Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015039.1 Kokia drynarioides strain JFW-HI SEQ_130083, 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: 570965
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 437 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:14095 original size:13 final size:13
Alignment explanation
Indices: 14079--14134 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
14069 TATTTTTGAG
*
14079 AAGTGCTTTTAAA
1 AAGTGATTTTAAA
14092 AAGT-ATTTTGAAA
1 AAGTGATTTT-AAA
* *
14105 AAATGATTTTGAA
1 AAGTGATTTTAAA
14118 AAGT-ACTTTTAAA
1 AAGTGA-TTTTAAA
14131 AAGT
1 AAGT
14135 TTGGTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.14
13 25 0.71
14 5 0.14
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.38
Consensus pattern (13 bp):
AAGTGATTTTAAA
Found at i:14551 original size:18 final size:17
Alignment explanation
Indices: 14520--14563 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
14510 TGTTTAGTAT
*
14520 TACTTTTGATTCAAAAA
1 TACTTTTTATTCAAAAA
14537 TACTTTTTATATCAAAAA
1 TACTTTTTAT-TCAAAAA
*
14555 TGCTTTTTA
1 TACTTTTTA
14564 AAAACACTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (17 bp):
TACTTTTTATTCAAAAA
Found at i:17924 original size:128 final size:128
Alignment explanation
Indices: 17696--17993 Score: 596
Period size: 128 Copynumber: 2.3 Consensus size: 128
17686 TTGTTATCTT
17696 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCAACTTCAATTGCTATTTTTGCCAT
1 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCAACTTCAATTGCTATTTTTGCCAT
17761 TTTATGATGTTGGGAATGGAAAGAACATGGTGATGTTTTATTTTTTAATTTATCCTTGTCATA
66 TTTATGATGTTGGGAATGGAAAGAACATGGTGATGTTTTATTTTTTAATTTATCCTTGTCATA
17824 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCAACTTCAATTGCTATTTTTGCCAT
1 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCAACTTCAATTGCTATTTTTGCCAT
17889 TTTATGATGTTGGGAATGGAAAGAACATGGTGATGTTTTATTTTTTAATTTATCCTTGTCATA
66 TTTATGATGTTGGGAATGGAAAGAACATGGTGATGTTTTATTTTTTAATTTATCCTTGTCATA
17952 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCA
1 TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCA
17994 TTGTCTTTTT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 170 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (128 bp):
TTAAGACAGCAAGATTCACATGTACATGTACTTTCCATATCAACTTCAATTGCTATTTTTGCCAT
TTTATGATGTTGGGAATGGAAAGAACATGGTGATGTTTTATTTTTTAATTTATCCTTGTCATA
Found at i:21188 original size:16 final size:18
Alignment explanation
Indices: 21149--21182 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21139 TCGATTTATA
21149 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
21166 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
21183 AATTTAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:23900 original size:15 final size:15
Alignment explanation
Indices: 23861--23894 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23851 ATCTTCCAGC
* *
23861 CCAAACCAAAGTGAA
1 CCAAACCCAATTGAA
23876 CCAAACCCAATTGAA
1 CCAAACCCAATTGAA
23891 CCAA
1 CCAA
23895 GTCCAAACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.32, G:0.09, T:0.09
Consensus pattern (15 bp):
CCAAACCCAATTGAA
Found at i:25095 original size:3 final size:3
Alignment explanation
Indices: 25048--25078 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25038 ATAATAATAA
25048 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
25079 TTGATTTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31191 original size:22 final size:22
Alignment explanation
Indices: 31163--31212 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
31153 AAGTCAAACT
31163 GTTGACTGGTCGTTGACCGACC
1 GTTGACTGGTCGTTGACCGACC
* *
31185 GTTGACTGGTTGTTGACTGACC
1 GTTGACTGGTCGTTGACCGACC
31207 GTTGAC
1 GTTGAC
31213 CAACCGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.22, G:0.32, T:0.32
Consensus pattern (22 bp):
GTTGACTGGTCGTTGACCGACC
Found at i:32085 original size:3 final size:3
Alignment explanation
Indices: 32040--32074 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
32030 TTTACAATAT
32040 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32075 TTGGATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:32174 original size:19 final size:19
Alignment explanation
Indices: 32150--32192 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
32140 CTTTTGGTAC
*
32150 TTTATTTTTTTTAGTTTTA
1 TTTATTTATTTTAGTTTTA
*
32169 TTTATTTATTTTATTTTTA
1 TTTATTTATTTTAGTTTTA
*
32188 GTTAT
1 TTTAT
32193 AGCTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTATTTATTTTAGTTTTA
Found at i:34756 original size:27 final size:27
Alignment explanation
Indices: 34695--34749 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
34685 CGGGGAGGAA
*
34695 GAAGAGATGGGCTTTTGCAGAGTATGT
1 GAAGAGATGGGCTTTTGCAGAGCATGT
34722 GAAGAGATGGGCTTTTGCAGAGCATGT
1 GAAGAGATGGGCTTTTGCAGAGCATGT
34749 G
1 G
34750 GATAGATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.27
Consensus pattern (27 bp):
GAAGAGATGGGCTTTTGCAGAGCATGT
Found at i:42223 original size:15 final size:14
Alignment explanation
Indices: 42199--42229 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42189 TCGATTAAAA
42199 TATCTTAATCGAAT
1 TATCTTAATCGAAT
42213 TATCATTAATCGAAT
1 TATC-TTAATCGAAT
42228 TA
1 TA
42230 CTCAAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
TATCTTAATCGAAT
Found at i:43466 original size:19 final size:20
Alignment explanation
Indices: 43432--43470 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43422 TAAAAAATTA
*
43432 TTAAAATATCATTAAATAAT
1 TTAAAAAATCATTAAATAAT
43452 TTAAAAAATCA-TAAATAAT
1 TTAAAAAATCATTAAATAAT
43471 GTGATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAAAAATCATTAAATAAT
Found at i:43480 original size:22 final size:20
Alignment explanation
Indices: 43422--43494 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 20
43412 TCAATAACAT
*
43422 TAAAAAATTATTAAAATATCA
1 TAAATAATTATTAAAA-ATCA
*
43443 TTAAATAATT-TAAAAAATCA
1 -TAAATAATTATTAAAAATCA
*
43463 TAAATAATGTGATTAAAATTCA
1 TAAATAAT-T-ATTAAAAATCA
43485 TAAAATAATT
1 T-AAATAATT
43495 CCCCATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 8 0.19
20 5 0.12
21 5 0.12
22 18 0.42
23 7 0.16
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAATAATTATTAAAAATCA
Found at i:44530 original size:16 final size:17
Alignment explanation
Indices: 44505--44537 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
44495 TATGTACGAA
*
44505 TAATTATAAAATAAAAT
1 TAATTATAAAACAAAAT
44522 TAATT-TAAAACAAAAT
1 TAATTATAAAACAAAAT
44538 ATAACTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATTATAAAACAAAAT
Found at i:44705 original size:23 final size:22
Alignment explanation
Indices: 44679--44731 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
44669 TTTTAAGAGG
44679 ATTAAAATGTAATTTTATTATAT
1 ATTAAAATGTAATTTT-TTATAT
** * *
44702 ATTAATTTATAATTTTTTATCT
1 ATTAAAATGTAATTTTTTATAT
44724 A-TAAAATG
1 ATTAAAATG
44732 ATTGAATTAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 4 0.17
22 6 0.26
23 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTAAAATGTAATTTTTTATAT
Found at i:44755 original size:16 final size:16
Alignment explanation
Indices: 44734--44765 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44724 ATAAAATGAT
44734 TGAATTAATTTTTAGG
1 TGAATTAATTTTTAGG
*
44750 TGAATTATTTTTTAGG
1 TGAATTAATTTTTAGG
44766 GGTTAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (16 bp):
TGAATTAATTTTTAGG
Found at i:48754 original size:16 final size:16
Alignment explanation
Indices: 48723--48763 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
48713 ACGTCAAGAA
*
48723 AAAAATAATTATTTTTT
1 AAAAAT-ATAATTTTTT
*
48740 TAAAATATAATTTTTT
1 AAAAATATAATTTTTT
48756 AAAAATAT
1 AAAAATAT
48764 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATATAATTTTTT
Found at i:48768 original size:11 final size:11
Alignment explanation
Indices: 48752--48777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48742 AAATATAATT
48752 TTTTAAAAATA
1 TTTTAAAAATA
48763 TTTTAAAAATA
1 TTTTAAAAATA
48774 TTTT
1 TTTT
48778 CCCTGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:49605 original size:17 final size:18
Alignment explanation
Indices: 49583--49659 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
49573 TCAAATCTAT
49583 TTTAAATTTA-ATTTAAG
1 TTTAAATTTATATTTAAG
* *
49600 TTTAAATTTATTTTTTAG
1 TTTAAATTTATATTTAAG
*
49618 TTTAAATTTATTTTTTAA-
1 TTTAAATTTA-TATTTAAG
* * *
49636 TTTAAAATTAT-TATAAA
1 TTTAAATTTATATTTAAG
49653 TTTAAAT
1 TTTAAAT
49660 AAATAAAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.08
17 17 0.33
18 24 0.47
19 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATATTTAAG
Found at i:49621 original size:18 final size:18
Alignment explanation
