Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1343785 original size:37 final size:41
Alignment explanation
Indices: 1343715--1343792 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 41
1343705 TTATTTATCA
*
1343715 TTTCTTTCTTTATTTTCTTTTTCTTTTTCTTTTTCCTTTTC
1 TTTCTTTCTTTATTTTCTTTTTCTTCTTCTTTTTCCTTTTC
* *
1343756 TTTCTTTC-TT-TTTTCTTTTT-TTCTTTTTTTTCTTTTT
1 TTTCTTTCTTTATTTTCTTTTTCTTCTTCTTTTTCCTTTT
1343793 TCGACTGTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 14 0.41
39 10 0.29
40 2 0.06
41 8 0.24
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (41 bp):
TTTCTTTCTTTATTTTCTTTTTCTTCTTCTTTTTCCTTTTC
Found at i:1345355 original size:10 final size:10
Alignment explanation
Indices: 1345323--1345359 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
1345313 ATAGAAGTGT
1345323 TAAA-AATGA
1 TAAAGAATGA
1345332 TAAAGAATG-
1 TAAAGAATGA
1345341 TAAAGAATGA
1 TAAAGAATGA
*
1345351 CAAAGAATG
1 TAAAGAATG
1345360 TGAAAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (10 bp):
TAAAGAATGA
Found at i:1345355 original size:19 final size:18
Alignment explanation
Indices: 1345323--1345367 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
1345313 ATAGAAGTGT
*
1345323 TAAAAATGATAAAGAATG
1 TAAAAATGACAAAGAATG
1345341 TAAAGAATGACAAAGAATG
1 TAAA-AATGACAAAGAATG
*
1345360 TGAAAATG
1 TAAAAATG
1345368 TATAAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.58, C:0.02, G:0.20, T:0.20
Consensus pattern (18 bp):
TAAAAATGACAAAGAATG
Found at i:1351754 original size:21 final size:20
Alignment explanation
Indices: 1351717--1351755 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1351707 TCTCCCGCAA
* *
1351717 CTCTCCCAACTATCCAAACT
1 CTCTCCCAACAAACCAAACT
1351737 CTCTCGCCAACAAACCAAA
1 CTCTC-CCAACAAACCAAA
1351756 AGCCAGCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.36, C:0.44, G:0.03, T:0.18
Consensus pattern (20 bp):
CTCTCCCAACAAACCAAACT
Found at i:1352700 original size:17 final size:16
Alignment explanation
Indices: 1352665--1352747 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 16
1352655 TTGGATCTGG
1352665 AAAATAAATAATGATA
1 AAAATAAATAATGATA
*
1352681 AAAATTAAATAAATGAAA
1 AAAA-TAAAT-AATGATA
*
1352699 AAGAATATAATAATAATA
1 AA-AATA-AATAATGATA
* *
1352717 ATAAT-AATAATAATA
1 AAAATAAATAATGATA
* *
1352732 ATAAT-AATAATAATA
1 AAAATAAATAATGATA
1352747 A
1 A
1352748 TATACTATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
15 26 0.44
16 4 0.07
17 8 0.14
18 16 0.27
19 5 0.08
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (16 bp):
AAAATAAATAATGATA
Found at i:1352713 original size:3 final size:3
Alignment explanation
Indices: 1352705--1352749 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1352695 GAAAAAGAAT
1352705 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1352750 TACTATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1352963 original size:2 final size:2
Alignment explanation
Indices: 1352954--1352988 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1352944 CAAAAAATAC
1352954 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1352989 GTTAAAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1365366 original size:20 final size:20
Alignment explanation
Indices: 1365324--1365381 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1365314 CTCAAAATTA
* * *
1365324 AACTCACCCAAACTCTCTTTC
1 AACTCTCCC-AACCCTCTATC
*
1365345 AACTCTTCCAACCCTCTATC
1 AACTCTCCCAACCCTCTATC
*
1365365 AACTCTCCCAACTCTCT
1 AACTCTCCCAACCCTCT
1365382 CCCAAACTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (20 bp):
AACTCTCCCAACCCTCTATC
Found at i:1366522 original size:45 final size:44
Alignment explanation
Indices: 1366393--1366522 Score: 111
Period size: 45 Copynumber: 2.9 Consensus size: 44
1366383 TATGTATATT
* * * *
1366393 AAAACTATAT-ATTTGAAAATTGTATAATATATATTATATTTTCA
1 AAAACTATATGATTTCAAAAAT-TATAATAAATAATATATTTTCA
* ** * * *
1366437 AAACCCGTATGATTTCAAAAATTAT-ATATATTAAACATATTTTTA
1 AAAACTATATGATTTCAAAAATTATAATA-AAT-AATATATTTTCA
*
1366482 AAAACTATATGTTTTCAAAAATATATAATAAATAATATATT
1 AAAACTATATGATTTCAAAAAT-TATAATAAATAATATATT
1366523 ATATATTATA
Statistics
Matches: 65, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
43 3 0.05
44 11 0.17
45 43 0.66
46 5 0.08
47 3 0.05
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.42
Consensus pattern (44 bp):
AAAACTATATGATTTCAAAAATTATAATAAATAATATATTTTCA
Found at i:1370723 original size:19 final size:19
Alignment explanation
Indices: 1370699--1370751 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
1370689 GAATGCATTT
*
1370699 CATGCATCGATGCACATAC
1 CATGCACCGATGCACATAC
*
1370718 CATGCACCTATGCACATAC
1 CATGCACCGATGCACATAC
*
1370737 CATGCACCTATGCAC
1 CATGCACCGATGCAC
1370752 CGAGGATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (19 bp):
CATGCACCGATGCACATAC
Found at i:1370796 original size:65 final size:63
Alignment explanation
Indices: 1370737--1370881 Score: 148
Period size: 64 Copynumber: 2.3 Consensus size: 63
1370727 ATGCACATAC
* * *
1370737 CATGCACCTATGCAC-CGAGGATGTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAG
1 CATGCACCGATGCACTC-AGGATATTATG-AAACATCGAATGCACTTGATGCATCGATGCA-CAG
1370801 T
63 T
* * * * * **
1370802 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATTCATCGATGCACTCT
1 CATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCACTTGATGCATCGATGCACAGT
*
1370865 TATTGCACCGATGCACT
1 CA-TGCACCGATGCACT
1370882 AAGGGTCCAA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
63 3 0.05
64 42 0.64
65 20 0.30
66 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (63 bp):
CATGCACCGATGCACTCAGGATATTATGAAACATCGAATGCACTTGATGCATCGATGCACAGT
Found at i:1379505 original size:19 final size:19
Alignment explanation
Indices: 1379481--1379532 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1379471 AATGCATTTG
1379481 ATGCATCGATGCACCAGTC
1 ATGCATCGATGCACCAGTC
1379500 ATGCATCGATGCACCAGTC
1 ATGCATCGATGCACCAGTC
*
1379519 ATGCATCAATGCAC
1 ATGCATCGATGCAC
1379533 TCTGGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACCAGTC
Found at i:1379522 original size:84 final size:82
Alignment explanation
Indices: 1379414--1379577 Score: 188
Period size: 84 Copynumber: 2.0 Consensus size: 82
1379404 CGAATACATT
* * * *
1379414 TCATGCATCGATGCACATACCATGCACCGATACAC-CGAGGATGTTATGAAAACATCGAATGCAT
1 TCATGCATCGATGCACATA-CATGCACCAATACACTC-AGGATATTATG-AAACATCAAATGCAC
1379478 TTGATGCATCGATGCACCAG
63 TTGATGCATCGATGCACCAG
* * * * *
1379498 TCATGCATCGATGCACCAGT-CATGCATCAATGCACTCTGGCTATTTTGAAACATCAAATGCACT
1 TCATGCATCGATGCA-CA-TACATGCACCAATACACTCAGGATATTATGAAACATCAAATGCACT
1379562 TGATGCATCGATGCAC
64 TGATGCATCGATGCAC
1379578 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
83 30 0.44
84 34 0.50
85 3 0.04
86 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (82 bp):
TCATGCATCGATGCACATACATGCACCAATACACTCAGGATATTATGAAACATCAAATGCACTTG
ATGCATCGATGCACCAG
Found at i:1379577 original size:17 final size:19
Alignment explanation
Indices: 1379555--1379597 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1379545 GAAACATCAA
*
1379555 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
1379572 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
1379591 ATGCACT
1 ATGCACT
1379598 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:1383215 original size:17 final size:17
Alignment explanation
Indices: 1383183--1383218 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1383173 AATTGTAATC
* *
1383183 ATCTTATATCTGTAAAT
1 ATCTTATAACTATAAAT
1383200 ATCTTATAACTATAAAT
1 ATCTTATAACTATAAAT
1383217 AT
1 AT
1383219 TTGATAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (17 bp):
ATCTTATAACTATAAAT
Found at i:1384834 original size:10 final size:10
Alignment explanation
Indices: 1384819--1384850 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1384809 AAGTCAAGGC
1384819 TCCAAATTGA
1 TCCAAATTGA
1384829 TCCAAATTGA
1 TCCAAATTGA
1384839 TCCAAATTGA
1 TCCAAATTGA
1384849 TC
1 TC
1384851 TCCAAGTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (10 bp):
TCCAAATTGA
Found at i:1386106 original size:16 final size:16
Alignment explanation
Indices: 1386082--1386112 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1386072 AATTGGAGGG
*
1386082 TTATTTTTAATTTAAT
1 TTATATTTAATTTAAT
1386098 TTATATTTAATTTAA
1 TTATATTTAATTTAA
1386113 ATAATTTTTC
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTTAATTTAAT
Found at i:1387772 original size:28 final size:28
Alignment explanation
Indices: 1387721--1387774 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1387711 TTATTTTATT
*
1387721 TTTTTATAAAGTTCCAGAGATTAATTCA
1 TTTTTATAAAGTTCCAAAGATTAATTCA
* * *
1387749 TTTTTGTAAAGTTCGAAAGTTTAATT
1 TTTTTATAAAGTTCCAAAGATTAATT
1387775 AATCTTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (28 bp):
TTTTTATAAAGTTCCAAAGATTAATTCA
Found at i:1390478 original size:21 final size:21
Alignment explanation
Indices: 1390445--1390489 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1390435 TCAAAAATAT
* *
1390445 TAAAAGTATTAATGTTTTAGG
