Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004327.1 Hibiscus syriacus cultivar Beakdansim tig00009486_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: 139079
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:273 original size:121 final size:120
Alignment explanation
Indices: 40--577 Score: 567
Period size: 111 Copynumber: 4.6 Consensus size: 120
30 ATGGATTTGA
*
40 GCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTT-TCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * *
104 TTATGAACTTCCTCTGGAAAAGTGTGTGCTAATCTATCTCCTTCTGTGATAGAGTCAT
66 TTATGAACTTTCTCTGG--AAGAGTATGCTAATCTATCTCCTTCTGTGAT-GAGTCAT
*
162 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
226 TTATGAAACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGAT-AGTCAT
66 TTATG-AACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGATGAGTCAT
* * *
281 GCAAAAGGTTGAACAAGTTCTTCTC---ATGAACTTC-TCTTCCTCTTCATATGAGTTTTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * ** * * *
342 TTATGAACTTTCTCTGG-A-A--ATGCTGATCCA--T-C--AAGTGAGGATTTGA-
66 TTATGAACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGATGA-GTCAT
388 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
* * ** * *
453 TTATGAACTTTCTCTGG-A-A--ATG-TGATCCA--T-C--AAGTGATGGATTGA-
66 TTATGAACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGAT-GAGTCAT
498 GCAAAAGGTTGGAAC-AGCTCTTCTCATTATGAACTTCTTCTCTTCTTCTTCTTCAGATGAGTTC
1 GCAAAAGGTT-GAACAAGCTCTTCTCATTATGAACTTC-T-TCTTC--C-TCTTCAGATGAGTTC
562 TTTCTCATTATGAACT
60 -TTCTCATTATGAACT
578 CTACCTGGAA
Statistics
Matches: 381, Mismatches: 18, Indels: 40
0.87 0.04 0.09
Matches are distributed among these distances:
106 4 0.01
107 25 0.07
108 3 0.01
109 1 0.00
110 60 0.16
111 63 0.17
112 5 0.01
113 1 0.00
114 2 0.01
115 28 0.07
116 52 0.14
119 31 0.08
121 50 0.13
122 45 0.12
123 11 0.03
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (120 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGATGAGTCAT
Found at i:517 original size:110 final size:110
Alignment explanation
Indices: 281--591 Score: 447
Period size: 110 Copynumber: 2.8 Consensus size: 110
271 TGATAGTCAT
* * *
281 GCAAAAGGTTGAACAAGTTCTTCTC---ATGAACTTC-TCTTCCTCTTCATATGAGTTTTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
342 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGAGGATTTGA
66 TTATGAACTTTCTCTGGAAATG-TGATCCATCAAGTGAGGATTTGA
388 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
453 TTATGAACTTTCTCTGGAAATGTGATCCATCAAGTGATGGA-TTGA
66 TTATGAACTTTCTCTGGAAATGTGATCCATCAAGTGA-GGATTTGA
498 GCAAAAGGTTGGAAC-AGCTCTTCTCATTATGAACTTCTTCTCTTCTTCTTCTTCAGATGAGTTC
1 GCAAAAGGTT-GAACAAGCTCTTCTCATTATGAACTTC-T-TCTTC--C-TCTTCAGATGAGTTC
*
562 TTTCTCATTATGAACTCTAC-CTGGAAATGT
60 -TTCTCATTATGAACT-TTCTCTGGAAATGT
592 TTTAAGAAAG
Statistics
Matches: 187, Mismatches: 4, Indels: 17
0.90 0.02 0.08
Matches are distributed among these distances:
107 24 0.13
110 60 0.32
111 55 0.29
112 5 0.03
114 1 0.01
115 15 0.08
116 25 0.13
117 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (110 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAATGTGATCCATCAAGTGAGGATTTGA
Found at i:560 original size:226 final size:225
Alignment explanation
Indices: 162--590 Score: 547
Period size: 226 Copynumber: 1.9 Consensus size: 225
152 ATAGAGTCAT
*
162 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCTCTTCAGATGAGTTCTTCTCAT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTCTTCAGATGAGTTCTTCTCAT
* ** **
227 TATGAAACTTTCTCTGGAAGAGTATGCTAATCTATCTCCTTCTGTGATAGTCATGCAAAAGGTTG
66 TATGAAACTTTCTCTGGAAGAG-ATGCTAATCCATCAACTGATGTGATA-TCATGCAAAAGGTTG
* * *
292 AACAAGTTCTTCTCATGAACTTCTCTTCCTCTTCATATGAGTT-TTTCTCATTATGAACT-TTCT
129 AACAAGCTCTTCTCATGAACTTCTCTTCCTCTTCAGATGAGTTCTTTCTCATTATGAACTCTAC-
355 CTGGAAATGCTGATCCATCAAGTGAGGATTTGA
193 CTGGAAATGCTGATCCATCAAGTGAGGATTTGA
388 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-TTCCTCTTCAGATGAGTTCTTCTCA
* * *
453 TTATG-AACTTTCTCTGG-A-A-ATG-TGATCCATCAAGTGATG-GAT-TGA-GCAAAAGGTTGG
65 TTATGAAACTTTCTCTGGAAGAGATGCTAATCCATCAACTGATGTGATATCATGCAAAAGGTT-G
510 AAC-AGCTCTTCTCATTATGAACTTCTTCTCTTCTTCTTCTTCAGATGAGTTCTTTCTCATTATG
129 AACAAGCTCTTCTC---ATGAA---CTTCTCTTC--C-TCTTCAGATGAGTTCTTTCTCATTATG
574 AACTCTACCTGGAAATG
185 AACTCTACCTGGAAATG
591 TTTTAAGAAA
