Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013316.1 Kokia drynarioides strain JFW-HI SEQ_128338, 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: 179042
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:413 original size:12 final size:12
Alignment explanation
Indices: 398--432 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
388 TTACGATGTT
398 TATTATTATTAA
1 TATTATTATTAA
*
410 TATTATTACTAA
1 TATTATTATTAA
*
422 CATTATTATTA
1 TATTATTATTA
433 TTAAAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:1307 original size:7 final size:6
Alignment explanation
Indices: 1211--1321 Score: 72
Period size: 6 Copynumber: 18.8 Consensus size: 6
1201 GTTTCAAATT
* * **
1211 ATTTCAA ATTTAA A-CTAA AATTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
1258 ATTTGAA A--T-A ATTTGAA ACTTAA ACTAAA ATTTAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
1305 A-ATAA ATTTTAA ATTTA
1 ATTTAA A-TTTAA ATTTA
1322 GAAATAAATG
Statistics
Matches: 82, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
3 2 0.02
5 13 0.16
6 52 0.63
7 15 0.18
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:1315 original size:18 final size:19
Alignment explanation
Indices: 1290--1330 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1280 AACTAAAATT
1290 TAAA-TTTAAATTTA-AAA
1 TAAATTTTAAATTTAGAAA
1307 TAAATTTTAAATTTAGAAA
1 TAAATTTTAAATTTAGAAA
1326 TAAAT
1 TAAAT
1331 GTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAATTTTAAATTTAGAAA
Found at i:1329 original size:24 final size:24
Alignment explanation
Indices: 1278--1329 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1268 ATTTGAAACT
* *
1278 TAAACTAAAATTTAAATTTAAATT
1 TAAAATAAAATTTAAATTTAAATA
*
1302 TAAAATAAATTTTAAATTTAGAA-A
1 TAAAATAAAATTTAAATTTA-AATA
1326 TAAA
1 TAAA
1330 TGTAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAATAAAATTTAAATTTAAATA
Found at i:1335 original size:18 final size:17
Alignment explanation
Indices: 1211--1335 Score: 66
Period size: 17 Copynumber: 7.4 Consensus size: 17
1201 GTTTCAAATT
*
1211 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
* *
1229 AATTAAATTTAAAACAA
1 ATTTAAATTTAAAATAA
1246 ATTTAAATTT-AAAT--
1 ATTTAAATTTAAAATAA
* **
1260 -TTGAAA--TAATTTGAA
1 ATTTAAATTTAAAAT-AA
* *
1275 ACTTAAA-CTAAAATTTAA
1 ATTTAAATTTAAAA--TAA
1293 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
1310 ATTTTAAATTTAGAAATAA
1 A-TTTAAATTTA-AAATAA
*
1329 ATGTAAA
1 ATTTAAA
1336 ATAATTTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
11 1 0.01
12 2 0.02
13 5 0.06
16 7 0.09
17 27 0.33
18 26 0.32
19 13 0.16
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1337 original size:19 final size:18
Alignment explanation
Indices: 1297--1337 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1287 ATTTAAATTT
* *
1297 AAATTTAAAATAAATTTT
1 AAATTTAAAATAAATGTA
1315 AAATTTAGAAATAAATGTA
1 AAATTTA-AAATAAATGTA
1334 AAAT
1 AAAT
1338 AATTTGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTTAAAATAAATGTA
Found at i:1822 original size:49 final size:49
Alignment explanation
Indices: 1714--1912 Score: 206
Period size: 50 Copynumber: 4.1 Consensus size: 49
1704 CCTCTAAATA
* * *
1714 TTCGTGGTACTTGATCCGCCATTGT-GACTTAGATCTTTCCCTTCGT-C
1 TTCGCGGTACTGGATCCGCCATTGTGGTCTTAGATCTTTCCCTTCGTGC
* * * * * *
1761 TTCGCAGTACTGGATCCGCCGTTGTGGTTTTAGATCCTACCCTTCATGC
1 TTCGCGGTACTGGATCCGCCATTGTGGTCTTAGATCTTTCCCTTCGTGC
* * * *
1810 TTCGCGGTACTGGATCCGCCACTGCGGTCTTAGATCTTTCCCGTCGTGTT
1 TTCGCGGTACTGGATCCGCCATTGTGGTCTTAGATCTTTCCCTTCGTG-C
* * *
1860 TTTGTGGTACTGGATCCGCCGTTGTGGTCTTTA-ATCTTTCCCTTCGTGTC
1 TTCGCGGTACTGGATCCGCCATTGTGGTC-TTAGATCTTTCCCTTCGTG-C
1910 TTC
1 TTC
1913 TGAGGTACAC
Statistics
Matches: 121, Mismatches: 27, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
47 21 0.17
48 16 0.13
49 40 0.33
50 41 0.34
51 3 0.02
ACGTcount: A:0.11, C:0.28, G:0.23, T:0.39
Consensus pattern (49 bp):
TTCGCGGTACTGGATCCGCCATTGTGGTCTTAGATCTTTCCCTTCGTGC
Found at i:6709 original size:18 final size:19
Alignment explanation
Indices: 6667--6709 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
6657 TCTTGTCGTG
6667 CTTTTCTCATCTCTCGCTT
1 CTTTTCTCATCTCTCGCTT
* **
6686 CCTTTCT-ATCTCTTTCTT
1 CTTTTCTCATCTCTCGCTT
6704 CTTTTC
1 CTTTTC
6710 CTTCACATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.05, C:0.35, G:0.02, T:0.58
Consensus pattern (19 bp):
CTTTTCTCATCTCTCGCTT
Found at i:13761 original size:29 final size:30
Alignment explanation
Indices: 13733--13945 Score: 150
Period size: 29 Copynumber: 6.9 Consensus size: 30
13723 ATCTAAGGGT
*
13733 AAAATGGTAA-TTTTTGAAAGTTTCGGGGTTA
1 AAAAT-GTAATTTTTTG-AAGTTTAGGGGTTA
* * * *
13764 AAAATGGAATTTTATGGAGGTTAGGGG-TA
1 AAAATGTAATTTTTTGAAGTTTAGGGGTTA
*
13793 AAAATGTAATTTTTTGAAGTTTTGGGGTTA
1 AAAATGTAATTTTTTGAAGTTTAGGGGTTA
*
13823 AAAATGTAATTTTTTGAAGTTTTGGAAAGTTCAGGGGTA
1 AAAATGTAATTTTTTGAAG-TTT----AG----GGGTTA
* * *
13862 AAAATGTAA-TTTTGGAAGTTTCGAGGTT-
1 AAAATGTAATTTTTTGAAGTTTAGGGGTTA
* *
13890 AAAATGGAATTTTTGGAAGTTT-GGGAG-TA
1 AAAATGTAATTTTTTGAAGTTTAGGG-GTTA
*
13919 AAAATGTAATTTTTGGAAAGTTTAGGG
1 AAAATGTAATTTTTTG-AAGTTTAGGG
13946 TCAAAATTAG
Statistics
Matches: 147, Mismatches: 19, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
28 11 0.07
29 55 0.37
30 38 0.26
31 16 0.11
33 1 0.01
35 1 0.01
37 3 0.02
38 8 0.05
39 14 0.10
ACGTcount: A:0.33, C:0.01, G:0.27, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTTGAAGTTTAGGGGTTA
Found at i:13767 original size:60 final size:60
Alignment explanation
Indices: 13611--13826 Score: 151
Period size: 60 Copynumber: 3.7 Consensus size: 60
13601 GACTCTCGAG
* * * * * * *
13611 AGGGCAAAATGGTAATTTTAGAAAAATTT-AGGGTT-AAAACATAA-TTTTAGG-CATCCA
1 AGGGTAAAATGGTAATTTTTG-AAAGTTTCGGGGTTAAAAACAGAATTTTTTGGACATCTA
** ** * * *
13668 AGGGTAAAACAGTAATTTTTAGAAA-AATCGAGATAAAAAACAGAATTTTTTGGACATCTA
1 AGGGTAAAATGGTAATTTTT-GAAAGTTTCGGGGTTAAAAACAGAATTTTTTGGACATCTA
** * **
13728 AGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTTAAAAATGGAATTTTATGGAGGT-TA
1 AGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTTAAAAACAGAATTTTTTGGACATCTA
* *
13787 GGGGTAAAAAT-GTAATTTTTTG-AAGTTTTGGGGTTAAAAA
1 AGGGT-AAAATGGTAA-TTTTTGAAAGTTTCGGGGTTAAAAA
13827 TGTAATTTTT
Statistics
Matches: 124, Mismatches: 27, Indels: 14
0.75 0.16 0.08
Matches are distributed among these distances:
56 1 0.01
57 21 0.17
58 9 0.07
59 37 0.30
60 56 0.45
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
AGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTTAAAAACAGAATTTTTTGGACATCTA
Found at i:13820 original size:59 final size:58
Alignment explanation
Indices: 13729--14014 Score: 224
Period size: 59 Copynumber: 4.7 Consensus size: 58
13719 GGACATCTAA
* * *
13729 GGGT-AAAATGGTAATTTTTGAAAGTTTCGGGGTTAAAAATGGAATTTTATGGAGGTTAG
1 GGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTT-TGGAAGTTAG
* *
13788 GGGTAAAAATGTAATTTTTTGAAGTTTTGGGGTTAAAAATGTAATTTTTTGAAGTTTTGGAAAGT
1 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATG---------GAATTTTTGG-AAGT
