Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3527
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: 52102
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:7012 original size:28 final size:26
Alignment explanation
Indices: 6970--7039 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
6960 GAAAGTAGCT
* * *
6970 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
6998 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
*
7024 AAATTACCGTTATACC
1 AAATTACTGTTATACC
7040 TGTAGGGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 18 0.49
27 1 0.03
28 18 0.49
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:7215 original size:28 final size:26
Alignment explanation
Indices: 7146--7233 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
7136 TGGAGGAAGC
*
7146 GTTCTGGTGGCTCTGCCACATATATCG
1 GTTCTGGTGGCTCTGCCACAT-TATCT
*
7173 GTTCTGATGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
7200 GTATCTGGTGACTCTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
*
7227 ATTCTGG
1 GTTCTGG
7234 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 5 0.09
27 32 0.60
28 16 0.30
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:8399 original size:52 final size:52
Alignment explanation
Indices: 8321--8423 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
8311 TGACTATTGC
8321 GGAAATTTAAATTTGAATATTGGTATGTTTATATATATTTTAAAATAACTTG
1 GGAAATTTAAATTTGAATATTGGTATGTTTATATATATTTTAAAATAACTTG
8373 GGAAATTTAAATTTGAATATTGGTATGTTTATATATATTTTAAAATAACTT
1 GGAAATTTAAATTTGAATATTGGTATGTTTATATATATTTTAAAATAACTT
8424 AATTGAAGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.47
Consensus pattern (52 bp):
GGAAATTTAAATTTGAATATTGGTATGTTTATATATATTTTAAAATAACTTG
Found at i:13165 original size:3 final size:3
Alignment explanation
Indices: 13157--13220 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
13147 GTAGGCTTCT
13157 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13205 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
13221 TGTAACACAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18403 original size:17 final size:17
Alignment explanation
Indices: 18381--18442 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
18371 ACAATAATAT
18381 AAAATA-ATGATATGTAC
1 AAAATATAT-ATATGTAC
*
18398 AAAATATATATATGTAT
1 AAAATATATATATGTAC
* *
18415 ATAATATAGT-TA--TAA
1 AAAATATA-TATATGTAC
18430 AAAATATATATAT
1 AAAATATATATAT
18443 TAAATTCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.30
17 22 0.59
18 3 0.08
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (17 bp):
AAAATATATATATGTAC
Found at i:19244 original size:16 final size:15
Alignment explanation
Indices: 19223--19261 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
19213 TTTTTTTGGT
19223 TTTTTTTTGCTGAAAA
1 TTTTTTTTGCT-AAAA
*
19239 TTTTTTTTGCTAGAA
1 TTTTTTTTGCTAAAA
19254 TTTTTTTT
1 TTTTTTTT
19262 TGCTCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (15 bp):
TTTTTTTTGCTAAAA
Found at i:19262 original size:16 final size:16
Alignment explanation
Indices: 19222--19265 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
19212 TTTTTTTTGG
19222 TTTTTTTTTGCTGAAA
1 TTTTTTTTTGCTGAAA
*
19238 ATTTTTTTTGCT-AGAA
1 TTTTTTTTTGCTGA-AA
19254 TTTTTTTTTGCT
1 TTTTTTTTTGCT
19266 CTTTTTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.16, C:0.07, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTTTTTTGCTGAAA
Found at i:19577 original size:31 final size:30
Alignment explanation
Indices: 19490--19577 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
19480 TGTAATTTTT
* * *
19490 AGAAAATTTAAG-GTTAAAATGTAATTTAA
1 AGAAAATTTAGGAGTCAAAATGAAATTTAA
* * * *
19519 GGAAAATTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAATTTAGGAGTCAAAATGAAATTTAA
*
19549 AGAAAAGTTTAGGAGTCAAAATGCAATTT
1 AGAAAA-TTTAGGAGTCAAAATGAAATTT
19578 TTTTTATTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 10 0.22
30 18 0.39
31 18 0.39
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.31
Consensus pattern (30 bp):
AGAAAATTTAGGAGTCAAAATGAAATTTAA
Found at i:19909 original size:78 final size:78
Alignment explanation
Indices: 19738--20231 Score: 563
Period size: 80 Copynumber: 6.3 Consensus size: 78
19728 TTATTCTTTA
* * * * *
19738 TTGAAAAAAAGAAATTGAAAATAGCTCGG-GATGCT-ACCTGAAGTTTAACTCACCTCTCG-AAT
1 TTGAAAAACAGAAATTGAAAATACCTCGGCG-TG-TGACCTGAGGCTCAACTCACCTCTCGCAA-
19800 TATGAGTTGA---TTT
63 TATGAGTTGATTTTTT
* * * *
19813 TTAAAAAAGCCAAAAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTTAACTCACCTCTCGCAA
1 TTGAAAAA--C-AGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAA
19878 TATGAGTTG-TTGTTTT
63 TATGAGTTGATT-TTTT
* * *
19894 TTGAAAAACAGAAATTGAAAAATACCTCGGCGTGTGACCCGAGGTTCAACTCATCTCTCGCAATA
1 TTGAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
19959 TGAGTTGATTTTTTTT
65 TGAGTTGA--TTTTTT
* * * * ** *
19975 TTGAAAAACAGAAATTGAAAATAACTCAGTGCGTGATTTGAGGCTCAACTCACCTCTCGTAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
20040 GAGTTGA-TTTTT
66 GAGTTGATTTTTT
* * * * *
20052 TTGAAAAACAGAAATTAAAAAATACCTCGGCGCGTGACCCGAGCCTCAACTCATCTCTCGCAATA
1 TTGAAAAACAGAAATT-GAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
20117 TGAGTTGATTTTTTT
65 TGAGTTGA-TTTTTT
* *
20132 TTGAAAAACAAAAATTGAAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCACAATA
1 TTGAAAAACAGAAATTG-AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
