Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:170304 original size:21 final size:20
Alignment explanation
Indices: 170277--170340 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
170267 TTTTTCAAAG
170277 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
170297 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
170312 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
170332 AAATCATTT
1 AAA-CATTT
170341 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:174880 original size:37 final size:37
Alignment explanation
Indices: 174822--174940 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
174812 TCCCATTATC
* *
174822 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
174858 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
*
174894 A-TTTTCAAAGAAACATTTACCAAACTTT-AAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
174929 ATTTTTTCAAAG
1 A-TTTTTCAAAG
174941 TTGATTACCA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 33 0.43
36 14 0.18
37 29 0.38
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACT
Found at i:176938 original size:23 final size:23
Alignment explanation
Indices: 176889--176970 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
176879 AAAACTACCA
* * * * *
176889 AAAGGCAGAGAAAAATTTGCCAC
1 AAAGGCAAAGATAAATGTGTCAT
176912 AAAGGCAAAGATAAATGTGTCAT
1 AAAGGCAAAGATAAATGTGTCAT
*
176935 AAA-G-ACAGATAAATGTGTCAT
1 AAAGGCAAAGATAAATGTGTCAT
176956 AAAGGCAAAGATAAA
1 AAAGGCAAAGATAAA
176971 CATGACGTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 19 0.38
22 2 0.04
23 29 0.58
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (23 bp):
AAAGGCAAAGATAAATGTGTCAT
Found at i:176946 original size:21 final size:21
Alignment explanation
Indices: 176920--176959 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
176910 ACAAAGGCAA
176920 AGATAAATGTGTCATAAAGAC
1 AGATAAATGTGTCATAAAGAC
176941 AGATAAATGTGTCATAAAG
1 AGATAAATGTGTCATAAAG
176960 GCAAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (21 bp):
AGATAAATGTGTCATAAAGAC
Found at i:180221 original size:23 final size:22
Alignment explanation
Indices: 180191--180263 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
180181 CAGTAGCTTG
*
180191 CAATTTGAGAAGTGATCTAAGAC
1 CAATTTGA-ATGTGATCTAAGAC
* *
180214 CAATTTGAATGCGATCTTAGAC
1 CAATTTGAATGTGATCTAAGAC
180236 CAATTTGAATGTGATCTAAGAC
1 CAATTTGAATGTGATCTAAGAC
180258 CAATTT
1 CAATTT
180264 ACCTCCTCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 37 0.82
23 8 0.18
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (22 bp):
CAATTTGAATGTGATCTAAGAC
Found at i:182287 original size:12 final size:13
Alignment explanation
Indices: 182270--182298 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
182260 ACTAAAATAC
182270 ATAAAAATATAT-
1 ATAAAAATATATG
182282 ATAAAAATATATG
1 ATAAAAATATATG
182295 ATAA
1 ATAA
182299 TTTTGCCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAAAAATATATG
Found at i:188484 original size:17 final size:17
Alignment explanation
Indices: 188464--188497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
188454 TCTTTATTCC
* *
188464 AGAATTGATTTTATTTG
1 AGAAGTGATATTATTTG
188481 AGAAGTGATATTATTTG
1 AGAAGTGATATTATTTG
188498 GTATTACCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (17 bp):
AGAAGTGATATTATTTG
Found at i:189969 original size:23 final size:23
Alignment explanation
Indices: 189911--189994 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
189901 ATCGCAATTA
189911 AATAAAAACTAATTATATTTTTTTG
1 AATAAAAA--AATTATATTTTTTTG
* * *
189936 AATTAATAAATTCATATTTTTTTT
1 AATAAAAAAATT-ATATTTTTTTG
* *
189960 AA-AAAAAAATTATAATTTTATG
1 AATAAAAAAATTATATTTTTTTG
*
189982 AATAAAAATATTA
1 AATAAAAAAATTA
189995 ATTATAAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 10 0.21
23 20 0.42
24 12 0.25
25 6 0.12
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AATAAAAAAATTATATTTTTTTG
Found at i:190054 original size:2 final size:2
Alignment explanation
Indices: 190047--190086 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
190037 TGAACCGTGA
190047 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
190087 TTAAAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193812 original size:24 final size:24
Alignment explanation
Indices: 193784--193855 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
193774 TGAAATACTT
193784 AAATGTTTTAGTTCAAAACATTAA
1 AAATGTTTTAGTTCAAAACATTAA
193808 AAATGTTTTAGTTCAAAACATTAA
1 AAATGTTTTAGTTCAAAACATTAA
193832 AAATGTTTTAGTTCAAAACATTAA
1 AAATGTTTTAGTTCAAAACATTAA
193856 CAATATTCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (24 bp):
AAATGTTTTAGTTCAAAACATTAA
Found at i:200081 original size:20 final size:21
Alignment explanation
Indices: 200056--200096 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
200046 GTTGTGGTCG
*
200056 TTTCTAGCCGTTT-GGGATGA
1 TTTCTAGCAGTTTGGGGATGA
200076 TTTCTAGCAGTTTGGGGATGA
1 TTTCTAGCAGTTTGGGGATGA
200097 AATCTCTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (21 bp):
TTTCTAGCAGTTTGGGGATGA
Found at i:200720 original size:18 final size:18
Alignment explanation
Indices: 200699--200781 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
200689 CTTAAACTTT
*
200699 ATATTATTTTTATTATAA
1 ATATAATTTTTATTATAA
*
200717 ATATAATATTTTA-AATAA
1 ATATAAT-TTTTATTATAA
200735 ATTATTAA-TTTTATT-TAA
1 A-TA-TAATTTTTATTATAA
200753 AT-TAATTTATTATTA-AA
1 ATATAATTT-TTATTATAA
*
200770 A-ATAACTTTTAT
1 ATATAATTTTTAT
200782 CATTTAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
15 3 0.06
16 6 0.11
17 14 0.26
18 20 0.38
19 7 0.13
20 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATAATTTTTATTATAA
Found at i:200882 original size:14 final size:16
Alignment explanation
Indices: 200851--200890 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
200841 TAAGTTAAAT
200851 TATAATTTTATTTATA
1 TATAATTTTATTTATA
200867 TATAATTTCT-TTTATA
1 TATAATTT-TATTTATA
*
200883 TATTATTT
1 TATAATTT
200891 ACAAATGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TATAATTTTATTTATA
Found at i:200996 original size:16 final size:16
Alignment explanation
Indices: 200917--201011 Score: 59
Period size: 16 Copynumber: 5.9 Consensus size: 16
200907 TAAGTACGAT
* *
200917 GTTCGGGTTAAATTCG
1 GTTCGGGTTAATTTTG
* * *
200933 GTTCGGTTTACTTTCG
1 GTTCGGGTTAATTTTG
200949 GATT-GGGTTAAAATTTT-
1 G-TTCGGGTT--AATTTTG
*
200966 ATTCGGGTTAATTTTG
1 GTTCGGGTTAATTTTG
**
200982 GTTCGGGTTTTTTTTG
1 GTTCGGGTTAATTTTG
* *
200998 GTTCAGTTTAATTT
1 GTTCGGGTTAATTT
201012 CACTTTCGGT
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
15 6 0.10
16 43 0.72
17 7 0.12
18 4 0.07
ACGTcount: A:0.16, C:0.08, G:0.25, T:0.51
Consensus pattern (16 bp):
GTTCGGGTTAATTTTG
Found at i:206026 original size:18 final size:19
Alignment explanation
Indices: 205988--206026 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
205978 ATTCCTATTT
*
205988 TCTATTATTTTTATTATAAA
1 TCTACTATTTTTA-TATAAA
206008 TCTACTATTTTTA-ATAAA
1 TCTACTATTTTTATATAAA
206026 T
1 T
206027 TATCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TCTACTATTTTTATATAAA
Found at i:207151 original size:22 final size:22
Alignment explanation
Indices: 207111--207152 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
207101 AGTCATTGGT
* **
207111 ATAATTTATCTTTTTATTTTAA
1 ATAATTTACCTTTAAATTTTAA
207133 ATAATTTACCTTTAAATTTT
1 ATAATTTACCTTTAAATTTT
207153 CAACTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTTACCTTTAAATTTTAA
Found at i:210597 original size:19 final size:21
Alignment explanation
Indices: 210555--210608 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
210545 TTTATTATAT
*
210555 TATATAATATATATGATAATA
1 TATATAATATATATCATAATA
*
210576 TATATAATA-ATTTCATAA-A
1 TATATAATATATATCATAATA
*
210595 TATATAATGTATAT
1 TATATAATATATAT
210609 AGTTTTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 9 0.32
20 10 0.36
21 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATAATATATATCATAATA
Found at i:210630 original size:24 final size:25
Alignment explanation
Indices: 210592--210643 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
210582 ATAATTTCAT
* *
210592 AAATATATAATGTATATAGTTTTTGA
1 AAATATATAATGTAT-GACTTTTTGA
210618 AAATATAT-A-GTATGACTTTTTGA
1 AAATATATAATGTATGACTTTTTGA
210641 AAA
1 AAA
210644 CAAATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 11 0.46
24 4 0.17
25 1 0.04
26 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (25 bp):
AAATATATAATGTATGACTTTTTGA
Found at i:210685 original size:33 final size:35
Alignment explanation
Indices: 210609--210696 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 35
210599 TAATGTATAT
* *
210609 AGTTTTTGAAAATATATAGTATGACTTTTTGAAAAC
1 AGTTTTTGAAAACATATA-TATGAATTTTTGAAAAC
**
210645 AAATTTTGAAAACATATATAT-AATTTTT-AAAAC
1 AGTTTTTGAAAACATATATATGAATTTTTGAAAAC
*
210678 GGTTTTTGAAAACA-ATATA
1 AGTTTTTGAAAACATATATA
210697 ATATATATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
32 5 0.11
33 16 0.36
34 6 0.13
35 3 0.07
36 15 0.33
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (35 bp):
AGTTTTTGAAAACATATATATGAATTTTTGAAAAC
Found at i:210763 original size:19 final size:19
Alignment explanation
Indices: 210696--210765 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
210686 AAAACAATAT
* *
210696 AATATATATAATTTTTTTA
1 AATAAATATAGTTTTTTTA
* * **
210715 CAT-ATTATAGTTTTTGAAA
1 AATAAATATAGTTTTT-TTA
210734 AATATAATATAGTTTTTTTA
1 AATA-AATATAGTTTTTTTA
210754 AATAAATATAGT
1 AATAAATATAGT
210766 GTACATATTA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
18 9 0.24
19 13 0.34
20 5 0.13
21 11 0.29
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (19 bp):
AATAAATATAGTTTTTTTA
Found at i:210787 original size:12 final size:12
Alignment explanation
Indices: 210771--210832 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
210761 ATAGTGTACA
210771 TATTAT-TTATT
1 TATTATATTATT
210782 ATATTATATTATT
1 -TATTATATTATT
210795 TA-TAGTATTA-T
1 TATTA-TATTATT
*
210806 TATTTTA-TATT
1 TATTATATTATT
210817 TATT-TCATTATT
1 TATTAT-ATTATT
210829 TATT
1 TATT
210833 TGTTTTTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 3 0.07
11 13 0.30
12 22 0.51
13 5 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (12 bp):
TATTATATTATT
Found at i:210792 original size:17 final size:17
Alignment explanation
Indices: 210770--210832 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
210760 TATAGTGTAC
210770 ATATTATTTATTATATT
1 ATATTATTTATTATATT
210787 ATATTATTTA-TAGTATT
1 ATATTATTTATTA-TATT
210804 ATTATT-TTATATT-TATT
1 A-TATTATT-TATTATATT
210821 -TCATTATTTATT
1 AT-ATTATTTATT
210833 TGTTTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
15 1 0.03
16 9 0.22
17 23 0.57
18 6 0.15
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
ATATTATTTATTATATT
Found at i:210797 original size:14 final size:14
Alignment explanation
Indices: 210770--210820 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
210760 TATAGTGTAC
210770 ATATTAT-TTA-TT
1 ATATTATATTATTT
210782 ATATTATATTATTT
1 ATATTATATTATTT
*
210796 ATAGTATTATTATTTT
1 ATATTA-TATTA-TTT
210812 ATATT-TATT
1 ATATTATATT
210821 TCATTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
14 11 0.33
15 5 0.15
16 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATATTATATTATTT
Found at i:210805 original size:22 final size:22
Alignment explanation
Indices: 210778--210819 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
210768 ACATATTATT
210778 TATTA-TATTATATTATTTATAG
1 TATTATTATTATA-TATTTATAG
*
210800 TATTATTATTTTATATTTAT
1 TATTATTATTATATATTTAT
210820 TTCATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTATTATTATATATTTATAG
Found at i:210828 original size:25 final size:23
Alignment explanation
Indices: 210771--210828 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
210761 ATAGTGTACA
210771 TATTATTTATTATATTATATTATT
1 TATTA-TTATTATATTATATTATT
*
210795 TATAGTATTATTATTTTATATTTATT
1 TAT--TATTATTATATTATA-TTATT
210821 TCATTATT
1 T-ATTATT
210829 TATTTGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 3 0.10
25 16 0.55
26 8 0.28
27 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTATTATTATATTATATTATT
Found at i:214135 original size:20 final size:20
Alignment explanation
Indices: 214099--214136 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
214089 ATCCTATTCC
**
214099 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
214119 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
214137 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:218524 original size:14 final size:14
Alignment explanation
Indices: 218502--218533 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
218492 TGACAATTAA
*
218502 CCTTTCATTAACCT
1 CCTTCCATTAACCT
218516 CCTTCCATTAACCT
1 CCTTCCATTAACCT
218530 CCTT
1 CCTT
218534 ATCCTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (14 bp):
CCTTCCATTAACCT
Found at i:226900 original size:31 final size:29
Alignment explanation
Indices: 226862--226919 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 29
226852 TTATAATATA
226862 TTGATTTATATGCATTTATCCTTTATTTTTT
1 TTGATTTATATGCATTTAT-CTTT-TTTTTT
226893 TTGATTTATATGCATTTATCTTTTTTT
1 TTGATTTATATGCATTTATCTTTTTTT
226920 ATATTGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 4 0.15
31 19 0.70
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.66
Consensus pattern (29 bp):
TTGATTTATATGCATTTATCTTTTTTTTT
Found at i:228731 original size:31 final size:30
Alignment explanation
Indices: 228696--228794 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 30
228686 TTGAAACATA
228696 AAATTTGTGAAGGATCCACTTGTTCCATCAC
1 AAATTTGTGAAGGATCCACTTGTTCC-TCAC
*
228727 AAATTTGTGACGGATCCACTTGTTCCGTCAC
1 AAATTTGTGAAGGATCCACTTGTTCC-TCAC
*
228758 AAATTTGTGACAGG-TCCACATGTTCCTCAC
1 AAATTTGTGA-AGGATCCACTTGTTCCTCAC
228788 AGAATTT
1 A-AATTT
228795 AGAATTTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.08
31 55 0.89
32 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (30 bp):
AAATTTGTGAAGGATCCACTTGTTCCTCAC
Found at i:228915 original size:93 final size:90
Alignment explanation
Indices: 228759--228946 Score: 270
Period size: 93 Copynumber: 2.1 Consensus size: 90
228749 TTCCGTCACA
* *
228759 AATTTGTGACAGGTCCACATGTTCCTCACAGAATTTAGAATTTTTTAATTACCCTCTCATTTCCT
1 AATTTGTGACAGGTCCACATGCTCCTCACAAAATTTAGAATTTTTTAATTACCCTCTCATTTCCT
*
228824 CCAATTTCCCTCCATTGAAACATAG
66 CCAATTTCCCTCCACTGAAACATAG
* * * *
228849 AATTTGTGACGGGTTCACATGCTCCGTCACAAAATTTAGAGGTTTTTTTACTTACCCGT-TCATT
1 AATTTGTGACAGGTCCACATGCTCC-TCACAAAATTTAGA--ATTTTTTAATTACCC-TCTCATT
228913 TCCTCCAATTTCCCTCCACTGAAACATAG
62 TCCTCCAATTTCCCTCCACTGAAACATAG
228942 AATTT
1 AATTT
228947 CAAACATACC
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
90 22 0.25
91 13 0.15
93 51 0.59
94 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (90 bp):
AATTTGTGACAGGTCCACATGCTCCTCACAAAATTTAGAATTTTTTAATTACCCTCTCATTTCCT
CCAATTTCCCTCCACTGAAACATAG
Found at i:229368 original size:19 final size:18
Alignment explanation
Indices: 229342--229385 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
229332 TTTTTATATG
229342 ATATTTTTTTATAAAAAA
1 ATATTTTTTTATAAAAAA
* *
229360 ATCATTTTTTTTTAGAAAA
1 AT-ATTTTTTTATAAAAAA
229379 ATATTTT
1 ATATTTT
229386 CAATTTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTTTTTTATAAAAAA
Found at i:229481 original size:31 final size:31
Alignment explanation
Indices: 229410--229481 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
229400 ATTTGTGGAC
*
229410 CCGTCACAAATTTCTGATAGATCCACCTATT
1 CCGTCACAAATTTCTGATAGATCCACATATT
* * * * * * *
229441 CAGTTACAAATTTGTGATGGGTCTACATGTT
1 CCGTCACAAATTTCTGATAGATCCACATATT
229472 CCGTCACAAA
1 CCGTCACAAA
229482 AAAAAATCAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (31 bp):
CCGTCACAAATTTCTGATAGATCCACATATT
Found at i:229579 original size:126 final size:124
Alignment explanation
Indices: 229367--229606 Score: 372
Period size: 126 Copynumber: 1.9 Consensus size: 124
229357 AAAATCATTT
* * * *
229367 TTTTTTAGAAAAATATTTTCAATTTGTGATGGAATTTGTGGACCCGTCACAAATTTCTGATAGAT
1 TTTTTTAGAAAAATATTTTAAATTTGTGATGAAATTTGTGAACCCGTCACAAATTTCTGACAGAT
* **
229432 CCACCTATTCAGTTACAAATTTGTGATGGGTCTACATGTTCCGTCACAAAAAAAAATCA
66 CCACCTATTCAGTCACAAATTTGTGATAAGTCTACATGTTCCGTCACAAAAAAAAATCA
* *
229491 TTTTTTAGAACAAATTATTTTAAATTTGTGATGAAATTTGTGAACTCGTCCCAAATTTCTGACAG
1 TTTTTTAGAA-AAA-TATTTTAAATTTGTGATGAAATTTGTGAACCCGTCACAAATTTCTGACAG
*
229556 ATCCACCTATTCTGTCACAAATTTGTGATAAGTCTACATGTTCCGTCACAA
64 ATCCACCTATTCAGTCACAAATTTGTGATAAGTCTACATGTTCCGTCACAA
229607 GTTTTTGGAG
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
124 10 0.10
125 3 0.03
126 91 0.88
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (124 bp):
TTTTTTAGAAAAATATTTTAAATTTGTGATGAAATTTGTGAACCCGTCACAAATTTCTGACAGAT
CCACCTATTCAGTCACAAATTTGTGATAAGTCTACATGTTCCGTCACAAAAAAAAATCA
Found at i:230197 original size:65 final size:65
Alignment explanation
Indices: 230120--230276 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
230110 CACACCCATT
* * *
230120 TCGAATGTATTTTGTATACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATAT-TTTGAAA
1 TCGAATGTATTTTGTGTACCGATGCACAGA-CCATGCATCAATGCACTCCTGAAT-TGTTTGAAA
230183 CA
64 CA
* **
230185 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGGCTTGTTTGAAACA
1 TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATTGTTTGAAACA
* * *
230250 TTGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGTATTTTGTGTACCGATGCAC
230277 CCATAGTGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 1 0.01
65 78 0.98
66 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (65 bp):
TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCAATGCACTCCTGAATTGTTTGAAACA
Found at i:232954 original size:17 final size:17
Alignment explanation
Indices: 232932--232965 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
232922 TATATTGAGT
232932 ATTAGTCAATTATGCGA
1 ATTAGTCAATTATGCGA
232949 ATTAGTCAATTATGCGA
1 ATTAGTCAATTATGCGA
232966 TAAAGGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
ATTAGTCAATTATGCGA
Found at i:236161 original size:23 final size:22
Alignment explanation
Indices: 236098--236170 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
236088 ACAATGTACC
236098 GATGC-TTCCCTTGAATGTGCAT
1 GATGCATT-CCTTGAATGTGCAT
* * *
236120 CGATACA--CCATGAAGGTGCACT
1 -GATGCATTCCTTGAATGTGCA-T
236142 GATGCATTCCTTGAATGTGCATT
1 GATGCATTCCTTGAATGTGCA-T
236165 GATGCA
1 GATGCA
236171 CTCTGTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 16 0.41
22 1 0.03
23 22 0.56
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (22 bp):
GATGCATTCCTTGAATGTGCAT
Found at i:238402 original size:65 final size:65
Alignment explanation
Indices: 238327--238481 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
238317 CACCCATTTT
*
238327 GAATGCATTTTATGTATCGATGCACA-AGCTATGCATCGATGCACTCATGAATAT-TTTGAAACA
1 GAATGCATTTTATGTACCGATGCACAGA-CTATGCATCGATGCACTCATGAAT-TGTTTGAAACA
238390 TC
64 TC
* * **
238392 GAATGCATTTTGTGTACCGATGCACAGACTATGCATCGATGCACTCCTGGCTTGTTTGAAACATC
1 GAATGCATTTTATGTACCGATGCACAGACTATGCATCGATGCACTCATGAATTGTTTGAAACATC
* *
238457 GAATGTA-ATTAGTGTACCGATGCAC
1 GAATGCATTTTA-TGTACCGATGCAC
238482 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
64 3 0.04
65 75 0.95
66 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (65 bp):
GAATGCATTTTATGTACCGATGCACAGACTATGCATCGATGCACTCATGAATTGTTTGAAACATC
Found at i:240652 original size:3 final size:3
Alignment explanation
Indices: 240644--240693 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
240634 TATATATGTA
*
240644 TAT TAT TAT TAT TAT TAT AAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
240690 TAT T
1 TAT T
240694 TACAAAACTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:247057 original size:171 final size:171
Alignment explanation
Indices: 246770--247101 Score: 488
Period size: 171 Copynumber: 1.9 Consensus size: 171
246760 TCATTTACAT
*
246770 TGATGTTGGCAAGCCAAAGCCTCCCACTTGTATTCCAATTAAGCTTTGTTCTTAAGTGTCTTTGT
1 TGATGTTGGCAAGCCAAAGCATCCCACTTGTATTCCAATTAAGCTTTGTTCTTAAGTGTCTTTGT
* * *
246835 GACGTCATACAAAAGCTCTGAACACTATACAAAGAGCTTCCCTGATTGAAAAATCTGGGCAGT-A
66 GACGTCATACAAAAGCTCTGAACAATATACAAAGAGCTTCCCTGATTGAAAAATCTAGACA-TAA
*
246899 GCTACAAGAAAGGATGAATGTGTTGTCAAATGTTCTCTGATA
130 GCTACAAGAAAGGATGAATGTGTTATCAAATGTTCTCTGATA
* * * * * *
246941 TGATGTTGGCAAGCTAAAGCATCCTATTTGTATTCCCATTGAGTTTTGTTCTTAAGTGTCTTTGT
1 TGATGTTGGCAAGCCAAAGCATCCCACTTGTATTCCAATTAAGCTTTGTTCTTAAGTGTCTTTGT
* * * *
247006 GATGTCATACAAAAGCTCTGAA-AATGATGCAAAGAGCTTCCCTGTTTGAAAAATCTAGATATAA
66 GACGTCATACAAAAGCTCTGAACAAT-ATACAAAGAGCTTCCCTGATTGAAAAATCTAGACATAA
*
247070 GCTACAGGAAAGGATGAATGTGTTATCAAATG
130 GCTACAAGAAAGGATGAATGTGTTATCAAATG
247102 CTCTATAAAT
Statistics
Matches: 143, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
170 3 0.02
171 140 0.98
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (171 bp):
TGATGTTGGCAAGCCAAAGCATCCCACTTGTATTCCAATTAAGCTTTGTTCTTAAGTGTCTTTGT
GACGTCATACAAAAGCTCTGAACAATATACAAAGAGCTTCCCTGATTGAAAAATCTAGACATAAG
CTACAAGAAAGGATGAATGTGTTATCAAATGTTCTCTGATA
Found at i:247780 original size:90 final size:90
Alignment explanation
Indices: 247627--247920 Score: 428
Period size: 90 Copynumber: 3.3 Consensus size: 90
247617 ATTAGATCAT
* *
247627 ATTTGGTCTCCACAGAAGAGTAGTAGAAGTGAATCAACCTCGAGTATGATCTTCACGGAAGAGTA
1 ATTTGGTCTCCACGGAAGAGTAGTGGAAGTGAATCAACCTCGAGTATGATCTTCACGGAAGAGTA
*
247692 GCGGAACATATTCTTCTTATTTTAG
66 GCGGAACATATTCTTCTTATTTCAG
* * * * *
247717 ATTTGGTCTCCATGGAAGAGTAATGGAAATGAATCAACCTCGAGTCTAATCTTCACGGAAGAGTA
1 ATTTGGTCTCCACGGAAGAGTAGTGGAAGTGAATCAACCTCGAGTATGATCTTCACGGAAGAGTA
* *
247782 GTGGAACATATTCTTCTTATTTCAT
66 GCGGAACATATTCTTCTTATTTCAG
** *
247807 ATTTGGTCTCCACGGAAGAGTAGTGGAAGCAAATCAACGTCGAGTATGATCTTCACGGAAGAGTA
1 ATTTGGTCTCCACGGAAGAGTAGTGGAAGTGAATCAACCTCGAGTATGATCTTCACGGAAGAGTA
247872 -CTGGAACATATTCTTCTTATTTCAG
66 GC-GGAACATATTCTTCTTATTTCAG
* * *
247897 ATTTAGCCTTCACGGAAGAGTAGT
1 ATTTGGTCTCCACGGAAGAGTAGT
247921 AAAGCAAAGT
Statistics
Matches: 180, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
90 180 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (90 bp):
ATTTGGTCTCCACGGAAGAGTAGTGGAAGTGAATCAACCTCGAGTATGATCTTCACGGAAGAGTA
GCGGAACATATTCTTCTTATTTCAG
Found at i:248256 original size:40 final size:40
Alignment explanation
Indices: 248201--248339 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 40
248191 TAACCAGATA
248201 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
* * ** * *
248241 TCCTCATCACAAAGGAGCAACATCATCC-TTAGAT-AGTCATATG
1 TCCTCATCACGAAGGAACAATGTCATCCACT-GATCAG--A-A-C
* *
248284 TCCTCATCACGAATGAACAATGTCATCCACCGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
248324 TCCTCATCACGAAGGA
1 TCCTCATCACGAAGGA
248340 GCAGCATCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
39 3 0.04
40 42 0.55
41 2 0.03
42 2 0.03
43 26 0.34
44 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (40 bp):
TCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAAC
Found at i:248310 original size:43 final size:41
Alignment explanation
Indices: 248241--248384 Score: 114
Period size: 43 Copynumber: 3.4 Consensus size: 41
248231 TGATCAGAAC
*
248241 TCCTCATCAC-AAAGGAGCAACATCATCCTTAGATAGTCATATG
1 TCCTCATCACGAAA-GAACAACATCATCCTTAGATAG-CA-ATG
* ** *** *
