Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 131 of 362
Found at i:43379814 original size:44 final size:44
Alignment explanation
Indices: 43379764--43379847 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
43379754 CAATACTCAT
43379764 ACACCAATCATCACATACTTGAATTTATCAGATTCACTACTTAG
1 ACACCAATCATCACATACTTGAATTTATCAGATTCACTACTTAG
*
43379808 ACACCAATCATCATATACTTGAATTTATCAGATTCACTAC
1 ACACCAATCATCACATACTTGAATTTATCAGATTCACTAC
43379848 CAATATACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (44 bp):
ACACCAATCATCACATACTTGAATTTATCAGATTCACTACTTAG
Found at i:43383142 original size:20 final size:20
Alignment explanation
Indices: 43383103--43383143 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43383093 AAACAGTAGC
**
43383103 TCATCCATATAAACTGTATT
1 TCATCCATATAAACAATATT
43383123 TCATCCATATAAACAATATT
1 TCATCCATATAAACAATATT
43383143 T
1 T
43383144 ATGCTCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (20 bp):
TCATCCATATAAACAATATT
Found at i:43383295 original size:25 final size:25
Alignment explanation
Indices: 43383241--43383298 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
43383231 TTCCACTTTT
* *
43383241 TTGAGCTATGAACAGTAAGTTCCTC
1 TTGAGCTATGAACAGTAAGCTCCTA
* *
43383266 CTGAGCTGATGGACAGTAAGCT-CTA
1 TTGAGCT-ATGAACAGTAAGCTCCTA
43383291 TTGAGCTA
1 TTGAGCTA
43383299 AAATGGTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.04
25 14 0.52
26 12 0.44
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (25 bp):
TTGAGCTATGAACAGTAAGCTCCTA
Found at i:43383331 original size:24 final size:24
Alignment explanation
Indices: 43383280--43383393 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
43383270 GCTGATGGAC
43383280 AGTAAGCTC-TATTGAGCT-AAAAT
1 AGTAAGCTCTTA-TGAGCTGAAAAT
* * * *
43383303 GGTAAGCTCTGACGAGCTGAAAAC
1 AGTAAGCTCTTATGAGCTGAAAAT
*
43383327 AGTAAGCTTTTATGAGCTG-AAAT
1 AGTAAGCTCTTATGAGCTGAAAAT
**
43383350 AGTAAGCTCCAATGAGCTGAAAAT
1 AGTAAGCTCTTATGAGCTGAAAAT
43383374 AGTAAGCTCTTATGAGCTGA
1 AGTAAGCTCTTATGAGCTGA
43383394 TATATCAGCA
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
23 32 0.43
24 42 0.57
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (24 bp):
AGTAAGCTCTTATGAGCTGAAAAT
Found at i:43383392 original size:47 final size:47
Alignment explanation
Indices: 43383278--43383393 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 47
43383268 GAGCTGATGG
* * **
43383278 ACAGTAAGCTC-TATTGAGCTAAAATGGTAAGCTCTGACGAGCTGAAA
1 ACAGTAAGCTCTTA-TGAGCTGAAATAGTAAGCTCCAACGAGCTGAAA
* *
43383325 ACAGTAAGCTTTTATGAGCTGAAATAGTAAGCTCCAATGAGCTGAAA
1 ACAGTAAGCTCTTATGAGCTGAAATAGTAAGCTCCAACGAGCTGAAA
*
43383372 ATAGTAAGCTCTTATGAGCTGA
1 ACAGTAAGCTCTTATGAGCTGA
43383394 TATATCAGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 58 0.97
48 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (47 bp):
ACAGTAAGCTCTTATGAGCTGAAATAGTAAGCTCCAACGAGCTGAAA
Found at i:43384590 original size:8 final size:8
Alignment explanation
Indices: 43384577--43384603 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
43384567 CTGTAAACTT
43384577 TAATAAAA
1 TAATAAAA
43384585 TAATAAAA
1 TAATAAAA
43384593 TAATAAAA
1 TAATAAAA
43384601 TAA
1 TAA
43384604 ATATTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:43393964 original size:11 final size:11
Alignment explanation
Indices: 43393950--43393974 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43393940 TCCCATAAAC
43393950 AATAAAATAAT
1 AATAAAATAAT
43393961 AATAAAATAAT
1 AATAAAATAAT
43393972 AAT
1 AAT
43393975 TTACTCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:43395960 original size:20 final size:19
Alignment explanation
Indices: 43395923--43395966 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
43395913 TATTAATGAA
*
43395923 TTTG-TGATGATTTTTAAG
1 TTTGATGATGATTTATAAG
43395941 TTTGATGATAGATTTATAAG
1 TTTGATGAT-GATTTATAAG
43395961 TTTGAT
1 TTTGAT
43395967 AGTTAAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52
Consensus pattern (19 bp):
TTTGATGATGATTTATAAG
Found at i:43396904 original size:22 final size:22
Alignment explanation
Indices: 43396836--43396904 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
43396826 ATTATGATTC
43396836 AAATGAATAAGACCATAGTTG-
1 AAATGAATAAGACCATAGTTGA
* *
43396857 AAA-GACACTATGACATCCTA-TTGA
1 AAATGA-A-TAAGAC--CATAGTTGA
43396881 AAATGAATAAGACCATAGTTGA
1 AAATGAATAAGACCATAGTTGA
43396903 AA
1 AA
43396905 GACACTATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
20 2 0.05
21 7 0.19
22 11 0.30
23 8 0.22
24 7 0.19
25 2 0.05
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (22 bp):
AAATGAATAAGACCATAGTTGA
Found at i:43396952 original size:46 final size:45
Alignment explanation
Indices: 43396753--43397055 Score: 290
Period size: 45 Copynumber: 6.7 Consensus size: 45
43396743 TGAAGACAAG
* * * * * *
43396753 TAAGACCATAGCTGAAAGA-AGCTATGGAATTATTATTCAGA-TGAG
1 TAAGACCATAGTTGAAAGACA-CTATGGCATCA-TATTGAAAGTGAA
* * * * *
43396798 TAAGACCTTAGTTGGAAGACGCTATGGCATTATGATTCAAA-TGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCAT-ATTGAAAGTGAA
* * *
43396843 TAAGACCATAGTTGAAAGACACTATGACATCCTATTGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATTGAAAGTGAA
43396888 TAAGACCATAGTTGAAAGACACTATGGCATCATATTAGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATATT-GAAAGTGAA
* * * * * *
43396934 TAAGACCATAGTTTAAAGACACTATGGCGTTATATCAGATAGTAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATAT-TGAAAGTGAA
* * * *
43396980 TAAGACCGTGGTTG-AAGACGCTATGGCATCATATCGGAAAGTGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCATAT-TGAAAGTGAA
* *
43397025 TAAGACCATGGTTGAAAGACACCATGGCATC
1 TAAGACCATAGTTGAAAGACACTATGGCATC
43397056 CTTCAATCAT
Statistics
Matches: 217, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
44 7 0.03
45 138 0.64
46 72 0.33
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCATATTGAAAGTGAA
Found at i:43396958 original size:91 final size:90
Alignment explanation
Indices: 43396793--43397057 Score: 300
Period size: 91 Copynumber: 2.9 Consensus size: 90
43396783 TATTATTCAG
* * * *
43396793 ATGAGTAAGACCTTAGTTGGAAGACGCTATGGCATTATGATTCAAA-TGAATAAGACCATAGTTG
1 ATGAATAAGACCATAGTT-GAAGACGCTATGGCATCAT-ATTGAAAGTGAATAAGACCATAGTTG
* *
43396857 AAAGACACTATGACATCCTAT-TGAAA
64 AAAGACACTATGGCATCCTATCAGAAA
* *
43396883 ATGAATAAGACCATAGTTGAAAGACACTATGGCATCATATTAGAAAGTGAATAAGACCATAGTTT
1 ATGAATAAGACCATAGTTG-AAGACGCTATGGCATCATATT-GAAAGTGAATAAGACCATAGTTG
* ** *
43396948 AAAGACACTATGGCGTTATATCAGATA
64 AAAGACACTATGGCATCCTATCAGAAA
* * * * * *
43396975 GTAAATAAGACCGTGGTTGAAGACGCTATGGCATCATATCGGAAAGTGAATAAGACCATGGTTGA
1 ATGAATAAGACCATAGTTGAAGACGCTATGGCATCATAT-TGAAAGTGAATAAGACCATAGTTGA
*
43397040 AAGACACCATGGCATCCT
65 AAGACACTATGGCATCCT
43397058 TCAATCATTG
Statistics
Matches: 146, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
89 4 0.03
90 35 0.24
91 89 0.61
92 18 0.12
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (90 bp):
ATGAATAAGACCATAGTTGAAGACGCTATGGCATCATATTGAAAGTGAATAAGACCATAGTTGAA
AGACACTATGGCATCCTATCAGAAA
Found at i:43400962 original size:12 final size:12
Alignment explanation
Indices: 43400947--43400976 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43400937 AATAATTAAA
43400947 TAAATTAGAAAT
1 TAAATTAGAAAT
*
43400959 TAAATTGGAAAT
1 TAAATTAGAAAT
43400971 TAAATT
1 TAAATT
43400977 CAGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:43403141 original size:47 final size:47
Alignment explanation
Indices: 43403070--43403568 Score: 827
Period size: 47 Copynumber: 10.6 Consensus size: 47
43403060 CCCTTCGGGA
* * * * * *
43403070 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43403117 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
43403164 CTTATCACATATATACACTTTCACATTCATCACATCGGTGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43403211 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43403258 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43403305 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43403352 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43403399 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43403446 CTTATCACATATATATACACTTTCACATTCAGCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43403495 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43403542 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43403569 TATTCAAATA
Statistics
Matches: 426, Mismatches: 24, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 383 0.90
49 43 0.10
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43403148 original size:25 final size:25
Alignment explanation
Indices: 43403120--43403198 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
43403110 ACTCGGCCCT
43403120 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
43403145 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
43403167 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
43403192 ATCACAT
1 ATCACAT
43403199 CGGTGATTAG
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:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:43409034 original size:10 final size:12
Alignment explanation
Indices: 43409004--43409037 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43408994 TTATGTATGT
43409004 TGTGAATATATA
1 TGTGAATATATA
43409016 TGTGAATATATA
1 TGTGAATATATA
43409028 T-TG-ATATATA
1 TGTGAATATATA
43409038 GTTGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 2 0.09
12 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (12 bp):
TGTGAATATATA
Found at i:43410219 original size:26 final size:25
Alignment explanation
Indices: 43410190--43410262 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
43410180 TCTCATCACT
43410190 ATTTTATCCCTAGTAAAATTTTGACG
1 ATTTTA-CCCTAGTAAAATTTTGACG
* *
43410216 ATTTTACCCCA-TAAAAAGTTTTGGCG
