Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 129 of 279
Found at i:41233264 original size:14 final size:14
Alignment explanation
Indices: 41233245--41233287 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
41233235 CTACAATTTA
*
41233245 ACTATTATGTTGTT
1 ACTATTTTGTTGTT
*
41233259 ACTATTTTCTTGTT
1 ACTATTTTGTTGTT
*
41233273 ATTATTTTGTTGTT
1 ACTATTTTGTTGTT
41233287 A
1 A
41233288 ATCTTGTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.19, C:0.07, G:0.12, T:0.63
Consensus pattern (14 bp):
ACTATTTTGTTGTT
Found at i:41236825 original size:29 final size:30
Alignment explanation
Indices: 41236753--41236825 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
41236743 CTTTTAAAAC
*
41236753 TTTTAAAAATTTTAATTAGATCTCTCAGTT
1 TTTTAAAAATTTTAATTAGATCTCTCAGTA
*
41236783 TTTTAAAAATTTTAATTAGA-CTCTTA-TA
1 TTTTAAAAATTTTAATTAGATCTCTCAGTA
*
41236811 TTTTGAAAATCTTTA
1 TTTTAAAAAT-TTTA
41236826 TTAAACCCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.26
29 9 0.23
30 20 0.51
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (30 bp):
TTTTAAAAATTTTAATTAGATCTCTCAGTA
Found at i:41236847 original size:30 final size:29
Alignment explanation
Indices: 41236811--41236868 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
41236801 GACTCTTATA
41236811 TTTTGAAAATCTTTA-TTAAACCCCTAAAAG
1 TTTTGAAAAT-TTTAGTTAAACCCC-AAAAG
*
41236841 TTTTGAAAATTTTAGTTAATCCCCAAAA
1 TTTTGAAAATTTTAGTTAAACCCCAAAA
41236869 TTAGTGGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTTGAAAATTTTAGTTAAACCCCAAAAG
Found at i:41236996 original size:23 final size:23
Alignment explanation
Indices: 41236966--41237012 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41236956 ATATATCATA
41236966 AACTTCAATTAATGTAGAAAACT
1 AACTTCAATTAATGTAGAAAACT
41236989 AACTTCAATTAATGTAGAAAACT
1 AACTTCAATTAATGTAGAAAACT
41237012 A
1 A
41237013 CTTTTAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
AACTTCAATTAATGTAGAAAACT
Found at i:41237019 original size:19 final size:21
Alignment explanation
Indices: 41236973--41237019 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
41236963 ATAAACTTCA
41236973 ATTAATGTAGAAAACTAACTT
1 ATTAATGTAGAAAACTAACTT
41236994 CAATTAATGTAGAAAACT-ACTT
1 --ATTAATGTAGAAAACTAACTT
41237016 -TTAA
1 ATTAA
41237020 CTTTATATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
22 4 0.17
23 16 0.67
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
ATTAATGTAGAAAACTAACTT
Found at i:41238683 original size:42 final size:42
Alignment explanation
Indices: 41238620--41238782 Score: 202
Period size: 42 Copynumber: 3.7 Consensus size: 42
41238610 CTTCGTTTAC
** *
41238620 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
41238663 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
41238704 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
41238753 TCGATGCCATAGCCCAGCTATGGTCTTACA
1 TCGATGCCATAGCCCAGCTATGGTCTTACA
41238783 TGAATCACAT
Statistics
Matches: 105, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
41 2 0.02
42 63 0.60
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.34
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:41238763 original size:49 final size:47
Alignment explanation
Indices: 41238703--41238869 Score: 180
Period size: 47 Copynumber: 3.5 Consensus size: 47
41238693 ATATTCATAT
*
41238703 ATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 ATCGATGCCATAGCCCAGATATGGTCTTACA-GTAATCACATATCACA
* *
41238751 TATCGATGCCATAGCCCAGCTATGGTCTTACA-TGAATCACATATCTCA
1 -ATCGATGCCATAGCCCAGATATGGTCTTACAGT-AATCACATATCACA
* * * *
41238799 CT-GATGCCATATCCCAGATATGGTCCTATACAGT-AGCATATATCAC-
1 ATCGATGCCATAGCCCAGATATGGT-CT-TACAGTAATCACATATCACA
* *
41238845 ACCGATGCCATATCCCAGATATGGT
1 ATCGATGCCATAGCCCAGATATGGT
41238870 ATTATACGGA
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
46 20 0.19
47 35 0.34
48 17 0.16
49 32 0.31
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (47 bp):
ATCGATGCCATAGCCCAGATATGGTCTTACAGTAATCACATATCACA
Found at i:41238894 original size:7 final size:7
Alignment explanation
Indices: 41238882--41238910 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
41238872 TATACGGAAA
41238882 TCACTTG
1 TCACTTG
41238889 TCACTTG
1 TCACTTG
41238896 TCACTTG
1 TCACTTG
41238903 TCACTTG
1 TCACTTG
41238910 T
1 T
41238911 AGCCGAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:41238944 original size:31 final size:31
Alignment explanation
Indices: 41238909--41239088 Score: 306
Period size: 31 Copynumber: 5.8 Consensus size: 31
41238899 CTTGTCACTT
*
41238909 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
41238940 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
41238971 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
41239002 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
41239033 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
41239064 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
41239089 TGTCATTTGT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 142 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:41243087 original size:42 final size:42
Alignment explanation
Indices: 41243040--41243124 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
41243030 ATAAAACTAT
41243040 AACACCCCTTACCCGAGCAAAGGATGCCACATTTTCGAGTCA
1 AACACCCCTTACCCGAGCAAAGGATGCCACATTTTCGAGTCA
41243082 AACACCCCTTACCCGAGCAAAGGATGCCACATTTTCGAGTCA
1 AACACCCCTTACCCGAGCAAAGGATGCCACATTTTCGAGTCA
41243124 A
1 A
41243125 TCACTTCACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (42 bp):
AACACCCCTTACCCGAGCAAAGGATGCCACATTTTCGAGTCA
Found at i:41243120 original size:22 final size:22
Alignment explanation
Indices: 41243053--41243120 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
41243043 ACCCCTTACC
41243053 CGAGCAAAGGATGCCACATTTT
1 CGAGCAAAGGATGCCACATTTT
* * **
41243075 CGAGTCAAA-CA--CC-CCTTACC
1 CGAG-CAAAGGATGCCACATT-TT
41243095 CGAGCAAAGGATGCCACATTTT
1 CGAGCAAAGGATGCCACATTTT
41243117 CGAG
1 CGAG
41243121 TCAATCACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 7 0.22
20 7 0.22
22 11 0.34
23 7 0.22
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (22 bp):
CGAGCAAAGGATGCCACATTTT
Found at i:41244891 original size:168 final size:168
Alignment explanation
Indices: 41244651--41244981 Score: 511
Period size: 168 Copynumber: 2.0 Consensus size: 168
41244641 CCCTCGCAGA
* * * * *
41244651 TTGTTTTTGGGTCATTTTCTGACATGCCAGCTGACGTATTCTATGATTCAACATTCGACGAAGCA
1 TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
* * * * *
41244716 CCACCTTCCAAGGTGGCCCGTGTCTCACCTCGTCCACCTGCACCTTCAGCCCCGGCAGGGGC-TT
66 ACACCTTCCAAGGTGGCCCATGTCTCACCTCCTCCACCTGCACCTCCAGCACCGGCAGGGGCATT
41244780 CTGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGT
131 -TGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGT
* * * *
41244819 TTGTTTTTGGGTCGTTTGGTGACATGTCAGGTCACGTATTCTATCATTCAACATTCAACCAAGCA
1 TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
*
41244884 ACACCTTCCAAGGTGGCCCATGTCTCACCTCCTCCACTTGCACCTCCAGCACCGGCAGGGGCATT
66 ACACCTTCCAAGGTGGCCCATGTCTCACCTCCTCCACCTGCACCTCCAGCACCGGCAGGGGCATT
41244949 TGAAAATGTGGCCAAAGATGATGAGAAACCAAA
131 TGAAAATGTGGCCAAAGATGATGAGAAACCAAA
41244982 AAATGCTAAA
Statistics
Matches: 147, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
168 145 0.99
169 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (168 bp):
TTGTTTTTGGGTCATTTGCTGACATGCCAGCTCACGTATTCTATCATTCAACATTCAACCAAGCA
ACACCTTCCAAGGTGGCCCATGTCTCACCTCCTCCACCTGCACCTCCAGCACCGGCAGGGGCATT
TGAAAATGTGGCCAAAGATGATGAGAAACCAAACAAGT
Found at i:41245720 original size:27 final size:28
Alignment explanation
Indices: 41245652--41245720 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
41245642 TGATAAAATA
*
41245652 ATTTCAATTTTATAAATACAAAAATTGT
1 ATTTCAATTTTAAAAATACAAAAATTGT
* * *
41245680 ATATCAATAGTTAAATAATA-AAATATT-T
1 ATTTCAAT-TTTAAA-AATACAAAAATTGT
41245708 ATTTCAATTTTAA
1 ATTTCAATTTTAA
41245721 TCAGTGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 4 0.12
28 15 0.45
29 10 0.30
30 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTTCAATTTTAAAAATACAAAAATTGT
Found at i:41253603 original size:3 final size:3
Alignment explanation
Indices: 41253595--41253652 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
41253585 ATTCAGTCAT
