Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012908.1 Kokia drynarioides strain JFW-HI SEQ_127922, 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: 429546
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:4740 original size:30 final size:30
Alignment explanation
Indices: 4706--4772 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
4696 ATTTTTGAGG
*
4706 AATTTGGGGATCAAAATTGAAATTTTGGAA
1 AATTTGAGGATCAAAATTGAAATTTTGGAA
* *
4736 AATTT-AGGATTAAAATTGAACTTTTGGAA
1 AATTTGAGGATCAAAATTGAAATTTTGGAA
4765 AATTTGAG
1 AATTTGAG
4773 TTTGAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 26 0.79
30 7 0.21
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (30 bp):
AATTTGAGGATCAAAATTGAAATTTTGGAA
Found at i:4789 original size:29 final size:28
Alignment explanation
Indices: 4718--4801 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
4708 TTTGGGGATC
4718 AAAATTGAAATTTTGGAAAATTT-AGGATT
1 AAAATTG-AATTTTGGAAAATTTGA-GATT
*
4747 AAAATTGAACTTTTGGAAAATTTGAGTTT
1 AAAATTGAA-TTTTGGAAAATTTGAGATT
**
4776 GAAAATGTG-ATTTTCAAAAATTTGAG
1 -AAAAT-TGAATTTTGGAAAATTTGAG
4802 GGTAAAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.04
29 37 0.77
30 7 0.15
31 2 0.04
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (28 bp):
AAAATTGAATTTTGGAAAATTTGAGATT
Found at i:4833 original size:29 final size:29
Alignment explanation
Indices: 4799--5140 Score: 329
Period size: 29 Copynumber: 11.7 Consensus size: 29
4789 TCAAAAATTT
*
4799 GAGGGTAAAAATGGTAA-TTTTGGATGTTC
1 GAGGGTAAAAAT-GTAATTTTTGGAAGTTC
* * *
4828 GGGGGT-AAAATGGTAATTTTTGGATGTTT
1 GAGGGTAAAAAT-GTAATTTTTGGAAGTTC
* *
4857 AAGGGTAAAAATGTAATTTTTGGAAGTTT
1 GAGGGTAAAAATGTAATTTTTGGAAGTTC
4886 G-GAGGTAAAAATGTAATTTTTGGAAAAGCTT-
1 GAG-GGTAAAAATGTAATTTTTGG--AAG-TTC
*
4917 G-GGGTAAAAATGTAATTTTTAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAGTTC
* * *
4945 GAGGGTAATAATGTGATTTTTGGAAGTTT
1 GAGGGTAAAAATGTAATTTTTGGAAGTTC
*
4974 GAGGGCAAAAATGTAATTTTTGAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTG-GAAGTTC
* *
5004 GAGGGT-AAAATGTGATTTTAGGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAGTTC
* * * *
5032 GAGGGTAAAAATATGATTTTTGAAAGTTTT
1 GAGGGTAAAAATGTAATTTTTGGAAG-TTC
** *
5062 G-GGACAAAAATGTAAATTTTGAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTG-GAAGTTC
* * *
5091 GAGGGTCAAAATGTAATTTTAGAAAAGTTC
1 GAGGGTAAAAATGTAATTTTTG-GAAGTTC
*
5121 GAGGGTTAAAATGTAATTTT
1 GAGGGTAAAAATGTAATTTT
5141 AGAAAAGTTT
Statistics
Matches: 264, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
27 2 0.01
28 28 0.11
29 145 0.55
30 82 0.31
31 5 0.02
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
GAGGGTAAAAATGTAATTTTTGGAAGTTC
Found at i:4893 original size:87 final size:88
Alignment explanation
Indices: 4805--5183 Score: 368
Period size: 87 Copynumber: 4.3 Consensus size: 88
4795 ATTTGAGGGT
* * * **
4805 AAAAATGGTAA-TTTTG-GATGTTCGGGGGT-AAAATGGTAATTTTTGGATGTTTAAGGGTAAAA
1 AAAAAT-GTAATTTTTGAGAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTCGAGGGTAAAA
* *
4867 ATGTAATTTTTGGAAGTTTGGAGGT
64 ATGTGATTTTTGGAAGTTTGGAGGC
* * *
4892 AAAAATGTAATTTTTGGAAAAGCTT-G-GGGTAAAAATGTAATTTTTAGAAGTTCGAGGGTAATA
1 AAAAATGTAATTTTT-GAGAAG-TTCGAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAA
4955 ATGTGATTTTTGGAAGTTT-GAGGGC
64 ATGTGATTTTTGGAAGTTTGGA-GGC
* *
4980 AAAAATGTAATTTTTGAGAAGTTCGAGGGT-AAAATGTGATTTTAGGAAGTTCGAGGGTAAAAAT
1 AAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAAT
* * *
5044 ATGATTTTTGAAAGTTTTGG-GAC
66 GTGATTTTTGGAAG-TTTGGAGGC
* * * * *
5067 AAAAATGTAAATTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTAGAAAAGTTCGAGGGTTAAAA
1 AAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTAATTTTTG-GAAGTTCGAGGGTAAAAA
* * * *
5132 TGTAATTTTAGAAAAGTTTGGAGTC
65 TGTGATTTTTG-GAAGTTTGGAGGC
5157 AAAATATG--ATTTTTG-GAAAGTTC-AGGG
1 AAAA-ATGTAATTTTTGAG-AAGTTCGAGGG
5184 ACCTTCTAGG
Statistics
Matches: 250, Mismatches: 26, Indels: 31
0.81 0.08 0.10
Matches are distributed among these distances:
86 6 0.02
87 91 0.36
88 88 0.35
89 50 0.20
90 12 0.05
91 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (88 bp):
AAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAAT
GTGATTTTTGGAAGTTTGGAGGC
Found at i:4925 original size:30 final size:31
Alignment explanation
Indices: 4799--5183 Score: 259
Period size: 29 Copynumber: 13.2 Consensus size: 31
4789 TCAAAAATTT
*
4799 GAGGGTAAAAATGGTAA-TTTTGG--ATGTTC
1 GAGGGTAAAAAT-GTAATTTTTGGAAAAGTTC
* * *
4828 GGGGGT-AAAATGGTAATTTTTGG--ATGTTT
1 GAGGGTAAAAAT-GTAATTTTTGGAAAAGTTC
* *
4857 AAGGGTAAAAATGTAATTTTTGG--AAGTTT
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
4886 G-GAGGTAAAAATGTAATTTTTGGAAAAGCTT-
1 GAG-GGTAAAAATGTAATTTTTGGAAAAG-TTC
*
4917 G-GGGTAAAAATGTAATTTTT--AGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* * *
4945 GAGGGTAATAATGTGATTTTTGG--AAGTTT
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* *
4974 GAGGGCAAAAATGTAATTTTT-GAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* *
5004 GAGGGT-AAAATGTGATTTTAGG--AAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* * *
5032 GAGGGTAAAAATATGATTTTT-G-AAAGTTTT
1 GAGGGTAAAAATGTAATTTTTGGAAAAG-TTC
** * *
5062 G-GGACAAAAATGTAAATTTT-GAGAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* *
5091 GAGGGTCAAAATGTAA-TTTTAGAAAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* * *
5121 GAGGGTTAAAATGTAA-TTTTAGAAAAGTTT
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
* * * *
5151 G-GAGTCAAAATATGATTTTTGG-AAAGTTC
1 GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
5180 -AGGG
1 GAGGG
5184 ACCTTCTAGG
Statistics
Matches: 295, Mismatches: 40, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 30 0.10
29 163 0.55
30 93 0.32
31 5 0.02
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (31 bp):
GAGGGTAAAAATGTAATTTTTGGAAAAGTTC
Found at i:5158 original size:59 final size:57
Alignment explanation
Indices: 4796--5183 Score: 256
Period size: 59 Copynumber: 6.6 Consensus size: 57
4786 TTTTCAAAAA
* * * * * *
4796 TTTGAGGGTAAAAATGGTAA-TTTTGGATGTTCGGGGGTAAAATGGTAATTTTTG-GATG
1 TTTG-GGGTCAAAAT-GTAATTTTTGAAAGTTCGAGGGTAAAAT-GTAATTTTAGAGAAG
* * * * * *
4854 TTTAAGGGTAAAAATGTAATTTTTGGAAGTTTG-GAGGTAAAAATGTAATTTTTGGAAAAG
1 TTT-GGGGTCAAAATGTAATTTTTGAAAGTTCGAG-GGT-AAAATGTAA-TTTTAGAGAAG
* * * *
4914 CTTGGGGTAAAAATGTAATTTTT-AGAAGTTCGAGGGTAATAATGTGATTTTTG-GAAG
1 TTTGGGGTCAAAATGTAATTTTTGA-AAGTTCGAGGGTAA-AATGTAATTTTAGAGAAG
*
4971 TTTGAGGG-CAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAATGTGATTTTAG-GAAG
1 TTTG-GGGTC-AAAATGTAATTTTTGA-AAGTTCGAGGGTAAAATGTAATTTTAGAGAAG
* * * * * **
5029 TTCGAGGGTAAAAATATGATTTTTGAAAGTTTTG-GGACAAAAATGTAAATTTT-GAGAAG
1 TTTG-GGGTCAAAATGTAATTTTTGAAAG-TTCGAGG-GTAAAATGT-AATTTTAGAGAAG
* * *
5088 TTCGAGGGTCAAAATGTAATTTTAGAAAAGTTCGAGGGTTAAAATGTAATTTTAGAAAAG
1 TTTG-GGGTCAAAATGTAATTTTTG-AAAGTTCGAGGG-TAAAATGTAATTTTAGAGAAG
* * *
5148 TTTGGAGTCAAAATATGATTTTTGGAAAGTTC-AGGG
1 TTTGGGGTCAAAATGTAATTTTT-GAAAGTTCGAGGG
5184 ACCTTCTAGG
Statistics
Matches: 271, Mismatches: 37, Indels: 44
0.77 0.11 0.12
Matches are distributed among these distances:
57 16 0.06
58 107 0.39
59 121 0.45
60 27 0.10
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (57 bp):
TTTGGGGTCAAAATGTAATTTTTGAAAGTTCGAGGGTAAAATGTAATTTTAGAGAAG
Found at i:6316 original size:18 final size:18
Alignment explanation
Indices: 6295--6329 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6285 AACGGTAATA
6295 TAATAAATAAATATATAT
1 TAATAAATAAATATATAT
*
6313 TAATAAATAAATGTATA
1 TAATAAATAAATATATA
6330 GGATTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TAATAAATAAATATATAT
Found at i:6907 original size:11 final size:10
Alignment explanation
Indices: 6872--6929 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
6862 ACATTAGTAC
6872 ATTTAAATAA
1 ATTTAAATAA
6882 ATTTAAACTTAA
1 ATTTAAA--TAA
6894 ATTTACAATAA
1 ATTTA-AATAA
6905 ATTTAAAT--
1 ATTTAAATAA
*
6913 -TTCAAATAA
1 ATTTAAATAA
6922 ATTTAAAT
1 ATTTAAAT