Statistics
Matches: 178, Mismatches: 12, Indels: 25
0.83 0.06 0.12
Matches are distributed among these distances:
217 19 0.11
218 6 0.03
220 8 0.04
221 10 0.06
222 3 0.02
223 9 0.05
224 1 0.01
225 2 0.01
226 63 0.35
227 55 0.31
228 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (225 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTCTTCAGATGAGTTCTTCTCAT
TATGAAACTTTCTCTGGAAGAGATGCTAATCCATCAACTGATGTGATATCATGCAAAAGGTTGAA
CAAGCTCTTCTCATGAACTTCTCTTCCTCTTCAGATGAGTTCTTTCTCATTATGAACTCTACCTG
GAAATGCTGATCCATCAAGTGAGGATTTGA
Found at i:738 original size:75 final size:73
Alignment explanation
Indices: 606--780 Score: 242
Period size: 75 Copynumber: 2.3 Consensus size: 73
596 AGAAAGAAAA
* * * *
606 AAACATTCTGCACTGTAGGGCTTACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCAA
1 AAACA-TCAGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC-CCCAA
671 AGGCTTTTTGG
64 AGGC-TTTTGG
* *
682 AAACATCAGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCCCCGAAG
1 AAACATCAGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCCCCAAAG
747 GCTTTTGG
66 GCTTTTGG
* *
755 ACACATCATGCATTGTAGGACTTACA
1 AAACATCA-GCACTGTAGGACTTACA
781 TATGTGAGAA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
73 13 0.14
74 24 0.27
75 48 0.53
76 5 0.06
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (73 bp):
AAACATCAGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCCCCAAAG
GCTTTTGG
Found at i:4198 original size:114 final size:113
Alignment explanation
Indices: 3983--4205 Score: 383
Period size: 114 Copynumber: 2.0 Consensus size: 113
3973 AGACTATCAT
* *
3983 CAAATTCATCTTTCAAATTCAATGATTGGTTTTGGGGTTCCTACCAACCAGATCAGATAACTCAA
1 CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACCAACCAGATCAGATAACTCAA
*
4048 AAAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAC
66 AAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAC
*
4096 CAAATTCATCTTTCAAATTTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACC-AACCAGATCAGATAACTCA
* *
4161 AAGAACACTTCCAGAAGATGCTATTGGGGCTCTTTATTTCTACTA
65 AAAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
4206 CGAGAACATG
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 42 0.41
114 61 0.59
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (113 bp):
CAAATTCATCTTTCAAATTCAATGATTGGTTTTAGGGTTCATACCAACCAGATCAGATAACTCAA
AAAACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAC
Found at i:12955 original size:3 final size:3
Alignment explanation
Indices: 12937--13027 Score: 57
Period size: 3 Copynumber: 32.0 Consensus size: 3
12927 TTTGGGCCTG
* * * * * * *
12937 TAA T-A TAA TAA AAA TAA TAA AAA TAA AAA TAA AAA AAA TAA AAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
12984 TAA T-A TTA TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13028 ATGAAATAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
2 10 0.14
3 60 0.86
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:12963 original size:15 final size:15
Alignment explanation
Indices: 12943--12986 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
12933 CCTGTAATAT
12943 AATAAAAATAATAAA
1 AATAAAAATAATAAA
*
12958 AATAAAAATAAAAAA
1 AATAAAAATAATAAA
*
12973 AATAAAAAAAATAA
1 AATAAAAATAATAA
12987 TATTATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:12967 original size:21 final size:21
Alignment explanation
Indices: 12941--12988 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
12931 GGCCTGTAAT
*
12941 ATAATAAAAATAATAAAAATAA
1 ATAATAAAAAAAATAAAAA-AA
12963 A-AATAAAAAAAATAAAAAAA
1 ATAATAAAAAAAATAAAAAAA
12983 ATAATA
1 ATAATA
12989 TTATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAATAAAAAAAATAAAAAAA
Found at i:12973 original size:24 final size:24
Alignment explanation
Indices: 12941--12986 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12931 GGCCTGTAAT
* *
12941 ATAATAAAAATAATAAAAATAAAA
1 ATAAAAAAAATAAAAAAAATAAAA
12965 ATAAAAAAAATAAAAAAAATAA
1 ATAAAAAAAATAAAAAAAATAA
12987 TATTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (24 bp):
ATAAAAAAAATAAAAAAAATAAAA
Found at i:13006 original size:19 final size:19
Alignment explanation
Indices: 12977--13026 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12967 AAAAAAAATA
* * *
12977 AAAAAAATAATATTATAAT
1 AAAATAATAATATTAAAAC
*
12996 ATAATAATAATATTAAAAC
