576459 TCTA-CATATTGGCACCTTCATCTTTAAAACCAATGTCGCTA-CCTTGAACCAGTATAT
129 TC-AGCATATTGGCACCTTTATCTTTAAGACCAATGTC-CCAGCCTTGAATCAGTACAT
576516 TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTT
1 TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTT
* *
576581 AAGACCAATGTCGCCGA-TCTTGAATCAGTACATTGGCATCTTCATCCTTCAGTCCGATATCGCT
66 AAGACCAATGTCG-CGAGCCTTGAATCAGCACATTGGCA---T-A------AGTCCGATATCGCT
* * *
576645 GGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCACCGGCCTTGAATCAGGAC
120 GGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC-CCAGCCTTGAATCAGTAC
576710 AT
184 AT
* *
576712 TGGCATCTTCATCCTTAAGTCTGATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTT
1 TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTT
* ** * *
576777 AAGACCAATGTTGTTAGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATC
66 AAGACCAATGTCGCGAGCCTTGAATCAGCACATTGGCATAAGTCCGATATCGCTGGCCTTGAATC
* *
576842 AGCATATTGGCACCTTTATTCTTTAAGACTAATGTCGCTAGCCTTGAATCAGTACAT
131 AGCATATTGGCACCTTTA-TCTTTAAGACCAATGTC-CCAGCCTTGAATCAGTACAT
* * * *
576899 TGGCACCTTCATCTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCA
1 TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCA
576953 TTTTTAACAT
Statistics
Matches: 377, Mismatches: 40, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
182 10 0.03
183 3 0.01
184 42 0.11
185 33 0.09
186 42 0.11
187 80 0.21
189 1 0.00
192 1 0.00
193 1 0.00
194 1 0.00
195 56 0.15
196 107 0.28
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (185 bp):
TGGCATCTTCATCCTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCTTT
AAGACCAATGTCGCGAGCCTTGAATCAGCACATTGGCATAAGTCCGATATCGCTGGCCTTGAATC
AGCATATTGGCACCTTTATCTTTAAGACCAATGTCCCAGCCTTGAATCAGTACAT
Found at i:576902 original size:89 final size:88
Alignment explanation
Indices: 576735--576903 Score: 275
Period size: 89 Copynumber: 1.9 Consensus size: 88
576725 CTTAAGTCTG
* *
576735 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTTGTTAGCCTTGA
1 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCTAGCCTTGA
576800 ATCAGCACATTGGCATAAGCCCA
66 ATCAGCACATTGGCATAAGCCCA
* * *
576823 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATTCTTTAAGACTAATGTCGCTAGCCTTG
1 ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTA-CCTTTAAGACCAATGTCGCTAGCCTTG
*
576888 AATCAGTACATTGGCA
65 AATCAGCACATTGGCA
576904 CCTTCATCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
88 36 0.49
89 38 0.51
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (88 bp):
ATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCTTTAAGACCAATGTCGCTAGCCTTGA
ATCAGCACATTGGCATAAGCCCA
Found at i:576935 original size:138 final size:137
Alignment explanation
Indices: 576694--576953 Score: 349
Period size: 138 Copynumber: 1.9 Consensus size: 137
576684 CAATGTCACC
* * * * *
576694 GGCCTTGAATCAGGACATTGGCATCTTCATCCTTAAGTCTGATATCGCTAGCCTTGAATCAGCAT
1 GGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGACTAATATCGCTAGCCTTGAATCAGCAC
* * *
576759 ATTGGCACCTTTACCTTTAAGACCAATGTTGTTAGCCTTGAATCAGCACATTGGCATAAGCCCAA
66 ATTGGCACCTTCACCTTTAAGACCAATATCGTTAGCCTTGAATCAGCACATTGGCATAAGCCCAA
576824 TATCGCT
131 TATCGCT
* * * * *
576831 GGCCTTGAATCAGCATATTGGCACCTTTATTCTTTAAGACTAATGTCGCTAGCCTTGAATCAGTA
1 GGCCTTGAATCAGCACATTGGCACCTTCA-TCCTTAAGACTAATATCGCTAGCCTTGAATCAGCA
* * * * *
576896 CATTGGCACCTTCATCTTTAAGCCCGATATCGTTGGCCTTGAATCAGCATATTGGCAT
65 CATTGGCACCTTCACCTTTAAGACCAATATCGTTAGCCTTGAATCAGCACATTGGCAT
576954 TTTTAACATT
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
137 25 0.24
138 79 0.76
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (137 bp):
GGCCTTGAATCAGCACATTGGCACCTTCATCCTTAAGACTAATATCGCTAGCCTTGAATCAGCAC
ATTGGCACCTTCACCTTTAAGACCAATATCGTTAGCCTTGAATCAGCACATTGGCATAAGCCCAA
TATCGCT
Found at i:583981 original size:28 final size:28
Alignment explanation
Indices: 583930--584240 Score: 385
Period size: 28 Copynumber: 11.1 Consensus size: 28
583920 TGGAACCAGG
* *
583930 ACAAATCAGTGGC-CCCTTTCAAAGTCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
* *
583957 ACAAGTCAGTGGTACCCTTTCAAAGTCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
583985 ACAAGTCAGTGGC-CCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
* **
584012 ATAAGTCAGTGGCACCCTTTTGAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
*
584040 ACAAGTTAGTGGCACCCTTTCAAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
* *
584068 ACAAGTCAGTGGCACTCTTTTAAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
*
584096 ACAAGTCAGTGGCACCCTCTCAAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
* * **
584124 ACAGGTCAGTGGCACCTTTTTGAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
*
584152 ACAAGTTAGTGGCACCCTTTCGAAA-CCC
1 ACAAGTCAGTGGCACCCTTTC-AAAGCCC
* * *
584180 ACAAATCAGTGGCATCCTTTTAAAGCCC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCC
* *
584208 ACAAGTTAGTGGCAACCTTCTCTAAAGCCC
1 ACAAGTCAGTGGCACCCTT-TC-AAAGCCC
584238 ACA
1 ACA
584241 CAAGTTGGTG
Statistics
Matches: 243, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
27 39 0.16
28 191 0.79
29 3 0.01
30 10 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
ACAAGTCAGTGGCACCCTTTCAAAGCCC
Found at i:585291 original size:24 final size:24
Alignment explanation
Indices: 585274--585332 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 24
585264 TTTTACCTAG
585274 ATGTATCGATACATTTTTCAATGA
1 ATGTATCGATACATTTTTCAATGA
*
585298 ATGTATCGATACA---TTC-ATCA
1 ATGTATCGATACATTTTTCAATGA
585318 ATGTATCGATACATT
1 ATGTATCGATACATT
585333 CTGTCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 16 0.50
21 3 0.09
24 13 0.41
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (24 bp):
ATGTATCGATACATTTTTCAATGA
Found at i:585333 original size:74 final size:75
