Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 375 of 425
Found at i:115405913 original size:5 final size:5
Alignment explanation
Indices: 115405905--115405967 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
115405895 TCTTTATTTT
* * *
115405905 TATTA TATTA TATTA TATTA TATTA TTATT- TATTG TCTTA T-TT- TATTT
1 TATTA TATTA TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA
*
115405953 TATTT TATTA T-TTA T
1 TATTA TATTA TATTA T
115405968 TACTTTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
3 1 0.02
4 12 0.24
5 34 0.67
6 4 0.08
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (5 bp):
TATTA
Found at i:115405976 original size:15 final size:15
Alignment explanation
Indices: 115405898--115405969 Score: 69
Period size: 15 Copynumber: 4.9 Consensus size: 15
115405888 TTTATTTTCT
115405898 TTATT-TTTATTATA
1 TTATTATTTATTATA
115405912 TTA-TATTATATTATA
1 TTATTATT-TATTATA
* *
115405927 TTATTATTTATTGTC
1 TTATTATTTATTATA
* *
115405942 TTATT-TTATTTTATT
1 TTATTATT-TATTATA
115405957 TTATTATTTATTA
1 TTATTATTTATTA
115405970 CTTTATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
13 1 0.02
14 7 0.15
15 33 0.70
16 6 0.13
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (15 bp):
TTATTATTTATTATA
Found at i:115405976 original size:30 final size:30
Alignment explanation
Indices: 115405887--115405978 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
115405877 GCAACCCAAT
*
115405887 TTTTATTTT-CTTTATT-TTTATTATATTA
1 TTTTATTTTATTTTATTATTTATTATATTA
* * * * *
115405915 TATTATATTATATTATTATTTATTGTCTTA
1 TTTTATTTTATTTTATTATTTATTATATTA
115405945 TTTTATTTTATTTTATTATTTATTACT-TTA
1 TTTTATTTTATTTTATTATTTATTA-TATTA
115405975 TTTT
1 TTTT
115405979 TGGATATTGA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
28 7 0.14
29 5 0.10
30 38 0.75
31 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (30 bp):
TTTTATTTTATTTTATTATTTATTATATTA
Found at i:115407922 original size:23 final size:23
Alignment explanation
Indices: 115407892--115407942 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
115407882 GCCAAAAATA
115407892 CAAAATGTGAAAGATTTTGGGAG
1 CAAAATGTGAAAGATTTTGGGAG
* *
115407915 CAAAATGTGGAAGATTTTGGGTG
1 CAAAATGTGAAAGATTTTGGGAG
115407938 CAAAA
1 CAAAA
115407943 ATGCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.25
Consensus pattern (23 bp):
CAAAATGTGAAAGATTTTGGGAG
Found at i:115407952 original size:24 final size:23
Alignment explanation
Indices: 115407892--115407952 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
115407882 GCCAAAAATA
**
115407892 CAAAATGTGAAAGATTTTGGGAG
1 CAAAATGCAAAAGATTTTGGGAG
*** *
115407915 CAAAATGTGGAAGATTTTGGGTG
1 CAAAATGCAAAAGATTTTGGGAG
115407938 CAAAAATGCAAAAGA
1 C-AAAATGCAAAAGA
115407953 AGAGATTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.43, C:0.07, G:0.28, T:0.23
Consensus pattern (23 bp):
CAAAATGCAAAAGATTTTGGGAG
Found at i:115414183 original size:28 final size:28
Alignment explanation
Indices: 115414143--115414198 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
115414133 AGAAACGGTG
115414143 TAAGCAATGGAATTGTAAATCATGAGAT
1 TAAGCAATGGAATTGTAAATCATGAGAT
115414171 TAAGCAATGGAATTGTAAATCATGAGAT
1 TAAGCAATGGAATTGTAAATCATGAGAT
115414199 ATAATAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (28 bp):
TAAGCAATGGAATTGTAAATCATGAGAT
Found at i:115415790 original size:29 final size:28
Alignment explanation
Indices: 115415751--115415834 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
115415741 CACTTTGTGC
115415751 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
* *
115415780 TATTCTGGTGTGTTTGGGAGGATTCTAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
115415808 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
115415835 CTGGTGTGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 31 0.63
29 18 0.37
ACGTcount: A:0.18, C:0.05, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:115415835 original size:23 final size:25
Alignment explanation
Indices: 115415755--115415848 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 25
115415745 TTGTGCTATT
115415755 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGATTATA-TA
*
115415782 TTCTGGTGTGTTTGGGAGGATTCTATGATA
1 --CTGGTGTGTTTTGGAGGA-T-TAT-ATA
115415812 CTGGTGTGTTTTGGAGGA-T-TATA
1 CTGGTGTGTTTTGGAGGATTATATA
115415835 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
115415849 TTGGACATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
23 17 0.28
24 1 0.02
25 1 0.02
28 20 0.33
29 15 0.25
30 5 0.08
31 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.34, T:0.46
Consensus pattern (25 bp):
CTGGTGTGTTTTGGAGGATTATATA
Found at i:115416066 original size:21 final size:21
Alignment explanation
Indices: 115416040--115416096 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
115416030 CTTTACTGAT
115416040 CAGGCACTTTGTGTGTCGCAG
1 CAGGCACTTTGTGTGTCGCAG
* * ***
115416061 CAGGCACCTCGTGTGTCGTTT
1 CAGGCACTTTGTGTGTCGCAG
115416082 CAGGCACTTATGTGT
1 CAGGCACTT-TGTGT
115416097 CGTATTCTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.32
Consensus pattern (21 bp):
CAGGCACTTTGTGTGTCGCAG
Found at i:115417660 original size:31 final size:31
Alignment explanation
Indices: 115417625--115417692 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
115417615 TTCTATTTTA
115417625 ATATGTTGGAAATGAAGTTAATGGTAAAAAT
1 ATATGTTGGAAATGAAGTTAATGGTAAAAAT
115417656 ATATGTTGGAAATGAAGTTAATGGTAAAAAT
1 ATATGTTGGAAATGAAGTTAATGGTAAAAAT
*
115417687 TTATGT
1 ATATGT
115417693 GAGACTATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (31 bp):
ATATGTTGGAAATGAAGTTAATGGTAAAAAT
Found at i:115418483 original size:2 final size:2
Alignment explanation
Indices: 115418476--115418505 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
115418466 AAATGTACAA
115418476 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
115418506 TAAAATAATT
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
Found at i:115421124 original size:15 final size:15
Alignment explanation
Indices: 115421087--115421115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
115421077 TTTCCCTATC
115421087 TAATAATAATAATTA
1 TAATAATAATAATTA
115421102 TAATAATAATAATT
1 TAATAATAATAATT
115421116 TTATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:115421943 original size:12 final size:12
Alignment explanation
Indices: 115421926--115421960 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
115421916 ACCATTAATA
*
115421926 AATAAATGAGTC
1 AATAAATGAGCC
115421938 AATAAATGAGCC
1 AATAAATGAGCC
115421950 AATAAATGAGC
1 AATAAATGAGC
115421961 TTTTAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.20
Consensus pattern (12 bp):
AATAAATGAGCC
Found at i:115427978 original size:60 final size:60
Alignment explanation
Indices: 115427885--115428009 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
115427875 TGTAGTTCAA
*
115427885 TGAGCATTGAGCTCAATTCCTTATCCTCACATCTAGTACGGGTGAGTTTGGATGAGTTAT
1 TGAGCATTGAGCTCAATTCCTTATCCTCACATCTAGTACAGGTGAGTTTGGATGAGTTAT
115427945 TGAGCATTGAGCTCAATTCCTTATCCTCACATCTAGTACAGGTGAGTTTGGATGAGTTAT
1 TGAGCATTGAGCTCAATTCCTTATCCTCACATCTAGTACAGGTGAGTTTGGATGAGTTAT
115428005 TGAGC
1 TGAGC
115428010 GTGGTGCGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (60 bp):
TGAGCATTGAGCTCAATTCCTTATCCTCACATCTAGTACAGGTGAGTTTGGATGAGTTAT
Found at i:115429228 original size:29 final size:30
Alignment explanation
Indices: 115429194--115429250 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
115429184 AAATACTTAG
115429194 AATTTAAAGGGTTAA-AGTGTAAATATAAA
1 AATTTAAAGGGTTAATAGTGTAAATATAAA
115429223 AATTTAAAGGGTTAATAGTGTAAATATA
1 AATTTAAAGGGTTAATAGTGTAAATATA
115429251 TTAAGAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (30 bp):
AATTTAAAGGGTTAATAGTGTAAATATAAA
Found at i:115431038 original size:27 final size:27
Alignment explanation
Indices: 115431000--115431056 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
115430990 GAAATTAAAC
115431000 TTAGTATGATTTTTTAGTACAATAATT
1 TTAGTATGATTTTTTAGTACAATAATT
*
115431027 TTAGTGTGATTTTTTAGTACAATAATT
1 TTAGTATGATTTTTTAGTACAATAATT
115431054 TTA
1 TTA
115431057 CTCTTGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (27 bp):
TTAGTATGATTTTTTAGTACAATAATT
Found at i:115442336 original size:13 final size:12
Alignment explanation
Indices: 115442316--115442353 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
115442306 TGTACTTATC
115442316 TCATTCATTCAA
1 TCATTCATTCAA
*
115442328 TCAATTCATACAA
1 TC-ATTCATTCAA
115442341 TCA-TCATTCAA
1 TCATTCATTCAA
115442352 TC
1 TC
115442354 TCAATCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 9 0.39
12 3 0.13
13 11 0.48
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (12 bp):
TCATTCATTCAA
Found at i:115443346 original size:24 final size:25
Alignment explanation
Indices: 115443319--115443419 Score: 95
Period size: 24 Copynumber: 4.1 Consensus size: 25
115443309 CATCGTATTT
* *
115443319 GCTCTTTCGAGCT-ATGATCGGTAA
1 GCTCTTTCGAGCTGATGAACAGTAA
*
115443343 GCTCTTTCTGAGTTGATGAACAGTAA
1 GCTCTTTC-GAGCTGATGAACAGTAA
*
115443369 GCTCTATT-GAGCTGA-AAACAGTAA
1 GCTCT-TTCGAGCTGATGAACAGTAA
*
115443393 GCT-TTGACGAGCTGA-GAACAGTAA
1 GCTCTT-TCGAGCTGATGAACAGTAA
115443417 GCT
1 GCT
115443420 TTTAGGAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 37 0.57
25 10 0.15
26 14 0.22
27 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (25 bp):
GCTCTTTCGAGCTGATGAACAGTAA
Found at i:115443420 original size:24 final size:23
Alignment explanation
Indices: 115443360--115443456 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 23
115443350 CTGAGTTGAT
* *
115443360 GAACAGTAAGCTCTATTGAGCTGA
1 GAACAGTAAGCTTTA-CGAGCTGA
*
115443384 AAACAGTAAGCTTTGACGAGCTGA
1 GAACAGTAAGCTTT-ACGAGCTGA
* *
115443408 GAACAGTAAGCTTTTAGGAGCTAA
