Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 3 of 32
Found at i:948729 original size:43 final size:43
Alignment explanation
Indices: 948682--948764 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
948672 TTCTAAGTAA
948682 TAAAAT-CAAAATAACTTTTACTATAATTAAATAATATTTTCAC
1 TAAAATACAAAAT-ACTTTTACTATAATTAAATAATATTTTCAC
* * *
948725 TAAAATACAAAATATTTTTATTATAATTTAATAATATTTT
1 TAAAATACAAAATACTTTTACTATAATTAAATAATATTTT
948765 TATTAGAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 30 0.83
44 6 0.17
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (43 bp):
TAAAATACAAAATACTTTTACTATAATTAAATAATATTTTCAC
Found at i:948760 original size:22 final size:22
Alignment explanation
Indices: 948697--948806 Score: 91
Period size: 22 Copynumber: 5.0 Consensus size: 22
948687 TCAAAATAAC
*
948697 TTTTACTATAATTAAATAATAT
1 TTTTATTATAATTAAATAATAT
* * *
948719 TTTCACTA-AAATACAA-AATAT
1 TTTTATTATAATTA-AATAATAT
*
948740 TTTTATTATAATTTAATAATAT
1 TTTTATTATAATTAAATAATAT
* * * *
948762 TTTTATTAGAAGATAATTAA-ACC
1 TTTTATTATAA-TTAAATAATA-T
948785 TTTTATTATAATTAAATAATAT
1 TTTTATTATAATTAAATAATAT
948807 GTAATATTAA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
21 17 0.25
22 34 0.51
23 16 0.24
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTATTATAATTAAATAATAT
Found at i:950738 original size:13 final size:13
Alignment explanation
Indices: 950720--950771 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
950710 CAAGCTTATG
950720 TTATTAATATAAC
1 TTATTAATATAAC
950733 TTATT-ATATTAAC
1 TTATTAATA-TAAC
**
950746 TTATTTTTATATAC
1 TTATTAATATA-AC
950760 ATTATTAATATA
1 -TTATTAATATA
950772 TTATGCTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.09
13 16 0.50
14 4 0.12
15 9 0.28
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (13 bp):
TTATTAATATAAC
Found at i:952022 original size:14 final size:15
Alignment explanation
Indices: 951995--952032 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
951985 TTTCAATTTA
*
951995 TATTATTAATTTTATT
1 TATTATTTA-TTTATT
952011 TA-TATTTATTTATT
1 TATTATTTATTTATT
952025 TATTATTT
1 TATTATTT
952033 CTATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 10 0.50
16 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTTATTTATT
Found at i:952054 original size:26 final size:27
Alignment explanation
Indices: 951998--952054 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
951988 CAATTTATAT
* * *
951998 TATTAATTTTATTTATATTTATTTATT
1 TATTAATTTTATTTATATTCATTCATA
952025 TATT-ATTTCTATTT-TATTCATTCATA
1 TATTAATTT-TATTTATATTCATTCATA
952051 TATT
1 TATT
952055 CGAAGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTAATTTTATTTATATTCATTCATA
Found at i:952086 original size:14 final size:14
Alignment explanation
Indices: 952067--952110 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
952057 AAGTTTCTAT
952067 AAATTTTTTTTCTC
1 AAATTTTTTTTCTC
952081 AAA--TTTTTT-T-
1 AAATTTTTTTTCTC
*
952091 AAATTTTCTTTCTC
1 AAATTTTTTTTCTC
952105 AAATTT
1 AAATTT
952111 CTACAAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 3 0.12
11 1 0.04
12 11 0.44
13 1 0.04
14 9 0.36
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.61
Consensus pattern (14 bp):
AAATTTTTTTTCTC
Found at i:953346 original size:21 final size:20
Alignment explanation
Indices: 953322--953366 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
953312 TTAAAGTAAT
953322 TTAAAATAAAATAATATAAAA
1 TTAAAATAAAATAAT-TAAAA
* *
953343 TTAAACTAAAATAATTTAAA
1 TTAAAATAAAATAATTAAAA
953363 TTAA
1 TTAA
953367 TTACTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAATAAAATAATTAAAA
Found at i:953786 original size:15 final size:18
Alignment explanation
Indices: 953751--953790 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
953741 TATCCTATAG
953751 TAATATAACTTATATTAA
1 TAATATAACTTATATTAA
953769 TAAT-TAAC-TATATT-A
1 TAATATAACTTATATTAA
953784 TAATATA
1 TAATATA
953791 TAACAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 4 0.19
18 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATAACTTATATTAA
Found at i:953794 original size:18 final size:18
Alignment explanation
Indices: 953753--953810 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
953743 TCCTATAGTA
953753 ATATAACT-TA-TATTAAT
1 ATATAACTATATTA-TAAT
953770 A-ATTAACTATATTATAAT
1 ATA-TAACTATATTATAAT
953788 ATATAACAATATATTAT-AT
1 ATATAAC--TATATTATAAT
953807 ATAT
1 ATAT
953811 TATATAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 6 0.17
18 11 0.31
19 9 0.26
20 8 0.23
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAACTATATTATAAT
Found at i:955277 original size:21 final size:20
Alignment explanation
Indices: 955252--955318 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 20
955242 CCAGAGTTGC
955252 AAGCTGAAAATCAGAGGATGA
1 AAGCTG-AAATCAGAGGATGA
955273 AAGCTGAAATCGAGAGGATGA
1 AAGCTGAAATC-AGAGGATGA
*
955294 AAGCTGAAATGGAGAGGATGA
1 AAGCTGAAAT-CAGAGGATGA
955315 AAGC
1 AAGC
955319 GGGGCAAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 5 0.12
21 38 0.88
ACGTcount: A:0.45, C:0.09, G:0.33, T:0.13
Consensus pattern (20 bp):
AAGCTGAAATCAGAGGATGA
Found at i:960476 original size:35 final size:35
Alignment explanation
Indices: 960430--960504 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
960420 TAAGTTAATA
960430 TATATTTAAAGGATTATTGTTTTAAGAATGGGTTC
1 TATATTTAAAGGATTATTGTTTTAAGAATGGGTTC
960465 TATATTTAAAGGATTATTGTTTTAAGAATGGGTTC
1 TATATTTAAAGGATTATTGTTTTAAGAATGGGTTC
960500 TATAT
1 TATAT
960505 ATTTTCCTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47
Consensus pattern (35 bp):
TATATTTAAAGGATTATTGTTTTAAGAATGGGTTC
Found at i:967466 original size:292 final size:293
Alignment explanation
Indices: 967151--967713 Score: 862
Period size: 292 Copynumber: 1.9 Consensus size: 293
967141 CTTGAGTCGG
* ** *
967151 CCTCTGTGTTTGATGCGCTAGATAATCTTGATATCAGTTCTCTTTTCACTGATCATGACCTTGCT
1 CCTCTGTGTTTGATGCGCTAGATAATCATGATATCAGTGATCTTTCCACTGATCATGACCTTGCT
* * * *
967216 GCCGGTAATCAATCAAGTCTTTACGTTCCATCATATTGTTTCATCTTGTTTGCATCTTATTCTTC
66 GCCGGTAATCAATCAAGTCTTCACGTTCCATCATATTGTTTCATCTTATTTACATCTTATTATTC
* *
967281 CCTCAATTTTGCCTTTTGTGTTAGTTAATTTTAACTCTT-AACTACAATGTCTTCTTATGTATAG
131 CCTCAAATTTGCCTTTTGTGTTAGTTAAATTTAACTCTTGAACTACAATGTCTTCTTATGTATAG
** * *
967345 CTTCTTAAATTTACTCATCCTGATTATTTTCTTGGT-TGATTTAGAATTTCCAAA-TCTCTCAGC
196 CTTAGTAAACTTACTCATCCTGATTATTTTCTT-GTATAATTTAGAATTTCCAAATTC-CTCAGC
967408 AGCTGGCCCCTCCTTTATCACAGATCATGACTTGA
259 AGCTGGCCCCTCCTTTATCACAGATCATGACTTGA
*
967443 CCTCTGTGTTTGATGCGCTAGATAGTCATGATATCAGTGATCTTTCCACTGATCATGACCTTGCT
1 CCTCTGTGTTTGATGCGCTAGATAATCATGATATCAGTGATCTTTCCACTGATCATGACCTTGCT
* * *
967508 GCGGGTAATCAATCAAGTCTTCACGTTCCATCGTATTGTTTCATCTTATTTATATCTTATTATTC
66 GCCGGTAATCAATCAAGTCTTCACGTTCCATCATATTGTTTCATCTTATTTACATCTTATTATTC
*
967573 CCTCAAATTTGCCTTTTGTGTTAGTTAAATTTAACTCTTGAACTGCAATGTCTTCTTATGTATAG
131 CCTCAAATTTGCCTTTTGTGTTAGTTAAATTTAACTCTTGAACTACAATGTCTTCTTATGTATAG
* * * *
967638 CTTAGTGAACTTACTTATCCTGATTATTTTCTTGTAGTAATTTAGAATTTCCAACTTCCTCTGCA
196 CTTAGTAAACTTACTCATCCTGATTATTTTCTTGTA-TAATTTAGAATTTCCAAATTCCTCAGCA
*
967703 GCTGGCTCCTC
260 GCTGGCCCCTC
967714 ATTTGTTGCA
Statistics
Matches: 243, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
292 157 0.65
293 52 0.21
294 32 0.13
295 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (293 bp):
CCTCTGTGTTTGATGCGCTAGATAATCATGATATCAGTGATCTTTCCACTGATCATGACCTTGCT
GCCGGTAATCAATCAAGTCTTCACGTTCCATCATATTGTTTCATCTTATTTACATCTTATTATTC
CCTCAAATTTGCCTTTTGTGTTAGTTAAATTTAACTCTTGAACTACAATGTCTTCTTATGTATAG
CTTAGTAAACTTACTCATCCTGATTATTTTCTTGTATAATTTAGAATTTCCAAATTCCTCAGCAG
CTGGCCCCTCCTTTATCACAGATCATGACTTGA
Found at i:970506 original size:2 final size:2
Alignment explanation
Indices: 970499--970537 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
970489 AGCAGGAAAG
970499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
970538 CCATTAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:976664 original size:35 final size:35
Alignment explanation
Indices: 976625--976695 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
976615 TGGCTATTAA
976625 TAGGATTAATTCTTTTATAAAATAAAGAAAAGCAT
1 TAGGATTAATTCTTTTATAAAATAAAGAAAAGCAT
976660 TAGGATTAATTCTTTTATAAAATAAAGAAAAGCAT
1 TAGGATTAATTCTTTTATAAAATAAAGAAAAGCAT
976695 T
1 T
976696 CTCTCTGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (35 bp):
TAGGATTAATTCTTTTATAAAATAAAGAAAAGCAT
Found at i:995038 original size:28 final size:28
Alignment explanation
Indices: 995007--995065 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
994997 AATATATTAC
995007 AAACAAATAAATTACATCAAAAATAAAT
1 AAACAAATAAATTACATCAAAAATAAAT
* *
995035 AAACAAATACATTACATCAAATATAAAT
1 AAACAAATAAATTACATCAAAAATAAAT
995063 AAA
1 AAA
995066 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (28 bp):
AAACAAATAAATTACATCAAAAATAAAT
Found at i:998481 original size:27 final size:27
Alignment explanation
Indices: 998424--998481 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
998414 GTCCATCTGG
* *
998424 TGAACTAAGGTATCCTTTGTGCACTTT
1 TGAACTAAGGTATCCTTTGCGCACTTC
*
998451 TGAACTAAGGTATCCTTTGCGCAGTTC
1 TGAACTAAGGTATCCTTTGCGCACTTC
998478 TGAA
1 TGAA
998482 AGGCTGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (27 bp):
TGAACTAAGGTATCCTTTGCGCACTTC
Found at i:1003637 original size:51 final size:51
Alignment explanation
Indices: 1003556--1003660 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
1003546 CAAAGTTGAA
*
1003556 GGCCCTCGAGAAGGATTACTTTCTTCTACTACTAAACTATGCTCTTTTGGT
1 GGCCCTCGAGAAGGACTACTTTCTTCTACTACTAAACTATGCTCTTTTGGT
* * *
1003607 GGCCCTTGAGAAGTACTACTTTCTTGTACTACTAAACTATGCTCTTTTGGT
1 GGCCCTCGAGAAGGACTACTTTCTTCTACTACTAAACTATGCTCTTTTGGT
1003658 GGC
1 GGC
1003661 TTTTGAATCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (51 bp):
GGCCCTCGAGAAGGACTACTTTCTTCTACTACTAAACTATGCTCTTTTGGT
Found at i:1013863 original size:2 final size:2
