Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1422
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: 293460
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 3 of 3
Found at i:260828 original size:17 final size:17
Alignment explanation
Indices: 260806--260872 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
260796 TTTTTTATTA
260806 ATAATATAAATATAAAT
1 ATAATATAAATATAAAT
260823 ATAATATAAATTATTAAAT
1 ATAATATAAA-TA-TAAAT
* * * *
260842 ATATTAAAAATTTAAAA
1 ATAATATAAATATAAAT
260859 ATAA-ATATAATATA
1 ATAATATA-AATATA
260873 TGTATTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
16 2 0.05
17 22 0.55
18 3 0.08
19 13 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATATAAATATAAAT
Found at i:264621 original size:29 final size:27
Alignment explanation
Indices: 264573--264637 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
264563 CAATCTTTTG
264573 ATAAAAATAAAAACTTATTTTAATATA-A
1 ATAAAAATAAAAACTTA-TTTAA-ATACA
*
264601 ATTAAAAATAATAA-TTGATTTAAATACA
1 A-TAAAAATAAAAACTT-ATTTAAATACA
264629 ATAAAAATA
1 ATAAAAATA
264638 TTTATTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 11 0.33
28 10 0.30
29 12 0.36
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAAAAATAAAAACTTATTTAAATACA
Found at i:264884 original size:5 final size:5
Alignment explanation
Indices: 264865--264950 Score: 58
Period size: 5 Copynumber: 17.8 Consensus size: 5
264855 ACGATATAAA
* *
264865 AATAT AATAT CAATAT AATAT -ATTT AAT-T AATA- AAAATT AATAT AATA-
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT
* * *
264913 AATAT GATAT AATAT -ATTT AAATAT GAT-T AATAT AATA
1 AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATA
264951 CACTTAATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
4 20 0.32
5 32 0.51
6 11 0.17
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:264936 original size:20 final size:19
Alignment explanation
Indices: 264901--264947 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
264891 ATTAATAAAA
*
264901 ATTAATATA-ATAAATATG
1 ATTAATATATTTAAATATG
264919 ATATAATATATTTAAATATG
1 AT-TAATATATTTAAATATG
264939 ATTAATATA
1 ATTAATATA
264948 ATACACTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
ATTAATATATTTAAATATG
Found at i:265653 original size:27 final size:28
Alignment explanation
Indices: 265623--265684 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
265613 ATATTAATTT
* *
265623 TTTTAATAT-ATAATTAATAGTTAAA-AA
1 TTTTAATATCA-AATAAATAATTAAATAA
* *
265650 TTTTTACATCAAATAAATAATTAAATAA
1 TTTTAATATCAAATAAATAATTAAATAA
265678 TTTTAAT
1 TTTTAAT
265685 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTTAATATCAAATAAATAATTAAATAA
Found at i:266550 original size:15 final size:17
Alignment explanation
Indices: 266530--266561 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
266520 TTATTTATAA
266530 ATTAAA-AA-AAATATT
1 ATTAAATAATAAATATT
266545 ATTAAATAATAAATATT
1 ATTAAATAATAAATATT
266562 TACAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAATAATAAATATT
Found at i:267918 original size:2 final size:2
Alignment explanation
Indices: 267911--267945 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
267901 CATTTATGTT
267911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
267946 GAAAATATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:271367 original size:22 final size:22
Alignment explanation
Indices: 271315--271374 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
271305 CTAGCCGTAT
*
271315 TTTTTTTTAC-CTTATTGTTTCTA
1 TTTTTTTT-CTCTT-TTCTTTCTA
* *
271338 TTTCTTTTCTCTTTTCTTTCTC
1 TTTTTTTTCTCTTTTCTTTCTA
*
271360 TTTTTTTTTTCTTTT
1 TTTTTTTTCTCTTTT
271375 TTTTAGTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTTTTCTCTTTTCTTTCTA
Found at i:271375 original size:11 final size:11
Alignment explanation
Indices: 271332--271378 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
271322 TACCTTATTG
* *
271332 TTTCTATTTCT
1 TTTCTCTTTTT
*
271343 TTTCTCTTTTC
1 TTTCTCTTTTT
271354 TTTCTCTTTTT
1 TTTCTCTTTTT
*
271365 TTTTTCTTTTT
1 TTTCTCTTTTT
271376 TTT
1 TTT
271379 AGTTGAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:272965 original size:85 final size:82
Alignment explanation
Indices: 272743--273227 Score: 377
Period size: 85 Copynumber: 5.8 Consensus size: 82
272733 TGACTTGTAA
* * * ** * *
272743 GCTTTGAAAATGTGCCATTAACTTGTTGGCTTTTG-AAATGTGACACTGACTTATGGGCTTTGAA
1 GCTTTGAAAATGTGCCACTGACTT-ATGGC-TTTGAAAAAATGCCACTGACTTGTGGGCTTTGAA
* * *
272807 AGGTGCCATTGACTTGTGA
64 AGGTGCCACTAACTTGTGG
* * * * * *
272826 GCTTTG-AAAGGTGCCACCGACTTGTGGGCTTTGAAAAAGATGTCGCTGACTTGTGGGCTCTCGA
1 GCTTTGAAAATGTGCCACTGACTTAT-GGCTTTGAAAAA-ATGCCACTGACTTGTGGGCT-TTGA
272890 AAGGTGCCACTAACTTGTGG
63 AAGGTGCCACTAACTTGTGG
* * *
272910 GTTTTGAAAATGTGCCATTGACTTATGAGCTTTTGAAAAAATGCCATTGACTTGTGGGCTTTGAA
1 GCTTTGAAAATGTGCCACTGACTTATG-GC-TTTGAAAAAATGCCACTGACTTGTGGGCTTTG-A
* * * *
272975 AAGGTACCCCTAATTTATGG
63 AAGGTGCCACTAACTTGTGG
* * * * ** *
272995 ACTTGGAAAATATGCCACTGATTTATGGACTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA
1 GCTTTGAAAATGTGCCACTGACTTATGG-CTTTGAAAAAATGCCACTGACTTGTGGGCTTTG--A
*
273060 AAGGTGCTA-TAACTTGTGG
63 AAGGTGCCACTAACTTGTGG
* * * * * *
273079 GCTTTCGAAAAGGTGCCACTGATTTTTGGACTATGAAAAGATGCCACTAACTTGTGGGCTTTGAA
1 GCTTT-GAAAATGTGCCACTGACTTATGG-CTTTGAAAAAATGCCACTGACTTGTGGGCTTTGAA
* *
273144 AGGATGCCATTGACTTGTGG
64 AGG-TGCCACTAACTTGTGG
* * * * * * *
273164 GCTTTGGAAGA-GTGACACTGACTTGTGGGCTTTGGAAGAGTGCCACTAACTTGTGGGC-TTGAA
