Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 34 of 35
Found at i:5068157 original size:51 final size:51
Alignment explanation
Indices: 5068080--5068467 Score: 233
Period size: 52 Copynumber: 7.4 Consensus size: 51
5068070 CAATTCTCCT
* * *
5068080 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTA
* * *
5068131 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTC-A
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAACAC-TAATTTTCTA
** * * * *
5068185 CAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAACCCCGTTA-TTTC--
1 CAATCGGGGATACTCCAACCCCGATT--T--T-----ATTTTCAAAACAC-TAATTTTCTA
* * * *
5068242 CAA--GGGGATACTCCAACCCCTG-CTTTATTCTT-AAAATATTGA-TTTCTCA
1 CAATCGGGGATACTCCAACCCC-GATTTTATT-TTCAAAACACTAATTTTCT-A
* * * *
5068291 TAATCGGGGATACTCGAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
* *
5068343 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTA
* * * * *
5068395 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAA-ACATCAATTTTTTCA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC-T-AATTTTCT-A
*
5068448 CAATCGAGGATACTCCAACC
1 CAATCGGGGATACTCCAACC
5068468 TCGTTATTTC
Statistics
Matches: 259, Mismatches: 48, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
46 6 0.02
47 4 0.02
48 1 0.00
49 3 0.01
50 2 0.01
51 64 0.25
52 75 0.29
53 30 0.12
54 30 0.12
55 25 0.10
56 2 0.01
57 4 0.02
58 4 0.02
59 5 0.02
62 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTA
Found at i:5068221 original size:27 final size:29
Alignment explanation
Indices: 5068187--5068261 Score: 111
Period size: 27 Copynumber: 2.7 Consensus size: 29
5068177 AATTTTCACA
5068187 ATCGGGGATACTCCAACCCCGTTA-AT-C
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
5068214 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
5068243 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
5068262 TGCTTTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.55
28 18 0.41
29 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATATCC
Found at i:5068478 original size:31 final size:28
Alignment explanation
Indices: 5068450--5068526 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
5068440 TTTTTTCACA
*
5068450 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
5068478 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
5068506 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
5068527 ACTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:5068549 original size:264 final size:263
Alignment explanation
Indices: 5068080--5068576 Score: 766
Period size: 264 Copynumber: 1.9 Consensus size: 263
5068070 CAATTCTCCT
* * *
5068080 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
*
5068145 CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGGGGATACTCCAACCCCGTT
66 CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGAGGATACTCCAACCCCGTT
** **
5068210 AATCATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCTGCTTTATTCTTA
131 AATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTGCTTTATTCCCA
*
5068275 AAATATTGATTTCTCATAATCGGGGATACTCGAACCCCGATTTTATTGCTAAAACACTAATTTTT
196 AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTT
5068340 CCA
261 CCA
* *
5068343 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTTTAATCGGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATAC
* * ** *
5068408 TCCAGCTCCGATTTTA-TTTC-CAAAAACATCAATTTTTTCACAATCGAGGATACTCCAACCTCG
65 TCCAACTCCGATTTTATTTTCAAAAAAACA-CAAAATTTTCACAATCGAGGATACTCCAACCCCG
* *
5068471 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCC-GACTTTATT
129 TTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTG-CTTTATT
*
5068535 CCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCC
192 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCC
5068577 ATTATTTTCG
Statistics
Matches: 211, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
262 7 0.03
263 82 0.39
264 122 0.58
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGAGGATACTCCAACCCCGTT
AATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTGCTTTATTCCCA
AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTT
CCA
Found at i:5068629 original size:79 final size:79
Alignment explanation
Indices: 5068480--5068671 Score: 215
Period size: 79 Copynumber: 2.4 Consensus size: 79
5068470 GTTATTTCAT
** * *
5068480 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAATAT
* * *
5068545 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * * *
5068559 TGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCAAATCCCGATTTTTTTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAAT-A
5068623 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
5068638 CGGGGATACTCCAGCCCCGTCATTTTCAAGGGGA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
5068672 CACCCCAACC
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 90 0.97
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:5072748 original size:27 final size:28
Alignment explanation
Indices: 5072713--5072787 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
5072703 ATTTTTCACA
*
5072713 ATCGAGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
5072740 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
5072768 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
5072788 TGCTTTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:5072896 original size:52 final size:52
Alignment explanation
Indices: 5072818--5072993 Score: 228
Period size: 52 Copynumber: 3.4 Consensus size: 52
5072808 GATTTCTCAT
* *
5072818 AATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCCAC
* **
5072870 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAA-TTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCC-AC
* * * * *
5072922 AATCGGGGATACTCCAGCTCTGATTTTATTTCCAAAAGCACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAA-CACCAATTTTTCCAC
*
5072975 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
5072994 TTGTTATTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
51 6 0.06
52 72 0.69
53 22 0.21
54 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTCCAC
Found at i:5072987 original size:53 final size:52
Alignment explanation
Indices: 5072607--5072993 Score: 222
Period size: 52 Copynumber: 7.4 Consensus size: 52
5072597 AATTCTCTGT
* * * * * *
5072607 AATCGGGGATATTCTATCTCCGATTTTATTT-TCAAAACACTAATTTTTT-AT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTTTCAC
* * * *
5072658 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACAC-CAATTTTTTCAC
* * * ** ** *
5072712 AATCGAGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAAC-CCCGTTATTTC-C
1 AATCGGGGATACTCCAACCCCGATT--TTAT------TTCTAAAACACCAATTTTTTCAC
* * * *** * *
5072769 GA--GGGGATACTCCAACCCCTG-CTTTA-TTCTTAAAATATTGA-TTTCTCAT
1 AATCGGGGATACTCCAACCCC-GATTTTATTTC-TAAAACACCAATTTTTTCAC
* * *
5072818 AATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCAC
* *
5072870 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT--T
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTT--TTCAC
* * * *
5072922 AATCGGGGATACTCCAGCTCTGATTTTATTTCCAAAAGCACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAA-CACCAATTTTTTCAC
*
5072975 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
5072994 TTGTTATTTC
Statistics
Matches: 252, Mismatches: 58, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
47 2 0.01
48 7 0.03
49 1 0.00
50 1 0.00
51 56 0.22
52 92 0.37
53 35 0.14
54 25 0.10
55 18 0.07
56 2 0.01
57 2 0.01
58 6 0.02
59 1 0.00
60 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCAC
Found at i:5073027 original size:28 final size:28
Alignment explanation
Indices: 5072976--5073052 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
5072966 TTTTTTCACA
* ** **
5072976 ATCGAGGATACTCCAACCTTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
5073004 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
5073032 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
5073053 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:5073076 original size:264 final size:263
Alignment explanation
Indices: 5072607--5073103 Score: 764
Period size: 264 Copynumber: 1.9 Consensus size: 263
5072597 AATTCTCTGT
* * * * *
5072607 AATCGGGGATATTCTATCTCCGATTTTATTTTCAAAACACTAATTTTTTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTTATAATCGGGGATACTC
*
5072672 CAACTCCGATTTTATTTTCAAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
66 CAACTCCGATTTTATTTCCAAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
** * **
5072737 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCTGCTTTATTCTTAA
131 ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
5072802 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
5072867 CAC
261 CAC
*
5072870 AATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTCCTT-TAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT--TTATAATCGGGGATAC
* * ** * **
5072934 TCCAGCTCTGATTTTATTTCCAAAAGCAC-CAATTTTTTCACAATCGAGGATACTCCAACCTTGT
