Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold205
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: 1179939
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 53951 characters in sequence are not A, C, G, or T
File 4 of 7
Found at i:598936 original size:20 final size:21
Alignment explanation
Indices: 598911--598950 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
598901 TATAAAACTC
598911 CCCCCTTAAT-AAAATTTTCT
1 CCCCCTTAATAAAAATTTTCT
598931 CCCCCTTAATAAAAATTTTC
1 CCCCCTTAATAAAAATTTTC
598951 CTTTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (21 bp):
CCCCCTTAATAAAAATTTTCT
Found at i:600771 original size:31 final size:31
Alignment explanation
Indices: 600736--600802 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
600726 TGGTGAAGAT
*
600736 TTTGAAGAAAAAT-G-AAAGGAAATGATGTAAA
1 TTTGAAG-AAAATCGAAAAAGAAATGATG-AAA
* *
600767 TTTGATGAAATTCGAAAAAGAAATGATGAAA
1 TTTGAAGAAAATCGAAAAAGAAATGATGAAA
600798 TTTGA
1 TTTGA
600803 GATTAAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 4 0.13
31 15 0.48
32 12 0.39
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.27
Consensus pattern (31 bp):
TTTGAAGAAAATCGAAAAAGAAATGATGAAA
Found at i:600930 original size:13 final size:13
Alignment explanation
Indices: 600897--600937 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
600887 ATAGTGCTCT
* *
600897 TGTATCGATATAT
1 TGTATCGATACAA
*
600910 TGTTTCGATACAA
1 TGTATCGATACAA
600923 TGTATCGATACAA
1 TGTATCGATACAA
600936 TG
1 TG
600938 ATCCTTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:603669 original size:13 final size:13
Alignment explanation
Indices: 603651--603676 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
603641 TACACAAAGT
603651 ATGTATCGATACA
1 ATGTATCGATACA
603664 ATGTATCGATACA
1 ATGTATCGATACA
603677 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:603674 original size:32 final size:33
Alignment explanation
Indices: 603633--603696 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
603623 TAGCCAAACT
**
603633 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
603665 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
603697 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:608285 original size:13 final size:13
Alignment explanation
Indices: 608267--608292 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
608257 TACACAAAGT
608267 ATGTATCGATACA
1 ATGTATCGATACA
608280 ATGTATCGATACA
1 ATGTATCGATACA
608293 TAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:608290 original size:32 final size:33
Alignment explanation
Indices: 608249--608312 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
608239 TAGCCAAACT
**
608249 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
608281 TGTATCGATACATAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
608313 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:609043 original size:13 final size:13
Alignment explanation
Indices: 609025--609050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
609015 TACAGCAAGT
609025 ATGTATCGATACA
1 ATGTATCGATACA
609038 ATGTATCGATACA
1 ATGTATCGATACA
609051 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:611314 original size:21 final size:22
Alignment explanation
Indices: 611268--611312 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
611258 TTGCAAGATG
611268 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
611290 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
611310 AAA
1 AAA
611313 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:613121 original size:15 final size:15
Alignment explanation
Indices: 613101--613131 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
613091 TAAAAATGCC
*
613101 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
613116 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
613131 C
1 C
613132 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:615220 original size:13 final size:13
Alignment explanation
Indices: 615202--615227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
615192 ACATTTTTCT
615202 TTGTATCGATACA
1 TTGTATCGATACA
615215 TTGTATCGATACA
1 TTGTATCGATACA
615228 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:617033 original size:21 final size:21
Alignment explanation
Indices: 617009--617052 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
616999 TTTTTGATAT
*
617009 GAATTACTTAATTAA-GGGGGA
1 GAATTA-TTAATAAACGGGGGA
617030 GAATTATTAATAAACGGGGGA
1 GAATTATTAATAAACGGGGGA
617051 GA
1 GA
617053 TAAAGGGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.25
Consensus pattern (21 bp):
GAATTATTAATAAACGGGGGA
Found at i:617048 original size:20 final size:21
Alignment explanation
Indices: 617009--617048 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
616999 TTTTTGATAT
* *
617009 GAATTACTTAATTAAGGGGGA
1 GAATTACTTAATAAACGGGGA
617030 GAATTA-TTAATAAACGGGG
1 GAATTACTTAATAAACGGGG
617049 GAGATAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.28
Consensus pattern (21 bp):
GAATTACTTAATAAACGGGGA
Found at i:617769 original size:13 final size:13
Alignment explanation
Indices: 617751--617776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
617741 TACACCAAGT
617751 ATGTATCGATACA
1 ATGTATCGATACA
617764 ATGTATCGATACA
1 ATGTATCGATACA
617777 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:617776 original size:32 final size:33
Alignment explanation
Indices: 617735--617796 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
617725 GCCAAACTTA
* **
617735 TATCGATACACCAAGTA-TGTATCGATACAATG
1 TATCGATACACAAAAAATTGTATCGATACAATG
617767 TATCGATACACAAAAAATTGTATCGATACA
1 TATCGATACACAAAAAATTGTATCGATACA
617797 TTGGCTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (33 bp):
TATCGATACACAAAAAATTGTATCGATACAATG
Found at i:620496 original size:20 final size:21
Alignment explanation
Indices: 620473--620544 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
620463 CACGTCCAAA
620473 TGTATCGATACATAATGCT-T
1 TGTATCGATACATAATGCTAT
*
620493 TGTATCG--AGAT-ATGCTCAT
1 TGTATCGATACATAATGCT-AT
* *
620512 TGTATCGATACATACT-CAAT
1 TGTATCGATACATAATGCTAT
*
620532 TGTATCAATACAT
1 TGTATCGATACAT
620545 GAAACTGGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
17 5 0.12
18 3 0.07
19 8 0.19
20 21 0.50
21 4 0.10
22 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATAATGCTAT
Found at i:620608 original size:13 final size:13
Alignment explanation
Indices: 620590--620619 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
620580 GATACATGGG
620590 ACATTGTATCGAT
1 ACATTGTATCGAT
620603 ACATTGTATCGAT
1 ACATTGTATCGAT
620616 ACAT
1 ACAT
620620 GAAGAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:620616 original size:33 final size:33
Alignment explanation
Indices: 620574--620640 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
620564 CTAAGTGAAA
*
620574 TGTATCGATACATG-GGACATTGTATCGATACAT
1 TGTATCGATACATGAAGA-ATTGTATCGATACAT
*
620607 TGTATCGATACATGAAGAATTGTGTCGATACAT
1 TGTATCGATACATGAAGAATTGTATCGATACAT
620640 T
1 T
620641 ATGTCCAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATACAT
Found at i:624067 original size:82 final size:82
Alignment explanation
Indices: 623970--624330 Score: 381
Period size: 82 Copynumber: 4.4 Consensus size: 82
623960 CAATCGAAAA
* *
623970 CTCTAATAGCTTCAGGCAGCAGTAGCATCCATCAATACC-GCAGTAGCTTCGAGCCTCTTCCAGC
1 CTCTAGTAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGTAGC-TCGAGCCTCTTCCAGC
*
624034 CCACGAACACGGTGGCAG
65 CCACGAACACGGTAGCAG
* * * *
624052 CTCTAGTAGCTTCAGGCAGTAGCAGCATCCATCAATACCGACAGTAGCTCGAGCCTTTTCCATCC
1 CTCTAGTAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGTAGCTCGAGCCTCTTCCAGCC
624117 CACGAACACGGTAGCAG
66 CACGAACACGGTAGCAG
** * * * * *
624134 CTCTAACAGCTTCAGGCAACAACAGCATTCATCAATACCTGGCAGCAGCTCGAGCTTCTTCCAGC
1 CTCTAGTAGCTTCAGGCAGCAGCAGCATCCATCAATACC-GGCAGTAGCTCGAGCCTCTTCCAGC
* *
624199 CTACGAACACAGTAGCAG
65 CCACGAACACGGTAGCAG
* * * * * * *
624217 CTCCAGCAACTTTAGGTAGTAGCAGCATCCATCAATACCGGCA-TCAG-TGCGAGCCTCTTCTAG
1 CTCTAGTAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGT-AGCT-CGAGCCTCTTCCAG
* *
624280 CCCATGAACACTGGCAGCAG
64 CCCACGAACAC-GGTAGCAG
* *
624300 CTCCAGTAGTTTCCA-GCAGCA-CTAGCATCCA
1 CTCTAGTAGCTT-CAGGCAGCAGC-AGCATCCA
624331 CCAACACTAG
Statistics
Matches: 230, Mismatches: 42, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
81 1 0.00
82 128 0.56
83 100 0.43
84 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (82 bp):
CTCTAGTAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGTAGCTCGAGCCTCTTCCAGCC
CACGAACACGGTAGCAG
Found at i:624272 original size:165 final size:165
Alignment explanation
Indices: 623970--624302 Score: 413
Period size: 165 Copynumber: 2.0 Consensus size: 165
623960 CAATCGAAAA
* * ** *
623970 CTCTAATAGCTTCAGGCAGCAGTAGCATCCATCAATACCGCAGTAGCTTCGAGCCTCTTCCAGCC
1 CTCTAACAGCTTCAGGCAACAACAGCATCCATCAATACCGCAGCAGCTTCGAGCCTCTTCCAGCC
* * * * *
624035 CACGAACACGGTGGCAGCTCTAGTAGCTTCAGGCAGTAGCAGCATCCATCAATACCGACAGTAGC
66 CACGAACACAGTAGCAGCTCCAGCAACTTCAGGCAGTAGCAGCATCCATCAATACCGACAGTAGC
* * *
624100 TCGAGCCTTTTCCATCCCACGAACAC-GGTAGCAG
131 TCGAGCCTCTTCCAGCCCACGAACACTGGCAGCAG
* *
624134 CTCTAACAGCTTCAGGCAACAACAGCATTCATCAATACCTGGCAGCAGC-TCGAGCTTCTTCCAG
1 CTCTAACAGCTTCAGGCAACAACAGCATCCATCAATACC--GCAGCAGCTTCGAGCCTCTTCCAG
* * * *
624198 CCTACGAACACAGTAGCAGCTCCAGCAACTTTAGGTAGTAGCAGCATCCATCAATACCGGCA-TC
64 CCCACGAACACAGTAGCAGCTCCAGCAACTTCAGGCAGTAGCAGCATCCATCAATACCGACAGT-
* *
624262 AG-TGCGAGCCTCTTCTAGCCCATGAACACTGGCAGCAG
128 AGCT-CGAGCCTCTTCCAGCCCACGAACACTGGCAGCAG
624300 CTC
1 CTC
624303 CAGTAGTTTC
Statistics
Matches: 143, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
164 36 0.25
165 90 0.63
166 17 0.12
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (165 bp):
CTCTAACAGCTTCAGGCAACAACAGCATCCATCAATACCGCAGCAGCTTCGAGCCTCTTCCAGCC
CACGAACACAGTAGCAGCTCCAGCAACTTCAGGCAGTAGCAGCATCCATCAATACCGACAGTAGC
TCGAGCCTCTTCCAGCCCACGAACACTGGCAGCAG
Found at i:632502 original size:21 final size:21
Alignment explanation
Indices: 632469--632509 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
632459 AGTTATATAA
632469 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
632490 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
632510 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:632574 original size:20 final size:19
Alignment explanation
Indices: 632549--632619 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