1 ATTTTACCCTAGT-AAAA-TTTTGACG
43410242 ATTTTACCTCTAGTAAAATTT
1 ATTTTACC-CTAGTAAAATTT
43410263 AGAGAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 1 0.03
25 8 0.20
26 24 0.60
27 6 0.15
28 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (25 bp):
ATTTTACCCTAGTAAAATTTTGACG
Found at i:43410421 original size:6 final size:6
Alignment explanation
Indices: 43410411--43410446 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
43410401 GCAAATGAAT
*
43410411 CATTTT CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
43410447 GGAAACCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:43429582 original size:19 final size:19
Alignment explanation
Indices: 43429560--43429596 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43429550 AAGCAATTTA
43429560 ATGTTATTTAT-ATGAAATG
1 ATGTTA-TTATCATGAAATG
43429579 ATGTTATTATCATGAAAT
1 ATGTTATTATCATGAAAT
43429597 ATTATGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (19 bp):
ATGTTATTATCATGAAATG
Found at i:43433167 original size:14 final size:14
Alignment explanation
Indices: 43433142--43433178 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
43433132 CAGAAGTAAA
43433142 CAAATA-AAAAATT
1 CAAATATAAAAATT
43433155 CAAATATAAAAATT
1 CAAATATAAAAATT
43433169 -AAAT-TAAAAA
1 CAAATATAAAAA
43433179 AATATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 10 0.43
14 7 0.30
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (14 bp):
CAAATATAAAAATT
Found at i:43433181 original size:22 final size:21
Alignment explanation
Indices: 43433156--43433199 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
43433146 TAAAAAATTC
43433156 AAATATAAAAATTAAATTAAAA
1 AAATATAAAAATTAAA-TAAAA
*
43433178 AAATATTAAAATTAAATAAAA
1 AAATATAAAAATTAAATAAAA
43433199 A
1 A
43433200 TGGCTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATATAAAAATTAAATAAAA
Found at i:43439471 original size:224 final size:224
Alignment explanation
Indices: 43439081--43439511 Score: 790
Period size: 224 Copynumber: 1.9 Consensus size: 224
43439071 ACAAAGCACT
43439081 GTTCATATAGGGCTCGCATATCTCTATTCATAAAAACACACATATAATCACAAAACAGAGTTTAG
1 GTTCATATAGGGCTCGCATATCTCTATTCATAAAAACACACATATAATCACAAAACAGAGTTTAG
*
43439146 AAAAGACTTACTCTTAAAATTTAGAATAAAGCCCTAAGTTTTTTATTTACATTATAGTTCGTACA
66 AAAAGACTTACTCTCAAAATTTAGAATAAAGCCCTAAGTTTTTTATTTACATTATAGTTCGTACA
*
43439211 TACATGATGCGATCCCTGAACACTCACCAATTTGCTAAAAGCTTAAACGAGCTTCACTTTCCTCT
131 TACATGATACGATCCCTGAACACTCACCAATTTGCTAAAAGCTTAAACGAGCTTCACTTTCCTCT
*
43439276 TATCTTTGCTTGTAGACTATAACATTATA
196 TATCTTTACTTGTAGACTATAACATTATA
*
43439305 GTTCATATAGGGCTCGCATATCTCTATTCATAAAAACACACATATAATCACAAAATAGAGTTTAG
1 GTTCATATAGGGCTCGCATATCTCTATTCATAAAAACACACATATAATCACAAAACAGAGTTTAG
*
43439370 AAAAGACTTACTCTCAAAATTTAGAATAAAGCCCTAATTTTTTTATTTACATTATAGTTCGTACA
66 AAAAGACTTACTCTCAAAATTTAGAATAAAGCCCTAAGTTTTTTATTTACATTATAGTTCGTACA
* * *
43439435 TACATGATATGATCCCTGAACACTCACCAATTTGCTAAAAGCTTAAACGAGCTTCGCTTTTCTCT
131 TACATGATACGATCCCTGAACACTCACCAATTTGCTAAAAGCTTAAACGAGCTTCACTTTCCTCT
43439500 TATCTTTACTTG
196 TATCTTTACTTG
43439512 CAAACTGTAA
Statistics
Matches: 199, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
224 199 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (224 bp):
GTTCATATAGGGCTCGCATATCTCTATTCATAAAAACACACATATAATCACAAAACAGAGTTTAG
AAAAGACTTACTCTCAAAATTTAGAATAAAGCCCTAAGTTTTTTATTTACATTATAGTTCGTACA
TACATGATACGATCCCTGAACACTCACCAATTTGCTAAAAGCTTAAACGAGCTTCACTTTCCTCT
TATCTTTACTTGTAGACTATAACATTATA
Found at i:43440747 original size:46 final size:46
Alignment explanation
Indices: 43440689--43440904 Score: 197
Period size: 46 Copynumber: 4.6 Consensus size: 46
43440679 GGGTTATTGT
* * *
43440689 GAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCA-CACTATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGTATCGGCCATCA-GATGA
* * * * *
43440735 GAGCCAGTGTAAGACCATGTTTGGGACATGGAATTGG-CATCGAGACGA
1 GAGCCAGTGTAAGA-CATGTCTAGGACAT-GTATCGGCCATC-AGATGA
* *
43440783 GTGCTAGTGTAAGACATGTCTAGGACATGTATCGGCC-TCAAGATGTA
1 GAGCCAGTGTAAGACATGTCTAGGACATGTATCGGCCATC-AGATG-A
* * * *
43440830 -AGCCAGTGTAAGACATGTCTGGGACATGTATCGACTATGAGATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGTATCGGCCATCAGATGA
* *
43440875 TAGTCAGTGTAAGACCATGTCTAGGACATG
1 GAGCCAGTGTAAGA-CATGTCTAGGACATG
43440905 GCATAGACTT
Statistics
Matches: 138, Mismatches: 23, Indels: 17
0.78 0.13 0.10
Matches are distributed among these distances:
45 1 0.01
46 72 0.52
47 43 0.31
48 21 0.15
49 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTAGGACATGTATCGGCCATCAGATGA
Found at i:43440918 original size:47 final size:48
Alignment explanation
Indices: 43440830--43440955 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 48
43440820 TCAAGATGTA
* *
43440830 AGCCAGTGTAAGA-CATGTCTGGGACAT-GTATCGACTATGAGATGAT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATAGACTATGAGAT-ATG
* *
43440876 AGTCAGTGTAAGACCATGTCTAGGACATGGCATAGACT-TGAGATATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATAGACTATGAGATATG
* * *
43440923 AGCCAGTATAAGACTATATCTGGGACATGGCAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCAT
43440956 CGGCACCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 14 0.21
47 47 0.69
48 7 0.10
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATAGACTATGAGATATG
Found at i:43462315 original size:19 final size:18
Alignment explanation
Indices: 43462287--43462327 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
43462277 TTTATTTACG
43462287 TTTTTATATTTCAGCATA
1 TTTTTATATTTCAGCATA
* *
43462305 TTTTATATATTTTAGCTTA
1 TTTT-TATATTTCAGCATA
43462324 TTTT
1 TTTT
43462328 GACCATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTTATATTTCAGCATA
Found at i:43463471 original size:40 final size:40
Alignment explanation
Indices: 43463388--43463573 Score: 268
Period size: 40 Copynumber: 4.7 Consensus size: 40
43463378 TTCTAGCGCA
* * * * *
43463388 AGCCTACGGGTCTTTAA-CCCGGATACCATTCTAGTACGA-
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCA-TAT
*
43463427 AGCCTGCGGGTCTTTATGCCCGGATACAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
*
43463467 AGCCTGCGGGTCTTTAAGCCTGGATACAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
* *
43463507 AGCCTGTGGGTCTTTAAGCCCGGATACAATTCTAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
43463547 AGCCTGCGGGTCTTTAAGCCCGGATAC
1 AGCCTGCGGGTCTTTAAGCCCGGATAC
43463574 CACATCAAAT
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.12
40 117 0.88
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCATAT
Found at i:43464857 original size:21 final size:21
Alignment explanation
Indices: 43464832--43464872 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43464822 CGGCAATTTC
43464832 AATTCATACCT-TTCAACCATG
1 AATTCA-ACCTATTCAACCATG
*
43464853 AATTCAACTTATTCAACCAT
1 AATTCAACCTATTCAACCAT
43464873 CATTTAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (21 bp):
AATTCAACCTATTCAACCATG
Found at i:43464882 original size:21 final size:21
Alignment explanation
Indices: 43464843--43464882 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43464833 ATTCATACCT
* *
43464843 TTCAACCATGAATTCAACTTA
1 TTCAACCATCAATTAAACTTA
*
43464864 TTCAACCATCATTTAAACT
1 TTCAACCATCAATTAAACT
43464883 ACTTAACATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (21 bp):
TTCAACCATCAATTAAACTTA
Found at i:43467530 original size:46 final size:44
Alignment explanation
Indices: 43467472--43467695 Score: 166
Period size: 46 Copynumber: 4.8 Consensus size: 44
43467462 GGGTTATTGT
* *
43467472 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATACTATGA-
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-T-CGA-GAC
** *
43467518 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTATCGAGAT
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGAC
* * **
43467564 GAATGCTAGTGCAAGACA-GTTCTAAGACATGCATCGGCCTCGAGAC
1 G-A-GCCAGTGTAAGACATG-TCTGGGACATGCATCGGCCTCGAGAC
* * * *
43467610 GTAAGCCAGTGTAAGTCATGTTTGGAACATGCATCGG-CTACGAGAT
1 G--AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGAC
*
43467656 GATAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 G--AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
43467696 ACCTTACCCC
Statistics
Matches: 141, Mismatches: 25, Indels: 21
0.75 0.13 0.11
Matches are distributed among these distances:
45 4 0.03
46 72 0.51
47 41 0.29
48 24 0.17
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGAC
Found at i:43467692 original size:94 final size:94
Alignment explanation
Indices: 43467474--43467695 Score: 237
Period size: 94 Copynumber: 2.4 Consensus size: 94
43467464 GTTATTGTGA
*
43467474 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATACTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATACGATGAGAGCCAGTGTAAGACCATGTC
*
43467539 TGGGACATGGCATCGGTATCGAGATGAAT
66 TGGAACATGGCATCGGTATCGAGATGAAT
* ** *
43467568 GCTAGTGCAAGACA-GTTCTAAGACATGCATCGGCC-T-CGA-GACGTAAGCCAGTGTAAG-TCA
1 GCTAGTGTAAGACATG-TCTGGGACATGCATCGGCCATACGATGA-G--AGCCAGTGTAAGACCA
*
43467628 TGTTTGGAACAT-GCATCGGCTA-CGAGATG-AT
62 TGTCTGGAACATGGCATCGG-TATCGAGATGAAT
43467659 AG-TCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 -GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
43467696 ACCTTACCCC
Statistics
Matches: 108, Mismatches: 10, Indels: 20
0.78 0.07 0.14
Matches are distributed among these distances:
91 5 0.05
92 26 0.24
93 26 0.24
94 51 0.47
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATACGATGAGAGCCAGTGTAAGACCATGTC
TGGAACATGGCATCGGTATCGAGATGAAT
Found at i:43471831 original size:29 final size:28
Alignment explanation
Indices: 43471777--43471832 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 28
43471767 ACATGGCCAA
43471777 ACACACGCCCGTGTTCTAGGCTGTGTGGC
1 ACACACGCCCGTGTTCTA-GCTGTGTGGC
43471806 ACACACGCCCGTGTCTCT-GCTCGTGTG