Indices: 49583--49647 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
49573 TCAAATCTAT
* *
49583 TTTAAATTTA-ATTTAAG
1 TTTAAATTTATTTTTTAG
49600 TTTAAATTTATTTTTTAG
1 TTTAAATTTATTTTTTAG
*
49618 TTTAAATTTATTTTTTAA
1 TTTAAATTTATTTTTTAG
*
49636 TTTAAAATTATT
1 TTTAAATTTATT
49648 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 10 0.23
18 33 0.77
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAAATTTATTTTTTAG
Found at i:49691 original size:15 final size:16
Alignment explanation
Indices: 49664--49698 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
49654 TTAAATAAAT
49664 AAAA-GTCTAAATTAC
1 AAAATGTCTAAATTAC
49679 AAAATGTCT-AATTAC
1 AAAATGTCTAAATTAC
49694 AAAAT
1 AAAAT
49699 TCATTAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATGTCTAAATTAC
Found at i:51410 original size:49 final size:49
Alignment explanation
Indices: 51366--51858 Score: 301
Period size: 49 Copynumber: 10.1 Consensus size: 49
51356 GTTTAAGTTA
* * **
51366 CAACGGCGAACCTTGTACCTCAGAGACATGAAAGGAAATATTTAAGCTA
1 CAACGGCGAACCTAGTACCTCAGAGACATGAAAGGAAAGATTTAAGCCG
* * *
51415 CAACGGCGAATCC-AGTACCAC-GAAGACA-CAAAGGAAA-AGTTTAAGTCG
1 CAACGGCGAA-CCTAGTACCTCAG-AGACATGAAAGGAAAGA-TTTAAGCCG
* *
51463 CAATGGCGAACCTAGTACCTCAG-GTCCAT-AAAGGGAAAGATTTAAGCCG
1 CAACGGCGAACCTAGTACCTCAGAG-ACATGAAA-GGAAAGATTTAAGCCG
* * * *
51512 CAACAGCGAATCC-AGTACCAC-GAAGAC-TCAAAGGGAAATG-TTTAAGTCG
1 CAACGGCGAA-CCTAGTACCTCAG-AGACATGAAA-GGAAA-GATTTAAGCCG
* * * *
51561 CAACGGTGAACCTTGTACCTCAGAGACATGAAGGGAAATATTTAAGCCG
1 CAACGGCGAACCTAGTACCTCAGAGACATGAAAGGAAAGATTTAAGCCG
* * * * **
51610 CAATGGCGAATCC-AGT-TCT-ACGAAGACACGAAGGGAAAGATTTAAGTTG
1 CAACGGCGAA-CCTAGTACCTCA-G-AGACATGAAAGGAAAGATTTAAGCCG
* * *
51659 CAACGGCGAACCTTA-TACATCAGAGATAT-AAAGGGAAAGATTTAAGCTG
1 CAACGGCGAACC-TAGTACCTCAGAGACATGAAA-GGAAAGATTTAAGCCG
* * *
51708 CAACGGTGAATCC-AGTACCAC-GAAGACAT-AAAGGGAAAATATTTAAGCCG
1 CAACGGCGAA-CCTAGTACCTCAG-AGACATGAAA-GG-AAAGATTTAAGCCG
* * * * *
51758 CAACGGTGAATCC-AGTACCACAAAGACATG-AAGGAAAAGGTTTAGGCCG
1 CAACGGCGAA-CCTAGTACCTCAGAGACATGAAAGG-AAAGATTTAAGCCG
* * *
51807 CAATGGCGAACCTTA-TACCTCAGAAACAT-AAAGGGAAAGGTTTAAGCCG
1 CAACGGCGAACC-TAGTACCTCAGAGACATGAAA-GGAAAGATTTAAGCCG
51856 CAA
1 CAA
51859 TAGCAAATCC
Statistics
Matches: 354, Mismatches: 54, Indels: 72
0.74 0.11 0.15
Matches are distributed among these distances:
47 5 0.01
48 51 0.14
49 235 0.66
50 62 0.18
51 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (49 bp):
CAACGGCGAACCTAGTACCTCAGAGACATGAAAGGAAAGATTTAAGCCG
Found at i:51597 original size:98 final size:98
Alignment explanation
Indices: 51330--51816 Score: 520
Period size: 98 Copynumber: 5.0 Consensus size: 98
51320 TACAAGTCTT
* **
51330 AGTACCACGAAGA-T-ATAGAGGGAAAGGTTTAAGTTACAACGGCGAACCTTGTACCTCAGAGAC
1 AGTACCACGAAGACTCA-A-AGGGAAATGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGAC
* * **
51393 ATGAAAGGAAATATTTAAGCTACAACGGCGAATCC
64 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * * *
51428 AGTACCACGAAGACACAAA-GGAAAAGTTTAAGTCGCAATGGCGAACCTAGTACCTCAG-GTCCA
1 AGTACCACGAAGACTCAAAGGGAAATGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAG-ACA
* *
51491 TAAAGGGAAAGATTTAAGCCGCAACAGCGAATCC
65 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
*
51525 AGTACCACGAAGACTCAAAGGGAAATGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAGACAT
1 AGTACCACGAAGACTCAAAGGGAAATGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGACAT
* *
51590 GAAGGGAAATATTTAAGCCGCAATGGCGAATCC
66 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * * * * * *
51623 AGTTCTACGAAGACACGAAGGGAAA-GATTTAAGTTGCAACGGCGAACCTTATACATCAGAGATA
1 AGTACCACGAAGACTCAAAGGGAAATG-TTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGACA
* * *
51687 TAAAGGGAAAGATTTAAGCTGCAACGGTGAATCC
65 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * * * *
51721 AGTACCACGAAGACAT-AAAGGGAAAATATTTAAGCCGCAACGGTGAATCC-AGTACCACAAAGA
1 AGTACCACGAAGAC-TCAAAGGG-AAATGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAGA
* * * *
51784 CATGAAGGAAAAGGTTTAGGCCGCAATGGCGAA
63 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAA
51817 CCTTATACCT
Statistics
Matches: 321, Mismatches: 58, Indels: 19
0.81 0.15 0.05
Matches are distributed among these distances:
96 1 0.00
97 83 0.26
98 180 0.56
99 54 0.17
100 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (98 bp):
AGTACCACGAAGACTCAAAGGGAAATGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAGACAT
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
Found at i:51868 original size:98 final size:99
Alignment explanation
Indices: 51733--51939 Score: 247
Period size: 98 Copynumber: 2.1 Consensus size: 99
51723 TACCACGAAG
* * ** *
51733 ACATAAAGGGAAAATATTTAAGCCGCAACGGTGAATCCAGTACCAC-AAAGACATGAAGGAAAAG
1 ACATAAAGGGAAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAA-ACACGAAGGAAAAG
*
51797 GTTTAGGCCGCAATGGCGAACCTTATACCTCAGAA
65 GTTTAAGCCGCAATGGCGAACCTTATACCTCAGAA
* * * * *
51832 ACATAAAGGG-AAAGGTTTAAGCCGCAATAGCAAATCCAGTACCGCGAAAATACGAAGGGAAAGG
1 ACATAAAGGGAAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAAACACGAAGGAAAAGG
* * *
51896 TTTAAGTCGTAATGGCGAACCTTATACCTTAGAA
66 TTTAAGCCGCAATGGCGAACCTTATACCTCAGAA
*
51930 GCATGAAAGG
1 ACAT-AAAGG
51940 AAATTTAAGC
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
98 73 0.80
99 18 0.20
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (99 bp):
ACATAAAGGGAAAAGATTTAAGCCGCAACAGCAAATCCAGTACCACGAAAACACGAAGGAAAAGG
TTTAAGCCGCAATGGCGAACCTTATACCTCAGAA
Found at i:51868 original size:148 final size:147
Alignment explanation
Indices: 51366--51879 Score: 397
Period size: 148 Copynumber: 3.5 Consensus size: 147
51356 GTTTAAGTTA
* * * * ** * *
51366 CAACGGCGAACCTTGTACCTCAGAGACATGAAA-GGAAATATTTAAGCTACAACGGCGAATCCAG
1 CAACGGCGAACCTTATACATCAGAAACAT-AAAGGGAAAGATTTAAGCCGCAACAGCAAATCCAG
* * * * * *
51430 TACCACGAAGACACAAA-GGAAA-AGTTTAAGTCGCAATGGCGAA-CCTAGTACCTC-AGGTCCA
65 TACCACGAAGACATAAAGGGAAATA-TTTAAGCCGCAACGGCGAATCC-AGTACCACAAAG-ACA
** *
51491 TAAAGGGAAAGATTTAAGCCG
127 CGAAGGAAAAGATTTAAGCCG
* * * **
51512 CAACAGCGAATCC--AGTAC--CACGAAGAC-TCAAAGGGAAATG-TTTAAGTCGCAACGGTGAA
1 CAACGGCGAA-CCTTA-TACATCA-GAA-ACAT-AAAGGGAAA-GATTTAAGCCGCAACAGCAAA
* * * * * * *
51571 -CCTTGTACCTC-AGAGACATGAAGGGAAATATTTAAGCCGCAATGGCGAATCCAGTTCTACGAA
60 TCC-AGTACCACGA-AGACATAAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACAAA
* **
51634 GACACGAAGGGAAAGATTTAAGTTG
123 GACACGAAGGAAAAGATTTAAGCCG
* * * * **
51659 CAACGGCGAACCTTATACATCAGAGATATAAAGGGAAAGATTTAAGCTGCAACGGTGAATCCAGT
1 CAACGGCGAACCTTATACATCAGAAACATAAAGGGAAAGATTTAAGCCGCAACAGCAAATCCAGT
* *
51724 ACCACGAAGACATAAAGGGAAAATATTTAAGCCGCAACGGTGAATCCAGTACCACAAAGACATGA
66 ACCACGAAGACATAAAGGG-AAATATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACGA
* *
51789 AGGAAAAGGTTTAGGCCG
130 AGGAAAAGATTTAAGCCG
* * * *
51807 CAATGGCGAACCTTATACCTCAGAAACATAAAGGGAAAGGTTTAAGCCGCAATAGCAAATCCAGT
1 CAACGGCGAACCTTATACATCAGAAACATAAAGGGAAAGATTTAAGCCGCAACAGCAAATCCAGT
*
51872 ACCGCGAA
66 ACCACGAA
51880 AATACGAAGG
Statistics
Matches: 294, Mismatches: 53, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
144 2 0.01
145 9 0.03
146 50 0.17
147 105 0.36
148 126 0.43
149 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (147 bp):
CAACGGCGAACCTTATACATCAGAAACATAAAGGGAAAGATTTAAGCCGCAACAGCAAATCCAGT
ACCACGAAGACATAAAGGGAAATATTTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACGAA
GGAAAAGATTTAAGCCG
Found at i:52912 original size:17 final size:17
Alignment explanation
Indices: 52872--52995 Score: 146
Period size: 17 Copynumber: 7.4 Consensus size: 17
52862 CTAAACCCAT
52872 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
52890 -TAAAATATATTTTAAA
1 TTTAAATTTATTTTAAA
*
52906 TTTAAATCTATTTTAAA
1 TTTAAATTTATTTTAAA
52923 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
52940 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
52957 TTT--ATTTTTTTTAAA
1 TTTAAATTTATTTTAAA
* *
52972 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
52989 TTTAAAT
1 TTTAAAT
52996 AAAAAAAAGT
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.13
16 1 0.01
17 76 0.85
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:52937 original size:28 final size:28
Alignment explanation
Indices: 52906--52964 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
52896 ATATTTTAAA
*
52906 TTTAAATCT-ATTTTAAATTTAAATTTAT
1 TTTAAATCTAAATTT-AATTTAAATTTAT
* *
52934 TTTAAATTTAAATTTAATTTAAGTTTAT
1 TTTAAATCTAAATTTAATTTAAATTTAT
52962 TTT
1 TTT
52965 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTAAATCTAAATTTAATTTAAATTTAT
Found at i:52952 original size:11 final size:11
Alignment explanation
Indices: 52904--52960 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
52894 ATATATTTTA
*
52904 AATTTAAATCT
1 AATTTAAATTT
