Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000784.1 Hibiscus syriacus cultivar Beakdansim tig00001521_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 169721
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2870 original size:22 final size:20
Alignment explanation
Indices: 2825--2872 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2815 AGAAAATAAA
2825 AGAGAGAATTTCATAAAGCT
1 AGAGAGAATTTCATAAAGCT
* *
2845 AGAGAGAATTTTATAAAGTT
1 AGAGAGAATTTCATAAAGCT
2865 AGAGAGAA
1 AGAGAGAA
2873 AGAATAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (20 bp):
AGAGAGAATTTCATAAAGCT
Found at i:12931 original size:13 final size:14
Alignment explanation
Indices: 12906--12935 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12896 ACTTAGAATA
12906 TTTAAAAACAAAAC
1 TTTAAAAACAAAAC
*
12920 TTTAAAAAAAAAAC
1 TTTAAAAACAAAAC
12934 TT
1 TT
12936 GAAAGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (14 bp):
TTTAAAAACAAAAC
Found at i:16022 original size:2 final size:2
Alignment explanation
Indices: 16015--16068 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
16005 GCCATTTTAA
16015 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
16057 AT AT AT AT AT AT
1 AT AT AT AT AT AT
16069 TATTAAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20581 original size:14 final size:16
Alignment explanation
Indices: 20543--20584 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
20533 AAATAGAATG
20543 AATAATATTATATATT
1 AATAATATTATATATT
*
20559 AATAATATTAT-TTTT
1 AATAATATTATATATT
20574 AA-AATATTATA
1 AATAATATTATA
20585 ATAATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAATATTATATATT
Found at i:20685 original size:33 final size:37
Alignment explanation
Indices: 20646--20724 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
20636 ACAACTTTGT
*
20646 AAATAAAAACATTA-AGA-T-TATT-ATAATTTATTA
1 AAATAAAAACATTATAAATTATATTAATAATTTATTA
** *
20679 AAATAAAATTATTATAAATTATATTAATTATTTATTA
1 AAATAAAAACATTATAAATTATATTAATAATTTATTA
20716 AAATAAAAA
1 AAATAAAAA
20725 TAATATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 12 0.32
34 2 0.05
35 1 0.03
36 4 0.11
37 18 0.49
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (37 bp):
AAATAAAAACATTATAAATTATATTAATAATTTATTA
Found at i:20719 original size:37 final size:39
Alignment explanation
Indices: 20662--20814 Score: 127
Period size: 40 Copynumber: 3.9 Consensus size: 39
20652 AAACATTAAG
*
20662 ATTATT-ATAATTTATTAAAATAA-AATTATTATAAATT
1 ATTATTAATTATTTATTAAAATAATAATTATTATAAATT
*
20699 A-TATTAATTATTTATTAAAATAAAAATAATATATTATTAATT
1 ATTATTAATTATTTATTAAAAT---AATAAT-TATTATAAATT
* * *
20741 ATTATTATTTACTTATTAAAATAATAA-TATTATTAAAAT
1 ATTATTAATTATTTATTAAAATAATAATTATTA-TAAATT
** * * *
20780 ATTAAAAAATATAATATTAAAATAACAA-TATTATA
1 ATTATTAATTAT-TTATTAAAATAATAATTATTATA
20815 GTATATTTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
36 4 0.04
37 15 0.16
38 5 0.05
39 13 0.14
40 25 0.27
41 3 0.03
42 11 0.12
43 18 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (39 bp):
ATTATTAATTATTTATTAAAATAATAATTATTATAAATT
Found at i:20725 original size:43 final size:43
Alignment explanation
Indices: 20678--20769 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
20668 ATAATTTATT
*
20678 AAAATAAAATTATTATAAATTA-TATTAATTATTTATTAAAATA
1 AAAATAAAA-TATTATAAATTATTATTAATTACTTATTAAAATA
* * *
20721 AAAATAATATATTATTAATTATTATTATTTACTTATTAAAATA
1 AAAATAAAATATTATAAATTATTATTAATTACTTATTAAAATA
*
20764 ATAATA
1 AAAATA
20770 TTATTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 11 0.26
43 32 0.74
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (43 bp):
AAAATAAAATATTATAAATTATTATTAATTACTTATTAAAATA
Found at i:20801 original size:23 final size:25
Alignment explanation
Indices: 20754--20803 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 25
20744 ATTATTTACT
*
20754 TATTAAAATAATAATATTATTAAAA
1 TATTAAAATAATAATAATATTAAAA
20779 TATTAAAA-AAT-ATAATATTAAAA
1 TATTAAAATAATAATAATATTAAAA
20802 TA
1 TA
20804 ACAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 13 0.54
24 3 0.12
25 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAATAATAATAATATTAAAA
Found at i:21207 original size:22 final size:23
Alignment explanation
Indices: 21151--21207 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
21141 GTAATGGAAC
21151 TTCAGTTGACCAGGAAAATGAAT
1 TTCAGTTGACCAGGAAAATGAAT
21174 TTCAGTTGACCAGGAAAATGAAT
1 TTCAGTTGACCAGGAAAATGAAT
21197 TTCA-TTGACCA
1 TTCAGTTGACCA
21208 TTTGTTTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.21
23 27 0.79
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (23 bp):
TTCAGTTGACCAGGAAAATGAAT
Found at i:30286 original size:25 final size:25
Alignment explanation
Indices: 30252--30300 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
30242 GGCTGGAACA
*
30252 TTTAGGGTTTGAAACCCTAATCTGG
1 TTTAGGGTTTAAAACCCTAATCTGG
30277 TTTAGGGTTTAAAACCCTAATCTG
1 TTTAGGGTTTAAAACCCTAATCTG
30301 ATGGGTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (25 bp):
TTTAGGGTTTAAAACCCTAATCTGG
Found at i:30387 original size:16 final size:14
Alignment explanation
Indices: 30373--30422 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
30363 TTGTAATATG
*
30373 TAATATTAATAATA
1 TAATAATAATAATA
30387 TAATAATAATAATA
1 TAATAATAATAATA
30401 -AATAATAATAATAA
1 TAATAATAATAAT-A
30415 TAA-AATAA
1 TAATAATAA
30423 CGATAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 12 0.36
14 19 0.58
15 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:30392 original size:3 final size:3
Alignment explanation
Indices: 30373--30422 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
30363 TTGTAATATG
*
30373 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
30418 -AA TAA
1 TAA TAA
30423 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:30428 original size:27 final size:27
Alignment explanation
Indices: 30374--30429 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
30364 TGTAATATGT
* *
30374 AATATTAATAATATAATAATAATAATA
1 AATAATAATAATATAATAATAACAATA
*
30401 AATAATAATAATAATAA-AATAACGATA
1 AATAATAATAAT-ATAATAATAACAATA
30428 AA
1 AA
30430 AAAACCCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (27 bp):
AATAATAATAATATAATAATAACAATA
Found at i:30641 original size:43 final size:44
Alignment explanation
Indices: 30580--30926 Score: 172
Period size: 43 Copynumber: 8.0 Consensus size: 44
30570 TGTTGGGGAC
* * * *
30580 GACACTGCTCATACGTGATGAAGAGTT-TGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
*
30623 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
* * * * *** *
30667 GATAACACGGTTCCTACGTGACGAGGACG-GCT-GTTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTCTGGGCCATCTAAAGG-T
* * **
30713 GACACGGCTCCTACGTGATGAGGAGATCT-GG---TCT-GGGGAT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGG-T
*
30753 GACACGGCTCATACGTGATGAAGAGTTCT-GGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
* * * * ** *
30796 GATAACATGGTTCCTACGTGATGAGGACG-GCT-GGTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTCTGGGCCATCTAAAGG-T
* * * ****
30842 AACACGGCTCCTACGTGATGAAGAGATCT-GGTC-GGGGAA--T
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
*
30882 GACACGGCTCATACGTGATGAAGAGTTCT-GGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
30925 GA
1 GA
30927 TAACACGGTT
Statistics
Matches: 232, Mismatches: 51, Indels: 42
0.71 0.16 0.13
Matches are distributed among these distances:
40 64 0.28
41 2 0.01
42 2 0.01
43 83 0.36
44 16 0.07
45 6 0.03
46 35 0.15
47 23 0.10
48 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (44 bp):
GACACGGCTCCTACGTGATGAAGAGTTCTGGGCCATCTAAAGGT
Found at i:30768 original size:40 final size:41
Alignment explanation
Indices: 30712--30912 Score: 158
Period size: 40 Copynumber: 4.8 Consensus size: 41
30702 TATCTATGGT
*
30712 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGGA
* * *
