Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013461.1 Kokia drynarioides strain JFW-HI SEQ_128487, 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: 46827
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:475 original size:15 final size:16
Alignment explanation
Indices: 455--490 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
445 TTGGGCCTAT
*
455 TTGGGTCA-TTTGTAA
1 TTGGGTCATTTTCTAA
470 TTGGGTCATTTTCTAA
1 TTGGGTCATTTTCTAA
486 TTGGG
1 TTGGG
491 CCAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.17, C:0.08, G:0.28, T:0.47
Consensus pattern (16 bp):
TTGGGTCATTTTCTAA
Found at i:572 original size:34 final size:33
Alignment explanation
Indices: 534--602 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
524 TTGGACATTT
* *
534 TAAATTTAAATTT-ATAATAAATTTAAATTTCAAA
1 TAAATTT-AATTTAAAAATAAACTT-AATTTCAAA
*
568 TAAATTTAATTTAAAAATAAACTTAATTTCCAA
1 TAAATTTAATTTAAAAATAAACTTAATTTCAAA
601 TA
1 TA
603 GGCCCAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (33 bp):
TAAATTTAATTTAAAAATAAACTTAATTTCAAA
Found at i:585 original size:17 final size:17
Alignment explanation
Indices: 534--593 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
524 TTGGACATTT
*
534 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
551 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
568 TAAATTT-AATTTAAAAA
1 TAAATTTAAATTT-AAAA
*
585 TAAACTTAA
1 TAAATTTAA
594 TTTCCAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 5 0.14
17 31 0.84
18 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1323 original size:206 final size:207
Alignment explanation
Indices: 969--1440 Score: 777
Period size: 206 Copynumber: 2.3 Consensus size: 207
959 TTTATTGCGA
* *
969 GTGGGTTTGATTTGGTCATCTTCTCAGTATTTCATCAGGAAGATGACCGCGTCGTTTGTTTCAAT
1 GTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAAT
** * * * *
1034 TTTCTTTTCTGTATCTTATCAGGAAGACGAATTTGGTTCATTCCTCAGTATCTCATCAGGAAGCT
66 TCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCT
**
1099 ATTTGTTTTATTACTTCGAACTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTT-
131 ATCCGTTTTATTACTTCGAACTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
1163 CTCACTTTGAA-C
196 CTCACTTT-AAGC
* *
1175 GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCTGATCGCGTCGTTTGTTTCAAT
1 GTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAAT
*
1240 TCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCTTCAGTATCTCATCAGGAAGCT
66 TCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCT
*
1305 ATCCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
131 ATCCGTTTTATTACTTCGAACTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
*
1370 CTCGCTTTAAGC
196 CTCACTTTAAGC
*
1382 GTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGCTAACCGCGTCGTTTGT
1 GTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGCTGACCGCGTCGTTTGT
1441 GGGTATCGCA
Statistics
Matches: 246, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
206 182 0.74
207 64 0.26
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (207 bp):
GTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAAT
TCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATCTCATCAGGAAGCT
ATCCGTTTTATTACTTCGAACTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTTG
CTCACTTTAAGC
Found at i:1946 original size:29 final size:29
Alignment explanation
Indices: 1907--1963 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1897 GTCGTATTCC
*
1907 AAAAAAAAGGATCAAAGGAAACGATCATA
1 AAAAAAAAGGATCAAAGGAAACAATCATA
1936 AAAAAAAAGGATCAAAGGAAACAATCAT
1 AAAAAAAAGGATCAAAGGAAACAATCAT
1964 TAGTTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.11, G:0.16, T:0.11
Consensus pattern (29 bp):
AAAAAAAAGGATCAAAGGAAACAATCATA
Found at i:13311 original size:30 final size:28
Alignment explanation
Indices: 13270--13502 Score: 193
Period size: 29 Copynumber: 8.0 Consensus size: 28
13260 CAAACATCCG
13270 GGGGT-AAAATGGTAATTTTTGGAAGTTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTC
*
13298 AGGGGTAAAAATGGAATTTTTGG-AGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTC
* *
13327 GGGGTCAAAAATGCG-GTTTTTGGAAGTTTA
1 GGGGT-AAAAATG-GAATTTTTGGAAG-TTC
* * *
13357 AGGGTAAAATTGGAATTTATGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAG-TTC
* *
13386 GGGGCCAAAAATGGGATTTTTGGAAGTTC
1 GGGG-TAAAAATGGAATTTTTGGAAGTTC
* * *
13415 GAGGGTAAAAATAGAATTTTTGAAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTC
* *
13445 AGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTC
**
13474 GGAGGTAAAAACAGAATTTTTGGACAGTT
1 GG-GGTAAAAATGGAATTTTTGGA-AGTT
13503 TAGAGACCTT
Statistics
Matches: 165, Mismatches: 27, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
28 8 0.05
29 94 0.57
30 63 0.38
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTC
Found at i:13505 original size:59 final size:60
Alignment explanation
Indices: 13275--13503 Score: 263
Period size: 59 Copynumber: 3.9 Consensus size: 60
13265 ATCCGGGGGT
* * * *
13275 AAAATGGTAATTTTTGGAAGTTCAG-GGGTAAAAATGGAATTTTTGG-AGTTTTGGGGTCA
1 AAAATGG-GATTTTTGGAAGTTCGGAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTCA
** * * * ** *
13334 AAAATGCGG-TTTTTGGAAGTT-TAAGGGTAAAATTGGAATTTATGGAAGTTTCGGGGCCA
1 AAAATG-GGATTTTTGGAAGTTCGGAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTCA
*
13393 AAAATGGGATTTTTGGAAGTTC-GAGGGTAAAAATAGAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGGGATTTTTGGAAGTTCGGAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTCA
*
13452 AAAATGGGATTTTTGGAAGTTCGGA-GGTAAAAACAGAATTTTTGGACAGTTT
1 AAAATGGGATTTTTGGAAGTTCGGAGGGTAAAAATAGAATTTTTGGA-AGTTT
13504 AGAGACCTTC
Statistics
Matches: 146, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
58 33 0.23
59 105 0.72
60 8 0.05
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (60 bp):
AAAATGGGATTTTTGGAAGTTCGGAGGGTAAAAATAGAATTTTTGGAAGTTTTAGGGTCA
Found at i:15306 original size:16 final size:15
Alignment explanation
Indices: 15280--15320 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
15270 GGCCTATTTG
15280 GGCCATTTGTAATTA
1 GGCCATTTGTAATTA
*
15295 GGCCATTTTGTAATTG
1 GGCCA-TTTGTAATTA
15311 GGCCAATTTG
1 GGCC-ATTTG
15321 ATCTGTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (15 bp):
