Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007464.1 Hibiscus syriacus cultivar Beakdansim tig00020478_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: 74203
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Found at i:880 original size:13 final size:13
Alignment explanation
Indices: 836--881 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
826 TCATTTTTTC
836 TTTAAAAAATGATTT
1 TTTAAAAAA--ATTT
851 TTTAAAAAAATTAT
1 TTTAAAAAAATT-T
*
865 TTTAAAAAACTTT
1 TTTAAAAAAATTT
878 TTTA
1 TTTA
882 GGTATTCGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 8 0.28
14 12 0.41
15 9 0.31
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTAAAAAAATTT
Found at i:8050 original size:8 final size:7
Alignment explanation
Indices: 8036--8125 Score: 57
Period size: 7 Copynumber: 12.9 Consensus size: 7
8026 GATCAAATCA
8036 AAAAAAG
1 AAAAAAG
8043 ATAAAAAG
1 A-AAAAAG
8051 CAAAGAAAG
1 -AAA-AAAG
8060 AAAAAAG
1 AAAAAAG
*
8067 --CAAAG
1 AAAAAAG
8072 AAAAAA-
1 AAAAAAG
8078 AAGAAAAG
1 AA-AAAAG
8086 AAAAAA-
1 AAAAAAG
*
8092 ACAAAGAG
1 A-AAAAAG
8100 AAAAAA-
1 AAAAAAG
8106 AGAAAAA-
1 A-AAAAAG
*
8113 AATAAAG
1 AAAAAAG
8120 AAAAAA
1 AAAAAA
8126 AGAAGATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
5 4 0.06
6 8 0.12
7 35 0.53
8 14 0.21
9 5 0.08
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:8059 original size:17 final size:16
Alignment explanation
Indices: 8034--8126 Score: 75
Period size: 16 Copynumber: 5.8 Consensus size: 16
8024 AAGATCAAAT
*
8034 CAAAAAAAGATAAAAAG
1 CAAAGAAAGA-AAAAAG
8051 CAAAGAAAGAAAAAAG
1 CAAAGAAAGAAAAAAG
8067 CAAAG-AA-AAAAAAG
1 CAAAGAAAGAAAAAAG
* *
8081 AAAAGAAAAAAACAAAG
1 CAAAGAAAGAAA-AAAG
* * *
8098 AGAAAAAAAGAAAAAAA
1 -CAAAGAAAGAAAAAAG
*
8115 TAAAGAAA-AAAA
1 CAAAGAAAGAAAA
8127 GAAGATAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
14 11 0.17
15 8 0.12
16 20 0.31
17 16 0.25
18 9 0.14
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (16 bp):
CAAAGAAAGAAAAAAG
Found at i:8073 original size:12 final size:11
Alignment explanation
Indices: 8052--8138 Score: 61
Period size: 11 Copynumber: 7.4 Consensus size: 11
8042 GATAAAAAGC
8052 AAAGAAAGAAA
1 AAAGAAAGAAA
8063 AAAGCAAAGAAAAA
1 AAAG-AAAG--AAA
8077 AAAGAAAAGAAAA
1 AAAG-AAAG-AAA
* *
8090 AAACAAAGAGA
1 AAAGAAAGAAA
8101 AAA-AAAGAAAA
1 AAAGAAAG-AAA
*
8112 AAATAAAGAAA
1 AAAGAAAGAAA
8123 AAA-AGAAGATAA
1 AAAGA-AAGA-AA
8135 AAAG
1 AAAG
8139 CACATGCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
10 5 0.08
11 24 0.38
12 17 0.27
13 7 0.11
14 11 0.17
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:8075 original size:26 final size:25
Alignment explanation
Indices: 8052--8114 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
8042 GATAAAAAGC
8052 AAAGAAAGAAAAAAGCAAAGAAAAA
1 AAAGAAAGAAAAAAGCAAAGAAAAA
*
8077 AAAGAAAAGAAAAAAACAAAGAGAAAA
1 AAAG-AAAGAAAAAAGCAAAGA-AAAA
8104 AAAGAAA-AAAA
1 AAAGAAAGAAAA
8115 TAAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 8 0.23
26 19 0.54
27 8 0.23
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAAAAAGCAAAGAAAAA
Found at i:8077 original size:14 final size:14
Alignment explanation
Indices: 8045--8119 Score: 77
Period size: 14 Copynumber: 5.4 Consensus size: 14
8035 AAAAAAAGAT
8045 AAAAAGCAAAGAAAGA
1 AAAAAGCAAAG-AA-A
8061 AAAAAGCAAAGAAA
1 AAAAAGCAAAGAAA
*
8075 AAAAAGAAAAG-AA
1 AAAAAGCAAAGAAA
8088 AAAAA-CAAAGAGAA
1 AAAAAGCAAAGA-AA
8102 AAAAAG-AAA-AAA