Alignment explanation
Indices: 585224--585371 Score: 208
Period size: 74 Copynumber: 2.0 Consensus size: 75
585214 TTTTACCCAG
** * * * *
585224 ATGTAACGATACATTTTTCAATGTATTGATACATTCTATC-TTTTACCTAGATGTATCGATACAT
1 ATGTAACGATACATTCATCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAG
585288 TTTTCAATGA
66 TTTTCAATGA
* * *
585298 ATGTATCGATACATTCATCAATGTATCGATACATTCTGTCTTTTTACCCAAATGTATTGATACAG
1 ATGTAACGATACATTCATCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAG
585363 TTTTCAATG
66 TTTTCAATG
585372 TATCGACACA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
74 35 0.55
75 29 0.45
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (75 bp):
ATGTAACGATACATTCATCAATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACAG
TTTTCAATGA
Found at i:586280 original size:20 final size:22
Alignment explanation
Indices: 586240--586287 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
586230 TAGCCTTTGA
*
586240 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
586262 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
586281 CCA-GCAT
1 CCATGCAT
586288 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:592931 original size:21 final size:21
Alignment explanation
Indices: 592906--592964 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
592896 TACTGCCAAA
592906 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
592927 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
592948 AAATGTATCGATACATT
1 AAATGTATCGATACATT
592965 GTATCGATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:592969 original size:13 final size:13
Alignment explanation
Indices: 592951--592975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
592941 ATTACTCAAA
592951 TGTATCGATACAT
1 TGTATCGATACAT
592964 TGTATCGATACA
1 TGTATCGATACA
592976 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:593040 original size:52 final size:52
Alignment explanation
Indices: 592984--593108 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
592974 CACTGATCTT
* *
592984 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
593036 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
593088 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
593109 CTTTTCATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:597741 original size:13 final size:13
Alignment explanation
Indices: 597723--597748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
597713 CAATTTTTTG
597723 TGTATCGATACAT
1 TGTATCGATACAT
597736 TGTATCGATACAT
1 TGTATCGATACAT
597749 ACTTGGTGTA
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:597763 original size:32 final size:33
Alignment explanation
Indices: 597703--597766 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
597693 TACAAGCCAA
** *
597703 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
597736 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
597767 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:598487 original size:21 final size:21
Alignment explanation
Indices: 598446--598489 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
598436 CTCTCCTTTA
* *
598446 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
598467 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
598488 TC
1 TC
598490 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:604245 original size:21 final size:21
Alignment explanation
Indices: 604216--604260 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
604206 AAGTTTTCAT
*
604216 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
604236 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
604258 TTT
1 TTT
604261 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:606500 original size:13 final size:13
Alignment explanation
Indices: 606482--606507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
606472 CAATTTTTTG
606482 TGTATCGATACAT
1 TGTATCGATACAT
606495 TGTATCGATACAT
1 TGTATCGATACAT
606508 ACTTGGTGTA
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:606982 original size:15 final size:15
Alignment explanation
Indices: 606962--607009 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
606952 ATTCTGCCAA
606962 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
606977 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
606992 ACCCACCACAAAATC
1 ATCCACCACAAAATC
607007 ATC
1 ATC
607010 AATACACGGC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:612096 original size:14 final size:14
Alignment explanation
Indices: 612011--612098 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 14
612001 CAATTCGCCA
*
612011 TTTGTCAAGAAATG
1 TTTGTCAAGAAATT
*
612025 GTTGTCAAGAAATT
1 TTTGTCAAGAAATT
* * *
612039 ATCGTCAAG-AACT
1 TTTGTCAAGAAATT
* * *
612052 TCTGTCGAG-AATG
1 TTTGTCAAGAAATT
* *
612065 TTTG-CTAGAAA-C
1 TTTGTCAAGAAATT
612077 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
612091 TTTGTCAA
1 TTTGTCAA
612099 TACGACCCTT
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
12 7 0.13
13 21 0.38
14 27 0.49
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:612179 original size:28 final size:28
Alignment explanation
Indices: 612108--612794 Score: 358
Period size: 28 Copynumber: 24.6 Consensus size: 28
612098 ATACGACCCT
*
612108 TTTCAAAGTCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
612136 TTCTCAAAGCCCACAAGACAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
*
612165 TTTCAAAGCCCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
612193 TTTTAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
612221 GTTCAAAGCCCACATGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
612249 TTTCAAAACCCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
612276 TTTCAAAGCCCACGAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** *** ** * *
