Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 47 of 150
Found at i:13361176 original size:30 final size:30
Alignment explanation
Indices: 13361113--13361177 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
13361103 TTAAATCAAG
* * *
13361113 AAAAAAACAAAAAAAGACAAAAAGATAGAA
1 AAAAAAACAAAAAAAGAAAAAAAGAAACAA
* *
13361143 AAAAAAACAAAAAAGGAAAAAAAGAAACCA
1 AAAAAAACAAAAAAAGAAAAAAAGAAACAA
13361173 AAAAA
1 AAAAA
13361178 TAAAGAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.82, C:0.08, G:0.09, T:0.02
Consensus pattern (30 bp):
AAAAAAACAAAAAAAGAAAAAAAGAAACAA
Found at i:13361632 original size:42 final size:42
Alignment explanation
Indices: 13361572--13361909 Score: 387
Period size: 42 Copynumber: 8.1 Consensus size: 42
13361562 AAGGAAAACA
* * * *
13361572 TTCATTACAATTAGAGACCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
*
13361614 TTCATTGCATTCAAAGACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
13361656 TTCGTTGCATTTAGAA-ACCCAGTTCTGGAAGTCCATTCACTT
1 TTCATTGCATTTA-AAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
13361698 TTCATTGCATCTAGAGACCCAGGTGTAGAGGTCTATTCACTT
1 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
* * *
13361740 TTCATTACGTTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
*
13361782 TTCATTGCATCTAGAA-ACCCAGGTGTGGAGGT-CATTCACTT
1 TTCATTGCATTTA-AAGACCCAGGTGTGGAGGTCCATTCACTT
* * * * *
13361823 TTCATTGCATTTAGAGACCCAGGTGCGGAGGTTCTTTGACTT
1 TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
13361865 TTCATTGCATTTAGAA-ACCCAAGTGTAGAGGTCCGTTTACTT
1 TTCATTGCATTTA-AAGACCCAGGTGTGGAGGTCCATTCACTT
13361907 TTC
1 TTC
13361910 TAGTTTACTT
Statistics
Matches: 251, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.00
41 37 0.15
42 209 0.83
43 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
TTCATTGCATTTAAAGACCCAGGTGTGGAGGTCCATTCACTT
Found at i:13361797 original size:126 final size:125
Alignment explanation
Indices: 13361583--13361909 Score: 449
Period size: 126 Copynumber: 2.6 Consensus size: 125
13361573 TCATTACAAT
* * * *
13361583 TAGAGACCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTCAAAGACCCAGGTGTGGAGGTCC
1 TAGAGACCCAGGTGTGGAGGTCTATTCACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCC
* * *
13361648 ATTCACTTTTCGTTGCATTTAGAAACCCAGTTCTGGAAGTCCATTCACTTTTCATTGCATC
66 ATTCACTTTTCATTGCATCTAGAAACCCAGGTCTGGAAGT-CATTCACTTTTCATTGCATC
* * *
13361709 TAGAGACCCAGGTGTAGAGGTCTATTCACTTTTCATTACGTTTAGAGACCCAGGTGTGGAGGTCC
1 TAGAGACCCAGGTGTGGAGGTCTATTCACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCC
* * *
13361774 ATTCACTTTTCATTGCATCTAGAAACCCAGGTGTGGAGGTCATTCACTTTTCATTGCATT
66 ATTCACTTTTCATTGCATCTAGAAACCCAGGTCTGGAAGTCATTCACTTTTCATTGCATC
* * * * *
13361834 TAGAGACCCAGGTGCGGAGGTTCT-TTGACTTTTCATTGCATTTAGAAACCCAAGTGTAGAGGTC
1 TAGAGACCCAGGTGTGGAGG-TCTATTCACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTC
* *
13361898 CGTTTACTTTTC
65 CATTCACTTTTC
13361910 TAGTTTACTT
Statistics
Matches: 177, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
125 81 0.46
126 96 0.54
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (125 bp):
TAGAGACCCAGGTGTGGAGGTCTATTCACTTTTCATTGCATTTAGAGACCCAGGTGTGGAGGTCC
ATTCACTTTTCATTGCATCTAGAAACCCAGGTCTGGAAGTCATTCACTTTTCATTGCATC
Found at i:13362973 original size:146 final size:147
Alignment explanation
Indices: 13362727--13362995 Score: 375
Period size: 147 Copynumber: 1.8 Consensus size: 147
13362717 TTTAAAAGAG
* * *
13362727 AGTTTAGATTTTGAAAAAAAAAATCTATTTTTTTAGTCATTTTAAAGGATAGTTTAAAATTTTAA
1 AGTTTAGATTTTGAAAAAAAAAA-CTATTTTTTTAGTCATTTAAAAAGATAATTTAAAATTTTAA
*
13362792 AATAAAGTTTTGAATTTTTTCAACTATTTCAAAATAAAATGTTTAATCTTTAAGGAAAATAGTGT
65 AATAAAATTTTGAATTTTTTCAACTATTTCAAAATAAAAT-TTTAATCTTTAA-GAAAATAGTGT
13362857 TTTTTTTTAAAAAGGGAGAA
128 TTTTTTTTAAAAAGGGAGAA
* *
13362877 AGTTTAGATTTTGAAAAATAAAA-T-TTTTTTTAGTCATTTAAAAAGA-AATTCTAAATTTTTAA
1 AGTTTAGATTTTGAAAAAAAAAACTATTTTTTTAGTCATTTAAAAAGATAATT-TAAAATTTTAA
* * ** *
13362939 AATAAAATTTTG-ATTTTTTTAACTATTTCGAAATAAGGTTTTAATTTTTAAGAAAAT
65 AATAAAATTTTGAATTTTTTCAACTATTTCAAAATAAAATTTTAATCTTTAAGAAAAT
13362996 TAATGATTTT
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
144 6 0.06
145 11 0.10
146 26 0.24
147 41 0.38
148 1 0.01
150 22 0.21
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (147 bp):
AGTTTAGATTTTGAAAAAAAAAACTATTTTTTTAGTCATTTAAAAAGATAATTTAAAATTTTAAA
ATAAAATTTTGAATTTTTTCAACTATTTCAAAATAAAATTTTAATCTTTAAGAAAATAGTGTTTT
TTTTTAAAAAGGGAGAA
Found at i:13364359 original size:3 final size:3
Alignment explanation
Indices: 13364351--13364400 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
13364341 AATCTTTTAA
13364351 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13364399 AA
1 AA
13364401 AAGATCGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13371606 original size:45 final size:45
Alignment explanation
Indices: 13371538--13371631 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
13371528 AACAGATACT
* * * *
13371538 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTC
*
13371583 CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTT
1 CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTC
13371628 CGGT
1 CGGT
13371632 TCACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAACACATAACAACCACCTTACTAATCAATGATGTC
Found at i:13374429 original size:15 final size:17
Alignment explanation
Indices: 13374399--13374435 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
13374389 TGTTTGTTAG
13374399 TTTTTATAATAATTTC-
1 TTTTTATAATAATTTCA
*
13374415 TTTTTATAAT-TTTTCA
1 TTTTTATAATAATTTCA
13374431 TTTTT
1 TTTTT
13374436 TGAATTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATAATAATTTCA
Found at i:13375094 original size:109 final size:109
Alignment explanation
Indices: 13374892--13375104 Score: 306
Period size: 109 Copynumber: 2.0 Consensus size: 109
13374882 AATCAGATAG
*
13374892 TATACTGATATCTGATTCTGACACGAAAAAAAACGAATTTTTTTTAAATTGTACTAGGTGCCAGC
1 TATACTGATATCTGACTCTGACACGAAAAAAAACGAATTTTTTTTAAATTGTACTAGGTGCCAGC
*
13374957 CATTGACAGACCAACACCTAAACATTTTTATTTTTATTTTTTTCA
66 CATTGACAGACCAACACCCAAACATTTTT-TTTTTATTTTTTTCA
* *
13375002 TATACTGATATCTGACTCTGACAC-AAAAAAAA-GAATTTTTTTTAAAATTGTACTGGGTGCCGG
1 TATACTGATATCTGACTCTGACACGAAAAAAAACGAATTTTTTTT-AAATTGTACTAGGTGCCAG
** * * *
13375065 CCATTGACAGGTCAGCACCCAAA-TTTTTTTTTTTGTTTTT
65 CCATTGACAGACCAACACCCAAACATTTTTTTTTTATTTTT
13375105 CTTTTTTCCC
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 10 0.11
108 16 0.17
109 44 0.47
110 23 0.25
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (109 bp):
TATACTGATATCTGACTCTGACACGAAAAAAAACGAATTTTTTTTAAATTGTACTAGGTGCCAGC
CATTGACAGACCAACACCCAAACATTTTTTTTTTATTTTTTTCA
Found at i:13376103 original size:22 final size:22
Alignment explanation
Indices: 13376077--13376149 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
13376067 TTTTTGCCGC
**
13376077 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAAA
* * *
13376099 CATGAGGGTTTAGTTCGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
13376121 CATGAGAGCTTAGTACGTTAAA
1 CATGAGAGCTTAGTACGTTAAA
13376143 CATGAGA
1 CATGAGA
13376150 TGTGGAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAAA
Found at i:13381474 original size:95 final size:95
Alignment explanation
Indices: 13381289--13381467 Score: 324
Period size: 95 Copynumber: 1.9 Consensus size: 95
13381279 AATGTGTGGA
*
13381289 TTTGATAATACAGGAATTAGAGAAGAGAAAGATCACTAATGCTTACACTCTTGCTTATCAGGTAC
1 TTTGATAATACAGGAATTAGAGAAGAGAAAGATCACTAATGCATACACTCTTGCTTATCAGGTAC
13381354 TTATATTTGGAATATTACTCTAGACTAATC
66 TTATATTTGGAATATTACTCTAGACTAATC
*
13381384 TTTGATAATAGAGGAATTAGAGAAGAGAAAGATCACTAATGCATACACTCTTGCTTATC-GGATA
1 TTTGATAATACAGGAATTAGAGAAGAGAAAGATCACTAATGCATACACTCTTGCTTATCAGG-TA
13381448 CTTATATTTGGAATATTACT
65 CTTATATTTGGAATATTACT
13381468 TCAGACTCAT
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
94 2 0.02
95 79 0.98
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (95 bp):
TTTGATAATACAGGAATTAGAGAAGAGAAAGATCACTAATGCATACACTCTTGCTTATCAGGTAC
TTATATTTGGAATATTACTCTAGACTAATC
Found at i:13382492 original size:12 final size:12
Alignment explanation
Indices: 13382475--13382499 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13382465 AGTGCAGTAG
13382475 CCACTAGTGGAT
1 CCACTAGTGGAT
13382487 CCACTAGTGGAT
1 CCACTAGTGGAT
13382499 C
1 C
13382500 TTTTTTCAGT
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:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (12 bp):
CCACTAGTGGAT
Found at i:13399596 original size:12 final size:12
Alignment explanation
Indices: 13399579--13399604 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13399569 AAATACAACA
13399579 CATAATGAATAG
1 CATAATGAATAG
13399591 CATAATGAATAG
1 CATAATGAATAG
13399603 CA
1 CA
13399605 AACACTACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (12 bp):
CATAATGAATAG
Found at i:13414695 original size:16 final size:16
Alignment explanation
Indices: 13414674--13414707 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
13414664 TATTTACTTT
13414674 ACTAGCTAACCAGAAG
1 ACTAGCTAACCAGAAG
*
13414690 ACTAGCTAACCAGTAG
1 ACTAGCTAACCAGAAG
13414706 AC
1 AC
13414708 GTGATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.18, T:0.15
Consensus pattern (16 bp):
ACTAGCTAACCAGAAG
Found at i:13417522 original size:85 final size:85
Alignment explanation
Indices: 13417348--13417582 Score: 250
Period size: 85 Copynumber: 2.8 Consensus size: 85
13417338 TTATATCATT
* * * * *
13417348 AAATCAAAATAAAATC-TATTAAACAGTAG-GAATAAATCTCGAAATAGA-ATTATTTGA-TT-A
1 AAATC-AAATAAAATCTTGTTAAA-TGTAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAA
***
13417408 TTTCTTTGTTTGGAAACAAAACA
64 TTTC-GAATTTGGAAACAAAACA
* * * *
13417431 ATATCAAATAAAATCTTGTTAAACTG-CGGGAATAAATC-CTGAATCAGATTTTATTTAATTTAA
1 AAATCAAATAAAATCTTGTTAAA-TGTAGAGAATAAATCTC-GAAACAGATTTTATTTAATTTAA
*
13417494 TTTCGAATTTGGAAACAAAATA
64 TTTCGAATTTGGAAACAAAACA