13853 TCAG
56 T-AG
* * *
13857 GGGTAAAAATGTAA-TTTTGGAAGTTTCGAGGTT-AAAATGGAATTTTTGGAAGTTTG
1 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTAG
* * * * *
13913 GGAGTAAAAATGTAATTTTTGGAAAG-TTTAGGGTCAAAATTAGAATTTTTGGAAGTTCG
1 GG-GTAAAAATGTAATTTTTGG-AAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTAG
* * * *
13972 AGGGTACAAATGTTA-TTTTGAAAAG-TTTGGGGTAAAAAATGGA
1 -GGGTAAAAATGTAATTTTTG-GAAGTTTTGGGGTTAAAAATGGA
14015 TTAAATTAAA
Statistics
Matches: 185, Mismatches: 24, Indels: 37
0.75 0.10 0.15
Matches are distributed among these distances:
56 3 0.02
57 17 0.09
58 42 0.23
59 65 0.35
60 7 0.04
67 9 0.05
68 26 0.14
69 16 0.09
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTAG
Found at i:13952 original size:58 final size:56
Alignment explanation
Indices: 13842--14014 Score: 177
Period size: 58 Copynumber: 3.0 Consensus size: 56
13832 TTTTTTGAAG
* *
13842 TTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTGG-AAGTTTCGAGGTTAAAATGGAAT
1 TTTTGG-AAGTT-AGGGGTAAAAATGTAATTTTGGAAAGTTTAG-GGTAAAAATGGAAT
* * *
13900 TTTTGGAAGTTTGGGAGTAAAAATGTAATTTTTGGAAAGTTTAGGGTCAAAATTAGAAT
1 TTTTGGAAGTTAGGG-GTAAAAATGTAA-TTTTGGAAAGTTTAGGGT-AAAAATGGAAT
* * * * *
13959 TTTTGGAAGTTCGAGGGTACAAATGTTATTTTGAAAAGTTTGGGGTAAAAAATGGA
1 TTTTGGAAGTTAG-GGGTAAAAATGTAATTTTGGAAAGTTTAGGGT-AAAAATGGA
14015 TTAAATTAAA
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.03
57 17 0.18
58 38 0.39
59 37 0.38
60 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (56 bp):
TTTTGGAAGTTAGGGGTAAAAATGTAATTTTGGAAAGTTTAGGGTAAAAATGGAAT
Found at i:13960 original size:30 final size:29
Alignment explanation
Indices: 13842--14009 Score: 141
Period size: 29 Copynumber: 5.8 Consensus size: 29
13832 TTTTTTGAAG
*
13842 TTTTGGAAAGTTCAGGGGTAAAAATGTAA-
1 TTTTGGAAAGTTTA-GGGTAAAAATGTAAT
* * *
13871 TTTTGG-AAGTTTCGAGGTTAAAATGGAAT
1 TTTTGGAAAGTTTAG-GGTAAAAATGTAAT
*
13900 TTTTGG-AAGTTTGGGAGTAAAAATGTAAT
1 TTTTGGAAAGTTTAGG-GTAAAAATGTAAT
*
13929 TTTTGGAAAGTTTAGGGTCAAAAT-TAGAAT
1 TTTTGGAAAGTTTAGGGTAAAAATGT--AAT
* * *
13959 TTTTGG-AAGTTCGAGGGTACAAATGTTA-
1 TTTTGGAAAGTT-TAGGGTAAAAATGTAAT
* *
13987 TTTTGAAAAGTTTGGGGTAAAAA
1 TTTTGGAAAGTTTAGGGTAAAAA
14010 ATGGATTAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
27 1 0.01
28 31 0.27
29 54 0.48
30 26 0.23
31 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTAAAAATGTAAT
Found at i:13972 original size:87 final size:87
Alignment explanation
Indices: 13842--14009 Score: 202
Period size: 87 Copynumber: 1.9 Consensus size: 87
13832 TTTTTTGAAG
*
13842 TTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTGGAAGTTTCGAGGTTA-AAATGGAATTTTTG-
1 TTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTGGAAGTTTCGAGGGTACAAATGGAA-TTTTGA
*
13905 GAAGTTTGGGAGTAAAAATGTAAT
65 AAAGTTTGGG-GTAAAAATGTAAT
* * **
13929 TTTTGGAAAGTTTA-GGGTCAAAAT-TAGAATTTTTGGAAG-TTCGAGGGTACAAATGTTATTTT
1 TTTTGGAAAGTTCAGGGGTAAAAATGT--AA-TTTTGGAAGTTTCGAGGGTACAAATGGAATTTT
13991 GAAAAGTTTGGGGTAAAAA
63 GAAAAGTTTGGGGTAAAAA
14010 ATGGATTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
85 1 0.01
86 9 0.13
87 36 0.51
88 24 0.34
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (87 bp):
TTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTGGAAGTTTCGAGGGTACAAATGGAATTTTGAA
AAGTTTGGGGTAAAAATGTAAT
Found at i:14938 original size:12 final size:12
Alignment explanation
Indices: 14923--14957 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14913 TTACGATGTT
14923 TATTATTATTAA
1 TATTATTATTAA
*
14935 TATTATTACTAA
1 TATTATTATTAA
*
14947 CATTATTATTA
1 TATTATTATTA
14958 TTAAAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:15762 original size:6 final size:6
Alignment explanation
Indices: 15736--15807 Score: 69
Period size: 6 Copynumber: 12.2 Consensus size: 6
15726 GTTTCAAATT
* **
15736 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
15783 ATTTAA A-GTAA ATTTTAA ATTTAA A
1 ATTTAA ATTTAA A-TTTAA ATTTAA A
15808 AATAAATCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
5 11 0.21
6 34 0.64
7 8 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:15777 original size:23 final size:24
Alignment explanation
Indices: 15751--15807 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 24
15741 AAATTTAAAC
15751 TAAATTTAAATTTAAAACAAA-TT
1 TAAATTTAAATTTAAAACAAATTT
**
15774 TAAATTTAAATTTAAAGTAAATTT
1 TAAATTTAAATTTAAAACAAATTT
15798 TAAATTTAAA
1 TAAATTTAAA
15808 AATAAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATTTAAATTTAAAACAAATTT
Found at i:15797 original size:17 final size:17
Alignment explanation
Indices: 15736--15783 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
15726 GTTTCAAATT
15736 ATTTCAAATTT-AAACTAA
1 ATTT-AAATTTAAAAC-AA
15754 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
15771 ATTTAAATTTAAA
1 ATTTAAATTTAAA
15784 TTTAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:18391 original size:76 final size:75
Alignment explanation
Indices: 18260--18408 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 75
18250 CTCAAAGCTT
* * *
18260 GAATTTTTGAAACTCATTAACCCAAATAAACTTAACGGGAAGAAGATATTAGAATAAAAAATATT
1 GAATCTTTGAAACCCATTAACCCAAAGAAACTTAACGGGAAGAAGATATTAGAATAAAAAATATT
18325 GAATGCTTTGA
66 GAAT-CTTTGA
* *
18336 GAATCTTTGAAACCCATTAACCCAAAGAAACTTAATGGGAAGAAGATATTGGAATAAAAAATATT
1 GAATCTTTGAAACCCATTAACCCAAAGAAACTTAACGGGAAGAAGATATTAGAATAAAAAATATT
18401 GAATCTTT
66 GAATCTTT
18409 AGGTTAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 4 0.06
76 64 0.94
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (75 bp):
GAATCTTTGAAACCCATTAACCCAAAGAAACTTAACGGGAAGAAGATATTAGAATAAAAAATATT
GAATCTTTGA
Found at i:20294 original size:28 final size:29
Alignment explanation
Indices: 20233--20301 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
20223 AGTATAGCTG
*
20233 GAGCTTTGCAATATGTTGTCATCACTCAACTT
1 GAGC-TTGC-ATATGCTGTCA-CACTCAACTT
*
20265 GAGCTTGCATATGCTGTCA-ACTCGACTT
1 GAGCTTGCATATGCTGTCACACTCAACTT
*
20293 GAGCATGCA
1 GAGCTTGCA
20302 CCCTTGGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.47
30 10 0.29
31 4 0.12
32 4 0.12
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (29 bp):
GAGCTTGCATATGCTGTCACACTCAACTT
Found at i:24199 original size:11 final size:12
Alignment explanation
Indices: 24176--24207 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
24166 CTATCAACTC
24176 TCTCAATTC-TT
1 TCTCAATTCTTT
24187 TCTC-ATTCTTT
1 TCTCAATTCTTT
24198 TCTCAATTCT
1 TCTCAATTCT
24208 CTCTTAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.21
11 10 0.53
12 5 0.26
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
TCTCAATTCTTT
Found at i:27897 original size:3 final size:3
Alignment explanation
Indices: 27889--27920 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
27879 AAAGATTCTC
27889 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
27921 GAGAAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:29033 original size:12 final size:12