6930 TTAAATTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:6910 original size:17 final size:18
Alignment explanation
Indices: 6885--6932 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
6875 TAAATAAATT
*
6885 TAAACTTAAATTTAC-AA
1 TAAATTTAAATTTACAAA
6902 TAAATTTAAATTT-CAAA
1 TAAATTTAAATTTACAAA
6919 TAAATTTAAATTTA
1 TAAATTTAAATTTA
6933 AATTCTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTACAAA
Found at i:6911 original size:6 final size:6
Alignment explanation
Indices: 6879--6936 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
6869 TACATTTAAA
*
6879 TAAATT TAAACT TAAATT TACAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
6925 TAAATT TAAATT
1 TAAATT TAAATT
6937 CTGTTTGGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 5 0.11
5 3 0.07
6 31 0.70
7 5 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:8917 original size:16 final size:16
Alignment explanation
Indices: 8896--9033 Score: 80
Period size: 16 Copynumber: 7.7 Consensus size: 16
8886 TAAATATTCG
8896 GGCTTTGTGCCTAGTA
1 GGCTTTGTGCCTAGTA
* *
8912 GGCTTTGTGTCAGTGTATTCA
1 GGCTTTGTG-C---CTAGT-A
8933 GGCTTTGTGCCTAGTA
1 GGCTTTGTGCCTAGTA
* *
8949 AGCTTTGTGCCGGTGTAATCA
1 GGCTTTGTGCC----TAGT-A
8970 GGCTTTGTGCCTAGTA
1 GGCTTTGTGCCTAGTA
*
8986 GGCTTTGTGTCGGT-GTA
1 GGCTTTGTG-C-CTAGTA
9003 TTCGAGCTTTGTGCCTAGTA
1 ---G-GCTTTGTGCCTAGTA
9023 GGCTTTGTGCC
1 GGCTTTGTGCC
9034 GGTGTAATCG
Statistics
Matches: 95, Mismatches: 10, Indels: 34
0.68 0.07 0.24
Matches are distributed among these distances:
16 40 0.42
17 12 0.13
18 1 0.01
19 1 0.01
20 12 0.13
21 29 0.31
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.38
Consensus pattern (16 bp):
GGCTTTGTGCCTAGTA
Found at i:8940 original size:37 final size:37
Alignment explanation
Indices: 8890--9101 Score: 280
Period size: 37 Copynumber: 5.7 Consensus size: 37
8880 TGCATTTAAA
* *
8890 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGTCAGTG
1 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
* *
8927 TATTCAGGCTTTGTGCCTAGTAAGCTTTGTGCCGGTG
1 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
* * *
8964 TAATCAGGCTTTGTGCCTAGTAGGCTTTGTGTCGGTG
1 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
*
9001 TATTCGAGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
* * * ** *
9038 TAATCGGGCTTTGTGCCTAATAGGCTTCGTGCCTATT
1 TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
* *
9075 TATTCGGGCTATGTGCCTAGAAGGCTT
1 TATTCGGGCTTTGTGCCTAGTAGGCTT
9102 GTTACCGGTG
Statistics
Matches: 153, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 153 1.00
ACGTcount: A:0.14, C:0.18, G:0.30, T:0.38
Consensus pattern (37 bp):
TATTCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:8976 original size:21 final size:20
Alignment explanation
Indices: 8911--9054 Score: 73
Period size: 21 Copynumber: 7.6 Consensus size: 20
8901 TGTGCCTAGT
* *
8911 AGGCTTTGTGTCAGTGTATTC
1 AGGCTTTGTG-CCGTGTAATC
8932 AGGCTTTGTGCC-TAGT-A--
1 AGGCTTTGTGCCGT-GTAATC
8949 A-GCTTTGTGCCGGTGTAATC
1 AGGCTTTGTGCC-GTGTAATC
*
8969 AGGCTTTGTGCC---TAGT-
1 AGGCTTTGTGCCGTGTAATC
* *
8985 AGGCTTTGTGTCGGTGTATTC
1 AGGCTTTGTG-CCGTGTAATC
*
9006 -GAGCTTTGTGCC---TAGT-
1 AG-GCTTTGTGCCGTGTAATC
9022 AGGCTTTGTGCCGGTGTAATC
1 AGGCTTTGTGCC-GTGTAATC
*
9043 GGGCTTTGTGCC
1 AGGCTTTGTGCC
9055 TAATAGGCTT
Statistics
Matches: 95, Mismatches: 9, Indels: 38
0.67 0.06 0.27
Matches are distributed among these distances:
16 30 0.32
17 11 0.12
18 2 0.02
19 1 0.01
20 12 0.13
21 39 0.41
ACGTcount: A:0.12, C:0.18, G:0.32, T:0.38
Consensus pattern (20 bp):
AGGCTTTGTGCCGTGTAATC
Found at i:12137 original size:18 final size:18
Alignment explanation
Indices: 12116--12163 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
12106 AATTAATTCC
12116 ATTAACCGAATTCGATCG
1 ATTAACCGAATTCGATCG
** *
12134 ATTAACTTAATTTGATCG
1 ATTAACCGAATTCGATCG
12152 ATTAACCGAATT
1 ATTAACCGAATT
12164 AATTCAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
ATTAACCGAATTCGATCG
Found at i:15580 original size:61 final size:61
Alignment explanation
Indices: 15485--15606 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
15475 CCATCATTTC
15485 TTCTTAAGTGTTAGATGTAAGTATTGTACAGGGGTGTGTTTAAAAGAAAATGAAAAACATG
1 TTCTTAAGTGTTAGATGTAAGTATTGTACAGGGGTGTGTTTAAAAGAAAATGAAAAACATG
15546 TTCTTAAGTGTTAGATGTAAGTATTGTACAGGGGTGTGTTTAAAAGAAAATGAAAAACATG
1 TTCTTAAGTGTTAGATGTAAGTATTGTACAGGGGTGTGTTTAAAAGAAAATGAAAAACATG
15607 GATAACGTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (61 bp):
TTCTTAAGTGTTAGATGTAAGTATTGTACAGGGGTGTGTTTAAAAGAAAATGAAAAACATG
Found at i:28496 original size:124 final size:124
Alignment explanation
Indices: 28276--28534 Score: 518
Period size: 124 Copynumber: 2.1 Consensus size: 124
28266 AAAATAAAAA
28276 GTATCGATACCCTTAACAAAGTATTGATATTTATCGATACCCTTCTTGGTATCGATGACTTTTTA
1 GTATCGATACCCTTAACAAAGTATTGATATTTATCGATACCCTTCTTGGTATCGATGACTTTTTA
28341 AGGATAGATGTTTTGGAAAATCAAATAAAAATTGCTCGAGTATCAATACCCTCCCCAAG
66 AGGATAGATGTTTTGGAAAATCAAATAAAAATTGCTCGAGTATCAATACCCTCCCCAAG
28400 GTATCGATACCCTTAACAAAGTATTGATATTTATCGATACCCTTCTTGGTATCGATGACTTTTTA
1 GTATCGATACCCTTAACAAAGTATTGATATTTATCGATACCCTTCTTGGTATCGATGACTTTTTA
28465 AGGATAGATGTTTTGGAAAATCAAATAAAAATTGCTCGAGTATCAATACCCTCCCCAAG
66 AGGATAGATGTTTTGGAAAATCAAATAAAAATTGCTCGAGTATCAATACCCTCCCCAAG
28524 GTATCGATACC
1 GTATCGATACC
28535 TCATAGTAAG
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 135 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (124 bp):
GTATCGATACCCTTAACAAAGTATTGATATTTATCGATACCCTTCTTGGTATCGATGACTTTTTA
AGGATAGATGTTTTGGAAAATCAAATAAAAATTGCTCGAGTATCAATACCCTCCCCAAG
Found at i:34517 original size:63 final size:63
Alignment explanation
Indices: 34432--34568 Score: 256
Period size: 63 Copynumber: 2.2 Consensus size: 63
34422 GTGATGTGAA
*
34432 ATCATATTTTATAAAAATAATTAAAAGCATAAAAATAAAGAAGGAAAAACAATTTGTAGATTTT
1 ATCA-ATTCTATAAAAATAATTAAAAGCATAAAAATAAAGAAGGAAAAACAATTTGTAGATTTT
34496 ATCAATTCTATAAAAATAATTAAAAGCATAAAAATAAAGAAGGAAAAACAATTTGTAGATTTT
1 ATCAATTCTATAAAAATAATTAAAAGCATAAAAATAAAGAAGGAAAAACAATTTGTAGATTTT
34559 ATCAATTCTA
1 ATCAATTCTA
34569 AGGATAGAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 68 0.94
64 4 0.06
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.31
Consensus pattern (63 bp):
ATCAATTCTATAAAAATAATTAAAAGCATAAAAATAAAGAAGGAAAAACAATTTGTAGATTTT
Found at i:36000 original size:24 final size:24
Alignment explanation
Indices: 35968--36026 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
35958 CAATTTCATT
35968 ACGTTTACGCTCGTCAGCTAGCAC
1 ACGTTTACGCTCGTCAGCTAGCAC
* *
35992 ACGTTTACGCTCGTCAGGTTGCAC
1 ACGTTTACGCTCGTCAGCTAGCAC
*
36016 ACTTTTACGCT
1 ACGTTTACGCT
36027 ACTATGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.20, T:0.31
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTAGCAC
Found at i:43022 original size:48 final size:48
Alignment explanation
Indices: 42950--43078 Score: 159
Period size: 48 Copynumber: 2.7 Consensus size: 48
42940 GCAGTTTCAT
* **
42950 TACGTTTACGCTCGTCAACTTGCACATGTTTACACTCTTCAGCTTATA
1 TACGTTTACGCTCGTCAACTTGCACACGTTTACACTCGCCAGCTTATA
* * * ** *
42998 TACGTTTGCGCTTGTCAGCTTGCACACGTTTATGCTCGCCATCTTATA
1 TACGTTTACGCTCGTCAACTTGCACACGTTTACACTCGCCAGCTTATA
* *
43046 TACATTTACGCTCGTCAACTTGCACACATTTAC
1 TACGTTTACGCTCGTCAACTTGCACACGTTTAC
43079 GCTACTATGA
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (48 bp):
TACGTTTACGCTCGTCAACTTGCACACGTTTACACTCGCCAGCTTATA
Found at i:43074 original size:24 final size:24
Alignment explanation
Indices: 42951--43081 Score: 100
Period size: 24 Copynumber: 5.5 Consensus size: 24
42941 CAGTTTCATT
42951 ACGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAACTTGCAC
* * * * ** *
42975 ATGTTTACACTCTTCAGCTTATAT
1 ACGTTTACGCTCGTCAACTTGCAC
* * *
42999 ACGTTTGCGCTTGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAACTTGCAC
* * * ** *
43023 ACGTTTATGCTCGCCATCTTATAT
1 ACGTTTACGCTCGTCAACTTGCAC
*
43047 ACATTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAACTTGCAC
*
43071 ACATTTACGCT
1 ACGTTTACGCT
43082 ACTATGAAAT
Statistics
Matches: 77, Mismatches: 30, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 77 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAACTTGCAC
Found at i:51874 original size:36 final size:36
Alignment explanation
Indices: 51834--51910 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
51824 TGATGATTGG
** **
51834 TGTGAAAGTGAATATATGGGTATGTGCTTCATGCCA
1 TGTGAAAGAAAATATATAAGTATGTGCTTCATGCCA
* * *
51870 TGTGACAGAAAATATGTAAGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATATAAGTATGTGCTTCATGCCA
51906 TGTGA
1 TGTGA
51911 TTGATTATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.34
Consensus pattern (36 bp):
TGTGAAAGAAAATATATAAGTATGTGCTTCATGCCA
Found at i:55155 original size:18 final size:19
Alignment explanation
Indices: 55134--55183 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
55124 TGTTGGTCAA
55134 GAGGAA-CCTGTTAGAGAG
1 GAGGAATCCTGTTAGAGAG
*
55152 GAGGAAGTTGCTGTTAGAGAG
1 GAGGAA--TCCTGTTAGAGAG
55173 GAGGAAATCCT
1 GAGG-AATCCT
55184 TGTTGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.23
20 3 0.12
21 15 0.58
22 2 0.08
ACGTcount: A:0.32, C:0.10, G:0.38, T:0.20
Consensus pattern (19 bp):
GAGGAATCCTGTTAGAGAG
Found at i:55187 original size:21 final size:21
Alignment explanation
Indices: 55140--55183 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55130 TCAAGAGGAA
*
55140 CCTGTTAGAGAGGAGGAAGTT
1 CCTGTTAGAGAGGAGGAAGAT
*
55161 GCTGTTAGAGAGGAGGAA-AT
1 CCTGTTAGAGAGGAGGAAGAT
55181 CCT
1 CCT
55184 TGTTGAAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.23
Consensus pattern (21 bp):
CCTGTTAGAGAGGAGGAAGAT
Found at i:57407 original size:14 final size:14
Alignment explanation
Indices: 57388--57414 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57378 TTTAGTACAT
57388 TGACATTTAACTTC
1 TGACATTTAACTTC
57402 TGACATTTAACTT
1 TGACATTTAACTT
57415 TGATTGCGTT
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:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (14 bp):
TGACATTTAACTTC
Found at i:64065 original size:272 final size:272
Alignment explanation
Indices: 63579--64131 Score: 1097
Period size: 272 Copynumber: 2.0 Consensus size: 272
63569 TGTAAAAGCT
63579 CGTGTCGAGGTTATCTGCAGCATGAATTACCTCATTTGCAAGCTAAACATGAACCTACTACTTGG
1 CGTGTCGAGGTTATCTGCAGCATGAATTACCTCATTTGCAAGCTAAACATGAACCTACTACTTGG
63644 GCAACAATAAAACCAATCCTACGTACTATCACATAACCAAAATATATCAAATCATACCATAATAA
66 GCAACAATAAAACCAATCCTACGTACTATCACATAACCAAAATATATCAAATCATACCATAATAA
63709 GCAAATCAAATGACAAATAAGAAGCATAAAGATCAAGAGATCAAAGTAAACCACTTCATAAACAC
131 GCAAATCAAATGACAAATAAGAAGCATAAAGATCAAGAGATCAAAGTAAACCACTTCATAAACAC
63774 ATAATCATCCATTTAAAATATGACCACCTCCGAACAAACTCCCATTCGACGTATATTTTTGGGCT
196 ATAATCATCCATTTAAAATATGACCACCTCCGAACAAACTCCCATTCGACGTATATTTTTGGGCT
63839 TCCTCAAGTATA
261 TCCTCAAGTATA
63851 CGTGTCGAGGTTATCTGCAGCATGAATTACCTCATTTGCAAGCTAAACATGAACCTACTACTTGG
1 CGTGTCGAGGTTATCTGCAGCATGAATTACCTCATTTGCAAGCTAAACATGAACCTACTACTTGG
63916 GCAACAATAAAACCAATCCTACGTACTATCACATAACCAAAATATATCAAATCATACCATAATAA
66 GCAACAATAAAACCAATCCTACGTACTATCACATAACCAAAATATATCAAATCATACCATAATAA
63981 GCAAATCAAATGACAAATAAGAAGCATAAAGATCAAGAGATCAAAGTAAACCACTTCATAAACAC
131 GCAAATCAAATGACAAATAAGAAGCATAAAGATCAAGAGATCAAAGTAAACCACTTCATAAACAC
*
64046 ATAATCATCCATTTAAAATATGACCACCTTCGAACAAACTCCCATTCGACGTATATTTTTGGGCT
196 ATAATCATCCATTTAAAATATGACCACCTCCGAACAAACTCCCATTCGACGTATATTTTTGGGCT
64111 TCCTCAAGTATA
261 TCCTCAAGTATA
64123 CGTGTCGAG
1 CGTGTCGAG
64132 TTGTAATATA
Statistics
Matches: 280, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
272 280 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (272 bp):
CGTGTCGAGGTTATCTGCAGCATGAATTACCTCATTTGCAAGCTAAACATGAACCTACTACTTGG
GCAACAATAAAACCAATCCTACGTACTATCACATAACCAAAATATATCAAATCATACCATAATAA
GCAAATCAAATGACAAATAAGAAGCATAAAGATCAAGAGATCAAAGTAAACCACTTCATAAACAC
ATAATCATCCATTTAAAATATGACCACCTCCGAACAAACTCCCATTCGACGTATATTTTTGGGCT
TCCTCAAGTATA
Found at i:68350 original size:21 final size:21
Alignment explanation
Indices: 68296--68362 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
68286 ATTTAGAAAC
*
68296 AGTGCAAACTTCTACCGATACT
1 AGTG-AAACTTCTACCGATACA
* * *
68318 TGGGAAAATTCTACCGATACA
1 AGTGAAACTTCTACCGATACA
* * *
68339 AGTGTAACTTCTACCAAAACA
1 AGTGAAACTTCTACCGATACA
68360 AGT
1 AGT
68363 CATGCTTCTA
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (21 bp):
AGTGAAACTTCTACCGATACA
Found at i:69028 original size:52 final size:52
Alignment explanation
Indices: 68950--69081 Score: 169
Period size: 52 Copynumber: 2.5 Consensus size: 52
68940 AAAGCTTAGT
* *
68950 CATATACTCAC-AATGATACATAGTCATCGGACCTCATAATT-CGTAAAGGATC
1 CATATACTCACGAA-GACACATAGTCATCGGAACTCAT-ATTCCGTAAAGGATC
* *
69002 CATATACTCACGAAGACACATAGTCATTGGAACTCATATTCCGTAAAGGATT
1 CATATACTCACGAAGACACATAGTCATCGGAACTCATATTCCGTAAAGGATC
* * *
69054 CAAATACTCACGATGACACATTGTCATC
1 CATATACTCACGAAGACACATAGTCATC
69082 AAACCTTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 3 0.04
52 65 0.93
53 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (52 bp):
CATATACTCACGAAGACACATAGTCATCGGAACTCATATTCCGTAAAGGATC
Found at i:69140 original size:37 final size:37
Alignment explanation
Indices: 69099--69172 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
69089 TTACATTTAA
69099 AGCTCAAGGCCCGTTAGCCATTCCTTTCCTTTGTTCC
1 AGCTCAAGGCCCGTTAGCCATTCCTTTCCTTTGTTCC
*
69136 AGCTCAAGGCCCGTTAGCCTTTCCTTTCCTTTGTTCC
1 AGCTCAAGGCCCGTTAGCCATTCCTTTCCTTTGTTCC
69173 CGCCTTCCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.12, C:0.35, G:0.16, T:0.36
Consensus pattern (37 bp):
AGCTCAAGGCCCGTTAGCCATTCCTTTCCTTTGTTCC
Found at i:75012 original size:21 final size:21
Alignment explanation
Indices: 74988--75041 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
74978 ATTGGGAAAA
*
74988 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* *
75009 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
75030 TTCTACCGATAC
1 TTCTACCGATAC
75042 TAAAAACTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:75830 original size:52 final size:52
Alignment explanation
Indices: 75774--75909 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 52
75764 ATTTCATTTG
*
75774 ATACTCACCATGACACATAGTTATCGGACCTTATAATTCA-TAAAGGATTCAT
1 ATACTCACGATGACACATAGTTATCGGACCTTATAA-TCAGTAAAGGATTCAT
*
75826 ATACTCACGATGACACATAGTTATCGGACCTCATAATCAGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTTATCGGACCTTATAATCAGTAAAGGATTCAT
* * *
75878 ATACTCACGATGATACATAGTCATCGAACCTT
1 ATACTCACGATGACACATAGTTATCGGACCTT
75910 TTACATTTAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 3 0.04
52 74 0.96
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTTATCGGACCTTATAATCAGTAAAGGATTCAT
Found at i:83411 original size:15 final size:15
Alignment explanation
Indices: 83391--83420 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
83381 AAGTCTGAAA
83391 GTGCTCATTTAACCG
1 GTGCTCATTTAACCG
83406 GTGCTCATTTAACCG
1 GTGCTCATTTAACCG
83421 ATGCCTCTAA
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:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
GTGCTCATTTAACCG
Found at i:86981 original size:20 final size:20
Alignment explanation
Indices: 86953--87092 Score: 113
Period size: 20 Copynumber: 7.0 Consensus size: 20
86943 GGGTTTAGAG
*
86953 TTTATAAATATTGATAAAAT
1 TTTAAAAATATTGATAAAAT
86973 TTTAAAAATATTGAT-AAAT
1 TTTAAAAATATTGATAAAAT
* * *
86992 TCTTAGATATTTTGATAAAAT
1 T-TTAAAAATATTGATAAAAT
* *
87013 TTTAAAAATATCGATAAAAC
1 TTTAAAAATATTGATAAAAT
* * * *
87033 CTTAAATAT-TTTAGTAAAGT
1 TTTAAAAATATTGA-TAAAAT
* *
87053 CTTAGAAATATTGATAAAAT
1 TTTAAAAATATTGATAAAAT
* *
87073 CTTTAAATATTTTGATAAAA
1 -TTTAAAAATATTGATAAAA
87093 GATAATTTTG
Statistics
Matches: 92, Mismatches: 23, Indels: 9
0.74 0.19 0.07
Matches are distributed among these distances:
19 7 0.08
20 62 0.67
21 23 0.25
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (20 bp):
TTTAAAAATATTGATAAAAT
