Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_pilon, whole genome shotgun sequence
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: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1583557 original size:21 final size:21
Alignment explanation
Indices: 1583533--1583590 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
1583523 GACCAAATAT
1583533 ATGTCTCAAAAGACCTCATAC
1 ATGTCTCAAAAGACCTCATAC
* ***
1583554 ATGT-TCCAAAGAAGACATAC
1 ATGTCTCAAAAGACCTCATAC
* *
1583574 ATGTCCCGAAAGACCTC
1 ATGTCTCAAAAGACCTC
1583591 GTAGACCCTC
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.21
Consensus pattern (21 bp):
ATGTCTCAAAAGACCTCATAC
Found at i:1594359 original size:29 final size:29
Alignment explanation
Indices: 1594317--1594380 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1594307 CACATATTAG
1594317 GATTGTTCTACAATTTCTGCTAGAGAAGC
1 GATTGTTCTACAATTTCTGCTAGAGAAGC
* *
1594346 GATTGTTCTGCAATTTCTGTTAGAGAAGC
1 GATTGTTCTACAATTTCTGCTAGAGAAGC
*
1594375 AATTGT
1 GATTGT
1594381 ATGTAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (29 bp):
GATTGTTCTACAATTTCTGCTAGAGAAGC
Found at i:1597740 original size:49 final size:50
Alignment explanation
Indices: 1597625--1597882 Score: 378
Period size: 50 Copynumber: 5.2 Consensus size: 50
1597615 GTGCATTGAG
**
1597625 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTGGGCATAAA
1 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
* * *
1597675 AGGTGTTC-CTAATGAAAGCTAAATGCATAACGATGCA-TTTCAGCATAAA
1 AGGTG-CCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
* * **
1597724 AGATGCCACTAATGAAAGTTAAATGCATAACGATGCATTTTCAGTGTAAA
1 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
*
1597774 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAA
1 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
* *
1597823 AAGTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCAGCATAAA
1 AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
1597873 AGGTGCCACT
1 AGGTGCCACT
1597883 TATGGTATTC
Statistics
Matches: 185, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
48 1 0.01
49 86 0.46
50 97 0.52
51 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (50 bp):
AGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAA
Found at i:1597748 original size:99 final size:99
Alignment explanation
Indices: 1597627--1597882 Score: 390
Period size: 99 Copynumber: 2.6 Consensus size: 99
1597617 GCATTGAGAG
** *
1597627 GTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTGGGCATAAAAGGTGTTC-CTAATGAA
1 GTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAAAGGTG-CCACTAATGAA
1597691 AGCTAAATGCATAACGATGCATTTCAGCAT-AAAA
65 AGCTAAATGCATAACGATGCATTTCAGCATAAAAA
* **
1597725 GATGCCACTAATGAAAGTTAAATGCATAACGATGCATTTTCAGTGTAAAAGGTGCCACTAATGAA
1 G-TGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAAAGGTGCCACTAATGAA
* * *
1597790 AGTTAAATGCATAACGGTGCATTTCGGCATAAAAA
65 AGCTAAATGCATAACGATGCATTTCAGCATAAAAA
*
1597825 GTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCAGCATAAAAGGTGCCACT
1 GTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAAAGGTGCCACT
1597883 TATGGTATTC
Statistics
Matches: 142, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
98 2 0.01
99 135 0.95
100 5 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (99 bp):
GTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCAGCATAAAAGGTGCCACTAATGAAA
GCTAAATGCATAACGATGCATTTCAGCATAAAAA
Found at i:1601015 original size:2 final size:2
Alignment explanation
Indices: 1601008--1601074 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
1600998 TATAACAATA
1601008 AT AT AT AT AT AT AT AT AT AT AT A- 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 AT AT AT AT
1601049 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
1601075 GCTGTTCATG
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1608812 original size:49 final size:50
Alignment explanation
Indices: 1608693--1608953 Score: 382
Period size: 50 Copynumber: 5.3 Consensus size: 50
1608683 ATTGAGAGTC
* *
1608693 AAAAGGTACCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCAT
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
* * * *
1608743 AAAAGGTGCCACTAAAGAAAGCTAAATGCATAACGATGCA-TTTCAGCAT
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
* *
1608792 AAAAGGTGCCACTAATGAAAGTTAAATACATAACGGTGCACTTTCGGCAT
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
* *
1608842 AAAAGATGCCACTAATGAAAGTTAAATGCATAATGGTGCA-TTTCGGCAT
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
* * *
1608891 AAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTACATTTTCAGCAT
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
*
1608941 AAAAGGTGTCACT
1 AAAAGGTGCCACT
1608954 CATGGTATTC
Statistics
Matches: 191, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 91 0.48
50 100 0.52
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (50 bp):
AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTGCATTTTCGGCAT
Found at i:1608852 original size:99 final size:99
Alignment explanation
Indices: 1608693--1608945 Score: 398
Period size: 99 Copynumber: 2.6 Consensus size: 99
1608683 ATTGAGAGTC
* *
1608693 AAAAGGTACCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCATAAAAGGTGCCACTAA
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCATAAAAGATGCCACTAA
1608758 AGAAAGCTAAATGCATAACGATGCATTTCAGCAT
66 AGAAAGCTAAATGCATAACGATGCATTTCAGCAT
* * *
1608792 AAAAGGTGCCACTAATGAAAGTTAAATACATAACGGTGCACTTTCGGCATAAAAGATGCCACTAA
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCATAAAAGATGCCACTAA
* * * * *
1608857 TGAAAGTTAAATGCATAATGGTGCATTTCGGCAT
66 AGAAAGCTAAATGCATAACGATGCATTTCAGCAT
* *
1608891 AAAAGGTGCCACTAATGAAAGTTAAATGCATAATGGTACATTTTCAGCATAAAAG
1 AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCATAAAAG
1608946 GTGTCACTCA
Statistics
Matches: 139, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 139 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (99 bp):
AAAAGGTGCCACTAATGAAAGTTAAATGCATAACGGTACATTTTCGGCATAAAAGATGCCACTAA
AGAAAGCTAAATGCATAACGATGCATTTCAGCAT
Found at i:1609481 original size:21 final size:20
Alignment explanation
Indices: 1609448--1609486 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1609438 TTTGGTAATA
1609448 TATTACATAAAATGTTTTAT
1 TATTACATAAAATGTTTTAT
*
1609468 TATTATATCAAAATGTTTT
1 TATTACAT-AAAATGTTTT
1609487 GTTTTAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TATTACATAAAATGTTTTAT
Found at i:1618354 original size:20 final size:20
Alignment explanation
Indices: 1618329--1618373 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1618319 TGAGAAACTT
* *
1618329 CATACTGGAGGGTTGGTATC
1 CATACTAGAGGGTTAGTATC
1618349 CATACTAGAGGGTTAGTATC
1 CATACTAGAGGGTTAGTATC
*
1618369 TATAC
1 CATAC
1618374 CAAAGATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (20 bp):
CATACTAGAGGGTTAGTATC
Found at i:1624308 original size:35 final size:35
Alignment explanation
Indices: 1624187--1624313 Score: 139
Period size: 36 Copynumber: 3.6 Consensus size: 35
1624177 AAGGGTAACT
* *
1624187 ATCTCAAGTGGGATAAAATTTGTTTCAAGAGAAACA
1 ATCTCAAGTGAGATAAAATTTGTTTTAAGA-AAACA
* * ** * *
1624223 ATATCTAGTGAGATAATGTTTATTTTAAGAAAAATA
1 ATCTCAAGTGAGATAAAATTTGTTTTAAG-AAAACA
1624259 ATCT-ATAGTGAGATAAAATTTGTTTTAAGAAAACA
1 ATCTCA-AGTGAGATAAAATTTGTTTTAAGAAAACA
*
1624294 ATCTCAAGTAAGATAAAATT
1 ATCTCAAGTGAGATAAAATT
1624314 GGATTGGATC
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
35 22 0.30
36 50 0.68
37 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (35 bp):
ATCTCAAGTGAGATAAAATTTGTTTTAAGAAAACA
Found at i:1624983 original size:50 final size:50
Alignment explanation
Indices: 1624929--1625036 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 50
1624919 ATGACATAAA
* *
1624929 ATCATTTTT-CCTCAACCTTAGGTATTATTC-CCATTATTGAACTCATCATC
1 ATCATTTTTACCTCAACCTTAAGCATTA-TCACCATTATTG-ACTCATCATC
*
1624979 ATCATTTTTACCTCAACCTTAAGCATTATCACCTTTATTGACTCATCATC
1 ATCATTTTTACCTCAACCTTAAGCATTATCACCATTATTGACTCATCATC
*
1625029 ACCATTTT
1 ATCATTTT
1625037 CTCTCATTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 28 0.54
51 24 0.46
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.42
Consensus pattern (50 bp):
ATCATTTTTACCTCAACCTTAAGCATTATCACCATTATTGACTCATCATC
Found at i:1627074 original size:46 final size:46
Alignment explanation
Indices: 1626970--1627163 Score: 221
Period size: 46 Copynumber: 4.2 Consensus size: 46
1626960 TAATATACCA
* ** * * *
1626970 TTATGTATTTTCATTGGTGGCATCCTTTTATGC-CAAATATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCTTATA-ATGCACCG
* * * * *
1627016 TTAAGCAATTTCATTTACGGCA-CCTTTTCATGCTTATAATGTACTG
1 TTATGCATTTTCATTTATGGCATCC-TTTCATGCTTATAATGCACCG
*
1627062 TTATGCATTTTCATTTATGGCATCCTTTCACGCTTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCTTATAATGCACCG
** *
1627108 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCTTATAATGCACCG
1627154 TTATGCATTT
1 TTATGCATTT
1627164 AGTCTTTTAC
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
45 2 0.02
46 118 0.95
47 4 0.03
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCTTATAATGCACCG
Found at i:1627288 original size:81 final size:81
Alignment explanation
Indices: 1627166--1627735 Score: 802
Period size: 81 Copynumber: 7.1 Consensus size: 81
1627156 ATGCATTTAG
* * * * * **
1627166 TCTTTTACCCAAAGGCATTTAGTCTTTCATCTAACTTGCATGATTGCCACCTTTCTGAAAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
* *
1627231 ACATCTAGGCATTTAA
66 ACAGCTAGGCAATTAA
* * *
1627247 TATTTAACTCAAAGGCATTTAGCCTTTCATCTTACTGGCATGATTGACACCTTTCTTCCAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
*
1627312 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
1627328 TCTTTAACTCAAAGGCATTTAACC-TTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
*
1627392 AAAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* *
1627408 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGATACCTTTCTGTCAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
*
1627473 ACA-CTAGACAATTAA
66 ACAGCTAGGCAATTAA
* * *
1627488 TCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACACCTTTCTGCCAAATAC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
*
1627553 ACAGCTAGGAAATTAA
66 ACAGCTAGGCAATTAA
* * *
1627569 TCTTTAACTCAAAGGGATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
1627634 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * * * * ** *
1627650 TCTTTTACTCAAAGGTATTTAACCTTTCATGTAACTGGCATAATTGACATATTTATGCCAAATGC
1 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
*
1627715 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
1627731 TCTTT
1 TCTTT
1627736 TATTTAAAAC
Statistics
Matches: 437, Mismatches: 50, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
80 147 0.34
81 290 0.66
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (81 bp):
TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCAATTAA
Found at i:1627416 original size:161 final size:162
Alignment explanation
Indices: 1627166--1627735 Score: 797
Period size: 161 Copynumber: 3.5 Consensus size: 162
1627156 ATGCATTTAG
* * ** * * * *
1627166 TCTTTTACCCAAAGGCATTTAGTCTTTCATCTAACTTGCATGATTGCCACCTTTCTGAAAAATGC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
* * * * *
1627231 ACATCTAGGCATTTAATATTTAACTCAAAGGCATTTAGCCTTTCATCTTACTGGCATGATTGACA
66 AAAGCTAGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACA
1627296 CCTTTCT-TCCAAATGCACAACTAGGCAATTAA
131 CCTTTCTGT-CAAATGCACAACTAGGCAATTAA
1627328 TCTTTAACTCAAAGGCATTTAACC-TTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
*
1627392 AAAGCTAGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGATA
66 AAAGCTAGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACA
*
1627457 CCTTTCTGTCAAATGCAC-ACTAGACAATTAA
131 CCTTTCTGTCAAATGCACAACTAGGCAATTAA
* * * * * *
1627488 TCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACACCTTTCTGCCAAATAC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
* * * *
1627553 ACAGCTAGGAAATTAATCTTTAACTCAAAGGGATTTAGCCTTTCATCTAACTGGCATAATTGACA
66 AAAGCTAGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACA
*
1627618 CCTTTCTGTCAAATGCACAGCTAGGCAATTAA
131 CCTTTCTGTCAAATGCACAACTAGGCAATTAA
* * * * * * *
1627650 TCTTTTACTCAAAGGTATTTAACCTTTCATGTAACTGGCATAATTGACATATTTATGCCAAATGC
1 TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
1627715 ACAA-CTAGGCAATTAATCTTT
66 A-AAGCTAGGCAATTAATCTTT
1627736 TATTTAAAAC
Statistics
Matches: 363, Mismatches: 41, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
160 34 0.09
161 225 0.62
162 103 0.28
163 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (162 bp):
TCTTTAACTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGCAAAATGC
AAAGCTAGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACA
CCTTTCTGTCAAATGCACAACTAGGCAATTAA
Found at i:1627617 original size:242 final size:241
Alignment explanation
Indices: 1627166--1627732 Score: 812
Period size: 242 Copynumber: 2.3 Consensus size: 241
1627156 ATGCATTTAG
* * * * *
1627166 TCTTTTACCCAAAGGCATTTAGTCTTTCATCTAACTTGCATGATTGCCACCTTTCTGAAAAATGC
1 TCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGACAAATGC
* ** * *
1627231 ACATCTAGGCATTTAATATTTAACTCAAAGGCATTTAGCCTTTCATCTTACTGGCATGATTGACA
66 ACA-CTAGGCAATTAATCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACA
* * *
1627296 CCTTTCTTCCAAATGCACAACTAGGCAATTAATCTTTAACTCAAAGGCATTTAACCTTCATCTAA
130 CCTTTCTGCCAAATACACAACTAGGAAATTAATCTTTAACTCAAAGGCATTTAACCTTCATCTAA
*
1627361 CTGGCATGATTGACACATTTCTG-CAAAATGCAAAGCTAGGCAATTAA
195 CTGGCATAATTGACACATTTCTGTC-AAATGCAAAGCTAGGCAATTAA
* * *
1627408 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGATACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGACAAATGC
*
1627473 ACACTAGACAATTAATCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACAC
66 ACACTAGGCAATTAATCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACAC
* * *
1627538 CTTTCTGCCAAATACACAGCTAGGAAATTAATCTTTAACTCAAAGGGATTTAGCCTTTCATCTAA
131 CTTTCTGCCAAATACACAACTAGGAAATTAATCTTTAACTCAAAGGCATTTAACC-TTCATCTAA
* *
1627603 CTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
195 CTGGCATAATTGACACATTTCTGTCAAATGCAAAGCTAGGCAATTAA
* * * * ** * *
1627650 TCTTTTACTCAAAGGTATTTAACCTTTCATGTAACTGGCATAATTGACATATTTATGCCAAATGC
1 TCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGACAAATGC
1627715 ACAACTAGGCAATTAATC
66 AC-ACTAGGCAATTAATC
1627733 TTTTATTTAA
Statistics
Matches: 288, Mismatches: 34, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
241 105 0.36
242 168 0.58
243 15 0.05
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.33
Consensus pattern (241 bp):
TCTTTTACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATGATTGACACCTTTCTGACAAATGC
ACACTAGGCAATTAATCCTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCACGATTGACAC
CTTTCTGCCAAATACACAACTAGGAAATTAATCTTTAACTCAAAGGCATTTAACCTTCATCTAAC
TGGCATAATTGACACATTTCTGTCAAATGCAAAGCTAGGCAATTAA
Found at i:1627818 original size:20 final size:21
Alignment explanation
Indices: 1627793--1627832 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1627783 ACACACATTA
*
1627793 TAAATATATA-TAATATAAAG
1 TAAATATACATTAATATAAAG
1627813 TAAATATACATTAATATAAA
1 TAAATATACATTAATATAAA
1627833 CATTTGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAATATACATTAATATAAAG
Found at i:1633074 original size:46 final size:46
Alignment explanation
Indices: 1632962--1633137 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
1632952 TTTTCATTGG
* * * *
1632962 TGGCATCCTTTCATGCCAATTATGCA-TCGTTAAT-CATTTTCA-TTA
1 TGGCATCATTTCATGCCTATAATGCACT-GTT-ATGCATTTTTATTTA
* * *
1633007 TGGCATCCTTTCATCCCTATAATGTACTGTTATGCATTTTTATTTA
1 TGGCATCATTTCATGCCTATAATGCACTGTTATGCATTTTTATTTA
* *
1633053 TGGCATCATTTCTTGCTTATAATGCACTGTTATGCATTTTTATTTA
1 TGGCATCATTTCATGCCTATAATGCACTGTTATGCATTTTTATTTA
* * *
1633099 TGACATCATTTCATGCCGATAATGCACCGTTATGCATTT
1 TGGCATCATTTCATGCCTATAATGCACTGTTATGCATTT
1633138 AATCTTTTAC
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
44 2 0.02
45 32 0.28
46 79 0.70
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.44
Consensus pattern (46 bp):
TGGCATCATTTCATGCCTATAATGCACTGTTATGCATTTTTATTTA
Found at i:1633314 original size:80 final size:81
Alignment explanation
Indices: 1633136--1633314 Score: 198
Period size: 80 Copynumber: 2.2 Consensus size: 81
1633126 CGTTATGCAT
* * * * * *
1633136 TTAATCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATAATTGACACATTTCTACCAA
1 TTAATCTTTAACTCAAAGACATTTAGCCTTTCACCTAACTTACATAATTGACACATTTATACCAA
** * *
1633201 ATTTACAATTAGCCAT
66 ATGCACAACTAGCCAA
* * * *
1633217 TTAATCTTTAACTCAAAGACATTTAGCCTTTCACCTAAC-TACATCATTGACACCTTTATGCTAA
1 TTAATCTTTAACTCAAAGACATTTAGCCTTTCACCTAACTTACATAATTGACACATTTATACCAA
* *
1633281 ATGCACAGCTAGGCAA
66 ATGCACAACTAGCCAA
*
1633297 TTAATGTTTAACTCAAAG
1 TTAATCTTTAACTCAAAG
1633315 GCAATCAATC
Statistics
Matches: 81, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
80 46 0.57
81 35 0.43
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.35
Consensus pattern (81 bp):
TTAATCTTTAACTCAAAGACATTTAGCCTTTCACCTAACTTACATAATTGACACATTTATACCAA
ATGCACAACTAGCCAA
Found at i:1633316 original size:22 final size:22
Alignment explanation
Indices: 1633291--1633337 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1633281 ATGCACAGCT
* *
1633291 AGGCAATTAATGTTTAACTCAA
1 AGGCAATCAATCTTTAACTCAA
1633313 AGGCAATCAATCTTTAACTCAA
1 AGGCAATCAATCTTTAACTCAA
1633335 AGG
1 AGG
1633338 TAGTTAGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGCAATCAATCTTTAACTCAA
Found at i:1633410 original size:103 final size:102
Alignment explanation
Indices: 1633219--1633420 Score: 289
Period size: 103 Copynumber: 2.0 Consensus size: 102
1633209 TTAGCCATTT
* * *
1633219 AATCTTTAACTCAAAGACATTTAGCCTTTCACCTAACTACATCATTGACACCTTTATGCTAAATG
1 AATCTTTAACTCAAAGACAGTTAGCCTTTCACCTAACTACATAATTGACACCATTATGCTAAATG
* *
1633284 CACAGCTAGGCAATTAATGTTTAACTCAAAGGCAATC
66 CAAAGCTAGGCAATTAATCTTTAACTCAAAGGCAATC
** * * *
1633321 AATCTTTAACTCAAAGGTAGTTAGCCTTTCATCTAACTGGCATAATTGACACCATTCTG-TCAAA
1 AATCTTTAACTCAAAGACAGTTAGCCTTTCACCTAACT-ACATAATTGACACCATTATGCT-AAA
1633385 TGCAAAGCTAGGCAATTAATCTTTAACTCAAAGGCA
64 TGCAAAGCTAGGCAATTAATCTTTAACTCAAAGGCA
1633421 TTTAGCCTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 35 0.40
103 53 0.60
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (102 bp):
AATCTTTAACTCAAAGACAGTTAGCCTTTCACCTAACTACATAATTGACACCATTATGCTAAATG
CAAAGCTAGGCAATTAATCTTTAACTCAAAGGCAATC
Found at i:1633895 original size:81 final size:81
Alignment explanation
Indices: 1633313--1633893 Score: 803
Period size: 81 Copynumber: 7.2 Consensus size: 81
1633303 TTTAACTCAA
* * *
1633313 AGGCAATCAATCTTTAACTCAAAGGTAGTTAGCCTTTCATCTAACTGGCATAATTGACACCA-TT
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACA-CATTT
*
1633377 CTGTCAAATGCAAAGCT
65 CTGTCAAATGCACAGCT
** *
1633394 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTTCCA-AGATTGACACCTTT
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATA-ATTGACACATTT
*
1633458 CTGTCAAATGCACAGTT
65 CTGTCAAATGCACAGCT
* * *
1633475 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCTTCTAACTGGCATGATTGACACCTTTC
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACATTTC
*
1633540 TGTCAAATGCACAACT
66 TGTCAAATGCACAGCT
* * * *
1633556 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTAGTATGATTGAAACCA-TT
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACA-CATTT
1633620 CTGTCAAATGCACAGCT
65 CTGTCAAATGCACAGCT
* * * *
1633637 AGGCATTTAACCTTTAACTCAAAGTCATTTAGCCTTTCATCGAACTGGCATAATTGACATC-TTT
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACA-CATTT
*
1633701 CTGTCAAATACACAGCT
65 CTGTCAAATGCACAGCT
* *
1633718 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGACAT-ATTGACATATTTC
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACATTTC
1633782 TGTCAAATGCACAGCT
66 TGTCAAATGCACAGCT
* * * * *
1633798 AGACAATTAATCTTTTACTCAAAAGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTC
1 AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACATTTC
* *
1633863 TGCCAAATGCAAAGCT
66 TGTCAAATGCACAGCT
**
1633879 AGAAAATTAATCTTT
1 AGGCAATTAATCTTT
1633894 TATTTAAAAC
Statistics
Matches: 446, Mismatches: 47, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
80 73 0.16
81 372 0.83
82 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (81 bp):
AGGCAATTAATCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACATTTC
TGTCAAATGCACAGCT
Found at i:1640567 original size:24 final size:24
Alignment explanation
