Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005887.1 Kokia drynarioides strain JFW-HI SEQ_120223, 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: 22749
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1037 original size:12 final size:11
Alignment explanation
Indices: 1016--1077 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
1006 AACTAAACCC
1016 ATTT-TTTTAAA
1 ATTTATTTT-AA
1027 ATTTATTTTAA
1 ATTTATTTTAA
*
1038 ATTTAAATTT-A
1 ATTT-ATTTTAA
*
1049 ATTTACGTTTAA
1 ATTTA-TTTTAA
1061 ATTTATTTTCAA
1 ATTTATTTT-AA
1073 ATTTA
1 ATTTA
1078 ATCTTACTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
10 1 0.02
11 21 0.49
12 21 0.49
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTTATTTTAA
Found at i:1047 original size:17 final size:17
Alignment explanation
Indices: 1025--1097 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
1015 CATTTTTTTA
1025 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* **
1042 AAATTTAATTTACGTTT
1 AAATTTATTTTAAATTT
1059 AAATTTATTTTCAAATTT
1 AAATTTATTTT-AAATTT
* *
1077 -AATCTTACTCTAAATTT
1 AAAT-TTATTTTAAATTT
1094 AAAT
1 AAAT
1098 AAATAAAAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:1065 original size:29 final size:30
Alignment explanation
Indices: 1033--1097 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1023 TAAAATTTAT
*
1033 TTTAAATTT-AAATTTAAT-TTACGTTTAAA
1 TTTAAATTTCAAATTTAATCTTAC-TCTAAA
*
1062 TTT-ATTTTCAAATTTAATCTTACTCTAAA
1 TTTAAATTTCAAATTTAATCTTACTCTAAA
1091 TTTAAAT
1 TTTAAAT
1098 AAATAAAAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.13
29 20 0.67
30 6 0.20
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTAAATTTCAAATTTAATCTTACTCTAAA
Found at i:1838 original size:3 final size:3
Alignment explanation
Indices: 1832--1867 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1822 TGCATTAAAT
1832 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1868 CAAAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2977 original size:29 final size:29
Alignment explanation
Indices: 2939--3295 Score: 155
Period size: 29 Copynumber: 12.2 Consensus size: 29
2929 CAGAAATCAT
* *
2939 ATTTTGACCTCAAACTTTCTAAAAATTAC
1 ATTTTAACCTCGAACTTTCTAAAAATTAC
*
2968 ATTTTAACCTCGTACTTTCTAAAAATTAC
1 ATTTTAACCTCGAACTTTCTAAAAATTAC
* * * * * *
2997 ATTTTTACCCCTAAACTTCACAAAAAATTAT
1 ATTTTAACCTC-GAACTT-TCTAAAAATTAC
** ** * *
3028 ATTTTTGCCATTAAAC-TTCCAAAAATTCC
1 ATTTTAACC-TCGAACTTTCTAAAAATTAC
* *
3057 ATTTCTACCCTCGAAC-TTC-CAAAATTACC
1 ATTT-TAACCTCGAACTTTCTAAAAATTA-C
* * *
3086 ATTTTACCCTTGAA--TT-TACAAAATTCC
1 ATTTTAACCTCGAACTTTCTA-AAAATTAC
*
3113 ATTTTTGACCTCGAACTTT-TCAAAAATTACC
1 A-TTTTAACCTCGAACTTTCT-AAAAATTA-C
* * *
3144 ATTTTACCCTCGAA-TTTCCAAAAATTCC
1 ATTTTAACCTCGAACTTTCTAAAAATTAC
* *
3172 ATTTTTAACCTTGAAC-TTCCAAAAATTATC
1 A-TTTTAACCTCGAACTTTCTAAAAATTA-C
