Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010105.1 Kokia drynarioides strain JFW-HI SEQ_124891, 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: 523673
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1042 original size:51 final size:51
Alignment explanation
Indices: 974--1159 Score: 198
Period size: 51 Copynumber: 3.6 Consensus size: 51
964 GCTATAAACG
*
974 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGG-TCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
1026 AAAAGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** * **
1077 AAAGGTCCGATGACTCCGTGTCATCGTGAGT--ATGAATTCCTATACGGAAC
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
* *
1127 AAGAGGTTTAATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCTGATGACTA-AGTGTCATCGTGAGTA
1160 TTAAATGAAT
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
49 5 0.05
50 9 0.08
51 92 0.84
52 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:1098 original size:102 final size:103
Alignment explanation
Indices: 974--1159 Score: 245
Period size: 102 Copynumber: 1.8 Consensus size: 103
964 GCTATAAACG
* ** *
974 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AAGTCTGAT
1 AAAGGATCCGATGACTAAGTGTCATCGTGAGT--ATGAATTCCTATACGGAACAAGAAGTCTAAT
1037 GACTA-AGTGTCATCGTGAGTAAATGAATCCATGATGGATT
64 GACTATA-TGTCATCGTGAGTAAATGAATCCATGATGGATT
** * *
1077 AAAGG-TCCGATGACTCCGTGTCATCGTGAGTATGAATTCCTATACGGAACAAGAGGTTTAATGA
1 AAAGGATCCGATGACTAAGTGTCATCGTGAGTATGAATTCCTATACGGAACAAGAAGTCTAATGA
1141 CTATATGTCATCGTGAGTA
66 CTATATGTCATCGTGAGTA
1160 TTAAATGAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
100 5 0.07
101 12 0.17
102 49 0.68
103 6 0.08
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (103 bp):
AAAGGATCCGATGACTAAGTGTCATCGTGAGTATGAATTCCTATACGGAACAAGAAGTCTAATGA
CTATATGTCATCGTGAGTAAATGAATCCATGATGGATT
Found at i:5901 original size:17 final size:17
Alignment explanation
Indices: 5871--5960 Score: 60
Period size: 17 Copynumber: 5.2 Consensus size: 17
5861 AATAACATTC
5871 AAACAACTAA-AACAGCAA
1 AAACAA-TAACAACA-CAA
*
5889 TAA-AATAACAACA-AA
1 AAACAATAACAACACAA
5904 ACAACAATAACAACAACAA
1 A-AACAATAACAAC-ACAA
* *
5923 AAATAATAACAAAACAA
1 AAACAATAACAACACAA
* * *
5940 CAACAAAAATAACAGCAA
1 AAACAATAACAACA-CAA
5958 AAA
1 AAA
5961 TAGAAACAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
15 2 0.04
16 5 0.09
17 28 0.50
18 18 0.32
19 3 0.05
ACGTcount: A:0.71, C:0.19, G:0.02, T:0.08
Consensus pattern (17 bp):
AAACAATAACAACACAA
Found at i:5909 original size:3 final size:3
Alignment explanation
Indices: 5895--5945 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
5885 GCAATAAAAT
* * * *
5895 AAC AAC AA- AAC AAC AAT AAC AAC AAC AAA AAT AAT AAC AA- AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
5941 AAC AA
1 AAC AA
5946 AAATAACAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.73, C:0.22, G:0.00, T:0.06
Consensus pattern (3 bp):
AAC
Found at i:5920 original size:20 final size:20
Alignment explanation
Indices: 5872--5953 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
5862 ATAACATTCA
* *
5872 AACAACTAAAACAGCAATAAAAT
1 AACAAC-AAAACAACAAT--AAC
5895 AACAACAAAACAACAATAAC
1 AACAACAAAACAACAATAAC
*
5915 AACAAC-AAA-AATAATAAC
1 AACAACAAAACAACAATAAC
*
5933 AA-AACAACAACAAAAATAAC
1 AACAACAA-AACAACAATAAC
5953 A
1 A
5954 GCAAAAATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.06
18 11 0.21
19 5 0.10
20 17 0.33
22 10 0.19
23 6 0.12
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.09
Consensus pattern (20 bp):
AACAACAAAACAACAATAAC
Found at i:5933 original size:35 final size:35
Alignment explanation
Indices: 5892--5989 Score: 103
Period size: 35 Copynumber: 2.8 Consensus size: 35
5882 ACAGCAATAA
*
5892 AATAACAACAA-AACAACAATAACAACAACAAAAAT
1 AATAACAA-AACAACAACAAAAACAACAACAAAAAT
* *
5927 AATAACAAAACAACAACAAAAATAACAGCAAAAAT
1 AATAACAAAACAACAACAAAAACAACAACAAAAAT
*
5962 AGA-AACAAAA-ATAGCAACAAAAATAACA
1 A-ATAACAAAACA-A-CAACAAAAACAACA
5990 GTAAAACAGC
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
34 3 0.05
35 38 0.68
36 15 0.27
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.08
Consensus pattern (35 bp):
AATAACAAAACAACAACAAAAACAACAACAAAAAT
Found at i:5938 original size:23 final size:24
Alignment explanation
Indices: 5906--5951 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
5896 ACAACAAAAC
5906 AACAATAACAACAACAAAAATAAT
1 AACAATAACAACAACAAAAATAAT
5930 AACAA-AACAACAACAAAAATAA
1 AACAATAACAACAACAAAAATAA
5952 CAGCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.09
Consensus pattern (24 bp):
AACAATAACAACAACAAAAATAAT
Found at i:5995 original size:12 final size:12
Alignment explanation
Indices: 5903--5989 Score: 97
Period size: 12 Copynumber: 7.3 Consensus size: 12
5893 ATAACAACAA
* *
5903 AACAACAATAAC
1 AACAACAAAAAT
5915 AACAACAAAAAT
1 AACAACAAAAAT
* *
5927 AATAAC-AAAAC
1 AACAACAAAAAT
5938 AACAACAAAAAT
1 AACAACAAAAAT
*
5950 AACAGCAAAAAT
1 AACAACAAAAAT
5962 AGA-AACAAAAAT
1 A-ACAACAAAAAT
*
5974 AGCAACAAAAAT
1 AACAACAAAAAT
5986 AACA
1 AACA
5990 GTAAAACAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
11 9 0.15
12 52 0.84
13 1 0.02
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:6016 original size:44 final size:43
Alignment explanation
Indices: 5976--6062 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
5966 ACAAAAATAG
* *
5976 CAACA-AAAATAACAGTAAAACAGCAATCAAAACAATAAAAAAAA
1 CAACACAAAATAACA--AAAAAAGCAACCAAAACAATAAAAAAAA
* *
6020 CAACACCAAAATAACAAAAAAAGCAACCAAAATAGTAAAAAAA
1 CAACA-CAAAATAACAAAAAAAGCAACCAAAACAATAAAAAAA
6063 TAGCACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 28 0.76
46 9 0.24
ACGTcount: A:0.70, C:0.17, G:0.05, T:0.08
Consensus pattern (43 bp):
CAACACAAAATAACAAAAAAAGCAACCAAAACAATAAAAAAAA
Found at i:6018 original size:23 final size:22
Alignment explanation
Indices: 5992--6079 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 22
5982 AAATAACAGT
* *
5992 AAAACAGCAATCAAAACAATAA
1 AAAAAAGCAACCAAAACAATAA
* *
6014 AAAAAA-CAACACCAAAATAA-CA
1 AAAAAAGC-A-ACCAAAACAATAA
* *
6036 AAAAAAGCAACCAAAATAGTAA
1 AAAAAAGCAACCAAAACAATAA
6058 AAAAATAGC-ACCAAAACAATAA
1 AAAAA-AGCAACCAAAACAATAA
6080 TATAATTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 10 0.19
22 31 0.58
23 12 0.23
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.08
Consensus pattern (22 bp):
AAAAAAGCAACCAAAACAATAA
Found at i:6038 original size:22 final size:22
Alignment explanation
Indices: 6013--6073 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
6003 CAAAACAATA
6013 AAAAAAACAACACCAAAATAAC
1 AAAAAAACAACACCAAAATAAC
**
6035 AAAAAAAGC-A-ACCAAAATAGT
1 AAAAAAA-CAACACCAAAATAAC
* *
6056 AAAAAAATAGCACCAAAA
1 AAAAAAACAACACCAAAA
6074 CAATAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 16 0.50
22 15 0.47
23 1 0.03
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAAAACAACACCAAAATAAC
Found at i:6041 original size:11 final size:11
Alignment explanation
Indices: 5879--6051 Score: 73
Period size: 12 Copynumber: 15.1 Consensus size: 11
5869 TCAAACAACT
* *
5879 AAAACAGCAAT
1 AAAACAACAAA
* *
5890 AAAATAACAAC
1 AAAACAACAAA
5901 AAAACAACAATA
1 AAAACAACAA-A
*
5913 ACAACAACAAA
1 AAAACAACAAA
*
5924 AATAATAACAAA
1 AA-AACAACAAA
*
5936 ACAACAACAAA
1 AAAACAACAAA
*
5947 AATAACAGCAAA
1 AA-AACAACAAA
5959 AATAGA-AACAAA
1 AA-A-ACAACAAA
*
5971 AATAGCAAC--A
1 AA-AACAACAAA
* **
5981 AAAATAACAGT
1 AAAACAACAAA
* *
5992 AAAACAGCAATC
1 AAAACAACAA-A
*
6004 AAAACAATAAAA
1 AAAACAA-CAAA
**
6016 AAAACAACACC
1 AAAACAACAAA
*
6027 AAAATAACAAA
1 AAAACAACAAA
6038 AAAAGCAACCAAA
1 AAAA-CAA-CAAA
6051 A
1 A
6052 TAGTAAAAAA
Statistics
Matches: 120, Mismatches: 31, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
9 4 0.03
10 3 0.03
11 48 0.40
12 57 0.47
13 8 0.07
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.08
Consensus pattern (11 bp):
AAAACAACAAA
Found at i:9675 original size:29 final size:29
Alignment explanation
Indices: 9611--9676 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
9601 GACATATATG
* *
9611 TCGTTTTTATAATTATTTAAGGGTTTGCA
1 TCGTTTTTAAAATTATTTAAGGGTTAGCA
*
9640 TCATTTTTAAAATTATTT-AGGGATATAG-A
1 TCGTTTTTAAAATTATTTAAGGG-T-TAGCA
9669 TCGTTTTT
1 TCGTTTTT
9677 GGCTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 25 0.81
30 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (29 bp):
TCGTTTTTAAAATTATTTAAGGGTTAGCA
Found at i:9714 original size:16 final size:16
Alignment explanation
Indices: 9693--9723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9683 AAAAATATTC
9693 TATTTATTTATTTACT
1 TATTTATTTATTTACT
*
9709 TATTTATTTCTTTAC
1 TATTTATTTATTTAC
9724 ATCATAAAAT
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:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTATTTACT
Found at i:12034 original size:15 final size:15
Alignment explanation
Indices: 12014--12048 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
12004 AATTAATAAA
12014 AAATTAATAAAATTT
1 AAATTAATAAAATTT
12029 AAATTAATAAAATTT
1 AAATTAATAAAATTT
12044 AAATT
1 AAATT
12049 TTCGTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTAATAAAATTT
Found at i:12519 original size:17 final size:18
Alignment explanation
Indices: 12487--12524 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
12477 CTAATATTTT
*
12487 TTTTATAAATTTTAATAA
1 TTTTATAAATTCTAATAA
*
12505 TTTTAT-AATTCTAATTA
1 TTTTATAAATTCTAATAA
12522 TTT
1 TTT
12525 CTTTGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATAAATTCTAATAA
Found at i:14045 original size:31 final size:30
Alignment explanation
Indices: 13981--14046 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
13971 AATAGTTTAT
* *
13981 ATTTTTATTATTTTTAAAAGATTAAATCAA
1 ATTTTTATCATTTTTAAAAGATAAAATCAA
*
14011 ATTTTTATCATTTTTGAAAAGCTAAAAT-ATA
1 ATTTTTATCATTTTT-AAAAGATAAAATCA-A
14042 ATTTT
1 ATTTT
14047 ATAATTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (30 bp):