1 GCTTT-GAAAATGTGCCACTGACTTAT-GGCTTTGAAAAAATGCCACTGACTTGTGGGCTTTGAA
273227 A
64 A
273228 AGATGCTACG
Statistics
Matches: 327, Mismatches: 61, Indels: 28
0.79 0.15 0.07
Matches are distributed among these distances:
81 5 0.02
82 19 0.06
83 33 0.10
84 108 0.33
85 153 0.47
86 9 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (82 bp):
GCTTTGAAAATGTGCCACTGACTTATGGCTTTGAAAAAATGCCACTGACTTGTGGGCTTTGAAAG
GTGCCACTAACTTGTGG
Found at i:273029 original size:113 final size:111
Alignment explanation
Indices: 272786--273233 Score: 361
Period size: 113 Copynumber: 4.0 Consensus size: 111
272776 TGAAATGTGA
* * * * *
272786 CACTGACTTATGGGCTTTGAAAGG-TGCCATTGACTTGTGAGCTTTG-AAAGGTGCCACCGACTT
1 CACTAACTTATGGACTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAAAGTGCCA-TGACTT
* ** * * * * * * *
272849 GTGGGCTTTGAAAAAGATGTCGCTGACTTGTGGGCTCTCG-AAAGGTGC
65 GTGGGCTTTG-AAAAGGTACCACTAATTTATGGACTAT-GAAAAGATGC
* ** * * * *
272897 CACTAACTTGTGGGTTTTGAAAATG-TGCCATTGACTTATGAGCTTTTGAAAAAATGCCATTGAC
1 CACTAACTTATGGACTTTG-AAAGGATGCCATTGACTTGTGGGC-TTTGAAAAAGTGCCA-TGAC
* *
272961 TTGTGGGCTTTGAAAAGGTACCCCTAATTTATGGACT-TGGAAAATATGC
63 TTGTGGGCTTTGAAAAGGTACCACTAATTTATGGACTAT-GAAAAGATGC
* * * * * *
273010 CACTGATTTATGGACTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGGTGCTATAACTT
1 CACTAACTTATGGACTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAAA-GTGCCATGACTT
* * *
273075 GTGGGCTTTCGAAAAGGTGCCACTGATTTTTGGACTATGAAAAGATGC
65 GTGGGCTTT-GAAAAGGTACCACTAATTTATGGACTATGAAAAGATGC
* * * * *
273123 CACTAACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGGAAGAGTGACACTGACTT
1 CACTAACTTATGGACTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAAAGTGCCA-TGACTT
* * * * *
273188 GTGGGCTTTG-GAAGAGTGCCACTAACTTGTGGGCT-TGAAAAGATGC
65 GTGGGCTTTGAAAAG-GTACCACTAATTTATGGACTATGAAAAGATGC
273234 TACGGAGTTG
Statistics
Matches: 273, Mismatches: 54, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
111 30 0.11
112 71 0.26
113 148 0.54
114 24 0.09
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (111 bp):
CACTAACTTATGGACTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAAAGTGCCATGACTTG
TGGGCTTTGAAAAGGTACCACTAATTTATGGACTATGAAAAGATGC
Found at i:273083 original size:141 final size:140
Alignment explanation
Indices: 272755--273223 Score: 331
Period size: 141 Copynumber: 3.3 Consensus size: 140
272745 TTTGAAAATG
* * * * * * ** *
272755 TGCCATTAACTTGTTGGCTTTTGAAATGTGACACTGACTTATGGGCTTT-G-AAAGGTGCCATTG
1 TGCCACTAACTTGTGGGC-TTTGAAAAGTGCCACTAACTTGTGGGCTTTCGAAAAAATGCCACTG
* * * ** * * * * * *
272818 ACTTGT-GAGCTTTG-AAAGGTGCCACCGACTTGTGGGCTTTGAAAAAGATGTCGCTGACTTGTG
65 ACTTGTGGA-CTATGAAAAGATACCACTAACTTATGGAC-TTGGAAAAGATGCCACTGACTTATG
* *
272881 GGCTCTCGAAAGG-
128 GACT-TTGAAAGGA
* * * * * * *
272894 TGCCACTAACTTGTGGGTTTTGAAAATGTGCCATTGACTTATGAGCTTTTGAAAAAATGCCATTG
1 TGCCACTAACTTGTGGGCTTTGAAAA-GTGCCACTAACTTGTGGGCTTTCGAAAAAATGCCACTG
* * * * * * *
272959 ACTTGTGGGCTTTGAAAAGGTACCCCTAATTTATGGACTTGGAAAATATGCCACTGATTTATGGA
65 ACTTGTGGACTATGAAAAGATACCACTAACTTATGGACTTGGAAAAGATGCCACTGACTTATGGA
273024 CTTTGAAAGGA
130 CTTTGAAAGGA
* **
273035 TGCCACTAACTTGTGGGCTTTGAAAAAGGTGCTA-TAACTTGTGGGCTTTCGAAAAGGTGCCACT
1 TGCCACTAACTTGTGGGCTTTG-AAAA-GTGCCACTAACTTGTGGGCTTTCGAAAAAATGCCACT
* * * * * * * * *
273099 GATTTTTGGACTATGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTGG
64 GACTTGTGGACTATGAAAAGATACCACTAACTTATGGACTTGGAAAAGATGCCACTGACTTATGG
* *
273164 GCTTTGGAA-GA
129 ACTTTGAAAGGA
* * *
273175 GTGACACTGACTTGTGGGCTTTGGAAGAGTGCCACTAACTTGTGGGCTT
1 -TGCCACTAACTTGTGGGCTTT-GAAAAGTGCCACTAACTTGTGGGCTT
273224 GAAAAGATGC
Statistics
Matches: 263, Mismatches: 57, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
138 7 0.03
139 34 0.13
140 15 0.06
141 180 0.68
142 27 0.10
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (140 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGTGCCACTAACTTGTGGGCTTTCGAAAAAATGCCACTGA
CTTGTGGACTATGAAAAGATACCACTAACTTATGGACTTGGAAAAGATGCCACTGACTTATGGAC
TTTGAAAGGA
Found at i:273230 original size:28 final size:29
Alignment explanation
Indices: 272713--273230 Score: 362
Period size: 28 Copynumber: 18.4 Consensus size: 29
272703 ACTTGTGTAA
* **
272713 GCTTTGAAAAGAGTTGCCTCTGACTTGTAA
1 GCTTTGAAAAGAG-TGCCACTGACTTGTGG
* * * *
272743 GCTTTGAAAA-TGTGCCATTAACTTGTTG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* * *
272771 GCTTTTG-AAA-TGTGACACTGACTTATGG
1 GC-TTTGAAAAGAGTGCCACTGACTTGTGG
* *
272799 GCTTTG-AAAG-GTGCCATTGACTTGTGA
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
*
272826 GCTTTG-AAAG-GTGCCACCGACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
272853 GCTTTGAAAA-AGATGTCGCTGACTTGTGG
1 GCTTTGAAAAGAG-TGCCACTGACTTGTGG
* *
272882 GCTCTCG-AAAG-GTGCCACTAACTTGTGG
1 GCT-TTGAAAAGAGTGCCACTGACTTGTGG
* * * * *
272910 GTTTTGAAAA-TGTGCCATTGACTTATGA
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
272938 GCTTTTGAAAA-AATGCCATTGACTTGTGG
1 GC-TTTGAAAAGAGTGCCACTGACTTGTGG
* * * * *
272967 GCTTTGAAAAG-GTACCCCTAATTTATGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* * * * *
272995 ACTTGGAAAATA-TGCCACTGATTTATGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* * *
273023 ACTTTGAAAGGA-TGCCACTAACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
273051 GCTTTGAAAA-AGGTGCTA-TAACTTGTGG
1 GCTTTGAAAAGA-GTGCCACTGACTTGTGG
* *
273079 GCTTTCGAAAAG-GTGCCACTGATTTTTGG
1 GCTTT-GAAAAGAGTGCCACTGACTTGTGG
* * *
273108 ACTATGAAAAGA-TGCCACTAACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