20197 TGAGTTGATTTTTT
65 TGAGTTGATTTTTT
* *
20211 TTGAAAAATAGAAATTAAAAA
1 TTGAAAAACAGAAATTGAAAA
20232 CAGAATTTGA
Statistics
Matches: 357, Mismatches: 44, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
75 7 0.02
77 22 0.06
78 107 0.30
79 73 0.20
80 115 0.32
81 31 0.09
82 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (78 bp):
TTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTT
Found at i:20356 original size:75 final size:75
Alignment explanation
Indices: 20230--20375 Score: 204
Period size: 75 Copynumber: 1.9 Consensus size: 75
20220 AGAAATTAAA
* * * * *
20230 AACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTG
1 AACAGAAATTGAAAAGACCTCAGCATGTGGCCCAAGACTCAACTCACCTCTCACAATATGAGTTG
20295 ATTTTTGACG
66 ATTTTTGACG
* * *
20305 AACAGAAATTGAAAATACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAAATTGAAAAGACCTCAGCATGTG-GCCCAAGACTCAACTCACCTCTCACAATATGAGTT
20369 GATTTTT
65 GATTTTT
20376 TTTTTGAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 61 0.98
76 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (75 bp):
AACAGAAATTGAAAAGACCTCAGCATGTGGCCCAAGACTCAACTCACCTCTCACAATATGAGTTG
ATTTTTGACG
Found at i:20431 original size:168 final size:168
Alignment explanation
Indices: 20055--20971 Score: 1527
Period size: 168 Copynumber: 5.4 Consensus size: 168
20045 GATTTTTTTG
** * ** * *
20055 AAAAACAGAAATTAAAAAATACCTCGGCGCGTGACCCGAGCCTCAACTCATCTCTCGCAATATGA
1 AAAAACAG-AATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGA
** * * *
20120 GTTGATTTTTTTTTGAAAAACAAAAATTGAAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTC
65 GTTGA----TTTTTGACGAACAGAAATTG-AAAATACCTCAGCGTGTGAGCC-AAGGCTCAACTC
20184 ACCTCTCACAATATGAGTTGA--TTTTTTTTGAAAAATAGAAATT
124 ACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
20227 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
20292 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
20357 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
* * * *
20395 AAAAACAGAATTTGAAAAGACCTCGGCTTGTGGCCCGAGACTTAACTCATCTCACGCAGTATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
20460 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
*
20525 ACAATATGAGTTGATTTTTTTTTTGAAACATAGAAATT
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
*
20563 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
*
20628 TTGATTTTTGACGAACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
20693 ACAATATGAGTTGA-TTTTTTTTTGAAAAATAGAAATT
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
*
20730 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
*
20795 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
20860 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
* * *
20898 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
20963 TTGATTTTT
66 TTGATTTTT
20972 TTTTTGAAAA
Statistics
Matches: 711, Mismatches: 30, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
166 50 0.07
167 183 0.26
168 416 0.59
171 54 0.08
172 8 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (168 bp):
AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
Found at i:20464 original size:93 final size:93
Alignment explanation
Indices: 20305--21064 Score: 648
Period size: 93 Copynumber: 8.8 Consensus size: 93
20295 ATTTTTGACG
* * * * *
20305 AACAGAAATTGAAAATACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAATTTGAAAAGACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGAGTT
20369 GATTTTTTTTTTGAAAAATAGAAATTAAA
65 GATTTTTTTTTTGAAAAATAGAAATTAAA
* * * * * * *
20398 AACAGAATTTGAAAAGACCTCGGCTTGTGGCCCGAGACTTAACTCATCTCACGCAGTATGAGTTG
1 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
** *
20463 A-----TTTTTGACGAACAGAAATT---
66 ATTTTTTTTTTGAAAAATAGAAATTAAA
* * * *
20483 GA-A-AA--T------ACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAATTTGAAAAGACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGAGTT
*
20537 GATTTTTTTTTTGAAACATAGAAATTAAA
65 GATTTTTTTTTTGAAAAATAGAAATTAAA
* * **
20566 AACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAGTTG
1 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
** *
20631 A-----TTTTTGACGAACAGAAATT---
66 ATTTTTTTTTTGAAAAATAGAAATTAAA
* * * *
20651 GA-A-AA--T----AG--CTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAATTTGAAAAGACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGAGTT
20705 GA-TTTTTTTTTGAAAAATAGAAATTAAA
65 GATTTTTTTTTTGAAAAATAGAAATTAAA
* * **
20733 AACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAGTTG
1 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
** *
20798 A-----TTTTTGACGAACAGAAATT---
66 ATTTTTTTTTTGAAAAATAGAAATTAAA
* * * * *
20818 GA-A-AA--T------ACCTCAGCGTATGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAATTTGAAAAGACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGAGTT
20872 GATTTTTTTTTTGAAAAATAGAAATTAAA
65 GATTTTTTTTTTGAAAAATAGAAATTAAA
20901 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
1 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
*
20966 ATTTTTTTTTTGAAAAATAGAAATGAAA
66 ATTTTTTTTTTGAAAAATAGAAATTAAA
* * *
20994 AATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCTGACAATATGAGTTG
1 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
21059 ATTTTT
66 ATTTTT
21065 GACGAACAGA
Statistics
Matches: 524, Mismatches: 83, Indels: 120
0.72 0.11 0.17
