Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 13 of 20
Found at i:5046168 original size:12 final size:13
Alignment explanation
Indices: 5046136--5046168 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5046126 CATGCTACAA
5046136 CTTTTTTTCTTTG
1 CTTTTTTTCTTTG
*
5046149 CTTTTTTT-TTTT
1 CTTTTTTTCTTTG
5046161 CTTTTTTT
1 CTTTTTTT
5046169 GTGGGGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (13 bp):
CTTTTTTTCTTTG
Found at i:5068412 original size:105 final size:104
Alignment explanation
Indices: 5068093--5068414 Score: 234
Period size: 105 Copynumber: 3.1 Consensus size: 104
5068083 AGACTTTATT
* * * * *
5068093 TATATGATTACACTTAATAACTTTATTAGTTATCACTTTAGATTTTATAACATATTGTTTATAAT
1 TATATAATTACATTTAATAAATTTATTAG-TATCACTTTAAATTTTATAACATATTATTTATAAT
* *
5068158 TAGTTATTATTTATACAAACTTTGATATAAAACATTTTAA
65 TAGTTATTATTTATACAAACTTTGATATAAAATATTATAA
* * * * * * * * ** * *
5068198 CATATAATT-TATACTATTAATTTTATATA-TAATAAAGTGATGTATTATGTAGACATA-TATTT
1 TATATAATTACAT-TTAATAAATTTAT-TAGT-AT-CACT-TTAAATTTTATA-ACATATTATTT
* * * *
5068260 A-ATTTA-TACATTAAGATTGT-TAC-AA-TTT-ATAATAAACT-TTAT-T
60 ATAATTAGT-TATT---ATT-TATACAAACTTTGAT-ATAAAATATTATAA
5068303 TATATAATTACATTTAATAAATTTATTAGCTATCACTTTAAATTTTATAACATATTATTTATAAT
1 TATATAATTACATTTAATAAATTTATTAG-TATCACTTTAAATTTTATAACATATTATTTATAAT
5068368 TAGTTATTATTTATACAAACTTTGATATAAAATATTATAA
65 TAGTTATTATTTATACAAACTTTGATATAAAATATTATAA
5068408 TATATAA
1 TATATAA
5068415 GTTATATCAT
Statistics
Matches: 156, Mismatches: 37, Indels: 48
0.65 0.15 0.20
Matches are distributed among these distances:
100 1 0.01
101 6 0.04
102 7 0.04
103 22 0.14
104 19 0.12
105 48 0.31
106 19 0.12
107 20 0.13
108 7 0.04
109 6 0.04
110 1 0.01
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (104 bp):
TATATAATTACATTTAATAAATTTATTAGTATCACTTTAAATTTTATAACATATTATTTATAATT
AGTTATTATTTATACAAACTTTGATATAAAATATTATAA
Found at i:5068429 original size:210 final size:211
Alignment explanation
Indices: 5068046--5068439 Score: 614
Period size: 210 Copynumber: 1.9 Consensus size: 211
5068036 TTATATATAC
* * *
5068046 ATTTAATTTATACATAAGTATTATTATAACTTATAATAGACTTTATTTATATGATTACACTTAAT
1 ATTTAATTTATACATAAGTATTATTACAACTTATAATAAACTTTATTTATATAATTACACTTAAT
* * * *
5068111 AACTTTATTAGTTATCACTTTAGATTTTATAACATATTGTTTATAATTAGTTATTATTTATACAA
66 AAATTTATTAGCTATCACTTTAAATTTTATAACATATTATTTATAATTAGTTATTATTTATACAA
* * *
5068176 ACTTTGATATAAAACATTTTAACATATAATTTATACTATTAATT-TTATATATAATAAAGTGATG
131 ACTTTGATATAAAACATTATAACATATAAGTTATACTATTAATTCATATATATAATAAAGTGATG
5068240 TATTATGTAGACATAT
196 TATTATGTAGACATAT
* * *
5068256 ATTTAATTTATACATTAAG-ATTGTTACAATTTATAATAAACTTTATTTATATAATTACATTTAA
1 ATTTAATTTATACA-TAAGTATTATTACAACTTATAATAAACTTTATTTATATAATTACACTTAA
5068320 TAAATTTATTAGCTATCACTTTAAATTTTATAACATATTATTTATAATTAGTTATTATTTATACA
65 TAAATTTATTAGCTATCACTTTAAATTTTATAACATATTATTTATAATTAGTTATTATTTATACA
* *
5068385 AACTTTGATATAAAATATTATAATATATAAGTTATA-TCATTAATTCATATATATA
130 AACTTTGATATAAAACATTATAACATATAAGTTATACT-ATTAATTCATATATATA
5068440 TATATATATA
Statistics
Matches: 166, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
209 1 0.01
210 153 0.92
211 12 0.07
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (211 bp):
ATTTAATTTATACATAAGTATTATTACAACTTATAATAAACTTTATTTATATAATTACACTTAAT
AAATTTATTAGCTATCACTTTAAATTTTATAACATATTATTTATAATTAGTTATTATTTATACAA
ACTTTGATATAAAACATTATAACATATAAGTTATACTATTAATTCATATATATAATAAAGTGATG
TATTATGTAGACATAT
Found at i:5081992 original size:2 final size:2
Alignment explanation
Indices: 5081987--5082032 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
5081977 AGAAAAAATC
*
5081987 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5082029 GA GA
1 GA GA
5082033 ATGAAGGGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5085426 original size:17 final size:16
Alignment explanation
Indices: 5085400--5085434 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5085390 TGAAAATCGA
*
5085400 TTCTTTCTTTCTTATAT
1 TTCTTACTTTCTT-TAT
5085417 TTCTTACTTTCTTTAT
1 TTCTTACTTTCTTTAT
5085433 TT
1 TT
5085435 AATTCTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.71
Consensus pattern (16 bp):
TTCTTACTTTCTTTAT
Found at i:5089767 original size:17 final size:17
Alignment explanation
Indices: 5089745--5089778 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5089735 AAAATAATTT
5089745 TTATT-AAATAATTAATA
1 TTATTAAAATAA-TAATA
5089762 TTATTAAAATAATAATA
1 TTATTAAAATAATAATA
5089779 AAAATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATTAAAATAATAATA
Found at i:5100053 original size:2 final size:2
Alignment explanation
Indices: 5100046--5100082 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5100036 AACCCTTCAC
5100046 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
5100083 TAATTCCTCA
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:5117948 original size:1 final size:1
Alignment explanation
Indices: 5117944--5117970 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5117934 CGCGGGAGCC
5117944 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
5117971 CTTCATTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:5124884 original size:16 final size:16
Alignment explanation
Indices: 5124865--5124936 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
5124855 GTAGATTTTG
5124865 TTAAAAAATTTATATA
1 TTAAAAAATTTATATA
*
5124881 TTAATAATATTTTAATATTA
1 TTAA-AA-AATTT-ATA-TA
* ** *
5124901 TCAAAAAATAAATTTA
1 TTAAAAAATTTATATA
*
5124917 TTAAAAAAATTATATA
1 TTAAAAAATTTATATA
5124933 TTAA
1 TTAA
5124937 TATTAAATAA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
16 21 0.51
17 4 0.10
18 6 0.15
19 5 0.12
20 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAAAATTTATATA
Found at i:5125951 original size:47 final size:47
Alignment explanation
Indices: 5125882--5125974 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
5125872 CACATAGTAG
* *
5125882 GCCTCCCAAGAGAAATGTAATTTCATTTCAGTTTGAAAGCGATGGTC
1 GCCTCCCAAGAGAAAGGTAATTTCATTTCACTTTGAAAGCGATGGTC
* *
5125929 GCCTCCCAAGAGGAAGGTAATTTTATTTCACTTTGAAAGCGATGGT
1 GCCTCCCAAGAGAAAGGTAATTTCATTTCACTTTGAAAGCGATGGT
5125975 TCTGACACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (47 bp):
GCCTCCCAAGAGAAAGGTAATTTCATTTCACTTTGAAAGCGATGGTC
Found at i:5136182 original size:15 final size:17
Alignment explanation
Indices: 5136151--5136182 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5136141 ATAATTTATA
5136151 ATTAAATATTAATATTT
1 ATTAAATATTAATATTT
5136168 ATTAAAT-TT-ATATTT
1 ATTAAATATTAATATTT
5136183 TACTAAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAAATATTAATATTT
Found at i:5145178 original size:23 final size:25
Alignment explanation
Indices: 5145143--5145204 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 25
5145133 TCAAATACTT
*
5145143 AAAT-ATTCTAATTTGA-TATATTA
1 AAATAATTTTAATTTGATTATATTA
* * *
5145166 ATATAA-TTTAA-TTAATTATTTTA
1 AAATAATTTTAATTTGATTATATTA
5145189 AAATAATTTTAATTTG
1 AAATAATTTTAATTTG
5145205 GTGTGTTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
22 3 0.10
23 18 0.62
24 6 0.21
25 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (25 bp):
AAATAATTTTAATTTGATTATATTA
Found at i:5146768 original size:21 final size:19
Alignment explanation
Indices: 5146744--5146808 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 19
5146734 ACTCTTCTTT
5146744 TTCTTCACCTTCTCCTTCTCC
1 TTCTTCACC-TCTCCTTCT-C
* *
5146765 TTCTCCATCTCTTCCTTCTAC
1 TTCTTCACCTC-TCCTTCT-C
*
5146786 TTCTT-ACCTCTCTTTCTC
1 TTCTTCACCTCTCCTTCTC
5146804 TTCTT
1 TTCTT
5146809 ACCACACACA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
18 6 0.16
19 6 0.16
20 6 0.16
21 19 0.51
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.52
Consensus pattern (19 bp):
TTCTTCACCTCTCCTTCTC
Found at i:5157162 original size:18 final size:18
Alignment explanation
Indices: 5157130--5157175 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
5157120 TAAATATTAA
*
5157130 ATTTTTATTATTTATT-TT
1 ATTTTT-TTACTTATTATT
5157148 ATGTTTTTTACTTATTATT
1 AT-TTTTTTACTTATTATT
5157167 ATTTTTTTA
1 ATTTTTTTA
5157176 AAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTTTTTACTTATTATT
Found at i:5157191 original size:11 final size:10
Alignment explanation
Indices: 5157174--5157198 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5157164 ATTATTTTTT
5157174 TAAAAAAAAA
1 TAAAAAAAAA
5157184 TAAAAAAAAA
1 TAAAAAAAAA
5157194 TAAAA
1 TAAAA
5157199 TAAAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:5162742 original size:13 final size:15
Alignment explanation
Indices: 5162726--5162757 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5162716 CACATTGCCA
5162726 TCTCC-CTGTTT-TT
1 TCTCCTCTGTTTCTT
5162739 TCTCCTCTGTTTCTT
1 TCTCCTCTGTTTCTT
5162754 TCTC
1 TCTC
5162758 TACTCTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 6 0.35
15 6 0.35
ACGTcount: A:0.00, C:0.34, G:0.06, T:0.59
Consensus pattern (15 bp):
TCTCCTCTGTTTCTT
Found at i:5163861 original size:14 final size:14
Alignment explanation
Indices: 5163842--5163870 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5163832 GCATCAGTGT
5163842 ACTTCGGCAGCTGC
1 ACTTCGGCAGCTGC
5163856 ACTTCGGCAGCTGC
1 ACTTCGGCAGCTGC
5163870 A
1 A
5163871 ATTTCAGCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (14 bp):
ACTTCGGCAGCTGC
Found at i:5172600 original size:14 final size:15
Alignment explanation
