Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014026.1 Kokia drynarioides strain JFW-HI SEQ_129057, 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: 272674
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 268 characters in sequence are not A, C, G, or T
Found at i:2003 original size:14 final size:13
Alignment explanation
Indices: 1981--2022 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
1971 TAAAATTGAA
1981 TTTTAATTTTAATT
1 TTTTAATTTT-ATT
*
1995 TTTTTATTTTATT
1 TTTTAATTTTATT
*
2008 TTTTGA-TTTATT
1 TTTTAATTTTATT
2020 TTT
1 TTT
2023 GGGTTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 9 0.35
13 8 0.31
14 9 0.35
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:7923 original size:101 final size:101
Alignment explanation
Indices: 7818--7999 Score: 229
Period size: 101 Copynumber: 1.8 Consensus size: 101
7808 TTAAAGCTAC
* * * * *
7818 GAAAGCGAATCCTTATTTCTCTGAAGTTACAGTAGAGCAGGATGAAGCTACAAAACCAAATCCTA
1 GAAAGCAAATCCTTATCTCCCTGAAGTTACAGTAGAACAAGATGAAGCTACAAAACCAAATCCTA
*
7883 TACCCCCAAAGTTGCAATGGGTCAGTTTAAAATCAT
66 TACCCCCAAAATTGCAATGGGTCAGTTTAAAATCAT
* * ** * * *
7919 GAAAGTAAATCTTTATCTCCCTGAAGTTGTAGTGGAACAAGATGAAGCTACAACATCAAATCCTA
1 GAAAGCAAATCCTTATCTCCCTGAAGTTACAGTAGAACAAGATGAAGCTACAAAACCAAATCCTA
* *
7984 TATCCCTAAAATTGCA
66 TACCCCCAAAATTGCA
8000 GTGGATTGGA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
101 66 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (101 bp):
GAAAGCAAATCCTTATCTCCCTGAAGTTACAGTAGAACAAGATGAAGCTACAAAACCAAATCCTA
TACCCCCAAAATTGCAATGGGTCAGTTTAAAATCAT
Found at i:8344 original size:17 final size:17
Alignment explanation
Indices: 8325--8361 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
8315 ATTATTTTAT
8325 AAATATAAATAAAATATA
1 AAATA-AAATAAAATATA
*
8343 AAATAAAATAAAATTTA
1 AAATAAAATAAAATATA
8360 AA
1 AA
8362 CCCAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAATAAAATATA
Found at i:10269 original size:25 final size:25
Alignment explanation
Indices: 10241--10290 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10231 AAAAATCTTA
10241 CAAGGTGATCCAATTACACCTATTT
1 CAAGGTGATCCAATTACACCTATTT
10266 CAAGGTGATCCAATTACACCTATTT
1 CAAGGTGATCCAATTACACCTATTT
10291 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (25 bp):
CAAGGTGATCCAATTACACCTATTT
Found at i:10607 original size:9 final size:9
Alignment explanation
Indices: 10593--10677 Score: 58
Period size: 9 Copynumber: 11.2 Consensus size: 9
10583 ATTTCAAAAA
10593 AATAATTTT
1 AATAATTTT
10602 AATAATTTT
1 AATAATTTT
10611 -AT-ATTTT
1 AATAATTTT
10618 AA-AA----
1 AATAATTTT
10622 AATAATTTT
1 AATAATTTT
10631 AATAATTTT
1 AATAATTTT
10640 -AT-ATTTT
1 AATAATTTT
10647 AA-AA----
1 AATAATTTT
10651 AATAATTTT
1 AATAATTTT
10660 AATAATTTT
1 AATAATTTT
10669 -AT-ATTTT
1 AATAATTTT
10676 AA
1 AA
10678 AAAATAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 31
0.66 0.00 0.34
Matches are distributed among these distances:
4 4 0.07
5 4 0.07
7 15 0.25
8 11 0.18
9 27 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATAATTTT
Found at i:10631 original size:29 final size:29
Alignment explanation
Indices: 10568--10728 Score: 268
Period size: 29 Copynumber: 5.4 Consensus size: 29
10558 ATTAAACTTA
*
10568 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTT-TAAAAAATAAT
10599 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
10628 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
10657 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAATAAT
* *
10686 TTTAAAAAGTTTATATTTTTAAAAAATAAT
1 TTTAATAATTTTATA-TTTTAAAAAATAAT
10716 TTTAATAATTTTA
1 TTTAATAATTTTA
10729 AAATCATTTG
Statistics
Matches: 124, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
29 81 0.65
30 30 0.24
31 13 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:13092 original size:292 final size:292
Alignment explanation
Indices: 12568--13158 Score: 1038
Period size: 292 Copynumber: 2.0 Consensus size: 292
12558 AATTTGTCAC
*
12568 TAGTTTCGCCATTAATACCCACCGTGTAAGAGTCTGAAGATACGTATCGATGGTCATGAAATCTC
1 TAGTTTCGCCATTAATACCCACCGTGTAAGAGACTGAAGATACGTATCGATGGTCATGAAATCTC
*
12633 AAATTTTCCATCGTTCCACTTATAAAACCCCACTCCACCGTATCATACGCTTTGCTCATATTGAG
66 AAATTTTCCATCGTTCCACTTATAAAACCCCACTCCACCGCATCATACGCTTTGCTCATATTGAG
12698 CTTAAGCGCAAAAGTACCCAACGATCTCGAACGCTTCATCTTCAACAAACGCAAGACTTCATATG
131 CTTAAGCGCAAAAGTACCCAACGATCTCGAACGCTTCATCTTCAACAAACGCAAGACTTCATATG
12763 CAATTAACACATTATCTAATATTTGCCTACCAGGGATGAAAGCTCCTTGGGCCTCATCAATGTAG
196 CAATTAACACATTATCTAATATTTGCCTACCAGGGATGAAAGCTCCTTGGGCCTCATCAATGTAG
*
12828 CTATATAAGAAACCCTTCATTCTACAAACTAA
261 CTATATAAGAAACCCCTCATTCTACAAACTAA
*
12860 TAGTTTCGCCATTAATACCCACCGTGTAAGAGACTGAAGATACGTATCGCTGGTCATGAAATCTC
1 TAGTTTCGCCATTAATACCCACCGTGTAAGAGACTGAAGATACGTATCGATGGTCATGAAATCTC
* * *
12925 AATTTTTCCATCGTTCCACTTATAAAACCTCACTCCACCGCATCATATGCTTTGCTCATATTGAG
66 AAATTTTCCATCGTTCCACTTATAAAACCCCACTCCACCGCATCATACGCTTTGCTCATATTGAG
* * *
12990 CTTAAGCGCAAAAGTACCTAACGATCTCGAACGCTTCATCTTTAACAAATGCAAGACTTCATATG
131 CTTAAGCGCAAAAGTACCCAACGATCTCGAACGCTTCATCTTCAACAAACGCAAGACTTCATATG
* * * *
13055 CAATTAACACATTATGTGATATTTTCCTATCAGGGATGAAAGCTCCTTGGGCCTCATCAATGTAG
196 CAATTAACACATTATCTAATATTTGCCTACCAGGGATGAAAGCTCCTTGGGCCTCATCAATGTAG
*
13120 CTATATAAGACACCCCTCATTCTACAAACTAA
261 CTATATAAGAAACCCCTCATTCTACAAACTAA
*
13152 TATTTTC
1 TAGTTTC
13159 ACAATAATTT
Statistics
Matches: 283, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
292 283 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (292 bp):
TAGTTTCGCCATTAATACCCACCGTGTAAGAGACTGAAGATACGTATCGATGGTCATGAAATCTC
AAATTTTCCATCGTTCCACTTATAAAACCCCACTCCACCGCATCATACGCTTTGCTCATATTGAG
CTTAAGCGCAAAAGTACCCAACGATCTCGAACGCTTCATCTTCAACAAACGCAAGACTTCATATG
CAATTAACACATTATCTAATATTTGCCTACCAGGGATGAAAGCTCCTTGGGCCTCATCAATGTAG
CTATATAAGAAACCCCTCATTCTACAAACTAA
Found at i:14216 original size:2 final size:2
Alignment explanation
Indices: 14209--14242 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14199 CAACTCCTTT
