Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002332.1 Kokia drynarioides strain JFW-HI SEQ_114380, 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: 68881
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:100 original size:7 final size:7
Alignment explanation
Indices: 73--135 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
63 TCTTCTTCCC
73 CTTC-TT
1 CTTCTTT
*
79 CTCCTTT
1 CTTCTTT
*
86 -TTCCTT
1 CTTCTTT
92 CTTCTTT
1 CTTCTTT
99 CTTTCTTT
1 C-TTCTTT
107 CTTTCTTT
1 C-TTCTTT
115 C-TCTTT
1 CTTCTTT
*
121 TTTCTTT
1 CTTCTTT
*
128 CTTTTTT
1 CTTCTTT
135 C
1 C
136 CTTCATTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
6 12 0.26
7 19 0.41
8 15 0.33
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
CTTCTTT
Found at i:102 original size:4 final size:4
Alignment explanation
Indices: 93--135 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
83 TTTTTCCTTC
*
93 TTCT TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
136 CTTCATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:110 original size:25 final size:23
Alignment explanation
Indices: 82--139 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
72 CCTTCTTCTC
82 CTTTTTCCTTCTTCTTTCTTTCTTT
1 CTTTTTCCTTC-TCTTT-TTTCTTT
*
107 C--TTTCTTTCTCTTTTTTCTTT
1 CTTTTTCCTTCTCTTTTTTCTTT
128 CTTTTTTCCTTC
1 C-TTTTTCCTTC
140 ATTTTTCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
21 8 0.29
22 5 0.18
23 7 0.25
24 7 0.25
25 1 0.04
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
CTTTTTCCTTCTCTTTTTTCTTT
Found at i:144 original size:12 final size:11
Alignment explanation
Indices: 83--146 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
73 CTTCTTCTCC
*
83 TTTTTCCTTCT
1 TTTTTCTTTCT
*
94 TCTTTCTTTCT
1 TTTTTCTTTCT
105 TTCTTTCTTTCTCT
1 TT-TTTC-TT-TCT
119 TTTTTCTTTCT
1 TTTTTCTTTCT
* *
130 TTTTTCCTTCA
1 TTTTTCTTTCT
141 TTTTTC
1 TTTTTC
147 GTTGGTCCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 28 0.62
12 6 0.13
13 6 0.13
14 5 0.11
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:144 original size:21 final size:21
Alignment explanation
Indices: 85--135 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
75 TCTTCTCCTT
*
85 TTTCCTTCTTCTTTCTTTCTTTC
1 TTTCTTTC-TCTTT-TTTCTTTC
108 TTTCTTTCTCTTTTTTCTTTC
1 TTTCTTTCTCTTTTTTCTTTC
129 TTT-TTTC
1 TTTCTTTC
136 CTTCATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 5 0.19
23 7 0.26
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTCTTTCTCTTTTTTCTTTC
Found at i:1025 original size:3 final size:3
Alignment explanation
Indices: 1012--1048 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1002 TCGACTATTT
*
1012 CAC CGC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1049 CGCATCAAAT
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:0.30, C:0.68, G:0.03, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:3932 original size:20 final size:21
Alignment explanation
Indices: 3896--3945 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
3886 ATTGGCATGG
*
3896 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
3917 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
3938 -TTAATTAA
1 TTTAATTAA
3946 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:4042 original size:3 final size:3
Alignment explanation
Indices: 4034--4063 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4024 TTCATCCCAT