*
52915 ATTTTAAATTT
1 AATTTAAATTT
*
52926 AAATTT-ATTTT
1 -AATTTAAATTT
52937 AAATTTAAATTT
1 -AATTTAAATTT
*
52949 AATTTAAGTTT
1 AATTTAAATTT
52960 A
1 A
52961 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 30 0.79
12 8 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:52977 original size:6 final size:6
Alignment explanation
Indices: 52900--52960 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
52890 TAAAATATAT
* * *
52900 TTTAAA TTTAAA TCT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
52946 TTT-AA TTTAAG TTTA
1 TTTAAA TTTAAA TTTA
52961 TTTTTTTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:53027 original size:15 final size:16
Alignment explanation
Indices: 52999--53033 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52989 TTTAAATAAA
52999 AAAAAGTCCAAATTAC
1 AAAAAGTCCAAATTAC
*
53015 AAAATGTCC-AATTAC
1 AAAAAGTCCAAATTAC
53030 AAAA
1 AAAA
53034 CCTATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (16 bp):
AAAAAGTCCAAATTAC
Found at i:54848 original size:30 final size:30
Alignment explanation
Indices: 54762--54846 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 30
54752 CCTAGAGGTT
* * * * *
54762 CCTAAACTGTTCAGAAATCATATTTTGACC
1 CCTAAACTTTTCAAAAATTACATTTTAACC
* * *
54792 CCTAAAGTTTTCCAAAATTCCATTTTAACC
1 CCTAAACTTTTCAAAAATTACATTTTAACC
54822 CC-AAACTTTTCAAAAATTACATTTT
1 CCTAAACTTTTCAAAAATTACATTTT
54847 TACTCTCGAG
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
29 20 0.45
30 24 0.55
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
CCTAAACTTTTCAAAAATTACATTTTAACC
Found at i:54866 original size:30 final size:29
Alignment explanation
Indices: 54800--54994 Score: 116
Period size: 29 Copynumber: 6.7 Consensus size: 29
54790 CCCCTAAAGT
* * * *
54800 TTTCC-AAAATTCCATTTTAACCCCAAAC
1 TTTCCAAAAATTACATTTTTACCTCGAAC
* *
54828 TTTTCAAAAATTACATTTTTACTCTCGAGC
1 TTTCCAAAAATTACATTTTTAC-CTCGAAC
*
54858 TTTCC-AAAATT-CTATTTCTGACCTCGAAC
1 TTTCCAAAAATTAC-ATTT-TTACCTCGAAC
* **
54887 -TTCCAAAAATTCCATTTTTGACCTCGATT
1 TTTCCAAAAATTACATTTTT-ACCTCGAAC
*
54916 TTTCCAAAAATTATCA-TTTTACCGCTGAAC
1 TTTCCAAAAATTA-CATTTTTACCTC-GAAC
* * * **
54946 -TTCCAAAAAACTCCATTTTGAACC-CGATT
1 TTTCC-AAAAATTACATTTT-TACCTCGAAC
54975 TTTCCAAAAATTACCATTTT
1 TTTCCAAAAATTA-CATTTT
54995 ATTCTCGGAT
Statistics
Matches: 129, Mismatches: 23, Indels: 28
0.72 0.13 0.16
Matches are distributed among these distances:
28 10 0.08
29 65 0.50
30 49 0.38
31 5 0.04
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTTACCTCGAAC
Found at i:54867 original size:58 final size:58
Alignment explanation
Indices: 54800--54924 Score: 146
Period size: 58 Copynumber: 2.2 Consensus size: 58
54790 CCCCTAAAGT
*
54800 TTTCCAAAATTCCATTT-TAACCCCAAACTTTTCAAAAATTACATTTTT-ACTCTCGAGC
1 TTTCCAAAATTCCATTTCTAACCCCAAAC-TTCCAAAAATTACATTTTTGAC-CTCGAGC
* * * * * **
54858 TTTCCAAAATTCTATTTCTGACCTCGAACTTCCAAAAATTCCATTTTTGACCTCGATT
1 TTTCCAAAATTCCATTTCTAACCCCAAACTTCCAAAAATTACATTTTTGACCTCGAGC
54916 TTTCCAAAA
1 TTTCCAAAA
54925 ATTATCATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
58 47 0.82
59 10 0.18
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (58 bp):
TTTCCAAAATTCCATTTCTAACCCCAAACTTCCAAAAATTACATTTTTGACCTCGAGC
Found at i:54965 original size:59 final size:59
Alignment explanation
Indices: 54883--54995 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 59
54873 TTCTGACCTC
* *
54883 GAACTTCCAAAAATTCCATTTTTG-ACCTCGATTTTTCCAAAAATTATCATTTTACCGCT
1 GAACTTCCAAAAACTCCATTTTTGAACC-CGATTTTTCCAAAAATTACCATTTTACCGCT
54942 GAACTTCCAAAAAACTCCA-TTTTGAACCCGATTTTTCCAAAAATTACCATTTTA
1 GAACTTCC-AAAAACTCCATTTTTGAACCCGATTTTTCCAAAAATTACCATTTTA
54996 TTCTCGGATG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 38 0.76
60 12 0.24
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (59 bp):
GAACTTCCAAAAACTCCATTTTTGAACCCGATTTTTCCAAAAATTACCATTTTACCGCT
Found at i:54983 original size:29 final size:30
Alignment explanation
Indices: 54887--55052 Score: 104
Period size: 30 Copynumber: 5.7 Consensus size: 30
54877 GACCTCGAAC
*
54887 TTCCAAAAATT-CCATTTTTGACCTCGATTT
1 TTCCAAAAATTACCA-TTTTGACCGCGATTT
* **
54917 TTCCAAAAATTATCATTTT-ACCGCTGA-AC
1 TTCCAAAAATTACCATTTTGACCGC-GATTT
*
54946 TTCCAAAAAACT-CCATTTTGAACC-CGATTT
1 TTCC-AAAAATTACCATTTTG-ACCGCGATTT
54976 TTCCAAAAATTACCATTTT-ATTCTCG-GA--T
1 TTCCAAAAATTACCATTTTGA--C-CGCGATTT
* * *
55005 GT-CTAAAATT-CCATTTTGACCCCGAATTT
1 TTCCAAAAATTACCATTTTGACCGCG-ATTT
55034 TTCC-AAAATTACCATTTTG
1 TTCCAAAAATTACCATTTTG
55053 CCCTCCGAGT
Statistics
Matches: 105, Mismatches: 13, Indels: 36
0.68 0.08 0.23
Matches are distributed among these distances:
25 1 0.01
26 2 0.02
27 8 0.08
28 9 0.09
29 32 0.30
30 45 0.43
31 8 0.08
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTCCAAAAATTACCATTTTGACCGCGATTT
Found at i:55072 original size:58 final size:57
Alignment explanation
Indices: 54892--55087 Score: 175
Period size: 59 Copynumber: 3.4 Consensus size: 57
54882 CGAACTTCCA
* * *
54892 AAAATTCCATTTTTGACCTCGATTTTTCCAAAAATTATCATTTTACCGCT--GAACT-TCC
1 AAAATTCCA-TTTTGACCCCGATTTTTCCAAAAATTACCATTTTACC-CTCCG-A-TGACC
* * ** * * *
54950 AAAAAACTCCATTTTGAACCCGATTTTTCCAAAAATTACCATTTTATTCTCGGATGTCT
1 --AAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCCGATGACC
*
55009 AAAATTCCATTTTGACCCCGAATTTTTCC-AAAATTACCATTTTGCCCTCCGAGTGACC
1 AAAATTCCATTTTGACCCCG-ATTTTTCCAAAAATTACCATTTTACCCTCCGA-TGACC
*
55067 AAAATTACCATTTTGGCCCCG
1 AAAATT-CCATTTTGACCCCG
55088 GGTATCCAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
57 37 0.32
58 20 0.18
59 48 0.42
60 9 0.08
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCTCCGATGACC
Found at i:56707 original size:6 final size:6
Alignment explanation
Indices: 56696--56726 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
56686 GTGTTCACAC
*
56696 GTGGCA GTGGCA ATGGCA GTGGCA GTGGCA G
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA G
56727 GTTGAAGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.16, G:0.48, T:0.16
Consensus pattern (6 bp):
GTGGCA
Found at i:59962 original size:19 final size:20
Alignment explanation
Indices: 59940--59985 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
59930 TTTTTTTTCA
*
59940 AATTTAT-CTAAAATTTTTG
1 AATTTATCCTAAAATATTTG
*
59959 AATTTATCCCTAACATATTTG
1 AATTTAT-CCTAAAATATTTG
59980 AATTTA
1 AATTTA
59986 AATAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
21 16 0.70
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTTATCCTAAAATATTTG
Found at i:60810 original size:22 final size:22
Alignment explanation
Indices: 60782--60828 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
60772 TGATGTAACA
60782 TATAATTAA-TATTAAAATAAAT
1 TATAATTAATTA-TAAAATAAAT
* *
60804 TATAATTTATTATAAAATATAT
1 TATAATTAATTATAAAATAAAT
60826 TAT
1 TAT
60829 TATGACAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATAATTAATTATAAAATAAAT
Found at i:69619 original size:3 final size:3
Alignment explanation
Indices: 69611--69637 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
69601 ATGGTTTATG
69611 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
69638 TATGAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:79861 original size:25 final size:25
Alignment explanation
Indices: 79813--79878 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
79803 TTTTAATAAA
* * *
79813 ATAAATAAATTATATATTATATTCAT
1 ATAAATATATT-TAAATTACATTCAT
*
79839 GTAAATATATTTAAATTACATTCAT
1 ATAAATATATTTAAATTACATTCAT
79864 ATAATTATATATTTA
1 ATAA--ATATATTTA
79879 TATTTAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 15 0.45
26 9 0.27
27 9 0.27
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAAATATATTTAAATTACATTCAT
Found at i:82348 original size:2 final size:2
Alignment explanation
Indices: 82341--82368 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82331 TCATAAACAG
82341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82369 TATTGTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85576 original size:39 final size:39
Alignment explanation
Indices: 85522--85600 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
85512 AGGGTGGACA
*
85522 TACAATCTTTGTATCTTGCTCCTTTTCTTTTTCTTTTTC
1 TACAATCTTTATATCTTGCTCCTTTTCTTTTTCTTTTTC
85561 TACAATCTTTATATCTTGCTCCTTTTCTTTTTCTTTTTC
1 TACAATCTTTATATCTTGCTCCTTTTCTTTTTCTTTTTC
85600 T
1 T
85601 TTTTTGTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.11, C:0.23, G:0.04, T:0.62
Consensus pattern (39 bp):
TACAATCTTTATATCTTGCTCCTTTTCTTTTTCTTTTTC
Found at i:86627 original size:6 final size:6
Alignment explanation
Indices: 86616--86641 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
86606 ATTATTCTTT
86616 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