Alignment explanation
Indices: 29016--29040 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29006 CTGGTCTGAA
29016 AGCTGCTTCAAC
1 AGCTGCTTCAAC
29028 AGCTGCTTCAAC
1 AGCTGCTTCAAC
29040 A
1 A
29041 ATGACGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
AGCTGCTTCAAC
Found at i:29196 original size:21 final size:21
Alignment explanation
Indices: 29141--29204 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
29131 TTGCTTCCTT
*
29141 AACACGCTCCAGGATTTCTTG
1 AACACGCTCCAGGATTTCTTC
* * **
29162 TACATGCTTAAGGATTTCTTC
1 AACACGCTCCAGGATTTCTTC
*
29183 AACGCGCTCCAGGATTTTCTTC
1 AACACGCTCCAGGA-TTTCTTC
29205 TGCAGTTCAG
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
21 25 0.78
22 7 0.22
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (21 bp):
AACACGCTCCAGGATTTCTTC
Found at i:33339 original size:18 final size:17
Alignment explanation
Indices: 33295--33341 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
33285 TATTTCATAT
33295 AAATATTTTTATTTTAA
1 AAATATTTTTATTTTAA
33312 AAAGT-TTTTTATTTTTAA
1 AAA-TATTTTTA-TTTTAA
33330 ACAATATTTTTA
1 A-AATATTTTTA
33342 CATACACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
AAATATTTTTATTTTAA
Found at i:34995 original size:21 final size:20
Alignment explanation
Indices: 34969--35107 Score: 64
Period size: 21 Copynumber: 6.3 Consensus size: 20
34959 CTCCTCTTAT
34969 AATTTTATATCATGTTTAAAC
1 AATTTTATAT-ATGTTTAAAC
* * *
34990 AATTTTAAATGGTTTTTAAA-
1 AATTTTATAT-ATGTTTAAAC
* *
35010 ATTGTTTAACATATGTATTAAAC
1 AAT-TTT-ATATATGT-TTAAAC
* * *
35033 ATATATTATATTTAAATTTTTTAAAT
1 A-AT-TT-TA--TATATGTT-TAAAC
35059 AATTTTATATTATGTTTAAAC
1 AATTTTATA-TATGTTTAAAC
* *
35080 AATTTTAAATAGTTTTTAAAC
1 AATTTTATATA-TGTTTAAAC
35101 AATTTTA
1 AATTTTA
35108 ATTTTTCAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
20 4 0.05
21 50 0.57
22 12 0.14
23 3 0.03
24 6 0.07
25 4 0.05
26 9 0.10
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTATATATGTTTAAAC
Found at i:35108 original size:21 final size:20
Alignment explanation
Indices: 35043--35108 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
35033 ATATATTATA
*
35043 TTTAAAT-TTTTTAAATAAT
1 TTTAAATATTTTTAAACAAT
* *
35062 TTTATATTATGTTTAAACAAT
1 TTTA-AATATTTTTAAACAAT
35083 TTTAAATAGTTTTTAAACAAT
1 TTTAAATA-TTTTTAAACAAT
35104 TTTAA
1 TTTAA
35109 TTTTTCAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 4 0.10
20 5 0.13
21 30 0.77
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTAAATATTTTTAAACAAT
Found at i:36268 original size:39 final size:39
Alignment explanation
Indices: 36214--36291 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
36204 AATTCGGGTC
36214 GTGGATCCATTCATCCTCCATTATCTTCCGAGCAGAACG
1 GTGGATCCATTCATCCTCCATTATCTTCCGAGCAGAACG
36253 GTGGATCCATTCATCCTCCATTATCTTCCGAGCAGAACG
1 GTGGATCCATTCATCCTCCATTATCTTCCGAGCAGAACG
36292 TGGTACTCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (39 bp):
GTGGATCCATTCATCCTCCATTATCTTCCGAGCAGAACG
Found at i:43518 original size:76 final size:76
Alignment explanation
Indices: 43392--43535 Score: 288
Period size: 76 Copynumber: 1.9 Consensus size: 76
43382 TTCTTGATGT
43392 TTGCATTGAAAAATTGTGAAGCACTTTTGTACTTGGTAGGTTGATTTTTGATAATATTCTACTTC
1 TTGCATTGAAAAATTGTGAAGCACTTTTGTACTTGGTAGGTTGATTTTTGATAATATTCTACTTC
43457 CCTTGGAAAAG
66 CCTTGGAAAAG
43468 TTGCATTGAAAAATTGTGAAGCACTTTTGTACTTGGTAGGTTGATTTTTGATAATATTCTACTTC
1 TTGCATTGAAAAATTGTGAAGCACTTTTGTACTTGGTAGGTTGATTTTTGATAATATTCTACTTC
43533 CCT
66 CCT
43536 ATGAACTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (76 bp):
TTGCATTGAAAAATTGTGAAGCACTTTTGTACTTGGTAGGTTGATTTTTGATAATATTCTACTTC
CCTTGGAAAAG
Found at i:46131 original size:40 final size:40
Alignment explanation
Indices: 46076--46153 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
46066 ACTTTGTGAA
* *
46076 TGACAGATGAGTGATGGGGACGGGCATCCTTTTTCTAAAT
1 TGACAGATGAGTGATGAGGACGGGCATACTTTTTCTAAAT
46116 TGACAGATGAGTGATGAGGACGGGCATACTTTTTCTAA
1 TGACAGATGAGTGATGAGGACGGGCATACTTTTTCTAA
46154 GGAAGTGGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.29
Consensus pattern (40 bp):
TGACAGATGAGTGATGAGGACGGGCATACTTTTTCTAAAT
Found at i:49998 original size:6 final size:6
Alignment explanation
Indices: 49987--50072 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
49977 GGCCCAATAG
* * * *
49987 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
50032 -ATTAGA AATTTA AATTT- -ATTATA AATTTA AATTTA AATTTA
1 AATT-TA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA
50073 TTTAATGTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
4 6 0.10
5 9 0.14
6 42 0.67
7 6 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:50015 original size:17 final size:17
Alignment explanation
Indices: 49987--50066 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
49977 GGCCCAATAG
*
49987 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* * *
50004 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
50021 AATTTAAATTTATTAGA
1 AATTTAAATTTATTATA
50038 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
50055 AATTTAAATTTA
1 AATTTAAATTTA
50067 AATTTATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:50043 original size:23 final size:21
Alignment explanation
Indices: 50017--50074 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 21
50007 TTAAGTTTAT
50017 TTTAAATTTAAATTTATTAGAAA
1 TTTAAATTTAAATTTATT--AAA
50040 TTTAAATTT--A-TTA-TAAA
1 TTTAAATTTAAATTTATTAAA
50057 TTTAAATTTAAATTTATT
1 TTTAAATTTAAATTTATT
50075 TAATGTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 12 0.39
19 2 0.06
20 6 0.19
21 2 0.06
23 9 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAAATTTAAATTTATTAAA
Found at i:50097 original size:13 final size:13
Alignment explanation
Indices: 50079--50104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50069 TTTATTTAAT
50079 GTCCAATTACAAA
1 GTCCAATTACAAA
50092 GTCCAATTACAAA
1 GTCCAATTACAAA
50105 TCAAGCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:50776 original size:3 final size:3
Alignment explanation
Indices: 50770--50831 Score: 94
Period size: 3 Copynumber: 21.7 Consensus size: 3
50760 TTATGGCATC
50770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
50817 AA- AAT -AT ATT AAT AA
1 AAT AAT AAT AAT AAT AA
50832 GTATTAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 6 0.11
3 48 0.89
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:51969 original size:29 final size:29
Alignment explanation
Indices: 51925--52222 Score: 201
Period size: 29 Copynumber: 10.0 Consensus size: 29
51915 TCCTAAATTA
* * * *
51925 TCCAAAAATCATATTTTGACCCCGAACTT
1 TCCAAAAATTACATTTTTACCCCAAACTT
*
51954 TCCAAAAATTACATTTTTACCCTTAAACTT
1 TCCAAAAATTACATTTTTACCC-CAAACTT
*** * *
51984 T-TTTAAATTATATTTTTAGACCCCAAATTT
1 TCCAAAAATTACATTTTT--ACCCCAAACTT
* *
52014 TCCAAAAATTATATTTTTTACCCTCGAACTT
1 TCCAAAAATTACA-TTTTTACCC-CAAACTT
* ** **
52045 TCC-AAAATTTCATTTTTGACCTTAATTTT
1 TCCAAAAATTACATTTTT-ACCCCAAACTT
* *
52074 TCTAAAAATTACATCTTTACCCCTAAACTT
