Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 138 of 438
Found at i:41124512 original size:40 final size:40
Alignment explanation
Indices: 41124468--41124694 Score: 397
Period size: 40 Copynumber: 5.7 Consensus size: 40
41124458 GCTACTTGCT
41124468 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41124508 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41124548 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
41124588 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41124627 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
41124666 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
41124695 CATCCGAATA
Statistics
Matches: 180, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
38 11 0.06
39 52 0.29
40 116 0.64
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41129344 original size:40 final size:40
Alignment explanation
Indices: 41129288--41129422 Score: 191
Period size: 40 Copynumber: 3.4 Consensus size: 40
41129278 TTCACAAACC
* * * *
41129288 ACTTAACCCGGATATAGCT-ACTTGCTCAAATGCCTTCGGG
1 ACTTAGCCCGGTTATAG-TAACTCGCACAAATGCCTTCGGG
* * *
41129328 ACTTAGCCCAGTTATAGTAACTCGCACAAGTGCCTTTGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
41129368 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
1 ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
41129408 ACTTAGCCCGGTTAT
1 ACTTAGCCCGGTTAT
41129423 CATCCGAATA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 83 0.99
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
ACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGG
Found at i:41134682 original size:29 final size:29
Alignment explanation
Indices: 41134645--41134719 Score: 150
Period size: 29 Copynumber: 2.6 Consensus size: 29
41134635 CTGATATGTG
41134645 ATGTGCGAGTAAGACCATGGCATCGATAT
1 ATGTGCGAGTAAGACCATGGCATCGATAT
41134674 ATGTGCGAGTAAGACCATGGCATCGATAT
1 ATGTGCGAGTAAGACCATGGCATCGATAT
41134703 ATGTGCGAGTAAGACCA
1 ATGTGCGAGTAAGACCA
41134720 CGTTTTATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (29 bp):
ATGTGCGAGTAAGACCATGGCATCGATAT
Found at i:41138829 original size:50 final size:50
Alignment explanation
Indices: 41138770--41138865 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
41138760 AAGTGCTAAT
41138770 ATTTTGTTATATATGGTATGTCATGTATGCTTTATAAATGGAGTTTGCAA
1 ATTTTGTTATATATGGTATGTCATGTATGCTTTATAAATGGAGTTTGCAA
**
41138820 ATTTTGTTATATATGGTATGTGGTGTATGCTTTATAAATGGAGTTT
1 ATTTTGTTATATATGGTATGTCATGTATGCTTTATAAATGGAGTTT
41138866 TAGCTTTGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (50 bp):
ATTTTGTTATATATGGTATGTCATGTATGCTTTATAAATGGAGTTTGCAA
Found at i:41139501 original size:21 final size:21
Alignment explanation
Indices: 41139475--41139544 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
41139465 ATTTAGAAGT
41139475 TTTAAAAACAAGTTGAAACCA
1 TTTAAAAACAAGTTGAAACCA
* *
41139496 TTTAAAAACAA-TT--CACGA
1 TTTAAAAACAAGTTGAAACCA
*
41139514 -GTAAAAACAAGTTGAAACCA
1 TTTAAAAACAAGTTGAAACCA
*
41139534 TTTAGAAACAA
1 TTTAAAAACAA
41139545 TTCACGAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 9 0.24
18 5 0.13
20 5 0.13
21 19 0.50
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.23
Consensus pattern (21 bp):
TTTAAAAACAAGTTGAAACCA
Found at i:41139519 original size:38 final size:38
Alignment explanation
Indices: 41139477--41139553 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
41139467 TTAGAAGTTT
41139477 TAAAAACAAGTTGAAACCATTTAAAAACAATTCACGAG
1 TAAAAACAAGTTGAAACCATTTAAAAACAATTCACGAG
*
41139515 TAAAAACAAGTTGAAACCATTTAGAAACAATTCACGAG
1 TAAAAACAAGTTGAAACCATTTAAAAACAATTCACGAG
41139553 T
1 T
41139554 TATTGGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.22
Consensus pattern (38 bp):
TAAAAACAAGTTGAAACCATTTAAAAACAATTCACGAG
Found at i:41147358 original size:105 final size:105
Alignment explanation
Indices: 41147223--41147435 Score: 381
Period size: 105 Copynumber: 2.0 Consensus size: 105
41147213 AAAACCCTAC
* *
41147223 ACATCACAGTAGTGACAACTGACAACACAAAACTAAAGAACCAATAACTGCTAGCAGTGAAGTGT
1 ACATCACAGTAGTGACAACTGACAAAACAAAACTAAAGAACCAATAACTGCTAGCAGTAAAGTGT
*
41147288 ATTAACCAAAGTTCATGTGCAGTCTCATTTTCACAGGCAT
66 ATTAACCAAAGTTCACGTGCAGTCTCATTTTCACAGGCAT
*
41147328 ACATCACAGTAGTGACAACTGACAAAACAAAACTAAAGAATCAATAACTGCTAGCAGTAAAGTGT
1 ACATCACAGTAGTGACAACTGACAAAACAAAACTAAAGAACCAATAACTGCTAGCAGTAAAGTGT
*
41147393 ATTAACCACAGTTCACGTGCAGTCTCATTTTCACAGGCAT
66 ATTAACCAAAGTTCACGTGCAGTCTCATTTTCACAGGCAT
41147433 ACA
1 ACA
41147436 CCAATGCATG
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (105 bp):
ACATCACAGTAGTGACAACTGACAAAACAAAACTAAAGAACCAATAACTGCTAGCAGTAAAGTGT
ATTAACCAAAGTTCACGTGCAGTCTCATTTTCACAGGCAT
Found at i:41151048 original size:15 final size:15
Alignment explanation
Indices: 41151028--41151068 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
41151018 TCATCTTCTT
41151028 CTTCTATACAATCTG
1 CTTCTATACAATCTG
41151043 CTTCTATACAATCTG
1 CTTCTATACAATCTG
*
41151058 CTACTATACAA
1 CTTCTATACAA
41151069 CCCAAGGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (15 bp):
CTTCTATACAATCTG
Found at i:41164453 original size:57 final size:57
Alignment explanation
Indices: 41164386--41164500 Score: 221
Period size: 57 Copynumber: 2.0 Consensus size: 57
41164376 ATAAGTGAGA
41164386 AAAAATACATCAACCAGATGAGTTTTACTTTTCAATTTTTATTTTAATAAAAAGAGT
1 AAAAATACATCAACCAGATGAGTTTTACTTTTCAATTTTTATTTTAATAAAAAGAGT
*
41164443 AAAAATACATCAACTAGATGAGTTTTACTTTTCAATTTTTATTTTAATAAAAAGAGT
1 AAAAATACATCAACCAGATGAGTTTTACTTTTCAATTTTTATTTTAATAAAAAGAGT
41164500 A
1 A
41164501 TTGCCAAAAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (57 bp):
AAAAATACATCAACCAGATGAGTTTTACTTTTCAATTTTTATTTTAATAAAAAGAGT
Found at i:41164735 original size:22 final size:22
Alignment explanation
Indices: 41164710--41164754 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41164700 AATGTTAGTG
41164710 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
41164732 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
41164754 T
1 T
41164755 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:41169317 original size:22 final size:22
Alignment explanation
Indices: 41169289--41169333 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41169279 AGGGGGAGTG
41169289 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
41169311 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
41169333 T
1 T
41169334 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:41174726 original size:33 final size:33
Alignment explanation
Indices: 41174681--41174779 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
41174671 TTTCTTCTTG
* *
41174681 ACATTCCTGCTCCTGTCCAGCAACTAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
41174714 ACATTCCAGCTCCTGTCCAGCAACCAGACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
41174747 ACATCCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
41174780 CCACTCAGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.28, C:0.42, G:0.10, T:0.19
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:41180793 original size:46 final size:46
Alignment explanation
Indices: 41180725--41180814 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
41180715 TTTATTGCAA
* *
41180725 TAAGAGTTTTAGTTTTATTTATTTTCTTTATTATATCAGGTTTTAT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTTAT
*
41180771 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTT
41180815 TATTTCCTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (46 bp):
TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTTTTAT
Found at i:41182238 original size:46 final size:46
Alignment explanation
Indices: 41182170--41182259 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
41182160 TTTATTGCAA
* *
41182170 TAAGAGTTTTAGTTTTATTTATTTTCTTTATTATATTAGGTTTTAT
1 TAAGAGTTTTAATTTTACTTATTTTCTTTATTATATTAGGTTTTAT
41182216 TAAGAGTTTTAATTTTACTTATTTTCTTTATTATATTAGGTTTT
1 TAAGAGTTTTAATTTTACTTATTTTCTTTATTATATTAGGTTTT
41182260 TATTTCCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.03, G:0.10, T:0.62
Consensus pattern (46 bp):
TAAGAGTTTTAATTTTACTTATTTTCTTTATTATATTAGGTTTTAT
Found at i:41192862 original size:31 final size:31
Alignment explanation
Indices: 41192824--41192890 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
41192814 TACATTAGTA
41192824 GTCACCTAACTATT-AGTAAA-TTTCTTTTCTG
1 GTCACCTAACTATTCA--AAATTTTCTTTTCTG
*
41192855 GTCACCTAACTATTCAAAATTTTCTTTTTTG
1 GTCACCTAACTATTCAAAATTTTCTTTTCTG
41192886 GTCAC
1 GTCAC
41192891 TGGTTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 3 0.09
31 29 0.88
32 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45
Consensus pattern (31 bp):
GTCACCTAACTATTCAAAATTTTCTTTTCTG
Found at i:41201160 original size:19 final size:19
Alignment explanation
Indices: 41201136--41201206 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 19
41201126 ACTACCTACC
41201136 AGAAAGAGAAAGAAAAAAA
1 AGAAAGAGAAAGAAAAAAA
*
41201155 AGAAAG-GCGAAG-AAAAAA
1 AGAAAGAG-AAAGAAAAAAA
41201173 AG-AAGA-AGAAGAAAAAAA
1 AGAAAGAGA-AAGAAAAAAA
41201191 AGAAAGAAGAAA-AAAA
1 AGAAAG-AGAAAGAAAA
41201207 GGTAATGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
17 6 0.14
18 17 0.40
19 16 0.37
20 3 0.07
21 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.23, T:0.00
Consensus pattern (19 bp):
AGAAAGAGAAAGAAAAAAA
Found at i:41202366 original size:13 final size:15