Alignment explanation
Indices: 1013856--1013892 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1013846 TAGTCTAATT
1013856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1013893 TTGGTTGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1014826 original size:2 final size:2
Alignment explanation
Indices: 1014819--1014851 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1014809 CAATATCAAC
1014819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1014852 AAGAGAGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1029139 original size:26 final size:28
Alignment explanation
Indices: 1029089--1029159 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 28
1029079 AAATGACGTG
* *
1029089 ATATTAATAATTTATTTTAAAATAA-AA
1 ATATTAATAATTTAATTGAAAATAATAA
*
1029116 AT-TTAATAATTTAATTGAACATAATAA
1 ATATTAATAATTTAATTGAAAATAATAA
* *
1029143 ATAATAAAAATTTAATT
1 ATATTAATAATTTAATT
1029160 AATTATTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.51
27 6 0.16
28 12 0.32
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
ATATTAATAATTTAATTGAAAATAATAA
Found at i:1031575 original size:14 final size:14
Alignment explanation
Indices: 1031556--1031585 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1031546 TACATATACA
1031556 GGAGGTCAGGTTGT
1 GGAGGTCAGGTTGT
1031570 GGAGGTCAGGTTGT
1 GGAGGTCAGGTTGT
1031584 GG
1 GG
1031586 TGATATCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.53, T:0.27
Consensus pattern (14 bp):
GGAGGTCAGGTTGT
Found at i:1041668 original size:2 final size:2
Alignment explanation
Indices: 1041663--1041687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1041653 ACACACACAC
1041663 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1041688 TAATCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1043778 original size:24 final size:23
Alignment explanation
Indices: 1043751--1043804 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
1043741 TTTAAAATGT
1043751 ATAAACAAA-AAAGAATTAAAAGAA
1 ATAAA-AAACAAAGAATTAAAA-AA
*
1043775 ATAAAAAACTAAGAATTAAAAAA
1 ATAAAAAACAAAGAATTAAAAAA
1043798 ATAAAAA
1 ATAAAAA
1043805 TGAAAAAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.15
Consensus pattern (23 bp):
ATAAAAAACAAAGAATTAAAAAA
Found at i:1043788 original size:15 final size:15
Alignment explanation
Indices: 1043770--1043811 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1043760 AAAGAATTAA
*
1043770 AAGAAATAAAAAACT
1 AAGAAATAAAAAAAT
*
1043785 AAGAATTAAAAAAAT
1 AAGAAATAAAAAAAT
1043800 AA-AAATGAAAAA
1 AAGAAAT-AAAAA
1043812 GTGAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.14
Consensus pattern (15 bp):
AAGAAATAAAAAAAT
Found at i:1058827 original size:16 final size:15
Alignment explanation
Indices: 1058780--1058827 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1058770 GACCCTTTTG
*
1058780 AATAAAAATAAAATAA
1 AATAAAAA-AAAAAAA
*
1058796 AATAAAAAAAGGAAAA
1 AATAAAAAAA-AAAAA
*
1058812 GATAAAAAAAAAAAA
1 AATAAAAAAAAAAAA
1058827 A
1 A
1058828 CGGAAATCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.10
Consensus pattern (15 bp):
AATAAAAAAAAAAAA
Found at i:1062938 original size:11 final size:11
Alignment explanation
Indices: 1062909--1062949 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
1062899 AAATATTTAA
1062909 ATATTTTTATT
1 ATATTTTTATT
1062920 -TATGTTTTATT
1 ATAT-TTTTATT
*
1062931 AAATTTTTA-T
1 ATATTTTTATT
1062941 ATATTTTTA
1 ATATTTTTA
1062950 AGTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 12 0.46
11 12 0.46
12 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
ATATTTTTATT
Found at i:1062961 original size:27 final size:25
Alignment explanation
Indices: 1062930--1062997 Score: 77
Period size: 24 Copynumber: 2.7 Consensus size: 25
1062920 TATGTTTTAT
*
1062930 TAAATTTTTATATATTTTTAAGTTAAA
1 TAAATTTTTATATATTTATAA-TT-AA
*
1062957 TAAATTTTTATA-ATTAATAATTAA
1 TAAATTTTTATATATTTATAATTAA
*
1062981 TAAATTATTAT-TATTTA
1 TAAATTTTTATATATTTA
1062998 AAATACTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 16 0.44
25 2 0.06
26 6 0.17
27 12 0.33
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TAAATTTTTATATATTTATAATTAA
Found at i:1063296 original size:8 final size:8
Alignment explanation
Indices: 1063271--1063330 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
1063261 GGGCTAAAAA
1063271 AATAATTTT
1 AATAA-TTT
1063280 AATTAATTT
1 AA-TAATTT
1063289 AATAATTT
1 AATAATTT
*
1063297 TATATATTT
1 AATA-ATTT
* *
1063306 AATTATAT
1 AATAATTT
1063314 AA-AA-TT
1 AATAATTT
1063320 AATAATTT
1 AATAATTT
1063328 AAT
1 AAT
1063331 TATTAATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 19 0.46
9 13 0.32
10 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATAATTT
Found at i:1066614 original size:15 final size:15
Alignment explanation
Indices: 1066594--1066625 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1066584 CAAAATTGGG
1066594 AAGAAGAACAATAAC
1 AAGAAGAACAATAAC
1066609 AAGAAGAACAATAAC
1 AAGAAGAACAATAAC
1066624 AA
1 AA
1066626 TAACAGCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (15 bp):
AAGAAGAACAATAAC
Found at i:1074340 original size:21 final size:21
Alignment explanation
Indices: 1074319--1074357 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1074309 ATTTAATTTA
1074319 AAATAAAAAT-ATAAAAAATT
1 AAATAAAAATAATAAAAAATT
* *
1074339 AATTAAACATAATAAAAAA
1 AAATAAAAATAATAAAAAA
1074358 GATTTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAAAAATAATAAAAAATT
Found at i:1096416 original size:20 final size:20
Alignment explanation
Indices: 1096378--1096415 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1096368 AATCTTAAAT
*
1096378 TTAAAAAAATATTAATTTTC
1 TTAAAAAAATAATAATTTTC
1096398 TTAAAAAAATAAT-ATTTT
1 TTAAAAAAATAATAATTTT
1096416 TAAATATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAAAATAATAATTTTC
Found at i:1119174 original size:27 final size:27
Alignment explanation
Indices: 1119060--1119308 Score: 167
Period size: 27 Copynumber: 9.0 Consensus size: 27
1119050 CATTATGACG
1119060 TGTAATAATTAAATTTTTAGA-ATACGACA
1 TGTAATAATTAAATTTTTA-ACATA--ACA
* * * * *
1119089 TGTAACAACTAAATGTTTAACATTATA
1 TGTAATAATTAAATTTTTAACATAACA
* * * * *
1119116 TATAACAATTACATTTTTTAACATGACG
1 TGTAATAATTA-AATTTTTAACATAACA
* *
1119144 TGTAATAATTACATTTTTAATATAACA
1 TGTAATAATTAAATTTTTAACATAACA
* * *
1119171 TGTAACAATTACATTTTTTAACATGACA
1 TGTAATAATTA-AATTTTTAACATAACA
* *
1119199 TGTAATAACTAAATTTTTAACATAATA
1 TGTAATAATTAAATTTTTAACATAACA
** * * *
1119226 CATAATAATTAAATCTTCAATATAACA
1 TGTAATAATTAAATTTTTAACATAACA
* * * **
1119253 TGTAATAACTATATTTTTCAACCTAATG
1 TGTAATAATTAAATTTTT-AACATAACA
* * *
1119281 TGTAACAATTAAATCTTCAACATAACA
1 TGTAATAATTAAATTTTTAACATAACA
1119308 T
1 T
1119309 ATGACAATTA
Statistics
Matches: 162, Mismatches: 54, Indels: 10
0.72 0.24 0.04
Matches are distributed among these distances:
27 84 0.52
28 60 0.37
29 18 0.11
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.39
Consensus pattern (27 bp):
TGTAATAATTAAATTTTTAACATAACA
Found at i:1119285 original size:82 final size:82
Alignment explanation
Indices: 1119146--1119305 Score: 185
Period size: 82 Copynumber: 2.0 Consensus size: 82
1119136 ACATGACGTG
* * * * * * *
1119146 TAATAATTACATTTTTAATATAACATGTAACAATTACATTTTTTAACATGACATGTAATAACTAA
1 TAATAATTAAATCTTCAATATAACATGTAACAACTACATTTTTCAACATAACATGTAACAACTAA
* *
1119211 ATTTTTAACATAATACA
66 ATCTTCAACATAATACA
* * * ** *
1119228 TAATAATTAAATCTTCAATATAACATGTAATAACTATATTTTTCAACCTAATGTGTAACAATTAA
1 TAATAATTAAATCTTCAATATAACATGTAACAACTACATTTTTCAACATAACATGTAACAACTAA
1119293 ATCTTCAACATAA
66 ATCTTCAACATAA
1119306 CATATGACAA
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (82 bp):
TAATAATTAAATCTTCAATATAACATGTAACAACTACATTTTTCAACATAACATGTAACAACTAA
ATCTTCAACATAATACA
Found at i:1119307 original size:55 final size:54
Alignment explanation
Indices: 1119086--1119308 Score: 203
Period size: 55 Copynumber: 4.1 Consensus size: 54
1119076 TTAGAATACG
* * * * * * * *
1119086 ACATGTAACAACTAAATGTTTAACATTATATATAACAATTACATTTTTTAACATG
1 ACATGTAATAACTAAATTTTTAACATAATATGTAACAATTA-AATCTTCAACATA
* * * * * * * * *
1119141 ACGTGTAATAATTACATTTTTAATATAACATGTAACAATTACATTTTTTAACATG
1 ACATGTAATAACTAAATTTTTAACATAATATGTAACAATTA-AATCTTCAACATA
** * *
1119196 ACATGTAATAACTAAATTTTTAACATAATACATAATAATTAAATCTTCAATATA
1 ACATGTAATAACTAAATTTTTAACATAATATGTAACAATTAAATCTTCAACATA
* * *
1119250 ACATGTAATAACTATATTTTTCAACCTAATGTGTAACAATTAAATCTTCAACATA
1 ACATGTAATAACTAAATTTTT-AACATAATATGTAACAATTAAATCTTCAACATA
1119305 ACAT
1 ACAT
1119309 ATGACAATTA
Statistics
Matches: 138, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
54 28 0.20
55 110 0.80
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (54 bp):
ACATGTAATAACTAAATTTTTAACATAATATGTAACAATTAAATCTTCAACATA
Found at i:1128475 original size:21 final size:21
Alignment explanation
Indices: 1128434--1128476 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1128424 TTTCTCGATA
* *
1128434 TTATAATGTAGTATTGATATT
1 TTATAATATAATATTGATATT
1128455 TTATAATATAATA-TGATTATT
1 TTATAATATAATATTGA-TATT
1128476 T
1 T
1128477 GTAATATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (21 bp):
TTATAATATAATATTGATATT
Found at i:1128552 original size:21 final size:21
Alignment explanation
Indices: 1128499--1128555 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1128489 AAATTAATGG
*
1128499 AATTATAAA-AGATTTTATAT
1 AATTATAAATATATTTTATAT
*
1128519 AATTTTAAATATATTTTATAT
1 AATTATAAATATATTTTATAT
*
1128540 -ATTATATATTATATTT
1 AATTATA-AATATATTT
1128556 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTATAAATATATTTTATAT
Found at i:1134052 original size:78 final size:78
Alignment explanation
Indices: 1133919--1134072 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 78
1133909 TAGTGGCATT
*
1133919 CAGCGAGAGTTCAAAAAGTCAAGGACCCTCGCCCTCCATCGGCCCCACCCACGGCGCGCGCTTCT
1 CAGCGAGAGTTCAAAAAGTCAAGGACCCTCACCCTCCATCGGCCCCACCCACGGCGCGCGCTTCT