30752 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG--ATCT---GGGGA
* * * * * ** *
30798 TAACATGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAAGA-GATCTGG--ATCTGGGGA
*
30841 TAACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGG-A
* *
30881 TGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGG
30913 CCATCTAAAG
Statistics
Matches: 126, Mismatches: 26, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
39 2 0.02
40 60 0.48
42 1 0.01
43 30 0.24
46 32 0.25
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (41 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGATCTGGGGA
Found at i:30814 original size:129 final size:129
Alignment explanation
Indices: 30622--30964 Score: 598
Period size: 129 Copynumber: 2.7 Consensus size: 129
30612 CGTCTAAAGG
*
30622 TGACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
* * *
30687 ACGAGGACGGCTGTTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGG-
65 ACGAGGACGGCTGGTTATCTATGGTTAACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGA
30751 A
129 A
*
30752 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
*
30817 TGAGGACGGCTGGTTATCTATGGTTAACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
66 CGAGGACGGCTGGTTATCTATGGTTAACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
*
30881 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGA
1 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
30946 CGAGGACGGCTGGTTATCT
66 CGAGGACGGCTGGTTATCT
30965 CTAGGATAAT
Statistics
Matches: 203, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
128 4 0.02
129 171 0.84
130 28 0.14
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
CGAGGACGGCTGGTTATCTATGGTTAACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAA
Found at i:30836 original size:46 final size:45
Alignment explanation
Indices: 30624--30964 Score: 169
Period size: 46 Copynumber: 7.8 Consensus size: 45
30614 TCTAAAGGTG
* ** **
30624 ACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGC-TGGTTATCT-AAGGTGATA
* * * * *
30671 ACACGGTTCCTACGTGACGAGGACG-GCTGTTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTGATA
* * *
30714 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCT--GGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTGATA
* * ** **
30754 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTGATA
* * *
30800 ACATGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TA
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTGATA
* * * *
30843 ACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG-ATA
* * ** **
30883 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTGATA
* * *
30929 ACACGGTTCCTACATGACGAGGACG-GCTGGTTATCT
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCT
30965 CTAGGATAAT
Statistics
Matches: 226, Mismatches: 45, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
40 63 0.28
42 2 0.01
43 56 0.25
45 8 0.04
46 66 0.29
47 26 0.12
48 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTGATA
Found at i:31345 original size:35 final size:36
Alignment explanation
Indices: 31298--31380 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
31288 ACAAAATTCA
**
31298 TTTCAAGAGAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACAGAT-TCAAAGATGGTAAATTTTG
*
31333 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
31369 TTTCCAA-AGAAA
1 TTT-CAAGAGAAA
31381 TAAACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 20 0.49
36 18 0.44
37 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:31485 original size:28 final size:28
Alignment explanation
Indices: 31423--31488 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
31413 GAGAGACACA
*
31423 ATTTTGTTTCAAAGGAAACAAACTCAAAG
1 ATTTT-TTTCAAAAGAAACAAACTCAAAG
* *
31452 A-TTTTTTCAAAAGAAACAATCTCAAAT
1 ATTTTTTTCAAAAGAAACAAACTCAAAG
31479 ATTTTTTTCA
1 ATTTTTTTCA
31489 CAAAATTGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.64
28 11 0.33
29 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAAACTCAAAG
Found at i:31548 original size:90 final size:87
Alignment explanation
Indices: 31369--31559 Score: 231
Period size: 87 Copynumber: 2.1 Consensus size: 87
31359 GTAAATTTTG
* * * * *
31369 TTTCCAAAGAAATAAACTCAAAGATTTTTCTCAAAGACTGTCTCGAGAGACACAATTTTGTTTCA
1 TTTCAAAAGAAACAAACTCAAAGATTTTTCTCAAAAACTGTCTCGAGAGACAAAACTTTGTTTCA
31434 AAGGAAACAAACTCAAAGATTT
66 AAGGAAACAAACTCAAAGATTT
* * * *
31456 TTTCAAAAGAAACAATCTCAAATATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 TTTCAAAAGAAACAAACTCAAAGATTTTTCTCA-AAAACTGTCTC--GAGAGACAAAACTTTGTT
*
31521 TCAAAGTAAA-ATAGACTCAAAGATTTT
63 TCAAAGGAAACA-A-ACTCAAAGA-TTT
31548 TTTCAAAAGAAA
1 TTTCAAAAGAAA
31560 TTGTCTTTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
87 28 0.32
88 9 0.10
89 1 0.01
90 26 0.30
91 9 0.10
92 15 0.17
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (87 bp):
TTTCAAAAGAAACAAACTCAAAGATTTTTCTCAAAAACTGTCTCGAGAGACAAAACTTTGTTTCA
AAGGAAACAAACTCAAAGATTT
Found at i:31601 original size:64 final size:63
Alignment explanation
Indices: 31456--31605 Score: 171
Period size: 64 Copynumber: 2.3 Consensus size: 63
31446 TCAAAGATTT
* *
31456 TTTCAAAAGAAACA-ATCTCAAATATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAACAGA-CTCAAAGATTTTTTTCAAAAAATTGTCTCAAGAGAGACAAAACTTTG
* ** * *
31519 TTTC-AAAGTAAAATAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTA-AGAGATAAAATTT
1 TTTCAAAAG--AAACAGACTCAAAGATTTTTTTC-AAA-AAATTGTCTCAAGAGAGACAAAACTT
31582 TG
62 TG
31584 TTTCAAAAGAAACAGACTCAAA
1 TTTCAAAAGAAACAGACTCAAA
31606 TGATGGATCT
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
62 4 0.05
63 4 0.05
64 31 0.42
65 20 0.27
66 14 0.19
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (63 bp):
TTTCAAAAGAAACAGACTCAAAGATTTTTTTCAAAAAATTGTCTCAAGAGAGACAAAACTTTG
Found at i:31877 original size:66 final size:67
Alignment explanation
Indices: 31760--31986 Score: 257
Period size: 67 Copynumber: 3.4 Consensus size: 67
31750 ACTCAAAGAT
* * ** * *
31760 TTTCAAAATG-AACATATTCAAAGA--TTTGCTTCAAAAGAAACGGTCTCAAGAGATACAAAATT
1 TTTCAAAA-GAAACAGATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT
31822 CAT-
65 -ATG
* * *
31825 TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTT
1 TTTCAAAAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTA
31889 TG
66 TG
* * *
31891 TTTCAAAAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTT
1 TTTCAAAAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTA
31956 TG
66 TG
* * * *
31958 TTTCCAAAGAACCAAACTCAAAGATTTTT
1 TTTCAAAAGAAACAGATTCAAAGATTTTT
31987 CAAGAGAAAC
Statistics
Matches: 141, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 16 0.11
65 4 0.03
66 35 0.25
67 85 0.60
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (67 bp):
TTTCAAAAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTA
TG
Found at i:31898 original size:37 final size:36
Alignment explanation
Indices: 31849--31968 Score: 112
Period size: 37 Copynumber: 3.4 Consensus size: 36
31839 ATTCAAAGAT
31849 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAA-TATCTTAAGAGAGACAAAA
**
31886 TTTTGTTTCAAAAG-AA-A-C-----AGACTCAAAGA
1 TTTTGTTTCAAAAGAAATATCTTAAGAGAGACAAA-A
*
31915 TTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAA
1 -TTTTGTTTCAAAAGAAA-TATCTTAAGAGAGACAAAA
*
31953 TTTTGTTTCCAAAGAA
1 TTTTGTTTCAAAAGAA
31969 CCAAACTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
28 7 0.11
29 1 0.02
30 14 0.21
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 29 0.44
38 1 0.02
39 6 0.09
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAATATCTTAAGAGAGACAAAA
Found at i:31923 original size:67 final size:67
Alignment explanation
Indices: 31831--31986 Score: 258
Period size: 67 Copynumber: 2.3 Consensus size: 67
31821 TCATTTTAAG
* * *
31831 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
31896 AA
66 AA
*
31898 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
31963 AA
66 AA
* *