*
13417516 AAATCAAATAAAATCTTGTTAAATGTAGAGAATAAATTTCGAAACAGATTTTATTTAATTTAATT
1 AAATCAAATAAAATCTTGTTAAATGTAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAATT
13417581 TC
66 TC
13417583 TCGTTTTTGG
Statistics
Matches: 127, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
82 12 0.09
83 27 0.21
84 9 0.07
85 73 0.57
86 6 0.05
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (85 bp):
AAATCAAATAAAATCTTGTTAAATGTAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAATT
TCGAATTTGGAAACAAAACA
Found at i:13417714 original size:78 final size:77
Alignment explanation
Indices: 13417620--13418054 Score: 487
Period size: 77 Copynumber: 5.5 Consensus size: 77
13417610 AATAAATCTA
* * * * *
13417620 TTGAATGGCGGGAATCAATCTCGAAATGGATTTTATGTTACTCGTTTTTGGAAATAAAACAAATT
1 TTGAACGGCAGGAATCAATCCCGAAA-CGATTTTATTTTACTCGTTTTTGGAAATAAAACAAATT
* *
13417685 TGAAATAAAATAG
65 TGGAATAAAATCG
* * * *
13417698 TTGAACGGC-GGAAATCAATCTCGAAAGGATTTTTTTTTTATTTTTCTCATTTTTGGAAATAAAA
1 TTGAACGGCAGG-AATCAATCCCGAAACGA------TTTTATTTTACTCGTTTTTGGAAATAAAA
13417762 CAAATTTGGAATAAAATCG
59 CAAATTTGGAATAAAATCG
**** * *
13417781 TTGAACGGCAGGAATCAATCCCGAATTTTTTTTATTTTACTTGTTTTTAGAAATAAAACAAATTT
1 TTGAACGGCAGGAATCAATCCCGAAACGATTTTATTTTACTCGTTTTTGGAAATAAAACAAATTT
13417846 GGAATAAAATCG
66 GGAATAAAATCG
* ** * *
13417858 TTGAACGGCGGGAATTTATCCCGAAACGATTTTATTTTACTTGTTTTTGGAAATAAAACAATTTT
1 TTGAACGGCAGGAATCAATCCCGAAACGATTTTATTTTACTCGTTTTTGGAAATAAAACAAATTT
*
13417923 AGAATAAAATCG
66 GGAATAAAATCG
* * *
13417935 TTGAACGACAGGAATCGATCCCGAAACGATTTTATTTTACTCGTTTTAGGAAATAAAA-AAATTT
1 TTGAACGGCAGGAATCAATCCCGAAACGATTTTATTTTACTCGTTTTTGGAAATAAAACAAA--T
*
13417999 TTGGAATAAAATCA
64 TTGGAATAAAATCG
* * *
13418013 TTGAACGACAGGAATCAATCCCAAAATGATTTTTATTTTACT
1 TTGAACGGCAGGAATCAATCCCGAAACGA-TTTTATTTTACT
13418055 TTAAATTTCC
Statistics
Matches: 309, Mismatches: 37, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
76 2 0.01
77 168 0.54
78 61 0.20
79 12 0.04
83 64 0.21
84 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (77 bp):
TTGAACGGCAGGAATCAATCCCGAAACGATTTTATTTTACTCGTTTTTGGAAATAAAACAAATTT
GGAATAAAATCG
Found at i:13417764 original size:83 final size:81
Alignment explanation
Indices: 13417650--13418129 Score: 402
Period size: 77 Copynumber: 5.9 Consensus size: 81
13417640 TCGAAATGGA
* * *
13417650 TTTTATGTTACTCGTTTTTGGAAATAAAACAAATTTGAAATAAAATAGTTGAACGGCGGAAATCA
1 TTTTATTTTACTCGTTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGG-AATCA
*
13417715 ATCTCGAAAGGATTTTTT
65 ATCCCGAAA-GATTTTTT
* *
13417733 TTTTATTTTTCTCATTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCAGGAATCA
1 TTTTATTTTACTCGTTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGC-GGAATCA
13417798 ATCCCG--A-A--TTTT
65 ATCCCGAAAGATTTTTT
* * **
13417810 TTTTATTTTACTTGTTTTTAGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGGAATTT
1 TTTTATTTTACTCGTTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGC-GGAATCA
13417875 ATCCCGAAACGA------
65 ATCCCGAAA-GATTTTTT
* * * * *
13417887 TTTTATTTTACTTGTTTTTGGAAATAAAACAATTTTAGAATAAAATCGTTGAACGACAGGAATCG
1 TTTTATTTTACTCGTTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGC-GGAATCA
13417952 ATCCCGAAACGA------
65 ATCCCGAAA-GATTTTTT
* * *
13417964 TTTTATTTTACTCGTTTTAGGAAATAAAA-AAATTTTTGGAATAAAATCATTGAACGACAGGAAT
1 TTTTATTTTACTCGTTTTTGGAAATAAAACAAA--TTTGGAATAAAATCGTTGAACGGC-GGAAT
* *
13418028 CAATCCCAAAATGATTTTTA
63 CAATCCCGAAA-GATTTTTT
* * *** * *
13418048 TTTTACTTTAAATTTCCCCGTTTGGAAATAAAATAAAATTAATGGTATAAAATCCGTTGAACGGC
1 TTTTA-TTT-TA-CT-CGTTTTTGGAAATAAAA-CAAATT--TGGAATAAAAT-CGTTGAACGGC
*
13418113 TAGAATCAATCCCGAAA
58 -GGAATCAATCCCGAAA
13418130 CGGATTTTAC
Statistics
Matches: 335, Mismatches: 40, Indels: 36
0.82 0.10 0.09
Matches are distributed among these distances:
76 2 0.01
77 165 0.49
78 39 0.12
79 2 0.01
81 2 0.01
83 62 0.19
84 7 0.02
85 3 0.01
86 1 0.00
87 1 0.00
88 15 0.04
90 13 0.04
91 23 0.07
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (81 bp):
TTTTATTTTACTCGTTTTTGGAAATAAAACAAATTTGGAATAAAATCGTTGAACGGCGGAATCAA
TCCCGAAAGATTTTTT
Found at i:13419626 original size:33 final size:33
Alignment explanation
Indices: 13419555--13419649 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
13419545 AGGATATCTA
* * *
13419555 AAATAATTTAATATGATGAA-A-A-ATAATATTT
1 AAATAATTTAATATAAT-AATACATAAAATATTC
* * *
13419586 AATTAATTTAATTTAATAATACATGAAATATTC
1 AAATAATTTAATATAATAATACATAAAATATTC
* *
13419619 AAATAATTTAATATAATGATATATAAAATAT
1 AAATAATTTAATATAATAATACATAAAATAT
13419650 AAAGTAGTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 2 0.04
31 15 0.30
32 1 0.02
33 32 0.64
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (33 bp):
AAATAATTTAATATAATAATACATAAAATATTC
Found at i:13419753 original size:2 final size:2
Alignment explanation
Indices: 13419746--13419779 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13419736 CACTTAAATA
13419746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13419780 TAATTGTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13420712 original size:26 final size:25
Alignment explanation
Indices: 13420683--13420742 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
13420673 ATTTAAATTA
*
13420683 TTTTTATTTTTTA-AAATTTTGGAGAG
1 TTTTTATTTTTCACAAATTTT-GA-AG
*
13420709 TTTTTAATTTTTCACAAATTTTTAAG
1 TTTTT-ATTTTTCACAAATTTTGAAG
13420735 TTTTTATT
1 TTTTTATT
13420743 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.10
26 12 0.40
27 8 0.27
28 7 0.23
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTTATTTTTCACAAATTTTGAAG
Found at i:13435307 original size:12 final size:12
Alignment explanation
Indices: 13435282--13435314 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13435272 AAGTTAGTCG
13435282 AACAATTATTCA
1 AACAATTATTCA
13435294 AACCAATT-TTCA
1 AA-CAATTATTCA
13435306 AACAATTAT
1 AACAATTAT
13435315 AATCTATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (12 bp):
AACAATTATTCA
Found at i:13435815 original size:17 final size:17
Alignment explanation
Indices: 13435801--13435849 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
13435791 TTTTCATATG
13435801 AAATAACAGTTCATACC
1 AAATAACAGTTCATACC
* *
13435818 AAATGACAGTTCATTCC
1 AAATAACAGTTCATACC
* *
13435835 AATTAATAGTTCATA
1 AAATAACAGTTCATA
13435850 ACACGTAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (17 bp):
AAATAACAGTTCATACC
Found at i:13435858 original size:17 final size:17
Alignment explanation
Indices: 13435838--13435884 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
13435828 TCATTCCAAT
*
13435838 TAATAGTTCATA-ACACG
1 TAATAGTTCATACA-ACA
13435855 TAATAGTTCATACAACA
1 TAATAGTTCATACAACA
*
13435872 TAATAGTTAATAC
1 TAATAGTTCATAC
13435885 TCCATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (17 bp):
TAATAGTTCATACAACA
Found at i:13436102 original size:20 final size:20
Alignment explanation
Indices: 13436077--13436119 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
13436067 ATGCTCACAC
13436077 TCTGCAAACATACCACGCTA
1 TCTGCAAACATACCACGCTA
13436097 TCTGCAAACATACCACGCTA
1 TCTGCAAACATACCACGCTA
13436117 TCT
1 TCT
13436120 TTTCAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.23
Consensus pattern (20 bp):
TCTGCAAACATACCACGCTA
Found at i:13441570 original size:7 final size:6
Alignment explanation
Indices: 13441539--13441588 Score: 55
Period size: 7 Copynumber: 7.5 Consensus size: 6
13441529 ATTTGGTTTA
13441539 TTTATT TTTATT TTTATT TAATTATT CTTTATT CTTTATT CTTTATT TTT
1 TTTATT TTTATT TTTATT T--TTATT -TTTATT -TTTATT -TTTATT TTT
13441589 TGTGATTTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.39
7 19 0.46
8 5 0.12
9 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:13441577 original size:14 final size:13
Alignment explanation
Indices: 13441539--13441588 Score: 66
Period size: 14 Copynumber: 3.7 Consensus size: 13
13441529 ATTTGGTTTA
13441539 TTTATTTTTATT-
1 TTTATTTTTATTC
13441551 TTTATTTAATTATTC
1 TTTATTT--TTATTC
13441566 TTTATTCTTTATTC
1 TTTATT-TTTATTC
13441580 TTTATTTTT
1 TTTATTTTT
13441589 TGTGATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 17 0.50
15 6 0.18
16 1 0.03
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTTATTC
Found at i:13448753 original size:104 final size:104
Alignment explanation
Indices: 13448573--13448781 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
13448563 TTGCAATCAA
*
13448573 AGTGATGCTTAGAAACAATGTTTGTTAAGAAGTTAGCCCATATGTGATAGCTTTTGAAAAGAGTT
1 AGTGATGCTTAAAAACAATGTTTGTTAAGAAGTTAGCCCATATGTGATAGCTTTTGAAAAGAGTT
13448638 ATATTTCATGCCCTTAGACTTAGTTAATTACCTATACTT
66 ATATTTCATGCCCTTAGACTTAGTTAATTACCTATACTT
13448677 AGTGATGCTTAAAAACAATGTTTGTTAAGAAGTTAGCCCATATGTGATAGCTTTTGAAAAGAGTT
1 AGTGATGCTTAAAAACAATGTTTGTTAAGAAGTTAGCCCATATGTGATAGCTTTTGAAAAGAGTT
13448742 ATATTTCATGCCCTTAGACTTAGTTAATTACCTATACTT
66 ATATTTCATGCCCTTAGACTTAGTTAATTACCTATACTT
13448781 A
1 A
13448782 AGTGTTTTTA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (104 bp):
AGTGATGCTTAAAAACAATGTTTGTTAAGAAGTTAGCCCATATGTGATAGCTTTTGAAAAGAGTT
ATATTTCATGCCCTTAGACTTAGTTAATTACCTATACTT
Found at i:13451463 original size:17 final size:18
Alignment explanation
Indices: 13451430--13451471 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
13451420 TGGAATAGTT
*
13451430 AATAAT-AATTTATATTC
1 AATAATCAATTCATATTC
13451447 AATAATCAATTCA-ATTC
1 AATAATCAATTCATATTC
*
13451464 CATAATCA
1 AATAATCA
13451472 CAAGTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATCAATTCATATTC
Found at i:13452658 original size:37 final size:37
Alignment explanation
Indices: 13452558--13452659 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 37
13452548 AGCTTACTCG
* * * * *
13452558 GTATATCAGTAAATAACTCTCAGTTCAGCTTTATTTA
1 GTATATCAGTAGATAACGCTCAGTTGAGCTTTAGTCA
** * *
13452595 GTATATCAGTAGATATTGCTCGGTTGAGGTTTAGTCA
1 GTATATCAGTAGATAACGCTCAGTTGAGCTTTAGTCA
* *
13452632 GTATATCAGTAGGTAACGCTTAGTTGAG
1 GTATATCAGTAGATAACGCTCAGTTGAG
