Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000640.1 Hibiscus syriacus cultivar Beakdansim tig00001240_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: 131012
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1573 original size:20 final size:20
Alignment explanation
Indices: 1544--1590 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1534 ATTCCACCAC
1544 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
1564 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
1584 ATG-AACT
1 ATGCAACT
1591 CTTAGACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:10855 original size:2 final size:2
Alignment explanation
Indices: 10848--10874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10838 TTTAATCCAA
10848 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
10875 ATTGTTATTA
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:12941 original size:23 final size:22
Alignment explanation
Indices: 12910--12954 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
12900 ATCCATCCAT
*
12910 GCATGCATGTATGTGTTATATGG
1 GCATCCATGTATGTG-TATATGG
12933 GCATCCATGTATGTGTATATGG
1 GCATCCATGTATGTGTATATGG
12955 TTATTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
GCATCCATGTATGTGTATATGG
Found at i:15936 original size:18 final size:18
Alignment explanation
Indices: 15913--15950 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
15903 CGTGAACGCT
15913 TACTTTTTAAGGCAAATC
1 TACTTTTTAAGGCAAATC
15931 TACTTTTTAAGGCAAATC
1 TACTTTTTAAGGCAAATC
15949 TA
1 TA
15951 ATTATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (18 bp):
TACTTTTTAAGGCAAATC
Found at i:16008 original size:3 final size:3
Alignment explanation
Indices: 16000--16053 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
15990 AACTATTTGA
* *
16000 TAT TAT TAT TAT TAT TAT TAT TAT AAT TA- TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16047 CAT TAT T
1 TAT TAT T
16054 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:16196 original size:5 final size:5
Alignment explanation
Indices: 16186--16211 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16176 TTTTTGGTCC
16186 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
16212 GAATAATGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:17496 original size:26 final size:26
Alignment explanation
Indices: 17456--17506 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
17446 TAAACCACCT
* *
17456 AAGGGGTCATCCAATGTTTGTATCCC
1 AAGGGGCCATACAATGTTTGTATCCC
17482 AAGGGGCCATACAATGTTTGTATCC
1 AAGGGGCCATACAATGTTTGTATCC
17507 ATTCATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (26 bp):
AAGGGGCCATACAATGTTTGTATCCC
Found at i:17986 original size:2 final size:2
Alignment explanation
Indices: 17979--18192 Score: 192
Period size: 2 Copynumber: 108.5 Consensus size: 2
17969 CACGTGAGTA
17979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * * *
18063 AT AT AT AT AG CT -T GT TT ACT AT GCT AT GT CAT TT CT -T GT GT
1 AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT -AT AT AT AT AT AT
* * * * *
18104 GT AT CT AC AT AT -T AT GGT -T TT A- AT -T AGT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT
18143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18185 AT A- AT AT A
1 AT AT AT AT A
18193 CATGTTTGAA
Statistics
Matches: 181, Mismatches: 18, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
1 8 0.04
2 167 0.92
3 6 0.03
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19296 original size:18 final size:20
Alignment explanation
Indices: 19255--19298 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
19245 TAAAACAATA
19255 ATAATATAACAAATCATAAC
1 ATAATATAACAAATCATAAC
*
19275 -TAATAT-ACAAAT-ATTAC
1 ATAATATAACAAATCATAAC
19292 ATAATAT
1 ATAATAT
19299 GAGTACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATATAACAAATCATAAC
Found at i:20962 original size:43 final size:43
Alignment explanation
Indices: 20914--21103 Score: 118
Period size: 43 Copynumber: 4.3 Consensus size: 43
20904 GATGGTGATA
*
20914 ACACGGTTCCTACACGATGAGGACGGCTGGTTATCTTGGGATG
1 ACACGGTTCCTACACGATGAGGATGGCTGGTTATCTTGGGATG
* ** * *
20957 ACACGGCTCCTACGTGATGAGGA-GGTCTGGTCA--GT-GGATG
1 ACACGGTTCCTACACGATGAGGATGG-CTGGTTATCTTGGGATG
* * * *
20997 AGACAGTTCCTACATGATGAGGATGTCTTGGTTATCTTTAGGGATGGTG
1 ACACGGTTCCTACACGATGAGGATGGC-TGGTTATC-TT-GGGA---TG
* * * * *
21046 ATAACACGGTTTCTACACGATGAGGATAGCTGGATATCTAGGGGTG
1 ---ACACGGTTCCTACACGATGAGGATGGCTGGTTATCTTGGGATG
*
21092 ACACGGCTCCTA
1 ACACGGTTCCTA
21104 TGTGATGAGG
Statistics
Matches: 110, Mismatches: 23, Indels: 28
0.68 0.14 0.17
Matches are distributed among these distances:
40 25 0.23
41 7 0.06
42 2 0.02
43 36 0.33
44 1 0.01
46 5 0.05
49 5 0.05
50 1 0.01
51 7 0.06
52 21 0.19
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (43 bp):
ACACGGTTCCTACACGATGAGGATGGCTGGTTATCTTGGGATG
Found at i:21036 original size:135 final size:134
Alignment explanation
Indices: 20816--21176 Score: 440
Period size: 135 Copynumber: 2.7 Consensus size: 134
20806 TAGTCGTCTA
* * *
20816 AGGG-TGACACAGCTCCTACGTGATGAGGAGATTTGGTCAGGGGAT-AACATTGTTCCTACATGA
1 AGGGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGAACA--GTTCCTACATGA
* *
20879 TGAGGATGACTTGGACATCTTTAATGATGGTGATAACACGGTTCCTACACGATGAGGACGGCTGG
64 TGAGGATGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACAGCTGG
*
20944 TTATCT
129 ATATCT
* *
20950 TGGGATGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGAGACAGTTCCTACATGAT
1 AGGGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGA-ACAGTTCCTACATGAT
* ** * * *
21015 GAGGATGTCTTGGTTATCTTTAGGGATGGTGATAACACGGTTTCTACACGATGAGGATAGCTGGA
65 GAGGATGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACAGCTGGA
21080 TATCT
130 TATCT
* * * * * **
21085 AGGGGTGACACGGCTCCTATGTGATGAGGAGATGTGGTCGGTGGATGACACGGTTCCTACGCGAT
