Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold339
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: 1314099
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 3 of 9
Found at i:299096 original size:20 final size:20
Alignment explanation
Indices: 299051--299126 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
299041 CTGCCAAGAA
***
299051 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
299072 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
299092 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
*
299112 GTGTATCGATACATT
1 ATGTATCGATACATT
299127 TAAGGGTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.04
20 30 0.65
21 14 0.30
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:301330 original size:11 final size:11
Alignment explanation
Indices: 301314--301346 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
301304 TTTACACCCC
301314 AAAAAAAACAA
1 AAAAAAAACAA
301325 AAAAAAAACAA
1 AAAAAAAACAA
301336 AAAAAACAACA
1 AAAAAA-AACA
301347 GGAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:302683 original size:28 final size:28
Alignment explanation
Indices: 302585--303720 Score: 1545
Period size: 28 Copynumber: 39.5 Consensus size: 28
302575 TGTTCATCCG
302585 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
* *
302614 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
302643 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
302671 TTTCCAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
302699 TTTCAAAACCCACAAGTCAGTAGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
302728 TTTCAAAGCCCACAAGTCAGTTGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
302756 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
302785 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
302813 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
* *
302842 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
302871 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
302899 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
302927 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
302956 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
* *
302985 TTTCAAAGCCCACAAATCAGTGGCACACT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
303014 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
303042 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
*
303071 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
* *
303100 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
303129 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
303157 TTTCGAAGCCCACAAGTTAGTGTCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
303185 TTTCAGAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
303213 TTTCGAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
303241 TTGCGAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
303269 TTTCAAAGCCCACACAAGTCAATGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
*
303300 TTTCAAAGCCCATGCAAGTCAATGGCA-CC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCC
*
303329 TTTTAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCC
*
303359 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
303387 TTTCAAAGCCCACAAGTTAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
303415 TTTCAGAGCCTACAAGTCAGTGGAACTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* *
303443 TTTCAAAGCCCACAAGCCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
303471 TTTCAAAGCCCACACAAGTCAGTGGCACTCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
* *
303502 TTTTAAAGCCCGCGCAAGTCAGTGGCACACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
* *
303533 TTTTCAAAGCCCACGAGTCAGTGGCACCT
1 -TTTCAAAGCCCACAAGTCAGTGGCACCC
303562 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
*
303590 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
* **
303618 TTTCAAAGCCCACGAGTCAGTGGCATTC
1 TTTCAAAGCCCACAAGTCAGTGGCACCC
303646 TTTCAAAGCCCACGCAAGTCAGTGGCACCC
1 TTTCAAAGCCCA--CAAGTCAGTGGCACCC
* ** *
303676 TTTTAAAGCCCACACAAGTCAGTAACACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
303707 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
303721 TGTGTCAGTG
Statistics
Matches: 1001, Mismatches: 86, Indels: 40
0.89 0.08 0.04
Matches are distributed among these distances:
28 477 0.48
29 359 0.36
30 93 0.09
31 63 0.06
32 9 0.01
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:302787 original size:114 final size:113
Alignment explanation
Indices: 302585--303720 Score: 1587
Period size: 114 Copynumber: 9.9 Consensus size: 113
302575 TGTTCATCCG
* *
302585 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
*
302650 GCCCACAAGTCAGTGGCACCCTTTCCAAGCCCACAAGTCAGTGGCACCC
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * *
302699 TTTCAAAACCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTTGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
302764 CCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACCC
66 CCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
* *
302813 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
*
302878 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCC
65 GCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
302927 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
* * *
302992 GCCCACAAATCAGTGGCACACTTTTCAAAGCCCACAAGTTAGTGGCACCC
65 GCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
*
303042 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
* *
303107 GCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC
65 GCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * *
303157 TTTCGAAGCCCACAAGTTAGTGTCAC-CCTTTCAGAGCCCACAAGTCAGTGGCACCCTTTCGAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
303221 CCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAAGTCAGTGGCACCC
66 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
303269 TTTCAAAGCCCACACAAGTCAATGGCACTCCTTTCAAAGCCCATGCAAGTCAATGGCA-CCTTTT
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTC
*
303333 AAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCC
62 AAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * * * * *
303387 TTTCAAAGCCCACAAGTTAGTGGCAC-CTTTTCAGAGCCTACAAGTCAGTGGAACTCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
303451 CCCACAAGCCAGTGGCACCTTTTCAAAGCCCACACAAGTCAGTGGCACTCC
66 CCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC-CC
* * * * *
303502 TTTTAAAGCCCGCGCAAGTCAGTGGCACACCTTTTCAAAGCCCACGAGTCAGTGGCACCTTTTCA
1 TTTCAAAG-CC-CACAAGTCAGTGGCACTCC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
*
303567 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCC
63 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
* * *
303618 TTTCAAAGCCCACGAGTCAGTGGCA-TTCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAA
** *
303682 AGCCCACACAAGTCAGTAACACTCTTTTCAAAGCCCACA
64 AG-CC-CACAAGTCAGTGGCAC-CCTTTCAAAGCCCACA
303721 TGTGTCAGTG
Statistics
Matches: 923, Mismatches: 76, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
112 68 0.07
113 68 0.07
114 341 0.37
115 229 0.25
116 51 0.06
117 58 0.06
118 52 0.06
119 56 0.06
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.21
Consensus pattern (113 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
Found at i:303764 original size:33 final size:33
Alignment explanation
Indices: 303359--303775 Score: 84
Period size: 28 Copynumber: 14.1 Consensus size: 33
303349 AGTGGCACCC
**
303359 TTTCAAAGCCCACAAGT-T-AGTGGCAC---CC
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
*
303387 TTTCAAAGCCCACAAGT-T-AGTGGCAC---CT
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
* * * *
303415 TTTCAGAGCCTACAA--GTCAGTGG-A-A-CTC
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
* *
303443 TTTCAAAGCCCACAA--GCCAGTGGCAC---CT
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
* **
303471 TTTCAAAGCCCACACA-AGTCAGTGGCAC-TCCT
1 TTTCAAAGCCCACA-AGTGTCAGTGGCACATTTT
* **
303503 TTT-AAAGCCCGCGCAA--GTCAGTGGCACA-CCT
1 TTTCAAAG-CC-CACAAGTGTCAGTGGCACATTTT
* *
303534 TTTCAAAGCCCAC--GAGTCAGTGGCAC---CT
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
**
303562 TTTCAAAGCCCACAA--GTCAGTGGCAC---CC
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
**
303590 TTTCAAAGCCCACAA--GTCAGTGG--CA-TCC
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
* *
303618 TTTCAAAGCCCAC--GAGTCAGTGG--CA-TTC
1 TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
**
303646 TTTCAAAGCCCACGCAA--GTCAGTGGCAC--CCT
1 TTTCAAAGCCCA--CAAGTGTCAGTGGCACATTTT
* * * *
303677 TTT-AAAGCCCACACA-AGTCAGT--AACACTCT
1 TTTCAAAGCCCACA-AGTGTCAGTGGCACATTTT
*
303707 TTTCAAAGCCCACATGTGTCAGTGGCA-ACTTTT
1 TTTCAAAGCCCACAAGTGTCAGTGGCACA-TTTT
303740 TTTCAAAGCCTACACAAGT-T-AGTGGCACATTTT
1 TTTCAAAGCC--CACAAGTGTCAGTGGCACATTTT
303773 TTT
1 TTT
303776 AAAAAACAAA
Statistics
Matches: 323, Mismatches: 26, Indels: 75
0.76 0.06 0.18
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 172 0.53
29 3 0.01
30 51 0.16
31 42 0.13
32 14 0.04
33 30 0.09
34 2 0.01
35 6 0.02
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (33 bp):
TTTCAAAGCCCACAAGTGTCAGTGGCACATTTT
Found at i:304356 original size:20 final size:20
Alignment explanation
Indices: 304328--304402 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
304318 TTTTACCCTG
304328 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
304348 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
304368 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
304388 ATGTATCGATACATT
1 ATGTATCGATACATT
304403 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:304395 original size:40 final size:39
Alignment explanation
Indices: 304328--304405 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
304318 TTTTACCCTG
* *
304328 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
304368 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
304406 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:309327 original size:11 final size:11
Alignment explanation
Indices: 309275--309329 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
309265 AATAATTACC
309275 AAAATAAAATT
1 AAAATAAAATT
* *
309286 --AATAATAGT
1 AAAATAAAATT
309295 AAAATAAATATT
1 AAAATAAA-ATT
* *
309307 TAACTAAAATT
1 AAAATAAAATT
309318 AAAATAAAATT
1 AAAATAAAATT
309329 A
1 A
309330 TATTAATTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
9 7 0.21
11 18 0.55
12 8 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:310984 original size:50 final size:50
Alignment explanation
Indices: 310896--311209 Score: 232
Period size: 50 Copynumber: 6.4 Consensus size: 50
310886 ATTAGGCTTT
* * * * * * *
