Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004729.1 Kokia drynarioides strain JFW-HI SEQ_118309, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 157108
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 133 characters in sequence are not A, C, G, or T
Found at i:4472 original size:16 final size:17
Alignment explanation
Indices: 4438--4475 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4428 ATTTTGAGTA
*
4438 ATTTAATTTTTTATGTT
1 ATTTTATTTTTTATGTT
*
4455 ATTTTATTTTTTCT-TT
1 ATTTTATTTTTTATGTT
4471 ATTTT
1 ATTTT
4476 TTATTATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTTTATGTT
Found at i:5838 original size:22 final size:22
Alignment explanation
Indices: 5810--5851 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
5800 AACTTGTTTT
5810 ATAAAAATAATGTTTTTTTTAA
1 ATAAAAATAATGTTTTTTTTAA
5832 ATAAAAATAATGTTTTTTTT
1 ATAAAAATAATGTTTTTTTT
5852 TTATCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATAAAAATAATGTTTTTTTTAA
Found at i:5939 original size:21 final size:21
Alignment explanation
Indices: 5915--5959 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5905 TAGATATTTT
*
5915 AATTATAATATAAATTAAAAA
1 AATTATAAGATAAATTAAAAA
** *
5936 AATTATTGGATAAATTACAAA
1 AATTATAAGATAAATTAAAAA
5957 AAT
1 AAT
5960 AGTCACTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
AATTATAAGATAAATTAAAAA
Found at i:8985 original size:61 final size:61
Alignment explanation
Indices: 8871--8985 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 61
8861 AAAAAATTTA
* * * * *
8871 GGTGTTGGCTATGCAATGGTCGACACCCCTTTTTTCAGATAAAAAAATTTCAAAATTTTTT
1 GGTGTTAGCCATGCAATGGTCGACACCCCTTTTATCAGACAAAAAAATATCAAAATTTTTT
* *
8932 GGTGTTAGCCATGCAATGG-CAGACATCCCTATTTATCTGACAAAAAAA-ATCAAA
1 GGTGTTAGCCATGCAATGGTC-GACACCCCT-TTTATCAGACAAAAAAATATCAAA
8986 TCTTTGCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
60 1 0.02
61 30 0.67
62 14 0.31
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (61 bp):
GGTGTTAGCCATGCAATGGTCGACACCCCTTTTATCAGACAAAAAAATATCAAAATTTTTT
Found at i:9970 original size:30 final size:30
Alignment explanation
Indices: 9922--10027 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
9912 AAATTTTCAA
* *
9922 AAAATAATAATTAGAATATACAGGAGATTAG
1 AAAATAA-AATTAAAATATACAGGAAATTAG
* *
9953 AAAATAAAATTAAAATATATAGTAAATTAG
1 AAAATAAAATTAAAATATACAGGAAATTAG
** * * * * *
9983 AATTTAAATTTAAAATAAAAACGAAATTAC
1 AAAATAAAATTAAAATATACAGGAAATTAG
* *
10013 AAATTAAATTTAAAA
1 AAAATAAAATTAAAA
10028 AGTAAACGGA
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
30 55 0.89
31 7 0.11
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (30 bp):
AAAATAAAATTAAAATATACAGGAAATTAG
Found at i:11234 original size:20 final size:20
Alignment explanation
Indices: 11191--11234 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11181 AAAAAATTCG
* * *
11191 AAAATATAAAAAACATTTTG
1 AAAATAGAAAAAACATTATA
*
11211 AAAATAGAAAAAATATTATA
1 AAAATAGAAAAAACATTATA
11231 AAAA
1 AAAA
11235 ATTCGAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAATAGAAAAAACATTATA
Found at i:12652 original size:60 final size:62
Alignment explanation
Indices: 12580--12745 Score: 187
Period size: 62 Copynumber: 2.7 Consensus size: 62
12570 TTTACCAAAT
* *
12580 AAAAAAA-TGGTGTCGGCCATGGCATGACCAATACAAAAAAA-TTTG-AA-TTTTTTATCTG
1 AAAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAAATTTTGAAATTTTTTTATCTG
* ** * *
12638 ACAAAAAGGGGGTGTCGATCATGGCATGAACGACACAAAAAAATTTTGAAATTTTTTTATCTG
1 A-AAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAAATTTTGAAATTTTTTTATCTG
* * * **
12701 AAAAAAAGGGATGTTGGCCATTGCATGACCAACACCCAAAAATTT
1 AAAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAAATTT
12746 ATTTATTTTT
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
58 1 0.01
59 5 0.06
60 28 0.33
61 4 0.05
62 36 0.42
63 12 0.14
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (62 bp):
AAAAAAAGGGGTGTCGGCCATGGCATGACCAACACAAAAAAATTTTGAAATTTTTTTATCTG
Found at i:12727 original size:62 final size:58
Alignment explanation
Indices: 12555--12745 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 58
12545 GGTCAACATA
* * * *