64 TCCAACTCCGATTTTATTTCCAAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGT
*
5072998 TATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCC
129 TA-ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCC
*
5073063 CAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
5073104 TTATTTTCGA
Statistics
Matches: 210, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
263 75 0.36
264 133 0.63
265 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTTATAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
CAC
Found at i:5073155 original size:79 final size:79
Alignment explanation
Indices: 5073006--5073210 Score: 223
Period size: 79 Copynumber: 2.6 Consensus size: 79
5072996 GTTATTTCAT
** * *
5073006 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
5073071 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * * *
5073085 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCTGATTTTTTTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
5073149 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * * *
5073164 CGGGGATACTCCAGCCCCGTCATTTTCAAGGGGACACCCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
5073211 TTATTATCTC
Statistics
Matches: 103, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 100 0.97
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:5074588 original size:23 final size:23
Alignment explanation
Indices: 5074554--5074597 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5074544 CCTCTCAATC
*
5074554 TCTTCAAGAATTATACCCCAAAT
1 TCTTCAAGAATTATAACCCAAAT
*
5074577 TCTT-AAGAAATTGTAACCCAA
1 TCTTCAAG-AATTATAACCCAA
5074598 GGTTGAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (23 bp):
TCTTCAAGAATTATAACCCAAAT
Found at i:5075120 original size:19 final size:20
Alignment explanation
Indices: 5075074--5075124 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5075064 CTGCCAATTT
5075074 CATGTATCGATACAAATGAG
1 CATGTATCGATACAAATGAG
** *
5075094 TGTTTATCGATAC-AATGAG
1 CATGTATCGATACAAATGAG
5075113 CATGTATCGATA
1 CATGTATCGATA
5075125 TAATATATCG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAAATGAG
Found at i:5075818 original size:26 final size:28
Alignment explanation
Indices: 5075789--5075854 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
5075779 TAAATATTTA
5075789 TTTCTTCATTTTTTTTCCTCTA-CTT-C
1 TTTCTTCATTTTTTTTCCTCTATCTTGC
* * *
5075815 TTTCTGT--TTTTTTTTTCTTTATCTTGT
1 TTTCT-TCATTTTTTTTCCTCTATCTTGC
5075842 TTTCTTCATTTTT
1 TTTCTTCATTTTT
5075855 CATTTTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
25 12 0.38
26 9 0.28
27 6 0.19
28 5 0.16
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (28 bp):
TTTCTTCATTTTTTTTCCTCTATCTTGC
Found at i:5077345 original size:28 final size:27
Alignment explanation
Indices: 5077272--5077345 Score: 62
Period size: 28 Copynumber: 2.6 Consensus size: 27
5077262 AATGCATGAA
*
5077272 CCTAAAATGCATAGAATTGCATAAAAGC
1 CCTAAAATGCAT-GAAATGCATAAAAGC
* *
5077300 CTCTAAAA--CATGAAAAATGCCTAAATAGG
1 C-CTAAAATGCATG--AAATGCATAAA-AGC
5077329 CCTAAAATGCATGAAAT
1 CCTAAAATGCATGAAAT
5077346 TACAACATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 20 0.54
29 9 0.24
30 4 0.11
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (27 bp):
CCTAAAATGCATGAAATGCATAAAAGC
Found at i:5077381 original size:57 final size:57
Alignment explanation
Indices: 5077271--5077566 Score: 192
Period size: 58 Copynumber: 5.1 Consensus size: 57
5077261 AAATGCATGA
* * *
5077271 ACCTAAAATGCAT-AGAATTGCATAAAAGCCTCTAAAACATGAAAAATGCCT-AAATAG
1 ACCTAAAATGCATGA-AATTACATAAAAGCCTATAAAACATGAAAAATGACTAAAAT-G
* * * *
5077328 GCCTAAAATGCATGAAATTACA-ACATAGCCTATAAATCATGAAAAATTACTAAAATG
1 ACCTAAAATGCATGAAATTACATA-AAAGCCTATAAAACATGAAAAATGACTAAAATG
* * * ** *
5077385 ACATAAAAATGCATGAAATGACATTAAAGTCCTA-AAGTCATGAAAAATGAATAAAATGG
1 ACCT-AAAATGCATGAAATTACATAAAAG-CCTATAAAACATGAAAAATGACTAAAAT-G
** ** * ** * *
5077444 TTCTGCAATGCATGAAATTACATAATAATCCT-TAAGTCATGGAAAATGAATAAAATG
1 ACCTAAAATGCATGAAATTACATAA-AAGCCTATAAAACATGAAAAATGACTAAAATG
** * * * *
5077501 -CCATCAAAACACATGAAATGACATAAAAGTCCT-TAAATCATGAGAAATGACTAAAGTG
1 ACC-T-AAAATGCATGAAATTACATAAAAG-CCTATAAAACATGAAAAATGACTAAAATG
*
5077559 ACATAAAA
1 ACCTAAAA
5077567 ACGTATGAAA
Statistics
Matches: 189, Mismatches: 37, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
56 2 0.01
57 51 0.27
58 127 0.67
59 9 0.05
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (57 bp):
ACCTAAAATGCATGAAATTACATAAAAGCCTATAAAACATGAAAAATGACTAAAATG
Found at i:5077403 original size:29 final size:28
Alignment explanation
Indices: 5077332--5077403 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
5077322 AAATAGGCCT
* *
5077332 AAAATGCATGAAATTACAACATAGCCTA
1 AAAATGCATGAAATTACAAAATAGCATA
*
5077360 TAAAT-CATGAAAAATTACTAAAAT-GACATA
1 AAAATGCATG--AAATTAC-AAAATAG-CATA
5077390 AAAATGCATGAAAT
1 AAAATGCATGAAAT
5077404 GACATTAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
27 4 0.11
28 4 0.11
29 12 0.34
30 11 0.31
31 4 0.11
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (28 bp):
AAAATGCATGAAATTACAAAATAGCATA
Found at i:5077426 original size:58 final size:58
Alignment explanation
Indices: 5077332--5077579 Score: 200
Period size: 58 Copynumber: 4.3 Consensus size: 58
5077322 AAATAGGCCT
* ** * * * *
5077332 AAAATGCATGAAATTACAACATAG-CCTATAAATCATGAAAAATTACTAAAATGACATA
1 AAAATGCATGAAATGACATTAAAGTCCTA-AAGTCATGAAAAATGAATAAAATGACATA
*
5077390 AAAATGCATGAAATGACATTAAAGTCCTAAAGTCATGAAAAATGAATAAAATGGTTC-T-
1 AAAATGCATGAAATGACATTAAAGTCCTAAAGTCATGAAAAATGAATAAAAT-G-ACATA
** * * * * * *
5077448 GCAATGCATGAAATTACA-TAATAATCCTTAAGTCATGGAAAATGAATAAAATGCCATC
1 AAAATGCATGAAATGACATTAA-AGTCCTAAAGTCATGAAAAATGAATAAAATGACATA
** * * * *
5077506 AAAACACATGAAATGACATAAAAGTCCTTAAA-TCATGAGAAATGACTAAAGTGACATA
1 AAAATGCATGAAATGACATTAAAGTCC-TAAAGTCATGAAAAATGAATAAAATGACATA
* *
5077564 AAAACGTATGAAATGA
1 AAAATGCATGAAATGA
5077580 TAAGAAGGTT
Statistics
Matches: 151, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
56 1 0.01
57 5 0.03
58 133 0.88
59 11 0.07
60 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (58 bp):
AAAATGCATGAAATGACATTAAAGTCCTAAAGTCATGAAAAATGAATAAAATGACATA
Found at i:5077484 original size:116 final size:116
Alignment explanation
Indices: 5077334--5077555 Score: 288
Period size: 116 Copynumber: 1.9 Consensus size: 116
5077324 ATAGGCCTAA
* * **
5077334 AATGCATGAAATTACAACATAGCCTATAAATCATGAAAAATTACTAAAATGACATAAAAATGCAT
1 AATGCATGAAATTACAACATAGCCTATAAATCATGAAAAATGAATAAAATGACATAAAAACACAT
*
5077399 GAAATGACATTAAAGTCC-TAAAGTCATGAAAAATGAATAAAATGGTTCTGC
66 GAAATGACATAAAAGTCCTTAAA-TCATGAAAAATGAATAAAATGGTTCTGC
* * * * *
5077450 AATGCATGAAATTACATA-ATAATCCT-TAAGTCATGGAAAATGAATAAAATGCCATCAAAACAC
1 AATGCATGAAATTACA-ACAT-AGCCTATAAATCATGAAAAATGAATAAAATGACATAAAAACAC
* *
5077513 ATGAAATGACATAAAAGTCCTTAAATCATGAGAAATGACTAAA
64 ATGAAATGACATAAAAGTCCTTAAATCATGAAAAATGAATAAA
5077556 GTGACATAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 82 0.90
117 9 0.10
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.24
Consensus pattern (116 bp):
AATGCATGAAATTACAACATAGCCTATAAATCATGAAAAATGAATAAAATGACATAAAAACACAT
GAAATGACATAAAAGTCCTTAAATCATGAAAAATGAATAAAATGGTTCTGC
Found at i:5079871 original size:21 final size:21
Alignment explanation
Indices: 5079829--5079871 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5079819 TTGTCAAAAT
* *
5079829 GTATCGATACATGCCCTTAAC
1 GTATCGATACAGGCCCTCAAC
5079850 GTATCGATACAAGGCCC-CAAC
1 GTATCGATAC-AGGCCCTCAAC
5079871 G
1 G
5079872 GTTAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (21 bp):
GTATCGATACAGGCCCTCAAC
Found at i:5079922 original size:20 final size:20
Alignment explanation
Indices: 5079897--5080020 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 20
5079887 TTTTCACAAT
5079897 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
5079917 TTGTATCGATACATTCTAGGTTAACCCA
1 TTGTATCGATACA-T-T--GTT----CA
* *
5079945 GATGTATCGATACATT-TCGCA
1 -TTGTATCGATACATTGT-TCA
*
5079966 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
5079986 TTGTATCGATAAATT-TTACA
1 TTGTATCGATACATTGTT-CA
* *
5080006 ATGCATCGATACATT
1 TTGTATCGATACATT
5080021 CAGGCATTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
19 1 0.01
20 57 0.70
21 3 0.04
22 1 0.01
24 4 0.05
27 1 0.01
28 3 0.04
29 12 0.15
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:5082415 original size:51 final size:53
Alignment explanation
Indices: 5082320--5082435 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 53
5082310 TTTTCATCTC
* * * * **
5082320 GAGGATACTTCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAAT-G
1 GAGGATACTCCAACTCCCGATTTCATTTCCAAAACACCAACTTTTCACAATCG
* *
5082371 GAGGATACTCCAACT-CCGATTTTATTTCCAAAACACCGACTTTTCACAATCG
1 GAGGATACTCCAACTCCCGATTTCATTTCCAAAACACCAACTTTTCACAATCG
5082423 G-GGATACTCCAAC
1 GAGGATACTCCAAC
5082436 CCTGTTCTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