1 ACACACGCCCGTGT-TCTAGCT-GTGTG
43471833 CCCAATTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 3 0.12
29 19 0.76
30 3 0.12
ACGTcount: A:0.12, C:0.34, G:0.29, T:0.25
Consensus pattern (28 bp):
ACACACGCCCGTGTTCTAGCTGTGTGGC
Found at i:43478982 original size:13 final size:13
Alignment explanation
Indices: 43478964--43478996 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
43478954 ATTGGGACAC
43478964 GCCCGTGTCCCTA
1 GCCCGTGTCCCTA
*
43478977 GCCCGTGTCCTTA
1 GCCCGTGTCCCTA
43478990 GCCCGTG
1 GCCCGTG
43478997 CTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.42, G:0.27, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTA
Found at i:43481440 original size:47 final size:48
Alignment explanation
Indices: 43481182--43481448 Score: 189
Period size: 47 Copynumber: 5.6 Consensus size: 48
43481172 TGAGAGCCAA
* *
43481182 TGTAAGACCATGTCTGGGACATGGAATC-AGCATTGA-GACGA-GAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGA-C-TTGATGA-GATGAGGTAG
* * *
43481230 TGTAAGA-CATGTCTAGGACAT-GCATCGGC-T-ATGAGATG-TGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAGATGAGGT-AG
* ** * * **
43481274 TGTAAGACCATGTCTGGGACATGACATCGGCACGAAGATGTG-GGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-G-AC-TTGATGAGATGAGGTAG
* * * **
43481324 TGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCGAT-A-GTCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-TGAGATGAGGT-AG
*
43481373 TGTAAGACCATGTTTGGGACATGGCATCGACTTGATG-GATGAGGTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAGATGAGGTAG
*
43481420 TGTAAGACCATGTCTAGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
43481449 GTATTACACC
Statistics
Matches: 171, Mismatches: 31, Indels: 35
0.72 0.13 0.15
Matches are distributed among these distances:
43 4 0.02
44 13 0.08
45 13 0.08
46 12 0.07
47 45 0.26
48 17 0.10
49 32 0.19
50 31 0.18
51 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACTTGATGAGATGAGGTAG
Found at i:43483163 original size:95 final size:93
Alignment explanation
Indices: 43483000--43483316 Score: 320
Period size: 95 Copynumber: 3.3 Consensus size: 93
43482990 GGTGAATTGC
* * * * * **
43483000 CGATGCCATATTCCAAACATGGTCTTACACTGGCTCACAT-GTCGAGGCTAATGCCATGTCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-CATAAT-GTGGCCGATGCCATGTCCAGA
* *
43483064 CATGGTCTTACACTAGCTCTTGTCTCAATG
64 CATGGTCTTACACTAGCTCTTATATCAATG
*
43483094 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCATAATGTGGTCGATGCCATGTCCCAGA
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCATAATGTGGCCGATGCCATGT-CCAGA
* **
43483159 CATGGTCATACACTAG-TGCACATATCAATG
64 CATGGTCTTACACTAGCT-CTTATATCAATG
* * *
43483189 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATTACAT-T-GCCGGTGCGAGGTTCC
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-CA-TA-ATGTGGCCGATGCCATG-TCC
* * *
43483252 AAACATGGTCTTACACTGGCTCTTATATC-GTGG
61 AGACATGGTCTTACACTAGCTCTTATATCAAT-G
43483285 CCGATGCCATGTCCCAGACATGGTCTTACACT
1 -CGATGCCATGTCCCAGACATGGTCTTACACT
43483317 AACACACATA
Statistics
Matches: 188, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
94 17 0.09
95 98 0.52
96 65 0.35
97 6 0.03
98 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCCATAATGTGGCCGATGCCATGTCCAGACA
TGGTCTTACACTAGCTCTTATATCAATG
Found at i:43483328 original size:48 final size:48
Alignment explanation
Indices: 43482998--43483316 Score: 285
Period size: 48 Copynumber: 6.7 Consensus size: 48
43482988 AGGGTGAATT
* * * *
43482998 GCCGATGCCATATTCCAAACATGGTCTTACACTGGCTCACATGTCGA-G
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-ATG
** * *** *
43483046 GCTAATGCCATGT-CCAGACATGGTCTTACACTAGCTCTTGTCTCAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-ATG
* *
43483093 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-CATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-ATCATG
* * *
43483140 GTCGATGCCATGTCCCAGACATGGTCATACACTAG-TGCACATATCAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-CACATATC-ATG
* * *
43483188 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-TACATT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATAT-CATG
* * * * * ** *
43483236 GCCGGTGCGAGGTTCCAAACATGGTCTTACACTGGCTCTTATATCGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
43483284 GCCGATGCCATGTCCCAGACATGGTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
43483317 AACACACATA
Statistics
Matches: 219, Mismatches: 40, Indels: 24
0.77 0.14 0.08
Matches are distributed among these distances:
46 2 0.01
47 76 0.35
48 138 0.63
49 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCATG
Found at i:43484842 original size:20 final size:20
Alignment explanation
Indices: 43484817--43484861 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
43484807 AGCACATGTA
*
43484817 TTCATAAAATTTCAGAATTT
1 TTCATAAAATTTCAGAAATT
*
43484837 TTCATAAAATTTTAGAAATT
1 TTCATAAAATTTCAGAAATT
43484857 TTCAT
1 TTCAT
43484862 TTTATTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (20 bp):
TTCATAAAATTTCAGAAATT
Found at i:43487656 original size:48 final size:48
Alignment explanation
Indices: 43487580--43487807 Score: 194
Period size: 48 Copynumber: 4.8 Consensus size: 48
43487570 GATATGTGCA
* * * * *
43487580 CTAGTGTAAGACCATGCCTGGCATATGGCTTCGGCCA-CGATATGAGAG
1 CTAGTGTAAGACCATGTCTGGAACATGGCATCGG-CATTGATATGAGAG
* * * * *
43487628 CTAGTGTAAAACCATGTTTGGAACATGGCATCGGTATTGAGATGAAAG
1 CTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAG
* * * * * *
43487676 CCAGTGTAAGACCATGTCAGGGACATGGCATCGACATTGATATGTGCG
1 CTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAG
* *
43487724 CTAGTGTAAGATCATGTTTGGAACATGGCATCGGGCACATT-ATA-G-GAG
1 CTAGTGTAAGACCATGTCTGGAACATGGCATC-GG--CATTGATATGAGAG
* * * *
43487772 CCAGTATAAGACCATGCCTGGGACATGGCATCGGCA
1 CTAGTGTAAGACCATGTCTGGAACATGGCATCGGCA
43487808 ATTCACTCTC
Statistics
Matches: 142, Mismatches: 34, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
45 2 0.01
47 3 0.02
48 128 0.90
49 2 0.01
50 3 0.02
51 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
CTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTGATATGAGAG
Found at i:43487774 original size:96 final size:96
Alignment explanation
Indices: 43487618--43487804 Score: 236
Period size: 96 Copynumber: 1.9 Consensus size: 96
43487608 CTTCGGCCAC
* *
43487618 GATATGAGAGCTAGTGTAAAACCATGTTTGGAACATGGCATCGGTATTGAGATGAAAGCCAGTGT
1 GATATGAGAGCTAGTGTAAAACCATGTTTGGAACATGGCATCGGCATTGAGATGAAAGCCAGTAT
*
43487683 AAGACCATGTCAGGGACATGGCATCGACATT
66 AAGACCATGCCAGGGACATGGCATCGACATT
* * * * * *
43487714 GATATGTGCGCTAGTGTAAGATCATGTTTGGAACATGGCATCGGGCACATT-ATA-G-GAGCCAG
1 GATATGAGAGCTAGTGTAAAACCATGTTTGGAACATGGCATC-GG--CATTGAGATGAAAGCCAG
*
43487776 TATAAGACCATGCCTGGGACATGGCATCG
63 TATAAGACCATGCCAGGGACATGGCATCG
43487805 GCAATTCACT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 70 0.90
97 3 0.04
98 2 0.03
99 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (96 bp):
GATATGAGAGCTAGTGTAAAACCATGTTTGGAACATGGCATCGGCATTGAGATGAAAGCCAGTAT
AAGACCATGCCAGGGACATGGCATCGACATT
Found at i:43490470 original size:30 final size:29
Alignment explanation
Indices: 43490436--43490494 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
43490426 AAATTAGATC
43490436 AAATCAAAATTTCATGTATAAAATTATACA
1 AAATCAAAATTT-ATGTATAAAATTATACA
* * *
43490466 AAATCGAAGTTTATGTATATAATTATACA
1 AAATCAAAATTTATGTATAAAATTATACA
43490495 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATCAAAATTTATGTATAAAATTATACA
Found at i:43491799 original size:60 final size:60
Alignment explanation
Indices: 43491732--43491856 Score: 187
Period size: 60 Copynumber: 2.1 Consensus size: 60
43491722 TTCATCTGGT
* * *
43491732 GGGTCTGGTGCAGGTTCTGAAGCTGGTTCATCCGCAGGTTCTTACGCTGGGTCTCGAGCC
1 GGGTCTGGTGCAGGTTCGGAAGCTGGTTCATCCGCAGGTTCCTACGCTGGCTCTCGAGCC
* * * *
43491792 GGGTCTGGTGCAGGTTCGGAAGCTGGTTCATCTGCCGGTTCCTATGCTGGCTCTCGAGCT
1 GGGTCTGGTGCAGGTTCGGAAGCTGGTTCATCCGCAGGTTCCTACGCTGGCTCTCGAGCC
43491852 GGGTC
1 GGGTC
43491857 AGGACGAGGC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.10, C:0.25, G:0.36, T:0.29
Consensus pattern (60 bp):
GGGTCTGGTGCAGGTTCGGAAGCTGGTTCATCCGCAGGTTCCTACGCTGGCTCTCGAGCC
Found at i:43495964 original size:18 final size:18
Alignment explanation
Indices: 43495937--43495972 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43495927 TGGTGAAGGT
*
43495937 TATGGCGAGGGACATGGC
1 TATGGAGAGGGACATGGC
*
43495955 TATGGAGAGGGTCATGGC
1 TATGGAGAGGGACATGGC
43495973 AGCGGTGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.44, T:0.19
Consensus pattern (18 bp):
TATGGAGAGGGACATGGC
Found at i:43498579 original size:26 final size:27
Alignment explanation
Indices: 43498519--43498582 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
43498509 ATGGAGGAAG
* *
43498519 TACTG-TACTGGTGACTATGTCACATT
1 TACTGTTACTGGTGACTATGCCACACT
* * *
43498545 TATTATTACTGGTGGCT-TGCCACACT
1 TACTGTTACTGGTGACTATGCCACACT
43498571 TACTGTTACTGG
1 TACTGTTACTGG
43498583 AAGCTACGCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (27 bp):
TACTGTTACTGGTGACTATGCCACACT
Found at i:43501907 original size:20 final size:20
Alignment explanation
Indices: 43501882--43501922 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43501872 ACAACATTTA
43501882 GGACTCGTTATGATCACTAT
1 GGACTCGTTATGATCACTAT
43501902 GGACTCGTTATGATCACTAT
1 GGACTCGTTATGATCACTAT
43501922 G
1 G
43501923 AGTTCTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
GGACTCGTTATGATCACTAT
Found at i:43514813 original size:46 final size:45
Alignment explanation
Indices: 43514762--43514890 Score: 195
Period size: 46 Copynumber: 2.8 Consensus size: 45
43514752 TATTTGGGCA
43514762 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
* *
43514807 GTCCGAACTCATTGAGTTGAGTTCGAGTTCACTTATGGATGCGAAC
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
* * *
