Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 17 of 356
Found at i:5963139 original size:20 final size:20
Alignment explanation
Indices: 5963101--5963140 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5963091 CGTAAAATGA
**
5963101 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGACTTACT
*
5963121 TTTCTGTAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
5963141 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:5972836 original size:65 final size:65
Alignment explanation
Indices: 5972757--5972888 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
5972747 AAAATACAAT
5972757 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
1 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
5972822 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
1 GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
5972887 GC
1 GC
5972889 ACCATTGAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (65 bp):
GCTTGCTTAATTAATATGTTTCAATGGTAGTGTGCTCCGAAATCCACTGTTCCCAACAAGGATTA
Found at i:5975281 original size:13 final size:14
Alignment explanation
Indices: 5975248--5975287 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
5975238 ATTACTTATG
5975248 TATAAAAT-TATAT
1 TATAAAATATATAT
5975261 TA-AAAATATAT-T
1 TATAAAATATATAT
*
5975273 TATAAAATATTTAT
1 TATAAAATATATAT
5975287 T
1 T
5975288 CATTTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 8 0.35
13 13 0.57
14 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATAAAATATATAT
Found at i:5982397 original size:13 final size:13
Alignment explanation
Indices: 5982379--5982408 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5982369 CGGCTGAGGC
5982379 AGCCGTGTACATA
1 AGCCGTGTACATA
5982392 AGCCGTGTACATA
1 AGCCGTGTACATA
5982405 AGCC
1 AGCC
5982409 ATCCACCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (13 bp):
AGCCGTGTACATA
Found at i:5983418 original size:11 final size:14
Alignment explanation
Indices: 5983386--5983418 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5983376 TTGAAGAATG
5983386 ATATTATTGTAATT
1 ATATTATTGTAATT
5983400 ATATTATTGTAATT
1 ATATTATTGTAATT
5983414 ATATT
1 ATATT
5983419 TGTATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
ATATTATTGTAATT
Found at i:5991485 original size:10 final size:10
Alignment explanation
Indices: 5991472--5991537 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
5991462 AAAAAATTCA
5991472 AAAAATATAT
1 AAAAATATAT
5991482 AAAAATATAT
1 AAAAATATAT
* * *
5991492 AAATATTTTT
1 AAAAATATAT
*
5991502 AAAAAAATTAT
1 AAAAATA-TAT
5991513 AATAAAT-T-T
1 AA-AAATATAT
5991522 AAAAATATAT
1 AAAAATATAT
5991532 AAAAAT
1 AAAAAT
5991538 GAAAAATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 29 0.66
11 4 0.09
12 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATATAT
Found at i:5991542 original size:17 final size:18
Alignment explanation
Indices: 5991504--5991547 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5991494 ATATTTTTAA
*
5991504 AAAAATTATAATAAATTT
1 AAAAATTATAATAAATTG
5991522 AAAAATATATAA-AAA-TG
1 AAAAAT-TATAATAAATTG
5991539 AAAAATTAT
1 AAAAATTAT
5991548 TGTTGACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 7 0.29
18 9 0.38
19 5 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATTATAATAAATTG
Found at i:5991640 original size:17 final size:18
Alignment explanation
Indices: 5991601--5991638 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5991591 AATTAAATAT
5991601 TTTAAAAAATATAATAAA
1 TTTAAAAAATATAATAAA
*
5991619 TTTAAAATAA-ATATTAAA
1 TTTAAAA-AATATAATAAA
5991637 TT
1 TT
5991639 AATAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAAAAAATATAATAAA
Found at i:5992170 original size:21 final size:21
Alignment explanation
Indices: 5992109--5992173 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
5992099 TATAATTATA
*
5992109 TTTTTAAAATATTT-T-TTTT
1 TTTTTAAAATATTTATATATT
*
5992128 ATTTTTAAAATTTATTATTATATT
1 -TTTTTAAAATAT-TTA-TATATT
5992152 TTTTTAAAATATTTATATATT
1 TTTTTAAAATATTTATATATT
5992173 T
1 T
5992174 ATATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 11 0.29
21 9 0.24
22 3 0.08
23 12 0.32
24 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTAAAATATTTATATATT
Found at i:5998938 original size:6 final size:6
Alignment explanation
Indices: 5998927--5998956 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5998917 TAATTTTTTA
5998927 AATATT AATATT AATATT AATATT AATATT
1 AATATT AATATT AATATT AATATT AATATT
5998957 TTTGTGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATATT
Found at i:6012759 original size:15 final size:15
Alignment explanation
Indices: 6012741--6012794 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
6012731 TCCAAGACAG
6012741 AGAAACCCAGAATAA
1 AGAAACCCAGAATAA
*
6012756 AGAAATCCAGAATAA
1 AGAAACCCAGAATAA
* * *
6012771 AGAGATCCAGGATAA
1 AGAAACCCAGAATAA
6012786 AGAAACCCA
1 AGAAACCCA
6012795 AGATATGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.56, C:0.19, G:0.17, T:0.09
Consensus pattern (15 bp):
AGAAACCCAGAATAA
Found at i:6012799 original size:15 final size:15
Alignment explanation
Indices: 6012723--6012799 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
6012713 CAAGAAAACC
6012723 TAAAGAAATCCAAGA
1 TAAAGAAATCCAAGA
* * *
6012738 CAGAGAAA-CCCAGAA
1 TAAAGAAATCCAAG-A
6012753 TAAAGAAATCC-AGAA
1 TAAAGAAATCCAAG-A
* *
6012768 TAAAGAGATCCAGGA
1 TAAAGAAATCCAAGA
*
6012783 TAAAGAAACCCAAGA
1 TAAAGAAATCCAAGA
6012798 TA
1 TA
6012800 TGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
14 4 0.08
15 42 0.86
16 3 0.06
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.10
Consensus pattern (15 bp):
TAAAGAAATCCAAGA
Found at i:6015825 original size:93 final size:93
Alignment explanation
Indices: 6015719--6015889 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
6015709 GCCCATAAGT
* * *
6015719 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
6015784 CGAGTTCGGATGCCTAGTTACATTTCTC
66 CGAGTTCGGATGCCTAGTTACATTTCTC
*
6015812 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
6015877 CGAGTTCGGATGC
66 CGAGTTCGGATGC
6015890 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCTC
Found at i:6015886 original size:46 final size:45
Alignment explanation
Indices: 6015711--6015886 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 45
6015701 TGCAACCCGC
* *
6015711 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAC-TTTGCAT
* * *
6015757 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CTTTGCAT
* ***
6015803 ACATTTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGAC-TTTGCAT
*
6015850 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
6015887 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.65
47 36 0.33
48 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACTTTGCAT
Found at i:6017454 original size:67 final size:67
Alignment explanation
Indices: 6017308--6017442 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
6017298 TTGTACGTGA
6017308 AAATTGAACCAAATCAACATTCCATATATAAAAAGACATAAAATTAAATTTCATGGTATAACATT
1 AAATTGAACCAAATCAACATTCCATATATAAAAAGACATAAAATTAAATTTCATGGTATAACATT
6017373 GC
66 GC
6017375 AAATTGAACCAAATCAACATTCCATATATAAAAAGACATAAAATTAAATTTCATGGTATAACATT
1 AAATTGAACCAAATCAACATTCCATATATAAAAAGACATAAAATTAAATTTCATGGTATAACATT
6017440 GC
66 GC
6017442 A
1 A
6017443 TGTTGGACCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (67 bp):
AAATTGAACCAAATCAACATTCCATATATAAAAAGACATAAAATTAAATTTCATGGTATAACATT
GC
Found at i:6020163 original size:16 final size:16
Alignment explanation
Indices: 6020142--6020173 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6020132 TCAAATGATT
6020142 TAAATTTTCTTTTATG
1 TAAATTTTCTTTTATG
6020158 TAAATTTTCTTTTATG
1 TAAATTTTCTTTTATG
6020174 GCAGGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TAAATTTTCTTTTATG
Found at i:6021796 original size:11 final size:11
Alignment explanation
Indices: 6021782--6021839 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
6021772 TTGATGTTGA
*
6021782 TTTGTTATTGT
1 TTTGTTATTAT
* *
6021793 TTTGCTACTAT
1 TTTGTTATTAT
*
6021804 TTTGCTATTAT
1 TTTGTTATTAT
6021815 ATATTGTTATTAT
1 -T-TTGTTATTAT
*
6021828 TTTGTTGTTAT
1 TTTGTTATTAT
6021839 T
1 T
6021840 ATTTGGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 28 0.72
12 2 0.05
13 9 0.23
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (11 bp):
TTTGTTATTAT
Found at i:6022536 original size:25 final size:26
Alignment explanation
Indices: 6022507--6022562 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
6022497 TTAATTTAAT
*
6022507 TTATTAAAAATTATAAAAATATA-AG
1 TTATTAAAAATGATAAAAATATATAG