1 AGGGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGA-ACAGTTCCTACATGAT
* * * *
21150 GAGAATGA-TAGGCCATCTTTAGGGATG
65 GAGGATGACTTGGACATCTTTAAGGATG
21177 ATATTTCAAG
Statistics
Matches: 195, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
134 19 0.10
135 172 0.88
136 1 0.01
137 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (134 bp):
AGGGATGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGAACAGTTCCTACATGATG
AGGATGACTTGGACATCTTTAAGGATGGTGATAACACGGTTCCTACACGATGAGGACAGCTGGAT
ATCT
Found at i:21302 original size:36 final size:36
Alignment explanation
Indices: 21245--21376 Score: 115
Period size: 36 Copynumber: 3.7 Consensus size: 36
21235 CAAAGATAGG
21245 TGTTTCAAAAGAAACTGACTCAAAAGAGACAAAATT
1 TGTTTCAAAAGAAACTGACTCAAAAGAGACAAAATT
** **** *
21281 TGTTTCAAGGGAAA-TGCACTC-AAAGATTTTTAATTT
1 TGTTTCAAAAGAAACTG-ACTCAAAAGA-GACAAAATT
* * *
21317 TGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGACTCAAAAGAGACAAAATT
** *
21353 TGTTTCAAGGGAAACAGACTCAAA
1 TGTTTCAAAAGAAACTGACTCAAA
21377 GATGATGTTT
Statistics
Matches: 69, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
35 7 0.10
36 56 0.81
37 6 0.09
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGACTCAAAAGAGACAAAATT
Found at i:21339 original size:72 final size:72
Alignment explanation
Indices: 21180--21379 Score: 234
Period size: 72 Copynumber: 2.8 Consensus size: 72
21170 AGGGATGATA
* * * * *
21180 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAGAATCAAAGA----
1 TTTCAAAAGAAACTGACTCAAAAGAGACAAAA-TTTGTTTCAAGGGAAACAGACTCAAAGATTTT
**
21241 T-A-GGTG
65 TAATTTTG
*
21247 TTTCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAA-TGCACTCAAAGATTTT
1 TTTCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAG-ACTCAAAGATTTT
21311 TAATTTTG
65 TAATTTTG
* * *
21319 TTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGAT
1 TTTCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGAT
21380 GATGTTTCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
65 1 0.01
66 23 0.20
67 29 0.26
70 1 0.01
71 1 0.01
72 57 0.50
73 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (72 bp):
TTTCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAACAGACTCAAAGATTTTT
AATTTTG
Found at i:21441 original size:138 final size:134
Alignment explanation
Indices: 21178--21514 Score: 378
Period size: 138 Copynumber: 2.5 Consensus size: 134
21168 TTAGGGATGA
* * *
21178 TATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTATTTCAAGGGAAACAGAATCAAAGATA
1 TATTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAGACTCAAAGATA
* * *
21243 GGTGTTTCAAAAGAAACTGACTCAAAAGAGACAAAATTTGTTTCAAGGGAAATGCACTCAAAGAT
66 GATGTTTCAAAAGAAACTGACTCAAAAGAGAAAAAATTCGTTTCAAGGGAAA-GCACTCAAAGA-
21308 TTTTAATTT
129 ---TAATTT
* *
21317 TGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACAGACTCAAAGAT-
1 TATTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAGACTCAAAGATA
* *
21380 GATGTTTCAAGAA-AAACTGTA-TTAAGAGAGAAAAAAATTCGTTTCAAGGGAAA-CAATCTCAA
66 GATGTTTCAA-AAGAAACTG-ACTCAAAAGAG-AAAAAATTCGTTTCAAGGGAAAGC-A-CTCAA
**
21442 AGATGGTTT
126 AGATAATTT
* * * * * * *
21451 TATTTCAAGAGAGACTGCCTCAAGAGAGATAAAATTTTGTTTGAAGAGAAAAAGACTCAAAGAT
1 TATTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAGACTCAAAGAT
21515 TTGTGTTTCA
Statistics
Matches: 171, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
134 32 0.19
135 26 0.15
136 1 0.01
137 23 0.13
138 58 0.34
139 31 0.18
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (134 bp):
TATTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAGACTCAAAGATA
GATGTTTCAAAAGAAACTGACTCAAAAGAGAAAAAATTCGTTTCAAGGGAAAGCACTCAAAGATA
ATTT
Found at i:24113 original size:10 final size:10
Alignment explanation
Indices: 24100--24147 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
24090 AGTCTTTTTC
24100 TTTCTTTGTT
1 TTTCTTTGTT
*
24110 TTTCTTTTTT
1 TTTCTTTGTT
24120 TTTCCTTT-TT
1 TTT-CTTTGTT
24130 TTTCTTTGTTT
1 TTTCTTTG-TT
24141 TTTCTTT
1 TTTCTTT
24148 TGCTTCTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.12
10 17 0.50
11 13 0.38
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83
Consensus pattern (10 bp):
TTTCTTTGTT
Found at i:24117 original size:20 final size:19
Alignment explanation
Indices: 24092--24148 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
24082 GTGTTTCTAG
*
24092 TCTTTTTCTTTCTTTGTTTT
1 TCTTTTTTTTTCTTT-TTTT
24112 TCTTTTTTTTTCCTTTTTTT
1 TCTTTTTTTTT-CTTTTTTT
24132 TCTTTGTTTTTTCTTTT
1 TCTTT-TTTTTTCTTTT
24149 GCTTCTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 24 0.71
21 10 0.29
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (19 bp):
TCTTTTTTTTTCTTTTTTT
Found at i:24154 original size:20 final size:20
Alignment explanation
Indices: 24111--24157 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24101 TTCTTTGTTT
**
24111 TTCTTTTTTTTTCCTTTTTT
1 TTCTTTTTTTTTCCTTTTGC
24131 TTCTTTGTTTTTT-CTTTTGC
1 TTCTTT-TTTTTTCCTTTTGC
24151 TTCTTTT
1 TTCTTTT
24158 CTCTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.71
21 6 0.25
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (20 bp):
TTCTTTTTTTTTCCTTTTGC
Found at i:24157 original size:27 final size:25
Alignment explanation
Indices: 24114--24168 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
24104 TTTGTTTTTC
*
24114 TTTTTTTTTCCTTTTTTTTCTTTGT
1 TTTTTTTTTCCTTTTTTCTCTTTGT
*
24139 TTTTTCTTTTGCTTCTTTTCTCTTTGT
1 TTTTT-TTTTCCTT-TTTTCTCTTTGT
24166 TTT
1 TTT
24169 GATTGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 5 0.19
26 7 0.27
27 14 0.54
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (25 bp):
TTTTTTTTTCCTTTTTTCTCTTTGT
Found at i:26014 original size:3 final size:3
Alignment explanation
Indices: 26006--26059 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
25996 AAAATGTGTA
*