612304 TTCTCAAAGTGGCATCCTTCTCAAAGCCCA-CA
1 TT-TCAAAG-CCCA--CAAGTCAGTG-GCATCC
** ** ** * *
612336 AGTCAGTGGCACC-C-CTTTA--AGC--CC
1 TTTCA-AAGC-CCACAAGTCAGTGGCATCC
* * * ** *
612360 --ACACAAG---TC-GGT--G-GCAACCTC
1 TTTCA-AAGCCCACAAGTCAGTGGCATC-C
*
612381 TCTCAAAGCCCACAAGTCAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
*
612409 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
612437 TTTTAAAGCCCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * * * *
612464 TTTTTTATGCCTACAAGTTAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
612493 TTTTAAAGCCCATAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
612520 TTTTCCAAGCCCACGAGTCACTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
**
612549 TTCTCAAAGTGCACAAGTCAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * * *
612578 TTCTCAAAGCCCACAAGTTAATCGCACCCC
1 TT-TCAAAGCCCACAAGTCAGTGGCA-TCC
* *
612608 TTT--AAGCCCACACAAGTCAGTGGAAACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCC
* *
612636 TCTCTCAAAGCCCTCAAGTCAGTGGCACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
*
612666 TTTCAAAGCCCACAAGTTAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
*
612694 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * * * *
612722 TTTTGAAGCCCATAAGTTAGTAGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * *
612750 TTTTGATGCCCACAAATCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
612778 TTTTAAAGCCTACAAGT
1 TTTCAAAGCCCACAAGT
612795 TGGTGGAAAC
Statistics
Matches: 512, Mismatches: 109, Indels: 76
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.00
20 1 0.00
21 1 0.00
22 6 0.01
23 2 0.00
24 1 0.00
25 2 0.00
26 2 0.00
27 32 0.06
28 325 0.63
29 97 0.19
30 23 0.04
31 5 0.01
32 11 0.02
33 2 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:612227 original size:56 final size:56
Alignment explanation
Indices: 612103--612794 Score: 605
Period size: 56 Copynumber: 12.4 Consensus size: 56
612093 TGTCAATACG
* * *
612103 ACCCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGACAGTGGC
1 ACCC-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC
* * * *
612161 ATCCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTAAAGCCCACAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC
* * * * *
612217 ACCCGTTCAAAGCCCACATGTCAGTGGCACCCTTTCAAAACCCATAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC
* *
612273 A-CCTTTCAAAGCCCACGAGTCAGTGGCATCC--TT-------CTCAA---AGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
612317 ATCCTTCTCAAAGCCCACAAGTCAGTGGCACCCCTTT--AAGCCCACACAAGTCGGTGGC
1 ACCCTT-TCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAG-CC-CACAAGTCAGTGGC
*
612375 AACCTCTCTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGC
1 -ACC-CTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGC
* * ** * * *
612433 ACCCTTTTAAAGCCCATAAGTCAGTGGCACCTTTTTTATGCCTACAAGTTAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC
* * * * *
612489 ACCCTTTTAAAGCCCATAAGTCAGTGGCACCTTTTCCAAGCCCACGAGTCACTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC
* ** * * * *
612545 ATCCTTCTCAAAGTGCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAATCGC
1 ACCCTT-TCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
612603 ACCCCTTT--AAGCCCACACAAGTCAGTGGAAACCTCTCTCAAAGCCCTCAAGTCAGTGGC
1 A-CCCTTTCAAAG-CC-CACAAGTCAGTGG-CACCT-TTTCAAAGCCCACAAGTCAGTGGC
*
612662 ACCCTTTCAAAGCCCACAAGTTAGTGGCA-CTCTTTCAAAGCCCACAAGTCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGTCAGTGGC
** * * * * * *
612718 ACCCTTTTGAAGCCCATAAGTTAGTAGCACCCTTTT-GATGCCCACAAATCAGTGGC
1 ACCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC
* * *
612774 ATCCTTTTAAAGCCTACAAGT
1 ACCCTTTCAAAGCCCACAAGT
612795 TGGTGGAAAC
Statistics
Matches: 524, Mismatches: 78, Indels: 66
0.78 0.12 0.10
Matches are distributed among these distances:
44 7 0.01
45 4 0.01
46 24 0.05
47 3 0.01
48 2 0.00
54 2 0.00
55 28 0.05
56 255 0.49
57 53 0.10
58 83 0.16
59 55 0.10
60 8 0.02
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (56 bp):
ACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGC
Found at i:612316 original size:17 final size:17
Alignment explanation
Indices: 612294--612329 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
612284 CCCACGAGTC
612294 AGTGGCATCCTTCTCAA
1 AGTGGCATCCTTCTCAA
612311 AGTGGCATCCTTCTCAA
1 AGTGGCATCCTTCTCAA
612328 AG
1 AG
612330 CCCACAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (17 bp):
AGTGGCATCCTTCTCAA
Found at i:612772 original size:257 final size:258
Alignment explanation
Indices: 612311--612781 Score: 746
Period size: 257 Copynumber: 1.8 Consensus size: 258
612301 TCCTTCTCAA
* * * *
612311 AGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCACCCCTTTAAGCCCACACAAGTCGGTGGCA
1 AGTGGCATCCTTCTCAAAGCCCACAAGTCAATCGCACCCCTTTAAGCCCACACAAGTCAGTGGAA
* *
612376 ACCTCTCTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTT
66 ACCTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * * * * * *
612441 AAAGCCCATAAGTCAGTGGCACCTTTTTTATGCCTACAAGTTAGTGGCACCCTTTTAAAGCCCAT
131 AAAGCCCACAAGTCAGTGGCACCCTTTTGAAGCCCACAAGTTAGTAGCACCCTTTTAAAGCCCAC
*
612506 AAGTCAGTGGCA-CCTTTTCCAAGCCCACGAGTCACTGGCATCCTTCTCAAAGTGCACAAGTC
196 AAATCAGTGGCATCCTTTTCCAAGCCCACGAGTCACTGGCATCCTTCTCAAAGTGCACAAGTC
*
612568 AGTGGCATCCTTCTCAAAGCCCACAAGTTAATCGCACCCCTTTAAGCCCACACAAGTCAGTGGAA
1 AGTGGCATCCTTCTCAAAGCCCACAAGTCAATCGCACCCCTTTAAGCCCACACAAGTCAGTGGAA
* * *
612633 ACCTCTCTCAAAGCCCTCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTC
66 ACCTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
* * *
612698 AAAGCCCACAAGTCAGTGGCACCCTTTTGAAGCCCATAAGTTAGTAGCACCCTTTTGATGCCCAC
131 AAAGCCCACAAGTCAGTGGCACCCTTTTGAAGCCCACAAGTTAGTAGCACCCTTTTAAAGCCCAC