13452660 TAACACTCTG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (37 bp):
GTATATCAGTAGATAACGCTCAGTTGAGCTTTAGTCA
Found at i:13481199 original size:14 final size:14
Alignment explanation
Indices: 13481180--13481206 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13481170 CATTTCTTGG
13481180 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
13481194 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
13481207 ACTGGATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:13482551 original size:22 final size:22
Alignment explanation
Indices: 13482525--13482570 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13482515 TTATTCTATG
13482525 AATTGATATATGT-TTATAAATT
1 AATTGA-ATATGTGTTATAAATT
* *
13482547 AATTGAATATTTGTTCTAAATT
1 AATTGAATATGTGTTATAAATT
13482569 AA
1 AA
13482571 GACAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
AATTGAATATGTGTTATAAATT
Found at i:13485272 original size:30 final size:30
Alignment explanation
Indices: 13485238--13485436 Score: 154
Period size: 30 Copynumber: 6.7 Consensus size: 30
13485228 AGTTTTGACT
* *
13485238 ATCAAATTATGAAAAGGGATGATAACAACC
1 ATCAAATTATGAAAAGGGATGGTGACAACC
*
13485268 ATCAACA--ATGAAAAGGGATGGTGACGACC
1 ATCAA-ATTATGAAAAGGGATGGTGACAACC
* ** * * *
13485297 ATCGAGCTATGAAAAGGGATGGCT-TCAGCT
1 ATCAAATTATGAAAAGGGATGG-TGACAACC
* * ****
13485327 ATCAAATTATGAAAAGGGATAGCT-CCGGTT
1 ATCAAATTATGAAAAGGGAT-GGTGACAACC
* *
13485357 ATCAAATAATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTGACAACC
** *
13485387 ATCAAACGATGAAAAGGGATGGTGGCAACC
1 ATCAAATTATGAAAAGGGATGGTGACAACC
*
13485417 ATCAAAATATGAAAAGGGAT
1 ATCAAATTATGAAAAGGGAT
13485437 AGCTTCGACT
Statistics
Matches: 135, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
29 25 0.19
30 107 0.79
31 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTGACAACC
Found at i:13485282 original size:29 final size:30
Alignment explanation
Indices: 13485246--13485317 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
13485236 CTATCAAATT
13485246 ATGAAAAGGGATGATAACAACCATC-AACA
1 ATGAAAAGGGATGATAACAACCATCGAACA
* * * * *
13485275 ATGAAAAGGGATGGTGACGACCATCGAGCT
1 ATGAAAAGGGATGATAACAACCATCGAACA
13485305 ATGAAAAGGGATG
1 ATGAAAAGGGATG
13485318 GCTTCAGCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.43, C:0.14, G:0.28, T:0.15
Consensus pattern (30 bp):
ATGAAAAGGGATGATAACAACCATCGAACA
Found at i:13485400 original size:90 final size:90
Alignment explanation
Indices: 13485274--13485440 Score: 255
Period size: 90 Copynumber: 1.9 Consensus size: 90
13485264 AACCATCAAC
* * * * * * *
13485274 AATGAAAAGGGATGGTGACGACCATCGAGCTATGAAAAGGGATGGCT-TCAGCTATCAAATTATG
1 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGG-TGGCAACCATCAAAATATG
13485338 AAAAGGGATAGCTCCGGTTATCAAAT
65 AAAAGGGATAGCTCCGGTTATCAAAT
13485364 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGTGGCAACCATCAAAATATGA
1 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGTGGCAACCATCAAAATATGA
13485429 AAAGGGATAGCT
66 AAAGGGATAGCT
13485441 TCGACTATCG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
89 1 0.01
90 68 0.99
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (90 bp):
AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGTGGCAACCATCAAAATATGA
AAAGGGATAGCTCCGGTTATCAAAT
Found at i:13485459 original size:90 final size:90
Alignment explanation
Indices: 13485274--13485468 Score: 250
Period size: 90 Copynumber: 2.2 Consensus size: 90
13485264 AACCATCAAC
* * * * * * *
13485274 AATGAAAAGGGATGGTGACGACCATCGAGCTATGAAAAGGGATGGCTTCAGCTATCAAATTATGA
1 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGCTGCAACCATCAAAATATGA
**
13485339 AAAGGGATAGCTCCGGTTATCAAAT
66 AAAGGGATAGCTCCGACTATCAAAT
13485364 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGG-TGGCAACCATCAAAATATG
1 AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGCT-GCAACCATCAAAATATG
* **
13485428 AAAAGGGATAGCTTCGACTATCGAGGT
65 AAAAGGGATAGCTCCGACTATC-AAAT
13485455 -ATGAAAAGGGATGG
1 AATGAAAAGGGATGG
13485469 GATAACTGAT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
89 1 0.01
90 88 0.97
91 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.19
Consensus pattern (90 bp):
AATGAAAAGGGATGGTGACGACCATCAAACGATGAAAAGGGATGGCTGCAACCATCAAAATATGA
AAAGGGATAGCTCCGACTATCAAAT
Found at i:13490521 original size:28 final size:28
Alignment explanation
Indices: 13490489--13490629 Score: 203
Period size: 28 Copynumber: 5.1 Consensus size: 28
13490479 TAACAGTTTT
* * *
13490489 GTGTGGACCTTAGACCATTACAGTAATA
1 GTGTGGGCCTTAGACCAATACAGTAACA
*
13490517 GTGTGGGCCTTAGCCCAATACAGTAACA
1 GTGTGGGCCTTAGACCAATACAGTAACA
13490545 GTGTGGGCCTTAGACCAATACAGTAACA
1 GTGTGGGCCTTAGACCAATACAGTAACA
* * *
13490573 GTGTGAGCCTTAGACCAATATAG-AAAA
1 GTGTGGGCCTTAGACCAATACAGTAACA
*
13490600 GTGTGGGCCTTAGCCCAATACAGTAACA
1 GTGTGGGCCTTAGACCAATACAGTAACA
13490628 GT
1 GT
13490630 ACAATGCAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
27 23 0.23
28 77 0.77
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (28 bp):
GTGTGGGCCTTAGACCAATACAGTAACA
Found at i:13490764 original size:26 final size:26
Alignment explanation
Indices: 13490735--13490809 Score: 107
Period size: 25 Copynumber: 2.9 Consensus size: 26
13490725 CACCAATATC
* *
13490735 GCAGCAAAGCTGCTAGTAATAGTAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
*
13490761 GCAGCAAAG-TTCCAGTAACAGTAAT
1 GCAGCAAAGCTGCCAGTAACAGTAAT
*
13490786 GCAGCAAAGTTGCCAGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
13490810 TATGTGGCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 22 0.50
26 22 0.50
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAT
Found at i:13491031 original size:27 final size:27
Alignment explanation
Indices: 13490953--13491458 Score: 413
Period size: 27 Copynumber: 18.9 Consensus size: 27
13490943 GGTATAATAG
* * * *
13490953 TCATTTTTCCCTAT-GGGGTAATTCGG
1 TCATTTTACCCTTTGGGGGTATTTCGA
* *
13490979 TCATTTTACCC-TTCGGGGTAATTCGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
13491005 TCATTTTACCCTTTGGGGGTCA-TTCGA
1 TCATTTTACCCTTTGGGGGT-ATTTCGA
*
13491032 TTATTTTACCCTTTGGGGGTCA-TTCGA
1 TCATTTTACCCTTTGGGGGT-ATTTCGA
* * *
13491059 TTATTTTACCCTTTGAGGGTCA-TTCGG
1 TCATTTTACCCTTTGGGGGT-ATTTCGA
** *
13491086 TCATTTTACCCTTCAGGGTTATTTC-A
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * *
13491112 GTTATTTTACCTTTTGAGGGTATTTCAGA
1 -TCATTTTACCCTTTGGGGGTATTTC-GA
* *
13491141 -CATTTTACCCTTCGGGGATATTTCGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * *
13491167 TCATTTTACCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * *
13491194 TCATTTTACCC-TTCGGGGTATTTTGG
1 TCATTTTACCCTTTGGGGGTATTTCGA
* *
13491220 TCATTTTA-CCTTTTGGGGTATTTTGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * * *
13491246 TCATTTTACCCTTCGAGGGTATTTTGG
1 TCATTTTACCCTTTGGGGGTATTTCGA
*
13491273 TCATTTTA-CCTTTCGGGGGTATTTTGA
1 TCATTTTACCCTTT-GGGGGTATTTCGA
*
13491300 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
**
13491327 TCATTTTACCCTTCAGGGGTATTTC-A
1 TCATTTTACCCTTTGGGGGTATTTCGA
* ** *
13491353 GTCATTTTACACTTCAGGGTTATTTCGA
1 -TCATTTTACCCTTTGGGGGTATTTCGA
* ****
13491381 TGATTTTACCCTTTGAAATTATTTCGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * ***
13491408 TGATTTTACCCTTCGAAAGTATTTCGA
1 TCATTTTACCCTTTGGGGGTATTTCGA
* * *
13491435 TCATATTACCCTATGGGGCTATTT
1 TCATTTTACCCTTTGGGGGTATTT
13491459 TGGTCATAAC
Statistics
Matches: 404, Mismatches: 62, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
25 3 0.01
26 80 0.20
27 314 0.78
28 6 0.01
29 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTTTGGGGGTATTTCGA
Found at i:13496352 original size:16 final size:15
Alignment explanation
Indices: 13496315--13496354 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
13496305 AGGAATAAAA
13496315 TACTGAGAAAAAAGC
1 TACTGAGAAAAAAGC
* *
13496330 TATTGAGAAAAAATTC
1 TACTGAGAAAAAA-GC
13496346 TACTGAGAA
1 TACTGAGAA
13496355 CGTTGTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (15 bp):
TACTGAGAAAAAAGC
Found at i:13496785 original size:17 final size:17
Alignment explanation
Indices: 13496763--13496795 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
13496753 GTTAGTGCAC
13496763 ATTGTCATTGCATTTTT
1 ATTGTCATTGCATTTTT
13496780 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
13496796 AATGTTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:13513103 original size:11 final size:11
Alignment explanation
Indices: 13513087--13513137 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
13513077 CAATAAGGAA
13513087 AATAAAAAAAT
1 AATAAAAAAAT
13513098 AATAAAAAAAT
1 AATAAAAAAAT
*
13513109 AA-AAACAACAGT
1 AATAAA-AA-AAT
13513121 AA-AACAAAAAT
1 AATAA-AAAAAT
13513132 AATAAA
1 AATAAA
13513138 TTAATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 3 0.09
11 20 0.59
12 10 0.29
13 1 0.03
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:13521863 original size:13 final size:13
Alignment explanation
Indices: 13521845--13521910 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
13521835 AGTTCTTCAT
*
13521845 TGCTTTTGAAAAC
1 TGCTTTTGAAAAG
13521858 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
13521871 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
* *
13521884 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
13521897 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
13521910 T
1 T
13521911 TCGGTTTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:13529894 original size:25 final size:25
Alignment explanation
Indices: 13529858--13529906 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
13529848 GTAGTGGCAA
*
13529858 GGTGGCGACACAGGTTTGGCAAGGG
1 GGTGGCGACACAGGTGTGGCAAGGG
* *
13529883 GGTGGCGTCACAGGTGTGGTAAGG
1 GGTGGCGACACAGGTGTGGCAAGG
13529907 AGGTCAGAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.14, G:0.49, T:0.18
Consensus pattern (25 bp):
GGTGGCGACACAGGTGTGGCAAGGG
Found at i:13544465 original size:15 final size:16