ATTTTTATCATTTTTAAAAGATAAAATCAA
Found at i:14047 original size:30 final size:29
Alignment explanation
Indices: 13978--14048 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
13968 TTTAATAGTT
* * *
13978 TATATTTTTATTATTTTTAAAAGATTAAA
1 TATAATTTTATCATTTTTAAAAGATAAAA
*
14007 TCA-AATTTTTATCATTTTTGAAAAGCTAAAA
1 T-ATAA-TTTTATCATTTTT-AAAAGATAAAA
14038 TATAATTTTAT
1 TATAATTTTAT
14049 AATTACTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
29 2 0.06
30 20 0.59
31 12 0.35
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (29 bp):
TATAATTTTATCATTTTTAAAAGATAAAA
Found at i:14057 original size:22 final size:23
Alignment explanation
Indices: 14032--14084 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
14022 TTTTGAAAAG
* *
14032 CTAAAATATAATTTTAT-AATTA
1 CTAAAATAAAATATTATAAATTA
**
14054 CTAATTTAAAATATTATAAATTA
1 CTAAAATAAAATATTATAAATTA
14077 -TAAAATAA
1 CTAAAATAA
14085 CTTAAATAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
CTAAAATAAAATATTATAAATTA
Found at i:15861 original size:20 final size:20
Alignment explanation
Indices: 15797--15865 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
15787 TAATAATTTT
15797 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* * ***
15817 AATTAA-TATAAATTTT-TTT
1 AA-TAATTTTATATTTTAAAA
15836 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
15856 AATAATTTTA
1 AATAATTTTA
15866 AATTAATTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 3 0.08
19 10 0.28
20 20 0.56
21 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:16538 original size:21 final size:23
Alignment explanation
Indices: 16514--16559 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
16504 AAAACTCTAA
16514 AAATAATTCAA-AT-TTTGAATT
1 AAATAATTCAATATATTTGAATT
* *
16535 AAATAGTTCAATTTATTTGAATT
1 AAATAATTCAATATATTTGAATT
16558 AA
1 AA
16560 TCAAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (23 bp):
AAATAATTCAATATATTTGAATT
Found at i:16610 original size:17 final size:17
Alignment explanation
Indices: 16588--16621 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16578 CTCGAATAAA
16588 AAATTAAGTTTTTCGGT
1 AAATTAAGTTTTTCGGT
16605 AAATTAAGTTTTTCGGT
1 AAATTAAGTTTTTCGGT
16622 TTAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
AAATTAAGTTTTTCGGT
Found at i:23123 original size:68 final size:71
Alignment explanation
Indices: 23045--23187 Score: 195
Period size: 71 Copynumber: 2.1 Consensus size: 71
23035 AATGGTAAGA
* * * *
23045 AATGGCAGTA-TTTTTTTTCCTT-A-ATGTACATGAAT-TTAATGACTTTTTCTTTCATGTGTTG
1 AATGGAAGTATTTTTTTTTCCTTAATATATACATGAATATT-ATGACATTTTCTTTCATATGTTG
*
23106 AGAGAAT
65 AGAGAAC
*
23113 AATGGAAGTATTTTTTTTTCTTTAATATATACATGAATATTATGACATTTTCTTTCATATGTTGA
1 AATGGAAGTATTTTTTTTTCCTTAATATATACATGAATATTATGACATTTTCTTTCATATGTTGA
23178 GAGAAC
66 GAGAAC
23184 AATG
1 AATG
23188 ACAGTATACG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
68 9 0.14
69 11 0.17
70 1 0.02
71 42 0.65
72 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (71 bp):
AATGGAAGTATTTTTTTTTCCTTAATATATACATGAATATTATGACATTTTCTTTCATATGTTGA
GAGAAC
Found at i:32571 original size:9 final size:9
Alignment explanation
Indices: 32557--32597 Score: 54
Period size: 8 Copynumber: 5.0 Consensus size: 9
32547 TAACCATTTA
32557 AAATAAATT
1 AAATAAATT
32566 AAATAAATT
1 AAATAAATT
32575 -AA-AAATT
1 AAATAAATT
32582 AAA-AAA-T
1 AAATAAATT
32589 AAATAAATT
1 AAATAAATT
32598 TCTTATCACC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 9 0.31
8 10 0.34
9 10 0.34
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAATAAATT
Found at i:39643 original size:43 final size:42
Alignment explanation
Indices: 39530--39673 Score: 193
Period size: 43 Copynumber: 3.4 Consensus size: 42
39520 TTCAAGTCAA
* *
39530 GAGTCTTCC-TTA-ACATAGTCTCATGCTCCTTCCGAGACAT
1 GAGTCTTCCTTTATACATAATCTCATGCTCATTCCGAGACAT
* * *
39570 GAGTCTTCCTTTAAACATAATCTCATGCTCATTCTGAGTCAT
1 GAGTCTTCCTTTATACATAATCTCATGCTCATTCCGAGACAT
* *
39612 GAGTCTTCCTTTTATACATAATCTCACGCTCATCCCGAGACAT
1 GAGTCTTCC-TTTATACATAATCTCATGCTCATTCCGAGACAT
39655 GAGTCTTCCATTTATACAT
1 GAGTCTTCC-TTTATACAT
39674 CAGGTGATTC
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
40 9 0.10
41 3 0.03
42 33 0.36
43 46 0.51
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (42 bp):
GAGTCTTCCTTTATACATAATCTCATGCTCATTCCGAGACAT
Found at i:48594 original size:25 final size:25
Alignment explanation
Indices: 48560--48611 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
48550 TCAAGAGTAC
48560 ACACTATCGTCCTCACTTTTGGTAG
1 ACACTATCGTCCTCACTTTTGGTAG
48585 ACACTATCGTCCTCACTTTTGGTAG
1 ACACTATCGTCCTCACTTTTGGTAG
48610 AC
1 AC
48612 TTTTAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (25 bp):
ACACTATCGTCCTCACTTTTGGTAG
Found at i:54326 original size:24 final size:24
Alignment explanation
Indices: 54299--54477 Score: 243
Period size: 24 Copynumber: 7.5 Consensus size: 24
54289 TTTAGCCCAC
* *
54299 ACGAACCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
54323 ACGAGCCCAGAATGGTTAGCTCTG
1 ACGAGCCCAGAATGGTTAGCTCTT
** *
54347 ACGAGTCTTA-AATGATTAGCTCTT
1 ACGAG-CCCAGAATGGTTAGCTCTT
*
54371 ATGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
54395 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
54419 ACGAGCCCAGAATGATTAACTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
54443 ACGAGCCCAGAATGGTTAGCACTT
1 ACGAGCCCAGAATGGTTAGCTCTT
54467 ACGAGCCCAGA
1 ACGAGCCCAGA
54478 CAAAGTTTAA
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
23 2 0.01
24 132 0.97
25 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:58307 original size:587 final size:587
Alignment explanation
Indices: 57195--58370 Score: 2156
Period size: 587 Copynumber: 2.0 Consensus size: 587
57185 TCCTTATTTG
*
57195 TTTTTATTTCGCACAGAAGGGTTTTGGACGTTGTTGTCTCTAGCTCAAAGAAATGATACTATGGT
1 TTTTTATTTCGCACAGAAAGGTTTTGGACGTTGTTGTCTCTAGCTCAAAGAAATGATACTATGGT
*
57260 AGGCATGAAAGTTTGTCGTGGGAGTCTCTCTATTACTCACCTCTTCTTTGTAGACGATAGTATAG
66 AGGCATGAAAGCTTGTCGTGGGAGTCTCTCTATTACTCACCTCTTCTTTGTAGACGATAGTATAG
* *
57325 TTTCTGGAGAGGCCACTGATAGAGTAGGGGCGACTATAAAGGAAATATTAGCTCATTGTGAACGT
131 TTTCTGGAGAGGCCACTAATAGAGGAGGGGCGACTATAAAGGAAATATTAGCTCATTGTGAACGT
* *
57390 GCCTCGGGACAACAGATGAATTTTGATAAATTAGTGATCTTTTTTAGTTCTAATACTACTAACTA
196 GCCTCGAGACAACAGATGAATTTTCATAAATTAGTGATCTTTTTTAGTTCTAATACTACTAACTA
*
57455 CATGTGCAATGGGATTGTTGATCTTTTGGGTGTTAGACGAGCTTTCAACTTAGAGGGTTGGGAAT
261 CATGTGCAATGGGATTGTTGATCTTTTGGGTGTTAGACGAGCTTTCAACTTAGAGGGTTGAGAAT
57520 TGGAGTAATCGATTTCTTTCTCAGGGTGGGAAAGAAGTTTTTATAAAAGAGGTCCTACAAGCACT
326 TGGAGTAATCGATTTCTTTCTCAGGGTGGGAAAGAAGTTTTTATAAAAGAGGTCCTACAAGCACT
* *
57585 GCCTACTTATTTGATGTCGTGCTTCCTATTGCCAAAAACGTTGTGTAAGGCTATGGAACAAATTA
391 GCCTACTTATTCGATGTCATGCTTCCTATTGCCAAAAACGTTGTGTAAGGCTATGGAACAAATTA
57650 TGAGGAATTTTTGGTGGAATAAAAGTGGTTGACGATTCGGGATGCATTGGTGCAAGTGGTTAGAG
456 TGAGGAATTTTTGGTGGAATAAAAGTGGTTGACGATTCGGGATGCATTGGTGCAAGTGGTTAGAG
57715 CTAAGTAAGCCTAAGATTGTTGGAAGTATGGGTTTTTGCGATCTTTGCAAATTTAAGATAGCGTT
521 CTAAGTAAGCCTAAGATTGTTGGAAGTATGGGTTTTTGCGATCTTTGCAAATTTAAGATAGCGTT
57780 GC
586 GC
* *
57782 TTTTTATTTTGCACAGAAAGGTTTTGGACGTTGTTGTCTCTAGCTCAAAGAAATGGTACTATGGT
1 TTTTTATTTCGCACAGAAAGGTTTTGGACGTTGTTGTCTCTAGCTCAAAGAAATGATACTATGGT
*
57847 AGGCATGAAGGCTTGTCGTGGGAGTCTCTCTATTACTCACCTCTTCTTTGTAGACGATAGTATAG
66 AGGCATGAAAGCTTGTCGTGGGAGTCTCTCTATTACTCACCTCTTCTTTGTAGACGATAGTATAG
* *
57912 TTTGTGGTGAGGCCACTAATAGAGGAGGGGC-AGCTATAAAGGAAATATTAGCTCATTGTGAACG
131 TTTCTGGAGAGGCCACTAATAGAGGAGGGGCGA-CTATAAAGGAAATATTAGCTCATTGTGAACG
*
57976 TGCCTCGAGACAACAGATGAATTTTCATAAATTAGTGATCTTTTTTAGTTCTAATACTACTGACT
195 TGCCTCGAGACAACAGATGAATTTTCATAAATTAGTGATCTTTTTTAGTTCTAATACTACTAACT
* *
58041 ACATGTGCAATGGGATTGTTGATCTTTTGGGTGTTAGACGGGCTTTCAACTTGGAGGGTTGAGAA
260 ACATGTGCAATGGGATTGTTGATCTTTTGGGTGTTAGACGAGCTTTCAACTTAGAGGGTTGAGAA
*
58106 TTGGAGTAATCGATTTCTTTCTCAGGGTGGGAAAGAAGTTTTTATAAAATAGGTCCTACAAGCAC
325 TTGGAGTAATCGATTTCTTTCTCAGGGTGGGAAAGAAGTTTTTATAAAAGAGGTCCTACAAGCAC
*
58171 TGCCTACTTATTCGATGTCATGCTTCCTATTGTCAAAAACGTTGTGTAAGGCTATGGAACAAATT
390 TGCCTACTTATTCGATGTCATGCTTCCTATTGCCAAAAACGTTGTGTAAGGCTATGGAACAAATT
*
58236 ATGAGGCATTTTTGGTGGAATAAAAGTGGTTGACGATTCGGGATGCATTGGTGCAAGTGGTTAGA
455 ATGAGGAATTTTTGGTGGAATAAAAGTGGTTGACGATTCGGGATGCATTGGTGCAAGTGGTTAGA
58301 GCTAAGTAAGCCTAAGATTGTTGGAAGTATGGGTTTTTGCGATCTTTGCAAATTTAAGATAGCGT
520 GCTAAGTAAGCCTAAGATTGTTGGAAGTATGGGTTTTTGCGATCTTTGCAAATTTAAGATAGCGT
58366 TGC
585 TGC
58369 TT
1 TT
58371 GCTAAGCAAG
Statistics
Matches: 568, Mismatches: 20, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
586 1 0.00
587 567 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (587 bp):
TTTTTATTTCGCACAGAAAGGTTTTGGACGTTGTTGTCTCTAGCTCAAAGAAATGATACTATGGT
AGGCATGAAAGCTTGTCGTGGGAGTCTCTCTATTACTCACCTCTTCTTTGTAGACGATAGTATAG
TTTCTGGAGAGGCCACTAATAGAGGAGGGGCGACTATAAAGGAAATATTAGCTCATTGTGAACGT
GCCTCGAGACAACAGATGAATTTTCATAAATTAGTGATCTTTTTTAGTTCTAATACTACTAACTA
CATGTGCAATGGGATTGTTGATCTTTTGGGTGTTAGACGAGCTTTCAACTTAGAGGGTTGAGAAT
TGGAGTAATCGATTTCTTTCTCAGGGTGGGAAAGAAGTTTTTATAAAAGAGGTCCTACAAGCACT
GCCTACTTATTCGATGTCATGCTTCCTATTGCCAAAAACGTTGTGTAAGGCTATGGAACAAATTA
TGAGGAATTTTTGGTGGAATAAAAGTGGTTGACGATTCGGGATGCATTGGTGCAAGTGGTTAGAG
CTAAGTAAGCCTAAGATTGTTGGAAGTATGGGTTTTTGCGATCTTTGCAAATTTAAGATAGCGTT
GC
Found at i:60415 original size:20 final size:21
Alignment explanation
Indices: 60380--60421 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
60370 ATAACATAAG
60380 AAATAAATAACAAATA-AAAA
1 AAATAAATAACAAATATAAAA
**
60400 AAATAAATAATGAATATAAAA
1 AAATAAATAACAAATATAAAA
60421 A
1 A
60422 TGATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (21 bp):
AAATAAATAACAAATATAAAA
Found at i:61592 original size:100 final size:100
Alignment explanation
Indices: 61412--62025 Score: 395
Period size: 100 Copynumber: 6.2 Consensus size: 100
61402 ATTTCTCTGC
* * * * * * * *
61412 AACTTCAGGAAAATAGGATTTGATATTGTAGTCTT-ATCCTGCTCCACTACATCATCAGGGAGAT