12555 AAAAAAATTT-AATTTTTTACCAAAT-AAAAAAATGGTGTCGGCCATGGCATGACCAATAC
1 AAAAAAATTTGAATTTTTTATC---TGAAAAAAAGGGTGTCGGCCATGGCATGAACAACAC
* ** *
12614 AAAAAAATTTGAATTTTTTATCTGACAAAAAGGGGGTGTCGATCATGGCATGAACGACAC
1 AAAAAAATTTGAATTTTTTATCTGA-AAAAA-AGGGTGTCGGCCATGGCATGAACAACAC
* * *
12674 AAAAAAATTTTGAAATTTTTTTATCTGAAAAAAAGGGATGTTGGCCATTGCATGACCAACAC
1 AAAAAAA-TTTG-AA-TTTTTTATCTGAAAAAAAGGG-TGTCGGCCATGGCATGAACAACAC
**
12736 CCAAAAATTT
1 AAAAAAATTT
12746 ATTTATTTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 15 0.14
60 38 0.36
61 10 0.09
62 30 0.28
63 12 0.11
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (58 bp):
AAAAAAATTTGAATTTTTTATCTGAAAAAAAGGGTGTCGGCCATGGCATGAACAACAC
Found at i:15295 original size:36 final size:36
Alignment explanation
Indices: 15248--15319 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
15238 ATCAAGTCTG
*
15248 GGTTTCTTTTCCTTCTTAATTTGGGTGGATGTTTGC
1 GGTTTCTTTTCCCTCTTAATTTGGGTGGATGTTTGC
*
15284 GGTTTCTTTTCCCTCTTAGTTTGGGTGGATGTTTGC
1 GGTTTCTTTTCCCTCTTAATTTGGGTGGATGTTTGC
15320 ATAAATCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.51
Consensus pattern (36 bp):
GGTTTCTTTTCCCTCTTAATTTGGGTGGATGTTTGC
Found at i:15463 original size:48 final size:48
Alignment explanation
Indices: 15408--15505 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
15398 ATACAAGGTA
15408 TCACCACTAATTGGGTAAGTATTTGGTACATCAGTGGAAAGTTTTAAC
1 TCACCACTAATTGGGTAAGTATTTGGTACATCAGTGGAAAGTTTTAAC
15456 TCACCACTAATTGGGTAAGTATTTGGTACATCAGTGGAAAGTTTTAAC
1 TCACCACTAATTGGGTAAGTATTTGGTACATCAGTGGAAAGTTTTAAC
15504 TC
1 TC
15506 CATAAGTGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (48 bp):
TCACCACTAATTGGGTAAGTATTTGGTACATCAGTGGAAAGTTTTAAC
Found at i:20929 original size:28 final size:28
Alignment explanation
Indices: 20883--20944 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
20873 AAACTCGAAC
**
20883 TTTAAA-TTAAAATTTTGAA-CTCTAAAT
1 TTTAAATTTAAAATACTGAATCTC-AAAT
20910 TTTAAATTTAAAATACTGAATCTCAAAT
1 TTTAAATTTAAAATACTGAATCTCAAAT
*
20938 ATTAAAT
1 TTTAAAT
20945 CGTAAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 6 0.20
28 21 0.70
29 3 0.10
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAATTTAAAATACTGAATCTCAAAT
Found at i:21872 original size:21 final size:20
Alignment explanation
Indices: 21848--21903 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
21838 ATTTTTTAAA
21848 ATATAAAAATTTTCAAAAAAT
1 ATATAAAAATTTT-AAAAAAT
*
21869 ATATAAAATATTTTAAAAATT
1 ATATAAAA-ATTTTAAAAAAT
*
21890 TTA-AAAAATTTTAA
1 ATATAAAAATTTTAA
21904 TTAAATGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.22
20 4 0.12
21 16 0.50
22 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAAAAATTTTAAAAAAT
Found at i:21909 original size:11 final size:10
Alignment explanation
Indices: 21852--21903 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
21842 TTTAAAATAT
21852 AAAAATTTTCA
1 AAAAATTTT-A
*
21863 AAAAATATATA
1 AAAAAT-TTTA
*
21874 AAATATTTT-
1 AAAAATTTTA
21883 AAAAATTTTA
1 AAAAATTTTA
21893 AAAAATTTTA
1 AAAAATTTTA
21903 A
1 A
21904 TTAAATGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 8 0.23
10 13 0.37
11 12 0.34
12 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:25662 original size:6 final size:6
Alignment explanation
Indices: 25651--25683 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
25641 AAATTATATT
25651 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATA
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATA
25684 CACGAGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAC
Found at i:27257 original size:15 final size:15
Alignment explanation
Indices: 27239--27284 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
27229 TTTGGATGAG
27239 AAATATTTATATAAA
1 AAATATTTATATAAA
*
27254 AAATATATTA-ATTAA
1 AAATAT-TTATATAAA
*
27269 AAAT-TTAATATAAA
1 AAATATTTATATAAA
27283 AA
1 AA
27285 TTACAATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.08
14 7 0.27
15 14 0.54
16 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATTTATATAAA
Found at i:27379 original size:20 final size:20
Alignment explanation
Indices: 27342--27381 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
