Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 136 of 175
Found at i:42064067 original size:35 final size:35
Alignment explanation
Indices: 42063972--42064091 Score: 122
Period size: 35 Copynumber: 3.5 Consensus size: 35
42063962 TCGAAATTTT
*
42063972 CGTGTTTTCAAAATTTTTCGTG--TCAAAAAATTC
1 CGTGTTTTCAAAAATTTTCGTGTTTCAAAAAATTC
* * * * *
42064005 TCATG-TATCGAAAATTTCCTTGTTTTCAAAAAATTC
1 -CGTGTTTTCAAAAATTTTCGTG-TTTCAAAAAATTC
*
42064041 CGTGTTTTCAAAAATTTTCGTGTTTC-AAAAATCTT
1 CGTGTTTTCAAAAATTTTCGTGTTTCAAAAAAT-TC
42064076 CGTGTTTTCAAAAATT
1 CGTGTTTTCAAAAATT
42064092 ATTATTGTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
33 12 0.17
34 9 0.13
35 24 0.35
36 24 0.35
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (35 bp):
CGTGTTTTCAAAAATTTTCGTGTTTCAAAAAATTC
Found at i:42064851 original size:20 final size:19
Alignment explanation
Indices: 42064799--42064870 Score: 58
Period size: 20 Copynumber: 3.7 Consensus size: 19
42064789 TTTAAATGAT
*
42064799 TTTTTATTAATTTTTAAT-
1 TTTTTATAAATTTTTAATA
*
42064817 TTTTT-TGAACTTTTTTGAATA
1 TTTTTAT-AA-ATTTTT-AATA
*
42064838 TTTTTATAAATTTTAATATA
1 TTTTTATAAATTTTTA-ATA
*
42064858 TTTTTACAAATTT
1 TTTTTATAAATTT
42064871 ATAGCTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.02
18 6 0.14
19 6 0.14
20 22 0.51
21 7 0.16
22 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATAAATTTTTAATA
Found at i:42068158 original size:16 final size:16
Alignment explanation
Indices: 42068137--42068171 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42068127 GATTAAGATT
42068137 TTAAAT-GTTGTTAGTA
1 TTAAATAGTT-TTAGTA
42068153 TTAAATAGTTTTAGTA
1 TTAAATAGTTTTAGTA
42068169 TTA
1 TTA
42068172 GGGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
TTAAATAGTTTTAGTA
Found at i:42074077 original size:25 final size:24
Alignment explanation
Indices: 42074028--42074080 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
42074018 ACATAATGTC
*
42074028 AATAAATAATTTAAAAATTATAAA
1 AATAAATAAATTAAAAATTATAAA
* *
42074052 AATAAATCAAATTCAAAATTCAAAAA
1 AATAAAT-AAATTAAAAATT-ATAAA
42074078 AAT
1 AAT
42074081 TAGCATGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AATAAATAAATTAAAAATTATAAA
Found at i:42082473 original size:24 final size:24
Alignment explanation
Indices: 42082446--42082497 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42082436 TTTCTAGAAG
* **
42082446 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
42082470 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
42082494 ATTT
1 ATTT
42082498 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:42098923 original size:18 final size:18
Alignment explanation
Indices: 42098894--42098962 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
42098884 AAGGGGATCA
* *
42098894 CATATTAGAACTCCATAT
1 CATATCAGAACTCCACAT
* *
42098912 AATATCATAACTCCACAT
1 CATATCAGAACTCCACAT
42098930 CATATCAGAACTCCACAT
1 CATATCAGAACTCCACAT
*
42098948 CATATTAGAACTCCA
1 CATATCAGAACTCCA
42098963 TACTAAATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.41, C:0.28, G:0.04, T:0.28
Consensus pattern (18 bp):
CATATCAGAACTCCACAT
Found at i:42100122 original size:44 final size:44
Alignment explanation
Indices: 42100085--42101055 Score: 598
Period size: 44 Copynumber: 22.3 Consensus size: 44
42100075 ACTACTGCTT
* * *
42100085 AGGGAGATAGGATTTACAATCTTCAACCTATTCCACTACTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * * * **
42100129 AGGGAGATGGGACATATAATCTTCCACCTATTCCACTGCTATTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
42100173 AGGGAGATAAGACTTACAATCTTCCACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
42100217 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
42100261 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
42100305 AGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * **
42100349 AGGGAGATAAGA-TT----T-GT--ACCT-TGT--A--GCTTCTC
1 AGGGAGATAGGACTTACAATCTTCAACCTAT-TCCACTGCTGGTC
** * ** * * * * * * ***
42100381 AAAAGA-ACAAAATTTGCTATCTTTAGCCTGTTCCACTGCAACTTC
1 -AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGC-TGGTC
* ** * * * ** *** *
42100426 -GGAGAGATAAGACTT-GTAGCTTCAACTTGTTCTGCTGCAACTTT
1 AGG-GAGATAGGACTTACAATCTTCAACCTATTCCACTGC-TGGTC
* * * * * * * * *
42100470 A--AAGATAAGTCTGATGCGATC-T--ACTCTATTGCAACTCCAGAG-A
1 AGGGAGATAGGACT--TACAATCTTCAAC-CTATT-CCACTGCTG-GTC
*** ** * *** * * * *
42100513 AATAAGATTTG-TTGTTGTAGCTTCAATCTATTCGACTGCAAT-GTT
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGC--TGGTC
* * * ** * ** * * *
42100558 GGGGA-AGTAAGA-TTCGCCGTCTTCAATCTGCTCCACTAC-AGCC
1 AGGGAGA-TAGGACTT-ACAATCTTCAACCTATTCCACTGCTGGTC
* * * *
42100601 TAGGGAGACA-GAATCTACAATCTTCAACCTATTCCACTGTTGTTC
1 -AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGGTC
* * *
42100646 AGGGAGATAGGACATACAATCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * *
42100690 AGGGAGATAGGACTTACAATCTTCCACATATTCCACTGTTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
42100734 AAGGAGATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* * * * *
42100778 AGGGAGATAGGACTTGCAAACTTTAACCTATTTCACTGCTGGTT
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
42100822 AGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* *
42100866 AGGGAGATAGGACTTGCAATC--GAACCTATTCCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
*
42100908 AGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
* ** * * *
42100952 AGGGAGATAGGATTTGTAATCTTCAACCTATTACAACTGTTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATT-CCACTGCTGGTC
* ** *
42100997 AGGGAGATAGGAATTGTAATCTTCAACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
42101041 AGGGAGATAGGACTT
1 AGGGAGATAGGACTT
42101056 GTGGTTTCAC
Statistics
Matches: 741, Mismatches: 140, Indels: 92
0.76 0.14 0.09
Matches are distributed among these distances:
32 9 0.01
33 5 0.01
34 1 0.00
35 1 0.00
36 5 0.01
37 1 0.00
38 2 0.00
39 1 0.00
40 4 0.01
41 1 0.00
42 52 0.07
43 13 0.02
44 561 0.76
45 84 0.11
46 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTC
Found at i:42100808 original size:517 final size:517
Alignment explanation
Indices: 42099833--42100874 Score: 1726
Period size: 517 Copynumber: 2.0 Consensus size: 517
42099823 TGCAATGTCG
*
42099833 GGGAGATAGGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCC
1 GGGAGATAAGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCC
*
42099898 ACTGCAACTTTAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGT
66 ACTGCAACTTGAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGT
*
42099963 CTGATGCAATCTGCTCTACTGCAACTCCAGAGAAATAAGATTCACTGTTGTAGCTTCAACCTATT
131 CTGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCACTGTTGTAGCTTCAACCTATT
* * * * *
42100028 TGACTACAATGTTGGGGAAGTAAGATTCACCGTCTCCGATCTGCTCCACTACTGCTTAGGGAGAT
196 CGACTACAATGTTGGGGAAGTAAGATTCACCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGAC
* * * *
42100093 AGGATTTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATGGGACATATAATCTTCCACCT
261 AGAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACCT
* *
42100158 ATTCCACTGCTATTCAGGGAGATAAGACTTACAATCTTCCACCTATTCCACTGCTGGTCAGGGAG
326 ATTCCACTGCTATTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGAG
* * *
42100223 ATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCAGGGAGATAGGACTTGCAATCTTCAAC
391 ATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGGGAGATAGGACTTGCAAACTTCAAC
*
42100288 CTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTCA
456 CTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCA
*
42100350 GGGAGATAAGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGTTCC
1 GGGAGATAAGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCC
*
42100415 ACTGCAACTTCGGA-GAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAG
66 ACTGCAACTT-GAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAG
* * *** *
42100479 TCTGATGCGATCTACTCTATTGCAACTCCAGAGAAATAAGATTTGTTGTTGTAGCTTCAATCTAT
130 TCTGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCACTGTTGTAGCTTCAACCTAT
* * *
42100544 TCGACTGCAATGTTGGGGAAGTAAGATTCGCCGTCTTCAATCTGCTCCACTACAGCCTAGGGAGA
195 TCGACTACAATGTTGGGGAAGTAAGATTCACCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGA
**
42100609 CAGAATCTACAATCTTCAACCTATTCCACTGTTGTTCAGGGAGATAGGACATACAATCTTCCACC
260 CAGAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACC
* * *
42100674 TATTCCACTGCTGTTCAGGGAGATAGGACTTACAATCTTCCACATATTCCACTGTTGGTCAAGGA
325 TATTCCACTGCTATTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGA
*
42100739 GATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGGGAGATAGGACTTGCAAACTTTAA
390 GATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGGGAGATAGGACTTGCAAACTTCAA
* * *
42100804 CCTATTTCACTGCTGGTTAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGGTCA
455 CCTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCA
42100867 GGGAGATA
1 GGGAGATA
42100875 GGACTTGCAA
Statistics
Matches: 486, Mismatches: 38, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
517 485 1.00
518 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (517 bp):
GGGAGATAAGATTTGTACCTTGTAGCTTCTCAAAAGAACAAAATTTGCTATCTTTAGCCTGCTCC
ACTGCAACTTGAAGGAGATAAGACTTGTAGCTTCAACTTGTTCTGCTGCAACTTTAAAGATAAGT
CTGATGCAATCTACTCTACTGCAACTCCAGAGAAATAAGATTCACTGTTGTAGCTTCAACCTATT
CGACTACAATGTTGGGGAAGTAAGATTCACCGTCTCCAATCTGCTCCACTACAGCCTAGGGAGAC
AGAATCTACAATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGGACATACAATCTTCCACCT
ATTCCACTGCTATTCAGGGAGATAAGACTTACAATCTTCCACATATTCCACTGCTGGTCAAGGAG
ATAGGACTTACAATCTTCAACCTATTCAACTGCTGGTCAGGGAGATAGGACTTGCAAACTTCAAC
CTATTCCACTGCTGGTCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCA
Found at i:42102015 original size:28 final size:28
Alignment explanation
Indices: 42101983--42102038 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
42101973 ATAAATAGTA
* *
42101983 TGAAAATTGGGTGTCCTATATATCGCAG
1 TGAAAATTGGGTGTCCCAGATATCGCAG
42102011 TGAAAATTGGGTGTCCCAGATATCGCAG
1 TGAAAATTGGGTGTCCCAGATATCGCAG
42102039 CTTGAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
TGAAAATTGGGTGTCCCAGATATCGCAG
Found at i:42108522 original size:37 final size:37
Alignment explanation
Indices: 42108461--42108606 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
42108451 TACGTATGAT
* *
42108461 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
42108496 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
42108533 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
42108570 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
42108607 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:42108623 original size:46 final size:46