* * *
3202 ATTTTACCCTCGAA-TGTCCAAAAATT-C
1 ATTTTAACCTCGAACTTTCTAAAAATTAC
* * * *
3229 TATTTTTGACCTCGATC-CTCCAAAAATTAC
1 -A-TTTTAACCTCGAACTTTCTAAAAATTAC
* * *
3259 TATTTTACCCTCCGAAGTGTCT-AAAATTATC
1 -ATTTTAACCT-CGAACTTTCTAAAAATTA-C
3290 ATTTTA
1 ATTTTA
3296 CCCCCGGGTG
Statistics
Matches: 254, Mismatches: 50, Indels: 47
0.72 0.14 0.13
Matches are distributed among these distances:
27 5 0.02
28 34 0.13
29 139 0.55
30 49 0.19
31 27 0.11
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
ATTTTAACCTCGAACTTTCTAAAAATTAC
Found at i:3147 original size:58 final size:58
Alignment explanation
Indices: 2940--3270 Score: 314
Period size: 58 Copynumber: 5.7 Consensus size: 58
2930 AGAAATCATA
* * * * * *
2940 TTTTGACCTCAAACTTTCTAAAAATTA-CATTTTAACCTCGTACTTTCTAAAAATTACAT
1 TTTTGACCTCGAAC-TTCCAAAAATTACCATTTTACCCTCG-AATTTCCAAAAATTCCAT
* * * * * ** *
2999 TTTT-ACCCCTAAACTTCACAAAAAATTA-TATTTTTGCCATTAAACTTCCAAAAATTCCAT
1 TTTTGACCTC-GAACTTC-C-AAAAATTACCA-TTTTACCCTCGAATTTCCAAAAATTCCAT
* * *
3059 TTCT-ACCCTCGAACTTCC-AAAATTACCATTTTACCCTTGAATTTAC-AAAATTCCAT
1 TTTTGA-CCTCGAACTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCAT
*
3115 TTTTGACCTCGAACTTTTCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCAT
1 TTTTGACCTCGAAC-TTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCAT
* * * * *
3174 TTTTAACCTTGAACTTCCAAAAATTATCATTTTACCCTCGAATGTCCAAAAATTCTAT
1 TTTTGACCTCGAACTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCAT
* * *
3232 TTTTGACCTCGATCCTCCAAAAATTACTATTTTACCCTC
1 TTTTGACCTCGAACTTCCAAAAATTACCATTTTACCCTC
3271 CGAAGTGTCT
Statistics
Matches: 225, Mismatches: 37, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
56 21 0.09
57 24 0.11
58 107 0.48
59 31 0.14
60 33 0.15
61 9 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
TTTTGACCTCGAACTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCAT
Found at i:3242 original size:87 final size:85
Alignment explanation
Indices: 3045--3322 Score: 230
Period size: 87 Copynumber: 3.2 Consensus size: 85
3035 CCATTAAACT
* * *
3045 TCCAAAAATTCCATTTCTACCCTCGAACTTCC-AAAATTACCA-TTTTACCCTTGAATTTACAAA
1 TCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATT-CCATTTTTACCCTTGAACTT-CAAA
* *
3108 ATT-CCATTTTTGA-CCTCGAACTT
64 ATTATCA-TTTT-ACCCTCGAA-TG
* *
3131 TTCAAAAATTACCA-TTTTACCCTCGAATTTCCAAAAATTCCATTTTTAACCTTGAACTTCCAAA
1 TCCAAAAATT-CCATTTTTACCCTCGAATTTCCAAAAATTCCATTTTTACCCTTGAACTT-C-AA
3195 AATTATCATTTTACCCTCGAATG
63 AATTATCATTTTACCCTCGAATG
* * * * *
3218 TCCAAAAATTCTATTTTTGA-CCTCG-ATCCTCCAAAAATTAC-TATTTTACCCTCCGAAGTGTC
1 TCCAAAAATTCCATTTTT-ACCCTCGAAT-TTCCAAAAATTCCAT-TTTTACCCT-TGAACT-TC
* **
3280 TAAAATTATCATTTTACCCCCGGGTG
61 -AAAATTATCATTTTACCCTCGAATG
*
3306 TCCAAAAATTGCATTTT
1 TCCAAAAATTCCATTTT
3323 GTCCCGTCTG
Statistics
