Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 179 of 318
Found at i:55506554 original size:28 final size:28
Alignment explanation
Indices: 55506491--55506556 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
55506481 CTACGGATCA
** *
55506491 AGTCAAACGAATATATCATCTAATCCAG
1 AGTCAAATAAATAAATCATCTAATCCAG
* *
55506519 AGTCAAATAAATAAATCATCTTATTCAG
1 AGTCAAATAAATAAATCATCTAATCCAG
55506547 AGTCAAATAA
1 AGTCAAATAA
55506557 CAAGTGAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27
Consensus pattern (28 bp):
AGTCAAATAAATAAATCATCTAATCCAG
Found at i:55510319 original size:16 final size:16
Alignment explanation
Indices: 55510286--55510324 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
55510276 GGTGTTTAAA
*
55510286 ATTTTTTATTTTTATT
1 ATTTTTTATTTGTATT
55510302 ATTTTTTATTTGGT-TT
1 ATTTTTTATTT-GTATT
55510318 ATTTTTT
1 ATTTTTT
55510325 GTTCGGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (16 bp):
ATTTTTTATTTGTATT
Found at i:55514588 original size:2 final size:2
Alignment explanation
Indices: 55514581--55514608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55514571 TCGGCTTAGC
55514581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55514609 GTTTGCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55515452 original size:80 final size:80
Alignment explanation
Indices: 55515316--55515493 Score: 225
Period size: 80 Copynumber: 2.2 Consensus size: 80
55515306 CGAATGATAT
* * *
55515316 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTCAATTCCGAAGGCAATTG
* *
55515381 TGCGAGTTACCAAAA
66 TGCGAATCACCAAAA
* * *
55515396 CCGGGTTAAGTCCCGAAGGCATTTATGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTC-AATT-CCGAAGGCAAT
* *
55515459 TGTGCGAATCACTATAA
64 TGTGCGAATCACCAAAA
*
55515476 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
55515494 ACAATCGAGC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 1 0.01
79 19 0.23
80 64 0.76
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTATGCTAAGTGACTAAATCCGGGTCAATTCCGAAGGCAATTG
TGCGAATCACCAAAA
Found at i:55515480 original size:40 final size:40
Alignment explanation
Indices: 55515314--55515493 Score: 179
Period size: 40 Copynumber: 4.5 Consensus size: 40
55515304 TTCGAATGAT
* * * *
55515314 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAA-TTACTAA
* *
55515355 ATCCGGG-TCAATT-CCGAAGGCATTTGTGCGAGTTACCAA
1 ATCCGGGCT-AATTCCCGAAGGCATTTGTGCGAATTACTAA
* * * * *
55515394 AACCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACTAA
1 ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAATTACTAA
* *
55515434 ATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATA
1 ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAATTACTA-A
55515475 A-CCGGGCT-ATGTCCCGAAG
1 ATCCGGGCTAAT-TCCCGAAG
55515494 ACAATCGAGC
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
39 16 0.14
40 89 0.76
41 12 0.10
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAATTCCCGAAGGCATTTGTGCGAATTACTAA
Found at i:55515514 original size:40 final size:40
Alignment explanation
Indices: 55515436--55515519 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
55515426 GTTACTAAAT
* * *
55515436 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
55515476 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
55515516 CCGG
1 CCGG
55515520 TTAAATTCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:55515518 original size:80 final size:79
Alignment explanation
Indices: 55515350--55515532 Score: 183
Period size: 80 Copynumber: 2.3 Consensus size: 79
55515340 GTGCTAAGTG
* * * * *
55515350 ACTAAATCCGGGTCAATTCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGG
1 ACTAAATCCGGGTCAATTCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAGA
** *
55515415 CATTTATGCGAGTT
66 CATCGATGCGAGTC
* * *
55515429 ACTAAATCCGGG-CTAATTCCCGAAGGCAATTGTGCGAATCACTATAACCGGGCTATGTCCCGAA
1 ACTAAATCCGGGTC-AATT-CCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAA
55515493 GACAATCGA-GCGAGTC
64 GAC-ATCGATGCGAGTC
* * * *
55515509 GCTATATCCGGTTAAATT-CGAAGG
1 ACTAAATCCGGGTCAATTCCGAAGG
55515533 TACGTGATTC
Statistics
Matches: 85, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
78 7 0.08
79 16 0.19
80 59 0.69
81 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (79 bp):
ACTAAATCCGGGTCAATTCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAGA
CATCGATGCGAGTC
Found at i:55523482 original size:39 final size:40
Alignment explanation
Indices: 55523333--55523512 Score: 204
Period size: 40 Copynumber: 4.5 Consensus size: 40
55523323 TTCGAATGGT
* * *
55523333 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
55523374 ATCCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAA
1 ATCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
55523414 AACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
55523454 ATCCGGGCTAA-TTCCGAAGGCAATTGTGCGAATCACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
55523494 A-CCGGGCTATGTCCCGAAG
1 ATCCGGGCTAAGTCCCGAAG
55523513 ACAATCGAGC
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 31 0.26
40 61 0.51
41 27 0.23
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:55523508 original size:79 final size:81
Alignment explanation
Indices: 55523335--55523512 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 81
55523325 CGAATGGTAT
* *
55523335 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
* *
55523400 GTGCGAGTTACCAAAA
66 GTGCGAATCACCAAAA
* * *
55523416 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGG-CTAATT-CCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTC-AATTCCCGAAGGCAAT
* *
55523478 TGTGCGAATCACTATAA
65 TGTGCGAATCACCAAAA
*
55523495 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
55523513 ACAATCGAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 40 0.47
80 19 0.22
81 26 0.31
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
GTGCGAATCACCAAAA
Found at i:55523525 original size:79 final size:79
Alignment explanation
Indices: 55523369--55523552 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 79
55523359 GTGCTAAGTG
* * * * *
55523369 ACTAAATCCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGTAAATT-CCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAG
* * * * *
55523434 GCATTTGTGCGAGTT
65 ACAATCGAGCGAGTC
* * *
55523449 ACTAAATCCGGGCT-AATTCCGAAGGCAATTGTGCGAATCACTATAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGG-TAAATTCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAG
55523513 ACAATCGAGCGAGTC
65 ACAATCGAGCGAGTC
* * *
55523528 GCTATATCCGGTTAAATTCCGAAGG
1 ACTAAATCCGGGTAAATTCCGAAGG
55523553 TACGTGATTC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
79 69 0.79
80 16 0.18
81 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (79 bp):
ACTAAATCCGGGTAAATTCCGAAGGCAATTGTGCGAATCACCAAAACCGGGCTAAGTCCCGAAGA
CAATCGAGCGAGTC
Found at i:55525710 original size:40 final size:40
Alignment explanation
Indices: 55525644--55525746 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 40
55525634 AAATTGAATG
* **
55525644 ATATCCGGGCTAAG-CCCGAAGACAATTATGCT-GAAATTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAG-AAGCT
* * *
55525683 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAGCT
55525723 ATATCCGGGCTAAGA-CCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
55525747 TTCGTGCAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 22 0.40
40 32 0.58
41 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAGCT
Found at i:55525774 original size:38 final size:38
Alignment explanation
Indices: 55525685--55525793 Score: 130
Period size: 38 Copynumber: 2.8 Consensus size: 38
55525675 TGAAATTTAT
* * *
55525685 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTAT
1 ATCCGGGCTAAGA-CCGAAGGC-ATTGTGCAAGTAGCTAA
* *
55525725 ATCCGGGCTAAGACCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCGAAGGCATT-GTGCAAGTAGCTAA
55525764 AT-CGGGCTAAGACCGAAGGCATTTGTGCAA
1 ATCCGGGCTAAGACCGAAGGCA-TTGTGCAA
55525794 TCGTGATATC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
38 28 0.45
39 22 0.35
40 12 0.19
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (38 bp):
ATCCGGGCTAAGACCGAAGGCATTGTGCAAGTAGCTAA
Found at i:55533811 original size:40 final size:39
Alignment explanation
Indices: 55533643--55533813 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
55533633 AGAAATTGAA
* *
55533643 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
55533683 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
55533723 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
55533763 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
55533803 TGATATCCGGG
