Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 9 of 25
Found at i:1250104 original size:14 final size:15
Alignment explanation
Indices: 1250080--1250108 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1250070 CGGCCGATCT
1250080 TCCCTACTTCAATTA
1 TCCCTACTTCAATTA
1250095 TCCC-ACTTCAATTA
1 TCCCTACTTCAATTA
1250109 ACATTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (15 bp):
TCCCTACTTCAATTA
Found at i:1250956 original size:20 final size:19
Alignment explanation
Indices: 1250931--1250983 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
1250921 TTCTACAATT
1250931 TGTATCGATACATAAGTAA
1 TGTATCGATACATAAGTAA
1250950 CTGTATCGATACATAAGTAA
1 -TGTATCGATACATAAGTAA
*
1250970 AGATATCGATACAT
1 TG-TATCGATACAT
1250984 GCCTAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATAAGTAA
Found at i:1250990 original size:20 final size:20
Alignment explanation
Indices: 1250932--1251009 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1250922 TCTACAATTT
* **
1250932 GTATCGATACATAAGTAACT
1 GTATCGATACATAACTAAAA
*
1250952 GTATCGATACATAAGT-AAA
1 GTATCGATACATAACTAAAA
**
1250971 GATATCGATACATGCCTAAAA
1 G-TATCGATACATAACTAAAA
*
1250992 TGTATCGATACAAAACTA
1 -GTATCGATACATAACTA
1251010 CCTTACATAC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 28 0.60
21 16 0.34
22 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (20 bp):
GTATCGATACATAACTAAAA
Found at i:1252658 original size:19 final size:19
Alignment explanation
Indices: 1252634--1252671 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1252624 TTCCATTGTT
1252634 CCAAACTACGCTGGGATTG
1 CCAAACTACGCTGGGATTG
*
1252653 CCAAACTACTCTGGGATTG
1 CCAAACTACGCTGGGATTG
1252672 TGGAATGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (19 bp):
CCAAACTACGCTGGGATTG
Found at i:1253607 original size:79 final size:79
Alignment explanation
Indices: 1253514--1253889 Score: 377
Period size: 79 Copynumber: 4.8 Consensus size: 79
1253504 AAATATCGAT
* * * * *
1253514 TTTTCATCTC-GGGATATTCAAACCCCATTATTTTTGAGGAGATACTCTTACCTCGTTTTTATTT
1 TTTTCATCTCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCTAACCTCATTTTTATTT
1253578 CAAAAATATTAAAA
66 CAAAAATATTAAAA
* * * *
1253592 TTTTCATCTCAGGGATACTCCAACCCCATTATTTTTGAGGAGATACTCCAA-CTCCGTTTTTATT
1 TTTTCATCTCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCTAACCT-CATTTTTATT
1253656 TCAAAAATATTAAAA
65 TCAAAAATATTAAAA
* * * * * * *
1253671 TTTTCATCTTGGGGATACTCTAACCCTATCAATTCTGAGGGGATACTCCAACC-CTATTTTTATT
1 TTTTCATCTCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCTAACCTC-ATTTTTATT
*
1253735 TCCAAAATATTAAAA
65 TCAAAAATATTAAAA
* * * * *
1253750 TTTTCATCTTGGGGATACTCCAACCTC-TGTATTTCTAAGGGGATACTCTAAACCCCATTTTTAT
1 TTTTCATCTCGGGGATACTCCAACCCCAT-TATTTTTGAGGGGATACTCT-AACCTCATTTTTAT
* * *
1253814 TTCTAAAATA-TAGAT
64 TTCAAAAATATTAAAA
* * * ** *
1253829 TTTTTACCATCGGGGATATTCCAACCCCAGCATTTTCGAGGGGATACTCTAAACC-CATTTT
1 TTTTCATC-TCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCT-AACCTCATTTT
1253890 CACTCCTAAA
Statistics
Matches: 255, Mismatches: 34, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
78 14 0.05
79 181 0.71
80 59 0.23
81 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (79 bp):
TTTTCATCTCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCTAACCTCATTTTTATTT
CAAAAATATTAAAA
Found at i:1253906 original size:159 final size:158
Alignment explanation
Indices: 1253580--1253935 Score: 362
Period size: 159 Copynumber: 2.2 Consensus size: 158
1253570 TTTTATTTCA
* * * * * *
1253580 AAAATATTAAAATTTTCATCTCAGGGATACTCCAACCCCATTATTTTTGAGGAGATACTCCAACT
1 AAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTCATTATTTCTAAGGAGATACTCAAACC
* * * * * *
1253645 CCGTTTTTATTTCAAAAATATTAAAATTTTCATCTTGGGGATACTCTAACCCTATCAATTCTGAG
66 CCATTTTTATTTCAAAAATATTAAAATTTTCACCTCGGGGATACTCCAACCCCAGCAATTCTGAG
* * *
1253710 GGGATACTCCAACCCTATTTTTATTTCC
131 GGGATACTCAAACCCTATTTTCATCTCC
* *
1253738 AAAATATTAAAATTTTCATCTTGGGGATACTCCAACCTC-TGTATTTCTAAGGGGATACTCTAAA
1 AAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTCAT-TATTTCTAAGGAGATACTC-AAA
* * * * * *
1253802 CCCCATTTTTATTTCTAAAATA-TAGATTTTTTACCATCGGGGATATTCCAACCCCAGC-ATTTT
64 CCCCATTTTTATTTCAAAAATATTAAAATTTTCACC-TCGGGGATACTCCAACCCCAGCAATTCT
1253865 CGAGGGGATACTCTAAACCC-ATTTTCA-CTCC
128 -GAGGGGATACTC-AAACCCTATTTTCATCTCC
* ** * * *
1253896 TAAAACATTAATTTTTTTATCTCGAGGATACTCTAACCTC
1 -AAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTC
1253936 GATTTTCACC
Statistics
Matches: 162, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
157 1 0.01
158 68 0.42
159 88 0.54
160 5 0.03
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (158 bp):
AAAATATTAAAATTTTCATCTCGGGGATACTCCAACCTCATTATTTCTAAGGAGATACTCAAACC
CCATTTTTATTTCAAAAATATTAAAATTTTCACCTCGGGGATACTCCAACCCCAGCAATTCTGAG
GGGATACTCAAACCCTATTTTCATCTCC
Found at i:1254872 original size:20 final size:20
Alignment explanation
Indices: 1254847--1254898 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1254837 TCATAATTTC
1254847 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
* *
1254867 TATCGATGCATGGTTCATTG
1 TATCGATACATTGTTCATTG
*
1254887 TATCAATACATT
1 TATCGATACATT
1254899 CTGGGTTTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TATCGATACATTGTTCATTG
Found at i:1257390 original size:52 final size:50
Alignment explanation
Indices: 1257328--1257446 Score: 157
Period size: 52 Copynumber: 2.3 Consensus size: 50
1257318 TTATTTCCGA
** *
1257328 GGGGATACTCCAACCCTGATTTTATTTTTAAAACACCAATTTTTCGCAATC
1 GGGGATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTTCACAATC
*
1257379 GGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATC
1 -GGGGATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTTTCACAATC
**
1257431 GAAGATACTCCAACCC
1 GGGGATACTCCAACCC
1257447 CGTTATTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 2 0.03
51 12 0.20
52 44 0.73
53 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTTCACAATC
Found at i:1257483 original size:79 final size:78
Alignment explanation
Indices: 1257380--1257606 Score: 292
Period size: 79 Copynumber: 2.9 Consensus size: 78
1257370 TTCGCAATCG
* ** * * *
1257380 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGAAGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACA-TGATTTTTCACAATCGAGGATACTCCAAC
1257445 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * * *
1257459 GGGGATACTCCATCCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATCGAGGATGCTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACA-TGATTTTTCACAATCGAGGATACTCCAAC
*
1257524 CCCGTTATTTTCGC
65 CCCGTTATTTTCGA
* * * *
1257538 GGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACAT-GATTTTTCACAATCGAGGATACTCCAAC
1257603 CCCG
65 CCCG
1257607 ATTTTATTTT
Statistics
Matches: 127, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
78 1 0.01
79 126 0.99
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATGATTTTTCACAATCGAGGATACTCCAACC
CCGTTATTTTCGA
Found at i:1257483 original size:131 final size:131
Alignment explanation
Indices: 1257249--1257491 Score: 355
Period size: 131 Copynumber: 1.9 Consensus size: 131
1257239 TTTTCATCTC
* ** *
1257249 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGAAGATACTCCAAC
* * *
1257314 CCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTTTAAAACACCAATTTTTCGCAATC
66 CCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTTTCGCAATC
1257379 G
131 G
*
1257380 GGGGATACTCCAACTCC-GATTTTATTTCCAAAACA-CTAATTTTTCACAATCGAAGATACTCCA
1 GGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATC-AATTTTTCACAATCGAAGATACTCCA
* * *
1257443 ACCCCGTTATTTTCGAGGGGATACTCCATCCCCGGCTTTATTTCTAAAA
64 ACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAA
1257492 TATTGATTTC
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
130 2 0.02
131 97 0.98
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (131 bp):
GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGAAGATACTCCAAC
CCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTTTCGCAATC
G
Found at i:1257509 original size:131 final size:130
Alignment explanation
Indices: 1257247--1257526 Score: 348
Period size: 131 Copynumber: 2.1 Consensus size: 130
1257237 ATTTTTCATC
* **
1257247 TCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCA
1 TCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGAAGATACTCCA
* * * * * *
1257312 ATCCCGTTATTTCCGAGGGGATACTCCAACCCTGATTTTATTTTTAAAACACCAATTTTTCGCAA
66 ACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTCACAA
*
1257377 TCGGGGGATACTCCAACTCC-GATTTTATTTCCAAAACA-CTAATTTTTCACAATCGAAGATACT
1 TC-GGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATC-AATTTTTCACAATCGAAGATACT
* * * * ***
1257440 CCAACCCCGTTATTTTCGAGGGGATACTCCATCCCCGGCTTTATTTCTAAAATATTGATTTCTCA
63 CCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTCA
1257505 CAA
128 CAA
* *
1257508 TCGAGGATGCTCCAACCCC
1 TCGGGGATACTCCAACCCC
1257527 GTTATTTTCG
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 18 0.14
131 109 0.86
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (130 bp):
TCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGAAGATACTCCA
ACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTCACAA
Found at i:1257614 original size:51 final size:50
Alignment explanation
Indices: 1257537--1257708 Score: 186
Period size: 51 Copynumber: 3.4 Consensus size: 50
1257527 GTTATTTTCG
* *** * *
1257537 CGGGGATACTCCAACCCTGGCCTTA-TTTCTAAAGCATCGATTTTTCACAAT
1 CGGGGATACTCCAACCCCGATTTTATTTTC-AAA-CACCGATTTTTCATAAT
1257588 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGA-TTTTCTATAAT
1 CGGGGATACTCCAACCCCGATTTTATTTTC-AAACACCGATTTTTC-ATAAT
* * * *
1257639 CAGGGATACTCTAACCCTGATTTTATTTTCAGAACACCGATTTTCCATAAT
1 CGGGGATACTCCAACCCCGATTTTATTTTCA-AACACCGATTTTTCATAAT
*
1257690 CGGGGATACTCCAGCCCCG
1 CGGGGATACTCCAACCCCG
1257709 TTGTTATCCC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 6 0.06
51 85 0.83
52 11 0.11
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (50 bp):
CGGGGATACTCCAACCCCGATTTTATTTTCAAACACCGATTTTTCATAAT
Found at i:1265476 original size:12 final size:11
Alignment explanation
Indices: 1265449--1265487 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1265439 AAGTTTTTAG
1265449 GAAAAATGTTT
1 GAAAAATGTTT
1265460 GAAAAATGTTT
1 GAAAAATGTTT
*
1265471 GAAAAAT-TTG
1 GAAAAATGTTT
1265481 GAAAAAT
1 GAAAAAT
1265488 CATCTAGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (11 bp):
GAAAAATGTTT
Found at i:1266584 original size:19 final size:20
Alignment explanation
Indices: 1266560--1266607 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
1266550 TAGCCAAACT
1266560 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
1266579 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
1266600 TGTATCGA
1 TGTATCGA
1266608 AACATTGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.48
21 14 0.52
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:1270677 original size:15 final size:15
Alignment explanation
Indices: 1270657--1270687 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1270647 TAAAAATATC
*
1270657 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1270672 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1270687 C
1 C
1270688 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1272786 original size:13 final size:13
Alignment explanation
Indices: 1272768--1272805 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1272758 CATTTTTCTT
1272768 TGTATCGATACAA
1 TGTATCGATACAA
*
1272781 TGTATCGATACAC
1 TGTATCGATACAA
1272794 TGTATCGATACA
1 TGTATCGATACA
1272806 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1275333 original size:19 final size:20
Alignment explanation
Indices: 1275309--1275356 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
1275299 TAGCCAAACT
1275309 TGTATCGATACAC-AAAATA
1 TGTATCGATACACAAAAATA
1275328 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC-AAAAATA
1275349 TGTATCGA
1 TGTATCGA
1275357 AACATTGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 13 0.48
21 14 0.52
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACAAAAATA
Found at i:1277134 original size:20 final size:20
Alignment explanation
Indices: 1277060--1277131 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
1277050 AAAAGGATAG
*
1277060 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* *
1277080 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* * *
1277100 CATGTATTGATATATTGAAA
1 AATGTATCGATACATTGAAA
1277120 AATGTATCGATA
1 AATGTATCGATA
1277132 TATCTGGGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1278100 original size:28 final size:28
Alignment explanation
Indices: 1278018--1278851 Score: 1103
Period size: 28 Copynumber: 29.4 Consensus size: 28
1278008 CTAACTTGTA
* *
1278018 TGGGCTTTGAGAAGAGTTGCCATTGACTTGTG
1 TGGGCTTTGA-AAG-GGTGCCACTGAC-T-TG
*
1278050 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
* *
1278079 TGGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
1278107 TGGGCTTTGAAAAGAGTGTCACTAACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
