Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 107 of 171
Found at i:34428900 original size:200 final size:200
Alignment explanation
Indices: 34428552--34428919 Score: 569
Period size: 200 Copynumber: 1.8 Consensus size: 200
34428542 AGTTGAAGTA
* * * *
34428552 GAGTGAAACTTCAAACCTCCATCTTCTTGATAAGATATAAAGAACTGGATCAAAATAATGAAGCG
1 GAGTAAAACTTCAAACCTCCATCTTCTTGATAAGATACAAAGAACTGGATCAAAACAATGAAACG
* *
34428617 GTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGACGCGAAGCTCAATGTAAGTGA
66 GTCATCGTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGA
*
34428682 AACTTCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGGGCCAAAAAAATAAAGCGAAGCTC
131 AACTTCAAACCCCCATCTTCCTAATGAGATACAAAGAAGTGGGCCAAAAAAATAAAGCGAAGCTC
34428747 AATGT
196 AATGT
* * *
34428752 GAGTAAAACTTCAAAACC-CCATCTT-TCTGATGAGATACAAAGAAGTGGATCAAAACGATGAAA
1 GAGTAAAACTTC-AAACCTCCATCTTCT-TGATAAGATACAAAGAACTGGATCAAAACAATGAAA
* * * *
34428815 TGGTCATCGTCCTGATGAGATACAGAGAAGTGGACCAAAATAATTAAGCGAAGCTCAATGTGAGT
64 CGGTCATCGTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGT
*
34428880 GAAACTTCAAACCCCCATCTTCCTAATGAGATACAGAGAA
129 GAAACTTCAAACCCCCATCTTCCTAATGAGATACAAAGAA
34428920 ATGTATCAAA
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
199 1 0.01
200 145 0.96
201 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (200 bp):
GAGTAAAACTTCAAACCTCCATCTTCTTGATAAGATACAAAGAACTGGATCAAAACAATGAAACG
GTCATCGTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGA
AACTTCAAACCCCCATCTTCCTAATGAGATACAAAGAAGTGGGCCAAAAAAATAAAGCGAAGCTC
AATGT
Found at i:34428957 original size:48 final size:48
Alignment explanation
Indices: 34428896--34428988 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
34428886 TCAAACCCCC
* * *
34428896 ATCTTCCTAATGAGATACAGAGAAATGTATCAAAACAATGAAGCGGTA
1 ATCTTCCTAATGAGATACAAAGAAATGGACCAAAACAATGAAGCGGTA
* * * * *
34428944 ATCTTCTTGATGAGATATAAAGAAGTGGACCAAAACAATGGAGCG
1 ATCTTCCTAATGAGATACAAAGAAATGGACCAAAACAATGAAGCG
34428989 AAGCTCAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (48 bp):
ATCTTCCTAATGAGATACAAAGAAATGGACCAAAACAATGAAGCGGTA
Found at i:34429811 original size:30 final size:30
Alignment explanation
Indices: 34429777--34429967 Score: 138
Period size: 30 Copynumber: 6.4 Consensus size: 30
34429767 TTAAAAATGG
*
34429777 TATTTTGACCCCCAAACTTTTCAAAAATTA
1 TATTTTGACCCTCAAACTTTTCAAAAATTA
* * *
34429807 TATTTTGAGCCTCGAGC-TTTCTAAAAATTA
1 TATTTTGACCCTCAAACTTTTC-AAAAATTA
* * *
34429837 TGTTTTGACCCTTAAACTTTCCAAAAATTA
1 TATTTTGACCCTCAAACTTTTCAAAAATTA
* * * ** *
34429867 TTTTTTGACCTTTATATTTTTTTAAAAATTA
1 TATTTTGACCCTCA-AACTTTTCAAAAATTA
* * *
34429898 TATATTGACCCTTAAACTTTCCAAAAATTCA
1 TATTTTGACCCTCAAACTTTTCAAAAATT-A
* * * *
34429929 -AATTT-ATCCCCCAAAC-TTTCCAAAATTT
1 TATTTTGA-CCCTCAAACTTTTCAAAAATTA
34429957 TATTTTGACCC
1 TATTTTGACCC
34429968 ATTTTTCCTT
Statistics
Matches: 123, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
29 21 0.17
30 75 0.61
31 27 0.22
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (30 bp):
TATTTTGACCCTCAAACTTTTCAAAAATTA
Found at i:34429862 original size:60 final size:60
Alignment explanation
Indices: 34429768--34429926 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
34429758 CTGTGTTATT
** ** * *
34429768 TAAAAATGGTATTTTGACCCCCAAACTTTTCAAAAATTATATTTTGAGCC-TCGAGCTTTC
1 TAAAAATTATATTTTGACCCTTAAACTTTCCAAAAATTATATTTTGA-CCTTAGAGCTTTC
* * * ** *
34429828 TAAAAATTATGTTTTGACCCTTAAACTTTCCAAAAATTATTTTTTGACCTTTATATTTTTT
1 TAAAAATTATATTTTGACCCTTAAACTTTCCAAAAATTATATTTTGACC-TTAGAGCTTTC
*
34429889 TAAAAATTATATATTGACCCTTAAACTTTCCAAAAATT
1 TAAAAATTATATTTTGACCCTTAAACTTTCCAAAAATT
34429927 CAAATTTATC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.02
60 40 0.48
61 41 0.49
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (60 bp):
TAAAAATTATATTTTGACCCTTAAACTTTCCAAAAATTATATTTTGACCTTAGAGCTTTC
Found at i:34429897 original size:31 final size:30
Alignment explanation
Indices: 34429768--34429926 Score: 140
Period size: 30 Copynumber: 5.3 Consensus size: 30
34429758 CTGTGTTATT
** **
34429768 TAAAAATGGTATTTTGACCCCCAAACTTT-
1 TAAAAATTATATTTTGACCCTTAAACTTTC
* ** *
34429797 TCAAAAATTATATTTTGAGCCTCGAGCTTTC
1 T-AAAAATTATATTTTGACCCTTAAACTTTC
*
34429828 TAAAAATTATGTTTTGACCCTTAAACTTTC
1 TAAAAATTATATTTTGACCCTTAAACTTTC
* * * ** *
34429858 CAAAAATTATTTTTTGACCTTTATATTTTTT
1 TAAAAATTATATTTTGACCCTTA-AACTTTC
*
34429889 TAAAAATTATATATTGACCCTTAAACTTTC
1 TAAAAATTATATTTTGACCCTTAAACTTTC
*
34429919 CAAAAATT
1 TAAAAATT
34429927 CAAATTTATC
Statistics
Matches: 102, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 77 0.75
31 24 0.24
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (30 bp):
TAAAAATTATATTTTGACCCTTAAACTTTC
Found at i:34434466 original size:40 final size:40
Alignment explanation
Indices: 34434365--34434466 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
34434355 AACTGAGTAG
* * * *
34434365 GCGGTGACACTGTAAACACTGAAATGCTATCATTGAACTG
1 GCGGTGACACTGTAAACACTGCAATACTAGCATTGAACTA
* *
34434405 GCAGTGACACTGTAAACACTGCGATACT-GCAATTGAACTA
1 GCGGTGACACTGTAAACACTGCAATACTAGC-ATTGAACTA
34434445 GCGGTGACACTGTAAACACTGC
1 GCGGTGACACTGTAAACACTGC
34434467 TAGATTACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.02
40 53 0.98
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (40 bp):
GCGGTGACACTGTAAACACTGCAATACTAGCATTGAACTA
Found at i:34438747 original size:19 final size:19
Alignment explanation
Indices: 34438715--34438753 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34438705 TACATGTGGC
34438715 ATTTTAATTAAATA-AAAT
1 ATTTTAATTAAATATAAAT
*
34438733 ATTTTAAATTTAATATAAAT
1 ATTTT-AATTAAATATAAAT
34438753 A
1 A
34438754 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTTAATTAAATATAAAT
Found at i:34438973 original size:20 final size:21
Alignment explanation
Indices: 34438937--34438978 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
34438927 TTTTTTTTAA
*
34438937 TATTAGTTACTATAAAAAAAT
1 TATTAGTTACGATAAAAAAAT
34438958 TATTAG-TACGATAAAAAAAT
1 TATTAGTTACGATAAAAAAAT
34438978 T
1 T
34438979 CTAAACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (21 bp):
TATTAGTTACGATAAAAAAAT
Found at i:34441203 original size:8 final size:8
Alignment explanation
Indices: 34441190--34441216 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
34441180 CGATGATAGA
34441190 GAGAGAGG
1 GAGAGAGG
34441198 GAGAGAGG
1 GAGAGAGG
34441206 GAGAGAGG
1 GAGAGAGG
34441214 GAG
1 GAG
34441217 CAGATAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (8 bp):
GAGAGAGG
Found at i:34443008 original size:32 final size:31
Alignment explanation
Indices: 34442972--34443044 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
34442962 TAATTAAAAT
34442972 TTTTTTATTCAATTT-ATTATTCAAAT-TAGACA
1 TTTTTTATT-AATTTGA-TATTCAAATCTA-ACA
* *
34443004 TTTTTTCTTAATTTGATATTTAAATCTAACA
1 TTTTTTATTAATTTGATATTCAAATCTAACA
34443035 TTTTTT-TTAA
1 TTTTTTATTAA
34443045 GTTGGTACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 4 0.11
31 22 0.59
32 11 0.30
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTTTATTAATTTGATATTCAAATCTAACA
Found at i:34445040 original size:31 final size:31
Alignment explanation
Indices: 34444969--34445027 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
34444959 AAAAAAAGTT
*
34444969 AACTTTTAAGGGTTCAAAATTTTTTTTTACC
1 AACTTTTAAGGGATCAAAATTTTTTTTTACC
*
34445000 AACTTTTAAGGGATCTAAATTTTTTTTT
1 AACTTTTAAGGGATCAAAATTTTTTTTT
34445028 CTCTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (31 bp):
AACTTTTAAGGGATCAAAATTTTTTTTTACC
Found at i:34452851 original size:18 final size:18
Alignment explanation
Indices: 34452828--34452867 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
34452818 GCCCGTTCAT
34452828 TTTATTTTT-TTTAAAATA
1 TTTATTTTTATTT-AAATA
*
34452846 TTTATTTTTATTTTAATA
1 TTTATTTTTATTTAAATA
34452864 TTTA
1 TTTA
34452868 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTTTATTTAAATA
Found at i:34454338 original size:15 final size:16
Alignment explanation
Indices: 34454308--34454341 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
34454298 TTCAGTTGTA
34454308 AAATTTTCAATTAATT
1 AAATTTTCAATTAATT
*
34454324 AAATTTT-ATTTAATT
1 AAATTTTCAATTAATT
34454339 AAA
1 AAA
34454342 AATTTATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTCAATTAATT
Found at i:34455214 original size:22 final size:22
Alignment explanation
Indices: 34455189--34455236 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
34455179 AAATAATAGA
*
34455189 AAAATAACAATAAAACAGCACC
1 AAAATAACAAAAAAACAGCACC
** *
34455211 AAAATAGTAAAAAAATAGCACC
1 AAAATAACAAAAAAACAGCACC
34455233 AAAA
1 AAAA
34455237 CAGCAACCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAATAACAAAAAAACAGCACC
Found at i:34455225 original size:33 final size:33
Alignment explanation
Indices: 34455154--34455281 Score: 121
Period size: 34 Copynumber: 3.8 Consensus size: 33
34455144 CCAAACAACC
* * *
34455154 AAAATAACAACCAAAACAGCAGCAAAAATAATAGA
1 AAAATAACAA-CAAAACAGCA-CCAAAATAGTAAA
*
34455189 AAAATAACAATAAAACAGCACCAAAATAGTAAA
1 AAAATAACAACAAAACAGCACCAAAATAGTAAA
* * *
34455222 AAAATAGCACCAAAACAGCAACCAAAACAGTAAA
1 AAAATAACAACAAAACAGC-ACCAAAATAGTAAA
* * * * *
34455256 AACACAACACCAAAACAACACAAAAA
1 AAAATAACAACAAAACAGCACCAAAA
34455282 AGCACCAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
33 32 0.41
34 37 0.47
35 10 0.13
ACGTcount: A:0.66, C:0.21, G:0.06, T:0.07
Consensus pattern (33 bp):
AAAATAACAACAAAACAGCACCAAAATAGTAAA
Found at i:34455245 original size:12 final size:11
Alignment explanation
Indices: 34455200--34455293 Score: 66
Period size: 11 Copynumber: 8.5 Consensus size: 11
34455190 AAATAACAAT
34455200 AAAACAGCACC
1 AAAACAGCACC
* * **
34455211 AAAATAGTAAA
1 AAAACAGCACC
*
34455222 AAAATAGCACC
1 AAAACAGCACC
34455233 AAAACAGCAACC
1 AAAACAGC-ACC
* *
34455245 AAAACAGTA-A
1 AAAACAGCACC
*
34455255 AAACACAACACC
1 AAA-ACAGCACC
*
34455267 AAAACAACA-C
1 AAAACAGCACC
*
34455277 AAAAAAGCACC
1 AAAACAGCACC
34455288 AAAACA
1 AAAACA
34455294 ATAATATAAT
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
10 11 0.17
11 39 0.62
12 13 0.21
ACGTcount: A:0.64, C:0.26, G:0.06, T:0.04
Consensus pattern (11 bp):
AAAACAGCACC
Found at i:34455674 original size:31 final size:31
Alignment explanation
Indices: 34455623--34455688 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
34455613 TGAACTTTAA
*
34455623 TTTGGTGCAATTATACACTTGAAAATCTAAT
1 TTTGGTGCAAATATACACTTGAAAATCTAAT
* * * *
34455654 TTTGGTTCAAATATATACTTGAAACTTTAAT
1 TTTGGTGCAAATATACACTTGAAAATCTAAT
34455685 TTTG
1 TTTG
34455689 ATTTAATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (31 bp):
TTTGGTGCAAATATACACTTGAAAATCTAAT
Found at i:34458203 original size:21 final size:22
Alignment explanation
Indices: 34458159--34458201 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34458149 ACAAAATCCA
*
34458159 ATTTTATTTATTTTATATTTTT
1 ATTTTATTGATTTTATATTTTT