86642 GTCATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:86888 original size:20 final size:20
Alignment explanation
Indices: 86863--86903 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
86853 TGGAACTTGG
86863 CAATTTTTTTCATTTTGATT
1 CAATTTTTTTCATTTTGATT
86883 CAATTTTTTTCATTTTGATT
1 CAATTTTTTTCATTTTGATT
86903 C
1 C
86904 TTAAATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.63
Consensus pattern (20 bp):
CAATTTTTTTCATTTTGATT
Found at i:126125 original size:33 final size:31
Alignment explanation
Indices: 126084--126146 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
126074 ACTTGTTTTA
**
126084 ACTCATTATGTTAACAAATTCTTATTTTGGTG
1 ACTCATTATGCCAA-AAATTCTTATTTTGGTG
*
126116 ACTCTATTATGCCCAAAATTCTTATTTTGGT
1 ACTC-ATTATGCCAAAAATTCTTATTTTGGT
126147 CATTTAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (31 bp):
ACTCATTATGCCAAAAATTCTTATTTTGGTG
Found at i:127757 original size:29 final size:31
Alignment explanation
Indices: 127692--127762 Score: 101
Period size: 30 Copynumber: 2.3 Consensus size: 31
127682 TTTAGGTCCA
127692 TTAAAAGTTGGTAAAAAAAAAAATTTTGAGCCC
1 TTAAAAGTTGGT--AAAAAAAAATTTTGAGCCC
*
127725 TTAAAAGTTGGT-AAAAAAAATTTTG-GCCT
1 TTAAAAGTTGGTAAAAAAAAATTTTGAGCCC
127754 TTAAAAGTT
1 TTAAAAGTT
127763 AAAAAGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 12 0.32
30 13 0.35
33 12 0.32
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.32
Consensus pattern (31 bp):
TTAAAAGTTGGTAAAAAAAAATTTTGAGCCC
Found at i:127773 original size:28 final size:29
Alignment explanation
Indices: 127706--127775 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
127696 AAGTTGGTAA
127706 AAAAAAAAATTTTGAGCCCTTAAAAGTTGG
1 AAAAAAAAATTTTGAGCCCTTAAAAGTT-G
* *
127736 TAAAAAAAATTTTG-GCCTTTAAAAGTT-
1 AAAAAAAAATTTTGAGCCCTTAAAAGTTG
127763 AAAAAGAAAATTT
1 AAAAA-AAAATTT
127776 GTTTGGCCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.11
28 7 0.19
29 12 0.33
30 13 0.36
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (29 bp):
AAAAAAAAATTTTGAGCCCTTAAAAGTTG
Found at i:130960 original size:26 final size:26
Alignment explanation
Indices: 130921--130981 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
130911 ACCAAGCTTT
* *
130921 TCAAAAGTACTTTTTAAAA-TCACTTC
1 TCAAAAGCATTTTTTAAAAGT-ACTTC
*
130947 TCCAAAGCATTTTTTAAAAGTACTTC
1 TCAAAAGCATTTTTTAAAAGTACTTC
130973 TCAAAAGCA
1 TCAAAAGCA
130982 ATGCTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (26 bp):
TCAAAAGCATTTTTTAAAAGTACTTC
Found at i:135836 original size:17 final size:17
Alignment explanation
Indices: 135814--135851 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
135804 TTATCTTGTA
*
135814 CTATTTTGGTAAATAAT
1 CTATTTTGATAAATAAT
*
135831 CTATTTTGATATATAAT
1 CTATTTTGATAAATAAT
135848 -TATT
1 CTATT
135852 ATTTTTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (17 bp):
CTATTTTGATAAATAAT
Found at i:135860 original size:47 final size:47
Alignment explanation
Indices: 135786--135878 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 47
135776 TGAGGATACC
* * * *
135786 ATTTTGGTATATAAATATTTATCTTGTACTATTTTGGTAAATAATCT
1 ATTTTGATATATAAATATTTATCTTGTACTATATTGATAAAAAATCT
* * *
135833 ATTTTGATATATAATTA-TTATTTTTGTATTATATTGATAAAAAATC
1 ATTTTGATATATAAATATTTA-TCTTGTACTATATTGATAAAAAATC
135879 ATAAAAATCA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 3 0.08
47 35 0.92
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (47 bp):
ATTTTGATATATAAATATTTATCTTGTACTATATTGATAAAAAATCT
Found at i:136325 original size:3 final size:3
Alignment explanation
Indices: 136317--136375 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
136307 ATCAAAAGGT
136317 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
136365 ATA ATA ATA AT
1 ATA ATA ATA AT
136376 CAAACATCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:136944 original size:45 final size:44
Alignment explanation
Indices: 136895--136980 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 44
136885 ACTAAACTCA
*
136895 TAACCCT-AAATCTTAAACGATAAAAATCTAATACCCTAAAATATT
1 TAACCCTAAAATCTTAAAC-AT-AAAATCTAAAACCCTAAAATATT
* * *
136940 TAACCTTAAAAATCTTAAACCTTAAATCTAAAACCCTAAAA
1 TAACCCT-AAAATCTTAAACATAAAATCTAAAACCCTAAAA
136981 AACCCAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
45 23 0.66
46 1 0.03
47 11 0.31
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.28
Consensus pattern (44 bp):
TAACCCTAAAATCTTAAACATAAAATCTAAAACCCTAAAATATT
Found at i:136949 original size:15 final size:16
Alignment explanation
Indices: 136902--137028 Score: 70
Period size: 15 Copynumber: 8.1 Consensus size: 16
136892 TCATAACCCT
**
136902 AAATCTTAAACGATAA
1 AAATCTTAAACCTTAA
*
136918 AAATC-TAATACCCTAA
1 AAATCTTAA-ACCTTAA
136934 AATAT-TT-AACCTTAA
1 AA-ATCTTAAACCTTAA
136949 AAATCTTAAACCTT--
1 AAATCTTAAACCTTAA
* *
136963 AAATCTAAAACCCTAAA
1 AAATCTTAAA-CCTTAA
* **
136980 AAACCCAAAACCTT-A
1 AAATCTTAAACCTTAA
136995 AAA-CATTAAACCTTAA
1 AAATC-TTAAACCTTAA
* *
137011 TTAATCATAAACCTTAA
1 -AAATCTTAAACCTTAA
137028 A
1 A
137029 CCATGAACCG
Statistics
Matches: 86, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
14 12 0.14
15 27 0.31
16 23 0.27
17 23 0.27
18 1 0.01
ACGTcount: A:0.52, C:0.20, G:0.01, T:0.27
Consensus pattern (16 bp):
AAATCTTAAACCTTAA
Found at i:136982 original size:31 final size:32
Alignment explanation
Indices: 136947--137047 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 32
136937 ATTTAACCTT
* *
136947 AAAAATCTTAAACCTTAAATC-TAAAACCCTA
1 AAAAATCATAAACCTTAAAACATAAAACCCTA
* * *
136978 AAAAACCCA-AAACCTTAAAACATTAAACCTTA
1 AAAAA-TCATAAACCTTAAAACATAAAACCCTA
** * * *
137010 ATTAATCATAAACCTTAAACCAT-GAACCGTA
1 AAAAATCATAAACCTTAAAACATAAAACCCTA
137041 AAAAATC
1 AAAAATC
137048 CACGAAACGA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
31 29 0.54
32 25 0.46
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (32 bp):
AAAAATCATAAACCTTAAAACATAAAACCCTA
Found at i:139710 original size:17 final size:17
Alignment explanation
Indices: 139685--139727 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
139675 TAAAGACCGA
*
139685 TCATTGTCTCCACGTCT
1 TCATCGTCTCCACGTCT
*
139702 TCATCGTCTCCATGTCT
1 TCATCGTCTCCACGTCT
139719 TCATCGTCT
1 TCATCGTCT
139728 ACAAGTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.35, G:0.12, T:0.42
Consensus pattern (17 bp):
TCATCGTCTCCACGTCT
Found at i:140280 original size:3 final size:3
Alignment explanation
Indices: 140272--140300 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
140262 TTTGGTGCCC
140272 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
140301 GAAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:142731 original size:408 final size:399
Alignment explanation
Indices: 141973--142830 Score: 1220
Period size: 407 Copynumber: 2.1 Consensus size: 399
141963 ACATCTTTCA
* * *
141973 TTGTACTAGAGTTAAATTCA-TGAGGCAATGGCACAATTAGTGTTGTCAATGATGCAAACACAAG
1 TTGTACTAGAGCTAAATTCACT-AGGCAATGGCACAACTAGTGTTGTCAAGGATGCAAACACAAG
* *
142037 GTAGAACCTTTCATTAAAAAGAGTTCTTATTGTGTTTGTGTGTGTCTCATTCTAAAGGGTTTGAG
65 GTAGAACCTTGCATTAAAAAGAGTTCTTATTGTGTTTGTGTGTGTCTCATTCTAAAGGGTTCGAG
* *
142102 ACATTTTTTTACTAAAACTAAATTCATTAGGCAATGGCAGAAAGGGTGCAAAGACAAGCTAGAAC
130 ACATTTTTGTACTAAAACTAAATTCATTAGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAAC
*
142167 CCTTAAATTGTCTTGCATTTGAAAGAGCTTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATT
195 CCTTAAATTGTCTTGCATTCGAAAGAGCTTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATT
*
142232 TTTGTAGTAGAGCTAAATTCACTAACCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGTCGAG
260 TTAGTAGTAGAGCTAAATTCACTAACCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGTCGAG
* * *
142297 CTAGAACCCTTATCTTGTCTTGCATTCGAAAGGGTTTTTTTTTTCTGTGTGTCTCTCTCATTCGA
325 CTAAAACCCTTATATTGTCTTGCATTCG-AA------TTTTTCTCTGTGTGTCTCTCTCATTCGA
* * *
142362 AAGGGTTGGAGACATTT
383 AAGGATTCGAGACACTT
* * * * *
142379 TTGTACTAGAGCTAAATTCACTAAGCAATGACAAAACTAGTGTTGTCAAGGATGCAAATACGAGG
1 TTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACTAGTGTTGTCAAGGATGCAAACACAAGG
* * * * *
142444 TAGAACCTTGCATTCAAAAGGGTTTTTTTTTGTGTTTGTGTGTGTCTTA-TCTGAAAGGGTTCGA
66 TAGAACCTTGCATTAAAAAGAG-TTCTTATTGTGTTTGTGTGTGTCTCATTCT-AAAGGGTTCGA
* * *
142508 GATATTTTTGTACTAAAACTAAATTCATTAGGCAATTGCAGAAAGGGCGCAAAGCCAAGCTAGAA
129 GACATTTTTGTACTAAAACTAAATTCATTAGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAA
* * *
142573 CCCTTAAATTGTCTTGCATTCGAAAGAG-TTTTGTGTGTGTGTGTCATTCGAAAGGGTTTGAGAC
194 CCCTTAAATTGTCTTGCATTCGAAAGAGCTTTT-T-TGTGTCTCTCATTCGAAAGGGTTTAAGAC
** *
142637 ATTTTAGTAGTAGAGCTAAATTCACTAGGCAATGACACAACTAGTGTTGTTAGGGGTGCAAAG-C
257 ATTTTAGTAGTAGAGCTAAATTCACTAACCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGTC
* * *
142701 GGAGCTAAAACCCTTGTATTGTCTTGCATTCGAATTTTTCTGTGTTTGTCTCTCTCATTCGAAAG
