Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015068.1 Kokia drynarioides strain JFW-HI SEQ_130112, 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: 452914
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 400 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9886 original size:28 final size:28
Alignment explanation
Indices: 9850--10229 Score: 170
Period size: 30 Copynumber: 12.9 Consensus size: 28
9840 ATTTTAAACA
* *
9850 TTCGGGGGTAAAAGGGTAATTTTGGTAG
1 TTCGAGGGTAAAAGGGTAATTTTGGAAG
*
9878 ATTC-AGGGTCAAAAATGGG-ATTTTTGGAAG
1 -TTCGAGGGT--AAAA-GGGTAATTTTGGAAG
* *
9908 TTCGGGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGGTAAAAGGGTAA-TTTTGGAA-G
* *
9938 TTCG-GAGTAAAAAATGGG-ATTTTTGGAAG
1 TTCGAGGGT--AAAA-GGGTAATTTTGGAAG
* *
9967 TTCGAGAGTAAAATGGTAATTTTTGGAAG
1 TTCGAGGGTAAAAGGGTAA-TTTTGGAAG
*
9996 TTTCGA-GGTCAAAAATGG-AATTTTTGGAAG
1 -TTCGAGGGT--AAAAGGGTAA-TTTTGGAAG
* *
10026 TTCGGGGGTAAAATGGTAATTTTGGAAGG
1 TTCGAGGGTAAAAGGGTAATTTTGGAA-G
* *
10055 TTTTG-GAGTCAAAAATGGG-AATTTTGGAAG
1 -TTCGAGGGT--AAAA-GGGTAATTTTGGAAG
* * *
10085 TTCGGGGGTAAAATGGTAATTTTTGAAAG
1 TTCGAGGGTAAAAGGGTAA-TTTTGGAAG
** *
10114 TTTTAGGGTCAAAAATGGG-ATTTTTGGAAG
1 TTCGAGGGT--AAAA-GGGTAATTTTGGAAG
* **
10144 CTCGAGGGTAAAATTGTAATTTTTGGAAG
1 TTCGAGGGTAAAAGGGTAA-TTTTGGAAG
* *
10173 TTTTG-GGGTCAAAAATGGG-ATTTTTGGAAG
1 -TTCGAGGGT--AAAA-GGGTAATTTTGGAAG
* * *
10203 TTCGGGGGTAAAATGGTAGTTATTGGA
1 TTCGAGGGTAAAAGGGTAATT-TTGGA
10230 TAGCTTAGGG
Statistics
Matches: 273, Mismatches: 40, Indels: 76
0.70 0.10 0.20
Matches are distributed among these distances:
27 9 0.03
28 47 0.17
29 81 0.30
30 90 0.33
31 39 0.14
32 7 0.03
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (28 bp):
TTCGAGGGTAAAAGGGTAATTTTGGAAG
Found at i:9961 original size:59 final size:59
Alignment explanation
Indices: 9850--10229 Score: 518
Period size: 59 Copynumber: 6.5 Consensus size: 59
9840 ATTTTAAACA
* * *
9850 TTCGGGGGTAAAAGGGTAA-TTTTGGTAGATTCAGG-GTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTC-GGAGTCAAAAATGGGATTTTTGGAAG
* *
9908 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAG
* * *
9967 TTCGAGAGTAAAATGGTAATTTTTGGAAGTTTC-GAGGTCAAAAATGGAATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGA-GTCAAAAATGGGATTTTTGGAAG
* *
10026 TTCGGGGGTAAAATGGTAA-TTTTGGAAGGTTTTGGAGTCAAAAATGGGAATTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAA-GTTTCGGAGTCAAAAATGGGATTTTTGGAAG
* *
10085 TTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGG-GTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAG-TTTCGGAGTCAAAAATGGGATTTTTGGAAG
* * * * *
10144 CTCGAGGGTAAAATTGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAG
* *
10203 TTCGGGGGTAAAATGGTAGTTATTGGA
1 TTCGGGGGTAAAATGGTAATTTTTGGA
10230 TAGCTTAGGG
Statistics
Matches: 287, Mismatches: 27, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
58 35 0.12
59 238 0.83
60 14 0.05
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAG
Found at i:10157 original size:177 final size:176
Alignment explanation
Indices: 9850--10229 Score: 573
Period size: 177 Copynumber: 2.1 Consensus size: 176
9840 ATTTTAAACA
* * *
9850 TTCGGGGGTAAAAGGGTAATTTTGGTAGATTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
1 TTCGGGGGTAAAATGGTAATTTTGGAAGATTCAGGGTCAAAAATGGGAATTTTGGAAGTTCGGGG
* * *
9915 GTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGAGAGTAAAA
66 GTAAAATGGTAATTTTTGAAAGGTTAGGAGTAAAAAATGGGATTTTTGGAAGCTCGAGAGTAAAA
9980 TGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
131 TGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
* **
10026 TTCGGGGGTAAAATGGTAATTTTGGAAGGTTTTGGAGTCAAAAATGGGAATTTTGGAAGTTCGGG
1 TTCGGGGGTAAAATGGTAATTTTGGAAGATTCAGG-GTCAAAAATGGGAATTTTGGAAGTTCGGG
* * *
10091 GGTAAAATGGTAATTTTTGAAAGTTTTAGG-GTCAAAAATGGGATTTTTGGAAGCTCGAGGGTAA
65 GGTAAAATGGTAATTTTTGAAAG-GTTAGGAGTAAAAAATGGGATTTTTGGAAGCTCGAGAGTAA
* * * *
10155 AATTGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
129 AATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
*
10203 TTCGGGGGTAAAATGGTAGTTATTGGA
1 TTCGGGGGTAAAATGGTAATT-TTGGA
10230 TAGCTTAGGG
Statistics
Matches: 184, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
176 30 0.16
177 145 0.79
178 9 0.05
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.33
Consensus pattern (176 bp):
TTCGGGGGTAAAATGGTAATTTTGGAAGATTCAGGGTCAAAAATGGGAATTTTGGAAGTTCGGGG
GTAAAATGGTAATTTTTGAAAGGTTAGGAGTAAAAAATGGGATTTTTGGAAGCTCGAGAGTAAAA
TGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAG
Found at i:10996 original size:78 final size:78
Alignment explanation
Indices: 10867--11018 Score: 214
Period size: 78 Copynumber: 1.9 Consensus size: 78
10857 TCGCGATTCC
* * * **
10867 GTAGCCACGCGCCGTTGTGCGCCTCCGCCAAGGCAACGTCCGACCGCCCACGCGACCTGCATCTC
1 GTAGCCACGCGCCGTTGTGCGCCTCCACCAAGACAACCTCCGACCGCCCACGCGACCCACATCTC
10932 CGGTCACCGGTCT
66 CGGTCACCGGTCT
* * * * *
10945 GTAGCCATGCGCCGTTGTGCGCTTCCACCAAGACAACCTCCGACCGTCCACGCGCCCCACATCTT
1 GTAGCCACGCGCCGTTGTGCGCCTCCACCAAGACAACCTCCGACCGCCCACGCGACCCACATCTC
11010 CGGTCACCG
66 CGGTCACCG
11019 ATAAGTTCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.16
Consensus pattern (78 bp):
GTAGCCACGCGCCGTTGTGCGCCTCCACCAAGACAACCTCCGACCGCCCACGCGACCCACATCTC
CGGTCACCGGTCT
Found at i:12081 original size:18 final size:18
Alignment explanation
Indices: 12055--12153 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
12045 TTATTTATTT
*
12055 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTAAAA
* * *
12074 TAATTTTAAA-CTTAAAT
1 TAAATTTAAATTTTAAAA
12091 TAAATTTAAATTTTAAAA
1 TAAATTTAAATTTTAAAA
* *
12109 TAAATTTTAATTTTTAAA
1 TAAATTTAAATTTTAAAA
*
12127 CAAATTT-AATTTTAAAA
1 TAAATTTAAATTTTAAAA
12144 TAAATTTAAA
1 TAAATTTAAA
12154 GGGAGTGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
17 28 0.42
18 35 0.53
19 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (18 bp):
TAAATTTAAATTTTAAAA
Found at i:12099 original size:35 final size:35
Alignment explanation
Indices: 12054--12153 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 35
12044 TTTATTTATT
*
12054 TTAAACTTTAAATTTGAAAATAATTTTAAACTTAAA
1 TTAAA-TTTAAATTTTAAAATAATTTTAAACTTAAA
**
12090 TTAAATTTAAATTTTAAAATAAATTTTAATTTTTAAA
1 TTAAATTTAAATTTTAAAAT-AATTTTAA-ACTTAAA
* *
12127 -CAAATTT-AATTTTAAAATAAATTTAAA
1 TTAAATTTAAATTTTAAAATAATTTTAAA
12154 GGGAGTGGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
34 7 0.12
35 25 0.45
36 19 0.34
37 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
TTAAATTTAAATTTTAAAATAATTTTAAACTTAAA
Found at i:12136 original size:17 final size:17
Alignment explanation
Indices: 12064--12152 Score: 97
Period size: 17 Copynumber: 5.1 Consensus size: 17
12054 TTAAACTTTA
* *
12064 AATTTGAAAATAATTTT
1 AATTTTAAAATAAATTT
** *
12081 AAACTTAAATTAAATTT
1 AATTTTAAAATAAATTT
12098 AAATTTTAAAATAAATTTT
1 -AATTTTAAAATAAA-TTT
* *
12117 AATTTTTAAACAAATTT
1 AATTTTAAAATAAATTT
12134 AATTTTAAAATAAATTT
1 AATTTTAAAATAAATTT
12151 AA
1 AA
12153 AGGGAGTGGG
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
17 32 0.55
18 23 0.40
19 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
AATTTTAAAATAAATTT
Found at i:12465 original size:15 final size:15
Alignment explanation
Indices: 12445--12478 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
12435 GAGATTGGAG
12445 TTCATGTTGTGAAAT
1 TTCATGTTGTGAAAT
12460 TTCATGTTGTGAAAT
1 TTCATGTTGTGAAAT
12475 TTCA
1 TTCA
12479 AGGAGATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (15 bp):
TTCATGTTGTGAAAT
Found at i:13084 original size:139 final size:138
Alignment explanation
Indices: 12725--13063 Score: 520
Period size: 139 Copynumber: 2.4 Consensus size: 138
12715 CGTGGGTTTG
* * *
12725 GTTT-GGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-CCACGTCGTCTATTTCAATTCGCTTC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCA--TCGT-TGTTTCAATCCGCTTC
* *
12788 TCTGTATCTCACCAAGAAGACAAATTTGGTTCACTTCTCAGTACCTCATCTGGAAGATTTGCTCG
63 TCTGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTACCTCATCTGGAAGATTTGCTCG
12853 TTTCGAGCCTC
128 TTTCGAGCCTC
* **
12864 GTTTGGGTCTTCTTCTCAGTGTCTCATAAGGAAGATGATCCCATCACTGTTTCAATCCGCTTCTC
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGAT-CCATCGTTGTTTCAATCCGCTTCTC
* *
12929 TGTATCTCATCAGGAAGACGAATTTGGTTTACTTCTCAGTACCTCATCTGGAAGATTTGCTCGTT
65 TGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTACCTCATCTGGAAGATTTGCTCGTT
12994 TCGAGCCTC
130 TCGAGCCTC
*
13003 GTTTGGGTCTTCTTATCAGTGTCTCATCAGGAAGATGATCCTATCGTTGTTTCAATCCGCT
1 GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCC-ATCGTTGTTTCAATCCGCT
13064 CCTTTGTACC
Statistics
Matches: 182, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
138 2 0.01
139 144 0.79
140 33 0.18
142 3 0.02
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (138 bp):
GTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCCATCGTTGTTTCAATCCGCTTCTCT
GTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTACCTCATCTGGAAGATTTGCTCGTTT
CGAGCCTC
Found at i:13719 original size:27 final size:28
Alignment explanation
Indices: 13689--13749 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
13679 CCAAGAATTC
*
13689 TATTAAAA-GAGGATCGAAGGAAACAAT
1 TATTAAAAGGAGGATCAAAGGAAACAAT
*
13716 TATTAAAAGGAGGATTAAAGGAAACAAT
1 TATTAAAAGGAGGATCAAAGGAAACAAT
*
13744 CATTAA
1 TATTAA
13750 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (28 bp):
TATTAAAAGGAGGATCAAAGGAAACAAT
Found at i:18278 original size:34 final size:34
Alignment explanation
Indices: 18235--18301 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
18225 GATGATATTG
18235 TAGGTACAGGTATTTTCTTCCCTTCTGAAATGAA
1 TAGGTACAGGTATTTTCTTCCCTTCTGAAATGAA
*
18269 TAGGTACAGGTATTTTCTTCCTTTCTGAAATGA
1 TAGGTACAGGTATTTTCTTCCCTTCTGAAATGA
18302 CGGTTGCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.40
Consensus pattern (34 bp):
TAGGTACAGGTATTTTCTTCCCTTCTGAAATGAA
Found at i:19394 original size:45 final size:45
Alignment explanation
Indices: 19330--19421 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
19320 TCTCGTTGCA
19330 TTACGAATAATCACCTTGGGACGATTGCTTCTGTAAGTCTTAGCT
1 TTACGAATAATCACCTTGGGACGATTGCTTCTGTAAGTCTTAGCT
19375 TTACGAATAATCACCTTGGGACGATTGCTTCTGTAAGTCTTAGCT
1 TTACGAATAATCACCTTGGGACGATTGCTTCTGTAAGTCTTAGCT
19420 TT
1 TT
19422 CCCGTCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (45 bp):
TTACGAATAATCACCTTGGGACGATTGCTTCTGTAAGTCTTAGCT
Found at i:21374 original size:59 final size:58
Alignment explanation
Indices: 21267--21613 Score: 266
Period size: 59 Copynumber: 5.9 Consensus size: 58
21257 CAAACATTTG
* * * * * *