34458181 ATTTTATTGA-TTTATCATTTT
1 ATTTTATTGATTTTAT-ATTTT
34458202 ATAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
ATTTTATTGATTTTATATTTTT
Found at i:34458363 original size:21 final size:20
Alignment explanation
Indices: 34458332--34458395 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
34458322 TTATCTATTT
*
34458332 ATAAATATAAATAAATACAA
1 ATAAAAATAAATAAATACAA
34458352 ATGAAAAATAAATAAAT---A
1 AT-AAAAATAAATAAATACAA
*
34458370 ATAAAATTAAATAAATACAA
1 ATAAAAATAAATAAATACAA
34458390 ACTAAA
1 A-TAAA
34458396 TACACATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 13 0.35
18 3 0.08
20 4 0.11
21 17 0.46
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (20 bp):
ATAAAAATAAATAAATACAA
Found at i:34458375 original size:17 final size:17
Alignment explanation
Indices: 34458335--34458386 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
34458325 TCTATTTATA
* *
34458335 AATATAAATAAATACA-
1 AATAAAAATAAATAAAT
34458351 AATGAAAAATAAATAAAT
1 AAT-AAAAATAAATAAAT
*
34458369 AATAAAATTAAATAAAT
1 AATAAAAATAAATAAAT
34458386 A
1 A
34458387 CAAACTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.81
18 3 0.10
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (17 bp):
AATAAAAATAAATAAAT
Found at i:34459448 original size:30 final size:29
Alignment explanation
Indices: 34459414--34459503 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
34459404 TTATGTTTTA
* *
34459414 ACCCCCAAACTATCAAATAATTCAAATTTG
1 ACCCCCAAACTTTCAAA-AATTCGAATTTG
* *
34459444 ACCCCTAAACTTTTTAAAAATTCGAATTTG
1 ACCCCCAAAC-TTTCAAAAATTCGAATTTG
*
34459474 ACCCTCAAACTTTCCAAAAATTCGAATTTG
1 ACCCCCAAACTTT-CAAAAATTCGAATTTG
34459504 CCCTAGTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
29 3 0.06
30 43 0.84
31 5 0.10
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (29 bp):
ACCCCCAAACTTTCAAAAATTCGAATTTG
Found at i:34459730 original size:37 final size:35
Alignment explanation
Indices: 34459662--34459730 Score: 84
Period size: 37 Copynumber: 1.9 Consensus size: 35
34459652 ATTTACTTAA
** *
34459662 TTTATTATTTTATTGTATTTCATGTATATATTATT
1 TTTATTATTTTATTGTAAATCATGTACATATTATT
*
34459697 TTTATTATTTATAATTGTAAATCATGTGCATATT
1 TTTATTATTT-T-ATTGTAAATCATGTACATATT
34459731 TTTGTATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 10 0.36
36 1 0.04
37 17 0.61
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.59
Consensus pattern (35 bp):
TTTATTATTTTATTGTAAATCATGTACATATTATT
Found at i:34462608 original size:15 final size:16
Alignment explanation
Indices: 34462588--34462617 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34462578 GGGGATGATA
34462588 TAAAAAG-TGAGTTGC
1 TAAAAAGCTGAGTTGC
34462603 TAAAAAGCTGAGTTG
1 TAAAAAGCTGAGTTG
34462618 AAAGCCCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
TAAAAAGCTGAGTTGC
Found at i:34473147 original size:72 final size:72
Alignment explanation
Indices: 34473025--34473235 Score: 251
Period size: 79 Copynumber: 2.8 Consensus size: 72
34473015 TCGACCATGA
* * *
34473025 GGCAAATTGAAGACCATCCGATTTCTTACCCCGACCATGGGGCAGATTGAAGCAATCCAACCCTA
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAACCCTA
*
34473090 ACTAGAG
66 ACCAGAG
* *
34473097 GGCAGATTGAAGACCATCCAATCTCTTACCCCAACCATGGGGCAAATTGAAGCAATCCAATCTTT
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCC-A-----
34473162 TACCCTAACCAGAG
60 -ACCCTAACCAGAG
* * * * * *
34473176 GGCAGATTGAAGAACATCTGATCTCTTATCCTGACCATGGGGAAAATTAAAGCAATCCAA
1 GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAA
34473236 TCTTTTACCC
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
72 54 0.46
73 1 0.01
78 1 0.01
79 62 0.53
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (72 bp):
GGCAGATTGAAGACCATCCGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATCCAACCCTA
ACCAGAG
Found at i:34473165 original size:39 final size:39
Alignment explanation
Indices: 34473096--34473246 Score: 142
Period size: 39 Copynumber: 3.8 Consensus size: 39
34473086 CCTAACTAGA
* *
34473096 GGGCAGATTGAAGACCATCCAATCTCTTACCCCAACCATG
1 GGGCAAATTGAAG-CAATCCAATCTCTTACCCCAACCATG
* *
34473136 GGGCAAATTGAAGCAATCCAATCTTTTACCCTAACCA-G
1 GGGCAAATTGAAGCAATCCAATCTCTTACCCCAACCATG
* * ** * **
34473174 AGGGCAGATTGAAGAACATCTGATCTCTTATCCTGACCATG
1 -GGGCAAATTGAAGCA-ATCCAATCTCTTACCCCAACCATG
* * *
34473215 GGGAAAATTAAAGCAATCCAATCTTTTACCCC
1 GGGCAAATTGAAGCAATCCAATCTCTTACCCC
34473247 TAAAGCTATA
Statistics
Matches: 88, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 46 0.52
40 40 0.45
41 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (39 bp):
GGGCAAATTGAAGCAATCCAATCTCTTACCCCAACCATG
Found at i:34473408 original size:51 final size:50
Alignment explanation
Indices: 34473349--34473462 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 50
34473339 TTGATCTTCA
* * *
34473349 CTGAAGTTGCAG-AGA-AATGGAGTGAAGCTATAA-AGGCGAATCCTTATCTCT
1 CTGAAGTTGCAGTAGAGAA-GGA-TGAAGCTATAAGA-ACAAAT-CTTATATCT
*
34473400 CTGAAGTTGCAGTAGAGCAGGATGAAGCTATAAGAACAAATCTTATATCT
1 CTGAAGTTGCAGTAGAGAAGGATGAAGCTATAAGAACAAATCTTATATCT
*
34473450 CTGAAGTTACAGT
1 CTGAAGTTGCAGT
34473463 GGGTCGGATT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
50 20 0.36
51 27 0.49
52 7 0.13
53 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (50 bp):
CTGAAGTTGCAGTAGAGAAGGATGAAGCTATAAGAACAAATCTTATATCT
Found at i:34474330 original size:5 final size:5
Alignment explanation
Indices: 34474320--34474362 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
34474310 TGGAAGACCT
* * *
34474320 AGAAA AGAAA AGAAA AGAGA AGACA A-AAC AGAAA AGAAA AGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
34474363 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
4 2 0.06
5 30 0.94
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:34481145 original size:112 final size:111
Alignment explanation
Indices: 34480999--34481223 Score: 333
Period size: 112 Copynumber: 2.0 Consensus size: 111
34480989 AATGTTTGTC
* * * *
34480999 ATTTTTAATCTTTCATTCATGTGAGTTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAAC
1 ATTTTTAATCTTTCATTCACGTGAGCTTTACCTCCAACAAAATTCAATTTTATCCACCTTACAAC
**
34481064 CTTGTTCAAGAATGTTTGCATTGAAATAACAGTTAGTGGACTAATG
66 CGAGTTCAAGAATGTTTGCATTGAAATAACAGTTAGTGGACTAATG
34481110 ATTTTTAATCTTTTCATTCACGTGAGCTTTACCTCCAACAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATC-TTTCATTCACGTGAGCTTTACCTCCAACAAAATTCAATTTTATCCACCTTACAA
* * * * * *
34481175 TCGAGTTCAAGCATTTTTGCATTGAAATGACGGTTAGTGGTCTAATG
65 CCGAGTTCAAGAATGTTTGCATTGAAATAACAGTTAGTGGACTAATG
34481222 AT
1 AT
34481224 ATAAGGAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
111 10 0.10
112 91 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (111 bp):
ATTTTTAATCTTTCATTCACGTGAGCTTTACCTCCAACAAAATTCAATTTTATCCACCTTACAAC
CGAGTTCAAGAATGTTTGCATTGAAATAACAGTTAGTGGACTAATG
Found at i:34481787 original size:98 final size:97
Alignment explanation
Indices: 34481613--34481939 Score: 370
Period size: 98 Copynumber: 3.4 Consensus size: 97
34481603 GGTTTGAAGG
* * * * *
34481613 GAAAGATTGAAG-TCGCAACGGCAAATCTAATACCCTAGAGATATGGAGGGAAAAGTTGAAGCCG
1 GAAAGATTAAAGCT-GCAACGGCAAATCTTATACCATGGAGATATGGAGGGAAAGGTTGAAGCCG
* *
34481677 CAACGATTAACCTTATACCTTAGAGACGTAATGA
65 CAACG-TGAACCTTATACCTTAGAGAAGTAATGA
* * * **
34481711 GAAAGATTAAAGCTGCAATGACAAATCTTATACCATGGAGATATGGAGAGAAAGGTTGAAGTTGC
1 GAAAGATTAAAGCTGCAACGGCAAATCTTATACCATGGAGATATGGAGGGAAAGGTTGAAGCCGC
* *
34481776 AACAGTGAACCTTATACCTTAGAAAAATAATGA
66 AAC-GTGAACCTTATACCTTAGAGAAGTAATGA
* * * *
34481809 GAAAGATTGAA-CTGCAACGGCGAATCTTATACCGTGTAGATATGGAGGGAAAGGTTGAAGCCGC
1 GAAAGATTAAAGCTGCAACGGCAAATCTTATACCATGGAGATATGGAGGGAAAGGTTGAAGCCGC
* * * * *
34481873 AACGGTGAACCTTATACGTTAAAGATGTGATGG
66 AAC-GTGAACCTTATACCTTAGAGAAGTAATGA
* * *
34481906 GAAAGATTATAGCCGCAACGGCGAATCTTATACC
1 GAAAGATTAAAGCTGCAACGGCAAATCTTATACC
34481940 CTGAGGATGA
Statistics
Matches: 192, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
97 79 0.41
98 111 0.58
99 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (97 bp):
GAAAGATTAAAGCTGCAACGGCAAATCTTATACCATGGAGATATGGAGGGAAAGGTTGAAGCCGC
AACGTGAACCTTATACCTTAGAGAAGTAATGA
Found at i:34481790 original size:49 final size:49
Alignment explanation
Indices: 34481650--34481889 Score: 162
Period size: 49 Copynumber: 4.9 Consensus size: 49
34481640 TAATACCCTA
* * * * * * *
34481650 GAGATATGGAGGGAAAAGTTGAAGCCGCAACGATTAACCTTATACCTTA
1 GAGATATGGAGAGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCATG
** * * * * *** *
34481699 GAGACGT-AATGAGAAAGATTAAAGCTGCAATGACAAATCTTATACCATG
1 GAGATATGGA-GAGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCATG
* * * *
34481748 GAGATATGGAGAGAAAGGTTGAAGTTGCAACAGTGAACCTTATACCTTA
1 GAGATATGGAGAGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCATG
* * * * * * *
34481797 GAAAAAT-AATGAGAAAGATTGAA-CTGCAACGGCGAATCTTATACCGTG
1 GAGATATGGA-GAGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCATG
* * *
34481845 TAGATATGGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATAC
1 GAGATATGGAGAGAAAGGTTGAAGCTGCAACGGTGAACCTTATAC
34481890 GTTAAAGATG
Statistics
Matches: 139, Mismatches: 47, Indels: 10
0.71 0.24 0.05
Matches are distributed among these distances:
48 36 0.26
49 102 0.73
50 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (49 bp):
GAGATATGGAGAGAAAGGTTGAAGCTGCAACGGTGAACCTTATACCATG
Found at i:34481908 original size:49 final size:48
Alignment explanation
Indices: 34481782--34481938 Score: 133
Period size: 49 Copynumber: 3.2 Consensus size: 48
34481772 TTGCAACAGT
* ** * * *
34481782 GAACCTTATACCTTAGAAAAATAATGAGAAAGATTGAA-CTGCAACGGC
1 GAACCTTATACGTTA-AAATGTGATGGGAAAGATTGAAGCCGCAACGGC
* * * *
34481830 GAATCTTATACCGTGTAGATATG-GA-GGGAAAGGTTGAAGCCGCAACGGT
1 GAACCTTATA-CGT-TA-AAATGTGATGGGAAAGATTGAAGCCGCAACGGC
34481879 GAACCTTATACGTTAAAGATGTGATGGGAAAGATT-ATAGCCGCAACGGC
1 GAACCTTATACGTTAAA-ATGTGATGGGAAAGATTGA-AGCCGCAACGGC
*
34481928 GAATCTTATAC
1 GAACCTTATAC
34481939 CCTGAGGATG
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
46 1 0.01
47 5 0.06
48 26 0.30
49 50 0.57
50 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (48 bp):
GAACCTTATACGTTAAAATGTGATGGGAAAGATTGAAGCCGCAACGGC
Found at i:34482182 original size:38 final size:38
Alignment explanation
Indices: 34482130--34482554 Score: 202
Period size: 40 Copynumber: 10.9 Consensus size: 38
34482120 TTACCCCGAT
* * *
34482130 CATGTGGCAGATTGAAGCAACCAATCTTTTGTCTC-AAC
1 CATGAGGCAGATTGAAGCAACCAATCTTTT-ACCCGAAC
* * * *
34482168 CATGAGGCAAATTGAAGACCATCCGATCTTTTACCCGGAC
1 CATGAGGCAGATTGAAG--CAACCAATCTTTTACCCGAAC
* * *
34482208 CATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAAT
1 CATGAGGCAGATTGAAGCAA-CCAATCTTTTACCCGAAC
* * *
34482247 CA-GAGGGCAGATTGAAGACACACTAATCTCTTACCCTG-AT
1 CATGA-GGCAGATTGAAG-CA-ACCAATCTTTTACCC-GAAC
* * * * **
34482287 CATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAGT
1 CATGAGGCAGATTGAAGCAACCAATCTTTTACCCGAAC
* * *