1 TAAAAATAATAATGTTTTAGG
1390466 TAAAAATAATAATGTTTTAGG
1 TAAAAATAATAATGTTTTAGG
1390487 TAA
1 TAA
1390490 TTTTTTACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATGTTTTAGG
Found at i:1396016 original size:36 final size:36
Alignment explanation
Indices: 1395976--1396091 Score: 105
Period size: 36 Copynumber: 3.2 Consensus size: 36
1395966 CTAATCAGTG
*
1395976 TTGAACATATATAAGGAATTAACAGCTTGATCAGAA
1 TTGAACCTATATAAGGAATTAACAGCTTGATCAGAA
* *
1396012 TTGAACCTACAATAAGGAATT-ACATG-TTAATC-G-A
1 TTGAACCTA-TATAAGGAATTAACA-GCTTGATCAGAA
* * *
1396046 TGCTAAACCTATATAAGGAATTACCAGCTTGATCAAAA
1 T--TGAACCTATATAAGGAATTAACAGCTTGATCAGAA
*
1396084 CTGAACCT
1 TTGAACCT
1396092 GCAAAGACTT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
34 2 0.03
35 12 0.19
36 36 0.58
37 11 0.18
38 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (36 bp):
TTGAACCTATATAAGGAATTAACAGCTTGATCAGAA
Found at i:1399906 original size:86 final size:87
Alignment explanation
Indices: 1399815--1400015 Score: 228
Period size: 86 Copynumber: 2.3 Consensus size: 87
1399805 TTCAATCCCT
* *
1399815 TTTTTATCTTTATAATTGAGTA-CCCTAATTTTGTAATCTTAC-TT-TTAACTTTATAATCGAGA
1 TTTTTAACTTTATAATTGAG-ACCCCTAATTTTGTAATCTCACTTTCTTAACTTTATAATCGAGA
** *
1399877 CTTTTAAGTTTTTTTCAATATCAC
65 CCCTTAAGTTCTTTT-AATATCAC
* * * * * *
1399901 TTTTTACCTCTATAATTAAGACCCCTAATTTTTTAATCTCACTTTCTTAACTTTATAATTGAGGC
1 TTTTTAACTTTATAATTGAGACCCCTAATTTTGTAATCTCACTTTCTTAACTTTATAATCGAGAC
*
1399966 CCTTAAGTTCTTTTAATCTCAC
66 CCTTAAGTTCTTTTAATATCAC
* * *
1399988 TTTCTAACTTTCTAATTGAGGCCCCTAA
1 TTTTTAACTTTATAATTGAGACCCCTAA
1400016 GAATTTTCAA
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
85 1 0.01
86 35 0.37
87 31 0.33
88 28 0.29
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (87 bp):
TTTTTAACTTTATAATTGAGACCCCTAATTTTGTAATCTCACTTTCTTAACTTTATAATCGAGAC
CCTTAAGTTCTTTTAATATCAC
Found at i:1399933 original size:44 final size:44
Alignment explanation
Indices: 1399796--1400089 Score: 198
Period size: 43 Copynumber: 6.8 Consensus size: 44
1399786 ATTGAAATAT
* * *
1399796 CTAATTCTTTTCAATC-C-CTTTTTTATCTTTATAATTGAGTA-CC
1 CTAATTTTTTTCAATCTCAC-TTTCTACCTTTATAATTGAG-ACCC
* * * * **
1399839 CTAA-TTTTGT-AATCTTACTTT-TAACTTTATAATCGAGACTT
1 CTAATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACCC
* * * * *
1399880 TTAAGTTTTTTTCAATATCACTTTTTACCTCTATAATTAAGACCC
1 CTAA-TTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACCC
* *
1399925 CTAA-TTTTTT-AATCTCACTTTCTTAACTTTATAATTGAGGCCC
1 CTAATTTTTTTCAATCTCACTTTC-TACCTTTATAATTGAGACCC
* * * * *
1399968 TTAAGTTCTTTT-AATCTCACTTTCTAACTTTCTAATTGAGGCCC
1 CTAA-TTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACCC
*** * *
1400012 CTAAGAATTTTCAATCTCA-ATTATACCTTTATAATTGAGA-CC
1 CTAATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACCC
* * *
1400054 CT-ATTTTTTTCAATTTCAATTACTACCTTTATAATT
1 CTAATTTTTTTCAATCTCACTTTCTACCTTTATAATT
1400090 AAGGCATGTA
Statistics
Matches: 196, Mismatches: 43, Indels: 25
0.74 0.16 0.09
Matches are distributed among these distances:
40 1 0.01
41 33 0.17
42 35 0.18
43 55 0.28
44 38 0.19
45 34 0.17
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (44 bp):
CTAATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACCC
Found at i:1399982 original size:45 final size:43
Alignment explanation
Indices: 1399815--1400054 Score: 202
Period size: 43 Copynumber: 5.6 Consensus size: 43
1399805 TTCAATCCCT
* * *
1399815 TTTTTATCTTTATAATTGAGTA-CCCTAA-TTTTGTAATCTTAC
1 TTTTTAACTTTATAATTGAG-ACCCCTAAGTTTTTTAATCTCAC
* *** *
1399857 -TTTTAACTTTATAATCGAGACTTTTAAGTTTTTTTCAATATCAC
1 TTTTTAACTTTATAATTGAGACCCCTAAG-TTTTTT-AATCTCAC
* * *
1399901 TTTTTACCTCTATAATTAAGACCCCTAA-TTTTTTAATCTCAC
1 TTTTTAACTTTATAATTGAGACCCCTAAGTTTTTTAATCTCAC
* *
1399943 TTTCTTAACTTTATAATTGAGGCCCTTAAGTTCTTTTAATCTCAC
1 TTT-TTAACTTTATAATTGAGACCCCTAAGTT-TTTTAATCTCAC
* * * * *
1399988 TTTCTAACTTTCTAATTGAGGCCCCTAAGAATTTTCAATCTCA-
1 TTTTTAACTTTATAATTGAGACCCCTAAG-TTTTTTAATCTCAC
* * *
1400031 ATTATACCTTTATAATTGAGACCC
1 TTTTTAACTTTATAATTGAGACCC
1400055 TATTTTTTTC
Statistics
Matches: 158, Mismatches: 31, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 20 0.13
42 10 0.06
43 50 0.32
44 41 0.26
45 36 0.23
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTTTAACTTTATAATTGAGACCCCTAAGTTTTTTAATCTCAC
Found at i:1401918 original size:16 final size:16
Alignment explanation
Indices: 1401898--1401941 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1401888 GTTTAATAAG
* *
1401898 CAACGAGCTTAATGAG
1 CAACGAGCTTAAGGAA
* *
1401914 TAACGAGTTTAAGGAA
1 CAACGAGCTTAAGGAA
1401930 CAACGAGCTTAA
1 CAACGAGCTTAA
1401942 CGAAGATGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (16 bp):
CAACGAGCTTAAGGAA
Found at i:1403092 original size:51 final size:52
Alignment explanation
Indices: 1403028--1403138 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 52
1403018 ACTTTGCAGA
* * * * * * *
1403028 AAGGCGC-GACCCATGC-TCCTCGTCTTACGCTGATGTGTCGCCATGTGTGGT
1 AAGGCGCAGACCCATGCAT-CGCGCCTTACGCTAATGTGGCACCACGTGGGGT
1403079 AAGGCGCAG-CCCATGCATCGCGCCTTACGCTAATGTGGCACCACGTGGGGT
1 AAGGCGCAGACCCATGCATCGCGCCTTACGCTAATGTGGCACCACGTGGGGT
1403130 AAGGCGCAG
1 AAGGCGCAG
1403139 TGCATAGGCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
51 49 0.96
52 2 0.04
ACGTcount: A:0.18, C:0.30, G:0.32, T:0.21
Consensus pattern (52 bp):
AAGGCGCAGACCCATGCATCGCGCCTTACGCTAATGTGGCACCACGTGGGGT
Found at i:1403317 original size:30 final size:29
Alignment explanation
Indices: 1403266--1403328 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
1403256 AAATGCTATG
*
1403266 CTCTCAACCCGTAAAATCACACAACAATC
1 CTCTCAACCCGAAAAATCACACAACAATC
1403295 CTCTCAACCCGAAAACATCACACAACAATC
1 CTCTCAACCCGAAAA-ATCACACAACAATC
1403325 CTCT
1 CTCT
1403329 TATCTTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.40, C:0.40, G:0.03, T:0.17
Consensus pattern (29 bp):
CTCTCAACCCGAAAAATCACACAACAATC
Found at i:1403402 original size:18 final size:16
Alignment explanation
Indices: 1403370--1403402 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1403360 CGTTATAAGG
1403370 TAATTTTTTTAATATA
1 TAATTTTTTTAATATA
1403386 TAATATTTTTT-ATATA
1 TAAT-TTTTTTAATATA
1403402 T
1 T
1403403 GATTATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTTTTTTAATATA
Found at i:1409297 original size:20 final size:19
Alignment explanation
Indices: 1409270--1409333 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
1409260 GTAAAAAAAT
1409270 AATTAAATAAAATACTAAA
1 AATTAAATAAAATACTAAA
*
1409289 AATTTAAAT--AATAC-AAT
1 AA-TTAAATAAAATACTAAA
1409306 AATTAAATAAAATACTAAAA
1 AATTAAATAAAATACT-AAA
1409326 AATTAAAT
1 AATTAAAT
1409334 GGATTATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.16
17 4 0.11
18 10 0.26
19 2 0.05
20 16 0.42
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAATAAAATACTAAA
Found at i:1410029 original size:23 final size:22
Alignment explanation
Indices: 1409999--1410063 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
1409989 TCCATTGATG
1409999 AGGATTTTGTACAAGAAAAAGGA
1 AGGATTTTGTA-AAGAAAAAGGA
1410022 AGGATTTTGTAAAAGAAAAAGGA
1 AGGATTTTGT-AAAGAAAAAGGA
* * *
1410045 TGAATTTTGTAAAGGAAAA
1 AGGATTTTGTAAAGAAAAA
1410064 TTCGAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.21
23 29 0.76
24 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.25
Consensus pattern (22 bp):
AGGATTTTGTAAAGAAAAAGGA
Found at i:1411117 original size:32 final size:32
Alignment explanation
Indices: 1411061--1411123 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1411051 CATATTTATA
* *
1411061 TTACTTTATGGTATATTAATGTCATTTGTGAT
1 TTACTTTATGGTATACTAACGTCATTTGTGAT
* *
1411093 TTACTTTATGGTATGCTAGCGTCATTTGTGA
1 TTACTTTATGGTATACTAACGTCATTTGTGA
1411124 GTCTTACCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (32 bp):
TTACTTTATGGTATACTAACGTCATTTGTGAT
Found at i:1418245 original size:39 final size:39
Alignment explanation
Indices: 1418161--1418246 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
1418151 ATGAGTAATG
* * * *
1418161 AATAAAAATAATGTTTCTATTCTATCATAATTCCTAAAA
1 AATAATAATAATGTTTCAACTCAATCATAATTCCTAAAA
* * *
1418200 ACTAATAATAATGTTT-AACTCAATCTTAATTCTTAATAA
1 AATAATAATAATGTTTCAACTCAATCATAATTCCTAA-AA
1418239 AATAATAA
1 AATAATAA
1418247 ATCTAATCCT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
38 15 0.39
39 23 0.61
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (39 bp):
AATAATAATAATGTTTCAACTCAATCATAATTCCTAAAA
Found at i:1419205 original size:2 final size:2
Alignment explanation
Indices: 1419198--1419242 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
1419188 TCTTTTAATG
1419198 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
1419240 AT A
1 AT A
1419243 AATTACAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1421292 original size:15 final size:15
Alignment explanation
Indices: 1421274--1421303 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1421264 AAAACCATGT
1421274 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1421289 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1421304 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1421310 original size:15 final size:15