322 -GAGCTAAAACCCTTATATTGTCTTGCATTCGAATTTTTCTCTGTGTGTCTCTCTCATTCGAAAG
142766 GATTCGAGACACTT
386 GATTCGAGACACTT
* *
142780 TTGTACTAGAGCTAAATTCACTAGGCAATGGCACGACTAGTGTTGTTAAGG
1 TTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACTAGTGTTGTCAAGG
142831 GCGCAGAGCC
Statistics
Matches: 404, Mismatches: 42, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
401 85 0.21
406 81 0.20
407 125 0.31
408 113 0.28
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (399 bp):
TTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACTAGTGTTGTCAAGGATGCAAACACAAGG
TAGAACCTTGCATTAAAAAGAGTTCTTATTGTGTTTGTGTGTGTCTCATTCTAAAGGGTTCGAGA
CATTTTTGTACTAAAACTAAATTCATTAGGCAATGGCAGAAAGGGCGCAAAGACAAGCTAGAACC
CTTAAATTGTCTTGCATTCGAAAGAGCTTTTTTGTGTCTCTCATTCGAAAGGGTTTAAGACATTT
TAGTAGTAGAGCTAAATTCACTAACCAATGACACAACTAGTGTTGTTAAGGGTGCAAAGTCGAGC
TAAAACCCTTATATTGTCTTGCATTCGAATTTTTCTCTGTGTGTCTCTCTCATTCGAAAGGATTC
GAGACACTT
Found at i:142805 original size:139 final size:135
Alignment explanation
Indices: 142550--142973 Score: 406
Period size: 139 Copynumber: 3.1 Consensus size: 135
142540 CAATTGCAGA
* * * * ** *
142550 AAGGGCGCAAAGCCAAGCTAGAACCCTTAA-ATTGTCTTGCATTCG-AAAGAGTTTTGTGTGTGT
1 AAGGGCGCAAAGCCGAGCTA-AAACCTTAATATTGTCTTGCACTAGAAAAGA-TTTCCT-TCT-T
* * * * *
142613 GTGTCATTCGAAAGGGTTTGAGACATTTTAGTAGTAGAGCTAAATTCACTAGGCAATGACACAAC
62 CTCTCATTCGAAAGGGTTCGAGACATTTT-GTACTAGAGCTAAATTCACTAGGCAATGGCACAAC
142678 TAGTGTTGTT
126 TAGTGTTGTT
* * * * * * **** ** *
142688 AGGGGTGCAAAGCGGAGCTAAAACCCTT-GTATTGTCTTGCATTCGAATTTTTCTGTGTTTGTCT
1 AAGGGCGCAAAGCCGAGCTAAAA-CCTTAATATTGTCTTGCACTAGAAAAGAT-T-TCCTTCT-T
* *
142752 CTCTCATTCGAAAGGATTCGAGACACTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACGAC
62 CTCTCATTCGAAAGGGTTCGAGACA-TTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACAAC
142817 TAGTGTTGTT
126 TAGTGTTGTT
* * *
142827 AAGGGCGCAGAGCCGAGCTAGAACCTTAATATTGTCTTGCACTAGAAAAGATTTCCTTCTTGTCT
1 AAGGGCGCAAAGCCGAGCTAAAACCTTAATATTGTCTTGCACTAGAAAAGATTTCCTTCTTCTCT
* *
142892 CATTCGAAAGGGTTCGAGACATTTT-TATGCTAAAGCTAAATTCACTAGGCAATGGCACAACTAA
66 CATTCGAAAGGGTTCGAGACATTTTGTA--CTAGAGCTAAATTCACTAGGCAATGGCACAACTAG
*
142956 TATTGTT
129 TGTTGTT
*
142963 AAGGACGCAAA
1 AAGGGCGCAAA
142974 ACCAAGGTAG
Statistics
Matches: 234, Mismatches: 43, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
134 2 0.01
135 4 0.02
136 71 0.30
137 6 0.03
138 41 0.18
139 104 0.44
140 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (135 bp):
AAGGGCGCAAAGCCGAGCTAAAACCTTAATATTGTCTTGCACTAGAAAAGATTTCCTTCTTCTCT
CATTCGAAAGGGTTCGAGACATTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACAACTAGTG
TTGTT
Found at i:142948 original size:136 final size:137
Alignment explanation
Indices: 142550--143015 Score: 462
Period size: 136 Copynumber: 3.4 Consensus size: 137
142540 CAATTGCAGA
* ** *
142550 AAGGGCGCAAAGCCAAGCTAGAACCCTTAA-ATTGTCTTGCATTCG-AAAGAGTTTTGTGTGTGT
1 AAGGGCGCAAAGCCGAGCTAGAACCCTTAATATTGTCTTGCATTCGAAAAGA-TTTCCT-TGTCT
* * *
142613 GTGTCATTCGAAAGGGTTTGAGACATTTTAGTAG-TAGAGCTAAATTCACTAGGCAATGACACAA
64 GTCTCATTCGAAAGGGTTCGAGACATTTTA-T-GCTAGAGCTAAATTCACTAGGCAATGGCACAA
142677 CTAGTGTTGTT
127 CTAGTGTTGTT
* * * * * **** **
142688 AGGGGTGCAAAGCGGAGCTAAAACCCTT-GTATTGTCTTGCATTCGAATTTTTCTGTGTTTGTCT
1 AAGGGCGCAAAGCCGAGCTAGAACCCTTAATATTGTCTTGCATTCGAAAAGAT-T-TCCTTGTCT
* * * * *
142752 CTCTCATTCGAAAGGATTCGAGACACTTTTGTACTAGAGCTAAATTCACTAGGCAATGGCACGAC
64 GTCTCATTCGAAAGGGTTCGAGACA-TTTTATGCTAGAGCTAAATTCACTAGGCAATGGCACAAC
142817 TAGTGTTGTT
128 TAGTGTTGTT
* * * *
142827 AAGGGCGCAGAGCCGAGCTAGAA-CCTTAATATTGTCTTGCACTAGAAAAGATTTCCTTCT-TGT
1 AAGGGCGCAAAGCCGAGCTAGAACCCTTAATATTGTCTTGCATTCGAAAAGATTTCCTTGTCTGT
*
142890 CTCATTCGAAAGGGTTCGAGACATTTTTATGCTAAAGCTAAATTCACTAGGCAATGGCACAACTA
66 CTCATTCGAAAGGGTTCGAGACA-TTTTATGCTAGAGCTAAATTCACTAGGCAATGGCACAACTA
* *
142955 ATATTGTT
130 GTGTTGTT
* * * * * * *
142963 AAGGACGCAAAACCAAGGTAGAACCC-TGATATTGT-TTCGCATTTGAAAGGATT
1 AAGGGCGCAAAGCCGAGCTAGAACCCTTAATATTGTCTT-GCATTCGAAAAGATT
143016 ATTTTATTTT
Statistics
Matches: 265, Mismatches: 54, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
135 2 0.01
136 105 0.40
137 6 0.02
138 44 0.17
139 102 0.38
140 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (137 bp):
AAGGGCGCAAAGCCGAGCTAGAACCCTTAATATTGTCTTGCATTCGAAAAGATTTCCTTGTCTGT
CTCATTCGAAAGGGTTCGAGACATTTTATGCTAGAGCTAAATTCACTAGGCAATGGCACAACTAG
TGTTGTT
Found at i:144569 original size:169 final size:169
Alignment explanation
Indices: 144290--144624 Score: 643
Period size: 169 Copynumber: 2.0 Consensus size: 169
144280 CTTTGTTTTC
144290 CAGAATTTGTTGCTTAGTACTGCCAATCGTTTGATTCTTGTGATTGAAGACATAGATTGTTCTAT
1 CAGAATTTGTTGCTTAGTACTGCCAATCGTTTGATTCTTGTGATTGAAGACATAGATTGTTCTAT
* *
144355 TAAGTTGCAGAACAGAGAATCTGGGATAGAACAACCTATAAAGTATCAGCTACGAAACAAGGTTA
66 TAAGTTGCAGAACAGAGAATCTGGGATAGAACAACCTATAAAGTATCAGCAACAAAACAAGGTTA
144420 GTCTGTCATGTAAGCTGTCATGAAATTCTATGGTGATTG
131 GTCTGTCATGTAAGCTGTCATGAAATTCTATGGTGATTG
144459 CAGAATTTGTTGCTTAGTACTGCCAATCGTTTGATTCTTGTGATTGAAGACATAGATTGTTCTAT
1 CAGAATTTGTTGCTTAGTACTGCCAATCGTTTGATTCTTGTGATTGAAGACATAGATTGTTCTAT
144524 TAAGTTGCAGAACAGAGAATCTGGGATAGAACAACCTATAAAGTATCAGCAACAAAACAAGGTTA
66 TAAGTTGCAGAACAGAGAATCTGGGATAGAACAACCTATAAAGTATCAGCAACAAAACAAGGTTA
*
144589 GTCTTTCATGTAAGCTGTCATGAAATTCTATGGTGA
131 GTCTGTCATGTAAGCTGTCATGAAATTCTATGGTGA
144625 ACTCATTGAA
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
169 163 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (169 bp):
CAGAATTTGTTGCTTAGTACTGCCAATCGTTTGATTCTTGTGATTGAAGACATAGATTGTTCTAT
TAAGTTGCAGAACAGAGAATCTGGGATAGAACAACCTATAAAGTATCAGCAACAAAACAAGGTTA
GTCTGTCATGTAAGCTGTCATGAAATTCTATGGTGATTG
Found at i:151956 original size:139 final size:139
Alignment explanation
Indices: 151708--151992 Score: 387
Period size: 139 Copynumber: 2.0 Consensus size: 139
151698 CATTTAACAT
* * * *
151708 TTAAATTAACGATTTTAGTAATAAAATAACCTAATTGATATAACGTTGATAGTTTAGGGATATGT
1 TTAAATTAACGATTTTAGTAATAAAAGAACCTAATTGATATAACATTGATAGTTTA-GAAGATGT
* * * ** *
151773 TTAGAATGGTTTAAAGTTTATGGAGCAATTTAGAATGAGGGTCATAGTTTGGGGATGTTTTGTGC
65 TTAGAATGGTTTAAAGTTTATGGACCAATTTAAAATGAGAGTCATAGTTTGGGGATGTTTAATGA
151838 AATTAACTC-
130 AATTAACTCA
* * *
151847 TTAAATTAACGATTTTAGTAATAGAAGAACTTTATTGATATAACATTGATAGTTT-GAAGATGTA
1 TTAAATTAACGATTTTAGTAATAAAAGAACCTAATTGATATAACATTGATAGTTTAGAAGATGT-
*
151911 ATTAGAATGTTTTAAAAGTTTA-GGACCAATTTAAAATGAGAGTCATAGTTTGGGGATGTTTAAT
65 -TTAGAATGGTTT-AAAGTTTATGGACCAATTTAAAATGAGAGTCATAGTTTGGGGATGTTTAAT
151975 GAAATTAACTCA
128 GAAATTAACTCA
151987 TTAAAT
1 TTAAAT
151993 CAACCCAAAG
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
137 6 0.05
139 108 0.84
140 14 0.11
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (139 bp):
TTAAATTAACGATTTTAGTAATAAAAGAACCTAATTGATATAACATTGATAGTTTAGAAGATGTT
TAGAATGGTTTAAAGTTTATGGACCAATTTAAAATGAGAGTCATAGTTTGGGGATGTTTAATGAA
ATTAACTCA
Found at i:173364 original size:160 final size:159
Alignment explanation
Indices: 172980--173516 Score: 921
Period size: 159 Copynumber: 3.4 Consensus size: 159
172970 AAAAATCTGG
* *
172980 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATAGCCATTGATGAATTTATTCGGT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
* * * *
173045 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACATGTAAGAATGTGAAAGCATCTTCGGCT
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
173110 CGAATGAATGTTTTTGGATATTTTTCTCA
131 CGAATGAATGTTTTTGGATATTTTTCTCA
* **
173139 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGTACATATTCGAT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
173204 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
* *
173269 CCAATGAATGTTTTTTTGATATTTTTCTCA
131 CGAATGAATG-TTTTTGGATATTTTTCTCA
173299 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
* *
173364 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCAGTC
66 TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
*
173429 CGAATGAATGTTTTTGGATACTTTTCTCA
131 CGAATGAATGTTTTTGGATATTTTTCTCA
*
173458 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGAATTGCCATTTGATGAATTT
1 TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCA-TTGATGAATTT
173517 GTTTGGCTCT
Statistics
Matches: 356, Mismatches: 20, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
159 193 0.54
160 163 0.46
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.40
Consensus pattern (159 bp):
TATCTAGTGAGTTGATGAACACAATTTGATATGTTTATGGATTGCCATTGATGAATTTATTCGAT
TCTTTTGTTGATTTAAAGCATGTGAAAATGAGTGTACTTGTAAGAATGAGAAAGCATTTTCGGCC
CGAATGAATGTTTTTGGATATTTTTCTCA
Found at i:175565 original size:31 final size:31
Alignment explanation
Indices: 175527--175596 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
175517 GTAATATACC
175527 ATTTGGTACCCGAGTTTAGCTTCAATGTTCA