14209 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
14243 AGGAATAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17639 original size:21 final size:20
Alignment explanation
Indices: 17613--17651 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17603 ATGATTCAAT
*
17613 ATATATAATTTATTATTTAAC
1 ATATATAATTAATT-TTTAAC
17634 ATATATAATTAATTTTTA
1 ATATATAATTAATTTTTA
17652 TAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATAATTAATTTTTAAC
Found at i:21630 original size:3 final size:3
Alignment explanation
Indices: 21622--21650 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21612 ATAACATTGA
21622 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
21651 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:25157 original size:16 final size:17
Alignment explanation
Indices: 25136--25168 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
25126 GGTCTTATTT
25136 AATAAATC-ATTAAAAA
1 AATAAATCAATTAAAAA
25152 AATAAATCAATTAAAAA
1 AATAAATCAATTAAAAA
25169 TTAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAATCAATTAAAAA
Found at i:25722 original size:14 final size:14
Alignment explanation
Indices: 25699--25728 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25689 TAATTTTTAC
*
25699 TAAATTTTTATTTT
1 TAAATATTTATTTT
25713 TAAATATTTATTTT
1 TAAATATTTATTTT
25727 TA
1 TA
25729 TATTTGTATA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TAAATATTTATTTT
Found at i:25739 original size:20 final size:20
Alignment explanation
Indices: 25702--25745 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
25692 TTTTTACTAA
* *
25702 ATTTTTATTTTTAAATATTT
1 ATTTTTATATTTAAATATAT
**
25722 ATTTTTATATTTGTATATAT
1 ATTTTTATATTTAAATATAT
25742 ATTT
1 ATTT
25746 ATAAATATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
ATTTTTATATTTAAATATAT
Found at i:31839 original size:30 final size:32
Alignment explanation
Indices: 31792--31851 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 32
31782 AAAGGTTAAT
*
31792 AACCAAATTTAATAAAAATA-ATA-ATAAAAA
1 AACCAAATTGAATAAAAATATATATATAAAAA
31822 AACCAAATTGACA-AAAAATATATATATAAA
1 AACCAAATTGA-ATAAAAATATATATATAAA
31852 TATTAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 17 0.65
31 4 0.15
32 5 0.19
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (32 bp):
AACCAAATTGAATAAAAATATATATATAAAAA
Found at i:37414 original size:15 final size:13
Alignment explanation
Indices: 37381--37438 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
37371 TTAAAAAATA
37381 TATTTATATTATAT
1 TATTT-TATTATAT
37395 TATTTTATTATAAT
1 TATTTTATTAT-AT
37409 TAATTTTA-TATA-
1 T-ATTTTATTATAT
37421 T-TTTTATT-TAT
1 TATTTTATTATAT
37432 TGATTTT
1 T-ATTTT
37439 TTTTATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
10 7 0.18
11 2 0.05
12 1 0.03
13 11 0.29
14 11 0.29
15 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TATTTTATTATAT
Found at i:41489 original size:72 final size:72
Alignment explanation
Indices: 41395--41541 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 72
41385 TAAAAAATAA
*
41395 ATGAACAAAGAGAAATAAATAAAAGAAAGGTTAAGAGGGCATACCTTGATTCAAAATGTCGCCGC
1 ATGAACAAAGAGAAATAAATAAAAGAAAGGTTAAGAGGGCATACCTTGATTCAAAATGTCGCCAC
41460 CAGAGCC
66 CAGAGCC
* * *
41467 ATGAACAAAGAGAAATAAATAAAAGAAAGGTTAAGAGGGCATACCTTGATTCGAAATGTTGTCAC
1 ATGAACAAAGAGAAATAAATAAAAGAAAGGTTAAGAGGGCATACCTTGATTCAAAATGTCGCCAC
41532 CAGAGCC
66 CAGAGCC
41539 ATG
1 ATG
41542 GACAGAATCC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (72 bp):
ATGAACAAAGAGAAATAAATAAAAGAAAGGTTAAGAGGGCATACCTTGATTCAAAATGTCGCCAC
CAGAGCC
Found at i:53941 original size:18 final size:18
Alignment explanation
Indices: 53918--53953 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53908 CATCTAATAC
53918 TGTTCCTTGTAAATATTT
1 TGTTCCTTGTAAATATTT
53936 TGTTCCTTGTAAATATTT
1 TGTTCCTTGTAAATATTT
53954 GGCAATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:58162 original size:33 final size:33
Alignment explanation
Indices: 58122--58195 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
58112 TTTATTAGGA
* *
58122 GATATTATTAT-TTAGCAATTTGATTTCTAATGG
1 GATATTATT-TCTTAGCAATTTGATTGCTAATAG
*
58155 GATATTATTTCTTAGTAATTTGATTGCTAATAG
1 GATATTATTTCTTAGCAATTTGATTGCTAATAG
58188 GATATTAT
1 GATATTAT
58196 AGGATATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (33 bp):
GATATTATTTCTTAGCAATTTGATTGCTAATAG
Found at i:59629 original size:19 final size:18
Alignment explanation
Indices: 59605--59656 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
59595 TTTGAATTTT
59605 TTTTTTATGTTCTTTTAAC
1 TTTTTTAT-TTCTTTTAAC
**
59624 TTTTTT-TTTCTTTTTTC
1 TTTTTTATTTCTTTTAAC
*
59641 TTTTTCATTTTCTTTT
1 TTTTTTA-TTTCTTTT
59657 GCTTATCCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTATTTCTTTTAAC
Found at i:62781 original size:3 final size:3
Alignment explanation
Indices: 62775--62815 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
62765 AGAAGAAGAA
*
62775 GAC GAC GAA GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
62816 TGATTCAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.34, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:65821 original size:2 final size:2
Alignment explanation
Indices: 65814--65847 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65804 CCATGAGCAC
65814 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65848 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:77735 original size:16 final size:16
Alignment explanation
Indices: 77714--77749 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
77704 TAAAAAATTG
77714 TTATATATTTAATTT-T
1 TTATATATTT-ATTTAT
77730 TTATATATTTATTTAT
1 TTATATATTTATTTAT
77746 TTAT
1 TTAT
77750 TAATTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATATTTATTTAT
Found at i:84187 original size:31 final size:31
Alignment explanation
Indices: 84152--84213 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
84142 CTACCTTCCT
84152 TAGGTTCCACTTCCTCTTTTTTGTTGGTTGC
1 TAGGTTCCACTTCCTCTTTTTTGTTGGTTGC