21267 GGGGTAAAAGGGTAA-TTTTGGTAGATTTAGGGTTAAAAATGG-GATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAG-GTTAGGGGT-AAAATGGTAATTTTTGGAAGTTTT
* * * *
21325 GGGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGG-GATTTTTGGAAG-TTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTAGGGGT--AAAATGGTAATTTTTGGAAGTTTT
* * *
21383 GAGGGTAAAATGATAATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTAGGGGTAAAATGGTAATTTTTGGAA-GTTTT
* * *
21443 GGAGTCAAAAATGGGAA-TTTTGGAA-GTTTGAGGGTAAAATGGTAATTTTTGGAAGTTTT
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTAG-GGGTAAAATGGTAATTTTTGGAAGTTTT
* * * *
21502 GGGGTCAAAAAT-G-AGATTTTTGGAA-GCTCGAGGGTAAAATTGTAATTTTTGGAATTTTT
1 GGGGT--AAAATGGTA-ATTTTTGGAAGGTTAG-GGGTAAAATGGTAATTTTTGGAAGTTTT
* * *
21561 GGGGTCAAAAATGG-GATTTTTGGAA-GTTCGAGGGTAAAATGGTAATTATTGGA
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTAG-GGGTAAAATGGTAATTTTTGGA
21614 TAGCTTAGGG
Statistics
Matches: 250, Mismatches: 27, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
57 8 0.03
58 34 0.14
59 165 0.66
60 35 0.14
61 8 0.03
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.35
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTAGGGGTAAAATGGTAATTTTTGGAAGTTTT
Found at i:21471 original size:60 final size:59
Alignment explanation
Indices: 21302--21613 Score: 343
Period size: 59 Copynumber: 5.3 Consensus size: 59
21292 TTTAGGGTTA
* * * *
21302 AAAATGG-GATTTTTGGAAGTTTAGGGGT--AAAATGGTAATTTTTGGAAGGTTCG-GAGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG-GATTTTTGGAA-GTTCGAGGGT
* * ** * *
21359 AAAAAATGG-GATTTTTGGAAG-TTCGAGGGT--AAAATGATAATTTTTGGAAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTTG-GGGTCAAAAATG-GGATTTTTGGAAGTTCGAGGGT
* * *
21418 AAAATGGTAATTTTTGGAAGGTTTTGGAGTCAAAAATGGGAATTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAA-GTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
21478 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGCTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
21537 AAAATTGTAATTTTTGGAATTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
21596 AAAATGGTAATTATTGGA
1 AAAATGGTAATTTTTGGA
21614 TAGCTTAGGG
Statistics
Matches: 223, Mismatches: 22, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
57 7 0.03
58 17 0.08
59 153 0.69
60 40 0.18
61 6 0.03
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:21476 original size:89 final size:88
Alignment explanation
Indices: 21310--21527 Score: 323
Period size: 89 Copynumber: 2.5 Consensus size: 88
21300 TAAAAATGGG
*
21310 ATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTT
1 ATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGAATTTT
21375 GGAAGTTCGAGGGTAAAATGATA
66 GGAAGTTCGAGGGTAAAATGATA
* * *
21398 ATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTTGGAGTCAAAAATGGGAATTT
1 ATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGG-TTCGGAGTAAAAAATGGGAATTT
* *
21463 TGGAAGTTTGAGGGTAAAATGGTA
65 TGGAAGTTCGAGGGTAAAATGATA
*
21487 ATTTTTGGAAGTTTTGGGGTCAAAAAT-G-AGATTTTTGGAAG
1 ATTTTTGGAAGTTTAGGGGT--AAAATGGTA-ATTTTTGGAAG
21528 CTCGAGGGTA
Statistics
Matches: 119, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
88 40 0.34
89 62 0.52
90 12 0.10
91 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (88 bp):
ATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGAATTTT
GGAAGTTCGAGGGTAAAATGATA
Found at i:21481 original size:148 final size:147
Alignment explanation
Indices: 21263--21586 Score: 440
Period size: 148 Copynumber: 2.2 Consensus size: 147
21253 ATTTCAAACA
* * * *
21263 TTTGGGGGTAAAAGGGTAA-TTTTGGTAGATTTAGGGTTAAAAATGGGATTTTTGGAAGTTTAGG
1 TTTGGGGGTAAAATGGTAATTTTTGGAAGATTTAGGGTCAAAAATGGGAATTTTGGAAGTTTAGG
* *
21327 GGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGAGGGTAAA
66 GGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGAGATTTTTGGAAGCTCGAGGGTAAA
21392 A-TGATAATTTTTGGAAG
131 ATTG-TAATTTTTGGAAG
* *
21409 TTTGGGGGTAAAATGGTAATTTTTGGAAGGTTTTGGAGTCAAAAATGGGAATTTTGGAAGTTT-G
1 TTTGGGGGTAAAATGGTAATTTTTGGAAGATTTAGG-GTCAAAAATGGGAATTTTGGAAGTTTAG
* * * *
21473 AGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGCTCGAGGGTA
65 -GGGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGAGATTTTTGGAAGCTCGAGGGTA
*
21538 AAATTGTAATTTTTGGAAT
129 AAATTGTAATTTTTGGAAG
* *
21557 TTTTGGGGTCAAAAATGG-GATTTTTGGAAG
1 TTTGGGGGT--AAAATGGTAATTTTTGGAAG
21587 TTCGAGGGTA
Statistics
Matches: 157, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
146 18 0.11
147 14 0.09
148 105 0.67
149 13 0.08
150 7 0.04
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.36
Consensus pattern (147 bp):
TTTGGGGGTAAAATGGTAATTTTTGGAAGATTTAGGGTCAAAAATGGGAATTTTGGAAGTTTAGG
GGTAAAATGGTAATTTTTGGAAGGTTCGGAGTAAAAAATGAGATTTTTGGAAGCTCGAGGGTAAA
ATTGTAATTTTTGGAAG
Found at i:21623 original size:29 final size:28
Alignment explanation
Indices: 21268--21623 Score: 258
Period size: 29 Copynumber: 12.1 Consensus size: 28
21258 AAACATTTGG
* *
21268 GGGTAAAAGGGTAA-TTTTGGTAGATTTA
1 GGGTAAAATGGTAATTTTTGGAAG-TTTA
*
21296 GGGTTAAAAATGG-GATTTTTGGAAGTTTA
1 GGG-T-AAAATGGTAATTTTTGGAAGTTTA
* *
21325 GGGGTAAAATGGTAATTTTTGGAAGGTTC
1 -GGGTAAAATGGTAATTTTTGGAAGTTTA
* *
21354 GGAGTAAAAAATGG-GATTTTTGGAAGTTCGA
1 GG-GT--AAAATGGTAATTTTTGGAAGTT-TA
* *
21385 GGGTAAAATGATAATTTTTGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGAAGTTT-A
*
21414 GGGTAAAATGGTAATTTTTGGAAGGTTTT
1 GGGTAAAATGGTAATTTTTGGAA-GTTTA
*
21443 GGAGTCAAAAATGGGAA-TTTTGGAAGTTTGA
1 GG-GT--AAAATGGTAATTTTTGGAAGTTT-A
*
21474 GGGTAAAATGGTAATTTTTGGAAGTTTTG
1 GGGTAAAATGGTAATTTTTGGAAG-TTTA
**
21503 GGGTCAAAAAT-G-AGATTTTTGGAAGCTCGA
1 GGGT--AAAATGGTA-ATTTTTGGAAG-TTTA
* * *
21533 GGGTAAAATTGTAATTTTTGGAATTTTTG
1 GGGTAAAATGGTAATTTTTGGAA-GTTTA
* *
21562 GGGTCAAAAATGG-GATTTTTGGAAGTTCGA
1 GGGT--AAAATGGTAATTTTTGGAAGTT-TA
* *
21592 GGGTAAAATGGTAATTATTGGATAGCTTA
1 GGGTAAAATGGTAATTTTTGGA-AGTTTA
21621 GGG
1 GGG
21624 ACCTCCGGGG
Statistics
Matches: 262, Mismatches: 37, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
28 39 0.15
29 103 0.39
30 81 0.31
31 30 0.11
32 9 0.03
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTA
Found at i:22342 original size:78 final size:78
Alignment explanation
Indices: 22234--22390 Score: 210
Period size: 78 Copynumber: 2.0 Consensus size: 78
22224 NNGTCGCGAT
* * * *
22234 TCCGTAGCCACGCGACGTTGTGTGCCTCCGCCGAGGCAACATCCGACCGCCCACGCGCCCTTA-A
1 TCCGTAGCCACGCGACGTTGTGCGCCTCCGCCAAGACAACATCCAACCGCCCACGCGCCC-TACA
22298 TCTCCGGTCACCGG
65 TCTCCGGTCACCGG
* * * *
22312 TCCGTAGCCATGC-ACCGTTGTGCGCTTCCGCCAAGACAACCTCCAACCGTCCACGCGCCCTACA
1 TCCGTAGCCACGCGA-CGTTGTGCGCCTCCGCCAAGACAACATCCAACCGCCCACGCGCCCTACA
22376 TCTCCGGTCACCGG
65 TCTCCGGTCACCGG
22390 T
1 T
22391 AAGTTCAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
77 3 0.04
78 66 0.96
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.18
Consensus pattern (78 bp):
TCCGTAGCCACGCGACGTTGTGCGCCTCCGCCAAGACAACATCCAACCGCCCACGCGCCCTACAT
CTCCGGTCACCGG
Found at i:23456 original size:17 final size:17
Alignment explanation
Indices: 23419--23516 Score: 124
Period size: 17 Copynumber: 5.6 Consensus size: 17
23409 TTATTTATTT
23419 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* *
23438 TAATTTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
23455 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
23472 TAAATTTAAAATTTTAAA
1 TAAATTT-AAATTTAAAA
* *
23490 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
23507 TAAATTTAAA
1 TAAATTTAAA
23517 GGGAGTGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
17 42 0.62
18 23 0.34
19 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:23463 original size:35 final size:34
Alignment explanation
Indices: 23419--23516 Score: 115
Period size: 35 Copynumber: 2.8 Consensus size: 34
23409 TTATTTATTT
23419 TAAACTTTAAATTTGAAAATAATTTTAAACTTAAAA
1 TAAA-TTTAAATTT-AAAATAATTTTAAACTTAAAA
* * *
23455 TAAATTTAAATTTAAAATAAATTTAAAATTTTAAA
1 TAAATTTAAATTTAAAAT-AATTTTAAACTTAAAA
* * *
23490 CAAATTTAATTTTAAAATAAATTTAAA
1 TAAATTTAAATTTAAAATAATTTTAAA
23517 GGGAGTGGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 12 0.22
35 38 0.70
36 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATAATTTTAAACTTAAAA
Found at i:26870 original size:271 final size:271
Alignment explanation
Indices: 26387--26930 Score: 822
Period size: 271 Copynumber: 2.0 Consensus size: 271
26377 TAATTCCATG
** * * * *
26387 ATCCAAGGTGCCACAGAGATAACGAAGTAAACATTTGGCTGCAGGTCAATGCTTCTTTGTTGGTT
1 ATCCAAGGTGCCACAGAGATAACGAAGTAAACATTTGGCTGCACCTCAATGCTCCGTCGTTAGTT
* * * * *
26452 TATGCATGAATTGAAATAGTTTGTTGATTGTGTAAGCGATGTTTGGGCGAGTGAGGGAAAGATAC
66 TATGCATGAATTGAAATAGTTTGTTGACTATGTAAGCGATGTCTAGGCAAGTGAGGGAAAGATAC
*
26517 TGAAGACTCCTAACAGTGGTACGATACTCTGTAGAATCAAACAATAGAGTACCTGCATGCAAGGT
131 TGAAGACTCCTAACAGTGGTACGATACTCTGTAGAATCAAACAATAGAGTACCTGCACGCAAGGT
26582 GAGAAGCAGAGTTGTTGCAAGAGGAGAT-GAAACGAGTTTGGCATCGACCATATGAGTCTTCTAA
196 GAGAAGCAGAGTTGTTGCAAGAGGAG-TGGAAACGAGTTTGGCATCGACCATATGAGTCTTCTAA
26646 AGGAGGTCAGCA
260 AGGAGGTCAGCA
* *
26658 ATCCAAGGTGCCACAGAGATAGCGAAGTAAACGTTTGGCTGCACCTCAATGCTCCGTCGTTAGTT
1 ATCCAAGGTGCCACAGAGATAACGAAGTAAACATTTGGCTGCACCTCAATGCTCCGTCGTTAGTT
* * * *
26723 TGTGCATGAATTGAGATAGTTTGTTGACTATGTAAGTGATGTCTAGGTAAGTGAGGGAAAGATAC
66 TATGCATGAATTGAAATAGTTTGTTGACTATGTAAGCGATGTCTAGGCAAGTGAGGGAAAGATAC
* * * *
26788 TGAAGA-TTCTCAACAGTGGTACGATACTCTGTAGGATCAGACAATAGAGTACCTGCACGTAAGG
131 TGAAGACTCCT-AACAGTGGTACGATACTCTGTAGAATCAAACAATAGAGTACCTGCACGCAAGG
* * * *
26852 TGAGAGGCGGAGTTGTTGCAAGAGGAGTGGAAACGGGTTTGGCATCGACCATATGAGTCTTCTGA
195 TGAGAAGCAGAGTTGTTGCAAGAGGAGTGGAAACGAGTTTGGCATCGACCATATGAGTCTTCTAA
26917 AGGAGGTCAGCA
260 AGGAGGTCAGCA
26929 AT
1 AT
26931 ATATTTTCAC
Statistics
Matches: 245, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
270 4 0.02
271 241 0.98
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (271 bp):
ATCCAAGGTGCCACAGAGATAACGAAGTAAACATTTGGCTGCACCTCAATGCTCCGTCGTTAGTT
TATGCATGAATTGAAATAGTTTGTTGACTATGTAAGCGATGTCTAGGCAAGTGAGGGAAAGATAC
TGAAGACTCCTAACAGTGGTACGATACTCTGTAGAATCAAACAATAGAGTACCTGCACGCAAGGT
GAGAAGCAGAGTTGTTGCAAGAGGAGTGGAAACGAGTTTGGCATCGACCATATGAGTCTTCTAAA
GGAGGTCAGCA
Found at i:32237 original size:18 final size:19
Alignment explanation
Indices: 32214--32254 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
32204 AGCACTGCTG
32214 CTCTTTCTGTAGAAACAC-
1 CTCTTTCTGTAGAAACACA
32232 CTCTTTCTGTAGAAACACA
1 CTCTTTCTGTAGAAACACA
32251 CTCT
1 CTCT
32255 ACAATCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (19 bp):
CTCTTTCTGTAGAAACACA
Found at i:35897 original size:15 final size:16
Alignment explanation
