Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009211.1 Kokia drynarioides strain JFW-HI SEQ_123916, 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: 19133
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:412 original size:13 final size:13
Alignment explanation
Indices: 394--421 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
384 CGAGAAGGGG
394 TGAGAGGTTTTTT
1 TGAGAGGTTTTTT
407 TGAGAGGTTTTTT
1 TGAGAGGTTTTTT
420 TG
1 TG
422 GTTTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.54
Consensus pattern (13 bp):
TGAGAGGTTTTTT
Found at i:997 original size:29 final size:29
Alignment explanation
Indices: 954--1291 Score: 329
Period size: 29 Copynumber: 11.5 Consensus size: 29
944 CGGAGTCCCT
*
954 AAACTATCCAAAAATCCCATTTTTACCCCC
1 AAACT-TCCAAAAATCCCATTTTTACCCCA
*
984 AAACTTCCAAAAATCCCATTTTTTACCCTA
1 AAACTTCCAAAAATCCCA-TTTTTACCCCA
* *
1014 AAACTTTCAAAAATTCCATTTTTACCCTC-
1 AAACTTCCAAAAATCCCATTTTTACCC-CA
* **
1043 GAACTTCCAAAAATCCCATTTTTGACCTTA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
* * *
1073 AAACTTCAAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* ** *
1102 GAACTTCCAAAAATATCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
* *
1132 AAACTTCCAAAAATCCCATTTTGACCCTA
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* * * * *
1161 AAACTACCAAAAATCACATTTTAACTCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* *
1190 AAACTTCCAAAAATTCCATTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
1219 AAACTTCCAAAAATTCCATTTTTACACCC-
1 AAACTTCCAAAAATCCCATTTTTAC-CCCA
* * * ***
1248 GAGCTTCCAAAAATCTCATTTTTGACCTTG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
1278 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
1292 TATCATTTTA
Statistics
Matches: 251, Mismatches: 49, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
29 158 0.63
30 93 0.37
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCA
Found at i:1048 original size:59 final size:59
Alignment explanation
Indices: 950--1241 Score: 331
Period size: 59 Copynumber: 5.0 Consensus size: 59
940 ACCCCGGAGT
*
950 CCCT-AAACTATCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
* * * *
1009 CCCTAAAACTTTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
* * * **
1068 CCTTAAAACTTCAAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATATCA-TTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
* * * ** * * *
1126 ACCTCAAAACTTCCAAAAATCCCATTTTGACCCTAAAACTACCAAAAATCACA-TTTTAA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
* * * *
1185 CTCC-GAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTT
1 C-CCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTT
1242 ACACCCGAGC
Statistics
Matches: 198, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
58 49 0.25
59 142 0.72
60 7 0.04
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA
Found at i:1113 original size:88 final size:89