1 AAAAAGCAAAGAAA
*
8114 ATAAAG
1 AAAAAG
8120 AAAAAAAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
12 11 0.21
13 8 0.15
14 21 0.40
15 2 0.04
16 11 0.21
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (14 bp):
AAAAAGCAAAGAAA
Found at i:8125 original size:14 final size:13
Alignment explanation
Indices: 8035--8129 Score: 75
Period size: 14 Copynumber: 6.8 Consensus size: 13
8025 AGATCAAATC
*
8035 AAAAAAAGATAAA
1 AAAAAAAGAAAAA
**
8048 AAGCAAAGAAAGAA
1 AAAAAAAGAAA-AA
8062 AAAAGCAAAGAAAAA
1 AAAA--AAAGAAAAA
8077 AAAGAAAAGAAAAA
1 AAA-AAAAGAAAAA
*
8091 AACAAAGAGAAAAA
1 AA-AAAAAGAAAAA
8105 AAGAAAAA-AATAAA
1 AA-AAAAAGAA-AAA
8119 GAAAAAAAGAA
1 -AAAAAAAGAA
8130 GATAAAAAGC
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.15
14 38 0.58
15 10 0.15
16 8 0.12
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:15948 original size:34 final size:34
Alignment explanation
Indices: 15908--15997 Score: 153
Period size: 34 Copynumber: 2.6 Consensus size: 34
15898 TAGTTTTTCT
* *
15908 GGGCTAAACTATAACCTTTCCCTAGCTTTTACAC
1 GGGCTAAGCTAGAACCTTTCCCTAGCTTTTACAC
15942 GGGCTAAGCTAGAACCTTTCCCTAGCTTTTACAC
1 GGGCTAAGCTAGAACCTTTCCCTAGCTTTTACAC
*
15976 GGGCTAAGTTAGAACCTTTCCC
1 GGGCTAAGCTAGAACCTTTCCC
15998 CTTTAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (34 bp):
GGGCTAAGCTAGAACCTTTCCCTAGCTTTTACAC
Found at i:16378 original size:19 final size:20
Alignment explanation
Indices: 16342--16422 Score: 101
Period size: 19 Copynumber: 4.0 Consensus size: 20
16332 CCGTTAGACA
**
16342 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTATACCCCCTG
* *
16362 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCTATACCCCCT-G
16383 GGGGGAATCTATACCCCCT-
1 GGGGGAATCTATACCCCCTG
*
16402 GGGGGAATCTATTCCCCCTG
1 GGGGGAATCTATACCCCCTG
16422 G
1 G
16423 ACAATCTGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 18 0.33
20 18 0.33
21 18 0.33
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTATACCCCCTG
Found at i:16379 original size:21 final size:21
Alignment explanation
Indices: 16342--16422 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
16332 CCGTTAGACA
*
16342 GGGGGAATC-GGTACCCCCTG
1 GGGGGAATCTGTTACCCCCTG
16362 GGGGGAATCTGTT-CCCCCTGG
1 GGGGGAATCTGTTACCCCCT-G
*
16383 GGGGGAATCT-ATACCCCCT-
1 GGGGGAATCTGTTACCCCCTG
*
16402 GGGGGAATCTATT-CCCCCTG
1 GGGGGAATCTGTTACCCCCTG
16422 G
1 G
16423 ACAATCTGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
19 16 0.30
20 18 0.34
21 19 0.36
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGAATCTGTTACCCCCTG
Found at i:16428 original size:18 final size:19
Alignment explanation
Indices: 16388--16429 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
16378 CCTGGGGGGG
**
16388 AATCTATACCCCCTGGGGG
1 AATCTATACCCCCTGGGAC
*
16407 AATCTATTCCCCCT-GGAC
1 AATCTATACCCCCTGGGAC
16425 AATCT
1 AATCT
16430 GATTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (19 bp):
AATCTATACCCCCTGGGAC
Found at i:18808 original size:34 final size:34
Alignment explanation
Indices: 18761--18885 Score: 214
Period size: 34 Copynumber: 3.7 Consensus size: 34
18751 CTAGTTTTTC
*
18761 CGGGCTAAACTAGAACATTTCCCTAGCTTTTACA
1 CGGGCTAAGCTAGAACATTTCCCTAGCTTTTACA
18795 CGGGCTAAGCTAGAACATTTCCCTAGCTTTTACA
1 CGGGCTAAGCTAGAACATTTCCCTAGCTTTTACA
*
18829 CGGGCTAAGCTAGAACCTTTCCCTAGCTTTTACA
1 CGGGCTAAGCTAGAACATTTCCCTAGCTTTTACA
* *
18863 TGGGCTAAGCTAGAACCTTTCCC
1 CGGGCTAAGCTAGAACATTTCCC