Alignment explanation
Indices: 1421277--1421311 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1421267 ACCATGTTAG
* *
1421277 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1421292 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1421307 ATAAA
1 ATAAA
1421312 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1421480 original size:23 final size:22
Alignment explanation
Indices: 1421391--1421509 Score: 70
Period size: 23 Copynumber: 5.3 Consensus size: 22
1421381 AATAGTAAGT
1421391 AAAATAA-ATATAAAAAATAAA
1 AAAATAATATATAAAAAATAAA
* * *
1421412 GAAA-AAGA-AGAAAAAGGA-AAA
1 AAAATAATATATAAAAA--ATAAA
* *
1421433 AAAATATAGAAATTAAACAAATAAA
1 AAAATA-ATATA-TAAA-AAATAAA
1421458 TAAAATAATA-ATAAAAAAGTAAA
1 -AAAATAATATATAAAAAA-TAAA
*
1421481 AATAAT-ATATATATAAAATAAA
1 AA-AATAATATATAAAAAATAAA
1421503 AAAATAA
1 AAAATAA
1421510 AAAAAGTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 27
0.70 0.05 0.24
Matches are distributed among these distances:
20 8 0.10
21 13 0.17
22 17 0.22
23 21 0.27
24 3 0.04
25 8 0.10
26 8 0.10
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (22 bp):
AAAATAATATATAAAAAATAAA
Found at i:1421503 original size:30 final size:31
Alignment explanation
Indices: 1421462--1421525 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
1421452 AATAAATAAA
*
1421462 ATAATAATAAAAAAGTAAAAATAA-TATATAT
1 ATAATAATAAAAAAATAAAAA-AAGTATATAT
1421493 ATAA-AATAAAAAAATAAAAAAAGTATATAT
1 ATAATAATAAAAAAATAAAAAAAGTATATAT
1421523 ATA
1 ATA
1421526 TATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 2 0.06
30 25 0.81
31 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (31 bp):
ATAATAATAAAAAAATAAAAAAAGTATATAT
Found at i:1421575 original size:44 final size:42
Alignment explanation
Indices: 1421455--1421577 Score: 101
Period size: 44 Copynumber: 2.9 Consensus size: 42
1421445 TTAAACAAAT
* *
1421455 AAATAAAATAATAATAAAAAAGTA-A-AAAT-AATATATATATA
1 AAATAAAAAAATAA-AAAAAA-TATATATATAAATATATATATA
* *
1421496 AAATAAAAAAATAAAAAAAGTATATATATATATATATATATA
1 AAATAAAAAAATAAAAAAAATATATATATAAATATATATATA
* ** *
1421538 TTAATAAAATTGATAATAAAAAATA-ATATTTAAATATATA
1 -AAATAAAA-AAATAA-AAAAAATATATATATAAATATATA
1421578 ATCTAAAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 9
0.78 0.12 0.11
Matches are distributed among these distances:
39 2 0.03
40 6 0.09
41 16 0.24
42 11 0.17
43 7 0.11
44 17 0.26
45 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (42 bp):
AAATAAAAAAATAAAAAAAATATATATATAAATATATATATA
Found at i:1421646 original size:23 final size:22
Alignment explanation
Indices: 1421583--1421652 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
1421573 ATATAATCTA
*
1421583 AAAAG-AATAAAAATATATAC-T
1 AAAAGTAAAAAAAATAT-TACAT
*
1421604 -AAAGTAAAAAAGAA-AATACAT
1 AAAAGTAAAAAA-AATATTACAT
1421625 AAAATGTAAAAAAAATATTACAT
1 AAAA-GTAAAAAAAATATTACAT
1421648 GAAAA
1 -AAAA
1421653 AAAAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
20 7 0.18
21 7 0.18
22 7 0.18
23 14 0.36
24 4 0.10
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAGTAAAAAAAATATTACAT
Found at i:1421972 original size:37 final size:36
Alignment explanation
Indices: 1421922--1422059 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
1421912 GTGCTTGTGG
* * * * *
1421922 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
1421959 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
1421996 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
1422030 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1422060 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:1422033 original size:34 final size:35
Alignment explanation
Indices: 1421956--1422056 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1421946 TTAGTAGAAC
1421956 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
1421994 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
1422027 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1422057 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:1422900 original size:105 final size:105
Alignment explanation
Indices: 1422605--1423121 Score: 704
Period size: 105 Copynumber: 5.0 Consensus size: 105
1422595 CATTGTTCCA
* * * * ** *
1422605 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTC-TGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
1422669 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTAGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
** * *
1422711 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATC-T-GAAT--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
*
1422771 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
1422811 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
**
1422876 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
*
1422916 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
* *
1422981 AGCGGTCCATTCGTCGTGAAGTTGAACTTGTGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
* * * * *
1423021 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTG-TTGTTGACAAG
* *
1423086 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTG
1423122 CCTCGAGTGC
Statistics
Matches: 376, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
100 81 0.22
101 1 0.00
102 9 0.02
104 6 0.02
105 202 0.54
106 77 0.20
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
Found at i:1423854 original size:68 final size:65
Alignment explanation
Indices: 1423764--1423921 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 65
1423754 AAGATATCTG
* * * **
1423764 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTATAAGGGAAATAAATTCAAAGA-
1423829 TT
64 TT
* * *
1423831 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTATAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTATAAGGGAAATAAATTCAAAGAT
1423896 T
65 T
*
1423897 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1423922 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 32 0.40
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTATAAGGGAAATAAATTCAAAGATT
Found at i:1423933 original size:65 final size:66
Alignment explanation
Indices: 1423764--1424072 Score: 227
Period size: 65 Copynumber: 4.6 Consensus size: 66
1423754 AAGATATCTG
* * * * **
1423764 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTATAAGGGAAATAAATTCAAAGAT
1423829 TT
65 TT
* *
1423831 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTATAGGGGAAATAAATTCAAAGA-
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTATAAGGGAAATAAATTCAAAGAT
1423895 TT
65 TT
* ** * *
1423897 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTT-TCAAGAGAAACTGTCTCAAGA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTAT-AAGGGAAA-----T-AA-ATT
* **
1423960 -AGACGAAAT
58 CA-AAGATTT
* * * * * *
1423969 TTGTTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATTTGTT-TCAGAGAAA-ACATATTCAAAT
1 TTGTTT-CAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTATAAGGGAAATA-A-ATTCAAAG
1424032 A-TT
63 ATTT
* *
1424035 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1424073 ATTTCAAGTG
Statistics
Matches: 195, Mismatches: 32, Indels: 32
0.75 0.12 0.12
Matches are distributed among these distances:
64 1 0.01
65 69 0.35
66 12 0.06
67 26 0.13
68 33 0.17
70 2 0.01
71 6 0.03
72 15 0.08
73 31 0.16
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTATAAGGGAAATAAATTCAAAGATT
T
Found at i:1423941 original size:21 final size:21
Alignment explanation
Indices: 1423917--1423975 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
1423907 GGAAACTGTC
1423917 TCAAGATAGACGAAATTTGTT
1 TCAAGATAGACGAAATTTGTT
* *
1423938 TC---A-AGA-GAAA-CTGTC
1 TCAAGATAGACGAAATTTGTT
1423953 TCAAGATAGACGAAATTTGTT
1 TCAAGATAGACGAAATTTGTT
1423974 TC
1 TC
1423976 CAAAAGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 5 0.18
16 4 0.14
17 3 0.11
18 2 0.07
19 3 0.11
20 4 0.14
21 7 0.25
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (21 bp):
TCAAGATAGACGAAATTTGTT
Found at i:1423948 original size:36 final size:36
Alignment explanation
Indices: 1423896--1424273 Score: 321
Period size: 36 Copynumber: 10.9 Consensus size: 36
1423886 ATTCAAAGAT
*
1423896 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* *
1423932 TTTGTTTCAAGAGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
** * *
1423968 TTTGTTTCCAAAAGAAACTGTCTCAAGGGGGACGAAA
1 TTTGTTT-CAAGGGAAACTGTCTCAAGAGAGACGAAA
* * * *
1424005 TTTGTTTC-AGAGAAAACATAT-TC---A-A-A--TAT
1 TTTGTTTCAAG-GGAAAC-TGTCTCAAGAGAGACGAAA
*
1424034 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * *
1424070 TTTATTTCAAGTGAAACTGTCTCAA-AGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* *
1424105 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
1424141 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACG-AAA
* * * * *
1424179 TTTATTTTAAGGGAAA-TGTTTTC-----A-ATG--T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACGAAA
* *
