Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010547.1 Kokia drynarioides strain JFW-HI SEQ_125467, 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: 149239
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:118 original size:4 final size:4
Alignment explanation
Indices: 111--157 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
101 TTCTTCCTTC
* * *
111 TTCT TTCT TTCT ATCT TTCT TTCT CTTTT TTCT TTCT TTTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TT
158 ATTTTTCGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
4 33 0.92
5 3 0.08
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:143 original size:25 final size:25
Alignment explanation
Indices: 109--157 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
99 CCTTCTTCCT
109 TCTTCTTTCTTTCTATCTTTCTTTC
1 TCTTCTTTCTTTCTATCTTTCTTTC
* * *
134 TCTTTTTTCTTTCTTTTTTTCTTT
1 TCTTCTTTCTTTCTATCTTTCTTT
158 ATTTTTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (25 bp):
TCTTCTTTCTTTCTATCTTTCTTTC
Found at i:157 original size:12 final size:12
Alignment explanation
Indices: 114--163 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
104 TTCCTTCTTC
* *
114 TTTCTTTCTATC
1 TTTCTTTCTTTT
126 TTTCTTTCTCTTT
1 TTTCTTTCT-TTT
139 TTTCTTTCTTTT
1 TTTCTTTCTTTT
*
151 TTTCTTTATTTT
1 TTTCTTTCTTTT
163 T
1 T
164 CGTTGGTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:461 original size:13 final size:13
Alignment explanation
Indices: 443--477 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
433 TGGGTGTCAG
443 GTATTTTTTTGTC
1 GTATTTTTTTGTC
456 GTA--TTTTTGTC
1 GTATTTTTTTGTC
467 GTATTTTTTTG
1 GTATTTTTTTG
478 AAAAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.69
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:5519 original size:50 final size:51
Alignment explanation
Indices: 5444--5541 Score: 189
Period size: 50 Copynumber: 1.9 Consensus size: 51
5434 TGCGTGTTTT
5444 ATCGAATCACAAATTATCAACAAAGTAGGATGAT-AAAGTATGAATTTCAA
1 ATCGAATCACAAATTATCAACAAAGTAGGATGATAAAAGTATGAATTTCAA
5494 ATCGAATCACAAATTATCAACAAAGTAGGATGATAAAAGTATGAATTT
1 ATCGAATCACAAATTATCAACAAAGTAGGATGATAAAAGTATGAATTT
5542 TAATTTATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 34 0.72
51 13 0.28
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (51 bp):
ATCGAATCACAAATTATCAACAAAGTAGGATGATAAAAGTATGAATTTCAA
Found at i:14707 original size:23 final size:23
Alignment explanation
Indices: 14664--14707 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14654 TTGTTTCTAT
**
14664 TTTGTCATTTTGATATTTCTTCA
1 TTTGTCATTTTGATACGTCTTCA
14687 TTTGTCAATTTTGAT-CGTCTT
1 TTTGTC-ATTTTGATACGTCTT
14708 TCATAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (23 bp):
TTTGTCATTTTGATACGTCTTCA
Found at i:26385 original size:20 final size:21
Alignment explanation
Indices: 26360--26398 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26350 TGCATTTTTA
26360 ACATTTT-TAACTTAGTGACT
1 ACATTTTCTAACTTAGTGACT
26380 ACATTTTCTAACTTAGTGA