31965 AGAACCAAACTCAAAGATTTTT
1 AGAAACAGACTCAAAGATTTTT
31987 CAAGAGAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 83 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
AA
Found at i:32488 original size:105 final size:101
Alignment explanation
Indices: 32308--32540 Score: 281
Period size: 105 Copynumber: 2.3 Consensus size: 101
32298 TAGAGCAATT
* * *
32308 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCCACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
32373 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
32410 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
32474 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
32515 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
32541 AAAATTCTCA
Statistics
Matches: 113, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
101 5 0.04
102 21 0.19
103 2 0.02
104 4 0.04
105 76 0.67
106 5 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:32649 original size:11 final size:12
Alignment explanation
Indices: 32628--32654 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32618 CAAAATAAAA
32628 TTTGTTTTTTTT
1 TTTGTTTTTTTT
32640 TTTGTTTTTTTT
1 TTTGTTTTTTTT
32652 TTT
1 TTT
32655 TAAATTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTGTTTTTTTT
Found at i:33081 original size:16 final size:15
Alignment explanation
Indices: 33034--33085 Score: 65
Period size: 16 Copynumber: 3.5 Consensus size: 15
33024 ATATGTATAT
33034 ATGTATGTATGAATTG
1 ATGTATGTATG-ATTG
33050 ATGTATGTAT-A-T-
1 ATGTATGTATGATTG
33062 ATGTATGTATGAGTTG
1 ATGTATGTATGA-TTG
33078 ATGTATGT
1 ATGTATGT
33086 TTCTCAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 10 0.31
13 2 0.06
14 1 0.03
15 1 0.03
16 18 0.56
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (15 bp):
ATGTATGTATGATTG
Found at i:33085 original size:4 final size:4
Alignment explanation
Indices: 33000--33072 Score: 73
Period size: 4 Copynumber: 19.0 Consensus size: 4
32990 ATGCAAATTT
* *
33000 TATG TAT- TATG TATG TATG --TG TATA TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
33045 AAT- TGATG TATG TATA TATG TATG TATG
1 TATG T-ATG TATG TATG TATG TATG TATG
33073 AGTTGATGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 3 0.05
4 50 0.89
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:34265 original size:12 final size:11
Alignment explanation
Indices: 34237--34274 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
34227 TCTTCTTTTG
*
34237 TTCTTTGCTTT
1 TTCTTTGATTT
34248 TTCTTTGATTT
1 TTCTTTGATTT
34259 TTGCTTTGATTT
1 TT-CTTTGATTT
34271 TTCT
1 TTCT
34275 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:34926 original size:26 final size:24
Alignment explanation
Indices: 34896--34966 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
34886 CAAGGTGGAA
34896 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
34920 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
34942 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
34966 A
1 A
34967 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:34951 original size:20 final size:20
Alignment explanation
Indices: 34883--34957 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
34873 AAATACAGTG
*
34883 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
34902 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
34928 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
34948 TTTCAAGGTC
1 TTTCAAGGTC
34958 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:34971 original size:26 final size:26
Alignment explanation
Indices: 34893--34972 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
34883 TTTCAAGGTG
34893 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
34919 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
34940 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
34965 GATAGAAT
1 GAAAGAAT
34973 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:34973 original size:46 final size:45
Alignment explanation
Indices: 34881--34974 Score: 152
Period size: 46 Copynumber: 2.1 Consensus size: 45
34871 ATAAATACAG
* *
34881 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
34926 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
34972 TGT
1 TGT
34975 CAAAAATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 11 0.24
46 34 0.76
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:40920 original size:25 final size:25
Alignment explanation
Indices: 40886--40934 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40876 GGCTGGAACA
*
40886 TTTAGGGTTTGAAACCCTAATCTGG
1 TTTAGGGTTTAAAACCCTAATCTGG
40911 TTTAGGGTTTAAAACCCTAATCTG
1 TTTAGGGTTTAAAACCCTAATCTG
40935 ATGGGTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (25 bp):
TTTAGGGTTTAAAACCCTAATCTGG
Found at i:41021 original size:16 final size:14
Alignment explanation
Indices: 41007--41056 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
40997 TTGTAATATG
*
41007 TAATATTAATAATA
1 TAATAATAATAATA
41021 TAATAATAATAATA
1 TAATAATAATAATA
41035 -AATAATAATAATAA
1 TAATAATAATAAT-A
41049 TAA-AATAA
1 TAATAATAA
41057 CGATAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 12 0.36
14 19 0.58
15 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:41026 original size:3 final size:3
Alignment explanation
Indices: 41007--41056 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
40997 TTGTAATATG
*
41007 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
41052 -AA TAA
1 TAA TAA
41057 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41062 original size:27 final size:27
Alignment explanation
Indices: 41008--41063 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40998 TGTAATATGT
* *
41008 AATATTAATAATATAATAATAATAATA
1 AATAATAATAATATAATAATAACAATA
*
41035 AATAATAATAATAATAA-AATAACGATA
1 AATAATAATAAT-ATAATAATAACAATA
41062 AA
1 AA
41064 AAAACCCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (27 bp):
AATAATAATAATATAATAATAACAATA
Found at i:46703 original size:136 final size:136
Alignment explanation
Indices: 46371--47133 Score: 883
Period size: 136 Copynumber: 5.6 Consensus size: 136
46361 CTTAGACCAT
* * *
46371 AAGTTCTTCTCATCT-TG-TCTTCTTCTCCCTCT-TTGAATGAGTTCTTCTCATTATGAACTCTC
1 AAGTTCTTCTCAT-TATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTC
* * * * * *
46433 CATTGTAAATGTTAATCCCTCGAGTGAGGTGTTGATGATTCAACTCCATATG-TGATGAATCGAG
65 CATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAA----A-ATGTTG-TGAATCGAG
*
46497 CCAAT--GTAGAAC
124 -CAATAGGTCGAAC
*** *
46509 AAGTTCTTCTCATTATGAACTTAGCCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCC
* * *
46574 ATTGGAAATATCAATCCCTCAAGCGAGGTGTTTCTGATTCAAAATGTTGTGAATCGAGCAATAGG
66 ATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAAAATGTTGTGAATCGAGCAATAGG
*
46639 CCGAAC
131 TCGAAC
* * *
46645 AAGTTCTTCTCATTATAAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATAATGAACTCTCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCC
* * * * *
46710 ATTGGAAATGTCAATCCCTCAAGCAAGGCGTTGTTGATTCGAAGTGTTGTGAATCAAGCAATAGG
66 ATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAAAATGTTGTGAATCGAGCAATAGG
*
46775 TGGAAC
131 TCGAAC
* * * * * * *
46781 AAGTTCTTTTCATTATGAACTTCTTCTCCCTTTGTCGGACGAGTTCTTCTCAATATGGACTATCT
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCC
* * * *
46846 ATTGGAAATGTCAATCCCTCAAGCGTGGCGTTACTGATTCGAAGTGTTGTGAATCGAGCAATAGG
66 ATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAAAATGTTGTGAATCGAGCAATAGG
46911 TCGAAC
131 TCGAAC
*
46917 AAGTTCTTCTCATTATAAACTTCTTCTCCCTCTGTCTGG-TGAGTTCTTCTCATTATGAACTCTC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTC-GGATGAGTTCTTCTCATTATGAACTCTC
** * * * * *** * **
46981 CATTTTAAAGGTTAATCCCTTAAGCGAGGCGTCGCTGATTCAAAATGACATTAATTTAGCAATAG
65 CATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAAAATGTTGTGAATCGAGCAATAG
*
47046 ATCGAAC
130 GTCGAAC
* * * *
