Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007556.1 Hibiscus syriacus cultivar Beakdansim tig00021262_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: 138814
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:178 original size:21 final size:22
Alignment explanation
Indices: 132--185 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
122 TCATAATATT
* *
132 TAAAAA-ATTAAATAACAATAC
1 TAAAAACATTTAATAACAAAAC
*
153 CAAAAACATTTAATAA-AAAAC
1 TAAAAACATTTAATAACAAAAC
174 TAAAAACATTTA
1 TAAAAACATTTA
186 GGTTGAACCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAACATTTAATAACAAAAC
Found at i:2435 original size:15 final size:15
Alignment explanation
Indices: 2415--2443 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2405 TAACATCTCT
2415 AATAACAACGACTCC
1 AATAACAACGACTCC
2430 AATAACAACGACTC
1 AATAACAACGACTC
2444 GATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.31, G:0.07, T:0.14
Consensus pattern (15 bp):
AATAACAACGACTCC
Found at i:3244 original size:18 final size:18
Alignment explanation
Indices: 3218--3268 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
3208 TGTAAATTTG
*
3218 TCCCAAATGACCACTATA
1 TCCCGAATGACCACTATA
* *
3236 TCCCGAATGATCACTATG
1 TCCCGAATGACCACTATA
*
3254 TCCCGAAGGACCACT
1 TCCCGAATGACCACT
3269 CATTAAGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (18 bp):
TCCCGAATGACCACTATA
Found at i:4199 original size:22 final size:21
Alignment explanation
Indices: 4150--4228 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
4140 AAGTTTCTCG
4150 GGTATCGATACCCTCCATATA
1 GGTATCGATACCCTCCATATA
4171 GGTATCGATACCTCTACCATAT-
1 GGTATCGATACC-CT-CCATATA
** * *
4193 GGTATCGAT-CATGTTCATACA
1 GGTATCGATAC-CCTCCATATA
4214 GGTATCGATACCCTC
1 GGTATCGATACCCTC
4229 TGCAACAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 4 0.09
21 24 0.52
22 12 0.26
23 6 0.13
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCCTCCATATA
Found at i:8319 original size:22 final size:21
Alignment explanation
Indices: 8270--8348 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
8260 AAGTTTCCCG
8270 GGTATCGATACCCTCCATATA
1 GGTATCGATACCCTCCATATA
8291 GGTATCGATACCTCTACCATAT-
1 GGTATCGATACC-CT-CCATATA
*** * *
8313 GGTATCGATATTGTTCATACA
1 GGTATCGATACCCTCCATATA
8334 GGTATCGATACCCTC
1 GGTATCGATACCCTC
8349 TGCAACAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 4 0.09
21 24 0.52
22 12 0.26
23 6 0.13
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (21 bp):
GGTATCGATACCCTCCATATA
Found at i:8976 original size:25 final size:25
Alignment explanation
Indices: 8948--8997 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
8938 TTATTAAGGG
*
8948 GAAAAAATCTCTTTTAAGCTTAAAT
1 GAAAAAATCTCTTTTAAGCTGAAAT
8973 GAAAAAATCTCTTTTAAGCTGAAAT
1 GAAAAAATCTCTTTTAAGCTGAAAT
8998 TTCCATAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (25 bp):
GAAAAAATCTCTTTTAAGCTGAAAT
Found at i:10764 original size:21 final size:20
Alignment explanation
Indices: 10735--10773 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
10725 AATATAAATA
* *
10735 TAAATTGAATTAAGAATATTT
1 TAAACTGAAATAA-AATATTT
10756 TAAACTGAAATAAAATAT
1 TAAACTGAAATAAAATAT
10774 ATTATAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAACTGAAATAAAATATTT
Found at i:14009 original size:21 final size:22
Alignment explanation
Indices: 13972--14013 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13962 AGGGAGTGTC
13972 CAAGTGATGGGGCTAGGGGTGG
1 CAAGTGATGGGGCTAGGGGTGG
13994 CAAGT-ATGGTGG-TAGGGGTG
1 CAAGTGATGG-GGCTAGGGGTG
14014 ATCGTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.19, C:0.07, G:0.52, T:0.21
Consensus pattern (22 bp):
CAAGTGATGGGGCTAGGGGTGG
Found at i:16352 original size:86 final size:86
Alignment explanation
Indices: 16251--16418 Score: 248
Period size: 86 Copynumber: 2.0 Consensus size: 86
16241 TACCTAAACA
* * **
16251 TCCATTCCCAAAGAAATAACACTCTAAAAATAAATGACTTCCACTCTCATCAACACCTT-GACAT
1 TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACA-CTTCGACAT
*
16315 AGTATGCAAGTCTACACCGATC
65 AGTATGCAAATCTACACCGATC
* * *
16337 TCCATTCCCAGAGAAAGAACACTCAAAAAATAAATGACTGATACTCTCATCAACACTTCTACATA
1 TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACACTTCGACATA
16402 GTATGCAAATCTACACC
66 GTATGCAAATCTACACC
16419 CAGTCCCATT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 3 0.04
86 70 0.96
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (86 bp):
TCCATTCCCAAAGAAAGAACACTCAAAAAATAAATGACTGACACTCTCATCAACACTTCGACATA
GTATGCAAATCTACACCGATC
Found at i:18289 original size:63 final size:63
Alignment explanation
Indices: 18190--18317 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
18180 TACCAAGTCT
* *
18190 CAAATTCCCATTATCATGTCCATTGTTTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
1 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
* *
18253 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGACACGGATGCAGATGGAAG
1 CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
18316 CA
1 CA
18318 CATACTTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (63 bp):
CAAATTCCCATTATCATGTCCACTGTCTACATTCCTTTGCTATGAAACGGATGCAAATGGAAG
Found at i:19099 original size:35 final size:35
Alignment explanation
Indices: 19060--19139 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
19050 TTACATTATT
* *
19060 GTGTTTGGTTTGTTTTAAATGAATATATGATTACA
1 GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
* * *
19095 GTGTTTGATTTGTTTGATAGGAATGTATGATTACA
1 GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
