Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 10 of 129
Found at i:1207312 original size:110 final size:109
Alignment explanation
Indices: 1207076--1207473 Score: 419
Period size: 110 Copynumber: 3.6 Consensus size: 109
1207066 CGACTCGCGA
* * * * * *
1207076 TGTTATCCCAATCAATTCTTTATTTTTTGAC-TAC-GATGTTATCCCGATTGATTCTGTAAGACC
1 TGTTGTCCCGATCGATTCTTTATTTTTTGACTTGCAG-TGTTATCTCGATCGATTCTGTAAGACC
* * *
1207139 TTCGGATATGATTTTTAAGGCTTCCGGGCATAATTTTGATTTGTA-G
65 TTCGGACATGATTTTTAAGACCTCCGGGCATAATTTTGA-TTG-ACG
* ** * * *
1207185 TGTTGTCCTGATCGATTCTTTATTTTTCAACTTGTAGTGTTATTTCGATCCATTCTGTAAGACCT
1 TGTTGTCCCGATCGATTCTTTATTTTTTGACTTGCAGTGTTATCTCGATCGATTCTGTAAGACCT
* *
1207250 TC-GAGCATGATTTTTAAGACCTCCGAGCATAATTTCGATTGACG
66 TCGGA-CATGATTTTTAAGACCTCCGGGCATAATTTTGATTGACG
* * * * * * *
1207294 ATGTTGTCCCGATTGATTCTTTATTTTTTGACTCGCAATGTTGTCTCGGTCGATTCTATAAAACC
1 -TGTTGTCCCGATCGATTCTTTATTTTTTGACTTGCAGTGTTATCTCGATCGATTCTGTAAGACC
* * *
1207359 TTCGGTCATGATTTTTAA-AGCCTTCGGGCATAATTTTGATTCACTG
65 TTCGGACATGATTTTTAAGA-CCTCCGGGCATAATTTTGATTGAC-G
* * * *
1207405 TGTTGTCCCAATCGATTCTTTATTTTTTGACTTGCGGTATTATCTCAATCGATTCTGTAAGACCT
1 TGTTGTCCCGATCGATTCTTTATTTTTTGACTTGCAGTGTTATCTCGATCGATTCTGTAAGACCT
1207470 TCGG
66 TCGG
1207474 TGTAATTTTG
Statistics
Matches: 235, Mismatches: 46, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
108 1 0.00
109 32 0.14
110 199 0.85
111 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (109 bp):
TGTTGTCCCGATCGATTCTTTATTTTTTGACTTGCAGTGTTATCTCGATCGATTCTGTAAGACCT
TCGGACATGATTTTTAAGACCTCCGGGCATAATTTTGATTGACG
Found at i:1207382 original size:22 final size:22
Alignment explanation
Indices: 1207352--1207395 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1207342 GTCGATTCTA
* *
1207352 TAAAACCTTCGGTCATGATTTT
1 TAAAACCTTCGGGCATAATTTT
*
1207374 TAAAGCCTTCGGGCATAATTTT
1 TAAAACCTTCGGGCATAATTTT
1207396 GATTCACTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (22 bp):
TAAAACCTTCGGGCATAATTTT
Found at i:1207663 original size:37 final size:37
Alignment explanation
Indices: 1207609--1207708 Score: 128
Period size: 37 Copynumber: 2.7 Consensus size: 37
1207599 CGTAGTTTTT
*
1207609 TCGATCGATTCTTTATTTTTTGACTCACAGTGTTGTC
1 TCGATCGATTCTTTATTTTTTGACTCACAGTATTGTC
* * * * *
1207646 TCGATCAATTCTCTATTTCTTGACTTACGGTATTGTC
1 TCGATCGATTCTTTATTTTTTGACTCACAGTATTGTC
* *
1207683 CCGATCGATTCTTTATTTTTTAACTC
1 TCGATCGATTCTTTATTTTTTGACTC
1207709 GTAATGTCAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (37 bp):
TCGATCGATTCTTTATTTTTTGACTCACAGTATTGTC
Found at i:1207897 original size:3 final size:3
Alignment explanation
Indices: 1207889--1207925 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1207879 TTTATGTTAA
1207889 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1207926 TATTTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1207971 original size:10 final size:11
Alignment explanation
Indices: 1207948--1207982 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1207938 ATTAATTATT
1207948 AAGAAAAAAGA
1 AAGAAAAAAGA
1207959 AAGAAAAAA-A
1 AAGAAAAAAGA
*
1207969 AAGAAAACAGA
1 AAGAAAAAAGA
1207980 AAG
1 AAG
1207983 TAGACGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:1218992 original size:6 final size:6
Alignment explanation
Indices: 1218926--1218990 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
1218916 TGATATTTAT
* * *
1218926 TATTAT TATTAT TATTAT TATTAC TATTAC TATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
*
1218974 TATTAC TATTAT TATTA
1 TATTAC TATTAC TATTA
1218991 TTTATTTTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (6 bp):
TATTAC
Found at i:1219001 original size:10 final size:10
Alignment explanation
Indices: 1218919--1219001 Score: 57
Period size: 9 Copynumber: 8.3 Consensus size: 10
1218909 GGTCAATTGA
1218919 TATTTATTAT
1 TATTTATTAT
1218929 TA-TTATTAT
1 TATTTATTAT
1218938 TA-TTATTAT
1 TATTTATTAT
* *
1218947 TA-CTATTAC
1 TATTTATTAT
*
1218956 TA-TTACTAT
1 TATTTATTAT
*
1218965 TACTATTACTAT
1 TA-T-TTATTAT
1218977 TACTATTATTAT
1 TA-T-TTATTAT
*
1218989 TATTTATTTT
1 TATTTATTAT
1218999 TAT
1 TAT
1219002 CTTTTTCTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
9 31 0.49
10 11 0.17
11 1 0.02
12 20 0.32
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATTAT
Found at i:1219817 original size:7 final size:7
Alignment explanation
Indices: 1219800--1219855 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
1219790 GGTTTTCCTT
*
1219800 TTTTCTA
1 TTTTATA
*
1219807 TTTTATTT
1 TTTTA-TA
1219815 TTTTATCA
1 TTTTAT-A
1219823 TTTTATA
1 TTTTATA
1219830 TTTTA-A
1 TTTTATA
1219836 GTTTTATA
1 -TTTTATA
1219844 TTTTATA
1 TTTTATA
1219851 TTTTA
1 TTTTA
1219856 GTTTTAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 1 0.02
7 28 0.67
8 13 0.31
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:1219848 original size:21 final size:20
Alignment explanation
Indices: 1219815--1219875 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
1219805 TATTTTATTT
1219815 TTTTATCATTTTATATTTTAAG
1 TTTTAT-ATTTTATATTTT-AG
1219837 TTTTATATTTTATATTTTAG
1 TTTTATATTTTATATTTTAG
*
1219857 TTTTAGTTTTTTATTATTT
1 TTTTA-TATTTTA-TATTT
1219876 ATTTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 7 0.19
21 18 0.50
22 11 0.31
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATATTTTATATTTTAG
Found at i:1219891 original size:13 final size:12
Alignment explanation
Indices: 1219842--1219899 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
1219832 TTAAGTTTTA
1219842 TATTTTATATTT
1 TATTTTATATTT
*
1219854 TAGTTTTAGTTTTT
1 TA-TTTTA-TATTT
1219868 TATTATT-TATTT
1 TATT-TTATATTT
1219880 TATTTTACTATTT
1 TATTTTA-TATTT
1219893 T-TTTTAT
1 TATTTTAT
1219900 TGAGTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.08
12 15 0.38
13 13 0.33
14 8 0.21
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (12 bp):
TATTTTATATTT
Found at i:1219891 original size:17 final size:17
Alignment explanation
Indices: 1219865--1219900 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1219855 AGTTTTAGTT
*
1219865 TTTTATTATTTATTTTA
1 TTTTACTATTTATTTTA
*
1219882 TTTTACTATTTTTTTTA
1 TTTTACTATTTATTTTA
1219899 TT
1 TT
1219901 GAGTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTACTATTTATTTTA
Found at i:1219893 original size:26 final size:26
Alignment explanation
Indices: 1219849--1219900 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1219839 TTATATTTTA
*
1219849 TATTTTAGTTTTAGTTTTTTATTATT
1 TATTTTAGTTTTACTTTTTTATTATT
*
1219875 TATTTTA-TTTTACTATTTTTTTTATT
1 TATTTTAGTTTTACT-TTTTTATTATT
1219901 GAGTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (26 bp):
TATTTTAGTTTTACTTTTTTATTATT
Found at i:1220199 original size:13 final size:13
Alignment explanation
Indices: 1220181--1220208 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1220171 TTACCAAACT
1220181 ATTGGAAGATTTA
1 ATTGGAAGATTTA
1220194 ATTGGAAGATTTA
1 ATTGGAAGATTTA
1220207 AT
1 AT
1220209 GAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (13 bp):
ATTGGAAGATTTA
Found at i:1233572 original size:2 final size:2
Alignment explanation
Indices: 1233554--1233596 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1233544 GTGTGTGCGC
* *
1233554 AT AT TT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1233596 A
1 A
1233597 CAAACACACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1235599 original size:2 final size:2
Alignment explanation
Indices: 1235592--1235632 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1235582 TTGATGGAAA
* * *
1235592 AT AT AT AT AT GT GT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1235633 CCTACAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1239306 original size:2 final size:2
Alignment explanation
Indices: 1239299--1239324 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1239289 AATTTGTATC
1239299 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
1239325 TATGTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1245297 original size:21 final size:21
Alignment explanation
Indices: 1245273--1245314 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1245263 AGTTTATGAG
** *
1245273 TTTTAATTCATTTTTTGTTTA
1 TTTTAATAAATTTTTTATTTA
1245294 TTTTAATAAATTTTTTATTTA
1 TTTTAATAAATTTTTTATTTA
1245315 ATTATAGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTAATAAATTTTTTATTTA
Found at i:1246842 original size:30 final size:29
Alignment explanation
Indices: 1246808--1246888 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 29
1246798 GTTATTAAAC
1246808 TTAATTAATTAAAACAAACA-TTTTGTTTAA
1 TTAATTAATTAAAACAAA-AGTTTTGTTT-A
*
1246838 TTAATGAATGT-AAACAAAAGTTTTGTTTA
1 TTAATTAAT-TAAAACAAAAGTTTTGTTTA
