Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002883.1 Kokia drynarioides strain JFW-HI SEQ_115295, 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: 70470
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1508 original size:205 final size:203
Alignment explanation
Indices: 1092--1739 Score: 789
Period size: 205 Copynumber: 3.2 Consensus size: 203
1082 AAACAACAAT
* * *
1092 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCATATCAAACCCACACTC---G-----AT
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGAACAAAT
* * * * * *
1149 -TTCGAATCCCAGCTTTCGGATAAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCT
66 CTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAACGGTTAGCTTCC
*
1213 TGATAAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAA
131 TGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAA
1278 CAAATGAC
196 CAAATGAC
*
1286 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAA-CCTACGCTCTATGTGAGA-
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCC-ACGCTCGA--TGA-AC
*
1349 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCAAAGCAATAAACGGTTAGC
62 AAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAACGGTTAGC
* *
1414 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCAGATT
127 TTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATT
1479 GAAACAAATGAC
192 GAAACAAATGAC
*
1491 GCGATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGAACAAAT
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGAACAAAT
* * * * * *
1556 CTTCAAACCCCAGCTTCCTGTTGAGATACTGAGAAACGGGTCGAAA-TAATAAAACGGTTAGCTT
66 CTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTC-AAAGCAAT-AAACGGTTAGCTT
* * * * * * * * * **
1620 CCTGATGAAAATACGGGGAAGTAAACCAAAATCATCTTCCTGATGAAACACAGAGAAGTAAATCA
129 CCTGATG-AGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTG
* *
1685 AAACAAGTGAT
193 AAACAAATGAC
** * * * *
1696 ATGGTCATCTTTCAGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
1740 TGAAACCAGA
Statistics
Matches: 394, Mismatches: 43, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
193 2 0.01
194 49 0.12
199 1 0.00
202 1 0.00
203 46 0.12
204 25 0.06
205 268 0.68
206 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (203 bp):
GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAATCCACGCTCGATGAACAAAT
CTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAACGGTTAGCTTCC
TGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAA
CAAATGAC
Found at i:2058 original size:6 final size:6
Alignment explanation
Indices: 2047--2163 Score: 53
Period size: 6 Copynumber: 20.7 Consensus size: 6
2037 TTGGACCCAA
* *
2047 TAAATT TAAATT T-ATTT TAGAA-T TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT -TAAATT TAAATT
* *
2093 T-ATTT TAGAA-T TAAGTT T--ATT CTAAATT TAAATT T--ATT TGAAATT
1 TAAATT TA-AATT TAAATT TAAATT -TAAATT TAAATT TAAATT T-AAATT
2138 TAAA-T T--ATT ATAAATT TAAATT TAAA
1 TAAATT TAAATT -TAAATT TAAATT TAAA
2164 ATCTATTTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 38
0.65 0.06 0.29
Matches are distributed among these distances:
3 1 0.01
4 9 0.11
5 15 0.18
6 44 0.52
7 15 0.18
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:2077 original size:17 final size:17
Alignment explanation
Indices: 2047--2161 Score: 137
Period size: 17 Copynumber: 6.8 Consensus size: 17
2037 TTGGACCCAA
2047 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
2064 TAGAA-TTAAGTTTATTC
1 TA-AATTTAAATTTATTT
2081 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
2098 TAGAA-TTAAGTTTATTC
1 TA-AATTTAAATTTATTT
2115 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
2132 GAAATTTAAA-TTATTA
1 TAAATTTAAATTTATTT