273136 GCTTTGAAAGGA-TGCCATTGACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
273164 GCTTTG-GAAGAGTGACACTGACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
* *
273192 GCTTTG-GAAGAGTGCCACTAACTTGTGG
1 GCTTTGAAAAGAGTGCCACTGACTTGTGG
273220 GC-TTGAAAAGA
1 GCTTTGAAAAGA
273231 TGCTACGGAG
Statistics
Matches: 389, Mismatches: 79, Indels: 42
0.76 0.15 0.08
Matches are distributed among these distances:
27 59 0.15
28 250 0.64
29 68 0.17
30 12 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (29 bp):
GCTTTGAAAAGAGTGCCACTGACTTGTGG
Found at i:273326 original size:55 final size:55
Alignment explanation
Indices: 273214--273595 Score: 511
Period size: 55 Copynumber: 6.9 Consensus size: 55
273204 TGCCACTAAC
* * * * *
273214 TTGTGGGCTTGAAAA-GATGCTACGGAGTTGGGGAC-TTAAAAGGATGCCACGGTG
1 TTGTGGACTT-AAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
* *
273268 TTGTGGACTTAAAAGGATGCCACAAAGTTGTAGACTTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
* * *
273323 TTGTAGACTTAAAAGGATGCCATGGAGTTGTGGACTTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
* * * *
273378 TTGTGGACTTCAAAAGGATGCCACGGAGTTGTGGGCTTTAAAAAGATGCCACGAAG
1 TTGTGGACTT-AAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
* * * *
273434 TTGTGGACTTAAAAAGACGCCACGGAGTTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
*
273488 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
*
273543 TTGTGGACTTTAAAA-GATGCCACGAAGTTGTGGACTTTGAAAAGAAATGCCAC
1 TTGTGGAC-TTAAAAGGATGCCACGAAGTTGTGGACTTT-AAAAG-GATGCCAC
273596 TAAATCGTGG
Statistics
Matches: 292, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
53 4 0.01
54 73 0.25
55 147 0.50
56 61 0.21
57 7 0.02
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (55 bp):
TTGTGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAAGGATGCCACGGAG
Found at i:273580 original size:27 final size:28
Alignment explanation
Indices: 273214--273595 Score: 501
Period size: 27 Copynumber: 13.9 Consensus size: 28
273204 TGCCACTAAC
* * *
273214 TTGTGGGCTTGAAAA-GATGCTACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
* *
273241 TTGGGGAC-TTAAAAGGATGCCACGGTG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
**
273268 TTGTGGAC-TTAAAAGGATGCCACAAAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273295 TTGTAGACTTTAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
* *
273323 TTGTAGAC-TTAAAAGGATGCCATGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
273350 TTGTGGACTTTAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273378 TTGTGGACTTCAAAAGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
* * *
273406 TTGTGGGCTTTAAAAAGATGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
* *
273434 TTGTGGAC-TTAAAAAGACGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273461 TTGTGGAC-TTAAAACGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273488 TTGTGGAC-TTAAAAGGATGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273515 TTGTGGACTTTAAAGGGATGCCACGGAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273543 TTGTGGACTTTAAAA-GATGCCACGAAG
1 TTGTGGACTTTAAAAGGATGCCACGGAG
*
273570 TTGTGGACTTTGAAAAGAAATGCCAC
1 TTGTGGACTTT-AAAAG-GATGCCAC
273596 TAAATCGTGG
Statistics
Matches: 316, Mismatches: 32, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
26 5 0.02
27 168 0.53
28 136 0.43
30 7 0.02
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
TTGTGGACTTTAAAAGGATGCCACGGAG
Found at i:278941 original size:27 final size:27
Alignment explanation
Indices: 278903--278960 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
278893 ATGACATGAG
278903 ATCCGCTTAGAGGAAAAGGGTTGGAGT
1 ATCCGCTTAGAGGAAAAGGGTTGGAGT
278930 ATCCGCTTAGAGGAAAAGGGTTGGAGT
1 ATCCGCTTAGAGGAAAAGGGTTGGAGT
278957 ATCC
1 ATCC
278961 CGATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.22
Consensus pattern (27 bp):
ATCCGCTTAGAGGAAAAGGGTTGGAGT
Found at i:280498 original size:1 final size:1
Alignment explanation
Indices: 280494--280589 Score: 75
Period size: 1 Copynumber: 96.0 Consensus size: 1
280484 TTCTTTTTTC
* * * * ** * * *
280494 AAAAAAAAAACAAAAAACAACAAAAAAACAAAAAAAAATGAAAAAACAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
280559 AAAAAAAAACAAACAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
280590 GAAGAATCTG
Statistics
Matches: 70, Mismatches: 25, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:280510 original size:10 final size:10
Alignment explanation
Indices: 280494--280589 Score: 90
Period size: 11 Copynumber: 9.5 Consensus size: 10
280484 TTCTTTTTTC
280494 AAAAAAAA-A
1 AAAAAAAACA
*
280503 ACAAAAAACA
1 AAAAAAAACA
280513 ACAAAAAAAC-
1 A-AAAAAAACA
280523 AAAAAAAA-A
1 AAAAAAAACA
**
280532 TGAAAAAACA
1 AAAAAAAACA
280542 AAAAAAAACA
1 AAAAAAAACA
*
280552 AAAAAACAAAA
1 AAAAAA-AACA
280563 AAAAACAAACA
1 AAAAA-AAACA
*
280574 AAGAAAAAAGA
1 AA-AAAAAACA
280585 AAAAA
1 AAAAA
280590 GAAGAATCTG
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
9 20 0.28
10 21 0.30
11 26 0.37
12 4 0.06
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.01
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:280520 original size:18 final size:18
Alignment explanation
Indices: 280497--280582 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
280487 TTTTTTCAAA
*
280497 AAAAAAACAAAAAACAAC
1 AAAAAAACAAAAAAAAAC
*
280515 AAAAAAACAAAAAAAAAT
1 AAAAAAACAAAAAAAAAC
*
280533 GAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAAAAAC
280551 AAAAAAACAAAAAAAAAC
