Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011679.1 Kokia drynarioides strain JFW-HI SEQ_126671, 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: 161215
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 202 characters in sequence are not A, C, G, or T
Found at i:4775 original size:115 final size:114
Alignment explanation
Indices: 4584--4904 Score: 500
Period size: 115 Copynumber: 2.8 Consensus size: 114
4574 GCTCAAAGCA
* * *
4584 AGCAAATCTTCGGACTCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAAAAATAAAATGGT
1 AGCAAGTCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTC-AAAAAATAAAATGGT
4649 TAGCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAGGGCTCGATGTG
65 TAGCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAGGGCTCGATGTG
*
4699 AGCAAGTCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCAAAATAATAAAATGGT
1 AGCAAGTCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCAAAA-AATAAAATGGT
4764 TAGCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAGGGCTCGATGTG
65 TAGCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAGGGCTCGATGTG
* * * **
4814 AGCAAGTCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGGCGAAGCAATAAAA-GGT
1 AGCAAGTCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTC-AAAAAATAAAATGGT
* * *
4878 TAGCTTCTTGATGAGATACTGAGAAGT
65 TAGCTTCCTGATGAGGTACAGAGAAGT
4905 GGACCAAATT
Statistics
Matches: 191, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
114 31 0.16
115 158 0.83
116 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (114 bp):
AGCAAGTCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCAAAAAATAAAATGGTT
AGCTTCCTGATGAGGTACAGAGAAGTATACCAACTCAGGGCTCGATGTG
Found at i:5387 original size:206 final size:206
Alignment explanation
Indices: 4804--5403 Score: 781
Period size: 209 Copynumber: 2.9 Consensus size: 206
4794 CCAACTCAGG
* * *
4804 GCTCGATGTGAGCAAGTCTTCGAACCCCAGCTTCCTGATAAGATACTGAGAAGCAGGGCGAAGCA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
* * *
4869 ATAAAAGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCCTCCTGATGAGGTAC
66 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTAC
* * *
4934 AGAGAAGCGGATTAAAACAAACGACGCGGCCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
131 AGAGAAGCGGATTAAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAA
* *
4999 TCAAGTAAAACGAG
196 TC-A--AAAACCAC
* * *
5013 GCTC-AAAGCGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGC
1 GCTCGATA-TGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGC
5077 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTA
65 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTA
* *
5142 CAGAGAAACGGATTAAGACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAA
130 CAGAGAAGCGGATTAAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAA
*
5207 ATC-AAACCCAC
195 ATCAAAAACCAC
* * * * *
5218 GCTCGATATGAGCAAATCTTTGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTA
1 GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
* * * * ** * ***
5283 ATAAAACGGTTAGCTTCCTGATGAAATACGGGGAAGTAAACCAAAACCATCTTCCTGATGAAACA
66 ATAAAA-GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTA
** * ** ** *
5348 CAGAGAAGTTGATCAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTGAGAA
130 CAGAGAAGCGGATTAAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAA
5404 GAAGGCAAAG
Statistics
Matches: 343, Mismatches: 45, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
205 65 0.19
206 96 0.28
208 1 0.00
209 181 0.53
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (206 bp):
GCTCGATATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCA
ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTAC
AGAGAAGCGGATTAAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAA
TCAAAAACCAC
Found at i:5763 original size:17 final size:17
Alignment explanation
Indices: 5740--5832 Score: 116
Period size: 17 Copynumber: 5.4 Consensus size: 17
5730 TCAAACTCAT
5740 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
5758 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
5775 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
5792 TTTAAATTCATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
5810 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
5827 TTTAAA
1 TTTAAA
5833 ATAGATAAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
17 38 0.58
18 28 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5786 original size:35 final size:35
Alignment explanation
Indices: 5740--5832 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
5730 TCAAACTCAT
**
5740 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTCATTTTAAAA
*
5775 TTTAAATTTATTTTAAATTTAAATTCATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTCATTTTAAAA
* *
5810 TTTAAAATTATTATAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAA
5833 ATAGATAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
34 1 0.02
35 51 0.98
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTCATTTTAAAA
Found at i:6581 original size:3 final size:3
Alignment explanation
Indices: 6575--6636 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
6565 ATGATAGCAT
* **
6575 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TTA TTT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
6621 TAA TAA TAAA TAA TAA
1 TAA TAA T-AA TAA TAA
6637 AAAAGGGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:6609 original size:25 final size:25
Alignment explanation
Indices: 6575--6636 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
6565 ATGATAGCAT
6575 TAAT-AATAATAATAATAATAATAA
1 TAATAAATAATAATAATAATAATAA
* **
6599 TAATAAATAATTATTTTAATAATAA
1 TAATAAATAATAATAATAATAATAA
6624 TAATAAATAATAA
1 TAATAAATAATAA
6637 AAAAGGGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TAATAAATAATAATAATAATAATAA
Found at i:7776 original size:30 final size:29
Alignment explanation
Indices: 7723--8068 Score: 248
Period size: 29 Copynumber: 11.8 Consensus size: 29
7713 GGAGGTCTCT
7723 AAACTGTCCAAAAATTCCATTTTTACCCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* *
7753 AAACTTCCAAAAATCCCATTTTTTTACCCCC
1 AAACTTCCAAAAATTCCA--TTTTTACCCTC
* *
7784 GAACTTCCAAAAATTCCATTTTCGACCC-C
1 AAACTTCCAAAAATTCCATTTT-TACCCTC
*
7813 AAAACTTTCAAAAATTCCA-TTTTACCC-C
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
7841 TGAACTTCCAAAAATTCCATTTTGA-CCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
*
7870 GAAACTTCCAAAAAATCCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* * *
7900 GAACTTCTAAAAATTCCATTTTTACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
7929 AAATTTCCGAAAATTACCA-TTTTACCC-C
1 AAACTTCCAAAAATT-CCATTTTTACCCTC
** * *
7957 TGGA-TGTCCAAAAACTCCATTTTCGA-CCTC
1 -AAACT-TCCAAAAATTCCATTTT-TACCCTC
*
7987 GAAAC-TCTC-AAAATTACCA-TTTTACCCCC
1 -AAACTTC-CAAAAATT-CCATTTTTACCCTC
* * *
8016 GAA-TGTCTAAAAATTCCATTTTTAACCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* *
8045 AAATTTTCCCAAAATTACCATTTT
1 AAA-CTTCCAAAAATT-CCATTTT
8069 GCCCCACGGG
Statistics
Matches: 249, Mismatches: 43, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
28 33 0.13
29 135 0.54
30 47 0.19
31 34 0.14
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:7951 original size:116 final size:117
Alignment explanation
Indices: 7724--8073 Score: 421
Period size: 116 Copynumber: 3.0 Consensus size: 117
7714 GAGGTCTCTA
* *
7724 AACTGTCCAAAAATTCCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTTTACCCCCGAAC
1 AACTGTCCAAAAATTCCATTTTGA-CCTCGAAACTTCCAAAAATACCA--TTTTTACCCCCGAAC
* * *
7788 TTCCAAAAATTCCATTTTCGACCCCAAAACTTT-CAAAAATT-CCATTTTACCCCTG
63 TTCTAAAAATTCCATTTT-TACCCTAAAA-TTTCCAAAAATTACCATTTTACCCCTG
*
7843 AACT-TCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAA-ATCCATTTTTACCCTCGAACTT
1 AACTGTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATA-CCATTTTTACCCCCGAACTT
*
7906 CTAAAAATTCCATTTTTACCCTAAAATTTCCGAAAATTACCATTTTACCCCTG
65 CTAAAAATTCCATTTTTACCCTAAAATTTCCAAAAATTACCATTTTACCCCTG