Alignment explanation
Indices: 41202355--41202384 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41202345 TGTATTTTTT
41202355 TAATGTAATTTTTATA
1 TAATGTAA-TTTTATA
41202371 TAATGTAATTTTAT
1 TAATGTAATTTTAT
41202385 TTGATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TAATGTAATTTTATA
Found at i:41220756 original size:46 final size:46
Alignment explanation
Indices: 41220600--41220863 Score: 193
Period size: 46 Copynumber: 5.7 Consensus size: 46
41220590 ATATATTGCC
* * *
41220600 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-TACGCATGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTATG-A--CT
* * * * *
41220650 GATGCATGTCCCAGACATGTCTTACACTAGC-A-CA-ACTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCATAGTATGA-CT
* *
41220694 GATGCATGTCCTAGACACGTCTTACACTGGCTATCATAGTATGACT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCATAGTATGACT
* * *
41220740 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTC-TAG-ATG-CC
1 GATGCATGTCCCAGACATGTCTTACACT-G-GCT-ATCATAGTATGACT
* * * * * *
41220786 GGTGCCATGT-CCAGATATGGTCTTACATTGGCTATCATAATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTATGACT
*
41220833 GAAGCATGTCCCAGACATGTCTTACACTGGC
1 GATGCATGTCCCAGACATGTCTTACACTGGC
41220864 GCACAAATCA
Statistics
Matches: 170, Mismatches: 31, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
44 32 0.19
45 7 0.04
46 63 0.37
47 32 0.19
48 17 0.10
49 15 0.09
50 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTATCATAGTATGACT
Found at i:41220842 original size:93 final size:92
Alignment explanation
Indices: 41220596--41220860 Score: 306
Period size: 93 Copynumber: 2.9 Consensus size: 92
41220586 TTGGATATAT
* * *
41220596 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATACGCAT-GCTGATGCATGTC
1 TGCCGATGCCATGT-CCAGACATGGTCTTACACTGGCTATCATA-ATG--TGGCTGATGCATGTC
*
41220660 CCAGACATGTCTTACACTAGCACAACTCTTA
62 CCAGACATGTCTTACACTAGCACAACTCTGA
* * * *
41220691 -GCCGATG-CATGTCCTAGACA-CGTCTTACACTGGCTATCATAGTATGACTGATGCATGTCCCA
1 TGCCGATGCCATGTCC-AGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCA
**
41220753 GACATGTCTTACACTAGC-CCTCGTCTAGA
65 GACATGTCTTACACTAGCACAAC-TCT-GA
* * * *
41220782 TGCCGGTGCCATGTCCAGATATGGTCTTACATTGGCTATCATAATGTGGCTGAAGCATGTCCCAG
1 TGCCGATGCCATGTCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAG
41220847 ACATGTCTTACACT
66 ACATGTCTTACACT
41220861 GGCGCACAAA
Statistics
Matches: 145, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
89 3 0.02
90 36 0.25
91 1 0.01
92 31 0.21
93 67 0.46
94 7 0.05
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (92 bp):
TGCCGATGCCATGTCCAGACATGGTCTTACACTGGCTATCATAATGTGGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCACAACTCTGA
Found at i:41221234 original size:30 final size:30
Alignment explanation
Indices: 41221193--41221250 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
41221183 AAATTTACAT
* *
41221193 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
41221223 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
41221251 TGCCCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:41223492 original size:37 final size:37
Alignment explanation
Indices: 41223442--41223528 Score: 156
Period size: 37 Copynumber: 2.3 Consensus size: 37
41223432 TGCGAAGTCT
41223442 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
*
41223479 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCT
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
41223516 TACCCGGAACATA
1 TACCCGG-ACATA
41223529 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 43 0.90
38 5 0.10
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (37 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTCG
Found at i:41223667 original size:49 final size:49
Alignment explanation
Indices: 41223597--41223752 Score: 276
Period size: 49 Copynumber: 3.2 Consensus size: 49
41223587 TTTGCCACAT
* * *
41223597 ATATATATACACTTTCGCATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
41223646 ATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
41223695 ACATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
41223744 ATATATACA
1 ATATATACA
41223753 TCTCATACAT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 102 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (49 bp):
ATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:41226894 original size:24 final size:23
Alignment explanation
Indices: 41226867--41226915 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
41226857 TTATTTCCAT
41226867 TCTGCTAAATTTTGTGTCTGTTGC
1 TCTGCTAAATTTTGTGTCTG-TGC
41226891 TCTGCTAAATTTTGTGTCTGTGC
1 TCTGCTAAATTTTGTGTCTGTGC
41226914 TC
1 TC
41226916 ATTTGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.49
Consensus pattern (23 bp):
TCTGCTAAATTTTGTGTCTGTGC
Found at i:41227022 original size:27 final size:27
Alignment explanation
Indices: 41226992--41227085 Score: 107
Period size: 27 Copynumber: 3.5 Consensus size: 27
41226982 TGCGCCTTTG
* * *
41226992 AGATAGGCACAACTAGTTGCACCTGTC
1 AGATAGGCTCAACTAGTCGCACCTCTC
* *
41227019 AGATAGGTTCAACTAGTCGCACCTCTG
1 AGATAGGCTCAACTAGTCGCACCTCTC
* ** *
41227046 AGAAAGGCTCAACTAGTCGTGCCTCTG
1 AGATAGGCTCAACTAGTCGCACCTCTC
41227073 AGATAGGCTCAAC
1 AGATAGGCTCAAC
41227086 CTGTATTCGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (27 bp):
AGATAGGCTCAACTAGTCGCACCTCTC
Found at i:41228259 original size:24 final size:24
Alignment explanation
Indices: 41228206--41228267 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
41228196 TTTGGAATCC
*
41228206 AAAGCT-AAATGT-AAAATTATCG
1 AAAGCTAAAATCTAAAAATTATCG
*
41228228 AAAGCTAAAATCTAAAAATTATTG
1 AAAGCTAAAATCTAAAAATTATCG
* * *
41228252 ATATCTAAATTCTAAA
1 AAAGCTAAAATCTAAA
41228268 TAAAAACTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 6 0.18
23 5 0.15
24 22 0.67
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.31
Consensus pattern (24 bp):
AAAGCTAAAATCTAAAAATTATCG
Found at i:41232461 original size:42 final size:42
Alignment explanation
Indices: 41232414--41232564 Score: 185
Period size: 42 Copynumber: 3.6 Consensus size: 42
41232404 TAAGTCTATG
* * *
41232414 TGTAAGACCATATCTGGGATATGACAACAATATGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
* * *
41232456 TGTAAGACCATAACTGGGATATGGCATCGATGTGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
* * ** * *
41232498 TGTAAGACCATAGCTGGGTTATTGGCATCGATACAATATTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTCA
41232541 TGTAAGACCATATCTGGGATATGG
1 TGTAAGACCATATCTGGGATATGG
41232565 TATTGGTATG
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
42 58 0.63
43 34 0.37
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
Found at i:41236955 original size:40 final size:40
Alignment explanation
Indices: 41236910--41237077 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41236900 CGGAATATAA
41236910 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41236950 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41236990 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
41237030 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41237070 CCGGATAT
1 CCGGATAT
41237078 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41242134 original size:46 final size:48
Alignment explanation
Indices: 41242063--41242186 Score: 152
Period size: 46 Copynumber: 2.7 Consensus size: 48
41242053 TATGTATGCT
*
41242063 AGTGTAAGACATGTCTGGGAAATGCATAGGCCACATT-ATGA-GA-A-CC
1 AGTGTAAGACATGTCTGGGACATGCATAGGCC-CATTGA-GACGAGAGCC
*
41242109 AGTGTAAGACATGTCTGGGACATGCATCGG--CATTGAGACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATAGGCCCATTGAGACGAGAGCC
* *
41242155 AGTGTAAAACATGTCTGGGACATGCATTGGCC
1 AGTGTAAGACATGTCTGGGACATGCATAGGCC
41242187 TCGAGATATG
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
43 6 0.09
44 3 0.04
45 1 0.01
46 58 0.85
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATAGGCCCATTGAGACGAGAGCC
Found at i:41242258 original size:49 final size:49
Alignment explanation
Indices: 41242151--41242281 Score: 174
Period size: 49 Copynumber: 2.7 Consensus size: 49
41242141 TTGAGACGAG
*
41242151 AGCCAGTGTAAAACATGTCTGGGACAT-GCATTGGCCTCGAGATATGCA
1 AGCCAGTGTAAAACCTGTCTGGGACATGGCATTGGCCTCGAGATATGCA
* * * * *
41242199 AGCCAATGTAAAACCTATCTAGGACATGGCATTGGCCTCGATATATGGA
1 AGCCAGTGTAAAACCTGTCTGGGACATGGCATTGGCCTCGAGATATGCA
* * *
41242248 AGTCAGTGTAAGACCTGTTTGGGACATGGCATTG
1 AGCCAGTGTAAAACCTGTCTGGGACATGGCATTG
41242282 TGTAAGACCT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
48 23 0.33
49 47 0.67
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (49 bp):
AGCCAGTGTAAAACCTGTCTGGGACATGGCATTGGCCTCGAGATATGCA
Found at i:41242293 original size:28 final size:28
Alignment explanation
Indices: 41242253--41242306 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
41242243 ATGGAAGTCA
*
41242253 GTGTAAGACCTGTTTGGGACATGGCATT
1 GTGTAAGACCTGTTTGGAACATGGCATT
41242281 GTGTAAGACCTGTTTGGAACATGGCA
1 GTGTAAGACCTGTTTGGAACATGGCA
41242307 ATGACTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (28 bp):
GTGTAAGACCTGTTTGGAACATGGCATT
Found at i:41246658 original size:40 final size:40
Alignment explanation
Indices: 41246599--41246767 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
41246589 CGGGACTTTA
* * *
41246599 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
41246639 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