51 52 0.95
52 3 0.05
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (53 bp):
GAGGATACTCCAACTCCCGATTTCATTTCCAAAACACCAACTTTTCACAATCG
Found at i:5082473 original size:79 final size:77
Alignment explanation
Indices: 5082377--5082594 Score: 235
Period size: 76 Copynumber: 2.8 Consensus size: 77
5082367 AATGGAGGAT
* * *
5082377 ACTCCAACTCC-GATTTTATTTCCAAAACACCGACTTTTCACAATCGGGGATACTCCAACCCTGT
1 ACTCCAACCCCAG-TTTTATTTCTAAAACA-C-AATTTTCACAATCGGGGATACTCCAACCCTGT
*
5082441 TCTTTCCGAGGGGAC
63 TATTTCCGAGGGGAC
* *
5082456 ACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTT-TC-ATCGGGGATACTCCAACCCCGTTA
1 ACTCCAACCCCAGTTTTATTTCTAAAACA-CAATTTTCACAATCGGGGATACTCCAACCCTGTTA
** *
5082519 TTTTTGAGGGGAT
65 TTTCCGAGGGGAC
* * * * *
5082532 ACCCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATCGGGGATACTCCAACCCTG
1 ACTCCAACCCCAGTTTTATTTCTAAAACA-CAATTT-TCACAATCGGGGATACTCCAACCCTG
5082595 GTTTTATTTC
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
76 64 0.54
77 2 0.02
78 5 0.04
79 46 0.39
80 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (77 bp):
ACTCCAACCCCAGTTTTATTTCTAAAACACAATTTTCACAATCGGGGATACTCCAACCCTGTTAT
TTCCGAGGGGAC
Found at i:5082539 original size:76 final size:78
Alignment explanation
Indices: 5082418--5082592 Score: 237
Period size: 76 Copynumber: 2.3 Consensus size: 78
5082408 GACTTTTCAC
* * * *
5082418 AATCGGGGATACTCCAACCCTGTTCTTTCCGAGGGGACACTCCAACCCCAGTTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCAGCTTTATTTCTAAAA
5082483 CATCAATTT-T-T
66 CATCAATTTATAT
* ** *
5082494 CATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACCCCAACCCCAGCTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCAGCTTTATTTCTAAAA
* *
5082559 TATTAATTTATCAT
66 CATCAATTTAT-AT
5082573 AATCGGGGATACTCCAACCC
1 AATCGGGGATACTCCAACCC
5082593 TGGTTTTATT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
76 64 0.75
77 1 0.01
79 20 0.24
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (78 bp):
AATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCAGCTTTATTTCTAAAA
CATCAATTTATAT
Found at i:5082602 original size:51 final size:51
Alignment explanation
Indices: 5082526--5082644 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
5082516 TTATTTTTGA
*
5082526 GGGGATACCCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATC
** * *
5082577 GGGGATACTCCAACCCTGGTTTTATTTCTAAAATATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATC
*
5082628 GGAGATACTCCAACCCC
1 GGGGATACTCCAACCCC
5082645 GTTATTTTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATC
Found at i:5082660 original size:79 final size:77
Alignment explanation
Indices: 5082577--5082859 Score: 334
Period size: 79 Copynumber: 3.6 Consensus size: 77
5082567 TATCATAATC
*
5082577 GGGGATACTCCAACCCTGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCC-GGTTTTATTTCTAAAATATCAATTTCTCATAATCGG-GATACTCCAAC
5082642 CCCGTTATTTTCGA
64 CCCGTTATTTTCGA
* * * *
5082656 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAGTCGGGGATACTCCAAC
1 GGGGATACTCCAA-CCCGGTTTTATTTCTAAAATATCAATTTCTCATAATC-GGGATACTCCAAC
*
5082721 CCCGTTATTTCCGA
64 CCCGTTATTTTCGA
* * * * *
5082735 GGGGATACTCCAATCCCGATTTTTTTTCT-AAATCATCGATTTTTCACAATCTGGGATACTCCAA
1 GGGGATACTCCAA-CCCGGTTTTATTTCTAAAAT-ATCAATTTCTCATAATC-GGGATACTCCAA
5082799 CCCCGTTATTTTCGA
63 CCCCGTTATTTTCGA
* * * * *
5082814 GGAGATACTCCAACCCCGTTATTATCTCCAAAATATTAAATTTCTC
1 GGGGATACTCCAACCCGGTT-TTATTTCTAAAATA-TCAATTTCTC
5082860 GTCGGGAGAT
Statistics
Matches: 173, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
78 8 0.05
79 149 0.86
80 16 0.09
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.35
Consensus pattern (77 bp):
GGGGATACTCCAACCCGGTTTTATTTCTAAAATATCAATTTCTCATAATCGGGATACTCCAACCC
CGTTATTTTCGA
Found at i:5082680 original size:130 final size:127
Alignment explanation
Indices: 5082450--5082723 Score: 377
Period size: 130 Copynumber: 2.1 Consensus size: 127
5082440 TTCTTTCCGA
* * *
5082450 GGGGACACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTAATCGGAGATACTCCAACCCC
* * *
5082515 GTTATTTTTGAGGGGATACCCCAACCCCAGCTTTATTTCTAAAATATTAATTTATCATAATC
66 GTTATTTTCGAGGGGATACCCCAACCCCAGCTTTATTTCTAAAACATCAATTTATCATAATC
** * *
5082577 GGGGATACTCCAACCCTGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTT-T--TAATCGGAGATACTCCAAC
* * * * * *
5082642 CCCGTTATTTTCGAGGGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAGTC
63 CCCGTTATTTTCGAGGGGATACCCCAACCCCAGCTTTATTTCTAAAACATCAATTTATCATAATC
5082707 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
5082724 GTTATTTCCG
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
127 37 0.29
128 1 0.01
130 89 0.70
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (127 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTAATCGGAGATACTCCAACCCC
GTTATTTTCGAGGGGATACCCCAACCCCAGCTTTATTTCTAAAACATCAATTTATCATAATC
Found at i:5084201 original size:15 final size:15
Alignment explanation
Indices: 5084165--5084202 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5084155 GGTTGTTCAT
5084165 ATTTTTTTTCAATGA
1 ATTTTTTTTCAATGA
**
5084180 AAGTTTTTTCAATGA
1 ATTTTTTTTCAATGA
5084195 ATTTTTTT
1 ATTTTTTT
5084203 GTATTTTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (15 bp):
ATTTTTTTTCAATGA
Found at i:5091041 original size:13 final size:13
Alignment explanation
Indices: 5091023--5091048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5091013 ACAATCCTTC
5091023 ATGTATCGATACA
1 ATGTATCGATACA
5091036 ATGTATCGATACA
1 ATGTATCGATACA
5091049 TCCGAGTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5091383 original size:51 final size:50
Alignment explanation
Indices: 5091319--5091432 Score: 183
Period size: 51 Copynumber: 2.3 Consensus size: 50
5091309 TTTTACTATT
* * *
5091319 TGTATCGATACATTATTCATTGTATCGATATATTCTGGGTTTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCT-GGATTTTACCCAAA
*
5091370 TGTATCGATACATTCTTCATTGTATCGATACATTCTGGATTTTACCCAAA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGATTTTACCCAAA
5091420 TGTATCGATACAT
1 TGTATCGATACAT
5091433 GCAGGCAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 25 0.42
51 34 0.58
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (50 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTGGATTTTACCCAAA
Found at i:5094253 original size:15 final size:15
Alignment explanation
Indices: 5094233--5094266 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5094223 AAATAATGAT
5094233 AAACTGAAATAGAGG
1 AAACTGAAATAGAGG
5094248 AAACTGAAATAGAGG
1 AAACTGAAATAGAGG
5094263 AAAC
1 AAAC
5094267 CAATATTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.24, T:0.12
Consensus pattern (15 bp):
AAACTGAAATAGAGG
Found at i:5095306 original size:21 final size:21
Alignment explanation
Indices: 5095282--5095323 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5095272 CAATATATAA
* *
5095282 CTCCCCTTTAATAAAATTTTT
1 CTCCCCCTTAAAAAAATTTTT
5095303 CTCCCCCTTAAAAAAATTTTT
1 CTCCCCCTTAAAAAAATTTTT
5095324 AATGCTCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCCCCCTTAAAAAAATTTTT
Found at i:5095443 original size:34 final size:34
Alignment explanation
Indices: 5095403--5095473 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
5095393 AATAAATTTA
* *
5095403 TTTC-AAATATCTCTCCCCTTTTTTATCTCTCCCC
1 TTTCAAAATATCTCT-CCATTTTTCATCTCTCCCC
* *
5095437 TTTCAAAATATCTGTCCATTTTTCATCTTTCCCC
1 TTTCAAAATATCTCTCCATTTTTCATCTCTCCCC
5095471 TTT
1 TTT
5095474 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 23 0.72
35 9 0.28
ACGTcount: A:0.17, C:0.32, G:0.01, T:0.49
Consensus pattern (34 bp):
TTTCAAAATATCTCTCCATTTTTCATCTCTCCCC
Found at i:5100255 original size:52 final size:52
Alignment explanation
Indices: 5100177--5100305 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
5100167 CGAAATATGA
5100177 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
5100229 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
5100281 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5100306 AAGATCAGCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:5100416 original size:33 final size:33
Alignment explanation
Indices: 5100379--5100445 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5100369 AGTGGCTTAA
5100379 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5100412 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5100445 A
1 A
5100446 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5100419 original size:13 final size:13
Alignment explanation
Indices: 5100401--5100425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5100391 CAAAAAAATA
5100401 TGTATCGATACAT
1 TGTATCGATACAT
5100414 TGTATCGATACA
1 TGTATCGATACA
5100426 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5101340 original size:67 final size:67
Alignment explanation
Indices: 5101217--5101345 Score: 154
Period size: 67 Copynumber: 1.9 Consensus size: 67
5101207 CGTCATTTTT
* * * *