1 TGATATCCGGG
55533814 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:55536830 original size:29 final size:29
Alignment explanation
Indices: 55536798--55536870 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
55536788 CTTCGAGCTC
*
55536798 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55536827 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55536856 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
55536871 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:55541085 original size:28 final size:28
Alignment explanation
Indices: 55541044--55541104 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
55541034 AAAGGCTCAA
55541044 ACACGGGCGCGTCATGGCCGTGTGAGGG
1 ACACGGGCGCGTCATGGCCGTGTGAGGG
* *
55541072 ACACGGGGGTGTCATGGCCGTGTGAGGG
1 ACACGGGCGCGTCATGGCCGTGTGAGGG
55541100 ACACG
1 ACACG
55541105 AGCATGTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.16, C:0.23, G:0.46, T:0.15
Consensus pattern (28 bp):
ACACGGGCGCGTCATGGCCGTGTGAGGG
Found at i:55545981 original size:17 final size:16
Alignment explanation
Indices: 55545947--55546005 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
55545937 AAAATAAAAT
* *
55545947 AATAAAATTGAAATGAA
1 AATAAAAAT-AAAAGAA
55545964 AATAAAAATCAAAAGAAA
1 AATAAAAAT-AAAAG-AA
**
55545982 AATAAAAATAAAACTA
1 AATAAAAATAAAAGAA
55545998 AATAAAAA
1 AATAAAAA
55546006 AATAGGAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.25
17 16 0.44
18 11 0.31
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (16 bp):
AATAAAAATAAAAGAA
Found at i:55545983 original size:6 final size:6
Alignment explanation
Indices: 55545957--55546009 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
55545947 AATAAAATTG
* * * *
55545957 AAATGA AAATAA AAATCA AAAGAA AAATAA AAATAA AACTAA ATAA-AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-AATAA
55546005 AAATA
1 AAATA
55546010 GGAGGATTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 2 0.05
6 35 0.92
7 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:55547519 original size:23 final size:21
Alignment explanation
Indices: 55547493--55547539 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
55547483 AACTAAAGGC
*
55547493 TGTTGTATGGCGGTGCACGGGCG
1 TGTTG-ATGGC-GAGCACGGGCG
*
55547516 TGTTGATGTCGAGCACGGGCG
1 TGTTGATGGCGAGCACGGGCG
55547537 TGT
1 TGT
55547540 GACGCGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 4 0.18
23 5 0.23
ACGTcount: A:0.11, C:0.17, G:0.45, T:0.28
Consensus pattern (21 bp):
TGTTGATGGCGAGCACGGGCG
Found at i:55556017 original size:47 final size:47
Alignment explanation
Indices: 55555945--55556341 Score: 623
Period size: 47 Copynumber: 8.3 Consensus size: 47
55555935 CCCTTCGGGA
* * * * * * *
55555945 CTTATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
55555992 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55556039 CTTATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55556086 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
55556135 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55556182 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55556229 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55556278 CTTATCACATATATACACACTTTCACGTTCATCACATTGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
55556327 CTTATCACATATATA
1 CTTATCACATATATA
55556342 TATCTCATAC
Statistics
Matches: 333, Mismatches: 13, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 193 0.58
49 140 0.42
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55556023 original size:25 final size:25
Alignment explanation
Indices: 55555995--55556073 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
55555985 ACTCGGCCCT
*
55555995 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACATTCACATTC
** * *
55556020 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACATTC-ACATTC
*
55556042 ATCACATATATACACCTTCACATTC
1 ATCACATATATACACATTCACATTC
55556067 ATCACAT
1 ATCACAT
55556074 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACATTCACATTC
Found at i:55556205 original size:143 final size:143
Alignment explanation
Indices: 55555945--55556341 Score: 654
Period size: 143 Copynumber: 2.8 Consensus size: 143
55555935 CCCTTCGGGA
* * * * * * * *
55555945 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
55556008 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACCTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACCTTCACATTCATCACA
55556073 TCGGCCATTAGGC
131 TCGGCCATTAGGC
55556086 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
55556151 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACCTTCACATTCATCACA
55556216 TCGGCCATTAGGC
131 TCGGCCATTAGGC
55556229 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT--
*
55556294 ACACTTTCACGTTCATCACATTGGCCATTAGGCCTTATCACATATATA
64 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
55556342 TATCTCATAC
Statistics
Matches: 239, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
141 10 0.04
142 1 0.00
143 182 0.76
145 46 0.19
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (143 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACCTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:55557650 original size:2 final size:2
Alignment explanation
Indices: 55557643--55557686 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55557633 TACCTTCGGC
55557643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55557685 AT
1 AT
55557687 GTTAATGACG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55563529 original size:49 final size:49
Alignment explanation
Indices: 55563467--55563594 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
55563457 CGTGTGCTAG
* * *
55563467 TGTAAGACATGTCTGGGACATGGCATTGACAC-CGATAAATGAGAGCCAA
1 TGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAAATGAAAGCCAA
* * * * *
55563516 TGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAAGTCAG
1 TGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAAATGAAAGCCAA
*
55563565 TGTAAGGCCTGTCTGGGACATGGCATCGAC
1 TGTAAGACCTGTCTGGGACATGGCATCGAC
55563595 TTTGAAGTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
48 1 0.01
49 66 0.99
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
TGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAAATGAAAGCCAA
Found at i:55564134 original size:3 final size:3
Alignment explanation
Indices: 55564126--55564176 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
55564116 ATTATAAGTA
*
55564126 AAT AAT AAT AAT AAT AATT ACT AA- AAT -AT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
55564169 -AT AAT AAT
1 AAT AAT AAT
55564177 TAAAGTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 8 0.20
3 31 0.76
4 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:55565100 original size:6 final size:6
Alignment explanation
Indices: 55565089--55565141 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
55565079 GTGTACCGCC
*
55565089 ACTGTT ACTGTT ACTGTT ACTATT ACTGTT ACTGTT ACTGTT ACTGTT
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT
55565137 ACTGT
1 ACTGT
55565142 GTATTCCAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ACTGTT
Found at i:55571406 original size:9 final size:9
Alignment explanation
Indices: 55571392--55571416 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55571382 AATCATTCAA
55571392 TCATTCATT
1 TCATTCATT
55571401 TCATTCATT
1 TCATTCATT
55571410 TCATTCA
1 TCATTCA
55571417 ATTTAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (9 bp):
TCATTCATT
Found at i:55577650 original size:45 final size:45
Alignment explanation
Indices: 55577599--55577699 Score: 193
Period size: 45 Copynumber: 2.2 Consensus size: 45
55577589 GGGGTATTAC
55577599 ACATGGCATCGGCTTGATATGTGTCAGTGTAAGACCATGTCTGGG
1 ACATGGCATCGGCTTGATATGTGTCAGTGTAAGACCATGTCTGGG
*
55577644 ACATGGCATTGGCTTGATATGTGTCAGTGTAAGACCATGTCTGGG
1 ACATGGCATCGGCTTGATATGTGTCAGTGTAAGACCATGTCTGGG
55577689 ACATGGCATCG
1 ACATGGCATCG
55577700 ACATCGACAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (45 bp):
ACATGGCATCGGCTTGATATGTGTCAGTGTAAGACCATGTCTGGG
Found at i:55578005 original size:56 final size:56
Alignment explanation
Indices: 55577919--55578037 Score: 220
Period size: 56 Copynumber: 2.1 Consensus size: 56
55577909 TTATATGATT
55577919 AGTAAGTCTTAATACGAGCACAATTTATGTTATATGATTAGTAAGGGCAAAAAATG
1 AGTAAGTCTTAATACGAGCACAATTTATGTTATATGATTAGTAAGGGCAAAAAATG
**
55577975 AGTAAGTCTTAATACGAGCACAATTTATGTTATATGATTAGTAAGGGCTGAAAATG
1 AGTAAGTCTTAATACGAGCACAATTTATGTTATATGATTAGTAAGGGCAAAAAATG
55578031 AGTAAGT
1 AGTAAGT
55578038 TATGCTTACG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (56 bp):