Matches: 159, Mismatches: 21, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
86 33 0.21
87 63 0.40
88 60 0.38
89 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (85 bp):
TCCAAAAATTCCATTTTTACCCTCGAATTTCCAAAAATTCCATTTTTACCCTTGAACTTCAAAAT
TATCATTTTACCCTCGAATG
Found at i:12035 original size:28 final size:28
Alignment explanation
Indices: 11995--12052 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
11985 GCCAAGCAAA
11995 TAATGAGATTTGGGTTTTACTGGTGTAC
1 TAATGAGATTTGGGTTTTACTGGTGTAC
12023 TAATGAGATTTGGGTTTTACTGGTGTAC
1 TAATGAGATTTGGGTTTTACTGGTGTAC
12051 TA
1 TA
12053 TGAAAGGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (28 bp):
TAATGAGATTTGGGTTTTACTGGTGTAC
Found at i:14554 original size:209 final size:208
Alignment explanation
Indices: 13941--14617 Score: 960
Period size: 209 Copynumber: 3.3 Consensus size: 208
13931 TAACGAGCTA
* * * * *
13941 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGATGAAACCA-AGCTCAATA-TGAGA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGA-CTCAA-AGTGAGC
* * ** * *
14004 AAAACTTTGAACTTCAGCTTCCTGATGAGATACTAAGAAGCAAGTCGAAGCAATAAATTGGTTAG
64 AAATCTTTAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAA-CAATAAAATGGTTAG
* * * * *
14069 CTTCCTGATGAGATACTAAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAGAGAAGCAGTT
128 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAAAAGCGGAT
*
14134 TGAAACAAGTGATGTG
193 TGAAACAAGTGATGCG
* * * * *
14150 GTCATCTTCCTGATGAAATACTGAGAAGTAGACCAAATCAATGAAGCCAGGCTTAAAGTTAGCAA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGACTCAAAGTGAGCAA
14215 ATCTTTAAACCCCAGCTTCCTGATGAGATACTGAGAA--AAGT-----AATAAAATGGTTAGCTT
66 ATCTTTAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAACAATAAAATGGTTAGCTT
14273 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATA-AACAAGCGGATTG
131 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAA-AAGCGGATTG
14337 AAACAAGTGATGCG
195 AAACAAGTGATGCG
* * *
14351 ATCATCTTCCTGATGAGATATTGAGAAGTAGACCAAATCAATGAAGCCAGACTCAAAGTGAGCAA
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGACTCAAAGTGAGCAA
* *
14416 ATCTTCAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCT
66 ATCTTTAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCG-AACAATAAAATGGTTAGCT
*
14481 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAAAAGCGGATTG
130 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAAAAGCGGATTG
14546 AAACAAGTGATGCG
195 AAACAAGTGATGCG
* * *
14560 GTCATCTTCTTGATGAGATACTGAGAAATAGATCAAATCAATGAAACCAGACTCAAAG
1 GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGACTCAAAG
14618 ACTACGGTGA
Statistics
Matches: 419, Mismatches: 37, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
200 1 0.00
201 181 0.43
203 3 0.01
207 4 0.01
208 1 0.00
209 227 0.54
210 2 0.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (208 bp):
GTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGACTCAAAGTGAGCAA
ATCTTTAAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAACAATAAAATGGTTAGCTT
CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAAAAGCGGATTGA
AACAAGTGATGCG
Found at i:14970 original size:11 final size:12
Alignment explanation
Indices: 14954--15020 Score: 68
Period size: 11 Copynumber: 5.8 Consensus size: 12
14944 TATTTTAAGA
*
14954 TTAAATTT-ATT
1 TTAAATTTAAAT
14965 TTAAATTTAAAT
1 TTAAATTTAAAT
*
14977 TT-ACTTTAAAT
1 TTAAATTTAAAT
*
14988 TT-AATTTAAGT
1 TTAAATTTAAAT
**
14999 TTAAATTTATTT
1 TTAAATTTAAAT
15011 TTAAATTTAA
1 TTAAATTTAA
15021 TCTTACTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
11 27 0.57
12 20 0.43
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:14973 original size:6 final size:6
Alignment explanation
Indices: 14954--15020 Score: 68
Period size: 6 Copynumber: 11.7 Consensus size: 6
14944 TATTTTAAGA
* * *
14954 TTAAAT TT-ATT TTAAAT TTAAAT TT-ACT TTAAAT TT-AAT TTAAGT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
**
14999 TTAAAT TTATTT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAA
15021 TCTTACTCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 13 0.27
6 35 0.73
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (6 bp):
TTAAAT
Found at i:15006 original size:17 final size:16
Alignment explanation
Indices: 14940--15037 Score: 80
Period size: 17 Copynumber: 6.1 Consensus size: 16
14930 CATTTTTTAA
* *
14940 AATTTATTTTAAGATTA
1 AATTTACTTTAA-ATTT
*
14957 AATTTATTTTAAATTT
1 AATTTACTTTAAATTT
14973 AAATTTACTTTAAATTT
1 -AATTTACTTTAAATTT
*
14990 AATTTAAGTTTAAATTT
1 AATTT-ACTTTAAATTT
15007 -A-TT--TTTAAATTT
1 AATTTACTTTAAATTT
15019 AATCTTACTCTT-AATTT
1 AAT-TTACT-TTAAATTT
15036 AA
1 AA
15038 ATAAATAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.13
13 1 0.01
15 4 0.06
16 9 0.13
17 45 0.64
18 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (16 bp):
AATTTACTTTAAATTT
Found at i:16875 original size:30 final size:30
Alignment explanation
Indices: 16828--16905 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
16818 GTTCAAAGGT
* * *
16828 CCCT-AAACTATCCAAAAATCATAATTTAA
1 CCCTCAAACTTTCTAAAAATCACAATTTAA
* * *
16857 CCC-CTAAACTTTTTAAAAATTACATTTTAA
1 CCCTC-AAACTTTCTAAAAATCACAATTTAA
16887 CCCTCAAACTTTCTAAAAA
1 CCCTCAAACTTTCTAAAAA
16906 AATACATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 3 0.08
30 35 0.90
31 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (30 bp):
CCCTCAAACTTTCTAAAAATCACAATTTAA
Found at i:16890 original size:29 final size:29
Alignment explanation
Indices: 16871--17155 Score: 228
Period size: 29 Copynumber: 9.7 Consensus size: 29
16861 TAAACTTTTT
* * *
16871 AAAAATTACATTTTAACCCTCAAACTTTCTA
1 AAAAATTACATTTTTACCCT-GAACTTTC-C
* *
16902 AAAAAATACATTTTTTCCCTCGAAC-TTCAC
