Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001618.1 Hibiscus syriacus cultivar Beakdansim tig00003215_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: 104193
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2810 original size:20 final size:20
Alignment explanation
Indices: 2787--2834 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2777 TAAAGAAGTG
2787 GGTGAAAGCTCAAAGGCCAA
1 GGTGAAAGCTCAAAGGCCAA
*
2807 GGTGAAAGCTCAAAGGCGAA
1 GGTGAAAGCTCAAAGGCCAA
*
2827 GGGGAAAG
1 GGTGAAAG
2835 AGAAAGCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.38, T:0.08
Consensus pattern (20 bp):
GGTGAAAGCTCAAAGGCCAA
Found at i:5167 original size:16 final size:19
Alignment explanation
Indices: 5135--5174 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
5125 ATGAAAATTG
5135 ATTTATCTTTGATTAATA-
1 ATTTATCTTTGATTAATAT
5153 ATTTAT-TTT-ATTAATAT
1 ATTTATCTTTGATTAATAT
5170 ATTTA
1 ATTTA
5175 CCTTGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTATCTTTGATTAATAT
Found at i:5360 original size:2 final size:2
Alignment explanation
Indices: 5347--5386 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5337 TCCGTCACTA
*
5347 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5387 TAAGCTTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6602 original size:30 final size:30
Alignment explanation
Indices: 6537--6608 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
6527 ATATTAAGAA
* * * *
6537 AATAAATTTAAATTTATGAGTTTTTAATAG
1 AATAAAATTAAATTTATAAATTTTAAATAG
*
6567 GATAAAATTAAATTTATAAAATTTTAAAT-G
1 AATAAAATTAAATTTAT-AAATTTTAAATAG
*
6597 AATAAAAATAAA
1 AATAAAATTAAA
6609 AAAATTAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (30 bp):
AATAAAATTAAATTTATAAATTTTAAATAG
Found at i:6731 original size:35 final size:35
Alignment explanation
Indices: 6680--6748 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
6670 GACGTTGTTG
6680 TTATTTATTTCACTAGTTCCATCCATGATTATAGC
1 TTATTTATTTCACTAGTTCCATCCATGATTATAGC
6715 TTATTTATTT-AGCTAGTTCCATCCATGATTATAG
1 TTATTTATTTCA-CTAGTTCCATCCATGATTATAG
6749 AGACGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.46
Consensus pattern (35 bp):
TTATTTATTTCACTAGTTCCATCCATGATTATAGC
Found at i:7951 original size:2 final size:2
Alignment explanation
Indices: 7944--7991 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
7934 ATTCTAACCC
7944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7986 AT AT AT
1 AT AT AT
7992 CACATCTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21730 original size:18 final size:18
Alignment explanation
Indices: 21709--21744 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21699 CCTCATTATC
21709 CTTCATTCCT-TCTTTCTT
1 CTTCATT-CTATCTTTCTT
21727 CTTCATTCTATCTTTCTT
1 CTTCATTCTATCTTTCTT
21745 TATCTCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.61
Consensus pattern (18 bp):
CTTCATTCTATCTTTCTT
Found at i:27818 original size:19 final size:20
Alignment explanation
Indices: 27794--27851 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
27784 AATACCTTTA
*
27794 CATATTTTTT-AATTAAAAT
1 CATATTTTTTGAATAAAAAT
27813 CATATTTTTATTGAATAAAAAT
1 CATA-TTTT-TTGAATAAAAAT
* *
27835 AATATTTTTTTAATAAA
1 CATATTTTTTGAATAAA
27852 TGTTTTGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 4 0.12
20 12 0.36
21 6 0.18
22 11 0.33
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
CATATTTTTTGAATAAAAAT
Found at i:27851 original size:20 final size:20
Alignment explanation
Indices: 27798--27851 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
27788 CCTTTACATA
* *
27798 TTTTTTAATTAAAATCATAT
1 TTTTTTAATAAAAATAATAT
27818 TTTTATTGAATAAAAATAATAT
1 TTTT-TT-AATAAAAATAATAT
27840 TTTTTTAATAAA
1 TTTTTTAATAAA
27852 TGTTTTGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
21 4 0.13
22 16 0.53
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTTTAATAAAAATAATAT
Found at i:34524 original size:3 final size:3
Alignment explanation
Indices: 34516--34552 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
34506 ATAATTATTC
34516 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34553 AAGAACAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39942 original size:15 final size:15
Alignment explanation
Indices: 39922--39952 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39912 TTGTTCCTAT
39922 TATAGATGACTACCG
1 TATAGATGACTACCG
39937 TATAGATGACTACCG
1 TATAGATGACTACCG
39952 T
1 T
39953 GAAAATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29
Consensus pattern (15 bp):
TATAGATGACTACCG
Found at i:41070 original size:24 final size:24
Alignment explanation
Indices: 41025--41076 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
41015 TTACTACTGT
* *
41025 CTTTCCCACTGTGTCTGCCTCTGC
1 CTTTACCACTGTCTCTGCCTCTGC
* * *
41049 CTTTACCACTGTCTTTGTCTCTGT
1 CTTTACCACTGTCTCTGCCTCTGC
41073 CTTT
1 CTTT
41077 GGTTCTGCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.35, G:0.13, T:0.46
Consensus pattern (24 bp):
CTTTACCACTGTCTCTGCCTCTGC
Found at i:41084 original size:36 final size:36
Alignment explanation
Indices: 41044--41112 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
41034 TGTGTCTGCC
* *
41044 TCTGCCTTTACCACTGTCTTTGTCTCTGTCTTTGGT
1 TCTGCCTTTACCACTGTCTTTGGCTCTGCCTTTGGT
* *
41080 TCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTT
1 TCTGCCTTTACCACTGTCTTTGGCTCTGCCTTT
41113 ACCACTGTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.04, C:0.29, G:0.16, T:0.51
Consensus pattern (36 bp):
TCTGCCTTTACCACTGTCTTTGGCTCTGCCTTTGGT
Found at i:41088 original size:24 final size:24
Alignment explanation
Indices: 41067--41338 Score: 167
Period size: 24 Copynumber: 10.8 Consensus size: 24
41057 CTGTCTTTGT
*
41067 CTCTGTCTTTGGTTCTGCCTTTAC
1 CTCTGTCTTTGGCTCTGCCTTTAC
*
41091 CTCTGTTTTTGGCTCTGCCTTTAC
1 CTCTGTCTTTGGCTCTGCCTTTAC
* * *
41115 CACTGTC-TTGGCTTCCGCCTTTAA
1 CTCTGTCTTTGGC-TCTGCCTTTAC
* * *
41139 CTCTGTTTTTGGCACTTCCTTTAC
1 CTCTGTCTTTGGCTCTGCCTTTAC
* *
41163 CACTG-CCTTGGCTTCTGCCTTTAC
1 CTCTGTCTTTGGC-TCTGCCTTTAC
* * * *
41187 CTCTGTCTTTTGTTTTTCCATTATCACC
1 CTCTGTCTTTGGCTCTGCC-TT-T-A-C
* *
41215 GTCTCTGCCTCTGTG-TCTGCCTTTTCCTTTAC
1 --CTCTGTCTTTG-GCTCTG-C-----CTTTAC
41247 CTCTGTCTTTGGCTCTGCCTTTAC
1 CTCTGTCTTTGGCTCTGCCTTTAC
* *
41271 CACTGTCTTT-GCTTCCGCCTTTAC
1 CTCTGTCTTTGGC-TCTGCCTTTAC
*
41295 CTCTGTCTTT-GCTTCCGCCTTTAC
1 CTCTGTCTTTGGC-TCTGCCTTTAC
**
41319 CTCTGTCTTTGTTTCTGCCT
1 CTCTGTCTTTGGCTCTGCCT
41339 CAGGCTCTGC
Statistics
Matches: 192, Mismatches: 36, Indels: 40
0.72 0.13 0.15
Matches are distributed among these distances:
23 12 0.06
24 133 0.69
25 11 0.06
26 1 0.01
27 1 0.01
28 1 0.01
29 2 0.01
30 23 0.12
31 2 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 2 0.01
36 1 0.01
ACGTcount: A:0.06, C:0.33, G:0.14, T:0.47
Consensus pattern (24 bp):
CTCTGTCTTTGGCTCTGCCTTTAC
Found at i:41121 original size:48 final size:48
Alignment explanation
Indices: 41069--41338 Score: 197
Period size: 48 Copynumber: 5.4 Consensus size: 48
41059 GTCTTTGTCT
41069 CTGTCTTTGGTTCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCA
1 CTGTCTTTGGTTCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCA
* * * *
41117 CTGTC-TTGGCTTCCGCCTTTAACTCTGTTTTTGGCACTTCCTTTACCA
1 CTGTCTTTGG-TTCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCA
* * * * *
41165 CTG-CCTTGGCTTCTGCCTTTACCTCTGTCTTTT-GTTTTTCCATTATCACCGTCT
1 CTGTCTTTGG-TTCTGCCTTTACCTCTGT-TTTTGGCTCTGCC-TT-T-A-C--CA
* * * *
41219 CTGCCTCTGTGTCTGCCTTTTCCTTTACCTCTGTCTTTGGCTCTGCCTTTACCA
1 CTGTCTTTG-GT-T--C--TGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCA
* * * * *
41273 CTGTCTTTGCTTCCGCCTTTACCTCTGTCTTT-GCTTCCGCCTTTACCT
1 CTGTCTTTGGTTCTGCCTTTACCTCTGTTTTTGGC-TCTGCCTTTACCA