* * *
7959 GA-TGTCCAAAAACTCCATTTTCGACCTCGAAAC-TCTCAAAATTACCA-TTTTACCCCCGAA-T
1 AACTGTCCAAAAATTCCATTTT-GACCTCGAAACTTC-CAAAAATACCATTTTTACCCCCGAACT
* * * *
8020 GTCTAAAAATTCCATTTTTAACCTCAAATTTTCCCAAAATTACCATTTTGCCCC
64 -TCTAAAAATTCCATTTTTACCCT-AAAATTTCCAAAAATTACCATTTTACCCC
8074 ACGGGTATCC
Statistics
Matches: 206, Mismatches: 15, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
114 3 0.01
115 17 0.08
116 98 0.48
117 49 0.24
118 35 0.17
119 4 0.02
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (117 bp):
AACTGTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATACCATTTTTACCCCCGAACTTC
TAAAAATTCCATTTTTACCCTAAAATTTCCAAAAATTACCATTTTACCCCTG
Found at i:8044 original size:58 final size:57
Alignment explanation
Indices: 7724--8073 Score: 311
Period size: 58 Copynumber: 6.0 Consensus size: 57
7714 GAGGTCTCTA
* *
7724 AACTGTCCAAAAATTCCATTTTT-ACCCTCAAACTTCCAAAAATCCCATTTTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTGA-CCTCAAACTTCCAAAATTACCA---TTTTACCCCCG
* * * *
7785 AACTTCCAAAAATTCCATTTTCGACCCCAAAACTTTCAAAAATT-CCATTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTGACCTC-AAAC-TTCCAAAATTACCATTTTACCCCCG
* *
7843 AACTTCCAAAAATTCCA-TTTTGACCTCGAAACTTCCAAAA-AATCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCTC-AAACTTCCAAAATTA-CCA-TTTTACCCCCG
* * * *
7901 AACTTCTAAAAATTCCATTTTT-ACCCTAAAATTTCCGAAAATTACCATTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTGA-CCTCAAACTTCC-AAAATTACCATTTTACCCCCG
* * *
7959 GA-TGTCCAAAAACTCCATTTTCGACCTCGAAAC-TCTCAAAATTACCATTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTGACCTC-AAACTTC-CAAAATTACCATTTTACCCCCG
* * * *
8017 AA-TGTCTAAAAATTCCATTTTTAACCTCAAATTTTCCCAAAATTACCATTTTGCCCC
1 AACT-TCCAAAAATTCCATTTTTGACCTCAAA-CTT-CCAAAATTACCATTTTACCCC
8074 ACGGGTATCC
Statistics
Matches: 240, Mismatches: 32, Indels: 36
0.78 0.10 0.12
Matches are distributed among these distances:
56 7 0.03
57 19 0.08
58 133 0.55
59 39 0.16
60 22 0.09
61 12 0.05
62 8 0.03
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (57 bp):
AACTTCCAAAAATTCCATTTTTGACCTCAAACTTCCAAAATTACCATTTTACCCCCG
Found at i:9433 original size:20 final size:20
Alignment explanation
Indices: 9400--9438 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9390 TATTCTAAAA
*
9400 GAAAAGCATGTGAATATGGG
1 GAAAAACATGTGAATATGGG
*
9420 GAAAAACATTTGAATATGG
1 GAAAAACATGTGAATATGG
9439 AAATAATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (20 bp):
GAAAAACATGTGAATATGGG
Found at i:12601 original size:9 final size:9
Alignment explanation
Indices: 12587--12625 Score: 78
Period size: 9 Copynumber: 4.3 Consensus size: 9
12577 AATTATCATG
12587 ATGCAAGAA
1 ATGCAAGAA
12596 ATGCAAGAA
1 ATGCAAGAA
12605 ATGCAAGAA
1 ATGCAAGAA
12614 ATGCAAGAA
1 ATGCAAGAA
12623 ATG
1 ATG
12626 AATAAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.23, T:0.13
Consensus pattern (9 bp):
ATGCAAGAA
Found at i:14714 original size:20 final size:21
Alignment explanation
Indices: 14691--14729 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14681 TTTTATATAT
14691 ATTTTTAAAT-TTTCTAAAAC
1 ATTTTTAAATATTTCTAAAAC
*
14711 ATTTTTATATATTTCTAAA
1 ATTTTTAAATATTTCTAAA
14730 CTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTAAATATTTCTAAAAC
Found at i:15994 original size:22 final size:22
Alignment explanation
Indices: 15969--16022 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
15959 TATTCTCATG
*
15969 TAAAAATTTAATTTTTTTTAAT
1 TAAAAATTTAATTTCTTTTAAT
* ***
15991 TAAATACAGAATTTCTTTTAAT
1 TAAAAATTTAATTTCTTTTAAT
16013 TAAAGAATTT
1 TAAA-AATTT
16023 TCAACTAGCC
Statistics
Matches: 22, Mismatches: 9, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (22 bp):
TAAAAATTTAATTTCTTTTAAT
Found at i:19527 original size:5 final size:5
Alignment explanation
Indices: 19519--19556 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
19509 TCTATTTAAA
* *
19519 AATCG AATCG AATCG AACCG AACCG AATCG AATCG AAT
1 AATCG AATCG AATCG AATCG AATCG AATCG AATCG AAT
19557 TTACCCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (5 bp):
AATCG
Found at i:23135 original size:31 final size:29
Alignment explanation
Indices: 23099--23164 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
23089 TATTTTTTAA
23099 ATATATACTT-TTGAACCATAATCAAAGTTTC
1 ATATATA-TTATTGAACCA-AATCAAAG-TTC
* *
23130 ATATATATTATTGCATCAAATCAAAGTTC
1 ATATATATTATTGAACCAAATCAAAGTTC
23159 ATATAT
1 ATATAT
23165 CAAATTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.28
30 10 0.31
31 13 0.41
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (29 bp):
ATATATATTATTGAACCAAATCAAAGTTC
Found at i:23171 original size:29 final size:30
Alignment explanation
Indices: 23118--23188 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 30
23108 TTTGAACCAT
*
23118 AATCAAAGTTTCATATATATTATTGCAT-CA
1 AATCAAAG-TTCATATATATAATTGCATACA
*
23148 AATCAAAGTTCATATATCA-AATTGCATAATA
1 AATCAAAGTTCATATAT-ATAATTGCAT-ACA
23179 AATCAAAGTT
1 AATCAAAGTT
23189 TATTTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 16 0.44
30 9 0.25
31 11 0.31
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (30 bp):
AATCAAAGTTCATATATATAATTGCATACA
Found at i:23747 original size:23 final size:23
Alignment explanation
Indices: 23705--23749 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23695 AAATATATAA
* **
23705 TAAATTTTAATAAATGATATTTT
1 TAAAATTTAATAAAACATATTTT
23728 TAAAATTTAATAAAACATATTT
1 TAAAATTTAATAAAACATATTT
23750 AAAAGCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAAATTTAATAAAACATATTTT
Found at i:23803 original size:29 final size:29
Alignment explanation
Indices: 23757--23812 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
23747 TTTAAAAGCT
* *
23757 TATAAAAATTCATAAAAATTTATAAATAA
1 TATAAAAATTCAGAAAAATATATAAATAA
23786 TATAGAAAATT-AGAAAAATATATAAAT
1 TATA-AAAATTCAGAAAAATATATAAAT
23813 TATGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (29 bp):
TATAAAAATTCAGAAAAATATATAAATAA
Found at i:24013 original size:34 final size:34
Alignment explanation
Indices: 23975--24049 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
23965 GATATTCTCC
23975 TTTTTATTGATAAATTATTGTTTTTATTTTTAAA
1 TTTTTATTGATAAATTATTGTTTTTATTTTTAAA
24009 TTTTTATTGATAAATTATTGTTTTTATTTTTAAA
1 TTTTTATTGATAAATTATTGTTTTTATTTTTAAA
24043 TTTTTAT
1 TTTTTAT
24050 CTCCAGTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (34 bp):
TTTTTATTGATAAATTATTGTTTTTATTTTTAAA
Found at i:24044 original size:20 final size:20
Alignment explanation
Indices: 23975--24036 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
23965 GATATTCTCC
23975 TTTTTATTGATAAATTATTG
1 TTTTTATTGATAAATTATTG
**
23995 TTTTTATT--T---TTA-AA
1 TTTTTATTGATAAATTATTG
24009 TTTTTATTGATAAATTATTG
1 TTTTTATTGATAAATTATTG
24029 TTTTTATT
1 TTTTTATT
24037 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
14 8 0.25
15 3 0.09
16 1 0.03
18 1 0.03
19 3 0.09
20 16 0.50
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (20 bp):
TTTTTATTGATAAATTATTG
Found at i:24311 original size:9 final size:9
Alignment explanation
Indices: 24240--24454 Score: 64
Period size: 10 Copynumber: 22.4 Consensus size: 9
24230 TAATCTTACT
24240 TAAAAATTA
1 TAAAAATTA
24249 TTAGAAATATT-
1 -TA-AAA-ATTA
24260 TAAAAATCT-
1 TAAAAAT-TA
*
24269 TAAAATTTTA
1 TAAAA-ATTA
*
24279 TATAAACTTA
1 TA-AAAATTA
*
24289 -AAAATTTA
1 TAAAAATTA
24297 TAAAAAATTA
1 T-AAAAATTA
**
24307 TAAAAAAAAA
1 T-AAAAATTA
*
24317 CACAAAAATTTA
1 TA-AA-AATT-A
*
24329 TAAATATTA
1 TAAAAATTA
24338 TAAAAATATA
1 TAAAAAT-TA
24348 TAATAAATTA
1 TAA-AAATTA
***
24358 TAATCTTTTA
1 TAA-AAATTA
*
24368 TAAAAATAA
1 TAAAAATTA
**
24377 TAAAACCTA
1 TAAAAATTA
*
24386 T-AATATT-
1 TAAAAATTA
*
24393 TAAAAGCTTA
1 TAAAA-ATTA
24403 TAAAAATTGA
1 TAAAAATT-A
*
24413 TGAAAACTTA
1 T-AAAAATTA
24423 TAAATAA-TA
1 TAAA-AATTA
24432 TTAAAAATTA
1 -TAAAAATTA
*
24442 TAAAATTTA
1 TAAAAATTA
24451 TAAA
1 TAAA
24455 TTATTAAAAA
Statistics
Matches: 153, Mismatches: 31, Indels: 43
0.67 0.14 0.19