4034 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4064 ACACGGCAAC
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:5635 original size:3 final size:3
Alignment explanation
Indices: 5627--5656 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5617 ATTTCTTCAT
5627 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5657 ACAGACAAAT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6976 original size:94 final size:94
Alignment explanation
Indices: 6813--7001 Score: 360
Period size: 94 Copynumber: 2.0 Consensus size: 94
6803 GTTCGTTTGT
6813 TAAGTTTTATATTTGAATTGCTAATTGATGTTAACTTGGAAGTTTCTTGGACTATTTGATAAATA
1 TAAGTTTTATATTTGAATTGCTAATTGATGTTAACTTGGAAGTTTCTTGGACTATTTGATAAATA
6878 AAAGACTTGGTGATTACTAAAAGGAAGAC
66 AAAGACTTGGTGATTACTAAAAGGAAGAC
* *
6907 TAAGTTTTATATTTGAATTGCTAATTGATGTTAACTTGGAAGTTTCTTGGACTATTTGATAATTG
1 TAAGTTTTATATTTGAATTGCTAATTGATGTTAACTTGGAAGTTTCTTGGACTATTTGATAAATA
6972 AAAGACTTGGTGATTACTAAAAGGAAGAC
66 AAAGACTTGGTGATTACTAAAAGGAAGAC
7001 T
1 T
7002 CATGTCTCTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 93 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (94 bp):
TAAGTTTTATATTTGAATTGCTAATTGATGTTAACTTGGAAGTTTCTTGGACTATTTGATAAATA
AAAGACTTGGTGATTACTAAAAGGAAGAC
Found at i:7193 original size:44 final size:43
Alignment explanation
Indices: 6989--7200 Score: 230
Period size: 43 Copynumber: 4.9 Consensus size: 43
6979 TGGTGATTAC
* * * * *
6989 TAAAAGGAAGACTCATGTCTCTGATAGAGCATGAGGTTATTTA
1 TAAAAGGAAAACTTATGTCTCGGTTAGAGCATAAGGTTATTTA
* ** * *
7032 TAAATGGAAGGCTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAAACTTATGTCTCGGTTAGAGCATAAGGTTATTTA
* *
7075 TAAAAGGAAAACTTATGTCTCGGTTAGAGCATAAGATTGTTTA
1 TAAAAGGAAAACTTATGTCTCGGTTAGAGCATAAGGTTATTTA
* *
7118 TAAAAGGAAAACTTATGTCTCAG-TAGGAGCATAAGGTTATTTG
1 TAAAAGGAAAACTTATGTCTCGGTTA-GAGCATAAGGTTATTTA
* **
7161 TAAATGGAAGAACTTATCACTCGGTT-GAAGCATAAGGTTA
1 TAAAAGGAA-AACTTATGTCTCGGTTAG-AGCATAAGGTTA
7201 ATATAGTTCG
Statistics
Matches: 146, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
42 2 0.01
43 120 0.82
44 23 0.16
45 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (43 bp):
TAAAAGGAAAACTTATGTCTCGGTTAGAGCATAAGGTTATTTA
Found at i:9891 original size:79 final size:79
Alignment explanation
Indices: 9758--9969 Score: 325
Period size: 79 Copynumber: 2.7 Consensus size: 79
9748 AAAACCGATG
* * * *
9758 ATCCTAGCACCTAGTGCCTAGCGGATAAACCACAAAAGCGAGTCCAGCTCTAGTTGGATTAACCA
1 ATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
9823 ACAATATCCGTCAA
66 ACAATATCCGTCAA
* * *
9837 ATCCTAGCACCCAGTGCTTAACGGATAAACCGCAAAAGTGAGCCCAGCTTTAGTTGGATTAACCA
1 ATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
9902 ACAATATCCGTCAA
66 ACAATATCCGTCAA
* * * *
9916 ATTCTAGCACCCAATGCCTAGCGGATAAACCGTAAAAATGAGCCCAGCTCTAGT
1 ATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGT
9970 CAGTTAAACT
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 119 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (79 bp):
ATCCTAGCACCCAGTGCCTAGCGGATAAACCGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
ACAATATCCGTCAA
Found at i:13474 original size:21 final size:22
Alignment explanation
Indices: 13417--13477 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
13407 AAACTGTACA
* **