84183 TAGGTTCCACTTCCTCTTTTTTGTTGGTTGC
1 TAGGTTCCACTTCCTCTTTTTTGTTGGTTGC
84214 GGAGAACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.06, C:0.23, G:0.19, T:0.52
Consensus pattern (31 bp):
TAGGTTCCACTTCCTCTTTTTTGTTGGTTGC
Found at i:85304 original size:269 final size:269
Alignment explanation
Indices: 84825--85338 Score: 852
Period size: 269 Copynumber: 1.9 Consensus size: 269
84815 AACTTAGCTT
* *
84825 GAGCTTTCTTCTCGACATATTGAGGGTAAAACTGCTCCTTGAACTCTTTTTGGATCTCATCGTAA
1 GAGCTTTCTTCTCAACATATTGAGGGTAAAACTGCTCCTTGAACTCTTTTTGGATCTCATCGCAA
*
84890 GTTCCAATTGTGTCTTGACCACGCCATTTATTTTTGGACTGATACTGCCACCATATAAGAGCAAA
66 GTTCCAATTGTGTCTTGACCACGCCATTTATTTTTGGACTGATACTACCACCATATAAGAGCAAA
*
84955 ATTAGTAAAATATCTTGCAATAGTATTTACTTGAGCATCATCATCCTTGATGCCCACAACATGAA
131 ATTAGTAAAATATCTTGCAATAGTATTTACCTGAGCATCATCATCCTTGATGCCCACAACATGAA
*
85020 AGTATTGCTCCATCTCCCACAA-AAGGTTATCCACTTCCTAAATGCTCCTTAACGCATTTATGTC
196 AGTACTGCTCCATCTCCCACAAGAA-GTTATCCACTTCCTAAATGCTCCTTAACGCATTTATGTC
85084 GATGCTCCTC
260 GATGCTCCTC
* * *
85094 GAGCTTTCTTCTCAACATATTGGGGGTAAAATTGCTTCTTGAACTCTTTTTGGATCTCATCGCAA
1 GAGCTTTCTTCTCAACATATTGAGGGTAAAACTGCTCCTTGAACTCTTTTTGGATCTCATCGCAA
* *
85159 GTTCCAATTGTGT-TCTGACCACGCCGTTTATTTTTGGACTGATACTACTACCATATAAGAGCAA
66 GTTCCAATTGTGTCT-TGACCACGCCATTTATTTTTGGACTGATACTACCACCATATAAGAGCAA
* * *
85223 AATTAGTAAAATATCTTGCAATAGTATTTACCTGAGCATCATTATCCTTGATGCCCATAACATGG
130 AATTAGTAAAATATCTTGCAATAGTATTTACCTGAGCATCATCATCCTTGATGCCCACAACATGA
* **
85288 AAGTACTGCTCCATCTCCCACAAGAAGTTGTCCACTTTTTAAATGCTCCTT
195 AAGTACTGCTCCATCTCCCACAAGAAGTTATCCACTTCCTAAATGCTCCTT
85339 GACTCGTGTG
Statistics
Matches: 227, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
268 1 0.00
269 224 0.99
270 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (269 bp):
GAGCTTTCTTCTCAACATATTGAGGGTAAAACTGCTCCTTGAACTCTTTTTGGATCTCATCGCAA
GTTCCAATTGTGTCTTGACCACGCCATTTATTTTTGGACTGATACTACCACCATATAAGAGCAAA
ATTAGTAAAATATCTTGCAATAGTATTTACCTGAGCATCATCATCCTTGATGCCCACAACATGAA
AGTACTGCTCCATCTCCCACAAGAAGTTATCCACTTCCTAAATGCTCCTTAACGCATTTATGTCG
ATGCTCCTC
Found at i:86578 original size:22 final size:22
Alignment explanation
Indices: 86550--86598 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
86540 AACAATGTTA
*
86550 CGACATCTAGGTTTCAGTGTCG
1 CGACATCTAGGTTTCAATGTCG
*
86572 CGACATCTCGGTTTCAATGTCG
1 CGACATCTAGGTTTCAATGTCG
*
86594 TGACA
1 CGACA
86599 CCTTCGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
CGACATCTAGGTTTCAATGTCG
Found at i:95101 original size:38 final size:38
Alignment explanation
Indices: 95059--95135 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
95049 ATAAAATTAT
*
95059 TTCATTAAATAATAAAAATATAAATGTTCGTATTCATG
1 TTCATTAAATAATAAAAATATAAACGTTCGTATTCATG
*
95097 TTCATTAAATAATAAAAATATAAACGTTTGTATTCATG
1 TTCATTAAATAATAAAAATATAAACGTTCGTATTCATG
95135 T
1 T
95136 GCGATACCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (38 bp):
TTCATTAAATAATAAAAATATAAACGTTCGTATTCATG
Found at i:99810 original size:26 final size:27
Alignment explanation
Indices: 99779--99841 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
99769 AAATGTACTA
**
99779 AACGGAGAGCACTTTACGTGCT-AA-T
1 AACGGAGAGCACAATACGTGCTAAATT
99804 AATCGGAGAGCACAATACGTGCTAAATT
1 AA-CGGAGAGCACAATACGTGCTAAATT
99832 AACGGAGAGC
1 AACGGAGAGC
99842 GCGCTAGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 2 0.06
26 18 0.55
27 10 0.30
28 3 0.09
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (27 bp):
AACGGAGAGCACAATACGTGCTAAATT
Found at i:104663 original size:15 final size:14
Alignment explanation
Indices: 104621--104663 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
104611 AGTAATCAAG
104621 TAAAAAATATTTTT
1 TAAAAAATATTTTT
104635 TAAAAACCAT-TTTTT
1 TAAAAA--ATATTTTT
104650 TAAAAAATGATTTT
1 TAAAAAAT-ATTTT
104664 AAAATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.08
14 6 0.24
15 15 0.60
16 2 0.08
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAAAAATATTTTT
Found at i:105410 original size:30 final size:31
Alignment explanation
Indices: 105357--105428 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
105347 ATTTTAAATT
105357 AATAATAGTAAAATTGTACTTTAATCTCTTAAA
1 AATAATA--AAAATTGTACTTTAATCTCTTAAA
* *
105390 AATAATAAAAATTTTA-TTTAATCTTTTAAA
1 AATAATAAAAATTGTACTTTAATCTCTTAAA
*
105420 AATCATAAA
1 AATAATAAA
105429 GATATAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.58
31 8 0.22
33 7 0.19
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (31 bp):
AATAATAAAAATTGTACTTTAATCTCTTAAA
Found at i:107923 original size:21 final size:21
Alignment explanation
Indices: 107893--107953 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
107883 AATTATTGGA
*
107893 ATTGTAAAACCTCA-AGGTTTT
1 ATTGTGAAACCT-ATAGGTTTT
107914 ATTGTGAAA-CTATAGGTTTT
1 ATTGTGAAACCTATAGGTTTT
107934 ATTGTGAAA-CTATAGTGTTT
1 ATTGTGAAACCTATAG-GTTT
107954 ACAGGGTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.65
21 12 0.32
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (21 bp):
ATTGTGAAACCTATAGGTTTT
Found at i:107954 original size:20 final size:20
Alignment explanation
Indices: 107907--107953 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
107897 TAAAACCTCA
107907 AGGTTTTATTGTGAAACTAT
1 AGGTTTTATTGTGAAACTAT
107927 AGGTTTTATTGTGAAACTAT
1 AGGTTTTATTGTGAAACTAT
107947 AGTGTTT
1 AG-GTTT
107954 ACAGGGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (20 bp):
AGGTTTTATTGTGAAACTAT
Found at i:108601 original size:45 final size:45
Alignment explanation
Indices: 108372--108625 Score: 212
Period size: 45 Copynumber: 5.7 Consensus size: 45
108362 CTGGAATGTA
* * *
108372 TAAGACCATAGTTGAAAGATACTATGGCATCAAA-CTGGAAATATG
1 TAAGACCATAGTTGAAAGATACTATGGCATCAAATC-GGGATTGTG
* * * *
108417 CAAGACCACAGTTGAAAGATACTATGGCATTAACTCGGGATTGTG
1 TAAGACCATAGTTGAAAGATACTATGGCATCAAATCGGGATTGTG
* * * * ** *
108462 TAAGA-CATAGTTAAAATATATTATGGCATTAAAT-TAGATATGTA
1 TAAGACCATAGTTGAAAGATACTATGGCATCAAATCGGGAT-TGTG
* * * **