1246867 TTGAATGTAATTAAAACAAAAG
1 TT-AAT-TAATTAAAACAAAAG
1246889 GGGTTTTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.09
30 27 0.61
31 13 0.30
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (29 bp):
TTAATTAATTAAAACAAAAGTTTTGTTTA
Found at i:1248164 original size:20 final size:20
Alignment explanation
Indices: 1248139--1248177 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1248129 AAAAAATTAC
1248139 AATAAATAAAAAAC-AATACA
1 AATAAA-AAAAAACTAATACA
*
1248159 AATAAAAAAGAACTAATAC
1 AATAAAAAAAAACTAATAC
1248178 CCAGTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (20 bp):
AATAAAAAAAAACTAATACA
Found at i:1253347 original size:54 final size:54
Alignment explanation
Indices: 1253260--1253365 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
1253250 TTGTTTGTGC
* * * *
1253260 TTGTCTTTGTAGCATCGATCTGCCTGCAATAACCTTAAAAATTTCCAAATCCTG
1 TTGTCTCTGCAGCATCAATCTGCCTGCAATAACCTCAAAAATTTCCAAATCCTG
* **
1253314 TTGTCTCTGCAGCATCAATCTGCCTGCACTAACCTCAGCAATTTCCAAATCC
1 TTGTCTCTGCAGCATCAATCTGCCTGCAATAACCTCAAAAATTTCCAAATCC
1253366 CGTAGCCGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (54 bp):
TTGTCTCTGCAGCATCAATCTGCCTGCAATAACCTCAAAAATTTCCAAATCCTG
Found at i:1257016 original size:68 final size:69
Alignment explanation
Indices: 1256898--1257037 Score: 192
Period size: 68 Copynumber: 2.0 Consensus size: 69
1256888 ATGCCAAAAT
* * *
1256898 ATCAAGCAACAAGTCATAATAAGTAAAACATGGGTGTTGTTGGATCCAAAAGGAAAACATAACGA
1 ATCAAGCAACAAGTC--AATAAGTAAAACACGGGTGTTGTTGGATCCAAAAAGAAAACATAACAA
1256963 TAGAAA
64 TAGAAA
* * * *
1256969 ATCAAGCAACAAGTC-ATAAGTACAATACGGGTGTTGTTGGATGCAAAAAGAAAACATAATAATA
1 ATCAAGCAACAAGTCAATAAGTAAAACACGGGTGTTGTTGGATCCAAAAAGAAAACATAACAATA
1257033 GAAA
66 GAAA
1257037 A
1 A
1257038 GGTTACCATT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
68 47 0.76
71 15 0.24
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (69 bp):
ATCAAGCAACAAGTCAATAAGTAAAACACGGGTGTTGTTGGATCCAAAAAGAAAACATAACAATA
GAAA
Found at i:1259331 original size:2 final size:2
Alignment explanation
Indices: 1259324--1259374 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
1259314 AAAGTATAAG
* * *
1259324 AT AT AT AT -T AT GT AT AT AT AT AT AT AT AT AT CT -T AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1259364 -T AT AT AT AT AT
1 AT AT AT AT AT AT
1259375 GAGGTGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1264977 original size:31 final size:31
Alignment explanation
Indices: 1264942--1265036 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 31
1264932 TATATAAATG
* * *
1264942 ATCCATGTACTCATACAAAATTTAAAATTTA
1 ATCCATATACTAACACAAAATTTAAAATTTA
1264973 ATCCATATACTAACACAAAATTTAAAATTTA
1 ATCCATATACTAACACAAAATTTAAAATTTA
* *** ** *
1265004 GTTTTTATACTCGCACGAAATTTAAAATTTA
1 ATCCATATACTAACACAAAATTTAAAATTTA
1265035 AT
1 AT
1265037 TCCTCTAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (31 bp):
ATCCATATACTAACACAAAATTTAAAATTTA
Found at i:1265187 original size:14 final size:14
Alignment explanation
Indices: 1265170--1265261 Score: 50
Period size: 14 Copynumber: 6.6 Consensus size: 14
1265160 TTTATTATAT
1265170 ATAAT-TAATTATTA
1 ATAATATAA-TATTA
*
1265184 ATAATATCATATTA
1 ATAATATAATATTA
* *
1265198 ATAACATTATTATT-
1 ATAATA-TAATATTA
* *
1265212 ATCAT-TTATATTA
1 ATAATATAATATTA
1265225 ATCAATTATAATATTA
1 AT-AA-TATAATATTA
* *
1265241 ATATTTTAA-ATTA
1 ATAATATAATATTA
1265254 AT-ATATAA
1 ATAATATAA
1265262 AAATTAAATT
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
12 9 0.16
13 8 0.14
14 23 0.40
15 9 0.16
16 9 0.16
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAATATAATATTA
Found at i:1265209 original size:43 final size:43
Alignment explanation
Indices: 1265161--1265243 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
1265151 ATATTAGTTT
*
1265161 TTATTATATATAATTAATTATTAAT-AA-TATCATATTAATAACA
1 TTATTAT-TATAATTAA-TATTAATCAATTATAATATTAATAACA
* *
1265204 TTATTATTATCATTTATATTAATCAATTATAATATTAATA
1 TTATTATTATAATTAATATTAATCAATTATAATATTAATA
1265244 TTTTAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 7 0.20
42 9 0.26
43 19 0.54
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (43 bp):
TTATTATTATAATTAATATTAATCAATTATAATATTAATAACA
Found at i:1266171 original size:20 final size:19
Alignment explanation
Indices: 1266131--1266178 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1266121 TTTAAATTTT
1266131 AATATTTTTAAAAAACTAG
1 AATATTTTTAAAAAACTAG
*
1266150 AA-ATTTTCTAAAAAATTCAG
1 AATATTTT-TAAAAAACT-AG
1266170 AATATTTTT
1 AATATTTTT
1266179 TATATTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 5 0.20
21 5 0.20
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (19 bp):
AATATTTTTAAAAAACTAG
Found at i:1267413 original size:2 final size:2
Alignment explanation
Indices: 1267406--1267431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1267396 AGAACCATCT
1267406 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1267432 GACACATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1269449 original size:36 final size:35
Alignment explanation
Indices: 1269403--1269493 Score: 130
Period size: 34 Copynumber: 2.6 Consensus size: 35
1269393 CACAAGTTAG
* * *
1269403 TATATAATAAATCTTTGGTTTTTTTTTTTTAACACA
1 TATATAATAAATATTTGGTTTTTTTTTCTCAA-ACA
1269439 TATATAATAAATATTTGG-TTTTTTTTCTCAAACA
1 TATATAATAAATATTTGGTTTTTTTTTCTCAAACA
*
1269473 TATATAATAAATTTTTGGTTT
1 TATATAATAAATATTTGGTTT
1269494 AGCATATACT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 20 0.40
35 13 0.26
36 17 0.34
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (35 bp):
TATATAATAAATATTTGGTTTTTTTTTCTCAAACA
Found at i:1272151 original size:56 final size:56
Alignment explanation
Indices: 1272065--1272176 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
1272055 GAGACTGGTA
** * * * *
1272065 TTATGAGCAGCGTCCTGTTCAAAAGATAGACTTCCCTTCCCCTTGCAACCCCACTT
1 TTATGAGCAAAGTCCCGTTCAAAAGATAGACTGCCCTTACCCTTGCAAACCCACTT
*
1272121 TTATGAGCAAAGTCCCGTTCAAAAGATAGACTGCCCTTACCGTTGCAAACCCACTT
1 TTATGAGCAAAGTCCCGTTCAAAAGATAGACTGCCCTTACCCTTGCAAACCCACTT
1272177 ACCAAAACAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (56 bp):
TTATGAGCAAAGTCCCGTTCAAAAGATAGACTGCCCTTACCCTTGCAAACCCACTT
Found at i:1273452 original size:23 final size:21
Alignment explanation
Indices: 1273422--1273474 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
1273412 TTTGAAATTA
1273422 ATAAAATATTATTTTTTTAAAAT
1 ATAAAATATTA--TTTTTAAAAT
1273445 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
1273466 AT-AAATATT
1 ATAAAATATT
1273475 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
23 11 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:1273480 original size:8 final size:8
Alignment explanation
Indices: 1273460--1273500 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1273450 ATATTATTTT
1273460 TAAA-ATA
1 TAAATATA
*
1273467 TAAATATT
1 TAAATATA
1273475 TAAATATA
1 TAAATATA
*
1273483 TAATTATA
1 TAAATATA
1273491 TAAATATA
1 TAAATATA
1273499 TA
1 TA
1273501 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:1278384 original size:3 final size:3
Alignment explanation
Indices: 1278376--1278401 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1278366 ATGTGCGGGA
1278376 GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GT
1278402 TGGAAAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GTG
Found at i:1287887 original size:17 final size:16
Alignment explanation
Indices: 1287860--1287892 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1287850 ATAGTTGTGA
1287860 TTATTTAAATAATTAT
1 TTATTTAAATAATTAT
1287876 TTATTATAAATAATTAT
1 TTATT-TAAATAATTAT
1287893 GATATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTAAATAATTAT
Found at i:1290633 original size:31 final size:31
Alignment explanation
Indices: 1290598--1290674 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
1290588 TGAATCCCTT
1290598 TCTATTCTCTTCTTAGTCTCTTCAATTCTTC
1 TCTATTCTCTTCTTAGTCTCTTCAATTCTTC
* * *
1290629 TCTATTCTCTACTTAGTCTTTTCAATTCTTT
1 TCTATTCTCTTCTTAGTCTCTTCAATTCTTC
*
1290660 TATATTCTCTTCTTA
1 TCTATTCTCTTCTTA
1290675 ATCCTAAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.57
Consensus pattern (31 bp):
TCTATTCTCTTCTTAGTCTCTTCAATTCTTC
Found at i:1302137 original size:17 final size:17
Alignment explanation
Indices: 1302115--1302150 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1302105 ATAATATAAA
*
1302115 ATATATAAGCTAAGAAC
1 ATATATAAGCTAAAAAC
1302132 ATATATAAGCTAAAAAC
1 ATATATAAGCTAAAAAC
1302149 AT
1 AT
1302151 CCCTCCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (17 bp):
ATATATAAGCTAAAAAC
Found at i:1305474 original size:2 final size:2
Alignment explanation