41253595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41253643 TAA TAA TAA T
1 TAA TAA TAA T
41253653 CTAAAAGTCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41257655 original size:106 final size:103
Alignment explanation
Indices: 41257513--41257802 Score: 341
Period size: 106 Copynumber: 2.7 Consensus size: 103
41257503 ATAAAAACCA
* * * *
41257513 GACTGGATCTTCCTTTTTTTGTTGATTTTTTTAAGTTTAAAATTAATAGTTTATCCTTGAATTTA
1 GACTGGATCTTCTTTTTTTTGTTGA--TTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATTTA
*
41257578 ATCGTATTTTTAAATATATTTGTGGAATTTCTAAGAAATAC-
64 ATCGTATTTCT-AATATATTTGTGGAATTTCTAAGAAAT-CG
* * * *
41257619 GACTGGATCGTCTTTTCTTTTGTTGATCTTTCAAGTTTTGAATTAATAGTTTATTCTTGAATTAA
1 GACTGGATCTTCTTTT-TTTTGTTGAT-TTTAAAGTTTTAAATTAATAGTTTATTCTTGAATT-T
* * * *
41257684 AAT-GTATTTCTAATATTTTTGTGTAATTTCTTAGCAATCG
63 AATCGTATTTCTAATATATTTGTGGAATTTCTAAGAAATCG
*
41257724 GACTGGATCCTTACTTTTTTCTGTTGTGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATT
1 GACTGGAT-CTT-CTTTTTTTTG-T-TGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATT
41257789 TAATCGTATTTCTA
62 TAATCGTATTTCTA
41257803 GTATTTTTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
104 1 0.01
105 32 0.20
106 61 0.39
107 60 0.38
108 4 0.03
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.51
Consensus pattern (103 bp):
GACTGGATCTTCTTTTTTTTGTTGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATTTAAT
CGTATTTCTAATATATTTGTGGAATTTCTAAGAAATCG
Found at i:41257780 original size:107 final size:106
Alignment explanation
Indices: 41257513--41257810 Score: 340
Period size: 107 Copynumber: 2.8 Consensus size: 106
41257503 ATAAAAACCA
* * * *
41257513 GACTGGATCTTCCTTTTTT-TGTTGAT-TTTTTTAAGTTTAAAATTAATAGTTTATCCTTGAATT
1 GACTGGATCTT-CTTTTTTCTGTTGATGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATT
* *
41257576 TAATCGTATTTTTAAATATATTTGTGGAATTTCTAAGAAATAC
65 TAATCGTATTTCT-AATATTTTTGTGGAATTTCTAAGAAATAC
* * * * *
41257619 GACTGGATCGTCTTTTCTTTTGTTGAT--CTTTCAAGTTTTGAATTAATAGTTTATTCTTGAATT
1 GACTGGATCTTCTTTT-TTCTGTTGATGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATT
* * * *
41257682 AAAAT-GTATTTCTAATATTTTTGTGTAATTTCTTAGCAAT-C
65 -TAATCGTATTTCTAATATTTTTGTGGAATTTCTAAGAAATAC
41257723 GGACTGGATCCTTACTTTTTTCTGTTG-TGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAA
1 -GACTGGAT-CTT-CTTTTTTCTGTTGATGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAA
*
41257787 TTTAATCGTATTTCTAGTATTTTT
63 TTTAATCGTATTTCTAATATTTTT
41257811 TTAGCAATCA
Statistics
Matches: 164, Mismatches: 19, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
104 1 0.01
105 37 0.23
106 62 0.38
107 64 0.39
ACGTcount: A:0.26, C:0.09, G:0.13, T:0.51
Consensus pattern (106 bp):
GACTGGATCTTCTTTTTTCTGTTGATGATTTTAAAGTTTTAAATTAATAGTTTATTCTTGAATTT
AATCGTATTTCTAATATTTTTGTGGAATTTCTAAGAAATAC
Found at i:41261191 original size:106 final size:105
Alignment explanation
Indices: 41261081--41261281 Score: 251
Period size: 106 Copynumber: 1.9 Consensus size: 105
41261071 TCAGCTGCCT
* * * **
41261081 TTTTTTTTTAAAAAAAAGTTTAAAATTAATAGTTTATCCTTGAA-TTAGATTGTATTTCTGATAT
1 TTTTTGTTGAAAAAAAAGTTTAAAATTAATAGTTTAACCTTGAATTTA-ATCCTATTTCTGAT-T
*
41261145 TTTTGTGTAATTTCTTAGCAATCCGACTGGATCGTCTTTTTC
64 TTTAGTGTAATTTCTTAGCAATCCGACTGGATCGTCTTTTTC
***** * *
41261187 TTTTTGTTGATTTTTAAGTTTTAAATTAATAGTTTAAGCTTGAATTTAATCCTATTTCTGATTTT
1 TTTTTGTTGAAAAAAAAGTTTAAAATTAATAGTTTAACCTTGAATTTAATCCTATTTCTGATTTT
*
41261252 TAGTGTAATTTCTTAGCAATCCGATTGGAT
66 TAGTGTAATTTCTTAGCAATCCGACTGGAT
41261282 ATTTTTTTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
105 31 0.39
106 46 0.57
107 3 0.04
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.50
Consensus pattern (105 bp):
TTTTTGTTGAAAAAAAAGTTTAAAATTAATAGTTTAACCTTGAATTTAATCCTATTTCTGATTTT
TAGTGTAATTTCTTAGCAATCCGACTGGATCGTCTTTTTC
Found at i:41261675 original size:109 final size:108
Alignment explanation
Indices: 41261370--41261689 Score: 403
Period size: 108 Copynumber: 3.0 Consensus size: 108
41261360 CTTACTTTTA
* ** * * * *
41261370 AGTTTAAAATTAATAGTTTATCCTTTAATTGAATCGTAGT-TCTGGTATTTTTGTCTAATTTCTT
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCATA-TCTCTGGTATTTTTGTGTAAATTCTT
41261434 AGCAATTCGACTGGATCGTCTCTTTTCTTGTTGA-TTTTTTTGT
65 AGCAATTCGACTGGATCGTCTCTTTTCTTGTTGATTTTTTTTGT
* * *
41261477 CGTTTTAAATTAATAGTGTATCCTAGAATTAAATCATATATCTCTGGT-TTTTTGTGTAACTTCT
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATC--ATATCTCTGGTATTTTTGTGTAAATTCT
* * *
41261541 TAGCAATTCGACCGGATCGGCTCTTTTCCTGTTGATTTTTTTTGT
64 TAGCAATTCGACTGGATCGTCTCTTTTCTTGTTGATTTTTTTTGT
*
41261586 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCATATCTCTGGTATCTTTGTGTAAATTCTTA
1 AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCATATCTCTGGTATTTTTGTGTAAATTCTTA
* * * * * *
41261651 GTAATCCAACTAGATCCTCTTCTTTTTTTGTTGATTTTT
66 GCAATTCGACTGGATCGTC-TCTTTTCTTGTTGATTTTT
41261690 CTTTTTTAAT
Statistics
Matches: 182, Mismatches: 25, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
107 40 0.22
108 75 0.41
109 67 0.37
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (108 bp):
AGTTTTAAATTAATAGTTTATCCTAGAATTAAATCATATCTCTGGTATTTTTGTGTAAATTCTTA
GCAATTCGACTGGATCGTCTCTTTTCTTGTTGATTTTTTTTGT
Found at i:41264386 original size:33 final size:31
Alignment explanation
Indices: 41264330--41264393 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
41264320 AGAAAGAAAG
*
41264330 AACATTATTATTTGGAATAGAGAT-ATAAAA
1 AACATTATTATTTGCAATAGAGATAATAAAA
41264360 AACATTATTATTTGCATGATACGAGATAATAAAA
1 AACATTATTATTTGCA--ATA-GAGATAATAAAA
41264394 TTTATAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 15 0.52
32 3 0.10
33 5 0.17
34 6 0.21
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (31 bp):
AACATTATTATTTGCAATAGAGATAATAAAA
Found at i:41265641 original size:13 final size:13
Alignment explanation
Indices: 41265615--41265648 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
41265605 TTATGAATGG
41265615 AAAAAAGTTGTAAT
1 AAAAAA-TTGTAAT
*
41265629 AAAAAATTTTAAT
1 AAAAAATTGTAAT
41265642 AAAAAAT
1 AAAAAAT
41265649 AATATACGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
AAAAAATTGTAAT
Found at i:41267509 original size:31 final size:31
Alignment explanation
Indices: 41267474--41267533 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
41267464 AACCAAAAGG
41267474 GTAAATTGT-ATTTGTAGTCATCCAACTATTA
1 GTAAATT-TCATTTGTAGTCATCCAACTATTA
* * *
41267505 GTAAATTTCTTTTTTGGTCATCCAACTAT
1 GTAAATTTCATTTGTAGTCATCCAACTAT
41267534 AAAAAGTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (31 bp):
GTAAATTTCATTTGTAGTCATCCAACTATTA
Found at i:41268016 original size:267 final size:266
Alignment explanation
Indices: 41267526--41268029 Score: 713
Period size: 267 Copynumber: 1.9 Consensus size: 266
41267516 TTTTGGTCAT
* ** * *
41267526 CCAACTATAAAAAGTTACAAAATGGTTACTCAAATATTTAATTTTGTTTTTTAGTCACCCAACTA
1 CCAACTATAAAAAGTTACAAAATAGTTACTCAAATATACAATTGTCTTTTTTAGTCACCCAACTA
* * * * * * * * **
41267591 CCTTAGATTTTTGAGTGTTTCTATTTTTACGTTAGCTAGCTGGTGGCAGAAAAAGTGATCGAATT
66 CCTTAGATTTTTGAGTGTTGCCATTTTTACATTAGCCAACTGGTGACAAAAAAAGTGATCAAACA
* **
41267656 ATGAAAAGTTACAAAATAGTAACTCAACTGTTCATGTTTATCTATTTTAGTCACCCAACTATCTT
131 ATGAAAAGTTACAAAATAGTAACGCAACTAATCATGTTTATCTATTTTAGTCACCCAACTATCTT
*
41267721 GAATTTTTGGGTGTTTTACTGTTTTCATTTTTACGTTAGCCAACAAGACAAAATTGAATAGTCGT
196 GAATTTTTGGGTGTTTTACTGGTTTCATTTTTACGTTAGCCAACAAGACAAAATTGAATAGTCGT
41267786 GGTTAC
261 GGTTAC
*
41267792 CCAACTATAAAAAGTTACAAAATAGTTACTCAATTATACAATTGTCTTTTTTAGTCACCCAACTA
1 CCAACTATAAAAAGTTACAAAATAGTTACTCAAATATACAATTGTCTTTTTTAGTCACCCAACTA
* * * *
41267857 TCTTGGATTTTTGGGTGTTGCCATTTTTACATTAGCCAACTGGTGACAAAAAAAAGTTATCAAAC
66 CCTTAGATTTTTGAGTGTTGCCATTTTTACATTAGCCAACTGGTGAC-AAAAAAAGTGATCAAAC
* * * * *
41267922 AATGAAAAGTTACAAAATAGTAACGGAACTAATCAAT-TTTGTCTTTTTTAGTCACCCAATTCTC
130 AATGAAAAGTTACAAAATAGTAACGCAACTAATC-ATGTTTATCTATTTTAGTCACCCAACTATC
*
41267986 TTGGATTTTTGGGTGTTTTACTGGTTTCATTTTTACGTTAGCCA
194 TTGAATTTTTGGGTGTTTTACTGGTTTCATTTTTACGTTAGCCA
41268030 GCTGGTGATA
Statistics
Matches: 206, Mismatches: 30, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
266 97 0.47
267 107 0.52
268 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (266 bp):
CCAACTATAAAAAGTTACAAAATAGTTACTCAAATATACAATTGTCTTTTTTAGTCACCCAACTA