1 AAAAAAACAAAAAAAAAC
* *
280569 AAACAAAGAAAAAA
1 AAAAAAACAAAAAA
280583 GAAAAAAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.01
Consensus pattern (18 bp):
AAAAAAACAAAAAAAAAC
Found at i:281939 original size:55 final size:55
Alignment explanation
Indices: 281728--282590 Score: 853
Period size: 55 Copynumber: 15.0 Consensus size: 55
281718 CTTTTCAGTC
* * *
281728 AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
281783 AGCGGGACACCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAG
1 AGCAGG--A-CGTCT--TTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
** * * *
281844 AGCAGGACACCTTTCAAAG-CCACACAAGTTGGCGGCACCTTTCAGTCCTCAAAA
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
*
281898 AGTAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* *
281952 AGCAGGACGCCTTTTCTTTTAAAGCCCACATAAGTTGGTAGCACC-TTCAGTCCTCAAAG
1 AGCAGGACG-----TCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
282011 AGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGATGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGA--C---GTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
282072 AGCAGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAG
1 AGCAGGACG-----TCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * *
282131 AGCAGGACGCCTTCTCCTTTCAAAGCCCATACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAA
1 AGCAGGACG---TCT--TTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
* * * *
282192 AGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAG
* *
282247 AGCAGGATGCTTTTTCTTTTCAAAGCTCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
1 AGCAGGA--C---GTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * * *
282308 AGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAG
* *
282363 AGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAG
1 AGCAGGA--C---GTCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
** * * *
282424 AGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAG
** *
282479 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
* * * * *
282534 AGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAG
1 AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
282589 AG
1 AG
282591 GTAGGATGCA
Statistics
Matches: 685, Mismatches: 74, Indels: 98
0.80 0.09 0.11
Matches are distributed among these distances:
54 76 0.11
55 242 0.35
56 15 0.02
57 5 0.01
58 8 0.01
59 79 0.12
60 88 0.13
61 164 0.24
62 8 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (55 bp):
AGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
Found at i:282285 original size:116 final size:115
Alignment explanation
Indices: 281663--282599 Score: 1103
Period size: 116 Copynumber: 8.2 Consensus size: 115
281653 TTCGCCCTTT
* * * * *
281663 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AAAGCCCACGCAAGTTGGTGGCACTTTTCAG-
1 AGTCCTCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
281726 --TC----AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
65 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* ** * * * *
281772 AGTCCTCAAAGAGCGGGACACCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTC
1 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * *
281837 CTCAAAGAGCAGGACACCTTTCAAAG-CCACACAAGTTGGCGGCACCTTTC
66 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * *
281887 AGTCCTCAAAAAGTAGGA--C---GTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTC
1 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* * **
281945 CTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACATAAGTTGGTAGCACCTTC
66 CTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTC
* * *
282000 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTTAAAGCCCACACAAGTTGATGGCA-TTTTCCAGT
1 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
* **
282064 CCTCAAAGAGCAGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
65 CCTCAAAGAGCAGGACGC-----CTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * * * * *
282120 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTCAAAGCCCATACAAGTTGGTGGCA-TTTTCCAGT
1 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
* *
282184 CCTCAAAAAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
65 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
*
282235 TAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCTCACACAAGTTGGTGGCACCTTTCAGT
1 -AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
*
282300 CCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
65 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
282351 TAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 -AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* * *
282416 CCCCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCC
65 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT-C
** *
282468 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
1 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
* *
282527 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
66 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
*
282578 AGTCCTCAAAGAGGTAGGATGC
1 AGTCCTCAAAGA-GCAGGATGC
282600 ACTTTATTTT
Statistics
Matches: 728, Mismatches: 66, Indels: 64
0.85 0.08 0.07
Matches are distributed among these distances:
108 29 0.04
109 75 0.10
110 91 0.12
111 13 0.02
112 2 0.00
113 26 0.04
114 16 0.02
115 68 0.09
116 249 0.34
117 4 0.01
118 6 0.01
119 24 0.03
120 121 0.17
124 3 0.00
125 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (115 bp):
AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTC
CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:283420 original size:19 final size:18
Alignment explanation
Indices: 283396--283458 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
283386 AAACAGAAAA
283396 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
283415 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
283428 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
283447 TGTATCGATACA
1 TGTATCGATACA
283459 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:283433 original size:13 final size:13
Alignment explanation
Indices: 283415--283439 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
283405 ACATAAGTGT
283415 TGTATCGATACAA
1 TGTATCGATACAA
283428 TGTATCGATACA
1 TGTATCGATACA
283440 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:283435 original size:32 final size:32
Alignment explanation
Indices: 283394--283466 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
283384 ACAAACAGAA
283394 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
283426 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
283458 AATGTATCG
1 AATGTATCG
283467 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:283529 original size:13 final size:13
Alignment explanation
Indices: 283511--283536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283501 ATTAAGAAAA
283511 TGTATCGATACAT
1 TGTATCGATACAT
283524 TGTATCGATACAT
1 TGTATCGATACAT
283537 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:285949 original size:52 final size:52
Alignment explanation
Indices: 285876--286010 Score: 175
Period size: 52 Copynumber: 2.6 Consensus size: 52
285866 GTTAAGTTTC
* *
285876 CCAATTGTT-CACAATAGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACA
1 CCAATT-TTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACA
** *
285927 CCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACA
1 CCAATTTTCC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACA
* *
285980 CCAATTTTTCACAATCGAGGATACTCCAACC
1 CCAATTTTCCACAATCGGGGATACTCCAACC
286011 TCTTTATTTC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
50 2 0.03
51 7 0.10
52 47 0.66
53 15 0.21
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (52 bp):
CCAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACA
Found at i:286139 original size:79 final size:79
Alignment explanation
Indices: 286024--286205 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 79
286014 TTATTTCATC
** *
286024 GGGGATACTCCAACCCCGTTACCTCCGCGGGCATACTCCAACCTCGG-CTTTATTTCCAAAAT-A
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGCATACTCCAACC-CGGACTTTATTTCC-AAATCA
* * *
286087 TTGATTTCTCATAATT
64 TCGATTTCTCACAACT
* * * * *
286103 GGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCGGATTTTATTTCCTAATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGCATACTCCAACCCGGACTTTATTTCCAAATCATC
*
286168 GATTTTTCACAACT
66 GATTTCTCACAACT
*
286182 GGGGATACTCTAACCCCGTTATTT
1 GGGGATACTCCAACCCCGTTATTT
286206 TCAAGGGGAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 6 0.07
79 82 0.93
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGCATACTCCAACCCGGACTTTATTTCCAAATCATC
GATTTCTCACAACT
Found at i:288005 original size:21 final size:21
Alignment explanation
Indices: 287980--288035 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
287970 TTTTTTTCTA
*
287980 TCTCTTTGTTTCTATTTCTTC
1 TCTCTTTCTTTCTATTTCTTC
* *
288001 TCTCTTTTCTTTCTTTTTTTTC
1 TCTC-TTTCTTTCTATTTCTTC
* *
288023 TCTTTTTTTTTCT
1 TCTCTTTCTTTCT
288036 TTCTTTTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (21 bp):
TCTCTTTCTTTCTATTTCTTC
Found at i:288036 original size:21 final size:21
Alignment explanation
Indices: 287969--288042 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
287959 GCTAGCCTTA
* *
287969 TTTTTTTTCTATCTCTTTGTTTC
1 TTTTTTTTC--TCTTTTTCTTTC
* *
287992 TATTTCTTCTCTCTTTTCTTTC
1 TTTTTTTTCTCT-TTTTCTTTC
*
288014 TTTTTTTTCTCTTTTTTTTTC
1 TTTTTTTTCTCTTTTTCTTTC
*
288035 TTTCTTTT
1 TTTTTTTT
288043 AGTTGAACCT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.43
22 17 0.40
23 7 0.17
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTTTTTTCTCTTTTTCTTTC
Found at i:289434 original size:22 final size:22
Alignment explanation
Indices: 289415--289462 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
289405 AAGCAAAAGC
289415 AAAAAAAA-TG-AAAAGAAAAA
1 AAAAAAAAGTGCAAAAGAAAAA
*
289435 AAAAAAAAGTGCAAAAGTAAAA
1 AAAAAAAAGTGCAAAAGAAAAA
*
289457 TAAAAA
1 AAAAAA
289463 GGGAACAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.08
Consensus pattern (22 bp):
AAAAAAAAGTGCAAAAGAAAAA
Found at i:290328 original size:912 final size:912
Alignment explanation
Indices: 288694--290442 Score: 2958
Period size: 912 Copynumber: 1.9 Consensus size: 912
288684 AAGGAAAAAG
*
288694 CAACTTTTGATGATGAGTCACGTTGAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAATTTCAA
1 CAACTTTTGACGATGAGTCACGTTGAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAATTTCAA
288759 GACAACCTATTTACCTTTGCCCAATGGCATGTAGAGATCTTGTGCAATGGCACATTTATCAAATA
66 GACAACCTATTTACCTTTGCCCAATGGCATGTAGAGATCTTGTGCAATGGCACATTTATCAAATA
288824 TTATCAATGAAAATAAATTTTGCATAAATCATTTCGTCATCCCTATTCAACTTGTTATCCATACA
131 TTATCAATGAAAATAAATTTTGCATAAATCATTTCGTCATCCCTATTCAACTTGTTATCCATACA
*
288889 TGTTCCTATCTTCAACTTTATCTTTTGCCCATCACATTTTGTCAAATTGTTTGTTCTTACACTTA
196 TGTTCCTATCTTCAACTTTATCTTTTGCCCATCACATTTTGTCAAATTGTTTGTTCTCACACTTA