612763 AAATCAGTGGCATCCTTTT
196 AAATCAGTGGCATCCTTTT
612782 AAAGCCTACA
Statistics
Matches: 192, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
257 186 0.97
258 6 0.03
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (258 bp):
AGTGGCATCCTTCTCAAAGCCCACAAGTCAATCGCACCCCTTTAAGCCCACACAAGTCAGTGGAA
ACCTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC
AAAGCCCACAAGTCAGTGGCACCCTTTTGAAGCCCACAAGTTAGTAGCACCCTTTTAAAGCCCAC
AAATCAGTGGCATCCTTTTCCAAGCCCACGAGTCACTGGCATCCTTCTCAAAGTGCACAAGTC
Found at i:612800 original size:28 final size:28
Alignment explanation
Indices: 612311--612794 Score: 434
Period size: 28 Copynumber: 17.0 Consensus size: 28
612301 TCCTTCTCAA
* *
612311 AGTGGCATCCTTCTCAAAGCCCACAAGTC
1 AGTGGCACCCTT-TTAAAGCCCACAAGTC
*
612340 AGTGGCACCCCTTT-AAGCCCACACAAGTC
1 AGTGGCACCCTTTTAAAG-CC-CACAAGTC
* * *
612369 GGTGGCAACCTCTCTCAAAGCCCACAAGTC
1 AGTGGC-ACC-CTTTTAAAGCCCACAAGTC
* *
612399 AGTGGCACTCTTTCAAAGCCCACAAGTC
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
*
612427 AGTGGCACCCTTTTAAAGCCCATAAGTC
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* * * * *
612455 AGTGGCACCTTTTTTATGCCTACAAGTT
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
*
612483 AGTGGCACCCTTTTAAAGCCCATAAGTC
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* *
612511 AGTGGCA-CCTTTTCCAAGCCCACGAGTC
1 AGTGGCACCCTTTT-AAAGCCCACAAGTC
* * * **
612539 ACTGGCATCCTTCTCAAAGTGCACAAGTC
1 AGTGGCACCCTT-TTAAAGCCCACAAGTC
* * *
612568 AGTGGCATCCTTCTCAAAGCCCACAAGTT
1 AGTGGCACCCTT-TTAAAGCCCACAAGTC
* * *
612597 AATCGCACCCCTTT-AAGCCCACACAAGTC
1 AGTGGCACCCTTTTAAAG-CC-CACAAGTC
* * * *
612626 AGTGGAAACCTCTCTCAAAGCCCTCAAGTC
1 AGTGG-CACC-CTTTTAAAGCCCACAAGTC
* *
612656 AGTGGCACCCTTTCAAAGCCCACAAGTT
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* *
612684 AGTGGCACTCTTTCAAAGCCCACAAGTC
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* * *
612712 AGTGGCACCCTTTTGAAGCCCATAAGTT
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* * * *
612740 AGTAGCACCCTTTTGATGCCCACAAATC
1 AGTGGCACCCTTTTAAAGCCCACAAGTC
* *
612768 AGTGGCATCCTTTTAAAGCCTACAAGT
1 AGTGGCACCCTTTTAAAGCCCACAAGT
612795 TGGTGGAAAC
Statistics
Matches: 369, Mismatches: 73, Indels: 27
0.79 0.16 0.06
Matches are distributed among these distances:
27 12 0.03
28 226 0.61
29 85 0.23
30 32 0.09
31 8 0.02
32 6 0.02
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
AGTGGCACCCTTTTAAAGCCCACAAGTC
Found at i:612815 original size:30 final size:32
Alignment explanation
Indices: 612779--612842 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
612769 GTGGCATCCT
*
612779 TTTAAAG-CCTACAAGTTGGTGGAAA-CCTTC
1 TTTAAAGCCCCACAAGTTGGTGGAAACCCTTC
612809 TTTAAAGCCCCCACAAGTTGGTGGAAACCCTTC
1 TTTAAAG-CCCCACAAGTTGGTGGAAACCCTTC
612842 T
1 T
612843 AAACCCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.23
32 17 0.57
33 6 0.20
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (32 bp):
TTTAAAGCCCCACAAGTTGGTGGAAACCCTTC
Found at i:613868 original size:20 final size:20
Alignment explanation
Indices: 613843--613970 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
613833 CTTTTACCCA
613843 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
613863 AATGTAACGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
613883 AATGTATCGATGCATTCTTC
1 AATGTATCGATACATTTTTC
*
613903 AATGTATGGATATATTCTACCTTTTTACCC
1 AATGTATCG--ATA--C-A--TTTTT---C
613933 AGATGTATCGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
613954 AATGTATCGATACATTT
1 AATGTATCGATACATTT
613971 AGTTAAAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
20 54 0.65
21 2 0.02
22 2 0.02
24 6 0.07
25 1 0.01
26 1 0.01
27 5 0.06
29 3 0.04
30 2 0.02
31 7 0.08
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:613956 original size:91 final size:90
Alignment explanation
Indices: 613794--613968 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 90
613784 TTTTACCAAG
* * **
613794 ATGTATTGATACATTTTTCAATGTATCGATATATTCTGTCTTTTACCCAAATGTATCGATACATT
1 ATGTATCGATACATTCTTCAATGTATCGATATATTCTACCTTTTACCCAAATGTATCGATACATT
613859 TTTCAATGTAACGATACATGTATGA
66 TTTCAATGTAACGATACATGTATGA
* * *
613884 ATGTATCGATGCATTCTTCAATGTATGGATATATTCTACCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATCGATATATTCTACC-TTTTACCCAAATGTATCGATACAT
*
613949 TTTTCAATGTATCGATACAT
65 TTTTCAATGTAACGATACAT
613969 TTAGTTAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
90 34 0.45
91 42 0.55
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (90 bp):
ATGTATCGATACATTCTTCAATGTATCGATATATTCTACCTTTTACCCAAATGTATCGATACATT
TTTCAATGTAACGATACATGTATGA
Found at i:614874 original size:19 final size:19
Alignment explanation
Indices: 614840--614878 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
614830 ACCATGCATT
*
614840 TTTTTACTATGTTCCATGCA
1 TTTTTAATATGTTCCA-GCA
614860 TTTTTAATATG-TCCAGCA
1 TTTTTAATATGTTCCAGCA
614878 T
1 T
614879 CTCATTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (19 bp):
TTTTTAATATGTTCCAGCA
Found at i:616291 original size:98 final size:98
Alignment explanation
Indices: 616116--616329 Score: 302
Period size: 98 Copynumber: 2.2 Consensus size: 98
616106 ATTTTTATTC
* * * * *
616116 ATCGAGGATACTCCAATCTGATTCCTCCGAGGAGATACTCTAACCTAATTTTTAAAACTTGTCAA
1 ATCGGGGATACTCCAACCTGATTCCTCCGAGGAAAAACTCTAACCCAATTTTTAAAACTTGTCAA
* *
616181 GATCTGACACTTATTTTTGCCTAAATTATCATT
66 GATCTGAAACTTATTCTTGCCTAAATTATCATT
* * * **
616214 GTCGGGGATACTCCAACCTTATTCCTCTGAGGAAAAACTCTAACCCCTTTTTTAAAACTTGTCAA
1 ATCGGGGATACTCCAACCTGATTCCTCCGAGGAAAAACTCTAACCCAATTTTTAAAACTTGTCAA
*
616279 GATTTGAAACTTATTCTTGCCTAAATTATCATT
66 GATCTGAAACTTATTCTTGCCTAAATTATCATT
*
616312 ATCGGGGACACTCCAACC
1 ATCGGGGATACTCCAACC
616330 CCATTCTTTC