1133984 CTTCCACAAACTC
66 CTTCCACAAACTC
*
1133997 CAGCGAGAGTTCAAAAAGTCAAGGACCCTCACCCTCCATCGGCCCCACCCCCGGCGCGCGCTTCT
1 CAGCGAGAGTTCAAAAAGTCAAGGACCCTCACCCTCCATCGGCCCCACCCACGGCGCGCGCTTCT
*
1134062 CTTCTACAAAC
66 CTTCCACAAAC
1134073 CACCCTCGCC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 73 1.00
ACGTcount: A:0.23, C:0.42, G:0.19, T:0.16
Consensus pattern (78 bp):
CAGCGAGAGTTCAAAAAGTCAAGGACCCTCACCCTCCATCGGCCCCACCCACGGCGCGCGCTTCT
CTTCCACAAACTC
Found at i:1134108 original size:53 final size:53
Alignment explanation
Indices: 1134021--1134136 Score: 187
Period size: 53 Copynumber: 2.2 Consensus size: 53
1134011 AAAGTCAAGG
* * *
1134021 ACCCTCACCCTCCATCGGCCCCACCCCCGGCGCGCGCTTCTCTTCTACAAACC
1 ACCCTCGCCCTCCATCGGCCCCACACACGGCGCGCGCTTCTCTTCTACAAACC
* *
1134074 ACCCTCGCCCTCCATCGGCCCCACACACGTCGCGCGCTTGTCTTCTACAAACC
1 ACCCTCGCCCTCCATCGGCCCCACACACGGCGCGCGCTTCTCTTCTACAAACC
1134127 ACCCTCGCCC
1 ACCCTCGCCC
1134137 ACAGCAGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.16, C:0.53, G:0.14, T:0.17
Consensus pattern (53 bp):
ACCCTCGCCCTCCATCGGCCCCACACACGGCGCGCGCTTCTCTTCTACAAACC
Found at i:1135131 original size:2 final size:2
Alignment explanation
Indices: 1135126--1135152 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1135116 TATATATATA
1135126 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1135153 TTTGATGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1145591 original size:17 final size:16
Alignment explanation
Indices: 1145558--1145592 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1145548 GTGAAGCGCG
1145558 TTTTAATTAATTATTT
1 TTTTAATTAATTATTT
1145574 TTTTAATTTAA-TATTT
1 TTTTAA-TTAATTATTT
1145590 TTT
1 TTT
1145593 GCCACCCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTAATTATTT
Found at i:1148029 original size:20 final size:21
Alignment explanation
Indices: 1147991--1148029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1147981 CTGAAAAGAG
*
1147991 ACAAGTGATCAGCACCTTGTC
1 ACAAGTGATCAGAACCTTGTC
1148012 ACAAGTGATCA-AACCTTG
1 ACAAGTGATCAGAACCTTG
1148030 CTCNNNNNNN
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
ACAAGTGATCAGAACCTTGTC
Found at i:1159501 original size:3 final size:3
Alignment explanation
Indices: 1159487--1159527 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1159477 TACATTTCCT
* *
1159487 TGC TGC TCC TGC TGC TGC TGC TGT TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1159528 ATGATGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.37
Consensus pattern (3 bp):
TGC
Found at i:1176230 original size:29 final size:28
Alignment explanation
Indices: 1176155--1176232 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 28
1176145 AATTAATTAA
* *
1176155 AAATTTAAATAAAATTATATATTTTTATT
1 AAATTT-AATAAATTTTTATATTTTTATT
* *
1176184 ATATTAAATCAAATTTTT-TAATTTTTATTTT
1 AAATTTAAT-AAATTTTTAT-ATTTTTA--TT
1176215 AAATTTAATAAATTTTTA
1 AAATTTAATAAATTTTTA
1176233 CAAAATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.11
29 17 0.45
30 8 0.21
31 9 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATTTAATAAATTTTTATATTTTTATT
Found at i:1188139 original size:57 final size:57
Alignment explanation
Indices: 1188051--1188165 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
1188041 AGAAAAACTA
1188051 TGGCAAACATTAACATGAACCTACTGTACAGGGCATCTCTAGATTTGCCAATGATTT
1 TGGCAAACATTAACATGAACCTACTGTACAGGGCATCTCTAGATTTGCCAATGATTT
1188108 TGGCAAACATTAACATGAACCTACTGTACAGGGCATCTCTAGATTTGCCAATGATTT
1 TGGCAAACATTAACATGAACCTACTGTACAGGGCATCTCTAGATTTGCCAATGATTT
1188165 T
1 T
1188166 AACAAAAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (57 bp):
TGGCAAACATTAACATGAACCTACTGTACAGGGCATCTCTAGATTTGCCAATGATTT
Found at i:1192246 original size:18 final size:19
Alignment explanation
Indices: 1192223--1192266 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1192213 GAAAGAAAAA
1192223 TAAAAATGATAT-AA-TATT
1 TAAAAAT-ATATAAATTATT
*
1192241 TAAAAATTTATAAATTATT
1 TAAAAATATATAAATTATT
1192260 TAAAAAT
1 TAAAAAT
1192267 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 9 0.39
19 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAAATATATAAATTATT
Found at i:1192259 original size:19 final size:19
Alignment explanation
Indices: 1192237--1192279 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1192227 AATGATATAA
1192237 TATTTAAAAATTTATAAAT
1 TATTTAAAAATTTATAAAT
*
1192256 TATTTAAAAATTTTTAAAT
1 TATTTAAAAATTTATAAAT
*
1192275 AATTT
1 TATTT
1192280 TTTATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAAAAATTTATAAAT
Found at i:1192297 original size:27 final size:26
Alignment explanation
Indices: 1192267--1192324 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1192257 ATTTAAAAAT
*
1192267 TTTTAAAT-AATTTTTTATTATTTATTA
1 TTTTAAATCAAATTTTTA-TATTT-TTA
*
1192294 TTTTTAATCAAATTTTTATATTTTTA
1 TTTTAAATCAAATTTTTATATTTTTA
1192320 TTTTA
1 TTTTA
1192325 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.26
27 12 0.44
28 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTAAATCAAATTTTTATATTTTTA
Found at i:1192298 original size:29 final size:27
Alignment explanation
Indices: 1192266--1192342 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
1192256 TATTTAAAAA
1192266 TTTTTAAATAATTTTT-TATTATTTATT
1 TTTTTAAATAATTTTTATATT-TTTATT
1192293 ATTTTT-AATCAAATTTTTATATTTTTATT
1 -TTTTTAAAT--AATTTTTATATTTTTATT
*
1192322 TTATTTAAATAAATATTTATA
1 TT-TTTAAAT-AATTTTTATA
1192343 ATTAATGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 3 0.07
28 7 0.16
29 26 0.60
30 7 0.16
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTAAATAATTTTTATATTTTTATT
Found at i:1192309 original size:28 final size:26
Alignment explanation
Indices: 1192265--1192342 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 26
1192255 TTATTTAAAA
*
1192265 ATTTTTAAATAATTTTTTATTATTTATT
1 ATTTTTAAATAAATTTTTA-TATTT-TT
1192293 ATTTTT-AATCAAATTTTTATATTTTT
1 ATTTTTAAAT-AAATTTTTATATTTTT
*
1192319 ATTTTATTTAAATAAATATTTATA
1 A--TT-TTTAAATAAATTTTTATA
1192343 ATTAATGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 3 0.07
27 8 0.19
28 16 0.37
29 13 0.30
30 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTTAAATAAATTTTTATATTTTT
Found at i:1192331 original size:25 final size:28
Alignment explanation
Indices: 1192265--1192323 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1192255 TTATTTAAAA
*
1192265 ATTTTTAAAT-AATTTTTTATTATTTATT
1 ATTTTT-AATCAAATTTTTATTATTTATT
1192293 ATTTTTAATCAAATTTTTA-TATTT-TT
1 ATTTTTAATCAAATTTTTATTATTTATT
1192319 ATTTT
1 ATTTT
1192324 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.24
27 8 0.28
28 14 0.48
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
ATTTTTAATCAAATTTTTATTATTTATT
Found at i:1192591 original size:30 final size:28
Alignment explanation
Indices: 1192556--1192629 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1192546 AACTATTAAT
**
1192556 AATAAAAATTTATTTGATTTAAAATAAAA
1 AATAAAAATTTATTT-AAATAAAATAAAA
* *
1192585 ATATAAAAATTTAATTAAATATAATAAAA
1 A-ATAAAAATTTATTTAAATAAAATAAAA
*
1192614 AATAAAAAGTTATTTA
1 AATAAAAATTTATTTA
1192630 TACCAAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 13 0.34
29 12 0.32
30 13 0.34
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAAAAATTTATTTAAATAAAATAAAA
Found at i:1193154 original size:17 final size:16
Alignment explanation
Indices: 1193132--1193180 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1193122 TTTAAATAAA
1193132 AAAATTATAATATTTTT
1 AAAATTATAAT-TTTTT
*
1193149 AAAATTTTAATTTTTT
1 AAAATTATAATTTTTT
1193165 AATTAATTA-AATTTTT
1 AA--AATTATAATTTTT
1193181 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 17 0.61
18 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAAATTATAATTTTTT
Found at i:1206132 original size:209 final size:206
Alignment explanation
Indices: 1205728--1206110 Score: 473
Period size: 209 Copynumber: 1.8 Consensus size: 206
1205718 ACCTGGAATT
* * * * *
1205728 CAATGCAATTCAACGAAGTCTCGGATTTTTAAAGGAGAATTCCAGTATTGAAGCATAATTTTTGT
1 CAATGCAATTCAACAAAG-CTCGAATTTTTAAAGGAGAATTCAAATATTGAAGCAAAATTTTTGT
** * * *
1205793 TAGGGGAAGAGAAAATCTTATTATATAATATAAAATTGTATAAGTTGAGAAATTTAAATTATAAA
65 TAGAAGAAGAGAAAATC-T-TTATATAATATAAAACTGTACAAGTTGAGAAATATAAATTATAAA
*
1205858 TCGAAAAATCTAAAATCTAAATATATATAATGTTAATCTTACTAAATATAATTTTGACTAACTAA
128 TCGAAAAATCTAAAATCTAAATATATATAAGGTTAATCTTACTAAATATAATTTT-A-TAACTAA
1205923 CAGAATTATAGTATAA
191 CAGAATTATAGTATAA
* * * *
1205939 CAATGTAATTCAACAAAG-TCGAATTTTTATAGGAGAGTTCAAATATTTAAGCAAAATTTTTGTT
1 CAATGCAATTCAACAAAGCTCGAATTTTTAAAGGAGAATTCAAATATTGAAGCAAAATTTTTGTT
*
1206003 AGAAGAAGAGAAAATC-TTATATAATATAAAACTGTACAAGTTATAGAGAGATATAAATTATAAA
66 AGAAGAAGAGAAAATCTTTATATAATATAAAACTGTACAAG-T-T-GAGAAATATAAATTATAAA
* * *
1206067 TTGAGAAATTTAAAATCTATATATATATATAAAAGGTTAATCTT
128 TCGAAAAATCTAAAATCTA-A-ATATATAT--AAGGTTAATCTT
1206111 TTTAAGTCTA
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
206 22 0.15
207 1 0.01
208 1 0.01
209 86 0.59
210 1 0.01
211 24 0.16
213 11 0.08
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (206 bp):
CAATGCAATTCAACAAAGCTCGAATTTTTAAAGGAGAATTCAAATATTGAAGCAAAATTTTTGTT
AGAAGAAGAGAAAATCTTTATATAATATAAAACTGTACAAGTTGAGAAATATAAATTATAAATCG
AAAAATCTAAAATCTAAATATATATAAGGTTAATCTTACTAAATATAATTTTATAACTAACAGAA
TTATAGTATAA
Found at i:1209413 original size:2 final size:2
Alignment explanation
Indices: 1209406--1209430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1209396 TAAGGATCAA
1209406 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1209431 GAGACTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1210745 original size:42 final size:42
Alignment explanation
Indices: 1210686--1210768 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
1210676 CAACCATTGG
1210686 TGGTGGGGCAGATATGAGTGCAGCGGCTTCTGCTGTTAATGC
1 TGGTGGGGCAGATATGAGTGCAGCGGCTTCTGCTGTTAATGC
1210728 TGGTGGGGCAGATATGAGTGCAGCGGCTTCTGCTGTTAATG