GGCCATTTGTAATTA
Found at i:15365 original size:6 final size:6
Alignment explanation
Indices: 15354--15432 Score: 69
Period size: 6 Copynumber: 13.8 Consensus size: 6
15344 AATTGGACAT
*
15354 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * **
15400 TTTAAA -ATAAA CTT-AA TTTAAA AATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
15433 TTTCCAATAG
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
4 2 0.03
5 14 0.24
6 40 0.69
7 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:15435 original size:17 final size:17
Alignment explanation
Indices: 15356--15432 Score: 120
Period size: 17 Copynumber: 4.5 Consensus size: 17
15346 TTGGACATTT
*
15356 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
15373 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
15390 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
15407 TAAACTT-AATTTAAAAA
1 TAAATTTAAATTT-AAAA
15424 TAAATTTAA
1 TAAATTTAA
15433 TTTCCAATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.09
17 49 0.89
18 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:16164 original size:207 final size:208
Alignment explanation
Indices: 15809--16267 Score: 787
Period size: 207 Copynumber: 2.2 Consensus size: 208
15799 ATTTATCGCG
* * *
15809 CGTGGGTTTGATTTGGTCATCTTCTCAGTATTTCATCAGGAAGATGACCGCGTCGTTTGTTTCAA
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAA
* * *
15874 TCCGCTTTTCTGTATCTTATCAGGAAGACGAATTTGGTTCACTCCTTAGTATCTCATAAGGAAGC
66 TCCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTTAGTATCTCATAAGGAAGC
*
15939 TATCCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTT
131 TATCCGTTTTATTACTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTT
16004 GCTCACTTTGA-A
196 GCTCACTTTGAGA
*
16016 CGTGGGTTTGATTTGGTCTTCTTCTAAGTATCTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAA
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAA
* * *
16081 TTCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTTAGTATTTCATCAGGAAGC
66 TCCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTTAGTATCTCATAAGGAAGC
* *
16146 TATCCGTTTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGTTGGGGTTCGAAGATTTT
131 TATCCGTTTTATTACTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTT
16211 GCTCACTTTGAGA
196 GCTCACTTTGAGA
16224 -GTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCT
1 CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCT
16268 AACCACGTTT
Statistics
Matches: 237, Mismatches: 14, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
207 236 1.00
208 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (208 bp):
CGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGCTGACCGCGTCGTTTGTTTCAA
TCCGCTTCTCCGTATCTCATCAGGAAGACGAATTTGGTTCACTCCTTAGTATCTCATAAGGAAGC
TATCCGTTTTATTACTTCGACCTGCTTCTCAATATCTCATCAAGAAGCTGGGGTTCGAAGATTTT
GCTCACTTTGAGA
Found at i:17278 original size:278 final size:278
Alignment explanation
Indices: 16774--17325 Score: 960
Period size: 278 Copynumber: 2.0 Consensus size: 278
16764 GGCCCAATGA
*
16774 TTTTCACAGTTTTTCAATTTAGCCCCTCAACCTTTTAAAAGCACCAGGAGCTGCCACGTGTCATG
1 TTTTCACAGTTTTTCAATTTAGCCCCTCAACCTTTTAAAAGCACCAGGAGCTACCACGTGTCATG
*
16839 ATTTTGGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCTTAAATC
66 ATTTTAGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCTTAAATC
*
16904 AGGTTCGCTTTAATTACAAAATTACCCCAAAAATTTTCCATGGTTTTCAAAATAGTCCTCTGACT
131 AAGTTCGCTTTAATTACAAAATTACCCCAAAAATTTTCCATGGTTTTCAAAATAGTCCTCTGACT
* * * *
16969 TCAGGATGCCTGAGGGGCTGCCACGTGTCACCTGTTTTTGGTTTTATTACCCCGGAGGTCTCTAA
196 TCAGGATGCCTGAGGGGCTGCCACATGTCACCCGTTTTTGGTTTTATTACCCCGAAGGTCCCTAA
17034 ACTGTCCAAAAATTCTAT
261 ACTGTCCAAAAATTCTAT
* * * *
17052 TTTTCACAGTTTTTCAATTTAGCCCTTCGACCTTTTAAAAGGACTAGGAGCTACCACGTGTCATG
1 TTTTCACAGTTTTTCAATTTAGCCCCTCAACCTTTTAAAAGCACCAGGAGCTACCACGTGTCATG
17117 ATTTTAGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCTTAAATC
66 ATTTTAGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCTTAAATC
* * * * *
17182 AAGTTCGCTTTATTTACAAAATTGCCCCATAAATTTTCCATGGTTTTCAAAGTATTCCTCTGACT
131 AAGTTCGCTTTAATTACAAAATTACCCCAAAAATTTTCCATGGTTTTCAAAATAGTCCTCTGACT
17247 TCAGGATGCCTGAGGGGCTGCCACATGTCACCCGTTTTTGGTTTTATTACCCCGAAGGTCCCTAA
196 TCAGGATGCCTGAGGGGCTGCCACATGTCACCCGTTTTTGGTTTTATTACCCCGAAGGTCCCTAA
17312 ACTGTCCAAAAATT
261 ACTGTCCAAAAATT
17326 TTGTTTTTAC
Statistics
Matches: 258, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
278 258 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (278 bp):
TTTTCACAGTTTTTCAATTTAGCCCCTCAACCTTTTAAAAGCACCAGGAGCTACCACGTGTCATG
ATTTTAGCTTATTTATGCAAATGGTCCCTTTTATTTCTAATTTGTTTTAATTTAATCCTTAAATC
AAGTTCGCTTTAATTACAAAATTACCCCAAAAATTTTCCATGGTTTTCAAAATAGTCCTCTGACT
TCAGGATGCCTGAGGGGCTGCCACATGTCACCCGTTTTTGGTTTTATTACCCCGAAGGTCCCTAA
ACTGTCCAAAAATTCTAT
Found at i:17361 original size:29 final size:28
Alignment explanation
Indices: 17329--17488 Score: 142
Period size: 29 Copynumber: 5.4 Consensus size: 28
17319 AAAAATTTTG
17329 TTTTTACCCCCGAACTTCCAAAATTCCCA
1 TTTTTACCCCCGAACTTCCAAAATT-CCA
* **
17358 TTTTTGACCTCAAAACTTCCAAAAATTCCA
1 TTTTT-ACCCCCGAACTTCC-AAAATTCCA
* *
17388 TTTTTACCCTCGAACTTCCAAAAATCCCA
1 TTTTTACCCCCGAACTTCC-AAAATTCCA
**
17417 TTTTTTGACCCCAAAACTTCCCAAAATTCCA
1 -TTTTT-ACCCCCGAACTT-CCAAAATTCCA
* **
17448 TTTTAACCCTTGAACTTCCAAAAATTACCA
1 TTTTTACCCCCGAACTTCC-AAAATT-CCA
17478 -TTTTACCCCCG
1 TTTTTACCCCCG
17489 GATGTCCGAA
Statistics
Matches: 105, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.02
29 47 0.45
30 31 0.30
31 23 0.22
32 2 0.02
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.33
Consensus pattern (28 bp):
TTTTTACCCCCGAACTTCCAAAATTCCA
Found at i:17377 original size:30 final size:29
Alignment explanation
Indices: 17341--17451 Score: 127
Period size: 30 Copynumber: 3.7 Consensus size: 29
17331 TTTACCCCCG
17341 AACTTCCAAAATTCCCATTTTTGACCTCAA
1 AACTTCCAAAATT-CCATTTTTGACCTCAA
*
17371 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
1 AACTTCC-AAAATTCCATTTTTGA-CCTCAA
* *
17400 AACTTCCAAAAATCCCATTTTTTGACCCCAA
1 AACTTCC-AAAATTCCA-TTTTTGACCTCAA
17431 AACTTCCCAAAATTCCATTTT
1 AACTT-CCAAAATTCCATTTT
17452 AACCCTTGAA
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.24
30 31 0.44
31 20 0.29
32 2 0.03