27332 ATTAAAATAT
* * *
27342 CTTTATAATAATATAATTTA
1 CTTTATAAAAAAAAAATTTA
27362 CTTTATAAAAAAAAAATTTA
1 CTTTATAAAAAAAAAATTTA
27382 ATTATTTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
CTTTATAAAAAAAAAATTTA
Found at i:37072 original size:70 final size:71
Alignment explanation
Indices: 36937--37087 Score: 250
Period size: 70 Copynumber: 2.1 Consensus size: 71
36927 CTTGGCCAAG
* **
36937 GTATCGGTAGAAGTCCCAAGCCACAACTTCTTTGCTCACTGGAGTTTGTTCTGTCGATAAAAGTC
1 GTATCGGTAGAAGTCCCAAGCCACAACTTCTTTGCTCACTGGAATTTGTTCTACCGATAAAAGTC
37002 TTGATT
66 TTGATT
37008 GTATCGGTAGAAGTCCCAAGCCACAACTTC-TTGCTCACTGGAATTTGTTCTACCGATAAAAGTC
1 GTATCGGTAGAAGTCCCAAGCCACAACTTCTTTGCTCACTGGAATTTGTTCTACCGATAAAAGTC
*
37072 TTGGTT
66 TTGATT
*
37078 GTATCTGTAG
1 GTATCGGTAG
37088 TTATTCTAGT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 45 0.60
71 30 0.40
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (71 bp):
GTATCGGTAGAAGTCCCAAGCCACAACTTCTTTGCTCACTGGAATTTGTTCTACCGATAAAAGTC
TTGATT
Found at i:46338 original size:361 final size:361
Alignment explanation
Indices: 45572--46821 Score: 1736
Period size: 361 Copynumber: 3.5 Consensus size: 361
45562 AAAGTTGTGG
* * * * * * *
45572 TATGCTAGTAACCTTATGGTAATCTAGAGTAACGGCTATTAGCTTTTAATAGATGACTAAAAATG
1 TATGCTATTAACCTTATGATAGTCCAGAGTAACGACTATTAGCTTTTAATAAATGGCTAAAAATG
* * * * * **
45637 GTAATTACAGATCATTTATCGAATGACACTCAGCCCAATTTGCATTGGTTGTCATTGTTGATGTT
66 ATAATTACAGATCATTTATCAAATGACACTCAACCCAATTTGCGTTGGCTACCATTGTTGATGTT
* * * *
45702 ATTTTTATTTGGTTAGAGCATGCTATTAGCCGTTATATGTTTTGGTTCTTATACTTAGTTAATAT
131 ATTTTTATTTGGTTAAAGCATGCTATTAGCCGTTATATTTTTTGGTCCTTATACTTAGATAATAT
* * *
45767 TTAAAATTTAGTCTCTGTACCTAAATTATTAAAACTTAAGCCCTTTTACTTTTTTAATTTAAAAA
196 TTAAAATTTAGTCTCTGTACCTAAACTATTAAAACTTAAGCCCTCTTGCTTTTTTAATTTAAAAA
*
45832 TCATAGTCCCATCATTAAAATTATTAGTATTTTCATCAAATTTTGCAAAA-TTAACATGTTGATT
261 TCATAGTCCCATCATTAAAATTATTAGTATTTTCATCAAAATTTG-AAAACTTAACATGTTGATT
*
45896 AGACTATAATTGACATTTTACACAAAGAAATACTATGA
325 AGACTATAATTGACATTTTACAGAAA-AAATACTATGA
* *
45934 TATGCTATTAACCTTATGATAGTCCAAAGTAACGACTATTAGCTTTTAATAAATAGCTAAAAATG
1 TATGCTATTAACCTTATGATAGTCCAGAGTAACGACTATTAGCTTTTAATAAATGGCTAAAAATG
* * * *
45999 ATAATTACAGATCATTTATCGAATGACACTCAGCCCAATCTGCGTTGACTACCATTGTTGATGTT
66 ATAATTACAGATCATTTATCAAATGACACTCAACCCAATTTGCGTTGGCTACCATTGTTGATGTT
* *
46064 ATTTTTATTTGGTTAAAGCATGCTATTAGTCATTATATTTTTTGGTCCTTATACTT-GAATAATA
131 ATTTTTATTTGGTTAAAGCATGCTATTAGCCGTTATATTTTTTGGTCCTTATACTTAG-ATAATA
* * * *
46128 TGTAAAATTTAGTATTTATACCTAAA-TATTAAAACTTAAGCCCTCTTGCTTTTTTAATTTAAAA
195 TTTAAAATTTAGTCTCTGTACCTAAACTATTAAAACTTAAGCCCTCTTGCTTTTTTAATTTAAAA
*
46192 ATCATAGTCCCTTCATTAAAATTATTAGTATTTTCATCAAAATTTGAAAACTTAACATGTTGATT
260 ATCATAGTCCCATCATTAAAATTATTAGTATTTTCATCAAAATTTGAAAACTTAACATGTTGATT
** *
46257 AGACTATAAACGACATTTTATATGAAAAAATACTATGA
325 AGACTATAATTGACATTTTACA-GAAAAAATACTATGA
** *
46295 TATGCTATTAACCTTATGATAGTCCAGAGTAATAACCATTAGCTTTTAATAAATGGCTAAAAATG
1 TATGCTATTAACCTTATGATAGTCCAGAGTAACGACTATTAGCTTTTAATAAATGGCTAAAAATG
** * * ** *
46360 GCAATTACAGATCATTTATCAAATGACACTTAATCCAATTTGTTTTGGTTACCATTGTTGATGTT
66 ATAATTACAGATCATTTATCAAATGACACTCAACCCAATTTGCGTTGGCTACCATTGTTGATGTT
* * * * *
46425 ATTTTTATTTGGTTAAAGCATGTTACTAACCGTCATATGTTTTTGGTCTTTATACTTAGATAATA
131 ATTTTTATTTGGTTAAAGCATGCTATTAGCCGTTATAT-TTTTTGGTCCTTATACTTAGATAATA
* * * *
46490 TTTAAAATTTAGTCTCTGTGCCTAAACGATTAAAACTTAAGCCCTCTTGCTTTTCTAATTCAAAA
195 TTTAAAATTTAGTCTCTGTACCTAAACTATTAAAACTTAAGCCCTCTTGCTTTTTTAATTTAAAA
* * *
46555 GTCACAGTCCCATCATTAAAATTATTAATATTTTCATCAAAATTT-ACAAACTTAACATGTTGAT
260 ATCATAGTCCCATCATTAAAATTATTAGTATTTTCATCAAAATTTGA-AAACTTAACATGTTGAT
* *
46619 TAGACTATAATTGACATTTTACACGAATAAAGACTATGA
324 TAGACTATAATTGACATTTTACA-GAAAAAATACTATGA
* * * *
46658 TATGCTATTAACCTTATAATAGTCCAGAGTAACTG-TTATTAGCTTTTAATAAGTGGTTAAAAAT
1 TATGCTATTAACCTTATGATAGTCCAGAGTAAC-GACTATTAGCTTTTAATAAATGGCTAAAAAT
* * *
46722 GATAATTACAGACCATTTATCAAATGACACTCAATCCAATTTGCGTTGGCTACCATTATTGATGT
65 GATAATTACAGATCATTTATCAAATGACACTCAACCCAATTTGCGTTGGCTACCATTGTTGATGT
* * *
46787 TATTTTGATTTTGTTAAAACATGCTATTAGCCGTT
130 TATTTTTATTTGGTTAAAGCATGCTATTAGCCGTT