26006 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26053 AAT AAT A
1 AAT AAT A
26060 TTTTTTTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32361 original size:19 final size:20
Alignment explanation
Indices: 32318--32365 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
32308 TCTAAATCCT
*
32318 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
32338 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
32357 TTTTCAAAA
1 TTTTCAAAA
32366 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:33914 original size:9 final size:8
Alignment explanation
Indices: 33892--33942 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
33882 TGTTTCAACA
33892 TTTTGGAT
1 TTTTGGAT
33900 ATTTTGGAT
1 -TTTTGGAT
33909 TGTTT-GAT
1 T-TTTGGAT
33917 TTTGTGGAT
1 TTT-TGGAT
*
33926 TGTTGGA-
1 TTTTGGAT
33933 TTTTGGAT
1 TTTTGGAT
33941 TT
1 TT
33943 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:33926 original size:17 final size:17
Alignment explanation
Indices: 33894--33937 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
33884 TTTCAACATT
33894 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
33911 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
33928 TTGGATTTTG
1 TTGGATTTTG
33938 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:34729 original size:76 final size:77
Alignment explanation
Indices: 34528--34737 Score: 268
Period size: 75 Copynumber: 2.8 Consensus size: 77
34518 CAAAGCCAAA
* * * **
34528 AATTTCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
34592 TTTTGGCCTCGAG
65 TTTTGGCCTCGAG
* *
34605 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
34669 TTT-G-CTCCGAG
66 TTTGGCCT-CGAG
* * *
34680 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATA-GGAGGAACCGATTCCCCCCT
34738 TGTACAACGG
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
74 2 0.02
75 53 0.45
76 39 0.33
77 23 0.20
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCTCGAG
Found at i:37278 original size:21 final size:22
Alignment explanation
Indices: 37245--37287 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
37235 AACGTAGGCA
* *
37245 TTTAATATTTTTACGTTATTAT
1 TTTAATATGTTTAAGTTATTAT
*
37267 TTTAA-ATGTTTAATTTATTAT
1 TTTAATATGTTTAAGTTATTAT
37288 AATTATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTAATATGTTTAAGTTATTAT
Found at i:49678 original size:13 final size:13
Alignment explanation
Indices: 49660--49687 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49650 AAGTACACAA
49660 ATATAAGATTATT
1 ATATAAGATTATT
49673 ATATAAGATTATT
1 ATATAAGATTATT
49686 AT
1 AT
49688 GTTGAGTCTA
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:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATATAAGATTATT
Found at i:50095 original size:59 final size:61
Alignment explanation
Indices: 49990--50115 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 61
49980 AAACATGTGA
* * * * *
49990 ATAATCAAGTGATCATTTTATAACATTTGATACTCATATGATTCAATAAAATAATG-ACAT
1 ATAATCAAATGATCATTTTATAACATTTAATAATCAAATGACTCAATAAAATAATGTACAT
* * *
50050 ATAATCAAATGAT-ATTTTATAA-ATTTTAATAATCAAATGGCTCAATAAGATTATGTACAT
1 ATAATCAAATGATCATTTTATAACA-TTTAATAATCAAATGACTCAATAAAATAATGTACAT
50110 A-AATCA
1 ATAATCA
50116 GTTGTGTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.02
59 38 0.68
60 17 0.30
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (61 bp):
ATAATCAAATGATCATTTTATAACATTTAATAATCAAATGACTCAATAAAATAATGTACAT
Found at i:54870 original size:24 final size:24
Alignment explanation
Indices: 54835--54884 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
54825 TTCTTTTAGT
54835 ACATGCACACTAAATATAACAAGG
1 ACATGCACACTAAATATAACAAGG
54859 ACATGC-CAACTAAATATAACAAGG
1 ACATGCAC-ACTAAATATAACAAGG
54883 AC
1 AC
54885 CCCATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (24 bp):
ACATGCACACTAAATATAACAAGG
Found at i:55268 original size:2 final size:2
Alignment explanation
Indices: 55261--55290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55251 ATCATACATC
55261 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
55291 TAGATACATT
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:55516 original size:32 final size:31
Alignment explanation
Indices: 55464--55566 Score: 154
Period size: 32 Copynumber: 3.3 Consensus size: 31
55454 GTTTCGAAGA
55464 ACATAGGTAAT-TGTCCATATGTCCCGAAAG
1 ACATAGGTAATATGTCCATATGTCCCGAAAG
55494 ACATAGGTAATCATGTCCATATGTCCCGAAAG
1 ACATAGGTAAT-ATGTCCATATGTCCCGAAAG
* * * *
55526 ACATAGGTAAAATATCCATATGTCTCAAAAG
1 ACATAGGTAATATGTCCATATGTCCCGAAAG
55557 ACATAGGTAA
1 ACATAGGTAA
55567 CCCTCGACTC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
30 11 0.16
31 27 0.40
32 29 0.43
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (31 bp):
ACATAGGTAATATGTCCATATGTCCCGAAAG
Found at i:62249 original size:18 final size:18
Alignment explanation
Indices: 62226--62264 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62216 ACCATAAACA
*
62226 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
62244 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
62262 GAA
1 GAA
62265 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:62413 original size:33 final size:31
Alignment explanation
Indices: 62370--62437 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
62360 ACTATATACC
62370 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
62402 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
62434 ATAT
1 ATAT
62438 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:62498 original size:107 final size:109
Alignment explanation
Indices: 62371--62572 Score: 263
Period size: 107 Copynumber: 1.9 Consensus size: 109
62361 CTATATACCA
* * *
62371 TATAGTTTTCAAAAATGATTTTAAAA-ATA-TTATATGAGTTTTCCAAAATATTTTTAAAAC-TA
1 TATAGTTTTCAAAAATGATTTCAAAATATAGTTATAT-AATTTT-C-AAAT-GTTTTAAAACTTA