310896 CTTTCCATCTTTAAGGCTTAACCTCCCTACCATGTGCCAACTAAATAGGT
1 CTTTCTATCTATAGGGCTTAACCTTCCTACCATATGCCAACTAAATTGGA
* * * *
310946 TTTTCTATCTATGGGGCTTAACATTCCTATCATATGCCAACTAAATTGGA
1 CTTTCTATCTATAGGGCTTAACCTTCCTACCATATGCCAACTAAATTGGA
* * *
310996 ATTTGTATCTATAGGGCTTAACC-TCTTTACCATATG-CAACTAAATTGGA
1 CTTTCTATCTATAGGGCTTAACCTTC-CTACCATATGCCAACTAAATTGGA
** * ** *
311045 CTTTCTATCTATACAGCTTAACCTTACTAAAAAATGCCAACTAAATTGGA
1 CTTTCTATCTATAGGGCTTAACCTTCCTACCATATGCCAACTAAATTGGA
* * ** *
311095 CTTTCTATCTATA--G---AACCTCCCAACCAGGTGCCAATTAAATTGGA
1 CTTTCTATCTATAGGGCTTAACCTTCCTACCATATGCCAACTAAATTGGA
* * * ** **
311140 TTTTCTATTTATAAGG-TTGAACC-TCCTTACCAGGTGCCAACTAAATTAAA
1 CTTTCTATCTATAGGGCTT-AACCTTCC-TACCATATGCCAACTAAATTGGA
* *
311190 CTTTCTATTTATAAGGCTTA
1 CTTTCTATCTATAGGGCTTA
311210 CCTCCATATC
Statistics
Matches: 212, Mismatches: 42, Indels: 20
0.77 0.15 0.07
Matches are distributed among these distances:
45 34 0.16
47 1 0.00
48 1 0.00
49 42 0.20
50 132 0.62
51 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (50 bp):
CTTTCTATCTATAGGGCTTAACCTTCCTACCATATGCCAACTAAATTGGA
Found at i:311054 original size:99 final size:100
Alignment explanation
Indices: 310910--311108 Score: 247
Period size: 99 Copynumber: 2.0 Consensus size: 100
310900 CCATCTTTAA
* ** *** *
310910 GGCTTAACCTCCCTACCATGTGCCAACTAAATAGGTTTTTCTATCTATGGGGCTTAACATTCCTA
1 GGCTTAACCTCCCTACCATATGCCAACTAAATAGGACTTTCTATCTATACAGCTTAACATTACTA
** * *
310975 TCATATGCCAACTAAATTGGAATTTGTATCTATAG
66 AAAAATGCCAACTAAATTGGAATTTCTATCTATAG
** * *
311010 GGCTTAACCTCTTTACCATATG-CAACTAAATTGGACTTTCTATCTATACAGCTTAACCTTACTA
1 GGCTTAACCTCCCTACCATATGCCAACTAAATAGGACTTTCTATCTATACAGCTTAACATTACTA
*
311074 AAAAATGCCAACTAAATTGGACTTTCTATCTATAG
66 AAAAATGCCAACTAAATTGGAATTTCTATCTATAG
311109 AACCTCCCAA
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
99 64 0.77
100 19 0.23
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (100 bp):
GGCTTAACCTCCCTACCATATGCCAACTAAATAGGACTTTCTATCTATACAGCTTAACATTACTA
AAAAATGCCAACTAAATTGGAATTTCTATCTATAG
Found at i:324793 original size:23 final size:24
Alignment explanation
Indices: 324743--324793 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
324733 AATGTCATCT
* *
324743 AAATAAAAGTCAAATTAATCTTAC
1 AAATAAAAGTCAAATTAACCTTAA
324767 AAATAAAA-T-AAATTATACCTTAA
1 AAATAAAAGTCAAATTA-ACCTTAA
324790 AAAT
1 AAAT
324794 TTTTAACTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 10 0.42
24 8 0.33
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATAAAAGTCAAATTAACCTTAA
Found at i:324957 original size:73 final size:72
Alignment explanation
Indices: 324767--325168 Score: 358
Period size: 73 Copynumber: 5.6 Consensus size: 72
324757 TTAATCTTAC
* * * * *
324767 AAAT-AAAATAAATTATACCTTAAAAATTTTTAACTCGTATAATTAACCTAAAAAATAAATTTAA
1 AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAATCAA-ATAAAAAACAAATTTAA
* *
324831 ACTTCTA-
65 AGTTTTAT
* * * * *
324838 AAATAAAAATTAAAATAAAAATACCTT---AATTTTAAACTCGTGTAATCAAAGTAGAAAATAAA
1 AAATAAAAA-T-AAAT---TATACCTTAAAAAATTTAAACTCGTATAATCAAA-TAAAAAACAAA
324900 TTTAAAGTTTTAT
60 TTTAAAGTTTTAT
* ** * **
324913 AAATAAAAATAAATTACATGTTAAAAATTTTAAACTCGTATAATCGAAGCAAAAAACAAATTTAA
1 AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAATC-AAATAAAAAACAAATTTAA
324978 AGTTTTAT
65 AGTTTTAT
* * * * * * *
324986 AAATAAAAACAAGTTATACATTAAAAAATTTAAACTCATATAATCATACACAAAA-AAA-TTAAA
1 AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAATCAAATAAAAAACAAATTTAAA
* *
325049 --CTTCT
66 GTTTTAT
* *
325054 -AATAAAAATAAA-AATACCTTAAAAAATTTAAACTCGTATAATCAAATCAGAAAACAAATTTAA
1 AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAATCAAAT-AAAAAACAAATTTAA
*
325117 AGTTCTAT
65 AGTTTTAT
* *
325125 AAATAAAAATAAATTATATCTTAAAAAATTAAAACTCGTATAAT
1 AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAAT
325169 TATATCTTAA
Statistics
Matches: 269, Mismatches: 43, Indels: 36
0.77 0.12 0.10
Matches are distributed among these distances:
66 30 0.11
67 15 0.06
68 6 0.02
69 5 0.02
70 9 0.03
71 9 0.03
72 23 0.09
73 110 0.41
74 46 0.17
75 9 0.03
77 7 0.03
ACGTcount: A:0.55, C:0.10, G:0.04, T:0.31
Consensus pattern (72 bp):
AAATAAAAATAAATTATACCTTAAAAAATTTAAACTCGTATAATCAAATAAAAAACAAATTTAAA
GTTTTAT
Found at i:325110 original size:139 final size:140
Alignment explanation
Indices: 324933--325191 Score: 378
Period size: 139 Copynumber: 1.9 Consensus size: 140
324923 AAATTACATG
* * *
324933 TTAAAAATTTTAAACTCGTATAATCGAAGCAAAAAACAAATTTAAAGTTTTATAAATAAAAACAA
1 TTAAAAAATTTAAACTCGTATAATCAAAGCAAAAAACAAATTTAAAGTTCTATAAATAAAAACAA
* *
324998 GTTATA-CATTAAAAAATTTAAACTCATATAATCATA-CACAAAAAAATTAAACTTCTAATAAAA
66 ATTATATC-TTAAAAAATTAAAACTCATATAATCATATCACAAAAAAATTAAACTTCTAATAAAA
325061 ATAAAAATACC
130 ATAAAAATACC
* * *
325072 TTAAAAAATTTAAACTCGTATAATCAAATCAGAAAACAAATTTAAAGTTCTATAAATAAAAATAA
1 TTAAAAAATTTAAACTCGTATAATCAAAGCAAAAAACAAATTTAAAGTTCTATAAATAAAAACAA
* * ** *
325137 ATTATATCTTAAAAAATTAAAACTCGTATAATTATATCTTAAAAAATTTAAACTT
66 ATTATATCTTAAAAAATTAAAACTCATATAATCATATCACAAAAAAATTAAACTT
325192 GTTAATCAAA
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
139 89 0.85
140 16 0.15
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.31
Consensus pattern (140 bp):
TTAAAAAATTTAAACTCGTATAATCAAAGCAAAAAACAAATTTAAAGTTCTATAAATAAAAACAA
ATTATATCTTAAAAAATTAAAACTCATATAATCATATCACAAAAAAATTAAACTTCTAATAAAAA
TAAAAATACC
Found at i:325197 original size:29 final size:30
Alignment explanation
Indices: 325136--325218 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
325126 AATAAAAATA
*
325136 AATTATATCTTAAAAAATTAAAACTCGTAT
1 AATTATATCTTAAAAAATTTAAACTCGTAT
*
325166 AATTATATCTTAAAAAATTTAAACTTGT-T
1 AATTATATCTTAAAAAATTTAAACTCGTAT
* * *
325195 AATCAAACCTGTAAAAAATTTAAA
1 AATTATATCT-TAAAAAATTTAAA
325219 GTTCTACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 8 0.17
30 39 0.83
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.36
Consensus pattern (30 bp):
AATTATATCTTAAAAAATTTAAACTCGTAT
Found at i:325221 original size:101 final size:102
Alignment explanation
Indices: 325071--325272 Score: 318
Period size: 101 Copynumber: 2.0 Consensus size: 102
325061 ATAAAAATAC
* *
325071 CTTAAAAAATTTAAACTCGTATAATCAAATCAGAAAACAAATTTAAAGTTCTATAAATAAAAATA
1 CTTAAAAAATTTAAACTCGTATAATCAAACCAGAAAACAAATTTAAAGTTCTACAAATAAAAATA
*
325136 AATTATATCTTAAAAAATTAAAACTCGTATAATTATAT
66 AATCATATCTT-AAAAATTAAAACTCGTATAATTATAT
* * *
325174 CTTAAAAAATTTAAACTTGT-TAATCAAACCTGTAAA-AAATTTAAAGTTCTACAAATAAAAATA
1 CTTAAAAAATTTAAACTCGTATAATCAAACCAGAAAACAAATTTAAAGTTCTACAAATAAAAATA
*
325237 AATCATATCTTAAAAATTTAAACTCGTATAATTATA
66 AATCATATCTTAAAAATTAAAACTCGTATAATTATA
325273 CCCAAAAAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 24 0.26
101 36 0.39
102 13 0.14
103 19 0.21
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (102 bp):
CTTAAAAAATTTAAACTCGTATAATCAAACCAGAAAACAAATTTAAAGTTCTACAAATAAAAATA
AATCATATCTTAAAAATTAAAACTCGTATAATTATAT
Found at i:325309 original size:73 final size:73
Alignment explanation
Indices: 325170--326946 Score: 1489
Period size: 73 Copynumber: 24.5 Consensus size: 73
325160 TCGTATAATT
* * *** *
325170 ATATCTTAAAAAATTTAAACTTGT-TAATCA-AACCTGTAAA-AAATTTAAAGTTCTACAAATAA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAA
*
325232 AAATAAATC
65 AAATAAATA
* * *
325241 ATATCTTAAAAATTTAAACTCGTATAATTATACCCAAAAAATAAATTTAAACTTCTACGAATAGA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
* *
325306 AATAAGTT
66 AATAAATA
* * * * * * *
325314 ATACCTTAAAAAAGTTAAACTCCTACAATTATA-CCAAAAAAT---TTTAAACTTTTATAAATAA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAA
325375 AAATAAA-A
65 AAATAAATA
* * * * * *
325383 ATATCTTAAAAAATTTAAACTAGTATAATCA-AACCAGAACACAAATTTTAAA-TTCTAAAAATA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCCAAAAAATAAA-TTTAAACTTCTACAAATA
* *
325446 AAATTAAATC
64 AAAATAAATA
*
325456 ATATCTTAAAAAATTTAAACTCGTATAATCATACCCAAAAAAATAAATTTAACCTTCTACAAATA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCC-AAAAAATAAATTTAAACTTCTACAAATA
325521 AAAATAAA-A
64 AAAATAAATA
* * * * *
325530 ATACCTTAAAAAATTTAAACTCATATAATCGAATA---AGAAAATAAATTTAAAGTTCTACAAAC
1 ATATCTT-AAAAATTTAAACTCGTATAATC--ATACCCAAAAAATAAATTTAAACTTCTACAAAT
*
325592 AAAAATAAATC
63 AAAAATAAATA
*
325603 ATATCTTAAAAATTTAAACTCGTATAATTATAACCC-AAAAATAAATTTAAACTTCTACAAATAA
1 ATATCTTAAAAATTTAAACTCGTATAATCAT-ACCCAAAAAATAAATTTAAACTTCTACAAATAA
325667 AAATAAA-A
65 AAATAAATA
* * * * * *
325675 ATA-CATTAAAAATTTTAAACTCGTATAATCA-AACTAGAGAACAAATTTAAAGTTCTACAAATA
1 ATATC-TTAAAAA-TTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATA
* *
325738 AAAATAAGTC
64 AAAATAAATA
* * *
325748 ATATCTTAAAAATTTAAACTCATATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAGA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
*
325813 AATAAATT
66 AATAAATA
* * * ** * * *
325821 ATATCTTTAAAAAGTTAAACTCTTATAACCATACTTAGAAAACA-AAATTTAGACTTCGATAAAT
1 ATATC-TTAAAAATTTAAACTCGTATAATCATACCCA-AAAA-ATAAATTTAAACTTCTACAAAT
*
325885 AAACATAAATA
63 AAAAATAAATA
** * * **
325896 ATCCCTTAAAAATTTAAACTCATATAATTA-AATCAAAAAATAAATTTAAAGCTT-TACAAATAA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAA-CTTCTACAAATAA
*
325959 AAATAAATT
65 AAATAAATA
* * * * *
325968 ATACCTTGAAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAATTTAAACTGCTATAAATA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATA-CCCAAAAAATAAATTTAAACTTCTACAAATA
326033 AAAATAAA-A
64 AAAATAAATA
** * * * *
326042 ATAAATTAAAAATTTAAATTCGTATAATCA-A-ACAAAAAA-AAATTTAAAGTTCTACATATAAA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
*
326104 AATAAATC
66 AATAAATA
* * * *
326112 ATATCTTAAAAAACTTAAACTCTTATAATCATACCTAAAAAATAAATTTAAACTTCTATAAATAA
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAA
326177 AAATAAA-A
65 AAATAAATA
* ** * *
326185 ATACCTTAAAAATTTTTAAA-TCGTATAATCA-AAGCAAAAAA-AAA-TT-AAGTTATACAAATA
1 ATATCTTAAAAA--TTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATA
* *
326245 AAAGTAAATC
64 AAAATAAATA
** * * * * *
326255 ATATCTTAAAAATTTAAACTTATATAATTATATCC-AAAAA-AAA-TTAAAATTTTACAAATAGA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
326317 AATAAAGT-
66 AATAAA-TA
* ** * *
326325 ATACCTTAAAAAATTTAAACTTATATAATCATA--TAAAAACCAT-AATTTAAACTTATACAAAT
1 ATATCTT-AAAAATTTAAACTCGTATAATCATACCCAAAAA--ATAAATTTAAACTTCTACAAAT
*
326387 AAAGATAAATA
63 AAAAATAAATA
* * * **
326398 ATA-CTATATAAATTTAAACTCATATAGT--TAAACAGAAAAATAAATTTAAA-TATCTACAAAT
1 ATATCT-TAAAAATTTAAACTCGTATAATCATACCCA-AAAAATAAATTTAAACT-TCTACAAAT
*
326459 AATAATAAAAATAA
63 AA-AA-ATAAAT-A
* * * * *
326473 ATTATACCTT-AAAATTTAAACTTGCATAATCATACTCAAAAAAGAAATTTTAAACTTTTACAAA
1 A-TAT--CTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAA-TTTAAACTTCTACAAA