*
41321 CTGTCTTTGTTTCTGCCT
1 CTGTCTTTGGTTCTGCCT
41339 CAGGCTCTGC
Statistics
Matches: 177, Mismatches: 27, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
47 7 0.04
48 112 0.63
49 6 0.03
50 2 0.01
51 1 0.01
52 2 0.01
53 1 0.01
54 12 0.07
55 4 0.02
56 3 0.02
57 1 0.01
58 2 0.01
59 5 0.03
60 19 0.11
ACGTcount: A:0.06, C:0.33, G:0.14, T:0.47
Consensus pattern (48 bp):
CTGTCTTTGGTTCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCA
Found at i:41143 original size:72 final size:72
Alignment explanation
Indices: 41067--41338 Score: 206
Period size: 72 Copynumber: 3.6 Consensus size: 72
41057 CTGTCTTTGT
*
41067 CTCTGTCTTTGGTTCTGCCTTTACCTCTGTTTTTGGCTCTGCCTTTACCACTGTCTTGGCTTCCG
1 CTCTGTCTTTGGTTCTGCCTTTACCTCTGTCTTTGGCTCTGCCTTTACCACTGTCTTGGCTTCCG
41132 CCTTTAA
66 CCTTTAA
* ** * * * * **
41139 CTCTGTTTTTGGCACTTCCTTTACCACTG-CCTTGGCTTCTGCCTTTACCTCTGTCTTTTGTTTT
1 CTCTGTCTTTGGTTCTGCCTTTACCTCTGTCTTTGGC-TCTGCCTTTACCACTGTC--TTGGCTT
* * *
41203 TC-CATTATCACCGT
63 CCGCCTT-T-A---A
* * * *
41217 CTCTGCCTCTGTGTCTGCCTTTTCCTTTACCTCTGTCTTTGGCTCTGCCTTTACCACTGTCTTTG
1 CTCTGTCTTTG-GT-T--C--TGCCTTTACCTCTGTCTTTGGCTCTGCCTTTACCACTGTCTTGG
*
41282 CTTCCGCCTTTAC
60 CTTCCGCCTTTAA
* * **
41295 CTCTGTCTTTGCTTCCGCCTTTACCTCTGTCTTTGTTTCTGCCT
1 CTCTGTCTTTGGTTCTGCCTTTACCTCTGTCTTTGGCTCTGCCT
41339 CAGGCTCTGC
Statistics
Matches: 150, Mismatches: 34, Indels: 32
0.69 0.16 0.15
Matches are distributed among these distances:
71 5 0.03
72 66 0.44
73 3 0.02
74 8 0.05
75 1 0.01
76 1 0.01
77 1 0.01
78 17 0.11
79 1 0.01
81 1 0.01
82 7 0.05
83 3 0.02
84 30 0.20
85 6 0.04
ACGTcount: A:0.06, C:0.33, G:0.14, T:0.47
Consensus pattern (72 bp):
CTCTGTCTTTGGTTCTGCCTTTACCTCTGTCTTTGGCTCTGCCTTTACCACTGTCTTGGCTTCCG
CCTTTAA
Found at i:41280 original size:12 final size:12
Alignment explanation
Indices: 41241--41328 Score: 68
Period size: 12 Copynumber: 7.3 Consensus size: 12
41231 CTGCCTTTTC
41241 CTTTACCTCTGT
1 CTTTACCTCTGT
** *
41253 CTTTGGCTCTGC
1 CTTTACCTCTGT
*
41265 CTTTACCACTGT
1 CTTTACCTCTGT
* * * *
41277 CTTTGCTTCCGC
1 CTTTACCTCTGT
41289 CTTTACCTCTGT
1 CTTTACCTCTGT
* * * *
41301 CTTTGCTTCCGC
1 CTTTACCTCTGT
41313 CTTTACCTCTGT
1 CTTTACCTCTGT
41325 CTTT
1 CTTT
41329 GTTTCTGCCT
Statistics
Matches: 52, Mismatches: 24, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.06, C:0.35, G:0.12, T:0.47
Consensus pattern (12 bp):
CTTTACCTCTGT
Found at i:41774 original size:39 final size:39
Alignment explanation
Indices: 41709--41900 Score: 217
Period size: 39 Copynumber: 4.9 Consensus size: 39
41699 TAGGCTCATG
* * * * * *
41709 TTCATTTCGTCGTTCCGAAGCTGCACTAGAACTATCGAG
1 TTCATTTTGTTGTTCCGAAACTGCACTAGAAATATCTAC
* * * *
41748 TTCTTTTTGTTGTTCCGACACTGCACTGGAAATATC-AGG
1 TTCATTTTGTTGTTCCGAAACTGCACTAGAAATATCTA-C
* *
41787 TTCATTTTGTTGTTTCGAAACTGCACTAGAAATATCTCC
1 TTCATTTTGTTGTTCCGAAACTGCACTAGAAATATCTAC
*
41826 TTCATTTCGTTGTTCCGAAACTGCACTAGAAATAT-TAC
1 TTCATTTTGTTGTTCCGAAACTGCACTAGAAATATCTAC
* *
41864 TTCCGTTTTGTTGTTCCGAAATTGCACTAGAAATATC
1 TT-CATTTTGTTGTTCCGAAACTGCACTAGAAATATC
41901 ATCGGTATCT
Statistics
Matches: 130, Mismatches: 19, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
38 5 0.04
39 125 0.96
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (39 bp):
TTCATTTTGTTGTTCCGAAACTGCACTAGAAATATCTAC
Found at i:42038 original size:39 final size:39
Alignment explanation
Indices: 41995--42093 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
41985 TCCACTCTCT
* * *
41995 TCAGCTTTTGGTAGAT-TGGCACCATCCGCTTCACCTTGA
1 TCAGCATTTGGT-GATATGGCACCATACGCTCCACCTTGA
* * *
42034 TCAGCGTTTGGTGCTATGGCATCATACGCTCCACCTTGA
1 TCAGCATTTGGTGATATGGCACCATACGCTCCACCTTGA
*
42073 TCAGCATTTGGTGCTATGGCA
1 TCAGCATTTGGTGATATGGCA
42094 TCATTCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 2 0.04
39 51 0.96
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (39 bp):