47053 AAGCTCTTCTCATTATGAACTTCCTCTCCCTCGGTCGGATGAGTTCTTCTCATTATGAACTATCC
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCC
*
47118 ATTGGAAATGTTAATC
66 ATTGGAAATGTCAATC
47134 GGTTTATCTT
Statistics
Matches: 536, Mismatches: 81, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
134 4 0.01
135 14 0.03
136 425 0.79
137 3 0.01
138 15 0.03
139 11 0.02
140 64 0.12
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (136 bp):
AAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCC
ATTGGAAATGTCAATCCCTCAAGCGAGGCGTTGCTGATTCAAAATGTTGTGAATCGAGCAATAGG
TCGAAC
Found at i:48004 original size:41 final size:41
Alignment explanation
Indices: 47953--48071 Score: 132
Period size: 42 Copynumber: 2.9 Consensus size: 41
47943 AATGTGAAAA
* * * * *
47953 CATCCTGCTCGAAGGTCTTATGAATGGCCCGAATGACTT-AT
1 CATCATGCTCGAAAGACTTAT-AATGGCCCGAAGGACTTAAG
* * *
47994 CATCTTGCTCGAAAGACTTATATATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTATA-ATGGCCCGAAGGACTTAAG
48036 CATCATGCTCGAAAGACTTACTAATGGCCCGAAGGA
1 CATCATGCTCGAAAGACTTA-TAATGGCCCGAAGGA
48072 TTTTTTCTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
40 1 0.02
41 31 0.47
42 32 0.48
43 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAATGGCCCGAAGGACTTAAG
Found at i:48320 original size:54 final size:54
Alignment explanation
Indices: 48145--48364 Score: 248
Period size: 54 Copynumber: 4.1 Consensus size: 54
48135 ACAGTTATCG
* * * *
48145 TCAAGAAACCCCTAAAAATTAGGATTAGCTTTTTTAAAAATTCTTTGGAAATAATCA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCTTTTG-AA-AA-CA
* * * * *
48202 TTAAGAAACCCCTGAAAATCAGGCTTAG-TT-TCTAAAAACTCATTTTCAAAACA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTC-TTTTGAAAACA
* *
48255 TCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAAATTCTTTTGAAAACA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCTTTTGAAAACA
* * * *
48309 TCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-CAATTTCGTTTGAAAACA
1 TCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCTTTTGAAAACA
48362 TCA
1 TCA
48365 TAACAAGAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
53 45 0.32
54 47 0.34
55 19 0.14
56 5 0.04
57 24 0.17
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (54 bp):
TCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCTTTTGAAAACA
Found at i:50316 original size:4 final size:4
Alignment explanation
Indices: 50300--50356 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
50290 TTTGATATGT
* * * *
50300 TTTC TTTC -ATC TTTC TTTC TTT- TTT- TTTC TTTT TTTT TTTC TTTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
50345 TTTC -TTC TTTC T
1 TTTC TTTC TTTC T
50357 CTTTTTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 11 0.25
4 33 0.75
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:50324 original size:22 final size:22
Alignment explanation
Indices: 50299--50364 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 22
50289 ATTTGATATG
*
50299 TTTTCTTTC-ATCTTTCTTTCT
1 TTTTTTTTCTATCTTTCTTTCT
*
50320 TTTTTTTTCT-T-TTT-TTTTT
1 TTTTTTTTCTATCTTTCTTTCT
50339 TCTTTTTTTCT-TCTTTC--TCT
1 T-TTTTTTTCTATCTTTCTTTCT
50359 TTTTTT
1 TTTTTT
50365 ATGTTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 10 0.26
20 16 0.42
21 12 0.32
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTTCTATCTTTCTTTCT
Found at i:50330 original size:10 final size:10
Alignment explanation
Indices: 50315--50374 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
50305 TTCATCTTTC
50315 TTTCTTTTTT
1 TTTCTTTTTT
50325 TTTCTTTTTT
1 TTTCTTTTTT
50335 TTT-TTCTTTT
1 TTTCTT-TTTT
*
50345 TTTC-TTCTT
1 TTTCTTTTTT
*
50354 TCTCTTTTTT
1 TTTCTTTTTT
* *
50364 TATGTTTTTT
1 TTTCTTTTTT
50374 T
1 T
50375 GCTATATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 8 0.19
10 34 0.81
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:50333 original size:11 final size:11
Alignment explanation
Indices: 50315--50354 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
50305 TTCATCTTTC
50315 TTTC-TTTTTT
1 TTTCTTTTTTT
50325 TTTCTTTTTTTT
1 TTTC-TTTTTTT
50337 TTTCTTTTTTT
1 TTTCTTTTTTT
*
50348 CTTCTTT
1 TTTCTTT
50355 CTCTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
12 10 0.37
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:50340 original size:37 final size:37
Alignment explanation
Indices: 50299--50374 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
50289 ATTTGATATG
* * *
50299 TTTTCTTTCATCT-TTCTTTCTTTTTTTTTCTTTTTTT
1 TTTTCTTT-ATCTCTTCTTTCTCTTTTTTTATGTTTTT
* *
50336 TTTTCTTTTTTTCTTCTTTCTCTTTTTTTATGTTTTT
1 TTTTCTTTATCTCTTCTTTCTCTTTTTTTATGTTTTT
50373 TT
1 TT
50375 GCTATATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (37 bp):
TTTTCTTTATCTCTTCTTTCTCTTTTTTTATGTTTTT
Found at i:50344 original size:17 final size:17
Alignment explanation
Indices: 50315--50364 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
50305 TTCATCTTTC
50315 TTTCTTTT-TTTTTCTTT
1 TTTCTTTTCTTTTT-TTT
*
50332 TTTTTTTTC-TTTTTTT
1 TTTCTTTTCTTTTTTTT
*
50348 CTTCTTTCTCTTTTTTT
1 TTTCTTT-TCTTTTTTT
50365 ATGTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 8 0.30
17 13 0.48
18 6 0.22
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCTTTTCTTTTTTTT
Found at i:50349 original size:30 final size:29
Alignment explanation
Indices: 50311--50364 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 29
50301 TTCTTTCATC
50311 TTTCTTTCTTT-TT-TTT-TCTTTTTTTT
1 TTTCTTTCTTTCTTCTTTCTCTTTTTTTT
*
50337 TTTCTTTTTTTCTTCTTTCTCTTTTTTT
1 TTTCTTTCTTTCTTCTTTCTCTTTTTTT
50365 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 2 0.08
28 3 0.12
29 9 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (29 bp):
TTTCTTTCTTTCTTCTTTCTCTTTTTTTT
Found at i:67416 original size:20 final size:19
Alignment explanation
Indices: 67385--67429 Score: 81
Period size: 20 Copynumber: 2.3 Consensus size: 19
67375 TGGTGCAGTC
67385 AGTAATAGAAGTGAATAAT
1 AGTAATAGAAGTGAATAAT
67404 AGTAATAAGAAGTGAATAAT
1 AGTAAT-AGAAGTGAATAAT
67424 AGTAAT
1 AGTAAT
67430 GAGGTATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27
Consensus pattern (19 bp):
AGTAATAGAAGTGAATAAT
Found at i:68309 original size:31 final size:30
Alignment explanation
Indices: 68229--68315 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
68219 TAAGGTGGCC
* * *
68229 CTTGGGTAGGCTCTGTGGCCCCAAGATCTT
1 CTTGAGTAGGCCCTGTGGCCCCGAGATCTT
* * *
68259 TTTAAGGTAGGCCATGTGGCCCCGAGATCCTT
1 CTTGA-GTAGGCCCTGTGGCCCCGAGAT-CTT
* *
68291 CTTGAGTAGGCCCCGTGGCCTCGAG
1 CTTGAGTAGGCCCTGTGGCCCCGAG
68316 TAACTTTCTT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.82
32 6 0.14
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (30 bp):
CTTGAGTAGGCCCTGTGGCCCCGAGATCTT
Found at i:69602 original size:12 final size:12
Alignment explanation
Indices: 69572--69604 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
69562 TGAGCATTAC
*
69572 ATTAGTATAAAA
1 ATTAGTCTAAAA
69584 ATTAGTCTAAAA
1 ATTAGTCTAAAA
69596 ATTAGTCTA
1 ATTAGTCTA
69605 TTGTTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (12 bp):
ATTAGTCTAAAA
Found at i:70864 original size:17 final size:17
Alignment explanation
Indices: 70842--70881 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
70832 TAATCGCGAT
70842 AAATACAATACAATTAA
1 AAATACAATACAATTAA
70859 AAATACAATACAATTAA
1 AAATACAATACAATTAA
70876 AAATAC
1 AAATAC
70882 GATCGTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATACAATACAATTAA
Found at i:75408 original size:42 final size:42
Alignment explanation
Indices: 75331--75432 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
75321 TTCTTATTTT
* * *
75331 TTTTACCTTTATAATTGATGTTCTAATATTATTCAAT-CTCAC
1 TTTTACCTTTATAATTGAAGTTCAAAGATTATTCAATCCT-AC
* * **
75373 TTTTATCTTTATAATTGAAGTCTCAAAGCTT-TTCAATCCTTT
1 TTTTACCTTTATAATTGAAGT-TCAAAGATTATTCAATCCTAC
75415 TTTTACCTTTATAATTGA
1 TTTTACCTTTATAATTGA
75433 GGCCCCTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 42 0.84
43 8 0.16