AGTAAGTCTTAATACGAGCACAATTTATGTTATATGATTAGTAAGGGCAAAAAATG
Found at i:55581161 original size:31 final size:31
Alignment explanation
Indices: 55581103--55581161 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
55581093 TTCTGATAGG
**
55581103 AAAAAAGAAAAAAAAGAAAAATGGAAGACAT
1 AAAAAAGAAAAAAAAGAAAAAAAGAAGACAT
*
55581134 AAAAAGGAAATAAAAA-AAAAAAAGAAGA
1 AAAAAAGAAA-AAAAAGAAAAAAAGAAGA
55581162 GAAAATACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.79
32 5 0.21
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (31 bp):
AAAAAAGAAAAAAAAGAAAAAAAGAAGACAT
Found at i:55587442 original size:24 final size:23
Alignment explanation
Indices: 55587414--55587466 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 23
55587404 TATTTAGTAT
*
55587414 TAAATATTTTTATAATATAAAATA
1 TAAATATTTTAATAATAT-AAATA
55587438 TAAATATTTTAATAATATAAATA
1 TAAATATTTTAATAATATAAATA
55587461 TAAATA
1 TAAATA
55587467 ATGATTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATATTTTAATAATATAAATA
Found at i:55587767 original size:14 final size:15
Alignment explanation
Indices: 55587750--55587782 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
55587740 AAATTTTTTA
*
55587750 AAAAAATATTTTC-C
1 AAAAAATAATTTCTC
55587764 AAAAAATAATTTCTC
1 AAAAAATAATTTCTC
55587779 AAAA
1 AAAA
55587783 GCGTCTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAATAATTTCTC
Found at i:55591122 original size:40 final size:39
Alignment explanation
Indices: 55591077--55591206 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
55591067 CGGAATACAA
55591077 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
55591117 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * * *
55591157 CCGAATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
55591197 CCGGATATAA
1 CCGGATATAA
55591207 TTTCCAGCAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.04
40 72 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:55598420 original size:19 final size:19
Alignment explanation
Indices: 55598396--55598433 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55598386 AAATTTAAAT
*
55598396 ACATTTTTAAATTTTTATA
1 ACATTTCTAAATTTTTATA
*
55598415 ACATTTCTCAATTTTTATA
1 ACATTTCTAAATTTTTATA
55598434 TATTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.55
Consensus pattern (19 bp):
ACATTTCTAAATTTTTATA
Found at i:55598697 original size:8 final size:7
Alignment explanation
Indices: 55598681--55598737 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
55598671 AAAAGTATTT
55598681 TTTAATA
1 TTTAATA
55598688 TTTAAATA
1 TTT-AATA
55598696 TTTAATA
1 TTTAATA
55598703 TTATAAT-
1 TT-TAATA
*
55598710 TTT-ATT
1 TTTAATA
*
55598716 TTTTA-A
1 TTTAATA
55598722 TTTAA-A
1 TTTAATA
55598728 TTTAATA
1 TTTAATA
55598735 TTT
1 TTT
55598738 TATTTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
5 2 0.05
6 14 0.33
7 16 0.37
8 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:55600051 original size:45 final size:42
Alignment explanation
Indices: 55599909--55600055 Score: 105
Period size: 48 Copynumber: 3.1 Consensus size: 42
55599899 CCCAATGTGA
* *
55599909 AAAAAAAAATAGAATAGAGAAGAAGAACAAGAAAAAGAGAACGAACGG
1 AAAAAAAAA-AGAATAGAG-AGAAG-A-AA-AAGAAGAGAA-GAAAGG
* * *
55599957 AAAAAAAAAAGGAGAGAAGAGTAGTAGAATAAAGAAGACAAGTAGAAGG
1 AAAAAAAAAA-GA-A-TAGAG-AGAAGAA-AAAGAAGAGAAG-A-AAGG
55600006 AAAAAAAAAAGAATAGTAGAGAAGATAAAAGAAGAGAATGAAAGG
1 AAAAAAAAAAGAATAG-AGAGAAGA-AAAAGAAGAGAA-GAAAGG
55600051 AAAAA
1 AAAAA
55600056 CAAAGGAGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
45 9 0.11
46 18 0.22
47 7 0.09
48 23 0.28
49 16 0.20
50 8 0.10
ACGTcount: A:0.66, C:0.03, G:0.24, T:0.07
Consensus pattern (42 bp):
AAAAAAAAAAGAATAGAGAGAAGAAAAAGAAGAGAAGAAAGG
Found at i:55601688 original size:9 final size:9
Alignment explanation
Indices: 55601674--55601700 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55601664 TCACTAGAGC
55601674 GCACATTAT
1 GCACATTAT
55601683 GCACATTAT
1 GCACATTAT
55601692 GCACATTAT
1 GCACATTAT
55601701 AGGGGGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
GCACATTAT
Found at i:55603773 original size:43 final size:43
Alignment explanation
Indices: 55603725--55603807 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
55603715 TTTCATTTAA
*
55603725 TTTCTCATCTCATAATCATTTATCATATTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
* * *
55603768 TTTCTCATCTCATACTCATTTCTCATCTTTGCCATTTCAA
1 TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAA
55603808 AATCAATTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.01, T:0.49
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:55615202 original size:39 final size:40
Alignment explanation
Indices: 55615076--55615255 Score: 204
Period size: 40 Copynumber: 4.5 Consensus size: 40
55615066 ATTCGAATGT
* * *
55615076 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* *
55615117 ATCCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAA
1 ATCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
55615157 AACCGGGTTAAGTCCCGAAGGCATTT-TGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
55615196 ATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
*
55615237 A-CCGGGCTATGTCCCGAAG
1 ATCCGGGCTAAGTCCCGAAG
55615256 ACAATCGAGC
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 34 0.29
40 56 0.47
41 29 0.24
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:55615211 original size:79 final size:81
Alignment explanation
Indices: 55615078--55615255 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 81
55615068 TCGAATGTAT
* *
55615078 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
* *
55615143 GTGCGAGTTACCAAAA
66 GTGCGAATCACCAAAA
* * *
55615159 CCGGGTTAAGTCCCGAAGGCATTT-TGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTC-AATTCCCGAAGGCAAT
* *
55615221 TGTGCGAATCACTATAA
65 TGTGCGAATCACCAAAA
*
55615238 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
55615256 ACAATCGAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 1 0.01
79 59 0.69
80 3 0.04
81 22 0.26
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
GTGCGAATCACCAAAA
Found at i:55615276 original size:40 final size:40
Alignment explanation
Indices: 55615198--55615281 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
55615188 GTTACTAAAT
* * *
55615198 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
55615238 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
55615278 CCGG
1 CCGG
55615282 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:55623208 original size:40 final size:40
Alignment explanation
Indices: 55623104--55623256 Score: 173
Period size: 40 Copynumber: 3.8 Consensus size: 40
55623094 TTCGAATGAT
* * * *
55623104 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
* * *
55623145 ATCCGGGTCAATTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAA
* *
55623186 AT-CGAGTTAAGTCCCGAAGGCATTTATGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * *
55623225 ATCCGGGCTAATTCCCGAAGGCAATTGTGCGA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGA
55623257 ATCACTATAA
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 5 0.05
40 57 0.61
41 31 0.33
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:55623272 original size:40 final size:39
Alignment explanation
Indices: 55623106--55623274 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 39
55623096 CGAATGATAT
* * * *
55623106 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGCTAATTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
55623146 TCCGGG-TCAATTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 -CCGGGCT-AATTCCCGAAGGCATTTGTGCGAGTTA-CTAAA
* * * * *
55623187 TCGAGTTAAGTCCCGAAGGCATTTATGCGAGTTACTAAA
1 CCGGGCTAATTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
55623226 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 -CCGGGCTAATTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
55623267 GCGGGCTA
1 CCGGGCTA
55623275 TGTCTCAAAG
Statistics
Matches: 104, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
39 4 0.04
40 69 0.66
41 31 0.30
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (39 bp):
CCGGGCTAATTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:55633775 original size:34 final size:34
Alignment explanation
Indices: 55633728--55633837 Score: 132
Period size: 34 Copynumber: 3.2 Consensus size: 34
55633718 AGTGACAATC
* * *
55633728 CAGTTTCAGTGTGAGACTTAGCCCATAACAATAA
1 CAGTATCAATGTGAGCCTTAGCCCATAACAATAA
*
55633762 CAGTATCAATGTGAGCCTTAGCCCATAGCAATAA
1 CAGTATCAATGTGAGCCTTAGCCCATAACAATAA
* * * *
55633796 GAGTATCAATATGGGCCTTAGCCCATTACAGA-AA