18886 CTTTACAAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 88 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (34 bp):
CGGGCTAAGCTAGAACATTTCCCTAGCTTTTACA
Found at i:22139 original size:37 final size:37
Alignment explanation
Indices: 22098--22177 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
22088 TGATAAACCA
*
22098 TTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCT-TAC
1 TTGAGATGGTTTCTCTCGAAACAAAGTTTTGTCTCT-C
*
22135 TTGAGATGGTTTCTCTTGAAACAAAGTTTTGTCTCTC
1 TTGAGATGGTTTCTCTCGAAACAAAGTTTTGTCTCTC
22172 TTGAGA
1 TTGAGA
22178 CAGTTTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
37 39 0.98
38 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (37 bp):
TTGAGATGGTTTCTCTCGAAACAAAGTTTTGTCTCTC
Found at i:22184 original size:37 final size:37
Alignment explanation
Indices: 22106--22193 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
22096 CATTGAGATT
* **
22106 GTTTCTCTCGAAACAAAGTTTTGTCTTACTTGAGATG
1 GTTTCTCTTGAAACAAAGTTTTGTCTTACTTGAGACA
22143 GTTTCTCTTGAAACAAAGTTTTGTCTCT-CTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCT-TACTTGAGACA
*
22180 GTTTCTTTTGAAAC
1 GTTTCTCTTGAAAC
22194 TTAAACAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
37 45 0.98
38 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTTACTTGAGACA
Found at i:22255 original size:81 final size:81
Alignment explanation
Indices: 22168--22337 Score: 259
Period size: 81 Copynumber: 2.1 Consensus size: 81
22158 AAGTTTTGTC
* * * * *
22168 TCTCTTGAGACAGTTTCTTTTGAAACTTAAACAATTGAGATTGTTTCCCATGAAATAAGTTTTCT
1 TCTCTTGAGACAGATTCTTTTGAAACTCAAACAATTGAGATTATTTCCCATGAAACAAATTTTCT
22233 CTCGCTTGAGACAGTT
66 CTCGCTTGAGACAGTT
* *
22249 TCTCTTGAGACAGATTCTTTTGAAACTCAAACAATTGAGATTATTTCCCTTGAAACAAATTTTGT
1 TCTCTTGAGACAGATTCTTTTGAAACTCAAACAATTGAGATTATTTCCCATGAAACAAATTTTCT
* *
22314 CTCGTTTGAGATAGTT
66 CTCGCTTGAGACAGTT
22330 TCTCTTGA
1 TCTCTTGA
22338 AACAAAGTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (81 bp):
TCTCTTGAGACAGATTCTTTTGAAACTCAAACAATTGAGATTATTTCCCATGAAACAAATTTTCT
CTCGCTTGAGACAGTT
Found at i:22257 original size:15 final size:15
Alignment explanation
Indices: 22237--22271 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22227 TTTTCTCTCG
*
22237 CTTGAGACAGTTTCT
1 CTTGAGACAGATTCT
22252 CTTGAGACAGATTCT
1 CTTGAGACAGATTCT
*
22267 TTTGA
1 CTTGA
22272 AACTCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (15 bp):
CTTGAGACAGATTCT
Found at i:22337 original size:36 final size:36
Alignment explanation
Indices: 22283--22376 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
22273 ACTCAAACAA
* *
22283 TTGAGATTA-TTTCCCTTGAAACAAATTTTGTCTCGT-
1 TTGAGA-TAGTTTCTCTTGAAACAAAGTTTGTCTC-TC
22319 TTGAGATAGTTTCTCTTGAAACAAAGTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAACAAAGTTTGTCTCTC
* * *
22355 TTGAGACAGTTTATTTTGAAAC
1 TTGAGATAGTTTCTCTTGAAAC
22377 TTAAACAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 3 0.06
36 48 0.94
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (36 bp):
TTGAGATAGTTTCTCTTGAAACAAAGTTTGTCTCTC
Found at i:22362 original size:102 final size:101
Alignment explanation
Indices: 22249--22440 Score: 296
Period size: 102 Copynumber: 1.9 Consensus size: 101
22239 TGAGACAGTT
* *
22249 TCTCTTGAGACAGATTCTTTTGAAACTCAAACAATTGAGATTATTTCCCTTGAAACAAATTTTGT
1 TCTCTTGAGACAGATTATTTTGAAACTCAAACAATTGAGATTATTTCCCTTGAAACAAAATTTGT
* *
22314 CTCGT-TTGAGATAGTTTCTCTTGAAACAAAGTTTGTC