Indices: 35865--35898 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35855 AATTAAAAGA
*
35865 AAAAAAAGATAAGTTC
1 AAAAAAAGATAAGATC
35881 AAAAAAAGATAA-ATC
1 AAAAAAAGATAAGATC
35896 AAA
1 AAA
35899 CTAAAGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAAAAAGATAAGATC
Found at i:36913 original size:81 final size:81
Alignment explanation
Indices: 36778--36941 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 81
36768 AAATTATATA
36778 AACCCTTATATGATAGGTTCAAAAAGAATTCACAACCTTAGACAAGTGACCACACCAATATTATT
1 AACCCTTATATGATAGGTTCAAAAAGAATTCACAACCTTAGACAAGTGACCACACCAATATTATT
36843 ATCCAAATCAAAAAAC
66 ATCCAAATCAAAAAAC
* *
36859 AACCCTTATATGATAGGTTCAAAAAGAATTCACAACCTTGGACAAGTGACCACACCAATATTGTT
1 AACCCTTATATGATAGGTTCAAAAAGAATTCACAACCTTAGACAAGTGACCACACCAATATTATT
36924 ATCCAAATCAAAAAAC
66 ATCCAAATCAAAAAAC
36940 AA
1 AA
36942 ATTACTAAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (81 bp):
AACCCTTATATGATAGGTTCAAAAAGAATTCACAACCTTAGACAAGTGACCACACCAATATTATT
ATCCAAATCAAAAAAC
Found at i:52441 original size:22 final size:22
Alignment explanation
Indices: 52413--52455 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
52403 GCATCATGCC
52413 TTCCTTTGATATCAATTTTCTA
1 TTCCTTTGATATCAATTTTCTA
52435 TTCCTTTGATATCAATTTTCT
1 TTCCTTTGATATCAATTTTCT
52456 TTTCAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.56
Consensus pattern (22 bp):
TTCCTTTGATATCAATTTTCTA
Found at i:52748 original size:95 final size:95
Alignment explanation
Indices: 52579--52769 Score: 301
Period size: 95 Copynumber: 2.0 Consensus size: 95
52569 CATTAAGAAG
* * *
52579 GTTCTAAACCATGCCCATTGAGCTGATCTATTCCCTGCAGTTCAAGTCTATTGCTTTTGGACCTG
1 GTTCCAAACCATGCCCATTGAACTGATCTATTCCCTGCAGTTCAAGTCTATTGCTTTTGGACCCG
** * *
52644 ATTTGATGTCGTTTTGGCATTGGCTGTTGA
66 ATTCAATGTCATTGTGGCATTGGCTGTTGA
* *
52674 GTTCCAAACCATGCCCATTGAACTGATCTATTCCTTTCAGTTCAAGTCTATTGCTTTTGGACCCG
1 GTTCCAAACCATGCCCATTGAACTGATCTATTCCCTGCAGTTCAAGTCTATTGCTTTTGGACCCG
52739 ATTCAATGTCATTGTGGCATTGGCTGTTGA
66 ATTCAATGTCATTGTGGCATTGGCTGTTGA
52769 G
1 G
52770 ATCAAATAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (95 bp):
GTTCCAAACCATGCCCATTGAACTGATCTATTCCCTGCAGTTCAAGTCTATTGCTTTTGGACCCG
ATTCAATGTCATTGTGGCATTGGCTGTTGA
Found at i:54641 original size:5 final size:5
Alignment explanation
Indices: 54631--54664 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
54621 AGCATTATTA
*
54631 TTTGT TTTGT TTTGT TTTGT TTTTT TTATGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TT-TGT TTT
54665 ACCCCTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (5 bp):
TTTGT
Found at i:63468 original size:16 final size:16
Alignment explanation
Indices: 63447--63479 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
63437 AAATGGATCA
63447 TTTCCATTTTCATTTT
1 TTTCCATTTTCATTTT
*
63463 TTTCCATTTTTATTTT
1 TTTCCATTTTCATTTT
63479 T
1 T
63480 AGAAACCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCCATTTTCATTTT
Found at i:65928 original size:26 final size:26
Alignment explanation
Indices: 65899--65977 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
65889 TTTATTAATG
65899 TATGATTTTCCTATTCACTTCTTAGT
1 TATGATTTTCCTATTCACTTCTTAGT
* *
65925 TATGA--TT-ATAAT-A-TT-TT-GAT
1 TATGATTTTCCTATTCACTTCTTAG-T
65945 TATGATTTTCCTATTCACTTCTTAGT
1 TATGATTTTCCTATTCACTTCTTAGT
65971 TATGATT
1 TATGATT
65978 ATAATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
19 1 0.02
20 8 0.20
21 2 0.05
22 3 0.07
23 6 0.15
24 3 0.07
25 2 0.05
26 15 0.37
27 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (26 bp):
TATGATTTTCCTATTCACTTCTTAGT
Found at i:65952 original size:46 final size:46
Alignment explanation
Indices: 65899--65993 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
65889 TTTATTAATG
65899 TATGATTTTCCTATTCACTTCTTAGTTATGATTATAATATTTTGAT
1 TATGATTTTCCTATTCACTTCTTAGTTATGATTATAATATTTTGAT
65945 TATGATTTTCCTATTCACTTCTTAGTTATGATTATAATATTTTGAT
1 TATGATTTTCCTATTCACTTCTTAGTTATGATTATAATATTTTGAT
65991 TAT
1 TAT
65994 TGATGCTAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (46 bp):
TATGATTTTCCTATTCACTTCTTAGTTATGATTATAATATTTTGAT
Found at i:65985 original size:26 final size:26
Alignment explanation
Indices: 65910--65985 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 26
65900 ATGATTTTCC
65910 TATTCACTTCTTAGTTATGATTATAA
1 TATTCACTTCTTAGTTATGATTATAA
* * **
65936 TA-T---TT-TGA-TTATGATTTTCC
1 TATTCACTTCTTAGTTATGATTATAA
65956 TATTCACTTCTTAGTTATGATTATAA
1 TATTCACTTCTTAGTTATGATTATAA
65982 TATT
1 TATT
65986 TTGATTATTG
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 11 0.31
21 3 0.08
22 2 0.06
24 2 0.06
25 3 0.08
26 15 0.42
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.54
Consensus pattern (26 bp):
TATTCACTTCTTAGTTATGATTATAA
Found at i:67282 original size:16 final size:16
Alignment explanation
Indices: 67248--67302 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
67238 GTCATCTTCG
*
67248 TTCTTCTTCCCCATTGT
1 TTCTTCTT-TCCATTGT
*
67265 TTCTTCTTTCCATGGT
1 TTCTTCTTTCCATTGT
*
67281 TTCTTTTTTCCCATTGT
1 TTCTTCTTT-CCATTGT
67298 TTCTT
1 TTCTT
67303 TGCAAACCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 14 0.42
17 19 0.58
ACGTcount: A:0.05, C:0.27, G:0.07, T:0.60
Consensus pattern (16 bp):
TTCTTCTTTCCATTGT
Found at i:67303 original size:17 final size:17
Alignment explanation
Indices: 67257--67303 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
67247 GTTCTTCTTC
*
67257 CCCATTGTTTCTTCTTT
1 CCCATTGTTTCTTTTTT
*
67274 -CCATGGTTTCTTTTTT
1 CCCATTGTTTCTTTTTT
67290 CCCATTGTTTCTTT
1 CCCATTGTTTCTTT
67304 GCAAACCTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.06, C:0.26, G:0.09, T:0.60
Consensus pattern (17 bp):
CCCATTGTTTCTTTTTT
Found at i:74109 original size:17 final size:17
Alignment explanation
Indices: 74083--74117 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
74073 GGAGAACTTA
* *
74083 TTCGTTGAGAATTTTTG
1 TTCGTAGAGAATTCTTG
74100 TTCGTAGAGAATTCTTG
1 TTCGTAGAGAATTCTTG
74117 T
1 T
74118 CAAGGTGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (17 bp):
TTCGTAGAGAATTCTTG
Found at i:74782 original size:21 final size:21
Alignment explanation
Indices: 74756--74807 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
74746 TGAGACAATA
74756 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* *
74777 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
74798 CTACCGATAC
1 CTACCGATAC
74808 TAAAACTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:86715 original size:25 final size:24
Alignment explanation
Indices: 86686--86742 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
86676 AATATTTATT
*
86686 TAATTTTTTAAAAATTATAAAAATA
1 TAATTTTTT-AAAATAATAAAAATA
* * *
86711 TAATTTATTAAAATAATGAAATTA
1 TAATTTTTTAAAATAATAAAAATA
86735 TAATTTTT
1 TAATTTTT
86743 ATCATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTTTTTAAAATAATAAAAATA
Found at i:87425 original size:22 final size:22
Alignment explanation
Indices: 87374--87417 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
87364 AACTTTATTA
*
87374 AAATTTATCTTTATTTTTAATT
1 AAATTTATCTTTATTTTGAATT
87396 AAATTTAT-TTTATTATTGAATT
1 AAATTTATCTTTATT-TTGAATT
87418 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATTTATCTTTATTTTGAATT
Found at i:96573 original size:21 final size:21
Alignment explanation
Indices: 96549--96602 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
96539 CAATACCATA
96549 AACTATCGATACTTGTATCTT
1 AACTATCGATACTTGTATCTT
96570 AACTATCGATACTTGTATCTT
1 AACTATCGATACTTGTATCTT
96591 AACTATCGATAC
1 AACTATCGATAC
96603 AACCCAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
AACTATCGATACTTGTATCTT
Found at i:97219 original size:24 final size:24
Alignment explanation
Indices: 97192--97267 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
97182 CACATGAGTG
97192 CAGAATGATTAGCTCTTACGAGCC
1 CAGAATGATTAGCTCTTACGAGCC
*
97216 CAGAATGGTTAGCTCTTACGAGCC
1 CAGAATGATTAGCTCTTACGAGCC
*
97240 CAAAATGATTAGCTCTTACGAGCC
1 CAGAATGATTAGCTCTTACGAGCC
97264 CAGA
1 CAGA
97268 CAGAGTTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (24 bp):
CAGAATGATTAGCTCTTACGAGCC
Found at i:98723 original size:19 final size:19
Alignment explanation
Indices: 98682--98723 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
98672 TCCATAACAA
*
98682 TTAACTTACTCTTTTTTAC
1 TTAATTTACTCTTTTTTAC
*
98701 --AATTTACTCTTTTTTCC
1 TTAATTTACTCTTTTTTAC
98718 TTAATT
1 TTAATT
98724 AAACAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 15 0.79
19 4 0.21
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTACTCTTTTTTAC
Found at i:101515 original size:21 final size:20
Alignment explanation
Indices: 101491--101530 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
101481 GTGTGCGACA
101491 AAAATCAAAAGAAAAAGAGAG
1 AAAAT-AAAAGAAAAAGAGAG
**
101512 AAAATGGAAGAAAAAGAGA
1 AAAATAAAAGAAAAAGAGA
101531 ATTTTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.70, C:0.03, G:0.23, T:0.05
Consensus pattern (20 bp):
AAAATAAAAGAAAAAGAGAG
Found at i:104271 original size:24 final size:24
Alignment explanation
Indices: 104244--104289 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
104234 ATTTTTAATT
104244 TTATAT-TTAATAATTTTATATATC
1 TTATATATTAA-AATTTTATATATC
*
104268 TTATTTATTAAAATTTTATATA
1 TTATATATTAAAATTTTATATA
104290 CATACATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATATATTAAAATTTTATATATC
Found at i:104299 original size:24 final size:25
Alignment explanation
Indices: 104250--104299 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
104240 AATTTTATAT
* *
104250 TTAATAATTTTATATATCTTATTTA
1 TTAATAATTTTATATATCATAATTA
104275 TTAA-AATTTTATATA-CATACATTA
1 TTAATAATTTTATATATCATA-ATTA
104299 T
1 T
104300 ACTACTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.14
24 15 0.68
25 4 0.18
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (25 bp):
TTAATAATTTTATATATCATAATTA
Found at i:105600 original size:60 final size:61
Alignment explanation
Indices: 105455--105686 Score: 183
Period size: 62 Copynumber: 3.8 Consensus size: 61
105445 AAAAAAATTA
* * * **
105455 GTGTTGGCCATTGCATGGCCTACACCTCCTTTTAATCTGAT--AAA-AAATCAA-ATTTTTGA
1 GTGTTGGCCATTGAATGGCCGACA-CTCCTTTT-ATCTGATAAAAATAAATCAATTTTTTTTT
* * * **
105514 GTGTT-GACAATGTAATGACTAACACTCCTATTTATCTGATAAAAATAAAT-AA-TTTTTTTT
1 GTGTTGGCCATTG-AATGGCCGACACTCCT-TTTATCTGATAAAAATAAATCAATTTTTTTTT
* * **
105574 GTGTTGGCCATTGAATGGCCGACACTCCCTTTTTTCAGATAACAAA-ATTTCAATTTTTTTTT
1 GTGTTGGCCATTGAATGGCCGACACT-CCTTTTATCTGATAA-AAATAAATCAATTTTTTTTT
* * *
105636 GTGTTGGCCATTGCATGGTCGACACTCTTTTTTATCTGAATAAAAATAAAT