1278136 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278164 TGGGCTTTGAAAAGAGTGCCACTTACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
1278193 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278221 TGGGCTTTGAAAGGGTGCCACTAACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278249 TGGGCTTTGAAAGGATGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278277 TGGGCTTTGAAAAGAGTGCCACAGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
1278306 TGGGCTTTGAAAGGGTGCCACTAACTTGCG
1 TGGGCTTTGAAAGGGTGCCACTGACTT--G
*
1278336 TGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
1278364 TGGGCTTTGAAAAGATGCCACTAACTTT
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278392 TGGGCTTTGAAAAGAGTGCCACTGGCTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
1278421 TGGGGTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
1278449 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278477 TGGGCTTTAAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
1278505 TGGGCTTTGAAAAGATGCTACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278533 TGGGCTTTGAAACGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278561 TGGGCTTTGGAAAGAGTGCCACTGACTTG
1 TGGGCTTT-GAAAGGGTGCCACTGACTTG
*
1278590 TGGGCTTTGAAAGGGTGCCATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278618 TGGGCTTTGAAAGGGTG-CATTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
1278645 TGGGCTTTAAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
1278673 TGGGCTTTGAAAAGATGCCATTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278701 TGGGCTTTAAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
1278729 TGGGCTTTGAAAAGATGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278757 TGGGCTTTGAAAGGGTCCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
1278785 TGAGCTTTGAAAGGATACCACTGACTTT
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
1278813 TGGGCTTTAAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
1278841 TGGGCTTTGAA
1 TGGGCTTTGAA
1278852 TAGATGAACA
Statistics
Matches: 707, Mismatches: 86, Indels: 22
0.87 0.11 0.03
Matches are distributed among these distances:
27 26 0.04
28 497 0.70
29 133 0.19
30 29 0.04
31 9 0.01
32 12 0.02
33 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:1280108 original size:9 final size:9
Alignment explanation
Indices: 1280085--1280145 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
1280075 TTTTTGCTAT
1280085 TTTTTTCTTG
1 TTTTTT-TTG
*
1280095 GTTTTTTTG
1 TTTTTTTTG
1280104 TTTTTTGTTG
1 TTTTTT-TTG
1280114 TTTTTTTTG
1 TTTTTTTTG
*
1280123 TTTTTTCTG
1 TTTTTTTTG
*
1280132 -TTTTTATG
1 TTTTTTTTG
1280140 TTTTTT
1 TTTTTT
1280146 CTGGGCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
8 7 0.16
9 24 0.53
10 14 0.31
ACGTcount: A:0.02, C:0.03, G:0.13, T:0.82
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1280109 original size:19 final size:19
Alignment explanation
Indices: 1280085--1280147 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
1280075 TTTTTGCTAT
1280085 TTTTTTCTTGGTTTTTTTG
1 TTTTTTCTTGGTTTTTTTG
* *
1280104 TTTTTTGTTGTTTTTTTTG
1 TTTTTTCTTGGTTTTTTTG
*
1280123 TTTTTTC-T-GTTTTTATG
1 TTTTTTCTTGGTTTTTTTG
1280140 TTTTTTCT
1 TTTTTTCT
1280148 GGGCATAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
17 14 0.37
18 1 0.03
19 23 0.61
ACGTcount: A:0.02, C:0.05, G:0.13, T:0.81
Consensus pattern (19 bp):
TTTTTTCTTGGTTTTTTTG
Found at i:1291385 original size:13 final size:13
Alignment explanation
Indices: 1291367--1291392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1291357 CAATTTTTTG
1291367 TGTATCGATACAT
1 TGTATCGATACAT
1291380 TGTATCGATACAT
1 TGTATCGATACAT
1291393 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1292150 original size:21 final size:20
Alignment explanation
Indices: 1292108--1292146 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1292098 TATTAATAAA
1292108 TCTCCCCCTTAATCAAGTAT
1 TCTCCCCCTTAATCAAGTAT
1292128 TCTCCCCCTTAATCAAGTA
1 TCTCCCCCTTAATCAAGTA
1292147 ATTCATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (20 bp):
TCTCCCCCTTAATCAAGTAT
Found at i:1293970 original size:13 final size:13
Alignment explanation
Indices: 1293952--1293977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1293942 ATAATCACCC
1293952 TGTATCGATACAA
1 TGTATCGATACAA
1293965 TGTATCGATACAA
1 TGTATCGATACAA
1293978 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1294034 original size:20 final size:20
Alignment explanation
Indices: 1293963--1294042 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1293953 GTATCGATAC
*
1293963 AATGTATCGATACAAAGAAA
1 AATGTATCGATACATAGAAA
*
1293983 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACATAGAA-----A
*
1294008 GATGTATCGATACATAGAAA
1 AATGTATCGATACATAGAAA
*
1294028 CATGTATCGATACAT
1 AATGTATCGATACAT
1294043 TTTAGACATT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATAGAAA
Found at i:1296075 original size:15 final size:15
Alignment explanation
Indices: 1296055--1296085 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1296045 ATTTCGTTTG
*
1296055 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1296070 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1296085 G
1 G
1296086 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1297909 original size:21 final size:21
Alignment explanation
Indices: 1297880--1297924 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1297870 AAGTTTTCAT
*
1297880 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1297900 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1297922 TTT
1 TTT
1297925 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1300160 original size:13 final size:13
Alignment explanation
Indices: 1300142--1300167 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1300132 CAATTTTTTG
1300142 TGTATCGATACAT
1 TGTATCGATACAT
1300155 TGTATCGATACAT
1 TGTATCGATACAT
1300168 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1303984 original size:20 final size:19
Alignment explanation
Indices: 1303955--1304103 Score: 96
Period size: 20 Copynumber: 7.9 Consensus size: 19
1303945 GGAAAAAAGA
1303955 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
1303974 CATACATGTATCGATACATT
1 CATA-ATGTATCGATACATT
* *
1303994 GAAAAATGTATCGATACA-T
1 -CATAATGTATCGATACATT
* * * *
1304013 C-T-AGGTA---AAAAAAT
1 CATAATGTATCGATACATT
* *
1304027 -AGAATATATCGATACATT
1 CATAATGTATCGATACATT
* *
1304045 GAAGAATGTATCGATACATT
1 -CATAATGTATCGATACATT
1304065 CATACATGTATCGATACATT
1 CATA-ATGTATCGATACATT
* *
1304085 GAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
1304104 CTGGGTAAGA
Statistics
Matches: 100, Mismatches: 18, Indels: 23
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.03
14 1 0.01
15 3 0.03
16 4 0.04
18 4 0.04
19 7 0.07
20 74 0.74
21 4 0.04
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:1304044 original size:71 final size:71
Alignment explanation
Indices: 1303928--1304083 Score: 199
Period size: 71 Copynumber: 2.2 Consensus size: 71
1303918 TTTTAACTAG
* * *
1303928 ATGTATCGATACATCTGGGAAAAAAGACATAATGTATCGATACATTCATA-CATGTATCGATACA
1 ATGTATCGATACATCTGGGAAAAAAGACAGAATATATCGATACATTCA-AGAATGTATCGATACA
*
1303992 TTGAAAA
65 TTCAAAA
* * *
1303999 ATGTATCGATACATCTAGGTAAAAAA-ATAGAATATATCGATACATTGAAGAATGTATCGATACA
1 ATGTATCGATACATCT-GGGAAAAAAGACAGAATATATCGATACATTCAAGAATGTATCGATACA
* *
1304063 TTCATAC
65 TTCAAAA
1304070 ATGTATCGATACAT
1 ATGTATCGATACAT
1304084 TGAAAAATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
70 1 0.01
71 65 0.88
72 8 0.11
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACATCTGGGAAAAAAGACAGAATATATCGATACATTCAAGAATGTATCGATACAT
TCAAAA
Found at i:1304122 original size:91 final size:91
Alignment explanation
Indices: 1303958--1304134 Score: 318
Period size: 91 Copynumber: 1.9 Consensus size: 91
1303948 AAAAAGACAT
1303958 AATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
1 AATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
*
1304023 AAATAGAATATATCGATACATTGAAG
66 AAACAGAATATATCGATACATTGAAG
* *
1304049 AATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAGA
1 AATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
*
1304114 AGACAGAATATATCGATACAT
66 AAACAGAATATATCGATACAT
1304135 CTGGGTAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (91 bp):
AATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
AAACAGAATATATCGATACATTGAAG
Found at i:1305478 original size:21 final size:22
Alignment explanation
Indices: 1305454--1305511 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
1305444 GAACTAGAGG
*
1305454 AGAAAATGAATGAGTTGGAA-A
1 AGAAAATGAATGAGTTGCAAGA
1305475 AGAAAA-GAAATGAGTTGCAAGA
1 AGAAAATG-AATGAGTTGCAAGA
*
1305497 TGAAAAT-AATGAGTT
1 AGAAAATGAATGAGTT
1305512 AACTAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.78
22 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.21
Consensus pattern (22 bp):
AGAAAATGAATGAGTTGCAAGA
Found at i:1308136 original size:79 final size:79
Alignment explanation
Indices: 1308014--1308239 Score: 285
Period size: 79 Copynumber: 2.9 Consensus size: 79
1308004 TGAGAAATTT
* * *
1308014 AATATTTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
*
1308078 CGGTTATGAAAAATC
65 CGATTATGAAAAATC
* * * *
1308093 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
* *
1308157 CAATTATGAGAAATC
65 CGATTATGAAAAATC
* * * **
1308172 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
1308237 GAT
66 GAT
1308240 GAAATAACGA
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
78 3 0.02
79 121 0.97
80 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
GATTATGAAAAATC
Found at i:1308247 original size:28 final size:28
Alignment explanation
Indices: 1308191--1308262 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1308181 GAAATAAAGC
** **
1308191 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1308219 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1308247 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1308263 TTGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1308465 original size:262 final size:262
Alignment explanation
Indices: 1308142--1308907 Score: 1311
Period size: 262 Copynumber: 2.9 Consensus size: 262
1308132 GAAAATAACA
*
1308142 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
*
1308207 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGATTGTG
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
* * *
1308272 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGT
131 AAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
* * *
1308337 TTTGAAAATAAAACTGAGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAT
196 TTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
1308402 CG
261 CG
**
1308404 GGGTTGGAGTATCCCCGATTATGAGAAA-CTAATATTTTGGAAATAAAATCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTATGAGAAATC-AATATTTTGGAAATAAAGCCGGGGTTGGAGTATC
*
1308468 CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTAGAGTATCCTCGATTGT
65 CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
*
1308533 GAAAAATTGGTGTTTTTGAAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
130 GAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
*
1308598 TTTTCAAAATAAAA-TCGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
195 TTTTGAAAATAAAACT-GGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAA
1308662 ACCG
259 ACCG
*
1308666 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTTGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
* * * *
1308731 CCTCGGAGGTAATGGGGTTGGAGTATCCCTGATGAAATAACGAGGTTGGAGTATCCTCAATTATG
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
1308796 AAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCCGATTAAAGGAAAATTGGTG
131 AAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTAT-CCCCGATTAAAGGAAAATTGGTG
* *
1308861 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATT
195 TTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGAAAAATT
1308908 GAGAAACTTA
Statistics
Matches: 474, Mismatches: 25, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
261 2 0.00
262 405 0.85
263 67 0.14
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (262 bp):
GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
AAAAATTGGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
TTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
CG
Found at i:1308509 original size:28 final size:28
Alignment explanation
Indices: 1308453--1308529 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
1308443 GAAATAAAAT
*** **
1308453 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1308481 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
1308509 CGAGGTTAGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1308530 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1308614 original size:211 final size:210
Alignment explanation
Indices: 1308303--1308681 Score: 566
Period size: 211 Copynumber: 1.8 Consensus size: 210
1308293 TAAAATCGGA
*
1308303 GTTAGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACTGAGGTTGGAGTATCCC
1 GTTAGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACAGAGGTTGGAGTATCCC
** *
1308368 CGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAGAAAC
66 CGATTAAGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAAAAAC
* *
1308433 TAATATTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCC
131 TAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCC
1308498 CGATGAAATAACGAG
196 CGATGAAATAACGAG
* ***
1308513 GTTAGAGTATCCTCGATTGTGA-AAAATTGGTGTTTTTGAAAATAAAATCAGA-GTTGGAGTATC
1 GTTAGAGTATCCCCGATTAAAAGAAAATTGGTG-TTTTGAAAATAAAA-CAGAGGTTGGAGTATC
* *
1308576 CCCGATTAAAGGAAAATTGGTGTTTTCA-AAATAAAATCGGGGTTGGAGTATCCCCGATTGTGAA
64 CCCGATT-AAGGAAAATTAGTGTTTT-AGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAA
* * *
1308640 AAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
127 AAACTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1308682 GATTATGAGA
Statistics
Matches: 150, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
209 10 0.07
210 50 0.33
211 89 0.59
212 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (210 bp):
GTTAGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACAGAGGTTGGAGTATCCC
CGATTAAGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAAAAAC
TAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCC
CGATGAAATAACGAG
Found at i:1308709 original size:51 final size:51
Alignment explanation
Indices: 1308250--1308907 Score: 348
Period size: 51 Copynumber: 12.6 Consensus size: 51
1308240 GAAATAACGA
** * * *
1308250 GGTTGGAGTATCCTTGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTG-TTTTGGAAATAAAATCGG
* * ** * * *
1308302 AGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAA-CTGA
1 GGTTGGAGTATCCCCGATTATGAG-AAATTAGTGTTTTGGAAATAAAATC-GG
* *
1308354 GGTTGGAGTATCCCCGATTGTG-GAAAATTAGTGTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAG-AAATTAGTGTTTTGGAAATAAAATCGG
* * *
1308405 GGTTGGAGTATCCCCGATTATGAGAAACTAATATTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCGG
* *** * * * ***** * *
1308456 GGTTGGAGTATCCCCTCGGAGGTA--ACGGGGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTAT-CCC-C-GA-TTATGA-GAAATTAGTGTTTTGGAAAT-AAA-ATCGG
* * * * * * *
1308512 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGAAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTG-TTTTGGAAATAAAATCGG
* * * **
1308564 AGTTGGAGTATCCCCGATTA-AAGGAAAATTGGTGTTTTCAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-G-AAATTAGTGTTTTGGAAATAAAATCGG
* * * *
1308616 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCGG
* * * **
1308667 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCGG
* * ** * ** *
1308718 GGTTTGAGTATCCCCTCGGAGGTAATG-G-GGTTGGAGTATCCCTGATGAAAT--AA-CGA
1 GGTTGGAGTAT-CCC-C-GA--TTATGAGAAATT--AGTGT-TTTG--GAAATAAAATCGG
* * * * *
1308774 GGTTGGAGTATCCTCAATTATGAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTATGAGAAATTAGTG-TTTTGGAAATAAAATCGG
* * * * *
1308826 AGTTGGAGTATCCCCCGATTA-AAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTAT-CCCCGATTATGA-G-AAATTAGTGTTTTGGAAATAAAATCGG
*
1308879 GGTTGGAGTATCCCCGATTATGAAAAATT
1 GGTTGGAGTATCCCCGATTATGAGAAATT
1308908 GAGAAACTTA
Statistics
Matches: 453, Mismatches: 116, Indels: 75
0.70 0.18 0.12
Matches are distributed among these distances:
49 5 0.01
51 172 0.38
52 130 0.29
53 68 0.15
54 27 0.06
55 10 0.02
56 33 0.07
57 3 0.01
59 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:1311248 original size:21 final size:21
Alignment explanation
Indices: 1311222--1311263 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1311212 GTATCGATAC
*
1311222 AATGTATCGATTCATTTCCTT
1 AATGTATCGATACATTTCCTT
1311243 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1311264 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1311312 original size:19 final size:18
Alignment explanation
Indices: 1311288--1311350 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1311278 AGCAATACAT
1311288 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1311307 TGTATCGATAC--A-TT-
1 TGTATCGATACAAACTTA
1311321 T-TATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1311339 TGTATCGATACA
1 TGTATCGATACA
1311351 TTTACGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 2 0.05
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.55
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1311326 original size:32 final size:32
Alignment explanation
Indices: 1311282--1311353 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1311272 CTTCATAGCA
*
1311282 ATACATTGTATCGATACAAAACTTATGTATCG
1 ATACATTTTATCGATACAAAACTTATGTATCG
*
1311314 ATACATTTTATCGATACAACACTTATGTATCG
1 ATACATTTTATCGATACAAAACTTATGTATCG
1311346 ATACATTT
1 ATACATTT
1311354 ACGGTTTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (32 bp):
ATACATTTTATCGATACAAAACTTATGTATCG
Found at i:1312371 original size:55 final size:55
Alignment explanation
Indices: 1312227--1312779 Score: 738
Period size: 55 Copynumber: 10.0 Consensus size: 55
1312217 ATAAAGTGCA
* ** *
1312227 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGGAAAGGAG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT------GAAAGGCG
* ** *
1312288 TCCTGCTTTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1312343 TCCTGCTCTTTGGGGACTAGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* ** *
1312398 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTCATGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1312453 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1312508 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1312563 TCCTGCTCTTTGAGGGCTGGAAAATGCCACCAACTGGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1312618 TCCTACTTTTTGAGGACTGGAAAATGCCACCAACTCGTGTGGGCTTTGAAAGGC-
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
** *
1312672 AACTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1312727 TCCTGCTCTTTAAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGG
1312780 AGAAGGCATC
Statistics
Matches: 442, Mismatches: 44, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
53 4 0.01
54 47 0.11
55 347 0.79
56 4 0.01
61 38 0.09
62 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1312580 original size:28 final size:28
Alignment explanation
Indices: 1312438--1312580 Score: 71
Period size: 28 Copynumber: 5.2 Consensus size: 28
1312428 CAACTCATGT
*
1312438 GGGCTTTGAAAGGTGTCCTGCTCTTTGA
1 GGGCTTTGAAAGGCGTCCTGCTCTTTGA
* * ** * *
1312466 GGAC--TGAAAGGTG-CCACCAACTTGTGT
1 GGGCTTTGAAAGGCGTCCTGC-TCTT-TGA
1312493 GGGCTTTGAAAGGCGTCCTGCTCTTTGA
1 GGGCTTTGAAAGGCGTCCTGCTCTTTGA
* * * ** ** ** *
1312521 GGAC-TGGAAAATGCCACCAACT-GGTGT
1 GGGCTTTG-AAAGGCGTCCTGCTCTTTGA
1312548 GGGCTTTGAAAGGCGTCCTGCTCTTTGA
1 GGGCTTTGAAAGGCGTCCTGCTCTTTGA
1312576 GGGCT
1 GGGCT
1312581 GGAAAATGCC
Statistics
Matches: 76, Mismatches: 31, Indels: 16
0.62 0.25 0.13
Matches are distributed among these distances:
25 3 0.04
26 12 0.16
27 21 0.28
28 26 0.34
29 11 0.14
30 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.28
Consensus pattern (28 bp):
GGGCTTTGAAAGGCGTCCTGCTCTTTGA
Found at i:1312901 original size:100 final size:100
Alignment explanation
Indices: 1312726--1312908 Score: 303
Period size: 100 Copynumber: 1.8 Consensus size: 100
1312716 TTTGAAAGGC
* * *
1312726 GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCATCT
1 GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
*
1312791 TGCTCTTTGAGGACTAAAGGGCGAAAGAAGAGAGT
66 TGCTCGTTGAGGACTAAAGGGCGAAAGAAGAGAGT
* **
1312826 GTCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
1 GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
1312891 TGCTCGTTGAGGACTAAA
66 TGCTCGTTGAGGACTAAA
1312909 AAGTGGAAGG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (100 bp):
GTCCTGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATCC
TGCTCGTTGAGGACTAAAGGGCGAAAGAAGAGAGT
Found at i:1313884 original size:1 final size:1
Alignment explanation
Indices: 1313878--1313939 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
1313868 TAGATTCTTC
* * * * * * *
1313878 TTTTTTTTTTCTCTTTTTTTTCTTTGTTTTTTTTTGTTTTTTTTTTTGTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1313940 AAAAAGAATG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.05, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:1313900 original size:25 final size:25
Alignment explanation
Indices: 1313872--1313938 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
1313862 CTTAAGTAGA
1313872 TTCTTCTTTTTTTTTT-CTCTTTTTT
1 TTCTT-TTTTTTTTTTGCTCTTTTTT
* *
1313897 TTCTTTGTTTTTTTTTGTTTTTTTTT
1 TTCTTT-TTTTTTTTTGCTCTTTTTT
*
1313923 TTGTTGTTTTTTTTTT
1 TTCTT-TTTTTTTTTT
1313939 TAAAAAGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.03
25 14 0.39
26 20 0.56
27 1 0.03
ACGTcount: A:0.00, C:0.07, G:0.06, T:0.87
Consensus pattern (25 bp):
TTCTTTTTTTTTTTTGCTCTTTTTT
Found at i:1315577 original size:54 final size:50
Alignment explanation
Indices: 1315518--1315643 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 50
1315508 AAATAATGGG
* * *
1315518 GTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGAAAA-TTAGTG---TCTTGAAAATAAAATCGAA
* *
1315572 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAATTAGTGTCTTGAAAATAAAATCGAA
*
1315623 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1315644 GAGAATTGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.02
51 34 0.53
54 24 0.38
55 5 0.08
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAATTAGTGTCTTGAAAATAAAATCGAA
Found at i:1317467 original size:14 final size:14
Alignment explanation
Indices: 1317441--1317478 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
1317431 TGGAATAGTG
*
1317441 TTTTTCTTT-GTTT
1 TTTTTTTTTGGTTT
1317454 TTTTTTTTTGGTTT
1 TTTTTTTTTGGTTT
1317468 TTTCTTTTTTG
1 TTT-TTTTTTG
1317479 CTAAAGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 7 0.32
15 7 0.32
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTGGTTT
Found at i:1318009 original size:13 final size:13
Alignment explanation
Indices: 1317991--1318016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1317981 ACAAAGATCC
1317991 ATGTATCGATACA
1 ATGTATCGATACA
1318004 ATGTATCGATACA
1 ATGTATCGATACA
1318017 CAGAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1318031 original size:33 final size:33
Alignment explanation
Indices: 1317971--1318037 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1317961 AATTTTCAAG
*** *
1317971 ATGTATCGATACAAAGATCCATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATATATCGATACA
*
1318004 ATGTATCGATACACAGAAAAATATATCGATACA
1 ATGTATCGATACAAAGAAAAATATATCGATACA
1318037 A
1 A
1318038 CATTTATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATATATCGATACA
Found at i:1318121 original size:21 final size:22
Alignment explanation
Indices: 1318095--1318171 Score: 106
Period size: 21 Copynumber: 3.6 Consensus size: 22
1318085 TGGGACCCTA
*
1318095 TATCGATACATTTGTA-GAATG
1 TATCGATACATTTGTACAAATG
**
1318116 TATCGATACA-TTCCACAAATG
1 TATCGATACATTTGTACAAATG
1318137 TATCGATACATTT-TACAAATG
1 TATCGATACATTTGTACAAATG
1318158 TATCGATACATTTG
1 TATCGATACATTTG
1318172 GATAATAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 3 0.06
21 44 0.90
22 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCGATACATTTGTACAAATG
Found at i:1330421 original size:79 final size:79
Alignment explanation
Indices: 1330288--1330486 Score: 231
Period size: 79 Copynumber: 2.5 Consensus size: 79
1330278 AATAACGGGG
* * * * ** * *
1330288 TTGGAGTATCCCATTGAAAATAACGGGGTTCGAGTATCCCCGGTTGTGAAAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTTAG
*
1330352 GAAATAAAATCGAGA
65 GAAATAAAACCGAGA
*
1330367 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTAT-AAGAAATCAATATTTTG
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAA-AAATCAATATTTAG
* * *
1330431 GAAATAAAGCCGGGG
65 GAAATAAAACCGAGA
**
1330446 TTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
1330487 GATGAAATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
78 3 0.03
79 100 0.97
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTAGG
AAATAAAACCGAGA
Found at i:1330497 original size:28 final size:28
Alignment explanation
Indices: 1330441--1330517 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1330431 GAAATAAAGC
*** **
1330441 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1330469 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1330497 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1330518 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1330570 original size:52 final size:51
Alignment explanation
Indices: 1330497--1330633 Score: 186
Period size: 52 Copynumber: 2.6 Consensus size: 51
1330487 GATGAAATAA
* * * *
1330497 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGAAAATAAAAC
*
1330549 CG-GAGTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGAAAATAAAAC
*
1330601 CGAGGTTGGAGTATCCCCGATTATGAACAATTG
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTG
1330634 AGAAACTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