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTTACCTTTATAATTGAAGTTCAAAGATTATTCAATCCTAC
Found at i:75533 original size:44 final size:45
Alignment explanation
Indices: 75362--75705 Score: 201
Period size: 42 Copynumber: 8.0 Consensus size: 45
75352 TCTAATATTA
* * * * * *
75362 TTCAATCTCACTTT-TATCTTTAT-AATTGAAGTCTCAAAG-CTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
** *
75404 TTCAATC-CTTTTTTTACCTTTAT-AATTGAGGCCCCTAA-TTTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
* * * * ***
75446 GT-AATCCCACTTT-TAACTTTAT-AATCGAGGCTTTTAAGTTTTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAG-TTTT
*
75489 TTCAATCTCACTTTCTACCTTT-TCAATTGGGGCCCCTAAGTTTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
* * *
75533 TTCGATCTCAATTTCTACCTTTATC-GTTGAGGCCCCTAA-TTTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
* * *
75576 TT-AATCCCACTTTTTCAACTTTAT-AATTGAGGCCCCTAAGTTTT
1 TTCAATCTCACTTTCT-ACCTTTATCAATTGAGGCCCCTAAGTTTT
*** * * * * *
75620 TTTTCTCTCA-ATTATACCTTAAT-ATTTGTGGCCCCT-A-TTTT
1 TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
* *
75661 TT-AGATCTCGA-TTTCTACCTTTAT-AATTAAGGCCTCTAA-TTTT
1 TTCA-ATCTC-ACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
75704 TT
1 TT
75706 ATAATTTCAT
Statistics
Matches: 234, Mismatches: 52, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
41 37 0.16
42 63 0.27
43 55 0.24
44 56 0.24
45 23 0.10
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.47
Consensus pattern (45 bp):
TTCAATCTCACTTTCTACCTTTATCAATTGAGGCCCCTAAGTTTT
Found at i:75566 original size:130 final size:128
Alignment explanation
Indices: 75418--75703 Score: 346
Period size: 130 Copynumber: 2.2 Consensus size: 128
75408 ATCCTTTTTT
***
75418 TACCTTTATAATTGAGGCCCCTAATTTTGTAATCCCAC-TTTT-AACTTTATAATCGAGGCTTTT
1 TACCTTTATAATTGAGGCCCCTAATTTTGTAATCCCACTTTTTCAACTTTATAATCGAGGCCCCT
* * * *
75481 AAG-TTTTTTTCAATCTCACTTTCTACCTT-TTCAATTGGGGCCCCTAAGTTTTTTCGATCTCAA
66 AAGTTTTTTTTC--TCTCA-ATTATACCTTAAT-AATTGGGGCCCCT-A-TTTTTTAGATCTCAA
75544 TTTC
125 TTTC
** * *
75548 TACCTTTATCGTTGAGGCCCCTAATTTTTTAATCCCACTTTTTCAACTTTATAATTGAGGCCCCT
1 TACCTTTATAATTGAGGCCCCTAATTTTGTAATCCCACTTTTTCAACTTTATAATCGAGGCCCCT
* * *
75613 AAGTTTTTTTTCTCTCAATTATACCTTAATATTTGTGGCCCCTATTTTTTAGATCTCGATTTC
66 AAGTTTTTTTTCTCTCAATTATACCTTAATAATTGGGGCCCCTATTTTTTAGATCTCAATTTC
* *
75676 TACCTTTATAATTAAGGCCTCTAATTTT
1 TACCTTTATAATTGAGGCCCCTAATTTT
75704 TTATAATTTC
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
128 41 0.31
129 1 0.01
130 54 0.40
131 10 0.07
132 20 0.15
133 8 0.06
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (128 bp):
TACCTTTATAATTGAGGCCCCTAATTTTGTAATCCCACTTTTTCAACTTTATAATCGAGGCCCCT
AAGTTTTTTTTCTCTCAATTATACCTTAATAATTGGGGCCCCTATTTTTTAGATCTCAATTTC
Found at i:75576 original size:86 final size:84
Alignment explanation
Indices: 75485--75705 Score: 232
Period size: 86 Copynumber: 2.6 Consensus size: 84
75475 GCTTTTAAGT
* *
75485 TTTTTTCAATCTCACTTTCTACCTTT-TCAATTGGGGCCCCTAAGTTTTTTCGATCTCAATTTCT
1 TTTTTT-AATCTCACTTTCTACCTTTAT-AATTGAGGCCCCTAAGTTTTTTCGATCTCAA-TTAT
* *
75549 ACCTTTATCGTTGAGGCCCCTAA
63 ACCTTAATAGTTGAGGCCCCT-A
* * * ***
75572 TTTTTTAATCCCACTTTTTCAACTTTATAATTGAGGCCCCTAAGTTTTTTTTCTCTCAATTATAC
1 TTTTTTAATCTCACTTTCT-ACCTTTATAATTGAGGCCCCTAAGTTTTTTCGATCTCAATTATAC
* *
75637 CTTAATATTTGTGGCCCCTA
65 CTTAATAGTTGAGGCCCCTA
* *
75657 TTTTTTAGATCTCGA-TTTCTACCTTTATAATTAAGGCCTCTAA-TTTTTT
1 TTTTTTA-ATCTC-ACTTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTT
75706 ATAATTTCAT
Statistics
Matches: 113, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
84 6 0.05
85 28 0.25
86 39 0.35
87 39 0.35
88 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.47
Consensus pattern (84 bp):
TTTTTTAATCTCACTTTCTACCTTTATAATTGAGGCCCCTAAGTTTTTTCGATCTCAATTATACC
TTAATAGTTGAGGCCCCTA
Found at i:75598 original size:43 final size:44
Alignment explanation
Indices: 75421--75621 Score: 198
Period size: 44 Copynumber: 4.6 Consensus size: 44
75411 CTTTTTTTAC
*
75421 CTTTATAATTGAGGCCCCTAA-TTTTGT-AATCCCACTTT-TAA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCCCACTTTCTAA
* *** * *
75462 CTTTATAATCGAGGCTTTTAAGTTTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTGAGGCCCCTAAG-TTTTTTCAATCCCACTTTCTAA
* * * * *
75507 CTTT-TCAATTGGGGCCCCTAAGTTTTTTCGATCTCAATTTCTAC
1 CTTTAT-AATTGAGGCCCCTAAGTTTTTTCAATCCCACTTTCTAA
** *
75551 CTTTATCGTTGAGGCCCCTAA-TTTTTT-AATCCCACTTTTTCAA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCCCACTTTCT-AA
75594 CTTTATAATTGAGGCCCCTAAGTTTTTT
1 CTTTATAATTGAGGCCCCTAAGTTTTTT
75622 TTCTCTCAAT
Statistics
Matches: 128, Mismatches: 24, Indels: 13
0.78 0.15 0.08
Matches are distributed among these distances:
41 17 0.13
42 9 0.07
43 31 0.24
44 53 0.41
45 18 0.14
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (44 bp):
CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCCCACTTTCTAA
Found at i:77501 original size:14 final size:14
Alignment explanation
Indices: 77479--77512 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
77469 ATTTGTAAGA
*
77479 ATTTGTTTTATTGT
1 ATTTTTTTTATTGT
77493 ATTTTTTTTATTGT
1 ATTTTTTTTATTGT
77507 ACTTTT
1 A-TTTT
77513 GGATTTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (14 bp):
ATTTTTTTTATTGT
Found at i:80926 original size:44 final size:44
Alignment explanation
Indices: 80877--80960 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
80867 GGGTATATAT
80877 ATTTAAATTAAATATATAAATATTATATATATATATATAATTTA
1 ATTTAAATTAAATATATAAATATTATATATATATATATAATTTA
* * *
80921 ATTTAATTTAAATTTATTAATATTATATATATATATATAA
1 ATTTAAATTAAATATATAAATATTATATATATATATATAA
80961 AATAATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (44 bp):
ATTTAAATTAAATATATAAATATTATATATATATATATAATTTA
Found at i:87213 original size:16 final size:16
Alignment explanation
Indices: 87192--87240 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
87182 AAGCTCTCCA
87192 TTCTCTCTAAATTCCC
1 TTCTCTCTAAATTCCC
*
87208 TTCTCTCTAAATTCCA
1 TTCTCTCTAAATTCCC
*
87224 TTCTCTTTAAATTCCC
1 TTCTCTCTAAATTCCC
87240 T
1 T
87241 CATCAGAGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCTCTCTAAATTCCC
Found at i:90099 original size:41 final size:44
Alignment explanation
Indices: 90030--90110 Score: 123
Period size: 41 Copynumber: 1.9 Consensus size: 44
90020 TTGGTAGCAA
* *
90030 GAAAAATATATCCTAACCTCATGCTTTCTAGTTC-CATGCTTTG
1 GAAAAATATATCCTAACCGCATGATTTCTAGTTCGCATGCTTTG
90073 GAAAAATA-A-CCTAACCGCATGATTTCTAGTTCGCATGC
1 GAAAAATATATCCTAACCGCATGATTTCTAGTTCGCATGC
90111 ATTTATTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 21 0.60
42 6 0.17
43 8 0.23
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (44 bp):
GAAAAATATATCCTAACCGCATGATTTCTAGTTCGCATGCTTTG
Found at i:93218 original size:82 final size:83
Alignment explanation
Indices: 93027--93263 Score: 316
Period size: 82 Copynumber: 2.9 Consensus size: 83
93017 GGATTACTCC
* * * * *
93027 ACTACTCTTCTGTGAAGATTTCATACTTTTCTGAAAAATCCGTTCCACTATTCTTTCGTGGA-GT
1 ACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTTCACTACTCTTTCGTGGAGGC
* * *
93091 TCAGATTTGCTCTTGCTTC
66 TGA-ATTTGCTCTTACTTA
* * *
93110 ACTACTCTTCCGTGAAGATTTTATACTTTGCTGAAAAATCCATTTCACTACTC-TTCGTTGAGGC
1 ACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTTCACTACTCTTTCGTGGAGGC
* *
93174 TGAATTTGTTTTTACTTA
66 TGAATTTGCTCTTACTTA
* *
93192 ACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTTAACTACTCTTTCGTGGAGAC
1 ACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTTCACTACTCTTTCGTGGAGGC
93257 TGAATTT
66 TGAATTT
93264 TGATTTTGCT
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
82 68 0.51
83 66 0.49
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (83 bp):
ACTACTCTTCCGTGAAGATTTCATACTTTGCTGAAAAATCCGTTTCACTACTCTTTCGTGGAGGC
TGAATTTGCTCTTACTTA
Found at i:93836 original size:22 final size:22
Alignment explanation
Indices: 93798--93842 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