46822 TTTTCAATAT
Statistics
Matches: 783, Mismatches: 97, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
360 4 0.01
361 271 0.35
362 240 0.31
363 268 0.34
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (361 bp):
TATGCTATTAACCTTATGATAGTCCAGAGTAACGACTATTAGCTTTTAATAAATGGCTAAAAATG
ATAATTACAGATCATTTATCAAATGACACTCAACCCAATTTGCGTTGGCTACCATTGTTGATGTT
ATTTTTATTTGGTTAAAGCATGCTATTAGCCGTTATATTTTTTGGTCCTTATACTTAGATAATAT
TTAAAATTTAGTCTCTGTACCTAAACTATTAAAACTTAAGCCCTCTTGCTTTTTTAATTTAAAAA
TCATAGTCCCATCATTAAAATTATTAGTATTTTCATCAAAATTTGAAAACTTAACATGTTGATTA
GACTATAATTGACATTTTACAGAAAAAATACTATGA
Found at i:50053 original size:22 final size:21
Alignment explanation
Indices: 50025--50072 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
50015 TCCAAATAAT
* *
50025 AACAACAATATAATAGTAAAAC
1 AACAACAAAACAATA-TAAAAC
*
50047 AACAACAAAACAATATCAAAC
1 AACAACAAAACAATATAAAAC
50068 AACAA
1 AACAA
50073 TAGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (21 bp):
AACAACAAAACAATATAAAAC
Found at i:53647 original size:6 final size:6
Alignment explanation
Indices: 53636--53670 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
53626 CATCTATTAT
*
53636 ATTTAA ATTTAA ATTTAA TATTTAT ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTT
53671 TGATATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
ATTTAA
Found at i:53658 original size:19 final size:19
Alignment explanation
Indices: 53634--53670 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
53624 TCCATCTATT
53634 ATATTTAAATTTAAATTTA
1 ATATTTAAATTTAAATTTA
*
53653 ATATTTATATTTAAATTT
1 ATATTTAAATTTAAATTT
53671 TGATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTAAATTTAAATTTA
Found at i:53679 original size:25 final size:25
Alignment explanation
Indices: 53632--53679 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53622 GATCCATCTA
*
53632 TTATATTTAAATTTAAATTTAATAT
1 TTATATTTAAATTTAAATATAATAT
**
53657 TTATATTTAAATTTTGATATAAT
1 TTATATTTAAATTTAAATATAAT
53680 TTGATTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATATTTAAATTTAAATATAATAT
Found at i:54631 original size:3 final size:3
Alignment explanation
Indices: 54623--54647 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54613 CGCTTTAAAA
54623 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
54648 GTTCAGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:60035 original size:14 final size:14
Alignment explanation
Indices: 60012--60042 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
60002 TAAAAGAGAG
60012 ATTTTCTTTGATGA
1 ATTTTCTTTGATGA
*
60026 ATTTTTTTTGATGA
1 ATTTTCTTTGATGA
60040 ATT
1 ATT
60043 AAAATAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (14 bp):
ATTTTCTTTGATGA
Found at i:64564 original size:13 final size:12
Alignment explanation
Indices: 64546--64579 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
64536 GGCTCCCACA
64546 TTGTTTTTTTGTT
1 TTGTTTTTTT-TT
64559 TTGTTTTTTTTT
1 TTGTTTTTTTTT
64571 TT-TTTTTTT
1 TTGTTTTTTT
64580 AAATTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 4 0.19
13 10 0.48
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:71201 original size:27 final size:25
Alignment explanation
Indices: 71163--71220 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
71153 CAATTAGATT
*
71163 TAAATTTTGAAATAAAAAATATGAC
1 TAAATTTTGAAATAAAAAATAAGAC
*
71188 TAAATATTTAGAAATAAAATATAAGAC
1 TAAAT-TTT-GAAATAAAAAATAAGAC
*
71215 TTAATT
1 TAAATT
71221 CCAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.18
26 4 0.14
27 19 0.68
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (25 bp):
TAAATTTTGAAATAAAAAATAAGAC
Found at i:85158 original size:30 final size:30
Alignment explanation
Indices: 85124--85181 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
85114 AAGTGATGTT
*
85124 ATGTGACGTAATTCATCCAATCTAAGTGGC
1 ATGTGACGTAACTCATCCAATCTAAGTGGC
*
85154 ATGTGACGTAACTCATCCAATCTGAGTG
1 ATGTGACGTAACTCATCCAATCTAAGTG
85182 ACAGATGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (30 bp):
ATGTGACGTAACTCATCCAATCTAAGTGGC
Found at i:87354 original size:823 final size:830
Alignment explanation
Indices: 84583--87924 Score: 4040