Indices: 1640535--1640653 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
1640525 ATTTGAATTC
1640535 TGATCTGATACTTGACATGGATTT
1 TGATCTGATACTTGACATGGATTT
* *
1640559 TGATCTGATA-TCTGATATGGATTC
1 TGATCTGATACT-TGACATGGATTT
* *
1640583 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTT
* *
1640607 TGATCCGATACTTGACTTGGATTT
1 TGATCTGATACTTGACATGGATTT
* *
1640631 TGATATGATACTTGATAT-GATTT
1 TGATCTGATACTTGACATGGATTT
1640654 ATGTTTTGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 6 0.07
24 76 0.92
25 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTT
Found at i:1643050 original size:23 final size:23
Alignment explanation
Indices: 1642996--1643061 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1642986 CACCAAACTG
* *
1642996 CCACACAGATTTGTCCCGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
*** *
1643019 CCGTGTAGAATTGTCCGGAAGGA
1 CCACATAGAATTGTCCCGAAGGA
*
1643042 CCACATAGAATTATCCCGAA
1 CCACATAGAATTGTCCCGAA
1643062 TGATTGCGTA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (23 bp):
CCACATAGAATTGTCCCGAAGGA
Found at i:1643211 original size:15 final size:15
Alignment explanation
Indices: 1643177--1643227 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1643167 AAGTATATTT
1643177 TATTCACATAG-ACTA
1 TATTCACATAGAAC-A
*
1643192 CATTCACATAGAACA
1 TATTCACATAGAACA
* *
1643207 TATTCCCATAAAACA
1 TATTCACATAGAACA
*
1643222 TTTTCA
1 TATTCA
1643228 GGTATAACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.31
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:1658109 original size:18 final size:18
Alignment explanation
Indices: 1658086--1658138 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
1658076 ACTGAATATT
*
1658086 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1658104 TGTCCCAAAGGACTACTA
1 TGTCCCGAAGGACCACTA
*
1658122 TGTTCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1658139 GATAATCCCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1675664 original size:20 final size:20
Alignment explanation
Indices: 1675639--1675686 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1675629 AAATTTATGT
1675639 GCAATAAAGCCTTCGTTGAA
1 GCAATAAAGCCTTCGTTGAA
1675659 GCAATAAAGCCTTCGTTGAA
1 GCAATAAAGCCTTCGTTGAA
1675679 GCAATAAA
1 GCAATAAA
1675687 ATCATGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
GCAATAAAGCCTTCGTTGAA
Found at i:1678741 original size:20 final size:20
Alignment explanation
Indices: 1678713--1678768 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1678703 TTAATAGGAG
* *
1678713 TATCAATATTTAGAGGGCAA
1 TATCGATATTCAGAGGGCAA
1678733 TATCGATATTCAGAGGGCAA
1 TATCGATATTCAGAGGGCAA
*
1678753 TATCGATACTCAGAGG
1 TATCGATATTCAGAGG
1678769 CAAATATGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (20 bp):
TATCGATATTCAGAGGGCAA
Found at i:1680087 original size:29 final size:31
Alignment explanation
Indices: 1680026--1680089 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
1680016 ATTTTGGTCC
*
1680026 CTAAACTTTTCCAAACATTATAGTTTGGCTA
1 CTAAACTTTTCCAAACATTATAGTTTGACTA
*
1680057 CTAAAC-TTT-CAAA-ATGTATAGTTTGATTA
1 CTAAACTTTTCCAAACAT-TATAGTTTGACTA
1680086 CTAA
1 CTAA
1680090 CCAAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.07
29 19 0.63
30 3 0.10
31 6 0.20
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (31 bp):
CTAAACTTTTCCAAACATTATAGTTTGACTA
Found at i:1685686 original size:19 final size:20
Alignment explanation
Indices: 1685662--1685704 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1685652 AGCATTTATC
*
1685662 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
1685681 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
1685701 TTCA
1 TTCA
1685705 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1686122 original size:35 final size:35
Alignment explanation
Indices: 1686047--1686175 Score: 181
Period size: 35 Copynumber: 3.7 Consensus size: 35
1686037 TACTATCTGT
*
1686047 TCATCACCATCTTCCATTACCATTTTCACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* *
1686083 TCATCACCATCTTCCATCACCATTGCATGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
* *
1686118 TCATCACCATCTTCTATCACCATTTCACGCTTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
*
1686153 TCATCACCAT-TTCC-TTACCATTT
1 TCATCACCATCTTCCATCACCATTT
1686176 ATTCACCATT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
33 8 0.10
34 3 0.04
35 52 0.62
36 21 0.25
ACGTcount: A:0.25, C:0.36, G:0.03, T:0.36
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:1686828 original size:16 final size:15
Alignment explanation
Indices: 1686771--1686831 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
1686761 TGAGATGTAA
*
1686771 CTTATCTTCATTTTT
1 CTTATTTTCATTTTT
1686786 CTTACTATTTCATTTCCTT
1 CTTA-T-TTTCATTT--TT
*
1686805 GTTA-TTTCATCTTTT
1 CTTATTTTCAT-TTTT
1686820 CTTATTTTCATT
1 CTTATTTTCATT
1686832 ACTTTATCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
15 10 0.27
16 13 0.35
17 9 0.24
19 5 0.14
ACGTcount: A:0.15, C:0.20, G:0.02, T:0.64
Consensus pattern (15 bp):
CTTATTTTCATTTTT
Found at i:1696233 original size:20 final size:20
Alignment explanation
Indices: 1696187--1696237 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1696177 CCCTAATAGG
*
1696187 AGTATCGATACTTAGAGGAC
1 AGTATCGATACTGAGAGGAC
**
1696207 AACATCGATACTGAGAGG-C
1 AGTATCGATACTGAGAGGAC
1696226 TAGTATCGATAC
1 -AGTATCGATAC
1696238 CAGAGTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
AGTATCGATACTGAGAGGAC
Found at i:1697432 original size:29 final size:29
Alignment explanation
Indices: 1697389--1697451 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1697379 CCCTGCGAGC
1697389 AATTTATCTTCTATTATAATTTATAAAAA
1 AATTTATCTTCTATTATAATTTATAAAAA
* *
1697418 GATTTATCTGT-TATTGTAATTTATAAAAA
1 AATTTATCT-TCTATTATAATTTATAAAAA
1697447 AATTT
1 AATTT
1697452 GTCCTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (29 bp):
AATTTATCTTCTATTATAATTTATAAAAA
Found at i:1697464 original size:29 final size:29
Alignment explanation
Indices: 1697405--1697474 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1697395 TCTTCTATTA
* * *
1697405 TAATTTATAAAAAGATTTATCTGTTATTG
1 TAATTTATAAAAAAATTTATCTGTAAATG
*
1697434 TAATTTATAAAAAAATTTGTCCT-TAAATG
1 TAATTTATAAAAAAATTTAT-CTGTAAATG
1697463 TAATTTATAAAA
1 TAATTTATAAAA
1697475 TATATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 34 0.94
30 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (29 bp):
TAATTTATAAAAAAATTTATCTGTAAATG
Found at i:1697490 original size:24 final size:24
Alignment explanation
Indices: 1697463--1697511 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1697453 TCCTTAAATG
1697463 TAATTTATAAAATATATTTAATTT
1 TAATTTATAAAATATATTTAATTT
* * *
1697487 TAATTTGTATAATTTATTTAATTT
1 TAATTTATAAAATATATTTAATTT
1697511 T
1 T
1697512 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TAATTTATAAAATATATTTAATTT
Found at i:1698518 original size:61 final size:61
Alignment explanation
Indices: 1698423--1698538 Score: 214
Period size: 61 Copynumber: 1.9 Consensus size: 61
1698413 CATATAGTGG
*
1698423 TATGACACATAAGGTCATGTCCACCACCTACACTAAGTGTCTTGGGTATACACTTTAGTAC
1 TATGACACATAAGGTCATGCCCACCACCTACACTAAGTGTCTTGGGTATACACTTTAGTAC
*
1698484 TATGACACATAAGGTCGTGCCCACCACCTACACTAAGTGTCTTGGGTATACACTT
1 TATGACACATAAGGTCATGCCCACCACCTACACTAAGTGTCTTGGGTATACACTT
1698539 AACTGCTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (61 bp):
TATGACACATAAGGTCATGCCCACCACCTACACTAAGTGTCTTGGGTATACACTTTAGTAC
Found at i:1704562 original size:65 final size:64
Alignment explanation
Indices: 1704487--1704638 Score: 198
Period size: 65 Copynumber: 2.4 Consensus size: 64
1704477 CACACCCATT
* * *
1704487 TCGAATGCATTTTGTGTACCGATACACAAGCCATGCATCGATGCACACTTGAATAT-TTTGAAAC
1 TCGAATGCATTTTGTGTACCGATACACAAACCATGCATCAATGCACACCTG-AT-TCTTTGAAAC
1704551 A
64 A
* * *
1704552 TCGAATGCATTTTGTGTACCGATACATAAACCATGCATCAATGCACTCCTGGTTCTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATACACAAACCATGCATCAATGCACACCTGATTCTTTGAAACA
* * *
1704616 TCGAATACAATTAGTGTACCGAT
1 TCGAATGCATTTTGTGTACCGAT
1704639 GCACCCCCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.01
64 30 0.39
65 46 0.60
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTGTGTACCGATACACAAACCATGCATCAATGCACACCTGATTCTTTGAAACA
Found at i:1710490 original size:44 final size:43
Alignment explanation
Indices: 1710405--1710502 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
1710395 TTTTGTGCTT
*
1710405 TGTGCATCGATACACTAGACAATGTACCGATGCATCTCTTGAA
1 TGTGCATCGATACACTAGACAATGCACCGATGCATCTCTTGAA
1710448 TGTGCATCGATACA-TCATGA-AGATGCACCGATGCAT-TCCTTGAA
1 TGTGCATCGATACACT-A-GACA-ATGCACCGATGCATCT-CTTGAA
*
1710492 TGTACATCGAT
1 TGTGCATCGAT
1710503 GCACCCTGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
42 1 0.02
43 17 0.35
44 31 0.63
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (43 bp):
TGTGCATCGATACACTAGACAATGCACCGATGCATCTCTTGAA
Found at i:1712741 original size:64 final size:64
Alignment explanation
Indices: 1712625--1712751 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 64
1712615 ATATCGAATG
* ** *
1712625 CATTTTGTGTACCGATGCACAAGCCATGCATCGATGCGTTCTTGAATATTTGAAACATCAAATT
1 CATTTTCTGTACCGATGCACAAGCCATGCATCGATGCACTCTAGAATATTTGAAACATCAAATT
* ** *
1712689 CATTTTCTGTACTGATGCAC-AGACCATGCATCGATGCACTCTAGGCTCTTTGAAACATCAAAT
1 CATTTTCTGTACCGATGCACAAG-CCATGCATCGATGCACTCTAGAATATTTGAAACATCAAAT
1712752 GCAATTTGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 52 0.96
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (64 bp):
CATTTTCTGTACCGATGCACAAGCCATGCATCGATGCACTCTAGAATATTTGAAACATCAAATT
Found at i:1712770 original size:64 final size:63
Alignment explanation
Indices: 1712621--1712772 Score: 148
Period size: 64 Copynumber: 2.4 Consensus size: 63
1712611 ACCCATATCG
** *
1712621 AATGCATTTTG-TGTACCGATGCACAAGCCATGCATCGATGCGTTCTTGAATATTTGAAACATCA
1 AATGCA-TTTGATGTA-CGATGCACAAGCCATGCATCGATGCACTCTAGAATATTTGAAACATCA
* ** ** *
1712685 AATTCATTTTCTGTACTGATGCAC-AGACCATGCATCGATGCACTCTAGGCTCTTTGAAACATCA
1 AATGCATTTGATGTAC-GATGCACAAG-CCATGCATCGATGCACTCTAGAATATTTGAAACATCA
1712749 AATGCAATTTGAT-TATCGATGCAC
1 AATGC-ATTTGATGTA-CGATGCAC
1712773 CCCCTAATGT
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
63 6 0.08
64 60 0.83
65 6 0.08