1 AACTTCAGGGATATAGGATTTGATGTCGTAG-CTTCATCTTGCTCTACTGCATCTTCAGGGAGAT
* * ** * ** **
61476 AGGACTTGCTAATGTAGTTTCATTATGATCCATTGC
65 AAGATTTGCTTTTGTAGTTTCAATCCGATCCATTAA
* * *
61512 AACTTCAGGGATATAGGATTTGATGTCGTAACTTCATATTGCTCTACTGTATCTTCAGGGAGATA
1 AACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCATCTTCAGGGAGATA
* * * * * *
61577 AGATTTACTTTTGTAGCTCCAA-CTTGACCCACTAA
66 AGATTTGCTTTTGTAGTTTCAATC-CGATCCATTAA
* * * * * *
61612 AACTTCATGGG-TATAGGATTTGATATTG-ATGCTTCATTTTTCTCTACTGCAACTTCAGAGAGA
1 AACTTCA-GGGATATAGGATTTGATGTCGTA-GCTTCATCTTGCTCTACTGCATCTTCAGGGAGA
* * * *
61675 TAAAGATTTGCTATTGTAGTTTTAATCCGGTCC-TTGA
64 T-AAGATTTGCTTTTGTAGTTTCAATCCGATCCATTAA
* * * * * *
61712 AACTTCAGGGATATAAGATTTTATGTCATAGTTTCATCTTGCTCCATTGCATCTTCAGGGAGATA
1 AACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCATCTTCAGGGAGATA
* *
61777 AGATTTGTTTTTGTAGCTTT-AATCCGATCCATTAC
66 AGATTTGCTTTTGTAG-TTTCAATCCGATCCATTAA
* * * * * ** * *
61812 AACTTTAGGGGTATAGGATTTGATGTTGTAGCCTCATCTTGCTCTATTGCAAATTTAGAGAGATA
1 AACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCATCTTCAGGGAGATA
* * ** * * **
61877 AGATTTGTTTTTGTAACTTTTGATCCAATCCACTGC
66 AGATTTGCTTTTGT-AGTTTCAATCCGATCCATTAA
* * * * * * *
61913 AACTTCAAGGATATAGG-TCTTGATGT--T-GTTTCCTCTTGCTCCACTGTAACTTCAGAGAGAT
1 AACTTCAGGGATATAGGAT-TTGATGTCGTAGCTTCATCTTGCTCTACTGCATCTTCAGGGAGAT
* * * * *
61974 CAAGATTTG-TTTCTGTAGCTTCAATCTGACCCACTAC
65 -AAGATTTGCTTT-TGTAGTTTCAATCCGATCCATTAA
*
62011 AACTTCAGGGGTATA
1 AACTTCAGGGATATA
62026 AGATCTGGTG
Statistics
Matches: 401, Mismatches: 98, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
98 55 0.14
99 43 0.11
100 244 0.61
101 58 0.14
102 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (100 bp):
AACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCATCTTCAGGGAGATA
AGATTTGCTTTTGTAGTTTCAATCCGATCCATTAA
Found at i:61773 original size:200 final size:199
Alignment explanation
Indices: 61503--62025 Score: 547
Period size: 200 Copynumber: 2.6 Consensus size: 199
61493 TTTCATTATG
* * * ** * *
61503 ATCCATTGCAACTTCAGGGATATAGGATTTGATGTCGTAACTTCATATTGCTCTACTGTATCTTC
1 ATCCACTGAAACTTCAGGGATATAAGATTTGATGTC-TAGTTTCATCTTGCTCCACTGTATCTTC
* * *
61568 AGGGAGATAAGATTTACTTTTGTAGCTCCAA-CTTGACCCACTAAAACTTCATGGGTATAGGATT
65 AGGGAGATAAGATTT-CTTTTGTAGCTTCAATC-TGACCCACTACAACTTCAGGGGTATAGGATT
* * * * *
61632 TGATATTG-ATGCTTCATTTTTCTCTACTGCAACTTCAGAGAGATAAAGATTTGCTATTGT-AGT
128 TGATATTGTA-GCCTCATCTTGCTCTACTGCAAATTCAGAGAGAT-AAGATTTGCTATTGTAACT
*
61695 TTTAATCCG
191 TTTAATCCA
* * * * *
61704 GTCC-TTGAAACTTCAGGGATATAAGATTTTATGTCATAGTTTCATCTTGCTCCATTGCATCTTC
1 ATCCACTGAAACTTCAGGGATATAAGATTTGATGTC-TAGTTTCATCTTGCTCCACTGTATCTTC
* * * * * *
61768 AGGGAGATAAGATTTGTTTTTGTAGCTTTAATCCGATCCATTACAACTTTAGGGGTATAGGATTT
65 AGGGAGATAAGATTT-CTTTTGTAGCTTCAATCTGACCCACTACAACTTCAGGGGTATAGGATTT
* * * * *
61833 GATGTTGTAGCCTCATCTTGCTCTATTGCAAATTTAGAGAGATAAGATTTGTTTTTGTAACTTTT
129 GATATTGTAGCCTCATCTTGCTCTACTGCAAATTCAGAGAGATAAGATTTGCTATTGTAACTTTT
*
61898 GATCCA
194 AATCCA
* * * * *
61904 ATCCACTGCAACTTCAAGGATAT-AGGTCTTGATGT-T-GTTTCCTCTTGCTCCACTGTAACTTC
1 ATCCACTGAAACTTCAGGGATATAAGAT-TTGATGTCTAGTTTCATCTTGCTCCACTGTATCTTC
* *
61966 AGAGAGATCAAGATTTGTTTCTGTAGCTTCAATCTGACCCACTACAACTTCAGGGGTATA
65 AGGGAGAT-AAGATTTCTTT-TGTAGCTTCAATCTGACCCACTACAACTTCAGGGGTATA
62026 AGATCTGGTG
Statistics
Matches: 265, Mismatches: 50, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
198 32 0.12
199 55 0.21
200 152 0.57
201 26 0.10
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (199 bp):
ATCCACTGAAACTTCAGGGATATAAGATTTGATGTCTAGTTTCATCTTGCTCCACTGTATCTTCA
GGGAGATAAGATTTCTTTTGTAGCTTCAATCTGACCCACTACAACTTCAGGGGTATAGGATTTGA
TATTGTAGCCTCATCTTGCTCTACTGCAAATTCAGAGAGATAAGATTTGCTATTGTAACTTTTAA
TCCA
Found at i:61808 original size:50 final size:49
Alignment explanation
Indices: 61659--61919 Score: 134
Period size: 50 Copynumber: 5.2 Consensus size: 49
61649 TTTTCTCTAC
* * *
61659 TGCAACTTCAGAGAGATAAAGATTTGCTATTGTAGTTTTAATCCGGTCC-T
1 TGCAACTTCAGGGAGAT-AAGATTTGTTATTGTAG-TTTAATCCGATCCAT
* * * * * *
61709 TGAAACTTCAGGGATATAAGA-TT-TTATGTCATAGTTTCATCTTGCTCCAT
1 TGCAACTTCAGGGAGATAAGATTTGTTAT-T-GTAGTTTAATC-CGATCCAT
* *
61759 TGCATCTTCAGGGAGATAAGATTTGTTTTTGTAGCTTTAATCCGATCCAT
1 TGCAACTTCAGGGAGATAAGATTTGTTATTGTAG-TTTAATCCGATCCAT
* * * * * ** * * * *
61809 TACAACTTTAGGG-GTATAGGATTTGATGTTGTAGCCTCATCTTGCTCTAT
1 TGCAACTTCAGGGAG-ATAAGATTTGTTATTGTAGTTTAATC-CGATCCAT
* * * * * * * *
61859 TGCAAATTTAGAGAGATAAGATTTGTTTTTGTAACTTTTGATCCAATCCAC
1 TGCAACTTCAGGGAGATAAGATTTGTTATTGT-A-GTTTAATCCGATCCAT
61910 TGCAACTTCA
1 TGCAACTTCA
61920 AGGATATAGG
Statistics
Matches: 154, Mismatches: 45, Indels: 23
0.69 0.20 0.10
Matches are distributed among these distances:
47 3 0.02
48 9 0.06
49 16 0.10
50 97 0.63
51 22 0.14
52 7 0.05
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (49 bp):
TGCAACTTCAGGGAGATAAGATTTGTTATTGTAGTTTAATCCGATCCAT
Found at i:62728 original size:21 final size:21
Alignment explanation
Indices: 62681--62732 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
62671 TGATAAGATT
* * **
62681 TAAAAAAATGGTAGACATTGG
1 TAAAAAAATGGCAAACATCAG
*
62702 TCAAAAAATGGCAAACATCAG
1 TAAAAAAATGGCAAACATCAG
62723 TAAAAAAATG
1 TAAAAAAATG
62733 CTAATCACAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (21 bp):
TAAAAAAATGGCAAACATCAG
Found at i:71105 original size:4 final size:4
Alignment explanation
Indices: 71084--71162 Score: 50
Period size: 4 Copynumber: 18.2 Consensus size: 4
71074 GGCAAAATAA
* * * *
71084 AAAT ACAT ACAT ACAT AAAT AAAAT AAAAT AAAT AACAT TAAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AA-AT AAAT AAAT -AAAT
* *
71136 TAAT AACAT AAAT AAAA AAAT ATAAT A
1 AAAT AA-AT AAAT AAAT AAAT A-AAT A
71163 GTAATGATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
4 38 0.61
5 24 0.39
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:71107 original size:27 final size:27
Alignment explanation
Indices: 71077--71135 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
71067 TGATGATGGC
*
71077 AAAATAAAAATACAT-ACA-TACATAAAT
1 AAAAT-AAAATAAATAACATTA-ATAAAT
71104 AAAATAAAATAAATAACATTAATAAAT
1 AAAATAAAATAAATAACATTAATAAAT
71131 AAAAT
1 AAAAT
71136 TAATAACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.28
27 19 0.66
28 2 0.07
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (27 bp):
AAAATAAAATAAATAACATTAATAAAT
Found at i:71117 original size:9 final size:9
Alignment explanation
Indices: 71098--71162 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
71088 ACATACATAC
71098 ATAAATAAA
1 ATAAATAAA
71107 ATAAA-ATAA
1 ATAAATA-AA
*
71116 ATAACAT-TA
1 ATAA-ATAAA
71125 ATAAATAAA
1 ATAAATAAA
* *
71134 ATTAATAAC
1 ATAAATAAA
71143 ATAAATAAA
1 ATAAATAAA
*
71152 A-AAATATA
1 ATAAATAAA
71160 ATA
1 ATA
71163 GTAATGATGA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
8 10 0.23
9 33 0.75
10 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAAATAAA
Found at i:71129 original size:13 final size:13
Alignment explanation
Indices: 71098--71147 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
71088 ACATACATAC
*
71098 ATAAATAAAATAAA
1 ATAAATAAAAT-TA
*
71112 ATAAATAACATTA
1 ATAAATAAAATTA
71125 ATAAATAAAATTA
1 ATAAATAAAATTA
71138 ATAACATAAA
1 ATAA-ATAAA
71148 TAAAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 17 0.53
14 15 0.47
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAATAAAATTA
Found at i:71133 original size:22 final size:22
Alignment explanation
Indices: 71096--71162 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
71086 ATACATACAT
71096 ACATAAATAAAATAAAATAAATA
1 ACATAAAT-AAATAAAATAAATA
* *
71119 ACATTAATAAATAAAATTAATA
1 ACATAAATAAATAAAATAAATA
71141 ACATAAATAAA-AAAATATAATA
1 ACATAAATAAATAAAATA-AATA
71163 GTAATGATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
21 5 0.13
22 27 0.69
23 7 0.18
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.25
Consensus pattern (22 bp):
ACATAAATAAATAAAATAAATA
Found at i:71367 original size:19 final size:19
Alignment explanation
Indices: 71343--71404 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
71333 ATGATATAAG
71343 AAATAAATAAAAAATAAAA
1 AAATAAATAAAAAATAAAA
***
71362 AAATAAATATTGAATATAAA
1 AAATAAATAAAAAATA-AAA
* *
71382 AAAT-GATAAAATATAAAA
1 AAATAAATAAAAAATAAAA
71400 AAATA
1 AAATA
71405 GTAAAAAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
18 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
AAATAAATAAAAAATAAAA
Found at i:77235 original size:21 final size:22
Alignment explanation
Indices: 77205--77262 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
77195 TCTCTAGAGT
77205 TTTTGGTATCGGTAGATGCAT-C
1 TTTT-GTATCGGTAGATGCATAC
*
77227 TTTTGTATCGGTAGAATTCATAC
1 TTTTGTATCGGTAG-ATGCATAC
77250 --TTGTATCGGTAGA
1 TTTTGTATCGGTAGA
77263 GCTAGCACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.03
21 22 0.67
22 9 0.27
23 1 0.03
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (22 bp):
TTTTGTATCGGTAGATGCATAC
Found at i:77435 original size:2 final size:2
Alignment explanation
Indices: 77430--77487 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
77420 TATATATATA
*
77430 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
77472 TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG
77488 AAGTGATAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.02, G:0.50, T:0.48
Consensus pattern (2 bp):
TG
Found at i:77746 original size:25 final size:25
Alignment explanation
Indices: 77718--77769 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
77708 GTTTTCACTC
77718 TTGAAAAATTCTTTTTTTTTTTTCT
1 TTGAAAAATTCTTTTTTTTTTTTCT
77743 TTGAAAAATTCTTTTTTTTTTTTCT
1 TTGAAAAATTCTTTTTTTTTTTTCT
77768 TT
1 TT
77770 CTCTCCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TTGAAAAATTCTTTTTTTTTTTTCT
Found at i:78076 original size:51 final size:49
Alignment explanation
Indices: 78003--78143 Score: 144