*
62433 TATATTATATA-AAATTTTCAAAAATGTTTTTATTTTAAACTATACAT
62 TATATTATATATAAATTTTCAAAAACGTTTTTATTTTAAACTATACAT
62480 TATA-TTTTC-AAAATGATTTCAAAATATATGTTATATAATTTTCAAATGTTTTAAAACTTATAT
1 TATAGTTTTCAAAAATGATTTCAAAATATA-GTTATATAATTTTCAAATGTTTTAAAACTTATAT
* *
62543 ATTGTATATAAGTTTTCAAAAACGTTTTTA
65 ATTATATATAAATTTTCAAAAACGTTTTTA
62573 AAAAAAACTA
Statistics
Matches: 82, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
106 9 0.11
107 30 0.37
108 28 0.34
109 9 0.11
110 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (109 bp):
TATAGTTTTCAAAAATGATTTCAAAATATAGTTATATAATTTTCAAATGTTTTAAAACTTATATA
TTATATATAAATTTTCAAAAACGTTTTTATTTTAAACTATACAT
Found at i:62542 original size:34 final size:35
Alignment explanation
Indices: 62483--62562 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 35
62473 TATACATTAT
62483 ATTTTCAAAATGATTTCAAAATATAT-GT-TATATA
1 ATTTTC-AAATGATTTCAAAATATATAGTGTATATA
* *
62517 ATTTTCAAATG-TTTTAAAACTTATATATTGTATATA
1 ATTTTCAAATGATTTCAAAA--TATATAGTGTATATA
62553 AGTTTTCAAA
1 A-TTTTCAAA
62563 AACGTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 7 0.18
33 5 0.13
34 11 0.28
35 1 0.03
36 7 0.18
37 8 0.21
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (35 bp):
ATTTTCAAATGATTTCAAAATATATAGTGTATATA
Found at i:62581 original size:108 final size:107
Alignment explanation
Indices: 62370--62597 Score: 250
Period size: 108 Copynumber: 2.1 Consensus size: 107
62360 ACTATATACC
* * *
62370 ATATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATA
1 ATATA-TTTTC-AAAATGATTTCAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATA
* ****
62435 TATTATATAAAATTTTCAAAAATGTTTTTATTTTAAACTATACAT
64 TATTATATAAAATTTTCAAAAACGTTTTTAAAAAAAACTATA-AT
62480 -TATATTTTCAAAATGATTTCAAAATATATGTTATAT-AATTTT-C-AAAT-GTTTTAAAACTTA
1 ATATATTTTCAAAATGATTTCAAAA-ATA--TTATATGAATTTTCCAAAATAGTTTTAAAAC-TA
* * *
62540 TATATTGTATATAAGTTTTCAAAAACGTTTTTAAAAAAAACTATATT
62 TATATTATATA-AAATTTTCAAAAACGTTTTTAAAAAAAACTATAAT
62587 ATATATTTTCA
1 ATATATTTTCA
62598 GAAACCATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
106 9 0.09
107 31 0.31
108 46 0.46
109 9 0.09
110 6 0.06
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (107 bp):
ATATATTTTCAAAATGATTTCAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATATA
TTATATAAAATTTTCAAAAACGTTTTTAAAAAAAACTATAAT
Found at i:70284 original size:21 final size:20
Alignment explanation
Indices: 70259--70332 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
70249 GATCGCTAAT
70259 TCGCAACGCGATAATACAAAA
1 TCGCAACGCGATAATAC-AAA
* **
70280 TCGCAACGCGATACTGAC-TT
1 TCGCAACGCGATAAT-ACAAA
*
70300 TCGCAACGAGATAATACATAA
1 TCGCAACGCGATAATACA-AA
*
70321 TCGCAATGCGAT
1 TCGCAACGCGAT
70333 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGATAATACAAA
Found at i:70315 original size:41 final size:39
Alignment explanation
Indices: 70234--70332 Score: 128
Period size: 41 Copynumber: 2.5 Consensus size: 39
70224 AAAATGATCA
*
70234 ACAAAATCGCAATGCGATCGCTAATTCGCAACGCGATAAT
1 ACAAAATCGCAATGCGATCGCT-ATTCGCAACGAGATAAT
*
70274 ACAAAATCGCAACGCGATACTGACT-TTCGCAACGAGATAAT
1 ACAAAATCGCAATGCGAT-C-G-CTATTCGCAACGAGATAAT
*
70315 ACATAATCGCAATGCGAT
1 ACAAAATCGCAATGCGAT
70333 TTTCAAAGCG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
40 17 0.33
41 32 0.62
42 1 0.02
43 2 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (39 bp):
ACAAAATCGCAATGCGATCGCTATTCGCAACGAGATAAT
Found at i:70527 original size:22 final size:22
Alignment explanation
Indices: 70499--70542 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
70489 CACTCTCTCA
70499 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
70521 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
70543 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:70856 original size:20 final size:20
Alignment explanation
Indices: 70807--70865 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
70797 TTTATTCTCT
* **
70807 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
70827 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
70847 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
70866 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:71056 original size:25 final size:24
Alignment explanation
Indices: 71002--71056 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
70992 TGTTTATTAT
* *
71002 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
71026 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
71052 TGTTT
1 TGTTT
71057 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:72213 original size:18 final size:18
Alignment explanation
Indices: 72187--72234 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
72177 TCCACTTCGG
*
72187 GAGCCATCACCTCACCTA
1 GAGCCATCACCTCACCCA
*
72205 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
72223 GAGCCATCACCT
1 GAGCCATCACCT
72235 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:72706 original size:12 final size:13
Alignment explanation
Indices: 72676--72707 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
72666 ACTGCTAAAC
72676 TGTTTTTGGTATT
1 TGTTTTTGGTATT
72689 TG-TTTTGGT-TT
1 TGTTTTTGGTATT
72700 TGTTTTTG
1 TGTTTTTG
72708 TCTTTTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 12 0.67
13 2 0.11
ACGTcount: A:0.03, C:0.00, G:0.25, T:0.72
Consensus pattern (13 bp):
TGTTTTTGGTATT
Found at i:72805 original size:20 final size:19
Alignment explanation
Indices: 72782--72837 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
72772 CGCGACACGA
72782 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* * *
72802 AAATGGCTATCACAATGCG
1 AAATGACTATCGCAACGCG
**
72821 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
72838 ACAAAATTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:72848 original size:21 final size:21
Alignment explanation