Alignment explanation
Indices: 42108570--42108929 Score: 410
Period size: 52 Copynumber: 7.6 Consensus size: 46
42108560 TAAGTGTAGC
* **
42108570 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
42108616 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
42108662 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
42108714 CACTTATCAC----T---TTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
42108753 CACTTATAACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
42108805 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
42108851 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
42108903 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
42108930 AGTACTCAAA
Statistics
Matches: 275, Mismatches: 14, Indels: 50
0.81 0.04 0.15
Matches are distributed among these distances:
39 37 0.13
42 1 0.00
46 112 0.41
48 1 0.00
49 3 0.01
50 1 0.00
52 120 0.44
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:42108736 original size:39 final size:39
Alignment explanation
Indices: 42108675--42108765 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
42108665 TTATCACTTT
*
42108675 TCACTTGTCAC-TTGATCAGATAAGTGTAGCCGAAGCTA
1 TCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTA
42108713 TCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTA
1 TCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTA
*
42108752 TCACTTATAACTTT
1 TCACTTATCACTTT
42108766 TCACTTGTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 10 0.20
39 40 0.80
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (39 bp):
TCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTA
Found at i:42108737 original size:91 final size:91
Alignment explanation
Indices: 42108634--42108916 Score: 440
Period size: 91 Copynumber: 3.0 Consensus size: 91
42108624 ACTTTGTCTC
42108634 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
1 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
42108699 TGTAGCCGAAGCTATCACTTATCACT
66 TGTAGCCGAAGCTATCACTTATCACT
* *
42108725 TTGATCAGATAAGTGTAGCCGAAGCTATCACTTATAACTTTTCACTTGTCACTTGATCAGATAAG
1 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
42108790 TGTAGCCGAAGCTATCACTTATCACTTTGT
66 TGTAGCCGAAGCTATCACTTATCAC----T
* *
42108820 CACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGAT
1 ---TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGAT
** *
42108885 AAGTGTAGCTAAAGCTACCACTTATCACT
63 AAGTGTAGCCGAAGCTATCACTTATCACT
42108914 TTG
1 TTG
42108917 TCACTTGATC
Statistics
Matches: 176, Mismatches: 9, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
91 91 0.52
94 1 0.01
95 1 0.01
98 83 0.47
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (91 bp):
TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
TGTAGCCGAAGCTATCACTTATCACT
Found at i:42108909 original size:189 final size:190
Alignment explanation
Indices: 42108571--42108916 Score: 595
Period size: 189 Copynumber: 1.8 Consensus size: 190
42108561 AAGTGTAGCC
* * *
42108571 ACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTT
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
*
42108636 GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTG
66 GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
* *
42108701 TAGCCGAAGCTATCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATA
131 TAGCCAAAGCTACCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATA
* *
42108761 ACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
*
42108825 GATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
66 GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
*
42108890 TAGCTAAAGCTACCACTTATCACTTTG
131 TAGCCAAAGCTACCACTTATCACTTTG
42108917 TCACTTGATC
Statistics
Matches: 146, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
189 138 0.95
190 8 0.05
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (190 bp):
ACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
TAGCCAAAGCTACCACTTATCACTTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATA
Found at i:42108914 original size:98 final size:98
Alignment explanation
Indices: 42108570--42108929 Score: 554
Period size: 98 Copynumber: 3.7 Consensus size: 98
42108560 TAAGTGTAGC
* * * *
42108570 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACT
42108635 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
42108669 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC----T---TT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
*
42108727 GATCAGATAAGTGTAGCCGAAGCTATCACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
42108760 AACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
*
42108825 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
42108858 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
42108923 GATCAGA
66 GATCAGA
42108930 AGTACTCAAA
Statistics
Matches: 241, Mismatches: 13, Indels: 15
0.90 0.05 0.06
Matches are distributed among these distances:
91 88 0.37
94 1 0.00
95 1 0.00
98 142 0.59
99 9 0.04
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:42110972 original size:3 final size:3
Alignment explanation
Indices: 42110964--42111016 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
42110954 ATAATCAAAT
* * *
42110964 ATA ATA ATA ATA ATA ACA ATA ATAA ATA GTA A-A ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
42111009 ATA ATA AT
1 ATA ATA AT
42111017 TAAGTGATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:42110991 original size:27 final size:27
Alignment explanation
Indices: 42110954--42111015 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
42110944 ATAGCTAAAT
42110954 ATAATCAAATA-TAATAATAATAATAACA
1 ATAAT-AAATAGTAA-AATAATAATAACA
* *
42110982 ATAATAAATAGTAAAATAATACTAATA
1 ATAATAAATAGTAAAATAATAATAACA
42111009 ATAATAA
1 ATAATAA
42111016 TTAAGTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (27 bp):
ATAATAAATAGTAAAATAATAATAACA
Found at i:42111395 original size:33 final size:33
Alignment explanation
Indices: 42111353--42111431 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
42111343 GAGGCTTCTG
42111353 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
1 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
*
42111386 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAG
1 AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
42111419 AACGGCGTCGTTT
1 AACGGCGTCGTTT
42111432 CCTTCACATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (33 bp):
AACGGCGTCGTTTTTAAAGCTACTGAAGCATAA
Found at i:42114832 original size:24 final size:24
Alignment explanation
Indices: 42114805--42114856 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42114795 AAGTAATCAT
* * *
42114805 ATTTTAATTGGAAAAAGATAGTAG
1 ATTTTAACTGGAAAAAGAAACTAG
*
42114829 ATTTTAACTGGGAAAAGAAACTAG
1 ATTTTAACTGGAAAAAGAAACTAG
42114853 ATTT
1 ATTT
42114857 ATGTGGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (24 bp):
ATTTTAACTGGAAAAAGAAACTAG
Found at i:42129988 original size:29 final size:30
Alignment explanation
Indices: 42129929--42129989 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
42129919 CATTTTAGGT
42129929 AAGTGTAAAATTATTAAAAAAATATATAAA
1 AAGTGTAAAATTATTAAAAAAATATATAAA
* *
42129959 AAGT-TAATAATTATTTAAAAAA-GTATAAA
1 AAGTGTAA-AATTATTAAAAAAATATATAAA
42129988 AA
1 AA
42129990 TTATTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (30 bp):
AAGTGTAAAATTATTAAAAAAATATATAAA
Found at i:42129991 original size:21 final size:19
Alignment explanation
Indices: 42129956--42130006 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
42129946 AAAAATATAT
*
42129956 AAAAAGTTAATAATTATTTA
1 AAAAAGTTAAAAATTA-TTA
42129976 AAAAAGTATAAAAATTATTA
1 AAAAAGT-TAAAAATTATTA
*
42129996 AAAAATTTAAA
1 AAAAAGTTAAA
42130007 TATGTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 16 0.57
21 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAAAGTTAAAAATTATTA
Found at i:42136474 original size:17 final size:17
Alignment explanation
Indices: 42136443--42136513 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
42136433 CAATTACAAA
*
42136443 AAAATATATTTAAAATAT
1 AAAA-ATATTAAAAATAT
*
42136461 AAAAATATTAAAAAAAT
1 AAAAATATTAAAAATAT
** *
42136478 TCAAATAGTAAATAATTAT
1 AAAAATATTAAA-AA-TAT
*
42136497 AAAAAATAATAAAAATA
1 -AAAAATATTAAAAATA
42136514 GCACATCGGA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
17 20 0.49
18 8 0.20
19 4 0.10
20 9 0.22
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAAATATTAAAAATAT
Found at i:42136484 original size:25 final size:26
Alignment explanation
Indices: 42136455--42136503 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42136445 AATATATTTA
42136455 AAATA-TAAAAATATTA-AAAAAATTC
1 AAATAGTAAAAA-ATTATAAAAAATTC
*
42136480 AAATAGTAAATAATTATAAAAAAT
1 AAATAGTAAAAAATTATAAAAAAT
42136504 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (26 bp):
AAATAGTAAAAAATTATAAAAAATTC
Found at i:42145087 original size:3 final size:3
Alignment explanation
Indices: 42145079--42145119 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42145069 ATCACATGTT
42145079 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42145120 TGGATGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42145201 original size:72 final size:72
Alignment explanation
Indices: 42145120--42145288 Score: 338
Period size: 72 Copynumber: 2.3 Consensus size: 72
42145110 TATTATTATT
42145120 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
42145185 TTTTAAG
66 TTTTAAG
42145192 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
42145257 TTTTAAG
66 TTTTAAG
42145264 TGGATGTAATGATGTAACTTAGTTG
1 TGGATGTAATGATGTAACTTAGTTG
42145289 GAAGTGGATG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:42145303 original size:29 final size:29
Alignment explanation
Indices: 42145261--42145317 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
42145251 GATTTATTTT
42145261 AAGTGGATGTAATGATGTAACTTAGTTGG
1 AAGTGGATGTAATGATGTAACTTAGTTGG
42145290 AAGTGGATGTAATGATGTAACTTAGTTG
1 AAGTGGATGTAATGATGTAACTTAGTTG
42145318 TATTCCAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
AAGTGGATGTAATGATGTAACTTAGTTGG
Found at i:42145364 original size:101 final size:101
Alignment explanation
Indices: 42145189--42145389 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
42145179 GATTTATTTT
42145189 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
1 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
*
42145254 TTATTTTAAGTGGATGTAATGATGTAACTTAGTTGG
66 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTGG
42145290 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
1 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
