Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 134 of 325
Found at i:41835309 original size:3 final size:3
Alignment explanation
Indices: 41835301--41835343 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
41835291 AAAGAACGTG
41835301 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ACAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA
41835344 ACCCATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41837527 original size:82 final size:82
Alignment explanation
Indices: 41837424--41837626 Score: 363
Period size: 82 Copynumber: 2.5 Consensus size: 82
41837414 TGGTATACAT
41837424 ATTTCAA-AAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAATAG
1 ATTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAATAG
41837488 TAAGATGTTAACTAACC
66 TAAGATGTTAACTAACC
* *
41837505 ATTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATGCTAACAAAATGATCCTATAGTAG
1 ATTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAATAG
41837570 TAAGATGTTAACTAACC
66 TAAGATGTTAACTAACC
* *
41837587 ATTTCAACGAATCATTTCAAAAAATAAACAAAATATGTTA
1 ATTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTA
41837627 ATCATCTCAA
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 7 0.06
82 110 0.94
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.29
Consensus pattern (82 bp):
ATTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAATAG
TAAGATGTTAACTAACC
Found at i:41838017 original size:159 final size:155
Alignment explanation
Indices: 41837703--41838175 Score: 499
Period size: 159 Copynumber: 3.0 Consensus size: 155
41837693 CATGCCATCC
* * *
41837703 TTTTTTGGCTTCTAGTTTTCATACTCGTACCAGACTGAGAAAAAAAATCAGAACCCCAAATTAGA
1 TTTTTTGGCTTCTAGTTTT-GTACTCGTACCAGACTAAGAAAAAAAATCAGAAACCCAAATTAGA
* * ** * * *
41837768 TTTAATTAATTTGGAATAAACATTAAAAAAAGTGTTTACA--ATATACTTGTGATCCGGTTATGT
65 TTTAAATATTTTGGAATTGACATT--AAAAA--GTTTACACGATATACCTGTGATCCAGTTGTGT
* * * *
41837831 TAGGCTGAATGCAT-AGTGTTCTATTGTTCT
126 TAGGTTGAATGCATGA-TGTTATGTTGTTAT
41837861 TTTTTTGGCTTCTAGTTTGTGTACTCGTACCAGACTAAGACCAAAAAAATCAGAAACCCAAATTA
1 TTTTTTGGCTTCTAGTTT-TGTACTCGTACCAGACTAAGA--AAAAAAATCAGAAACCCAAATTA
* * * *
41837926 GATTAAAATATTTTTGAATTGACATTAAAATAGTTTACACGATATACCTGGGATCCAGTTGTATT
63 GATTTAAATATTTTGGAATTGACATTAAAA-AGTTTACACGATATACCTGTGATCCAGTTGTGTT
*
41837991 AGGTTGGATGCATGATGTTATGTTGTTAT
127 AGGTTGAATGCATGATGTTATGTTGTTAT
* *
41838020 TTTTTGGGCTTATAGTTCTTGTACTCGTACCAGACTAAGATAAAAAAAATTCA-AAACCCAAATT
1 TTTTTTGGCTTCTAGTT-TTGTACTCGTACCAGACTAAG--AAAAAAAA-TCAGAAACCCAAATT
* * * * *
41838084 AGATTTTAATATTTTGGAATTGATAATGAAAAAGTATT-TACGATATACCTGTGTTCCTA-TTGT
62 AGATTTAAATATTTTGGAATTGA-CATTAAAAAGT-TTACACGATATACCTGTGATCC-AGTTGT
* *
41838147 GTTAGGTTGAATGCATGATCTTTTGTTGT
124 GTTAGGTTGAATGCATGATGTTATGTTGT
41838176 GACCCACACC
Statistics
Matches: 268, Mismatches: 33, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
157 7 0.03
158 40 0.15
159 164 0.61
160 56 0.21
161 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.38
Consensus pattern (155 bp):
TTTTTTGGCTTCTAGTTTTGTACTCGTACCAGACTAAGAAAAAAAATCAGAAACCCAAATTAGAT
TTAAATATTTTGGAATTGACATTAAAAAGTTTACACGATATACCTGTGATCCAGTTGTGTTAGGT
TGAATGCATGATGTTATGTTGTTAT
Found at i:41843455 original size:28 final size:28
Alignment explanation
Indices: 41843423--41843487 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41843413 ATTTACTAGA
*
41843423 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
41843451 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41843479 ATACCCCTA
1 ATACCCCTA
41843488 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41843649 original size:26 final size:27
Alignment explanation
Indices: 41843605--41843681 Score: 111
Period size: 26 Copynumber: 2.8 Consensus size: 27
41843595 GGTGGCTATC
*
41843605 CCACAAATTATCTGTTCTGGTGGCCCTG
1 CCACAAA-TATCTGTTCTGGTGGCACTG
41843633 CCAC-AATATCTGTTCTGGTGGCACTG
1 CCACAAATATCTGTTCTGGTGGCACTG
41843659 CCACAAAATATCTGTATCTGGTG
1 CCAC-AAATATCTGT-TCTGGTG
41843682 ACTCTGTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 23 0.51
27 2 0.04
28 13 0.29
29 7 0.16
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (27 bp):
CCACAAATATCTGTTCTGGTGGCACTG
Found at i:41850158 original size:12 final size:13
Alignment explanation
Indices: 41850130--41850162 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41850120 TTATTTCTTT
41850130 TTCTCCATCTACC
1 TTCTCCATCTACC
*
41850143 TTCTCC-TCTTCC
1 TTCTCCATCTACC
41850155 TTCTCCAT
1 TTCTCCAT
41850163 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:41851259 original size:28 final size:28
Alignment explanation
Indices: 41851227--41851291 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41851217 ATTTACTAGA
*
41851227 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
41851255 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41851283 ATACCCCTA
1 ATACCCCTA
41851292 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41851498 original size:29 final size:28
Alignment explanation
Indices: 41851397--41851487 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
41851387 AGGAAGCGTC
41851397 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
41851425 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
41851453 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
41851482 CTGGTG
1 CTGGTG
41851488 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:41851512 original size:56 final size:55
Alignment explanation
Indices: 41851397--41851512 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 55
41851387 AGGAAGCGTC
* *
41851397 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTT
* * *
41851453 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-T
41851509 CTGG
1 CTGG
41851513 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
55 9 0.17
56 29 0.56
57 14 0.27
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTT
Found at i:41851979 original size:18 final size:18
Alignment explanation
Indices: 41851940--41851980 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
41851930 TAATAAGGCC
* *
41851940 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
41851958 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
41851976 TTTTA
1 TTTTA
41851981 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:41853719 original size:19 final size:19
Alignment explanation
Indices: 41853681--41853724 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41853671 ATTTTCTACA
**
41853681 TATTTTTTTAAATTTTAAT
1 TATTTTTTTAAATTGAAAT
*
41853700 TATTTTTTTAAGTTGAAAT
1 TATTTTTTTAAATTGAAAT
41853719 TCATTT
1 T-ATTT
41853725 GCTGATGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TATTTTTTTAAATTGAAAT
Found at i:41859303 original size:19 final size:19
Alignment explanation
Indices: 41859279--41859332 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
41859269 AATGTCTCTT
41859279 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTTCAT-CA
41859298 TTTGCATTACATTTCATCA
1 TTTGCATTACATTTCATCA
* *
41859317 TATGCATTAAATTTCA
1 TTTGCATTACATTTCA
41859333 CAAAAAGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (19 bp):
TTTGCATTACATTTCATCA
Found at i:41865361 original size:335 final size:335
Alignment explanation
Indices: 41864751--41865420 Score: 1223
Period size: 335 Copynumber: 2.0 Consensus size: 335
41864741 ATAAAGATCT
41864751 AATGTATGTTACAACCACTAAAGAAGACTCTCAAGAAGGCTATCCTTAGAAACTAAACTTTGACG
1 AATGTATGTTACAACCACTAAAGAAGACTCTCAAGAAGGCTATCCTTAGAAACTAAACTTTGACG
*
41864816 GAGCCTCAAATGTTGTAAATAATAGAATTGGGGTAGTCCTGGTATCCCAAGATGGAGATCATTAT
66 GAGCCTCAAATGCTGTAAATAATAGAATTGGGGTAGTCCTGGTATCCCAAGATGGAGATCATTAT
* *
41864881 CCATTCACTAGTAAATTGGATTTTAATTACACGAACAATATGGTAGAATACGAAGCATGCATCAT
131 CCATTCACTAGTAAATTAGATTTTAATTACACGAACAATATGGTAGAATACAAAGCATGCATCAT
*
41864946 GGGTATCCGTACAGCCATAAAACGTAACATTAAAGTACTAGAGGTATATGGAGATTCTGCATTAG
196 GGGTATCCGTACAGCCATAAAACGTAACATCAAAGTACTAGAGGTATATGGAGATTCTGCATTAG
*
41865011 TGATCTATCAACTCAAAGGTGAATGGGAGACAAGAGACCCCAAATTGATTAATTATTGTAGGCTG
261 TGATCTATCAACTCAAAGGTGAATGAGAGACAAGAGACCCCAAATTGATTAATTATTGTAGGCTG
*
41865076 GTTCTGGAGC
326 GTTCTAGAGC
* *
41865086 AATGTATGTTGCAACCACTAAAGAAGACTCTCAAGAAGGCTATCCTTGGAAACTAAACTTTGACG
1 AATGTATGTTACAACCACTAAAGAAGACTCTCAAGAAGGCTATCCTTAGAAACTAAACTTTGACG
* *
41865151 GAGCCTCAAATGCTGTGAATAGTAGAATTGGGGTAGTCCTGGTATCCCAAGATGGAGATCATTAT
66 GAGCCTCAAATGCTGTAAATAATAGAATTGGGGTAGTCCTGGTATCCCAAGATGGAGATCATTAT
41865216 CCATTCACTAGTAAATTAGATTTTAATTACACGAACAATATGGTAGAATACAAAGCATGCATCAT
131 CCATTCACTAGTAAATTAGATTTTAATTACACGAACAATATGGTAGAATACAAAGCATGCATCAT
* * *
41865281 GGGTATCCGTGCAGCCATATAACGTAACATCAAAGTACTAGAGGTATATGGGGATTCTGCATTAG
196 GGGTATCCGTACAGCCATAAAACGTAACATCAAAGTACTAGAGGTATATGGAGATTCTGCATTAG
41865346 TGATCTATCAACTCAAAGGTGAATGAGAGACAAGAGACCCCAAATTGATTAATTATTGTAGGCTG
261 TGATCTATCAACTCAAAGGTGAATGAGAGACAAGAGACCCCAAATTGATTAATTATTGTAGGCTG
41865411 GTTCTAGAGC
326 GTTCTAGAGC
41865421 TGATTGAAGA
Statistics
Matches: 322, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
335 322 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (335 bp):
AATGTATGTTACAACCACTAAAGAAGACTCTCAAGAAGGCTATCCTTAGAAACTAAACTTTGACG
GAGCCTCAAATGCTGTAAATAATAGAATTGGGGTAGTCCTGGTATCCCAAGATGGAGATCATTAT
CCATTCACTAGTAAATTAGATTTTAATTACACGAACAATATGGTAGAATACAAAGCATGCATCAT
GGGTATCCGTACAGCCATAAAACGTAACATCAAAGTACTAGAGGTATATGGAGATTCTGCATTAG
TGATCTATCAACTCAAAGGTGAATGAGAGACAAGAGACCCCAAATTGATTAATTATTGTAGGCTG
GTTCTAGAGC
Found at i:41867959 original size:94 final size:95
Alignment explanation
Indices: 41867814--41868085 Score: 411
Period size: 94 Copynumber: 2.9 Consensus size: 95
41867804 TTAAAGCCAC
*
41867814 AAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGTTAATCTTATTTCCCTAAAGTC