248284 TCCTCATCACGAATGAACAATGTCATCCACCGATCAG-AA-C
1 TCCTCATCACGAAAGAACAACATCATCCTTAGAT-AGCAATG
* * *
248324 TCCTCATCACGAAGGAGCAGCATCATCCTTAGATAGCCAGATG
1 TCCTCATCACGAAAGAACAACATCATCCTTAGATAG-CA-ATG
248367 TCCTCATCACGAAAGAAC
1 TCCTCATCACGAAAGAAC
248385 CTTGTTATCT
Statistics
Matches: 76, Mismatches: 19, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
39 2 0.03
40 26 0.34
41 2 0.03
42 2 0.03
43 40 0.53
44 4 0.05
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (41 bp):
TCCTCATCACGAAAGAACAACATCATCCTTAGATAGCAATG
Found at i:248327 original size:83 final size:83
Alignment explanation
Indices: 248188--248384 Score: 313
Period size: 83 Copynumber: 2.4 Consensus size: 83
248178 ATATCTAAAA
* * * *
248188 AGATAACCAGATATCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCACAA
1 AGATAGCCAGATGTCCTCATCACGAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCACAA
248253 AGGAGCAACATCATCCTT
66 AGGAGCAACATCATCCTT
* * * *
248271 AGATAGTCATATGTCCTCATCACGAATGAACAATGTCATCCACCGATCAGAACTCCTCATCACGA
1 AGATAGCCAGATGTCCTCATCACGAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCACAA
*
248336 AGGAGCAGCATCATCCTT
66 AGGAGCAACATCATCCTT
248354 AGATAGCCAGATGTCCTCATCACGAAAGAAC
1 AGATAGCCAGATGTCCTCATCACGAAAGAAC
248385 CTTGTTATCT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 103 1.00
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (83 bp):
AGATAGCCAGATGTCCTCATCACGAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCACAA
AGGAGCAACATCATCCTT
Found at i:248510 original size:220 final size:220
Alignment explanation
Indices: 248121--248526 Score: 598
Period size: 220 Copynumber: 1.8 Consensus size: 220
248111 AATAGTGAAC
* *
248121 CAGCATCATCCTTAGATAGCCAGAGCTCCTCATCATGAATGAACCATGTTATCTCAAATATCTAA
1 CAGCATCATCCTTAGATAGCCAGAGCTCCTCATCACGAAAGAACCATGTTATCTCAAATATCTAA
* * *
248186 AAAGATAACCAGATATCCTCATCACGAAGGAACAATGTCATCCACTGATCAGAACTCCTCATCAC
66 AAAGATAACCAGATATCCTCATCACAAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
* * ** * * *
248251 AAAGGAGCAACATCATCCTTAGATAGTCATATGTCCTCATCACGAATGAACAATGTCATCCACCG
131 AAAGGAGCAACATAATCCTTAAATAACCAGATATCCTCATCACGAAGGAACAATGTCATCCACCG
248316 ATCAGAACTCCTCATCACGAAGGAG
196 ATCAGAACTCCTCATCACGAAGGAG
* *
248341 CAGCATCATCCTTAGATAGCCAGATG-TCCTCATCACGAAAGAACCTTGTTATCTCAAATATCTG
1 CAGCATCATCCTTAGATAGCCAGA-GCTCCTCATCACGAAAGAACCATGTTATCTCAAATATCTA
* * * *
248405 AAAATATGACCATATGTCCTCATCACAAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCA
65 AAAAGATAACCAGATATCCTCATCACAAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCA
** * *
248470 TGAAGGAGCAGCATAATCCTTAAATAACCAGATATCCTCATCACGAAGGAACCATGT
130 CAAAGGAGCAACATAATCCTTAAATAACCAGATATCCTCATCACGAAGGAACAATGT
248527 TATCTCAAAT
Statistics
Matches: 163, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
220 162 0.99
221 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (220 bp):
CAGCATCATCCTTAGATAGCCAGAGCTCCTCATCACGAAAGAACCATGTTATCTCAAATATCTAA
AAAGATAACCAGATATCCTCATCACAAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
AAAGGAGCAACATAATCCTTAAATAACCAGATATCCTCATCACGAAGGAACAATGTCATCCACCG
ATCAGAACTCCTCATCACGAAGGAG
Found at i:248528 original size:137 final size:137
Alignment explanation
Indices: 248283--249034 Score: 999
Period size: 137 Copynumber: 5.5 Consensus size: 137
248273 ATAGTCATAT
* * *
248283 GTCCTCATCACGAATGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAGCATC
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCAGCGTC
* * * *
248348 ATCCTTAGATAGCCAGATGTCCTCATCACGAAAGAACCTTGTTATCTCAAATATCTGAAAATATG
66 ATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGATG
* *
248413 ACCATAT
131 ACCAGAC
* * * * * *
248420 GTCCTCATCACAAAAGAACAATGTCATCCACCGATCAGAACTCCTCATCATGAAGGAGCAGCATA
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCAGCGTC
* * **
248485 ATCCTTAAATAACCAGATATCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATG
66 ATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGATG
*
248550 GCCAGAC
131 ACCAGAC
* **
248557 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCTTCATCACGAAGGAGCCCCGTC
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCAGCGTC
** * * *
248622 ATCCTTAGATAATTAGATGTCATCATCGCGAAGGAACCGTGTTATCTCAAATATCTGAAAAGATG
66 ATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGATG
*
248687 ATCAGAC
131 ACCAGAC
* * *
248694 ATCCTCATCACGAAGGAACAATGTCATCCACCGACCAAAACTCCTCATCAGGAAGGAGACA-CGT
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAG-CAGCGT
** * * * **
248758 CATTTTTAGATAATCAGATGTCCTTATCATGAAGGAACCATGTTATCTCAAATA-CTTTAAAGAT
65 CATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGAT
*
248822 GGCCAGAC
130 GACCAGAC
* * * *
248830 GTCCTCATCACGAAGGAAAAATGTCATCCATCGACCAGAACT-CTCATCACAAAGGATTC-GCGT
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGA-GCAGCGT
* *
248893 TATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTGAAAAGAT
65 CATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGAT
248958 GACCAGAC
130 GACCAGAC
* * * **
248966 ATCCTCATCACGAAGGAACAATGTCATCCACCGACCATAAATCCTCATCACGAAGGAGCAATGTC
1 GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCAGCGTC
249031 ATCC
66 ATCC
249035 ACCGAACAGA
Statistics
Matches: 530, Mismatches: 79, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
135 63 0.12
136 105 0.20
137 361 0.68
138 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (137 bp):
GTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCAGCGTC
ATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTGAAAAGATG
ACCAGAC
Found at i:249074 original size:40 final size:40
Alignment explanation
Indices: 248961--249063 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
248951 AAAAGATGAC
* * *
248961 CAGACATCCTCATCACGAAGGAACAATGTCATCCACCGAC
1 CAGAAATCCTCATCACGAAGGAGCAATGTCATCCACCGAA
*
249001 CATAAATCCTCATCACGAAGGAGCAATGTCATCCACCGAA
1 CAGAAATCCTCATCACGAAGGAGCAATGTCATCCACCGAA
*
249041 CAGAACTCCTCATCACGAAGGAG
1 CAGAAATCCTCATCACGAAGGAG
249064 TTACGTCATC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.16
Consensus pattern (40 bp):
CAGAAATCCTCATCACGAAGGAGCAATGTCATCCACCGAA
Found at i:249149 original size:176 final size:177
Alignment explanation
Indices: 248831--249372 Score: 739
Period size: 176 Copynumber: 3.1 Consensus size: 177
248821 TGGCCAGACG
* *
248831 TCCTCATCACGAAGGAAAAATGTCATCCATCGACCAGAACT-CTCATCACAAAGGA-TTCGCGTT
1 TCCTCATCACGAAGGAAAAATGTCATCCACCGACCAGAACTCCTCATCACAAAGGAGTT-GCGTC
* **
248894 ATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTGAAAAGATG
65 ATCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATG
* * * *
248959 ACCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGACCATAAA
130 GCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAAC
** * * *
249007 TCCTCATCACGAAGGAGCAATGTCATCCACCGAACAGAACTCCTCATCACGAAGGAGTTACGTCA
1 TCCTCATCACGAAGGAAAAATGTCATCCACCGACCAGAACTCCTCATCACAAAGGAGTTGCGTCA
* * * *
249072 TCCTTAGATAATCATATGTCTTCATCAAGAAGGAATCGTGTTATCTCAAATA-CTTTAAAGATGG
66 TCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGG
* *
249136 CCAGACGTCCTCATCATGAAGGAATAATGTCATCCACCGACCAGAAC
131 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAAC
* * ** *
249183 TCCTCATCACGAAGGAATAATGTCATCCACCGACCATAACTCCTCATCACAAAGGAGCCGTGTCA
1 TCCTCATCACGAAGGAAAAATGTCATCCACCGACCAGAACTCCTCATCACAAAGGAGTTGCGTCA
* * * *
249248 TCCTTAGATAATCAGATGTCCTCATCTCGAATGAACCATGTTATCTCAAATATCTTTAAATATGG
66 TCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGG
* * * ** *
249313 CCAAACGTCCTCATCACGAAGGAACAATATCATTCAATGATCAGAAC
131 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAAC
249360 TCCTCATCACGAA
1 TCCTCATCACGAA
249373 AGAGAAGCAT
Statistics
Matches: 318, Mismatches: 45, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
176 189 0.59
177 127 0.40
178 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (177 bp):
TCCTCATCACGAAGGAAAAATGTCATCCACCGACCAGAACTCCTCATCACAAAGGAGTTGCGTCA
TCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGG
CCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAAC
Found at i:249191 original size:40 final size:40
Alignment explanation
Indices: 249143--249238 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
249133 TGGCCAGACG
*
249143 TCCTCATCATGAAGGAATAATGTCATCCACCGACCAGAAC
1 TCCTCATCACGAAGGAATAATGTCATCCACCGACCAGAAC
*
249183 TCCTCATCACGAAGGAATAATGTCATCCACCGACCATAAC
1 TCCTCATCACGAAGGAATAATGTCATCCACCGACCAGAAC
*
249223 TCCTCATCACAAAGGA
1 TCCTCATCACGAAGGA
249239 GCCGTGTCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (40 bp):
TCCTCATCACGAAGGAATAATGTCATCCACCGACCAGAAC
Found at i:249429 original size:137 final size:137
Alignment explanation
Indices: 249183--249472 Score: 350
Period size: 137 Copynumber: 2.1 Consensus size: 137
249173 CGACCAGAAC
* * * * ** **
249183 TCCTCATCACGAAGGAATAATGTCATCCACCGACCATAACTCCTCATCACAAAGGAGCCGTGTCA
1 TCCTCATCACGAAGGAACAATATCATCCAACGACCAGAACTCCTCATCACAAAGGAGAAGCATCA
* * * * *
249248 TCCTTAGATAATCAGATGTCCTCATCTCGAATGAACCATGTTATCTCAAATATCTTTAAATATGG
66 TCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCCTCAAAGATGG
249313 CCAAACG
131 CCAAACG
* * *
249320 TCCTCATCACGAAGGAACAATATCATTCAATGATCAGAACTCCTCATCACGAAA-GAGAAGCATC
1 TCCTCATCACGAAGGAACAATATCATCCAACGACCAGAACTCCTCATCAC-AAAGGAGAAGCATC
* * *
249384 ATCCTTAGAT-AGCTAGATGTCCTCATCACGAAGGAATCGTGTTATCTCAAATATCCTCAAAGAT
65 ATCCTTAGATAATC-AGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCCTCAAAGAT
* * *
249448 GTCCAGATG
129 GGCCAAACG
249457 TCCTCATCACGAAGGA
1 TCCTCATCACGAAGGA
249473 TTAATGTCAT
Statistics
Matches: 129, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
136 2 0.02
137 124 0.96
138 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (137 bp):
TCCTCATCACGAAGGAACAATATCATCCAACGACCAGAACTCCTCATCACAAAGGAGAAGCATCA
TCCTTAGATAATCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCCTCAAAGATGG
CCAAACG
Found at i:251341 original size:17 final size:17
Alignment explanation
Indices: 251321--251353 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
251311 ATATTTATTC
251321 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
251338 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
251354 TATGATATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:251446 original size:15 final size:16
Alignment explanation
Indices: 251421--251462 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
251411 CTCAAAATTA
*
251421 AATATTATTTTA-AAT
1 AATAATATTTTACAAT
*
251436 AATTATATTTTACAAT
1 AATAATATTTTACAAT
251452 AATAATATTTT
1 AATAATATTTT
251463 CACCTCGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AATAATATTTTACAAT
Found at i:256000 original size:58 final size:58
Alignment explanation
Indices: 255932--256050 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 58
255922 TAATGAATAC
* *
255932 ATAAAGAGGTTTAAATTTTAAAATATATATTATTCTTAAATTCTGAATAAGATCATAT
1 ATAAAGAGGTTTAAATTTTAAAATACATAGTATTCTTAAATTCTGAATAAGATCATAT
* *
255990 ATAAAGAGGTTTAAATTTTAAAATGCATAGTATTCTTAAATTCTGAATAAGATTATAT
1 ATAAAGAGGTTTAAATTTTAAAATACATAGTATTCTTAAATTCTGAATAAGATCATAT
256048 ATA
1 ATA
256051 TTCATGGATA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (58 bp):
ATAAAGAGGTTTAAATTTTAAAATACATAGTATTCTTAAATTCTGAATAAGATCATAT
Found at i:260156 original size:30 final size:30
Alignment explanation
Indices: 260115--260181 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
260105 GTAATTGAAC
260115 AATTCTTATAGAACTCGTCATTCCGGAATAT
1 AATT-TTATAGAACTCGTCATTCCGGAATAT
260146 AATTTTATAGAACTCGTCATTCCGGAATAT
1 AATTTTATAGAACTCGTCATTCCGGAATAT
260176 AATTTT
1 AATTTT
260182 TTAATGGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (30 bp):
AATTTTATAGAACTCGTCATTCCGGAATAT
Found at i:260512 original size:32 final size:32