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAATTCCATTTTTGACCTCAA
Found at i:17426 original size:60 final size:60
Alignment explanation
Indices: 17310--17481 Score: 229
Period size: 60 Copynumber: 2.9 Consensus size: 60
17300 GAAGGTCCCT
*** * * *
17310 AAACTGTCCAAAAATTTTGTTTTTACCCCCGAACTTCCAAAATTCCCA-TTTTTGACCTCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACCCCA
17370 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACCCCA
* * * *
17430 AAACTTCCCAAAATTCCATTTTAACCCTTGAACTTCCAAAAATTACCATTTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAA-TCCCATTTT
17482 ACCCCCGGAT
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
59 37 0.37
60 55 0.55
61 8 0.08
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGACCCCA
Found at i:19813 original size:111 final size:112
Alignment explanation
Indices: 19660--19882 Score: 283
Period size: 111 Copynumber: 2.0 Consensus size: 112
19650 CACAGTAGAA
* * * *
19660 AATTGTTGTTTTATTTTTACGGTTTCTTTGTACGGCAAGTTCTTTGGTATATTGTCCCTTATCAA
1 AATTGTTGTTTTATTTTCACGGTTTCTTTGTACGACAAGTTCTTTGATATATTGTCACTTATCAA
19725 T-TACATGTTATTCC-T-TTTTTAT-AAGTCAAATTAAATTTATATTAAC
66 TCT-CATGTTATTCCATATTTTT-TCAAGT-AAATTAAATTTATATTAAC
* * * * *
19771 AATTTTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGATATATTGTCACTTGTCAA
1 AATTGTTGTTTTATTTTCACGGTTTCTTTGTACGACAAGTTCTTTGATATATTGTCACTTATCAA
* * *
19836 TCTTATGTTATTCCATATTTTTTCAGGTAAATTAAATTTCTATTAAC
66 TCTCATGTTATTCCATATTTTTTCAAGTAAATTAAATTTATATTAAC
19883 TTAAAATTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
111 67 0.70
112 21 0.22
113 8 0.08
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.52
Consensus pattern (112 bp):
AATTGTTGTTTTATTTTCACGGTTTCTTTGTACGACAAGTTCTTTGATATATTGTCACTTATCAA
TCTCATGTTATTCCATATTTTTTCAAGTAAATTAAATTTATATTAAC
Found at i:20557 original size:218 final size:215
Alignment explanation
Indices: 19771--20592 Score: 800
Period size: 215 Copynumber: 3.8 Consensus size: 215
19761 TTATATTAAC
* *
19771 AATTTTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGATATATTGTCACTTGTCAA
1 AATTTTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGTTATATTGTCACTTATCAA
** * * * *
19836 TCTTATGTTATTCCATATTTTTTCAGGT-AAATTAAATTTCTATTAACTTAAAATTTTAAAATTT
66 TCACATGGTATTCCATA-TTTTT-AAGTCAAATTAAATTTATATTAACTTAAAATTTTAAAAATT
* * * *
19900 TTATAATAGTGTAATGAGAAAATTTTCATTGTAGGGGTCGTAGCCCCCTAATTAAAATTTTATTT
129 TTAAAAGAGTGTAATGAGAAAATTTTCATT-TAAGGGTTGTAG-CCCCTAATTAAAATTTTATTT
* * * * *
19965 CTTTCATCGAAATGGGCACGACATAC
192 ATGTCAACGAAATGGACACGA-A-AA
* * * * *
19991 AATTTATGATTTGTTTTCA-TGTTTTCTTTGTAC-AGTAGGTTCTTTTTTATATTGTCACTTGTC
1 AATTTTTGTTTTATTTTCACTG-TTTCTTTGTACGA-TAGGTTCTTTGTTATATTGTCACTTATC
** * * * * * *
20054 GGTCACATGGTATTCTATATTTCTTAAGTCATATTATATTTATATTAAATTTAAATTTTATAAAT
64 AATCACATGGTATTCCATATTT-TTAAGTCAAATTAAATTTATATTAACTTAAAATTTTAAAAAT
* * * * *
20119 TTTAAAAGAGTATAATGAGAAAATGTTCATTTAAGGGTTGCAGCCCCTAATTAAAAATTTATATA
128 TTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTTGTAGCCCCTAATTAAAATTTTATTTA
* * * *
20184 TGTTATA-AAAATTGACACG-ACA
193 TGTCA-ACGAAATGGACACGAAAA
* ** * *
20206 TATTATTT-TTTTATTTTCACAATTTCTTTGTACGATAGGTTTTTTGGTATATTGT---TTGATG
1 AATT-TTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGTTATATTGTCACTT-AT-
* * * * *
20267 CCAATCACATGCTCTTACATAGTTTTTAGGTCAAATTAAATTTATATTAACTTAAAATTTTATAA
63 -CAATCACATGGTATTCCATA-TTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTAAAA
* * * *
20332 GTTTTAAAAGGGTGTAATGAGAAAATTTTCATTTAAGGGTTATAGCCTCTAATTAAAATTTTATT
126 ATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTTGTAGCCCCTAATTAAAATTTTATT
* * *
20397 TATGTGAACGAAATGGTCAAGATAGAA
191 TATGTCAACGAAATGGACACGA-A-AA
* * *
20424 AATTTTTGTTTTATTTTCACGGTTTTTTTGTACGATAGGTTCTTTGTTATATTGTCACTTATCAG
1 AATTTTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGTTATATTGTCACTTATCAA
* * * *
20489 TCATATGGTATTCCGAT-TTTTTAAAGTTAAATTATATTTATATTAACTTAAAACTTTAAAAATT
66 TCACATGGTATTCC-ATATTTTT-AAGTCAAATTAAATTTATATTAACTTAAAATTTTAAAAATT
* * *
20553 TTAAAAGAATGTAATGACAAAATTTTTATTTTAAGGGTTG
129 TTAAAAGAGTGTAATGAGAAAATTTTCA-TTTAAGGGTTG
20593 CTACCTTGAT
Statistics
Matches: 484, Mismatches: 95, Indels: 47
0.77 0.15 0.08
Matches are distributed among these distances:
212 2 0.00
213 1 0.00
214 1 0.00
215 159 0.33
216 7 0.01
217 9 0.02
218 148 0.31
219 30 0.06
220 125 0.26
221 2 0.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (215 bp):
AATTTTTGTTTTATTTTCACTGTTTCTTTGTACGATAGGTTCTTTGTTATATTGTCACTTATCAA
TCACATGGTATTCCATATTTTTAAGTCAAATTAAATTTATATTAACTTAAAATTTTAAAAATTTT
AAAAGAGTGTAATGAGAAAATTTTCATTTAAGGGTTGTAGCCCCTAATTAAAATTTTATTTATGT
CAACGAAATGGACACGAAAA
Found at i:22487 original size:220 final size:216
Alignment explanation
Indices: 21093--23513 Score: 1490
Period size: 216 Copynumber: 11.1 Consensus size: 216
21083 CAGACTCATG
* * * * * * * **
21093 ATATTTATATTAATTTAAAATTTTATACATTTTAAAAAATTTTAATGAGAAATTTTTCATATTTT
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCAT-TTAG
*** * * *
21158 GACCTACAACCCCCTAATTAAAATATT-TTTCTAT-AATTGAAATGAG-CACGATAGA-AATTTT
65 GGGTTACAA--CCCTAATTAAAATTTTATTTCTATGAATCGAAATG-GTCAAGATAGATAATTTT
* * * * * * *
21219 TATTTTATTCTC-TCGATTTCTTTGTAAGGTAGGTTCTTTGGTATATTGTCATTTGTCAATCACA
127 TGTTTTATTTTCAT-GGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGTC-TA
* * *
21283 TGTTATTCC-TTTTTTTTAAGTTAAATT
189 TGGTATTCCATATTTTTTAAGTCAAATT
* * * * * * * * *
21310 AAATTTACATTAATTTAAAATTTGATAAATTTTGAAAGAATGTAATGAGAAAATTTTCATTAAGT
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAGG
* * * * ** * * * * * *
21375 GGCTGCATCCCGTTATTTAAAAACTTATTTCTGT-CATCGAATTGGGCATGACAGATAA-TTTT-
66 GGTTACAACCC--TAATTAAAATTTTATTTCTATGAATCGAAATGGTCAAGATAGATAATTTTTG
* * * * * * * * *
21437 TTTTATTTTCACGGTTTCTTTATATGTTAGGTTCTTTGGTGTATTGTCACTAGTCAATCACATGT
129 TTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGTC-TATGG
*
21502 TATTCCATA--TTTTAAGCCAAATT
192 TATTCCATATTTTTTAAGTCAAATT
* * * * * * * *
21525 AAATTTATATTAACTTAAAATTTTATAAATTTAAAAAAAATGTAAAGATAAAATTTTCATTTAGG
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAGG
* * * * * * * * * * ** * *
21590 GGCTGCAGTCCCCTAATTAAATTTTTTTTTCTGT-CATTGAAATTGTCACGACGGA-CATTTTTA
66 GGTTACA--ACCCTAATTAAAATTTTATTTCTATGAATCGAAATGGTCAAGATAGATAATTTTTG