Period size: 52 Copynumber: 2.8 Consensus size: 49
77993 TCAAATCTTG
*
78003 TTTAATTAAATTA--TT-TTCAGATATGATATTTTATATAAAAATAAATA
1 TTTATTTAAATTATTTTATTCAGATATG-TATTTTATATAAAAATAAATA
* * * *
78050 TTTATTTAAATTGATTTTGTTTAGATATGCTGATTTTACATAAATATAAATA
1 TTTATTTAAATT-ATTTTATTCAGATATG-T-ATTTTATATAAAAATAAATA
* * *
78102 TTTGTTTATATTATTTTATTCAGATATTGTATTTAATATAAA
1 TTTATTTAAATTATTTTATTCAGATA-TGTATTTTATATAAA
78144 TATTTATATT
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
47 11 0.14
48 1 0.01
50 12 0.16
51 23 0.30
52 30 0.39
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (49 bp):
TTTATTTAAATTATTTTATTCAGATATGTATTTTATATAAAAATAAATA
Found at i:78480 original size:84 final size:85
Alignment explanation
Indices: 78285--78525 Score: 231
Period size: 84 Copynumber: 2.8 Consensus size: 85
78275 AATTAAAATC
* * * * * *
78285 GAATGAATCTGTTTGGGGATTTATTCCCGCCGTTCAACAGATTTTATTTTATTTTATTTTAATTT
1 GAATAAATCTATTTCGGGATTTATTTCCGCCGTTCAACAGATTTTATTCTA---TATTTGAATTT
* *
78350 TGTTTTCAATTAATAAATTAATT
63 TGTTTCCAATTAATAAATTAAGT
* * *
78373 GAATAAATCTATTTCAGGATTTATTTCCGCCGCTCAATAGATTTTATTCTATATTTGAATTTTGT
1 GAATAAATCTATTTCGGGATTTATTTCCGCCGTTCAACAGATTTTATTCTATATTTGAATTTTGT
*
78438 TTCCAGA-TAGT-AATTAAGT
66 TTCCA-ATTAATAAATTAAGT
* * * * * * *
78457 GAATTATTTTATTTCGGGATTTA-TTCTCGCCTTTTAACAAATTTTGTTCTAT-TTTG-ATTTTG
1 GAATAAATCTATTTCGGGATTTATTTC-CGCCGTTCAACAGATTTTATTCTATATTTGAATTTTG
78519 TTTCCAA
65 TTTCCAA
78526 AACAAGAATA
Statistics
Matches: 129, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
81 1 0.01
82 12 0.09
83 7 0.05
84 45 0.35
85 20 0.16
86 1 0.01
88 43 0.33
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (85 bp):
GAATAAATCTATTTCGGGATTTATTTCCGCCGTTCAACAGATTTTATTCTATATTTGAATTTTGT
TTCCAATTAATAAATTAAGT
Found at i:84865 original size:13 final size:14
Alignment explanation
Indices: 84849--84877 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
84839 AAATAAAGGC
84849 AAAA-TTGATAAAA
1 AAAATTTGATAAAA
84862 AAAATTTGATAAAA
1 AAAATTTGATAAAA
84876 AA
1 AA
84878 TAGGCCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (14 bp):
AAAATTTGATAAAA
Found at i:88691 original size:23 final size:25
Alignment explanation
Indices: 88665--88710 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
88655 CCAATTAGGG
88665 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
88688 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
88711 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:89786 original size:6 final size:6
Alignment explanation
Indices: 89777--89833 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
89767 TACTTTAGCC
* * * *
89777 ATTTTT ATTTTT GTTTTACT ATTTAT ATTTTT AATTTA ATTTTT ATATTTT
1 ATTTTT ATTTTT ATTTT--T ATTTTT ATTTTT ATTTTT ATTTTT AT-TTTT
89828 ATTTTT
1 ATTTTT
89834 TCCCTTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
6 30 0.75
7 6 0.15
8 4 0.10
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:89805 original size:20 final size:20
Alignment explanation
Indices: 89777--89827 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
89767 TACTTTAGCC
* ** *
89777 ATTTTTATTTTTGTTTTACT
1 ATTTATATTTTTAATTTAAT
89797 ATTTATATTTTTAATTTAAT
1 ATTTATATTTTTAATTTAAT
*
89817 TTTTATATTTT
1 ATTTATATTTT
89828 ATTTTTTCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTATATTTTTAATTTAAT
Found at i:89820 original size:13 final size:13
Alignment explanation
Indices: 89790--89833 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
89780 TTTATTTTTG
89790 TTTTACTATTTATAT
1 TTTTA-TATTTA-AT
89805 TTTTA-ATTTAAT
1 TTTTATATTTAAT
*
89817 TTTTATATTTTAT
1 TTTTATATTTAAT
89830 TTTT
1 TTTT
89834 TCCCTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 15 0.56
15 5 0.19
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTTAAT
Found at i:93693 original size:16 final size:17
Alignment explanation
Indices: 93674--93713 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
93664 AAAAAAAGTC
*
93674 AAAAAGAAAATTTA-AA
1 AAAAAGAAAATTGAGAA
*
93690 AAAAAAAAAATTGAGAA
1 AAAAAGAAAATTGAGAA
93707 AAAAAGA
1 AAAAAGA
93714 GAAGAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAGAAAATTGAGAA
Found at i:94806 original size:25 final size:23
Alignment explanation
Indices: 94766--94811 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
94756 CCAATTAAGG
94766 AATTATTATTTAAATTTAATTCT
1 AATTATTATTTAAATTTAATTCT
*
94789 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTA-AATTTAATT
94812 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAAATTTAATTCT
Found at i:104111 original size:36 final size:36
Alignment explanation
Indices: 104064--104169 Score: 203
Period size: 36 Copynumber: 2.9 Consensus size: 36
104054 TCAGAATAGG
104064 TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATGGA
1 TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATGGA
*
104100 TTTGCTTTTTGGCTCTAACTGCTTCCGAACAATGGA
1 TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATGGA
104136 TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATG
1 TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATG
104170 CCTTAGGTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (36 bp):
TTTGCTTTTTGGCTCTAAGTGCTTCCGAACAATGGA
Found at i:106939 original size:79 final size:80
Alignment explanation
Indices: 106802--107011 Score: 255
Period size: 79 Copynumber: 2.6 Consensus size: 80
106792 AGTTTAACTG
* * * *
106802 ACTAGTGCTAGGCAT-ACATTTGCGGTTTATCCGCTTGGCACTAGGTGCCAGGATTTGATGGATA
1 ACTAGAGCTAGGC-TCACCTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATA
*
106866 -TTGTTGGTTAATCAAA
65 TTTGTTAGTTAA-CAAA
* *
106882 AC-AGAGCTAGGCTCACTTTTGCGGTTTACCCGCTAGGCACTAGGTGCCAAGATTTGATGGATAT
1 ACTAGAGCTAGGCTCACCTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATAT
**
106946 TTGTTAGTTAACCCA
66 TTGTTAGTTAACAAA
* * ** *
106961 ACTAGAGCTGGGCTCACCTTTACGGTTTATCATCTAGGCACCAGGTGCCAA
1 ACTAGAGCTAGGCTCACCTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAA
107012 AATCGTCGGT
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
79 58 0.52
80 53 0.47
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
ACTAGAGCTAGGCTCACCTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATAT
TTGTTAGTTAACAAA
Found at i:106998 original size:80 final size:79
Alignment explanation
Indices: 106824--107011 Score: 243
Period size: 80 Copynumber: 2.4 Consensus size: 79
106814 CATACATTTG
* * *
106824 CGGTTTATCCGCTTGGCACTAGGTGCCAGGATTTGATGGATATTGTTGGTTAATCAAAACAGAGC
1 CGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATATTGTTAGTTAATCAAAACAGAGC
* *
106889 TAGGCTCACTTTTG
66 TAGGCTCACCTTTA
* **
106903 CGGTTTACCCGCTAGGCACTAGGTGCCAAGATTTGATGGATATTTGTTAGTTAA-CCCAACTAGA
1 CGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATA-TTGTTAGTTAATCAAAAC-AGA
*
106967 GCTGGGCTCACCTTTA
64 GCTAGGCTCACCTTTA
** *
106983 CGGTTTATCATCTAGGCACCAGGTGCCAA
1 CGGTTTATCCGCTAGGCACTAGGTGCCAA
107012 AATCGTCGGT
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 43 0.46
80 51 0.54
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (79 bp):
CGGTTTATCCGCTAGGCACTAGGTGCCAAGATTTGATGGATATTGTTAGTTAATCAAAACAGAGC
TAGGCTCACCTTTA
Found at i:107198 original size:80 final size:80
Alignment explanation
Indices: 107049--107212 Score: 211
Period size: 80 Copynumber: 2.0 Consensus size: 80
107039 GGCACAAACC
* * * * ** * *
107049 GTTGGTTAATCCAACTAGAGTTGGGCTCATTTATTGTTGTTTATCCACTAAGCACTAGATGCTAA
1 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTTATCCACTAAGCACCAGATGCCAA
107114 GAATTGACGGATTTT
66 GAATTGACGGATTTT
* * * *
107129 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTTATCCACTAGGCACCGGGTGCCAT
1 GTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTTATCCACTAAGCACCAGATGCCAA
*
107194 GAATTGATGGATTTT
66 GAATTGACGGATTTT
107209 GTTG
1 GTTG
107213 AAAGTAAAGA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (80 bp):
GTTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCGGTTTATCCACTAAGCACCAGATGCCAA
GAATTGACGGATTTT
Found at i:110810 original size:18 final size:18
Alignment explanation
Indices: 110769--110811 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
110759 ACAGTCAACG
110769 AGTCAACGGTCAACAGTC
1 AGTCAACGGTCAACAGTC
*
110787 -GATCAACGGTCAACGGTC
1 AG-TCAACGGTCAACAGTC
110805 AGTCAAC
1 AGTCAAC
110812 TTGGCTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (18 bp):
AGTCAACGGTCAACAGTC
Found at i:113262 original size:42 final size:41
Alignment explanation
Indices: 113231--113395 Score: 224
Period size: 42 Copynumber: 4.0 Consensus size: 41
113221 CTTTTTCAAT
*
113231 CATAATCTCACTCTCAT-TAAGACATGAGTCTTCCTTTAAA
1 CATAATCTCATTCTCATCTAAGACATGAGTCTTCCTTTAAA
113271 CATAATCTCATTCTCATCCTAAGACATGAGTCTTCCTTTAAA
1 CATAATCTCATTCTCAT-CTAAGACATGAGTCTTCCTTTAAA
* * *
113313 CATAGTCTCATTCTTATCTCGAGACATGAGTCTTCCTTTAAA
1 CATAATCTCATTCTCATCT-AAGACATGAGTCTTCCTTTAAA
* * *
113355 TATAGTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTA
1 CATAATCTCATTCTCAT-CTAAGACATGAGTCTTCC-TTTA
113396 TGCATCAAGA
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
40 16 0.14
41 2 0.02
42 89 0.79
43 5 0.04
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (41 bp):
CATAATCTCATTCTCATCTAAGACATGAGTCTTCCTTTAAA
Found at i:120409 original size:81 final size:81
Alignment explanation
Indices: 120274--120436 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
120264 GAGGGACCTG
120274 TCACTGCCATATTGGTATCTTTAGTACTCAAGCTCATCTATGGCCATCGTTCTCTTCATGTTTGT
1 TCACTGCCATATTGGTATCTTTAGTACTCAAGCTCATCTATGGCCATCGTTCTCTTCATGTTTGT
120339 CGTTCTTGTTAGTTGT
66 CGTTCTTGTTAGTTGT
*
120355 TCACTGCCATATTGGTATCTTTAGTACTCAAGCTCATCTATGGCCATGGTTCTCTTCATGTTTGT
1 TCACTGCCATATTGGTATCTTTAGTACTCAAGCTCATCTATGGCCATCGTTCTCTTCATGTTTGT
120420 CGTTCTTGTTAGTTGT
66 CGTTCTTGTTAGTTGT
120436 T
1 T
120437 GCTTCTTTCC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (81 bp):
TCACTGCCATATTGGTATCTTTAGTACTCAAGCTCATCTATGGCCATCGTTCTCTTCATGTTTGT
CGTTCTTGTTAGTTGT