CCTTAGATTTTTGAGTGTTGCCATTTTTACATTAGCCAACTGGTGACAAAAAAAGTGATCAAACA
ATGAAAAGTTACAAAATAGTAACGCAACTAATCATGTTTATCTATTTTAGTCACCCAACTATCTT
GAATTTTTGGGTGTTTTACTGGTTTCATTTTTACGTTAGCCAACAAGACAAAATTGAATAGTCGT
GGTTAC
Found at i:41280720 original size:13 final size:12
Alignment explanation
Indices: 41280702--41280745 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
41280692 ACCAAACTAG
41280702 GAGAGAAAGAAAA
1 GAGAGAAA-AAAA
41280715 GAGAGAAAAAAA
1 GAGAGAAAAAAA
* *
41280727 AAAAGAAAAAAA
1 GAGAGAAAAAAA
41280739 GAG-GAAA
1 GAGAGAAA
41280746 TTGTAGCTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 4 0.15
12 15 0.56
13 8 0.30
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
GAGAGAAAAAAA
Found at i:41287511 original size:92 final size:90
Alignment explanation
Indices: 41287346--41287515 Score: 232
Period size: 92 Copynumber: 1.9 Consensus size: 90
41287336 TGGATCACTA
* * *
41287346 GATTTAGCACAACTTCCATTTAGGCCATAAACTTTTAATTTTGTTAAATTACTTAGTTGAACTTC
1 GATTTAGCACAACTTCCATTTAAGCCATAAACTTTTAATTTTATTAAATTACATAGTTGAACTTC
*
41287411 TATTATTAATAAAATAAGGATGATTG
66 TACTATTAA-AAAATAAGGATGATTG
* * * * *
41287437 GATTTAGTACAACTTTCATTTAAGTCATAAACTTTTTAATTTTATTAAATTACATGGTTGAATTT
1 GATTTAGCACAACTTCCATTTAAGCCATAAAC-TTTTAATTTTATTAAATTACATAGTTGAACTT
*
41287502 CTGCTATTAAAAAA
65 CTACTATTAAAAAA
41287516 GTAAATCACT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
91 32 0.47
92 36 0.53
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (90 bp):
GATTTAGCACAACTTCCATTTAAGCCATAAACTTTTAATTTTATTAAATTACATAGTTGAACTTC
TACTATTAAAAAATAAGGATGATTG
Found at i:41295870 original size:20 final size:20
Alignment explanation
Indices: 41295841--41295879 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41295831 GGAGTAAATG
41295841 TGTTTAAAAT-TAGTTCTACA
1 TGTTTAAAATATA-TTCTACA
*
41295861 TGTTTTAAATATATTCTAC
1 TGTTTAAAATATATTCTAC
41295880 GTCATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
TGTTTAAAATATATTCTACA
Found at i:41296203 original size:23 final size:24
Alignment explanation
Indices: 41296169--41296222 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
41296159 CAGCCACGTC
41296169 AATTTTTAATAGTAGAAATGGATG
1 AATTTTTAATAGTAGAAATGGATG
41296193 AATTTTT-ATAGTAGAAATGGATG
1 AATTTTTAATAGTAGAAATGGATG
41296216 AATTTTT
1 AATTTTT
41296223 TAACAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.43
Consensus pattern (24 bp):
AATTTTTAATAGTAGAAATGGATG
Found at i:41296232 original size:22 final size:23
Alignment explanation
Indices: 41296184--41296233 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
41296174 TTAATAGTAG
** *
41296184 AAATGGATGAATTTTTATAGTAG
1 AAATGGATGAATTTTTATAACAA
41296207 AAATGGATGAATTTTT-TAACAA
1 AAATGGATGAATTTTTATAACAA
41296229 AAATG
1 AAATG
41296234 ACTGATTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (23 bp):
AAATGGATGAATTTTTATAACAA
Found at i:41302365 original size:3 final size:3
Alignment explanation
Indices: 41302357--41302391 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41302347 AACAAATAGG
41302357 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41302392 GTACTAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41304460 original size:23 final size:23
Alignment explanation
Indices: 41304431--41304476 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41304421 TTGCAACACT
41304431 CAATTTCTTCAACAACTAAACTA
1 CAATTTCTTCAACAACTAAACTA
41304454 CAATTTCTTCAACAACTAAACTA
1 CAATTTCTTCAACAACTAAACTA
41304477 GAAAAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (23 bp):
CAATTTCTTCAACAACTAAACTA
Found at i:41305573 original size:30 final size:31
Alignment explanation
Indices: 41305529--41305604 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
41305519 TTTTAGGTCC
41305529 AATTTAGTACTTAAACTTAACAAATTTTCTT
1 AATTTAGTACTTAAACTTAACAAATTTTCTT
* * **
41305560 AATTTAG-ACTTAAAGTTGACACTTTTTCTT
1 AATTTAGTACTTAAACTTAACAAATTTTCTT
*
41305590 AAATT-GATACTTAAA
1 AATTTAG-TACTTAAA
41305605 GTCTTAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 1 0.03
30 23 0.61
31 14 0.37
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTTAGTACTTAAACTTAACAAATTTTCTT
Found at i:41310587 original size:19 final size:17
Alignment explanation
Indices: 41310563--41310679 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
41310553 TAATATTAGA
41310563 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
41310582 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
41310602 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
41310619 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
41310635 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
41310651 -ATATA-ATATAATATT
1 AAAATATATATAATATT
41310666 AAAATATA-ATAATA
1 AAAATATATATAATA
41310680 CGACATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:41326562 original size:85 final size:85
Alignment explanation
Indices: 41326419--41326584 Score: 323
Period size: 85 Copynumber: 2.0 Consensus size: 85
41326409 GGTTCTCCGG
41326419 CGACGCGTCCGTGGTTTCAGGTGAGGTTTACTTATTTCTTTTCTTTTACTTTTGTCTATTTTCGT
1 CGACGCGTCCGTGGTTTCAGGTGAGGTTTACTTATTTCTTTTCTTTTACTTTTGTCTATTTTCGT
41326484 ATATAAAAAAGAAAAACACA
66 ATATAAAAAAGAAAAACACA
*
41326504 CGACGCGTCCGTGGTTTCAGGTGAGGTTTACTTATTTCTTTTCTTTTACTTTTTTCTATTTTCGT
1 CGACGCGTCCGTGGTTTCAGGTGAGGTTTACTTATTTCTTTTCTTTTACTTTTGTCTATTTTCGT
41326569 ATATAAAAAAGAAAAA
66 ATATAAAAAAGAAAAA
41326585 GAAAAAACAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (85 bp):
CGACGCGTCCGTGGTTTCAGGTGAGGTTTACTTATTTCTTTTCTTTTACTTTTGTCTATTTTCGT
ATATAAAAAAGAAAAACACA
Found at i:41329671 original size:15 final size:16
Alignment explanation
Indices: 41329651--41329681 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
41329641 AATTTATTTT
41329651 TATATTTGAT-TTAAA
1 TATATTTGATATTAAA
41329666 TATATTTGATATTAAA
1 TATATTTGATATTAAA
41329682 ATTTCAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TATATTTGATATTAAA
Found at i:41335562 original size:88 final size:88
Alignment explanation
Indices: 41335413--41335575 Score: 308
Period size: 88 Copynumber: 1.9 Consensus size: 88
41335403 CAGAAGCTGC
41335413 AAAATCAAGCACAACAGAAAAATATTGAAGCTCAAGTGGCTGAAGATAGTAGTGACAATGAGGAG
1 AAAATCAAGCACAACAGAAAAATATTGAAGCTCAAGTGGCTGAAGATAGTAGTGACAATGAGGAG
*
41335478 CGGGTCTTTAGGCAGACCTAGGG
66 CGGATCTTTAGGCAGACCTAGGG
*
41335501 AAAATCAAGCACAACAGAAAAATATTGAAGCTCAAGTGGCTGAAGATAGTAGTGACCATGAGGAG
1 AAAATCAAGCACAACAGAAAAATATTGAAGCTCAAGTGGCTGAAGATAGTAGTGACAATGAGGAG
41335566 CGGATCTTTA
66 CGGATCTTTA
41335576 CTGTGTCATG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (88 bp):
AAAATCAAGCACAACAGAAAAATATTGAAGCTCAAGTGGCTGAAGATAGTAGTGACAATGAGGAG
CGGATCTTTAGGCAGACCTAGGG
Found at i:41338629 original size:16 final size:16
Alignment explanation
Indices: 41338608--41338639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41338598 ACCAAGGAGA
*
41338608 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
41338624 AATTCATGCACATAAG
1 AATTCATGCACATAAG
41338640 TCTTACGAAT
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:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:41339429 original size:16 final size:16
Alignment explanation
Indices: 41339393--41339434 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41339383 CGGTTACAGA
*
41339393 TTATTTA-ATTTAATT
1 TTATTTATATTAAATT
*
41339408 TAATTTATATTAAATT
1 TTATTTATATTAAATT
41339424 TTATTTATATT
1 TTATTTATATT
41339435 TCATATGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTATATTAAATT
Found at i:41343931 original size:14 final size:14
Alignment explanation
Indices: 41343912--41343942 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41343902 TTACACACAC
41343912 ATACATATATAGAT
1 ATACATATATAGAT
41343926 ATACATATATAGAT
1 ATACATATATAGAT
41343940 ATA
1 ATA
41343943 TACACGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
ATACATATATAGAT
Found at i:41352413 original size:15 final size:15
Alignment explanation
Indices: 41352395--41352424 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41352385 AAATTTTAAT
*
41352395 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
41352410 TTTTTATAATTTATA
1 TTTTTATAATTTATA
41352425 AAGGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:41353728 original size:26 final size:26
Alignment explanation