1424207 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC--AA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1424242 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1424274 AAAACTCTTC
Statistics
Matches: 280, Mismatches: 37, Indels: 52
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.01
29 30 0.11
30 4 0.01
31 3 0.01
32 2 0.01
33 1 0.00
34 30 0.11
35 38 0.14
36 84 0.30
37 81 0.29
38 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:1424028 original size:138 final size:136
Alignment explanation
Indices: 1423835--1424150 Score: 418
Period size: 138 Copynumber: 2.3 Consensus size: 136
1423825 AGATTTTGTG
* * * * *
1423835 TTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTAT-AGGGGAAATAAATTCAAAGATTTT
1 TTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTT-TCAGAGAAAACAAATTCAAAGATTTT
* * * *
1423899 GTTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGATAGAC
65 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAA-AGAGAC
* *
1423964 GAAATTTG
129 AAAATTTA
* * * *
1423972 TTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATTTGTTTCAGAGAAAACATATTCAAATATTTT
1 TTT-CAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAGAGAAAACAAATTCAAAGATTTT
*
1424037 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGTGAAACTGTCTCAAAGAGACA
65 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAGAGACA
1424102 AAATTTA
130 AAATTTA
** *
1424109 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCA
1 TTTCAAAAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCA
1424151 AGGGAAACTA
Statistics
Matches: 155, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
136 24 0.15
137 27 0.17
138 104 0.67
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (136 bp):
TTTCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAGAGAAAACAAATTCAAAGATTTTG
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAAGAGACAA
AATTTA
Found at i:1424177 original size:173 final size:173
Alignment explanation
Indices: 1423900--1424277 Score: 478
Period size: 173 Copynumber: 2.2 Consensus size: 173
1423890 AAAGATTTTG
* * * * *
1423900 TTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAGAGAAACTGTCTCAAGATAGACG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACA
* * * *
1423965 AAATTTGTTTCCAAAAGAAACTGTCTCAAGGGGGACG-AAATTTGTTTC-AGAGAAAACATATTC
66 AAATTTGTTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAG-GAAAACATATTC
*
1424028 AAATATTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
130 -AATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC--AATTTA
* *
1424074 TTTCAAGTGAAACTGTCTCAA-AGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACA
** * * ** *
1424138 AAATTTTGTTT-CAAGGGAAACTATCTCAAGAGAGACGAAAATTTATTTTAAGGGAAATGTTTTC
66 AAA-TTTGTTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAGGAAAACATATTC
* * *
1424202 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTTG
130 AATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTTA
1424246 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1424278 CTCTTCTAGT
Statistics
Matches: 176, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
172 25 0.14
173 77 0.44
174 72 0.41
175 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (173 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACA
AAATTTGTTTCCAAAAGAAACTATCTCAAGAGAGACGAAAATTTATTTCAAGGAAAACATATTCA
ATATTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAATTTA
Found at i:1424232 original size:15 final size:15
Alignment explanation
Indices: 1424214--1424270 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1424204 TGTTTATGTT
1424214 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
* *
1424229 TCAAGGGAGACAATTTGTT
1 TCAA--GAGA-AA-CTGTC
*
1424248 TCAAGGGAAACTGTC
1 TCAAGAGAAACTGTC
1424263 TCAAGAGA
1 TCAAGAGA
1424271 GACAAAACTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 14 0.44
16 2 0.06
17 7 0.22
18 2 0.06
19 7 0.22
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.23
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:1424258 original size:34 final size:34
Alignment explanation
Indices: 1424210--1424275 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
1424200 TCAATGTTTA
*
1424210 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATT
*
1424244 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1424276 AACTCTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAATT
Found at i:1424327 original size:35 final size:35
Alignment explanation
Indices: 1424210--1424327 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 35
1424200 TCAATGTTTA
*
1424210 TGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAT-T
1 TGTTTCAAGA-AAACTGTCTCAAGAGAGACAAATCT
* *
1424244 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC-
1 TGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATCT
* * * *
1424279 T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATCT
1 TGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATCT
*
1424315 TGTTTTAAGAAAA
1 TGTTTCAAGAAAA
1424328 ACAATCATGA
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
34 29 0.45
35 32 0.49
36 2 0.03
37 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.25
Consensus pattern (35 bp):
TGTTTCAAGAAAACTGTCTCAAGAGAGACAAATCT
Found at i:1425253 original size:22 final size:22
Alignment explanation
Indices: 1425228--1425271 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1425218 CATTTTTGTT
1425228 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
1425250 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
1425272 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1425933 original size:8 final size:8
Alignment explanation
Indices: 1425922--1425989 Score: 59
Period size: 8 Copynumber: 8.8 Consensus size: 8
1425912 TTTTTGCTTT
1425922 TTTTTTTC
1 TTTTTTTC
*
1425930 TTTTGTTC
1 TTTTTTTC
*
1425938 -TTGTTTC
1 TTTTTTTC
*
1425945 TCTTTTTC
1 TTTTTTTC
*
1425953 TTTGTTT-
1 TTTTTTTC
*
1425960 TTTTTTGC
1 TTTTTTTC
*
1425968 TTTTTTGC
1 TTTTTTTC
*
1425976 TTCTTTTC
1 TTTTTTTC
1425984 TTTTTT
1 TTTTTT
1425990 GTTCTTGATT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
7 10 0.22
8 36 0.78
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.79
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1425972 original size:22 final size:22
Alignment explanation
Indices: 1425923--1425990 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
1425913 TTTTGCTTTT
* *
1425923 TTTTTTCTTTTGTTCTTGTTT-C
1 TTTTTTC-TTTGTTTTTTTTTGC
1425945 TCTTTTTCTTTGTTTTTTTTTGC
1 T-TTTTTCTTTGTTTTTTTTTGC
1425968 TTTTTTGCTTCT-TTTCTTTTTTG
1 TTTTTT-CTT-TGTTT-TTTTTTG
1425991 TTCTTGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 17 0.44
23 14 0.36
24 8 0.21
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTTTCTTTGTTTTTTTTTGC
Found at i:1425988 original size:16 final size:16
Alignment explanation
Indices: 1425913--1425995 Score: 59
Period size: 17 Copynumber: 5.1 Consensus size: 16
1425903 TCTTTTTGAT
*
1425913 TTTTGCTTTTTTTTTTC
1 TTTTGC-TTTTTTGTTC
1425930 TTTTG-TTCTTGTT-TCTC
1 TTTTGCTT-TT-TTGT-TC
*
1425947 TTTTTCTTTGTTT-TT-
1 TTTTGCTTT-TTTGTTC
1425962 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
1425979 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
1425994 TT
1 TT
1425996 GATTGGATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
14 3 0.05
15 15 0.27
16 14 0.25
17 21 0.38
18 3 0.05
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:1425992 original size:34 final size:36
Alignment explanation
Indices: 1425912--1425989 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 36
1425902 TTCTTTTTGA
* *
1425912 TTTTTGCTTTTTTTTTTCTTTTGTTCTTGTTTCTCTTT
1 TTTTTG-TTTTTTTTTGCTTTTGTTCTTCTTTCTC-TT
1425950 TTCTTTGTTTTTTTTTGCTTTT-TTGCTTCTTT-TCTT
1 TT-TTTGTTTTTTTTTGCTTTTGTT-CTTCTTTCTCTT
1425986 TTTT
1 TTTT
1425990 GTTCTTGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
35 2 0.06
36 4 0.11
37 4 0.11
38 22 0.61
39 4 0.11
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (36 bp):
TTTTTGTTTTTTTTTGCTTTTGTTCTTCTTTCTCTT
Found at i:1427169 original size:8 final size:8
Alignment explanation
Indices: 1427153--1427191 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1427143 AATGTAGATG
1427153 AAAATGCA
1 AAAATGCA
*
1427161 AAAAGGCA
1 AAAATGCA
1427169 AAAATGC-
1 AAAATGCA
1427176 AAAATGCA
1 AAAATGCA
*
1427184 AGAATGCA
1 AAAATGCA
1427192 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1427179 original size:15 final size:15
Alignment explanation
Indices: 1427153--1427191 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1427143 AATGTAGATG
1427153 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1427169 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1427184 AGAATGCA
1 AAAATGCA
1427192 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1427733 original size:18 final size:18
Alignment explanation
Indices: 1427710--1427749 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1427700 ATTAGTCTTT
1427710 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
1427728 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
1427746 CAGA
1 CAGA