19130 GTGTTTGGTT
1 GTGTTTGGTT
19140 AAAGGAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.24, C:0.03, G:0.25, T:0.49
Consensus pattern (35 bp):
GTGTTTGGTTTGTTTGAAAGGAATATATGATTACA
Found at i:23829 original size:42 final size:41
Alignment explanation
Indices: 23756--23850 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
23746 AGCCAAACAA
* * * * *
23756 GATGGCTCACCTTCGCGGTTTAAGTTGGTCTTGATTATTTG
1 GATGACTCCCCTTCGAGGTTTAAATCGGTCTTGATTATTTG
* *
23797 GGTGACTCCCCTTCGAGGTTCTAAATCGGTCTTGATTCTTTG
1 GATGACTCCCCTTCGAGGTT-TAAATCGGTCTTGATTATTTG
23839 GATGACTCCCCT
1 GATGACTCCCCT
23851 CACAGGTCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (41 bp):
GATGACTCCCCTTCGAGGTTTAAATCGGTCTTGATTATTTG
Found at i:24222 original size:34 final size:34
Alignment explanation
Indices: 24037--24288 Score: 143
Period size: 34 Copynumber: 7.2 Consensus size: 34
24027 GGTGGGACAA
**
24037 AAATTTTTCAAGAGAAAATATCTCAAGTTAGATG
1 AAATTTTTCAAGAGAAAATATCTCAAGGGAGATG
* * * * *
24071 AAATTTTGGTTTCGAG-GAAAACTGTCTCGAGTGAGACG
1 AAA--TT--TTTCAAGAGAAAA-TATCTCAAGGGAGATG
*
24109 AAAATTTTTCAAG-G--AATATCTCAAGTGAGATTG
1 -AAATTTTTCAAGAGAAAATATCTCAAGGGAGA-TG
* * * * * * *
24142 AATTTTCGTTCTAAGAGGAATTGTCTCGAGTGAGATA
1 AAATTT--TTC-AAGAGAAAATATCTCAAGGGAGATG
** *
24179 AAAAATTTCAAGAAAAAATATCTCAAGGGAGATG
1 AAATTTTTCAAGAGAAAATATCTCAAGGGAGATG
* * ** ** *
24213 AAATTTTTCAAGAGAAACTGTCTCGTGTAAGACGG
1 AAATTTTTCAAGAGAAAATATCTCAAGGGAGA-TG
*
24248 AAAGTTTTCAAGAGAAAATATCTCAAGGGAGATG
1 AAATTTTTCAAGAGAAAATATCTCAAGGGAGATG
24282 AAATTTT
1 AAATTTT
24289 AGTTTCAAGA
Statistics
Matches: 161, Mismatches: 43, Indels: 28
0.69 0.19 0.12
Matches are distributed among these distances:
32 17 0.11
33 3 0.02
34 54 0.34
35 39 0.24
36 3 0.02
37 11 0.07
38 31 0.19
39 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (34 bp):
AAATTTTTCAAGAGAAAATATCTCAAGGGAGATG
Found at i:24306 original size:141 final size:141
Alignment explanation
Indices: 24032--24344 Score: 377
Period size: 142 Copynumber: 2.2 Consensus size: 141
24022 TATCAGGTGG
** ** *
24032 GACAAAAATTTTTCAAGAGAAAATATCTCAAGTTAGATGAAATTTTGGTTTCGAGGAAAACTGTC
1 GACAAAAAAATTTCAAGAGAAAATATCTCAAGGGAGATGAAA-TTT-GTTTCAAGGAAAACTGTC
* * * * *
24097 TCGAGTGAGACGAAAATTTTTCAAGGAATATCTCAAGTGAGATTGAATTTTCGTTCTAAGAGGAA
64 TCGAGTAAGACGAAAAGTTTTCAAGGAATATCTCAAGGGAGATTGAATTTTAGTTCTAAGAGAAA
24162 TTGTCTCGAGTGA
129 TTGTCTCGAGTGA
* *
24175 GA-TAAAAAATTTCAAGAAAAAATATCTCAAGGGAGATGAAA-TT-TTTCAA-GAGAAACTGTCT
1 GACAAAAAAATTTCAAGAGAAAATATCTCAAGGGAGATGAAATTTGTTTCAAGGA-AAACTGTCT
* *
24236 CGTGTAAGACGGAAAGTTTTCAAGAGAAAATATCTCAAGGGAGA-TGAAATTTTAGTT-TCAAGA
65 CGAGTAAGACGAAAAGTTTTCAAG-G--AATATCTCAAGGGAGATTG-AATTTTAGTTCT-AAGA
24299 GAAATTGTCTCGAGTGA
125 GAAATTGTCTCGAGTGA
*
24316 GACAAAAAAATTTCAAGAGAAACTATCTC
1 GACAAAAAAATTTCAAGAGAAAATATCTC
24345 TAGTGAAACG
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
137 2 0.01
138 34 0.23
139 1 0.01
140 5 0.03
141 46 0.32
142 56 0.38
143 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (141 bp):
GACAAAAAAATTTCAAGAGAAAATATCTCAAGGGAGATGAAATTTGTTTCAAGGAAAACTGTCTC
GAGTAAGACGAAAAGTTTTCAAGGAATATCTCAAGGGAGATTGAATTTTAGTTCTAAGAGAAATT
GTCTCGAGTGA
Found at i:28032 original size:3 final size:3
Alignment explanation
Indices: 28018--28178 Score: 56
Period size: 3 Copynumber: 50.0 Consensus size: 3
28008 GTTATAAGAT
* * * * * * *
28018 TAA TACA TAA TAA TAC TAG TAAA TAT TAA CAA TAC TAA TAC TAA TAC
1 TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
28065 TAA TAA TAA TAA TGAA -AC TGT TAA TAA TAA TAA AAA CTAA TAA TAGG
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A
* * *
28112 TAA TAT TAA TAAA TAA TATA TAA TGACA T-A TAG TAAA TAC TATA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA T-A-A TAA TAA T-AA TAA TA-A TAA
28159 TAA TAGGA TAA TAA TAA TAA
1 TAA TA--A TAA TAA TAA TAA
28179 GTAAGTATAA
Statistics
Matches: 115, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
2 3 0.03
3 85 0.74
4 22 0.19
5 5 0.04
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:28989 original size:30 final size:31
Alignment explanation
Indices: 28955--29020 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
28945 GCCGTAGATT
28955 CCAAAATAAT-TT-TTTGTGTGCCCTATTAAG
1 CCAAAATAATCTTATTTG-GTGCCCTATTAAG
* **
28985 CC-AAATAATCTTATTTGGTGCGCTATTGGG
1 CCAAAATAATCTTATTTGGTGCCCTATTAAG
29015 CCAAAA
1 CCAAAA
29021 ACACCTGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 16 0.53
31 7 0.23
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
CCAAAATAATCTTATTTGGTGCCCTATTAAG
Found at i:31147 original size:40 final size:40
Alignment explanation
Indices: 31069--31147 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
31059 ATGAAAAATG
* * *
31069 CAAGCAACCCAACATTTAATACTTGGAAACTTGAAATTTT
1 CAAGCAACCCAACATTAAATACCTGGAAACTTAAAATTTT
31109 CAAGCAACCCAAC-TTGAAATACCTGGAAA-TTAATAATTT
1 CAAGCAACCCAACATT-AAATACCTGGAAACTTAA-AATTT
31148 GTGTGTTGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (40 bp):
CAAGCAACCCAACATTAAATACCTGGAAACTTAAAATTTT
Found at i:48650 original size:31 final size:28
Alignment explanation
Indices: 48584--48657 Score: 76
Period size: 31 Copynumber: 2.5 Consensus size: 28
48574 TAGAGTGAAA
*
48584 AATATTTTATTTAATTTAAAAAATATAAT
1 AATATTTTATAT-ATTTAAAAAATATAAT
**
48613 TTTATTTTATATATTTAAAAATAATTATAAT
1 AATATTTTATATATTT-AAAA-AA-TATAAT
*
48644 AATATTTTTTATAT
1 AATATTTTATATAT
48658 ATTATTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.11
29 13 0.36
30 2 0.06