Indices: 1305467--1305491 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1305457 GCACTAGCAT
1305467 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
1305492 GTAAGATACC
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:1310205 original size:6 final size:6
Alignment explanation
Indices: 1310194--1310230 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1310184 AGTGTTTGGG
1310194 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC A
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC A
1310231 AGAGTTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:1315415 original size:42 final size:42
Alignment explanation
Indices: 1315368--1315450 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
1315358 GTCTTGACCT
*
1315368 GTGACAAGTGGTATCAGAGCCA-ACCTTAAACCGTTCGATCCC
1 GTGACAAGTGGTATCAGAGCCAGACC-AAAACCGTTCGATCCC
*
1315410 GTGACAAGTGGTATCAGAGCCAGTCCAAAACCGTTCGATCC
1 GTGACAAGTGGTATCAGAGCCAGACCAAAACCGTTCGATCC
1315451 ACGTCAAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (42 bp):
GTGACAAGTGGTATCAGAGCCAGACCAAAACCGTTCGATCCC
Found at i:1319241 original size:131 final size:129
Alignment explanation
Indices: 1318923--1319255 Score: 348
Period size: 131 Copynumber: 2.5 Consensus size: 129
1318913 ATTAATATCA
* * *
1318923 TTGTTTAATATTTTATACAATAACAAAAAAAAATTATTACAAAAAAATTGATCATATTCGTAACC
1 TTGTTTAATATTTTATACAATAAC--AAAAAAATTAATAC-AAAAAATTTATCATATTCGTAACA
* * * *
1318988 AAATAAAAAATTATTGTGTAAACTTATTTTATTTGCAATGATTTTTTGAAGTCATTACTTAAAAT
63 AAAGAAAAAATTATTGTGAAAACTTATTTTATTTGCAATGATTTTTTCAAATCATTACTTAAAAT
1319053 AT
128 AT
** * *
1319055 TT-TTTAATATTTTATACAATAACAAATAAAATTGCTACAAAAAAGTGTATAATATTCGTAACAA
1 TTGTTTAATATTTTATACAATAACAAA-AAAATTAATACAAAAAA-TTTATCATATTCGTAACAA
* * * * * * * * * *
1319119 CAAGATAAAATTGTTTTGAAAATTTATTTTATTTGTAATTA-TTTTTCAATATCGTTGCTTCAAT
64 -AAGAAAAAATTATTGTGAAAACTTATTTTATTTGCAATGATTTTTTCAA-ATCATTACTTAAAA
1319183 TAT
127 TAT
** **
1319186 TTGTTTAATATTTTATACAATAACAAAAAAATTAATATGAAAAATTTAATCATATTTATAACAAA
1 TTGTTTAATATTTTATACAATAACAAAAAAATTAATACAAAAAATTT-ATCATATTCGTAACAAA
1319251 A-AAAA
65 AGAAAA
1319256 TTGTTGATAT
Statistics
Matches: 166, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
129 12 0.07
130 35 0.21
131 93 0.56
132 26 0.16
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (129 bp):
TTGTTTAATATTTTATACAATAACAAAAAAATTAATACAAAAAATTTATCATATTCGTAACAAAA
GAAAAAATTATTGTGAAAACTTATTTTATTTGCAATGATTTTTTCAAATCATTACTTAAAATAT
Found at i:1319637 original size:2 final size:2
Alignment explanation
Indices: 1319624--1319654 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1319614 TGAATTGTTG
*
1319624 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1319655 GGACTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1325342 original size:43 final size:42
Alignment explanation
Indices: 1325260--1325350 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 42
1325250 TCTCCTTTTC
* *
1325260 ATAA-TTTTATTTATTATTTTTTTAAATTAACTTTTGTAATTA
1 ATAATTTTTATTTAATATTTTTTTAAATTAACTTTAGTAA-TA
*
1325302 ATTAATTTTTATTTAATATTTTTTT-GATTAA-TTGTAGTAATA
1 A-TAATTTTTATTTAATATTTTTTTAAATTAACTT-TAGTAATA
1325344 ATAATTT
1 ATAATTT
1325351 GATTAATTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 6 0.14
42 6 0.14
43 13 0.30
44 18 0.42
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (42 bp):
ATAATTTTTATTTAATATTTTTTTAAATTAACTTTAGTAATA
Found at i:1326429 original size:196 final size:197
Alignment explanation
Indices: 1326094--1326490 Score: 760
Period size: 196 Copynumber: 2.0 Consensus size: 197
1326084 ACAGTAAGTA
1326094 CTAATTGTTGGTTCTGTCAATGAACGTGAATGTGATGGACAAGTAATATGATCAGCAGATATGCT
1 CTAATTGTTGGTTCTGTCAATGAACGTGAATGTGATGGACAAGTAATATGATCAGCAGATATGCT
* *
1326159 TTTCTATTTGGCAAAAACCATGATCATGTTCCATTCTTTATATAGTCAAATTAGCTAAAAAACAA
66 TTTCTAATTGGCAAAAACCATGATCATGTTCCATTCTTCATATAGTCAAATTAGCTAAAAAACAA
1326224 AACAATTTCAGCATTGCGATCTCATCAGCGGCTGACTCATCACTCACCGTCTGATTGGTTCAAAA
131 AACAATTTCAGCATTGCGATCTCATCAGCGGCTGACTCATCACTCACCGTCTGATTGGTTCAAAA
1326289 TC
196 TC
*
1326291 CTAATTGTTGGTTCTGTCAATGAACGTGAATGTGATGGACAAGTAATCTGATCAGCAGATATGC-
1 CTAATTGTTGGTTCTGTCAATGAACGTGAATGTGATGGACAAGTAATATGATCAGCAGATATGCT
1326355 TTTCTAATTGGCAAAAACCATGATCATGTTCCATTCTTCATATAGTCAAATTAGCTAAAAAACAA
66 TTTCTAATTGGCAAAAACCATGATCATGTTCCATTCTTCATATAGTCAAATTAGCTAAAAAACAA
1326420 AACAATTTCAGCATTGCGATCTCATCAGCGGCTGACTCATCACTCACCGTCTGATTGGTTCAAAA
131 AACAATTTCAGCATTGCGATCTCATCAGCGGCTGACTCATCACTCACCGTCTGATTGGTTCAAAA
1326485 TC
196 TC
1326487 CTAA
1 CTAA
1326491 AGTGTTTTTC
Statistics
Matches: 197, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
196 134 0.68
197 63 0.32
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (197 bp):
CTAATTGTTGGTTCTGTCAATGAACGTGAATGTGATGGACAAGTAATATGATCAGCAGATATGCT
TTTCTAATTGGCAAAAACCATGATCATGTTCCATTCTTCATATAGTCAAATTAGCTAAAAAACAA
AACAATTTCAGCATTGCGATCTCATCAGCGGCTGACTCATCACTCACCGTCTGATTGGTTCAAAA
TC
Found at i:1326888 original size:2 final size:2
Alignment explanation
Indices: 1326883--1326908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1326873 ACACGCGTAC
1326883 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
1326909 TTGTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1327040 original size:2 final size:2
Alignment explanation
Indices: 1327033--1327060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1327023 AACCAATGTA
1327033 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1327061 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1327065 original size:2 final size:2
Alignment explanation
Indices: 1327060--1327088 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1327050 TCTCTCTCTC
1327060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1327089 GAATATGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1327921 original size:23 final size:26
Alignment explanation
Indices: 1327895--1327943 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 26
1327885 TGTTACGAAG
*
1327895 TAATAATC-ACAA-CAAT-ATAAAAA
1 TAATAAACAACAATCAATAATAAAAA
1327918 TAATAAACAACAATCAATAATAAAAA
1 TAATAAACAACAATCAATAATAAAAA
1327944 ATATAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 4 0.18
26 7 0.32
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.20
Consensus pattern (26 bp):
TAATAAACAACAATCAATAATAAAAA
Found at i:1331487 original size:256 final size:256
Alignment explanation
Indices: 1331032--1331545 Score: 974
Period size: 256 Copynumber: 2.0 Consensus size: 256
1331022 ATCATCAATA
1331032 AAAGTAACAAAATATCTGCTATCACCTAATGACTCAACCTCAATGGGACCACATACGTCAGAATA
1 AAAGTAACAAAATATCTGCTATCACCTAATGACTCAACCTCAATGGGACCACATACGTCAGAATA
*
1331097 AATTAATTCTAATATATTTTCTTTTCTCTGAGAACTTTTACGAAAAGGAACTCTATGATGCTTAC
66 AATTAATTCTAATATATTTTCTTTTCTCTGAGAACTTTTACGAAAAGAAACTCTATGATGCTTAC
1331162 CAAACAAACAATAATCACATGAATCGAGAGACATACCTTTGGTCAAGGGAATAAGAGACTATCTT
131 CAAACAAACAATAATCACATGAATCGAGAGACATACCTTTGGTCAAGGGAATAAGAGACTATCTT
1331227 GCCAAAACCTGTAACCTCTTTTCACTCATGTGTGCCAACCTCTTGTGCCACAAGTTTGCTG
196 GCCAAAACCTGTAACCTCTTTTCACTCATGTGTGCCAACCTCTTGTGCCACAAGTTTGCTG
* *
1331288 AAAGTAACAAAATATCTGCTATCACCTAATGACTCAACCTTAATTGGACCACATACGTCAGAATA
1 AAAGTAACAAAATATCTGCTATCACCTAATGACTCAACCTCAATGGGACCACATACGTCAGAATA
*
1331353 AATTAATTCTAATCTATTTTCTTTTCTCTGAGAACTTTTACGAAAAGAAACTCTATGATGCTTAC
66 AATTAATTCTAATATATTTTCTTTTCTCTGAGAACTTTTACGAAAAGAAACTCTATGATGCTTAC
*
1331418 CAAACAAATAATAATCACATGAATCGAGAGACATACCTTTGGTCAAGGGAATAAGAGACTATCTT
131 CAAACAAACAATAATCACATGAATCGAGAGACATACCTTTGGTCAAGGGAATAAGAGACTATCTT
*
1331483 GCCAAAACCTGTAACCTCTTTTCACTCATGTGTGCCAACCTCTTGTGTCACAAGTTTGCTG
196 GCCAAAACCTGTAACCTCTTTTCACTCATGTGTGCCAACCTCTTGTGCCACAAGTTTGCTG
1331544 AA
1 AA
1331546 GCATCATTTT
Statistics
Matches: 252, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
256 252 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (256 bp):
AAAGTAACAAAATATCTGCTATCACCTAATGACTCAACCTCAATGGGACCACATACGTCAGAATA
AATTAATTCTAATATATTTTCTTTTCTCTGAGAACTTTTACGAAAAGAAACTCTATGATGCTTAC
CAAACAAACAATAATCACATGAATCGAGAGACATACCTTTGGTCAAGGGAATAAGAGACTATCTT
GCCAAAACCTGTAACCTCTTTTCACTCATGTGTGCCAACCTCTTGTGCCACAAGTTTGCTG
Found at i:1333281 original size:18 final size:17
Alignment explanation
Indices: 1333260--1333293 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1333250 TTTCAACTAA
1333260 CTCTCTCTTTTCTTTTTT
1 CTCTCTCTTTT-TTTTTT
1333278 CTCTCTCTTTTTTTTT
1 CTCTCTCTTTTTTTTT
1333294 AGTTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (17 bp):
CTCTCTCTTTTTTTTTT
Found at i:1333765 original size:1 final size:1
Alignment explanation
Indices: 1333759--1333784 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1333749 TATATACCCT