1 ACATTTTCTAACTTAGTGA
26399 TGCTCGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (21 bp):
ACATTTTCTAACTTAGTGACT
Found at i:44505 original size:15 final size:15
Alignment explanation
Indices: 44482--44515 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44472 ATAAGGTTCG
*
44482 ACCACTCAAAACACT
1 ACCAATCAAAACACT
*
44497 ACCAATCAAAACATT
1 ACCAATCAAAACACT
44512 ACCA
1 ACCA
44516 CCACGCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (15 bp):
ACCAATCAAAACACT
Found at i:53124 original size:22 final size:22
Alignment explanation
Indices: 53094--53140 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53084 AAATATTAAT
* *
53094 AAATGAAAATTTGTAAAAAAAA
1 AAATGAAAAATTGAAAAAAAAA
*
53116 AAATTAAAAATTGAAAAAAAAA
1 AAATGAAAAATTGAAAAAAAAA
53138 AAA
1 AAA
53141 ACAGGAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (22 bp):
AAATGAAAAATTGAAAAAAAAA
Found at i:61799 original size:50 final size:50
Alignment explanation
Indices: 61730--61887 Score: 194
Period size: 50 Copynumber: 3.2 Consensus size: 50
61720 ATGGCTTATT
*
61730 TAAATCCTTTATGGTAATTTACTTGGGAAGCCTTTATGGCGAGTCACCTG
1 TAAAGCCTTTATGGTAATTTACTTGGGAAGCCTTTATGGCGAGTCACCTG
* * * **
61780 TAAAGCCTTTATGGCAATTTACTTGGGAAGCCTTTGTGGTGAGTCATTTG
1 TAAAGCCTTTATGGTAATTTACTTGGGAAGCCTTTATGGCGAGTCACCTG
* * * *
61830 TAAAGCCTTTATGGTGATTTATTTGGGAAGTCCTTGA-GGC-ATGTTACCTG
1 TAAAGCCTTTATGGTAATTTACTTGGGAAG-CCTTTATGGCGA-GTCACCTG
61880 TAAAGCCT
1 TAAAGCCT
61888 ATGTGCCGTA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 86 0.95
51 4 0.04
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (50 bp):
TAAAGCCTTTATGGTAATTTACTTGGGAAGCCTTTATGGCGAGTCACCTG
Found at i:61854 original size:25 final size:25
Alignment explanation
Indices: 61730--61850 Score: 98
Period size: 25 Copynumber: 4.8 Consensus size: 25
61720 ATGGCTTATT
* *
61730 TAAATCCTTTATGGTAATTTACTTG
1 TAAAGCCTTTATGGTGATTTACTTG
** * * * *
61755 GGAAGCCTTTATGGCGAGTCACCTG
1 TAAAGCCTTTATGGTGATTTACTTG
**
61780 TAAAGCCTTTATGGCAATTTACTTG
1 TAAAGCCTTTATGGTGATTTACTTG
** * * * *
61805 GGAAGCCTTTGTGGTGAGTCATTTG
1 TAAAGCCTTTATGGTGATTTACTTG
61830 TAAAGCCTTTATGGTGATTTA
1 TAAAGCCTTTATGGTGATTTA
61851 TTTGGGAAGT
Statistics
Matches: 69, Mismatches: 27, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (25 bp):
TAAAGCCTTTATGGTGATTTACTTG
Found at i:66006 original size:21 final size:21
Alignment explanation
Indices: 65982--66022 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
65972 TTCTACCCTG
* *
65982 TACTTCTATCGATACATGTAA
1 TACTTCTACCGAAACATGTAA
66003 TACTTCTACCGAAACATGTA
1 TACTTCTACCGAAACATGTA
66023 TGCAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TACTTCTACCGAAACATGTAA
Found at i:70640 original size:40 final size:40
Alignment explanation
Indices: 70583--70679 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
70573 CTTCATAGGT
* * *
70583 TCACAAGTCTTCTTTTTAGTCAATCTTATGCTCTATCGAG
1 TCACAAGTCTTCCTTTTAATCAATCTTATGCTCTATCAAG
*
70623 TCACAAGTCTTCCTTTTAATCACTCTTATGCTCTATCAAG