5101217 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAAGATTGGACTTAAAGAT-AAGATG
5101282 AGA
65 AGA
* * * *
5101285 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGAGATTGG-GTTCAAAGATAAGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAAGATTGGACTT-AAAGATAAGA
5101346 AAAAGGATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
66 6 0.12
67 42 0.81
68 4 0.08
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.22
Consensus pattern (67 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAAGATTGGACTTAAAGATAAGATGA
GA
Found at i:5101571 original size:52 final size:52
Alignment explanation
Indices: 5101510--5101795 Score: 380
Period size: 52 Copynumber: 5.7 Consensus size: 52
5101500 AGATGAAGGT
*
5101510 GCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGAC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
5101562 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
*
5101614 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
* *
5101666 GCCAATATGCTGATTCAAGGCTAGCGATATTGGACTT-AA-A-G-----G-T
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
* * * * * *
5101709 GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA--A-GAAGAT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
* *
5101758 GCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
5101796 CAAGGGTTGC
Statistics
Matches: 213, Mismatches: 14, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
43 32 0.15
44 3 0.01
45 1 0.00
48 1 0.00
49 35 0.16
50 1 0.00
51 2 0.01
52 138 0.65
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (52 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGAC
Found at i:5101646 original size:104 final size:96
Alignment explanation
Indices: 5101608--5101800 Score: 241
Period size: 95 Copynumber: 2.1 Consensus size: 96
5101598 TAAAGATGAC
* * *
5101608 AAAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATA
1 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATA
*
5101673 TGCTGATTCAAGGCTAGCGATATTGGACTT-
66 TGCTGATTCAAGGCCAGCGATATTGGACTTA
* * * * * *
5101703 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA--A-GAAGATGCCAATA
1 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATA
* *
5101765 TGCTGATTCAAGGCCAGCAATATTGGGCTTA
66 TGCTGATTCAAGGCCAGCGATATTGGACTTA
*
5101796 CAAGG
1 AAAGG
5101801 GTTGCCACCG
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 37 0.44
93 5 0.06
95 42 0.50
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (96 bp):
AAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGACGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTTA
Found at i:5101721 original size:43 final size:44
Alignment explanation
Indices: 5101661--5101800 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 44
5101651 AAAGATGACA
* * *
5101661 AAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAC
* * * * *
5101704 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT--AC
*
5101750 AAGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAC
1 AAG--G-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAC
5101797 AAGG
1 AAGG
5101801 GTTGCCACCG
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
43 36 0.46
45 2 0.03
46 3 0.04
47 4 0.05
48 1 0.01
49 33 0.42
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAC
Found at i:5101822 original size:30 final size:31
Alignment explanation
Indices: 5101788--5101855 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
5101778 CCAGCAATAT
5101788 TGGGCTTACA-AGGGTTGCCACCGACTTATG
1 TGGGCTTACAGAGGGTTGCCACCGACTTATG
* *
5101818 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGC-TTACAGAGGGTTGCCACCGACTTATG
5101850 TGGGCT
1 TGGGCT
5101856 GAAAAAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 5 0.15
31 5 0.15
32 24 0.71
ACGTcount: A:0.16, C:0.21, G:0.35, T:0.28
Consensus pattern (31 bp):
TGGGCTTACAGAGGGTTGCCACCGACTTATG
Found at i:5101903 original size:56 final size:56
Alignment explanation
Indices: 5101816--5101943 Score: 161
Period size: 56 Copynumber: 2.2 Consensus size: 56
5101806 CACCGACTTA
* *
5101816 TGTGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGC-TGAAAAAGATGCCACTGACT
1 TGTGGGCTTT-GA-AGGGTTGCCACCAAC-T-TGTGGACTTGAAAAAGATGCCACTGACT
*
5101875 TGTGGGCTTTGAA-GGTTGCCACTAACTTGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAGGGTTGCCACCAACTTGTGGAC-TTGAAAAAGATGCCACTGACT
*
5101931 TGTGGACTTTGAA
1 TGTGGGCTTTGAA
5101944 AAAGATGCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
54 6 0.10
55 1 0.02
56 43 0.68
57 1 0.02
58 2 0.03
59 10 0.16
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (56 bp):
TGTGGGCTTTGAAGGGTTGCCACCAACTTGTGGACTTGAAAAAGATGCCACTGACT
Found at i:5101969 original size:29 final size:29
Alignment explanation
Indices: 5101848--5101969 Score: 171
Period size: 29 Copynumber: 4.3 Consensus size: 29
5101838 CACCGACTTG
5101848 TGTGGGC--TGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * *
5101875 TGTGGGCTTTG--AAGGTTGCCACTAACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
5101902 TGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
5101931 TGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
5101960 TGTGGGCTTT
1 TGTGGGCTTT
5101970 TGAAGGGTGA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
27 30 0.36
29 53 0.64
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:5103121 original size:1 final size:1
Alignment explanation
Indices: 5103115--5103167 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
5103105 GTTGTTGTTG
* * * * *
5103115 TTTTTTTATTTTGTTTTGTTTTTTTTTTGTTTTTTTTCTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5103168 GTGGAGGACG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.02, C:0.02, G:0.06, T:0.91
Consensus pattern (1 bp):
T
Found at i:5103136 original size:16 final size:15
Alignment explanation
Indices: 5103109--5103166 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 15
5103099 GTTGTTGTTG
5103109 TTGTTGTTTTTTTATT
1 TTGTT-TTTTTTTATT
*
5103125 TTGTTTTGTTTTTTTT
1 TTGTTTT-TTTTTATT
5103141 TTGTTTTTTTTCT-TT
1 TTGTTTTTTTT-TATT
5103156 TT-TTTTTTTTT
1 TTGTTTTTTTTT
5103167 TGTGGAGGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 1 0.03
14 8 0.21
15 10 0.26
16 20 0.51
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (15 bp):
TTGTTTTTTTTTATT
Found at i:5103147 original size:9 final size:9
Alignment explanation
Indices: 5103091--5103167 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
5103081 ATCCGGACCC
*
5103091 TTTTTGTTG
1 TTTTTGTTT
* *
5103100 TTGTTGTTG
1 TTTTTGTTT
*
5103109 TTGTTGTTT
1 TTTTTGTTT
5103118 TTTTAT-TTT
1 TTTT-TGTTT
*
5103127 GTTTTGTTTTT
1 -TTTT-TGTTT
5103138 TTTTTGTTT
1 TTTTTGTTT
*
5103147 TTTTTCTTT
1 TTTTTGTTT
5103156 TTTTT-TTT
1 TTTTTGTTT
5103164 TTTT
1 TTTT
5103168 GTGGAGGACG
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
8 7 0.12
9 39 0.66
10 10 0.17
11 3 0.05
ACGTcount: A:0.01, C:0.01, G:0.13, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:5116973 original size:52 final size:52
Alignment explanation
Indices: 5116888--5117016 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
5116878 CGAAATATGA
5116888 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
5116940 AAATCTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
5116992 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
5117017 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:5117114 original size:33 final size:33
Alignment explanation
Indices: 5117077--5117143 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5117067 AGTAGCTTAA
5117077 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5117110 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5117143 A
1 A
5117144 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5117117 original size:13 final size:13
Alignment explanation
Indices: 5117099--5117123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5117089 CAAAAAAATA
5117099 TGTATCGATACAT
1 TGTATCGATACAT
5117112 TGTATCGATACA
1 TGTATCGATACA
5117124 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5122216 original size:12 final size:12
Alignment explanation
Indices: 5122195--5122225 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5122185 AACTTCTTTT
*
5122195 TCATCATCATCA
1 TCATCTTCATCA
5122207 TCATCTTCATCA
1 TCATCTTCATCA
5122219 TCATCTT
1 TCATCTT
5122226 TGATGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCA
Found at i:5123833 original size:20 final size:20
Alignment explanation
Indices: 5123808--5123862 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5123798 GTTAGGCTCA
*
5123808 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTCCACC
* **
5123828 ATGTATCGATACAATCCTTC
1 ATGTATCGATACATTCCACC
5123848 ATGTATCGATACATT
1 ATGTATCGATACATT
5123863 GTATCGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTCCACC
Found at i:5123867 original size:13 final size:13
Alignment explanation
Indices: 5123849--5123873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5123839 CAATCCTTCA