108506 TAAGACCTTAGTTGAAAGATACTATGGCATCATATCGAGAACGAT-
1 TAAGACCATAGTTGAAAGATACTATGGCATCAAATCGGGATTG-TG
* **
108551 CAAGACCATAGTTGAAAGATACTATGGCATCATTTCGGGATTGTG
1 TAAGACCATAGTTGAAAGATACTATGGCATCAAATCGGGATTGTG
* * * *
108596 TAAGACCTTGGTTGAAA-ATACCATGTCATC
1 TAAGACCATAGTTGAAAGATACTATGGCATC
108626 CTCGGAATAA
Statistics
Matches: 167, Mismatches: 36, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
43 3 0.02
44 44 0.26
45 115 0.69
46 5 0.03
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGATACTATGGCATCAAATCGGGATTGTG
Found at i:112162 original size:3 final size:3
Alignment explanation
Indices: 112156--112199 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
112146 TTCCCTCCTC
112156 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
112200 GAGCCAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:117714 original size:30 final size:31
Alignment explanation
Indices: 117661--117719 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
117651 CAAAAAAATT
* *
117661 CAACTTTTAAGGGGCTCAAAAATTTTTTTAC
1 CAACGTTTAAGCGGCTCAAAAATTTTTTTAC
*
117692 CAACGTTTAAGCGGC-CTAAAATTTTTTT
1 CAACGTTTAAGCGGCTCAAAAATTTTTTT
117720 TTTCAACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (31 bp):
CAACGTTTAAGCGGCTCAAAAATTTTTTTAC
Found at i:117720 original size:31 final size:31
Alignment explanation
Indices: 117661--117743 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
117651 CAAAAAAATT
* *
117661 CAACTTTTAAGGGGCTCAAAAATTTTTTTAC
1 CAACGTTTAAGGGCCTCAAAAATTTTTTTAC
* **
117692 CAACGTTTAAGCGGCCT-AAAATTTTTTTTTT
1 CAACGTTTAAG-GGCCTCAAAAATTTTTTTAC
* *
117723 CAACTTTTAAGGG-ATCAAAAA
1 CAACGTTTAAGGGCCTCAAAAA
117744 CTTTAATTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
29 1 0.02
30 6 0.14
31 31 0.74
32 4 0.10
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (31 bp):
CAACGTTTAAGGGCCTCAAAAATTTTTTTAC
Found at i:124480 original size:22 final size:22
Alignment explanation
Indices: 124450--124493 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
124440 TAACAAAAAC
*
124450 GAAATGAAACAACTAAACCTAA
1 GAAAAGAAACAACTAAACCTAA
**
124472 GAAAAGAAATGACTAAACCTAA
1 GAAAAGAAACAACTAAACCTAA
124494 ATTACAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (22 bp):
GAAAAGAAACAACTAAACCTAA
Found at i:124543 original size:14 final size:14
Alignment explanation
Indices: 124526--124552 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
124516 TAAAGAAAAG
124526 GTGTAAAATTAGGT
1 GTGTAAAATTAGGT
124540 GTGTAAAATTAGG
1 GTGTAAAATTAGG
124553 AGCTTAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (14 bp):
GTGTAAAATTAGGT
Found at i:129529 original size:17 final size:17
Alignment explanation
Indices: 129485--129532 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
129475 TTCAAACCCA
*
129485 AAAATAAAAATAATTACT
1 AAAATAAAAA-AATAACT
* * *
129503 AAATTTAAAAACTAACT
1 AAAATAAAAAAATAACT
129520 AAAATAAAAAAAT
1 AAAATAAAAAAAT
129533 TCAAACCCCA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAATAAAAAAATAACT
Found at i:130820 original size:89 final size:89
Alignment explanation
Indices: 130501--130909 Score: 399
Period size: 89 Copynumber: 4.6 Consensus size: 89
130491 CTTCGGATAC
* * * * *
130501 TTGGGG-AAAAAATGGTAATTTTTGGGAGGTTCGAGGTTAAAAGATGAAATTTTTAGACA--TTC
1 TTGGGGTAAAAAATGG-AATTTTT-GGAAGTTCGAGGGTAAAA-ATGGAATTTTTA-AAAGTTTT
*
130563 GGGG-TAAAAATGGAATTTTTGG-ACTT
62 GGGGTTAAAAATGGAATTTTTGGAAGTT
** * * * * *
130589 TTAAGGTTAGAAATGGAAATTTTGG-AGTTTCGA-GGTCAAAAATGGAATTTTTAGAAG-TTCGG
1 TTGGGGTAAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTAAAAGTTTTGG
* *
130651 GGGTAAAAATGGATTTTTTTTTGGAAGTT
64 GGTTAAAAATGGA---ATTTTTGGAAGTT
* * *
130680 TTGGGGTCAAAAATGGAATTTTTTGAAGTTTG-GGGATAAAAATGGAATTTTTAAAAGTTTTGGG
1 TTGGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGG-TAAAAATGGAATTTTTAAAAGTTTTGGG
130744 GTTAAAAATGGAATTTTTTGGAAGTT
65 GTTAAAAATGGAA-TTTTTGGAAGTT
* * * * *
130770 TTGGGGT-TAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATTGGATTTTTTGAAAGTTTTAGGG
1 TTGGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTTTGGGG
*
130834 TCAAAAATGGAATTTTTGGAAGTT
66 TTAAAAATGGAATTTTTGGAAGTT
* *
130858 TTGGGGTAAAAAAT-GAGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTT
1 TTGGGGTAAAAAATGGA-ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT
130910 GAACAATTTA
Statistics
Matches: 268, Mismatches: 36, Indels: 33
0.80 0.11 0.10
Matches are distributed among these distances:
85 1 0.00
86 21 0.08
87 21 0.08
88 31 0.12
89 100 0.37
90 29 0.11
91 46 0.17
92 19 0.07
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (89 bp):
TTGGGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAAAAGTTTTGGGG
TTAAAAATGGAATTTTTGGAAGTT
Found at i:130910 original size:29 final size:28
Alignment explanation
Indices: 130501--130910 Score: 322
Period size: 29 Copynumber: 13.8 Consensus size: 28
130491 CTTCGGATAC
* *
130501 TTGGGGAAAAAATGGTAATTTTTGGGAGGT
1 TTGGGGTAAAAATGG-AATTTTT-GGAAGT
* * * *
130531 TCGAGGTTAAAAGATGAAATTTTTAGACA-T
1 TTG-GGGTAAAA-ATGGAATTTTTGGA-AGT
* **
130561 TCGGGGTAAAAATGGAATTTTTGGACTT
1 TTGGGGTAAAAATGGAATTTTTGGAAGT
* * * *
130589 TTAAGGTTAGAAATGGAAATTTTGG-AGT
1 TT-GGGGTAAAAATGGAATTTTTGGAAGT
* *
130617 TTCGAGGTCAAAAATGGAATTTTTAGAAGT
1 TT-GGGGT-AAAAATGGAATTTTTGGAAGT
* *
130647 TCGGGGGTAAAAATGGATTTTTTTTTGGAAGTT
1 T-TGGGGTAAAAATGGA---ATTTTTGGAAG-T
*
130680 TTGGGGTCAAAAATGGAATTTTTTGAAGT
1 TTGGGGT-AAAAATGGAATTTTTGGAAGT
**
130709 TTGGGGATAAAAATGGAATTTTTAAAAGTT
1 TTGGGG-TAAAAATGGAATTTTTGGAAG-T
130739 TTGGGGTTAAAAATGGAATTTTTTGGAAGTT
1 TTGGGG-TAAAAATGGAA-TTTTTGGAAG-T
*
130770 TTGGGGTTAAAATGGAATTTTTGGAAGT
1 TTGGGGTAAAAATGGAATTTTTGGAAGT
* * * *
130798 TCGAGGGTAAAATTGGATTTTTTGAAAGTT
1 TTG-GGGTAAAAATGGAATTTTTGGAAG-T
*
130828 TTAGGGTCAAAAATGGAATTTTTGGAAGTT
1 TTGGGGT-AAAAATGGAATTTTTGGAAG-T
130858 TTGGGGTAAAAAAT-GAGATTTTTGGAAGT
1 TTGGGGT-AAAAATGGA-ATTTTTGGAAGT
*
130887 TTGAGGGTAAAAATGAAATTTTTG
1 TTG-GGGTAAAAATGGAATTTTTG
130911 AACAATTTAG
Statistics
Matches: 308, Mismatches: 50, Indels: 45