34482325 TA-GAGGGCAGATTGAAGACAAACCAATCTCTTACCCCG-AT
1 CATGA-GGCAGATTGAAG-C-AACCAATCTTTTA-CCCGAAC
* * * * * **
34482365 CATGGGGCAAATTAAAGCATCCAATCTTTTACCCTAGT
1 CATGAGGCAGATTGAAGCAACCAATCTTTTACCCGAAC
* * * * *
34482403 CA-GAGGGTAGATTGAAGACACACCAATCTCTTGCCTTG-AT
1 CATGA-GGCAGATTGAAG-CA-ACCAATCTTTTACC-CGAAC
* * * * *
34482443 CATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAAT
1 CATGAGGCAGATTGAAGCAACCAATCTTTTACCCGAAC
* * *
34482481 CA-GAGGGCAGACTGAAGACACACCAATCTCTTACCCCG-AT
1 CATGA-GGCAGATTGAAG-CA-ACCAATCTTTTA-CCCGAAC
* * *
34482521 CATGGGGCAGATTAAAGCATCCAATCTTTTACCC
1 CATGAGGCAGATTGAAGCAACCAATCTTTTACCC
34482555 TAGTCAAAGG
Statistics
Matches: 291, Mismatches: 69, Indels: 55
0.70 0.17 0.13
Matches are distributed among these distances:
37 9 0.03
38 101 0.35
39 42 0.14
40 128 0.44
41 11 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (38 bp):
CATGAGGCAGATTGAAGCAACCAATCTTTTACCCGAAC
Found at i:34482340 original size:78 final size:78
Alignment explanation
Indices: 34482114--34482571 Score: 598
Period size: 78 Copynumber: 5.9 Consensus size: 78
34482104 GCAAAGAAAA
* * * ** *
34482114 AATCTCTTACCCCGATCATGTGGCAGATTGAAGCAACCAATCTTTT-GTCTCAACCATGA-GGCA
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCT-AATCA-GAGGGCA
*
34482177 AATTGAAGAC-CATCC
64 GATTGAAGACACA-CC
* * * * *
34482192 GATCTTTTACCCGGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAGGGCAG
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGC-ATCCAATCTTTTACCCTAATCAGAGGGCAG
*
34482257 ATTGAAGACACACT
65 ATTGAAGACACACC
* * *
34482271 AATCTCTTACCCTGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAGTTAGAGGGCAGA
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
*
34482336 TTGAAGACAAACC
66 TTGAAGACACACC
* * *
34482349 AATCTCTTACCCCGATCATGGGGCAAATTAAAGCATCCAATCTTTTACCCTAGTCAGAGGGTAGA
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
34482414 TTGAAGACACACC
66 TTGAAGACACACC
* ** * *
34482427 AATCTCTTGCCTTGATCATGGGGCAAATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
*
34482492 CTGAAGACACACC
66 TTGAAGACACACC
* * *
34482505 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAGTCAAAGGGTAGA
1 AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
34482570 TT
66 TT
34482572 AAAGCCACCA
Statistics
Matches: 335, Mismatches: 41, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
78 273 0.81
79 58 0.17
80 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (78 bp):
AATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGA
TTGAAGACACACC
Found at i:34482784 original size:138 final size:135
Alignment explanation
Indices: 34482538--34482795 Score: 358
Period size: 138 Copynumber: 1.9 Consensus size: 135
34482528 CAGATTAAAG
34482538 CATCCAATCTTTTACCCTAGTCAAAGGGTAGATTAAAGCCACCATCCAATATTTTACCCCCTAAG
1 CATCCAATCTTTTACCCTAGTCAAAGGGTAGATTAAAGCCACCATCCAATATTTTACCCCCTAAG
* * *
34482603 TCAAGAAGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAAGTCAAGAGGGCCAAATTAAA
66 TCAAGAAGGGAAGATTAAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAGGGCCAAATTAAA
34482668 GCCAC
131 GCCAC
* * * *
34482673 CATCCAATCTTTTACCTGTAAGTCAAGAGGG-AGAAATTGAAGCCACTATCCAATCTTTTA-CCC
1 CATCCAATCTTTTACC-CT-AGTCAA-AGGGTAG--ATTAAAGCCACCATCCAATATTTTACCCC
* * * *
34482736 CTAATTCAAGAAGGGAAGATTAAAGCTACTATCCAATCTTTTATCCCTAAATCAAGAGGG
61 CTAAGTCAAGAAGGGAAGATTAAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAGGG
34482796 GTAGATTGAA
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
135 16 0.15
136 1 0.01
137 8 0.07
138 60 0.56
139 22 0.21
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (135 bp):
CATCCAATCTTTTACCCTAGTCAAAGGGTAGATTAAAGCCACCATCCAATATTTTACCCCCTAAG
TCAAGAAGGGAAGATTAAAGCCACCATCCAATCTTTTACCCCTAAATCAAGAGGGCCAAATTAAA
GCCAC
Found at i:34482802 original size:46 final size:46
Alignment explanation
Indices: 34482460--34482814 Score: 316
Period size: 46 Copynumber: 8.1 Consensus size: 46
34482450 CAAATTGAAG
* * *
34482460 CATCCAATCTTTTA-CCCTAA-TC-AGA-GGGCAGACTGAAGACA-
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
* * *
34482501 CA-CCAATCTCTTACCCC-GA-TC-A-TGGGGCAGATTAAAG----
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
*
34482538 CATCCAATCTTTTA-CCCT-AGTCAA-A-GGGTAGATTAAAGCCAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
* * *
34482580 CATCCAATATTTTACCCCCTAAGTCAAGAAGGGCAGATTGAAGCCAC
1 CATCCAATCTTTTA-CCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
* *
34482627 CATCCAATCTTTTACCCCTAAGTCAAGAGGGCCAAATTAAAGCCAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
** * *
34482673 CATCCAATCTTTTACCTGTAAGTCAAGAGGGAG-AAATTGAAGCCAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGG-GCAGATTAAAGCCAC
* * * * *
34482719 TATCCAATCTTTTACCCCTAATTCAAGAAGGGAAGATTAAAGCTAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
* * * * * *
34482765 TATCCAATCTTTTATCCCTAAATCAAGAGGGGTAGATTGAAGCTAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
34482811 CATC
1 CATC
34482815 TCATAAAAGC
Statistics
Matches: 263, Mismatches: 34, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
37 6 0.02
38 24 0.09
39 1 0.00
40 25 0.10
41 5 0.02
42 13 0.05
44 4 0.02
45 7 0.03
46 150 0.57
47 28 0.11
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (46 bp):
CATCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTAAAGCCAC
Found at i:34483594 original size:27 final size:27
Alignment explanation
Indices: 34483541--34483594 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
34483531 GGAAGACCTG
* * * * *
34483541 CAAAAGAAAAGAAAAGAGAAGACAAAA
1 CAAAACAAAACAAAAAAGAACAAAAAA
34483568 CAAAACAAAACAAAAAAGAACAAAAAA
1 CAAAACAAAACAAAAAAGAACAAAAAA
34483595 ATATATGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (27 bp):
CAAAACAAAACAAAAAAGAACAAAAAA
Found at i:34484909 original size:21 final size:21
Alignment explanation
Indices: 34484876--34484929 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
34484866 ATATTATTTG
34484876 TTTTGT-TATTTTGTGAATGCA
1 TTTTGTCTA-TTTGTGAATGCA
* *
34484897 TTTTGTCTATTTGTTATTGCA
1 TTTTGTCTATTTGTGAATGCA
34484918 TTATTGATCTAT
1 TT-TTG-TCTAT
34484930 GTGCATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 18 0.64
22 5 0.18
23 5 0.18
ACGTcount: A:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (21 bp):
TTTTGTCTATTTGTGAATGCA
Found at i:34487014 original size:30 final size:30
Alignment explanation
Indices: 34486937--34487014 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
34486927 CCCCATACAA
* * * *
34486937 TCCAAAAATTTGAATTTAAGCCTTAAACTT
1 TCCAAAAATTCGAATTTGACCCTCAAACTT
* *
34486967 TTCAAAAATTCTAATTTGACCCTCAAACTT
1 TCCAAAAATTCGAATTTGACCCTCAAACTT
34486997 TCCAAAAATTCGAATTTG
1 TCCAAAAATTCGAATTTG
34487015 CCCCGATTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (30 bp):
TCCAAAAATTCGAATTTGACCCTCAAACTT
Found at i:34488648 original size:27 final size:27
Alignment explanation
Indices: 34488618--34488671 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
34488608 TTATTTTAAT
* *
34488618 AAATAAAATATTATTTAATATTTATTA
1 AAATAAAATATTAATTAAAATTTATTA
* *
34488645 AAATAATATCTTAATTAAAATTTATTA
1 AAATAAAATATTAATTAAAATTTATTA
34488672 TTTTTATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATAAAATATTAATTAAAATTTATTA
Found at i:34488651 original size:15 final size:17
Alignment explanation
Indices: 34488633--34488665 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
34488623 AAATATTATT
34488633 TAATAT-TT-ATTAAAA
1 TAATATCTTAATTAAAA
34488648 TAATATCTTAATTAAAA
1 TAATATCTTAATTAAAA
34488665 T
1 T
34488666 TTATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATCTTAATTAAAA
Found at i:34508149 original size:46 final size:47
Alignment explanation
Indices: 34508054--34508174 Score: 118
Period size: 46 Copynumber: 2.6 Consensus size: 47
34508044 TAATTCTTTT
* * * * * **
34508054 TGGCAACTTATCTGCAATTATAGTGGCTAGACCACATATATCTGTTC
1 TGGCAGCTTAACTGCAACTATGGTGGCTAGACCACATATACCTAATC
* * * *
34508101 TGGCAGCTTAGCTGCAA-TATGGTGGTTTGACGACATATACCTAATC
1 TGGCAGCTTAACTGCAACTATGGTGGCTAGACCACATATACCTAATC
*
34508147 TGGCAGCTTTAACTGCAACTCTGGTGGC
1 TGGCAGC-TTAACTGCAACTATGGTGGC
34508175 AATGTCCACA
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
46 29 0.48
47 24 0.40
48 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (47 bp):
TGGCAGCTTAACTGCAACTATGGTGGCTAGACCACATATACCTAATC
Found at i:34510716 original size:135 final size:135
Alignment explanation
Indices: 34510518--34510774 Score: 419
Period size: 135 Copynumber: 1.9 Consensus size: 135
34510508 TGCTCATTTT
*
34510518 ATCTTGTAATATTCTATATTGTACTAGTCACGTTAGGTGTGTATATATAAGATTATTATTATGCC
1 ATCTTGTAATATTCTATATTGCACTAGTCACGTTAGGTGTGTATATATAAGATTATTATTATGCC
* *
34510583 ATCAACTATAGGCGTTTTTTGTTTAATTTTTATTATTAAATCAACAAAATTCATTAAATCCGTGA
66 ATCAACTATAGGCG-CTTTT-TTTAATTTGTATTATTAAATCAACAAAATTCATTAAATCCGTGA
34510648 TTAATCC
129 TTAATCC
* * *
34510655 ATCTTGTTATATTCT-TA-TGCATTAGTCGCGTTAGGTGTGTATATATAAGATTATTATTATGCC
1 ATCTTGTAATATTCTATATTGCACTAGTCACGTTAGGTGTGTATATATAAGATTATTATTATGCC
*
34510718 ATCAACTATAGGTGCTTTTTTTAATTTGTATTATTAAATCAACAAAATTCATTAAAT
66 ATCAACTATAGGCGCTTTTTTTAATTTGTATTATTAAATCAACAAAATTCATTAAAT
34510775 TTAGTTTATT
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
133 37 0.33
134 4 0.04
135 56 0.50
136 2 0.02
137 14 0.12
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (135 bp):
ATCTTGTAATATTCTATATTGCACTAGTCACGTTAGGTGTGTATATATAAGATTATTATTATGCC
ATCAACTATAGGCGCTTTTTTTAATTTGTATTATTAAATCAACAAAATTCATTAAATCCGTGATT
AATCC
Found at i:34513018 original size:58 final size:55
Alignment explanation
Indices: 34512956--34513125 Score: 141
Period size: 58 Copynumber: 3.0 Consensus size: 55
34512946 ACGTAGGTTA
* * *
34512956 TATATTATTTTTA-TAATATTATATATTATAATTTTTTTAATTCATATTTAATAATAAT
1 TATATTATTGTTATTAA-ATTATATATTAT--TTTATTAAATT-ATATTTAATAATAAT
* *
34513014 TATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTTTATTTAATAATAAT
1 TATATT---ATTGTTATTAAATTATATATTATTTTATTAAATTATATTTAATAATAAT
* * * * *
34513072 TATGTTATAATATGATTAAATTATTTATTATTTT-TT-TATTA-ATTTAATAATAAT
1 TATATTAT--TGTTATTAAATTATATATTATTTTATTAAATTATATTTAATAATAAT
34513126 CTTATTAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
54 13 0.14
55 4 0.04
56 2 0.02
57 21 0.22
58 25 0.27
59 9 0.10
61 17 0.18
62 3 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (55 bp):
TATATTATTGTTATTAAATTATATATTATTTTATTAAATTATATTTAATAATAAT
Found at i:34513124 original size:54 final size:55
Alignment explanation
Indices: 34512981--34513133 Score: 157
Period size: 58 Copynumber: 2.7 Consensus size: 55
34512971 ATATTATATA
* * *
34512981 TTATAATTTTTTTAATTCATATTTAATAATAATTATATTAAGAATGTTATTAAATTAT
1 TTATTATTTTTTT-ATT-A-ATTTAATAATAATTATATTAAGAATATGATTAAATTAT
* * * * *
34513039 ATATTATTTTATTAAATTTTATTTAATAATAATTATGTT-ATAATATGATTAAATTAT
1 TTATTATTTT-TT-TA-TTAATTTAATAATAATTATATTAAGAATATGATTAAATTAT
34513096 TTATTATTTTTTTATTAATTTAATAATAATCT-TATTAA