1333759 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
1333785 GCGGTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1334122 original size:2 final size:2
Alignment explanation
Indices: 1334115--1334152 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1334105 AGCTAGGTTA
1334115 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
1334153 TCTAGTTGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335262 original size:31 final size:30
Alignment explanation
Indices: 1335218--1335275 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
1335208 TCTAGTAAAA
*
1335218 TTAAAAAAATTATTATTATTATAATTATGG
1 TTAAAAAAATTATTATAATTATAATTATGG
*
1335248 TTAAAATAAATTATTATAATTGTAATTA
1 TTAAAA-AAATTATTATAATTATAATTA
1335276 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
TTAAAAAAATTATTATAATTATAATTATGG
Found at i:1335543 original size:14 final size:14
Alignment explanation
Indices: 1335477--1335544 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
1335467 ATATCATATT
*
1335477 TAATAATTTA-AAA
1 TAATTATTTATAAA
* *
1335490 TAAATAATTATAAA
1 TAATTATTTATAAA
*
1335504 TTATATATTTA-AAA
1 TAAT-TATTTATAAA
* *
1335518 T-ATTCTTAATAAA
1 TAATTATTTATAAA
1335531 TAATTATTTATAAA
1 TAATTATTTATAAA
1335545 ATTTTAATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
12 4 0.10
13 13 0.32
14 19 0.46
15 5 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATTATTTATAAA
Found at i:1336960 original size:2 final size:2
Alignment explanation
Indices: 1336953--1336990 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1336943 CGTTGATGCC
*
1336953 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1336991 GATAGATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1337576 original size:2 final size:2
Alignment explanation
Indices: 1337569--1337601 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1337559 TAAAGACTTA
*
1337569 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1337602 ATGAGAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1339680 original size:3 final size:3
Alignment explanation
Indices: 1339672--1339696 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1339662 GTTGTATCAC
1339672 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1339697 TAAAACCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1342709 original size:13 final size:13
Alignment explanation
Indices: 1342682--1342719 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1342672 TCTATGCAGC
*
1342682 AACAAAAAAAGAAA
1 AACAAAAACA-AAA
1342696 AACAAAAACAAAA
1 AACAAAAACAAAA
1342709 AACAAAAACAA
1 AACAAAAACAA
1342720 TAGCACGCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (13 bp):
AACAAAAACAAAA
Found at i:1349035 original size:27 final size:28
Alignment explanation
Indices: 1348989--1349041 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1348979 TTGTATATTT
*
1348989 TTAATAAAATAAAATAATTAATTTTTTA
1 TTAATAAAATAAAATAATTAACTTTTTA
* *
1349017 TTAAT-AAATTAAATTATTAACTTTT
1 TTAATAAAATAAAATAATTAACTTTT
1349042 AGGTGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAATAAAATAAAATAATTAACTTTTTA
Found at i:1351540 original size:63 final size:63
Alignment explanation
Indices: 1351437--1351620 Score: 239
Period size: 63 Copynumber: 2.9 Consensus size: 63
1351427 TGTTTTTACT
* * * **
1351437 TTTACCAACAGTTGACTATTGGTGGCGTCAATATAGCCTAAAATATTCCAACAGAAAA-AGGGC
1 TTTACCAACAGTTGACTATTGGTGGCATCAGTATAACCTAAAATATTCCAACAGAAAATA-AAC
* *
1351500 TTTACCAACAGTTGACTATTGGTGGCATCAGTATAACCTAAAATATTCTAA-TGAAAATAAAC
1 TTTACCAACAGTTGACTATTGGTGGCATCAGTATAACCTAAAATATTCCAACAGAAAATAAAC
* **
1351562 TTTACCAACGGTTGA-TAATTGGTGGCATCAGTATAATATAAAATATTCCAACAGAAAAT
1 TTTACCAACAGTTGACT-ATTGGTGGCATCAGTATAACCTAAAATATTCCAACAGAAAAT
1351621 GGTGTTAGTA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
61 1 0.01
62 51 0.48
63 54 0.51
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (63 bp):
TTTACCAACAGTTGACTATTGGTGGCATCAGTATAACCTAAAATATTCCAACAGAAAATAAAC
Found at i:1352096 original size:13 final size:13
Alignment explanation
Indices: 1352078--1352102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1352068 TGGTTTCTAT
1352078 CAATATTGTTTCG
1 CAATATTGTTTCG
1352091 CAATATTGTTTC
1 CAATATTGTTTC
1352103 ATTAATAGAT
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CAATATTGTTTCG
Found at i:1357052 original size:15 final size:14
Alignment explanation
Indices: 1357026--1357116 Score: 89
Period size: 14 Copynumber: 6.4 Consensus size: 14
1357016 CATCAAAAGT
1357026 CTAAAATCAAAGCC
1 CTAAAATCAAAGCC
*
1357040 CTAAATTTCAAAGCC
1 CTAAA-ATCAAAGCC
*
1357055 CTAAAATCAAAGTC
1 CTAAAATCAAAGCC
1357069 CTAAAATCTAAA-CC
1 CTAAAATC-AAAGCC
1357083 CTAAACATCTAAA-CTC
1 CTAAA-ATC-AAAGC-C
*
1357099 C-AAAATCAAAACC
1 CTAAAATCAAAGCC
1357112 CTAAA
1 CTAAA
1357117 TAGTAAACAC
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
13 5 0.07
14 33 0.49
15 27 0.40
16 2 0.03
ACGTcount: A:0.49, C:0.27, G:0.03, T:0.20
Consensus pattern (14 bp):
CTAAAATCAAAGCC
Found at i:1357110 original size:29 final size:28
Alignment explanation
Indices: 1357017--1357116 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
1357007 TTTTTGAGGC
**
1357017 ATCAAAAGTCTAAAATCAAAGC-CCTAAA
1 ATCAAAACCCTAAAATCAAA-CTCCTAAA
* * *
1357045 TTTCAAAGCCCTAAAATCAAAGTCCTAAA
1 -ATCAAAACCCTAAAATCAAACTCCTAAA
*
1357074 ATCTAAACCCTAAACATCTAAACTCC-AAA
1 ATCAAAACCCTAAA-ATC-AAACTCCTAAA
1357103 ATCAAAACCCTAAA
1 ATCAAAACCCTAAA
1357117 TAGTAAACAC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 11 0.19
29 41 0.71
30 6 0.10
ACGTcount: A:0.50, C:0.26, G:0.04, T:0.20
Consensus pattern (28 bp):
ATCAAAACCCTAAAATCAAACTCCTAAA
Found at i:1357219 original size:41 final size:41
Alignment explanation
Indices: 1357137--1357219 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
1357127 TTGAAACTCG
** *
1357137 AAACTTCTAAACTTTTAAAACCCTAAAATCCAAAACTCTAA
1 AAACTTCTAAACCCTTAAAACCCTAAAATCCAAAACCCTAA
* * **
1357178 AAACTTCTAAACCCTTAAAACTCTGAAATCTGAAACCCTAA
1 AAACTTCTAAACCCTTAAAACCCTAAAATCCAAAACCCTAA
1357219 A
1 A
1357220 TCCTTCAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.25
Consensus pattern (41 bp):
AAACTTCTAAACCCTTAAAACCCTAAAATCCAAAACCCTAA
Found at i:1357238 original size:31 final size:31
Alignment explanation
Indices: 1357184--1357250 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1357174 CTAAAAACTT
* *
1357184 CTAAACCCTTAAAACTCTGAAATC-TGAAACC
1 CTAAACCCTTAAAACACTAAAATCTTGAAA-C
* *
1357215 CTAAATCCTTCAAACACTAAAATCTTGAAAC
1 CTAAACCCTTAAAACACTAAAATCTTGAAAC
1357246 CTAAA
1 CTAAA
1357251 AAAAAACCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.45, C:0.27, G:0.04, T:0.24
Consensus pattern (31 bp):
CTAAACCCTTAAAACACTAAAATCTTGAAAC
Found at i:1363643 original size:18 final size:17
Alignment explanation
Indices: 1363620--1363653 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1363610 TGGTGAAAAA
1363620 AAAGGAAAAAATAAAAGG
1 AAAGG-AAAAATAAAAGG
*
1363638 AAAGGAAGAATAAAAG
1 AAAGGAAAAATAAAAG
1363654 AAGAAAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (17 bp):
AAAGGAAAAATAAAAGG
Found at i:1364551 original size:32 final size:32
Alignment explanation
Indices: 1364515--1364601 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
1364505 CTAAAATAAT
**
1364515 ATTTAAGCCCAAT-TTAACTAGCATTAATGAAG
1 ATTTAAGCCCAATATTAACTAGCACCAATG-AG
** *
1364547 ATTTAAG-CTTATATTATCTAGCACCAATGAG
1 ATTTAAGCCCAATATTAACTAGCACCAATGAG
*
1364578 ATTTAAGCCCAGTATT-ACTAGCAC
1 ATTTAAGCCCAATATTAACTAGCAC
1364602 GTAAACCCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
ATTTAAGCCCAATATTAACTAGCACCAATGAG
Found at i:1364699 original size:31 final size:31
Alignment explanation
Indices: 1364658--1364731 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
1364648 GCTGGCACGC
*
1364658 AAGCCCATATTATCTGGCACCAATGAGATTT
1 AAGCCCATATTATATGGCACCAATGAGATTT
* *
1364689 AAGCCTATATTATATGGCATCAATGAGATTT
1 AAGCCCATATTATATGGCACCAATGAGATTT
1364720 AAGCCCAATATT
1 AAGCCC-ATATT
1364732 GCTAGCGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (31 bp):
AAGCCCATATTATATGGCACCAATGAGATTT
Found at i:1364793 original size:138 final size:138
Alignment explanation
Indices: 1364540--1364831 Score: 404
Period size: 138 Copynumber: 2.1 Consensus size: 138
1364530 AACTAGCATT
* * * **
1364540 AATGAAGATTTAAGCTTATATTATCTAGCACCAATGAGATTTAAGCCCAGTATTACTAGCACGTA
1 AATG-AGATTTAAGCCTATATTATATAGCACCAATGAGATTTAAGCCCAATATTACTAGCACACA
* * *
1364605 AACCCAAATTATTTGGCATTAATAAAGTTTTAAGCTTACTTTAGCTGGCACGCAAGCCCATATTA
65 AACCCAAATTATCTGGCATTAATAAAGTTTTAAGCCTACTTTAGCTGGCACGCAAGCCCAGATTA
1364670 TCTGGCACC
130 TCTGGCACC
* * * *
1364679 AATGAGATTTAAGCCTATATTATATGGCATCAATGAGATTTAAGCCCAATATTGCTAGCGCACAA