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (63 bp):
AATGCATTTGATGTACGATGCACAAGCCATGCATCGATGCACTCTAGAATATTTGAAACATCA
Found at i:1726382 original size:16 final size:16
Alignment explanation
Indices: 1726361--1726392 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1726351 AAAAAATATT
1726361 TCCATTAAGAAACATA
1 TCCATTAAGAAACATA
1726377 TCCATTAAGAAACATA
1 TCCATTAAGAAACATA
1726393 ATAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
TCCATTAAGAAACATA
Found at i:1739024 original size:21 final size:20
Alignment explanation
Indices: 1738974--1739025 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
1738964 CTCTTGATAG
* *
1738974 GTATTGGTACTACTAGTATA
1 GTATTGATACTACTAGAATA
** *
1738994 GTATCAATACTACTTGAATGA
1 GTATTGATACTACTAGAAT-A
1739015 GTATTGATACT
1 GTATTGATACT
1739026 GTTCATCCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATTGATACTACTAGAATA
Found at i:1741475 original size:20 final size:20
Alignment explanation
Indices: 1741437--1741476 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1741427 AATACGTAAA
* *
1741437 TTAATTTTAAGATTTTATTT
1 TTAATTTAAAGATTATATTT
*
1741457 TTAATTTAAATATTATATTT
1 TTAATTTAAAGATTATATTT
1741477 GATTCAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTAATTTAAAGATTATATTT
Found at i:1743455 original size:20 final size:20
Alignment explanation
Indices: 1743417--1743456 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1743407 AATGCTTAAA
* *
1743417 TTAATTTTAAGATTTTATTT
1 TTAATTTAAAGATTATATTT
*
1743437 TTAATTTAAATATTATATTT
1 TTAATTTAAAGATTATATTT
1743457 GATTCAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTAATTTAAAGATTATATTT
Found at i:1743837 original size:24 final size:24
Alignment explanation
Indices: 1743809--1743887 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
1743799 ACCAGGTTCG
1743809 GTATCGATACTACTATACATAGTA
1 GTATCGATACTACTATACATAGTA
* * *
1743833 ATATCGATATTCCT-TGA-AT-G--
1 GTATCGATACTACTAT-ACATAGTA
*
1743853 GTATCGATACTACTACACATAGTA
1 GTATCGATACTACTATACATAGTA
1743877 GTATCGATACT
1 GTATCGATACT
1743888 CCTTGAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
20 12 0.29
21 2 0.05
22 2 0.05
23 3 0.07
24 23 0.55
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (24 bp):
GTATCGATACTACTATACATAGTA
Found at i:1743858 original size:44 final size:44
Alignment explanation
Indices: 1743808--1743906 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 44
1743798 TACCAGGTTC
* *
1743808 GGTATCGATACTACTATACATAGTAATATCGATATTCCTTGA-A
1 GGTATCGATACTACTACACATAGTAATATCGATACTCCTTGAGA
*
1743851 TGGTATCGATACTACTACACATAGTAGTATCGATACTCCTTGAGA
1 -GGTATCGATACTACTACACATAGTAATATCGATACTCCTTGAGA
*
1743896 GGTATTGATAC
1 GGTATCGATAC
1743907 CTTTGTGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 49 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (44 bp):
GGTATCGATACTACTACACATAGTAATATCGATACTCCTTGAGA
Found at i:1745485 original size:21 final size:21
Alignment explanation
Indices: 1745434--1745490 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1745424 GGTCTTGATA
*
1745434 GTATCGATACTACTATTCACG
1 GTATCGATACTACTGTTCACG
** *
1745455 GTATTAATACTACTGTTCATG
1 GTATCGATACTACTGTTCACG
1745476 GTATCGATAC-ACTGT
1 GTATCGATACTACTGT
1745491 AGCAGTATCG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
GTATCGATACTACTGTTCACG
Found at i:1745551 original size:18 final size:18
Alignment explanation
Indices: 1745528--1745577 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 18
1745518 GAATATTTTA
*
1745528 GTATCGGTACTGTTCATG
1 GTATCGATACTGTTCATG
1745546 GTATCGATACAACTGTTCATG
1 GTATCGAT---ACTGTTCATG
1745567 GTATCGATACT
1 GTATCGATACT
1745578 ACTATTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
21 18 0.64
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (18 bp):
GTATCGATACTGTTCATG
Found at i:1745562 original size:21 final size:21
Alignment explanation
Indices: 1745536--1745585 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1745526 TAGTATCGGT
1745536 ACTGTTCATGGTATCGATACA
1 ACTGTTCATGGTATCGATACA
*
1745557 ACTGTTCATGGTATCGATACT
1 ACTGTTCATGGTATCGATACA
*
1745578 ACTATTCA
1 ACTGTTCA
1745586 CACATATAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
ACTGTTCATGGTATCGATACA
Found at i:1745601 original size:19 final size:19
Alignment explanation
Indices: 1745577--1745623 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1745567 GTATCGATAC
1745577 TACTATTCACAC-ATATAGG
1 TACTATTCACACAATAT-GG
* *
1745596 TACTATTTATACAATATGG
1 TACTATTCACACAATATGG
1745615 TACTATTCA
1 TACTATTCA
1745624 TAAGAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (19 bp):
TACTATTCACACAATATGG
Found at i:1747252 original size:22 final size:22
Alignment explanation
Indices: 1747224--1747266 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1747214 ATCGGTTTAG
1747224 CACTAAAGGAT-ACTTAGTGCAA
1 CACTAAAGGATAAC-TAGTGCAA
1747246 CACTAAAGGATAACTAGTGCA
1 CACTAAAGGATAACTAGTGCA
1747267 TATTGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (22 bp):
CACTAAAGGATAACTAGTGCAA
Found at i:1766847 original size:54 final size:54
Alignment explanation
Indices: 1766782--1766941 Score: 239
Period size: 54 Copynumber: 3.0 Consensus size: 54
1766772 TATACTTTCA
* * * *
1766782 ACACTGTGTGTGCAACCCATGGAATTCGTAATGAGTTTTTGAATTACCATTTAG
1 ACACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTAG
* * * *
1766836 GCACTATGTGTGCAATCAATGGAATTCATAATCAGTTTGTGAATTACCATTTTG
1 ACACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTAG
*
1766890 ACACTATGTGTACAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTT
1 ACACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTT
1766942 CAACACTTAG
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (54 bp):
ACACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTAG
Found at i:1767467 original size:26 final size:24
Alignment explanation
Indices: 1767412--1767467 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1767402 ATGTTATAAC
*
1767412 ATTAAGACCATTTTATGTATTAAA
1 ATTAAGAACATTTTATGTATTAAA
1767436 AGTTAATGAACATTTTAT-TATTATTAA
1 A-TTAA-GAACATTTTATGTATTA--AA
1767463 ATTAA
1 ATTAA
1767468 AATGTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.04
25 9 0.33
26 14 0.52
27 3 0.11
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (24 bp):
ATTAAGAACATTTTATGTATTAAA
Found at i:1768479 original size:14 final size:15
Alignment explanation
Indices: 1768440--1768485 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1768430 AAAGCATTCC
*
1768440 ATGAGCTAAGTATATG
1 ATGAGCTAA-TATATA
1768456 ATGATG-TAATAT-TA
1 ATGA-GCTAATATATA
1768470 ATGAGCTAATATATA
1 ATGAGCTAATATATA
1768485 A
1 A
1768486 GCCTTATGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 6 0.23
16 7 0.27
17 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (15 bp):
ATGAGCTAATATATA
Found at i:1809562 original size:21 final size:21
Alignment explanation
Indices: 1809538--1809578 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1809528 GAACTAATAT
*
1809538 GATATAGTGAGGTTCTAATCA
1 GATATAATGAGGTTCTAATCA
* *
1809559 GATATAATGATGTTTTAATC
1 GATATAATGAGGTTCTAATC
1809579 TACCTTAGAA
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:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (21 bp):
GATATAATGAGGTTCTAATCA
Found at i:1818555 original size:20 final size:19
Alignment explanation
Indices: 1818511--1818560 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1818501 GACCAAGAGC
*
1818511 ATGTATCTTCATTAAAATA
1 ATGTATTTTCATTAAAATA
1818530 ATGTATTTTCATTAAAAATCA
1 ATGTATTTTCATT-AAAAT-A
1818551 A-GTATTTTCA
1 ATGTATTTTCA
1818561 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATA
Found at i:1822485 original size:19 final size:19
Alignment explanation
Indices: 1822461--1822510 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1822451 GGCCCAAGAG
* *
1822461 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
*
1822480 CATGTATTTTAATCAAAAT
1 CATGTATTTTCATCAAAAT
1822499 CATGTATTTTCA
1 CATGTATTTTCA
1822511 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:1837111 original size:13 final size:13
Alignment explanation
Indices: 1837089--1837118 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1837079 ACTAAACACC
1837089 TTTC-ACATACCT
1 TTTCAACATACCT
1837101 TTTCAACATACCT
1 TTTCAACATACCT
1837114 TTTCA
1 TTTCA
1837119 TATTTGGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1845559 original size:20 final size:19
Alignment explanation
Indices: 1845534--1845580 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1845524 TTTCTTTTTT
1845534 TTTTCTTTAAGTGCTTACAA
1 TTTTCTTTAAGTGCTT-CAA
*
1845554 TTTTCTTTTGAGTGCTTCAA
1 TTTTC-TTTAAGTGCTTCAA
1845574 -TTTCTTT
1 TTTTCTTT
1845581 GCTGATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 8 0.32
21 10 0.40
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTCTTTAAGTGCTTCAA
Found at i:1856835 original size:51 final size:49
Alignment explanation
Indices: 1856631--1856875 Score: 280
Period size: 49 Copynumber: 5.0 Consensus size: 49
1856621 AAAATGAATA
* *
1856631 AATGAAAGTTAAATGCATACCGGTGCATTTCGGCATAAAAGGTACCAC-
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * * *
1856679 AATTAAAG-TAAATGTATAATGGTGCATTTCGGCAT-AAAGGTGCCACA
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * ** * *
1856726 AATGAAAGTTAATTGTATAATAGTGCATTTCGACATAAAATGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * *
1856775 AATGAAAGTTAAATGCATAACGGTGCATTTCGGCAAACAAAATGTGTCACT
1 AATGAAAGTTAAATGCATAACGGTGCATTTCGGC--ATAAAAGGTGCCACT
* * *
1856826 AATGAAAGTTAAATGCATAACAGTGTATTTTCAGCATAAAAGGTGCCACT
1 AATGAAAGTTAAATGCATAACGGTGCA-TTTCGGCATAAAAGGTGCCACT
1856876 CATGGTATTT
Statistics
Matches: 167, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
46 10 0.06
47 31 0.19
48 31 0.19
49 39 0.23
50 12 0.07
51 38 0.23
52 6 0.04
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (49 bp):
AATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
Found at i:1861430 original size:21 final size:21
Alignment explanation
Indices: 1861370--1861423 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1861360 CATTCTAGGA
**
1861370 ATTT-ATGGCTTCGGTAAAAG
1 ATTTCATGGCTTCGAAAAAAG
1861390 ATTTCATGGCTTCGAAAAAAG
1 ATTTCATGGCTTCGAAAAAAG
1861411 ATTTCATGGCTTC