51 10 0.13
52 52 0.69
53 13 0.17
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:1333012 original size:13 final size:13
Alignment explanation
Indices: 1332994--1333019 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1332984 ACAAAGATCG
1332994 ATGTATCGATACA
1 ATGTATCGATACA
1333007 ATGTATCGATACA
1 ATGTATCGATACA
1333020 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1333030 original size:21 final size:21
Alignment explanation
Indices: 1333006--1333047 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1332996 GTATCGATAC
1333006 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1333027 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1333048 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1333096 original size:19 final size:18
Alignment explanation
Indices: 1333072--1333134 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1333062 AGCGATACAT
1333072 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1333091 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
1333104 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1333123 TGTATCGATACA
1 TGTATCGATACA
1333135 TTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1333105 original size:32 final size:32
Alignment explanation
Indices: 1333064--1333136 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
1333054 AGCTTCGTAG
1333064 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1333096 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1333128 CGATACATT
1 CGATACATT
1333137 TACGGTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1337139 original size:20 final size:20
Alignment explanation
Indices: 1337110--1337184 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1337100 AAAAAGACAT
*
1337110 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
1337130 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
1337150 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
1337170 AATGTATCGATACAT
1 AATGTATCGATACAT
1337185 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:1337178 original size:40 final size:39
Alignment explanation
Indices: 1337107--1337184 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1337097 GGTAAAAAGA
* *
1337107 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1337146 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1337185 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1338924 original size:32 final size:36
Alignment explanation
Indices: 1338838--1338908 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1338828 CTAAGTAATT
**
1338838 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
1338874 GAGAGGTTCTATCTTAGCCCATG-AAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
1338909 AGTTTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 12 0.36
36 21 0.64
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
Found at i:1339308 original size:11 final size:11
Alignment explanation
Indices: 1339287--1339337 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
1339277 AATTTTTCAA
1339287 TTTTTTCTTTTC
1 TTTTTT-TTTTC
1339299 TTTTTTTTTTC
1 TTTTTTTTTTC
1339310 --TTTTTTTTC
1 TTTTTTTTTTC
**
1339319 TTTTTAATTTC
1 TTTTTTTTTTC
1339330 TTTTTTTT
1 TTTTTTTT
1339338 CAAAAGTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 9 0.27
11 18 0.55
12 6 0.18
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:1339308 original size:16 final size:16
Alignment explanation
Indices: 1339287--1339337 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1339277 AATTTTTCAA
1339287 TTTTTTCTTTTCTTTT
1 TTTTTTCTTTTCTTTT
1339303 TTTTTTCTTTT-TTTT
1 TTTTTTCTTTTCTTTT
* **
1339318 CTTTTTAATTTCTTTT
1 TTTTTTCTTTTCTTTT
1339334 TTTT
1 TTTT
1339338 CAAAAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTCTTTTCTTTT
Found at i:1339317 original size:20 final size:20
Alignment explanation
Indices: 1339279--1339338 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1339269 TGGCACTTAA
*
1339279 TTTTTCAATTT-TTTCTTTTC
1 TTTTT-AATTTCTTTTTTTTC
**
1339299 TTTTTTTTTTCTTTTTTTTC
1 TTTTTAATTTCTTTTTTTTC
1339319 TTTTTAATTTCTTTTTTTTC
1 TTTTTAATTTCTTTTTTTTC
1339339 AAAAGTTTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTAATTTCTTTTTTTTC
Found at i:1343681 original size:16 final size:16
Alignment explanation
Indices: 1343655--1343833 Score: 106
Period size: 16 Copynumber: 11.1 Consensus size: 16
1343645 AAATTTTTGA
*
1343655 GTCATTTTTGGGTTTGG
1 GTCA-TTTTGGGTTCGG
*
1343672 CTCATTTTGGGTTCGG
1 GTCATTTTGGGTTCGG
* * *
1343688 GTCATTTCGAGTTTGG
1 GTCATTTTGGGTTCGG
1343704 GTCATTTTGGGTTCGG
1 GTCATTTTGGGTTCGG
* **
1343720 ATCATTTCAGGTTCGG
1 GTCATTTTGGGTTCGG
** * *
1343736 GTCATTTCAGATTCGA
1 GTCATTTTGGGTTCGG
* * *
1343752 GTCATTTTAGATTCGA
1 GTCATTTTGGGTTCGG
* * *
1343768 GTCATTTCGAGTTTGG
1 GTCATTTTGGGTTCGG
** *
1343784 GTCATTTCAGGTTCAG
1 GTCATTTTGGGTTCGG
* * **
1343800 ATTATTTCAGGTTCGG
1 GTCATTTTGGGTTCGG
* *
1343816 GTCATTTCGGATTCGG
1 GTCATTTTGGGTTCGG
1343832 GT
1 GT
1343834 TATCGGGTTT
Statistics
Matches: 129, Mismatches: 33, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
16 126 0.98
17 3 0.02
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.42
Consensus pattern (16 bp):
GTCATTTTGGGTTCGG
Found at i:1343757 original size:32 final size:32
Alignment explanation
Indices: 1343683--1343833 Score: 128
Period size: 32 Copynumber: 4.7 Consensus size: 32
1343673 TCATTTTGGG
* ** *
1343683 TTCGGGTCATTTC-GAGTTTGGGTCATTTTGGG
1 TTCGGGTCATTTCAG-GTTCGGGTCATTTCAGA
*
1343715 TTCGGATCATTTCAGGTTCGGGTCATTTCAGA
1 TTCGGGTCATTTCAGGTTCGGGTCATTTCAGA
* * * *
1343747 TTCGAGTCATTTTAGATTCGAGTCATTTC-GA
1 TTCGGGTCATTTCAGGTTCGGGTCATTTCAGA
* * * * *
1343778 GTTTGGGTCATTTCAGGTTCAGATTATTTCAGG
1 -TTCGGGTCATTTCAGGTTCGGGTCATTTCAGA
1343811 TTCGGGTCATTTC-GGATTCGGGT
1 TTCGGGTCATTTCAGG-TTCGGGT
1343834 TATCGGGTTT
Statistics
Matches: 93, Mismatches: 22, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
31 4 0.04
32 87 0.94
33 2 0.02
ACGTcount: A:0.16, C:0.15, G:0.28, T:0.41
Consensus pattern (32 bp):
TTCGGGTCATTTCAGGTTCGGGTCATTTCAGA
Found at i:1343773 original size:48 final size:46
Alignment explanation
Indices: 1343653--1343833 Score: 150
Period size: 48 Copynumber: 3.7 Consensus size: 46
1343643 TAAAATTTTT
* * * *
1343653 GAGTCATTTTTGGGTTTGGCTCATTTTGGGTTCGGGTCATTTC-GAGTTT
1 GAGTCA-TTTTAGGTTCGG-TCA-TTTCGGTTCGGGTCATTTCAGA-TTC
* *
1343702 GGGTCATTTTGGGTTCGGATCATTTCAGGTTCGGGTCATTTCAGATTC
1 GAGTCATTTTAGGTTCGG-TCATTTC-GGTTCGGGTCATTTCAGATTC
* * *
1343750 GAGTCATTTTAGATTCGAGTCATTTCGAGTTTGGGTCATTTCAGGTTC
1 GAGTCATTTTAGGTTCG-GTCATTTCG-GTTCGGGTCATTTCAGATTC
* *
1343798 -AGATTATTTCAGGTTCGGGTCATTTCGGATTCGGGT
1 GAG-TCATTTTAGGTTC-GGTCATTTCGG-TTCGGGT
1343834 TATCGGGTTT
Statistics
Matches: 111, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
47 7 0.06
48 95 0.86
49 9 0.08
ACGTcount: A:0.15, C:0.14, G:0.29, T:0.42
Consensus pattern (46 bp):
GAGTCATTTTAGGTTCGGTCATTTCGGTTCGGGTCATTTCAGATTC
Found at i:1344655 original size:39 final size:39
Alignment explanation
Indices: 1344598--1344681 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
1344588 TAAATTCAGT
* * * *
1344598 TCATTTCGAGTTAATTGTTTGGGTTATTTCAGGTTCGGG
1 TCATTTCAAGTTAATTGTTCGGATTATTTCAGGTTCGCG
*
1344637 TCATTTCAAGTTACTTGTTCGGATTATTTCAGGTTCGCG
1 TCATTTCAAGTTAATTGTTCGGATTATTTCAGGTTCGCG
1344676 TCATTT
1 TCATTT
1344682 TTGTGTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (39 bp):
TCATTTCAAGTTAATTGTTCGGATTATTTCAGGTTCGCG
Found at i:1345105 original size:147 final size:148
Alignment explanation
Indices: 1344910--1345203 Score: 371
Period size: 147 Copynumber: 2.0 Consensus size: 148
1344900 ACTTCAAAAG
* * * *
1344910 ATAAAAATAAATCTACTCTTAATTCATACTTTTGACAAAGAAGCGGACCTAG-TAGCTTT-ATAG
1 ATAAAAACAAACCTACTCTTAATTCATACCTTCGACAAAGAAGCGGACC-AGATAG-TTTCATAG
* * * *
1344973 GACTAGGTTTTGGG-GGATGCTATAATATCCCCAAGATTTACCATCAACTTAGAAGTACCCAGTG
64 GACTAGGTTTTGGGAGAATACTAAAATATCCCCAAGATTTACCATCAACTTAGAAATACCCAGTG
1345037 ATCCCAAGGGCA-TTGATAAT
129 ATCCCAAGGG-ATTTGATAAT
* * * *
1345057 ATAAAAACAAACCTACTCTTAATTCGTACCTTCGACATAGAAGTGGACCCGATAGTTTCATAGGA
1 ATAAAAACAAACCTACTCTTAATTCATACCTTCGACAAAGAAGCGGACCAGATAGTTTCATAGGA
* * * * *
1345122 CTAGGTTTTGGGAGAATACTAAAATATCCCTAAGGTTTACCATCAACTTATAAATGCCTAGTGAT
66 CTAGGTTTTGGGAGAATACTAAAATATCCCCAAGATTTACCATCAACTTAGAAATACCCAGTGAT
*
1345187 CCTAAGGGATTTGATAA
131 CCCAAGGGATTTGATAA
1345204 AATTTTTTTT
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
146 4 0.03
147 64 0.51
148 57 0.46
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (148 bp):
ATAAAAACAAACCTACTCTTAATTCATACCTTCGACAAAGAAGCGGACCAGATAGTTTCATAGGA
CTAGGTTTTGGGAGAATACTAAAATATCCCCAAGATTTACCATCAACTTAGAAATACCCAGTGAT
CCCAAGGGATTTGATAAT
Found at i:1345763 original size:141 final size:141
Alignment explanation
Indices: 1345509--1345903 Score: 483
Period size: 141 Copynumber: 2.8 Consensus size: 141
1345499 TGAAAATCTC
* * * * * * * *
1345509 ATTTCGTAACGTAATGGAGAATCGAAAAGATACGAAAAGTTTCGTAGCTTTCTATACCCTTACGA
1 ATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATACCCCTACGG
* *
1345574 AAAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAATTTTTAATTT
66 ATAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAA-ATTTAATTT
1345639 CTAAAAA-ATTT
130 CTAAAAATATTT
** * *
1345650 ATTTCGTTTCTTAATAGAGAACCGAAAAGATATGAAAAGTTTTGAAGATTTCTATACCCCTACGG
1 ATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATACCCCTACGG
* * *
1345715 ATAATTATAGGAATATTAGAAATCTTAAAAAATTAAGATAATAATTTTTATTTAAATTTAGTTTC
66 ATAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAAATTTAATTTC
1345780 TAAAAATATTT
131 TAAAAATATTT
* * * * *
1345791 ATTTTGTACCTTAACGGAGAACTGAAAAGATACAAAAAGTTTTGAAAATTT-TCATACCCC-ACG
1 ATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCT-ATACCCCTACG
** * * * *
1345854 GATACCCAT-GGAAATATTAGAAATTTTGAAAAATTGAGGTGATAATTTTT
65 GATAATCATAGG-AATATTAGAAATCTTGAAAAATTAAGATAATAATTTTT
1345904 GTTGGATAAA
Statistics
Matches: 218, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
139 2 0.01
140 57 0.26
141 159 0.73
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (141 bp):
ATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTCTATACCCCTACGG
ATAATCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAAATTTAATTTC
TAAAAATATTT
Found at i:1346794 original size:23 final size:23
Alignment explanation
Indices: 1346746--1346798 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1346736 TTGTAACTAG
*
1346746 TTTT-TCTATTTTTTTCTTTTGCT
1 TTTTCTCTATTTTTTTCATTT-CT
1346769 TTTTCTCTATTTTTTCTCATTT-T
1 TTTTCTCTATTTTTT-TCATTTCT
1346792 TTTTCTC
1 TTTTCTC
1346799 ACTTGCCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 12 0.44
24 10 0.37
25 5 0.19
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTCTCTATTTTTTTCATTTCT
Found at i:1347652 original size:167 final size:167
Alignment explanation
Indices: 1347398--1347718 Score: 368
Period size: 167 Copynumber: 1.9 Consensus size: 167
1347388 AATCCTCCCA
** *
1347398 AAAACCTTTATAGAATAGAAAATTCAATTTTTCAAAACTATGGACATTTCAAGAAAAAATGAAAA
1 AAAACCTTTATAGAATAGAAAAAACAATTTTTCAAAACTAAGGACATTTCAAGAAAAAATGAAAA
* ** * * *
1347463 ACCCATGAAAATAAATGAATTTTTTAAAACTGATTTACT-ATAATTTAAATGAT-GATATTTTAT
66 ACCCATGAAAATAAAGGAATTTTACAAAACTGATTTAATGATAA-TTAAATAATAG-TATTTAAT
* *
1347526 GAATATTAAAAATTTTGAACCGAGAAGAAACCCCCCCCG
129 GAATATTAAAAATTTTAAACCAAGAAGAAACCCCCCCCG
1347565 AAAACCTTTATAGAAT-GAAAAAACACGATTTTTCGAAAA-TAAGGA-ATTTCAAGGAAAAAATG
1 AAAACCTTTATAGAATAGAAAAAACA--ATTTTTC-AAAACTAAGGACATTTCAA-GAAAAAATG
**** * *
1347627 -AAATTTGATG-AAATAAAGGGAATTTTACAAAACTGATTTAATGGTGATTAAATAATAGTATTT
62 AAAAACCCATGAAAATAAA-GGAATTTTACAAAACTGATTTAATGATAATTAAATAATAGTATTT
*
1347690 AATGAATTTTAAAAATTTTAAACCAAGAA
126 AATGAATATTAAAAATTTTAAACCAAGAA
1347719 AAATCTCTTC
Statistics
Matches: 129, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
166 14 0.11
167 87 0.67
168 24 0.19
169 4 0.03
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (167 bp):
AAAACCTTTATAGAATAGAAAAAACAATTTTTCAAAACTAAGGACATTTCAAGAAAAAATGAAAA
ACCCATGAAAATAAAGGAATTTTACAAAACTGATTTAATGATAATTAAATAATAGTATTTAATGA
ATATTAAAAATTTTAAACCAAGAAGAAACCCCCCCCG
Found at i:1347865 original size:166 final size:165
Alignment explanation
Indices: 1347443--1347865 Score: 401
Period size: 166 Copynumber: 2.5 Consensus size: 165
1347433 AACTATGGAC
** * * *
1347443 ATTTCAAGAAAAAATGAAAAACCCATGAAAATAAATGAATTTTTTAAAACTGATTT-ACTATAAT
1 ATTTCAAGAAAAAATGAAAAATTCATG-AAATAAAGGAATTTTTCAAAACTGATTTAATTATAA-
* * * * *
1347507 TTAAATGATGATATTTTATGAATATTAAAAATTTTGAACCGAGAAGAAACCCCCCCCGAAAACCT
64 TTAAATGATGATA-TTTAAGAATTTTAAAAATTTTAAACCAAGAAGAAACCCCCCCCGAAAACAT
** **
1347572 TTATAGAATGAAAAAACACGATTTTTCGAAAATAAGGA
128 TTATAGAATGAAAAAACACGATACTTCGAAAATAAAAA
* * * ** *
1347610 ATTTCAAGGAAAAAATG-AAATTTGATGAAATAAAGGGAATTTTACAAAACTGATTTAATGGTGA
1 ATTTCAA-GAAAAAATGAAAAATTCATGAAATAAA-GGAATTTTTCAAAACTGATTTAATTATAA
* * * **
1347674 TTAAATAAT-AGTATTTAATGAATTTTAAAAATTTTAAACCAAGAA-AAA-TCTCTTCGAAAACA
64 TTAAATGATGA-TATTTAA-GAATTTTAAAAATTTTAAACCAAGAAGAAACCCCCCCCGAAAACA