Found at i:125369 original size:107 final size:107
Alignment explanation
Indices: 125183--125402 Score: 413
Period size: 107 Copynumber: 2.1 Consensus size: 107
125173 TAAAAATGGA
125183 AATTATTTAATTTAAGTTCAAAAAGAAGTTGATAGTTTAATAATTGTATTACAAGGCATAGTACA
1 AATTATTTAATTTAAGTTCAAAAAGAAGTTGATAGTTTAATAATTGTATTACAAGGCATAGTACA
125248 AATTTGAAATATATAAATAAAAGTTATAATTTCCACGATATT
66 AATTTGAAATATATAAATAAAAGTTATAATTTCCACGATATT
*
125290 AATTATTTAATTTAAGTTCAAAAAGAAGTTGATAGTTTAATAATTGTATTACGAGGCATAGTACA
1 AATTATTTAATTTAAGTTCAAAAAGAAGTTGATAGTTTAATAATTGTATTACAAGGCATAGTACA
* *
125355 AATTTGAAATATATAAATAAATGTTATAATTTCCACGCTATT
66 AATTTGAAATATATAAATAAAAGTTATAATTTCCACGATATT
125397 AATTAT
1 AATTAT
125403 AAAAGTTAAA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 110 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (107 bp):
AATTATTTAATTTAAGTTCAAAAAGAAGTTGATAGTTTAATAATTGTATTACAAGGCATAGTACA
AATTTGAAATATATAAATAAAAGTTATAATTTCCACGATATT
Found at i:125833 original size:18 final size:18
Alignment explanation
Indices: 125810--125857 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
125800 AAAAATTATA
*
125810 AAAAAATTCAATAAAAAT
1 AAAAAATTCAAGAAAAAT
*
125828 AAAAAATTTCAAGAAACAT
1 AAAAAA-TTCAAGAAAAAT
*
125847 ATAAAATTCAA
1 AAAAAATTCAA
125858 AAACTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAATTCAAGAAAAAT
Found at i:125866 original size:17 final size:19
Alignment explanation
Indices: 125811--125867 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
125801 AAAATTATAA
* * * *
125811 AAAAATTCAATAAAAATAA
1 AAAATTTCAAGAAACATAT
125830 AAAATTTCAAGAAACATAT
1 AAAATTTCAAGAAACATAT
*
125849 AAAA-TTCAA-AAACTTAT
1 AAAATTTCAAGAAACATAT
125866 AA
1 AA
125868 TGGGTGAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 19 0.58
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATTTCAAGAAACATAT
Found at i:129131 original size:43 final size:43
Alignment explanation
Indices: 129066--129151 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
129056 ACTTATACAA
*
129066 TATTGGTAACAACAATCGTATGGCTCACTTAGCCCTCTTTTGG
1 TATTGGTAACAACAATCATATGGCTCACTTAGCCCTCTTTTGG
129109 TATTGGTAACAACAATCATATGGCTCACTTAGCCCTCTTTTGG
1 TATTGGTAACAACAATCATATGGCTCACTTAGCCCTCTTTTGG
129152 CGTAGACCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (43 bp):
TATTGGTAACAACAATCATATGGCTCACTTAGCCCTCTTTTGG
Found at i:129954 original size:29 final size:28
Alignment explanation
Indices: 129909--129984 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
129899 GACCATAAGG
**
129909 GCTCACATATACCAGAATATACCAAAAAA
1 GCTCACATATAATAGAATA-ACCAAAAAA
* * *
129938 GCTCACATATAATAGAATAGCCACAAAT
1 GCTCACATATAATAGAATAACCAAAAAA
129966 GCTTCCACATATAATAGAA
1 GC-T-CACATATAATAGAA
129985 CAGCCATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 8 0.20
29 18 0.45
30 14 0.35
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.21
Consensus pattern (28 bp):
GCTCACATATAATAGAATAACCAAAAAA
Found at i:129977 original size:30 final size:30
Alignment explanation
Indices: 129941--130007 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
129931 CAAAAAAGCT
*
129941 CACATATAATAGAATAGCCACAAA-TGCTTC
1 CACATATAATAGAACAGCCACAAAGT-CTTC
*
129971 CACATATAATAGAACAGCCATAAAGTCTTC
1 CACATATAATAGAACAGCCACAAAGTCTTC
130001 CACATAT
1 CACATAT
130008 CGGTAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (30 bp):
CACATATAATAGAACAGCCACAAAGTCTTC
Found at i:130737 original size:24 final size:24
Alignment explanation
Indices: 130689--130735 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
130679 AAGAGTTAAT
*
130689 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAAAGCAAATATAAAATAAA
*
130713 TTGTCAAAGCAAAT-TAAGATAAA
1 TTGTCAAAGCAAATATAAAATAAA
130736 ATGAATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (24 bp):
TTGTCAAAGCAAATATAAAATAAA
Found at i:132891 original size:17 final size:17
Alignment explanation
Indices: 132871--132930 Score: 93
Period size: 17 Copynumber: 3.5 Consensus size: 17
132861 AAATGAACTA
* *
132871 ACAAGTAAAATGCAACG
1 ACAATTAAAATGCAATG
*
132888 ACAACTAAAATGCAATG
1 ACAATTAAAATGCAATG
132905 ACAATTAAAATGCAATG
1 ACAATTAAAATGCAATG
132922 ACAATTAAA
1 ACAATTAAA
132931 TGAGATGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.18
Consensus pattern (17 bp):
ACAATTAAAATGCAATG
Found at i:132899 original size:34 final size:33
Alignment explanation
Indices: 132844--132932 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 33
132834 ATAAGAATGG
* *
132844 AAATGCAACTACAATGCAAATG-AACTAACAAGTA
1 AAATGCAACGACAAT-AAAATGCAA-TAACAAGTA
* *
132878 AAATGCAACGACAACTAAAATGCAATGACAATTA
1 AAATGCAACGACAA-TAAAATGCAATAACAAGTA
* *
132912 AAATGCAATGACAATTAAATG
1 AAATGCAACGACAATAAAATG
132933 AGATGCATGC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
33 6 0.13
34 38 0.81
35 3 0.06
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (33 bp):
AAATGCAACGACAATAAAATGCAATAACAAGTA
Found at i:139596 original size:18 final size:18
Alignment explanation
Indices: 139575--139614 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
139565 TTATATGAAT
**
139575 GCATCTGATTTTGTAATC
1 GCATCTGATCATGTAATC
*
139593 GCATCTGGTCATGTAATC
1 GCATCTGATCATGTAATC
139611 GCAT
1 GCAT
139615 ATTATCTGGT
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:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (18 bp):
GCATCTGATCATGTAATC
Found at i:160361 original size:22 final size:22
Alignment explanation
Indices: 160336--160412 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
160326 TTTCATGCCC
* *
160336 TCTGTTCAACATTGTGTGTGCT
1 TCTGTTCAGCATTGTATGTGCT
160358 TCTGTTCAGCATTGTATGTGCT
1 TCTGTTCAGCATTGTATGTGCT
* *
160380 TCTATTCAGCACTGTATGTGCT
1 TCTGTTCAGCATTGTATGTGCT
160402 TCTGTTCAGCA
1 TCTGTTCAGCA
160413 CTTTGTGTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (22 bp):
TCTGTTCAGCATTGTATGTGCT
Found at i:160413 original size:22 final size:22
Alignment explanation
Indices: 160336--160446 Score: 116
Period size: 22 Copynumber: 5.0 Consensus size: 22
160326 TTTCATGCCC
* * *
160336 TCTGTTCAACATTGTGTGTGCT
1 TCTGTTCAGCACTGTATGTGCT
*
160358 TCTGTTCAGCATTGTATGTGCT
1 TCTGTTCAGCACTGTATGTGCT
*
160380 TCTATTCAGCACTGTATGTGCT
1 TCTGTTCAGCACTGTATGTGCT
* *
160402 TCTGTTCAGCACTTTGTGTGCCT
1 TCTGTTCAGCACTGTATGTG-CT
*
160425 ACTGTTGTCAGCACT-TATGTGC
1 TCTG-T-TCAGCACTGTATGTGC
160447 CCTCTGTTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
22 57 0.74
23 6 0.08
24 6 0.08
25 8 0.10
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (22 bp):
TCTGTTCAGCACTGTATGTGCT
Found at i:167615 original size:22 final size:22
Alignment explanation
Indices: 167589--167653 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
167579 TTTTATGCCA
*
167589 TCTGTTCAACATTGTGTGTGCT
1 TCTGTTCAACACTGTGTGTGCT
*
167611 TCTGTTCAGCACTGTGTGTGCT
1 TCTGTTCAACACTGTGTGTGCT
* * * *
167633 TCTATTTAGCACTTTGTGTGC
1 TCTGTTCAACACTGTGTGTGC
167654 CTACTGTTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (22 bp):
TCTGTTCAACACTGTGTGTGCT
Found at i:168124 original size:34 final size:34
Alignment explanation
Indices: 168086--168154 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
168076 TTGGGGATGC
168086 TTTGATTTGATGAAATGAAATGATGAATTTTGGT
1 TTTGATTTGATGAAATGAAATGATGAATTTTGGT
168120 TTTGATTTGATGAAATGAAATGATGAATTTTGGT
1 TTTGATTTGATGAAATGAAATGATGAATTTTGGT
168154 T
1 T
168155 GAAACTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (34 bp):
TTTGATTTGATGAAATGAAATGATGAATTTTGGT
Found at i:175509 original size:11 final size:11
Alignment explanation
Indices: 175493--175518 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
175483 CCACAAATTT
175493 TATTATTATTA
1 TATTATTATTA
175504 TATTATTATTA
1 TATTATTATTA
175515 TATT
1 TATT
175519 TTTTCCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:176061 original size:7 final size:7
Alignment explanation
Indices: 176049--176096 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
176039 AATGAAACCT
176049 AATTTTA
1 AATTTTA
176056 AATTTTA
1 AATTTTA
*
176063 AATTCTA
1 AATTTTA
176070 AATTTTA
1 AATTTTA
* *
176077 ATTTATTT
1 AATT-TTA
*
176085 AAGTTTA
1 AATTTTA
176092 AATTT
1 AATTT
176097 AAACTTATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:176091 original size:6 final size:6
Alignment explanation
Indices: 176052--176150 Score: 64
Period size: 6 Copynumber: 17.0 Consensus size: 6
176042 GAAACCTAAT
* *
176052 TTTAAA TTTTAAA TTCTAAA TTTTAA TTT--A TTTAAG TTTAAA TTTAAA
1 TTTAAA -TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
176100 CTT-AT TTTGAG TTTAAA TTT-AT TTTAAA -TTAAA TTTAAA ATTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
176145 TTTAAA
1 TTTAAA
176151 ATGTCCAAAT
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
4 4 0.06
5 12 0.17
6 43 0.61
7 12 0.17
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:176096 original size:22 final size:23
Alignment explanation
Indices: 176057--176120 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
176047 CTAATTTTAA
* * *
176057 ATTTTAAATTCTAAATTTTAATTT
1 ATTTTAAGTT-TAAATTTAAACTT
176081 A-TTTAAGTTTAAATTTAAACTT
1 ATTTTAAGTTTAAATTTAAACTT
*
176103 ATTTTGAGTTTAAATTTA
1 ATTTTAAGTTTAAATTTA
176121 TTTTAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.34
23 22 0.63
24 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTAAGTTTAAATTTAAACTT
Found at i:176133 original size:16 final size:16
Alignment explanation
Indices: 176088--176136 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
176078 TTTATTTAAG
*
176088 TTTAAATTTAAACTTAT
1 TTTAAA-TTAAATTTAT
**
176105 TTTGAGTTTAAATTTAT
1 TTT-AAATTAAATTTAT
176122 TTTAAATTAAATTTA
1 TTTAAATTAAATTTA
176137 AAATTAAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.38
17 15 0.58
18 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTAAATTTAT
Found at i:177872 original size:58 final size:57
Alignment explanation
Indices: 177791--178110 Score: 243
Period size: 59 Copynumber: 5.5 Consensus size: 57