1 GTGTTGGCCATTGAATGGCCGACACTC-CTTTTATCTG-ATAAAAATAAAT
105687 TTTTGGGTGT
Statistics
Matches: 135, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
58 17 0.13
59 15 0.11
60 37 0.27
61 18 0.13
62 42 0.31
63 6 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (61 bp):
GTGTTGGCCATTGAATGGCCGACACTCCTTTTATCTGATAAAAATAAATCAATTTTTTTTT
Found at i:106002 original size:60 final size:58
Alignment explanation
Indices: 105777--106062 Score: 258
Period size: 60 Copynumber: 4.8 Consensus size: 58
105767 CCATGGTTGG
* * * *
105777 TAAAAAATT--AATTTTTTTGTGTTAGCCATGCAATGGCCGACACCCCTTTTTTTATCTGG
1 TAAAAAATTCAAATTTTTTGGTGTTGGCCATGC-ATGGCCGACACCCC--TTTTTATCAGA
* *
105836 TAAAAAATTTTCAAATTTTTTTGGTGTTGGCTATTGCATGGCCGACACCCCTTTTTATCTGAA
1 TAAAAAA--TTCAAA-TTTTTTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTATCAG-A
* ** * * * *
105899 TAAAAAA-TCAAAATTTTAAGTGTTGGGCATGCCATGGCTGACACACCTTTTTTGTCAGA
1 TAAAAAATTCAAATTTTTTGGTGTTGGCCATG-CATGGCCGACAC-CCCTTTTTATCAGA
* *
105958 TAAAAAATTC-AATTTGTTTGGTATTGGCCATGTCATGGCCGACACCCCTATTTATCTA-A
1 TAAAAAATTCAAATTT-TTTGGTGTTGGCCATG-CATGGCCGACACCCCTTTTTATC-AGA
*
106017 TAAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACAC
1 T-AAAAAATTCAAATTTTTTGGTGTTGGCCATGC-ATGGCCGACAC
106063 TAACTTTCCC
Statistics
Matches: 187, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
58 2 0.01
59 53 0.28
60 75 0.40
61 7 0.04
62 10 0.05
63 9 0.05
64 28 0.15
65 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (58 bp):
TAAAAAATTCAAATTTTTTGGTGTTGGCCATGCATGGCCGACACCCCTTTTTATCAGA
Found at i:106013 original size:119 final size:122
Alignment explanation
Indices: 105795--106062 Score: 330
Period size: 119 Copynumber: 2.2 Consensus size: 122
105785 TAATTTTTTT
* * * * *
105795 GTGTTAGCCATGCAATGGCCGACACCCCTTTTTTTATCTGGTAAAAAATTTTCAAATTTTTTTGG
1 GTGTTGGCCATGCAATGGCCGACACACCTTTTTTTATCAGATAAAAAA-TTTCAAATTTGTTTGG
* * *
105860 TGTTGGCTATTGCATGGCCGACACCCCTTTTTATCTGAAT-AAAAAATCAAAATTTTAA
65 TATTGGCCATTGCATGGCCGACACCCCTATTTATCT-AATAAAAAAATCAAAATTTTAA
* * * *
105918 GTGTTGGGCATGCCATGGCTGACACACC-TTTTTTGTCAGATAAAAAA-TTC-AATTTGTTTGGT
1 GTGTTGGCCATGCAATGGCCGACACACCTTTTTTTATCAGATAAAAAATTTCAAATTTGTTTGGT
* **
105980 ATTGGCCA-TGTCATGGCCGACACCCCTATTTATCTAATAAAAAAAATCAAATTTTTTG
66 ATTGGCCATTG-CATGGCCGACACCCCTATTTATCTAAT-AAAAAAATCAAAATTTTAA
106038 GTGTTGGCCATGCAATGGCCGACAC
1 GTGTTGGCCATGCAATGGCCGACAC
106063 TAACTTTCCC
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
118 5 0.04
119 40 0.32
120 40 0.32
122 16 0.13
123 23 0.19
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (122 bp):
GTGTTGGCCATGCAATGGCCGACACACCTTTTTTTATCAGATAAAAAATTTCAAATTTGTTTGGT
ATTGGCCATTGCATGGCCGACACCCCTATTTATCTAATAAAAAAATCAAAATTTTAA
Found at i:106890 original size:17 final size:17
Alignment explanation
Indices: 106868--106922 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
106858 AAAAAATAAT
*
106868 AATTAGAATATACAGGA
1 AATTAGAATATATAGGA
106885 AATTAGAA-AT-TA--A
1 AATTAGAATATATAGGA
*
106898 AATTAAAATATATAGGA
1 AATTAGAATATATAGGA
106915 AATTAGAA
1 AATTAGAA
106923 ATTAAATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.26
14 2 0.06
15 3 0.10
16 2 0.06
17 16 0.52
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.27
Consensus pattern (17 bp):
AATTAGAATATATAGGA
Found at i:106902 original size:30 final size:30
Alignment explanation
Indices: 106868--106965 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 30
106858 AAAAAATAAT
*
106868 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
106898 AATTAAAATATATAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
* * * * * *
106928 ATTTGAAATAAAAACGAAATTAAAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
106958 ATTTAAAA
1 AATTAAAA
106966 AGTAAACGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAATTAA
Found at i:106973 original size:30 final size:29
Alignment explanation
Indices: 106883--106976 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 29
106873 GAATATACAG
* * *
106883 GAAATTAGAAATTAAAATTAAAATATATAG
1 GAAATTAGAAATTAAATTTAAAA-ATAAAC
106913 GAAATTAGAAATTAAATTTGAAATAA-AAAC
1 GAAATTAGAAATTAAATTT-AAA-AATAAAC
*
106943 GAAATTAAAAATTAAATTTAAAAAGTAAAC
1 GAAATTAGAAATTAAATTTAAAAA-TAAAC
106973 GAAA
1 GAAA
106977 AAAAATCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.04
29 3 0.05
30 46 0.82
31 4 0.07
32 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.27
Consensus pattern (29 bp):
GAAATTAGAAATTAAATTTAAAAATAAAC
Found at i:109255 original size:22 final size:22
Alignment explanation
Indices: 109206--109264 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
109196 TTGGGGTGTT
* * *
109206 GGTGAGCAGGAAATTCGATTTT
1 GGTGAGCTGGAATTTCGATTTA
*
109228 GATGAGCTGGAATTTCGATTTA
1 GGTGAGCTGGAATTTCGATTTA
109250 GGTGAGCTGGAATTT
1 GGTGAGCTGGAATTT
109265 GAGTGGTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.08, G:0.32, T:0.34
Consensus pattern (22 bp):
GGTGAGCTGGAATTTCGATTTA
Found at i:109451 original size:84 final size:84
Alignment explanation
Indices: 109357--109737 Score: 595
Period size: 84 Copynumber: 4.5 Consensus size: 84
109347 TAAATTTAAA
* *
109357 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATTTTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
*
109422 ATTGTCAAATTAACACATT
66 ATTGTCAAATCAACACATT
* * * *
109441 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTCAAATTTGGTAAATAATGA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
* *
109506 ATTATCAAATCAACTCATT
66 ATTGTCAAATCAACACATT
* *
109525 ATTTGATAAAAAATGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTAATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAATATTAAAATTTGATAAATAATG
*
109590 TATTGTCAAATTAACACATT
65 TATTGTCAAATCAACACATT
109610 ATTTGATAAAAATTGTAATATAATAAT--TTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
109673 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
109692 ATTTGATATAAATTGAAATATAATAATAATATTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATA
109738 ATGTTAAATT
Statistics
Matches: 271, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
82 78 0.29
84 105 0.39
85 73 0.27
86 15 0.06
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGATAAATAATGT
ATTGTCAAATCAACACATT
Found at i:109635 original size:169 final size:167
Alignment explanation
Indices: 109357--109737 Score: 620
Period size: 169 Copynumber: 2.3 Consensus size: 167
109347 TAAATTTAAA
* * *
109357 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTAATTTAAATTTTAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTAATAAATAATG
109421 TATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATAT
66 TATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAAT--TTTTTAATTTAAATAT
* * *
109486 TCAAATTTGGTAAATAATGAATTATCAAATCAACTCATT
129 TAAAATTTGATAAATAATGAATTATCAAATCAACACATT
*
109525 ATTTGATAAAAAATGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTAATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTAATAAATAATG
*
109590 TATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAATTTTTTTATTTAAATATTA
66 TATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAATTTTTTAATTTAAATATTA
* *
109655 AAATTTGATAAATAATGTATTGTCAAATCAACACATT
131 AAATTTGATAAATAATGAATTATCAAATCAACACATT
* *
109692 ATTTGATATAAATTGAAATATAATAATAATATTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAAT-TTTTTTATTTAAATA
109738 ATGTTAAATT
Statistics
Matches: 198, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
167 76 0.38
168 43 0.22
169 79 0.40
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (167 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTAATAAATAATG
TATTGTCAAATTAACACATTATTTGATAAAAATTGTAATATAATAATTTTTTAATTTAAATATTA
AAATTTGATAAATAATGAATTATCAAATCAACACATT
Found at i:109908 original size:28 final size:28
Alignment explanation
Indices: 109852--109908 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
109842 AACATGTACC
**
109852 TTAATTTTCAAATCAATTTCAACTTAAA
1 TTAATTTTCAAATCAATTTCAACACAAA
* **
109880 TTAATTTTCAAATTAATTTTTACACAAA
1 TTAATTTTCAAATCAATTTCAACACAAA
109908 T
1 T
109909 ATTCTTCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (28 bp):
TTAATTTTCAAATCAATTTCAACACAAA
Found at i:112889 original size:11 final size:12
Alignment explanation
Indices: 112846--112893 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
112836 TTATTTTCGT
*
112846 TTATTTCTTAAAA
1 TTATTT-TTAATA
*
112859 TTAATTTTAATTA
1 TTATTTTTAA-TA
112872 TTATTTTTAATA
1 TTATTTTTAATA
112884 -TATTTTTAAT
1 TTATTTTTAAT
112894 TTGTCGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 15 0.48
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTTTAATA
Found at i:113729 original size:59 final size:58
Alignment explanation
Indices: 113656--114158 Score: 262
Period size: 60 Copynumber: 8.4 Consensus size: 58
113646 ACCAACATAA
* * *
113656 AAAAATT-GATTTTTTACCAGATAAAAAAAGGGGTGTCGGCCATGCAATGGCTAACACC
1 AAAAATTCAATTTTTTATCAGA-AAAAAAAGGGGTGTCGGCCATGCAATGGCCAACACC
* *
113714 AAAAATTCAAATTTTTTATCTGACAAAAAAA-GGGTGTCGACCATTGC-ATGGCCAACAACC
1 AAAAATTC-AATTTTTTATCAGA-AAAAAAAGGGGTGTCGGCCA-TGCAATGGCCAAC-ACC
* * *
113774 AAAAAAATT-GATTTTTTA-CTAGATAAAAAAGGGAGTGTCGGCCATG-ACATGGCCAACACAAA
1 --AAAAATTCAATTTTTTATC-AGAAAAAAAAGGG-GTGTCGGCCATGCA-ATGGCCAACAC--C
* * * *
113836 AAAAATTCGAATTTTTTATCTG-ACAAAAAGGGATGTTGGCCATG-ACATGGCCAACACCC
1 AAAAATTC-AATTTTTTATCAGAAAAAAAAGGGGTGTCGGCCATGCA-ATGGCCAACA-CC
* ** * * *
113895 AACAATTTGATTTTTTATTCAGAAAAAAAA-GGGTGTCGACCATACAATGACCAACACC
1 AAAAATTCAATTTTTTA-TCAGAAAAAAAAGGGGTGTCGGCCATGCAATGGCCAACACC
* * *
113953 AAAAAATTTTTTTTAATTTTTTTATCTG---AAAAAGGGAGTGTCGGCCATTGC-ATGACCAACA
1 -AAAAA-----TTCAA-TTTTTTATCAGAAAAAAAAGGG-GTGTCGGCCA-TGCAATGGCCAACA
114014 CC
57 CC
* * * ** * ** *
114016 AAAAAATTTGATTTTTTTATCA-AATAAATGGGGGTATCGGCCATGGTATGGTCAACACC
1 -AAAAA-TTCAATTTTTTATCAGAAAAAAAAGGGGTGTCGGCCATGCAATGGCCAACACC
* * * * ** **
114075 AAAAAAATTAAATTTTTTATCTGACAAAAAGGGGGTGTAAGCCATTG-AATAACCAACACCC
1 --AAAAATTCAATTTTTTATCAGAAAAAAAAGGGGTGTCGGCCA-TGCAATGGCCAACA-CC
*
114136 AAAAATTTAATTTTTTTATCAGA
1 AAAAATTCAA-TTTTTTATCAGA
114159 TGCCAACACC
Statistics
Matches: 349, Mismatches: 57, Indels: 76
0.72 0.12 0.16
Matches are distributed among these distances:
58 28 0.08
59 102 0.29
60 121 0.35
61 36 0.10
62 18 0.05
63 28 0.08
64 9 0.03
65 7 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (58 bp):
AAAAATTCAATTTTTTATCAGAAAAAAAAGGGGTGTCGGCCATGCAATGGCCAACACC
Found at i:114166 original size:34 final size:34
Alignment explanation
Indices: 114127--114192 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
114117 CATTGAATAA
* *
114127 CCAACACCCAAAAATTTAATTTTTTTATCAGATG