42145355 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTG
66 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTG
42145390 TATTCCAACT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.40
Consensus pattern (101 bp):
AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
TTATTTTAAGTGGATGTAATGATGAAACTTAGTTGG
Found at i:42149631 original size:3 final size:3
Alignment explanation
Indices: 42149623--42149663 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42149613 ATCACATGTT
42149623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42149664 TGGATGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42149745 original size:72 final size:72
Alignment explanation
Indices: 42149664--42149832 Score: 338
Period size: 72 Copynumber: 2.3 Consensus size: 72
42149654 TATTATTATT
42149664 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
42149729 TTTTAAG
66 TTTTAAG
42149736 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
42149801 TTTTAAG
66 TTTTAAG
42149808 TGGATGTAATGATGTAACTTAGTTG
1 TGGATGTAATGATGTAACTTAGTTG
42149833 GAAGTGGATG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:42149847 original size:29 final size:29
Alignment explanation
Indices: 42149805--42149861 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
42149795 GATTTATTTT
42149805 AAGTGGATGTAATGATGTAACTTAGTTGG
1 AAGTGGATGTAATGATGTAACTTAGTTGG
42149834 AAGTGGATGTAATGATGTAACTTAGTTG
1 AAGTGGATGTAATGATGTAACTTAGTTG
42149862 TATTCCAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
AAGTGGATGTAATGATGTAACTTAGTTGG
Found at i:42149908 original size:101 final size:101
Alignment explanation
Indices: 42149733--42149933 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
42149723 GATTTATTTT
42149733 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
1 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
*
42149798 TTATTTTAAGTGGATGTAATGATGTAACTTAGTTGG
66 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTGG
42149834 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
1 AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
42149899 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTG
66 TTATTTTAAGTGGATGTAATGATGAAACTTAGTTG
42149934 TATTCCAACT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.40
Consensus pattern (101 bp):
AAGTGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGAT
TTATTTTAAGTGGATGTAATGATGAAACTTAGTTGG
Found at i:42151394 original size:33 final size:33
Alignment explanation
Indices: 42151357--42151420 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
42151347 TTGCAGCAGA
*
42151357 CTTGCGACGTGGCTGT-ATCACACAGCTAATAGG
1 CTTGCAACGTGGCTGTGAT-ACACAGCTAATAGG
* *
42151390 CTTGCAATGTGGCTGTGATATACAGCTAATA
1 CTTGCAACGTGGCTGTGATACACAGCTAATA
42151421 TTTGCTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (33 bp):
CTTGCAACGTGGCTGTGATACACAGCTAATAGG
Found at i:42155467 original size:43 final size:43
Alignment explanation
Indices: 42155412--42155660 Score: 369
Period size: 43 Copynumber: 5.8 Consensus size: 43
42155402 TTTTAGAAAT
42155412 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
42155455 AAATGCTGCTATAGATTAGGACCTTTAGCGGCGCTTCTT-CCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT-TTCCCAC
* *
42155498 AAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTT-GCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
42155540 AAACGCCGCTATAGCTCAAGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
42155583 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
42155626 AAACGCCGATATAGAACAA-ACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT
42155661 CTCACAAAAA
Statistics
Matches: 185, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
42 55 0.30
43 128 0.69
44 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:42155586 original size:85 final size:86
Alignment explanation
Indices: 42155412--42155662 Score: 382
Period size: 85 Copynumber: 2.9 Consensus size: 86
42155402 TTTTAGAAAT
* * * *
42155412 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAATGCTGCTATAGATTAGGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
42155477 CTTTAGCGGCGCTTCTTCCAC
66 CTTTAGCGACGCTTCTTCCAC
* * *
42155498 AAACGCCGCTGTAGATCAAGACCTTTAGCGGCGCTTTT-GCACAAACGCCGCTATAGCTCAAGAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
42155562 CTTTAGCGACGCTT-TTCCCAC
66 CTTTAGCGACGCTTCTT-CCAC
* *
42155583 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGATATAGAACAA-AC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
42155647 CTTTAGCGACGCTTCT
66 CTTTAGCGACGCTTCT
42155663 CACAAAAAGG
Statistics
Matches: 149, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
84 2 0.01
85 90 0.60
86 57 0.38
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAGCGACGCTTCTTCCAC
Found at i:42160087 original size:11 final size:12
Alignment explanation
Indices: 42160058--42160090 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42160048 TTCAGCTTGG
*
42160058 ATGCTGGTCTGC
1 ATGCTGGTTTGC
42160070 ATGCTGGTTTGC
1 ATGCTGGTTTGC
42160082 -TGCTGGTTT
1 ATGCTGGTTT
42160091 CCTGTTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.33, T:0.42
Consensus pattern (12 bp):
ATGCTGGTTTGC
Found at i:42166491 original size:26 final size:28
Alignment explanation
Indices: 42166442--42166496 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
42166432 ATATTTCTAT
*
42166442 TTTTTTAATGAATATTTTTCTATATTTA
1 TTTTTAAATGAATATTTTTCTATATTTA
42166470 TTTTTAAATGAATA-TTTT-TATATTTA
1 TTTTTAAATGAATATTTTTCTATATTTA
42166496 T
1 T
42166497 ACGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 9 0.35
27 4 0.15
28 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTTTAAATGAATATTTTTCTATATTTA
Found at i:42178873 original size:217 final size:217
Alignment explanation
Indices: 42178491--42179353 Score: 1433
Period size: 217 Copynumber: 4.0 Consensus size: 217
42178481 TCGGTGGCCA
* * **
42178491 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTCATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
* * * *
42178556 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTAAAGTTACAGTGGAGCATACTGAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * *
42178621 AGTCTTATCCTCCTAAAGTTGCAGTGAGACAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
*
42178686 GCATTGGAGCAGATTAAAGCCG
196 GCAGTGGAGCAGATTAAAGCCG
*
42178708 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
42178773 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
42178838 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGAAAAATTTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
*
42178903 GCAGTGGAGCAGATTAAAGCTG
196 GCAGTGGAGCAGATTAAAGCCG
* * * * *
42178925 ATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAA-TTTCAGATCTCATCACTCTGAAG
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTT-AGATCTCATCTCTCTGAAG
*
42178989 TTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
65 TTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
*
42179054 AAGTCTTATCCTCCTAAAGTTACAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGT
130 AAGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGT
*
42179119 TGCATTGGAGCAGATTAAAGCCG
195 TGCAGTGGAGCAGATTAAAGCCG
* *
42179142 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
42179207 TGCAGAGAGCA-ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
42179271 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATTTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
* *
42179336 GCAGTAGAGCGGATTAAA
196 GCAGTGGAGCAGATTAAA
42179354 ACCTTGGATC
Statistics
Matches: 603, Mismatches: 41, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
216 131 0.22
217 470 0.78
218 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (217 bp):
ATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACCTTAGATCTCATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCG
Found at i:42179327 original size:172 final size:173
Alignment explanation
Indices: 42179149--42179483 Score: 600
Period size: 173 Copynumber: 1.9 Consensus size: 173
42179139 CCGATAATCC
*
42179149 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTCGCAGTAGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
42179214 AGCA-ATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
* *
42179278 TCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATTT
131 TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGATGGAAAATTT
* * *
42179321 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTCGCAGTAGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
*
42179386 AGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
66 AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
42179451 TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGA
131 TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGA
42179484 AAGCAAGTCT
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
172 65 0.42
173 90 0.58
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (173 bp):
TATCTCCCTGAAGTCGCAGTAGAGCGGATTAAAACATTAGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTA
TCCTCCTAAAGTTGCAGTAAGGCAGACTGAAGATGGAAAATTT
Found at i:42179463 original size:44 final size:42
Alignment explanation
Indices: 42178498--42179525 Score: 432
Period size: 44 Copynumber: 23.7 Consensus size: 42
42178488 CCAATAATCC
* * *
42178498 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCACAGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCT
* * * * * *
42178542 CATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* * * *
42178582 TATCTCCCTAAAGTTACAGTGGAGCATACTGAGTAAGCAAGTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
42178626 TATCCTCCTAAAGTTGCAGT-GAGACAGACTGAAGATGGCAAATCT
1 TAT-CTCCTGAAGTTGCAGTGGAG-CAGACT-AAGA-AGCAAGTCT
* * * *
42178671 TATCTCTCTGAAGTTGCATTGGAGCAGA-TTA-AAGCCGATAATCC
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * * * *
42178715 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAA-AACCTTAGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
42178759 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
42178799 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * * *
42178843 TATCCTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGAAAAATTT
1 TAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGAAG-CAAGTCT
* * *
42178888 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCTGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC--A-AGTCT
* * * * *
42178932 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAA-AATTTC-AGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAA--GCAAG-TCT
* * * * * * *