13417 AATTTCTACTGATACTTGTGCT
1 AATTTCTACCGATACAAGTGCT
* *
13439 AGTTT-TACCGGTACAAGTG-T
1 AATTTCTACCGATACAAGTGCT
13459 AATTTCTACCGATACAAGT
1 AATTTCTACCGATACAAGT
13478 CATGCATCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 5 0.16
21 22 0.71
22 4 0.13
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (22 bp):
AATTTCTACCGATACAAGTGCT
Found at i:17052 original size:43 final size:42
Alignment explanation
Indices: 16973--17141 Score: 152
Period size: 43 Copynumber: 4.1 Consensus size: 42
16963 AGAATTTCCT
* * * *
16973 CTTTAAAC--ATTCTTATGCTCTA-TCGAGTCATAAGTCTTC
1 CTTTAAACATATTCTCATGCTCAATTCGAGACATGAGTCTTC
* *
17012 CTTTCAAACATAATCTCACGCTCAATTCGAGACATGAGTCTTC
1 CTTT-AAACATATTCTCATGCTCAATTCGAGACATGAGTCTTC
* * *
17055 CTTT-ATCATATTCTCATGCTC-ATTCCAGTCATGAGTCTTC
1 CTTTAAACATATTCTCATGCTCAATTCGAGACATGAGTCTTC
* * **
17095 CATTTATACA-ATTTTTCATGCTCAACCCGAGACATGAGTCTTC
1 C-TTTAAACATA-TTCTCATGCTCAATTCGAGACATGAGTCTTC
17138 CTTT
1 CTTT
17142 TTATACATCG
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
39 4 0.04
40 22 0.21
41 18 0.17
42 25 0.24
43 35 0.34
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (42 bp):
CTTTAAACATATTCTCATGCTCAATTCGAGACATGAGTCTTC
Found at i:17085 original size:83 final size:83
Alignment explanation
Indices: 16981--17141 Score: 193
Period size: 83 Copynumber: 1.9 Consensus size: 83
16971 CTCTTTAAAC
* * **
16981 ATTCTTATGCTCTATCGAGTCATAAGTCTTCC-TTTCAAAC-ATAATCTCACGCTCAATTCGAGA
1 ATTCTCATGCTCTATCCAGTCATAAGTCTTCCATTT-AAACAAT-ATCTCACGCTCAACCCGAGA
17044 CATGAGTCTTCCTTTATCAT
64 CATGAGTCTTCCTTTATCAT
* * * * *
17064 ATTCTCATGCTC-ATTCCAGTCATGAGTCTTCCATTTATACAATTTTTCATGCTCAACCCGAGAC
1 ATTCTCATGCTCTA-TCCAGTCATAAGTCTTCCATTTAAACAATATCTCACGCTCAACCCGAGAC
17128 ATGAGTCTTCCTTT
65 ATGAGTCTTCCTTT
17142 TTATACATCG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
82 1 0.02
83 60 0.91
84 5 0.08
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (83 bp):
ATTCTCATGCTCTATCCAGTCATAAGTCTTCCATTTAAACAATATCTCACGCTCAACCCGAGACA
TGAGTCTTCCTTTATCAT
Found at i:24367 original size:27 final size:27
Alignment explanation
Indices: 24317--24574 Score: 178
Period size: 27 Copynumber: 9.6 Consensus size: 27
24307 TCCTTCATAG
* *
24317 TTTGCCACAAGGGCT-TATCTTTCATGA
1 TTTGCCACAAAGGCTAT-TCATTCATGA
* *
24344 TTCGCCACAAAGGCTATTTATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* ** ** * * *
24371 CTCACCGTAATGGTTATTCATTCATGT
1 TTTGCCACAAAGGCTATTCATTCATGA
** * *
24398 TTTGCCGTAATGGTTATTCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* ** *
24425 CTTGCCACAAAAACTATCCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * * * *
24452 TTTTCCATAAAGGATACTCATTAATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * *
24479 TTTTCCATAAAGGTTATTCATTCATGA
1 TTTGCCACAAAGGCTATTCATTCATGA
* *
24506 TTTTCCACAAAGGCTATTCATTCATAA
1 TTTGCCACAAAGGCTATTCATTCATGA
* * *
24533 TTTGTCACAACGGCT-TCTCATTAATGA
1 TTTGCCACAAAGGCTAT-TCATTCATGA
*
24560 TTTGTCACAAAGGCT
1 TTTGCCACAAAGGCT
24575 TTTCTTTTCT
Statistics
Matches: 184, Mismatches: 45, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
26 1 0.01
27 182 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (27 bp):
TTTGCCACAAAGGCTATTCATTCATGA
Found at i:24422 original size:81 final size:80
Alignment explanation
Indices: 24337--24530 Score: 210
Period size: 81 Copynumber: 2.4 Consensus size: 80