Matches are distributed among these distances:
75 118 0.23
76 3 0.01
77 2 0.00
79 16 0.03
80 31 0.06
81 3 0.01
82 1 0.00
83 9 0.02
84 7 0.01
85 7 0.01
86 1 0.00
87 2 0.00
88 47 0.09
90 2 0.00
91 1 0.00
92 42 0.08
93 232 0.44
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (93 bp):
AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTTTTGAAAAATAGAAATTAAA
Found at i:20533 original size:75 final size:74
Alignment explanation
Indices: 20454--20878 Score: 191
Period size: 75 Copynumber: 5.2 Consensus size: 74
20444 TCTCACGCAG
20454 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCA
1 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATA-CTCAGCGTGTGAGCCAAGGCTCAACTCA
20519 CCTCTCACAA
65 CCTCTCACAA
*** ** *
20529 TATGAGTTGATTTTTTTTTTGAAACATAGAAATT-AAAA-A--CAGAATTTGAAAAGACCTCGGC
1 TATGAGTTGA--TTTTTGACG-AAC--AGAAATTGAAAATACTCAGCGTGTG---AG----C--C
* * *
20590 ATGTGGCCCGAGACTCAACTCATCTCTCGTAA
52 A--AGGCTC-A-ACTC-AC-C-TCTCAC--AA
20622 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCA
1 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATA-CTCAGCGTGTGAGCCAAGGCTCAACTCA
20687 CCTCTCACAA
65 CCTCTCACAA
** * ** *
20697 TATGAGTTGATTTTTTTTTGAAAAATAGAAATT-AAAA-A--CAGAATTTGAAAAGACCTCGGCA
1 TATGAGTTGA----TTTTTGACGAACAGAAATTGAAAATACTCAGCGTGTG---AG----C--CA
* * *
20758 TGTGGCCCGAGACTCAACTCATCTCTCGTAA
53 --AGGCTC-A-ACTC-AC-C-TCTCAC--AA
*
20789 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGGCTCAACTCA
1 TATGAGTTGATTTTTGACGAACAGAAATTGAAAATA-CTCAGCGTGTGAGCCAAGGCTCAACTCA
20854 CCTCTCACAA
65 CCTCTCACAA
20864 TATGAGTTGATTTTT
1 TATGAGTTGATTTTT
20879 TTTTTGAAAA
Statistics
Matches: 259, Mismatches: 36, Indels: 110
0.64 0.09 0.27
Matches are distributed among these distances:
74 6 0.02
75 45 0.17
77 19 0.07
78 12 0.05
79 24 0.09
80 15 0.06
81 3 0.01
82 9 0.03
83 2 0.01
84 6 0.02
85 4 0.02
86 7 0.03
87 5 0.02
88 29 0.11
89 11 0.04
90 15 0.06
91 11 0.04
92 12 0.05
93 24 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (74 bp):
TATGAGTTGATTTTTGACGAACAGAAATTGAAAATACTCAGCGTGTGAGCCAAGGCTCAACTCAC
CTCTCACAA
Found at i:20793 original size:428 final size:418
Alignment explanation
Indices: 20305--21574 Score: 1297
Period size: 428 Copynumber: 3.0 Consensus size: 418
20295 ATTTTTGACG
* * * * *
20305 AACAGAAATTGAAAATACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTT
1 AACAGAATTTGAAAATACCTCGGCATGTG-GCCCGAGGCTCAACTCA-CTCTCGCAATATGAGTT
* *
20369 GATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCTTGTGGCCCGAG
64 GA---TTTTTTTGAAAAATAGAAATT---AACAGAA-TTGAAAATACCTCAGCTTGTGG-CCGAG
* * * *
20434 ACTTAACTCATCTCACGCAGTATGAGTTGA-TTTTTGACGAACAGAAATTGAAAATACCTCAGCG
121 ACTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-GAACAGAAATTGAAAATACCTCAGCG
*
20498 TGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAACATAGAAATT
185 TGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
* * *
20563 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAG
250 AAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAG
*
20628 TTGATTTTTGACGAACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
315 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
* * *
20693 ACAATATGAGTTGATTTTTTTTTGAAAAATAGAAATTAAA
380 GCAATATGAGTTGA-TTTTTTTTGAAAAATAAAAATTGAA
* * *
20733 AACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAGTTG
1 AACAGAATTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTG
* * * * *
20798 A--TTTTTG----A-CG-----AACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGGCTCAAC
65 ATTTTTTTGAAAAATAGAAATTAACAG-AATTGAAAATACCTCAGCTTGTG-GCCGAGACTCAAC
* *
20851 TCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAA
128 TCACCTCTCGCAATATGAGTTGA----TTTTTTG------AG--------AACAGAAATTGAAAA
* * * *
20916 GACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAA
175 TACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAA
*
20980 AAATAGAAATGAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCT
239 AAATAGAAATTAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCT
*
21045 -GACAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTTAGCGTGTGAGCCAAGGCTC
304 CG-CAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTC
* ** *
21109 AACTCACCTCTTGCAATATGAGTTGA-TTTTTTTGACGAACAAAAATTGAA
368 AACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAATAAAAATTGAA
* * * * * *
21159 AATAGATTTTGAAAATACCTCGACATGTGACCCGAGGCCCAACTCACATCTCGCAATGTGAGTTG
1 AACAGAATTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCAC-TCTCGCAATATGAGTTG
* * *
21224 ATTTTTTTGAAAAATATAAATT----GAA---AAAATACCTCAG-TGTGTGATCTGA-AGCTCAA
65 ATTTTTTTGAAAAATAGAAATTAACAGAATTGAAAATACCTCAGCT-TGTG-GCCGAGA-CTCAA
* * *
21280 CTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGA
127 CTCACCTCTCGCAATATGAGTTGA-TTTTTTGAGA-ACAGAAATTGAAAATACCTCAGCGTGTGA
* * ***
21345 GCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGA-TTTTTTTTTGAAAGGCAGAAATTGAAAA
190 GCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT-AAAA
* * * ** * * * * *
21409 ATGGAAATTGAAAATACCTCGGTGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGA
254 ATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAGTTGA
* *
21474 TTTTTTTGAC-AACAGAAATTGAAATTACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCG
319 --TTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCG
*
21535 CAATATGAGTTGATTTTTTTTGAAAGATAAAAATTGAA