1 AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTTAATCTTATTTCCCTAAAGTC
41867879 ACAGTGGAACAGATTAAAGCTACAAGCTAA
66 ACAGTGGAACAGATTAAAGCTACAAGCTAA
* *
41867909 AAATCTTATCTTCCTGAAGTTGCA-TAGAGCAGATTGAAGATGTTAGTCTTATTTCCCTGAAGTC
1 AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTTAATCTTATTTCCCTAAAGTC
* *
41867973 ACAGTGAAACAGATTAAAGCTACAAGCTAT
66 ACAGTGGAACAGATTAAAGCTACAAGCTAA
* * * * * *
41868003 AAATCTTATCTCCCTGAAGCTGTAGTAGAGCAGATTGAAGATGCTAATCTTATTTCCCTTAAGTT
1 AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTTAATCTTATTTCCCTAAAGTC
* * *
41868068 GCAGTGGAGCAGGTTAAA
66 ACAGTGGAACAGATTAAA
41868086 AATAACAAAT
Statistics
Matches: 160, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
94 86 0.54
95 74 0.46
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
AAATCTTATCTTCCTGAAGTTGCAGTAGAGCAGATTGAAGATGTTAATCTTATTTCCCTAAAGTC
ACAGTGGAACAGATTAAAGCTACAAGCTAA
Found at i:41868112 original size:45 final size:45
Alignment explanation
Indices: 41867771--41868409 Score: 265
Period size: 44 Copynumber: 13.8 Consensus size: 45
41867761 CATCGTGATG
* ***
41867771 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATT-AAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * * ***
41867815 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-GTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * ** *
41867859 AATCTTATTTCCCTAAAGTCACAGTGGAACAGATTAAAGCTACAAGCTAA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA---A-AA--TAACA
* * * * ***
41867910 AATCTTATCTTCCTGAAGTTGCA-TAGAGCAGATTGAAGAT-GTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * ** * * * *
41867953 AGTCTTATTTCCCTGAAGTCACAGTGAAACAGATTAAAGCTACAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA--AATAA-C---A
* * * * * * *
41868004 AATCTTATCTCCCTGAAGCTGTAGTAGAGCAGATTGAAGAT-GCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * *
41868048 AATCTTATTTCCCTTAAGTTGCAGTGGAGCAGGTTAAAAATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * * ** * *
41868093 AATCTTATCTCTCTAAAGTTGCAGTAGAATAGATT-AAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * * *
41868137 AATCTCATAC-CCCTGAAGTTGTAGTGG-GACAGATTGAAGTTATTATAACG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATT-AA---A-AATAACA
* * * *** *
41868187 AATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATT-GAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * * * * * *
41868231 AA-CATTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGATAGCG
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
* * * * *
41868276 AATCTTATTTCCCTGAAATTGCAGTGGAACAAATTAAAACTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---A--A-AAATAACA
* * * * * **
41868327 AGTCTTATCTCTCTGAAGTTGTAGTGGAGAAAATTAAAAATAATG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
41868372 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
41868410 GCCACTAACC
Statistics
Matches: 423, Mismatches: 134, Indels: 75
0.67 0.21 0.12
Matches are distributed among these distances:
43 20 0.05
44 167 0.39
45 101 0.24
46 5 0.01
47 1 0.00
48 2 0.00
49 5 0.01
50 42 0.10
51 80 0.19
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAATAACA
Found at i:41868302 original size:89 final size:89
Alignment explanation
Indices: 41868181--41868441 Score: 270
Period size: 96 Copynumber: 2.9 Consensus size: 89
41868171 TGAAGTTATT
* * *
41868181 ATAACGAATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACTAACATTATCTCTCTG
1 ATAACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAACATTATCTCTCTG
* ** * *
41868246 AAGTTGCAGTAGAGCAGGTTGAAG
66 AAGTTGCAGTAGAGAAAATTAAAA
* * * * * * * *
41868270 ATAGCGAATCTTATTTCCCTGAAATTGCAGTGGAACAAATTAAAACTACAAATTACAAGTCTTAT
1 ATAACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C-ACTAAC-A---TTAT
* *
41868335 CTCTCTGAAGTTGTAGTGGAGAAAATTAAAA
59 CTCTCTGAAGTTGCAGTAGAGAAAATTAAAA
* * *
41868366 ATAATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAACCTTATCTCTCTA
1 ATAACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAACATTATCTCTCTG
41868431 AAGTTGCAGTA
66 AAGTTGCAGTA
41868442 AGTTAGAACG
Statistics
Matches: 134, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
89 56 0.42
91 1 0.01
92 4 0.03
93 5 0.04
94 1 0.01
96 67 0.50
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (89 bp):
ATAACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAACATTATCTCTCTG
AAGTTGCAGTAGAGAAAATTAAAA
Found at i:41868322 original size:183 final size:182
Alignment explanation
Indices: 41868004--41868441 Score: 458
Period size: 183 Copynumber: 2.4 Consensus size: 182
41867994 ACAAGCTATA
* * *** * * *
41868004 AATCTTATCTCCCTGAAGCTGTAGTAGAGCAGATTGAAGATGCTAATCTTATTTCCCTTAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACTAA-CTTATCTCTCTAAAGTTG
* * * * **
41868069 CAGTGGAGCAGGTTAAAAATAACAAATCTTATCTCTCTAAAGTTGCAGTAGAATAGATTAAAGTT
65 CAGTAGAGCAGGTTAAAAATAACAAATCTTATCTCCCTAAAGTTGCAGTAGAACAAATTAAAACT
* *
41868134 ACAAA-T-C-TCATA-C-CCCTGAAGTTGTAGTGG-GACAGATTGAAGTTATTATAACG
130 ACAAATTACATCATATCTCCCTGAAGTTGTAGTGGAGA-AAATT-AA---A-AATAACG
* *
41868187 AATCTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGCCACTAACATTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACTAAC-TTATCTCTCTAAAGTTG
* * * * * *
41868252 CAGTAGAGCAGGTTGAAGATAGCGAATCTTATTTCCCTGAAA-TTGCAGTGGAACAAATTAAAAC
65 CAGTAGAGCAGGTTAAAAATAACAAATCTTATCTCCCT-AAAGTTGCAGTAGAACAAATTAAAAC
* * *
41868316 TACAAATTACAAGTCTTATCTCTCTGAAGTTGTAGTGGAGAAAATTAAAAATAATG
129 TACAAATTAC-A-TCATATCTCCCTGAAGTTGTAGTGGAGAAAATTAAAAATAACG
* *
41868372 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAACCTTATCTCTCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACTAA-CTTATCTCTCTAAAGTTG
41868437 CAGTA
65 CAGTA
41868442 AGTTAGAACG
Statistics
Matches: 214, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
182 1 0.00
183 108 0.50
184 4 0.02
185 70 0.33
186 2 0.01
188 4 0.02
189 3 0.01
190 20 0.09
191 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (182 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCCACTAACTTATCTCTCTAAAGTTGC
AGTAGAGCAGGTTAAAAATAACAAATCTTATCTCCCTAAAGTTGCAGTAGAACAAATTAAAACTA
CAAATTACATCATATCTCCCTGAAGTTGTAGTGGAGAAAATTAAAAATAACG
Found at i:41868438 original size:44 final size:45
Alignment explanation
Indices: 41868330--41868440 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 45
41868320 AATTACAAGT
* * *
41868330 CTTATCTCTCTGAAGTTGTAGTGGAGAAAATTAAAAATAATGAAT
1 CTTATCTCTCTGAAGTTGCAGTGGAGAAAATTAAAAACAATGAAC
* * * ** *
41868375 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACT-AAC
1 CTTATCTCTCTGAAGTTGCAGTGGAGAAAATTAAAAACAATGAAC
*
41868419 CTTATCTCTCTAAAGTTGCAGT
1 CTTATCTCTCTGAAGTTGCAGT
41868441 AAGTTAGAAC
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
44 22 0.40
45 33 0.60
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (45 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGAAAATTAAAAACAATGAAC
Found at i:41874015 original size:28 final size:24
Alignment explanation
Indices: 41873984--41874034 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
41873974 ATGGAGAATA
41873984 ATTAAATTCCTTAAATAAATAAAAAAAG
1 ATTAAATT--TTAAAT--ATAAAAAAAG
41874012 ATTAAATTTTAAATATAAAAAAA
1 ATTAAATTTTAAATATAAAAAAA
41874035 TACAGGGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.39
26 6 0.26
28 8 0.35
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (24 bp):
ATTAAATTTTAAATATAAAAAAAG
Found at i:41874405 original size:23 final size:24
Alignment explanation
Indices: 41874374--41874431 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
41874364 TTGTATCAAA
*
41874374 AAAAT-AAATATA-ATAAAAATAT
1 AAAATAAAATATATATAAAAAAAT
* * *
41874396 ATAATGAAAT-TATTTAAAAAAAT
1 AAAATAAAATATATATAAAAAAAT
41874419 AAAATAAAATATA
1 AAAATAAAATATA
41874432 GTAGCATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
22 6 0.21
23 20 0.71
24 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATAAAATATATATAAAAAAAT
Found at i:41876123 original size:19 final size:19
Alignment explanation
Indices: 41876099--41876136 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41876089 TACCTATAAT
41876099 TTTTTTACAATTTTTCCAA
1 TTTTTTACAATTTTTCCAA
41876118 TTTTTTACAATTTTTCCAA
1 TTTTTTACAATTTTTCCAA
41876137 ATGAAACACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTACAATTTTTCCAA
Found at i:41876181 original size:32 final size:32
Alignment explanation
Indices: 41876142--41876206 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41876132 TCCAAATGAA
41876142 ACACTTACCTACAATTTCAAGTTAACTTATGC
1 ACACTTACCTACAATTTCAAGTTAACTTATGC
41876174 ACACTTACCTACAATTTCAAGTTAACTTATGC
1 ACACTTACCTACAATTTCAAGTTAACTTATGC
41876206 A
1 A
41876207 TGAATTCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (32 bp):
ACACTTACCTACAATTTCAAGTTAACTTATGC
Found at i:41877418 original size:19 final size:20
Alignment explanation
Indices: 41877394--41877431 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
41877384 CCATCATCTT
41877394 TTCCTTTTT-CAAAATTTCG
1 TTCCTTTTTCCAAAATTTCG
41877413 TTCCTTTTTCCAAAATTTC
1 TTCCTTTTTCCAAAATTTC
41877432 TGAAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (20 bp):
TTCCTTTTTCCAAAATTTCG
Found at i:41878151 original size:17 final size:17
Alignment explanation
Indices: 41878129--41878161 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41878119 TTGGACCATG
41878129 TGGGCCACACGGGTGTA
1 TGGGCCACACGGGTGTA
*
41878146 TGGGCCACATGGGTGT
1 TGGGCCACACGGGTGT
41878162 GTGAGCTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.21, G:0.42, T:0.21
Consensus pattern (17 bp):
TGGGCCACACGGGTGTA
Found at i:41888779 original size:23 final size:23
Alignment explanation
Indices: 41888752--41888798 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41888742 CTGCGAAGTT
41888752 ATCAGCACCCTCAGTTATCCCTA
1 ATCAGCACCCTCAGTTATCCCTA