1 AATGAGATTTAAGCCTATATTATATAGCACCAATGAGATTTAAGCCCAATATTACTAGCACACAA
* * * *
1364744 GCTCAAATTATCTGGCATTAATGAAGTTTTAAGCCTACTTTAGCTGGCACGCAAGCTCAGATTAT
66 ACCCAAATTATCTGGCATTAATAAAGTTTTAAGCCTACTTTAGCTGGCACGCAAGCCCAGATTAT
*
1364809 CTGGCATC
131 CTGGCACC
*
1364817 AATAGAGTTTTAAGC
1 AAT-GAGATTTAAGC
1364832 TCAGTTTAAT
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
138 120 0.90
139 14 0.10
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (138 bp):
AATGAGATTTAAGCCTATATTATATAGCACCAATGAGATTTAAGCCCAATATTACTAGCACACAA
ACCCAAATTATCTGGCATTAATAAAGTTTTAAGCCTACTTTAGCTGGCACGCAAGCCCAGATTAT
CTGGCACC
Found at i:1365271 original size:33 final size:32
Alignment explanation
Indices: 1365226--1365312 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
1365216 CTCTTAGTGA
*
1365226 AAATTTATGCCTAGTTTATCTAGCCCCCAAGG
1 AAATTTAAGCCTAGTTTATCTAGCCCCCAAGG
* * * * *
1365258 AAATCTTAAGCCTAGTTTATTTGGTCTCCAATG
1 AAAT-TTAAGCCTAGTTTATCTAGCCCCCAAGG
*
1365291 AAGTTTTAAGCCTAGTTTATCT
1 AA-ATTTAAGCCTAGTTTATCT
1365313 GACTTTCGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
32 4 0.09
33 40 0.89
34 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (32 bp):
AAATTTAAGCCTAGTTTATCTAGCCCCCAAGG
Found at i:1365452 original size:33 final size:34
Alignment explanation
Indices: 1365387--1365452 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
1365377 GGTCCCAAGG
*
1365387 AAATCTTAAACCTAGTTTATTTGACCCTAAAAAA
1 AAATCTTAAACCTAGTTTATTTGACCATAAAAAA
* *
1365421 AAAT-TTAAGCCTAGTTTATTTG-GCATAAAAAA
1 AAATCTTAAACCTAGTTTATTTGACCATAAAAAA
1365453 TTTTAAGCCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.28
33 17 0.59
34 4 0.14
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (34 bp):
AAATCTTAAACCTAGTTTATTTGACCATAAAAAA
Found at i:1365594 original size:33 final size:33
Alignment explanation
Indices: 1365540--1365687 Score: 163
Period size: 33 Copynumber: 4.5 Consensus size: 33
1365530 ATCTGACCTC
* * *
1365540 TAATGAAA-TTTAAGCCAAGTTTATCTAGCATT
1 TAATGAAATTTTAAGCCTAGTTTAGCTAGCACT
* * * *
1365572 TAATGAAATTTTAAACCTAGTTTAGCTGGCCCA
1 TAATGAAATTTTAAGCCTAGTTTAGCTAGCACT
* * * *
1365605 TAATAAAATTTTAAGCCCAGTTTATCTAGCATT
1 TAATGAAATTTTAAGCCTAGTTTAGCTAGCACT
* * *
1365638 TAATGAAATTTTAAGCCTAGTTTAGCTGGCCCC
1 TAATGAAATTTTAAGCCTAGTTTAGCTAGCACT
1365671 TAATGAAATTTTAAGCC
1 TAATGAAATTTTAAGCC
1365688 CAATTTATCT
Statistics
Matches: 93, Mismatches: 22, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
32 8 0.09
33 85 0.91
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (33 bp):
TAATGAAATTTTAAGCCTAGTTTAGCTAGCACT
Found at i:1365630 original size:66 final size:66
Alignment explanation
Indices: 1365540--1365728 Score: 274
Period size: 66 Copynumber: 2.9 Consensus size: 66
1365530 ATCTGACCTC
* *
1365540 TAATGAAA-TTTAAGCCAAGTTTATCTAGCATTTAATGAAATTTTAAACCTAGTTTAGCTGGCCC
1 TAATGAAATTTTAAGCCCAGTTTATCTAGCATTTAATGAAATTTTAAGCCTAGTTTAGCTGGCCC
1365604 A
66 A
*
1365605 TAATAAAATTTTAAGCCCAGTTTATCTAGCATTTAATGAAATTTTAAGCCTAGTTTAGCTGGCCC
1 TAATGAAATTTTAAGCCCAGTTTATCTAGCATTTAATGAAATTTTAAGCCTAGTTTAGCTGGCCC
*
1365670 C
66 A
* * * **
1365671 TAATGAAATTTTAAGCCCAATTTATCTGGTATCAAAT-AAAGTTTTAAGCCTAGTTTAG
1 TAATGAAATTTTAAGCCCAGTTTATCTAGCATTTAATGAAA-TTTTAAGCCTAGTTTAG
1365729 TTTACATACA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
65 10 0.09
66 102 0.91
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (66 bp):
TAATGAAATTTTAAGCCCAGTTTATCTAGCATTTAATGAAATTTTAAGCCTAGTTTAGCTGGCCC
A
Found at i:1365709 original size:99 final size:98
Alignment explanation
Indices: 1365517--1365727 Score: 228
Period size: 99 Copynumber: 2.1 Consensus size: 98
1365507 GTATCTAATC
* * * **
1365517 TTAAGCTCAGTTTATCTGACCTCTAATGAAATTTAAGCCAAGTTTATCTAGCATTTAATGAAATT
1 TTAAGCCCAGTTTATCTGACATCTAATGAAATTTAAGCCAAGTTTAGCTAGCACCTAATGAAATT
* * *
1365582 TTAAACCTAGTTTAGCTGGCCCATAATAAAATT
66 TTAAACCCAATTTAGCTGGACCATAATAAAATT
* * * *
1365615 TTAAGCCCAGTTTATCT-AGCATTTAATGAAATTTTAAGCCTAGTTTAGCTGGCCCCTAATGAAA
1 TTAAGCCCAGTTTATCTGA-CATCTAATGAAA-TTTAAGCCAAGTTTAGCTAGCACCTAATGAAA
* * * *
1365679 TTTTAAGCCCAATTTATCTGGTATCA-AATAAAGTT
64 TTTTAAACCCAATTTAGCTGG-ACCATAATAAAATT
*
1365714 TTAAGCCTAGTTTA
1 TTAAGCCCAGTTTA
1365728 GTTTACATAC
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
97 1 0.01
98 26 0.28
99 64 0.69
100 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (98 bp):
TTAAGCCCAGTTTATCTGACATCTAATGAAATTTAAGCCAAGTTTAGCTAGCACCTAATGAAATT
TTAAACCCAATTTAGCTGGACCATAATAAAATT
Found at i:1366192 original size:36 final size:35
Alignment explanation
Indices: 1366144--1366230 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 35
1366134 CAATTGATTC
* *
1366144 TTTATTTCTTAACTTGCAGTATT-GTCCTAATCATTT
1 TTTATTTTTTAACTTACAGTATTAGTCCT-ATCA-TT
* * *
1366180 TTTATTTTTTAACTTACAGTGTTATTTCTATCATT
1 TTTATTTTTTAACTTACAGTATTAGTCCTATCATT
*
1366215 TTTATTTTTTGACTTA
1 TTTATTTTTTAACTTA
1366231 TGATGTCGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 17 0.39
36 24 0.55
37 3 0.07
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.59
Consensus pattern (35 bp):
TTTATTTTTTAACTTACAGTATTAGTCCTATCATT
Found at i:1366253 original size:36 final size:36
Alignment explanation
Indices: 1366172--1366255 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 36
1366162 GTATTGTCCT
* *
1366172 AATCATTTTTTATTTTTTAACTTACAGTGTTATTTC
1 AATCATTTTTTATTTTTTAACTTACAGTGTCATCTC
* * * *
1366208 TATCA-TTTTTATTTTTTGACTTA-TGATGTCGTCTC
1 AATCATTTTTTATTTTTTAACTTACAG-TGTCATCTC
1366243 AATCATTTTTTAT
1 AATCATTTTTTAT
1366256 CACTTGATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 1 0.03
35 27 0.69
36 11 0.28
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (36 bp):
AATCATTTTTTATTTTTTAACTTACAGTGTCATCTC
Found at i:1366298 original size:18 final size:18
Alignment explanation
Indices: 1366275--1366322 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
1366265 TGCGGTTCAG
1366275 TAAAAA-AAATAACAAAAA
1 TAAAAATAAA-AACAAAAA
1366293 TAAAAATAAAAACAAAAA
1 TAAAAATAAAAACAAAAA
*
1366311 CAAAACATAAAA
1 TAAAA-ATAAAA
1366323 CTTTTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.10
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:1366303 original size:12 final size:12
Alignment explanation
Indices: 1366276--1366322 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1366266 GCGGTTCAGT
1366276 AAAAA-AAATAAC
1 AAAAATAAA-AAC
*
1366288 AAAAATAAAAAT
1 AAAAATAAAAAC
*
1366300 AAAAACAAAAAC
1 AAAAATAAAAAC
1366312 AAAACATAAAA
1 AAAA-ATAAAA
1366323 CTTTTGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 21 0.72
13 8 0.28
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAATAAAAAC
Found at i:1368307 original size:14 final size:14
Alignment explanation
Indices: 1368265--1368386 Score: 50
Period size: 14 Copynumber: 8.3 Consensus size: 14
1368255 TCCAAACGCT
*
1368265 AAATTTCAAAACCTA
1 AAATTT-AAACCCTA
* **
1368280 AAATTGAAGTCCTA
1 AAATTTAAACCCTA
1368294 AAATTTAAACCCTA
1 AAATTTAAACCCTA
* *
1368308 AACATCTAAATTCC-A
1 AA-ATTTAAA-CCCTA
**
1368323 AAATGAAAACCCTA
1 AAATTTAAACCCTA
* *
1368337 AAA-TCAAAACCTCA
1 AAATTTAAACCCT-A
*
1368351 AACATTTGAAACCCCA
1 AA-ATTT-AAACCCTA
*
1368367 AACTTTCAAACCCTTA
1 AAATTT-AAACCC-TA
1368383 AAAT
1 AAAT
1368387 GAAATCCAAA
Statistics
Matches: 78, Mismatches: 21, Indels: 15
0.68 0.18 0.13
Matches are distributed among these distances:
13 8 0.10
14 31 0.40
15 24 0.31
16 10 0.13
17 5 0.06
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATTTAAACCCTA
Found at i:1370430 original size:12 final size:11
Alignment explanation
Indices: 1370419--1370449 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
1370409 AAATAAAAAT
1370419 TTAAAATTAAA
1 TTAAAATTAAA
1370430 TTAAAATATAAA
1 TTAAAAT-TAAA
1370442 TTAAAATT
1 TTAAAATT
1370450 TGGGTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:1370430 original size:18 final size:17
Alignment explanation
Indices: 1370407--1370446 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1370397 GTATTCTTTC
*
1370407 TTAAATAAAAATTTAAAA
1 TTAAATAAAAATAT-AAA
*
1370425 TTAAATTAAAATATAAA
1 TTAAATAAAAATATAAA
1370442 TTAAA
1 TTAAA
1370447 ATTTGGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAATAAAAATATAAA
Found at i:1375987 original size:3 final size:3
Alignment explanation
Indices: 1375975--1376057 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
1375965 TTTTTTAGTT
* ** * * * *
1375975 TAA TAT TAA TAA TAA TTT TGA TAA TAA TAT TAA TAA TAA CAT TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1376022 GTTAA AAA TAAA TAA TAA TAA TAC TAA TAA TAA TAA
1 --TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
1376058 AAAGAAAAAA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
2 2 0.03