0.76 0.12 0.11
Matches are distributed among these distances:
28 22 0.07
29 126 0.41
30 103 0.33
31 29 0.09
32 17 0.06
33 11 0.04
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (28 bp):
TTGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:130910 original size:59 final size:58
Alignment explanation
Indices: 130501--130910 Score: 332
Period size: 59 Copynumber: 6.9 Consensus size: 58
130491 CTTCGGATAC
* * * * *
130501 TTGGGGAAAAAATGGTAATTTTTGGGAGGTTCGAGGTTAAAAGATGAAATTTTTAGACA--T
1 TTGGGGTAAAAATGG-AATTTTT-GGAAGTTTGAGGGTAAAA-ATGAAATTTTTGGA-AGTT
* ** * * *
130561 TCGGGGTAAAAATGGAATTTTTGGACTTTTAAGGTTAGAAATGGAAA-TTTTGG-AGTT
1 TTGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAAT-GAAATTTTTGGAAGTT
* * * * * **
130618 TCGAGGTCAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGGATTTTTTTTTGGAAGTT
1 TTGGGGT-AAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAAT-GA--AATTTTTGGAAGTT
* * **
130680 TTGGGGTCAAAAATGGAATTTTTTGAAGTTTG-GGGATAAAAATGGAATTTTTAAAAGTT
1 TTGGGGT-AAAAATGGAATTTTTGGAAGTTTGAGGG-TAAAAATGAAATTTTTGGAAGTT
* *
130739 TTGGGGTTAAAAATGGAATTTTTTGGAAGTTTTG-GGGTTAAAATGGAATTTTTGGAAG-T
1 TTGGGG-TAAAAATGGAA-TTTTTGGAAG-TTTGAGGGTAAAAATGAAATTTTTGGAAGTT
* * * * * *
130798 TCGAGGGTAAAATTGGATTTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTT
1 TTG-GGGTAAAAATGGAATTTTTGGAAGTTTGAGGGT-AAAAATGAAATTTTTGGAAGTT
130858 TTGGGGTAAAAAAT-GAGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTG
1 TTGGGGT-AAAAATGGA-ATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTG
130911 AACAATTTAG
Statistics
Matches: 288, Mismatches: 44, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
55 1 0.00
57 17 0.06
58 60 0.21
59 85 0.30
60 69 0.24
61 17 0.06
62 39 0.14
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (58 bp):
TTGGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGGAAGTT
Found at i:132033 original size:3 final size:3
Alignment explanation
Indices: 132025--132097 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
132015 TCATTTTCCT
* **
132025 TTA TTA TTA TTA TTA TTA TTA -AA ACA GTTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
132071 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
132098 ATGCTATCAG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 1 0.02
3 58 0.92
4 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:132137 original size:15 final size:15
Alignment explanation
Indices: 132072--132143 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 15
132062 TATTTATTAT
* **
132072 TATTATTATTATTAT
1 TATTATTATTAATGC
132087 TATTATTATTAATGC
1 TATTATTATTAATGC
* ** * *
132102 TATCAGCATCACAT-T
1 TATTATTATTA-ATGC
132117 TATTATTATTAATGC
1 TATTATTATTAATGC
132132 TATTATTATTAA
1 TATTATTATTAA
132144 AAAGTTTGAA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
14 2 0.05
15 38 0.90
16 2 0.05
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (15 bp):
TATTATTATTAATGC
Found at i:132810 original size:18 final size:18
Alignment explanation
Indices: 132787--132840 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
132777 CTTTTTAATT
132787 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
132805 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
132822 ATTTAAA-TTTAAACTTA
1 AATTAAATTTTAAACTTA
132839 AA
1 AA
132841 AGAAGAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:146873 original size:17 final size:17
Alignment explanation
Indices: 146839--146886 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
146829 AAAGTAAGAG
*
146839 GTATATTATGAATGAAAA
1 GTATATT-TGAATTAAAA
*
146857 -TTTATATTGAATTAAAA
1 GTATAT-TTGAATTAAAA
146874 GTATATTTGAATT
1 GTATATTTGAATT
146887 GAATTTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
GTATATTTGAATTAAAA
Found at i:163925 original size:17 final size:17
Alignment explanation
Indices: 163881--163945 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
163871 TACGAGTTAT
*
163881 AAACCAAAAAT-AAAT-
1 AAACTAAAAATAAAATA
163896 AAAC-AAGAAATAACAA-A
1 AAACTAA-AAATAA-AATA
*
163913 ATACTAAAAATAAAATA
1 AAACTAAAAATAAAATA
163930 AAACTAAAAATTAAAA
1 AAACTAAAAA-TAAAA
163946 CCCGTATCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 2 0.05
15 8 0.20
16 3 0.07
17 21 0.51
18 7 0.17
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.15
Consensus pattern (17 bp):
AAACTAAAAATAAAATA
Found at i:174862 original size:17 final size:17
Alignment explanation
Indices: 174842--174909 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 17
174832 ACTACAATGC
174842 AAATGCACTGACAA-ATA
1 AAATGCA-TGACAATATA
*
174859 AAATGCATAGACAATTTA
1 AAATGCAT-GACAATATA
174877 AAATGCAATGACAACTATA
1 AAATGC-ATGACAA-TATA
174896 TGAAATGCAT-ACAA
1 --AAATGCATGACAA
174910 CTAAACTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.02
17 12 0.28
18 13 0.30
19 9 0.21
20 2 0.05
21 6 0.14
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (17 bp):
AAATGCATGACAATATA
Found at i:175303 original size:3 final size:3
Alignment explanation
Indices: 175295--175395 Score: 70
Period size: 3 Copynumber: 34.0 Consensus size: 3
175285 TTGTGACAAA
* * *
175295 TTC TTC TTC TTT TTA TTT TTC -TC TTGC TTC TTC TCTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC T-TC TTC TTC TTC
* *
175340 TTC TTC TTC TT- TTT TTT TTC -TC TTGC TTC TTC TCTC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC T-TC TTC TTC TTC
175384 TTCC TTC -TC TTC
1 TT-C TTC TTC TTC
175396 CTCATCACCC
Statistics
Matches: 82, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
2 12 0.15
3 55 0.67
4 15 0.18
ACGTcount: A:0.01, C:0.30, G:0.02, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:175328 original size:12 final size:11
Alignment explanation
Indices: 175296--175395 Score: 70
Period size: 11 Copynumber: 9.5 Consensus size: 11
175286 TGTGACAAAT
175296 TCTTCTTCTT-
1 TCTTCTTCTTC
* *
175306 T-TTATTTTTC
1 TCTTCTTCTTC
175316 TCTTGCTTCTTC
1 TCTT-CTTCTTC
175328 TC-TCTTC-TC
1 TCTTCTTCTTC
175337 TTCTTCTTCTTC
1 -TCTTCTTCTTC
* * *
175349 TTTTTTTTTTC