1 AAAATAATAATATTAAAAC
13015 AAAATAATAATA
1 AAAATAATAATA
13027 AATGAAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAATAATATTAAAAC
Found at i:13040 original size:22 final size:22
Alignment explanation
Indices: 12996--13040 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12986 ATATTATAAT
* *
12996 ATAATAATAATATTAAAACAAA
1 ATAATAATAATATGAAAAAAAA
13018 ATAATAATAA-ATGAAATAAAAA
1 ATAATAATAATATGAAA-AAAAA
13040 A
1 A
13041 CTAGTGTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAATAATAATATGAAAAAAAA
Found at i:15162 original size:38 final size:37
Alignment explanation
Indices: 15109--15202 Score: 127
Period size: 37 Copynumber: 2.5 Consensus size: 37
15099 TTATAAATCC
* *
15109 TCCACCCGATTCGAACCCGACCAAAAAAATATACACCT
1 TCCACCCGATCCGAACCCGACC-AAAAAATATACACAT
* *
15147 TCCACCCAATCCGAACTCC-ACCCAAAAATATACACAT
1 TCCACCCGATCCGAAC-CCGACCAAAAAATATACACAT
15184 TCCACCCGATCCGAACCCG
1 TCCACCCGATCCGAACCCG
15203 GCCCGCTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
36 2 0.04
37 28 0.57
38 17 0.35
39 2 0.04
ACGTcount: A:0.36, C:0.41, G:0.07, T:0.15
Consensus pattern (37 bp):
TCCACCCGATCCGAACCCGACCAAAAAATATACACAT
Found at i:15605 original size:14 final size:14
Alignment explanation
Indices: 15587--15619 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15577 TTCTAGGGAT
15587 AAAAAAAT-TATTA
1 AAAAAAATATATTA
*
15600 ATAAAAATATATTA
1 AAAAAAATATATTA
15614 AAAAAA
1 AAAAAA
15620 TCCTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAAATATATTA
Found at i:15607 original size:13 final size:13
Alignment explanation
Indices: 15586--15620 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
15576 ATTCTAGGGA
15586 TAAAAAAAT-TAT
1 TAAAAAAATATAT
15598 TAATAAAAATATAT
1 TAA-AAAAATATAT
15612 TAAAAAAAT
1 TAAAAAAAT
15621 CCTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 12 0.57
14 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAAAATATAT
Found at i:18668 original size:16 final size:15
Alignment explanation
Indices: 18642--18671 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18632 ATGAAATCTC
18642 ATGTCTGTCCCTTTA
1 ATGTCTGTCCCTTTA
18657 ATGTCATGTCCCTTT
1 ATGTC-TGTCCCTTT
18672 TATAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGTCTGTCCCTTTA
Found at i:19658 original size:3 final size:3
Alignment explanation
Indices: 19650--19681 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19640 CATCCATTTC
19650 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19682 AGAGGGTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:31731 original size:22 final size:22
Alignment explanation
Indices: 31702--31749 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
31692 CTCTAGAGAG
31702 ACTACAAAATATT-TTTAAATT
1 ACTACAAAATATTATTTAAATT
31723 ACTATCAAAATATTATTTAAATT
1 ACTA-CAAAATATTATTTAAATT
31746 ACTA
1 ACTA
31750 ATGGGGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.16
22 9 0.36
23 12 0.48
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
ACTACAAAATATTATTTAAATT
Found at i:32076 original size:3 final size:3
Alignment explanation
Indices: 32068--32120 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
32058 TATTTAACCA
32068 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32116 AAT AA
1 AAT AA
32121 GCTATTAGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33199 original size:19 final size:18
Alignment explanation
Indices: 33164--33200 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
33154 AATTCTCCCC
*
33164 AAAATTATTACAAATATA
1 AAAATTATTAAAAATATA
33182 AAAATTATTATAAAATATA
1 AAAATTATTA-AAAATATA
33201 TTATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTATTAAAAATATA
Found at i:33847 original size:31 final size:31
Alignment explanation
Indices: 33812--33873 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
33802 GAGACATGGC
* *
33812 CAAATTGTGTGGAGATCAATACATGAGAGGT
1 CAAATTGTGTGCAGATCAATAAATGAGAGGT
*
33843 CAAATTGTGTGCATATCAATAAATGAGAGGT
1 CAAATTGTGTGCAGATCAATAAATGAGAGGT
33874 GGCTTCTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (31 bp):
CAAATTGTGTGCAGATCAATAAATGAGAGGT
Found at i:40827 original size:2 final size:2
Alignment explanation
Indices: 40820--40859 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40810 AATGGGAGAC