41888775 ATCAGCACCCTCAGTTATCCCTA
1 ATCAGCACCCTCAGTTATCCCTA
41888798 A
1 A
41888799 GGTCATCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (23 bp):
ATCAGCACCCTCAGTTATCCCTA
Found at i:41892156 original size:8 final size:8
Alignment explanation
Indices: 41892143--41892170 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
41892133 TTAAAATATA
41892143 AATTTTGT
1 AATTTTGT
41892151 AATTTTGT
1 AATTTTGT
41892159 AATTTTGT
1 AATTTTGT
41892167 AATT
1 AATT
41892171 ACTACTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (8 bp):
AATTTTGT
Found at i:41892674 original size:21 final size:20
Alignment explanation
Indices: 41892650--41892693 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41892640 ATTTATCTCC
* *
41892650 AATCTTAATGAATATAAAGAA
1 AATCATAATAAATA-AAAGAA
*
41892671 AATCATAATAAATAAAATAA
1 AATCATAATAAATAAAAGAA
41892691 AAT
1 AAT
41892694 ACATTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (20 bp):
AATCATAATAAATAAAAGAA
Found at i:41904783 original size:25 final size:25
Alignment explanation
Indices: 41904745--41904893 Score: 219
Period size: 25 Copynumber: 6.0 Consensus size: 25
41904735 AGTTAAGCTT
* *
41904745 GTTAAA-TTGTTCTTAATAATTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
* *
41904769 GTTAAATTTGTTCTTAATAATTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
41904794 GTTAAATTTGCTCTTAATATTTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
*
41904819 ATTAAATTTGCTCTTAATATTTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
41904844 GTTAAATTTGCTCTTAATATTTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
* * *
41904869 ATTAAATTTGCCCTTATTATTTCCG
1 GTTAAATTTGCTCTTAATATTTCCG
41904894 AATAAGTTAC
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
24 6 0.05
25 111 0.95
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (25 bp):
GTTAAATTTGCTCTTAATATTTCCG
Found at i:41904873 original size:13 final size:12
Alignment explanation
Indices: 41904807--41904877 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
41904797 AAATTTGCTC
41904807 TTAATATTTCCGA
1 TTAA-ATTTCCGA
* **
41904820 TTAAATTTGCTC
1 TTAAATTTCCGA
*
41904832 TTAATATTTCCGG
1 TTAA-ATTTCCGA
* **
41904845 TTAAATTTGCTC
1 TTAAATTTCCGA
41904857 TTAATATTTCCGA
1 TTAA-ATTTCCGA
41904870 TTAAATTT
1 TTAAATTT
41904878 GCCCTTATTA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
12 22 0.50
13 22 0.50
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.49
Consensus pattern (12 bp):
TTAAATTTCCGA
Found at i:41905757 original size:45 final size:45
Alignment explanation
Indices: 41905693--41905958 Score: 355
Period size: 45 Copynumber: 6.0 Consensus size: 45
41905683 ATATCGTACA
* * *
41905693 ATACTATTTGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAT
1 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
* *
41905738 ATACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAT
1 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
41905783 ATACTATTCGGGCCCTT-GAGCCTAGCAGGCTATAATGCCGGTGAT
1 ATACTATTCGGG-CCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
* * *
41905828 ATACTATTCGGGCCTTCGAGCCTAGTAGGTTATAATGCCGATGAT
1 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
* *
41905873 ATACTATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCCAGTGA-
1 ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
* *
41905917 AT--TGATATCGGG-CTTCGAGCCTAGCAGGCGA-AATACCGGTGA
1 ATACT-AT-TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
41905959 ATGAATTCGG
Statistics
Matches: 203, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
42 10 0.05
43 19 0.09
44 11 0.05
45 159 0.78
46 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (45 bp):
ATACTATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAT
Found at i:41908308 original size:19 final size:20
Alignment explanation
Indices: 41908258--41908301 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
41908248 AAATAGATAT
*
41908258 TTATT-TAAATATTAAATTA
1 TTATTATAATTATTAAATTA
*
41908277 TTGTTATAATTATT-AATTA
1 TTATTATAATTATTAAATTA
41908296 TTATTA
1 TTATTA
41908302 ATATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATTATAATTATTAAATTA
Found at i:41911382 original size:30 final size:30
Alignment explanation
Indices: 41911347--41911409 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
41911337 TTTTATTTTA
*
41911347 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
*
41911377 TTGTTAATTTTTTTATTATTTTAAAAGCAT
1 TTGTTAATTTTCTTATTATTTTAAAAGCAT
41911407 TTG
1 TTG
41911410 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAAGCAT
Found at i:41912371 original size:28 final size:28
Alignment explanation
Indices: 41912331--41912387 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
41912321 GAAGTGTGAA
41912331 CCCAACTTCAACTATATGACAATGCTTT
1 CCCAACTTCAACTATATGACAATGCTTT
**
41912359 CCCAACTTCAACTATATGACGGTGCTTT
1 CCCAACTTCAACTATATGACAATGCTTT
41912387 C
1 C
41912388 TTTCAACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.32
Consensus pattern (28 bp):
CCCAACTTCAACTATATGACAATGCTTT
Found at i:41915291 original size:29 final size:29
Alignment explanation
Indices: 41915230--41915294 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
41915220 CCTTATGGCA
* *
41915230 CAATGTTATACATGAACTTTGATTTTGTG
1 CAATTTTATACATGAACTTTGAATTTGTG
* *
41915259 CAATTTTATACATGAA-TTTTAATTTGATT
1 CAATTTTATACATGAACTTTGAATTTG-TG
41915288 CAATTTT
1 CAATTTT
41915295 CATAAACTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (29 bp):
CAATTTTATACATGAACTTTGAATTTGTG
Found at i:41924891 original size:3 final size:3
Alignment explanation
Indices: 41924883--41924921 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
41924873 AATCTAGTCC
* *
41924883 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41924922 CCTTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:41936434 original size:1 final size:1
Alignment explanation
Indices: 41936428--41936453 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
41936418 TTTGCTTCCT
41936428 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
41936454 CTTTGGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41937957 original size:38 final size:38
Alignment explanation
Indices: 41937862--41937961 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 38
41937852 AGTTGAAGCA
*
41937862 AGATCTTATCTCCCTGA-TTACAGCGGAGCAGATCAAAG
1 AGATCTTATCT-CCTGAGTTACAACGGAGCAGATCAAAG
* * * * *
41937900 ATAATCCTATCTCCTTGAGTTACAATGGAGCGGATTAAAG
1 A-GATCTTATCTCC-TGAGTTACAACGGAGCAGATCAAAG
41937940 -GATCTTATCTCTCTGAGTTACA
1 AGATCTTATCTC-CTGAGTTACA
41937962 GTAGAGAAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
38 21 0.42
39 12 0.24
40 17 0.34
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (38 bp):
AGATCTTATCTCCTGAGTTACAACGGAGCAGATCAAAG
Found at i:41938129 original size:44 final size:44
Alignment explanation
Indices: 41937863--41938351 Score: 217
Period size: 44 Copynumber: 11.5 Consensus size: 44
41937853 GTTGAAGCAA
* *
41937863 GATCTTATCTCCCTG-A-TTACAGCGGAGCAGATCAAAGAT--A-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATACAG
* * * *
41937903 -ATCCTATCTCCTTG-AGTTACAATGGAGCGGATT---A-A-AG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* * * * *
41937940 GATCTTATCTCTCTG-AGTTACAGTAGAGAAGA-TCACAT-CAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* ** *
41937981 G-TCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAGAATGCA-
1 GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGA-TTAA-AATACAG
* * * * *
41938025 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAATACAG
* * *
41938069 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* * * ***
41938112 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* * * ** *
41938154 G-TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TACAG
* **
41938199 GATCTTATC-CCCTG-AGTTACAGTGGAGCAGATT-GAAGCCAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* * ** * *
41938240 AGATCTTATCTCCCCG-AGATTACAGCGGAGCAGA-TCGAAGACAC
1 -GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATACAG
* * ** * *
41938284 TATCCTATCTCCCTGAAGTTACAGTGGAGTGGGTTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
* *
41938328 GATCTTATCTCTCTGAGGTTACAG
1 GATCTTATCTCCCTGAAGTTACAG
41938352 CAGAGTAGGC
Statistics
Matches: 340, Mismatches: 77, Indels: 60
0.71 0.16 0.13
Matches are distributed among these distances:
36 2 0.01
37 1 0.00
38 24 0.07
39 13 0.04
40 30 0.09
41 46 0.14
42 18 0.05
43 63 0.19
44 96 0.28
45 37 0.11
46 10 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATACAG
Found at i:41938159 original size:173 final size:166
Alignment explanation
Indices: 41937862--41938235 Score: 542
Period size: 173 Copynumber: 2.2 Consensus size: 166
41937852 AGTTGAAGCA
*
41937862 AGATCTTATCTCCCTGA-TTACAGCGGAGCAGATC-AA-AGATAATCCTATCTCCTTGAGTTACA
1 AGATCTTATCTCCCTGAGTTACAGCGGAGCAGATCGAAGAGATAATCCTATCTCCCTGAGTTACA
41937924 ATGGAGCGGATTAAAGGATCTTATCTCTCTGAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
66 ATGGAGCGGATTAAAGGATCTTATCTCTCTGAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
41937989 TCCCTGAGATTACAGTGGAACAGACCGAAGAA-TGC
131 TCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
*
41938024 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGA-GTTACAGCGGAGCAGATCGAAGAGATAATCCTATCTCCCTG-AGTTA
* * *
41938089 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
64 CAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTG-AGTTACAGTAGAGAAGATCACATCAG
* * **
41938154 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGC
123 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
* *
41938198 AGATCTTATC-CCCTGAGTTACAGTGGAGCAGATTGAAG
1 AGATCTTATCTCCCTGAGTTACAGCGGAGCAGATCGAAG
41938236 CCAGAGATCT
Statistics
Matches: 189, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