Alignment explanation
Indices: 13544445--13544475 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13544435 AAAGTCATGG
13544445 ATTAAAATT-CATAGT
1 ATTAAAATTACATAGT
13544460 ATTAAAATTACATAGT
1 ATTAAAATTACATAGT
13544476 TGAATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTAAAATTACATAGT
Found at i:13544576 original size:39 final size:38
Alignment explanation
Indices: 13544532--13544724 Score: 233
Period size: 39 Copynumber: 5.0 Consensus size: 38
13544522 TACGTAAGTT
*
13544532 ATACCCATTATCGCACTTACGTGCCCCTGTTGTACTTTG
1 ATACCC-TTATCGCACTTACGTGCCCCTGTTGTACTTCG
* * *
13544571 GTACCCTAATTGCACTTACGTGCCCCTGTTGTACTTCG
1 ATACCCTTATCGCACTTACGTGCCCCTGTTGTACTTCG
* * *
13544609 ATACTCTTGATTGCACTTACGTGCCCCTATTGTACTTCG
1 ATACCCTT-ATCGCACTTACGTGCCCCTGTTGTACTTCG
* * *
13544648 ATACCCCTAAACGCACTTACGTGGCCCTGTTGTACTTCG
1 ATA-CCCTTATCGCACTTACGTGCCCCTGTTGTACTTCG
* * *
13544687 GTACCCTTGATCTCACTTACGTGCCCCTGTTGCACTTC
1 ATACCCTT-ATCGCACTTACGTGCCCCTGTTGTACTTC
13544725 AGTACTCCTG
Statistics
Matches: 131, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 38 0.29
39 90 0.69
40 3 0.02
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (38 bp):
ATACCCTTATCGCACTTACGTGCCCCTGTTGTACTTCG
Found at i:13544606 original size:19 final size:19
Alignment explanation
Indices: 13544546--13544723 Score: 76
Period size: 19 Copynumber: 9.2 Consensus size: 19
13544536 CCATTATCGC
13544546 ACTTACGTGCCCCTGTTGT
1 ACTTACGTGCCCCTGTTGT
** * * *
13544565 ACTTTGGT-ACCCTAATTGC
1 ACTTACGTGCCCCT-GTTGT
13544584 ACTTACGTGCCCCTGTTGT
1 ACTTACGTGCCCCTGTTGT
* * * *
13544603 ACTT-CGATACTCTTGATTGC
1 ACTTACG-TGCCCCTG-TTGT
*
13544623 ACTTACGTGCCCCTATTGT
1 ACTTACGTGCCCCTGTTGT
* *** *
13544642 ACTT-CGATACCCCTAAACGC
1 ACTTACG-TGCCCCT-GTTGT
*
13544662 ACTTACGTGGCCCTGTTGT
1 ACTTACGTGCCCCTGTTGT
* * * *
13544681 ACTT-CGGTACCCTTGATCT
1 ACTTAC-GTGCCCCTGTTGT
*
13544700 CACTTACGTGCCCCTGTTGC
1 -ACTTACGTGCCCCTGTTGT
13544720 ACTT
1 ACTT
13544724 CAGTACTCCT
Statistics
Matches: 109, Mismatches: 39, Indels: 22
0.64 0.23 0.13
Matches are distributed among these distances:
18 9 0.08
19 57 0.52
20 38 0.35
21 5 0.05
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.35
Consensus pattern (19 bp):
ACTTACGTGCCCCTGTTGT
Found at i:13544683 original size:78 final size:78
Alignment explanation
Indices: 13544532--13544724 Score: 259
Period size: 78 Copynumber: 2.5 Consensus size: 78
13544522 TACGTAAGTT
* * **
13544532 ATACCCATT-ATC-GCACTTACGTGCCCCTGTTGTACTTTGGTACCCTAATTGCACTTACGTGCC
1 ATACCC-TTGATCTGCACTTACGTGCCCCTGTTGTACTTCGATACCCTAAACGCACTTACGTGCC
13544595 CCTGTTGTACTTCG
65 CCTGTTGTACTTCG
* * *
13544609 ATACTCTTGAT-TGCACTTACGTGCCCCTATTGTACTTCGATACCCCTAAACGCACTTACGTGGC
1 ATACCCTTGATCTGCACTTACGTGCCCCTGTTGTACTTCGATA-CCCTAAACGCACTTACGTGCC
13544673 CCTGTTGTACTTCG
65 CCTGTTGTACTTCG
* *
13544687 GTACCCTTGATCT-CACTTACGTGCCCCTGTTGCACTTC
1 ATACCCTTGATCTGCACTTACGTGCCCCTGTTGTACTTC
13544725 AGTACTCCTG
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
76 2 0.02
77 34 0.34
78 64 0.63
79 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (78 bp):
ATACCCTTGATCTGCACTTACGTGCCCCTGTTGTACTTCGATACCCTAAACGCACTTACGTGCCC
CTGTTGTACTTCG
Found at i:13546564 original size:17 final size:16
Alignment explanation
Indices: 13546533--13546566 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13546523 AAATATTATG
13546533 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
13546549 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
13546566 A
1 A
13546567 CGCCATCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:13548140 original size:48 final size:48
Alignment explanation
Indices: 13548067--13548193 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 48
13548057 GGCAAAAATA
* *
13548067 ATACAAGGGTGGCACGGACTGTGTGCAGGCCACCAATAACCTGTTCA-G
1 ATACAAGGGTGGCACGGACTATGTGCAGGCCACCAAGAACCTGTT-ATG
* * *
13548115 ATACAAGGGTGGCACGGACTATGTGCAGGCCACCGAGAATCTGTTATT
1 ATACAAGGGTGGCACGGACTATGTGCAGGCCACCAAGAACCTGTTATG
* * * *
13548163 ACACAAAGGTGGTACGGACTCTGTGCAGGCC
1 ATACAAGGGTGGCACGGACTATGTGCAGGCC
13548194 GCCGAGAAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.01
48 68 0.99
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.20
Consensus pattern (48 bp):
ATACAAGGGTGGCACGGACTATGTGCAGGCCACCAAGAACCTGTTATG
Found at i:13552311 original size:119 final size:119
Alignment explanation
Indices: 13552100--13552318 Score: 284
Period size: 119 Copynumber: 1.8 Consensus size: 119
13552090 TTGTTACCGC
* *
13552100 CCCTTTTCATAGTTCGATAGCCGAAGCTATCCCTTTCCATATTTTGATAACCGAAGCTATACCTT
1 CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTCCATAATTTGATAACCGAAGCTATACCTT
* * *
13552165 TTCATAATTTGATGGTCGACGCCATCCCTTTTCATTGTTGATGCTCATCATCAT
66 TTCATAATTCGATAGTCGAAGCCATCCCTTTTCATTGTTGATGCTCATCATCAT
* * * *
13552219 CCCTTTTCATAATTTGATAGCTGAAG-TCATCCCCTTT-CATAATTTGATAGCCGGAG-TCAT-C
1 CCCTTTTCATAATTCGATAGCCGAAGCT-AT-CCCTTTCCATAATTTGATAACCGAAGCT-ATAC
*
13552280 CTTTTTCATAATTCGATAGTTGAAGCCATCCCTTTTCAT
63 C-TTTTCATAATTCGATAGTCGAAGCCATCCCTTTTCAT
13552319 AATTTGATAG
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
118 4 0.05
119 76 0.88
120 6 0.07
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (119 bp):
CCCTTTTCATAATTCGATAGCCGAAGCTATCCCTTTCCATAATTTGATAACCGAAGCTATACCTT
TTCATAATTCGATAGTCGAAGCCATCCCTTTTCATTGTTGATGCTCATCATCAT
Found at i:13552369 original size:30 final size:30
Alignment explanation
Indices: 13552100--13552468 Score: 295
Period size: 30 Copynumber: 12.3 Consensus size: 30
13552090 TTGTTACCGC
* * * *
13552100 CCCTTTTCATAGTTCGATAGCCGAAGCTAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
* * ** *
13552130 CCCTTTCCATATTTTGATAACCGAAGCTAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
* * *
13552160 ACCTTTTCATAATTTGATGGTCGACGCCAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
*
13552190 CCCTTTTCAT--TGTTGAT-GCTC-ATCA-TCAT
1 CCCTTTTCATAAT-TTGATAG-TCGA--AGCCAT
*
13552219 CCCTTTTCATAATTTGATAG-CTGAAGTCAT
1 CCCTTTTCATAATTTGATAGTC-GAAGCCAT
* * * *
13552249 CCCCTTTCATAATTTGATAGCCGGAGTCAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
* * *
13552279 CCTTTTTCATAATTCGATAGTTGAAGCCAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
13552309 CCCTTTTCATAATTTGATAGTCGAAGCCAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
* * *
13552339 CCCTTTTCATAATTCGATGGTCGTCA-CCAT
1 CCCTTTTCATAATTTGATAGTCG-AAGCCAT
*** * *
13552369 CCCTTTTCATTGCTTGATGGTCGTCA-CCAT
1 CCCTTTTCATAATTTGATAGTCG-AAGCCAT
* ** *
13552399 CCCTTTTAATAATTCAATAGTCGAAGCTAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
* * *
13552429 CCCTTTCCATATTTTGATAGTCGAAACCAT
1 CCCTTTTCATAATTTGATAGTCGAAGCCAT
13552459 CCCTTTTCAT
1 CCCTTTTCAT
13552469 TGGTCAATAC
Statistics
Matches: 275, Mismatches: 51, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
28 3 0.01
29 23 0.08
30 244 0.89
31 5 0.02
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (30 bp):
CCCTTTTCATAATTTGATAGTCGAAGCCAT
Found at i:13553615 original size:107 final size:109
Alignment explanation
Indices: 13553418--13553618 Score: 257
Period size: 107 Copynumber: 1.9 Consensus size: 109
13553408 TATACGACAC
* *
13553418 TACTAACATGCTGTAGACATTAAAATAATAATAAAATAAATATTTCCACTTCAGATTTGTGGTCC
1 TACTAACATGCTATAGACATT-AAATAATAATAAAATAAATATTTCCACATCAGATTTGTGGTCC
* *
13553483 TAAAACCACTATTCTGATTTTACTAAAAATGGGTTGTTACAATAA
65 TAAAACCACTATTCTGATGTCACTAAAAATGGGTTGTTACAATAA
* ** *
13553528 TACTAACATGCTATAGACATT-AA-AATAATAAAATAATTATTTTTACATCTGATTTGTGGTTCC
1 TACTAACATGCTATAGACATTAAATAATAATAAAATAAATATTTCCACATCAGATTTGTGG-TCC
* *
13553591 -GAAACCACTGTT-TCGATGTCACTAAAAA
65 TAAAACCACTATTCT-GATGTCACTAAAAA
13553619 CAAGTTGTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
106 1 0.01
107 53 0.67
108 5 0.06
110 20 0.25
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (109 bp):
TACTAACATGCTATAGACATTAAATAATAATAAAATAAATATTTCCACATCAGATTTGTGGTCCT
AAAACCACTATTCTGATGTCACTAAAAATGGGTTGTTACAATAA
Found at i:13559027 original size:36 final size:36
Alignment explanation
Indices: 13558980--13559053 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
13558970 CAATGAAGAG
13558980 TTGGTGTCCGAGGCATCCTTGGTAGCTATAACTAGC
1 TTGGTGTCCGAGGCATCCTTGGTAGCTATAACTAGC
13559016 TTGGTGTCCGAGGCATCCTTGGTAGCTATAACTAGC
1 TTGGTGTCCGAGGCATCCTTGGTAGCTATAACTAGC
13559052 TT
1 TT
13559054 ATTGGAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (36 bp):
TTGGTGTCCGAGGCATCCTTGGTAGCTATAACTAGC
Found at i:13559777 original size:21 final size:20
Alignment explanation
Indices: 13559751--13559797 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
13559741 AATTTCCTTT
*
13559751 TAATAATCGAAATTTATTTTA
1 TAATAATCGAAA-ATATTTTA
*
13559772 TAATAA--GAAAATATTTTG
1 TAATAATCGAAAATATTTTA
13559790 TAATAATC
1 TAATAATC
13559798 AATGTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 12 0.55
19 4 0.18
21 6 0.27
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (20 bp):
TAATAATCGAAAATATTTTA
Found at i:13559823 original size:16 final size:17
Alignment explanation
Indices: 13559804--13559835 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13559794 AATCAATGTC
13559804 ATAAATAAA-CTTAATA
1 ATAAATAAAGCTTAATA
13559820 ATAAATAAAGCTTAAT
1 ATAAATAAAGCTTAAT
13559836 TAAAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAATAAAGCTTAATA
Found at i:13559959 original size:23 final size:26
Alignment explanation
Indices: 13559932--13559987 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
13559922 TTATTTAAAC
13559932 AAATATCCA-TATTTATA-TA-ATTA
1 AAATATCCATTATTTATACTAGATTA
* *
13559955 AAATATTCATTTATTTATACTAGGTTA
1 AAATATCCA-TTATTTATACTAGATTA
13559982 AAATAT
1 AAATAT
13559988 GTCATAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 8 0.30
25 8 0.30
26 2 0.07
27 9 0.33
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (26 bp):
AAATATCCATTATTTATACTAGATTA
Found at i:13559971 original size:25 final size:28
Alignment explanation