1 TGGTGGGGCAGATATGAGTGCAGCGGCTTCTGCTGTTAATG
1210769 AGGTTGCCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.39, T:0.29
Consensus pattern (42 bp):
TGGTGGGGCAGATATGAGTGCAGCGGCTTCTGCTGTTAATGC
Found at i:1211190 original size:3 final size:3
Alignment explanation
Indices: 1211182--1211221 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1211172 GTTAAAATTG
* *
1211182 TTA TTA TTA TGA TTA TTA CTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1211222 GTGGTTTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1216090 original size:20 final size:19
Alignment explanation
Indices: 1216037--1216103 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
1216027 ATTTAGGGTA
1216037 AAATATTTTAAATTTTAAAT
1 AAATATTTT-AATTTTAAAT
*
1216057 TAAT-TTATTAATTTTTAATAT
1 AAATATT-TTAA-TTTTAA-AT
1216078 AAATATTTT-ATTTTAAA-
1 AAATATTTTAATTTTAAAT
1216095 AAATATTTT
1 AAATATTTT
1216104 CTACTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 9 0.22
18 1 0.02
19 10 0.24
20 12 0.29
21 7 0.17
22 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATTTTAATTTTAAAT
Found at i:1217336 original size:768 final size:772
Alignment explanation
Indices: 1215840--1217364 Score: 1919
Period size: 768 Copynumber: 2.0 Consensus size: 772
1215830 CCTCTTGTAC
*
1215840 CTGTGGCTGTACAAATTGAAAATCAAATTAAATTAAACGACTTCATTCTATTACACACCAACTTT
1 CTGTGGCTGTACAAATTGAAAATCAAATTAAATGAAACGACTTCATTCTATTACACACCAAC-TT
* * *
1215905 TCGACAGTGATGTAAACCGGTTTGCCTTTTAATGACAAAGCATCCTTCGTCATAAGGAAGACACA
65 TCGACACTGATGTAAACCGGTTTGCCTTTTAATGACAAAGCATCCTTCGTCACAAAGAAGACACA
* *
1215970 AGAAGAACAAAACAGCTGATTTTGCTCAACACGTGGAGGTGTTTGAATTAAAACATAATTTAGGG
130 AGAAGAACAAAACAACTGATTTTGCTCAACACGTGGAGGTGTTTGAATTAAAACATAATTTAAGG
* * * *
1216035 TAAAATATTTTAAATTTTAAATTAATTTATTAATTTTTAATATAAATATTTTATTTTAAAAAATA
195 AAAAATATTTTAAAATTTAAATTAATTTATTAATTTTTAATATAAATACTCTATTTTAAAAAATA
* * * * *
1216100 TTTTCTACTATATATATAAATTCAGTAGTTAATTATTAATGTTTTTTATTCATTAAATAACATGA
260 TCTTCTACTAAACATATAAATCCAGTAGTTAATTATTAATGTTTTTTATTAATTAAATAACA-GA
* * * ** ** *
1216165 TAATATTGAAAATAAAATTTTACTCTTTATTAATTTTAAAAATTACTATTATATAACTTTTTATC
324 T-ATATT---AAT-AAATATAACTCTTTATTAATTTTAAAAATAAAGAGCATATAACTCTTTAT-
* * *
1216230 AGTTCTTTTAAAAAAATTACATGATAATTTTTTAAATTAATAAAAAAAATTTAAAATTTTTTATG
383 A-TTCTTTTAAAAAAATTA-ATAATAATTTTTTAAATTAATAAAAAAAATTTAAAATCTTTTATA
* * * * *
1216295 TTATCTGTTAACGGTATCTACACTTTGTAAAATGTTCATTTTAAAAATTAATAGATTCGTTTATA
446 TTATCTATTAACCGTATCTACACTTTATAAAATGTCCATTTCAAAAATTAATAGA-T-G----TA
* * * *
1216360 ATTTTGATTAAAATTTAAAAAATAAAAATATTTTATAATTATGAACTTTTCATCCAATAATTTTA
505 ATTTTGATTAAAATTTAAAAAATAAAAATATTTTACAATTATGAACTTCTAATCCAATAATTTAA
* * * *
1216425 AATTTAAAATTTAAAAATATGAGGTTGACGTTAAAACCAAATGCAATAATTGGGAGATAGTAAAA
570 AATTTAAAATTTAAAAACATGAGATTGACGTTAAAACAAAATGCAATAATTGAGAGATAGTAAAA
*
1216490 ATTAATTGCAACAGGGATTCTTACGTAAAGAGAAGGAAAGAACACAGAACAAATTCATTCTCTAC
635 ATTAATTGCAACAGGGATTCTTACGTAAAGAGAAGGAAAGAACACAGAACAAATTCATACTCTAC
*
1216555 AATAAGCATAGCATGTTAATCT-GTCTAAAGAAATAGTGCTAACGGTATCGCTTTCTTTAAAACT
700 AATAAGCATAGCATGTTAATCTATTC-AAAGAAATAGTGCTAACGGTATCGCTTTCTTTAAAACT
1216619 TTCATTTGT
764 TTCATTTGT
* * *
1216628 CTGTGGCTGTACAAATTGAAAATCTAATTAAATGAACCGACTTCATTCTATTATACACCAAC-TT
1 CTGTGGCTGTACAAATTGAAAATCAAATTAAATGAAACGACTTCATTCTATTACACACCAACTTT
* * * * *
1216692 CGACACTGATGTAAACCGGTTTG-CTTTTAATGATATAGCATCCTT-GATCACAAATAAGATATA
66 CGACACTGATGTAAACCGGTTTGCCTTTTAATGACAAAGCATCCTTCG-TCACAAAGAAGACACA
* *
1216755 AGAAGAACAAAACAACTGATTTTGCTCAACACGTGGAGGTGTTTGAATT-TAATATAATTTAAGG
130 AGAAGAACAAAACAACTGATTTTGCTCAACACGTGGAGGTGTTTGAATTAAAACATAATTTAAGG
* *
1216819 AAAAATATTTTAAAATTTAAA-TATATTTATTATTTTTTAA-ATATATACTCTATTTTAAAAACA
195 AAAAATATTTTAAAATTTAAATTA-ATTTATTAATTTTTAATATAAATACTCTATTTTAAAAA-A
* *
1216882 TATCTTCTATTAAACATATAAATCCAACTGATAGTTAATTATTAATG-TTTTTATTAATT-TA-A
258 TATCTTCTACTAAACATATAAATCC-A--G-TAGTTAATTATTAATGTTTTTTATTAATTAAATA
* *
1216944 ACA-AT-TATT-AT-TATATAACTTTTTATTAATTTTAAAAAATAAGAGAGCACTTATCAATGCT
319 ACAGATATATTAATAAATATAACTCTTTATTAATTTT-AAAAATAA-AGAGCA--TAT-AA--CT
* **
1217005 CTTTAT-TT-TTTTAAAAAAATT-ATAATAATTTTTTTAATTAATAAAAAAATATTT-TTATCTT
377 CTTTATATTCTTTTAAAAAAATTAATAATAATTTTTTAAATTAATAAAAAAA-ATTTAAAATCTT
* * * *
1217066 TTATATTATCTATTAACCGTATTTTACATTTTATAAAATGTCCATTTCGAAAGTTAATAGA-G-A
441 TTATATTATCTATTAACCGTA-TCTACACTTTATAAAATGTCCATTTCAAAAATTAATAGATGTA
* * ** *
1217129 ATTTTGATTAAAATTTAAAAAGTAAGAATATTTTACCAACTT-TTCA-TTCTAAT-CAATGATTT
505 ATTTTGATTAAAATTTAAAAAATAAAAATATTTTA-CAA-TTATGAACTTCTAATCCAATAATTT
1217191 AAAATTTAAAATTTAAAAACATGAGATTGAC-TCTAAAACAAAATGCAATAATTGAGAGATAGTA
568 AAAATTTAAAATTTAAAAACATGAGATTGACGT-TAAAACAAAATGCAATAATTGAGAGATAGTA
*
1217255 AAAATTAATTGCAACAGGGATTCTTACGTAAGGAGAAGGAAAGAACACAGAACAAATTCATACTC
632 AAAATTAATTGCAACAGGGATTCTTACGTAAAGAGAAGGAAAGAACACAGAACAAATTCATACTC
*
1217320 TACAATAATCATAGCATGTTAATCTATTCAAAGAAATAGTGCTAA
697 TACAATAAGCATAGCATGTTAATCTATTCAAAGAAATAGTGCTAA
1217365 TTCTAATCTG
Statistics
Matches: 646, Mismatches: 71, Indels: 60
0.83 0.09 0.08
Matches are distributed among these distances:
767 1 0.00
768 168 0.26
769 41 0.06
770 4 0.01
771 2 0.00
774 1 0.00
775 18 0.03
776 55 0.09
777 40 0.06
778 13 0.02
779 5 0.01
780 2 0.00
781 4 0.01
782 7 0.01
783 22 0.03
784 68 0.11
785 84 0.13
786 25 0.04
787 12 0.02
788 74 0.11
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (772 bp):
CTGTGGCTGTACAAATTGAAAATCAAATTAAATGAAACGACTTCATTCTATTACACACCAACTTT
CGACACTGATGTAAACCGGTTTGCCTTTTAATGACAAAGCATCCTTCGTCACAAAGAAGACACAA
GAAGAACAAAACAACTGATTTTGCTCAACACGTGGAGGTGTTTGAATTAAAACATAATTTAAGGA
AAAATATTTTAAAATTTAAATTAATTTATTAATTTTTAATATAAATACTCTATTTTAAAAAATAT
CTTCTACTAAACATATAAATCCAGTAGTTAATTATTAATGTTTTTTATTAATTAAATAACAGATA
TATTAATAAATATAACTCTTTATTAATTTTAAAAATAAAGAGCATATAACTCTTTATATTCTTTT
AAAAAAATTAATAATAATTTTTTAAATTAATAAAAAAAATTTAAAATCTTTTATATTATCTATTA
ACCGTATCTACACTTTATAAAATGTCCATTTCAAAAATTAATAGATGTAATTTTGATTAAAATTT
AAAAAATAAAAATATTTTACAATTATGAACTTCTAATCCAATAATTTAAAATTTAAAATTTAAAA
ACATGAGATTGACGTTAAAACAAAATGCAATAATTGAGAGATAGTAAAAATTAATTGCAACAGGG
ATTCTTACGTAAAGAGAAGGAAAGAACACAGAACAAATTCATACTCTACAATAAGCATAGCATGT
TAATCTATTCAAAGAAATAGTGCTAACGGTATCGCTTTCTTTAAAACTTTCATTTGT
Found at i:1252531 original size:72 final size:72
Alignment explanation
Indices: 1252448--1252732 Score: 401
Period size: 72 Copynumber: 3.9 Consensus size: 72
1252438 CATCTGCCTG
* * * *
1252448 TCCTTTGGCTTCAACATTTGATTTTTCTTGATCCTTATGCACATTATCACCTTCTGTCTCACCAT
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTTTCTCACCAT
1252513 CCATCTT
66 CCATCTT
* * * * * * *
1252520 TCCTTTTGCTTCAACCTTTGATTCTTCCCGATCCTTATGCACATTACCACCTCCTTTTTCACCAT
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTTTCTCACCAT
1252585 CCATCTT
66 CCATCTT
1252592 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATCATGCACATTATCACCTTCATTT-TCA
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCC-T-T-ATGCACATTATCACCTTC-TTTCTCA
1252656 CCATCCATCTT
62 CCATCCATCTT
* * *
1252667 TCCTTTGGCTTCAACGTTTGATTCTCCCTGACCCTCATGCACATTATCACCTTCTTTCTCACCAT
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTTTCTCACCAT
1252732 C
66 C
1252733 AGTTGTTGCC
Statistics
Matches: 190, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
71 3 0.02
72 119 0.63
73 1 0.01
74 2 0.01
75 62 0.33
76 3 0.02
ACGTcount: A:0.18, C:0.33, G:0.07, T:0.41
Consensus pattern (72 bp):
TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTTTCTCACCAT
CCATCTT
Found at i:1252751 original size:147 final size:144
Alignment explanation
Indices: 1252448--1252732 Score: 412
Period size: 147 Copynumber: 2.0 Consensus size: 144
1252438 CATCTGCCTG
* * *
1252448 TCCTTTGGCTTCAACATTTGATTTTTCTTGATCCTTATGCACATTATCACCTTCTGTCTCACCAT
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTGTCTCACCAT
* * * *
1252513 CCATCTTTCCTTTTGCTTCAACCTTTGATTCTTCCCGATCCTTATGCACATTACCACCTCCTTTT
66 CCATCTTTCCTTTGGCTTCAACCTTTGATTCTTCCCGACCCTCATGCACATTACCACCTCCTTTC
1252578 TCACCATCCATCTT
131 TCACCATCCATCTT
*
1252592 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATCATGCACATTATCACCTTCAT-TTTCA
1 TCCTTTGGCTTCAACATTTGATTCTTCCTGACCC-T-T-ATGCACATTATCACCTTC-TGTCTCA
* * *
1252656 CCATCCATCTTTCCTTTGGCTTCAACGTTTGATTC-TCCCTGACCCTCATGCACATTATCACCTT
62 CCATCCATCTTTCCTTTGGCTTCAACCTTTGATTCTTCCC-GACCCTCATGCACATTACCACCTC
1252720 CTTTCTCACCATC
126 CTTTCTCACCATC
1252733 AGTTGTTGCC
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
144 31 0.25
145 1 0.01
146 5 0.04
147 87 0.70
148 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.07, T:0.41
Consensus pattern (144 bp):
TCCTTTGGCTTCAACATTTGATTCTTCCTGACCCTTATGCACATTATCACCTTCTGTCTCACCAT
CCATCTTTCCTTTGGCTTCAACCTTTGATTCTTCCCGACCCTCATGCACATTACCACCTCCTTTC
TCACCATCCATCTT
Found at i:1262035 original size:22 final size:22
Alignment explanation
Indices: 1262007--1262051 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1261997 GTTAATCAGA
*
1262007 TTTGAGATCACTCTCTATAGGG
1 TTTGAGATCACGCTCTATAGGG
1262029 TTTGAGATCACGCTCTATAGGG
1 TTTGAGATCACGCTCTATAGGG
1262051 T
1 T
1262052 AAGGGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (22 bp):
TTTGAGATCACGCTCTATAGGG
Found at i:1271132 original size:15 final size:15
Alignment explanation
Indices: 1271114--1271190 Score: 64
Period size: 15 Copynumber: 5.0 Consensus size: 15
1271104 TTATTAGATG
1271114 TATAATTATTAAAAA
1 TATAATTATTAAAAA
* * *
1271129 TATAATTTTTTAACA
1 TATAATTATTAAAAA
* *
1271144 TTTGATATTATAAAAAA
1 TAT-A-ATTATTAAAAA
* *
1271161 AATAATTATAAAAAA
1 TATAATTATTAAAAA
*
1271176 TATGATTATTAAAAA
1 TATAATTATTAAAAA
1271191 AATTACATTA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
15 37 0.79
16 2 0.04
17 8 0.17
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (15 bp):
TATAATTATTAAAAA
Found at i:1272066 original size:17 final size:17
Alignment explanation
Indices: 1272044--1272076 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1272034 AATGGCTCTT