5123849 TGTATCGATACAT
1 TGTATCGATACAT
5123862 TGTATCGATACA
1 TGTATCGATACA
5123874 ATGTGAGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5125616 original size:20 final size:21
Alignment explanation
Indices: 5125573--5125622 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5125563 TTACAATTTC
*
5125573 TATCGATACAACAAGGGAATG
1 TATCGATACAACAAGGGAACG
* *
5125594 TATCGATAC-GCAAGTGAACG
1 TATCGATACAACAAGGGAACG
5125614 TATCGATAC
1 TATCGATAC
5125623 TAGACTTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TATCGATACAACAAGGGAACG
Found at i:5125776 original size:51 final size:52
Alignment explanation
Indices: 5125659--5125795 Score: 174
Period size: 51 Copynumber: 2.7 Consensus size: 52
5125649 TCTAGAAAGA
* * * *
5125659 AAATGTATCGATATATT-TT-GTTGTATCGATACATTCTGGGTTTTTGATCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTGTGATCC
* *
5125709 AAATGTATTGATACATTCTTCATTGTATCAATACATTCTAGG-TTGTGA-CC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTGTGATCC
*
5125759 TAAATGTATCGATACATTCTTCAATGTATCGATACAT
1 -AAATGTATCGATACATTCTTCATTGTATCGATACAT
5125796 CCAGTTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 17 0.23
51 40 0.53
52 18 0.24
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTAGGTTTGTGATCC
Found at i:5130477 original size:48 final size:47
Alignment explanation
Indices: 5130406--5130561 Score: 120
Period size: 48 Copynumber: 3.3 Consensus size: 47
5130396 CAATTTTGTA
* *
5130406 AGAAAGTACAAACTA-ACGTTAAAAAACTTGATTTTAGTCGCTTTTGAC
1 AGAAAGTACAAACTACAC--TAAAAAACTTGATTTTAGTCGATTTTAAC
* ** * * *
5130454 A-AAAGTACAAAACTAGCACTAAAAGACTCAATTTTGGTTGATTTTAAT
1 AGAAAGTAC-AAACTA-CACTAAAAAACTTGATTTTAGTCGATTTTAAC
* ** *
5130502 AGAAAGTATCAAACTACCCTAAAAAACTTGATTTCGGTC-AGTTTTAAT
1 AGAAAGTA-CAAACTACACTAAAAAACTTGATTTTAGTCGA-TTTTAAC
*
5130550 AGAAAATACAAA
1 AGAAAGTACAAA
5130562 AATAACCTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
47 12 0.14
48 60 0.69
49 12 0.14
50 3 0.03
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (47 bp):
AGAAAGTACAAACTACACTAAAAAACTTGATTTTAGTCGATTTTAAC
Found at i:5130587 original size:49 final size:48
Alignment explanation
Indices: 5130472--5130599 Score: 134
Period size: 48 Copynumber: 2.6 Consensus size: 48
5130462 AAAACTAGCA
* * * * *
5130472 CTAAAAGACTCAATTTTGGT-TGATTTTAATAGAAAGTATCAAACTACC
1 CTAAAAGACTTAATTTCGGTCAG-TTTTAATAGAAAATATCAAAATACC
* *
5130520 CTAAAAAACTTGATTTCGGTCAGTTTTAATAGAAAATA-CAAAAATAACC
1 CTAAAAGACTTAATTTCGGTCAGTTTTAATAGAAAATATC-AAAAT-ACC
* *
5130569 TTAAAAGACTTAATTTCGGTCAGTTGTAATA
1 CTAAAAGACTTAATTTCGGTCAGTTTTAATA
5130600 TGAGTTATAG
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 34 0.52
49 31 0.47
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (48 bp):
CTAAAAGACTTAATTTCGGTCAGTTTTAATAGAAAATATCAAAATACC
Found at i:5130739 original size:29 final size:28
Alignment explanation
Indices: 5130698--5130791 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
5130688 CAAAAATTAT
* *
5130698 TAAATGGTCCCTAGATTATAAAAAATAACC
1 TAAATGAT-CCTAGATTAT-GAAAATAACC
* **
5130728 TAAATGATCCTAAAATGTATGAAAAT-TGC
1 TAAATGATCCT-AGAT-TATGAAAATAACC
5130757 TAAATGATCCATAGATTATGGAAAATAACC
1 TAAATGATCC-TAGATTAT-GAAAATAACC
5130787 TAAAT
1 TAAAT
5130792 AACACTTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 3 0.06
29 23 0.45
30 22 0.43
31 3 0.06
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (28 bp):
TAAATGATCCTAGATTATGAAAATAACC
Found at i:5130761 original size:59 final size:58
Alignment explanation
Indices: 5130698--5130885 Score: 223
Period size: 59 Copynumber: 3.2 Consensus size: 58
5130688 CAAAAATTAT
** * *
5130698 TAAATGGTCCCTAGATTATAAAAAATAACCTAAATGATCCTAAAATGTATGAAAATTGC
1 TAAATGGTCCCTAGATTATGGAAAATAACCTAAAT-AACCTAAAATGCATGAAAATTGC
* * * * * **
5130757 TAAATGATCCATAGATTATGGAAAATAACCTAAATAACACTTAAATCCAAGAAAATTAT
1 TAAATGGTCCCTAGATTATGGAAAATAACCTAAATAAC-CTAAAATGCATGAAAATTGC
* * *
5130816 TAAATAGTCCCTACATTATGGAAAATAACCAAAATAACCATAAAATGCATGAAAATTGC
1 TAAATGGTCCCTAGATTATGGAAAATAACCTAAATAACC-TAAAATGCATGAAAATTGC
5130875 TAAATGGTCCC
1 TAAATGGTCCC
5130886 CAATATGTAT
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
58 3 0.03
59 102 0.97
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (58 bp):
TAAATGGTCCCTAGATTATGGAAAATAACCTAAATAACCTAAAATGCATGAAAATTGC
Found at i:5132607 original size:24 final size:24
Alignment explanation
Indices: 5132568--5132613 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5132558 TTTTTTATAA
*
5132568 ATATGTCCTTAGAAAAGGCTTTTG
1 ATATGTCCTTAGAAAAAGCTTTTG
5132592 ATATGTCCTTTA-AAAAAGCTTT
1 ATATGTCC-TTAGAAAAAGCTTT
5132614 GAAATCTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (24 bp):
ATATGTCCTTAGAAAAAGCTTTTG
Found at i:5132748 original size:35 final size:35
Alignment explanation
Indices: 5132709--5132862 Score: 123
Period size: 35 Copynumber: 4.3 Consensus size: 35
5132699 GAGAAAGTAT
*
5132709 TTTGAAAATCTTGATGAAATATCCTTAAGAAAAGC
1 TTTGAAAATCTTGATAAAATATCCTTAAGAAAAGC
* * *
5132744 TTTGAAAATTTCTAATAAAATAT-CTTAGAGAGAAGCC
1 TTTGAAAATCT-TGATAAAATATCCTTA-AGAAAAG-C
* * * *
5132781 TTTGAAATGTTACTTTGATAAAATATCCTCAAGATAGGC
1 TTTGAAA--AT-C-TTGATAAAATATCCTTAAGAAAAGC
* * *
5132820 TTTAAAAATCTTGATAAAATATCCCT-AGAAAAGT
1 TTTGAAAATCTTGATAAAATATCCTTAAGAAAAGC
*
5132854 TTTTAAAAT
1 TTTGAAAAT
5132863 GTTTTTCTGA
Statistics
Matches: 93, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
34 13 0.14
35 28 0.30
36 16 0.17
37 9 0.10
39 8 0.09
40 15 0.16
41 4 0.04
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (35 bp):
TTTGAAAATCTTGATAAAATATCCTTAAGAAAAGC
Found at i:5143856 original size:53 final size:53
Alignment explanation
Indices: 5143753--5143857 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 53
5143743 AATGTAATAT
* * *
5143753 TACCTAAATAACCCTAATGAATATTTATAAACATGAAAGTCCTCATATGACCA
1 TACCTAAATAACCCTAATGAATATATATAAACATAAAAGTCCTCACATGACCA
** * **
5143806 TACCTAAATAACTTTAATGGATATATATCGACATAAAAGTTCCT-ACATGACC
1 TACCTAAATAACCCTAATGAATATATATAAACATAAAAG-TCCTCACATGACC
5143858 TTAGAGACTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 39 0.91
54 4 0.09
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (53 bp):
TACCTAAATAACCCTAATGAATATATATAAACATAAAAGTCCTCACATGACCA
Found at i:5144214 original size:30 final size:29
Alignment explanation
Indices: 5144179--5144332 Score: 75
Period size: 30 Copynumber: 5.2 Consensus size: 29
5144169 CGAAAATTTT
5144179 TAAATGGTCTCTAGATTATAGAAAATAACC
1 TAAATGGTC-CTAGATTATAGAAAATAACC
** * * *
5144209 TAAATGACCCTAAAATACATA-AAAATTACC
1 TAAATGGTCCT-AGAT-TATAGAAAATAACC
* *
5144239 -AAATAGTCCTTAGATTATGGAAAATAACC
1 TAAATGGTCC-TAGATTATAGAAAATAACC
* * * * *
5144268 TAAGTGATCCTAAAATACATA-AAAATTA-C
1 TAAATGGTCCT-AGAT-TATAGAAAATAACC
* *
5144297 TAAATGATCTTTAGATTAT-GAAAAATAACC
1 TAAATGGTC-CTAGATTATAG-AAAATAACC
5144327 TAAATG
1 TAAATG
5144333 ACTCTAAAAT
Statistics
Matches: 89, Mismatches: 24, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
28 4 0.04
29 38 0.43
30 42 0.47
31 5 0.06
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (29 bp):
TAAATGGTCCTAGATTATAGAAAATAACC
Found at i:5144221 original size:59 final size:59
Alignment explanation
Indices: 5144135--5144360 Score: 235
Period size: 59 Copynumber: 3.9 Consensus size: 59
5144125 TCATCCTTAT
* ** * ** **
5144135 ATTATA-AAAATAACCTATACAACCCTAAAATGCACGAAAATTTTTAAATGGTCTCTAG
1 ATTATAGAAAATAACCTAAATGACCCTAAAATACATAAAAATTACTAAATGGTCTCTAG
* *
5144193 ATTATAGAAAATAACCTAAATGACCCTAAAATACATAAAAATTACCAAATAGTC-CTTAG
1 ATTATAGAAAATAACCTAAATGACCCTAAAATACATAAAAATTACTAAATGGTCTC-TAG
* * * * *
5144252 ATTATGGAAAATAACCTAAGTGATCCTAAAATACATAAAAATTACTAAATGATCTTTAG
1 ATTATAGAAAATAACCTAAATGACCCTAAAATACATAAAAATTACTAAATGGTCTCTAG
* * * *
5144311 ATTAT-GAAAAATAACCTAAATGACTCTAAAATGCAT-GAAATTGCTAAATG
1 ATTATAG-AAAATAACCTAAATGACCCTAAAATACATAAAAATTACTAAATG
5144361 TCCTTAATAT
Statistics
Matches: 141, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
58 20 0.14
59 121 0.86
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (59 bp):
ATTATAGAAAATAACCTAAATGACCCTAAAATACATAAAAATTACTAAATGGTCTCTAG
Found at i:5144333 original size:30 final size:29
Alignment explanation
Indices: 5144190--5144333 Score: 105
Period size: 29 Copynumber: 4.9 Consensus size: 29
5144180 AAATGGTCTC
*
5144190 TAGATTATAGAAAATAACCTAAATGACCCT
1 TAGATTATA-AAAATAACCTAAATGATCCT
* * * *
5144220 AAAATACATAAAAATTACC-AAAT-AGTCCT
1 TAGAT-TATAAAAATAACCTAAATGA-TCCT
* *
5144249 TAGATTATGGAAAATAACCTAAGTGATCCT
1 TAGATTAT-AAAAATAACCTAAATGATCCT
* * * * *
5144279 AAAATACATAAAAATTA-CTAAATGATCTT
1 TAGAT-TATAAAAATAACCTAAATGATCCT
5144308 TAGATTATGAAAAATAACCTAAATGA
1 TAGATTAT-AAAAATAACCTAAATGA
5144334 CTCTAAAATG
Statistics
Matches: 84, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
28 5 0.06
29 38 0.45
30 35 0.42
31 6 0.07
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (29 bp):
TAGATTATAAAAATAACCTAAATGATCCT
Found at i:5144376 original size:59 final size:59