177781 TTTTCTCTCG
* * *
177791 AACTTCTAAAAATTACATTTTTACCCTTAAACTTCAAAAAATTACAATTTTACCCTA
1 AACTTCTAAAAATTACATTTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCTA
* * * *
177848 AACTTCTAAAAAATTACATTTTTACCCCCAAACTTCCAAAAATCACATTTTTACCTTCG
1 AACTTCT-AAAAATTACATTTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCT-A
* * * *
177907 AACTTCTCGAAATTTACATTTTTACCCCTGAACTTCTAAAAATCACATTTTTACCCTA
1 AACTTCT-AAAAATTACATTTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCTA
* * ** * * ** *
177965 AACTTTCTTAAAATGACATTTTTATGCCTAAAACTTTC-CAAAATTATGTTTTTACTCC-G
1 AAC-TTCTAAAAATTACATTTTTACCCCT-AAAC-TTCAAAAAATCACATTTTTAC-CCTA
* * * * * * *
178024 AACTTTCCAAAAATGACTTTTTTACCCCTAAATCTTTC-TAAAATTACATTTTAACCCCA
1 AAC-TTCTAAAAATTACATTTTTACCCCTAAA-C-TTCAAAAAATCACATTTTTACCCTA
* * *
178083 AACTCTCCAAAACTT-CATTTTTAACCCT
1 AACT-TCTAAAAATTACATTTTTACCCCT
178111 GGTTTTTTTT
Statistics
Matches: 214, Mismatches: 40, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
57 7 0.03
58 79 0.37
59 123 0.57
60 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (57 bp):
AACTTCTAAAAATTACATTTTTACCCCTAAACTTCAAAAAATCACATTTTTACCCTA
Found at i:177925 original size:59 final size:59
Alignment explanation
Indices: 177681--178075 Score: 288
Period size: 59 Copynumber: 6.7 Consensus size: 59
177671 AAATCTTTCT
** * * * *
177681 AAAATTACATTTTTATCCCCCGAACTTTCCAAAAATTACATCTTGACCCGTCGAACTTCTCC
1 AAAATTACATTTTTA-CCCCTAAAC-TTCCAAAAATTACATTTTTA-CCTTCGAACTTCTCA
* * ** * **
177743 AAAACTATATTTTTGGCCCTAAAATTATAAAAATTACA-TTTT--CTCTCGAACTTCT-A
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCT-TCGAACTTCTCA
* * * * * *
177799 AAAATTACATTTTTACCCTTAAACTTCAAAAAATTACAATTTTACCCT-AAACTTCTAA
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCTTCGAACTTCTCA
* * *
177857 AAAATTACATTTTTACCCCCAAACTTCCAAAAATCACATTTTTACCTTCGAACTTCTCG
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCTTCGAACTTCTCA
* * * * * * *
177916 AAATTTACATTTTTACCCCTGAACTTCTAAAAATCACATTTTTACCCT-AAACTT-TCTT
1 AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCTTCGAACTTCTC-A
* ** ** *
177974 AAAATGACATTTTTATGCCTAAAACTTTCC-AAAATTATGTTTTTA-CTCCGAACTT-TCCA
1 AAAATTACATTTTTACCCCT-AAAC-TTCCAAAAATTACATTTTTACCTTCGAACTTCT-CA
* * * *
178033 AAAATGACTTTTTTACCCCTAAATCTTTCTAAAATTACATTTT
1 AAAATTACATTTTTACCCCTAAA-CTTCCAAAAATTACATTTT
178076 AACCCCAAAC
Statistics
Matches: 262, Mismatches: 58, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
56 31 0.12
57 23 0.09
58 72 0.27
59 103 0.39
60 16 0.06
61 5 0.02
62 12 0.05
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCTTCGAACTTCTCA
Found at i:177978 original size:88 final size:87
Alignment explanation
Indices: 177794--178111 Score: 254
Period size: 88 Copynumber: 3.6 Consensus size: 87
177784 TCTCTCGAAC
* * * * * *
177794 TTCTAAAAATTACATTTTTACCCTTAAAC-TTCAAAAAATTACAATTTTA-CCCTAAACTTCTAA
1 TTCT-AAAATCACATTTTTAGCCTAAAACTTTC-CAAAATTACATTTTTACCCCTGAACTTCT-A
* *
177857 AAAATTACATTTTTACCCCCAAACT
63 AAAATCACATTTTTACCCCTAAACT
* * ** * *
177882 TCCAAAAATCACATTTTTA-CCTTCGAACTTCTCGAAATTTACATTTTTACCCCTGAACTTCTAA
1 TTCTAAAATCACATTTTTAGCC-TAAAACTT-TCCAAAATTACATTTTTACCCCTGAACTTCTAA
177946 AAATCACATTTTTA-CCCTAAACT
64 AAATCACATTTTTACCCCTAAACT
* ** * *
177969 TTCTTAAAATGACATTTTTATGCCTAAAACTTTCCAAAATTATGTTTTTACTCC-GAACTTTCCA
1 TTC-TAAAATCACATTTTTA-GCCTAAAACTTTCCAAAATTACATTTTTACCCCTGAAC-TTCTA
* *
178033 AAAATGACTTTTTTACCCCTAAATCT
63 AAAATCACATTTTTACCCCTAAA-CT
* * ** * *
178059 TTCTAAAATTACA-TTTTAACCCCAAACTCTCCAAAACTT-CATTTTTAACCCTG
1 TTCTAAAATCACATTTTTAGCCTAAAACTTTCCAAAA-TTACATTTTTACCCCTG
178112 GTTTTTTTTT
Statistics
Matches: 185, Mismatches: 33, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
86 2 0.01
87 54 0.29
88 87 0.47
89 35 0.19
90 7 0.04
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (87 bp):
TTCTAAAATCACATTTTTAGCCTAAAACTTTCCAAAATTACATTTTTACCCCTGAACTTCTAAAA
ATCACATTTTTACCCCTAAACT
Found at i:178026 original size:117 final size:117
Alignment explanation
Indices: 177771--178086 Score: 324
Period size: 117 Copynumber: 2.7 Consensus size: 117
177761 CTAAAATTAT
* * *
177771 AAAAATTACA-TTTT-CTCTCGAACTTCT-AAAAATTACATTTTTACCCTTAAACTTCAAAAAAT
1 AAAAATCACATTTTTACTC-CGAACTTCTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAAT
* * *
177833 TACAATTTTACCCTAAAC-TTCTAAAAAATTACATTTTTACCCCCAAACTTCC
65 TACATTTTTACCCTAAACTTTCTAAAAAATGACATTTTTACCCCAAAACTTCC
* * * *
177885 AAAAATCACATTTTTACCTTCGAACTTCTCGAAATTTACATTTTTACCCCTGAACTTCTAAAAAT
1 AAAAATCACATTTTTA-CTCCGAACTTCTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAAT
* * * *
177950 CACATTTTTACCCTAAACTTTCT-TAAAATGACATTTTTATGCCTAAAACTTTCC
65 TACATTTTTACCCTAAACTTTCTAAAAAATGACATTTTTA-CCCCAAAAC-TTCC
* ** * *
178004 -AAAATTATGTTTTTACTCCGAACTT-TCCAAAAATGACTTTTTTACCCCTAAATCTTTCT-AAA
1 AAAAATCACATTTTTACTCCGAACTTCT-CAAAAATTACATTTTTACCCCTAAA-C-TTCTAAAA
* *
178066 ATTACATTTTAACCCCAAACT
63 ATTACATTTTTACCCTAAACT
178087 CTCCAAAACT
Statistics
Matches: 166, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
114 9 0.05
115 4 0.02
116 10 0.06
117 91 0.55
118 44 0.27
119 8 0.05
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (117 bp):
AAAAATCACATTTTTACTCCGAACTTCTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAATT
ACATTTTTACCCTAAACTTTCTAAAAAATGACATTTTTACCCCAAAACTTCC
Found at i:178075 original size:29 final size:29
Alignment explanation
Indices: 177635--178110 Score: 233
Period size: 29 Copynumber: 16.2 Consensus size: 29
177625 TCATAATTTG
* * **
177635 ACCCCTAAACTTTTTTAAAATTATATTTAA
1 ACCCCTAAAC-TTTCTAAAATTACATTTTT
*
177665 ACCCTTAAATCTTTCTAAAATTACATTTTT
1 ACCCCTAAA-CTTTCTAAAATTACATTTTT
** * * *
177695 ATCCCCCGAACTTTCCAAAAATTACATCTTG
1 A-CCCCTAAACTTT-CTAAAATTACATTTTT
* * * * *
177726 ACCCGTCGAACTTCTCCAAAACTATATTTTT
1 ACCCCT-AAACTT-TCTAAAATTACATTTTT
** * *
177757 GGCCCTAAAATTAT-AAAAATTACA-TTTT
1 ACCCCTAAACTT-TCTAAAATTACATTTTT
* *
177785 --CTCTCGAAC-TTCTAAAAATTACATTTTT
1 ACCCCT-AAACTTTCT-AAAATTACATTTTT
* * *
177813 ACCCTTAAAC-TTCAAAAAATTACAATTTT
1 ACCCCTAAACTTTC-TAAAATTACATTTTT
177842 A-CCCTAAAC-TTCTAAAAAATTACATTTTT
1 ACCCCTAAACTTTCT--AAAATTACATTTTT
* * * *
177871 ACCCCCAAACTTCCAAAAATCACATTTTT
1 ACCCCTAAACTTTCTAAAATTACATTTTT
* * * *
177900 A-CCTTCGAACTTCTCGAAATTTACATTTTT
1 ACCCCT-AAACTT-TCTAAAATTACATTTTT
* *
177930 ACCCCTGAAC-TTCTAAAAATCACATTTTT
1 ACCCCTAAACTTTCT-AAAATTACATTTTT
*
177959 A-CCCTAAACTTTCTTAAAATGACATTTTT
1 ACCCCTAAACTTTC-TAAAATTACATTTTT
** * **
177988 ATGCCTAAAACTTTCCAAAATTATGTTTTT
1 ACCCCT-AAACTTTCTAAAATTACATTTTT
* * * * *
178018 ACTCC-GAACTTTCCAAAAATGACTTTTTT
1 ACCCCTAAACTTT-CTAAAATTACATTTTT
*
178047 ACCCCTAAATCTTTCTAAAATTACATTTTA
1 ACCCCTAAA-CTTTCTAAAATTACATTTTT
* *
178077 ACCCC-AAACTCTCCAAAACTT-CATTTTT
1 ACCCCTAAACTTTCTAAAA-TTACATTTTT
*
178105 AACCCT
1 ACCCCT
178111 GGTTTTTTTT
Statistics
Matches: 339, Mismatches: 78, Indels: 59
0.71 0.16 0.12
Matches are distributed among these distances:
25 1 0.00
26 4 0.01
27 11 0.03
28 53 0.16
29 112 0.33
30 100 0.29
31 57 0.17
32 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
ACCCCTAAACTTTCTAAAATTACATTTTT
Found at i:189341 original size:16 final size:16
Alignment explanation
Indices: 189320--189372 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
189310 TCTAAATTTT
189320 AATTTATTTTAGTTTA
1 AATTTATTTTAGTTTA
* *
189336 AATTTA-TTGAGTTTG
1 AATTTATTTTAGTTTA
**
189351 AATTTATTTTAAATTA
1 AATTTATTTTAGTTTA
189367 AATTTA
1 AATTTA
189373 AAATTAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 13 0.43
16 17 0.57
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (16 bp):
AATTTATTTTAGTTTA
Found at i:189348 original size:15 final size:15
Alignment explanation
Indices: 189320--189358 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
189310 TCTAAATTTT
*
189320 AATTTATTTTAGTTTA
1 AATTTA-TTGAGTTTA
*
189336 AATTTATTGAGTTTG
1 AATTTATTGAGTTTA
189351 AATTTATT
1 AATTTATT
189359 TTAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (15 bp):
AATTTATTGAGTTTA
Found at i:190753 original size:30 final size:30
Alignment explanation
Indices: 190714--190888 Score: 149
Period size: 30 Copynumber: 5.8 Consensus size: 30
190704 AACTTTCCAG
* * *
190714 AAATCATATTTTAACCCCTAAATTTTTTGA
1 AAATTATATTTTAACCCCTAAACTTTTTCA
* * *
190744 AAATTATATTTTAACCCTTAACCTTTTGCA
1 AAATTATATTTTAACCCCTAAACTTTTTCA
* *
190774 AAATTATATTTTTACCTCC-AAA-TCTTTCCA
1 AAATTATATTTTAACC-CCTAAACT-TTTTCA
* * * *
190804 AATTTACATTTTAACCCCTTAAACTTTCTAA
1 AAATTATATTTTAACCCC-TAAACTTTTTCA
* * *
190835 AAATTATATCTTGACCCCTAAACTTCTTCA
1 AAATTATATTTTAACCCCTAAACTTTTTCA
* *
190865 TAATTACATTTT-ACCCCTAAACTT
1 AAATTATATTTTAACCCCTAAACTT
190889 CCAAAAATTA
Statistics
Matches: 114, Mismatches: 26, Indels: 11
0.75 0.17 0.07
Matches are distributed among these distances:
29 15 0.13
30 77 0.68
31 21 0.18
32 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.02, T:0.42
Consensus pattern (30 bp):
AAATTATATTTTAACCCCTAAACTTTTTCA
Found at i:191011 original size:30 final size:29
Alignment explanation
Indices: 190704--191071 Score: 243
Period size: 29 Copynumber: 12.5 Consensus size: 29
190694 AAGGTCCTTG
* * *
190704 AACTTTCCAGAAATCATATTTTAACCCCTA
1 AACTTTCCA-AAATTACATTTTTACCCCTA
* ** * * *
190734 AATTTTTTGAAAATTATATTTTAACCCTTA
1 AA-CTTTCCAAAATTACATTTTTACCCCTA
* * *
190764 ACCTTTTGCAAAATTATATTTTTACCTCC-A
1 AAC-TTTCCAAAATTACATTTTTACC-CCTA
* *
190794 AATCTTTCCAAATTTACATTTTAACCCCTTA
1 AA-CTTTCCAAAATTACATTTTTACCCC-TA
* * * *
190825 AACTTTCTAAAAATTATATCTTGACCCCTA
1 AACTTTC-CAAAATTACATTTTTACCCCTA
* *
190855 AACTTCTTCATAATTACA-TTTTACCCCTA
1 AACTT-TCCAAAATTACATTTTTACCCCTA
*
190884 AAC-TTCCAAAAATTACATTTTTACCCCCA
1 AACTTTCC-AAAATTACATTTTTACCCCTA
* * *
190913 AGC-TTCGAAAAATTACATTTTT--CCCTCG
1 AACTTTC-CAAAATTACATTTTTACCCCT-A
* *
190941 AACTTCTCAAAAATTACATTTTTACCTC-A
1 AACTT-TCCAAAATTACATTTTTACCCCTA
*
190970 AACTTTACCAAAATAACATTTTTACCCCTA