* * * ** * * *
21653 TTTTATTTTCACGATTTCTTTGTATGGTAAATTATTTTGTATATTGTCACTTGTCAGTCCAATGG
129 TTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGT-CTATGG
* * * *
21718 TATTTCTTATTTCTTAAATCAAATT
192 TATTCCATATTTTTTAAGTCAAATT
* * * *
21743 ATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTAATCAGAAAATTTTCATTTTA-
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA-TTTAG
** * * * * * *
21807 GGCCTAC-A----AATTAAATCTTGTTTTTTCTAT-TATCGAAATGGGCACGATAAAT-ATTTTT
65 GGGTTACAACCCTAATTAAA-ATT-TTATTTCTATGAATCGAAATGGTCAAGATAGATAATTTTT
*** * * * * * * *
21865 GTTTTATTTTCACAATTTCTTTTTACGGTGGGTTCTTTGGTTTATTTTCGCTTGTTAATCACATG
128 GTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATA-TTTCACTTGTCAGTC-TATG
* * *
21930 TTATTCCATATTTTTCAAGTTAAATT
191 GTATTCCATATTTTTTAAGTCAAATT
* * * * * *
21956 AAATTTATATTAACTTAAAAATTGATAAATTTTGAAAGAGTGTAATGAGAAAAATTTT-ATTTAG
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAG-AAAATTTTCATTTAG
* * * * * * *
22020 GGGTTACAGTCGCCTAATTAAAAATTTGTTTCT-T-CATC-AAATTGGGCAGGATAGATATTTTT
65 GGGTTACA-AC-CCTAATTAAAATTTTATTTCTATGAATCGAAA-TGGTCAAGATAGATA--ATT
* * * * * * *
22082 TTTTTTTGTTTTTTCAAGGTTTTTTTGTACGGTAGATTCTTTGGTATATTGTCACTTTTCAATCA
125 TTTGTTT-TATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGTC-
* ** * **
22147 CATACTCTTAAATATTTTTTTAAGTCAAATT
187 TATGGTATTCCATA-TTTTTTAAGTCAAATT
* * * * *
22178 AAATTTATATTAATTTAATATTTT-ATAATGTTTAAAAGAGTGTAATGA-AAACTTTTCATTTAG
1 ATATTTATATTAAATTAAAATTTTAAAAAT-TTTAAAAGAGTGTAATGAGAAAATTTTCATTTAG
*
22241 GGGTTGTAGC-ACCCTAATTAAAAATTTATTTCTATGAAT-GAAATGGTCAAGATAGATAATTTT
65 GGG-T-TA-CAACCCTAATTAAAATTTTATTTCTATGAATCGAAATGGTCAAGATAGATAATTTT
* * * * * *
22304 TGTTTTATCTTCATGGTTTTTTTTTGTACGATAGGTTCTTTGTTATATTCTCATTTATCAGTCCT
127 TGTTTTATTTTCATGG--TTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGT-CT
* *
22369 ACGGTATTCCGAT-TTTTTTAAGTTAAATT
188 ATGGTATTCC-ATATTTTTTAAGTCAAATT
* *
22398 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAATGTAATTAGAAAATTTTCATTTTAG
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCA-TTTAG
* ** ** * * * *
22463 GGGTTACTACCCTTGCTTAAAATTTTATTT-T-TGTTTCCGATATGGGCACGATAGATAATTCTT
65 GGGTTACAACCC-TAATTAAAATTTTATTTCTATGAAT-CGAAATGGTCAAGATAGATAATTTTT
* * ** * *
22526 GTTTCATTTTTACCGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAGTCTCATG
128 GTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCAGTCT-ATG
* * *
22591 GTATTCCATATATCTTAAGTCAATTT
191 GTATTCCATATTTTTTAAGTCAAATT
* * * *
22617 ATATTTATATTTATATTAGTTTCAAA-TTTAATAAATTTTAATAGTGTTTAATGAGAAAATTTTC
1 ATATTTATA-TTA-A--A--TTAAAATTTTAA-AAATTTTAAAAGAGTGTAATGAGAAAATTTTC
* * * ** * *
22681 ATTTAGGGGCTGTAGC-TCCCTAATTAAAATTTTATTT-T-TGTAATAGAAAAGAACATGGTAGA
59 ATTTAGGGG-T-TA-CAACCCTAATTAAAATTTTATTTCTATG-AATCGAAATGGTCAAGATAGA
* *
22743 CAATTTTTGTTTTATTTTCATGGTTTCTTTGTACTGTAGGTTCTTTGGTATATTATCACTTGTCA
120 TAATTTTTGTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATT-TCACTTGTCA
* * * * *
22808 ATCAAATGTTATTCCATAGTTTTTAATTCAAATT
184 GTC-TATGGTATTCCATATTTTTTAAGTCAAATT
* * * * *
22842 AAATTTATATGAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTCTT-ATTTAG
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATT-TTCATTTAG
* * * * *
22906 GGGCTGCAATCCCCTAATTAAAATTTTTATTTCTAT-CATCGAAATGGTCACA-ACAGACAATTT
65 GGGTTACAA--CCCTAATTAAAA-TTTTATTTCTATGAATCGAAATGGTCA-AGATAGATAATTT
* * * *
22969 TTATTTTATTTTCATGGTTTCTTTTTACGTTAGGTTTTTTGGTATA-TTCACTTGTCAGTCTCAT
126 TTGTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTTCACTTGTCAGTCT-AT
*
23033 GGTATTCC-TTTTTTCTTAAGTCAAATT
190 GGTATTCCATATTTT-TTAAGTCAAATT
* * * * **
23060 ATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTAATGAGAAATTTTTCATTTCCG
1 ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAGG
*** *
23125 ACCTACAACCCCCTAATTAAAA---TAGTTTCTAT-AATCGAAATGAG-CACGATAGAT-ATTTT
66 GGTTACAA--CCCTAATTAAAATTTTA-TTTCTATGAATCGAAATG-GTCAAGATAGATAATTTT
* *
23184 TGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATATTTTCACTTGTCAGT-TACA
127 TGTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATA-TTTCACTTGTCAGTCT--A
* * *
23248 TGCTATTCCATATTTTTCAAGTTAAATT
189 TGGTATTCCATATTTTTTAAGTCAAATT
* * * * * * *
23276 -TAATTTACATTAACTTAAAATTTGATAAATTTTGAAAGAGTGTAATGAGAAAATTTTTATTTAA
1 AT-ATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAG
*** * * * * * * * * * *
23340 GACCTGCAGCCCGCTATTTAAAATTTTATTTCTGTTAA-C-AAGTTGGGCACGACAAATAATTTT
65 GGGTTACA-ACC-CTAATTAAAATTTTATTTCTATGAATCGAA-ATGGTCAAGATAGATAATTTT
* * * * * *
23403 TGTTTTTTTTTCACGGTTTCTTTGTATGGTAGG-TCATTTGGTATATTATTACTTGTCAATCACA
127 TGTTTTATTTTCATGGTTTCTTTGTACGGTAGGTTC-TTTGGTATATT-TCACTTGTCAGTC-TA
* *
23467 TGCTATTACATATTTTTTTAAGTCAAATT
189 TGGTATTCCATA-TTTTTTAAGTCAAATT
* *
23496 AAATTTATATTAACTTAA
1 ATATTTATATTAAATTAA
23514 TATATTGTCA
Statistics
Matches: 1756, Mismatches: 344, Indels: 205
0.76 0.15 0.09
Matches are distributed among these distances:
211 7 0.00
212 7 0.00
213 142 0.08
214 60 0.03
215 135 0.08
216 242 0.14
217 111 0.06
218 204 0.12
219 205 0.12
220 196 0.11
221 185 0.11
222 79 0.04
223 9 0.01
224 16 0.01
225 151 0.09
226 6 0.00
227 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (216 bp):
ATATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAGTGTAATGAGAAAATTTTCATTTAGG
GGTTACAACCCTAATTAAAATTTTATTTCTATGAATCGAAATGGTCAAGATAGATAATTTTTGTT
TTATTTTCATGGTTTCTTTGTACGGTAGGTTCTTTGGTATATTTCACTTGTCAGTCTATGGTATT
CCATATTTTTTAAGTCAAATT
Found at i:23238 original size:434 final size:432
Alignment explanation
Indices: 21095--23513 Score: 2089
Period size: 434 Copynumber: 5.5 Consensus size: 432
21085 GACTCATGAT
* * * * * * * ** *
21095 ATTTATATTAATTTAAAATTTTATACATTTTAAAAAATTTTAATGAGAAATTTTTCATATTTTGA
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTT-AT-TTAGGG
* * * * * * * * *
21160 CCTACAACCCCCTAATTAAAATATT-TTTCTATAATTGAAATGAGCACGATAGA-AATTTTTATT
64 GCTGCAATCCCCTAATTAAAATTTTATTTCTGTCATCGAAATGGGCACGACAGATAATTTTTATT
* * * * * * *
21223 TTATTCTCTCGATTTCTTTGTAAGGTAGGTTCTTTGGTATATTGTCATTTGTCAATCACATGTTA
129 TTATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATGGTA
* * * * * *
21288 TTCCTTTTTTTTAAGTTAAATTAAATTTACATTAATTTAAAATTTGATAAATTTTGAAAGAATGT