1 TTATTATTTTTTTATTAATTTAATAATAAT-TATATTAA
34513134 AACTTAATAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
54 18 0.23
55 3 0.04
56 2 0.03
57 24 0.31
58 26 0.33
59 3 0.04
60 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (55 bp):
TTATTATTTTTTTATTAATTTAATAATAATTATATTAAGAATATGATTAAATTAT
Found at i:34520534 original size:2 final size:2
Alignment explanation
Indices: 34520527--34520556 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34520517 AATTTTAATC
*
34520527 CA CA CA CA CA CA AA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
34520557 TAAATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:34526913 original size:15 final size:15
Alignment explanation
Indices: 34526895--34526947 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
34526885 TAGTATTTAT
34526895 ATTTTAAATTGATTA
1 ATTTTAAATTGATTA
**
34526910 ATTTTAAATTTTTTTA
1 ATTTTAAA-TTGATTA
* *
34526926 TTTTTTAAATTGGTTA
1 -ATTTTAAATTGATTA
34526942 ATTTTA
1 ATTTTA
34526948 GTCTTGACCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 13 0.43
16 10 0.33
17 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
ATTTTAAATTGATTA
Found at i:34526946 original size:16 final size:16
Alignment explanation
Indices: 34526896--34526946 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
34526886 AGTATTTATA
34526896 TTTTAAATTGATTAA-
1 TTTTAAATTGATTAAT
** *
34526911 TTTTAAATTTTTTTATT
1 TTTTAAA-TTGATTAAT
*
34526928 TTTTAAATTGGTTAAT
1 TTTTAAATTGATTAAT
34526944 TTT
1 TTT
34526947 AGTCTTGACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTTAAATTGATTAAT
Found at i:34532025 original size:19 final size:19
Alignment explanation
Indices: 34531989--34532026 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34531979 AAAAAATACA
*
34531989 AAAATAAATTTTTCTATTT
1 AAAATAAATTTATCTATTT
34532008 AAAATAAATTATAT-TATTT
1 AAAATAAATT-TATCTATTT
34532027 GAGTGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATAAATTTATCTATTT
Found at i:34533298 original size:24 final size:23
Alignment explanation
Indices: 34533261--34533307 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
34533251 TCCACTTTGA
*
34533261 ATTTACTCTGAATAGTAATTAAAT
1 ATTTACTCTGAATACT-ATTAAAT
34533285 ATTTATCTCT-AATACTATTAAAT
1 ATTTA-CTCTGAATACTATTAAAT
34533308 TTGCATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 10 0.48
25 4 0.19
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (23 bp):
ATTTACTCTGAATACTATTAAAT
Found at i:34533396 original size:25 final size:25
Alignment explanation
Indices: 34533342--34533396 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
34533332 AAATCAAATA
*
34533342 TTAA-AAAAATTAAAAATATATATT
1 TTAATAAAAATTAAAAATAGATATT
* *
34533366 TGAATAAAAATTAAAAATAGATTTT
1 TTAATAAAAATTAAAAATAGATATT
34533391 TTAATA
1 TTAATA
34533397 TTAATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAATAAAAATTAAAAATAGATATT
Found at i:34538191 original size:16 final size:16
Alignment explanation
Indices: 34538170--34538201 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
34538160 ACGTCATTTC
34538170 TATCCCTTCTCAATAG
1 TATCCCTTCTCAATAG
34538186 TATCCCTTCTCAATAG
1 TATCCCTTCTCAATAG
34538202 GAGAATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
TATCCCTTCTCAATAG
Found at i:34538711 original size:22 final size:21
Alignment explanation
Indices: 34538686--34538740 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
34538676 AATTAGACTA
*
34538686 ATATTTATTTAATTATTAAAAT
1 ATATTTATTTAATT-GTAAAAT
*
34538708 ATATTT-TTGATATTGTAAAAT
1 ATATTTATTTA-ATTGTAAAAT
34538729 ATA-TTATTTAAT
1 ATATTTATTTAAT
34538741 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
ATATTTATTTAATTGTAAAAT
Found at i:34539981 original size:21 final size:22
Alignment explanation
Indices: 34539956--34540000 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
34539946 ATATTTATTT
*
34539956 TATATCATACAA-AAATTAAAA
1 TATATCATACAATAAATAAAAA
* *
34539977 TATATTATATAATAAATAAAAA
1 TATATCATACAATAAATAAAAA
34539999 TA
1 TA
34540001 AAATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TATATCATACAATAAATAAAAA
Found at i:34545058 original size:31 final size:30
Alignment explanation
Indices: 34544963--34545060 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 30
34544953 TTTACTTAAA
*
34544963 TTGGTACTTGAACTTGACATTTTTTCCTAAT
1 TTGGTACTTGAACTTG-TATTTTTTCCTAAT
**
34544994 TTGGTACCTAT-AA-TT-T-TTTTGGACCCT-AT
1 TTGGTA-CT-TGAACTTGTATTTT--TTCCTAAT
34545023 TTGGTACTTGAACTTGGTATTTTTTCCTAAT
1 TTGGTACTTGAACTT-GTATTTTTTCCTAAT
34545054 TTGGTAC
1 TTGGTAC
34545061 CTAAATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
27 1 0.02
28 8 0.15
29 10 0.19
30 6 0.12
31 18 0.35
32 8 0.15
33 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.49
Consensus pattern (30 bp):
TTGGTACTTGAACTTGTATTTTTTCCTAAT
Found at i:34545085 original size:60 final size:60
Alignment explanation
Indices: 34544931--34545089 Score: 198
Period size: 60 Copynumber: 2.7 Consensus size: 60
34544921 TTCTTTTTTT
* * *
34544931 TAATTTGATACCTAAACTTTTTTTTA-CTT-AAATTGGTACTTGAACTTGACATTTTTTCC
1 TAATTTGGTACCTAAA-TTTTTTTTAGATTCAATTTGGTACTTGAACTTGACATTTTTTCC
* ** * **
34544990 TAATTTGGTACCTATAA-TTTTTTTGGACCCTATTTGGTACTTGAACTTGGTATTTTTTCC
1 TAATTTGGTACCTA-AATTTTTTTTAGATTCAATTTGGTACTTGAACTTGACATTTTTTCC
34545050 TAATTTGGTACCTAAATTTTTTTTAGATTCAATTTGGTAC
1 TAATTTGGTACCTAAATTTTTTTTAGATTCAATTTGGTAC
34545090 CTAAATTTAT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
58 7 0.08
59 15 0.18
60 61 0.73
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.50
Consensus pattern (60 bp):
TAATTTGGTACCTAAATTTTTTTTAGATTCAATTTGGTACTTGAACTTGACATTTTTTCC
Found at i:34545336 original size:30 final size:31
Alignment explanation
Indices: 34545281--34545359 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 31
34545271 AGACCTCAAA
* *
34545281 AAGTTTAAGTACTAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
34545312 AAGTTTAAGTACCAAATT-AAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* *
34545342 AAATTTAAGTATCAAATT
1 AAGTTTAAGTACCAAATT
34545360 GACCAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 28 0.64
31 16 0.36
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:34545887 original size:20 final size:20
Alignment explanation
Indices: 34545859--34545896 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
34545849 TGAGATGTTG
* *
34545859 ATATGTTTTTAATTTTATAA
1 ATATATTTTTAATGTTATAA
34545879 ATATATTTTTAATGTTAT
1 ATATATTTTTAATGTTAT
34545897 TTGAAGAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
ATATATTTTTAATGTTATAA
Found at i:34555208 original size:24 final size:22
Alignment explanation
Indices: 34555160--34555208 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
34555150 AAAATCACAT
*
34555160 ACATAACAATATATCAATTTCA
1 ACATAACAATATAACAATTTCA
* *
34555182 ACATAATAATATACACACATTTTA
1 ACATAACAATATA-ACA-ATTTCA
34555206 ACA
1 ACA
34555209 CTGATATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 12 0.55
23 2 0.09
24 8 0.36
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (22 bp):
ACATAACAATATAACAATTTCA
Found at i:34555457 original size:50 final size:49
Alignment explanation
Indices: 34555394--34555520 Score: 155
Period size: 50 Copynumber: 2.6 Consensus size: 49
34555384 CTGTTATGAA
* * * *
34555394 CAAGCCACCCTAATTTGTATATATACTGCCACTAATATATTTTTGTGTC
1 CAAGCCACACTAATTTGCAGATATACTGCCACTAATATAATTTTGTGTC
**
34555443 CAAGCCATCACTAATTTGCAGATATACTGCCACTAATATAATTTTGTGGA
1 CAAGCCA-CACTAATTTGCAGATATACTGCCACTAATATAATTTTGTGTC
* * *
34555493 CATGCTACCACTGATTTGCAGATATACT
1 CAAGCCA-CACTAATTTGCAGATATACT
34555521 ACCTTTGCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
49 7 0.10
50 60 0.90
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (49 bp):
CAAGCCACACTAATTTGCAGATATACTGCCACTAATATAATTTTGTGTC
Found at i:34557143 original size:20 final size:20
Alignment explanation
Indices: 34557103--34557149 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
34557093 AAGGTATCGA
* *
34557103 TAGAAGTGGAATTGTATCGG
1 TAGAAGTGGAATTCTACCGG
* *
34557123 TATAAGTGGAGTTCTACCGG
1 TAGAAGTGGAATTCTACCGG
34557143 TAGAAGT
1 TAGAAGT
34557150 CTCATTGGAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.32, T:0.30
Consensus pattern (20 bp):
TAGAAGTGGAATTCTACCGG
Found at i:34560182 original size:20 final size:20
Alignment explanation
Indices: 34560159--34560205 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
34560149 AAGGTATCTA
* * *
34560159 TAGAAGTGGTGTTTTATCGG
1 TAGAAGTGGAGTTCTACCGG
34560179 TAGAAGTGGAGTTCTACCGG
1 TAGAAGTGGAGTTCTACCGG
34560199 TAGAAGT
1 TAGAAGT
34560206 CTCACTAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.32
Consensus pattern (20 bp):
TAGAAGTGGAGTTCTACCGG
Found at i:34565778 original size:18 final size:18
Alignment explanation
Indices: 34565735--34565771 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34565725 GGCCTTGCAA
*
34565735 TTATCCTTAGGCTTTGCC
1 TTATCCTTAGGCTTTACC
34565753 TTATCCTTAGGC-TTACC
1 TTATCCTTAGGCTTTACC
34565770 TT
1 TT
34565772 TTCCCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.46
Consensus pattern (18 bp):
TTATCCTTAGGCTTTACC
Found at i:34568624 original size:29 final size:28
Alignment explanation
Indices: 34568588--34568659 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
34568578 CATATAACAT
34568588 AGACAGAACACACAACAAATACGTAGCAC
1 AGACAGAACACACAAC-AATACGTAGCAC
* *
34568617 AGATAGAAACACACAACAATATGTAGCAC
1 AGACAG-AACACACAACAATACGTAGCAC
34568646 AGACAGAGACACAC
1 AGACAGA-ACACAC
34568660 CTCTAGTGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 27 0.71
30 10 0.26
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.08
Consensus pattern (28 bp):
AGACAGAACACACAACAATACGTAGCAC
Found at i:34569251 original size:26 final size:27
Alignment explanation
Indices: 34569222--34569298 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
34569212 TATTGGGGCT
*
34569222 CAATTTGGGT-TTAAGGT-TTTGGGTTA
1 CAATTAGGGTATTAA-GTCTTTGGGTTA
*
34569248 CAATTAGGGTATTCAGTCTTTGGGTTA
1 CAATTAGGGTATTAAGTCTTTGGGTTA
*
34569275 CAATTAGGGTATTCAGTCTTTGGG
1 CAATTAGGGTATTAAGTCTTTGGG
34569299 ATTTTGGTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 11 0.23
27 36 0.77
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.42
Consensus pattern (27 bp):
CAATTAGGGTATTAAGTCTTTGGGTTA
Found at i:34569274 original size:27 final size:27
Alignment explanation
Indices: 34569239--34569298 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
34569229 GGTTTAAGGT
34569239 TTTGGGTTACAATTAGGGTATTCAGTC
1 TTTGGGTTACAATTAGGGTATTCAGTC
34569266 TTTGGGTTACAATTAGGGTATTCAGTC
1 TTTGGGTTACAATTAGGGTATTCAGTC
34569293 TTTGGG
1 TTTGGG
34569299 ATTTTGGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (27 bp):
TTTGGGTTACAATTAGGGTATTCAGTC
Found at i:34576628 original size:16 final size:16
Alignment explanation
Indices: 34576604--34576652 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