1 CAGTATCAATGTGAGCCTTAGCCCATAACA-ATAA
55633830 CAGTATCA
1 CAGTATCA
55633838 GTAATGCAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
34 64 0.98
35 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (34 bp):
CAGTATCAATGTGAGCCTTAGCCCATAACAATAA
Found at i:55635451 original size:18 final size:18
Alignment explanation
Indices: 55635416--55635466 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
55635406 TAAACTATAC
*
55635416 CAAATTATACTATCATAAT
1 CAAATTAAACT-TCATAAT
55635435 CAAATTAAACTTCATAAT
1 CAAATTAAACTTCATAAT
55635453 CAAATTAAACTTCA
1 CAAATTAAACTTCA
55635467 ATCTTATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 21 0.68
19 10 0.32
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (18 bp):
CAAATTAAACTTCATAAT
Found at i:55641222 original size:40 final size:40
Alignment explanation
Indices: 55641167--55641244 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
55641157 GGAAAAAAAA
55641167 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
55641207 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
55641245 GCTACATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:55644044 original size:40 final size:40
Alignment explanation
Indices: 55643947--55644127 Score: 190
Period size: 40 Copynumber: 4.5 Consensus size: 40
55643937 CAAATTATTA
* * * *
55643947 CACACTAAGTGACAAAACATAGCCGAAGCTAT-TTTAACCTCG
1 CACACTAAGTG-CCATACATAGCCAAAGCTATCTTGAA--TCG
55643989 CACACTAAGTGCCATACATAGCCAAAGCTATCTTGAATCG
1 CACACTAAGTGCCATACATAGCCAAAGCTATCTTGAATCG
* * *
55644029 TACACTAAGTGCCATA-AGTAGCCGAAGCTATCTTAAATCG
1 CACACTAAGTGCCATACA-TAGCCAAAGCTATCTTGAATCG
* * * * *
55644069 CACACCAAGTGCCATATATAGCCAAAGCTATGTCGGATCG
1 CACACTAAGTGCCATACATAGCCAAAGCTATCTTGAATCG
55644109 CACACTAAGTG-C-TACATAG
1 CACACTAAGTGCCATACATAG
55644128 AGTTGATTTG
Statistics
Matches: 120, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.05
39 2 0.02
40 79 0.66
41 18 0.15
42 15 0.12
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCCAAAGCTATCTTGAATCG
Found at i:55644082 original size:80 final size:82
Alignment explanation
Indices: 55643947--55644120 Score: 235
Period size: 80 Copynumber: 2.1 Consensus size: 82
55643937 CAAATTATTA
* * * *
55643947 CACACTAAGTGACAAAACATAGCCGAAGCTATTTTAACCTCGCACACTAAGTGCCATACATAGCC
1 CACACTAAGTGCCAAAACATAGCCGAAGCTATCTTAACATCGCACACCAAGTGCCATACATAGCC
*
55644012 AAAGCTATCTTGAATCG
66 AAAGCTATCTCGAATCG
* * * *
55644029 TACACTAAGTGCCATAA-GTAGCCGAAGCTATCTTAA-ATCGCACACCAAGTGCCATATATAGCC
1 CACACTAAGTGCCAAAACATAGCCGAAGCTATCTTAACATCGCACACCAAGTGCCATACATAGCC
* *
55644092 AAAGCTATGTCGGATCG
66 AAAGCTATCTCGAATCG
55644109 CACACTAAGTGC
1 CACACTAAGTGC
55644121 TACATAGAGT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 49 0.61
81 17 0.21
82 14 0.17
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (82 bp):
CACACTAAGTGCCAAAACATAGCCGAAGCTATCTTAACATCGCACACCAAGTGCCATACATAGCC
AAAGCTATCTCGAATCG
Found at i:55644645 original size:21 final size:20
Alignment explanation
Indices: 55644621--55644659 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
55644611 CTTGTTTAAT
55644621 TATCAACAACCATTCAAAATC
1 TATCAACAACCA-TCAAAATC
* *
55644642 TATCATCAATCATCAAAA
1 TATCAACAACCATCAAAA
55644660 CTCAAACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (20 bp):
TATCAACAACCATCAAAATC
Found at i:55645566 original size:30 final size:30
Alignment explanation
Indices: 55645530--55645590 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
55645520 TCCAAGGAGA
55645530 CATCATTTTTGCACTCATGGTAATTGTTTT
1 CATCATTTTTGCACTCATGGTAATTGTTTT
55645560 CATCATTTTTGCACTCATGGTAATTGTTTT
1 CATCATTTTTGCACTCATGGTAATTGTTTT
55645590 C
1 C
55645591 CTTCTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (30 bp):
CATCATTTTTGCACTCATGGTAATTGTTTT
Found at i:55652007 original size:27 final size:27
Alignment explanation
Indices: 55651930--55651997 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
55651920 GCCTCTCATG
55651930 GAATAGCCATTCCATGCTACCACCAAA
1 GAATAGCCATTCCATGCTACCACCAAA
55651957 GAATAGCCATTCCATGCTACCACCAAA
1 GAATAGCCATTCCATGCTACCACCAAA
55651984 GAATAGCCATTCCA
1 GAATAGCCATTCCA
55651998 GCCTTTCACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.19
Consensus pattern (27 bp):
GAATAGCCATTCCATGCTACCACCAAA
Found at i:55654978 original size:46 final size:44
Alignment explanation
Indices: 55654886--55654979 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
55654876 ATTACAACAT
*
55654886 CATTCTATTCAACCAAACACAATAATACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
**
55654930 CATTCCATTCAACCAAACA-TTTGAATTACTGATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACAAT-AA-TACT-ATTACAGCTCTATTC
55654976 CATT
1 CATT
55654980 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.45
45 4 0.09
46 19 0.43
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAATAATACTATTACAGCTCTATTC
Found at i:55654982 original size:16 final size:16
Alignment explanation
Indices: 55654961--55655015 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
55654951 TGAATTACTG
*
55654961 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
55654977 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
55654993 ATTACAG-TCTTGTTCA
1 ATTACAGCTC-TATTCA
55655009 ATTACAG
1 ATTACAG
55655016 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 2 0.06
16 34 0.94
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:55677937 original size:29 final size:29
Alignment explanation
Indices: 55677905--55677977 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
55677895 CTTCGAGCTC
*
55677905 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55677934 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55677963 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
55677978 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:55692570 original size:28 final size:28
Alignment explanation
Indices: 55692505--55692605 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
55692495 ATGGTGAATC
*
55692505 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
55692534 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
55692562 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
55692592 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55692606 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55702292 original size:19 final size:19
Alignment explanation
Indices: 55702261--55702301 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
55702251 AATGTATACA
*
55702261 AAAATTTATTAAAAATTGT
1 AAAATTTATTAAAAATTAT
55702280 AAAATATTA-TAAAAATTAT
1 AAAAT-TTATTAAAAATTAT
55702299 AAA
1 AAA
55702302 TAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATTTATTAAAAATTAT
Found at i:55702297 original size:9 final size:9
Alignment explanation
Indices: 55702241--55702301 Score: 59
Period size: 9 Copynumber: 6.1 Consensus size: 9
55702231 TGTAACTTTT
55702241 AAATTATAA
1 AAATTATAA
55702250 AAATGTATACAA
1 AAAT-TAT--AA
55702262 AAATTTATTAA
1 AAA-TTA-TAA
*
55702273 AAATTGTAA
1 AAATTATAA
55702282 AATATTATAA
1 AA-ATTATAA
55702292 AAATTATAA
1 AAATTATAA
55702301 A
1 A
55702302 TAAAAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
9 17 0.39
10 13 0.30
11 5 0.11
12 7 0.16
13 2 0.05
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:55702939 original size:24 final size:24
Alignment explanation
Indices: 55702893--55702949 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
55702883 TTTGCTAGAA
* *
55702893 AGAAAGAAGGGAAAGTAAGAAAAT
1 AGAAAAAAGGGAAAATAAGAAAAT
55702917 AGAAAAAAGGGAAAATGAA-AAAAT
1 AGAAAAAAGGGAAAAT-AAGAAAAT
*
55702941 AAAAAAAAG
1 AGAAAAAAG
55702950 AGAGGAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (24 bp):
AGAAAAAAGGGAAAATAAGAAAAT
Found at i:55714469 original size:40 final size:39
Alignment explanation
Indices: 55714310--55714471 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
55714300 TGTGTATGAA
*
55714310 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
55714349 TGTGCGA-TTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
55714387 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
55714426 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
55714466 TGTGCG
1 TGTGCG
55714472 GGTTACCATA
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
38 37 0.33
39 59 0.52
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:55714487 original size:40 final size:40
Alignment explanation
Indices: 55714327--55714507 Score: 154
Period size: 39 Copynumber: 4.6 Consensus size: 40
55714317 ATTGTGATAT
* *** *
55714327 CCGGGCTAAG-CCCGAAGGCAATTGTGCGA-TTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* * * ** *