24327 GGGCTTATCT
* * * * * *
24337 TTCATGATTCGCCACAAAGGCTATTTATTCATGACTCACCGTAATGGTTATTCATTCATG-TTTT
1 TTCATGATT-GCCACAAAGGCTATTCATTCATGACTCACCATAAAGGATACTCATTAATGATTTT
* *
24401 GCCGTAATGGTTATTCA
65 -CCATAAAGGTTATTCA
** * * **
24418 TTCATGACTTGCCACAAAAACTATCCATTCATGATTTTCCATAAAGGATACTCATTAATGATTTT
1 TTCATGA-TTGCCACAAAGGCTATTCATTCATGACTCACCATAAAGGATACTCATTAATGATTTT
24483 CCATAAAGGTTATTCA
65 CCATAAAGGTTATTCA
*
24499 TTCATGATTTTCCACAAAGGCTATTCATTCAT
1 TTCATGA-TTGCCACAAAGGCTATTCATTCAT
24531 AATTTGTCAC
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
81 86 0.93
82 6 0.07
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (80 bp):
TTCATGATTGCCACAAAGGCTATTCATTCATGACTCACCATAAAGGATACTCATTAATGATTTTC
CATAAAGGTTATTCA
Found at i:24553 original size:81 final size:81
Alignment explanation
Indices: 24409--24562 Score: 202
Period size: 81 Copynumber: 1.9 Consensus size: 81
24399 TTGCCGTAAT
* *
24409 GGTTATTCATTCATGACTTGCCACAAAAACTATCCATTCATGATTTTCCATAAAGGATACTCATT
1 GGTTATTCATTCATGACTTGCCACAAAAACTATCCATTCATAATTTTCCACAAAGGATACTCATT
24474 AATGATTTTCCATAAA
66 AATGATTTTCCATAAA
* * ** * * * *
24490 GGTTATTCATTCATGATTTTCCACAAAGGCTATTCATTCATAATTTGT-CACAACGGCTTCTCAT
1 GGTTATTCATTCATGACTTGCCACAAAAACTATCCATTCATAATTT-TCCACAAAGGATACTCAT
24554 TAATGATTT
65 TAATGATTT
24563 GTCACAAAGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
81 61 0.98
82 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.38
Consensus pattern (81 bp):
GGTTATTCATTCATGACTTGCCACAAAAACTATCCATTCATAATTTTCCACAAAGGATACTCATT
AATGATTTTCCATAAA
Found at i:39549 original size:29 final size:30
Alignment explanation
Indices: 39506--39564 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
39496 GAATTAGATC
*
39506 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
* *
39536 AAATCAAAA-TTCATATATACAATTTCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
39565 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCACA
Found at i:40370 original size:17 final size:18
Alignment explanation
Indices: 40338--40371 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40328 AGTCTAAATC
40338 AAATAAAAATAATACAAT
1 AAATAAAAATAATACAAT
*
40356 AAATAAAGA-AATACAA
1 AAATAAAAATAATACAA
40372 AACTTAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAATACAAT
Found at i:41416 original size:27 final size:27
Alignment explanation
Indices: 41380--41432 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
41370 CATGTTTTTT
* *
41380 TTTTTTACCAAGTAAGTTGTTGTAAAC
1 TTTTTCACCAAATAAGTTGTTGTAAAC
41407 TTTTTCACCAAATAAGTTGTTGTAAA
1 TTTTTCACCAAATAAGTTGTTGTAAA
41433 GGGGCCTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (27 bp):
TTTTTCACCAAATAAGTTGTTGTAAAC
Found at i:45220 original size:42 final size:42
Alignment explanation
Indices: 45154--45599 Score: 506
Period size: 42 Copynumber: 10.8 Consensus size: 42
45144 TTATAACTTT
* * *
45154 AATCTACCCTCTGGTTAGGGTAAAATATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* *
45196 AATTTGTCCTCTTGTTAGGGTAAAAGATTGGAT-G-GT-TTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* * * * * *
45235 AATCTGCCC-CATGGTTGGGGTAAGAGATTGAATTGTGTTTTC
1 AATCTGCCCTC-TTGTTAGGGTAAAAGATTGGATGGTGTCTTC
*
45277 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGAT-G-G-CTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* * *