1 AAAAATTACATTTTTACCCT-GAACTTTC-C
*
16932 AAAAATTACATTTTTTACCTTGAAC-TTCC
1 AAAAATTACA-TTTTTACCCTGAACTTTCC
**
16961 AAAAATTACATTTTTACCCTCGAACTTAAC
1 AAAAATTACATTTTTACCCT-GAACTTTCC
* *
16991 AAAAATTACATTTTTTCCCCT-AAATTTCC
1 AAAAATTACA-TTTTTACCCTGAACTTTCC
*
17020 AAAAATTCCATTTTTAACCCTGAACTTTCC
1 AAAAATTACATTTTT-ACCCTGAACTTTCC
17050 AAAAATTATCA-TTTTACCCTCGAA-TTTCC
1 AAAAATTA-CATTTTTACCCT-GAACTTTCC
* *
17079 AAAAATTTCATTTTGA-CCTCGAACTTT-C
1 AAAAATTACATTTTTACCCT-GAACTTTCC
* * *
17107 AAAAATTAACA-TTTTATCCCCGTA-TATCC
1 AAAAATT-ACATTTTTA-CCCTGAACTTTCC
*
17136 AAAAATTCCATTTTTTACCC
1 AAAAATTACA-TTTTTACCC
17156 CAAACCTCTA
Statistics
Matches: 210, Mismatches: 28, Indels: 34
0.77 0.10 0.12
Matches are distributed among these distances:
28 39 0.19
29 72 0.34
30 59 0.28
31 40 0.19
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTGAACTTTCC
Found at i:16942 original size:30 final size:29
Alignment explanation
Indices: 16871--17151 Score: 232
Period size: 30 Copynumber: 9.6 Consensus size: 29
16861 TAAACTTTTT
** * *
16871 AAAAATTACATTTTAACCCTCAAACTTTCTA
1 AAAAATTACATTTTTTCCCTCGAAC-TTC-C
*
16902 AAAAAATACATTTTTTCCCTCGAACTTCAC
1 AAAAATTACATTTTTTCCCTCGAACTTC-C
* *
16932 AAAAATTACATTTTTTACCTTGAACTTCC
1 AAAAATTACATTTTTTCCCTCGAACTTCC
* *
16961 AAAAATTACATTTTTACCCTCGAACTTAAC
1 AAAAATTACATTTTTTCCCTCGAACTT-CC
* *
16991 AAAAATTACATTTTTTCCC-CTAAATTTCC
1 AAAAATTACATTTTTTCCCTC-GAACTTCC
* *
17020 AAAAATTCCATTTTTAACCCT-GAACTTTCC
1 AAAAATTACATTTTT-TCCCTCGAAC-TTCC
* *
17050 AAAAATTATCA-TTTTACCCTCGAATTTCC
1 AAAAATTA-CATTTTTTCCCTCGAACTTCC
* ** *
17079 AAAAATTTCA-TTTTGACCTCGAACTTTC
1 AAAAATTACATTTTTTCCCTCGAACTTCC
* *
17107 AAAAATTAACATTTTATCCC-CGTA-TATCC
1 AAAAATT-ACATTTTTTCCCTCGAACT-TCC
*
17136 AAAAATTCCATTTTTT
1 AAAAATTACATTTTTT
17152 ACCCCAAACC
Statistics
Matches: 204, Mismatches: 36, Indels: 23
0.78 0.14 0.09
Matches are distributed among these distances:
28 31 0.15
29 73 0.36
30 77 0.38
31 23 0.11
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAAATTACATTTTTTCCCTCGAACTTCC
Found at i:16986 original size:59 final size:59
Alignment explanation
Indices: 16902--17121 Score: 245
Period size: 59 Copynumber: 3.7 Consensus size: 59
16892 AAACTTTCTA
* * *
16902 AAAAAATACATTTTTTCCCTCGAACTTCACAAAAATTACATTTTTTACCTTGAACTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCACAAAAATTACATTTTTTACCTTGAATTTCC
* * * *
16961 AAAAATTACATTTTTACCCTCGAACTTAACAAAAATTACATTTTTTCCCCTAAATTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCACAAAAATTACATTTTTTACCTTGAATTTCC
* *
17020 AAAAATTCCATTTTTAACCCT-GAACTTTC-CAAAAATTATCA--TTTTACCCTCGAATTTCC
1 AAAAATTACATTTTT-ACCCTCGAAC-TTCACAAAAATTA-CATTTTTTA-CCTTGAATTTCC
* * *
17079 AAAAATTTCATTTTGA-CCTCGAACTT-TCAAAAATTAACATTTT
1 AAAAATTACATTTTTACCCTCGAACTTCACAAAAATT-ACATTTT
17122 ATCCCCGTAT
Statistics