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 101 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (98 bp):
ATCGGGGATACTCCAACCTGATTCCTCCGAGGAAAAACTCTAACCCAATTTTTAAAACTTGTCAA
GATCTGAAACTTATTCTTGCCTAAATTATCATT
Found at i:616352 original size:98 final size:98
Alignment explanation
Indices: 616136--616355 Score: 289
Period size: 98 Copynumber: 2.2 Consensus size: 98
616126 CTCCAATCTG
* * * * *
616136 ATTCCTCCGAGGAGATACTCTAACCTAATTTTTAAAACTTGTCAAGATCTGACACTTATTTTTGC
1 ATTCCTCTGAGGAAATACTCTAACCCAATTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTGC
* * **
616201 CTAAATTATCATTGTCGGGGATACTCCAACCTT
66 CTAAATTATCATTATCGGGGACACTCCAACCCC
* ** *
616234 ATTCCTCTGAGGAAAAACTCTAACCCCTTTTTTAAAACTTGTCAAGATTTGAAACTTATTCTTGC
1 ATTCCTCTGAGGAAATACTCTAACCCAATTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTGC
616299 CTAAATTATCATTATCGGGGACACTCCAACCCC
66 CTAAATTATCATTATCGGGGACACTCCAACCCC
* *
616332 ATT-CTTTCGAGGGAATACTCTAAC
1 ATTCCTCT-GAGGAAATACTCTAAC
616356 TCTGCTTTTT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
97 3 0.03
98 102 0.97
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (98 bp):
ATTCCTCTGAGGAAATACTCTAACCCAATTTTTAAAACTTGTCAAGATCTGAAACTTATTCTTGC
CTAAATTATCATTATCGGGGACACTCCAACCCC
Found at i:624839 original size:13 final size:13
Alignment explanation
Indices: 624821--624846 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
624811 TATACCAAGT
624821 ATGTATCGATACA
1 ATGTATCGATACA
624834 ATGTATCGATACA
1 ATGTATCGATACA
624847 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:624840 original size:32 final size:33
Alignment explanation
Indices: 624803--624866 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
624793 TAGCCAAACT
* **
624803 TGTATCGATATACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
624835 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
624867 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:627100 original size:21 final size:21
Alignment explanation
Indices: 627067--627116 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
627057 TTGCAAGTTG
*
627067 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
627089 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
627110 AAATAAA
1 AAATAAA
627117 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:631043 original size:13 final size:13
Alignment explanation
Indices: 631025--631050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
631015 ACATTTTTCT
631025 TTGTATCGATACA
1 TTGTATCGATACA
631038 TTGTATCGATACA
1 TTGTATCGATACA
631051 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:631214 original size:20 final size:20
Alignment explanation
Indices: 631171--631216 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
631161 AAATCTTTTG
631171 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
631192 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
631212 CAAAA
1 CAAAA
631217 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:633620 original size:13 final size:13
Alignment explanation
Indices: 633602--633627 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
633592 TACACCAAGT
633602 ATGTATCGATACA
1 ATGTATCGATACA
633615 ATGTATCGATACA
1 ATGTATCGATACA
633628 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:633625 original size:32 final size:33
Alignment explanation
Indices: 633584--633647 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
633574 TAGCCAAACT
**
633584 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
633616 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
633648 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:634954 original size:155 final size:155
Alignment explanation
Indices: 634733--635253 Score: 647
Period size: 155 Copynumber: 3.4 Consensus size: 155
634723 ACCGAGTCAA
* * * **
634733 GTGGGTATTTAGGATAGGTTCATCACTTTTAT-AGTCCTTTTTAAGTTTTTTAGGGGTACCAGGA
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGT-CTTTTTAAGTCCTTTAGGGGTACCAGGA
* * * *
634797 TACTTTCACGTTGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTGGAACTAACTCCCAGGTCA
65 TACTTTCACGTTGAAGGTATCCTTTAGAGGAATTTTCGTAATTTTTAGAACTAACTCCTAGGTCA
634862 TCATCGGGTCCACTTTTATATCGAAG
130 TCATCGGGTCCACTTTTATATCGAAG
* *
634888 GTGGGTATTTAAAATAGGTTCATCCCTTTTAT-AGTCTTTTTTAAGTCCTTTAGGGGTACC-GAG
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTC-TTTTTAAGTCCTTTAGGGGTACCAG-G
* * * * *
634951 ATACTTTCACGTTGAATGTATCCTCTCGAGGAATTTTCGTAATTTTTAGAACCAACTCTTAGGTC
64 ATACTTTCACGTTGAAGGTATCCTTTAGAGGAATTTTCGTAATTTTTAGAACTAACTCCTAGGTC
**
635016 ATCATCGGGTCTGCTTTTATATCGAAG
129 ATCATCGGGTCCACTTTTATATCGAAG
* * *
635043 GTGGGCATTT-AGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGTTGCTAGGAT
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGGTACCAGGAT
* * * * * * *
635107 ACTTTTACGTCGAAGGTATACCCTTAGGGGCATTTTGGTAATTTTTTAGAACTAACTCCTAGTTC
66 ACTTTCACGTTGAAGGTAT-CCTTTAGAGGAATTTTCGTAA-TTTTTAGAACTAACTCCTAGGTC
* * * *
635172 GTCA-CTAGGTCCTCTTTTATGTCGAAG
129 ATCATC-GGGTCCACTTTTATATCGAAG
* *
635199 GTGGGCATTTAGGATAGGTTCATCCCTTGTATGAGTCTTTTTAAGTCCTTTAGGG
1 GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGG
635254 CTGTTAGGAT
Statistics
Matches: 318, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
154 61 0.19
155 165 0.52
156 50 0.16
157 42 0.13
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (155 bp):
GTGGGCATTTAAGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGGTACCAGGAT
ACTTTCACGTTGAAGGTATCCTTTAGAGGAATTTTCGTAATTTTTAGAACTAACTCCTAGGTCAT
CATCGGGTCCACTTTTATATCGAAG
Found at i:635306 original size:311 final size:309
Alignment explanation
Indices: 634733--635308 Score: 705
Period size: 311 Copynumber: 1.9 Consensus size: 309
634723 ACCGAGTCAA
* **
634733 GTGGGTATTTAGGATAGGTTCATCACTTTTATAGTCCTTTTTAAGTTTTTTAGGGGTACCAGGAT