381 CAATATGAGTTGATTTTTTTTGAAAAATAAAAATTGAA
21573 AA
1 AA
21575 TACCTTAGCA
Statistics
Matches: 705, Mismatches: 90, Indels: 108
0.78 0.10 0.12
Matches are distributed among these distances:
410 50 0.07
411 3 0.00
412 2 0.00
413 51 0.07
414 133 0.19
415 34 0.05
416 8 0.01
418 1 0.00
419 1 0.00
420 1 0.00
421 2 0.00
423 6 0.01
425 1 0.00
426 74 0.10
427 11 0.02
428 277 0.39
430 46 0.07
432 1 0.00
433 2 0.00
434 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (418 bp):
AACAGAATTTGAAAATACCTCGGCATGTGGCCCGAGGCTCAACTCACTCTCGCAATATGAGTTGA
TTTTTTTGAAAAATAGAAATTAACAGAATTGAAAATACCTCAGCTTGTGGCCGAGACTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTTGAGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAG
GCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAATAGAAT
TTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
CGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTTGAAAAATAAAAATTGAA
Found at i:20799 original size:335 final size:336
Alignment explanation
Indices: 20055--20971 Score: 1527
Period size: 335 Copynumber: 2.7 Consensus size: 336
20045 GATTTTTTTG
** * ** * *
20055 AAAAACAGAAATTAAAAAATACCTCGGCGCGTGACCCGAGCCTCAACTCATCTCTCGCAATATGA
1 AAAAACAG-AATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGA
** * * *
20120 GTTGATTTTTTTTTGAAAAACAAAAATTGAAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTC
65 GTTGA----TTTTTGACGAACAGAAATTG-AAAATACCTCAGCGTGTGAGCC-AAGGCTCAACTC
20184 ACCTCTCACAATATGAGTTGA--TTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGA
124 ACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGA
20247 CCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTGACGAACAGAA
189 CCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTGACGAACAGAA
20312 ATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTT
254 ATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTT
20377 TTTTGAAAAATAGAAATT
319 TTTTGAAAAATAGAAATT
* * * *
20395 AAAAACAGAATTTGAAAAGACCTCGGCTTGTGGCCCGAGACTTAACTCATCTCACGCAGTATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
20460 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
*
20525 ACAATATGAGTTGATTTTTTTTTTGAAACATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGC
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGC
*
20590 ATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAGTTGATTTTTGACGAACAGAAATTGAAA
196 ATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAA
*
20655 ATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTTTTTGAA
261 ATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAA
20719 AAATAGAAATT
326 AAATAGAAATT
*
20730 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAG
1 AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
*
20795 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGGCTCAACTCACCTCTC
66 TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
*
20860 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCAGC
131 ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGC
* *
20925 ATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTGATTTTT
196 ATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTT
20972 TTTTTGAAAA
Statistics
Matches: 545, Mismatches: 29, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
334 50 0.09
335 273 0.50
336 163 0.30
339 51 0.09
340 8 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (336 bp):
AAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAG
TTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTC
ACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGC
ATGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAA
ATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAA
AAATAGAAATT
Found at i:21008 original size:13 final size:14
Alignment explanation
Indices: 20974--21008 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
20964 TGATTTTTTT
20974 TTTGAAAAATAGAA
1 TTTGAAAAATAGAA
*
20988 -ATGAAAAATAGAA
1 TTTGAAAAATAGAA
21001 TTTGAAAA
1 TTTGAAAA
21009 GACCTCGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (14 bp):
TTTGAAAAATAGAA
Found at i:21060 original size:261 final size:258
Alignment explanation
Indices: 20641--21480 Score: 1005
Period size: 261 Copynumber: 3.3 Consensus size: 258
20631 ATTTTTGACG
* * * *
20641 AACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTG
1 AACAGAAATTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTG
*
20706 ATTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGAC
66 ATTTTTTTTTGAAAAATAGAAA-TAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGAC
* * *
20771 TCAACTCATCTCTCGTAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTAT
130 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGT
* *
20836 GAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAA
195 GAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTGAAAAACAGAAATTAAA
* * * *
20901 AACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAGTTG
1 AACAGAAATTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTG
20966 ATTTTTTTTTTGAAAAATAGAAATGAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGA
66 A-TTTTTTTTTGAAAAATAGAAAT-AAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGA
*
21031 CTCAACTCACCTCT-GACAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTTAGCGT
129 CTCAACTCACCTCTCG-CAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGT
* ** * *