Matches: 137, Mismatches: 15, Indels: 18
0.81 0.09 0.11
Matches are distributed among these distances:
57 15 0.11
58 10 0.07
59 103 0.75
60 9 0.07
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTCGAACTTCACAAAAATTACATTTTTTACCTTGAATTTCC
Found at i:17171 original size:57 final size:58
Alignment explanation
Indices: 16957--17156 Score: 212
Period size: 59 Copynumber: 3.4 Consensus size: 58
16947 TACCTTGAAC
* * *
16957 TTCCAAAAATTACATTTTT-ACCCTCGAACTTAACAAAAATT-ACATTTTTTCCCC-TAAAT
1 TTCCAAAAATTCCATTTTTAACCC-CGAACTT-TCAAAAATTAACATTTTATCCCCGT--AT
* * *
17016 TTCCAAAAATTCCATTTTTAACCCTGAACTTTCCAAAAATTATCATTTTA-CCCTCGAAT
1 TTCCAAAAATTCCATTTTTAACCCCGAACTTT-CAAAAATTAACATTTTATCCC-CGTAT
* * *
17075 TTCCAAAAATTTCA-TTTTGACCTCGAACTTTCAAAAATTAACATTTTATCCCCGTAT
1 TTCCAAAAATTCCATTTTTAACCCCGAACTTTCAAAAATTAACATTTTATCCCCGTAT
* *
17132 ATCCAAAAATTCCATTTTTTACCCC
1 TTCCAAAAATTCCATTTTTAACCCC
17157 AAACCTCTAA
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
57 32 0.27
58 25 0.21
59 50 0.42
60 11 0.09
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (58 bp):
TTCCAAAAATTCCATTTTTAACCCCGAACTTTCAAAAATTAACATTTTATCCCCGTAT
Found at i:17178 original size:57 final size:58
Alignment explanation
Indices: 16958--17197 Score: 204
Period size: 59 Copynumber: 4.1 Consensus size: 58
16948 ACCTTGAACT
* * * * *
16958 TCCAAAAATTACATTTTT-ACCCTCGAACTTAACAAAAATTA-CATTTTTTCCC-CTAAATT
1 TCCAAAAATTCCATTTTTAACCC-CGAACTT-TCAAAAATTATCA-TTTTACCCTC-GAATA
* *
17017 TCCAAAAATTCCATTTTTAACCCTGAACTTTCCAAAAATTATCATTTTACCCTCGAATT
1 TCCAAAAATTCCATTTTTAACCCCGAACTTT-CAAAAATTATCATTTTACCCTCGAATA
* * * * *
17076 TCCAAAAATTTCA-TTTTGACCTCGAACTTTCAAAAATTAACATTTTATCCC-CGTATA
1 TCCAAAAATTCCATTTTTAACCCCGAACTTTCAAAAATTATCATTTTA-CCCTCGAATA
* * * * * * *
17133 TCCAAAAATTCCATTTTTTACCCCAAAC-CTCTAAAATTATTATTTTGCCCTCGAAGTG
1 TCCAAAAATTCCATTTTTAACCCCGAACTTTCAAAAATTATCATTTTACCCTCGAA-TA
17191 TCCAAAA
1 TCCAAAA
17198 TTATCGTTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
56 3 0.02
57 49 0.33
58 36 0.24
59 55 0.37
60 7 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTAACCCCGAACTTTCAAAAATTATCATTTTACCCTCGAATA
Found at i:17226 original size:29 final size:29
Alignment explanation
Indices: 17047--17227 Score: 113
Period size: 29 Copynumber: 6.3 Consensus size: 29
17037 CCCTGAACTT
* * *
17047 TCCAAAAATTATCATTTTACCCTCGAATT
1 TCCAAAAATTATCATTTTGCCCCCGAATA
* *
17076 TCCAAAAATT-TCATTTTGACCTCGAACT-
1 TCCAAAAATTATCATTTTGCCCCCGAA-TA
* * ** *
17104 TTCAAAAATTAACATTTTATCCCCGTATA
1 TCCAAAAATTATCATTTTGCCCCCGAATA
* **
17133 TCCAAAAATT-CCATTTTTTACCCC-AA-A
1 TCCAAAAATTATCA-TTTTGCCCCCGAATA
* * * * *
17160 CCTCTAAAATTATTATTTTGCCCTCGAAGTG
1 TC-CAAAAATTATCATTTTGCCCCCGAA-TA
*
17191 TCC-AAAATTATCGTTTTGCCCCCGAATA
1 TCCAAAAATTATCATTTTGCCCCCGAATA
17219 TCCAAAAAT
1 TCCAAAAAT
17228 AGCATTGTAT