Found at i:87012 original size:40 final size:40
Alignment explanation
Indices: 86963--87092 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
86953 TTTATAAATA
* *
86963 TTGATAAAATTTTAAAAATATTGATAAATTCTTAGATATT
1 TTGATAAAATTTTAAAAATATTGATAAAATCTTAAATATT
* *
87003 TTGATAAAATTTTAAAAATATCGATAAAACCTTAAATATT
1 TTGATAAAATTTTAAAAATATTGATAAAATCTTAAATATT
* * *
87043 TT-AGTAAAGTCTTAGAAATATTGATAAAATCTTTAAATATT
1 TTGA-TAAAATTTTAAAAATATTGATAAAATC-TTAAATATT
87084 TTGATAAAA
1 TTGATAAAA
87093 GATAATTTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.01
40 60 0.78
41 15 0.19
42 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (40 bp):
TTGATAAAATTTTAAAAATATTGATAAAATCTTAAATATT
Found at i:97459 original size:6 final size:6
Alignment explanation
Indices: 97448--97479 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
97438 TGGAGCTGCA
97448 TTTTAT TTTTAT TTTTA- TTTTA- TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
97480 TAATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:97468 original size:11 final size:11
Alignment explanation
Indices: 97447--97479 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
97437 TTGGAGCTGC
97447 ATTTTATTTTT
1 ATTTTATTTTT
97458 ATTTT-TATTTT
1 ATTTTAT-TTTT
97469 ATTTTATTTTT
1 ATTTTATTTTT
97480 TAATTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:97481 original size:17 final size:17
Alignment explanation
Indices: 97447--97479 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
97437 TTGGAGCTGC
97447 ATTTTATTTTTATTTTT
1 ATTTTATTTTTATTTTT
97464 ATTTTA-TTTTATTTTT
1 ATTTTATTTTTATTTTT
97480 TAATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTATTTTTATTTTT
Found at i:97486 original size:17 final size:17
Alignment explanation
Indices: 97449--97487 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
97439 GGAGCTGCAT
*
97449 TTTATTTTTATTTTTAT
1 TTTATTTTTATTTTTAA
97466 TTTA-TTTTATTTTTTAA
1 TTTATTTTTA-TTTTTAA
97483 TTTAT
1 TTTAT
97488 AATCATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTTATTTTTAA
Found at i:98610 original size:13 final size:13
Alignment explanation
Indices: 98592--98657 Score: 64
Period size: 13 Copynumber: 5.1 Consensus size: 13
98582 ATTGAATCAA
*
98592 ACTTTTCAAAAGT
1 ACTTTTTAAAAGT
98605 ACTTTTTAAAA-T
1 ACTTTTTAAAAGT
98617 CACTTTTTTAAAA-T
1 -AC-TTTTTAAAAGT
*
98631 ATTTTTTAAAAGT
1 ACTTTTTAAAAGT
* *
98644 ACTTCTCAAAAGT
1 ACTTTTTAAAAGT
98657 A
1 A
98658 ATGCTAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 10 0.22
13 25 0.56
14 10 0.22
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (13 bp):
ACTTTTTAAAAGT
Found at i:98635 original size:12 final size:14
Alignment explanation
Indices: 98607--98641 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
98597 TCAAAAGTAC
98607 TTTTTAAAATCACT
1 TTTTTAAAATCACT
98621 TTTTTAAAAT-A-T
1 TTTTTAAAATCACT
98633 TTTTTAAAA
1 TTTTTAAAA
98642 GTACTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 1 0.05
14 10 0.48
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTTAAAATCACT
Found at i:102337 original size:16 final size:15
Alignment explanation
Indices: 102311--102371 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
102301 AATGTAAAAT
102311 TAAAGATGAAATGCAA
1 TAAA-ATGAAATGCAA
***
102327 TAATAATGAAATGGTT
1 TAA-AATGAAATGCAA
*
102343 TAAAGATGATATGCAA
1 TAAA-ATGAAATGCAA
102359 TAACAATGAAATG
1 TAA-AATGAAATG
102372 GGGTCCTTGA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
15 1 0.03
16 31 0.91
17 2 0.06
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (15 bp):
TAAAATGAAATGCAA
Found at i:102348 original size:32 final size:32
Alignment explanation
Indices: 102310--102372 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
102300 TAATGTAAAA
*
102310 TTAAAGATGAAATGCAATAATAATGAAATGGT
1 TTAAAGATGAAATGCAATAACAATGAAATGGT
*
102342 TTAAAGATGATATGCAATAACAATGAAATGG
1 TTAAAGATGAAATGCAATAACAATGAAATGG
102373 GGTCCTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (32 bp):
TTAAAGATGAAATGCAATAACAATGAAATGGT
Found at i:104833 original size:17 final size:17
Alignment explanation
Indices: 104794--104837 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
104784 TGATAGATGG
*
104794 AAATGCAATGACAATGC
1 AAATGCAATGACAATGA
* * *
104811 AGATGCAGTGACAATTA
1 AAATGCAATGACAATGA
104828 AAATGCAATG
1 AAATGCAATG
104838 TCAAAGGAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:107111 original size:20 final size:20
Alignment explanation
Indices: 107075--107112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
107065 AGACTAACAG
*
107075 AAATAACTGAAAGATAAAAA
1 AAATAACTGAAAAATAAAAA
107095 AAATAAACT-AAAAATAAA
1 AAAT-AACTGAAAAATAAA
107113 TGATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAACTGAAAAATAAAAA
Found at i:122453 original size:17 final size:17
Alignment explanation
Indices: 122429--122486 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
122419 ATATATATGG
**
122429 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
*
122446 AGATGCAATGACAATAA
1 AAATGCAATGACAATAA
*
122463 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
122480 TAATGCA
1 AAATGCA
122487 GGGACAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:122493 original size:34 final size:34
Alignment explanation
Indices: 122429--122494 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
122419 ATATATATGG
* *
122429 AAATGCAATGACAATGTAGATGCAATGACAATAA
1 AAATGCAATGACAATATAGATGCAAGGACAATAA
* *
122463 AAATGCAATGACATTAATA-ATGCAGGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAAGGACAAT
122495 TATACTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAAGGACAATAA
Found at i:127714 original size:11 final size:10
Alignment explanation
Indices: 127698--127733 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
127688 GTCACATGAA
127698 AAAAGAAGAAG
1 AAAAGAA-AAG
127709 AAAAGAAAAG
1 AAAAGAAAAG
127719 AAAAGAAAAAG
1 AAAAG-AAAAG
127730 AAAA
1 AAAA
127734 ATATTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAG
Found at i:127716 original size:5 final size:5
Alignment explanation
Indices: 127698--127733 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
127688 GTCACATGAA
127698 AAAAG AAGAAG AAAAG AAAAG AAAAG AAAAAG AAAA
1 AAAAG AA-AAG AAAAG AAAAG AAAAG -AAAAG AAAA
127734 ATATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:127719 original size:16 final size:16
Alignment explanation
Indices: 127698--127733 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
127688 GTCACATGAA
127698 AAAAGAAGAAG-AAAAG
1 AAAAGAA-AAGAAAAAG
127714 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
127730 AAAA
1 AAAA
127734 ATATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:135194 original size:37 final size:38
Alignment explanation
Indices: 135101--135194 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
135091 ATTTTCGGAA
* * *
135101 TGCACCCAAGACTGTCATTGCATAAATATTCTTCAAAT
1 TGCACCCAAGAATGTCGTTACATAAATATTCTTCAAAT
* * * *
135139 TGCA-TCTAGAACTATCGTTACATAAGTATTCTTC-AAT
1 TGCACCCAAGAA-TGTCGTTACATAAATATTCTTCAAAT
135176 TGCACCCAAGAATGTCGTT
1 TGCACCCAAGAATGTCGTT
135195 GCATGAACAT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
37 17 0.39
38 27 0.61
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (38 bp):
TGCACCCAAGAATGTCGTTACATAAATATTCTTCAAAT
Found at i:140071 original size:14 final size:15
Alignment explanation
Indices: 140046--140075 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
140036 ACCGTAACGA
140046 GGGTGTGGTGAGAAT
1 GGGTGTGGTGAGAAT
140061 GGGTG-GGTGAGAAT
1 GGGTGTGGTGAGAAT
140075 G
1 G
140076 TCAACGCCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.00, G:0.57, T:0.23
Consensus pattern (15 bp):
GGGTGTGGTGAGAAT
Found at i:146070 original size:18 final size:18
Alignment explanation
Indices: 146047--146086 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
146037 TTATATGAAT
**
146047 GCATCTGATTTTGTGATC
1 GCATCTGATCATGTGATC
*
146065 GCATCTGGTCATGTGATC
1 GCATCTGATCATGTGATC
146083 GCAT