1 ATTTGGTACCCGAGTTTAGCTTCAATGTTCA
** * * *
175558 ATTTGGTACTTGAGTTTGGCTTCCATGTTTA
1 ATTTGGTACCCGAGTTTAGCTTCAATGTTCA
175589 ATTTGGTA
1 ATTTGGTA
175597 GCTGAGGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCCGAGTTTAGCTTCAATGTTCA
Found at i:177255 original size:29 final size:28
Alignment explanation
Indices: 177184--177256 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
177174 CAAATACAAT
*
177184 TAATAATACAATAAAAATATAATTATAG
1 TAATAATACAATAAAAATATAATCATAG
* * *
177212 TATTAAATAAAATAACAATATAATCATAG
1 TAAT-AATACAATAAAAATATAATCATAG
*
177241 TAATAATGACCATAAA
1 TAATAAT-ACAATAAA
177257 TATTAATTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
28 6 0.17
29 29 0.83
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (28 bp):
TAATAATACAATAAAAATATAATCATAG
Found at i:177623 original size:16 final size:16
Alignment explanation
Indices: 177593--177650 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
177583 AAATGGCATG
177593 AAAATAAAT-AACAAA
1 AAAATAAATAAACAAA
*
177608 AAGATAAATAAACAAA
1 AAAATAAATAAACAAA
177624 AAAATAAAATAAA-AATA
1 AAAAT-AAATAAACAA-A
177641 AAAATTAAAT
1 AAAA-TAAAT
177651 GTTAAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 8 0.22
16 12 0.32
17 16 0.43
18 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAACAAA
Found at i:177638 original size:6 final size:6
Alignment explanation
Indices: 177593--177672 Score: 65
Period size: 6 Copynumber: 13.2 Consensus size: 6
177583 AAATGGCATG
* * *
177593 AAAATA AATAACA AAAAGA TAAATA AACAA-A AAAAT- AAAATA AAAATA
1 AAAATA AA-AATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
** *
177641 AAAATTA AATGTT AAAATA AAAATA AAAATA A
1 AAAA-TA AAAATA AAAATA AAAATA AAAATA A
177673 TTGGGATTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
5 7 0.12
6 40 0.69
7 11 0.19
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:179608 original size:14 final size:14
Alignment explanation
Indices: 179589--179615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
179579 ACATTTATTA
179589 TCAAAAAAATTTGG
1 TCAAAAAAATTTGG
179603 TCAAAAAAATTTG
1 TCAAAAAAATTTG
179616 ATTGTATTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (14 bp):
TCAAAAAAATTTGG
Found at i:179955 original size:17 final size:16
Alignment explanation
Indices: 179911--179956 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
179901 GATACAAATT
*
179911 ATTTTAAATTCAAAAC
1 ATTTTGAATTCAAAAC
*
179927 ATTTTGAATTCAAATC
1 ATTTTGAATTCAAAAC
*
179943 ATATTTGATTTCAA
1 AT-TTTGAATTCAA
179957 TTATTAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.43
Consensus pattern (16 bp):
ATTTTGAATTCAAAAC
Found at i:182630 original size:4 final size:4
Alignment explanation
Indices: 182623--182653 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
182613 ATTAAAAAAA
182623 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
182654 TAAGAAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:198003 original size:101 final size:102
Alignment explanation
Indices: 197857--198042 Score: 252
Period size: 101 Copynumber: 1.8 Consensus size: 102
197847 GCAATATCAC
* * * *** *
197857 GCCTTTGATTCAATGTATGGAAAAGATATAATACCTTATAAGATGATTTTGGTGCTAATGCATTG
1 GCCTTTGATTCAATGTATGAAAAAGACATAATACCTTACAAGATGATTTCAATGCTAATGCATTC
197922 GTTGTGATTT-AAGTTCATTTAGCGCGTGCGATAGCAA
66 GTT-TGATTTAAAGTTCATTTAGCGCGTGCGATAGCAA
* *
197959 GCCTTTG-TTCCAATGTATGAAAAATACATAA-ACCTTACATGATGATTTCAATGCTAATGCATT
1 GCCTTTGATT-CAATGTATGAAAAAGACATAATACCTTACAAGATGATTTCAATGCTAATGCATT
198022 CGTTTGATTTAAAGTTCATTT
65 CGTTTGATTTAAAGTTCATTT
198043 TGTTGACATA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 6 0.08
101 42 0.58
102 25 0.34
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (102 bp):
GCCTTTGATTCAATGTATGAAAAAGACATAATACCTTACAAGATGATTTCAATGCTAATGCATTC
GTTTGATTTAAAGTTCATTTAGCGCGTGCGATAGCAA
Found at i:200815 original size:13 final size:13
Alignment explanation
Indices: 200792--200825 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
200782 CCAAATGCTA
*
200792 AAAAATTAAATAT
1 AAAATTTAAATAT
*
200805 TAAATTTAAATAT
1 AAAATTTAAATAT
200818 AAAATTTA
1 AAAATTTA
200826 TTTGATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTTAAATAT
Found at i:202125 original size:36 final size:34
Alignment explanation
Indices: 202051--202125 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
202041 TGAATTGATT
* *
202051 AAAACTCAAAATCAAATCATAATAACCCAATCCG
1 AAAACTCAAAATCAAATCATAATAACCAAATCCA
*
202085 AAAACTCAAATATCATATCCA-AATGAACCAAATCCA
1 AAAACTCAAA-ATCAAAT-CATAAT-AACCAAATCCA
202121 AAAAC
1 AAAAC
202126 ACTCAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 10 0.29
35 9 0.26
36 16 0.46
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (34 bp):
AAAACTCAAAATCAAATCATAATAACCAAATCCA
Found at i:205527 original size:2 final size:2
Alignment explanation
Indices: 205520--205544 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
205510 ATGAAAAGAA
205520 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
205545 TATATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:209748 original size:7 final size:7
Alignment explanation
Indices: 209736--209790 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
209726 AAGTAAACTA
209736 TCAACGG
1 TCAACGG
*
209743 TCAACGA
1 TCAACGG
209750 TCAACGG
1 TCAACGG
*
209757 TCAGCGG
1 TCAACGG
*
209764 TCAACGA
1 TCAACGG
* *
209771 TCAATGA
1 TCAACGG
*
209778 TCAACCG
1 TCAACGG
209785 TCAACG
1 TCAACG
209791 ATTAATGGGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (7 bp):
TCAACGG
Found at i:209754 original size:14 final size:14
Alignment explanation
Indices: 209735--209792 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
209725 AAAGTAAACT
209735 ATCAACGGTCAACG
1 ATCAACGGTCAACG
*
209749 ATCAACGGTCAGCG
1 ATCAACGGTCAACG
* * *
209763 GTCAACGATCAATG
1 ATCAACGGTCAACG
*
209777 ATCAACCGTCAACG
1 ATCAACGGTCAACG
209791 AT
1 AT
209793 TAATGGGTGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (14 bp):
ATCAACGGTCAACG
Found at i:209797 original size:21 final size:21
Alignment explanation
Indices: 209735--209797 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
209725 AAAGTAAACT
*
209735 ATCAACGGTCAACGATCAACG
1 ATCAACGGTCAACGATCAATG
* *
209756 GTCAGCGGTCAACGATCAATG
1 ATCAACGGTCAACGATCAATG
* *
209777 ATCAACCGTCAACGATTAATG
1 ATCAACGGTCAACGATCAATG
209798 GGTGGGGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCAACGGTCAACGATCAATG
Found at i:213454 original size:22 final size:22
Alignment explanation
Indices: 213426--213467 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
213416 TCGTTATCAT
213426 TAAATTAATATTAAATTTACGC
1 TAAATTAATATTAAATTTACGC
213448 TAAATTAATATTAAATTTAC
1 TAAATTAATATTAAATTTAC
213468 ATTTTGATTA
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:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTAATATTAAATTTACGC
Found at i:225527 original size:27 final size:27
Alignment explanation
Indices: 225487--225569 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 27
225477 TATTTCGGAA
225487 ACCAACAAAGGTACGTTGATACAAGGG
1 ACCAACAAAGGTACGTTGATACAAGGG
* * * *
225514 ATCAACAAAGGTACGTCGATCCGAGGG
1 ACCAACAAAGGTACGTTGATACAAGGG
*
225541 ACCAACAAAGGTATGTTGATACAAGGG
1 ACCAACAAAGGTACGTTGATACAAGGG
225568 AC
1 AC
225570 TGTGATTTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (27 bp):
ACCAACAAAGGTACGTTGATACAAGGG
Found at i:228797 original size:4 final size:4
Alignment explanation
Indices: 228788--228838 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
228778 CTTTCTAAGT
* * *
228788 CATA CATA CATG CATA CATG CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
228836 CAT
1 CAT
228839 CGACATGAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:230963 original size:12 final size:11
Alignment explanation
Indices: 230940--230969 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
230930 CTTTTGGTAC
230940 AAAAAAGGAAA
1 AAAAAAGGAAA
230951 AAAAAAGGAAA
1 AAAAAAGGAAA
230962 AAAAAAGG
1 AAAAAAGG
230970 TCCGATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAAGGAAA
Found at i:234749 original size:120 final size:120
Alignment explanation
Indices: 234536--234773 Score: 370
Period size: 120 Copynumber: 2.0 Consensus size: 120
234526 ATATGCACAG
* * * *
234536 ATACCGTATCGATGGCTGAGGTACCACATATGTTGTGAATCCTTGACATCTCGTGTGAGCAGCAT
1 ATACCGTATCAATGGCTGAGGTACCACATATGTTGTCAATCCTGGACAGCTCGTGTGAGCAGCAT
234601 CGTATACTAGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAAC
66 CGTATACTAGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAAC
* * **
234656 ATACCGTATCAATGGCTGGGGTATCGTATATGTTG-CAAGTCCTGGACAGCTCGTGTGAGCAGCA
1 ATACCGTATCAATGGCTGAGGTACCACATATGTTGTCAA-TCCTGGACAGCTCGTGTGAGCAGCA
* *
234720 TCTTATACTAGTAACAGAGTTGATACAGACATGAGGATGAAATTCTGGATTATA