Alignment explanation
Indices: 5144113--5144379 Score: 233
Period size: 59 Copynumber: 4.5 Consensus size: 59
5144103 ATTATGTATG
* * ** * **
5144113 AAAATTGCTAAATCA-TCCTTATATTAT-AAAAATAACCTATACAACCCTAAAATGCACG
1 AAAATTACTAAAT-AGTCCTTATATTATGAAAAATAACCTAAATGACCCTAAAATACATA
** * *
5144171 AAAATTTTTAAATGGT-CTCTAGATTAT-AGAAAATAACCTAAATGACCCTAAAATACATA
1 AAAATTACTAAATAGTCCT-TATATTATGA-AAAATAACCTAAATGACCCTAAAATACATA
* * * * *
5144230 AAAATTACCAAATAGTCCTTAGATTATGGAAAATAACCTAAGTGATCCTAAAATACATA
1 AAAATTACTAAATAGTCCTTATATTATGAAAAATAACCTAAATGACCCTAAAATACATA
* * * *
5144289 AAAATTACTAAAT-GATCTTTAGATTATGAAAAATAACCTAAATGACTCTAAAATGCAT-
1 AAAATTACTAAATAG-TCCTTATATTATGAAAAATAACCTAAATGACCCTAAAATACATA
* *
5144347 GAAATTGCTAAAT-GTCCTTAATATATATGAAAA
1 AAAATTACTAAATAGTCCTT-ATAT-TATGAAAA
5144380 TATTTTTAAA
Statistics
Matches: 173, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
57 6 0.03
58 36 0.21
59 129 0.75
60 2 0.01
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (59 bp):
AAAATTACTAAATAGTCCTTATATTATGAAAAATAACCTAAATGACCCTAAAATACATA
Found at i:5144993 original size:10 final size:9
Alignment explanation
Indices: 5144978--5145025 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
5144968 AAAAACTATA
5144978 TTTTCTTCTT
1 TTTTCTT-TT
5144988 TTTTCTTTT
1 TTTTCTTTT
*
5144997 CTTTTCTCTT
1 -TTTTCTTTT
*
5145007 TTTCCTTTT
1 TTTTCTTTT
*
5145016 TTTTATTTT
1 TTTTCTTTT
5145025 T
1 T
5145026 CTGCTCAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:5145008 original size:19 final size:19
Alignment explanation
Indices: 5144978--5145019 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5144968 AAAAACTATA
*
5144978 TTTTCTTCTTTTTTCTTTT
1 TTTTCTTCTTTTTCCTTTT
5144997 CTTTTC-TCTTTTTCCTTTT
1 -TTTTCTTCTTTTTCCTTTT
5145016 TTTT
1 TTTT
5145020 ATTTTTCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 12 0.57
20 5 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTCTTCTTTTTCCTTTT
Found at i:5145501 original size:20 final size:20
Alignment explanation
Indices: 5145476--5145525 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
5145466 TTTCATAATG
5145476 TATCGATACACAAGGTGATA
1 TATCGATACACAAGGTGATA
* *
5145496 TATCGATACACAGGGTGATG
1 TATCGATACACAAGGTGATA
*
5145516 TATCAATACA
1 TATCGATACA
5145526 TTATGGGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (20 bp):
TATCGATACACAAGGTGATA
Found at i:5147884 original size:20 final size:19
Alignment explanation
Indices: 5147854--5147905 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
5147844 AATAAAATTT
5147854 TAAATAATTTTAATTTAATTA
1 TAAA-AATTTTAATTT-ATTA
* * *
5147875 TTAAAATTTTTATTTTTTA
1 TAAAAATTTTAATTTATTA
5147894 TAAAAATTTTAA
1 TAAAAATTTTAA
5147906 AAAAACTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.50
20 10 0.38
21 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAAAATTTTAATTTATTA
Found at i:5148369 original size:31 final size:32
Alignment explanation
Indices: 5148328--5148441 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 32
5148318 TTGAAATTAA
*
5148328 TATTA-AAATTTATCATTATATATTATATTTT
1 TATTATAATTTTATCATTATATATTATATTTT
*
5148359 TATTATAATTTCT-T-ATTGTA-ATTTATAAATTTT
1 TATTATAATTT-TATCATTATATA-TTAT--ATTTT
* *
5148392 T-TGT-TGAATTTTATTATTATAT-TTTTATTTT
1 TAT-TAT-AATTTTATCATTATATATTATATTTT
5148423 TATTA-AATTTTATCATTAT
1 TATTATAATTTTATCATTAT
5148442 CTGTTTATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
30 14 0.21
31 21 0.32
32 9 0.14
33 17 0.26
34 5 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (32 bp):
TATTATAATTTTATCATTATATATTATATTTT
Found at i:5150223 original size:13 final size:14
Alignment explanation
Indices: 5150197--5150226 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5150187 TATTTATTAT
5150197 ATTTTAATTATAAA
1 ATTTTAATTATAAA
5150211 ATTTTAA-TATAAA
1 ATTTTAATTATAAA
5150224 ATT
1 ATT
5150227 AAAATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTAATTATAAA
Found at i:5150769 original size:13 final size:13
Alignment explanation
Indices: 5150753--5150787 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5150743 ATTTTTTTAA
*
5150753 AATATTTATATTT
1 AATATTTATATCT
5150766 AATATTTATATCT
1 AATATTTATATCT
*
5150779 AACATTTAT
1 AATATTTAT
5150788 TTAAATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTATATCT
Found at i:5150801 original size:13 final size:12
Alignment explanation
Indices: 5150759--5150822 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
5150749 TTAAAATATT
*
5150759 TATATTTAATATT
1 TATATTTAA-ATA
*
5150772 TATATCTAACAT-
1 TATATTTAA-ATA
5150784 T-TATTTAAATCA
1 TATATTTAAAT-A
5150796 TATATTTAAATA
1 TATATTTAAATA
*
5150808 TAAATTTAAAGTA
1 TATATTTAAA-TA
5150821 TA
1 TA
5150823 ATTCTCTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 2 0.05
11 6 0.14
12 12 0.28
13 23 0.53
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (12 bp):
TATATTTAAATA
Found at i:5151532 original size:20 final size:21
Alignment explanation
Indices: 5151512--5151552 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5151502 TTATTATTAA
5151512 TAAAATTATTTAATTT-ATAAT
1 TAAAATT-TTTAATTTCATAAT
5151533 TAAAATTTTTAATTTCATAA
1 TAAAATTTTTAATTTCATAA
5151553 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATTTTTAATTTCATAAT
Found at i:5151798 original size:16 final size:15
Alignment explanation
Indices: 5151777--5151812 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5151767 TTATACATAA
5151777 AATAAAATTTCATGTT
1 AATAAAATTTCA-GTT
5151793 AATAAAAATTTCAGTT
1 AAT-AAAATTTCAGTT
5151809 AATA
1 AATA
5151813 TACTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 1 0.05
16 9 0.47
17 9 0.47
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AATAAAATTTCAGTT
Found at i:5151802 original size:17 final size:16
Alignment explanation
Indices: 5151780--5151812 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5151770 TACATAAAAT
5151780 AAAATTTCATGTTAATA
1 AAAATTTCA-GTTAATA
5151797 AAAATTTCAGTTAATA
1 AAAATTTCAGTTAATA
5151813 TACTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
AAAATTTCAGTTAATA
Found at i:5151953 original size:18 final size:19
Alignment explanation
Indices: 5151924--5151962 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5151914 AAATAATTAA
5151924 AATATGAAAATTTA-TATTT
1 AATATGAAAA-TTACTATTT
5151943 AATAT-AAAATTACTATTT
1 AATATGAAAATTACTATTT
5151961 AA
1 AA
5151963 CATTCAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 11 0.58
19 5 0.26
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
AATATGAAAATTACTATTT
Found at i:5152105 original size:25 final size:24
Alignment explanation
Indices: 5152077--5152157 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 24
5152067 CATATTATAT
5152077 TTATATTATAATTATTTTTAAAATA
1 TTATATTATAATTA-TTTTAAAATA
* *
5152102 TTATATATTTAA-TATATTAATAAT-
1 TTATAT-TATAATTATTTTAA-AATA
* *
5152126 TTATATTAT-ATAAATTTTAATATA
1 TTATATTATAAT-TATTTTAAAATA
5152150 TTTATATT
1 -TTATATT
5152158 TTTAAATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.02
23 4 0.09
24 17 0.39
25 18 0.41
26 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATATTATAATTATTTTAAAATA
Found at i:5152118 original size:16 final size:16
Alignment explanation
Indices: 5152068--5152158 Score: 61
Period size: 16 Copynumber: 5.8 Consensus size: 16
5152058 TTCATTTATC
*
5152068 ATATTATAT-TTATATT
1 ATATTATATATT-TAAT
*
5152084 ATAATTAT-T-TTTAAA
1 AT-ATTATATATTTAAT
5152099 ATATTATATATTTAAT
1 ATATTATATATTTAAT
5152115 ATATTA-ATAATTT-AT
1 ATATTATAT-ATTTAAT
*
5152130 AT-TATATAAATTTTAAT
1 ATAT-TATATA-TTTAAT
5152147 ATATT-TATATTT
1 ATATTATATATTT
5152159 TTAAATTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 6 0.10
15 17 0.28
16 27 0.44
17 10 0.16
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTATATATTTAAT
Found at i:5152159 original size:16 final size:16
Alignment explanation
Indices: 5152071--5152192 Score: 81
Period size: 17 Copynumber: 7.4 Consensus size: 16
5152061 ATTTATCATA
* *
5152071 TTATATTTATATTATAA
1 TTATATTT-TAATATAT
*
5152088 TTAT-TTTTAAAATA-
1 TTATATTTTAATATAT
5152102 TTATATATTTAATATAT
1 TTATAT-TTTAATATAT
* *
5152119 TAATAATTT-ATATTAT
1 TTATATTTTAATA-TAT
* *
5152135 ATAAATTTTAATATAT
1 TTATATTTTAATATAT
5152151 TTATATTTTTAA-ATTAT
1 TTATA-TTTTAATA-TAT
*
5152168 GTTATATTTTAATTATTT
1 -TTATATTTTAA-TATAT
5152186 TTATATT
1 TTATATT
5152193 ATATAAATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
14 4 0.05
15 9 0.11
16 29 0.35
17 33 0.40
18 7 0.08
19 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
TTATATTTTAATATAT
Found at i:5152162 original size:49 final size:47
Alignment explanation
Indices: 5152068--5152158 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 47
5152058 TTCATTTATC
* *
5152068 ATATTATATTTATATTATAATTATTTTTAAAATATTATATATTTAAT
1 ATATTATATTTATATTATAATAAATTTTAAAATATTATATATTTAAT
*
5152115 ATATTAATAATTTATATTAT-ATAAATTTTAATATATT-TATATTT
1 ATATT-AT-ATTTATATTATAATAAATTTTAAAATATTATATATTT