1 TCACAAGTCTTCCTTTTAATCAATCTTATGCTCTATCAAG
*
70663 TCATAAGTCTTCCTTTT
1 TCACAAGTCTTCCTTTT
70680 TAAAAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (40 bp):
TCACAAGTCTTCCTTTTAATCAATCTTATGCTCTATCAAG
Found at i:70757 original size:41 final size:41
Alignment explanation
Indices: 70706--70849 Score: 270
Period size: 41 Copynumber: 3.5 Consensus size: 41
70696 GCTTATTTTA
70706 AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
1 AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
70747 AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
1 AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
*
70788 AGATATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
1 AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
70829 AGACATGAGTCTTCCATTTAA
1 AGACATGAGTCTTCC-TTTAA
70850 ATATCAAGTT
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
41 95 0.95
42 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (41 bp):
AGACATGAGTCTTCCTTTAATATAATCTCATTCTCATCCCG
Found at i:76688 original size:21 final size:20
Alignment explanation
Indices: 76664--76723 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
76654 GAAGCATGCA
*
76664 ATGTTTCGGTAGAAGTCTTAC
1 ATGTATCGGTAGAAGTCTT-C
* *
76685 ATGTATCGGTAGTACTACTTC
1 ATGTATCGGTAGAAGT-CTTC
*
76706 AAGTATCGGTAGAAGTCT
1 ATGTATCGGTAGAAGTCT
76724 GCACTGTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
ATGTATCGGTAGAAGTCTTC
Found at i:80842 original size:194 final size:194
Alignment explanation
Indices: 80495--80931 Score: 504
Period size: 194 Copynumber: 2.3 Consensus size: 194
80485 GAAATCGACG
* * * * *
80495 CGATGTTTGAGGTACCGCATATGTTACGAGTCCTCAACAACTTGTGTGAGCATCATCGTGAGTTG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTGTGAGCATCATCGTGAGTTC
* * * *
80560 GGAAATGAGAAATGAATCCAAGAACGGATTACAGGCCCTACGATGGCTAGGATTTATACATAAAT
66 GAAAAAGAGAAATAAATCCAAGAACGGATTACAGGCCCTACGAAGGCTAGGATTTATACATAAAT
* * * *
80625 GCATATTCTCGATAACTCGTGTGAGCAGCATCATTAGGGAAATAGTTATACGCACAGACACCGTA
131 GCATATTCTCGACAACTCGTGTGAGCAGCACCATTA-GGAAACAGTT-TACACACAGACACCGTA
80690 T
194 T
* * * *
80691 CGATGGTTGAGGTACCGCATATATTGCGAGTCCTCGACAGCTCGTGTGATC-TGTATCGTGAG-T
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTGTGAGCAT-CATCGTGAGTT
* * * * * * * * *
80754 CGAAAAAGAGATATAAATCCTA-AATGGATTATAGGCCTTACGAAGGTTGGGATTTATGCTTAAA
65 CGAAAAAGAGAAATAAATCCAAGAACGGATTACAGGCCCTACGAAGGCTAGGATTTATACATAAA
* * * * *
80818 TGCATATTCTCGACAGCTCGTGTGAGCAGCACCGTTAGGAGACAGTTTACATATAGACACCGTAT
130 TGCATATTCTCGACAACTCGTGTGAGCAGCACCATTAGGAAACAGTTTACACACAGACACCGTAT
* * *
80883 TGATGGTTG-GGCTACTGTATATGTTGCGAGTCCTCAACAGCTCGTGTGA
1 CGATGGTTGAGG-TACCGCATATGTTGCGAGTCCTCAACAGCTCGTGTGA
80932 ATAACATCGG
Statistics
Matches: 203, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
191 2 0.01
192 56 0.28
193 8 0.04
194 67 0.33
195 18 0.09
196 52 0.26
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (194 bp):
CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTGTGAGCATCATCGTGAGTTC
GAAAAAGAGAAATAAATCCAAGAACGGATTACAGGCCCTACGAAGGCTAGGATTTATACATAAAT
GCATATTCTCGACAACTCGTGTGAGCAGCACCATTAGGAAACAGTTTACACACAGACACCGTAT
Found at i:90130 original size:25 final size:26
Alignment explanation
Indices: 90102--90173 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
90092 AATTTTCTCG
*
90102 AAATTTTATCG-GGGTAAAATCATCA
1 AAATTTTATAGAGGGTAAAATCATCA
* **
90127 AAATCTTATAGAGGGTAAAATTGTCA
1 AAATTTTATAGAGGGTAAAATCATCA
* * *
90153 AAATTTTGTTGAGAGTAAAAT
1 AAATTTTATAGAGGGTAAAAT
90174 AGGGATGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (26 bp):
AAATTTTATAGAGGGTAAAATCATCA
Found at i:93818 original size:2 final size:2
Alignment explanation
Indices: 93811--93835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93801 AATTCAAGAG
93811 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
93836 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94103 original size:23 final size:22
Alignment explanation
Indices: 94037--94105 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
94027 TGCACTAATG
* * *
94037 AACGAAAAGCACCAAGGTGCTA
1 AACGAAGAGCACAAACGTGCTA
* * *
94059 GACGGAGAGCACAAATGTGCTA
1 AACGAAGAGCACAAACGTGCTA
*
94081 AACGAAGAGCATAATACGTGCTA
1 AACGAAGAGCACAA-ACGTGCTA
94104 AA
1 AA
94106 TAACGGAGAG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 28 0.76
23 9 0.24
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (22 bp):
AACGAAGAGCACAAACGTGCTA
Found at i:96558 original size:17 final size:19
Alignment explanation
Indices: 96536--96570 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
96526 TAATTCTAAA
96536 TTAAAT-TCTA-AATATAT
1 TTAAATATCTATAATATAT
96553 TTAAATATCTATAATATA
1 TTAAATATCTATAATATA
96571 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATATCTATAATATAT
Found at i:125038 original size:158 final size:154
Alignment explanation
Indices: 124750--125228 Score: 430
Period size: 158 Copynumber: 3.0 Consensus size: 154
124740 GTAACCATAT
* * * * **
124750 ATGCTCACACGAGCTGTGAAATGGGTTTGCTCG-CTCGAGCTGTGGGTTGAGATGTGGGGCTACA
1 ATGCTCACACGAGCTGTGAAATGAGTATGCT-GAAT-GAGCTGTGGGTCGAGATGTTAGGCTACA
* * * * *
124814 CGATGCTTCTCACACGAGCTGTGAAGAATCCGCAATAAATGC-CGAACCTCAGCCATC-AGTAAG
64 CGATGCTGCTCACACGAGCTGTGGAGAATCCAC-A-AAATGCAAG-ACCTCAGCCATCGA-TAGG
124877 ACATCTAAGACTAGCACCCATATAACCTGTA
125 ACATC-AAGACTAGCACCCATATAACCTGTA
* * *
124908 ATGCTCACACAAGCTGTGAAATGAGTCTGCTGAAATGAGCTGTGGGTCGAGATGTTAGGCTACGC
1 ATGCTCACACGAGCTGTGAAATGAGTATGCTG-AATGAGCTGTGGGTCGAGATGTTAGGCTACAC
* *
124973 GATGCTGCTCACATGAGTTGTGGAGAATCCACAACCAATGCAAGACCTCAGCCATCGATAGGACA
65 GATGCTGCTCACACGAGCTGTGGAGAATCCACAA--AATGCAAGACCTCAGCCATCGATAGGACA
125038 TC---ACTAGCACCCATATAACCTGTA
128 TCAAGACTAGCACCCATATAACCTGTA
* * * *
125062 ATGTTCACACGAGCTGTAACTGTAACATGTAATTATATATGCTCATATGAGCTGTGGGTCGGGAT
1 ATGCTCACACGAGCTG----TG-AA-ATG-----A-GTATGCTGA-ATGAGCTGTGGGTCGAGAT
* * * * * *
125127 GTTAGGCTACATGATGTTGCTCACACGAGCTATGGAGAATTCGCATAAAATGCAGGACCTTAGCC