TCAGCATTTGGTGATATGGCACCATACGCTCCACCTTGA
Found at i:42094 original size:39 final size:39
Alignment explanation
Indices: 42011--42097 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
42001 TTTGGTAGAT
* * * *
42011 TGGCACCATCCGCTTCACCTTGATCAGCGTTTGGTGCTA
1 TGGCATCATACGCTCCACCTTGATCAGCATTTGGTGCTA
42050 TGGCATCATACGCTCCACCTTGATCAGCATTTGGTGCTA
1 TGGCATCATACGCTCCACCTTGATCAGCATTTGGTGCTA
42089 TGGCATCAT
1 TGGCATCAT
42098 TCAATTCATC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (39 bp):
TGGCATCATACGCTCCACCTTGATCAGCATTTGGTGCTA
Found at i:42111 original size:39 final size:39
Alignment explanation
Indices: 42024--42124 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
42014 CACCATCCGC
**
42024 TTCACCTTGATCAGCGTTTGGTGCTATGGCATCATACGC
1 TTCACCTTGATCAGCGTTTGGTGCTATGGCATCATACAA
* * *
42063 TCCACCTTGATCAGCATTTGGTGCTATGGCATCATTCAA
1 TTCACCTTGATCAGCGTTTGGTGCTATGGCATCATACAA
* *
42102 TTCATCTTGACCAGCGTTTGGTG
1 TTCACCTTGATCAGCGTTTGGTG
42125 TTCTAGCATC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (39 bp):
TTCACCTTGATCAGCGTTTGGTGCTATGGCATCATACAA
Found at i:42173 original size:78 final size:78
Alignment explanation
Indices: 42024--42344 Score: 225
Period size: 78 Copynumber: 4.1 Consensus size: 78
42014 CACCATCCGC
* * * * * *** *
42024 TTCACCTTGATCAGCGTTTGGTGCTATGGCATCATACGCTCCACCTTGATCAGCA-TTTGGTGCT
1 TTCACCTTGATCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAG-ATTTTGGTGTT
* * *
42088 ATGGCATCATTCAA
65 CTCGCATCATCCAA
* *
42102 TTCATCTTGACCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGATTTTGGTGTTC
1 TTCACCTTGATCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGATTTTGGTGTTC
**
42167 TCGCATCATCCGC
66 TCGCATCATCCAA
*** ** * * * *
42180 TTCACCCCCATCAGATTTTGGTGTTCTCGCATCATCCGCTTGACTCCTATCAGATTTTGGTGTTC
1 TTCACCTTGATCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGATTTTGGTGTTC
**
42245 TCGCATCATCCGC
66 TCGCATCATCCAA
* ** * *** ** ** *
42258 TTCACCCCT-ATCAGATTTTGGTGTTCTGGTGCCATTTGCTTCACCCTGATCAGTTTTTGGTGTT
1 TTCA-CCTTGATCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGATTTTGGTGTT
* *
42322 -TCTGTATCATCCAC
65 CTC-GCATCATCCAA
42336 TTCACCTTG
1 TTCACCTTG
42345 TTCATCTTTC
Statistics
Matches: 197, Mismatches: 42, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
77 6 0.03
78 188 0.95
79 3 0.02
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (78 bp):
TTCACCTTGATCAGCGTTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGATTTTGGTGTTC
TCGCATCATCCAA
Found at i:42299 original size:39 final size:39
Alignment explanation
Indices: 42118--42341 Score: 290
Period size: 39 Copynumber: 5.7 Consensus size: 39
42108 TTGACCAGCG
* *
42118 TTTGGTGTTCTAGCATCATCCGCTTCACCCCCATCAGAT
1 TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
*
42157 TTTGGTGTTCTCGCATCATCCGCTTCACCCCCATCAGAT
1 TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
* *
42196 TTTGGTGTTCTCGCATCATCCGCTTGACTCCTATCAGAT
1 TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
42235 TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
1 TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
* *** ** *
42274 TTTGGTGTTCTGGTGCCATTTGCTTCA-CCCTGATCAGTT
1 TTTGGTGTTCTCGCATCATCCGCTTCACCCCT-ATCAGAT
* *
42313 TTTGGTGTT-TCTGTATCATCCACTTCACC
1 TTTGGTGTTCTC-GCATCATCCGCTTCACC
42342 TTGTTCATCT
Statistics
Matches: 163, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
38 5 0.03
39 157 0.96
40 1 0.01
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (39 bp):
TTTGGTGTTCTCGCATCATCCGCTTCACCCCTATCAGAT
Found at i:42828 original size:3 final size:3
Alignment explanation
Indices: 42820--42849 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42810 TGTAGCCTTG
42820 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
42850 TCAGTGCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:43484 original size:3 final size:3