31 17 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTTTATATATTTAAAAAATATAAT
Found at i:49217 original size:12 final size:12
Alignment explanation
Indices: 49200--49237 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
49190 GTCTTTTATT
49200 AGGCTGGGTGTA
1 AGGCTGGGTGTA
49212 AGGCTGGGTGTA
1 AGGCTGGGTGTA
*
49224 AGGATGGGTAGTA
1 AGGCTGGGT-GTA
49237 A
1 A
49238 TCAGGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.24, C:0.05, G:0.47, T:0.24
Consensus pattern (12 bp):
AGGCTGGGTGTA
Found at i:49823 original size:25 final size:25
Alignment explanation
Indices: 49795--49842 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
49785 TCAATAATTT
49795 TTTTAAAAATATATAAA-ATTTATAA
1 TTTTAAAAAT-TATAAATATTTATAA
**
49820 TTTTTTAAATTATAAATATTTAT
1 TTTTAAAAATTATAAATATTTAT
49843 CATCACCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAAATTATAAATATTTATAA
Found at i:50335 original size:343 final size:340
Alignment explanation
Indices: 49702--50525 Score: 1241
Period size: 343 Copynumber: 2.4 Consensus size: 340
49692 AAAAATATTG
49702 AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
* * *
49767 AATAATTAATTTTAAAAG-TCAATAATTTTTTTAAAAATATATAAAATTTATAATTTTTTAAATT
66 AATAATTAATTTTAAAAGAT-AAT-ATTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATT
* *
49831 AT--AAA-TA-T-TTATCATCACCATCGTCATTTTGTAAAAGAAATATTAGTTATAAAACTTTTA
129 ATAAAAATTATTATTATCATCACCATCATCATTTTGTAAAAGAAATAGTAGTTATAAAACTTTTA
* *
49891 TAAAATTATTTATATTTTAAAATACTTACCATCAAAGTTTTTATATACTAGATTATATGTATTGT
194 TAAAATTATTCATATTTTAAAATACTTACCATCAAAGTTTTTATATACTAGATTATACGTATTGT
* ** * *
49956 GTAATTTTAATATAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAATTGTTGTTA
259 GTAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTAGTAATTGTTGTTA
*
50021 AAAATTAAAAATTAATA
324 AAAAATAAAAATTAATA
*
50038 AATAATAATTCATTTGATCCCTCAATTATAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
1 AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
50103 AATAATTAATTTTAAAAGATAATATTTTTTTCCAAAATATATGAAATTTATAATTTTTAAAATTA
66 AATAATTAATTTTAAAAGATAATATTTTTTT-CAAAATATATGAAATTTATAATTTTTAAAATTA
* *
50168 TAAAATATTTATTATTATCATTATCATCATCATTTTGTAAAAGAAATAGTAGTTATAAAACTTTT
130 TAAAA-A-TTATTATTATCATCACCATCATCATTTTGTAAAAGAAATAGTAGTTATAAAACTTTT
* * *
50233 ATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCT-TATATTATATTATACGTATT
193 ATAAAATTATTCATATTTTAAAATACTTACCATCAAAGTTTT-TATATACTAGATTATACGTATT
* *
50297 GTGTAATTTTAATGCAAAACTCAAAATAATTTTATTAAAAATAAATAAACATTAGTAATTGTTGT
257 GTGTAATTTTAATACAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTAGTAATTGTTGT
*
50362 TAAAAAATAAAAATTAATG
322 TAAAAAATAAAAATTAATA
* *** * * * *
50381 AATAATAATTCATTTAATTTATTAATTGTAATTAAAAATTTAATTTAATATTTTTTATACTTTTA
1 AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
*
50446 AATAATTAATTTTAAAAGAAAATA-TTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
66 AATAATTAATTTTAAAAGATAATATTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
50510 AAAAAAATTATTATTA
131 --AAAAATTATTATTA
50526 AAAAAAATAA
Statistics
Matches: 444, Mismatches: 32, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
335 8 0.02
336 116 0.26
337 1 0.00
338 2 0.00
339 1 0.00
341 45 0.10
342 8 0.02
343 262 0.59
344 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (340 bp):
AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
AATAATTAATTTTAAAAGATAATATTTTTTTCAAAATATATGAAATTTATAATTTTTAAAATTAT
AAAAATTATTATTATCATCACCATCATCATTTTGTAAAAGAAATAGTAGTTATAAAACTTTTATA
AAATTATTCATATTTTAAAATACTTACCATCAAAGTTTTTATATACTAGATTATACGTATTGTGT
AATTTTAATACAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTAGTAATTGTTGTTAAA
AAATAAAAATTAATA
Found at i:55187 original size:5 final size:5
Alignment explanation
Indices: 55177--55214 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
55167 ATCATCTTCT
* *
55177 TTTTA TTTTA TTTTA TTTTA TTTTA TATTA TTATA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
55215 CTGTACCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:55995 original size:31 final size:31
Alignment explanation
Indices: 55957--56030 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
55947 ATTTGTACAC
* ** *
55957 TTTTGGTCATTTATGTTATCGTTTTATTATG
1 TTTTGGTCACTTACATTATCGTTTTATTAAG
55988 TTTTGGTCACTTACATTATCGTTTTATTAAG
1 TTTTGGTCACTTACATTATCGTTTTATTAAG
56019 TTTTGGTCACTT
1 TTTTGGTCACTT
56031 GGACGTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.11, G:0.15, T:0.57
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCGTTTTATTAAG
Found at i:56795 original size:31 final size:31
Alignment explanation
Indices: 56757--56825 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
56747 TTTTCGAGTG
* *
56757 ACCAAAACTTAACAAAACGATAACGTAAGTA
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
* *
56788 ACCAAAACTTAATAAAACGATAAAGTAAATG
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
56819 ACCAAAA
1 ACCAAAA
56826 GTGTACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.16
Consensus pattern (31 bp):
ACCAAAACTTAACAAAACGATAAAGTAAATA
Found at i:59454 original size:5 final size:5
Alignment explanation
Indices: 59444--59481 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
59434 ATCATCTTCT
* *
59444 TTTTA TTTTA TTTTA TTTTA TTTTA TATTA TTATA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
59482 CTGTACCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:60265 original size:31 final size:31
Alignment explanation
Indices: 60227--60300 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