2148 TAAATTTAAATTTA
1 TAAATTTAAATTTA
2162 AAATCTATTT
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
16 18 0.22
17 60 0.73
18 4 0.05
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:2090 original size:34 final size:34
Alignment explanation
Indices: 2047--2161 Score: 180
Period size: 34 Copynumber: 3.4 Consensus size: 34
2037 TTGGACCCAA
2047 TAAATTTAAATTTATTTTAGAATTAAGTTTATTC
1 TAAATTTAAATTTATTTTAGAATTAAGTTTATTC
2081 TAAATTTAAATTTATTTTAGAATTAAGTTTATTC
1 TAAATTTAAATTTATTTTAGAATTAAGTTTATTC
* * *
2115 TAAATTTAAATTTATTTGA-AATTTAA-ATTATTA
1 TAAATTTAAATTTATTTTAGAA-TTAAGTTTATTC
2148 TAAATTTAAATTTA
1 TAAATTTAAATTTA
2162 AAATCTATTT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
33 21 0.27
34 56 0.73
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (34 bp):
TAAATTTAAATTTATTTTAGAATTAAGTTTATTC
Found at i:2165 original size:23 final size:23
Alignment explanation
Indices: 2128--2175 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2118 ATTTAAATTT
2128 ATTTGAAATTTAAAT-TATTATAA
1 ATTTGAAATTTAAATCTATT-TAA
2151 ATTT-AAATTTAAAATCTATTTAA
1 ATTTGAAATTT-AAATCTATTTAA
2174 AT
1 AT
2176 AATGTCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTGAAATTTAAATCTATTTAA
Found at i:2855 original size:15 final size:15
Alignment explanation
Indices: 2835--2864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2825 ATTAAATGTT
*
2835 TAATATTTTTAATAA
1 TAATATTTCTAATAA
2850 TAATATTTCTAATAA
1 TAATATTTCTAATAA
2865 CATTAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATTTCTAATAA
Found at i:3944 original size:30 final size:29
Alignment explanation
Indices: 3895--4223 Score: 349
Period size: 29 Copynumber: 11.2 Consensus size: 29
3885 CTAAAAATTT
** *
3895 CATTTTTACCCTTAAACTTCAAAAAATCC
1 CATTTTTACCCCAAAACTTCCAAAAATCC
*
3924 CATTTTTAACCCCAAAACTTCCAAAAATTC
1 CATTTTT-ACCCCAAAACTTCCAAAAATCC
3954 CATTTTTACCCTC-AAACTTCCAAAAATCC
1 CATTTTTACCC-CAAAACTTCCAAAAATCC
* * *
3983 CATTTTTGACCCTAAAACTTTCAAAAATTC
1 CATTTTT-ACCCCAAAACTTCCAAAAATCC
** *
4013 CATTTTTACCCCCTAACTTCCAAAAATCT
1 CATTTTTACCCCAAAACTTCCAAAAATCC
* **
4042 CATTTTCAACCCCAAAACTTCCAAAAATTT
1 CATTTT-TACCCCAAAACTTCCAAAAATCC
4072 CATTTTTACCCTC-AAACTTCCAAAAATCC
1 CATTTTTACCC-CAAAACTTCCAAAAATCC
* * * **
4101 CATTTTAACCCTAAAACTTTCAAAAATTT
1 CATTTTTACCCCAAAACTTCCAAAAATCC
**
4130 CATTTTTACCCCCGAACTTCCAAAAATCC
1 CATTTTTACCCCAAAACTTCCAAAAATCC
* * **
4159 CATTTTCGATCCCAAAACTTCCAAAAATTT
1 CATTTT-TACCCCAAAACTTCCAAAAATCC
*
4189 CATTTTTAACCCAAAACTTCC-AAAATCTC
1 CATTTTTACCCCAAAACTTCCAAAAATC-C
4218 CATTTT
1 CATTTT
4224 CGACCTCTAA
Statistics
Matches: 248, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
28 5 0.02
29 143 0.58
30 100 0.40
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (29 bp):
CATTTTTACCCCAAAACTTCCAAAAATCC
Found at i:4224 original size:59 final size:59
Alignment explanation
Indices: 3887--4228 Score: 465
Period size: 59 Copynumber: 5.8 Consensus size: 59
3877 TAAATTATCT
* * **
3887 AAAAATTTCATTTTTACCCTTAAACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCC
1 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
* * * *
3946 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTTC
1 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
* * * * *
4005 AAAAATTCCATTTTTACCCCCTAACTTCCAAAAATCTCATTTTCAACCCCAAAACTTCC
1 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
* * *
4064 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTT-AACCCTAAAACTTTC
1 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
* * *
4122 AAAAATTTCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTCGATCCCAAAACTTCC
1 AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
*