Indices: 72824--72867 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
72814 CAATGCGAAA
72824 TGAAAATCGCAACGACAAAAT
1 TGAAAATCGCAACGACAAAAT
72845 TGAAAATCGCAACGACAAAAT
1 TGAAAATCGCAACGACAAAAT
72866 TG
1 TG
72868 CAATGCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.18, G:0.16, T:0.16
Consensus pattern (21 bp):
TGAAAATCGCAACGACAAAAT
Found at i:72882 original size:33 final size:32
Alignment explanation
Indices: 72826--72921 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 32
72816 ATGCGAAATG
*
72826 AAAATCGCAACGACAAAATTGAAAATCGCAACGAC
1 AAAATCGCAACG-C-GAA-TGAAAATCGCAACGAC
* *
72861 AAAATTGCAATGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCG-AATGAAAATCGCAACGAC
72894 AAAATCGCAACGCGAATGAAAATCGCAA
1 AAAATCGCAACGCGAATGAAAATCGCAA
72922 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.25
33 28 0.51
34 3 0.05
35 10 0.18
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (32 bp):
AAAATCGCAACGCGAATGAAAATCGCAACGAC
Found at i:72899 original size:14 final size:14
Alignment explanation
Indices: 72847--72905 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
72837 GACAAAATTG
72847 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
72861 AAAATTGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
72880 AAAATCGCAACGAC
1 AAAATCGCAACGAC
72894 AAAATCGCAACG
1 AAAATCGCAACG
72906 CGAATGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:72997 original size:20 final size:20
Alignment explanation
Indices: 72972--73035 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
72962 TTCATTCGCA
*
72972 TGCGATAGCCATTTCCGCGT
1 TGCGATAGTCATTTCCGCGT
72992 TGCGATAGTCATTTCCGCGT
1 TGCGATAGTCATTTCCGCGT
*
73012 TGCGATAGTCATTTTCGCG-
1 TGCGATAGTCATTTCCGCGT
73031 TGCGA
1 TGCGA
73036 AAGTAAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 5 0.12
20 37 0.88
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.33
Consensus pattern (20 bp):
TGCGATAGTCATTTCCGCGT
Found at i:73046 original size:19 final size:20
Alignment explanation
Indices: 72987--73061 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
72977 TAGCCATTTC
* *
72987 CGCGTTGCGATAGTCA-TTT
1 CGCGTTGCGAAAGTAAGTTT
* * *
73006 CCGCGTTGCGATAGTCATTTT
1 -CGCGTTGCGAAAGTAAGTTT
73027 CGCG-TGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
73046 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
73062 ACTATTCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.31
20 31 0.63
21 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:73053 original size:39 final size:40
Alignment explanation
Indices: 72972--73055 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
72962 TTCATTCGCA
* *
72972 TGCGATAGCCATTTCCGCGTTGCGATAGTCATTTCCGCGT
1 TGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCGT
* * *
73012 TGCGATAGTCATTTTCGCG-TGCGAAAGTAAGTTT-CGTGT
1 TGCGATAGCCATTTCCGCGTTGCGAAAGTAA-TTTCCGCGT
73051 TGCGA
1 TGCGA
73056 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 18 0.47
40 20 0.53
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (40 bp):
TGCGATAGCCATTTCCGCGTTGCGAAAGTAATTTCCGCGT
Found at i:73419 original size:21 final size:20
Alignment explanation
Indices: 73393--73462 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
73383 CTGTCATTCC
73393 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
73414 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
73435 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
73456 TCAAGAG
1 TCAAGAG
73463 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:73483 original size:42 final size:42
Alignment explanation
Indices: 73386--73474 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
73376 GACTCACCTG
* * * *
73386 TCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
* *
73428 TCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
73470 TCATC
1 TCATC
73475 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCCACTA
Found at i:75045 original size:14 final size:14
Alignment explanation
Indices: 75026--75079 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
75016 CGAAATGACT
75026 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
75040 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
75059 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
75073 ATCGCAA
1 ATCGCAA
75080 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:75097 original size:33 final size:33
Alignment explanation
Indices: 75007--75084 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
74997 AAAACAGACT
** **
75007 ATCGCAACACGAAATGACTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
75040 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
75073 ATCGCAATGCGA
1 ATCGCAATGCGA
75085 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:75128 original size:20 final size:20
Alignment explanation
Indices: 75103--75149 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
75093 TCGCATTGCG
*
75103 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
75123 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
75143 ATTTTCG
1 ATTTTCG
75150 CATTGCCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:75150 original size:20 final size:20
Alignment explanation
Indices: 75111--75155 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
75101 CGATTTTCTA
75111 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
75131 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
75151 ATTGC
1 GTTGC
75156 CATTTCCCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:75396 original size:20 final size:20
Alignment explanation
Indices: 75371--75420 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
75361 TTGAAGATGA
75371 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
75391 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
75411 TTGCGATTTT