162 17 0.09
164 17 0.09
165 2 0.01
166 17 0.09
167 16 0.08
168 1 0.01
172 40 0.21
173 66 0.35
174 13 0.07
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (166 bp):
AGATCTTATCTCCCTGAGTTACAGCGGAGCAGATCGAAGAGATAATCCTATCTCCCTGAGTTACA
ATGGAGCGGATTAAAGGATCTTATCTCTCTGAGTTACAGTAGAGAAGATCACATCAGGTCTTATC
TCCCTGAGATTACAGTGGAACAGACCGAAGAATTGC
Found at i:41938217 original size:85 final size:85
Alignment explanation
Indices: 41937940--41938280 Score: 303
Period size: 88 Copynumber: 3.9 Consensus size: 85
41937930 CGGATTAAAG
* * * *
41937940 GATCTTATCTCTCTGAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGT
1 GATCTTATCTCCCTGAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
*
41938005 GGAACAGACCGAAGAATGCA
66 GGAGCAGACCGAAGAATGCA
** * ** * *
41938025 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTGAAGTTA
1 GATCTTATCTCCCTGA-GTTACAGTAGAGCAGATCG--CATCA-GGTCTTATCTCCCTGAGGTTA
* ** **
41938089 CAGTGGAGCGGA-TTAA-AATAAA
62 CAGTGGAGCAGACCGAAGAATGCA
* * *
41938111 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACA
1 -GATCTTATCTCCCTG-AGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACA
*
41938176 GTGGAGTAGACCGAAGAATTGCA
64 GTGGAGCAGACCGAAGAA-TGCA
* * * * * *
41938199 GATCTTATC-CCCTGAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCCGAGATTAC
1 GATCTTATCTCCCTGAGTTACAGTAGAGCAGATCGCA-TCAG-G-TCTTATCTCCCTGAGGTTAC
* *
41938263 AGCGGAGCAGATCGAAGA
63 AGTGGAGCAGACCGAAGA
41938281 CACTATCCTA
Statistics
Matches: 198, Mismatches: 45, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
85 61 0.31
86 29 0.15
87 45 0.23
88 63 0.32
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (85 bp):
GATCTTATCTCCCTGAGTTACAGTAGAGCAGATCGCATCAGGTCTTATCTCCCTGAGGTTACAGT
GGAGCAGACCGAAGAATGCA
Found at i:41938263 original size:129 final size:128
Alignment explanation
Indices: 41938027--41938264 Score: 279
Period size: 128 Copynumber: 1.9 Consensus size: 128
41938017 AGAATGCAGA
*
41938027 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGTTACAG
* * * *
41938092 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 TGGAGCAGATTAAAACAAAGGATCTTATCTCCCCGAAGTTACAGTAGAGTAGATCGCATCAGG
* * * *
41938155 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGA-ATTGCAGATCTTATC-CCCTG-AGTT
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATA-T--A-ATCCTATCTCCCTGAAGTT
* * *
41938217 ACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCCG-AGATTACAG
62 ACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCCGAAG-TTACAG
41938265 CGGAGCAGAT
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
127 1 0.01
128 39 0.42
129 39 0.42
130 6 0.07
131 7 0.08
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (128 bp):
TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATATAATCCTATCTCCCTGAAGTTACAG
TGGAGCAGATTAAAACAAAGGATCTTATCTCCCCGAAGTTACAGTAGAGTAGATCGCATCAGG
Found at i:41938279 original size:88 final size:88
Alignment explanation
Indices: 41937940--41938312 Score: 308
Period size: 85 Copynumber: 4.3 Consensus size: 88
41937930 CGGATTAAAG
* * * *
41937940 GATCTTATCTCTCTGAGTTACAGTAGAGAAGATC-ACA-TCAG-G-TCTTATCTCCCTGAGATTA
1 GATCTTATCTCCCTGAGTTACAGTGGAGCAGATCGA-AGACAGAGATCTTATCTCCCTGAGATTA
*
41938001 CAGTGGAACAGACCGAAGAATGCA
65 CAGTGGAGCAGACCGAAGAATGCA
* * * *
41938025 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATA-ATCCTATCTCCCTGA-AGTT
1 GATCTTATCTCCCTGA-GTTACAGTGGAGCAGATCGAAGACAGAGATCTTATCTCCCTGAGA-TT
* ** **
41938088 ACAGTGGAGCGGA-TTAA-AATAAA
64 ACAGTGGAGCAGACCGAAGAATGCA
* * * * * * *
41938111 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCAG-G-TCTTATCTCTCTGAGGTT
1 -GATCTTATCTCCCTG-AGTTACAGTGGAGCAGATCGAAGACAGAGATCTTATCTCCCTGAGATT
*
41938173 ACAGTGGAGTAGACCGAAGAATTGCA
64 ACAGTGGAGCAGACCGAAGAA-TGCA
* * *
41938199 GATCTTATC-CCCTGAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCCGAGATTAC
1 GATCTTATCTCCCTGAGTTACAGTGGAGCAGATCGAAGACAGAGATCTTATCTCCCTGAGATTAC
* *
41938263 AGCGGAGCAGATCGAAG-A--CA
66 AGTGGAGCAGACCGAAGAATGCA
* *
41938283 CTATCCTATCTCCCTGAAGTTACAGTGGAG
1 -GATCTTATCTCCCTG-AGTTACAGTGGAG
41938313 TGGGTTAAAA
Statistics
Matches: 224, Mismatches: 45, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
84 2 0.01
85 65 0.29
86 35 0.16
87 62 0.28
88 60 0.27
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (88 bp):
GATCTTATCTCCCTGAGTTACAGTGGAGCAGATCGAAGACAGAGATCTTATCTCCCTGAGATTAC
AGTGGAGCAGACCGAAGAATGCA
Found at i:41938429 original size:216 final size:216
Alignment explanation
Indices: 41938024--41938425 Score: 556
Period size: 216 Copynumber: 1.9 Consensus size: 216
41938014 CGAAGAATGC
* * *
41938024 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
* * *
41938089 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAA
* * * * *** * * *
41938154 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTGCAGATCTTATCCCCTGAGTTAC
131 GTCTTATCTCCCTGAAGATACAGTGGAATAGACCGAAGAACCACAAACCTCATCCCCTGAGTTAC
41938219 AGTGGAGCAGATTGAAGCCAG
196 AGTGGAGCAGATTGAAGCCAG
41938240 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACA-TAATCCTATCTCCCTGAAGTT
* * * *
41938304 ACAGTGGAGTGGGTTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGGCCGCATCA
65 ACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCA
* * ** *
41938369 AGTCTTATTTCCCTGAAGATGCAGTGGAATAGATTGAA-AACCACAAACCTCGTCCCC
130 AGTCTTATCTCCCTGAAGATACAGTGGAATAGACCGAAGAACCACAAACCTCATCCCC
41938426 CTGAAGTTGC
Statistics
Matches: 160, Mismatches: 25, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
215 12 0.08
216 147 0.92
217 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (216 bp):
AGATCTTATCTCCCCGAGATTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGACCGCATCAA
GTCTTATCTCCCTGAAGATACAGTGGAATAGACCGAAGAACCACAAACCTCATCCCCTGAGTTAC
AGTGGAGCAGATTGAAGCCAG
Found at i:41939741 original size:3 final size:3
Alignment explanation
Indices: 41939733--41939771 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
41939723 AATCTAGTCC
* *
41939733 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41939772 CCTTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:41948549 original size:46 final size:46
Alignment explanation
Indices: 41948499--41948671 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
41948489 TGGTTGAGCA
41948499 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41948545 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
41948590 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41948638 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41948672 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41948655 original size:93 final size:93
Alignment explanation
Indices: 41948496--41948667 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
41948486 GGATGGTTGA
* * * *
41948496 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
41948561 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
*
41948589 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
41948654 TGAGTCCGAGTTCA
66 TGAGTCCGAGTTCA
41948668 CTTAGGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:41956104 original size:46 final size:46
Alignment explanation
Indices: 41956049--41956176 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
41956039 GATGGTTGAG
41956049 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA
** *
41956095 TGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA
* * *
41956141 CACCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41956177 GGGGCGGGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA
Found at i:41959025 original size:19 final size:20
Alignment explanation
Indices: 41958987--41959027 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41958977 ATTTTAAACC
*
41958987 TACCTAGTTCAATCAACATT
1 TACCTAATTCAATCAACATT
*
41959007 TACCTAATT-AATGAACATT
1 TACCTAATTCAATCAACATT
41959026 TA
1 TA
41959028 TGCACTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (20 bp):
TACCTAATTCAATCAACATT
Found at i:41959683 original size:37 final size:41
Alignment explanation
Indices: 41959616--41959728 Score: 130
Period size: 37 Copynumber: 2.9 Consensus size: 41
41959606 CGGATAATTT
41959616 GAAGTAATA-AGTTGACACCCAGTGTCTCATCGGCTAAAT-C
1 GAAGTAATAGA-TTGACACCCAGTGTCTCATCGGCTAAATCC
* ** *
41959656 GAAGT-A-A-ATTGGCACCCAGTG-CATCATCGAATTAATCC
1 GAAGTAATAGATTGACACCCAGTGTC-TCATCGGCTAAATCC
41959694 GAAGTAATAGATTGACACCCAGTGTCTCATCGGCT
1 GAAGTAATAGATTGACACCCAGTGTCTCATCGGCT
41959729 CGATGTCGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
36 1 0.02
37 22 0.37
38 8 0.13
39 2 0.03
40 6 0.10
41 20 0.33
42 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (41 bp):
GAAGTAATAGATTGACACCCAGTGTCTCATCGGCTAAATCC
Found at i:41960734 original size:19 final size:21
Alignment explanation
Indices: 41960699--41960740 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
41960689 GTATTTCATA
*
41960699 TATTATTATTTTATACATATG
1 TATTATTATTTTATACACATG
41960720 TATT-TTATTTT-TACACATG
1 TATTATTATTTTATACACATG
41960739 TA
1 TA
41960741 CACACAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTATTATTTTATACACATG
Found at i:41967109 original size:37 final size:40
Alignment explanation
Indices: 41967041--41967154 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 40
41967031 TCGGATAATT
41967041 CGAAGTAATA-AGTTGACACCCAGTGTCTCATCGGCTAAAC
1 CGAAGTAATAGA-TTGACACCCAGTGTCTCATCGGCTAAAC
* ** *
41967081 CGAAGT-A-A-ATTGGCACCCAGTG-CATCATCGAATTAATC
1 CGAAGTAATAGATTGACACCCAGTGTC-TCATCG-GCTAAAC
41967119 CGAAGTAATAGATTGACACCCAGTGTCTCATCGGCT
1 CGAAGTAATAGATTGACACCCAGTGTCTCATCGGCT
41967155 CGATGTCGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
36 1 0.02
37 18 0.30
38 12 0.20
39 2 0.03
40 8 0.13
41 19 0.31
42 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAGATTGACACCCAGTGTCTCATCGGCTAAAC