41246679 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
41246719 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
41246759 CCCGGATAT
1 CCCGGATAT
41246768 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:41254689 original size:40 final size:40
Alignment explanation
Indices: 41254630--41254798 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
41254620 CGGGACTTTA
* * *
41254630 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
41254670 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
41254710 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
41254750 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
41254790 CCCGGATAT
1 CCCGGATAT
41254799 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:41259676 original size:79 final size:79
Alignment explanation
Indices: 41259528--41259764 Score: 383
Period size: 79 Copynumber: 3.0 Consensus size: 79
41259518 GATGATAATG
41259528 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATTCCGGGCTAAGTCCCGAAGGCATTTGTG
41259593 CGAGTTACTA-ATTCC
65 CGAGTTACTATA-TCC
41259608 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTCCGGGCTAAGTCCCGAAGGCATTTGTGC
41259673 GAGTTACTATATCC
66 GAGTTACTATATCC
** *
41259687 GGGCTAAGTCCCGAAGGCA-TTGTGCGAACTACTATATCC-GGCTAAGTCCCGAAGGCATTTGAG
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-TCCGGGCTAAGTCCCGAAGGCATTTGTG
41259750 CGAG-TAGCTATATCC
65 CGAGTTA-CTATATCC
41259765 AGTTAAATCC
Statistics
Matches: 151, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
77 2 0.01
78 49 0.32
79 65 0.43
80 35 0.23
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (79 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTCCGGGCTAAGTCCCGAAGGCATTTGTGC
GAGTTACTATATCC
Found at i:41259780 original size:39 final size:40
Alignment explanation
Indices: 41259528--41259764 Score: 378
Period size: 40 Copynumber: 6.0 Consensus size: 40
41259518 GATGATAATG
41259528 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
41259568 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
41259608 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-TCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
41259647 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
**
41259687 GGGCTAAGTCCCGAAGGCA-TTGTGCGAACTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
41259726 -GGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
41259765 AGTTAAATCC
Statistics
Matches: 189, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
38 20 0.11
39 72 0.38
40 97 0.51
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:41265642 original size:39 final size:39
Alignment explanation
Indices: 41265595--41265777 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
41265585 AATGTTCGAG
41265595 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
*
41265634 TGATATCCGGGCTAAGCCCGAAGGCAATTGGGCGAGTTA
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* * *
41265673 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
* ** *
41265712 TGATATCCGGGTTAAGTCCCGAAGGCCTTTGTGCGGGTTA
1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA
** * *
41265752 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
41265778 GTTTGAACGA
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23
Consensus pattern (39 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA
Found at i:41270722 original size:40 final size:40
Alignment explanation
Indices: 41270667--41270882 Score: 332
Period size: 40 Copynumber: 5.5 Consensus size: 40
41270657 CGGATGATAA
41270667 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
41270707 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
41270746 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
**
41270786 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
41270826 CGGCCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
41270866 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
41270883 TACTTGGTTT
Statistics
Matches: 165, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 54 0.33
40 111 0.67
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:41270798 original size:79 final size:80
Alignment explanation
Indices: 41270667--41270882 Score: 332
Period size: 79 Copynumber: 2.7 Consensus size: 80
41270657 CGGATGATAA
41270667 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTG
**
41270731 TGCGAGTTACTAT-TC
65 TGCGAACTACTATATC
41270746 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
41270811 GCGAACTACTATATC
66 GCGAACTACTATATC
* * * *
41270826 CGGCCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
41270883 TACTTGGTTT
Statistics
Matches: 128, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
79 89 0.70
80 39 0.30
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAACTACTATATC
Found at i:41270878 original size:119 final size:119
Alignment explanation
Indices: 41270667--41270882 Score: 330
Period size: 119 Copynumber: 1.8 Consensus size: 119
41270657 CGGATGATAA
** * *
41270667 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAATTCCGGCCTAAGTCCCGAAGGCATTTGA
*
41270732 GCGAGTTACTATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
66 GCGAGTTACTATTCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATATC
41270786 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACT-ATATCCGGCCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAAT-TCCGGCCTAAGTCCCGAAGGCATTTG
*
41270850 AGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
65 AGCGAGTTA-CTAT-TCCGGGCTAAATCCCGAAGG
41270883 TACTTGGTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
118 4 0.05
119 81 0.92
120 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (119 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTAATTCCGGCCTAAGTCCCGAAGGCATTTGA
GCGAGTTACTATTCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:41272394 original size:15 final size:16
Alignment explanation
Indices: 41272367--41272396 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41272357 GATAAACCTC
41272367 AGTAAGATTATGATTG
1 AGTAAGATTATGATTG
41272383 AGTAAG-TTATGATT
1 AGTAAGATTATGATT
41272397 ATAAGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (16 bp):
AGTAAGATTATGATTG
Found at i:41278078 original size:59 final size:58
Alignment explanation
Indices: 41277962--41278085 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 58
41277952 TAAATACTAT
* * * *
41277962 TAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTGTATTTAA
1 TAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
* * *
41278020 TAATAATTATGTTAA-AATATGATTAAATTATTTTTTTATTTTTATTAAAATATATTTAA
1 TAATAATTATATTAAGAATATGATTAAATTA-TATATTA-TTTTATTAAAATATATTTAA
*
41278079 CAATAAT
1 TAATAAT
41278086 CTTATTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 13 0.23
58 19 0.34
59 24 0.43
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (58 bp):
TAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
Found at i:41278238 original size:44 final size:45
Alignment explanation
Indices: 41278183--41278275 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 45
41278173 TACAATATTT
41278183 ATTCCATTCAACCAAATACAA-GAA-TACT-ATTACAACTCTATTCC
1 ATTCCATTCAACC-AA-ACAATGAATTACTGATTACAACTCTATTCC
*
41278227 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACAA-TGAATTACTGATTACAACTCTATTCC
41278273 ATT
1 ATT
41278276 ACAATCCTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 4 0.09
43 2 0.05
44 16 0.36
45 4 0.09
46 18 0.41
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (45 bp):
ATTCCATTCAACCAAACAATGAATTACTGATTACAACTCTATTCC
Found at i:41278278 original size:16 final size:15
Alignment explanation
Indices: 41278257--41278308 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
41278247 TGAATTACTG
41278257 ATTACAGCTCTATTCC
1 ATTACA-CTCTATTCC
* *
41278273 ATTACAATCCTATTCA
1 ATTACACT-CTATTCC
*
41278289 ATTACAACCCTATTCC
1 ATTAC-ACTCTATTCC
41278305 ATTA
1 ATTA
41278309 TAGTGAACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTACACTCTATTCC
Found at i:41280994 original size:46 final size:47
Alignment explanation
Indices: 41280907--41281267 Score: 307
Period size: 46 Copynumber: 7.7 Consensus size: 47
41280897 TTTGTGTGCC
* *
41280907 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGA-TGCT
* *
41280955 AGTGTAAGA-CATGTCCGGGACAT-GCATCGGCCTCGAGATGTAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATG-ATGCT
** *
41281001 AGTGTAAGA-CATGTCTGGGACAT-GCATC-AACTACGAGA-CATG-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGATGCT
* * * * * *
41281044 CAGTGGAAGACCATGTCTGGGACATGGCATTGACATGGATACGCAAGA-GCT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG--A-G-ATGATGCT
* * * *
41281095 AGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATAATGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGAT-GCT
* *
41281144 AGTGTAAGA-CATGTCTGGGACAT--CATCGG-CTAAGAGTTG-TGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGATGCT
* *
41281187 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATGAGGATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGAT-GCT
* *
41281236 ACTGTAAGACCATGTCTGGGACATGCCATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
41281268 TAACTTAACC
Statistics
Matches: 253, Mismatches: 38, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
43 12 0.05
44 25 0.10
45 20 0.08
46 70 0.28
47 23 0.09
48 25 0.10
49 44 0.17