Alignment explanation
Indices: 954--1241 Score: 338
Period size: 88 Copynumber: 3.3 Consensus size: 89
944 CGGAGTCCCT
** * ***
954 AAACTATCCAAAAATCCCATTTTT-ACCCCCAAACTTCCAAAAATCCCATTTTTTACCCTAAAAC
1 AAACT-TCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCA-TTTTTACCCCCGAAC
*
1018 TTTCAAAAATTCCATTTTTACCCTC-
64 TTCCAAAAATTCCATTTTTACCCTCA
* * *
1043 GAACTTCCAAAAATCCCATTTTTGACCTTAAAACTTCAAAAAATTCCATTTTTACCCCCGAACTT
1 AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
*
1108 CCAAAAATAT-CATTTTTAACCTCA
66 CCAAAAAT-TCCATTTTTACCCTCA
* * *
1132 AAACTTCCAAAAATCCCA-TTTTGACCCTAAAACTACCAAAAA-TCACA-TTTTAACTCCGAAAC
1 AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTC-CATTTTTACCCCCG-AAC
*
1194 TTCCAAAAATTCCATTTTGACCC-CA
64 TTCCAAAAATTCCATTTTTACCCTCA
*
1219 AAACTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATCCCATTTTT
1242 ACACCCGAGC
Statistics
Matches: 172, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
87 31 0.18
88 100 0.58
89 41 0.24
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (89 bp):
AAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
CCAAAAATTCCATTTTTACCCTCA
Found at i:1283 original size:59 final size:57
Alignment explanation
Indices: 955--1292 Score: 247
Period size: 59 Copynumber: 5.8 Consensus size: 57
945 GGAGTCCCTA
* * ** * * *
955 AACTATCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCTAA
1 AACT-TCCAAAAATCTCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTAACCC--G
* * ** * * **
1015 AACTTTCAAAAAT-TCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTAA
1 AACTTCCAAAAATCT-CATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTAACC--CG
* * *** *
1074 AACTTCAAAAAAT-TCCATTTTTACCCCCGAACTTCCAAAAATAT-CATTTTTAACCTCAA
1 AACTTCCAAAAATCT-CATTTTGACCCTAAAACTTCCAAAAAT-TCCATTTTTAACC-C-G
* *
1133 AACTTCCAAAAATCCCATTTTGACCCTAAAACTACCAAAAA-TCACA-TTTTAACTCCG
1 AACTTCCAAAAATCTCATTTTGACCCTAAAACTTCCAAAAATTC-CATTTTTAAC-CCG
*
1190 AAACTTCCAAAAAT-TCCATTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACACCCG
1 -AACTTCCAAAAATCT-CATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTA-ACCCG
* * *
1249 AGCTTCCAAAAATCTCATTTTTGACCTTGAAACTTCCAAAAATT
1 AACTTCCAAAAATCTCA-TTTTGACCCTAAAACTTCCAAAAATT
1293 ATCATTTTAC
Statistics
Matches: 235, Mismatches: 27, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
57 1 0.00
58 62 0.26
59 166 0.71
60 6 0.03
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (57 bp):
AACTTCCAAAAATCTCATTTTGACCCTAAAACTTCCAAAAATTCCATTTTTAACCCG
Found at i:1290 original size:88 final size:85
Alignment explanation
Indices: 954--1305 Score: 334
Period size: 88 Copynumber: 4.0 Consensus size: 85
944 CGGAGTCCCT
* * **
954 AAACTATCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTTACCCTAAAACT
1 AAACT-TCCAAAAATCCCATTTTTA-CCCAAAACTTCCAAAAATCTCA-TTTTTACCCCGAAACT
*
1019 TTCAAAAATTCCATTTTTACCCTC-