* * * *
1347736 TTTA-CGAAGTG-CAAAACTCTATACTTCGAAAATAAAAAA
127 TTTATAGAA-TGAAAAAACACGATACTTCGAAAAT-AAAAA
* * *
1347775 ATTTCAAGAAAAAAATGAAAAATTCATGAAATAATAGCAATTTTTCAAAACTAATTTAATTTTAA
1 ATTTCAAG-AAAAAATGAAAAATTCATGAAATAA-AGGAATTTTTCAAAACTGATTTAATTATAA
1347840 TTAAATGATGATATTTGAAGAATTTT
64 TTAAATGATGATATTT-AAGAATTTT
1347866 GATATTTAAA
Statistics
Matches: 206, Mismatches: 38, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
164 21 0.10
165 33 0.16
166 72 0.35
167 68 0.33
168 12 0.06
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (165 bp):
ATTTCAAGAAAAAATGAAAAATTCATGAAATAAAGGAATTTTTCAAAACTGATTTAATTATAATT
AAATGATGATATTTAAGAATTTTAAAAATTTTAAACCAAGAAGAAACCCCCCCCGAAAACATTTA
TAGAATGAAAAAACACGATACTTCGAAAATAAAAA
Found at i:1348824 original size:14 final size:14
Alignment explanation
Indices: 1348802--1348831 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1348792 ATTTGAAACT
*
1348802 TTAATTTAATTAAA
1 TTAACTTAATTAAA
1348816 TTAACTTAATTAAA
1 TTAACTTAATTAAA
1348830 TT
1 TT
1348832 TCAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAACTTAATTAAA
Found at i:1350358 original size:17 final size:18
Alignment explanation
Indices: 1350303--1350352 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
1350293 CATTGCATTG
* *
1350303 CATTGCATTCCATAGGTTT
1 CATTGCATTGCAT-GCTTT
1350322 CATTGCATTGCATGCTTT
1 CATTGCATTGCATGCTTT
*
1350340 CATTTCA-TGCATG
1 CATTGCATTGCATG
1350353 TGTTCACACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 6 0.21
18 10 0.36
19 12 0.43
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (18 bp):
CATTGCATTGCATGCTTT
Found at i:1351346 original size:22 final size:22
Alignment explanation
Indices: 1351309--1351385 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
1351299 CGCAACAGTC
1351309 CAGCAAGCAAAGCAAAACCAAAA
1 CAGCAAGC-AAGCAAAACCAAAA
*
1351332 TAGCAAGCAAGCAAAACCAAAA
1 CAGCAAGCAAGCAAAACCAAAA
* * *
1351354 CAGCAAGCAAGGAAAAACGAAA
1 CAGCAAGCAAGCAAAACCAAAA
*
1351376 CAACAAGCAA
1 CAGCAAGCAA
1351386 AGAACGAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 41 0.85
23 7 0.15
ACGTcount: A:0.60, C:0.23, G:0.16, T:0.01
Consensus pattern (22 bp):
CAGCAAGCAAGCAAAACCAAAA
Found at i:1351397 original size:22 final size:22
Alignment explanation
Indices: 1351351--1351439 Score: 99
Period size: 22 Copynumber: 4.0 Consensus size: 22
1351341 AGCAAAACCA
*
1351351 AAACAGCAAGCAAGGAAA-AACG
1 AAACAGCAAGCAAAGAAAGAA-G
* *
1351373 AAACAACAAGCAAAGAACGAAG
1 AAACAGCAAGCAAAGAAAGAAG
* *
1351395 AAATAGTAAGCAAAGAAAGAAG
1 AAACAGCAAGCAAAGAAAGAAG
1351417 AAACAGCAAGCAAAAGTAAAGAA
1 AAACAGCAAGC-AAAG-AAAGAA
1351440 AAAGCTTACG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 43 0.78
23 6 0.11
24 6 0.11
ACGTcount: A:0.63, C:0.13, G:0.20, T:0.03
Consensus pattern (22 bp):
AAACAGCAAGCAAAGAAAGAAG
Found at i:1353386 original size:2 final size:2
Alignment explanation
Indices: 1353379--1353413 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1353369 AAAACACTAA
1353379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1353414 CATCAATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1365027 original size:38 final size:42
Alignment explanation
Indices: 1364941--1365033 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 42
1364931 GCCTGACGTA
* * *
1364941 TGGTTACCACCCTAGTCATATTTTTCTCATTCTAATTTGACGTG
1 TGGTTACCACCCTAGTCAGATTTTTCTCA-TC-AATTTGACATC
1364985 TGGTTACCACCCTAGTCAGA-TTTT-TC-TC-ATTTGACATC
1 TGGTTACCACCCTAGTCAGATTTTTCTCATCAATTTGACATC
1365023 TGGTTACCACC
1 TGGTTACCACC
1365034 TTGGTCAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 19 0.41
40 2 0.04
42 2 0.04
43 4 0.09
44 19 0.41
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
TGGTTACCACCCTAGTCAGATTTTTCTCATCAATTTGACATC
Found at i:1365270 original size:42 final size:41
Alignment explanation
Indices: 1365199--1366467 Score: 617
Period size: 42 Copynumber: 30.2 Consensus size: 41
1365189 TCTTACCTTC
* * * *
1365199 AGTCTGCCTATTGGCTTTGACCTTGGAGACTGCTTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * *
1365241 AGTTTACCTGTCGGCTTTGACTCTGGAGACT-TTCCCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT--CACCTCA
* * * *
1365283 AGTCTGCTTGTCGGCTTTGACCTTGGAGACTACCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * *
1365325 AGTCTACCTGTTGGCTTTGACCCTAGAGACTTTCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCT-TCACCTCA
* * * *
1365367 AGTCTGCCTATCGACTTTGACCTTAGAGACTACCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * *
1365409 AGTCTACCTATTGGCTTTGACCCT-GAAGACT-TTCTTACCTTC-
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTCTTC--ACC-TCA
* * *
1365451 AGTATGCCTGTCGGCTTTGACCCTAGAGACTACCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* ** * * **
1365493 AGTTTGTTTGTCGACTTTAACCCTAGAGACT-TTCCTACCTTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-ACCTCA
* * * *
1365535 AGTCTACCTGTCAGCTTTGACCCTAAAGACTGCCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * *
1365577 AGTCTGCCTATCGGCTTTGACTCTGGAGTCT-TTCCTACCTTC-
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-ACC-TCA
* * *
1365619 AGTTTGCCTGTCGACTTTGACCCTAGAGACTGCTTCACTTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * *
1365661 AGTCTGCCTGTCGGCTTTAACCTTAGAGACTTTTCTACCCTC-
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTTC-A-CCTCA
* * * *
1365703 AGTCTGTCTGTCGGCTTTGACCCTAAATACTGCCTT-ATCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT--CTTCACCTCA
* *
1365745 AGTCTGCCTGTCGGCTTTGACCTTAGAGACT-TTCCTACC-CTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-ACCTC-A
* * ** * *
1365787 AGTTTACCTGTCCACTTTGACCCTAGAGACTACCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * * *
1365829 AGTCTGCCTATCGACTTT-AACCTTGAAGACT-TTCTTACCCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAG-AGACTCTTC--A-CCTCA
* * * * * * *
1365872 AGTCTACTTATCAGTTTTGACCCTAAAGACT-TTCCTATCTTC-
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-A-CCTCA
* * * * * *
1365914 AGTCTGCTTGTCGACTTTGACCTTAGGGACTGCCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * * * *
1365956 AGTGTACCTGTCGACTTTGACCTTGGAGACTGCCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * *
1365998 AGTCTGCCTGTCGGCTTTGACCTTGGAGACT-TTCCTACCTTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-ACC-TCA
* * *
1366041 A-TCTACCTATCGGCTTTGACCATAGAGACTGCCTT-ACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT--CTTCACCTCA
* **
1366082 AGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTCCTACCTTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTT-C-ACCTCA
** * * * * *
1366124 AGTCTGCCTGTCAACTTTAACCATGGAGACTGCCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * *
1366166 AGTTTGCCTGTTGGCTTTAACCCTAGAAACT-TTCTTACTCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTTC--AC-CTCA
* * * ** * * *
1366209 A-TTTGTCTATCAACTTTGACCATGGAGACTGTCTT-ATCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC--TCTTCACCTCA
* * * *
1366250 AGTCTGCCTGTCGACTTTGACCCTAGAGGCTTTTCTACC-CTT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTTC-ACCTC-A
** * * *
1366292 AGTCTGTTTGTCAGCTTTGACCCTAGAGATTGTTTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
* * * * * *
1366334 AGTCTGCCTATCGGCTTTAACCTTGGAGACTTTTTTACCCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TCTTCA-CCTCA
* * ** * *
1366377 AGTTTGCTTGTAAGCTTTGATCCTAAAGACT-TGTCTACCTTC-
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCT-TC-ACC-TCA
* * * * * *
1366419 AGTTTGCCTATCAGCTTTGACCCTGGAGACTACCTCATCTCA
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACT-CTTCACCTCA
1366461 AGTCTGC
1 AGTCTGC
1366468 TTGTTGACTT
Statistics
Matches: 931, Mismatches: 219, Indels: 154
0.71 0.17 0.12
Matches are distributed among these distances:
39 4 0.00
40 14 0.02
41 33 0.04
42 774 0.83
43 85 0.09
44 17 0.02
45 4 0.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (41 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTCTTCACCTCA
Found at i:1365341 original size:84 final size:83
Alignment explanation
Indices: 1365199--1366467 Score: 894
Period size: 84 Copynumber: 15.1 Consensus size: 83
1365189 TCTTACCTTC
* * * * * * *
1365199 AGTCTGCCTATTGGCTTTGACCTTGGAGACTGCTTCACCTCAAGTTTACCTGTCGGCTTTGACTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGAC-C
*
1365264 TGGAGACTTTCCCACCTCA
65 TGGAGACTTTCCTACCTCA
* * * * * *
1365283 AGTCTGCTTGTCGGCTTTGACCTTGGAGACTACCTCACCTCAAGTCTACCTGTTGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
*
1365348 TAGAGACTTT-CTCACCTCA
65 TGGAGACTTTCCT-ACCTCA
* * * * * * *
1365367 AGTCTGCCTATCGACTTTGACCTTAGAGACTACCTCACCTCAAGTCTACCTATTGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
* *
1365432 TGAAGACTTTCTTACCTTC-
65 TGGAGACTTTCCTACC-TCA
* * * * ** * *
1365451 AGTATGCCTGTCGGCTTTGACCCTAGAGACTACCTCACCTTAAGTTTGTTTGTCGACTTTAACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
* **
1365516 TAGAGACTTTCCTACCTTT
65 TGGAGACTTTCCTACCTCA
* * * *
1365535 AGTCTACCTGTCAGCTTTGACCCTAAAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACTC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGAC-C
*
1365600 TGGAGTCTTTCCTACCTTC-
65 TGGAGACTTTCCTACC-TCA
* * * * *
1365619 AGTTTGCCTGTCGACTTTGACCCTAGAGACTGCTTCACTTCAAGTCTGCCTGTCGGCTTTAACCT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACC-
* *
1365684 TAGAGACTTTTCTACCCTC-
65 TGGAGACTTTCCTA-CCTCA
* * * * *
1365703 AGTCTGTCTGTCGGCTTTGACCCTAAATACTGCCTTATCTCAAGTCTGCCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACC-
* *
1365768 TAGAGACTTTCCTACC-CTT
65 TGGAGACTTTCCTACCTC-A
* * ** * * * * *
1365787 AGTTTACCTGTCCACTTTGACCCTAGAGACTACCTCACCTTAAGTCTGCCTATCGACTTTAACCT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACC-
* * *
1365852 TGAAGACTTTCTTACCCTTA
65 TGGAGACTTTCCTA-CCTCA
* * * * * * * * * *
1365872 AGTCTACTTATCAGTTTTGACCCTAAAGACTTTCCT-ATCTTC-AGTCTGCTTGTCGACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTCA-CCTCAAGTCTGCCTGTCGGCTTTGAC
* *
1365935 CTTAGG-GAC-TGCCTCACCTTA
64 C-T-GGAGACTTTCCT-ACCTCA
* * * * *
1365956 AGTGTACCTGTCGACTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACC-
*
1366021 TGGAGACTTTCCTACCTTTA
65 TGGAGACTTTCCTACC-TCA
* * * *
1366041 A-TCTACCTATCGGCTTTGACCATAGAGACTGCCTTACCTCAAGTCTGCCTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
**
1366105 TGGAGACTTTCCTACCTTT
65 TGGAGACTTTCCTACCTCA
** * * * * * * *
1366124 AGTCTGCCTGTCAACTTTAACCATGGAGACTGCCTCACCTTAAGTTTGCCTGTTGGCTTTAACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
* * *
1366189 TAGAAACTTTCTTACTCTCA
65 TGGAGACTTTCCTAC-CTCA
* * * ** * * * * * *
1366209 A-TTTGTCTATCAACTTTGACCATGGAGACTGTCTTATCTCAAGTCTGCCTGTCGACTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGA-CC
* * * *
1366273 TAGAGGCTTTTCTACC-CTT
65 TGGAGACTTTCCTACCTC-A
** * * ** * *
1366292 AGTCTGTTTGTCAGCTTTGACCCTAGAGATTGTTTCACCTCAAGTCTGCCTATCGGCTTTAACCT
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACC-
**
1366357 TGGAGACTTTTTTACCCTCA
65 TGGAGACTTTCCTA-CCTCA
* * ** * * * * * *
1366377 AGTTTGCTTGTAAGCTTTGATCCTAAAGACTTGTCT-ACCTTC-AGTTTGCCTATCAGCTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCCTAGAGAC-TGCCTCACC-TCAAGTCTGCCTGTCGGCTTTGA-
* *
1366440 CCTGGAGAC-TACCTCATCTCA
63 CCTGGAGACTTTCCT-ACCTCA
1366461 AGTCTGC
1 AGTCTGC
1366468 TTGTTGACTT
Statistics
Matches: 958, Mismatches: 193, Indels: 68
0.79 0.16 0.06
Matches are distributed among these distances:
82 2 0.00
83 22 0.02
84 793 0.83
85 125 0.13
86 16 0.02
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (83 bp):
AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCT
GGAGACTTTCCTACCTCA
Found at i:1365482 original size:168 final size:169
Alignment explanation
Indices: 1365187--1366379 Score: 996
Period size: 168 Copynumber: 7.1 Consensus size: 169
1365177 CCATTTGAAT
* * * * * * *
1365187 TTTCT-TACCTTC-AGTCTGCCTATTGGCTTTGACCTTGGAGACTGCTTCACCTCAAGTTTACCT
1 TTTCTCTACC-TCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCT
* * * * * * *
1365250 GTCGGCTTTGACTCTGGAGACTTTCCCACC-TCAAGTCTGCTTGTCGGCTTTGACCTTGGAGACT
65 GTCGGCTTTGACCCTGAAGACTTTCCTACCTTC-AGTCTGCCTGTCGACTTTGACCCTAGAGACT
* * * *
1365314 ACCTCACCTCAAGTCTACCTGTTGGCTTTGACCCTAGAGAC
129 GCCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
* * * *
1365355 TTTCTC-ACCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACTACCTCACCTCAAGTCTACCTA
1 TTTCTCTACCTCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTG
* * * * *
1365419 TTGGCTTTGACCCTGAAGACTTTCTTACCTTCAGTATGCCTGTCGGCTTTGACCCTAGAGACTAC
66 TCGGCTTTGACCCTGAAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGC
* * ** *
1365484 CTCACCTTAAGTTTGTTTGTCGACTTTAACCCTAGAGAC
131 CTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
** * * *
1365523 TTTC-CTACCTTTAGTCTACCTGTC-AGCTTTGACCCTAAAGACTGCCTCACCTCAAGTCTGCCT
1 TTTCTCTACCTCAAGTCTGCCTATCGA-CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCT
* * * * *
1365586 ATCGGCTTTGACTCTGGAGTCTTTCCTACCTTCAGTTTGCCTGTCGACTTTGACCCTAGAGACTG
65 GTCGGCTTTGACCCTGAAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTG
* * *
1365651 CTTCACTTCAAGTCTGCCTGTCGGCTTTAACCTTAGAGAC