1 ATTTCATGGCTTC
1861424 AACAAAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (21 bp):
ATTTCATGGCTTCGAAAAAAG
Found at i:1876563 original size:49 final size:49
Alignment explanation
Indices: 1876510--1876696 Score: 225
Period size: 49 Copynumber: 3.8 Consensus size: 49
1876500 TCTAAAATGA
* *
1876510 ATAAATGAAAGTTAAACGAATAACAGTGCATTTCGGCATAAAAGGTGCC
1 ATAAATGAAAGTTAAATGCATAACAGTGCATTTCGGCATAAAAGGTGCC
* * * *
1876559 ATAAATTAAAATTAAATGCATAACGGTGCATATCGGCATAAAAGGTGCC
1 ATAAATGAAAGTTAAATGCATAACAGTGCATTTCGGCATAAAAGGTGCC
* * * *
1876608 ACAAATGAAAGTTAAATGCATAAC-GATTCATTTTGGCATAAAAGATGCC
1 ATAAATGAAAGTTAAATGCATAACAG-TGCATTTCGGCATAAAAGGTGCC
* * *
1876657 ACT-AATGAAATTTAAATGTATAATAGTGCATTTCGGCATA
1 A-TAAATGAAAGTTAAATGCATAACAGTGCATTTCGGCATA
1876697 GATGGTTCCA
Statistics
Matches: 116, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 114 0.98
50 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (49 bp):
ATAAATGAAAGTTAAATGCATAACAGTGCATTTCGGCATAAAAGGTGCC
Found at i:1878203 original size:28 final size:28
Alignment explanation
Indices: 1878144--1878206 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1878134 AAGTTAAGTT
* *
1878144 AAGAAAGAAAGGTAATGAACGGGTAGGA
1 AAGAAAGAAAGATAATGAACGGGTAAGA
**
1878172 AAGAAAGAAAAGATAATGATTGGGTAAG-
1 AAGAAAG-AAAGATAATGAACGGGTAAGA
1878200 AAGAAAG
1 AAGAAAG
1878207 TTAAAGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.54, C:0.02, G:0.32, T:0.13
Consensus pattern (28 bp):
AAGAAAGAAAGATAATGAACGGGTAAGA
Found at i:1880373 original size:26 final size:25
Alignment explanation
Indices: 1880343--1880391 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1880333 ATAATATAAG
*
1880343 CTAAGTATATGAATTATTATAAAGTA
1 CTAAGAATATGAA-TATTATAAAGTA
* *
1880369 CTAAGAATGTGCATATTATAAAG
1 CTAAGAATATGAATATTATAAAG
1880392 ATGTGAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (25 bp):
CTAAGAATATGAATATTATAAAGTA
Found at i:1882793 original size:16 final size:15
Alignment explanation
Indices: 1882764--1882802 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1882754 TGTAGGAGTC
1882764 TTTTTCTTTCTCTTT
1 TTTTTCTTTCTCTTT
*
1882779 TTTTTCTTCTTTCTTT
1 TTTTTCTT-TCTCTTT
*
1882795 TTCTTCTT
1 TTTTTCTT
1882803 GTTATAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTCTCTTT
Found at i:1882795 original size:13 final size:13
Alignment explanation
Indices: 1882762--1882802 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
1882752 GTTGTAGGAG
1882762 TCTTTTTCTTTCTCT
1 TCTTTTTC-TTCT-T
*
1882777 TTTTTTTCTTCTT
1 TCTTTTTCTTCTT
1882790 TCTTTTTCTTCTT
1 TCTTTTTCTTCTT
1882803 GTTATAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 4 0.17
15 7 0.29
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTTCTTCTT
Found at i:1884843 original size:14 final size:14
Alignment explanation
Indices: 1884824--1884850 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1884814 TATGAGTATG
1884824 GTGATGGTGATGGC
1 GTGATGGTGATGGC
1884838 GTGATGGTGATGG
1 GTGATGGTGATGG
1884851 AATATGGAAG
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:0.04, G:0.52, T:0.30
Consensus pattern (14 bp):
GTGATGGTGATGGC
Found at i:1887182 original size:35 final size:35
Alignment explanation
Indices: 1887107--1887222 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
1887097 TACTATCTGT
* *
1887107 TCATCACCATCTTCCATCACAATTTTTACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* *
1887143 TCATCACCATCTTCCATCACCATTGCATGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
* *
1887178 TCATCACCTTCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
1887213 TCATCACCAT
1 TCATCACCAT
1887223 TCCCTTACCA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 50 0.70
36 21 0.30
ACGTcount: A:0.26, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:1891947 original size:21 final size:21
Alignment explanation
Indices: 1891921--1891969 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1891911 TAAAACACTT
1891921 GATGTCTCTTGATCGTTCAGG
1 GATGTCTCTTGATCGTTCAGG
*
1891942 GATGTCTCTTGATTGTTCAGG
1 GATGTCTCTTGATCGTTCAGG
1891963 GATGTCT
1 GATGTCT
1891970 TTTCCTCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (21 bp):
GATGTCTCTTGATCGTTCAGG
Found at i:1893685 original size:23 final size:26
Alignment explanation
Indices: 1893655--1893706 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1893645 GGAATACGAT
1893655 TAATAAAG-GAAG-AA-TAAATGAAA
1 TAATAAAGAGAAGAAATTAAATGAAA
*
1893678 TAATAAAGATAAGAAATTAAATGAAA
1 TAATAAAGAGAAGAAATTAAATGAAA
1893704 TAA
1 TAA
1893707 AATGGAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 3 0.12
25 2 0.08
26 12 0.48
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (26 bp):
TAATAAAGAGAAGAAATTAAATGAAA
Found at i:1902057 original size:20 final size:20
Alignment explanation
Indices: 1902011--1902060 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1902001 TTCATTCATT
*
1902011 CATTAACTCATGTCATGTTA
1 CATTAGCTCATGTCATGTTA
* *
1902031 -TTCTAGCTCATGTTATGTTA
1 CAT-TAGCTCATGTCATGTTA
1902051 CATTAGCTCA
1 CATTAGCTCA
1902061 CTAGCTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (20 bp):
CATTAGCTCATGTCATGTTA
Found at i:1907055 original size:21 final size:21
Alignment explanation
Indices: 1907010--1907057 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1907000 AAAACACCCG
* * *
1907010 ATGTCTCTTGATCATTCAGGG
1 ATGTCTCTTGATCATCCAAGA
1907031 ATGTCTCTTGATCATCCAAGA
1 ATGTCTCTTGATCATCCAAGA
1907052 ATGTCT
1 ATGTCT
1907058 TTTTCTCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (21 bp):
ATGTCTCTTGATCATCCAAGA
Found at i:1909409 original size:15 final size:15
Alignment explanation
Indices: 1909389--1909418 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1909379 CTTGGATGAA
1909389 AAGGCATCTTCATGG
1 AAGGCATCTTCATGG
1909404 AAGGCATCTTCATGG
1 AAGGCATCTTCATGG
1909419 GCAGCATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
AAGGCATCTTCATGG
Found at i:1909425 original size:15 final size:16
Alignment explanation
Indices: 1909389--1909433 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1909379 CTTGGATGAA
1909389 AAGGCATCTTCAT-GG
1 AAGGCATCTTCATGGG
1909404 AAGGCATCTTCATGGG
1 AAGGCATCTTCATGGG
*
1909420 CA-GCATCATTCATG
1 AAGGCATC-TTCATG
1909434 AAAGGTCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (16 bp):
AAGGCATCTTCATGGG
Found at i:1913083 original size:29 final size:29
Alignment explanation
Indices: 1913041--1913102 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
1913031 TTGGCAACTC
1913041 AGCTTCAAATAGTCCAACTAGCTGAGATT
1 AGCTTCAAATAGTCCAACTAGCTGAGATT
1913070 AGCTTCAAATAGTCCAACTAGCTGAGATT
1 AGCTTCAAATAGTCCAACTAGCTGAGATT
1913099 AGCT
1 AGCT
1913103 AGCCTTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTTCAAATAGTCCAACTAGCTGAGATT
Found at i:1917447 original size:5 final size:5
Alignment explanation
Indices: 1917437--1917462 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1917427 TCAACTTTTA
1917437 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
1917463 CTTTTGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1917508 original size:23 final size:23
Alignment explanation
Indices: 1917456--1917505 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1917446 TTTTCTTTTC
* *
1917456 TTTTCTTCTTTTGAGTGCTGGAA
1 TTTTCTTCTTTTGAGTACTGCAA
*
1917479 TTTTCTTCTTTTGGAGTACTTCAA
1 TTTTCTTCTTTT-GAGTACTGCAA
1917503 TTT
1 TTT
1917506 CTTTTCTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (23 bp):
TTTTCTTCTTTTGAGTACTGCAA
Found at i:1918313 original size:161 final size:161
Alignment explanation
Indices: 1918048--1918341 Score: 455
Period size: 161 Copynumber: 1.8 Consensus size: 161
1918038 AGATGGAAGA
* * **
1918048 TTGTATCTCCATAAGACATATTGACCAAATAAGATCAGGATCTCATTCAAAAAGTTATCGTAAGT
1 TTGTATCTCCAGAAGACATATTGACCAAATAAGATCAGGATCTCATTCAAAAAGTCATCACAAGT
* *
1918113 CTGATGTTATTCTGGTCTTCTATTCCAAGGCTTGGACGAGTGGATCATTTGGAAGAATTATTAGT
66 CTGATGTTATTCTGGTCTTCTATTCCAAGGATTGGACGAGTGGATCATTTGGAAGAATTATTACT
1918178 TCTAACTGTTGGAAAGATAAGAGACAGACAG
131 TCTAACTGTTGGAAAGATAAGAGACAGACAG
* * *
1918209 TTGTATCTCTAGAAGACATGTTGACCAAATAAGATCAGGATC-CTATTCACAAAGTCATCACAAG
1 TTGTATCTCCAGAAGACATATTGACCAAATAAGATCAGGATCTC-ATTCAAAAAGTCATCACAAG
* * * *
1918273 TCTGATGTTGTTCTGGTCTTCTTTTTCAAGGATTGGACGAGTGGATCATTTGGAAGAGTTATTAC
65 TCTGATGTTATTCTGGTCTTCTATTCCAAGGATTGGACGAGTGGATCATTTGGAAGAATTATTAC
1918338 TTCT
130 TTCT
1918342 TCATTTGATG
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
160 1 0.01
161 118 0.99
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (161 bp):
TTGTATCTCCAGAAGACATATTGACCAAATAAGATCAGGATCTCATTCAAAAAGTCATCACAAGT
CTGATGTTATTCTGGTCTTCTATTCCAAGGATTGGACGAGTGGATCATTTGGAAGAATTATTACT
TCTAACTGTTGGAAAGATAAGAGACAGACAG
Found at i:1920480 original size:295 final size:294
Alignment explanation
Indices: 1919951--1920539 Score: 1144
Period size: 295 Copynumber: 2.0 Consensus size: 294
1919941 CTCAAGAGAC
1919951 ATACGATAGAGCTCCATGCCTATTCGACCACACACATGTGAGCCTTTGGCACCAAACATGAGGAG
1 ATACGATAGAGCTCCATGCCTATTCGACCACACACATGTGAGCCTTTGGCACCAAACATGAGGAG
1920016 ACACATCACCATTCGGCCAAGGGGAGAAAAATGGCGCCAATGAATAAGCATTGCCCATTCGGCCA
66 ACACATCACCATTCGGCCAAGGGGAGAAAAATGGCGCCAATGAATAAGCATTGCCCATTCGGCCA
*
1920081 AGGGAGATGTCTTCCCATCCTTAGCCAAATCATCAAGCCCCTTAATGAAGGGTTAGCCGAACCAT
131 AGGGAGATGTCTTCCCATCCTTAGCCAAATCATCAAGCCCCTTAATGAAGGGTTAGCCAAACCAT
1920146 CACAAGCACAAAGGACTCAATCATTCATTTTAAGCATTATGTATTTTCATCAAAATTCATGTATC
196 CACAAGCACAAAGGACTCAATCATTCATTTTAAGCATTATGTATTTTCATCAAAATTCATGTATC
1920211 AATCGAATAGCTATGTAACCATTCGACCAAGCCA
261 AATCGAATAGCTATGTAACCATTCGACCAAGCCA
1920245 ATACGATAGAGCTCCATGCCTATTCGACCACACACATGTGAGCCTTTGGCACCAAACATGAGGAG
1 ATACGATAGAGCTCCATGCCTATTCGACCACACACATGTGAGCCTTTGGCACCAAACATGAGGAG
1920310 ACACATCACCATTCGGCCAAGGGGAGAAAAATGGCGCCAAGATGAATAAGCA-TGCCCATTCGGC
66 ACACATCACCATTCGGCCAAGGGGAGAAAAATGGCGCC-A-ATGAATAAGCATTGCCCATTCGGC
1920374 CAAGGGAGATGTCTTCCCATCCTTAGCCAAATCATCAAGCCCCTTAATGAAGGGTTAGCCAAACC
129 CAAGGGAGATGTCTTCCCATCCTTAGCCAAATCATCAAGCCCCTTAATGAAGGGTTAGCCAAACC
1920439 ATCACAAGCACAAAGGACTCAATCATTCATTTTAAGCATTATGTATTTTCATCAAAATTCATGTA
194 ATCACAAGCACAAAGGACTCAATCATTCATTTTAAGCATTATGTATTTTCATCAAAATTCATGTA
1920504 TCAATCGAATAGCTATGTAACCATTCGACCAAGCCA
259 TCAATCGAATAGCTATGTAACCATTCGACCAAGCCA