60217 ATTTGTACAC
* ** *
60227 TTTTGGTCATTTATGTTATCGTTTTATTATG
1 TTTTGGTCACTTACATTATCGTTTTATTAAG
60258 TTTTGGTCACTTACATTATCGTTTTATTAAG
1 TTTTGGTCACTTACATTATCGTTTTATTAAG
60289 TTTTGGTCACTT
1 TTTTGGTCACTT
60301 GGACGTTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.18, C:0.11, G:0.15, T:0.57
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCGTTTTATTAAG
Found at i:61065 original size:31 final size:31
Alignment explanation
Indices: 61027--61095 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
61017 TTTTCGAGTG
* *
61027 ACCAAAACTTAACAAAACGATAACGTAAGTA
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
* *
61058 ACCAAAACTTAATAAAACGATAAAGTAAATG
1 ACCAAAACTTAACAAAACGATAAAGTAAATA
61089 ACCAAAA
1 ACCAAAA
61096 GTGTACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.58, C:0.17, G:0.09, T:0.16
Consensus pattern (31 bp):
ACCAAAACTTAACAAAACGATAAAGTAAATA
Found at i:73578 original size:16 final size:16
Alignment explanation
Indices: 73557--73589 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
73547 TACTATTTAC
*
73557 GTGAATAGTGAATTTT
1 GTGAATAGTGAAATTT
73573 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
73589 G
1 G
73590 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.39
Consensus pattern (16 bp):
GTGAATAGTGAAATTT
Found at i:81041 original size:23 final size:23
Alignment explanation
Indices: 81009--81063 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
80999 GACGAACGTA
* * *
81009 TAAACAAATATATTTATAAACAT
1 TAAACGAATATACTCATAAACAT
* *
81032 TAAACGAATATGCTCATAAATAT
1 TAAACGAATATACTCATAAACAT
81055 TAAACGAAT
1 TAAACGAAT
81064 CGAACATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (23 bp):
TAAACGAATATACTCATAAACAT
Found at i:81612 original size:20 final size:20
Alignment explanation
Indices: 81589--81640 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
81579 AACGCGATCC
81589 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
81609 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
81629 CCAAAATCGCAA
1 CCAGAATCGCAA
81641 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:81657 original size:21 final size:20
Alignment explanation
Indices: 81631--81728 Score: 70
Period size: 21 Copynumber: 4.8 Consensus size: 20
81621 ATCAGTTTCC
81631 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * * *
81652 AAAATCGCGATGCGATAGTAG
1 AAAATCGCAACGCGAT-TTTG
* ** *
81673 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
81694 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
81714 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
81729 ACACATAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 15 0.26
21 42 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:81721 original size:20 final size:20
Alignment explanation
Indices: 81696--81889 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
81686 GATTTTCCAT
* *
81696 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
81716 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
81736 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
81756 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
81776 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
81796 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
81816 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
81836 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
81857 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
81877 AATCGCAACGCGA
1 AATCGCAACGCGA
81890 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:81741 original size:40 final size:39
Alignment explanation
Indices: 81692--81889 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
81682 TTGCGATTTT
* ** *
81692 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
81730 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
81771 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
81811 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
81850 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
81890 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:81779 original size:60 final size:60
Alignment explanation
Indices: 81696--81888 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
81686 GATTTTCCAT
* ** * *
81696 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
81756 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
81816 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
81877 AATCGCAACGCG
1 AATCGCAACGCG
81889 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:82308 original size:33 final size:33
Alignment explanation
Indices: 82269--82339 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82259 TTCACTTAGA
*
82269 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
82302 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
82335 TTTCA
1 TTTCA
82340 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:82479 original size:14 final size:14
Alignment explanation
Indices: 82460--82514 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
82450 AGAATGACTG
82460 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
82474 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
82493 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
82507 TCGCAACG
1 TCGCAACG
82515 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:82497 original size:33 final size:33
Alignment explanation
Indices: 82460--82530 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
82450 AGAATGACTG