1 CCAACACCCAAAAAATTAATTTTTTTACCAGATG
*
114161 CCAACACCCAAAAAATTGATTTTTTTACCAGA
1 CCAACACCCAAAAAATTAATTTTTTTACCAGA
114193 ATAAAAGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (34 bp):
CCAACACCCAAAAAATTAATTTTTTTACCAGATG
Found at i:118129 original size:12 final size:13
Alignment explanation
Indices: 118114--118156 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
118104 ATATCTTTAT
*
118114 TATAATCTATA-A
1 TATAATATATATA
118126 TATAATATATATA
1 TATAATATATATA
118139 TATATATATATATA
1 TATA-ATATATATA
118153 TATA
1 TATA
118157 TTAATACGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 13 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TATAATATATATA
Found at i:118176 original size:2 final size:2
Alignment explanation
Indices: 118121--118157 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
118111 TATTATAATC
118121 TA TA -A TA TA -A 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 TA TA TA TA T
118158 TAATACGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:118384 original size:17 final size:18
Alignment explanation
Indices: 118326--118386 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
118316 GCCCTTTTAC
*
118326 TATATTATATAATGCTATA
1 TATATTATATAAT-ATATA
118345 TCATATTATATAATATATAA
1 T-ATATTATATAATATAT-A
* *
118365 TATATTA-ATAGTTTATA
1 TATATTATATAATATATA
118382 TATAT
1 TATAT
118387 GCATCAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.16
18 7 0.19
19 10 0.27
20 14 0.38
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TATATTATATAATATATA
Found at i:119112 original size:23 final size:24
Alignment explanation
Indices: 119080--119137 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
119070 ATTCTCATTT
* *
119080 AATTAGTAAATATATATTTTTAA-A
1 AATTA-TAAAAATATATTATTAATA
119104 AATTATAAAAATATATTATTAATA
1 AATTATAAAAATATATTATTAATA
119128 AATT-TAAAAA
1 AATTATAAAAA
119138 ATAAACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AATTATAAAAATATATTATTAATA
Found at i:119138 original size:25 final size:23
Alignment explanation
Indices: 119091--119140 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
119081 ATTAGTAAAT
* *
119091 ATATATTTTTAAAAATTATAAAA
1 ATATATTATTAAAAATTAAAAAA
*
119114 ATATATTATTAATAAATTTAAAAA
1 ATATATTATTAA-AAATTAAAAAA
119138 ATA
1 ATA
119141 AACATGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATATTATTAAAAATTAAAAAA
Found at i:120335 original size:19 final size:19
Alignment explanation
Indices: 120307--120350 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
120297 TTTCTCTCCA
*
120307 TCTTCCTTCC-CTCTCTATC
1 TCTTCTTTCCTCTCT-TATC
*
120326 TTTTCTTTCCTCTCTTATC
1 TCTTCTTTCCTCTCTTATC
120345 TCTTCT
1 TCTTCT
120351 GTGCCCTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.57
Consensus pattern (19 bp):
TCTTCTTTCCTCTCTTATC
Found at i:128629 original size:17 final size:17
Alignment explanation
Indices: 128607--128641 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
128597 TACAACCCTA
128607 AAAATAGGATGACATAT
1 AAAATAGGATGACATAT
128624 AAAATAGGATGACATAT
1 AAAATAGGATGACATAT
128641 A
1 A
128642 TCTATCAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AAAATAGGATGACATAT
Found at i:129623 original size:19 final size:19
Alignment explanation
Indices: 129569--129623 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
129559 AATGTTAAAA
*
129569 TATT-AAATTGATATAAACT
1 TATTAAAATT-ATAAAAACT
*
129588 TATTAAAATTATGAAAACT
1 TATTAAAATTATAAAAACT
129607 TATATAAAA-TATAAAAA
1 TAT-TAAAATTATAAAAA
129624 ATTCTAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (19 bp):
TATTAAAATTATAAAAACT
Found at i:129665 original size:19 final size:19
Alignment explanation
Indices: 129643--129778 Score: 54
Period size: 20 Copynumber: 7.1 Consensus size: 19
129633 AATTCTATAC
129643 ATTATAAAAAATTTATAAA
1 ATTATAAAAAATTTATAAA
*
129662 ATTAATAAAACTTATTT-TAAA
1 ATT-ATAAAA--AATTTATAAA
129683 TATT-T--AAAATTTCA-AAA
1 -ATTATAAAAAATTT-ATAAA
* * *
129700 ATGTATTAAAATTCTTAAAAA
1 AT-TATAAAAAAT-TTATAAA
*
129721 ATTATAAAAAAAATTATAAA
1 ATTAT-AAAAAATTTATAAA
*
129741 A-TAT-TAAAATTGATATAAA
1 ATTATAAAAAATT--TATAAA
* *
129760 TTTTTAAAAAA-TTATAAA
1 ATTATAAAAAATTTATAAA
129778 A
1 A
129779 AAATCATAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 35
0.64 0.10 0.26
Matches are distributed among these distances:
16 6 0.07
17 9 0.10
18 9 0.10
19 12 0.14
20 25 0.29
21 19 0.22
22 7 0.08
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (19 bp):
ATTATAAAAAATTTATAAA
Found at i:129733 original size:12 final size:12
Alignment explanation
Indices: 129716--129741 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
129706 TAAAATTCTT
129716 AAAAAATTATAA
1 AAAAAATTATAA
129728 AAAAAATTATAA
1 AAAAAATTATAA
129740 AA
1 AA
129742 TATTAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:130298 original size:83 final size:83
Alignment explanation
Indices: 130201--130361 Score: 304
Period size: 83 Copynumber: 1.9 Consensus size: 83
130191 TAATTTTGAT
*
130201 AATTTATTTAGAATTTTGTCGATTGAGTTTTAGCGTGAGTTTAAATAAGCGGTGTAATATATATA
1 AATTTATTTAGAATTTTGTCGATTGAGTTTTAGCATGAGTTTAAATAAGCGGTGTAATATATATA
130266 ATTTATTTTTCATAACTC
66 ATTTATTTTTCATAACTC
*
130284 AATTTATTTAGAATTTTGTCGATTGAGTTTTAGCATGAGTTTAGATAAGCGGTGTAATATATATA
1 AATTTATTTAGAATTTTGTCGATTGAGTTTTAGCATGAGTTTAAATAAGCGGTGTAATATATATA
130349 ATTTATTTTTCAT
66 ATTTATTTTTCAT
130362 TTCATGCTAC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (83 bp):
AATTTATTTAGAATTTTGTCGATTGAGTTTTAGCATGAGTTTAAATAAGCGGTGTAATATATATA
ATTTATTTTTCATAACTC
Found at i:133942 original size:11 final size:11
Alignment explanation
Indices: 133926--133954 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
133916 GACCCATCTG
133926 AACATGACTTA
1 AACATGACTTA
133937 AACATGACTTA
1 AACATGACTTA
133948 AACATGA
1 AACATGA
133955 TTTCGCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.24
Consensus pattern (11 bp):
AACATGACTTA
Found at i:138616 original size:6 final size:6
Alignment explanation
Indices: 138600--138631 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
138590 AGTCCATCAA
138600 TCCCTAC TCCCAC TCCCAC TCCCAC TCCCAC T
1 TCCC-AC TCCCAC TCCCAC TCCCAC TCCCAC T
138632 AAAGTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.16, C:0.62, G:0.00, T:0.22
Consensus pattern (6 bp):
TCCCAC
Found at i:141619 original size:6 final size:6
Alignment explanation
Indices: 141609--141641 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
141599 TTTCAACATA
*
141609 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
141642 GCAACGACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:142149 original size:2 final size:2
Alignment explanation
Indices: 142142--142166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
142132 GACTTCCTAT
142142 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
142167 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:146065 original size:15 final size:15
Alignment explanation
Indices: 146035--146064 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
146025 TGGGCCCCCC
146035 TAAAGTTTAATTTTT
1 TAAAGTTTAATTTTT
146050 TAAA-TTTAATTTTT
1 TAAAGTTTAATTTTT
146064 T
1 T
146065 TGTAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TAAAGTTTAATTTTT
Found at i:147483 original size:27 final size:27
Alignment explanation
Indices: 147446--147518 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
147436 TTTATATATT
147446 TTTTAG-AATTTTTTAAATAATATAAA
1 TTTTAGAAATTTTTTAAATAATATAAA
* * * *
147472 TTTTAGAAATTTTATAAATATTTTGAA
1 TTTTAGAAATTTTTTAAATAATATAAA
* *
147499 TTTTAAAAATTACTTTAAAT
1 TTTTAGAAATT-TTTTAAAT
147519 TTTTGAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 6 0.16
27 26 0.68
28 6 0.16
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (27 bp):
TTTTAGAAATTTTTTAAATAATATAAA
Found at i:147487 original size:18 final size:17
Alignment explanation
Indices: 147466--147509 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
147456 TTTTAAATAA
147466 TATAAATTTTAGAAATTT
1 TATAAATTTTAG-AATTT
*
147484 TATAAATATTTTGAATTT
1 TATAAAT-TTTAGAATTT
*
147502 TAAAAATT
1 TATAAATT
147510 ACTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 18 0.78
19 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:147521 original size:19 final size:19
Alignment explanation
Indices: 147478--147531 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
147468 TAAATTTTAG
* *
147478 AAATTTTATAAA-TATTTT
1 AAATTTTAAAAATTACTTT
*
147496 GAATTTTAAAAATTACTTT
1 AAATTTTAAAAATTACTTT
147515 AAATTTTTGAAAAATTA
1 AAA-TTTT-AAAAATTA
147532 TTTTGAACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
20 4 0.14
21 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
AAATTTTAAAAATTACTTT
Found at i:147543 original size:21 final size:19
Alignment explanation
Indices: 147479--147543 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
147469 AAATTTTAGA
*
147479 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTG
* *
147497 AATTTTAAAAATTACTTTA
1 AATTTTAAAAATTATTTTG
147516 AATTTTTGAAAAATTATTTTG
1 AA-TTTT-AAAAATTATTTTG
147537 AACTTTT
1 AA-TTTT
147544 TTTGTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.26
19 7 0.18
20 4 0.11
21 17 0.45
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTG
Found at i:150946 original size:16 final size:17
Alignment explanation
Indices: 150914--150948 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
150904 TTAGATCAAG
*
150914 GATGAACAATAATGAAA
1 GATGAACAATAAAGAAA
150931 GATGAA-AATAAAGAAA
1 GATGAACAATAAAGAAA
150947 GA
1 GA
150949 GGAATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.14
Consensus pattern (17 bp):
GATGAACAATAAAGAAA
Found at i:154135 original size:10 final size:10
Alignment explanation
Indices: 154120--154174 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
154110 GGGAATTATA
154120 AATAAATATT
1 AATAAATATT
154130 AATAAAT-TT
1 AATAAATATT
* *
154139 ATTTGAATA-T
1 A-ATAAATATT
154149 AATTAAATATT
1 AA-TAAATATT
154160 ACATAAATATT
1 A-ATAAATATT
154171 AATA
1 AATA
154175 TTTATTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
9 3 0.08
10 21 0.58
11 11 0.31
12 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (10 bp):
AATAAATATT
Found at i:156769 original size:10 final size:10
Alignment explanation
Indices: 156754--156778 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
156744 AATTTAGAAA
156754 AAAAAAAAAG
1 AAAAAAAAAG
156764 AAAAAAAAAG
1 AAAAAAAAAG
156774 AAAAA
1 AAAAA
156779 GGGTGATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:173577 original size:17 final size:18
Alignment explanation
