Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011834.1 Kokia drynarioides strain JFW-HI SEQ_126830, 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: 294964
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 520 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:254500 original size:6 final size:6
Alignment explanation
Indices: 254452--254519 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
254442 TCATTTTGGG
* ***
254452 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTCT TTTAAA GTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA
254501 -TTAAGA -TTAAA TTTAAA TT
1 TTTAA-A TTTAAA TTTAAA TT
254520 GAATTAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
5 10 0.20
6 30 0.61
7 9 0.18
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:255264 original size:3 final size:3
Alignment explanation
Indices: 255256--255323 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
255246 ATAACTTATT
* *
255256 TAA TAA TAA TAT TAA TAA TAT TCAA TAA TAA TTAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA
*
255302 TAA TAA TAA TAAA TAG TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA
255324 AAAAGAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:255857 original size:30 final size:29
Alignment explanation
Indices: 255821--255900 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
255811 GAAAATGAAA
* *
255821 AAAAAATTCCTTTTTTAACCCCGAACTTTC
1 AAAAAATTCCATTTTTAACCCCGAA-GTTC
* *
255851 AAAAAATTACATTTTTACCCCCCGAAGTTC
1 AAAAAATTCCATTTTTA-ACCCCGAAGTTC
*
255881 CAAAAATTCCATTTTTAACC
1 AAAAAATTCCATTTTTAACC
255901 TTGAAACTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.05
30 33 0.79
31 7 0.17
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAAATTCCATTTTTAACCCCGAAGTTC
Found at i:256001 original size:30 final size:29
Alignment explanation
Indices: 255833--256105 Score: 164
Period size: 30 Copynumber: 9.3 Consensus size: 29
255823 AAAATTCCTT
*
255833 TTTTAACCCCGAACTTTCAAAAAATTA-CA
1 TTTT-ACCCCGAACTTTCCAAAAATTACCA
*
255862 TTTTTACCCCCCGAA-GTTCCAAAAATT-CCA
1 -TTTTA--CCCCGAACTTTCCAAAAATTACCA
**
255892 TTTTTAACCTTGAAAC-TTCCAAAAATTA-CA
1 -TTTT-ACCCCG-AACTTTCCAAAAATTACCA
*
255922 -TTTACTCCCCGAACTTTCC-AAAA-TCCCA
1 TTTTA--CCCCGAACTTTCCAAAAATTACCA
* *
255950 TTTTGACTCCG-ATTTTGCCAAAAATTACCA
1 TTTT-ACCCCGAACTTT-CCAAAAATTACCA
255980 TTTTACCCTCGAACTTTCC-AAAATT-CCA
1 TTTTACCC-CGAACTTTCCAAAAATTACCA
* *
256008 TTTTTTATCCC-AA-TTTCACCAAAATTACCA
1 --TTTTACCCCGAACTTTC-CAAAAATTACCA
*
256038 TTTTACCCCCAAACTTTCC-AAAATT-CCA
1 TTTTA-CCCCGAACTTTCCAAAAATTACCA
*
256066 TTTTTAACCCCG-ATTTTACCAAAAATTACCA
1 -TTTT-ACCCCGAACTTT-CCAAAAATTACCA
256097 TTTTACCCC
1 TTTTACCCC
256106 CGGACATCCA
Statistics
Matches: 196, Mismatches: 16, Indels: 63
0.71 0.06 0.23
Matches are distributed among these distances:
27 10 0.05
28 36 0.18
29 58 0.30
30 73 0.37
31 19 0.10
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTACCCCGAACTTTCCAAAAATTACCA
Found at i:256107 original size:30 final size:28
Alignment explanation
Indices: 255908--256107 Score: 128
Period size: 29 Copynumber: 6.9 Consensus size: 28