Indices: 13559941--13559992 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
13559931 CAAATATCCA
13559941 TATTTATA-TA-ATTAAAATAT-TCATT
1 TATTTATACTAGATTAAAATATGTCATT
*
13559966 TATTTATACTAGGTTAAAATATGTCAT
1 TATTTATACTAGATTAAAATATGTCAT
13559993 AAGTCCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 2 0.09
27 9 0.39
28 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (28 bp):
TATTTATACTAGATTAAAATATGTCATT
Found at i:13560919 original size:36 final size:37
Alignment explanation
Indices: 13560857--13560937 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 37
13560847 GCTTCAGCCG
* * *
13560857 ATTTGCTCTCTTGTTTCTTTTCTTTTCTTTTCTGTCA
1 ATTTGCTCTCTAGTTTATTTTCTTTTCTTTTCTGCCA
*
13560894 ATTTGCTCTC-AGTTTATTTTCTTTTCTTTTCTGCCG
1 ATTTGCTCTCTAGTTTATTTTCTTTTCTTTTCTGCCA
13560930 ATTTGCTC
1 ATTTGCTC
13560938 CCTCTATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 30 0.75
37 10 0.25
ACGTcount: A:0.07, C:0.22, G:0.10, T:0.60
Consensus pattern (37 bp):
ATTTGCTCTCTAGTTTATTTTCTTTTCTTTTCTGCCA
Found at i:13560947 original size:23 final size:23
Alignment explanation
Indices: 13560921--13560965 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
13560911 TTTCTTTTCT
*
13560921 TTTCTGCCGATTTGCTCCCTCTA
1 TTTCTGCCAATTTGCTCCCTCTA
13560944 TTTCTGCCAATTTGCTCCCTCT
1 TTTCTGCCAATTTGCTCCCTCT
13560966 GTCCCTCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.36, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTCTGCCAATTTGCTCCCTCTA
Found at i:13568230 original size:23 final size:23
Alignment explanation
Indices: 13568202--13568248 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
13568192 GGGCAGAGGG
*
13568202 ACAGAGGGAGCAAATTGGCAGAA
1 ACAGAGGGAGCAAATCGGCAGAA
*
13568225 ACAGAGGGAGCAAATCGGTAGAA
1 ACAGAGGGAGCAAATCGGCAGAA
13568248 A
1 A
13568249 AGAAAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.34, T:0.09
Consensus pattern (23 bp):
ACAGAGGGAGCAAATCGGCAGAA
Found at i:13572074 original size:32 final size:32
Alignment explanation
Indices: 13572033--13572097 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
13572023 CTGCATGAAT
*
13572033 TGTTTCTTCATTTTTTTTACCCAAATTCAAGA
1 TGTTTCTTCATTTTTCTTACCCAAATTCAAGA
13572065 TGTTTCTTCATTTTTCTTACCCAAATTCAAGA
1 TGTTTCTTCATTTTTCTTACCCAAATTCAAGA
13572097 T
1 T
13572098 TTTGCTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (32 bp):
TGTTTCTTCATTTTTCTTACCCAAATTCAAGA
Found at i:13582550 original size:2 final size:2
Alignment explanation
Indices: 13582543--13582567 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13582533 CTTCAGACTT
13582543 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
13582568 GCAATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13584868 original size:30 final size:31
Alignment explanation
Indices: 13584832--13584928 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 31
13584822 TAGCGCAACC
* * * *
13584832 TAAAGAAGTGTTTTTGTGGCTATCTTTGAT-
1 TAAAGAAGAGTCTTTGTGGCAATCTCTGATA
*
13584862 TAAAGAA-AGTCTTTGTGGCAATCTCTGTTA
1 TAAAGAAGAGTCTTTGTGGCAATCTCTGATA
* *
13584892 TAAAG-A-AGCCTTTGTGGCGATCTCT-ATTA
1 TAAAGAAGAGTCTTTGTGGCAATCTCTGA-TA
13584921 TAAAGAAG
1 TAAAGAAG
13584929 CCTCTATGGC
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
29 42 0.76
30 13 0.24
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (31 bp):
TAAAGAAGAGTCTTTGTGGCAATCTCTGATA
Found at i:13584879 original size:29 final size:28
Alignment explanation
Indices: 13584844--13584998 Score: 125
Period size: 29 Copynumber: 5.4 Consensus size: 28
13584834 AAGAAGTGTT
* *
13584844 TTTGTGGCTATCTTTGATTAAAGAAAGTC
1 TTTGTGGCTATCTCTG-TTAAAGAAAGCC
*
13584873 TTTGTGGCAATCTCTGTTATAA-AGAAGCC
1 TTTGTGGCTATCTCTGTTA-AAGA-AAGCC
* *
13584902 TTTGTGGCGATCTCTATTATAA-AGAAGCC
1 TTTGTGGCTATCTCTGTTA-AAGA-AAGCC
* * * * * *
13584931 TCTATGGCGATTTTTGTTAAAAGGAAGCC
1 TTTGTGGCTATCTCTGTT-AAAGAAAGCC
* *
13584960 TTTGTGGCTATCTCTGTTAAAGGAAGTC
1 TTTGTGGCTATCTCTGTTAAAGAAAGCC
13584988 TTTGTGGCTAT
1 TTTGTGGCTAT
13584999 TGTAATGCGT
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
28 24 0.23
29 80 0.76
30 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (28 bp):
TTTGTGGCTATCTCTGTTAAAGAAAGCC
Found at i:13584909 original size:58 final size:58
Alignment explanation
Indices: 13584844--13584995 Score: 168
Period size: 58 Copynumber: 2.6 Consensus size: 58
13584834 AAGAAGTGTT
*
13584844 TTTGTGGCTATCTTTGATTAAAGAAAGTCTTTGTGGCAATCTCTGTTATAAA-GAAGCC
1 TTTGTGGCTATCTCTGATTAAAGAAAGTCTTTGTGGCAATCTCTGTTA-AAAGGAAGCC
* * * * * * *
13584902 TTTGTGGCGATCTCT-ATTATAA-AGAAGCCTCTATGGCGATTTTTGTTAAAAGGAAGCC
1 TTTGTGGCTATCTCTGATTA-AAGA-AAGTCTTTGTGGCAATCTCTGTTAAAAGGAAGCC
*
13584960 TTTGTGGCTATCTCTG-TTAAAGGAAGTCTTTGTGGC
1 TTTGTGGCTATCTCTGATTAAAGAAAGTCTTTGTGGC
13584996 TATTGTAATG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
57 20 0.26
58 56 0.74
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (58 bp):
TTTGTGGCTATCTCTGATTAAAGAAAGTCTTTGTGGCAATCTCTGTTAAAAGGAAGCC
Found at i:13585966 original size:13 final size:15
Alignment explanation
Indices: 13585950--13585990 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 15
13585940 TTTAAATTTT
*
13585950 ATTTTAATAA-AA-A
1 ATTTTAAAAATAATA
13585963 ATTTTAAAAATAATA
1 ATTTTAAAAATAATA
13585978 ATTTTAAATAATA
1 ATTTTAAA-AATA
13585991 TTATTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 9 0.38
14 2 0.08
15 9 0.38
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAAAATAATA
Found at i:13585990 original size:16 final size:15
Alignment explanation
Indices: 13585950--13585990 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13585940 TTTAAATTTT
13585950 ATTTT-AATAA-AAA
1 ATTTTAAATAATAAA
13585963 ATTTTAAA-AATAATA
1 ATTTTAAATAATAA-A
13585978 ATTTTAAATAATA
1 ATTTTAAATAATA
13585991 TTATTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.29
14 4 0.17
15 9 0.38
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:13586557 original size:14 final size:14
Alignment explanation
Indices: 13586538--13586575 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
13586528 CTAGAAAACT
13586538 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
13586552 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
13586566 AAGTCATTTT
1 AAATCATTTT
13586576 TAGTAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:13590712 original size:42 final size:42
Alignment explanation
Indices: 13590607--13590698 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
13590597 GGGACATGCG
* ** * *
13590607 GTCGTGTCTCAACCTATGTAACTTACTGAGATGGGCCACATT
1 GTCGTGTCTCAGCCCGTGTAACTTACTAAGATGAGCCACATT
13590649 GTCGTGTCTCAGCCCGTGTAACTTACTAAGATGAGCCACA-T
1 GTCGTGTCTCAGCCCGTGTAACTTACTAAGATGAGCCACATT
13590690 GATCGTGTC
1 G-TCGTGTC
13590699 GTAGGTCGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (42 bp):
GTCGTGTCTCAGCCCGTGTAACTTACTAAGATGAGCCACATT
Found at i:13592168 original size:25 final size:25
Alignment explanation
Indices: 13592093--13592207 Score: 92
Period size: 25 Copynumber: 4.6 Consensus size: 25
13592083 ATACATGTAT
* * *
13592093 GCTCATATGAGCTCAA-AATCGGTAT
1 GCTCATACGAGCTGAATAAT-GGTAA
* * *
13592118 GCTCTTACAAGCTGTA-AATGGTAA
1 GCTCATACGAGCTGAATAATGGTAA
* * *
13592142 GCTCTTTCGAGCTGAGTAATGGTAA
1 GCTCATACGAGCTGAATAATGGTAA
* *
13592167 GCTCATGCGAGTTGAAT-ATCGGTAA
1 GCTCATACGAGCTGAATAAT-GGTAA
13592192 GCTCATACGAGCTGAA
1 GCTCATACGAGCTGAA
13592208 ACCGGTAACC
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
24 18 0.25
25 54 0.75
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAATGGTAA
Found at i:13594299 original size:36 final size:36
Alignment explanation
Indices: 13594259--13594375 Score: 110
Period size: 36 Copynumber: 3.2 Consensus size: 36
13594249 AATTGCTTTG
* * *
13594259 AAGAGCTAGTCCAACCTAAACACGCCAAATGGTCAT
1 AAGAGCTAGTCTAACCAAAACACGCCAAATGCTCAT
* * * * **
13594295 AAGAGCTCA-ACTACCCGATAACACGCCAATTGCTCCG
1 AAGAGCT-AGTCTAACC-AAAACACGCCAAATGCTCAT
* *
13594332 AAGAGTTAGTCTAACCAAAACATGCCAAATGCTCAT
1 AAGAGCTAGTCTAACCAAAACACGCCAAATGCTCAT
13594368 AAGAGCTA
1 AAGAGCTA
13594376 AACCACTCGA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
36 34 0.57
37 26 0.43
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.18
Consensus pattern (36 bp):
AAGAGCTAGTCTAACCAAAACACGCCAAATGCTCAT
Found at i:13594335 original size:73 final size:73
Alignment explanation
Indices: 13594210--13594390 Score: 238
Period size: 73 Copynumber: 2.5 Consensus size: 73
13594200 TGAAAATAGA
* * **
13594210 CCAAATGCTCATAAGAGCTC-ATTCACTCGATAACATGCCAATTGCTTTGAAGAGCTAGTCCAAC
1 CCAAATGCTCATAAGAGCTCAACT-ACTCGATAACACGCCAATTGCTCCGAAGAGCTAGTCCAAC
*
13594274 CTAAACACG
65 CAAAACACG
* * * *
13594283 CCAAATGGTCATAAGAGCTCAACTACCCGATAACACGCCAATTGCTCCGAAGAGTTAGTCTAACC
1 CCAAATGCTCATAAGAGCTCAACTACTCGATAACACGCCAATTGCTCCGAAGAGCTAGTCCAACC
*
13594348 AAAACATG
66 AAAACACG
* *
13594356 CCAAATGCTCATAAGAGCTAAACCACTCGATAACA
1 CCAAATGCTCATAAGAGCTCAACTACTCGATAACA
13594391 TGTCAAAACA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 91 0.98
74 2 0.02
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (73 bp):
CCAAATGCTCATAAGAGCTCAACTACTCGATAACACGCCAATTGCTCCGAAGAGCTAGTCCAACC
AAAACACG
Found at i:13594624 original size:10 final size:10
Alignment explanation
Indices: 13594601--13594629 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13594591 AAATAAAACA
13594601 ATTATATC-T
1 ATTATATCAT
13594610 ATTATATCAT
1 ATTATATCAT
13594620 ATTATATCAT
1 ATTATATCAT
13594630 CAATCATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTATATCAT
Found at i:13607619 original size:29 final size:27
Alignment explanation
Indices: 13607588--13607649 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
13607578 AAAGCATTAA
13607588 AAAAAA-AATTTTAAAATTTAAAAAATTTA
1 AAAAAAGAATTTTAAAA-TTAAAAAA--TA
*
13607617 AAAAAAGTATTTTAAAATTAAAAAATA
1 AAAAAAGAATTTTAAAATTAAAAAATA
13607644 AAAAAA
1 AAAAAA
13607650 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 8 0.26