Indices: 173533--173577 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
173523 AAATTTCAAT
*
173533 AAATAAAA-AAATGTATA
1 AAATAAAATAAATATATA
*
173550 AAAT-AATTAAATAT-TA
1 AAATAAAATAAATATATA
173566 AAATAAAATAAA
1 AAATAAAATAAA
173578 AAAAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAAATAAATATATA
Found at i:173590 original size:21 final size:21
Alignment explanation
Indices: 173519--173595 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 21
173509 ATGTTTATAT
*
173519 AAAAAAATTTCAAT-AAAT--
1 AAAAAAATTTAAATAAAATAA
*
173537 AAAAAAATGT--ATAAAATAA
1 AAAAAAATTTAAATAAAATAA
** * *
173556 TTAAATATTAAAATAAAATAA
1 AAAAAAATTTAAATAAAATAA
173577 AAAAAAATTTAAATTAAAA
1 AAAAAAATTTAAA-TAAAA
173596 ATAATATTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
16 2 0.05
17 4 0.09
18 9 0.21
19 5 0.12
21 18 0.42
22 5 0.12
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (21 bp):
AAAAAAATTTAAATAAAATAA
Found at i:175221 original size:3 final size:3
Alignment explanation
Indices: 175213--175282 Score: 88
Period size: 3 Copynumber: 23.7 Consensus size: 3
175203 TGCAATCAAT
* *
175213 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC ATC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
175261 TT- TTT TTC TTT TTC TCC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TT
175283 AAACCCTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:179751 original size:25 final size:26
Alignment explanation
Indices: 179723--179775 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
179713 TACTAGTGTT
*
179723 TGTCCTCTGTGACACGAG-TTTTGTC
1 TGTCCTCTATGACACGAGATTTTGTC
179748 TGTCCTCTATGACACGAGTATTTTGTC
1 TGTCCTCTATGACACGAG-ATTTTGTC
179775 T
1 T
179776 TGTTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 17 0.68
27 8 0.32
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (26 bp):
TGTCCTCTATGACACGAGATTTTGTC
Found at i:181284 original size:97 final size:98
Alignment explanation
Indices: 181108--181302 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 98
181098 AACTTTGGAA
* * * *
181108 AAGGGTATTCGATTATCTCGATTTGAAGAAAAAGTCGTACCTAGTAAGTTTAGGTACAAATTTTC
1 AAGGATATTCGATTATCTCGATTCGAAGAAAAAGTCGTACCTAGTAAGTTAAGGCACAAATTTTC
* * *
181173 AGAATCAGAGAT-AAAGAAACATTGCCTTGATTT
66 AAAATCAGAAATAAAAG-AACATTGCCTCGATTT
*
181206 AAGGATATTCGATTAT-TCCGATTCGAAGAAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CGATTCGAAGAAAAAGTCGTACCTAGTAAGTTAAGGCACAAATTTT
*
181269 CAAAACTC-GAAATAAAAGAATATTGCCTCGATTT
65 CAAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
181303 TAAAGTTTTC
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
97 50 0.59
98 35 0.41
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (98 bp):
AAGGATATTCGATTATCTCGATTCGAAGAAAAAGTCGTACCTAGTAAGTTAAGGCACAAATTTTC
AAAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:181658 original size:58 final size:59
Alignment explanation
Indices: 181556--182175 Score: 598
Period size: 59 Copynumber: 10.6 Consensus size: 59
181546 TTTTGGTCAC
* * * * * *
181556 TCGAGGGTAAAATGATAA-TTTTGGGAAAGTTGAGGGTTAAAAATGGAATTTTTAGACA-T
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATT-AGGGTCAAAAATGGAA-TTTTGGAAAGT
* * * *
181615 TCGGGGGTAAAATGGT-ACTTTTGGAAGAATTAGGGTCAAAAATGAAATTATTGG-AAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATT-TTGGAAAGT
*** *
181673 TCGAGGGTAAAACAATAATTTTTGGAAAAATCGAGGGTCAAAAATGGAATTTTTGG-AAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAAT-TAGGGTCAAAAATGGAA-TTTTGGAAAGT
* *
181733 T-TAGGGGTAAAATGGTAA-TTTTGGAAAAATTAGGGTCAAAAATAGAATTTTTGG-AAGT
1 TCGA-GGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAA-TTTTGGAAAGT
* * *
181791 TCGAGGGTAAAATGGTAATTTTTGGAAAGATTAGGGTC-AAAATGGAATTTTGTAAAAT
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGT
* * * *
181849 TCGGGGGTAAAAAT-GTAA-TTTT-CAAAAAGTTTGAGGTCAAAAATGGAATTTTGGAAAAT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAA-TTAG-GGTCAAAAATGGAATTTTGGAAAGT
* * * *
181908 TCGAGAGTAAAAAT-GTAATTTTT-GAAAAGTTCGTGGTTAAAAATGGAATTTTGG-AAGT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTGGAAAGT
* * * * *
181966 TTGA-GG-AAAATGGTAATTTTTGGAAAAATCAGGGTAAAAAATGGAATTTTAGAAAAT
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGT
*
182023 TC-AGGGGTAAAAAT-GTAATTTTTGGAAAAATTAAGGTCAAAAATGGAATTTTGGAAAGT
1 TCGA-GGGT-AAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGT
* * *
182082 TCGAGGGTAAAAT-GTAATTTTTGGAAAAA-TCGAGGTCAAAAATAGAATTTTAGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTGGAAAGT
** * *
182140 TCGAGGGTAAAAAAGTAATTTTTGGACAATTTAGGG
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGG
182176 ACCTGTAGGG
Statistics
Matches: 472, Mismatches: 63, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
55 5 0.01
56 32 0.07
57 28 0.06
58 162 0.34
59 192 0.41
60 51 0.11
61 2 0.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (59 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGT
Found at i:181697 original size:29 final size:28
Alignment explanation
Indices: 181556--182165 Score: 100
Period size: 29 Copynumber: 20.9 Consensus size: 28
181546 TTTTGGTCAC
* *
181556 TCGAGGGTAAAATGATAATTTTGGGAAAGT
1 TCGAGGGTAAAA-AATAATTTTTGG-AAGT
* *
181586 T-GAGGGTTAAAAATGGAATTTTTAGACA-T
1 TCGAGGGTAAAAAAT--AATTTTTGGA-AGT
* ** *
181615 TCGGGGGTAAAATGGT-ACTTTTGGAAGAAT
1 TCGAGGGTAAAA-AATAATTTTTGGAAG--T
* *
181645 T--AGGGTCAAAAATGAAATTATTGGAAGT
1 TCGAGGGTAAAAAAT--AATTTTTGGAAGT
**
181673 TCGAGGGTAAAACAATAATTTTTGGAAAAA
1 TCGAGGGTAAAA-AATAATTTTTGG-AAGT
*
181703 TCGAGGGTCAAAAATGGAATTTTTGGAAGT
1 TCGAGGGTAAAAAAT--AATTTTTGGAAGT
* ** *
181733 T-TAGGGGTAAAATGGTAA-TTTTGGAAAAAT
1 TCGA-GGGTAAAA-AATAATTTTTGG--AAGT
*
181763 T--AGGGTCAAAAATAGAATTTTTGGAAGT
1 TCGAGGGT-AAAAA-ATAATTTTTGGAAGT
**
181791 TCGAGGGTAAAATGGTAATTTTTGGAAAGAT
1 TCGAGGGTAAAA-AATAATTTTTGG-AAG-T
* * *
181822 T--AGGGT-CAAAATGGAA-TTTTGTAAAAT
1 TCGAGGGTAAAAAAT--AATTTTTG-GAAGT
* * ***
181849 TCGGGGGTAAAAATGTAATTTTCAAAAAGT
1 TCGAGGGTAAAAA-ATAATTTT-TGGAAGT
* * *
181879 TTGA-GGTCAAAAATGGAA-TTTTGGAAAAT
1 TCGAGGGTAAAAAAT--AATTTTTGG-AAGT
* * *
181908 TCGAGAGTAAAAATGTAATTTTTGAAAAGT
1 TCGAGGGTAAAAA-ATAATTTTTG-GAAGT
* *
181938 TCG-TGGTTAAAAATGGAA-TTTTGGAAGT
1 TCGAGGGTAAAAAAT--AATTTTTGGAAGT
* ** **
181966 TTGA-GG-AAAATGGTAATTTTTGGAAAAA
1 TCGAGGGTAAAA-AATAATTTTTGG-AAGT
* * *
181994 TC-AGGGTAAAAAATGGAATTTTAGAAAAT
1 TCGAGGGTAAAAAAT--AATTTTTGGAAGT
* *
182023 TC-AGGGGTAAAAATGTAATTTTTGGAAAAAT
1 TCGA-GGGTAAAAA-ATAATTTTTGG--AAGT
* *
182054 T--AAGGTCAAAAATGGAA-TTTTGGAAAGT
1 TCGAGGGTAAAAAAT--AATTTTTGG-AAGT
** **
182082 TCGAGGGTAAAATGTAATTTTTGGAAAAA
1 TCGAGGGTAAAAAATAATTTTTGG-AAGT
* * *
182111 TCGA-GGTCAAAAATAGAATTTTAGAAAGT
1 TCGAGGGT-AAAAA-ATAATTTTTGGAAGT
182140 TCGAGGGTAAAAAAGTAATTTTTGGA
1 TCGAGGGTAAAAAA-TAATTTTTGGA
182166 CAATTTAGGG
Statistics
Matches: 412, Mismatches: 100, Indels: 137
0.63 0.15 0.21
Matches are distributed among these distances:
26 2 0.00
27 15 0.04
28 70 0.17
29 154 0.37
30 147 0.36
31 24 0.06
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (28 bp):
TCGAGGGTAAAAAATAATTTTTGGAAGT
Found at i:182175 original size:29 final size:28
Alignment explanation
Indices: 181633--182175 Score: 131
Period size: 29 Copynumber: 18.6 Consensus size: 28
181623 AAAATGGTAC
* * *
181633 TTTTGGAAGAATTAGGGTCAAAAATGAAAT
1 TTTTGGAA-ATTTAGGGT-AAAAAAGTAAT
* * *
181663 TATTGGAAGTTCGAGGGTAAAACAA-TAAT
1 TTTTGGAAATT-TAGGGTAAAA-AAGTAAT
** * *
181692 TTTTGGAAAAATCGAGGGTCAAAAATGGAAT
1 TTTTGG--AAATTTAGGGT-AAAAAAGTAAT
* **
181723 TTTTGGAAGTTTAGGGGTAAAATGGTAA-
1 TTTTGGAAATTTA-GGGTAAAAAAGTAAT
*
181751 TTTTGGAAAAATTAGGGTCAAAAATAG-AAT
1 TTTTGG-AAATTTAGGGT-AAAAA-AGTAAT
* * **
181781 TTTTGGAAGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAATT-TAGGGTAAAAAAGTAAT
* * * *
181810 TTTTGGAAAGATTAGGGTCAAAATGGAA-
1 TTTTGGAAA-TTTAGGGTAAAAAAGTAAT
* ** *
181838 TTTTGTAAAATTCGGGGGTAAAAATGTAAT
1 TTTTG-GAAATT-TAGGGTAAAAAAGTAAT
*** * *
181868 TTTCAAAAAGTTT-GAGGTCAAAAATGGAA-
1 TTTTGGAAA-TTTAG-GGT-AAAAAAGTAAT
* * *
181897 TTTTGGAAAATTCGAGAGTAAAAATGTAAT
1 TTTTGG-AAATT-TAGGGTAAAAAAGTAAT
* * * * *
181927 TTTTGAAAAGTTCGTGGTTAAAAATGGAA-
1 TTTTGGAAATTTAG-GG-TAAAAAAGTAAT
* **
181956 TTTTGGAAGTTT-GAGG-AAAATGGTAAT
1 TTTTGGAAATTTAG-GGTAAAAAAGTAAT
* * *
181983 TTTTGGAAAAATCAGGGTAAAAAATGGAAT
1 TTTTGG-AAATTTAGGGTAAAAAA-GTAAT
* * * *
182013 TTTAGAAAATTCAGGGGTAAAAATGTAAT
1 TTTTGGAAATTTA-GGGTAAAAAAGTAAT
* * * *
182042 TTTTGGAAAAATTAAGGTCAAAAATGGAA-
1 TTTTGG-AAATTTAGGGT-AAAAAAGTAAT
* *
182071 TTTTGGAAAGTTCGAGGGT-AAAATGTAAT
1 TTTTGGAAA-TT-TAGGGTAAAAAAGTAAT
** *
182100 TTTTGGAAAAATCGAGGTCAAAAATAG-AA-
1 TTTTGGAAATTTAG-GGT-AAAAA-AGTAAT
* *
182129 TTTTAGAAAGTTCGAGGGTAAAAAAGTAAT
1 TTTTGGAAA-TT-TAGGGTAAAAAAGTAAT
182159 TTTTGGACAATTTAGGG
1 TTTTGGA-AATTTAGGG
182176 ACCTGTAGGG
Statistics
Matches: 372, Mismatches: 95, Indels: 93
0.66 0.17 0.17
Matches are distributed among these distances:
26 7 0.02
27 7 0.02
28 43 0.12
29 171 0.46
30 123 0.33
31 21 0.06
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (28 bp):
TTTTGGAAATTTAGGGTAAAAAAGTAAT
Found at i:182944 original size:3 final size:3
Alignment explanation
Indices: 182936--182985 Score: 82
Period size: 3 Copynumber: 16.0 Consensus size: 3
182926 TTCGTTTTCT
182936 TTA TTA TTA TTA TTA TTAA TTA TTAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA
182983 TTA
1 TTA
182986 GTGCTATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:183659 original size:6 final size:6
Alignment explanation
Indices: 183635--183719 Score: 54
Period size: 6 Copynumber: 14.2 Consensus size: 6
183625 GTTTAAAACT
** *
183635 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTAAAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA
*
183682 ATGGATAA ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A
1 AT--TTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA A
183720 AATAAATTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
4 3 0.05
5 10 0.16
6 35 0.57
7 9 0.15
8 4 0.07
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (6 bp):
ATTTAA
Found at i:183670 original size:17 final size:18
Alignment explanation
Indices: 183649--183727 Score: 90
Period size: 17 Copynumber: 4.3 Consensus size: 18
183639 CAAATTTAAT
183649 TAAATTTAAATTTAAAG-
1 TAAATTTAAATTTAAAGA
* *
183666 CAAATTTAAATTAAAAATGGA
1 TAAATTTAAATT-TAAA--GA
183687 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAGA
*
183704 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGA
183722 TAAATT
1 TAAATT
183728 CAAAACCCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
17 26 0.50
18 12 0.23
19 2 0.04
20 1 0.02
21 11 0.21