1 GAACAGTAAGC-TTTACGAGCTGA
*
115443432 TATATCAGTAAGCTTATACGAGCTG
1 GA-A-CAGTAAGCTT-TACGAGCTG
115443457 CAGTGAGTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
24 37 0.63
25 7 0.12
26 15 0.25
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (23 bp):
GAACAGTAAGCTTTACGAGCTGA
Found at i:115467591 original size:26 final size:24
Alignment explanation
Indices: 115467476--115467592 Score: 85
Period size: 24 Copynumber: 4.7 Consensus size: 24
115467466 CTATGACCGA
* * *
115467476 TAAGCTCTTTCTGAGCTAATGAATAG
1 TAAGCTCTTAC-GAGCTGA-GAACAG
* *
115467502 TAAGCTC-TATCGAGCT-AGAAATAA
1 TAAGCTCTTA-CGAGCTGAG-AACAG
115467526 TAAGCTCTTACGAGCTGAGAACAG
1 TAAGCTCTTACGAGCTGAGAACAG
* *
115467550 TAAGCTCTTACAAGCTGATATATCAG
1 TAAGCTCTTACGAGCTGAGA-A-CAG
* *
115467576 TAAGCTCATGCGAGCTG
1 TAAGCTCTTACGAGCTG
115467593 TGGTGAGTCC
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.01
24 39 0.51
25 11 0.14
26 25 0.33
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (24 bp):
TAAGCTCTTACGAGCTGAGAACAG
Found at i:115470450 original size:88 final size:88
Alignment explanation
Indices: 115470301--115470472 Score: 308
Period size: 88 Copynumber: 2.0 Consensus size: 88
115470291 CTAAACCAGA
* *
115470301 TTTCCCCACAATGGGTTTCTAAGGTCATGGTCCTATCCCACCATGACATATGAAATGTATGTGTA
1 TTTCCCCACAATAGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
* *
115470366 TTAAGATGTGTTATCACATCTCC
66 TTAAGACGCGTTATCACATCTCC
115470389 TTTCCCCACAATAGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
1 TTTCCCCACAATAGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
115470454 TTAAGACGCGTTATCACAT
66 TTAAGACGCGTTATCACAT
115470473 TCCCGACCCC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (88 bp):
TTTCCCCACAATAGGTTTCTAAGGTCATAGTCCTATCCCACCATGACATATGAAATGTATGTGTA
TTAAGACGCGTTATCACATCTCC
Found at i:115471622 original size:43 final size:43
Alignment explanation
Indices: 115471557--115471642 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
115471547 TATTAATGAA
115471557 TGAATGAATCTCAAGTTATGATCTATTGATTAAGTGTTCACTT
1 TGAATGAATCTCAAGTTATGATCTATTGATTAAGTGTTCACTT
*
115471600 TGAATGAATCTCAAGTTTTGATCTATTGATTAAGTGTTCACTT
1 TGAATGAATCTCAAGTTATGATCTATTGATTAAGTGTTCACTT
115471643 ACTCAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (43 bp):
TGAATGAATCTCAAGTTATGATCTATTGATTAAGTGTTCACTT
Found at i:115474486 original size:37 final size:37
Alignment explanation
Indices: 115474444--115474514 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
115474434 TTGTGCACAT
115474444 TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
1 TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
115474481 TGATCACGTTGGATTTGTTTACAAATATTTTTTT
1 TGATCACGTTGGATTTGTTTACAAATATTTTTTT
115474515 TCCGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (37 bp):
TGATCACGTTGGATTTGTTTACAAATATTTTTTTCAG
Found at i:115477960 original size:46 final size:46
Alignment explanation
Indices: 115477891--115477982 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
115477881 AAAGATTTAT
* *
115477891 GATACTACATTTTAACAAAATATTTATTGGATTGTCCATTCTAAAG
1 GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
*
115477937 GATACTACATTTTAACAAGATATTTATTGAATTGTCCACTCTAAAG
1 GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
115477983 ATTAGGTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (46 bp):
GATACTACATTTTAACAAAATATTTATTGAATTGTCCACTCTAAAG
Found at i:115478473 original size:64 final size:64
Alignment explanation
Indices: 115478339--115478460 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
115478329 TATGATAAAC
* ****
115478339 TATATAAAATATAAAATGAATTAAGCTATAAAGTCAACACAATATGAATTTTTTTTAAAACAAT
1 TATATAAAATACAAAATGAATTAAGCTATAAAGTCAACACAATATGAATAAAATTTAAAACAAT
* **
115478403 TATATAAAATACAAAATGAATTAAGCTATACAGTCAACACAATAATGTGTAAAATTTA
1 TATATAAAATACAAAATGAATTAAGCTATAAAGTCAACACAAT-ATGAATAAAATTTA
115478461 TATAAATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
64 41 0.84
65 8 0.16
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (64 bp):
TATATAAAATACAAAATGAATTAAGCTATAAAGTCAACACAATATGAATAAAATTTAAAACAAT
Found at i:115480271 original size:3 final size:3
Alignment explanation
Indices: 115480265--115480292 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
115480255 TTTTGAACTA
115480265 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
115480293 TGGCATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:115482441 original size:4 final size:4
Alignment explanation
Indices: 115482434--115482458 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
115482424 TAATTAAACC
115482434 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
115482459 TATGGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:115496383 original size:146 final size:147
Alignment explanation
Indices: 115496121--115496453 Score: 379
Period size: 146 Copynumber: 2.3 Consensus size: 147
115496111 AAAAATATTG
* * * * * *
115496121 AATGTGTAACTAATTTTATGGTAGATTATAAAATATA-TAGTTAATATTATATAATTAAGGTAGA
1 AATGTGTAACTAA-CTTATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGA
* * * *
115496185 TTATTAATAATATGTATATCTATGTATAGCTATGCTATTATAATATACATTTTTATATTAATGAG
65 TTATTAATAATATGTATATCTATATAAAACTATGATATTATAATATACATTTTTATATTAATGAG
* *
115496250 ATGTAATC-TTAAACCCTA
130 ACGCAA-CATTAAACCCTA
*
115496268 AATGTATAACTAACTGTATGGTAGATTATAATATATACAAG-AAACA-TATATAATTAAGATAGA
1 AATGTGTAACTAACT-TATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGA
* * * *
115496331 TTATTAATAATATGTA-ATCCTATATAAAATTATGATATTTTAATGTATATTTTTATATTAATGA
65 TTATTAATAATATGTATAT-CTATATAAAACTATGATATTATAATATACATTTTTATATTAATGA
* * *
115496395 TACGCAACATTAGACTCTA
129 GACGCAACATTAAACCCTA
* * *
115496414 AACGTGTAATTAACTTCATAGTAGATTATAATATATACAA
1 AATGTGTAACTAACTT-ATGGTAGATTATAATATATACAA
115496454 TTAGCATGGA
Statistics
Matches: 157, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
145 4 0.03
146 116 0.74
147 35 0.22
148 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (147 bp):
AATGTGTAACTAACTTATGGTAGATTATAATATATACAAGTAAACATTATATAATTAAGATAGAT
TATTAATAATATGTATATCTATATAAAACTATGATATTATAATATACATTTTTATATTAATGAGA
CGCAACATTAAACCCTA
Found at i:115500783 original size:17 final size:17
Alignment explanation
Indices: 115500763--115500815 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
115500753 TTCATAAACA
115500763 TATATCATTCATTTCAT-
1 TATATCATT-ATTTCATG
*
115500780 TATATCAATATTTCATG
1 TATATCATTATTTCATG
115500797 TACTATCA-T-TTTCATG
1 TA-TATCATTATTTCATG
115500813 TAT
1 TAT
115500816 TTCAGGCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 1 0.03
16 16 0.48
17 11 0.33
18 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (17 bp):
TATATCATTATTTCATG
Found at i:115501074 original size:33 final size:33
Alignment explanation
Indices: 115501028--115501156 Score: 100
Period size: 33 Copynumber: 3.8 Consensus size: 33
115501018 GTTTTCTTTA
*
115501028 TGCCATAGTCCAACTATGGTCTTACACTTGTAT
1 TGCCATAGCCCAACTATGGTCTTACACTTGTAT
* * * * ** *
115501061 TGCCATGGCCCAACCATGGCCTTACTCACGTAG
1 TGCCATAGCCCAACTATGGTCTTACACTTGTAT
* *
115501094 TGCCATATCCCAGA-TATGGTCTTATCATCTT-CAT
1 TGCCATAGCCCA-ACTATGGTCTTA-CA-CTTGTAT
*
115501128 GATGCCATAGCCCAGCTATGGTCTTACAC
1 --TGCCATAGCCCAACTATGGTCTTACAC
115501157 ATGCATATAT
Statistics
Matches: 71, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
33 43 0.61
34 4 0.06
35 3 0.04
36 21 0.30
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.30
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTACACTTGTAT
Found at i:115501220 original size:108 final size:100
Alignment explanation
Indices: 115501026--115501260 Score: 235
Period size: 108 Copynumber: 2.3 Consensus size: 100
115501016 TCGTTTTCTT
* *
115501026 TATGCCATAGTCCAACTATGGTCTTACACTTGTATTGCCATGGCCCAACCATGGCCTTACTCACG
1 TATGCCATAGCCCAACTATGGTCTTACACATGTATTGCCATGGCCCAACCATGGCCTTACTCACG
* **
115501091 TAGTGCCATATCCCAGATATGGTCTTATCATCTTCA
66 TAGTGCCATAACCCAGATATGGTCTTATCA-CTGAA
* * *
115501127 TGATGCCATAGCCCAGCTATGGTCTTACACATGCATATATACCGCCATGGTCCAACCATGGTCTT
1 T-ATGCCATAGCCCAACTATGGTCTTACACATG--TAT-T---GCCATGGCCCAACCATGGCCTT
** *
115501192 ACGTTCACG-A-TGTTATAACCCA-ATTATGGTCTTTTCACTGAA
59 AC--TCACGTAGTGCCATAACCCAGA-TATGGTCTTATCACTGAA
*
115501234 T-TGCCATAGCTCAACTATGGTCTTACA
1 TATGCCATAGCCCAACTATGGTCTTACA
115501261 TTTACACACT
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
101 1 0.01
102 28 0.25
104 3 0.03
105 25 0.23
107 5 0.05
108 43 0.39
109 1 0.01
110 5 0.05
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (100 bp):
TATGCCATAGCCCAACTATGGTCTTACACATGTATTGCCATGGCCCAACCATGGCCTTACTCACG
TAGTGCCATAACCCAGATATGGTCTTATCACTGAA
Found at i:115504544 original size:40 final size:40
Alignment explanation
Indices: 115504485--115504670 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
115504475 CATTGGAATG
* * * *
115504485 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
* *
115504525 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTATT
* **
115504565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
* * * * *
115504605 AAAT-CGGGTTAAGACCCGAAGGCAATCGTGCGAA-TCACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTATT
* * * *
115504644 ATAACCGGGCTAGGTCCCGAAGACAAT
1 ATATCCGGGCTAAGACCCGAAGGCAAT
115504671 CGAGCGAGTC
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
39 32 0.27
40 86 0.72
41 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT
Found at i:115504587 original size:80 final size:79
Alignment explanation
Indices: 115504485--115504637 Score: 207
Period size: 80 Copynumber: 1.9 Consensus size: 79
115504475 CATTGGAATG
* * ** *
115504485 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAAT-CGGGCTAAGACCCGAAGGCA
*
115504550 TTCGTGCGAGTTGTT
65 ATCGTGCGAGTTGTT