1 TCTTCTTCTTC
175360 TCTTGCTTCTTC
1 TCTT-CTTCTTC
*
175372 TC-TCTTCTTT
1 TCTTCTTCTTC
175382 TCTTC--CTTC
1 TCTTCTTCTTC
175391 TCTTC
1 TCTTC
175396 CTCATCACCC
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
9 16 0.23
10 16 0.23
11 22 0.31
12 16 0.23
ACGTcount: A:0.01, C:0.30, G:0.02, T:0.67
Consensus pattern (11 bp):
TCTTCTTCTTC
Found at i:175331 original size:14 final size:14
Alignment explanation
Indices: 175314--175377 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
175304 TTTTTATTTT
175314 TCTCTTGCTTCTTC
1 TCTCTTGCTTCTTC
*
175328 TCTCTTCTCTTCTTC
1 TCTCTT-GCTTCTTC
* * *
175343 TTCTTCTT-TTTTTTT
1 -TC-TCTTGCTTCTTC
175358 TCTCTTGCTTCTTC
1 TCTCTTGCTTCTTC
175372 TCTCTT
1 TCTCTT
175378 CTTTTCTTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
13 4 0.10
14 18 0.46
15 11 0.28
16 2 0.05
17 4 0.10
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (14 bp):
TCTCTTGCTTCTTC
Found at i:175369 original size:44 final size:45
Alignment explanation
Indices: 175295--175391 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 45
175285 TTGTGACAAA
175295 TTCTTCTTCTTTTTATTTTTCTCTTGCTTCTTCTCTCTTCTCTTC
1 TTCTTCTTCTTTTTATTTTTCTCTTGCTTCTTCTCTCTTCTCTTC
*
175340 TTCTTCTTCTTTTT-TTTTTCTCTTGCTTCTTCTCTCTTCTTTTC
1 TTCTTCTTCTTTTTATTTTTCTCTTGCTTCTTCTCTCTTCTCTTC
175384 TTCCTTCT
1 TT-CTTCT
175392 CTTCCTCATC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 31 0.62
45 19 0.38
ACGTcount: A:0.01, C:0.29, G:0.02, T:0.68
Consensus pattern (45 bp):
TTCTTCTTCTTTTTATTTTTCTCTTGCTTCTTCTCTCTTCTCTTC
Found at i:175900 original size:18 final size:17
Alignment explanation
Indices: 175873--175906 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
175863 GCATGGGATT
*
175873 CCTTGTCTTTCTTCTTTG
1 CCTTGCCTTTC-TCTTTG
175891 CCTTGCCTTTCTCTTT
1 CCTTGCCTTTCTCTTT
175907 CTTTGATGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.32, G:0.09, T:0.59
Consensus pattern (17 bp):
CCTTGCCTTTCTCTTTG
Found at i:191795 original size:70 final size:70
Alignment explanation
Indices: 191683--191835 Score: 182
Period size: 70 Copynumber: 2.2 Consensus size: 70
191673 GAACTACTAA
* * * * * * ** *
191683 GTTTGTCGCGAGACGGACATGCCTATTTTGTGACATAGGGGGCGGGCTGCTGGAACA-TCAAGAC
1 GTTTGTCGCGACACAGACATGCCTATGTTGCGACATAAGGGGCAGGCCACTAGAACACT-AAGAC
191747 TGAAGG
65 TGAAGG
* * *
191753 GTTTGTCGCGACACAGACATGCCTATGTTGCGATATAAGGGGCAGGCCACTAGACCACTAGGACT
1 GTTTGTCGCGACACAGACATGCCTATGTTGCGACATAAGGGGCAGGCCACTAGAACACTAAGACT
191818 GAAGG
66 GAAGG
191823 GTTTGTCGCGACA
1 GTTTGTCGCGACA
191836 TAGAGGGAGC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
70 69 0.99
71 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (70 bp):
GTTTGTCGCGACACAGACATGCCTATGTTGCGACATAAGGGGCAGGCCACTAGAACACTAAGACT
GAAGG
Found at i:197436 original size:12 final size:12
Alignment explanation
Indices: 197414--197453 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
197404 GAGTTGTTTG
197414 AAAGCATAAAATA
1 AAAG-ATAAAATA
197427 AAAGATAAAATA
1 AAAGATAAAATA
*
197439 AAATATAAAATA
1 AAAGATAAAATA
197451 AAA
1 AAA
197454 ACAAAGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAGATAAAATA
Found at i:197441 original size:17 final size:17
Alignment explanation
Indices: 197419--197453 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
197409 GTTTGAAAGC
197419 ATAAAATA-AAAGATAAA
1 ATAAAATATAAA-ATAAA
197436 ATAAAATATAAAATAAA
1 ATAAAATATAAAATAAA
197453 A
1 A
197454 ACAAAGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
ATAAAATATAAAATAAA
Found at i:198705 original size:21 final size:22
Alignment explanation
Indices: 198675--198716 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
198665 ATTCACATGT
198675 TTTCTTACTCATGCTTCTTTTG
1 TTTCTTACTCATGCTTCTTTTG
**
198697 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGCTTCTTTT
198717 CTTTTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.10, C:0.21, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGCTTCTTTTG
Found at i:208926 original size:19 final size:19
Alignment explanation
Indices: 208904--208943 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
208894 TTTAGAAAAC
208904 TTACAAAGTCATCTTAGTT
1 TTACAAAGTCATCTTAGTT
208923 TTACAAAGTCATCTTAGTT
1 TTACAAAGTCATCTTAGTT
208942 TT
1 TT
208944 GTCTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (19 bp):
TTACAAAGTCATCTTAGTT
Found at i:214839 original size:31 final size:31
Alignment explanation
Indices: 214801--214931 Score: 226
Period size: 31 Copynumber: 4.2 Consensus size: 31
214791 TTAGATAATA
**
214801 AAAAATAAATGCAAAGACAAAAATAGACATC
1 AAAAATAAATATAAAGACAAAAATAGACATC
214832 AAAAATAAATATAAAGACAAAAATAGACATC
1 AAAAATAAATATAAAGACAAAAATAGACATC
214863 AAAAATAAATATAAAGACAAAAATAGACATC
1 AAAAATAAATATAAAGACAAAAATAGACATC
*
214894 AAAAATAAATATAAAGACAAAAATGGACATC
1 AAAAATAAATATAAAGACAAAAATAGACATC
214925 AACAAAT
1 AA-AAAT
214932 GTCATCCTCG
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 92 0.96
32 4 0.04
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.15
Consensus pattern (31 bp):
AAAAATAAATATAAAGACAAAAATAGACATC
Found at i:214854 original size:18 final size:18
Alignment explanation
Indices: 214831--214917 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 18
214821 AAATAGACAT
214831 CAAAAATAAATATAAAGA
1 CAAAAATAAATATAAAGA
* *
214849 CAAAAATAGACAT-----
1 CAAAAATAAATATAAAGA
214862 CAAAAATAAATATAAAGA
1 CAAAAATAAATATAAAGA
* *
214880 CAAAAATAGACAT-----
1 CAAAAATAAATATAAAGA
214893 CAAAAATAAATATAAAGA
1 CAAAAATAAATATAAAGA
214911 CAAAAAT
1 CAAAAAT
214918 GGACATCAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 22 0.43
18 29 0.57
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (18 bp):
CAAAAATAAATATAAAGA
Found at i:215168 original size:16 final size:16
Alignment explanation
Indices: 215147--215177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
215137 ATAATGAGAA
215147 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
215163 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