326537 TAAAAATAAATA
62 TAAAAATAAATA
** * * * *
326549 ATAAATTAAAATTTTAAACTCATATAATCA-A-AC-AAAAAGAAA-TTACAACTTCTACAAATAA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTA-AACTTCTACAAATAA
*
326610 AAATAAATT
65 AAATAAATA
* ** * * *
326619 ATATCTTAAGAAATTTAAACTCATATAATCATACTTAAAAAACAAA-TTAAATTTTTACAAATAA
1 ATATCTTAA-AAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAA
326683 AAATAAATA
65 AAATAAATA
** ** * * * *
326692 ATAAATTAAATTTTTAAACTCGTATAATTA-AACCAAAAATTAAATTTAAACTTTTACAAATAAA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
326756 TAA-AAATAA
66 -AATAAAT-A
*** * * *
326765 ATTATACCTTAAAAATTTAAACTCGTATAATCATATTTAAAAAATAAAATTAAACTTCAATAAAT
1 A-TAT--CTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAAT
326830 AAAAATAAAAATA
63 AAAAAT--AAATA
* * * * * *
326843 ATAGC-TAAATATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAAACTTCTATAAATAAA
1 ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
*
326906 AATAAATT
66 AATAAATA
*
326914 ATACCTTAAAAATTTAAACTCGTATAATCATAC
1 ATATCTTAAAAATTTAAACTCGTATAATCATAC
326947 TAAAATATTT
Statistics
Matches: 1387, Mismatches: 230, Indels: 176
0.77 0.13 0.10
Matches are distributed among these distances:
68 7 0.01
69 95 0.07
70 124 0.09
71 114 0.08
72 283 0.20
73 349 0.25
74 203 0.15
75 92 0.07
76 32 0.02
77 48 0.03
78 13 0.01
79 26 0.02
80 1 0.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (73 bp):
ATATCTTAAAAATTTAAACTCGTATAATCATACCCAAAAAATAAATTTAAACTTCTACAAATAAA
AATAAATA
Found at i:325945 original size:365 final size:356
Alignment explanation
Indices: 325210--326951 Score: 1641
Period size: 365 Copynumber: 4.8 Consensus size: 356
325200 AACCTGTAAA
*
325210 AAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCGTATAATTAT-AC
1 AAATTTAAAGTTCTACAAATAAAAATAAATCATACCTTAAAAATTTAAACTCGTATAATTATAAC
* * ** * * *
325274 CCAAAAAATAAATTTAAACTTCTACGAATAGAAATAAGTTATACCTTAAAAAAGTTAAACTCCTA
66 CC-AAAAATAAATTTAAACTTCTACAAATAAAAATAA-AAATACATT-AAAAATTTAAACTCGTA
* * * * * * *
325339 CAATTATACCAAAA-AATTTTAAACTTTTATAAATAAAAATAAA-AATATCTTAAAAAATTTAAA
128 TAATCAAACAAAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTT-AAAAATTTAAA
* * * * * * *
325402 CT-AGTATAATCA-AACCAGAACACAAATTTTAAA-TTCTAAAAATAAAATTAAATCATATCTTA
192 CTCA-TATAATCATACCCAAAAAACAAA-TTTAAACTTCTACAAATAAAAATAAATAATACCTT-
325464 AAAAATTTAAACTCGTATAATCATACCCAAAAAAATAAATTTAACCTTCTACAAATAAAAATAAA
254 AAAAATTTAAACTCGTATAATCATA--C-AAAAAA-AAATTTAA-CTTCTACAAATAAAAATAAA
*
325529 -AATACCTTAAAAAATTTAAACTCATATAATCGAAT-AAGAAAAT
314 TAATACCTT-AAAAATTTAAACTCATATAATCAAATCAA-AAAAT
* *
325572 AAATTTAAAGTTCTACAAACAAAAATAAATCATATCTTAAAAATTTAAACTCGTATAATTATAAC
1 AAATTTAAAGTTCTACAAATAAAAATAAATCATACCTTAAAAATTTAAACTCGTATAATTATAAC
325637 CCAAAAATAAATTTAAACTTCTACAAATAAAAATAAAAATACATTAAAAATTTTAAACTCGTATA
66 CCAAAAATAAATTTAAACTTCTACAAATAAAAATAAAAATACATTAAAAA-TTTAAACTCGTATA
* * * * *
325702 ATCAAACTAGAGAACAAATTTAAAGTTCTACAAATAAAAATAAGTCATATCTTAAAAATTTAAAC
130 ATCAAAC-A-AAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAAC
* * *
325767 TCATATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAGAAATAAATTATATCTTTAAA
193 TCATATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATAATA-CCTTAAA
* * * * * *
325832 AAGTTAAACTCTTATAACCATACTTAGAAAACAAAATTTAGACTTCGATAAATAAACATAAATAA
257 AATTTAAACTCGTATAATCATAC--A-AAAA-AAAATTTA-ACTTCTACAAATAAAAATAAATAA
* *
325897 TCCCTTAAAAATTTAAACTCATATAATTAAATCAAAAAAT
317 TACCTTAAAAATTTAAACTCATATAATCAAATCAAAAAAT
* * *
325937 AAATTTAAAGCTT-TACAAATAAAAATAAATTATACCTTGAAAAATTTAAACTTGTATAATCATA
1 AAATTTAAAG-TTCTACAAATAAAAATAAATCATACCTT-AAAAATTTAAACTCGTATAATTATA
* * * * * *
326001 CCCCAAAAAAGAAATTTAAACTGCTATAAATAAAAATAAAAATAAATTAAAAATTTAAATTCGTA
64 ACCC-AAAAATAAATTTAAACTTCTACAAATAAAAATAAAAATACATTAAAAATTTAAACTCGTA
* * * * *
326066 TAATCAAACAAAAAAAAATTTAAAGTTCTACATATAAAAATAAATCATATCTTAAAAAACTTAAA
128 TAATCAAACAAAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTT-AAAAATTTAAA
* * * *
326131 CTCTTATAATCATACCTAAAAAATAAATTTAAACTTCTATAAATAAAAATAAA-AATACCTTAAA
192 CTCATATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAA
* * * * *
326195 AATTTTTAAA-TCGTATAATCAAAGCAAAAAAAAA-TTAAGTTATACAAATAAAAGTAAATCATA
257 AA--TTTAAACTCGTATAATCATA-CAAAAAAAAATTTAACTTCTACAAATAAAAATAAATAATA
* * * * *
326258 TCTTAAAAATTTAAACTTATATAATTATATCCAAAAA-
319 CCTTAAAAATTTAAACTCATATAATCAAATCAAAAAAT
* * * **
326295 AAA-TTAAAATTTTACAAATAGAAATAAAGT-ATACCTTAAAAAATTTAAACTTATATAATCATA
1 AAATTTAAAGTTCTACAAATAAAAATAAA-TCATACCTT-AAAAATTTAAACTCGTATAAT--TA
* * * *
326358 TAA---AAACCAT-AATTTAAACTTATACAAATAAAGATAAATAATAC-TATATAAATTTAAACT
62 TAACCCAAA-AATAAATTTAAACTTCTACAAATAAAAATAAA-AATACAT-TAAAAATTTAAACT
* * * *
326418 CATATAGTTAAACAGAAAAATAAATTTAAA-TATCTACAAATAATAATAAAAATAAATTATACCT
124 CGTATAATCAAAC--AAAAATAAATTTAAACT-TCTACAAATAA-AA-ATAAAT-AA-TAT--CT
*** * * *
326482 T-AAAATTTAAACTTGCATAATCATACTCAAAAAAGAAATTTTAAACTTTTACAAATAAAAATAA
180 TAAAAATTTAAACTCATATAATCATACCCAAAAAACAAA-TTTAAACTTCTACAAATAAAAATAA
** * * * * *
326546 ATAATAAATTAAAATTTTAAACTCATATAATCAAACAAAAAGAAATTACAACTTCTACAAATAAA
244 ATAATACCTTAAAAATTTAAACTCGTATAATCATACAAAAAAAAATT-TAACTTCTACAAATAAA
* * * * *
326611 AATAAATTATATCTTAAGAAATTTAAACTCATATAATCATACTTAAAAAAC
308 AATAAATAATACCTTAA-AAATTTAAACTCATATAATCA-AATCAAAAAAT
* * * ** **
326662 AAA-TTAAATTTTTACAAATAAAAATAAATAATAAATTAAATTTTTAAACTCGTATAATTA-AA-
1 AAATTTAAAGTTCTACAAATAAAAATAAATCATACCTTAAAAATTTAAACTCGTATAATTATAAC
* * *
326724 CCAAAAATTAAATTTAAACTTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTC
66 CCAAAAA-TAAATTTAAACTTCTAC----AAATAAAAATAAA-AATACATTAAAAATTTAAACTC
* * * *
326789 GTATAATCATATTTA-AAAAATAAAATTAAACTTCAATAAATAAAAATAAAAATAATAGC-TAAA
125 GTATAATCA-A---ACAAAAATAAATTTAAACTTCTACAAATAAAAAT--AAATAATATCTTAAA
* * * * * *
326852 TATTTAAACTCATATAATCA-AACTAAAAAATAAATTTAAACTTCTATAAATAAAAATAAATTAT
184 AATTTAAACTCATATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATAAT
*
326916 ACCTTAAAAATTTAAACTCGTATAATCATACTAAAA
249 ACCTTAAAAATTTAAACTCGTATAATCATACAAAAA
326952 TATTTTCACA
Statistics
Matches: 1153, Mismatches: 162, Indels: 127
0.80 0.11 0.09
Matches are distributed among these distances:
355 28 0.02
356 29 0.03
357 48 0.04
358 28 0.02
359 56 0.05
360 13 0.01
361 27 0.02
362 145 0.13
363 56 0.05
364 149 0.13
365 295 0.26
366 110 0.10
367 94 0.08
369 3 0.00
370 41 0.04
371 29 0.03
372 1 0.00
374 1 0.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (356 bp):
AAATTTAAAGTTCTACAAATAAAAATAAATCATACCTTAAAAATTTAAACTCGTATAATTATAAC
CCAAAAATAAATTTAAACTTCTACAAATAAAAATAAAAATACATTAAAAATTTAAACTCGTATAA
TCAAACAAAAATAAATTTAAACTTCTACAAATAAAAATAAATAATATCTTAAAAATTTAAACTCA
TATAATCATACCCAAAAAACAAATTTAAACTTCTACAAATAAAAATAAATAATACCTTAAAAATT
TAAACTCGTATAATCATACAAAAAAAAATTTAACTTCTACAAATAAAAATAAATAATACCTTAAA
AATTTAAACTCATATAATCAAATCAAAAAAT
Found at i:326243 original size:507 final size:500
Alignment explanation
Indices: 325207--326941 Score: 1966
Period size: 507 Copynumber: 3.4 Consensus size: 500
325197 TCAAACCTGT
* *
325207 AAAAAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCGTATAATTAT
1 AAAAAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAATCAT
* * *
325272 ACCCAAAAAATAAATTTAAACTTCTACGAATAGAAATAAGTTATACCTTAAAAAAGTTAAACTCC
66 ACCCAAAAAATAAATTTAAACTTCTACAAATAGAAATAAATTATACCTTAAAAAAGTTAAACTCT
* * * * *
325337 TACAAT--TATACCAAAAAATTTTAAACTTTTATAAATAAAAATAAA-AATATCTTAAAAAATTT
131 TATAATCATATA-AAAAAAAATTTAAACTTCTATAAATAAAAATAAATAATACCTT-AAAAATTT
* * * * * * * *
325399 AAACT-AGTATAATCAAACCAGAACACAAATTTTAAATTCTAAAAATAAAATTAAATCATATCTT
194 AAACTCA-TATAATTAAA-CAAAAAATAAA-TTTAAATT-TACAAATAAAAATAAATTATACCTT
* * * *
325463 AAAAAATTTAAACTCGTATAATCATACCCAAAAAAATAAATTTAACCTTCTACAAATAAAAATAA
255 -AAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAATTTAAACTTCTACAAATAAAAATAA
** * * *
325528 AAATACCTTAAAAAATTTAAACTCATATAATCGAATAAGAAAATAAATTTAAAGTTCTACAAACA
319 AAATAAATT-AAAAATTTAAACTCATATAATCAAACAA-AAAA-AAATTTAAAGTTCTACAAATA
* * *
325593 AAAATAAATCATATCTT-AAAAATTTAAACTCGTATAATTATAACC-CAAAAATAAATTTAAACT
381 AAAATAAATCATATCTTAAAAAATTTAAACTCATATAATCAT-ACCTAAAAAATAAATTTAAACT
325656 TCTACAAATAAAAATAAAAATACATTAAAAA-TTTTAAACTCGTATAATCAAACTAGA
445 TCTACAAATAAAAATAAAAATACATTAAAAATTTTTAAACTCGTATAATCAAAC-A-A
* *
325713 GAACAAATTTAAAGTTCTACAAATAAAAATAAGTCATATCTTAAAAATTTAAACTCATATAATCA
1 -AAAAAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAATCA
* * *
325778 TACCCAAAAAACAAATTTAAACTTCTACAAATAGAAATAAATTATATCTTTAAAAAGTTAAACTC
65 TACCCAAAAAATAAATTTAAACTTCTACAAATAGAAATAAATTATACCTTAAAAAAGTTAAACTC
* * * * *
325843 TTATAACCATACTTAGAAAACAAAATTTAGACTTCGATAAATAAACATAAATAATCCCTTAAAAA
130 TTATAATCATA--TA-AAAA-AAAATTTAAACTTCTATAAATAAAAATAAATAATACCTTAAAAA
325908 TTTAAACTCATATAATTAAATCAAAAAATAAATTTAAAGCTTTACAAATAAAAATAAATTATACC
191 TTTAAACTCATATAATTAAA-CAAAAAATAAATTTAAA--TTTACAAATAAAAATAAATTATACC
* *
325973 TTGAAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAATTTAAACTGCTATAAATAAAAAT
253 TT-AAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAATTTAAACTTCTACAAATAAAAAT
* * *
326038 AAAAATAAATTAAAAATTTAAATTCGTATAATCAAACAAAAAAAAATTTAAAGTTCTACATATAA
317 AAAAATAAATTAAAAATTTAAACTCATATAATCAAACAAAAAAAAATTTAAAGTTCTACAAATAA
* *
326103 AAATAAATCATATCTTAAAAAACTTAAACTCTTATAATCATACCTAAAAAATAAATTTAAACTTC
382 AAATAAATCATATCTTAAAAAATTTAAACTCATATAATCATACCTAAAAAATAAATTTAAACTTC
* *
326168 TATAAATAAAAATAAAAATACCTTAAAAATTTTTAAA-TCGTATAATCAAAGCAA
447 TACAAATAAAAATAAAAATACATTAAAAATTTTTAAACTCGTATAATCAAA-CAA
* * * * *
326222 AAAAAAATT-AAGTTATACAAATAAAAGTAAATCATATCTTAAAAATTTAAACTTATATAATTAT
1 AAAAAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAATCAT
* * * * *
326286 ATCC-AAAAA-AAA-TTAAAATTTTACAAATAGAAATAAAGTATACCTTAAAAAATTTAAACT-T
66 ACCCAAAAAATAAATTTAAACTTCTACAAATAGAAATAAATTATACCTTAAAAAAGTTAAACTCT
* * * * *
326347 ATATAATCATATAAAAACCATAATTTAAACTTATACAAATAAAGATAAATAATA-CTATATAAAT
131 -TATAATCATATAAAAA--AAAATTTAAACTTCTATAAATAAAAATAAATAATACCT-TAAAAAT
*
326411 TTAAACTCATATAGTTAAACAGAAAAATAAATTTAAATATCTACAAATAATAATAAAAATAAATT
192 TTAAACTCATATAATTAAACA-AAAAATAAATTTAAAT-T-TAC-----A-AATAAAAATAAATT
* * *
326476 ATACCTT-AAAATTTAAACTTGCATAATCATA-CTCAAAAAAGAAATTTTAAACTTTTACAAATA
248 ATACCTTAAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAA-TTTAAACTTCTACAAATA
* * *
326539 AAAATAAATAATAAATTAAAATTTTAAACTCATATAATCAAACAAAAAGAAA-TTACAACTTCTA
312 AAAATAAA-AATAAATTAAAAATTTAAACTCATATAATCAAACAAAAAAAAATTTA-AAGTTCTA
* * * *
326603 CAAATAAAAATAAATTATATCTTAAGAAATTTAAACTCATATAATCATACTTAAAAAACAAA-TT
375 CAAATAAAAATAAATCATATCTTAAAAAATTTAAACTCATATAATCATACCTAAAAAATAAATTT
* * * *
326667 AAATTTTTACAAATAAAAATAAATAATAAATT--AAATTTTTAAACTCGTATAATTAAACCAA