66 CTC-TCTTGAGACAGTTT-ACTTGAAACAAAGTTTGTC
* * *
22351 TCTCTTGAGACAGTTTATTTTGAAACTTAAACAATTGAGATTGTTTCCCTTGAAACAAAATTTGT
1 TCTCTTGAGACAGATTATTTTGAAACTCAAACAATTGAGATTATTTCCCTTGAAACAAAATTTGT
22416 CTCTCTTGAGACAGTTTACTTGAAA
66 CTCTCTTGAGACAGTTTACTTGAAA
22441 TATAAACAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 8 0.10
102 74 0.90
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (101 bp):
TCTCTTGAGACAGATTATTTTGAAACTCAAACAATTGAGATTATTTCCCTTGAAACAAAATTTGT
CTCTCTTGAGACAGTTTACTTGAAACAAAGTTTGTC
Found at i:22403 original size:66 final size:67
Alignment explanation
Indices: 22319--22507 Score: 285
Period size: 65 Copynumber: 2.9 Consensus size: 67
22309 TTTGTCTCGT
* * * *
22319 TTGAGATAGTTTCTCTTGAAACAAAGTTTGTCTCTCTTGAGACAGTTTATTTTGAAACT-TAAAC
1 TTGAGATTGTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTATCTTGAAACTATAAAC
22383 AA
66 AA
22385 TTGAGATTGTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTA-CTTGAAA-TATAAAC
1 TTGAGATTGTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTATCTTGAAACTATAAAC
22448 AA
66 AA
* * * *
22450 TTGAGGTTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAAC
1 TTGAGATTGTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTATCTTGAAAC
22508 AAATTATCCC
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
64 1 0.01
65 58 0.52
66 53 0.47
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAAATTTGTCTCTCTTGAGACAGTTTATCTTGAAACTATAAAC
AA
Found at i:22426 original size:183 final size:185
Alignment explanation
Indices: 22092--22432 Score: 533
Period size: 183 Copynumber: 1.9 Consensus size: 185
22082 CAAAATTGAT
* * * * *
22092 AAACCATTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTTACTTGAGATGGTTTCTCTTGAAAC
1 AAACAATTGAGATTATTTCCCTCGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAAC
*
22157 AAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACTTAAACAATTGAGATTGTTTCCCATGAA
66 AAAGTTTTGTCTCTCTTGAGACAGTTTATTTTGAAACTTAAACAATTGAGATTGTTTCCCATGAA
* **
22222 ATAAGTTTTCTCTCGCTTGAGACAGTTTCTCTTGAGACAGATTCTTTTGAAACTC
131 ACAAAATTTCTCTCGCTTGAGACAGTTTCTCTTGAGACAGATTCTTTTGAAACTC
* **
22277 AAACAATTGAGATTATTTCCCTTGAAACAAA-TTTTGTCTCGTTTGAGATAGTTTCTCTTGAAAC
1 AAACAATTGAGATTATTTCCCTCGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAAC
*
22341 AAAG-TTTGTCTCTCTTGAGACAGTTTATTTTGAAACTTAAACAATTGAGATTGTTTCCCTTGAA
66 AAAGTTTTGTCTCTCTTGAGACAGTTTATTTTGAAACTTAAACAATTGAGATTGTTTCCCATGAA
* *
22405 ACAAAATTTGTCTCTCTTGAGACAGTTT
131 ACAAAATTTCTCTCGCTTGAGACAGTTT
22433 ACTTGAAATA
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
183 81 0.57
184 33 0.23
185 27 0.19
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (185 bp):
AAACAATTGAGATTATTTCCCTCGAAACAAAGTTTTGTCTCACTTGAGATAGTTTCTCTTGAAAC
AAAGTTTTGTCTCTCTTGAGACAGTTTATTTTGAAACTTAAACAATTGAGATTGTTTCCCATGAA
ACAAAATTTCTCTCGCTTGAGACAGTTTCTCTTGAGACAGATTCTTTTGAAACTC
Found at i:22781 original size:138 final size:138
Alignment explanation
Indices: 22511--22901 Score: 543
Period size: 138 Copynumber: 2.8 Consensus size: 138
22501 TTGAAACAAA
* * *
22511 TTATCCCTAAAGAT-GCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCAACCAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACCGACCAGATCTC
* * *
22575 CTCATCACATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGAATCGTGTT
66 CTCATCGCATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAAGAATCGTGAT
22640 ATCTCTAT
131 ATCTCTAT
* *