29 14 0.45
30 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAAAGAATTTTAAAATTAAAAAATA
Found at i:13607620 original size:30 final size:28
Alignment explanation
Indices: 13607583--13607649 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
13607573 AAAAAAAAGC
13607583 ATTAAAAAAAAAATTTTAAAATTTAAAAA
1 ATTAAAAAAAAAATTTTAAAA-TTAAAAA
**
13607612 ATTTAAAAAAAGTATTTTAAAATTAAAAA
1 A-TTAAAAAAAAAATTTTAAAATTAAAAA
13607641 A-TAAAAAAA
1 ATTAAAAAAA
13607650 TAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.23
29 9 0.26
30 18 0.51
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (28 bp):
ATTAAAAAAAAAATTTTAAAATTAAAAA
Found at i:13607708 original size:6 final size:5
Alignment explanation
Indices: 13607670--13607709 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
13607660 TTATTATATT
13607670 CGGGC CGGGC C-GGC C-GGC CGGGC CGGGC CGGGCC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGC CGGG-C CGGGC C
13607710 AAAAAAGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.00, C:0.45, G:0.55, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:13609100 original size:29 final size:29
Alignment explanation
Indices: 13609026--13609092 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
13609016 AGAGTTTATA
*
13609026 GCTATCTCTATAAAAAGGACGCCTTTGTG
1 GCTATCTCTATAAAAAGGACACCTTTGTG
* *
13609055 ACTATATCTATAAAAAGGACACCTTTGTG
1 GCTATCTCTATAAAAAGGACACCTTTGTG
13609084 GCTATCTCT
1 GCTATCTCT
13609093 GTTAAAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (29 bp):
GCTATCTCTATAAAAAGGACACCTTTGTG
Found at i:13612521 original size:31 final size:33
Alignment explanation
Indices: 13612481--13612548 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
13612471 GAATTTTAAA
13612481 TTAGAGTTTAGGG-TTTTTTAATTTGTAAGTGT
1 TTAGAGTTTAGGGTTTTTTTAATTTGTAAGTGT
* *
13612513 TTAG-GTTTAGGGTTTTTTTTTATTTTTAAGTGT
1 TTAGAGTTTAGGG-TTTTTTTAATTTGTAAGTGT
13612546 TTA
1 TTA
13612549 TTAATTATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 8 0.25
32 4 0.12
33 20 0.62
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (33 bp):
TTAGAGTTTAGGGTTTTTTTAATTTGTAAGTGT
Found at i:13612614 original size:14 final size:14
Alignment explanation
Indices: 13612595--13612643 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
13612585 GATTTAAGGG
13612595 TTTTGAAAAAATAA
1 TTTTGAAAAAATAA
* *
13612609 TTTTGACAAGATGAA
1 TTTTGAAAAAAT-AA
* *
13612624 ATCTGAAAAAATAA
1 TTTTGAAAAAATAA
13612638 TTTTGA
1 TTTTGA
13612644 CGAAATAGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.49, C:0.04, G:0.12, T:0.35
Consensus pattern (14 bp):
TTTTGAAAAAATAA
Found at i:13623173 original size:64 final size:64
Alignment explanation
Indices: 13623094--13623218 Score: 250
Period size: 64 Copynumber: 2.0 Consensus size: 64
13623084 GCTGATCCCC
13623094 TGCTATCACGATGTTCAATCTAACAACCTGAAAATAATAACTAGGTAAGTTCGTGAGAACTCAT
1 TGCTATCACGATGTTCAATCTAACAACCTGAAAATAATAACTAGGTAAGTTCGTGAGAACTCAT
13623158 TGCTATCACGATGTTCAATCTAACAACCTGAAAATAATAACTAGGTAAGTTCGTGAGAACT
1 TGCTATCACGATGTTCAATCTAACAACCTGAAAATAATAACTAGGTAAGTTCGTGAGAACT
13623219 TAATGAGTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (64 bp):
TGCTATCACGATGTTCAATCTAACAACCTGAAAATAATAACTAGGTAAGTTCGTGAGAACTCAT
Found at i:13623754 original size:305 final size:305
Alignment explanation
Indices: 13623196--13623808 Score: 1075
Period size: 305 Copynumber: 2.0 Consensus size: 305
13623186 TGAAAATAAT
*
13623196 AACTAGGTAAGTTCGTGAGAACTTAATGAGTTCTTGAGACACAAATCCCACAATAAATATCATTA
1 AACTAGGTAAGTTCGTGAGAACTTAATGAATTCTTGAGACACAAATCCCACAATAAATATCATTA
*
13623261 AACATTAAGAGATTAGACTCAAACTTACAGACTAGCACGCCATATTTGGAGGATACAACTCTCTC
66 AACATTAAGAGATTAGACTCAAACTGACAGACTAGCACGCCATATTTGGAGGATACAACTCTCTC
* * *
13623326 TGATTCGAAATATCCACTGGCAGGTACTACTGTAATCAGAGTCAGCCTACTGGTGGACACTAACT
131 TAATTCGAAATATCCACTGGCAGGTACTACCGCAATCAGAGTCAGCCTACTGGTGGACACTAACT
*
13623391 ATTTTTGGAAACTTGTATATGATGAACACGACACAATTGCTTTGCATGTACATCACTTTTGCGGA
196 ATTTTTGGAAACTTGTATATGATGAACACGACACAATTGCTTTGCATGTACATCACTTTTGCAGA
* *
13623456 CCATCCTGTCATAGCTATCAGACTTATTGTTTAAACATTTCATGC
261 CCATCCTGTCATAACTATCAAACTTATTGTTTAAACATTTCATGC
*
13623501 AACTAGGTAAGTTCGTGAGTACTTAATGAATTCTTGAGACACAAATCCCACAATAAATATCATTA
1 AACTAGGTAAGTTCGTGAGAACTTAATGAATTCTTGAGACACAAATCCCACAATAAATATCATTA
* *
13623566 AACATTAAGAGGTTAGACTCAAACTGATAGACTAGCACGCCATATTTGGAGGATACAACTCTCTC
66 AACATTAAGAGATTAGACTCAAACTGACAGACTAGCACGCCATATTTGGAGGATACAACTCTCTC
* *
13623631 TAATTCGAAATGTCCACTGGC-GGATACTACCGCAATTAGAGTCAGCCTACTGGTGGACACTAAC
131 TAATTCGAAATATCCACTGGCAGG-TACTACCGCAATCAGAGTCAGCCTACTGGTGGACACTAAC
* *
13623695 TATTTTTGGAAACTTGTATATGATGAACATGACACAATTGCTTTGCATGTACGTCACTTTTGCAG
195 TATTTTTGGAAACTTGTATATGATGAACACGACACAATTGCTTTGCATGTACATCACTTTTGCAG
13623760 ACCATCCTGTCATAACTATCAAACTTATTGTTTAAACATTTCATGC
260 ACCATCCTGTCATAACTATCAAACTTATTGTTTAAACATTTCATGC
13623806 AAC
1 AAC
13623809 GCGCACTCCT
Statistics
Matches: 292, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
304 2 0.01
305 290 0.99
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (305 bp):
AACTAGGTAAGTTCGTGAGAACTTAATGAATTCTTGAGACACAAATCCCACAATAAATATCATTA
AACATTAAGAGATTAGACTCAAACTGACAGACTAGCACGCCATATTTGGAGGATACAACTCTCTC
TAATTCGAAATATCCACTGGCAGGTACTACCGCAATCAGAGTCAGCCTACTGGTGGACACTAACT
ATTTTTGGAAACTTGTATATGATGAACACGACACAATTGCTTTGCATGTACATCACTTTTGCAGA
CCATCCTGTCATAACTATCAAACTTATTGTTTAAACATTTCATGC
Found at i:13627969 original size:41 final size:42
Alignment explanation
Indices: 13627728--13627969 Score: 291
Period size: 41 Copynumber: 5.9 Consensus size: 42
13627718 TTGTATAAAA
* ** *
13627728 CACCGGCAT-AAAGCCTGCTAGGCACAAAGCCTG--ATACATT
1 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATA-ATT
* * * * *
13627768 CCACCGGCA-CAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
* * *
13627810 CACCGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
*
13627851 CACCGGCATC-AATCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
13627892 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
*
13627934 CACCGGCATC-AAGCCTGCTAGACGTAAAGTTTGAAA
1 CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAA
13627970 CATCTTATTT
Statistics
Matches: 179, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
41 134 0.75
42 43 0.24
43 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (42 bp):
CACCGGCATCAAAGCCTGCTAGACGTAAAGTCTGAAATAATT
Found at i:13628641 original size:16 final size:17
Alignment explanation
Indices: 13628620--13628654 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13628610 ATCTAATAAT
13628620 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
13628636 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
13628653 TT
1 TT
13628655 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:13633382 original size:40 final size:40
Alignment explanation
Indices: 13633329--13633407 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
13633319 GCGTTTGGAT
13633329 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
1 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
* * * * *
13633369 AAAAAACGCCGCTAAAGATCGAGTATTAGCGGCGCTTTT
1 AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTT
13633408 TGGAAAGCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAAAACACCGCTAAAAATCAAGCATTACCGGCGCTTTTA
Found at i:13633653 original size:41 final size:41
Alignment explanation
Indices: 13633497--13633654 Score: 149
Period size: 41 Copynumber: 3.9 Consensus size: 41
13633487 CTTTGAGTTT
* * * * **
13633497 TCGGGGCTTTAGTGTCGTTTTT-GAAAAAGCGTCACTAACGC
1 TCGGGGCTTTAGCGGCGTTTTTAG-AAAAGCGCCGCTAATAC
* *
13633538 AT-GGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
1 -TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
* * *
13633579 TTGGGGCTTTAGCGGCGCTTCTAGAAAAGCGCCGCTAATAC
1 TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
* * * *
13633620 TCGGGGCTTTAGCTGCATTTTTTGAAAAACGCCGC
1 TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGC
13633655 AAAAATATTT
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 95 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATAC
Found at i:13634057 original size:14 final size:14
Alignment explanation
Indices: 13634047--13634080 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
13634037 GGTTTAAGGT
13634047 TTAGGGGTTAAATG
1 TTAGGGGTTAAATG
13634061 TTAGGGGTT-AATAG
1 TTAGGGGTTAAAT-G
13634075 TTAGGG
1 TTAGGG
13634081 CTTTAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (14 bp):
TTAGGGGTTAAATG
Found at i:13635951 original size:16 final size:16
Alignment explanation
Indices: 13635930--13635969 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
13635920 CGTTTGGTTC
13635930 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
13635946 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
13635962 ACTGTAAT
1 GCTGTAAT
13635970 AATAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:13636015 original size:45 final size:44
Alignment explanation
Indices: 13635951--13636043 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
13635941 ATAGAGCTGT
13635951 AATGGAATAGAACTGTAATAATAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAAT-ATTC-ATGTGTTTGGTTGAATGG
* *
13635996 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
13636040 AATG
1 AATG
13636044 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:13636263 original size:54 final size:54
Alignment explanation
Indices: 13636156--13636265 Score: 134
Period size: 54 Copynumber: 2.0 Consensus size: 54
13636146 ATTATTAACA
* * *
13636156 TAAATAATTTAATAAAAATAATAAATAATTTAACCATATTTTAACAATTATTAT
1 TAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTTAACAATAATTAT
* * *
13636210 TAAATATATTTAAT-AAAATAATATATAATTTAATAAAATTCTTAA-TATAATTAT
1 TAAATA-ATTTAATAAAAATAATAAATAATTTAACAAAATT-TTAACAATAATTAT
13636264 TA
1 TA
13636266 TTATATGAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 37 0.77
55 11 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (54 bp):
TAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTTAACAATAATTAT
Found at i:13638680 original size:16 final size:16
Alignment explanation
Indices: 13638630--13638680 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13638620 ATGTCGAGGA
13638630 AGAAATCTGGTGAAAG
1 AGAAATCTGGTGAAAG
* * *
13638646 TGAAAAC-GATG-AAG
1 AGAAATCTGGTGAAAG
13638660 AAGAAATCTGGTGAAAG
1 -AGAAATCTGGTGAAAG
13638677 AGAA
1 AGAA
13638681 GATATGAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
14 3 0.12
15 8 0.31
16 12 0.46
17 3 0.12
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.16
Consensus pattern (16 bp):
AGAAATCTGGTGAAAG
Found at i:13642244 original size:25 final size:26
Alignment explanation
Indices: 13642199--13642255 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
13642189 TTAATTTTAT
*
13642199 AATTAATCTATTTAATTAATAGTAGA
1 AATTAATCTATTTAATAAATAGTAGA
**
13642225 AATTAAT-TATTATAA-AAATAGTTTA
1 AATTAATCTATT-TAATAAATAGTAGA
13642250 AATTAA
1 AATTAA
13642256 ATTTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (26 bp):
AATTAATCTATTTAATAAATAGTAGA
Found at i:13643048 original size:17 final size:17
Alignment explanation
Indices: 13643022--13643091 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 17
13643012 AATTTACAAG
*
13643022 TATTTTATTTTAAGATT
1 TATTTAATTTTAAGATT
*
13643039 TATTTAATTTCATAATTGATGAA
1 TATTTAATTT--TAA--GAT--T
*
13643062 TATTTTATATTTAAGATT
1 TATTTAAT-TTTAAGATT
13643080 TATTTAATTTTA
1 TATTTAATTTTA
13643092 TTATTTGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
17 13 0.32
18 7 0.17
19 3 0.07
20 3 0.07
21 3 0.07
22 3 0.07
23 7 0.17
24 2 0.05
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTAATTTTAAGATT
Found at i:13643105 original size:41 final size:40
Alignment explanation
Indices: 13643022--13643108 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 40
13643012 AATTTACAAG
*
13643022 TATTTTATTTTAAGATTTATTTAATTTCATAATTGATGAA
1 TATTTTATTTTAAGATTTATTTAATTTCATAATTGATAAA
* *
13643062 TATTTTATATTTAAGATTTATTTAATTTTATTATTTG-TAAA
1 TATTTTAT-TTTAAGATTTATTTAATTTCA-TAATTGATAAA
13643103 TATTTT
1 TATTTT
13643109 TTATATACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 8 0.19
41 29 0.69
42 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (40 bp):
TATTTTATTTTAAGATTTATTTAATTTCATAATTGATAAA
Found at i:13644689 original size:15 final size:16
Alignment explanation
Indices: 13644664--13644693 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13644654 TTTGTGCAGT
13644664 TTTTCTATTTTTATTG
1 TTTTCTATTTTTATTG
13644680 TTTT-TATTTTTATT
1 TTTTCTATTTTTATT
13644694 TAAAAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTCTATTTTTATTG
Found at i:13645511 original size:27 final size:27
Alignment explanation
Indices: 13645481--13645537 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
13645471 CAGAGCCGAT
* * *
13645481 ACCAGTCAAGCCTTTCCCATAGGCGGC
1 ACCAATCAAGCCATCCCCATAGGCGGC
*
13645508 ACCAATCAAGCCATCCCCATAGGTGGC
1 ACCAATCAAGCCATCCCCATAGGCGGC
13645535 ACC
1 ACC
13645538 CACTCCCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.39, G:0.19, T:0.16
Consensus pattern (27 bp):
ACCAATCAAGCCATCCCCATAGGCGGC
Found at i:13645558 original size:6 final size:6
Alignment explanation
Indices: 13645536--13645572 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
13645526 ATAGGTGGCA
13645536 CCCACTC CCCA-C CCCATC CCCATC CCCATC CCCATC C
1 CCCA-TC CCCATC CCCATC CCCATC CCCATC CCCATC C
13645573 GACTCTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 20 0.69
7 4 0.14
ACGTcount: A:0.16, C:0.70, G:0.00, T:0.14
Consensus pattern (6 bp):
CCCATC
Found at i:13649514 original size:62 final size:64
Alignment explanation
Indices: 13649438--13649602 Score: 194
Period size: 62 Copynumber: 2.6 Consensus size: 64
13649428 CAATGTAGCT
* *
13649438 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAAT-TTAT-A-TAA-CA
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGT-TGTAATGTTATAATTAATC-
13649499 A
64 A
* * * * *
13649500 AATTTATATTACAAAGTTTGTTACAAGTTTTAGTGTTTTAATGTTGTAATGTTTTAATTAATCT
1 AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTATAATTAATCA
**
13649564 AATTTATGACCACAAAGTTTGTTCCAAGTTTTAATGTTG
1 AATTTAT-ATTACAAAGTTTGTTCCAAGTTTTAATGTTG
13649603 CAATTAATCT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
61 5 0.06
62 43 0.50
63 1 0.01
64 10 0.12
65 27 0.31
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (64 bp):
AATTTATATTACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTTGTAATGTTATAATTAATCA
Found at i:13649592 original size:65 final size:69
Alignment explanation
Indices: 13649465--13649601 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 69
13649455 TTGTTCCAAT
**
13649465 TTTTAATGTTGTAATGTATTTAATTTATATAACAAAATTTATATTACAAAGTTTGTTACAAGTTT
1 TTTTAATGTTGTAATGTATTTAATTTATAT-ACAAAATTTATACCACAAAGTTTGTTACAAGTTT
*
13649530 TAGTG
65 TAATG
* *
13649535 TTTTAATGTTGTAATGT-TTTAA-TTA-AT-C-TAATTTATGACCACAAAGTTTGTTCCAAGTTT
1 TTTTAATGTTGTAATGTATTTAATTTATATACAAAATTTAT-ACCACAAAGTTTGTTACAAGTTT
13649595 TAATG
65 TAATG
13649600 TT
1 TT
13649602 GCAATTAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
64 7 0.11
65 27 0.44
67 2 0.03
68 3 0.05
69 5 0.08
70 17 0.28
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (69 bp):
TTTTAATGTTGTAATGTATTTAATTTATATACAAAATTTATACCACAAAGTTTGTTACAAGTTTT
AATG
Found at i:13652016 original size:26 final size:26
Alignment explanation
Indices: 13651973--13652025 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
13651963 ATTTTATATT
*
13651973 AAAATACTAAAAATAACATGCCAATAA
1 AAAATACTAAAAATAACATACC-ATAA
13652000 AAAATA-TAACAAA-AACATACCATAA
1 AAAATACTAA-AAATAACATACCATAA
13652025 A
1 A
13652026 CGATACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.21
26 10 0.42
27 9 0.38
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAATACTAAAAATAACATACCATAA
Found at i:13652708 original size:14 final size:14
Alignment explanation
Indices: 13652691--13652717 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13652681 ACCTTTTCTT
13652691 TTCTATTTTTTTCA
1 TTCTATTTTTTTCA
13652705 TTCTATTTTTTTC
1 TTCTATTTTTTTC
13652718 TTTTTTCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTATTTTTTTCA
Found at i:13654870 original size:21 final size:21
Alignment explanation
Indices: 13654844--13654884 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13654834 CAATAATGTT
*
13654844 AGAAAAATTCTGGTGTAAGAA
1 AGAAAAATTCTGGTGCAAGAA
* *
13654865 AGAAAATTTGTGGTGCAAGA
1 AGAAAAATTCTGGTGCAAGA
13654885 TAACGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.27, T:0.24
Consensus pattern (21 bp):
AGAAAAATTCTGGTGCAAGAA
Found at i:13655654 original size:20 final size:20
Alignment explanation
Indices: 13655611--13655659 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13655601 AGGAGCCAAT
* *
13655611 AAATCAATTTGATTAAAATT
1 AAATCAAATTGATTAAAATA
*
13655631 AAATCAAATTGATTAGAATA
1 AAATCAAATTGATTAAAATA
*
13655651 AAATAAAAT
1 AAATCAAAT
13655660 AAGATAATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:13659281 original size:27 final size:27
Alignment explanation
Indices: 13659251--13659333 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 27
13659241 AACTCTGAGA
13659251 GAATGATATGTGTGACGAACTCTAAAG
1 GAATGATATGTGTGACGAACTCTAAAG
* ** *
13659278 GAATAATATGTACGACAAACTCTAAAG
1 GAATGATATGTGTGACGAACTCTAAAG
* * ** *
13659305 GAACGGTATGTGTGGTGAACTCTGAAG
1 GAATGATATGTGTGACGAACTCTAAAG
13659332 GA
1 GA
13659334 TTAGTACGTA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (27 bp):
GAATGATATGTGTGACGAACTCTAAAG
Found at i:13664357 original size:50 final size:50
Alignment explanation
Indices: 13664246--13664536 Score: 316
Period size: 50 Copynumber: 5.7 Consensus size: 50
13664236 ATTTGGGTAA
* * *
13664246 AGAGATCCCATGTACGACCATGTCTGGGACATGGC-ATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGA-TGGCA-C--CGAG---ATG
13664302 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * *
13664352 AGAGGTCCCATGTAAGACTATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * **
13664402 AGAGGCCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
* * *
13664452 AGAGGTCCCGTGTAAGACCATGTCTGGGACATGGC-ATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGAT-GGCACCGAGATG
** ** * * *
13664502 AGAACTCTTATGTAAGACCATATGTGGGATATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
13664537 ATTGGCAGTA
Statistics
Matches: 208, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.00
50 164 0.79
53 3 0.01
55 1 0.00
56 38 0.18
57 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGATGGCACCGAGATG
Found at i:13664530 original size:150 final size:154
Alignment explanation
Indices: 13664252--13664543 Score: 387
Period size: 150 Copynumber: 1.9 Consensus size: 154
13664242 GTAAAGAGAT
* *
13664252 CCCATGTACGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-T-AGATGATGAGAGGTCCCATGTAA
** * * *
13664317 GACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAGGTCCCATGTAAGACTATGTTTGGGAC
64 GACCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGAC
*
13664382 ATGGCGTTGGCACCGAGATGAGAGGC
129 ATGGCATTGGCACCGAGATGAGAGGC
* *
13664408 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CA-A-A-GATGAGAGGTCCCGTGTAAGA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATGATGAGAGGTCCCATGTAAGA
* * ** *
13664469 CCATGTCTGGGACATGGC-ATGGGCACCTATATGAGAACTCTTATGTAAGACCATATGTGGGATA
66 CCATGTCTGGGACATGGCGAT-GGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGACA
13664533 TGGCATTGGCA
130 TGGCATTGGCA
13664544 GTACAAGAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
149 2 0.02
150 80 0.67
151 1 0.01
152 1 0.01
155 2 0.02
156 34 0.28
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (154 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATAGATGATGAGAGGTCCCATGTAAGA
CCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCCCATGTAAGACCATATGTGGGACAT
GGCATTGGCACCGAGATGAGAGGC