1 GTGGGCATTTAGGATAGGTTCATCACTTTTATAGTCCTTTTTAAGTCCTTTAGGGGTACCAGGAT
* * * *
634798 ACTTTCACGTTGAAGGTATCCTTTAGAGGTATTTTCATAATTTTTGGAACTAACTCCCAGGTCAT
66 ACTTTCACGTCGAAGGTATCCCTTAGAGGCATTTTCATAATTTTTAGAACTAACTCCCAGGTCAT
* * *
634863 CATCGGGTCCACTTTTATATCGAAGGTGGGTATTTAAAATAGGTTCATCCCTTTTATAGTCTTTT
131 CATCAGGTCCACTTTTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTATAGTCTTTT
* * ** * **
634928 TTAAGTCCTTTAGGGGTACCGAGATACTTTCACGTTGAATGTATCCTCTCGAGGAATTTTCGTAA
196 TTAAGTCCTTTAGGGGTA-CGAGATACTTTCACATTAAAAATATCCCCTAAAGGAATTTTCGTAA
634993 TTTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATATCGAAG
260 TTTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATATCGAAG
* * * *
635043 GTGGGCATTTA-GATAGGTTCATCCCTTTTATGAGT-CTTTTTAAGTCCTTTAGGGTTGCTAGGA
1 GTGGGCATTTAGGATAGGTTCATCACTTTTAT-AGTCCTTTTTAAGTCCTTTAGGGGTACCAGGA
* * ** * *
635106 TACTTTTACGTCGAAGGTATACCCTTAGGGGCATTTTGGTAATTTTTTAGAACTAACTCCTAGTT
65 TACTTTCACGTCGAAGGTAT-CCCTTAGAGGCATTTTCATAA-TTTTTAGAACTAACTCCCAGGT
* * * **
635171 CGTCA-CTAGGTCCTCTTTTATGTCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTGTATGAGT
128 CATCATC-AGGTCCACTTTTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTAT-AGT
* **
635235 C-TTTTTAAGTCCTTTAGGGCTGTTA-G-GATACTTTTACATTAAAAATATCCCCTAAAGGCTTT
191 CTTTTTTAAGTCCTTTAGGG--G-TACGAGATACTTTCACATTAAAAATATCCCCTAAAGGAATT
*
635297 TTTGTAATTTTT
253 TTCGTAATTTTT
635309 CTTGAACTTA
Statistics
Matches: 222, Mismatches: 36, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
309 60 0.27
310 30 0.14
311 124 0.56
312 5 0.02
313 1 0.00
314 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (309 bp):
GTGGGCATTTAGGATAGGTTCATCACTTTTATAGTCCTTTTTAAGTCCTTTAGGGGTACCAGGAT
ACTTTCACGTCGAAGGTATCCCTTAGAGGCATTTTCATAATTTTTAGAACTAACTCCCAGGTCAT
CATCAGGTCCACTTTTATATCGAAGGTGGGCATTTAAAATAGGTTCATCCCTTGTATAGTCTTTT
TTAAGTCCTTTAGGGGTACGAGATACTTTCACATTAAAAATATCCCCTAAAGGAATTTTCGTAAT
TTTTAGAACCAACTCTTAGGTCATCATCGGGTCTGCTTTTATATCGAAG
Found at i:639788 original size:79 final size:79
Alignment explanation
Indices: 639657--639817 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
639647 GCTACATTAG
*
639657 TTAAAACAATTTTTAACCAAGTTCTTAACTTTTAGGAAATTTGTAAGAAAAATATAGTACACTAT
1 TTAAAACAATTTTTAACCAAGTTCTTAACTTGTAGGAAATTTGTAAGAAAAATATAGTACACTAT
639722 GAAATTTAAAAAAA
66 GAAATTTAAAAAAA
639736 TTAAAACAATTTTTAACCAAGTTCTTAACTTGTAGGAAATTTGTAAGAAAAATATAGTACACTAT
1 TTAAAACAATTTTTAACCAAGTTCTTAACTTGTAGGAAATTTGTAAGAAAAATATAGTACACTAT
639801 GAAATTTAAAAAAA
66 GAAATTTAAAAAAA
639815 TTA
1 TTA
639818 TTTTAATGGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (79 bp):
TTAAAACAATTTTTAACCAAGTTCTTAACTTGTAGGAAATTTGTAAGAAAAATATAGTACACTAT
GAAATTTAAAAAAA
Found at i:642459 original size:52 final size:50
Alignment explanation
Indices: 642403--642572 Score: 164
Period size: 52 Copynumber: 3.3 Consensus size: 50
642393 GCCAATGTGT
*
642403 TGATTCAAGGCCAGTGGCATTAGACCTAAAAATGAC-AAGAGTGCTAATATG
1 TGATTCAAGGCCAGTGGCATT-GACTTAAAAATGACAAAG-GTGCTAATATG
* * *
642454 ATGATTCAAGGCTAGTAGCATTGAGCTTAAAAATGACAAAGGTGCCT-ATGTG
1 -TGATTCAAGGCCAGTGGCATTGA-CTTAAAAATGACAAAGGTG-CTAATATG
* * * * *
642506 CTGATTCAAGGCCAGCGACATTGGACTTAGAAAAAGATAAAGGTACTAATATG
1 -TGATTCAAGGCCAGTGGCATT-GACTTA-AAAATGACAAAGGTGCTAATATG
642559 TCGATTCAAGGCCA
1 T-GATTCAAGGCCA
642573 ACGATTTTGG
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
51 2 0.02
52 61 0.62
53 35 0.36
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (50 bp):
TGATTCAAGGCCAGTGGCATTGACTTAAAAATGACAAAGGTGCTAATATG
Found at i:642729 original size:52 final size:52
Alignment explanation
Indices: 642613--642735 Score: 140
Period size: 52 Copynumber: 2.4 Consensus size: 52
642603 AGAAGAGTTC
* * * *
642613 CAATGTGCTGATTCATGGCTAGCGACATTAGACTTGAAGATGAGAAGAATAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAATAT
* * * * *
642665 CAATATGCTGATTCAAGGCCAGCGACTTTGGACTTAAAAATTAGAAGAAT-G
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAATAT
*
642716 CTAATGTGTTGATTCAAGGC
1 C-AATGTGCTGATTCAAGGC
642736 TTGCAACATT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 1 0.02
52 58 0.98
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (52 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGAATAT
Found at i:642822 original size:52 final size:52
Alignment explanation
Indices: 642766--642895 Score: 129
Period size: 52 Copynumber: 2.5 Consensus size: 52
642756 ATGATAAAAA
* * * **
642766 TGCCAATTTGTTGATTCAAGGCCAACGATATCAGACTTAA-AGATGACCAAGG
1 TGCCAATATGATGATTCAAGGCCAACGATATCAGACTTAAGA-AAGAAAAAGG
* * * * **
642818 TGCCAATATGCTGATCCAAAGCCAGCGATATTGGACTTAAGAAAGAAAAAGG
1 TGCCAATATGATGATTCAAGGCCAACGATATCAGACTTAAGAAAGAAAAAGG
642870 TGCCAA-AGTGATGATTCAAGGCCAAC
1 TGCCAATA-TGATGATTCAAGGCCAAC
642896 AACATTGGAC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
51 1 0.02
52 60 0.97
53 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (52 bp):
TGCCAATATGATGATTCAAGGCCAACGATATCAGACTTAAGAAAGAAAAAGG
Found at i:642997 original size:31 final size:30
Alignment explanation
Indices: 642962--643516 Score: 349
Period size: 32 Copynumber: 17.2 Consensus size: 30
642952 AATGACATTA
* * *
642962 GGCTTATAAAGAGATGCCATCGACTTGTGTG
1 GGCTT-TAAAGGGTTGCCACCGACTTGTGTG
* * * *
642993 GGCTTTTGAGAGGGTTGCCACCAATTTTTGTG
1 GGC-TTT-AAAGGGTTGCCACCGACTTGTGTG
* **
643025 GGCTTTTAAGAGGGTTGTCGTCGACTTGTGTG
1 GGC-TTTAA-AGGGTTGCCACCGACTTGTGTG
*
643057 GGCTTTTGAAGGGGATTGCCACCGACTTAG-GTG
1 GGC-TTT-AAAGGG-TTGCCACCGACTT-GTGTG
* *
643090 GGCTTTAGAAGAGGATTGCCACCAACTTGTGTA
1 GGCTTTA-AAG-GG-TTGCCACCGACTTGTGTG
643123 GGCTTTAGAAGGGTTGCCACCGACTTGTGTG
1 GGCTTTA-AAGGGTTGCCACCGACTTGTGTG
** * *
643154 GGCTTTAGAAGGGTTGCCATTGACTTATATG
1 GGCTTTA-AAGGGTTGCCACCGACTTGTGTG