22648 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATATCATGCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACCGACCAGATCTC
* * *
22713 CTCATCGCGTAGGAGCAACATCATCCTTAGATAACCAGACTTCCTCATCACGTAAGAA-CAGTGA
66 CTCATCGCATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAAGAATC-GTGA
22777 TATCTCTAT
130 TATCTCTAT
* * * * * * * *
22786 TTATCCCTAAAGATGGCTAGACGGCTTCATTATGCATGAACAATGTCATCCATCGACTAGATCTC
1 TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACCGACCAGATCTC
** * * *
22851 CTTGTCGCATAGGAGCAGTGCCATCCTTAGATAACCAGACTTCCTTATCAC
66 CTCATCGCATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCAC
22902 ATATAAATCG
Statistics
Matches: 223, Mismatches: 29, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
137 15 0.07
138 208 0.93
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (138 bp):
TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAAGAACAATGTCATCCACCGACCAGATCTC
CTCATCGCATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAAGAATCGTGAT
ATCTCTAT
Found at i:24328 original size:19 final size:20
Alignment explanation
Indices: 24290--24328 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24280 TTATATGTTC
*
24290 CATATAGTCACTTAATTCAT
1 CATATAGTCACGTAATTCAT
*
24310 CATATATTCACGT-ATTCAT
1 CATATAGTCACGTAATTCAT
24329 ATCATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (20 bp):
CATATAGTCACGTAATTCAT
Found at i:32004 original size:8 final size:8
Alignment explanation
Indices: 31991--32023 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
31981 GCATGTATCA
31991 AAACATAT
1 AAACATAT
31999 AAACATAT
1 AAACATAT
32007 AAACATAT
1 AAACATAT
32015 AAACATAT
1 AAACATAT
32023 A
1 A
32024 TCACTTATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AAACATAT
Found at i:32250 original size:20 final size:20
Alignment explanation
Indices: 32206--32251 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
32196 AATGTTTTAA
*
32206 TGAACAGTACCGATACTGTG
1 TGAACAGTACCGATACTATG
* *
32226 GGAACAGTACTGATACTATG
1 TGAACAGTACCGATACTATG
32246 TGAACA
1 TGAACA
32252 TTAATGAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
TGAACAGTACCGATACTATG
Found at i:32733 original size:34 final size:33
Alignment explanation
Indices: 32694--32764 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
32684 TTTTGTAAAG
*
32694 GGGAAAGGTTCTAGCTTAGCCCATGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCATG-AAAAACTA
* * *
32728 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCATGAAAAACTA
32761 GGGA
1 GGGA
32765 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCATGAAAAACTA
Found at i:33459 original size:35 final size:35
Alignment explanation
Indices: 33399--33467 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
33389 TATTTCAAAA
*
33399 TGGTATCGATACTTGCCTTATGGTATCAATACCCT
1 TGGTATCGATACTTCCCTTATGGTATCAATACCCT
*
33434 TGGTATCGATA-TTACCCTT-TAGGTATCGATACCC
1 TGGTATCGATACTT-CCCTTAT-GGTATCAATACCC
33468 CTTGAATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 3 0.10
35 27 0.90
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (35 bp):
TGGTATCGATACTTCCCTTATGGTATCAATACCCT
Found at i:38622 original size:12 final size:12
Alignment explanation
Indices: 38589--38622 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
38579 TACATGAATT
38589 GAATATGTGTTC
1 GAATATGTGTTC
38601 GAAGTA-GTGTTC
1 GAA-TATGTGTTC
38613 GAATATGTGT
1 GAATATGTGT