* *
6022532 TTATT-AAAATGATAAAATTATATAT
1 TTATTAAAAATGATAAAAATATATAG
6022557 TTATTA
1 TTATTA
6022563 TAGTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
TTATTAAAAATGATAAAAATATATAG
Found at i:6022546 original size:24 final size:25
Alignment explanation
Indices: 6022507--6022577 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
6022497 TTAATTTAAT
*
6022507 TTATTAAAAATTATAAAAATATA-AG
1 TTATT-AAAATGATAAAAATATATAG
* *
6022532 TTATTAAAATGATAAAATTATATAT
1 TTATTAAAATGATAAAAATATATAG
*
6022557 TTATT-ATA-G-TAAAAATATATA
1 TTATTAAAATGATAAAAATATATA
6022578 ATTTAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 11 0.28
23 1 0.03
24 17 0.43
25 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
TTATTAAAATGATAAAAATATATAG
Found at i:6023222 original size:31 final size:31
Alignment explanation
Indices: 6023184--6023246 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
6023174 AGAGGACACG
6023184 TGCTAATCTTAAGAGAGGATATGTGTTGACA
1 TGCTAATCTTAAGAGAGGATATGTGTTGACA
6023215 TGCTAATCTTAAGAGAGGATATGTGTTGACA
1 TGCTAATCTTAAGAGAGGATATGTGTTGACA
6023246 T
1 T
6023247 ACATAAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (31 bp):
TGCTAATCTTAAGAGAGGATATGTGTTGACA
Found at i:6039754 original size:14 final size:14
Alignment explanation
Indices: 6039730--6039767 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
6039720 AAAATATGAG
6039730 TTAATTATAAAAAT
1 TTAATTATAAAAAT
6039744 ATTAA-TATAAAAAT
1 -TTAATTATAAAAAT
6039758 TTAATTATAA
1 TTAATTATAA
6039768 GTAATTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTATAAAAAT
Found at i:6040473 original size:18 final size:19
Alignment explanation
Indices: 6040450--6040487 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6040440 AAATAATATC
6040450 ATATTTAAATATATT-TTT
1 ATATTTAAATATATTATTT
*
6040468 ATATTTATATATATTATTT
1 ATATTTAAATATATTATTT
6040487 A
1 A
6040488 CTTTCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTTAAATATATTATTT
Found at i:6053396 original size:132 final size:132
Alignment explanation
Indices: 6053159--6053409 Score: 344
Period size: 132 Copynumber: 1.9 Consensus size: 132
6053149 CTTTCCCACC
* * * *
6053159 GATTCGGATTTCACCTTGCTCGAATCATAATAGTGTACACCAGGCACAGTTTTTTCAGATTGCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * *
6053224 TGAACGAAAGGAGTTAGAACCCTTATGATCATCAATGGGATG-TTTGAAGGAAGATTTGCTTCTC
66 CGAACGAAAGGAATCAGAACCCTTATGATCATCAATGGGATGCTTTG-AGGAAGATTTGCTTCTC
6053288 ACT
130 ACT
* * *
6053291 GATTCAGATTTCACCTTACTCGAGTCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* ** *
6053356 CGAAGCG-ATGGAATCAGAAGTCTTATGATCATCGATGGGATGCTTTGAGGAAGA
66 CGAA-CGAAAGGAATCAGAACCCTTATGATCATCAATGGGATGCTTTGAGGAAGA
6053410 CTTGATTGCA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
132 97 0.94
133 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (132 bp):
GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
CGAACGAAAGGAATCAGAACCCTTATGATCATCAATGGGATGCTTTGAGGAAGATTTGCTTCTCA
CT
Found at i:6053582 original size:150 final size:150
Alignment explanation
Indices: 6053291--6053626 Score: 390
Period size: 150 Copynumber: 2.2 Consensus size: 150
6053281 GCTTCTCACT
* * * * *
6053291 GATTCAGATTTCACCTTACTCGAGTCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
* * *
6053356 CGAAGCGATGGAATCAGAAGTCTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGATTGCAG
66 CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGATTGCAG
* * *
6053421 TTGTCAGAATCTTTCCCACC
131 CTGCCAAAATCTTTCCCACC
* * *
6053441 GATTCGGATTTTACCTTACTAGAATCATAACAGTGTACACCAGACACA-GTTTGTTCGTATTCCA
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTT-TTCATATTCCA
* ** * * *
6053505 ATGAAGCAATGGAATTGGAACTCTTATGGTCATCAATGGGATG-TTTGAAGGAAGATTTGCTTGC
65 ACGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGATTG-
**
6053569 CA-CTGCCAAAATCTTTCCCGTC
128 CAGCTGCCAAAATCTTTCCCACC
* * * *
6053591 AATTCGGATTTCATCTTGCTTGAATCATAATAGTGT
1 GATTCGGATTTCACCTTACTAGAATCATAATAGTGT
6053627 TTTGCTATAT
Statistics
Matches: 155, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
149 8 0.05
150 145 0.94
151 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (150 bp):
GATTCGGATTTCACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGATTGCAG
CTGCCAAAATCTTTCCCACC
Found at i:6054814 original size:14 final size:13
Alignment explanation
Indices: 6054785--6054835 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
6054775 CTTAAACTCT
*
6054785 TTTCTTTTTCTT-
1 TTTCTTTTTTTTC
6054797 TTTCTTTTTTTTCC
1 TTTCTTTTTTTT-C
*
6054811 TTTCTTTCTTTTAC
1 TTTCTTT-TTTTTC
*
6054825 TTTATTTTTTT
1 TTTCTTTTTTT
6054836 GTTTCCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 11 0.33
13 4 0.12
14 14 0.42
15 4 0.12
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:6054819 original size:30 final size:31
Alignment explanation
Indices: 6054785--6054844 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6054775 CTTAAACTCT
*
6054785 TTTCTTTTTCTTT-TTCTTTTT-TTTCCTTTC
1 TTTCTTTTACTTTATT-TTTTTGTTTCCTTTC
6054815 TTTCTTTTACTTTATTTTTTTGTTTCCTTT
1 TTTCTTTTACTTTATTTTTTTGTTTCCTTT
6054845 TTGCTTTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (31 bp):
TTTCTTTTACTTTATTTTTTTGTTTCCTTTC
Found at i:6057204 original size:5 final size:5
Alignment explanation
Indices: 6057196--6057261 Score: 50
Period size: 5 Copynumber: 14.0 Consensus size: 5
6057186 AAATAAAAAT
* * * * *
6057196 TTAAG TTAAA TTAAA TTGAG TAAAA TT-AT TTAAA TTAAA TTAAA --AAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
*
6057243 TTAAA -TATA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA
6057262 ATTTTATTAC
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
3 3 0.07
4 6 0.13
5 37 0.80
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (5 bp):
TTAAA
Found at i:6057245 original size:22 final size:22
Alignment explanation
Indices: 6057184--6057262 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
6057174 TTAAATCGAA
* *
6057184 TAAAATAAAAATTTAAGTTAAAT
1 TAAATTAAAAAATTAA-TTAAAT
* *
6057207 TAAATTGAGTAAAATTATTTAAAT
1 TAAATT-A-AAAAATTAATTAAAT
* *
6057231 TAAATTAAAAAATTAAATATAT
1 TAAATTAAAAAATTAATTAAAT
6057253 TAAATTAAAA
1 TAAATTAAAA
6057263 TTTTATTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 21 0.46
23 6 0.13
24 13 0.28
25 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAATTAAAAAATTAATTAAAT
Found at i:6060119 original size:28 final size:29
Alignment explanation
Indices: 6060074--6060135 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
6060064 GTATTTTTGA
*
6060074 TAAAAAAGTGAAATTTAAATTTTGTAT-T
1 TAAAAAAGTGAAAATTAAATTTTGTATCT
* * *
6060102 TAAAAAATTTAAAATTAAATTTTTTATCT
1 TAAAAAAGTGAAAATTAAATTTTGTATCT
6060131 TAAAA
1 TAAAA
6060136 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (29 bp):
TAAAAAAGTGAAAATTAAATTTTGTATCT
Found at i:6060140 original size:21 final size:19
Alignment explanation
Indices: 6060110--6060169 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
6060100 TTTAAAAAAT
6060110 TTAAAA-TTAAATTTTTTA
1 TTAAAATTTAAATTTTTTA
*
6060128 TCTTAAAATTTAAATTTAATTA
1 --TTAAAATTTAAATTT-TTTA
6060150 TTAAAATTGTAAAGTTTTTT
1 TTAAAATT-TAAA-TTTTTT
6060170 TTTTAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 14 0.41
21 14 0.41
22 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAAATTTAAATTTTTTA
Found at i:6063245 original size:16 final size:17
Alignment explanation
Indices: 6063224--6063258 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6063214 TTTAAATTTT
6063224 TTAAAATAATTA-AAAA
1 TTAAAATAATTATAAAA
*
6063240 TTAAAATATTTATAAAA
1 TTAAAATAATTATAAAA
6063257 TT
1 TT
6063259 CCAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAATAATTATAAAA
Found at i:6063255 original size:18 final size:18
Alignment explanation
Indices: 6063234--6063294 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
6063224 TTAAAATAAT
6063234 TAAAAATTAAAATATTTA
1 TAAAAATTAAAATATTTA
* *
6063252 T-AAAATTCCAAATTTTTA
1 TAAAAATT-AAAATATTTA
* *
6063270 TATATATTTAAAATA-TTA
1 TA-AAAATTAAAATATTTA
6063288 TAAAAAT
1 TAAAAAT
6063295 CTTTAAAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
17 9 0.28
18 15 0.47
19 4 0.12
20 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAATTAAAATATTTA
Found at i:6063301 original size:20 final size:20
Alignment explanation
Indices: 6063276--6063313 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6063266 TTTATATATA
*
6063276 TTTAAAATATTATAAAAATC
1 TTTAAAAAATTATAAAAATC
*
6063296 TTTAAAAAATTCTAAAAA
1 TTTAAAAAATTATAAAAA
6063314 ATATATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTAAAAAATTATAAAAATC
Found at i:6073256 original size:32 final size:32
Alignment explanation
Indices: 6073215--6073281 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
6073205 TTATATGGGC
6073215 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
1 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
*
6073247 ATAGGAATGCTTTAAAGTTAACCTGAGATCGA
1 ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
6073279 ATA
1 ATA
6073282 AGAACTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (32 bp):
ATAGGAATGCTTTAAAGTTAACCTGAGATCAA
Found at i:6073974 original size:23 final size:23
Alignment explanation
Indices: 6073961--6074013 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
6073951 AATCAAGCAT
*
6073961 ATTCAAGGATCAAACTCAAGAAC
1 ATTCAAAGATCAAACTCAAGAAC
6073984 ATTCAAAGATCAAACTCAAGAAC
1 ATTCAAAGATCAAACTCAAGAAC
6074007 ATTCAAA
1 ATTCAAA
6074014 TTAAGCACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (23 bp):
ATTCAAAGATCAAACTCAAGAAC
Found at i:6075051 original size:31 final size:30
Alignment explanation
Indices: 6075016--6075077 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
6075006 AGTTAAAAGA
*
6075016 AGAAAGCAAACGAAAC-AGAGAAGAACAGGGG
1 AGAAAG-AAACGAAACAAGA-AAGAAAAGGGG
* *
6075047 AGAAAGAAAGGAAAGAAGAAAGAAAAGGGG
1 AGAAAGAAACGAAACAAGAAAGAAAAGGGG
6075077 A
1 A
6075078 AATAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.60, C:0.06, G:0.34, T:0.00
Consensus pattern (30 bp):
AGAAAGAAACGAAACAAGAAAGAAAAGGGG
Found at i:6076646 original size:39 final size:39
Alignment explanation
Indices: 6076539--6076673 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
6076529 GACCTCGAGT
* * *
6076539 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
6076580 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
6076618 CGATGAGACACTGGGTGTCAACTATTACTTCGAACT-GTC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
6076657 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
6076674 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 37 0.49
40 3 0.04
41 15 0.20
42 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:6083367 original size:22 final size:22
Alignment explanation
Indices: 6083340--6083385 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
6083330 GTATATTTAT
6083340 TTTAGGTTTAATATTTGATGAA
1 TTTAGGTTTAATATTTGATGAA
6083362 TTTAGGTTTAATATTTGATGAA
1 TTTAGGTTTAATATTTGATGAA
6083384 TT
1 TT
6083386 GTGATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (22 bp):
TTTAGGTTTAATATTTGATGAA
Found at i:6083497 original size:14 final size:14
Alignment explanation
Indices: 6083474--6083514 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
6083464 GATTATAATG
*
6083474 TTTAGATATTTTAT
1 TTTAAATATTTTAT
*
6083488 TTTAATTATTTTA-
1 TTTAAATATTTTAT
6083501 TTTAAATATTTTAT
1 TTTAAATATTTTAT
6083515 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAAATATTTTAT
Found at i:6083510 original size:13 final size:13
Alignment explanation
Indices: 6083474--6083519 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6083464 GATTATAATG
*
6083474 TTTAGATATTTTA
1 TTTAAATATTTTA
*
6083487 TTTTAATTATTTTA
1 -TTTAAATATTTTA
6083501 TTTAAATATTTTA
1 TTTAAATATTTTA
*
6083514 TATAAA
1 TTTAAA
6083520 AATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTAAATATTTTA
Found at i:6085732 original size:23 final size:23
Alignment explanation
Indices: 6085705--6085749 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6085695 AATTGTAAAA
*
6085705 TTAAATGTTTAAAATTTATTATG
1 TTAAAAGTTTAAAATTTATTATG
*
6085728 TTAAAAGTTTAAATTTTATTAT
1 TTAAAAGTTTAAAATTTATTAT
6085750 TGATGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TTAAAAGTTTAAAATTTATTATG
Found at i:6089352 original size:31 final size:29
Alignment explanation
Indices: 6089291--6089350 Score: 75
Period size: 32 Copynumber: 2.0 Consensus size: 29
6089281 TTAAAATTTT
*
6089291 TTATATTAATTTTATTATTTTAATTAAAA
1 TTATATTAATTTTATTATTTTAAATAAAA
*
6089320 TTATATTTAATTTTTATATTTTTTAAATAAA
1 TTATA-TTAA-TTTTAT-TATTTTAAATAAA
6089351 TTTGTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 6 0.23
32 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATTAATTTTATTATTTTAAATAAAA
Found at i:6095862 original size:10 final size:10
Alignment explanation
Indices: 6095847--6095881 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
6095837 AAAGATTATT
6095847 TTTTTTTTAA
1 TTTTTTTTAA
6095857 TTTTTTTTAA
1 TTTTTTTTAA
6095867 --TTTTTTAA
1 TTTTTTTTAA
6095875 TTTTTTT
1 TTTTTTT
6095882 CTCTTCGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.35
10 15 0.65
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:6096926 original size:26 final size:26
Alignment explanation
Indices: 6096853--6097139 Score: 220
Period size: 26 Copynumber: 11.2 Consensus size: 26
6096843 CTTAAATTGC
6096853 TTATTTTAAATCTGTTTT-TACGTATTAT
1 TTATTTTAAAT-TGTTTTATA--TATTAT
* * *
6096881 TTTTTTTAAATAG--TT-T-TATTAC
1 TTATTTTAAATTGTTTTATATATTAT
* *
6096903 TTAGTTTAAATTGTTCTATATATTAT
1 TTATTTTAAATTGTTTTATATATTAT
* *
6096929 TTATCTTTAAAATGTTTTGTATATTAT
1 TTAT-TTTAAATTGTTTTATATATTAT
* * * *
6096956 GTATTTTAATTTTCTTTTTACATATTAT
1 TTATTTTAA-ATT-GTTTTATATATTAT
* *
6096984 TTATCTTAAA--CTTTT-TATA-TA-
1 TTATTTTAAATTGTTTTATATATTAT
* *
6097005 TTACTTTAAATTGTCTTATATATTAT
1 TTATTTTAAATTGTTTTATATATTAT
* *
6097031 TTATTTTAAATTGCTTTGTATATTAT
1 TTATTTTAAATTGTTTTATATATTAT
* *
6097057 TTGTTTTAAATTGTTTTACATATTAT
1 TTATTTTAAATTGTTTTATATATTAT
*
6097083 TTATTTTAAATTG-TTT-TATACTAT
1 TTATTTTAAATTGTTTTATATATTAT
* * *
6097107 TTACTTCAAATTGTTTTATACATTATT
1 TTATTTTAAATTGTTTTATATATTA-T
6097134 TTATTT
1 TTATTT
6097140 CATTTTCTTT
Statistics
Matches: 201, Mismatches: 43, Indels: 31
0.73 0.16 0.11
Matches are distributed among these distances:
21 8 0.04
22 17 0.08
23 6 0.03
24 26 0.13
25 12 0.06
26 74 0.37
27 30 0.15
28 28 0.14
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (26 bp):
TTATTTTAAATTGTTTTATATATTAT
Found at i:6097032 original size:102 final size:99
Alignment explanation
Indices: 6096854--6097139 Score: 317
Period size: 102 Copynumber: 2.8 Consensus size: 99
6096844 TTAAATTGCT
* * *
6096854 TATTTTAAATCTGTTTTTACGTATTATTTTTTTTAAATAGTTTTAT-TACTTAGTTTAAATTGTT
1 TATTTTAAAT-T-TTTTTACATATTATTTATTTTAAAT-GTTTTATATACTTACTTTAAATTGTT
*
6096918 CTATATATTATTTATCTTTAAAATGTTTTGTATATTATG
63 -TATATATTATTTAT-TTTAAAATGCTTTGTATATTATG
* *
6096957 TATTTTAATTTTCTTTTTACATATTATTTATCTTAAACT-TTTTATATA-TTACTTTAAATTGTC
1 TATTTTAA-ATT-TTTTTACATATTATTTATTTTAAA-TGTTTTATATACTTACTTTAAATTGT-
* *
6097020 TTATATATTATTTATTTTAAATTGCTTTGTATATTATT
62 TTATATATTATTTATTTTAAAATGCTTTGTATATTATG
* * * *
6097058 TGTTTTAAATTGTTTTACATATTATTTATTTTAAATTGTTTTATACTATTTACTTCAAATTGTTT
1 TATTTTAAATTTTTTTACATATTATTTATTTTAAA-TGTTTTATA-TACTTACTTTAAATTG-TT
*
6097123 TATACATTATTTTATTT
63 TATATATTA-TTTATTT
6097140 CATTTTCTTT
Statistics
Matches: 158, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
99 23 0.15
100 9 0.06
101 29 0.18
102 54 0.34
103 41 0.26
104 2 0.01
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.60
Consensus pattern (99 bp):
TATTTTAAATTTTTTTACATATTATTTATTTTAAATGTTTTATATACTTACTTTAAATTGTTTAT
ATATTATTTATTTTAAAATGCTTTGTATATTATG
Found at i:6117936 original size:96 final size:96
Alignment explanation
Indices: 6117772--6117959 Score: 270
Period size: 96 Copynumber: 2.0 Consensus size: 96
6117762 TTGCTGCAGT
* * * * *
6117772 GTAGGAGGCATTGGGAAGTGTTGACTTGGAGCCTCCTGAGTTTGGCCAGGTGGTGTATAGTAAGC
1 GTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTATAGTAAGC
* *
6117837 ATCTCGC-TGAGGGACAGGTGGAACTTGCTGA
66 ATCTC-CTTGAGCGACAGGAGGAACTTGCTGA
* * *
6117868 GTAGGAGGCATAGGGAATTGCTGACTTGGAATCTCCTGAGTTTGGGCAGGGGGAGTATAGTAAGC
1 GTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTATAGTAAGC
6117933 ATCTCCTTGAGCGACAGGAGGAACTTG
66 ATCTCCTTGAGCGACAGGAGGAACTTG
6117960 GCTCTGAGGG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (96 bp):
GTAGGAGGCATAGGGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGGGGAGTATAGTAAGC
ATCTCCTTGAGCGACAGGAGGAACTTGCTGA
Found at i:6121947 original size:17 final size:16
Alignment explanation
Indices: 6121921--6121961 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
6121911 AGAAATAAGA
6121921 TTTT-TATTTTTTACT
1 TTTTCTATTTTTTACT
*
6121936 TTTTGCTATTTTTTAGT
1 TTTT-CTATTTTTTACT
6121953 TTTTCTATT
1 TTTTCTATT
6121962 CTATCACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 14 0.61
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (16 bp):
TTTTCTATTTTTTACT
Found at i:6122242 original size:11 final size:11
Alignment explanation
Indices: 6122226--6122258 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6122216 TTATTATAAA