* * * *
115504565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCGGGTTAAGACCCGAAGGCAA
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCGGGCTAAGACCCGAAGGCAA
115504630 TCGTGCGA
66 TCGTGCGA
115504638 ATCACTATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 27 0.43
80 36 0.57
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCGGGCTAAGACCCGAAGGCAA
TCGTGCGAGTTGTT
Found at i:115504652 original size:79 final size:80
Alignment explanation
Indices: 115504489--115504670 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 80
115504479 GGAATGATAT
* ** * *
115504489 CCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
* *** *
115504554 TGCGAGTTGTTATAT
66 TGCGAATCACTATAA
* * * * *
115504569 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT-CGGGTTAAGACCCGAAGGCAATCG
1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
115504633 TGCGAATCACTATAA
66 TGCGAATCACTATAA
* *
115504648 CCGGGCTAGGTCCCGAAGACAAT
1 CCGGGCTAAGTCCCGAAGGCAAT
115504671 CGAGCGAGTC
Statistics
Matches: 83, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
79 51 0.61
80 32 0.39
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG
TGCGAATCACTATAA
Found at i:115511160 original size:23 final size:23
Alignment explanation
Indices: 115511088--115511153 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
115511078 TATCAAATTT
* *
115511088 TCATAATCAATCTCAGTTTCT-TTC
1 TCAT-ATCAATTTCA-TTTCTACTC
115511112 TCATATCAATTTCATTTCTACTC
1 TCATATCAATTTCATTTCTACTC
* *
115511135 TCATTTCCATTCTCATTTC
1 TCATATCAATT-TCATTTC
115511154 AGTCTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
23 20 0.56
24 11 0.31
ACGTcount: A:0.23, C:0.27, G:0.02, T:0.48
Consensus pattern (23 bp):
TCATATCAATTTCATTTCTACTC
Found at i:115513334 original size:8 final size:8
Alignment explanation
Indices: 115513292--115513316 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
115513282 ATATAGACTA
115513292 AATAAAAT
1 AATAAAAT
115513300 AATAAAAT
1 AATAAAAT
115513308 AATAAAAT
1 AATAAAAT
115513316 A
1 A
115513317 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:115513368 original size:41 final size:41
Alignment explanation
Indices: 115513290--115513371 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
115513280 ATATATAGAC
*
115513290 TAAATAAAATAATAAAATAATAAAATATCTTATTAAAATAT
1 TAAATAAAATAATAAAATAATAAAATAACTTATTAAAATAT
*
115513331 TAAAT-AAATAATAATTATATAATTAAATAAC-TA-TAAAATAT
1 TAAATAAAATAATAA--A-ATAATAAAATAACTTATTAAAATAT
115513372 CACCAACATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
40 9 0.25
41 13 0.36
42 3 0.08
43 11 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (41 bp):
TAAATAAAATAATAAAATAATAAAATAACTTATTAAAATAT
Found at i:115513626 original size:29 final size:30
Alignment explanation
Indices: 115513568--115513636 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
115513558 CCACCCTTAA
* * * *
115513568 AATATTTTCACTATTAGTCCTTCAACTTTT
1 AATATTTACACTATTAATCCCTCAAATTTT
*
115513598 CATATTTACACT-TTAATCCCTCAAATTTT
1 AATATTTACACTATTAATCCCTCAAATTTT
115513627 AAGTATTTAC
1 AA-TATTTAC
115513637 TCTTGGGCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.46
Consensus pattern (30 bp):
AATATTTACACTATTAATCCCTCAAATTTT
Found at i:115514717 original size:7 final size:7
Alignment explanation
Indices: 115514707--115514749 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
115514697 TAATATTTAT
115514707 TTAAGTA
1 TTAAGTA
115514714 TTAAGTA
1 TTAAGTA
*
115514721 TTAAATA
1 TTAAGTA
115514728 TTAAGTA
1 TTAAGTA
115514735 TTAAGTA
1 TTAAGTA
115514742 TTAAGTA
1 TTAAGTA
115514749 T
1 T
115514750 ATATTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TTAAGTA
Found at i:115515752 original size:41 final size:40
Alignment explanation
Indices: 115515696--115515820 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 40
115515686 GACTTTGAGT
*
115515696 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATC
* * ** *
115515737 CGATGA-ATCACTGGGT-ACCAA-T-TTACTTCGGTTTAGC
1 CGATGAGA-CACTGGGTGTCAAATTATTACTTCGAATTATC
*
115515774 CGATGAGACACTGGGTGTCAAATTATTACTTCAAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
115515814 CGATGAG
1 CGATGAG
115515821 GTAATGGGTG
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
37 15 0.22
38 14 0.21
39 2 0.03
40 22 0.33
41 14 0.21
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:115516195 original size:17 final size:18
Alignment explanation
Indices: 115516165--115516199 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
115516155 AATGTGAATT
115516165 TTAATTATTCAATTGTGC
1 TTAATTATTCAATTGTGC
*
115516183 TTAA-TATTTAATTGTGC
1 TTAATTATTCAATTGTGC
115516200 CTATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTAATTATTCAATTGTGC
Found at i:115528811 original size:23 final size:22
Alignment explanation
Indices: 115528779--115528834 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
115528769 TAATTTTGGT
115528779 ATATGATGAAGT-TATCTT-ATAA
1 ATATGATGAA-TCTATCTTGA-AA
115528801 ATATGCATGAATCTATCTTGAAA
1 ATATG-ATGAATCTATCTTGAAA
*
115528824 ATATGTTGAAT
1 ATATGATGAAT
115528835 TGGATTGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.37
23 18 0.60
24 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (22 bp):
ATATGATGAATCTATCTTGAAA
Found at i:115529983 original size:22 final size:21
Alignment explanation
Indices: 115529958--115529998 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
115529948 TTGATTTGAG
115529958 GAAAAGAAATTAGGGAAAAATA
1 GAAAA-AAATTAGGGAAAAATA
* *
115529980 GAAAAAGATTTGGGAAAAA
1 GAAAAAAATTAGGGAAAAA
115529999 AACTTTGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (21 bp):
GAAAAAAATTAGGGAAAAATA
Found at i:115530216 original size:39 final size:40
Alignment explanation
Indices: 115530167--115530242 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
115530157 GCATTTATGA
* * **
115530167 AAAAATGCCGCTATTGC-TTACCTTTTGTGGCGTTTATTC
1 AAAAACGCCGCTAATGCTTTACCTTTTACGGCGTTTATTC
115530206 AAAAACGCCGCTAATGCTTTACCTTTTACGGCGTTTA
1 AAAAACGCCGCTAATGCTTTACCTTTTACGGCGTTTA
115530243 AAAATGCCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.47
40 17 0.53
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (40 bp):
AAAAACGCCGCTAATGCTTTACCTTTTACGGCGTTTATTC
Found at i:115536174 original size:23 final size:24
Alignment explanation
Indices: 115536148--115536195 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
115536138 GAAAGTAAAA
115536148 AGAGAA-CGTGCCAAAAGGCAGAC
1 AGAGAACCGTGCCAAAAGGCAGAC
**
115536171 AGAGAATCCGTGCCAACGGGCAGAC
1 AGAGAA-CCGTGCCAAAAGGCAGAC
115536196 TAATTTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
25 15 0.71
ACGTcount: A:0.38, C:0.25, G:0.31, T:0.06
Consensus pattern (24 bp):
AGAGAACCGTGCCAAAAGGCAGAC
Found at i:115537471 original size:21 final size:21
Alignment explanation
Indices: 115537442--115537482 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
115537432 TTTTCAAAGA
* *
115537442 TATGTATTGGATTGAATTGAG
1 TATGAATTGGATTAAATTGAG
*
115537463 TATGAATTGTATTAAATTGA
1 TATGAATTGGATTAAATTGA
115537483 TGTTAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (21 bp):
TATGAATTGGATTAAATTGAG
Found at i:115538021 original size:25 final size:25
Alignment explanation
Indices: 115537991--115538069 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
115537981 ATTCCCAATT
*
115537991 ATGGCTCGGATGAGCTTCCCGTTAC
1 ATGGCTCGAATGAGCTTCCCGTTAC
* * * *
115538016 ATGGCTC-ACATAAGTTTCCAGTTAT
1 ATGGCTCGA-ATGAGCTTCCCGTTAC
*
115538041 ATGGCTCGAAAGAGCTTCCCGTTTAC
1 ATGGCTCGAATGAGCTTCCCG-TTAC
115538067 ATG
1 ATG
115538070 TTTGCATGAG
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
25 34 0.83
26 7 0.17
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (25 bp):
ATGGCTCGAATGAGCTTCCCGTTAC
Found at i:115543314 original size:32 final size:32
Alignment explanation
Indices: 115543278--115543342 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
115543268 TGTATGCATT
115543278 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
115543310 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
115543342 T
1 T
115543343 GGTAAGCATT
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:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:115546245 original size:94 final size:94
Alignment explanation
Indices: 115546076--115546252 Score: 225
Period size: 94 Copynumber: 1.9 Consensus size: 94
115546066 TCATTTGTGT
* * *
115546076 GCTAGTGTAAGAAATGTCTAGGACATGCATCTGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTAATGTAAGAAATGTCTAGGACATGCATCTGCCACAATATGAGAGCCAGGGTAAGACCATGTC
115546141 AAGGACATGGCATCGGCATTGAGACGAGA
66 AAGGACATGGCATCGGCATTGAGACGAGA
* * * *
115546170 GCTAATGTAAGACATGTCTGGGACATGCATCTGCCTCGAGATAT-A-AGCCAGGGTAAGATCATG
1 GCTAATGTAAGAAATGTCTAGGACATGCATCTGCCAC-A-ATATGAGAGCCAGGGTAAGACCATG
* *
115546233 T-ATGGAATATGGCATCGGCA
64 TCAAGG-ACATGGCATCGGCA
115546253 CGGATAGAGT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 3 0.04
94 63 0.89
95 2 0.03
96 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (94 bp):
GCTAATGTAAGAAATGTCTAGGACATGCATCTGCCACAATATGAGAGCCAGGGTAAGACCATGTC
AAGGACATGGCATCGGCATTGAGACGAGA
Found at i:115546388 original size:99 final size:96
Alignment explanation
Indices: 115546264--115546439 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 96
115546254 GGATAGAGTT
115546264 GTCAGTGTAAGACCATGTCTGGGACATGGTATCGGCACGGAT-ATGTGA-GAGCCAATGTAAGAC
1 GTCAGTGTAAGACCATGTCTGGGACATGGTATC-G-AC--ATGATGT-ATGAGCCAATGTAAGAC
115546327 CATGCCTGGGACATGGCGCCGGCCTTAATCGTGATA
61 CATGCCTGGGACATGGCGCCGGCCTTAATCGTGATA
* * * * *
115546363 GTCATTGTGAGACCATGTCTGGGACATGGTATCGACTTGATGTATGAGCCACTGTAAGACCATGT
1 GTCAGTGTAAGACCATGTCTGGGACATGGTATCGACATGATGTATGAGCCAATGTAAGACCATGC
115546428 CTGGGACATGGC
66 CTGGGACATGGC