**
82460 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82493 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82526 TCGCA
1 TCGCA
82531 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:82548 original size:19 final size:19
Alignment explanation
Indices: 82526--82623 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
82516 GAAACCAAAA
*
82526 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82545 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
82559 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82578 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
82592 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
82611 TCGCGTTGCGATT
1 TCGCGTTGCGATT
82624 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:82567 original size:14 final size:14
Alignment explanation
Indices: 82548--82637 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
82538 TTTCATTTCG
82548 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
82562 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
82581 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
82595 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
82612 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
82628 CGTTGCGATT
1 CGTTGCGATT
82638 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:82573 original size:33 final size:33
Alignment explanation
Indices: 82531--82645 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
82521 CAAAATCGCA
82531 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
82564 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
82597 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
82630 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
82646 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:84759 original size:93 final size:93
Alignment explanation
Indices: 84341--84904 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
84331 TAGATTGCTT
*
84341 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84406 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84434 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84498 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84526 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84590 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84617 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84682 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84710 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84775 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84803 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84868 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84896 AGTAAATTT
1 AGTAAATTT
84905 ATCCATTCAA
Statistics
Matches: 468, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 79 0.17
92 116 0.25
93 273 0.58
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:84988 original size:19 final size:19
Alignment explanation
Indices: 84948--85076 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
84938 TAGTTTACTT
* *
84948 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
84968 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
84987 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
85006 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
85020 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
85039 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
85053 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
85072 TCGCA
1 TCGCA
85077 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:85027 original size:33 final size:32
Alignment explanation
Indices: 84984--85076 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
84974 CGCGAAACCA
**
84984 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
85016 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
85049 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
85077 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:85074 original size:52 final size:52
Alignment explanation
Indices: 84948--85076 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
84938 TAGTTTACTT
**
84948 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
85000 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
85053 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
85077 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:85094 original size:19 final size:19
Alignment explanation
Indices: 85072--85206 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
85062 GAAACCAAAA
*
85072 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
85091 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
85107 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
85124 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
85140 T--CGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
85157 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
85176 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
85196 TCGTGTTGCGA
1 TCGCGTTGCGA
85207 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 10 0.11
17 11 0.12
19 46 0.49
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:85113 original size:14 final size:14
Alignment explanation
Indices: 85094--85150 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
85084 TTTCATTTCG
85094 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
85108 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
85125 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
85141 CGTTGCGATT
1 CGTTGCGATT