6122226 AATTTTAATTT
1 AATTTTAATTT
6122237 AATTTTAATTT
1 AATTTTAATTT
*
6122248 -TTTTTAATTT
1 AATTTTAATTT
6122258 A
1 A
6122259 GTTTCGCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTAATTT
Found at i:6122535 original size:33 final size:33
Alignment explanation
Indices: 6122468--6122541 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
6122458 TCAACATCAA
*
6122468 TAATTTCTTATTTTTTTAATTTTAACTATATTTT
1 TAATTT-TAATTTTTTTAATTTTAACTATATTTT
* *
6122502 TTATTTTAATTTTTTTAATATTT-TCTCAT-TTTT
1 TAATTTTAATTTTTTTAAT-TTTAACT-ATATTTT
6122535 TAATTTT
1 TAATTTT
6122542 TTGAAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 24 0.71
34 10 0.29
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (33 bp):
TAATTTTAATTTTTTTAATTTTAACTATATTTT
Found at i:6122628 original size:24 final size:24
Alignment explanation
Indices: 6122577--6122630 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
6122567 TTTATTTTTG
*
6122577 AATTTTATATATATTAATTTTTTA
1 AATTTTATATATATTAATTTCTTA
6122601 AATTTTATA-ATA-TATATTTCTTA
1 AATTTTATATATATTA-ATTTCTTA
6122624 TAATTTT
1 -AATTTT
6122631 TCTGGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 10 0.37
24 15 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTTTATATATATTAATTTCTTA
Found at i:6126103 original size:16 final size:17
Alignment explanation
Indices: 6126076--6126108 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
6126066 ATATTTAATT
6126076 TTTAAGATTAAATTTTA
1 TTTAAGATTAAATTTTA
6126093 TTTAA-ATTAAATTTTA
1 TTTAAGATTAAATTTTA
6126109 AAAATGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAGATTAAATTTTA
Found at i:6129075 original size:11 final size:11
Alignment explanation
Indices: 6129059--6129093 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
6129049 TTTTACTATC
6129059 TCGTTGTTATT
1 TCGTTGTTATT
6129070 TCGTTGTTATT
1 TCGTTGTTATT
* *
6129081 TTGTTGTCATT
1 TCGTTGTTATT
6129092 TC
1 TC
6129094 ATTATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.11, G:0.17, T:0.63
Consensus pattern (11 bp):
TCGTTGTTATT
Found at i:6129501 original size:91 final size:91
Alignment explanation
Indices: 6129346--6129527 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 91
6129336 CTTTTTTTTA
* *
6129346 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAGTTTGGACAAAAT
1 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
6129411 TTTAGGCCCATTTTTCGACCCGAATC
66 TTTAGGCCCATTTTTCGACCCGAATC
* * * * *
6129437 AATATGGGCAGGTCTTATTAAGCTCGAATTTAGCATTTTTAATCTAGTTTAAATTTAGACAAAAT
1 AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
* *
6129502 TTTAGGCCTATTTTTCGACCTGAATC
66 TTTAGGCCCATTTTTCGACCCGAATC
6129528 CGAGTCTGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (91 bp):
AATATGGACAGGTCGTATCAAGCTCAAATTTAGCATTTTTAATCTAGTTCAAATTTAGACAAAAT
TTTAGGCCCATTTTTCGACCCGAATC
Found at i:6132559 original size:7 final size:7
Alignment explanation
Indices: 6132549--6132585 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
6132539 GTTAATAATT
6132549 AATTTTA
1 AATTTTA
6132556 AATTTTA
1 AATTTTA
6132563 AATTTTA
1 AATTTTA
6132570 AATTTTA
1 AATTTTA
6132577 AATTTTA
1 AATTTTA
6132584 AA
1 AA
6132586 AAGGACTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTTA
Found at i:6155725 original size:14 final size:14
Alignment explanation
Indices: 6155706--6155753 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
6155696 TAAGTAAAAC
6155706 ATAATATAAAATTT
1 ATAATATAAAATTT
6155720 ATAATATATAACATTT
1 ATAATATA-AA-ATTT
*
6155736 ATAA-ATAATATTT
1 ATAATATAAAATTT
6155749 -TAATA
1 ATAATA
6155754 AATTGTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.10
13 5 0.17
14 9 0.30
15 5 0.17
16 8 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:6155730 original size:16 final size:16
Alignment explanation
Indices: 6155709--6155739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6155699 GTAAAACATA
6155709 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
6155725 ATATAACATTTATAA
1 ATATAAAATTTATAA
6155740 ATAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:6158466 original size:20 final size:20
Alignment explanation
Indices: 6158429--6158500 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
6158419 AATATTTTGA
* * *
6158429 TATATCGAAGTTTCTAAGCT
1 TATATCAAAATTTTTAAGCT
6158449 TATATCAAAATTTTTAAGGC-
1 TATATCAAAATTTTTAA-GCT
* * *
6158469 TACAT-AAAAATTTTAAGAT
1 TATATCAAAATTTTTAAGCT
*
6158488 TTTATCAAAATTT
1 TATATCAAAATTT
6158501 CTAATGATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.03
19 13 0.32
20 24 0.60
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (20 bp):
TATATCAAAATTTTTAAGCT
Found at i:6158511 original size:20 final size:19
Alignment explanation
Indices: 6158475--6158523 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6158465 AGGCTACATA
6158475 AAAATTT-TAAGATTTTATC
1 AAAATTTCTAAGATTTTA-C
6158494 AAAATTTCTAATGA-TTTAC
1 AAAATTTCTAA-GATTTTAC
6158513 AAAATTTCTAA
1 AAAATTTCTAA
6158524 AAGTATACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 19 0.68
20 7 0.25
21 2 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (19 bp):
AAAATTTCTAAGATTTTAC
Found at i:6158643 original size:18 final size:20
Alignment explanation
Indices: 6158596--6158652 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
6158586 TTAATATATT
6158596 AAAATTCTTAAGATTATACCA
1 AAAATT-TTAAGATTATACCA
*
6158617 AAAATTTTAAGGTTATA-CA
1 AAAATTTTAAGATTATACCA
6158636 AAAATTTATAATGATTA
1 AAAATTT-TAA-GATTA
6158653 AGCAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 9 0.28
20 13 0.41
21 10 0.31
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
AAAATTTTAAGATTATACCA
Found at i:6159033 original size:16 final size:16
Alignment explanation
Indices: 6159012--6159053 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
6159002 ATATTTCTTG
*
6159012 ATATATTTTTTTATAA
1 ATATATTTTTATATAA
*
6159028 ATATATATTTAATATAA
1 ATATAT-TTTTATATAA
6159045 AT-TATTTTT
1 ATATATTTTT
6159054 GTTCAATCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 9 0.41
17 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTTTTATATAA
Found at i:6159357 original size:16 final size:15
Alignment explanation
Indices: 6159336--6159373 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
6159326 TTGTTATTTT
6159336 TAATATATATATAATA
1 TAATATATATATAA-A
*
6159352 TAATATATATTTAAA
1 TAATATATATATAAA
6159367 TAA-ATAT
1 TAATATAT
6159374 GTAGACAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 4 0.19
16 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATATATATAAA
Found at i:6159598 original size:15 final size:16
Alignment explanation
Indices: 6159572--6159601 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6159562 AATTTGTTTT
6159572 ATAGATAAAAATAAAA
1 ATAGATAAAAATAAAA
6159588 ATAGA-AAAAATAAA
1 ATAGATAAAAATAAA
6159602 GTTGCGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
ATAGATAAAAATAAAA
Found at i:6167063 original size:13 final size:14
Alignment explanation
Indices: 6167047--6167092 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
6167037 ATGATTTTAT
6167047 TTTTATT-TATATA
1 TTTTATTATATATA
*
6167060 TTTT-TTATAAATA
1 TTTTATTATATATA
*
6167073 TATTTATTATATAAA
1 T-TTTATTATATATA
6167088 TTTTA
1 TTTTA
6167093 GTGAGACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 2 0.07
13 10 0.37
14 7 0.26
15 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTATTATATATA
Found at i:6167085 original size:17 final size:15
Alignment explanation
Indices: 6167055--6167088 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
6167045 ATTTTTATTT
6167055 ATATATTTTTTATAA
1 ATATATTTTTTATAA
6167070 ATATATTTATTATATAA
1 ATATATTT-TT-TATAA
6167087 AT
1 AT
6167089 TTTAGTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATTTTTTATAA
Found at i:6168534 original size:33 final size:36
Alignment explanation
Indices: 6168453--6168536 Score: 86
Period size: 37 Copynumber: 2.4 Consensus size: 36
6168443 TAGAGCACCA
* *
6168453 ATTTAATTAAAATAATTTATTATTTTTTACAAAATT
1 ATTTAAATAAAATAATTTATTATCTTTTACAAAATT
*
6168489 ATATTATTATAAAGAT-ATTT-TTATCTTTTA-AAAA-T
1 AT-TTA-AATAAA-ATAATTTATTATCTTTTACAAAATT
6168524 ATTTAAATAAAAT
1 ATTTAAATAAAAT
6168537 GAATAAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
32 2 0.05
33 5 0.12
34 3 0.07
35 3 0.07
36 6 0.15
37 12 0.29
38 8 0.20
39 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (36 bp):
ATTTAAATAAAATAATTTATTATCTTTTACAAAATT
Found at i:6178904 original size:12 final size:12
Alignment explanation
Indices: 6178887--6178912 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6178877 TCATGACAAC