115546440 ATCGGCATCC
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
95 2 0.03
96 34 0.49
97 2 0.03
98 1 0.01
99 31 0.44
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (96 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGTATCGACATGATGTATGAGCCAATGTAAGACCATGC
CTGGGACATGGCGCCGGCCTTAATCGTGATA
Found at i:115546429 original size:47 final size:49
Alignment explanation
Indices: 115546120--115546444 Score: 176
Period size: 48 Copynumber: 6.8 Consensus size: 49
115546110 CACATTATGA
* ** *
115546120 GAGCCAGTGTAAGACCATGTCAAGGACATGGCATCGG-CATTGA-GACGA-
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGAC-TTGATG-TGAT
* * * *
115546168 GAGCTAATGTAAGA-CATGTCTGGGACAT-GCATCTGCCTCGA-GAT-AT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGACTTGATG-TGAT
* ** * * * * * *
115546214 AAGCCAGGGTAAGATCATGTATGGAATATGGCATCGGCAC-GGAT-AGA-
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGG-ACTTGATGTGAT
* * * * *
115546261 GTTGTCAGTGTAAGACCATGTCTGGGACATGGTATCGGCAC-GGATATGTGA-
1 G-AGCCAATGTAAGACCATGTCTGGGACATGGCATCGG-ACTTG--ATGTGAT
* ** * *
115546312 GAGCCAATGTAAGACCATGCCTGGGACATGGCGCCGGCCTTAATCGTGAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGACTTGAT-GTGAT
* * * *
115546362 -AGTCATTGTGAGACCATGTCTGGGACATGGTATC-GACTTGATGT-AT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGACTTGATGTGAT
*
115546408 GAGCCACTGTAAGACCATGTCTGGGACATGGCATCGG
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGG
115546445 CATCCTACCC
Statistics
Matches: 210, Mismatches: 51, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
45 1 0.00
46 23 0.11
47 56 0.27
48 63 0.30
49 33 0.16
50 31 0.15
51 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (49 bp):
GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGACTTGATGTGAT
Found at i:115552858 original size:94 final size:92
Alignment explanation
Indices: 115552697--115552961 Score: 299
Period size: 94 Copynumber: 2.8 Consensus size: 92
115552687 CCATTTGTGT
* * **
115552697 GCTAGTGTAAGACATGTCTGGGACATGCATGGGCCACGTTATG-AGAGCCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCT-GGACATGCATCGGCCTCGAGATGTA-AGCCAGTGTAAGACCATGT
*
115552761 CTGGGACATGGCATCAG-TATTGAGACGAG
64 CTGGGACATGGCATCAGCCA-TGAGACGAG
*
115552790 AGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCAAGATGTAAGCCAGTGTAAGACCATGT
1 -GCTAGTGTAAGACATGTCT-GGACATGCATCGGCCTCGAGATGTAAGCCAGTGTAAGACCATGT
* * *
115552855 CTGGGACATGGCATCGGCCATGAGATGTG
64 CTGGGACATGGCATCAGCCATGAGACGAG
* * *
115552884 TC-AGTATAAGACCATGTCTGAGACATGGCATCGGCCAT-GAGATGT--GTCAGTGTAAGACCAT
1 GCTAGTGTAAGA-CATGTCTG-GACAT-GCATCGGCC-TCGAGATGTAAGCCAGTGTAAGACCAT
115552945 GTCTGGGACATGGCATC
62 GTCTGGGACATGGCATC
115552962 TACATGGATA
Statistics
Matches: 151, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
92 41 0.27
93 13 0.09
94 94 0.62
95 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGACATGCATCGGCCTCGAGATGTAAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCAGCCATGAGACGAG
Found at i:115552894 original size:46 final size:46
Alignment explanation
Indices: 115552694--115553015 Score: 291
Period size: 46 Copynumber: 6.9 Consensus size: 46
115552684 GGGCCATTTG
* * *
115552694 TGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATGGGCCACGTTATGA
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA--TGA-GA
* * *
115552741 -GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-TATTGAGA
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGAGA
* * * * *
115552786 CGAGAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCC-TCAAGA
1 --TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-GAGA
115552832 TGTAAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAGA
1 TGT--GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAGA
* * *
115552880 TGTGTCAGTATAAGACCATGTCTGAGACATGGCATCGGCCATGAGA
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAGA
* ** *
115552926 TGTGTCAGTGTAAGACCATGTCTGGGACATGGCATC-TACATGGATA
1 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-GAGA
*
115552972 TGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCC
1 TGT----GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCC
115553016 TTAATCGCGA
Statistics
Matches: 228, Mismatches: 29, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
44 1 0.00
45 6 0.03
46 114 0.50
47 41 0.18
48 33 0.14
49 1 0.00
50 31 0.14
51 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAGA
Found at i:115552961 original size:140 final size:143
Alignment explanation
Indices: 115552700--115553015 Score: 353
Period size: 140 Copynumber: 2.2 Consensus size: 143
115552690 TTTGTGTGCT
* * *
115552700 AGTGTAAGA-CATGTCTGGGACAT-GCATGGGCCACGTTATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-TGATGAGAGCCAGTATAAGACCATGTCT
* * * *
115552763 GGGACATGGCATCAGTATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTC
65 GAGACATGGCATCAGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATCGACATC
115552828 AAGATGT-A-AGCC
130 AAGATGTGAGAGCC
* *
115552840 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGA-GATGTGTCAGTATAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACTGATGA-GAGCCAGTATAAGACCATGTCT
* * * * * *
115552903 GAGACATGGCATCGGCCA-TGAGATGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCTAC
65 GAGACATGGCATCAG-CATTGAGACGAGAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGAC
** *
115552965 ATGGATATGTGAGAGCC
127 ATCAAGATGTGAGAGCC
*
115552982 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC
115553016 TTAATCGCGA
Statistics
Matches: 149, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
138 9 0.06
139 16 0.11
140 62 0.42
141 16 0.11
142 46 0.31
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (143 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACTGATGAGAGCCAGTATAAGACCATGTCTG
AGACATGGCATCAGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATCGACATCA
AGATGTGAGAGCC
Found at i:115552975 original size:92 final size:91
Alignment explanation
Indices: 115552694--115553016 Score: 273
Period size: 94 Copynumber: 3.5 Consensus size: 91
115552684 GGGCCATTTG
* * * * *** *
115552694 TGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATGGGCCACGTTATGAGAGCCAGTGTAAGACC
1 TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCAAGATG-TAGCCAGTGTAAGACC
*
115552757 ATGTCTGGGACATGGCATCAGTATTGAGA
65 ATGTCTGGGACATGGCATCA-CA-TGAGA
* * *
115552786 CGAGAGCTAGTGTAAGA-CATGTCT-AGGACAT-GCATCGGCCTCAAGATGTAAGCCAGTGTAAG
1 --TGTGCCAGTGTAAGACCATGTCTGA-GACATGGCATCGGCCTCAAGATGT-AGCCAGTGTAAG
*
115552848 ACCATGTCTGGGACATGGCATCGGCCATGAGA
62 ACCATGTCTGGGACATGGCATC--ACATGAGA
* * * *
115552880 TGTGTCAGTATAAGACCATGTCTGAGACATGGCATCGGCCAT-GAGATGT-GTCAGTGTAAGACC
1 TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCC-TCAAGATGTAGCCAGTGTAAGACC
*
115552943 ATGTCTGGGACATGGCATCTACATGGATA
65 ATGTCTGGGACATGGCATC-ACAT-GAGA
* *
115552972 TGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCT
1 TGT----GCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCT
115553017 TAATCGCGAT
Statistics
Matches: 191, Mismatches: 25, Indels: 25
0.79 0.10 0.10
Matches are distributed among these distances:
91 3 0.02
92 48 0.25
93 12 0.06
94 92 0.48
95 3 0.02
96 33 0.17
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (91 bp):
TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCAAGATGTAGCCAGTGTAAGACCA
TGTCTGGGACATGGCATCACATGAGA
Found at i:115557976 original size:41 final size:41
Alignment explanation
Indices: 115557477--115557997 Score: 664
Period size: 41 Copynumber: 12.9 Consensus size: 41
115557467 AGTCGTGAAA
* * *
115557477 TAGCGGCGTTTTCGGAAAAACGCCGCCAAAAGTCCGAGAAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* *
115557518 TAGCGGCGTTTTT-CAAGAAACGCCGCCAAAAGTCTGAGAAT
1 TAGCGGCGTTTTTGGAA-AAACGCCGCCAAAAGTCTGAGCAT
* * **
115557559 TCGCGGCATTTTTCCAAAAACGCCGCCAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* *
115557600 TAGCGGCATTTTTAGAAAAACGCCGCCAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* * *
115557641 TAGCGGCGTTGTTGGAAAAGCGCCGCTAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* *
115557682 TAGCGGCGTTGTTGGAAAAACGCCGCTAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* * *
115557723 TAGCGGCGTTGTTGGAAAAACGCCGCTAAAAGTCTGAGAAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
*
115557764 TAGCGGCGTTTGTCGG-AAAACGCCGCCAAAA-TACTGAGCAT
1 TAGCGGCGTTT-TTGGAAAAACGCCGCCAAAAGT-CTGAGCAT
* ** *
115557805 TAGCAGC------CCAAAAACGCCGCCAAAAGTCTGAGTAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
** *
115557840 TAGCGGCGTTTTTCCAAAAACGCCGCCAAAAGTCTGAGTAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* *
115557881 TCGCTGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
115557922 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
* * *
115557963 TAGCGGCGTTTTTGGAGAAACGCCGCTAAACGTCT
1 TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCT
115557998 TTTTTGAATT
Statistics
Matches: 433, Mismatches: 35, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
35 28 0.06
36 1 0.00
40 3 0.01
41 395 0.91
42 6 0.01
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (41 bp):
TAGCGGCGTTTTTGGAAAAACGCCGCCAAAAGTCTGAGCAT
Found at i:115558225 original size:22 final size:21
Alignment explanation
Indices: 115558198--115558242 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
115558188 TTTAGCGGTA
*
115558198 TTAAGGGTTTATGGGTTTAGGT
1 TTAAGGGTTCAT-GGTTTAGGT
*
115558220 TTAAGGGTTCATGGTTTATGT
1 TTAAGGGTTCATGGTTTAGGT
115558241 TT
1 TT
115558243 TTGTGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.49
Consensus pattern (21 bp):
TTAAGGGTTCATGGTTTAGGT
Found at i:115558280 original size:15 final size:15
Alignment explanation
Indices: 115558217--115558280 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