194 TTCCTTTTTTTTAAGTCAAATTAAATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTT
* ** * * * *
21353 AATGAGAAAATTTTCA-TTAAGTGGCTGCATCCCGTTATTTAAAAACTTATTTCTGTCATCGAAT
259 AATGAGAAAATTTTCATTTAAG-GGCTGCAACCCCCTAATT-AAAA-TTATTTCTATAATCGAAA
* * * * * * * * *
21417 TGGGCATGACAGATAATTTT-TTTTATTTTCACGGTTTCTTTATATGTTAGGTTCTTTGGTGTAT
321 TGAGCACGATAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATAT
* * **
21481 TGTCACTAGTCAATCACATGTTATTCCATA-TTTTAAGCCAAATTAA
386 TTTCACTTGTCAATCACATGTTATTCCATATTTTTAAGTTAAATTAA
* * * * *
21527 ATTTATATTAACTTAAAATTTTATAAATTTAAAAAAAATGTAAAGATAAAATTTTCATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTT-ATTTAGGGG
* * * * * * * *
21592 CTGCAGTCCCCTAATTAAATTTTTTTTTCTGTCATTGAAATTGTCACGACGGA-CATTTTTATTT
65 CTGCAATCCCCTAATTAAAATTTTATTTCTGTCATCGAAATGGGCACGACAGATAATTTTTATTT
* ** * *
21656 TATTTTCACGATTTCTTTGTATGGTAAATTATTTTGTATATTGTCACTTGTCAGTC-CAATGGTA
130 TATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCAC-ATGGTA
* * * *
21720 TTTCTTATTTCTTAAATCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTT
194 TTCCTT-TTTTTTAAGTCAAATTAAATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTT
* * * * ** * **** * *
21785 TAATCAGAAAATTTTCATTTTAGGCCTACAA---ATTAAATCTTGTTTTTTCTATTATCGAAATG
258 TAATGAGAAAATTTTCATTTAAGGGCTGCAACCCCCTAATTAAAATTATTTCTATAATCGAAATG
* * * * * *
21847 GGCACGATAAATATTTTTGTTTTATTTTCACAATTTCTTTTTACGGTGGGTTCTTTGGTTTATTT
323 AGCACGATAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATATTT
* *
21912 TCGCTTGTTAATCACATGTTATTCCATATTTTTCAAGTTAAATTAA
388 TCACTTGTCAATCACATGTTATTCCATATTTTT-AAGTTAAATTAA
* * *
21958 ATTTATATTAACTTAAAAATTGATAAATTTTGAAAGAGTGTAATGAGAAAAATTTTATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGA-AAAAATTTTATTTAGGGG
* * * * * * * * * *
22023 TTACAGTCGCCTAATTAAAAATTTGTTTCT-TCATC-AAATTGGGCAGGATAGATATTTTTTTTT
65 CTGCAATCCCCTAATTAAAATTTTATTTCTGTCATCGAAA-TGGGCACGACAGATA--ATTTTTA
* * * * * * * *
22086 TTTGTTTTTTCAAGGTTTTTTTGTACGGTAGATTCTTTGGTATATTGTCACTTTTCAATCACATA
127 TTT-TATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATG
* * ** *
22151 CTCTTAAATATTTTTTTAAGTCAAATTAAATTTATATTAATTTAATATTTTAT-AATGTTTAAAA
191 GTATT-CCT-TTTTTTTAAGTCAAATTAAATTTATATTAATTTAAAATTTTATAAAT-TTTAAAA
* * * * * * *
22215 GAGTGTAATGA-AAACTTTTCATTTAGGGGTTGTAGCACCCTAATTAAAAATTTATTTCTATGAA
253 GAGTTTAATGAGAAAATTTTCATTTAAGGGCTGCAACCCCCTAATT-AAAA-TTATTTCTAT-AA
* * * * * *
22279 T-GAAATG-GTCAAGATAGATAATTTTTGTTTTATCTTCATGGTTTTTTTTTGTACGATAGGTTC
315 TCGAAATGAG-CACGATAGAT-ATTTTTGTTTTATTTTCA-CG-ATTTCTTTGTACGGTAGGTTC
* * * * * * * * *
22342 TTTGTTATATTCTCATTTATCAGTC-CTACGGTATTCCGATTTTTTTAAGTTAAATTAT
376 TTTGGTATATTTTCACTTGTCAATCAC-ATGTTATTCC-ATATTTTTAAGTTAAATTAA
* * * * *
22400 ATTTATATTAAATTAAAATTTTAAAAATTTTAAAAGAATGTAATTAGAAAATTTTCATTTTAGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTT-A-TTTAGGG
* * * * ** * * * * * *
22465 GTTACTA-CCCTTGCTTAAAATTTTATTTTTGT-TTCCGATATGGGCACGATAGATAATTCTTGT
64 GCTGCAATCCCCTAATTAAAATTTTATTTCTGTCAT-CGAAATGGGCACGACAGATAATTTTTAT
* * * * *
22528 TTCATTTTTACCGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAGTCTCATGGT
128 TTTATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATGGT
* * * * * * *
22593 ATTCCATATATCTTAAGTCAATTTATATTTATATTTATATTAGTTTCAAATTTAATAAATTTTAA
193 ATTCC-TTTTTTTTAAGTC-A---A-A-TTAAATTTATATTAATTTAAAATTTTATAAATTTTAA
* * * * * * * *
22658 TAGTGTTTAATGAGAAAATTTTCATTTAGGGGCTGTAGCTCCCTAATTAAAATTTTATTTTTGTA
251 AAGAGTTTAATGAGAAAATTTTCATTTAAGGGCTGCAACCCCCTAATTAAAA--TTATTTCTATA
* * * * * * * * *
22723 ATAGAAAAGAACATGGTAGACAATTTTTGTTTTATTTTCATGGTTTCTTTGTACTGTAGGTTCTT
314 ATCGAAATGAGCACGATAGA-TATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTT
* *
22788 TGGTATATTATCACTTGTCAATCAAATGTTATTCCATAGTTTTTAA-TTCAAATTAA
378 TGGTATATTTTCACTTGTCAATCACATGTTATTCCATA-TTTTTAAGTT-AAATTAA
*
22844 ATTTATATGAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTCTTATTTAGGGG
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATT-TTATTTAGGGG
* * * *
22909 CTGCAATCCCCTAATTAAAATTTTTATTTCTATCATCGAAATGGTCACAACAGACAATTTTTATT
65 CTGCAATCCCCTAATTAAAA-TTTTATTTCTGTCATCGAAATGGGCACGACAGATAATTTTTATT
* * * * * * *
22974 TTATTTTCATGGTTTCTTTTTACGTTAGGTTTTTTGGTATA-T-TCACTTGTCAGTCTCATGGTA
129 TTATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATGGTA
*
23037 TTCCTTTTTTCTTAAGTCAAATTATATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTT
194 TTCCTTTTTT-TTAAGTCAAATTAAATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTT
* ** ** *
23102 TAATGAGAAATTTTTCATTTCCGACCTACAACCCCCTAATTAAAA-TAGTTTCTATAATCGAAAT
258 TAATGAGAAAATTTTCATTTAAGGGCTGCAACCCCCTAATTAAAATTA-TTTCTATAATCGAAAT
23166 GAGCACGATAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATATT
322 GAGCACGATAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATATT
* * * *
23231 TTCACTTGTCAGTTACATGCTATTCCATATTTTTCAAGTTAAATTTA
387 TTCACTTGTCAATCACATGTTATTCCATATTTTT-AAGTTAAATTAA
* * * * * **
23278 ATTTACATTAACTTAAAATTTGATAAATTTTGAAAGAGTGTAATGAGAAAATTTTTATTTAAGAC
1 ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGA-AAAAATTTTATTTAGGGG
* * * * * * *
23343 CTGC-AGCCCGCTATTTAAAATTTTATTTCTGTTAAC-AAGTTGGGCACGACAAATAATTTTTGT
65 CTGCAATCCC-CTAATTAAAATTTTATTTCTGTCATCGAA-ATGGGCACGACAGATAATTTTTAT
* * * * *
23406 TTTTTTTTCACGGTTTCTTTGTATGGTAGGTCATTTGGTATATTATTACTTGTCAATCACATGCT
128 TTTATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATGGT
* *
23471 ATTACATATTTTTTTAAGTCAAATTAAATTTATATTAACTTAA
193 ATT-CCT-TTTTTTTAAGTCAAATTAAATTTATATTAATTTAA
23514 TATATTGTCA
Statistics
Matches: 1587, Mismatches: 335, Indels: 126
0.77 0.16 0.06
Matches are distributed among these distances:
428 30 0.02
429 66 0.04
430 20 0.01
431 105 0.07
432 148 0.09
433 153 0.10
434 221 0.14
435 104 0.07
436 31 0.02
437 84 0.05
438 2 0.00
439 33 0.02
440 72 0.05
441 16 0.01
442 113 0.07
443 83 0.05
444 120 0.08
445 113 0.07
446 73 0.05
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (432 bp):
ATTTATATTAACTTAAAATTTTATAAATTTTAAAAGAGTGTAATGAAAAAATTTTATTTAGGGGC
TGCAATCCCCTAATTAAAATTTTATTTCTGTCATCGAAATGGGCACGACAGATAATTTTTATTTT
ATTTTCACGGTTTCTTTGTATGGTAGGTTATTTGGTATATTGTCACTTGTCAATCACATGGTATT
CCTTTTTTTTAAGTCAAATTAAATTTATATTAATTTAAAATTTTATAAATTTTAAAAGAGTTTAA