6178887 AAGAAGGAGGAG
1 AAGAAGGAGGAG
6178899 AAGAAGGAGGAG
1 AAGAAGGAGGAG
6178911 AA
1 AA
6178913 ACTTGTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (12 bp):
AAGAAGGAGGAG
Found at i:6184684 original size:12 final size:13
Alignment explanation
Indices: 6184667--6184695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6184657 CATGGTTTAG
6184667 AGTTTG-GGTTCA
1 AGTTTGTGGTTCA
6184679 AGTTTGTGGTTCA
1 AGTTTGTGGTTCA
6184692 AGTT
1 AGTT
6184696 CAAGTTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.17, C:0.07, G:0.31, T:0.45
Consensus pattern (13 bp):
AGTTTGTGGTTCA
Found at i:6184715 original size:19 final size:20
Alignment explanation
Indices: 6184672--6184718 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
6184662 TTTAGAGTTT
6184672 GGGTTCAAGTTTGTGGTTCA
1 GGGTTCAAGTTTGTGGTTCA
*
6184692 -AGTTCAAG-TTG-GGATTCA
1 GGGTTCAAGTTTGTGG-TTCA
6184710 GGGTTCAAG
1 GGGTTCAAG
6184719 GTTTAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 14 0.61
ACGTcount: A:0.21, C:0.11, G:0.34, T:0.34
Consensus pattern (20 bp):
GGGTTCAAGTTTGTGGTTCA
Found at i:6187134 original size:3 final size:3
Alignment explanation
Indices: 6187126--6187159 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6187116 CAATTTTATG
*
6187126 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6187160 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6207194 original size:28 final size:27
Alignment explanation
Indices: 6207154--6207230 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 27
6207144 AATTCTTTCT
6207154 ATTTTTTATAGTTTATATATATATTAGA
1 ATTTTTTATAGTTTATATATAT-TTAGA
* * *
6207182 TTTTTTTCTAGTTT-TAT-TATTTATA
1 ATTTTTTATAGTTTATATATATTTAGA
* *
6207207 ATTTTTTAAAATTTATATATATTT
1 ATTTTTTATAGTTTATATATATTT
6207231 TTAGTAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
27 8 0.20
28 12 0.30
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTTTATAGTTTATATATATTTAGA
Found at i:6210908 original size:51 final size:51
Alignment explanation
Indices: 6210828--6210984 Score: 205
Period size: 51 Copynumber: 3.1 Consensus size: 51
6210818 GACGAAGCTC
* * * *
6210828 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
6210879 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* * *
6210930 CTGCTGCCGCTGATGCTCCAACTG-C--TGCTGCCT-CTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATG-CTGCTGAAGCTCCAACTG
*
6210978 ATGCTGC
1 CTGCTGC
6210985 TGCCGTTGTA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
48 25 0.26
49 2 0.02
50 1 0.01
51 69 0.71
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.25
Consensus pattern (51 bp):
CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
Found at i:6210982 original size:27 final size:24
Alignment explanation
Indices: 6210828--6211011 Score: 170
Period size: 24 Copynumber: 7.3 Consensus size: 24
6210818 GACGAAGCTC
*
6210828 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
6210852 CCGTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
*
6210879 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
6210903 ACGTTGATGCTGCTGAAGCTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
*
6210930 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
6210954 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCGCTGAAGCTCCAAC---TG
* * *
6210981 CTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
6211005 CCGCTGC
1 CTGCTGC
6211012 TGTTCAAATT
Statistics
Matches: 132, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
24 67 0.51
25 2 0.02
26 2 0.02
27 61 0.46
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.26
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:6211012 original size:27 final size:27
Alignment explanation
Indices: 6210828--6211013 Score: 117
Period size: 27 Copynumber: 7.2 Consensus size: 27
6210818 GACGAAGCTC
* * *
6210828 CTGCTGCCGCTGAAGTTCCAACTGCCG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
6210855 TTGATG-CTGCTGAAGTTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
6210879 CTGCTGCCGCTGAAGCTCCAACAGACG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* *
6210906 TTGATG-CTGCTGAAGCTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
6210930 CTGCTGCCGCTGATGCTCCAACT---G
1 CTGCTGCCTCTGAAGCTCCAACTGACG
*
6210954 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
6210981 CTGCTGCCGT-TGTAGTTCCAACTGCCG
1 CTGCTGCC-TCTGAAGCTCCAACTGACG
6211008 CTGCTG
1 CTGCTG
6211014 TTCAAATTGA
Statistics
Matches: 126, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
24 57 0.45
25 2 0.02
26 2 0.02
27 64 0.51
28 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.26
Consensus pattern (27 bp):
CTGCTGCCTCTGAAGCTCCAACTGACG
Found at i:6220510 original size:30 final size:29
Alignment explanation
Indices: 6220440--6220516 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
6220430 ATGATGCTAG
*
6220440 AGATATTTGATA-TTTATAATTATTTAATT
1 AGATATTT-ATATTTTATAATTATTTAATA
**
6220469 AGATAAATATATTTTAATAA-TATTTTAATA
1 AGATATTTATATTTT-ATAATTA-TTTAATA
6220499 AGATATTTATATTATTAT
1 AGATATTTATATT-TTAT
6220517 TATATAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 3 0.08
29 11 0.28
30 23 0.59
31 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (29 bp):
AGATATTTATATTTTATAATTATTTAATA
Found at i:6222153 original size:39 final size:39
Alignment explanation
Indices: 6222093--6222230 Score: 113
Period size: 39 Copynumber: 3.4 Consensus size: 39
6222083 AATATGTAGA
* *
6222093 CATGGTTGAAAGTACCTGGCAACATGATAGAAAGTGTAAGAC
1 CATGG-TGAAA-TACATGGCAACATGATAGAAA-TGAAAGAC
* *
6222135 CATGGTGAAAT-TATGGCAACGTGAT-GAAAAT-AAAGAC
1 CATGGTGAAATACATGGCAACATGATAG-AAATGAAAGAC
*
6222172 CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGAC
1 CATGG-TG-AA-ATA-CATGGCAACATGA-TAGAAATGAAAGAC
*
6222216 CAT-GTGAAATCCATG
1 CATGGTGAAATACATG
6222231 CAGCGTGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
37 10 0.13
38 4 0.05
39 20 0.25
40 5 0.06
41 7 0.09
42 18 0.23
43 5 0.06
44 10 0.13
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (39 bp):
CATGGTGAAATACATGGCAACATGATAGAAATGAAAGAC
Found at i:6222195 original size:42 final size:43
Alignment explanation
Indices: 6222093--6222219 Score: 135
Period size: 42 Copynumber: 3.1 Consensus size: 43
6222083 AATATGTAGA
* *
6222093 CATGGTTGAAAG-TACC-TGGCAACATGATAGAAAGTGTAAGAC
1 CATGGTTGAAAGATACCATGGCAACATGAT-GAAAATGAAAGAC
* *
6222135 CATGG-TG-AA-AT--TATGGCAACGTGATGAAAAT-AAAGAC
1 CATGGTTGAAAGATACCATGGCAACATGATGAAAATGAAAGAC
*
6222172 CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGAC
1 CATGGTTGAAAGATACCATGGCAACATGATGA-AAATGAAAGAC
6222216 CATG
1 CATG
6222220 TGAAATCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
37 10 0.14
38 7 0.10
39 13 0.19
40 5 0.07
41 2 0.03
42 18 0.26
43 4 0.06
44 10 0.14
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (43 bp):
CATGGTTGAAAGATACCATGGCAACATGATGAAAATGAAAGAC
Found at i:6222195 original size:81 final size:79
Alignment explanation
Indices: 6222093--6222274 Score: 211
Period size: 81 Copynumber: 2.3 Consensus size: 79
6222083 AATATGTAGA
* * *
6222093 CATGGTTGAAAG-TACC-TGGCAACATGA-TAGAAAGTGTAAGACCATGGTGAAAT-TATGGCAA
1 CATGGTTGAAAGATACCATGGCAACATGACGAGAAA-TGAAAGACCAT-GTGAAATCCAT-GCAA
6222154 CGTG-ATGAAA-ATAAAGAC
63 CGTGAATGAAAGAT--AG-C
*
6222172 CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGACCATGTGAAATCCATGCAGCGT
1 CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGACCATGTGAAATCCATGCAACGT
6222237 GAATGAAAGATAGC
66 GAATGAAAGATAGC
6222251 C-TGG-TGAAAGATACCATGG-AACAT
1 CATGGTTGAAAGATACCATGGCAACAT
6222275 ACATGAAAGA
Statistics
Matches: 93, Mismatches: 4, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
76 5 0.05
77 15 0.16
78 3 0.03
79 14 0.15
80 20 0.22
81 29 0.31
82 7 0.08
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (79 bp):
CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGACCATGTGAAATCCATGCAACGT
GAATGAAAGATAGC
Found at i:6222224 original size:42 final size:42
Alignment explanation
Indices: 6222093--6222302 Score: 122
Period size: 38 Copynumber: 5.4 Consensus size: 42
6222083 AATATGTAGA
* *
6222093 CATGGTTGAAAG-TACC-TGGCAACATGATAGAAAGTGTAAGAC
1 CATGG-TGAAAGATACCATGGCAACATGAGAGAAA-TGAAAGAC
* *
6222135 CATGGTG-AA-AT--TATGGCAACGTGATGA-AAAT-AAAGAC
1 CATGGTGAAAGATACCATGGCAACATGA-GAGAAATGAAAGAC
6222172 CATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAAAGAC
1 CATGG-TGAAAGATACCATGGCAACATGA-GAGAAATGAAAGAC
* * *
6222216 CAT-GTG-AA-AT-CCAT-GCAGCGTGA-ATGAAA-GATAG-C
1 CATGGTGAAAGATACCATGGCAACATGAGA-GAAATGAAAGAC
* *
6222251 C-TGGTGAAAGATACCATGG-AACAT-ACATGAAA-GATA-AC