63 TCCAAAAATTCCA-TTTTACCC-CA
* * *
1043 GAACTTCCAAAAATCCCATTTTTGACCTTAAAACTTCAAAAAAT-TCCATTTTTACCCCCG-AAC
1 AAACTTCCAAAAATCCCATTTTT-ACC-CAAAACTTCCAAAAATCT-CATTTTTA-CCCCGAAAC
*
1106 TTCCAAAAATAT-CATTTTTAACCTCA
62 TTCCAAAAAT-TCCA-TTTT-ACCCCA
* * * * *
1132 AAACTTCCAAAAATCCCATTTTGACCCTAAAACTACCAAAAATCACATTTTAACTCCGAAACTTC
1 AAACTTCCAAAAATCCCATTTTTACCC-AAAACTTCCAAAAATCTCATTTTTACCCCGAAACTTC
1197 CAAAAATTCCATTTTGACCCCA
65 CAAAAATTCCATTTT-ACCCCA
* ** * **
1219 AAACTTCCAAAAATTCCATTTTTACACCCGAGCTTCCAAAAATCTCATTTTTGACCTTGAAACTT
1 AAACTTCCAAAAATCCCATTTTTAC-CCAAAACTTCCAAAAATCTCATTTTT-ACCCCGAAACTT
*
1284 CCAAAAATTATCATTTTACCCC
64 CCAAAAATT-CCATTTTACCCC
1306 TGGATGTCCG
Statistics
Matches: 218, Mismatches: 31, Indels: 29
0.78 0.11 0.10
Matches are distributed among these distances:
87 55 0.25
88 109 0.50
89 54 0.25
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (85 bp):
AAACTTCCAAAAATCCCATTTTTACCCAAAACTTCCAAAAATCTCATTTTTACCCCGAAACTTCC
AAAAATTCCATTTTACCCCA
Found at i:6829 original size:21 final size:21
Alignment explanation
Indices: 6805--6856 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
6795 AAATGTATCA
*
6805 ATACTTTTTGAAAATATATAG
1 ATACTTTTTGAAAAGATATAG
* *
6826 ATACATTTTGAAAAGATATCG
1 ATACTTTTTGAAAAGATATAG
6847 ATACTTTTTG
1 ATACTTTTTG
6857 TCATTGTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (21 bp):
ATACTTTTTGAAAAGATATAG
Found at i:8516 original size:22 final size:22
Alignment explanation
Indices: 8479--8536 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
8469 TTTTATAATA
*
8479 ATTATTA-TAAATATAAT-TTT
1 ATTATTATTTAATATAATATTT
8499 AGTTATTATTTAATATAATATTT
1 A-TTATTATTTAATATAATATTT
8522 A-TATTATTTTAATAT
1 ATTATTA-TTTAATAT
8537 TTTATTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 17 0.52
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
ATTATTATTTAATATAATATTT
Found at i:11813 original size:31 final size:31
Alignment explanation
Indices: 11752--11815 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
11742 ACACGGGATC
*
11752 AAAACGTAAATTTAGAAAAGTTTAGGGGGTAA
1 AAAACGTAAATTTAGAAAAATTTA-GGGGTAA
* *
11784 AAAATGTAATTTTAGGAAAAATTTA-GGGTAA
1 AAAACGTAAATTTA-GAAAAATTTAGGGGTAA
11815 A
1 A
11816 TATGTGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.25
32 12 0.43
33 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.28
Consensus pattern (31 bp):
AAAACGTAAATTTAGAAAAATTTAGGGGTAA
Found at i:11869 original size:29 final size:29
Alignment explanation
Indices: 11808--12145 Score: 245
Period size: 29 Copynumber: 11.7 Consensus size: 29
11798 GGAAAAATTT
*
11808 AGGGTAAATATGTGATTTTTGAGAAGTTCG
1 AGGGTAAAAATGTGATTTTTGAGAAGTT-G
*
11838 AGGGTGAAAATGTGATTTTTG-GAAGCTTG
1 AGGGTAAAAATGTGATTTTTGAGAAG-TTG
* *
11867 AGGGTAAAAATGTAATTCTTGAGAAGTTCG
1 AGGGTAAAAATGTGATTTTTGAGAAGTT-G
* *
11897 -GGAGTAAAAAAGTGATTTTTG-GAAGCTCG
1 AGG-GTAAAAATGTGATTTTTGAGAAG-TTG
* *