93788 AAGCTTTTGT
* *
93798 TCTTTGAAAATATAATCGATCA
1 TCTTTGAAAAGAGAATCGATCA
*
93820 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCGATCA
93842 T
1 T
93843 TCTTGCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCGATCA
Found at i:103640 original size:26 final size:26
Alignment explanation
Indices: 103604--103656 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
103594 ATAAATGAGA
*
103604 AGATTACAATTTTATTAGATCTATCG
1 AGATTACAATTTTATTAGATCCATCG
* *
103630 AGATTATAATTTTTTTAGATCCATCG
1 AGATTACAATTTTATTAGATCCATCG
103656 A
1 A
103657 TGTCTCTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (26 bp):
AGATTACAATTTTATTAGATCCATCG
Found at i:105860 original size:16 final size:17
Alignment explanation
Indices: 105817--105861 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
105807 CCATTTTTTA
105817 ATTACAATT-AATAAAT
1 ATTACAATTAAATAAAT
*
105833 ATT--AACTAAATAAAT
1 ATTACAATTAAATAAAT
105848 -TTACAATTAAATAA
1 ATTACAATTAAATAA
105862 TCAAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 12 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTACAATTAAATAAAT
Found at i:107364 original size:21 final size:21
Alignment explanation
Indices: 107322--107364 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
107312 TTTTTGGGCT
* * *
107322 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
107343 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
107364 A
1 A
107365 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:107416 original size:20 final size:20
Alignment explanation
Indices: 107391--107428 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
107381 GAATGCTAGA
107391 GGGGAACCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
107411 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
107429 TGAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:108098 original size:149 final size:149
Alignment explanation
Indices: 107905--108208 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
107895 GGGTAGAGGG
* *
107905 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
107970 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
108035 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
108054 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
108119 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
108184 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
108203 TCTACG
1 TCTACG
108209 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:108231 original size:23 final size:23
Alignment explanation
Indices: 108187--108231 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
108177 ATCATTATAT
*
108187 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
108210 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
108232 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:114305 original size:21 final size:21
Alignment explanation
Indices: 114263--114305 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
114253 TTTTCGGGCT
* * *
114263 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
114284 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
114305 A
1 A
114306 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:114357 original size:20 final size:20
Alignment explanation
Indices: 114332--114369 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
114322 GAATGCTAGA
114332 GGGGAACCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
114352 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
114370 TGAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:115143 original size:148 final size:149
Alignment explanation
Indices: 114845--115147 Score: 572
Period size: 148 Copynumber: 2.0 Consensus size: 149
114835 GGGTAGAGGG
* *
114845 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
114910 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
114975 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
114994 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
115059 ACTTGATCCATAG-ATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
115123 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
115142 TCTACG
1 TCTACG
115148 GGGCACTTCG
Statistics
Matches: 151, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
148 76 0.50
149 75 0.50
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:115170 original size:23 final size:23
Alignment explanation
Indices: 115126--115170 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
115116 ATCATTATAT
*
115126 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
115149 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
115171 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:116580 original size:44 final size:44
Alignment explanation
Indices: 116525--116610 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
116515 CAGCTCGTAA
* *
116525 TTTACACCGAAGTGCCACATAATTT-T-CCTAATGGACCACATAGG
1 TTTACAACGAAGTGCCACAT-ATTTGTCCCGAA-GGACCACATAGG
116569 TTTACAACGAAGTGCCACATATTTGTCCCGAAGGACCACATA
1 TTTACAACGAAGTGCCACATATTTGTCCCGAAGGACCACATA
116611 ATTATCCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 4 0.11
44 30 0.79
45 4 0.11
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (44 bp):
TTTACAACGAAGTGCCACATATTTGTCCCGAAGGACCACATAGG
Found at i:116607 original size:21 final size:21
Alignment explanation
Indices: 116583--116675 Score: 91
Period size: 21 Copynumber: 4.3 Consensus size: 21
116573 CAACGAAGTG
*
116583 CCACATATTTGTCCCGAAGGA
1 CCACATATTTATCCCGAAGGA
* *
116604 CCACATAATTATCCCGAATGA
1 CCACATATTTATCCCGAAGGA
*
116625 CCACATAGGTTT-GCACCGAAGTG-
1 CCACATA--TTTATC-CCGAAG-GA
*
116648 CCACATATTTATCCCGAAAGA
1 CCACATATTTATCCCGAAGGA
116669 CCACATA
1 CCACATA
116676 AAACCCTCGA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 40 0.69
22 2 0.03
23 14 0.24
24 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.23
Consensus pattern (21 bp):
CCACATATTTATCCCGAAGGA
Found at i:116635 original size:65 final size:65
Alignment explanation
Indices: 116531--116676 Score: 206
Period size: 65 Copynumber: 2.2 Consensus size: 65
116521 GTAATTTACA
* * *
116531 CCGAAGTG-CCACATAATTTTCCTAATGGACCACATAGGTTTACAACGAAGTGCCACATATTTGT
1 CCGAAG-GACCACATAATTTCCCGAATGGACCACATAGGTTTACAACGAAGTGCCACATATTTAT
116595 C
65 C
* *
116596 CCGAAGGACCACATAATTATCCCGAAT-GACCACATAGGTTTGCACCGAAGTGCCACATATTTAT
1 CCGAAGGACCACATAATT-TCCCGAATGGACCACATAGGTTTACAACGAAGTGCCACATATTTAT
116660 C
65 C
*
116661 CCGAAAGACCACATAA
1 CCGAAGGACCACATAA
116677 AACCCTCGAC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.01
65 66 0.90
66 6 0.08
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (65 bp):
CCGAAGGACCACATAATTTCCCGAATGGACCACATAGGTTTACAACGAAGTGCCACATATTTATC
Found at i:122386 original size:44 final size:44
Alignment explanation
Indices: 122333--122418 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
122323 CATCTCATAA
* * *
122333 TTTGCACCGAAGTTCCATATAATTGTCCTGAAGGACCACATAGG
1 TTTGCACCGAAGTTCCACATAATTATCCCGAAGGACCACATAGG
*
122377 TTTGCACCGAAGTTCCACATATTTATCCCGAAGGACCACATA
1 TTTGCACCGAAGTTCCACATAATTATCCCGAAGGACCACATA
122419 ATTGTCCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
TTTGCACCGAAGTTCCACATAATTATCCCGAAGGACCACATAGG
Found at i:122409 original size:21 final size:21
Alignment explanation
Indices: 122355--122483 Score: 111
Period size: 21 Copynumber: 6.0 Consensus size: 21
122345 TTCCATATAA
*
122355 TTGTCCTGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATA--T
**
122378 TTG-CACCGAAGTTCCACATAT
1 TTGTC-CCGAAGGACCACATAT
* *
122399 TTATCCCGAAGGACCACATAA
1 TTGTCCCGAAGGACCACATAT
122420 TTGTCCCGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATA--T
*
122443 TT-TCACCAAAGTG-CCACATAT
1 TTGTC-CCGAAG-GACCACATAT
*
122464 TTGTCCCGAAGAACCACATA
1 TTGTCCCGAAGGACCACATA
122484 AAACCCTCGA
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