53 GTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA-TC-CACAAAATGCAAGACCTCAGCC
* *
125192 ATCGGTAGGACATCCAAGACCAGCACCCATATAACCT
116 ATCGATAGGACAT-CAAGACTAGCACCCATATAACCT
125229 ATAAATAACC
Statistics
Matches: 264, Mismatches: 32, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
154 36 0.14
156 1 0.00
157 2 0.01
158 107 0.41
159 5 0.02
160 3 0.01
165 2 0.01
166 83 0.31
167 3 0.01
168 4 0.02
170 18 0.07
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (154 bp):
ATGCTCACACGAGCTGTGAAATGAGTATGCTGAATGAGCTGTGGGTCGAGATGTTAGGCTACACG
ATGCTGCTCACACGAGCTGTGGAGAATCCACAAAATGCAAGACCTCAGCCATCGATAGGACATCA
AGACTAGCACCCATATAACCTGTA
Found at i:127169 original size:13 final size:13
Alignment explanation
Indices: 127151--127181 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
127141 TTCTACAATT
127151 TATTTTTAATAAA
1 TATTTTTAATAAA
*
127164 TATTTTTATTAAA
1 TATTTTTAATAAA
127177 TATTT
1 TATTT
127182 ACGGATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTTAATAAA
Found at i:133336 original size:24 final size:24
Alignment explanation
Indices: 133304--133372 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
133294 AATCTTTTAG
133304 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
*
133328 TTAACCTCTATTTATTTGTTTCAA
1 TTAAACTCTATTTATTTGTTTCAA
* *
133352 TTAAACTCTGTTTAGTTGTTT
1 TTAAACTCTATTTATTTGTTT
133373 GAGTCAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.13, G:0.07, T:0.55
Consensus pattern (24 bp):
TTAAACTCTATTTATTTGTTTCAA
Found at i:135538 original size:16 final size:18
Alignment explanation
Indices: 135507--135539 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
135497 GAATTTAGTG
135507 TTTATGTTTTGAGGGTTC
1 TTTATGTTTTGAGGGTTC
135525 TTTAT-TTTTG-GGGTT
1 TTTATGTTTTGAGGGTT
135540 TAGTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.09, C:0.03, G:0.27, T:0.61
Consensus pattern (18 bp):
TTTATGTTTTGAGGGTTC
Found at i:136197 original size:111 final size:110
Alignment explanation
Indices: 135962--136208 Score: 284
Period size: 111 Copynumber: 2.2 Consensus size: 110
135952 ATTGATGACT
* * * * **
135962 GAATTGACAGATCATGATACATGATTGTGTGCAAGTTCATGTGGCTAAAACCCATGGTAAAATTG
1 GAATTGGCAGATCACGATACATGAATATGTGCAAGCCCATGTGGCTAAAACCCATGGTAAAATTG
*
136027 TAATTGTAAGAATGTTCATGGCGTAGCCTTCAATATGTATGAATC
66 TAATTGTAAGAATGTTCATGGCGTAGCCTTCAATATATATGAATC
* * * *
136072 GAATGGGTAGATCACGATACATGAATATGTGTAAGCCCATGTGGCTGAAACCCATGGCATAAAA-
1 GAATTGGCAGATCACGATACATGAATATGTGCAAGCCCATGTGGCTAAAACCCATGG--TAAAAT
* * * *
136136 TG--ATATGATATGAATGTTCATGGTGTAGCCTTCGATATATGTGAATC
64 TGTAAT-TG-TAAGAATGTTCATGGCGTAGCCTTCAATATATATGAATC
* *
136183 GAATTGGCAAATCACAATACATGAAT
1 GAATTGGCAGATCACGATACATGAAT
136209 TTATGTCTAG
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
109 2 0.02
110 49 0.43
111 58 0.51
112 5 0.04
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (110 bp):
GAATTGGCAGATCACGATACATGAATATGTGCAAGCCCATGTGGCTAAAACCCATGGTAAAATTG
TAATTGTAAGAATGTTCATGGCGTAGCCTTCAATATATATGAATC
Done.