50 32 0.13
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGATGCT
Found at i:41281203 original size:142 final size:138
Alignment explanation
Indices: 41280901--41281217 Score: 381
Period size: 142 Copynumber: 2.3 Consensus size: 138
41280891 GGGTGATTTG
* * * *
41280901 TGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGTGCTAGTGTAAGACA
1 TGTG-CAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGAGACGAGAGCTAGTGTAAGACA
* * *
41280966 TGTCCGGGACATGCATCGGCCTCGAGATGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCAA
65 TGTCCGGGACATGCATCAGCCTCGAAATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAA
41281031 CTACGAGACA
130 CTAC-AGACA
* * *
41281041 TGT-CAGTGGAAGACCATGTCTGGGACATGGCATTGACATGGATACGCAAGAGCTAGTGTAAGAC
1 TGTGCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGAGACG--AGAGCTAGTGTAAGA-
**
41281105 CATGTTTGGGACATGGCATCAGCCTCGATAATG-ATAGCCAGTGTAAGACATGTCTGGGACAT-C
63 CATGTCCGGGACAT-GCATCAGCCTCGA-AATGTA-AGCCAGTGTAAGACATGTCTGGGACATGC
** **
41281168 ATCGGCTA-AGAGT
125 ATCAACTACAGACA
41281181 TGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 TGTGC-AGTGTAAGACCATGTCTGGGACATGGCATCG
41281218 GCCTCGATGA
Statistics
Matches: 151, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
138 37 0.25
140 23 0.15
141 13 0.09
142 49 0.32
143 29 0.19
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (138 bp):
TGTGCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGAGACGAGAGCTAGTGTAAGACAT
GTCCGGGACATGCATCAGCCTCGAAATGTAAGCCAGTGTAAGACATGTCTGGGACATGCATCAAC
TACAGACA
Found at i:41298772 original size:25 final size:25
Alignment explanation
Indices: 41298738--41298790 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
41298728 AATTTTCCAT
41298738 TAATGAATCATCCAAAAATATCTAC
1 TAATGAATCATCCAAAAATATCTAC
41298763 TAATGAATCATCCAAAAATATCTAC
1 TAATGAATCATCCAAAAATATCTAC
41298788 TAA
1 TAA
41298791 CTTTTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (25 bp):
TAATGAATCATCCAAAAATATCTAC
Found at i:41306496 original size:24 final size:24
Alignment explanation
Indices: 41306464--41306550 Score: 165
Period size: 24 Copynumber: 3.6 Consensus size: 24
41306454 AATCTCAAAT
41306464 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
41306488 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
41306512 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
41306536 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
41306551 ACATAATAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:41306516 original size:48 final size:48
Alignment explanation
Indices: 41306464--41306572 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
41306454 AATCTCAAAT
** *
41306464 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATA-A
41306512 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
41306560 GCACTATGTGTGC
1 GCACTATGTGTGC
41306573 AACGTTTGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 52 0.91
49 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
Found at i:41306563 original size:24 final size:24
Alignment explanation
Indices: 41306464--41306572 Score: 157
Period size: 24 Copynumber: 4.5 Consensus size: 24
41306454 AATCTCAAAT
*
41306464 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
41306488 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATA
*
41306512 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
** *
41306536 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCG-ATTTACTATA
41306560 GCACTATGTGTGC
1 GCACTATGTGTGC
41306573 AACGTTTGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
24 73 0.94
25 5 0.06
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATA
Found at i:41314369 original size:24 final size:24
Alignment explanation
Indices: 41314337--41314423 Score: 165
Period size: 24 Copynumber: 3.6 Consensus size: 24
41314327 AATCTCAAAT
41314337 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
*
41314361 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATG
41314385 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
41314409 GCACTATGTGTGCGA
1 GCACTATGTGTGCGA
41314424 ACATAATAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:41314389 original size:48 final size:48
Alignment explanation
Indices: 41314337--41314445 Score: 175
Period size: 48 Copynumber: 2.3 Consensus size: 48
41314327 AATCTCAAAT
** *
41314337 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCG-ATTTACTATA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATA-A
41314385 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
1 GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
41314433 GCACTATGTGTGC
1 GCACTATGTGTGC
41314446 AACGTTTGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 52 0.91
49 5 0.09
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (48 bp):
GCACTATGTGTGCGATTTACTATGGCACTATGTGTGCGAACATAATAA
Found at i:41314436 original size:24 final size:24
Alignment explanation
Indices: 41314337--41314445 Score: 157
Period size: 24 Copynumber: 4.5 Consensus size: 24
41314327 AATCTCAAAT
*
41314337 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
41314361 GCACTATGTGTGCGATTTACTATA
1 GCACTATGTGTGCGATTTACTATA
*
41314385 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATA
** *
41314409 GCACTATGTGTGCGAACATAATA-A
1 GCACTATGTGTGCG-ATTTACTATA
41314433 GCACTATGTGTGC
1 GCACTATGTGTGC
41314446 AACGTTTGGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
24 73 0.94
25 5 0.06
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATA
Found at i:41316011 original size:15 final size:15
Alignment explanation
Indices: 41315991--41316022 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41315981 CATTTCACTA
*
41315991 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
41316006 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
41316021 TT
1 TT
41316023 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:41318262 original size:43 final size:43
Alignment explanation
Indices: 41318214--41318372 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
41318204 AAGCTCTACA
* *
41318214 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
* * * *
41318257 ATGCC-ACTGTCCCAAACAG-GATCTTACGTGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
* ** *
41318299 ATGCCAACGTCCCAGATGTGGTCTTACACATAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGT-AATCA-AATATCG
*
41318343 ATGCCAACATCCCAGACGTGGTCTTACATG
1 ATGCCAACGTCCCAGACGTGGTCTTACATG
41318373 ATAACACATA
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
41 1 0.01
42 21 0.23
43 39 0.43
44 30 0.33
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
Found at i:41323838 original size:40 final size:40
Alignment explanation
Indices: 41323793--41323959 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41323783 CGGAATATAA
41323793 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41323833 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
41323873 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41323913 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41323952 CCGGATAT
1 CCGGATAT
41323960 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41323943 original size:80 final size:79
Alignment explanation
Indices: 41323793--41323959 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
41323783 CGGAATATAA
* *
41323793 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
41323858 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
41323873 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
41323935 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
41323952 CCGGATAT
1 CCGGATAT
41323960 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:41324805 original size:17 final size:19
Alignment explanation
Indices: 41324782--41324827 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41324772 AAGAAGCATG
41324782 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41324800 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41324818 AATCATGCTC
1 AATCATGCTC
41324828 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41331840 original size:40 final size:40
Alignment explanation
Indices: 41331795--41331961 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41331785 CGGAATATAA
41331795 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41331835 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
41331875 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
41331915 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41331954 CCGGATAT
1 CCGGATAT
41331962 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41331945 original size:80 final size:79
Alignment explanation
Indices: 41331795--41331961 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
41331785 CGGAATATAA
* *
41331795 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
41331860 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
41331875 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
41331937 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
41331954 CCGGATAT
1 CCGGATAT
41331962 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:41332805 original size:17 final size:19
Alignment explanation
Indices: 41332782--41332827 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
41332772 AAGAAGCATG
41332782 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