1 CATGGTGAAAGATACCATGGCAACATGAGA-GAAATGAAAGAC
6222289 CATGGTGAAA-ATAC
1 CATGGTGAAAGATAC
6222303 ATGACATGAA
Statistics
Matches: 137, Mismatches: 12, Indels: 42
0.72 0.06 0.22
Matches are distributed among these distances:
34 1 0.01
35 5 0.04
36 7 0.05
37 17 0.12
38 33 0.24
39 28 0.20
40 8 0.06
41 4 0.03
42 20 0.15
43 5 0.04
44 9 0.07
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (42 bp):
CATGGTGAAAGATACCATGGCAACATGAGAGAAATGAAAGAC
Found at i:6223849 original size:46 final size:45
Alignment explanation
Indices: 6223782--6223948 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 45
6223772 TGTAACCCGC
6223782 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
* * * * *
6223828 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCG-GGCTTCGCAT
* *** * *
6223873 ACATCTCCGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGCAT
*
6223918 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGCGAACTCGGACTCAACTCAACGAG
6223949 TTGGATGCCC
Statistics
Matches: 96, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.01
44 21 0.22
45 20 0.21
46 52 0.54
47 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGCAT
Found at i:6223897 original size:90 final size:91
Alignment explanation
Indices: 6223789--6223957 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 91
6223779 CGCCCATAAG
* *
6223789 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
6223854 ACGAGCTCGATGCCTAGTTACATCTC
66 ACGAGCTCGATGCCTAGTTACATCTC
*
6223880 CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
6223944 ACGAGTTGGATGCC
66 ACGAGCTCGATGCC
6223958 CAAATATCCT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
90 66 0.90
91 7 0.10
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGATGCCTAGTTACATCTC
Found at i:6225842 original size:17 final size:19
Alignment explanation
Indices: 6225822--6225861 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
6225812 CAACATATCT
*
6225822 AATTTAGT-CAATATCA-C
1 AATTTAGTACAAAATCACC
6225839 AATTTAGTACAAAATCACC
1 AATTTAGTACAAAATCACC
6225858 AATT
1 AATT
6225862 GTCATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (19 bp):
AATTTAGTACAAAATCACC
Found at i:6238904 original size:33 final size:33
Alignment explanation
Indices: 6238867--6238981 Score: 103
Period size: 33 Copynumber: 3.4 Consensus size: 33
6238857 AATTATTTAT
6238867 TTTTATTTTTTTTATTTGTCTCTTTTTTTTTTG
1 TTTTATTTTTTTTATTTGTCTCTTTTTTTTTTG
* *
6238900 TTTTA-TTTTATTATTTTGTCCTTCGTTTATTTCTTTG
1 TTTTATTTTTTTTA-TTTGT-C-TC-TTT-TTTTTTTG
* *
6238937 TTTT-TATTTTTTATCTT-TTTCTTTTTTTTTT-
1 TTTTATTTTTTTTAT-TTGTCTCTTTTTTTTTTG
6238968 TTATTATTTTTTTT
1 TT-TTATTTTTTTT
6238982 TATACTTTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
31 2 0.03
32 15 0.23
33 20 0.30
34 3 0.05
35 2 0.03
36 5 0.08
37 19 0.29
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (33 bp):
TTTTATTTTTTTTATTTGTCTCTTTTTTTTTTG
Found at i:6238916 original size:24 final size:23
Alignment explanation
Indices: 6238862--6238948 Score: 59
Period size: 24 Copynumber: 3.7 Consensus size: 23
6238852 TAACCAATTA
6238862 TTTATTTTTATTTTTTTTATTTG
1 TTTATTTTTATTTTTTTTATTTG
* * *
6238885 TCTCTTTTTTTTTTGTTTTATTT-
1 TTTATTTTTATTTT-TTTTATTTG
** ** *
6238908 TATTATTTTGTCCTTCGTTTATTTC
1 T-TTATTTT-TATTTTTTTTATTTG
*
6238933 TTTGTTTTTATTTTTT
1 TTTATTTTTATTTTTT
6238949 ATCTTTTTCT
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
23 16 0.35
24 26 0.57
25 4 0.09
ACGTcount: A:0.09, C:0.07, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTATTTTTATTTTTTTTATTTG
Found at i:6238955 original size:8 final size:7
Alignment explanation
Indices: 6238937--6238984 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
6238927 TATTTCTTTG
6238937 TTTTTAT
1 TTTTTAT
6238944 TTTTTAT
1 TTTTTAT
*
6238951 CTTTTTCT
1 -TTTTTAT
6238959 TTTTT-T
1 TTTTTAT
6238965 TTTTTAT
1 TTTTTAT
*
6238972 TATTT-T
1 TTTTTAT
6238978 TTTTTAT
1 TTTTTAT
6238985 ACTTTGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 11 0.31
7 18 0.51
8 6 0.17
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:6238961 original size:21 final size:20
Alignment explanation
Indices: 6238937--6238984 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
6238927 TATTTCTTTG
6238937 TTTTTATTTTTTATCT-TTTT
1 TTTTTATTTTTTAT-TATTTT
*
6238957 CTTTTTTTTTTTTATTATTTT
1 -TTTTTATTTTTTATTATTTT
6238978 TTTTTAT
1 TTTTTAT
6238985 ACTTTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.10, C:0.04, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTATTTTTTATTATTTT
Found at i:6238974 original size:24 final size:25
Alignment explanation
Indices: 6238929--6238980 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
6238919 CCTTCGTTTA
6238929 TTTCTTTGTTTTTATTTTTTATCTT
1 TTTCTTTGTTTTTATTTTTTATCTT
*
6238954 TTTCTTT-TTTTT-TTTTATTATTTT
1 TTTCTTTGTTTTTATTTT-TTATCTT
6238978 TTT
1 TTT
6238981 TTATACTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 4 0.16
24 14 0.56
25 7 0.28
ACGTcount: A:0.08, C:0.06, G:0.02, T:0.85
Consensus pattern (25 bp):
TTTCTTTGTTTTTATTTTTTATCTT
Found at i:6251073 original size:44 final size:43
Alignment explanation
Indices: 6250963--6251341 Score: 182
Period size: 44 Copynumber: 8.7 Consensus size: 43
6250953 ATTATACAGG
* * ** * *
6250963 TCTTATCTCCCTGAGATTACAGGGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCA---GAGA
* * *
6251009 TCTTATCTCCATGAGGTTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAG-CAGAGA
* * *
6251053 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAG-CAGAGA
* * ** *
6251097 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCAGAGA
* ** * * * *
6251136 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTAAAGCAGAGA
* * * ** * *
6251177 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTAAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCA---GAGA
** **
6251223 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAG-CAGAGA
* * * ** *
6251266 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATT-AAAGCAGAGA
* * * *
6251310 TCTTATCTCTCTGAGGTTACAGCAGAGTAGAT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGAT
6251342 CGCATCAAGT
Statistics
Matches: 252, Mismatches: 65, Indels: 34
0.72 0.19 0.10
Matches are distributed among these distances:
38 1 0.00
39 25 0.10
40 3 0.01
41 28 0.11
42 5 0.02
43 31 0.12
44 94 0.37
45 1 0.00
46 62 0.25
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCAGAGA
Found at i:6251362 original size:174 final size:170
Alignment explanation
Indices: 6251050--6251382 Score: 474
Period size: 174 Copynumber: 1.9 Consensus size: 170
6251040 TTGAAGCCAG
* * *
6251050 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTGATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTGATCCTATCTCCCTGAGATT
* * *
6251115 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
6251180 TATTTCCCTG-AGATTACAGTGGAACAGACCAAAGAATTTA
131 TATTTCCCTGAAGA-TACAGTGGAACAGACCAAAGAATTTA
*
6251220 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTGATCCTATCTCCCTGAGA-T
* * * *
6251283 TACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
*
6251348 AAGTCTTATTTCCCTGAAGATGCAGTGGAACAGAC
125 AAGTCTTATTTCCCTGAAGATACAGTGGAACAGAC
6251383 TGAAAACAAG
Statistics
Matches: 144, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
168 1 0.01
169 28 0.19
170 43 0.30
174 69 0.48
175 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTGATCCTATCTCCCTGAGATT
ACAATGGAGCGGATTAAAAGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATTTCCCTGAAGATACAGTGGAACAGACCAAAGAATTTA
Found at i:6253068 original size:3 final size:3
Alignment explanation
Indices: 6253060--6253090 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6253050 CAATTTTATG
*
6253060 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6253091 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:6253210 original size:12 final size:12
Alignment explanation
Indices: 6253195--6253219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6253185 TATATTTGCT
6253195 TATATATGTATA
1 TATATATGTATA
6253207 TATATATGTATA
1 TATATATGTATA
6253219 T
1 T
6253220 GTATTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATATATGTATA
Found at i:6257481 original size:22 final size:21
Alignment explanation
Indices: 6257456--6257502 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 21
6257446 TGTCTAATTG
6257456 AAAAGATAATTTTGTAAAAGTT
1 AAAAGATAATTTTGTAAAAG-T
6257478 AAAAGATAATTTTGTAAAAGT
1 AAAAGATAATTTTGTAAAAGT
6257499 AAAA
1 AAAA
6257503 CCTTATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (21 bp):
AAAAGATAATTTTGTAAAAGT
Found at i:6262493 original size:2 final size:2