43514853 ACCGGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43514891 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
45 2 0.03
46 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
Found at i:43518197 original size:51 final size:49
Alignment explanation
Indices: 43518131--43518414 Score: 299
Period size: 50 Copynumber: 5.7 Consensus size: 49
43518121 TGAGGTCGCA
*
43518131 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CT-AAGACTGTGATCACG
* *
43518182 TGTGTAGTACTAAGTGCAGGCTACTATGTGTA-TTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAAGACT-GTGA--TCACG
* *
43518232 TGTGTAGTACTAAGTGCAGGCTGCTATGCGTACTCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACT--AAGACTGTGATCACG
* * * *
43518283 TGTGTCGTACTAAGTGCAGGCTACTACGTGTA-TTAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAAGACT-GTGA--TCACG
* * * * * *
43518333 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGACTGTTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAAGACTG-TGATCACG
43518382 TGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
1 TGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
43518415 CAGATAGCTT
Statistics
Matches: 200, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
47 2 0.01
48 12 0.06
49 35 0.17
50 76 0.38
51 68 0.34
53 6 0.03
54 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAAGACTGTGATCACG
Found at i:43518295 original size:101 final size:100
Alignment explanation
Indices: 43518120--43518409 Score: 440
Period size: 101 Copynumber: 2.9 Consensus size: 100
43518110 ATGATCTATT
* *
43518120 GTGAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGAAAACTGTGATCACGTGT
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GAAAACTGTGATCACGTGT
43518185 GTAGTACTAAGTGCAGGCTACTATGTGTATTAGATG
65 GTAGTACTAAGTGCAGGCTACTATGTGTATTAGATG
*
43518221 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTGCTATGCGTACTCGAAAACTGTGATCACGTGT
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTAC-CGAAAACTGTGATCACGTGT
* *
43518286 GTCGTACTAAGTGCAGGCTACTACGTGTATTAGATG
65 GTAGTACTAAGTGCAGGCTACTATGTGTATTAGATG
* * * * * *
43518322 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC--AGACTGTTGGTCGCATGT
1 GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGAAAACTG-TGATCACGTGT
43518385 GTAGTACTAAGTGCAGGCTACTATG
65 GTAGTACTAAGTGCAGGCTACTATG
43518410 CGTACCAGAT
Statistics
Matches: 173, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
98 5 0.03
99 31 0.18
100 1 0.01
101 135 0.78
102 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (100 bp):
GTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCGAAAACTGTGATCACGTGTG
TAGTACTAAGTGCAGGCTACTATGTGTATTAGATG
Found at i:43519805 original size:50 final size:49
Alignment explanation
Indices: 43519692--43519867 Score: 176
Period size: 50 Copynumber: 3.5 Consensus size: 49
43519682 TTGGTACGCA
* * **
43519692 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* * *
43519741 TAGTAGCCTACACTTAGTACTACACACGTGACCTCACCA-TCTAATATACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
* *** * *
43519791 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAG---TCTAATACACG
43519842 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
43519868 TGCGACCTCA
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 28 0.27
50 39 0.37
51 35 0.33
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:43519865 original size:101 final size:99
Alignment explanation
Indices: 43519692--43519878 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 99
43519682 TTGGTACGCA
* * *
43519692 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGCCTACACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTACACTTA
*
43519757 GTACTACACACGTGACCTCACCATCTAATATACG
66 GTACTACACACGCGACCTCACCATCTAATATACG
* * * *
43519791 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAGTAGCCTACAC
*
43519855 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
43519879 AATAGATCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 42 0.55
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCTCACCATCTAATATACG
Found at i:43522690 original size:15 final size:15
Alignment explanation
Indices: 43522648--43522691 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
43522638 CATAGTATCG
*
43522648 TATCTTGGATTTCTT
1 TATCTTGGATTTCTC
*
43522663 TAT-TCTGGGTTTCTC
1 TATCT-TGGATTTCTC
43522678 TATCTTGGATTTCT
1 TATCTTGGATTTCT
43522692 TTATTCTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:43525184 original size:46 final size:46
Alignment explanation
Indices: 43525129--43525257 Score: 179
Period size: 46 Copynumber: 2.8 Consensus size: 46
43525119 TATTTGGGCA
*
43525129 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGGACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
43525175 TCCGGACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGGACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
43525221 -CCCGAGCTCATTGAGTTGAGTGCGACTTCGCTTATGG
1 TCCGGA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43525258 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
45 4 0.05
46 71 0.95
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGGACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:43541030 original size:41 final size:41
Alignment explanation
Indices: 43540965--43541047 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
43540955 TGTGCGACAT
*
43540965 GCCCATGTCCCTACCCATCATCAAGACTGTCAAAAGAACAC
1 GCCCATGTCCCCACCCATCATCAAGACTGTCAAAAGAACAC
* **
43541006 GCCCGTGTCCCCACCCATGGTCAAGACTGTCAAAAGAACAC
1 GCCCATGTCCCCACCCATCATCAAGACTGTCAAAAGAACAC
43541047 G
1 G
43541048 AGCGTGCGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.16
Consensus pattern (41 bp):
GCCCATGTCCCCACCCATCATCAAGACTGTCAAAAGAACAC
Found at i:43551896 original size:28 final size:27
Alignment explanation
Indices: 43551821--43551915 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 27
43551811 CTACACTACA
43551821 ATTATCTG-ATCTGGTGGCTCTGTCAC
1 ATTATCTGTATCTGGTGGCTCTGTCAC
*
43551847 ATATATCTGT-TCTGGTGGCTCTGCCAC
1 AT-TATCTGTATCTGGTGGCTCTGTCAC
* *
43551874 GATTATCTGTATTTGGTGACTCTGTCAC
1 -ATTATCTGTATCTGGTGGCTCTGTCAC
*
43551902 ATTATTTGT-TCTGG
1 ATTATCTGTATCTGG
43551916 CAGTCATGCT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
26 6 0.10
27 37 0.63
28 16 0.27
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (27 bp):
ATTATCTGTATCTGGTGGCTCTGTCAC
Found at i:43559380 original size:27 final size:26
Alignment explanation
Indices: 43559350--43559421 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
43559340 AGAATAGTGT
43559350 AATTACTTGA-ATACCCCTATGTGTG-AA
1 AATTAC-TGATATACCCCTA-G-GTGCAA
43559377 AATTACTGATATACCCCTAGGTGCAA
1 AATTACTGATATACCCCTAGGTGCAA
*
43559403 AATTAC-CATTATACCCCTA
1 AATTACTGA-TATACCCCTA
43559422 AGGTTACTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 4 0.10
26 22 0.54
27 15 0.37
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (26 bp):
AATTACTGATATACCCCTAGGTGCAA
Found at i:43559569 original size:27 final size:26
Alignment explanation
Indices: 43559539--43559638 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 26
43559529 GGTGGCTACA
*
43559539 CCACAATTATTTGATCTGGTGGCTCTG
1 CCAC-ATTATCTGATCTGGTGGCTCTG
*
43559566 CCACATATATCTGTTCTGGTGGCTCTG
1 CCACAT-TATCTGATCTGGTGGCTCTG
* *
43559593 CCAGGATTATCTGTATCTGGTGACTCTG
1 CCA-CATTATCTG-ATCTGGTGGCTCTG
* *
43559621 TCACATTATCTGTTCTGG
1 CCACATTATCTGATCTGG
43559639 CAGCCATGCT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
26 7 0.11
27 39 0.63
28 16 0.26
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
CCACATTATCTGATCTGGTGGCTCTG
Found at i:43561391 original size:41 final size:41
Alignment explanation
Indices: 43561316--43561507 Score: 187
Period size: 41 Copynumber: 4.7 Consensus size: 41
43561306 ATTCCTAACC
* * *
43561316 TTTTCAACTTTTTCA-TTAATAT-TTTCTTCAAATATAT-TCA
1 TTTTCAACCTTTTCATTTGATATCTTT-TTCGAATAT-TGTCA
* *
43561356 TTTTAAACCTTTTCATTTGATATTCTTTTT-GAATATTGACA
1 TTTTCAACCTTTTCATTTGATA-TCTTTTTCGAATATTGTCA
* * ** *
43561397 TTTTCAACCTTTTCATTTGATATCTTTTTGGGATATCAT-T
1 TTTTCAACCTTTTCATTTGATATCTTTTTCGAATATTGTCA
* *
43561437 TTTTCAACCTTTTCATTTGATATCTTTTTCTAATATTGTCC
1 TTTTCAACCTTTTCATTTGATATCTTTTTCGAATATTGTCA
* *
43561478 TTTTCAACATTTTCATTTGTTATCCTTTTT
1 TTTTCAACCTTTTCATTTGATAT-CTTTTT
43561508 GGATAACTTC
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
40 55 0.44
41 59 0.47
42 9 0.07
43 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.05, T:0.56
Consensus pattern (41 bp):
TTTTCAACCTTTTCATTTGATATCTTTTTCGAATATTGTCA
Found at i:43561411 original size:81 final size:80
Alignment explanation
Indices: 43561316--43561494 Score: 202
Period size: 81 Copynumber: 2.2 Consensus size: 80
43561306 ATTCCTAACC
*
43561316 TTTTCAACTTTTTCATTAATAT-TTTCTTCAAATAT-ATTCATTTTAAACCTTTTCATTTGATAT
1 TTTTCAACATTTTCATTAATATCTTT-TTCAAATATCATT--TTTTAAACCTTTTCATTTGATA-
43561379 TCTTTTT-GAATATTGACA
62 TCTTTTTCGAATATTGACA
* * *** *
43561397 TTTTCAACCTTTTCATTTGATATCTTTTTGGGATATCATTTTTTCAACCTTTTCATTTGATATCT
1 TTTTCAACATTTTCA-TTAATATCTTTTTCAAATATCATTTTTTAAACCTTTTCATTTGATATCT
* * *
43561462 TTTTCTAATATTGTCC
65 TTTTCGAATATTGACA
43561478 TTTTCAACATTTTCATT
1 TTTTCAACATTTTCATT
43561495 TGTTATCCTT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
80 9 0.11
81 57 0.68
82 12 0.14
83 6 0.07
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (80 bp):
TTTTCAACATTTTCATTAATATCTTTTTCAAATATCATTTTTTAAACCTTTTCATTTGATATCTT
TTTCGAATATTGACA
Found at i:43561496 original size:81 final size:82
Alignment explanation
Indices: 43561356--43561509 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 82
43561346 AATATATTCA
*
43561356 TTTTAAACCTTTTCATTTGATATTCTTTTTGAATATTGACATTTTCAACCTTTTCATTTGATAT-
1 TTTTAAACCTTTTCATTTGATATTCTTTTTGAATATTGACATTTTCAACATTTTCATTTGATATC