5152159 TTAAATTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 12 0.31
48 16 0.41
49 11 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
ATATTATATTTATATTATAATAAATTTTAAAATATTATATATTTAAT
Found at i:5152163 original size:24 final size:24
Alignment explanation
Indices: 5152092--5152165 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
5152082 TTATAATTAT
* *
5152092 TTTTAAAATA-TTATATATTTAATA
1 TTTTAATATATTTATATTTTTAA-A
* *
5152116 TATTAATA-ATTTATATTATATAAA
1 TTTTAATATATTTATATT-TTTAAA
5152140 TTTTAATATATTTATATTTTTAAA
1 TTTTAATATATTTATATTTTTAAA
5152164 TT
1 TT
5152166 ATGTTATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 27 0.66
25 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATATATTTATATTTTTAAA
Found at i:5153247 original size:59 final size:59
Alignment explanation
Indices: 5153182--5153298 Score: 234
Period size: 59 Copynumber: 2.0 Consensus size: 59
5153172 TTCTTTTATT
5153182 TCTGAATTCGGTGAATCTTGAATAGTGCTTTTAATCCTTCTAATTTTCGCATATACGCC
1 TCTGAATTCGGTGAATCTTGAATAGTGCTTTTAATCCTTCTAATTTTCGCATATACGCC
5153241 TCTGAATTCGGTGAATCTTGAATAGTGCTTTTAATCCTTCTAATTTTCGCATATACGC
1 TCTGAATTCGGTGAATCTTGAATAGTGCTTTTAATCCTTCTAATTTTCGCATATACGC
5153299 GCCTAACTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (59 bp):
TCTGAATTCGGTGAATCTTGAATAGTGCTTTTAATCCTTCTAATTTTCGCATATACGCC
Found at i:5158172 original size:6 final size:6
Alignment explanation
Indices: 5158161--5158199 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
5158151 TGCATTGGGA
5158161 AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGG
1 AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG AGG
5158200 CGGTTGGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:5161212 original size:10 final size:10
Alignment explanation
Indices: 5161197--5161226 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5161187 AATAACTGAA
5161197 TTTTTTTCTT
1 TTTTTTTCTT
5161207 TTTTTTTCTT
1 TTTTTTTCTT
*
5161217 TTTTTCTCTT
1 TTTTTTTCTT
5161227 CAAATCCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:5163984 original size:15 final size:16
Alignment explanation
Indices: 5163954--5163987 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
5163944 TTACCTTCTC
5163954 AATAAGAGACTAAGAA
1 AATAAGAGACTAAGAA
5163970 AATAAGAGA-TAAGAA
1 AATAAGAGACTAAGAA
5163985 AAT
1 AAT
5163988 CATACCCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.65, C:0.03, G:0.18, T:0.15
Consensus pattern (16 bp):
AATAAGAGACTAAGAA
Found at i:5164606 original size:95 final size:95
Alignment explanation
Indices: 5164323--5164596 Score: 539
Period size: 95 Copynumber: 2.9 Consensus size: 95
5164313 AGTTAGGTGG
5164323 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
1 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
5164388 ATTTTTTGAGTTTGAATCAAACCAATTTTT
66 ATTTTTTGAGTTTGAATCAAACCAATTTTT
5164418 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
1 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
*
5164483 ATTTTTTGAGTTTGAATTAAACCAATTTTT
66 ATTTTTTGAGTTTGAATCAAACCAATTTTT
5164513 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
1 AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
5164578 ATTTTTTGAGTTTGAATCA
66 ATTTTTTGAGTTTGAATCA
5164597 TTTCGATTTT
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 177 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.47
Consensus pattern (95 bp):
AAAGGGTTGATTTCGAATCAAACCAATTTGGATTATATCATTTTAGATTTTTAAATTTTTAAATT
ATTTTTTGAGTTTGAATCAAACCAATTTTT
Found at i:5164613 original size:16 final size:16
Alignment explanation
Indices: 5164585--5164626 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5164575 ATTATTTTTT
*
5164585 GAGTTTGAATCATTTC
1 GAGTTTGAGTCATTTC
*
5164601 GATTTTGAGTCATTTC
1 GAGTTTGAGTCATTTC
5164617 GAGTTTGAGT
1 GAGTTTGAGT
5164627 TTATTCACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (16 bp):
GAGTTTGAGTCATTTC
Found at i:5164653 original size:37 final size:38
Alignment explanation
Indices: 5164582--5164653 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
5164572 TAAATTATTT
* *
5164582 TTTGAGTTTGAATCATTTCGATTTTGAGTCATTTCGAG
1 TTTGAGTTTGAATCACTTCAATTTTGAGTCATTTCGAG
* * *
5164620 TTTGAGTTT-ATTCACTTCAATTTTGGGTTATTTC
1 TTTGAGTTTGAATCACTTCAATTTTGAGTCATTTC
5164654 ATATTCAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 20 0.69
38 9 0.31
ACGTcount: A:0.19, C:0.11, G:0.18, T:0.51
Consensus pattern (38 bp):
TTTGAGTTTGAATCACTTCAATTTTGAGTCATTTCGAG
Found at i:5164743 original size:28 final size:28
Alignment explanation
Indices: 5164711--5164767 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5164701 TGAATTTTAG
5164711 TTTAATGCTCGAGTTAATTAAGTTCAAA
1 TTTAATGCTCGAGTTAATTAAGTTCAAA
5164739 TTTAATGCTCGAGTTAATTAAGTTCAAA
1 TTTAATGCTCGAGTTAATTAAGTTCAAA
5164767 T
1 T
5164768 CATTTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (28 bp):
TTTAATGCTCGAGTTAATTAAGTTCAAA
Found at i:5164775 original size:16 final size:16
Alignment explanation
Indices: 5164756--5164790 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5164746 CTCGAGTTAA
5164756 TTAAGTTCAAATCATT
1 TTAAGTTCAAATCATT
*
5164772 TTAAGTTCGAATCATT
1 TTAAGTTCAAATCATT
5164788 TTA
1 TTA
5164791 GGATCAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (16 bp):
TTAAGTTCAAATCATT
Found at i:5164931 original size:16 final size:16
Alignment explanation
Indices: 5164904--5164956 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
5164894 AGCTTCAAAT
5164904 TTTTCAAATTTGAATCA
1 TTTT-AAATTTGAATCA
* *
5164921 TTTTGAATTTGAGTCA
1 TTTTAAATTTGAATCA
*
5164937 TTTTAAATTTAAATCA
1 TTTTAAATTTGAATCA
5164953 TTTT
1 TTTT
5164957 TGGATTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
TTTTAAATTTGAATCA
Found at i:5167892 original size:16 final size:15
Alignment explanation
Indices: 5167870--5167916 Score: 76
Period size: 16 Copynumber: 3.0 Consensus size: 15
5167860 GGTTATTTCG
5167870 AATTTAAATTTATTT
1 AATTTAAATTTATTT
5167885 AGATTTAAATTTATTT
1 A-ATTTAAATTTATTT
5167901 AAGTTTAAATTTATTT
1 AA-TTTAAATTTATTT
5167917 GGGTTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.07
16 28 0.93
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
AATTTAAATTTATTT
Found at i:5167933 original size:16 final size:16
Alignment explanation
Indices: 5167862--5167944 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
5167852 GGTGTTTGGG
* *
5167862 TTATTTCGAATTTAAAT
1 TTATTT-GAGTTTGAAT
*
5167879 TTATTT-AGATTTAAAT
1 TTATTTGAG-TTTGAAT
* *
5167895 TTATTTAAGTTTAAAT
1 TTATTTGAGTTTGAAT
*
5167911 TTATTTGGGTTTGAAT
1 TTATTTGAGTTTGAAT
* *
5167927 TTTTTTGAGTTTGGAT
1 TTATTTGAGTTTGAAT
5167943 TT
1 TT
5167945 GAGTTCAGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.02
16 48 0.84
17 8 0.14
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (16 bp):
TTATTTGAGTTTGAAT
Found at i:5168178 original size:18 final size:17
Alignment explanation
Indices: 5168116--5168171 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
5168106 TAATTATTTA
5168116 TTTAT-TAAAATCTATATT
1 TTTATATAAAAT-TA-ATT
5168134 TTTATATAAAATTAATT
1 TTTATATAAAATTAATT
5168151 TGTTATATAAAATTAATT
1 T-TTATATAAAATTAATT
5168169 TTT
1 TTT
5168172 CAAATAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.17
18 24 0.67
19 6 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATATAAAATTAATT
Found at i:5168366 original size:24 final size:23
Alignment explanation
Indices: 5168322--5168369 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5168312 AATTAATATT
* *
5168322 TAAAAAATTTAAAATATATTTAA
1 TAAAAAATTTAAAACACATTTAA
*
5168345 TAAAATATTTAAAAACACATTTAA
1 TAAAAAATTT-AAAACACATTTAA
5168369 T
1 T
5168370 CTTAACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAAATTTAAAACACATTTAA
Found at i:5169420 original size:16 final size:16
Alignment explanation
Indices: 5169401--5169432 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5169391 TTTAGTTAGA
5169401 GCTTTTACGGATTCGG
1 GCTTTTACGGATTCGG
*
5169417 GCTTTTATGGATTCGG
1 GCTTTTACGGATTCGG
5169433 ACTATCTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.31, T:0.41
Consensus pattern (16 bp):
GCTTTTACGGATTCGG
Found at i:5172274 original size:6 final size:6
Alignment explanation
Indices: 5172263--5172288 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5172253 TTTTGTCATA
5172263 ATATTT ATATTT ATATTT ATATTT AT
1 ATATTT ATATTT ATATTT ATATTT AT
5172289 TGTAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATATTT
Found at i:5173823 original size:35 final size:35
Alignment explanation
Indices: 5173784--5173863 Score: 160
Period size: 35 Copynumber: 2.3 Consensus size: 35
5173774 TTGACAGTGT
5173784 CATGATTAATCGCCACTAGCGCGAAATGACTTTTA
1 CATGATTAATCGCCACTAGCGCGAAATGACTTTTA
5173819 CATGATTAATCGCCACTAGCGCGAAATGACTTTTA
1 CATGATTAATCGCCACTAGCGCGAAATGACTTTTA
5173854 CATGATTAAT
1 CATGATTAAT
5173864 TGCCCAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (35 bp):
CATGATTAATCGCCACTAGCGCGAAATGACTTTTA
Found at i:5174273 original size:21 final size:23