440 AAACTTCTACAAATAAAAATAAA-AATACATTAAAAATTTTTAAACTCGTATAATCAAA-CAA
* * * * *
326728 AAATTAAATTTAAACTTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTAT
1 AAA--AAATTTAAAGTTCTAC----AAATAAAAATAAATCATATCTTAAAAATTTAAACTCATAT
*** * * * * * * * *
326793 AATCATATTTAAAAAATAAAATTAAACTTCAATAAATAAAAATAAAAATAATAGC-T-AAATATT
60 AATCATACCCAAAAAATAAATTTAAACTTCTACAAATAGAAAT--AAATTATACCTTAAAAAAGT
* * *
326856 TAAACTCATATAATCAAACTAAAAAATAAATTTAAACTTCTATAAATAAAAATAAATTATACCTT
123 TAAACTCTTATAATCATA-TAAAAAA-AAATTTAAACTTCTATAAATAAAAATAAATAATACCTT
*
326921 AAAAATTTAAACTCGTATAAT
186 AAAAATTTAAACTCATATAAT
326942 CATACTAAAA
Statistics
Matches: 1053, Mismatches: 129, Indels: 83
0.83 0.10 0.07
Matches are distributed among these distances:
500 1 0.00
501 9 0.01
502 73 0.07
503 1 0.00
504 51 0.05
505 26 0.02
506 94 0.09
507 285 0.27
508 33 0.03
509 49 0.05
510 85 0.08
511 43 0.04
512 141 0.13
513 51 0.05
514 5 0.00
515 4 0.00
516 86 0.08
517 9 0.01
518 7 0.01
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (500 bp):
AAAAAATTTAAAGTTCTACAAATAAAAATAAATCATATCTTAAAAATTTAAACTCATATAATCAT
ACCCAAAAAATAAATTTAAACTTCTACAAATAGAAATAAATTATACCTTAAAAAAGTTAAACTCT
TATAATCATATAAAAAAAAATTTAAACTTCTATAAATAAAAATAAATAATACCTTAAAAATTTAA
ACTCATATAATTAAACAAAAAATAAATTTAAATTTACAAATAAAAATAAATTATACCTTAAAAAT
TTAAACTTGTATAATCATACCCCAAAAAAGAAATTTAAACTTCTACAAATAAAAATAAAAATAAA
TTAAAAATTTAAACTCATATAATCAAACAAAAAAAAATTTAAAGTTCTACAAATAAAAATAAATC
ATATCTTAAAAAATTTAAACTCATATAATCATACCTAAAAAATAAATTTAAACTTCTACAAATAA
AAATAAAAATACATTAAAAATTTTTAAACTCGTATAATCAAACAA
Found at i:326985 original size:146 final size:147
Alignment explanation
Indices: 325226--326951 Score: 735
Period size: 143 Copynumber: 11.9 Consensus size: 147
325216 AAAGTTCTAC
* * * * * *
325226 AAATAAAAAT--AAATCATATCTTAAAAATTTAAACTCGTATAATTATACCCAAAAAATAAATTT
1 AAATAAAAATAAAAATAATAGC-TAAATATTTAAACTCATATAATCA-AACCAAAAAATAAATTT
* * * * * * * *
325289 AAACTTCTAC----GAATAGAAATAAGTTATACCTTAAAAAAGTTAAACTCCTACAATTATA-CC
64 AAACTT-TACAAATAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATATCT
* *
325349 AAAAAAT---TTTAAACTTTTAT
127 AAAAAATAAAATTAAAC--TAAT
* * * *
325369 AAATAAAAATAAAAAT-AT--CTTAAAAAATTTAAACT-AGTATAATCAAACCAGAACACAAATT
1 AAATAAAAATAAAAATAATAGC-T-AAATATTTAAACTCA-TATAATCAAACCAAAAAATAAA-T
* * * * *
325430 TTAAA--TT-CTAA-AAATAAAATTAAATCATATCTTAAAAAATTTAAACTCGTATAATCATACC
62 TTAAACTTTACAAATAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATA-T
* * * * *
325491 CAAAAAAATAAATTTAACCTTCTAC
125 CTAAAAAATAAAATTAAAC-T-AAT
* * * *
325516 AAATAAAAAT--AAA-AATACCTTAAAAAATTTAAACTCATATAATCGAA-TAAGAAAATAAATT
1 AAATAAAAATAAAAATAATAGC-T-AAATATTTAAACTCATATAATCAAACCAA-AAAATAAATT
* * * * * * *
325577 TAAAGTTCTAC----AAACAAAAATAAATCATATCTTAAAAATTTAAACTCGTATAATTATAACC
63 TAAACTT-TACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCT
* * * *
325638 CAAAAATAAATTTAAACTTCTAC
127 AAAAAATAAAATTAAAC-T-AAT
* * * * * *
325661 AAATAAAAATAAAAATACAT---TAAAAATTTTAAACTCGTATAATCAAACTAGAGAACAAATTT
1 AAATAAAAATAAAAATA-ATAGCTAAATA-TTTAAACTCATATAATCAAACCAAAAAATAAATTT
* * * * * * *
325723 AAAGTTCTAC----AAATAAAAATAAGTCATATCTTAAAAATTTAAACTCATATAATCATACCCA
64 AAACTT-TACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCTA
* * * *
325784 AAAAACAAATTTAAACTTCTAC
128 AAAAATAAAATTAAAC-T-AAT
* * * * * * * * *
325806 AAATAGAAAT--AAATTATATCTTTAAAAAGTTAAACTCTTATAACCATACTTAGAAAACA-AAA
1 AAATAAAAATAAAAATAATAGC--TAAATATTTAAACTCATATAATCAAAC-CA-AAAA-ATAAA
* * * * * * * *
325868 TTTAGAC-TT-C-GATAAATAAACATAAATAATCCCTTAAAAATTTAAACTCATATAATTAAATC
61 TTTAAACTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATC
* * *
325930 -AAAAAATAAATTTAAAGCTTTAC
126 TAAAAAATAAAATTAAA-C-TAAT
* * * ** * *
325953 AAATAAAAAT--AAATTATACCTTGAAAAATTTAAACTTGTATAATCATACCCCAAAAAAGAAAT
1 AAATAAAAATAAAAATAATAGC-T-AAATATTTAAACTCATATAATCA-A-ACCAAAAAATAAAT
* * * ** * *
326016 TTAAAC--TGC-TATAAATAAAAATAAA-AATAAATTAAAAATTTAAATTCGTATAATCA-AAC-
62 TTAAACTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCT
* * **
326075 AAAAAA-AAATTTAAAGTTCT
127 AAAAAATAAAATTAAACTAAT
* * * * * *
326095 ACATATAAAAAT--AAATCATATCTTAAAAAACTTAAACTCTTATAATCATACCTAAAAAATAAA
1 A-A-ATAAAAATAAAAATAATAGC-T-AAATATTTAAACTCATATAATCAAACC-AAAAAATAAA
* * *
326158 TTTAAAC-TT-C-TATAAATAAAAATAAA-AATACCTTAAAAATTTTTAAA-TCGTATAATCAAA
61 TTTAAACTTTACAAATAAATAAAAATAAATTATACCTTAAAAA--TTTAAACTCGTATAATCATA
* ** *
326218 GC--AAAAA-AAAATTAAGTTATAC
124 TCTAAAAAATAAAATTAAACTA-AT
* * * * * * * *
326240 AAATAAAAGT--AAATCATATCTTAAAAATTTAAACTTATATAATTATATCC-AAAAA-AAATTA
1 AAATAAAAATAAAAATAATAGC-TAAATATTTAAACTCATATAATCA-AACCAAAAAATAAATTT
* * * **
326301 AAATTTTAC----AAATAGAAATAAAGTATACCTTAAAAAATTTAAACTTATATAATCATA--TA
64 AAACTTTACAAATAAATAAAAATAAATTATACCTT-AAAAATTTAAACTCGTATAATCATATCTA
* *
326360 AAAACCAT-AATTTAAACTTATAC
128 AAAA--ATAAAATTAAAC-TA-AT
* * * *
326383 AAATAAAGAT--AAATAATA-CTATATAAATTTAAACTCATATAGTTAAA-CAGAAAAATAAATT
1 AAATAAAAATAAAAATAATAGCTA-A-ATATTTAAACTCATATAATCAAACCA-AAAAATAAATT
* *
326444 TAAA-TATCTACAAATAATAATAAAAATAAATTATACCTT-AAAATTTAAACTTGCATAATCATA
63 TAAACT-T-TACAAAT-A-AATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA
* * * *
326507 -CTCAAAAAAGAAATTTTAAACTTTTAC
124 TCT-AAAAAATAAA-ATTAAAC--TAAT
* *
326534 AAATAAAAATAAATAATAA-A-TTAAA-ATTTTAAACTCATATAATCAAA-C-AAAAAGAAA-TT
1 AAATAAAAATAAA-AATAATAGCTAAATA-TTTAAACTCATATAATCAAACCAAAAAATAAATTT
* *
326593 ACAACTTCTAC----AAATAAAAATAAATTATATCTTAAGAAATTTAAACTCATATAATCATA-C
64 A-AACTT-TACAAATAAATAAAAATAAATTATACCTTAA-AAATTTAAACTCGTATAATCATATC
* * * *
326653 TTAAAAAA-CAAATTAAATTTTTAC
126 -TAAAAAATAAAATTAAA--CTAAT
* * * * *
326677 AAATAAAAATAAATAATAA-A-TTAAATTTTTAAACTCGTATAATTAAACCAAAAATTAAATTTA
1 AAATAAAAATAAA-AATAATAGCTAAATATTTAAACTCATATAATCAAACCAAAAAATAAATTTA
*
326740 AACTTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATTTAA
65 AAC-TTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCTAA
326805 AAAATAAAATTAAACTTCAAT
129 AAAATAAAATTAAAC-T-AAT
*
326826 AAATAAAAATAAAAATAATAGCTAAATATTTAAACTCATATAATCAAACTAAAAAATAAATTTAA
1 AAATAAAAATAAAAATAATAGCTAAATATTTAAACTCATATAATCAAACCAAAAAATAAATTTAA
*
326891 AC-TT-C-TATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA-CTAAAA
66 ACTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCTAAAA
326952 TATTTTCACA
Statistics
Matches: 1309, Mismatches: 164, Indels: 218
0.77 0.10 0.13
Matches are distributed among these distances:
139 19 0.01
140 30 0.02
141 16 0.01
142 88 0.07
143 223 0.17
144 102 0.08
145 220 0.17
146 137 0.10
147 166 0.13
148 98 0.07
149 89 0.07
150 47 0.04
151 62 0.05
152 3 0.00
153 4 0.00
154 5 0.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (147 bp):
AAATAAAAATAAAAATAATAGCTAAATATTTAAACTCATATAATCAAACCAAAAAATAAATTTAA
ACTTTACAAATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATATCTAAAA
AATAAAATTAAACTAAT
Found at i:327101 original size:17 final size:15
Alignment explanation
Indices: 327074--327117 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
327064 AACTAATCTT
*
327074 ATAAATAAAAATAAA
1 ATAAATTAAAATAAA
*
327089 TTATATATTAAAATAAA
1 --ATAAATTAAAATAAA
327106 ATAAATTAAAAT
1 ATAAATTAAAAT
327118 TTTTACAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAATTAAAATAAA
Found at i:327217 original size:13 final size:13
Alignment explanation
Indices: 327199--327227 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
327189 ATATTTTATA
327199 AAAATTACTTAAT
1 AAAATTACTTAAT
327212 AAAATTACTTAAT
1 AAAATTACTTAAT
327225 AAA
1 AAA
327228 TGTTTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAATTACTTAAT
Found at i:328950 original size:11 final size:11
Alignment explanation
Indices: 328936--328979 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
328926 TTTTATTGTT
*
328936 TTAAAAAAATT
1 TTAAAAAAATC
328947 TTAAAAAAAATC
1 TT-AAAAAAATC
*
328959 TTCAAAAAATC
1 TTAAAAAAATC
*
328970 TAAAAAAAAT
1 TTAAAAAAAT
328980 AATAATCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
TTAAAAAAATC
Found at i:331166 original size:15 final size:16
Alignment explanation
Indices: 331143--331176 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
331133 GTTTAATTAA
331143 TTTATATTTAAATATT
1 TTTATATTTAAATATT
*
331159 TTTA-ATTTTAATATT
1 TTTATATTTAAATATT
331174 TTT
1 TTT
331177 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTAAATATT
Found at i:333392 original size:35 final size:36
Alignment explanation
Indices: 333338--333408 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
333328 ATTATTCAAA
*
333338 AAATATTTATATTTTTTAAT-AATTA-AATTTAAAT
1 AAATATTTATATTTTTTAATAAATAATAATTTAAAT
333372 AAATATTT-TATTTTAATTAATAAATAATAATTTAAAT
1 AAATATTTATATTTT--TTAATAAATAATAATTTAAAT
333409 CAGATCGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 6 0.19
34 8 0.25
35 5 0.16
36 4 0.12
37 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AAATATTTATATTTTTTAATAAATAATAATTTAAAT
Found at i:334222 original size:16 final size:15
Alignment explanation
Indices: 334197--334226 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
334187 TATATTATTA
334197 ATTTATTATATAAAT
1 ATTTATTATATAAAT
334212 ATTTATATATATAAA
1 ATTTAT-TATATAAA
334227 AAAGAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTATATAAAT
Found at i:334952 original size:2 final size:2
Alignment explanation
Indices: 334945--334969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
334935 TGTATTACGT
334945 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
334970 GAGGTCGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:335051 original size:19 final size:19
Alignment explanation
Indices: 335009--335044 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
334999 ATTAAACTAG
*
335009 TTTTATATATTTTAATATA
1 TTTTATATATATTAATATA
335028 TTTTATATA-ATTAATAT
1 TTTTATATATATTAATAT
335045 TTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATATATATTAATATA
Found at i:335556 original size:4 final size:4
Alignment explanation
Indices: 335547--335596 Score: 55
Period size: 4 Copynumber: 11.5 Consensus size: 4
335537 GAAGAAAATT
*
335547 TTAA TTAA TTAA TTTAA TTAA TTCAA TTAGA TCAA TTAAA TTAA TTAA
1 TTAA TTAA TTAA -TTAA TTAA TT-AA TTA-A TTAA TT-AA TTAA TTAA
335595 TT
1 TT
335597 TAAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 25 0.62
5 15 0.38
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:335563 original size:9 final size:9
Alignment explanation
Indices: 335547--335599 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
335537 GAAGAAAATT
335547 TTAA-TTAA
1 TTAATTTAA
335555 TTAATTTAA
1 TTAATTTAA
*
335564 TTAATTCAA
1 TTAATTTAA
*
335573 TTAGA-TCAA
1 TTA-ATTTAA
*
335582 TTAAATTAA
1 TTAATTTAA