43561420 CTTTTTGGGATATCATT
66 CTTTTTGGGATATCATT
* * * * *
43561437 TTTTCAACCTTTTCATTTGATA-TCTTTTTCTAATATTGTCCTTTTCAACATTTTCATTTGTTAT
1 TTTTAAACCTTTTCATTTGATATTCTTTTT-GAATATTGACATTTTCAACATTTTCATTTGATAT
43561501 CCTTTTTGG
65 CCTTTTTGG
43561510 ATAACTTCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 7 0.11
81 50 0.77
82 8 0.12
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.56
Consensus pattern (82 bp):
TTTTAAACCTTTTCATTTGATATTCTTTTTGAATATTGACATTTTCAACATTTTCATTTGATATC
CTTTTTGGGATATCATT
Found at i:43561520 original size:41 final size:40
Alignment explanation
Indices: 43561356--43561529 Score: 142
Period size: 41 Copynumber: 4.3 Consensus size: 40
43561346 AATATATTCA
* * * *
43561356 TTTTAAACCTTTTCATTTGATATTCTTTTTGAAT-A-TTGACA
1 TTTTCAACATTTTCATTTGATA-TCTTTTTGGATAACTT--CC
* *
43561397 TTTTCAACCTTTTCATTTGATATCTTTTTGGGATATCATT--
1 TTTTCAACATTTTCATTTGATATCTTTTT-GGATAAC-TTCC
* ** *
43561437 TTTTCAACCTTTTCATTTGATATCTTTTTCTA-ATATTGTCC
1 TTTTCAACATTTTCATTTGATATCTTTTTGGATA-ACT-TCC
*
43561478 TTTTCAACATTTTCATTTGTTATCCTTTTTGGATAACTTCC
1 TTTTCAACATTTTCATTTGATAT-CTTTTTGGATAACTTCC
43561519 TTTTCAACATT
1 TTTTCAACATT
43561530 GATATGAACT
Statistics
Matches: 111, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 36 0.32
41 59 0.53
42 9 0.08
43 1 0.01
44 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.55
Consensus pattern (40 bp):
TTTTCAACATTTTCATTTGATATCTTTTTGGATAACTTCC
Found at i:43561708 original size:41 final size:41
Alignment explanation
Indices: 43561651--43561731 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
43561641 AAACAAGAAA
* *
43561651 AGGTTTAAATGTATAAGATGTAAAGATAGGTTTCATTTTCT
1 AGGTTTAAACGTATAAGATGTAAAGATAGGTTTCAGTTTCT
*
43561692 AGGTTTAAGCGTATAAGATGTAAAGATAGGTTTCAGTTTC
1 AGGTTTAAACGTATAAGATGTAAAGATAGGTTTCAGTTTC
43561732 AGTTTCAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (41 bp):
AGGTTTAAACGTATAAGATGTAAAGATAGGTTTCAGTTTCT
Found at i:43564056 original size:24 final size:24
Alignment explanation
Indices: 43564028--43564132 Score: 83
Period size: 23 Copynumber: 4.5 Consensus size: 24
43564018 TCAGCTCGTA
* *
43564028 AGAGCTTACTGTTTTTAGCTTATT
1 AGAGCTTACTGTTTTTAGCTCAAT
* **
43564052 GGAGCTTAC-CATTTTAGCTCAAT
1 AGAGCTTACTGTTTTTAGCTCAAT
* *
43564075 AGAGCTTACTG--TTCAGCTCGAT
1 AGAGCTTACTGTTTTTAGCTCAAT
* * * *
43564097 ATAGCTTACCG-TTTCAGCTCATT
1 AGAGCTTACTGTTTTTAGCTCAAT
43564120 AGAGCTTACTGTT
1 AGAGCTTACTGTT
43564133 CATCAACTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 18 0.29
23 36 0.57
24 9 0.14
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (24 bp):
AGAGCTTACTGTTTTTAGCTCAAT
Found at i:43564102 original size:22 final size:21
Alignment explanation
Indices: 43564067--43564134 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 21
43564057 TTACCATTTT
43564067 AGCTCAATAGAGCTTACTGTTC
1 AGCTC-ATAGAGCTTACTGTTC
* *
43564089 AGCTCGATATAGCTTACCGTTTC
1 AGCTC-ATAGAGCTTACTG-TTC
43564112 AGCTCATTAGAGCTTACTGTTC
1 AGCTCA-TAGAGCTTACTGTTC
43564134 A
1 A
43564135 TCAACTTAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 21 0.54
23 18 0.46
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (21 bp):
AGCTCATAGAGCTTACTGTTC
Found at i:43569417 original size:46 final size:47
Alignment explanation
Indices: 43569184--43569502 Score: 189
Period size: 47 Copynumber: 6.8 Consensus size: 47
43569174 AGGGTATAAT
* ** * **
43569184 GCCGATGCCATGTCCCAGACATGGTCTTACA-TTGGATCATCCATCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTCAT-CTTGTA
* * **
43569231 GTCGATGCCATGTCCCAGACATGGTCTTACTCT-GACTATCAAAATTG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CT-TC-ATCTTGTA
* **
43569279 GGCCGACT-TCATGTCTTAGACATGGTCTTACACTAGCTCTCA-CATATCCGT-
1 -GCCGA-TGCCATGTCCCAGACATGGTCTTACACTAGCT-TCATC-T-T--GTA
* * * *
43569330 GTCGATGTCATGTCCCAGGCATGGTCTTACACT-GAC-ACATCTTGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTTCATCTTGTA
*
43569376 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTTCATCTT-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC-TTCATCTTGTA
* * ** *
43569421 TGCCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCTCAT-AAGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT-TCATCTTGTA
*
43569469 GCCGAT-ACATGTCCCAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
43569503 ACACAAATAA
Statistics
Matches: 215, Mismatches: 33, Indels: 50
0.72 0.11 0.17
Matches are distributed among these distances:
44 11 0.05
45 29 0.13
46 32 0.15
47 51 0.24
48 23 0.11
49 37 0.17
50 31 0.14
51 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTTCATCTTGTA
Found at i:43574650 original size:43 final size:43
Alignment explanation
Indices: 43574549--43574656 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
43574539 GATTAACGAG
* *
43574549 ATGTGATTATGTGAAAGACCATGTCTGGGACATTAACATCATT
1 ATGTGATTATATGTAAGACCATGTCTGGGACATTAACATCATT
* ** *
43574592 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTATATGTAAGACCATGTCTGGGACATTAACATCATT
* *
43574635 ATTTTATT-TCATGTAAGACCAT
1 ATGTGATTAT-ATGTAAGACCAT
43574657 AGCTAGGCTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 56 0.98
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (43 bp):
ATGTGATTATATGTAAGACCATGTCTGGGACATTAACATCATT
Found at i:43578713 original size:33 final size:33
Alignment explanation
Indices: 43578671--43578738 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
43578661 ATCAATTCCC
43578671 ATACATATATGCTCATACGAGCTATGAATAAGT
1 ATACATATATGCTCATACGAGCTATGAATAAGT
*
43578704 ATACATATATGCTCATACGAGCTGTGAATAAGT
1 ATACATATATGCTCATACGAGCTATGAATAAGT
43578737 AT
1 AT
43578739 GCTCACAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (33 bp):
ATACATATATGCTCATACGAGCTATGAATAAGT
Found at i:43580570 original size:39 final size:40
Alignment explanation
Indices: 43580475--43580651 Score: 132
Period size: 39 Copynumber: 4.5 Consensus size: 40
43580465 ACTTGAAACC
** * *
43580475 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGCGGGACCTTAAGCCCGGACAT
* * * *
43580514 AATACTAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGCGGGACCTTAAGCCCGGACAT
* * * * **
43580553 ATTTCCAGCACGTAGCCTAC-GGACCTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGGACCTTAAGCCCGGACAT
* *
43580592 AATTCCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
1 AATTCCAGCACATAGCCTGCGGGACCTTAAGCCCGGACAT
* *
43580631 AATTCCAACACATAGCTTGCG
1 AATTCCAGCACATAGCCTGCG
43580652 ACCCTAAGTC
Statistics
Matches: 110, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
38 16 0.15
39 94 0.85
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
AATTCCAGCACATAGCCTGCGGGACCTTAAGCCCGGACAT
Found at i:43587943 original size:50 final size:51
Alignment explanation
Indices: 43587865--43587984 Score: 206
Period size: 50 Copynumber: 2.4 Consensus size: 51
43587855 GACCATGGCA
*
43587865 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATG
43587916 A-AAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATG
* *
43587966 ACAAGTGAAAAGTGGTAGC
1 ACAAGTGATAAGTGATAGC
43587985 ATCTGCTACC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 49 0.75
51 16 0.25
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.24
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAAGGACAAATG
Found at i:43588007 original size:31 final size:30
Alignment explanation
Indices: 43587969--43588055 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 30
43587959 ACAAATGACA
*
43587969 AGTGAAAAGTGGTAGCATCTGCTACCTGATC
1 AGTGAAAAGTGGTAGC-TCGGCTACCTGATC
43588000 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-CGGCTACCTGATC
*
43588031 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGC-TCGGCTAC
43588056 AAGTGACAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.02
31 50 0.96
32 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (30 bp):
AGTGAAAAGTGGTAGCTCGGCTACCTGATC
Found at i:43588143 original size:47 final size:46
Alignment explanation
Indices: 43588073--43588196 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 46
43588063 AAGTGATTTC
* * *
43588073 CGTATAAGACCATATTTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * * *
43588119 CTGTATAAGACCATATCTAGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
43588166 CGTGTAAGACCATAGCTGGGTTATGGCATCG
1 CGTATAAGACCATATCTGGGATATGGCATCG
43588197 ATATGTGATA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 26 0.40
47 39 0.60
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:43588227 original size:12 final size:12
Alignment explanation
Indices: 43588210--43588235 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43588200 TGTGATATGT
43588210 GATTACGTGTAA
1 GATTACGTGTAA
43588222 GATTACGTGTAA
1 GATTACGTGTAA
43588234 GA
1 GA
43588236 CCATAGCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATTACGTGTAA
Found at i:43588307 original size:56 final size:57
Alignment explanation
Indices: 43588222--43588328 Score: 189
Period size: 56 Copynumber: 1.9 Consensus size: 57
43588212 TTACGTGTAA
*
43588222 GATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTG-ATATGTGATATAT
1 GATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTGATATAT
*
43588278 GATTATGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
1 GATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTG
43588329 TAAGACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 41 0.85
57 7 0.15
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (57 bp):
GATTACGTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATATGTGATATAT
Found at i:43588330 original size:42 final size:42
Alignment explanation
Indices: 43588271--43588398 Score: 186
Period size: 42 Copynumber: 3.0 Consensus size: 42
43588261 TGTGATATGT
*
43588271 GATATATGATTATGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
43588313 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