21 50 0.58
22 6 0.07
23 29 0.34
24 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACATAT
Found at i:122443 original size:65 final size:65
Alignment explanation
Indices: 122351--122484 Score: 214
Period size: 65 Copynumber: 2.1 Consensus size: 65
122341 GAAGTTCCAT
* * * *
122351 ATAATTGTCCTGAAGGACCACATAGGTTTGCACCGAAGTTCCACATATTTATCCCGAAGGACCAC
1 ATAATTGTCCCGAAGGACCACATAGGTTTGCACCAAAGTGCCACATATTTATCCCGAAGAACCAC
* *
122416 ATAATTGTCCCGAAGGACCACATAGGTTTTCACCAAAGTGCCACATATTTGTCCCGAAGAACCAC
1 ATAATTGTCCCGAAGGACCACATAGGTTTGCACCAAAGTGCCACATATTTATCCCGAAGAACCAC
122481 ATAA
1 ATAA
122485 AACCCTCGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (65 bp):
ATAATTGTCCCGAAGGACCACATAGGTTTGCACCAAAGTGCCACATATTTATCCCGAAGAACCAC
Found at i:123430 original size:22 final size:22
Alignment explanation
Indices: 123402--123455 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
123392 TACCCTGATG
123402 GTATCGATACCTCTATCAACAA
1 GTATCGATACCTCTATCAACAA
123424 GTATCGATACCTCTATCAACAA
1 GTATCGATACCTCTATCAACAA
123446 GTATCGATAC
1 GTATCGATAC
123456 AACCCTCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (22 bp):
GTATCGATACCTCTATCAACAA
Found at i:128147 original size:22 final size:22
Alignment explanation
Indices: 128089--128149 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
128079 CATATAATAT
128089 TATATATATATATATTTAAAAAAC
1 TATATA-ATAT-TATTTAAAAAAC
* * **
128113 TAAAT-ATACTATTTTTAAAAC
1 TATATAATATTATTTAAAAAAC
128134 TATATAATATTATTTA
1 TATATAATATTATTTA
128150 TTATTTTCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.48
22 11 0.38
24 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATAATATTATTTAAAAAAC
Found at i:128931 original size:132 final size:132
Alignment explanation
Indices: 128548--128966 Score: 481
Period size: 132 Copynumber: 3.2 Consensus size: 132
128538 TTAGATTTGG
* *
128548 AAAATTTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCGGGGTAG--TTGTTCCACTGCT
1 AAAATTTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCAGGGTAGATTTGCTCCACTGCT
* * * ** *
128611 TTTTAGGGAAGATCAAATCTGGGAAAAA-AGATATGCTCGACTGCTCTTCAGGGAAGATCAGATC
66 CTTAAGGGAAGATCAAATCT-GGAAAAAGAGATATGCTCTACTTTTCTTCAGGGAATATCAGATC
128675 TAA
130 TAA
* * * * *
128678 AAAATTTTGATTCACTCCACTATTCTTCAGGGATGATTAAATAAGGGTAGATTTGGTCCACTGCT
1 AAAATTTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCAGGGTAGATTTGCTCCACTGCT
** * *
128743 CTTAAAAGAAGATCAAATCTGGAAAAAGAGATATGCTCT-GTTGTTCTTCAGAGAATATCAGATC
66 CTTAAGGGAAGATCAAATCTGGAAAAAGAGATATGCTCTACTT-TTCTTCAGGGAATATCAGATC
128807 TAA
130 TAA
* * ** *
128810 AAAATTTTGATTCATTCCACTGCTCTTCAGAAAAGATTGAATCAGGCTAGATTTGCTCCACTGCT
1 AAAATTTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCAGGGTAGATTTGCTCCACTGCT
* * * * * * * *
128875 CTTCAGGGAAGATCAAATATGAAAAAAGAGATGTGCTATACTTTTATGCAGGGAATATCAAATC-
66 CTTAAGGGAAGATCAAATCTGGAAAAAGAGATATGCTCTACTTTTCTTCAGGGAATATCAGATCT
128939 AA
131 AA
* **
128941 AAAA-CTTGATTCACTTTACTACTCTT
1 AAAATTTTGATTCACTCCACTACTCTT
128967 TAGCAAAGAT
Statistics
Matches: 241, Mismatches: 43, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
130 62 0.26
131 14 0.06
132 163 0.68
133 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (132 bp):
AAAATTTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCAGGGTAGATTTGCTCCACTGCT
CTTAAGGGAAGATCAAATCTGGAAAAAGAGATATGCTCTACTTTTCTTCAGGGAATATCAGATCT
AA
Found at i:130511 original size:27 final size:26
Alignment explanation
Indices: 130472--130551 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
130462 ATCTTGAACC
*
130472 TCCTTTTTATTTTAGTTTTCTTTTTTTT
1 TCCTTCTT-TTTTA-TTTTCTTTTTTTT
*
130500 TCCTTCTTTTTTATTTTTTTTATTTTT
1 TCCTTCTTTTTTATTTTCTTT-TTTTT
* *
130527 TTC-TCTTTTTATATTTTCTTCTTTT
1 TCCTTCTTTTT-TATTTTCTTTTTTT
130552 CCTTCAGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.40
27 20 0.44
28 7 0.16
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.79
Consensus pattern (26 bp):
TCCTTCTTTTTTATTTTCTTTTTTTT
Found at i:130535 original size:18 final size:18
Alignment explanation
Indices: 130514--130548 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
130504 TCTTTTTTAT
* *
130514 TTTTTTTATTTTTTTCTC
1 TTTTTATATTTTCTTCTC
130532 TTTTTATATTTTCTTCT
1 TTTTTATATTTTCTTCT
130549 TTTCCTTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTATATTTTCTTCTC
Found at i:130549 original size:16 final size:14
Alignment explanation
Indices: 130489--130551 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
130479 TATTTTAGTT
*
130489 TTCTTTTTTTTTCC
1 TTCTTTTTTTTTTC
130503 TTCTTTTTTATTTT-
1 TTCTTTTTT-TTTTC
*
130517 TT-TTATTTTTTTC
1 TTCTTTTTTTTTTC
130530 -TCTTTTTATATTTTC
1 TTCTTTTT-T-TTTTC
130545 TTCTTTT
1 TTCTTTT
130552 CCTTCAGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 5 0.12
13 9 0.22
14 12 0.30
15 8 0.20
16 6 0.15
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTTTTTTTC
Found at i:136439 original size:29 final size:29
Alignment explanation
Indices: 136419--136477 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
136409 TATTTTCAAC
136419 TACTATA-TATTTTCAAAACTATATATATA
1 TACTATATTATTTTC-AAACTATATATATA
*
136448 TACTATATTATTTTCAAACTATATTTATA
1 TACTATATTATTTTCAAACTATATATATA
136477 T
1 T
136478 TATTTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (29 bp):
TACTATATTATTTTCAAACTATATATATA
Found at i:136441 original size:16 final size:17
Alignment explanation
Indices: 136409--136444 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
136399 ATATATTTAC
*
136409 TATTTTCAACTACTATA
1 TATTTTCAACAACTATA
136426 TATTTTCAA-AACTATA
1 TATTTTCAACAACTATA
136442 TAT
1 TAT
136445 ATATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTCAACAACTATA
Found at i:136462 original size:47 final size:50
Alignment explanation
Indices: 136381--136508 Score: 149
Period size: 45 Copynumber: 2.6 Consensus size: 50
136371 AAAAATAGAC
* * *
136381 TATTTTAAAAACTATATA-ATATATTTACTATTTTC-AAC-TA-CTATA-
1 TATTTTCAAAACTATATATATATATATATTATTTTCAAACATATCTATAT
*
136426 TATTTTCAAAACTATATATATATACTATATTATTTTCAAACTATATTTATAT
1 TATTTTCAAAACTATATATATATA-TATATTATTTTCAAAC-ATATCTATAT
136478 TATTTTCAAAAACTATATAATATATATATAT
1 TATTTTC-AAAACTATAT-ATATATATATAT
136509 ATATATATAT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
45 17 0.24
46 5 0.07
47 10 0.14
48 3 0.04
50 2 0.03
51 4 0.06
52 7 0.10
53 15 0.21
54 7 0.10
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (50 bp):
TATTTTCAAAACTATATATATATATATATTATTTTCAAACATATCTATAT
Found at i:136470 original size:16 final size:16
Alignment explanation
Indices: 136409--136472 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
136399 ATATATTTAC
136409 TATTTTC-AACTACTAT
1 TATTTTCAAACTA-TAT
136425 ATATTTTCAAAACTATA-
1 -TATTTTC-AAACTATAT
* *
136442 TA-TAT-ATACTATAT
1 TATTTTCAAACTATAT
136456 TATTTTCAAACTATAT
1 TATTTTCAAACTATAT
136472 T
1 T
136473 TATATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
13 7 0.18
14 2 0.05
15 4 0.11
16 11 0.29
17 7 0.18
18 2 0.05
19 5 0.13
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTTCAAACTATAT
Found at i:136518 original size:47 final size:47
Alignment explanation
Indices: 136381--136524 Score: 113
Period size: 45 Copynumber: 3.0 Consensus size: 47
136371 AAAAATAGAC
* * *
136381 TATTTT-AAAAACTATATAATATATTTACTATTTTCA-ACTA-CTATA-
1 TATTTTCAAAAACTATATAATATATATACTATTAT-ATA-TATTTATAT
* *
136426 TATTTTC-AAAACTATATATATATACTATATTATTTTCAAACTATATTTATAT
1 TATTTTCAAAAACTATATA-ATATA-TATACTA--TT-ATA-TATATTTATAT
136478 TATTTTCAAAAACTATATAATATATATA-TATATATATATATTT-TAT
1 TATTTTCAAAAACTATATAATATATATACTAT-TATATATATTTATAT
136524 T
1 T
136525 TATGACTCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
45 17 0.21
46 9 0.11
47 12 0.15
48 3 0.04
49 4 0.05
50 4 0.05
51 9 0.11
52 12 0.15
53 11 0.14
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.49
Consensus pattern (47 bp):
TATTTTCAAAAACTATATAATATATATACTATTATATATATTTATAT