1 GCAT
146087 ATTATCTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (18 bp):
GCATCTGATCATGTGATC
Found at i:153929 original size:38 final size:38
Alignment explanation
Indices: 153873--153988 Score: 205
Period size: 38 Copynumber: 3.1 Consensus size: 38
153863 GGAAGCACAA
*
153873 ATCAATAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
1 ATCAGTAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
153911 ATCAGTAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
1 ATCAGTAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
* *
153949 ATCAGTAGAAAGGATTTAAGGTGCTGTCTCACATCTTC
1 ATCAGTAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
153987 AT
1 AT
153989 GTGGCAGTCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (38 bp):
ATCAGTAGAAAGGATTTAAGGTGCTCTCTCGCATCTTC
Found at i:157385 original size:94 final size:94
Alignment explanation
Indices: 157271--157453 Score: 348
Period size: 94 Copynumber: 1.9 Consensus size: 94
157261 CAGATTTATC
157271 CAAGATTCAAAGAGTGATACTATTCATCCATTACTAATGCAATCTAAGTCATTCATCCAAGAATT
1 CAAGATTCAAAGAGTGATACTATTCATCCATTACTAATGCAATCTAAGTCATTCATCCAAGAATT
157336 AAAGATACAACATTCAATCAAATTTCATT
66 AAAGATACAACATTCAATCAAATTTCATT
**
157365 CAAGATTTGAAGAGTGATACTATTCATCCATTACTAATGCAATCTAAGTCATTCATCCAAGAATT
1 CAAGATTCAAAGAGTGATACTATTCATCCATTACTAATGCAATCTAAGTCATTCATCCAAGAATT
157430 AAAGATACAACATTCAATCAAATT
66 AAAGATACAACATTCAATCAAATT
157454 CATCTAACTC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.31
Consensus pattern (94 bp):
CAAGATTCAAAGAGTGATACTATTCATCCATTACTAATGCAATCTAAGTCATTCATCCAAGAATT
AAAGATACAACATTCAATCAAATTTCATT
Found at i:157731 original size:17 final size:17
Alignment explanation
Indices: 157694--157733 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
157684 TTGATGCAAC
*
157694 GACAATAAAAATGCAGT
1 GACAATAAAAATGCAGG
**
157711 GACAATAAAAATGTGGG
1 GACAATAAAAATGCAGG
157728 GACAAT
1 GACAAT
157734 TATACTATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (17 bp):
GACAATAAAAATGCAGG
Found at i:161087 original size:37 final size:37
Alignment explanation
Indices: 160987--161101 Score: 108
Period size: 37 Copynumber: 3.1 Consensus size: 37
160977 TTTATGCAGT
* *
160987 GACAGTCTTGGGTGC-ATTTCAGAAGTGCTCATGCGGC
1 GACAGTTTTGGGAGCAATTT-AGAAGTGCTCATGCGGC
* * * **
161024 GACAATTTTGGGTA-TAATCTAGAAGTGCTCATTTGGC
1 GACAGTTTTGGG-AGCAATTTAGAAGTGCTCATGCGGC
* * *
161061 GACAGTTTTGGGAGCAATTTAAAAGTGCCCATGCAGC
1 GACAGTTTTGGGAGCAATTTAGAAGTGCTCATGCGGC
161098 GACA
1 GACA
161102 TTAGTAGTAA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
36 1 0.02
37 56 0.93
38 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (37 bp):
GACAGTTTTGGGAGCAATTTAGAAGTGCTCATGCGGC
Found at i:165996 original size:26 final size:26
Alignment explanation
Indices: 165953--166006 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
165943 ATTTTGGGTG
*
165953 CAATTCTGGATATATTCATGCAGCGA
1 CAATTCTGGACATATTCATGCAGCGA
*
165979 CAATTCTGGACATGTTCATGCAGCGA
1 CAATTCTGGACATATTCATGCAGCGA
166005 CA
1 CA
166007 TTCCTAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (26 bp):
CAATTCTGGACATATTCATGCAGCGA
Found at i:166037 original size:37 final size:38
Alignment explanation
Indices: 165996--166083 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
165986 GGACATGTTC
165996 ATGCAGCGACA-TTCCTAGG-TGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTT--TAGGATGCAATTTGAAGAATACTT
* * * *
166033 ATGCAGTGATAGTTTTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACAGTTTAGGATGCAATTTGAAGAATACTT
166071 ATGCAGCGACAGT
1 ATGCAGCGACAGT
166084 ATTGGGTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
36 3 0.07
37 14 0.33
38 25 0.60
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (38 bp):
ATGCAGCGACAGTTTAGGATGCAATTTGAAGAATACTT
Found at i:166616 original size:4 final size:4
Alignment explanation
Indices: 166607--166641 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
166597 TTATATAGTA
166607 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
166642 TCTATCTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:166671 original size:6 final size:6
Alignment explanation
Indices: 166660--166770 Score: 123
Period size: 6 Copynumber: 18.5 Consensus size: 6
166650 TCTATCTATC
* * * * *
166660 TATATA TATATA TCTATA GATATA GATATA TATATA TAGATA TAGATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
166708 TAGATA TATATA TATAGA TATAGA TATAGA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
166756 TAGATA GATATA TAT
1 TATATA TATATA TAT
166771 TTGTTTTCCA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (6 bp):
TATATA
Found at i:166688 original size:20 final size:20
Alignment explanation
Indices: 166660--166770 Score: 136
Period size: 20 Copynumber: 5.7 Consensus size: 20
166650 TCTATCTATC
* *
166660 TATATATATATATCTATAGA
1 TATAGATATATATATATAGA
166680 TATAGATATATATATATAGA
1 TATAGATATATATATATAGA
* *
166700 TATAGATATAGATATATATA
1 TATAGATATATATATATAGA
*
166720 TATAG--ATATAGATATAGA
1 TATAGATATATATATATAGA
* *
166738 TATATATATATATATATATA
1 TATAGATATATATATATAGA
*
166758 GATAGATATATAT
1 TATAGATATATAT
166771 TTGTTTTCCA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
18 14 0.18
20 63 0.82
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (20 bp):
TATAGATATATATATATAGA
Found at i:166689 original size:26 final size:26
Alignment explanation
Indices: 166660--166770 Score: 177
Period size: 26 Copynumber: 4.3 Consensus size: 26
166650 TCTATCTATC
**
166660 TATATATATATATCTATAGATATAGA
1 TATATATATATAGATATAGATATAGA
166686 TATATATATATAGATATAGATATAGA
1 TATATATATATAGATATAGATATAGA
166712 TATATATATATAGATATAGATATAGA
1 TATATATATATAGATATAGATATAGA
* * *
166738 TATATATATATATATATATAGATAGA
1 TATATATATATAGATATAGATATAGA
166764 TATATAT
1 TATATAT
166771 TTGTTTTCCA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.41
Consensus pattern (26 bp):
TATATATATATAGATATAGATATAGA
Found at i:170508 original size:26 final size:26
Alignment explanation
Indices: 170448--170501 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
170438 ATTTTGGGTG
*
170448 CAATTCTGGACACATTCATTCAGAGA
1 CAATTCTGGACACATTCATGCAGAGA
** *
170474 CAATTCTGGACATGTTCATGCAGTGA
1 CAATTCTGGACACATTCATGCAGAGA
170500 CA
1 CA
170502 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (26 bp):
CAATTCTGGACACATTCATGCAGAGA
Found at i:170666 original size:37 final size:37
Alignment explanation
Indices: 170572--170680 Score: 128
Period size: 37 Copynumber: 2.9 Consensus size: 37
170562 ATTTATGCAA
* * * * ** *
170572 CGACAGTCTTGGGTACATTCCGGAAATATTCTTGCGG
1 CGACAGTTTTGGGTACAATCTGGAAGTGCTCATGCGG
* *
170609 CGACATTTTTGGGTAAAATCTGGAAGTGCTCATGCGG
1 CGACAGTTTTGGGTACAATCTGGAAGTGCTCATGCGG
*
170646 CGACAGTTTTGGGTACAATCTAGAAGTGCTCATGC
1 CGACAGTTTTGGGTACAATCTGGAAGTGCTCATGC
170681 AGTGACATTA
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (37 bp):
CGACAGTTTTGGGTACAATCTGGAAGTGCTCATGCGG
Found at i:173724 original size:30 final size:30
Alignment explanation
Indices: 173688--173765 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
173678 TCCACTTAAC
* * **
173688 TTAGATAGCCACAGAGGCGTTCACACATTG
1 TTAGATAGCCACAAAGGCGCTCACACATCA
*
173718 TTAGATAGGCACAAAGGCGCTCACACATCA
1 TTAGATAGCCACAAAGGCGCTCACACATCA
*
173748 TTAGATAACCACAAAGGC
1 TTAGATAGCCACAAAGGC
173766 ATCCACTCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (30 bp):
TTAGATAGCCACAAAGGCGCTCACACATCA
Found at i:174007 original size:30 final size:30
Alignment explanation
Indices: 173973--174078 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
173963 GAATAGCCAA
* * * *
173973 AAAGGATTCCACATATGAGAGAATAACCAC
1 AAAGGCTTTCACATATCAGAGAACAACCAC
* * *
174003 AAAGGCTTTCATATATTAAAGAACAACCAC
1 AAAGGCTTTCACATATCAGAGAACAACCAC
174033 AAAGGCTTTCACATATCAGAGAACAACCAC
1 AAAGGCTTTCACATATCAGAGAACAACCAC
*
174063 AAAGGCTTTCATATAT
1 AAAGGCTTTCACATAT
174079 AGGTAATGGT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.22
Consensus pattern (30 bp):
AAAGGCTTTCACATATCAGAGAACAACCAC