55714365 CCGGGCTAAG-CCCGAAGGCAATGGTGCGAGCTATGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *** *
55714404 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
55714443 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
* *
55714483 CCGGGCTATGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
55714508 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
38 28 0.22
39 52 0.42
40 45 0.36
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAA
Found at i:55722363 original size:40 final size:39
Alignment explanation
Indices: 55722203--55722365 Score: 245
Period size: 39 Copynumber: 4.2 Consensus size: 39
55722193 TGTGTATGAA
* *
55722203 TGTGCGAATTGTGATATCCAGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
55722242 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
55722281 GGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
55722320 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
55722360 TGTGCG
1 TGTGCG
55722366 GGTTACCATA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 96 0.85
40 17 0.15
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:55722381 original size:40 final size:40
Alignment explanation
Indices: 55722223--55722401 Score: 148
Period size: 39 Copynumber: 4.5 Consensus size: 40
55722213 GTGATATCCA
* * *** *
55722223 GGCTAAG-CCCGAAGGCAATTGTGCGAATTGTGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* * * ** *
55722262 GGCTAAG-CCCGAAGGCAATGGTGCGAGCTATGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *** *
55722301 GGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *
55722340 GGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
* *
55722380 GGCTATGTCCCGAAGGCGTTTG
1 GGCTAAGTCCCGAAGGCATTTG
55722402 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 77 0.63
40 45 0.37
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATAACCG
Found at i:55725469 original size:15 final size:16
Alignment explanation
Indices: 55725438--55725470 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55725428 ATGATAAACC
55725438 ATAAAAAGATTAATAAG
1 ATAAAAAGA-TAATAAG
55725455 ATAAAAAGA-AATAAG
1 ATAAAAAGATAATAAG
55725470 A
1 A
55725471 AAATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (16 bp):
ATAAAAAGATAATAAG
Found at i:55725476 original size:27 final size:26
Alignment explanation
Indices: 55725438--55725495 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
55725428 ATGATAAACC
55725438 ATAAAAAGATT-AATAAGATAAAAAGAA
1 ATAAAAAGATTAAATAA-ATAAAAA-AA
*
55725465 ATAAGAAA-ATTAAATAAATAAGAAAA
1 ATAA-AAAGATTAAATAAATAAAAAAA
55725491 ATAAA
1 ATAAA
55725496 CTAACCACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 1 0.04
26 6 0.21
27 13 0.46
28 8 0.29
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (26 bp):
ATAAAAAGATTAAATAAATAAAAAAA
Found at i:55725485 original size:17 final size:17
Alignment explanation
Indices: 55725463--55725495 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55725453 AGATAAAAAG
*
55725463 AAATAAGAAAATTAAAT
1 AAATAAGAAAAATAAAT
55725480 AAATAAGAAAAATAAA
1 AAATAAGAAAAATAAA
55725496 CTAACCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATAAGAAAAATAAAT
Found at i:55726436 original size:2 final size:2
Alignment explanation
Indices: 55726429--55726459 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55726419 GAGACTAGTC
55726429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55726460 CATGTCATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55731646 original size:29 final size:29
Alignment explanation
Indices: 55731618--55731720 Score: 143
Period size: 29 Copynumber: 3.6 Consensus size: 29
55731608 CCTCCGAGCT
** * * *
55731618 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
55731647 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
55731676 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
55731705 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
55731721 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:55733645 original size:5 final size:6
Alignment explanation
Indices: 55733633--55733657 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55733623 AAATTAGATT
55733633 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
55733658 GTGTATCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:55739851 original size:29 final size:28
Alignment explanation
Indices: 55739801--55739855 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
55739791 ATTAGGTTAA
* *
55739801 TTTATTTTAATTAGTGACCTTAATTAAAG
1 TTTATTTTAATTAATCACCTT-ATTAAAG
55739830 TTTATTTTAATTTAATCA-CTTATTAA
1 TTTATTTTAA-TTAATCACCTTATTAA
55739856 CCATTTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 13 0.57
30 5 0.22
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
TTTATTTTAATTAATCACCTTATTAAAG
Found at i:55747013 original size:29 final size:29
Alignment explanation
Indices: 55746977--55747139 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
55746967 AATAAACGAT
***
55746977 CTCGCACACTTAGTGCCATGCGATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
55747006 CTCGCACACATAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* *
55747035 TTTGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
*
55747064 TTCGCACACTTAGTGCCATATAATTTAAG
1 CTCGCACACTTAGTGCCATATAATTTAAG
* ** *
55747093 TTCGCACACTTAGTGCCATA-CCTTCCAAG
1 CTCGCACACTTAGTGCCATATAATT-TAAG
*
55747122 CCCGCACACTTAGTGCCA
1 CTCGCACACTTAGTGCCA
55747140 ATCTTGTCAC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
28 2 0.02
29 118 0.98
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CTCGCACACTTAGTGCCATATAATTTAAG
Found at i:55750527 original size:46 final size:46
Alignment explanation
Indices: 55750472--55750652 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
55750462 TAGGATGGTT
55750472 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
55750518 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
55750564 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
55750611 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55750653 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:55750633 original size:93 final size:93
Alignment explanation
Indices: 55750474--55750644 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
55750464 GGATGGTTGA
* *
55750474 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55750539 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
55750567 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55750632 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55750645 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55753656 original size:15 final size:15
Alignment explanation
Indices: 55753617--55753696 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
55753607 GTATCTTGGG
*
55753617 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
55753632 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
55753647 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
55753662 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
55753677 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
55753691 TTTCTT
1 TTTCTT
55753697 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:55753686 original size:30 final size:30
Alignment explanation
Indices: 55753608--55753695 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
55753598 CATAGTATCG
* * *
55753608 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
55753638 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
55753668 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
55753696 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:55757416 original size:40 final size:40
Alignment explanation
Indices: 55757361--55757570 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
55757351 AACATTGGAA
55757361 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
55757401 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
55757441 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
55757481 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
55757520 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
55757561 CTATATCCGG
1 ATATATCCGG
55757571 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:55765552 original size:40 final size:40
Alignment explanation
Indices: 55765497--55765706 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
55765487 AACATTGGAA
55765497 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
55765537 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
55765577 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
55765617 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