Matches are distributed among these distances:
7 1 0.01
8 13 0.08
9 51 0.33
10 63 0.41
11 20 0.13
12 5 0.03
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Found at i:24950 original size:19 final size:19
Alignment explanation
Indices: 24918--24954 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24908 TCTTAAAGTT
* *
24918 TTATATAAACTTATAAAAC
1 TTATAGAAAATTATAAAAC
24937 TTATAGAAAATTATAAAA
1 TTATAGAAAATTATAAAA
24955 AAAATAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
TTATAGAAAATTATAAAAC
Found at i:29438 original size:15 final size:15
Alignment explanation
Indices: 29418--29447 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29408 TAGTATTACG
29418 TACATAACATTGATA
1 TACATAACATTGATA
29433 TACATAACATTGATA
1 TACATAACATTGATA
29448 GTTGAAATAA
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:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
TACATAACATTGATA
Found at i:30052 original size:18 final size:18
Alignment explanation
Indices: 29996--30052 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
29986 TTTTGAATTT
*
29996 TTTTGAATTATTTATATAA
1 TTTTGAA-TATTTTTATAA
* **
30015 TTTTG-A-ACTTTTATTT
1 TTTTGAATATTTTTATAA
30031 TTTTGAATATTTTTATAA
1 TTTTGAATATTTTTATAA
30049 TTTT
1 TTTT
30053 ACAATTATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 11 0.38
17 1 0.03
18 12 0.41
19 5 0.17
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTGAATATTTTTATAA
Found at i:31625 original size:30 final size:29
Alignment explanation
Indices: 31585--31876 Score: 293
Period size: 30 Copynumber: 9.9 Consensus size: 29
31575 GGATACCCAT
31585 GGGT-AAAATGGAATTTTTGGAAGTTTCG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
* *
31613 GGGTCAAAAATGGAAGTTTCGGAAG-TTCGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTC-G
* *
31643 GGGTAAAGATGGAATTTTTGGAAATTTCG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
* * *
31672 AGGTCAAAAATGGAATTTTTGAAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCG
* * * *
31702 GGGTAAAAATGAAACTTTTAGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
*
31731 GGGTTAAAAATGGGATTTTTGGAAG-TTCG
1 GGG-TAAAAATGGAATTTTTGGAAGTTTCG
* * *
31760 AGGGTAAAAACGTAATTTTTGGAAGTTTTG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCG
* * *
31790 GGGTCAAAAATGGGATTTTTAGAAGTTTAG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCG
* *
31820 GGGTAAAAATAGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
** *
31849 GGGTTATCAATGGAATTTTTAGAAGTTT
1 GGG-TAAAAATGGAATTTTTGGAAGTTT
31877 AGGGACCTCC
Statistics
Matches: 215, Mismatches: 39, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.02
29 95 0.44
30 116 0.54
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCG
Found at i:31659 original size:59 final size:59
Alignment explanation
Indices: 31585--31875 Score: 341
Period size: 59 Copynumber: 4.9 Consensus size: 59
31575 GGATACCCAT
* * *
31585 GGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAAGTTTCGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * * * * *
31643 GGGTAAAGATGGAATTTTTGGAAATTTCGAGGTCAAAAATGGAATTTTTGAAAGTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * * * * *
31702 GGGTAAAAATGAAACTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * * * **
31761 GGGTAAAAACGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTAGAAGTTTAG
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * ** *
31820 GGGTAAAAATAGAATTTTTGGAAGTTTTGGGGTTATCAATGGAATTTTTAGAAGTT
1 GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
31876 TAGGGACCTC
Statistics
Matches: 197, Mismatches: 35, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
58 4 0.02
59 193 0.98
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTCGG
Found at i:33879 original size:99 final size:99
Alignment explanation
Indices: 33748--33941 Score: 259
Period size: 99 Copynumber: 2.0 Consensus size: 99
33738 CCTGTCTCGT
* * * *
33748 TTCTAAGGTGTTAGGTTCACCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGAT
1 TTCTAAGGTATTAGGTTCACCATTACGACCTCAACCTTTCCCTTCATATCTCCATGGTATCGGAT
* *
33813 TCGCCGTTGC-ATCCTCAATCC-TTCTCATCGCATC
66 TCACAGTTGCGA-CCTCAA-CCTTTCTCATCGCATC
* * *
33847 TTCTAAGGTATT-GTGTTCACCATTACGACCTCAACCTTTCCCTTCATATCTCCGTGGTATTGGG
1 TTCTAAGGTATTAG-GTTCACCATTACGACCTCAACCTTTCCCTTCATATCTCCATGGTATCGGA
33911 TTCACAGTTGCGACCTCAACCTTTCTCATCG
65 TTCACAGTTGCGACCTCAACCTTTCTCATCG
33942 ATGTCGGGTT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
98 3 0.04
99 79 0.95
100 1 0.01
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (99 bp):
TTCTAAGGTATTAGGTTCACCATTACGACCTCAACCTTTCCCTTCATATCTCCATGGTATCGGAT
TCACAGTTGCGACCTCAACCTTTCTCATCGCATC
Found at i:33914 original size:49 final size:48
Alignment explanation
Indices: 33761--34284 Score: 185
Period size: 49 Copynumber: 10.8 Consensus size: 48
33751 TAAGGTGTTA
* *
33761 GGTTCACCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCG
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC-TGGTATTG
* * * * * **
33810 GATTCGCCGTTGC-ATCCTCAATCC-TTCTCATCGCATCTTCTAAGGTATTG
1 GGTTCACCATTGCGA-CCTCAA-CCTTTCCCTTCATATCTTCT--GGTATTG
* * *
33860 TGTTCACCATTACGACCTCAACCTTTCCCTTCATATCTCCGTGGTATTG
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC-TGGTATTG
* * *
33909 GGTTCA-CAGTTGCGACCTCAACCTTT--C-TC--A---TC-GATGTCG
1 GGTTCACCA-TTGCGACCTCAACCTTTCCCTTCATATCTTCTGGTATTG
* * * * *
33948 GGTTCACCGTTGCGGCCTCAACCTTTCCTTTCGA-ATCTTCATGGTACTA
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTC-ATATCTTC-TGGTATTG
* * * * * * **
33997 AGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC-T-GGTATTG
* * * * *
34047 GGTTCGCCATTGCAACCTCAACCTTTTCCTTCGTATCTTCATGGTATAG
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC-TGGTATTG
**** * ** * * **
34096 GGTTCGTTGTTGTGGTCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTCT--GGTATTG
* * * * * * * * ***
34146 GATTCACCGTCGCGGCCTCGATCC-TTCCCTTTAAATCTTCACGGTACCA
1 GGTTCACCATTGCGACCTC-AACCTTTCCCTTCATATCTTC-TGGTATTG
* * ** * * *
34195 AGTTCACCGTCACGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTATTT
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC-T-GGTATTG
* * * * *
34245 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC
1 GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTC
34285 AGGGTATTAG
Statistics
Matches: 355, Mismatches: 93, Indels: 53
0.71 0.19 0.11
Matches are distributed among these distances:
39 26 0.07
40 1 0.00
41 1 0.00
42 2 0.01
44 2 0.01
46 2 0.01
47 3 0.01
48 8 0.02
49 165 0.46
50 140 0.39
51 5 0.01
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.34
Consensus pattern (48 bp):
GGTTCACCATTGCGACCTCAACCTTTCCCTTCATATCTTCTGGTATTG
Found at i:34066 original size:50 final size:50
Alignment explanation
Indices: 33946--34284 Score: 267
Period size: 50 Copynumber: 6.8 Consensus size: 50
33936 TCATCGATGT
* ** *
33946 CGGGTTCACCGTTGCGGCCTCAACCTTTCCTTTCGA-ATCTTCAT-GGTAC
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC-ACATCTTCTTAGGTAC
***
33995 TAAGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
* ** * * ** * *
34045 CGGGTTCGCCATTGCAACCTCAACCTTTTCCTTCGTATCTTCAT-GGTAT
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
* ** * * *
34094 AGGGTTCGTTGTTGTGGTCTCAACCTTTCCCATCACATCTTCTAAGGTAC
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
* * * * * * *
34144 CGGATTCACCGTCGCGGCCTCGATCC-TTCCCTTTAAATCTTC--ACGGTAC
1 CGGGTTCGCCGTTGCGGCCTC-AACCTTTCCCATCACATCTTCTTA-GGTAC
** * ** * *
34193 CAAGTTCACCGTCACGGCCTCAACCTTTCCCTTCACATCTTCTTAGGTAT
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
**
34243 TTGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC
1 CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC
34285 AGGGTATTAG
Statistics
Matches: 221, Mismatches: 61, Indels: 15
0.74 0.21 0.05
Matches are distributed among these distances:
48 5 0.02
49 105 0.48
50 107 0.48
51 4 0.02
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (50 bp):
CGGGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTAC
Found at i:34118 original size:187 final size:192
Alignment explanation
Indices: 33761--34291 Score: 502
Period size: 187 Copynumber: 2.8 Consensus size: 192
33751 TAAGGTGTTA
* * ** **
33761 GGTTCACCATTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTA-TCGGATTCGCCGTTGCAT
1 GGTTCACCGTTGCGGCCTCAACCTTTCCTTTCA-ATCTTCATGGTACTAAG-TTCGCCGTTGCGG
* * * * * *
33825 CCTCAATCC-TTCTCATCGCATCTTCTAAGGTATTGTGTTCACCATTACGACCTCAACCTTTCCC
64 CCTCAA-CCTTTCCCATCACATCTTCTTAGGTATTGGGTTCGCCATTGCGACCTCAACCTTTCCC
* * * *
33889 TTCATATCTCCGTGGTATTGGGTTCACAGTTGCGACCTCAACCTTT-C-T-CA-TC-GATGT-CG
128 TTCATATCTCCATGGTATAGGGTTCACAGTTGCGACCTCAACCTTTCCATACATTCTAAGGTACG
33948 GGTTCACCGTTGCGGCCTCAACCTTTCCTTTCGAATCTTCATGGTACTAAGTTCGCCGTTGCGGC
1 GGTTCACCGTTGCGGCCTCAACCTTTCCTTTC-AATCTTCATGGTACTAAGTTCGCCGTTGCGGC
** * *
34013 CTCAACCTTTCCCATCACATCTTCTTAGGTACCGGGTTCGCCATTGCAACCTCAACCTTTTCCTT
65 CTCAACCTTTCCCATCACATCTTCTTAGGTATTGGGTTCGCCATTGCGACCTCAACCTTTCCCTT
* * *** * **
34078 CGTATCTTCATGGTATAGGGTTCGTTGTTGTGGTCTCAACCTTTCCCATCACATCTTCTAAGGTA
130 CATATCTCCATGGTATAGGGTTCACAGTTGCGACCTCAACCTTT-CCAT-ACA--TTCTAAGGTA
34143 CCG
191 -CG
* * * * * * * * **
34146 GATTCACCGTCGCGGCCTCGATCCTTCCCTTTAAATCTTCACGGTACCAAGTTCACCGTCACGGC
1 GGTTCACCGTTGCGGCCTC-AACCTTTCCTTTCAATCTTCATGGTACTAAGTTCGCCGTTGCGGC
* * * * *
34211 CTCAACCTTTCCCTTCACATCTTCTTAGGTATTTGGTTCGCCGTTGCGGCCTCAACCTTTCCCAT
65 CTCAACCTTTCCCATCACATCTTCTTAGGTATTGGGTTCGCCATTGCGACCTCAACCTTTCCCTT
* * *
34276 CACATCTTCAGGGTAT
130 CATATCTCCATGGTAT
34292 TAGATTTGTC
Statistics
Matches: 279, Mismatches: 50, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
186 2 0.01
187 140 0.50
188 3 0.01
189 1 0.00
190 1 0.00
192 2 0.01
195 2 0.01
196 3 0.01
198 115 0.41
199 10 0.04
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (192 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCTTTCAATCTTCATGGTACTAAGTTCGCCGTTGCGGCC
TCAACCTTTCCCATCACATCTTCTTAGGTATTGGGTTCGCCATTGCGACCTCAACCTTTCCCTTC
ATATCTCCATGGTATAGGGTTCACAGTTGCGACCTCAACCTTTCCATACATTCTAAGGTACG
Found at i:34273 original size:99 final size:98
Alignment explanation
Indices: 33948--34273 Score: 352
Period size: 99 Copynumber: 3.3 Consensus size: 98
33938 ATCGATGTCG
33948 GGTTCACCGTTGCGGCCTCAACCTTT-CCTTTCGAATCTTCATGGTACTAAGTTCGCCGTTGCGG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCTTT-GAATCTTCATGGTACTAAGTTCGCCGTTGCGG
34012 CCTCAACCTTTCCCATCACATCTTCTTAGGTACC
65 CCTCAACCTTTCCCATCACATCTTCTTAGGTACC
* * ** * * * * ** *
34046 GGGTTCGCCATTGCAACCTCAACCTTTTCCTTCGTATCTTCATGGTA-TAGGGTTCGTTGTTGTG
1 -GGTTCACCGTTGCGGCCTCAACCTTTCCCTTTGAATCTTCATGGTACTA-AGTTCGCCGTTGCG
* *
34110 GTCTCAACCTTTCCCATCACATCTTCTAAGGTACC
64 GCCTCAACCTTTCCCATCACATCTTCTTAGGTACC
* * * * * * **
34145 GGATTCACCGTCGCGGCCTCGATCC-TTCCCTTTAAATCTTCACGGTACCAAGTTCACCGTCACG
1 GG-TTCACCGTTGCGGCCTC-AACCTTTCCCTTTGAATCTTCATGGTACTAAGTTCGCCGTTGCG
* **
34209 GCCTCAACCTTTCCCTTCACATCTTCTTAGGTATTT
64 GCCTCAACCTTTCCCATCACATCTTCTTAGGTA-CC
*
34245 GGTTCGCCGTTGCGGCCTCAACCTTTCCC
1 GGTTCACCGTTGCGGCCTCAACCTTTCCC
34274 ATCACATCTT
Statistics
Matches: 181, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
98 7 0.04
99 164 0.91
100 10 0.06
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.33
Consensus pattern (98 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCCTTTGAATCTTCATGGTACTAAGTTCGCCGTTGCGGC
CTCAACCTTTCCCATCACATCTTCTTAGGTACC
Found at i:34309 original size:99 final size:97
Alignment explanation
Indices: 33948--34314 Score: 344
Period size: 99 Copynumber: 3.7 Consensus size: 97
33938 ATCGATGTCG
* *
33948 GGTTCACCGTTGCGGCCTCAACCTTTCCTTTCGAATCTTCATGGTACTAAGTTCGCCGTTGCGGC
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCTTC-AATCTTCATGGTACTAAGTTCGCCGTTACGGC
34013 CTCAACCTTTCCCATCACATCTTCTTAGGTACC
65 CTCAACCTTTCCCATCACATCTTCTTAGGTACC
* * ** * * * ** **
34046 GGGTTCGCCATTGCAACCTCAACCTTTTCCTTCGTATCTTCATGGTA-TAGGGTTCGTTGTTGTG
1 -GGTTCACCGTTGCGGCCTCAACCTTTCCCTTC-AATCTTCATGGTACTA-AGTTCGCCGTTACG
* *
34110 GTCTCAACCTTTCCCATCACATCTTCTAAGGTACC
63 GCCTCAACCTTTCCCATCACATCTTCTTAGGTACC
* * * * * * *
34145 GGATTCACCGTCGCGGCCTCGATCC-TTCCCTTTAAATCTTCACGGTACCAAGTTCACCGTCACG
1 GG-TTCACCGTTGCGGCCTC-AACCTTTCCC-TTCAATCTTCATGGTACTAAGTTCGCCGTTACG
* **
34209 GCCTCAACCTTTCCCTTCACATCTTCTTAGGTATTT
63 GCCTCAACCTTTCCCATCACATCTTCTTAGGTA-CC
* * * * * *
34245 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCAGGGTA-TTAGATTTGTCGTTACGG
1 GGTTCACCGTTGCGGCCTCAACCTTTCCCTTCA-ATCTTCATGGTACTAAG-TTCGCCGTTACGG
34309 CCTCAA
64 CCTCAA
34315 TCTTCTCTGT
Statistics
Matches: 211, Mismatches: 48, Indels: 18
0.76 0.17 0.06
Matches are distributed among these distances:
98 11 0.05
99 192 0.91
100 8 0.04
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (97 bp):
GGTTCACCGTTGCGGCCTCAACCTTTCCCTTCAATCTTCATGGTACTAAGTTCGCCGTTACGGCC
TCAACCTTTCCCATCACATCTTCTTAGGTACC
Found at i:35161 original size:19 final size:19
Alignment explanation
Indices: 35133--35176 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35123 TTAGATTTTA
* *
35133 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
35152 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
35171 AAATTA
1 AAATTA
35177 CACTCATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:36091 original size:16 final size:16
Alignment explanation
Indices: 36072--36173 Score: 64
Period size: 16 Copynumber: 5.8 Consensus size: 16
36062 ATACAAATTC
36072 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
36088 AGGCTTTGTGCCGGT-GTTAT
1 AGGCTTTGTGCC--TAG---T
36108 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
* *
36125 AGGTTTTGTG-CTGGTGTTAT
1 AGGCTTTGTGCCT--AG---T
36145 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
36162 AGGCTTTGTGCC
1 AGGCTTTGTGCC
36174 GATGTTATCA
Statistics
Matches: 68, Mismatches: 4, Indels: 28
0.68 0.04 0.28
Matches are distributed among these distances:
15 2 0.03
16 33 0.49
17 4 0.06
18 1 0.01
19 1 0.01
20 4 0.06
21 21 0.31
22 2 0.03
ACGTcount: A:0.11, C:0.18, G:0.32, T:0.39
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:36114 original size:21 final size:20
Alignment explanation
Indices: 36088--36190 Score: 73
Period size: 21 Copynumber: 5.4 Consensus size: 20
36078 TGTGCCTAGT
36088 AGGCTTTGTGCCGGTGTTATC
1 AGGCTTTGTGCC-GTGTTATC
36109 AGGCTTTGTGCC----TAGT-
1 AGGCTTTGTGCCGTGTTA-TC
* *
36125 AGGTTTTGTGCTGGTGTTATC
1 AGGCTTTGTGC-CGTGTTATC
36146 AGGCTTTGTGCC----TAGT-
1 AGGCTTTGTGCCGTGTTA-TC
36162 AGGCTTTGTGCCGATGTTATC
1 AGGCTTTGTGCCG-TGTTATC
36183 AGGCTTTG
1 AGGCTTTG
36191 AGCCAGTGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
16 26 0.41
17 2 0.03
20 2 0.03
21 34 0.53
ACGTcount: A:0.12, C:0.17, G:0.32, T:0.40
Consensus pattern (20 bp):
AGGCTTTGTGCCGTGTTATC
Found at i:36120 original size:37 final size:37
Alignment explanation
Indices: 36070--36190 Score: 215
Period size: 37 Copynumber: 3.3 Consensus size: 37
36060 TTATACAAAT
36070 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTA
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTA
* *
36107 TCAGGCTTTGTGCCTAGTAGGTTTTGTGCTGGTGTTA
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTA
*
36144 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGATGTTA
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTA
36181 TCAGGCTTTG
1 TCAGGCTTTG
36191 AGCCAGTGAT
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 79 1.00
ACGTcount: A:0.12, C:0.17, G:0.31, T:0.40
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTTA
Found at i:44704 original size:30 final size:30
Alignment explanation
Indices: 44638--45003 Score: 241
Period size: 30 Copynumber: 12.3 Consensus size: 30
44628 GGGAATTCAA
* *
44638 GGTTAAAATGTAATTTT-GGAAAAGTTT-AG
1 GGTTAAAATATAATTTTAGG-GAAGTTTAAG
*
44667 GGTTAAAATATGATTTTAGGGAAGTTT-AG
1 GGTTAAAATATAATTTTAGGGAAGTTTAAG
* * *
44696 ATGTTAAAATGTGATTTT-GGGAAGTTTAAG
1 -GGTTAAAATATAATTTTAGGGAAGTTTAAG
* *
44726 GGTTAAAATATAATTTTAGAGAAATTTAAG
1 GGTTAAAATATAATTTTAGGGAAGTTTAAG
* * *