TGAGAAAATTTTCATTTAAGGGCTGCAACCCCCTAATTAAAATTATTTCTATAATCGAAATGAGC
ACGATAGATATTTTTGTTTTATTTTCACGATTTCTTTGTACGGTAGGTTCTTTGGTATATTTTCA
CTTGTCAATCACATGTTATTCCATATTTTTAAGTTAAATTAA
Found at i:24599 original size:17 final size:17
Alignment explanation
Indices: 24577--24610 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
24567 CACTAGCACT
*
24577 AAAATGCAATGACAATG
1 AAAATGCAACGACAATG
24594 AAAATGCAACGACAATG
1 AAAATGCAACGACAATG
24611 CTTACTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATG
Found at i:27828 original size:50 final size:50
Alignment explanation
Indices: 27774--28644 Score: 321
Period size: 50 Copynumber: 17.4 Consensus size: 50
27764 TTACAACATG
* * *
27774 AAATCCTATATCCCTGAAGATGCAATGGATCGGATTAAAACTACAGTAGC
1 AAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAGTAGC
* * * * * * * ** *
27824 AAATCCTATCTCCCTGAAGGTGCAGTGGAGCAAAATGAAGCTAAAACATC
1 AAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAGTAGC
* * *
27874 AAATCCTATATCCCTGAAGTTGTAGTGGAT-TGAATTGAAACTAC-GATAGC
1 AAATCCTATATCCCTGAAGATGCAGTGGATCAG-ATTGAAACTACAG-TAGC
* * * *
27924 AAAT-CTCATCTCCTTGAAGATGCAGTGGATCAAGA-TGAAGCTACA-TCATC
1 AAATCCT-ATATCCCTGAAGATGCAGTGGATC-AGATTGAAACTACAGT-AGC
* * * *
27974 AAATCCTATATCCTTGAAGATGCAGTGGATCAGATTAAAACAACAGTAAC
1 AAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAGTAGC
** * * * * * ** *
28024 AAATATTATCTACGTGAAGATACAGTGGAGCAAGA-TGAAGA-TACAACATC
1 AAATCCTATATCCCTGAAGATGCAGTGGATC-AGATTGAA-ACTACAGTAGC
* * *
28074 AAATCCTATATCCCTGAAG-TCACAGAGGATCGGATTGAAACTAC-GATAGC
1 AAATCCTATATCCCTGAAGAT-GCAGTGGATCAGATTGAAACTACAG-TAGC
* * * ** *
28124 TAAT-CT-TATCTCCTAGAAGATGCAGTGGAGCAAGA-TGAAACTATAACATC
1 AAATCCTATATC-CCT-GAAGATGCAGTGGATC-AGATTGAAACTACAGTAGC
* * * * * *
28174 AAATCCTATATCCTTGAAG-TCGTAGAGGACCGGATTGAAATTAC-GATAGC
1 AAATCCTATATCCCTGAAGAT-GCAGTGGATCAGATTGAAACTACAG-TAGC
* * * * * ** *
28224 TAAT-CT-CATCTCTTGGAAGATGCAGTGGAGCA-ATATGAAGCTACAACATC
1 AAATCCTATATC-CCT-GAAGATGCAGTGGATCAGAT-TGAAACTACAGTAGC
* * * *
28274 AAATCCTATATCTCTGAAG-TCGTAGAGGATCGGATTGAAACTAC-GATAGC
1 AAATCCTATATCCCTGAAGAT-GCAGTGGATCAGATTGAAACTACAG-TAGC
* * * * * ** *
28324 TAAT-CTCATCTCCC-GAAAGATACAGTGGAGCAAGA-T-AACGCTACAACATC
1 AAATCCT-ATATCCCTG-AAGATGCAGTGGATC-AGATTGAA-ACTACAGTAGC
* * * * * *
28374 AAATCCTATATCCTTGAAG-TCGTAGAGGATCGGATTTAAACTA-TGATAGC
1 AAATCCTATATCCCTGAAGAT-GCAGTGGATCAGATTGAAACTACAG-TAGC
* * * * * * * ** *
28424 TAAT-CTCATCTCCCGGAAGATGTAGAGGAGCAAGA-TGAAGCTACAACATC
1 AAATCCT-ATATCCCTGAAGATGCAGTGGATC-AGATTGAAACTACAGTAGC
*
28474 AAATCCTATATCCCTGAAG-TCGTAGTGGATCAGATTGAAACTAC-GATAGC
1 AAATCCTATATCCCTGAAGAT-GCAGTGGATCAGATTGAAACTACAG-TAGC
* ** * * ** *
28524 AAAT-CTCATCTCCCTGAAGAAACAGTGGAGCAAGA-TGAAGCTACAACATC
1 AAATCCT-ATATCCCTGAAGATGCAGTGGATC-AGATTGAAACTACAGTAGC
* * ** * *
28574 AAATCCTATATACCTGAAGTTGCAGTGGATTGGATTGAAACTATAATAGC
1 AAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAGTAGC
*
28624 AAAT-CTCATCTCCCTGAAGAT
1 AAATCCT-ATATCCCTGAAGAT
28645 ACAATGGAGC
Statistics
Matches: 585, Mismatches: 173, Indels: 126
0.66 0.20 0.14
Matches are distributed among these distances:
48 7 0.01
49 46 0.08
50 485 0.83
51 39 0.07
52 8 0.01
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (50 bp):
AAATCCTATATCCCTGAAGATGCAGTGGATCAGATTGAAACTACAGTAGC
Found at i:27872 original size:100 final size:99
Alignment explanation
Indices: 27759--28676 Score: 1021
Period size: 100 Copynumber: 9.2 Consensus size: 99
27749 TGAAATGGAG
* * * *
27759 TGAAGTTACAACATGAAATCCTATATCCCTGAAGATGCAATGGATCGGATTAAAACTAC-AGTAG
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAG-TGTAATGGATCGGATTGAAACTACGA-TAG
* *
27823 CAAATC-CTATCTCCCTGAAGGTGCAGTGGAGCAAAA
64 CAAATCTC-ATCTCCCTGAAGATGCAGTGGAGCAAGA
* * * *
27859 TGAAGCTAAAACATCAAATCCTATATCCCTGAAGTTGTAGTGGATTGAATTGAAACTACGATAGC
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAG-TGTAATGGATCGGATTGAAACTACGATAGC
* *
27924 AAATCTCATCTCCTTGAAGATGCAGTGGATCAAGA
65 AAATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
* * * * * * * *
27959 TGAAGCTACATCATCAAATCCTATATCCTTGAAGATGCAGTGGATCAGATTAAAACAAC-AGTAA
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAG-TGTAATGGATCGGATTGAAACTACGA-TAG
* * * * *
28023 CAAATATTATCTACGTGAAGATACAGTGGAGCAAGA
64 CAAATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
* * *
28059 TGAAGATACAACATCAAATCCTATATCCCTGAAGT-CACAGAGGATCGGATTGAAACTACGATAG
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAGTGTA-A-TGGATCGGATTGAAACTACGATAG
* *
28123 CTAATCTTATCT-CCTAGAAGATGCAGTGGAGCAAGA
64 CAAATCTCATCTCCCT-GAAGATGCAGTGGAGCAAGA
* * * * *
28159 TGAAACTATAACATCAAATCCTATATCCTTGAAGTCGTAGA-GGACCGGATTGAAATTACGATAG
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAGT-GTA-ATGGATCGGATTGAAACTACGATAG
* * *
28223 CTAATCTCATCT-CTTGGAAGATGCAGTGGAGCAATA
64 CAAATCTCATCTCCCT-GAAGATGCAGTGGAGCAAGA
*
28259 TGAAGCTACAACATCAAATCCTATATCTCTGAAGTCGTAGA-GGATCGGATTGAAACTACGATAG
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAGT-GTA-ATGGATCGGATTGAAACTACGATAG
* *
28323 CTAATCTCATCTCCC-GAAAGATACAGTGGAGCAAGA
64 CAAATCTCATCTCCCTG-AAGATGCAGTGGAGCAAGA
* * *
28359 T-AACGCTACAACATCAAATCCTATATCCTTGAAGTCGTAGA-GGATCGGATTTAAACTATGATA
1 TGAA-GCTACAACATCAAATCCTATATCCCTGAAGT-GTA-ATGGATCGGATTGAAACTACGATA
* * * *
28422 GCTAATCTCATCTCCCGGAAGATGTAGAGGAGCAAGA
63 GCAAATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
* *
28459 TGAAGCTACAACATCAAATCCTATATCCCTGAAGTCGTAGTGGATCAGATTGAAACTACGATAGC
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAGT-GTAATGGATCGGATTGAAACTACGATAGC
**
28524 AAATCTCATCTCCCTGAAGAAACAGTGGAGCAAGA
65 AAATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
* * * * **
28559 TGAAGCTACAACATCAAATCCTATATACCTGAAGTTGCAGTGGATTGGATTGAAACTATAATAGC
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAG-TGTAATGGATCGGATTGAAACTACGATAGC
* * *
28624 AAATCTCATCTCCCTGAAGATACAATGGAGCTAGA
65 AAATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
*
28659 TGAAGCTATAACATCAAA
1 TGAAGCTACAACATCAAA
28677 ACGACATCAT
Statistics
Matches: 710, Mismatches: 92, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
98 2 0.00
99 7 0.01
100 691 0.97
101 8 0.01
102 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (99 bp):