3 52 0.88
4 3 0.05
5 2 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1375998 original size:12 final size:12
Alignment explanation
Indices: 1375975--1376056 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 12
1375965 TTTTTTAGTT
1375975 TAATATTAATAA
1 TAATATTAATAA
* *
1375987 TAATTTTGATAA
1 TAATATTAATAA
1375999 TAATATTAATAA
1 TAATATTAATAA
*
1376011 TAACATTAAAAGTTAA
1 TAATATT--AA--TAA
* *
1376027 AAATAAATAATAA
1 TAAT-ATTAATAA
*
1376040 TAATACTAATAA
1 TAATATTAATAA
1376052 TAATA
1 TAATA
1376057 AAAAGAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
12 38 0.69
13 6 0.11
14 2 0.04
15 2 0.04
16 5 0.09
17 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:1377075 original size:18 final size:17
Alignment explanation
Indices: 1377030--1377076 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1377020 TTCTTTTTAT
* *
1377030 TTTTTTATATATTATTA
1 TTTTTTATATTTTAGTA
1377047 TTTTTGT-TATTTTGAGTA
1 TTTTT-TATATTTT-AGTA
1377065 TTTTTTATATTT
1 TTTTTTATATTT
1377077 ATGCATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTTATATTTTAGTA
Found at i:1377499 original size:16 final size:16
Alignment explanation
Indices: 1377475--1377536 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
1377465 CTAGGATTCT
1377475 AAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
* *
1377491 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
1377507 -AAACCCCTTAAAATCC
1 AAAACCCC-TAAAATCC
* *
1377523 AAAATCCCTTAAAT
1 AAAACCCCTAAAAT
1377537 TCTAAACCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 6 0.16
16 26 0.68
17 6 0.16
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:1377503 original size:17 final size:17
Alignment explanation
Indices: 1377483--1377535 Score: 83
Period size: 16 Copynumber: 3.2 Consensus size: 17
1377473 CTAAAACCCC
1377483 TAAAATCCAAAATCCCT
1 TAAAATCCAAAATCCCT
*
1377500 T-AAATCC-AAACCCCT
1 TAAAATCCAAAATCCCT
1377515 TAAAATCCAAAATCCCT
1 TAAAATCCAAAATCCCT
1377532 TAAA
1 TAAA
1377536 TTCTAAACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.25
16 12 0.38
17 12 0.38
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAATCCAAAATCCCT
Found at i:1377519 original size:32 final size:31
Alignment explanation
Indices: 1377476--1377536 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 31
1377466 TAGGATTCTA
1377476 AAACCCCTAAAATCCAAAATCCCTTAAATCC
1 AAACCCCTAAAATCCAAAATCCCTTAAATCC
1377507 AAACCCCTTAAAATCCAAAATCCCTTAAAT
1 AAACCCC-TAAAATCCAAAATCCCTTAAAT
1377537 TCTAAACCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (31 bp):
AAACCCCTAAAATCCAAAATCCCTTAAATCC
Found at i:1377815 original size:14 final size:14
Alignment explanation
Indices: 1377798--1377824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1377788 TAATAACCAA
1377798 TTATTAATAAAATT
1 TTATTAATAAAATT
1377812 TTATTAATAAAAT
1 TTATTAATAAAAT
1377825 GGGATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATTAATAAAATT
Found at i:1378893 original size:7 final size:7
Alignment explanation
Indices: 1378881--1378914 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1378871 TATTTTATTC
1378881 TTATTTT
1 TTATTTT
1378888 TTA-TTT
1 TTATTTT
1378894 TTATTTT
1 TTATTTT
*
1378901 TTATTAT
1 TTATTTT
1378908 TTATTTT
1 TTATTTT
1378915 ATTTTAGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:1378914 original size:13 final size:13
Alignment explanation
Indices: 1378873--1378914 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1378863 GTGTTTGTTA
*
1378873 TTTTATTCTTATT
1 TTTTATTTTTATT
1378886 TTTTATTTTTATT
1 TTTTATTTTTATT
1378899 TTTTATTATTTATT
1 TTTTATT-TTTATT
1378913 TT
1 TT
1378915 ATTTTAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 19 0.70
14 8 0.30
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:1378915 original size:19 final size:19
Alignment explanation
Indices: 1378870--1378919 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1378860 TAGGTGTTTG
* *
1378870 TTATTTTA-TTCTTATTTT
1 TTATTTTATTTTTTATTAT
1378888 TTATTTTTATTTTTTATTAT
1 TTA-TTTTATTTTTTATTAT
1378908 TTATTTTATTTT
1 TTATTTTATTTT
1378920 AGGATATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 14 0.50
20 11 0.39
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TTATTTTATTTTTTATTAT
Found at i:1381033 original size:28 final size:28
Alignment explanation
Indices: 1380993--1381050 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1380983 GGACGATGAT
1380993 GTAAGGAATAATTTAGAAACCTTTAGTG
1 GTAAGGAATAATTTAGAAACCTTTAGTG
*
1381021 GTAAGGAATAATTTAGAAATCTTTAGTG
1 GTAAGGAATAATTTAGAAACCTTTAGTG
1381049 GT
1 GT
1381051 CAAAATCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (28 bp):
GTAAGGAATAATTTAGAAACCTTTAGTG
Found at i:1383684 original size:16 final size:16
Alignment explanation
Indices: 1383654--1383683 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1383644 CTCAAAGAGA
1383654 GAAAGAAAAGAAAAAT
1 GAAAGAAAAGAAAAAT
1383670 GAAAG-AAAGAAAAA
1 GAAAGAAAAGAAAAA
1383684 AAATGCCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (16 bp):
GAAAGAAAAGAAAAAT
Found at i:1384047 original size:10 final size:10
Alignment explanation
Indices: 1384032--1384112 Score: 59
Period size: 9 Copynumber: 8.8 Consensus size: 10
1384022 ATCAACAATG
1384032 GATGAAAAAA
1 GATGAAAAAA
1384042 GATG-AAAAA
1 GATGAAAAAA
*
1384051 GA-G-AAAGA
1 GATGAAAAAA
*
1384059 GA-AAAAAAA
1 GATGAAAAAA
* *
1384068 G-GGAAAACA
1 GATGAAAAAA
1384077 GATGAAAAAA
1 GATGAAAAAA
*
1384087 -AAGAAAAAA
1 GATGAAAAAA
1384096 -ATGAAAAAA
1 GATGAAAAAA
*
1384105 AATGAAAA
1 GATGAAAA
1384113 TGAAAAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
8 7 0.12
9 34 0.59
10 17 0.29
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (10 bp):
GATGAAAAAA
Found at i:1384067 original size:18 final size:18
Alignment explanation
Indices: 1384046--1384126 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 18
1384036 AAAAAAGATG
1384046 AAAAAGAGAAAGAG-AAA
1 AAAAAGAGAAAGAGAAAA
* *
1384063 AAAAAGGGAAAACAGATGAAA
1 AAAAAGAG-AAAGAGA--AAA
* *
1384084 AAAAAGAAAAAAATGAAAA
1 AAAAAGAGAAAGA-GAAAA
*
1384103 AAAATGA-AAATGA-AAAA
1 AAAAAGAGAAA-GAGAAAA
1384120 AAAAAGA
1 AAAAAGA
1384127 TTAAAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
17 17 0.34
18 8 0.16
19 10 0.20
20 4 0.08
21 11 0.22
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAAGAGAAAGAGAAAA
Found at i:1384085 original size:21 final size:18
Alignment explanation
Indices: 1384046--1384112 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
1384036 AAAAAAGATG
* *
1384046 AAAAAGAGAAAGA-GAAA
1 AAAAAGAAAAAAATGAAA
*
1384063 AAAAAGGGAAAACAGATGAAA
1 AAAAA--GAAAA-AAATGAAA
1384084 AAAAAGAAAAAAATGAAA
1 AAAAAGAAAAAAATGAAA
1384102 AAAAATGAAAA
1 AAAAA-GAAAA
1384113 TGAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.12
18 12 0.28
19 14 0.33
20 3 0.07
21 9 0.21
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAAAGAAAAAAATGAAA
Found at i:1384104 original size:16 final size:15
Alignment explanation
Indices: 1384083--1384124 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1384073 AACAGATGAA
1384083 AAAAAAGAAAAAAATG
1 AAAAAA-AAAAAAATG
*
1384099 AAAAAAAATGAAAATG
1 AAAAAAAA-AAAAATG
1384115 AAAAAAAAAA
1 AAAAAAAAAA
1384125 GATTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAAAAATG
Found at i:1384122 original size:10 final size:10
Alignment explanation
Indices: 1384059--1384112 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
1384049 AAGAGAAAGA
*
1384059 GAAAAAAAAGG
1 GAAAAAAAA-T
* *
1384070 GAAAACAGAT
1 GAAAAAAAAT
1384080 GAAAAAAAA-
1 GAAAAAAAAT
1384089 G-AAAAAAAT
1 GAAAAAAAAT
1384098 GAAAAAAAAT
1 GAAAAAAAAT
1384108 GAAAA
1 GAAAA
1384113 TGAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.19
9 2 0.06
10 20 0.56
11 7 0.19
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06
Consensus pattern (10 bp):
GAAAAAAAAT
Found at i:1384718 original size:17 final size:18
Alignment explanation
Indices: 1384679--1384719 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 18
1384669 TGGATTGCTC
1384679 AATATGATCTAAAAAGATG
1 AATATGATC-AAAAAGATG
1384698 -ATATGATC-AAAAGATG
1 AATATGATCAAAAAGATG
1384714 AATATG
1 AATATG
1384720 GTGATAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
18 8 0.38
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (18 bp):
AATATGATCAAAAAGATG
Found at i:1385283 original size:46 final size:45
Alignment explanation
Indices: 1385230--1385351 Score: 129
Period size: 46 Copynumber: 2.6 Consensus size: 45
1385220 TCTTTTGATA
* * *
1385230 AGAATCTTGATTTTTTAAATGAAAATCTTTAAAAAAT-TTTCAAATG
1 AGAATCTTGA-GTCTTAAATGAAAATCTTTAAAAAATCCTT-AAATG
* *
1385276 AGAATCTTTGAGTCTTAAATGAGAATCTTTAAGAAATCCTTAAATG
1 AGAATC-TTGAGTCTTAAATGAAAATCTTTAAAAAATCCTTAAATG