1 TCCAAAAATTACATTTTTACCCC-AAACTT
* *
52104 TCC-AAAATTCCATTTTTAACCCTAAA-TT
1 TCCAAAAATTACATTTTT-ACCCCAAACTT
* *
52132 TTCTAAAATTACATTTTTACCCCCTAAACTT
1 TCCAAAAATTACATTTTTA-CCCC-AAACTT
* * * *
52163 TCC-AAAATTCCATTTTTAACCTCGAATTT
1 TCCAAAAATTACATTTTT-ACCCCAAACTT
*
52192 TCCAAAAATTACATCTTTACCCCTAAACTT
1 TCCAAAAATTACATTTTTACCCC-AAACTT
52222 T
1 T
52223 ACCCCTAAAT
Statistics
Matches: 205, Mismatches: 47, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
28 5 0.02
29 86 0.42
30 84 0.41
31 25 0.12
32 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCCAAACTT
Found at i:52103 original size:59 final size:59
Alignment explanation
Indices: 51952--52222 Score: 314
Period size: 59 Copynumber: 4.6 Consensus size: 59
51942 GACCCCGAAC
* *** ** *
51952 TTTCCAAAAATTACATTTTTACCCTTAAACTTTTTTAAATTATATTTTTAGACCCCAAAT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTA-ACCCTAAAT
* * * * * *
52012 TTTCCAAAAATTATATTTTTTA-CCCTCGAACTTTCCAAAATTTCATTTTTGACCTTAATT
1 TTTCCAAAAATTACA-TTTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCTAAAT
* *
52072 TTTCTAAAAATTACATCTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAAAT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAAAT
* *
52131 TTT-CTAAAATTACATTTTTACCCCCTAAACTTTCCAAAATTCCATTTTTAA-CCTCGAAT
1 TTTCCAAAAATTACATTTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTAACCCT-AAAT
*
52190 TTTCCAAAAATTACATCTTTACCCCTAAACTTT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTT
52223 ACCCCTAAAT
Statistics
Matches: 179, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
58 17 0.09
59 84 0.47
60 55 0.31
61 23 0.13
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.42
Consensus pattern (59 bp):
TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAAAT
Found at i:52200 original size:30 final size:29
Alignment explanation
Indices: 51919--52214 Score: 188
Period size: 30 Copynumber: 10.0 Consensus size: 29
51909 GGAGGTTCCT
* * *
51919 AAATTATCCAAAAAT-CATATTTTGACCCC
1 AAATTTTCCAAAATTACAT-TTTTAACCCC
* * *
51948 GAACTTTCCAAAAATTACATTTTT-ACCCTT
1 AAATTTTCC-AAAATTACATTTTTAACCC-C
** *
51978 AAACTTTT-TTAAATTATATTTTTAGACCCC
1 AAA-TTTTCCAAAATTACATTTTTA-ACCCC
* *
52008 AAATTTTCCAAAAATTATATTTTTTACCCTC
1 AAATTTTCC-AAAATTACATTTTTAACCC-C
* * * * **
52039 GAACTTTCCAAAATTTCATTTTTGACCTT
1 AAATTTTCCAAAATTACATTTTTAACCCC
* * *
52068 AATTTTTCTAAAAATTACATCTTT-ACCCC
1 AAATTTTC-CAAAATTACATTTTTAACCCC
* * *
52097 TAAACTTTCCAAAATTCCATTTTTAACCCT
1 -AAATTTTCCAAAATTACATTTTTAACCCC
* *
52127 AAATTTTCTAAAATTACATTTTTACCCCC
1 AAATTTTCCAAAATTACATTTTTAACCCC
* * *
52156 TAAACTTTCCAAAATTCCATTTTTAACCTC
1 -AAATTTTCCAAAATTACATTTTTAACCCC
* *
52186 GAATTTTCCAAAAATTACATCTTT-ACCCC
1 AAATTTTCC-AAAATTACATTTTTAACCCC
52215 TAAACTTTAC
Statistics
Matches: 203, Mismatches: 50, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
29 81 0.40
30 91 0.45
31 31 0.15
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (29 bp):
AAATTTTCCAAAATTACATTTTTAACCCC
Found at i:52224 original size:13 final size:13
Alignment explanation
Indices: 52206--52231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52196 AAAATTACAT
52206 CTTTACCCCTAAA
1 CTTTACCCCTAAA
52219 CTTTACCCCTAAA
1 CTTTACCCCTAAA
52232 TGTCTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
CTTTACCCCTAAA
Found at i:52368 original size:60 final size:59
Alignment explanation
Indices: 52222--52392 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 59
52212 CCCTAAACTT
* * * *
52222 TACCCCTAAATGTCTAAAAATTCCTTTTTTGA-CTCGAA-CTTT-ACAAAATTACCATTT
1 TACCCCTGAATGTCTAAAAATTCCATTTTTAACCTCGAACCTTTCA-AAAATTACCATTC
* * * * *
52279 TACCCTTGAATGTCTAAAAGTGCCATTTTTCACCCCGAACCTTTCAAAAATTACCATTC
1 TACCCCTGAATGTCTAAAAATTCCATTTTTAACCTCGAACCTTTCAAAAATTACCATTC
* * * **
52338 TACCCCCTGGATGTCTAAAAATTTCATTTTTAACCTCAAACCTTTCGCAAATTAC
1 TA-CCCCTGAATGTCTAAAAATTCCATTTTTAACCTCGAACCTTTCAAAAATTAC
52393 AATTTTGTTC
Statistics
Matches: 92, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
57 26 0.28
58 5 0.05
59 18 0.20
60 43 0.47
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (59 bp):
TACCCCTGAATGTCTAAAAATTCCATTTTTAACCTCGAACCTTTCAAAAATTACCATTC
Found at i:63051 original size:3 final size:3
Alignment explanation
Indices: 63045--63097 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
63035 CAACAACAAC
63045 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
63093 AAT AA
1 AAT AA
63098 ATATATTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:64254 original size:30 final size:30
Alignment explanation
Indices: 64230--64401 Score: 165
Period size: 30 Copynumber: 5.8 Consensus size: 30
64220 TTTTTGACCT
* *
64230 TAAATTTTCCAAAAATTACATTTTT-ACCCT
1 TAAACTTTCC-AAAATTACATTTTTAACCCC
* *
64260 TAAACTTTACAAAATTCCATTTTTAA-CCC
1 TAAACTTTCCAAAATTACATTTTTAACCCC
**
64289 TAATTTTTCCAAAATTTACA-TTTTAACCCC
1 TAAACTTTCCAAAA-TTACATTTTTAACCCC
* * *
64319 TAAACTTTCCAAAATTCCATTTTTAA-TCA
1 TAAACTTTCCAAAATTACATTTTTAACCCC
* **
64348 TAAATTTTTTGAAAATTACATTTTT-ACCCC
1 TAAA-CTTTCCAAAATTACATTTTTAACCCC
64378 TAAACTTTCCAAAATTATCATTTT
1 TAAACTTTCCAAAATTA-CATTTT
64402 ACCCTCGAGT
Statistics
Matches: 113, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
29 52 0.46
30 61 0.54
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (30 bp):
TAAACTTTCCAAAATTACATTTTTAACCCC
Found at i:64297 original size:59 final size:59
Alignment explanation
Indices: 64175--64393 Score: 242
Period size: 59 Copynumber: 3.7 Consensus size: 59
64165 GACCCTGAAC
* * * * *** * * * *
64175 TTTCCAAAAAATACAATTTTACCCTTACACTTTTTGAAATTCTATTTTTTGACCTTAAAT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCA-TTTTTAACCATAATT
* * *
64235 TTTCCAAAAATTACATTTTTACCCTTAAACTTTACAAAATTCCATTTTTAACCCTAATT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCATAATT
* * *
64294 TTTCCAAAATTTACATTTTAACCCCTAAACTTTCCAAAATTCCATTTTTAATCATAAATT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCAT-AATT
**
64354 TTT-TGAAAATTACATTTTTACCCCTAAACTTTCCAAAATT
1 TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATT
64394 ATCATTTTAC
Statistics
Matches: 138, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
59 94 0.68
60 44 0.32
ACGTcount: A:0.35, C:0.21, G:0.01, T:0.43
Consensus pattern (59 bp):
TTTCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCATAATT
Found at i:64460 original size:60 final size:57
Alignment explanation
Indices: 64359--64580 Score: 205
Period size: 60 Copynumber: 3.8 Consensus size: 57
64349 AAATTTTTTG
* * * * * *
64359 AAAATTACATTTTTACCCCT-AAACTTTCCAAAATTATCATTTTACCCTCGAGTGTCTA
1 AAAATTCCATTTTTAACCCTGAACCTTT-AAAAATTACCATTTTACCC-CGAATGTCTA
* * *
64417 CAAAATTCCATTTTTGACCCTGAACCTTATAAAAATTACCATTTTACCCCTAAATTTCTA
1 -AAAATTCCATTTTTAACCCTGAACCTT-TAAAAATTACCATTTTACCCC-GAATGTCTA
* * * *
64477 AAAATGCCA-TTTTAACCCTCAACCTTCCAAAAATTACCATTATACCCCCCGAATGTCTA
1 AAAATTCCATTTTTAACCCTGAACCTT-TAAAAATTACCATTTTA--CCCCGAATGTCTA
* * *
64536 AAAATTCTATTTTTAACCTTGAACCTTTCGAAAATTACCATTTTA
1 AAAATTCCATTTTTAACCCTGAACCTTT-AAAAATTACCATTTTA