21095 GTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGTTGA--TTTTTTTGACGAACAAAAATTGA
193 GTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTAA
21158 A
258 A
* ** * * * *
21159 AATAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCCCAACTCACATCTCGCAATGTGAGTT
1 AACAGAAATTGAAAATACCTCAG-CATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTT
* * * ** ** *
21223 GA--TTTTTTTGAAAAAT----AT--AAATTGAA----AAAATACCTCAGTGTGTGATCTGA-AG
65 GATTTTTTTTTGAAAAATAGAAATAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGA-
* *
21275 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAGACAGAAATTGAAAATAGCTCAGC
129 CTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGACGA-ACAGAAATTGAAAATACCTCAGC
* * **
21339 GCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTGAAAGGCAGAAATT
191 GTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATT
21404 GAAA
256 -AAA
** * ** * * * *
21408 AATGGAAATTGAAAATACCTCGGTGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTG
1 AACAGAAATTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTG
21473 ATTTTTTT
66 ATTTTTTT
21481 GACAACAGAA
Statistics
Matches: 505, Mismatches: 60, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
243 1 0.00
244 44 0.09
245 2 0.00
246 67 0.13
248 23 0.05
249 55 0.11
250 1 0.00
251 7 0.01
255 14 0.03
257 1 0.00
258 74 0.15
260 60 0.12
261 156 0.31
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (258 bp):
AACAGAAATTGAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTTTGAAAAATAGAAATAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACT
CAACTCACCTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTG
AGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTAAA
Found at i:21075 original size:168 final size:165
Alignment explanation
Indices: 20898--21312 Score: 458
Period size: 168 Copynumber: 2.5 Consensus size: 165
20888 AATAGAAATT
* * * *
20898 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGG-CCGAGACTCAACTCACCTCTCGCAATATGAG
*** * *
20963 TTGATTTTTTTTTTGAAAAATAGAAATGAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCCG
65 TTGATTTTTTTGACGAAAAA-A-AAATG-AAAATAGAATTTGAAAAGACCTCGACATGTGACCCG
* *
21028 AGACTCAACTCACCTCT-GACAATATGAGTTGA-TTTTTG
127 AGACCCAACTCACATCTCG-CAATATGAGTTGATTTTTTG
** * * * *
21066 ACGAACAGAAATTGAAAATACCTTAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTG-GCCGAGACTCAACTCACCTCTCGCAATATGAG
* * * * *
21131 TTGATTTTTTTGACGAACAAAAATTGAAAATAGATTTTGAAAATACCTCGACATGTGACCCGAGG
65 TTGATTTTTTTGACGAAAAAAAAATGAAAATAGAATTTGAAAAGACCTCGACATGTGACCCGAGA
*
21196 CCCAACTCACATCTCGCAATGTGAGTTGATTTTTTTG
130 CCCAACTCACATCTCGCAATATGAGTTGA-TTTTTTG
* * * * *
21233 AAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGA-AGCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAATTG--AAAATACCTCAGCGTGTG-GCCGAGA-CTCAACTCACCTCTCGCAATAT
21297 GAGTTGATTTTTTTGA
62 GAGTTGATTTTTTTGA
21313 AAGACAGAAA
Statistics
Matches: 206, Mismatches: 34, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
165 58 0.28
166 5 0.02
167 17 0.08
168 69 0.33
169 57 0.28
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (165 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGGCCGAGACTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGACGAAAAAAAAATGAAAATAGAATTTGAAAAGACCTCGACATGTGACCCGAGAC
CCAACTCACATCTCGCAATATGAGTTGATTTTTTG
Found at i:21083 original size:503 final size:486
Alignment explanation
Indices: 20018--21816 Score: 1540
Period size: 503 Copynumber: 3.6 Consensus size: 486
20008 TGATTTGAGG
* ** *
20018 CTCAACTCACCTCTCG-TAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAATACCTCGG
1 CTCAACTCACCTCT-GACAATATGAGTTGA-TTTTTTGACGAACAGAAATT-GAAAATACCTCGG
* * * **
20082 CGCGTGACCCGAGCCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAAAAAT
63 CGTGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGA---TTTTTTGACGAACAAAAAT
* * *
20147 TGAAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTT
125 TG-AAAATAGCTCAGCGTGTGACCTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTT
20212 TGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCAT
189 TGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCAT
*
20277 CTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGG
254 CTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGG
20342 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATT
319 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATT
* * * * * * *
20407 TGAAAAGACCTCGGCTTGTGGCCCGAGACTTAACTCATCTCACGCAGTATGAGTTGATTTTTGAC
384 TGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCACACAATATGAGTTGATTTTTGAA
* * *
20472 GAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGG
449 GAACAGAAATTGAAAAGACCTCAGCATGTGAGCCAAGA
* *
20510 CTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAACATAGAAATTAAAAACAGAATT
1 CTCAACTCACCTCTGACAATATGAGTTGA----TTTTTTG--AC---G--------AACAGAAAT
* * *
20575 TGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGTAATATGAGTTGA-TTTTTGA
49 TGAAAATACCTCGGCGTGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGA
*
20639 CGAACAGAAATTGAAAATAGCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCACAATATGAG
114 CGAACAAAAATTGAAAATAGCTCAGCGTGTGA-CCTAAGGCTCAACTCACCTCTCACAATATGAG
20703 TTGATTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGA
178 TTGA-TTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGA
*
20768 GACTCAACTCATCTCTCGTAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCG
242 GACTCAACTCATCTCTCGCAATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCG
20833 TATGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
307 TATGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATT
*
20898 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCTCACAATATGAG
372 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCACACAATATGAG
*
20963 TTGATTTTTTTTTTGAAAAATAGAA-ATGAAAAATAGAATTTGAAAAGACCTCGGCATGTG-GCC
437 TTGA-----TTTTTG----A-AGAACA-G------A-AA-TTGAAAAGACCTCAGCATGTGAG-C
*
21026 CGAGA
482 CAAGA
**
21031 CTCAACTCACCTCTGACAATATGAGTTGA-TTTTTGACGAACAGAAATTGAAAATACCTTAGCGT
1 CTCAACTCACCTCTGACAATATGAGTTGATTTTTTGACGAACAGAAATTGAAAATACCTCGGCGT
* * * *
21095 GTGAG-CCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTGACGAACAAAAATTGAA
66 GTG-GCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGA-TTTTTTGACGAACAAAAATTGAA
* ** * * * *
21159 AATAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCCCAACTCACATCTCGCAATGTGAGTT
129 AAT--A----G-------CTCAG-CGTGTGACCTAAGGCTCAACTCACCTCTCACAATATGAGTT
* * * ** ** *
21223 GA-TTTTTTTGAAAAATATAAATT-------GAA----AAAATACCTCAGTGTGTGATCTGA-AG
180 GATTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGA-
* * *
21275 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA-AAGACAGAAATTGAAAATAGCTCAGC
244 CTCAACTCATCTCTCGCAATATGAGTTGA--TTTTTGACGA-ACAGAAATTGAAAATACCTCAGC
** * * ***
21339 GCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGA-TTTTTTTTTGAAAGGCAGAAAT
306 GTATGAGCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAAT
** * * * ** * * * * * * *
21403 TGAAAAATGGAAATTGAAAATACCTCGGTGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACG
371 T-AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCCGAGACTCAACTCACCTCACACAATATG
* ** * * *
21468 AGTTGATTTTTTTG-ACAACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGG
435 AGTTGA--TTTTTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-AAGA
* *
21519 CTCAACTCACCTCTCG-CAATATGAGTTGATTTTTTTTGAAAGATA-A-AAATTGAAAATACCTT
1 CTCAACTCACCTCT-GACAATATGAGTTGA--TTTTTTG-ACGA-ACAGAAATTGAAAATACCTC
* * ** * * ** *
21581 AGCATGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAA
61 GGCGTGTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGA---TTTTTTGACGAACAAAA
** * * * **
21644 ATTGAAAATAATTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGTTGA---TTT
123 ATTGAAAATAGCTCAGCGTGTGACCTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTT
* * * * * * * * ** *
21704 TTGAAAAACATAAATT--GAACAGAAATTGAAAATACCTC--AACGTGTCTTGAGGCTCAACTCA
188 TTGAAAAATAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCA
* * *
21765 CCTCTCGCAATATGAGTTGATTTTTTGA-AAAGAAGAAATTGAAAATACCTCA
253 TCTCTCGCAATATGAGTTGA-TTTTTGACGAA-CAGAAATTGAAAATACCTCA
21817 ATGTGTCTTG
Statistics
Matches: 1103, Mismatches: 119, Indels: 182
0.79 0.08 0.13
Matches are distributed among these distances:
474 18 0.02
476 29 0.03
478 7 0.01
479 5 0.00
480 28 0.03
481 35 0.03
483 10 0.01
487 2 0.00
488 33 0.03
489 31 0.03
490 13 0.01
491 54 0.05
492 31 0.03
493 1 0.00
495 8 0.01
497 1 0.00
498 4 0.00
499 1 0.00
502 49 0.04
503 323 0.29
504 10 0.01
505 68 0.06
506 21 0.02
507 173 0.16
508 15 0.01
509 3 0.00
511 2 0.00
512 2 0.00
513 4 0.00
514 2 0.00
516 26 0.02
517 3 0.00
518 37 0.03
519 1 0.00
520 3 0.00
521 50 0.05
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (486 bp):
CTCAACTCACCTCTGACAATATGAGTTGATTTTTTGACGAACAGAAATTGAAAATACCTCGGCGT
GTGGCCCGAGACTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGACGAACAAAAATTGAAAA
TAGCTCAGCGTGTGACCTAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTGAAAAA
TAGAAATTAAAAACAGAATTTGAAAAGACCTCGGCATGTGGCCCGAGACTCAACTCATCTCTCGC
AATATGAGTTGATTTTTGACGAACAGAAATTGAAAATACCTCAGCGTATGAGCCAAGGCTCAACT
CACCTCTCACAATATGAGTTGATTTTTTTTTTGAAAAATAGAAATTAAAAACAGAATTTGAAAAG
ACCTCAGCATGTGGCCCGAGACTCAACTCACCTCACACAATATGAGTTGATTTTTGAAGAACAGA
AATTGAAAAGACCTCAGCATGTGAGCCAAGA
Found at i:21245 original size:90 final size:90
Alignment explanation
Indices: 21077--21250 Score: 224
Period size: 90 Copynumber: 1.9 Consensus size: 90
21067 CGAACAGAAA
* * * * * *
21077 TTGAAAATACCTTAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTT
1 TTGAAAATACCTGAGCATGTGACCCAAGGCCCAACTCACATCTCGCAATATGAGTTGATTTTTTT
**
21142 GACGAACAAAAATTGAAAATAGATT
66 GAAAAACAAAAATTGAAAATAGATT
* *
21167 TTGAAAATACCTCGA-CATGTGACCCGAGGCCCAACTCACATCTCGCAATGTGAGTTGATTTTTT
1 TTGAAAATACCT-GAGCATGTGACCCAAGGCCCAACTCACATCTCGCAATATGAGTTGATTTTTT
* *
21231 TGAAAAATATAAATTGAAAA
65 TGAAAAACAAAAATTGAAAA
21251 AATACCTCAG
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 70 0.99
91 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (90 bp):
TTGAAAATACCTGAGCATGTGACCCAAGGCCCAACTCACATCTCGCAATATGAGTTGATTTTTTT
GAAAAACAAAAATTGAAAATAGATT
Found at i:21282 original size:79 final size:75
Alignment explanation
Indices: 21192--21947 Score: 564
Period size: 77 Copynumber: 9.7 Consensus size: 75
21182 CATGTGACCC
* * * * *
21192 GAGGCCCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG--AAAATACC
* *
21257 TCAGTGTGTGATCT
64 TCAGCGTGT-CT-T
* * *
21271 GAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTC
* *
21336 AGCGCGTGAGC-C
66 A--GCGTG-TCTT
* * **
21348 AAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTGAAAGGCAGAAATTGAAAAATGG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAACAGAAATTG-AAAAT--