65 TCGTATACTAGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATA
234774 GATAGTGTGA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
119 2 0.02
120 105 0.98
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (120 bp):
ATACCGTATCAATGGCTGAGGTACCACATATGTTGTCAATCCTGGACAGCTCGTGTGAGCAGCAT
CGTATACTAGTAACAGAGTTGATACAGACATGAGAATGAAATTCTGGATTATAAC
Found at i:235013 original size:30 final size:30
Alignment explanation
Indices: 234979--235041 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
234969 AAATGATTTT
*
234979 AAATTTATTTTTTAAAATATAAAAATATAA
1 AAATTTAATTTTTAAAATATAAAAATATAA
* *
235009 AAA-TTAATTTTTAAAATATAAAATTATTA
1 AAATTTAATTTTTAAAATATAAAAATATAA
235038 AAAT
1 AAAT
235042 CATCATCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
AAATTTAATTTTTAAAATATAAAAATATAA
Found at i:235470 original size:6 final size:6
Alignment explanation
Indices: 235456--235499 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
235446 TTCATTTCTT
*
235456 GGAAGG GGAAAG GGAAAG GG-AAG GGAAAG GGAAAG GGAGAAG GG
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGA-AAG GG
235500 GAATAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 5 0.14
6 25 0.71
7 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:235483 original size:17 final size:18
Alignment explanation
Indices: 235456--235493 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
235446 TTCATTTCTT
235456 GGAAGGGGAAAGGGAAAG
1 GGAAGGGGAAAGGGAAAG
235474 GGAA-GGGAAAGGGAAAG
1 GGAAGGGGAAAGGGAAAG
235491 GGA
1 GGA
235494 GAAGGGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
GGAAGGGGAAAGGGAAAG
Found at i:236079 original size:10 final size:10
Alignment explanation
Indices: 236064--236115 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
236054 TATATTTTAA
236064 AAATAATTTT
1 AAATAATTTT
236074 AAATAATTTT
1 AAATAATTTT
*
236084 AAAT--TTTAAA
1 AAATAATTT--T
236094 AAATAATTTT
1 AAATAATTTT
236104 -AATAATTTT
1 AAATAATTTT
236113 AAA
1 AAA
236116 ATCATTTGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 3 0.09
9 9 0.26
10 20 0.57
12 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAATAATTTT
Found at i:236082 original size:29 final size:29
Alignment explanation
Indices: 236041--236115 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
236031 GATGATGATG
*
236041 ATTTTAATAATTTTATATTTT-AAAAATA
1 ATTTTAATAATTTTAAATTTTAAAAAATA
236069 ATTTTAAATAATTTTAAATTTTAAAAAATA
1 ATTTT-AATAATTTTAAATTTTAAAAAATA
236099 ATTTTAATAATTTTAAA
1 ATTTTAATAATTTTAAA
236116 ATCATTTGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 5 0.11
29 27 0.61
30 12 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTTAATAATTTTAAATTTTAAAAAATA
Found at i:236097 original size:20 final size:22
Alignment explanation
Indices: 236074--236116 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
236064 AAATAATTTT
236074 AAATAATTTT-A-AATTTTAAA
1 AAATAATTTTAATAATTTTAAA
236094 AAATAATTTTAATAATTTTAAA
1 AAATAATTTTAATAATTTTAAA
236116 A
1 A
236117 TCATTTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATAATTTTAATAATTTTAAA
Found at i:236117 original size:20 final size:20
Alignment explanation
Indices: 236065--236122 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
236055 ATATTTTAAA
236065 AATAATTTT-AAATAATTTT
1 AATAATTTTAAAATAATTTT
236084 -A-AATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
236104 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
236123 GCTGATGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
20 19 0.58
21 1 0.03
22 6 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:241603 original size:22 final size:22
Alignment explanation
Indices: 241550--241595 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
241540 TCGAATTGAG
* *
241550 TTTAAGGTTTGAGTGATTTGGT
1 TTTAAGGTTTGGGTGATTGGGT
241572 TTTAAGGTTTGGGT-ATTGGGT
1 TTTAAGGTTTGGGTGATTGGGT
241593 TTT
1 TTT
241596 CATGGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (22 bp):
TTTAAGGTTTGGGTGATTGGGT
Found at i:251125 original size:17 final size:17
Alignment explanation
Indices: 251099--251132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
251089 ATAATGATAA
*
251099 AAAAATTTACAATGATG
1 AAAAAGTTACAATGATG
*
251116 AAAAAGTTACTATGATG
1 AAAAAGTTACAATGATG
251133 GCCATGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (17 bp):
AAAAAGTTACAATGATG
Found at i:263352 original size:6 final size:6
Alignment explanation
Indices: 263341--263369 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
263331 CTGCGCCTTT
263341 CCTGTG CCTGTG CCTGTG CCTGTG CCTGT
1 CCTGTG CCTGTG CCTGTG CCTGTG CCTGT
263370 TATATCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (6 bp):
CCTGTG
Found at i:270304 original size:25 final size:23
Alignment explanation
Indices: 270267--270313 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
270257 TAGTATTTAA
270267 TTTTTGAACTTTATAATTTATTTTC
1 TTTTTGAACTTTA-AATTT-TTTTC
270292 TTTTTGATA-TTTAAATTTTTTT
1 TTTTTGA-ACTTTAAATTTTTTT
270314 GTCACATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 11 0.52
26 1 0.05
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTTTGAACTTTAAATTTTTTTC
Found at i:275839 original size:2 final size:2
Alignment explanation
Indices: 275834--275865 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
275824 TATACACGCG
*
275834 CA CA CA GA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
275866 AACATAGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.47, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:278980 original size:4 final size:4
Alignment explanation
Indices: 278971--279024 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
278961 GAACATATAC
* * * *
278971 ACAT ACAT ACAT ACAT GCAT GCAT GCAT AAAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
279019 ACAT AC
1 ACAT AC
279025 GATAAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:300219 original size:3 final size:3
Alignment explanation
Indices: 300211--300237 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
300201 TACATACATC
300211 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
300238 GAGGAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:302301 original size:6 final size:6
Alignment explanation
Indices: 302287--302318 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
302277 TGTGAACCAT
*
302287 GTGGGG GTGGTG GTGGGG GTGGGG GTGGGG GT
1 GTGGGG GTGGGG GTGGGG GTGGGG GTGGGG GT
302319 TGCAGCTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.78, T:0.22
Consensus pattern (6 bp):
GTGGGG
Found at i:304398 original size:26 final size:26
Alignment explanation
Indices: 304369--304418 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
304359 TATTTCTAAC
304369 TTTTTCT-AATATTTTTAATTTTTAGA
1 TTTTTCTAAAT-TTTTTAATTTTTAGA
* *
304395 TTTTTTTAAATTTTTTTATTTTTA
1 TTTTTCTAAATTTTTTAATTTTTA
304419 ATGATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTCTAAATTTTTTAATTTTTAGA
Found at i:307011 original size:21 final size:21
Alignment explanation
Indices: 306987--307028 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
306977 CCAATACCTT
306987 TACAAATTCTACCGATACAAG
1 TACAAATTCTACCGATACAAG
*
307008 TACAATTTCTACCGATACAAG
1 TACAAATTCTACCGATACAAG
307029 CCATGCAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (21 bp):
TACAAATTCTACCGATACAAG
Found at i:307347 original size:35 final size:35
Alignment explanation
Indices: 307301--307372 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
307291 TCATAACTTC
307301 AAAATACAACATGCTATTACATTGCCCATACTTTT
1 AAAATACAACATGCTATTACATTGCCCATACTTTT
*
307336 AAAATACAACATGCTATTACATTGTCCATACTTTT
1 AAAATACAACATGCTATTACATTGCCCATACTTTT
307371 AA
1 AA
307373 GACATCTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (35 bp):
AAAATACAACATGCTATTACATTGCCCATACTTTT
Found at i:307919 original size:51 final size:51
Alignment explanation
Indices: 307840--308013 Score: 240
Period size: 51 Copynumber: 3.4 Consensus size: 51
307830 CCGTATAGGA
* * * *
307840 ATTCATATACTCACGATGACACTGAGTCATTGGACCTTTAATTCATCATGG
1 ATTCATTTACTCACGATGACACTCAGTCATCGGACCTTTAATTCGTCATGG
* * *
307891 ATTCATTTACTCATGATGACACTCAGTCAACAGACCTTTAATTCGTCATGG
1 ATTCATTTACTCACGATGACACTCAGTCATCGGACCTTTAATTCGTCATGG
* * * * *
307942 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGA
1 ATTCATTTACTCACGATGACACTCAGTCATCGGACCTTTAATTCGTCATGG
307993 ATTCATTTACTCACGATGACA
1 ATTCATTTACTCACGATGACA
308014 TTACTCACGA
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 108 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTCAGTCATCGGACCTTTAATTCGTCATGG
Found at i:308019 original size:15 final size:15
Alignment explanation
Indices: 307999--308028 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
307989 AAGAATTCAT
307999 TTACTCACGATGACA
1 TTACTCACGATGACA