Alignment explanation
Indices: 6262488--6262519 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6262478 GTGTGTGTGT
6262488 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6262520 CGGAGAGGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6271233 original size:14 final size:13
Alignment explanation
Indices: 6271215--6271255 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 13
6271205 TTAAAGAGAG
6271215 ATTTTATTATTTT
1 ATTTTATTATTTT
6271228 AGTTTTATTATTTT
1 A-TTTTATTATTTT
6271242 ATTATTATTTATTT
1 ATT-TTA-TTATTT
6271256 AGTATAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTATTATTTT
Found at i:6272379 original size:3 final size:3
Alignment explanation
Indices: 6272371--6272395 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6272361 GGAATAGAGT
6272371 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
6272396 AATAAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:6273233 original size:46 final size:46
Alignment explanation
Indices: 6273114--6273343 Score: 291
Period size: 46 Copynumber: 5.0 Consensus size: 46
6273104 GTTTTCTGAA
* *
6273114 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
6273160 ATGAAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATG--AAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
6273208 ATGGAATGTATAAGACCATGGTTGAAAGATACAATGGCAACGTGAC
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
6273254 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGTAACATGAC
1 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
6273300 AGGAAATG-AGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATGAAATGTA-TAAGACCATGGTTGAAAGATACCATGGCAACATG
6273344 TCAAAGATAA
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 116 0.71
48 46 0.28
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (46 bp):
ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:6274476 original size:15 final size:15
Alignment explanation
Indices: 6274456--6274486 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6274446 ATGAAATGGG
6274456 TGTAATAAAATATTT
1 TGTAATAAAATATTT
6274471 TGTAATAAAATATTT
1 TGTAATAAAATATTT
6274486 T
1 T
6274487 TAAGTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TGTAATAAAATATTT
Found at i:6282574 original size:22 final size:22
Alignment explanation
Indices: 6282557--6282608 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6282547 TATAATTTTA
*
6282557 AAATATATGTTAAATAATAATT
1 AAATATATATTAAATAATAATT
* *
6282579 AAATATATATTAAGTAATAAAT
1 AAATATATATTAAATAATAATT
*
6282601 ATATATAT
1 AAATATAT
6282609 CAAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATATATATTAAATAATAATT
Found at i:6282757 original size:12 final size:13
Alignment explanation
Indices: 6282726--6282759 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6282716 ATAATATTTA
6282726 TATTAAAATAAAT
1 TATTAAAATAAAT
*
6282739 TAATAAAAT-AAT
1 TATTAAAATAAAT
6282751 TATTAAAAT
1 TATTAAAAT
6282760 GTTAAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAAAATAAAT
Found at i:6283611 original size:5 final size:5
Alignment explanation
Indices: 6283596--6283626 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
6283586 TAAGGGTAAT
6283596 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAAA
6283627 AGCTATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:6283918 original size:16 final size:15
Alignment explanation
Indices: 6283884--6283942 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 15
6283874 ATACACACAT
*
6283884 TTATAATTTTTATACAA
1 TTAT-ATTTTAATA-AA
6283901 TTAATATTTTAATAAA
1 TT-ATATTTTAATAAA
*
6283917 TTA-ATTTTAAT-AT
1 TTATATTTTAATAAA
6283930 TTCATATTTTAAT
1 TT-ATATTTTAAT
6283943 CACATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 3 0.08
14 9 0.24
15 9 0.24
16 4 0.11
17 10 0.27
18 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATTTTAATAAA
Found at i:6283925 original size:14 final size:15
Alignment explanation
Indices: 6283887--6283928 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
6283877 CACACATTTA
*
6283887 TAATTTTTATACAAT
1 TAATTTTAATACAAT
6283902 TAATATTTTAATA-AAT
1 T-A-ATTTTAATACAAT
6283918 TAATTTTAATA
1 TAATTTTAATA
6283929 TTTCATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 5 0.21
17 8 0.33
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTTTAATACAAT
Found at i:6287785 original size:247 final size:244
Alignment explanation
Indices: 6287387--6287839 Score: 560
Period size: 247 Copynumber: 1.8 Consensus size: 244
6287377 CGGGTCGATT
*
6287387 TTGGTTTTGAAAATGAAAACGAACATGGGAGTCGACCAATCCTTGTTATAAGGTGTGATTGAATC
1 TTGGTTTTGAAAATGAAAACGAAAATGGGAGTCGACCAATCCTTGTTATAAGGTGTGATTGAATC
* * * * *
6287452 ACCTTGTAATTTGATCGTTTTAATAAACAATTTCGATTTACTAAAACGGCGATTTTAGTCTACGA
66 ACCTTGTAATTTAATCATTTTAATAAACAATTTAGATTTACTAAAACGACAATTTTAGTCTACGA
*** * * * **
6287517 AATTTGAGAAAACGGGTTCGGGATTCGGTTATGTGCAAGGAAGGATTAGCACCCTCG-TCACGCC
131 AATAACAGAAAACGAGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTCGAT-ACGCC
6287581 CAAAATTGGTACTGTCGTAACCATTTTTTTTTTGGAAAACGGTAGTCGAC
195 CAAAATTGGTACTGTCGTAACCATTTTTTTTTTGGAAAACGGTAGTCGAC
* *
6287631 TTGGATTTTGAAAATGAAAACGAAAAACT-GGAGTCGCCACCAATCTTTTTTGATAAGGTGTGAT
1 TTGG-TTTTGAAAATGAAAACG-AAAA-TGGGAGTCG--ACCAATCCTTGTT-ATAAGGTGTGAT
* * *
6287695 TGGATCACCTT-TGA-TTAATCATTTTAAT-AA-AATTTAAGATTTACTAAAACGATAATTTTTT
60 TGAATCACCTTGTAATTTAATCATTTTAATAAACAATTT-AGATTTACTAAAACGACAA--TTTT
* * * *
6287756 GGTCTACGAAA-AACAGAAAATGAGTTCGGGAGTCGGTTACGCACGAGGAAGGGTTAGCACCCTC
122 AGTCTACGAAATAACAGAAAACGAGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTC
6287820 GATACGCCCAAAATTGGTAC
187 GATACGCCCAAAATTGGTAC
6287840 CTAGTTGATT
Statistics
Matches: 176, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
244 4 0.02
245 22 0.12
246 27 0.15
247 73 0.41
248 28 0.16
249 22 0.12
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (244 bp):
TTGGTTTTGAAAATGAAAACGAAAATGGGAGTCGACCAATCCTTGTTATAAGGTGTGATTGAATC
ACCTTGTAATTTAATCATTTTAATAAACAATTTAGATTTACTAAAACGACAATTTTAGTCTACGA
AATAACAGAAAACGAGTTCGGGAGTCGGTTACGCACAAGGAAGGATTAGCACCCTCGATACGCCC
AAAATTGGTACTGTCGTAACCATTTTTTTTTTGGAAAACGGTAGTCGAC
Found at i:6288582 original size:6 final size:6
Alignment explanation
Indices: 6288567--6288601 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6288557 TAAAAATGAC
*
6288567 AACGAT AACGAA AACGAA AACGAA AACGAA AACGA
1 AACGAA AACGAA AACGAA AACGAA AACGAA AACGA
6288602 TAATAATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.63, C:0.17, G:0.17, T:0.03
Consensus pattern (6 bp):
AACGAA
Found at i:6289004 original size:25 final size:25
Alignment explanation
Indices: 6288985--6289032 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6288975 TAAATATGGT
6288985 ATAATAATG-GAAATATAAATATAAG
1 ATAAT-ATGAGAAATATAAATATAAG
*
6289010 ATAATATGAGAAATAAAAATATA
1 ATAATATGAGAAATATAAATATA
6289033 GAAGTGACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.27
Consensus pattern (25 bp):
ATAATATGAGAAATATAAATATAAG
Found at i:6291317 original size:24 final size:24
Alignment explanation
Indices: 6291250--6291326 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
6291240 TGGAAAAATA
* * *
6291250 AATTTAAAATAGATACTATAAAAC
1 AATTTAAAGTAAATAATATAAAAC
* *
6291274 AATTTTAAGTAAATAGTATAAAAC
1 AATTTAAAGTAAATAATATAAAAC
* *
6291298 AATTTAAAGTCACTAATATACAAAAC
1 AATTTAAAGTAAATAATAT--AAAAC
6291324 AAT
1 AAT
6291327 AAAATAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 35 0.81
26 8 0.19
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (24 bp):
AATTTAAAGTAAATAATATAAAAC
Found at i:6291524 original size:22 final size:22
Alignment explanation
Indices: 6291490--6291538 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6291480 TTCTGAAAAT
6291490 AAAT-AATAATAAAA-AAGTTTA
1 AAATAAATAATAAAAGAA-TTTA
* *
6291511 CAATAAATAGTAAAAGAATTTA
1 AAATAAATAATAAAAGAATTTA
6291533 AAATAA
1 AAATAA
6291539 TTAACATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (22 bp):
AAATAAATAATAAAAGAATTTA
Found at i:6291669 original size:25 final size:25
Alignment explanation
Indices: 6291576--6291703 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 25
6291566 GACACATGAT
6291576 AAATTTAAAATAAATATTATATATATA
1 AAATTTAAAATAAATA--ATATATATA
*
6291603 AGATAGTCTAAAATAAA-AAGGTATATATACA
1 A-A-A-TTTAAAATAAATAA--TATATAT--A
* *
6291634 AAACTTCAAAAT-AATAATATGTATA
1 AAA-TTTAAAATAAATAATATATATA
*
6291659 ATAGTTTAAAATAAATAATATATATA
1 A-AATTTAAAATAAATAATATATATA
*
6291685 AAATTTAAAATGAATAATA
1 AAATTTAAAATAAATAATA
6291704 GTTTAAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
25 25 0.31