115558207 TATGGGTTTA
*
115558217 GGTTTAAGGGTTCA-T
1 GGTTTAA-GGTTTAGT
* * *
115558232 GGTTTATGTTTTTGT
1 GGTTTAAGGTTTAGT
*
115558247 GGTTTAAGGTTTAGG
1 GGTTTAAGGTTTAGT
115558262 GGTTTAATGG-TTAGT
1 GGTTTAA-GGTTTAGT
115558277 GGTT
1 GGTT
115558281 AGGGGTTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
14 3 0.08
15 33 0.87
16 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (15 bp):
GGTTTAAGGTTTAGT
Found at i:115559076 original size:14 final size:14
Alignment explanation
Indices: 115559034--115559077 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
115559024 GCGGTATTAA
115559034 GGTTTAAGGGTTAG
1 GGTTTAAGGGTTAG
*
115559048 TGG-TTAGGGGTTAG
1 -GGTTTAAGGGTTAG
*
115559062 GGTTTAAGGGATAG
1 GGTTTAAGGGTTAG
115559076 GG
1 GG
115559078 GATAAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.32
Consensus pattern (14 bp):
GGTTTAAGGGTTAG
Found at i:115559501 original size:22 final size:22
Alignment explanation
Indices: 115559476--115559529 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
115559466 TATCTAGAAT
115559476 TTAGGGTTTAAT-GTTTATAAGG
1 TTAGGGTTTAATGGTTTA-AAGG
* *
115559498 TTAGGGTTT-ATGGTTTAGAGT
1 TTAGGGTTTAATGGTTTAAAGG
115559519 TTAGGGTTTAA
1 TTAGGGTTTAA
115559530 GATTTAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (22 bp):
TTAGGGTTTAATGGTTTAAAGG
Found at i:115559514 original size:7 final size:7
Alignment explanation
Indices: 115559498--115559546 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
115559488 GTTTATAAGG
115559498 TTAGGGT
1 TTAGGGT
*
115559505 TTATGGT
1 TTAGGGT
*
115559512 TTAGAGT
1 TTAGGGT
115559519 TTAGGGT
1 TTAGGGT
* *
115559526 TTAAGAT
1 TTAGGGT
115559533 TTAGGGT
1 TTAGGGT
115559540 TTAGGGT
1 TTAGGGT
115559547 CTGATTTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:115559524 original size:21 final size:21
Alignment explanation
Indices: 115559470--115559546 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
115559460 ATTTAGTATC
*
115559470 TAGAATTTAGGGTTTAAT-GTT
1 TAGAGTTTAGGGTTT-ATGGTT
* *
115559491 TATAAGGTTAGGGTTTATGGTT
1 TA-GAGTTTAGGGTTTATGGTT
* *
115559513 TAGAGTTTAGGGTTTAAGATT
1 TAGAGTTTAGGGTTTATGGTT
*
115559534 TAGGGTTTAGGGT
1 TAGAGTTTAGGGT
115559547 CTGATTTTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 31 0.67
22 15 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
TAGAGTTTAGGGTTTATGGTT
Found at i:115560969 original size:25 final size:26
Alignment explanation
Indices: 115560941--115560996 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
115560931 AATTTTTTTA
* *
115560941 ATTAAT-CGAAATTTTTTTATCTAAT
1 ATTAATCCGAAATTTTTATATATAAT
* *
115560966 ATT-ATCCTAAATTTTTATATATTAT
1 ATTAATCCGAAATTTTTATATATAAT
115560991 ATTAAT
1 ATTAAT
115560997 TTAATTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 21 0.84
26 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTAATCCGAAATTTTTATATATAAT
Found at i:115562941 original size:9 final size:9
Alignment explanation
Indices: 115562900--115563036 Score: 112
Period size: 9 Copynumber: 14.6 Consensus size: 9
115562890 ATTGATCATT
*
115562900 ACTTAAATA
1 ACTTACATA
*
115562909 AGTTACATA
1 ACTTACATA
* *
115562918 ACTCACGTA
1 ACTTACATA
115562927 ACTTACATA
1 ACTTACATA
*
115562936 ATTTACATAACA
1 ACTTACAT---A
*
115562948 ACCTACATA
1 ACTTACATA
115562957 ACTTACATA
1 ACTTACATA
115562966 ACTTACATA
1 ACTTACATA
* *
115562975 ATTTATATA
1 ACTTACATA
*
115562984 ACTCACATA
1 ACTTACATA
* *
115562993 ACGTATATAACA
1 AC-T-TA-CATA
115563005 ACTTACATA
1 ACTTACATA
*
115563014 ACTCACATA
1 ACTTACATA
115563023 ACTTACATA
1 ACTTACATA
115563032 ACTTA
1 ACTTA
115563037 ACTAATACAT
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
9 83 0.84
10 3 0.03
11 2 0.02
12 11 0.11
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:115562974 original size:57 final size:57
Alignment explanation
Indices: 115562900--115563034 Score: 162
Period size: 57 Copynumber: 2.4 Consensus size: 57
115562890 ATTGATCATT
* * * * **
115562900 ACTTAAATAAGTTACATAACTCACGTAACTTACATAATTTACATAACAACCTACATA
1 ACTTACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACCTACATA
* * * * *
115562957 ACTTACATAACTTACATAATTTATATAACTCACATAACGTATATAACAACTTACATA
1 ACTTACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACCTACATA
*
115563014 ACTCACATAACTTACATAACT
1 ACTTACATAACTTACATAACT
115563035 TAACTAATAC
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.31
Consensus pattern (57 bp):
ACTTACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACCTACATA
Found at i:115562992 original size:48 final size:48
Alignment explanation
Indices: 115562905--115563034 Score: 145
Period size: 48 Copynumber: 2.7 Consensus size: 48
115562895 TCATTACTTA
* * * * *
115562905 AATAAGTTACATAACTCACGTAACTTACATAATTTACATAAC-AACCT
1 AATAACTTACATAACTCACATAACTTACATAACTCACATAACGAACAT
* * * * *
115562952 ACATAACTTACATAACTTACATAATTTATATAACTCACATAACGTATAT
1 A-ATAACTTACATAACTCACATAACTTACATAACTCACATAACGAACAT
*
115563001 AACAACTTACATAACTCACATAACTTACATAACT
1 AATAACTTACATAACTCACATAACTTACATAACT
115563035 TAACTAATAC
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
47 1 0.01
48 63 0.94
49 3 0.04
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (48 bp):
AATAACTTACATAACTCACATAACTTACATAACTCACATAACGAACAT
Found at i:115568655 original size:24 final size:21
Alignment explanation
Indices: 115568607--115568667 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
115568597 TCTAACCGAT
*
115568607 GCAGCAGAGAGGGAGGCAGCG
1 GCAGCAGCGAGGGAGGCAGCG
*
115568628 GCAGCAGCGAGGGAGGTAGCG
1 GCAGCAGCGAGGGAGGCAGCG
* * *
115568649 ACAGCAGCAAGCGAGGCAG
1 GCAGCAGCGAGGGAGGCAG
115568668 AGCAGAGCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.21, G:0.48, T:0.02
Consensus pattern (21 bp):
GCAGCAGCGAGGGAGGCAGCG
Found at i:115569052 original size:43 final size:43
Alignment explanation
Indices: 115569003--115569110 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 43
115568993 TTTAGCGGCG
*
115569003 TTTGTGGGGAAAGCGCCGCTAAAGGACTCTACTTTTGGCAGCA
1 TTTGTGGAGAAAGCGCCGCTAAAGGACTCTACTTTTGGCAGCA
* * * *
115569046 TTTGTGGAGAAAGCGCCGCTAAAAGGTCTGTACTTTTGGCGGCG
1 TTTGTGGAGAAAGCGCCGCT-AAAGGACTCTACTTTTGGCAGCA
* * *
115569090 TTTTTGGTGTAAGCGCCGCTA
1 TTTGTGGAGAAAGCGCCGCTA
115569111 TAGGTCTGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 20 0.36
44 36 0.64
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.29
Consensus pattern (43 bp):
TTTGTGGAGAAAGCGCCGCTAAAGGACTCTACTTTTGGCAGCA
Found at i:115569131 original size:43 final size:42
Alignment explanation
Indices: 115568992--115569350 Score: 249
Period size: 43 Copynumber: 8.3 Consensus size: 42
115568982 CAATCTATAA
* *
115568992 TTTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGACTCTAC
1 TTTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCTGTAC
* * *
115569035 TTTTGGCAGCATTTGTGGAGAAAGCGCCGCTAAAAGGTCTGTAC
1 TTTTAGCGGCGTTTGTGG-GAAAGCGCCGCT-AAAGGTCTGTAC
* * * * *
115569079 TTTTGGCGGCGTTTTTGGTGTAAGCGCCGCTATAGGTCTGTAA
1 TTTTAGCGGCGTTTGTGG-GAAAGCGCCGCTAAAGGTCTGTAC
* * * *
115569122 ATTTAGCGGCTTTTTTGGGCAAAAGCTCCGCTAAAGGTCTGTAC
1 TTTTAGCGGCGTTTGTGGG--AAAGCGCCGCTAAAGGTCTGTAC
*** * *
115569166 TTTTAGCGGCGATTTG-CAAACAAACG-CGCTAAAGGTCTGCAC
1 TTTTAGCGGCG-TTTGTGGGA-AAGCGCCGCTAAAGGTCTGTAC
* * * **
115569208 TTTTAGCGGTGCTTT-TCCCGGAAA-CGCCGCTAAAGATCTACAC
1 TTTTAGCGGCG-TTTGT--GGGAAAGCGCCGCTAAAGGTCTGTAC
* * * * * **
115569251 CTTTAGTGGCGTTTGTGGGTAAAACGCCGCTAAAGGTATATGT
1 TTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTGTAC
* ** *
115569294 TTTTAGCGGCGTTTGTTTGCTAAGCGCCGCTAAAGGTCTATAC
1 TTTTAGCGGCGTTTG-TGGGAAAGCGCCGCTAAAGGTCTGTAC
*
115569337 TATTAGCGGCGTTT
1 TTTTAGCGGCGTTT
115569351 TTCGTTCAAA
Statistics
Matches: 249, Mismatches: 53, Indels: 28
0.75 0.16 0.08
Matches are distributed among these distances:
41 2 0.01
42 40 0.16
43 136 0.55
44 68 0.27
45 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (42 bp):
TTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTGTAC
Found at i:115573423 original size:15 final size:17
Alignment explanation
Indices: 115573393--115573428 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
115573383 TATATTTTAT
115573393 ATTTACTTTCTTATATA
1 ATTTACTTTCTTATATA
115573410 ATTTA-TTT-TTATATA
1 ATTTACTTTCTTATATA
115573425 ATTT
1 ATTT
115573429 TAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTACTTTCTTATATA
Found at i:115580153 original size:33 final size:33
Alignment explanation
Indices: 115580116--115580182 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
115580106 GTCCACCTAG
115580116 TTTGATCCCTTTTATCTCATAATCACCGATGTA
1 TTTGATCCCTTTTATCTCATAATCACCGATGTA
* *
115580149 TTTGATCCTTTTTATCTCATAATCACTGATGTA
1 TTTGATCCCTTTTATCTCATAATCACCGATGTA
115580182 T
1 T
115580183 CTTTCGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (33 bp):
TTTGATCCCTTTTATCTCATAATCACCGATGTA
Found at i:115582313 original size:10 final size:10
Alignment explanation
Indices: 115582292--115582328 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
115582282 TTTTAAGAAA
115582292 ATTTTTAA-T
1 ATTTTTAATT
115582301 ATTTTTAATT
1 ATTTTTAATT
115582311 ATTTTTAATT
1 ATTTTTAATT
115582321 ATTTTTAA
1 ATTTTTAA
115582329 AATACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTTAATT
Found at i:115583595 original size:22 final size:21
Alignment explanation
Indices: 115583548--115583621 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
115583538 TATTTGCTTA
*
115583548 TTTGAATCGATTATTTTGTTG
1 TTTGAATCGATTCTTTTGTTG
* *
115583569 ATTGACTCGATTCTTTATGTTG
1 TTTGAATCGATTCTTT-TGTTG
*
115583591 TTTGAATCAATTC-TTTGTTG
1 TTTGAATCGATTCTTTTGTTG
115583611 TTT-AACTCGAT
1 TTTGAA-TCGAT
115583622 CCAAATGCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.05
20 12 0.27
21 15 0.34
22 15 0.34