42178976 CATCACTCTGAAGTTGCAG-AGAGCAGA-TCA-CATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
42179016 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * * *
42179060 TATCCTCCTAAAGTTACAGT-GAGGCAGACTGAAGATGGAAAATCT
1 TAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * * *
42179105 TATCTCCCTGAAGTTGCATTGGAGCAGA-TTA-AAGCCGATAATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCT
* * *
42179149 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAA-AA-CATTAGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA--AG-TCT
* * * * *
42179193 TATCTCTCTGAAGTTGCAG-AGAGCA-A-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
42179232 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * * *
42179276 TATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAAAATTT
1 TAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * * * **
42179321 TATCTCCCTGAAGTTGCAGTAGAGCGGATTAA-AACCTTGGATCT
1 TATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
42179365 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
42179405 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCC-TGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* *
42179449 TATCCTCCTAAAGTTGCAGT-AAGGCAGACTGAAGAAAGCAAGTCT
1 TAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAG-AAGCAAGTCT
* * * * *
42179494 TATCCCCCTAAAATTGTAGTGGGGCAGACTAA
1 TAT-CTCCTGAAGTTGCAGTGGAGCAGACTAA
42179526 ATGAACAAAT
Statistics
Matches: 760, Mismatches: 138, Indels: 172
0.71 0.13 0.16
Matches are distributed among these distances:
39 21 0.03
40 85 0.11
41 44 0.06
42 27 0.04
43 60 0.08
44 338 0.44
45 175 0.23
46 9 0.01
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
TATCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:42181091 original size:19 final size:19
Alignment explanation
Indices: 42181067--42181106 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
42181057 TTAATTGATA
42181067 ATGTAATTATTTTATATAT
1 ATGTAATTATTTTATATAT
*
42181086 ATGTAATTATTTTATCTAT
1 ATGTAATTATTTTATATAT
42181105 AT
1 AT
42181107 ATGCATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
ATGTAATTATTTTATATAT
Found at i:42181119 original size:23 final size:19
Alignment explanation
Indices: 42181071--42181121 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
42181061 TTGATAATGT
*
42181071 AATTATTTTATATATATGT
1 AATTATTTTATATATATGC
42181090 AATTATTTTATCTATATATGC
1 AATTATTTTA--TATATATGC
42181111 ATATATATTTT
1 A-AT-TATTTT
42181122 TGTTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
21 9 0.33
22 2 0.07
23 6 0.22
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
AATTATTTTATATATATGC
Found at i:42181163 original size:29 final size:27
Alignment explanation
Indices: 42181124--42181180 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 27
42181114 TATATTTTTG
*
42181124 TTTTTTTAATGAATATTTTTCTATATTTA
1 TTTTTTAAATGAATA-TTTT-TATATTTA
42181153 TTTTTTAAATGAATATTTTTATATTTA
1 TTTTTTAAATGAATATTTTTATATTTA
42181180 T
1 T
42181181 ACGTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.33
28 4 0.15
29 14 0.52
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTTTAAATGAATATTTTTATATTTA
Found at i:42181719 original size:24 final size:24
Alignment explanation
Indices: 42181691--42181743 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
42181681 CACCTTTGAA
*
42181691 ACCCTTTCCACAGCTCCTTTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
42181715 ACCCTTTCCACAGCTCCTCTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
42181739 ACCCT
1 ACCCT
42181744 ATCGATTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.49, G:0.04, T:0.34
Consensus pattern (24 bp):
ACCCTTTCCACAGCTCCTCTCTTC
Found at i:42184797 original size:49 final size:49
Alignment explanation
Indices: 42184743--42184842 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
42184733 AAAGATAGTT
42184743 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
42184792 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
42184841 AA
1 AA
42184843 TATTAAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (49 bp):
AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
Found at i:42185131 original size:20 final size:20
Alignment explanation
Indices: 42185106--42185145 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42185096 AATATTTTTT
*
42185106 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
42185126 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
42185146 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:42185152 original size:14 final size:14
Alignment explanation
Indices: 42185129--42185168 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42185119 ACAGAAAAGT
*
42185129 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42185143 AAATCATTTTACGG
1 AAAACATTTTACAG
42185157 AAAACATTTTAC
1 AAAACATTTTAC
42185169 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42185247 original size:15 final size:15
Alignment explanation
Indices: 42185227--42185261 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
42185217 TTTCTATGCC
42185227 ATTGTTATATTTATT
1 ATTGTTATATTTATT
*
42185242 ATTGTTGTATTTATT
1 ATTGTTATATTTATT
42185257 ATTGT
1 ATTGT
42185262 GGCATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
ATTGTTATATTTATT
Found at i:42186658 original size:98 final size:98
Alignment explanation
Indices: 42186434--42186658 Score: 308
Period size: 98 Copynumber: 2.3 Consensus size: 98
42186424 TTCAATGTAT
* * * * *
42186434 TACCATCCCAGATGGCCCGAAAACAATGGCTTCCACACTTTACCTATACTATCATCCCGAATGGC
1 TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
*
42186499 TCGACAATTATAACATTCATGATCAATTCATTC
66 TCGACAATGATAACATTCATGATCAATTCATTC
* * * * * *
42186532 TATCATTCTGGATGGCTCAACGACGATGGCTTCCACACTTTACCTATATTACCATCCCGAATGGC
1 TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
*
42186597 TCTACAATGATGAA-ATTCATGATCAATTCATTC
66 TCGACAATGAT-AACATTCATGATCAATTCATTC
*
42186630 TACCATTCCGGATGGCCCGACAATGATGG
1 TACCATTCCGGATGGCCCGACAACGATGG
42186659 TTTTCACTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
98 105 0.98
99 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (98 bp):
TACCATTCCGGATGGCCCGACAACGATGGCTTCCACACTTTACCTATACTACCATCCCGAATGGC
TCGACAATGATAACATTCATGATCAATTCATTC
Found at i:42186683 original size:98 final size:98
Alignment explanation
Indices: 42186434--42186685 Score: 276
Period size: 98 Copynumber: 2.6 Consensus size: 98
42186424 TTCAATGTAT
* * * * * *
42186434 TACCATCCCAGATGGCCCGAA-AACAATGGCTTCCACACTTTACCTATACTATCATCCCGAATGG
1 TACCATTCCGGATGGCCC-AACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGG
*
42186498 CTCGACAATTATAACATTCATGATCAATTCATTC
65 CTCGACAATGATAACATTCATGATCAATTCATTC
* * * * * * *
42186532 TATCATTCTGGATGGCTCAACGACGATGGCTTCCACACTTTACCTATATTACCATCCCGAATGGC
1 TACCATTCCGGATGGCCCAACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGGC
*
42186597 TCTACAATGATGAA-ATTCATGATCAATTCATTC
66 TCGACAATGAT-AACATTCATGATCAATTCATTC
* * * * *
42186630 TACCATTCCGGATGGCCCGACAATGATGGTTTTCACTA-TATACATATCCTACCATC
1 TACCATTCCGGATGGCCCAACAACGATGGCTTCCAC-ACTATACATATACTACCATC
42186686 ACGGTTGGCC
Statistics
Matches: 128, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
97 2 0.02
98 123 0.96
99 3 0.02
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (98 bp):
TACCATTCCGGATGGCCCAACAACGATGGCTTCCACACTATACATATACTACCATCCCGAATGGC
TCGACAATGATAACATTCATGATCAATTCATTC
Found at i:42196771 original size:33 final size:34
Alignment explanation
Indices: 42196684--42196771 Score: 78
Period size: 33 Copynumber: 2.6 Consensus size: 34
42196674 TAATATATGA
*
42196684 AATATAAATTTTAAATATTTT--TAAGCAATAAAT
1 AATATATATTTTAAAT-TTTTAATAAGCAATAAAT
* * *
42196717 ATTA-ATTATTTATAAA-ATTTAATTAG-AATAAAT
1 AATATA-TATTT-TAAATTTTTAATAAGCAATAAAT
42196750 AATATATATTTTAAATTTTTAA
1 AATATATATTTTAAATTTTTAA
42196772 ATATAACCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
32 8 0.19
33 27 0.63
34 8 0.19
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (34 bp):
AATATATATTTTAAATTTTTAATAAGCAATAAAT
Found at i:42197492 original size:22 final size:21
Alignment explanation
Indices: 42197464--42197510 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42197454 ATTAAATTTT
*
42197464 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAA-ATAAAAATAA
* *
42197486 AAAATTTTAAAATTAAAATAA
1 AAAATTTGAAAATAAAAATAA
42197507 AAAA
1 AAAA
42197511 AGGGAGGAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATTTGAAAATAAAAATAA
Found at i:42197503 original size:21 final size:21
Alignment explanation
Indices: 42197449--42197510 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
42197439 ATACTAATAA
* *
42197449 TTAAAATTAAATTTTAAAATT
1 TTAAAATTAAAATTAAAAATT
* *
42197470 TGAAATATAAAAATTAAAAATT
1 TTAAA-ATTAAAATTAAAAATT
*
42197492 TTAAAATTAAAATAAAAAA
1 TTAAAATTAAAATTAAAAA
42197511 AGGGAGGAGG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TTAAAATTAAAATTAAAAATT
Found at i:42199572 original size:16 final size:16
Alignment explanation
Indices: 42199551--42199589 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42199541 GTTTAGTTCA
*
42199551 CTGTAATGGAATAGAG
1 CTGTAATGGAATAAAG
*
42199567 CTGTAATGGACTAAAG
1 CTGTAATGGAATAAAG
42199583 CTGTAAT
1 CTGTAAT
42199590 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:42199765 original size:12 final size:12
Alignment explanation
Indices: 42199748--42199772 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42199738 AATTTAATAA
42199748 AATTATTATTAT
1 AATTATTATTAT
42199760 AATTATTATTAT
1 AATTATTATTAT
42199772 A
1 A
42199773 TGAATTAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTATTATTAT
Found at i:42203821 original size:29 final size:27
Alignment explanation
Indices: 42203751--42203822 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 27
42203741 TAATAAAGAT
*
42203751 ATCAAAAATAAAAATAGTTTAAAAATAT
1 ATCAAAAAT-AAAATAGTTTAAAAATAC
*
42203779 ATTAAAAGATTAAAATAGTTTTAAATGAA-AC
1 ATCAAAA-A-TAAAATAG-TTTAAA--AATAC
42203810 ATCAAAAATAAAA
1 ATCAAAAATAAAA
42203823 ACATGTCGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
28 6 0.17
29 13 0.36
30 8 0.22
31 7 0.19
32 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (27 bp):
ATCAAAAATAAAATAGTTTAAAAATAC
Found at i:42206587 original size:11 final size:11
Alignment explanation
Indices: 42206557--42206591 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
42206547 ATCAAAAGGC
42206557 CTCTCTATTTT
1 CTCTCTATTTT
42206568 CTGTCTCTATTTT
1 C--TCTCTATTTT
42206581 CTCTCTATTTT
1 CTCTCTATTTT
42206592 GTCAAAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.09, C:0.26, G:0.03, T:0.63
Consensus pattern (11 bp):
CTCTCTATTTT