Alignment explanation
Indices: 43478--43514 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
43468 TTTATTATCT
*
43478 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43515 GGTATTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:43747 original size:80 final size:78
Alignment explanation
Indices: 43657--43810 Score: 175
Period size: 78 Copynumber: 1.9 Consensus size: 78
43647 TCGCTAATTA
* * ** *
43657 ATTTTCGGTAGAACCCAATATTAACATTTTCGGT-ATAAAAAAATAATATTTTACGTAACGCTTT
1 ATTTTAGGTAGAACCAAATATTAACATTTT---TAATAAAAAAATAATATTTTAAATAACACTTT
*
43721 ACCAGAAATATTAAAC
63 ACCAAAAATATTAAAC
** * * *
43737 ATTTTAGGTAGCGCCAAATATTAATATTTTTAATAAAAAAATATTATTTTAAATAACACTTTACT
1 ATTTTAGGTAGAACCAAATATTAACATTTTTAATAAAAAAATAATATTTTAAATAACACTTTACC
43802 AAAAATATT
66 AAAAATATT
43811 TAAAAAAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 1 0.02
78 36 0.58
80 25 0.40
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (78 bp):
ATTTTAGGTAGAACCAAATATTAACATTTTTAATAAAAAAATAATATTTTAAATAACACTTTACC
AAAAATATTAAAC
Found at i:45971 original size:14 final size:14
Alignment explanation
Indices: 45952--45983 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
45942 AATAGGAAGT
45952 AATCCCTGCAAATA
1 AATCCCTGCAAATA
45966 AATCCCTGCAAATA
1 AATCCCTGCAAATA
45980 AATC
1 AATC
45984 ATTGCGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (14 bp):
AATCCCTGCAAATA
Found at i:55140 original size:23 final size:23
Alignment explanation
Indices: 55110--55155 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55100 GTAAAAAAAA
*
55110 TACCTAAAACATTATTATTTTTT
1 TACCTAAAACATTAATATTTTTT
*
55133 TACCTAAAACATTAATGTTTTTT
1 TACCTAAAACATTAATATTTTTT
55156 AACATTTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (23 bp):
TACCTAAAACATTAATATTTTTT
Found at i:67894 original size:21 final size:21
Alignment explanation
Indices: 67861--67905 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
67851 AGTTTTGAAA
* *
67861 AAAATTGAAAGTTTAGGTACT
1 AAAACTGAAAGTTTAGGCACT
*
67882 AAAACTGACAGTTTAGGCACT
1 AAAACTGAAAGTTTAGGCACT
67903 AAA
1 AAA
67906 CGCATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (21 bp):
AAAACTGAAAGTTTAGGCACT
Found at i:72586 original size:21 final size:22
Alignment explanation
Indices: 72562--72603 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
72552 GACTTCTTCT
72562 CCTCC-AACAACTTTGTTGCCG
1 CCTCCAAACAACTTTGTTGCCG
*
72583 CCTCCAAAACAGCTTTGTTGC
1 CCTCC-AAACAACTTTGTTGC
72604 AAAAATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (22 bp):
CCTCCAAACAACTTTGTTGCCG
Found at i:75039 original size:18 final size:18
Alignment explanation
Indices: 75016--75050 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
75006 TATTGCTGAT
75016 TGTTTCTCACCAGAGCTA
1 TGTTTCTCACCAGAGCTA
75034 TGTTTCTCACCAGAGCT
1 TGTTTCTCACCAGAGCT
75051 TTTGGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (18 bp):
TGTTTCTCACCAGAGCTA
Found at i:76436 original size:38 final size:37
Alignment explanation
Indices: 76362--76437 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
76352 GTTGGAAAAT
* *
76362 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
* *
76399 ATTTATATATTTTTTTTTACAAAATTGAAAAAT-ATAAA
1 ATTTATATA-TTTTATTTAAAAAATT-AAAAATCATAAA
76437 A
1 A
76438 AAATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 9 0.27
38 20 0.61
39 4 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
Found at i:82740 original size:23 final size:23
Alignment explanation
Indices: 82714--82761 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
82704 ATAAAGTACA
*
82714 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
82737 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
82760 AT
1 AT
82762 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:83167 original size:21 final size:20
Alignment explanation