Found at i:174530 original size:15 final size:16
Alignment explanation
Indices: 174506--174539 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
174496 CATGTAACTT
*
174506 ATGCACAGACTT-CTC
1 ATGCAAAGACTTACTC
174521 ATGCAAAGACTTACTC
1 ATGCAAAGACTTACTC
174537 ATG
1 ATG
174540 AAGAAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (16 bp):
ATGCAAAGACTTACTC
Found at i:180976 original size:15 final size:15
Alignment explanation
Indices: 180961--180990 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
180951 CTACGATGAT
180961 GATATCTATGAAGATG
1 GATA-CTATGAAGATG
180977 GATACTATGAAGAT
1 GATACTATGAAGAT
180991 TGGGAGATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (15 bp):
GATACTATGAAGATG
Found at i:199836 original size:19 final size:19
Alignment explanation
Indices: 199812--199851 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
199802 TTATAGCAAT
199812 TTTTCTTTT-TCTTTTCTCA
1 TTTTCTTTTCT-TTTTCTCA
199831 TTTTCTTTTCTTTTTCTCA
1 TTTTCTTTTCTTTTTCTCA
199850 TT
1 TT
199852 CAACATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTCTCA
Found at i:200616 original size:21 final size:21
Alignment explanation
Indices: 200591--200637 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
200581 CTCTCTTTCC
* *
200591 TCCTTGTGTTTCTTCTTTTTG
1 TCCTTGTGCTTCCTCTTTTTG
200612 TCCTTGTGCTTCCTCTTTTTG
1 TCCTTGTGCTTCCTCTTTTTG
200633 TCCTT
1 TCCTT
200638 CGTACCAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.13, T:0.62
Consensus pattern (21 bp):
TCCTTGTGCTTCCTCTTTTTG
Found at i:213990 original size:11 final size:11
Alignment explanation
Indices: 213974--214000 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
213964 TGAAATCAAG
213974 TATTTTCATAA
1 TATTTTCATAA
213985 TATTTTCATAA
1 TATTTTCATAA
213996 TATTT
1 TATTT
214001 AGTTAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTCATAA
Found at i:218325 original size:46 final size:46
Alignment explanation
Indices: 218241--218329 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
218231 AAATTGCATG
* * **
218241 CTTTGCCACGACACCGGTTCTGGTGTGTCGTAAAATCGACCCCTTT
1 CTTTGCCACAACACCGGTCCTGGTGTGTCACAAAATCGACCCCTTT
* * *
218287 CTTTGTCACAACACCGGTCCTGGTGTGTCACGACATCGACCCC
1 CTTTGCCACAACACCGGTCCTGGTGTGTCACAAAATCGACCCC
218330 AGACTTCAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.27
Consensus pattern (46 bp):
CTTTGCCACAACACCGGTCCTGGTGTGTCACAAAATCGACCCCTTT
Found at i:219486 original size:15 final size:15
Alignment explanation
Indices: 219453--219500 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
219443 TGACATTTAT
* *
219453 GATGATATCTCTGAC
1 GATGATATCTATGAA
219468 GATGATATCTATGAA
1 GATGATATCTATGAA
*
219483 GATGGGTAT-TATGAA
1 GAT-GATATCTATGAA
219498 GAT
1 GAT
219501 TGAAAGATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (15 bp):
GATGATATCTATGAA
Found at i:224695 original size:27 final size:27
Alignment explanation
Indices: 224664--224726 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
224654 TTGGTCTTTT
224664 CTTCTTCTTGTGGCGCTCTTAATTGCG
1 CTTCTTCTTGTGGCGCTCTTAATTGCG
*
224691 CTTCTTCTTGTGGCGCTCTTACTTGCG
1 CTTCTTCTTGTGGCGCTCTTAATTGCG
224718 CTTCTTCTT
1 CTTCTTCTT
224727 ATCATTGTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.05, C:0.29, G:0.19, T:0.48
Consensus pattern (27 bp):
CTTCTTCTTGTGGCGCTCTTAATTGCG
Found at i:224715 original size:15 final size:14
Alignment explanation
Indices: 224666--224715 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
224656 GGTCTTTTCT
224666 TCTTCTTGTGGCGC
1 TCTTCTTGTGGCGC
**
224680 TCTTAAT-T-GCGC
1 TCTTCTTGTGGCGC
224692 TTCTTCTTGTGGCGC
1 -TCTTCTTGTGGCGC
224707 TCTTACTTG
1 TCTT-CTTG
224716 CGCTTCTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 10 0.36
15 8 0.29
ACGTcount: A:0.06, C:0.26, G:0.22, T:0.46
Consensus pattern (14 bp):
TCTTCTTGTGGCGC
Found at i:258501 original size:26 final size:26
Alignment explanation
Indices: 258463--258536 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
258453 ACTAATGTAG
*
258463 CTGCATGAGCATGTCTAGAATTGTCA
1 CTGCATGAGCATGTCCAGAATTGTCA
* *
258489 CTGCATGAACATGTCCAGAATTGTCG
1 CTGCATGAGCATGTCCAGAATTGTCA
*
258515 TTGCATGAGCATGTCCAGAATT
1 CTGCATGAGCATGTCCAGAATT
258537 ATGCCTAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (26 bp):
CTGCATGAGCATGTCCAGAATTGTCA
Found at i:259037 original size:35 final size:35
Alignment explanation
Indices: 258998--259068 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
258988 ATCTATTTAA
258998 TCTTGCTTCTATTTTTTAATCTTTGGGTTTGAAAG
1 TCTTGCTTCTATTTTTTAATCTTTGGGTTTGAAAG
259033 TCTTGCTTCTATTTTTTAATCTTTGGGTTTGAAAG
1 TCTTGCTTCTATTTTTTAATCTTTGGGTTTGAAAG
259068 T
1 T
259069 TTTTAGCACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (35 bp):
TCTTGCTTCTATTTTTTAATCTTTGGGTTTGAAAG
Found at i:263899 original size:21 final size:21
Alignment explanation
Indices: 263873--263919 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
263863 TTAGTACCAA
* * *
263873 TAGAAGCATGATTTGTTTCGG
1 TAGAAGCATCACTTGTATCGG
*
263894 TAGAAGCTTCACTTGTATCGG
1 TAGAAGCATCACTTGTATCGG
263915 TAGAA
1 TAGAA
263920 TTGTCATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (21 bp):
TAGAAGCATCACTTGTATCGG
Found at i:272294 original size:19 final size:19
Alignment explanation
Indices: 272270--272319 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
272260 AAAAATTTCA
*
272270 TTCTTTTTTTTTTCTCTTT
1 TTCTTTTTTTTTTCTCATT
**
272289 TTCTTTCCTTTTTCTCATT
1 TTCTTTTTTTTTTCTCATT
*
272308 TTGTTTCTTTTT
1 TTCTTT-TTTTT
272320 CAAATGACTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (19 bp):
TTCTTTTTTTTTTCTCATT
Found at i:272317 original size:18 final size:19
Alignment explanation
Indices: 272278--272320 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
272268 CATTCTTTTT
*
272278 TTTTTCTCTTTTTCTTTCC
1 TTTTTCTCATTTTCTTTCC
*
272297 TTTTTCTCATTTTGTTT-C
1 TTTTTCTCATTTTCTTTCC
272315 TTTTTC
1 TTTTTC
272321 AAATGACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTCTCATTTTCTTTCC
Found at i:276957 original size:52 final size:52
Alignment explanation
Indices: 276882--277072 Score: 301
Period size: 52 Copynumber: 3.7 Consensus size: 52
276872 TTGTTCTGTA
* * *
276882 AAGGAATTCATATACTCATGATGACACTTAGTCATCGGACCATATAATCCATG
1 AAGG-ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATG
*
276935 AAGGATTCATGTACTCACGATGACACTTAGTCATCAGACCTTATAATCCATG
1 AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATG
* * * *
276987 AAAGATTCATGTACTCACGATAACACTTAATCATCGAACCTTATAATCCATG
1 AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATG
277039 AAGGATTCATGTACTCACGATGACACTTAGTCAT
1 AAGGATTCATGTACTCACGATGACACTTAGTCAT
277073 TAGAACTTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
52 122 0.97
53 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (52 bp):
AAGGATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATG
Found at i:277981 original size:20 final size:21
Alignment explanation
Indices: 277946--277989 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
277936 ACTTTCATCA
* *
277946 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
277967 TTAACCTTT-ATTAAACATAT
1 TTAACCTTTAATTAAACATAT
277987 TTA
1 TTA
277990 TAATCAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:284060 original size:34 final size:34
Alignment explanation
Indices: 284016--284121 Score: 113
Period size: 34 Copynumber: 3.0 Consensus size: 34
284006 ACATGAGTCT
* *
284016 ATTCAAAATAGTTCCTAGAATTGTCACTGCATGA
1 ATTCAAAATAGTGCCCAGAATTGTCACTGCATGA
*
284050 ATTCAGAATAGTGCCCAGAATTGTCACTGCATGA
1 ATTCAAAATAGTGCCCAGAATTGTCACTGCATGA
* * * *
284084 CGATGTCCAATATTGCGCCCAAAATTGTCACTGCATGA
1 --AT-T-CAAAATAGTGCCCAGAATTGTCACTGCATGA
284122 CGATGTCCAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 31 0.52
36 2 0.03
37 1 0.02
38 26 0.43
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (34 bp):
ATTCAAAATAGTGCCCAGAATTGTCACTGCATGA
Found at i:285897 original size:45 final size:45
Alignment explanation