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTGAATCGATTCTTTTGTTG
Found at i:115586142 original size:5 final size:5
Alignment explanation
Indices: 115586126--115586182 Score: 53
Period size: 6 Copynumber: 10.4 Consensus size: 5
115586116 CTAATTTAAT
115586126 ATAAA ATCAAA ATAAA ATAAAAA ATAAA AT-AA ATAAAA ATAAAA ATAAA
1 ATAAA AT-AAA ATAAA AT--AAA ATAAA ATAAA AT-AAA AT-AAA ATAAA
115586175 ATAGAA AT
1 ATA-AA AT
115586183 TTCAATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.09
5 18 0.39
6 19 0.41
7 5 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:115586151 original size:12 final size:11
Alignment explanation
Indices: 115586126--115586182 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
115586116 CTAATTTAAT
*
115586126 ATAAAATCAAA
1 ATAAAATAAAA
115586137 ATAAAATAAAAA
1 ATAAAAT-AAAA
*
115586149 ATAAAATAAAT
1 ATAAAATAAAA
115586160 A-AAAATAAAA
1 ATAAAATAAAA
*
115586170 ATAAAATAGAA
1 ATAAAATAAAA
115586181 AT
1 AT
115586183 TTCAATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.22
11 21 0.52
12 10 0.25
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:115586962 original size:19 final size:19
Alignment explanation
Indices: 115586938--115586980 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
115586928 TTTTATTCAT
115586938 TTATTTATGTACAAGCAAA
1 TTATTTATGTACAAGCAAA
115586957 TTATTTATGTACAAGCAAA
1 TTATTTATGTACAAGCAAA
115586976 -TATTT
1 TTATTT
115586981 TTTTCAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (19 bp):
TTATTTATGTACAAGCAAA
Found at i:115589302 original size:6 final size:6
Alignment explanation
Indices: 115589287--115589321 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
115589277 AAATAAAAGG
*
115589287 CGGGGA CGGGGG CGGGGA CGGGGA CGGGGA CGGGG
1 CGGGGA CGGGGA CGGGGA CGGGGA CGGGGA CGGGG
115589322 GCATGGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.11, C:0.17, G:0.71, T:0.00
Consensus pattern (6 bp):
CGGGGA
Found at i:115589302 original size:12 final size:12
Alignment explanation
Indices: 115589285--115589323 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
115589275 AGAAATAAAA
115589285 GGCGGGGACGGG
1 GGCGGGGACGGG
115589297 GGCGGGGACGGG
1 GGCGGGGACGGG
*
115589309 GACGGGGACGGG
1 GGCGGGGACGGG
115589321 GGC
1 GGC
115589324 ATGGATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.18, G:0.72, T:0.00
Consensus pattern (12 bp):
GGCGGGGACGGG
Found at i:115592024 original size:23 final size:22
Alignment explanation
Indices: 115591990--115592063 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 22
115591980 AAAGTGAATG
115591990 GAATTATATTAAATTGAAAATAT
1 GAATTA-ATTAAATTGAAAATAT
115592013 -ATAGTTAATT-AATT-AAAATAT
1 GA-A-TTAATTAAATTGAAAATAT
*
115592034 GAATTAATTGAAAATTGAAAA-GT
1 GAATTAATT--AAATTGAAAATAT
115592057 GAATTAA
1 GAATTAA
115592064 ATACCCTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
20 6 0.14
21 8 0.19
22 6 0.14
23 16 0.37
24 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (22 bp):
GAATTAATTAAATTGAAAATAT
Found at i:115592040 original size:16 final size:16
Alignment explanation
Indices: 115592019--115592052 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
115592009 ATATATAGTT
115592019 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
115592035 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
115592051 AA
1 AA
115592053 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:115592283 original size:53 final size:54
Alignment explanation
Indices: 115592222--115592342 Score: 149
Period size: 53 Copynumber: 2.3 Consensus size: 54
115592212 TGTCGGATAT
* * * *
115592222 TGTT-CTGTTATTGTTTC-GGATTTGTTCCGATGAGGTACTCTGTGTACCGTAC
1 TGTTACTGTTATTGTTTCTAGATTTATTCCGATGAAGTACTCTGGGTACCGTAC
* * * *
115592274 TGTTACTGTTACT-ATTCTAGATTTATTCTGATGAAGTACTCTGGGTATCGTAC
1 TGTTACTGTTATTGTTTCTAGATTTATTCCGATGAAGTACTCTGGGTACCGTAC
115592327 TGTTACTGTTATTGTT
1 TGTTACTGTTATTGTT
115592343 ACTGTTACTG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
52 7 0.12
53 48 0.86
54 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.46
Consensus pattern (54 bp):
TGTTACTGTTATTGTTTCTAGATTTATTCCGATGAAGTACTCTGGGTACCGTAC
Found at i:115592335 original size:6 final size:6
Alignment explanation
Indices: 115592324--115592354 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
115592314 CTGGGTATCG
*
115592324 TACTGT TACTGT TATTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
115592355 CCGGCTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (6 bp):
TACTGT
Found at i:115592578 original size:18 final size:18
Alignment explanation
Indices: 115592554--115592630 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
115592544 AATTGATTGA
115592554 TACTGAATAACTGATTAT
1 TACTGAATAACTGATTAT
* * * *
115592572 TATTGAATAATTTATTGT
1 TACTGAATAACTGATTAT
*
115592590 TACTGAATAACTGACTAT
1 TACTGAATAACTGATTAT
* * *
115592608 TACTAAATAAATAATTAT
1 TACTGAATAACTGATTAT
115592626 T-CTGA
1 TACTGA
115592631 TTGACTGATC
Statistics
Matches: 45, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 3 0.07
18 42 0.93
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (18 bp):
TACTGAATAACTGATTAT
Found at i:115592617 original size:36 final size:36
Alignment explanation
Indices: 115592544--115592617 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
115592534 ATAACCAATC
* * *
115592544 AATTGATTGATACTGAATAACTGATTATTATTGAAT
1 AATTGATTGATACTGAATAACTGACTATTACTAAAT
* *
115592580 AATTTATTGTTACTGAATAACTGACTATTACTAAAT
1 AATTGATTGATACTGAATAACTGACTATTACTAAAT
115592616 AA
1 AA
115592618 ATAATTATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (36 bp):
AATTGATTGATACTGAATAACTGACTATTACTAAAT
Found at i:115593074 original size:20 final size:18
Alignment explanation
Indices: 115593049--115593088 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
115593039 ATAATAGAAT
115593049 TTGATTAATTTGGTATGAAA
1 TTGATTAATTT-G-ATGAAA
*
115593069 TTGATTTATTTGATGAAA
1 TTGATTAATTTGATGAAA
115593087 TT
1 TT
115593089 TGATATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (18 bp):
TTGATTAATTTGATGAAA
Found at i:115595549 original size:18 final size:18
Alignment explanation
Indices: 115595523--115595561 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
115595513 TAACTAATTT
*
115595523 AATATAAAATCAAAAT-GA
1 AATAAAAAAT-AAAATAGA
115595541 AATAAAAAATAAAATAGA
1 AATAAAAAATAAAATAGA
115595559 AAT
1 AAT
115595562 TTCTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AATAAAAAATAAAATAGA
Found at i:115602931 original size:15 final size:16
Alignment explanation
Indices: 115602911--115602940 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115602901 AAAATTATTT
115602911 TATAC-TAATATTTTA
1 TATACTTAATATTTTA
115602926 TATACTTAATATTTT
1 TATACTTAATATTTT
115602941 TGATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TATACTTAATATTTTA
Found at i:115603937 original size:19 final size:18
Alignment explanation
Indices: 115603905--115603953 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
115603895 ATAAGTCTTT
*
115603905 TTTTTTTA-ATTTTTTAA
1 TTTTTTTATATTTTTAAA
115603922 TTTTTTTATATATTTTAAA
1 TTTTTTTATAT-TTTTAAA
*
115603941 TTATTTTAT-TTTT
1 TTTTTTTATATTTT
115603954 AAGTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTATATTTTTAAA
Found at i:115604271 original size:17 final size:16
Alignment explanation
Indices: 115604244--115604276 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
115604234 ATAAATAAAT
115604244 AATTATTAATTTAATA
1 AATTATTAATTTAATA
115604260 AATTATTTAATTTAATA
1 AATTA-TTAATTTAATA
115604277 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTATTAATTTAATA
Found at i:115604470 original size:28 final size:29
Alignment explanation
Indices: 115604434--115604509 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
115604424 ATTTTAATTA
115604434 TATAAATTAAATTTTAATTAGATATT-AT
1 TATAAATTAAATTTTAATTAGATATTGAT
* *
115604462 T-TATTATTAAA-TTTATATAAGATATTGAT
1 TATA-AATTAAATTTTA-ATTAGATATTGAT
*
115604491 TATAAAATAAATTTTAATT
1 TATAAATTAAATTTTAATT
115604510 GTTAAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
27 6 0.16
28 16 0.42
29 10 0.26
30 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
TATAAATTAAATTTTAATTAGATATTGAT
Found at i:115604591 original size:14 final size:13
Alignment explanation
Indices: 115604572--115604605 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
115604562 TTGTTTAATT
115604572 AAAAATAACTTTTA
1 AAAAATAA-TTTTA
115604586 AAAAATAATTTTA
1 AAAAATAATTTTA
115604599 AGAAAAT
1 A-AAAAT
115604606 TTGTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:115605582 original size:3 final size:3
Alignment explanation
Indices: 115605574--115605598 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
115605564 TAATTTTTGT
115605574 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
115605599 TATTACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:115606691 original size:24 final size:24
Alignment explanation
Indices: 115606659--115606717 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
115606649 GAGTCACCTG
115606659 TCCCAAAATATGTAAGCTTTTTAA
1 TCCCAAAATATGTAAGCTTTTTAA
115606683 TCCCAAAATATGTAAGCTTTTTAA
1 TCCCAAAATATGTAAGCTTTTTAA
115606707 TCCCAAAATAT
1 TCCCAAAATAT
115606718 TCCTTGCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (24 bp):
TCCCAAAATATGTAAGCTTTTTAA
Found at i:115614224 original size:21 final size:19
Alignment explanation
Indices: 115614155--115614274 Score: 86
Period size: 18 Copynumber: 6.3 Consensus size: 19
115614145 TAAAAATTAG
115614155 AAAAAAATTAT-AAATTTT
1 AAAAAAATTATAAAATTTT
* * *
115614173 ATAAAAGTTATTAAATTTT
1 AAAAAAATTATAAAATTTT
115614192 AATAAAAA-TATAAAATATATT
1 AA-AAAAATTATAAAAT-T-TT
**
115614213 AAAAAAATTAT-ATTTTTT
1 AAAAAAATTATAAAATTTT
* * **