Statistics
Matches: 116, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
27 2 0.02
28 45 0.39
29 67 0.58
30 1 0.01
31 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTGCCCCCGAATA
Found at i:19825 original size:29 final size:29
Alignment explanation
Indices: 19755--19931 Score: 187
Period size: 29 Copynumber: 6.0 Consensus size: 29
19745 ATTATGTTTG
* *
19755 GACCACCAAAATTTCCAAAAATCCAAATTT
1 GACC-CCAAACTTTCCAAAAATTCAAATTT
* * * *
19785 TACCCTTAAACTTTTCAAAAATTTAAATTT
1 GACCC-CAAACTTTCCAAAAATTCAAATTT
**
19815 GACCCCAAACTTTCCAAAAATTTGAATTT
1 GACCCCAAACTTTCCAAAAATTCAAATTT
* ***
19844 GACCCCTAAGCTTTCCAAAAATTTGCATTT
1 GACCCC-AAACTTTCCAAAAATTCAAATTT
19874 -AGCCCCAAACTTTTCC-AAAATTCAAATTT
1 GA-CCCCAAAC-TTTCCAAAAATTCAAATTT
19903 GACCCCAAACTTTCCAAAAATTCAAATTT
1 GACCCCAAACTTTCCAAAAATTCAAATTT
19932 TGACTCGGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
28 5 0.04
29 63 0.50
30 57 0.46
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (29 bp):
GACCCCAAACTTTCCAAAAATTCAAATTT
Found at i:19835 original size:59 final size:58
Alignment explanation
Indices: 19755--19931 Score: 196
Period size: 59 Copynumber: 3.0 Consensus size: 58
19745 ATTATGTTTG
* * * *
19755 GACCACCAAAATTTCCAAAAATCCAAATTTTACCCTTAAACTTTTCAAAAATTTAAATTT
1 GACC-CCAAACTTTCCAAAAATTCAAATTTGACCC-TAAACTTTCCAAAAATTTAAATTT
** * **
19815 GACCCCAAACTTTCCAAAAATTTGAATTTGACCCCTAAGCTTTCCAAAAATTTGCATTT
1 GACCCCAAACTTTCCAAAAATTCAAATTTGA-CCCTAAACTTTCCAAAAATTTAAATTT
* *
19874 -AGCCCCAAACTTTTCC-AAAATTCAAATTTGACCCCAAACTTTCCAAAAATTCAAATTT
1 GA-CCCCAAAC-TTTCCAAAAATTCAAATTTGACCCTAAACTTTCCAAAAATTTAAATTT
19932 TGACTCGGTT
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 23 0.23
59 63 0.64
60 12 0.12
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (58 bp):
GACCCCAAACTTTCCAAAAATTCAAATTTGACCCTAAACTTTCCAAAAATTTAAATTT
Found at i:20137 original size:18 final size:19
Alignment explanation
Indices: 20106--20159 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
20096 ATCTACTTAA
*
20106 TTTATTAT-TTTATTGTAT
1 TTTATTATATATATTGTAT
*
20124 TTTA-TATATATATTAT-T
1 TTTATTATATATATTGTAT
*
20141 TTTATTATTTATACTTGTA
1 TTTATTATATATA-TTGTA
20160 AATCATGTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 8 0.29
18 17 0.61
19 3 0.11
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTATTATATATATTGTAT
Found at i:21683 original size:29 final size:28
Alignment explanation
Indices: 21643--21698 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
21633 ATAAAATAAT
* *
21643 TTTTTTATA-TTTAAATTTAAATAAAACA
1 TTTTTTAAATTTTAAAATTAAA-AAAACA
21671 TTTTTTACAATTTTAAAATTAAAAAAAC
1 TTTTTTA-AATTTTAAAATTAAAAAAAC
21699 CACCAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.29
29 6 0.25
30 11 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTTTAAATTTTAAAATTAAAAAAACA
Done.