** * * * *
21413 AAATTGAAAATACCTCGGTGTGT
61 -ACCT---CA-GCGT--GTCT-T
* * * * * *
21436 GA-CCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTG-ACAACAGAAATTGAAAT
1 GAGGCTCA-ACTC-A----CCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA
*
21499 TACCTCAGCGTGTCCT
60 TACCTCAGCGTGTCTT
* * *
21515 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGATAAAAATTGAAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAATACCT
* *
21580 TAGCATGTCTT
65 CAGCGTGTCTT
** **
21591 GAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTGAAAAACAGAAATTGAAAATAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAACAGAAATTGAAAATACC
*
21656 TCAGCATGTCTT
64 TCAGCGTGTCTT
** * *
21668 GAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTGAAAAACAT-AAATTGAACAGAAATTG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-------TTGAAA---AACAGAAATTG
*
21732 AAAATACCTCAACGTGTCTT
56 AAAATACCTCAGCGTGTCTT
21752 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAGA-AGAAATTGAAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-ACAGAAATTGAAAATACCT
**
21815 CAATGTGTCTT
65 CAGCGTGTCTT
** * * * *
21826 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTG-AAAACAAAAATTGAAATTACCTA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTC
*
21888 AACGTGTCTT
66 AGCGTGTCTT
** *
21898 GAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTTG--AAACAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT
21948 AAAAGCATCA
Statistics
Matches: 555, Mismatches: 82, Indels: 87
0.77 0.11 0.12
Matches are distributed among these distances:
71 1 0.00
72 69 0.12
73 10 0.02
74 78 0.14
75 14 0.03
76 57 0.10
77 112 0.20
78 1 0.00
79 79 0.14
80 10 0.02
81 3 0.01
82 3 0.01
83 7 0.01
84 57 0.10
85 2 0.00
86 3 0.01
87 4 0.01
88 4 0.01
89 5 0.01
90 10 0.02
91 8 0.01
93 18 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (75 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTC
AGCGTGTCTT
Found at i:21308 original size:169 final size:164
Alignment explanation
Indices: 20898--21332 Score: 471
Period size: 169 Copynumber: 2.6 Consensus size: 164
20888 AATAGAAATT
* * * * * *
20898 AAAAACAGAATTTGAAAAGACCTCAGCATGTG-GCCCGAGACTCAACTCACCTCTCACAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGAG-CCAAGGCTCAACTCACCTCTCGCAATATGA
** * * * *
20962 GTTGATTTTTTTTTTGAAAAATAGAAATGAAAAATAGAATTTGAAAAGACCTCGGCATGTGGCCC
65 GTTGA-TTTTTTTGAGAACAA-A-AATTG-AAAATAGAATTTGAAAAGACCTCGACATGTGACCC
* *
21027 GAGACTCAACTCACCTCTGACAATATGAGTTGATTTTTG
126 GAGACCCAACTCACATCTGACAATATGAGTTGATTTTTG
** * *
21066 ACGAACAGAAATTGAAAATACCTTAGCGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
* * *
21131 TTGATTTTTTTGACGAACAAAAATTGAAAATAGATTTTGAAAATACCTCGACATGTGACCCGAGG
66 TTGATTTTTTTGA-GAACAAAAATTGAAAATAGAATTTGAAAAGACCTCGACATGTGACCCGAGA
*
21196 CCCAACTCACATCTCG-CAATGTGAGTTGATTTTTTTG
130 CCCAACTCACATCT-GACAATATGAGTTGA--TTTTTG
* * * * *
21233 AAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATAT
1 AAAAACAGAAATTG--AAAATACCTCAGCGTGTGAGC-CAAGGCTCAACTCACCTCTCGCAATAT
* *
21297 GAGTTGATTTTTTTGAAAGACAGAAATTGAAAATAG
63 GAGTTGATTTTTTTGAGA-ACAAAAATTGAAAATAG
21333 CTCAGCGCGT
Statistics
Matches: 225, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
165 58 0.26
166 5 0.02
167 24 0.11
168 63 0.28
169 73 0.32
170 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (164 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTGAGAACAAAAATTGAAAATAGAATTTGAAAAGACCTCGACATGTGACCCGAGAC
CCAACTCACATCTGACAATATGAGTTGATTTTTG
Found at i:21535 original size:74 final size:74
Alignment explanation
Indices: 21412--21947 Score: 569
Period size: 74 Copynumber: 7.1 Consensus size: 74
21402 TTGAAAAATG
* * * *** *
21412 GAAATTGAAAATACCTCGGTGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTT
*
21477 TTTTGACAACA
64 TTTTGAAAACA
* * **
21488 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTT
*
21553 TTTGAAAGATA
65 TTTGAAA-ACA
* * *
21564 AAAATTGAAAATACCTTAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTT
21629 TTTTGAAAAACA
64 TTTTG-AAAACA
** * *
21641 GAAATTGAAAATAATTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
* *
21706 GAAAAACATAAATTGAACA
66 -------TTGAA---AACA
* **
21725 GAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
*
21789 TTGAAAAGAA
66 TTGAAAA-CA
** *
21799 GAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
21862 TTGAAAACA
66 TTGAAAACA
* * * * *
21871 AAAATTGAAATTACCTAAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTT
1 GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
21935 TTG-AAACA
66 TTGAAAACA
21943 GAAAT
1 GAAAT
21948 AAAAGCATCA
Statistics
Matches: 401, Mismatches: 43, Indels: 36
0.84 0.09 0.08
Matches are distributed among these distances:
72 66 0.16
73 16 0.04
74 92 0.23
75 15 0.04
76 79 0.20
77 66 0.16
78 3 0.01
81 2 0.00
82 1 0.00
83 4 0.01
84 57 0.14
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (74 bp):
GAAATTGAAAATACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
TTGAAAACA
Found at i:21942 original size:72 final size:73
Alignment explanation
Indices: 21721--21940 Score: 352
Period size: 72 Copynumber: 3.0 Consensus size: 73
21711 ACATAAATTG
* ** *
21721 AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
21786 TTTTTGAA
66 TTTTTGAA
* *