40820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40860 GTTAGTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44945 original size:60 final size:58
Alignment explanation
Indices: 44834--44945 Score: 134
Period size: 60 Copynumber: 1.9 Consensus size: 58
44824 CATGATAGTC
* * * * * *
44834 ATCATTTTGTAACTTTTATAGTTGAGAACTCAACAAAATAATATCATATAGTCGATAA
1 ATCATTTTATAACTTTTATAGTCGAAAACTCAACAAAACAACACCATATAGTCGATAA
* *
44892 ATCATTTTATAACTTTTAATAGTCGATAAACTCAACAAAGCAACACCTTATAGT
1 ATCATTTTATAACTTTT-ATAGTCGA-AAACTCAACAAAACAACACCATATAGT
44946 TAGAGACAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
58 16 0.36
59 7 0.16
60 21 0.48
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (58 bp):
ATCATTTTATAACTTTTATAGTCGAAAACTCAACAAAACAACACCATATAGTCGATAA
Found at i:47335 original size:17 final size:17
Alignment explanation
Indices: 47313--47347 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
47303 TTGACAAAAG
47313 TCGATAGGGAATTGCAA
1 TCGATAGGGAATTGCAA
47330 TCGATAGGGAATTGCAA
1 TCGATAGGGAATTGCAA
47347 T
1 T
47348 GCAGCAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (17 bp):
TCGATAGGGAATTGCAA
Found at i:50733 original size:20 final size:20
Alignment explanation
Indices: 50708--50745 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50698 GACTCAGAAA
50708 TCAGAAT-TCATATTAAAGGG
1 TCAGAATAT-ATATTAAAGGG
50728 TCAGAATATATATTAAAG
1 TCAGAATATATATTAAAG
50746 AACCACTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (20 bp):
TCAGAATATATATTAAAGGG
Found at i:51820 original size:24 final size:26
Alignment explanation
Indices: 51777--51831 Score: 96
Period size: 24 Copynumber: 2.2 Consensus size: 26
51767 GAACTTTTTT
51777 TATTTTTTATTTTCATTTTAAAAAAA
1 TATTTTTTATTTTCATTTTAAAAAAA
51803 TATTTTTTATTTT-A-TTTAAAAAAA
1 TATTTTTTATTTTCATTTTAAAAAAA
51827 TATTT
1 TATTT
51832 AATTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 15 0.52
25 1 0.03
26 13 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTTTTATTTTCATTTTAAAAAAA
Found at i:51841 original size:25 final size:24
Alignment explanation
Indices: 51793--51841 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
51783 TTATTTTCAT
* *
51793 TTTAAAAAAATATTTTTTATTTTA
1 TTTAAAAAAATATTTATTAATTTA
51817 TTTAAAAAAATATTTAATTAATTTA
1 TTTAAAAAAATATTT-ATTAATTTA
51842 GATGAAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAAAAATATTTATTAATTTA
Found at i:52376 original size:23 final size:23
Alignment explanation
Indices: 52350--52395 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
52340 AAAAGCATAT
*
52350 AAAAGCGCGCCACAAGAACAGAG
1 AAAAGCACGCCACAAGAACAGAG
* *
52373 AAAAGCATGTCACAAGAACAGAG
1 AAAAGCACGCCACAAGAACAGAG
52396 GTTCTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.22, G:0.24, T:0.04
Consensus pattern (23 bp):
AAAAGCACGCCACAAGAACAGAG
Found at i:62969 original size:29 final size:29
Alignment explanation
Indices: 62923--63005 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
62913 CTCACCTAAC
*
62923 TAAATTGATGTAAACAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
62953 TAAATGATATAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
62982 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
63006 ATTTAGTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:66390 original size:15 final size:15
Alignment explanation
Indices: 66370--66399 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66360 CTTTCTTATA
66370 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
66385 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
66400 CCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:67732 original size:29 final size:29
Alignment explanation
Indices: 67689--67771 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
67679 CTCACCTAAC
67689 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
* *
67719 TAAATGATATAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
67748 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
67772 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:69203 original size:17 final size:18
Alignment explanation
Indices: 69181--69214 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69171 CGGTTTTAGC
69181 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
69198 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