45316 AATCTACCC-CATGGTT-GGTGTAAGAGATTGGAT-G-G-CTTC
1 AATCTGCCCTC-TTGTTAGG-GTAAAAGATTGGATGGTGTCTTC
* * * *
45355 AATTTGCCC-CATGGTTGGGGTAAGAGATTGGATGGTGTCTTC
1 AATCTGCCCTC-TTGTTAGGGTAAAAGATTGGATGGTGTCTTC
45397 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
* * *
45439 AATCTACCCTCTTGTTAAGGTAAAAGATTAGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
** * *
45481 AATCTATCCTCTTATTAGGGTAAAATATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
*
45523 AATCTGCCTTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
1 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
45565 AATCTGCCCTCTTGTTTA-GGTAAAAGATTGGATGG
1 AATCTGCCCTCTTG-TTAGGGTAAAAGATTGGATGG
45600 GATGATGTAA
Statistics
Matches: 354, Mismatches: 37, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
38 4 0.01
39 91 0.26
40 7 0.02
41 5 0.01
42 242 0.68
43 5 0.01
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (42 bp):
AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTC
Found at i:45370 original size:120 final size:122
Alignment explanation
Indices: 45154--45599 Score: 508
Period size: 120 Copynumber: 3.6 Consensus size: 122
45144 TTATAACTTT
* * * * * *
45154 AATCTACCCTCTGGTTAGGGTAAAATATTGGATGGTGTCTTCAATTTGTCCTCTTGTTAGGGTAA
1 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCT-ACCCCTGGTTAGGGTAA
* * *
45219 AAGATTGGATGGTTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGAATTGTGTTTTC
65 AAGATTGGATGGCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGAATGGTGTCTTC
45277 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGAT-G-G-CTTCAATCTACCCCATGGTT-GGTGTA
1 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTACCCC-TGGTTAGG-GTA
* * *
45338 AGAGATTGGATGGCTTCAATTTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTCTTC
64 AAAGATTGGATGGCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGAATGGTGTCTTC
* * *
45397 AATCTGCCCTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTACCCTCTTGTTAAGGTAA
1 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTACCC-CTGGTTAGGGTAA
* * * ** * * * *
45462 AAGATTAGATGGTGTCTTCAATCTATCCTC-TTATTAGGGTAAAATATTGGATGGTGTCTTC
65 AAGATTGGAT-G-G-CTTCAATCT-GCCCCATGGTTGGGGTAAGAGATTGAATGGTGTCTTC
* * * *
45523 AATCTGCCTTCTTGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTTGTTTA-GGTA
1 AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTACCC-C-TGGTTAGGGTA
45587 AAAGATTGGATGG
64 AAAGATTGGATGG
45600 GATGATGTAA
Statistics
Matches: 281, Mismatches: 30, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
119 5 0.02
120 100 0.36
121 2 0.01
122 2 0.01
123 60 0.21
124 4 0.01
125 2 0.01
126 99 0.35
127 7 0.02
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (122 bp):
AATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTACCCCTGGTTAGGGTAAA
AGATTGGATGGCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTGAATGGTGTCTTC
Found at i:61105 original size:21 final size:21
Alignment explanation
Indices: 61072--61138 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
61062 GTTAAGGAAT
*
61072 AGTGCAGACTTCTACCAATATA
1 AGTG-AGACTTCTACCAATACA
* *
61094 AGTGAGAGTTCTACCGATACA
1 AGTGAGACTTCTACCAATACA
**
61115 AGTGACTCTTCTACCGAA-ACA
1 AGTGAGACTTCTACC-AATACA
61136 AGT
1 AGT
61139 CTTACTTCTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGAGACTTCTACCAATACA
Found at i:62389 original size:18 final size:18