38623 CCTCAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (12 bp):
GAATATGTGTTC
Found at i:47388 original size:23 final size:23
Alignment explanation
Indices: 47356--47401 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
47346 TTAGTGAATC
* *
47356 GACCGGAACCGCTAAATCGTTCA
1 GACCGAAACCGCTAAACCGTTCA
*
47379 GACCGAAACCGCTGAACCGTTCA
1 GACCGAAACCGCTAAACCGTTCA
47402 AACCAGACCG
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:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (23 bp):
GACCGAAACCGCTAAACCGTTCA
Found at i:48702 original size:32 final size:32
Alignment explanation
Indices: 48633--48702 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
48623 AAACCAGATA
** * *
48633 TCGGATACCCGATTATTGAGTACCCGTAAAAT
1 TCGGATACCCGATTACCGAATACCCATAAAAT
* *
48665 CCGGATACCCGATTACCGAATACCCATAACAT
1 TCGGATACCCGATTACCGAATACCCATAAAAT
48697 TCGGAT
1 TCGGAT
48703 CGAGACACGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (32 bp):
TCGGATACCCGATTACCGAATACCCATAAAAT
Found at i:48752 original size:16 final size:16
Alignment explanation
Indices: 48728--48782 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
48718 AAAATCATCG
*
48728 ACCCGAAAATTCCAAAT
1 ACCC-AAAAATCCAAAT
48745 ACCCAAAAAT-CAAAT
1 ACCCAAAAATCCAAAT
* *
48760 ACCCAAAAATCCGAGT
1 ACCCAAAAATCCAAAT
48776 ACCCAAA
1 ACCCAAA
48783 TTTGCACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 15 0.44
16 15 0.44
17 4 0.12
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (16 bp):
ACCCAAAAATCCAAAT
Found at i:49566 original size:21 final size:23
Alignment explanation
Indices: 49520--49572 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
49510 AACGTGTAAT
*
49520 TATAAATTAGTTAAAAATCTAAA
1 TATAAATTAGTTAAAAATCAAAA
*
49543 TATAAATT-GTTTAAAAT-AAAA
1 TATAAATTAGTTAAAAATCAAAA
*
49564 TATTAATTA
1 TATAAATTA
49573 CATTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 10 0.38
22 8 0.31
23 8 0.31
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TATAAATTAGTTAAAAATCAAAA
Found at i:52172 original size:8 final size:8
Alignment explanation
Indices: 52128--52188 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
52118 TTTGGTGGTC
52128 AAAGAAGTA
1 AAAGAAG-A
* *
52137 GAAGAACA
1 AAAGAAGA
52145 AAAGAAGA
1 AAAGAAGA
*
52153 AATATAAAGA
1 AA-A-GAAGA
52163 AAAGAAGA
1 AAAGAAGA
*
52171 AAA-TAGA
1 AAAGAAGA
52178 AAAGAAGA
1 AAAGAAGA
52186 AAA
1 AAA
52189 AGATTGGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
7 6 0.15
8 22 0.54
9 7 0.17
10 6 0.15
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.07
Consensus pattern (8 bp):
AAAGAAGA
Found at i:52178 original size:15 final size:16
Alignment explanation
Indices: 52144--52188 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
52134 GTAGAAGAAC
52144 AAAAGAAGAAATATAAAG
1 AAAAGAAGAAA-AT-AAG
52162 AAAAGAAGAAAAT-AG
1 AAAAGAAGAAAATAAG
52177 AAAAGAAGAAAA
1 AAAAGAAGAAAA
52189 AGATTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.52
17 2 0.07
18 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
AAAAGAAGAAAATAAG
Found at i:54921 original size:17 final size:18
Alignment explanation
Indices: 54899--54935 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
54889 AAATTAATGA
*
54899 AAATAAATGAATAA-AAT
1 AAATAAATAAATAATAAT
54916 AAATAAATAAATAATAAT
1 AAATAAATAAATAATAAT
54934 AA
1 AA
54936 TGAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATAAATAAATAATAAT
Found at i:54944 original size:21 final size:19