Alignment explanation
Indices: 260471--260548 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
260461 GTTGTGGACA
*
260471 TCATCTTCAATCTCTTACATTAGACAATTC-TT
1 TCATCTTCAATCTCTTACATTAGAC-ACTCATT
260503 TCATCTTCAATCTCTTACATTAGACACTCATT
1 TCATCTTCAATCTCTTACATTAGACACTCATT
*
260535 TTATCTTCAATCTC
1 TCATCTTCAATCTC
260549 CTACGCGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 3 0.07
32 40 0.93
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.44
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACATTAGACACTCATT
Found at i:266332 original size:23 final size:23
Alignment explanation
Indices: 266306--266387 Score: 155
Period size: 23 Copynumber: 3.6 Consensus size: 23
266296 ATTAAAGACA
266306 AAGTGAACGTTTATTATCTTTGT
1 AAGTGAACGTTTATTATCTTTGT
*
266329 AAGTGAATGTTTATTATCTTTGT
1 AAGTGAACGTTTATTATCTTTGT
266352 AAGTGAACGTTTATTATCTTTGT
1 AAGTGAACGTTTATTATCTTTGT
266375 AAGTGAACGTTTA
1 AAGTGAACGTTTA
266388 AACACAAAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.46
Consensus pattern (23 bp):
AAGTGAACGTTTATTATCTTTGT
Found at i:269287 original size:49 final size:50
Alignment explanation
Indices: 269233--269341 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 50
269223 AATAAATTTT
* *
269233 TTATTAAATTACACATTTTGACA-ACACAATTTAATAAAAATTAATTAAA
1 TTATTAAATTACACATTTTGAAATACACAATTAAATAAAAATTAATTAAA
* * * *
269282 TTATTAAATTATACATTTTGAAATATATAATTAAATATAAATTAATTAAA
1 TTATTAAATTACACATTTTGAAATACACAATTAAATAAAAATTAATTAAA
*
269332 ATA-TAAATTA
1 TTATTAAATTA
269342 TTCACATATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
49 28 0.54
50 24 0.46
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (50 bp):
TTATTAAATTACACATTTTGAAATACACAATTAAATAAAAATTAATTAAA
Found at i:269350 original size:15 final size:16
Alignment explanation
Indices: 269309--269341 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
269299 TTGAAATATA
269309 TAATT-AAATATAAAT
1 TAATTAAAATATAAAT
269324 TAATTAAAATATAAAT
1 TAATTAAAATATAAAT
269340 TA
1 TA
269342 TTCACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTAAAATATAAAT
Found at i:269766 original size:18 final size:16
Alignment explanation
Indices: 269743--269785 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
269733 TGCTGTGCGG
269743 CGGTTAAAAAAGTGTGAT
1 CGGTTAAAAAA--GTGAT
*
269761 CGGTTAAACAAGTGAT
1 CGGTTAAAAAAGTGAT
269777 CGGTTAAAA
1 CGGTTAAAA
269786 TTTAGATCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (16 bp):
CGGTTAAAAAAGTGAT
Found at i:269870 original size:23 final size:23
Alignment explanation
Indices: 269835--269893 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
269825 ATCAAGCATA
* *
269835 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
269858 ATAATATAATAGGTAGTGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
269881 ATAATAAAATAGG
1 ATAATATAATAGG
269894 CATTTAACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.34
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:269948 original size:23 final size:23
Alignment explanation
Indices: 269922--269969 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
269912 ATCAAATACA
269922 ATAA-CAAATTAGGTAGCGCTTAT
1 ATAATCAAA-TAGGTAGCGCTTAT
**
269945 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTAGCGCTTAT
269968 AT
1 AT
269970 TGACCTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAATCAAATAGGTAGCGCTTAT
Found at i:269955 original size:87 final size:87
Alignment explanation
Indices: 269807--269969 Score: 263
Period size: 87 Copynumber: 1.9 Consensus size: 87
269797 TATGTTATAT
* * *
269807 CATTTAACCGAAAATATTATCAAGCATAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCGAAAATATTATCAAACACAATAACAAATTAGGTAGCGCTTATATAATATAATAGGT
*
269872 AGTGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
269894 CATTTAACCGGAAATATTATCAAATACAATAACAAATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAACACAATAACAAATTAGGTAGCGCTTATATAATATAATAGGT
269959 AGCGCTTATAT
66 AGCGCTTATAT
269970 TGACCTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAACACAATAACAAATTAGGTAGCGCTTATATAATATAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:270332 original size:197 final size:195
Alignment explanation
Indices: 269988--270484 Score: 544
Period size: 199 Copynumber: 2.5 Consensus size: 195
269978 TTTATCATAA
* * * * * *
269988 AATCGGTAAATTTAAACCGGTTACATTATAAATTGACCTATTACATTAT-GTATATCGGTTTCGA
1 AATCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAAT-TATCGATTTCGA
* * * *
270052 TGTTTTCGGGATCGATACAATTTT-AAATGTATCGACACTTATGCGTGCAACTCGTTTGTGCTTT
65 TG-TTTCGGGATCGATAC-TTTTTAAAATGTATCGACACTTATGCGTACAACTCGTTTGTCCTTC
* * *
270116 ATTTTGGAAAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCT
128 ATTTTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CT
*
270180 AATT
192 AATG
* * *
270184 AATC-GTATATTTTAACCAGTTACATTGTAAATTTACCTGTTACATAATAATTATCGATTTCGAT
1 AATCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT
*
270248 GTTTCGAGGATCGATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTG-CCATT
66 GTTTCG-GGATCGATACTTTTTA-AAATGTATCGACAC-TTATGCGTACAACTCGTTTGTCC-TT
* * *
270312 CATTTT-GAAAAAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTC
127 CATTTTGGAAAAAA-GTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTC
*
270376 TCATG
191 TAATG
* * * *
270381 AACCCGGTATATTTCT-ACCGGTTACATTGGAAATTTACCTATTATATTATAATTATCGGTCTCT
1 AA-TCGGTATATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC-G-AT-T
* *
270445 TTGAT-TTTC-GGATCGATACTTGTTATAAATGTATCGACAC
61 TCGATGTTTCGGGATCGATACTTTTTA-AAATGTATCGACAC
270485 AAAATCTAAT
Statistics
Matches: 255, Mismatches: 32, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
194 9 0.04
195 60 0.24
196 27 0.11
197 72 0.28
198 2 0.01
199 73 0.29
200 2 0.01
201 5 0.02
202 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (195 bp):
AATCGGTATATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGAT
GTTTCGGGATCGATACTTTTTAAAATGTATCGACACTTATGCGTACAACTCGTTTGTCCTTCATT
TTGGAAAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATG
Found at i:273991 original size:21 final size:21
Alignment explanation
Indices: 273965--274012 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
273955 TTTGGGATCG
273965 ACACTTGGTATAAATGTATCA
1 ACACTTGGTATAAATGTATCA
*
273986 ACACTTGGTATAAATGTATCG
1 ACACTTGGTATAAATGTATCA
274007 ACACTT
1 ACACTT
274013 TGTTCGTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
ACACTTGGTATAAATGTATCA
Found at i:274174 original size:221 final size:217
Alignment explanation
Indices: 273779--274212 Score: 534
Period size: 221 Copynumber: 2.0 Consensus size: 217
273769 ACACTTTTTC
** *
273779 TAAATGTATCAACACTTTTTCGTGAACTTGTTTGAAAAATTTATTATGGACATAAAGTGTCGACA
1 TAAATGTATCAACACTTTTTCGTGAACTTGTTTGAAAAATACATTATGGACATAAAGTATCGACA
* * * * * * *
273844 CGAATGTATAAAGTATCGATACATTATGTATACTTTTTTTAATAACCGATATATTTAGACCGGTT
66 CAAATGAATAAAGTATCGATACATTATGTAGACTTTTTTCAAAAACCGATAAATTTAAACCGGTT
* * * * * *
273909 ACATTGTTATGTTACCTATTACATTATAATGATGTGTTTCGATGTTTTTGGGATCGACACTTGGT
131 ACATTGTAAAGTGACCTATTACATTATAATGACGGGTTTCGATGTTTTTGGGATCGACACTTGAT
273974 ATAAATGTATCAACACTTGGTA
196 ATAAATGTATCAACACTTGGTA
* * * * *
273996 TAAATGTATCGACACTTTGTTCGTGCACTTGGTTTG-GAAATACATTCTGGACA-ACATGTATCG
1 TAAATGTATCAACACTTT-TTCGTGAACTT-GTTTGAAAAATACATTATGGACATA-AAGTATCG
* *
274059 ACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCAGAAAACCGGTAAATTTA
63 ACACAAATGAATAAAGTATCGATACATTA-TGTAGA-CT-TTTT-TCA-AAAACCGATAAATTTA
* *
274123 AACCGGTTACATTGTAAAGTGA-CTATTACATTATAGTTACGGGTTTCGATGTTTTTGGGATCGA
123 AACCGGTTACATTGTAAAGTGACCTATTACATTATAATGACGGGTTTCGATGTTTTTGGGATCGA
*
274187 CACTTGATATAAATGTATCGACACTT
188 CACTTGATATAAATGTATCAACACTT
274213 ATTTGTGAAC
Statistics
Matches: 183, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
217 20 0.11
218 57 0.31
219 7 0.04
220 4 0.02
221 64 0.35
222 31 0.17
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (217 bp):
TAAATGTATCAACACTTTTTCGTGAACTTGTTTGAAAAATACATTATGGACATAAAGTATCGACA
CAAATGAATAAAGTATCGATACATTATGTAGACTTTTTTCAAAAACCGATAAATTTAAACCGGTT
ACATTGTAAAGTGACCTATTACATTATAATGACGGGTTTCGATGTTTTTGGGATCGACACTTGAT
ATAAATGTATCAACACTTGGTA
Found at i:276668 original size:15 final size:15
Alignment explanation
Indices: 276648--276699 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
276638 TGATTTCCTC
*
276648 AGAAGAGCTGGGTTG
1 AGAAGAGATGGGTTG
*
276663 AGAAGAGGTGGGTTG
1 AGAAGAGATGGGTTG
276678 AGAAGAGATGGGTTG
1 AGAAGAGATGGGTTG
276693 AGAAGAG
1 AGAAGAG
276700 TCCCGATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.02, G:0.48, T:0.17
Consensus pattern (15 bp):
AGAAGAGATGGGTTG
Found at i:277530 original size:198 final size:198
Alignment explanation
Indices: 277192--277976 Score: 1322
Period size: 198 Copynumber: 3.9 Consensus size: 198
277182 CATTATGGAC
* *
277192 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAGAT
1 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
277257 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
66 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
* *
277322 ATGTATCGACACCTTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACATAAA
131 ATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAA
277387 TTA
196 TTA
277390 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
1 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
*
277455 TGATAATTTACCTATTACATTATAATTATGGGTCTTGATGTTTTTTGGATCGATACTTTTTATAA
66 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
*
277520 ATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCAACACAAA
131 ATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAA
*
277585 TTC
196 TTA
277588 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
1 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
*
277653 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAG
66 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
* *
277718 ATGTATTGACACATTATGGTGACCTTGGTAAGGAAATCATTGTGGACACAAAGTATGGAATCGAC
131 ATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAG--T---ATCGAC
277783 ACAAATTA
191 ACAAATTA
* * * * * *
277791 AAAAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAATCGGTGTATTTAGAACGGTTAGAT
1 AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
*
277856 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTTTTATAA
66 TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
**
277921 ATGTATCGACACATT-TCCATG-CACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
131 ATGTATCGACACATTAT-GGTGAC-CTTGGTAAGGAAATCATTCTGGACACAAAGTAT
277977 ACTTGGACAA
Statistics
Matches: 555, Mismatches: 25, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
198 372 0.67
200 1 0.00
201 1 0.00
202 2 0.00
203 179 0.32
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (198 bp):
AAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGAT
TGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATAA
ATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTATCGACACAAA
TTA
Found at i:277737 original size:396 final size:398
Alignment explanation
Indices: 277191--277976 Score: 1346
Period size: 401 Copynumber: 2.0 Consensus size: 398
277181 ACATTATGGA
* *
277191 CAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTATTTAGACCGGTTAGA
1 CAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGA
277256 TTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATA
66 TTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATA
* *
277321 AATGTATCGACACCTTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAG-T-ATCGACAT
131 AATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGATGATCGACAC
* *
277384 AAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAG
196 AAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCATAAACCGGTGTAATTAGAACAG
* *
277449 TTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTTGATGTTTTTTGGATCGATACTTT
261 TTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTT
**
277514 TTATAAATGTATCGACACATTAT-GGTG-ACCTTGGTAAGGAAATCATTCTGGACACAAAGTATC
326 TTATAAATGTATCGACACATT-TCCATGCA-CTTGGTAAGGAAATCATTCTGGACACAAAGTATC
277577 AACACAAATT
389 AACACAAATT
277587 CAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGA
1 CAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGA
277652 TTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATA
66 TTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATA
* * *
277717 GATGTATTGACACATTATGGTGACCTTGGTAAGGAAATCATTGTGGACACAAAGTATGGAATCGA
131 AATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAG-AT-G-ATCGA
* * *
277782 CACAAATTAAAAAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAATCGGTGTATTTAGAA
193 CACAAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCATAAACCGGTGTAATTAGAA
*
277847 CGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
258 CAGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATAC
277912 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
323 TTTTTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTAT
277977 ACTTGGACAA
Statistics
Matches: 366, Mismatches: 17, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
396 178 0.49
398 1 0.00
400 1 0.00
401 185 0.51
402 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (398 bp):
CAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCATAAACCGGTGTAATTAGACCAGTTAGA
TTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGGATCGATACTTTTTATA
AATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGATGATCGACAC
AAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCATAAACCGGTGTAATTAGAACAG
TTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACTTT
TTATAAATGTATCGACACATTTCCATGCACTTGGTAAGGAAATCATTCTGGACACAAAGTATCAA
CACAAATT
Found at i:278275 original size:19 final size:19
Alignment explanation
Indices: 278251--278300 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
278241 TTACATTCAC
*
278251 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
278270 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
278289 ATACAAAATTAA
1 ATACAAAATTAA
278301 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:279466 original size:17 final size:17
Alignment explanation
Indices: 279444--279479 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
279434 GAATCATTAG
279444 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
279461 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
279478 GA
1 GA
279480 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:280105 original size:15 final size:15
Alignment explanation
Indices: 280082--280111 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
280072 ACTCTGTTTT
280082 CCCTAACCGTAATCC
1 CCCTAACCGTAATCC
*
280097 CCCTGACCGTAATCC
1 CCCTAACCGTAATCC
280112 ACCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.10, T:0.20
Consensus pattern (15 bp):
CCCTAACCGTAATCC
Found at i:282369 original size:20 final size:20
Alignment explanation
Indices: 282323--282369 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
282313 ATTGATAGCG
282323 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
282343 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
282364 -TTTACC
1 CTTTACC
282370 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:282568 original size:181 final size:182
Alignment explanation
Indices: 282324--282942 Score: 913
Period size: 182 Copynumber: 3.4 Consensus size: 182
282314 TTGATAGCGC
* * * *
282324 TTTACCGGTTTTGTCATTTCGATACCGGTTTTGTCATATTTTTACCTATTATATTGTTATGGATC
1 TTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
* * *
282389 GATACGTTT-TCAAAAAGTATCGACACTTTTTAGGCGCTATAATTTCTTCTCTTTTAAATTACGA
66 GATACATTTGT-ATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGA
282453 AAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTATCTT
130 AAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTATCTT
* * *
282506 TTTACCGGTTTTATCATTTCGAGA-CTGTTTTGTCATATTATTACCTGCTATATTGCTATGGATC
1 TTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
* * * * *
282570 GACATATTTGTATAAAGTATCGACACCTTTTAGGCACTATTACTTCTTCTCTTTTAAATTACGAA
66 GATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAA
*
282635 AGTGTCGATACTTATATTAATGTATCGACACTTTCAATATATCCGGTAGT-TT
131 AGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTA-TCTT
*
282687 TTTACCGGTTTTATCATTTCGATACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
1 TTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
* * *
282752 GATACATTTGTATAAAGTATCGATACTTTTTAGGCGCTATAACTTGTTCTCTTTTAAATTACAAA
66 GATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAA
* * **
282817 AGTGTCGATACTTACATTAATTTATCGACACTTTCAATATATCCGGTAGCGG
131 AGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTATCTT
* * * * * *
282869 TTTACCAGTTTTATCATAAT-GACACCGGTTTTATCATATTTTTACCAGTTATATTGCTATGGAT
1 TTTACCGGTTTTATCAT-TTCGATACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGAT
282933 CGATACATTT
65 CGATACATTT
282943 TTCATTTGTA
Statistics
Matches: 394, Mismatches: 38, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
181 162 0.41
182 231 0.59
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TTTACCGGTTTTATCATTTCGATACCGGTTTTGTCATATTATTACCTGTTATATTGCTATGGATC
GATACATTTGTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAA
AGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTATCTT
Found at i:284399 original size:51 final size:51
Alignment explanation
Indices: 284252--284407 Score: 204
Period size: 51 Copynumber: 3.1 Consensus size: 51
284242 AATTTTTATT
* *
284252 AAAATGTATAATTTAATATTTTAATTAATTTTGTATTGGATTGTGTAATTC
1 AAAATGTATAATTTAATATTTTAATTAATTTTGTATTGAATTGTGTAGTTC
* * *
284303 AAAATGTATAATTTAATATTTTAATTAATTTTTTATTAAACTGTGTAGTTC
1 AAAATGTATAATTTAATATTTTAATTAATTTTGTATTGAATTGTGTAGTTC
* * * ****
284354 AAAATGTACAATTAAATATTTTAATAAAAAAAGTATTGAATTGTGTAGTTC
1 AAAATGTATAATTTAATATTTTAATTAATTTTGTATTGAATTGTGTAGTTC
284405 AAA
1 AAA
284408 TCTATGGCTA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 90 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (51 bp):
AAAATGTATAATTTAATATTTTAATTAATTTTGTATTGAATTGTGTAGTTC
Found at i:285534 original size:2 final size:2
Alignment explanation
Indices: 285527--285556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
285517 CTTTCAAATC
285527 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
285557 TATCGATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:291791 original size:55 final size:55
Alignment explanation
Indices: 291707--291819 Score: 163
Period size: 55 Copynumber: 2.1 Consensus size: 55
291697 CTTCCAGGGG
** * * *
291707 CTCTGCTTCGGGCATTGGGAAGCGTAACCCGATCACCAGACCATCCTCACTGCCC
1 CTCTGCTTCGGGCATCAGGAAGCCTAACCCGACCACCAAACCATCCTCACTGCCC
* *
291762 CTCTGCTTCGGGCATCAGGACGCCTAACCCGACCACCAAACTATCCTCACTGCCC
1 CTCTGCTTCGGGCATCAGGAAGCCTAACCCGACCACCAAACCATCCTCACTGCCC
291817 CTC
1 CTC
291820 GAACCACCCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.20, C:0.42, G:0.19, T:0.19
Consensus pattern (55 bp):
CTCTGCTTCGGGCATCAGGAAGCCTAACCCGACCACCAAACCATCCTCACTGCCC
Found at i:297854 original size:13 final size:13
Alignment explanation
Indices: 297836--297865 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
297826 TTAATTAGAG
297836 AAAATTAAAAATT
1 AAAATTAAAAATT
*
297849 AAAATTAAAATTT
1 AAAATTAAAAATT
297862 AAAA
1 AAAA
297866 CATTCGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:299316 original size:9 final size:9
Alignment explanation
Indices: 299299--299331 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
299289 AACCTGTAAA
299299 AATAATATT
1 AATAATATT
*
299308 AATAGTATT
1 AATAATATT
299317 AATAATA-T
1 AATAATATT
299325 AATAATA
1 AATAATA
299332 ATAGTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (9 bp):
AATAATATT
Found at i:299765 original size:22 final size:22
Alignment explanation
Indices: 299740--299781 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
299730 AAGAGAAAAA
299740 AATTAATAATTTAGA-AATATTG
1 AATT-ATAATTTAGAGAATATTG
*
299762 AATTATTATTTAGAGAATAT
1 AATTATAATTTAGAGAATAT
299782 ATTCACGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (22 bp):
AATTATAATTTAGAGAATATTG
Found at i:318561 original size:24 final size:25
Alignment explanation
Indices: 318534--318595 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
318524 TAAAGATACC
318534 CAAATAGTAAATAATCAAAGGA-AA
1 CAAATAGTAAATAATCAAAGGACAA
*
318558 CAAAT-G-AATATAAATCGAAGGACAA
1 CAAATAGTAA-AT-AATCAAAGGACAA
*
318583 -AAATATTAAATAA
1 CAAATAGTAAATAA
318596 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
22 2 0.06
23 3 0.10
24 20 0.65
25 4 0.13
26 2 0.06
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (25 bp):
CAAATAGTAAATAATCAAAGGACAA
Found at i:318605 original size:12 final size:12
Alignment explanation
Indices: 318590--318640 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
318580 CAAAAATATT
318590 AAATAAAATAAA
1 AAATAAAATAAA
** *
318602 AAATAATGT-CA
1 AAATAAAATAAA
318613 AAAT-AAATAAA
1 AAATAAAATAAA
318624 GAAATAAAATAAA
1 -AAATAAAATAAA
318637 AAAT
1 AAAT
318641 GATAAAAAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
10 2 0.07
11 6 0.20
12 15 0.50
13 7 0.23
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:318638 original size:23 final size:23
Alignment explanation
Indices: 318590--318638 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
318580 CAAAAATATT
** *
318590 AAATAAAATAAAAAATAATGTCA
1 AAATAAAATAAAAAATAAAATAA
318613 AAAT-AAATAAAGAAATAAAATAA
1 AAATAAAATAAA-AAATAAAATAA
318636 AAA
1 AAA
318639 ATGATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATAAAATAAAAAATAAAATAA
Found at i:320034 original size:5 final size:5
Alignment explanation
Indices: 320004--320086 Score: 73
Period size: 5 Copynumber: 16.2 Consensus size: 5
319994 CCTGGAAAGA
* *
320004 AAAAT AAAAT GAAAAT GAAAT -TAAT AAAAT AAAAT AAAAT AAAA- AGAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
*
320054 -ACAT AATAAT AATAAT AAAGAT AAAAT AAAAT A
1 AAAAT AA-AAT AA-AAT AAA-AT AAAAT AAAAT A
320087 TTTTCCAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
4 7 0.11
5 39 0.59
6 20 0.30
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:320227 original size:36 final size:35
Alignment explanation
Indices: 320181--320399 Score: 170
Period size: 36 Copynumber: 6.2 Consensus size: 35
320171 ACTACATAGT
* *
320181 TTTTAAAAATGTTTTTAAAACTATATACTATATAAG
1 TTTTCAAAATGTTTTAAAAACTATATA-TATATAAG
* *
320217 TTTTCAAAATGATTTT-AAAGCTATATA-ATATATG
1 TTTTCAAAATG-TTTTAAAAACTATATATATATAAG
*
320251 TTTTCAAAATGTTTTAAAAA--A-ACTATAT-T-TG
1 TTTTCAAAATGTTTTAAAAACTATA-TATATATAAG
*
320282 TTTTCAAAATGTTTTAAAAACTACATA-ATATACA-
1 TTTTCAAAATGTTTTAAAAACTATATATATATA-AG
** * *
320316 TTTTCAAAAACATTTTAAAAAATTATATATTATATTTA-
1 TTTTC-AAAATGTTTT-AAAAACTATATA-TATA-TAAG
*
320354 TTTTCAAAATGTTTTAAAAATTATATAATATATAAATG
1 TTTTCAAAATGTTTTAAAAACTATAT-ATATAT-AA-G
320392 TTTTCAAA
1 TTTTCAAA
320400 CTATAAAAAA
Statistics
Matches: 151, Mismatches: 13, Indels: 36
0.75 0.06 0.18
Matches are distributed among these distances:
31 23 0.15
32 6 0.04
33 10 0.07
34 26 0.17
35 9 0.06
36 46 0.30
37 13 0.09
38 17 0.11
39 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (35 bp):
TTTTCAAAATGTTTTAAAAACTATATATATATAAG
Found at i:320343 original size:65 final size:65
Alignment explanation
Indices: 320207--320337 Score: 165
Period size: 65 Copynumber: 2.0 Consensus size: 65