TGAAGCTACAACATCAAATCCTATATCCCTGAAGTGTAATGGATCGGATTGAAACTACGATAGCA
AATCTCATCTCCCTGAAGATGCAGTGGAGCAAGA
Found at i:28346 original size:300 final size:294
Alignment explanation
Indices: 27759--28676 Score: 1151
Period size: 300 Copynumber: 3.1 Consensus size: 294
27749 TGAAATGGAG
* * *
27759 TGAAGTTACAACATGAAATCCTATATCCCTGAAGATGCAA-TGGATCGGATTAAAACTAC-AGTA
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAG-T-CAAGAGGATCGGATTAAAACTACGA-TA
* * * *
27822 GCAAATCCTATCTCCCTGAAGGTGCAGTGGAGCAAAATGAAGCTAAAACATCAAATCCTATATCC
63 GCTAATCTTATCT-CCTGAAGATGCAGTGGAGCAAGATGAAGCTAAAACATCAAATCCTATATCC
* * *
27887 CTGAAGTTGTAGTGGATTGAATTGAAACTACGATAGCAAATCTCATCTCCTTGAAGATGCAGTGG
127 CTGAAGTCGTAGTGGATCGGATTGAAACTACGATAGCAAATCTCATCTCCTTGAAGATGCAGTGG
* * * * *
27952 ATCAAGATGAAGCTACATCATCAAATCCTATATCCTTGAAGATGCAGTGGATCAGATTAAAACAA
192 AGCAAGATGAAGCTACAACATCAAATCCTATATCC-TGAAG-TGCAGTGGATCGGATTGAAACTA
* * * **
28017 CAGTAACAAATATTATCTACGTGAAGATACAGTGGAGCAAGA
255 CA-TAGCAAATCTCATCT-CCCGAAGATACAGTGGAGCAAGA
* *
28059 TGAAGATACAACATCAAATCCTATATCCCTGAAGTCACAGAGGATCGGATTGAAACTACGATAGC
1 TGAAGCTACAACATCAAATCCTATATCCCTGAAGTCA-AGAGGATCGGATTAAAACTACGATAGC
* * *
28124 TAATCTTATCTCCTAGAAGATGCAGTGGAGCAAGATGAAACTATAACATCAAATCCTATATCCTT
65 TAATCTTATCTCCT-GAAGATGCAGTGGAGCAAGATGAAGCTAAAACATCAAATCCTATATCCCT
* * * *
28189 GAAGTCGTAGAGGACCGGATTGAAATTACGATAGCTAATCTCATCT-CTTGGAAGATGCAGTGGA
129 GAAGTCGTAGTGGATCGGATTGAAACTACGATAGCAAATCTCATCTCCTT-GAAGATGCAGTGGA
* * *
28253 GCAATATGAAGCTACAACATCAAATCCTATATCTCTGAAGTCGTAGAGGATCGGATTGAAACTAC
193 GCAAGATGAAGCTACAACATCAAATCCTATATC-CTGAAGT-GCAGTGGATCGGATTGAAACTAC
*
28318 GATAGCTAATCTCATCTCCCGAAAGATACAGTGGAGCAAGA
256 -ATAGCAAATCTCATCTCCCG-AAGATACAGTGGAGCAAGA
* * * *
28359 T-AACGCTACAACATCAAATCCTATATCCTTGAAGTCGTAGAGGATCGGATTTAAACTATGATAG
1 TGAA-GCTACAACATCAAATCCTATATCCCTGAAGTC-AAGAGGATCGGATTAAAACTACGATAG
* * * * *
28423 CTAATCTCATCTCCCGGAAGATGTAGAGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCC
64 CTAATCTTATCT-CCTGAAGATGCAGTGGAGCAAGATGAAGCTAAAACATCAAATCCTATATCCC
* * **
28488 TGAAGTCGTAGTGGATCAGATTGAAACTACGATAGCAAATCTCATCTCCCTGAAGAAACAGTGGA
128 TGAAGTCGTAGTGGATCGGATTGAAACTACGATAGCAAATCTCATCTCCTTGAAGATGCAGTGGA
*
28553 GCAAGATGAAGCTACAACATCAAATCCTATATACCTGAAGTTGCAGTGGATTGGATTGAAACTAT
193 GCAAGATGAAGCTACAACATCAAATCCTATAT-CCTGAAG-TGCAGTGGATCGGATTGAAACTA-
* * *
28618 AATAGCAAATCTCATCTCCCTGAAGATACAATGGAGCTAGA
255 CATAGCAAATCTCATCTCCC-GAAGATACAGTGGAGCAAGA
*
28659 TGAAGCTATAACATCAAA
1 TGAAGCTACAACATCAAA
28677 ACGACATCAT
Statistics
Matches: 539, Mismatches: 61, Indels: 36
0.85 0.10 0.06
Matches are distributed among these distances:
298 2 0.00
299 13 0.02
300 512 0.95
301 12 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (294 bp):
TGAAGCTACAACATCAAATCCTATATCCCTGAAGTCAAGAGGATCGGATTAAAACTACGATAGCT
AATCTTATCTCCTGAAGATGCAGTGGAGCAAGATGAAGCTAAAACATCAAATCCTATATCCCTGA
AGTCGTAGTGGATCGGATTGAAACTACGATAGCAAATCTCATCTCCTTGAAGATGCAGTGGAGCA
AGATGAAGCTACAACATCAAATCCTATATCCTGAAGTGCAGTGGATCGGATTGAAACTACATAGC
AAATCTCATCTCCCGAAGATACAGTGGAGCAAGA
Found at i:29157 original size:4 final size:4
Alignment explanation
Indices: 29148--29184 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
29138 CTTATTCTAT
29148 TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
29185 CTTTTAGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:29176 original size:13 final size:13
Alignment explanation
Indices: 29139--29190 Score: 79
Period size: 13 Copynumber: 3.9 Consensus size: 13
29129 ATTTATGTGC
29139 TTATTCTATTTTAT
1 TTATT-TATTTTAT
29153 TTATTTA-TTTAT
1 TTATTTATTTTAT
29165 TTATTTATTTTAT
1 TTATTTATTTTAT
29178 TTATTTACTTTTA
1 TTATTTA-TTTTA
29191 GCACTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.33
13 14 0.39
14 10 0.28
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:29359 original size:29 final size:30
Alignment explanation
Indices: 29326--29382 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
29316 CATTTCATGC
29326 CATTTATATTCTCACCCTTTAA-ATTATAT
1 CATTTATATTCTCACCCTTTAATATTATAT
* * *
29355 CATTTTTATTTTCATCCTTTAATATTAT
1 CATTTATATTCTCACCCTTTAATATTAT
29383 TTGCAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (30 bp):
CATTTATATTCTCACCCTTTAATATTATAT
Found at i:31575 original size:108 final size:107
Alignment explanation
Indices: 31412--31691 Score: 382
Period size: 108 Copynumber: 2.6 Consensus size: 107
31402 ATTCAAAAAA
* * *
31412 CTCAAACATACTGGGTATGATTTTTTTTCTTTGAACATAAATAATTGAGTATCCTATTTAAAATC
1 CTCAAACATACT-GGTATGA---TTTTTCTTTGAACCTAAATAATCGAATATCCTATTTAAAATC
* * *
31477 AATAAATGTTTGATGTTCTTTTATTTAG-GGGATTCGAGAAATTGTG
62 AATAAATGTTCGATGTTCTTTTATTTAGAGAG-TTCAAGAAATTGTG
* *
31523 CTCAAACATACTAGGTATGATTTTTCTTTAAACCTAAATAATCAAATATCCTATTTAAAATCAAT
1 CTCAAACATACT-GGTATGATTTTTCTTTGAACCTAAATAATCGAATATCCTATTTAAAATCAAT
31588 AAATGTTCGATGTTCTTTTATTTAGAGAGTTCAAGAAATTGTG
65 AAATGTTCGATGTTCTTTTATTTAGAGAGTTCAAGAAATTGTG
* * * *
31631 CTCAAACGTACTGGATATGATTTTTCTTTGAACCTAAGTAGTCGAATATTCTATTTAAAAT
1 CTCAAACATACTGG-TATGATTTTTCTTTGAACCTAAATAATCGAATATCCTATTTAAAAT
31692 TGATAATTGT
Statistics
Matches: 152, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
107 2 0.01
108 129 0.85
109 2 0.01
111 19 0.12
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (107 bp):
CTCAAACATACTGGTATGATTTTTCTTTGAACCTAAATAATCGAATATCCTATTTAAAATCAATA
AATGTTCGATGTTCTTTTATTTAGAGAGTTCAAGAAATTGTG
Found at i:32407 original size:19 final size:19
Alignment explanation
Indices: 32366--32424 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
32356 CTACTATTCC
* * **
32366 TATTATTATTTGATTGTCG
1 TATTATTATTTTATTTTAT
32385 TATTATTATTTTATTTTAT
1 TATTATTATTTTATTTTAT
32404 TATTCATGTA-TTTATTTTAT
1 TATT-AT-TATTTTATTTTAT
32424 T
1 T
32425 TTTGCCATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.56
20 13 0.38
21 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (19 bp):
TATTATTATTTTATTTTAT
Found at i:34356 original size:31 final size:31
Alignment explanation
Indices: 34321--34383 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
34311 ACAAAATATC
*
34321 TCAATCTAATTTTATTCCAATCAAATTGATT
1 TCAATCTAATTTGATTCCAATCAAATTGATT
* * *
34352 TCAATTTGATTTGATTCTAATCAAATTGATT
1 TCAATCTAATTTGATTCCAATCAAATTGATT
34383 T
1 T