64581 TTCTCGAAGC
Statistics
Matches: 132, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
58 30 0.23
59 40 0.30
60 61 0.46
61 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCCTGAACCTTTAAAAATTACCATTTTACCCCGAATGTCTA
Found at i:64481 original size:118 final size:118
Alignment explanation
Indices: 64359--64580 Score: 279
Period size: 118 Copynumber: 1.9 Consensus size: 118
64349 AAATTTTTTG
* * * * * * *
64359 AAAATTACATTTTTACCCCTAAACTTTCC-AAAATTATCATTTTA-CCCTCGAGTGTCTACAAAA
1 AAAATGACA-TTTTAACCCTAAACCTTCCAAAAATTACCATTATACCCCCCGAATGTCTA-AAAA
*
64422 TTCCATTTTTGACCCTGAACCTTAT-AAAAATTACCATTTTACCCCTAAATTTCTA
64 TTCCATTTTTAACCCTGAACCTT-TCAAAAATTACCATTTTACCCCTAAATTTCTA
* *
64477 AAAATGCCATTTTAACCCTCAACCTTCCAAAAATTACCATTATACCCCCCGAATGTCTAAAAATT
1 AAAATGACATTTTAACCCTAAACCTTCCAAAAATTACCATTATACCCCCCGAATGTCTAAAAATT
* * *
64542 CTATTTTTAACCTTGAACCTTTCGAAAATTACCATTTTA
66 CCATTTTTAACCCTGAACCTTTCAAAAATTACCATTTTA
64581 TTCTCGAAGC
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
117 17 0.19
118 59 0.67
119 12 0.14
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (118 bp):
AAAATGACATTTTAACCCTAAACCTTCCAAAAATTACCATTATACCCCCCGAATGTCTAAAAATT
CCATTTTTAACCCTGAACCTTTCAAAAATTACCATTTTACCCCTAAATTTCTA
Found at i:64517 original size:89 final size:87
Alignment explanation
Indices: 64236--64517 Score: 225
Period size: 89 Copynumber: 3.2 Consensus size: 87
64226 ACCTTAAATT
* * * *
64236 TTCCAAAAATTACATTTTTACCCTTAAACTTTACAAAATT-CCATTTTTAACCCTAATTTTTCCA
1 TTCCAAAAATTCCATTTTTACCCTAAAACTTTA-AAAATTACCATTTTTACCCCTAA-ATTTCCA
* * *
64300 AAATTTACATTTTAACCCCTAAACT
64 AAATTAACATTTTAA-CCCTCAACC
* * ** *
64325 TTCC-AAAATTCCATTTTTAATCATAAATTTTTTGAAAATTA-CATTTTTACCCCTAAACTTTCC
1 TTCCAAAAATTCCATTTTT-ACCCTAAA-ACTTTAAAAATTACCATTTTTACCCCTAAA-TTTCC
* * *
64388 AAAATTATCATTTT-ACCCTCGA-G
63 AAAATTAACATTTTAACCCTCAACC
* * *
64411 TGTCTACAAAATTCCATTTTTGACCCTGAACCTTATAAAAATTACCA-TTTTACCCCTAAATTTC
1 T-TCCA-AAAATTCCATTTTT-ACCCTAAAACTT-TAAAAATTACCATTTTTACCCCTAAATTTC
* * **
64475 TAAAAATGCCATTTTAACCCTCAACC
62 CAAAATTAACATTTTAACCCTCAACC
64501 TTCCAAAAATTACCATT
1 TTCCAAAAATT-CCATT
64518 ATACCCCCCG
Statistics
Matches: 152, Mismatches: 29, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
86 1 0.01
87 7 0.05
88 37 0.24
89 101 0.66
90 6 0.04
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (87 bp):
TTCCAAAAATTCCATTTTTACCCTAAAACTTTAAAAATTACCATTTTTACCCCTAAATTTCCAAA
ATTAACATTTTAACCCTCAACC
Found at i:64601 original size:29 final size:28
Alignment explanation
Indices: 64566--64626 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
64556 GAACCTTTCG
** *
64566 AAAATTACCATTTTATTCTCGAAGCATCC
1 AAAATTACCATTTTACCCCCG-AGCATCC
*
64595 AAAATTACCGTTTTACCCCCGAGCATCC
1 AAAATTACCATTTTACCCCCGAGCATCC
64623 AAAA
1 AAAA
64627 ATCACATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAGCATCC
Found at i:66887 original size:39 final size:39
Alignment explanation
Indices: 66841--66939 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 39
66831 TTAAATAAGG
66841 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGCTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGCTGT
*
66880 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGCTGT
* *
66919 TTTTAATATGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
66940 GACAAATTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGCTGT
Found at i:67021 original size:32 final size:32
Alignment explanation
Indices: 66985--67047 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
66975 AGTCGAAATT
* *
66985 AATTAGCTGATTAATGTGTTTCAGGAACATGC
1 AATTAGCTGATTAATATATTTCAGGAACATGC
*
67017 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGAACATG
67048 TATGGATGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGAACATGC
Found at i:70172 original size:18 final size:19
Alignment explanation
Indices: 70149--70184 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
70139 AGAGTGAGAA
*
70149 TGAAAAAGGAAA-GAAAAT
1 TGAAAAAAGAAAGGAAAAT
70167 TGAAAAAAGAAAGGAAAA
1 TGAAAAAAGAAAGGAAAA
70185 ATGAGAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (19 bp):
TGAAAAAAGAAAGGAAAAT
Found at i:73265 original size:8 final size:8
Alignment explanation
Indices: 73244--73290 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
73234 TTTAATTTGT
73244 TTTAGTTAA
1 TTTAGTT-A
73253 TTTAGTTA
1 TTTAGTTA
73261 TTTAG-T-
1 TTTAGTTA
*
73267 TTAAGTTAA
1 TTTAGTT-A
73276 TTTAGTTA
1 TTTAGTTA
73284 TTTAGTT
1 TTTAGTT
73291 TGATACATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 14 0.42
9 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.60
Consensus pattern (8 bp):
TTTAGTTA
Found at i:73268 original size:23 final size:23
Alignment explanation
Indices: 73238--73291 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
73228 TAAATATTTA
*
73238 ATTT-GTTTTAGTTAATTTAGTT
1 ATTTAGTTTAAGTTAATTTAGTT
73260 ATTTAGTTTAAGTTAATTTAGTT
1 ATTTAGTTTAAGTTAATTTAGTT
73283 ATTTAGTTT
1 ATTTAGTTT
73292 GATACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (23 bp):
ATTTAGTTTAAGTTAATTTAGTT
Found at i:73414 original size:32 final size:32
Alignment explanation
Indices: 73378--73472 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
73368 TGCCAAAATT
*
73378 AATTAGCTGATTAATGTGCTTCAGGTACATGC
1 AATTAGCTGATTAATGTGTTTCAGGTACATGC
73410 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATGTGTTTCAGGTACATGC
* * *
73442 AATTAGCTAATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATGTGTTTCAGGTACATG
73473 TATGGATAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
AATTAGCTGATTAATGTGTTTCAGGTACATGC
Found at i:78452 original size:26 final size:26
Alignment explanation
Indices: 78413--78554 Score: 169
Period size: 26 Copynumber: 5.5 Consensus size: 26
78403 ATACAAACCT
* *
78413 AGTT-AGTTTATCGCTCTTACGAGCC
1 AGTTCAGTATATCGCTCTTTCGAGCC
* * * * *
78438 AATTTAGTATGTCGCTCTTACGACCC
1 AGTTCAGTATATCGCTCTTTCGAGCC
*
78464 AGTTCAGTATATCTCTCTTTCGAGCC
1 AGTTCAGTATATCGCTCTTTCGAGCC
*
78490 AGTTCAATATATCGCTCTTTCGAGCC
1 AGTTCAGTATATCGCTCTTTCGAGCC
* *
78516 AGTTCAGTATATCACTCTTTTGAGCC
1 AGTTCAGTATATCGCTCTTTCGAGCC
*
78542 AGTTTAGTATATC
1 AGTTCAGTATATC
78555 TTCAGAGTCT
Statistics
Matches: 100, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
25 3 0.03
26 97 0.97
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (26 bp):
AGTTCAGTATATCGCTCTTTCGAGCC
Found at i:85112 original size:18 final size:18
Alignment explanation
Indices: 85086--85120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
85076 GATGAAATTC
85086 TCATATTTTTCATCTTCA
1 TCATATTTTTCATCTTCA
*
85104 TCATCTTTTTCATCTTC
1 TCATATTTTTCATCTTC
85121 TTCTTCCACG
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:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATATTTTTCATCTTCA
Found at i:85854 original size:36 final size:36
Alignment explanation
Indices: 85805--85908 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
85795 TGGTAACGAG