320197 AAAACTATAT
** * * ** **
320207 ACTATATAAGTTTTCAAAATGATTTTAAAGCTATATAATATATGTTTTCAAAATGTTTTAAAAAA
1 ACTATATTTGTTTTCAAAATGATTTTAAAACTACATAATATACATTTTCAAAACATTTTAAAAAA
320272 ACTATATTTGTTTTCAAAATG-TTTTAAAAACTACATAATATACATTTTCAAAAACATTTTAAAA
1 ACTATATTTGTTTTCAAAATGATTTT-AAAACTACATAATATACATTTTC-AAAACATTTTAAAA
320336 AA
64 AA
320338 TTATATATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 4 0.07
65 38 0.68
66 14 0.25
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.40
Consensus pattern (65 bp):
ACTATATTTGTTTTCAAAATGATTTTAAAACTACATAATATACATTTTCAAAACATTTTAAAAAA
Found at i:321241 original size:84 final size:83
Alignment explanation
Indices: 320811--321417 Score: 496
Period size: 84 Copynumber: 7.3 Consensus size: 83
320801 ATTTTATTGA
* * * * * * *
320811 CAGATAACCCTTCTTG-CATTGAGCTATGTTGTAAATGATATGCCTTGGAGTTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
320875 ACTCGAAGG--TTT-TTGG
65 ACTCAAAGGTCTTTGTTGG
* * * * * * * * * *
320891 TAGACAACCCTTCTAGCCTTGAGTTAT-ATCGCAAATGATATGCCGTT-GAGCTTAGTGTAATCT
1 CAGATAACCCTTCTAGACTTAAGTTATGCT-GCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCG
*
320954 AACTCAAAGGTCTTTTTTGG
64 AACTCAAAGGTCTTTGTTGG
* * * * *
320974 CAGATAACCCTTCTCGACTTAAGTTATGATGTAAATGATGTGCCTTAGAGCTGAGCGTAGTCCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
321039 CTCGAAGGTCTTTGGTGA
66 CTCAAAGGTCTTTGTTGG
* * * * * * * *
321057 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTTAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
* *
321122 ACTC-GAGAG--TAT-TTGG
65 ACTCAAAG-GTCTTTGTTGG
* * * * *
321138 CAGATAGCCCTTCTTGACTTAAGTTATTCTGCAAATAATGTGTCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
321203 CTCAAAGGTCTTTGGTTGG
66 CTCAAAGGTCTTT-GTTGG
* * * * * *
321222 CAGATAACCCTTCTCGACTTAATTTATGCCGCAAATGATATGCCTTGGAGCTGAACATAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
321287 CTCGAAGGTCTTTTATTGG
66 CTCAAAGGTC-TTTGTTGG
* * * * * * * * * * *
321306 CAAATAGCCTTTCTTGCCTTGAGCTATGTTGCAAATGATGCGTCTTAGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* *
321371 CTCAAAGGTCCTTGTCGG
66 CTCAAAGGTCTTTGTTGG
* *
321389 CAGATAACCCTTCTAGCCTTGAGTTATGC
1 CAGATAACCCTTCTAGACTTAAGTTATGC
321418 CGTAAATGTT
Statistics
Matches: 416, Mismatches: 95, Indels: 29
0.77 0.18 0.05
Matches are distributed among these distances:
79 1 0.00
80 75 0.18
81 42 0.10
82 9 0.02
83 134 0.32
84 152 0.37
85 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (83 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTGTTGG
Found at i:326420 original size:13 final size:15
Alignment explanation
Indices: 326402--326437 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
326392 TTTAATTGCG
326402 AAAATTATAAA-TT-
1 AAAATTATAAATTTA
326415 AAAATTA-AAATTTA
1 AAAATTATAAATTTA
326429 AAAATTATA
1 AAAATTATA
326438 TTCGAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 7 0.35
15 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTATAAATTTA
Found at i:328003 original size:6 final size:6
Alignment explanation
Indices: 327988--328059 Score: 51
Period size: 6 Copynumber: 11.7 Consensus size: 6
327978 ACTTGGAAAG
*
327988 AAAAAT -AAAAT AAAAAT GAAATTAAT -AAAAT AAAAAT AAAAA- AATAAT
1 AAAAAT AAAAAT AAAAAT -AAA--AAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
328036 AATAAT AATAAAG ATAAAAT AAAA
1 AAAAAT AA-AAAT A-AAAAT AAAA
328060 TATTTTCCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
5 12 0.22
6 26 0.48
7 12 0.22
8 1 0.02
9 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:328017 original size:26 final size:25
Alignment explanation
Indices: 327988--328054 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
327978 ACTTGGAAAG
*
327988 AAAAATAAAATAAAAATGAA-ATTAAT
1 AAAAATAAAATAAAAA--AATAATAAT
328014 -AAAATAAAAATAAAAAAATAATAAT
1 AAAAAT-AAAATAAAAAAATAATAAT
*
328039 AATAATAAAGATAAAA
1 AAAAATAAA-ATAAAA
328055 TAAAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 2 0.06
25 13 0.37
26 20 0.57
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (25 bp):
AAAAATAAAATAAAAAAATAATAAT
Found at i:328023 original size:31 final size:33
Alignment explanation
Indices: 327988--328061 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 33
327978 ACTTGGAAAG
*
327988 AAAAATAAAATAAA-AATGAA-ATTAATAAA-AT
1 AAAAATAAAATAAATAAT-AATAATAATAAAGAT
328019 AAAAATAAAA-AAATAATAATAATAATAAAGAT
1 AAAAATAAAATAAATAATAATAATAATAAAGAT
328051 -AAAATAAAATA
1 AAAAATAAAATA
328062 TTTTCCAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 5 0.13
31 30 0.79
32 3 0.08
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (33 bp):
AAAAATAAAATAAATAATAATAATAATAAAGAT
Found at i:328039 original size:20 final size:19
Alignment explanation
Indices: 327988--328059 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
327978 ACTTGGAAAG
327988 AAAAATAAAATAAAAATGAA
1 AAAAATAAAATAAAAAT-AA
**
328008 ATTAATAAAATAAAAATAA
1 AAAAATAAAATAAAAATAA
*
328027 AAAAAT--AATAATAATAA
1 AAAAATAAAATAAAAATAA
*
328044 TAAAGATAAAATAAAA
1 -AAAAATAAAATAAAA
328060 TATTTTCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 10 0.24
18 5 0.12
19 6 0.14
20 21 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAAATAAAATAAAAATAA
Found at i:328042 original size:17 final size:18
Alignment explanation
Indices: 328016--328061 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
328006 AAATTAATAA
*
328016 AATAAAAATAA-AAAAAT
1 AATAATAATAATAAAAAT
*
328033 AATAATAATAATAAAGAT
1 AATAATAATAATAAAAAT
328051 AA-AATAA-AATA
1 AATAATAATAATA
328062 TTTTCCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 4 0.15
17 15 0.58
18 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAATAATAATAAAAAT
Found at i:328135 original size:39 final size:38
Alignment explanation
Indices: 328051--328127 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 38
328041 TAATAAAGAT
328051 AAAATAAAATATTTTCCAAAAGCTTATATATATATATTTTC
1 AAAA-AAAATATTTT-CAAAA-CTTATATATATATATTTTC
328092 AAAAAAAATATTTT-AAAA-TTATATATCATATATTTT
1 AAAAAAAATATTTTCAAAACTTATATAT-ATATATTTT
328128 GTGAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 8 0.23
37 9 0.26
38 4 0.11
40 10 0.29
41 4 0.11
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.43
Consensus pattern (38 bp):
AAAAAAAATATTTTCAAAACTTATATATATATATTTTC
Found at i:328229 original size:34 final size:34
Alignment explanation
Indices: 328153--328357 Score: 135
Period size: 34 Copynumber: 6.0 Consensus size: 34
328143 AAAACTACAT
328153 AGTTTTCAAAAATGTTTTTAAAACTATATACTATATA
1 AGTTTTC-AAAATG-TTTTAAAACTATATAC-ATATA
*
328190 AGTTTTCAAAATGATTTTAAAGCTATATA-ATATA
1 AGTTTTCAAAATG-TTTTAAAACTATATACATATA
* * *
328224 TGTTTTCAAAATGTTTTAAAA--A-AAACTATATTT
1 AGTTTTCAAAATGTTTTAAAACTATATAC-ATA-TA
*
328257 A-TTTTCATAATGTTTTAAAA-TATACATA-ATATA
1 AGTTTTCAAAATGTTTTAAAACTAT--ATACATATA
* * * *
328290 CA-TTTTCAAAAACGTTTTAAAAAT-TATATATTTA
1 -AGTTTTC-AAAATGTTTTAAAACTATATACATATA
*
328324 TA-TTTTCAAAATGTTTTAAAAATTATATA-ATATA
1 -AGTTTTCAAAATGTTTT-AAAACTATATACATATA
328358 TAAACATTTT
Statistics
Matches: 138, Mismatches: 17, Indels: 29
0.75 0.09 0.16
Matches are distributed among these distances:
30 2 0.01
31 1 0.01
32 21 0.15
33 22 0.16
34 45 0.33
35 17 0.12
36 23 0.17
37 7 0.05
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (34 bp):
AGTTTTCAAAATGTTTTAAAACTATATACATATA
Found at i:328262 original size:66 final size:66
Alignment explanation
Indices: 328155--328359 Score: 191
Period size: 66 Copynumber: 3.0 Consensus size: 66
328145 AACTACATAG
* * ** * *
328155 TTTTCAAAAATGTTTTTAAAACTATATACTATATAAGTTTTCAAAATGATTTTAAAGCTATATAA
1 TTTTCAAAAACGTTTTAAAAAAAATATA-TTTAT-A-TTTTCAAAATG-TTTTAAA-ATATATAA
*
328220 TATATG
61 TATATA
* *
328226 TTTTC-AAAATGTTTTAAAAAAAACTATA-TT-TATTTTCATAATGTTTTAAAATATACATAATA
1 TTTTCAAAAACGTTTTAAAAAAAA-TATATTTATATTTTCAAAATGTTTTAAAATAT--ATAATA
*
328288 TACA
63 TATA
**
328292 TTTTCAAAAACGTTTTAAAAATTATATATTTATATTTTCAAAATGTTTTAAAAATTATATAATAT
1 TTTTCAAAAACGTTTTAAAAAAAATATATTTATATTTTCAAAATGTTTT-AAAA-TATATAATAT
328357 ATA
64 ATA
328360 AACATTTTCA
Statistics
Matches: 113, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
64 3 0.03
65 7 0.06
66 27 0.24
67 18 0.16
68 26 0.23
69 5 0.04
70 18 0.16
71 9 0.08
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (66 bp):
TTTTCAAAAACGTTTTAAAAAAAATATATTTATATTTTCAAAATGTTTTAAAATATATAATATAT
A
Found at i:332334 original size:19 final size:19
Alignment explanation
Indices: 332310--332347 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
332300 CCACTTGTTT
332310 TCTTTT-GTTAAATTGCCGG
1 TCTTTTCGTTAAA-TGCCGG
332329 TCTTTTCGGTTAAATGCCG
1 TCTTTTC-GTTAAATGCCG
332348 AGAACTCGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (19 bp):
TCTTTTCGTTAAATGCCGG
Found at i:334150 original size:13 final size:13
Alignment explanation
Indices: 334132--334156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334122 AATCTTAGAA
334132 ACAACTTTGAGAG
1 ACAACTTTGAGAG
334145 ACAACTTTGAGA
1 ACAACTTTGAGA
334157 CACACTTCAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
ACAACTTTGAGAG
Found at i:339131 original size:2 final size:2
Alignment explanation
Indices: 339124--339148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
339114 TTGATATACG
339124 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
339149 TGCAGCATTC
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:350986 original size:32 final size:31
Alignment explanation
Indices: 350949--351041 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 31
350939 GGTAGTCTTT
*
350949 ATGGCCCCGAGATCTTTTTTTGGGTAGGC-C
1 ATGGCCCCGAGATCTTTTCTTGGGTAGGCTC
* *
350979 ATGTGGCCCCGATAT-TTTTCTTGGGTACGCTC
1 A--TGGCCCCGAGATCTTTTCTTGGGTAGGCTC
*
351011 ATGGCCTCGAGAATC-TTTCTTGGGTAGGCTC
1 ATGGCCCCGAG-ATCTTTTCTTGGGTAGGCTC
351042 TCAGGCCCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 9 0.17
31 30 0.58
32 13 0.25
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (31 bp):
ATGGCCCCGAGATCTTTTCTTGGGTAGGCTC
Found at i:353766 original size:28 final size:29
Alignment explanation
Indices: 353698--353768 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
353688 TTTGGATATG
**
353698 AAATTACCAAAAGCAGCACTATGGGGTAA
1 AAATTACCAAAAATAGCACTATGGGGTAA
353727 AAATTACCAAAAATAGCACTATGGGGTAA
1 AAATTACCAAAAATAGCACTATGGGGTAA
353756 AAATTA-CAAAAAT
1 AAATTACCAAAAAT
353769 TCCCTTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.17
29 33 0.82
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (29 bp):
AAATTACCAAAAATAGCACTATGGGGTAA
Found at i:354911 original size:31 final size:31
Alignment explanation
Indices: 354873--354943 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
354863 TAAGGCAACC
** *
354873 CTTGGGTAGACTTTGCGGCCTCGAGATATTT
1 CTTGGGTAGACCCTGCGGCCCCGAGATATTT
* * *
354904 CTTGGGTAGGCCCTGTGGCCCCGAGATCTTT
1 CTTGGGTAGACCCTGCGGCCCCGAGATATTT
354935 CTTGGGTAG
1 CTTGGGTAG
354944 GCCCCGTGGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.32, T:0.32
Consensus pattern (31 bp):
CTTGGGTAGACCCTGCGGCCCCGAGATATTT
Found at i:354944 original size:31 final size:31
Alignment explanation
Indices: 354889--354953 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
354879 TAGACTTTGC
* *
354889 GGCCTCGAGATATTTCTTGGGTAGGCCCTGT
1 GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
*
354920 GGCCCCGAGATCTTTCTTGGGTAGGCCCCGT
1 GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
354951 GGC
1 GGC
354954 TTTTCTTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.11, C:0.28, G:0.34, T:0.28
Consensus pattern (31 bp):
GGCCCCGAGATATTTCTTGGGTAGGCCCCGT
Found at i:364222 original size:162 final size:161
Alignment explanation
Indices: 363955--364525 Score: 655