Found at i:42211195 original size:13 final size:13
Alignment explanation
Indices: 42211160--42211197 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
42211150 GATATATTTG
*
42211160 TAATTTGAAAGCT
1 TAATTTGAAAACT
42211173 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
42211187 TAATTTGAAAA
1 TAATTTGAAAA
42211198 TTTGGAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:42211235 original size:29 final size:27
Alignment explanation
Indices: 42211161--42211235 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
42211151 ATATATTTGT
* * * *
42211161 AATTTGAAAGCTTAAGTTTGAAAACTT
1 AATTTGAAAACTTAAATTTAAAAACTA
*
42211188 AATTTGAAAATTTGGAAATTTAAAAACTA
1 AATTTGAAAACTT--AAATTTAAAAACTA
42211217 AATTTTTGAAAACTTAAAT
1 AA--TTTGAAAACTTAAAT
42211236 GTCTTGAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.29
29 17 0.45
31 10 0.26
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (27 bp):
AATTTGAAAACTTAAATTTAAAAACTA
Found at i:42211514 original size:35 final size:35
Alignment explanation
Indices: 42211471--42211715 Score: 370
Period size: 35 Copynumber: 7.1 Consensus size: 35
42211461 GCAGGGAATA
*
42211471 TTTGTTGCAGAGAATCTCTT-CTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCT-TTCCTGTTCACGCATTAT
42211506 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
* *
42211541 TTTGTTGCAAGGAATCTTTCCTGTTCACGCATCA-
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
* *
42211575 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
42211610 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
* * *
42211645 TTTGTTGCAAGGAATCTTTCCTGTTCACACATCA-
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
* *
42211679 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
42211714 TT
1 TT
42211716 CTTTTTGGAC
Statistics
Matches: 190, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
34 61 0.32
35 129 0.68
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (35 bp):
TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTAT
Found at i:42211598 original size:69 final size:70
Alignment explanation
Indices: 42211471--42211715 Score: 345
Period size: 69 Copynumber: 3.5 Consensus size: 70
42211461 GCAGGGAATA
*
42211471 TTTGTTGC-AGAGAATCTCTT-CTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCAC
1 TTTGTTGCAAG-GAATCT-TTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTTTCCTGTTCAC
42211534 GCATTAT
64 GCATTAT
* *
42211541 TTTGTTGCAAGGAATCTTTCCTGTTCACGCATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACGC
1 TTTGTTGCAAGGAATCTTTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTTTCCTGTTCACGC
42211605 ATTAT
66 ATTAT
* * * *
42211610 TTTGTTGCAGGGAATCTTTCCTGTTCACGCATTATTTTGTTGCAAGGAATCTTTCCTGTTCACAC
1 TTTGTTGCAAGGAATCTTTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTTTCCTGTTCACGC
*
42211675 ATCA-
66 ATTAT
* * *
42211679 TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
1 TTTGTTGCAAGGAATCTTTCCTGTTCACGCATTATTT
42211716 CTTTTTGGAC
Statistics
Matches: 160, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
69 102 0.64
70 56 0.35
71 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (70 bp):
TTTGTTGCAAGGAATCTTTCCTGTTCACGCATTATTTTCTTGCAGGGAATCTTTCCTGTTCACGC
ATTAT
Found at i:42211655 original size:104 final size:104
Alignment explanation
Indices: 42211470--42211715 Score: 456
Period size: 104 Copynumber: 2.4 Consensus size: 104
42211460 TGCAGGGAAT
* * *
42211470 ATTTGTTGCAGAGAATCTCTTCTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCACG
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCACG
*
42211535 CATTATTTTGTTGCAAGGAATCTTTCCTGTTCACGCATC
66 CATTATTTTGTTGCAAGGAATCTTTCCTGTTCACACATC
42211574 ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCACG
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCACG
42211639 CATTATTTTGTTGCAAGGAATCTTTCCTGTTCACACATC
66 CATTATTTTGTTGCAAGGAATCTTTCCTGTTCACACATC
42211678 ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTT
42211716 CTTTTTGGAC
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 138 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.41
Consensus pattern (104 bp):
ATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTTTCCTGTTCACG
CATTATTTTGTTGCAAGGAATCTTTCCTGTTCACACATC
Found at i:42214540 original size:20 final size:23
Alignment explanation
Indices: 42214505--42214549 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
42214495 GAGCAAATCG
42214505 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
42214527 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
42214548 TT
1 TT
42214550 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:42220532 original size:79 final size:81
Alignment explanation
Indices: 42220398--42220580 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 81
42220388 GAATGATGTG
* *
42220398 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATTG
*
42220462 TGCGAGATACTA-ATTC
66 TGCGAGATACTATA-AC
* * * **
42220478 CGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAATT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAATT
* *
42220540 GTGTGAGTTACTATAAC
65 GTGCGAGATACTATAAC
* *
42220557 TGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
42220581 AATGAGTAGC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 55 0.63
80 31 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (81 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATTG
TGCGAGATACTATAAC
Found at i:42220587 original size:40 final size:40
Alignment explanation
Indices: 42220398--42220580 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
42220388 GAATGATGTG
* * * *
42220398 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTAAATC
* * * *
42220438 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTC
1 CGGGCTAAG-TCCCGAAGGCATTTGTGTGAGTTACTAAATC
*
42220478 CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAATC
* *
42220517 CGGGTTAAGTCCCGAAGGCAATTGTGTGAGTTACTATAA-C
1 CGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTA-AATC
* *
42220557 TGGGCTATGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTG
42220581 AATGAGTAGC
Statistics
Matches: 120, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAATC
Found at i:42228272 original size:79 final size:81
Alignment explanation
Indices: 42228136--42228320 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
42228126 TTGAATGATG
* *
42228136 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
42228200 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
42228215 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
42228277 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
42228295 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42228321 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:42228334 original size:40 final size:40
Alignment explanation
Indices: 42228137--42228320 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
42228127 TGAATGATGT
* * * *
42228137 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
42228177 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
42228217 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
42228255 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
42228296 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
42228321 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:42228342 original size:79 final size:79
Alignment explanation
Indices: 42228189--42228353 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
42228179 GGACTAAGAT
* * **
42228189 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
42228254 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
42228268 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
42228331 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
42228347 CCGAAGG
1 CCGAAGG
42228354 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:42229802 original size:35 final size:35
Alignment explanation
Indices: 42229759--42229935 Score: 225
Period size: 35 Copynumber: 5.1 Consensus size: 35
42229749 GCAGGGAATA
*
42229759 TTTGTTGCAGGGAATCTCTTATGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
*
42229794 TTTGTTGCAGGGAATCTCTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
42229829 TTTGTTGCAGGGAATCT-TTCCTGTTCACGCATTAT
1 TTTGTTGCAGGGAATCTCTT-CTGTTCACGCATTAT
* * * *
42229864 TTTGTAGCAAGGAATCT-TTCCTGTTCACACATCA-
1 TTTGTTGCAGGGAATCTCTT-CTGTTCACGCATTAT
* * * *
42229898 TTTCTTGCACGGAATCTCTCCTGTTCACTCATTAT
1 TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
42229933 TTT
1 TTT
42229936 ATTTTGGAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
34 27 0.21
35 99 0.79
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (35 bp):
TTTGTTGCAGGGAATCTCTTCTGTTCACGCATTAT
Found at i:42230125 original size:35 final size:35
Alignment explanation
Indices: 42230032--42230312 Score: 370
Period size: 35 Copynumber: 8.1 Consensus size: 35
42230022 GCTCCAAAAT
* * *
42230032 AAAATAATGAGTGAACAGGAGAGATTCCGTGCAA-
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
* * * * *
42230066 GAAATGATGTGTTAACAGGAAAGATTCCTTGCAAC
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
*
42230101 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAT
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
* *
42230136 AAAATAATGCGTGAACAGGAGAGATTCCCTACAA-
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
* * * *
42230170 GAAATGATGTGTGAACAGGAAAGATTCCTTGCAAC
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
*
42230205 AAAATAATGCGTGAACAGGAAAGATTCACTGCAAC
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
* *
42230240 AAAATAATGCGTGAACAGGAGAGATTTCCTGCAAC
1 AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
42230275 AAAATAATGCGTGAACA-GAAGAGATTCCCTGCAAC
1 AAAATAATGCGTGAACAGGAA-AGATTCCCTGCAAC
42230310 AAA
1 AAA
42230313 TATTCCCTGC
Statistics
Matches: 214, Mismatches: 30, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
34 58 0.27
35 156 0.73
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (35 bp):
AAAATAATGCGTGAACAGGAAAGATTCCCTGCAAC
Found at i:42230209 original size:104 final size:104
Alignment explanation
Indices: 42230029--42230312 Score: 444
Period size: 104 Copynumber: 2.7 Consensus size: 104
42230019 GATGCTCCAA
* * *
42230029 AATAAAATAATGAGTGAACAGGAGAGATTCCGTGCAAGAAATGATGTGTTAACAGGAAAGATTCC
1 AATAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAAAGATTCC
*
42230094 TTGCAACAAAATAATGCGTGAACAGGAAAGATTCCCTGC
66 TTGCAACAAAATAATGCGTGAACAGGAAAGATTCACTGC
*
42230133 AATAAAATAATGCGTGAACAGGAGAGATTCCCTACAAGAAATGATGTGTGAACAGGAAAGATTCC
1 AATAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAAAGATTCC
42230198 TTGCAACAAAATAATGCGTGAACAGGAAAGATTCACTGC
66 TTGCAACAAAATAATGCGTGAACAGGAAAGATTCACTGC
* * * * *
42230237 AACAAAATAATGCGTGAACAGGAGAGATTTCCTGCAACAAAATAATGCGTGAACA-GAAGAGATT
1 AATAAAATAATGCGTGAACAGGAGAGATTCCCTGCAA-GAAATGATGTGTGAACAGGAA-AGATT
*
42230301 CCCTGCAACAAA
64 CCTTGCAACAAA
42230313 TATTCCCTGC
Statistics
Matches: 166, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
104 136 0.82
105 30 0.18
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.20
Consensus pattern (104 bp):
AATAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAAAGATTCC
TTGCAACAAAATAATGCGTGAACAGGAAAGATTCACTGC
Found at i:42230291 original size:139 final size:138
Alignment explanation
Indices: 42230033--42230314 Score: 413
Period size: 139 Copynumber: 2.0 Consensus size: 138
42230023 CTCCAAAATA
* * * * *
42230033 AAATAATGAGTGAACAGGAGAGATTCCGTGCAAGAAATGATGTGTTAACAGGAAAGATTCCTTGC
1 AAATAATGAGTGAACAGGAAAGATTCCGTGCAAAAAATAATGCGTGAACAGGAAAGATTCCTTGC
* *
42230098 AACAAAATAATGCGTGAACAGGAAAGATTCCCTGCAATAAAATAATGCGTGAACAGGAGAGATTC
66 AACAAAATAATGCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGAAGAGATTC
*
42230163 CCTACAAG
131 CCTACAAC
* * *
42230171 AAATGATGTGTGAACAGGAAAGATTCCTTGCAACAAAATAATGCGTGAACAGGAAAGATTCAC-T
1 AAATAATGAGTGAACAGGAAAGATTCCGTGCAA-AAAATAATGCGTGAACAGGAAAGATTC-CTT
* *
42230235 GCAACAAAATAATGCGTGAACAGGAGAGATTTCCTGCAACAAAATAATGCGTGAACAGAAGAGAT
64 GCAACAAAATAATGCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGAAGAGAT
*
42230300 TCCCTGCAAC
129 TCCCTACAAC
42230310 AAATA
1 AAATA
42230315 TTCCCTGCAA
Statistics
Matches: 127, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
138 29 0.23
139 97 0.76
140 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (138 bp):
AAATAATGAGTGAACAGGAAAGATTCCGTGCAAAAAATAATGCGTGAACAGGAAAGATTCCTTGC
AACAAAATAATGCGTGAACAGGAAAGATTCCCTGCAACAAAATAATGCGTGAACAGAAGAGATTC
CCTACAAC
Found at i:42234908 original size:35 final size:35
Alignment explanation
Indices: 42234819--42235029 Score: 318
Period size: 35 Copynumber: 6.1 Consensus size: 35
42234809 GTCCAAAAAG
* *
42234819 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
* * * *
42234853 AAATGATGTGTGAATAGGAAAGATTCCTTGCAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
42234888 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
*
42234923 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
* *
42234958 AAATAATGCGTGAACAGGAGAGATTCCCTGCGACA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
42234993 AAATAATGCGTGAACA-GAAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAA-AGATTCCCTGCAACA
42235028 AA
1 AA
42235030 TATTCCCTGC
Statistics
Matches: 161, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
34 30 0.19
35 131 0.81
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAAAGATTCCCTGCAACA
Found at i:42235297 original size:29 final size:29
Alignment explanation
Indices: 42235265--42235337 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
42235255 TTCTCAAGAC
* *
42235265 ATTTAAGTTTTCAAAAATTTAGTTTTTAA
1 ATTTAAGTTTTCAAAAATTAAGTTTTCAA
*
42235294 ATTTCCAAATTTTC--AAATTAAGTTTTCAA
1 ATTT--AAGTTTTCAAAAATTAAGTTTTCAA
* *
42235323 ACTTAAGCTTTCAAA
1 ATTTAAGTTTTCAAA
42235338 TTACAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
27 6 0.18
29 21 0.62
31 7 0.21
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTTAAGTTTTCAAAAATTAAGTTTTCAA
Found at i:42235321 original size:13 final size:13
Alignment explanation
Indices: 42235303--42235340 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
42235293 AATTTCCAAA
42235303 TTTTCAAATTAAG
1 TTTTCAAATTAAG
42235316 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
42235330 CTTTCAAATTA
1 TTTTCAAATTA
42235341 CAAATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:42237659 original size:16 final size:16
Alignment explanation
Indices: 42237634--42237667 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42237624 TGTGTTTTGC
* *
42237634 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
42237650 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
42237666 TT
1 TT
42237668 CATCATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:42240185 original size:9 final size:9
Alignment explanation
Indices: 42240171--42240195 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42240161 AGAAACATGA
42240171 TGACCCAGT
1 TGACCCAGT
42240180 TGACCCAGT
1 TGACCCAGT
42240189 TGACCCA
1 TGACCCA
42240196 ATTATTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (9 bp):
TGACCCAGT
Found at i:42248094 original size:24 final size:24
Alignment explanation
Indices: 42248062--42248119 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
42248052 ATGTCCCAAA
42248062 ATTACAGTGGATTAAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
*
42248086 ATTACAGTGGATTGAACCTTGAAG
1 ATTACAGTGGATTAAACCTTGAAG
42248110 ATTACAGTGG
1 ATTACAGTGG
42248120 GGACAATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTACAGTGGATTAAACCTTGAAG
Found at i:42248472 original size:46 final size:46
Alignment explanation
Indices: 42248405--42248822 Score: 432
Period size: 46 Copynumber: 9.0 Consensus size: 46
42248395 GCAGTGGAGC
* * *
42248405 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
*
42248451 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGC-----AAT
*
42248502 AGATTAAAGCT-AACGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
42248547 AGATTAAAGCTGAAGGCAGCTAATCTT-TTTCCCTAGCGTTGCAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * * **
42248592 AGGTTAAAGCTGAAGGCAACGAATCTTATTTCCTTGACGTTGCCGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* ** * * ** *
42248638 GGA--GCAGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTTATAGT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
42248682 AGATCAAAGCTGAGGGTAGCGAATCTTATTT-CCTCGGCGTTGCAGTGGAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCT-GGCGTTGC-----AAT
* *
42248733 AGATTAAAGCTGAAGGCAGCGAATATTATTTCCCCGGCGTTGCAAT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
42248779 AGATTAAGGCTGAAGGCAGCGAATCTTATTTCTCTGGTGTTGCA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCA
42248823 GTGGAATAGA
Statistics
Matches: 307, Mismatches: 49, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
44 33 0.11
45 56 0.18
46 137 0.45
50 29 0.09
51 50 0.16
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (46 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
Found at i:42248691 original size:90 final size:89
Alignment explanation
Indices: 42248554--42248730 Score: 228
Period size: 90 Copynumber: 2.0 Consensus size: 89
42248544 AATAGATTAA
* * * *
42248554 AGCTGAAGGCAGCTAATCTTTTTCCCTAGCGTTGCAGTAGGTTAAAGCTGAAGGCAACGAATCTT
1 AGCTGAAGGCAGCAAATCTTTTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCTT
* *
42248619 ATTTCCTTGACGTTGCCGTGGAGC
66 ATTTCCTCGACGTTGCAGTGGAGC
* * * * * *
42248643 AGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTTATAGTAGATCAAAGCTGAGGGTAGCGAATCT
1 AGCTGAAGGCAGCAAATCTT-TTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCT
*
42248708 TATTTCCTCGGCGTTGCAGTGGA
65 TATTTCCTCGACGTTGCAGTGGA
42248731 ATAGATTAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 19 0.26
90 55 0.74
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (89 bp):
AGCTGAAGGCAGCAAATCTTTTTCCCTAGCGTTACAGTAGATCAAAGCTGAAGGCAACGAATCTT
ATTTCCTCGACGTTGCAGTGGAGC
Found at i:42248740 original size:141 final size:135
Alignment explanation
Indices: 42248405--42248815 Score: 439
Period size: 141 Copynumber: 2.9 Consensus size: 135
42248395 GCAGTGGAGC
* *
42248405 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCCTAGCGTTGTAGTAGATTAAAGCTGAAGGCAG
1 AGATCAAAGCTGAAGGCAGCGAATCTT-TTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAG
* *
42248470 CGAATCTTATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCT-AACGCAGCGAATCTTATTTCC
65 CGAATCTTATTTCCTTGGCGTTGCAGTGG---AG----AAGCTGAAGGCAGCGAATCTTATTTCT
*
42248534 CTGGCGTTGCAAT
123 CTGGCGTTACAAT
* * * *
42248547 AGATTAAAGCTGAAGGCAGCTAATCTTTTTCCCTAGCGTTGCAGTAGGTTAAAGCTGAAGGCAAC
1 AGATCAAAGCTGAAGGCAGCGAATCTTTTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAGC
* * * *
42248612 GAATCTTATTTCCTTGACGTTGCCGTGGAGCAGCTGAAGGCAGCAAATCTTATTTCTCTGGCGTT
66 GAATCTTATTTCCTTGGCGTTGCAGTGGAGAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCGTT
* *
42248677 ATAGT
131 ACAAT
* * *
42248682 AGATCAAAGCTGAGGGTAGCGAATCTTATTT-CCTCGGCGTTGCAGTGGAATAGATTAAAGCTGA
1 AGATCAAAGCTGAAGGCAGCGAATCTT-TTTCCCT-AGCGTTGCA---G--TAGATTAAAGCTGA
* ** * * *
42248746 AGGCAGCGAATATTATTTCCCCGGCGTTGCAATAGATTAAGGCTGAAGGCAGCGAATCTTATTTC
59 AGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGA-GAA-GCTGAAGGCAGCGAATCTTATTTC
42248811 TCTGG
122 TCTGG
42248816 TGTTGCAGTG
Statistics
Matches: 229, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
134 4 0.02
135 54 0.24
136 11 0.05
138 2 0.01
139 1 0.00
141 102 0.45
142 27 0.12
143 28 0.12
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (135 bp):
AGATCAAAGCTGAAGGCAGCGAATCTTTTTCCCTAGCGTTGCAGTAGATTAAAGCTGAAGGCAGC
GAATCTTATTTCCTTGGCGTTGCAGTGGAGAAGCTGAAGGCAGCGAATCTTATTTCTCTGGCGTT
ACAAT
Found at i:42248791 original size:97 final size:98
Alignment explanation
Indices: 42248405--42248840 Score: 434
Period size: 97 Copynumber: 4.6 Consensus size: 98
42248395 GCAGTGGAGC
* *
42248405 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCC-CTAGCGTT---GT--AGTAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
*
42248464 AGGCAGCGAATCTTATTTCCTTGGCGTTGCAGTGGAAT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGC-----AAT
*
42248502 AGATTAAAGCT-AACGCAGCGAATCTTATTTCC-CTGGCGTTGC-----AATAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* * *
42248560 AGGCAGCTAATCTT-TTTCCCTAGCGTTGCAGT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * * * *
42248592 AGGTTAAAGCTGAAGGCAACGAATCTTATTTCCT-TGACGTTGCCGTGG---AG----CAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* * ** *
42248649 AGGCAGCAAATCTTATTTCTCTGGCGTTATAGT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
42248682 AGATCAAAGCTGAGGGTAGCGAATCTTATTTCCTC-GGCGTTGCAGTGGAATAGATTAAAGCTGA
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
* *
42248746 AGGCAGCGAATATTATTTCCCCGGCGTTGCAAT
66 AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
* * *
42248779 AGATTAAGGCTGAAGGCAGCGAATCTTATTT-CTCTGGTGTTGCAGTGGAATAGATTGAAGCT
1 AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCT
42248841 ACTAATCCTA
Statistics
Matches: 282, Mismatches: 38, Indels: 38
0.79 0.11 0.11
Matches are distributed among these distances:
89 19 0.07
90 66 0.23
91 27 0.10
93 4 0.01
95 13 0.05
96 58 0.21
97 95 0.34