308014 TTACTCACGATGACA
1 TTACTCACGATGACA
308029 CTTAGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
TTACTCACGATGACA
Found at i:308054 original size:66 final size:66
Alignment explanation
Indices: 307948--308075 Score: 247
Period size: 66 Copynumber: 1.9 Consensus size: 66
307938 ATGGATTCAT
307948 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATTTACTCACGATGAC
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATTTACTCACGATGAC
308013 A
66 A
*
308014 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGAT
1 TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATTTACTCACGAT
308076 AACACTTAGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (66 bp):
TTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGAATTCATTTACTCACGATGAC
A
Found at i:309001 original size:20 final size:21
Alignment explanation
Indices: 308958--309001 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
308948 ACTTTCATGA
* * *
308958 TTAAGCTTTAATTAAGTATTT
1 TTAACCTTTAATTAAATATAT
308979 TTAACCTTT-ATTAAATATAT
1 TTAACCTTTAATTAAATATAT
308999 TTA
1 TTA
309002 CTCTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAACCTTTAATTAAATATAT
Found at i:309421 original size:60 final size:60
Alignment explanation
Indices: 309288--309421 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 60
309278 GACAAATTTG
*
309288 AATAGTTAGGTGACCATTTTGTAACTTTTCATAGTTGGATGATCAAAAAAGAAATTTACT
1 AATAGTTAGGTGACCATTTTGTAACTTTTCATAATTGGATGATCAAAAAAGAAATTTACT
* * * * * * *
309348 AATAATAAAGTGACCATTTTGTAATTTTTCATAATTGGATGATTAAAAAATAAATTTATT
1 AATAGTTAGGTGACCATTTTGTAACTTTTCATAATTGGATGATCAAAAAAGAAATTTACT
309408 AATAGTTAGGTGAC
1 AATAGTTAGGTGAC
309422 TACTAGTGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (60 bp):
AATAGTTAGGTGACCATTTTGTAACTTTTCATAATTGGATGATCAAAAAAGAAATTTACT
Found at i:310402 original size:52 final size:51
Alignment explanation
Indices: 310320--310417 Score: 144
Period size: 53 Copynumber: 1.9 Consensus size: 51
310310 TCACTTTTAA
*
310320 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTGATTTTGTTTGTTTGTTTG
1 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTT-AATTTG-TTGTTTGTTTG
* *
310373 TTTTTGGGGTTTGAATTAA-TTTTCTGGGAATTTAATTTGTTGTTT
1 TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTAATTTGTTGTTT
310418 AGGCGCTGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 6 0.14
51 5 0.12
52 14 0.33
53 17 0.40
ACGTcount: A:0.16, C:0.02, G:0.23, T:0.58
Consensus pattern (51 bp):
TTTTTAGGGTTTGAATGAATTTTTCTGGGAATTTAATTTGTTGTTTGTTTG
Found at i:319743 original size:13 final size:14
Alignment explanation
Indices: 319721--319784 Score: 53
Period size: 13 Copynumber: 4.7 Consensus size: 14
319711 TTTAGTATTA
*
319721 TTTTTGAAAAGT-G
1 TTTTTAAAAAGTAG
*
319734 TTTTTAAAAATTAG
1 TTTTTAAAAAGTAG
*
319748 TTTTAAAAAAGT-G
1 TTTTTAAAAAGTAG
* *
319761 ATTTTGAAAAA-TAT
1 -TTTTTAAAAAGTAG
319775 TTTTTAAAAA
1 TTTTTAAAAA
319785 TTTGATTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 21 0.51
14 20 0.49
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (14 bp):
TTTTTAAAAAGTAG
Found at i:320141 original size:20 final size:20
Alignment explanation
Indices: 320116--320154 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
320106 CCATCTGAAG
*
320116 AAAAATATT-TTTGAAAAGTC
1 AAAAAT-TTCTTTCAAAAGTC
320136 AAAAATTTCTTTCAAAAGT
1 AAAAATTTCTTTCAAAAGT
320155 TACTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (20 bp):
AAAAATTTCTTTCAAAAGTC
Found at i:329531 original size:4 final size:4
Alignment explanation
Indices: 329508--329587 Score: 54
Period size: 4 Copynumber: 19.8 Consensus size: 4
329498 TTTTACGATG
* * * * * ** *
329508 TAAA TAAG TAAG TAAG TAAA TAAA TAAAA TAAA TAAC TAAC TAGC TAAC
1 TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
*
329557 TAAA TAAA TAAA T-AA TCAAA TAAC TAAA TAA
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAA
329588 TTTTTTTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
3 3 0.05
4 55 0.85
5 7 0.11
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:329749 original size:16 final size:15
Alignment explanation
Indices: 329728--329758 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
329718 TAACCACTGG
329728 AAATAAATAAATATAT
1 AAATAAATAAA-ATAT
329744 AAATAAATAAAATAT
1 AAATAAATAAAATAT
329759 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAATAAAATAT
Found at i:348772 original size:12 final size:12
Alignment explanation
Indices: 348751--348785 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
348741 TTACATATAT
*
348751 ATACATATACAC
1 ATACACATACAC
348763 ATACACATACAC
1 ATACACATACAC
348775 ATACACATACA
1 ATACACATACA
348786 TATGAGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (12 bp):
ATACACATACAC
Found at i:348772 original size:18 final size:18
Alignment explanation
Indices: 348743--348788 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
348733 TTTAGCCCTT
* *
348743 ACATATATATACATATAC
1 ACATACATATACACATAC
*
348761 ACATACACATACACATAC
1 ACATACATATACACATAC
348779 ACATACATAT
1 ACATACATAT
348789 GAGCATAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (18 bp):
ACATACATATACACATAC
Found at i:354521 original size:10 final size:10
Alignment explanation
Indices: 354506--354537 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
354496 CTATAATATC
*
354506 AATAAAATAA
1 AATAAAACAA
354516 AATAAAACAA
1 AATAAAACAA
354526 AATAAAACAA
1 AATAAAACAA
354536 AA
1 AA
354538 CCTCTTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AATAAAACAA
Found at i:354529 original size:15 final size:15
Alignment explanation
Indices: 354509--354538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
354499 TAATATCAAT
*
354509 AAAATAAAATAAAAC
1 AAAATAAAACAAAAC
354524 AAAATAAAACAAAAC
1 AAAATAAAACAAAAC
354539 CTCTTTTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAATAAAACAAAAC
Found at i:363351 original size:60 final size:60
Alignment explanation
Indices: 363272--363390 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
363262 TGAGGATTCA
** * * * * *
363272 TCCTTCTTGAGATATTTGTGTTCGATTTTCATTTCTTGGGATTCTTTAACCCCGGCTTTG
1 TCCTTCTCAAGATACTTGTGTTCGATTTTCAGTCCTCGAGATTCTTTAACCCCGGCTTTG
*
363332 TCCTTCTCAAGATACTTGTGTTCGATTTTCAGTCCTCGAGATTCTTTAACCTCGGCTTT
1 TCCTTCTCAAGATACTTGTGTTCGATTTTCAGTCCTCGAGATTCTTTAACCCCGGCTTT
363391 CTTTGAGGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (60 bp):
TCCTTCTCAAGATACTTGTGTTCGATTTTCAGTCCTCGAGATTCTTTAACCCCGGCTTTG
Found at i:370114 original size:4 final size:4
Alignment explanation
Indices: 370107--370144 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
370097 AAAGAAATAA
* *
370107 ATAC ATAC ACAC ATAC ACAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
370145 TAAAACAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAC
Found at i:371170 original size:23 final size:22
Alignment explanation
Indices: 371137--371183 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
371127 TTGTATATAC
371137 TTAAAAAAAATACAATATTTTA
1 TTAAAAAAAATACAATATTTTA
*
371159 TTAAAAATAAATATAATATTTTA
1 TTAAAAA-AAATACAATATTTTA
371182 TT
1 TT
371184 TCTATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAAAAAATACAATATTTTA
Found at i:371206 original size:25 final size:26
Alignment explanation
Indices: 371178--371227 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
371168 AATATAATAT
*
371178 TTTATTTCT-ATATAAAATAAATAAA
1 TTTATTTATCATATAAAATAAATAAA
*
371203 TTTATTTATGCATATAATATAAATA
1 TTTATTTAT-CATATAAAATAAATA
371228 CGTAAACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
27 13 0.62
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTATTTATCATATAAAATAAATAAA
Found at i:371210 original size:29 final size:27
Alignment explanation
Indices: 371138--371227 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 27
371128 TGTATATACT
* *
371138 TAAAAAAAATACAATATTTTAT---TA
1 TAAAATAAATATAATATTTTATGCATA
*
371162 -AAAATAAATATAATATTTTATTTCTATA
1 TAAAATAAATATAATATTTTA-TGC-ATA
*
371190 TAAAATAAATA-AATTTATTTATGCATA
1 TAAAATAAATATAATAT-TTTATGCATA
*
371217 TAATATAAATA
1 TAAAATAAATA
371228 CGTAAACTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 18 0.33
24 1 0.02
27 13 0.24
28 8 0.15
29 14 0.26
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (27 bp):
TAAAATAAATATAATATTTTATGCATA
Found at i:371751 original size:29 final size:29
Alignment explanation
Indices: 371679--371744 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
371669 TTTATCAAAT
*
371679 ACAAATACTAGATTGGACCAAAACATAAC
1 ACAAATACTAGATTAGACCAAAACATAAC
*
371708 ACAAGTACTAGATTAGACCAAATA-ATAAC
1 ACAAATACTAGATTAGACCAAA-ACATAAC
371737 ACAAATAC
1 ACAAATAC
371745 CATATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.09, T:0.18
Consensus pattern (29 bp):
ACAAATACTAGATTAGACCAAAACATAAC
Done.