Found at i:136916 original size:110 final size:110
Alignment explanation
Indices: 136723--136943 Score: 424
Period size: 110 Copynumber: 2.0 Consensus size: 110
136713 GCAAAACATA
*
136723 AATATTTGCCGTCATTGGAAAAATGACGATAGTTTAAGACAAAAATATATATAATATATTAATAT
1 AATATTTGCCGTCATTGGAAAAATGACGATAGTTTAAGACAAAAAAATATATAATATATTAATAT
136788 CATTATTATTATTGTAATAATTTTGAAAATTATGGATTTGAAATG
66 CATTATTATTATTGTAATAATTTTGAAAATTATGGATTTGAAATG
*
136833 AATATTTGTCGTCATTGGAAAAATGACGATAGTTTAAGACAAAAAAATATATAATATATTAATAT
1 AATATTTGCCGTCATTGGAAAAATGACGATAGTTTAAGACAAAAAAATATATAATATATTAATAT
136898 CATTATTATTATTGTAATAATTTTGAAAATTATGGATTTGAAATG
66 CATTATTATTATTGTAATAATTTTGAAAATTATGGATTTGAAATG
136943 A
1 A
136944 TTGATTTATC
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (110 bp):
AATATTTGCCGTCATTGGAAAAATGACGATAGTTTAAGACAAAAAAATATATAATATATTAATAT
CATTATTATTATTGTAATAATTTTGAAAATTATGGATTTGAAATG
Found at i:138138 original size:16 final size:18
Alignment explanation
Indices: 138100--138139 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
138090 AAGTATTTAC
*
138100 TATTTAAATTTTAAATGA
1 TATTTAAATTTAAAATGA
138118 T-TTTAAA-TTAAAAT-A
1 TATTTAAATTTAAAATGA
138133 TATTTAA
1 TATTTAA
138140 TTCTAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 2 0.10
16 11 0.55
17 6 0.30
18 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTAAATTTAAAATGA
Found at i:138644 original size:38 final size:38
Alignment explanation
Indices: 138593--138681 Score: 178
Period size: 38 Copynumber: 2.3 Consensus size: 38
138583 TTTATTTATT
138593 TTTTGCTTAAATATTACTAATAAAAGAACCCAGTCCTG
1 TTTTGCTTAAATATTACTAATAAAAGAACCCAGTCCTG
138631 TTTTGCTTAAATATTACTAATAAAAGAACCCAGTCCTG
1 TTTTGCTTAAATATTACTAATAAAAGAACCCAGTCCTG
138669 TTTTGCTTAAATA
1 TTTTGCTTAAATA
138682 GATATTAAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (38 bp):
TTTTGCTTAAATATTACTAATAAAAGAACCCAGTCCTG
Found at i:148266 original size:15 final size:15
Alignment explanation
Indices: 148217--148266 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
148207 TCAAAATTTA
148217 AATATATGTTACTT-G
1 AATATATGTTA-TTCG
* *
148232 AAAATATATTATTC-
1 AATATATGTTATTCG
148246 AGATATATGTTATTCG
1 A-ATATATGTTATTCG
148262 AATAT
1 AATAT
148267 GTATGTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 3 0.11
15 24 0.86
16 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (15 bp):
AATATATGTTATTCG
Found at i:152306 original size:16 final size:16
Alignment explanation
Indices: 152285--152318 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
152275 CTAAACCTAG
152285 CCTCTATCACCCTTTC
1 CCTCTATCACCCTTTC
152301 CCTCTATCACCCTTTC
1 CCTCTATCACCCTTTC
152317 CC
1 CC
152319 ATAGCTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (16 bp):
CCTCTATCACCCTTTC
Found at i:153403 original size:19 final size:19
Alignment explanation
Indices: 153379--153417 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
153369 TCGAATGCAT
153379 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
153398 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
153417 T
1 T
153418 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:153545 original size:64 final size:64
Alignment explanation
Indices: 153365--153527 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
153355 GAATTAATTG
* * * *
153365 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
153430 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
153494 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
153528 TGGTGCACCA
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:156059 original size:20 final size:20
Alignment explanation
Indices: 155991--156066 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
155981 GATCTAGACG
* *
155991 ACCTGAACCGGTCCGAGTCA
1 ACCTGAACCGATCTGAGTCA
* * * *
156011 A-CTCGGACTGAACTGAATCA
1 ACCT-GAACCGATCTGAGTCA
**
156031 ACCCAAACCGATCTGAGTCA
1 ACCTGAACCGATCTGAGTCA
*
156051 ACCTGAACCGGTCTGA
1 ACCTGAACCGATCTGA
156067 CCCATTGACT
Statistics
Matches: 39, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (20 bp):
ACCTGAACCGATCTGAGTCA
Found at i:156137 original size:19 final size:19
Alignment explanation
Indices: 156065--156137 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
156055 GAACCGGTCT
156065 GACCCATTGACTTTGAAC-C
1 GACCCATTGACTTTG-ACTC
* * *
156084 GACCCGTTGAC-TTAAATC
1 GACCCATTGACTTTGACTC
* *
156102 GACCCATTAACTTTGACTT
1 GACCCATTGACTTTGACTC
*
156121 GACCCGTTGACTTTGAC
1 GACCCATTGACTTTGAC
156138 CAAAAAGTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
17 1 0.02
18 12 0.29
19 29 0.69
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (19 bp):
GACCCATTGACTTTGACTC
Found at i:167146 original size:2 final size:2
Alignment explanation
Indices: 167139--167182 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
167129 TTATACCTAT
167139 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
167181 TA
1 TA
167183 CACCAATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:169227 original size:114 final size:106
Alignment explanation
Indices: 169072--169305 Score: 240
Period size: 114 Copynumber: 2.1 Consensus size: 106
169062 GAATTCTCTT
* * *
169072 ATTATGAACTCTCCACTGGAAATGTTGATTCACCTCTTTCTGTGATGGAA-TCAAACCAGGTTGA
1 ATTATGAACTCT-CACTGGAAATATTGATTCACCCCCTTCTGTGAT-GAATTCAAA--A-G--GA
* *
169136 ACAAGTTCTTCTAATTATGAACTTCTTCTTCCTCATT-GGATGAGTTTTTCTC
59 ACAAGTTCTTCTAATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTC
* * * **
169188 ATTATGAACTCT-TCTGGAAATATTGGTTCACCCCCTTCTGTGGTGAATTTGAAAGGAACAAGTT
1 ATTATGAACTCTCACTGGAAATATTGATTCACCCCCTTCTGTGATGAATTCAAAAGGAACAAGTT
*
169252 CTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTC
66 CTTCTAATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTC
169293 ATTATGAACTCTC
1 ATTATGAACTCTC
169306 CATTAGAAAT
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
104 2 0.02
105 25 0.24
106 4 0.04
107 3 0.03
108 1 0.01
109 23 0.22
111 1 0.01
112 1 0.01
113 3 0.03
114 29 0.28
116 12 0.12
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (106 bp):
ATTATGAACTCTCACTGGAAATATTGATTCACCCCCTTCTGTGATGAATTCAAAAGGAACAAGTT
CTTCTAATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTC
Found at i:169477 original size:131 final size:133
Alignment explanation
Indices: 169243--169715 Score: 622
Period size: 131 Copynumber: 3.6 Consensus size: 133
169233 AATTTGAAAG
* * *
169243 GAACAAGTTCTTCTCATTATGAAC-TTTCTCCT-TTAGGACGAGTTCTTCTCATTATGAACTCTC
1 GAACAAGATCTTCTCATTATGAACTTTTCTCCTCTTCGGATGAGTTCTTCTCATTATGAACTCTC
* * ** * *
169306 CATTAGAAATTTCAATCCCTCAAGCGAGGCATCCCTGATTCGAAATGCCATGAATCGAGTGATAG
66 CATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAG
169371 GTC
131 GTC
*
169374 GAAC-AGATCTTCTCATTATGAACTTATTCT-CTCTTTGGATG-GTTCTTCTCATTATGAACTCT
1 GAACAAGATCTTCTCATTATGAACTT-TTCTCCTCTTCGGATGAGTTCTTCTCATTATGAACTCT
* * * **
169436 CCATTGGAAATGTCAATCCCTCAAGTGAGGTGTCATTGATTCAAAATGTTGTGAATCGAGTGATA
65 CCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATA
169501 GGTC
130 GGTC
* *
169505 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAG---TTCTCATTATAAACT
1 GAACAAGATCTTCTCATTATGAACTT-TTCT-CCTCT-TCGGATGAGTTCTTCTCATTATGAACT
* ** * * *
169567 CTTCATTGGAAATGTTGATCCCTCAAGCGAGGTGTCGCTGATTTGAAATGCCGTGAATCAAGTGA
63 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGA
169632 T-GGTC
128 TAGGTC
169637 GAACAAGATCTTCTCATTATGAACTTTTTCTCCCTCTTCGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGATCTTCTCATTATGAAC-TTTTCT-CCTCTTCGGATGAGTTCTTCTCATTATGAACTC
169702 TCCATTGGAAATGT
64 TCCATTGGAAATGT
169716 TGATCC
Statistics
Matches: 298, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
130 18 0.06
131 99 0.33
132 71 0.24
133 71 0.24
134 32 0.11
135 6 0.02
136 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (133 bp):
GAACAAGATCTTCTCATTATGAACTTTTCTCCTCTTCGGATGAGTTCTTCTCATTATGAACTCTC
CATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAG
GTC
Done.