Alignment explanation
Indices: 54897--54950 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
54887 TAAAATTAAT
54897 GAAAATAAATGAATAAAATA
1 GAAAATAAAT-AATAAAATA
*
54917 AATAAATAAATAATAATAATGA
1 GA-AAATAAATAATAA-AAT-A
54939 GAAAATAAATAA
1 GAAAATAAATAA
54951 AGTAGAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 6 0.21
21 21 0.72
22 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (19 bp):
GAAAATAAATAATAAAATA
Found at i:55560 original size:13 final size:14
Alignment explanation
Indices: 55530--55563 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55520 AGCATTGTGA
55530 AAAGAAAAAAAATG
1 AAAGAAAAAAAATG
*
55544 AAAGAAAATAAAT-
1 AAAGAAAAAAAATG
55557 AAAGAAA
1 AAAGAAA
55564 GATGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAGAAAAAAAATG
Found at i:56507 original size:5 final size:5
Alignment explanation
Indices: 56497--56523 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
56487 AGTAAAACAA
56497 TTTAG TTTAG TTTAG TTTAG TTTAG TT
1 TTTAG TTTAG TTTAG TTTAG TTTAG TT
56524 ATTACAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (5 bp):
TTTAG
Found at i:57065 original size:40 final size:40
Alignment explanation
Indices: 56986--57065 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
56976 ATAGGAGTCA
* * *
56986 AATATTGCACCGCAGTGTTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGCAGTGTTGAGGTCGAGCTTTACCCACCT
* *
57026 AATAATGCACCGTAGTGTTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGCAGTGTTGAGGTCGAGCTTTACCCACCT
57066 TCTAGACCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (40 bp):
AATAATGCACCGCAGTGTTGAGGTCGAGCTTTACCCACCT
Found at i:59264 original size:12 final size:12
Alignment explanation
Indices: 59247--59275 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
59237 CAAGCGCTTA
59247 TTTTTCCTCATT
1 TTTTTCCTCATT
59259 TTTTT-CTCATT
1 TTTTTCCTCATT
59270 TTTTTC
1 TTTTTC
59276 GTTTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTCCTCATT
Found at i:64824 original size:46 final size:45
Alignment explanation
Indices: 64746--64849 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 45
64736 ATAACTAATG
*
64746 AATAAAATAATAACAAACTAAACATTTCTTAACT-C-TAATTCCT
1 AATAAAATAATAACAAACTAAAAATTTCTTAACTACTTAATTCCT
* *
64789 AATAAAATAATAATAAACTAAAAATTATATTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAACAAACTAAAAA-T-T-TCTTAACT--A-CTTAATTCCT
64840 AATAAAATAA
1 AATAAAATAA
64850 AAAATCTAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
43 22 0.44
44 1 0.02
45 1 0.02
46 7 0.14
50 1 0.02
51 18 0.36
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (45 bp):
AATAAAATAATAACAAACTAAAAATTTCTTAACTACTTAATTCCT
Found at i:70101 original size:22 final size:22
Alignment explanation
Indices: 70076--70134 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
70066 CTTTCTACTA
*
70076 AGAGGTTATAAAACCCCTTTAT
1 AGAGGTTATAAAACCCCCTTAT
*
70098 AGAGGTTATGAAACCCCCTTAT
1 AGAGGTTATAAAACCCCCTTAT
70120 AGAGGTT-TAGAAACC
1 AGAGGTTATA-AAACC
70135 AGTAGAACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (22 bp):
AGAGGTTATAAAACCCCCTTAT
Found at i:71581 original size:13 final size:13
Alignment explanation
Indices: 71563--71587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71553 TTATATTGAT
71563 GCTTTAGAGGCTA
1 GCTTTAGAGGCTA
71576 GCTTTAGAGGCT
1 GCTTTAGAGGCT
71588 CATTTCCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (13 bp):
GCTTTAGAGGCTA
Done.