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (98 bp):
AGATTAAAGCTGAAGGCAGCGAATCTTATTTCCTCTGGCGTTGCAGTGGAATAGATTAAAGCTGA
AGGCAGCGAATCTTATTTCCCTGGCGTTGCAAT
Found at i:42262040 original size:14 final size:15
Alignment explanation
Indices: 42262018--42262094 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42262008 CAATCAAACA
42262018 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
42262032 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
* *
42262047 ACAGAAAAGTAAAATATTTT
1 CCAGAAAA-T----CATTTT
42262067 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
42262081 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
42262095 ACTAGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 15 0.31
16 1 0.02
18 1 0.02
19 3 0.06
20 8 0.16
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:42266962 original size:45 final size:44
Alignment explanation
Indices: 42266885--42266986 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 44
42266875 AATGGTAGCA
* *
42266885 GTAACAGTAACAGTAACAGTATTCAACGCACAAAGTG-CTGAATC
1 GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAATC
* *
42266929 TGTAATAGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATC
1 -GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
42266974 GATAATAGTAACA
1 G-TAATAGTAACA
42266987 ATAGTCAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
44 1 0.02
45 48 0.96
46 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (44 bp):
GTAATAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATC
Found at i:42267233 original size:40 final size:40
Alignment explanation
Indices: 42267189--42267275 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
42267179 AGTTCATTAC
* *
42267189 TTTAGTAA-TCTCACAGTTCAATGCAATACACATAACAATA
1 TTTAGTAACT-TCACAATTCAATGCAATACACAAAACAATA
* * *
42267229 TTTAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
*
42267269 TTCAGTA
1 TTTAGTA
42267276 TTCCATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (40 bp):
TTTAGTAACTTCACAATTCAATGCAATACACAAAACAATA
Found at i:42267949 original size:25 final size:23
Alignment explanation
Indices: 42267905--42267965 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
42267895 ATTTTGATTT
*
42267905 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
42267929 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
42267953 ATATAAATTATAT
1 AT-TTAATTATAT
42267966 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:42267968 original size:35 final size:35
Alignment explanation
Indices: 42267913--42267981 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
42267903 TTATTTAATA
* *
42267913 ATATAATATCATTATAATTTAATTATCATAAATTC
1 ATATAATATAATTATAATTTAAATATCATAAATTC
*
42267948 ATATAATATAAATTAT-ATTTAAATATCATTAATT
1 ATATAATAT-AATTATAATTTAAATATCATAAATT
42267982 AAATAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (35 bp):
ATATAATATAATTATAATTTAAATATCATAAATTC
Found at i:42273598 original size:25 final size:23
Alignment explanation
Indices: 42273554--42273614 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
42273544 ATTTTGATTT
*
42273554 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
42273578 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
42273602 ATATAAATTATAT
1 AT-TTAATTATAT
42273615 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:42273617 original size:35 final size:35
Alignment explanation
Indices: 42273562--42273641 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
42273552 TTATTTAATA
* *
42273562 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
42273596 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
42273631 ATATAAT-TAAA
1 ATATAATATAAA
42273642 ACAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:42275642 original size:17 final size:17
Alignment explanation
Indices: 42275620--42275653 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42275610 TTCTTTTTTA
42275620 ATTTAT-ATTTATTATTT
1 ATTTATGATTT-TTATTT
42275637 ATTTATGATTTTTATTT
1 ATTTATGATTTTTATTT
42275654 GTTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATGATTTTTATTT
Found at i:42277014 original size:26 final size:26
Alignment explanation
Indices: 42276985--42277061 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
42276975 AACATATTTC
* *
42276985 TCAAAATTTTAATAGGGGTAAAATTA
1 TCAAAATTTTACTAGGGGTAAAATCA
* * *
42277011 TCAAAAAATTTACCAGGGGTAAAATCG
1 TC-AAAATTTTACTAGGGGTAAAATCA
*
42277038 TTAAAATTTTACT-GAGGGTAAAAT
1 TCAAAATTTTACTAG-GGGTAAAAT
42277062 AGAGATGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.02
26 20 0.49
27 20 0.49
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:42297052 original size:40 final size:40
Alignment explanation
Indices: 42296861--42297045 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
42296851 TTGAATGATG
* * * * *
42296861 TCCGGGCTAAGTCCCGAAGG-GTTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42296901 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42296941 TTCGAGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42296980 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
42297021 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42297046 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 33 0.27
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42297067 original size:79 final size:79
Alignment explanation
Indices: 42296914--42297078 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
42296904 GGACTAAGAT
** **
42296914 CCGAAGGCATTTGTGCGAGATACTAATTTCGAGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAAACTCGAGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
42296979 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
42296993 CCGAAGGCATTTGTGCGAGTTACTATAACT-GGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTA-AACTCGAGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
42297056 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
42297072 CCGAAGG
1 CCGAAGG
42297079 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 46 0.63
80 27 0.37
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAACTCGAGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:42299392 original size:24 final size:24
Alignment explanation
Indices: 42299364--42299412 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42299354 TATCTTGAAA
42299364 AGAAGATAAAGTAAACGGACTGAC
1 AGAAGATAAAGTAAACGGACTGAC
42299388 AGAAGATAAAGTAAACGGACTGAC
1 AGAAGATAAAGTAAACGGACTGAC
42299412 A
1 A
42299413 TTTTTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.24, T:0.12
Consensus pattern (24 bp):
AGAAGATAAAGTAAACGGACTGAC
Found at i:42300611 original size:47 final size:47
Alignment explanation
Indices: 42300557--42300651 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
42300547 TAGTGCCTAG
* * *
42300557 TGATTGAAATAAAAACTTCTAAATAGTTGAGTGACTTGATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
*
42300604 TGATTGAAATAAAAACTTCTAAATAATTTAGTGAATTAATGAAAACT
1 TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
42300651 T
1 T
42300652 TCGAATAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (47 bp):
TGATTGAAATAAAAACTTCTAAATAATTGAGTGAATTAATGAAAACT
Found at i:42306161 original size:58 final size:58
Alignment explanation
Indices: 42306097--42306214 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
42306087 ATAAACTATA
42306097 AAACGAACATGAAAAATATAATATAGAGAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
1 AAACGAACATGAAAAATATAATATAGAGAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
*
42306155 AAACGAACATGAAAAATATAATATATAGAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
1 AAACGAACATGAAAAATATAATATAGAGAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
42306213 AA
1 AA
42306215 TGAGATGAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.11
Consensus pattern (58 bp):
AAACGAACATGAAAAATATAATATAGAGAGAGAGAGAAAAGAAAGAAAAAGAGAAATG
Found at i:42311270 original size:41 final size:41
Alignment explanation
Indices: 42311213--42311294 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
42311203 AAAATGGTGT
42311213 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
1 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
42311254 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
1 TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
42311295 CACTTTTGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (41 bp):
TGCTAAGCACAAACACAGGCACATTTTGGAAACTAGTCTTA
Found at i:42315067 original size:18 final size:17
Alignment explanation
Indices: 42315034--42315067 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42315024 GCAATTAATA
*
42315034 TAAAAAATAAAGATATT
1 TAAAAAATAAAAATATT
42315051 TAAAAAATATAAAATAT
1 TAAAAAATA-AAAATAT
42315068 AGCCTTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAATAAAAATATT
Found at i:42321604 original size:17 final size:18
Alignment explanation
Indices: 42321572--42321605 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42321562 AGTCAACAAA
*
42321572 ATAATAACAGTAAAATAC
1 ATAATAACAATAAAATAC
42321590 ATAATAA-AATAAAATA
1 ATAATAACAATAAAATA
42321606 AAACATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
ATAATAACAATAAAATAC
Found at i:42321790 original size:3 final size:3
Alignment explanation
Indices: 42321782--42321862 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
42321772 TAAAAATGGA
** *
42321782 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GGT AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42321830 -AT AAT AA- AACT AAT -AT AAT AAT AAAT AA- AAT AA
1 AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT AAT AA
42321863 ACAAAAAGAG
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 8 0.12
3 53 0.80
4 5 0.08
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:42331776 original size:23 final size:23
Alignment explanation
Indices: 42331746--42331791 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42331736 TTTCTAGAGA
42331746 AAGAACAGTAACTTTGGAGGGAT
1 AAGAACAGTAACTTTGGAGGGAT
42331769 AAGAACAGTAACTTTGGAGGGAT
1 AAGAACAGTAACTTTGGAGGGAT
42331792 TTTGATCTTC
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:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (23 bp):
AAGAACAGTAACTTTGGAGGGAT
Found at i:42336120 original size:19 final size:19
Alignment explanation
Indices: 42336096--42336140 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42336086 TCCCCCTTTT
* *
42336096 TTTATTTTAATGCAATTTA
1 TTTATTTTAATACAATATA
*
42336115 TTTATTTTTATACAATATA
1 TTTATTTTAATACAATATA
42336134 TTT-TTTT
1 TTTATTTT
42336141 CTTCATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTATTTTAATACAATATA
Found at i:42346086 original size:227 final size:227
Alignment explanation
Indices: 42345683--42346128 Score: 732
Period size: 227 Copynumber: 2.0 Consensus size: 227
42345673 TCATTGGTTG
*
42345683 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGGTGGAATACATTAACT
1 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
* * * *
42345748 TTTGTTGTGCCAAAAGAGAGGATTGCTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATATAT
66 TCTATTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATACAT
* * * *
42345813 CAGTCAGAGGTTTCTCGACCAGAAACGTAAAGAATTTTTAGAGCTTAAATAGGGTCATATGACAA
131 CAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACAA
*
42345878 TGTCCGAATATGAATTAGAATTTGTTCGGCTA
196 TGTCCGAATATGAACTAGAATTTGTTCGGCTA
*
42345910 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGCTTACCAGTGATGGAATACATTAACT
1 AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
* * * *
42345975 TCTATTGTGCCGAAAGAGATGATTACTTGGGAATTCTTTCAAATTGAG-TTCTGAAAGAAATACA
66 TCTATTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTC-AAAAGAAATACA
*
42346039 TCAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTGGAGCTTAAACAGGGTCATATGACA
130 TCAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACA
42346104 ATGTCCGAATATGAACTAGAATTTG
195 ATGTCCGAATATGAACTAGAATTTG
42346129 CTCGATTGAG
Statistics
Matches: 202, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
226 3 0.01
227 199 0.99
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (227 bp):
AATGTCTTAAGTGTGCAGTATCTCTGTTAAAAGATTCAGATTACCAGTGATGGAATACATTAACT
TCTATTGTGCCAAAAGAGAGGATTACTTGGGAATTCTTTCAAACTGAGTTTCAAAAGAAATACAT
CAGTCAGAGGTTTCTCGACCAAAAACGTAAAAAATTCTTAGAGCTTAAACAGGGTCATATGACAA
TGTCCGAATATGAACTAGAATTTGTTCGGCTA
Found at i:42350974 original size:25 final size:24
Alignment explanation
Indices: 42350946--42351026 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 24
42350936 GACACACCAC
*
42350946 AGCTCGTATGAGCTTCCCATTATAT
1 AGCTCGCATGAGCTTCCCATTAT-T
*
42350971 AGCTCACATGAGCTT-CCAGTTACTT
1 AGCTCGCATGAGCTTCCCA-TTA-TT
*
42350996 AGCTCGCATGAGCTTCCCTTTATT
1 AGCTCGCATGAGCTTCCCATTATT
42351020 CAGCTCG
1 -AGCTCG
42351027 GAGAAGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 5 0.10
25 40 0.83
26 3 0.06
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (24 bp):
AGCTCGCATGAGCTTCCCATTATT
Found at i:42357830 original size:24 final size:21
Alignment explanation
Indices: 42357777--42357820 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
42357767 ATATGGTCTT
42357777 TTGTTTTGCATGAGGCACATG
1 TTGTTTTGCATGAGGCACATG
42357798 TTGTTTTGCATGAGGCACATG
1 TTGTTTTGCATGAGGCACATG
42357819 TT
1 TT
42357821 CTTGTTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (21 bp):
TTGTTTTGCATGAGGCACATG
Found at i:42361147 original size:22 final size:23
Alignment explanation
Indices: 42361121--42361169 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
42361111 AAATATAAAC
42361121 TTTATTATTCTATTATTA-ATTA
1 TTTATTATTCTATTATTACATTA
* *
42361143 TTTATTTTTGTATTATTACTATTA
1 TTTATTATTCTATTATTAC-ATTA
42361167 TTT
1 TTT
42361170 TGTCTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
24 7 0.30
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTATTCTATTATTACATTA
Found at i:42364778 original size:30 final size:31
Alignment explanation
Indices: 42364737--42364812 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
42364727 CATAGAGGGA
* *
42364737 TTAATTAATTTTT-TATTATTTTATA-AGGAC
1 TTAATTGATTTTTAAATTATTTTA-AGAGGAC
*
42364767 TTAATTGATTTTTAAAATTATTTTAAGAGGTC
1 TTAATTGATTTTT-AAATTATTTTAAGAGGAC
42364799 TTAATTGATTTTTA
1 TTAATTGATTTTTA
42364813 GGGATTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 12 0.30
31 2 0.05
32 26 0.65
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (31 bp):
TTAATTGATTTTTAAATTATTTTAAGAGGAC
Found at i:42364802 original size:32 final size:32
Alignment explanation
Indices: 42364751--42364812 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
42364741 TTAATTTTTT
42364751 ATTATTTTATAAGGACTTAATTGATTTTTAAA
1 ATTATTTTATAAGGACTTAATTGATTTTTAAA
*
42364783 ATTATTTTA-AGAGGTCTTAATTGATTTTTA
1 ATTATTTTATA-AGGACTTAATTGATTTTTA
42364813 GGGATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (32 bp):
ATTATTTTATAAGGACTTAATTGATTTTTAAA
Found at i:42365462 original size:20 final size:19
Alignment explanation
Indices: 42365439--42365479 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42365429 ATTTTAAAAT
42365439 AATTTAAAAAATTAATTAAA
1 AATTTAAAAAA-TAATTAAA
**
42365459 AATTTGTAAAATAATTAAA
1 AATTTAAAAAATAATTAAA
42365478 AA
1 AA
42365480 ATCAATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTTAAAAAATAATTAAA
Found at i:42365480 original size:20 final size:21
Alignment explanation
Indices: 42365417--42365481 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
42365407 CATACTTTTC
42365417 AAAA-TTATAAAAATT--TTAA
1 AAAATTTA-AAAAATTAATTAA
42365436 AATAATTTAAAAAATTAATT-A
1 AA-AATTTAAAAAATTAATTAA
**
42365457 AAAATTTGTAAAA-TAATTAA
1 AAAATTTAAAAAATTAATTAA
42365477 AAAAT
1 AAAAT
42365482 CAATTAAGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 7 0.18
20 24 0.62
21 6 0.15
22 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTTAAAAAATTAATTAA
Found at i:42365763 original size:20 final size:20
Alignment explanation
Indices: 42365740--42365782 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
42365730 TTTAGTTATT
*
42365740 AAATGATAATTTTATAAATA
1 AAATGATAATCTTATAAATA
*
42365760 AAATTATAATCTTATAAATA
1 AAATGATAATCTTATAAATA
42365780 AAA
1 AAA
42365783 CAATTTAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATGATAATCTTATAAATA
Found at i:42366394 original size:32 final size:32
Alignment explanation
Indices: 42366358--42366419 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
42366348 AAAAATGAAC
* *
42366358 TTTTA-AATGTATATCTTTTTTAATTTTTAAAG
1 TTTTATAATGTAT-TATTTTTCAATTTTTAAAG
*
42366390 TTTTATTATGTATTATTTTTCAATTTTTAA
1 TTTTATAATGTATTATTTTTCAATTTTTAA
42366420 GAAGTAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTTATAATGTATTATTTTTCAATTTTTAAAG
Found at i:42367114 original size:22 final size:22
Alignment explanation
Indices: 42367081--42367141 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
42367071 GCCCGGCCCG
* *
42367081 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
42367104 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
42367126 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
42367142 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:42367154 original size:16 final size:16
Alignment explanation
Indices: 42367117--42367156 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42367107 TTAATAAAAT
* *
42367117 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
42367133 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
42367149 TAAAATTA
1 TAAAATTA
42367157 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:42367235 original size:59 final size:60
Alignment explanation
Indices: 42367167--42367345 Score: 261
Period size: 59 Copynumber: 2.9 Consensus size: 60
42367157 TCAAATTATT
* *
42367167 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCAA
42367226 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCAA
42367286 ATTATTAATTGTTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
1 A--ATT-A-----TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
42367346 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 9
0.91 0.02 0.08
Matches are distributed among these distances:
59 56 0.51
60 2 0.02
62 3 0.03
63 1 0.01
68 47 0.43
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (60 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAACTTATCAA
Found at i:42367452 original size:22 final size:24
Alignment explanation
Indices: 42367412--42367455 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
42367402 AAATAAACTT
42367412 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
42367436 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
42367456 CTTGCCCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:42372416 original size:28 final size:28
Alignment explanation
Indices: 42372358--42372438 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 28
42372348 TGATAAGCCT
42372358 AAAAATTACAAAAATA-TATAAAAGTGAA
1 AAAAATTA-AAAAATATTATAAAAGTGAA
42372386 AAAAATTAAAAAATATTAT-AAA-TGACTA
1 AAAAATTAAAAAATATTATAAAAGTGA--A
*
42372414 AAAAATTTAAAAAAAATTATTAAAA
1 AAAAA-TTAAAAAATATTA-TAAAA
42372439 TAAAGATTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
26 3 0.07
27 10 0.22
28 17 0.37
29 12 0.26
30 1 0.02
31 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (28 bp):
AAAAATTAAAAAATATTATAAAAGTGAA
Found at i:42372417 original size:29 final size:28
Alignment explanation
Indices: 42372358--42372438 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
42372348 TGATAAGCCT
*
42372358 AAAAATTACAAAAATA-TATAAAAGTGAA
1 AAAAATTA-AAAAATATTATAAAACTGAA
42372386 AAAAATTAAAAAATATTATAAATGACT-AA
1 AAAAATTAAAAAATATTATAAA--ACTGAA
* *
42372415 AAAATTTAAAAAAAATTATTAAAA
1 AAAAATTAAAAAATATTA-TAAAA
42372439 TAAAGATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
27 7 0.15
28 15 0.33
29 18 0.39
30 6 0.13
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (28 bp):
AAAAATTAAAAAATATTATAAAACTGAA
Found at i:42372504 original size:17 final size:18
Alignment explanation
Indices: 42372472--42372519 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
42372462 ATTAAAAATA
*
42372472 AAAATTTTAAAAATATGG
1 AAAATTTTAAAAATATAG
*
42372490 AAAATTTT-CAAATATAG
1 AAAATTTTAAAAATATAG
42372507 AAAATTATTAAAA
1 AAAATT-TTAAAA
42372520 TTATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 13 0.52
18 10 0.40
19 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.33
Consensus pattern (18 bp):
AAAATTTTAAAAATATAG
Found at i:42372539 original size:9 final size:9
Alignment explanation
Indices: 42372507--42372540 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
42372497 TCAAATATAG
42372507 AAAATTATT
1 AAAATTATT
42372516 AAAATTATT
1 AAAATTATT
*
42372525 AAAAATATAT
1 AAAATTAT-T
42372535 AAAATT
1 AAAATT
42372541 GTAAATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATTATT
Found at i:42372641 original size:20 final size:21
Alignment explanation
Indices: 42372613--42372661 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
42372603 CAAAGTAACT
*
42372613 CAAATAAATAATA-AAAAATA
1 CAAAAAAATAATATAAAAATA
* * *
42372633 CAAAAAAATGATATAAAATTG
1 CAAAAAAATAATATAAAAATA
42372654 CAAAAAAA
1 CAAAAAAA
42372662 AATTTTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18
Consensus pattern (21 bp):
CAAAAAAATAATATAAAAATA
Done.