Found at i:41967919 original size:17 final size:16
Alignment explanation
Indices: 41967897--41967928 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41967887 AGCTTTTCTC
41967897 CTTTTCTTTCTCTTTTT
1 CTTTTCTTTCT-TTTTT
41967914 CTTTTCTTTCTTTTT
1 CTTTTCTTTCTTTTT
41967929 CTTCTCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTTCTTTCTTTTTT
Found at i:41967940 original size:21 final size:21
Alignment explanation
Indices: 41967899--41967940 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
41967889 CTTTTCTCCT
*
41967899 TTTCTTTCTCTTTTTCTTTTC
1 TTTCTTTCTCTTTCTCTTTTC
*
41967920 TTTCTTTTTC-TTCTCTGTTTC
1 TTTCTTTCTCTTTCTCT-TTTC
41967941 GTTTTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTCTTTCTCTTTTC
Found at i:41969654 original size:26 final size:26
Alignment explanation
Indices: 41969625--41969698 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
41969615 CTCAATATAT
41969625 GGCTCTTCGTGAGCTTCCCGATAAAA
1 GGCTCTTCGTGAGCTTCCCGATAAAA
* * *
41969651 GGCTCTTCGTGAGCTTCCTGATTAAT
1 GGCTCTTCGTGAGCTTCCCGATAAAA
*
41969677 GGCTCTTC-AGAGCTTCCCGATA
1 GGCTCTTCGTGAGCTTCCCGATA
41969699 TGGCTCCCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 11 0.26
26 31 0.74
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATAAAA
Found at i:41972415 original size:20 final size:20
Alignment explanation
Indices: 41972392--41972437 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41972382 TAAGCTCGGT
41972392 TGAGCTCAAACGAGCTGAAA
1 TGAGCTCAAACGAGCTGAAA
* * *
41972412 TGAGCTTAAATGAGCTGAAT
1 TGAGCTCAAACGAGCTGAAA
41972432 TGAGCT
1 TGAGCT
41972438 GGACGGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (20 bp):
TGAGCTCAAACGAGCTGAAA
Found at i:41972438 original size:10 final size:10
Alignment explanation
Indices: 41972392--41972438 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
41972382 TAAGCTCGGT
*
41972392 TGAGCTCAAA
1 TGAGCTGAAA
*
41972402 CGAGCTGAAA
1 TGAGCTGAAA
*
41972412 TGAGCTTAAA
1 TGAGCTGAAA
*
41972422 TGAGCTGAAT
1 TGAGCTGAAA
41972432 TGAGCTG
1 TGAGCTG
41972439 GACGGAGCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (10 bp):
TGAGCTGAAA
Found at i:41974559 original size:30 final size:31
Alignment explanation
Indices: 41974488--41974570 Score: 100
Period size: 30 Copynumber: 2.7 Consensus size: 31
41974478 CTATTGTTTC
*
41974488 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTTTTCAATCTCA
*
41974519 AATTTC-TTTTC-GCTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATCT-TCTTTTTCAATCTCA
* *
41974548 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTCATCTTCTTTTT
41974571 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 7 0.16
30 30 0.68
31 7 0.16
ACGTcount: A:0.13, C:0.23, G:0.01, T:0.63
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTTTTCAATCTCA
Found at i:41974577 original size:12 final size:12
Alignment explanation
Indices: 41974546--41974570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41974536 TTTTTCAATC
41974546 TCATTTTCTTTT
1 TCATTTTCTTTT
41974558 TCATTTTCTTTT
1 TCATTTTCTTTT
41974570 T
1 T
41974571 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:41974588 original size:12 final size:12
Alignment explanation
Indices: 41974573--41974604 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
41974563 TTCTTTTTGC
41974573 TTTTCAAAGGCT
1 TTTTCAAAGGCT
41974585 TTTTCAAAGGCT
1 TTTTCAAAGGCT
41974597 TTTTCAAA
1 TTTTCAAA
41974605 TTCTCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:41974661 original size:5 final size:5
Alignment explanation
Indices: 41974651--41974713 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
41974641 CTCTTGCCTC
* * *
41974651 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTT TGCTTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-CTTT T-C-TTT
41974699 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
41974714 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 3 0.06
5 30 0.61
6 12 0.24
7 4 0.08
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:41975660 original size:12 final size:11
Alignment explanation
Indices: 41975644--41975686 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
41975634 TTTTTTCAGT
*
41975644 ATTTTTTTATA
1 ATTTTTTTTTA
*
41975655 ATTTTTTTTGA
1 ATTTTTTTTTA
*
41975666 ATTTTTTTTTCG
1 ATTTTTTTTT-A
41975678 ATTTTTTTT
1 ATTTTTTTT
41975687 AAACTTGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTTA
Found at i:41977317 original size:20 final size:20
Alignment explanation
Indices: 41977294--41977339 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
41977284 TAAGCTTGGT
41977294 TGAGCTCAAACGAGCTGAAA
1 TGAGCTCAAACGAGCTGAAA
* *
41977314 TGAGCTCAAATGAGCTGAAT
1 TGAGCTCAAACGAGCTGAAA
41977334 TGAGCT
1 TGAGCT
41977340 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (20 bp):
TGAGCTCAAACGAGCTGAAA
Found at i:41977340 original size:10 final size:10
Alignment explanation
Indices: 41977294--41977340 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
41977284 TAAGCTTGGT
*
41977294 TGAGCTCAAA
1 TGAGCTGAAA
*
41977304 CGAGCTGAAA
1 TGAGCTGAAA
*
41977314 TGAGCTCAAA
1 TGAGCTGAAA
*
41977324 TGAGCTGAAT
1 TGAGCTGAAA
41977334 TGAGCTG
1 TGAGCTG
41977341 GACGGAGCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (10 bp):
TGAGCTGAAA
Found at i:41978544 original size:79 final size:79
Alignment explanation
Indices: 41978413--41978566 Score: 308
Period size: 79 Copynumber: 1.9 Consensus size: 79
41978403 AGAGTGTTTC
41978413 CAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCTCGAA
1 CAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCTCGAA
41978478 GTCCAGTGCATTTG
66 GTCCAGTGCATTTG
41978492 CAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCTCGAA
1 CAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCTCGAA
41978557 GTCCAGTGCA
66 GTCCAGTGCA
41978567 CAATCCACAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (79 bp):
CAATGTACCTTACTCGCAGCATTTACTCATTTCGATTGCTTTTGTATTGCTTCTTTCCCCTCGAA
GTCCAGTGCATTTG
Found at i:41985661 original size:23 final size:23
Alignment explanation
Indices: 41985614--41985656 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41985604 CATTTCAACC
41985614 TACTAAATATTAACTAAATTATA
1 TACTAAATATTAACTAAATTATA
*
41985637 TACTACATATT-A-TAAATTAT
1 TACTAAATATTAACTAAATTAT
41985657 TTATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
TACTAAATATTAACTAAATTATA
Found at i:42008697 original size:20 final size:20
Alignment explanation
Indices: 42008672--42008717 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
42008662 AACGTTCGAC
42008672 ATCACTTTCTCATACACAAT
1 ATCACTTTCTCATACACAAT
42008692 ATCACTTTCTCATACACAAT
1 ATCACTTTCTCATACACAAT
*
42008712 CTCACT
1 ATCACT
42008718 CAATTCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (20 bp):
ATCACTTTCTCATACACAAT
Found at i:42025202 original size:14 final size:14
Alignment explanation
Indices: 42025183--42025216 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42025173 TCCTGAAGTG
*
42025183 GATGATATGATTAT
1 GATGATATGACTAT
*
42025197 GATGATATTACTAT
1 GATGATATGACTAT
42025211 GATGAT
1 GATGAT
42025217 GAAAGTCGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (14 bp):
GATGATATGACTAT
Found at i:42026101 original size:15 final size:15
Alignment explanation
Indices: 42026077--42026120 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
42026067 TATGATATCG
42026077 TATCTTGGATTTCTC
1 TATCTTGGATTTCTC
* *
42026092 TATTTTGGATTCCTC
1 TATCTTGGATTTCTC
*
42026107 TATCTTGGTTTTCT
1 TATCTTGGATTTCT
42026121 TGTCATCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.11, C:0.18, G:0.14, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTC
Found at i:42029036 original size:19 final size:20
Alignment explanation
Indices: 42029012--42029054 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
42029002 TTGAATTCTA
*
42029012 ATGCTTTATTATT-ATGAGT
1 ATGCTTGATTATTCATGAGT
42029031 ATGCTTGATTATTCCATGAGT
1 ATGCTTGATTATT-CATGAGT
42029052 ATG
1 ATG
42029055 TGATTGGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (20 bp):
ATGCTTGATTATTCATGAGT
Found at i:42029271 original size:45 final size:44
Alignment explanation
Indices: 42029186--42029271 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 44
42029176 TATGTAATCT
*
42029186 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATGTGACATTC
1 GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATTC
*
42029230 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATGA-ATGACA
1 GAACTCATTGAGTTGT-GTCTGAGTTCATGATAT-ATATGACA
42029272 CATCTTTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 16 0.42
45 21 0.55
46 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (44 bp):
GAACTCATTGAGTTGTGTCTGAGTTCATGATATATATGACATTC
Found at i:42033526 original size:90 final size:90
Alignment explanation
Indices: 42033415--42033594 Score: 333
Period size: 90 Copynumber: 2.0 Consensus size: 90
42033405 CGGAATTCCT
*
42033415 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATTCACGTTGAGTTGTCGA
1 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
*
42033480 AAGGCCTAGTAAACTTTGTGCTCTA
66 AAGGCCTAGTAAAATTTGTGCTCTA
*
42033505 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGTTTAAGATCCACGTTGAGTTGTCGA
1 CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
42033570 AAGGCCTAGTAAAATTTGTGCTCTA
66 AAGGCCTAGTAAAATTTGTGCTCTA
42033595 ACTCCAAGGG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (90 bp):
CTAGCTCATTGAGTTGGAGCATCTGTTTCTCTTTAGCGAGCTTAAGATCCACGTTGAGTTGTCGA
AAGGCCTAGTAAAATTTGTGCTCTA
Found at i:42039822 original size:44 final size:44
Alignment explanation
Indices: 42039772--42039925 Score: 160
Period size: 42 Copynumber: 3.6 Consensus size: 44
42039762 TGTGTTATTG
42039772 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