55765656 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
55765697 CTATATCCGG
1 ATATATCCGG
55765707 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:55767588 original size:46 final size:46
Alignment explanation
Indices: 55767533--55767713 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
55767523 TAGGATGGTT
55767533 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
55767579 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
55767625 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
55767672 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55767714 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:55767694 original size:93 final size:93
Alignment explanation
Indices: 55767535--55767705 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
55767525 GGATGGTTGA
* *
55767535 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55767600 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
55767628 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
55767693 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55767706 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:55769743 original size:20 final size:20
Alignment explanation
Indices: 55769718--55769758 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55769708 TGTTCGGAAT
55769718 ACCTTTTGGATAAGATAGTA
1 ACCTTTTGGATAAGATAGTA
*
55769738 ACCTTTTGGATATGATAGTA
1 ACCTTTTGGATAAGATAGTA
55769758 A
1 A
55769759 AATTTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
ACCTTTTGGATAAGATAGTA
Found at i:55769764 original size:20 final size:20
Alignment explanation
Indices: 55769721--55769764 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55769711 TCGGAATACC
**
55769721 TTTTGGATAAGATAGTAACC
1 TTTTGGATAAGATAGTAAAA
*
55769741 TTTTGGATATGATAGTAAAA
1 TTTTGGATAAGATAGTAAAA
55769761 TTTT
1 TTTT
55769765 TTGAGCTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (20 bp):
TTTTGGATAAGATAGTAAAA
Found at i:55774560 original size:16 final size:15
Alignment explanation
Indices: 55774535--55774564 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
55774525 TGGTTGAAAT
55774535 TTTAATTTTTTATAG
1 TTTAATTTTTTATAG
55774550 TTTATATTTTTTATA
1 TTTA-ATTTTTTATA
55774565 ATTTGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTAATTTTTTATAG
Found at i:55778758 original size:31 final size:31
Alignment explanation
Indices: 55778723--55778781 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
55778713 CACGTCCATG
55778723 TGGGCAGG-CTGTGTGGTCACACACGCCCGTA
1 TGGGCAGGTC-GTGTGGTCACACACGCCCGTA
55778754 TGGGCAGGTCGTGTGGTCACACACGCCC
1 TGGGCAGGTCGTGTGGTCACACACGCCC
55778782 ATGTCCCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.19
Consensus pattern (31 bp):
TGGGCAGGTCGTGTGGTCACACACGCCCGTA
Found at i:55780745 original size:47 final size:47
Alignment explanation
Indices: 55780682--55781215 Score: 881
Period size: 47 Copynumber: 11.4 Consensus size: 47
55780672 CCCTTCGGGA
* *
55780682 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
55780729 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
55780776 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55780823 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
55780870 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55780917 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55780964 CTTATCACATATACACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
55781011 CTTATCACATATATACACTTTCACATTCATCACA-TGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55781057 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
55781104 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
55781151 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
55781198 CTTATCACATATACACAC
1 CTTATCACATATATACAC
55781216 CTTGTACATC
Statistics
Matches: 453, Mismatches: 33, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
46 45 0.10
47 408 0.90
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:55784003 original size:29 final size:28
Alignment explanation
Indices: 55783971--55784042 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
55783961 TTCAAGCCCA
* *
55783971 CACACATAGTGCCATATAGTCCAAACTCG
1 CACAC-TAGTGCCATACAGTACAAACTCG
* *
55784000 CACACTTAGTGCCATACATTACAAGCTCG
1 CACAC-TAGTGCCATACAGTACAAACTCG
55784029 CACACTCAGTGCCA
1 CACACT-AGTGCCA
55784043 ATCTCGTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 36 0.97
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (28 bp):
CACACTAGTGCCATACAGTACAAACTCG
Found at i:55791266 original size:43 final size:43
Alignment explanation
Indices: 55791217--55791304 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
55791207 GAATCAAATA
* * * *
55791217 CGATGCCGATGTCCC-AATCATGGTCTTACACGTAACCACATAT
1 CGATGCCAACGTCCCTAAT-ATGGTCTTACACGAAAACACATAT
* *
55791260 CGATGCCAACGTCCCTGATGTGGTCTTACACGAAAACACATAT
1 CGATGCCAACGTCCCTAATATGGTCTTACACGAAAACACATAT
55791303 CG
1 CG
55791305 GATCCTATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 36 0.95
44 2 0.05
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
CGATGCCAACGTCCCTAATATGGTCTTACACGAAAACACATAT
Found at i:55791960 original size:24 final size:25
Alignment explanation
Indices: 55791928--55791998 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
55791918 ACTAACATTA
*
55791928 CATAGCTC-AAATATTCATCAATGG
1 CATAACTCAAAATATTCATCAATGG
*
55791952 CATAACTCAAAATAGTCATCAATGG
1 CATAACTCAAAATATTCATCAATGG
* * *
55791977 CAAAAATCAAAATGTTCATCAA
1 CATAACTCAAAATATTCATCAA
55791999 AATAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 7 0.17
25 33 0.82
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (25 bp):
CATAACTCAAAATATTCATCAATGG
Found at i:55793520 original size:15 final size:16
Alignment explanation
Indices: 55793491--55793520 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55793481 TAAACATGCT
55793491 TTAACACATTATCAAA
1 TTAACACATTATCAAA
55793507 TTAACACA-TATCAA
1 TTAACACATTATCAA
55793521 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:55802096 original size:43 final size:43
Alignment explanation
Indices: 55801980--55802097 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 43
55801970 GATTTGAGAT
* * * * *
55801980 TTACATGTAAGATCAT-GTCTGGGACATCGGTATCATATTTAA
1 TTACATGTAAGACCCTCGTCTGGGACGTTGGCATCATATTTAA
* * *
55802022 TTTCGTGTAAGACCCTC-TCTGAGACAG-TGGCATCGATATTTAA
1 TTACATGTAAGACCCTCGTCTGGGAC-GTTGGCATC-ATATTTAA
*
55802065 TTACATGTAAGA-CCTCGTTTGGGACGTTGGCAT
1 TTACATGTAAGACCCTCGTCTGGGACGTTGGCAT
55802098 TATACGAGCT
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
42 29 0.49
43 30 0.51
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (43 bp):
TTACATGTAAGACCCTCGTCTGGGACGTTGGCATCATATTTAA
Found at i:55805623 original size:28 final size:28
Alignment explanation
Indices: 55805592--55805654 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
55805582 TTGATATTTT
55805592 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
55805620 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
55805648 GTACACT
1 GCACACT
55805655 GAGTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:55811804 original size:20 final size:20
Alignment explanation
Indices: 55811779--55811816 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55811769 ACAACTGTAT
*
55811779 GCCAAATTTAGTAAGGGTAA
1 GCCAAATTTAGCAAGGGTAA
55811799 GCCAAATTTAGCAAGGGT
1 GCCAAATTTAGCAAGGGT
55811817 GAATTCTGGT
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:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (20 bp):
GCCAAATTTAGCAAGGGTAA
Found at i:55818858 original size:80 final size:81
Alignment explanation
Indices: 55818759--55818937 Score: 227
Period size: 80 Copynumber: 2.2 Consensus size: 81
55818749 GCTCGATTGT
* * * *
55818759 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTCGAGAATTAGA-CCGGATTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGAATT-GACCCGGATTTAG
* * *
55818823 TAAC-TCGCATAAATGC
65 TAACTTAGCACAAAAGC
* * * *
55818839 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGAATTGACCCGGATTTAGT
*
55818904 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
55818920 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
55818938 ATATCATTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 56 0.67
81 26 0.31
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (81 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGAATTGACCCGGATTTAGT
AACTTAGCACAAAAGC
Found at i:55818937 original size:41 final size:40
Alignment explanation
Indices: 55818759--55818939 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