41332800 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
41332818 AATCATGCTC
1 AATCATGCTC
41332828 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:41341006 original size:27 final size:27
Alignment explanation
Indices: 41340932--41340998 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
41340922 AAGAAAATAA
* * *
41340932 AAGCCTTTGTGGCAATATATTAAATTG
1 AAGCCTTCGTGGCAATATATGAAATGG
*
41340959 AAGCCCTT-GTGGCAATTTATGAAATGG
1 AAG-CCTTCGTGGCAATATATGAAATGG
41340986 AAGCCTTCGTGGC
1 AAGCCTTCGTGGC
41340999 GATCTATGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.11
27 27 0.77
28 4 0.11
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (27 bp):
AAGCCTTCGTGGCAATATATGAAATGG
Found at i:41341014 original size:27 final size:27
Alignment explanation
Indices: 41340932--41341023 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
41340922 AAGAAAATAA
* * * *
41340932 AAGCCTTTGTGGCAATATATTAAATTG
1 AAGCCTTCGTGGCAATCTATGAAATGG
*
41340959 AAGCCCTT-GTGGCAATTTATGAAATGG
1 AAG-CCTTCGTGGCAATCTATGAAATGG
*
41340986 AAGCCTTCGTGGCGATCTATGGAAA-GG
1 AAGCCTTCGTGGCAATCTAT-GAAATGG
*
41341013 AATGTCTTCGT
1 AA-GCCTTCGT
41341024 AGTGCATTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
26 4 0.07
27 36 0.65
28 15 0.27
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (27 bp):
AAGCCTTCGTGGCAATCTATGAAATGG
Found at i:41343789 original size:27 final size:27
Alignment explanation
Indices: 41343759--41343814 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
41343749 TCCTCTAGTG
* * * *
41343759 ATCCCTGTTTTGCCAAACCTGCTGGCA
1 ATCCCTGCTTCGCCAAACCCGCTAGCA
41343786 ATCCCTGCTTCGCCAAACCCGCTAGCA
1 ATCCCTGCTTCGCCAAACCCGCTAGCA
41343813 AT
1 AT
41343815 TATAGTTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (27 bp):
ATCCCTGCTTCGCCAAACCCGCTAGCA
Found at i:41344080 original size:55 final size:53
Alignment explanation
Indices: 41343977--41344107 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 53
41343967 ATCAAAACTG
* * * *
41343977 AAATGAAATTGGACCTCACAACTGCACCTTTACAATAAAATGTGACATAAATGAA
1 AAATGAAATTGGACCTCATAACTG-ACCTTTAAAACAAAATGTAACATAAAT-AA
* * *
41344032 TAATGAAATTGGACCTCATAA-TTAGCCTTCTAAAACAAAGTGTAACATAAATAA
1 AAATGAAATTGGACCTCATAACTGA-CCTT-TAAAACAAAATGTAACATAAATAA
* *
41344086 AAATGAAATCGAACCTCATAAC
1 AAATGAAATTGGACCTCATAAC
41344108 CAAGCTACTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
53 1 0.02
54 25 0.40
55 37 0.59
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (53 bp):
AAATGAAATTGGACCTCATAACTGACCTTTAAAACAAAATGTAACATAAATAA
Found at i:41344195 original size:59 final size:56
Alignment explanation
Indices: 41344124--41344299 Score: 155
Period size: 59 Copynumber: 3.1 Consensus size: 56
41344114 ACTTAAATAG
*
41344124 AATGCAATATAAATGAAAATGAAAAGAAATTGGACCTTAATACTAGGCCTCCAAAACAA
1 AATGCAACATAAATGAAAATGAAAAGAAA-T-GACC-TAATACTAGGCCTCCAAAACAA
* * * *
41344183 AATGCAACATAAATGAAAATGAAATCGAACATCA-C-AAT--TAGGCCTCTAAAACAT
1 AATGCAACATAAATGAAAATGAAA-AGAA-ATGACCTAATACTAGGCCTCCAAAACAA
* * * *
41344237 AATGCCACATAAATGAAAATGAAATGAAACTAGACCTCACA-ACTAAGCCTCCAAAACAG
1 AATGCAACATAAATGAAAATGAAAAGAAA-T-GACCT-A-ATACTAGGCCTCCAAAACAA
41344296 AATG
1 AATG
41344300 TGATTAAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 20
0.76 0.09 0.16
Matches are distributed among these distances:
52 1 0.01
53 4 0.04
54 38 0.40
55 1 0.01
56 3 0.03
57 1 0.01
58 2 0.02
59 41 0.43
60 4 0.04
61 1 0.01
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (56 bp):
AATGCAACATAAATGAAAATGAAAAGAAATGACCTAATACTAGGCCTCCAAAACAA
Found at i:41344234 original size:54 final size:54
Alignment explanation
Indices: 41344021--41344261 Score: 175
Period size: 54 Copynumber: 4.4 Consensus size: 54
41344011 ATAAAATGTG
* * * * * *
41344021 ACATAAATGAATAATGAAATTGGACCTCATAATTA-GCCTTCTAAAACAAAGTGTA
1 ACATAAATGAA-AATGAAATCGAACATCACAATTAGGCC-TCTAAAACAAAATGCA
* * * ** * * * *
41344076 ACATAAATAAAAATGAAATCGAACCTCATAACCAAG-CTACTTAAATAGAATGCA
1 ACATAAATGAAAATGAAATCGAACATCACAATTAGGCCT-CTAAAACAAAATGCA
* * * *
41344130 ATATAAATGAAAATGAAA-AGAA-ATTGGACCTTAATACTAGGCCTCCAAAACAAAATGCA
1 ACATAAATGAAAATGAAATCGAACA-T-CA-C--AAT--TAGGCCTCTAAAACAAAATGCA
* *
41344189 ACATAAATGAAAATGAAATCGAACATCACAATTAGGCCTCTAAAACATAATGCC
1 ACATAAATGAAAATGAAATCGAACATCACAATTAGGCCTCTAAAACAAAATGCA
41344243 ACATAAATGAAAATGAAAT
1 ACATAAATGAAAATGAAAT
41344262 GAAACTAGAC
Statistics
Matches: 145, Mismatches: 29, Indels: 25
0.73 0.15 0.13
Matches are distributed among these distances:
53 5 0.03
54 85 0.59
55 11 0.08
56 3 0.02
57 2 0.01
58 1 0.01
59 31 0.21
60 6 0.04
61 1 0.01
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (54 bp):
ACATAAATGAAAATGAAATCGAACATCACAATTAGGCCTCTAAAACAAAATGCA
Found at i:41344241 original size:113 final size:112
Alignment explanation
Indices: 41344025--41344299 Score: 270
Period size: 113 Copynumber: 2.4 Consensus size: 112
41344015 AATGTGACAT
* * *
41344025 AAATGAATAATGAAATTGGACCTCATAAT--TAGCCTTCTAAAACAAAGTGTAACATAAATAAAA
1 AAATGAA-AA-GAAATTGGACCT--TAATACTAGCC-TCCAAAACAAAATGCAACATAAATAAAA
* * * * *
41344088 ATGAAATCGAACCTCATAACCAAGCTACTTAAATAGAATGCAATATAAATGA
61 ATGAAATCGAACATCACAACCAAGCTACTAAAACAGAATGCAACATAAATGA
*
41344140 AAATGAAAAGAAATTGGACCTTAATACTAGGCCTCCAAAACAAAATGCAACATAAATGAAAATGA
1 AAATGAAAAGAAATTGGACCTTAATACTA-GCCTCCAAAACAAAATGCAACATAAATAAAAATGA
** * * *
41344205 AATCGAACATCACAATTAGGCCT-CTAAAACATAATGCCACATAAATGA
65 AATCGAACATCACAACCAAG-CTACTAAAACAGAATGCAACATAAATGA
* * * * *
41344253 AAATGAAATGAAACTAGACCTCACA-ACTAAGCCTCCAAAACAGAATG
1 AAATGAAAAGAAATTGGACCTTA-ATACT-AGCCTCCAAAACAAAATG
41344300 TGATTAAAAT
Statistics
Matches: 135, Mismatches: 19, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
111 4 0.03
113 115 0.85
114 9 0.07
115 7 0.05
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (112 bp):
AAATGAAAAGAAATTGGACCTTAATACTAGCCTCCAAAACAAAATGCAACATAAATAAAAATGAA
ATCGAACATCACAACCAAGCTACTAAAACAGAATGCAACATAAATGA
Found at i:41352565 original size:8 final size:8
Alignment explanation
Indices: 41352549--41352583 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
41352539 TTAAAGCGAT
41352549 AAATG-CG
1 AAATGCCG
*
41352556 AAAGGCCG
1 AAATGCCG
41352564 AAATGCCG
1 AAATGCCG
41352572 AAATGCCG
1 AAATGCCG
41352580 AAAT
1 AAAT
41352584 TCTGGCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.43, C:0.20, G:0.26, T:0.11
Consensus pattern (8 bp):
AAATGCCG
Found at i:41353080 original size:9 final size:9
Alignment explanation
Indices: 41353066--41353122 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
41353056 TTTTATAAAC
41353066 ATGATATGT
1 ATGATATGT
*
41353075 ATGATATGCAC
1 ATGATATG--T
*
41353086 ATGACATGT
1 ATGATATGT
*
41353095 ATGATATGCAC
1 ATGATATG--T
41353106 ATGATATGT
1 ATGATATGT
41353115 ATGATATG
1 ATGATATG
41353123 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:41353089 original size:20 final size:20
Alignment explanation
Indices: 41353064--41353134 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
41353054 ATTTTTATAA
41353064 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41353084 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
41353104 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41353124 ACATGAGATGT
1 ACATGATATGT
41353135 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:41353111 original size:11 final size:11
Alignment explanation
Indices: 41353075--41353129 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
41353065 CATGATATGT
41353075 ATGATATGCAC
1 ATGATATGCAC
* *
41353086 ATGACATG--T
1 ATGATATGCAC
41353095 ATGATATGCAC
1 ATGATATGCAC
*
41353106 ATGATATG--T
1 ATGATATGCAC
41353115 ATGATATGCAC
1 ATGATATGCAC
41353126 ATGA
1 ATGA
41353130 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41353211 original size:23 final size:23
Alignment explanation
Indices: 41353181--41353323 Score: 241
Period size: 23 Copynumber: 6.1 Consensus size: 23
41353171 AGGAAGTGCA
41353181 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
41353204 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
41353228 AAAGGGCTTATGCCCTAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41353251 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41353274 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
41353297 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
41353321 AAA
1 AAA
41353324 AGAGGCTAGG
Statistics
Matches: 113, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
23 70 0.62
24 43 0.38
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:41353248 original size:47 final size:47
Alignment explanation
Indices: 41353179--41353344 Score: 246
Period size: 47 Copynumber: 3.5 Consensus size: 47
41353169 GGAGGAAGTG
41353179 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
*
41353226 CAAAAGGGCTTATGCCCTAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
41353273 -TAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATT-AAAGGGCTTATGCCCCAGTTAT
* *
41353320 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 CAAAAG-GGCTTATGCC-CCAGTTAT
41353345 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
46 22 0.20
47 67 0.61
48 9 0.08
49 11 0.10
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:41353294 original size:70 final size:70
Alignment explanation
Indices: 41353181--41353323 Score: 259
Period size: 70 Copynumber: 2.0 Consensus size: 70
41353171 AGGAAGTGCA
*