* * *
42039816 TGTAAGACCATGTCTGGGACATTGGCATCGTATATG-G-TTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCG-ATTTGTGATTTACA
* *
42039858 TGTAAGAGCC-TGTCTGGGACAG-TGGCATTGATATT-TGA-TTATA
1 TGTAAGA-CCATGTCTGGGAC-GTTGGCATCGAT-TTGTGATTTACA
**
42039901 TGTAAGACCACATCTGGGACGTTGG
1 TGTAAGACCATGTCTGGGACGTTGG
42039926 TGTTGTACGA
Statistics
Matches: 91, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
41 2 0.02
42 32 0.35
43 23 0.25
44 30 0.33
45 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTACA
Found at i:42039875 original size:42 final size:44
Alignment explanation
Indices: 42039771--42039925 Score: 160
Period size: 44 Copynumber: 3.6 Consensus size: 44
42039761 ATGTGTTATT
* *
42039771 GTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTAC
*
42039815 ATGTAAGACCATGTCTGGGACATTGGCATCGTATATG-G-TTT-C
1 GTGTAAGACCATGTCTGGGACATTGGCATCG-ATATGTGATTTAC
* * *
42039857 GTGTAAGAGCC-TGTCTGGGACAGTGGCATTGATATTTGATTATA-
1 GTGTAAGA-CCATGTCTGGGACATTGGCATCGATATGTGATT-TAC
** *
42039901 -TGTAAGACCACATCTGGGACGTTGG
1 GTGTAAGACCATGTCTGGGACATTGG
42039926 TGTTGTACGA
Statistics
Matches: 93, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
41 4 0.04
42 29 0.31
43 25 0.27
44 31 0.33
45 4 0.04
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (44 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTAC
Found at i:42044161 original size:12 final size:12
Alignment explanation
Indices: 42044146--42044187 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
42044136 CTCCAGTTTT
42044146 CACACGGCCTAG
1 CACACGGCCTAG
42044158 CACACGGCCTAG
1 CACACGGCCTAG
*
42044170 CACACGGCCTGG
1 CACACGGCCTAG
42044182 CACACG
1 CACACG
42044188 TGCGTGTGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.24, C:0.43, G:0.26, T:0.07
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:42050232 original size:41 final size:42
Alignment explanation
Indices: 42050184--42050267 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
42050174 TTTAATTTGC
42050184 AAGTTTTGCACC-GTTACAATTTAGTCATTTTTCTTTAATTA
1 AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
*
42050225 AAGTTTTGCACCTTTTACAATTTAGTCATTTTTCTTTAATTA
1 AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
42050267 A
1 A
42050268 CTATCTATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 12 0.29
42 29 0.71
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.50
Consensus pattern (42 bp):
AAGTTTTGCACCTGTTACAATTTAGTCATTTTTCTTTAATTA
Found at i:42054313 original size:25 final size:25
Alignment explanation
Indices: 42054279--42054328 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42054269 ATTTATATTC
42054279 ATCTAGCATTCATATTAGAAACCAA
1 ATCTAGCATTCATATTAGAAACCAA
42054304 ATCTAGCATTCATATTAGAAACCAA
1 ATCTAGCATTCATATTAGAAACCAA
42054329 TCAAAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
ATCTAGCATTCATATTAGAAACCAA
Found at i:42064209 original size:27 final size:27
Alignment explanation
Indices: 42064179--42064270 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
42064169 ATTACCAAAG
* * * *
42064179 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
*
42064206 TACCCTCGATTTGCAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
42064233 TACCCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGA-TTTACAAAATTACCATTT
42064260 TACCCTCGATT
1 TACCCTCGATT
42064271 GTGAAATTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.02
27 55 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:42064210 original size:54 final size:52
Alignment explanation
Indices: 42064152--42064280 Score: 125
Period size: 54 Copynumber: 2.4 Consensus size: 52
42064142 ATTATTGAAA
* * * *
42064152 TACCCTCGACTTGTAAGATTACCAAAGTACCCTC-GATTTATAGAATTATCGTTT
1 TACCCTCGA-TTGTAA-ATTACCAAAGTACCCTCAG-TTTACAAAATTACCATTT
* ***
42064206 TACCCTCGATTTGCAAAATTACCATTTTACCCTCAGTTTACAAAATTACCATTT
1 TACCCTCGA-TTG-TAAATTACCAAAGTACCCTCAGTTTACAAAATTACCATTT
42064260 TACCCTCGATTGTGAAATTAC
1 TACCCTCGATTGT-AAATTAC
42064281 TAAAATACTC
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
53 10 0.16
54 49 0.79
55 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (52 bp):
TACCCTCGATTGTAAATTACCAAAGTACCCTCAGTTTACAAAATTACCATTT
Found at i:42064380 original size:107 final size:108
Alignment explanation
Indices: 42064269--42064510 Score: 274
Period size: 107 Copynumber: 2.2 Consensus size: 108
42064259 TTACCCTCGA
* * * *
42064269 TTGTGAAATTACTAAAATACTCTTGTAGAATAAAATTACCAAAATACCCCTAGTTTGTAAAATTA
1 TTGTGAAATTACTGAAATACCCTTGTAG--TAAAATTACCAAAATACCCCTAATTTATAAAATTA
* * *
42064334 C-CAAATACCCCT-AGTTTGT-AAAATTACCGAAATACCACTGGT
64 CAAAAATACCCCTGACTTTGTAAAAATTACAGAAATACCACTGGT
* * *
42064376 TTGTGAAATTACCGAAATACCCTTAATTTGTAAAATTACCAAAATACCCCTAATTTATAAAATTA
1 TTGTGAAATTACTGAAATACCCTT--GTAGTAAAATTACCAAAATACCCCTAATTTATAAAATTA
* * * *
42064441 CAAAAATACCCTTGACTTTTTAAAAATTATAGAAATACCATTGGT
64 CAAAAATACCCCTGACTTTGTAAAAATTACAGAAATACCACTGGT
***
42064486 TTACAAAATTACTGAAATACCCTTG
1 TTGTGAAATTACTGAAATACCCTTG
42064511 GTTTGTAGAT
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
107 55 0.50
108 9 0.08
109 7 0.06
110 40 0.36
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (108 bp):
TTGTGAAATTACTGAAATACCCTTGTAGTAAAATTACCAAAATACCCCTAATTTATAAAATTACA
AAAATACCCCTGACTTTGTAAAAATTACAGAAATACCACTGGT
Found at i:42064414 original size:54 final size:54
Alignment explanation
Indices: 42064299--42064529 Score: 214
Period size: 54 Copynumber: 4.3 Consensus size: 54
42064289 TCTTGTAGAA
* * * *
42064299 TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACC-AAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCACTAGTTTATAAAATTACCGAAATACCCTTAATTTG
* * * *
42064352 TAAAATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTTAATTTG
1 TAAAATTACCAAAATACCACTAGTTTATAAAATTACCGAAATACCCTTAATTTG
* * ** * *
42064406 TAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAATACCCTTGACTTTT
1 TAAAATTACCAAAATACCACTAGTTTATAAAATTACCGAAATACCCTT-AATTTG
* * * * * **
42064461 TAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTG
1 T-AAAATTACCA-AAATACCACTAGTTTATAAAATTACCGAAATACCCTTAATTTG
* *
42064516 TAGATTTACCAAAA
1 TAAAATTACCAAAA
42064530 CACCCTTGTA
Statistics
Matches: 143, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
53 33 0.23
54 62 0.43
55 11 0.08
56 37 0.26
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (54 bp):
TAAAATTACCAAAATACCACTAGTTTATAAAATTACCGAAATACCCTTAATTTG
Found at i:42064452 original size:26 final size:27
Alignment explanation
Indices: 42064299--42064451 Score: 209
Period size: 27 Copynumber: 5.7 Consensus size: 27
42064289 TCTTGTAGAA
42064299 TAAAATTACCAAAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
42064326 TAAAATTACC-AAATACCCCTAGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
* * *
42064352 TAAAATTACCGAAATACCACTGGTTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
* * * *
42064379 TGAAATTACCGAAATACCCTTAATTTG
1 TAAAATTACCAAAATACCCCTAGTTTG
* *
42064406 TAAAATTACCAAAATACCCCTAATTTA
1 TAAAATTACCAAAATACCCCTAGTTTG
*
42064433 TAAAATTACAAAAATACCC
1 TAAAATTACCAAAATACCC
42064452 TTGACTTTTT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
26 26 0.23
27 87 0.77
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.29
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTAGTTTG
Found at i:42064502 original size:27 final size:26
Alignment explanation
Indices: 42064459--42064514 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
42064449 CCCTTGACTT
42064459 TTTAAAAATTATAGAAATACCATTGG
1 TTTAAAAATTATAGAAATACCATTGG
*
42064485 TTTACAAAATTACT-GAAATACCCTTGG
1 TTTA-AAAATTA-TAGAAATACCATTGG
42064512 TTT
1 TTT
42064515 GTAGATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACCATTGG
Found at i:42064503 original size:110 final size:107
Alignment explanation
Indices: 42064299--42064534 Score: 283
Period size: 110 Copynumber: 2.2 Consensus size: 107
42064289 TCTTGTAGAA
* * * * *
42064299 TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAATACCCCTAGTTTGTAAAATTACCGA
1 TAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAATACCCCTACTTTGTAAAATTACAGA
***
42064364 AATACCACTGGTTTGTGAAATTACCGAAATACCCTTAATTTG
66 AATACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTG
* * *
42064406 TAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAAATACCCTTGACTTTTTAAAAATTAT
1 TAAAATTACCAAAATACCCCTAATTTATAAAATTAC-AAAATACCCCT-ACTTTGT-AAAATTAC
* * **
42064471 AGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTG
63 AGAAATACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTG
* * *
42064516 TAGATTTACCAAAACACCC
1 TAAAATTACCAAAATACCC
42064535 TTGTAGGATA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
107 34 0.31
108 9 0.08
109 5 0.05
110 60 0.56
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (107 bp):
TAAAATTACCAAAATACCCCTAATTTATAAAATTACAAAATACCCCTACTTTGTAAAATTACAGA
AATACCACTGGTTTACAAAATTACCGAAATACCCTTAATTTG
Found at i:42064598 original size:27 final size:27
Alignment explanation
Indices: 42064555--42064628 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
42064545 AAATGACTAA
*
42064555 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
42064582 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
42064609 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
42064629 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:42064632 original size:27 final size:27
Alignment explanation
Indices: 42064568--42064632 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
42064558 ACCCCTAATA
*
42064568 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
42064595 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
42064622 GGTAAAATGAC
1 GGTAAAATGAC
42064633 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:42065479 original size:25 final size:24