215178 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:216961 original size:17 final size:17
Alignment explanation
Indices: 216941--216983 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
216931 ATGTAGATGC
216941 AGTGACAATAAAAATGA
1 AGTGACAATAAAAATGA
*
216958 AGTGACAATAAAAATGC
1 AGTGACAATAAAAATGA
*
216975 AGGGACAAT
1 AGTGACAAT
216984 TATACTACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.16
Consensus pattern (17 bp):
AGTGACAATAAAAATGA
Found at i:220196 original size:37 final size:37
Alignment explanation
Indices: 220155--220250 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
220145 TATTTATGCA
* * *
220155 GCGACAGTCTTGGGTGCATTCTGGAAATATTCTTGTG
1 GCGACAGTTTTGGGTGCATTCTGGAAATACTCATGTG
* * *
220192 GCGACAGTTTTGGGTGCAATCTGGAAGTGCTCATGTG
1 GCGACAGTTTTGGGTGCATTCTGGAAATACTCATGTG
**
220229 GCGACAGTTTTGGACGCATTCT
1 GCGACAGTTTTGGGTGCATTCT
220251 AGAAGTGCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (37 bp):
GCGACAGTTTTGGGTGCATTCTGGAAATACTCATGTG
Found at i:220256 original size:37 final size:37
Alignment explanation
Indices: 220188--220263 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
220178 GAAATATTCT
** *
220188 TGTGGCGACAGTTTTGGGTGCAATCTGGAAGTGCTCA
1 TGTGGCGACAGTTTTGGACGCAATCTAGAAGTGCTCA
*
220225 TGTGGCGACAGTTTTGGACGCATTCTAGAAGTGCTCA
1 TGTGGCGACAGTTTTGGACGCAATCTAGAAGTGCTCA
220262 TG
1 TG
220264 CAGTGACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (37 bp):
TGTGGCGACAGTTTTGGACGCAATCTAGAAGTGCTCA
Found at i:234061 original size:51 final size:51
Alignment explanation
Indices: 233978--234177 Score: 283
Period size: 51 Copynumber: 3.9 Consensus size: 51
233968 GACATCTCAT
* * *
233978 TCCATAAAGGAATCTATTAACTCAGGATGACACTTAGTCATCAGACCTTTAA
1 TCCATAAAGGAATC-ATTTACTCACGATGACACTTAGTCATCAGACCATTAA
*
234030 TCCATAGAGGAATCATTTACTCACGATGACACTTAGTCATCAGACCATTAA
1 TCCATAAAGGAATCATTTACTCACGATGACACTTAGTCATCAGACCATTAA
* * * ** *
234081 TCCATAAAGGATTCATTTATTCACGATGACACATACACATCAGACCATAAA
1 TCCATAAAGGAATCATTTACTCACGATGACACTTAGTCATCAGACCATTAA
* *
234132 TCCATAAAGGATTCATTTACTCACGATGACACTTAGTCATCGGACC
1 TCCATAAAGGAATCATTTACTCACGATGACACTTAGTCATCAGACC
234178 CTTTCGTTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
51 119 0.90
52 13 0.10
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (51 bp):
TCCATAAAGGAATCATTTACTCACGATGACACTTAGTCATCAGACCATTAA
Found at i:241297 original size:51 final size:50
Alignment explanation
Indices: 241227--241403 Score: 248
Period size: 51 Copynumber: 3.5 Consensus size: 50
241217 GAATCTATAA
* *
241227 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATACAAGATTCGTTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATA-AAGATTCATTT
* *
241278 ACTCGCGATGACACATAGTCATCGGACCATTAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAA-GATTCATTT
* *
241329 ACTCACGATGACACTTAGTCATTC-GACCATTAATCCATGAAGGATTCATCT
1 ACTCACGATGACACTTAGTCA-TCGGACCATTAATCCAT-AAAGATTCATTT
*
241380 ACTTACGATGACACTTAGTCATCG
1 ACTCACGATGACACTTAGTCATCG
241404 ATCCCTTTCG
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
50 4 0.04
51 105 0.93
52 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (50 bp):
ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGATTCATTT
Found at i:245684 original size:45 final size:45
Alignment explanation
Indices: 245634--245726 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
245624 CAGAATAAAG
*
245634 AAATCATGAATTTTCCTTCGTTGTCACGAATGTCTATGTTGCAAT
1 AAATCATGAATTTGCCTTCGTTGTCACGAATGTCTATGTTGCAAT
245679 AAATCATGAATTTGCCTTCGTTGTCACGAATGTCTATGTTGCAAT
1 AAATCATGAATTTGCCTTCGTTGTCACGAATGTCTATGTTGCAAT
245724 AAA
1 AAA
245727 CCCCTTATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (45 bp):
AAATCATGAATTTGCCTTCGTTGTCACGAATGTCTATGTTGCAAT
Found at i:254737 original size:7 final size:7
Alignment explanation
Indices: 254721--254752 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
254711 ACCCAAATTC
254721 ATTTTT-
1 ATTTTTA
254727 ATTTTTA
1 ATTTTTA
254734 ATTTTTA
1 ATTTTTA
254741 ATTTTTA
1 ATTTTTA
254748 ATTTT
1 ATTTT
254753 CAAGTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTTA
Found at i:257331 original size:43 final size:42
Alignment explanation
Indices: 257266--257351 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
257256 TATGTATCTC
* *
257266 TTAATTTGTTTGAAATTATTATGTTTAAGTTGTTAGGTTTGT
1 TTAAATTGTTTGAAATTATTATGTTTAAGTTGTTAGGATTGT
* * *
257308 TTAAATTGTTATGAAATTGTTATGTTTAATTTGTTTGGATTGT
1 TTAAATTGTT-TGAAATTATTATGTTTAAGTTGTTAGGATTGT
257351 T
1 T
257352 ATTTAACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 9 0.24
43 29 0.76
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (42 bp):
TTAAATTGTTTGAAATTATTATGTTTAAGTTGTTAGGATTGT
Found at i:260229 original size:33 final size:34
Alignment explanation
Indices: 260191--260259 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
260181 TTATGCAAAA
*
260191 TAAAATGACA-CAAAATTA-ATAAAAAAAAAATAT
1 TAAAATG-CATCAAAATTATATAAAAAAAAAACAT
* *
260224 TAAAATGCATGAAAATTATATAAAAATAAAACAT
1 TAAAATGCATCAAAATTATATAAAAAAAAAACAT
260258 TA
1 TA
260260 GCATGTACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 2 0.06
33 14 0.45
34 15 0.48
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (34 bp):
TAAAATGCATCAAAATTATATAAAAAAAAAACAT
Found at i:264361 original size:20 final size:20
Alignment explanation
Indices: 264325--264378 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
264315 ATTACTTTGG
264325 ATTTTTTTT-TAAATTTT-A
1 ATTTTTTTTATAAATTTTAA
*
264343 ATTTTTTTTATATATTTTTAGA
1 ATTTTTTTTATA-AATTTTA-A
*
264365 AATTTTTTTATAAA
1 ATTTTTTTTATAAA
264379 ATATAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.31
19 2 0.07
20 5 0.17
21 1 0.03
22 12 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTTTATAAATTTTAA
Found at i:264445 original size:21 final size:20
Alignment explanation
Indices: 264407--264444 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
264397 TTAAAATTTA
264407 AAAATTATTTAGTATTTTTT
1 AAAATTATTTAGTATTTTTT