85805 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
*
85841 CATGACCTCTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* * * *
85877 TATGACTTTTGGATC-ATCAAGGAGTAAAACGA
1 CATGACCTTTGGGTCAAT-AGGGAGTAAAACGA
85909 ATAACGAACG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 2 0.03
36 59 0.97
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
Found at i:97653 original size:24 final size:24
Alignment explanation
Indices: 97626--97872 Score: 179
Period size: 24 Copynumber: 10.3 Consensus size: 24
97616 CTCATGTACA
* *
97626 TTTATGCTCGTCAGTTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* * ** *
97650 TTTACGCTCGTTAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
* *
97674 TTTACGCTCGTCAGCTTATGTACA
1 TTTACGCTCGTCAGCTTATATACG
** * * *
97698 TTTACGCTCACCAGCTTGTACACA
1 TTTACGCTCGTCAGCTTATATACG
97722 TTTACGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* ** * *
97746 TTTACGCTCGTTAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATATACG
* * * *
97770 TTTAAGCTTGTCAGCTTGTGTACG
1 TTTACGCTCGTCAGCTTATATACG
* * ** *
97794 TTTATGCTCATCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
* * ** * *
97818 TTTACACTCGTCAACTTGCACATG
1 TTTACGCTCGTCAGCTTATATACG
*
97842 TTTACGCTCGTCAACTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
97866 TTTACGC
1 TTTACGC
97873 AGTTCAATAA
Statistics
Matches: 171, Mismatches: 52, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 171 1.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.36
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTATATACG
Found at i:97687 original size:48 final size:48
Alignment explanation
Indices: 97623--97830 Score: 245
Period size: 48 Copynumber: 4.3 Consensus size: 48
97613 CATCTCATGT
* * * * *
97623 ACATTTATGCTCGTCAGTTTATATACGTTTACGCTCGTTAACTTGCAC
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAGCTTGCAC
* * * * *
97671 ACGTTTACGCTCGTCAGCTTATGTACATTTACGCTCACCAGCTTGTAC
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAGCTTGCAC
* *
97719 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAGCTTGCAC
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAGCTTGCAC
* * * * *
97767 ACATTTAAGCTTGTCAGCTTGTGTACGTTTATGCTCATCAGCTTGCAC
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAGCTTGCAC
* *
97815 ACGTTTACACTCGTCA
1 ACATTTACGCTCGTCA
97831 ACTTGCACAT
Statistics
Matches: 132, Mismatches: 28, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
48 132 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (48 bp):
ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCATCAGCTTGCAC
Found at i:97792 original size:96 final size:96
Alignment explanation
Indices: 97623--97858 Score: 301
Period size: 96 Copynumber: 2.5 Consensus size: 96
97613 CATCTCATGT
* * * *
97623 ACATTTATGCTCGTCAGTTTATATACGTTTACGCTCGTTAACTTGCACACGTTTACGCTCGTCAG
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAACTTGCACACATTTAAGCTCGTCAG
*
97688 CTTATGTACATTTACGCTCACCAGCTTGTAC
66 CTTATGTACATTTACGCTCACCAGCTTGCAC
* *
97719 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAGCTTGCACACATTTAAGCTTGTCAG
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAACTTGCACACATTTAAGCTCGTCAG
* * * *
97784 CTTGTGTACGTTTATGCTCATCAGCTTGCAC
66 CTTATGTACATTTACGCTCACCAGCTTGCAC
* * * ** * * *
97815 ACGTTTACACTCGTCAACTTGCACATGTTTACGCTCGTCAACTT
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAACTT
97859 ATATACGTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 120 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (96 bp):
ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAACTTGCACACATTTAAGCTCGTCAG
CTTATGTACATTTACGCTCACCAGCTTGCAC
Found at i:97866 original size:72 final size:70
Alignment explanation
Indices: 97623--97872 Score: 239
Period size: 72 Copynumber: 3.5 Consensus size: 70
97613 CATCTCATGT
* * * *
97623 ACATTTATGCTCGTCAGTTTATATACGTTTACGCTCGTTAACTTGCACACGTTTACGCTCGTCAG
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAG
*
97688 CTTATGT
66 C-T-TGC
** * * * ** * *
97695 ACATTTACGCTCACCAGCTTGTACACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAG
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAG
97760 CTTGCAC
66 CTTG--C
* * * * * * * *
97767 ACATTTAAGCTTGTCAGCTTGTGTACGTTTATGCTCATCAGCTTGCACACGTTTACACTCGTCAA
1 ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAG
97832 CTTGC
66 CTTGC
*
97837 ACATGTTTACGCTCGTCAACTTATATACGTTTACGC
1 ACA--TTTACGCTCGTCAGCTTATATACGTTTACGC
97873 AGTTCAATAA
Statistics
Matches: 139, Mismatches: 35, Indels: 8
0.76 0.19 0.04
Matches are distributed among these distances:
70 6 0.04
71 1 0.01
72 132 0.95
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (70 bp):
ACATTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCAG
CTTGC
Found at i:98723 original size:112 final size:112
Alignment explanation
Indices: 98526--98751 Score: 452
Period size: 112 Copynumber: 2.0 Consensus size: 112
98516 AGAAAAGGTA
98526 AAGTGCCAATTCTCCTTCCTTTCCTTTCTTTTTTTATTATTTTAATTCCTTTCTTAACATTTTTA
1 AAGTGCCAATTCTCCTTCCTTTCCTTTCTTTTTTTATTATTTTAATTCCTTTCTTAACATTTTTA
98591 TAATCTCTAAATATTTTTTCACCACATATTTTTCGTGATGATCTACT
66 TAATCTCTAAATATTTTTTCACCACATATTTTTCGTGATGATCTACT
98638 AAGTGCCAATTCTCCTTCCTTTCCTTTCTTTTTTTATTATTTTAATTCCTTTCTTAACATTTTTA
1 AAGTGCCAATTCTCCTTCCTTTCCTTTCTTTTTTTATTATTTTAATTCCTTTCTTAACATTTTTA
98703 TAATCTCTAAATATTTTTTCACCACATATTTTTCGTGATGATCTACT
66 TAATCTCTAAATATTTTTTCACCACATATTTTTCGTGATGATCTACT
98750 AA
1 AA
98752 CTCCTCCACT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.52
Consensus pattern (112 bp):
AAGTGCCAATTCTCCTTCCTTTCCTTTCTTTTTTTATTATTTTAATTCCTTTCTTAACATTTTTA
TAATCTCTAAATATTTTTTCACCACATATTTTTCGTGATGATCTACT
Found at i:105190 original size:17 final size:17
Alignment explanation
Indices: 105170--105202 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
105160 TAATCATGAT
105170 AAAAAATAA-TGGAAAGG
1 AAAAAA-AAGTGGAAAGG
105187 AAAAAAAAGTGGAAAG
1 AAAAAAAAGTGGAAAG
105203 TAATTGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (17 bp):
AAAAAAAAGTGGAAAGG
Found at i:115439 original size:27 final size:28
Alignment explanation
Indices: 115389--115460 Score: 119
Period size: 27 Copynumber: 2.5 Consensus size: 28
115379 CAAATGATTT
115389 TAAAATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTA--TTTTTAAAATA
115419 TAAAATTATTAAAATTA-TTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAATA
115446 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
115461 CATCATCATT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 25 0.60
30 17 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTAAAATA
Found at i:115443 original size:11 final size:9
Alignment explanation
Indices: 115388--115460 Score: 63
Period size: 9 Copynumber: 8.8 Consensus size: 9
115378 GCAAATGATT
115388 TTAAAATTA
1 TTAAAATTA
115397 TTAAAATTA
1 TTAAAATTA
*
115406 TT----TTT
1 TTAAAATTA
115411 TTAAAA-TA
1 TTAAAATTA
115419 -TAAAATTA
1 TTAAAATTA
115427 TTAAAATTA
1 TTAAAATTA
115436 TTTTAAAA-TA
1 --TTAAAATTA
115446 -TAAAATTA