Alignment explanation
Indices: 62366--62400 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62356 ACATTAAATC
62366 ACACAATTAAGTCATTTA
1 ACACAATTAAGTCATTTA
*
62384 ACACAATTTAGTCATTT
1 ACACAATTAAGTCATTT
62401 TAGGAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (18 bp):
ACACAATTAAGTCATTTA
Found at i:64659 original size:59 final size:58
Alignment explanation
Indices: 64450--65120 Score: 538
Period size: 60 Copynumber: 11.5 Consensus size: 58
64440 CAAAAAAAAA
* *
64450 TTGGTGTTGGCCATTGCATGGTCGACACCACCTTTTTAATCTGA-CAAAAAA-AA----T
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACCTTTTT-ATCTGATAAAAAAATAATTTTT
* * * * * ****
64504 TTGGTGTTAGTCATTTCATGGTCGACACCACCTTTTTATCTGATAAAAATAAAAAAAAAT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACCTTTTTATCTGATAAAAA-AATAATTTTT
* * *
64564 TTGGTATTGACCATGCATTGGCTGACACCACCTTTTTAT-TAGATAAAAAAATAATTTTT
1 TTGGTGTTGGCCATGCA-TGGCCGACACCACCTTTTTATCT-GATAAAAAAATAATTTTT
* *
64623 TTGGTGTTGGCCATTGCATGGCCGACACTACCTTTTTTATCTGATAAAAATCA-AATTTTT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACC-TTTTTATCTGATAAAAA-AATAATTTTT
* * *
64683 TTGGTGTTGGCCATTGCATGGCCGACGCCACCTTTTTTATCTGAGAAAAAATTCAAATTTTT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACC-TTTTTATCTGATAAAAAAAT--AATTTTT
* * *
64745 TGGGTGTTGGCCATGCATTGGTCGACACCACCTTTTTATCTGATAAAAAAATCAAAATTTT
1 TTGGTGTTGGCCATGCA-TGGCCGACACCACCTTTTTATCTGATAAAAAAAT--AATTTTT
* * ** * * *
64806 TTGGTGTTGGTCATTGCATGACCGACATTACCTTTTTATTTGACAAAAAATTCAATTTTTT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACCTTTTTATCTGATAAAAAAAT-AA-TTTTT
* * *
64867 TTTGTGTTGGCCATGCATTGGCCGACACTACCTTTTTATCTGATAAAAAAATCAAATTTT
1 TTGGTGTTGGCCATGCA-TGGCCGACACCACCTTTTTATCTGATAAAAAAAT-AATTTTT
* * * *
64927 TTGGTGTTGG-C---CAT------CA-C-CTTTTTTATCTAAGAAAAAATTTAATTTTT
1 TTGGTGTTGGCCATGCATGGCCGACACCACCTTTTTATCTGATAAAAAA-ATAATTTTT
* *
64974 TTGGTGTTAGCCATGCATTGGCCGACACCACC-TTTTATCTGATAAAAAAATCAAATTTT
1 TTGGTGTTGGCCATGCA-TGGCCGACACCACCTTTTTATCTGATAAAAAAAT-AATTTTT
* * * * *
65033 TTAGTGTTGACCATTGCATGACCGACACCACCTTTTTTATCTGACAAAAAAATTATTTTT
1 TTGGTGTTGGCCA-TGCATGGCCGACACCACC-TTTTTATCTGATAAAAAAATAATTTTT
** *
65093 TTTTTGTTGGCTATGCATTGGCCGACAC
1 TTGGTGTTGGCCATGCA-TGGCCGACAC
65121 TAACTTTCTA
Statistics
Matches: 502, Mismatches: 76, Indels: 72
0.77 0.12 0.11
Matches are distributed among these distances:
47 32 0.06
48 2 0.00
49 2 0.00
51 2 0.00
52 1 0.00
53 6 0.01
54 38 0.08
55 3 0.01
56 4 0.01
58 3 0.01
59 82 0.16
60 157 0.31
61 135 0.27
62 35 0.07
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (58 bp):
TTGGTGTTGGCCATGCATGGCCGACACCACCTTTTTATCTGATAAAAAAATAATTTTT
Found at i:65961 original size:17 final size:17
Alignment explanation
Indices: 65939--65971 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
65929 AATTAGAAAT
65939 GAAATTA-AAATATAAAC
1 GAAATTATAAAT-TAAAC
65956 GAAATTATAAATTAAA
1 GAAATTATAAATTAAA
65972 ATTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (17 bp):
GAAATTATAAATTAAAC
Found at i:65976 original size:30 final size:30
Alignment explanation
Indices: 65940--66049 Score: 139
Period size: 30 Copynumber: 3.7 Consensus size: 30
65930 ATTAGAAATG
*
65940 AAATTAAAATATAAACGAAATTATAAATTA
1 AAATTAAAATATAAACGAAATTACAAATTA
* * *
65970 AAATTAAAATATACACAAAATTAGAAATTA
1 AAATTAAAATATAAACGAAATTACAAATTA