130 CCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
* * * * * * *
1365691 TTT-TCTACCCTC-AGTCTGTCTGTCGGCTTTGACCCTAAATACTGCCTTATCTCAAGTCTGCCT
1 TTTCTCTA-CCTCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCT
* * * *
1365754 GTCGGCTTTGA-CCTTAGAGACTTTCCTACCCTT-AGTTTACCTGTCCACTTTGACCCTAGAGAC
65 GTCGGCTTTGACCCTGA-AGACTTTCCTA-CCTTCAGTCTGCCTGTCGACTTTGACCCTAGAGAC
* * * * *
1365817 TACCTCACCTTAAGTCTGCCTATCGACTTTAA-CCTTGAAGAC
128 TGCCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAG-AGAC
* * * * * * *
1365859 TTTCT-TACCCTTAAGTCTACTTATC-AGTTTTGACCCTAAAGACTTTCCT-ATCTTC-AGTCTG
1 TTTCTCTA-CCTCAAGTCTGCCTATCGA-CTTTGACCCTAGAGAC-TGCCTCA-CCTCAAGTCTG
* * * * * * * * * *
1365920 CTTGTCGACTTTGA-CCTTAGGGAC-TGCCTCACCTTAAGTGTACCTGTCGACTTTGACCTTGGA
62 CCTGTCGGCTTTGACCCTGA-AGACTTTCCT-ACCTTCAGTCTGCCTGTCGACTTTGACCCTAGA
* * *
1365983 GACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
125 GACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
* * * * *
1366028 TTTC-CTACCTTTAA-TCTACCTATCGGCTTTGACCATAGAGACTGCCTTACCTCAAGTCTGCCT
1 TTTCTCTACC-TCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCT
* * * * * *
1366091 GTCGGCTTTGACCCTGGAGACTTTCCTACCTTTAGTCTGCCTGTCAACTTTAACCATGGAGACTG
65 GTCGGCTTTGACCCTGAAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTG
* * * *
1366156 CCTCACCTTAAGTTTGCCTGTTGGCTTTAACCCTAGAAAC
130 CCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
* * * * * * * *
1366196 TTTCT-TACTCTCAA-TTTGTCTATCAACTTTGACCATGGAGACTGTCTTATCTCAAGTCTGCCT
1 TTTCTCTAC-CTCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCT
* * * **
1366259 GTCGACTTTGACCCT-AGAGGCTTTTCTACCCTT-AGTCTGTTTGTC-AGCTTTGACCCTAGAGA
65 GTCGGCTTTGACCCTGA-AGACTTTCCTA-CCTTCAGTCTGCCTGTCGA-CTTTGACCCTAGAGA
* ** * * *
1366321 TTGTTTCACCTCAAGTCTGCCTATCGGCTTTAACCTTGGAGAC
127 CTGCCTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
*
1366364 TTT-TTTACCCTCAAGT
1 TTTCTCTA-CCTCAAGT
1366380 TTGCTTGTAA
Statistics
Matches: 841, Mismatches: 150, Indels: 67
0.79 0.14 0.06
Matches are distributed among these distances:
167 18 0.02
168 672 0.80
169 142 0.17
170 9 0.01
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (169 bp):
TTTCTCTACCTCAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTG
TCGGCTTTGACCCTGAAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGC
CTCACCTCAAGTCTGCCTGTCGGCTTTAACCCTAGAGAC
Found at i:1366598 original size:42 final size:44
Alignment explanation
Indices: 1366507--1366601 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
1366497 TGTCTATCGA
* **
1366507 CTTTGACCCTGGAGACTTTCTTATCCTTTAAGTCTGCTTGTCGG
1 CTTTGACCCTGAAGACTTTCTTATCCTTTAAGTCTGCCCGTCGG
* *
1366551 CTTTGACCCTGAAGACTTT-TTCA-CCTTTTA-TCTGCCCGTTGG
1 CTTTGACCCTGAAGACTTTCTT-ATCCTTTAAGTCTGCCCGTCGG
1366593 CTTTGACCC
1 CTTTGACCC
1366602 GAGAGAATCT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 18 0.40
43 8 0.18
44 19 0.42
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (44 bp):
CTTTGACCCTGAAGACTTTCTTATCCTTTAAGTCTGCCCGTCGG
Found at i:1367830 original size:36 final size:34
Alignment explanation
Indices: 1367774--1367840 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
1367764 AACCGATGCA
*
1367774 GCAATGAAGGAAGCAATGAAGATATCAACGGGCT
1 GCAATGAAGGAAGCAATGAAGACATCAACGGGCT
* *
1367808 GCAATGAAGTTGATGCAATGAAGACATCGACGG
1 GCAATGAAG--GAAGCAATGAAGACATCAACGG
1367841 ACAGCAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 9 0.32
36 19 0.68
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.16
Consensus pattern (34 bp):
GCAATGAAGGAAGCAATGAAGACATCAACGGGCT
Found at i:1368073 original size:23 final size:23
Alignment explanation
Indices: 1368047--1368090 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1368037 GCAGCAAAAA
*
1368047 AAAAGAAAAAAAAAAAAGAAATC
1 AAAACAAAAAAAAAAAAGAAATC
*
1368070 AAAACAAAAAAAAAGAAGAAA
1 AAAACAAAAAAAAAAAAGAAA
1368091 AAGCTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (23 bp):
AAAACAAAAAAAAAAAAGAAATC
Found at i:1368092 original size:13 final size:13
Alignment explanation
Indices: 1368042--1368067 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1368032 AAATTGCAGC
1368042 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1368055 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1368068 TCAAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:1368446 original size:22 final size:22
Alignment explanation
Indices: 1368409--1368463 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1368399 CGCAACACTC
1368409 CAGCAAGCAAAGCAAAACCAAAA
1 CAGCAAGC-AAGCAAAACCAAAA
*
1368432 CAGCAAGCAAGCAAAACCGAAA
1 CAGCAAGCAAGCAAAACCAAAA
*
1368454 CAACAAGCAA
1 CAGCAAGCAA
1368464 AGAAAGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 22 0.73
23 8 0.27
ACGTcount: A:0.58, C:0.27, G:0.15, T:0.00
Consensus pattern (22 bp):
CAGCAAGCAAGCAAAACCAAAA
Found at i:1368475 original size:22 final size:22
Alignment explanation
Indices: 1368450--1368517 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 22
1368440 AAGCAAAACC
1368450 GAAACAACAAGCAAAGAAAGAA
1 GAAACAACAAGCAAAGAAAGAA
1368472 GAAACAACAAGCAAAGAAAGAA
1 GAAACAACAAGCAAAGAAAGAA
*
1368494 GAAACAGCAAGCAAAAGCAAAGAA
1 GAAACAACAAGC-AAAG-AAAGAA
1368518 CAAGCTTACG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 33 0.77
23 4 0.09
24 6 0.14
ACGTcount: A:0.66, C:0.15, G:0.19, T:0.00
Consensus pattern (22 bp):
GAAACAACAAGCAAAGAAAGAA
Found at i:1369399 original size:162 final size:163
Alignment explanation
Indices: 1369109--1369405 Score: 375
Period size: 162 Copynumber: 1.8 Consensus size: 163
1369099 TAAGGGCAAG
* * * * * * * *
1369109 ATAGTCTTTTTATGCTCACTCGATTCATATTTTTATATTCTTATGGTTTTTCGTAGAGGTATAAA
1 ATAGTCGTTTTATGCCCACTCGAGTCATATTCTCATATTCCTATAGTTTTTCATAGAGGTATAAA
* * * * * *
1369174 ATTTTTTATAACCTCTTGTATCCACTGGTTTTCTATTAGGTATGAAACGTAATTTTCAAAATTTA
66 AATTTTTAAAACCTCTTGTATCCACTGGTGTTCCATCAGATATGAAACGTAATTTTCAAAATTTA
1369239 AAAGTATTTGGCCCCTTTCATTGATATTAAAAA
131 AAAGTATTTGGCCCCTTTCATTGATATTAAAAA
*
1369272 ATAGTCGTTTT-TGCCCACTCGAGTCATGTTCTCATATTCCTATAGTTTTTCATAG-GAGTATAA
1 ATAGTCGTTTTATGCCCACTCGAGTCATATTCTCATATTCCTATAGTTTTTCATAGAG-GTATAA
* * * *
1369335 AAATTTTTAAAACCTTTTGTATCC-CATGGTGTTCCGTCAGATATGAAATGTAATTTTTAAAATT
65 AAATTTTTAAAACCTCTTGTATCCAC-TGGTGTTCCATCAGATATGAAACGTAATTTTCAAAATT
*
1369399 TAGAAGT
129 TAAAAGT
1369406 TAAATTTAAA
Statistics
Matches: 112, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
161 2 0.02
162 100 0.89
163 10 0.09
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (163 bp):
ATAGTCGTTTTATGCCCACTCGAGTCATATTCTCATATTCCTATAGTTTTTCATAGAGGTATAAA
AATTTTTAAAACCTCTTGTATCCACTGGTGTTCCATCAGATATGAAACGTAATTTTCAAAATTTA
AAAGTATTTGGCCCCTTTCATTGATATTAAAAA
Found at i:1372645 original size:205 final size:204
Alignment explanation
Indices: 1372274--1372663 Score: 507
Period size: 205 Copynumber: 1.9 Consensus size: 204
1372264 TAATGTTTTG
* * ** * * * * *
1372274 ATAATTTTTTGAAATATATTAAAACCCACTTACCTTAAAGTTATTCATGTAATTAAAAAAACCAC
1 ATAATTTTTTAAAATAAAACAAAACCCACTCACCCTAAAATTACTCATGTAATTAAAAAAACCAA
* * * * * * * *
1372339 TCATTTTTTCTTTTTTAAACTTTTACAACTACTTAGTTCTTTCTTCTATTTTAGAAAAGTATTTT
66 TCACTCTCTATTTCTCAAACTTTCACAACTACTTAGGTCTTTCTTCTATTTTAGAAAAGTATTTT
1372404 TTTATTATTTTTACATATATTTTTTAAATTAAAAACTATCCAATTATACAAAAAAATTCTATATT
131 TTTATTATTTTTA-ATATATTTTTTAAATTAAAAACTATCCAATTATACAAAAAAATTCTATATT
1372469 TAATAAATTA
195 TAATAAATTA
*
1372479 ATAATTTTTTAAAATAAAACAAAACCCACTCACCCTAAAATTACTCATGTAATTAAAAAAATCAA
1 ATAATTTTTTAAAATAAAACAAAACCCACTCACCCTAAAATTACTCATGTAATTAAAAAAACCAA
* * *
1372544 TCACTCTCTATTTCTCAAAGTTTCACAACTACTT-GGTCATTTCTTC-ATTTTTAGAATAGTTTT
66 TCACTCTCTATTTCTCAAACTTTCACAACTACTTAGGTC-TTTCTTCTA-TTTTAGAAAAGTATT
* *
1372607 TATTTTATTATTTTT-GTATATTTTTTAAATTAAAAAACTATCCACTTATACAAAAAA
129 T-TTTTATTATTTTTAATATATTTTTTAAATT-AAAAACTATCCAATTATACAAAAAA
1372664 TTACCAATAT
Statistics
Matches: 158, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
204 19 0.12
205 126 0.80
206 13 0.08
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (204 bp):
ATAATTTTTTAAAATAAAACAAAACCCACTCACCCTAAAATTACTCATGTAATTAAAAAAACCAA
TCACTCTCTATTTCTCAAACTTTCACAACTACTTAGGTCTTTCTTCTATTTTAGAAAAGTATTTT
TTTATTATTTTTAATATATTTTTTAAATTAAAAACTATCCAATTATACAAAAAAATTCTATATTT
AATAAATTA
Found at i:1373813 original size:20 final size:20
Alignment explanation
Indices: 1373788--1373825 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1373778 TCATTTACGT
1373788 TTATATATA-TACATATTTAA
1 TTATAT-TAGTACATATTTAA
1373808 TTATATTAGTACATATTT
1 TTATATTAGTACATATTT
1373826 TTATTATGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
TTATATTAGTACATATTTAA
Found at i:1380293 original size:2 final size:2
Alignment explanation
Indices: 1380286--1380322 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1380276 CCTCAGGTTG
1380286 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1380323 ACTCACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1380331 original size:2 final size:2
Alignment explanation
Indices: 1380326--1380355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1380316 CTCTCTCACT
1380326 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1380356 TATACGAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1381399 original size:7 final size:7
Alignment explanation
Indices: 1381387--1381420 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
1381377 TCAAGAATTG
1381387 AAAAATA
1 AAAAATA
1381394 AAAAATA
1 AAAAATA
*
1381401 AAACATA
1 AAAAATA
1381408 AAAAATA
1 AAAAATA
1381415 AAAAAT
1 AAAAAT
1381421 TTTCGTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:1381848 original size:3 final size:3
Alignment explanation
Indices: 1381842--1381871 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1381832 TATATTATTT
1381842 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1381872 TTATTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1381876 original size:3 final size:3
Alignment explanation
Indices: 1381870--1381900 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1381860 ATAATAATAA
1381870 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1381901 AATGCATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1388515 original size:147 final size:143
Alignment explanation
Indices: 1388198--1388875 Score: 697
Period size: 146 Copynumber: 4.7 Consensus size: 143
1388188 AAAAGTGAAT
* * * * * * *
1388198 CTACGCCTAATATGTACCCTTGGCATAGAAGTGACCCGATGATAAATTAGGACTCGATTCTAGAA
1 CTACGCCTAATACGTACCCTCGACATAGAAGTGACTCGATGACAAATTAGGACTCGATTTTAAAA
** * * * *
1388263 ATTATGAATATACCTCTATGAGTTTACCTTCGACATGAAAATATCTAGTAA-CCTAAAGGACTTA
66 ATTACAAAAATACC-CTATG-GTATACCTTCGACATGAAAGTATCTAGTAACCCTAAAAGACTTA
*
1388327 AAAAAAAAAGTAAAC
129 AAAAAAAAAGCAAAC
* * *
1388342 CTACGCCTAATACGTACCCTCGACATAGAAATGA-TCTAATGACAAATTAGGACTTGATTTTAAA
1 CTACGCCTAATACGTACCCTCGACATAGAAGTGACTC-GATGACAAATTAGGACTCGATTTTAAA
* * **
1388406 AATTACAAAAATATCCCTATGGTTATATCGTCGACATGAAAGTATCCTAGTAACCCTAATGGACT
65 AATTACAAAAATA-CCCTATGG-TATACCTTCGACATGAAAGTAT-CTAGTAACCCTAAAAGACT
*
1388471 TAAAAGGAAAAAGCAAAC
127 TAAAA-AAAAAAGCAAAC
* * * * *
1388489 CTATGCCTAATACATACCCTCGACATAGAAGCGACTCGATGACAAATTAGGACTCGATTCTAGAA
1 CTACGCCTAATACGTACCCTCGACATAGAAGTGACTCGATGACAAATTAGGACTCGATTTTAAAA
* * * *
1388554 ATTACAAAAATACCCTTAAGGGATACCTTCGACTTGAAAGTATCTCGGTAACCCTAAAAGACTTA
66 ATTACAAAAATACCC-TATGGTATACCTTCGACATGAAAGTATCT-AGTAACCCTAAAAGACTTA
1388619 AAAAAGAAAAGCAAAC
129 AAAAA-AAAAGCAAAC
* * * *
1388635 TTACGCCTAATACGTACCTTC-AGCATAGAAGTGACTCGATAACAAATTAAGG-CTTGATTTTAA
1 CTACGCCTAATACGTACCCTCGA-CATAGAAGTGACTCGATGACAAATT-AGGACTCGATTTTAA
* * * *
1388698 AAATTACAAAAATGCTCTTATAGGTATACCTTCGACATGAAAGTATCCCAATAACCCT-AAAGAC
64 AAATTACAAAAATAC-CCTAT-GGTATACCTTCGACATGAAAGTAT-CTAGTAACCCTAAAAGA-
**
1388762 CTT---AAAAAAAGTGAAC
125 CTTAAAAAAAAAAGCAAAC
* * * * * *
1388778 CTATGCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAGTTAGGACTCAATTTTAGAA
1 CTACGCCTAATACGTACCCTCGACATAGAAGTGACTCGATGACAAATTAGGACTCGATTTTAAAA
* * *
1388843 ATTACAAAAATACTCTTAGGGGATACCTTCGAC
66 ATTACAAAAATAC-CCTATGGTATACCTTCGAC
1388876 TTAGAAGTGT
Statistics
Matches: 447, Mismatches: 69, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
142 16 0.04
143 77 0.17
144 88 0.20
145 13 0.03
146 134 0.30
147 116 0.26
148 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (143 bp):
CTACGCCTAATACGTACCCTCGACATAGAAGTGACTCGATGACAAATTAGGACTCGATTTTAAAA
ATTACAAAAATACCCTATGGTATACCTTCGACATGAAAGTATCTAGTAACCCTAAAAGACTTAAA
AAAAAAAGCAAAC
Found at i:1388735 original size:293 final size:286
Alignment explanation
Indices: 1388202--1388877 Score: 835
Period size: 293 Copynumber: 2.3 Consensus size: 286
1388192 GTGAATCTAC
* * *
1388202 GCCTAATATGTACCCTTGGCATAGAAGTGACCCGATGATAAATTAGGACTCGATTCTAGAAATTA
1 GCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAATTAGGACTCGATTCTAGAAATTA
** * * ** * *
1388267 TGAATATA-CCTCTATGAGTTTACCTTCGACATGAAAATATCTAGTAACCTAAAGGACTTAAAAA
66 CAAAAATACCCT-TAAG-GGATACCTTCGACTTGAAAATATCTAGTAACCTAAAAGACTTAAAAA
* *
1388331 AAAAAGTAAACCTACGCCTAATACGTACCCTCGACATAGAAATGATCTAATGACAAATTAGGACT