41353181 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCTAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
41353246 TTATT
66 TTATT
* *
41353251 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAG
1 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
41353316 TTATT
66 TTATT
41353321 AAA
1 AAA
41353324 AGAGGCTAGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (70 bp):
AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAG
TTATT
Found at i:41360491 original size:9 final size:9
Alignment explanation
Indices: 41360479--41360535 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
41360469 TTTGATAAAC
41360479 ATGATATGT
1 ATGATATGT
*
41360488 ATGATATGCAC
1 ATGATATG--T
*
41360499 ATGACATGT
1 ATGATATGT
*
41360508 ATGATATGCAC
1 ATGATATG--T
41360519 ATGATATGT
1 ATGATATGT
41360528 ATGATATG
1 ATGATATG
41360536 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:41360502 original size:20 final size:20
Alignment explanation
Indices: 41360477--41360547 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
41360467 ATTTTGATAA
41360477 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41360497 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
41360517 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41360537 ACATGAGATGT
1 ACATGATATGT
41360548 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:41360524 original size:11 final size:11
Alignment explanation
Indices: 41360488--41360542 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
41360478 CATGATATGT
41360488 ATGATATGCAC
1 ATGATATGCAC
* *
41360499 ATGACATG--T
1 ATGATATGCAC
41360508 ATGATATGCAC
1 ATGATATGCAC
*
41360519 ATGATATG--T
1 ATGATATGCAC
41360528 ATGATATGCAC
1 ATGATATGCAC
41360539 ATGA
1 ATGA
41360543 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41360624 original size:23 final size:23
Alignment explanation
Indices: 41360594--41360760 Score: 280
Period size: 23 Copynumber: 7.1 Consensus size: 23
41360584 AGGAAGTGCA
41360594 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
41360617 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
41360641 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
41360665 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41360688 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
41360711 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
41360734 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
41360758 AAA
1 AAA
41360761 AGAGGCTAGG
Statistics
Matches: 139, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
23 71 0.51
24 68 0.49
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:41360649 original size:24 final size:23
Alignment explanation
Indices: 41360593--41360782 Score: 274
Period size: 24 Copynumber: 8.0 Consensus size: 23
41360583 GAGGAAGTGC
41360593 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
41360616 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
41360639 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
41360663 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
41360687 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
41360710 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
41360734 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
*
41360758 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
41360782 A
1 A
41360783 TGATAAAGCA
Statistics
Matches: 156, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
23 66 0.42
24 80 0.51
25 10 0.06
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:41360661 original size:47 final size:47
Alignment explanation
Indices: 41360592--41360760 Score: 286
Period size: 47 Copynumber: 3.6 Consensus size: 47
41360582 AGAGGAAGTG
41360592 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
*
41360639 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
*
41360687 -TAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
41360733 TAAAAGGGCTTTTGCCCCAGTTATTAAA
1 CAAAAGGGCTTATGCCCCAGTTATTAAA
41360761 AGAGGCTAGG
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
46 22 0.19
47 71 0.62
48 22 0.19
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:41362849 original size:29 final size:29
Alignment explanation
Indices: 41362816--41362917 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
41362806 TGACGAGATC
41362816 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
41362845 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
41362874 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
41362903 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
41362918 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:41370870 original size:29 final size:29
Alignment explanation
Indices: 41370837--41370938 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
41370827 TGACGAGATC
41370837 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
41370866 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
41370895 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
41370924 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
41370939 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:41377874 original size:20 final size:21
Alignment explanation
Indices: 41377849--41377888 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41377839 CTCTTGAAAT
41377849 AGGGC-ACATGCCCGTGTGGA
1 AGGGCAACATGCCCGTGTGGA
*
41377869 AGGGCAACATGGCCGTGTGG
1 AGGGCAACATGCCCGTGTGG
41377889 TCATTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.23, G:0.42, T:0.15
Consensus pattern (21 bp):
AGGGCAACATGCCCGTGTGGA
Found at i:41381337 original size:27 final size:27
Alignment explanation
Indices: 41381306--41381361 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
41381296 CTTTGTTACC
*
41381306 CAAGTCATGCTGAACCTACACCATGTT
1 CAAGTCATGCCGAACCTACACCATGTT
41381333 CAAGTCATGCCGAACCTACACCATGTT
1 CAAGTCATGCCGAACCTACACCATGTT
41381360 CA
1 CA
41381362 TATTAGCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.23
Consensus pattern (27 bp):
CAAGTCATGCCGAACCTACACCATGTT
Found at i:41382348 original size:10 final size:10
Alignment explanation
Indices: 41382333--41382358 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41382323 TGATCATGAG
41382333 ATTATGGTAA
1 ATTATGGTAA
41382343 ATTATGGTAA
1 ATTATGGTAA
41382353 ATTATG
1 ATTATG
41382359 TTATCTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
ATTATGGTAA
Found at i:41385487 original size:2 final size:2
Alignment explanation
Indices: 41385480--41385508 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41385470 GTGAAATGGA
41385480 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41385509 TTTTGGCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41387660 original size:11 final size:12
Alignment explanation
Indices: 41387639--41387665 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41387629 GAGCTTCCTC
41387639 TTTCTTTTTTTT
1 TTTCTTTTTTTT
41387651 TTTCTTTTTTTT
1 TTTCTTTTTTTT
41387663 TTT
1 TTT
41387666 TGTAAACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:41395176 original size:57 final size:56
Alignment explanation
Indices: 41395055--41395196 Score: 146
Period size: 57 Copynumber: 2.5 Consensus size: 56
41395045 TATTGTTTAA
*
41395055 CAAGATTACCAGTCCAGGCTAAATCCTTTATATAACGTATACTCAGGGAAGCTCAAT
1 CAAGATTACCAGTCCAGGCTAAATCCTTAATATAACGTATACTCAGGGAA-CTCAAT
* * * * * *
41395112 TAGGATTATCAGTCCAGGCTAAA-CCTTAATCATAACGTATGCTCAGAGGTA-TTATAT
1 CAAGATTACCAGTCCAGGCTAAATCCTTAAT-ATAACGTATACTCAG-GGAACTCA-AT
*
41395169 CAAGATTACCCA-TCCGGGCTAAATCCTT
1 CAAGATTA-CCAGTCCAGGCTAAATCCTT
41395197 TTTATAACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
56 8 0.12
57 52 0.75
58 9 0.13
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (56 bp):
CAAGATTACCAGTCCAGGCTAAATCCTTAATATAACGTATACTCAGGGAACTCAAT
Found at i:41400109 original size:26 final size:26
Alignment explanation
Indices: 41400080--41400139 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
41400070 TCCCTTTGAA
* * *
41400080 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
41400106 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
41400134 TCATTC
1 TCATTC
41400140 TCAATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.17
27 2 0.07
28 22 0.76
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:41400125 original size:28 final size:28
Alignment explanation
Indices: 41400094--41400156 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
41400084 TCGATATTTT
41400094 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
41400122 GCACACTAAGTGTCATTCTCAATATTTC
1 GCACACTAAGTGTCATTCTCAATATCTC
*
41400150 GTACACT
1 GCACACT
41400157 GAGTACCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGTCATTCTCAATATCTC
Found at i:41400371 original size:31 final size:32
Alignment explanation
Indices: 41400314--41400377 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
41400304 CTGGCTAAAT
41400314 TGTAGAGATACCAAAGTTCAGGGGCATTTTGG
1 TGTAGAGATACCAAAGTTCAGGGGCATTTTGG
41400346 TGTAGAGATACCAAAGTT-AGGGGCATTTTGG
1 TGTAGAGATACCAAAGTTCAGGGGCATTTTGG
41400377 T
1 T
41400378 AATTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (32 bp):
TGTAGAGATACCAAAGTTCAGGGGCATTTTGG
Found at i:41416127 original size:24 final size:24
Alignment explanation
Indices: 41416100--41416162 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
41416090 CTTATTATGT