85151 TTAATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:85119 original size:33 final size:33
Alignment explanation
Indices: 85077--85169 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
85067 CAAAATCGCA
*
85077 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
85110 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
85143 TTGCGATTTTAATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
85170 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:87151 original size:14 final size:14
Alignment explanation
Indices: 87129--87165 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
87119 GATTGTTTAA
87129 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
87143 ATT-ATTTGTAAAAG
1 -TTGATTTGTAAAAG
87157 TTGATTTGT
1 TTGATTTGT
87166 GTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:87287 original size:19 final size:19
Alignment explanation
Indices: 87271--87372 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
87261 CAAAATGACT
87271 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
87309 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
87323 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87342 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
87362 ATCGCAATGCG
1 ATCGCAATGCG
87373 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:87425 original size:19 final size:19
Alignment explanation
Indices: 87401--87660 Score: 344
Period size: 19 Copynumber: 14.7 Consensus size: 19
87391 GATTATCTCG
87401 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87420 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87439 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
87453 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87472 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87491 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87510 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
87524 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87543 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87562 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
87576 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87595 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87614 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
87628 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
87648 TTGCGATTTTCAT
1 TTGCGATTTTCAT
87661 GTTGGGATTT
Statistics
Matches: 214, Mismatches: 6, Indels: 41
0.82 0.02 0.16
Matches are distributed among these distances:
14 24 0.11
16 29 0.14
17 27 0.13
18 2 0.01
19 119 0.56
20 13 0.06
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:87441 original size:52 final size:49
Alignment explanation
Indices: 87379--87688 Score: 298
Period size: 52 Copynumber: 5.9 Consensus size: 49
87369 TGCGTTTATA
*
87379 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-T-TCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
*
87431 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-T-TTTCGTTGCGA-TTTCATTTCGCGTTGCGATTTTC
* * *
87483 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTCTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATTTC-G-CGTTGCGATTTTC
* * * *
87535 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* * * *
87587 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCGTTGCG-ATTTC-ATT-TCGCGTTGCGATTTTC
* *
87639 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTACGATT
1 ATTT-CGCATTGCGATTTTC--GTTGCGA-TTTCATTTCGCGTTGCGATT
87689 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 11, Indels: 23
0.87 0.04 0.09
Matches are distributed among these distances:
50 14 0.06
51 4 0.02
52 175 0.74
53 29 0.12
54 7 0.03
55 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (49 bp):
ATTTCGCATTGCGATTTTCGTTGCGATTTCATTTCGCGTTGCGATTTTC
Found at i:87476 original size:71 final size:71
Alignment explanation
Indices: 87401--87688 Score: 366
Period size: 71 Copynumber: 4.1 Consensus size: 71
87391 GATTATCTCG
87401 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
87466 TTCGCA
66 TTCGCA
*
87472 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
87537 TTCGCA
66 TTCGCA
*
87543 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATT
87603 TTCATTTCGCA
61 TTCATTTCGCA
* *
87614 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTTTC--GTTGCGATTTT
*
87672 CATTTCGCG
63 CATTTCGCA
*
87681 TTACGATT
1 TTGCGATT
87689 GTATTTTCCG
Statistics
Matches: 194, Mismatches: 8, Indels: 32
0.83 0.03 0.14
Matches are distributed among these distances:
66 12 0.06
67 26 0.13
68 14 0.07
69 14 0.07
70 2 0.01
71 120 0.62
72 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:89989 original size:12 final size:12
Alignment explanation
Indices: 89972--89996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89962 TCTTCGGGGA
89972 CTTTTTCTTCTT
1 CTTTTTCTTCTT
89984 CTTTTTCTTCTT
1 CTTTTTCTTCTT
89996 C
1 C
89997 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:90205 original size:24 final size:24
Alignment explanation
Indices: 90171--90217 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
90161 CTGAAACATC
90171 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
90195 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
90218 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:90928 original size:20 final size:20
Alignment explanation
Indices: 90900--91268 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
90890 AAATTTCAGT
* * * *
90900 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