34576594 AACACTTATC
* *
34576604 TCACTATCTATTGTTT
1 TCACAATCTATAGTTT
*
34576620 TCACAATCTAGAGTTTT
1 TCACAATCTATAG-TTT
*
34576637 TCTCAATCTATAGTTT
1 TCACAATCTATAGTTT
34576653 CCTATAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.49
Consensus pattern (16 bp):
TCACAATCTATAGTTT
Found at i:34576643 original size:17 final size:17
Alignment explanation
Indices: 34576617--34576652 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34576607 CTATCTATTG
34576617 TTTTCACAATCTAGAGT
1 TTTTCACAATCTAGAGT
* *
34576634 TTTTCTCAATCTATAGT
1 TTTTCACAATCTAGAGT
34576651 TT
1 TT
34576653 CCTATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (17 bp):
TTTTCACAATCTAGAGT
Found at i:34577684 original size:50 final size:50
Alignment explanation
Indices: 34577550--34577743 Score: 221
Period size: 50 Copynumber: 3.9 Consensus size: 50
34577540 CAAATCACCA
34577550 TTTGTGGACAAGCCACCACTGATTTGCAAATCA-ACTGCCATTGATA-ACACT
1 TTTGTGGACAAGCCACCACTGATTTGCAAAT-ATACTGCCATTGATATA-A-T
* * * * * *
34577601 ATTGTGGACAAGTCACCACTAATTTGTAGATATACTGCCATTGATATATT
1 TTTGTGGACAAGCCACCACTGATTTGCAAATATACTGCCATTGATATAAT
* * ** *
34577651 TTTGTGGCCAAGCTACCACTCCTTTGCAAATATACTGCCACTGATATAAT
1 TTTGTGGACAAGCCACCACTGATTTGCAAATATACTGCCATTGATATAAT
* * *
34577701 TTTGTGGGCATGCCACCACTGATTTGCAGATATACTGCCATTG
1 TTTGTGGACAAGCCACCACTGATTTGCAAATATACTGCCATTG
34577744 CTTTAACCTT
Statistics
Matches: 118, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
50 78 0.66
51 39 0.33
52 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (50 bp):
TTTGTGGACAAGCCACCACTGATTTGCAAATATACTGCCATTGATATAAT
Found at i:34579669 original size:24 final size:24
Alignment explanation
Indices: 34579642--34579687 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
34579632 CACAGAAAAC
34579642 TTAGCTCACACGAGCCCAGAATGG
1 TTAGCTCACACGAGCCCAGAATGG
** *
34579666 TTAGCTCTTACGAGCCTAGAAT
1 TTAGCTCACACGAGCCCAGAAT
34579688 CAAAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCTCACACGAGCCCAGAATGG
Found at i:34579715 original size:27 final size:27
Alignment explanation
Indices: 34579676--34579743 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
34579666 TTAGCTCTTA
*
34579676 CGAGCCTAGAATCAAAATAATGCTATTT
1 CGAGCC-AGAATCAAAATAACGCTATTT
*
34579704 CGAGCCAGAATCAAAATAACGCTCTTT
1 CGAGCCAGAATCAAAATAACGCTATTT
*
34579731 TGAGCCAGAATCA
1 CGAGCCAGAATCA
34579744 GATTACTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (27 bp):
CGAGCCAGAATCAAAATAACGCTATTT
Found at i:34584683 original size:33 final size:33
Alignment explanation
Indices: 34584641--34584707 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
34584631 CTTGGACCAC
34584641 TGGGATAACTAAAGAGACATTAAACCACTAGAT
1 TGGGATAACTAAAGAGACATTAAACCACTAGAT
34584674 TGGGATAACTAAAGAGACATTAAACCACTAGAT
1 TGGGATAACTAAAGAGACATTAAACCACTAGAT
34584707 T
1 T
34584708 ACACAGTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (33 bp):
TGGGATAACTAAAGAGACATTAAACCACTAGAT
Found at i:34585880 original size:30 final size:30
Alignment explanation
Indices: 34585835--34585922 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
34585825 AGTTACCGAT
*
34585835 ATGTGGAAGCCTTTGTGGTTGTTCTTTGAA
1 ATGTGGAAGCTTTTGTGGTTGTTCTTTGAA
* * * *
34585865 ATGTGAAAGCTTTTGTGGTTGTACTCTGAT
1 ATGTGGAAGCTTTTGTGGTTGTTCTTTGAA
* *
34585895 ATGTGGAAG-TCTTTGTGGCTATTCTTTG
1 ATGTGGAAGCT-TTTGTGGTTGTTCTTTG
34585923 TTATATTGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 1 0.02
30 46 0.98
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.44
Consensus pattern (30 bp):
ATGTGGAAGCTTTTGTGGTTGTTCTTTGAA
Found at i:34587846 original size:2 final size:2
Alignment explanation
Indices: 34587839--34587871 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34587829 TAATATTTTC
34587839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34587872 AACAAGAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34601650 original size:224 final size:221
Alignment explanation
Indices: 34601145--34601879 Score: 1130
Period size: 224 Copynumber: 3.3 Consensus size: 221
34601135 TACTTTATAG
* * * * * *
34601145 ATAAGTGGCAAATTTTTTCACTATTTTGATTAAAAAATTAATTTTAATCTCATATTAATTAGAGA
1 ATAAGTGTC-AATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATTGACTAGAGA
* *
34601210 ATACTCTCATGCTTCACTTCTTCACAATTTCCATTAAAAAGATAATTTTAATTTCACATTGACTA
65 ATACTCTCATGCCTCACTTCTTCACTATTTCCATTAAAAAGATAATTTTAA-TTCACATTGACTA
* *
34601275 AAAAAAATACTCTCATAGCTCTTTTTTCATTAAAAATTAATTTTAATCCATCACTGGTTAGAGAA
129 AAAAAAATACTCTCATAGCTCTTTTTTCATTAAAAATTAATTTTAATCCATCGCTGGCTAGAGAA
* * *
34601340 CACTCTCGTGTTCACACTTAATCTATAA
194 TACTCTCGTGCTCACACTTAATCCATAA
* *
34601368 ATAAGTGTCAATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCATATTGACTAGAGAG
1 ATAAGTGTCAATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATTGACTAGAGAA
* * * *
34601433 TACTCTCATGCCTCACTTTTTCGCTATTTCCATTAAAATGATCATTTTAATCTCACATTGACTAA
66 TACTCTCATGCCTCACTTCTTCACTATTTCCATTAAAAAGATAATTTTAAT-TCACATTGACT-A
* * *
34601498 AAAAAAATGCTCTCATAGCTCTTTTTTCATTAAAAATTAATTTTTAATCCATCGCTAGCGAGAGA
129 AAAAAAATACTCTCATAGCTCTTTTTTCATTAAAAATTAA-TTTTAATCCATCGCTGGCTAGAGA
*
34601563 ATACTCTCGTGCTCACACTTAATCCACAA
193 ATACTCTCGTGCTCACACTTAATCCATAA
* * *
34601592 ATAAATGTCTATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATATCACATTGACTAGAGAA
1 ATAAGTGTCAATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATTGACTAGAGAA
*
34601657 TACTCTCATGCCTCACTTCTTCACTATTTTCATTAAAAAGATAATTTTAATTCCACATTGACTAA
66 TACTCTCATGCCTCACTTCTTCACTATTTCCATTAAAAAGATAATTTTAATT-CACATTGACTAA
*
34601722 AAAAAATACTCTCATAGCT-ATTTTTCATTAAAAATTAATTTTAATCCATCGCTGGCTAGAGAAT
130 AAAAAATACTCTCATAGCTCTTTTTTCATTAAAAATTAATTTTAATCCATCGCTGGCTAGAGAAT
34601786 ACTCTCGTGCTCACACTTAATCCATAA
195 ACTCTCGTGCTCACACTTAATCCATAA
* * *
34601813 ATAAGTGTCCATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTTACATTGACTAAAGAA
1 ATAAGTGTCAATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATTGACTAGAGAA
34601878 TA
66 TA
34601880 TTATCATATC
Statistics
Matches: 467, Mismatches: 41, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
221 113 0.24
222 124 0.27
223 69 0.15
224 161 0.34
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (221 bp):
ATAAGTGTCAATTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATTGACTAGAGAA
TACTCTCATGCCTCACTTCTTCACTATTTCCATTAAAAAGATAATTTTAATTCACATTGACTAAA
AAAAATACTCTCATAGCTCTTTTTTCATTAAAAATTAATTTTAATCCATCGCTGGCTAGAGAATA
CTCTCGTGCTCACACTTAATCCATAA
Found at i:34601878 original size:93 final size:94
Alignment explanation
Indices: 34601743--34601983 Score: 240
Period size: 95 Copynumber: 2.6 Consensus size: 94
34601733 TCATAGCTAT
** * *
34601743 TTTTCATT-AAAAATTAATTTTAATCCATCGCTGGCTAGAGAATACTCTCGT-GCTCACACT-TA
1 TTTTCATTAAAAAATTAATTTTAATCCA-CATTGACTAGAGAATACTCTCATAGCTCACA-TGTA
* *
34601805 -ATCCATAAATAAGTGTCCA-TTTCTTCACTA
64 CAT-CATAAATAAGTGACAATTTTCTTCACTA
* * * * *
34601835 TTTTCATTAAAAAATTAATTTTAATCTTACATTGACTAAAGAATATTATCATATCTCACATGTAC
1 TTTTCATTAAAAAATTAATTTTAATC-CACATTGACTAGAGAATACTCTCATAGCTCACATGTAC
* * *
34601900 ATTATAAATGAGTGACAATTTTCTTCGCTA
65 ATCATAAATAAGTGACAATTTTCTTCACTA
* * * *
34601930 TTTTCATTAAAAAGTTAATTTTAGTCCGACATTGACTAGAGAACACTCTTATAG
1 TTTTCATTAAAAAATTAATTTTAATCC-ACATTGACTAGAGAATACTCTCATAG
34601984 TTTGTTTCTT
Statistics
Matches: 119, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
92 8 0.07
93 34 0.29
94 21 0.18
95 56 0.47
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (94 bp):
TTTTCATTAAAAAATTAATTTTAATCCACATTGACTAGAGAATACTCTCATAGCTCACATGTACA
TCATAAATAAGTGACAATTTTCTTCACTA
Found at i:34602486 original size:15 final size:14
Alignment explanation
Indices: 34602462--34602514 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
34602452 TTTACAAATT
34602462 AAAAAATAATTATA
1 AAAAAATAATTATA
34602476 AAAAGAATAATTATA
1 AAAA-AATAATTATA
* *
34602491 TTAAAAATAAATAATA
1 -AAAAAAT-AATTATA
*
34602507 TAAAAATA
1 AAAAAATA
34602515 TTCAATATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 5 0.15
15 20 0.59
16 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AAAAAATAATTATA
Found at i:34602508 original size:18 final size:16
Alignment explanation
Indices: 34602462--34602512 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
34602452 TTTACAAATT
34602462 AAAAAATAAT-TATAA
1 AAAAAATAATATATAA
*
34602477 AAAGAATAATTATATTAA
1 AAAAAATAA-TATA-TAA
34602495 AAATAAATAATATA-AA
1 AAA-AAATAATATATAA
34602511 AA
1 AA
34602513 TATTCAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 2 0.07
18 10 0.33
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAAAATAATATATAA
Found at i:34603014 original size:58 final size:58
Alignment explanation
Indices: 34602907--34603019 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
34602897 TAGAGCTTAT
* *
34602907 AGTTTAAAATTATTTATATATAATTGATATGAATGATGGTGATTTTAATAAAATACTA
1 AGTTTAAAATTATTTATATATAATTAATATGAATGATGGTGATTCTAATAAAATACTA
* * * *
34602965 AGTTTAAAGTTATTTATATATTATTAATATGAATGGTAGG-GATTCTAATACAATA
1 AGTTTAAAATTATTTATATATAATTAATATGAATGAT-GGTGATTCTAATAAAATA
34603020 GTAATACTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (58 bp):
AGTTTAAAATTATTTATATATAATTAATATGAATGATGGTGATTCTAATAAAATACTA
Found at i:34604208 original size:169 final size:173
Alignment explanation
Indices: 34603918--34604265 Score: 569
Period size: 169 Copynumber: 2.0 Consensus size: 173
34603908 ATAAATTTTG
34603918 TATTAATAATGTGTACAGCAGGGGGAATTTAGGTATTGACAGGATCCGGTCCTCTTAAAATGACA
1 TATTAATAATGTGTACAGCAGGGGGAATTT--GTA-TG--AGGATCCGGTCCTCTTAAAATGACA
* *
34603983 TATTTTTTATTTAGGTTTTTAAAATTTTTAAAATTTTAAATTAGTAAAATTAAAATTACATTTTA
61 TATTTTTTATTTAAGTTTTTAAAATTTTTAAAATTTTAAATTAGTAAAAATAAAATTACATTTTA
* *
34604048 ATTTCCCTAAAAATAATAATTTTTGATTTAATTTTTTAAAAATTATAT
126 ATCTCCCTAAAAATAATAAATTTTGATTTAATTTTTTAAAAATTATAT
34604096 TATTAATAATGTGTACAGCAGGGGGAA-TT-TA-G-GGATCCGGTCCTCTTAAAATGACATATTT
1 TATTAATAATGTGTACAGCAGGGGGAATTTGTATGAGGATCCGGTCCTCTTAAAATGACATATTT
* *
34604157 TTTATTTAAGTTTTTAAAATTTTTAAAATTTTAAATTAGTAAAAATAAAATTATATTTTGATCTC
66 TTTATTTAAGTTTTTAAAATTTTTAAAATTTTAAATTAGTAAAAATAAAATTACATTTTAATCTC
34604222 CCTAAAAATAATAAATTTTGATTTAATTTTTTAAAAATTATAT
131 CCTAAAAATAATAAATTTTGATTTAATTTTTTAAAAATTATAT
34604265 T
1 T
34604266 TTTACTATCG
Statistics
Matches: 164, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
169 132 0.80
172 1 0.01
174 2 0.01
177 2 0.01
178 27 0.16
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (173 bp):
TATTAATAATGTGTACAGCAGGGGGAATTTGTATGAGGATCCGGTCCTCTTAAAATGACATATTT
TTTATTTAAGTTTTTAAAATTTTTAAAATTTTAAATTAGTAAAAATAAAATTACATTTTAATCTC
CCTAAAAATAATAAATTTTGATTTAATTTTTTAAAAATTATAT
Found at i:34610662 original size:16 final size:14
Alignment explanation
Indices: 34610649--34610690 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34610639 TGTACGAATG
34610649 AATAAATATACGAA
1 AATAAATATACGAA
* *
34610663 AATAGATATAAGAAA
1 AATAAATATACG-AA
34610678 AATAAA-ATACGAA