44756 GGTTAAAATGTAATTTTAAGAAAGTTTAAG
1 GGTTAAAATATAATTTTAGGGAAGTTTAAG
* **
44786 GGTTAAAATATAATTTTAGAGAAGTTTGGGG
1 GGTTAAAATATAATTTTAGGGAAGTTT-AAG
* * * * *
44817 GGTCAAACTGTGATTTT-GGAAATGTTT-AG
1 GGTTAAAATATAATTTTAGGGAA-GTTTAAG
* **
44846 AGATTAAAATATAATTTT-GGGAAAGTTTGGG
1 -GGTTAAAATATAATTTTAGGG-AAGTTTAAG
*
44877 GGTTAAAAT-TCAATTTT-TGGAAGTTTAAG
1 GGTTAAAATAT-AATTTTAGGGAAGTTTAAG
* ** *** *
44906 GGTCAAAATGCAATTTTAAAAAAGTTTAGG
1 GGTTAAAATATAATTTTAGGGAAGTTTAAG
* * **
44936 GGTTAAAATGTGATTTT-GTAAAAGTTTAAG
1 GGTTAAAATATAATTTTAG-GGAAGTTTAAG
* * * *
44966 GGTTAAAATGTGATTTTAGAGAAGTTT-GG
1 GGTTAAAATATAATTTTAGGGAAGTTTAAG
44995 GGTTAAAAT
1 GGTTAAAAT
45004 GTTGTTTTTA
Statistics
Matches: 271, Mismatches: 52, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
29 79 0.29
30 170 0.63
31 22 0.08
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.37
Consensus pattern (30 bp):
GGTTAAAATATAATTTTAGGGAAGTTTAAG
Found at i:44713 original size:59 final size:60
Alignment explanation
Indices: 44638--45022 Score: 385
Period size: 59 Copynumber: 6.5 Consensus size: 60
44628 GGGAATTCAA
* * * *
44638 GGTTAAAATGTAATTTTGGAAAAGTTT-AGGGTTAAAATATGATTTTAGGGAAGTTTAGA
1 GGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTAGG
* * * *
44697 TGTTAAAATGTGATTTTGG-GAAGTTTAAGGGTTAAAATATAATTTTAGAGAAATTTAAG
1 GGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTAGG
* * *
44756 GGTTAAAATGTAATTTT-AAGAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGG
1 GGTTAAAATGTGATTTTGGA-AAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTT-AGG
* * * * * *
44817 GGTCAAACTGTGATTTTGGAAATGTTT-AGAGATTAAAATATAATTTT-GGGAAAGTTTGGG
1 GGTTAAAATGTGATTTTGGAAAAGTTTAAG-GGTTAAAATATAATTTTAGAG-AAGTTTAGG
* * ** * *
44877 GGTTAAAAT-TCAATTTTTGG--AAGTTTAAGGGTCAAAATGCAATTTTAAAAAAGTTTAGG
1 GGTTAAAATGT-GA-TTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTAGG
* * *
44936 GGTTAAAATGTGATTTTGTAAAAGTTTAAGGGTTAAAATGTGATTTTAGAGAAGTTT-GG
1 GGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTAGG
* *
44995 GGTTAAAATGTTGTTTTTAG-AAAGTTTA
1 GGTTAAAATG-TGATTTTGGAAAAGTTTA
45023 GAGACTTATT
Statistics
Matches: 267, Mismatches: 44, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
58 11 0.04
59 116 0.43
60 90 0.34
61 49 0.18
62 1 0.00
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (60 bp):
GGTTAAAATGTGATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTAGG
Found at i:44903 original size:180 final size:179
Alignment explanation
Indices: 44650--44996 Score: 468
Period size: 180 Copynumber: 1.9 Consensus size: 179
44640 TTAAAATGTA
* * * *
44650 ATTTTGGAAAAGTTTAGGGTTAAAATATGATTTTAGGGAAGTTTAGATGTTAAAATGTGATTTTG
1 ATTTTGGAAAAGTTTAGGATTAAAATATAATTTTAGGGAAGTTTAGAGGTTAAAATGTAATTTTG
* * *
44715 GGAAGTTTAAGGGTTAAAATATAATTTTAGAGAAA-TTTAAGGGTTAAAATGTAATTTT-AAGAA
66 GGAAGTTTAAGGGTCAAAATACAATTTTA-AAAAAGTTTAAGGGTTAAAATGTAATTTTGAA-AA
44778 AGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGGGGTCAAACTGTG
129 AGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGGGGTCAAACTGTG
* * *
44829 ATTTTGGAAATGTTTAGAGATTAAAATATAATTTT-GGGAAAGTTTGGGGGTTAAAAT-TCAATT
1 ATTTTGGAAAAGTTTAG-GATTAAAATATAATTTTAGGG-AAGTTTAGAGGTTAAAATGT-AATT
* * * * *
44892 TTTGGAAGTTTAAGGGTCAAAATGCAATTTTAAAAAAGTTTAGGGGTTAAAATGTGATTTTGTAA
63 TTGGGAAGTTTAAGGGTCAAAATACAATTTTAAAAAAGTTTAAGGGTTAAAATGTAATTTTGAAA
* *
44957 AAGTTTAAGGGTTAAAATGTGATTTTAGAGAAGTTTGGGG
128 AAGTTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGG
44997 TTAAAATGTT
Statistics
Matches: 146, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
179 24 0.16
180 121 0.83
181 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (179 bp):
ATTTTGGAAAAGTTTAGGATTAAAATATAATTTTAGGGAAGTTTAGAGGTTAAAATGTAATTTTG
GGAAGTTTAAGGGTCAAAATACAATTTTAAAAAAGTTTAAGGGTTAAAATGTAATTTTGAAAAAG
TTTAAGGGTTAAAATATAATTTTAGAGAAGTTTGGGGGGTCAAACTGTG
Found at i:48892 original size:5 final size:5
Alignment explanation
Indices: 48882--48913 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
48872 TGGGTCATAT
48882 GAAAG GAAAG GAAAG GAAAG GAAAG GCAAAG G
1 GAAAG GAAAG GAAAG GAAAG GAAAG G-AAAG G
48914 TGGCTGCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.56, C:0.03, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAAG
Found at i:55789 original size:14 final size:14
Alignment explanation
Indices: 55770--55824 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
55760 AGCCAGGTAA
55770 TCCTTTCTTTCTCT
1 TCCTTTCTTTCTCT
*
55784 TCCTTTCTTT-TAT
1 TCCTTTCTTTCTCT
*
55797 TCTTTTCCTCTTCTCT
1 TCCTTT-CT-TTCTCT
55813 TCCTTCTCTTTC
1 TCCTT-TCTTTC
55825 CAGATTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 7 0.21
14 12 0.36
15 5 0.15
16 8 0.24
17 1 0.03
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (14 bp):
TCCTTTCTTTCTCT
Found at i:59438 original size:21 final size:23
Alignment explanation
Indices: 59412--59453 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
59402 CCAAAATTGA
*
59412 ATGCAAG-CCAA-TTTTTTAACC
1 ATGCAAGTCCAAGATTTTTAACC
59433 ATGCAAGTCCAAGATTTTTAA
1 ATGCAAGTCCAAGATTTTTAA
59454 TCTCTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (23 bp):
ATGCAAGTCCAAGATTTTTAACC
Found at i:60515 original size:7 final size:7
Alignment explanation
Indices: 60503--60528 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
60493 AATAGCAGAA
60503 AAAGAGC
1 AAAGAGC
60510 AAAGAGC
1 AAAGAGC
60517 AAAGAGC
1 AAAGAGC
60524 AAAGA
1 AAAGA
60529 AAGAGGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAGC
Found at i:60910 original size:14 final size:15
Alignment explanation
Indices: 60891--60938 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
60881 GAAGGTGTAA
60891 TTAATTTAAATTT-T
1 TTAATTTAAATTTAT
60905 TTAATTAATTAAATTTAT
1 TTAA-T--TTAAATTTAT
*
60923 TTAATTAAAATTTAT
1 TTAATTTAAATTTAT
60938 T
1 T
60939 CTTGTCCTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.14
15 11 0.38
17 9 0.31
18 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTTAAATTTAT
Found at i:60911 original size:18 final size:18
Alignment explanation
Indices: 60888--60930 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
60878 GTTGAAGGTG
60888 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
60906 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
60924 TAATTAA
1 TAATTAA
60931 AATTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:64377 original size:29 final size:29
Alignment explanation
Indices: 64334--64513 Score: 102
Period size: 30 Copynumber: 6.2 Consensus size: 29
64324 TGAATCACTA
* *
64334 CAAAATGGTAATTTTTGGATGTTTGGGGG
1 CAAAATGGTATTTTTTGGATGTTTGAGGG
* **
64363 CAAAATGGTTTTTTTTTTTATGTTTGAGGG
1 CAAAATGG-TATTTTTTGGATGTTTGAGGG
* * *
64393 TAAAATGGTATTTTTTGGAAAAG-TTAAGGG
1 CAAAATGGTATTTTTTGG--ATGTTTGAGGG
* * *
64423 TCAAAAT-GTAATTTTTGGATATTTTGGAGTG
1 -CAAAATGGTATTTTTTGGAT-GTTT-GAGGG
* *
64454 --AAATAGTA-ATTTTGGATGTTTCG-GGG
1 CAAAATGGTATTTTTTGGATGTTT-GAGGG
* * * *
64480 AAAAATGGTAATTTTTGGATATTCGAGGG
1 CAAAATGGTATTTTTTGGATGTTTGAGGG
64509 CAAAA
1 CAAAA
64514 ATATAATTTT
Statistics
Matches: 113, Mismatches: 26, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
26 2 0.02
27 4 0.04
28 21 0.19
29 35 0.31
30 41 0.36
31 10 0.09
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.40
Consensus pattern (29 bp):
CAAAATGGTATTTTTTGGATGTTTGAGGG
Found at i:64466 original size:28 final size:28
Alignment explanation
Indices: 64425--64525 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
64415 GTTAAGGGTC
* *
64425 AAAATGTAATTTTTGGATATTTTGGAGT
1 AAAATGTAATTTTTGGATATTTCGGAGA
* * *
64453 GAAATAGTAA-TTTTGGATGTTTCGGGGA
1 AAAAT-GTAATTTTTGGATATTTCGGAGA
*
64481 AAAATGGTAATTTTTGGATA-TTCGAGGGCA
1 AAAAT-GTAATTTTTGGATATTTCG-GAG-A
*
64511 AAAATATAATTTTTG
1 AAAATGTAATTTTTG
64526 AGAAATTCGA
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 30 0.50
29 24 0.40
30 6 0.10
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.40
Consensus pattern (28 bp):
AAAATGTAATTTTTGGATATTTCGGAGA