1920540 TCTCATTTCC
Statistics
Matches: 292, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
294 103 0.35
295 178 0.61
296 11 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (294 bp):
ATACGATAGAGCTCCATGCCTATTCGACCACACACATGTGAGCCTTTGGCACCAAACATGAGGAG
ACACATCACCATTCGGCCAAGGGGAGAAAAATGGCGCCAATGAATAAGCATTGCCCATTCGGCCA
AGGGAGATGTCTTCCCATCCTTAGCCAAATCATCAAGCCCCTTAATGAAGGGTTAGCCAAACCAT
CACAAGCACAAAGGACTCAATCATTCATTTTAAGCATTATGTATTTTCATCAAAATTCATGTATC
AATCGAATAGCTATGTAACCATTCGACCAAGCCA
Found at i:1920925 original size:21 final size:22
Alignment explanation
Indices: 1920890--1920937 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
1920880 TCTCTATTCC
1920890 ATCTTTATTTTATTTCATTTATT
1 ATCTTTA-TTTATTTCATTTATT
1920913 ATCTTTA-TTATTTCATTTATT
1 ATCTTTATTTATTTCATTTATT
1920934 -TCTT
1 ATCTT
1920938 CCTTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.16
21 14 0.56
23 7 0.28
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (22 bp):
ATCTTTATTTATTTCATTTATT
Found at i:1921236 original size:16 final size:17
Alignment explanation
Indices: 1921204--1921237 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1921194 TGAAGACAAC
*
1921204 AATCAGAAAAAGAAGAA
1 AATCAAAAAAAGAAGAA
1921221 AATCAAAAAAAG-AGAA
1 AATCAAAAAAAGAAGAA
1921237 A
1 A
1921238 GCAAGCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.06
Consensus pattern (17 bp):
AATCAAAAAAAGAAGAA
Found at i:1922671 original size:21 final size:21
Alignment explanation
Indices: 1922647--1922694 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1922637 ATCGAGGAAA
*
1922647 AGACATCCCTGAATGATCAAG
1 AGACATCCCTGAACGATCAAG
1922668 AGACATCCCTGAACGATCAAG
1 AGACATCCCTGAACGATCAAG
1922689 AGACAT
1 AGACAT
1922695 TAGGTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (21 bp):
AGACATCCCTGAACGATCAAG
Found at i:1925500 original size:21 final size:23
Alignment explanation
Indices: 1925463--1925510 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
1925453 TCTCTATTCC
1925463 ATCTTTATTTCATTTCATTTATT
1 ATCTTTATTTCATTTCATTTATT
1925486 ATCTTTA-TT-ATTTCATTTATT
1 ATCTTTATTTCATTTCATTTATT
1925507 -TCTT
1 ATCTT
1925511 CCTTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 2 0.08
23 7 0.28
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (23 bp):
ATCTTTATTTCATTTCATTTATT
Found at i:1928634 original size:91 final size:91
Alignment explanation
Indices: 1928479--1929322 Score: 1239
Period size: 91 Copynumber: 9.3 Consensus size: 91
1928469 TTCAAACAAA
1928479 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * ** *
1928544 CTCTCCACTGGTAATATTGAGTCATG
66 CTCTCCACTGGAAATCTTGAACCAAG
* * * *
1928570 GTTGAACAAGTTCTTCTCATTATGAA-TGTCTTCTCCCTCATTTGACGAGTTATTCTCATTATGA
1 GTTGAACAAGTTCTTCTCATTATGAACT-TCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGA
* * *
1928634 ACTCTCCACTGGTAA-CGTTGAATCAAT
65 ACTCTCCACTGGAAATC-TTGAACCAAG
* *
1928661 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCT-GTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
*
1928725 CTCTCCACTAGAAATCTTGAACCAAG
66 CTCTCCACTGGAAATCTTGAACCAAG
* *
1928751 GTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCGTTGGATGAGTTCTTCTCATTACGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
*
1928816 CTCTCTACTGGAAATCTTGAACCAAG
66 CTCTCCACTGGAAATCTTGAACCAAG
* * *
1928842 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCACTTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
1928907 CTCTCCACTGGAAATTTTGAGCCAAG
66 CTCTCCACTGGAAATCTTGAACCAAG
* * *
1928933 GTTGAACAAGTTCTTCTGATTATGAACTTATTCTCCCT-GTTGGATGAGTTCTTTTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1928997 CTCTCCACTGGAAATCTTGAACCAAG
66 CTCTCCACTGGAAATCTTGAACCAAG
* * * *
1929023 GTTGAACAAGTTATTTTCATTATGAACTCCTTCTCCCTCCTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
*
1929088 CTCTCCACTGGAAATCTTGAACCAAT
66 CTCTCCACTGGAAATCTTGAACCAAG
* * *
1929114 GTTGAACAAGTTCTTATCATTATGTAC-TCTTCTACCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
*
1929178 CTCTCCACTAGAAATCTTGAACCAAG
66 CTCTCCACTGGAAATCTTGAACCAAG
* * * *
1929204 GTTGAACAAGTTATTCTCAATATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTAATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * *
1929269 CTCTACACTGGAAATGTTCAACCAAT
66 CTCTCCACTGGAAATCTTGAACCAAG
*
1929295 GTTGAACAAGTTCTTCTCGTTATGAACT
1 GTTGAACAAGTTCTTCTCATTATGAACT
1929323 CTCCACTGGA
Statistics
Matches: 674, Mismatches: 72, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
90 239 0.35
91 434 0.64
92 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATCTTGAACCAAG
Found at i:1928809 original size:181 final size:182
Alignment explanation
Indices: 1928479--1929322 Score: 1239
Period size: 181 Copynumber: 4.7 Consensus size: 182
1928469 TTCAAACAAA
1928479 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * ** *
1928544 CTCTCCACTGGTAATATTGAGTCATGGTTGAACAAGTTCTTCTCATTATGAA-TGTCTTCTCCCT
66 CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACT-TCTTCTCCCT
* * * * * * *
1928608 CATTTGACGAGTTATTCTCATTATGAACTCTCCACTGGTAA-CGTTGAATCAAT
130 CGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATC-TTGAACCAAG
* *
1928661 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCCCT-GTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
1928725 CTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTC
66 CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
* *
1928790 GTTGGATGAGTTCTTCTCATTACGAACTCTCTACTGGAAATCTTGAACCAAG
131 GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAG
* * *
1928842 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCACTTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * *
1928907 CTCTCCACTGGAAATTTTGAGCCAAGGTTGAACAAGTTCTTCTGATTATGAACTTATTCTCCCT-
66 CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
*
1928971 GTTGGATGAGTTCTTTTCATTATGAACTCTCCACTGGAAATCTTGAACCAAG
131 GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAG
* * * *
1929023 GTTGAACAAGTTATTTTCATTATGAACTCCTTCTCCCTCCTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * *
1929088 CTCTCCACTGGAAATCTTGAACCAATGTTGAACAAGTTCTTATCATTATGTAC-TCTTCTACCTC
66 CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
*
1929152 GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAG
131 GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAG
* * * *
1929204 GTTGAACAAGTTATTCTCAATATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTAATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * * * *
1929269 CTCTACACTGGAAATGTTCAACCAATGTTGAACAAGTTCTTCTCGTTATGAACT
66 CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACT
1929323 CTCCACTGGA
Statistics
Matches: 597, Mismatches: 60, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
180 8 0.01
181 468 0.78
182 121 0.20
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (182 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAG
Found at i:1928969 original size:272 final size:271
Alignment explanation
Indices: 1928479--1929322 Score: 1246
Period size: 272 Copynumber: 3.1 Consensus size: 271
1928469 TTCAAACAAA
1928479 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * ** *
1928544 CTCTCCACTGGTAATATTGAGTCATGGTTGAACAAGTTCTTCTCATTATGAA-TGTCTTCTCCCT
66 CTCTCCACTGGAAATCTTGAACCA-AGTTGAACAAGTTCTTCTCATTATGAACT-TCTTCTCCCT
* * * * *
1928608 CATTT-GACGAGTTATTCTCATTATGAACTCTCCACTGGTAA-CGTTGAATCAATGTTGAACAAG
129 C-TTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATC-TTGAACCAAGGTTGAACAAG
* *
1928671 TTCTTCTCATTATAAACTTCTTCTCCCTGTTGGATAAGTTCTTCTCATTATGAACTCTCCACTAG
192 TTCTTCTCATTATAAACTTCTTCTCCCTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGG
1928736 AAATCTTGAACCAAG
257 AAATCTTGAACCAAG
* *
1928751 GTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCGTTGGATGAGTTCTTCTCATTACGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
1928816 CTCTCTACTGGAAATCTTGAACCAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCAC
66 CTCTCCACTGGAAATCTTGAACCAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
* *
1928881 TTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATTTTGAGCCAAGGTTGAACAAGTTC
130 TTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTC
* * * *
1928946 TTCTGATTATGAACTTATTCTCCCTGTTGGATGAGTTCTTTTCATTATGAACTCTCCACTGGAAA
195 TTCTCATTATAAACTTCTTCTCCCTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAA
1929011 TCTTGAACCAAG
260 TCTTGAACCAAG
* * * *
1929023 GTTGAACAAGTTATTTTCATTATGAACTCCTTCTCCCTCCTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* * *
1929088 CTCTCCACTGGAAATCTTGAACCAATGTTGAACAAGTTCTTATCATTATGTAC-TCTTCTACCTC
66 CTCTCCACTGGAAATCTTGAACCAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC
* * *
1929152 GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTA
130 TTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTC
* * *
1929217 TTCTCAATATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTAATTATGAACTCTACACTGGAA
195 TTCTCATTATAAACTTCTTCTCCCT-GTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
* * *
1929282 ATGTTCAACCAAT
259 ATCTTGAACCAAG
*
1929295 GTTGAACAAGTTCTTCTCGTTATGAACT
1 GTTGAACAAGTTCTTCTCATTATGAACT
1929323 CTCCACTGGA
Statistics
Matches: 515, Mismatches: 51, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
271 94 0.18
272 419 0.81
273 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (271 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATCTTGAACCAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCT
TTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCT
TCTCATTATAAACTTCTTCTCCCTGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAAT
CTTGAACCAAG
Found at i:1929330 original size:52 final size:52
Alignment explanation
Indices: 1929251--1929374 Score: 194
Period size: 52 Copynumber: 2.4 Consensus size: 52
1929241 TCGTTGGATG
* *
1929251 AGTTCTTCTAATTATGAACTCTACACTGGAAATGTTCAACCAATGTTGAACA
1 AGTTCTTCTAATTATGAACTCTACACTGGAAATCTTCAACCAAGGTTGAACA
** * *
1929303 AGTTCTTCTCGTTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACA
1 AGTTCTTCTAATTATGAACTCTACACTGGAAATCTTCAACCAAGGTTGAACA
1929355 AGTTCTTCTAATTATGAACT
1 AGTTCTTCTAATTATGAACT
1929375 TATTTTCCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTCTTCTAATTATGAACTCTACACTGGAAATCTTCAACCAAGGTTGAACA
Found at i:1929421 original size:143 final size:143