1427750 CTTGAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:1429693 original size:15 final size:15
Alignment explanation
Indices: 1429675--1429704 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1429665 AAAACCATGT
1429675 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1429690 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1429705 GAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1429711 original size:15 final size:15
Alignment explanation
Indices: 1429678--1429712 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1429668 ACCATGTTAG
* *
1429678 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1429693 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1429708 ATAAA
1 ATAAA
1429713 TTAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1429743 original size:11 final size:11
Alignment explanation
Indices: 1429727--1429756 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1429717 TTAATTAAAT
1429727 TAAATAAAAGA
1 TAAATAAAAGA
1429738 TAAATAAAAGA
1 TAAATAAAAGA
1429749 TAAGATAA
1 TAA-ATAA
1429757 GTAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (11 bp):
TAAATAAAAGA
Found at i:1429817 original size:13 final size:12
Alignment explanation
Indices: 1429797--1429874 Score: 52
Period size: 13 Copynumber: 6.3 Consensus size: 12
1429787 AAGAAAAAGG
1429797 AAAA-AAAATAT
1 AAAATAAAATAT
* *
1429808 AGAAATAAAACAA
1 A-AAATAAAATAT
1429821 ATAAATAAAATA-
1 A-AAATAAAATAT
* *
1429833 ATAATAAAAAAGT
1 AAAATAAAATA-T
*
1429846 AAAATAATATAT
1 AAAATAAAATAT
*
1429858 ATAAATAAAAAAT
1 A-AAATAAAATAT
1429871 AAAA
1 AAAA
1429875 AAAGTATATA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
11 9 0.18
12 9 0.18
13 33 0.65
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:1429830 original size:29 final size:29
Alignment explanation
Indices: 1429760--1429866 Score: 71
Period size: 29 Copynumber: 3.7 Consensus size: 29
1429750 AAGATAAGTA
*
1429760 AAATAAATATAAAAAATAAAGAAAAAGAAG
1 AAATAAATA-AAAAAATAAAGAAAAAGAAC
*
1429790 AAA-AAGGA-AAAAAAATATAGAAATAA-AAC
1 AAATAA--ATAAAAAAATAAAGAAA-AAGAAC
* *
1429819 AAATAAATAAAATAATAATA-AAAAAGTA-
1 AAATAAATAAAAAAATAA-AGAAAAAGAAC
* *
1429847 AAATAATATATATAAATAAA
1 AAATAA-ATAAAAAAATAAA
1429867 AAATAAAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
28 10 0.16
29 41 0.67
30 9 0.15
31 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.18
Consensus pattern (29 bp):
AAATAAATAAAAAAATAAAGAAAAAGAAC
Found at i:1429864 original size:26 final size:26
Alignment explanation
Indices: 1429790--1429884 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 26
1429780 GAAAAAGAAG
* *
1429790 AAAAAGGAAAA-AAAATATAGAAATA
1 AAAAAGTAAAATAAAATATATAAATA
*
1429815 AAACAAAT-AAATAAAATA-AT-AATA
1 AAA-AAGTAAAATAAAATATATAAATA
*
1429839 AAAAAGTAAAATAATATATATAAATA
1 AAAAAGTAAAATAAAATATATAAATA
*
1429865 AAAAA-TAAAA-AAAGTATATA
1 AAAAAGTAAAATAAAATATATA
1429885 TATATATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
23 3 0.05
24 24 0.41
25 14 0.24
26 17 0.29
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (26 bp):
AAAAAGTAAAATAAAATATATAAATA
Found at i:1429885 original size:26 final size:26
Alignment explanation
Indices: 1429790--1429886 Score: 96
Period size: 26 Copynumber: 3.8 Consensus size: 26
1429780 GAAAAAGAAG
* *
1429790 AAAAAGGAAAAAAA-ATATAGAAATA
1 AAAAAGTAAAAAAATATATATAAATA
* *
1429815 AAACAAATAAATAAA-ATA-AT-AATA
1 AAA-AAGTAAAAAAATATATATAAATA
*
1429839 AAAAAGTAAAATAATATATATAAATA
1 AAAAAGTAAAAAAATATATATAAATA
1429865 AAAAA-TAAAAAAAGTATATATA
1 AAAAAGTAAAAAAA-TATATATA
1429887 TATATATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
23 8 0.14
24 10 0.17
25 13 0.22
26 28 0.47
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAAAGTAAAAAAATATATATAAATA
Found at i:1429892 original size:36 final size:37
Alignment explanation
Indices: 1429821--1429899 Score: 110
Period size: 36 Copynumber: 2.2 Consensus size: 37
1429811 AATAAAACAA
1429821 ATAAATAAAATAATAATAAAAAAGTAAAATAATATAT
1 ATAAATAAAATAATAATAAAAAAGTAAAATAATATAT
*
1429858 ATAAATAAAA-AAT-A-AAAAAAGTATATATATATATAT
1 ATAAATAAAATAATAATAAAAAAGTA-AAATA-ATATAT
1429894 ATAAAT
1 ATAAAT
1429900 TAATAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
34 9 0.23
35 5 0.13
36 15 0.38
37 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (37 bp):
ATAAATAAAATAATAATAAAAAAGTAAAATAATATAT
Found at i:1430009 original size:23 final size:22
Alignment explanation
Indices: 1429954--1430015 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1429944 TAAAAAAAAT
1429954 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
1429975 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
1429998 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
1430016 AAAAAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:1430325 original size:37 final size:36
Alignment explanation
Indices: 1430284--1430421 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
1430274 GTGCTTGTGG
* * * * *
1430284 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
1430321 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
1430358 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
1430392 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1430422 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:1430395 original size:34 final size:35
Alignment explanation
Indices: 1430318--1430418 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
1430308 TTAGTAGAAC
1430318 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
1430356 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
1430389 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1430419 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:1439057 original size:18 final size:18
Alignment explanation
Indices: 1439036--1439071 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1439026 GTACAAAAAG
1439036 AAATCACAACATAAAATA
1 AAATCACAACATAAAATA
*
1439054 AAATCACCACATAAAATA
1 AAATCACAACATAAAATA
1439072 TATATGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.19, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCACAACATAAAATA
Found at i:1440515 original size:25 final size:24
Alignment explanation
Indices: 1440470--1440538 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
1440460 TAAAAAACAT
1440470 AAGAAATAAATAAAATA-GAAATAGAA
1 AAGAAA-AAATAAAA-AGGAAAT-GAA
*
1440496 AGGAAAAAATAAAAAGGAAATGAA
1 AAGAAAAAATAAAAAGGAAATGAA
* *
1440520 AAG-ATAAATCAAAAGGAAA
1 AAGAAAAAATAAAAAGGAAA
1440539 ACAAATGCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 14 0.37
24 6 0.16
25 13 0.34
26 5 0.13
ACGTcount: A:0.71, C:0.01, G:0.16, T:0.12
Consensus pattern (24 bp):
AAGAAAAAATAAAAAGGAAATGAA
Found at i:1440582 original size:17 final size:16
Alignment explanation
Indices: 1440549--1440593 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1440539 ACAAATGCAG
1440549 AATAAATAAAAAGA-AA
1 AATAAATAAAAA-ACAA
1440565 AATAAATAAAAAACAA
1 AATAAATAAAAAACAA
1440581 AATAAAATAAAAA
1 AAT-AAATAAAAA
1440594 TATACATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.04
16 17 0.63
17 9 0.33
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.13
Consensus pattern (16 bp):
AATAAATAAAAAACAA
Found at i:1441864 original size:3 final size:3
Alignment explanation
Indices: 1441856--1441914 Score: 55
Period size: 3 Copynumber: 17.7 Consensus size: 3
1441846 ATGGATAAGA
*
1441856 AAT AAT AAT AAAT AAT AAT AAAT AAC AAT AAT AAAT AAT AAAT AAAT
1 AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT -AAT AAT -AAT -AAT
1441903 AAAT AAT AAT AA
1 -AAT AAT AAT AA
1441915 ATAAATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
3 30 0.60
4 20 0.40
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1441868 original size:10 final size:10
Alignment explanation
Indices: 1441850--1441923 Score: 91
Period size: 10 Copynumber: 7.5 Consensus size: 10
1441840 AAATAAATGG
*
1441850 ATAAGAAATA
1 ATAATAAATA
1441860 ATAATAAATA
1 ATAATAAATA
1441870 ATAATAAATA
1 ATAATAAATA
*
1441880 ACAAT-AATAA
1 ATAATAAAT-A
1441890 ATAATAAAT-
1 ATAATAAATA
1441899 A-AATAAATA
1 ATAATAAATA
1441908 ATAATAAATAA
1 ATAATAAAT-A
1441919 ATAAT
1 ATAAT
1441924 TATATTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
8 7 0.12
9 5 0.09
10 35 0.62
11 9 0.16
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (10 bp):
ATAATAAATA
Found at i:1441869 original size:7 final size:7
Alignment explanation
Indices: 1441855--1441923 Score: 74
Period size: 7 Copynumber: 10.0 Consensus size: 7
1441845 AATGGATAAG
1441855 AAATAAT
1 AAATAAT
1441862 -AATAA-
1 AAATAAT
1441867 ATAATAAT
1 A-AATAAT
1441875 AAATAA-
1 AAATAAT
*
1441881 CAATAAT
1 AAATAAT
1441888 AAATAAT
1 AAATAAT
1441895 AAATAAAT
1 AAAT-AAT
1441903 AAATAAT
1 AAATAAT
1441910 -AATAAAT
1 AAAT-AAT
1441917 AAATAAT
1 AAATAAT
1441924 TATATTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 13 0.25
7 29 0.55
8 11 0.21
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:1441879 original size:4 final size:4
Alignment explanation
Indices: 1441862--1441922 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