Indices: 41353679--41353730 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
41353669 AATTTTAATT
*
41353679 TAAAATTAATGATTTTTTAATAAAAAA
1 TAAAATAAATGATTTTTT-ATAAAAAA
41353706 TAAAATAATATGATTTTTT-TAAAAA
1 TAAAATAA-ATGATTTTTTATAAAAA
41353731 TGATTTAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 7 0.30
28 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
TAAAATAAATGATTTTTTATAAAAAA
Found at i:41355859 original size:31 final size:31
Alignment explanation
Indices: 41355802--41355868 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
41355792 ATTTTTTATC
* * *
41355802 CCTT-AATTTGATAATTAGGTTCATTTTGGT
1 CCTTGAATTTGACAATTAGATTCATTTTAGT
*
41355832 CTTTGAATTTGACAATTAGA-TCTATTTTAGT
1 CCTTGAATTTGACAATTAGATTC-ATTTTAGT
41355863 CCTTGA
1 CCTTGA
41355869 CTCGAATTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (31 bp):
CCTTGAATTTGACAATTAGATTCATTTTAGT
Found at i:41363943 original size:18 final size:18
Alignment explanation
Indices: 41363912--41363946 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41363902 ACAAAGATTT
41363912 TGTTTTTTTGAGTTTGAG
1 TGTTTTTTTGAGTTTGAG
41363930 TGTTTGTTTT-AGTTTGA
1 TGTTT-TTTTGAGTTTGA
41363947 AAGTGAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (18 bp):
TGTTTTTTTGAGTTTGAG
Found at i:41376259 original size:30 final size:30
Alignment explanation
Indices: 41376225--41376283 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
41376215 AAAGACTCTA
*
41376225 TGGCATGTCAATTATATCTAATTTAGTTTT
1 TGGCATGTCAACTATATCTAATTTAGTTTT
*
41376255 TGGCATGTCAACTATATCTGATTTAGTTT
1 TGGCATGTCAACTATATCTAATTTAGTTT
41376284 AACTTAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (30 bp):
TGGCATGTCAACTATATCTAATTTAGTTTT
Found at i:41377355 original size:13 final size:13
Alignment explanation
Indices: 41377337--41377361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41377327 GAAAGATATC
41377337 TTTCTCTTTTATT
1 TTTCTCTTTTATT
41377350 TTTCTCTTTTAT
1 TTTCTCTTTTAT
41377362 ATATATATAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTCTTTTATT
Found at i:41382570 original size:20 final size:21
Alignment explanation
Indices: 41382537--41382575 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41382527 ATGGAATCAA
41382537 AAAAAATTCAAACTTTAATGC
1 AAAAAATTCAAACTTTAATGC
*
41382558 AAAAAATT-GAACTTTAAT
1 AAAAAATTCAAACTTTAAT
41382576 TGTAAATCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (21 bp):
AAAAAATTCAAACTTTAATGC
Found at i:41382987 original size:12 final size:12
Alignment explanation
Indices: 41382972--41382996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41382962 CCCAGCTTGC
41382972 GCCTCCGCCTCA
1 GCCTCCGCCTCA
41382984 GCCTCCGCCTCA
1 GCCTCCGCCTCA
41382996 G
1 G
41382997 GCCGGTGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.56, G:0.20, T:0.16
Consensus pattern (12 bp):
GCCTCCGCCTCA
Found at i:41384267 original size:51 final size:53
Alignment explanation
Indices: 41384192--41384294 Score: 156
Period size: 51 Copynumber: 2.0 Consensus size: 53
41384182 AAAAGAAGAA
41384192 TTTTTTGGGTGCTAGTCATGTAATGGCCGACACCAGATATG-AAAAA-AAAAT
1 TTTTTTGGGTGCTAGTCATGTAATGGCCGACACCAGATATGTAAAAATAAAAT
* * * *
41384243 TTTTTTTGGTGCTGGTCATTTAATGGCCGACACCAGCTATGTAAAAATAAAA
1 TTTTTTGGGTGCTAGTCATGTAATGGCCGACACCAGATATGTAAAAATAAAA
41384295 ATAAAAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 37 0.80
52 5 0.11
53 4 0.09
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (53 bp):
TTTTTTGGGTGCTAGTCATGTAATGGCCGACACCAGATATGTAAAAATAAAAT
Found at i:41400688 original size:4 final size:4
Alignment explanation
Indices: 41400673--41400724 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
41400663 AGAAAAAAAC
* * * *
41400673 GTAT GCAT GTAT GTAT GTAT ATAC ATAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
41400721 GTAT
1 GTAT
41400725 TGATATTTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:41414767 original size:38 final size:39
Alignment explanation
Indices: 41414683--41414817 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
41414673 ACCAATATGG
*
41414683 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
41414722 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
41414760 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
41414801 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
41414818 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:41416399 original size:5 final size:5
Alignment explanation
Indices: 41416381--41416411 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
41416371 TTTCTTTTAT
41416381 ATATA ATAATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA
41416412 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:41416451 original size:27 final size:26
Alignment explanation
Indices: 41416387--41416451 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 26
41416377 TTATATATAA
41416387 TAATAATATAATATAATATAATATACT
1 TAATAATA-AATATAATATAATATACT
* **
41416414 TAATTATTAAATA-AATATATATATTTT
1 TAA-TAATAAATATAATATA-ATATACT
41416441 TAATCAATAAA
1 TAAT-AATAAA
41416452 ATCTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 7 0.23
27 20 0.65
28 4 0.13
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATAATAAATATAATATAATATACT
Found at i:41419426 original size:130 final size:131
Alignment explanation
Indices: 41419218--41419482 Score: 370
Period size: 130 Copynumber: 2.0 Consensus size: 131
41419208 CATTCATTCA
** ** **
41419218 AAAATTCTTCAAAACGAAGACGAGATTCGAGGTTGGGCAATTCGTGGAATCGTGCCCTAACGTGT
1 AAAATTCTTCAAAACGAAGACGAGATTCGAGACTAAGCAATTAATGGAATCGTGCCCTAACGTGT
* *
41419283 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCGAAATTTCACTCACATCTTT
66 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACATCTTC
41419348 T
131 T
* * *
41419349 AAAATTCTTCAAAACGAAGACGAGGTTCGATACTAAGCAA-TAATGGAATCGTGCTCTAACGTGT
1 AAAATTCTTCAAAACGAAGACGAGATTCGAGACTAAGCAATTAATGGAATCGTGCCCTAACGTGT
* * * * * *
41419413 TGGGTTGCAATTTCGCGTTTGCTCAAAGTAATTGAGTATCCCTTCAAAATTTCATTCATATCTTC
66 TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACATCTTC
41419478 T
131 T
41419479 AAAA
1 AAAA
41419483 ATTATTTAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
130 83 0.71
131 34 0.29
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (131 bp):
AAAATTCTTCAAAACGAAGACGAGATTCGAGACTAAGCAATTAATGGAATCGTGCCCTAACGTGT
TGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCACTTCAAAATTTCACTCACATCTTC
T
Found at i:41419868 original size:130 final size:130
Alignment explanation
Indices: 41419621--41419857 Score: 332
Period size: 130 Copynumber: 1.8 Consensus size: 130
41419611 AAAATGCTTA
* **
41419621 AAAACGAAGACGATGTTCAATGTTTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCGCT
1 AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCAAGCCCTATCGTGCTGGGTTGCGCT
* * * * *
41419686 TTTTCATTGGTTCGAAACAATTGAAGATCCCTTCGGAGTTTCACTCACATTTTCTAAAATCTTTC
66 TTTTCATTGGTCCAAAACAATCGAAGATCCCTTCGGAATTTCACACACATTTTCTAAAATCTTTC
* * *
41419751 AAAATGAAGGCGATGTTCGATGTTTGACGATTTGAGAATCAAGCCCTATCGTGCTGGGTTGCGCT
1 AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCAAGCCCTATCGTGCTGGGTTGCGCT
* * *
41419816 TTTTCATTTGTCCAAAATAATCGAATATCTCCTT-GGAATTTC
66 TTTTCATTGGTCCAAAACAATCGAAGATC-CCTTCGGAATTTC
41419858 GCACGTATTT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
130 89 0.96
131 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (130 bp):
AAAACGAAGACGATGTTCAATGTTTGACGATTTGAGAATCAAGCCCTATCGTGCTGGGTTGCGCT
TTTTCATTGGTCCAAAACAATCGAAGATCCCTTCGGAATTTCACACACATTTTCTAAAATCTTTC
Found at i:41423623 original size:16 final size:17
Alignment explanation
Indices: 41423604--41423635 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41423594 ATAACATCAT
41423604 TATATA-TGTACGAATC
1 TATATAGTGTACGAATC
41423620 TATATAGTGTACGAAT
1 TATATAGTGTACGAAT
41423636 AGTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (17 bp):
TATATAGTGTACGAATC
Found at i:41423710 original size:21 final size:22
Alignment explanation
Indices: 41423666--41423710 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
41423656 AGTATAAATA
*
41423666 TATATACATATATCATATAAGTT
1 TATATACA-ATATCATACAAGTT
*
41423689 TATATAC-ATATCATACATGTT
1 TATATACAATATCATACAAGTT
41423710 T
1 T
41423711 CCTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (22 bp):
TATATACAATATCATACAAGTT