632539 ACCCTGAAAA
632549 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
632569 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
632588 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
632609 GTATCGATACA
1 GTATCGATACA
632620 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:632672 original size:53 final size:53
Alignment explanation
Indices: 632589--632725 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
632579 AGATTGCATA
632589 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
632643 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
632696 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
632726 TTGGTAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:632866 original size:13 final size:13
Alignment explanation
Indices: 632848--632873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
632838 TCACTATTCA
632848 TGTATCGATACAT
1 TGTATCGATACAT
632861 TGTATCGATACAT
1 TGTATCGATACAT
632874 CATAAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:639092 original size:128 final size:128
Alignment explanation
Indices: 638738--639694 Score: 455
Period size: 128 Copynumber: 7.5 Consensus size: 128
638728 TTTTTTTATG
* * * *
638738 CCCTCAGTCTGCCTGTTGGCTTTGACCCTGGAGAC-TACCT--CCTTAAGTCTGCCTATCGGCTT
1 CCCTAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTT-AGTCTGCCTATCGGCTT
* * ** *
638800 TGACCCTA-GAGACTTTCCT-ATCCCT-TAGTCT-GTTTATCGGCTTTAACCCTAGAGAC-TGCC
65 TGA-CCTAGGAAAC-TTCCTCAT--CTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTCC
638860 TCAT
126 T-AT
** * * ** * * * * *
638864 --CTACA-TTCTATCTGTCGGCGTTGACTCAAGAGACATTT-CTTCTCTTAGTCTGCTTGTCGAC
1 CCCTA-AGTT-TGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTACCCTTAGTCTGCCTATCGGC
* * * * *
638925 TTCGACCCTA-GAGACTGCCTCATCTAAAGTCT-GCCTATCGGTTTTAACCCTGGAGACTTTCCT
63 TTTGA-CCTAGGAAACTTCCTCATCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTCCT
638988 AT
127 AT
* * * *
638990 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTTAGTTTGCCTATCAGCTT
1 CCCTAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTA-CCCTTAGTCTGCCTATCGGCTT
* * * * * *
639055 TGACCTAGGAAACTACCTCATCTAAAGT-TGGCATATCGACTTTGACCTTGGAGACTTTTTCC--
65 TGACCTAGGAAACTTCCTCATCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGAC--TTTCCTA
639117 T
128 T
* * *
639118 CCCTAAGTTTGCTTGTCGACTTTGACTCTGGAGACTTTCCTACCCTTCAGTCTGCCTATCGGCTT
1 CCCTAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTT-AGTCTGCCTATCGGCTT
* * * * * *
639183 TGACCTAAGAGACCTTCCTTC-CCTCAA-TCT-GTCTGTCGGCTTTAACCCTAGAGAC-TTCCTT
65 TGACCTAGGA-AACTTCC-TCATCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTCC-T
639244 AT
127 AT
* ** * * *
639246 --CTAAAGTTTGCCTGTTGGCTTTGACCCTAAAAACTTTCCTATCCCTAAGTCTGCCTATCGACT
1 CCCT-AAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTA-CCCTTAGTCTGCCTATCGGCT
* * * * * * * *
639309 TTAACCTTGGAGACTTTCCT-ATCTCTAAGT-TTGCCTGTCAGCTTTGACCCTAGAGACTATT-C
64 TTGACCTAGGAAAC-TTCCTCATCT-AAAGTCTGGCCTATCGGCTTTAACCCTAGAGACT-TTCC
639371 TAT
126 TAT
* * * * *
639374 CCCTTAA-TTTGCCTATCGGCTTTAACCTTGGAGACTTTCTTACCCTTTAGTCTGCCTGTCGGCT
1 CCC-TAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTACCC-TTAGTCTGCCTATCGGCT
* * * * * * * * **
639438 TTGACCCTA-GAGACTGCCTC-CCT-TAGTCT-GCTTGTCAGCTTTGACCCGGGAGACTTTCCT-
64 TTGA-CCTAGGAAACTTCCTCATCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTCCTA
639498 T
128 T
* * * * * * * * *
639499 CCCTCAGTCT-CCTTGTCAGCTTTGACCCTGAAGA-TTGCCT-CATCTAAAGTTTGCCTGTCGGC
1 CCCTAAGTTTGCC-TGTCGGCTTTGACCCTGGAGACTTTCCTAC-CCT-TAGTCTGCCTATCGGC
* * * * * * ** *
639561 TTTGACCCTA-GAGACTT-TTCTACCCT-TAGTCT-GCGTGTTAGCTTTGACCCTAGAGACTTTC
63 TTTGA-CCTAGGAAACTTCCTC-A-TCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTC
639622 CTA-
125 CTAT
* * * * * * * *
639625 CCCTAAGTCTGTCTCTCGGCTTTGACCTTGGAAACTTTCCTATCCCTAAGTCTGTCTGTCGGCTT
1 CCCTAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTA-CCCTTAGTCTGCCTATCGGCTT
639690 TGACC
65 TGACC
639695 CTGGAGACTT
Statistics
Matches: 646, Mismatches: 131, Indels: 108
0.73 0.15 0.12
Matches are distributed among these distances:
123 4 0.01
124 42 0.07
125 50 0.08
126 134 0.21
127 153 0.24
128 185 0.29
129 62 0.10
130 15 0.02
131 1 0.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (128 bp):
CCCTAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTACCCTTAGTCTGCCTATCGGCTTT
GACCTAGGAAACTTCCTCATCTAAAGTCTGGCCTATCGGCTTTAACCCTAGAGACTTTCCTAT
Found at i:639360 original size:86 final size:86
Alignment explanation
Indices: 638738--639752 Score: 679
Period size: 85 Copynumber: 12.0 Consensus size: 86
638728 TTTTTTTATG
* * * * * *
638738 CCCTCAGTCTGCCTGTTGGCTTTGACCCTGGAGAC-TACC--TCCTTAAGTCTGCCTATCGGCTT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCTT
* *
638800 TGACCCTAGAGACTTTCCTAT
66 TGACCTTGGAGACTTTCCTAT
* ** * * * * **
638821 CCCTTAGTCTGTTTATCGGCTTTAACCCTAGAGAC-TGCCTCAT--CTACATTCTATCTGTCGGC
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-ATCCCTA-AGTCTGCCTGTCGGC
* **
638883 GTTGA-CTCAAGAGACATTT-CT-T
64 TTTGACCT-TGGAGAC-TTTCCTAT
* * * * * * * *
638905 CTCTTAGTCTGCTTGTCGACTTCGACCCTAGAGAC-TGCCTCAT--CTAAAGTCTGCCTATCGGT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCT-ATCCCT-AAGTCTGCCTGTCGGC
* *
638967 TTTAACCCTGGAGACTTTCCTAT
64 TTTGACCTTGGAGACTTTCCTAT
* * * * * *
638990 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTTAGTTTGCCTATCAGCTT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCTT
* * *
639055 TGACCTAGGAAAC-TACCTCAT
66 TGACCTTGGAGACTTTCCT-AT
* * * * * * *
639076 --CTAAAGT-TGGCATATCGACTTTGACCTTGGAGACTTTTTCC--TCCCTAAGTTTGCTTGTCG
1 CCCT-AAGTCT-GCCTGTCGGCTTTGACCCTAGAGAC--TTTCCTATCCCTAAGTCTGCCTGTCG
*
639136 ACTTTGA-CTCTGGAGACTTTCCTA-
62 GCTTTGACCT-TGGAGACTTTCCTAT
* * * *
639160 CCCTTCAGTCTGCCTATCGGCTTTGA-CCTAAGAGACCTTCCT-TCCCTCAA-TCTGTCTGTCGG
1 CCC-TAAGTCTGCCTGTCGGCTTTGACCCT-AGAGACTTTCCTATCCCT-AAGTCTGCCTGTCGG
* * *
639222 CTTTAACCCTAGAGAC-TTCCTTAT
63 CTTTGACCTTGGAGACTTTCC-TAT
* * * * * *
639246 --CTAAAGTTTGCCTGTTGGCTTTGACCCTAAAAACTTTCCTATCCCTAAGTCTGCCTATCGACT
1 CCCT-AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCT
*
639309 TTAACCTTGGAGACTTTCCTAT
65 TTGACCTTGGAGACTTTCCTAT
* * * * *
639331 CTCTAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTATT-CTATCCCTTAA-TTTGCCTATCGGC
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACT-TTCCTATCCC-TAAGTCTGCCTGTCGGC
* *
639394 TTTAACCTTGGAGACTTTCTTA-
64 TTTGACCTTGGAGACTTTCCTAT
* * * * *
639416 CCCTTTAGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCC--TCCCTTAGTCTGCTTGTCAGCT
1 CCC-TAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCT
**
639478 TTGACCCGGGAGACTTTCCT-T
65 TTGACCTTGGAGACTTTCCTAT
* * * *
639499 CCCTCAGTCT-CCTTGTCAGCTTTGACCCT-GAAGA-TTGCCTCAT--CTAAAGTTTGCCTGTCG
1 CCCTAAGTCTGCC-TGTCGGCTTTGACCCTAG-AGACTTTCCT-ATCCCT-AAGTCTGCCTGTCG
* * *
639559 GCTTTGACCCTAGAGACTTTTCTA-
62 GCTTTGACCTTGGAGACTTTCCTAT
* * ** * *
639583 CCCTTAGTCTGCGTGTTAGCTTTGACCCTAGAGACTTTCCTA-CCCTAAGTCTGTCTCTCGGCTT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCTT
*
639647 TGACCTTGGAAACTTTCCTAT
66 TGACCTTGGAGACTTTCCTAT
* * * *
639668 CCCTAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTCATATCCCTTAGTCTGCCTGTCGGCTT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCTT
* *
639733 TGATCTTGGAAACTTTCCTA
66 TGACCTTGGAGACTTTCCTA
639753 CTGTTAGGTT
Statistics
Matches: 737, Mismatches: 137, Indels: 113
0.75 0.14 0.11
Matches are distributed among these distances:
81 3 0.00
82 30 0.04
83 70 0.09
84 195 0.26
85 223 0.30
86 200 0.27
87 16 0.02
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (86 bp):
CCCTAAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTATCCCTAAGTCTGCCTGTCGGCTT
TGACCTTGGAGACTTTCCTAT
Found at i:639748 original size:43 final size:43
Alignment explanation
Indices: 638738--639752 Score: 675
Period size: 43 Copynumber: 24.0 Consensus size: 43
638728 TTTTTTTATG
* * *
638738 CCCTCAGTCTGCCTGTTGGCTTTGACCCTGGAGAC-TACC--T
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * *
638778 CCTTAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCCTAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* ** * * * *
638821 CCCTTAGTCTGTTTATCGGCTTTAACCCTAGAGAC-TGCCTCAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-AT
* ** * * **
638864 --CTACATTCTATCTGTCGGCGTTGACTCAAGAGACATTT-CT-T
1 CCCTA-AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTCCTAT
* * * * * * *
638905 CTCTTAGTCTGCTTGTCGACTTCGACCCTAGAGAC-TGCCTCAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-AT
* * *
638948 --CTAAAGTCTGCCTATCGGTTTTAACCCTGGAGACTTTCCTAT
1 CCCT-AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
*
638990 CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * * * *
639033 CCCTTAGTTTGCCTATCAGCTTTGA-CCTAGGAAAC-TACCTCAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTCCT-AT
* * * *
639076 --CTAAAGT-TGGCATATCGACTTTGACCTTGGAGACTTTTTCC--T
1 CCCT-AAGTCT-GCCTGTCGGCTTTGACCCTGGAGAC--TTTCCTAT
* * * *
639118 CCCTAAGTTTGCTTGTCGACTTTGACTCTGGAGACTTTCCTA-
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639160 CCCTTCAGTCTGCCTATCGGCTTTGA-CCTAAGAGACCTTCCT-T
1 CCC-TAAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTTCCTAT
* * *
639203 CCCTCAA-TCTGTCTGTCGGCTTTAACCCTAGAGAC-TTCCTTAT
1 CCCT-AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC-TAT
* * ** *
639246 --CTAAAGTTTGCCTGTTGGCTTTGACCCTAAAAACTTTCCTAT
1 CCCT-AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639288 CCCTAAGTCTGCCTATCGACTTTAACCTTGGAGACTTTCCTAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639331 CTCTAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTATT-CTAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTCCTAT
* * * * *
639374 CCCTTAA-TTTGCCTATCGGCTTTAACCTTGGAGACTTTCTTA-
1 CCC-TAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * *
639416 CCCTTTAGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCC--T
1 CCC-TAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639457 CCCTTAGTCTGCTTGTCAGCTTTGACCCGGGAGACTTTCCT-T
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639499 CCCTCAGTCT-CCTTGTCAGCTTTGACCCTGAAGA-TTGCCTCAT
1 CCCTAAGTCTGCC-TGTCGGCTTTGACCCTGGAGACTTTCCT-AT
* * *
639542 --CTAAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTA-
1 CCCT-AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * ** *
639583 CCCTTAGTCTGCGTGTTAGCTTTGACCCTAGAGACTTTCCTA-
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639625 CCCTAAGTCTGTCTCTCGGCTTTGACCTTGGAAACTTTCCTAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* *