41416100 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
41416124 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
41416148 TCGCACACATAGTGC
1 TCGCACACATAGTGC
41416163 ATTTGAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:41424095 original size:146 final size:146
Alignment explanation
Indices: 41423812--41424089 Score: 356
Period size: 146 Copynumber: 1.9 Consensus size: 146
41423802 TAGGGTATAA
* * * *
41423812 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCTATCAAGTCGATGCCATGTCCCA
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACATCTATCAAGTCGATACCATATCCCA
41423877 GACATGGTCTTACACTAACTATCAAAATCGAGGCTGACGCCATGTCCCAGACATGGTCTTACACT
66 GACATGGTCTTACACTAACTATCAAAATCGAGGCTGACGCCATGTCCCAGACATGGTCTTACACT
41423942 AGCTCTCACTTATCCG
131 AGCTCTCACTTATCCG
* * * *
41423958 TGCCGATGCCATGTCCTAGACATGGTCTTACACTGACACCT-TAT-ACGTACCGATACCATATCC
1 TGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACATCTATCAAGT--CGATACCATATCC
* ** *
41424021 CAGACATGGTCTTACACTGAC-A-C-ATCTCGTA-GCTGATG-CATGTCCCAGACAT-GTCTTAC
64 CAGACATGGTCTTACACTAACTATCAAAATCG-AGGCTGACGCCATGTCCCAGACATGGTCTTAC
*
41424080 TCTAGCTCTC
128 ACTAGCTCTC
41424090 GTCTCAATGC
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
141 16 0.14
142 14 0.12
143 10 0.09
144 5 0.04
145 4 0.03
146 67 0.58
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (146 bp):
TGCCGATGCCATGTCCCAAACATGGTCTTACACTGACACATCTATCAAGTCGATACCATATCCCA
GACATGGTCTTACACTAACTATCAAAATCGAGGCTGACGCCATGTCCCAGACATGGTCTTACACT
AGCTCTCACTTATCCG
Found at i:41424142 original size:48 final size:48
Alignment explanation
Indices: 41424083--41424177 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
41424073 GTCTTACTCT
41424083 AGCTCTCGTCTCAATGCCGATGCCATGTACAAGACATGGTATTACACA
1 AGCTCTCGTCTCAATGCCGATGCCATGTACAAGACATGGTATTACACA
* * *
41424131 AGCTCTCGTCTCAATGCCGATGCCATGTCCTAGACATGGTCTTACAC
1 AGCTCTCGTCTCAATGCCGATGCCATGTACAAGACATGGTATTACAC
41424178 TGGCTCTCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (48 bp):
AGCTCTCGTCTCAATGCCGATGCCATGTACAAGACATGGTATTACACA
Found at i:41424184 original size:48 final size:47
Alignment explanation
Indices: 41423810--41424227 Score: 300
Period size: 47 Copynumber: 8.8 Consensus size: 47
41423800 CATAGGGTAT
*
41423810 AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCATCTATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATC
* ** * *
41423858 AA-GTCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCAAAATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--TATC
* * * * *
41423906 GAGGCTGACGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACTTATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--C-TATC
** * * *
41423956 CGTGCCGATGCCATGTCCTAGACATGGTCTTACACTGACAC-CTTAT-
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATC
* * * * * *
41424002 ACGTACCGATACCATATCCCAGACATGGTCTTACACTGACACATC--TC
1 A-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATC
* * * * *
41424049 -GTAGCTGATG-CATGTCCCAGACAT-GTCTTACTCTAGCTCTCGTCTC
1 AAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATC
* * * ** *
41424095 AATGCCGATGCCATGTACAAGACATGGTATTACACAAGCTCTCGTCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATC
*
41424143 AATGCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCTC-ATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATC
* * *
41424189 ATGTGTCCGATG-CAGGTCCTAGACAT-GTCTTACACTGGC
1 A-ATG-CCGATGCCATGTCCCAGACATGGTCTTACACTGGC
41424228 ACACAATTAA
Statistics
Matches: 301, Mismatches: 51, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.01
44 11 0.04
45 15 0.05
46 31 0.10
47 102 0.34
48 69 0.23
49 35 0.12
50 35 0.12
51 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (47 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATC
Found at i:41425356 original size:10 final size:11
Alignment explanation
Indices: 41425341--41425369 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
41425331 GCTATAACAC
41425341 ATAAAATAAT-
1 ATAAAATAATA
41425351 ATAAAATAATA
1 ATAAAATAATA
41425362 ATAAAATA
1 ATAAAATA
41425370 GTTTCTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:41428819 original size:30 final size:29
Alignment explanation
Indices: 41428725--41428826 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
41428715 TATAGTGAAT
* * *
41428725 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
41428754 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
41428782 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
41428812 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
41428827 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:41436662 original size:30 final size:29
Alignment explanation
Indices: 41436568--41436669 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
41436558 TATAGTGAAT
* * *
41436568 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
41436597 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
41436625 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
41436655 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
41436670 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:41439434 original size:42 final size:42
Alignment explanation
Indices: 41439329--41439505 Score: 178
Period size: 43 Copynumber: 4.1 Consensus size: 42
41439319 CAGAGAACAT
* * * *
41439329 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAA
* * *
41439371 ACATCGATGCCACTGTCCCAGACAG-GGTCTTTCACGAAATCAA
1 ATA-CGATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAA
* * * *
41439414 ATACGATGTCAATGTCCCAGACATGGTCTTACACATAAAACAGA
1 ATACGATGCCAATGTCCCAGACGTGGTCTTACAC-GAAATCA-A
* *
41439458 AGT-TGATGCCAACGTCCCAGACGTGGTCTTACACGAAATCAA
1 A-TACGATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAA
41439500 ATACGA
1 ATACGA
41439506 AATCCTATAT
Statistics
Matches: 107, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.01
42 32 0.30
43 43 0.40
44 30 0.28
45 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAA
Found at i:41449448 original size:39 final size:40
Alignment explanation
Indices: 41449393--41449561 Score: 215
Period size: 39 Copynumber: 4.3 Consensus size: 40
41449383 GGACTAAGAT
* *
41449393 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
41449432 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
* *
41449471 CCGAAGGCA-TT-TGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
* * *
41449509 CCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGGTT-TGTC
1 CCGAAGGCATTTGTGCGAGTTAATA-AATCC-GGGTTAAGTC
41449549 CCGAAGGCATTTG
1 CCGAAGGCATTTG
41449562 AGCTAGTCGT
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
37 23 0.19
38 12 0.10
39 47 0.40
40 29 0.25
41 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC
Found at i:41449527 original size:77 final size:77
Alignment explanation
Indices: 41449406--41449561 Score: 219
Period size: 77 Copynumber: 2.0 Consensus size: 77
41449396 AAGGCGTTCG
* *
41449406 TGCGAGTTAATAAATCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTAATA-AATCC-GGGTTAA
1 TGCGAGTTAATAAACCCGGGTTAAGCCCGAAGGCATTCGTGCGAGTTAATATAA-CCGGGGTT-A
41449469 G-CCCGAAGGCATT
64 GTCCCGAAGGCATT
* * *
41449482 TGCGAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAACCGGGGTTTG
1 TGCGAGTTAATAAACCCGGGTTAAG-CCCGAAGGCATTCGTGCGAGTTAATATAACCGGGGTTAG
41449547 TCCCGAAGGCATT
65 TCCCGAAGGCATT
41449560 TG
1 TG
41449562 AGCTAGTCGT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
76 23 0.32
77 27 0.38
78 21 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (77 bp):
TGCGAGTTAATAAACCCGGGTTAAGCCCGAAGGCATTCGTGCGAGTTAATATAACCGGGGTTAGT
CCCGAAGGCATT
Found at i:41457517 original size:40 final size:39
Alignment explanation
Indices: 41457481--41457587 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
41457471 ATATCCGGAC
*
41457481 TAAGATCCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGT
1 TAAG-TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
* * * *
41457521 TAAGCCCGAAGGCATTTGTGCGAGTTACTAAACCCGGGT
1 TAAGTCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
41457560 TAAGTCCCGAAGGCATTCGTGCGAGTTA
1 TAAGT-CCGAAGGCATTCGTGCGAGTTA
41457588 CTATAACCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.58
40 25 0.42
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGT
Found at i:41457588 original size:40 final size:40
Alignment explanation
Indices: 41457487--41457616 Score: 183
Period size: 40 Copynumber: 3.3 Consensus size: 40
41457477 GGACTAAGAT
* * *
41457487 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
*
41457526 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
* *
41457566 CCGAAGGCATTCGTGCGAGTTACTATAACCGGGGTT-TGTC
1 CCGAAGGCATTCGTGCGAGTTACTA-AACCCGGGTTAAGTC
41457606 CCGAAGGCATT
1 CCGAAGGCATT
41457617 TGAGCTAGTC
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 34 0.41
40 39 0.48
41 9 0.11
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAACCCGGGTTAAGTC
Found at i:41457649 original size:79 final size:79
Alignment explanation
Indices: 41457486--41457651 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 79
41457476 CGGACTAAGA
* * *
41457486 TCCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGCCCGAAGGCATTTGAGCGAGTCACTA
*
41457551 AACCCGGGTTAAGT
66 AACCCGGGTTAAAT
* * * * *
41457565 CCCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGGTT-TGTCCCGAAGGCATTTGAGCTAGTCG