1 AATAAATATACGAA
34610691 TCATGAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:34610846 original size:39 final size:39
Alignment explanation
Indices: 34610797--34610876 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
34610787 ATGAAGCTTC
*
34610797 GGAGAGTTTAGCGTTAAAATGTAATTTTGGAAAGTTTTA
1 GGAGAATTTAGCGTTAAAATGTAATTTTGGAAAGTTTTA
* *
34610836 GGAGAATTTAGGGTTAAAGTGTAATTTTGGAAAGTTTTA
1 GGAGAATTTAGCGTTAAAATGTAATTTTGGAAAGTTTTA
34610875 GG
1 GG
34610877 GGTAAAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.01, G:0.29, T:0.38
Consensus pattern (39 bp):
GGAGAATTTAGCGTTAAAATGTAATTTTGGAAAGTTTTA
Found at i:34610929 original size:58 final size:57
Alignment explanation
Indices: 34610859--34611128 Score: 215
Period size: 58 Copynumber: 4.6 Consensus size: 57
34610849 TTAAAGTGTA
* * * *
34610859 ATTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTAGGAAGTTCGAGGTAAAAATGTC
1 ATTTTGGGAAGTTTGA-GGGTAAAAATGTAATTTTAGGAAGTTCGAGGTAAAAATGTG
* * * *
34610917 ATTTTGGGAAGTTTGAGGGTAAAAATGTACTTTTTTA-AAAGTTCGTGGGTAAAAATATG
1 ATTTTGGGAAGTTTGAGGGTAAAAATGTA--ATTTTAGGAAGTTCG-AGGTAAAAATGTG
* * * *
34610976 ATTTTTGAAAGTTTG-GGG-ACAAAATTTAATTTTTGAGAAGTTCGAGGATAAAAATGTG
1 ATTTTGGGAAGTTTGAGGGTA-AAAATGTAATTTTAG-GAAGTTCGAGG-TAAAAATGTG
** * * * * * *
34611034 ATTTCT-GGAAGTTCAAGAGCAAAAATGTAATTTTTGGAAGTTTGAGGGCAAAAATGTA
1 ATTT-TGGGAAGTTTGAGGGTAAAAATGTAATTTTAGGAAGTTCGA-GGTAAAAATGTG
* * *
34611092 ATTTTAGAGAAGTTTGAGGGTCAAAATGTGATTTTAG
1 ATTTT-GGGAAGTTTGAGGGTAAAAATGTAATTTTAG
34611129 AAAAGTTTAG
Statistics
Matches: 167, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
56 4 0.02
57 16 0.10
58 77 0.46
59 69 0.41
60 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (57 bp):
ATTTTGGGAAGTTTGAGGGTAAAAATGTAATTTTAGGAAGTTCGAGGTAAAAATGTG
Found at i:34611095 original size:88 final size:87
Alignment explanation
Indices: 34610880--34611125 Score: 246
Period size: 88 Copynumber: 2.8 Consensus size: 87
34610870 TTTTAGGGGT
* * * * * *
34610880 AAAAATGTCATTTTAGGAAGTTCGAGGTAAAAATGTCA-TTTTGGGAAGTTTGAGGGTAAAAATG
1 AAAAATGTAATTTTTGGAAGTTTGAGGGAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATG
* ** * *
34610944 T-ACTTTTTTAAAAGTTCGTGGGT
66 TGA--TTTCTAAAAGTTCAAGAGC
* * * * * *
34610967 AAAAATATGATTTTTGAAAGTTTG-GGGACAAAATTTAATTTTTGAGAAGTTCGAGGATAAAAAT
1 AAAAATGTAATTTTTGGAAGTTTGAGGGA-AAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAAT
**
34611031 GTGATTTCTGGAAGTTCAAGAGC
65 GTGATTTCTAAAAGTTCAAGAGC
* *
34611054 AAAAATGTAATTTTTGGAAGTTTGAGGGCAAAAATGTAATTTTAGAGAAGTTTGAGGGTCAAAAT
1 AAAAATGTAATTTTTGGAAGTTTGAGGG-AAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAAT
34611119 GTGATTT
65 GTGATTT
34611126 TAGAAAAGTT
Statistics
Matches: 128, Mismatches: 26, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
86 3 0.02
87 59 0.46
88 64 0.50
89 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAGTTTGAGGGAAAAATGTAATTTTTGAGAAGTTTGAGGGTAAAAATG
TGATTTCTAAAAGTTCAAGAGC
Found at i:34611106 original size:30 final size:30
Alignment explanation
Indices: 34610837--34611200 Score: 238
Period size: 30 Copynumber: 12.5 Consensus size: 30
34610827 AAAGTTTTAG
* * *
34610837 GAGAA-TTT-AGGGTTAAAGTGTAATTTTG
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* * *
34610865 GA-AAGTTTTAGGGGTAAAAATGTCATTTTA
1 GAGAAGTTTGA-GGGTAAAAATGTAATTTTT
* *
34610895 G-GAAGTTCGA-GGTAAAAATGTCA-TTTT
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* *
34610922 GGGAAGTTTGAGGGTAAAAATGTACTTTTT
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* * * * * *
34610952 TAAAAGTTCGTGGGTAAAAATATGATTTTT
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
*
34610982 GA-AAGTTTG-GGG-ACAAAATTTAATTTTT
1 GAGAAGTTTGAGGGTA-AAAATGTAATTTTT
* * * *
34611010 GAGAAGTTCGAGGATAAAAATGTGATTTCT
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
** * *
34611040 G-GAAGTTCAAGAGCAAAAATGTAATTTTT
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* *
34611069 G-GAAGTTTGAGGGCAAAAATGTAATTTTA
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* * *
34611098 GAGAAGTTTGAGGGTCAAAATGTGATTTTA
1 GAGAAGTTTGAGGGTAAAAATGTAATTTTT
* * * *
34611128 GAAAAGTTT-AGTGGTTAAAATGAAATTTTG
1 GAGAAGTTTGAG-GGTAAAAATGTAATTTTT
* *
34611158 GAAAAGTTTGGGGGTCAAAACATG--ATTTTT
1 GAGAAGTTTGAGGGT-AAAA-ATGTAATTTTT
34611188 G-GATAGTTT-AGGG
1 GAGA-AGTTTGAGGG
34611201 ACCTTCCAGG
Statistics
Matches: 269, Mismatches: 50, Indels: 33
0.76 0.14 0.09
Matches are distributed among these distances:
27 7 0.03
28 43 0.16
29 78 0.29
30 133 0.49
31 5 0.02
32 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
GAGAAGTTTGAGGGTAAAAATGTAATTTTT
Found at i:34612277 original size:3 final size:3
Alignment explanation
Indices: 34612269--34612321 Score: 70
Period size: 3 Copynumber: 16.7 Consensus size: 3
34612259 TTTTTGTTAT
*
34612269 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTTA TTA TGTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA -TTA
34612317 TTA TT
1 TTA TT
34612322 TAATGAAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 37 0.82
4 7 0.16
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:34613023 original size:6 final size:6
Alignment explanation
Indices: 34613012--34613083 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
34613002 ACATTTTTAA
* * *
34613012 TTAAAT TTAAAT TT-AAT TTAAA- ATAAGT TTAAAT TTAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
34613057 TTAAAC TTAAA- -TAAAT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
34613084 ATTGGGTTCC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
4 4 0.08
5 12 0.23
6 36 0.69
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:34613028 original size:16 final size:16
Alignment explanation
Indices: 34613019--34613083 Score: 78
Period size: 16 Copynumber: 4.0 Consensus size: 16
34613009 TAATTAAATT
34613019 TAAATTT-AATTTAAAA
1 TAAATTTAAATTT-AAA
*
34613035 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
34613052 TAAATTTAAACTTAAA
1 TAAATTTAAATTTAAA
*
34613068 TAAATTAAAATTTAAA
1 TAAATTTAAATTTAAA
34613084 ATTGGGTTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 23 0.53
17 20 0.47
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:34613046 original size:17 final size:17
Alignment explanation
Indices: 34613019--34613085 Score: 93
Period size: 17 Copynumber: 4.1 Consensus size: 17
34613009 TAATTAAATT
34613019 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
*
34613035 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
34613052 TAAATTTAAACTT-AAA
1 TAAATTTAAATTTAAAA
*
34613068 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
34613085 T
1 T
34613086 TGGGTTCCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
16 20 0.45
17 24 0.55
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:34613967 original size:17 final size:17
Alignment explanation
Indices: 34613941--34613991 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
34613931 TTCACCCCAA
*
34613941 CCTCTCTTTTTCTTTTT
1 CCTCTTTTTTTCTTTTT
34613958 CCTC-TTTTTTCTTTTT
1 CCTCTTTTTTTCTTTTT
* *
34613974 TCTTTTTTCTTTCTTTTT
1 CCTCTTTT-TTTCTTTTT
34613992 TATTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 13 0.45
17 7 0.24
18 9 0.31
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
CCTCTTTTTTTCTTTTT
Found at i:34613970 original size:7 final size:7
Alignment explanation
Indices: 34613947--34613985 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
34613937 CCAACCTCTC
34613947 TTTTTCT
1 TTTTTCT
34613954 TTTTCCTCT
1 TTTT--TCT
34613963 TTTTTCT
1 TTTTTCT
34613970 TTTTTCT
1 TTTTTCT
34613977 TTTTTCT
1 TTTTTCT
34613984 TT
1 TT
34613986 CTTTTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 23 0.77
9 7 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:34613977 original size:14 final size:15
Alignment explanation
Indices: 34613942--34613985 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
34613932 TCACCCCAAC
34613942 CTCTCTTTTTCTTTTT
1 CTCT-TTTTTCTTTTT
34613958 CCTCTTTTTTCTTTTT
1 -CTCTTTTTTCTTTTT
34613974 -TCTTTTTTCTTT
1 CTCTTTTTTCTTT
34613986 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.44
16 11 0.41
17 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
CTCTTTTTTCTTTTT
Found at i:34618750 original size:16 final size:14
Alignment explanation
Indices: 34618737--34618778 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
34618727 TGTACGAATG
34618737 AATAAATATACGAA
1 AATAAATATACGAA
* *
34618751 AATAGATATAAGAAA
1 AATAAATATACG-AA
34618766 AATAAA-ATACGAA
1 AATAAATATACGAA
34618779 TCATGAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:34618921 original size:28 final size:28
Alignment explanation
Indices: 34618889--34619018 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 28
34618879 AGCTTCGGAG
* *
34618889 AGTTTGAAGTTAAAACATAATTTTGGAA
1 AGTTTTAAGGTAAAACATAATTTTGGAA
* *
34618917 AGTTTTAGGGGTAAAA-ATGTCATTTTGGAAA
1 AGTTTTA-AGGTAAAACA--TAATTTTGG-AA
* *
34618948 AG-TTTAGGGTAAAACGTAATTTTGGAA
1 AGTTTTAAGGTAAAACATAATTTTGGAA
*
34618975 AGTTTTAAGGTAAAA-ATGTCATTTTGGGAA
1 AGTTTTAAGGTAAAACA--TAATTTT-GGAA
34619005 AG-TTTAAGGTAAAA
1 AGTTTTAAGGTAAAA
34619019 ATGTGATTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 17
0.76 0.08 0.15
Matches are distributed among these distances:
27 4 0.05
28 26 0.31
29 32 0.38
30 18 0.21
31 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (28 bp):
AGTTTTAAGGTAAAACATAATTTTGGAA
Found at i:34619000 original size:29 final size:29
Alignment explanation
Indices: 34618906--34619113 Score: 180
Period size: 29 Copynumber: 7.2 Consensus size: 29
34618896 AGTTAAAACA
34618906 TAATTTTGGAAAGTTTTAGGGGTAAAAATG
1 TAATTTTGGAAAGTTTTA-GGGTAAAAATG
* *
34618936 TCATTTTGGAAAAG-TTTAGGGT-AAAACG
1 TAATTTTGG-AAAGTTTTAGGGTAAAAATG
*
34618964 TAATTTTGGAAAGTTTTAAGGTAAAAATG
1 TAATTTTGGAAAGTTTTAGGGTAAAAATG
* *
34618993 TCATTTTGGGAAAG-TTTAAGGTAAAAATG
1 TAATTTT-GGAAAGTTTTAGGGTAAAAATG
* * *
34619022 TGATTTT-TAGAAGTTTGAGGGTAAAAATG
1 TAATTTTGGA-AAGTTTTAGGGTAAAAATG
** *
34619051 TAATTTTTAAGAAG-TTTGGGGTAAAAATG
1 TAATTTTGGA-AAGTTTTAGGGTAAAAATG
* **
34619080 TGATTTTTGG-AAGTTCGAGGG--AAAATG
1 T-AATTTTGGAAAGTTTTAGGGTAAAAATG
34619107 TAATTTT
1 TAATTTT
34619114 TAAAAAGGTC
Statistics
Matches: 148, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
26 5 0.03
27 12 0.08
28 26 0.18
29 73 0.49
30 28 0.19
31 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TAATTTTGGAAAGTTTTAGGGTAAAAATG
Found at i:34619016 original size:57 final size:58
Alignment explanation
Indices: 34618889--34619018 Score: 199
Period size: 57 Copynumber: 2.2 Consensus size: 58
34618879 AGCTTCGGAG
* *
34618889 AGTTTGAAGTTAAAACATAATTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTGGAAA
1 AGTTT-AAGGTAAAACATAATTTTGGAAAGTTTTAGAGGTAAAAATGTCATTTTGGAAA
* * *
34618948 AGTTTAGGGTAAAACGTAATTTTGGAAAGTTTTA-AGGTAAAAATGTCATTTTGGGAA
1 AGTTTAAGGTAAAACATAATTTTGGAAAGTTTTAGAGGTAAAAATGTCATTTTGGAAA