1272044 ATTGTAA-TATGATTATA
1 ATTGTAAGTAT-ATTATA
1272061 ATTGTAAGTATATTAT
1 ATTGTAAGTATATTAT
1272077 TTTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
ATTGTAAGTATATTATA
Found at i:1275518 original size:24 final size:24
Alignment explanation
Indices: 1275491--1275538 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1275481 GTTAAATTCT
1275491 GTGAGGGCCTTCTTTACAATTTGA
1 GTGAGGGCCTTCTTTACAATTTGA
1275515 GTGAGGGCCTTCTTTACAATTTGA
1 GTGAGGGCCTTCTTTACAATTTGA
1275539 TCACATCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (24 bp):
GTGAGGGCCTTCTTTACAATTTGA
Found at i:1277615 original size:15 final size:15
Alignment explanation
Indices: 1277595--1277634 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1277585 TTCCTCTCCA
1277595 TGGTGATGGTGGCGG
1 TGGTGATGGTGGCGG
*
1277610 TGGTGATGGTGGTGG
1 TGGTGATGGTGGCGG
1277625 TGGTGATGGT
1 TGGTGATGGT
1277635 ATCATGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.07, C:0.03, G:0.57, T:0.33
Consensus pattern (15 bp):
TGGTGATGGTGGCGG
Found at i:1292264 original size:9 final size:9
Alignment explanation
Indices: 1292202--1292264 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
1292192 CTCAGACTTT
1292202 TTTTCCTTC
1 TTTTCCTTC
*
1292211 TTTTCTTTC
1 TTTTCCTTC
* *
1292220 ATTTCTTTC
1 TTTTCCTTC
*
1292229 TTCTCCTTC
1 TTTTCCTTC
1292238 TTTT-CTT-
1 TTTTCCTTC
1292245 TTATT--TTC
1 TT-TTCCTTC
1292253 TTTTCCTTC
1 TTTTCCTTC
1292262 TTT
1 TTT
1292265 CCATGGCAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 6 0.14
8 7 0.16
9 31 0.70
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTCCTTC
Found at i:1299131 original size:52 final size:52
Alignment explanation
Indices: 1299039--1299155 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
1299029 AACTTTAGAA
* * * *
1299039 CCTCTTGGATTTTTTTGCTTCCATTATCTTTTTATAGTTTGTTTGATCAGGG
1 CCTCTTGGATTTTTTTGCTTCCAATAACTATTAATAGTTTGTTTGATCAGGG
** * *
1299091 TGTCTTGGATTTTTTTGCTTCCAATAACTATTAATCGTTTGTTTGATCTGGG
1 CCTCTTGGATTTTTTTGCTTCCAATAACTATTAATAGTTTGTTTGATCAGGG
1299143 CCTCTTGGATTTT
1 CCTCTTGGATTTT
1299156 CAATTTTGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.52
Consensus pattern (52 bp):
CCTCTTGGATTTTTTTGCTTCCAATAACTATTAATAGTTTGTTTGATCAGGG
Found at i:1299683 original size:27 final size:28
Alignment explanation
Indices: 1299653--1299711 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1299643 ATGGCCCGAA
*
1299653 GAAGAAATGAGA-AGGATGAAAGATTTG
1 GAAGAAATGACAGAGGATGAAAGATTTG
1299680 GAAGAAATGACAGAGGATGAAAGATTTG
1 GAAGAAATGACAGAGGATGAAAGATTTG
1299708 GAAG
1 GAAG
1299712 CTGTGGGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.47, C:0.02, G:0.34, T:0.17
Consensus pattern (28 bp):
GAAGAAATGACAGAGGATGAAAGATTTG
Found at i:1307757 original size:39 final size:39
Alignment explanation
Indices: 1307684--1307759 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1307674 AAATGCAGTA
* * **
1307684 GTAGTTTTTATGATTTTTTGACAATTTTGGTATTTGTCG
1 GTAGGTTTTATGATTATTTGACAATTACGGTATTTGTCG
*
1307723 GTAGGTTTTATGATTATTTGACAATTACGTTATTTGT
1 GTAGGTTTTATGATTATTTGACAATTACGGTATTTGT
1307760 AGGTCAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.21, C:0.05, G:0.20, T:0.54
Consensus pattern (39 bp):
GTAGGTTTTATGATTATTTGACAATTACGGTATTTGTCG
Found at i:1312770 original size:79 final size:79
Alignment explanation
Indices: 1312639--1312794 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 79
1312629 AGAGAACTAC
* **
1312639 AGGTTTGTGTGGTAGTTTTATTGGTTTGGAAAGATTCTGGTGATTACTTGCTAGTTTTGAAAGAT
1 AGGTTTGTGTGGTAGTTTTATTGGTTTGGAAAGATTCTGGTGATCACTTGCTAGTTTCAAAAGAT
*
1312704 TGTGAGTGTCCTGA
66 TGTGAATGTCCTGA
*
1312718 AGGTTTGTGTGGTCGCTTTT-TTGGTTTGGAAAGATTCTGGTGATCACTTGCTAGTTTCAAAAGA
1 AGGTTTGTGTGGTAG-TTTTATTGGTTTGGAAAGATTCTGGTGATCACTTGCTAGTTTCAAAAGA
1312782 TTGTGAATGTCCT
65 TTGTGAATGTCCT
1312795 TGCTGGTTGG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 67 0.94
80 4 0.06
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.42
Consensus pattern (79 bp):
AGGTTTGTGTGGTAGTTTTATTGGTTTGGAAAGATTCTGGTGATCACTTGCTAGTTTCAAAAGAT
TGTGAATGTCCTGA
Found at i:1319184 original size:31 final size:31
Alignment explanation
Indices: 1319146--1319240 Score: 109
Period size: 36 Copynumber: 2.9 Consensus size: 31
1319136 TTGTTACTCT
1319146 TTATGTGCAGAGGTTGGTTAAGTCATCCTCG
1 TTATGTGCAGAGGTTGGTTAAGTCATCCTCG
*
1319177 TTATGTGCTGAGATGAGTTGGGTTAAGTCATCCTCT
1 TTATGTGC--AGA-G-GTT-GGTTAAGTCATCCTCG
* * *
1319213 TTATGTGCTGAGATGGGTTAAGTCATCC
1 TTATGTGCAGAGGTTGGTTAAGTCATCC
1319241 GATAAGTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 21 0.38
32 1 0.02
33 4 0.07
34 3 0.05
35 3 0.05
36 23 0.42
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (31 bp):
TTATGTGCAGAGGTTGGTTAAGTCATCCTCG
Found at i:1324904 original size:2 final size:2
Alignment explanation
Indices: 1324897--1324928 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1324887 TTACTCCTAC
*
1324897 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1324929 TTATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1325795 original size:87 final size:90
Alignment explanation
Indices: 1325663--1325843 Score: 244
Period size: 87 Copynumber: 2.0 Consensus size: 90
1325653 TTGCTTTCGT
* * *
1325663 CATAGCCGTAAGCTTCAGTTGTTTCATAGTTTGCGTGATTACTGAAGCCATGGCCCATT-C-C-A
1 CATAGCCGTAAGCTTCAGTTGCTTCATAGCTTGCGAGATTACTGAAGCCATGGCCCATTCCACTA
* * * *
1325725 TTTTTGTGGTTGCCATGGGTTGAGC
66 TTTTTCTGGTTACCATGGGCTGAAC
* *
1325750 CATAGCCAG-AAGCTTCAGTTGCTTCGTAGCTTGCGAGATTGCTGAAGCCATGGCCCATTCCACT
1 CATAGCC-GTAAGCTTCAGTTGCTTCATAGCTTGCGAGATTACTGAAGCCATGGCCCATTCCACT
1325814 ATTTTTCTGGTTACCATGGGCTGAAC
65 ATTTTTCTGGTTACCATGGGCTGAAC
1325840 CATA
1 CATA
1325844 ACCATGGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
87 52 0.64
88 2 0.02
89 1 0.01
90 26 0.32
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (90 bp):
CATAGCCGTAAGCTTCAGTTGCTTCATAGCTTGCGAGATTACTGAAGCCATGGCCCATTCCACTA
TTTTTCTGGTTACCATGGGCTGAAC
Found at i:1326900 original size:2 final size:2
Alignment explanation
Indices: 1326887--1326924 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1326877 CGAGGAATGG
*
1326887 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1326925 CAAGCCCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1341587 original size:27 final size:30
Alignment explanation
Indices: 1341548--1341630 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 30
1341538 CCCGCCTTCC
1341548 AAAATTTTTAAATTTT-TTTTTA-TTTTT-T
1 AAAA-TTTTAAATTTTATTTTTATTTTTTAT
1341576 AAAATTTTAAATTTTTATTTTTATTTTTTAT
1 AAAATTTTAAA-TTTTATTTTTATTTTTTAT
1341607 AAATATTTTATAATTTTATTTTTA
1 AAA-ATTTTA-AATTTTATTTTTA
1341631 CAAATATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
27 7 0.14
28 8 0.16
29 6 0.12
30 5 0.10
31 4 0.08
32 17 0.35
33 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (30 bp):
AAAATTTTAAATTTTATTTTTATTTTTTAT
Found at i:1341614 original size:25 final size:24
Alignment explanation
Indices: 1341586--1341646 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
1341576 AAAATTTTAA
*
1341586 ATTTTTATTTTTATTTTTTATAAAT
1 ATTTTTATTTTTA-TTTTTACAAAT
*
1341611 ATTTTATAATTTTATTTTTACAAAT
1 ATTTT-TATTTTTATTTTTACAAAT
*
1341636 ATTATTATTTT
1 ATTTTTATTTT
1341647 CGTCACTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 5 0.16
25 19 0.61
26 7 0.23
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTTATTTTTATTTTTACAAAT
Found at i:1341625 original size:19 final size:18
Alignment explanation
Indices: 1341550--1341623 Score: 52
Period size: 19 Copynumber: 4.3 Consensus size: 18
1341540 CGCCTTCCAA
* *
1341550 AATTTTTAAATTTTTTTTT
1 AATTTTTAAA-TATTTTAT
*
1341569 ATTTTTTAAA-ATTTTA-
1 AATTTTTAAATATTTTAT
1341585 AATTTTT--AT-TTTTAT
1 AATTTTTAAATATTTTAT
*
1341600 -TTTTTATAAATATTTTAT
1 AATTTT-TAAATATTTTAT
1341618 AATTTT
1 AATTTT
1341624 ATTTTTACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 6 0.14
17 6 0.14
18 6 0.14
19 13 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATTTTTAAATATTTTAT
Found at i:1345413 original size:17 final size:18
Alignment explanation
Indices: 1345383--1345418 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1345373 AATAGGTAAA
1345383 AAGGTGGACATAAAGTTT
1 AAGGTGGACATAAAGTTT
*
1345401 AAGGTGG-CATAAATTTT
1 AAGGTGGACATAAAGTTT
1345418 A
1 A
1345419 CCATAATGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.31
Consensus pattern (18 bp):
AAGGTGGACATAAAGTTT
Found at i:1350584 original size:35 final size:35
Alignment explanation
Indices: 1350545--1350633 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
1350535 ATAATTATGA
* *
1350545 TTGTTCGAAAGTTATACTT-ATTTATACAATTAAGT
1 TTGTTCAAAAGTTATA-TTCATTTAAACAATTAAGT
* * *
1350580 TTGTTTAAAAGTTGTATTCATTTAAATAATTAAGT
1 TTGTTCAAAAGTTATATTCATTTAAACAATTAAGT
* *
1350615 TTATTCAAATAATTATATT
1 TTGTTCAAA-AGTTATATT
1350634 TATTAAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
34 2 0.05
35 34 0.79
36 7 0.16
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (35 bp):
TTGTTCAAAAGTTATATTCATTTAAACAATTAAGT
Found at i:1351076 original size:24 final size:24
Alignment explanation
Indices: 1351020--1351076 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1351010 AAAATAATTA
* *
1351020 TATTGAAAAACAAACAATTATATC
1 TATTGAAAAACAAACAATTACAAC
** *
1351044 TATCAAAAAACCAACAATTACAAC
1 TATTGAAAAACAAACAATTACAAC
*
1351068 TGTTGAAAA
1 TATTGAAAA
1351077 TAATGATTGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.16, G:0.05, T:0.25
Consensus pattern (24 bp):
TATTGAAAAACAAACAATTACAAC
Found at i:1355263 original size:23 final size:23
Alignment explanation
Indices: 1355206--1355284 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
1355196 AATTTTTAAA
1355206 ATTTTTATTATTATATATATATAATT
1 ATTTTTA-TA-TATATA-ATATAATT
* *
1355232 -TGATATATATATATAATATAATT
1 AT-TTTTATATATATAATATAATT
* *
1355255 ATTTTTATA-ATTATATTTTAATT
1 ATTTTTATATA-TATAATATAATT