Found at i:64534 original size:30 final size:29
Alignment explanation
Indices: 64388--64613 Score: 135
Period size: 29 Copynumber: 7.7 Consensus size: 29
64378 TTTTATGTTT
*
64388 GAGGGT-AAAATGGTATTTTTTGGAAAAGTT-
1 GAGGGTAAAAAT-GTAATTTTTGG-AAA-TTC
* * * *
64418 AAGGGTCAAAATGTAATTTTTGGATATTTT
1 GAGGGTAAAAATGTAATTTTTGGA-AATTC
* * **
64448 G-GAGT-GAAATAGTAA-TTTTGGATGTTTC
1 GAGGGTAAAAAT-GTAATTTTTGGA-AATTC
*
64476 G-GGG-AAAAATGGTAATTTTTGGATATTC
1 GAGGGTAAAAAT-GTAATTTTTGGAAATTC
* *
64504 GAGGGCAAAAATATAATTTTTGAGAAATTC
1 GAGGGTAAAAATGTAATTTTTG-GAAATTC
* * *
64534 GA-GGTAAATATGTGATTTTTGGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAATTC
* * * *
64562 GGGGGTAAAAATGTAATCTTTGAGAAGTTT
1 GAGGGTAAAAATGTAATTTTTG-GAAATTC
64592 GAGGGGTAAAAATGTAATTTTT
1 GA-GGGTAAAAATGTAATTTTT
64614 AGACAAAATA
Statistics
Matches: 157, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
28 37 0.24
29 60 0.38
30 37 0.24
31 23 0.15
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
GAGGGTAAAAATGTAATTTTTGGAAATTC
Found at i:64601 original size:31 final size:31
Alignment explanation
Indices: 64476--64613 Score: 139
Period size: 29 Copynumber: 4.6 Consensus size: 31
64466 TGGATGTTTC
64476 GGGG-AAAAATGGTAATTTTTG-GATA-TTCGA
1 GGGGTAAAAAT-GTAATTTTTGAGA-AGTTCGA
* * *
64506 -GGGCAAAAATATAATTTTTGAGAAATTCGA
1 GGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
64536 --GGTAAATATGTGATTTTTG-GAAGTTCG-
1 GGGGTAAAAATGTAATTTTTGAGAAGTTCGA
* *
64563 GGGGTAAAAATGTAATCTTTGAGAAGTTTGA
1 GGGGTAAAAATGTAATTTTTGAGAAGTTCGA
64594 GGGGTAAAAATGTAATTTTT
1 GGGGTAAAAATGTAATTTTT
64614 AGACAAAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
28 7 0.08
29 44 0.49
30 20 0.22
31 19 0.21
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (31 bp):
GGGGTAAAAATGTAATTTTTGAGAAGTTCGA
Found at i:65698 original size:11 final size:11
Alignment explanation
Indices: 65682--65718 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
65672 TCCCTTTTTA
65682 TTATTAAATAT
1 TTATTAAATAT
*
65693 TTATTATATA-
1 TTATTAAATAT
65703 TTATT-AATAT
1 TTATTAAATAT
65713 TTATTA
1 TTATTA
65719 TAAAACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.14
10 10 0.45
11 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATTAAATAT
Found at i:65713 original size:20 final size:21
Alignment explanation
Indices: 65680--65720 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
65670 TCTCCCTTTT
65680 TATTATTAAATATTTATTATA
1 TATTATTAAATATTTATTATA
65701 TATTATT-AATATTTATTATA
1 TATTATTAAATATTTATTATA
65721 AAACATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATTAAATATTTATTATA
Found at i:66323 original size:17 final size:17
Alignment explanation
Indices: 66301--66347 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
66291 ACTTTCAAAT
*
66301 TTTAAATTTGAAATAAA
1 TTTAAATTTAAAATAAA
66318 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
66335 TTTAAAATTAAAA
1 TTTAAATTTAAAA
66348 ATTGGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:66841 original size:39 final size:38
Alignment explanation
Indices: 66762--67609 Score: 516
Period size: 39 Copynumber: 21.8 Consensus size: 38
66752 GACTCCAATA
* * * ** * *
66762 TGCCCCATGATCGGGGTAAGAGATTGGCTGATGATGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGTG-TAATC
* * * * *
66801 TGACCTAGGCTCGGGGTAAAAGATCAAATGGTGGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * * * ** * *
66840 TGCCCCAAGCTCGAGGTAAAAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * * * **
66879 TGCCCCAAGTTCGGGGTAAAAGAT-TAGATAGCCGTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGA-AT-GGTGTAATC
* * * * * ** * *
66918 CGTCCTAGGCTCGGGGTAAAAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * *
66957 TGCCTCAGGCTCGAGGTAAGAGATCGAATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
* * * *
66996 TGCCCCAAGCTCGGGGTAAGAAATCGAATGATGGTTATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
** * **
67035 TGCCTTAGGCTCGAGGTAAGAGATCGAATGGCTACAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
** * * * * *
67074 TGCCCCAAACTCGGGGTAAGAGATTGATTGATGGTGATT
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * * *
67113 TGCCCCAGGTTCGGGGTAAAAGATCGAATGGCTGCAATT
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
* * * * * * *
67152 TACCCCAAGCTCGAGGTAAAAGATTGACTGGTGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * *
67191 TACCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
* * ** * *
67230 TGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * * * *
67269 TACCCCAGGCTCGGGGTAAGATATCGAACGACTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATG-GTGTAATC
* * * *
67308 TGCCTCAGGCTCGGGGTAAGAGATTGACTGGTGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGGT-GTAATC
* * * * * *
67347 TGCCCTAAGCTCAGGGTAAGAGATCGAATGACTGCAATT
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATG-GTGTAATC
*
67386 TGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTG-AA-C
1 TGCCCCAGGCTCGGGGTAAGAGA-T--CGAATGGTGTAATC
* * * *
67425 TACCCCAAGCTTGGGGTAAGAAATCGAATGGCTGTAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
* * * *
67464 TGCCCCAGGCTCGAGGTAAGAGAT-TAACTGATGGTGATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAA-TGGT-GTAATC
* *
67503 TGCCCCAGGTTCGGGGTAAGAGATCGAATGGTTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
* *
67542 TGCCCCAGGTTCGGGGTAAGAGATCGAATGGCTGCAATC
1 TGCCCCAGGCTCGGGGTAAGAGATCGAATGG-TGTAATC
*
67581 TGCCCCAGGCTCGGGGTAAAAGATCGAAT
1 TGCCCCAGGCTCGGGGTAAGAGATCGAAT
67610 CTTTAATTCG
Statistics
Matches: 609, Mismatches: 174, Indels: 52
0.73 0.21 0.06
Matches are distributed among these distances:
36 6 0.01
37 2 0.00
38 12 0.02
39 568 0.93
40 14 0.02
41 2 0.00
42 5 0.01
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (38 bp):
TGCCCCAGGCTCGGGGTAAGAGATCGAATGGTGTAATC
Found at i:66893 original size:78 final size:78
Alignment explanation
Indices: 66748--67609 Score: 924
Period size: 78 Copynumber: 11.1 Consensus size: 78
66738 TTATTACTTT
* * * * * * * * *
66748 GAATGACTCCAATATGCCCCATGATCGGGGTAAGAGATTGGCTGATGATGATCTGACCTAGGCTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
66813 GGGGTAAAAGATC
66 GGGGTAAGAGATC
* * * * * * *
66826 AAATGG-TGGCAATCTGCCCCAAGCTCGAGGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGTT
1 GAATGGCT-GCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCT
*
66890 CGGGGTAAAAGAT-
65 CGGGGTAAGAGATC
* * * * * * * * * *
66903 TAGATAGCCGTAATCCGTCCTAGGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCTCAGGCT
1 GA-ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCT
*
66968 CGAGGTAAGAGATC
65 CGGGGTAAGAGATC
* * * * * **
66982 GAATGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAAATCGAATGATGGTTATCTGCCTTAGGCTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
67047 GAGGTAAGAGATC
66 GGGGTAAGAGATC
* ** * * *
67060 GAATGGCTACAATCTGCCCCAAACTCGGGGTAAGAGATTGATTGATGGTGATTTGCCCCAGGTTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
67125 GGGGTAAAAGATC
66 GGGGTAAGAGATC
* * * * * * * *
67138 GAATGGCTGCAATTTACCCCAAGCTCGAGGTAAAAGATTGACTGGTGGTGATCTACCTCAGGCTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
67203 GGGGTAAGAGATC
66 GGGGTAAGAGATC
* * *
67216 GAATGGCTGCAATCTGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTACCCCAGGCTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
67281 GGGGTAAGATATC
66 GGGGTAAGAGATC
* * * * * *
67294 GAACGACTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGACTGGTGGTGATCTGCCCTAAGCTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
67359 AGGGTAAGAGATC
66 GGGGTAAGAGATC
* * * * * * * *
67372 GAATGACTGCAATTTGCCCCAGGCTCGGGGTAAGAGATTGGCTAATGGTGAACTACCCCAAGCTT
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
*
67437 GGGGTAAGAAATC
66 GGGGTAAGAGATC
* * * *
67450 GAATGGCTGTAATCTGCCCCAGGCTCGAGGTAAGAGATTAACTGATGGTGATCTGCCCCAGGTTC
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
67515 GGGGTAAGAGATC
66 GGGGTAAGAGATC
* * *
67528 GAATGGTTGCAATCTGCCCCAGGTTCGGGGTAAGAGATCGA---ATGGCTGCAATCTGCCCCAGG