Indices: 5172570--5172602 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5172560 ATAAATATTC
*
5172570 TATTAATATTGTAAA
1 TATTAATAATGTAAA
5172585 TATTAATAAT-TAAA
1 TATTAATAATGTAAA
5172599 TATT
1 TATT
5172603 TTTTGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TATTAATAATGTAAA
Found at i:5188443 original size:2 final size:2
Alignment explanation
Indices: 5188438--5188466 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5188428 TTCAACTGTT
5188438 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 T
5188467 CTTGTTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5208715 original size:22 final size:22
Alignment explanation
Indices: 5208690--5208732 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5208680 ATCATATTCA
5208690 ATGTCA-CATTAATAAAAAAATC
1 ATGTCAGCA-TAATAAAAAAATC
*
5208712 ATGTCAGCATAATTAAAAAAT
1 ATGTCAGCATAATAAAAAAAT
5208733 TTAATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (22 bp):
ATGTCAGCATAATAAAAAAATC
Found at i:5209008 original size:31 final size:30
Alignment explanation
Indices: 5208973--5209034 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
5208963 CAATTTTAAA
* *
5208973 ATATTTACAAATAT-TTTTCATATTAATAATT
1 ATATTT-CAAATATATTTTAAAATTAA-AATT
*
5209004 ATATTTTAAATATATTTTAAAATTAAAATT
1 ATATTTCAAATATATTTTAAAATTAAAATT
5209034 A
1 A
5209035 AATAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
ATATTTCAAATATATTTTAAAATTAAAATT
Found at i:5209671 original size:16 final size:16
Alignment explanation
Indices: 5209648--5209680 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
5209638 ATAAATTATG
5209648 TCTTTTTTTTT-TCCT
1 TCTTTTTTTTTGTCCT
5209663 TCTTTTTTTTTGTCCT
1 TCTTTTTTTTTGTCCT
5209679 TC
1 TC
5209681 AATAATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTTTTTTTTTGTCCT
Found at i:5217485 original size:2 final size:2
Alignment explanation
Indices: 5217448--5217472 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5217438 TGGCTATGGC
5217448 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
5217473 GTGTGTGTAT
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:5218471 original size:20 final size:21
Alignment explanation
Indices: 5218436--5218474 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5218426 TTTGATAAAT
*
5218436 ATAAACTAATTGATTAAAAAA
1 ATAAACTAAATGATTAAAAAA
5218457 ATAAAC-AAATGATTAAAA
1 ATAAACTAAATGATTAAAA
5218475 TATAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
ATAAACTAAATGATTAAAAAA
Found at i:5219505 original size:2 final size:2
Alignment explanation
Indices: 5219498--5219527 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5219488 AGTAAGATAT
5219498 TC TC TC TC TC TC TC TC TC T- TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5219528 TTCTGTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5221289 original size:18 final size:20
Alignment explanation
Indices: 5221251--5221290 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5221241 CACATATGGG
*
5221251 TAATTGCTTCATTTTTCATT
1 TAATTGCTTCATTTCTCATT
5221271 TAATT-CTTC-TTTCTCATT
1 TAATTGCTTCATTTCTCATT
5221289 TA
1 TA
5221291 CTTTAGTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (20 bp):
TAATTGCTTCATTTCTCATT
Found at i:5229186 original size:23 final size:20
Alignment explanation
Indices: 5229139--5229176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5229129 TGCTTTCTCC
*
5229139 ATAAAGAATGATTATAATTG
1 ATAAAGAATGATGATAATTG
*
5229159 ATAAAGGATGATGATAAT
1 ATAAAGAATGATGATAAT
5229177 GTAGATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (20 bp):
ATAAAGAATGATGATAATTG
Found at i:5231622 original size:5 final size:5
Alignment explanation
Indices: 5231612--5231762 Score: 55
Period size: 5 Copynumber: 30.4 Consensus size: 5
5231602 TAATGTCATA
* *
5231612 TATTT TATTT TATTTT TATTAT AATTT TA-TA TATTT TATTTT TATTT
1 TATTT TATTT TA-TTT TATT-T TATTT TATTT TATTT TA-TTT TATTT
* * * * * * * *
5231659 T-TTAA TATAAT T-TTT AATAT TA-TA TATTT TATTT TAATT TCTTA TATTT
1 TATT-T TAT-TT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
* * * * * *
5231708 TATTT TA-TT T-TTT GATTTT TATAT TA-TA TATTT TATTT AAATA TATTT
1 TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT TATTT TATTT
5231756 TATTT TA
1 TATTT TA
5231763 ATTATAACAT
Statistics
Matches: 101, Mismatches: 32, Indels: 26
0.64 0.20 0.16
Matches are distributed among these distances:
4 15 0.15
5 66 0.65
6 20 0.20
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:5231650 original size:20 final size:19
Alignment explanation
Indices: 5231625--5231718 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 19
5231615 TTTATTTTAT
5231625 TTTTATTATAATTTTATATA
1 TTTTATT-TAATTTTATATA
* *
5231645 TTTTATTTTTATTTTTTAATA
1 TTTTA-TTTAATTTTAT-ATA
* *
5231666 TAATT-TTTAATATTATATA
1 T-TTTATTTAATTTTATATA
5231685 TTTTATTTTAATTTCT-TATA
1 TTTTA-TTTAATTT-TATATA
*
5231705 TTTTATTTTATTTT
1 TTTTATTTAATTTT
5231719 TTGATTTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.05
19 11 0.19
20 36 0.61
21 7 0.12
22 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATTTAATTTTATATA
Found at i:5231668 original size:33 final size:33
Alignment explanation
Indices: 5231609--5231693 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
5231599 TTTTAATGTC
*
5231609 ATATATTTTA-TTTTA-TTTTTATTATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATTTT
5231640 ATATATTTTATTTTTATTTTTTAATATAATTTT
1 ATATATTTTATTTTTATTTTTTAATATAATTTT
*
5231673 -TAATATTATATATTTTATTTT
1 AT-ATATTTTAT-TTTTATTTT
5231694 AATTTCTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
31 10 0.21
32 6 0.12
33 23 0.48
34 9 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAATATAATTTT
Found at i:5231714 original size:40 final size:40
Alignment explanation
Indices: 5231621--5231714 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
5231611 ATATTTTATT
* * * *
5231621 TTAT-TTTTATTATAATTTTATATATTTTATTTTTATTTT
1 TTATATTTTATTTTAATATTATATATTTTATTTTAATTTC
* *
5231660 TTA-ATATAATTTTTAATATTATATATTTTATTTTAATTTC
1 TTATATTTTA-TTTTAATATTATATATTTTATTTTAATTTC
5231700 TTATATTTTATTTTA
1 TTATATTTTATTTTA
5231715 TTTTTTGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
39 6 0.14
40 34 0.77
41 4 0.09
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (40 bp):
TTATATTTTATTTTAATATTATATATTTTATTTTAATTTC
Found at i:5231739 original size:60 final size:62
Alignment explanation
Indices: 5231610--5231745 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 62
5231600 TTTAATGTCA
*
5231610 TATATT-T-TATTTTATTTTTATTATAATTTTATATATTTTATTTTTATTTTTTAATATAAT
1 TATATTATATATTATATTTTTATTATAATTTTATATATTTTATTTTTATTTTTTAATATAAT
* * *
5231670 T-T-TTA-ATATTATATATTTTATTTTAATTTCT-TATATTTTA-TTTTATTTTTTGAT-T-TT
1 TATATTATATATTATAT-TTTTATTATAATTT-TATATATTTTATTTTTATTTTTTAATATAAT
*
5231727 TATATTATATATTTTATTT
1 TATATTATATATTATATTT
5231746 AAATATATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
57 2 0.03
58 4 0.06
59 26 0.41
60 31 0.48
61 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.71
Consensus pattern (62 bp):
TATATTATATATTATATTTTTATTATAATTTTATATATTTTATTTTTATTTTTTAATATAAT
Found at i:5231760 original size:53 final size:54
Alignment explanation
Indices: 5231640--5231762 Score: 151
Period size: 53 Copynumber: 2.3 Consensus size: 54
5231630 TTATAATTTT
*
5231640 ATATATTTTATTTTTATTTTTTAATATAATTTTTAATATTATATATTTTATTTTA
1 ATATATTTTA-TTTTATTTTTTAATATAATTTTTAATATTATATATTTTATTTAA
* * * * * *
5231695 ATTTCTTATATTTTATTTTATT-TTTTGATTTTT-ATATTATATATTTTATTTAA
1 ATATATTTTATTTTATTTT-TTAATATAATTTTTAATATTATATATTTTATTTAA
5231748 ATATATTTTATTTTA
1 ATATATTTTATTTTA
5231763 ATTATAACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 31 0.54
54 17 0.30
55 9 0.16
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (54 bp):
ATATATTTTATTTTATTTTTTAATATAATTTTTAATATTATATATTTTATTTAA
Found at i:5232104 original size:27 final size:27
Alignment explanation
Indices: 5232070--5232123 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5232060 GGTTTGGATG
5232070 TTCTTTGGGCCCATGACTAATTCTGTT
1 TTCTTTGGGCCCATGACTAATTCTGTT
5232097 TTCTTTGGGCCCATGACTAATTCTGTT
1 TTCTTTGGGCCCATGACTAATTCTGTT
5232124 GTAGGTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (27 bp):
TTCTTTGGGCCCATGACTAATTCTGTT
Found at i:5259960 original size:2 final size:2
Alignment explanation
Indices: 5259955--5259979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5259945 AGTGTGTGTG
5259955 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
5259980 GATTAATATT
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:5261832 original size:2 final size:2
Alignment explanation
Indices: 5261825--5261854 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5261815 AACCGTGAAA
5261825 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5261855 GCTGGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5263685 original size:14 final size:14
Alignment explanation
Indices: 5263666--5263693 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5263656 ACTTCACATC
5263666 TGATCACTCTCTCT
1 TGATCACTCTCTCT
5263680 TGATCACTCTCTCT
1 TGATCACTCTCTCT
5263694 CTCTCTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.07, T:0.43
Consensus pattern (14 bp):
TGATCACTCTCTCT
Found at i:5264682 original size:2 final size:2
Alignment explanation
Indices: 5264675--5264713 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5264665 TTAGCTGATA