1355278 ATTTTTA
1 ATTTTTA
1355285 ATGTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.02
23 30 0.68
24 7 0.16
25 3 0.07
26 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
ATTTTTATATATATAATATAATT
Found at i:1355265 original size:12 final size:12
Alignment explanation
Indices: 1355248--1355284 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1355238 ATATATATAA
1355248 TATAATTATTTT
1 TATAATTATTTT
*
1355260 TATAATTATATT
1 TATAATTATTTT
1355272 T-TAATTATTTT
1 TATAATTATTTT
1355283 TA
1 TA
1355285 ATGTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATAATTATTTT
Found at i:1357592 original size:12 final size:12
Alignment explanation
Indices: 1357562--1357594 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1357552 AATATAATTT
*
1357562 TTATAAATTAAA
1 TTATAAAATAAA
1357574 TTA-AAAATAAA
1 TTATAAAATAAA
1357585 TTATAAAATA
1 TTATAAAATA
1357595 TTACTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTATAAAATAAA
Found at i:1358387 original size:2 final size:2
Alignment explanation
Indices: 1358380--1358422 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1358370 ATATTTGCCA
1358380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1358422 A
1 A
1358423 GAGAGGGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1375795 original size:21 final size:21
Alignment explanation
Indices: 1375761--1375800 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1375751 AGAGCTTCTT
* * *
1375761 CCTCCTTTTTCTGCTTGTAAA
1 CCTCCATTTCCTGCATGTAAA
1375782 CCTCCATTTCCTGCATGTA
1 CCTCCATTTCCTGCATGTA
1375801 TTTCTCCTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.33, G:0.10, T:0.42
Consensus pattern (21 bp):
CCTCCATTTCCTGCATGTAAA
Found at i:1381799 original size:82 final size:82
Alignment explanation
Indices: 1381690--1381844 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 82
1381680 GTTAACTTTG
* * *
1381690 CTTTATTAACAGGTGGCGGTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTAC
1 CTTTATTAACAGATGACAGTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTAC
1381755 TAAAGTAACGTTTGCTA
66 TAAAGTAACGTTTGCTA
* * * *
1381772 CTTTATTAATAGATGACAGTTAGGACAGCTTGAATAGTTTATTAAGAAAAGGACGTGATTATTAC
1 CTTTATTAACAGATGACAGTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTAC
1381837 TAAAGTAA
66 TAAAGTAA
1381845 TATTTAATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (82 bp):
CTTTATTAACAGATGACAGTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTAC
TAAAGTAACGTTTGCTA
Found at i:1381859 original size:82 final size:81
Alignment explanation
Indices: 1381708--1381863 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 81
1381698 ACAGGTGGCG
* **
1381708 GTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTACTAAAGTAACGTTTGCTAC
1 GTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTACTAAAGTAACATTTAATAC
1381773 TTTATTAATAGATGACA
66 TTTA-TAATAGATGACA
* * * * *
1381790 GTTAGGACAGCTTGAATAGTTTATTAAGAAAAGGACGTGATTATTACTAAAGTAATATTTAATAT
1 GTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTACTAAAGTAACATTTAATAC
1381855 TTTATAATA
66 TTTATAATA
1381864 TAATATGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 5 0.08
82 61 0.92
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (81 bp):
GTTAAGACAGCTTGAATAGTTTATTAAGAAAAGAAAGTGATTATTACTAAAGTAACATTTAATAC
TTTATAATAGATGACA
Found at i:1381869 original size:15 final size:15
Alignment explanation
Indices: 1381856--1381940 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
1381846 ATTTAATATT
1381856 TTATAATATAATATGA
1 TTATAA-ATAATATGA
* *
1381872 TTATAAATAATGTAA
1 TTATAAATAATATGA
1381887 TTATAAATAATATGA
1 TTATAAATAATATGA
* *
1381902 TAATAAAAAATGAT-A
1 TTATAAATAAT-ATGA
*
1381917 TTAT-AAT-ATTTGA
1 TTATAAATAATATGA
1381930 TATATAAATAA
1 T-TATAAATAA
1381941 AATAAAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
12 1 0.02
13 4 0.07
14 5 0.09
15 36 0.65
16 9 0.16
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TTATAAATAATATGA
Found at i:1381899 original size:30 final size:30
Alignment explanation
Indices: 1381856--1381940 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
1381846 ATTTAATATT
1381856 TTATAATATAATATGATTATAAATAATG-TAA
1 TTATAA-ATAATATGATTATAAATAATGAT-A
* *
1381887 TTATAAATAATATGATAATAAAAAATGATA
1 TTATAAATAATATGATTATAAATAATGATA
*
1381917 TTAT-AAT-ATTTGATATATAAATAA
1 TTATAAATAATATGAT-TATAAATAA
1381941 AATAAAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 6 0.13
29 10 0.21
30 24 0.51
31 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (30 bp):
TTATAAATAATATGATTATAAATAATGATA
Found at i:1382144 original size:32 final size:33
Alignment explanation
Indices: 1382108--1382171 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1382098 CTTAAATATA
1382108 ATTTTAATATTATATA-TTTATTTTCATTTTTT
1 ATTTTAATATTATATATTTTATTTTCATTTTTT
*
1382140 ATTTTAATATTATATATTTTATTTTTATTTTT
1 ATTTTAATATTATATATTTTATTTTCATTTTT
1382172 AATATAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (33 bp):
ATTTTAATATTATATATTTTATTTTCATTTTTT
Found at i:1382149 original size:27 final size:26
Alignment explanation
Indices: 1382119--1382186 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
1382109 TTTTAATATT
*
1382119 ATATATTTATTTTCATTTTT-TATTTTA
1 ATATATATATTTT-ATTTTTAT-TTTTA
1382146 ATATTATATATTTTATTTTTATTTTTA
1 ATA-TATATATTTTATTTTTATTTTTA
*
1382173 ATATA-ATTTTTTAT
1 ATATATATATTTTAT
1382187 ATTATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 8 0.22
26 2 0.05
27 17 0.46
28 10 0.27
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
ATATATATATTTTATTTTTATTTTTA
Found at i:1382188 original size:32 final size:32
Alignment explanation
Indices: 1382112--1382203 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
1382102 AATATAATTT
* * * *
1382112 TAATATTATATA-TTTATTTTCATTTTTTATTT
1 TAATATTTTATATTTTATTTTTA-TTTTTAATA
*
1382144 TAATATTATATATTTTATTTTTATTTTTAATA
1 TAATATTTTATATTTTATTTTTATTTTTAATA
* * *
1382176 TAATTTTTTATATTATATATTTTCTTTT
1 TAATATTTTATATTTTAT-TTTTATTTT
1382204 CTTTTCTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 34 0.67
33 17 0.33
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TAATATTTTATATTTTATTTTTATTTTTAATA
Found at i:1382296 original size:28 final size:27
Alignment explanation
Indices: 1382055--1382307 Score: 110
Period size: 26 Copynumber: 9.5 Consensus size: 27
1382045 ATAAATTTAA
*
1382055 TATATTTATATT-TTTTATTATTAATTTT
1 TATA-TTATATTATATTATT-TTAATTTT
* * * *
1382083 TATATAATATTATCTCTTAAATATAATTTT
1 TATATTATATTA--TATT-ATTTTAATTTT
* *
1382113 AATATTATA-TAT-TTATTTTCATTTTT
1 TATATTATATTATATTATTTT-AATTTT
*
1382139 TATTTTAATATTATA-TATTTT-A-TTT
1 TATATT-ATATTATATTATTTTAATTTT
1382164 T-TATT-T-TTA-A-TA---TAATTTTT
1 TATATTATATTATATTATTTTAA-TTTT
* * **
1382184 TATATTATA-TATTTTCTTTTCTTTTCT
1 TATATTATATTATATTATTTTAATTT-T
* *
1382211 TTTATCTATATTATATAAATTTTAATTTTT
1 TATAT-TATATTATAT-TATTTTAA-TTTT
1382241 TATATTATATTATATT-TTTTAATTTT
1 TATATTATATTATATTATTTTAATTTT
*
1382267 TATATTATA-TATTTTATTTTAATATGTT
1 TATATTATATTATATTATTTTAAT-T-TT
*
1382295 TATTTTA-ATTATA
1 TATATTATATTATA
1382308 ACATTGTAAA
Statistics
Matches: 169, Mismatches: 28, Indels: 56
0.67 0.11 0.22
Matches are distributed among these distances:
17 1 0.01
18 1 0.01
20 7 0.04
21 7 0.04
22 4 0.02
24 4 0.02
25 12 0.07
26 34 0.20
27 24 0.14
28 28 0.17
29 16 0.09
30 26 0.15
31 5 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
TATATTATATTATATTATTTTAATTTT
Found at i:1382298 original size:14 final size:13
Alignment explanation
Indices: 1382229--1382303 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 13
1382219 TATTATATAA
*
1382229 ATTTTAATTTTTT
1 ATTTTAATATTTT
*
1382242 ATATT-ATATTATAT
1 ATTTTAATATT-T-T
*
1382256 TTTTTAAT-TTTT
1 ATTTTAATATTTT
*
1382268 ATATTATATATTTT
1 ATTTTA-ATATTTT
1382282 ATTTTAATATGTTT
1 ATTTTAATAT-TTT
1382296 ATTTTAAT
1 ATTTTAAT
1382304 TATAACATTG
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 9 0.18
13 12 0.24
14 26 0.53
15 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (13 bp):
ATTTTAATATTTT
Found at i:1399818 original size:285 final size:284
Alignment explanation
Indices: 1399273--1400677 Score: 1976
Period size: 285 Copynumber: 4.9 Consensus size: 284
1399263 AGATTTATGG
** * * * *
1399273 TTCTCCATTTCAGTCAGTCTTTCTGATGATTCTTGTTTCTCCCTCTCGAGCTGCAACTCCTGTTC
1 TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTTC
* * * * * * *
1399338 GTTTCTCTGGGTCTGTAAGGAATCCAATTCCTGCTGCAAATTGTTGACCTGCACCACTAAGGCCG
66 ATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAATT-TTAACCTGCACCTCTAGGGCTG
* * * * **********
1399403 TTAATTGGGAAGAAGTTTCATTCTCTGTGCTTNNNNNNNNNNCCTGGAGAGCAGTGAACTCAAGC
130 TTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAGC
* * *
1399468 CCTCTTTCTGCCAATGTTTTCTCTAATTCTAAGATTAGACCCTGTAA-CCACACCTTTTCCTCCC
195 CCTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCTCTAAGCC-CACCTTTTCCTCCC
*****
1399532 TTAACTGACCATTCTCCAATTNNNNN
259 TTAACTGACCATTCTCCAATTTCTGA
*****
1399558 NNNNNCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTTC
1 TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTTC
1399623 ATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAATGTTTAACCTGCACCTCTAGGGCTG
66 ATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAAT-TTTAACCTGCACCTCTAGGGCTG
1399688 TTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAGC
130 TTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAGC
* * * * * *
1399753 CCTCTTTCTGCCAATGTTTTCTCAAATTCAAGGATTCGATCCTCTAAGTCCAGCTTTTTCTCCCT
195 CCTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCTCTAAGCCCACCTTTTCCTCCCT
1399818 TAACTGACCATTCTCCAATTTCTGA
260 TAACTGACCATTCTCCAATTTCTGA
1399843 TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCT-TCCTCTCAAGCTGCAATTCCAGTT
1 TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCT-CTCTCAAGCTGCAATTCCAGTT
*
1399907 CATTTCTCTGGGTCTGTAAGGAATCCAGCTCCTGCTTCAAATGTTTAACCTGCACCTCTAGGGCT