* * * **
43588355 -ATTATGTGAAGATGTGTAAGACCATAGTTGAACTATGGCATC
1 GA-TATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
43588397 GA
1 GA
43588399 GAAAACAAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.01
42 76 0.97
43 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
GATATATGAATATGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:43592482 original size:47 final size:47
Alignment explanation
Indices: 43592359--43592735 Score: 607
Period size: 47 Copynumber: 8.1 Consensus size: 47
43592349 GAAATGATAG
*
43592359 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43592406 TAAGGCC-AATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43592452 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43592499 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43592546 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43592592 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43592639 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
43592685 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43592732 TAAG
1 TAAG
43592736 TCCCGAAGGG
Statistics
Matches: 313, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 131 0.42
47 182 0.58
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43592595 original size:93 final size:94
Alignment explanation
Indices: 43592359--43592735 Score: 607
Period size: 93 Copynumber: 4.0 Consensus size: 94
43592349 GAAATGATAG
*
43592359 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCC-AATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
43592423 GTGATGAATGTGAAAGTGTATATGTGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* *
43592452 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
43592517 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
*
43592546 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
43592610 GTGATGAATGTGAAAGTGTATATATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
* * * * * *
43592639 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * *
43592703 GTGATGGATGTGAAAGTGCATAAATGTGA
66 GTGATGAATGTGAAAGTGTATATATGTGA
43592732 TAAG
1 TAAG
43592736 TCCCGAAGGG
Statistics
Matches: 267, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
92 23 0.09
93 164 0.61
94 80 0.30
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43592611 original size:140 final size:140
Alignment explanation
Indices: 43592359--43592735 Score: 605
Period size: 140 Copynumber: 2.7 Consensus size: 140
43592349 GAAATGATAG
*
43592359 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAATGGCCGATG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAATGGCCGATG
*
43592424 TGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
43592489 ATATGTGTGA
131 ATATATGTGA
* *
43592499 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC-AATGGCCGAT
43592564 GTGATGAATGTGAAAGTGTATATATGT-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
65 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
43592628 TATATATGTGA
130 TATATATGTGA
* * * * *
43592639 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC-AATGGCCGAT
* * *
43592703 GTGATGGATGTGAAAGTGCATAAATGTGATAAG
65 GTGATGAATGTGAAAGTGTATATATGTGATAAG
43592736 TCCCGAAGGG
Statistics
Matches: 219, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
139 60 0.27
140 124 0.57
141 35 0.16
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (140 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCAATGGCCGATG
TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATGTGA
Found at i:43592910 original size:37 final size:37
Alignment explanation
Indices: 43592854--43592932 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
43592844 CCGAGCTCTA
* * *
43592854 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
43592891 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
43592928 AAGAC
1 AAGAC
43592933 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:43594929 original size:39 final size:39
Alignment explanation
Indices: 43594806--43594999 Score: 169
Period size: 39 Copynumber: 5.0 Consensus size: 39
43594796 ACTTGAAACC
** **
43594806 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGC-GGACCTTAAGTCCGGATAT
* * * * * * *
43594845 AATACCAGCTCAAAGCCTGTGGGA-CTTTAGCCCGGACAT
1 AATTCCAGCACATAGCCTG-CGGACCTTAAGTCCGGATAT
* * *
43594884 ATTTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
* *
43594923 AATTCCAGCACATAGCCTGCAGACCTTAAGTCTGGATAT
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
* * *
43594962 AATTCCAACACATAGCCTGCGGACCCTAAGTCTGGATA
1 AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATA
43595000 AACATCACTG
Statistics
Matches: 126, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
38 18 0.14
39 108 0.86
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (39 bp):
AATTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATAT
Found at i:43601438 original size:2 final size:2
Alignment explanation
Indices: 43601431--43601456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43601421 GAGTCATAAT
43601431 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
43601457 ATGCAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43608850 original size:21 final size:21
Alignment explanation
Indices: 43608826--43608902 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
43608816 GTTATAATGA
43608826 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
43608847 CCACACGGGCATGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
* *
43608868 CCACACGGACGTGTTGCCTTT
1 CCACACGGGCGTGTTGCCCTT
43608889 CCACACGGGCGTGT
1 CCACACGGGCGTGT
43608903 GCCTTGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:43618432 original size:42 final size:42
Alignment explanation
Indices: 43618385--43618502 Score: 155
Period size: 43 Copynumber: 2.8 Consensus size: 42
43618375 TGTGATATCG
* *
43618385 TGTAAGACCATGTCTAGGACATTGGCATCGTATTTGATTTCA
1 TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTACA
* * *
43618427 TGTAAGACCCTGTCTGGGACAGTGGCATCGATGTTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATCG-TATTTGATTACA
** *
43618470 TGTAAGACCATGTCTGGGATGTTGGCATTGTAT
1 TGTAAGACCATGTCTGGGACATTGGCATCGTAT
43618503 ATGCTTTCCG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 29 0.45
43 35 0.55
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTACA
Found at i:43623737 original size:93 final size:90
Alignment explanation
Indices: 43623550--43623801 Score: 267
Period size: 93 Copynumber: 2.7 Consensus size: 90
43623540 TTAAGGATGT
* * * *
43623550 AAAAAGTCCTCGAACTTTTTTAAAAAAAGCAATTAAGCCCCTACTCTTTTTTTTGCATTCAATTG
1 AAAAAGGCCTCAAACTTTTTTAAAAAAAGCAACTAAGCCCCTACTCTTTTTTTTGCACTCAATTG
* *
43623615 GATACTTGAACTTTCAAAATGCATC
66 GATACTTGAACTTCCAAAATGCATA
*
43623640 AAAAAGGCCTCAAACTTTTTTAAAAAAAGTAACTAAGCCCCTATTTCTTCTTTTTTTT-CACTCA
1 AAAAAGGCCTCAAACTTTTTTAAAAAAAGCAACTAAGCCCCTA---C-TCTTTTTTTTGCACTCA
* *
43623704 ATTGGGTACTTGAA-TTGCCAGAATGCATA
62 ATTGGATACTTGAACTT-CCAAAATGCATA
* * * * *
43623733 AAAAAGGTCTTCAAACTTTTTCATAAAAAACCAATTAAGCCCTTGCTA-TTTTTTTTTTGCACTC
1 AAAAAGG-CCTCAAACTTTTTTA-AAAAAAGCAACTAAGCCC---CTACTCTTTTTTTTGCACTC
43623797 AATTG
61 AATTG
43623802 AGTACTAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
90 39 0.29
92 2 0.01
93 44 0.32
94 33 0.24
95 15 0.11
98 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (90 bp):
AAAAAGGCCTCAAACTTTTTTAAAAAAAGCAACTAAGCCCCTACTCTTTTTTTTGCACTCAATTG
GATACTTGAACTTCCAAAATGCATA
Found at i:43624389 original size:22 final size:22
Alignment explanation
Indices: 43624346--43624410 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
43624336 TTATAAAAAG
*
43624346 TTTACAA-TTTT-TAATTTTTT
1 TTTACAATTTTTATAAATTTTT
43624366 TTTACAATTTTTATAAATTTTT
1 TTTACAATTTTTATAAATTTTT
43624388 TTT-CTAATTTTTAATAAATTTTT
1 TTTAC-AATTTTT-ATAAATTTTT
43624411 AATATTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 7 0.17
21 5 0.12
22 18 0.45
23 10 0.25
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTACAATTTTTATAAATTTTT
Found at i:43624417 original size:20 final size:21
Alignment explanation
Indices: 43624392--43624448 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
43624382 ATTTTTTTTC
43624392 TAATTTTTAATAAATTTTTAA
1 TAATTTTTAATAAATTTTTAA
* *
43624413 T-ATTTTTATTAAA-ATTTAA
1 TAATTTTTAATAAATTTTTAA
43624432 TAATTTTT-ATAAATTTT
1 TAATTTTTAATAAATTTT
43624449 ATTTTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.33
20 19 0.63
21 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTTTTAATAAATTTTTAA
Found at i:43626059 original size:16 final size:17
Alignment explanation
Indices: 43626032--43626065 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43626022 AATATTTTTG
43626032 TAATTATATTAAGTATT
1 TAATTATATTAAGTATT
*
43626049 TAATT-TATTAATTATT
1 TAATTATATTAAGTATT
43626065 T
1 T
43626066 TTTTAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TAATTATATTAAGTATT
Found at i:43626124 original size:20 final size:20
Alignment explanation
Indices: 43626087--43626127 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
43626077 TCATTAAAAA
*
43626087 TTATAAACAAAAACTAATTT
1 TTATAAACAAAAAATAATTT
43626107 TTATAAA-AAAAATATAATTT
1 TTATAAACAAAAA-ATAATTT
43626127 T
1 T
43626128 AATATATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATAAACAAAAAATAATTT
Found at i:43629906 original size:14 final size:14
Alignment explanation
Indices: 43629887--43629936 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
43629877 GCATGTGTGA
43629887 CCACACGGCCCCAC
1 CCACACGGCCCCAC
43629901 CCACACGGCCCCAC
1 CCACACGGCCCCAC
*
43629915 CCACATGGCCCCAC
1 CCACACGGCCCCAC
*
43629929 CCAAACGG
1 CCACACGG
43629937 GCGTGTGACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.24, C:0.58, G:0.16, T:0.02
Consensus pattern (14 bp):
CCACACGGCCCCAC