Found at i:41425932 original size:35 final size:35
Alignment explanation
Indices: 41425845--41425932 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
41425835 CGGGGTATAA
*
41425845 GGTTT-AGGTTTGAGG-TTTGAGGTTTAGAGTTTAT
1 GGTTTGAGGTTT-AGGATTTGAGGTTTAGAGTTCAT
* * * * * *
41425879 GATTGGATGTTCAAGATTTGAGGTTTAGGGTTCAT
1 GGTTTGAGGTTTAGGATTTGAGGTTTAGAGTTCAT
41425914 GGTTTGAGGTTTAGGATTT
1 GGTTTGAGGTTTAGGATTT
41425933 TGGATTTTGG
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.44
Consensus pattern (35 bp):
GGTTTGAGGTTTAGGATTTGAGGTTTAGAGTTCAT
Found at i:41426157 original size:14 final size:14
Alignment explanation
Indices: 41426138--41426177 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
41426128 TCTCGAACCC
41426138 TAAACCCCAAACTT
1 TAAACCCCAAACTT
41426152 TAAACCCCAAACTT
1 TAAACCCCAAACTT
* *
41426166 TGAACCTCAAAC
1 TAAACCCCAAAC
41426178 CCAAATCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.35, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAACCCCAAACTT
Found at i:41426182 original size:20 final size:21
Alignment explanation
Indices: 41426157--41426211 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
41426147 AACTTTAAAC
*
41426157 CCCAAACT-TTGAACCTCAAA
1 CCCAAACTCTCGAACCTCAAA
41426177 CCCAAA-TCTCGAACCTCAAA
1 CCCAAACTCTCGAACCTCAAA
* *
41426197 CACAAACACT-GAACC
1 CCCAAACTCTCGAACC
41426212 ATGAGCCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.42, C:0.38, G:0.05, T:0.15
Consensus pattern (21 bp):
CCCAAACTCTCGAACCTCAAA
Found at i:41426236 original size:6 final size:6
Alignment explanation
Indices: 41426205--41426264 Score: 66
Period size: 6 Copynumber: 9.3 Consensus size: 6
41426195 AACACAAACA
* *
41426205 CTGAAC CATGAGC CATGAACC CTGAAC CTGAAC CTGAAC CTGAAC CAGAAC
1 CTGAAC C-TGAAC C-TGAA-C CTGAAC CTGAAC CTGAAC CTGAAC CTGAAC
41426256 CTTGAAC CT
1 C-TGAAC CT
41426265 TGAAACTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 27 0.57
7 18 0.38
8 2 0.04
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
CTGAAC
Found at i:41426273 original size:7 final size:7
Alignment explanation
Indices: 41426256--41426289 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
41426246 GAACCAGAAC
*
41426256 CTTGAAC
1 CTTGAAA
41426263 CTTGAAA
1 CTTGAAA
41426270 CTTGAAA
1 CTTGAAA
41426277 CTTGAAA
1 CTTGAAA
41426284 CTTGAA
1 CTTGAA
41426290 CTTTGAACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (7 bp):
CTTGAAA
Found at i:41426275 original size:14 final size:14
Alignment explanation
Indices: 41426256--41426296 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
41426246 GAACCAGAAC
41426256 CTTGAACCTTGAAA
1 CTTGAACCTTGAAA
*
41426270 CTTGAAACTTGAAA
1 CTTGAACCTTGAAA
*
41426284 CTTGAACTTTGAA
1 CTTGAACCTTGAA
41426297 CACGAACCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (14 bp):
CTTGAACCTTGAAA
Found at i:41426521 original size:27 final size:27
Alignment explanation
Indices: 41426475--41426544 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
41426465 AACCATGAAC
*
41426475 TTGAGTTTAGAGTTTAAGGTTCGAGGT
1 TTGAGTTTTGAGTTTAAGGTTCGAGGT
41426502 TTGAGATTTTGAGTTT-AGGTTCGAGGT
1 TTGAG-TTTTGAGTTTAAGGTTCGAGGT
*
41426529 TTAGGGTTTTGAGTTT
1 TT-GAGTTTTGAGTTT
41426545 CGGATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 28 0.72
28 11 0.28
ACGTcount: A:0.19, C:0.03, G:0.33, T:0.46
Consensus pattern (27 bp):
TTGAGTTTTGAGTTTAAGGTTCGAGGT
Found at i:41426600 original size:22 final size:22
Alignment explanation
Indices: 41426575--41426616 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41426565 ATTATGTGTT
41426575 AATGACATGAAAAAATTGTAGA
1 AATGACATGAAAAAATTGTAGA
* * *
41426597 AATGTCATTAAATAATTGTA
1 AATGACATGAAAAAATTGTA
41426617 AAGGAACCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (22 bp):
AATGACATGAAAAAATTGTAGA
Found at i:41431683 original size:31 final size:30
Alignment explanation
Indices: 41431641--41431732 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
41431631 AAATTGTTGT
* *
41431641 TAAGCCCTTCAAAATTTATGAAAATTTTAGC
1 TAAGCCTTTCAAAATTTTTGAAAATTTTA-C
* * * *
41431672 TAGGTCTTTCAAAATTTTTAGAAATTTTTAT
1 TAAGCCTTTCAAAATTTTT-GAAAATTTTAC
*
41431703 TAAGCCTCTCAAAATTTTTGAAAAATTTTA
1 TAAGCCTTTCAAAATTTTTG-AAAATTTTA
41431733 ATTAAACCGC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.02
31 39 0.80
32 9 0.18
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (30 bp):
TAAGCCTTTCAAAATTTTTGAAAATTTTAC
Found at i:41431757 original size:30 final size:31
Alignment explanation
Indices: 41431680--41431826 Score: 133
Period size: 31 Copynumber: 4.8 Consensus size: 31
41431670 GCTAGGTCTT
* * *
41431680 TCAAAATTTTTAGAAATTTTTATTAAGCCTC
1 TCAAAATTTTTAAAAATTTTAATTAAACCTC
*
41431711 TCAAAATTTTTGAAAAATTTTAATTAAACCGC
1 TCAAAATTTTT-AAAAATTTTAATTAAACCTC
*
41431743 -C-AAATTTTATAAAAATTTTCATTAAACC-C
1 TCAAAATTTT-TAAAAATTTTAATTAAACCTC
* * *
41431772 TCCAAAAGTTTTGAAAGTTTTAATTAAACC-C
1 T-CAAAATTTTTAAAAATTTTAATTAAACCTC
* **
41431803 T-TAAATTTTTTGAAATTTTAATTA
1 TCAAAATTTTTAAAAATTTTAATTA
41431827 GCCCCTCAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
29 19 0.20
30 24 0.25
31 32 0.33
32 22 0.23
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (31 bp):
TCAAAATTTTTAAAAATTTTAATTAAACCTC
Found at i:41431798 original size:31 final size:30
Alignment explanation
Indices: 41431681--41431826 Score: 129
Period size: 30 Copynumber: 4.8 Consensus size: 30
41431671 CTAGGTCTTT
* *
41431681 CAAAATTTTTAGAAATTTTTATT-AAGCCTC
1 CAAAATTTTT-GAAATTTTAATTAAACCCTC
*
41431711 TCAAAATTTTTGAAAAATTTTAATTAAA-CCGC
1 -CAAAATTTTTG--AAATTTTAATTAAACCCTC
* *
41431743 C-AAATTTTATAAAAATTTTCATTAAACCCTC
1 CAAAATTTT-T-GAAATTTTAATTAAACCCTC
*
41431774 CAAAAGTTTTGAAAGTTTTAATTAAACCCT-
1 CAAAATTTTTGAAA-TTTTAATTAAACCCTC
* *
41431804 TAAATTTTTTGAAATTTTAATTA
1 CAAAATTTTTGAAATTTTAATTA
41431827 GCCCCTCAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
29 9 0.09
30 35 0.36
31 31 0.32
32 19 0.20
33 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (30 bp):
CAAAATTTTTGAAATTTTAATTAAACCCTC
Found at i:41431801 original size:61 final size:61
Alignment explanation
Indices: 41431683--41431837 Score: 165
Period size: 61 Copynumber: 2.6 Consensus size: 61
41431673 AGGTCTTTCA
* * * *
41431683 AAATTTTTAGAAATTTTTATTAAGCCTCTCAAAATTTTTGAAAAATTTTAATTAAACCGCC
1 AAATTTTTAAAAATTTTCATTAACCCTCTCAAAAGTTTTGAAAAATTTTAATTAAACCGCC
* *
41431744 AAATTTTATAAAAATTTTCATTAAACCCTC-CAAAAGTTTTG-AAAGTTTTAATTAAACC-CTT
1 AAATTTT-TAAAAATTTTCATT-AACCCTCTCAAAAGTTTTGAAAAATTTTAATTAAACCGC-C
** * *
41431805 AAATTTTTTGAAATTTTAATTAGCCC-CTCAAAA
1 AAATTTTTAAAAATTTTCATTAACCCTCTCAAAA
41431838 AAACTAACCT
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
58 1 0.01
59 9 0.11
60 12 0.15
61 30 0.38
62 22 0.28
63 6 0.08
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (61 bp):
AAATTTTTAAAAATTTTCATTAACCCTCTCAAAAGTTTTGAAAAATTTTAATTAAACCGCC
Found at i:41439332 original size:8 final size:8
Alignment explanation
Indices: 41439319--41439360 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
41439309 CTTATATTGA
41439319 ACATACAC
1 ACATACAC
41439327 ACATACAC
1 ACATACAC
*
41439335 ACAT--AT
1 ACATACAC
*
41439341 ACATACAT
1 ACATACAC
41439349 ACATACAC
1 ACATACAC
41439357 ACAT
1 ACAT
41439361 GCATGCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 5 0.17
8 25 0.83
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (8 bp):
ACATACAC
Found at i:41439344 original size:22 final size:22
Alignment explanation
Indices: 41439319--41439360 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41439309 CTTATATTGA
41439319 ACATACACACATACACACATAT
1 ACATACACACATACACACATAT
*
41439341 ACATACATACATACACACAT
1 ACATACACACATACACACAT
41439361 GCATGCATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (22 bp):
ACATACACACATACACACATAT
Found at i:41446610 original size:36 final size:35
Alignment explanation
Indices: 41446544--41446613 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
41446534 TACGAGAGTG
* *
41446544 AATAAACAAACATAATTGAAAACAATAATTAAAAT
1 AATAAACAAACATAATTGAAAAAAAAAATTAAAAT
41446579 AATAAACAAA-ATGAAATTGAAAAAAAAAATTAAAA
1 AATAAACAAACAT--AATTGAAAAAAAAAATTAAAA
41446614 GTCAGTCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 2 0.06
35 10 0.32
36 19 0.61
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (35 bp):