Alignment explanation
Indices: 42065441--42065510 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
42065431 AGGAAGTGCT
* *
42065441 AAAATGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
42065465 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
42065490 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
42065511 GTTAAAAGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 1 0.02
25 40 0.98
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:42065717 original size:42 final size:42
Alignment explanation
Indices: 42065658--42065750 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
42065648 TAGTCTCCCC
*
42065658 AAATGGGCTTGCATACATTCATTGACATT-ACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTCA-ATGTGATATTG
42065700 AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
42065742 AAATTGGGC
1 AAA-TGGGC
42065751 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 42 0.88
43 6 0.12
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTCAATGTGATATTG
Found at i:42065816 original size:31 final size:31
Alignment explanation
Indices: 42065774--42065914 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
42065764 CGTTTACAGT
42065774 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
42065805 AAAAGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42065836 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
42065867 AAAGGCTTCGACCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42065898 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
42065915 ACATGTCAAG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 105 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:42072808 original size:24 final size:24
Alignment explanation
Indices: 42072776--42072845 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
42072766 TACTTGGGTT
* *
42072776 ATTTTCCATCAATTCATCATTTGA
1 ATTTACCATCAATTCATCCTTTGA
**
42072800 ATTTACCATCAATTCATCCTTTTC
1 ATTTACCATCAATTCATCCTTTGA
*
42072824 ATTTACCA-AAATTCATCCTTTG
1 ATTTACCATCAATTCATCCTTTG
42072846 CCACATAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (24 bp):
ATTTACCATCAATTCATCCTTTGA
Found at i:42080577 original size:46 final size:46
Alignment explanation
Indices: 42080510--42080602 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
42080500 CGCCTTGTTT
* *
42080510 CCTAAGAGGGAGTCGTCGTATGTTAGACAAATATCAAATGACGGTA
1 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
* *
42080556 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAGATGGCGGTA
1 CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
42080602 C
1 C
42080603 ATTCTGCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (46 bp):
CCTAAGAGGGAGTCGACGTATGTTAGACAAATAGCAAATGACGGTA
Found at i:42083158 original size:26 final size:26
Alignment explanation
Indices: 42083122--42083231 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
42083112 TGATACAAAT
42083122 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
42083148 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
42083174 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
42083200 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
42083226 TGATAA
1 TGATAA
42083232 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:42084884 original size:27 final size:27
Alignment explanation
Indices: 42084843--42084980 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
42084833 GAGGAAGCGT
*
42084843 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
42084870 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
42084897 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
42084924 TCTGGTGGC-CTGCCAC-GATATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
42084950 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
42084976 TCTGG
1 TCTGG
42084981 CAGCCATGCT
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
25 7 0.07
26 20 0.20
27 72 0.73
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:42088961 original size:26 final size:26
Alignment explanation
Indices: 42088923--42089032 Score: 168
Period size: 26 Copynumber: 4.2 Consensus size: 26
42088913 TGATACAAAT
*
42088923 TGATAATAAGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
42088949 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
42088975 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
42089001 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
42089027 TGATAA
1 TGATAA
42089033 GAATTTCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:42090504 original size:28 final size:26
Alignment explanation
Indices: 42090462--42090536 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
42090452 AAAAGTAGCT
* *
42090462 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
42090490 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
42090516 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
42090537 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:42090681 original size:27 final size:27
Alignment explanation
Indices: 42090640--42090766 Score: 164
Period size: 27 Copynumber: 4.7 Consensus size: 27
42090630 GAGGAAGCGT
*
42090640 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
42090667 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
42090694 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * * *
42090721 TCTGGTGGCCCTGCCACGACTATCTTTA
1 TCTGGTGGCTCTGCCACAAATATC-TGA
* *
42090749 TCTGGTGACTCTGTCACA
1 TCTGGTGGCTCTGCCACA
42090767 TTATCTGTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 71 0.83
28 15 0.17
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:42092964 original size:11 final size:11
Alignment explanation
Indices: 42092932--42092964 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
42092922 CCCTAGTTTT
*
42092932 TTTCTTTCTCT
1 TTTCTTTCTCC
42092943 TTTCTTTCTCC
1 TTTCTTTCTCC
42092954 TTTCTTTCTCC
1 TTTCTTTCTCC
42092965 CTTTTCGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCTTTCTCC
Found at i:42092993 original size:18 final size:16
Alignment explanation
Indices: 42092967--42093020 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
42092957 CTTTCTCCCT
*
42092967 TTTCGTTTAAGCTTTTTG
1 TTTCTTTTAAGC--TTTG
*
42092985 TTTCTTTTATGCTTTG
1 TTTCTTTTAAGCTTTG
*
42093001 TTTCTTTTTAACCTTTG
1 TTTC-TTTTAAGCTTTG
42093018 TTT
1 TTT
42093021 TATTTACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 8 0.26
17 13 0.42
18 10 0.32
ACGTcount: A:0.09, C:0.13, G:0.11, T:0.67
Consensus pattern (16 bp):
TTTCTTTTAAGCTTTG
Found at i:42093300 original size:18 final size:18
Alignment explanation
Indices: 42093274--42093338 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
42093264 ATTACAAGTG
*
42093274 TATTTTCATGCACATGTT
1 TATTATCATGCACATGTT
* * *
42093292 TATTATCATTACCACAAGTG
1 TATTATCA-T-GCACATGTT
* *
42093312 TATTTTCATGCGCATGTT
1 TATTATCATGCACATGTT
42093330 TATTATCAT
1 TATTATCAT
42093339 TACCATACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
18 20 0.57
19 2 0.06
20 13 0.37
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TATTATCATGCACATGTT
Found at i:42093312 original size:38 final size:38
Alignment explanation
Indices: 42093267--42093343 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
42093257 CAAATATATT
42093267 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
1 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
*
42093305 ACAAGTGTATTTTCATGCGCATGTTTATTATCATTACC
1 ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
42093343 A
1 A
42093344 TACATCTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (38 bp):
ACAAGTGTATTTTCATGCACATGTTTATTATCATTACC
Found at i:42099556 original size:23 final size:23
Alignment explanation
Indices: 42099530--42099575 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42099520 GTACACGAAT
42099530 TCCAACCAAACACACCAGAATAA
1 TCCAACCAAACACACCAGAATAA
*
42099553 TCCAACCAAACGCACCAGAATAA
1 TCCAACCAAACACACCAGAATAA
42099576 ATAATCCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.35, G:0.07, T:0.09
Consensus pattern (23 bp):
TCCAACCAAACACACCAGAATAA
Found at i:42099578 original size:27 final size:27
Alignment explanation
Indices: 42099530--42099599 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
42099520 GTACACGAAT
42099530 TCCAACCAAACACACCAG----AATAA
1 TCCAACCAAACACACCAGAATAAATAA
*
42099553 TCCAACCAAACGCACCAGAATAAATAA
1 TCCAACCAAACACACCAGAATAAATAA
**
42099580 TCCTCCCAAACACACCAGAA
1 TCCAACCAAACACACCAGAA
42099600 AGGCATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.44
27 22 0.56
ACGTcount: A:0.49, C:0.36, G:0.06, T:0.10
Consensus pattern (27 bp):
TCCAACCAAACACACCAGAATAAATAA
Found at i:42100605 original size:16 final size:17
Alignment explanation
Indices: 42100584--42100623 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42100574 GTTTGAGCTT
*
42100584 TTTGTTTC-TTTTATGC
1 TTTGTTTCTTTTTAAGC
42100600 TTTGTTTCTTTTTAAGC
1 TTTGTTTCTTTTTAAGC
42100617 TTTGTTT
1 TTTGTTT
42100624 TATTTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.70
Consensus pattern (17 bp):
TTTGTTTCTTTTTAAGC
Found at i:42104998 original size:4 final size:4
Alignment explanation
Indices: 42104989--42105112 Score: 65
Period size: 4 Copynumber: 30.8 Consensus size: 4
42104979 TTTTAATTCT
* * * *
42104989 TTTA TTTA TTCA TTTA TTTA TTTA CTTG TTTA TTTA TTCA -TTA TTCCT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA
* * * * * * * *
42105037 TTTA TTCTA ATCA TTTG TTTG TTCA TTTA CTTA TCTA TTTA TCTA -TTA
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
42105085 TTCA TTTA CTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTT
42105113 TAATCCTTGT
Statistics
Matches: 87, Mismatches: 26, Indels: 14
0.69 0.20 0.11
Matches are distributed among these distances:
3 5 0.06