1 TTAAAATTA
115454 TTAAAAT
1 TTAAAAT
115461 CATCATCATT
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
5 4 0.08
7 10 0.19
8 5 0.10
9 25 0.48
10 2 0.04
11 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:115546 original size:19 final size:19
Alignment explanation
Indices: 115500--115547 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
115490 TTTCTGTTAT
*
115500 CTTTCCCCTTCCCTCTTCC
1 CTTTCCCTTTCCCTCTTCC
*
115519 CTTTCCCCTTTCTCT-TTCC
1 CTTT-CCCTTTCCCTCTTCC
115538 CATTTCCCTT
1 C-TTTCCCTT
115548 ATGTTTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (19 bp):
CTTTCCCTTTCCCTCTTCC
Found at i:116398 original size:9 final size:9
Alignment explanation
Indices: 116384--116431 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
116374 AAAATGTTAA
*
116384 AATAATGTT
1 AATAATTTT
116393 AATAATTTT
1 AATAATTTT
116402 AAATTAATTTT
1 -AA-TAATTTT
116413 AATAATTTT
1 AATAATTTT
*
116422 -ATATTTTT
1 AATAATTTT
116430 AA
1 AA
116432 AATAATTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 7 0.21
9 16 0.47
10 4 0.12
11 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
AATAATTTT
Found at i:116409 original size:11 final size:10
Alignment explanation
Indices: 116383--116439 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 10
116373 TAAAATGTTA
*
116383 AAATAATGTT
1 AAATAATTTT
116393 -AATAATTTT
1 AAATAATTTT
116402 AAATTAATTTT
1 AAA-TAATTTT
116413 -AATAATTTT
1 AAATAATTTT
*
116422 --ATATTTTT
1 AAATAATTTT
116430 AAAATAATTT
1 -AAATAATTT
116440 GCTGATGTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 7 0.18
9 15 0.38
10 4 0.10
11 13 0.33
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
AAATAATTTT
Found at i:116409 original size:20 final size:20
Alignment explanation
Indices: 116380--116422 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
116370 GATTAAAATG
116380 TTAAAATAATGTTAATAATT
1 TTAAAATAATGTTAATAATT
* *
116400 TTAAATTAATTTTAATAATT
1 TTAAAATAATGTTAATAATT
116420 TTA
1 TTA
116423 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAAATAATGTTAATAATT
Found at i:116429 original size:28 final size:29
Alignment explanation
Indices: 116384--116439 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
116374 AAAATGTTAA
*
116384 AATAATGTTAATAATTTTAAATTAATTTT
1 AATAATGTTAATAATTTTAAAATAATTTT
* *
116413 AATAAT-TTTATATTTTTAAAATAATTT
1 AATAATGTTAATAATTTTAAAATAATTT
116440 GCTGATGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
AATAATGTTAATAATTTTAAAATAATTTT
Found at i:128677 original size:24 final size:24
Alignment explanation
Indices: 128628--128678 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
128618 AGACCCGAGC
*
128628 AAAATCCCTCAGCCAAAAACTATG
1 AAAATCCCTCAGCCAAAAACCATG
* *
128652 AAAATTCCTCAG-CAAATACCATTG
1 AAAATCCCTCAGCCAAAAACCA-TG
128676 AAA
1 AAA
128679 TACATCAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.20
Consensus pattern (24 bp):
AAAATCCCTCAGCCAAAAACCATG
Found at i:139646 original size:40 final size:40
Alignment explanation
Indices: 139590--139670 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
139580 CGACCTAATC
* *
139590 TCCCCAAAACCGTTTATCGAATCTACATACCTCTTTTATT
1 TCCCCAAAACCATTTATCGAATCTACATACCTCTTTCATT
* * *
139630 TCCCCAAAACCATTTATTGGATCTACATATCTCTTTCATT
1 TCCCCAAAACCATTTATCGAATCTACATACCTCTTTCATT
139670 T
1 T
139671 ACTTTACTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.28, G:0.05, T:0.40
Consensus pattern (40 bp):
TCCCCAAAACCATTTATCGAATCTACATACCTCTTTCATT
Found at i:141508 original size:20 final size:20
Alignment explanation
Indices: 141483--141523 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
141473 TATCTGTATA
141483 TCACATAGTATTTGGTTAAC
1 TCACATAGTATTTGGTTAAC
141503 TCACATAGTATTTGGTTAAC
1 TCACATAGTATTTGGTTAAC
141523 T
1 T
141524 TAGCATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (20 bp):
TCACATAGTATTTGGTTAAC
Found at i:143184 original size:26 final size:26
Alignment explanation
Indices: 143154--143211 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
143144 GAGTAATTTC
* *
143154 TTTATCCTTTTTCATTTA-TTCTTTTA
1 TTTATACTTTTTCATTAACTTC-TTTA
* *
143180 TTTATATTTTTTCGTTAACTTCTTTA
1 TTTATACTTTTTCATTAACTTCTTTA
143206 TTTATA
1 TTTATA
143212 TTTGACATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTATACTTTTTCATTAACTTCTTTA
Found at i:150323 original size:3 final size:3
Alignment explanation
Indices: 150315--150372 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
150305 TGCCCTTTAT
150315 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
150363 CTA TTA TTA T
1 TTA TTA TTA T
150373 ATTTTTTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:152764 original size:7 final size:7
Alignment explanation
Indices: 152754--152787 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
152744 AACCTAAAAA
152754 GTCAACG
1 GTCAACG
152761 GTCAACG
1 GTCAACG
152768 GTCAACG
1 GTCAACG
*
152775 TGTTAACG
1 -GTCAACG
152783 GTCAA
1 GTCAA
152788 AACGGGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (7 bp):
GTCAACG
Found at i:152784 original size:15 final size:14
Alignment explanation
Indices: 152754--152787 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
152744 AACCTAAAAA
152754 GTCAACGGTCAACG
1 GTCAACGGTCAACG
*
152768 GTCAACGTGTTAACG
1 GTCAACG-GTCAACG
152783 GTCAA
1 GTCAA
152788 AACGGGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:157530 original size:23 final size:23
Alignment explanation
Indices: 157504--157653 Score: 185
Period size: 23 Copynumber: 6.4 Consensus size: 23
157494 AGTGCTGGGC
*
157504 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
157527 AACAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* *
157550 ATCAGAGAGCACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
157573 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
157596 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
157620 TAACAGAGAGCACGA-GATGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
157644 AACAGAGAGC
1 AACAGAGAGC
157654 GCGCTAGTGT
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
23 96 0.83
24 2 0.02
25 16 0.14
26 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:161683 original size:11 final size:11
Alignment explanation
Indices: 161667--161698 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
161657 TGCACCTAAC
*
161667 ACACTTAAGGT
1 ACACTTAAGAT
161678 ACACTTAAGAT
1 ACACTTAAGAT
161689 ACACTTAAGA
1 ACACTTAAGA
161699 GTTATTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (11 bp):
ACACTTAAGAT
Found at i:163403 original size:21 final size:21
Alignment explanation
Indices: 163357--163403 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
163347 AGACCTATGG
*
163357 CTTCTACCGATACAACTCTAA
1 CTTCTACCGATACAACTCCAA
* *
163378 GTTCTATCGATACAAC-CCAGA
1 CTTCTACCGATACAACTCCA-A
163399 CTTCT
1 CTTCT
163404 TTTGGTAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (21 bp):
CTTCTACCGATACAACTCCAA
Found at i:166551 original size:20 final size:21
Alignment explanation