AATAAACAAACATAATTGAAAAAAAAAATTAAAAT
Found at i:41450219 original size:21 final size:21
Alignment explanation
Indices: 41450193--41450236 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
41450183 AGACGAGCAA
* *
41450193 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41450214 TACTCCAAAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
41450235 TA
1 TA
41450237 ACAGCCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:41463473 original size:18 final size:18
Alignment explanation
Indices: 41463436--41463474 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41463426 TAAATTATTT
* *
41463436 AATATTTATTTTTATAAA
1 AATATTTATATTCATAAA
41463454 AATATTTATATTCATTAAA
1 AATATTTATATTCA-TAAA
41463473 AA
1 AA
41463475 GTTGGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATTTATATTCATAAA
Found at i:41467586 original size:34 final size:35
Alignment explanation
Indices: 41467520--41467587 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
41467510 AAATAGACAT
*
41467520 TTATATTTAATAACATAAAATAATTAATATTTTTA
1 TTATATTTAATAAAATAAAATAATTAATATTTTTA
* * *
41467555 TTAT-TTTAATAAAATTAATTAA-TAATAATTTTA
1 TTATATTTAATAAAATAAAATAATTAATATTTTTA
41467588 AATTCTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 10 0.34
34 15 0.52
35 4 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (35 bp):
TTATATTTAATAAAATAAAATAATTAATATTTTTA
Found at i:41468199 original size:3 final size:3
Alignment explanation
Indices: 41468191--41468221 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41468181 CCTCGAAATT
41468191 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
41468222 GGAGACGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:41470549 original size:18 final size:18
Alignment explanation
Indices: 41470515--41470552 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41470505 GCCTCCGTGG
*
41470515 TACTTTTACCTTTTTTTT
1 TACTTTTACCTTATTTTT
41470533 TACTTTT-CCTTGATTTTT
1 TACTTTTACCTT-ATTTTT
41470551 TA
1 TA
41470553 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (18 bp):
TACTTTTACCTTATTTTT
Found at i:41471633 original size:12 final size:12
Alignment explanation
Indices: 41471616--41471641 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41471606 TATAGCTTGC
41471616 AATGATGTTTTG
1 AATGATGTTTTG
41471628 AATGATGTTTTG
1 AATGATGTTTTG
41471640 AA
1 AA
41471642 CTTTGGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (12 bp):
AATGATGTTTTG
Found at i:41476382 original size:4 final size:4
Alignment explanation
Indices: 41476373--41476409 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
41476363 CAAAAATAAC
*
41476373 CATA CATA CATA CATA CATA CAT- -ATA TATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
41476410 TGAATGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:41478519 original size:47 final size:47
Alignment explanation
Indices: 41478450--41478543 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
41478440 GGGTAACATG
41478450 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGT
1 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGT
41478497 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGT
1 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGT
41478544 TTGGAGGGCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.34
Consensus pattern (47 bp):
ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGT
Found at i:41478600 original size:131 final size:131
Alignment explanation
Indices: 41478366--41478627 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
41478356 AGGTAACATG
41478366 ATCCGAAATGTGTTAGGTATAGCCAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
1 ATCCGAAATGTGTTAGGTATAGCCAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
*
41478431 ATTTTTGAAGGGTAACATGATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATG
66 ATTTTTGAAGGCTAACATGATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATG
41478496 T
131 T
*
41478497 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
1 ATCCGAAATGTGTTAGGTATAGCCAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
41478562 ATTTTTGAAGGCTAACATGATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATG
66 ATTTTTGAAGGCTAACATGATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATG
41478627 T
131 T
41478628 TTGGAGGGCC
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.27, C:0.11, G:0.29, T:0.33
Consensus pattern (131 bp):
ATCCGAAATGTGTTAGGTATAGCCAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
ATTTTTGAAGGCTAACATGATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATG
T
Found at i:41478638 original size:84 final size:84
Alignment explanation
Indices: 41478497--41478651 Score: 310
Period size: 84 Copynumber: 1.8 Consensus size: 84
41478487 GGGATTATGT
41478497 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
1 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
41478562 ATTTTTGAAGGCTAACATG
66 ATTTTTGAAGGCTAACATG
41478581 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
1 ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
41478646 ATTTTT
66 ATTTTT
41478652 AAAAAATTTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (84 bp):
ATCCGAAATGTGTTAGGTATAGCTAGTGGCAGATCTTGGGATTATGTTTGGAGGGCCTAATTAAA
ATTTTTGAAGGCTAACATG
Found at i:41482183 original size:42 final size:42
Alignment explanation
Indices: 41482094--41482188 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
41482084 TCCTAATTGG
* * * **
41482094 GAAAATAATTCCCTTATTTTAATAAATTACTAAAACATTAGG
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
* * *
41482136 GAAAATAGTTCCTTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
41482178 TAAAATAATTC
1 GAAAATAATTC
41482189 TAGAATATTA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (42 bp):
GAAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:41482885 original size:3 final size:3
Alignment explanation
Indices: 41482877--41482915 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
41482867 CGCAGCAACT
* * *
41482877 GCA GCA GCA GCA ACA ACA CCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
41482916 AAGGCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.38, C:0.36, G:0.26, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:41482888 original size:15 final size:15
Alignment explanation
Indices: 41482868--41482915 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
41482858 AGCAACAAAC
*
41482868 GCAGCAACTGCAGCA
1 GCAGCAACAGCAGCA
* *
41482883 GCAGCAACAACACCA
1 GCAGCAACAGCAGCA
*
41482898 GCAGCAGCAGCAGCA
1 GCAGCAACAGCAGCA
41482913 GCA
1 GCA
41482916 AAGGCAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.35, G:0.25, T:0.02
Consensus pattern (15 bp):
GCAGCAACAGCAGCA
Found at i:41482888 original size:27 final size:27
Alignment explanation
Indices: 41482857--41482916 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
41482847 ACCATCTCCT
*
41482857 CAGCAACAA-ACGCAGCAACTGCAGCAG
1 CAGCAACAACAC-CAGCAACAGCAGCAG
*
41482884 CAGCAACAACACCAGCAGCAGCAGCAG
1 CAGCAACAACACCAGCAACAGCAGCAG
41482911 CAGCAA
1 CAGCAA
41482917 AGGCAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.42, C:0.35, G:0.22, T:0.02
Consensus pattern (27 bp):
CAGCAACAACACCAGCAACAGCAGCAG
Found at i:41486779 original size:6 final size:6
Alignment explanation
Indices: 41486768--41486800 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41486758 TTCATGCATG
*
41486768 CATATA CATATA CATATA CATAGA CATATA CAT
1 CATATA CATATA CATATA CATATA CATATA CAT
41486801 GTATTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (6 bp):
CATATA
Found at i:41487527 original size:28 final size:28
Alignment explanation
Indices: 41487486--41487539 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
41487476 AACGTGCCAT
41487486 TTTTATAACCCATGGGATTATAATAAGG
1 TTTTATAACCCATGGGATTATAATAAGG
* *
41487514 TTTTATCACTCATGGGATTATAATAA
1 TTTTATAACCCATGGGATTATAATAA
41487540 AGATTTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (28 bp):
TTTTATAACCCATGGGATTATAATAAGG
Found at i:41487546 original size:28 final size:28
Alignment explanation
Indices: 41487487--41487547 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
41487477 ACGTGCCATT
* *
41487487 TTTATAACCCATGGGATTATAATAAGGT
1 TTTATAACCCATGGGATTATAATAAAGA
* *
41487515 TTTATCACTCATGGGATTATAATAAAGA