65 CATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAAT-TTTAACCTGCACCTCTAGGGCT
1399972 GTTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAG
129 GTTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAG
* * * * * *
1400037 CCCTCTTTCTGCCAATGTTTTCTCAAATTCAAGGATTCGATCCTCTAAGTCCAGCTTTTTCTCCC
194 CCCTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCTCTAAGCCCACCTTTTCCTCCC
1400102 TTAACTGACCATTCTCCAATTTCTGA
259 TTAACTGACCATTCTCCAATTTCTGA
*
1400128 TTCTCCATTTCAGAGAGTCTTCTATGATGATTCTTGTTTCTC-CTCTCAAGCTGCAATTCCAGTT
1 TTCTCCATTTCAGAGAGTCTT-TCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTT
* *
1400192 CATTTCTCTGGGTCTGTAAGGAATCCAGCTCCTGCTTCAAATTTTTAACCTGCACCTCTAAGGCT
65 CATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAA-TTTTAACCTGCACCTCTAGGGCT
* * * *
1400257 GTTAACCGTGAAGAAGCTTCATTCTCTACGTTTACATGTTTTTCCTGGAGAGCAGTGAACTCAAG
129 GTTAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAG
* * * *
1400322 CCCTCTTTCTGCCAATGTTTTCTCTAATTCAAAAATTTGACCCTGTAACCCCACCTTTTCCTCCC
194 CCCTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCTCTAAGCCCACCTTTTCCTCCC
1400387 TTAACTGACCATTCTCCAATTTCTGA
259 TTAACTGACCATTCTCCAATTTCTGA
* * *
1400413 TTCTCCATTTCAGAGATTCTTTCTAATGATTCTTGTTTCTCTCTCTCAAGCTGCAACTCCAGTTC
1 TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTTC
* *
1400478 ATTTCTCTGGGTCCGTAAGGAATCCAACTCCTGCTGCAAATTGTTAACCTG-ATCCTCTAGGGCT
66 ATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAATT-TTAACCTGCA-CCTCTAGGGCT
* * * * *
1400542 ATTAACTGGGAAGAAGCTTCATTCTCTGCAG-TTGCATGTTTTTCCTGGAGATCAGTGAACTCAA
129 GTTAACTGTGAAGAAGCTTCATTCTCTGC-GCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAA
* * *
1400606 GCCCTCTTTCTGCCAATTTTTTCTCTAATTCAAAGATTTGACCCTGC-AACCCCACCTTTTCCTC
193 GCCCTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCT-CTAAGCCCACCTTTTCCTC
1400670 CCTTAACT
257 CCTTAACT
1400678 CATTCTCTGC
Statistics
Matches: 1024, Mismatches: 85, Indels: 22
0.91 0.08 0.02
Matches are distributed among these distances:
284 22 0.02
285 980 0.96
286 22 0.02
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (284 bp):
TTCTCCATTTCAGAGAGTCTTTCTGATGATTCTTGTTTCTCTCTCTCAAGCTGCAATTCCAGTTC
ATTTCTCTGGGTCTGTAAGGAATCCAACTCCTGCTTCAAATTTTAACCTGCACCTCTAGGGCTGT
TAACTGTGAAGAAGCTTCATTCTCTGCGCTTACATGTTTCTCCTGGAGAGCAGTGAACTCAAGCC
CTCTTTCTGCCAATGTTTTCTCTAATTCAAAGATTCGACCCTCTAAGCCCACCTTTTCCTCCCTT
AACTGACCATTCTCCAATTTCTGA
Found at i:1400766 original size:117 final size:117
Alignment explanation
Indices: 1400560--1400786 Score: 391
Period size: 117 Copynumber: 1.9 Consensus size: 117
1400550 GGAAGAAGCT
* *
1400560 TCATTCTCTGCAGTTGCATGTTTTTCCTGGAGATCAGTGAACTCAAGCCCTCTTTCTGCCAATTT
1 TCATTCTCTGCACTTGCATGTTTTTCCTGGAGAGCAGTGAACTCAAGCCCTCTTTCTGCCAATTT
*
1400625 TTTCTCTAATTCAAAGATTTGACCCTGCAACCCCACCTTTTCCTCCCTTAAC
66 TTTCTCTAATTCAAAGATTTGACCCCGCAACCCCACCTTTTCCTCCCTTAAC
*
1400677 TCATTCTCTGCACTTGCATGTTTTTCCTGGAGAGCAGTGAACTCAAGCCCTGTTTCTGCCAATTT
1 TCATTCTCTGCACTTGCATGTTTTTCCTGGAGAGCAGTGAACTCAAGCCCTCTTTCTGCCAATTT
* **
1400742 TTTCTCTAATTCAAAGATTTGACCCCGTAATGCCACCTTTTCCTC
66 TTTCTCTAATTCAAAGATTTGACCCCGCAACCCCACCTTTTCCTC
1400787 TCTCAACTGA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 103 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (117 bp):
TCATTCTCTGCACTTGCATGTTTTTCCTGGAGAGCAGTGAACTCAAGCCCTCTTTCTGCCAATTT
TTTCTCTAATTCAAAGATTTGACCCCGCAACCCCACCTTTTCCTCCCTTAAC
Found at i:1411294 original size:32 final size:32
Alignment explanation
Indices: 1411266--1411345 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
1411256 TAAATTTGAT
1411266 AAATATTAATATTTAACTT-AAAA-TAATTTAAA
1 AAATATTAATATTTAACTTAAAAATTAATTT--A
** *
1411298 AAATAAAAATATTTAATTTAAAAATTAATTTA
1 AAATATTAATATTTAACTTAAAAATTAATTTA
1411330 AAATATTAATATTTAA
1 AAATATTAATATTTAA
1411346 ATTATACAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 31 0.76
33 4 0.10
34 6 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
AAATATTAATATTTAACTTAAAAATTAATTTA
Found at i:1411339 original size:13 final size:13
Alignment explanation
Indices: 1411303--1411339 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
1411293 TTAAAAAATA
1411303 AAAATATTTAATTT
1 AAAATA-TTAATTT
1411317 AAAA-ATTAATTT
1 AAAATATTAATTT
1411329 AAAATATTAAT
1 AAAATATTAAT
1411340 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATATTAATTT
Found at i:1411508 original size:74 final size:74
Alignment explanation
Indices: 1411430--1411568 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 74
1411420 ATAAATAGAA
* *
1411430 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATTATTTAAT-AAATACAAATTT
1 TAAATCGTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAAA-ACAAATTT
1411494 ATAAGAGGTT
65 ATAAGAGGTT
* * * *
1411504 TAAATCGTATTGATAATTATAATAAAAAATATTTTAATGATCATCATTTAATGAAAACATATTTA
1 TAAATCGTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAAAACAAATTTA
1411569 CAAGTATAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 55 0.95
75 3 0.05
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (74 bp):
TAAATCGTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAAAACAAATTTA
TAAGAGGTT
Found at i:1434090 original size:21 final size:21
Alignment explanation
Indices: 1434064--1434104 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1434054 ATTTCAGAGC
1434064 AGACTGACTTGATATCTGAAT
1 AGACTGACTTGATATCTGAAT
1434085 AGACTGACTTGATATCTGAA
1 AGACTGACTTGATATCTGAA
1434105 CAAACCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (21 bp):
AGACTGACTTGATATCTGAAT
Found at i:1436149 original size:15 final size:15
Alignment explanation
Indices: 1436129--1436157 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1436119 GAATCAAATA
1436129 TATATATATATATAC
1 TATATATATATATAC
1436144 TATATATATATATA
1 TATATATATATATA
1436158 TATTGATATA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAC
Found at i:1436149 original size:17 final size:17
Alignment explanation
Indices: 1436127--1436159 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1436117 TTGAATCAAA
1436127 TATATATATATATATAC
1 TATATATATATATATAC
1436144 TATATATATATATATA
1 TATATATATATATATA
1436160 TTGATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATATATATAC
Found at i:1436168 original size:2 final size:2
Alignment explanation
Indices: 1436126--1436160 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1436116 CTTGAATCAA
1436126 AT AT AT AT AT AT AT AT ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
1436161 TGATATATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1440623 original size:43 final size:43
Alignment explanation
Indices: 1440575--1440703 Score: 204
Period size: 43 Copynumber: 3.0 Consensus size: 43
1440565 TCACAGTACC
1440575 TGGAGCATTGGGTAGAAAACATTCTTAGCATATGCGGAAAGTG
1 TGGAGCATTGGGTAGAAAACATTCTTAGCATATGCGGAAAGTG
* * *
1440618 TGGAGCATTGGGCAGAAAACATTCTTAGCATATGCAGATAGTG
1 TGGAGCATTGGGTAGAAAACATTCTTAGCATATGCGGAAAGTG
* * *
1440661 TGGAGCATTGGGTTGAAAACATTCTTAGCGTATGTGGAAAGTG
1 TGGAGCATTGGGTAGAAAACATTCTTAGCATATGCGGAAAGTG
1440704 CCCATTACTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (43 bp):
TGGAGCATTGGGTAGAAAACATTCTTAGCATATGCGGAAAGTG
Found at i:1449801 original size:3 final size:3
Alignment explanation
Indices: 1449793--1449830 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1449783 TTACTCCTTT
*
1449793 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
1449831 TTCAAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1452192 original size:15 final size:15
Alignment explanation
Indices: 1452168--1452213 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
1452158 ACGTTACAAT
1452168 GTAATGTGATTACAG
1 GTAATGTGATTACAG
* *
1452183 GTAATATGATTACAA
1 GTAATGTGATTACAG
1452198 GTAATGTGATTACAG
1 GTAATGTGATTACAG
1452213 G
1 G
1452214 GAAAATAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (15 bp):
GTAATGTGATTACAG
Found at i:1452388 original size:19 final size:19
Alignment explanation
Indices: 1452366--1452494 Score: 66
Period size: 21 Copynumber: 6.4 Consensus size: 19
1452356 AGTTTAATAT
1452366 ATTTATATTTTTATTATTA
1 ATTTATATTTTTATTATTA
* * *
1452385 ATTTTTATATATATCATTCTTA
1 A--TTTATAT-TTTTATTATTA
* *
1452407 A-ATATATTTTTAATATCATA
1 ATTTATATTTTTATTAT--TA
* *
1452427 TTTTATTTTTTTATTATT-
1 ATTTATATTTTTATTATTA
* *
1452445 ATTATAATATTTTTTTTTAATA
1 ATT-T-ATA-TTTTTATTATTA
1452467 TATTTATA-TTTTATTATTA
1 -ATTTATATTTTTATTATTA
1452486 ATTTTATAT
1 A-TTTATAT
1452495 AATATCATTT
Statistics
Matches: 79, Mismatches: 18, Indels: 25
0.65 0.15 0.20
Matches are distributed among these distances:
18 8 0.10
19 23 0.29
20 4 0.05
21 31 0.39
22 10 0.13
23 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTATATTTTTATTATTA
Found at i:1452530 original size:55 final size:55
Alignment explanation
Indices: 1452471--1452664 Score: 179
Period size: 55 Copynumber: 3.5 Consensus size: 55
1452461 TTAATATATT
1452471 TATATTTTATTATTAATT-TTA-TATAATATCATTTCTTAAATATATTTTAATGTCA
1 TATATTTTATTATTAATTATTATTATAATATCATTT-TTAAATATATTTTAAT-TCA
* * * *
1452526 TATATTTTATTTTTATTTATTATTTATAATATTTATATTT---TAT-TTTTAATAT-A
1 TATATTTTATTATTAATTATTA-TTATAATA-TCATTTTTAAATATATTTTAAT-TCA
* * *
1452579 TTTATATTTATTTATTAATTTTTA-TATAATATCATATTTTAAATATATTTTAATACA
1 TATAT-TTTA-TTATTAATTATTATTATAATATCAT-TTTTAAATATATTTTAATTCA
* *
1452636 TATATTTTATTTTTATTTATTATTATAAT
1 TATATTTTATTATTAATTATTATTATAAT
1452665 TTTATATATT
Statistics
Matches: 110, Mismatches: 16, Indels: 25
0.73 0.11 0.17
Matches are distributed among these distances:
52 3 0.03
53 15 0.14
54 12 0.11
55 39 0.35
56 16 0.15
57 12 0.11
58 9 0.08
59 4 0.04
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (55 bp):
TATATTTTATTATTAATTATTATTATAATATCATTTTTAAATATATTTTAATTCA
Found at i:1452593 original size:58 final size:53
Alignment explanation
Indices: 1452515--1452680 Score: 162
Period size: 54 Copynumber: 3.0 Consensus size: 53
1452505 CTTAAATATA
*