34384 AAAGGTCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (31 bp):
TCAATCTAATTTGATTCCAATCAAATTGATT
Found at i:35896 original size:29 final size:30
Alignment explanation
Indices: 35843--35901 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
35833 GAATTAGAAT
*
35843 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
* *
35873 AAATCAAAA-TTCATATATACAATTGCACA
1 AAATCAAAATTTCATATATAAAATTACACA
35902 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:36116 original size:76 final size:76
Alignment explanation
Indices: 36036--36290 Score: 288
Period size: 76 Copynumber: 3.4 Consensus size: 76
36026 GTTAATTTAT
* * * * *
36036 AATTTTAATTGTTAGCTTTAAAAAGTTGGTTTTGCTTAAAAACCACTCTTCAAACTCAATACTAA
1 AATTTTAATTTTTAGCTTAAAAAAGTTGGTTTTGCTTAAAAACCACTTTTGAAAGTCAATACTAA
36101 AGAAAGCTTAA
66 AGAAAGCTTAA
* *
36112 AATTTTAATTTTTAACTTGAAAAAA-TTGAG-TTTGCTTAAAAACCAATTTTGAAAGTCAATACT
1 AATTTTAATTTTTAGCTT-AAAAAAGTTG-GTTTTGCTTAAAAACCACTTTTGAAAGTCAATACT
*
36175 AAAGAAAGTTTAA
64 AAAGAAAGCTTAA
* * * * *
36188 AAGTTT-ATTTTTTGACTTAAAAAAGTTGATTTTGCTTAAAAACCACTTTTGAATGTGAATACTA
1 AATTTTAATTTTTAG-CTTAAAAAAGTTGGTTTTGCTTAAAAACCACTTTTGAAAGTCAATACTA
36252 AAGAAAG-TCT-A
65 AAGAAAGCT-TAA
*
36263 AATATTTAATTTTTTA-CTTACAAAAGTT
1 AAT-TTTAA-TTTTTAGCTTAAAAAAGTT
36291 TTTATTTTTA
Statistics
Matches: 152, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
75 16 0.11
76 124 0.82
77 7 0.05
78 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (76 bp):
AATTTTAATTTTTAGCTTAAAAAAGTTGGTTTTGCTTAAAAACCACTTTTGAAAGTCAATACTAA
AGAAAGCTTAA
Found at i:36887 original size:114 final size:114
Alignment explanation
Indices: 36687--36916 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 114
36677 ATAGTGAAAG
*
36687 CAAAATTAGTTGAGCAAACATGGTCAAACCCCTTGCTTCTTTTGCTCCTCGTCTTAATCCTCAAC
1 CAAAATTAGTTGAGAAAACATGGTCAAACCCCTTGCTTCTTTTGCTCCTCGTCTTAATCCTCAAC
36752 TTATTCCTTAACTTCATCAAGCGTAGCAAGCTCAAATTGCCACCATCGC
66 TTATTCCTTAACTTCATCAAGCGTAGCAAGCTCAAATTGCCACCATCGC
36801 CAAAATTAGTTGAGAAAACATGGTCAAACCCCTTGCTTCTTTTGCTCCTCGTCTTAATCCTCAAC
1 CAAAATTAGTTGAGAAAACATGGTCAAACCCCTTGCTTCTTTTGCTCCTCGTCTTAATCCTCAAC
36866 TTATTCCTTAACTTCATCAAGCGTAGCAAGCTCAAATTGCCACCATCGC
66 TTATTCCTTAACTTCATCAAGCGTAGCAAGCTCAAATTGCCACCATCGC
36915 CA
1 CA
36917 CCCATACTCC
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (114 bp):
CAAAATTAGTTGAGAAAACATGGTCAAACCCCTTGCTTCTTTTGCTCCTCGTCTTAATCCTCAAC
TTATTCCTTAACTTCATCAAGCGTAGCAAGCTCAAATTGCCACCATCGC
Found at i:39364 original size:71 final size:70
Alignment explanation
Indices: 39266--39404 Score: 167
Period size: 71 Copynumber: 2.0 Consensus size: 70
39256 AAATTAAAAT
** * *
39266 AAATAAAAAAATAAATTCAAGTAAACAATGACAACATAACAAGATTATAATTAAAAA-ATAAGTA
1 AAATAAAAAAATAAATTCAAGTAAACAACAACAACACAACAAGATTATAA--AAAAACATAAGCA
39330 AAAGTTC
64 AAAGTTC
* *
39337 AAATAAACAACATAAA-TCTAAGT-AACAACAATAACACAACAAGATTATAAAAAAACATAAGCA
1 AAATAAA-AAAATAAATTC-AAGTAAACAACAACAACACAACAAGATTATAAAAAAACATAAGCA
39400 AAAGT
64 AAAGT
39405 CTAAAATACA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
69 5 0.08
70 11 0.19
71 32 0.54
72 11 0.19
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (70 bp):
AAATAAAAAAATAAATTCAAGTAAACAACAACAACACAACAAGATTATAAAAAAACATAAGCAAA
AGTTC
Found at i:40915 original size:14 final size:14
Alignment explanation
Indices: 40896--40925 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40886 CCCTAATCCT
*
40896 CCATAAACCTTAAA
1 CCATAAACATTAAA
40910 CCATAAACATTAAA
1 CCATAAACATTAAA
40924 CC
1 CC
40926 TCAAATCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (14 bp):
CCATAAACATTAAA
Found at i:40938 original size:21 final size:21
Alignment explanation
Indices: 40899--40938 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40889 TAATCCTCCA
*
40899 TAAACCTTAAACCATAAACAT
1 TAAACCTCAAACCATAAACAT
40920 TAAACCTCAAATCCA-AAAC
1 TAAACCTCAAA-CCATAAAC
40939 CCAAACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCTCAAACCATAAACAT
Found at i:41441 original size:20 final size:20
Alignment explanation
Indices: 41413--41466 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
41403 CTCCAGTGAG
* *
41413 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
*
41433 ACTTTTACCGATACAACTCC
1 ACTTCTACCGATACAACTCC
*
41453 ACTTCTACAGATAC
1 ACTTCTACCGATAC
41467 CTTGAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:41697 original size:20 final size:21
Alignment explanation
Indices: 41674--41734 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 21
41664 AGAACTCCTC
41674 TTCTACT-GATACAACTATAG
1 TTCTACTCGATACAACTATAG
* * *
41694 TTCTA-TCAATACAAGTATGG
1 TTCTACTCGATACAACTATAG
*
41714 TTCTACTGGA-ACAACTA-AG
1 TTCTACTCGATACAACTATAG
41733 TT
1 TT
41735 GCAGACTGCT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 4 0.12
20 26 0.81
21 2 0.06
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (21 bp):
TTCTACTCGATACAACTATAG
Found at i:44393 original size:33 final size:34
Alignment explanation
Indices: 44327--44391 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
44317 AAACCTTTAT
*
44327 GCTTTAAATTGAAAATGATTTTTATATAAGGGGA
1 GCTTTAAATTGAAAATGACTTTTATATAAGGGGA
44361 GCTTT-AATTGAAAATGACTTTTAT-TAAGGGG
1 GCTTTAAATTGAAAATGACTTTTATATAAGGGG
44392 GAAAAATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 7 0.23
33 18 0.60
34 5 0.17
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (34 bp):
GCTTTAAATTGAAAATGACTTTTATATAAGGGGA
Found at i:46001 original size:59 final size:59
Alignment explanation
Indices: 45882--46060 Score: 277
Period size: 60 Copynumber: 3.0 Consensus size: 59
45872 TAATGTGGCA
*
45882 CTATTTTAGTGGTGCATAAAAATTATACTTTTTACGATGATCCTAATATAATTTATTCTC
1 CTATTTTATTGGTGCATAAAAATTATACTTTTTA-GATGATCCTAATATAATTTATTCTC
* *
45942 CTATTTTATTGTTGCTTAAAAATTATACTTTTTAGATGATCCTAATATAATTTATTCTC
1 CTATTTTATTGGTGCATAAAAATTATACTTTTTAGATGATCCTAATATAATTTATTCTC
* * * *
46001 CTATTTTATTGGTGCCTAAAAATTTTACTTTTCAAGATGATCTTAATATAATTTATTCTC
1 CTATTTTATTGGTGCATAAAAATTATACTTTT-TAGATGATCCTAATATAATTTATTCTC
46061 TTGAAATAAA
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
59 54 0.49
60 56 0.51
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (59 bp):
CTATTTTATTGGTGCATAAAAATTATACTTTTTAGATGATCCTAATATAATTTATTCTC
Done.