1 GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGG-TG--ATCTGCCCCAGG
*
67590 CTCGGGGTAAAAGATC
63 CTCGGGGTAAGAGATC
67606 GAAT
1 GAAT
67610 CTTTAATTCG
Statistics
Matches: 658, Mismatches: 119, Indels: 14
0.83 0.15 0.02
Matches are distributed among these distances:
75 4 0.01
76 2 0.00
77 2 0.00
78 649 0.99
79 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (78 bp):
GAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTC
GGGGTAAGAGATC
Found at i:76611 original size:20 final size:20
Alignment explanation
Indices: 76588--76626 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
76578 AAACGAAGCT
76588 TCTTATAAACCTTCTTCAAG
1 TCTTATAAACCTTCTTCAAG
* **
76608 TCTTCTAAGTCTTCTTCAA
1 TCTTATAAACCTTCTTCAA
76627 CCTTTCTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (20 bp):
TCTTATAAACCTTCTTCAAG
Found at i:77759 original size:23 final size:23
Alignment explanation
Indices: 77729--77772 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
77719 ACGGTCAAAG
*
77729 TAATATAT-ATTTATATATAGTGT
1 TAATATATGATATATA-ATAGTGT
77752 TAATATATGATATATAATAGT
1 TAATATATGATATATAATAGT
77773 ATTATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
TAATATATGATATATAATAGTGT
Found at i:77792 original size:13 final size:13
Alignment explanation
Indices: 77752--77795 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
77742 TATATAGTGT
*
77752 TAATATATGATATA
1 TAATATATTATA-A
77766 TAATAGTATTATAA
1 TAATA-TATTATAA
77780 TAATATATTATAA
1 TAATATATTATAA
77793 TAA
1 TAA
77796 CAATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 11 0.39
15 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:78948 original size:17 final size:17
Alignment explanation
Indices: 78926--78959 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
78916 GGTTGATATG
* *
78926 GAAAATGTTATTGAAAT
1 GAAAATGCTATTAAAAT
78943 GAAAATGCTATTAAAAT
1 GAAAATGCTATTAAAAT
78960 AACGAGTGAT
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:0.03, G:0.15, T:0.32
Consensus pattern (17 bp):
GAAAATGCTATTAAAAT
Found at i:82426 original size:29 final size:28
Alignment explanation
Indices: 82386--82692 Score: 176
Period size: 29 Copynumber: 10.5 Consensus size: 28
82376 TTTGAAGTTG
* *
82386 AAAATGTGATTTTTGGAAATTTGGGGGC
1 AAAATGTAATTTTTGGAAATTTGGGGGT
* * *
82414 AAAATGGTAATTTTCGGATATTCGGGGGT
1 AAAAT-GTAATTTTTGGAAATTTGGGGGT
* * *
82443 AAAATGGTATTTTTTTTGGAAAAGTTAGGGGTT
1 AAAAT-GTA--ATTTTTGG-AAA-TTTGGGGGT
*
82476 AAAATGTAATTTTTGGATATTTGGGGGT
1 AAAATGTAATTTTTGGAAATTTGGGGGT
**
82504 AAAATGATAA--TTTGG--ATGTTCAGGGT
1 AAAATG-TAATTTTTGGAAAT-TTGGGGGT
* * **
82530 CAAAATGGTAATTTTTGGATATTCGGGAGCA
1 -AAAAT-GTAATTTTTGGAAATTTGGG-GGT
** **
82561 AAAACATAATTTTTGAGAAATTT-AAGGT
1 AAAATGTAATTTTTG-GAAATTTGGGGGT
* * *
82589 AAATATGTGATTTTTGGAAGTTTAGGGGT
1 AAA-ATGTAATTTTTGGAAATTTGGGGGT
* *
82618 AAAAATGTAATTTTTGAGAAGTTCGAGGGGT
1 -AAAATGTAATTTTTG-GAAATTTG-GGGGT
*
82649 AAAATGTAA-TTTTGGAAAATTTTGAGGGTT
1 AAAATGTAATTTTTGG-AAA-TTTG-GGGGT
82679 AAAATGTAATTTTT
1 AAAATGTAATTTTT
82693 AGACAAAATA
Statistics
Matches: 215, Mismatches: 41, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
25 2 0.01
26 6 0.03
27 13 0.06
28 30 0.14
29 76 0.35
30 53 0.25
31 18 0.08
32 5 0.02
33 12 0.06
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAATTTGGGGGT
Found at i:82462 original size:90 final size:88
Alignment explanation
Indices: 82366--82545 Score: 220
Period size: 90 Copynumber: 2.0 Consensus size: 88
82356 CAAATCGAAC
* * *
82366 TTTTGGAAAA-TTTGAAGTTGAAAATGTGATTTTTGGAAATTTGGGGGCAAAATGGTAATTTTCG
1 TTTTGGAAAAGTTAGAAGTT-AAAATGTAATTTTTGGAAATTTGGGGGCAAAATGATAA-TTT-G
* *
82430 GATATTCGGGGGT-AAAATGGTATTTT
63 GATATTC-AGGGTCAAAATGGTAATTT
** * *
82456 TTTTGGAAAAGTTAGGGGTTAAAATGTAATTTTTGGATATTTGGGGGTAAAATGATAATTTGGAT
1 TTTTGGAAAAGTTAGAAGTTAAAATGTAATTTTTGGAAATTTGGGGGCAAAATGATAATTTGGAT
*
82521 GTTCAGGGTCAAAATGGTAATTT
66 ATTCAGGGTCAAAATGGTAATTT
82544 TT
1 TT
82546 GGATATTCGG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
87 4 0.05
88 21 0.27
89 3 0.04
90 44 0.56
91 6 0.08
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (88 bp):
TTTTGGAAAAGTTAGAAGTTAAAATGTAATTTTTGGAAATTTGGGGGCAAAATGATAATTTGGAT
ATTCAGGGTCAAAATGGTAATTT
Found at i:84527 original size:17 final size:17
Alignment explanation
Indices: 84505--84540 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
84495 ACTTTCAAAT
* *
84505 TTTAAATTTGAAATAAA
1 TTTAAACTTAAAATAAA
84522 TTTAAACTTAAAATAAA
1 TTTAAACTTAAAATAAA
84539 TT
1 TT
84541 AAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:90939 original size:14 final size:15
Alignment explanation
Indices: 90922--90952 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
90912 CAGTTAACTC
90922 AAAAAATTATA-AAA
1 AAAAAATTATATAAA
90936 AAAAAATTATATAAA
1 AAAAAATTATATAAA
90951 AA
1 AA
90953 TATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAATTATATAAA
Found at i:114494 original size:2 final size:2
Alignment explanation
Indices: 114483--114521 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
114473 AAAGTTTTTC
114483 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
114522 TCTAAGTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:114710 original size:24 final size:24
Alignment explanation
Indices: 114683--114748 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
114673 GTGGGTTTCA
* *
114683 TATTTTTTCTCAGTTAAATTCTGT
1 TATTTTTTCTCAATTAAATTATGT
*
114707 TATTTTTAT-TTAATTAAATTATGT
1 TATTTTT-TCTCAATTAAATTATGT
114731 TATTTTTTCTCAATTAAA
1 TATTTTTTCTCAATTAAA
114749 CTTTAATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.59
Consensus pattern (24 bp):
TATTTTTTCTCAATTAAATTATGT
Found at i:122423 original size:29 final size:28
Alignment explanation
Indices: 122353--122423 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
122343 TTTTAAATTA
*
122353 ATAAAAA-TAAAATTATATATTGACTTC
1 ATAAAAATTATAATTATATATTGACTTC
* * * *
122380 CT-AAAATGATAAATTATATTTTTACTATC
1 ATAAAAATTAT-AATTATATATTGACT-TC
122409 ATAAAAATTATAATT
1 ATAAAAATTATAATT
122424 TAATTTCGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 13 0.39
29 7 0.21
30 7 0.21
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (28 bp):
ATAAAAATTATAATTATATATTGACTTC
Found at i:124058 original size:35 final size:32
Alignment explanation
Indices: 123989--124055 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
123979 AAATCACGGG
* *
123989 CAAAGGAGGAAAAATTCATTAATGTTGAAAAA
1 CAAAGAAGGAAAAATTCACTAATGTTGAAAAA
*
124021 CAAAGAAGGAGAAATTCACTAATGTTGAAAAA
1 CAAAGAAGGAAAAATTCACTAATGTTGAAAAA
124053 CAA
1 CAA
124056 CAATACAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.19
Consensus pattern (32 bp):
CAAAGAAGGAAAAATTCACTAATGTTGAAAAA
Found at i:126503 original size:15 final size:15
Alignment explanation
Indices: 126485--126534 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
126475 TGTCTTATTT
126485 TATATTTTAATCATC
1 TATATTTTAATCATC
*
126500 TATA-TTTAA-AATGC
1 TATATTTTAATCAT-C
* *
126514 TACATTTTAATCATT
1 TATATTTTAATCATC
126529 TATATT
1 TATATT
126535 ATTGTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
15 14 0.52
16 2 0.07
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (15 bp):
TATATTTTAATCATC
Found at i:145392 original size:15 final size:14
Alignment explanation
Indices: 145367--145395 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
145357 TTTAAAGTCT
145367 TTATGAAAAAAAAA
1 TTATGAAAAAAAAA
145381 TTATGAAAAAAAAA
1 TTATGAAAAAAAAA
145395 T
1 T
145396 GTAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (14 bp):
TTATGAAAAAAAAA
Found at i:145770 original size:28 final size:29
Alignment explanation
Indices: 145710--145909 Score: 253
Period size: 28 Copynumber: 6.9 Consensus size: 29
145700 GAGAGTTTTA
* *
145710 GGGTCAAAAATAGAATTTTTGGAAGTTCAG
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGG
*
145740 GGGTAAAAATAGAATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTCGG
145769 GGGT-AAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTCGG
**
145797 GGGT-AAAATGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTCGG
145825 GGGTCAAAAATGGAATTTTTGGAAGTTTC-G
1 GGGT-AAAAATGGAATTTTTGGAAG-TTCGG
* * *
145855 AGGTCAAAAATGGAATTTTTGAAAGTTTGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTCGG
* *
145885 GCGTACAAATGGAATTTTTGGAAGT
1 GGGTAAAAATGGAATTTTTGGAAGT
145910 CTCAAGACCT
Statistics
Matches: 154, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
28 53 0.34
29 49 0.32
30 50 0.32
31 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGG
Found at i:145837 original size:30 final size:29
Alignment explanation
Indices: 145703--145909 Score: 240
Period size: 30 Copynumber: 7.1 Consensus size: 29
145693 TAACTTTGAG
* *
145703 AGTTTTAGGGTCAAAAATAGAATTTTTGGA
1 AGTTTTGGGGT-AAAAATGGAATTTTTGGA
** *
145733 AGTTCAGGGGTAAAAATAGAATTTTTGGA
1 AGTTTTGGGGTAAAAATGGAATTTTTGGA
**
145762 AGTTCGGGGGT-AAAATGGAATTTTTGGA
1 AGTTTTGGGGTAAAAATGGAATTTTTGGA
**
145790 AGTTCGGGGGT-AAAATGGAATTTTTGGA
1 AGTTTTGGGGTAAAAATGGAATTTTTGGA
145818 AGTTTTGGGGTCAAAAATGGAATTTTTGGA
1 AGTTTTGGGGT-AAAAATGGAATTTTTGGA
* * *
145848 AGTTTCGAGGTCAAAAATGGAATTTTTGAA
1 AGTTTTGGGGT-AAAAATGGAATTTTTGGA
*
145878 AG-TTTGGGCGTACAAATGGAATTTTTGGA
1 AGTTTTGGG-GTAAAAATGGAATTTTTGGA
145907 AGT
1 AGT
145910 CTCAAGACCT
Statistics
Matches: 159, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
28 53 0.33
29 50 0.31
30 56 0.35
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
AGTTTTGGGGTAAAAATGGAATTTTTGGA
Found at i:146641 original size:23 final size:21
Alignment explanation
Indices: 146615--146657 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
146605 CCTTTTCTTT
*
146615 TTTAAAACTTATTTTCTTTTTAC
1 TTTAAAACCT-TTTT-TTTTTAC
146638 TTTAAAACCTTTTTTTTTTA
1 TTTAAAACCTTTTTTTTTTA
146658 AAAGATCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 9 0.47
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAAAACCTTTTTTTTTTAC
Found at i:147744 original size:17 final size:17
Alignment explanation
Indices: 147722--147788 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
147712 GATATTATTT
*
147722 ATTTTAAATTTATAATA
1 ATTTTAAATTTAAAATA
147739 ATTTTAAATTTAAAATA
1 ATTTTAAATTTAAAATA
* * *
147756 AATTTAAACTTAAATTA
1 ATTTTAAATTTAAAATA
* *
147773 AATTCAAATTTAAAAT
1 ATTTTAAATTTAAAAT
147789 TAAAATAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:147750 original size:6 final size:6
Alignment explanation
Indices: 147724--147809 Score: 65
Period size: 6 Copynumber: 15.0 Consensus size: 6
147714 TATTATTTAT
* * *
147724 TTTAAA TTTATAA --TAAT TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
147770 -TTAAA TTCAAA TTTAAA ATTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
147810 ACAAATTTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 1 0.02
5 15 0.24
6 45 0.71
7 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:147762 original size:34 final size:34
Alignment explanation
Indices: 147724--147837 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 34
147714 TATTATTTAT
*
147724 TTTAAATTTATAATAATTTTAAATTTAAAATAAA
1 TTTAAATTTATAATAAATTTAAATTTAAAATAAA
* *
147758 TTTAAACTTAAATTAAATTCAAATTTAAAATTAAAATAAA
1 TTTAAA-TT-TA-T-AA-T-AAATTTAAATTTAAAATAAA
* * *
147798 TCTAAATTTAAAACAAATTT-AATCTTAAAATAAA
1 TTTAAATTTATAATAAATTTAAAT-TTAAAATAAA
147832 TTTAAA
1 TTTAAA
147838 AGGGGCCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
33 2 0.03
34 27 0.42
35 2 0.03
36 3 0.05
37 1 0.02
38 3 0.05
39 3 0.05
40 23 0.36
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
TTTAAATTTATAATAAATTTAAATTTAAAATAAA
Found at i:147768 original size:23 final size:22
Alignment explanation
Indices: 147742--147809 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
147732 TATAATAATT
147742 TTAAATTTAAAATAAATTTAAAC
1 TTAAA-TTAAAATAAATTTAAAC
* *
147765 TTAAATTAAATTCAAATTTAAAA
1 TTAAATTAAAAT-AAATTTAAAC
* *
147788 TTAAAATAAATCTAAATTTAAA
1 TTAAATTAAA-ATAAATTTAAA
147810 ACAAATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.15
23 32 0.82
24 1 0.03
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAATTAAAATAAATTTAAAC
Found at i:147798 original size:17 final size:17
Alignment explanation
Indices: 147743--147838 Score: 88
Period size: 17 Copynumber: 5.6 Consensus size: 17
147733 ATAATAATTT
*
147743 TAAATTTAAAA-TAAATT
1 TAAATTTAAAATTAAA-A
* *
147760 TAAACTT-AAATTAAAT
1 TAAATTTAAAATTAAAA
147776 TCAAATTTAAAATTAAAA
1 T-AAATTTAAAATTAAAA
* *
147794 TAAATCTAAATTTAAAA
1 TAAATTTAAAATTAAAA
* **
147811 CAAATTTAATCTTAAAA
1 TAAATTTAAAATTAAAA
147828 TAAATTTAAAA
1 TAAATTTAAAA
147839 GGGGCCCGAT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
16 5 0.08
17 50 0.78
18 9 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAAATTAAAA
Found at i:147810 original size:23 final size:22
Alignment explanation
Indices: 147749--147810 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
147739 ATTTTAAATT
* * *
147749 TAAAATAAATTTAAACTTAAAT
1 TAAATTAAATTTAAAATTAAAA
147771 TAAATTCAAATTTAAAATTAAAA
1 TAAATT-AAATTTAAAATTAAAA
147794 TAAATCTAAATTTAAAA
1 TAAAT-TAAATTTAAAA
147811 CAAATTTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.14
23 29 0.83
24 1 0.03
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATTAAATTTAAAATTAAAA
Found at i:147838 original size:11 final size:11
Alignment explanation
Indices: 147743--147819 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 11
147733 ATAATAATTT
147743 TAAATTTAAAA
1 TAAATTTAAAA
*
147754 TAAATTTAAACT
1 TAAATTTAAA-A
*
147766 TAAA-TTAAAT
1 TAAATTTAAAA
147776 TCAAATTTAAAA
1 T-AAATTTAAAA
* *
147788 TTAAA-ATAAATC
1 -TAAATTTAAA-A
147800 TAAATTTAAAA
1 TAAATTTAAAA
*
147811 CAAATTTAA
1 TAAATTTAA
147820 TCTTAAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
10 2 0.04
11 34 0.64
12 16 0.30
13 1 0.02
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:149720 original size:31 final size:31
Alignment explanation
Indices: 149685--149754 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
149675 ACATGAATTT
*
149685 TAATTTTGGTGT-AATTGTACACGTGAAACTC
1 TAATTTTGGT-TCAAATGTACACGTGAAACTC
* * * *
149716 TAATTGTGGTTCAAATGTATACTTGAAACTT
1 TAATTTTGGTTCAAATGTACACGTGAAACTC
149747 TAATTTTG
1 TAATTTTG
149755 ATTTAATCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (31 bp):
TAATTTTGGTTCAAATGTACACGTGAAACTC
Found at i:149937 original size:29 final size:30
Alignment explanation
Indices: 149905--149973 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 30
149895 AAATCAAAAT
*
149905 TTCATGTATAAAATTTCACA-AAATCAG-AG
1 TTCATGTATAAAATTCCACATAAATC-GTAG
149934 TTCATGTATAAAATTCCACATTAAATCGTAG
1 TTCATGTATAAAATTCCACA-TAAATCGTAG
149965 TTCATGTAT
1 TTCATGTAT
149974 GGTTTTGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 19 0.53
30 1 0.03
31 16 0.44
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (30 bp):
TTCATGTATAAAATTCCACATAAATCGTAG
Found at i:150111 original size:16 final size:16
Alignment explanation
Indices: 150090--150123 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
150080 AAGCTCAATC
150090 TTATTTAACAAA-AAAT
1 TTATTT-ACAAACAAAT
150106 TTATTTACAAACAAAT
1 TTATTTACAAACAAAT
150122 TT
1 TT
150124 GTTGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
TTATTTACAAACAAAT
Found at i:154355 original size:11 final size:11
Alignment explanation
Indices: 154328--154370 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
154318 ACAATAACGA
*
154328 CAAAATAATAA
1 CAAAATAATAG
154339 CAAAATAATAG
1 CAAAATAATAG
** *
154350 TGAAATGATAG
1 CAAAATAATAG
154361 CAAAATAATA
1 CAAAATAATA
154371 TAAAAACAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:155467 original size:16 final size:17
Alignment explanation
Indices: 155437--155469 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
155427 AGTTAGAGAA
155437 GAAAAAAAAGGAAAATTT
1 GAAAAAAAA-GAAAATTT
155455 GAAAAAAAA-AAAATT
1 GAAAAAAAAGAAAATT
155470 AAAATGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
GAAAAAAAAGAAAATTT
Done.