115614231 ATAAAAATTGTAAAA-ACT
1 AAAAAAATTATAAAATTTT
*
115614249 AAAAAAATTGTAAAATTTT
1 AAAAAAATTATAAAATTTT
115614268 ATAAAAA
1 A-AAAAA
115614275 CCATAAAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
18 35 0.45
19 19 0.24
20 17 0.22
21 7 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAAAAATTATAAAATTTT
Found at i:115615053 original size:4 final size:4
Alignment explanation
Indices: 115615044--115615069 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
115615034 GGTGCTCCTT
115615044 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
115615070 AAGACAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:115615601 original size:6 final size:6
Alignment explanation
Indices: 115615590--115615624 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
115615580 TTCCAAAGGT
115615590 ACATCA ACATCA ACATCA ACATCA ACATCA ACATC
1 ACATCA ACATCA ACATCA ACATCA ACATCA ACATC
115615625 GCCATCATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATCA
Found at i:115616296 original size:21 final size:19
Alignment explanation
Indices: 115616261--115616308 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
115616251 TCTTAAACTT
115616261 TTTTAAAAAATTAAATTAA
1 TTTTAAAAAATTAAATTAA
*
115616280 TTTTAAAAACATATAAATTTA
1 TTTTAAAAA-AT-TAAATTAA
115616301 -TTTAAAAA
1 TTTTAAAAA
115616309 TTTATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 10 0.38
21 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTTAAAAAATTAAATTAA
Found at i:115618817 original size:15 final size:14
Alignment explanation
Indices: 115618797--115618851 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
115618787 TAGCATTATT
115618797 TATTATTATATTAAC
1 TATTATTATATT-AC
*
115618812 TGTTATTATTATTAC
1 TATTATTA-TATTAC
*
115618827 TATTATCATATT-C
1 TATTATTATATTAC
*
115618840 -ATTAATATATTA
1 TATTATTATATTA
115618852 TTATCATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.27
13 1 0.03
14 4 0.12
15 15 0.45
16 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTATTATATTAC
Found at i:115618886 original size:38 final size:39
Alignment explanation
Indices: 115618796--115618887 Score: 93
Period size: 38 Copynumber: 2.4 Consensus size: 39
115618786 GTAGCATTAT
* * * *
115618796 TTATTATTATAT-TAACTGTTATTATTATTACTATTATCA
1 TTATTATTATATAT-ATTATTATCATTATTACTATTACCA
*
115618835 -TATTCATTA-ATATATTATTATCATTTTTACTA-TACCA
1 TTATT-ATTATATATATTATTATCATTATTACTATTACCA
115618872 TTATTATTATATATAT
1 TTATTATTATATATAT
115618888 ATACCTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
37 8 0.18
38 31 0.70
39 5 0.11
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (39 bp):
TTATTATTATATATATTATTATCATTATTACTATTACCA
Found at i:115626481 original size:42 final size:42
Alignment explanation
Indices: 115626420--115626748 Score: 197
Period size: 43 Copynumber: 7.5 Consensus size: 42
115626410 AGATTTACAA
* *
115626420 ATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAA-TTGCAG
1 ATCTTAA-CCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAG
* *
115626462 ATCTTATCTCCCTAGGCAGTAGGGAAACAGATCGAAGATGAAG
1 ATCTTAAC-CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAG
*
115626505 ATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGAT-AATG
1 ATCTTAACC-CCTAAGCAGTAGGGAAACAGATCGAAGATGAA-G
* * * * *
115626548 AGCTTTAACCCCCTAAGTAGTAGGGTAATA-AGCT-GAAAATTACAG
1 ATC-TTAA-CCCCTAAGCAGTAGGG-AA-ACAGATCGAAGATGA-AG
* ** ** * * * *
115626593 ATTTTGTCTCCCTGAAGTTGCAGTGG-AACAAATCG-A-ATCCAGCG
1 ATCTTAAC-CCCT-AAGCAGTAG-GGAAACAGATCGAAGAT-GA-AG
** *
115626637 AATCTTGTCTCCCTAGGCAGTAGGGAAACAGATCGAAGATGAAG
1 -ATCTTAAC-CCCTAAGCAGTAGGGAAACAGATCGAAGATGAAG
*
115626681 ATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGAT-AATG
1 ATCTTAACC-CCTAAGCAGTAGGGAAACAGATCGAAGATGAA-G
* *
115626724 AGCTTTAACCCCCTAAGTAGTAGGG
1 ATC-TTAA-CCCCTAAGCAGTAGGG
115626749 TAATAAGCTA
Statistics
Matches: 226, Mismatches: 37, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
41 1 0.00
42 38 0.17
43 83 0.37
44 64 0.28
45 34 0.15
46 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (42 bp):
ATCTTAACCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAG
Found at i:115626933 original size:179 final size:178
Alignment explanation
Indices: 115626503--115627137 Score: 1039
Period size: 179 Copynumber: 3.6 Consensus size: 178
115626493 TCGAAGATGA
115626503 AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
1 AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
115626568 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
66 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
* * * * * *
115626633 AGCGAATCTTGTCTCCCTAGGCAG-T-AGGGAAACAGATCGAAGA-TGA-
131 AGCGAATCTTGTCTTCCT--GAAGTTCAGTGAAGCAGATTGAAGATTTAT
115626679 AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
1 AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
*
115626744 TAGGGTAATAAGCTAAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
66 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
115626809 AGCGAATCTTGTCTTCCTGAAGTTACAGTGAAGCAGATTGAAGATTTAT
131 AGCGAATCTTGTCTTCCTGAAGTT-CAGTGAAGCAGATTGAAGATTTAT
*
115626858 AGATCTTAATCC-CCTAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGTA
1 AGATCTTAA-CCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTA
*
115626922 GTAGGGTAATAAGCTGAAATTTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATC
65 GTAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATC
* *
115626987 CAGCGAATTTTGTCTTCCTGAAGTTGCAGTAAAGCAGATTGAAGATTTAT
130 CAGCGAATCTTGTCTTCCTGAAGTT-CAGTGAAGCAGATTGAAGATTTAT
*
115627037 AGATCTTAATCC-CCTAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGTA
1 AGATCTTAA-CCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTA
* * *
115627101 GTAGGGTAATAAGTTGAAAATTACAGATCTTGCCTCC
65 GTAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCC
115627138 TCGAATGCAG
Statistics
Matches: 436, Mismatches: 17, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
174 3 0.01
175 1 0.00
176 146 0.33
177 15 0.03
178 2 0.00
179 267 0.61
180 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (178 bp):
AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
AGCGAATCTTGTCTTCCTGAAGTTCAGTGAAGCAGATTGAAGATTTAT
Found at i:115627220 original size:355 final size:351
Alignment explanation
Indices: 115626503--115627250 Score: 971
Period size: 355 Copynumber: 2.1 Consensus size: 351
115626493 TCGAAGATGA
115626503 AGATCTTAACCTCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
1 AGATCTTAACC-CCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
115626568 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
65 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
115626633 AGCGAATCTTGTCTCCCTAGGCAGTAGGGAAACAGATCGAAGATGAAGATCTTAACCTCCTAAGC
130 AGCGAATCTTGTCTCCCTAGGCAGTA--GAAACAGATCGAAGATGAAGATCTTAACCTCCTAAGC
115626698 AGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAGTAGGGTAATAAGCTAAAAA
193 AGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAGTAGGGTAATAAGCTAAAAA
* * ** * * ** **
115626763 TTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCCAGCGAATCTTGTCTTCCTG
258 TTACAGATCTTGCCTCCCTGAAG-TGCAGTGGAACAAATCGAAAACAGCCAAGCTTAACCCCCTG
** * * *
115626828 AAGTTACAGTGAAGCAGATTGAAGATTTAT
322 AAGCGACAGGGAAGCAGACTGAAGATTCAT
*
115626858 AGATCTTAATCCCCTAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGTAG
1 AGATCTTAA-CCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAG
*
115626923 TAGGGTAATAAGCTGAAATTTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
65 TAGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCC
* * * * *
115626988 AGCGAATTTTGTCTTCCTGAAGTTGCAGTA-AAGCAGATTGAAGATTTATAGATCTTAATCC-CC
130 AGCGAATCTTGTCTCCCT--AG--GCAGTAGAAACAGATCGAAGA-TGA-AGATCTTAA-CCTCC
* *
115627051 TAAGCAGTAGGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGTAGTAGGGTAATAAGTT
188 TAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAGTAGGGTAATAAGCT
* *
115627116 GAAAATTACAGATCTTGCCT-CCTCGAA-TGCAGT-GAAGCAGATTC-AAAACA-CCAAGCTCTA
253 AAAAATTACAGATCTTGCCTCCCT-GAAGTGCAGTGGAA-CA-AATCGAAAACAGCCAAGCT-TA
*
115627176 ACCCCCT-AAGCCGA-AGGGTAA-CA-AGCTGATG-TTCAT
314 ACCCCCTGAAG-CGACAGGG-AAGCAGA-CTGAAGATTCAT
*
115627212 AGGATCTTAAACCCCTAAGCAGTAGGGAAACAGACCAAA
1 A-GATCTT-AACCCCTAAGCAGTAGGGAAACAGATCAAA
115627251 TTGTAGATCT
Statistics
Matches: 347, Mismatches: 29, Indels: 34
0.85 0.07 0.08
Matches are distributed among these distances:
354 6 0.02
355 193 0.56
356 36 0.10
357 10 0.03
358 94 0.27
359 8 0.02
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (351 bp):
AGATCTTAACCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAGT
AGGGTAATAAGCTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAAATCGAATCCA
GCGAATCTTGTCTCCCTAGGCAGTAGAAACAGATCGAAGATGAAGATCTTAACCTCCTAAGCAGT
AGGGAAACAGATCAAAGATAATGAGCTTTAACCCCCTAAGTAGTAGGGTAATAAGCTAAAAATTA
CAGATCTTGCCTCCCTGAAGTGCAGTGGAACAAATCGAAAACAGCCAAGCTTAACCCCCTGAAGC
GACAGGGAAGCAGACTGAAGATTCAT
Found at i:115627397 original size:86 final size:85
Alignment explanation
Indices: 115627217--115627502 Score: 324
Period size: 86 Copynumber: 3.3 Consensus size: 85
115627207 TTCATAGGAT
* *** * *
115627217 CTTAAACCCCTAAGCAGTAGGGAAACAGACCAAATTGTAGATCTTATCCCCTAAGCAGTAGTGGT
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATCCCCTAAGCAGTAGTGGA
*
115627282 GTAGATCGAAGAAGAAGAAC
66 GCAGATCGAAGAAGAAGAAC
115627302 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATC-CCCTAAGCAGTAGTGG
*
115627367 AGCAGATCGAAGACGAAGAAC
65 AGCAGATCGAAGAAGAAGAAC
* *** * * **
115627388 CTTAAACCCCTAAGCAGTAGGGTAATAGGTTGGGTATACAGATCTAAAACCCTAAGCAGTAG-GG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAAT-TGCAGATCTTATCCCCTAAGCAGTAGTGG
* * * *
115627452 AAACAGATCAAAGATGACA-AGC
65 -AGCAGATCGAAGAAGA-AGAAC
* *
115627474 CTTAATCCCTTAAGCAGTAGGGTAACAGG