639668 CCCTAAGTCTGTCTGTCGGCTTTGACCCTGGAGACTTTCATAT
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
* * * *
639711 CCCTTAGTCTGCCTGTCGGCTTTGATCTTGGAAACTTTCCTA
1 CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTA
639753 CTGTTAGGTT
Statistics
Matches: 764, Mismatches: 155, Indels: 109
0.74 0.15 0.11
Matches are distributed among these distances:
40 59 0.08
41 40 0.05
42 280 0.37
43 369 0.48
44 13 0.02
45 3 0.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (43 bp):
CCCTAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT
Found at i:640170 original size:32 final size:33
Alignment explanation
Indices: 640129--640191 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
640119 TAGCCAAACT
640129 TGTATCGATACAC-AAAATATGTATCGATATAA
1 TGTATCGATACACAAAAATATGTATCGATATAA
640161 TGTATCGATACACAAAAAATATGTATCGATA
1 TGTATCGATACAC-AAAAATATGTATCGATA
640192 CATTGGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.45
34 16 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATATAA
Found at i:646360 original size:13 final size:13
Alignment explanation
Indices: 646342--646375 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
646332 TTTCTTTGTG
646342 TCGATACAATGTA
1 TCGATACAATGTA
*
646355 TCGATACACTGTA
1 TCGATACAATGTA
646368 TCGATACA
1 TCGATACA
646376 GGGGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (13 bp):
TCGATACAATGTA
Found at i:648937 original size:13 final size:13
Alignment explanation
Indices: 648919--648955 Score: 60
Period size: 11 Copynumber: 3.0 Consensus size: 13
648909 TACACAAAAT
648919 ATGTATCGATACA
1 ATGTATCGATACA
648932 ATGTAT--ATACA
1 ATGTATCGATACA
648943 ATGTATCGATACA
1 ATGTATCGATACA
648956 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:649899 original size:84 final size:82
Alignment explanation
Indices: 649719--650717 Score: 475
Period size: 84 Copynumber: 11.9 Consensus size: 82
649709 TAAGCTTTCA
** * * * * *
649719 CCTACCCTTCAGTCTATCTGTCAGCTTTGACACTAGAGACTGCCTC-CCTCAA-TCTACCTATCA
1 CCTACCCTT-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTCACCT-AAGTCTGCCTGTCA
*
649782 GCTTTGACCC-AAGAAACTTT
64 -CTTTGACCCTAA-AGACTTT
* * * * * * * *
649802 CCTTCCCTCAGTCTGCTTGTCGGCTTTGACCTTAAAGACTGCCTCATCTAAAGTTTGCCTGTCAT
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTCACCT-AAGTCTGCCTGTCA-
649867 CTTTGACCCTAAAGACTTT
64 CTTTGACCCTAAAGACTTT
* * * * *
649886 TCTACCCTTAGTCTGCCTGTCAGCTTTGACCCT-GAAGACTTTCTTACCCTTAGTCTGCCTGTCG
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTCCTCA-CCTAAGTCTGCCTGTC-
*
649950 ACTTTGACCC-AGGAGACTTT
63 ACTTTGACCCTA-AAGACTTT
* * * * * * * * * *
649970 CCTTCCCTCAATCTGCCTGTCGGCTTTAACCTTAGAGACTGCCTTATCTAAAGTTTGCCTGTCGG
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTCACCT-AAGTCTGCCTGTC-A
* *
650035 CTTTGACTCTGAAGACTTT
64 CTTTGACCCTAAAGACTTT
* * * * *
650054 CCTATCCCTAAGTCTGCCTGTTGGCTTTGACCTTCGAGACTTTCCT-ATCCCTAAGTCTGCTTGT
1 CCTA-CCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TTCCTCA--CCTAAGTCTGCCTGT
*
650118 CAGCTTTGACTCTAAAGACTATT
62 CA-CTTTGACCCTAAAGACT-TT
* * * * *
650141 -CTATCCCTTAATCTGCCTGTCGGCTTTGATCTTGGAGACTTCC-CTACCCTTCAA-TCTGCCTA
1 CCTA-CCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTC-A-CC-T-AAGTCTGCCTG
* ** *
650203 TCGACTTTGACCTTGGAGAC-TG
61 TC-ACTTTGACCCTAAAGACTTT
* * * *
650225 CCT-CCCTTAGTCTGCCTGTCGACTTTGATCC-AGGAGACTTTCCTTC-CCTCAGTCTGCTTGTC
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTA-GAGAC-TTCC-TCACCTAAGTCTGCCTGTC
* *
650287 GACTTTGACCCTGAAGAC-TA
63 -ACTTTGACCCTAAAGACTTT
* * * * * * *
650307 CCT-CATCTAAATTTTGCCTGTCAGCTTTGACCCT-GAAGACTT-TTCTACCCTTAGTCTGCCTG
1 CCTAC-CCT-TAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTCCTC-A-CCTAAGTCTGCCTG
* *
650369 TCAGCTTTAACCCTGAAGACCTTT
61 TCA-CTTTGACCCTAAAGA-CTTT
* * *
650393 -CTACCCTCAGTCTGCCTGTCGGCTTTGACCCT-GAAGACTGCCTCATCTAAAGT-TCGCCTGTC
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTCCTCACCT-AAGTCT-GCCTGTC
*
650455 AACTTTGACCCTAGAGACTTT
63 -ACTTTGACCCTAAAGACTTT
* * ** * *
650476 TCTACCCTTAGTCTGCTTGTTAGCTTTGACCCTAGAGACTT-TTCTACCCTCAGTCTGCCTGTCG
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTC-A-CCTAAGTCTGCCTGTC-
* * *
650540 GCTTTGACCTTAAAGAC-TG
63 ACTTTGACCCTAAAGACTTT
* * * * * * * *
650559 CCTTA-TCTAAAGTTTACCTGTCGACTTTGACCTTGGAGACTAGT-CT-ACCCTTAGTCTGCCTG
1 CC-TACCCT-TAGTCTGCCTGTCGGCTTTGACCCTAGAGACT--TCCTCA-CCTAAGTCTGCCTG
* ** *
650621 TCAGCTTTGACCTTGGAGATTTT
61 TCA-CTTTGACCCTAAAGACTTT
* * * * * ** * *
650644 CCTACCCTCAGTTTGTCTATCAGCTTTGACCCT-GAAGACCACCTCATCTAAAGTTTGCCTGTCA
1 CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAG-AGACTTCCTCACCT-AAGTCTGCCTGTCA
650708 GCTTTGACCC
64 -CTTTGACCC
650718 GGGAGAATCT
Statistics
Matches: 709, Mismatches: 149, Indels: 115
0.73 0.15 0.12
Matches are distributed among these distances:
81 3 0.00
82 59 0.08
83 70 0.10
84 415 0.59
85 63 0.09
86 92 0.13
87 7 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (82 bp):
CCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTCCTCACCTAAGTCTGCCTGTCACT
TTGACCCTAAAGACTTT
Found at i:649967 original size:126 final size:125
Alignment explanation
Indices: 649736--650682 Score: 644
Period size: 126 Copynumber: 7.5 Consensus size: 125
649726 TTCAGTCTAT
* ** * * * * *
649736 CTGTCAGCTTTGACACTAGAGAC-TGCCT-CCCTCAATCTACCTATCAGCTTTGACCCAAGAA-A
1 CTGTCAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCC-TGAAGA
* * * ** * * *
649798 CTTTCCTT-CCCTCAGTCTGCTTGTCGGCTTTGACCTTAAAGACTGCCTCATCTAAAGTTTGC
65 C-TTCCTTACCCTAAGTCTGCCTGTCGACTTTGACCTTGGAGACTGCCTCACCT-TAGTCTGC
* * * *
649860 CTGTCATCTTTGACCCTAAAGACTTTTCTACCCTTAGTCTGCCTGTCAGCTTTGACCCTGAAGAC
1 CTGTCAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGAC
* * ** * * *
649925 TTTCTTACCCTTAGTCTGCCTGTCGACTTTGACCCAGGAGACTTTCCTTC-CCTCAATCTGC
66 TTCCTTACCCTAAGTCTGCCTGTCGACTTTGACCTTGGAGAC-TGCC-TCACCTTAGTCTGC
* * * ** * * * *
649986 CTGTCGGCTTTAACCTTAGAGAC-TGCCTTA-TCTAAAGTTTGCCTGTCGGCTTTGACTCTGAAG
1 CTGTCAGCTTTGACCCTAGAGACTTTTC-TACCCT-CAGTCTGCCTGTCGGCTTTGACCCTGAAG
* * * * *
650049 ACTTTCC-TATCCCTAAGTCTGCCTGTTGGCTTTGACCTTCGAGACTTTCCT-ATCCCTAAGTCT
64 AC-TTCCTTA-CCCTAAGTCTGCCTGTCGACTTTGACCTTGGAGAC-TGCCTCA--CCTTAGTCT
650112 GC
124 GC
* * * * * * * * *
650114 TTGTCAGCTTTGACTCTAAAGACTATTCTATCCCTTAATCTGCCTGTCGGCTTTGATCTTGGAGA
1 CTGTCAGCTTTGACCCTAGAGACTTTTCTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGA
* *
650179 CTTCCCTACCCTTCAA-TCTGCCTATCGACTTTGACCTTGGAGACTGCCTC-CCTTAGTCTGC
65 CTTCCTTACCC-T-AAGTCTGCCTGTCGACTTTGACCTTGGAGACTGCCTCACCTTAGTCTGC
* * * * *
650240 CTGTC-GACTTTGATCC-AGGAGACTTTCCTTCCCTCAGTCTGCTTGTCGACTTTGACCCTGAAG
1 CTGTCAG-CTTTGACCCTA-GAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAG
* * * * * * * **
650303 ACTACCTCA-TCTAAATTTTGCCTGTC-AGCTTTGACCCTGAAGACT-TTTCTACCCTTAGTCTG
64 ACTTCCTTACCCT-AAGTCTGCCTGTCGA-CTTTGACCTTGGAGACTGCCTC-A-CCTTAGTCTG
650365 C
125 C
* *
650366 CTGTCAGCTTTAACCCT-GAAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGA
1 CTGTCAGCTTTGACCCTAG-AGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGA
* * * * * * **
650430 CTGCCTCA-TCTAAAGT-TCGCCTGTCAACTTTGACCCTAGAGACT-TTTCTACCCTTAGTCTGC
65 CTTCCTTACCCT-AAGTCT-GCCTGTCGACTTTGACCTTGGAGACTGCCTC-A-CCTTAGTCTGC
* * * *
650492 TTGTTAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCTTAAAGAC
1 CTGTCAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGAC
* * * * *
650557 TGCCTTA-TCTAAAGTTTACCTGTCGACTTTGACCTTGGAGACTAGTCT-ACCCTTAGTCTGC
66 TTCCTTACCCT-AAGTCTGCCTGTCGACTTTGACCTTGGAGACT-GCCTCA-CCTTAGTCTGC
* * * * * *
650618 CTGTCAGCTTTGACCTTGGAGA-TTTTCCTACCCTCAGTTTGTCTATCAGCTTTGACCCTGAAGA
1 CTGTCAGCTTTGACCCTAGAGACTTTT-CTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGA
650682 C
65 C
650683 CACCTCATCT
Statistics
Matches: 661, Mismatches: 125, Indels: 72
0.77 0.15 0.08
Matches are distributed among these distances:
123 6 0.01
124 44 0.07
125 55 0.08
126 411 0.62
127 46 0.07
128 43 0.07
129 52 0.08
130 4 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (125 bp):
CTGTCAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAGAC
TTCCTTACCCTAAGTCTGCCTGTCGACTTTGACCTTGGAGACTGCCTCACCTTAGTCTGC
Found at i:650261 original size:83 final size:82
Alignment explanation
Indices: 650144--650310 Score: 217
Period size: 83 Copynumber: 2.0 Consensus size: 82
650134 GACTATTCTA
* **
650144 TCCCTTAATCTGCCTGTCGGCTTTGATCTTGGAGACTTCCCTACCCTTCAATCTGCCTATCGACT
1 TCCCTTAATCTGCCTGTCGACTTTGATCCAGGAGACTTCCCTACCC-TCAATCTGCCTATCGACT
* * *
650209 TTGACCTTGGAGACTGCC
65 TTGACCCTGAAGACTACC
* * * * * *
650227 TCCCTTAGTCTGCCTGTCGACTTTGATCCAGGAGACTTTCCTTCCCTCAGTCTGCTTGTCGACTT
1 TCCCTTAATCTGCCTGTCGACTTTGATCCAGGAGACTTCCCTACCCTCAATCTGCCTATCGACTT
650292 TGACCCTGAAGACTACC
66 TGACCCTGAAGACTACC
650309 TC
1 TC
650311 ATCTAAATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
82 32 0.44
83 40 0.56
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.34
Consensus pattern (82 bp):
TCCCTTAATCTGCCTGTCGACTTTGATCCAGGAGACTTCCCTACCCTCAATCTGCCTATCGACTT
TGACCCTGAAGACTACC
Found at i:650557 original size:42 final size:42
Alignment explanation
Indices: 649797--650682 Score: 528
Period size: 42 Copynumber: 21.0 Consensus size: 42
649787 GACCCAAGAA
* * * *
649797 ACTTTCCTTCCCTCAGTCTGCTTGTCGGCTTTGACCTTAAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * ** * *
649839 AC-TGCCT-CATCTAAAGTTTGCCTGTCATCTTTGACCCTAAAG
1 ACTTTCCTAC-CCT-AAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * *
649881 ACTTTTCTACCCTTAGTCTGCCTGTCAGCTTTGACCCTGAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * ** *
649923 ACTTTCTTACCCTTAGTCTGCCTGTCGACTTTGACCCAGGAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* *
649965 ACTTTCCTTCCCTCAA-TCTGCCTGTCGGCTTTAACCTT-AGAG
1 ACTTTCCTACCCT-AAGTCTGCCTGTCGGCTTTGACCTTGA-AG
* * *
650007 AC-TGCCTTA-TCTAAAGTTTGCCTGTCGGCTTTGA-CTCTGAAG
1 ACTTTCC-TACCCT-AAGTCTGCCTGTCGGCTTTGACCT-TGAAG
*
650049 ACTTTCCTATCCCTAAGTCTGCCTGTTGGCTTTGACCTTCG-AG
1 ACTTTCCTA-CCCTAAGTCTGCCTGTCGGCTTTGACCTT-GAAG
* * *
650092 ACTTTCCTATCCCTAAGTCTGCTTGTCAGCTTTGA-CTCTAAAG
1 ACTTTCCTA-CCCTAAGTCTGCCTGTCGGCTTTGACCT-TGAAG
* *
650135 ACTATT-CTATCCCTTAA-TCTGCCTGTCGGCTTTGATCTTGGAG
1 ACT-TTCCTA-CCC-TAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * *
650178 ACTTCCCTACCCTTCAA-TCTGCCTATCGACTTTGACCTTGGAG
1 ACTTTCCTACCC-T-AAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * * *
650221 AC-TGCCT-CCCTTAGTCTGCCTGTCGACTTTGATCC-AGGAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGA-CCTTGAAG
* * * * *
650261 ACTTTCCTTCCCTCAGTCTGCTTGTCGACTTTGACCCTGAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * * * *
650303 AC-TACCT-CATCTAAATTTTGCCTGTCAGCTTTGACCCTGAAG
1 ACTTTCCTAC-CCT-AAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * * *
650345 ACTTTTCTACCCTTAGTCTGCCTGTCAGCTTTAACCCTGAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* *
650387 ACCTTT-CTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAAG
1 A-CTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * ** *
650429 AC-TGCCT-CATCTAAAGT-TCGCCTGTCAACTTTGACCCT-AGAG
1 ACTTTCCTAC-CCT-AAGTCT-GCCTGTCGGCTTTGACCTTGA-AG
* * * ** *
650471 ACTTTTCTACCCTTAGTCTGCTTGTTAGCTTTGACCCT-AGAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGA-AG
* * *
650513 ACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCTTAAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * * * *
650555 AC-TGCCTTA-TCTAAAGTTTACCTGTCGACTTTGACCTTGGAG
1 ACTTTCC-TACCCT-AAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * *
650597 ACTAGT-CTACCCTTAGTCTGCCTGTCAGCTTTGACCTTGGAG
1 ACT-TTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
* * * * * * *
650639 ATTTTCCTACCCTCAGTTTGTCTATCAGCTTTGACCCTGAAG
1 ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
650681 AC
1 AC
650683 CACCTCATCT
Statistics
Matches: 676, Mismatches: 121, Indels: 94
0.76 0.14 0.11
Matches are distributed among these distances:
39 1 0.00
40 28 0.04
41 44 0.07
42 440 0.65
43 148 0.22
44 15 0.02
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (42 bp):
ACTTTCCTACCCTAAGTCTGCCTGTCGGCTTTGACCTTGAAG
Found at i:650693 original size:126 final size:125
Alignment explanation
Indices: 649857--650723 Score: 675
Period size: 126 Copynumber: 6.9 Consensus size: 125
649847 ATCTAAAGTT
* ** * * *
649857 TGCCTGTCATCTTTGACCCTAAAGACTTTTCTACCCTTAGTCTGCCTGTCAGCTTTGACCCTGAA
1 TGCCTGTCAGCTTTGACCCTGGAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAA
** * * * * * * * *
649922 GACTTTCTTACCCT-TAGTCTGCCTGTCGACTTTGACCCAGGAGACTT-TCCTTCCCTCAATC
66 GACTACCTCA-TCTAAAGTTTGCCTGTC-ACTTTGACCCTGGAGACTTGT-CTACCCTTAGTC
* * * * ** * * * *
649983 TGCCTGTCGGCTTTAACCTTAGAGA-CTGCCTTA-TCTAAAGTTTGCCTGTCGGCTTTGACTCTG
1 TGCCTGTCAGCTTTGACCCTGGAGACCTTTC-TACCCT-CAGTCTGCCTGTCGGCTTTGACCCTG
* * ** * * *
650046 AAGACTTTCCT-ATCCCT-AAGTCTGCCTGTTGGCTTTGACCTTCGAGACTT-TCCTATCCCTAA
64 AAGAC-TACCTCAT--CTAAAGTTTGCCTG-TCACTTTGACCCTGGAGACTTGT-CTA-CCCTTA
650108 GTC
123 GTC
* * ** * * * *
650111 TGCTTGTCAGCTTTGACTCTAAAGA-CTATTCTATCCCTTAATCTGCCTGTCGGCTTTGATCTTG
1 TGCCTGTCAGCTTTGACCCTGGAGACCT-TTCTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTG
* * * * * * * *
650175 GAGACTTCC-CTACCCTTCAA-TCTGCCTATCGACTTTGACCTTGGAGAC-TGCCT-CCCTTAGT
64 AAGACTACCTC-A-TC-TAAAGTTTGCCTGTC-ACTTTGACCCTGGAGACTTGTCTACCCTTAGT
650236 C
125 C
* * * * *
650237 TGCCTGTC-GACTTTGATCCAGGAGA-CTTTCCTTCCCTCAGTCTGCTTGTCGACTTTGACCCTG
1 TGCCTGTCAG-CTTTGACCCTGGAGACCTTT-CTACCCTCAGTCTGCCTGTCGGCTTTGACCCTG
* * *
650300 AAGACTACCTCATCTAAATTTTGCCTGTCAGCTTTGACCCTGAAGACTTTTCTACCCTTAGTC
64 AAGACTACCTCATCTAAAGTTTGCCTGTCA-CTTTGACCCTGGAGACTTGTCTACCCTTAGTC
* *
650363 TGCCTGTCAGCTTTAACCCTGAAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAA
1 TGCCTGTCAGCTTTGACCCTGGAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAA
* * * *
650428 GACTGCCTCATCTAAAGTTCGCCTGTCAACTTTGACCCTAGAGACTTTTCTACCCTTAGTC
66 GACTACCTCATCTAAAGTTTGCCTGTC-ACTTTGACCCTGGAGACTTGTCTACCCTTAGTC
* * * * * *
650489 TGCTTGTTAGCTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCTTAAA
1 TGCCTGTCAGCTTTGACCCTGGAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAA
* * * * *
650554 GACTGCCTTATCTAAAGTTTACCTGTCGACTTTGACCTTGGAGACTAGTCTACCCTTAGTC
66 GACTACCTCATCTAAAGTTTGCCTGTC-ACTTTGACCCTGGAGACTTGTCTACCCTTAGTC
* * * * * *
650615 TGCCTGTCAGCTTTGACCTTGGAGA-TTTTCCTACCCTCAGTTTGTCTATCAGCTTTGACCCTGA
1 TGCCTGTCAGCTTTGACCCTGGAGACCTTT-CTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGA
* *
650679 AGACCACCTCATCTAAAGTTTGCCTGTCAGCTTTGACCCGGGAGA
65 AGACTACCTCATCTAAAGTTTGCCTGTCA-CTTTGACCCTGGAGA
650724 ATCTTTTCTT
Statistics
Matches: 598, Mismatches: 114, Indels: 58
0.78 0.15 0.08
Matches are distributed among these distances:
123 4 0.01
124 23 0.04
125 47 0.08
126 390 0.65
127 41 0.07
128 40 0.07
129 49 0.08
130 4 0.01
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.34
Consensus pattern (125 bp):
TGCCTGTCAGCTTTGACCCTGGAGACCTTTCTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGAA
GACTACCTCATCTAAAGTTTGCCTGTCACTTTGACCCTGGAGACTTGTCTACCCTTAGTC
Found at i:652262 original size:20 final size:21
Alignment explanation
Indices: 652237--652283 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
652227 ATGAATAGTG
652237 ATACAAGTGTTCTTCCC-TTA
1 ATACAAGTGTTCTTCCCTTTA
652257 ATACAAGTGTTCTTCCCTTTA
1 ATACAAGTGTTCTTCCCTTTA
652278 ATACAA
1 ATACAA
652284 AATTTATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (21 bp):
ATACAAGTGTTCTTCCCTTTA
Found at i:653129 original size:13 final size:13
Alignment explanation
Indices: 653111--653135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
653101 ACTGAAGTAA
653111 TGTATCGATACAT
1 TGTATCGATACAT
653124 TGTATCGATACA
1 TGTATCGATACA
653136 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:653766 original size:23 final size:24
Alignment explanation
Indices: 653721--653767 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
653711 CAAAGAATTG
*
653721 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
653745 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
653768 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:656949 original size:53 final size:53
Alignment explanation
Indices: 656885--657021 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
656875 CTACTACCAA
656885 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
656938 TGTATCGATACATATTGTGTGTATCGATATAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
656991 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
657022 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:657054 original size:20 final size:20
Alignment explanation
Indices: 656991--657061 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
656981 GCCAATGTCC
**
656991 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
657011 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
657031 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
657051 TGTATCGATAC
1 TGTATCGATAC
657062 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:657127 original size:21 final size:21
Alignment explanation
Indices: 657101--657141 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
657091 GTCAACCTTG
657101 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
657122 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
657142 TTTACTTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:657908 original size:22 final size:22
Alignment explanation
Indices: 657880--657957 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
657870 CCACGAACAC
657880 GGCAGCAGCTCCAGCAGCTTCA
1 GGCAGCAGCTCCAGCAGCTTCA
* * * *
657902 GGCAGCAGCAGCATCCATCA-ATACC
1 -G--GCAGCAGC-TCCAGCAGCTTCA
*
657927 GGTAGCAGCTCCAGCAGCTTCA
1 GGCAGCAGCTCCAGCAGCTTCA
657949 GGCAGCAGC
1 GGCAGCAGC
657958 AGCATTCATC
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
21 6 0.15
22 17 0.41
23 1 0.02
24 1 0.02
25 10 0.24
26 6 0.15
ACGTcount: A:0.26, C:0.35, G:0.27, T:0.13
Consensus pattern (22 bp):
GGCAGCAGCTCCAGCAGCTTCA
Found at i:657981 original size:47 final size:47
Alignment explanation
Indices: 657881--657984 Score: 172
Period size: 47 Copynumber: 2.2 Consensus size: 47
657871 CACGAACACG
*
657881 GCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCG
1 GCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCA
* * *
657928 GTAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATTCATCAATACTA
1 GCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCA
657975 GCAGCAGCTC
1 GCAGCAGCTC
657985 GAGCCTCTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.15
Consensus pattern (47 bp):
GCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCA
Found at i:658012 original size:82 final size:82
Alignment explanation
Indices: 657926--658107 Score: 285
Period size: 82 Copynumber: 2.2 Consensus size: 82
657916 CCATCAATAC
*
657926 CGGTAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATTCATCAATACTAGCAGCAGC-TCGAGCC
1 CGGTAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACTAGCAGCAGCAT-GAGCC
*
657990 TCTTCCAGCCCACGAACA
65 TCTTCCAGCCCACAAACA
* * * *
658008 CGGTAGTAGCTCTAGCAGCTTCAGGTAGCAGCAGCATCCATCAATACTGGCAGCAGCATGAGCCT
1 CGGTAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACTAGCAGCAGCATGAGCCT
658073 CTTCCAGCCCACAAACA
66 CTTCCAGCCCACAAACA
*
658090 CGGCAGCAGCTCCAGCAG
1 CGGTAGCAGCTCCAGCAG
658108 TTTCTAGCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 89 0.99
83 1 0.01
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (82 bp):
CGGTAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACTAGCAGCAGCATGAGCCT
CTTCCAGCCCACAAACA
Found at i:658038 original size:129 final size:129
Alignment explanation
Indices: 657806--658064 Score: 383
Period size: 129 Copynumber: 2.0 Consensus size: 129
657796 CAATCGAAAA
* * * * * *
657806 CTCCAGTAGCTTCAAGTAGCAGCAGCATCCATCAATACCGGTAGCAGCTCGAGCCTTTTCTAGCC
1 CTCCAGCAGCTTCAAGCAGCAGCAGCATCCATCAATACCAGCAGCAGCTCGAGCCTCTTCCAGCC
*
657871 CACGAACACGGCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGTAGCAG
66 CACGAACACGGCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAG
* * *
657935 CTCCAGCAGCTTCAGGCAGCAGCAGCATTCATCAATACTAGCAGCAGCTCGAGCCTCTTCCAGCC
1 CTCCAGCAGCTTCAAGCAGCAGCAGCATCCATCAATACCAGCAGCAGCTCGAGCCTCTTCCAGCC
* * * * *
658000 CACGAACACGGTAGTAGCTCTAGCAGCTTCAGGTAGCAGCAGCATCCATCAATACTGGCAGCAG
66 CACGAACACGGCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAG
658064 C
1 C
658065 ATGAGCCTCT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 115 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.17
Consensus pattern (129 bp):
CTCCAGCAGCTTCAAGCAGCAGCAGCATCCATCAATACCAGCAGCAGCTCGAGCCTCTTCCAGCC
CACGAACACGGCAGCAGCTCCAGCAGCTTCAGGCAGCAGCAGCATCCATCAATACCGGCAGCAG
Found at i:666161 original size:21 final size:21
Alignment explanation
Indices: 666114--666162 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
666104 AGAGCTTTAA
666114 TTATTTTATCAAGGGAGAGAT
1 TTATTTTATCAAGGGAGAGAT