1 TTGCGATTTT
75421 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:75711 original size:12 final size:12
Alignment explanation
Indices: 75692--75725 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
75682 CTCTTCGGCG
75692 ACATCCGTTCCT
1 ACATCCGTTCCT
*
75704 ATATCCGTTCCT
1 ACATCCGTTCCT
75716 ACATCC-TTCC
1 ACATCCGTTCC
75726 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:76305 original size:24 final size:24
Alignment explanation
Indices: 76278--76331 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
76268 GTATTCGAAA
*
76278 TTTGATCTTGGTCAATACCCGGAT
1 TTTGATATTGGTCAATACCCGGAT
*
76302 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAT
76326 TTTGAT
1 TTTGAT
76332 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAT
Found at i:76512 original size:3 final size:3
Alignment explanation
Indices: 76504--76542 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
76494 ATATAATCCT
* * *
76504 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
76543 AAAGTCCCCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:76521 original size:12 final size:12
Alignment explanation
Indices: 76504--76542 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
76494 ATATAATCCT
76504 GAAGAAGAAAAA
1 GAAGAAGAAAAA
76516 GAAGAAGAAAAA
1 GAAGAAGAAAAA
76528 GAAGAAGAAAAA
1 GAAGAAGAAAAA
76540 GAA
1 GAA
76543 AAAGTCCCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:76565 original size:6 final size:6
Alignment explanation
Indices: 76508--76546 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
76498 AATCCTGAAG
* *
76508 AAGAAA AAGAAG AAGAAA AAGAAG AAGAAA AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
76547 TCCCCGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:78895 original size:33 final size:33
Alignment explanation
Indices: 78849--78975 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
78839 GGAAATTACT
* * *
78849 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
78882 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
* *
78915 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
78948 ATCGCAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
78976 CAAATTTAGT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:79004 original size:19 final size:19
Alignment explanation
Indices: 78980--79051 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
78970 GCAACGCAAA
*
78980 TTTAGTTTCGTGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
78999 TTTAGTTTCGCGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
79018 TTT-G--T--CGTTGCGAT
1 TTTAGTTTCGCGTTGCGAT
*
79032 TTTCA-TTTCGCATTGCGAT
1 TTT-AGTTTCGCGTTGCGAT
79051 T
1 T
79052 CTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
14 12 0.27
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.67
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.50
Consensus pattern (19 bp):
TTTAGTTTCGCGTTGCGAT
Found at i:79033 original size:33 final size:33
Alignment explanation
Indices: 78991--79116 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
78981 TTAGTTTCGT
* * *
78991 GTTGCGATTTT-AGTTTCGCGTTGCGATTTTGTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTATATC
* *
79024 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTATATC
79057 GTTGCGATTTTCATTTCGCATTGCGATTATATC
1 GTTGCGATTTTCATTTCGCATTGCGATTATATC
79090 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
79117 AGTAATTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
33 86 0.99
34 1 0.01
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTATATC
Found at i:79082 original size:19 final size:19
Alignment explanation
Indices: 79025--79116 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
79015 GATTTTGTCG
79025 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
79044 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
79058 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
79077 TTGCGA--TT-ATATCG--
1 TTGCGATTTTCATTTCGCA
79091 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
79110 TTGCGAT
1 TTGCGAT
79117 AGTAATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:79244 original size:14 final size:14
Alignment explanation
Indices: 79225--79259 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
79215 TCAATTAAAA
79225 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
79239 AAATCACCTTTTAC
1 AAATCAACTTTTAC
79253 AAATCAA
1 AAATCAA
79260 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:80695 original size:42 final size:42
Alignment explanation
Indices: 80649--80728 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
80639 CGATGACAGT
* * *
80649 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
* * *
80691 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
80729 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
Found at i:81124 original size:91 final size:90
Alignment explanation
Indices: 80950--81134 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
80940 ATTTCAAACT
* * *
80950 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGAAAAAACAAAGACAAATACTAAATTCACAGTGTT--A-AATAAACAGTTTAGC
81015 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
81043 TTCAACCAAAAGAAAAAACAAAAAGACAAATACTAAATTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGAAAAAAC--AAAGACAAATACTAAATTCACAGTGTTAAATAAACAGTTTAGCA
*
81107 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
81134 T
1 T
81135 AAGAAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 42 0.49
93 18 0.21
95 26 0.30
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGAAAAAACAAAGACAAATACTAAATTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:82889 original size:19 final size:19
Alignment explanation
Indices: 82834--82901 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
82824 TGAAATGAAA
* **
82834 ATCGCAACGAGATAATGAAA