1 CTTAAACCCCTAAGCAGTAGGGTAACAGG
115627503 CTGAAAATTA
Statistics
Matches: 174, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
85 45 0.26
86 119 0.68
87 10 0.06
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (85 bp):
CTTAAACCCCTAAGCAGTAGGGTAACAGGTTAAATTGCAGATCTTATCCCCTAAGCAGTAGTGGA
GCAGATCGAAGAAGAAGAAC
Found at i:115629013 original size:15 final size:14
Alignment explanation
Indices: 115628993--115629047 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
115628983 TAGCATTATT
115628993 TATTATTATATTAAC
1 TATTATTATATT-AC
*
115629008 TGTTATTATTATTAC
1 TATTATTA-TATTAC
*
115629023 TATTATCATATT-C
1 TATTATTATATTAC
*
115629036 -ATTAATATATTA
1 TATTATTATATTA
115629048 TTATCATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.27
13 1 0.03
14 4 0.12
15 15 0.45
16 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (14 bp):
TATTATTATATTAC
Found at i:115629082 original size:38 final size:39
Alignment explanation
Indices: 115628992--115629083 Score: 93
Period size: 38 Copynumber: 2.4 Consensus size: 39
115628982 GTAGCATTAT
* * * *
115628992 TTATTATTATAT-TAACTGTTATTATTATTACTATTATCA
1 TTATTATTATATAT-ATTATTATCATTATTACTATTACCA
*
115629031 -TATTCATTA-ATATATTATTATCATTTTTACTA-TACCA
1 TTATT-ATTATATATATTATTATCATTATTACTATTACCA
115629068 TTATTATTATATATAT
1 TTATTATTATATATAT
115629084 ATACCTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
37 8 0.18
38 31 0.70
39 5 0.11
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (39 bp):
TTATTATTATATATATTATTATCATTATTACTATTACCA
Found at i:115630694 original size:27 final size:27
Alignment explanation
Indices: 115630664--115630715 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
115630654 CATAAAACGA
* *
115630664 TTTAAAAAAAATCATATATACATAAAT
1 TTTAAAAAAAATAATATAGACATAAAT
* *
115630691 TTTATAACAAATAATATAGACATAA
1 TTTAAAAAAAATAATATAGACATAA
115630716 GTACATAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTAAAAAAAATAATATAGACATAAAT
Found at i:115632310 original size:31 final size:32
Alignment explanation
Indices: 115632269--115632330 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
115632259 CTCTGTTTGT
*
115632269 TTCTTCTTTGTTTTTGCT-TTTTGTTTTCTGC
1 TTCTTCTTTGTTTTTCCTATTTTGTTTTCTGC
*
115632300 TTCTTTTTTGTTTTTCCTAATTTTGTTTTCT
1 TTCTTCTTTGTTTTTCCT-ATTTTGTTTTCT
115632331 TGTATTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 16 0.59
33 11 0.41
ACGTcount: A:0.03, C:0.15, G:0.10, T:0.73
Consensus pattern (32 bp):
TTCTTCTTTGTTTTTCCTATTTTGTTTTCTGC
Found at i:115634518 original size:147 final size:147
Alignment explanation
Indices: 115634323--115634618 Score: 556
Period size: 147 Copynumber: 2.0 Consensus size: 147
115634313 TTAATCATCT
* *
115634323 AATTTACCGAGTTCATTTTTTTGTCATTTCTCCATCACTTACGATTAAGACTTGGATGATAGAAG
1 AATTTACCGAGTTCATTTTTTTGTCATTTCTCCATCACTAACGATTAAGACTTGAATGATAGAAG
*
115634388 GCGTATAAGTTTAAAAATGATATAATAATATATTTAGTCCTTAATAATTACATATTTTATTAATT
66 GCGTATAAGTTTAAAAATAATATAATAATATATTTAGTCCTTAATAATTACATATTTTATTAATT
115634453 TGATTATGATTATAAAA
131 TGATTATGATTATAAAA
*
115634470 AATTTACCGAGTTCATTTTTTTGTCATTTTTCCATCACTAACGATTAAGACTTGAATGATAGAAG
1 AATTTACCGAGTTCATTTTTTTGTCATTTCTCCATCACTAACGATTAAGACTTGAATGATAGAAG
115634535 GCGTATAAGTTTAAAAATAATATAATAATATATTTAGTCCTTAATAATTACATATTTTATTAATT
66 GCGTATAAGTTTAAAAATAATATAATAATATATTTAGTCCTTAATAATTACATATTTTATTAATT
115634600 TGATTATGATTATAAAA
131 TGATTATGATTATAAAA
115634617 AA
1 AA
115634619 ATTAACTCTC
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 145 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (147 bp):
AATTTACCGAGTTCATTTTTTTGTCATTTCTCCATCACTAACGATTAAGACTTGAATGATAGAAG
GCGTATAAGTTTAAAAATAATATAATAATATATTTAGTCCTTAATAATTACATATTTTATTAATT
TGATTATGATTATAAAA
Found at i:115638877 original size:22 final size:22
Alignment explanation
Indices: 115638852--115638895 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
115638842 GAGTTATATA
*
115638852 ATAGTAAAATTACATCAAAATG
1 ATAGCAAAATTACATCAAAATG
115638874 ATAGCAAAATTACATCAAAATG
1 ATAGCAAAATTACATCAAAATG
115638896 GTAACAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.25
Consensus pattern (22 bp):
ATAGCAAAATTACATCAAAATG
Found at i:115638903 original size:22 final size:22
Alignment explanation
Indices: 115638857--115638903 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
115638847 ATATAATAGT
*
115638857 AAAATTACATCAAAATGATAGC
1 AAAATTACATCAAAATGATAAC
*
115638879 AAAATTACATCAAAATGGTAAC
1 AAAATTACATCAAAATGATAAC
115638901 AAA
1 AAA
115638904 CAACAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAATTACATCAAAATGATAAC
Found at i:115639033 original size:20 final size:20
Alignment explanation
Indices: 115638985--115639024 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
115638975 AAAATAGACC
*
115638985 TTAT-TTTTTATTTAAACTT
1 TTATATTTTTATTCAAACTT
115639004 TTATATTTTTATTCAAA-TT
1 TTATATTTTTATTCAAACTT
115639023 TT
1 TT
115639025 CTCATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATTTTTATTCAAACTT
Found at i:115644450 original size:26 final size:26
Alignment explanation
Indices: 115644414--115644470 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
115644404 ACGAAGAAAG
115644414 GATCAAAAATTAAAAAAAGGGTATAA
1 GATCAAAAATTAAAAAAAGGGTATAA
115644440 GATCAAAAATTAAAAAAAGGGTATAA
1 GATCAAAAATTAAAAAAAGGGTATAA
115644466 GATCA
1 GATCA
115644471 TAACTCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (26 bp):
GATCAAAAATTAAAAAAAGGGTATAA
Found at i:115651516 original size:19 final size:21
Alignment explanation
Indices: 115651466--115651522 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
115651456 ATGTATCTGT
*
115651466 TCTTACGAGCTTCTATTTAGC
1 TCTTACGAGCTTCTATTCAGC
*
115651487 TCTTACGAGCTTCTGTTCAGC
1 TCTTACGAGCTTCTATTCAGC
115651508 T-TT-CGAGCTTCTATT
1 TCTTACGAGCTTCTATT
115651523 GGTGTATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 11 0.33
20 2 0.06
21 20 0.61
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.44
Consensus pattern (21 bp):
TCTTACGAGCTTCTATTCAGC
Found at i:115656380 original size:24 final size:24
Alignment explanation
Indices: 115656353--115656433 Score: 63
Period size: 24 Copynumber: 3.3 Consensus size: 24
115656343 CAGCTTGAAA
115656353 GAGCATCCCGTTATTAGCTCTTAT
1 GAGCATCCCGTTATTAGCTCTTAT
* * * * *
115656377 GAGCTTCTCGTTATATGGTTCTTGT
1 GAGCATCCCGTTAT-TAGCTCTTAT
* * * **
115656402 GAGCTTCCTGTTAATAGCTCTTCG
1 GAGCATCCCGTTATTAGCTCTTAT
115656426 GAGCATCC
1 GAGCATCC
115656434 TGATTAGTTG
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
24 25 0.58
25 18 0.42
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTTAT
Found at i:115656578 original size:24 final size:24
Alignment explanation
Indices: 115656549--115656617 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 24
115656539 TCCTGATTAA
115656549 TGGCTCTCTTAAGCTTCTCGATAT
1 TGGCTCTCTTAAGCTTCTCGATAT
* *
115656573 TGGCTCGCTTGAACCTTCTCGATAT
1 TGGCTCTCTT-AAGCTTCTCGATAT
*
115656598 TGGCT-TGTATAAGCTTCTCG
1 TGGCTCTCT-TAAGCTTCTCG
115656618 TTAATAACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (24 bp):
TGGCTCTCTTAAGCTTCTCGATAT
Found at i:115656592 original size:25 final size:24
Alignment explanation
Indices: 115656549--115656602 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
115656539 TCCTGATTAA
* *
115656549 TGGCTCTCTTAAGCTTCTCGATAT
1 TGGCTCGCTTAACCTTCTCGATAT
115656573 TGGCTCGCTTGAACCTTCTCGATAT
1 TGGCTCGCTT-AACCTTCTCGATAT
115656598 TGGCT
1 TGGCT
115656603 TGTATAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (24 bp):
TGGCTCGCTTAACCTTCTCGATAT
Found at i:115660097 original size:29 final size:29
Alignment explanation
Indices: 115660019--115660097 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
115660009 TTTAATCCCT
115660019 TTAAAAATAATAAAATTACGT-TTTAAATTTC
1 TTAAAAATAATAAAATTA--TATTT-AATTTC
* * *
115660050 TTAAATATAA-AAAAATATATTT-ATTTT
1 TTAAAAATAATAAAATTATATTTAATTTC
115660077 TTCAAAAATAATAAAATTATA
1 TT-AAAAATAATAAAATTATA
115660098 AATTATTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
27 6 0.15
28 8 0.20
29 11 0.28
30 6 0.15
31 9 0.22
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATATTTAATTTC
Found at i:115667280 original size:16 final size:17
Alignment explanation
Indices: 115667259--115667302 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
115667249 TGTTTACTTA
115667259 ATTTTATTTA-TTAAAC
1 ATTTTATTTATTTAAAC
* *
115667275 ATTTTATTAATTTAAAT
1 ATTTTATTTATTTAAAC
115667292 ATTTTAGTTTA
1 ATTTTA-TTTA
115667303 GAATAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 11 0.48
18 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTTATTTATTTAAAC
Found at i:115667822 original size:21 final size:22
Alignment explanation
Indices: 115667765--115667827 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
115667755 AAGTTTAATT
115667765 AATTTTAA-ATAAATTAATAAA
1 AATTTTAATATAAATTAATAAA
* *
115667786 AATTAT-ATATTGAAATT-TTAAA
1 AATTTTAATA-T-AAATTAATAAA
115667808 AATTTTAATATAAATTAATA
1 AATTTTAATATAAATTAATA
115667828 TAATGTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 13 0.39
23 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTTAATATAAATTAATAAA
Found at i:115667868 original size:22 final size:22
Alignment explanation
Indices: 115667835--115667916 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 22
115667825 ATATAATGTG
115667835 AATTCTAATTTTAAAAAATTATT
1 AATT-TAATTTTAAAAAATTATT
*
115667858 AATTTAATTTTAAATAAAATATT
1 AATTTAATTTTAAA-AAATTATT
* *
115667881 AAAATT-ATTTTATAAAATTATT
1 -AATTTAATTTTAAAAAATTATT
*
115667903 AATTTAAGTTTAAA
1 AATTTAATTTTAAA
115667917 TAAAAGTGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.08
22 23 0.47
23 18 0.37
24 4 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
AATTTAATTTTAAAAAATTATT
Done.