21794 AAGAAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AACAA-AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
21859 A-TTTTGAA
65 ATTTTTGAA
* *
21867 AACAAAAATTGAAATTACCTAAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
21932 TTTTTGAA
66 TTTTTGAA
21940 A
1 A
21941 CAGAAATAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
72 57 0.42
73 22 0.16
74 56 0.41
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (73 bp):
AACAAAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
TTTTTGAA
Found at i:29329 original size:24 final size:24
Alignment explanation
Indices: 29302--29351 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29292 ATGAAAGTTT
29302 AATGCAAATG-ATGCAATGCAATGC
1 AATGCAAATGTATGCAATG-AATGC
*
29326 AATGCAAATGTATGGAATGAATGC
1 AATGCAAATGTATGCAATGAATGC
29350 AA
1 AA
29352 AAGAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (24 bp):
AATGCAAATGTATGCAATGAATGC
Found at i:32911 original size:16 final size:16
Alignment explanation
Indices: 32890--32947 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
32880 TTTTTTGGTT
32890 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAAA
32906 TTTTTTTTGCTGG-AA
1 TTTTTTTTGCTGGAAA
*
32921 TTTTTTTTGCTGGAAT
1 TTTTTTTTGCTGGAAA
32937 TTTTTTTTGCT
1 TTTTTTTTGCT
32948 CTTTTTTCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 15 0.38
16 25 0.62
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (16 bp):
TTTTTTTTGCTGGAAA
Found at i:32943 original size:15 final size:15
Alignment explanation
Indices: 32890--32943 Score: 99
Period size: 15 Copynumber: 3.5 Consensus size: 15
32880 TTTTTTGGTT
32890 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGG-AA
32906 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
32921 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
32936 TTTTTTTT
1 TTTTTTTT
32944 TGCTCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 25 0.66
16 13 0.34
ACGTcount: A:0.13, C:0.06, G:0.17, T:0.65
Consensus pattern (15 bp):
TTTTTTTTGCTGGAA
Found at i:33259 original size:31 final size:30
Alignment explanation
Indices: 33187--33259 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
33177 ATTTAAGGTT
* * *
33187 AAAATGTAATTTAAGGAAAGTTTATGGCTC
1 AAAATGAAATTTAAGAAAAGTTTAGGGCTC
* * *
33217 TAAGTGAAATTTAAAGAAAAGTTTAGGGGTC
1 AAAATGAAATTT-AAGAAAAGTTTAGGGCTC
*
33248 AAAATGCAATTT
1 AAAATGAAATTT
33260 TTTTTTTTTG
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (30 bp):
AAAATGAAATTTAAGAAAAGTTTAGGGCTC
Found at i:40317 original size:12 final size:13
Alignment explanation
Indices: 40295--40325 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
40285 TGATTAGTGG
40295 TTTATCCAATATA
1 TTTATCCAATATA
40308 TTTA-CCAATATA
1 TTTATCCAATATA
40320 TTTATC
1 TTTATC
40326 ATTAGCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTATCCAATATA
Found at i:40752 original size:13 final size:13
Alignment explanation
Indices: 40734--40758 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40724 GGTTTGTTTA
40734 TTAAACTAATTAT
1 TTAAACTAATTAT
40747 TTAAACTAATTA
1 TTAAACTAATTA
40759 ACTAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTAATTAT
Found at i:44369 original size:28 final size:28
Alignment explanation
Indices: 44337--44397 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
44327 ATTTACTAGA
*
44337 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
44365 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
44393 ATACC
1 ATACC
44398 TCTAGGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:44569 original size:27 final size:27
Alignment explanation
Indices: 44527--44595 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
44517 TGCCACAAAT
*
44527 TATCTGTTCTGGTGGCCCTGCCACGTA
1 TATCTGTTCTGGTGGCACTGCCACGTA
*
44554 TATTTGTTCTGGTGGCACTGCCACGTA
1 TATCTGTTCTGGTGGCACTGCCACGTA
44581 TATCTGTATCTGGTG
1 TATCTGT-TCTGGTG
44596 ACTCTGTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.13, C:0.23, G:0.26, T:0.38
Consensus pattern (27 bp):
TATCTGTTCTGGTGGCACTGCCACGTA
Found at i:45111 original size:56 final size:56
Alignment explanation
Indices: 45051--45162 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
45041 ATAAGGCCTT
45051 TTAATTATTTTTTATGGTTTGGTTTTACTTTTATTATTTTATTTTATTACGATGAA
1 TTAATTATTTTTTATGGTTTGGTTTTACTTTTATTATTTTATTTTATTACGATGAA
*
45107 TTAATTATTTTTTATGGTTTGGTTTTACTTTTATTATTTTATTTTATTATGATGAA
1 TTAATTATTTTTTATGGTTTGGTTTTACTTTTATTATTTTATTTTATTACGATGAA
45163 AAAAAACTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (56 bp):
TTAATTATTTTTTATGGTTTGGTTTTACTTTTATTATTTTATTTTATTACGATGAA
Found at i:46019 original size:12 final size:12
Alignment explanation
Indices: 45980--46013 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
45970 GCGAGCAGCT
*
45980 CGAGGTAGAGGC
1 CGAGGAAGAGGC
*
45992 CGTGGAAGAGGC
1 CGAGGAAGAGGC
46004 CGAGGAAGAG
1 CGAGGAAGAG
46014 CTCGAGCGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.50, T:0.06
Consensus pattern (12 bp):
CGAGGAAGAGGC
Found at i:49594 original size:27 final size:28
Alignment explanation
Indices: 49556--49611 Score: 105
Period size: 27 Copynumber: 2.0 Consensus size: 28
49546 CGACAGACTT
49556 TCTCTTCAGAAGTTAGCCAAGTTG-ATG
1 TCTCTTCAGAAGTTAGCCAAGTTGTATG
49583 TCTCTTCAGAAGTTAGCCAAGTTGTATG
1 TCTCTTCAGAAGTTAGCCAAGTTGTATG
49611 T
1 T
49612 GGCGGAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (28 bp):
TCTCTTCAGAAGTTAGCCAAGTTGTATG
Done.