** *
643185 GGCTTTAGAAGGGGTTGCCACTAACTTGTGTA
1 GGCTTTA-AA-GGGTTGCCACCGACTTGTGTG
* *
643217 GGCTTTAGAAAAGGGTTGCCACCAACTTGTGTA
1 GGCTTT---AAAGGGTTGCCACCGACTTGTGTG
*
643250 GGCTTTGAAGAAGGGTTGCCATCGACTTGTGTG
1 GGCTTT--A-AAGGGTTGCCACCGACTTGTGTG
* * * * *
643283 GGCTTTGAAGAAGAGTTACCATCAATTTGTGTG
1 GGCTTT--A-AAGGGTTGCCACCGACTTGTGTG
* * *
643316 GGCTTTGAAAATGGTTGCTACCAACTTGTGTG
1 GGCTTT--AAAGGGTTGCCACCGACTTGTGTG
* * * *
643348 GGCTTTAAAGAAGGGTTCCCACCAACTTATGTA
1 GGCTTT--A-AAGGGTTGCCACCGACTTGTGTG
*
643381 GGCTTTGAAAGAGGTTGCCATCGACTTGTGTG
1 GGCTTT-AAAG-GGTTGCCACCGACTTGTGTG
* *
643413 GGTTTTAGATAAGGGTTGCCACAGACTTGTGT-
1 GGCTTT--A-AAGGGTTGCCACCGACTTGTGTG
* * *
643445 AGATTTGAAGAAGGGTTGCCACCGACTTATGTG
1 GGCTTT--A-AAGGGTTGCCACCGACTTGTGTG
* *
643478 GGTTTTGAAAAGGGTTGCCACCAACTTGTGTG
1 GGCTTT--AAAGGGTTGCCACCGACTTGTGTG
643510 GGCTTTA
1 GGCTTTA
643517 GAAAAGATTA
Statistics
Matches: 432, Mismatches: 73, Indels: 39
0.79 0.13 0.07
Matches are distributed among these distances:
30 1 0.00
31 62 0.14
32 182 0.42
33 180 0.42
34 6 0.01
35 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (30 bp):
GGCTTTAAAGGGTTGCCACCGACTTGTGTG
Found at i:643091 original size:33 final size:32
Alignment explanation
Indices: 642976--643519 Score: 403
Period size: 33 Copynumber: 16.8 Consensus size: 32
642966 TATAAAGAGA
* *
642976 TGCCATCGACTTGTGTGGGCTTTTG-AGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG-GGGT
* * * *
643008 TGCCACCAATTTTTGTGGGCTTT-TAAGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG-GGGT
* ** *
643040 TGTCGTCGACTTGTGTGGGCTTTTGAAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGG-T
*
643073 TGCCACCGACTTAG-GTGGGCTTTAGAAGAGGAT
1 TGCCACCGACTT-GTGTGGGCTTTAGAAG-GGGT
* *
643106 TGCCACCAACTTGTGTAGGCTTTAGAA-GGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
643137 TGCCACCGACTTGTGTGGGCTTTAGAA-GGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
** * *
643168 TGCCATTGACTTATATGGGCTTTAGAAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
** * *
643200 TGCCACTAACTTGTGTAGGCTTTAGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGGT
* *
643233 TGCCACCAACTTGTGTAGGCTTT-GAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG--GGGT
* *
643266 TGCCATCGACTTGTGTGGGCTTT-GAAGAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG--GGGT
* * * * **
643299 TACCATCAATTTGTGTGGGCTTT-GAAAATGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGGT
* *
643331 TGCTACCAACTTGTGTGGGCTTTA-AAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG--GGGT
* * * * *
643364 TCCCACCAACTTATGTAGGCTTT-GAAAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGGT
* * *
643396 TGCCATCGACTTGTGTGGGTTTTAGATAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGA-AGGGGT
* * *
643429 TGCCACAGACTTGTGT-AGATTT-GAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG--GGGT
* * *
643461 TGCCACCGACTTATGTGGG-TTTTGAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGGT
*
643493 TGCCACCAACTTGTGTGGGCTTTAGAA
1 TGCCACCGACTTGTGTGGGCTTTAGAA
643520 AAGATTACCA
Statistics
Matches: 413, Mismatches: 75, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.00
31 61 0.15
32 162 0.39
33 179 0.43
34 10 0.02
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGGT
Found at i:643385 original size:65 final size:65
Alignment explanation
Indices: 642984--643522 Score: 467
Period size: 65 Copynumber: 8.3 Consensus size: 65
642974 GATGCCATCG
* * * * * * * **
642984 ACTTGTGTGGGCTTTTG-AGAGGGTTGCCACCAATTTTTGTGGGCTTTTAAG-AGGGTTGTCGTC
1 ACTTGTGTAGGC-TTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACC
*
643047 G
65 A
* * *
643048 ACTTGTGTGGGCTTTTG-AAGGGGATTGCCACCGACTTAG-GTGGGCTTTAGAAG-AGGATTGCC
1 ACTTGTGTAGGC-TTTGAAAAGGG-TTGCCACCGACTT-GTGTGGGCTTTA-AAGAAGGGTTGCC
643110 ACCA
62 ACCA
* ***
643114 ACTTGTGTAGGCTTT-AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCATTG
1 ACTTGTGTAGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACCA
* * * * ** *
643176 ACTTATATGGGCTTT-AGAAGGGGTTGCCACTAACTTGTGTAGGCTTTAGAA-AAGGGTTGCCAC
1 ACTTGTGTAGGCTTTGA-AAAGGGTTGCCACCGACTTGTGTGGGCTTTA-AAGAAGGGTTGCCAC
643239 CA
64 CA
* * * * *
643241 ACTTGTGTAGGCTTTGAAGAAGGGTTGCCATCGACTTGTGTGGGCTTTGAAGAAGAGTTACCATC
1 ACTTGTGTAGGCTTTGAA-AAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACC
643306 A
65 A
* * * * * *
643307 ATTTGTGTGGGCTTTGAAAATGGTTGCTACCAACTTGTGTGGGCTTTAAAGAAGGGTTCCCACCA
1 ACTTGTGTAGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACCA
* * * * *
643372 ACTTATGTAGGCTTTG-AAAGAGGTTGCCATCGACTTGTGTGGGTTTTAGATAAGGGTTGCCA-C
1 ACTTGTGTAGGCTTTGAAAAG-GGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACC
643435 A
65 A
* * * *
643436 GACTTGTGTA-GATTTGAAGAAGGGTTGCCACCGACTTATGTGGGTTTTGAA-AAGGGTTGCCAC
1 -ACTTGTGTAGGCTTTGAA-AAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCAC
643499 CA
64 CA
*
643501 ACTTGTGTGGGCTTTAGAAAAG
1 ACTTGTGTAGGCTTT-GAAAAG
643523 ATTACCACGG
Statistics
Matches: 385, Mismatches: 70, Indels: 39
0.78 0.14 0.08
Matches are distributed among these distances:
61 2 0.01
62 22 0.06
63 26 0.07
64 72 0.19
65 182 0.47
66 81 0.21
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (65 bp):
ACTTGTGTAGGCTTTGAAAAGGGTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTGCCACCA
Found at i:644564 original size:19 final size:19
Alignment explanation
Indices: 644519--644575 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
644509 ACTGCCAGTT
*
644519 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATGG
644538 TCCATGTATCGATACAATGG
1 T-CATGTATCGATACAATGG
644558 TCATGTATCGATACAATG
1 TCATGTATCGATACAATG
644576 TATCGATACA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATGG
Found at i:644578 original size:13 final size:13
Alignment explanation