Alignment explanation
Indices: 1929160--1929464 Score: 468
Period size: 143 Copynumber: 2.1 Consensus size: 143
1929150 TCGTTGGATG
1929160 AGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTATTCTCAAT
1 AGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTATTCTCAAT
* * *
1929225 ATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTAATTATGAACTCTACACTGGAAATGTTCAA
66 ATAAACTTATTCTCCCTCGTTGGATGAGTTATTCTAATTATGAACTCTACACTGGAAATCTTCAA
1929290 CCAATGTTGAACA
131 CCAATGTTGAACA
* * *
1929303 AGTTCTTCTCGTTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCT-AAT
1 AGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTATTCTCAA-
* * * * * * *
1929367 TATGAACTTATTTTCCCTCGTTGGATTAGTTATTCTCATTATGATCTCTCCACTGGAAATCTTGA
65 TATAAACTTATTCTCCCTCGTTGGATGAGTTATTCTAATTATGAACTCTACACTGGAAATCTTCA
*
1929432 ACCCATGTTGAACA
130 ACCAATGTTGAACA
1929446 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
1929465 ATCTTCTCCC
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
142 2 0.01
143 144 0.99
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (143 bp):
AGTTCTTCTCATTATGAACTCTCCACTAGAAATCTTGAACCAAGGTTGAACAAGTTATTCTCAAT
ATAAACTTATTCTCCCTCGTTGGATGAGTTATTCTAATTATGAACTCTACACTGGAAATCTTCAA
CCAATGTTGAACA
Found at i:1929463 original size:91 final size:92
Alignment explanation
Indices: 1929303--1929522 Score: 336
Period size: 91 Copynumber: 2.4 Consensus size: 92
1929293 ATGTTGAACA
* *
1929303 AGTTCTTCTCGTTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTAATT
1 AGTTATTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTAATT
* *
1929368 ATGAACTTATTTTCCCTCGTTGGAT-T
66 ATGAACATATTCTCCCTCGTTGGATGT
* * * *
1929394 AGTTATTCTCATTATGATCTCTCCACTGGAAATCTTGAACCCATGTTGAACAAGTTCTTCTCATT
1 AGTTATTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTAATT
*
1929459 ATGAACATCTTCTCCCTCGTTGGATGT
66 ATGAACATATTCTCCCTCGTTGGATGT
*
1929486 -GTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA
1 AGTTATTCTCATTATGAACTCTCCACTGGAAATCTTGA
1929523 TTGTTTATCT
Statistics
Matches: 117, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 116 0.99
92 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (92 bp):
AGTTATTCTCATTATGAACTCTCCACTGGAAATCTTGAACCAAGGTTGAACAAGTTCTTCTAATT
ATGAACATATTCTCCCTCGTTGGATGT
Found at i:1929987 original size:66 final size:65
Alignment explanation
Indices: 1929916--1930212 Score: 280
Period size: 66 Copynumber: 4.6 Consensus size: 65
1929906 AAAGTTTTTG
* * * *
1929916 TGTTTCAAGAGAAACTTTATCCAGAGAGACAAAATTCAGTTCAAGGGACACGATCTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATT-
1929981 A
65 A
* * **
1929982 TGTTTCAAGGGAAACTATCTCAAGAGAGGA-AAAATTCCTTTCAAGGGAAACGATCTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGA-GACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATT
1930046 -
65 A
* * * * ** * * *
1930046 TTTTTCAAG-GGAACTGTCTCGAGAGAGACAAAATTCATTTCAATTGAAATGATCTCAAAGCTCA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGAT-T
1930110 A
65 A
* * * *
1930111 TGTTTCAATGA-AAACTGTCTCAAGAGAGACAAAACTC-GTTTCAAGGGAAACAACCTCAAAGGT
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTCAG-TTCAAGGGAAACGATCTCAAA-GA
*
1930174 TTT
63 TTA
* * *
1930177 TATTTCAAGATAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1930213 TGTTTCAAGA
Statistics
Matches: 189, Mismatches: 33, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
62 2 0.01
63 42 0.22
64 8 0.04
65 9 0.05
66 124 0.66
67 4 0.02
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATTA
Found at i:1930080 original size:129 final size:132
Alignment explanation
Indices: 1929918--1930212 Score: 346
Period size: 129 Copynumber: 2.3 Consensus size: 132
1929908 AGTTTTTGTG
* * * * **
1929918 TTTCAAGAGAAACTTTATCCAGAGAGACAAAATTCAGTTCAAGGGACACGATCTCAAAGATTGAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATCAAT
* * * *
1929983 GTTTCAAGGGAAACTATCTCAAGAGAGGA-AAAATTCCTTTCAAGGGAAACGATCTCAAA-GATT
66 GTTTCAAGGAAAACTATCTCAAGAGA-GACAAAACTCCTTTCAAGGGAAACAACCTCAAAGGATT
1930046 TT-
130 TTA
* * * ** * *
1930048 TTTCAAG-GGAACTGTCTCGAGAGAGACAAAATTCATTTCAATTGAAATGATCTCAAAGCTCAAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATCAAT
* * * *
1930112 GTTTCAATGAAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACAACCTCAAAGGTTTT
66 GTTTCAAGGAAAACTATCTCAAGAGAGACAAAACTCCTTTCAAGGGAAACAACCTCAAAGGATTT
1930177 TA
131 TA
* *
1930179 TTTCAAGATAAACTGTCTCAAGGGAGACAAAATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1930213 TGTTTCAAGA
Statistics
Matches: 137, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
128 2 0.01
129 94 0.69
130 12 0.09
131 7 0.05
132 22 0.16
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (132 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCAGTTCAAGGGAAACGATCTCAAAGATCAAT
GTTTCAAGGAAAACTATCTCAAGAGAGACAAAACTCCTTTCAAGGGAAACAACCTCAAAGGATTT
TA
Found at i:1930163 original size:21 final size:20
Alignment explanation
Indices: 1930121--1930163 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1930111 TGTTTCAATG
*
1930121 AAAACTGTCTCAAGAGAGAC
1 AAAACTGTCTCAAGAGAAAC
* *
1930141 AAAACTCGTTTCAAGGGAAAC
1 AAAACT-GTCTCAAGAGAAAC
1930162 AA
1 AA
1930164 CCTCAAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAACTGTCTCAAGAGAAAC
Found at i:1930218 original size:66 final size:63
Alignment explanation
Indices: 1929984--1930285 Score: 184
Period size: 66 Copynumber: 4.7 Consensus size: 63
1929974 AAGATTGATG
* * ** * *
1929984 TTTCAAGGGAAACTATCTCAAGAGAGGA-AAAATTCCTTTCAAGGGAAACGAT-CTCAAAGATTT
1 TTTCAA-GAAAACTGTCTCAAGAGA-GACAAAATTTGTTTCAAGAGAAAC-ATACTC-AAGTTTT
1930047 T-
62 TA
** * ** ** * ***
1930048 TTTCAAGGGAACTGTCTCGAGAGAGACAAAATTCATTTCAATTGAAATGAT-CTCAAAGCTCAAT
1 TTTCAAGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA-CATACTC-AAG-TTTTT
*
1930112 G
63 A
* * *
1930113 TTTCAATGAAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGGAAACA-ACCTCAAAGGTTTT
1 TTTCAA-GAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATA-CTC-AA-GTTTT
1930177 TA
62 TA
* * * * *
1930179 TTTCAAGATAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAATATATTCAATTTTTTT
1 TTTCAAGA-AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATACTCAAGTTTTTA
* *
1930243 TTTCAAAAGAAACTGTCTCAAGCA-AGATAAAATTTGTTTCAAG
1 TTTCAAGA-AAACTGTCTCAAG-AGAGACAAAATTTGTTTCAAG
1930286 TAAAACTGTC
Statistics
Matches: 192, Mismatches: 35, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
62 2 0.01
63 41 0.21
64 50 0.26
65 11 0.06
66 86 0.45
67 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (63 bp):
TTTCAAGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATACTCAAGTTTTTA
Found at i:1930283 original size:36 final size:35
Alignment explanation
Indices: 1930243--1930320 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
1930233 CAATTTTTTT
1930243 TTTCAA-AAGAAACTGTCTCAAGCAAGATA-AAATTTG
1 TTTCAAGAA-AAACTGTCTC-AG-AAGATACAAATTTG
* * *
1930279 TTTCAAGTAAAACTGTCTCAGTAGATACAACTTTG
1 TTTCAAGAAAAACTGTCTCAGAAGATACAAATTTG
1930314 TTTCAAG
1 TTTCAAG
1930321 GGAAACAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 5 0.14
35 15 0.41
36 16 0.43
37 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (35 bp):
TTTCAAGAAAAACTGTCTCAGAAGATACAAATTTG
Found at i:1930320 original size:35 final size:36
Alignment explanation
Indices: 1930252--1930320 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
1930242 TTTTCAAAAG
1930252 AAACTGTCTCAAGCAAGATAAAATTTGTTTCAAGTA
1 AAACTGTCTCAAGCAAGATAAAATTTGTTTCAAGTA
* *
1930288 AAACTGTCTC-AG-TAGATACAACTTTGTTTCAAG
1 AAACTGTCTCAAGCAAGATA-AAATTTGTTTCAAG
1930321 GGAAACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 5 0.17
35 15 0.50
36 10 0.33
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (36 bp):
AAACTGTCTCAAGCAAGATAAAATTTGTTTCAAGTA
Found at i:1930879 original size:42 final size:41
Alignment explanation
Indices: 1930766--1930879 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
1930756 TACTGAAGGT
* * * *
1930766 CTTATGGATGGCCCAAAGGACTTATTATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
* * * *
1930807 CTTATAGATGGCTCGAAGGATTTAAGCATCATGCTCGAAAGG
1 CTTATAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGA
1930849 CTTACT-GATGGCCCGAAGGACTTACTCATCA
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCA
1930880 AGAAACCCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGA
Found at i:1931017 original size:43 final size:43
Alignment explanation
Indices: 1930916--1931086 Score: 218
Period size: 43 Copynumber: 4.0 Consensus size: 43
1930906 TTCTTAGTTG
* * * * *
1930916 TCATCAAGGAAGCCATACAAATCACGTTGGTCCCTCTAG-TTG
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
*
1930958 TCATCAAGAAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
* *
1931001 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGATTC
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
* ** * *
1931044 TTATCAAGGAAAACCGACATATCACGTTGGTCCCTCGAGCTTA
1 TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
1931087 GTTTCTTATA
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 34 0.30
43 78 0.70
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (43 bp):
TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTA
Found at i:1932495 original size:15 final size:16
Alignment explanation
Indices: 1932472--1932505 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1932462 TCAGGCTGGC
*
1932472 TTCTTGCGTTC-TTGA
1 TTCTGGCGTTCATTGA
1932487 TTCTGGCGTTCATTGA
1 TTCTGGCGTTCATTGA
1932503 TTC
1 TTC
1932506 GATGAAGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (16 bp):
TTCTGGCGTTCATTGA
Found at i:1934868 original size:19 final size:19
Alignment explanation
Indices: 1934834--1934891 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
1934824 TGGATCTATC
1934834 TATTTTCTTCTTTCTTTTTTT
1 TATTTT-TT-TTTCTTTTTTT
1934855 TATTTTTTTTTC-TTTTTT
1 TATTTTTTTTTCTTTTTTT
*
1934873 TATATATTTTTTCTTTTTT
1 TAT-TTTTTTTTCTTTTTT
1934892 CTCTTTGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.26
19 12 0.35
20 7 0.21
21 6 0.18
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (19 bp):
TATTTTTTTTTCTTTTTTT
Found at i:1934873 original size:22 final size:23
Alignment explanation
Indices: 1934836--1934893 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