4181 AAAAATTTCATTTTTAACCC-AAAACTTCC-AAAATCTCCATTTTCGACC
1 AAAAATTTCATTTTT-ACCCTCAAACTTCCAAAAATC-CCATTTTCGACC
4229 TCTAAAGTCT
Statistics
Matches: 252, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
58 60 0.24
59 188 0.75
60 4 0.02
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.33
Consensus pattern (59 bp):
AAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTCGACCCCAAAACTTCC
Found at i:4257 original size:117 final size:116
Alignment explanation
Indices: 3909--4234 Score: 485
Period size: 117 Copynumber: 2.8 Consensus size: 116
3899 TTTACCCTTA
* * *
3909 AACTTCAAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTTC
1 AACTTCCAAAAATCCCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
*
3974 CAAAAATCCCATTTTTGACCCTAAAACTTTCAAAAATTCCATTTTTACCCCCT
66 CAAAAATCCCA-TTTTGACCCTAAAACTTTCAAAAATTCC-TTTTTACCCCCG
*
4027 AACTTCCAAAAATCTCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
1 AACTTCCAAAAATCCCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
* *
4092 CAAAAATCCCATTTTAACCCTAAAACTTTCAAAAATTTCATTTTTACCCCCG
66 CAAAAATCCCATTTTGACCCTAAAACTTTCAAAAA-TTCCTTTTTACCCCCG
* * *
4144 AACTTCCAAAAATCCCATTTTCGATCCCAAAACTTCCAAAAATTTCATTTTTAACCC-AAAACTT
1 AACTTCCAAAAATCCCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTT-ACCCTCAAACTT
4208 CC-AAAATCTCCATTTTCGACCTCTAAA
65 CCAAAAATC-CCATTTT-GACC-CTAAA
4235 GTCTCGAAAT
Statistics
Matches: 191, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
116 6 0.03
117 98 0.51
118 82 0.43
119 5 0.03
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.32
Consensus pattern (116 bp):
AACTTCCAAAAATCCCATTTTCAACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCAAACTTC
CAAAAATCCCATTTTGACCCTAAAACTTTCAAAAATTCCTTTTTACCCCCG
Found at i:12027 original size:2 final size:2
Alignment explanation
Indices: 12020--12072 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
12010 GCTATCTAGA
12020 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12062 AG AG AG AG AG A
1 AG AG AG AG AG A
12073 CTATTTTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20780 original size:15 final size:16
Alignment explanation
Indices: 20753--20782 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20743 TTAATATCAT
20753 TTTTAATTATTTGTTG
1 TTTTAATTATTTGTTG
20769 TTTTAA-TATTTGTT
1 TTTTAATTATTTGTT
20783 TTAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (16 bp):
TTTTAATTATTTGTTG
Found at i:20783 original size:12 final size:12
Alignment explanation
Indices: 20766--20791 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20756 TAATTATTTG
20766 TTGTTTTAATAT
1 TTGTTTTAATAT
20778 TTGTTTTAATAT
1 TTGTTTTAATAT
20790 TT
1 TT
20792 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:20784 original size:28 final size:27
Alignment explanation
Indices: 20738--20791 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
20728 GTTTTACGAA
20738 TTGTTTTAATATCATTTTTAATTATTTG
1 TTGTTTTAATATCATTTTTAA-TATTTG
*
20766 TTGTTTTAATAT-TTGTTTTAATATTT
1 TTGTTTTAATATCAT-TTTTAATATTT
20792 TTAAATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (27 bp):
TTGTTTTAATATCATTTTTAATATTTG
Found at i:20817 original size:26 final size:24
Alignment explanation
Indices: 20786--20833 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
20776 ATTTGTTTTA
*
20786 ATATTTTTAAATGTATTTGATATATC
1 ATATTTTAAAAT-TATTT-ATATATC
20812 ATATTTTAAAATTATTTATATA
1 ATATTTTAAAATTATTTATATA
20834 ATAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
ATATTTTAAAATTATTTATATATC
Found at i:35829 original size:63 final size:63
Alignment explanation
Indices: 35751--35878 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
35741 CACTCCATTG
*
35751 TTACTTCTCAAGAACAAGGGTACCATAATGTAATGATATCCCTTAAAAAAAGATATATATATA