** * * *
666135 AAATTTTATTAAGGGGGAGTT
1 TTATTTTATCAAGGGAGAGAT
666156 TTATTTT
1 TTATTTT
666163 TACTTTTGAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (21 bp):
TTATTTTATCAAGGGAGAGAT
Found at i:666832 original size:20 final size:19
Alignment explanation
Indices: 666787--666841 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
666777 TATATTGATA
* *
666787 CATTTTATCGATGCATACT
1 CATTGTATCGATACATACT
666806 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
666825 CAATTGTATCGATACAT
1 C-ATTGTATCGATACAT
666842 GAAACTGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:670383 original size:19 final size:19
Alignment explanation
Indices: 670336--670422 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
670326 TACTAGTTTT
***
670336 ATGTATCGATACAATTCTTC
1 ATGTATCGATACAA-TGAAC
670356 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
*
670375 ATGTTTCGAT---AT--A-
1 ATGTATCGATACAATGAAC
*
670388 ATGGATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
670407 ATGTATCGATACAATG
1 ATGTATCGATACAATG
670423 TATCGATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
13 8 0.15
14 1 0.02
16 4 0.07
18 1 0.02
19 26 0.48
20 14 0.26
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:670401 original size:32 final size:32
Alignment explanation
Indices: 670360--670451 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
670350 TTCTTCATGT
* *
670360 ATCGATACAATGAACATGTTTCGATATAATGG
1 ATCGATACAATGAACATGTATCGATACAATGG
*
670392 ATCGATACAATGAACATGTATCGATACAATGT
1 ATCGATACAATGAACATGTATCGATACAATGG
* *
670424 ATCGATACAAAGCAATATGTATCGATAC
1 ATCGATACAATG-AACATGTATCGATAC
670452 TTCTGGGCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 40 0.74
33 14 0.26
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (32 bp):
ATCGATACAATGAACATGTATCGATACAATGG
Found at i:670425 original size:13 final size:13
Alignment explanation
Indices: 670407--670433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
670397 TACAATGAAC
670407 ATGTATCGATACA
1 ATGTATCGATACA
670420 ATGTATCGATACA
1 ATGTATCGATACA
670433 A
1 A
670434 AGCAATATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:671208 original size:20 final size:20
Alignment explanation
Indices: 671185--671232 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
671175 GCAAATTGTG
* *
671185 TCGATATATTTAGGAATGTA
1 TCGATACATTTACGAATGTA
**
671205 TCGATACATTTACTTATGTA
1 TCGATACATTTACGAATGTA
671225 TCGATACA
1 TCGATACA
671233 ATTTTTTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (20 bp):
TCGATACATTTACGAATGTA
Found at i:671311 original size:20 final size:20
Alignment explanation
Indices: 671282--671354 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
671272 ATTTGAGACA
*
671282 TGTATTGATACATTTACTTT
1 TGTATTGATACATTCACTTT
*
671302 TGTATCGATACATTCA-TTT
1 TGTATTGATACATTCACTTT
*
671321 ATGTATTGATACATTCACTAAT
1 -TGTATTGATACATTCACT-TT
671343 TGTATTGATACA
1 TGTATTGATACA
671355 AATCGTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.07
20 29 0.63
21 13 0.28
22 1 0.02
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (20 bp):
TGTATTGATACATTCACTTT
Found at i:672447 original size:16 final size:16
Alignment explanation
Indices: 672428--672459 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
672418 TTATTAATGT
672428 ATAAAATTTTATAATA
1 ATAAAATTTTATAATA
*
672444 ATAAATTTTTATAATA
1 ATAAAATTTTATAATA
672460 TTTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAAAATTTTATAATA
Found at i:672567 original size:40 final size:41
Alignment explanation
Indices: 672504--672582 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
672494 ATTTTTCTCA
* * *
672504 TTTTTCTTTCTTATATCTCTTTTTC-CT-TTTTTCTTTTAT
1 TTTTTCTTTCTCACATCTCTTTTTCTCTCATTTTCTTTTAT
*
672543 TTTTTCCTTTCTCACATCTTTTTTTCTCTCATTTTCTTTT
1 TTTTT-CTTTCTCACATCTCTTTTTCTCTCATTTTCTTTT
672583 TTCTCTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 5 0.15
40 17 0.52
41 2 0.06
42 9 0.27
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.71
Consensus pattern (41 bp):
TTTTTCTTTCTCACATCTCTTTTTCTCTCATTTTCTTTTAT
Found at i:672582 original size:15 final size:15
Alignment explanation
Indices: 672544--672599 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
672534 TTCTTTTATT
* *
672544 TTTTCCTTTCTCACA
1 TTTTCTTTTCTCTCA
672559 TCTTT-TTTTCTCTCA
1 T-TTTCTTTTCTCTCA
*
672574 TTTTCTTTTTTCTC-
1 TTTTCTTTTCTCTCA
672588 TTTTCTTCTTCT
1 TTTTCTT-TTCT
672600 TTCTTCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.29
15 21 0.62
16 3 0.09
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCTTTTCTCTCA
Found at i:672589 original size:27 final size:28
Alignment explanation
Indices: 672559--672618 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
672549 CTTTCTCACA
*
672559 TCTTTTTTTCTCTCATT-TTCTTTTTTC-
1 TCTTTTCTTCT-TCATTCTTCTTTTTTCT
*
672586 TCTTTTCTTCTTCTTTCTTCTTTTTTCT
1 TCTTTTCTTCTTCATTCTTCTTTTTTCT
672614 TCTTT
1 TCTTT
672619 GGTACTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 20 0.69
28 5 0.17
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (28 bp):
TCTTTTCTTCTTCATTCTTCTTTTTTCT
Found at i:672596 original size:17 final size:16
Alignment explanation
Indices: 672562--672614 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
672552 TCTCACATCT
*
672562 TTTTTTCTCTCATTTTC
1 TTTTTTCTCT-TTTTTC
672579 TTTTTTCTCTTTTCTTC
1 TTTTTTCTCTTTT-TTC
*
672596 TTCTTTCTTCTTTTTTC
1 TTTTTTC-TCTTTTTTC
672613 TT
1 TT
672615 CTTTGGTACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.06
17 24 0.75
18 6 0.19
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:672599 original size:20 final size:20
Alignment explanation
Indices: 672576--672617 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
672566 TTCTCTCATT
*
672576 TTCTTTTTTCTCTTTTCTTC
1 TTCTTTCTTCTCTTTTCTTC
*
672596 TTCTTTCTTCTTTTTTCTTC
1 TTCTTTCTTCTCTTTTCTTC
672616 TT
1 TT
672618 TGGTACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTCTTTCTTCTCTTTTCTTC
Found at i:672617 original size:10 final size:10
Alignment explanation
Indices: 672576--672618 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
672566 TTCTCTCATT
672576 TTCTTTTTTC
1 TTCTTTTTTC
672586 -TC--TTTTC
1 TTCTTTTTTC
*
672593 TTCTTCTTTC
1 TTCTTTTTTC
672603 TTCTTTTTTC
1 TTCTTTTTTC
672613 TTCTTT
1 TTCTTT
672619 GGTACTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 5 0.18
8 2 0.07
9 2 0.07
10 19 0.68
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:676309 original size:13 final size:13
Alignment explanation
Indices: 676291--676315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
676281 TACCAGTTTT
676291 ATGTATCGATACA
1 ATGTATCGATACA
676304 ATGTATCGATAC
1 ATGTATCGATAC
676316 TTCTGGACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:677153 original size:20 final size:20
Alignment explanation
Indices: 677128--677192 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
677118 GACATATATT
677128 GATACATTCACTTTTGTATC
1 GATACATTCACTTTTGTATC
*
677148 GATACATTGA-TTTATGTATC
1 GATACATTCACTTT-TGTATC
*
677168 GATACATTCACTAATTGTATC
1 GATACATTCACT-TTTGTATC
677189 GATA
1 GATA
677193 TAAATCATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.08
20 24 0.62
21 11 0.28
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
GATACATTCACTTTTGTATC
Found at i:678412 original size:15 final size:15
Alignment explanation
Indices: 678386--678455 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
678376 TTCTTTTATT
*
678386 TTTTCCTTTCTCTCA
1 TTTTCTTTTCTCTCA
678401 TCTTT-TTTTCTCTCA
1 T-TTTCTTTTCTCTCA
*
678416 TTTTCTTTTTTCTC-
1 TTTTCTTTTCTCTCA
*
678430 TTTTCTTCTTCTTTC-
1 TTTTCTT-TTCTCTCA
*
678445 TTCTCTTTTCT
1 TTTTCTTTTCT
678456 TCTTTGGTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
14 14 0.30
15 30 0.64
16 3 0.06
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCTTTTCTCTCA
Found at i:678430 original size:17 final size:17
Alignment explanation
Indices: 678361--678456 Score: 58
Period size: 17 Copynumber: 5.7 Consensus size: 17
678351 CTCTCTTATA
*
678361 TCTCTTTTTCCTTTTTTC
1 TCTCATTTT-CTTTTTTC
* * *
678379 TTTTATTTT-TTCCTTTC
1 TCTCATTTTCTT-TTTTC
*
678396 TCTCA-TCT-TTTTTTC
1 TCTCATTTTCTTTTTTC
678411 TCTCATTTTCTTTTTTC
1 TCTCATTTTCTTTTTTC
* *
678428 TCT-TTTCTTCTTCTTTC
1 TCTCATT-TTCTTTTTTC
678445 TTCTC-TTTTCTT
1 -TCTCATTTTCTT
678457 CTTTGGTACT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
15 9 0.15
16 10 0.16
17 31 0.51
18 11 0.18
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTCATTTTCTTTTTTC
Found at i:678438 original size:10 final size:10
Alignment explanation
Indices: 678419--678458 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
678409 TCTCTCATTT
678419 TCTTTT-TTC
1 TCTTTTCTTC
678428 TCTTTTCTTC
1 TCTTTTCTTC
678438 T-TCTTTCTTC
1 TCT-TTTCTTC
678448 TCTTTTCTTC
1 TCTTTTCTTC
678458 T
1 T
678459 TTGGTACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 7 0.25
10 20 0.71
11 1 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TCTTTTCTTC
Found at i:678441 original size:20 final size:20
Alignment explanation
Indices: 678363--678459 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
678353 CTCTTATATC
* *
678363 TCTTTTTCCTTTTTTCTT-T
1 TCTTTTTTCTCTTTTCTTCT
* *
678382 TATTTTTTC-C-TTTCTCTCA
1 TCTTTTTTCTCTTTTCT-TCT
*
678401 TCTTTTTT-TC-TCTCATT-T
1 TCTTTTTTCTCTTTTC-TTCT
678419 TCTTTTTTCTCTTTTCTTCT
1 TCTTTTTTCTCTTTTCTTCT
*
678439 TCTTTCTTCTCTTTTCTTCT
1 TCTTTTTTCTCTTTTCTTCT
678459 T
1 T
678460 TGGTACTCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.08
18 9 0.15
19 23 0.37
20 25 0.40
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTTTTCTCTTTTCTTCT
Found at i:678449 original size:37 final size:36
Alignment explanation
Indices: 678379--678450 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 36
678369 TCCTTTTTTC
678379 TTTTATTTTTTCCTTTCTCTCATCTTTTTTTCTCTCA
1 TTTTATTTTTTCCTTTCTCT-ATCTTTTTTTCTCTCA
*
678416 TTTTCTTTTTTCTCTTT-TCT-TCTTCTTTCTTCTCT
1 TTTTATTTTTTC-CTTTCTCTATCTT-TTT-TTCTCT
678451 TTTCTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
35 4 0.13
36 3 0.10
37 20 0.65
38 4 0.13
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (36 bp):
TTTTATTTTTTCCTTTCTCTATCTTTTTTTCTCTCA
Found at i:678457 original size:17 final size:16
Alignment explanation
Indices: 678407--678460 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
678397 CTCATCTTTT
*
678407 TTTCTCTCATTTTCTTT
1 TTTCTCTC-TTTTCTTC
*
678424 TTTCTCTTTTCTTCTTC
1 TTTCTCTCTT-TTCTTC
678441 TTTCTTCTCTTTTCTTC
1 TTTC-TCTCTTTTCTTC
678458 TTT