Period size: 162 Copynumber: 3.4 Consensus size: 161
363945 TGGCGGTTTA
* * * *
363955 TGTCGATACTTTATAAAACTGTATTGATCCACATCAATATAACAGGTAAAAATATAACAAAACCG
1 TGTCGATACTTTATAAAA-TGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
*
364020 GTAATGCGGTACCAGATATATTGAAAGTTTCGATACTTTAATATAAGTATCGACACTTTGTGAAT
65 GTAAAGCGGTACCAGATATATTGAAAGTTTCGATACTTTAATATAAGTATCGACACTTTGTGAAT
* *
364085 TTAAAAGAGAAGCAGTTTTAGCGCTCACAATG
130 TTAAAAGAGAAGCAGTTTTAGCGCCCACAAAG
* *
364117 TGTCGATACTTTATAACAATGGATCGATCCACAACGACATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
364182 GTATAGAGC-G-ACC-GAATATATTTAAAGTGTT-GATACTTTAATATAAGTATCGACTCTTTGT
65 GTA-A-AGCGGTACCAG-ATATATTGAAAGT-TTCGATACTTTAATATAAGTATCGACACTTTGT
* * *
364243 GAATTTAAAAGAGAAGTAGTTTTAGTGCCCATAAAG
126 GAATTTAAAAGAGAAGCAGTTTTAGCGCCCACAAAG
* *
364279 TGTCGATACTTTATAATAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* *
364344 GTCCTTAAAGGAAAAAATCGGTATAGAGCGACCAGATATATTTAAAGTGTCGATACTTTAATATA
65 G----TAAA-G-------CGG--T------ACCAGATATATTGAAAGTTTCGATACTTTAATATA
* * * *
364409 AGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAA
110 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCCACAAAG
*
364461 TGTCGATACTTTATAACAATGTATCGGTCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAA-AATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
364526 ATATTGAAAT
Statistics
Matches: 350, Mismatches: 30, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
161 1 0.00
162 195 0.56
163 6 0.02
164 3 0.01
165 2 0.01
166 2 0.01
172 1 0.00
173 1 0.00
181 1 0.00
182 137 0.39
183 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (161 bp):
TGTCGATACTTTATAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGG
TAAAGCGGTACCAGATATATTGAAAGTTTCGATACTTTAATATAAGTATCGACACTTTGTGAATT
TAAAAGAGAAGCAGTTTTAGCGCCCACAAAG
Found at i:364499 original size:182 final size:182
Alignment explanation
Indices: 364175--364588 Score: 625
Period size: 182 Copynumber: 2.3 Consensus size: 182
364165 AAAATATGAC
* * *
364175 AAAACCGGTATAGAGCGACCGAATATATTTAAAGTGTTGATACTTTAATATAAGTATCGACTCTT
1 AAAATCGGTATAGAGCGACCGAATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
** * * *
364240 TGTGAATTTAAAAGAGAAGTAGTTTTAGTGCCCATAAAGTGTCGATACTTTATAATAATGTATCG
66 TGTGAATTTAAAAGAGAAACAGTTTTAGCGCCCATAAAATGTCGATACTTTATAACAATGTATCG
* * *
364305 ATCCAAAACGATATAACAGGTAAAAATATGACAAAATCGGTCCTT-AAAGGAA
131 ATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGAT-ATTGAAAGGAA
364357 AAAATCGGTATAGAGCGACC-AGATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACT
1 AAAATCGGTATAGAGCGACCGA-ATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACT
*
364421 TTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAATGTCGATACTTTATAACAATGTATC
65 TTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCCATAAAATGTCGATACTTTATAACAATGTATC
* * *
364486 GGTCCACAACGATATAACAGGTAAAAATATGACAAAACCGATATTGAAATGAA
130 GATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGATATTGAAAGGAA
* * * *
364539 AAAATCGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTAATA
1 AAAATCGGTATAGAGCGACCGAATATATTTAAAGTGTCGATACTTTAATA
364589 AGTACACGTA
Statistics
Matches: 210, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
181 3 0.01
182 206 0.98
183 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (182 bp):
AAAATCGGTATAGAGCGACCGAATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAGAAACAGTTTTAGCGCCCATAAAATGTCGATACTTTATAACAATGTATCG
ATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGATATTGAAAGGAA
Found at i:368045 original size:21 final size:21
Alignment explanation
Indices: 368021--368064 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
368011 AAGACAATTA
*
368021 AGAGTCCAAGAGAGACTTGAG
1 AGAGTCCAAGAGACACTTGAG
* *
368042 AGAGTCGAAGATACACTTGAG
1 AGAGTCCAAGAGACACTTGAG
368063 AG
1 AG
368065 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCCAAGAGACACTTGAG
Found at i:368137 original size:33 final size:33
Alignment explanation
Indices: 368098--368197 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
368088 AAATAGATGG
*
368098 AGTGGTGAAAGAAGTTAAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
368131 ATTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
*
368164 AGTGGTTAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
368197 A
1 A
368198 CTTAAGGTGG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:368403 original size:18 final size:18
Alignment explanation
Indices: 368380--368418 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
368370 AAAAAAATAT
368380 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
368398 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
368416 GAA
1 GAA
368419 ATAAAGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:369966 original size:19 final size:19
Alignment explanation
Indices: 369942--369987 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
369932 AAATGTAGGT
*
369942 TAATTTTGCATAAGATTTA
1 TAATTTTGAATAAGATTTA
*
369961 TAATTTTGAATATGATTTA
1 TAATTTTGAATAAGATTTA
369980 TAATTTTG
1 TAATTTTG
369988 TATGTGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (19 bp):
TAATTTTGAATAAGATTTA
Found at i:370608 original size:199 final size:198
Alignment explanation
Indices: 370253--371813 Score: 1880
Period size: 199 Copynumber: 7.8 Consensus size: 198
370243 GTAAGCAGAT
* * ** * *
370253 GTGTTGATACATTTATAAAAAGCATCGATCAAAAAAACATCAAAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATC-GAAACCCATAATTATAATGTAAT
* * *
370318 AGGTAATTTTGTAATATAATCGGTATAAATATATCGGTTTTATGTA-AGAATAGGTCTACATAAT
65 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATG-AGAGAATAGGTCTACATAAT
* *
370382 GTATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGAACG
129 GTATCGACACTTTT-AAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACG
370447 CATAAA
193 CATAAA
* *
370453 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACTCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
370518 GGTAATTTT-TCAACGTAACTGGTA-AAACTGTACCTGTTTTATGAGAGAATATGTCTACATAAT
66 GGTAATTTTGT-AATGTAACCGGTATAAA-TATACCGGTTTTATGAGAGAATAGGTCTACATAAT
* *
370581 GTATCGACACTTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGGGTGCAC
129 GTATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTGCAC
**
370646 AAATAAA
192 GCATAAA
* * * * * *
370653 GTGTCGATACATTTTTTAAAAGTGTCAATCCCAGAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
370718 GGTAATTTTGTAATGTAACCAGTATAAATATACCGATTTTATGTGAAAATATGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * *
370783 ATCGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAGTAAATGTCCAAAAAATGGTGCAC
131 ATCGACACTTTTAAATT-TGTGTCGATACTTTTTGTCCAGAATGAA--TCC-CAAAATGGTGCAC
*
370848 ACATAAA
192 GCATAAA
* * *
370855 GTGTCGATACATTTATAAAAATTATCGATCCCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
370920 GGTAATATTT-CAATGTAACTGGTATAAATATACCAGTTTTCTGTGAGAATAGGTCTAGAAAATG
66 GGTAAT-TTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
** * * * *
370984 TATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCC
130 TATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGC
*
371049 ATTAA
194 ATAAA
* * *
371054 GTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * *
371119 GGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAAGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * *
371184 ATCGACACATTTGAAATTGGTGTCGGTACTTTTTGTCTAGAATGAATGCCCAAAATGGTGAACGC
131 ATCGACAC-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAAT-CCCAAAATGGTGCACGC
371249 ATAAA
194 ATAAA
* * * ** * * *
371254 GTGTCGATACATTTTTAAAAAAGTGTCTATCTGAGAGACAT-TAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
*
371318 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTAT-ATGAGAATAGGTCTATATAAT
65 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGA-GAGAATAGGTCTACATAAT
* * * *
371382 GTATCGACACTTTTTAATTGTGTGTCGATACATTTTGTCCAGAGTAAATGCCCAAAAAATGGTGC
129 GTATCGACACTTTTAAATT-TGTGTCGATACTTTTTGTCCAGAATGAAT-CCC--AAAATGGTGC
371447 ACGCATAAA
190 ACGCATAAA
* * *
371456 GTGTCGATACATTTATAAAAAGTATCGATCTCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
371521 GGTAATTTT-TCAATGTAACCGGTATAAATATATCGATTTTATGCGAGAATAGGTCTAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
** * * * * *
371585 TATCGACACTTATGGAATTTGTGTCGATACTTTTTGTTCAGAAGGAATGCCAAAAGGGTGCACCC
130 TATCGACACTT-TTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGC
* *
371650 GTTAA
194 ATAAA
* *
371655 GTGTCGATACATTTTTAAAAAG-AGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTA-TCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * *
371719 AGGTAATTTTGTAATGTAACTGGTATAAATATACCAGTTTTATGAGAAAATAGGTC-AGCATAAA
65 AGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAAT
*
371783 GTATCGACAATTGTTAAATTTGTGTCGATAC
129 GTATCGACACTT-TTAAATTTGTGTCGATAC
371814 CATTTTAAAA
Statistics
Matches: 1175, Mismatches: 158, Indels: 57
0.85 0.11 0.04
Matches are distributed among these distances:
198 10 0.01
199 444 0.38
200 355 0.30
201 48 0.04
202 305 0.26
203 13 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGCACGCAT
AAA
Found at i:371383 original size:601 final size:600
Alignment explanation
Indices: 370253--371813 Score: 2301
Period size: 601 Copynumber: 2.6 Consensus size: 600
370243 GTAAGCAGAT
* * * * * * *
370253 GTGTTGATACATTTATAAAAAGCATCGATCAAAAAAACATCAAAAACTCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATC-GAAACCCATGATTATAATGTAAT
* * * * *
370318 AGGTAATTTTGTAATATAA-TCGGTATAAATATATCGGTTTTATGTAAGAATAGGTCTACATAAT
65 AGGTAATTTT-CAATGTAACT-GGTATAAATATATC-GTTTTATGTGAGAATAGGTCTAGAAAAT
* * * * * * * *
370382 GTATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATCCCAAAATGGTGAACG
127 GTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACC
* * * * *
370447 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACTCATAATTATAAT
192 CATTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * *
370512 GTAATAGGTAATTTT-TCAACGTAACTGGTA-AAACTGTACCTGTTTTATGAGAGAATATGTCTA
257 GTAATAGGTAATTTTGT-AATGTAACTGGTATAAA-TATACCAGTTTTATGAGAGAATAAGTCTA
370575 CATAATGTATCGACAC-TTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAG
320 CATAATGTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAG
* *
370639 GGTGCACAAATAAAGTGTCGATACATTTTTTAAAAGTGTCAATCCCAGAGACATCGAAACCCATA
385 GGTGAACAAATAAAGTGTCGATACATTTTTAAAAAGTGTCAATCCCAGAGACATCGAAACCCATA
*
370704 ATTATAATGTAATAGGTAATTTTGTAATGTAACCAGTATAAATATACCGATTTTATGTGAAAATA
450 ATTATAATGTAATAGGTAATTTTGTAATGTAACCAGTATAAATATACCGATTTTATATGAAAATA
* *
370769 TGTCTACATAATGTATCGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAGTAAATGTCC
515 GGTCTACATAATGTATCGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAGTAAATGCCC
370834 AAAAAATGGTGCACACATAAA
580 AAAAAATGGTGCACACATAAA
* *
370855 GTGTCGATACATTTATAAAAATTATCGATCCCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATGATTATAATGTAATA
* *
370920 GGTAATATTTCAATGTAACTGGTATAAATATACCAGTTTTCTGTGAGAATAGGTCTAGAAAATGT
66 GGTAAT-TTTCAATGTAACTGGTATAAATATATC-GTTTTATGTGAGAATAGGTCTAGAAAATGT
370985 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
129 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
*
371050 TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCTCAAAAACATCGAAACCCATAATTATAATGT
194 TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* * * *
371115 AATAGGTAATTTTGTAATGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAAGTCTACATA
259 AATAGGTAATTTTGTAATGTAACTGGTATAAATATACCAGTTTTATGAGAGAATAAGTCTACATA
* * * * * *
371180 ATGTATCGACACATT-TGAAATTGGTGTCGGTACTTTTTGTCTAGAATGAATGCCCAAAATGGTG
324 ATGTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGGGTG
** * ** *
371244 AACGCATAAAGTGTCGATACATTTTTAAAAAAGTGTCTATCTGAGAGACAT-TAAACCCATAATT
389 AACAAATAAAGTGTCGATACATTTTT-AAAAAGTGTCAATCCCAGAGACATCGAAACCCATAATT
* * *
371308 ATAATGTAATAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATATGAGAATAGGT
453 ATAATGTAATAGGTAATTTTGTAATGTAACCAGTATAAATATACCGATTTTATATGAAAATAGGT
* * *
371373 CTATATAATGTATCGACACTTTTTAATTGTGTGTCGATACATTTTGTCCAGAGTAAATGCCCAAA
518 CTACATAATGTATCGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAGTAAATGCCCAAA
*
371438 AAATGGTGCACGCATAAA
583 AAATGGTGCACACATAAA
*
371456 GTGTCGATACATTTATAAAAAGTATCGATCTCATAAACATCGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATGATTATAATGTAATA
* *
371521 GGTAATTTTTCAATGTAACCGGTATAAATATATCGATTTTATGCGAGAATAGGTCTAGAAAATGT
66 GGTAA-TTTTCAATGTAACTGGTATAAATATATCG-TTTTATGTGAGAATAGGTCTAGAAAATGT
* *
371586 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTTCAGAAGGAATGCCAAAAGGGTGCACCCG
129 ATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCA
* *
371651 TTAAGTGTCGATACATTTTTAAAAAGAGTCGATCCCAAAAATATCGAAACCCATAATTATAATGT
194 TTAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* *
371716 AATAGGTAATTTTGTAATGTAACTGGTATAAATATACCAGTTTTATGAGAAAATAGGTC-AGCAT
259 AATAGGTAATTTTGTAATGTAACTGGTATAAATATACCAGTTTTATGAGAGAATAAGTCTA-CAT
* *
371780 AAAGTATCGACA-ATTGTTAAATTTGTGTCGATAC
323 AATGTATCGACACATTATTAAATTTGTGTCGATAC
371814 CATTTTAAAA
Statistics
Matches: 866, Mismatches: 83, Indels: 21
0.89 0.09 0.02
Matches are distributed among these distances:
600 5 0.01
601 795 0.92
602 66 0.08
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (600 bp):
GTGTCGATACATTTATAAAAAGTATCGATCACATAAACATCGAAACCCATGATTATAATGTAATA
GGTAATTTTCAATGTAACTGGTATAAATATATCGTTTTATGTGAGAATAGGTCTAGAAAATGTAT
CGACACTTATGGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCAAAAGGGTGCACCCATT
AAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
TAGGTAATTTTGTAATGTAACTGGTATAAATATACCAGTTTTATGAGAGAATAAGTCTACATAAT
GTATCGACACATTATTAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAAGGGTGAA
CAAATAAAGTGTCGATACATTTTTAAAAAGTGTCAATCCCAGAGACATCGAAACCCATAATTATA
ATGTAATAGGTAATTTTGTAATGTAACCAGTATAAATATACCGATTTTATATGAAAATAGGTCTA
CATAATGTATCGACACTTTTTAATTATGCGTCGATACATTTTGTCCAGAGTAAATGCCCAAAAAA
TGGTGCACACATAAA
Found at i:374704 original size:24 final size:24
Alignment explanation
Indices: 374653--374705 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
374643 TTTCATATGT
* * *
374653 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
374677 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTCAATATA
374701 AATTT
1 AATTT
374706 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:375488 original size:199 final size:199
Alignment explanation
Indices: 375013--376180 Score: 1418
Period size: 200 Copynumber: 5.9 Consensus size: 199
375003 TAAAGTTTCC
* * *
375013 CATAAAGTGTCGATACATGTTTT-AAAAGTATCGATCCTAAAAACATCGAAACCGAAAATTATAG
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * * * * * *
375077 TGTAATAGGTAAATTTACAATGTAACTGGTATAAATATACCCGTTTTTTTTTAGAAAATAGATAT
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA-CCG-ATTTTATGAGAGAATAGGTCT
* *
375142 ACATAATGTATCGACACTTGTGGAATTGGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGT
128 ACATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAG-
*
375207 GGTGCACC
192 GGTGCACG
* * * *
375215 CATACATTGTCGATACATTTTTAAAAAGTATTGATCCCAAAAACATCGAAACCAATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* ** * * *
375280 GTAATAGGTAATTTTGTAATATAGCCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACA
* * * * * * *
375345 TAATATGTCGACACTT-TTGAATTTTGTGTCGATACTTTTTTTCCAGAATGAATCCCAAAATGGT
131 TAATGTATCGACACTTGTGGAA-TTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGT
* **
375409 GAAAT
195 GCACG
* * * * * * *
375414 CATAAAATGTCAATACATTTATAAAAAGTATCGATCTCAGAAACATTGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
** * *
375479 GTAATAGGTAAATTTACAATGTAA-TAGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACA
* *
375543 TAATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAAAAGGGTT
131 TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG-T
375608 GCACG
195 GCACG
* *
375613 CATAAAGTGTCGATAGATTTTTAAAAAGTATCGAT-CCATAAAACATCGAAACTGATAATTATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCA-AAAACATCGAAACCGATAATTATAA
* * *
375677 TGTACTAGGTAAATTTACAATGTAACCTGTATAACTATACC-AGTTTTATGAGAGAATAGGTCTA
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTTATGAGAGAATAGGTCTA
*
375741 CATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAAAAGGG
129 CATAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG
375806 TTGCACG
194 -TGCACG
* *
375813 CATAAAGTGTCGATAGATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * * * **
375878 ATAATAGGTAAATTTACAATATAACCGTTATAAATTTACCGGTTTTATGAGAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACA
* * *
375943 TAATGTATCGACACGTTTTAG-ATTTGTGTCGATACATTTTT-TCCAAAATGAATGCCAAACGGG
131 TAATGTATCGACAC-TTGTGGAATTTGTGTCGATAC-TTTTTGTCCAAAATGAATGCCAAA-AGG
**
376006 GTGCAAA
193 GTGCACG
* * * * ** * *
376013 CAAAAAGTATTGATACA-TTTGAAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * * *
376077 GTAATAAGTAAATTTATAATGTAACCGGTATAAATATACCAATTTTATAAGAGAATAGGTCAACT
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACA
**
376142 TAATGTATCGACACTT-TTAAATTTGTGTCGATACTTTTT
131 TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTT
376181 AAATAACACG
Statistics
Matches: 836, Mismatches: 117, Indels: 31
0.85 0.12 0.03
Matches are distributed among these distances:
197 6 0.01
198 103 0.12
199 275 0.33
200 345 0.41
201 22 0.03
202 85 0.10
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACA
TAATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTG
CACG
Found at i:380640 original size:178 final size:178
Alignment explanation
Indices: 380313--380650 Score: 464
Period size: 178 Copynumber: 1.9 Consensus size: 178
380303 GCTAAATAGG
380313 TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
1 TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
* * ** * * *
380378 GTAAATTAACAATGTAACCGGTATAAATATATTGGTTAATTAGAAAACAAGTCAATATAATGTAT
66 ATAAATTAACAATATAACCGGTATAAATATACCGGTTAATAAGAAAACAAGTCAACATAAAGTAT
* *
380443 CGACACTTTTTTTAATTTGTGTCGATACTTATTATCCAGAATATAAAC
131 CGACACTTATTTAAATTTGTGTCGATACTTATTATCCAGAATATAAAC
* * *
380491 TGTCGATACATTTAT-TAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATGTAATA
1 TGTCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * * * * **
380555 GATAAATTTACAATATAACTGGTATAAATATACCGATTTTATAAGAAAATAGGTCTGCATAAAGT
65 GATAAATTAACAATATAACCGGTATAAATATACCG-GTTAATAAGAAAACAAGTCAACATAAAGT
380620 ATCGACAC-TATTTAAATTTGTGTCGATACTT
129 ATCGACACTTATTTAAATTTGTGTCGATACTT
380651 TTTGTCTATA
Statistics
Matches: 138, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
178 109 0.79
179 29 0.21
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (178 bp):
TGTCGATACATTTTCTAAAAGTATCGACCCCAAAAACATCGAAACCAATAATTATAATGTAATAG
ATAAATTAACAATATAACCGGTATAAATATACCGGTTAATAAGAAAACAAGTCAACATAAAGTAT
CGACACTTATTTAAATTTGTGTCGATACTTATTATCCAGAATATAAAC
Found at i:380804 original size:200 final size:198
Alignment explanation
Indices: 380485--380968 Score: 585
Period size: 200 Copynumber: 2.4 Consensus size: 198
380475 TATCCAGAAT
*
380485 ATAAACTGTCGATACATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAA-AACATCGAAACCGATAATTATAATG
* * *** * * **
380550 TAATAGATAAATTTACAATATAACTGGTATAAATATACCGATTTTATAAGAAAATAGGTCTGCAT
65 TAATAGGTAAATTTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGATCTAAAT
* * *
380615 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTGTCTATAATGAATGCCAAACGGGGTG
130 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAAACGAGGTG
380680 CACAC
194 CACAC
* * ** *
380685 ATAAAGTGTCGATATATTTATTAAAAGTATAGATCCCACAAACATCGAAAGTGATAATTACAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA-AAACATCGAAACCGATAATTATAATG
* * * * *
380750 TGATAGGTAAATTTACAATGTATCCAATAGAAATATACCGGTTTTATGAGAAAATATATCTAAAT
65 TAATAGGTAAATTTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGATCTAAAT
* * * *
380815 AATGTATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGC
130 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGC
**
380880 ATGC
195 ACAC
* * * * * *
380884 ATAAAGTATTGATACATTTA--AAATTGTATCGATCCAAAAAATATCAAAACCGATAATTATAAT
1 ATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC-CAAAACATCGAAACCGATAATTATAAT
*
380947 GTAATAGGTAAATTTGCAATGT
64 GTAATAGGTAAATTTACAATGT
380969 TACCTTACCG
Statistics
Matches: 239, Mismatches: 42, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
197 3 0.01
198 49 0.21
199 42 0.18
200 144 0.60
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.32
Consensus pattern (198 bp):
ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAACATCGAAACCGATAATTATAATGT
AATAGGTAAATTTACAATGTAACCAATAGAAATATACCGATTTTATAAGAAAATAGATCTAAATA
AAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGCA
CAC
Found at i:381125 original size:23 final size:23
Alignment explanation
Indices: 381075--381119 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
381065 TGCCTATTTT
*
381075 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
381098 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
381120 TGTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:384394 original size:3 final size:3
Alignment explanation
Indices: 384374--384470 Score: 167
Period size: 3 Copynumber: 32.3 Consensus size: 3
384364 GAACCAACAG
* *
384374 AGA AGG AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
384422 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
384470 A
1 A
384471 ACATCCTACC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:385309 original size:14 final size:14
Alignment explanation
Indices: 385290--385324 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
385280 TGACCAATTT
385290 TGCCACCCCATTAA
1 TGCCACCCCATTAA
385304 TGCCACCCCATTAA
1 TGCCACCCCATTAA
385318 TGCCACC
1 TGCCACC
385325 AAATTGCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.46, G:0.09, T:0.20
Consensus pattern (14 bp):
TGCCACCCCATTAA
Found at i:390743 original size:2 final size:2
Alignment explanation
Indices: 390736--390762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
390726 GGAAAATAAA
390736 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
390763 CTTTGTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:399834 original size:33 final size:33
Alignment explanation
Indices: 399787--399857 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
399777 ATAAAGTTTA
* *
399787 CGAT-AATTGAAATACTTAAATACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
*
399819 TGATAAATTCAAATACTTAAAAACTTTCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTTCAAGTT
399852 CGATAA
1 CGATAA
399858 TTGAAACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTTCAAGTT
Found at i:399877 original size:21 final size:21
Alignment explanation
Indices: 399852--399893 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
399842 CTTTCAAGTT
399852 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
399873 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
399894 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:404937 original size:23 final size:22
Alignment explanation
Indices: 404906--404950 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
404896 AGTAAAATAT
*
404906 TAAATAAAT-TAAAATACTTAAA
1 TAAATAAATACAAAATA-TTAAA
404928 TAAATTAAATACAAAATATTAAA
1 TAAA-TAAATACAAAATATTAAA
404951 AATATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 10 0.50
24 6 0.30
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATAAATACAAAATATTAAA
Done.