Indices: 644560--644586 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
644550 TACAATGGTC
644560 ATGTATCGATACA
1 ATGTATCGATACA
644573 ATGTATCGATACA
1 ATGTATCGATACA
644586 A
1 A
644587 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:645046 original size:31 final size:32
Alignment explanation
Indices: 644999--645079 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 32
644989 GCATCTTTTT
* *
644999 TCTAAAGCCTATACAAGTCAGTGGCAACCCTT-
1 TCTAAAGCCCACACAAGTCAGTGGCAA-CCTTA
* **
645031 T-TAAAGCCCACACAAGTCGGTGGTTACCTTA
1 TCTAAAGCCCACACAAGTCAGTGGCAACCTTA
*
645062 TCAAAAGCCCACACAAGT
1 TCTAAAGCCCACACAAGT
645080 TGGTGGCATC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.10
31 21 0.51
32 16 0.39
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (32 bp):
TCTAAAGCCCACACAAGTCAGTGGCAACCTTA
Found at i:645232 original size:52 final size:52
Alignment explanation
Indices: 645149--645464 Score: 350
Period size: 52 Copynumber: 6.1 Consensus size: 52
645139 TCAAACTATC
* * * *
645149 TCATTTTTAAGCCTAATGTCACTAGCCTTGAATCAACACATTGGCACCCTTA
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * *
645201 TCATGTTTAAGTCTAATGTCACTGGCCTTGAATCAGCACAGTGGCACCTTTG
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * *
645253 TCATCTTTAAGTTTGATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTG
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * *
645305 TCATCTTTAAGTTTGATATCACTAGCCTTGAATCAGCATATTGGCA-CCTCTA
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCT-TA
*
645357 TCAT-TTTAA-TCCCAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
1 TCATCTTTAAGT-CTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
* * * * * * *
645408 TCATGTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTAGCACTCTTC
1 TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
645460 TCATC
1 TCATC
645465 CTTATCATCT
Statistics
Matches: 229, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
50 1 0.00
51 43 0.19
52 184 0.80
53 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (52 bp):
TCATCTTTAAGTCTAATATCACTAGCCTTGAATCAGCACATTGGCACCCTTA
Found at i:645437 original size:155 final size:156
Alignment explanation
Indices: 645167--645454 Score: 402
Period size: 155 Copynumber: 1.9 Consensus size: 156
645157 AAGCCTAATG
* * *
645167 TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCTAATGTCACTGGCCTTGA
1 TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCCAATATCACTAGCCTTGA
* * * * * *
645232 ATCAGCACAGTGGCACCTTTGTCATCTTTAAGTTTGATATCGCTAGCCTTGAATCAGCATATTGG
66 ATCAGCACAGTGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATTAG
645297 CACCTTTGTCATCTTTAAGTTTGATA
131 CACCTTTGTCATCTTTAAGTTTGATA
* *
645323 TCACTAGCCTTGAATCAGCATATTGGCA-CCTCTATCAT-TTTAA-TCCCAATATCACTAGCCTT
1 TCACTAGCCTTGAATCAACACATTGGCACCCT-TATCATGTTTAAGT-CCAATATCACTAGCCTT
* * * *
645385 GAATCAGCACATTGGCACCCTTATCATGTTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATT
64 GAATCAGCACAGTGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATT
645450 AGCAC
129 AGCAC
645455 TCTTCTCATC
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
154 1 0.01
155 82 0.71
156 32 0.28
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (156 bp):
TCACTAGCCTTGAATCAACACATTGGCACCCTTATCATGTTTAAGTCCAATATCACTAGCCTTGA
ATCAGCACAGTGGCACCCTTATCATCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATTAG
CACCTTTGTCATCTTTAAGTTTGATA
Found at i:652082 original size:17 final size:17
Alignment explanation
Indices: 652060--652094 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
652050 CACTTCATGA
652060 TTTTATTTCAGGTTGAT
1 TTTTATTTCAGGTTGAT
652077 TTTTATTTCAGGTTGAT
1 TTTTATTTCAGGTTGAT
652094 T
1 T
652095 CGAAGGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
TTTTATTTCAGGTTGAT
Found at i:654113 original size:19 final size:19
Alignment explanation
Indices: 654065--654116 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
654055 CAAACCCCAA
* *
654065 AATGTATTGACACAATAAT
1 AATGTATCGATACAATAAT
654084 AATGTATCGATACAATAAT
1 AATGTATCGATACAATAAT
654103 AATGTATCGATACA
1 AATGTATCGATACA
654117 TTTGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (19 bp):
AATGTATCGATACAATAAT
Found at i:654150 original size:70 final size:71
Alignment explanation
Indices: 654015--654168 Score: 179
Period size: 70 Copynumber: 2.2 Consensus size: 71
654005 AATTTAACTG
* * * * *
654015 ATGTATTGATACATTGAAGAATTTATCAATACATTTGAGTCAAACCCCAAAATGTATTGACACAA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGAGTCAAAACCCAAAATGTATCGACACAA
*
654080 T-AATA
66 TGAAAA
* * * *
654085 ATGTATCGATACAAT-AATAATGTATCGATACATTTGGGTCAAAAACCCAGAAA-GTATCGATAC
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGAGTC-AAAACCCA-AAATGTATCGACAC
654148 AATGAAAA
64 AATGAAAA
654156 ATGTATCGATACA
1 ATGTATCGATACA
654169 TTTGGATCAA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
69 21 0.30
70 31 0.44
71 19 0.27
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACAATGAAGAATGTATCAATACATTTGAGTCAAAACCCAAAATGTATCGACACAA
TGAAAA
Found at i:654208 original size:50 final size:50
Alignment explanation
Indices: 654082--654221 Score: 192
Period size: 50 Copynumber: 2.8 Consensus size: 50
654072 TGACACAATA
* *
654082 ATAATGTATCGATACAATAATAATGTATCGATACATTTGGGTCAAAAACCC
1 ATAATGTATCGATACAATAAAAATGTATCGATACATTTGGATC-AAAACCC
* * *
654133 AGAAAGTATCGATACAATGAAAAATGTATCGATACATTTGGATC-AATCCC
1 ATAATGTATCGATACAAT-AAAAATGTATCGATACATTTGGATCAAAACCC
*
654183 ATAATGTATCAATACAATAAAAAATGTATCGATACATTT
1 ATAATGTATCGATACAAT-AAAAATGTATCGATACATTT
654222 TCTTTCCTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
50 40 0.51
51 16 0.20
52 23 0.29
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (50 bp):
ATAATGTATCGATACAATAAAAATGTATCGATACATTTGGATCAAAACCC
Done.