1441852 AAGAAATAAT
1441862 AATA AAT- AAT- AATA AATA ACA-A TAATA AAT- AATA AATA AATA AAT-
1 AATA AATA AATA AATA AATA A-ATA -AATA AATA AATA AATA AATA AATA
1441907 AAT- AATA AATA AATA A
1 AATA AATA AATA AATA A
1441923 TTATATTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
3 15 0.29
4 33 0.65
5 3 0.06
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1442034 original size:18 final size:18
Alignment explanation
Indices: 1442008--1442070 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
1441998 CAAAAATGTT
*
1442008 TTTTAAAAAACTATATAA
1 TTTTCAAAAACTATATAA
* *
1442026 TTTTCAAAAA--AAATACT
1 TTTTCAAAAACTATATA-A
* *
1442043 TTTTTAAAAACTATATGA
1 TTTTCAAAAACTATATAA
1442061 TTTTCAAAAA
1 TTTTCAAAAA
1442071 ATGTTTTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
18 18 0.53
19 3 0.09
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (18 bp):
TTTTCAAAAACTATATAA
Found at i:1442151 original size:37 final size:37
Alignment explanation
Indices: 1442054--1442316 Score: 254
Period size: 37 Copynumber: 7.2 Consensus size: 37
1442044 TTTTAAAAAC
* * * * *
1442054 TATATGATTTTCAAAAAATGTTTTCAAAAATTAAATTT
1 TATATAATTTTC-AAAAATGTTTTTAAAAACTATATAT
1442092 TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAAATGTTTTTAAAAACTATATAT
*
1442130 TATATAAATTTCAAAAATG-TTTT-AAAACTATATAT
1 TATATAATTTTCAAAAATGTTTTTAAAAACTATATAT
* *
1442165 TATGTAAGTTTTCCAAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTT-CAAAAATGTTTTTAAAAACTATATAT
* *
1442204 TATAT-ATTTTCCTAAAAT-ATTTTAAAAACTATATAT
1 TATATAATTTT-CAAAAATGTTTTTAAAAACTATATAT
* * * * *
1442240 TATACAGTTTT--TAAGTG-TTTTAAAAACCATATAT
1 TATATAATTTTCAAAAATGTTTTTAAAAACTATATAT
* * *
1442274 TATATGCATTTT-TAAAATGTTTTTAGAAACTATATAT
1 TATAT-AATTTTCAAAAATGTTTTTAAAAACTATATAT
1442311 TATATA
1 TATATA
1442317 CGTATTTTCA
Statistics
Matches: 192, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
34 23 0.12
35 22 0.11
36 33 0.17
37 54 0.28
38 39 0.20
39 21 0.11
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATAATTTTCAAAAATGTTTTTAAAAACTATATAT
Found at i:1443097 original size:84 final size:83
Alignment explanation
Indices: 1442921--1443593 Score: 617
Period size: 84 Copynumber: 8.1 Consensus size: 83
1442911 TGAGCTATAT
*** * * * *
1442921 TGCAAATGATGTGCCCTCAAAGTTGAGTGTAATCGAACTCGAAGGTCTTTGATTGGCAGATAGCC
1 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTG-GTGGCAGATAACC
* * *
1442986 CTTCTCGACTTAAGCTATGT
64 CTTCTAGACTTAAGTTATGC
* * * * * *
1443006 TGCAAATGATGTGCCTTGGAGCTGAACGTAGTTGAACTTGAATGTCTTTTGGTGACAGATAACCC
1 TGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTGGCAGATAACCC
* *
1443071 TTCTAGCCTTGAGTTATGC
65 TTCTAGACTTAAGTTATGC
* * * * * ** *
1443090 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGGGGGTC-TT--TGGCAGATAGCCC
1 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCC
* * *
1443152 TTCTCGATTTAAGCTATGC
65 TTCTAGACTTAAGTTATGC
* * * * * * *
1443171 TGCAATTGATATTCCGTT-GAGCTGAGCATAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACC
1 TGCAAATGATGTGCC-TTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTGGCAGATAACC
*
1443235 CTTCTAGACTTAAGTTGTGC
64 CTTCTAGACTTAAGTTATGC
* * * **
1443255 TGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTGGTGATAGATAACCCT
1 TGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCT
* * *
1443320 TATAGCCTTGAGTTATGC
66 TCTAGACTTAAGTTATGC
* *** * * * *
1443338 TGTAAATGATGTGCCCTCAAAGTTGAGAGTAATCGAACTCGAGGGTC-TT--TGGCAGATAGCCC
1 TGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCC
* *
1443400 TTCTCGACTTAAGCTATGC
65 TTCTAGACTTAAGTTATGC
* * *
1443419 TGCGAATGATGTGCCTTGGAGCTAAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAACCC
1 TGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGG-TGGCAGATAACCC
* *
1443484 TTCTCA-ACCTGAGTTATGC
65 TTCT-AGACTTAAGTTATGC
* * *
1443503 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCT
1 TGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCT
*
1443568 TCTA-ACCTTGAGTTATGC
66 TCTAGA-CTTAAGTTATGC
1443586 TGCAAATG
1 TGCAAATG
1443594 TTGTCTTAAA
Statistics
Matches: 467, Mismatches: 106, Indels: 32
0.77 0.18 0.05
Matches are distributed among these distances:
80 48 0.10
81 72 0.15
82 4 0.01
83 83 0.18
84 220 0.47
85 40 0.09
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
TGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGGCAGATAACCCT
TCTAGACTTAAGTTATGC
Found at i:1443237 original size:165 final size:167
Alignment explanation
Indices: 1442924--1443593 Score: 502
Period size: 165 Copynumber: 4.0 Consensus size: 167
1442914 GCTATATTGC
* * *
1442924 AAATGATGTGCCCTCAAAGTTGAGTGTAATCGAACTCGAAGGTCTTTGATTGGCAGATAGCCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTC-TT-ATTGGCAGATAGCCCTT
* * * * * ** *
1442989 CTCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAACGTAGTTGAACTTGAATGTCTT
64 CTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAACATAATCGAACTCAAAGGTCTT
* * *
1443054 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
129 TTGGTGACAGACAACCCTTCTAGACTTAAGTTATGCTGT
**
1443093 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGGGGGTC-T-TTGGCAGATAGCCCTTCT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTATTGGCAGATAGCCCTTCT
* * * *
1443156 CGATTTAAGCTATGCTGCAATTGATATTCCGTT-GAGCTGAGCATAATCGAACTCAAAGGTCTTT
66 CGACTTAAGCTATGCTGCAAATGATATGCC-TTGGAGCTGAACATAATCGAACTCAAAGGTCTTT
* * *
1443220 TGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGT
130 TGGTGACAGACAACCCTTCTAGACTTAAGTTATGCTGT
* * * * * * ** *
1443258 AAATGATATG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATT-TGGTGATAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTAT--TGGCAGATAGCCCTT
* * * * * * * *** * * * *
1443321 ATAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGTTGAGA-GTAATCGAACTCGAGGGTC
64 CTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGA-ACATAATCGAACTCAAAGGTC
* * * * *
1443385 -TTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGC
127 TTTTGGTGACAGACAACCCTTCTAGACTTAAGTTATGCTGT
* * * * * * * * *
1443422 GAATGATGTG-CCTTGGAGCTAAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTC-TT-ATTGGCAGATAGCCCTT
* * * * * * * *
1443486 CTCAACCTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-T
64 CTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAACATAATCGAACTCAAAGGTCTT
* * * * *
1443550 TTGTTGGCAGATAACCCTTCTA-ACCTTGAGTTATGCTGC
129 TTGGTGACAGACAACCCTTCTAGA-CTTAAGTTATGCTGT
1443589 AAATG
1 AAATG
1443594 TTGTCTTAAA
Statistics
Matches: 401, Mismatches: 85, Indels: 32
0.77 0.16 0.06
Matches are distributed among these distances:
164 118 0.29
165 149 0.37
166 4 0.01
167 68 0.17
168 23 0.06
169 39 0.10
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (167 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAAGGTCTTATTGGCAGATAGCCCTTCT
CGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAACATAATCGAACTCAAAGGTCTTTT
GGTGACAGACAACCCTTCTAGACTTAAGTTATGCTGT
Found at i:1443389 original size:248 final size:248
Alignment explanation
Indices: 1442950--1443593 Score: 884
Period size: 248 Copynumber: 2.6 Consensus size: 248
1442940 AAGTTGAGTG
* * * * *
1442950 TAATCGAACTCGAAGGTC-TTTGATTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATG
1 TAATCGAACTCAAAGGTCTTTTG-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
* * * * * *
1443014 ATGTGCCTTGGAGCTGAACGTAGTTGAACTTGAATGTCTTTTGGTGACAGATAACCCTTCTAGCC
65 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-ATTTGGTGACAGATAACCCTTCTAGCC
* * *
1443079 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGGGGGTCTTTGGCA
129 TTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGAGTAATCGAACTAGAGGGTCTTTGGCA
* * *
1443144 GATAGCCCTTCTCGATTTAAGCTATGCTGC-AATTGATATTCCGTT-GAGCTGAGCA
194 GATAGCCCTTCTCGACTTAAGCTATGCTGCGAA-TGATATGCC-TTGGAGCTAAGCA
* * *
1443199 TAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGTAAATGA
1 TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
* * *
1443264 TATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTGGTGATAGATAACCCTTATAGCCTT
66 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAACCCTTCTAGCCTT
* *
1443329 GAGTTATGCTGTAAATGATGTGCCCTCAAAGTTGAGAGTAATCGAACTCGAGGGTCTTTGGCAGA
131 GAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGAGTAATCGAACTAGAGGGTCTTTGGCAGA
* *
1443394 TAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATGTGCCTTGGAGCTAAGCG
196 TAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATATGCCTTGGAGCTAAGCA
* * *
1443447 TAATCGAACTCGAAA-GTCTTTGGTTGGCAGATAACCCTTCTCA-ACCTGAGTTATGCTGCAAAT
1 TAATCGAACTC-AAAGGTCTTTTGTTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAAT
* * * *
1443510 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAACC
64 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAACCCTTCTAGCC
*
1443575 TTGAGTTATGCTGCAAATG
129 TTGAGTTATGCTGTAAATG
1443594 TTGTCTTAAA
Statistics
Matches: 349, Mismatches: 41, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
247 2 0.01
248 255 0.73
249 88 0.25
250 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (248 bp):
TAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGA
TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTGGTGACAGATAACCCTTCTAGCCTT
GAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGAGTAATCGAACTAGAGGGTCTTTGGCAGA
TAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATATGCCTTGGAGCTAAGCA
Found at i:1443392 original size:164 final size:166
Alignment explanation
Indices: 1443190--1443593 Score: 469
Period size: 164 Copynumber: 2.4 Consensus size: 166
1443180 TATTCCGTTG
* * *
1443190 AGCTGAGCA-TAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 AGCTGAG-AGTAATCGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTAGACTTAAGTTATG
* * * *
1443254 CTGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTATTTGG-TGATAGATAACC
63 CTGCAAATGATATGCCTTGGAGCTAAGCGTAATCGAACTCGAAAGTATTTGGTTGACAGATAACC
* * *
1443318 CTTAT-AGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAA
128 CTTATCAACC-TGAGTTATGCTGCAAATGATATG-CCTCAA
* * * * *
1443358 AGTTGAGAGTAATCGAACTCGAGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
1 AGCTGAGAGTAATCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
* * * *
1443421 CGAATGATGTGCCTTGGAGCTAAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAACCCTT
66 CAAATGATATGCCTTGGAGCTAAGCGTAATCGAACTCGAAAGTATTTGGTTGACAGATAACCCTT
* ***
1443486 CTCAACCTGAGTTATGCTGCAAATGATATGCCTTGG
131 ATCAACCTGAGTTATGCTGCAAATGATATGCCTCAA
* * *
1443522 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTA-ACCTTGAGTTATGC
1 AGCTGAGAGTAATCGAACTCGAAGGTC-TTGTTGGCAGATAACCCTTCTAGA-CTTAAGTTATGC
1443586 TGCAAATG
64 TGCAAATG
1443594 TTGTCTTAAA
Statistics
Matches: 197, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
164 99 0.50
165 36 0.18
166 5 0.03
167 35 0.18
168 22 0.11
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (166 bp):
AGCTGAGAGTAATCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTG
CAAATGATATGCCTTGGAGCTAAGCGTAATCGAACTCGAAAGTATTTGGTTGACAGATAACCCTT
ATCAACCTGAGTTATGCTGCAAATGATATGCCTCAA
Found at i:1448827 original size:24 final size:24
Alignment explanation
Indices: 1448782--1448836 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
1448772 AAAAATATTT
*
1448782 AAATAAATAAAAAATCATAAGAACA
1 AAATAAATAAAAAATCAAAAGAA-A
1448807 AAATAAGAT-AAAAA-CAAAAGAAA
1 AAATAA-ATAAAAAATCAAAAGAAA
1448830 ACAATAA
1 A-AATAA
1448837 TAATAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 12 0.44
25 11 0.41
26 2 0.07
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.13
Consensus pattern (24 bp):
AAATAAATAAAAAATCAAAAGAAA
Found at i:1450310 original size:10 final size:9
Alignment explanation
Indices: 1450295--1450366 Score: 63
Period size: 10 Copynumber: 7.3 Consensus size: 9
1450285 TAAATGGATA
1450295 AAAAATAAT
1 AAAAATAAT
1450304 AAGAAATAAT
1 AA-AAATAAT
*
1450314 AATAATAAAT
1 AAAAAT-AAT
*
1450324 AATAATAAAT
1 AAAAAT-AAT
*
1450334 AACAATAAT
1 AAAAATAAT
1450343 AAATAATAAAT
1 AAA-AAT-AAT
1450354 AAATAATAAT
1 AAA-AATAAT
1450364 AAA
1 AAA
1450367 TAAATAATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
9 10 0.18
10 36 0.64
11 10 0.18
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (9 bp):
AAAAATAAT
Found at i:1450311 original size:7 final size:7
Alignment explanation
Indices: 1450292--1450369 Score: 74
Period size: 7 Copynumber: 11.1 Consensus size: 7
1450282 AAATAAATGG
*
1450292 ATAAAAA
1 ATAAATA
1450299 AT-AATA
1 ATAAATA
*
1450305 AGAAATA
1 ATAAATA
1450312 AT-AATA
1 ATAAATA
1450318 ATAAATA
1 ATAAATA
1450325 AT-AATAA
1 ATAAAT-A
1450332 ATAACAATA
1 AT-A-AATA
1450341 ATAAATA
1 ATAAATA
1450348 ATAAATA
1 ATAAATA
1450355 A-ATAATA
1 ATA-AATA
1450362 ATAAATA
1 ATAAATA
1450369 A
1 A
1450370 ATAATTATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
6 14 0.23
7 38 0.63
8 2 0.03
9 3 0.05
10 3 0.05
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (7 bp):
ATAAATA
Found at i:1450314 original size:3 final size:3
Alignment explanation
Indices: 1450298--1450365 Score: 64
Period size: 3 Copynumber: 20.7 Consensus size: 3
1450288 ATGGATAAAA
* *
1450298 AAT AAT AAGA AAT AAT AAT AAT AAAT AAT AAT AAAT AAC AAT AAT AAAT
1 AAT AAT AA-T AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT -AAT
1450347 AAT AAAT AAAT AAT AAT AA
1 AAT -AAT -AAT AAT AAT AA
1450366 ATAAATAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
3 38 0.68
4 18 0.32
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1450314 original size:13 final size:13
Alignment explanation
Indices: 1450292--1450374 Score: 95
Period size: 13 Copynumber: 6.7 Consensus size: 13
1450282 AAATAAATGG
*
1450292 ATAAAAAATAATA
1 ATAAATAATAATA
*
1450305 AGAAATAATAATA
1 ATAAATAATAATA
1450318 AT--A-AATAATA
1 ATAAATAATAATA
*
1450328 ATAAATAACAATA
1 ATAAATAATAATA
1450341 ATAAATAAT-A-A
1 ATAAATAATAATA
1450352 ATAAATAATAATAA
1 ATAAATAATAAT-A
1450366 ATAAATAAT
1 ATAAATAAT
1450375 TATATTAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
10 9 0.15
11 11 0.19
12 3 0.05
13 26 0.44
14 10 0.17
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (13 bp):
ATAAATAATAATA
Found at i:1450367 original size:10 final size:10
Alignment explanation
Indices: 1450311--1450374 Score: 83
Period size: 10 Copynumber: 5.9 Consensus size: 10
1450301 AATAAGAAAT
1450311 AATAATAATA
1 AATAATAATA
1450321 AATAATAATA
1 AATAATAATA
1450331 AATAACAATAATA
1 AAT---AATAATA
1450344 AATAATAAATA
1 AATAAT-AATA
1450355 AATAATAATA
1 AATAATAATA
1450365 AATAAATAAT
1 AAT-AATAAT
1450375 TATATTAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
10 23 0.47
11 16 0.33
13 10 0.20
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (10 bp):
AATAATAATA
Found at i:1450487 original size:17 final size:16
Alignment explanation
Indices: 1450462--1450521 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 16
1450452 CAAAAATGTT
1450462 TTTTAAAAACTATATAA
1 TTTTAAAAACTATAT-A
*
1450479 TTTTCAAAAA--ATACTT
1 TTTT-AAAAACTATA-TA
1450495 TTTTAAAAACTATATGA
1 TTTTAAAAACTATAT-A
1450512 TTTTCAAAAA
1 TTTT-AAAAA
1450522 ATGTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 5 0.14
16 8 0.23
17 12 0.34
18 10 0.29
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTTAAAAACTATATA
Found at i:1450502 original size:33 final size:32
Alignment explanation
Indices: 1450440--1450528 Score: 126
Period size: 33 Copynumber: 2.8 Consensus size: 32
1450430 CTACATATTA
*
1450440 TATATAATTTTTC-AAAAATGTTTTTTAAAAAC
1 TATATAA-TTTTCAAAAAATCTTTTTTAAAAAC
1450472 TATATAATTTTCAAAAAATACTTTTTTAAAAAC
1 TATATAATTTTCAAAAAAT-CTTTTTTAAAAAC
* *
1450505 TATATGATTTTCAAAAAATGTTTT
1 TATATAATTTTCAAAAAATCTTTT
1450529 CAAAAATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 5 0.10
32 17 0.33
33 30 0.58
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (32 bp):
TATATAATTTTCAAAAAATCTTTTTTAAAAAC
Found at i:1450648 original size:39 final size:38
Alignment explanation
Indices: 1450505--1450770 Score: 280
Period size: 38 Copynumber: 7.2 Consensus size: 38
1450495 TTTTAAAAAC
* * * * * *
1450505 TATATGATTTTCAAAAAATGTTTTCAAAAATTAAATTT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
*
1450543 TATATAAGTTTT-CAAAAATGTTTTTAAATACTATATAT
1 TATATAA-TTTTCCAAAAATGTTTTTAAAAACTATATAT
* *
1450581 TATATAAATTTCAAAAAATGTTTTTAAAAACTATATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
*
1450619 TATATAAGTTTTCCAAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCCAAAAATGTTTTTAAAAACTATATAT
* *
1450658 TATAT-ATTTTCCTAAAAT-ATTTTAAAAACTATATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
* * * *
1450694 TATACAGTTTT-C--AAGTG-TTTTAAAAACCATATAT
1 TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
* *
1450728 TATATACATTTT--TAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCCAAAAATGTTTTTAAAAACTATATAT
1450765 TATATA
1 TATATA
1450771 CGTATTTTCA
Statistics
Matches: 196, Mismatches: 23, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
34 24 0.12
35 4 0.02
36 27 0.14
37 39 0.20
38 65 0.33
39 37 0.19
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (38 bp):
TATATAATTTTCCAAAAATGTTTTTAAAAACTATATAT
Found at i:1456524 original size:16 final size:16
Alignment explanation
Indices: 1456503--1456538 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1456493 AACAATGACT
1456503 TCAACACTTTTAAATA
1 TCAACACTTTTAAATA
1456519 TCAACACTTTTAAATA
1 TCAACACTTTTAAATA
1456535 TCAA
1 TCAA
1456539 GATGATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (16 bp):
TCAACACTTTTAAATA
Found at i:1459666 original size:4 final size:4
Alignment explanation
Indices: 1459657--1459683 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1459647 GTGTTTTATT
1459657 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1459684 TATATTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1460947 original size:30 final size:30
Alignment explanation
Indices: 1460913--1460973 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1460903 TTCGATATAA
*
1460913 CAAATTAAGTTAAA-TGGATTTTAAGATTTT
1 CAAATTAAGTTAAAGT-AATTTTAAGATTTT
1460943 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1 CAAATTAAGTTAAAGTAATTTTAAGATTTT
1460973 C
1 C