335591 TTAATTTAA
1 TTAATTTAA
335600 ATAAATATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
8 5 0.13
9 33 0.85
10 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (9 bp):
TTAATTTAA
Found at i:335867 original size:36 final size:33
Alignment explanation
Indices: 335827--335899 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 33
335817 TAAAAATTAG
335827 TAAAATTATATTTACATTAAACAATATAATATATAT
1 TAAAATTATATTTACATTAAA-AAT-TAATA-ATAT
* *
335863 TAAAATTATATTTATATTAAAAATTATTAATAT
1 TAAAATTATATTTACATTAAAAATTAATAATAT
335896 TAAA
1 TAAA
335900 TAAAACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 8 0.23
34 4 0.11
35 3 0.09
36 20 0.57
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
TAAAATTATATTTACATTAAAAATTAATAATAT
Found at i:335872 original size:18 final size:17
Alignment explanation
Indices: 335827--335899 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 17
335817 TAAAAATTAG
* *
335827 TAAAATTATATTTACAT
1 TAAAATTATATATATAT
*
335844 TAAACAATATAATATATAT
1 TAAA-ATTAT-ATATATAT
*
335863 TAAAATTATATTTATAT
1 TAAAATTATATATATAT
335880 TAAAAATTAT-TA-ATAT
1 T-AAAATTATATATATAT
335896 TAAA
1 TAAA
335900 TAAAACTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.06
16 5 0.11
17 13 0.28
18 16 0.34
19 10 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTATATATATAT
Found at i:335880 original size:17 final size:17
Alignment explanation
Indices: 335827--335899 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
335817 TAAAAATTAG
* *
335827 TAAAATTATATTTACAT
1 TAAAAATATATTTATAT
*
335844 TAAACAATATAATATATAT
1 TAAA-AATAT-ATTTATAT
*
335863 TAAAATTATATTTATAT
1 TAAAAATATATTTATAT
*
335880 TAAAAAT-TATTAATAT
1 TAAAAATATATTTATAT
335896 TAAA
1 TAAA
335900 TAAAACTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 12 0.26
17 17 0.36
18 8 0.17
19 10 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAAATATATTTATAT
Found at i:335973 original size:35 final size:29
Alignment explanation
Indices: 335926--336001 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 29
335916 TATGTTCATT
335926 AATTAAATAAAACTTATTTATTTAATATATCAAA
1 AATTAAATAAAACTTA--TATTT-ATAT-T-AAA
335960 ATATTAAATAAAACTTATATTTATATTAAA
1 A-ATTAAATAAAACTTATATTTATATTAAA
335990 AATTAAATAAAA
1 AATTAAATAAAA
336002 TTTTTAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.27
30 4 0.10
31 1 0.02
32 4 0.10
33 5 0.12
34 1 0.02
35 15 0.37
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (29 bp):
AATTAAATAAAACTTATATTTATATTAAA
Found at i:343680 original size:20 final size:20
Alignment explanation
Indices: 343636--343693 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
343626 TTTAATTATA
*
343636 AAATATATAAAT-A-TTAAT
1 AAATATAAAAATAATTTAAT
343654 ATTAATATAAAAATAATTTAAT
1 A--AATATAAAAATAATTTAAT
343676 AAATA-AGAAAATAGATTT
1 AAATATA-AAAATA-ATTT
343694 TTTAGTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 20 0.61
21 5 0.15
22 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATATAAAAATAATTTAAT
Found at i:344215 original size:3 final size:3
Alignment explanation
Indices: 344207--344235 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
344197 TAAGTTCAAA
344207 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
344236 AAAACAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:344678 original size:2 final size:2
Alignment explanation
Indices: 344673--344704 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
344663 ATTATTAAAA
344673 AT AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344705 GTAACAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344777 original size:91 final size:90
Alignment explanation
Indices: 344617--344795 Score: 313
Period size: 91 Copynumber: 2.0 Consensus size: 90
344607 TTCAGATGAC
* * *
344617 AACAAAAATTTTTTATAACCCAAGTTGATCACCCATCATCCAAAAAATTATTAAAAATATATAAT
1 AACAAAAATTTTGTATAACCCAAGTTGATCACCCATCATCAAAAAAATTATTAAAAAAATATAAT
344682 ATTATATATATATATATATATATGT
66 ATTATATATATATATATATATATGT
344707 AACAAAAATTTTGTATAACCCAAGTTGATCATCCCATCATCAAAAAAATTATTAAAAAAATATAA
1 AACAAAAATTTTGTATAACCCAAGTTGATCA-CCCATCATCAAAAAAATTATTAAAAAAATATAA
*
344772 TATTATGTATATATATATATATAT
65 TATTATATATATATATATATATAT
344796 ATCAAAACAA
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
90 30 0.36
91 54 0.64
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (90 bp):
AACAAAAATTTTGTATAACCCAAGTTGATCACCCATCATCAAAAAAATTATTAAAAAAATATAAT
ATTATATATATATATATATATATGT
Found at i:346644 original size:3 final size:3
Alignment explanation
Indices: 346636--346680 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
346626 AAAAAAGTCA
346636 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
346681 AACAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:348314 original size:21 final size:20
Alignment explanation
Indices: 348280--348321 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
348270 ATATTTTATT
* *
348280 TAAATTTTATTATAAAATATA
1 TAAATATTAATATAAAA-ATA
348301 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
348321 T
1 T
348322 TTTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATATTAATATAAAAATA
Found at i:348566 original size:27 final size:27
Alignment explanation
Indices: 348535--348587 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
348525 AAATTTAAAT
348535 TTTGAAATTTGAATGTTCTAAAAATTA
1 TTTGAAATTTGAATGTTCTAAAAATTA
* * *
348562 TTTGAATTTTTAATTTTCTAAAAATT
1 TTTGAAATTTGAATGTTCTAAAAATT
348588 TTATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (27 bp):
TTTGAAATTTGAATGTTCTAAAAATTA
Found at i:349399 original size:21 final size:24
Alignment explanation
Indices: 349375--349430 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
349365 GTAACTACCC
349375 TTTTTAAAAAATT-ATTT-AT--A
1 TTTTTAAAAAATTAATTTAATAAA
* *
349395 TTTTTTATAAATTAATTTAATAAA
1 TTTTTAAAAAATTAATTTAATAAA
349419 TTTTTAAAAAAT
1 TTTTTAAAAAAT
349431 GCTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 2 0.07
24 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTAAAAAATTAATTTAATAAA
Found at i:350313 original size:54 final size:52
Alignment explanation
Indices: 350251--350353 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 52
350241 AAAATTAAAA
* *
350251 TTTTAAATAAAACAATTCCATATGAACTTTTAATTTTTTCTGATTTATTATAAT
1 TTTTAAATAAAACAATTCCATATAAACTTTTAATTCTTT-T-ATTTATTATAAT
* *
350305 TTTTAAATAAAACAATTTCTTATAAACTTTTAATTCTTTTATTTATTAT
1 TTTTAAATAAAACAATTCCATATAAACTTTTAATTCTTTTATTTATTAT
350354 CAAATTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 9 0.20
53 1 0.02
54 35 0.78
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (52 bp):
TTTTAAATAAAACAATTCCATATAAACTTTTAATTCTTTTATTTATTATAAT
Found at i:350447 original size:17 final size:19
Alignment explanation
Indices: 350409--350453 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
350399 TTCCTTATAC
350409 AATAAAAAAATATCATTAAT
1 AATAAAAAAATAT-ATTAAT
*
350429 AATAAAAAAATATTTATAAT
1 AATAAAAAAATATAT-TAAT
350449 AATAA
1 AATAA
350454 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAAAAAATATATTAAT
Found at i:350520 original size:2 final size:2
Alignment explanation
Indices: 350513--350554 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
350503 TCTCACATTC
350513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350555 TTCAGTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351549 original size:29 final size:30
Alignment explanation
Indices: 351527--351589 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
351517 TTTATTTAAT
* *
351527 TTTTTATATTTTTA-TTATATTTAAATAAA
1 TTTTTAAATTTTAATTTATATTTAAATAAA
351556 TTTTTAAATTTTAATTTATATTTAAATAAA
1 TTTTTAAATTTTAATTTATATTTAAATAAA
351586 TTTT
1 TTTT
351590 GACTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAAATTTTAATTTATATTTAAATAAA
Found at i:351701 original size:29 final size:30
Alignment explanation
Indices: 351636--351712 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
351626 ATATTTTTTT
*
351636 ATATAAAATTTTATTTGAATATAAATAAAA
1 ATATAAAATTTTATTTAAATATAAATAAAA
*
351666 AAATAAAATTTTATTTAAATAT-AATAAAA
1 ATATAAAATTTTATTTAAATATAAATAAAA
351695 ATATAAAATTTTACTTTA
1 ATATAAAATTTTA-TTTA
351713 TAAAATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 19 0.44
30 24 0.56
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (30 bp):
ATATAAAATTTTATTTAAATATAAATAAAA
Found at i:351893 original size:16 final size:16
Alignment explanation
Indices: 351872--351902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
351862 ACATTCGAAT
351872 TTAAATTTAATTTAGA
1 TTAAATTTAATTTAGA
*
351888 TTAAATTTGATTTAG
1 TTAAATTTAATTTAG
351903 TTTATAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (16 bp):
TTAAATTTAATTTAGA
Found at i:352356 original size:16 final size:17
Alignment explanation
Indices: 352335--352367 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
352325 TAAATATATT
352335 TAATAAAT-AATTTTAA
1 TAATAAATAAATTTTAA
352351 TAATAAATAAATTTTAA
1 TAATAAATAAATTTTAA
352368 ATGTGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAAATAAATTTTAA
Found at i:352397 original size:17 final size:19
Alignment explanation
Indices: 352377--352423 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
352367 AATGTGATAA
352377 ATATTTAATAAA-AATAT-
1 ATATTTAATAAATAATATG
*
352394 ATATTTAGTTAAATAATATG
1 ATATTTA-ATAAATAATATG
*
352414 ATTTTTAATA
1 ATATTTAATA
352424 TAGATCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 4 0.17
19 7 0.29
20 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
ATATTTAATAAATAATATG
Found at i:352787 original size:20 final size:20
Alignment explanation
Indices: 352755--352792 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
352745 TATATTTATA
352755 TTATTTTTAAATATTTTTTC
1 TTATTTTTAAATATTTTTTC
352775 TTATATTTT-AATATTTTT
1 TTAT-TTTTAAATATTTTT
352793 ATAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTTAAATATTTTTTC
Found at i:355721 original size:2 final size:2
Alignment explanation
Indices: 355714--355756 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
355704 CTGATAGGTT
355714 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
355756 T
1 T
355757 TCCTTTTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:360428 original size:2 final size:2
Alignment explanation
Indices: 360421--360457 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
360411 TAAGAATACT
360421 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
360458 TCTTTCGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:361431 original size:13 final size:13
Alignment explanation
Indices: 361413--361440 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
361403 TATAAATAAT
361413 AATTATTTTTTTA
1 AATTATTTTTTTA