Indices: 83137--83190 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
83127 GATAGACACT
*
83137 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
83158 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
83181 TTACATTATA
1 TTACATTATA
83191 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:83178 original size:23 final size:23
Alignment explanation
Indices: 83152--83214 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
83142 ATATAACCAT
83152 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
83175 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
83198 TACCTATTACATCATAT
1 TACCTATTACATTATAT
83215 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:83533 original size:430 final size:431
Alignment explanation
Indices: 82873--84174 Score: 2590
Period size: 430 Copynumber: 3.0 Consensus size: 431
82863 GGATCGATAC
82873 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
82938 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-ATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
83002 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
83067 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
83132 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
261 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
83197 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
326 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
83262 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
83303 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
83368 ATTTGATTGTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
83432 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
83497 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
83562 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
261 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
83627 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
326 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
83692 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
83733 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
83798 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
83863 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
83928 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
83993 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
261 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
84058 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
326 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
84123 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
84164 TTTAACAGTGT
1 TTTAACAGTGT
84175 ACTGCGAATT
Statistics
Matches: 870, Mismatches: 0, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
429 31 0.04
430 486 0.56
431 353 0.41
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (431 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
Found at i:83597 original size:21 final size:20
Alignment explanation
Indices: 83567--83620 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
83557 GATAGACACT
*
83567 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
83588 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
83611 TTACATTATA
1 TTACATTATA
83621 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:83608 original size:23 final size:23
Alignment explanation
Indices: 83582--83644 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
83572 ATATAACCAT
83582 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
83605 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
83628 TACCTATTACATCATAT
1 TACCTATTACATTATAT
83645 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:84028 original size:21 final size:20
Alignment explanation
Indices: 83998--84051 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
83988 GATAGACACT
*