5264675 AT AT AT AT AT AT AT A- 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
5264714 TAATAAGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5276003 original size:26 final size:26
Alignment explanation
Indices: 5275970--5276024 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5275960 ACTGTAGAAA
5275970 ATTGCCAATTAAAGATTCCTCTGTTG
1 ATTGCCAATTAAAGATTCCTCTGTTG
5275996 ATTGCCAATTAAAGATTCCTCTGTTG
1 ATTGCCAATTAAAGATTCCTCTGTTG
5276022 ATT
1 ATT
5276025 TGTAGAGATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (26 bp):
ATTGCCAATTAAAGATTCCTCTGTTG
Found at i:5280689 original size:52 final size:51
Alignment explanation
Indices: 5280622--5280721 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 51
5280612 CCTGGGAATG
* *
5280622 GTGATTCCTGTAGACAATATAAAAAGACAATTAAGGT-GCCTTGTATATTACA
1 GTGATTCCTGCAGACAATATAAAAAG-CAATTAA-GTCGACTTGTATATTACA
* *
5280674 GTGATTCCTGCAGACAATATAGAAAGCAATTTAGTCGACTTGTATATT
1 GTGATTCCTGCAGACAATATAAAAAGCAATTAAGTCGACTTGTATATT
5280722 TTGTCTCAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.05
51 17 0.40
52 24 0.56
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (51 bp):
GTGATTCCTGCAGACAATATAAAAAGCAATTAAGTCGACTTGTATATTACA
Found at i:5286849 original size:12 final size:12
Alignment explanation
Indices: 5286832--5286856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5286822 CAAGTATAAG
5286832 TCTTGAAAACAT
1 TCTTGAAAACAT
5286844 TCTTGAAAACAT
1 TCTTGAAAACAT
5286856 T
1 T
5286857 TTTCAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTTGAAAACAT
Found at i:5288011 original size:16 final size:15
Alignment explanation
Indices: 5287990--5288044 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
5287980 ATTATAAAAA
5287990 TAATTTTACATTTTAT
1 TAATTTTA-ATTTTAT
**
5288006 TAATTTTAAAAATTAT
1 TAATTTT-AATTTTAT
*
5288022 TAATATATAATTTTAT
1 TAAT-TTTAATTTTAT
5288038 TAATTTT
1 TAATTTT
5288045 TTATTAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 2 0.06
16 26 0.84
17 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTTAATTTTAT
Found at i:5288556 original size:23 final size:24
Alignment explanation
Indices: 5288526--5288571 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5288516 GAATAAAAAA
5288526 TATTAA-TTCATATTAAAATTAAT
1 TATTAATTTCATATTAAAATTAAT
**
5288549 TATTAATTTTGTATTAAAATTAA
1 TATTAATTTCATATTAAAATTAA
5288572 AAATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TATTAATTTCATATTAAAATTAAT
Found at i:5288581 original size:24 final size:24
Alignment explanation
Indices: 5288536--5288581 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5288526 TATTAATTCA
**
5288536 TATTAAAATTAATTATTAATTTTG
1 TATTAAAATTAAAAATTAATTTTG
*
5288560 TATTAAAATTAAAAATTTATTT
1 TATTAAAATTAAAAATTAATTT
5288582 AAATACGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTAAAATTAAAAATTAATTTTG
Found at i:5298968 original size:31 final size:31
Alignment explanation
Indices: 5298902--5299001 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
5298892 AATAAAAAAT
* *
5298902 ATTAAAATAAAATATAAAATATACG-AATCAGAA
1 ATTAAAAT-AAA-ATAAAATATAAGAAATTA-AA
5298935 ATTAAAATAAAATAAAATATAAGAAATTAAA
1 ATTAAAATAAAATAAAATATAAGAAATTAAA
* * * *
5298966 ATTTATATAATATAAGGA-A-AAGAAATTAAA
1 ATTAAAATAAAATAA-AATATAAGAAATTAAA
5298996 A-TAAAA
1 ATTAAAA
5299002 CATATAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.05
30 12 0.21
31 26 0.46
32 8 0.14
33 8 0.14
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (31 bp):
ATTAAAATAAAATAAAATATAAGAAATTAAA
Found at i:5299315 original size:15 final size:15
Alignment explanation
Indices: 5299295--5299339 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
5299285 TTATTTTCTC
5299295 TGCAATCACATTACT
1 TGCAATCACATTACT
*
5299310 TGCAATCACATTATT
1 TGCAATCACATTACT
5299325 TGCAATCACATTACT
1 TGCAATCACATTACT
5299340 AATAATCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:5299347 original size:30 final size:30
Alignment explanation
Indices: 5299295--5299351 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5299285 TTATTTTCTC
**
5299295 TGCAATCACATTACTTGCAATCACATTATT
1 TGCAATCACATTACTAACAATCACATTATT
*
5299325 TGCAATCACATTACTAATAATCACATT
1 TGCAATCACATTACTAACAATCACATT
5299352 GCATTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
TGCAATCACATTACTAACAATCACATTATT
Found at i:5303879 original size:22 final size:22
Alignment explanation
Indices: 5303802--5303897 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 22
5303792 TTCTTATTAT
*
5303802 ATTTAATTATTTTATT-TTAAAA
1 ATTTAATT-TTTTATTATAAAAA
* * * * *
5303824 TTTTTATTTTTAATTTTAAAAT
1 ATTTAATTTTTTATTATAAAAA
**
5303846 A-TTAATACTTTATTATAAAAA
1 ATTTAATTTTTTATTATAAAAA
* *
5303867 ATTTAATTTTTTATAATTAAAA
1 ATTTAATTTTTTATTATAAAAA
*
5303889 TTTTAATTT
1 ATTTAATTT
5303898 AATTTTATAA
Statistics
Matches: 55, Mismatches: 17, Indels: 4
0.72 0.22 0.05
Matches are distributed among these distances:
21 21 0.38
22 34 0.62
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTAATTTTTTATTATAAAAA
Found at i:5303890 original size:21 final size:20
Alignment explanation
Indices: 5303802--5303897 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 20
5303792 TTCTTATTAT
*
5303802 ATTTAATTATTTTATTTTAAA
1 ATTTAATT-TTTTATATTAAA
* * *
5303823 ATTTTTATTTTTAATTTTAAA
1 A-TTTAATTTTTTATATTAAA
*
5303844 ATATTAATACTTTATTATA-AAAA
1 AT-TTAAT--TTT-TTATATTAAA
5303867 ATTTAATTTTTTATAATTAAA
1 ATTTAATTTTTTAT-ATTAAA
5303888 ATTTTAATTT
1 A-TTTAATTT
5303898 AATTTTATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.07
20 5 0.08
21 21 0.35
22 19 0.32
23 8 0.13
24 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAATTTTTTATATTAAA
Found at i:5304344 original size:22 final size:22
Alignment explanation
Indices: 5304301--5304366 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
5304291 TTATTCTCTA
* *
5304301 TTTTTGAAATAATTGTTATCAAAT
1 TTTTTAAAATAATT-AT-TCAAAT
*
5304325 TTTTTTAAATAATTATTCAAAT
1 TTTTTAAAATAATTATTCAAAT
5304347 TTCTTTAAGAATAATTATTC
1 TT-TTTAA-AATAATTATTC
5304367 CGATAAATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 8 0.22
23 5 0.14
24 24 0.65
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTTAAAATAATTATTCAAAT
Found at i:5304831 original size:16 final size:16
Alignment explanation
Indices: 5304810--5304842 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5304800 ATTTAGTTAC
*
5304810 TAATAATATTTTTTAT
1 TAATAATATTATTTAT
5304826 TAATAATATTATTTAT
1 TAATAATATTATTTAT
5304842 T
1 T
5304843 TTATATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATAATATTATTTAT
Found at i:5305718 original size:21 final size:21
Alignment explanation
Indices: 5305692--5305734 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5305682 TCTTCAGCAG
5305692 TCGCAAATTGTACATATATTA
1 TCGCAAATTGTACATATATTA
5305713 TCGCAAATTGTACATATATTA
1 TCGCAAATTGTACATATATTA
5305734 T
1 T
5305735 GAACCCCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
TCGCAAATTGTACATATATTA
Found at i:5307585 original size:20 final size:21
Alignment explanation
Indices: 5307560--5307600 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
5307550 TTTAAACTTA
5307560 TAAAATT-AATATTTTTAATT
1 TAAAATTAAATATTTTTAATT
5307580 TAAAATTAAAATATTTTTAAT
1 TAAAATT-AAATATTTTTAAT
5307601 ATTCTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATTAAATATTTTTAATT
Found at i:5307916 original size:22 final size:21
Alignment explanation
Indices: 5307863--5307942 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
5307853 AATATTAATG
5307863 ATTAA-ATTATAAATAA-AA-T
1 ATTAATATT-TAAATAATAACT
**
5307882 ATTAATACCTAAATAATCAACT
1 ATTAATATTTAAATAAT-AACT
*
5307904 ATTAATATTTAAA-AGATAAGT
1 ATTAATATTTAAATA-ATAACT
5307925 GATTAATATTATAAATAA
1 -ATTAATATT-TAAATAA
5307943 AATATAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 12 0.25
20 1 0.02
21 6 0.12
22 23 0.48
23 5 0.10
24 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (21 bp):
ATTAATATTTAAATAATAACT
Found at i:5307944 original size:27 final size:26
Alignment explanation
Indices: 5307913--5307965 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
5307903 TATTAATATT
*
5307913 TAAAAGATAAGTGATTAATATTATAAA
1 TAAAAGATAAATGATTAATATT-TAAA
* *
5307940 TAAAATATAAATTATTAATATTTAAA
1 TAAAAGATAAATGATTAATATTTAAA
5307966 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (26 bp):
TAAAAGATAAATGATTAATATTTAAA
Found at i:5307966 original size:22 final size:22
Alignment explanation
Indices: 5307873--5307972 Score: 74
Period size: 22 Copynumber: 4.3 Consensus size: 22
5307863 ATTAAATTAT
* **
5307873 AAATAAAATATTAATACCTAAA
1 AAATAAATTATTAATATTTAAA
* * *
5307895 TAATCAACTATTAATATTTAAA
1 AAATAAATTATTAATATTTAAA
* * *
5307917 AGATAAGTGATTAATATTATAAATAA
1 AAATAAATTATTAATATT-T--A-AA
5307943 AATATAAATTATTAATATTTAAA
1 AA-ATAAATTATTAATATTTAAA
5307966 AAATAAA
1 AAATAAA
5307973 AATAAAAGAT
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 34 0.58
23 5 0.08
24 1 0.02
25 1 0.02
26 4 0.07
27 14 0.24
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (22 bp):
AAATAAATTATTAATATTTAAA
Found at i:5308052 original size:178 final size:174
Alignment explanation
Indices: 5307774--5308091 Score: 476
Period size: 178 Copynumber: 1.8 Consensus size: 174
5307764 TTGCATTAAA
* *
5307774 AAATTATTAATATTTAAAAAATACAATAAAAAATAATCATAATAACATTTAAATTTTAAATAAAA
1 AAATTATTAATATTTAAAAAATAAAATAAAAAATAATCATAATAACATTTAAATTATAAATAAAA
5307839 CAATAGTATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATACCTAAATAATCAACT
66 CAATAGTATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATACCTAAATAATCAACT
5307904 ATTAATATTTAAAAGATAAGTGATTAATATTATAAATAAAATAT
131 ATTAATATTTAAAAGATAAGTGATTAATATTATAAATAAAATAT
*
5307948 AAATTATTAATATTTAAAAAATAAAAATAAAAGATAAATACTCATAATAACATTTAAATTATAAA
1 AAATTATTAATATTTAAAAAAT-AAAAT--AA-A-AAATAATCATAATAACATTTAAATTATAAA
* * * * ** *
5308013 TTAAATATTATTATTTT-TAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATGAT
61 TAAAACAATAGTATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATACCTAAATAAT
* *
5308077 CAATTTTTAATATTT
126 CAACTATTAATATTT
5308092 TAAATAAATA
Statistics
Matches: 127, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
174 22 0.17
175 4 0.03
177 2 0.02
178 58 0.46
179 41 0.32
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (174 bp):
AAATTATTAATATTTAAAAAATAAAATAAAAAATAATCATAATAACATTTAAATTATAAATAAAA
CAATAGTATTTTATAATATTAATGATTAAATTATAAATAAAATATTAATACCTAAATAATCAACT
ATTAATATTTAAAAGATAAGTGATTAATATTATAAATAAAATAT
Found at i:5308071 original size:26 final size:26
Alignment explanation
Indices: 5308031--5308142 Score: 94
Period size: 26 Copynumber: 4.5 Consensus size: 26
5308021 TATTATTTTT
5308031 AATATTAATGA-TTAAATTATAAATAA
1 AATATTAAT-ATTTAAATTATAAATAA
* *
5308057 AATATTAATATTTAAATGATCAAT--
1 AATATTAATATTTAAATTATAAATAA
* *
5308081 --TTTTAATATTTTAA--ATAAATAA
1 AATATTAATATTTAAATTATAAATAA
* * *
5308103 TTATAATAACATTTAAATTATAAATAA
1 -AATATTAATATTTAAATTATAAATAA
5308130 AATATTAATATTT
1 AATATTAATATTT
5308143 TATAATGTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.08
22 12 0.18
25 11 0.17
26 30 0.45
27 8 0.12
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
AATATTAATATTTAAATTATAAATAA
Found at i:5323652 original size:17 final size:17
Alignment explanation
Indices: 5323630--5323664 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5323620 TTTTATTTTT
*
5323630 ATTAAAAATATTTAAGA
1 ATTAAAAATAATTAAGA
5323647 ATTAAAAATAATTAAGA
1 ATTAAAAATAATTAAGA
5323664 A
1 A
5323665 AATAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
ATTAAAAATAATTAAGA
Found at i:5348533 original size:16 final size:15
Alignment explanation
Indices: 5348512--5348579 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
5348502 CGTTTGATAC
5348512 ATTACAATGTAATGTG
1 ATTACAA-GTAATGTG
*
5348528 ATTACAAGTAAATATG
1 ATTACAAGT-AATGTG
**
5348544 ATTGTAAGTAATGTG
1 ATTACAAGTAATGTG
* *
5348559 ATTGCAAGCAATGTG
1 ATTACAAGTAATGTG
5348574 ATTACA
1 ATTACA
5348580 GGGAAAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
15 25 0.57
16 19 0.43
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:5348768 original size:27 final size:27
Alignment explanation
Indices: 5348738--5348833 Score: 68
Period size: 27 Copynumber: 3.4 Consensus size: 27
5348728 TAATATATTT
5348738 ATATTTTTTATTATTAATTTTTATATA
1 ATATTTTTTATTATTAATTTTTATATA
** * * *
5348765 ATATCATTTCTTAAATATATTTTTAATATC
1 ATATTTTTTATT-ATTA-ATTTTT-ATATA
* * *
5348795 ATATATTTTATT-TTTATTTATTTTATA
1 ATATTTTTTATTATTAATTT-TTATATA
*
5348822 ATATTTTATATT
1 ATATTTTTTATT
5348834 TTATTTATAT
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
27 26 0.51
28 6 0.12
29 6 0.12
30 13 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTTTTTATTATTAATTTTTATATA
Found at i:5348785 original size:43 final size:43
Alignment explanation
Indices: 5348737--5348884 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
5348727 TTAATATATT
5348737 TATATTTTT-TATTATTAATTTTTATATAATATCATTTCTTAAA
1 TATATTTTTATATTATTAATTTTTATATAATATCATTT-TTAAA
* ** *
5348780 TATATTTTTAATATCATATATTTTATTTTTATTTATTTTATAATATTTT--A
1 TATA-TTTT--TAT-AT-TA-TTAATTTTTA--TATAATATCAT-TTTTAAA
*
5348830 TATTTTATTTATATTATTAATTTTTATATAATATCATTTTTTAAA
1 TATATT-TTTATATTATTAATTTTTATATAATATCA-TTTTTAAA
5348875 TATATTTTTA
1 TATATTTTTA
5348885 ATGTCATATA
Statistics
Matches: 81, Mismatches: 10, Indels: 27
0.69 0.08 0.23
Matches are distributed among these distances:
43 15 0.19
44 9 0.11
45 15 0.19
46 3 0.04
47 3 0.04
48 5 0.06
49 4 0.05
50 15 0.19
52 10 0.12
53 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (43 bp):
TATATTTTTATATTATTAATTTTTATATAATATCATTTTTAAA
Found at i:5348841 original size:26 final size:27
Alignment explanation
Indices: 5348797--5349428 Score: 108
Period size: 26 Copynumber: 24.3 Consensus size: 27
5348787 TTAATATCAT
*
5348797 ATATTTTAT-TTTTATTTATTTTA-TA
1 ATATTTTATATTTTATTTATATTATTA
5348822 ATATTTTATATTTTATTTATATTATTA
1 ATATTTTATATTTTATTTATATTATTA
** * *
5348849 AT-TTTTATATAATA-TCAT-TTTTTA
1 ATATTTTATATTTTATTTATATTATTA
*
5348873 A-A-TATAT-TTTTAATGTCATATATT-TT-
1 ATATTTTATATTTT-AT-T--TATATTATTA
5348899 AT-TTTTAT-TTATTATTATAATATT-TT-
1 ATATTTTATATT-TTATT-T-ATATTATTA
* * *
5348925 ATATTTTAT-TTTTAATATATTTATATTT
1 ATATTTTATATTTT-ATTTATAT-TATTA
* * *
5348953 ATATTATTA-ATTTT-TATATAATA-TC
1 ATATT-TTATATTTTATTTATATTATTA
* * * * *
5348978 ATATTTTA-AATATATTTTTAATATCA
1 ATATTTTATATTTTATTTATATTATTA
5349004 TATATTTTAT-TTTTATTTATTATTA-TA
1 -ATATTTTATATTTTATTTA-TATTATTA
* *
5349031 AT-TTTATATATTTTATTTTTAATATATTT
1 ATATTT-TATATTTTATTTAT-AT-TATTA
* *
5349060 AT-TTTTTTATTATTATTTTTA-TA-TA
1 ATATTTTATATT-TTATTTATATTATTA
* * ** * * *
5349085 ATATCATT-TCTTAAATATATTTTCAATGTC
1 ATAT-TTTATATTTTATTTATATT--AT-TA
5349115 ATATATTT-TATTTTATTTATTATTA-TA
1 ATAT-TTTATATTTTATTTA-TATTATTA
5349142 ATATTTTATATTTTA-TT-T-TT-TTA
1 ATATTTTATATTTTATTTATATTATTA
*
5349165 ATATCTT-TA---TATTTATATTATTA
1 ATATTTTATATTTTATTTATATTATTA
**
5349188 AT-TTTTATATAATA-TTATATT-TTA
1 ATATTTTATATTTTATTTATATTATTA
*
5349212 A-A-TATAT-TTTTAATATATATATT-TT-
1 ATATTTTATATTTT-AT-T-TATATTATTA
5349237 AT-TTTTAT-TTATTA-TTATATT-TTA
1 ATATTTTATATT-TTATTTATATTATTA
* *
5349261 TATATTTTAT-TTTTATTTCT-TAATATA
1 -ATATTTTATATTTTATTTATATTAT-TA
*
5349288 AT-TTTTATATTATATATT-TATT-TTA
1 ATATTTTATATTTTAT-TTATATTATTA
* * * *
5349313 ATTTGTTTTACCTATATTA-TTA-AATGTTA
1 A--TATTTTA--TATTTTATTTATATTATTA
*
5349342 ATTTTTTATA-TTTATTT-TATT-TTA
1 ATATTTTATATTTTATTTATATTATTA
*
5349366 AT-TTTTATATTATATATTTTTATT-TTA
1 ATATTTTATATT-T-TATTTATATTATTA
* *
5349393 ATATTTT-TATTTAATTATAATATTATAAA
1 ATATTTTATATTTTATT-T-ATATTAT-TA
5349422 ATATTTT
1 ATATTTT
5349429 TAATAAGGTA
Statistics
Matches: 458, Mismatches: 65, Indels: 164
0.67 0.09 0.24
Matches are distributed among these distances:
19 2 0.00
20 2 0.00
21 1 0.00
22 11 0.02
23 42 0.09
24 27 0.06
25 75 0.16
26 103 0.22
27 103 0.22
28 36 0.08
29 34 0.07
30 19 0.04
31 3 0.01
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (27 bp):
ATATTTTATATTTTATTTATATTATTA
Found at i:5348847 original size:21 final size:20
Alignment explanation
Indices: 5348802--5348847 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
5348792 ATCATATATT
5348802 TTATTTTTATTTATTTTATA
1 TTATTTTTATTTATTTTATA
*
5348822 ATATTTTATATTT-TATTTATA
1 TTATTTT-TATTTAT-TTTATA
5348843 TTATT
1 TTATT
5348848 AATTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTTTTATTTATTTTATA
Found at i:5348856 original size:95 final size:96
Alignment explanation
Indices: 5348731--5348935 Score: 358
Period size: 95 Copynumber: 2.1 Consensus size: 96
5348721 ATAAGTTTAA
*
5348731 TATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCA
1 TATATTT-TA-TTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCA
5348796 TATATTTTATTTTTATTTATT-TTATAATATTT
64 TATATTTTATTTTTATTTATTATTATAATATTT
* *
5348828 TATATTTTATTTATATTATTAATTTTTATATAATATCATTTTTTAAATATATTTTTAATGTCATA
1 TATATTTTATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATA
5348893 TATTTTATTTTTATTTATTATTATAATATTT
66 TATTTTATTTTTATTTATTATTATAATATTT
5348924 TATATTTTATTT
1 TATATTTTATTT
5348936 TTAATATATT
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
95 72 0.69
96 25 0.24
97 7 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (96 bp):
TATATTTTATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATA
TATTTTATTTTTATTTATTATTATAATATTT
Found at i:5348911 original size:15 final size:15
Alignment explanation
Indices: 5348795--5349276 Score: 216
Period size: 15 Copynumber: 30.1 Consensus size: 15
5348785 TTTTAATATC
5348795 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
5348810 ATTTATTTTATAATATTT
1 ATATATTTTAT--T-TTT
*
5348828 -TATATTTTATTTAT
1 ATATATTTTATTTTT
*
5348842 AT-TA-TTAATTTTT
1 ATATATTTTATTTTT
* *
5348855 ATATAATATCATTTTTT
1 ATAT-ATTTTA-TTTTT
* * *
5348872 AAATATATTTTTAATGTC
1 --ATATA-TTTTATTTTT
5348890 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
5348905 ATTTATTATTATAATATTT
1 ATATATT-TTAT--T-TTT
5348924 -TATATTTTATTTTT
1 ATATATTTTATTTTT
*
5348938 A-ATATATTTATATTT
1 ATATAT-TTTATTTTT
*
5348953 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
* *
5348968 ATATAATATCATATTTTAA
1 ATAT-AT-T-TTATTTT-T
* * *
5348987 ATATATTTTTAATATC
1 ATATA-TTTTATTTTT
5349003 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
5349018 ATTTATTATTATAATTTT
1 ATATATT-TTAT--TTTT
5349036 ATATATTTTATTTTT
1 ATATATTTTATTTTT
5349051 A-ATATATTTATTTTT
1 ATATAT-TTTATTTTT
5349066 -T-TATTATTATTTTT
1 ATATATT-TTATTTTT
* *
5349080 ATATAATATCATTTCTT
1 ATAT-ATTTTATTT-TT
* * *
5349097 AAATATATTTTCAATGTC
1 --ATATATTTT-ATTTTT
5349115 ATATATTTTA-TTTT
1 ATATATTTTATTTTT
*
5349129 ATTTATTATTATAATATTT
1 ATATATT-TTAT--T-TTT
5349148 -TATATTTTATTTTT
1 ATATATTTTATTTTT
* *
5349162 TTAATATCTTTATATTT
1 AT-ATAT-TTTATTTTT
*
5349179 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
*