1934826 GATCTATCTA
* *
1934836 TTTTCTTCTTTCTTTTTTTTATT
1 TTTTCTTCTTTCTTTTATATATT
*
1934859 TTTTTTTCTTT-TTTTATATATT
1 TTTTCTTCTTTCTTTTATATATT
*
1934881 TTTTCTTTTTTCT
1 TTTTCTTCTTTCT
1934894 CTTTGGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCTTCTTTCTTTTATATATT
Found at i:1951099 original size:5 final size:5
Alignment explanation
Indices: 1951089--1951150 Score: 55
Period size: 5 Copynumber: 13.4 Consensus size: 5
1951079 TTGGAGTGAA
*
1951089 AAAAG AAAAG AAAAG -ATA- AAAAG AAAAG AAAA- AAAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG
*
1951136 --AAG AAAAA AAAAG AA
1 AAAAG AAAAG AAAAG AA
1951151 GAAATTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.06
4 10 0.21
5 32 0.68
6 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:1951111 original size:18 final size:17
Alignment explanation
Indices: 1951087--1951150 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 17
1951077 ACTTGGAGTG
1951087 AAAAAAGAAAAGAAAAGA
1 AAAAAAGAAAAGAAAA-A
*
1951105 TAAAAAGAAAAGAAAAAA
1 AAAAAAGAAAAG-AAAAA
1951123 AAAAGAAGAAAAGAAGAAA
1 AAAA-AAGAAAAGAA-AAA
1951142 AAAAAAGAA
1 AAAAAAGAA
1951151 GAAATTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 22 0.54
19 19 0.46
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAA
Found at i:1951112 original size:13 final size:12
Alignment explanation
Indices: 1951094--1951150 Score: 71
Period size: 13 Copynumber: 4.6 Consensus size: 12
1951084 GTGAAAAAAG
1951094 AAAAGAAAAGATA
1 AAAAGAAAAGA-A
1951107 AAAAGAAAAGAA
1 AAAAGAAAAGAA
1951119 AAAA-AAAAGAA
1 AAAAGAAAAGAA
*
1951130 GAAAAGAAGAAAAA
1 -AAAAGAA-AAGAA
1951144 AAAAGAA
1 AAAAGAA
1951151 GAAATTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 7 0.17
12 9 0.22
13 20 0.50
14 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:1951132 original size:32 final size:31
Alignment explanation
Indices: 1951087--1951150 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
1951077 ACTTGGAGTG
* *
1951087 AAAAAAGAAAAGAAAAGATA-AAAAGAAAAGA
1 AAAAAAAAAAAGAAAAGA-AGAAAAAAAAAGA
1951118 AAAAAAAAAGAAGAAAAGAAGAAAAAAAAAGA
1 AAAAAAAAA-AAGAAAAGAAGAAAAAAAAAGA
1951150 A
1 A
1951151 GAAATTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (31 bp):
AAAAAAAAAAAGAAAAGAAGAAAAAAAAAGA
Found at i:1951152 original size:24 final size:24
Alignment explanation
Indices: 1951089--1951154 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 24
1951079 TTGGAGTGAA
*
1951089 AAAAG-AAAAGAAAAGATA-AAAAG
1 AAAAGAAAAAAAAAAGA-AGAAAAG
1951112 AAAAGAAAAAAAAAAGAAGAAAAG
1 AAAAGAAAAAAAAAAGAAGAAAAG
1951136 --AAG-AAAAAAAAAGAAGAAA
1 AAAAGAAAAAAAAAAGAAGAAA
1951155 TTCAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
21 16 0.40
22 3 0.08
23 6 0.15
24 15 0.38
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAAAAAAAGAAGAAAAG
Found at i:1951154 original size:13 final size:12
Alignment explanation
Indices: 1951086--1951150 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
1951076 AACTTGGAGT
*
1951086 GAAAAAAGAAAA
1 GAAAAAAAAAAA
*
1951098 GAAAAGATAAAAA
1 GAAAA-AAAAAAA
1951111 GAAAAGAAAAAAA
1 GAAAA-AAAAAAA
* *
1951124 -AAAGAAGAAAA
1 GAAAAAAAAAAA
1951135 GAAGAAAAAAAAA
1 GAA-AAAAAAAAA
1951148 GAA
1 GAA
1951151 GAAATTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
11 6 0.14
12 10 0.23
13 27 0.63
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:1951163 original size:21 final size:20
Alignment explanation
Indices: 1951117--1951164 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1951107 AAAAGAAAAG
*
1951117 AAAAAAAAAAGAAGAAAAGA
1 AAAAAAAAAAGAAGAAAACA
*
1951137 AGAAAAAAAAAGAAGAAATTCA
1 A-AAAAAAAAAGAAGAAA-ACA
1951159 AAAAAA
1 AAAAAA
1951165 GAGAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAGAAGAAAACA
Found at i:1952582 original size:21 final size:21
Alignment explanation
Indices: 1952556--1952604 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1952546 ATCGAGGAAA
*
1952556 AGACATCC-CTGAACGATCAAT
1 AGACATCCAC-GAACGATCAAG
1952577 AGACATCCACGAACGATCAAG
1 AGACATCCACGAACGATCAAG
1952598 AGACATC
1 AGACATC
1952605 ATGTATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.41, C:0.29, G:0.16, T:0.14
Consensus pattern (21 bp):
AGACATCCACGAACGATCAAG
Found at i:1956740 original size:14 final size:14
Alignment explanation
Indices: 1956721--1956758 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1956711 TGTTTTTCAA
1956721 CTTTTCTTGTTT-TT
1 CTTTTCTT-TTTCTT
1956735 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
*
1956749 TTTTTCTTTT
1 CTTTTCTTTT
1956759 CTTATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:1956752 original size:19 final size:20
Alignment explanation
Indices: 1956722--1956761 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1956712 GTTTTTCAAC
1956722 TTTTCTTGTTTTTCTTTTCT
1 TTTTCTTGTTTTTCTTTTCT
1956742 TTTTCTT-TTTTTCTTTTCT
1 TTTTCTTGTTTTTCTTTTCT
1956761 T
1 T
1956762 ATTTTGAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTGTTTTTCTTTTCT
Found at i:1959095 original size:20 final size:20
Alignment explanation
Indices: 1959067--1959105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1959057 TATTTCATTT
*
1959067 ATTTTAGTTCATTTCTTTGG
1 ATTTAAGTTCATTTCTTTGG
**
1959087 ATTTAAGTTGTTTTCTTTG
1 ATTTAAGTTCATTTCTTTG
1959106 CACATACATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTTAAGTTCATTTCTTTGG
Found at i:1961809 original size:54 final size:54
Alignment explanation
Indices: 1961739--1961860 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
1961729 TCGTAAAATA
1961739 TTTT-ACAACACATTCATTCTTTACTGTCGCTTCTGCCCAGATGTTCGTAAAGC
1 TTTTGACAACACATTCATTCTTTACTGTCGCTTCTGCCCAGATGTTCGTAAAGC
* * * *
1961792 TTTTGACAACATATTCATTCTTTCCTGTGGCTTCTGCCCAGATGTTTGTAAAGC
1 TTTTGACAACACATTCATTCTTTACTGTCGCTTCTGCCCAGATGTTCGTAAAGC
*
1961846 TTTTGA-AAAACATTC
1 TTTTGACAACACATTC
1961861 GTCATTTCCT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
53 11 0.18
54 51 0.82
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (54 bp):
TTTTGACAACACATTCATTCTTTACTGTCGCTTCTGCCCAGATGTTCGTAAAGC
Found at i:1968549 original size:7 final size:7
Alignment explanation
Indices: 1968531--1968638 Score: 66
Period size: 7 Copynumber: 15.6 Consensus size: 7
1968521 TACAAACGTA
1968531 AAAATGC
1 AAAATGC
1968538 AAAAATGC
1 -AAAATGC
1968546 AAAATGC
1 AAAATGC
1968553 AAAATGC
1 AAAATGC
1968560 -AAATGC
1 AAAATGC
*
1968566 -AAATGT
1 AAAATGC
1968572 AACAAT--
1 AA-AATGC
1968578 AAGAATGC
1 AA-AATGC
* *
1968586 AAATTGT
1 AAAATGC
** *
1968593 GCAATAC
1 AAAATGC
1968600 AAAA-GC
1 AAAATGC
1968606 AAACATG-
1 AAA-ATGC
1968613 AAAATGC
1 AAAATGC
*
1968620 GAAGATGC
1 -AAAATGC
1968628 AAAATGC
1 AAAATGC
1968635 AAAA
1 AAAA
1968639 GCATGTATGA
Statistics
Matches: 78, Mismatches: 14, Indels: 17
0.72 0.13 0.16
Matches are distributed among these distances:
6 23 0.29
7 36 0.46
8 19 0.24
ACGTcount: A:0.56, C:0.13, G:0.16, T:0.16
Consensus pattern (7 bp):
AAAATGC
Found at i:1968565 original size:20 final size:19
Alignment explanation
Indices: 1968494--1968568 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
1968484 TTATGTAAAG
1968494 ATGCAAATGCAAAAATGAAA
1 ATGCAAATGC-AAAATGAAA
* * * *
1968514 ATGTAAATACAAACGTAAAA
1 ATGCAAATGCAAA-ATGAAA
1968534 ATGCAAAAATGCAAAATGCAAA
1 ATGC--AAATGCAAAATG-AAA
1968556 ATGCAAATGCAAA
1 ATGCAAATGCAAA
1968569 TGTAACAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 24 0.56
21 1 0.02
22 15 0.35
ACGTcount: A:0.59, C:0.12, G:0.13, T:0.16
Consensus pattern (19 bp):
ATGCAAATGCAAAATGAAA
Found at i:1968797 original size:43 final size:44
Alignment explanation
Indices: 1968720--1968802 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
1968710 GCATCAAACA
* * *
1968720 AAACTTTTACATGTAGGGGACAACTTTGAGTCCTAACTTCAATG
1 AAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAATG
* *
1968764 AAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
1968803 TCTAAGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 30 0.88
44 4 0.12
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (44 bp):
AAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAATG
Found at i:1970350 original size:9 final size:9
Alignment explanation
Indices: 1970336--1970369 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1970326 CATGCATCGG
1970336 AAAAAATAA
1 AAAAAATAA
1970345 AAAAAAT-A
1 AAAAAATAA
1970353 AAAAAATAA
1 AAAAAATAA
1970362 AATAAAAT
1 AA-AAAAT
1970370 GGTTAGTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1970356 original size:17 final size:18
Alignment explanation
Indices: 1970336--1970369 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1970326 CATGCATCGG
1970336 AAAAAATAAAA-AAAATA
1 AAAAAATAAAATAAAATA
1970353 AAAAAATAAAATAAAAT
1 AAAAAATAAAATAAAAT
1970370 GGTTAGTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAATAAAATAAAATA
Found at i:1971912 original size:28 final size:28
Alignment explanation
Indices: 1971849--1971916 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1971839 TTGTAGTTAA
*
1971849 AAATG-AAAATA-TTAAAATTAGTGTTT
1 AAATGTAAAATATTTAAAATTAGTGTCT
1971875 AAAATGTAAAATATTTAAAATTAGTGCTCT
1 -AAATGTAAAATATTTAAAATTAGTG-TCT
*
1971905 -AATTTAAAATAT
1 AAATGTAAAATAT
1971917 CACAAGATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 17 0.47
29 12 0.33
30 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (28 bp):
AAATGTAAAATATTTAAAATTAGTGTCT
Found at i:1973120 original size:3 final size:3
Alignment explanation
Indices: 1973112--1973164 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1973102 AATATTTATT
*
1973112 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1973159 TAA TAA
1 TAA TAA
1973165 CAAAAAAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1989769 original size:29 final size:28
Alignment explanation
Indices: 1989719--1989786 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
1989709 ATTGGCTTGC
*
1989719 TTTCTCTTTTTGAATTTGTTCTTTTTCT
1 TTTCTCTTTTTGAATTTGTTCTTCTTCT
1989747 TTTCATCTTTTCTGAATTT-TTCTTCTTCT
1 TTTC-TCTTTT-TGAATTTGTTCTTCTTCT
*
1989776 TTTTTCTTTTT
1 TTTCTCTTTTT
1989787 TTTTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 1 0.03
28 10 0.28
29 18 0.50
30 7 0.19
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.72
Consensus pattern (28 bp):
TTTCTCTTTTTGAATTTGTTCTTCTTCT
Done.