288954 TTAGATGCATTGATAAAAATGACATAAATGTTCACGATAAGCAACTAGAGATCAATTTCGAAAGT
261 TTAGATGCATTGATAAAAATGACATAAATGTTCACGATAAGCAACTAGAGATCAATTTCGAAAGT
*
289019 GAACTTGCCAAATCAACTGGGCAATGCCACAAGATTGCCCTACGGCACCATCATGATTCTTAGTC
326 GAACTTGCCAAATCAACTGGGCAATGCCACAAGATTACCCTACGGCACCATCATGATTCTTAGTC
289084 TTGCCTTTCCACTTTAACTTCCAAAGTTAACTTTCTCTAAGAGATAGCTTTCAGTTCACAAGGCA
391 TTGCCTTTCCACTTTAACTTCCAAAGTTAACTTTCTCTAAGAGATAGCTTTCAGTTCACAAGGCA
* *
289149 GAGTGATCGAAATGAGAAATGACCTTATTTGATCATCCGTTCTTAAAAAAAAATCCTTTGCCACC
456 CAGTGATCGAAATGAGAAATGACCTTATTTCATCATCCGTTCTTAAAAAAAAATCCTTTGCCACC
*
289214 CCTTGAGCCTGACAAATTCTTTTTTTTTGAAACCCTGATCAAGGATCACTTCCTACATTTTGGGG
521 CCTTGAGCCTGACAAATTCTTTTTTTTTGAAACCCTGATCAAGGATCACTTCCTACATTTGGGGG
289279 GCAAATAAAAATTCGTCTAGAAGTATGGGTGTAGAAATGTTTGTCCTTAAATTTTGAGAATGCCC
586 GCAAATAAAAATTCGTCTAGAAGTATGGGTGTAGAAATGTTTGTCCTTAAATTTTGAGAATGCCC
* * *
289344 CAACAATAATGGGCGAATCAAAAAAGTACAAAGTTCATTTAAAATGACGAAAAAAAGTT-G-AAA
651 CAACAATAAGGGGCGAATAAAAAAAGTACAAAGTTCAGTTAAAATGACG-AAAAAAGTTAGAAAA
*
289407 GCAAAAGCAAAA-AAAATGAAAAGAAAAAAAAAAAAAG-T-GCAAAAGTA-AAAT-AAAAAGGGA
715 GCAAAA-CAAAATAAAATG-AAAG-AAAACAAAAAAAGTTGGCAAAAGTATAAATAAAAAAGGGA
*
289467 A-CAACAAAAGTAAAAAAATAAGGACATGAATGCCCATATAAACAAAAATGATCATCAATGGAAC
777 ACCAACAAAAAT-AAAAAATAAGGACATGAATGCCCATATAAACAAAAATGATCATCAATGGAAC
289531 CCCCTACCGAGCCATACTGAGCCAGCAAACCATCAATCTTGAGCAAAGGAATCCATCCCCATCCG
841 CCCCTACCGAGCCATACTGAGCCAGCAAACCATCAATCTTGAGCAAAGGAATCCATCCCCATCCG
289596 TTAGAGT
906 TTAGAGT
289603 CAACTTTTGACGATGGAGTCGA-GTTGAAAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAATT
1 CAACTTTTGACGAT-GAGTC-ACGTTG--AATCCTTGCACTTTTCTTGCTTATTTTGTGTAAATT
*
289667 TCAAGACAACCTATTTACCTTTGCCCAATGGCATGTAGAGATCTTGTGCAATGGCACCTTTATCA
62 TCAAGACAACCTATTTACCTTTGCCCAATGGCATGTAGAGATCTTGTGCAATGGCACATTTATCA
289732 AATATTATCAATGAAAATAAATTTTGCATAAATCATTTCGTCATCCCTATTCAACTTGTTATCCA
127 AATATTATCAATGAAAATAAATTTTGCATAAATCATTTCGTCATCCCTATTCAACTTGTTATCCA
*
289797 TACATGTTCCTATCTTCAACTTTATCTTTTGCCCATCACATTTTGTCAATTTTGTTTGTTCTCAC
192 TACATGTTCCTATCTTCAACTTTATCTTTTGCCCATCACATTTTGTCAA-ATTGTTTGTTCTCAC
*
289862 ACTTCTTAGATGCATTGATAAAAATGACATAAATGTTCACGATAAGCAACTAGAGATCAATTTCG
256 ACTTATTAGATGCATTGATAAAAATGACATAAATGTTCACGATAAGCAACTAGAGATCAATTTCG
289927 AAAGTGAACTTGCCAAATCAAATCTGGGGCAATGCCACAAGATTACCCTACGGCACCATCATGAT
321 AAAGTGAACTTGCCAAATC-AA-CT-GGGCAATGCCACAAGATTACCCTACGGCACCATCATGAT
*
289992 TCTTAGTCTTGCCTTTCCACTTTAAACTTCCAAAGTTAACTTTCTCTAAGAGATAGTTTCTCAGT
383 TCTTAGTCTTGCCTTTCCACTTT-AACTTCCAAAGTTAACTTTCTCTAAGAGATAGCTT-TCAGT
*
290057 TCACAA-G-ACAGTGATCGAAATGAGAAATGACCTTCTTTCATCATCC-TCTCTTAAAAAAAAAT
446 TCACAAGGCACAGTGATCGAAATGAGAAATGACCTTATTTCATCATCCGT-TCTTAAAAAAAAAT
290119 CCTTTGCCAACCCCTTTGAGCCTGACAAATTC-TTTTTTTTGAAACCCTGATCAAGGATCACTTC
510 CCTTTGCC-ACCCC-TTGAGCCTGACAAATTCTTTTTTTTTGAAACCCTGATCAAGGATCACTTC
* *
290183 TTACATTTGGGGGGCAAATGAAAATTCGTCTAAGAAGTATGGGTGTAGAAATG-TTGTCCTTAAA
573 CTACATTTGGGGGGCAAATAAAAATTCGTCT-AGAAGTATGGGTGTAGAAATGTTTGTCCTTAAA
290247 TTTTGAGAATG-CCCAACAATAAGGGGCGAATAAAAAAAGTACCAAAGTTCCCAGTTAAAATTGA
637 TTTTGAGAATGCCCCAACAATAAGGGGCGAATAAAAAAAGTA-CAAAGTT--CAGTTAAAA-TGA
* * *
290311 TG-AAAAAGTT-G-AAAGCAAAAGCAAAATAAAATGAAAGAAAACAAAAAAAGTTGGTAAACGTA
698 CGAAAAAAGTTAGAAAAGCAAAA-CAAAATAAAATGAAAGAAAACAAAAAAAGTTGGCAAAAGTA
*
290373 TAAATAAAAAAGGGAACCAACAAAAATAAAAAATAAGGACATGAATGCCTATATAAACAAAAATG
762 TAAATAAAAAAGGGAACCAACAAAAATAAAAAATAAGGACATGAATGCCCATATAAACAAAAATG
290438 ATCAT
827 ATCAT
290443 TGCTCCAATC
Statistics
Matches: 794, Mismatches: 22, Indels: 36
0.93 0.03 0.04
Matches are distributed among these distances:
909 13 0.02
910 9 0.01
911 1 0.00
912 214 0.27
913 96 0.12
914 2 0.00
915 3 0.00
916 147 0.19
917 141 0.18
918 78 0.10
919 21 0.03
920 8 0.01
921 52 0.07
922 9 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (912 bp):
CAACTTTTGACGATGAGTCACGTTGAATCCTTGCACTTTTCTTGCTTATTTTGTGTAAATTTCAA
GACAACCTATTTACCTTTGCCCAATGGCATGTAGAGATCTTGTGCAATGGCACATTTATCAAATA
TTATCAATGAAAATAAATTTTGCATAAATCATTTCGTCATCCCTATTCAACTTGTTATCCATACA
TGTTCCTATCTTCAACTTTATCTTTTGCCCATCACATTTTGTCAAATTGTTTGTTCTCACACTTA
TTAGATGCATTGATAAAAATGACATAAATGTTCACGATAAGCAACTAGAGATCAATTTCGAAAGT
GAACTTGCCAAATCAACTGGGCAATGCCACAAGATTACCCTACGGCACCATCATGATTCTTAGTC
TTGCCTTTCCACTTTAACTTCCAAAGTTAACTTTCTCTAAGAGATAGCTTTCAGTTCACAAGGCA
CAGTGATCGAAATGAGAAATGACCTTATTTCATCATCCGTTCTTAAAAAAAAATCCTTTGCCACC
CCTTGAGCCTGACAAATTCTTTTTTTTTGAAACCCTGATCAAGGATCACTTCCTACATTTGGGGG
GCAAATAAAAATTCGTCTAGAAGTATGGGTGTAGAAATGTTTGTCCTTAAATTTTGAGAATGCCC
CAACAATAAGGGGCGAATAAAAAAAGTACAAAGTTCAGTTAAAATGACGAAAAAAGTTAGAAAAG
CAAAACAAAATAAAATGAAAGAAAACAAAAAAAGTTGGCAAAAGTATAAATAAAAAAGGGAACCA
ACAAAAATAAAAAATAAGGACATGAATGCCCATATAAACAAAAATGATCATCAATGGAACCCCCT
ACCGAGCCATACTGAGCCAGCAAACCATCAATCTTGAGCAAAGGAATCCATCCCCATCCGTTAGA
GT
Found at i:291824 original size:28 final size:28
Alignment explanation
Indices: 291711--292464 Score: 713
Period size: 28 Copynumber: 27.2 Consensus size: 28
291701 AGTAGTATTT
*
291711 CTTTTCAAAATCCACAACTCCGTGGCAT-
1 CTTTT-AAAGTCCACAACTCCGTGGCATC
* *
291739 CTTTTTATGTCCACAACTCCGTGGCAT-
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * *
291766 CTTTTTATGTCCACAACTCTGTGGCAATC
1 CTTTTAAAGTCCACAACTCCGTGGC-ATC
* *
291795 CCTTTAAAGTCCACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* *
291823 CCTTTAAAGTCCACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
*
291851 CCTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
*