1 TCCGAAGGCATTCGTGCGAGTTAATA-AATCC-GGGTTAAG-CCCGAAGGCATTTGAGCGAGTCA
* * *
41457628 TTATATCC-GGTTAAAT
63 CTAAACCCGGGTTAAAT
41457644 TCCGAAGG
1 TCCGAAGG
41457652 TACGTGATTC
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
79 40 0.56
80 31 0.44
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGAAGGCATTCGTGCGAGTTAATAAATCCGGGTTAAGCCCGAAGGCATTTGAGCGAGTCACTA
AACCCGGGTTAAAT
Found at i:41460397 original size:34 final size:33
Alignment explanation
Indices: 41460334--41460400 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
41460324 CAGTTCAATT
41460334 TCAGTTGGAGCCTTAGCCCATTACTGTAGCAGTA
1 TCAGTTGGAGCCTTAGCCCATTAC-GTAGCAGTA
41460368 TCAGTGTGG-GCCTTAGCCCAATTTA-GTAGCAGT
1 TCAGT-TGGAGCCTTAGCCC-A-TTACGTAGCAGT
41460401 CACTGTACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
34 23 0.77
35 4 0.13
36 3 0.10
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (33 bp):
TCAGTTGGAGCCTTAGCCCATTACGTAGCAGTA
Found at i:41463513 original size:40 final size:40
Alignment explanation
Indices: 41463288--41463513 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
41463278 GCTACTTGTT
* *
41463288 CAAATGCCTTCAGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
41463328 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
41463368 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
41463408 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
41463448 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41463489 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41463514 CATCATTCGA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 153 0.91
41 13 0.08
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41465575 original size:12 final size:12
Alignment explanation
Indices: 41465560--41465597 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
41465550 CTTTGATCCA
41465560 CTCCTCAAATCT
1 CTCCTCAAATCT
*
41465572 CTCCCCAAATCT
1 CTCCTCAAATCT
*
41465584 CTCCTCTAATCT
1 CTCCTCAAATCT
41465596 CT
1 CT
41465598 TCATCAGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (12 bp):
CTCCTCAAATCT
Found at i:41476079 original size:47 final size:47
Alignment explanation
Indices: 41475955--41476090 Score: 177
Period size: 46 Copynumber: 2.9 Consensus size: 47
41475945 ACCATAATCT
* * *
41475955 CACCCATAATGAACTTGGAACGCAACTCAACGAGCTCGGGTG-TTCG
1 CACCCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCG
* * ** *
41476001 CATCCATAATGAACTCGAAACAAAACTCAACGAGTTTGGATGCTT-G
1 CACCCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCG
41476047 CACCCATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGATGC
1 CACCCATAA-TGAACTCGGAACGCAACTCAACGAGTTCGGATGC
41476091 CTCATAATTC
Statistics
Matches: 75, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
46 43 0.57
47 32 0.43
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (47 bp):
CACCCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGCTTCG
Found at i:41478384 original size:46 final size:46
Alignment explanation
Indices: 41478334--41478509 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
41478324 TGGTTGAGCA
41478334 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41478380 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41478425 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41478473 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41478510 GCGGGTTACA
Statistics
Matches: 113, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 4 0.04
46 63 0.56
47 29 0.26
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41478490 original size:93 final size:93
Alignment explanation
Indices: 41478331--41478501 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41478321 GGATGGTTGA
* *
41478331 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41478396 TGAGTCCGAGTTCCTGAGATGTAACTAG
66 TGAGTCCGAGTTCCTGAGATGTAACTAG
*
41478424 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41478489 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41478502 GCTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCCTGAGATGTAACTAG
Found at i:41486186 original size:42 final size:42
Alignment explanation
Indices: 41486139--41486227 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
41486129 TCCTAATTGG
* *
41486139 GAAAATAATTCCCTCATTCTAATAAACTACTAAAACATAAAA
1 GAAAATAATTCCCTAACTCTAATAAACTACTAAAACATAAAA
* * *
41486181 GAAAATAGTTTCCTAACTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAATTCCCTAACTCTAATAAACTACTAAAACATAAAA
*
41486223 TAAAA
1 GAAAA
41486228 ATATTCCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (42 bp):
GAAAATAATTCCCTAACTCTAATAAACTACTAAAACATAAAA
Found at i:41486248 original size:43 final size:41
Alignment explanation
Indices: 41486158--41486249 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
41486148 TCCCTCATTC
* * *
41486158 TAATAAACTACTAAAACATAAAAGAAAATAGTTTCCTAACTC
1 TAATAAACTACTAAAACATAAAAAAAAATAG-TTCCTAAATA
*
41486200 TAATAAACTACTAAAAGATAAAATAAAAATA-TTCCTAAAATA
1 TAATAAACTACTAAAACATAAAA-AAAAATAGTTCCT-AAATA
41486242 TGAATAAA
1 T-AATAAA
41486250 ATTTATCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
41 5 0.12
42 26 0.60
43 12 0.28
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.26
Consensus pattern (41 bp):
TAATAAACTACTAAAACATAAAAAAAAATAGTTCCTAAATA
Found at i:41486272 original size:19 final size:18
Alignment explanation
Indices: 41486248--41486291 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
41486238 AATATGAATA
41486248 AAATTTATCTACCTAAAT
1 AAATTTATCTACCTAAAT
*
41486266 AATATTTATCTACTTAAAT
1 AA-ATTTATCTACCTAAAT
41486285 AAATTTA
1 AAATTTA
41486292 AAATATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:41490666 original size:42 final size:42
Alignment explanation
Indices: 41490619--41490707 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
41490609 TCCTAATTGG
* * *
41490619 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTAACTCTAATAAACTACTAAAAGATAAAA
*
41490661 GAAAATAGTTTCCTAACTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTAACTCTAATAAACTACTAAAAGATAAAA
*
41490703 TAAAA
1 GAAAA
41490708 ATATTCCTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (42 bp):
GAAAATAGTTCCCTAACTCTAATAAACTACTAAAAGATAAAA
Found at i:41490728 original size:43 final size:41
Alignment explanation
Indices: 41490620--41490729 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
41490610 CCTAATTGGG
* * * * *
41490620 AAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAAG
1 AAAATAGTT-CCTAAATATAATAAACTACTAAAAGATAAAAA
* *
41490662 AAAATAGTTTCCTAACTCTAATAAACTACTAAAAGATAAAATA
1 AAAATAG-TTCCTAAATATAATAAACTACTAAAAGATAAAA-A
41490705 AAAATA-TTCCTAAAATATGAATAAA
1 AAAATAGTTCCT-AAATAT-AATAAA
41490730 ACTTATCTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 5 0.09
42 39 0.67
43 14 0.24
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.29
Consensus pattern (41 bp):
AAAATAGTTCCTAAATATAATAAACTACTAAAAGATAAAAA
Found at i:41490754 original size:19 final size:18
Alignment explanation
Indices: 41490732--41490771 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
41490722 TGAATAAAAC
41490732 TTATCTACCTAAATAATAT
1 TTATCTACCTAAATAA-AT
41490751 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
41490769 TTA
1 TTA
41490772 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:41493935 original size:21 final size:23
Alignment explanation
Indices: 41493911--41493956 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
41493901 TAATGATAAA
*
41493911 TATTTTAAT-GTA-AAATATTAT
1 TATTTTAATAGTATAAACATTAT
41493932 TATTTTAATAGTATAAACATTAT
1 TATTTTAATAGTATAAACATTAT
41493955 TA
1 TA
41493957 AAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TATTTTAATAGTATAAACATTAT
Found at i:41496002 original size:16 final size:16
Alignment explanation
Indices: 41495981--41496017 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41495971 TAAGGAAAAA
41495981 ATAGTGTTG-AAGCAAC
1 ATAGTGTTGCAAGC-AC
41495997 ATAGTGTTGCAAGCAC
1 ATAGTGTTGCAAGCAC
41496013 ATAGT
1 ATAGT
41496018 TAAGCAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (16 bp):
ATAGTGTTGCAAGCAC
Found at i:41500596 original size:38 final size:38
Alignment explanation
Indices: 41500545--41500624 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
41500535 TTATTCGAGA
41500545 AGTAAGGACCATTTTAAAAATTTTCAAAATCTAACTTG
1 AGTAAGGACCATTTTAAAAATTTTCAAAATCTAACTTG
41500583 AGTAAGGACCATTTTAAAAATTTTCAAAATCTAACTTG
1 AGTAAGGACCATTTTAAAAATTTTCAAAATCTAACTTG
41500621 AGTA
1 AGTA
41500625 TCAATATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (38 bp):
AGTAAGGACCATTTTAAAAATTTTCAAAATCTAACTTG
Found at i:41500773 original size:14 final size:14
Alignment explanation
Indices: 41500743--41500784 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
41500733 TATTTTCCGA
41500743 AAAATGATTTCTGG
1 AAAATGATTTCTGG
41500757 AAAATGATTTACT-G
1 AAAATGATTT-CTGG
41500771 AAAAT-ATTTTCTGG
1 AAAATGA-TTTCTGG
41500785 TGTTTGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 20 0.80
15 2 0.08
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:41500892 original size:20 final size:20
Alignment explanation
Indices: 41500867--41500905 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41500857 GTTTTTACAT
41500867 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
41500887 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
41500906 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Done.