1452515 TTTTAATGTCATATATTTTATTTTTATTTATTATTTATAATATTTATATTTTAT
1 TTTTAAT-ACATATATTTTATTTTTATTTATTATTTATAATATTTATATTTTAT
* * *
1452569 TTTTAATATATTTATATTTATTTATTAATTT-TTA--TATAATA-TCATATTTTAAATAT
1 TTTTAATACATATAT-TTTATTT-TT-ATTTATTATTTATAATATTTATA-TTT---TAT
*
1452625 ATTTTAATACATATATTTTATTTTTATTTATTA-TTATAATTTTATATATTTTAT
1 -TTTTAATACATATATTTTATTTTTATTTATTATTTATAATATT-TATATTTTAT
1452679 TT
1 TT
1452681 CATTTCTTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
52 4 0.04
53 17 0.18
54 21 0.23
55 10 0.11
56 20 0.22
57 17 0.18
58 3 0.03
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (53 bp):
TTTTAATACATATATTTTATTTTTATTTATTATTTATAATATTTATATTTTAT
Found at i:1452598 original size:110 final size:110
Alignment explanation
Indices: 1452358--1452680 Score: 451
Period size: 110 Copynumber: 3.0 Consensus size: 110
1452348 AAAATATAAG
*
1452358 TTTAATATATTTATATTTTTATTATTAATTTTTATAT-ATATCAT-TCTTAAATATATTTTTAAT
1 TTTAATATATTTATA-TTTTATTATTAATTTTTATATAATATCATATTTTAAATATA-TTTTAAT
1452421 --ATCATATTTTA-TTTT-TTTATTATTAT--TA-TA-ATATTTT-TT
64 ACAT-ATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
1452460 TTTAATATATTTATATTTTATTATTAA-TTTTATATAATATCAT-TTCTTAAATATATTTTAATG
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTAAT-
*
1452523 TCATATATTTTATTTTTATTTATTATTTATAATATT-TATATTTTATT
64 ACATATATTTTATTTTTATTTATTA-TTATAATATTATATATTTTATT
1452570 TTTAATATATTTATA-TTTATTTATTAATTTTTATATAATATCATATTTTAAATATATTTTAATA
1 TTTAATATATTTATATTTTA-TTATTAATTTTTATATAATATCATATTTTAAATATATTTTAATA
*
1452634 CATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 CATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
1452680 T
1 T
1452681 CATTTCTTTA
Statistics
Matches: 201, Mismatches: 3, Indels: 26
0.87 0.01 0.11
Matches are distributed among these distances:
100 8 0.04
101 27 0.13
102 24 0.12
103 8 0.04
104 6 0.03
105 7 0.03
106 4 0.02
108 2 0.01
109 21 0.10
110 60 0.30
111 32 0.16
112 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (110 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATATTTTAAATATATTTTAATAC
ATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
Found at i:1452606 original size:22 final size:22
Alignment explanation
Indices: 1452534--1452606 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 22
1452524 CATATATTTT
*
1452534 ATTTTTATTTA-TTATTTA-TA
1 ATTTTTATATATTTATTTATTA
*
1452554 ATATTTATAT-TTTATTT-TTA
1 ATTTTTATATATTTATTTATTA
*
1452574 ATATATT-TATATTTATTTATTA
1 AT-TTTTATATATTTATTTATTA
1452596 ATTTTTATATA
1 ATTTTTATATA
1452607 ATATCATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 21 0.50
21 12 0.29
22 9 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTTATATATTTATTTATTA
Found at i:1452677 original size:33 final size:33
Alignment explanation
Indices: 1452635--1452719 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
1452625 ATTTTAATAC
*
1452635 ATATATTTTATTTTTATTTA-TTATTATAATTTT
1 ATATATTTTATTTTTATTTATTTAATAT-ATTTT
* *
1452668 ATATATTTTA-TTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTTAATATATTTT
*
1452700 TTATATTTTATATTTTATTT
1 ATATATTTTAT-TTTTATTT
1452720 TAATTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
32 21 0.48
33 16 0.36
34 7 0.16
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTTAATATATTTT
Found at i:1452727 original size:58 final size:58
Alignment explanation
Indices: 1452526--1452727 Score: 129
Period size: 59 Copynumber: 3.5 Consensus size: 58
1452516 TTTAATGTCA
* **
1452526 TATATTTTAT-TTTTATTTATTATTTATAATA-TTTATATTTTATTTTTAATATA---TT
1 TATATTTTATATTTTATTT-TAATTTATAATATTTTATATCAT-TTTTTAATATATTTTT
* * * * *
1452581 TATA-TTTAT-TTATTAATTTTTATATAATATCATATTTTAAAT-ATATTTTAATACATATATTT
1 TATATTTTATATT-TT-A-TTTTA-AT-TTATAATATTTTATATCATTTTTTAAT--ATATTTTT
* *
1452643 TAT-TTTTAT-TTATTATTATAATTT-TATATATTTTATTTCATTTCTTTAATATATTTTT
1 TATATTTTATATT-TTATTTTAATTTATA-ATATTTTATATCATTT-TTTAATATATTTTT
1452701 TATATTTTATATTTTATTTTAATTTAT
1 TATATTTTATATTTTATTTTAATTTAT
1452728 TTTACCTATA
Statistics
Matches: 115, Mismatches: 14, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
54 7 0.06
55 6 0.05
56 2 0.02
57 13 0.11
58 27 0.23
59 31 0.27
60 13 0.11
61 1 0.01
62 15 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (58 bp):
TATATTTTATATTTTATTTTAATTTATAATATTTTATATCATTTTTTAATATATTTTT
Found at i:1452729 original size:49 final size:48
Alignment explanation
Indices: 1452674--1452824 Score: 119
Period size: 49 Copynumber: 3.0 Consensus size: 48
1452664 TTTTATATAT
*
1452674 TTTATTTCATTTCTTTAATATATTTTTTATATTTTATATTTTATTTTAA
1 TTTATTT-ATTTCTTTAATATATATTTTATATTTTATATTTTATTTTAA
** * * * *
1452723 TTTATTT-TACCTATATTATATAAATGTTA-ATTTTTATATTTTATTTTAT
1 TTTATTTATTTCT-T-TAATATATATTTTATA-TTTTATATTTTATTTTAA
* * *
1452772 TTTAATTTTTATTCTTATATTATATATTTTAT-TTTAATATTTTTATTTTAA
1 TTT-ATTTAT-TTCTT-TAATATATATTTTATATTTTATA-TTTTATTTTAA
1452823 TT
1 TT
1452825 ATAATATTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
47 3 0.04
48 2 0.03
49 37 0.47
50 10 0.13
51 25 0.32
52 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (48 bp):
TTTATTTATTTCTTTAATATATATTTTATATTTTATATTTTATTTTAA
Found at i:1452801 original size:20 final size:19
Alignment explanation
Indices: 1452757--1452835 Score: 74
Period size: 20 Copynumber: 4.1 Consensus size: 19
1452747 TGTTAATTTT
*
1452757 TATATTTTATTTTATTTTA
1 TATATTTTATTTTATATTA
1452776 -AT-TTTTATTCTTATATTA
1 TATATTTTATT-TTATATTA
1452794 TATATTTTATTTTAATATT-
1 TATATTTTATTTT-ATATTA
* *
1452813 TTTATTTTAATTATAATATTA
1 TATATTTT-ATT-TTATATTA
1452834 TA
1 TA
1452836 AAATATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
17 7 0.14
18 9 0.18
19 11 0.22
20 20 0.41
21 2 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTTTATTTTATATTA
Found at i:1452809 original size:56 final size:54
Alignment explanation
Indices: 1452697--1452821 Score: 152
Period size: 54 Copynumber: 2.3 Consensus size: 54
1452687 TTTAATATAT
1452697 TTTTTATATTTTATATTTTATTTTAATTTATTTTACCTATATTATATAAATGTTAA
1 TTTTTATA-TTT-TATTTTATTTTAATTTATTTTACCTATATTATATAAATGTTAA
* *
1452753 TTTTTATATTTTATTTTATTTTAATTT-TTATT-CTTATATTATAT--AT-TTTA
1 TTTTTATATTTTATTTTATTTTAATTTATT-TTACCTATATTATATAAATGTTAA
*
1452803 TTTTAATATTTTTATTTTA
1 TTTTTATA-TTTTATTTTA
1452822 ATTATAATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
50 10 0.16
51 12 0.19
53 13 0.20
54 18 0.28
55 3 0.05
56 8 0.12
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (54 bp):
TTTTTATATTTTATTTTATTTTAATTTATTTTACCTATATTATATAAATGTTAA
Found at i:1452822 original size:14 final size:15
Alignment explanation
Indices: 1452358--1452823 Score: 84
Period size: 14 Copynumber: 30.4 Consensus size: 15
1452348 AAAATATAAG
1452358 TTTAATATATTTATAT
1 TTTAATATATTT-TAT
* *
1452374 TTTTAT-TA-TTAAT
1 TTTAATATATTTTAT
* * *
1452387 TTTTATATATATCAT
1 TTTAATATATTTTAT
*
1452402 TCTTAA-ATATATT-T
1 T-TTAATATATTTTAT
*
1452416 TTAATATCATATTTTAT
1 TTTA-AT-ATATTTTAT
*
1452433 TTT--TTTATTATTAT
1 TTTAATATATT-TTAT
*
1452447 TATAATAT-TTTT-T
1 TTTAATATATTTTAT
1452460 TTTAATATATTTATAT
1 TTTAATATATTT-TAT
*
1452476 TTTATTATTAATTTTA-
1 TTTAATA-T-ATTTTAT
* *
1452492 TATAATATCA-TTT-C
1 TTTAATAT-ATTTTAT
* *
1452506 TTAAATATATTTTAA
1 TTTAATATATTTTAT
* *
1452521 TGTCATATATTTTAT
1 TTTAATATATTTTAT
* *
1452536 TTTTATTTATTATTTAT
1 TTTAATATA-T-TTTAT
** *
1452553 AATATTTATATTTTATT
1 TTTA-ATATATTTTA-T
1452570 TTTAATATA-TTTAT
1 TTTAATATATTTTAT
* *
1452584 ATTT-ATTTA-TTAATT
1 -TTTAATATATTTTA-T
**
1452599 TTTATATAATATCATAT
1 TTTA-AT-ATATTTTAT
1452616 TTTAAATATATTTTA-
1 TTT-AATATATTTTAT
*
1452631 -ATACATATATTTTAT
1 TTTA-ATATATTTTAT
* *
1452646 TTTTATTTATTATTAT
1 TTTAATATATT-TTAT
*
1452662 AATTTTATATATTTTA-
1 --TTTAATATATTTTAT
*
1452678 TTTCAT-T-TCTTTA-
1 TTTAATATAT-TTTAT
* *
1452691 -AT-ATATTTTTTAT
1 TTTAATATATTTTAT
1452704 ATTT--TATATTTTAT
1 -TTTAATATATTTTAT
*
1452718 TTTAATTTATTTTACCT
1 TTTAATATATTTTA--T
* *
1452735 ATATTATATAAATGTTAATT
1 -T-TTA-ATATAT-TTTA-T
*
1452755 TTTATATTTTATTTTAT
1 TTTA-A-TATATTTTAT
*
1452772 TTTAATTTTTATTCTTAT
1 TTTAA--TATATT-TTAT
*
1452790 ATT-ATATATTTTAT
1 TTTAATATATTTTAT
1452804 TTTAATAT-TTTTAT
1 TTTAATATATTTTAT
1452818 TTTAAT
1 TTTAAT
1452824 TATAATATTA
Statistics
Matches: 334, Mismatches: 63, Indels: 108
0.66 0.12 0.21
Matches are distributed among these distances:
11 2 0.01
12 7 0.02
13 33 0.10
14 85 0.25
15 66 0.20
16 51 0.15
17 41 0.12
18 34 0.10
19 7 0.02
20 5 0.01
21 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATATATTTTAT
Found at i:1452826 original size:32 final size:33
Alignment explanation
Indices: 1452764--1452832 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 33
1452754 TTTTATATTT
1452764 TATTTTATTTTAATTTTTATTCTTATATTAT-A
1 TATTTTATTTTAATTTTTATTCTTATATTATAA
1452796 TATTTTATTTTAATATTTTTATT-TTA-ATTATAA
1 TATTTTATTTT-A-ATTTTTATTCTTATATTATAA
1452829 TATT
1 TATT
1452833 ATAAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
32 16 0.47
33 9 0.26
34 9 0.26
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (33 bp):
TATTTTATTTTAATTTTTATTCTTATATTATAA
Found at i:1452827 original size:37 final size:30
Alignment explanation
Indices: 1452756--1452818 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 30
1452746 ATGTTAATTT
*
1452756 TTATATTTTATTTTATTTTAATTTTTATTC
1 TTATATTTTATTTTATTTTAATTTTTATTA
*
1452786 TTATATTATATATTTTATTTTAATATTT-TTA
1 TTATATT-T-TATTTTATTTTAATTTTTATTA
1452817 TT
1 TT
1452819 TTAATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 7 0.24
31 5 0.17
32 17 0.59
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (30 bp):
TTATATTTTATTTTATTTTAATTTTTATTA
Found at i:1460087 original size:2 final size:2
Alignment explanation
Indices: 1460080--1460122 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1460070 ATTGGTACTT
*
1460080 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1460122 T
1 T
1460123 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Done.