Indices: 285848--285938 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
285838 CTCAAATTGC
285848 TTCGAAAAATTATTCTCATACTTTTACTGCATTTTTTTATTTTAT
1 TTCGAAAAATTATTCTCATACTTTTACTGCATTTTTTTATTTTAT
285893 TTCGAAAAATTATTCTCATACTTTTACTGCATTTTTTTATTTTAT
1 TTCGAAAAATTATTCTCATACTTTTACTGCATTTTTTTATTTTAT
285938 T
1 T
285939 ACTCCAACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.56
Consensus pattern (45 bp):
TTCGAAAAATTATTCTCATACTTTTACTGCATTTTTTTATTTTAT
Found at i:292215 original size:17 final size:17
Alignment explanation
Indices: 292176--292224 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
292166 ATATATATGG
* **
292176 AAATGCAATGACAATGT
1 AAATGCAGTGACAATAA
*
292193 AGATGCAGTGACAATAA
1 AAATGCAGTGACAATAA
*
292210 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
292225 TATACTACAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.18
Consensus pattern (17 bp):
AAATGCAGTGACAATAA
Found at i:308800 original size:23 final size:23
Alignment explanation
Indices: 308769--308823 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
308759 CCATGAATTG
*
308769 TTTATGGTTGTCGAATTTGGAGAT
1 TTTA-GGTTATCGAATTTGGAGAT
* *
308793 TTTAGGTTATTGAATTTGGGGAT
1 TTTAGGTTATCGAATTTGGAGAT
308816 TTTAGGTT
1 TTTAGGTT
308824 TTGGGTGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (23 bp):
TTTAGGTTATCGAATTTGGAGAT
Found at i:308874 original size:27 final size:28
Alignment explanation
Indices: 308835--308907 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
308825 TGGGTGGTCG
*
308835 AATTTGGGGATTTTGGGTAAGGG-TTTT
1 AATTTGGGAATTTTGGGTAAGGGTTTTT
* * *
308862 AATTTGGGAATTTTTGTTTAGGGTTTTT
1 AATTTGGGAATTTTGGGTAAGGGTTTTT
* *
308890 GATTTTGGAGATTTTGGG
1 AATTTGGGA-ATTTTGGG
308908 CTAGTGCTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 19 0.53
28 11 0.31
29 6 0.17
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (28 bp):
AATTTGGGAATTTTGGGTAAGGGTTTTT
Found at i:309499 original size:11 final size:11
Alignment explanation
Indices: 309483--309520 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
309473 GATGATGATT
309483 ATAATTTTAAA
1 ATAATTTTAAA
309494 ATAATTTT--A
1 ATAATTTTAAA
309503 ATAATTTTAAA
1 ATAATTTTAAA
*
309514 ATCATTT
1 ATAATTT
309521 GCTGACGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:309508 original size:20 final size:20
Alignment explanation
Indices: 309483--309520 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
309473 GATGATGATT
309483 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
*
309503 ATAATTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
309521 GCTGACGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:317804 original size:14 final size:14
Alignment explanation
Indices: 317785--317816 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
317775 GGGTAATCCA
317785 AGTAGCCTAGAGAT
1 AGTAGCCTAGAGAT
317799 AGTAGCCTAGAGAT
1 AGTAGCCTAGAGAT
317813 AGTA
1 AGTA
317817 TATTCTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (14 bp):
AGTAGCCTAGAGAT
Found at i:319275 original size:23 final size:23
Alignment explanation
Indices: 319245--319296 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
319235 CATCTTGGAA
319245 TGCGTTAGCAACACAATTTGTTT
1 TGCGTTAGCAACACAATTTGTTT
319268 TGCGTTAGCAACACAATTTGTTT
1 TGCGTTAGCAACACAATTTGTTT
319291 TGCGTT
1 TGCGTT
319297 TCAATCTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (23 bp):
TGCGTTAGCAACACAATTTGTTT
Found at i:333727 original size:16 final size:18
Alignment explanation
Indices: 333679--333732 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 18
333669 TGTGGGTATT
333679 AAGGAAGTAAAAGAAGAAGAG
1 AAGGAAGT--AAGAA-AAGAG
333700 AAGGAAGT-AGAAAAG-G
1 AAGGAAGTAAGAAAAGAG
333716 AA-GAAGTAAGAAAAGAG
1 AAGGAAGTAAGAAAAGAG
333733 GAATTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.16
16 10 0.32
17 4 0.13
18 4 0.13
21 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (18 bp):
AAGGAAGTAAGAAAAGAG
Found at i:338540 original size:158 final size:158
Alignment explanation
Indices: 338131--338541 Score: 495
Period size: 158 Copynumber: 2.6 Consensus size: 158
338121 GTTAAGATGT
* * * * * *
338131 TACACGATGCTGCTCAGAAGAGCTGTGGAGAATCCGTAACAAAAGCTGGATCTTAGCCATCGATA
1 TACACGATGCTGCTCACACGAGCTGTGGAGAATCTGTAACAAATGTTGGATCTCAGCCATCGATA
* * ** **
338196 GGACATCTAAGACCAACACCCATATGACATGTAATGCTCACACAAGATATGAAGTAGGCCTGCTT
66 GGACATCTAAGACCAACACCCATATGACCTGTAATGCTCACACAAGATATCAAGTAGGCCAACAC
* * * *
338261 ACATAAGCTGTGGATCAATATGTTAGGC
131 ACACAAGCTGTGGATCAAGATATTAGAC
* * * * *
338289 TACACGATGCTACTCACACGAGCTGTGGAGAATCTGTTACAAATGTCGAATCTCAACCATCGATA
1 TACACGATGCTGCTCACACGAGCTGTGGAGAATCTGTAACAAATGTTGGATCTCAGCCATCGATA
* * *
338354 GGACATCTAAGACCAGA-ACCCATATGACCTGTAATGCTCACACAAGCTGTCAAGTGGGCCAACA
66 GGACATCTAAGACCA-ACACCCATATGACCTGTAATGCTCACACAAGATATCAAGTAGGCCAACA
* *
338418 CACACGAGCTGT-GAGTTAAGATATTAGAC
130 CACACAAGCTGTGGA-TCAAGATATTAGAC
* ** * *
338447 TACACGATGTTGCTCACACGAGCTGTGGAGAATCTACAATAAATGTTGGATCTCAGTCATC-AGT
1 TACACGATGCTGCTCACACGAGCTGTGGAGAATCTGTAACAAATGTTGGATCTCAGCCATCGA-T
338511 AGGACATCTAAGACCAACACCCATATGACCT
65 AGGACATCTAAGACCAACACCCATATGACCT
338542 ATAAATCCTG
Statistics
Matches: 213, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
157 4 0.02
158 208 0.98
159 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (158 bp):
TACACGATGCTGCTCACACGAGCTGTGGAGAATCTGTAACAAATGTTGGATCTCAGCCATCGATA
GGACATCTAAGACCAACACCCATATGACCTGTAATGCTCACACAAGATATCAAGTAGGCCAACAC
ACACAAGCTGTGGATCAAGATATTAGAC
Found at i:351724 original size:16 final size:16
Alignment explanation
Indices: 351700--351730 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
351690 AAGAAAACTA
351700 AAATCAAATAACAAAT
1 AAATCAAATAACAAAT
*
351716 AAATGAAATAACAAA
1 AAATCAAATAACAAA
351731 AGAAAGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.03, T:0.16
Consensus pattern (16 bp):
AAATCAAATAACAAAT
Found at i:361612 original size:89 final size:89
Alignment explanation
Indices: 361457--361625 Score: 275
Period size: 89 Copynumber: 1.9 Consensus size: 89
361447 TTGTGACCAA
* *
361457 TTTTCCTTAAAGTAAAAATGAATACCAAGTTGTATGACAAATTTTACTTTGGCCTTAAATTCAAA
1 TTTTCCTTAAAGTAAAAATGAATACCAAGTTGTATAACAAATTTTACTTTGACCTTAAATTCAAA
361522 ATGCCTTTTATTAAGGGGAAGCAG
66 ATGCCTTTTATTAAGGGGAAGCAG
* * * *
361546 TTTTCTTTAAAGTAAAAATGAATGCCAAGTTTTATAACAAATTTTACTTTGACCTTAAATTTAAA
1 TTTTCCTTAAAGTAAAAATGAATACCAAGTTGTATAACAAATTTTACTTTGACCTTAAATTCAAA
*
361611 ATGTCTTTTATTAAG
66 ATGCCTTTTATTAAG
361626 CGGGTGCAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (89 bp):
TTTTCCTTAAAGTAAAAATGAATACCAAGTTGTATAACAAATTTTACTTTGACCTTAAATTCAAA
ATGCCTTTTATTAAGGGGAAGCAG
Found at i:362902 original size:3 final size:3
Alignment explanation
Indices: 362894--362943 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
362884 GCAAAAAAGT
*
362894 AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
362942 AG
1 AG
362944 TTGATGATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:362951 original size:3 final size:3
Alignment explanation
Indices: 362945--362972 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
362935 AAGAAGAAGT
362945 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
362973 TCCATGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:363138 original size:6 final size:6
Alignment explanation
Indices: 363120--363157 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
363110 TAAATTGAGG
363120 AAAAG- AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
363158 AACCCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 8 0.26
6 23 0.74
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:376862 original size:275 final size:277
Alignment explanation
Indices: 376188--376958 Score: 1208
Period size: 277 Copynumber: 2.8 Consensus size: 277
376178 TACAGTTTCT
*
376188 GCTGCTCGTCAATGTGGATGATTCTGTCTAGCAAAATATTATCCAATGCTTAAACTGCCATTGAC
1 GCTGCTCGTCAATGTGGATGATTCTGTCTAGCAAAATATTATCCAATGC-TAAACAGCCATTGAC