291879 CTTTT-AAGT-CACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
291905 TTTTTTAAGTCCACAACTTCGTGGTATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* *
291933 TTTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
*
291961 CTTTTGAAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* **
291989 CTTTTAAAGTCCACAACTCCATGGTGTC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * *
292017 CCTTT-AAGTCCACAATTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
*
292044 CTTTTAAAGTCCACAACTTCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * *
292072 TTTTTAAAATCCACAACTCCGTGACATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
**
292100 CTTTTAAAGTCCACAACTCCGCAGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
292128 CTTTT-AAGTCCACAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* *
292155 TTTTTAAAGTCCACAACTCCATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
*
292183 TTTTTAAAGTCCACAACTCCGTGGCAT-
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * *
292210 CTTTTTAAGTCTATAACTCCGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * * *
292238 CTTTT-AAGCCCACAAGTCAGTGGCACC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
** * * * **
292265 CTTCCAAAGCCCATAAGTCAATGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * * * *
292293 CTTTCAAAGCCCACAAGTCAGTGACA-C
1 CTTTTAAAGTCCACAACTCCGTGGCATC
** * * *
292320 CTTCCAAAGCCCACAAGTCAGTGGCAT-
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* *
292347 CTTTTCAAAGTCCACAAATCAGTGGCA-C
1 CTTTT-AAAGTCCACAACTCCGTGGCATC
* * ** *
292375 CTTTTCAAAAGCCCACAAGTTAGTGGCACC
1 CTTTT--AAAGTCCACAACTCCGTGGCATC
* * * *
292405 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTTAAAGTCCACAACTCCGTGGCATC
* * * * *
292433 ATTTCAAAGTCCATAAATCAGTGGCA-C
1 CTTTTAAAGTCCACAACTCCGTGGCATC
292460 CTTTT
1 CTTTT
292465 CCAAGTGCAT
Statistics
Matches: 629, Mismatches: 84, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
26 20 0.03
27 172 0.27
28 394 0.63
29 38 0.06
30 5 0.01
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCGTGGCATC
Found at i:291882 original size:83 final size:83
Alignment explanation
Indices: 291721--292464 Score: 675
Period size: 83 Copynumber: 9.0 Consensus size: 83
291711 CTTTTCAAAA
* * * * *
291721 TCCACAACTCCGTGGCAT-CTTTTTATGTCCACAACTCCGTGGCAT-CTTTTTATGTCCACAACT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
* *
291784 CTGTGGCAATCCCTTTAAAG
66 CCGTGGC-AT-CCTTTTAAG
* * *
291804 TCCACAACTCCATGGCATCCCTTTAAAGTCCACAACTCCATGGCATCCCTTTAAAGTCCACAACT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
291869 CCGTGGCATCCTTTTAAG
66 CCGTGGCATCCTTTTAAG
* * * * * * * *
291887 T-CACAACTCCATGGCATCTTTTTTAAGTCCACAACTTCGTGGTATCTTTTTTAAGTCCACAACT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
291951 CCGTGGCATCCTTTTGAAG
66 CCGTGGCATCCTTTT-AAG
** * *
291970 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGTGTCCCTTT-AAGTCCACAATT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
*
292034 CCATGGCATCCTTTTAAAG
66 CCGTGGCATCCTTTT-AAG
* * * * *
292053 TCCACAACTTCGTGGCATCTTTTTAAAATCCACAACTCCGTGACATCCTTTTAAAGTCCACAACT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
**
292118 CCGCAGCATCCTTTTAAG
66 CCGTGGCATCCTTTTAAG
* *
292136 TCCACAACTCCGTGGCATCTTTTTAAAGTCCACAACTCCATGGCATCTTTTTAAAGTCCACAACT
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
*
292201 CCGTGGCATCTTTTTAAG
66 CCGTGGCATCCTTTTAAG
* * * * * ** * * *
292219 TCTATAACTCCGTGGCATCCTTTT-AAGCCCACAAGT-CAGTGGCACCCTTCCAAAGCCCATAAG
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCA-TGGCATCCTTTTAAAGTCCACAAC
** *
292282 TCAATGGCATCCTTTCAAAG
65 TCCGTGGCATCCTTT-TAAG
* * * * ** * *
292302 CCCACAAGTCAGTGACA-CCTTCCAAAGCCCACAAGT-CAGTGGCAT-CTTTTCAAAGTCCACAA
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCA-TGGCATCCTTTT-AAAGTCCACAA
* *
292364 ATCAGTGGCA-CCTTTTCAAAAG
64 CTCCGTGGCATCCTTTT---AAG
* * ** * * * * * * * *
292386 CCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGT-CAGTGGCATCATTTCAAAGTCCATAAA
1 TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCA-TGGCATCCTTTTAAAGTCCACAAC
*
292450 TCAGTGGCA-CCTTTT
65 TCCGTGGCATCCTTTT
292465 CCAAGTGCAT
Statistics
Matches: 559, Mismatches: 88, Indels: 26
0.83 0.13 0.04
Matches are distributed among these distances:
81 2 0.00
82 120 0.21
83 252 0.45
84 108 0.19
85 74 0.13
86 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (83 bp):
TCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACT
CCGTGGCATCCTTTTAAG
Found at i:291894 original size:111 final size:111
Alignment explanation
Indices: 291711--292308 Score: 677
Period size: 111 Copynumber: 5.4 Consensus size: 111
291701 AGTAGTATTT
* * * * * *
291711 CTTTTCAAAATCCACAACTCCGTGGCAT-CTTTTTATGTCCACAACTCCGTGGCATCTTTTTATG
1 CTTTT-AAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAG
* *
291775 TCCACAACTCTGTGGCAATCCCTTTAAAGTCCACAACTCCATGGCATC
65 TCCACAACTCCGTGGC-ATCCCTTTTAAGTCCACAACTCCATGGCATC
* *
291823 CCTTTAAAGTCCACAACTCCATGGCATCCCTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
1 CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
* ** * * *
291888 -CACAACTCCATGGCATCTTTTTTAAGTCCACAACTTCGTGGTATC
66 CCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCATGGCATC
* * * *
291933 TTTTTTAAGTCCACAACTCCGTGGCATCCTTTTGAAGTCCACAACTCCGTGGCATCCTTTTAAAG
1 CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAG
* ** *
291998 TCCACAACTCCATGGTGTCCC-TTTAAGTCCACAATTCCATGGCATC
65 TCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCATGGCATC
* * * * *
292044 CTTTTAAAGTCCACAACTTCGTGGCATCTTTTTAAAATCCACAACTCCGTGACATCCTTTTAAAG
1 CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTT-AAG
** *
292109 TCCACAACTCCGCAGCAT-CCTTTTAAGTCCACAACTCCGTGGCATC
65 TCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCATGGCATC
* * *
292155 TTTTTAAAGTCCACAACTCCATGGCATCTTTTTAAAGTCCACAACTCCGTGGCATCTTTTTAAGT
1 CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
* * * * *
292220 CTATAACTCCGTGGCAT-CCTTTTAAGCCCACAAGT-CAGTGGCACC
66 CCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCA-TGGCATC
** * * * * * *
292265 CTTCCAAAGCCCATAAGTCAATGGCATCCTTTCAAAGCCCACAA
1 CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAA
292309 GTCAGTGACA
Statistics
Matches: 413, Mismatches: 68, Indels: 12
0.84 0.14 0.02
Matches are distributed among these distances:
109 1 0.00
110 155 0.38
111 206 0.50
112 51 0.12
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (111 bp):
CTTTTAAAGTCCACAACTCCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAGT
CCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCATGGCATC
Found at i:292465 original size:28 final size:28
Alignment explanation
Indices: 291711--292805 Score: 440
Period size: 28 Copynumber: 39.1 Consensus size: 28
291701 AGTAGTATTT
* * * *
291711 CTTTTCAAAATCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * * * *
291739 CTTTT-TATGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * * *
291766 CTTTT-TATGTCCACAACTCTGTGGCAATC
1 CTTTTCAAAGTCCACAAGTCAGTGGC-A-C
* *
291795 CCTTT-AAAGTCCACAACTCCA-TGGCATC
1 CTTTTCAAAGTCCACAAGT-CAGTGGCA-C
* *
291823 CCTTT-AAAGTCCACAACTCCA-TGGCATC
1 CTTTTCAAAGTCCACAAGT-CAGTGGCA-C
* * *
291851 CCTTT-AAAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* *
291879 CTTTT--AAGT-CACAACTCCA-TGGCAT
1 CTTTTCAAAGTCCACAAGT-CAGTGGCAC
** * * *
291904 CTTTTTTAAGTCCACAACTTC-GTGGTAT
1 CTTTTCAAAGTCCACAA-GTCAGTGGCAC
** * *
291932 CTTTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* * *
291961 CTTTT-GAAGTCCACAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* *
291989 CTTTT-AAAGTCCACAACTCCATGGTGTC-C
1 CTTTTCAAAGTCCACAAGT-CA--GTGGCAC
*
292018 C-TTT--AAGTCCACAATTCCA-TGGCATC
1 CTTTTCAAAGTCCACAAGT-CAGTGGCA-C
* *
292044 CTTTT-AAAGTCCACAACTTC-GTGGCAT
1 CTTTTCAAAGTCCACAA-GTCAGTGGCAC
* * * * *
292071 CTTTTTAAAATCCACAACTCCGTGACATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* * **
292100 CTTTT-AAAGTCCACAACTCCGCAGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* * *
292128 CTTTT--AAGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * *
292154 CTTTTTAAAGTCCACAACTCCA-TGGCAT
1 CTTTTCAAAGTCCACAAGT-CAGTGGCAC
* * * *
292182 CTTTTTAAAGTCCACAACTCCGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * * * *
292210 CTTTT-TAAGTCTATAACTCCGTGGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
*
292238 CTTTT--AAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * * * *
292264 CCTTCCAAAGCCCATAAGTCAATGGCATC
1 CTTTTCAAAGTCCACAAGTCAGTGGCA-C
* *
292293 C-TTTCAAAGCCCACAAGTCAGTGACAC
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * *
292320 C-TTCCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
*
292347 CTTTTCAAAGTCCACAAATCAGTGGCAC
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* *
292375 CTTTTCAAAAGCCCACAAGTTAGTGGCAC
1 CTTTTC-AAAGTCCACAAGTCAGTGGCAC
* * *
292404 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * *
292432 CATTTCAAAGTCCATAAATCAGTGGCAC
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * * * * *
292460 CTTTTCCAAGTGCATAAATTAGTGGTAC
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* * ** *
292488 TTTTTAAAAACCCACAAGTCAGTGGCAT
1 CTTTTCAAAGTCCACAAGTCAGTGGCAC
* *
292516 TTTTTCAAAAG-CTCATAAGTCAGTGGCTAC
1 CTTTTC-AAAGTC-CACAAGTCAGTGGC-AC
*
292546 CTTTTCAAAAGT-CACAAGTCGGTGGCAC
1 CTTTTC-AAAGTCCACAAGTCAGTGGCAC
* * * * *
292574 CTTTTGACGAGCCCACAAGTCATTGATCCATC
1 CTTTTCA-AAGTCCACAAGTCAGTG--GCA-C
**
292606 C-TTTC-AAG-CCATACAAGTC-GTAACAC
1 CTTTTCAAAGTCC--ACAAGTCAGTGGCAC
* *
292632 C-TTTCAAAAGCCCAACAAAGTCGGTGGCA-
1 CTTTTC-AAAGTCC-AC-AAGTCAGTGGCAC
*
292661 CATTTCAAAG-CCTACAAGTCAGTGGCAC
1 CTTTTCAAAGTCC-ACAAGTCAGTGGCAC
*
292689 CTTTT-AAAG-CTCACAAGTCAGTGTCA-
1 CTTTTCAAAGTC-CACAAGTCAGTGGCAC
* * *
292715 CATTTCAAAAG-CCAACAAGTCAATGGTAC
1 CTTTTC-AAAGTCC-ACAAGTCAGTGGCAC
* * * *
292744 CTTTTCAAAGCCCACAAATTAGTAGCAACC
1 CTTTTCAAAGTCCACAAGTCAGTGGC-A-C
**
292774 CTTTTCAAAGCTCACACAAGTTGGTGGCAC
1 CTTTTCAAAG-TC-CACAAGTCAGTGGCAC
292804 CT
1 CT
292806 ATGTCCGAGT
Statistics
Matches: 877, Mismatches: 128, Indels: 122
0.78 0.11 0.11
Matches are distributed among these distances:
24 3 0.00
25 5 0.01
26 33 0.04
27 190 0.22
28 458 0.52
29 123 0.14
30 41 0.05
31 11 0.01
32 13 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (28 bp):
CTTTTCAAAGTCCACAAGTCAGTGGCAC
Found at i:292685 original size:27 final size:27
Alignment explanation
Indices: 292649--292760 Score: 109
Period size: 27 Copynumber: 4.1 Consensus size: 27
292639 AAGCCCAACA
*
292649 AAGTCGGTGGCACATTTCAAAGCCTAC
1 AAGTCAGTGGCACATTTCAAAGCCTAC
* *
292676 AAGTCAGTGGCACCTTTTAAAG-CTCAC
1 AAGTCAGTGGCACATTTCAAAGCCT-AC
* *
292703 AAGTCAGTGTCACATTTCAAAAGCCAAC
1 AAGTCAGTGGCACATTTC-AAAGCCTAC
* * * *
292731 AAGTCAATGGTACCTTTTCAAAGCCCAC
1 AAGTCAGTGGCA-CATTTCAAAGCCTAC
292759 AA
1 AA
292761 ATTAGTAGCA
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.03
27 36 0.52
28 25 0.36
29 6 0.09
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (27 bp):
AAGTCAGTGGCACATTTCAAAGCCTAC
Done.