5349194 ATATAATATTATATTTTAA
1 ATAT-AT-TT-TATTTT-T
* *
5349213 ATATATTTT-TAATAT
1 ATATATTTTAT-TTTT
5349228 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
5349243 ATTTATTATTATATTTT
1 ATATATT-TTAT-TTTT
5349260 ATATATTTTATTTTT
1 ATATATTTTATTTTT
5349275 AT
1 AT
5349277 TTCTTAATAT
Statistics
Matches: 358, Mismatches: 57, Indels: 104
0.69 0.11 0.20
Matches are distributed among these distances:
13 10 0.03
14 38 0.11
15 119 0.33
16 54 0.15
17 63 0.18
18 46 0.13
19 28 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:5348922 original size:21 final size:22
Alignment explanation
Indices: 5348898--5348971 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
5348888 TCATATATTT
5348898 TATTTT-TATTTATTATTATAA
1 TATTTTATATTTATTATTATAA
5348919 TATTTTATATTTTATT-TT-TAA
1 TATTTTATA-TTTATTATTATAA
5348940 TATATTTATATTTA-TATTATTAA
1 TAT-TTTATATTTATTATTA-TAA
5348963 T-TTTTATAT
1 TATTTTATAT
5348972 AATATCATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
22 11 0.23
23 10 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTATATTTATTATTATAA
Found at i:5348964 original size:113 final size:113
Alignment explanation
Indices: 5348828--5349275 Score: 723
Period size: 113 Copynumber: 4.0 Consensus size: 113
5348818 TATAATATTT
* *
5348828 TATATTT-TATTTATATTATTAATTTTTATATAATATCATTTTTTAAATATATTTTTAATGTCAT
1 TATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCAT
5348892 ATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTATTTTTAA
66 ATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATTTTTAA
5348940 TATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCAT
1 TATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCAT
5349005 ATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAA
66 ATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAA
* * * *
5349053 TATATTTATTTTTTTATTATT-ATTTTTATATAATATCAT-TTCTTAAATATATTTTCAATGTCA
1 TATATTTATATTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAATATCA
5349116 TATATTTTA-TTTTATTTATTATTATAATATTT-TATATTTTATTTTTTTAA
65 TATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTA--TTTTTAA
* *
5349166 TATCTTTATATTTATATTATTAATTTTTATATAATATTATATTTTAAATATATTTTTAATAT-AT
1 TATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCAT
5349230 ATATTTTATTTTTATTTATTATTAT-ATTTTATATATTTTATTTTTA
66 ATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTA
5349276 TTTCTTAATA
Statistics
Matches: 314, Mismatches: 12, Indels: 21
0.90 0.03 0.06
Matches are distributed among these distances:
111 36 0.11
112 62 0.20
113 164 0.52
114 50 0.16
115 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (113 bp):
TATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATATCAT
ATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTTTTAA
Found at i:5349019 original size:6 final size:6
Alignment explanation
Indices: 5349008--5349081 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
5348998 ATATCATATA
* * * *
5349008 TTTTAT TTTTAT TTATTAT TATAAT TTTATAT ATTTTAT TTTTA- ATATAT
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT -TTTTAT TTTTAT TTTTAT
*
5349058 TTATT-T TTTTAT TATTAT TTTTAT
1 TT-TTAT TTTTAT TTTTAT TTTTAT
5349082 ATAATATCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
5 5 0.10
6 33 0.63
7 11 0.21
8 3 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTAT
Found at i:5349121 original size:176 final size:171
Alignment explanation
Indices: 5348835--5349256 Score: 424
Period size: 171 Copynumber: 2.5 Consensus size: 171
5348825 TTTTATATTT
* * * *
5348835 TATTTATATTATTAATTTTTATATAATATCATTTTTTAAATATATTTTTAATGTCATATATTTTA
1 TATTTATATTATTAATTTTTATATAATATTATATATT--ATATATTTTTAATAT-ATATATTTTA
* * * * * * *
5348900 TTTTTATTTATTA-T-TATAATAT--TTT-AT-ATTTTATTTTTAATAT-ATTTATATTTATATT
63 TTTTTATTTATTATTATATAATATCATTTCTTAAATATATTTTCAATGTCATATAT-TTTATTTT
* *
5348958 ATTAATTTTTAT-ATAATATCATATTTTAAATATATTTTTAATATC-ATA
127 ATTTATTATTATAAT-ATATCATATTTT--AT-T-TTTTTAATATCTATA
* * *
5349006 TATTT-TATT-TTTATTTATTATTATAATTTTATATATT-T-TATTTTTAATATATTTATTTT-T
1 TATTTATATTATTAATTT-TTA-TATAATATTATATATTATATATTTTTAATATATATATTTTAT
*
5349066 TTATTA-TTATTTTTATATAATATCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTA
64 TT-TTATTTATTATTATATAATATCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTA
* * *
5349130 TTTATTATTATAATATTTTATATTTTATTTTTTTAATATCTTTA
128 TTTATTATTATAATATATCATATTTTATTTTTTTAATATCTATA
*
5349174 TATTTATATTATTAATTTTTATATAATATTATATTTTAAATATATTTTTAATATATATATTTTAT
1 TATTTATATTATTAATTTTTATATAATATTATATATT--ATATATTTTTAATATATATATTTTAT
5349239 TTTTATTTATTATTATAT
64 TTTTATTTATTATTATAT
5349257 TTTATATATT
Statistics
Matches: 206, Mismatches: 25, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
165 8 0.04
166 12 0.06
167 30 0.15
168 23 0.11
169 18 0.09
170 14 0.07
171 57 0.28
172 30 0.15
173 14 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (171 bp):
TATTTATATTATTAATTTTTATATAATATTATATATTATATATTTTTAATATATATATTTTATTT
TTATTTATTATTATATAATATCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTATTT
ATTATTATAATATATCATATTTTATTTTTTTAATATCTATA
Found at i:5349137 original size:62 final size:59
Alignment explanation
Indices: 5348813--5349252 Score: 290
Period size: 59 Copynumber: 7.6 Consensus size: 59
5348803 TATTTTTATT
**
5348813 TATTTTATAATATTTTATATTTTATTTATATTATTAATTTTTATATAATATCATTTTTTAAATA
1 TATTTT-TAATATCATATATTTTATTT-TATTATT-ATTTTTATATAATAT-A-TTTTTAAATA
* * * * *
5348877 TATTTTTAATGTCATATATTTTA-TTT-TTA-T-TTATTATTATAATAT-TTTAT-ATTT
1 TATTTTTAATATCATATATTTTATTTTATTATTATTTTTA-TATAATATATTTTTAAATA
* *
5348931 TATTTTTAATAT-ATTTATATTTATATTATTA--ATTTTTATATAATATCATATTTTAAATA
1 TATTTTTAATATCATATAT-TTTATTTTATTATTATTTTTATATAATAT-AT-TTTTAAATA
* * *
5348990 TATTTTTAATATCATATATTTTA-TTT-TTA-T-TTATTAT-T-ATA-ATTTTATATATTT
1 TATTTTTAATATCATATATTTTATTTTATTATTATTTTTATATAATATATTTT-TA-AATA
** *
5349044 TATTTTTAATATATT-TATTTTTTTATTATTATT-T--TTATATAATATCATTTCTTAAATA
1 TATTTTTAATATCATATATTTTATT-TTATTATTATTTTTATATAATAT-ATTT-TTAAATA
* * * * **
5349102 TATTTTCAATGTCATATATTTTATTTTATTTATTATTATAATATTTTATA-TTTT--AT-
1 TATTTTTAATATCATATATTTTATTTTA-TTATTATTTTTATATAATATATTTTTAAATA
* *
5349158 T-TTTTTAATATC-TTTATATTTATATTATTA--ATTTTTATATAATATTATATTTTAAATA
1 TATTTTTAATATCATATAT-TTTATTTTATTATTATTTTTATATAATA-TAT-TTTTAAATA
5349216 TATTTTTAATAT-ATATATTTTATTTTTATTTATTATT
1 TATTTTTAATATCATATATTTTA-TTTTA-TTATTATT
5349253 ATATTTTATA
Statistics
Matches: 294, Mismatches: 42, Indels: 82
0.70 0.10 0.20
Matches are distributed among these distances:
52 13 0.04
53 17 0.06
54 40 0.14
55 44 0.15
56 14 0.05
57 24 0.08
58 34 0.12
59 58 0.20
60 15 0.05
61 2 0.01
62 13 0.04
63 14 0.05
64 6 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (59 bp):
TATTTTTAATATCATATATTTTATTTTATTATTATTTTTATATAATATATTTTTAAATA
Found at i:5349205 original size:25 final size:23
Alignment explanation
Indices: 5349177--5349271 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 23
5349167 ATCTTTATAT
5349177 TTATATTATTAATTTTTATATAATA
1 TTATATT-TTAATTTTTAT-TAATA
5349202 TTATATTTTAAATATATTT-TTAATA
1 TTATATTTT-AAT-T-TTTATTAATA
*
5349227 TATATATTTT-ATTTTTATTTATTA
1 T-TATATTTTAATTTTTA-TTAATA
5349251 TTATATTTTATATATTTTATT
1 TTATATTTTA-AT-TTTTATT
5349272 TTTATTTCTT
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
22 3 0.05
23 9 0.15
24 10 0.17
25 20 0.33
26 15 0.25
27 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATATTTTAATTTTTATTAATA
Found at i:5349220 original size:88 final size:87
Alignment explanation
Indices: 5348874--5349309 Score: 239
Period size: 87 Copynumber: 5.1 Consensus size: 87
5348864 CATTTTTTAA
* *
5348874 ATATATTT-TTAATGTCATATATTTTATTTTTATTTATTATTATA----ATATTTTATATTTT-A
1 ATATATTTATTAATAT-ATATATTTTATTTTTATTTATTATTATATTTTATATATTATATTTTAA
5348933 TTT-TTAATAT-ATTTATAT-TT
65 TTTCTTAATATAATTTATATATT
* ** ** * * * * * *
5348953 ATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTA-ATATCATATATTTTATTTT
1 ATA-TATTTATTAATATAT-ATATTTTATTTT-TATTTATTATTATATTTTATATATTATATTTT
* * *
5349017 TATTTATTATTATAATTTTATATATT
63 AATTTCTTAATATAA-TTTATATATT
*
5349043 -T-TA-TT-TT--TA-ATATA-TTTA-TTTT-TTTATTATTAT-TTTTATATAATATCATTTCTT
1 ATATATTTATTAATATATATATTTTATTTTTATTTATTATTATATTTTATATATTAT-A-TT-TT
* * * *
5349097 AAATATATTTTCAATGTCA--TATATTTT
63 -AAT-T-TCTT-AATATAATTTATATATT
* *
5349124 ATTTTATTTATTATTATA-ATATTTTATATTTTATTT-TT-TTAATATCTTTATAT-TTATATTA
1 A-TATATTTATTAATATATATATTTTAT-TTTTATTTATTATT-ATAT-TTTATATATTATATT-
*
5349185 TTAATTT-TT-ATATAATATTATATTTT
61 TTAATTTCTTAATATAAT-TTATATATT
* *
5349211 AAATATATTT-TTAATATATATATTTTATTTTTATTTATTATTATATTTTATATATTTTATTTTT
1 --ATATATTTATTAATATATATATTTTATTTTTATTTATTATTATATTTTATATATTATATTTTA
*
5349275 ATTTCTTAATATAATTTTTATATT
64 ATTTCTTAATATAATTTATATATT
5349299 ATATATTTATT
1 ATATATTTATT
5349310 TTAATTTGTT
Statistics
Matches: 271, Mismatches: 38, Indels: 88
0.68 0.10 0.22
Matches are distributed among these distances:
77 17 0.06
78 1 0.00
79 8 0.03
80 10 0.04
81 27 0.10
82 12 0.04
83 6 0.02
84 10 0.04
85 16 0.06
86 17 0.06
87 47 0.17
88 43 0.16
89 26 0.10
90 8 0.03
91 9 0.03
92 7 0.03
93 7 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (87 bp):
ATATATTTATTAATATATATATTTTATTTTTATTTATTATTATATTTTATATATTATATTTTAAT
TTCTTAATATAATTTATATATT
Found at i:5349234 original size:225 final size:229
Alignment explanation
Indices: 5348796--5349275 Score: 803
Period size: 225 Copynumber: 2.1 Consensus size: 229