1 ATCGCAACGCGA-AATGACT
82854 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
82874 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
82893 ATCGCAACG
1 ATCGCAACG
82902 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.41
20 24 0.55
21 2 0.05
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:82912 original size:14 final size:14
Alignment explanation
Indices: 82893--82981 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
82883 CGAAATGACT
82893 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
82907 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
*
82926 ATCACAACGAGAGA
1 ATCGCAACGAGAGA
*
82940 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
82959 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
82973 ATCGCAACG
1 ATCGCAACG
82982 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.32
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:82916 original size:33 final size:33
Alignment explanation
Indices: 82833--82998 Score: 224
Period size: 33 Copynumber: 4.8 Consensus size: 33
82823 TTGAAATGAA
* *
82833 AATCGCAACGAGATAATGAAAATCGCAACGCGGAAATG
1 AATCGCAACGCGA-AATGAAAATCGCAA--C-GAGA-G
**
82871 ACTATCGCAACGCGAAATGACTATCGCAACGAGAG
1 A--ATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
82906 AATCGCAACGCGAAATGAAAATCACAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
82939 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
82972 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
82999 TGCGATTTTG
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
33 88 0.75
35 2 0.02
36 3 0.03
37 1 0.01
38 1 0.01
39 12 0.10
40 11 0.09
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:82933 original size:19 final size:19
Alignment explanation
Indices: 82825--83003 Score: 145
Period size: 19 Copynumber: 10.1 Consensus size: 19
82815 TCTTTTGGTT
*
82825 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
82844 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
82864 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
**
82884 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
82901 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
82917 GAAATGAAAATCACAA--C
1 GAAATGAAAATCGCAACGC
*
82934 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
82950 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
82967 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
82983 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
83002 GA
1 GA
83004 TTTTGGTTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 34
0.73 0.07 0.19
Matches are distributed among these distances:
14 28 0.22
15 3 0.02
16 6 0.05
17 6 0.05
18 3 0.02
19 51 0.39
20 31 0.24
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:83032 original size:19 final size:19
Alignment explanation
Indices: 82999--83083 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
82989 AAAATCGCAA
**
82999 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
83018 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
83037 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
83051 TGCGATAGTT-ATTTCCGCGT
1 TGCGAT-TTTCATTT-CGCGT
83071 TGCGATTTTCATT
1 TGCGATTTTCATT
83084 CTCGAAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
14 10 0.19
17 5 0.09
19 25 0.47
20 13 0.25
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:83633 original size:20 final size:20
Alignment explanation
Indices: 83592--83683 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
83582 GCTATGTAAA
* *
83592 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
83612 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
83632 TCGCATTGTGAATTT-CCTAAT
1 TCGCATTGCG-ATTTACGT-AT
* * *
83653 TCGCATTGCAATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
83673 TCGCGTTGCGA
1 TCGCATTGCGA
83684 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.05
20 39 0.67
21 16 0.28
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:83798 original size:21 final size:22
Alignment explanation
Indices: 83750--83798 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
83740 ACTTATTCGT
83750 ATTGCG-AATTGGGAAAATCGC
1 ATTGCGAAATTGGGAAAATCGC
** *
83771 AACGCGAAATT-GGAAAATTGC
1 ATTGCGAAATTGGGAAAATCGC
83792 ATTGCGA
1 ATTGCGA
83799 TTGTCATAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (22 bp):
ATTGCGAAATTGGGAAAATCGC
Found at i:83856 original size:20 final size:20
Alignment explanation
Indices: 83833--83878 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
83823 GGAAACTGAT
*
83833 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
83853 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
83872 TTGCGAT
1 TTGCGAT
83879 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:90730 original size:18 final size:18
Alignment explanation
Indices: 90707--90742 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
90697 TCTGCCCCTT
90707 CATTATCACCTATTTATG
1 CATTATCACCTATTTATG
90725 CATTATCACCTATTTATG
1 CATTATCACCTATTTATG
90743 AAGGTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
CATTATCACCTATTTATG
Found at i:95771 original size:30 final size:28
Alignment explanation
Indices: 95736--95833 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 28
95726 GAATTAATCT
95736 TTAATTTGACTATTAAATTTTAGAATAATA
1 TTAATTTGA-TATTAAATTTTAGAA-AATA
* *
95766 CTAATTTGATATTTAATTTTAGAGGAAATA
1 TTAATTTGATATTAAATTTTAGA--AAATA
* * *
95796 TTATTTTGATTTTAAATTTTAGACAATA
1 TTAATTTGATATTAAATTTTAGAAAATA
95824 TTAATTTGAT
1 TTAATTTGAT
95834 CTCTAATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 13 0.22
29 13 0.22
30 31 0.53
31 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (28 bp):
TTAATTTGATATTAAATTTTAGAAAATA
Found at i:97498 original size:35 final size:36
Alignment explanation
Indices: 97422--97498 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 36