361426 AATTATTTTTTTA
1 AATTATTTTTTTA
361439 AA
1 AA
361441 ATTTTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTATTTTTTTA
Found at i:361613 original size:4 final size:4
Alignment explanation
Indices: 361604--361628 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
361594 CGTTGGATAT
361604 ACCA ACCA ACCA ACCA ACCA ACCA A
1 ACCA ACCA ACCA ACCA ACCA ACCA A
361629 GTTGTCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (4 bp):
ACCA
Found at i:361845 original size:29 final size:29
Alignment explanation
Indices: 361813--361869 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
361803 CTTGATAGCT
361813 TTAAAA-AAAATAAAACATAAAAATAATAA
1 TTAAAATAAAATAAAACAT-AAAATAATAA
* *
361842 TTAAAATATAATAAAATATAAAATAATA
1 TTAAAATAAAATAAAACATAAAATAATA
361870 TAAATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (29 bp):
TTAAAATAAAATAAAACATAAAATAATAA
Found at i:361854 original size:17 final size:17
Alignment explanation
Indices: 361821--361866 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 17
361811 CTTTAAAAAA
*
361821 AATAAAACATAAAA-AT
1 AATAAAATATAAAATAT
361837 AAT--AAT-TAAAATAT
1 AATAAAATATAAAATAT
361851 AATAAAATATAAAATA
1 AATAAAATATAAAATA
361867 ATATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
16 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAATATAAAATAT
Found at i:361872 original size:17 final size:16
Alignment explanation
Indices: 361829--361877 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
361819 AAAATAAAAC
361829 ATAAAA-ATAAT-AAT
1 ATAAAATATAATAAAT
361843 -TAAAATATAATAAAAT
1 ATAAAATATAAT-AAAT
361859 ATAAAATA-ATATAAAT
1 ATAAAATATA-ATAAAT
361875 ATA
1 ATA
361878 TTTATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
16 11 0.37
17 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAATATAATAAAT
Found at i:362083 original size:2 final size:2
Alignment explanation
Indices: 362072--362137 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
362062 CCCATACAAT
* * * *
362072 TA TA TA -A TA TA TA TA TA TA TA CA TA T- TA TG TA TG TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
362111 TA TA TT TA TA TA TA TA -A TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
362138 TGTTATTTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:362126 original size:34 final size:34
Alignment explanation
Indices: 362081--362151 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 34
362071 TTATATAATA
*
362081 TATATATATATACATATTATGTATGTAATTTATATT
1 TATATATATA-ACATATTATAT-TGTAATTTATATT
* *
362117 TATATATATAATATATTATATTGTTATTTATATT
1 TATATATATAACATATTATATTGTAATTTATATT
362151 T
1 T
362152 TTAAAACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 13 0.41
35 9 0.28
36 10 0.31
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (34 bp):
TATATATATAACATATTATATTGTAATTTATATT
Found at i:362523 original size:19 final size:20
Alignment explanation
Indices: 362490--362534 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
362480 ATTTTTTAAA
**
362490 TATTTGAATTTATTTA-ATT
1 TATTTGAATCAATTTATATT
362509 TATTTGAATCAATTTATTATT
1 TATTTGAATCAATTTA-TATT
362530 TATTT
1 TATTT
362535 AATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTGAATCAATTTATATT
Found at i:363067 original size:64 final size:65
Alignment explanation
Indices: 362973--363110 Score: 217
Period size: 64 Copynumber: 2.1 Consensus size: 65
362963 TTTCATTGAC
*
362973 CAAATTATTTTTTACAAAACAATCACT-AAAATTATGAAAAAAAAAATTTT-AAAATCATTTTTC
1 CAAATTATTTTTTACAAAACAAACACTAAAAATTATG-AAAAAAAAATTTTAAAAATCATTTTTC
363036 A
65 A
* *
363037 CAAATTATTTTTTACAAAACAAACACTAAAAATTATGAAAAAAAAATTTTAAAAATTATTTTTTA
1 CAAATTATTTTTTACAAAACAAACACTAAAAATTATGAAAAAAAAATTTTAAAAATCATTTTTCA
*
363102 CAAAATATT
1 CAAATTATT
363111 CGTATCTTAG
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 39 0.57
65 29 0.43
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.36
Consensus pattern (65 bp):
CAAATTATTTTTTACAAAACAAACACTAAAAATTATGAAAAAAAAATTTTAAAAATCATTTTTCA
Found at i:370620 original size:15 final size:17
Alignment explanation
Indices: 370600--370631 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
370590 TCAATTAAGT
370600 ATTTAAA-AAAT-TTTA
1 ATTTAAATAAATATTTA
370615 ATTTAAATAAATATTTA
1 ATTTAAATAAATATTTA
370632 TATTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAAATAAATATTTA
Found at i:370728 original size:16 final size:16
Alignment explanation
Indices: 370709--370739 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
370699 TTAATTTTTA
370709 ATAAAAATAATATATG
1 ATAAAAATAATATATG
*
370725 ATAAAAATATTATAT
1 ATAAAAATAATATAT
370740 TATTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATAAAAATAATATATG
Found at i:379689 original size:17 final size:18
Alignment explanation
Indices: 379662--379695 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
379652 AAATTGATAG
*
379662 TTTGATTTATATCTTATT
1 TTTGATTTATATATTATT
379680 TTTG-TTTATATATTAT
1 TTTGATTTATATATTAT
379696 CAGCGAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (18 bp):
TTTGATTTATATATTATT
Found at i:383098 original size:22 final size:23
Alignment explanation
Indices: 383064--383108 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
383054 TAAACTTAAA
383064 AATTATAAATAAA-ATTTAATTT
1 AATTATAAATAAATATTTAATTT
*
383086 AATTA-AAATTAAATTTTTAATTT
1 AATTATAAA-TAAATATTTAATTT
383109 TTTATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 9 0.45
23 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATAAATAAATATTTAATTT
Found at i:384496 original size:16 final size:18
Alignment explanation
Indices: 384477--384516 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
384467 CAATAATTCG
384477 ATTTATAAA-TA-AATTT
1 ATTTATAAATTATAATTT
*
384493 ATTTTTAAATTATAATTT
1 ATTTATAAATTATAATTT
384511 -TTTATA
1 ATTTATA
384517 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATAAATTATAATTT
Found at i:385288 original size:15 final size:16
Alignment explanation
Indices: 385270--385299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
385260 AAAATTAAAT
385270 TTATTA-AAATTTTTA
1 TTATTATAAATTTTTA
385285 TTATTATAAATTTTT
1 TTATTATAAATTTTT
385300 TTACTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATAAATTTTTA
Found at i:385584 original size:15 final size:16
Alignment explanation
Indices: 385555--385587 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
385545 ACGTTTAAAA
385555 TTAAATTTCAAAATTT
1 TTAAATTTCAAAATTT
385571 TTAAATTT-AAAATTT
1 TTAAATTTCAAAATTT
385586 TT
1 TT
385588 GTTTGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAAATTTCAAAATTT
Found at i:385815 original size:13 final size:13
Alignment explanation
Indices: 385785--385828 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
385775 ATCAAAACAG
385785 AAAATTTTAATTT
1 AAAATTTTAATTT
*
385798 ATAAATTTAAAATTT
1 A-AAATTT-TAATTT
385813 AAAATTTTAATTT
1 AAAATTTTAATTT
385826 AAA
1 AAA
385829 TGAATGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 9 0.33
14 12 0.44
15 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTTTAATTT
Found at i:386264 original size:9 final size:9
Alignment explanation
Indices: 386247--386287 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
386237 AACTTTTTAA
*
386247 AAATAAAAT
1 AAATTAAAT
386256 AAATTAAAT
1 AAATTAAAT
*
386265 AAATCAAAT
1 AAATTAAAT
*
386274 AAATTAAAA
1 AAATTAAAT
386283 AAATT
1 AAATT
386288 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATTAAAT
Found at i:386273 original size:18 final size:18
Alignment explanation
Indices: 386245--386286 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
386235 AAAACTTTTT
386245 AAAAATAAAATAAATTAA
1 AAAAATAAAATAAATTAA
* *
386263 ATAAATCAAATAAATTAA
1 AAAAATAAAATAAATTAA
386281 AAAAAT
1 AAAAAT
386287 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATAAAATAAATTAA
Found at i:387942 original size:14 final size:14
Alignment explanation
Indices: 387923--387959 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
387913 AAATTTTGTG
387923 TTTTTTTATTTTAT
1 TTTTTTTATTTTAT
*
387937 TTTTTTAATTTTAT
1 TTTTTTTATTTTAT
387951 TATTTTTTA
1 T-TTTTTTA
387960 CTCGATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTATTTTAT
Found at i:388779 original size:22 final size:23
Alignment explanation
Indices: 388753--388840 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 23
388743 ATAAATTTAT
388753 TATTTATAAATATATTTTTAAT-
1 TATTTATAAATATATTTTTAATA
* *
388775 TATTTGTGAATATATTTAATT-ATA
1 TATTTATAAATATATTT--TTAATA
* *
388799 TATTTATAAAAATATTCATTTAATG
1 TATTTATAAATATATT--TTTAATA
*
388824 T-TTGTATAAATTTATTT
1 TATT-TATAAATATATTT
388841 AATTTAAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
22 15 0.29
23 3 0.06
24 19 0.37
25 13 0.25
26 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.56
Consensus pattern (23 bp):
TATTTATAAATATATTTTTAATA
Found at i:388792 original size:20 final size:20
Alignment explanation
Indices: 388741--388797 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
388731 AATAATATCA
*
388741 AAATAAATTT-ATTATTTAT
1 AAATATATTTAATTATTTAT
*
388760 AAATATATTTTTAATTATTTGT
1 AAATATA--TTTAATTATTTAT
*
388782 GAATATATTTAATTAT
1 AAATATATTTAATTAT
388798 ATATTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 9 0.28
21 3 0.09
22 14 0.44
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
AAATATATTTAATTATTTAT
Found at i:389379 original size:18 final size:20
Alignment explanation
Indices: 389356--389401 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
389346 AATAGACATC
389356 TAATTATT-AAT-TTTAATA
1 TAATTATTAAATATTTAATA
389374 TAATTATTACAATATTTAATA
1 TAATTATTA-AATATTTAATA
*
389395 TCATTAT
1 TAATTAT
389402 CACTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
20 3 0.12
21 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATTATTAAATATTTAATA
Found at i:389835 original size:19 final size:20
Alignment explanation
Indices: 389804--389843 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
389794 ATATATATAT
389804 ATATATAAATTAAAT-TAAA
1 ATATATAAATTAAATATAAA
389823 ATAT-TAAATTTAAATATAAA
1 ATATATAAA-TTAAATATAAA
389843 A
1 A
389844 AAGAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATAAATTAAATATAAA
Found at i:389959 original size:18 final size:20
Alignment explanation
Indices: 389927--389972 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
389917 AATTATATGA
389927 TATATATTAATTTT-ATGTTT
1 TATATATTAATTTTAAT-TTT
389947 TATATATT-A-TTTAATTTT
1 TATATATTAATTTTAATTTT
389965 TATTATAT
1 TA-TATAT
389973 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATATATTAATTTTAATTTT
Found at i:389971 original size:19 final size:20
Alignment explanation
Indices: 389927--389972 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