4 72 0.83
5 9 0.10
6 1 0.01
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:42105227 original size:21 final size:21
Alignment explanation
Indices: 42105198--42105239 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42105188 ATGCCTTCAT
*
42105198 TATTGTTACTATTTTATTATC
1 TATTATTACTATTTTATTATC
42105219 TATTATTACTATTTTATTATC
1 TATTATTACTATTTTATTATC
42105240 ATCTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTATTACTATTTTATTATC
Found at i:42105243 original size:24 final size:22
Alignment explanation
Indices: 42105193--42105236 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
42105183 TATTCATGCC
*
42105193 TTCAT-TATTGTTACTATTTTA
1 TTCATCTATTATTACTATTTTA
42105214 TT-ATCTATTATTACTATTTTA
1 TTCATCTATTATTACTATTTTA
42105235 TT
1 TT
42105237 ATCATCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
TTCATCTATTATTACTATTTTA
Found at i:42105952 original size:26 final size:26
Alignment explanation
Indices: 42105923--42106030 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
42105913 TGGTACAAAT
42105923 TGATAATAGG-TTAGGTAAATGTTCCA
1 TGATAAT-GGATTAGGTAAATGTTCCA
*
42105949 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
42105975 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
42106001 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
42106027 TGAT
1 TGAT
42106031 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 2 0.03
26 75 0.97
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:42109540 original size:22 final size:20
Alignment explanation
Indices: 42109503--42109543 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
42109493 ATTAAAGTAA
*
42109503 TAAAATGTAAATAATTAAAT
1 TAAAATGTAAAAAATTAAAT
42109523 TAAAATGGATAAAAAATTAAA
1 TAAAAT-G-TAAAAAATTAAA
42109544 ACAAAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
TAAAATGTAAAAAATTAAAT
Found at i:42115598 original size:15 final size:15
Alignment explanation
Indices: 42115578--42115609 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42115568 TATGAAAATT
*
42115578 GCATGTGAATTTATG
1 GCATGTAAATTTATG
42115593 GCATGTAAATTTATG
1 GCATGTAAATTTATG
42115608 GC
1 GC
42115610 TTTTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (15 bp):
GCATGTAAATTTATG
Found at i:42116490 original size:20 final size:20
Alignment explanation
Indices: 42116451--42116500 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
42116441 TGAATCAAAA
* *
42116451 AAAGGAAGAA-AAAAATATT
1 AAAGGAAAAATAAAAAAATT
42116470 AAAGGAAAAATAAAAAAATT
1 AAAGGAAAAATAAAAAAATT
42116490 AACA-GAAAAAT
1 AA-AGGAAAAAT
42116501 TGGGAGTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 17 0.63
21 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAGGAAAAATAAAAAAATT
Found at i:42120510 original size:26 final size:24
Alignment explanation
Indices: 42120481--42120535 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
42120471 TCTAAACTAA
42120481 TTTTAGGTAAATTTAATCGTTTATAT
1 TTTTAGGTAAATTTAAT--TTTATAT
** * *
42120507 TTTTTTGTTAATTTAATTTTTTAT
1 TTTTAGGTAAATTTAATTTTATAT
42120531 TTTTA
1 TTTTA
42120536 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 10 0.42
26 14 0.58
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.65
Consensus pattern (24 bp):
TTTTAGGTAAATTTAATTTTATAT
Found at i:42127169 original size:70 final size:70
Alignment explanation
Indices: 42127124--42127670 Score: 479
Period size: 70 Copynumber: 7.7 Consensus size: 70
42127114 TTTTCATATT
* * * *
42127124 AGTTGGGAGCTTTGGCTCGTGCTTACTATTTTGGAAGTCGCGATATTGAATCAACAAGCCTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
42127189 ATTAC
66 ATTAC
** * * * * * * *
42127194 AACTAGGAGC-TTGAGCTCGCACTGACTATTTTGGAGGTCACAATATTAAATCAACAAGCATTTG
1 AGTTGGGAGCTTTG-GCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTG
42127258 GATTAC
65 GATTAC
* * * *
42127264 AATTGGGAGCTTTGGCTCGCGCTAACTATTTTGGAGGTTGCGATATTAAATCAGCGAGCCTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
42127329 ATTAC
66 ATTAC
* * * * * * ** * *
42127334 AGCTGGGAGCTTTGGCTCACACTAACTATTTTGGAGGTCGCAATATTGAATCAGTGAGCTTTTGC
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
42127399 A-TATC
66 ATTA-C
** * ** * * * *
42127404 AGTTGGGAGCTTTGGCTTACGCTTATTGCTTTGGAGGTTGGGATATTGAATCAGCGAGCCTTTGG
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
* *
42127469 ACTAT
66 ATTAC
* * * * * * * ** *
42127474 AGCTAGGAGCTTGAGCTTGAGCTCGTGCTTATTGTTTTAGAGGCCATGATATTGAATCAACGAGC
1 AGTTGGGAGC-T----TTG-GCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGC
42127539 CTTTGGATTAC
60 CTTTGGATTAC
* * * * **
42127550 AGTTGAGAGCTTTGGCTCGCGCTTACTGTTTTGGAGGTCGTGATATTAAATCAGCGAGCCTTTTC
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
42127615 A-TATC
66 ATTA-C
* * *
42127620 AGTTGGGAGCTTTGGCTCTCGCTGACTATTTTAGAGGTCGCGATATTAAAT
1 AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAAT
42127671 TGGTTGGGAA
Statistics
Matches: 389, Mismatches: 77, Indels: 22
0.80 0.16 0.05
Matches are distributed among these distances:
69 7 0.02
70 318 0.82
71 9 0.02
75 4 0.01
76 51 0.13
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (70 bp):
AGTTGGGAGCTTTGGCTCGCGCTTACTATTTTGGAGGTCGCGATATTAAATCAACGAGCCTTTGG
ATTAC
Found at i:42134161 original size:15 final size:15
Alignment explanation
Indices: 42134129--42134166 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
42134119 TATAAAAATG
42134129 AATTAAAAATAAAGA
1 AATTAAAAATAAAGA
*
42134144 AATTACAAAATATA-A
1 AATTA-AAAATAAAGA
42134159 AATTAAAA
1 AATTAAAA
42134167 CAACAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 11 0.52
16 7 0.33
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AATTAAAAATAAAGA
Found at i:42142197 original size:21 final size:22
Alignment explanation
Indices: 42142171--42142211 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42142161 ATAATTATAT
42142171 TAATTATA-TTATGTTAAATAA
1 TAATTATATTTATGTTAAATAA
*
42142192 TAATTATATTTATTTTAAAT
1 TAATTATATTTATGTTAAAT
42142212 CATTAACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TAATTATATTTATGTTAAATAA
Found at i:42143157 original size:30 final size:30
Alignment explanation
Indices: 42143123--42143182 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
42143113 ACTTAACAAG
42143123 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
42143153 CAAATATCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
42143183 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:42143557 original size:24 final size:24
Alignment explanation
Indices: 42143511--42143557 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42143501 GATTATTGAA
*
42143511 TTTTCATAAAATAGTAATAAAAAG
1 TTTTCATAAAATAATAATAAAAAG
*
42143535 TTTTCATAAATTTAATAATAAAA
1 TTTTCATAAA-ATAATAATAAAA
42143558 TAAAAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTTCATAAAATAATAATAAAAAG
Found at i:42143934 original size:14 final size:14
Alignment explanation
Indices: 42143915--42143945 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42143905 TGCTTATCTT
*
42143915 TATAGGGTAAATTA
1 TATAGGGTAAACTA
42143929 TATAGGGTAAACTA
1 TATAGGGTAAACTA
42143943 TAT
1 TAT
42143946 TGGTAGCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (14 bp):
TATAGGGTAAACTA
Found at i:42153689 original size:188 final size:189
Alignment explanation
Indices: 42153319--42153729 Score: 646
Period size: 188 Copynumber: 2.2 Consensus size: 189
42153309 GCAGCAACCT
* *
42153319 TCACAATTCTATCTCAATGCCTAATCATATAATGCAAGTTCAAGAATCTAGAGCTTAATTCAGTC
1 TCACAATTCTATCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
* ** * *
42153384 GGTTCATGCAATCTTCCTTTAAAGATGGTATTTTGATACATCTCAAGTTAGATTCTCAACATTGC
66 AGTTCATGCAATCACCCTTTAAAGATGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTGC
42153449 AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
131 AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
* *
42153508 TCACAATTCTACCTCAATGCCTAATCAGATGATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
1 TCACAATTCTATCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
* *
42153573 AGTTCATGCAATCACCC-TT-ATGAGTGGTATTTTGAAACGTCTCAAGTTAGAGTCTCAACATTG
66 AGTTCATGCAATCACCCTTTAAAGA-TGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTG
* * * *
42153636 CAATCGTTCCCCTATCCCCATACTAAGGCCTCCTTTACACGAAATATTGCAAGTTCAACA
130 CAATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
* *
42153696 TCACAATTCTATCTCAATGCCTAACCAAATAATG
1 TCACAATTCTATCTCAATGCCTAATCAGATAATG
42153730 TGCTTAGTTG
Statistics
Matches: 202, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
187 3 0.01
188 124 0.61
189 75 0.37
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (189 bp):
TCACAATTCTATCTCAATGCCTAATCAGATAATGCAAGTTCAAGAACCTAGAGCTTAATTCAGTC
AGTTCATGCAATCACCCTTTAAAGATGGTATTTTGAAACATCTCAAGTTAGAGTCTCAACATTGC
AATCCTTCCCCTATCCCCATACTAAGGCCTCCTATACACAAAATAATGCAAGTTCAACA
Found at i:42154579 original size:7 final size:8
Alignment explanation
Indices: 42154568--42154595 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42154558 AAAATGAAAA
42154568 AAAAAAGG
1 AAAAAAGG
42154576 AAAAAAGG
1 AAAAAAGG
42154584 AAAAAAGG
1 AAAAAAGG
42154592 AAAA
1 AAAA
42154596 GAAGAAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:42154794 original size:3 final size:3
Alignment explanation
Indices: 42154786--42154827 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
42154776 GGTAAATAAC
42154786 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
42154828 TTTTCAAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42155478 original size:2 final size:2
Alignment explanation
Indices: 42155471--42155500 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42155461 AATTAAAGTA
42155471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42155501 TTTTAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.