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:183691 original size:38 final size:39
Alignment explanation
Indices: 183649--183722 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
183639 CAAATTTAAT
183649 TAAATTTAAATTTAA-AGCAAATTTAAA-TTAAAAATGGA
1 TAAATTTAAATTTAAGA-CAAATTTAAATTTAAAAATGGA
*
183687 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAAT
1 TAAATTTAAATTTAAGACAAATTTAAATTTAAAAAT
183723 AAATTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
38 24 0.73
39 9 0.27
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.38
Consensus pattern (39 bp):
TAAATTTAAATTTAAGACAAATTTAAATTTAAAAATGGA
Found at i:184306 original size:49 final size:49
Alignment explanation
Indices: 184248--184525 Score: 217
Period size: 49 Copynumber: 5.7 Consensus size: 49
184238 GTACTGGATC
* * *
184248 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTA-TAAGGTT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACT-AGGTT
* * * * * *
184297 TGCCGTTGCGACTTAAACCCTTCCCTTCGTATCT-TGGTGGTACT-GGATC
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACTAGG-TT
* * ** *
184346 CGCCGTTGCGGCTTAGATATTTCCCTTCATGTCTCTGAGGTACAAGGTT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* * * * * *
184395 CGCTGTTGCGACTTAAACCCTTCCCTTCGTATCT-TGGCGGTACT-GGATC
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACTAGG-TT
* * * * * *
184444 CGTCGTTGCGGCTTAGATCTTTCCCTCCATGTCTCCGAGGTACTAGGTT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
* *
184493 CGTCATTGCGACTTAAACCTTTCCCTTC-TGTCT
1 CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCT
184526 TCGTGGTACT
Statistics
Matches: 172, Mismatches: 48, Indels: 19
0.72 0.20 0.08
Matches are distributed among these distances:
48 11 0.06
49 155 0.90
50 6 0.03
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.35
Consensus pattern (49 bp):
CGCCGTTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTAGGTT
Found at i:184356 original size:98 final size:98
Alignment explanation
Indices: 184223--184520 Score: 472
Period size: 98 Copynumber: 3.0 Consensus size: 98
184213 CCTTTCATGT
*
184223 CTTCGTATCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGG
1 CTTCGTATCTTGGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGG
*
184288 TATAAGGTTTGCCGTTGCGACTTAAACCCTTCC
66 TATAAGGTTCGCCGTTGCGACTTAAACCCTTCC
* *
184321 CTTCGTATCTTGGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTTCATGTCTCTGAGG
1 CTTCGTATCTTGGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGG
* *
184386 TACAAGGTTCGCTGTTGCGACTTAAACCCTTCC
66 TATAAGGTTCGCCGTTGCGACTTAAACCCTTCC
* * *
184419 CTTCGTATCTTGGCGGTACTGGATCCGTCGTTGCGGCTTAGATCTTTCCCTCCATGTCTCCGAGG
1 CTTCGTATCTTGGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGG
* * *
184484 TACT-AGGTTCGTCATTGCGACTTAAACCTTTCC
66 TA-TAAGGTTCGCCGTTGCGACTTAAACCCTTCC
184517 CTTC
1 CTTC
184521 TGTCTTCGTG
Statistics
Matches: 183, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
98 183 1.00
ACGTcount: A:0.14, C:0.28, G:0.22, T:0.35
Consensus pattern (98 bp):
CTTCGTATCTTGGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGG
TATAAGGTTCGCCGTTGCGACTTAAACCCTTCC
Found at i:190416 original size:6 final size:6
Alignment explanation
Indices: 190405--190446 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
190395 TTTGCAGGTC
* * *
190405 GGCAGT GGCAGT GGCAGT CGCAGT GGCGGT GGCGGT GGCAGT
1 GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT GGCAGT
190447 TCAAGTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.12, C:0.19, G:0.52, T:0.17
Consensus pattern (6 bp):
GGCAGT
Found at i:190704 original size:17 final size:17
Alignment explanation
Indices: 190684--190729 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
190674 GTTTAAAACT
*
190684 ATTTCAAATTTAA-TTAA
1 ATTT-AAATTTAAGATAA
190701 ATTTAAATTTAAGATAA
1 ATTTAAATTTAAGATAA
190718 ATTTAAATTTAA
1 ATTTAAATTTAA
190730 AAATAAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTAAGATAA
Found at i:207943 original size:21 final size:21
Alignment explanation
Indices: 207917--207960 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
207907 ACAAAACATT
207917 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
207938 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
207959 AT
1 AT
207961 TGTCGAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:208601 original size:96 final size:96
Alignment explanation
Indices: 208427--208611 Score: 266
Period size: 96 Copynumber: 1.9 Consensus size: 96
208417 GAAAAGGATG
** * * *
208427 TTCGATTATCTCGATTTGAAGAAAGGTTGCACTTAGTAAGTTAAGGCGTAAATTTTTAAAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAAAATCGA
*
208492 AGATAAGGAAATATTGCCTCGATTAAGGGTA
66 AGATAAAGAAATATTGCCTCGATTAAGGGTA
* *
208523 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGAAACTCG
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTT-GAAAATCG
208588 AA-ATAAA-AGAATATTGCCTCGATT
65 AAGATAAAGA-AATATTGCCTCGATT
208612 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 1 0.01
96 70 0.89
97 8 0.10
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTGAAAATCGA
AGATAAAGAAATATTGCCTCGATTAAGGGTA
Found at i:209006 original size:30 final size:30
Alignment explanation
Indices: 208970--209214 Score: 225
Period size: 30 Copynumber: 8.3 Consensus size: 30
208960 GTAAAGTGGT
208970 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
* * * *
209000 AATTTTTTG--AGGTTCGGGGGTAAAAATGT
1 AA-TTTTTGAAAGTTTCGAGGTTAAAAATGG
* * *
209029 ATTTTTTGGAAGTTTCGAGGTTAAAAATAG
1 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
* * *
209059 AATTTTTGGAAGTTT-G-GGAGTAAAAATGT
1 AATTTTTGAAAGTTTCGAGG-TTAAAAATGG
* *
209088 AATTTTTGAAAGTTT-TAGGGTCAAAAATGG
1 AATTTTTGAAAGTTTCGA-GGTTAAAAATGG
* * **
209118 AATTTTTGAAAGTTT-GGGGGTAAAAATAT
1 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
*
209147 AATTTTT-AGAAGTTTTGAGGTTAAAAATGG
1 AATTTTTGA-AAGTTTCGAGGTTAAAAATGG
* * *
209177 AATTTTTGGAAGTTTCGAGGTCAAAAATAG
1 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
209207 AATTTTTG
1 AATTTTTG
209215 GAAGGTAGGG
Statistics
Matches: 173, Mismatches: 33, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.05
29 60 0.35
30 96 0.55
31 8 0.05
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AATTTTTGAAAGTTTCGAGGTTAAAAATGG
Found at i:209020 original size:59 final size:59
Alignment explanation
Indices: 208968--209255 Score: 300
Period size: 59 Copynumber: 4.9 Consensus size: 59
208958 GGGTAAAGTG
* *
208968 GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAGGTTCGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTAAAAAT
* * * * *
209027 GTATTTTTTGGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGAGTAAAAAT
1 GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTAAAAAT
* *
209086 GTAATTTTTGAAAGTTT-TAGGGTCAAAAATGGAA-TTTTTGAAAGTTTGGGGGTAAAAAT
1 GTAATTTTTGAAAGTTTCGA-GGTTAAAAATGGAATTTTTTG-AAGTTTGGGGGTAAAAAT
* * * * *
209145 ATAATTTTT-AGAAGTTTTGAGGTTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAAT
1 GTAATTTTTGA-AAGTTTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGT-AAAAAT
* * * * * * *
209205 AG-AATTTTTGGAAG-GTAG-GGGTCAAAATGTAATTTTTTGAAGTTTCGGGGT
1 -GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGT
209256 TTTCAGGGCA
Statistics
Matches: 192, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
58 35 0.18
59 135 0.70
60 22 0.11
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (59 bp):
GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTAAAAAT
Found at i:209047 original size:118 final size:117
Alignment explanation
Indices: 208844--209190 Score: 314
Period size: 118 Copynumber: 2.9 Consensus size: 117
208834 CCCGGGGGGC
* * * **
208844 AAAATGGTAATTTTGGGAAAGTTTGA-GGTTAAAAATGGAATTTTTAGACA-TTCAAGGGTAAAA
1 AAAAT-GTAATTTT-TGAAAGTTTGAGGGTCAAAAATGGAATTTTT-GAAAGTTCGGGGGTAAAA
** *** * *
208907 CCATAACTTTTTA-AAAAATCGAGATCAAAAACGAAATTTTTGGACA-TCTAGGG-GT-
63 ATATAA-TTTTTAGAAGTTTCGAGGTTAAAAA-GAAATTTTTGGA-AGT-TAGGGAGTA
* * *
208962 AAAGTGGTAATTTTTGAAAGTTTCGA-GGTTAAAAATGGAATTTTTTG-AGGTTCGGGGGTAAAA
1 AAAAT-GTAATTTTTGAAAGTTT-GAGGGTCAAAAATGGAA-TTTTTGAAAGTTCGGGGGTAAAA
* * * * *
209025 ATGTATTTTTTGGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGAGTA
63 ATATAATTTTTAGAAGTTTCGAGGTTAAAAAGA-AATTTTTGGAAGTTAGGGAGTA
* *
209081 AAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAATA
1 AAAATGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATA
* *
209146 TAATTTTTAGAAGTTTTGAGGTTAAAAATGGAATTTTTGGAAGTT
66 TAATTTTTAGAAGTTTCGAGGTTAAAAA-GAAATTTTTGGAAGTT
209191 TCGAGGTCAA
Statistics
Matches: 189, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
117 26 0.14
118 154 0.81
119 9 0.05
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (117 bp):
AAAATGTAATTTTTGAAAGTTTGAGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATA
TAATTTTTAGAAGTTTCGAGGTTAAAAAGAAATTTTTGGAAGTTAGGGAGTA
Found at i:209191 original size:118 final size:118
Alignment explanation
Indices: 208968--209254 Score: 352
Period size: 118 Copynumber: 2.4 Consensus size: 118
208958 GGGTAAAGTG
* * * * *
208968 GTAATTTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTTGAGGTTCGGGGGTAAAAATGTATTT
1 GTAATTTTTGAAAGTTTAGAGGTCAAAAATGGAATTTTTTGAAGTTCGGGGGTAAAAATATAATT
*
209033 TTTGGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGAGTAAAAAT
66 TTTAGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGAGTAAAAAT
*
209086 GTAATTTTTGAAAGTTTTAG-GGTCAAAAATGGAA-TTTTTGAAAGTTTGGGGGTAAAAATATAA
1 GTAATTTTTGAAAG-TTTAGAGGTCAAAAATGGAATTTTTTG-AAGTTCGGGGGTAAAAATATAA
* * *
209149 TTTTTAGAAGTTTTGAGGTTAAAAATGGAATTTTTGGAAGTTT-CGAGGTCAAAAAT
64 TTTTTAGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGA-GT-AAAAAT
* * * *
209205 AG-AATTTTTGGAAG-GTAGGGGTC-AAAATGTAATTTTTTGAAGTTTCGGGG
1 -GTAATTTTTGAAAGTTTAGAGGTCAAAAATGGAATTTTTTGAAG-TTCGGGG
209255 TTTTCAGGGC
Statistics
Matches: 147, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
117 22 0.15
118 103 0.70
119 21 0.14
120 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (118 bp):
GTAATTTTTGAAAGTTTAGAGGTCAAAAATGGAATTTTTTGAAGTTCGGGGGTAAAAATATAATT
TTTAGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGTTTGGGAGTAAAAAT
Found at i:209215 original size:30 final size:28
Alignment explanation
Indices: 208970--209251 Score: 212
Period size: 30 Copynumber: 9.6 Consensus size: 28
208960 GTAAAGTGGT
*
208970 AATTTTTGAAAGTTTCGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCGAGG-TAAAAAT-G
* * *
209000 AATTTTTTG-AGGTTCGGGGGTAAAAATG
1 AATTTTTGGAAGTTTC-GAGGTAAAAATG
*
209028 TATTTTTTGGAAGTTTCGAGGTTAAAAATAG
1 -AATTTTTGGAAGTTTCGAGG-TAAAAAT-G