389917 AATTATATGA
*
389927 TATATATTAATTTTATGTTT
1 TATATATTAATTTAATGTTT
389947 TATATATT-ATTTAAT-TTT
1 TATATATTAATTTAATGTTT
389965 TATTATAT
1 TA-TATAT
389973 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATATATTAATTTAATGTTT
Found at i:390074 original size:15 final size:14
Alignment explanation
Indices: 390033--390083 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
390023 AGTTATTTAT
390033 ATTTTAAAAATT-A
1 ATTTTAAAAATTAA
*
390046 A--TAAAAATATTAA
1 ATTTTAAAA-ATTAA
390059 ATTATTAAAAATTAA
1 ATT-TTAAAAATTAA
390074 ATTTTAAAAA
1 ATTTTAAAAA
390084 AATTATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.16
12 3 0.10
13 3 0.10
14 7 0.23
15 8 0.26
16 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTTAAAAATTAA
Found at i:390084 original size:16 final size:17
Alignment explanation
Indices: 390040--390088 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 17
390030 TATATTTTAA
* *
390040 AAATTAATAAAAATATT
1 AAATTATTAAAAAAATT
390057 AAATTATT--AAAAATT
1 AAATTATTAAAAAAATT
390072 AAATT-TTAAAAAAATT
1 AAATTATTAAAAAAATT
390088 A
1 A
390089 TGTTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
16 8 0.29
17 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTATTAAAAAAATT
Found at i:391134 original size:19 final size:20
Alignment explanation
Indices: 391099--391136 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
391089 AATTATTGAA
*
391099 TAAATTTTAATTATTTTTAT
1 TAAATTTAAATTATTTTTAT
391119 TAAATTTAAATT-TTTTTA
1 TAAATTTAAATTATTTTTA
391137 ATTTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAAATTTAAATTATTTTTAT
Found at i:391141 original size:15 final size:17
Alignment explanation
Indices: 391111--391152 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
391101 AATTTTAATT
391111 ATTTTTATTAAATTTAA
1 ATTTTTATTAAATTTAA
391128 ATTTTT-TT-AATTTATA
1 ATTTTTATTAAATTTA-A
391144 ATATTTTAT
1 AT-TTTTAT
391153 ATTTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.27
16 5 0.23
17 10 0.45
18 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTATTAAATTTAA
Found at i:391740 original size:20 final size:23
Alignment explanation
Indices: 391715--391758 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
391705 TAAATATTAT
391715 TAAAAAATTA-T-TTTTA-TAAA
1 TAAAAAATTAGTATTTTATTAAA
391735 TAAAAAATTAGTATTTTATTAAA
1 TAAAAAATTAGTATTTTATTAAA
391758 T
1 T
391759 TAATAATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 5 0.24
23 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAAAAATTAGTATTTTATTAAA
Found at i:391932 original size:20 final size:20
Alignment explanation
Indices: 391895--391933 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
391885 TCAAATTTAT
*
391895 TAATATATTTTATTATAAAA
1 TAATATATTTTATCATAAAA
391915 TAAT-TATTTTATACATAAA
1 TAATATATTTTAT-CATAAA
391934 TAAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATATTTTATCATAAAA
Found at i:393256 original size:23 final size:23
Alignment explanation
Indices: 393230--393280 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
393220 ATTAATCTAT
393230 TATATTTAAT-TTAATTATAAAAA
1 TATATTTAATATTAA-TATAAAAA
*
393253 TATA-TAAATATTAATATAAAAA
1 TATATTTAATATTAATATAAAAA
393275 TA-ATTT
1 TATATTT
393281 TTTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATATTTAATATTAATATAAAAA
Found at i:394335 original size:15 final size:16
Alignment explanation
Indices: 394315--394344 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
394305 TTTAAAAAAT
394315 TATGTATA-TATATTA
1 TATGTATATTATATTA
394330 TATGTATATTATATT
1 TATGTATATTATATT
394345 TTAAGTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TATGTATATTATATTA
Found at i:399474 original size:22 final size:22
Alignment explanation
Indices: 399447--399498 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
399437 ATTTAACATG
* *
399447 AATAATAAAAAAATAAAATATT
1 AATAATAAAAAAATAAAAAAAT
** *
399469 AATAATATCATAATAAAAAAAT
1 AATAATAAAAAAATAAAAAAAT
399491 AATAATAA
1 AATAATAA
399499 TTAACTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAATAAAAAAATAAAAAAAT
Found at i:399821 original size:43 final size:43
Alignment explanation
Indices: 399774--399953 Score: 198
Period size: 43 Copynumber: 4.0 Consensus size: 43
399764 CATTACATTT
* *
399774 CATGCATTTCATGTAATTTTCATTTCTTGCATTACATTTCATA
1 CATGCATTTCACGTAATTTTCATTTCATGCATTACATTTCATA
* *
399817 CATGCATTTCACGTAATTTTCATTTCCTGCATTACATTTCATG
1 CATGCATTTCACGTAATTTTCATTTCATGCATTACATTTCATA
* *
399860 CATGCATTTCACATAATTTTCATTTCATGCATTTCACACATTACATTTCATG
1 CATGCATTTCACGTAATTTTCATTTCATG---------CATTACATTTCATA
* * *
399912 CATGCATTTCACGTAATGTTCATTTCATGCATTTCGTTTCAT
1 CATGCATTTCACGTAATTTTCATTTCATGCATTACATTTCAT
399954 GCATTACATT
Statistics
Matches: 119, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
43 78 0.66
52 41 0.34
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (43 bp):
CATGCATTTCACGTAATTTTCATTTCATGCATTACATTTCATA
Found at i:399886 original size:29 final size:29
Alignment explanation
Indices: 399851--399943 Score: 108
Period size: 29 Copynumber: 3.4 Consensus size: 29
399841 TCCTGCATTA
399851 CATTTCATGCATGCATTTCACATAATTTT
1 CATTTCATGCATGCATTTCACATAATTTT
* *
399880 CA-TT--T-CATGCATTTCACA-CA-TTA
1 CATTTCATGCATGCATTTCACATAATTTT
* *
399903 CATTTCATGCATGCATTTCACGTAATGTT
1 CATTTCATGCATGCATTTCACATAATTTT
399932 CATTTCATGCAT
1 CATTTCATGCAT
399944 TTCGTTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 13 0.25
26 2 0.04
27 12 0.23
28 3 0.06
29 15 0.29
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.42
Consensus pattern (29 bp):
CATTTCATGCATGCATTTCACATAATTTT
Found at i:399907 original size:52 final size:52
Alignment explanation
Indices: 399846--399946 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
399836 TCATTTCCTG
*
399846 CATTACATTTCATGCATGCATTTCACATAATTTTCATTTCATGCATTTCACA
1 CATTACATTTCATGCATGCATTTCACATAATGTTCATTTCATGCATTTCACA
*
399898 CATTACATTTCATGCATGCATTTCACGTAATGTTCATTTCATGCATTTC
1 CATTACATTTCATGCATGCATTTCACATAATGTTCATTTCATGCATTTC
399947 GTTTCATGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.43
Consensus pattern (52 bp):
CATTACATTTCATGCATGCATTTCACATAATGTTCATTTCATGCATTTCACA
Found at i:400052 original size:15 final size:15
Alignment explanation
Indices: 400040--400075 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
400030 CATGCATTGT
400040 ATTGCATTGCATTTC
1 ATTGCATTGCATTTC
400055 ATTGCATTGC-TTTC
1 ATTGCATTGCATTTC
400069 A-TGCATT
1 ATTGCATT
400076 AAAGCTCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 5 0.24
15 10 0.48
ACGTcount: A:0.19, C:0.19, G:0.14, T:0.47
Consensus pattern (15 bp):
ATTGCATTGCATTTC
Found at i:401237 original size:22 final size:21
Alignment explanation
Indices: 401186--401253 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
401176 TGGTAGCAGC
* *
401186 AAAAAAAG-AAAGCAGCAAAC
1 AAAAACAGCAAAGCAGCAAAG
401206 AAAAACAGCAATAGCAGCAAAG
1 AAAAACAGCAA-AGCAGCAAAG
**
401228 AAAAGTAGCAAA-CAGCAAAGG
1 AAAAACAGCAAAGCAGCAAA-G
401249 AAAAA
1 AAAAA
401254 AACAAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.35
21 8 0.20
22 18 0.45
ACGTcount: A:0.65, C:0.15, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAAACAGCAAAGCAGCAAAG
Found at i:401898 original size:9 final size:9
Alignment explanation
Indices: 401884--401920 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
401874 CTTTGCTTAA
401884 TTGGATGTT
1 TTGGATGTT
401893 TTGGATGTT
1 TTGGATGTT
*
401902 TTGGATGTC
1 TTGGATGTT
401911 TTGGTATGTT
1 TTGG-ATGTT
401921 GTCAAGTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 21 0.84
10 4 0.16
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.54
Consensus pattern (9 bp):
TTGGATGTT
Found at i:404794 original size:9 final size:9
Alignment explanation
Indices: 404780--404807 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
404770 TTTTTCTCAG
404780 TTTAAAATT
1 TTTAAAATT
404789 TTTAAAATT
1 TTTAAAATT
404798 TTTAAAATT
1 TTTAAAATT
404807 T
1 T
404808 ATCAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTAAAATT
Found at i:404814 original size:18 final size:19
Alignment explanation
Indices: 404780--404819 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
404770 TTTTTCTCAG
*
404780 TTTAAAATTTTTAAAAT-T
1 TTTAAAATTTATAAAATAT
*
404798 TTTAAAATTTATCAAATAT
1 TTTAAAATTTATAAAATAT
404817 TTT
1 TTT
404820 CATTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTATAAAATAT
Found at i:407849 original size:154 final size:151
Alignment explanation
Indices: 407322--407837 Score: 458
Period size: 154 Copynumber: 3.4 Consensus size: 151
407312 CATATTTATT
* ** * * * * ** * *
407322 TATCA-TTTTGTGTCCTTTAGGATTACTAAGATACTTTTATGTCGAAGGTATACATAGGGGAATC
1 TATCATTTTTGTGTCCTTTAGGGTTACCGAGATACTTTCATGTCAAAGTTATACTTAAAGGCATT
* * * * * *
407386 TTGGTAATTTTTCTTAGAACCAAGTCTTAGGCAGTCACTGGT-TATTTCTAT-TCAAAGGTGTAC
66 TTGGTAA-TTTT-TTAGAACCGAGTCTTAGGTAGTCACTGATCTCTTT-TATGCCAAAAGTGTAC
*
407449 GTTTAGGATAGGTTCATCTTTTTTTA
128 GTTTAGAATAGGTTCA--TTTTTTTA
** * ** *
407475 TATCATTTTCATGTCCATTAGGGTTATTGGGATACTTTCATGTCAAAGTTATACTTAAAGGCATT
1 TATCATTTTTGTGTCCTTTAGGGTTACCGAGATACTTTCATGTCAAAGTTATACTTAAAGGCATT
* * * * *
407540 TTAGTAATTTTTTAAAATCGAGTCTTAGGTAGTCACCGAGTCACTTTTATGCCATAGACA-TG--
66 TTGGTAATTTTTTAGAACCGAGTCTTAGGTAGTCACTGA-TCTCTTTTATGCCA-A-A-AGTGTA
407602 CGTTTA-AGATAGGTTCATCCTTTTTT-
127 CGTTTAGA-ATAGGTTCAT--TTTTTTA
* * * * *
407628 TAT--TTTCCTTGTGTCCTTTAAGGTTACCAAGATACTTTCACGTCAAAGGTATACCCTAAAGGC
1 TATCATTT--TTGTGTCCTTTAGGGTTACCGAGATACTTTCATGTCAAAGTTATA-CTTAAAGGC
407691 ATTTTGGTAATTTCTTTAGAACCGAGTCTTAGGTAGTCACTTGATCTCTTTTATGCCAAAAGTGT
63 ATTTTGGTAATTT-TTTAGAACCGAGTCTTAGGTAGTCAC-TGATCTCTTTTATGCCAAAAGTGT
* *
407756 ACATTTAGAATATGTTCATTTTTTTA
126 ACGTTTAGAATAGGTTCATTTTTTTA
* * *
407782 TATCATTTTTGTATCCTTTTGGGTTACCGAGATATTTTCATGTCAAAGTTATACTT
1 TATCATTTTTGTGTCCTTTAGGGTTACCGAGATACTTTCATGTCAAAGTTATACTT
407838 TATGGGCATT
Statistics
Matches: 288, Mismatches: 53, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
151 3 0.01
152 24 0.08
153 62 0.22
154 138 0.48
155 52 0.18
156 9 0.03
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (151 bp):
TATCATTTTTGTGTCCTTTAGGGTTACCGAGATACTTTCATGTCAAAGTTATACTTAAAGGCATT
TTGGTAATTTTTTAGAACCGAGTCTTAGGTAGTCACTGATCTCTTTTATGCCAAAAGTGTACGTT
TAGAATAGGTTCATTTTTTTA
Found at i:410398 original size:30 final size:31
Alignment explanation
Indices: 410349--410413 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
410339 AATGGATACT
*
410349 TTATTCTTTGCAAATTTTATTTATAAATCAA
1 TTATTCTTTGCAAATTTTATTCATAAATCAA
* * *
410380 TTATT-TTTGTAATTTTTATTCATAAATTAA
1 TTATTCTTTGCAAATTTTATTCATAAATCAA
410410 TTAT
1 TTAT
410414 CTACACGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (31 bp):