1 TTTATAACCCATGGGATTATAATAAAGA
41487543 TTTAT
1 TTTAT
41487548 GATGAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (28 bp):
TTTATAACCCATGGGATTATAATAAAGA
Found at i:41488347 original size:22 final size:24
Alignment explanation
Indices: 41488295--41488347 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
41488285 TTAGCGATTA
41488295 TGAAATTGATGCTATAAATAAGTG
1 TGAAATTGATGCTATAAATAAGTG
** * *
41488319 TTTAATTG-TGCTA-ATATTAGTG
1 TGAAATTGATGCTATAAATAAGTG
41488341 TGAAATT
1 TGAAATT
41488348 TTATGGCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 12 0.52
23 5 0.22
24 6 0.26
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.42
Consensus pattern (24 bp):
TGAAATTGATGCTATAAATAAGTG
Found at i:41500559 original size:11 final size:11
Alignment explanation
Indices: 41500511--41500563 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
41500501 AAAAATATTT
*
41500511 ATTTTATTTAG
1 ATTTAATTTAG
41500522 AGGTTTAATTTAG
1 A--TTTAATTTAG
*
41500535 -TGTAATTCTAG
1 ATTTAATT-TAG
41500546 ATTTAATTTAG
1 ATTTAATTTAG
41500557 ATTTAAT
1 ATTTAAT
41500564 GTAATTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 14 0.40
12 6 0.17
13 9 0.26
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (11 bp):
ATTTAATTTAG
Found at i:41505167 original size:15 final size:15
Alignment explanation
Indices: 41505147--41505224 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
41505137 TTTATGGAAA
41505147 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
41505162 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41505176 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41505192 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41505206 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41505222 ATC
1 ATC
41505225 GAGATATTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41505175 original size:30 final size:30
Alignment explanation
Indices: 41505141--41505234 Score: 161
Period size: 30 Copynumber: 3.1 Consensus size: 30
41505131 TCCATATTTA
*
41505141 TGGAAAATCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
41505171 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
41505201 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
41505232 TGG
1 TGG
41505235 CATAATAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
30 53 0.87
31 8 0.13
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:41509830 original size:15 final size:15
Alignment explanation
Indices: 41509810--41509917 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
41509800 TTTATGGAAA
41509810 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
41509825 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
41509839 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41509855 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41509869 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41509885 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41509899 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41509915 ATC
1 ATC
41509918 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41509839 original size:30 final size:30
Alignment explanation
Indices: 41509803--41509917 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
41509793 ATCCATATTT
*
41509803 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
41509833 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
41509863 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
41509893 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
41509918 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:41512397 original size:34 final size:34
Alignment explanation
Indices: 41512359--41512432 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
41512349 TTTAGTCCCT
41512359 TAAAA-AAAAGATGAAATCATAAGTTCATACATGA
1 TAAAATAAAA-ATGAAATCATAAGTTCATACATGA
* *
41512393 TAAAATTACAATGAAATCATAAGTTCATACATGA
1 TAAAATAAAAATGAAATCATAAGTTCATACATGA
41512427 TAAAAT
1 TAAAAT
41512433 TACACTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.27
Consensus pattern (34 bp):
TAAAATAAAAATGAAATCATAAGTTCATACATGA
Found at i:41512433 original size:34 final size:34
Alignment explanation
Indices: 41512369--41512436 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41512359 TAAAAAAAAG
41512369 ATGAAATCATAAGTTCATACATGATAAAATTACA
1 ATGAAATCATAAGTTCATACATGATAAAATTACA
41512403 ATGAAATCATAAGTTCATACATGATAAAATTACA
1 ATGAAATCATAAGTTCATACATGATAAAATTACA
41512437 CTTTAACCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (34 bp):
ATGAAATCATAAGTTCATACATGATAAAATTACA
Found at i:41513587 original size:4 final size:4
Alignment explanation
Indices: 41513578--41513602 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41513568 AAATCAAAGG
41513578 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
41513603 ATATGAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:41517115 original size:20 final size:20
Alignment explanation
Indices: 41517090--41517131 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
41517080 AAACCAAGTG
*
41517090 GGGGGTCAACACGCCCTTGT
1 GGGGGTCAACACGCCCGTGT
41517110 GGGGGTCAACACGCCCGTGT
1 GGGGGTCAACACGCCCGTGT
41517130 GG
1 GG
41517132 ATGAGGTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (20 bp):
GGGGGTCAACACGCCCGTGT
Found at i:41530302 original size:24 final size:24
Alignment explanation
Indices: 41530228--41530306 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
41530218 AATTTGATAC
*
41530228 TTTTTTTCTAATTTGGTACCTAAA
1 TTTTTTTCTAATTTGGTACTTAAA
* * * * *
41530252 CCTTTTTTGT-ATCT-GAACTTGACA
1 -TTTTTTTCTAATTTGGTACTT-AAA
41530276 TTTTTTTCTAATTTGGTACTTAAA
1 TTTTTTTCTAATTTGGTACTTAAA
41530300 TTTTTTT
1 TTTTTTT
41530307 GGACCCAATT
Statistics
Matches: 40, Mismatches: 11, Indels: 7
0.69 0.19 0.12
Matches are distributed among these distances:
23 11 0.28
24 17 0.43
25 12 0.30
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTTTTCTAATTTGGTACTTAAA
Found at i:41530594 original size:4 final size:4
Alignment explanation
Indices: 41530585--41530610 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41530575 GTTTTCAATA
41530585 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
41530611 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:41530878 original size:31 final size:31
Alignment explanation
Indices: 41530833--41530911 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
41530823 GACCCCCAAA
* * *
41530833 AAGTTTAGGCACCAACTTAAGAAAAAGTATC
1 AAGTTGAGGTACCAAATTAAGAAAAAGTATC
* * *
41530864 AAGTTGAGGTACCAAATTAGGACAAAGTGTC
1 AAGTTGAGGTACCAAATTAAGAAAAAGTATC
41530895 AAGTTGAGGTACCAAAT
1 AAGTTGAGGTACCAAAT
41530912 GTTATATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (31 bp):
AAGTTGAGGTACCAAATTAAGAAAAAGTATC
Found at i:41540223 original size:27 final size:28
Alignment explanation
Indices: 41540182--41540239 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
41540172 TTGTCCTCTC
41540182 TACTAGAAAACGAGCAAATTAATCTTTA
1 TACTAGAAAACGAGCAAATTAATCTTTA
*
41540210 TACTA-AAAATGAGCAAATTAATCTTTA
1 TACTAGAAAACGAGCAAATTAATCTTTA
41540237 TAC
1 TAC
41540240 GTTAGATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (28 bp):
TACTAGAAAACGAGCAAATTAATCTTTA
Found at i:41556236 original size:19 final size:21
Alignment explanation
Indices: 41556199--41556239 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41556189 AGGTTTAGTG
*
41556199 TAAAAAATTGTATTAATAATA
1 TAAAAAAATGTATTAATAATA
41556220 TAAAAAAAT-TATT-ATAATA
1 TAAAAAAATGTATTAATAATA
41556239 T
1 T
41556240 TATTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAAAATGTATTAATAATA
Found at i:41558992 original size:31 final size:30
Alignment explanation
Indices: 41558946--41559006 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
41558936 ATAAATATTA
41558946 AATTTATACATAAATTTTGATTTAATGTAT
1 AATTTATACATAAATTTTGATTTAATGTAT
* *
41558976 AATTTAATATATAAATTTTGATTTAGTGTAT
1 AATTT-ATACATAAATTTTGATTTAATGTAT
41559007 TTATACACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (30 bp):
AATTTATACATAAATTTTGATTTAATGTAT
Found at i:41559916 original size:18 final size:19
Alignment explanation
Indices: 41559862--41559919 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
41559852 AAATTAGAAA
41559862 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