34619005 AGTTTAAGGTAAAA
1 AGTTTAAGGTAAAA
34619019 ATGTGATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 34 0.52
58 26 0.40
59 5 0.08
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (58 bp):
AGTTTAAGGTAAAACATAATTTTGGAAAGTTTTAGAGGTAAAAATGTCATTTTGGAAA
Found at i:34619028 original size:58 final size:58
Alignment explanation
Indices: 34618908--34619275 Score: 245
Period size: 58 Copynumber: 6.3 Consensus size: 58
34618898 TTAAAACATA
* *
34618908 ATTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTGGAAAAGTTTAGGGT-AAAACGTA
1 ATTTTGGAAAGTTTTA-GGGTAAAAATGTCATTTTGGAAAAGTTTAGGGTAAAAATGTG
* * *
34618966 ATTTTGGAAAGTTTTAAGGTAAAAATGTCATTTTGGGAAAGTTTAAGGTAAAAATGTG
1 ATTTTGGAAAGTTTTAGGGTAAAAATGTCATTTTGGAAAAGTTTAGGGTAAAAATGTG
* * * * *
34619024 ATTTT-TAGAAGTTTGAGGGTAAAAATGTAATTTT-TAAGAAGTTTGGGGTAAAAATGTG
1 ATTTTGGA-AAGTTTTAGGGTAAAAATGTCATTTTGGAA-AAGTTTAGGGTAAAAATGTG
** * ** * **
34619082 ATTTTTGG-AAGTTCGAGGG--AAAATGTAATTTTTAAAAAGGTCGGCGGTAAAAATGTG
1 A-TTTTGGAAAGTTTTAGGGTAAAAATGTCATTTTGGAAAAGTTTAG-GGTAAAAATGTG
* ** * * * * ** *
34619139 ATTTT-TAGAAGTTCGAGGG-CAAAATGTAATTTTAGAGAAGTTCGGGGGTTAAAATGTG
1 ATTTTGGA-AAGTTTTAGGGTAAAAATGTCATTTTGGAAAAGTT-TAGGGTAAAAATGTG
* * * * *
34619197 ATTTTAGAAAAG-TTTAGGGGTTAAAATG-CAATTTTGGAAAAGTGTAGGGGTCAAAATATG
1 ATTTT-GGAAAGTTTTA-GGGTAAAAATGTC-ATTTTGGAAAAGTTTA-GGGTAAAAATGTG
*
34619257 ATTTTTGGATAG-TTTAGGG
1 A-TTTTGGAAAGTTTTAGGG
34619276 ACCTTTTGGG
Statistics
Matches: 253, Mismatches: 39, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
56 23 0.09
57 58 0.23
58 115 0.45
59 15 0.06
60 38 0.15
61 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (58 bp):
ATTTTGGAAAGTTTTAGGGTAAAAATGTCATTTTGGAAAAGTTTAGGGTAAAAATGTG
Found at i:34619143 original size:29 final size:29
Alignment explanation
Indices: 34619012--34619202 Score: 185
Period size: 29 Copynumber: 6.6 Consensus size: 29
34619002 GAAAGTTTAA
* *
34619012 GGTAAAAATGTGATTTTTAGAAGTTTGAG
1 GGTAAAAATGTGATTTTAAGAAGTTCGAG
* *
34619041 GGTAAAAATGTAATTTTTAAGAAGTTTG-G
1 GGTAAAAATGTGA-TTTTAAGAAGTTCGAG
**
34619070 GGTAAAAATGTGATTTTTGGAAGTTCGAG
1 GGTAAAAATGTGATTTTAAGAAGTTCGAG
* * *
34619099 GG--AAAATGTAATTTTTAAAAAGGTCG-G
1 GGTAAAAATGTGA-TTTTAAGAAGTTCGAG
*
34619126 CGGTAAAAATGTGATTTTTAGAAGTTCGAG
1 -GGTAAAAATGTGATTTTAAGAAGTTCGAG
* * *
34619156 GG-CAAAATGTAATTTTAGAGAAGTTCGGG
1 GGTAAAAATGTGATTTTA-AGAAGTTCGAG
*
34619185 GGTTAAAATGTGATTTTA
1 GGTAAAAATGTGATTTTA
34619203 GAAAAGTTTA
Statistics
Matches: 132, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
27 9 0.07
28 35 0.27
29 53 0.40
30 35 0.27
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
GGTAAAAATGTGATTTTAAGAAGTTCGAG
Found at i:34619150 original size:57 final size:57
Alignment explanation
Indices: 34619012--34619205 Score: 268
Period size: 58 Copynumber: 3.4 Consensus size: 57
34619002 GAAAGTTTAA
* *
34619012 GGTAAAAATGTGATTTTTAGAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTGG
1 GGTAAAAATGTGATTTTTAGAAGTTCGAGGG-AAAAATGTAATTTTTAAGAAGTTCGG
* * *
34619070 GGTAAAAATGTGATTTTTGGAAGTTCGAGGG-AAAATGTAATTTTTAAAAAGGTCGG
1 GGTAAAAATGTGATTTTTAGAAGTTCGAGGGAAAAATGTAATTTTTAAGAAGTTCGG
*
34619126 CGGTAAAAATGTGATTTTTAGAAGTTCGAGGGCAAAATGTAA-TTTTAGAGAAGTTCGGG
1 -GGTAAAAATGTGATTTTTAGAAGTTCGAGGGAAAAATGTAATTTTTA-AGAAGTTC-GG
*
34619185 GGTTAAAATGTGA-TTTTAGAA
1 GGTAAAAATGTGATTTTTAGAA
34619206 AAGTTTAGGG
Statistics
Matches: 123, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
56 22 0.18
57 43 0.35
58 56 0.46
59 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (57 bp):
GGTAAAAATGTGATTTTTAGAAGTTCGAGGGAAAAATGTAATTTTTAAGAAGTTCGG
Found at i:34619195 original size:30 final size:30
Alignment explanation
Indices: 34619012--34619231 Score: 161
Period size: 30 Copynumber: 7.6 Consensus size: 30
34619002 GAAAGTTTAA
* * * *
34619012 GGTAAAAATGTGATTTT-TAGAAGTTTGAG
1 GGTAAAAATGTAATTTTAGAGAAGTTCGGG
*
34619041 GGTAAAAATGTAATTTTTA-AGAAGTT-TGG
1 GGTAAAAATGTAA-TTTTAGAGAAGTTCGGG
* * *
34619070 GGTAAAAATGTGATTTTTG-GAAGTTCGAG
1 GGTAAAAATGTAATTTTAGAGAAGTTCGGG
* * *
34619099 GG--AAAATGTAATTTTTA-AAAAGGTCGGC
1 GGTAAAAATGTAA-TTTTAGAGAAGTTCGGG
* * *
34619127 GGTAAAAATGTGATTTT-TAGAAGTTCGAG
1 GGTAAAAATGTAATTTTAGAGAAGTTCGGG
*
34619156 GG-CAAAATGTAATTTTAGAGAAGTTCGGG
1 GGTAAAAATGTAATTTTAGAGAAGTTCGGG
* * * **
34619185 GGTTAAAATGTGATTTTAGAAAAGTTTAGG
1 GGTAAAAATGTAATTTTAGAGAAGTTCGGG
* *
34619215 GGTTAAAATGCAATTTT
1 GGTAAAAATGTAATTTT
34619232 GGAAAAGTGT
Statistics
Matches: 151, Mismatches: 29, Indels: 21
0.75 0.14 0.10
Matches are distributed among these distances:
27 8 0.05
28 34 0.23
29 53 0.35
30 56 0.37
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
GGTAAAAATGTAATTTTAGAGAAGTTCGGG
Found at i:34619237 original size:30 final size:30
Alignment explanation
Indices: 34618897--34619253 Score: 144
Period size: 30 Copynumber: 12.3 Consensus size: 30
34618887 AGAGTTTGAA
** *
34618897 GTTAAAACATAATTTT-GGAAAGTTTTAGGG
1 GTTAAAATGTAATTTTAGAAAAG-TTTAGGG
* * *
34618927 GTAAAAATGTCATTTTGGAAAAGTTTA-GG
1 GTTAAAATGTAATTTTAGAAAAGTTTAGGG
* * *
34618956 G-TAAAACGTAATTTT-GGAAAGTTTTA-AG
1 GTTAAAATGTAATTTTAGAAAAG-TTTAGGG
* * * * *
34618984 GTAAAAATGTCATTTTGGGAAAGTTTA-AG
1 GTTAAAATGTAATTTTAGAAAAGTTTAGGG
* *
34619013 GTAAAAATGTGATTTTTAG--AAGTTT-GAGG
1 GTTAAAATGT-AATTTTAGAAAAGTTTAG-GG
* *
34619042 GTAAAAATGTAATTTTTA-AGAAGTTT-GGG
1 GTTAAAATGTAA-TTTTAGAAAAGTTTAGGG
* * * * *
34619071 GTAAAAATGTGATTTTTG-GAAG-TTCGAGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAG-GG
* *
34619100 G--AAAATGTAATTTTTA-AAAAG-GTCGGCG
1 GTTAAAATGTAA-TTTTAGAAAAGTTTAGG-G
* * *
34619128 GTAAAAATGTGATTTTTAG--AAG-TTCGAGG
1 GTTAAAATGT-AATTTTAGAAAAGTTTAG-GG
* * **
34619157 G-CAAAATGTAATTTTAGAGAAGTTCGGGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAGGG
*
34619186 GTTAAAATGTGATTTTAGAAAAGTTTAGGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAGGG
* * *
34619216 GTTAAAATGCAATTTTGGAAAAGTGTAGGG
1 GTTAAAATGTAATTTTAGAAAAGTTTAGGG
*
34619246 GTCAAAAT
1 GTTAAAAT
34619254 ATGATTTTTG
Statistics
Matches: 262, Mismatches: 40, Indels: 50
0.74 0.11 0.14
Matches are distributed among these distances:
27 23 0.09
28 52 0.20
29 76 0.29
30 105 0.40
31 6 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (30 bp):
GTTAAAATGTAATTTTAGAAAAGTTTAGGG
Found at i:34621075 original size:6 final size:6
Alignment explanation
Indices: 34621064--34621130 Score: 52
Period size: 6 Copynumber: 11.8 Consensus size: 6
34621054 ATATTTTTAA
* * * * *
34621064 TTAAAT TTAAAT TT-AAT TTAAA- ATAAAT TTAAAC TCAAA- ATAAGT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
34621109 TTAAAT TTAAA- ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAA
34621131 ATAAATAATT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
5 15 0.33
6 31 0.67
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:34621080 original size:16 final size:16
Alignment explanation
Indices: 34621071--34621129 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
34621061 TAATTAAATT
34621071 TAAATTTAATTTAAAA
1 TAAATTTAATTTAAAA
* *
34621087 TAAATTTAAACTCAAAA
1 TAAATTT-AATTTAAAA
*
34621104 TAAGTTTAAATTTAAAA
1 TAAATTT-AATTTAAAA
34621121 TAAATTTAA
1 TAAATTTAA
34621130 AATAAATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.25
17 27 0.75
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:34621081 original size:11 final size:11
Alignment explanation
Indices: 34621062--34621136 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
34621052 GGATATTTTT
34621062 AATTAAATTTA
1 AATTAAATTTA
*
34621073 AATTTAATTTA
1 AATTAAATTTA
*
34621084 AAATAAATTTA
1 AATTAAATTTA
* *
34621095 AACTCAAA-ATA
1 AA-TTAAATTTA
*
34621106 AGTTTAAATTTA
1 A-ATTAAATTTA
*
34621118 AAATAAATTTA
1 AATTAAATTTA
*
34621129 AAATAAAT
1 AATTAAAT
34621137 AATTTAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
11 44 0.88
12 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:34621116 original size:34 final size:32
Alignment explanation
Indices: 34621078--34621153 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 32
34621068 ATTTAAATTT
*
34621078 AATTTAAAATAAATTTAAACTCAAAATAAGTTT-A
1 AATTTAAAATAAATTTAAAAT--AAATAA-TTTAA
34621112 AATTTAAAATAAATTTAAAATAAATAATTTAA
1 AATTTAAAATAAATTTAAAATAAATAATTTAA
34621144 AATTTAAAAT
1 AATTTAAAAT
34621154 TGAGTTTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
31 3 0.08
32 17 0.43
34 20 0.50
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
AATTTAAAATAAATTTAAAATAAATAATTTAA
Found at i:34621142 original size:14 final size:15
Alignment explanation
Indices: 34621084--34621146 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 15
34621074 ATTTAATTTA
*
34621084 AAATAAATTTAAACT
1 AAATAAATTTAAAAT
* *
34621099 CAAAATAAGTTTAAATTT
1 --AAATAAATTTAAA-AT
34621117 AAAATAAATTTAAAAT
1 -AAATAAATTTAAAAT
34621133 AAAT-AATTTAAAAT
1 AAATAAATTTAAAAT
34621147 TTAAAATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.24
15 4 0.10
16 1 0.02
17 25 0.61
18 1 0.02
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATAAATTTAAAAT
Found at i:34622745 original size:15 final size:16
Alignment explanation
Indices: 34622725--34622754 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34622715 AAAAGGAAGA
34622725 GAAAAA-GAAAAAAAC
1 GAAAAAGGAAAAAAAC
34622740 GAAAAAGGAAAAAAA
1 GAAAAAGGAAAAAAA
34622755 AGGAAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
GAAAAAGGAAAAAAAC
Found at i:34623889 original size:98 final size:97
Alignment explanation
Indices: 34623714--34624018 Score: 346
Period size: 98 Copynumber: 3.1 Consensus size: 97
34623704 AGGAAATGTT
* * * * * *
34623714 GAATCATATACCCTAGAGATATGAAGGGAAAGG-TCAAGGCCGTAACGGTGAACCTTATACACTA
1 GAATCTTATA-CCTAGAGATGTGGAGGGAAAGGTTGAA-GCCGCAACGGTGAACCTTATACCCTA
* * * * *
34623778 GAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGT
64 GAGATGTAAAGGGAAAGATTGAAGCCACAACGGC
* * *
34623812 GAACCTTATACCATAGAGATGTGGAGGGAAAGGTTGAAGTCGCAACGGTGAACCTTCTACCCTAG
1 GAATCTTATACC-TAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCCTAG
* * *
34623877 AGAT-TATAAGGGAAATATTGAAGTCACAACGAC
65 AGATGTA-AAGGGAAAGATTGAAGCCACAACGGC
* * * *
34623910 GAATCTTATACTCTAGAGATGTAGAGGGAAAGGTTG-AGCCGCAACGGTGGACCTTAAACCTTAG
1 GAATCTTATAC-CTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCCTAG
*
34623974 AGATGTGAAGGGAAAGATTGAAGCCACAACGGC
65 AGATGTAAAGGGAAAGATTGAAGCCACAACGGC
34624007 GAATCTTATACC
1 GAATCTTATACC
34624019 CCGAAGATGA
Statistics
Matches: 174, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
96 1 0.01
97 65 0.37
98 104 0.60
99 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.20
Consensus pattern (97 bp):
GAATCTTATACCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCCTAGA
GATGTAAAGGGAAAGATTGAAGCCACAACGGC
Found at i:34624027 original size:49 final size:48
Alignment explanation
Indices: 34623720--34624019 Score: 298
Period size: 49 Copynumber: 6.1 Consensus size: 48
34623710 TGTTGAATCA