Period size: 823 Copynumber: 3.9 Consensus size: 830
84573 TTTCAAATAA
* * * * * *
84583 GAAGATAAAACATATTTAAGTGCA-TTTAA-ACTC-TCACATGACTACATTAAGTCTTATCTTTT
1 GAAGATAAAACACATTTAAGTGCACTTTAACCCACGTC-CA-GA-TACAGTAAATCTTATCCTTT
* * * * * *
84645 GGAATGAGTAGACGCTCATTATAGAAGAATGTTAATCCATTTTTGTGACTTATCCTTCATTTCAC
63 AGAATGAGTAGACACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCAC
* * *
84710 AGGAAGCCGCATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATCTATAA-GG
128 AAGAAGCCACATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATATATAATGG
* * *** ** * * * **
84774 AGTTTTGAGTTACACTAAAGAGTGTGTCAAAGTAAGATTTGATATTGTTATTAGCGAGTACCACA
193 AGCTCTGAGTTACACTAAAGAGTGTGTCAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGT
* * * * * *
84839 GCTGTAATGCCATGTAATTTATTAGATCCATTTATGGACAATTTTTTAACTTTCAACGATTTGGA
258 GCTGTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAACGATTTGGA
* * * * * * * *
84904 AACACTTAAATTTATTTTGATTGAAGGCATTAAGAATGATCGTTGAAAGCTTATTAGTTTAGTTC
323 AACACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTC
* * *
84969 TAATAGGATTATGAGTGATATGATCAAATATATTTTCATTTTTAACTTTCCAAATGGTCCATAAG
388 TAATAGGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAATGATCCATAAG
* * * * * * * *
85034 CCGACAATAAGATAAGTAAAGAACTTGTTACCTGTGTCAGTAGTAGCATCGATTGTATCAAGTCA
453 CTGACAATAAAATAAGTGAAGAACTCGTGACCTGTGTCACTAGTAGCATCAACTGTATCAAGTCA
* *
85099 ATCTTGTAGATTTTGAAGTGATGTTATGTGACGTAATTCATCCAATCTAAGTGGCATGTGACGTA
518 ACCCTGTAGATTTTG-A---A-G-TA----ACG--------------T---T---ATGTGACGTA
* * * *
85164 ACTCATCCAATCTGAGTGACAGATGGCATCGAAATCAAACTACTTAGCAAAATTACATTCCTTGA
553 ACTCATCCAATCTGAGTGACAGATGGCATCCAAACCAAACTACCTAGAAAAATTACATTCCTTGA
* * *
85229 ATAATTTCTTGACAGTTTCATTATGCTCCTAATACAAAGGACATTCTGAAAGTGCATTAATTGAG
618 ATAACTTCTCGACAGTTTCATTATGCTCCTAACACAAAGGACATTCTGAAAGTGCA-TAATTGAG
* * * * *
85294 CCTTTTTGTAGCTCCATTCACGTGGGAAGATGATTACGGCAATGTTTCCAAAAATAAAAAGAAGT
682 CCCTTCTATAGCTCCATTCA--TGTG-AGA-GA-TA-GGCAAAGTTTCC--AAATAAAAA-AAGT
* * * ** *
85359 ACCATTTTCTTGATTTGTTGAAATAGCACAATTTCACTTATATCTTTTATAGTGAAATATATTTG
738 ACCAATATCTTGAATTGTTGAAATAGCACAATCCCACTTATATC---T-T--T----TACA--T-
* * *
85424 GTAGTGTTTGAGGATGTAGGTGTAATTTGTCAAGCAATAGTAG
790 GTA--GTTTGAGAATGTAGGCGTAATTTGTCGAGCAATAGTAG
* * * * * *
85467 GAAGATAAAACACATTTAAGTGCACTTAAACCCATGTCCATAAATAGTAAATATTATCCTTTAGA
1 GAAGATAAAACACATTTAAGTGCACTTTAACCCACGTCCAGATACAGTAAATCTTATCCTTTAGA
* * * *
85532 ATGAGTAGACACTCGTTGTTGAAGAATGTTAATCCATTTTTGGGACTTATCGTTTAATTCACAAA
66 ATGAGTAGACACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
*
85597 AAGCCACATTGTAGTCTCAT-GTGGAAGCAATAGTAGTCGTGAGAATAATAATATATAATGGAGC
131 AAGCCACATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATATATAATGGAGC
* * * * *
85661 TCTGAGTTACACTAAAGAGTGTGCCAAAGTAAGATATGATCCCACAACTAGCGAGTACTAGTGTT
196 TCTGAGTTACACTAAAGAGTGTGTCAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGTGCT
* *
85726 GTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAATGGTTTGGAAAC
261 GTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAACGATTTGGAAAC
*
85791 ACTCAGATTTAATCTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCTAA
326 ACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCTAA
* ** * *
85856 TGGGATTATGAGTGATATGATCAAATAT-CCTTAATTTCTAACTTTCCAAATGATCCAGAAGCTG
391 TAGGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAATGATCCATAAGCTG
* *
85920 ACAATAAAATAAGTGAGGAACTCGTGCCCTGTGTCACTAGTAGCATCAACTGTATCAAGTCAACC
456 ACAATAAAATAAGTGAAGAACTCGTGACCTGTGTCACTAGTAGCATCAACTGTATCAAGTCAACC
* * *
85985 CTGTAGATTTT---G-AA-G-TA----ACGTAACTCAGCCAATATGAGTGACAGATGGCATCAAA
521 CTGTAGATTTTGAAGTAACGTTATGTGACGTAACTCATCCAATCTGAGTGACAGATGGCATCCAA
* *
86040 ACCAAACTACCTAGAAAAATTACATTCCTTGAATAACTTCTCGACGGTTTCATTATGTTCCTAAC
586 ACCAAACTACCTAGAAAAATTACATTCCTTGAATAACTTCTCGACAGTTTCATTATGCTCCTAAC
*
86105 ACAAAGGACATTTTGAAAGTGCATAATTGAGCCCTTCTATAGCTCCATTCATGTGGGAAGATGAT
651 ACAAAGGACATTCTGAAAGTGCATAATTGAGCCCTTCTATAGCTCCATTCATGT--G-AGA-GA-
*
86170 TATGGCAAAGTTTCCAAAAATAAAAAAAGTACCAGTATCTTGAATTGTTGAAATAGCACAATCCC
711 TA-GGCAAAGTTTCC--AAATAAAAAAAGTACCAATATCTTGAATTGTTGAAATAGCACAATCCC