1 TTACTTCTCAAGAACAAGGGTACAATAATGTAATGATATCCCTTAAAAAAAGATATATATATA
*
35814 TTACTTCTCAAGAACAAGGGTACAATAATGTACTGATATCCCTTAAAAAAAGATATATATATA
1 TTACTTCTCAAGAACAAGGGTACAATAATGTAATGATATCCCTTAAAAAAAGATATATATATA
35877 TT
1 TT
35879 TATGATATTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (63 bp):
TTACTTCTCAAGAACAAGGGTACAATAATGTAATGATATCCCTTAAAAAAAGATATATATATA
Found at i:38730 original size:21 final size:21
Alignment explanation
Indices: 38706--38745 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38696 ACAAGGGAAT
*
38706 TACAATTAACA-ACAACAGAAC
1 TACAATCAACACAC-ACAGAAC
38727 TACAATCAACACACACAGA
1 TACAATCAACACACACAGA
38746 TACATCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.28, G:0.05, T:0.12
Consensus pattern (21 bp):
TACAATCAACACACACAGAAC
Found at i:41244 original size:26 final size:26
Alignment explanation
Indices: 41215--41277 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
41205 AACAACTTTG
41215 GACATGTTCATGCAGTGATAATTCTA
1 GACATGTTCATGCAGTGATAATTCTA
*
41241 GACAAGTTTC-TGCAGTGATAATTCTA
1 GACATG-TTCATGCAGTGATAATTCTA
*
41267 GACATGCTCAT
1 GACATGTTCAT
41278 ACAACGACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.06
26 27 0.84
27 3 0.09
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (26 bp):
GACATGTTCATGCAGTGATAATTCTA
Found at i:42555 original size:18 final size:17
Alignment explanation
Indices: 42513--42556 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
42503 TGGCTGCATG
42513 GTGCTTTTTCTTCCTTCT
1 GTGC-TTTTCTTCCTTCT
* *
42531 ATTCTTTTCTTCCTTTCT
1 GTGCTTTTCTTCC-TTCT
42549 GTGCTTTT
1 GTGCTTTT
42557 TGTCCTTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.02, C:0.25, G:0.09, T:0.64
Consensus pattern (17 bp):
GTGCTTTTCTTCCTTCT
Found at i:45029 original size:11 final size:11
Alignment explanation
Indices: 45013--45043 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
45003 GTTAGATTAC
45013 TTTGATTCTTA
1 TTTGATTCTTA
45024 TTTGATTCTTA
1 TTTGATTCTTA
45035 TTTGATTCT
1 TTTGATTCT
45044 CCTCATCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (11 bp):
TTTGATTCTTA
Found at i:53688 original size:21 final size:21
Alignment explanation
Indices: 53658--53704 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
53648 GGTTGACTGG
53658 AAAGACAAGAAG-AGAAAGCGC
1 AAAGACAAGAAGAAG-AAGCGC
* *
53679 AAAGATAAGAAGAAGATGCGC
1 AAAGACAAGAAGAAGAAGCGC
53700 AAAGA
1 AAAGA
53705 AGAAGGCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.57, C:0.11, G:0.28, T:0.04
Consensus pattern (21 bp):
AAAGACAAGAAGAAGAAGCGC
Found at i:53853 original size:17 final size:18
Alignment explanation
Indices: 53819--53857 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
53809 TTTTATTTGG
*
53819 TTGTCATTGCATTTTCAT
1 TTGTCAATGCATTTTCAT
53837 TTGTCAATGCA-TTTCAT
1 TTGTCAATGCATTTTCAT
53854 TTGT
1 TTGT
53858 TAGTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.54
Consensus pattern (18 bp):
TTGTCAATGCATTTTCAT
Found at i:65356 original size:81 final size:81
Alignment explanation
Indices: 65221--65375 Score: 274
Period size: 81 Copynumber: 1.9 Consensus size: 81
65211 AGCGGTATTT
*
65221 CGGTGGTAAGAAATGATAAAAATGAACTAATCCCTACTCGCATTGCTACAGGTTGGCGAGTGTGC
1 CGGTGGTAAGAAATGATAAAAATAAACTAATCCCTACTCGCATTGCTACAGGTTGGCGAGTGTGC
*
65286 ATGGATTACGGCATTA
66 ATGAATTACGGCATTA
* *
65302 CGGTGGTAAGCAATGATAAAAATAAATTAATCCCTACTCGCATTGCTACAGGTTGGCGAGTGTGC
1 CGGTGGTAAGAAATGATAAAAATAAACTAATCCCTACTCGCATTGCTACAGGTTGGCGAGTGTGC
65367 ATGAATTAC
66 ATGAATTAC
65376 CGTCGTTTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (81 bp):
CGGTGGTAAGAAATGATAAAAATAAACTAATCCCTACTCGCATTGCTACAGGTTGGCGAGTGTGC
ATGAATTACGGCATTA
Done.