* * * *
376253 CATTCTACTTCCAAGTAGTCTACCAATCATGTGGATAGGATTTTCTACTGAGTAACCTTTTGCTC
65 CATTCTACTTCCAAGTAGACTACCATTCATGTGGATAGGATTTTCTACCGAGTAACCTTTTGCAC
* *
376318 AATGATCCATCTTTTTGGTCTAGCTGATTTATGGTAACCCTTTTTAGCAGTTCCAATGATACAAA
130 AATGATCCATCTTTTTGATCTAGCTGATTTATGGTAACCCTTTTAAGCAGTTCCAATGATACAAA
* * * *
376383 ATGTAGTTTGACCCTTACCCTTTCACGTGGATAGGATTTTCTACAAAGTAACCTTATGCTCAGTG
195 AAGTAGTTTGACCCATACCCATTCACGTGGATAGGATTTTCTACAAAGTAACCTTATGCTCAATG
376448 ATCCATCTTTTTGATCTA
260 ATCCATCTTTTTGATCTA
***
376466 GCTGCTCGTCAATGTGGATGATTCTGTCT-GACAAAATATTATCCAATGCTTGGCAGCCATTGAC
1 GCTGCTCGTCAATGTGGATGATTCTGTCTAG-CAAAATATTATCCAATGCTAAACAGCCATTGAC
* * * * *
376530 CATTCTACTTCCAAGCAGATTACCATTCATGTGGATAGGATTTTCTATCGGGTAACCTTTTGCCC
65 CATTCTACTTCCAAGTAGACTACCATTCATGTGGATAGGATTTTCTACCGAGTAACCTTTTGCAC
** *
376595 AATGATCCATCTTTTTGATCTAGCTGATTTATGGTAGTCCTTTTAAGCAGTTCCAATGATGCAAA
130 AATGATCCATCTTTTTGATCTAGCTGATTTATGGTAACCCTTTTAAGCAGTTCCAATGATACAAA
* ** *
376660 AAGTAGTTTGACCCATACCCATTCATGTGGATAGGATTTTCTA-TGAGTAACCTTTTGCTCAATG
195 AAGTAGTTTGACCCATACCCATTCACGTGGATAGGATTTTCTACAAAGTAACCTTATGCTCAATG
376724 ATCCA-CTTTTTGATCTA
260 ATCCATCTTTTTGATCTA
*
376741 GCTGCTCATCAATGTGGATGATTCTGTCTAGCAAAATATTATCCAATGCTAAACAGCCATTGACC
1 GCTGCTCGTCAATGTGGATGATTCTGTCTAGCAAAATATTATCCAATGCTAAACAGCCATTGACC
*
376806 ATTCTACTTACAAGTAGACTACCATTCATGTGGATAGGATTTTCTACCGAGTAACCTTTTTGCAC
66 ATTCTACTTCCAAGTAGACTACCATTCATGTGGATAGGATTTTCTACCGAGTAACC-TTTTGCAC
*
376871 AATGATCCATCCTTTTT-ATCTAGCTGATTTATGGTAACCCTTTTAAGCAGTTCCAATGATACAG
130 AATGATCCAT-CTTTTTGATCTAGCTGATTTATGGTAACCCTTTTAAGCAGTTCCAATGATACAA
*
376935 AAATTAGTTTGACCCATACCCATT
194 AAAGTAGTTTGACCCATACCCATT
376959 AGCTGGATCC
Statistics
Matches: 449, Mismatches: 40, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
275 122 0.27
276 106 0.24
277 174 0.39
278 47 0.10
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (277 bp):
GCTGCTCGTCAATGTGGATGATTCTGTCTAGCAAAATATTATCCAATGCTAAACAGCCATTGACC
ATTCTACTTCCAAGTAGACTACCATTCATGTGGATAGGATTTTCTACCGAGTAACCTTTTGCACA
ATGATCCATCTTTTTGATCTAGCTGATTTATGGTAACCCTTTTAAGCAGTTCCAATGATACAAAA
AGTAGTTTGACCCATACCCATTCACGTGGATAGGATTTTCTACAAAGTAACCTTATGCTCAATGA
TCCATCTTTTTGATCTA
Found at i:379112 original size:114 final size:114
Alignment explanation
Indices: 378912--379140 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
378902 ATATTGCATT
378912 GGAAGAAAATAGCTAGAAGAAACATAGTCCAGATGCTATGTAGCAATGCAGTTTCTTTTATTTCT
1 GGAAGAAAATAGCTAGAAGAAACATAGTCCAGATGCTATGTAGCAATGCAGTTTCTTTTATTTCT
378977 AAATTGGCTAATAAATCAGCCAATGCAAACATAGACACCAAGCTAGTTG
66 AAATTGGCTAATAAATCAGCCAATGCAAACATAGACACCAAGCTAGTTG
379026 GGAAGAAAATAGCTAGAAGAAACATAGTCCAGATGCTATGTAGCAATGCAGTTTCTTTTATTTCT
1 GGAAGAAAATAGCTAGAAGAAACATAGTCCAGATGCTATGTAGCAATGCAGTTTCTTTTATTTCT
379091 AAATTGGCTAATAAATCAGCCAATGCAAACATAGACACCAAGCTAGTTG
66 AAATTGGCTAATAAATCAGCCAATGCAAACATAGACACCAAGCTAGTTG
379140 G
1 G
379141 TTTCAGTTAC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (114 bp):
GGAAGAAAATAGCTAGAAGAAACATAGTCCAGATGCTATGTAGCAATGCAGTTTCTTTTATTTCT
AAATTGGCTAATAAATCAGCCAATGCAAACATAGACACCAAGCTAGTTG
Found at i:387197 original size:21 final size:21
Alignment explanation
Indices: 387158--387199 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
387148 ATGTGTTTAA
*
387158 TAATTAATTATCAAATTAAAT
1 TAATTAATAATCAAATTAAAT
* *
387179 TAATTAATAATTAATTTAAAT
1 TAATTAATAATCAAATTAAAT
387200 CATGTGAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAATAATCAAATTAAAT
Found at i:394098 original size:22 final size:22
Alignment explanation
Indices: 394071--394115 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
394061 AGCTTGATTG
**
394071 AAATTGGTAAATTTTATGTTGA
1 AAATTGGTAAATTAGATGTTGA
*
394093 AAATTGTTAAATTAGATGTTGA
1 AAATTGGTAAATTAGATGTTGA
394115 A
1 A
394116 TGGGTTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (22 bp):
AAATTGGTAAATTAGATGTTGA
Found at i:395658 original size:19 final size:18
Alignment explanation
Indices: 395634--395671 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
395624 ATTTAATTAA
395634 TAATGAA-ATTATATTTATT
1 TAATGAACA-TATA-TTATT
395653 TAATGAACATATATTATT
1 TAATGAACATATATTATT
395671 T
1 T
395672 CATAAGTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 11 0.61
20 1 0.06
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
TAATGAACATATATTATT
Found at i:429034 original size:36 final size:36
Alignment explanation
Indices: 428964--429248 Score: 275
Period size: 36 Copynumber: 7.9 Consensus size: 36
428954 GAGCTATTCC
* * * * * *
428964 TAGCATTATGCTATAACTGAGACATAAACTATCACA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* *
429000 TAGCATTA-GACTCTAGCCGAGATGTAAGCAATCACA
1 TAGCATTACG-CTCTAACCGAGACGTAAGCAATCACA
* * * *
429036 TATCGTTACGCTCTAACCGAGACATAAACAATCACA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* *
429072 TAGCATTACGCTCTAACTGAGACGTAAGCAATCATA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* * * * *
429108 TAACATTATGCTCAAATCGAGACGTAAACAATCACA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* * * * * *
429144 TATCATTATGCTCTAACTGAGACATAAGTAATCAAA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* * *
429180 TAGCATTACGCTCTAATCGAGACATAAGCAGTCACA
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
* * *
429216 TAGCATTATGCTCTAACTGAGATGTAAGCAATC
1 TAGCATTACGCTCTAACCGAGACGTAAGCAATC
429249 CATCAAAGTG
Statistics
Matches: 200, Mismatches: 47, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
35 1 0.00
36 198 0.99
37 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (36 bp):
TAGCATTACGCTCTAACCGAGACGTAAGCAATCACA
Found at i:429099 original size:72 final size:72
Alignment explanation
Indices: 428967--429248 Score: 332
Period size: 72 Copynumber: 3.9 Consensus size: 72
428957 CTATTCCTAG
* * * * * * *
428967 CATTATGCTATAACTGAGACATAAACTATCACATAGCATTA-GACTCTAGCCGAGATGTAAGCAA
1 CATTACGCTCTAACCGAGACATAAACAATCACATAGCATTATG-CTCTAACTGAGACGTAAGCAA
* *
429031 TCACATAT
65 TCAAATAA
* *
429039 CGTTACGCTCTAACCGAGACATAAACAATCACATAGCATTACGCTCTAACTGAGACGTAAGCAAT
1 CATTACGCTCTAACCGAGACATAAACAATCACATAGCATTATGCTCTAACTGAGACGTAAGCAAT
*
429104 CATATAA
66 CAAATAA
* * * * * * *
429111 CATTATGCTCAAATCGAGACGTAAACAATCACATATCATTATGCTCTAACTGAGACATAAGTAAT
1 CATTACGCTCTAACCGAGACATAAACAATCACATAGCATTATGCTCTAACTGAGACGTAAGCAAT
*
429176 CAAATAG
66 CAAATAA
* * * *
429183 CATTACGCTCTAATCGAGACATAAGCAGTCACATAGCATTATGCTCTAACTGAGATGTAAGCAAT
1 CATTACGCTCTAACCGAGACATAAACAATCACATAGCATTATGCTCTAACTGAGACGTAAGCAAT
429248 C
66 C
429249 CATCAAAGTG
Statistics
Matches: 179, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
72 178 0.99
73 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (72 bp):
CATTACGCTCTAACCGAGACATAAACAATCACATAGCATTATGCTCTAACTGAGACGTAAGCAAT
CAAATAA
Found at i:429157 original size:108 final size:108
Alignment explanation
Indices: 428964--429248 Score: 331
Period size: 108 Copynumber: 2.6 Consensus size: 108
428954 GAGCTATTCC
* * * * * * * *
428964 TAGCATTATGCTATAACTGAGACATAAACTATCACATAGCATTA-GACTCTAGCCGAGATGTAAG
1 TAGCATTACGCTCTAACTGAGACATAAGCAATCACATAGCATTATG-CTCAAACCGAGACGTAAA
* *
429028 CAATCACATATCGTTACGCTCTAACCGAGACATAAACAATCACA
65 CAATCACATATCATTACGCTCTAACCGAGACATAAACAATCAAA
* * * *
429072 TAGCATTACGCTCTAACTGAGACGTAAGCAATCATATAACATTATGCTCAAATCGAGACGTAAAC
1 TAGCATTACGCTCTAACTGAGACATAAGCAATCACATAGCATTATGCTCAAACCGAGACGTAAAC
* * **
429137 AATCACATATCATTATGCTCTAACTGAGACATAAGTAATCAAA
66 AATCACATATCATTACGCTCTAACCGAGACATAAACAATCAAA
* * * * *
429180 TAGCATTACGCTCTAA-TCGAGACATAAGCAGTCACATAGCATTATGCTCTAACTGAGATGTAAG
1 TAGCATTACGCTCTAACT-GAGACATAAGCAATCACATAGCATTATGCTCAAACCGAGACGTAAA
429244 CAATC
65 CAATC
429249 CATCAAAGTG
Statistics
Matches: 148, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
107 1 0.01
108 146 0.99
109 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (108 bp):
TAGCATTACGCTCTAACTGAGACATAAGCAATCACATAGCATTATGCTCAAACCGAGACGTAAAC
AATCACATATCATTACGCTCTAACCGAGACATAAACAATCAAA
Done.