*
86235 ACTTATATCTTTTACAATGAAATAAATTTTGTAGTGTTTAAGTGTAGGCGTAATTTGTCGAGCAA
773 ACTTATATCTTTTAC-ATG---T--AGTTTG-A--G---AA-TGTAGGCGTAATTTGTCGAGCAA
* *
86300 CAGTAA
825 TAGTAG
* * *
86306 GAAGATAAAACATATTTAAGTGCACTTGAACCCACGTCCAGATACAATAAATCTTATCCTTTAGA
1 GAAGATAAAACACATTTAAGTGCACTTTAACCCACGTCCAGATACAGTAAATCTTATCCTTTAGA
* *
86371 ATGAGTAGGCATTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
66 ATGAGTAGACACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
*
86436 AAGCCATC-TTGTAGTCTCATAGTGGAAGCAATAGTAGTCGTGAGAATAATAATATATAATGGAG
131 AAGCCA-CATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATATATAATGGAG
*
86500 CTCTGAGTTACACTAGAGAGTGT-TCCAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGTG
195 CTCTGAGTTACACTAAAGAGTGTGT-CAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGTG
* * * * * * *
86564 TTGTAATGTCATGTAATTCATTAGATCTATTTACGGACTATCTCTAAACCTTTAACGACTTGGAA
259 CTGTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAACGATTTGGAA
86629 ACACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCT
324 ACACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCT
* * *
86694 AATAGGATTATGAATGATATGATCAAATATCGTTTCATTTCTAAATTTCCAAATGATCCATAAG-
389 AATAGGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAATGATCCATAAGC
* * * *
86758 TCAACAATAAAAATAAGTGAGGAACTCGTAACCTGTGTCACTAGTAGCATCAATTGTATCAAGTC
454 T-GACAAT-AAAATAAGTGAAGAACTCGTGACCTGTGTCACTAGTAGCATCAACTGTATCAAGTC
*
86823 AACCATGTAGATTTTGAAGTAACGTTATGTGACGTAACTCATCCAATCTGAGTGACAGATGGCAT
517 AACCCTGTAGATTTTGAAGTAACGTTATGTGACGTAACTCATCCAATCTGAGTGACAGATGGCAT
* * *
86888 CCAAACCAAACTACCTAAAAAAATTACATTCCTTGAATAACTTCTCGACGGTTTCATTATGTTCC
582 CCAAACCAAACTACCTAGAAAAATTACATTCCTTGAATAACTTCTCGACAGTTTCATTATGCTCC
* *
86953 TAACACAAAAGACATTCTGAAAGTGCATAATTGAGCCCTTCTATAGTTCCATTCATGTG-G-GA-
647 TAACACAAAGGACATTCTGAAAGTGCATAATTGAGCCCTTCTATAGCTCCATTCATGTGAGAGAT
* * * *
87015 A-GCAAAGTTTCC-AA-AAAAAAAGTATCAATATCTTGAATTGTTGACATAGTACTATCCCACTT
712 AGGCAAAGTTTCCAAATAAAAAAAGTACCAATATCTTGAATTGTTGAAATAGCACAATCCCACTT
* * * *
87077 AAATCTTTTACA-GTA-TTTGAGCACGTAAGCGTAATTTGTCGAGCAATAGTAG
777 ATATCTTTTACATGTAGTTTGAGAATGTAGGCGTAATTTGTCGAGCAATAGTAG
* *
87129 GAAGATAAAACACATTTAAATGCACTTTAACTCACGTCCAGATACAGTAAATCTTATCCTTTAGA
1 GAAGATAAAACACATTTAAGTGCACTTTAACCCACGTCCAGATACAGTAAATCTTATCCTTTAGA
*
87194 ATGAGTAGGCACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
66 ATGAGTAGACACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
* *
87259 AAGCCACGTTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGACAATAATAATATATAATGGAGC
131 AAGCCACATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATATATAATGGAGC
* * * *
87324 TCTGAGTTACACTAGAGAGTGTGTCAAAGTAATATCTAATCCCGCAACTAGCAAGTACTAGTGCT
196 TCTGAGTTACACTAAAGAGTGTGTCAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGTGCT
* *
87389 GTAATGCAATGTAATTCATTAGATCTATTTACAGACAATCTTTGAACCTTCAACGATTTGGAAAC
261 GTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAACGATTTGGAAAC
* *
87454 ACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAACTTATTAATTTAGTTCTAA
326 ACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCTAA
* * *
87519 TAAGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAAAGACCCATAAGCTG
391 TAGGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAATGATCCATAAGCTG
* *
87584 ACAATAAAATAAGTGAAGAACTCGTGACCTATGTCACTAGAAGCATCAACTGTATCAAGTCAACC
456 ACAATAAAATAAGTGAAGAACTCGTGACCTGTGTCACTAGTAGCATCAACTGTATCAAGTCAACC
* * *
87649 CTGTAGATTTTGAAGTAACGTCATGTGATGTAACTCGTCCAATCTGAGTGACAGATGGCATCCAA
521 CTGTAGATTTTGAAGTAACGTTATGTGACGTAACTCATCCAATCTGAGTGACAGATGGCATCCAA
* * *
87714 ACTAAACTACCTAGAAAAATTACATTCCTTGAATAAATTCTAGACAGTTTCATTATGCTCCTAAC
586 ACCAAACTACCTAGAAAAATTACATTCCTTGAATAACTTCTCGACAGTTTCATTATGCTCCTAAC
* * * *
87779 ACAAAGGACATTCTGAAAGTGCATAATTGAGCCCTTCTGTATCTCCGTTCACGTGGGAAGATGAA
651 ACAAAGGACATTCTGAAAGTGCATAATTGAGCCCTTCTATAGCTCCATTCA--TGTG-AGA-G-A
* * *
87844 CATGGCAAAGTTTCCAAAAATAAAAAAAAAAGTACTC-GTATCTTGAATTGTTGAAATAGCGCAA
711 TA-GGCAAAGTTTCC--AAAT---AAAAAAAGTAC-CAATATCTTGAATTGTTGAAATAGCACAA
87908 TCCCACTTATATCTTTT
769 TCCCACTTATATCTTTT
87925 GAAGTGAAAT
Statistics