26 14 0.17
27 8 0.10
28 3 0.04
29 18 0.22
30 11 0.14
31 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (25 bp):
AAATTTAAAATAAATAATATATATA
Found at i:6299860 original size:27 final size:26
Alignment explanation
Indices: 6299812--6299865 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
6299802 TACTTATACG
*
6299812 TATAAAAATTAAATTTACTATACTATA
1 TATAAAAATTAAAATTACTATA-TATA
*
6299839 TATAAATATTAAAAATTA-TATATATA
1 TATAAAAATT-AAAATTACTATATATA
6299865 T
1 T
6299866 GAACTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 13 0.54
28 6 0.25
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAAAAATTAAAATTACTATATATA
Found at i:6307683 original size:27 final size:26
Alignment explanation
Indices: 6307644--6307706 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
6307634 TCCCATTCCT
*
6307644 CCACCCCCCCTCCTCCACCTTCACCC
1 CCACCCCACCTCCTCCACCTTCACCC
6307670 CCACCACCACCTCCTCCACCTTCACCC
1 CCACC-CCACCTCCTCCACCTTCACCC
6307697 CCACCTCCAC
1 CCACC-CCAC
6307707 TTGGCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.16, C:0.70, G:0.00, T:0.14
Consensus pattern (26 bp):
CCACCCCACCTCCTCCACCTTCACCC
Found at i:6308717 original size:494 final size:494
Alignment explanation
Indices: 6307790--6308788 Score: 1973
Period size: 494 Copynumber: 2.0 Consensus size: 494
6307780 TTTTGCCAAC
6307790 ACCAATCAAAAGCTAATACTAAACCTAATATACTTTCAACAGATGATTACTCTTAAAAAGTGCCA
1 ACCAATCAAAAGCTAATACTAAACCTAATATACTTTCAACAGATGATTACTCTTAAAAAGTGCCA
6307855 CCAATTCCATTCAATTAGAAGTGAATTTACTAGATACCGCAAAACCAAGTGGTAAATCCTACTTA
66 CCAATTCCATTCAATTAGAAGTGAATTTACTAGATACCGCAAAACCAAGTGGTAAATCCTACTTA
6307920 AAGTAATGACCCCATAATCACAAAAAAAAAGAAAAAAGAAAAAAAAACCCACATGATTCAGCCAA
131 AAGTAATGACCCCATAATCACAAAAAAAAAGAAAAAAGAAAAAAAAACCCACATGATTCAGCCAA
6307985 AAAATGACAAATCAAAAACATAAACAACAAATCACTCAATCCAAGTTATAAACAAAAATTCATGA
196 AAAATGACAAATCAAAAACATAAACAACAAATCACTCAATCCAAGTTATAAACAAAAATTCATGA
6308050 TAAACCTCATCAAACTAAACCATTAAAGCTGACAACAATAACCGACCAGTAATCAGAACAAAAAC
261 TAAACCTCATCAAACTAAACCATTAAAGCTGACAACAATAACCGACCAGTAATCAGAACAAAAAC
6308115 AACCAATAATACCAAAAAGAAAAAAGGCAAACTTTCATATAAGAACAAAACCAGCCATACAAACC
326 AACCAATAATACCAAAAAGAAAAAAGGCAAACTTTCATATAAGAACAAAACCAGCCATACAAACC
6308180 CTCAAGGGAAAAAAAAAACTTACGATTCAGGCCTTGAAGAACCAAATGGACGTTTAAAATGCGAA
391 CTCAAGGGAAAAAAAAAACTTACGATTCAGGCCTTGAAGAACCAAATGGACGTTTAAAATGCGAA
6308245 CCAGAATATAAATCATCTTTTACTCGCTTCATCCTCTAA
456 CCAGAATATAAATCATCTTTTACTCGCTTCATCCTCTAA
6308284 ACCAATCAAAAGCTAATACTAAACCTAATATACTTTCAACAGATGATTACTCTTAAAAAGTGCCA
1 ACCAATCAAAAGCTAATACTAAACCTAATATACTTTCAACAGATGATTACTCTTAAAAAGTGCCA
6308349 CCAATTCCATTCAATTAGAAGTGAATTTACTAGATACCGCAAAACCAAGTGGTAAATCCTACTTA
66 CCAATTCCATTCAATTAGAAGTGAATTTACTAGATACCGCAAAACCAAGTGGTAAATCCTACTTA
6308414 AAGTAATGACCCCATAATCACAAAAAAAAAGAAAAAAGAAAAAAAAAACCCACATGATTCAGCCA
131 AAGTAATGACCCCATAATCACAAAAAAAAAGAAAAAAG-AAAAAAAAACCCACATGATTCAGCCA
6308479 AAAAATGACAAATCAAAAACATAAACAACAAATCACTCAATCCAAGTTATAAACAAAAATTCATG
195 AAAAATGACAAATCAAAAACATAAACAACAAATCACTCAATCCAAGTTATAAACAAAAATTCATG
6308544 ATAAACCTCATCAAACTAAACCATTAAAGCTGACAACAATAACCGACCAGTAATCAGAACAAAAA
260 ATAAACCTCATCAAACTAAACCATTAAAGCTGACAACAATAACCGACCAGTAATCAGAACAAAAA
6308609 CAACCAATAATACCAAAAAGAAAAAAGGCAAACTTTCATATAAGAACAAAACCAGCCATACAAAC
325 CAACCAATAATACCAAAAAGAAAAAAGGCAAACTTTCATATAAGAACAAAACCAGCCATACAAAC
6308674 CCTCAAGGG-AAAAAAAAACTTACGATTCAGGCCTTGAAGAACCAAATGGACGTTTAAAATGCGA
390 CCTCAAGGGAAAAAAAAAACTTACGATTCAGGCCTTGAAGAACCAAATGGACGTTTAAAATGCGA
6308738 ACCAGAATATAAATCATCTTTTACTCGCTTCATCCTCTAA
455 ACCAGAATATAAATCATCTTTTACTCGCTTCATCCTCTAA
*
6308778 ACCAAACAAAA
1 ACCAATCAAAA
6308789 AACAAAAACA
Statistics
Matches: 503, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
494 273 0.54
495 230 0.46
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (494 bp):
ACCAATCAAAAGCTAATACTAAACCTAATATACTTTCAACAGATGATTACTCTTAAAAAGTGCCA
CCAATTCCATTCAATTAGAAGTGAATTTACTAGATACCGCAAAACCAAGTGGTAAATCCTACTTA
AAGTAATGACCCCATAATCACAAAAAAAAAGAAAAAAGAAAAAAAAACCCACATGATTCAGCCAA
AAAATGACAAATCAAAAACATAAACAACAAATCACTCAATCCAAGTTATAAACAAAAATTCATGA
TAAACCTCATCAAACTAAACCATTAAAGCTGACAACAATAACCGACCAGTAATCAGAACAAAAAC
AACCAATAATACCAAAAAGAAAAAAGGCAAACTTTCATATAAGAACAAAACCAGCCATACAAACC
CTCAAGGGAAAAAAAAAACTTACGATTCAGGCCTTGAAGAACCAAATGGACGTTTAAAATGCGAA
CCAGAATATAAATCATCTTTTACTCGCTTCATCCTCTAA
Found at i:6308972 original size:6 final size:6
Alignment explanation
Indices: 6308957--6308996 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
6308947 CTTTTTTATG
*
6308957 TTTCTC TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TTTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
6308997 AATCTTCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:6308978 original size:18 final size:17
Alignment explanation
Indices: 6308947--6308996 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
6308937 TCTTATGATC
6308947 CTTTTTTATGTTTCTCTTT
1 CTTTTTT-T-TTTCTCTTT
*
6308966 CTTTTTCTTTTTCTTTTT
1 CTTTTT-TTTTTCTCTTT
6308984 CTTTTTTTTTTCT
1 CTTTTTTTTTTCT
6308997 AATCTTCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.24
18 14 0.48
19 7 0.24
20 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (17 bp):
CTTTTTTTTTTCTCTTT
Found at i:6315597 original size:23 final size:24
Alignment explanation
Indices: 6315546--6315597 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
6315536 TTTTTATAAG
*
6315546 TATTTAAATAAATTATAAAAAATT
1 TATTTAAATAAATAATAAAAAATT
* * *
6315570 GATTTAAATAAA-AATTAAAACTT
1 TATTTAAATAAATAATAAAAAATT
6315593 TATTT
1 TATTT
6315598 TGTAGTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TATTTAAATAAATAATAAAAAATT
Found at i:6324821 original size:14 final size:14
Alignment explanation
Indices: 6324802--6324832 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
6324792 AAGCAGTAAC
6324802 GCATTCCCCAGTGA
1 GCATTCCCCAGTGA
6324816 GCATTCCCCAGTGA
1 GCATTCCCCAGTGA
6324830 GCA
1 GCA
6324833 ACAAGACGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (14 bp):
GCATTCCCCAGTGA
Found at i:6326267 original size:15 final size:15
Alignment explanation
Indices: 6326247--6326275 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6326237 CACTAAAATT
6326247 TTTACAATATTTATC
1 TTTACAATATTTATC
6326262 TTTACAATATTTAT
1 TTTACAATATTTAT
6326276 TTTCTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTACAATATTTATC
Found at i:6326330 original size:13 final size:13
Alignment explanation
Indices: 6326312--6326345 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6326302 TATCACATAA
6326312 AATTAAATTTAAC
1 AATTAAATTTAAC
* *
6326325 AATTAATTTTAAT
1 AATTAAATTTAAC
6326338 AATTAAAT
1 AATTAAAT
6326346 AATCTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAAATTTAAC
Found at i:6328972 original size:28 final size:27
Alignment explanation
Indices: 6328941--6328997 Score: 105
Period size: 28 Copynumber: 2.1 Consensus size: 27
6328931 TTAAAGTACA
6328941 TTTTAAAATTATTCTCTTATTTATGAGT
1 TTTTAAAATTATTCTCTTATTTATG-GT
6328969 TTTTAAAATTATTCTCTTATTTATGGT
1 TTTTAAAATTATTCTCTTATTTATGGT
6328996 TT
1 TT
6328998 AGAAAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (27 bp):
TTTTAAAATTATTCTCTTATTTATGGT
Found at i:6329004 original size:28 final size:28
Alignment explanation
Indices: 6328945--6329004 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
6328935 AGTACATTTT
**
6328945 AAAATTATTCTCTTATTTATGAGTTTTT
1 AAAATTATTCTCTTATTTATGAGTTTGA
6328973 AAAATTATTCTCTTATTTATG-GTTTAGA
1 AAAATTATTCTCTTATTTATGAGTTT-GA
6329001 AAAA
1 AAAA
6329005 GGGTTATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50
Consensus pattern (28 bp):
AAAATTATTCTCTTATTTATGAGTTTGA
Found at i:6330429 original size:33 final size:32
Alignment explanation
Indices: 6330356--6330435 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
6330346 AGTAATTTCG
* *
6330356 AAAGTTAGGATTTATGTATCACCAAAAAAAGT
1 AAAGTTAGGATTTATATATCACCAAAAAAAGA
*
6330388 AAAGTTAGGATTTATATGTCACCAAAAAAAGA
1 AAAGTTAGGATTTATATATCACCAAAAAAAGA
6330420 AAAGTTTAGGATTTAT
1 AAAG-TTAGGATTTAT
6330436 TTAAAAGATA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 33 0.75
33 11 0.25
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.30
Consensus pattern (32 bp):
AAAGTTAGGATTTATATATCACCAAAAAAAGA
Found at i:6331371 original size:15 final size:16
Alignment explanation
Indices: 6331345--6331374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6331335 TTAACTAAAA
6331345 AACTATAAATTAATTG
1 AACTATAAATTAATTG
6331361 AACTA-AAATTAATT
1 AACTATAAATTAATT
6331375 TTACTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (16 bp):
AACTATAAATTAATTG
Done.