90920 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
90940 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
90960 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
90980 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91000 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
91020 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
91040 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91060 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91080 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
91100 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
91120 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91140 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
91160 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
91180 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
91200 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
91220 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
91240 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
91260 GTTGCGATT
1 GTTGCGATT
91269 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:102242 original size:18 final size:18
Alignment explanation
Indices: 102219--102269 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
102209 AGGAAAACTT
102219 AATTATTATTGTTATTTA
1 AATTATTATTGTTATTTA
* *
102237 AATTA-TAGTTATAATTTA
1 AATTATTA-TTGTTATTTA
*
102255 AATAATTATTGTTAT
1 AATTATTATTGTTAT
102270 CGTTAGTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
AATTATTATTGTTATTTA
Found at i:103487 original size:32 final size:32
Alignment explanation
Indices: 103421--103488 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
103411 TATTAAGGGA
* *
103421 TAAAAGCAAAAATAAAATAATAGATGGATGAC
1 TAAAAGAAAAAATAAAATAATAGATGAATGAC
*
103453 TAAAAGAAAAAATAAAATAATA-ATTGAATTAC
1 TAAAAGAAAAAATAAAATAATAGA-TGAATGAC
103485 TAAA
1 TAAA
103489 TAAGCAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.22
Consensus pattern (32 bp):
TAAAAGAAAAAATAAAATAATAGATGAATGAC
Found at i:114112 original size:6 final size:6
Alignment explanation
Indices: 114101--114137 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
114091 TCTTATATCA
114101 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT T
114138 TTAATAACTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:114196 original size:23 final size:23
Alignment explanation
Indices: 114150--114193 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
114140 AATAACTTAT
*
114150 TCTTTATGACACGTTTTCTATTA
1 TCTTTATGACACGTTTTCAATTA
*
114173 TCTTT-TGTCACGTTTTCAATT
1 TCTTTATGACACGTTTTCAATT
114194 TATTGATCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (23 bp):
TCTTTATGACACGTTTTCAATTA
Found at i:116832 original size:59 final size:60
Alignment explanation
Indices: 116699--116835 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 60
116689 AACATAATGA
* * **
116699 ATAGTTGGGTGACCATTTTATAACTTTTAATAGTAGAGAGACTCAACAAAGCAACATTTT
1 ATAGTCGGGTGACCATTTTATAACTTTTAATAGTAGAAAGACTCAACAAAGCAACACCTT
* * * * *
116759 ATAGTCAGAG-GACCATTTTATAAC-TTTAATAGTCA-AAAGACTTAATAAAGTAATACCTT
1 ATAGTC-GGGTGACCATTTTATAACTTTTAATAGT-AGAAAGACTCAACAAAGCAACACCTT
116818 ATAGTCGGGTGACCATTT
1 ATAGTCGGGTGACCATTT
116836 GTGTACATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 40 0.62
60 20 0.31
61 2 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (60 bp):
ATAGTCGGGTGACCATTTTATAACTTTTAATAGTAGAAAGACTCAACAAAGCAACACCTT
Found at i:120518 original size:17 final size:17
Alignment explanation
Indices: 120496--120541 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
120486 ACTCATAGGG
120496 AGGAGATGCACAGTATA
1 AGGAGATGCACAGTATA
120513 AGGAGATGCACAGTATA
1 AGGAGATGCACAGTATA
120530 AGGAGAT-CACAG
1 AGGAGATGCACAG
120542 AGAGTACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.17
17 24 0.83
ACGTcount: A:0.41, C:0.13, G:0.30, T:0.15
Consensus pattern (17 bp):
AGGAGATGCACAGTATA
Found at i:121276 original size:5 final size:5
Alignment explanation
Indices: 121257--121453 Score: 65
Period size: 5 Copynumber: 39.4 Consensus size: 5
121247 GATTCATTTA
* * * * *
121257 TTATT TTATT ATTATT TTATT TT-TT AT-TT TTATT TAATG TT-TT CTCTT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
* *
121305 TGA-T TTATTT TTATT TATATAT ATT-TT TTATT TTTTT TTATCT TATATAT
1 TTATT TTA-TT TTATT T-TAT-T -TTATT TTATT TTATT TTAT-T T-TAT-T
* * ** * * *
121355 ATATT TT-TT TTACAT TT-TT TCCTT TGA-T TTATT TGA-T ATATTT TTATT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTAT-T TTATT
* * *
121403 TTATT TTATT TTCCTT TGA-T TTA-T TTATC TTATT TTATT TTATT TTATT
1 TTATT TTATT TT-ATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
121452 TT
1 TT
121454 TTCTCCTTTT
Statistics
Matches: 141, Mismatches: 32, Indels: 38
0.67 0.15 0.18
Matches are distributed among these distances:
4 31 0.22
5 75 0.53
6 28 0.20
7 6 0.04
8 1 0.01
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:121281 original size:18 final size:19
Alignment explanation
Indices: 121253--121291 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
121243 CTTTGATTCA
121253 TTTATTATTTTATTATTAT
1 TTTATTATTTTATTATTAT
*
121272 TTTATT-TTTTATTTTTAT
1 TTTATTATTTTATTATTAT
121290 TT
1 TT
121292 AATGTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTATTATTTTATTATTAT
Found at i:121352 original size:28 final size:28
Alignment explanation
Indices: 121307--121366 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
121297 TTTCTCTTTG