1 AACTTT-CCAAAATTACATTTTTACCCCTA
** *
191000 AATCTTTCCAAAATTAC-TTTTTACTTC-G
1 AA-CTTTCCAAAATTACATTTTTACCCCTA
* *
191028 AACTTCCCAAAATGACATTTTTA-CCCTA
1 AACTTTCCAAAATTACATTTTTACCCCTA
191056 AATCTTTCCAAAATTA
1 AA-CTTTCCAAAATTA
191072 TGTTTTAACT
Statistics
Matches: 265, Mismatches: 51, Indels: 45
0.73 0.14 0.12
Matches are distributed among these distances:
27 18 0.07
28 22 0.08
29 101 0.38
30 93 0.35
31 31 0.12
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
AACTTTCCAAAATTACATTTTTACCCCTA
Found at i:194145 original size:15 final size:16
Alignment explanation
Indices: 194118--194148 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
194108 CAGTAATTTA
194118 TTCTTTTTCTTTTTCT
1 TTCTTTTTCTTTTTCT
194134 TTCTTTTT-TTTTTCT
1 TTCTTTTTCTTTTTCT
194149 CATATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTCTTTTTCTTTTTCT
Found at i:203758 original size:25 final size:25
Alignment explanation
Indices: 203712--203759 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
203702 CTCACATATA
* *
203712 ATAGAAAAACCATAATGACTTCCGT
1 ATAGAAAAACCACAAAGACTTCCGT
* *
203737 ATAGAACAACCACAAAGGCTTCC
1 ATAGAAAAACCACAAAGACTTCC
203760 ACATATAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (25 bp):
ATAGAAAAACCACAAAGACTTCCGT
Found at i:206355 original size:21 final size:20
Alignment explanation
Indices: 206329--206402 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
206319 TGTTCTACCT
*
206329 GTAGAAGTCTGGGTTGTATCA
1 GTAGAAGTCT-AGTTGTATCA
**
206350 GTAGAACCCATAGTTGTATCA
1 GTAGAAGTC-TAGTTGTATCA
* *
206371 GTAGAAGTCTTAGTTCTATCG
1 GTAGAAGTC-TAGTTGTATCA
*
206392 GTAGAATTCTA
1 GTAGAAGTCTA
206403 AAGCTTTTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (20 bp):
GTAGAAGTCTAGTTGTATCA
Found at i:208468 original size:81 final size:80
Alignment explanation
Indices: 208378--208533 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 80
208368 TATCGATACA
* * * *
208378 ATCCATTTTATCGACTCACGATGTTGCTCATACAAGCT-ATCAAGAATCCATAACATATTCAAGA
1 ATCCATTTTATCCACTCACGATGCTGCTCACACAAGCTGAT-AAGAATCCATAACATATGCAAGA
208442 TCTTAGCCGTCAAAGG
65 TCTTAGCCGTCAAAGG
* * * * *
208458 ATCCATTTTTATCCACTCACGGTGCTGCTCACACAAGCTGATAATAATCCGTAACTTATGCAGGA
1 ATCCA-TTTTATCCACTCACGATGCTGCTCACACAAGCTGATAAGAATCCATAACATATGCAAGA
208523 TCTTAGCCGTC
65 TCTTAGCCGTC
208534 GGAGAGTCCT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
80 5 0.08
81 58 0.89
82 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (80 bp):
ATCCATTTTATCCACTCACGATGCTGCTCACACAAGCTGATAAGAATCCATAACATATGCAAGAT
CTTAGCCGTCAAAGG
Found at i:215362 original size:81 final size:80
Alignment explanation
Indices: 215214--215364 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 80
215204 CCATCGATAC
* * * *
215214 GGTCCATTTTATACACTCACGATGCTGCTCACACAAGCTGTCAAGAATTTGCAACATATGTAGGA
1 GGTCCATTTTATACACTCACAATGCTGCTCACACAAGCTGTCAAGAATTCGCAACATATGCAAGA
215279 TCTTATCCATCAGAG
66 TCTTATCCATCAGAG
* * * * * * * *
215294 GGTCCATATTTATCCACTCACAATTCTGCTCGCTCAAGTTGTTAAGAATTCGTAACTTATGCAAG
1 GGTCCAT-TTTATACACTCACAATGCTGCTCACACAAGCTGTCAAGAATTCGCAACATATGCAAG
215359 ATCTTA
65 ATCTTA
215365 GCTGTCGGAG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
80 7 0.12
81 51 0.88
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (80 bp):
GGTCCATTTTATACACTCACAATGCTGCTCACACAAGCTGTCAAGAATTCGCAACATATGCAAGA
TCTTATCCATCAGAG
Found at i:221597 original size:26 final size:22
Alignment explanation
Indices: 221550--221593 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
221540 TTAAACGAAA
221550 GGGTGAATAATTCATTTTTCTT
1 GGGTGAATAATTCATTTTTCTT
221572 GGGTGAATAATTCATTTTTCTT
1 GGGTGAATAATTCATTTTTCTT
221594 TCTTCTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (22 bp):
GGGTGAATAATTCATTTTTCTT
Found at i:229261 original size:81 final size:81
Alignment explanation
Indices: 229176--229326 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 81
229166 TACGGTCAAT
* * * *
229176 TTTATCCACTCACGATGCTGCTCACATAATCTGTCAATAATTTC-CAACATATGCAGGATCTTAG
1 TTTATCCACTCACGATGCTGCTCACACAAGCTGTCAAGAA-TCCGCAACATATGCAGGATCTTAG
229240 CCATCAAGGGGTCCATA
65 CCATCAAGGGGTCCATA
* * *
229257 TTTATCCACTCACGATTCTGCTCACACAAGCTGTCAAGAATCCGCAACTTATGCTGGATCTTAGC
1 TTTATCCACTCACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCTTAGC
229322 CATCA
66 CATCA
229327 GAGAGTCCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.03
81 60 0.97
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (81 bp):
TTTATCCACTCACGATGCTGCTCACACAAGCTGTCAAGAATCCGCAACATATGCAGGATCTTAGC
CATCAAGGGGTCCATA
Found at i:235134 original size:21 final size:21
Alignment explanation
Indices: 235108--235156 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
235098 TAACATAGGA
* *
235108 ATTTTTCATTATTTTTGTTTT
1 ATTTTTCATTACTTTCGTTTT
*
235129 ATTTTTTATTACTTTCGTTTT
1 ATTTTTCATTACTTTCGTTTT
*
235150 CTTTTTC
1 ATTTTTC
235157 TTTTTTGTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTCATTACTTTCGTTTT
Found at i:238018 original size:2 final size:2
Alignment explanation
Indices: 238011--238039 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
238001 ATAAGTTGAA
238011 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
238040 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:238044 original size:2 final size:2
Alignment explanation
Indices: 238039--238117 Score: 60
Period size: 2 Copynumber: 42.0 Consensus size: 2
238029 ACACACACAC
* *
238039 AT AT AT AT AT AT AT AA AC A- AT AT A- 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 AT
* * * * *
238079 GT AT GT AT A- AA AT TT AT AT A- AC A- 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 AT
238118 TAATAGAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
1 5 0.08
2 58 0.92
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:257444 original size:21 final size:21
Alignment explanation
Indices: 257418--257480 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
257408 CAAACAATGA
*
257418 CAAAAAGTATCTATACCTTTT
1 CAAAAAGTATCGATACCTTTT
257439 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
257460 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
257481 ATCAGGTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (21 bp):
CAAAAAGTATCGATACCTTTT
Found at i:258763 original size:25 final size:23
Alignment explanation
Indices: 258728--258780 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
258718 GGAAAATCAT
* *
258728 GTAAATTATAAAAAGGTAAAAGA
1 GTAAATTATAAAAACGTAAAAAA
*
258751 GTAAATTACATAAAAACTTAAAAAA
1 GTAAATT--ATAAAAACGTAAAAAA
258776 GTAAA
1 GTAAA
258781 CAAAAGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
25 18 0.72
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23
Consensus pattern (23 bp):
GTAAATTATAAAAACGTAAAAAA
Found at i:270115 original size:26 final size:29
Alignment explanation
Indices: 270064--270121 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
270054 TTTTCTTAAG
270064 AAATCAAAACCAAATTTTTATTAAAG-CA
1 AAATCAAAACCAAATTTTTATTAAAGTCA
270092 AAATC-AAACCAAA-TTTTATTAAAGTCA
1 AAATCAAAACCAAATTTTTATTAAAGTCA
270119 AAA
1 AAA
270122 CTTACATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 11 0.38
27 13 0.45
28 5 0.17
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (29 bp):
AAATCAAAACCAAATTTTTATTAAAGTCA
Found at i:271282 original size:4 final size:4
Alignment explanation
Indices: 271275--271314 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
271265 TTTGTTTATC
* *
271275 TTTA TTTA TTTA TTTA TTTA TTTTT TTTA GTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTT
271315 GTAGTCCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 28 0.90
5 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:271308 original size:21 final size:22
Alignment explanation
Indices: 271264--271314 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
271254 GGTTTAATTA
* *
271264 ATTTGTTTATCTTTATTTATTT
1 ATTTATTTATCTTTATTTAGTT
*
271286 ATTTATTTAT-TTTTTTTAGTT
1 ATTTATTTATCTTTATTTAGTT
271307 ATTTATTT
1 ATTTATTT
271315 GTAGTCCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTATTTATCTTTATTTAGTT
Found at i:284375 original size:37 final size:37
Alignment explanation
Indices: 284304--284375 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
284294 CTATAGTTTC
*
284304 CTATAATTTCACAATCACATTCCTATAGTCTCAAAAT
1 CTATAATTTCACAATCACATTCCTAGAGTCTCAAAAT
* * ** *
284341 CTATAGTTTCACATTCACATTTTTAGAGTTTCAAA
1 CTATAATTTCACAATCACATTCCTAGAGTCTCAAA
284376 TCATATCTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.39
Consensus pattern (37 bp):
CTATAATTTCACAATCACATTCCTAGAGTCTCAAAAT
Found at i:286304 original size:18 final size:19
Alignment explanation
Indices: 286281--286319 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
286271 TTAGTCACAT
* *
286281 AAGAAATCGACAA-AAGAA
1 AAGAAAACGAAAAGAAGAA
286299 AAGAAAACGAAAAGAAGAA
1 AAGAAAACGAAAAGAAGAA
286318 AA
1 AA
286320 AGGTCACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.18, T:0.03
Consensus pattern (19 bp):
AAGAAAACGAAAAGAAGAA
Found at i:288069 original size:30 final size:29
Alignment explanation
Indices: 288024--288180 Score: 116
Period size: 30 Copynumber: 5.6 Consensus size: 29
288014 ATCCCTGAAT
*
288024 AGGAAGCCTTTTGTGGCGAGTTCTAAATAA
1 AGGAAGCC-TTTGTGGCGAGTTCTGAATAA
* *
288054 AGGGAAGCCTTTGTGGC-AATCCCTGAAT--
1 A-GGAAGCCTTTGTGGCGAGT-TCTGAATAA
*
288082 AGGAAGCCTTTGTGGTGAGTTCTGAATGAA
1 AGGAAGCCTTTGTGGCGAGTTCTGAAT-AA
* *
288112 AAGAAGCCTTTGTGGC-AATCTCTGAAT--
1 AGGAAGCCTTTGTGGCGAGT-TCTGAATAA
* * **
288139 AGGAAGGCTTTGTGGCGA--CCT-ACGAA
1 AGGAAGCCTTTGTGGCGAGTTCTGAATAA
288165 AGGAAGCCTTTGTGGC
1 AGGAAGCCTTTGTGGC
288181 AATCTTTGAA
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
24 1 0.01
25 2 0.02
26 15 0.15
27 34 0.33
28 4 0.04
29 4 0.04
30 35 0.34
31 7 0.07
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (29 bp):
AGGAAGCCTTTGTGGCGAGTTCTGAATAA
Found at i:288090 original size:27 final size:27
Alignment explanation