* * *
1385322 AGAATCTTTGAGTGTCAAATGAGAATCTTT
1 AGAATC-TTGAGTCTTAAATGAAAATCTTT
1385352 GAGGTATGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 61 0.91
47 6 0.09
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (45 bp):
AGAATCTTGAGTCTTAAATGAAAATCTTTAAAAAATCCTTAAATG
Found at i:1385297 original size:21 final size:21
Alignment explanation
Indices: 1385271--1385563 Score: 135
Period size: 21 Copynumber: 13.8 Consensus size: 21
1385261 AAAAATTTTC
1385271 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
*
1385292 AAATGAGAATCTTTAAGAAATCCTT
1 AAATGAGAATCTTT--G-AGT-CTT
* *
1385317 AAATGAGAATCTTTGAGTGTC
1 AAATGAGAATCTTTGAGTCTT
* *
1385338 AAATGAGAATCTTTGAGGTATG
1 AAATGAGAATCTTTGA-GTCTT
* *
1385360 AAACTCA-AA-ATTT-A-TC--
1 AAA-TGAGAATCTTTGAGTCTT
* * * *
1385376 GAAT-ATGAATCTTCGAAT-TC
1 AAATGA-GAATCTTTGAGTCTT
* *
1385396 AAATGAGAATATTTAAAGAAT-TAT
1 AAATGAGAATCTTT---GAGTCT-T
* *
1385420 CAAATGAGAATCTTTGAGTGTC
1 -AAATGAGAATCTTTGAGTCTT
* *
1385442 AAAT-ATGAATCTTTGA-ACTC
1 AAATGA-GAATCTTTGAGTCTT
* * *
1385462 AAATGAGAATATTTGAATTCTC
1 AAATGAGAATCTTTG-AGTCTT
* *
1385484 AAATGAGAATCTGTGAGTGTT
1 AAATGAGAATCTTTGAGTCTT
*
1385505 AAATGAGAATCTTTGAAT-TT
1 AAATGAGAATCTTTGAGTCTT
*
1385525 CAAATGAGAATCTTTGAAT-TT
1 -AAATGAGAATCTTTGAGTCTT
1385546 AAAATGAGAATCTTTGAG
1 -AAATGAGAATCTTTGAG
1385564 GTGTGAAACT
Statistics
Matches: 215, Mismatches: 32, Indels: 50
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.00
15 1 0.00
16 4 0.02
17 2 0.01
18 2 0.01
19 1 0.00
20 27 0.13
21 106 0.49
22 29 0.13
23 10 0.05
24 2 0.01
25 30 0.14
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTT
Found at i:1385323 original size:25 final size:24
Alignment explanation
Indices: 1385244--1385330 Score: 99
Period size: 25 Copynumber: 3.7 Consensus size: 24
1385234 TCTTGATTTT
* * *
1385244 TTAAATGAAAATCTTTAAAAAATT
1 TTAAATGAGAATCTTTAAGAAATC
*
1385268 TTCAAATGAGAATCTTT--G-AGTC
1 TT-AAATGAGAATCTTTAAGAAATC
1385290 TTAAATGAGAATCTTTAAGAAATCC
1 TTAAATGAGAATCTTTAAGAAAT-C
1385315 TTAAATGAGAATCTTT
1 TTAAATGAGAATCTTT
1385331 GAGTGTCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
21 14 0.26
22 4 0.08
23 1 0.02
24 4 0.08
25 30 0.57
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (24 bp):
TTAAATGAGAATCTTTAAGAAATC
Found at i:1385515 original size:63 final size:62
Alignment explanation
Indices: 1385377--1385563 Score: 250
Period size: 63 Copynumber: 2.9 Consensus size: 62
1385367 AAATTTATCG
*
1385377 AATATGAATCTTCGAATTCAAATGAGAATATTTAAAGAATTATCAAATGAGAATCTTTGAGTGTC
1 AATATGAATCTTTGAATTCAAATGAGAATATTT---GAATT-TCAAATGAGAATCTTTGAGTGTC
1385442 A
62 A
* * *
1385443 AATATGAATCTTTGAACTCAAATGAGAATATTTGAATTCTCAAATGAGAATCTGTGAGTGTTA
1 AATATGAATCTTTGAATTCAAATGAGAATATTTGAATT-TCAAATGAGAATCTTTGAGTGTCA
* *
1385506 AATGA-GAATCTTTGAATTTCAAATGAGAATCTTTGAATTTAAAATGAGAATCTTTGAG
1 AAT-ATGAATCTTTGAA-TTCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAG
1385564 GTGTGAAACT
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
63 58 0.53
64 21 0.19
66 31 0.28
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (62 bp):
AATATGAATCTTTGAATTCAAATGAGAATATTTGAATTTCAAATGAGAATCTTTGAGTGTCA
Found at i:1385528 original size:42 final size:40
Alignment explanation
Indices: 1385421--1385718 Score: 161
Period size: 42 Copynumber: 7.3 Consensus size: 40
1385411 AAGAATTATC
* * * *
1385421 AAATGAGAATCTTTGAGTGTCAAAT-ATGAATCTTTGAACTC
1 AAATGAGAATCTTTGAATTTCAAATGA-GAATCTTTG-ATTT
* *
1385462 AAATGAGAATATTTGAATTCTCAAATGAGAATCTGTGAGTGTT
1 AAATGAGAATCTTTGAATT-TCAAATGAGAATCTTTGA-T-TT
1385505 AAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAATTT
1 AAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG-ATTT
* * * * * *
1385546 AAAATGAGAATCTTTGAGGTGTGAAACTCA-AA-ATTT-A-TC
1 -AAATGAGAATCTTTGA-ATTTCAAA-TGAGAATCTTTGATTT
* * * *
1385585 GAATGTGAATC-TTCAAATTCAAATGAGAATCTTTGAATTT
1 AAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG-ATTT
* * * * *
1385625 CAAATGAGAATCTTTGAGATGTGAAACTCA-AA-ATTT-A-TC
1 -AAATGAGAATCTTTGA-ATTTCAAA-TGAGAATCTTTGATTT
*
1385664 GAATGTA-AATCTTTGAA-TTCAAATGAGAATCTTTGAATTT
1 AAATG-AGAATCTTTGAATTTCAAATGAGAATCTTTG-ATTT
*
1385704 CAAATAAGAATCTTT
1 -AAATGAGAATCTTT
1385719 AAGATGTGAA
Statistics
Matches: 191, Mismatches: 41, Indels: 50
0.68 0.15 0.18
Matches are distributed among these distances:
35 4 0.02
36 12 0.06
37 10 0.05
38 22 0.12
39 5 0.03
40 5 0.03
41 38 0.20
42 56 0.29
43 35 0.18
44 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (40 bp):
AAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGATTT
Found at i:1385614 original size:20 final size:20
Alignment explanation
Indices: 1385586--1385638 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
1385576 AAATTTATCG
*
1385586 AATGTGAATCTTCAAATTCA
1 AATGAGAATCTTCAAATTCA
* *
1385606 AATGAGAATCTTTGAATTTCA
1 AATGAGAATC-TTCAAATTCA
1385627 AATGAGAATCTT
1 AATGAGAATCTT
1385639 TGAGATGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGAGAATCTTCAAATTCA
Found at i:1385616 original size:79 final size:79
Alignment explanation
Indices: 1385523--1385730 Score: 353
Period size: 79 Copynumber: 2.6 Consensus size: 79
1385513 ATCTTTGAAT
* *
1385523 TTCAAATGAGAATCTTTGAATTTAAAATGAGAATCTTTGAGGTGTGAAACTCAAAATTTATCGAA
1 TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTATCGAA
*
1385588 TGTGAATCTTCAAA
66 TGTAAATCTTCAAA
1385602 TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTATCGAA
1 TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTATCGAA
**
1385667 TGTAAATCTTTGAA
66 TGTAAATCTTCAAA
* *
1385681 TTCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTTAAGATGTGAAAC
1 TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGATGTGAAAC
1385731 CTTAAAGTTT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 122 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (79 bp):
TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAGATGTGAAACTCAAAATTTATCGAA
TGTAAATCTTCAAA
Found at i:1385628 original size:21 final size:21
Alignment explanation
Indices: 1385602--1385718 Score: 97
Period size: 21 Copynumber: 5.8 Consensus size: 21
1385592 AATCTTCAAA
1385602 TTCAAATGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
1385623 TTCAAATGAGAATCTTTGAGAT
1 TTCAAATGAGAATCTTTGA-AT
* * * *
1385645 GTGAAACTCA-AA-ATTT--A-
1 TTCAAA-TGAGAATCTTTGAAT
*
1385662 -TCGAATGTA-AATCTTTGAA-
1 TTCAAATG-AGAATCTTTGAAT
1385681 TTCAAATGAGAATCTTTGAAT
1 TTCAAATGAGAATCTTTGAAT
*
1385702 TTCAAATAAGAATCTTT
1 TTCAAATGAGAATCTTT
1385719 AAGATGTGAA
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.01
16 6 0.08
17 3 0.04
18 1 0.01
19 2 0.03
20 16 0.21
21 38 0.49
22 8 0.10
23 2 0.03
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (21 bp):
TTCAAATGAGAATCTTTGAAT
Found at i:1385706 original size:100 final size:100
Alignment explanation
Indices: 1385264--1385718 Score: 238
Period size: 100 Copynumber: 4.4 Consensus size: 100
1385254 ATCTTTAAAA
* *
1385264 AATTTTCAAATGAGAATCTTTGAGTCTT-AAATGAGAATCTTTAAGAAATCCTT-AAATGAGAAT
1 AATTATCAAATGAGAATCTTTGAAT-TTCAAATGAGAATCTTT--G-AAT--TTCAAATGAGAAT
* * * * * * ***
1385327 CTTTG-AGTGTCAAATGAGAATCTTTGAGGTATGAAACTCAA
60 CTTTGAATTG-AAAATCAAAATCTTTGAGATGTGAAACTTTG
* * *
1385368 AATTTATCGAAT-ATGAATCTTCGAA-TTCAAATGAGAATATTTAAAGAATTATCAAATGAGAAT
1 AA-TTATCAAATGA-GAATCTTTGAATTTCAAATGAGAATCTTT---GAATT-TCAAATGAGAAT
* * * * *
1385431 CTTTG-AGTGTCAAAT-ATGAATCTTTGA-ACTCAAATGAGAATATTTG
60 CTTTGAATTG-AAAATCA-AAATCTTTGAGA-T---GTGA-AA-CTTTG
* * *
1385477 AATTCTCAAATGAGAATCTGTGAGTGTT-AAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG
1 AATTATCAAATGAGAATCTTTGAAT-TTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG
* * * * ***
1385541 AATTTAAAATGAGAATCTTTGAGGTGTGAAACTCAA
65 AATTGAAAATCAAAATCTTTGAGATGTGAAACTTTG
* * * *
1385577 AATTTATCGAATGTGAATC-TTCAAATTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG
1 AA-TTATCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTG
*
1385641 AGATGTGAAACTCAAAAT-TTATCGA-ATGT-AAATCTTTG
65 A-AT-TGAAAATCAAAATCTT-T-GAGATGTGAAA-CTTTG
*
1385679 AA-T-TCAAATGAGAATCTTTGAATTTCAAATAAGAATCTTT
1 AATTATCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTT
1385719 AAGATGTGAA
Statistics
Matches: 279, Mismatches: 45, Indels: 58
0.73 0.12 0.15
Matches are distributed among these distances:
99 13 0.05
100 63 0.23
101 22 0.08
102 21 0.08
103 6 0.02
104 55 0.20
105 51 0.18
106 8 0.03
107 4 0.01
108 17 0.06
109 17 0.06
110 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (100 bp):
AATTATCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGAATTTCAAATGAGAATCTTTGA
ATTGAAAATCAAAATCTTTGAGATGTGAAACTTTG
Found at i:1385965 original size:114 final size:114
Alignment explanation