Alignment explanation
Indices: 5174249--5174294 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
5174239 ACTTAAATCC
*
5174249 AAACCCGATT-AAAATCTA-ATA
1 AAACCCAATTAAAAATCTATATA
*
5174270 AAACTCAATTAAAAATCTATATA
1 AAACCCAATTAAAAATCTATATA
5174293 AA
1 AA
5174295 CTTAAACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (23 bp):
AAACCCAATTAAAAATCTATATA
Found at i:5174338 original size:19 final size:19
Alignment explanation
Indices: 5174314--5174359 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5174304 AAACCCAATT
5174314 AAAAAAATAAAATAAAATA
1 AAAAAAATAAAATAAAATA
** *
5174333 AAAAAACCAAAGTAAAATA
1 AAAAAAATAAAATAAAATA
5174352 AAAAAAAT
1 AAAAAAAT
5174360 CACAATACAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAAAATAAAATAAAATA
Found at i:5174535 original size:17 final size:17
Alignment explanation
Indices: 5174509--5174544 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5174499 CAACAATATC
* *
5174509 AACCAGAAGCAGAATCA
1 AACCAAAAGCAAAATCA
5174526 AACCAAAAGCAAAATCA
1 AACCAAAAGCAAAATCA
5174543 AA
1 AA
5174545 TTAGAGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.22, G:0.11, T:0.06
Consensus pattern (17 bp):
AACCAAAAGCAAAATCA
Found at i:5174719 original size:13 final size:13
Alignment explanation
Indices: 5174703--5174731 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5174693 AAAAAATGGT
5174703 TGAAGAGAATGAA
1 TGAAGAGAATGAA
5174716 TGAAGAGAATGAA
1 TGAAGAGAATGAA
5174729 TGA
1 TGA
5174732 TCAGGTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (13 bp):
TGAAGAGAATGAA
Found at i:5174900 original size:19 final size:20
Alignment explanation
Indices: 5174867--5174906 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5174857 AACATTAATT
5174867 AATGAAAAAGATAATTTTAC
1 AATGAAAAAGATAATTTTAC
*
5174887 AATGAAAAA-TTAATTTTAC
1 AATGAAAAAGATAATTTTAC
5174906 A
1 A
5174907 CATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGAAAAAGATAATTTTAC
Found at i:5174951 original size:21 final size:22
Alignment explanation
Indices: 5174918--5174961 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
5174908 ATTTTTAAAA
5174918 TATTTTAAATGA-T-TTATATT
1 TATTTTAAATGATTATTATATT
*
5174938 TATTTTAATTTGATTATTATATT
1 TATTTTAA-ATGATTATTATATT
5174961 T
1 T
5174962 TATAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 1 0.05
23 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TATTTTAAATGATTATTATATT
Found at i:5175075 original size:17 final size:17
Alignment explanation
Indices: 5175040--5175073 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
5175030 ATTTAATTGA
5175040 TAATTAATATAAAATTT
1 TAATTAATATAAAATTT
5175057 TAATTAAT-TAAAATTT
1 TAATTAATATAAAATTT
5175073 T
1 T
5175074 TATATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAATATAAAATTT
Found at i:5176751 original size:19 final size:20
Alignment explanation
Indices: 5176707--5176762 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
5176697 TTGCCAGTTT
* *
5176707 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGATA
*
5176727 CATGTATCGATATAATGA-A
1 CATGTATCGATACAATGATA
5176746 CATGTATCGATACAATG
1 CATGTATCGATACAATG
5176763 TATCAATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:5177729 original size:33 final size:33
Alignment explanation
Indices: 5177679--5177742 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
5177669 TGCACTAAAA
*
5177679 TGCTCATCCATGCGCTGCGAGAGTGAAGTGAAG
1 TGCTCATCCATGCGCTGCGAAAGTGAAGTGAAG
*
5177712 TGCTCA-CTCATGTGCTGCGAAAGTGAAGTGA
1 TGCTCATC-CATGCGCTGCGAAAGTGAAGTGA
5177743 TCAACTCTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (33 bp):
TGCTCATCCATGCGCTGCGAAAGTGAAGTGAAG
Found at i:5179118 original size:21 final size:20
Alignment explanation
Indices: 5179068--5179119 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
5179058 AAAAGATGTT
* *
5179068 TTGATGTAAAATTGATAAAAT
1 TTGATG-AAAATTGAGAAAAA
* *
5179089 TTTAAGAAAATTTGAGAAAAA
1 TTGATGAAAA-TTGAGAAAAA
5179110 TTGATGAAAA
1 TTGATGAAAA
5179120 AATATTAGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGATGAAAATTGAGAAAAA
Found at i:5179231 original size:13 final size:13
Alignment explanation
Indices: 5179213--5179250 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5179203 TAGTAACCCA
5179213 TGTATCGATACAT
1 TGTATCGATACAT
* *
5179226 TGTATCAATATAT
1 TGTATCGATACAT
5179239 TGTATCGATACA
1 TGTATCGATACA
5179251 AAAAACATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5185481 original size:19 final size:20
Alignment explanation
Indices: 5185437--5185492 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
5185427 CTGCCAGTTT
* *
5185437 CATGTATCGATACAATTATG
1 CATGTATCGATACAATGATA
5185457 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
5185476 CATGTATCGATACAATG
1 CATGTATCGATACAATG
5185493 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:5185495 original size:13 final size:13
Alignment explanation
Indices: 5185477--5185503 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5185467 TACAATGAAC
5185477 ATGTATCGATACA
1 ATGTATCGATACA
5185490 ATGTATCGATACA
1 ATGTATCGATACA
5185503 A
1 A
5185504 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5187739 original size:24 final size:25
Alignment explanation
Indices: 5187712--5187759 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5187702 CCTATCGTTA
*
5187712 TGTTTATAATTATGCTT-ATGCTTG
1 TGTTTATAACTATGCTTAATGCTTG
* *
5187736 TGTTTGTAACTATGTTTAATGCTT
1 TGTTTATAACTATGCTTAATGCTT
5187760 TTAATTATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.54
Consensus pattern (25 bp):
TGTTTATAACTATGCTTAATGCTTG
Found at i:5188802 original size:20 final size:20
Alignment explanation
Indices: 5188777--5188830 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
5188767 ATTATAAGCA
5188777 ATGTATCGATACAAT-TCAT
1 ATGTATCGATACAATGTCAT
*
5188796 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCAT
5188817 ATGTATCGATACAA
1 ATGTATCGATACAA
5188831 ACATTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTCAT
Found at i:5188903 original size:19 final size:19
Alignment explanation
Indices: 5188859--5188911 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5188849 CTACCAGTTT
* **
5188859 CATGTATCGATACAATTGTC
1 CATGTATCGATAC-AGTGAA
5188879 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
*
5188898 CATGTATGGATACA
1 CATGTATCGATACA
5188912 ATGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAGTGAA
Found at i:5189539 original size:22 final size:22
Alignment explanation
Indices: 5189514--5189555 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5189504 AGATAAACAT
5189514 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
* *
5189536 ATTTCTCCCCTTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
5189556 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:5197485 original size:16 final size:16
Alignment explanation
Indices: 5197464--5197497 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5197454 TTAACATTTT
5197464 ATTATAAAATTTAGTA
1 ATTATAAAATTTAGTA
*
5197480 ATTATAGAATTTAGTA
1 ATTATAAAATTTAGTA
5197496 AT
1 AT
5197498 ATTTTGGTTC
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:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
ATTATAAAATTTAGTA
Found at i:5200309 original size:41 final size:40
Alignment explanation
Indices: 5200264--5200370 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
5200254 AGTTAATCCT
*
5200264 TCTAACTTATTGTCTTTATCTGTTTCATCCAAGCAAACCCC
1 TCTAACTTATTG-CTTTATCTGTTTCATCCAAGAAAACCCC
* * ***
5200305 TCTAACCTATTAGCTTTAT-TGATTTCGTCTTGGAAAACCCC
1 TCTAACTTATT-GCTTTATCTG-TTTCATCCAAGAAAACCCC
* *
5200346 TCTAACTTGTTGGCTTTATCGGTTT
1 TCTAACTTATT-GCTTTATCTGTTT
5200371 TGCCTTGGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
40 2 0.04
41 49 0.92
42 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (40 bp):
TCTAACTTATTGCTTTATCTGTTTCATCCAAGAAAACCCC
Found at i:5200378 original size:41 final size:41
Alignment explanation
Indices: 5200298--5200411 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
5200288 TCATCCAAGC
* * * * * *
5200298 AAACCCCTCTAACCTATTAGCTTTATTGATTTCGTCTTGGA
1 AAACCCCTCTAACTTGTTGGCTTTATCGGTTTCGCCTTGGA
* *
5200339 AAACCCCTCTAACTTGTTGGCTTTATCGGTTTTGCCTTGGC
1 AAACCCCTCTAACTTGTTGGCTTTATCGGTTTCGCCTTGGA
* *
5200380 CAACCTCTCTAACTTGTTGGCTTTATCGGTTT
1 AAACCCCTCTAACTTGTTGGCTTTATCGGTTT
5200412 AAGTTTTGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.40
Consensus pattern (41 bp):
AAACCCCTCTAACTTGTTGGCTTTATCGGTTTCGCCTTGGA
Found at i:5201309 original size:24 final size:25
Alignment explanation
Indices: 5201282--5201329 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5201272 TTTTGAAAAA
*
5201282 TTATAATCATTATATGA-ATTTTTC
1 TTATAATCAATATATGAGATTTTTC
**
5201306 TTATTCTCAATATATGAGATTTTT
1 TTATAATCAATATATGAGATTTTT
5201330 TACCTTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.54
Consensus pattern (25 bp):
TTATAATCAATATATGAGATTTTTC
Done.