121307 ATTTATTTTTATTTATATATAT-TTTTT
1 ATTTATTTTTATTTATATATATATTTTT
*
121334 ATTTTTTTTTATCTTATATATATATTTTT
1 ATTTATTTTTAT-TTATATATATATTTTT
121363 -TTTA
1 ATTTA
121367 CATTTTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.38
28 13 0.45
29 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (28 bp):
ATTTATTTTTATTTATATATATATTTTT
Found at i:121404 original size:6 final size:5
Alignment explanation
Indices: 121396--121453 Score: 66
Period size: 5 Copynumber: 11.8 Consensus size: 5
121386 TTTGATATAT
* * *
121396 TTTTA TTTTA TTTTA TTTTCC TTTGA -TTTA -TTTA TCTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
121445 TTTTA TTTT
1 TTTTA TTTT
121454 TTCTCCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 7 0.16
5 35 0.78
6 3 0.07
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:121413 original size:83 final size:83
Alignment explanation
Indices: 121303--121510 Score: 200
Period size: 83 Copynumber: 2.5 Consensus size: 83
121293 ATGTTTTCTC
* *
121303 TTTGATTTATTTTTA-TTTATATATATTTT-TTAT-TTTTTTTTATCTTATATATATATTTT-TT
1 TTTGA-TTATTTTTATTTTATATATATTTTCTT-TGATTTATTTATCTTAT-T-T-TATTTTATT
121364 TTACATTTTT-TCC-TTTGATTTA
61 TTA-ATTTTTCTCCTTTTGATTTA
*
121386 TTTGATATATTTTTATTTTAT-TTTATTTTCCTTTGATTTATTTATCTTATTTTATTTTATTTTA
1 TTTGAT-TATTTTTATTTTATATATATTTT-CTTTGATTTATTTATCTTATTTTATTTTATTTTA
*
121450 TTTTTTCTCCTTTTGATTTA
64 ATTTTTCTCCTTTTGATTTA
* * * *
121470 TTATTATTATTATTATTTTATGT-T-TTTTCCTTGATTTATTT
1 TT-TGATTATTTTTATTTTATATATATTTTCTTTGATTTATTT
121511 CAAATTTATG
Statistics
Matches: 108, Mismatches: 7, Indels: 21
0.79 0.05 0.15
Matches are distributed among these distances:
82 24 0.22
83 33 0.31
84 32 0.30
85 19 0.18
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (83 bp):
TTTGATTATTTTTATTTTATATATATTTTCTTTGATTTATTTATCTTATTTTATTTTATTTTAAT
TTTTCTCCTTTTGATTTA
Found at i:121425 original size:40 final size:38
Alignment explanation
Indices: 121272--121510 Score: 158
Period size: 39 Copynumber: 6.2 Consensus size: 38
121262 TTATTATTAT
* * * *
121272 TTTATTTTTTATTTTTATTTAATGTT-TTCT-CTTTGA
1 TTTATTTATTATTTTTATTTTATTTTATTTTCCTTTGA
* * *
121308 TTTATTT-TTATTTATATATATT-TTTTATTTT-TTTTTA
1 TTTATTTATTATTT-T-TATTTTATTTTATTTTCCTTTGA
* **
121345 TCTTATATA-TATATTTT-TTTTACATT-TTTTCCTTTGA
1 T-TTATTTATTAT-TTTTATTTTATTTTATTTTCCTTTGA
121382 TTTATTTGATATATTTTTATTTTATTTTATTTTCCTTTGA
1 TTTATTT-AT-TATTTTTATTTTATTTTATTTTCCTTTGA
121422 TTTATTTATCT-TATTTTATTTTATTTTATTTTTTCTCCTTTTGA
1 TTTATTTAT-TAT-TTTTATTTTATTTTA---TTT-TCC-TTTGA
* *
121466 TTTATTATTATTATTATTATTTTATGTT-TTTTCC-TTGA
1 TTTA-T-TTATTATTTTTATTTTATTTTATTTTCCTTTGA
121504 TTTATTT
1 TTTATTT
121511 CAAATTTATG
Statistics
Matches: 163, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
35 6 0.04
36 25 0.15
37 22 0.13
38 22 0.13
39 30 0.18
40 21 0.13
41 3 0.02
42 3 0.02
43 3 0.02
44 9 0.06
45 14 0.09
46 5 0.03
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (38 bp):
TTTATTTATTATTTTTATTTTATTTTATTTTCCTTTGA
Found at i:121444 original size:44 final size:39
Alignment explanation
Indices: 121341--121510 Score: 161
Period size: 40 Copynumber: 4.2 Consensus size: 39
121331 TTTATTTTTT
**
121341 TTTATCTTATATATATATTTT-TTTTACATTTTTTCCTTTGA
1 TTTAT-TTAT-TAT-TATTTTATTTTATTTTTTTTCCTTTGA
121382 TTTATTTGA-TA-TATTTTTATTTTATTTTATTTTCCTTTGA
1 TTTATTT-ATTATTA-TTTTATTTTATTTT-TTTTCCTTTGA
*
121422 TTTATTTATCTTATTTTATTTTATTTTATTTTTTCTCCTTTTGA
1 TTTATTTA--TTA--TTATTTTATTTTATTTTTTTTCC-TTTGA
*
121466 TTTA-TTATTATTATTATTATTTTATGTTTTTTCC-TTGA
1 TTTATTTATTATTATT-TTATTTTATTTTTTTTCCTTTGA
121504 TTTATTT
1 TTTATTT
121511 CAAATTTATG
Statistics
Matches: 111, Mismatches: 5, Indels: 28
0.77 0.03 0.19
Matches are distributed among these distances:
37 2 0.02
38 12 0.11
39 17 0.15
40 36 0.32
41 9 0.08
42 2 0.02
43 8 0.07
44 23 0.21
45 2 0.02
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (39 bp):
TTTATTTATTATTATTTTATTTTATTTTTTTTCCTTTGA
Found at i:125856 original size:60 final size:61
Alignment explanation
Indices: 125729--125860 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 61
125719 AATTGGGGAT
* * * *
125729 CAATATAGAATGAGAGTCATAGTTTGGGGGATGACATTATAATGTTCAAAAGTTTAGGAAC
1 CAATTTAGAATGAGAGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGAAC
** *
125790 TGATTTAGAATGAGAGTCATAGTTT-GAGAATGTA-ATTGGAATGTTCAAAAGTTTA-GAACC
1 CAATTTAGAATGAGAGTCATAGTTTGGAGAATG-ACATTAGAATGTTCAAAAGTTTAGGAA-C
125850 CAATTTAGAAT
1 CAATTTAGAAT
125861 AAAGGTCATA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.05
60 34 0.57
61 23 0.38
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (61 bp):
CAATTTAGAATGAGAGTCATAGTTTGGAGAATGACATTAGAATGTTCAAAAGTTTAGGAAC
Found at i:129720 original size:37 final size:38
Alignment explanation
Indices: 129657--129732 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
129647 AGTGACGGTG
* *
129657 AGGGTGTCTCTGAAAAATCTCGAGTTCATAATCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
* **
129695 AGGGTGT-TCAGAAGAATCCCGAGTTCATTGTCTATTC
1 AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
129732 A
1 A
129733 TTGATTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (38 bp):
AGGGTGTCTCAGAAAAATCCCGAGTTCATAATCTATTC
Found at i:133939 original size:12 final size:12
Alignment explanation
Indices: 133922--133947 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
133912 GAGTAAAATC
133922 GAAGCCGAACTT
1 GAAGCCGAACTT
133934 GAAGCCGAACTT
1 GAAGCCGAACTT
133946 GA
1 GA
133948 GAGGTTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (12 bp):
GAAGCCGAACTT
Done.