5348786 TTTAATATCA
* * *
5348796 TATATTTTATTTTTATTTATTTTATAATATTTTATATTTTATTTATATTATTAATTTTTATATAA
1 TATATTTTATATAT-TTTATTTT-TAATATATTATATTTTATTTATATTATTAATTTTTATATAA
* *
5348861 TATCATTTTTTAAATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTTTA
64 TATCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTTATTTATTATTATAATATTTTA
5348926 TATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATAT
129 TATTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATAT
5348991 ATTTTTAATATCATATATTTTATTTTTATTTATTAT
194 ATTTTTAATATCATATATTTTATTTTTATTTATTAT
5349027 TATAATTTTATATATTTTATTTTTAATATATT-TA-TTT-TTT-TATTATT-ATTTTTATATAAT
1 TAT-ATTTTATATATTTTATTTTTAATATATTATATTTTATTTATATTATTAATTTTTATATAAT
5349087 ATCATTTCTTAAATATATTTTCAATGTCATATATTTTA-TTTTATTTATTATTATAATATTTTAT
65 ATCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTTATTTATTATTATAATATTTTAT
* *
5349151 ATTTTATTTTTTTAATATCTTTATATTTATATTATTAATTTTTATATAATATTATATTTTAAATA
130 ATTTTA--TTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATA
5349216 TATTTTTAATAT-ATATATTTTATTTTTATTTATTAT
193 TATTTTTAATATCATATATTTTATTTTTATTTATTAT
5349252 TATATTTTATATATTTTATTTTTA
1 TATATTTTATATATTTTATTTTTA
5349276 TTTCTTAATA
Statistics
Matches: 239, Mismatches: 7, Indels: 13
0.92 0.03 0.05
Matches are distributed among these distances:
224 53 0.22
225 76 0.32
226 74 0.31
227 3 0.01
228 3 0.01
229 2 0.01
230 8 0.03
231 11 0.05
232 9 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (229 bp):
TATATTTTATATATTTTATTTTTAATATATTATATTTTATTTATATTATTAATTTTTATATAATA
TCATTTCTTAAATATATTTTCAATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATA
TTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATAT
TTTTAATATCATATATTTTATTTTTATTTATTAT
Found at i:5349242 original size:49 final size:48
Alignment explanation
Indices: 5349125--5349312 Score: 140
Period size: 49 Copynumber: 3.9 Consensus size: 48
5349115 ATATATTTTA
* **
5349125 TTTTATTTAT-TATTA-TAATATTTTATATTTTATT-T-TTTTA-ATAT
1 TTTTATATATATATTATTAAT-TTTTATATAATATTATATTTTATATAT
* *
5349169 CTTTATATTTATATTATTAATTTTTATATAATATTATATTTTAAATATAT
1 TTTTATATATATATTATTAATTTTTATATAATATTATATTTT--ATATAT
* *
5349219 TTTTAATATATATATT-TT-ATTTTTATTTATTATTATATTTTATATAT
1 TTTT-ATATATATATTATTAATTTTTATATAATATTATATTTTATATAT
* * * *
5349266 TTTATTTTTATTTCTTAATATAATTTTTATATTATATATT-TATTTTA
1 TTT-TATATATATATT-AT-TAATTTTTATA-TA-ATATTATATTTTA
5349313 ATTTGTTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
44 7 0.06
45 17 0.15
46 5 0.04
47 20 0.18
48 1 0.01
49 23 0.20
50 10 0.09
51 18 0.16
52 9 0.08
53 4 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (48 bp):
TTTTATATATATATTATTAATTTTTATATAATATTATATTTTATATAT
Found at i:5349297 original size:32 final size:32
Alignment explanation
Indices: 5349227--5349310 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
5349217 ATTTTTAATA
*
5349227 TATATATTTTATTTTTATTTATTATTATATTT
1 TATATATTTTATTTTTATTTATTAATATATTT
*
5349259 TATATATTTTATTTTTATTTCTTAATATAATTT
1 TATATATTTTATTTTTATTTATTAATAT-ATTT
* *
5349292 T-TATATTATATATTTATTT
1 TATATATTTTATTTTTATTT
5349311 TAATTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 42 0.89
33 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (32 bp):
TATATATTTTATTTTTATTTATTAATATATTT
Found at i:5349308 original size:38 final size:37
Alignment explanation
Indices: 5348873--5349316 Score: 136
Period size: 38 Copynumber: 11.9 Consensus size: 37
5348863 TCATTTTTTA
5348873 AATATATTTTTA-ATGTCATATATTTTATTTTTATTTATT
1 AATATATTTTTATAT-T-ATATA-TTTATTTTTATTTATT
* * * * *
5348912 ATTATAATATTTTATATTTTATTTTTA-ATATATTTA-T
1 AATAT-AT-TTTTATATTATATATTTATTTTTATTTATT
* * * * ** *
5348949 ATTTATATTATTA-ATT-TTTATATAATATCATATTT-TA
1 A-ATATATTTTTATATTATATAT-TTAT-TTTTATTTATT
*
5348986 AATATATTTTTAATATCATATATTTTATTTTTATTTATT
1 AATATATTTTT-ATATTATATA-TTTATTTTTATTTATT
* * *
5349025 ATTATA-ATTT-TA-TATAT-TTTATTTTTAATATATT
1 AATATATTTTTATATTATATATTTATTTTT-ATTTATT
* * *
5349059 --TAT-TTTTT-TATTATTATTTTTATATAATATCATTTCTT
1 AATATATTTTTATATTA-TATATTTAT-T--T-TTATTTATT
*
5349097 AAATATATTTTCA-ATGTCATATATTT-TATTTTATTTATT
1 -AATATATTTTTATAT-T-ATATATTTAT-TTTTATTTATT
* * * *
5349136 ATTATAATATTTTATATT-T-TATTT-TTTTAATATCTT
1 AATAT-AT-TTTTATATTATATATTTATTTTTATTTATT
* *
5349172 --TATATTTATATTATTA-ATTTTTATATAATATTATATT-TT
1 AATATATTTTTA-TATTATATATTTAT-T--T-TTAT-TTATT
5349211 AAATATATTTTTA-ATATATATATTTTATTTTTATTTATT
1 -AATATATTTTTATAT-TATATA-TTTATTTTTATTTATT
* *
5349250 -AT-TATATTT-TA-TATAT-TTTATTTTTATTTCTT
1 AATATATTTTTATATTATATATTTATTTTTATTTATT
*
5349282 AATATAATTTTTATATTATATATTTATTTTAATTT
1 AATAT-ATTTTTATATTATATATTTATTTTTATTT
5349317 GTTTTACCTA
Statistics
Matches: 303, Mismatches: 47, Indels: 111
0.66 0.10 0.24
Matches are distributed among these distances:
32 27 0.09
33 19 0.06
34 25 0.08
35 20 0.07
36 33 0.11
37 25 0.08
38 48 0.16
39 41 0.14
40 16 0.05
41 13 0.04
42 23 0.08
43 12 0.04
44 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (37 bp):
AATATATTTTTATATTATATATTTATTTTTATTTATT
Found at i:5349356 original size:24 final size:23
Alignment explanation
Indices: 5349325--5349376 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5349315 TTGTTTTACC
5349325 TATA-TTATTAAATGTTAATTTTT
1 TATATTTATTAAATGTTAA-TTTT
** *
5349348 TATATTTATTTTATTTTAATTTT
1 TATATTTATTAAATGTTAATTTT
5349371 TATATT
1 TATATT
5349377 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATATTTATTAAATGTTAATTTT
Found at i:5349399 original size:53 final size:52
Alignment explanation
Indices: 5349213--5349400 Score: 136
Period size: 53 Copynumber: 3.4 Consensus size: 52
5349203 TATATTTTAA
* * * *
5349213 ATATATTTTTAATATATATATTTTATTTTTA-TTTATTATTATATTTTATATATT
1 ATATATTTTTATTTTATATTTTTTATATTTATTTTATT-TTA-ATTTT-TATATT
*
5349267 -T-TATTTTTATTTCTTAATATAATTTTTATATTATATATTTATTTTAATTTGT-T-TT
1 ATATATTTTTA-TT-TT-ATAT--TTTTTATATT-TAT-TTTATTTTAATTTTTATATT
* *
5349322 ACCTATATTATTAAATGTTA-ATTTTTTATATTTATTTTATTTTAATTTTTATATT
1 A--TATATT-TT-TATTTTATATTTTTTATATTTATTTTATTTTAATTTTTATATT
5349377 ATATATTTTTATTTTAATATTTTT
1 ATATATTTTTATTTT-ATATTTTT
5349401 ATTTAATTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 37
0.69 0.07 0.24
Matches are distributed among these distances:
51 4 0.04
52 11 0.10
53 28 0.26
54 5 0.05
55 19 0.18
56 1 0.01
57 11 0.10
58 8 0.08
59 9 0.08
60 9 0.08
61 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (52 bp):
ATATATTTTTATTTTATATTTTTTATATTTATTTTATTTTAATTTTTATATT
Found at i:5349403 original size:6 final size:6
Alignment explanation
Indices: 5349344--5349404 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
5349334 AAATGTTAAT
* *
5349344 TTTTTA TATTTA -TTTTA TTTTAA TTTTTA TATTATATA TTTTTA TTTTAATA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T-TT-T-TA TTTTTA TTTT--TA
5349396 TTTTTA TTT
1 TTTTTA TTT
5349405 AATTATAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
5 4 0.09
6 26 0.58
7 3 0.07
8 9 0.20
9 3 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:5349404 original size:14 final size:14
Alignment explanation
Indices: 5349356--5349404 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
5349346 TTTATATTTA
5349356 TTTTATTTT-A-AT
1 TTTTATTTTAATAT
*
5349368 TTTTATATTATATAT
1 TTTTATTTTA-ATAT
5349383 TTTTATTTTAATAT
1 TTTTATTTTAATAT
5349397 TTTTATTT
1 TTTTATTT
5349405 AATTATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 8 0.25
14 13 0.41
15 11 0.34
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATTTTAATAT
Found at i:5349410 original size:78 final size:79
Alignment explanation
Indices: 5349109--5349410 Score: 241
Period size: 78 Copynumber: 4.0 Consensus size: 79
5349099 ATATATTTTC
* * *
5349109 AATGTCATATATTTTAT-TTTATTTATTATTATAATATTTTATATT-T-TATTT-TTTTAATATC
1 AATGTTATATATTTTATATTTATTTCTTAATATAAT-TTTTATATTATATATTTATTTTAATAT-
5349170 TTTATATTTATATTATT-
64 TTT-TATTTA-ATTATTA
* * *
5349187 AAT-TT-T-TATATAATATTATATTT-TAAATAT-ATTTTTA-A-TATATA--TA-TTT--TATT
1 AATGTTATATATTTTATATT-TATTTCTTAATATAATTTTTATATTATATATTTATTTTAATATT
5349240 TTTATTT-ATTATTA
65 TTTATTTAATTATTA
* * * *
5349254 TATTTTATATATTTTATTTTTATTTCTTAATATAATTTTTATATTATATATTTATTTTAATTTGT
1 AATGTTATATATTTTATATTTATTTCTTAATATAATTTTTATATTATATATTTATTTTAATAT-T
**
5349319 TTTACCTATATTATTA
65 TTTATTTA-ATTATTA
* * *
5349335 AATGTTA-ATTTTTTATATTTA-TT-TTATTTTAATTTTTATATTATATATTTTTATTTTAATAT
1 AATGTTATATATTTTATATTTATTTCTTAATATAATTTTTATATTATATA--TTTATTTTAATAT
5349397 TTTTATTTAATTAT
64 TTTTATTTAATTAT
5349411 AATATTATAA
Statistics
Matches: 179, Mismatches: 22, Indels: 46
0.72 0.09 0.19
Matches are distributed among these distances:
66 6 0.03
67 2 0.01
68 7 0.04
69 9 0.05
70 17 0.09
71 7 0.04
72 6 0.03
73 8 0.04
74 7 0.04
75 10 0.06
76 11 0.06
77 6 0.03
78 32 0.18
79 15 0.08
80 24 0.13
81 12 0.07
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (79 bp):
AATGTTATATATTTTATATTTATTTCTTAATATAATTTTTATATTATATATTTATTTTAATATTT
TTATTTAATTATTA
Found at i:5391813 original size:7 final size:7
Alignment explanation
Indices: 5391803--5391831 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5391793 AGCAATGAGT
5391803 TTAGCTG
1 TTAGCTG
5391810 TTAGCTG
1 TTAGCTG
5391817 TTAGCTG
1 TTAGCTG
5391824 TTAGCTG
1 TTAGCTG
5391831 T
1 T
5391832 CTTGGCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.28, T:0.45
Consensus pattern (7 bp):
TTAGCTG
Found at i:5398734 original size:30 final size:29
Alignment explanation