* * *
34623720 TATACCCTAGAGATATGAAGGGAAAGG-TCAAGGCCGTAACGGTGAACCT
1 TATACCCTAGAGATGT-AAGGGAAAGGTTGAA-GCCGCAACGGTGAACCT
* *
34623769 TATACACTAGAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGTGAACCT
1 TATACCCTAGAGATGTA-AGGGAAAGGTTGAAGCCGCAACGGTGAACCT
* * *
34623818 TATACCATAGAGATGTGGAGGGAAAGGTTGAAGTCGCAACGGTGAACCT
1 TATACCCTAGAGATGT-AAGGGAAAGGTTGAAGCCGCAACGGTGAACCT
* * ** * * ** *
34623867 TCTACCCTAGAGATTATAAGGGAAATATTGAAGTCACAACGACGAATCT
1 TATACCCTAGAGA-TGTAAGGGAAAGGTTGAAGCCGCAACGGTGAACCT
* *
34623916 TATACTCTAGAGATGTAGAGGGAAAGGTTG-AGCCGCAACGGTGGACCT
1 TATACCCTAGAGATGTA-AGGGAAAGGTTGAAGCCGCAACGGTGAACCT
* * * * * *
34623964 TAAACCTTAGAGATGTGAAGGGAAAGATTGAAGCCACAACGGCGAATCT
1 TATACCCTAGAGATGT-AAGGGAAAGGTTGAAGCCGCAACGGTGAACCT
34624013 TATACCC
1 TATACCC
34624020 CGAAGATGAG
Statistics
Matches: 204, Mismatches: 40, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
48 40 0.20
49 159 0.78
50 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.20
Consensus pattern (48 bp):
TATACCCTAGAGATGTAAGGGAAAGGTTGAAGCCGCAACGGTGAACCT
Found at i:34624061 original size:146 final size:147
Alignment explanation
Indices: 34623767--34624061 Score: 355
Period size: 146 Copynumber: 2.0 Consensus size: 147
34623757 AACGGTGAAC
*
34623767 CTTATACACTAGAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGTGAACCTTATACCATAGAGAT
1 CTTATACACTAGAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGTGAACCTTAAACCATAGAGAT
* * * * * * * *
34623832 GTGGAGGGAAAGGTTGAAGTCGCAACGGTGAACCTTCTACCCTAGAGATTATAAGGGAAATATTG
66 GTGAAGGGAAAGATTGAAGCCACAACGGCGAACCTTATACCCTAGAGATGATAAGGGAAAGATTG
* *
34623897 AAGTCACAACGACGAAT
131 AAGTCACAAAGACAAAT
* * * *
34623914 CTTATACTCTAGAGATGTAGAGGGAAAGGTT-GAGCCGCAACGGTGGACCTTAAACCTTAGAGAT
1 CTTATACACTAGAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGTGAACCTTAAACCATAGAGAT
* * *
34623978 GTGAAGGGAAAGATTGAAGCCACAACGGCGAATCTTATACCC-CGA-A-GATGAGGAGAAGCAGA
66 GTGAAGGGAAAGATTGAAGCCACAACGGCGAACCTTATACCCTAGAGATGATAAGG-GAA--AGA
* *
34624040 TTGAAGTCGCAAAGGCAAAT
128 TTGAAGTCACAAAGACAAAT
34624060 CT
1 CT
34624062 CAAGACTGTA
Statistics
Matches: 125, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
143 5 0.04
144 4 0.03
145 2 0.02
146 84 0.67
147 30 0.24
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (147 bp):
CTTATACACTAGAGATGTAGAGGGAAAGGTTAAAGCCGCAACGGTGAACCTTAAACCATAGAGAT
GTGAAGGGAAAGATTGAAGCCACAACGGCGAACCTTATACCCTAGAGATGATAAGGGAAAGATTG
AAGTCACAAAGACAAAT
Found at i:34624415 original size:96 final size:96
Alignment explanation
Indices: 34624307--34624503 Score: 331
Period size: 96 Copynumber: 2.1 Consensus size: 96
34624297 AGTGGGTCGA
* * *
34624307 GTCAAAATAATGAAGCAGAGCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAAT
1 GTCAAAATAATGAAGCAGAGCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAAACTTCAAAT
* * *
34624372 CCCATCTTCCTGGTGAGGTACAGAGAAGTGG
66 CACATATTCCCGGTGAGGTACAGAGAAGTGG
*
34624403 GTCAAAATAATGAATCAGAGCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAAACTTCAAAT
1 GTCAAAATAATGAAGCAGAGCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAAACTTCAAAT
34624468 CACATATTCCCGGTGAGGTACAGAGAAGTGG
66 CACATATTCCCGGTGAGGTACAGAGAAGTGG
34624499 GTCAA
1 GTCAA
34624504 TACAATGTGT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.21
Consensus pattern (96 bp):
GTCAAAATAATGAAGCAGAGCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAAACTTCAAAT
CACATATTCCCGGTGAGGTACAGAGAAGTGG
Found at i:34624604 original size:114 final size:114
Alignment explanation
Indices: 34624420--34625070 Score: 888
Period size: 114 Copynumber: 5.7 Consensus size: 114
34624410 TAATGAATCA
* * * * *
34624420 GAGCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAAACTTCAAATCACATATTCCCGGTGAG
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
*
34624485 GTACAGAGAAGTGGGTCAATACAATGTGTTGAATCAAAACAACGAAGCC
66 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
* * **
34624534 GAGCTCAACGTCCCTGAGGGTACAGTAAAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
* * *
34624599 GTACAGAAAAGTGGGTCAATACAGTATGTTGAATCAAAATAACGAAGCC
66 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
* * * * * *
34624648 GAGCTTAACGTCCTTAAGGATACAGTGGAGTAGAGTGAGACTTCAAAGCTCATCCTCCTGGTTAG
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
*
34624713 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAATGAAGCC
66 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
* * * * *
34624762 AAGCTCAACGTCCCTGAGGATATAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTAAA
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
* * * * *
34624827 GTACAGAGAAGTGGGTCAAAATAGTGTGTTTAATCAAAACAACAAAGTC
66 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
* * * * * *
34624876 GAGTTCAACATCCCTTAGGATATAGTGGAGTGGAGTGAAACTTCAAATCCCATCTTCCTGGTGAG
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
* * * * * *
34624941 GTATAGAGAAGTGGGTCAAAACAATGTGTTGAATAAAAACAATGAAGTC
66 GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
* * * *
34624990 GACCTCAACGTCCCTAAGGATACAGTGGAGTGGAGTGAGACTTCAAATCACATCTTCCTAGTGAG
1 GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
34625055 GTACAGAGAAGTGGGT
66 GTACAGAGAAGTGGGT
34625071 TAAAACAAAT
Statistics
Matches: 470, Mismatches: 67, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 470 1.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (114 bp):
GAGCTCAACGTCCCTAAGGATACAGTGGAGTAGAGTGAGACTTCAAATCCCATCTTCCTGGTGAG
GTACAGAGAAGTGGGTCAATACAGTGTGTTGAATCAAAACAACGAAGCC
Found at i:34625535 original size:11 final size:11
Alignment explanation
Indices: 34625506--34625539 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
34625496 AAATGTCCCT
*
34625506 TTAAAACCCAT
1 TTAAAACCCAA
34625517 TTACAAACCCAA
1 TTA-AAACCCAA
34625529 TTAAAACCCAA
1 TTAAAACCCAA
34625540 ACTACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (11 bp):
TTAAAACCCAA
Found at i:34633567 original size:24 final size:23
Alignment explanation
Indices: 34633497--34633567 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 23
34633487 CTATTAGAAC
*
34633497 TTTTAAAAATATTTTTTATTTGATA
1 TTTTAAAAATA-TTTTTATTT-AAA
*
34633522 TTTT--AAATATTTTTATAATAAA
1 TTTTAAAAATATTTTTAT-TTAAA
34633544 TTTTAAAAATATTTATTATTTAAA
1 TTTTAAAAATATTT-TTATTTAAA
34633568 GTGAATTTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 13 0.33
23 6 0.15
24 12 0.31
25 8 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (23 bp):
TTTTAAAAATATTTTTATTTAAA
Found at i:34635665 original size:31 final size:31
Alignment explanation
Indices: 34635624--34635692 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
34635614 TCAAATTTTA
34635624 AATTTT-AGTGTAGTATAAAAACCAAAATTG
1 AATTTTGAGTGTAGTATAAAAACCAAAATTG
34635654 AATTTTGAGTGTAGTATAAAAACCAAAATTG
1 AATTTTGAGTGTAGTATAAAAACCAAAATTG
34635685 AATTTTGA
1 AATTTTGA
34635693 CTATTGTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (31 bp):
AATTTTGAGTGTAGTATAAAAACCAAAATTG
Found at i:34637132 original size:42 final size:43
Alignment explanation
Indices: 34637031--34637144 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 43
34637021 CACACGAGTT
* *
34637031 GGCACACGGGGGTATGTCAGGGTGTGTGTCTAAACTATTTGGA
1 GGCACACGGGCGTGTGTCAGGGTGTGTGTCTAAACTATTTGGA
* *
34637074 GGCACACGGGCGTGTGTCAGGGTGTGTGTC-ATACTGTTTGGA
1 GGCACACGGGCGTGTGTCAGGGTGTGTGTCTAAACTATTTGGA
**
34637116 GGCACACGGGTATGTGTCAGGGTGTGTGT
1 GGCACACGGGCGTGTGTCAGGGTGTGTGT
34637145 GGCACACGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
42 37 0.57
43 28 0.43
ACGTcount: A:0.17, C:0.15, G:0.40, T:0.28
Consensus pattern (43 bp):
GGCACACGGGCGTGTGTCAGGGTGTGTGTCTAAACTATTTGGA
Found at i:34637252 original size:53 final size:53
Alignment explanation
Indices: 34637145--34637279 Score: 146
Period size: 53 Copynumber: 2.5 Consensus size: 53
34637135 GGGTGTGTGT
* * *
34637145 GGCACACGAGCTGGCACATGGACGTGTGTTAAGGGGTGTGTATACTATTCTAG
1 GGCACACGGGCTGACACATGGGCGTGTGTTAAGGGGTGTGTATACTATTCTAG
* ** *
34637198 GGCACACGGGCTGACAAATGGGCGTGTGTT-AGGGTGTGTGTATGTTATTTTAG
1 GGCACACGGGCTGACACATGGGCGTGTGTTAAGGG-GTGTGTATACTATTCTAG
* ** * *
34637251 GGAACATAGGCTGATACATGGGGGTGTGT
1 GGCACACGGGCTGACACATGGGCGTGTGT
34637280 ATATCGTTCT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 4 0.06
53 64 0.94
ACGTcount: A:0.21, C:0.13, G:0.37, T:0.28
Consensus pattern (53 bp):
GGCACACGGGCTGACACATGGGCGTGTGTTAAGGGGTGTGTATACTATTCTAG
Found at i:34637913 original size:40 final size:40
Alignment explanation
Indices: 34637806--34637915 Score: 166
Period size: 40 Copynumber: 2.8 Consensus size: 40
34637796 GAGAATATTT
* * *
34637806 ACTGAACTGGCAGTGACACTGTAAACACTACAAGATTTCA
1 ACTGAACTGGCAGTGACACTGTAAACATTGCAAGATTACA
* * *
34637846 ATTGAACCGGTAGTGACACTGTAAACATTGCAAGATTACA
1 ACTGAACTGGCAGTGACACTGTAAACATTGCAAGATTACA
34637886 ACTGAACTGGCAGTGACACTGTAAACATTG
1 ACTGAACTGGCAGTGACACTGTAAACATTG
34637916 TGACGTGTCA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (40 bp):
ACTGAACTGGCAGTGACACTGTAAACATTGCAAGATTACA
Found at i:34638042 original size:29 final size:29
Alignment explanation
Indices: 34638000--34638143 Score: 146
Period size: 29 Copynumber: 5.0 Consensus size: 29
34637990 CGGATGGGAG
34638000 TATCATGTTTGCATCTGTAACTGTATCTA
1 TATCATGTTTGCATCTGTAACTGTATCTA
*
34638029 TATCATGTCTGCATCTGTAACTGTATCTA
1 TATCATGTTTGCATCTGTAACTGTATCTA
* * *
34638058 TAGCATGTTTGCATCCGTAACTGTATCTG
1 TATCATGTTTGCATCTGTAACTGTATCTA
* * * * *
34638087 TGA-CATGATTGTATTTGTAATTGTATCTG
1 T-ATCATGTTTGCATCTGTAACTGTATCTA
** * * *
34638116 TGGCATGATTGTATTTGTAACTGTATCT
1 TATCATGTTTGCATCTGTAACTGTATCT
34638144 GTGACTGTAT
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
29 100 0.99
30 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (29 bp):
TATCATGTTTGCATCTGTAACTGTATCTA
Found at i:34638106 original size:58 final size:58
Alignment explanation
Indices: 34638003--34638148 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 58
34637993 ATGGGAGTAT
*
34638003 CATGTTTGCATCTGTAACTGTATCTAT-ATCATGTCTGCATCTGTAACTGTATCTATAG
1 CATGTTTGCATCTGTAACTGTATCTGTGA-CATGTCTGCATCTGTAACTGTATCTATAG
* * * * * *
34638061 CATGTTTGCATCCGTAACTGTATCTGTGACATGAT-TGTATTTGTAATTGTATCTGTGG
1 CATGTTTGCATCTGTAACTGTATCTGTGACATG-TCTGCATCTGTAACTGTATCTATAG
* * *
34638119 CATGATTGTATTTGTAACTGTATCTGTGAC
1 CATGTTTGCATCTGTAACTGTATCTGTGAC
34638149 TGTATCTGTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
58 73 0.97
59 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (58 bp):
CATGTTTGCATCTGTAACTGTATCTGTGACATGTCTGCATCTGTAACTGTATCTATAG
Found at i:34638150 original size:12 final size:12
Alignment explanation
Indices: 34638125--34638158 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34638115 GTGGCATGAT
* *
34638125 TGTATTTGTAAC
1 TGTATCTGTGAC
34638137 TGTATCTGTGAC
1 TGTATCTGTGAC
34638149 TGTATCTGTG
1 TGTATCTGTG
34638159 CCATGACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (12 bp):
TGTATCTGTGAC
Done.