Indices: 287999--288184 Score: 139
Period size: 27 Copynumber: 6.7 Consensus size: 27
287989 TAAATGAGCA
*
287999 GAAGCCTTTGTGACAATCCCTGAATAG
1 GAAGCCTTTGTGGCAATCCCTGAATAG
* * *
288026 GAAGCCTTTTGTGGCGAGT-TCTAAATAAAGG
1 GAAGCC-TTTGTGGC-AATCCCTGAAT--A-G
288057 GAAGCCTTTGTGGCAATCCCTGAATAG
1 GAAGCCTTTGTGGCAATCCCTGAATAG
* * * *
288084 GAAGCCTTTGTGGTGAGT-TCTGAATGAAAA
1 GAAGCCTTTGTGG-CAATCCCTGAAT---AG
*
288114 GAAGCCTTTGTGGCAATCTCTGAATAG
1 GAAGCCTTTGTGGCAATCCCTGAATAG
* *
288141 GAAGGCTTTGTGGCGA--CCTACGAA-AG
1 GAAGCCTTTGTGGCAATCCCT--GAATAG
288167 GAAGCCTTTGTGGCAATC
1 GAAGCCTTTGTGGCAATC
288185 TTTGAAAAGA
Statistics
Matches: 125, Mismatches: 19, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
25 2 0.02
26 16 0.13
27 44 0.35
28 15 0.12
29 6 0.05
30 35 0.28
31 7 0.06
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (27 bp):
GAAGCCTTTGTGGCAATCCCTGAATAG
Found at i:288121 original size:57 final size:57
Alignment explanation
Indices: 287981--288184 Score: 256
Period size: 57 Copynumber: 3.6 Consensus size: 57
287971 TGTTTGTGTT
** *
287981 GCGAGTTCTAAATGAGCAGAAGCCTTTGTGACAATCCCTGAATAGGAAGCCTTTTGTG
1 GCGAGTTCTAAATGAAAAGAAGCCTTTGTGGCAATCCCTGAATAGGAAGCC-TTTGTG
*
288039 GCGAGTTCTAAAT-AAAGGGAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTG
1 GCGAGTTCTAAATGAAA-AGAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTG
* * * *
288096 GTGAGTTCTGAATGAAAAGAAGCCTTTGTGGCAATCTCTGAATAGGAAGGCTTTGTG
1 GCGAGTTCTAAATGAAAAGAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTG
* * *
288153 GCGA--CCT--ACGAAAGGAAGCCTTTGTGGCAATC
1 GCGAGTTCTAAATGAAAAGAAGCCTTTGTGGCAATC
288185 TTTGAAAAGA
Statistics
Matches: 131, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
53 23 0.18
55 2 0.02
57 58 0.44
58 48 0.37
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (57 bp):
GCGAGTTCTAAATGAAAAGAAGCCTTTGTGGCAATCCCTGAATAGGAAGCCTTTGTG
Found at i:288201 original size:27 final size:27
Alignment explanation
Indices: 287999--288206 Score: 134
Period size: 27 Copynumber: 7.5 Consensus size: 27
287989 TAAATGAGCA
* ** *
287999 GAAGCCTTTGTGACAATCCCTGAATAG
1 GAAGCCTTTGTGGCAATCTATGAAAAG
* *
288026 GAAGCCTTTTGTGGCGAGTTCTAAAT-AAAGG
1 GAAGCC-TTTGTGGC-A-ATCT--ATGAAAAG
** *
288057 GAAGCCTTTGTGGCAATCCCTGAATAG
1 GAAGCCTTTGTGGCAATCTATGAAAAG
* *
288084 GAAGCCTTTGTGGTGAGTTCTGAATGAAAA-
1 GAAGCCTTTGTGG-CA-ATCT--ATGAAAAG
* *
288114 GAAGCCTTTGTGGCAATCTCTGAATAG
1 GAAGCCTTTGTGGCAATCTATGAAAAG
* * * *
288141 GAAGGCTTTGTGGCGACCTACG-AAAG
1 GAAGCCTTTGTGGCAATCTATGAAAAG
*
288167 GAAGCCTTTGTGGCAATCTTTGAAAAG
1 GAAGCCTTTGTGGCAATCTATGAAAAG
* *
288194 AAAGCCTTCGTGG
1 GAAGCCTTTGTGG
288207 AGAACTCTGT
Statistics
Matches: 136, Mismatches: 33, Indels: 24
0.70 0.17 0.12
Matches are distributed among these distances:
26 26 0.19
27 54 0.40
28 13 0.10
29 5 0.04
30 23 0.17
31 14 0.10
32 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (27 bp):
GAAGCCTTTGTGGCAATCTATGAAAAG
Found at i:288246 original size:22 final size:22
Alignment explanation
Indices: 288209--288264 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
288199 CTTCGTGGAG
*
288209 AACTCTGTA-GAATGCAAGGCA
1 AACTCTGAAGGAATGCAAGGCA
*
288230 AACTCTGAAGGAATGCAAGGCG
1 AACTCTGAAGGAATGCAAGGCA
* *
288252 AACCCTAAAGGAA
1 AACTCTGAAGGAA
288265 AGGAATGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (22 bp):
AACTCTGAAGGAATGCAAGGCA
Found at i:292333 original size:2 final size:2
Alignment explanation
Indices: 292326--292356 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
292316 CAACATAGGT
292326 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
292357 TAATATGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:293356 original size:27 final size:26
Alignment explanation
Indices: 293313--293381 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
293303 CGAGTTCTGA
293313 ATGAAAGGAAGCCTTTGTGGCAATCCT
1 ATGAAAGGAAGCCTTTGTGGCAA-CCT
*
293340 -TGAATAGGAAGCCTTTGTGGCGACCT
1 ATGAA-AGGAAGCCTTTGTGGCAACCT
*
293366 ATGAAAGAAAGCCTTT
1 ATGAAAGGAAGCCTTT
293382 ATGAAAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 17 0.45
27 21 0.55
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (26 bp):
ATGAAAGGAAGCCTTTGTGGCAACCT
Found at i:293376 original size:57 final size:57
Alignment explanation
Indices: 293267--293376 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
293257 TGAACAAAAA
* ** * *
293267 CCTTTGTGGAAATCCCTAAATAGGAAGCCTTTGAATCGAGTTCTGAATGAAAGGAAG
1 CCTTTGTGGAAATCCCTAAATAGGAAGCCTTTGAAGCGACCTATGAAAGAAAGGAAG
* * * **
293324 CCTTTGTGGCAATCCTTGAATAGGAAGCCTTTGTGGCGACCTATGAAAGAAAG
1 CCTTTGTGGAAATCCCTAAATAGGAAGCCTTTGAAGCGACCTATGAAAGAAAG
293377 CCTTTATGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (57 bp):
CCTTTGTGGAAATCCCTAAATAGGAAGCCTTTGAAGCGACCTATGAAAGAAAGGAAG
Found at i:296653 original size:38 final size:38
Alignment explanation
Indices: 296602--296677 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
296592 AGTTTTACTT
296602 ACCTAAATCAAGCTCACAAGTTCAACAATGGAAAACCC
1 ACCTAAATCAAGCTCACAAGTTCAACAATGGAAAACCC
296640 ACCTAAATCAAGCTCACAAGTTCAACAATGGAAAACCC
1 ACCTAAATCAAGCTCACAAGTTCAACAATGGAAAACCC
296678 TAGTTTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.16
Consensus pattern (38 bp):
ACCTAAATCAAGCTCACAAGTTCAACAATGGAAAACCC
Found at i:304765 original size:24 final size:24
Alignment explanation
Indices: 304733--304781 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
304723 TTATGTTAGA
304733 AATGTACATTGAGTATTGCTAATG
1 AATGTACATTGAGTATTGCTAATG
304757 AATGTACATTGAGTATTGCTAATG
1 AATGTACATTGAGTATTGCTAATG
304781 A
1 A
304782 CGAGCTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (24 bp):
AATGTACATTGAGTATTGCTAATG
Found at i:308580 original size:18 final size:18
Alignment explanation
Indices: 308559--308596 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
308549 TGAATTTTCG
308559 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAACT-GAAT
308577 AATTCGAATAAACTGAAT
1 AATTCGAATAAACTGAAT
308595 AA
1 AA
308597 AACTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACTGAAT
Found at i:314601 original size:5 final size:5
Alignment explanation
Indices: 314587--314625 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
314577 TAAACATCCT
* *
314587 CACCC TACCC CACCC CACCC CACCC CACCC CACCA CACC
1 CACCC CACCC CACCC CACCC CACCC CACCC CACCC CACC
314626 TTTTCTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.74, G:0.00, T:0.03
Consensus pattern (5 bp):
CACCC
Found at i:316078 original size:17 final size:16
Alignment explanation
Indices: 316058--316090 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
316048 TTTTTCTCCT
316058 TCTCTTTTCTCTCTCTC
1 TCTCTTTTCT-TCTCTC
316075 TCTCTTTTCTTCTCTC
1 TCTCTTTTCTTCTCTC
316091 ATTATGGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TCTCTTTTCTTCTCTC
Found at i:316172 original size:246 final size:244
Alignment explanation
Indices: 315731--316198 Score: 751
Period size: 246 Copynumber: 1.9 Consensus size: 244
315721 ATTATAACCC
*
315731 GCCACATCATTTAAACTTTAAAAAGTTATATTTTTTTTAAATTCTTTTACCTTATTTTCTTCTTT
1 GCCACATCATTTAAACTTTAAAAAATTATATTTTTTTTAAATTCTTTTACCTTATTTTCTTCTTT
* *
315796 TTATTTACATTTTTCTCCTATTTCCTCTCTTTCTCTCTTTTGTTCTCTCATTATGGCAGCATATT
66 TTATTTACATTTTTCTCCTATTTCCTCTCTCTCTCTCTTTTCTTCTCTCATTATGGCAGCATATT
* *
315861 CATCTCTGCAACTTGGTTATTTAAAGATCCTTGTAATTATCTCGCATATATCAATGAACATTCTT
131 CATCTCTGCAACTTGGTTATTTAAAGATCCTTGTAATTATCTCGCATATATCAATCAAAATTCTT
*
315926 TTGAATAAAGCTGTGATATTATAAGCTTTTAATTGTTCTATTATGACAT
196 TTGAATAAAGCTGTGATACTATAAGCTTTTAATTGTTCTATTATGACAT
*
315975 GCCACGTCATTTAAACTTTAAAAAAATTATA-TTTTTTT-AATTCTTTTACCTTATTTTCTTCTT
1 GCCACATCATTTAAACTTT-AAAAAATTATATTTTTTTTAAATTCTTTTACCTTATTTTCTTCTT
* *
316038 TTTATTTACATTTTTCTCCTTCTCTTTTCTCTCTCTCTCTCTTTTCTTCTCTCATTATGGCAGCA
65 TTTATTTACATTTTTCT-C--CTATTTCCTCTCTCTCTCTCTTTTCTTCTCTCATTATGGCAGCA
* * * * *
316103 TATTCATCTCTGCAACTTGGTTATTTTAAGTTCCTTGTAATTTTCTTGCATGTATCAATCAAAAT
127 TATTCATCTCTGCAACTTGGTTATTTAAAGATCCTTGTAATTATCTCGCATATATCAATCAAAAT
*
316168 TCTTTTGAATAAAGCTTTGATACTATAAGCT
192 TCTTTTGAATAAAGCTGTGATACTATAAGCT
316199 AGCACAAGAA
Statistics
Matches: 205, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
243 42 0.20
244 26 0.13
245 10 0.05
246 127 0.62
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (244 bp):
GCCACATCATTTAAACTTTAAAAAATTATATTTTTTTTAAATTCTTTTACCTTATTTTCTTCTTT
TTATTTACATTTTTCTCCTATTTCCTCTCTCTCTCTCTTTTCTTCTCTCATTATGGCAGCATATT
CATCTCTGCAACTTGGTTATTTAAAGATCCTTGTAATTATCTCGCATATATCAATCAAAATTCTT
TTGAATAAAGCTGTGATACTATAAGCTTTTAATTGTTCTATTATGACAT
Found at i:318137 original size:26 final size:26
Alignment explanation
Indices: 318108--318159 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
318098 GGATTTTATT
*
318108 CTTGTAGACTAAGAAACTAAAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
*
318134 CTTGTAGAATAAGAAACTATAATTAA
1 CTTGTAGAATAAGAAACTAAAATTAA
318160 GGAAACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (26 bp):
CTTGTAGAATAAGAAACTAAAATTAA
Found at i:321245 original size:16 final size:17
Alignment explanation
Indices: 321222--321266 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
321212 CATTTATCAC
321222 ATAT-ATATATATTTA-
1 ATATAATATATATTTAG
*
321237 ATATAATATAT-GTTAG
1 ATATAATATATATTTAG
*
321253 ATATATTATATATT
1 ATATAATATATATT
321267 ACAAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.29
16 16 0.67
17 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
ATATAATATATATTTAG
Found at i:332035 original size:22 final size:21
Alignment explanation
Indices: 332010--332051 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
332000 ATATATATAA
332010 AACAAAAATAAAAATGCAAAGC
1 AACAAAAAT-AAAATGCAAAGC
* *
332032 AACATATATAAAATGCAAAG
1 AACAAAAATAAAATGCAAAG
332052 GATCACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.64, C:0.12, G:0.10, T:0.14
Consensus pattern (21 bp):
AACAAAAATAAAATGCAAAGC
Done.