1 TTT
678461 GGTACTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 25 0.78
18 5 0.16
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCTCTCTTTTCTTC
Found at i:679763 original size:46 final size:44
Alignment explanation
Indices: 679696--679785 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 44
679686 ATTTGACAAA
*
679696 TTGAATTTTTCAAACTTCTAGTTTTGGATATATATGTATTATTGGG
1 TTGAATATTTCAAACTTCTAGTTTT-GA-ATATATGTATTATTGGG
679742 TTGAATATTTCAAACTTCTAGTTTTGAATATATGTATTATTGGG
1 TTGAATATTTCAAACTTCTAGTTTTGAATATATGTATTATTGGG
679786 ATATCTTAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 17 0.40
45 2 0.05
46 24 0.56
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.49
Consensus pattern (44 bp):
TTGAATATTTCAAACTTCTAGTTTTGAATATATGTATTATTGGG
Found at i:682436 original size:15 final size:16
Alignment explanation
Indices: 682416--682463 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
682406 AGATGTGAAA
682416 AAAATA-AAATATTAC
1 AAAATATAAATATTAC
*
682431 AAAATATAGAATAATA-
1 AAAATATA-AATATTAC
682447 AAAATTATAAATATTAC
1 AAAA-TATAAATATTAC
682464 GTAAATACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 6 0.22
16 11 0.41
17 10 0.37
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (16 bp):
AAAATATAAATATTAC
Found at i:686162 original size:25 final size:24
Alignment explanation
Indices: 686121--686169 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
686111 AATACTTTAT
686121 ATTTTATTATTTAATATAAATATA
1 ATTTTATTATTTAATATAAATATA
* *
686145 ATTTTAATTATTTTATATATATATA
1 ATTTT-ATTATTTAATATAAATATA
686170 TATATGCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTATTATTTAATATAAATATA
Found at i:691115 original size:2 final size:2
Alignment explanation
Indices: 691108--691133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
691098 TTTCTTGAAA
691108 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
691134 GATAAGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:692622 original size:13 final size:13
Alignment explanation
Indices: 692604--692629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
692594 TACTGGCTAT
692604 CAACTGCAGCTTA
1 CAACTGCAGCTTA
692617 CAACTGCAGCTTA
1 CAACTGCAGCTTA
692630 GAACATTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (13 bp):
CAACTGCAGCTTA
Found at i:693167 original size:44 final size:44
Alignment explanation
Indices: 693104--693187 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
693094 AAACCAAGCA
693104 GACTACCCTTTAAAAGTATGATAAGAATGACTGTAAGAATGTAT
1 GACTACCCTTTAAAAGTATGATAAGAATGACTGTAAGAATGTAT
693148 GACTACCCTTTAAAAGTATGATAAGAATGACTGTAAGAAT
1 GACTACCCTTTAAAAGTATGATAAGAATGACTGTAAGAAT
693188 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.29
Consensus pattern (44 bp):
GACTACCCTTTAAAAGTATGATAAGAATGACTGTAAGAATGTAT
Found at i:695823 original size:2 final size:2
Alignment explanation
Indices: 695816--695853 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
695806 AAATATTCAG
695816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
695854 ATAACATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:698456 original size:79 final size:76
Alignment explanation
Indices: 698340--698792 Score: 339
Period size: 79 Copynumber: 5.8 Consensus size: 76
698330 GTTGGAATGT
* * * * *
698340 TCCCTCGAAGATAACGAGGTTGGAGTATTCCCAATGGTAGAAAATTAGTGTTTTAGAAATAAAAT
1 TCCCTTGAAAATAACG-GGTTGGAGTATCCCCGATGGT-GAAAATCAGTGTTTTAGAAATAAAAT
*
698405 CGAGGTTGGAGTG
64 CGAGGTTGGAGTA
* * *
698418 TCCTCTTGAAAATAACGGGATTAGAGTATCCTCGATGGTGAAAAATC-GATATTTTAGAAATAAA
1 TCC-CTTGAAAATAACGGG-TTGGAGTATCCCCGATGGTG-AAAATCAG-TGTTTTAGAAATAAA
* *
698482 GTC-AGAGTTGGAGTG
62 ATCGAG-GTTGGAGTA
* * * * *
698497 TCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATC-GACGTTTTAAAAATAAA
1 TCCCTTGA-AAATAA-CGGGTTGGAGTATCCCCGATGGTG-AAAATCAG-TGTTTTAGAAATAAA
* * *
698561 A-CTGGGGTTGAAATA
62 ATC-GAGGTTGGAGTA
* * *
698576 TCCCTTCGAAAATAACGAGGTTGGAGTATCCCTGATGGTGGAAAATCGGTGTTTTAGAAATAAAG
1 TCCCTT-GAAAATAACG-GGTTGGAGTATCCCCGATGGT-GAAAATCAGTGTTTTAGAAATAAAA
* *
698641 TCGGGGTTAGAGTA
63 TCGAGGTTGGAGTA
** * * **
698655 TCCCCTAAAAAATAAC-----AGAGTATCCCCGATAGTGAAAAATCAGTGTTGCAGAAATAAAAT
1 T-CCCTTGAAAATAACGGGTTGGAGTATCCCCGATGGTG-AAAATCAGTGTTTTAGAAATAAAAT
*
698715 TGAGGTTGGAGTA
64 CGAGGTTGGAGTA
* * * * *
698728 TCTCCTCGAAAATAACGGGGTTGGAGTATCGCTGATAGTGAAAAATCGGTGTTTTAGAAATAAAA
1 TC-CCTTGAAAATAAC-GGGTTGGAGTATCCCCGATGGTG-AAAATCAGTGTTTTAGAAATAAAA
698793 CATCAGTGAA
Statistics
Matches: 300, Mismatches: 52, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
72 2 0.01
73 57 0.19
78 14 0.05
79 215 0.72
80 12 0.04
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (76 bp):
TCCCTTGAAAATAACGGGTTGGAGTATCCCCGATGGTGAAAATCAGTGTTTTAGAAATAAAATCG
AGGTTGGAGTA
Found at i:698621 original size:158 final size:154
Alignment explanation
Indices: 698329--698791 Score: 451
Period size: 158 Copynumber: 3.0 Consensus size: 154
698319 AAAGAAATAA
* * * * * * * *
698329 AGTTGGAATGTTCCCTC-GAAGATAACGAGGTTGGAGTATTCCCAATGGTAGAAAATTAGTGTTT
1 AGTTGGAGTGTCCCCTCAGAA-ATAATG-GGTTGGAGTATCCCCGATGGT-GAAAAATCGAGTTT
* *
698393 TAGAAATAAAATCGAGGTTGGAGTGTCCTCTT-GAAAATAACGGGATTAGAGTAT-CCTCGATGG
63 TAGAAATAAAAT-GAGGTTGGAGTATCC-CTTCGAAAATAACGGG-TTGGAGTATCCCT-GATGG
* *
698456 TGAAAAATCGATATTTTAGAAATAAAGTCAG
124 TGAAAAATCGGTGTTTTAGAAATAAAGTCAG
698487 AGTTGGAGTGTCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATGGTGAAAAATCGACGTTTT
1 AGTTGGAGTGTCCCCTCAGAAATAAT-GGGTTGGAGTATCCCCGATGGTGAAAAATCGA-GTTTT
* * * * *
698552 AAAAATAAAACTGGGGTTGAAATATCCCTTCGAAAATAACGAGGTTGGAGTATCCCTGATGGTGG
64 AGAAATAAAA-TGAGGTTGGAGTATCCCTTCGAAAATAACG-GGTTGGAGTATCCCTGATGGTGA
*
698617 AAAATCGGTGTTTTAGAAATAAAGTCGG
127 AAAATCGGTGTTTTAGAAATAAAGTCAG
* * * **** * *
698645 GGTTAGAGTATCCCCT-A-AAA-AAT--AACAGAGTATCCCCGATAGTGAAAAATC-AGTGTTGC
1 AGTTGGAGTGTCCCCTCAGAAATAATGGGTTGGAGTATCCCCGATGGTGAAAAATCGAGT-TT-T
* *
698704 AGAAATAAAATTGAGGTTGGAGTATCTCC-TCGAAAATAACGGGGTTGGAGTATCGCTGATAGTG
64 AGAAATAAAA-TGAGGTTGGAGTATC-CCTTCGAAAATAAC-GGGTTGGAGTATCCCTGATGGTG
698768 AAAAATCGGTGTTTTAGAAATAAA
126 AAAAATCGGTGTTTTAGAAATAAA
698792 ACATCAGTGA
Statistics
Matches: 259, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
150 2 0.01
151 3 0.01
152 98 0.38
153 3 0.01
155 3 0.01
156 3 0.01
157 11 0.04
158 126 0.49
159 10 0.04
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (154 bp):
AGTTGGAGTGTCCCCTCAGAAATAATGGGTTGGAGTATCCCCGATGGTGAAAAATCGAGTTTTAG
AAATAAAATGAGGTTGGAGTATCCCTTCGAAAATAACGGGTTGGAGTATCCCTGATGGTGAAAAA
TCGGTGTTTTAGAAATAAAGTCAG
Found at i:698727 original size:73 final size:73
Alignment explanation
Indices: 698599--698743 Score: 173
Period size: 73 Copynumber: 2.0 Consensus size: 73
698589 AACGAGGTTG
* * * * ** * *
698599 GAGTATCCCTGATGGTGGAAAATCGGTGTTTTAGAAATAAAGTCGGGGTTAGAGTATCCCCTAAA
1 GAGTATCCCCGATAGTGAAAAATCAGTGTTGCAGAAATAAAATCGAGGTTAGAGTATCCCCTAAA
698664 AAATAACA
66 AAATAACA
* * * **
698672 GAGTATCCCCGATAGTGAAAAATCAGTGTTGCAGAAATAAAATTGAGGTTGGAGTATCTCCTCGA
1 GAGTATCCCCGATAGTGAAAAATCAGTGTTGCAGAAATAAAATCGAGGTTAGAGTATCCCCTAAA
698737 AAATAAC
66 AAATAAC
698744 GGGGTTGGAG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (73 bp):
GAGTATCCCCGATAGTGAAAAATCAGTGTTGCAGAAATAAAATCGAGGTTAGAGTATCCCCTAAA
AAATAACA
Found at i:698752 original size:152 final size:154
Alignment explanation
Indices: 698380--698791 Score: 449
Period size: 152 Copynumber: 2.6 Consensus size: 154
698370 CCAATGGTAG
* * * * * *
698380 AAAATTAGTGTTTTAGAAATAAAATCGAGGTTGGAGTGTCCTCTTGAAAATAACGGGATTAGAGT
1 AAAATCAGTG-TTTAGAAATAAAATTGAGGTTGGAGTATCC-CTCGAAAATAACGGGGTTGGAGT
* * * *
698445 AT-CCTCGATGGTGAAAAATCGATATTTTAGAAATAAAGTCAGAGTTGGAGTGTCCCCTCAGAAA
64 ATCCCT-GATGGTGAAAAATCGGTGTTTTAGAAATAAAGTCAGAGTTAGAGTATCCCCTCAGAAA
**** *
698509 TAATGGGGTTGGAGTATCCCCGATGGTGA
128 TAAT--GAACAGAGTATCCCCGATAGTGA
* * * * * *
698538 AAAATCGACGT-TTTAAAAATAAAACTGGGGTTGAAATATCCCTTCGAAAATAACGAGGTTGGAG
1 AAAATC-A-GTGTTTAGAAATAAAATTGAGGTTGGAGTATCCC-TCGAAAATAACGGGGTTGGAG
* * *
698602 TATCCCTGATGGTGGAAAATCGGTGTTTTAGAAATAAAGTCGGGGTTAGAGTATCCCCT-A-AAA
63 TATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAGTCAGAGTTAGAGTATCCCCTCAGAAA
698665 -AAT-AACAGAGTATCCCCGATAGTGA
128 TAATGAACAGAGTATCCCCGATAGTGA
*
698690 AAAATCAGTGTTGCAGAAATAAAATTGAGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGT
1 AAAATCAGTGTT-TAGAAATAAAATTGAGGTTGGAGTATC-CCTCGAAAATAACGGGGTTGGAGT
* *
698755 ATCGCTGATAGTGAAAAATCGGTGTTTTAGAAATAAA
64 ATCCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAA
698792 ACATCAGTGA
Statistics
Matches: 213, Mismatches: 34, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
150 2 0.01
151 3 0.01
152 99 0.46
153 2 0.01
155 3 0.01
156 3 0.01
157 2 0.01
158 93 0.44
159 4 0.02
160 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (154 bp):
AAAATCAGTGTTTAGAAATAAAATTGAGGTTGGAGTATCCCTCGAAAATAACGGGGTTGGAGTAT
CCCTGATGGTGAAAAATCGGTGTTTTAGAAATAAAGTCAGAGTTAGAGTATCCCCTCAGAAATAA
TGAACAGAGTATCCCCGATAGTGA
Found at i:699421 original size:51 final size:51
Alignment explanation
Indices: 699345--699447 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
699335 AAATAGAATG
699345 CATTTTACTGATTCCAGGGTTTTTGAACAGCTTAAATTCAAAAAATCGTAA
1 CATTTTACTGATTCCAGGGTTTTTGAACAGCTTAAATTCAAAAAATCGTAA
* *
699396 CATTTTACTGATTCTAGGGTTTTTGAACAGCTTAGATTCAAAAAATCGTAA
1 CATTTTACTGATTCCAGGGTTTTTGAACAGCTTAAATTCAAAAAATCGTAA
699447 C
1 C
699448 TCCCTCATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (51 bp):
CATTTTACTGATTCCAGGGTTTTTGAACAGCTTAAATTCAAAAAATCGTAA
Found at i:701332 original size:21 final size:21
Alignment explanation
Indices: 701306--701362 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
701296 AGGGTGGCTT
701306 TGTATCGATACATTTTAAGCA
1 TGTATCGATACATTTTAAGCA
701327 TGTATCGATACATTTTAAGCA
1 TGTATCGATACATTTTAAGCA
*
701348 TGTATCAATACATTT
1 TGTATCGATACATTT
701363 ACTGTTTGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTTAAGCA
Found at i:702804 original size:21 final size:22
Alignment explanation
Indices: 702763--702807 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
702753 AAAAAAAACA
*
702763 AAAATAATATACTAAATAAATG
1 AAAATAAAATACTAAATAAATG
702785 AAAATAAAAT-CTAAGA-AAATG
1 AAAATAAAATACTAA-ATAAATG
702806 AA
1 AA
702808 GGAAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (22 bp):
AAAATAAAATACTAAATAAATG
Found at i:703263 original size:35 final size:34
Alignment explanation
Indices: 703219--703347 Score: 134
Period size: 35 Copynumber: 3.6 Consensus size: 34