Found at i:13670368 original size:50 final size:50
Alignment explanation
Indices: 13670257--13670544 Score: 373
Period size: 50 Copynumber: 5.7 Consensus size: 50
13670247 ATTTGGGTAA
* ** *
13670257 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCA-C--CGAG---ATG
*
13670313 AGAGGTCCCATGTAAGACCATGTCTGGGACACGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
* * *
13670363 AGAGGTCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGTACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
13670412 AGAGGTCCCATGTAAGA-CATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
* * *
13670461 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
** * *
13670511 AGAGGTCCCCCGTAAGACCATGTTTGGGGCATGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGG
13670545 CATGGGCAGC
Statistics
Matches: 212, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
48 11 0.05
49 67 0.32
50 92 0.43
53 3 0.01
55 1 0.00
56 38 0.18
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
Found at i:13670479 original size:148 final size:152
Alignment explanation
Indices: 13670256--13670538 Score: 412
Period size: 148 Copynumber: 1.9 Consensus size: 152
13670246 CATTTGGGTA
*
13670256 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-CGAG--TATGAGAGGTCC
* *
13670321 CATGTAAGACCATGTCTGGGACACGGTGTTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGT
63 CATGTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGT
13670386 CTGGGAATGGCGTTGGTACCGAGAT
128 CTGGGAATGGCGTTGGTACCGAGAT
* **
13670411 AAGAGGTCCCATGTAAGA-CATGTCTGGGACATGGTGTTGGCA-C-CGAG-ATGAGAGGTCCCAT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCAT
* * * * *
13670472 GTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATTAGAGGTCCCCCGTAAGACCATGTTTG
66 GTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGTCTG
13670537 GG
131 GG
13670539 GCATGGCATG
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
148 74 0.63
151 3 0.03
153 1 0.01
154 22 0.19
155 17 0.15
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (152 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCACGAGTATGAGAGGTCCCAT
GTAAGACCATGTCTGGGACACGGTGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGTCTG
GGAATGGCGTTGGTACCGAGAT
Found at i:13670581 original size:100 final size:98
Alignment explanation
Indices: 13670262--13670602 Score: 313
Period size: 98 Copynumber: 3.4 Consensus size: 98
13670252 GGTAAAGAGA
* * *
13670262 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCA---AGA-TA--AGAGGTCCCACGTA
* ** * **
13670327 AGACCATGTCTGGGACACGGTGTTGGCACCGAGATGAGAGG
59 AGA-CATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
13670368 TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGTACCGAGATAAGAGGTCCCATGTAAGACATG
1 TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGACATG
** * **
13670433 TCTGGGACATGGTGTTGGCACCGAGATGAGAGG
66 TCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * * *
13670466 TCCCATGTAAGACCATGTTTGGGACATGGTGTTGGCACCAAGATTAGAGGTCCCCCGTAAGACCA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGA-CA
* * * * *
13670531 TGTTTGGGGCATGGCATGGGCAGCTATATGAGAAC
64 TGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
** * *
13670566 TTTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGA-ATGGCGTTGGCA
13670603 GTACAAGAAG
Statistics
Matches: 204, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
98 59 0.29
99 48 0.24
100 57 0.28
101 2 0.01
102 3 0.01
105 11 0.05
106 24 0.12
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (98 bp):
TCCCATGTAAGACCATGTCTGGGAATGGCGTTGGCACCAAGATAAGAGGTCCCACGTAAGACATG
TCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:13673292 original size:22 final size:22
Alignment explanation
Indices: 13673267--13673310 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13673257 CACTAATCAC
13673267 AATAAGCTTATATTTGACTAGA
1 AATAAGCTTATATTTGACTAGA
* *
13673289 AATAAGTTTATATTTTACTAGA
1 AATAAGCTTATATTTGACTAGA
13673311 TTATGACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
AATAAGCTTATATTTGACTAGA
Found at i:13683438 original size:10 final size:11
Alignment explanation
Indices: 13683414--13683447 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13683404 GAAAAGTTGC
13683414 AGAAAAACCTA
1 AGAAAAACCTA
13683425 AGAAAAACCT-
1 AGAAAAACCTA
*
13683435 AGAAAAAACTA
1 AGAAAAACCTA
13683446 AG
1 AG
13683448 GTTAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.65, C:0.15, G:0.12, T:0.09
Consensus pattern (11 bp):
AGAAAAACCTA
Found at i:13686045 original size:46 final size:44
Alignment explanation
Indices: 13685980--13686065 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 44
13685970 ATAGTGTGGT
* * *
13685980 GTTCATCATACCAAGGTTCCTATCATCCTTGATAGTGGGTTGAG
1 GTTCATCATACCAAGGTTCCTACCATACTTGATAGAGGGTTGAG
*
13686024 GTTCATCTTATACCAAGGTTCCTACCATAGTTGATAGAGGGT
1 GTTCATC--ATACCAAGGTTCCTACCATACTTGATAGAGGGT
13686066 CAAGGTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 7 0.19
46 29 0.81
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (44 bp):
GTTCATCATACCAAGGTTCCTACCATACTTGATAGAGGGTTGAG
Found at i:13688976 original size:17 final size:18
Alignment explanation
Indices: 13688956--13688994 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
13688946 CTACTTCTTC
13688956 TTTAGGTTAATT-AGAGT
1 TTTAGGTTAATTGAGAGT
* *
13688973 TTTAGTTTACTTGAGAGT
1 TTTAGGTTAATTGAGAGT
13688991 TTTA
1 TTTA
13688995 TTTGGATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.51
Consensus pattern (18 bp):
TTTAGGTTAATTGAGAGT
Found at i:13690857 original size:2 final size:2
Alignment explanation
Indices: 13690850--13690909 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
13690840 CACGCGCATT
13690850 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13690892 CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA
13690910 TTATTGCTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13691830 original size:29 final size:31
Alignment explanation
Indices: 13691765--13691834 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
13691755 CCTACAAAAA
* **
13691765 TAGTCACTTTTGTTTGACTTAGATTACATTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
*
13691796 TAGTCACTTATGTTTGAAAT-G-TTACGTTT
1 TAGTCACTTATGTTTGAAATAGATTACATTT
13691825 TAGTCACTTA
1 TAGTCACTTA
13691835 CATTATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.49
30 1 0.03
31 17 0.49
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (31 bp):
TAGTCACTTATGTTTGAAATAGATTACATTT
Found at i:13692305 original size:55 final size:55
Alignment explanation
Indices: 13692221--13692328 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
13692211 ATTGACAGTT
13692221 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
1 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
13692276 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAG
1 TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAG
13692329 CCTTTTGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (55 bp):
TGTTTGTTTGTCCATCTCCAAAGAAGAAAGAGAGTCTAAAGATTGTTAGATAGTC
Found at i:13700904 original size:25 final size:23
Alignment explanation
Indices: 13700876--13700927 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
13700866 TTTTTTATAT
13700876 TTTTTTATAAGAATATGTTTTTGAA
1 TTTTTTAT-A-AATATGTTTTTGAA
*
13700901 TTTTTTATAATTATGTTTTTGAA
1 TTTTTTATAAATATGTTTTTGAA
13700924 TTTT
1 TTTT
13700928 AGAATTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 17 0.65
24 1 0.04
25 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTTTATAAATATGTTTTTGAA
Found at i:13700933 original size:21 final size:22
Alignment explanation
Indices: 13700885--13700933 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
13700875 TTTTTTTATA
13700885 AGAA-TATGTTTTTGAATTTTTT
1 AGAATTATGTTTTTGAA-TTTTT
*
13700907 ATAATTATGTTTTTGAA-TTTT
1 AGAATTATGTTTTTGAATTTTT
13700928 AGAATT
1 AGAATT
13700934 GAGACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 3 0.12
23 12 0.50
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (22 bp):
AGAATTATGTTTTTGAATTTTT
Found at i:13703480 original size:25 final size:25
Alignment explanation
Indices: 13703433--13703480 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13703423 ATTGTTAATC
** *
13703433 GTTTTTTTTTTTATTTTTTGTTGTT
1 GTTTTTTTTTTTAAATTTGGTTGTT
13703458 GTTTTTTTTTTTAAATTTGGTTG
1 GTTTTTTTTTTTAAATTTGGTTG
13703481 CTATTTATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (25 bp):
GTTTTTTTTTTTAAATTTGGTTGTT
Found at i:13706939 original size:23 final size:23
Alignment explanation
Indices: 13706883--13706969 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
13706873 TCTCTGTGAC
* * *
13706883 GCCTTTGTAGAGTATTTTGTAAA
1 GCCTTTGTGGTGTATTCTGTAAA
13706906 GCCTTTGTGGTGTATTCTGTAAA
1 GCCTTTGTGGTGTATTCTGTAAA
* * * *
13706929 GCCTTTTTGGTGTATTCAGTGAT
1 GCCTTTGTGGTGTATTCTGTAAA
* *
13706952 GCCTGTGTGGTATATTCT
1 GCCTTTGTGGTGTATTCT
13706970 ATGACATTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (23 bp):
GCCTTTGTGGTGTATTCTGTAAA
Found at i:13726783 original size:45 final size:45
Alignment explanation
Indices: 13726714--13726804 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
13726704 ATTTAAAGAC
* * *
13726714 AAAATGGGCCAGTATGCGAGATAGGAAATAAGTGGTGCCAAAAAT
1 AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
*
13726759 AAAATGGGCCAGCATGTGAAATAGGAAAGAAGTGGTGCCAAAAAT
1 AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
13726804 A
1 A
13726805 CAAAGTGTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (45 bp):
AAAATGGGCCAGCATGCGAAATAGGAAAGAAGTGGTGCCAAAAAT
Found at i:13728486 original size:16 final size:16
Alignment explanation
Indices: 13728467--13728501 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13728457 CATATAATAA
*
13728467 ATTATATTAATAATTT
1 ATTATATTAATAAGTT
*
13728483 ATTATTTTAATAAGTT
1 ATTATATTAATAAGTT
13728499 ATT
1 ATT
13728502 TAATATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTATATTAATAAGTT
Done.