69215 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:70811 original size:29 final size:29
Alignment explanation
Indices: 70777--70873 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
70767 AAGGTATGTC
*
70777 GTGTTCGTTTATTTATTTTTGAAGGTGTT
1 GTGTTCGTTTATTTATTTTTAAAGGTGTT
* * *
70806 GTGTTCATTTA---AGTTTTAATATTGTGTT
1 GTGTTCGTTTATTTATTTTTAA-A-GGTGTT
70834 CGTGTTCGTTTATTTATTTTTAAAGGTGTTT
1 -GTGTTCGTTTATTTATTTTTAAAGGTG-TT
70865 GTGTTCGTT
1 GTGTTCGTT
70874 ATGTATTGTT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
26 6 0.11
27 1 0.02
28 5 0.09
29 20 0.37
30 12 0.22
31 3 0.06
32 7 0.13
ACGTcount: A:0.15, C:0.05, G:0.22, T:0.58
Consensus pattern (29 bp):
GTGTTCGTTTATTTATTTTTAAAGGTGTT
Found at i:70907 original size:23 final size:24
Alignment explanation
Indices: 70866--70947 Score: 87
Period size: 23 Copynumber: 3.4 Consensus size: 24
70856 AAGGTGTTTG
*
70866 TGTTCGTTATGTATTGTTCACGAACA
1 TGTTCGTT-TATA-TGTTCACGAACA
* * *
70892 TGTTCATTTA-ATGTTCAAGAACG
1 TGTTCGTTTATATGTTCACGAACA
*
70915 TGTTTGTTTATATGTTCAC-AACA
1 TGTTCGTTTATATGTTCACGAACA
70938 TGTTCGTTTA
1 TGTTCGTTTA
70948 GCGTTCGTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 30 0.65
24 8 0.17
25 1 0.02
26 7 0.15
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.45
Consensus pattern (24 bp):
TGTTCGTTTATATGTTCACGAACA
Found at i:71068 original size:21 final size:22
Alignment explanation
Indices: 71024--71067 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
71014 TTAGCGTTCA
71024 TAGTGTTTGTTTAGCGTTGTTT
1 TAGTGTTTGTTTAGCGTTGTTT
*
71046 TAGTGTTT-TTTATCGTTCGTTT
1 TAGTGTTTGTTTAGCGTT-GTTT
71068 ATATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.09, C:0.07, G:0.23, T:0.61
Consensus pattern (22 bp):
TAGTGTTTGTTTAGCGTTGTTT
Found at i:78503 original size:29 final size:31
Alignment explanation
Indices: 78461--78525 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
78451 TTTTTCAAAA
78461 TAATATGTTACGTT-ATTTTTTATTTCA-TT
1 TAATATGTTACGTTAATTTTTTATTTCATTT
78490 TAATAT-TTATCGTTAATTTTTTATTTCATTT
1 TAATATGTTA-CGTTAATTTTTTATTTCATTT
78521 TAATA
1 TAATA
78526 ACTCGTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 3 0.09
29 10 0.30
30 13 0.39
31 7 0.21
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.62
Consensus pattern (31 bp):
TAATATGTTACGTTAATTTTTTATTTCATTT
Found at i:80389 original size:37 final size:37
Alignment explanation
Indices: 80317--80390 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
80307 TATATTTTTA
*
80317 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTG
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTG
* * *
80354 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTTG
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTTG
80391 TAATATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTG
Found at i:81181 original size:20 final size:20
Alignment explanation
Indices: 81143--81181 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
81133 GGAGTGGAAA
*
81143 ATTAAAGTAAATTTTAAAAT
1 ATTAAAGTAAATTTGAAAAT
* *
81163 ATTAAATTAAGTTTGAAAA
1 ATTAAAGTAAATTTGAAAA
81182 CGTATAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
ATTAAAGTAAATTTGAAAAT
Found at i:81917 original size:2 final size:2
Alignment explanation
Indices: 81910--81994 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
81900 TTTTGTGGCT
81910 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
81952 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
81994 G
1 G
81995 TAAATAAAAG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:86661 original size:29 final size:29
Alignment explanation
Indices: 86612--86667 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
86602 TTTGTCCCAT
* *
86612 TAAAATTTTATAATTTTAAGTTCGCTCAC
1 TAAAATTTTATAAGTTCAAGTTCGCTCAC
86641 TAAAATTTTATAAGTTCAAGTTCGCTC
1 TAAAATTTTATAAGTTCAAGTTCGCTC
86668 TCTTAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (29 bp):
TAAAATTTTATAAGTTCAAGTTCGCTCAC
Found at i:90684 original size:26 final size:26
Alignment explanation
Indices: 90644--90729 Score: 163
Period size: 26 Copynumber: 3.3 Consensus size: 26
90634 TCCTCACTAA
*
90644 TTATTTCTAAAAAATTCACTAATTTG
1 TTATTTCTAACAAATTCACTAATTTG
90670 TTATTTCTAACAAATTCACTAATTTG
1 TTATTTCTAACAAATTCACTAATTTG
90696 TTATTTCTAACAAATTCACTAATTTG
1 TTATTTCTAACAAATTCACTAATTTG
90722 TTATTTCT