97412 CTTTAAAAAA
* *
97422 AAAAAGGCAATTGCAAGAAGCAACCAATATCAAATTC
1 AAAAA-GCAATTGCAAGAAGCAACCAAGATCAAAGTC
* * *
97459 -AAAAGCAATTGCAAGATGCATCCAAGAT-GAAGTC
1 AAAAAGCAATTGCAAGAAGCAACCAAGATCAAAGTC
97493 AAAAAG
1 AAAAAG
97499 GCTTACTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
34 4 0.12
35 26 0.76
36 4 0.12
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.16
Consensus pattern (36 bp):
AAAAAGCAATTGCAAGAAGCAACCAAGATCAAAGTC
Found at i:101460 original size:227 final size:226
Alignment explanation
Indices: 101022--101654 Score: 887
Period size: 227 Copynumber: 2.8 Consensus size: 226
101012 GGCAAGTGGT
**
101022 AAAAAAA-ATGTATCACCCTAACACAGCCTAGCATGACC-GACTAAAATATTGGCAACAGGG---
1 AAAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAG-CTAAAATATTGGCAACAGGGAAA
*
101082 A-AGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCAC-AAAAATGTCTATTCTTCA
65 AGAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCC-CGAAAAATGTCTA-T-TACA
* * *
101145 TCTTACATGAGGG--CAACAACTTTAAGGTAGTTTGATAAAAACAATCAAAAGGTACTTTTAAAG
127 TCTTACACGAGGGAACACCAACTTTAAGGTAGTTTGATAAAAACAATCATAAGGTACTTTTAAAG
* * *
101208 AACATGTAGGTCCACTTATGCAATAGGTATAATCC
192 AACATGTAAGTCAACTTAGGCAATAGGTATAATCC
*
101243 AAAAAAAGATGTATCACCCTAATGCAGCCTAGCACGACCAGCTAAAATATTGGCAACAGGGAAAA
1 AAAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAGCTAAAATATTGGCAACAGGGAAAA
* * * *
101308 GAGGAGATTGCAAGAAAATAATCACCTCGGCAAAGTTGCCTCCCGACAAATGTCTATTACATATT
66 GAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCCGAAAAATGTCTATTACATCTT
*
101373 ACACGAGGGAAACACCAACTTTAAGGTCA-TTTGATAAAAACAATCATAAGGTAGTTTTAAAGAA
131 ACACGAGGG-AACACCAACTTTAAGGT-AGTTTGATAAAAACAATCATAAGGTACTTTTAAAGAA
101437 CATGTAAGTCAACTTAGGCAATAGGTATAATCC
194 CATGTAAGTCAACTTAGGCAATAGGTATAATCC
* * *
101470 AAAAAGAGATGTATCGCCCTAATGCAGCCTAGCATGACCAACTAAAATATTGGCAACAGGGAAAA
1 AAAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAGCTAAAATATTGGCAACAGGGAAAA
101535 GAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCT-CCGTAAAAAATGTCTATTCCACA
66 GAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCCG--AAAAATGTCTATT--ACA
* *
101599 TCTTACAC-AGGGCAACACCAACTTTAAGATAGTTTAATAAAAA-AATCATGAAGGTA
127 TCTTACACGAGGG-AACACCAACTTTAAGGTAGTTTGATAAAAACAATCAT-AAGGTA
101655 TTACCCACTT
Statistics
Matches: 369, Mismatches: 26, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
221 7 0.02
222 48 0.13
223 1 0.00
224 14 0.04
225 3 0.01
226 53 0.14
227 177 0.48
228 20 0.05
229 36 0.10
230 10 0.03
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (226 bp):
AAAAAAAGATGTATCACCCTAATGCAGCCTAGCATGACCAGCTAAAATATTGGCAACAGGGAAAA
GAGGAGATCGCAAGAAAATGATCACCTCGGCAAAGTTGCCTCCCGAAAAATGTCTATTACATCTT
ACACGAGGGAACACCAACTTTAAGGTAGTTTGATAAAAACAATCATAAGGTACTTTTAAAGAACA
TGTAAGTCAACTTAGGCAATAGGTATAATCC
Found at i:103279 original size:252 final size:250
Alignment explanation
Indices: 102837--103311 Score: 898
Period size: 252 Copynumber: 1.9 Consensus size: 250
102827 TAAAAACCCA
*
102837 TTTCCAATACGCTTTAGAAAATTCAAGTAAATAACAAAAGAGAATACTAACTGTTGACAATCTCA
1 TTTCCAATACGCTTTAGAAAATTCAAGTAAATAACAAAAGAAAATACTAACTGTTGACAATCTCA
102902 GCAGAGCTCTTGTACTGGTAACAACTTCAGAGGAGGTGAGATCCAGCTCCTTCTCCTCTCCTCAT
66 GCAGAGCTCTTGTACTGGTAACAACTTCAGAGGAGGTGAGATCCAGCTCCTTCTCCTCTCCTCAT
*
102967 ATTTTCCGACATCGTTTCCAGAGCTTATAAAAACCTATGAAAATTCCTTAAAAAATAAAATAAAA
131 ATTTTCCGACATCGTTTCCAGAGCTTATAAAAACCTATAAAAATTCCTTAAAAAATAAAATAAAA
103032 AAGATATCAGTG-ACGTCAAAGAAGATAAAACTACGGTAAAGAGAGAAAGGAGCC
196 AAGATATCAGTGAACGTCAAAGAAGATAAAACTACGGTAAAGAGAGAAAGGAGCC
103086 TTTCCAATACGCTTTAGAAAATTCAAGTAAATAACAAAAGATAAGATACTAACTGTTGACAATCT
1 TTTCCAATACGCTTTAGAAAATTCAAGTAAATAACAAAAGA-AA-ATACTAACTGTTGACAATCT
103151 CAGCAGAGCTCTTGTACTTGGTAACAACTTCAGAGGAGGTGAGATCCAGCTCCTTCTCCTCTCCT
64 CAGCAGAGCTCTTGTAC-TGGTAACAACTTCAGAGGAGGTGAGATCCAGCTCCTTCTCCTCTCCT
103216 CATATTTTCCGACATCGTTTCCAGAGCTTATAAAAACCTATAAAAATTCCTTAAAAAATAAAATA
128 CATATTTTCCGACATCGTTTCCAGAGCTTATAAAAACCTATAAAAATTCCTTAAAAAATAAAATA
103281 AAAAAGATATCAGTGAACGTCAAAGAAGATA
193 AAAAAGATATCAGTGAACGTCAAAGAAGATA
103312 CTGAGAAAAG
Statistics
Matches: 220, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
249 41 0.19
250 1 0.00
251 37 0.17
252 126 0.57
253 15 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (250 bp):
TTTCCAATACGCTTTAGAAAATTCAAGTAAATAACAAAAGAAAATACTAACTGTTGACAATCTCA
GCAGAGCTCTTGTACTGGTAACAACTTCAGAGGAGGTGAGATCCAGCTCCTTCTCCTCTCCTCAT
ATTTTCCGACATCGTTTCCAGAGCTTATAAAAACCTATAAAAATTCCTTAAAAAATAAAATAAAA
AAGATATCAGTGAACGTCAAAGAAGATAAAACTACGGTAAAGAGAGAAAGGAGCC
Found at i:104961 original size:28 final size:27
Alignment explanation
Indices: 104901--104974 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
104891 GAGATGGGCT
*
104901 TAAAATTTTATGTTAGAAATGAATTTA
1 TAAAATTTTATATTAGAAATGAATTTA
104928 TAAAATTTTATATTAGAGAATGAATTTA
1 TAAAATTTTATATTAGA-AATGAATTTA
* *
104956 TGAAATTTTATCTTA-AAAT
1 TAAAATTTTATATTAGAAAT
104975 CTTACAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 17 0.40
28 23 0.53
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (27 bp):
TAAAATTTTATATTAGAAATGAATTTA
Found at i:105095 original size:2 final size:2
Alignment explanation
Indices: 105090--105133 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
105080 GTTTTCTTGA
105090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105132 AT
1 AT
105134 GTTTGTTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114398 original size:19 final size:19
Alignment explanation
Indices: 114374--114411 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
114364 CTCTATTTAA
114374 AAAAAATAATTAAAAATAT
1 AAAAAATAATTAAAAATAT
* *
114393 AAAAAATTATTTAAAATAT
1 AAAAAATAATTAAAAATAT
114412 TTAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATAATTAAAAATAT
Done.