83998 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
84019 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
84042 TTACATTATA
1 TTACATTATA
84052 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:84039 original size:23 final size:23
Alignment explanation
Indices: 84013--84075 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
84003 ATATAACCAT
84013 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
84036 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
84059 TACCTATTACATCATAT
1 TACCTATTACATTATAT
84076 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:87057 original size:184 final size:184
Alignment explanation
Indices: 86630--87298 Score: 1263
Period size: 182 Copynumber: 3.7 Consensus size: 184
86620 TTTTAAATGG
*
86630 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
86695 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
86760 GATGTGTAAAATGTCGACAC-TTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
86813 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
86878 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
86943 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
86997 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
87062 TAAGACCGGTATA-TT-TACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
87125 GATGTGTAAAATGTCGACACTTTTTGAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
87179 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
87244 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
87299 ATGTTGAAAG
Statistics
Matches: 477, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
182 178 0.37
183 152 0.32
184 147 0.31
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:88673 original size:3 final size:3
Alignment explanation
Indices: 88665--88715 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
88655 ACTTGTTTGG
* * * *
88665 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
88713 ATC
1 ATC
88716 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:88682 original size:12 final size:12
Alignment explanation
Indices: 88665--88727 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
88655 ACTTGTTTGG
88665 ATCATCATCTTC
1 ATCATCATCTTC
*
88677 ATCATCATCGTC
1 ATCATCATCTTC
*
88689 ATCATCATCATC
1 ATCATCATCTTC
*
88701 ATCGTCATCTTC
1 ATCATCATCTTC
* *
88713 ATCGTCAGCTTC
1 ATCATCATCTTC
88725 ATC
1 ATC
88728 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:88726 original size:18 final size:18
Alignment explanation
Indices: 88669--88730 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
88659 GTTTGGATCA
88669 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
88687 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
88705 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
88723 TCATCTTC
1 TCATCTTC
88731 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:88730 original size:6 final size:6
Alignment explanation
Indices: 88669--88730 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
88659 GTTTGGATCA
* * * * * *
88669 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
88717 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
88731 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:91373 original size:198 final size:199
Alignment explanation
Indices: 90193--91405 Score: 2092
Period size: 196 Copynumber: 6.1 Consensus size: 199
90183 TTTAAATTAG
* *
90193 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
90258 ATTGTACCGGTTAGATTAAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
90322 CGACACTTTTTATATATGGATCGACACTTTATTGATTCACCTTG-TAAAAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGG-GAA
90386 AAAAA
195 AAAAA
90391 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
90456 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* ***
90521 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAA
90586 AAAAA
195 AAAAA
90591 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
90656 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
90720 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAAA
90781 AAAA
196 AAAA
90785 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
90849 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* ***
90914 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAAA
90978 AAAA
196 AAAA
90982 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
91045 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* ***
91109 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAAA
91174 AAAA
196 AAAA
91178 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
91243 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
91308 CGACACTTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAA
91372 AAAAA
195 AAAAA
*
91377 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
91406 TGACCCTTAA
Statistics
Matches: 974, Mismatches: 28, Indels: 25
0.95 0.03 0.02
Matches are distributed among these distances:
193 120 0.12
194 23 0.02
195 64 0.07
196 216 0.22
197 15 0.02
198 209 0.21
199 116 0.12
200 198 0.20
201 13 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTCTGGGAAA
AAAA
Found at i:91511 original size:37 final size:38
Alignment explanation
Indices: 91470--91549 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
91460 TCTCATTCAT
*
91470 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
91507 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
91545 AATTA
1 AATTA
91550 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:91513 original size:19 final size:19
Alignment explanation
Indices: 91486--91549 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
91476 ATTCACATAA
*
91486 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
91505 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
91524 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
91543 AAAATTA
1 AAAATTA
91550 ACTCGACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:93361 original size:33 final size:33
Alignment explanation
Indices: 93324--93389 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
93314 CATCTTAATA
*
93324 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
93357 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
93390 CCATATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:95745 original size:20 final size:19
Alignment explanation
Indices: 95699--95745 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
95689 TCCGGTATCA
*
95699 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
95718 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
95739 TTTTACC
1 TTTTACC
95746 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:95911 original size:20 final size:20
Alignment explanation
Indices: 95863--95912 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
95853 TCGACACTTT
95863 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTTATCA
*
95883 T-TTTGTTACCGGTTTTATCA
1 TAATT-TTACCGGTTTTATCA
95903 TAATTTTACC
1 TAATTTTACC
95913 TGGTATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (20 bp):
TAATTTTACCGGTTTTATCA
Found at i:99625 original size:4 final size:4
Alignment explanation
Indices: 99616--99645 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
99606 TGGGGTTGAA
99616 ATTT ATTT ATTT ATTT ATTT A-TT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
99646 ATGTATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:99633 original size:12 final size:11
Alignment explanation
Indices: 99616--99645 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
99606 TGGGGTTGAA
99616 ATTTATTTATTT
1 ATTTATTTA-TT
99628 ATTTATTTATT
1 ATTTATTTATT
99639 ATTTATT
1 ATTTATT
99646 ATGTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Done.