1 TTATTTCT
90730 TTTTTTAGTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (26 bp):
TTATTTCTAACAAATTCACTAATTTG
Found at i:92157 original size:2 final size:2
Alignment explanation
Indices: 92150--92177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
92140 TAATCGTGTA
92150 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
92178 GCGCGCGCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:92602 original size:20 final size:19
Alignment explanation
Indices: 92574--92649 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
92564 CACTGAATAT
92574 TTGTCCCGAAGGACCACTAA
1 TTGTCCCGAAGGACCACT-A
* * *
92594 TTGTTCCGAAGAACCGCTA
1 TTGTCCCGAAGGACCACTA
*
92613 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACT-A
92632 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
92650 GATAATCCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 14 0.30
19 1 0.02
20 32 0.68
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.22
Consensus pattern (19 bp):
TTGTCCCGAAGGACCACTA
Found at i:92658 original size:20 final size:20
Alignment explanation
Indices: 92615--92658 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
92605 AACCGCTATG
* **
92615 TCCCGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTGATAA
92635 TCCCGAAGGACCACTGATAA
1 TCCCGAAGGACCACTGATAA
92655 TCCC
1 TCCC
92659 TCGACTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATAA
Found at i:95295 original size:17 final size:19
Alignment explanation
Indices: 95262--95298 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
95252 TATGATGAAC
95262 TAAAACTTATGAAAAATAT
1 TAAAACTTATGAAAAATAT
95281 TAAAACTT-T-AAAAATAT
1 TAAAACTTATGAAAAATAT
95298 T
1 T
95299 CATCATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAACTTATGAAAAATAT
Found at i:101984 original size:24 final size:24
Alignment explanation
Indices: 101948--101995 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
101938 GTCAGACCGA
*
101948 CGCGAGAGGGAACG-AGACCGAGAC
1 CGCGAGAGAGAACGCAGA-CGAGAC
*
101972 CGCGATAGAGAACGCAGACGAGAC
1 CGCGAGAGAGAACGCAGACGAGAC
101996 AGAGATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.35, C:0.25, G:0.38, T:0.02
Consensus pattern (24 bp):
CGCGAGAGAGAACGCAGACGAGAC
Found at i:102002 original size:24 final size:24
Alignment explanation
Indices: 101957--102048 Score: 62
Period size: 24 Copynumber: 3.7 Consensus size: 24
101947 ACGCGAGAGG
* *
101957 GAACGAGACCGAGACCGCGATAGA
1 GAACGAGACCGAGACAGAGATAGA
*
101981 GAACGCAGA-CGAGACAGAGATATTCGC
1 GAACG-AGACCGAGACAGAGATA---GA
* * *
102008 GACCGCGACCGAGACCGAGATAGA
1 GAACGAGACCGAGACAGAGATAGA
*
102032 G-ACAGAGAGCGAGACAG
1 GAAC-GAGACCGAGACAG
102049 GGAACGGACG
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
23 1 0.02
24 28 0.55
25 3 0.06
26 2 0.04
27 17 0.33
ACGTcount: A:0.37, C:0.24, G:0.34, T:0.05
Consensus pattern (24 bp):
GAACGAGACCGAGACAGAGATAGA
Found at i:117827 original size:2 final size:2
Alignment explanation
Indices: 117820--117845 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117810 TTACTATTTC
117820 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
117846 TATCCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119399 original size:27 final size:27
Alignment explanation
Indices: 119362--119438 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
119352 ATTATAAATA
*
119362 TAAAGTATAATAAATAATATTATTTAT
1 TAAAATATAATAAATAATATTATTTAT
* *
119389 TAGAATATAATTAAT-ATAATTATTT-T
1 TAAAATATAATAAATAAT-ATTATTTAT
*
119415 TAAAATATTA-AAATAAT-TTATTTA
1 TAAAATATAATAAATAATATTATTTA
119439 ATATTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
24 6 0.15
25 3 0.07
26 13 0.32
27 19 0.46
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TAAAATATAATAAATAATATTATTTAT
Found at i:119446 original size:23 final size:23
Alignment explanation
Indices: 119383--119446 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
119373 AAATAATATT
* * *
119383 ATTTATTAGAATATAATTAATATA
1 ATTTATT-TAATATTATTAAAATA
* *
119407 ATTATTTTTAA-AATATTAAAATA
1 ATT-TATTTAATATTATTAAAATA
119430 ATTTATTTAATATTATT
1 ATTTATTTAATATTATT
119447 TTTTCAATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
22 6 0.19
23 17 0.55
24 5 0.16
25 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTATTTAATATTATTAAAATA
Found at i:120369 original size:18 final size:18
Alignment explanation
Indices: 120346--120384 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
120336 TATATATTGT
120346 TAAAATAAAAATATAATA
1 TAAAATAAAAATATAATA
** *
120364 TAAAATATTATTATAATA
1 TAAAATAAAAATATAATA
120382 TAA
1 TAA
120385 TTTAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATAAAAATATAATA
Found at i:120425 original size:27 final size:26
Alignment explanation
Indices: 120387--120447 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
120377 TAATATAATT
120387 TAATATATTATTA-TAATACTA-AAAATA
1 TAATAT-TTATTATTAATA-TATAAAA-A
120414 TAATATTGTATTATTAATATATAAAAA
1 TAATATT-TATTATTAATATATAAAAA
120441 TAATATT
1 TAATATT
120448 ATTTTAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
TAATATTTATTATTAATATATAAAAA
Found at i:122746 original size:60 final size:59
Alignment explanation
Indices: 122659--122810 Score: 141
Period size: 60 Copynumber: 2.5 Consensus size: 59
122649 GGAAATTATA
* *
122659 GGAAT-TTCAAAAGTTTAGGTACTAATTTAGAAAGAGGGTCAT-GATTTAAGG-ATGAATTT
1 GGAATGTTCAAAAGTTAAGG-ACCAATTTAGAAAGAGGGTCATAG-TTT-AGGAATGAATTT
* ** *
122718 GGAATGTTCAAAAGCTTAAGGACCAATTTAGAATGATTGTCATAGTTTGGGAATGAATTT
1 GGAATGTTCAAAAG-TTAAGGACCAATTTAGAAAGAGGGTCATAGTTTAGGAATGAATTT
* * *
122778 AGAATG-TCTAAAAGTTTAAGAATCAATTTAGAA
1 GGAATGTTC-AAAAG-TTAAGGACCAATTTAGAA
122811 TGTATTATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
59 9 0.12
60 63 0.81
61 6 0.08
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (59 bp):
GGAATGTTCAAAAGTTAAGGACCAATTTAGAAAGAGGGTCATAGTTTAGGAATGAATTT
Found at i:128334 original size:3 final size:3
Alignment explanation
Indices: 128326--128364 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
128316 GTTCATGGCT
128326 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
128365 GGAAACCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:130281 original size:50 final size:51
Alignment explanation
Indices: 130128--130311 Score: 291
Period size: 51 Copynumber: 3.6 Consensus size: 51
130118 CTTAAACCAA
* * * *
130128 TGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTGTTTACTAACACCGG
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGG
130179 TGTAAGTATGTGTTAAGTGCTACACTTTTTTTTATTTTATTCACTTACACCGG
1 TGTAAGTATGTGTTAAGTGCTACAC--TTTTTTATTTTATTCACTTACACCGG
*
130232 TGT-AGTATGTGTTAAGTGCTACACTTGTTTATTTTATTCACTTACACCGG
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGG
130282 TGTAAGTATGTGTTAAGTGCTACA-TTTTTT
1 TGTAAGTATGTGTTAAGTGCTACACTTTTTT
130312 GCAGTATGAA
Statistics
Matches: 124, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
50 33 0.27
51 44 0.35
52 21 0.17
53 26 0.21
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (51 bp):
TGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGG
Found at i:134485 original size:145 final size:144
Alignment explanation
Indices: 134326--134625 Score: 379
Period size: 145 Copynumber: 2.1 Consensus size: 144
134316 CAACATTTGG
* * * *
134326 AATGTTGATCGGAGATCCCGATCGCCGGCGAGAAGACAAAAACCATTCGGCTTATTTTTTTCGAT
1 AATGTTGATTGGAGATCCCGATCGCCGGCAAGAAGACAAAAACCATTCGGCTTATTTTCTCCGAT
* * *
134391 -C-TGTCGTCGTCCATCGTCCGATCGTCCTGAATTTTCAGTATGTTGTTTATGATGATCTCACGC
66 CCATGTC--CGTCCACCGTCCGATCGTCCTGAATATTCAGTATGTTGTTTATGATGATCTCACGA
134454 AACTTTTGACCATTCGA
129 AAC-TTTGACCATTCGA
* * * **
134471 AATGTTGATTGGAGATCCCGATCGCCGGCAAGAGGCCAAAAACCGTTCTTCTTATTTTCTCCGAT
1 AATGTTGATTGGAGATCCCGATCGCCGGCAAGAAGACAAAAACCATTCGGCTTATTTTCTCCGAT
* * * * *
134536 CCATTTCCGTCCACCGTCCGATCGTCCTGAATATTCAGTATGTTGTTTGTGATGGTTTTACGAAA
66 CCATGTCCGTCCACCGTCCGATCGTCCTGAATATTCAGTATGTTGTTTATGATGATCTCACGAAA
* *
134601 CTTTGACCGTTCGG
131 CTTTGACCATTCGA
*
134615 AATATTGATTG
1 AATGTTGATTG
134626 TGATTCTGAT
Statistics
Matches: 133, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
144 21 0.16
145 108 0.81
146 1 0.01
147 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (144 bp):
AATGTTGATTGGAGATCCCGATCGCCGGCAAGAAGACAAAAACCATTCGGCTTATTTTCTCCGAT
CCATGTCCGTCCACCGTCCGATCGTCCTGAATATTCAGTATGTTGTTTATGATGATCTCACGAAA
CTTTGACCATTCGA
Found at i:135393 original size:40 final size:40
Alignment explanation
Indices: 135342--135444 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 40
135332 AAAGATGATA
* * * *
135342 ACACAGTTCCTACATGATGATGAAACAC-AGTCGAGGGATG