Indices: 1385782--1386050 Score: 396
Period size: 114 Copynumber: 2.4 Consensus size: 114
1385772 TTTTAAACTT
*
1385782 TTGGATGTGAATCTCCAAAATTCAAACGAAAAGCTTTAAACTCAACTTTTGGATGCAAATCTCTA
1 TTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATGCAAATCTCTA
*
1385847 AATTTTTGAGTAAGAACCTTTGAACTTAGATGTGAAACTCTAAGATTTC
66 AATTTTTGAGTAAGAACCTTTAAACTTAGATGTGAAACTCTAAGATTTC
* * * * *
1385896 TTGGATGTGAATCTTCAAAATTCAAATAAAAAGCTTTGAACTCAACTTTTGTATGCGAATCTCTA
1 TTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATGCAAATCTCTA
* *
1385961 AATTTTTGAGTGAGTACCTTTAAACTTAGATGTGAAACTCTAAGATTTC
66 AATTTTTGAGTAAGAACCTTTAAACTTAGATGTGAAACTCTAAGATTTC
* **** *
1386010 TTGAATGTGAA-CTTTTGAATTCAAACGAAAAGCTTTAAACT
1 TTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACT
1386051 TTTGGATGAA
Statistics
Matches: 139, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
113 24 0.17
114 115 0.83
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (114 bp):
TTGGATGTGAATCTCCAAAATTCAAACAAAAAGCTTTAAACTCAACTTTTGGATGCAAATCTCTA
AATTTTTGAGTAAGAACCTTTAAACTTAGATGTGAAACTCTAAGATTTC
Found at i:1386376 original size:45 final size:45
Alignment explanation
Indices: 1386322--1386568 Score: 297
Period size: 45 Copynumber: 5.5 Consensus size: 45
1386312 TTGTAGTACA
* * *
1386322 TCTGTTTAGAAGAGCTTTATTTATTTTTCTCAAAGTCGTTGAGTC
1 TCTGATTAGAAGAGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
* * * * *
1386367 TCTGATTAGAGGAGCTTTGTTTATTTTT-TTAAAGTTGTAGAACC
1 TCTGATTAGAAGAGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
* * *
1386411 TCTAATTAGAAGAGCTGTGTTTATTTTTCTCAAAGTCGTTAAGCC
1 TCTGATTAGAAGAGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
*
1386456 TCTGATTAG-AGAAGCTTTGTTTATTTTTCTCAAAGTCGTTAAGCC
1 TCTGATTAGAAG-AGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
* *
1386501 TCTAATTA-AAGGAGCTTGGTTTATTTTT-TCAAAGTCGTTGAGCC
1 TCTGATTAGAA-GAGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
*
1386545 TCT-ATTTAGAGGAGCTTTGTTTAT
1 TCTGA-TTAGAAGAGCTTTGTTTAT
1386569 GTGTTCAAAA
Statistics
Matches: 173, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.01
44 71 0.41
45 100 0.58
46 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (45 bp):
TCTGATTAGAAGAGCTTTGTTTATTTTTCTCAAAGTCGTTGAGCC
Found at i:1386459 original size:89 final size:88
Alignment explanation
Indices: 1386303--1386577 Score: 342
Period size: 89 Copynumber: 3.1 Consensus size: 88
1386293 AGCCTTTTAC
* * ** * *
1386303 TTTTCAAAGTTGTAGTACATCTGTTTAGAAGAGCTTTATTTATTTTTCTCAAAGTCGTTGAGTCT
1 TTTTCAAAGTTGTAGAACCTCTAATTAGAAGAGC-TTGTTTATTTTTCTCAAAGTCGTTGAGCCT
1386368 CTGATTAGAGGAGCTTTGTTTATT
65 CTGATTAGAGGAGCTTTGTTTATT
* *
1386392 TTTTTAAAGTTGTAGAACCTCTAATTAGAAGAGCTGTGTTTATTTTTCTCAAAGTCGTTAAGCCT
1 TTTTCAAAGTTGTAGAACCTCTAATTAGAAGAGCT-TGTTTATTTTTCTCAAAGTCGTTGAGCCT
*
1386457 CTGATTAGAGAAGCTTTGTTTATT
65 CTGATTAGAGGAGCTTTGTTTATT
* *
1386481 TTTCTCAAAGTCGTTA-AGCCTCTAATTA-AAGGAGCTTGGTTTATTTTT-TCAAAGTCGTTGAG
1 TTT-TCAAAGTTG-TAGAACCTCTAATTAGAA-GAGCTT-GTTTATTTTTCTCAAAGTCGTTGAG
*
1386543 CCTCT-ATTTAGAGGAGCTTTGTTTATG
62 CCTCTGA-TTAGAGGAGCTTTGTTTATT
*
1386570 TGTTCAAA
1 TTTTCAAA
1386578 AAAAATGAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
88 7 0.04
89 122 0.74
90 33 0.20
91 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (88 bp):
TTTTCAAAGTTGTAGAACCTCTAATTAGAAGAGCTTGTTTATTTTTCTCAAAGTCGTTGAGCCTC
TGATTAGAGGAGCTTTGTTTATT
Found at i:1386591 original size:11 final size:11
Alignment explanation
Indices: 1386575--1386600 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1386565 TTATGTGTTC
1386575 AAAAAAAATGA
1 AAAAAAAATGA
1386586 AAAAAAAATGA
1 AAAAAAAATGA
1386597 AAAA
1 AAAA
1386601 GATAAAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:1386832 original size:16 final size:16
Alignment explanation
Indices: 1386804--1386849 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1386794 TGTTTGTTAT
1386804 TTTATTCTTATTTTTTA
1 TTTATT-TTATTTTTTA
*
1386821 TTT-TTATTATTTATTA
1 TTTATT-TTATTTTTTA
1386837 TTTATTTTATTTT
1 TTTATTTTATTTT
1386850 AGGATATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTATTTTTTA
Found at i:1387421 original size:18 final size:17
Alignment explanation
Indices: 1387398--1387438 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1387388 CCTAGAGAGA
1387398 GGAAGAGAGGAAAAAAGG
1 GGAAGAGAGG-AAAAAGG
*
1387416 GGAAGA-AGGAGAAAGG
1 GGAAGAGAGGAAAAAGG
1387432 GGAAGAG
1 GGAAGAG
1387439 CAATTTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 12 0.57
17 3 0.14
18 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (17 bp):
GGAAGAGAGGAAAAAGG
Found at i:1387707 original size:4 final size:4
Alignment explanation
Indices: 1387698--1387724 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1387688 GCGTTAAGAT
1387698 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1387725 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1388015 original size:59 final size:60
Alignment explanation
Indices: 1387938--1388052 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
1387928 TCCAATTTCT
* * *
1387938 AAAAAATATTTTTTAGGAAAAATTGAATGCATCAATTTT-TTTTAAAATAAAATTTTTTA
1 AAAAAATATTTTTGAGGAAAAATTGAAAGCATCAATTTTCTTTAAAAATAAAATTTTTTA
* *
1387997 AAAAAAGTA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTT
1 AAAAAA-TATTTTTGAGGAAAAATTGAAAGCATCAATTTTCTTTAAAAATAAAATTT
1388053 CTAAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 32 0.65
60 17 0.35
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (60 bp):
AAAAAATATTTTTGAGGAAAAATTGAAAGCATCAATTTTCTTTAAAAATAAAATTTTTTA
Found at i:1388058 original size:59 final size:58
Alignment explanation
Indices: 1387931--1388164 Score: 168
Period size: 71 Copynumber: 3.8 Consensus size: 58
1387921 AAATATTTCC
* * * * * *
1387931 AATTTCT-AAAAAATATTTTTTAGGAAAAATTGAATGCATCAATTTT-TTTTAAAATAA
1 AATTTCTAAAAAAATA-TTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAA
* *
1387988 AATTTTTTAAAAAAAGTATTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAA
1 AA-TTTCTAAAAAAA-TATTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAA
* * *
1388048 AATTTCTAAAATAAAAATTTCTAAAAGCATTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGA
1 AATTTCT--AA-AAAAA----T------ATTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTAA
*
1388113 AATTAA
53 AAATAA
* *
1388119 AATTTC-AGAAAAATATTTTTAAGACAAAGTTGAAAGTATCAATTTT
1 AATTTCTAAAAAAATATTTTGAAGA-AAAGTTGAAAGTATCAATTTT
1388165 TTTTGTATAA
Statistics
Matches: 144, Mismatches: 16, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
57 10 0.07
58 25 0.17
59 36 0.25
60 14 0.10
61 2 0.01
62 5 0.03
63 1 0.01
65 1 0.01
67 5 0.03
68 1 0.01
71 44 0.31
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (58 bp):
AATTTCTAAAAAAATATTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAA
Found at i:1388060 original size:14 final size:15
Alignment explanation
Indices: 1388041--1388073 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1388031 ATTTTCTTTA
1388041 AAAAT-AAAATTTCT
1 AAAATAAAAATTTCT
1388055 AAAATAAAAATTTCT
1 AAAATAAAAATTTCT
1388070 AAAA
1 AAAA
1388074 GCATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAAATTTCT
Found at i:1388194 original size:2 final size:2
Alignment explanation
Indices: 1388187--1388220 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1388177 GCAATAAGTT
1388187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1388221 AAACAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1392076 original size:13 final size:12
Alignment explanation
Indices: 1392058--1392088 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1392048 GCTCATTTGG
1392058 TTTTTTTTATTT
1 TTTTTTTTATTT
1392070 ATTTTTTTTATTT
1 -TTTTTTTTATTT
1392083 TTTTTT
1 TTTTTT
1392089 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:1392084 original size:10 final size:10
Alignment explanation
Indices: 1392060--1392095 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1392050 TCATTTGGTT
1392060 TTTTTTATTTA
1 TTTTTT-TTTA
1392071 -TTTTTTTTA
1 TTTTTTTTTA
1392080 TTTTTTTTTA
1 TTTTTTTTTA
1392090 TTTTTT
1 TTTTTT
1392096 ATAAATGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:1393788 original size:30 final size:31
Alignment explanation
Indices: 1393725--1393793 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1393715 CATATTGACA
*
1393725 TGGCATTGCCACATCATTTGTCAGGCACCATG
1 TGGCATTGCCACATCATTTGACAGG-ACCATG
** *
1393757 TGGCATTGCCATGTCATTTGACATG-CCATG
1 TGGCATTGCCACATCATTTGACAGGACCATG
1393787 TGGCATT
1 TGGCATT
1393794 ATATACTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 12 0.36
32 21 0.64
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (31 bp):
TGGCATTGCCACATCATTTGACAGGACCATG
Done.