Matches: 2180, Mismatches: 222, Indels: 157
0.85 0.09 0.06
Matches are distributed among these distances:
822 222 0.10
823 450 0.21
824 6 0.00
826 1 0.00
827 1 0.00
828 1 0.00
829 3 0.00
830 6 0.00
831 3 0.00
832 17 0.01
833 2 0.00
834 1 0.00
835 4 0.00
836 1 0.00
837 2 0.00
838 55 0.03
839 209 0.10
840 255 0.12
841 76 0.03
842 136 0.06
843 114 0.05
844 1 0.00
845 1 0.00
846 4 0.00
847 2 0.00
848 3 0.00
850 2 0.00
852 150 0.07
868 1 0.00
869 1 0.00
873 1 0.00
875 1 0.00
883 130 0.06
884 308 0.14
885 5 0.00
886 3 0.00
887 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (830 bp):
GAAGATAAAACACATTTAAGTGCACTTTAACCCACGTCCAGATACAGTAAATCTTATCCTTTAGA
ATGAGTAGACACTCATTGTAGAAGAATGTTAATCCATTTTTGGGACTTATCCTTTAATTCACAAG
AAGCCACATTGTAGTCTCATAGTGGAAGCAATAGTAGCCGTGAGAATAATAATATATAATGGAGC
TCTGAGTTACACTAAAGAGTGTGTCAAAGTAAGATTTGATCCCGCAACTAGCAAGTACTAGTGCT
GTAATGCCATGTAATTCATTAGATCTATTTACGGACAATCTTTGAACCTTCAACGATTTGGAAAC
ACTCAGATTTAATTTGATTGAAGGCATTGAGAATGGTCGATGAAAGCTTATTAATTCAGTTCTAA
TAGGATTATGAGTGATATGATCAAATATAGTTTCATTTCTAACTTTCCAAATGATCCATAAGCTG
ACAATAAAATAAGTGAAGAACTCGTGACCTGTGTCACTAGTAGCATCAACTGTATCAAGTCAACC
CTGTAGATTTTGAAGTAACGTTATGTGACGTAACTCATCCAATCTGAGTGACAGATGGCATCCAA
ACCAAACTACCTAGAAAAATTACATTCCTTGAATAACTTCTCGACAGTTTCATTATGCTCCTAAC
ACAAAGGACATTCTGAAAGTGCATAATTGAGCCCTTCTATAGCTCCATTCATGTGAGAGATAGGC
AAAGTTTCCAAATAAAAAAAGTACCAATATCTTGAATTGTTGAAATAGCACAATCCCACTTATAT
CTTTTACATGTAGTTTGAGAATGTAGGCGTAATTTGTCGAGCAATAGTAG
Found at i:94604 original size:20 final size:21
Alignment explanation
Indices: 94561--94611 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
94551 TTCAGAATAA
* *
94561 TAAAATTTTAATATAATTTTT
1 TAAAATTATAATATAATTTAT
94582 TAAAAATTATAATA-AA-TTAT
1 T-AAAATTATAATATAATTTAT
94602 TAAAATTATA
1 TAAAATTATA
94612 TGTAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 3 0.11
22 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTATAATATAATTTAT
Found at i:98565 original size:26 final size:22
Alignment explanation
Indices: 98520--98566 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
98510 CGCCATTAAA
98520 AATAATAAAAAATTTAAAATAT
1 AATAATAAAAAATTTAAAATAT
98542 AATATATAACAAAATTATATAAATA
1 AATA-ATAA-AAAATT-TA-AAATA
98567 ATTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 4 0.19
24 6 0.29
25 2 0.10
26 5 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAATAAAAAATTTAAAATAT
Found at i:98567 original size:24 final size:21
Alignment explanation
Indices: 98516--98568 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 21
98506 TAAACGCCAT
98516 TAAA-AATAATAAAAAATTTA
1 TAAATAATAATAAAAAATTTA
*
98536 AAATATAATATATAACAAAATTATA
1 TAA-ATAATA-ATAA-AAAATT-TA
98561 TAAATAAT
1 TAAATAAT
98569 TTAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 4 0.15
23 4 0.15
24 11 0.42
25 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAATAATAATAAAAAATTTA
Found at i:110410 original size:238 final size:238
Alignment explanation
Indices: 109992--110428 Score: 811
Period size: 238 Copynumber: 1.8 Consensus size: 238
109982 CAATAGTGGA
109992 TCAACAAAAATGATATAAAATTTAGCACAAATAATTTAATCTATAGTTAAACTCTATTTAACAAG
1 TCAACAAAAATGATATAAAATTTAGCACAAATAATTTAATCTATAGTTAAACTCTATTTAACAAG
110057 AAATTAGAACTCTTAAGTTGATTAAGTTTTAATTCGATTGGCATTGATCATTATTGTCAATACAA
66 AAATTAGAACTCTTAAGTTGATTAAGTTTTAATTCGATTGGCATTGATCATTATTGTCAATACAA
* * * *
110122 GAGAACGTAGGTTCGAGTACGTTGAAGTACATTATGGGTTGAGAGAAAATATGAGTAGTTTTAAG
131 GAGAACGTAGGTTCGAGTACATTGAAGCACATTATGGGTTGAGAGAAAATATGAATAGTTCTAAG
110187 TATTTGATTTTTTAAATATATTTATTACTACCTCGTACTTCGT
196 TATTTGATTTTTTAAATATATTTATTACTACCTCGTACTTCGT
110230 TCAACAAAAATGATATAAAATTTAGCACAAATAATTTAATCTATAGTTAAACTCTATTTAACAAG
1 TCAACAAAAATGATATAAAATTTAGCACAAATAATTTAATCTATAGTTAAACTCTATTTAACAAG
* *
110295 AAATTAGAACTCTTAAGTTGATTAAGTTTTAATTCGATTGGCATTGATTATTATTGTCAATATAA
66 AAATTAGAACTCTTAAGTTGATTAAGTTTTAATTCGATTGGCATTGATCATTATTGTCAATACAA
*
110360 GAGAACGTAGGTTCGAGTGCATTGAAGCACATTATGGGTTGAGAGAAAATATGAATAGTTCTAAG
131 GAGAACGTAGGTTCGAGTACATTGAAGCACATTATGGGTTGAGAGAAAATATGAATAGTTCTAAG
110425 TATT
196 TATT
110429 ATGTAAAAAA
Statistics
Matches: 192, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