264427 AAAATTATTT--TATTTTTT
1 AAAATTATTTAGTATTTTTT
264445 TGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
AAAATTATTTAGTATTTTTT
Found at i:265848 original size:15 final size:15
Alignment explanation
Indices: 265828--265873 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
265818 ACAAAACGAT
265828 AACGTAAATTATTAA
1 AACGTAAATTATTAA
265843 AACGTAATATT-TT-A
1 AACGTAA-ATTATTAA
* *
265857 AACATAAATAATTAA
1 AACGTAAATTATTAA
265872 AA
1 AA
265874 TATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
15 12 0.46
16 3 0.12
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (15 bp):
AACGTAAATTATTAA
Found at i:266440 original size:31 final size:30
Alignment explanation
Indices: 266397--266466 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
266387 AAAATTTTAA
266397 TAAAAATAATTAATTTAT-TCATTGATTAAAT
1 TAAAAA-AATTAATTTATCT-ATTGATTAAAT
* *
266428 ATACAAAAATTAATTTATCTATTTATTAAAT
1 -TAAAAAAATTAATTTATCTATTGATTAAAT
266459 TAAAAAAA
1 TAAAAAAA
266467 CAAAAAGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.21
31 21 0.62
32 6 0.18
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (30 bp):
TAAAAAAATTAATTTATCTATTGATTAAAT
Found at i:270834 original size:3 final size:3
Alignment explanation
Indices: 270826--270856 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
270816 AAAATGCTTG
270826 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
270857 ATGAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:271636 original size:48 final size:48
Alignment explanation
Indices: 271559--271873 Score: 325
Period size: 48 Copynumber: 6.6 Consensus size: 48
271549 GTAGAACTAT
* *
271559 GTAAACGTGTGCAAGCTGACGAGCATAAACGTATATAAGTTGACGAGC
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGC
* *
271607 GTAAACGTGTG-AATGCTGACAAGCGTAAACGTACATAAGCTGACGAGC
1 GTAAACGTGTGCAA-GCTGACGAGCGTAAACGTATATAAGCTGACGAGC
* * * * *
271655 GTAAACGTGTGCAAGCTGACAAGCGTAAACATGT-TCAAGTTGACGAAC
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATAT-AAGCTGACGAGC
* * ** * * * ** *
271703 GTAAATGTATATAAGCTGATGAGCATAAACGTGTGCAA---GACGAGA
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGC
* * ** *
271748 GTAAACATATATAAGTTGACGAGCGTAAACGTATATAAGCTGACGAGC
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGC
* *
271796 GTAAACGTGTGCAAGCTAACGAGCATAAACGTATATAAGCTGACGAGC
1 GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGC
* *
271844 ATAAACATGTGCAAGCTGACGAGCGTAAAC
1 GTAAACGTGTGCAAGCTGACGAGCGTAAAC
271874 ATACATGAGT
Statistics
Matches: 220, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
45 35 0.16
47 3 0.01
48 180 0.82
49 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (48 bp):
GTAAACGTGTGCAAGCTGACGAGCGTAAACGTATATAAGCTGACGAGC
Found at i:271849 original size:72 final size:72
Alignment explanation
Indices: 271571--271873 Score: 294
Period size: 72 Copynumber: 4.2 Consensus size: 72
271561 AAACGTGTGC
* * ** * * * * * *
271571 AAGCTGACGAGCATAAACGTATATAAGTTGACGAGCGTAAACGTGTGA-ATGCTGACAAGCGTAA
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAGCATAAACATAT-ATAAGCTGACGAGCGTAA
*
271635 ACGTACAT
65 ACGTATAT
* * * * *
271643 AAGCTGACGAGCGTAAACGTGTGCAAGCTGACAAGCGTAAACATGT-TCAAGTTGACGAACGTAA
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAGCATAAACATATAT-AAGCTGACGAGCGTAA
*
271707 ATGTATAT
65 ACGTATAT
* * *
271715 AAGCTGATGAGCATAAACGTGTGCAA---GACGAG-AGTAAACATATATAAGTTGACGAGCGTAA
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAGCA-TAAACATATATAAGCTGACGAGCGTAA
271776 ACGTATAT
65 ACGTATAT
* * *
271784 AAGCTGACGAGCGTAAACGTGTGCAAGCTAACGAGCATAAACGTATATAAGCTGACGAGCATAAA
1 AAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAGCATAAACATATATAAGCTGACGAGCGTAAA
* * **
271849 CATGTGC
66 CGTATAT
271856 AAGCTGACGAGCGTAAAC
1 AAGCTGACGAGCGTAAAC
271874 ATACATGAGT
Statistics
Matches: 193, Mismatches: 30, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
69 59 0.31
70 1 0.01
72 132 0.68
73 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (72 bp):
AAGCTGACGAGCGTAAACGTGTGCAAGCTGACGAGCATAAACATATATAAGCTGACGAGCGTAAA
CGTATAT
Found at i:271875 original size:24 final size:24
Alignment explanation
Indices: 271559--271873 Score: 260
Period size: 24 Copynumber: 13.2 Consensus size: 24
271549 GTAGAACTAT
*
271559 GTAAACGTGTGCAAGCTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* * * *
271583 ATAAACGTATATAAGTTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* *
271607 GTAAACGTGTGA-ATGCTGACAAGC
1 GTAAACGTGT-ACAAGCTGACGAGC
** *
271631 GTAAACGTACATAAGCTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* *
271655 GTAAACGTGTGCAAGCTGACAAGC
1 GTAAACGTGTACAAGCTGACGAGC
* * * *
271679 GTAAACATGTTCAAGTTGACGAAC
1 GTAAACGTGTACAAGCTGACGAGC
* * * *
271703 GTAAATGTATATAAGCTGATGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* * *
271727 ATAAACGTGTGCAA---GACGAGA
1 GTAAACGTGTACAAGCTGACGAGC
* * * *
271748 GTAAACATATATAAGTTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* *
271772 GTAAACGTATATAAGCTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* *
271796 GTAAACGTGTGCAAGCTAACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* * *
271820 ATAAACGTATATAAGCTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
* * *
271844 ATAAACATGTGCAAGCTGACGAGC
1 GTAAACGTGTACAAGCTGACGAGC
271868 GTAAAC
1 GTAAAC
271874 ATACATGAGT
Statistics
Matches: 225, Mismatches: 61, Indels: 10
0.76 0.21 0.03
Matches are distributed among these distances:
21 14 0.06
23 1 0.00
24 209 0.93
25 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (24 bp):
GTAAACGTGTACAAGCTGACGAGC
Found at i:272561 original size:21 final size:21
Alignment explanation
Indices: 272537--272588 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
272527 AGTAAGGGTA
272537 GTATCGGTAGTACCTATACTT
1 GTATCGGTAGTACCTATACTT
272558 GTATCGGTAGTACCTATACTT
1 GTATCGGTAGTACCTATACTT
272579 GTATCGGTAG
1 GTATCGGTAG
272589 AACTCCCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (21 bp):
GTATCGGTAGTACCTATACTT
Done.