129 AAAAAGCAAACCTACGCCTAATACGTACCCTCGACATAGAAATGATCTAATAACAAATTAGGACT
* * *
1388396 TGATTTTAAAAATTACAAAAATATCCCTATGGTTATATCGTCGACATGAAAGTATCCTAGTAACC
194 TGATTTTAAAAATTACAAAAATATCCCTATGGTTATACCGTCGACATGAAAGTATCCCAATAACC
*
1388461 CTAATGGA-CTTAAAAGGAAAAAGCAAACCTAT
259 CTAA-AGACCTT--AA--AAAAAGCAAACCTAT
* * * *
1388493 GCCTAATACATACCCTCGACATAGAAGCGACTCGATGACAAATTAGGACTCGATTCTAGAAATTA
1 GCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAATTAGGACTCGATTCTAGAAATTA
* *
1388558 CAAAAATACCCTTAAGGGATACCTTCGACTTGAAAGTATCTCGGTAACCCTAAAAGACTTAAAAA
66 CAAAAATACCCTTAAGGGATACCTTCGACTTGAAAATATCT-AGTAA-CCTAAAAGACTTAAAAA
* * * *
1388623 AGAAAAGCAAACTTACGCCTAATACGTACCTTC-AGCATAGAAGTGA-CTCGATAACAAATTAAG
129 A-AAAAGCAAACCTACGCCTAATACGTACCCTCGA-CATAGAAATGATCT-AATAACAAATT-AG
* * *
1388686 G-CTTGATTTTAAAAATTACAAAAAT-GCTCTTATAGG-TATACCTTCGACATGAAAGTATCCCA
190 GACTTGATTTTAAAAATTACAAAAATATC-CCTAT-GGTTATACCGTCGACATGAAAGTATCCCA
**
1388748 ATAACCCTAAAGACCTTAAAAAAAGTGAACCTAT
253 ATAACCCTAAAGACCTTAAAAAAAGCAAACCTAT
* * *
1388782 GCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAGTTAGGACTCAATTTTAGAAATTA
1 GCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAATTAGGACTCGATTCTAGAAATTA
* *
1388847 CAAAAATACTCTTAGGGGATACCTTCGACTT
66 CAAAAATACCCTTAAGGGATACCTTCGACTT
1388878 AGAAGTGTTT
Statistics
Matches: 334, Mismatches: 41, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
289 100 0.30
290 21 0.06
291 72 0.22
292 26 0.08
293 110 0.33
294 5 0.01
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (286 bp):
GCCTAATACGTACCCTCGGCATAGAAGTGACCCGATGACAAATTAGGACTCGATTCTAGAAATTA
CAAAAATACCCTTAAGGGATACCTTCGACTTGAAAATATCTAGTAACCTAAAAGACTTAAAAAAA
AAAGCAAACCTACGCCTAATACGTACCCTCGACATAGAAATGATCTAATAACAAATTAGGACTTG
ATTTTAAAAATTACAAAAATATCCCTATGGTTATACCGTCGACATGAAAGTATCCCAATAACCCT
AAAGACCTTAAAAAAAGCAAACCTAT
Found at i:1390421 original size:80 final size:81
Alignment explanation
Indices: 1390252--1390610 Score: 404
Period size: 80 Copynumber: 4.5 Consensus size: 81
1390242 AAACGAATAG
* * * * * *
1390252 AAGGGTTGACTAGGGCAAAA-CTGATAAAGTTATCCAATTAAAAGGTTAGTCAAGGCGAAATCGA
1 AAGGGTTGACCAGGGCAAAATC-GATAAAGTCAACCAATTAGAAGGTTAGCCAAGGCAAAATCGA
* *
1390316 TAAAGCCAACGGGTTAA
65 TAAAGCCAACAGATTAA
* * * * *
1390333 AAAGGTTGACCAGGGCAAAATTGATAAAGTCTACCAATTGGAA-GTTAGCCAAGGCGAAATCGAT
1 AAGGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTAGAAGGTTAGCCAAGGCAAAATCGAT
* * *
1390397 AAAGCTAATAGATTAT
66 AAAGCCAACAGATTAA
* * ** * * *
1390413 AAGGGTTGACCAAGGAAAAATCGATAAAGTCAATTAATTAGAAGGTTGGCTAGGGCAAAATCGAT
1 AAGGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTAGAAGGTTAGCCAAGGCAAAATCGAT
1390478 AAAGCCAACAGATTAA
66 AAAGCCAACAGATTAA
* * *
1390494 AAGGGTTGATCAGGGC-AAATCGATAAAGTCAACCAATTGGAAGGTTGGCCAAGGCAAAATCGAT
1 AAGGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTAGAAGGTTAGCCAAGGCAAAATCGAT
*
1390558 AAAGCTAACAGATTAGA
66 AAAGCCAACAGATTA-A
*
1390575 AA-GGTTGACCAAGGCAAAA-CAGATAAAGTCAACCAA
1 AAGGGTTGACCAGGGCAAAATC-GATAAAGTCAACCAA
1390611 GGATGAAAAG
Statistics
Matches: 233, Mismatches: 40, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
80 135 0.58
81 98 0.42
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (81 bp):
AAGGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTAGAAGGTTAGCCAAGGCAAAATCGAT
AAAGCCAACAGATTAA
Found at i:1390434 original size:41 final size:40
Alignment explanation
Indices: 1390302--1390602 Score: 233
Period size: 41 Copynumber: 7.5 Consensus size: 40
1390292 AAAGGTTAGT
* * * * *
1390302 CAAGGCGAAATCGATAAAGCCAACGGGTTAAAAAGGTTGAC
1 CAAGGCAAAATCGATAAAGCTAACAGATT-AGAAGGTTGAC
* * * *
1390343 CAGGGCAAAATTGATAAAGTCTACCA-ATTGGAA-GTT-AGC
1 CAAGGCAAAATCGATAAAG-CTAACAGATTAGAAGGTTGA-C
* * *
1390382 CAAGGCGAAATCGATAAAGCTAATAGATTATAAGGGTTGAC
1 CAAGGCAAAATCGATAAAGCTAACAGATTAGAA-GGTTGAC
* * *
1390423 CAAGGAAAAATCGATAAAG-TCAATTA-ATTAGAAGGTTGGC
1 CAAGGCAAAATCGATAAAGCT-AA-CAGATTAGAAGGTTGAC
* * * * *
1390463 TAGGGCAAAATCGATAAAGCCAACAGATTAAAAGGGTTGAT
1 CAAGGCAAAATCGATAAAGCTAACAGATTAGAA-GGTTGAC
* * *
1390504 CAGGGC-AAATCGATAAAG-TCAACCA-ATTGGAAGGTTGGC
1 CAAGGCAAAATCGATAAAGCT-AA-CAGATTAGAAGGTTGAC
1390543 CAAGGCAAAATCGATAAAGCTAACAGATTAGAAAGGTTGAC
1 CAAGGCAAAATCGATAAAGCTAACAGATTAG-AAGGTTGAC
1390584 CAAGGCAAAA-CAGATAAAG
1 CAAGGCAAAATC-GATAAAG
1390603 TCAACCAAGG
Statistics
Matches: 205, Mismatches: 37, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
38 5 0.02
39 38 0.19
40 71 0.35
41 85 0.41
42 6 0.03
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (40 bp):
CAAGGCAAAATCGATAAAGCTAACAGATTAGAAGGTTGAC
Found at i:1390473 original size:40 final size:39
Alignment explanation
Indices: 1390249--1390607 Score: 167
Period size: 41 Copynumber: 8.9 Consensus size: 39
1390239 GTCAAACGAA
* * *
1390249 TAGAAGGGTTGACTAGGGCAAAA-CTGATAAAGTTATCCAAT
1 TAGAA-GGTTGGCTAGGGCAAAATC-GATAAAGTCA-ACAAT
* * * * * **
1390290 TAAAAGGTTAG-TCAAGGCGAAATCGATAAAGCCAACGGGT
1 TAGAAGGTTGGCT-AGGGCAAAATCGATAAAGTCAAC-AAT
* * * * *
1390330 TAAAAAGGTTGACCAGGGCAAAATTGATAAAGTCTACCAAT
1 T-AGAAGGTTGGCTAGGGCAAAATCGATAAAGTC-AACAAT
* * * * * *
1390371 TGGAA-GTTAGCCAAGGCGAAATCGATAAAG-CTAATAGAT
1 TAGAAGGTTGGCTAGGGCAAAATCGATAAAGTC-AACA-AT
* * * * * *
1390410 TATAAGGGTTGACCAAGGAAAAATCGATAAAGTCAATTAAT
1 TAGAA-GGTTGGCTAGGGCAAAATCGATAAAGTCAA-CAAT
*
1390451 TAGAAGGTTGGCTAGGGCAAAATCGATAAAGCCAACAGAT
1 TAGAAGGTTGGCTAGGGCAAAATCGATAAAGTCAACA-AT
* *
1390491 TAAAAGGGTT-GATCAGGGC-AAATCGATAAAGTCAACCAAT
1 TAGAA-GGTTGGCT-AGGGCAAAATCGATAAAGTCAA-CAAT
* * *
1390531 TGGAAGGTTGGCCAAGGCAAAATCGATAAAG-CTAACAGAT
1 TAGAAGGTTGGCTAGGGCAAAATCGATAAAGTC-AACA-AT
* * *
1390571 TAGAAAGGTTGACCAAGGCAAAA-CAGATAAAGTCAAC
1 TAG-AAGGTTGGCTAGGGCAAAATC-GATAAAGTCAAC
1390608 CAAGGATGAA
Statistics
Matches: 244, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
38 4 0.02
39 39 0.16
40 96 0.39
41 99 0.41
42 6 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (39 bp):
TAGAAGGTTGGCTAGGGCAAAATCGATAAAGTCAACAAT
Found at i:1390547 original size:161 final size:161
Alignment explanation
Indices: 1390309--1390606 Score: 456
Period size: 161 Copynumber: 1.9 Consensus size: 161
1390299 AGTCAAGGCG
* * * *
1390309 AAATCGATAAAGCCAACGGGTTAAAAAGGTTGACCAGGGCAAAATTGATAAAGTCTACCAATTGG
1 AAATCGATAAAGCCAACAGATTAAAAAGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTGG
* * * *
1390374 AAGTTAGCCAAGGCGAAATCGATAAAGCTAATAGATTATAAGGGTTGACCAAGGAAAAATC-GAT
66 AAGTTAGCCAAGGCAAAATCGATAAAGCTAACAGATTAGAAAGGTTGACCAAGGAAAAA-CAGAT
1390438 AAAGTCAATTAATTAGAAGGTTGGCTAGGGCA
130 AAAGTCAATTAATTAGAAGGTTGGCTAGGGCA
* *
1390470 AAATCGATAAAGCCAACAGATTAAAAGGGTTGATCAGGGC-AAATCGATAAAGTCAACCAATTGG
1 AAATCGATAAAGCCAACAGATTAAAAAGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTGG
* *
1390534 AAGGTTGGCCAAGGCAAAATCGATAAAGCTAACAGATTAGAAAGGTTGACCAAGGCAAAACAGAT
66 AA-GTTAGCCAAGGCAAAATCGATAAAGCTAACAGATTAGAAAGGTTGACCAAGGAAAAACAGAT
1390599 AAAGTCAA
130 AAAGTCAA
1390607 CCAAGGATGA
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 25 0.20
161 98 0.80
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.19
Consensus pattern (161 bp):
AAATCGATAAAGCCAACAGATTAAAAAGGTTGACCAGGGCAAAATCGATAAAGTCAACCAATTGG
AAGTTAGCCAAGGCAAAATCGATAAAGCTAACAGATTAGAAAGGTTGACCAAGGAAAAACAGATA
AAGTCAATTAATTAGAAGGTTGGCTAGGGCA
Found at i:1390702 original size:35 final size:35
Alignment explanation
Indices: 1390663--1390983 Score: 324
Period size: 35 Copynumber: 9.2 Consensus size: 35
1390653 AATGAGGGTA
* * *
1390663 GAAAGAGTTTAACTAGATACAGTCAAATGATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
* ** * **
1390698 GAAAGAGTTTGACCAAATACAACCAAATGGCGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
* * * *
1390733 GGAAGAGTTTAACTAGATACAGTCAAACAATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
*
1390768 GAAAGAGTTTGACCAGATATAGTCAAACGATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
* * *
1390803 AAAAGCA-TTTGACCAGATATAGCCAAACGATGATG
1 GAAAG-AGTTTGACCAGATACAGTCAAACGATGATG
* * * *
1390838 GAAATAGTTTAACCAAATACAGTCAAACGATGATA
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
* * * *
1390873 GAAATAGTTTGACCAGATATAGCCAAACGATGGT-
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
* * * **
1390907 GAAAAAGTTTGACCAAATATAG-CTAAATAATGATG
1 GAAAGAGTTTGACCAGATACAGTC-AAACGATGATG
*
1390942 GAAAAAGTTTGACCAGATACAGTCAAACGATGATG
1 GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
1390977 GAAAGAG
1 GAAAGAG
1390984 CCAAATGATG
Statistics
Matches: 235, Mismatches: 46, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
33 1 0.00
34 28 0.12
35 204 0.87
36 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (35 bp):
GAAAGAGTTTGACCAGATACAGTCAAACGATGATG
Found at i:1390838 original size:105 final size:105
Alignment explanation
Indices: 1390663--1390983 Score: 403
Period size: 105 Copynumber: 3.1 Consensus size: 105
1390653 AATGAGGGTA
* * * * * * * *
1390663 GAAAGAGTTTAACTAGATACAGTCAAATGATGATGGAAAGAGTTTGACCAAATACAACCAAATGG
1 GAAAGAGTTTGACCAGATATAGTCAAACGATGATGAAAAGAGTTTGACCAAATATAGCCAAATGA
* * * * *
1390728 CGATGGGAAGAGTTTAACTAGATACAGTCAAACAATGATG
66 TGATGGAAAAAGTTTAACCAGATACAGTCAAACGATGATG
* *
1390768 GAAAGAGTTTGACCAGATATAGTCAAACGATGATGAAAAGCA-TTTGACCAGATATAGCCAAACG
1 GAAAGAGTTTGACCAGATATAGTCAAACGATGATGAAAAG-AGTTTGACCAAATATAGCCAAATG
* * *
1390832 ATGATGGAAATAGTTTAACCAAATACAGTCAAACGATGATA
65 ATGATGGAAAAAGTTTAACCAGATACAGTCAAACGATGATG
* * * * *
1390873 GAAATAGTTTGACCAGATATAGCCAAACGATGGTGAAAA-AGTTTGACCAAATATAGCTAAATAA
1 GAAAGAGTTTGACCAGATATAGTCAAACGATGATGAAAAGAGTTTGACCAAATATAGCCAAATGA
*
1390937 TGATGGAAAAAGTTTGACCAGATACAGTCAAACGATGATG
66 TGATGGAAAAAGTTTAACCAGATACAGTCAAACGATGATG
1390977 GAAAGAG
1 GAAAGAG
1390984 CCAAATGATG
Statistics
Matches: 185, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
103 1 0.01
104 61 0.33
105 122 0.66
106 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (105 bp):
GAAAGAGTTTGACCAGATATAGTCAAACGATGATGAAAAGAGTTTGACCAAATATAGCCAAATGA
TGATGGAAAAAGTTTAACCAGATACAGTCAAACGATGATG
Found at i:1391035 original size:54 final size:52
Alignment explanation
Indices: 1390935--1391036 Score: 141
Period size: 54 Copynumber: 1.9 Consensus size: 52
1390925 ATAGCTAAAT
* * **
1390935 AATGATGGAAAAAGTTTGACCAGATACAGTCAAACGATGATGGAAAGAGCCA
1 AATGATGCAAAAAGTTTGACCAGATACAGCCAAACGATGACAGAAAGAGCCA
*
1390987 AATGATGACAAAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGA
1 AATGATG-CAAAA-AGTTTGACCAGATACAGCCAAACGATGACAGAAAGA
1391037 TTTTGACTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 7 0.16
53 4 0.09
54 32 0.74
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.17
Consensus pattern (52 bp):
AATGATGCAAAAAGTTTGACCAGATACAGCCAAACGATGACAGAAAGAGCCA
Found at i:1391043 original size:35 final size:35
Alignment explanation
Indices: 1390982--1391291 Score: 228
Period size: 35 Copynumber: 9.1 Consensus size: 35
1390972 TGATGGAAAG
1390982 AGCCAAATGATGACA-AAAGAGTTTGACCAGATAC
1 AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
* * *
1391016 AGCCAAATGATGACAGAAAGATTTTGACTAGATAT
1 AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
* *
1391051 AGCCAAATAATGA-TGAAAAGAGTTTGACCAGATAC
1 AGCCAAATGATGACAG-AAAGAGTTTGACCAGATAC
* * *
1391086 AGTCGAACGAT----G--AGAGTTTGACCAGATAC
1 AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
** * *
1391115 AGCCAAATGATGATGGAAAGTGTTTGACTAGATAC
1 AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
* * * * * **
1391150 AGCCAAATAATGAC-GAAAAAAATTTGGCTAGATGT
1 AGCCAAATGATGACAG-AAAGAGTTTGACCAGATAC
* * * *
1391185 AGCTAAACGATGA-TGAAAGGAGTTTGATCAGATAC
1 AGCCAAATGATGACAGAAA-GAGTTTGACCAGATAC
* * * *
1391220 AGCCAAACGATGACAAAAAGAGTTTGACTAGATGC
1 AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
* * * *
1391255 AGCCAAACGATGAC-GAAAAACATTTAACCAGATAC
1 AGCCAAATGATGACAGAAAGA-GTTTGACCAGATAC
1391290 AG
1 AG
1391292 TCAGACAATG
Statistics
Matches: 216, Mismatches: 47, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
29 25 0.12
32 1 0.00
33 1 0.00
34 24 0.11
35 162 0.75
36 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (35 bp):
AGCCAAATGATGACAGAAAGAGTTTGACCAGATAC
Found at i:1391049 original size:89 final size:88
Alignment explanation
Indices: 1390908--1391072 Score: 195
Period size: 89 Copynumber: 1.9 Consensus size: 88
1390898 AACGATGGTG
* * ** * *
1390908 AAAAAGTTTGACCAAATATAGCTAAATAATGATGGAAAAAGTTTGACCAGATACAGTCAAACGAT
1 AAAAAGTTTGACCAAATACAGCCAAATAATGACAGAAAAAGTTTGACCAGATACAGCCAAACAAT
*
1390973 GATGGAAAGAGCCAAATGATGAC
66 GATGAAAAGAGCCAAATGATGAC
* * * * * * *
1390996 AAAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGATTTTGACTAGATATAGCCAAATAA
1 AAAA-AGTTTGACCAAATACAGCCAAATAATGACAGAAAAAGTTTGACCAGATACAGCCAAACAA
1391061 TGATGAAAAGAG
65 TGATGAAAAGAG
1391073 TTTGACCAGA
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
88 4 0.06
89 58 0.94
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (88 bp):
AAAAAGTTTGACCAAATACAGCCAAATAATGACAGAAAAAGTTTGACCAGATACAGCCAAACAAT
GATGAAAAGAGCCAAATGATGAC
Found at i:1391098 original size:70 final size:69
Alignment explanation
Indices: 1390982--1391291 Score: 292