*
209059 AATTTTTGGAAGTTT-GGGAGTAAAAATG
1 AATTTTTGGAAGTTTCGAG-GTAAAAATG
* *
209087 TAATTTTTGAAAGTTT-TAGGGTCAAAAATGG
1 -AATTTTTGGAAGTTTCGA-GGT-AAAAAT-G
* * * *
209118 AATTTTTGAAAGTTTGGGGGTAAAAATAT
1 AATTTTTGGAAGTTTCGAGGTAAAAAT-G
* *
209147 AATTTTTAGAAGTTTTGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTCGAGG-TAAAAAT-G
209177 AATTTTTGGAAGTTTCGAGGTCAAAAATAG
1 AATTTTTGGAAGTTTCGAGGT-AAAAAT-G
* * * *
209207 AATTTTTGGAAG-GTAGGGGTCAAAATG
1 AATTTTTGGAAGTTTCGAGGTAAAAATG
*
209234 TAATTTTTTGAAGTTTCG
1 -AATTTTTGGAAGTTTCG
209252 GGGTTTTCAG
Statistics
Matches: 204, Mismatches: 33, Indels: 31
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.00
28 18 0.09
29 77 0.38
30 106 0.52
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (28 bp):
AATTTTTGGAAGTTTCGAGGTAAAAATG
Found at i:210353 original size:17 final size:17
Alignment explanation
Indices: 210331--210365 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
210321 ATGTTATTTT
210331 TATTATTATCATTATTA
1 TATTATTATCATTATTA
*
210348 TATTATTATTATTATTA
1 TATTATTATCATTATTA
210365 T
1 T
210366 TAAAAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATTATCATTATTA
Found at i:210355 original size:20 final size:20
Alignment explanation
Indices: 210330--210367 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
210320 AATGTTATTT
210330 TTATTATTATCATTATTATA
1 TTATTATTATCATTATTATA
*
210350 TTATTATTATTATTATTA
1 TTATTATTATCATTATTA
210368 AAAACAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATCATTATTATA
Found at i:210380 original size:3 final size:3
Alignment explanation
Indices: 210324--210367 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
210314 TTAATAAATG
* *
210324 TTA TTT TTA TTA TTA TCA TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
210368 AAAACAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:210617 original size:12 final size:12
Alignment explanation
Indices: 210600--210625 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
210590 ATTCCTGGTC
210600 TTGGTATGACTA
1 TTGGTATGACTA
210612 TTGGTATGACTA
1 TTGGTATGACTA
210624 TT
1 TT
210626 CGGAGCTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGGTATGACTA
Found at i:211204 original size:14 final size:15
Alignment explanation
Indices: 211181--211209 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
211171 AATTTGGACA
211181 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
211196 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
211210 ATAATAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:211247 original size:6 final size:6
Alignment explanation
Indices: 211236--211314 Score: 85
Period size: 6 Copynumber: 13.7 Consensus size: 6
211226 ATTTTGAAAA
*
211236 TAAATT TAAATT TAAATT TAAATT TAAGA-T T-AATT TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT
* * *
211283 TAAA-A TAAATC TAAATT TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
211315 AGGGGCCCGG
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
4 1 0.02
5 11 0.18
6 48 0.79
7 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:211274 original size:23 final size:23
Alignment explanation
Indices: 211242--211303 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
211232 AAAATAAATT
*
211242 TAAATTTAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAATTTAAAA
* *
211265 TTAATTTAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAATTTAAAA
*
211288 TAAATCTAAATTTAAA
1 TAAATTTAAATTTAAA
211304 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAAA
Found at i:211314 original size:17 final size:17
Alignment explanation
Indices: 211221--211314 Score: 100
Period size: 17 Copynumber: 5.4 Consensus size: 17
211211 TAATAATTCT
211221 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAAATAAA
*
211240 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
**
211258 TTTAAGA-TTAATTTAAA
1 TTTAA-ATTTAAAATAAA
*
211275 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
211292 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
211309 TTTAAA
1 TTTAAA
211315 AGGGGCCCGG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.02
17 40 0.62
18 16 0.25
19 7 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:219261 original size:29 final size:30
Alignment explanation
Indices: 219225--219291 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
219215 TAAAATTTTT
* * *
219225 TGTATAAAATTGTACA-AAATTAAAGTTCA
1 TGTATAAAATTGCACATAAACTAAAATTCA
219254 TGTATAAAATTGCACATTAAACTAAAATTCA
1 TGTATAAAATTGCACA-TAAACTAAAATTCA
219285 TGTATAA
1 TGTATAA
219292 CTTAAGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 15 0.45
31 18 0.55
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (30 bp):
TGTATAAAATTGCACATAAACTAAAATTCA
Found at i:220991 original size:21 final size:21
Alignment explanation
Indices: 220967--221020 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
220957 GTTGTGACAG
*
220967 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* *
220988 TTCTACCAATACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
221009 TTCTACCGATAC
1 TTCTACCGATAC
221021 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:221102 original size:69 final size:69
Alignment explanation
Indices: 220986--221123 Score: 258
Period size: 69 Copynumber: 2.0 Consensus size: 69
220976 TACAAGTGTA
*
220986 ACTTCTACCAATACAAGTCATGCTTCTACCGATACTAAAAACTCCAGAGAACTAAGAAGTTTTTC
1 ACTTCTACCAATACAAGTCATGCTTCTACCGATACTAAAAACTCCAGAGAACTAAGAAGTTTTAC
221051 CCTG
66 CCTG
*
221055 ACTTGTACCAATACAAGTCATGCTTCTACCGATACTAAAAACTCCAGAGAACTAAGAAGTTTTAC
1 ACTTCTACCAATACAAGTCATGCTTCTACCGATACTAAAAACTCCAGAGAACTAAGAAGTTTTAC
221120 CCTG
66 CCTG
221124 CAACTTTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (69 bp):
ACTTCTACCAATACAAGTCATGCTTCTACCGATACTAAAAACTCCAGAGAACTAAGAAGTTTTAC
CCTG
Found at i:222815 original size:22 final size:19
Alignment explanation
Indices: 222786--222829 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 19
222776 ACTTTCATGA
222786 TTAACTTAATCAATCACCTAT
1 TTAACTTAATCAAT--CCTAT
*
222807 TTAATCTTAATTAATCCTAT
1 TTAA-CTTAATCAATCCTAT
222827 TTA
1 TTA
222830 TTATCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 9 0.43
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAACTTAATCAATCCTAT
Found at i:229024 original size:53 final size:53
Alignment explanation
Indices: 228960--229243 Score: 403
Period size: 53 Copynumber: 5.4 Consensus size: 53
228950 AAGTCCAATA
* *
228960 ACTATGTGTCATCGTGAGTTATATGAATCTTATAATGGATTAAAGG-TCTGATG
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTC-GATG
*
229013 ACTATGTGTCATCATGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
* *
229066 ACTATGTGTCATCGTGAGTTATATGAATCCTATTACGGATTAAAGGTTCGATG
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
* * * * *
229119 ACTATGTATCATCATGAGTTATATGAATCCTATTACGGATTAAGGGTTCGATG
1 ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
* * *
229172 AGCT-TGTGTCATCGTGAGATATACGAATCC-ATCATGGATTAAAGGTCCGATG
1 A-CTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
*
229224 ACTTTGTGTCATCGTGAGTT
1 ACTATGTGTCATCGTGAGTT
229244 TTCAAATGTG
Statistics
Matches: 210, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
51 2 0.01
52 34 0.16
53 170 0.81
54 4 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (53 bp):
ACTATGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAAAGGTTCGATG
Found at i:229937 original size:21 final size:23
Alignment explanation
Indices: 229911--229966 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
229901 GGAGTTTTTA
229911 GTATCGGTAGAATTA-AG-ACTT
1 GTATCGGTAGAATTAGAGCACTT
229932 GTATCGGTA-AA--AGAGTCACTT
1 GTATCGGTAGAATTAGAG-CACTT
229953 GTATCGGTAGAATT
1 GTATCGGTAGAATT
229967 CTGTACTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.03
19 2 0.07
20 2 0.07
21 22 0.76
22 2 0.07
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (23 bp):
GTATCGGTAGAATTAGAGCACTT
Found at i:230937 original size:41 final size:41
Alignment explanation
Indices: 230865--230992 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
230855 TAAGTATTAA
* * * *
230865 GCCCGATA-AATACACTGACACAAAGCCTGCTAGGCACAAG
1 GCCCGATACAGTACACTGACATAAAGCATGCTAGGCTCAAG
** *
230905 GCCCGATACAGTACACTGACATAAAGCATGCTAAACTCTAG
1 GCCCGATACAGTACACTGACATAAAGCATGCTAGGCTCAAG
* * ** *
230946 GTCTGATACAGTACA-TCGACATAAAGTTTGCTAGGCTTAAG
1 GCCCGATACAGTACACT-GACATAAAGCATGCTAGGCTCAAG
230987 GCCCGA
1 GCCCGA
230993 GTCATTACAC
Statistics
Matches: 69, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
40 9 0.13
41 60 0.87
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (41 bp):
GCCCGATACAGTACACTGACATAAAGCATGCTAGGCTCAAG
Found at i:236469 original size:17 final size:16
Alignment explanation
Indices: 236443--236474 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
236433 TACTTCTACT
236443 GATACTAAAAACTCCA
1 GATACTAAAAACTCCA
236459 GATAGCTAAAAACTCC
1 GATA-CTAAAAACTCC
236475 TACCCTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.47, C:0.25, G:0.09, T:0.19
Consensus pattern (16 bp):
GATACTAAAAACTCCA
Found at i:237179 original size:41 final size:41
Alignment explanation
Indices: 237103--237332 Score: 208
Period size: 41 Copynumber: 5.5 Consensus size: 41
237093 CCTTATGCTC
* * * * *
237103 TTTCGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCA
1 TTTCGAGACATGAGTCTTCC-TTAATCAAAATCTCATTCTCA
** * *
237145 ACTCGAGACATGAGTCTTCTTTAATCAAAATCTCATTCTTA
1 TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
* * * * *
237186 TTTCGAGACACGAGTTTTCCTTATTCATAATCTTATTCTCA
1 TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
* *
237227 TTTTGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTTA
1 TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
* * ** *
237268 TTTCGAAACATGAGTCTTCCATTTATACAATTTCTCATGCTCA
1 TTTCGAGACATGAGTCTTCC-TTAAT-CAAAATCTCATTCTCA
* * **
237311 ATCCGAGATGTGAGTCTTCCTT
1 TTTCGAGACATGAGTCTTCCTT
237333 TTTATACACC
Statistics
Matches: 149, Mismatches: 37, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
41 101 0.68
42 21 0.14
43 27 0.18
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (41 bp):
TTTCGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
Found at i:239798 original size:20 final size:20
Alignment explanation
Indices: 239773--239817 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
239763 AACCTATGGA
239773 TGCGATTCATCTGTCATCTT
1 TGCGATTCATCTGTCATCTT
239793 TGCGATTCATCTGTCATCTT
1 TGCGATTCATCTGTCATCTT
239813 TGCGA
1 TGCGA
239818 AGCAAATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.18, T:0.42
Consensus pattern (20 bp):
TGCGATTCATCTGTCATCTT
Done.