Found at i:43631647 original size:36 final size:36
Alignment explanation
Indices: 43631601--43631680 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
43631591 TTTAATTTTG
* * *
43631601 TATACATTTCA-TATGTTATTAT-TAATTGTTTTAAGT
1 TATATATTTCATTAT-TTATTATAT-ATTATTTTAAAT
43631637 TATATATTTCATTATTTATTATATATTATTTTAAAT
1 TATATATTTCATTATTTATTATATATTATTTTAAAT
43631673 TAATATAT
1 T-ATATAT
43631681 ATATTCTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
36 28 0.74
37 10 0.26
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (36 bp):
TATATATTTCATTATTTATTATATATTATTTTAAAT
Found at i:43631674 original size:17 final size:18
Alignment explanation
Indices: 43631654--43631696 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
43631644 TTCATTATTT
*
43631654 ATTATATAT-TATTTTAA
1 ATTATATATATATTCTAA
43631671 ATTAATATATATATTCTAA
1 ATT-ATATATATATTCTAA
43631690 A-TATATA
1 ATTATATA
43631697 ATTTACACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATATATATATTCTAA
Found at i:43633689 original size:12 final size:12
Alignment explanation
Indices: 43633672--43633696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43633662 ATAATAAAAT
43633672 ATAACAATAATA
1 ATAACAATAATA
43633684 ATAACAATAATA
1 ATAACAATAATA
43633696 A
1 A
43633697 AATATGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACAATAATA
Found at i:43633952 original size:12 final size:12
Alignment explanation
Indices: 43633935--43633961 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43633925 AATATATATA
43633935 TAAATGAAATAC
1 TAAATGAAATAC
43633947 TAAATGAAATAC
1 TAAATGAAATAC
43633959 TAA
1 TAA
43633962 GATAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (12 bp):
TAAATGAAATAC
Found at i:43633993 original size:17 final size:18
Alignment explanation
Indices: 43633973--43634010 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
43633963 ATAAAGGAGC
43633973 AAAAATATT-AAAAAA-AT
1 AAAAAT-TTGAAAAAAGAT
43633990 AAAAATTTGAAAAAAGAT
1 AAAAATTTGAAAAAAGAT
43634008 AAA
1 AAA
43634011 TTTAATTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.63
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATTTGAAAAAAGAT
Found at i:43635007 original size:20 final size:19
Alignment explanation
Indices: 43634984--43635021 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
43634974 TTTTTGAAAA
43634984 TTTTTAAGATTTTGGGCTAG
1 TTTTTAAG-TTTTGGGCTAG
43635004 TTTTTAAGTTTTGGGCTA
1 TTTTTAAGTTTTGGGCTA
43635022 TTCGGGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.05, G:0.24, T:0.53
Consensus pattern (19 bp):
TTTTTAAGTTTTGGGCTAG
Found at i:43640032 original size:24 final size:23
Alignment explanation
Indices: 43640000--43640052 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
43639990 AATTATTGTA
*
43640000 ATTTACCCCAAAAAAAAGTAAAGT
1 ATTTACCCC-AAAAAAAGCAAAGT
**
43640024 ATTTACCCCCCAAAAAGCAAAGT
1 ATTTACCCCAAAAAAAGCAAAGT
43640047 ATTTAC
1 ATTTAC
43640053 ACGAGTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (23 bp):
ATTTACCCCAAAAAAAGCAAAGT
Found at i:43650498 original size:31 final size:34
Alignment explanation
Indices: 43650463--43650539 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 34
43650453 AATATTAAAT
43650463 TTAATTTAATACTTATCTTGATAG-T-AT-TT-TA
1 TTAATTTAATACTTATCTT-ATAGATAATATTCTA
*
43650494 TTAATTTAATATTTATCTTATAGATAAATATTCTA
1 TTAATTTAATACTTATCTTATAGAT-AATATTCTA
43650529 TTAATTTAATA
1 TTAATTTAATA
43650540 GATTTAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 4 0.10
31 19 0.47
33 2 0.05
34 2 0.05
35 13 0.32
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAATTTAATACTTATCTTATAGATAATATTCTA
Found at i:43650558 original size:12 final size:12
Alignment explanation
Indices: 43650541--43650565 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43650531 AATTTAATAG
43650541 ATTTAATATTAA
1 ATTTAATATTAA
43650553 ATTTAATATTAA
1 ATTTAATATTAA
43650565 A
1 A
43650566 GTGATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:43653961 original size:16 final size:17
Alignment explanation
Indices: 43653940--43653973 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43653930 GTAGATTGGA
*
43653940 AATTGAAAGTG-GAATG
1 AATTGAAAATGTGAATG
43653956 AATTGAAAATGTGAATG
1 AATTGAAAATGTGAATG
43653973 A
1 A
43653974 CCTATTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (17 bp):
AATTGAAAATGTGAATG
Found at i:43656715 original size:43 final size:42
Alignment explanation
Indices: 43656641--43656763 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
43656631 CGGAAAGCTC
* * * * * *
43656641 ATACAATGCCAACGTCCCAGATATGGTCTTACATGTAATTAA
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAA
* * *
43656683 ATATCGATGTCACTGTCCCAGACAGGGTCTTACACGAAATCAA
1 ATA-CGATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAA
43656726 ATACGATGCCAATGTCCCAGAC-GTGGTCTTACACGTAA
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACACGTAA
43656764 ATCATAAGTC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 33 0.49
43 33 0.49
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAA
Found at i:43656767 original size:43 final size:43
Alignment explanation
Indices: 43656641--43656767 Score: 143
Period size: 43 Copynumber: 3.0 Consensus size: 43
43656631 CGGAAAGCTC
* * ** * *
43656641 ATACAATGCCAACGTCCCAGATATGGTCTTACATGT-AATTAA
1 ATACGATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAA
* *
43656683 ATATCGATGTCACTGTCCCAGACAG-GGTCTTACACG-AAATCAA
1 ATA-CGATGCCAATGTCCCAGAC-GTGGTCTTACACGTAAATCAA
43656726 ATACGATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCA
1 ATACGATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCA
43656768 TAAGTCAATG
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 31 0.44
43 38 0.54
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (43 bp):
ATACGATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAA
Found at i:43656800 original size:44 final size:42
Alignment explanation
Indices: 43656641--43656803 Score: 116
Period size: 43 Copynumber: 3.8 Consensus size: 42
43656631 CGGAAAGCTC
* * ** * * *
43656641 ATACAATGCCAACGTCCCAGATATGGTCTTACATGTAATTAA
1 ATACAATGCCAATGTCCCAAACGTGGTCTTACACGAAATCAA
* * * *
43656683 ATATCGATGTCACTGTCCCAGACAG-GGTCTTACACGAAATCAA
1 ATA-CAATGCCAATGTCCCAAAC-GTGGTCTTACACGAAATCAA
* *
43656726 ATACGATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCATA
1 ATACAATGCCAATGTCCCAAACGTGGTCTTACACG-AAATCA-A
* *
43656770 AGT-CAATGCCAACT-TCCCAAATGTGTTCTTACAC
1 A-TACAATGCCAA-TGTCCCAAACGTGGTCTTACAC
43656804 AAAAACACAT
Statistics
Matches: 99, Mismatches: 15, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 31 0.31
43 38 0.38
44 27 0.27
45 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
ATACAATGCCAATGTCCCAAACGTGGTCTTACACGAAATCAA
Found at i:43659969 original size:21 final size:22
Alignment explanation
Indices: 43659929--43659979 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
43659919 TTTTATAATT
* *
43659929 TATATATATTTCTAATTTTTTA
1 TATATTTATTTCTAATTTTTCA
*
43659951 TATATTTATTTC-GATTTTTCA
1 TATATTTATTTCTAATTTTTCA
*
43659972 TATTTTTA
1 TATATTTA
43659980 ATGTGTACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (22 bp):
TATATTTATTTCTAATTTTTCA
Found at i:43662587 original size:46 final size:45
Alignment explanation
Indices: 43662537--43662719 Score: 163
Period size: 46 Copynumber: 4.0 Consensus size: 45
43662527 ACATTTCATA
43662537 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCAAG
* * * * * *
43662583 GCCGATGCATGTCACAGACATGTCTTATACTAGCACTCTTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCAAG
* * ***
43662629 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCATATTGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCATCTCAAG
* * * * *
43662677 ACTGATGCATGTCCCAAATATGTCTTACACTAGC-TCA-CTCAAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCAAG
43662720 TGATCCAAAT
Statistics
Matches: 106, Mismatches: 27, Indels: 11
0.74 0.19 0.08
Matches are distributed among these distances:
43 2 0.02
44 3 0.03
46 57 0.54
47 24 0.23
48 20 0.19
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCAAG
Found at i:43662684 original size:94 final size:92
Alignment explanation
Indices: 43662537--43662710 Score: 215
Period size: 94 Copynumber: 1.9 Consensus size: 92
43662527 ACATTTCATA
* * * *
43662537 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAGGCCGATGCATGTCACAGAC
1 GCCGATGCATATCCCAGACATGTCTTACACTGGCTTACATATCAAGACCGATGCATGTCACAAAC
*
43662602 ATGTCTTATACTAGCACTCTTCTCAAT
66 ATGTCTTACACTAGCACTCTTCTCAAT
*** * *
43662629 GCCGATGCCATATCCCAGACATGGTCTTACACTGGCTCT-CATATTGTGACTGATGCATGTCCCA
1 GCCGATG-CATATCCCAGACAT-GTCTTACACTGGCT-TACATATCAAGACCGATGCATGTCACA
*
43662693 AATATGTCTTACACTAGC
63 AACATGTCTTACACTAGC
43662711 TCACTCAAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
92 7 0.10
93 13 0.19
94 47 0.69
95 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (92 bp):
GCCGATGCATATCCCAGACATGTCTTACACTGGCTTACATATCAAGACCGATGCATGTCACAAAC
ATGTCTTACACTAGCACTCTTCTCAAT
Found at i:43663096 original size:30 final size:30
Alignment explanation
Indices: 43663039--43663098 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43663029 AATAATTTAT
* * * *
43663039 ACTTTGGCAAAATGATCAATTTGCCCCTAG
1 ACTTTGACAAAATAACCAATTTACCCCTAG
*
43663069 ACTTTGACAAAATAACCATTTTACCCCTAG
1 ACTTTGACAAAATAACCAATTTACCCCTAG
43663099 GTTCGAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (30 bp):
ACTTTGACAAAATAACCAATTTACCCCTAG
Found at i:43665843 original size:7 final size:7
Alignment explanation
Indices: 43665823--43665855 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
43665813 TAAAAATATA
43665823 ATAAA-T
1 ATAAATT
43665829 AT-AATT
1 ATAAATT
43665835 ATAAATT
1 ATAAATT
43665842 ATAAATT
1 ATAAATT
43665849 ATAAATT
1 ATAAATT
43665856 TACATACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 2 0.08