TTATTCTTTGCAAATTTTATTCATAAATCAA
Found at i:411111 original size:12 final size:12
Alignment explanation
Indices: 411096--411150 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
411086 ATATTTTATT
411096 TTATTATATAAA
1 TTATTATATAAA
411108 TTATTAT-TATAA
1 TTATTATATA-AA
**
411120 TTATTATATTTTA
1 TTATTATA-TAAA
*
411133 TT-TTATAAAAA
1 TTATTATATAAA
411144 TTATTAT
1 TTATTAT
411151 TATATTGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
11 5 0.15
12 25 0.74
13 3 0.09
14 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTATATAAA
Found at i:411146 original size:36 final size:35
Alignment explanation
Indices: 411056--411177 Score: 117
Period size: 35 Copynumber: 3.3 Consensus size: 35
411046 AAAATAAAAA
*
411056 TTATTTTA-AAAAATTTAATT-TT-TTTTATTAATATT
1 TTATTTTATAAAAA-TT-ATTATTATATTATT-ATATT
411091 TTATTTTATTATATAAATTATTATTATAATTATTATATT
1 TTATTTTA-TA-A-AAATTATTATTAT-ATTATTATATT
*
411130 TTATTTTATAAAAATTATTATTATATT-GTATTATT
1 TTATTTTATAAAAATTATTATTATATTATTA-TATT
411165 TTATTTTAATAAA
1 TTATTTT-ATAAA
411178 CTAAATTTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
34 2 0.03
35 22 0.29
36 18 0.24
37 5 0.07
38 7 0.09
39 17 0.22
40 5 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.61
Consensus pattern (35 bp):
TTATTTTATAAAAATTATTATTATATTATTATATT
Found at i:411184 original size:39 final size:39
Alignment explanation
Indices: 411080--411184 Score: 121
Period size: 39 Copynumber: 2.7 Consensus size: 39
411070 TTAATTTTTT
* *
411080 TTATTAATATTTTATTTTATTATATAAATTATTATTATAA
1 TTATT-ATATTTTATTTTAATAAATAAATTATTATTATAA
411120 TTATTATATTTTATTTT-AT-AA-AAATTATTATTAT-A
1 TTATTATATTTTATTTTAATAAATAAATTATTATTATAA
*
411155 TT-GTATTATTTTATTTTAATAAACTAAATT
1 TTATTA-TATTTTATTTTAATAAA-TAAATT
411185 TATTGCAAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
34 2 0.04
35 14 0.25
36 15 0.26
37 3 0.05
38 1 0.02
39 17 0.30
40 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (39 bp):
TTATTATATTTTATTTTAATAAATAAATTATTATTATAA
Found at i:411947 original size:13 final size:13
Alignment explanation
Indices: 411931--411958 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
411921 ATGCTGGTTG
411931 GACTGATGATGAT
1 GACTGATGATGAT
411944 GACTGATGATGAT
1 GACTGATGATGAT
411957 GA
1 GA
411959 TCTTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (13 bp):
GACTGATGATGAT
Found at i:416057 original size:27 final size:28
Alignment explanation
Indices: 416010--416063 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
416000 ATTTTTATTT
416010 TAATTATTATTTTAAATTATATTTAAAG
1 TAATTATTATTTTAAATTATATTTAAAG
416038 TAATTGATT-TTTT-AATTATATTTAAA
1 TAATT-ATTATTTTAAATTATATTTAAA
416064 AAATATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 13 0.52
28 9 0.36
29 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TAATTATTATTTTAAATTATATTTAAAG
Found at i:418121 original size:36 final size:36
Alignment explanation
Indices: 418076--418145 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
418066 GCAAACACTA
*
418076 ATATAATATCTCTTTAAGTTCATATGAGGATTTGAT
1 ATATAATATCTCTTTAAGCTCATATGAGGATTTGAT
*
418112 ATATAATATCTCTTTAAGCTCGTATGAGGATTTG
1 ATATAATATCTCTTTAAGCTCATATGAGGATTTG
418146 TTATCATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (36 bp):
ATATAATATCTCTTTAAGCTCATATGAGGATTTGAT
Found at i:418739 original size:65 final size:65
Alignment explanation
Indices: 418658--418787 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
418648 CATTTTAGAT
* *
418658 TTTTATATTTATAAATAGAAAAATGATAAGGTATATTATTGTGTTTGAATATTAAATTTTCAAGA
1 TTTTATATTTATAAATAGAAAAATGATAAGATATATTATTGTGTTTAAATATTAAATTTTCAAGA
*
418723 TTTTATATTTATAAATAGAAAAATGGTAAGATATATTATTGTGTTTAAATATTAAATTTTCAAGA
1 TTTTATATTTATAAATAGAAAAATGATAAGATATATTATTGTGTTTAAATATTAAATTTTCAAGA
418788 ATTATCAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.45
Consensus pattern (65 bp):
TTTTATATTTATAAATAGAAAAATGATAAGATATATTATTGTGTTTAAATATTAAATTTTCAAGA
Found at i:419420 original size:32 final size:31
Alignment explanation
Indices: 419381--419481 Score: 112
Period size: 32 Copynumber: 3.1 Consensus size: 31
419371 TTAATTGTCC
419381 GGGTCATTTCGGGTTTGAATCATTTCGAGTTT
1 GGGTCATTTCGGGTTTG-ATCATTTCGAGTTT
* * * *
419413 GGGTCATTTCGAGTTCGCATCATTTTGAGTTC
1 GGGTCATTTCGGGTTTG-ATCATTTCGAGTTT
* *
419445 GGGTCATTTCAGGTTCTGGTCATTTCGAGTTT
1 GGGTCATTTCGGGTT-TGATCATTTCGAGTTT
419477 CGGGT
1 -GGGT
419482 TGGTCGGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
32 51 0.91
33 5 0.09
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.42
Consensus pattern (31 bp):
GGGTCATTTCGGGTTTGATCATTTCGAGTTT
Found at i:419451 original size:16 final size:16
Alignment explanation
Indices: 419380--419481 Score: 98
Period size: 16 Copynumber: 6.3 Consensus size: 16
419370 GTTAATTGTC
*
419380 CGGGTCATTTCGGGTT
1 CGGGTCATTTCGAGTT
* **
419396 TGAATCATTTCGAGTT
1 CGGGTCATTTCGAGTT
*
419412 TGGGTCATTTCGAGTT
1 CGGGTCATTTCGAGTT
** *
419428 CGCATCATTTTGAGTT
1 CGGGTCATTTCGAGTT
419444 CGGGTCATTTC-AGGTT
1 CGGGTCATTTCGA-GTT
*
419460 CTGGTCATTTCGAGTTT
1 CGGGTCATTTCGAG-TT
419477 CGGGT
1 CGGGT
419482 TGGTCGGTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.01
16 60 0.88
17 7 0.10
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (16 bp):
CGGGTCATTTCGAGTT
Found at i:419680 original size:20 final size:20
Alignment explanation
Indices: 419655--419696 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
419645 TATGTAACAA
*
419655 TTATTTTTATTAAATTAAAG
1 TTATTTATATTAAATTAAAG
* *
419675 TTATTTATATTTAATTTAAG
1 TTATTTATATTAAATTAAAG
419695 TT
1 TT
419697 TAAGCTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTTATATTAAATTAAAG
Found at i:420345 original size:2 final size:2
Alignment explanation
Indices: 420338--420375 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
420328 CGGATTTCGA
420338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
420376 TTTGAGAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:423010 original size:20 final size:20
Alignment explanation
Indices: 422964--423025 Score: 53
Period size: 22 Copynumber: 3.2 Consensus size: 20
422954 TATTTAATTT
422964 TATATTAAAA-ATAT-AAT-
1 TATATTAAAATATATAAATA
*
422981 TAT-TT-TAATATATAAATA
1 TATATTAAAATATATAAATA
*
422999 TATATTAAAATATTTTAAAATA
1 TATATTAAAATA-TAT-AAATA
423021 TATAT
1 TATAT
423026 ACAAATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 2 0.06
16 6 0.17
17 6 0.17
18 3 0.09
19 2 0.06
20 4 0.11
21 2 0.06
22 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATTAAAATATATAAATA
Found at i:423358 original size:24 final size:24
Alignment explanation
Indices: 423331--423397 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
423321 ACACTGATTT
423331 TTTTTTTTAATTTTATAAGATTAA
1 TTTTTTTTAATTTTATAAGATTAA
** *
423355 TTTTTTTGGATTTTATAAGATTAT
1 TTTTTTTTAATTTTATAAGATTAA
423379 TTTTTTTTAATTTTATAAG
1 TTTTTTTTAATTTTATAAG
423398 TAAAATTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.64
Consensus pattern (24 bp):
TTTTTTTTAATTTTATAAGATTAA
Found at i:424026 original size:21 final size:21
Alignment explanation
Indices: 424000--424039 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
423990 TTCTAATAAT
*
424000 ATTTATTAATAATAAATATTA
1 ATTTATTAATAACAAATATTA
*
424021 ATTTATTATTAACAAATAT
1 ATTTATTAATAACAAATAT
424040 GTACTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTATTAATAACAAATATTA
Found at i:426530 original size:21 final size:22
Alignment explanation
Indices: 426488--426530 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
426478 TTTTAATCTC
*
426488 TTAAAAACTATTATTAATATAT
1 TTAAAAACTAGTATTAATATAT
426510 TTAAAAA-TAGTATATAA-ATAT
1 TTAAAAACTAGTAT-TAATATAT
426531 GTTTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAAAACTAGTATTAATATAT
Found at i:435072 original size:2 final size:2
Alignment explanation
Indices: 435060--435098 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
435050 TTTGACTTCT
435060 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
435099 AATTGGTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:436865 original size:22 final size:21
Alignment explanation
Indices: 436820--436865 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
436810 AATTTTAAAA
* * *
436820 AAAGAAATGAAGAAATAAGTG
1 AAAGAAATGAAAAAAAAAGGG
436841 AAAGAAAATGAAAAAAAAAGGG
1 AAAG-AAATGAAAAAAAAAGGG
436863 AAA
1 AAA
436866 AGAGGAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.22, T:0.09
Consensus pattern (21 bp):
AAAGAAATGAAAAAAAAAGGG
Found at i:437421 original size:2 final size:2
Alignment explanation
Indices: 437408--437454 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
437398 TATTCTTTTG
*
437408 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
437450 TA TA T
1 TA TA T
437455 GACTTCACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:441227 original size:13 final size:13
Alignment explanation
Indices: 441209--441234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
441199 TACACCAAGT
441209 ATGTATCGATACA
1 ATGTATCGATACA
441222 ATGTATCGATACA
1 ATGTATCGATACA
441235 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:441253 original size:34 final size:32
Alignment explanation
Indices: 441191--441255 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
441181 TAGCCAAACT
**
441191 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
441223 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
441256 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:442901 original size:19 final size:20
Alignment explanation
Indices: 442877--442924 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
442867 GGCAGCACCA
442877 CCAGGTCGCGACCGGCACT-
1 CCAGGTCGCGACCGGCACTC
442896 CCAGGTCGCGACCGGCACTC
1 CCAGGTCGCGACCGGCACTC
442916 CCAGGTCGC
1 CCAGGTCGC
442925 AACCAAGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.15, C:0.44, G:0.31, T:0.10
Consensus pattern (20 bp):
CCAGGTCGCGACCGGCACTC
Found at i:445028 original size:13 final size:13
Alignment explanation
Indices: 445010--445035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
445000 TACACCAAGT
445010 ATGTATCGATACA
1 ATGTATCGATACA
445023 ATGTATCGATACA
1 ATGTATCGATACA
445036 CCAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:446901 original size:20 final size:20
Alignment explanation
Indices: 446876--446950 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
446866 ATTTGCCTGC
*
446876 ATGTATTGATACATTGAATA
1 ATGTATCGATACATTGAATA
* **
446896 ATGTATCAATACATTTGCGTA
1 ATGTATCGATACA-TTGAATA
* *
446917 TTGTATCGATACATTGACTA
1 ATGTATCGATACATTGAATA
446937 ATGTATCGATACAT
1 ATGTATCGATACAT
446951 CTGGGTGAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Done.