41559881 CAAAAATTCAAAATATTTAT
1 -AAAAATTCAAAATATTTAT
*
41559901 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
41559919 A
1 A
41559920 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 14 0.39
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:41561236 original size:29 final size:29
Alignment explanation
Indices: 41561203--41561259 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41561193 ATTATTTAAG
41561203 TTAGAAAAATTGTGAAGCAATGAAATGAT
1 TTAGAAAAATTGTGAAGCAATGAAATGAT
*
41561232 TTAGAAACATTGTGAAGCAATGAAATGA
1 TTAGAAAAATTGTGAAGCAATGAAATGA
41561260 AATTACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.26
Consensus pattern (29 bp):
TTAGAAAAATTGTGAAGCAATGAAATGAT
Found at i:41566916 original size:19 final size:19
Alignment explanation
Indices: 41566894--41566947 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 19
41566884 TATTTTTATG
41566894 ATTTAAAAATAAATATTTT
1 ATTTAAAAATAAATATTTT
41566913 ATTTATAAAAAAATAAATATTTT
1 A-TT-T--AAAAATAAATATTTT
*
41566936 ATATTTAAAATA
1 AT-TTAAAAATA
41566948 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
19 1 0.03
20 8 0.28
21 1 0.03
22 2 0.07
23 17 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAAAATAAATATTTT
Found at i:41566924 original size:23 final size:23
Alignment explanation
Indices: 41566898--41566945 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
41566888 TTTATGATTT
41566898 AAAAATAAATATTTTAT-TTATAA
1 AAAAATAAATATTTTATATT-TAA
41566921 AAAAATAAATATTTTATATTTAA
1 AAAAATAAATATTTTATATTTAA
41566944 AA
1 AA
41566946 TATTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAAATAAATATTTTATATTTAA
Found at i:41567144 original size:14 final size:15
Alignment explanation
Indices: 41567125--41567165 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
41567115 AAATAAGTTC
41567125 AAAAATCCAAAAT-A
1 AAAAATCCAAAATGA
*
41567139 AAAAAT-CAATATGA
1 AAAAATCCAAAATGA
*
41567153 AAAAATCGAAAAT
1 AAAAATCCAAAAT
41567166 TAAATCCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (15 bp):
AAAAATCCAAAATGA
Found at i:41574192 original size:56 final size:56
Alignment explanation
Indices: 41574090--41574251 Score: 193
Period size: 56 Copynumber: 2.9 Consensus size: 56
41574080 GAATAAAGAC
* * * *
41574090 AAGTTCATACTTCAATATGAGAACAATTGCCAAATTCAGGGACTAACTTAAAAAAA
1 AAGTTCATGCCTCAATATGAGAACAATTGCCAAGTTTAGGGACTAACTTAAAAAAA
* * *
41574146 AAGTTCATGCCTCAATATGAGAACAATTGCTAAGTTTAGGGGCTAACTTGAAACAAA
1 AAGTTCATGCCTCAATATGAGAACAATTGCCAAGTTTAGGGACTAACTT-AAAAAAA
* * * *
41574203 AA-TTCAAGTCC-CAATGTGGGAACAATTGCCAAGTTTAAGGACTAACTTA
1 AAGTTCATG-CCTCAATATGAGAACAATTGCCAAGTTTAGGGACTAACTTA
41574252 GACAACGAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 1 0.01
56 80 0.88
57 10 0.11
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (56 bp):
AAGTTCATGCCTCAATATGAGAACAATTGCCAAGTTTAGGGACTAACTTAAAAAAA
Found at i:41575114 original size:17 final size:17
Alignment explanation
Indices: 41575062--41575114 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
41575052 TTGAACTAAG
41575062 TTTT-ATTATTTTTTAAT
1 TTTTAATTATTTTTT-AT
**
41575079 TTTTAATT-TGTTTGAAT
1 TTTTAATTAT-TTTTTAT
41575096 TTTTAATTATTTTTTAT
1 TTTTAATTATTTTTTAT
41575113 TT
1 TT
41575115 AAACTAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 22 0.76
18 7 0.24
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (17 bp):
TTTTAATTATTTTTTAT
Found at i:41575938 original size:14 final size:14
Alignment explanation
Indices: 41575919--41575945 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41575909 ATTAAAAGTT
41575919 TATAAATTTTTATA
1 TATAAATTTTTATA
41575933 TATAAATTTTTAT
1 TATAAATTTTTAT
41575946 TTGGAGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATAAATTTTTATA
Found at i:41576640 original size:31 final size:31
Alignment explanation
Indices: 41576605--41576673 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
41576595 ATTAACTACC
*
41576605 CAATGACTTAAATAAAAACTTTTAAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
* * *
41576636 CAATGTCTTAAATGAAATCTTTCAAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
*
41576667 TAATGAC
1 CAATGAC
41576674 CAAATTATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTCAAATAGTT
Found at i:41580357 original size:24 final size:24
Alignment explanation
Indices: 41580330--41580381 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41580320 TTAGTAAGTC
*
41580330 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
41580354 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
41580378 AAAT
1 AAAT
41580382 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:41587473 original size:6 final size:6
Alignment explanation
Indices: 41587467--41587499 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41587457 AAATGATGAT
*
41587467 GAAGAT GAAGAC GAAGAC GAAGAC GAAGAC GAA
1 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAA
41587500 AGGAACTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.33, T:0.03
Consensus pattern (6 bp):
GAAGAC
Found at i:41588283 original size:30 final size:30
Alignment explanation
Indices: 41588227--41588283 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
41588217 TTAAGCTCGC
* **
41588227 TTATATTATTTTTATTTTTTAAAATTTATA
1 TTATATTATTTTTAGTAATTAAAATTTATA
41588257 TTATATTA-TTTTAGTAATTAATAATTT
1 TTATATTATTTTTAGTAATTAA-AATTT
41588284 TATGCAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTATATTATTTTTAGTAATTAAAATTTATA
Found at i:41593491 original size:5 final size:5
Alignment explanation
Indices: 41593481--41593518 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
41593471 ATCAGTCCCT
41593481 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
41593519 GGCAGTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:41596627 original size:25 final size:26
Alignment explanation
Indices: 41596599--41596671 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 26
41596589 TATTCAAGCA
* *
41596599 AAATGGATGAAATTTTTAACGGAA-G
1 AAATGGATGGAATTTTTAACGAAAGG
* *
41596624 AAATTGATGGAATTTTTAATAGAAAGTG
1 AAATGGATGGAATTTTTAA-CGAAAG-G
41596652 AAATGGATGGAATTTTTAAC
1 AAATGGATGGAATTTTTAAC
41596672 ATGGAGGAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 17 0.44
26 3 0.08
28 19 0.49
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (26 bp):
AAATGGATGGAATTTTTAACGAAAGG
Found at i:41602285 original size:43 final size:43
Alignment explanation
Indices: 41602193--41602288 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
41602183 GTTTATTTGA
*
41602193 AAAAACGCCACTAAAGATCATGACCTTTAGCGGCGCTTTTTCC
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCC
* *
41602236 ACAAACGCCGCTAAAGATTATGACCTTTAGCGGCGC-TTTTCTC
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTC-C
41602279 AAAAACGCCG
1 AAAAACGCCG
41602289 TCATGAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 5 0.10
43 43 0.90
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCC
Found at i:41607400 original size:16 final size:16
Alignment explanation
Indices: 41607379--41607446 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
41607369 TTTGGTTCGC
41607379 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41607395 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
41607411 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
*
41607427 TGTATTGGAATAGAGG
1 TGTATTGGATTAGAGG
41607443 TGTA
1 TGTA
41607447 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41607486 original size:45 final size:41
Alignment explanation
Indices: 41607427--41607536 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
41607417 GGATTAGAGG
*
41607427 TGTATTGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGG-T
* * ***
41607469 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
41607512 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
41607537 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGT
Found at i:41607699 original size:16 final size:16
Alignment explanation
Indices: 41607662--41607703 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41607652 TTAATCATAT
*
41607662 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41607678 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41607693 TTAAAATATAT
1 TTAAAATATAT
41607704 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Done.