6 5 0.20
7 18 0.72
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATAAATT
Found at i:43671359 original size:18 final size:18
Alignment explanation
Indices: 43671336--43671371 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43671326 TTTAGTCAAA
43671336 GAAATTTAATTAAAATAC
1 GAAATTTAATTAAAATAC
43671354 GAAATTTAATTAAAATAC
1 GAAATTTAATTAAAATAC
43671372 AATAAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (18 bp):
GAAATTTAATTAAAATAC
Found at i:43672519 original size:11 final size:11
Alignment explanation
Indices: 43672499--43672533 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
43672489 TTTTGCTACC
*
43672499 ATGTTATTATT
1 ATGTTGTTATT
43672510 ATGTTGTTATT
1 ATGTTGTTATT
*
43672521 ATTTTGTTATT
1 ATGTTGTTATT
43672532 AT
1 AT
43672534 TATTTGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (11 bp):
ATGTTGTTATT
Found at i:43672519 original size:14 final size:14
Alignment explanation
Indices: 43672500--43672537 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
43672490 TTTGCTACCA
43672500 TGTTATTATTATGT
1 TGTTATTATTATGT
*
43672514 TGTTATTATTTTGT
1 TGTTATTATTATGT
*
43672528 TATTATTATT
1 TGTTATTATT
43672538 TGAATATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (14 bp):
TGTTATTATTATGT
Found at i:43672782 original size:13 final size:11
Alignment explanation
Indices: 43672748--43672779 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
43672738 TATATATATT
43672748 TAAAAATAATA
1 TAAAAATAATA
43672759 TAAAAATAATA
1 TAAAAATAATA
43672770 TAAAAA-AATA
1 TAAAAATAATA
43672780 ATACGGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:43674592 original size:46 final size:46
Alignment explanation
Indices: 43674525--43674793 Score: 230
Period size: 46 Copynumber: 5.8 Consensus size: 46
43674515 TATTTGGGCA
*
43674525 TCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
43674571 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* *
43674616 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * * * *
43674664 TTCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
* ** *
43674709 CATCCGAGCTTATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
43674757 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43674794 GCGGGTTACA
Statistics
Matches: 177, Mismatches: 28, Indels: 36
0.73 0.12 0.15
Matches are distributed among these distances:
42 6 0.03
43 8 0.05
45 6 0.03
46 86 0.49
47 51 0.29
48 6 0.03
50 8 0.05
51 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:43674680 original size:93 final size:93
Alignment explanation
Indices: 43674521--43674786 Score: 442
Period size: 93 Copynumber: 2.9 Consensus size: 93
43674511 CGGATATTTG
* *
43674521 GGCATCCGAACGCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
43674586 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
43674614 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTTCGAACTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
43674679 TTGAGTCCAAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
** * * *
43674707 GGCATCCGAGCTTATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
43674772 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
43674787 CTTATGGGCG
Statistics
Matches: 160, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 160 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:43687417 original size:30 final size:30
Alignment explanation
Indices: 43687383--43687443 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
43687373 TCCTTAACTC
43687383 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
43687413 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
43687443 A
1 A
43687444 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:43692301 original size:46 final size:46
Alignment explanation
Indices: 43692234--43692356 Score: 230
Period size: 46 Copynumber: 2.7 Consensus size: 46
43692224 CCATGTAACC
43692234 CATCCATAAGTGAACTCAGACTCAACTCAACAATCTCTGGTGTGCG
1 CATCCATAAGTGAACTCAGACTCAACTCAACAATCTCTGGTGTGCG
43692280 CATCCATAAGTGAACTCAGACTCAACTCAACAATCTCTGGTGTGCG
1 CATCCATAAGTGAACTCAGACTCAACTCAACAATCTCTGGTGTGCG
43692326 CATCCATAAGTGAACTC-GAACTCAACTCAAC
1 CATCCATAAGTGAACTCAG-ACTCAACTCAAC
43692357 GAGTTCGGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
45 1 0.01
46 75 0.99
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (46 bp):
CATCCATAAGTGAACTCAGACTCAACTCAACAATCTCTGGTGTGCG
Found at i:43692890 original size:30 final size:29
Alignment explanation
Indices: 43692855--43692912 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
43692845 CCAAAATCAT
43692855 ATTTTGGCAAAATTACAATTTTTCCCCTAA
1 ATTTTGGCAAAATTAC-ATTTTTCCCCTAA
*
43692885 ATTTTGTCAAAATTACATTTTTCCCCTA
1 ATTTTGGCAAAATTACATTTTTCCCCTA
43692913 GGCTCGTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (29 bp):
ATTTTGGCAAAATTACATTTTTCCCCTAA
Found at i:43695374 original size:40 final size:40
Alignment explanation
Indices: 43695290--43695473 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
43695280 TTGAATGCTG
* * * *
43695290 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
43695329 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
43695370 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
43695410 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
43695450 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43695474 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:43695427 original size:80 final size:81
Alignment explanation
Indices: 43695290--43695470 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
43695280 TTGAATGCTG
* * *
43695290 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
43695354 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
43695370 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
43695431 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
43695450 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
43695471 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:43695494 original size:39 final size:39
Alignment explanation
Indices: 43695358--43695519 Score: 132
Period size: 40 Copynumber: 4.1 Consensus size: 39
43695348 GGTATTTGTG
* * * **
43695358 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
43695398 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
43695438 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
43695477 TGAGTTAATATAA-CCGGGCTATGT-CCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
43695516 CGAG
1 CGAG
43695520 GAGCTAATCC
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
38 9 0.09
39 27 0.26
40 67 0.64
41 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:43703213 original size:40 final size:40
Alignment explanation
Indices: 43703129--43703312 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
43703119 TTGAATGCTG
* * * *
43703129 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
43703168 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
43703209 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
43703249 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
43703289 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43703313 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:43703266 original size:80 final size:81
Alignment explanation
Indices: 43703129--43703309 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
43703119 TTGAATGCTG
* * *
43703129 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
43703193 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
43703209 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
43703270 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
43703289 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
43703310 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:43703333 original size:39 final size:38
Alignment explanation
Indices: 43703210--43703359 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
43703200 GTTATTAATT
* ** * *
43703210 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
43703250 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
43703289 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
43703329 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
43703360 GAGCTAATCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:43705512 original size:16 final size:16
Alignment explanation
Indices: 43705493--43705523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43705483 CTTCTTCACT
43705493 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
43705509 TACTTACTTACTTAA
1 TACTCACTTACTTAA
43705524 TCAAATTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:43705529 original size:20 final size:20
Alignment explanation
Indices: 43705490--43705529 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43705480 AAACTTCTTC
* *
43705490 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
43705510 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
43705530 TTAGTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:43712823 original size:27 final size:26
Alignment explanation
Indices: 43712789--43712966 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
43712779 AAAATTGTAC
43712789 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
43712816 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
43712842 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
43712870 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
43712898 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
43712925 GGCACTAAGTGTGCGAGTTGAATATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
43712952 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43712967 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 25 0.20
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Done.