238 192 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (238 bp):
TCAACAAAAATGATATAAAATTTAGCACAAATAATTTAATCTATAGTTAAACTCTATTTAACAAG
AAATTAGAACTCTTAAGTTGATTAAGTTTTAATTCGATTGGCATTGATCATTATTGTCAATACAA
GAGAACGTAGGTTCGAGTACATTGAAGCACATTATGGGTTGAGAGAAAATATGAATAGTTCTAAG
TATTTGATTTTTTAAATATATTTATTACTACCTCGTACTTCGT
Found at i:124300 original size:27 final size:28
Alignment explanation
Indices: 124267--124324 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
124257 ACATTTTTTT
** *
124267 TTAATTTAATATTTAAATTTTTTAAA-A
1 TTAATTTAATACCTAAATTTATTAAATA
124294 TTAATTTAATACCTAAATTTATTAAATA
1 TTAATTTAATACCTAAATTTATTAAATA
124322 TTA
1 TTA
124325 TACAAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAATTTAATACCTAAATTTATTAAATA
Found at i:124821 original size:31 final size:31
Alignment explanation
Indices: 124747--124823 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
124737 AATCTCCAAA
* * *
124747 AAGTTTAAATACCAATTTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
124778 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATGTC
* **
124809 TAGTTTGGGTACCAA
1 AAGTTTAAGTACCAA
124824 GTTGAACCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAATGTC
Found at i:128901 original size:18 final size:19
Alignment explanation
Indices: 128869--128912 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
128859 TTTTTTTATT
128869 AATTATTTATAATTTTTAA
1 AATTATTTATAATTTTTAA
*
128888 AATT-TTTATTATTTTT-A
1 AATTATTTATAATTTTTAA
128905 AATTATTT
1 AATTATTT
128913 GTTGATATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 14 0.61
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTTATAATTTTTAA
Found at i:132370 original size:31 final size:29
Alignment explanation
Indices: 132332--132401 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
132322 CTCCCAAAAC
*
132332 TATACATGAACGATGGTTTACTGTGTAATTG
1 TATACATGAACGATGATTT-C-GTGTAATTG
** *
132363 TATACATGAACTTTGATTTCGTGTAATTT
1 TATACATGAACGATGATTTCGTGTAATTG
132392 TATACATGAA
1 TATACATGAA
132402 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
30 1 0.03
31 16 0.46
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (29 bp):
TATACATGAACGATGATTTCGTGTAATTG
Found at i:132395 original size:29 final size:30
Alignment explanation
Indices: 132354--132411 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
132344 ATGGTTTACT
132354 GTGTAATTGTATACATG-AACTTTGATTTC
1 GTGTAATTGTATACATGAAACTTTGATTTC
* *
132383 GTGTAATTTTATACATGAAATTTTGATTT
1 GTGTAATTGTATACATGAAACTTTGATTT
132412 GATCCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (30 bp):
GTGTAATTGTATACATGAAACTTTGATTTC
Found at i:132590 original size:31 final size:28
Alignment explanation
Indices: 132554--132633 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 28
132544 GATTAAATTA
132554 AAATTAAAGTTTCATGTATAGATTTGAACC
1 AAATTAAAGTTTCATGTATA-A-TTGAACC
* * *
132584 ACAATTAGAATTTTACGTGTATAATTGCACC
1 A-AATTA-AAGTTT-CATGTATAATTGAACC
132615 AAATTAAAG-TTCATGTATA
1 AAATTAAAGTTTCATGTATA
132634 TAATTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 7 0.17
28 2 0.05
29 2 0.05
30 6 0.14
31 12 0.29
32 6 0.14
33 7 0.17
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (28 bp):
AAATTAAAGTTTCATGTATAATTGAACC
Found at i:146910 original size:10 final size:10
Alignment explanation
Indices: 146895--146919 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
146885 AAAGGTTAAG
146895 TTTTTTTTCT
1 TTTTTTTTCT
146905 TTTTTTTTCT
1 TTTTTTTTCT
146915 TTTTT
1 TTTTT
146920 CCCTTCCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:153744 original size:21 final size:21
Alignment explanation
Indices: 153675--153744 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
153665 ATTGGTCTTT
153675 TGTTTTCATATTCAGGAAATAA
1 TGTTTT-ATATTCAGGAAATAA
* **
153697 TGCTGTTTCTATTTCA--AAAGTTT
1 TG-T-TTTATA-TTCAGGAAA-TAA
153720 TGTTTTATATTCAGGAAATAA
1 TGTTTTATATTCAGGAAATAA
153741 TGTT
1 TGTT
153745 GTGAGTGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
20 4 0.11
21 10 0.28
22 9 0.25
23 6 0.17
24 7 0.19
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (21 bp):
TGTTTTATATTCAGGAAATAA
Done.