703209 AACATATGTA
*
703219 TATAATAAATAATTTAAAATTAATAAAATTATATT
1 TATATTAAATAA-TTAAAATTAATAAAATTATATT
*
703254 TAAATTAAATAA-TAAAATATAAATAAAATTATATT
1 TATATTAAATAATTAAAAT-T-AATAAAATTATATT
* *
703289 TATGTTGAATACTAATTAAAATTTTATTAAAATTATATT
1 TATATT-AA-A-TAATTAAAA--TTAATAAAATTATATT
*
703328 TATATTAAAAAATTAAAATT
1 TATATTAAATAATTAAAATT
703348 TTATCTACAT
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
33 6 0.08
34 3 0.04
35 28 0.35
36 10 0.13
37 2 0.03
38 5 0.06
39 23 0.29
40 1 0.01
41 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.43
Consensus pattern (34 bp):
TATATTAAATAATTAAAATTAATAAAATTATATT
Found at i:703273 original size:21 final size:21
Alignment explanation
Indices: 703220--703273 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
703210 ACATATGTAT
703220 ATAAT-AAATAATTTAAAATTA
1 ATAATAAAAT-ATTTAAAATTA
*
703241 ATAA-AATTATATTT-AAATTAA
1 ATAATAA-AATATTTAAAATT-A
703262 ATAATAAAATAT
1 ATAATAAAATAT
703274 AAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 18 0.67
22 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATAAAATATTTAAAATTA
Found at i:703320 original size:39 final size:36
Alignment explanation
Indices: 703242--703351 Score: 123
Period size: 39 Copynumber: 3.0 Consensus size: 36
703232 TTAAAATTAA
* * * * *
703242 TAAAATTATATTTAAATTAAATAA-TAAAATATAAA
1 TAAAATTATATTTATATTAAAAAATTAAAATTTTAT
* *
703277 TAAAATTATATTTATGTTGAATACTAATTAAAATTTTAT
1 TAAAATTATATTTATATT-AA-A-AAATTAAAATTTTAT
703316 TAAAATTATATTTATATTAAAAAATTAAAATTTTAT
1 TAAAATTATATTTATATTAAAAAATTAAAATTTTAT
703352 CTACATTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 16 0.25
36 16 0.25
37 2 0.03
38 5 0.08
39 25 0.39
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.45
Consensus pattern (36 bp):
TAAAATTATATTTATATTAAAAAATTAAAATTTTAT
Found at i:703345 original size:25 final size:25
Alignment explanation
Indices: 703314--703363 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
703304 TTAAAATTTT
* *
703314 ATTAAAATTATATTTATATTAAAAA
1 ATTAAAATTATATCTACATTAAAAA
*
703339 ATTAAAATTTTATCTACATTAAAAA
1 ATTAAAATTATATCTACATTAAAAA
703364 TAAAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAAAATTATATCTACATTAAAAA
Found at i:703407 original size:20 final size:19
Alignment explanation
Indices: 703379--703418 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
703369 TAATAAAATT
**
703379 AATATAAAAATTTAAAAAA
1 AATATAAAAAAGTAAAAAA
703398 AATATGAAAAAAGTAAAAAA
1 AATAT-AAAAAAGTAAAAAA
703418 A
1 A
703419 GGATTACCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AATATAAAAAAGTAAAAAA
Found at i:704724 original size:20 final size:20
Alignment explanation
Indices: 704682--704734 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
704672 ATCCATAAAA
* *
704682 TGTATCGATACAT-GTTCAT
1 TGTATCGATACATGGATAAT
704701 TGTATCGATACATGGATAAT
1 TGTATCGATACATGGATAAT
704721 TGTATCGATACATG
1 TGTATCGATACATG
704735 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGGATAAT
Found at i:710329 original size:78 final size:78
Alignment explanation
Indices: 710228--710418 Score: 224
Period size: 79 Copynumber: 2.4 Consensus size: 78
710218 TTGGATTGTT
* * * * * *
710228 CCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGAAAAAAAATT
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGAAAAAAAATC
710292 G-GGATTGGAGTATC
65 GAGG-TTGGAGTATC
* * * * *
710306 CCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGTC
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAGAAAAAAAATC
710371 GAGGTTGGAGTATC
65 GAGGTTGGAGTATC
* *
710385 CCTTCGGAAATAACGGGGTTGGAGTATCCCCGAT
1 CCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
710419 GATTAACGGG
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
77 1 0.01
78 42 0.44
79 51 0.53
80 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (78 bp):
CCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAATCG
AGGTTGGAGTATC
Found at i:710405 original size:28 final size:26
Alignment explanation
Indices: 710373--710444 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
710363 ATAAAGTCGA
710373 GGTTGGAGTATCCCTTCG-GAAATAACGG
1 GGTTGGAGTATCCC--CGAG-AATAACGG
*
710401 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGA-GAATAACGG
710428 GGTTGGAGTATCCCCGA
1 GGTTGGAGTATCCCCGA
710445 TTGTGAAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 2 0.05
27 24 0.59
28 15 0.37
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (26 bp):
GGTTGGAGTATCCCCGAGAATAACGG
Found at i:710542 original size:52 final size:53
Alignment explanation
Indices: 710425--710825 Score: 240
Period size: 52 Copynumber: 7.6 Consensus size: 53
710415 CGATGATTAA
* *
710425 CGGGGTTGGAGTATCCCCGATTGTGAAG-AAATTGGTGTTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTG--TTTTGAAAATAAAAT
* * *
710479 CGGAGTTGGAGTATCCCCGA-T-TAAAGGAAAATTGGTGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAA-GAAAATTAGTGTTTTGAAAATAAAAT
* * *
710531 CGGGGTTGGAGTATCCCCGATTGTGAA-AAAATTAGCGTTTT-AGCAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTGTTTTGA-AAATAAAAT
* * * * * *
710583 CGGGGTTGGAGTATCCCCGATTATG-A-AAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTGTTTTGAAAATAAAAT
* * * * * * * *
710634 CGGGGTTGGAGTATCCTC--TCG-GAA-ATAA-T-GGGGTTGGAGTATCCCCTATGATTAA-
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTGTTTTGA--A-----AAT-A-AAAT
* * * *
710689 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAAT--TA-GTGTTTTGAAAATAAAAT
* * * *
710745 CGGAGTTGGAGTATCCCCAATTAT--AGAAAATTAGTGTTTTAAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTGTTTTGAAAATAAAAT
* * * *
710796 CGGAGTTGGAATATCCCTGATTGTGGAGAA
1 CGGGGTTGGAGTATCCCCGATTGTGAAGAA
710826 TTGAGAAACT
Statistics
Matches: 263, Mismatches: 56, Indels: 57
0.70 0.15 0.15
Matches are distributed among these distances:
47 3 0.01
48 1 0.00
49 6 0.02
51 69 0.26
52 81 0.31
53 7 0.03
54 39 0.15
55 20 0.08
56 23 0.09
57 4 0.02
58 3 0.01
59 2 0.01
62 2 0.01
64 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (53 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAGAAAATTAGTGTTTTGAAAATAAAAT
Found at i:710634 original size:264 final size:264
Alignment explanation
Indices: 710319--710820 Score: 837
Period size: 264 Copynumber: 1.9 Consensus size: 264
710309 TCGAAAATAA
* *
710319 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGTCGAGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGTCGAGGTTGGAGTAT
710384 CC-CTTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTG
66 CCTC-TCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTG
*
710448 TGAAGAAATTGG-TGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATT
130 TGAAGAAATTGGATGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTAAA-GAAAATT
* * * *
710512 GGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGAAAAAATTAGCGTTTTAGCAA
194 AGTGTTTTAAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGAAAAAATTAGCGTTTTAGCAA
710577 TAAAAC
259 TAAAAC
* *
710583 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGTCGAGGTTGGAGTAT
* *
710648 CCTCTCGGAAATAATGGGGTTGGAGTATCCCCTATGATTAACGGGGTTGGAGTATCCCCGATTGT
66 CCTCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
* *
710713 GAAGAAATTGGTATTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTATAGAAAATTA
131 GAAGAAATTGG-ATGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAGAAAATTA
*
710778 GTGTTTTAAAAATAAAATCGGAGTTGGAATATCCCTGATTGTG
195 GTGTTTTAAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
710821 GAGAATTGAG
Statistics
Matches: 221, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
264 133 0.60
265 47 0.21
266 41 0.19
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (264 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGTCGAGGTTGGAGTAT
CCTCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
GAAGAAATTGGATGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCAATTAAAGAAAATTAG
TGTTTTAAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGAAAAAATTAGCGTTTTAGCAATA
AAAC
Found at i:710638 original size:51 final size:51
Alignment explanation
Indices: 710425--710649 Score: 261
Period size: 52 Copynumber: 4.3 Consensus size: 51
710415 CGATGATTAA
* *
710425 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAA-AAATTAGTG--TTTTGGAAATAAAAT
* * * * *
710479 CGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAAT
* * * * *
710531 CGGGGTTGGAGTATCCCCGATTGTGAAAAAATTAGCGTTTTAGCAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATG-AAAAATTAGTGTTTTGGAAATAAAAT
* * * *
710583 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAAT
710634 CGGGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
710650 TCTCGGAAAT
Statistics
Matches: 145, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
51 35 0.24
52 78 0.54
54 30 0.21
55 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAAT
Found at i:710701 original size:27 final size:28
Alignment explanation
Indices: 710634--710706 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
710624 GAAATAAAGT
* *
710634 CGGGGTTGGAGTATCCTCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTAGGAAATAA
* * *
710662 TGGGGTTGGAGTATCCCCTATG-ATTAA
1 CGGGGTTGGAGTATCCCCTAGGAAATAA
710689 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
710707 GATTGTGAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.27
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTAGGAAATAA
Found at i:713199 original size:13 final size:13
Alignment explanation
Indices: 713181--713206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
713171 ACAAAGATCC
713181 ATGTATCGATACA
1 ATGTATCGATACA
713194 ATGTATCGATACA
1 ATGTATCGATACA
713207 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:713202 original size:33 final size:33
Alignment explanation
Indices: 713160--713226 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
713150 AAAATTTCCA
***
713160 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
713193 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
713226 A
1 A
713227 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:713270 original size:19 final size:18
Alignment explanation
Indices: 713246--713313 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
713236 CAGTAGCTAA
713246 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
713265 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
713280 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
713297 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