Indices: 5398686--5398742 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
5398676 TTAGTTTTAG
*
5398686 TTTTAAAAGAGAAAAAAAAGAAGAATAAA
1 TTTTAAAAGAGAAAAAAAAGAAAAATAAA
5398715 TTTTAAAAGAGAGAAAAAAAGAAAAATA
1 TTTTAAAAGAGA-AAAAAAAGAAAAATA
5398743 TGGGGTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (29 bp):
TTTTAAAAGAGAAAAAAAAGAAAAATAAA
Found at i:5403682 original size:12 final size:12
Alignment explanation
Indices: 5403665--5403700 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5403655 TGTCGGGTTA
*
5403665 CTCTCTCTTTCT
1 CTCTCTCTGTCT
*
5403677 CTCTCTGTGTCT
1 CTCTCTCTGTCT
5403689 CTCTCTCTGTCT
1 CTCTCTCTGTCT
5403701 TTAAACTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.08, T:0.53
Consensus pattern (12 bp):
CTCTCTCTGTCT
Found at i:5412073 original size:15 final size:14
Alignment explanation
Indices: 5412042--5412080 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
5412032 TAATTAAACT
5412042 TAAAATATTAA-ATA
1 TAAAATA-TAATATA
5412056 TAAAACTATAATATA
1 TAAAA-TATAATATA
5412071 TAAAATATAA
1 TAAAATATAA
5412081 ATAGTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAATATAATATA
Found at i:5412076 original size:22 final size:21
Alignment explanation
Indices: 5412037--5412081 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5412027 ATTTCTAATT
*
5412037 AAACTTAAAATATTAAATATA
1 AAACTTAAAATATAAAATATA
*
5412058 AAACTATAATATATAAAATATA
1 AAACT-TAAAATATAAAATATA
5412080 AA
1 AA
5412082 TAGTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
AAACTTAAAATATAAAATATA
Found at i:5412083 original size:15 final size:15
Alignment explanation
Indices: 5412042--5412083 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5412032 TAATTAAACT
5412042 TAAAATATTAAATATA
1 TAAAATA-TAAATATA
*
5412058 -AAACTAT-AATATA
1 TAAAATATAAATATA
5412071 TAAAATATAAATA
1 TAAAATATAAATA
5412084 GTTAAATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATATAAATATA
Found at i:5415992 original size:10 final size:10
Alignment explanation
Indices: 5415933--5415992 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
5415923 TCCCTCAAAA
*
5415933 TTTTTAAAAT
1 TTTTTATAAT
5415943 TTTTTAT-AT
1 TTTTTATAAT
* *
5415952 ATTATAT-AT
1 TTTTTATAAT
5415961 TTTTTATAAT
1 TTTTTATAAT
5415971 TTTTTAAAATAAT
1 TTTTT---ATAAT
5415984 TTTTTATAA
1 TTTTTATAA
5415993 AATAATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
9 14 0.34
10 17 0.41
13 10 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:5415993 original size:15 final size:14
Alignment explanation
Indices: 5415966--5415999 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
5415956 TATATTTTTT
5415966 ATAA-TTTTTTAAA
1 ATAATTTTTTTAAA
5415979 ATAATTTTTTATAAA
1 ATAATTTTTT-TAAA
5415994 ATAATT
1 ATAATT
5416000 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 5 0.26
15 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTTTTTTAAA
Found at i:5416067 original size:18 final size:18
Alignment explanation
Indices: 5416044--5416081 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5416034 AATTCCATTC
5416044 AATTTTATTCAAATTTTT
1 AATTTTATTCAAATTTTT
* *
5416062 AATTTTTTTTAAATTTTT
1 AATTTTATTCAAATTTTT
5416080 AA
1 AA
5416082 GTTTCTNNNN
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
AATTTTATTCAAATTTTT
Found at i:5417175 original size:97 final size:96
Alignment explanation
Indices: 5417024--5417217 Score: 309
Period size: 97 Copynumber: 2.0 Consensus size: 96
5417014 TTACGTTTAA
* *
5417024 TGAAATTTTTATATTTTTATTTTAAACTAAATAAGTGTTCATAATTTATGGAGGACTAATTATTG
1 TGAAATTTTTATATTTTTATTTTAAACTAAATAAGTCTTCATAATTGATGGAGGACTAATTATTG
*
5417089 TTAATCAAACTTAAAG-TTTTTATATTTTATT
66 TTAATCAAAATT-AAGTTTTTTATATTTTATT
* * *
5417120 TGAAACTTTTTATATTTTTATTTTGAATTAAATAAGTCTTTATAATTGATGGAGGACTAATTATT
1 TGAAA-TTTTTATATTTTTATTTTAAACTAAATAAGTCTTCATAATTGATGGAGGACTAATTATT
5417185 GTTAATCAAAATTAAGTTTTTTATATTTTATT
65 GTTAATCAAAATTAAGTTTTTTATATTTTATT
5417217 T
1 T
5417218 TGAATTGAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
96 8 0.09
97 82 0.91
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.51
Consensus pattern (96 bp):
TGAAATTTTTATATTTTTATTTTAAACTAAATAAGTCTTCATAATTGATGGAGGACTAATTATTG
TTAATCAAAATTAAGTTTTTTATATTTTATT
Found at i:5417251 original size:75 final size:76
Alignment explanation
Indices: 5417126--5417271 Score: 222
Period size: 75 Copynumber: 1.9 Consensus size: 76
5417116 TATTTGAAAC
** * * *
5417126 TTTTTATATTTTTATTTTGAATTAAATAAGTCTTTATAATTGATGGAGGACTAATTATTGTTAAT
1 TTTTTATATTTTTATTTTGAATTAAATAAGTCTCCATAACTGATGAAGGACTAATTATTGTTAAC
5417191 CAAAATTAAGT
66 CAAAATTAAGT
* *
5417202 TTTTTATA-TTTTATTTTGAATTGAATAAGTCTCCCTAACTGATGAAGGACTAATTATTGTTAAC
1 TTTTTATATTTTTATTTTGAATTAAATAAGTCTCCATAACTGATGAAGGACTAATTATTGTTAAC
5417266 CAAAAT
66 CAAAAT
5417272 CATACTTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 55 0.87
76 8 0.13
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.46
Consensus pattern (76 bp):
TTTTTATATTTTTATTTTGAATTAAATAAGTCTCCATAACTGATGAAGGACTAATTATTGTTAAC
CAAAATTAAGT
Found at i:5417407 original size:29 final size:29
Alignment explanation
Indices: 5417356--5417436 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 29
5417346 ATAGTATCAC
* *
5417356 ATTAATACAACGTCATATTGAAAAAAAAAA
1 ATTATTAC-ACGTCATGTTGAAAAAAAAAA
* *
5417386 ATTGTTACACGTCATGTTG---AAAAAAT
1 ATTATTACACGTCATGTTGAAAAAAAAAA
*
5417412 ATTATTACACGTTATGTTGAAAAAA
1 ATTATTACACGTCATGTTGAAAAAA
5417437 TATTATTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
26 23 0.55
29 13 0.31
30 6 0.14
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (29 bp):
ATTATTACACGTCATGTTGAAAAAAAAAA
Found at i:5417419 original size:26 final size:26
Alignment explanation
Indices: 5417379--5417463 Score: 116
Period size: 26 Copynumber: 3.2 Consensus size: 26
5417369 CATATTGAAA
* *
5417379 AAAAAAAATTGTTACACGTCATGTTG
1 AAAAAATATTATTACACGTCATGTTG
*
5417405 AAAAAATATTATTACACGTTATGTTG
1 AAAAAATATTATTACACGTCATGTTG
**
5417431 AAAAAATATTATTACATATCATGTTG
1 AAAAAATATTATTACACGTCATGTTG
5417457 AAGAAAA
1 AA-AAAA
5417464 GCTGTTATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 48 0.92
27 4 0.08
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (26 bp):
AAAAAATATTATTACACGTCATGTTG
Found at i:5417548 original size:27 final size:26
Alignment explanation
Indices: 5417476--5417548 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 26
5417466 TGTTATACGT
*
5417476 CATATTAAAAAAAATGTTGTTATGCA
1 CATATTAAAAAAAATGTTATTATGCA
*
5417502 CTATATT---CAAAATGTTATTATGCAA
1 C-ATATTAAAAAAAATGTTATTATGC-A
*
5417527 CATATTAAAAAAAAAGTTATTA
1 CATATTAAAAAAAATGTTATTA
5417549 CATGTCATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
24 19 0.50
25 2 0.05
26 1 0.03
27 16 0.42
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (26 bp):
CATATTAAAAAAAATGTTATTATGCA
Found at i:5417559 original size:130 final size:127
Alignment explanation
Indices: 5417405--5417649 Score: 287
Period size: 130 Copynumber: 1.9 Consensus size: 127
5417395 CGTCATGTTG
* * * * * *
5417405 AAAAAATATTATTACACGTTATGTTGAAAAAATATTATTACATAT-C-ATGTTGAAGAAAAGCTG
1 AAAAAAAATTATTACACGTCATGTTAAAAAAAAATTA-TA-ATATGCTATATTGAAAAAAAGCTG
* * ** *
5417468 TTATACGTCATATTAAAAAAAATGTTGTTATGCACTATATTCAAAATGTTATTATGCAACATATT
64 TTATACATCATATTAAAAAAAA--TTATTACACACCATATTCAAAATGTTATTATGCAACATATT
5417533 A
127 A
* *
5417534 AAAAAAAAGTTATTACATGTCATGTTAAAAAAAAATTATAATATGCTATATTGAAAAAAAGTTGT
1 AAAAAAAA-TTATTACACGTCATGTTAAAAAAAAATTATAATATGCTATATTGAAAAAAAGCTGT
* * *
5417599 TTTATATTATATTAAAAAAAATTATTACACACCATATTCAAAATGTTATTA
65 TATACATCATATTAAAAAAAATTATTACACACCATATTCAAAATGTTATTA
5417650 CATGTTATGT
Statistics
Matches: 97, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
128 30 0.31
129 10 0.10
130 57 0.59
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (127 bp):
AAAAAAAATTATTACACGTCATGTTAAAAAAAAATTATAATATGCTATATTGAAAAAAAGCTGTT
ATACATCATATTAAAAAAAATTATTACACACCATATTCAAAATGTTATTATGCAACATATTA
Found at i:5435529 original size:16 final size:18
Alignment explanation
Indices: 5435498--5435530 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5435488 CAACAAACAT
5435498 TTCATCTCAGCTTCTCTC
1 TTCATCTCAGCTTCTCTC
5435516 TTCAT-TCA-CTTCTCT
1 TTCATCTCAGCTTCTCT
5435531 TAGGTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.12, C:0.36, G:0.03, T:0.48
Consensus pattern (18 bp):
TTCATCTCAGCTTCTCTC
Found at i:5456500 original size:21 final size:21
Alignment explanation
Indices: 5456462--5456501 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5456452 GTAGATTAAA
*
5456462 TTAATTAAATATTTTTAAAAG
1 TTAATTAAATATTATTAAAAG
5456483 TTAATTACAAT-TTATTAAA
1 TTAATTA-AATATTATTAAA
5456502 TGTAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAATTAAATATTATTAAAAG
Found at i:5460101 original size:24 final size:23
Alignment explanation
Indices: 5460058--5460103 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
5460048 TAATTATTTT
5460058 AATTATTATATATTTTTAATATA
1 AATTATTATATATTTTTAATATA
5460081 AATTAATTATAT-TTTTATAATAT
1 AATT-ATTATATATTTT-TAATAT
5460104 TATGAGGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATTATTATATATTTTTAATATA
Found at i:5464747 original size:35 final size:35
Alignment explanation
Indices: 5464690--5464764 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
5464680 TCACAAAAGT
* * * *
5464690 TATAACTTTTTATATGATAAAAACATAAATTTTCA
1 TATAACTTTTCAAATAAAAAAAACATAAATTTTCA