11926 -GGGCAAAAATGT-AATTTTGAGAAGTTCG
1 AGGGTAAAAATGTGATTTTTGAGAAGTT-G
11954 AGGGTAAAAATTGTGATTTTT-AGAAGTTTG
1 AGGGTAAAAA-TGTGATTTTTGAGAAG-TTG
* * *
11984 -GGGTCAAAATGTAATTTTTGTA-AAGTTT
1 AGGGTAAAAATGTGATTTTTG-AGAAGTTG
** *
12012 AGCATAAAAATGTGATTTTTTG-GAAGTTT
1 AGGGTAAAAATGTGA-TTTTTGAGAAGTTG
** *
12041 AGGGGCAAAA--TGACTTTTTGAGAAGTTCA
1 AGGGTAAAAATGTGA-TTTTTGAGAAGTT-G
* *
12070 AGGGTAAAAAAGTGATTTTTG-GAAGTTTA
1 AGGGTAAAAATGTGATTTTTGAGAAG-TTG
* *
12099 AGGG-AAAAATGT-AATTTTGAGAAGTTT
1 AGGGTAAAAATGTGATTTTTGAGAAGTTG
* *
12126 AGGGGTCAAAATGTAATTTT
1 A-GGGTAAAAATGTGATTTT
12146 GAAAAAGTTT
Statistics
Matches: 248, Mismatches: 35, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
27 25 0.10
28 44 0.18
29 99 0.40
30 70 0.28
31 10 0.04
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
AGGGTAAAAATGTGATTTTTGAGAAGTTG
Found at i:11957 original size:116 final size:115
Alignment explanation
Indices: 11824--12124 Score: 371
Period size: 116 Copynumber: 2.6 Consensus size: 115
11814 AATATGTGAT
* *
11824 TTTTGAGAAGTTCGAGGGTGAAAATGTGATTTTTGGAAGCTTGAGGGTAAAAATGTAATTCTTGA
1 TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAATT-TTGA
* * *
11889 GAAGTTCGGGAGTAAAAAAGTGA-TTTTTGGAAG-CTCGGGGCAAAAATGTA-A
65 GAAGTTCAGCA-TAAAAAAGTGATTTTTTGGAAGTCTAGGGGC-AAAATG-ACA
* *
11940 TTTTGAGAAGTTCGAGGGTAAAAATTGTGATTTTTAGAAGTTTG-GGGTCAAAATGTAATTTTTG
1 TTTTGAGAAGTTCGAGGGTAAAAA-TGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAA-TTTTG
* * * *
12004 TA-AAGTTTAGCATAAAAATGTGATTTTTTGGAAGTTTAGGGGCAAAATGACT
64 -AGAAGTTCAGCATAAAAAAGTGATTTTTTGGAAGTCTAGGGGCAAAATGACA
* * *
12056 TTTTGAGAAGTTCAAGGGTAAAAAAGTGATTTTTGGAAGTTTAAGGG-AAAAATGTAATTTTGAG
1 TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTGAG
12120 AAGTT
66 AAGTT
12125 TAGGGGTCAA
Statistics
Matches: 161, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
113 1 0.01
114 10 0.06
115 36 0.22
116 88 0.55
117 26 0.16
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (115 bp):
TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTGAG
AAGTTCAGCATAAAAAAGTGATTTTTTGGAAGTCTAGGGGCAAAATGACA
Found at i:11971 original size:58 final size:57
Alignment explanation
Indices: 11824--12124 Score: 312
Period size: 58 Copynumber: 5.2 Consensus size: 57
11814 AATATGTGAT
* *
11824 TTTTGAGAAGTTCGAGGGTGAAAATGTGATTTTTGGAAGCTT-GAGGGTAAAAATGTAA
1 TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAG-TTAG-GGGCAAAAATGTAA
* * *
11882 TTCTTGAGAAGTTCG-GGAGTAAAAAAGTGATTTTTGGAAGCTCGGGGCAAAAATGTAA
1 TT-TTGAGAAGTTCGAGG-GTAAAAATGTGATTTTTGGAAGTTAGGGGCAAAAATGTAA
* *
11940 TTTTGAGAAGTTCGAGGGTAAAAATTGTGATTTTTAGAAGTTTGGGGTC-AAAATGTAA
1 TTTTGAGAAGTTCGAGGGTAAAAA-TGTGATTTTTGGAAGTTAGGGG-CAAAAATGTAA
* ** *
11998 TTTTTGTA-AAGTT-TAGCATAAAAATGTGATTTTTTGGAAGTTTAGGGGC-AAAATG-ACT
1 -TTTTG-AGAAGTTCGAGGGTAAAAATGTGA-TTTTTGGAAG-TTAGGGGCAAAAATGTA-A
* * *
12056 TTTTGAGAAGTTCAAGGGTAAAAAAGTGATTTTTGGAAGTTTAAGGG-AAAAATGTAA