713314 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:713286 original size:13 final size:13
Alignment explanation
Indices: 713268--713292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
713258 ACAATACTTA
713268 TGTATCGATACAT
1 TGTATCGATACAT
713281 TGTATCGATACA
1 TGTATCGATACA
713293 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:713290 original size:32 final size:32
Alignment explanation
Indices: 713249--713311 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
713239 TAGCTAATTA
*
713249 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
713281 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
713312 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:713375 original size:21 final size:20
Alignment explanation
Indices: 713349--713425 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 20
713339 GTTGGGACCC
* *
713349 TGTATCGATACATTTGTAGAA
1 TGTATCGATACA-TTCTAAAA
*
713370 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTA-AAA
*
713391 TGTATCGATACATTCTACAGA
1 TGTATCGATACATTCTA-AAA
713412 TGTATCGATACATT
1 TGTATCGATACATT
713426 TGGATAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 47 0.94
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTCTAAAA
Found at i:715803 original size:23 final size:22
Alignment explanation
Indices: 715760--715812 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
715750 TATAATTGAA
* *
715760 TAATAAATAGGTTGTAGATGAT
1 TAATAAATAAGTTGTAAATGAT
*
715782 CTAATAAATAAGTTTTAAATGAT
1 -TAATAAATAAGTTGTAAATGAT
*
715805 TCATAAAT
1 TAATAAAT
715813 GGATTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (22 bp):
TAATAAATAAGTTGTAAATGAT
Found at i:717094 original size:3 final size:3
Alignment explanation
Indices: 717088--717116 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
717078 TTTTATTATT
717088 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
717117 TGGTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:718117 original size:36 final size:37
Alignment explanation
Indices: 718052--718121 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 37
718042 AATAGGATCA
* * * *
718052 TCATTTTTATTTTGTTTTTTATTTTACAATCATTATG
1 TCATTTCTATTTTCTTTTGTATTTGACAATCATTATG
718089 TCATTTCT-TTTTCTTTTGTATTTGACAATCATT
1 TCATTTCTATTTTCTTTTGTATTTGACAATCATT
718122 TTGAATTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 22 0.76
37 7 0.24
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (37 bp):
TCATTTCTATTTTCTTTTGTATTTGACAATCATTATG
Found at i:720324 original size:2 final size:2
Alignment explanation
Indices: 720317--720351 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
720307 TTAAATTTAC
720317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
720352 CACGTATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:724195 original size:24 final size:27
Alignment explanation
Indices: 724167--724217 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
724157 TCAAAAATTT
724167 TATTTATC-G-GG-GATACTCCAACTC
1 TATTTATCTGAGGAGATACTCCAACTC
*
724191 TATTTTTCTGAGGAGATACTCCAACTC
1 TATTTATCTGAGGAGATACTCCAACTC
724218 CGCTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 1 0.04
26 2 0.09
27 13 0.57
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (27 bp):
TATTTATCTGAGGAGATACTCCAACTC
Found at i:727472 original size:15 final size:15
Alignment explanation
Indices: 727452--727511 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
727442 GTTAGTCTTG
727452 AGTTCAAGTTCTTTT
1 AGTTCAAGTTCTTTT
*
727467 AGTTCATGTT-TTTT
1 AGTTCAAGTTCTTTT
* * *
727481 CAAGTTTAAGTTATTTG
1 --AGTTCAAGTTCTTTT
*
727498 AGTTCGAGTTCTTT
1 AGTTCAAGTTCTTT
727512 CAGGGTTTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 4 0.11
15 20 0.57
16 8 0.23
17 3 0.09
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.53
Consensus pattern (15 bp):
AGTTCAAGTTCTTTT
Found at i:727513 original size:31 final size:31
Alignment explanation
Indices: 727452--727513 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
727442 GTTAGTCTTG
* * *
727452 AGTTCAAGTTCTTTTAGTTCATGTTTTTTCA
1 AGTTCAAGTTATTTGAGTTCATGTTCTTTCA
*
727483 AGTTTAAGTTATTTGAGTTCGA-GTTCTTTCA
1 AGTTCAAGTTATTTGAGTTC-ATGTTCTTTCA
727514 GGGTTTAGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (31 bp):
AGTTCAAGTTATTTGAGTTCATGTTCTTTCA
Found at i:727898 original size:109 final size:110
Alignment explanation
Indices: 727684--727908 Score: 264
Period size: 108 Copynumber: 2.1 Consensus size: 110
727674 TTATATTTTG
* *
727684 TTATATCTATATCTATACTATTATAAAATTATTAATTGAATTTAGTATCGAGTCAAGTAATACTA
1 TTATATCTATATCTATACTATTATAAAATTATTAATTGAATTTAGTATCGAATCAAATAATACTA
* **
727749 ATTTAATTAAGAAAATTTTATAAAACTAAAATATAAAAT-AAAAA
66 ATATAATTAAGAAAATTACATAAAACTAAAATATAAAATAAAAAA
* * * *
727793 TTATAT-T-TATC-ATACTATTATAAAATTTTTTATTGAGTTTAATGTCAT-GAATCAAATGATA
1 TTATATCTATATCTATACTATTATAAAATTATTAATTGAATTT-A-GT-ATCGAATCAAATAATA
* *
727854 CTAATATAGTATAA-AAAATTACATAAAAATTAAAATATAAAATAAAAAA
63 CTAATATAAT-TAAGAAAATTACAT-AAAACTAAAATATAAAATAAAAAA
727903 TTATAT
1 TTATAT
727909 ATTAATAAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
106 26 0.26
107 5 0.05
108 29 0.29
109 28 0.28
110 11 0.11
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (110 bp):
TTATATCTATATCTATACTATTATAAAATTATTAATTGAATTTAGTATCGAATCAAATAATACTA
ATATAATTAAGAAAATTACATAAAACTAAAATATAAAATAAAAAA
Found at i:727915 original size:18 final size:18
Alignment explanation
Indices: 727894--727928 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
727884 TAAAATATAA
727894 AATAAAAA-ATTATATATT
1 AATAAAAATATT-TATATT
727912 AATAAAAATATTTATAT
1 AATAAAAATATTTATAT
727929 CTTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAAAATATTTATATT
Found at i:727920 original size:31 final size:31
Alignment explanation
Indices: 727864--727922 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
727854 CTAATATAGT
*
727864 ATAAAAAATTACATAAAAATTAAAATATAAA
1 ATAAAAAATTACATAAAAATAAAAATATAAA
* **
727895 ATAAAAAATTATATATTAATAAAAATAT
1 ATAAAAAATTACATAAAAATAAAAATAT
727923 TTATATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (31 bp):
ATAAAAAATTACATAAAAATAAAAATATAAA
Found at i:728382 original size:22 final size:23
Alignment explanation
Indices: 728357--728419 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
728347 TGGTCGTGAC
728357 AAAAAAGGAAAAAAAA-AATGAA
1 AAAAAAGGAAAAAAAAGAATGAA
*
728379 AAAAGAGGAAAAAAAAAGAATGAA
1 AAAAAAGG-AAAAAAAAGAATGAA
*
728403 ACGAAAAAGGTAAAAAA
1 A--AAAAAGGAAAAAAA
728420 GATGCAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 7 0.21
23 8 0.24
24 7 0.21
25 6 0.18
26 6 0.18
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (23 bp):
AAAAAAGGAAAAAAAAGAATGAA
Found at i:729623 original size:17 final size:20
Alignment explanation
Indices: 729587--729623 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
729577 CCCCCCCCCT
729587 TTTTTTCTTTCAATTAAAGA
1 TTTTTTCTTTCAATTAAAGA
729607 TTTTTT-TTT-AA-TAAAGA
1 TTTTTTCTTTCAATTAAAGA
729624 GTTAGGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 3 0.18
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTTCTTTCAATTAAAGA
Found at i:733258 original size:3 final size:3
Alignment explanation
Indices: 733250--733287 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
733240 AGGTTAGTTG
*
733250 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
733288 TATTTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:734428 original size:16 final size:15
Alignment explanation
Indices: 734407--734457 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
734397 CTGTTCCAGA
*
734407 TGTTATTTTATAGTTT
1 TGTTATATT-TAGTTT
734423 TGTTATATTTAGTTTT
1 TGTTATATTTAG-TTT
* *
734439 TTTTATAATTAGTTT
1 TGTTATATTTAGTTT
734454 TGTT
1 TGTT
734458 CGTTCCACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.69
Consensus pattern (15 bp):
TGTTATATTTAGTTT
Found at i:738598 original size:17 final size:18
Alignment explanation
Indices: 738576--738609 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
738566 GTTTTAAAAA
738576 AAATAT-TAACTCAAATT
1 AAATATATAACTCAAATT
*
738593 AAATATATAACTTAAAT
1 AAATATATAACTCAAAT
738610 AAGTAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATATAACTCAAATT
Found at i:742485 original size:17 final size:17
Alignment explanation
Indices: 742463--742509 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
742453 TTTTTTGTTT
*
742463 TATTTATTTAAGATATA
1 TATTTATTTAAGATAAA
742480 TATTTAATTTAAG-TAAA
1 TATTT-ATTTAAGATAAA
742497 TATTTATTTAAGA
1 TATTTATTTAAGA
742510 CAAGAATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 7 0.26
17 13 0.48
18 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TATTTATTTAAGATAAA
Found at i:742955 original size:34 final size:35
Alignment explanation
Indices: 742917--742983 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
742907 CCTTACAACA
742917 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
742951 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
742984 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:743460 original size:13 final size:13
Alignment explanation
Indices: 743442--743467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
743432 CAATTTTTTG
743442 TGTATCGATACAT
1 TGTATCGATACAT
743455 TGTATCGATACAT
1 TGTATCGATACAT
743468 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:743553 original size:20 final size:20
Alignment explanation
Indices: 743528--743600 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
743518 ATCTTTTTTT
743528 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
743548 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
743569 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
743589 ATGTATCGATAC
1 ATGTATCGATAC
743601 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:743579 original size:41 final size:42
Alignment explanation
Indices: 743506--743600 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
743496 CTGCCAAGAA
*
743506 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
743548 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
743589 ATGTATCGATAC
1 ATGTATCGATAC
743601 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:744174 original size:15 final size:15
Alignment explanation
Indices: 744154--744183 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
744144 TAAATTTTAC
744154 GAATTTGTACATTCT
1 GAATTTGTACATTCT
744169 GAATTTGTACATTCT
1 GAATTTGTACATTCT
744184 CCCCCTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GAATTTGTACATTCT
Done.