1460974 CAAACGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
CAAATTAAGTTAAAGTAATTTTAAGATTTT
Found at i:1467080 original size:18 final size:18
Alignment explanation
Indices: 1467057--1467097 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1467047 TCCCCTTTGA
1467057 AGGGGAACCGATACCCCC
1 AGGGGAACCGATACCCCC
*
1467075 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
*
1467093 TGGGG
1 AGGGG
1467098 TTCTGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (18 bp):
AGGGGAACCGATACCCCC
Found at i:1469523 original size:30 final size:29
Alignment explanation
Indices: 1469489--1469548 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1469479 TTCGATATAA
*
1469489 CAAATTAAGTTAAATGGATTTTAAGATTTT
1 CAAATTAAGTTAAA-GGAATTTAAGATTTT
*
1469519 CAAATTAAGTTAAAGTAATTTAAGATTTT
1 CAAATTAAGTTAAAGGAATTTAAGATTTT
1469548 C
1 C
1469549 CAAACGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (29 bp):
CAAATTAAGTTAAAGGAATTTAAGATTTT
Found at i:1479660 original size:44 final size:45
Alignment explanation
Indices: 1479559--1479861 Score: 312
Period size: 45 Copynumber: 6.8 Consensus size: 45
1479549 TTATAACATT
* *
1479559 TTTTCTGTTGATAGTGCACCCATATGCATTTCAACT-ATAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCA-AGCATAC
* * * *
1479604 TTTTCTATTGATAATGTACCCATATACATTTCAAC-CAAGTATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
* * ** *
1479648 TTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATGC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
* * * *
1479693 TCTTCTATTGATAATACACCCATATGCATTTCAACTCAAACATAC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
1479738 TTTTC-GATTGATAATGCACCC-TATGCATTTCAACTCAAGCATAC
1 TTTTCTG-TTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
* * * ** ** *
1479782 -TTTCTGTGGATAATGCACCCATATGCATTCCCACGAAATTATGC
1 TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
* *
1479826 TTTT-TCGTTGATAATGTACCCATATACATTTCAACT
1 TTTTCT-GTTGATAATGCACCCATATGCATTTCAACT
1479862 AGGGCATCCT
Statistics
Matches: 215, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
43 17 0.08
44 81 0.38
45 117 0.54
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
TTTTCTGTTGATAATGCACCCATATGCATTTCAACTCAAGCATAC
Found at i:1479714 original size:89 final size:89
Alignment explanation
Indices: 1479559--1479862 Score: 341
Period size: 89 Copynumber: 3.4 Consensus size: 89
1479549 TTATAACATT
* * * *
1479559 TTTTCTGTTGATAGTGCACCCATATGCATTTCAACTATAGTATACTTTTCTATTGATAATGTACC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATAC-TTTCTATTGATAATGCACC
* *
1479624 CATATACATTTCAAC-CAAGTATAC
65 CATATGCATTTCAACGCAAATATAC
* * * *
1479648 TTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATGCTCTTCTATTGATAATACACC
1 TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACT-TTCTATTGATAATGCACC
* *
1479713 CATATGCATTTCAACTCAAACATAC
65 CATATGCATTTCAACGCAAATATAC
* * *
1479738 TTTTC-GATTGATAATGCACCC-TATGCATTTCAACTCA-AGCATACTTTCTGTGGATAATGCAC
1 TTTTCTG-TTGATAATGCACCCATATACATTTCAACT-ATAGCATACTTTCTATTGATAATGCAC
* * *
1479800 CCATATGCATTCCCACG-AAATTATGC
64 CCATATGCATTTCAACGCAAA-TATAC
*
1479826 TTTT-TCGTTGATAATGTACCCATATACATTTCAACTA
1 TTTTCT-GTTGATAATGCACCCATATACATTTCAACTA
1479863 GGGCATCCTT
Statistics
Matches: 182, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
87 3 0.02
88 50 0.27
89 104 0.57
90 25 0.14
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (89 bp):
TTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACTTTCTATTGATAATGCACCC
ATATGCATTTCAACGCAAATATAC
Found at i:1479978 original size:18 final size:17
Alignment explanation
Indices: 1479947--1479996 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1479937 TATCATTTCA
1479947 ATATATTA-AATAAA-C
1 ATATATTACAATAAAGC
1479962 ATAGTAATTACAATAAAGC
1 ATA-T-ATTACAATAAAGC
1479981 ATATATTAACAATAAA
1 ATATATT-ACAATAAA
1479997 ACAAATCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 7 0.23
18 15 0.50
19 4 0.13
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (17 bp):
ATATATTACAATAAAGC
Found at i:1480326 original size:21 final size:21
Alignment explanation
Indices: 1480298--1480355 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1480288 AACCCTTCGA
*
1480298 TATCGATACCCCTTCTTATGG
1 TATCGATACCCCTTCTTAGGG
* *
1480319 TGTCGATACTACCC-TATTAGGG
1 TATCGATAC--CCCTTCTTAGGG
1480341 TATCGATACCCCTTC
1 TATCGATACCCCTTC
1480356 ATGTATCGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.10
21 9 0.31
22 14 0.48
23 3 0.10
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (21 bp):
TATCGATACCCCTTCTTAGGG
Found at i:1486332 original size:45 final size:44
Alignment explanation
Indices: 1486168--1486511 Score: 281
Period size: 45 Copynumber: 7.8 Consensus size: 44
1486158 GCTATAACAT
* * *
1486168 CTTTTCTATTGATAATGCACCCATATTCATTTCAAC-TATGTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCACCATAT-TATA
* * * * *
1486212 TTTTTCTGTTGATAATGTACCCATATATATGTCTACCATAATATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTC-ACCATATTATA
* * * *
1486257 CATTTATGTTGATAATGTACCAATATACATTTCTACCATATTATA
1 CTTTTCTGTTGATAATGCACCCATATACATTTC-ACCATATTATA
* * *
1486302 CTTTTCTGTTGATAATGTACCCATATACATTTCAAC-T-TTA-G
1 CTTTTCTGTTGATAATGCACCCATATACATTTCACCATATTATA
** ** **
1486343 CATGGTCTGTTGATAATGCACCCATATGTATTTCAACTC-TAGCATA
1 C-TTTTCTGTTGATAATGCACCCATATACATTTC-AC-CATATTATA
**
1486389 CTTTTCTGTTGATAATGCACCCATATGA-ATTTCGACTCA-AGCATA
1 CTTTTCTGTTGATAATGCACCCATAT-ACATTTC-AC-CATATTATA
* * * * *
1486434 CTTTTCTGTGGATAATGCACCCATATGCATTCCCACCAAATTATG
1 CTTTTCTGTTGATAATGCACCCATATACATT-TCACCATATTATA
*
1486479 CTTTTCTGTTGATAATGTA-CCATATACATTTCA
1 CTTTTCTGTTGATAATGCACCCATATACATTTCA
1486512 ACTAGGGCAT
Statistics
Matches: 245, Mismatches: 43, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 30 0.12
43 4 0.02
44 43 0.18
45 163 0.67
46 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.40
Consensus pattern (44 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCACCATATTATA
Found at i:1486421 original size:132 final size:134
Alignment explanation
Indices: 1486168--1486464 Score: 327
Period size: 132 Copynumber: 2.2 Consensus size: 134
1486158 GCTATAACAT
* * * ** *
1486168 CTTTTCTATTGATAATGCACCCATATTCATTTCAACTATGTATATTTTTCTGTTGATAATGTACC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATGTACATTGGTCTGTTGATAATGCACC
* * * *
1486233 CATATATATGTCTACCATAATATACATTTATGTTGATAATGTACCAATATACATTTCTAC-CATA
66 CATATATATGTCAACCATAACATACATTTATGTTGATAATGCACCAATATACATTTCGACTCA-A
**
1486297 TTATA
130 GCATA
*
1486302 CTTTTCTGTTGATAATGTACCCATATACATTTCAACT-T-TAGCA-TGGTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATGTA-CATTGGTCTGTTGATAATGCAC
* * * * * *
1486364 CCATATGTATTTCAACTC-TAGCATACTTTTCTGTTGATAATGCACCCATATGA-ATTTCGACTC
65 CCATATATATGTCAAC-CATAACATACATTTATGTTGATAATGCACCAATAT-ACATTTCGACTC
1486427 AAGCATA
128 AAGCATA
* *
1486434 CTTTTCTGTGGATAATGCACCCATATGCATT
1 CTTTTCTGTTGATAATGCACCCATATACATT
1486465 CCCACCAAAT
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
132 97 0.71
133 6 0.04
134 34 0.25
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (134 bp):
CTTTTCTGTTGATAATGCACCCATATACATTTCAACTATGTACATTGGTCTGTTGATAATGCACC
CATATATATGTCAACCATAACATACATTTATGTTGATAATGCACCAATATACATTTCGACTCAAG
CATA
Found at i:1486485 original size:177 final size:175
Alignment explanation
Indices: 1486176--1486514 Score: 450
Period size: 177 Copynumber: 1.9 Consensus size: 175
1486166 ATCTTTTCTA
* * *
1486176 TTGATAATGCACCCATATTCATTTCAACTATGTATATTTTTCTGTTGATAATGTACCCATATATA
1 TTGATAATGCACCCATATTCATTTCAACTATGCATACTTTTCTGTTGATAATGCACCCATATATA
* * * * * * *
1486241 TGTCTACCATAATATACATTTATGTTGATAATGTACCAATATACATTTCTACCATATTATACTTT
66 TGTCGACCATAACATACATTTATGTGGATAATGCACCAATATACATTCCCACCAAATTATACTTT
1486306 TCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATGGTCTG
131 TCTGTTGATAATGTA-CCATATACATTTCAACTTTAGCATGGTCTG
*
1486352 TTGATAATGCACCCATATGT-ATTTCAACTCTAGCATACTTTTCTGTTGATAATGCACCCATATG
1 TTGATAATGCACCCATAT-TCATTTCAACTAT-GCATACTTTTCTGTTGATAATGCACCCATAT-
* * * * * * *
1486416 A-ATTTCGACTCA-AGCATACTTTTCTGTGGATAATGCACCCATATGCATTCCCACCAAATTATG
63 ATATGTCGAC-CATAACATACATTTATGTGGATAATGCACCAATATACATTCCCACCAAATTATA
1486479 CTTTTCTGTTGATAATGTACCATATACATTTCAACT
127 CTTTTCTGTTGATAATGTACCATATACATTTCAACT
1486515 AGGGCATCAT
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
176 45 0.32
177 93 0.66
178 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (175 bp):
TTGATAATGCACCCATATTCATTTCAACTATGCATACTTTTCTGTTGATAATGCACCCATATATA
TGTCGACCATAACATACATTTATGTGGATAATGCACCAATATACATTCCCACCAAATTATACTTT
TCTGTTGATAATGTACCATATACATTTCAACTTTAGCATGGTCTG
Found at i:1487083 original size:22 final size:22
Alignment explanation
Indices: 1487053--1487110 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
1487043 CCCTCACCAT
*
1487053 GGTATCGATACCACTATGTTAC
1 GGTACCGATACCACTATGTTAC
1487075 GGTACCGATACCACTATGTTAC
1 GGTACCGATACCACTATGTTAC
1487097 GGTACCGATACCAC
1 GGTACCGATACCAC
1487111 CCTTAGGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (22 bp):
GGTACCGATACCACTATGTTAC
Done.