Period size: 70 Copynumber: 4.5 Consensus size: 69
1390972 TGATGGAAAG
* *
1390982 AGCCAAATGATGA-CAAAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGATTTTGACTA
1 AGCCAAATGATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGACAGAAAGA-TTTGACTA
*
1391046 GATAT
65 GATAC
* * * *
1391051 AGCCAAATAATGATGAAAAGAGTTTGACCAGATACAGTCGAACGATG--AG--AG-TTTGACCAG
1 AGCCAAATGATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGACAGAAAGATTTGACTAG
1391111 ATAC
66 ATAC
* * * ** * * *
1391115 AGCCAAATGATGATGGAAAGTGTTTGACTAGATACAGCCAAATAATGACGAAAAAAATTTGGCTA
1 AGCCAAATGATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGAC-AGAAAGATTTGACTA
**
1391180 GATGT
65 GATAC
* * * * *
1391185 AGCTAAACGATGATGAAAGGAGTTTGATCAGATACAGCCAAACGATGACAAAAAGAGTTTGACTA
1 AGCCAAATGATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGACAGAAAGA-TTTGACTA
*
1391250 GATGC
65 GATAC
* * * *
1391255 AGCCAAACGATGACGAAAA-ACATTTAACCAGATACAG
1 AGCCAAATGATGATGAAAAGA-GTTTGACCAGATACAG
1391292 TCAGACAATG
Statistics
Matches: 193, Mismatches: 39, Indels: 17
0.78 0.16 0.07
Matches are distributed among these distances:
64 50 0.26
66 2 0.01
67 1 0.01
68 2 0.01
69 20 0.10
70 118 0.61
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (69 bp):
AGCCAAATGATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGACAGAAAGATTTGACTAG
ATAC
Found at i:1391163 original size:134 final size:133
Alignment explanation
Indices: 1390982--1391232 Score: 333
Period size: 134 Copynumber: 1.9 Consensus size: 133
1390972 TGATGGAAAG
* * *
1390982 AGCCAAATGATGACAAAAGAGTTTGACCAGATACAGCCAAATGATGAC-AGAAAGATTTTGACTA
1 AGCCAAATGATGACAAAAGAGTTTGACCAGATACAGCCAAATAATGACGA-AAAAAATTTGACTA
* * *
1391046 GATATAGCCAAATAATGATGAAAAGAGTTTGACCAGATACAGTCGAACGATGAGAGTTTGACCAG
65 GATATAGCCAAACAATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGAGAGTTTGACCAG
1391111 ATAC
130 ATAC
** * * *
1391115 AGCCAAATGATGATGGAAAGTGTTTGACTAGATACAGCCAAATAATGACGAAAAAAATTTGGCTA
1 AGCCAAATGATGA-CAAAAGAGTTTGACCAGATACAGCCAAATAATGACGAAAAAAATTTGACTA
* * * * *
1391180 GATGTAGCTAAACGATGATGAAAGGAGTTTGATCAGATACAGCCAAACGATGA
65 GATATAGCCAAACAATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGA
1391233 CAAAAAGAGT
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
133 13 0.13
134 86 0.86
135 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (133 bp):
AGCCAAATGATGACAAAAGAGTTTGACCAGATACAGCCAAATAATGACGAAAAAAATTTGACTAG
ATATAGCCAAACAATGATGAAAAGAGTTTGACCAGATACAGCCAAACGATGAGAGTTTGACCAGA
TAC
Found at i:1391194 original size:99 final size:101
Alignment explanation
Indices: 1390998--1391302 Score: 332
Period size: 99 Copynumber: 3.0 Consensus size: 101
1390988 ATGATGACAA
*
1390998 AAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGAT-TTTGACTAGATATAGCCAAATAAT
1 AAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAG-TGTTTGACTAGATACAGCCAAATAAT
* * * *
1391062 GATGAAAAGAGTTTGACCAGATACAGTCGAAC-GATG
65 GACGAAAAAAATTTGACCAGATACAGTCAAACAGATG
**
1391098 -AGAGTTTGACCAGATACAGCCAAATGATGATGGAAAGTGTTTGACTAGATACAGCCAAATAATG
1 AAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGTGTTTGACTAGATACAGCCAAATAATG
* * **
1391162 ACGAAAAAAATTTGGCTAGATGTAG-CTAAACGATGATG
66 ACGAAAAAAATTTGACCAGATACAGTC-AAAC-A-GATG
* * * * * **
1391200 AAAGGAGTTTGATCAGATACAGCCAAACGATGACAAAAAGAGTTTGACTAGATGCAGCCAAACGA
1 -AA-GAGTTTGACCAGATACAGCCAAATGATGACAGAAAGTGTTTGACTAGATACAGCCAAATAA
* * *
1391265 TGACGAAAAACATTTAACCAGATACAGTCAGACA-ATG
64 TGACGAAAAAAATTTGACCAGATACAGTCAAACAGATG
1391302 A
1 A
1391303 TGAAATGAGT
Statistics
Matches: 169, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
98 2 0.01
99 80 0.47
101 1 0.01
102 7 0.04
104 2 0.01
105 76 0.45
106 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (101 bp):
AAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGTGTTTGACTAGATACAGCCAAATAATG
ACGAAAAAAATTTGACCAGATACAGTCAAACAGATG
Found at i:1391303 original size:105 final size:103
Alignment explanation
Indices: 1390997--1391314 Score: 351
Period size: 105 Copynumber: 3.1 Consensus size: 103
1390987 AATGATGACA
* *
1390997 AAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGATTTTGACTAGATATAGCCAAATAAT
1 AAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGAGTTTGACTAGATACAGCCAAATAAT
* * *
1391062 GATGAAAAGAGTTTGACCAGATACAGTC-G--AACGATG
66 GACGAAAA-AATTTGACCAGATACAGTCAGACAATGATG
** *
1391098 --AGAGTTTGACCAGATACAGCCAAATGATGATGGAAAGTGTTTGACTAGATACAGCCAAATAAT
1 AAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGAGTTTGACTAGATACAGCCAAATAAT
* * ** * *
1391161 GACGAAAAAAATTTGGCTAGATGTAG-CTAAACGATGATG
66 GACG-AAAAAATTTGACCAGATACAGTC-AGACAATGATG
* * * * **
1391200 AAAGGAGTTTGATCAGATACAGCCAAACGATGACAAAAAGAGTTTGACTAGATGCAGCCAAACGA
1 AAA-GAGTTTGACCAGATACAGCCAAATGATGACAGAAAGAGTTTGACTAGATACAGCCAAATAA
*
1391265 TGACGAAAAACATTTAACCAGATACAGTCAGACAATGATG
65 TGACGAAAAA-ATTTGACCAGATACAGTCAGACAATGATG
1391305 AAATGAGTTT
1 AAA-GAGTTT
1391315 AATCAATGAC
Statistics
Matches: 176, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
98 1 0.01
99 73 0.41
100 4 0.02
102 5 0.03
104 6 0.03
105 86 0.49
106 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (103 bp):
AAAGAGTTTGACCAGATACAGCCAAATGATGACAGAAAGAGTTTGACTAGATACAGCCAAATAAT
GACGAAAAAATTTGACCAGATACAGTCAGACAATGATG
Found at i:1391668 original size:89 final size:92
Alignment explanation
Indices: 1391463--1391676 Score: 260
Period size: 89 Copynumber: 2.3 Consensus size: 92
1391453 TTTGTGGTCA
* * *
1391463 TGTGATGCATCAATACCATCTAGTGGTTGGTTAAAGAAAGGGATATGATTGGGAATGAGTGATTG
1 TGTGATGCATCAATACCATCTAGTGGTTGGATAAAG--AGGAATATGATTAGGAATGAGTGA-TG
* *
1391528 GGATACCCTTGCCCTAAGGAAATAAGGCTT
63 GGATACCCTTACCCAAAGGAAATAAGGCTT
* *
1391558 TGTGATGCATCAACACCATCTAGTGGTTGGATAAAG-GGAATATGATTAGGAAT-A-TG-TGGGC
1 TGTGATGCATCAATACCATCTAGTGGTTGGATAAAGAGGAATATGATTAGGAATGAGTGATGGGA
*
1391619 TGCACCTTACCCAAAGGAAATTAA-GCTT
66 TAC-CCTTACCCAAAGGAAA-TAAGGCTT
*
1391647 TGTGATGCATCAATACTATCTAGT-GTTGGA
1 TGTGATGCATCAATACCATCTAGTGGTTGGA
1391677 GGGAAAAAGA
Statistics
Matches: 107, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
88 12 0.11
89 40 0.37
90 5 0.05
91 1 0.01
92 15 0.14
95 34 0.32
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (92 bp):
TGTGATGCATCAATACCATCTAGTGGTTGGATAAAGAGGAATATGATTAGGAATGAGTGATGGGA
TACCCTTACCCAAAGGAAATAAGGCTT
Found at i:1391694 original size:89 final size:89
Alignment explanation
Indices: 1391463--1391705 Score: 217
Period size: 89 Copynumber: 2.7 Consensus size: 89
1391453 TTTGTGGTCA
* * * *
1391463 TGTGATGCATCAATACCATCTAGTGGTTGGTTA-AAGAAAGGGATATGATTGGGAATGAGTGATT
1 TGTGATGCATCAACACCATCTAGTGGTTGG--AGAA-AAA-GAATAAGATTAGGAAT-A-TG--T
* * * *
1391527 GGGATAC-CCTTGCCCTAAGGAAATAAGGCTT
58 GGGCTGCACCTTACCCAAAGGAAATAAGGCTT
* ** *
1391558 TGTGATGCATCAACACCATCTAGTGGTTGGATAAAGGGAATATGATTAGGAATATGTGGGCTGCA
1 TGTGATGCATCAACACCATCTAGTGGTTGGAGAAAAAGAATAAGATTAGGAATATGTGGGCTGCA
1391623 CCTTACCCAAAGGAAATTAA-GCTT
66 CCTTACCCAAAGGAAA-TAAGGCTT
* * *
1391647 TGTGATGCATCAATACTATCTAGT-GTTGGAGGGAAAAAG-ATAAGATTAGGACTATGTGG
1 TGTGATGCATCAACACCATCTAGTGGTTGGA--GAAAAAGAATAAGATTAGGAATATGTGG
1391706 CTAGGAGTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
88 12 0.09
89 58 0.46
90 9 0.07
91 1 0.01
92 14 0.11
93 2 0.02
94 2 0.02
95 29 0.23
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (89 bp):
TGTGATGCATCAACACCATCTAGTGGTTGGAGAAAAAGAATAAGATTAGGAATATGTGGGCTGCA
CCTTACCCAAAGGAAATAAGGCTT
Found at i:1392403 original size:89 final size:88
Alignment explanation
Indices: 1392273--1392498 Score: 233
Period size: 89 Copynumber: 2.6 Consensus size: 88
1392263 CAAATGCACA
* * * * * *
1392273 TGAAATGATGTAAATGCAAACATCAAT-AAAATGATAGATGCATATGAGATGA-TGCAAATACCA
1 TGAAATGATGCAAATGCAAGCATCAATAAAAAGGA-AAATGCATATGAAAT-ATTGCAAACACCA
* ** *
1392336 GTGTCATCTAATGGTGCAGATGT-GTG
64 ATGTCATCTAA-AATGCAGAAGTAG-G
* * *
1392362 TGAAATAATGCAAATGCAAGCATCAATAAAAAGGAAAATGCATATAAAATATTGCAAACACTAAT
1 TGAAATGATGCAAATGCAAGCATCAATAAAAAGGAAAATGCATATGAAATATTGCAAACACCAAT
*
1392427 GTTATCTAAAATGCAGAAGTAGG
66 GTCATCTAAAATGCAGAAGTAGG
* * * *
1392450 TGAAACGATGCAAATGCAAGCATTAATAAAAAGGCAAATACATATGAAA
1 TGAAATGATGCAAATGCAAGCATCAATAAAAAGGAAAATGCATATGAAA
1392499 CAACGTAAAT
Statistics
Matches: 114, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
88 53 0.46
89 55 0.48
90 6 0.05
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (88 bp):
TGAAATGATGCAAATGCAAGCATCAATAAAAAGGAAAATGCATATGAAATATTGCAAACACCAAT
GTCATCTAAAATGCAGAAGTAGG
Found at i:1395636 original size:40 final size:40
Alignment explanation
Indices: 1395591--1395671 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
1395581 ATGATAGCAT
*
1395591 TAGTTTCATCCTCGTTTGATACTTGGAACAGATGACAACA
1 TAGTTTCATCCTCGTTTGATACCTGGAACAGATGACAACA
*
1395631 TAGTTTCATCCTTGTTTGATACCTGGAACAGATGACAACA
1 TAGTTTCATCCTCGTTTGATACCTGGAACAGATGACAACA
1395671 T
1 T
1395672 CTTGTAAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (40 bp):
TAGTTTCATCCTCGTTTGATACCTGGAACAGATGACAACA
Found at i:1395954 original size:16 final size:16
Alignment explanation
Indices: 1395933--1395966 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1395923 AATTGGGTAT
1395933 GGTCTTAACTAAGTGA
1 GGTCTTAACTAAGTGA
1395949 GGTCTTAACTAAGTGA
1 GGTCTTAACTAAGTGA
1395965 GG
1 GG
1395967 CCTTTACGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (16 bp):
GGTCTTAACTAAGTGA
Found at i:1398357 original size:141 final size:141
Alignment explanation
Indices: 1398076--1398632 Score: 685
Period size: 141 Copynumber: 3.9 Consensus size: 141
1398066 AAGTTATAAA
* * * *
1398076 TTTCGAAAATTTCATTTCATACCTTAATGGAGAACCGAAAAGATTCGAAAAGTTTTGAAGACT-T
1 TTTCAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTT-AA-A-TAT
* * * * * * ** *
1398140 TTTTATACCCAT-ACGAAAAACTATAAAAATATTAGAAATCTTGAAAAATTAAAATAATAATTTT
63 TTCTATATCC-TCACGGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAAATAATAATTTT
*
1398204 TATTTAAGTTTTTAT
127 TATTTAATTTTTTAT
*
1398219 TTTCAAAAAATTCATTTCGTACCTTAATGGAGAATCGAAAAGATACGAAAAGTTTTAAATATTTC
1 TTTCAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTAAATATTTC
* *
1398284 TATATCCTCACGGATACTCATGGGAATAATAGAAATCTTGAAAAATTAAAATAATAATTTTTATT
66 TATATCCTCACGGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAAATAATAATTTTTATT
1398349 TAATTTTTTAT
131 TAATTTTTTAT
* * ** ** ***
1398360 TTTTAAAAAATTTATTTCGTATTTTAATATAGAATTAAAAAGATACGAAAAGTTTTAAATATTT-
1 TTTCAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTAAATATTTC
* * * * * *
1398424 T-TATGCCTTATGGATACCCATGGGAACAATAGAAATCTTTAAAAATTAAGATAATAATTTTTAT
66 TATAT-CCTCACGGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAAATAATAATTTTTAT
1398488 TTAATTTTTTTAT
130 TTAA-TTTTTTAT
* *
1398501 TTTCAAAAAATTCATTTCGTACTTTAATGGAGAACCGAAAAGATACGAGAAGTTTTAAATATTTC
1 TTTCAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTAAATATTTC
*
1398566 TATA--CTCACATGGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAGATAATAATTTTTA
66 TATATCCTCAC--GGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAAATAATAATTTTTA
1398629 TTTA
129 TTTA
1398633 GTGATAAAAT
Statistics
Matches: 361, Mismatches: 45, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
139 3 0.01
140 63 0.17
141 186 0.52
142 56 0.16
143 53 0.15
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (141 bp):
TTTCAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTAAATATTTC
TATATCCTCACGGATACCCATGGAAATAATAGAAATCTTGAAAAATTAAAATAATAATTTTTATT
TAATTTTTTAT
Found at i:1399648 original size:20 final size:21
Alignment explanation
Indices: 1399609--1399652 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1399599 TTAAGTATAG
*
1399609 ATGTTTTTCAAGCATAAAAATA
1 ATGTTTTTAAAG-ATAAAAATA
1399631 ATGTTTTTAAAG-TAAAAATA
1 ATGTTTTTAAAGATAAAAATA
1399651 AT
1 AT
1399653 CCACAGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTTTTTAAAGATAAAAATA
Found at i:1399815 original size:19 final size:20
Alignment explanation
Indices: 1399768--1399822 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1399758 ACACCCAGAT
1399768 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCTTA
* *
1399788 GTATCGATACATGTT-CTTG
1 GTATCGATACATATTGCTTA
* *
1399807 GTATTGATACACATTG
1 GTATCGATACATATTG
1399823 AATTGTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:1400373 original size:32 final size:29
Alignment explanation
Indices: 1400332--1400486 Score: 121
Period size: 32 Copynumber: 4.9 Consensus size: 29
1400322 TTATTAAGAG
1400332 GTTCTATCTTAGCCTTGAAAGATAGTGTAGAA
1 GTTCTATCTTAGCCTTGAAAGATAG-G--GAA
*
1400364 GTTCTATCTTAGCCTTTGTAAAAGATAGGGAG
1 GTTCTATCTTAGCC-TTG--AAAGATAGGGAA
* * **
1400396 GTTTTGTCTTAGCCTACAAAAGATAGGGAGAAAA
1 GTTCTATCTTAGCCT-TGAAAGATA-GG-G--AA
* *
1400430 GTTCTATCTTAGCCCGTGAAAAGATAGGGAG
1 GTTCTATCTTAG-CCTTG-AAAGATAGGGAA
1400461 GTCTCTATCTTAGCCTTGAAAGATAG
1 GT-TCTATCTTAGCCTTGAAAGATAG
1400487 TATTGTAAGG
Statistics
Matches: 99, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
30 15 0.15
31 10 0.10
32 39 0.39
33 4 0.04
34 14 0.14
35 17 0.17
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (29 bp):
GTTCTATCTTAGCCTTGAAAGATAGGGAA
Done.