Indices: 166515--166553 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
166505 TTATAAATAG
*
166515 GATTAATTAAGGTTAATGAGT
1 GATTAAATAAGGTTAATGAGT
166536 GATTAAATAA-GTTAATGA
1 GATTAAATAAGGTTAATGA
166554 TGAAAGTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
GATTAAATAAGGTTAATGAGT
Found at i:166693 original size:15 final size:15
Alignment explanation
Indices: 166669--166699 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
166659 GAAAAACTAG
166669 GGTTTCCATTGTTGA
1 GGTTTCCATTGTTGA
*
166684 GGTTTTCATTGTTGA
1 GGTTTCCATTGTTGA
166699 G
1 G
166700 CATGTGAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.29, T:0.48
Consensus pattern (15 bp):
GGTTTCCATTGTTGA
Found at i:170919 original size:13 final size:13
Alignment explanation
Indices: 170901--170929 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
170891 AAATTCGAAA
170901 TTTTTTTCGATTT
1 TTTTTTTCGATTT
170914 TTTTTTTCGATTT
1 TTTTTTTCGATTT
170927 TTT
1 TTT
170930 CAAGTCGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTCGATTT
Found at i:173026 original size:26 final size:26
Alignment explanation
Indices: 172971--173132 Score: 118
Period size: 26 Copynumber: 6.3 Consensus size: 26
172961 GCTCAAAGCT
* * *
172971 TGCTATTTAATCACCAGC--AAGGCT
1 TGCTATATAATCACCGGCTTAAGGCC
* *
172995 TGCTATATGATCACCGGCTTAAAGCC
1 TGCTATATAATCACCGGCTTAAGGCC
* * *
173021 TGCTATTTAATCACTAGG-TCAAGGCC
1 TGCTATATAATCAC-CGGCTTAAGGCC
* * * **
173047 AGCTATTTAATCACCGGCTCGAA-GTT
1 TGCTATATAATCACCGGCT-TAAGGCC
* *
173073 TGCTATTTAATTACCGGC-TAAGGCC
1 TGCTATATAATCACCGGCTTAAGGCC
*
173098 TGCAATATAATCACCGGCTTAAGGCC
1 TGCTATATAATCACCGGCTTAAGGCC
*
173124 TGCCATATA
1 TGCTATATA
173133 GTCATTGCCT
Statistics
Matches: 107, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
24 17 0.16
25 18 0.17
26 68 0.64
27 4 0.04
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (26 bp):
TGCTATATAATCACCGGCTTAAGGCC
Found at i:173063 original size:52 final size:50
Alignment explanation
Indices: 172955--173126 Score: 166
Period size: 52 Copynumber: 3.4 Consensus size: 50
172945 CACTAGCTAT
* * * *
172955 TCACTGGCTCAAAGCTTGCTATTTAATCACCA-GCAAGGCTTGCTATATGA
1 TCACCGGCTCAAAGCCTGCTATTTAATCA-CAGGCAAGGCCTGCTATATAA
* * *
173005 TCACCGGCTTAAAGCCTGCTATTTAATCACTAGGTCAAGGCCAGCTATTTAA
1 TCACCGGCTCAAAGCCTGCTATTTAATCAC-AGG-CAAGGCCTGCTATATAA
* ** * * *
173057 TCACCGGCTCGAAGTTTGCTATTTAATTACCGGCTAAGGCCTGCAATATAA
1 TCACCGGCTCAAAGCCTGCTATTTAATCACAGGC-AAGGCCTGCTATATAA
* *
173108 TCACCGGCTTAAGGCCTGC
1 TCACCGGCTCAAAGCCTGC
173127 CATATAGTCA
Statistics
Matches: 97, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
49 1 0.01
50 28 0.29
51 30 0.31
52 38 0.39
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (50 bp):
TCACCGGCTCAAAGCCTGCTATTTAATCACAGGCAAGGCCTGCTATATAA
Found at i:173156 original size:103 final size:102
Alignment explanation
Indices: 172955--173164 Score: 235
Period size: 103 Copynumber: 2.0 Consensus size: 102
172945 CACTAGCTAT
* * * *
172955 TCACTGGCTCAAAGCTTGCTATTTAATCACCAGCAAGGCTTGCTATATGATCACCGGCTTAAAGC
1 TCACCGGCTCAAAGCTTGCTATTTAATCACCAGCAAGGCCTGCAATATAATCACCGGCTTAAAGC
* * * * *
173020 CTGCTATTTAATCACTAGGTCAAGGCCAGCTATTTAA
66 CTGCCATATAATCACTAGCTCAAGGCCAACTATTAAA
* * * * *
173057 TCACCGGCTCGAAGTTTGCTATTTAATTACCGGCTAAGGCCTGCAATATAATCACCGGCTTAAGG
1 TCACCGGCTCAAAGCTTGCTATTTAATCACCAGC-AAGGCCTGCAATATAATCACCGGCTTAAAG
* *
173122 CCTGCCATATAGTCA-TTGCCTCGAA-GCCAACTATTAAA
65 CCTGCCATATAATCACTAG-CTC-AAGGCCAACTATTAAA
173160 TCACC
1 TCACC
173165 TCTATTCTAA
Statistics
Matches: 89, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
102 31 0.35
103 56 0.63
104 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (102 bp):
TCACCGGCTCAAAGCTTGCTATTTAATCACCAGCAAGGCCTGCAATATAATCACCGGCTTAAAGC
CTGCCATATAATCACTAGCTCAAGGCCAACTATTAAA
Found at i:175564 original size:25 final size:25
Alignment explanation
Indices: 175535--175597 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
175525 ATTTAAATAC
175535 TTATCTTATTAAAAAACTATATAA-A
1 TTATCTTATTAAAAAACTATA-AACA
*
175560 TTATCTTGATAAAAAAACTATAAACA
1 TTATCTT-ATTAAAAAACTATAAACA
*
175586 TTATCTAATTAA
1 TTATCTTATTAA
175598 TTTTTCATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (25 bp):
TTATCTTATTAAAAAACTATAAACA
Found at i:175885 original size:30 final size:31
Alignment explanation
Indices: 175851--175923 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
175841 CATTTAACAC
175851 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACATTATCGAAAA-GTGACAA
175881 AACAGTCACTAACATTATCGAAAAGTGACAA
1 AACAGTCACTAACATTATCGAAAAGTGACAA
175912 AACAGTCACTAA
1 AACAGTCACTAA
175924 TTAACAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 3 0.08
30 12 0.30
31 20 0.50
32 5 0.12
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACATTATCGAAAAGTGACAA
Found at i:176203 original size:57 final size:57
Alignment explanation
Indices: 176131--176255 Score: 232
Period size: 57 Copynumber: 2.2 Consensus size: 57
176121 AAATCAAGTA
* *
176131 AACCCTAAATCAAAAATCACAATCAATATCAATATCAAATTCGAATAAACACAAAAC
1 AACCCTAAATAAAAAATCACAATCAATATCAACATCAAATTCGAATAAACACAAAAC
176188 AACCCTAAATAAAAAATCACAATCAATATCAACATCAAATTCGAATAAACACAAAAC
1 AACCCTAAATAAAAAATCACAATCAATATCAACATCAAATTCGAATAAACACAAAAC
176245 AACCCTAAATA
1 AACCCTAAATA
176256 CAAATATCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 66 1.00
ACGTcount: A:0.57, C:0.23, G:0.02, T:0.18
Consensus pattern (57 bp):
AACCCTAAATAAAAAATCACAATCAATATCAACATCAAATTCGAATAAACACAAAAC
Found at i:177946 original size:22 final size:22
Alignment explanation
Indices: 177921--177962 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
177911 TTTAACATAC
*
177921 AAATCTTAATTTATATCAACGA
1 AAATATTAATTTATATCAACGA
*
177943 AAATATTAATTTATGTCAAC
1 AAATATTAATTTATATCAAC
177963 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (22 bp):
AAATATTAATTTATATCAACGA
Found at i:178300 original size:17 final size:16
Alignment explanation
Indices: 178243--178305 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
178233 GGTCCGTTGG
*
178243 AAATTGAATTTATTTTA
1 AAATTAAATTTA-TTTA
* * *
178260 AATTTAAGTTAATTTGA
1 AAATTAAATTTATTT-A
*
178277 AATTTAAATTTATTATA
1 AAATTAAATTTATT-TA
178294 AAATTAAATTTA
1 AAATTAAATTTA
178306 GAAAAATCCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 3 0.08
17 33 0.89
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
AAATTAAATTTATTTA
Found at i:179000 original size:32 final size:31
Alignment explanation
Indices: 178940--179023 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
178930 GCGGTTTTTC
* * *
178940 AAAATATTTATTAATAATAAATTTTTTTAAA
1 AAAATAATAATTAATAATAAATTCTTTTAAA
178971 CAATAATAATAA-TAATAAT-AATATCTTTTAAA
1 -AA-AATAATAATTAATAATAAAT-TCTTTTAAA
179003 AAAATAATAATTAATAATAAA
1 AAAATAATAATTAATAATAAA
179024 AAAGGCATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
30 8 0.18
31 12 0.27
32 19 0.42
33 6 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
AAAATAATAATTAATAATAAATTCTTTTAAA
Done.