1 ACACGGTTCCTACGTGATGAGGAAAC-CTAGTCAAGGGATG
* *
135382 ACATGGTTCCTACGTGATGAGGAGACCTAGTCAAGGGATG
1 ACACGGTTCCTACGTGATGAGGAAACCTAGTCAAGGGATG
* *
135422 ACACGATTCCTACGTGATAAGGA
1 ACACGGTTCCTACGTGATGAGGA
135445 CGATTGGTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.21
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGAAACCTAGTCAAGGGATG
Found at i:135709 original size:121 final size:121
Alignment explanation
Indices: 135495--135719 Score: 317
Period size: 121 Copynumber: 1.9 Consensus size: 121
135485 GTTAATCCAT
* * * * *
135495 TGGGCACAATATCCTTCTTCGTGAAGTTGAAATCGTGGGTGGCTCATTCGTCGTGAAATTGAGCT
1 TGGGCACAATATCCTTCATCGTGAAGTTAAAATCGTGGGTAGCTCATTCGTCATGAAATTGAGCA
* *
135560 TTGAATTGGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTACTTG
66 TTGAATTGAATATCCTTCATCCTGAAGTTGAAATCCAAGGGTTGCATTGCTACTTG
* * * *
135616 TGGGCACGATATCCTTCATCGTGAAGTTAAAATTGTGGAG-AGCTCCTTCGTCATGAAGTTGAGC
1 TGGGCACAATATCCTTCATCGTGAAGTTAAAATCGTGG-GTAGCTCATTCGTCATGAAATTGAGC
* *
135680 ATTGACTTGAATATCCTTCGTCCTGAAGTTGAAATCCAAG
65 ATTGAATTGAATATCCTTCATCCTGAAGTTGAAATCCAAG
135720 CTTGTGTTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 89 0.99
122 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (121 bp):
TGGGCACAATATCCTTCATCGTGAAGTTAAAATCGTGGGTAGCTCATTCGTCATGAAATTGAGCA
TTGAATTGAATATCCTTCATCCTGAAGTTGAAATCCAAGGGTTGCATTGCTACTTG
Found at i:136121 original size:43 final size:43
Alignment explanation
Indices: 136055--136181 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
136045 TGTGTTGCGG
* * * * *
136055 GTGGACACGAT-TCCCTTCGTCGTGAAGTTGAAACCGTGG-TTGT
1 GTGGGCACGATAT-CCTCCGTCGTGGAGTTGAAATCGTGGATT-C
136098 GTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTC
1 GTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTC
*
136141 GTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 GTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
136182 GGCCTCTTCG
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 73 0.96
44 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (43 bp):
GTGGGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTC
Found at i:136147 original size:192 final size:197
Alignment explanation
Indices: 135870--136256 Score: 529
Period size: 206 Copynumber: 1.9 Consensus size: 197
135860 GCTTGTGTGT
135870 ACGATTCCCTTCGTCGTGAAATTGAAACGTGGATGGATAGGCACGATATCCTCCGTCGTGGAGTT
1 ACGATTCCCTTCGTCGTGAAATTGAAACGTGGATGGATAGGCACGATATCCTCCGTCGTGGAGTT
* *
135935 GAAATCGTGGATCTGTGGGTATGATATCAT-C-C-G-T-T-GTGGATGGCCCCTTCGTCGTGAAG
66 GAAATCGTGGATCTGTGGGTACGATATCATCCGCGGTTATCGTGGATGGCCCCTTCGTCGTGAAA
*
135994 TTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTGTGTTGCGGGTGG
131 TTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGG
136059 AC
196 AC
* * *
136061 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGTTGTG-TGGGCACGATATCCTCCGTCGTGGAG
1 ACGATTCCCTTCGTCGTGAAATTGAAA-CGTGGATG-GATAGGCACGATATCCTCCGTCGTGGAG
* *
136125 TTGAAATCGTGGAT-TCGTGGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCTCT
64 TTGAAATCGTGGATCT-GTGGGTACGATATCATCCG-C---G-GTT---ATCGTGGATGGCCCCT
**
136189 TCGTTTTGAAATTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTAT
120 TCGTCGTGAAATTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTAT
136254 GTT
185 GTT
136257 TCGAGTCTAA
Statistics
Matches: 169, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
191 27 0.16
192 60 0.36
193 2 0.01
195 1 0.01
200 1 0.01
201 1 0.01
205 1 0.01
206 76 0.45
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (197 bp):
ACGATTCCCTTCGTCGTGAAATTGAAACGTGGATGGATAGGCACGATATCCTCCGTCGTGGAGTT
GAAATCGTGGATCTGTGGGTACGATATCATCCGCGGTTATCGTGGATGGCCCCTTCGTCGTGAAA
TTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGG
AC
Found at i:136762 original size:29 final size:30
Alignment explanation
Indices: 136685--136768 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 30
136675 TCGCATCGGG
* *
136685 ATGTTGAAT-TCCCAAAGATGCCCCAATATT
1 ATGTTGAATCT-CGAAAGATGCCCCAACATT
136715 CGATGTTGAATCTCGAAAGATGCCCCAACATT
1 --ATGTTGAATCTCGAAAGATGCCCCAACATT
**
136747 -TGTTGAATCTTTAAAGATGCCC
1 ATGTTGAATCTCGAAAGATGCCC
136769 TCTATTGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 20 0.43
32 26 0.55
33 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (30 bp):
ATGTTGAATCTCGAAAGATGCCCCAACATT
Done.