1 TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAG-TTAGGGGCAAAAATGTAA
12113 TTTTGAGAAGTT
1 TTTTGAGAAGTT
12125 TAGGGGTCAA
Statistics
Matches: 208, Mismatches: 20, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
56 1 0.00
57 70 0.34
58 86 0.41
59 50 0.24
60 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (57 bp):
TTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAGTTAGGGGCAAAAATGTAA
Found at i:12146 original size:29 final size:29
Alignment explanation
Indices: 11760--12175 Score: 225
Period size: 29 Copynumber: 14.2 Consensus size: 29
11750 TCAAAACGTA
* *
11760 AATTTAGAAAAGTTTAGGGGGTAAAAAATGT
1 AATTTTGAGAAGTTTA-GGGGT-AAAAATGT
* * *
11791 AATTTTAGGAAAAATTTA-GGGTAAATATGT
1 AATTTT--GAGAAGTTTAGGGGTAAAAATGT
* * *
11821 GATTTTTGAGAAG-TTCGAGGGTGAAAATGT
1 -AATTTTGAGAAGTTTAG-GGGTAAAAATGT
* *
11851 GATTTTTG-GAAGCTT-GAGGGTAAAAATGT
1 -AATTTTGAGAAGTTTAG-GGGTAAAAATGT
* *
11880 AATTCTTGAGAAG-TTCGGGAGTAAAAAAGT
1 AATT-TTGAGAAGTTTAGGG-GTAAAAATGT
* * * *
11910 GATTTTTG-GAAG-CTCGGGGCAAAAATGT
1 -AATTTTGAGAAGTTTAGGGGTAAAAATGT
*
11938 AATTTTGAGAAG-TTCGAGGGTAAAAATTGT
1 AATTTTGAGAAGTTTAG-GGGTAAAAA-TGT
* * *
11968 GATTTTTAGAAGTTT-GGGGTCAAAATGT
1 AATTTTGAGAAGTTTAGGGGTAAAAATGT
**
11996 AATTTTTGTA-AAGTTTA-GCATAAAAATGT
1 AA-TTTTG-AGAAGTTTAGGGGTAAAAATGT
* *
12025 GATTTTTTG-GAAGTTTAGGGG-CAAAATG-
1 -A-ATTTTGAGAAGTTTAGGGGTAAAAATGT
* * * *
12053 ACTTTTTGAGAAGTTCAAGGGTAAAAAAGT
1 A-ATTTTGAGAAGTTTAGGGGTAAAAATGT
* *
12083 GATTTTTG-GAAGTTTAAGGG-AAAAATGT
1 -AATTTTGAGAAGTTTAGGGGTAAAAATGT
*
12111 AATTTTGAGAAGTTTAGGGGTCAAAATGT
1 AATTTTGAGAAGTTTAGGGGTAAAAATGT
* * * *
12140 AATTTTGAAAAAGTTTAAGGGTCAAAATAT
1 AATTTTG-AGAAGTTTAGGGGTAAAAATGT
12170 AATTTT
1 AATTTT
12176 TGGAAAGTTC
Statistics
Matches: 312, Mismatches: 44, Indels: 59
0.75 0.11 0.14
Matches are distributed among these distances:
27 19 0.06
28 52 0.17
29 115 0.37
30 97 0.31
31 20 0.06
33 9 0.03
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AATTTTGAGAAGTTTAGGGGTAAAAATGT
Found at i:18966 original size:23 final size:22
Alignment explanation
Indices: 18807--18975 Score: 121
Period size: 23 Copynumber: 7.3 Consensus size: 22
18797 CGAAGTACTT
18807 AACAGTAAGCACACAAGTGCTGGGAA
1 AACAGTAAGCACACAAGTGC---G-A
* *
18833 AACAATAAGCACACACAATGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
18855 ATCCAGTAAGCACACACAGTGC-A
1 A-ACAGTAAGCACACA-AGTGCGA
* * * *
18878 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
18900 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACAC-AAGTGCGA
18924 AACAGTAAGCACACGAAGTGCGA
1 AACAGTAAGCACAC-AAGTGCGA
18947 AACAGTAAGCACACACAGTGCTG-
1 AACAGTAAGCACACA-AGTGC-GA
18970 AACAGT
1 AACAGT
18976 GAGCGCGCTA
Statistics
Matches: 122, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
22 20 0.16
23 79 0.65
24 5 0.04
26 14 0.11
27 4 0.03
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Done.