*
5464725 TATAACTTTTCAAATAAAAAAAATATAAATTTTCA
1 TATAACTTTTCAAATAAAAAAAACATAAATTTTCA
5464760 TATAA
1 TATAA
5464765 AGACACACAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (35 bp):
TATAACTTTTCAAATAAAAAAAACATAAATTTTCA
Found at i:5487903 original size:2 final size:2
Alignment explanation
Indices: 5487890--5487929 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5487880 CTCTATTTAA
*
5487890 AT AT AT AA 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
5487930 TGGTTTCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5493807 original size:14 final size:15
Alignment explanation
Indices: 5493788--5493818 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5493778 AGTCTTATTG
5493788 TTATTTT-TTTTTCT
1 TTATTTTCTTTTTCT
5493802 TTATTTTCTTTTTCT
1 TTATTTTCTTTTTCT
5493817 TT
1 TT
5493819 TTCTTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (15 bp):
TTATTTTCTTTTTCT
Found at i:5497289 original size:24 final size:24
Alignment explanation
Indices: 5497262--5497314 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
5497252 CCTAGAGAAA
5497262 AAACAATGTGGTAATCCTTTTTTC
1 AAACAATGTGGTAATCCTTTTTTC
5497286 AAACAATGTGGTAATCCTTTTTTC
1 AAACAATGTGGTAATCCTTTTTTC
5497310 AAACA
1 AAACA
5497315 TATAGAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (24 bp):
AAACAATGTGGTAATCCTTTTTTC
Found at i:5499543 original size:51 final size:50
Alignment explanation
Indices: 5499488--5499633 Score: 161
Period size: 51 Copynumber: 2.8 Consensus size: 50
5499478 TTGAAGAATC
5499488 TATTAAAAAAATATATATATAATAAATAA-TTTCACAAATTTTAGAAAGGAA
1 TATTAAAAAAATATATATATAATAAA-AATTTTCA-AAATTTTAGAAAGGAA
* ** * *
5499539 TATTAAAAATATATATA-ATAAATAAAAATTTTCAAAAAATTGGAAAGGAC
1 TATTAAAAAAATATATATAT-AATAAAAATTTTCAAAATTTTAGAAAGGAA
*
5499589 TATTAGAATAAATATAAATATATAATAAAAATTTTCAAAAATTTT
1 TATTA-AA-AAA-ATATATATATAATAAAAATTTTC-AAAATTTT
5499634 GAGGGCAGTG
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
50 21 0.27
51 29 0.37
52 2 0.03
53 19 0.24
54 8 0.10
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (50 bp):
TATTAAAAAAATATATATATAATAAAAATTTTCAAAATTTTAGAAAGGAA
Found at i:5499619 original size:53 final size:51
Alignment explanation
Indices: 5499487--5499629 Score: 168
Period size: 53 Copynumber: 2.8 Consensus size: 51
5499477 TTTGAAGAAT
**
5499487 CTATTAAAAAA-ATATATATATAATAAATAA-TTTCACAAATTTTAGAAAGGA
1 CTATTAAAAAATATATATATATAATAAA-AATTTTCA-AAAAATTAGAAAGGA
* *
5499538 ATATT-AAAAATATATATA-ATAAATAAAAATTTTCAAAAAATTGGAAAGGA
1 CTATTAAAAAATATATATATAT-AATAAAAATTTTCAAAAAATTAGAAAGGA
*
5499588 CTATTAGAATAAATATAAATATATAATAAAAATTTTCAAAAA
1 CTATTA-AA-AAATATATATATATAATAAAAATTTTCAAAAA
5499630 TTTTGAGGGC
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
50 25 0.32
51 22 0.28
52 2 0.03
53 28 0.35
54 2 0.03
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (51 bp):
CTATTAAAAAATATATATATATAATAAAAATTTTCAAAAAATTAGAAAGGA
Found at i:5502044 original size:36 final size:34
Alignment explanation
Indices: 5501997--5502081 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 34
5501987 AAATTTTATT
*
5501997 AATATTAATATTTAA-TTTAAAATATTAAAAAATAAA
1 AATATTAATATTTAATTTTAAAAAATT---AAATAAA
* *
5502033 AATATTAATATTTAATTTTAAAAAATTAATTTAA
1 AATATTAATATTTAATTTTAAAAAATTAAATAAA
5502067 AATATTAATATTTAA
1 AATATTAATATTTAA
5502082 ATTATACAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 20 0.44
36 15 0.33
37 10 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AATATTAATATTTAATTTTAAAAAATTAAATAAA
Found at i:5502063 original size:14 final size:14
Alignment explanation
Indices: 5502044--5502082 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
5502034 ATATTAATAT
5502044 TTAATTTTAAAAAA
1 TTAATTTTAAAAAA
*
5502058 TTAA-TTTAAAATA
1 TTAATTTTAAAAAA
5502071 TTAATATTTAAA
1 TTAAT-TTTAAA
5502083 TTATACAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 4 0.18
15 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAATTTTAAAAAA
Found at i:5508305 original size:3 final size:3
Alignment explanation
Indices: 5508297--5508328 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5508287 AATTGGGTGC
5508297 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
5508329 AACGCTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:5511926 original size:24 final size:24
Alignment explanation
Indices: 5511899--5511956 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
5511889 GCTCCAGAAG
5511899 CTGCAGAGGAAAGTAGTAAGCCTA
1 CTGCAGAGGAAAGTAGTAAGCCTA
5511923 CTGCAGAGGAAAGTAGTAAGCCTA
1 CTGCAGAGGAAAGTAGTAAGCCTA
5511947 CTGCAGAGGA
1 CTGCAGAGGA
5511957 GAACTCAGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (24 bp):
CTGCAGAGGAAAGTAGTAAGCCTA
Found at i:5517317 original size:4 final size:4
Alignment explanation
Indices: 5517305--5517335 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
5517295 CCTTCAAAAT
5517305 ATAG TATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG AT
5517336 TGCTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (4 bp):
ATAG
Found at i:5526747 original size:2 final size:2
Alignment explanation
Indices: 5526740--5526767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5526730 CACGCAACAT
5526740 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5526768 ATACAGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5542213 original size:2 final size:2
Alignment explanation
Indices: 5542202--5542230 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5542192 AGATAACAAC
5542202 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5542231 AGTTTAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5544794 original size:29 final size:29
Alignment explanation
Indices: 5544737--5544830 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
5544727 TAAAAAATGT
5544737 TTACACATCATGTTAAAAAAAATATTATTA
1 TTACACATCATGTT-AAAAAAATATTATTA
*
5544767 TTATACATCATGTTAAAAAAATATTATTA
1 TTACACATCATGTTAAAAAAATATTATTA
* * ** *
5544796 TTACATATCATGTTGAAAAGTTATTATTG
1 TTACACATCATGTTAAAAAAATATTATTA
5544825 TTACAC
1 TTACAC
5544831 GTTATATTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 43 0.77
30 13 0.23
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (29 bp):
TTACACATCATGTTAAAAAAATATTATTA
Found at i:5558718 original size:43 final size:43
Alignment explanation
Indices: 5558657--5558753 Score: 185
Period size: 43 Copynumber: 2.3 Consensus size: 43
5558647 AGAGAAAGAG
5558657 AGAGAGGGGAGGCTTAGGACAATGACGGCAGAGCCCTATAGGC
1 AGAGAGGGGAGGCTTAGGACAATGACGGCAGAGCCCTATAGGC
*
5558700 AGAGAGGGGAGGCTTAGGACAATGACGGCGGAGCCCTATAGGC
1 AGAGAGGGGAGGCTTAGGACAATGACGGCAGAGCCCTATAGGC
5558743 AGAGAGGGGAG
1 AGAGAGGGGAG
5558754 AGCAGCTTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.30, C:0.16, G:0.43, T:0.10
Consensus pattern (43 bp):
AGAGAGGGGAGGCTTAGGACAATGACGGCAGAGCCCTATAGGC
Found at i:5558732 original size:22 final size:22
Alignment explanation
Indices: 5558664--5558732 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
5558654 GAGAGAGAGG
5558664 GGAGGCTTAGGACAATGACGGC
1 GGAGGCTTAGGACAATGACGGC
* *
5558686 AGAGCCCTATAGG-CAGA-GA-GG-
1 GGAG-GCT-TAGGACA-ATGACGGC
5558707 GGAGGCTTAGGACAATGACGGC
1 GGAGGCTTAGGACAATGACGGC
5558729 GGAG
1 GGAG
5558733 CCCTATAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 5 0.14
22 9 0.25
23 6 0.17
24 5 0.14
ACGTcount: A:0.29, C:0.17, G:0.42, T:0.12
Consensus pattern (22 bp):
GGAGGCTTAGGACAATGACGGC
Found at i:5558753 original size:21 final size:21
Alignment explanation
Indices: 5558687--5558753 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
5558677 AATGACGGCA
5558687 GAGCCCTATAGGCAGAGAGGG
1 GAGCCCTATAGGCAGAGAGGG
*
5558708 GAG-GCT-TAGGACA-ATGACGGCG
1 GAGCCCTATAGG-CAGA-GA-GG-G
5558730 GAGCCCTATAGGCAGAGAGGG
1 GAGCCCTATAGGCAGAGAGGG
5558751 GAG
1 GAG
5558754 AGCAGCTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
19 5 0.14
20 6 0.16
21 9 0.24
22 6 0.16
23 6 0.16
24 5 0.14
ACGTcount: A:0.28, C:0.18, G:0.43, T:0.10
Consensus pattern (21 bp):
GAGCCCTATAGGCAGAGAGGG
Found at i:5567272 original size:16 final size:15
Alignment explanation
Indices: 5567232--5567273 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5567222 GAAGGAAACT
5567232 TATGAGATTATGAATG
1 TATGA-ATTATGAATG
5567248 TCATG-ATTATGAAATG
1 T-ATGAATTATG-AATG
5567264 TATGAATTAT
1 TATGAATTAT
5567274 AAAAACACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.39
16 11 0.48
17 3 0.13
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (15 bp):
TATGAATTATGAATG
Found at i:5571213 original size:21 final size:23
Alignment explanation
Indices: 5571174--5571215 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5571164 TTTTTAAACA
*
5571174 GTTAATTTTTTTTTCAATATTAT
1 GTTAATTTTTTGTTCAATATTAT
5571197 GTTAA-TTTTTGTT-AATATT
1 GTTAATTTTTTGTTCAATATT
5571216 TTGAACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (23 bp):
GTTAATTTTTTGTTCAATATTAT
Found at i:5597395 original size:22 final size:24
Alignment explanation
Indices: 5597365--5597418 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
5597355 CAATCAAACT
5597365 ATTATATTTTTAT-T-TAA-GGTTA
1 ATTA-ATTTTTATATCTAACGGTTA
5597387 ATTGAATTTTTATATCTAACGGTTA
1 ATT-AATTTTTATATCTAACGGTTA
5597412 ATTAATT
1 ATTAATT
5597419 GATATTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 11 0.39
23 2 0.07
24 7 0.25
25 8 0.29
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (24 bp):
ATTAATTTTTATATCTAACGGTTA
Done.