* *
66000 AATTTAAAATATAAATGAAATTACAAATTA
1 AAATTAAAATATAAACGAAATTACAAATTA
* * *
66030 AATTTAAAAAATAATCGAAA
1 AAATTAAAATATAAACGAAA
66050 AAAATCAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATTAAAATATAAACGAAATTACAAATTA
Found at i:65982 original size:18 final size:18
Alignment explanation
Indices: 65929--66029 Score: 55
Period size: 18 Copynumber: 5.3 Consensus size: 18
65919 AAAAAATAAT
*
65929 AATTAGAAATGAAATTAA
1 AATTAGAAATTAAATTAA
65947 AATATAAACGAAATTATAAATTAA
1 AAT-T--A-GAAA-T-TAAATTAA
* *
65971 AATTA-AAATATACA-CAA
1 AATTAGAAAT-TAAATTAA
65988 AATTAGAAATTAAATTTAA
1 AATTAGAAATTAAA-TTAA
* *
66007 AA-TATAAATGAAATTACA
1 AATTAGAAATTAAATTA-A
66025 AATTA
1 AATTA
66030 AATTTAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
17 13 0.20
18 24 0.37
19 10 0.15
21 2 0.03
22 4 0.06
23 2 0.03
24 10 0.15
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTAGAAATTAAATTAA
Found at i:67256 original size:32 final size:32
Alignment explanation
Indices: 67207--67288 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
67197 AAAATTTCAT
* *
67207 TTTGAAGATATCAAAAAA-TA-ATTTAAAAATA
1 TTTGAAAATATAAAAAAATTATATTTAAAAA-A
*
67238 TTTCGAAAATATAAAAAAATTTATTTTTAAAAAA
1 TTT-GAAAATATAAAAAAA-TTATATTTAAAAAA
*
67272 ATTGAAAATATAAAAAA
1 TTTGAAAATATAAAAAA
67289 TATTTCGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 3 0.07
32 13 0.30
33 14 0.33
34 5 0.12
35 8 0.19
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (32 bp):
TTTGAAAATATAAAAAAATTATATTTAAAAAA
Found at i:67279 original size:33 final size:36
Alignment explanation
Indices: 67228--67293 Score: 102
Period size: 33 Copynumber: 1.9 Consensus size: 36
67218 CAAAAAATAA
*
67228 TTTAAAAATATTTCGAAAATATAAAAAA-ATTTATT
1 TTTAAAAATAATTCGAAAATATAAAAAATATTTATT
67263 TTTAAAAA-AATT-GAAAATATAAAAAATATTT
1 TTTAAAAATAATTCGAAAATATAAAAAATATTT
67294 CGAAAATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.48
34 7 0.24
35 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (36 bp):
TTTAAAAATAATTCGAAAATATAAAAAATATTTATT
Found at i:67313 original size:21 final size:20
Alignment explanation
Indices: 67275--67313 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
67265 TAAAAAAATT
*
67275 GAAAATATAAAAAATATTTC
1 GAAAATAGAAAAAATATTTC
67295 GAAAATAGAAAAAAGTATT
1 GAAAATAGAAAAAA-TATT
67314 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.26
Consensus pattern (20 bp):
GAAAATAGAAAAAATATTTC
Found at i:67328 original size:51 final size:53
Alignment explanation
Indices: 67231--67334 Score: 151
Period size: 53 Copynumber: 2.0 Consensus size: 53
67221 AAAATAATTT
* *
67231 AAAAATATTTCGAAAATATAAAAAAATTTATTTTTAAAAAAATTGAAAATATA
1 AAAAATATTTCGAAAATATAAAAAAATGTATTTATAAAAAAATTGAAAATATA
*
67284 AAAAATATTTCGAAAATA-GAAAAAA-GTA-TTATAAAAAAATTTGAAAATATA
1 AAAAATATTTCGAAAATATAAAAAAATGTATTTATAAAAAAA-TTGAAAATATA
67335 TCTTACATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
50 10 0.21
51 13 0.28
52 6 0.13
53 18 0.38
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (53 bp):
AAAAATATTTCGAAAATATAAAAAAATGTATTTATAAAAAAATTGAAAATATA
Found at i:68364 original size:22 final size:22
Alignment explanation
Indices: 68339--68388 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
68329 TCAACGATGG
*
68339 AATTTGGGTGGTGGTGAGCTGA
1 AATTTCGGTGGTGGTGAGCTGA
**
68361 AATTTCGGTTTTGGTGAGCT-A