55818749 GCTCGATTGT
* * * *
55818759 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGC
* * * *
55818799 CTTCGAGAATTAGACCGGATTTAGTAACTCGCATAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
55818839 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* * * *
55818879 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
55818920 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACTTAGCCCGGAT
55818940 ATCATTCGAA
Statistics
Matches: 114, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
40 84 0.74
41 29 0.25
42 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:55819654 original size:2 final size:2
Alignment explanation
Indices: 55819647--55819688 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
55819637 ATGTGCAAAC
55819647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55819689 GCTAGAGCCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55822830 original size:33 final size:33
Alignment explanation
Indices: 55822788--55822857 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
55822778 AAACACTAAC
* *
55822788 ACAT-AACCTAAAATTAAGTAGTTGCCTTTCTT
1 ACATAAACCTAAAATCAAGAAGTTGCCTTTCTT
* *
55822820 ACATAAACCTAGAATCAAGAAGTTTCCTTTCTT
1 ACATAAACCTAAAATCAAGAAGTTGCCTTTCTT
55822853 ACATA
1 ACATA
55822858 TAATTCTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (33 bp):
ACATAAACCTAAAATCAAGAAGTTGCCTTTCTT
Found at i:55837850 original size:9 final size:9
Alignment explanation
Indices: 55837836--55837860 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55837826 TGGATTATTT
55837836 TGAATGAAA
1 TGAATGAAA
55837845 TGAATGAAA
1 TGAATGAAA
55837854 TGAATGA
1 TGAATGA
55837861 TTGAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (9 bp):
TGAATGAAA
Found at i:55838310 original size:43 final size:42
Alignment explanation
Indices: 55838193--55838310 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
55838183 GATTTGAGAT
* * *
55838193 TTACATGTAAGACCATGTCTGAGACATCGACATCGTATCTAA
1 TTACATGTAAGACCATGTCTGGGACGTCGGCATCGTATCTAA
* * * * *
55838235 TTTCGTGTAAGACCTTGTCTAGGACAG-AGGCATCG-ATACTAAA
1 TTACATGTAAGACCATGTCTGGGAC-GTCGGCATCGTAT-CT-AA
*
55838278 TTACATGTAAGACCACGTCTGGGACGTCGGCAT
1 TTACATGTAAGACCATGTCTGGGACGTCGGCAT
55838311 TGTACTTGTC
Statistics
Matches: 58, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
41 2 0.03
42 29 0.50
43 27 0.47
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACGTCGGCATCGTATCTAA
Found at i:55846539 original size:40 final size:40
Alignment explanation
Indices: 55846432--55846599 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
55846422 CGGGATTTAA
* * * * *
55846432 CCGGATACAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * * * *
55846472 CCGGATTTGGTAATTTGCACCATTGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* *
55846512 CCGGATATAA-CAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
55846552 CCGGACATAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55846592 CCGGATAT
1 CCGGATAT
55846600 CATTCAAATG
Statistics
Matches: 101, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 100 0.99
41 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55854457 original size:40 final size:40
Alignment explanation
Indices: 55854408--55854559 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
55854398 ACAACCACAA
* * *** *
55854408 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
*
55854448 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
* *
55854488 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC
* * *
55854528 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
55854560 CATTCAAATG
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 2 0.02
40 92 0.96
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
Found at i:55857586 original size:47 final size:47
Alignment explanation
Indices: 55857476--55857596 Score: 140
Period size: 47 Copynumber: 2.6 Consensus size: 47
55857466 TTACTTGTGT
* * *
55857476 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCATATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGACATATGACGAGA
* * *
55857522 GCGAGTGTAAGACCATGTCTAGGACATGGTATC-GACAT-TGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGACATAT--GACGAGA
55857570 GCTAGTGTAAGACATGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
55857597 CGTCGGCCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
46 12 0.19
47 31 0.49
48 20 0.32
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGGACATATGACGAGA
Found at i:55861781 original size:26 final size:26
Alignment explanation
Indices: 55861752--55861853 Score: 91
Period size: 26 Copynumber: 3.9 Consensus size: 26
55861742 CCAACACACC
55861752 AATATCACAAAAAAGCTGCCAGTAAT
1 AATATCACAAAAAAGCTGCCAGTAAT
** *
55861778 AATATCACAGCAAAGCTACCAGT-AT
1 AATATCACAAAAAAGCTGCCAGTAAT
* * ** *
55861803 CAATAACGCAGCAAAGCTGCCAGTAAC
1 -AATATCACAAAAAAGCTGCCAGTAAT
*
55861830 AATATCGCAACAAAA-CTGCCAGTA
1 AATATCACAA-AAAAGCTGCCAGTA
55861854 TTAGTATATG
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
25 2 0.03
26 57 0.90
27 4 0.06
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.17
Consensus pattern (26 bp):
AATATCACAAAAAAGCTGCCAGTAAT
Found at i:55863363 original size:27 final size:28
Alignment explanation
Indices: 55863333--55863402 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
55863323 ATAGTGAATC
*
55863333 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
55863360 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
55863388 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55863403 GTACAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:55863474 original size:42 final size:42
Alignment explanation
Indices: 55863410--55863515 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
55863400 GCTGTACAAT
* *
55863410 TTTAAACCCGCACACGTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
55863452 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
1 TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
55863494 TTTATA-CCGCACACTTAGTGCC
1 TTTATACCCGCACACTTAGTGCC
55863516 GAGACCAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 16 0.26
42 46 0.74
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (42 bp):
TTTATACCCGCACACTTAGTGCCAATCTTGTCACCGTGTCCA
Found at i:55865548 original size:8 final size:8
Alignment explanation
Indices: 55865537--55865565 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55865527 AAAAGGCCAT
55865537 CTTTTCAG
1 CTTTTCAG
55865545 CTTTTCAG
1 CTTTTCAG
55865553 CTTTTCAG
1 CTTTTCAG
55865561 CTTTT
1 CTTTT
55865566 GCCGATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.24, G:0.10, T:0.55
Consensus pattern (8 bp):
CTTTTCAG
Found at i:55869272 original size:40 final size:40
Alignment explanation
Indices: 55869213--55869354 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
55869203 AAATTGAATG
* * *
55869213 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
55869253 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
55869293 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
55869333 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
55869355 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:55869378 original size:40 final size:40
Alignment explanation
Indices: 55869251--55869380 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
55869241 ATGCTGGAAA
* * *
55869251 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * **
55869291 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
55869331 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
55869371 TTATATCCGG
1 TTATATCCGG
55869381 TTATATTCCG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 74 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:55875879 original size:40 final size:40
Alignment explanation
Indices: 55875842--55876037 Score: 272
Period size: 40 Copynumber: 4.9 Consensus size: 40
55875832 GGATATAGCT
* *
55875842 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
55875882 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* *
55875922 ACTTGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* *
55875962 ACTCGCACAAATGCCTTCGGGACTTAGCCCAG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
55876002 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
55876038 CATCCGAATA
Statistics
Matches: 140, Mismatches: 12, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
40 137 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:55875941 original size:80 final size:80
Alignment explanation
Indices: 55875842--55876037 Score: 304
Period size: 80 Copynumber: 2.5 Consensus size: 80