1 AATTTCGGTGGTGGTGAGCTGA
68382 GAATTTC
1 -AATTTC
68389 AATTTAGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.20, C:0.08, G:0.34, T:0.38
Consensus pattern (22 bp):
AATTTCGGTGGTGGTGAGCTGA
Found at i:68398 original size:22 final size:22
Alignment explanation
Indices: 68351--68409 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
68341 TTTGGGTGGT
** *
68351 GGTGAGCT-GAAATTTCGGTTTT
1 GGTGAGCTAG-AATTTCAATTTA
68373 GGTGAGCTAGAATTTCAATTTA
1 GGTGAGCTAGAATTTCAATTTA
68395 GGTGAGCTAGAATTT
1 GGTGAGCTAGAATTT
68410 GGGTGGTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.37
Consensus pattern (22 bp):
GGTGAGCTAGAATTTCAATTTA
Found at i:68569 original size:45 final size:45
Alignment explanation
Indices: 68520--68664 Score: 105
Period size: 45 Copynumber: 3.2 Consensus size: 45
68510 ATTGAAATAT
*
68520 AATAATAGTTTTTTATTTGAATAAATTTAAAATTTAAATTTGGTA
1 AATAATAGTTTTTTATTTAAATAAATTTAAAATTTAAATTTGGTA
* * ** * * *** * * *
68565 AATAATA-TATTGTCAAATCAATATATTATTTGA-TAAAAATTGAAATA
1 AATAATAGT-TTTTTATTTAAATAAATT-TAAAATTTAAATTTG--GTA
68612 TAATAATAGTTTTTTATTTAAATAAATTTAAAATTTAAATTTGGTA
1 -AATAATAGTTTTTTATTTAAATAAATTTAAAATTTAAATTTGGTA
*
68658 ATTAATA
1 AATAATA
68665 TATTATCAAA
Statistics
Matches: 68, Mismatches: 25, Indels: 14
0.64 0.23 0.13
Matches are distributed among these distances:
44 1 0.01
45 32 0.47
46 4 0.06
47 4 0.06
48 26 0.38
49 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (45 bp):
AATAATAGTTTTTTATTTAAATAAATTTAAAATTTAAATTTGGTA
Found at i:68596 original size:93 final size:94
Alignment explanation
Indices: 68499--68878 Score: 588
Period size: 93 Copynumber: 4.1 Consensus size: 94
68489 TAAATTTAAA
* * *
68499 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTGAATAAATTTAAA-ATTTAAATTTGG
1 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
* *
68563 TAAATAATATATTGTCAAATCAATATATT
66 TAAATAATATATTGTCAAATCAACACATT
* *
68592 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAA-ATTTAAATTTGG
1 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
* * *
68656 TAATTAATATATTATCAAATCAACATATT
66 TAAATAATATATTGTCAAATCAACACATT
* *
68685 ATTTGATATAAATTGAAATATAATAATAATTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
1 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
**
68750 TAAATAACGTATTGTCAAATCAACACATT
66 TAAATAATATATTGTCAAATCAACACATT
*
68779 ATTTGATATAAATTGAAATATAATAAT--TTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
1 ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
*
68842 TAAATAATGTATTGTCAAATCAACACATT
66 TAAATAATATATTGTCAAATCAACACATT
68871 ATTTGATA
1 ATTTGATA
68879 TAA
Statistics
Matches: 272, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
92 72 0.26
93 139 0.51
94 61 0.22
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (94 bp):
ATTTGATAAAAATTGAAATATAATAATAGTTTTTTATTTAAATAAATTTAAATATTAAAATTTGA
TAAATAATATATTGTCAAATCAACACATT
Found at i:68830 original size:32 final size:33
Alignment explanation
Indices: 68777--68839 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
68767 AATCAACACA
*
68777 TTATTTGATATAAATTGAAATA-TAATAATTTTT
1 TTATTTGAAATAAATTGAAATATTAA-AATTTTT
*
68810 TTATTT-AAATAAATTTAAATATTAAAATTT
1 TTATTTGAAATAAATTGAAATATTAAAATTT
68840 GATAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
TTATTTGAAATAAATTGAAATATTAAAATTTTT
Done.