55875832 GGATATAGCT
* * *
55875842 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
* * *
55875907 AGCCCGGATTTGGTA
66 AGCCCAGAATTAGTA
* *
55875922 ACTTGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGACT
55875986 TAGCCCAGAATTAGTA
65 TAGCCCAGAATTAGTA
55876002 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
55876038 CATCCGAATA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 102 0.98
81 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCAGAATTAGTA
Found at i:55877124 original size:18 final size:19
Alignment explanation
Indices: 55877101--55877139 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
55877091 GTAAGGGAAT
55877101 AAAGAAATG-GAAAAAAAA
1 AAAGAAATGAGAAAAAAAA
55877119 AAAGAAATGATGAAAAAAAA
1 AAAGAAATGA-GAAAAAAAA
55877139 A
1 A
55877140 TGGTGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAGAAATGAGAAAAAAAA
Found at i:55878508 original size:28 final size:29
Alignment explanation
Indices: 55878468--55878539 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
55878458 AAAATTGTAC
*
55878468 AGCACTAAGTGTGCGAGTTTG-AT-TATAT
1 AGCACTAAGTGTGCGAG-CTGAATGTATAT
55878496 AGCACTAAGTGTGCGAGCTGAATGTATAT
1 AGCACTAAGTGTGCGAGCTGAATGTATAT
55878525 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55878540 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAATGTATAT
Found at i:55884958 original size:19 final size:21
Alignment explanation
Indices: 55884934--55884974 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
55884924 AAGGGAGAAT
55884934 AAAG-AAATG-GAAAAAAAAA
1 AAAGAAAATGAGAAAAAAAAA
55884953 AAAGAAAATGATGAAAAAAAAA
1 AAAGAAAATGA-GAAAAAAAAA
55884975 TGGGTGTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
22 10 0.53
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (21 bp):
AAAGAAAATGAGAAAAAAAAA
Found at i:55886348 original size:28 final size:28
Alignment explanation
Indices: 55886279--55886379 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
55886269 GACAAGATTG
* * * *
55886279 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
55886309 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55886337 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
55886366 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55886380 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55886373 original size:29 final size:28
Alignment explanation
Indices: 55886308--55886379 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
55886298 AAAATTGTAC
*
55886308 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
55886336 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
55886365 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55886380 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:55893934 original size:28 final size:29
Alignment explanation
Indices: 55893902--55894000 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 29
55893892 ATAATAAGCC
*
55893902 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* *
55893930 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
* * *
55893958 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
55893987 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55894001 CAATCTCATG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
27 2 0.03
28 37 0.61
29 19 0.31
30 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:55901984 original size:28 final size:28
Alignment explanation
Indices: 55901913--55901986 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
55901903 ATAATAAGCC
* *
55901913 CGCACACTTAGTGCT-TAATAGTCGAACT
1 CGCACACTTAGTGCTAT-ATAATCAAACT
55901941 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
55901969 CGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
55901987 CAATTTGATC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:55907829 original size:27 final size:28
Alignment explanation
Indices: 55907772--55907839 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 28
55907762 AAATTTGTAC
*
55907772 AGCACTAAGTGTGCGAGTTTGATTATTT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55907800 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
55907827 AGCACTAAGTGTG
1 AGCACTAAGTGTG
55907840 AGGACTCACT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:55913147 original size:2 final size:2
Alignment explanation
Indices: 55913142--55913170 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55913132 GAAACTAGGA
55913142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55913171 ATCATTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55919844 original size:19 final size:20
Alignment explanation
Indices: 55919820--55919858 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55919810 ATTAATAAGC
55919820 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
55919839 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
55919859 TTACACGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:55923535 original size:48 final size:48
Alignment explanation
Indices: 55923418--55923742 Score: 380
Period size: 48 Copynumber: 6.7 Consensus size: 48
55923408 GTAAAATGTA
* *
55923418 GATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATACATCAGTGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-A-CAATGCC
* * * *
55923468 GATGCCATGTCCCAGACATGGTTTTACGCTGGCTCACATAACAATGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
* * *** *
55923516 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
* * * * *
55923564 GATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATAGTGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
* ** * *** *
55923612 GATGCCATGTTCTGAACATGGTCTTACACTGGCTCGCATATTGAGGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
** *
55923660 GATGCCATGTCCCTGACATGGTCTTACACTAGCTCTCATAACAATGCC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
55923708 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC
55923743 ACACATAACC
Statistics
Matches: 229, Mismatches: 46, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
48 193 0.84
49 1 0.00
50 35 0.15
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAACAATGCC
Found at i:55923612 original size:96 final size:96
Alignment explanation
Indices: 55923418--55923742 Score: 481
Period size: 96 Copynumber: 3.4 Consensus size: 96
55923408 GTAAAATGTA
* * * * *
55923418 GATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATACATCAGTGCCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCATA-TTGAG-GCCGATGCCATGTCCTAG
* * * *
55923483 ACATGGTTTTACGCTGGCTCACATAACAATGCC
64 ACATGGTCTTACACTAGCTCTCATAACAATGCC
*
55923516 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGTCCTAGAC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGTCCTAGAC
* *
55923581 ATGGTCTTACACTAGCTCTCATAATAGTGCC
66 ATGGTCTTACACTAGCTCTCATAACAATGCC
* **
55923612 GATGCCATGTTCTGAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGTCCCT-GA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGT-CCTAGA
55923676 CATGGTCTTACACTAGCTCTCATAACAATGCC
65 CATGGTCTTACACTAGCTCTCATAACAATGCC
55923708 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTC
55923743 ACACATAACC
Statistics
Matches: 207, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
96 164 0.79
97 6 0.03
98 37 0.18
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (96 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGTCCTAGAC
ATGGTCTTACACTAGCTCTCATAACAATGCC
Found at i:55925255 original size:31 final size:31
Alignment explanation
Indices: 55925217--55925279 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
55925207 ATGTTACAGG
*
55925217 ATAGTTTATGATTGTTTTGCATGATAATTGT
1 ATAGTTTATGATTGTTTTGCACGATAATTGT
55925248 ATAGTTTATGATTGTTTTGCACGATAATTGT
1 ATAGTTTATGATTGTTTTGCACGATAATTGT
55925279 A
1 A
55925280 AAATGACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (31 bp):
ATAGTTTATGATTGTTTTGCACGATAATTGT
Found at i:55928262 original size:70 final size:67
Alignment explanation
Indices: 55928183--55928310 Score: 202
Period size: 70 Copynumber: 1.9 Consensus size: 67
55928173 TTTAACAAAA
*
55928183 TTTTTTCTCTCATTTTCTCACTTGCCAAACACCACTTTTTTTTTCTTCAAAACACATGGTTGTTG
1 TTTTTTCTCTCATTTTCTCACTTGCCAAACACCA--TTTTTCTTCTTC-AAACACATGGTTGTTG
55928248 CCATT
63 CCATT
* *
55928253 TTTTTTCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAACATATGGTT
1 TTTTTTCTCTCATTTTCTCACTTGCCAAACACCATTTTTCTTCTTCAAACACATGGTT
55928311 AGCTCATTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
67 11 0.20
68 11 0.20
70 33 0.60
ACGTcount: A:0.20, C:0.26, G:0.06, T:0.48
Consensus pattern (67 bp):
TTTTTTCTCTCATTTTCTCACTTGCCAAACACCATTTTTCTTCTTCAAACACATGGTTGTTGCCA
TT
Done.