255898 ACCTTGAAAC
255908 TTCCAAAAATTA-CA-TTTACTCCCCGAACT
1 TTCC-AAAATTACCATTTTAC-CCCCG-ACT
* * *
255937 TTCCAAAA-TCCCATTTTGA-CTCCGATT
1 TTCCAAAATTACCATTTT-ACCCCCGACT
*
255964 TTGCCAAAAATTACCATTTTACCCTCGAACT
1 TT-CC-AAAATTACCATTTTACCCCCG-ACT
* *
255995 TTCCAAAATT-CCATTTTTTA-TCCC-AAT
1 TTCCAAAATTACCA--TTTTACCCCCGACT
*
256022 TTCACCAAAATTACCATTTTACCCCCAAACT
1 TT--CCAAAATTACCATTTTACCCCC-GACT
* *
256053 TTCCAAAATT-CCATTTTTAACCCCGATT
1 TTCCAAAATTACCA-TTTTACCCCCGACT
256081 TTACCAAAAATTACCATTTTACCCCCG
1 TT-CC-AAAATTACCATTTTACCCCCG
256108 GACATCCAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
27 9 0.07
28 27 0.20
29 50 0.37
30 38 0.28
31 11 0.08
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (28 bp):
TTCCAAAATTACCATTTTACCCCCGACT
Found at i:256120 original size:59 final size:59
Alignment explanation
Indices: 255822--256218 Score: 305
Period size: 58 Copynumber: 6.7 Consensus size: 59
255812 AAAATGAAAA
* * * *
255822 AAAAATTCCTTTTTTAACCCCGAACTTTCAAAAAATTA-CATTTTTACCCCCCGAA-GTTCC
1 AAAAATTCCATTTTTAACCCCG-ATTTTCCAAAAATTACCA-TTTTA-CCCCCGAACTTTCC
** **
255882 AAAAATTCCATTTTTAACCTTGAAACTTCCAAAAATTA-CA-TTTACTCCCCGAACTTTCC
1 AAAAATTCCATTTTTAACCCCG-ATTTTCCAAAAATTACCATTTTAC-CCCCGAACTTTCC
* * * *
255941 -AAAATCCCA-TTTTGACTCCGATTTTGCCAAAAATTACCATTTTACCCTCGAACTTTCC
1 AAAAATTCCATTTTTAACCCCGATTTT-CCAAAAATTACCATTTTACCCCCGAACTTTCC
* * * * *
255999 -AAAATTCCATTTTTTATCCC-AATTTCACCAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAAATTCCATTTTTAACCCCGATTTTC-CAAAAATTACCATTTTACCCCCGAACTTTCC
* *
256057 -AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGGAC-ATCC
1 AAAAATTCCATTTTTAACCCCGATTTT-CCAAAAATTACCATTTTACCCCCGAACTTTCC
* * * * * ** * *
256115 AAAAATTCTATTTTTGATCTCGATTTATTCTAAAAATTACCATAATA-CCCCGGA-TGTCC
1 AAAAATTCCATTTTTAACCCCGA-TT-TTCCAAAAATTACCATTTTACCCCCGAACTTTCC
* * ** * *
256174 AAAAAATCCTTTTTTAACCCTAAACTTTCCCAAAATTACCATTTT
1 AAAAATTCCATTTTTAACCC-CGATTTTCCAAAAATTACCATTTT
256219 TTGCCTCGAG
Statistics
Matches: 272, Mismatches: 51, Indels: 30
0.77 0.14 0.08
Matches are distributed among these distances:
56 3 0.01
57 19 0.07
58 109 0.40
59 86 0.32
60 53 0.19
61 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATTCCATTTTTAACCCCGATTTTCCAAAAATTACCATTTTACCCCCGAACTTTCC
Found at i:256122 original size:117 final size:115
Alignment explanation
Indices: 255823--256129 Score: 313
Period size: 117 Copynumber: 2.6 Consensus size: 115
255813 AAATGAAAAA
* * * *
255823 AAAATTCCTTTTTTAACCCCGAACTTTCAAAAAATTA-CATTTTTACCCCCCGA-AGTTCCAAAA
1 AAAATTCCATTTTTAACCCCG-ATTTTCCAAAAATTACCA-TTTTACCCCCGGACA--TCCAAAA
*
255886 ATTCCA-TTTTTAACCTTGAAACTTCCAAAAATTACATTTACTCCCCGAACTTTCC
62 ATTCCATTTTTTAACC-T-AAACTTCCAAAAATTACATTTACTCCCCAAACTTTCC
* * * * * *
255941 AAAATCCCA-TTTTGACTCCGATTTTGCCAAAAATTACCATTTTACCCTCGAACTTTCC-AAAAT
1 AAAATTCCATTTTTAACCCCGATTTT-CCAAAAATTACCATTTTACCCCCGGAC-ATCCAAAAAT
* * * *
256004 TCCATTTTTTATCC-CAATTTCACCAAAATTACCATTTTAC-CCCCAAACTTTCC
64 TCCATTTTTTAACCTAAACTTC-CAAAAATTA-CA-TTTACTCCCCAAACTTTCC
256057 AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGGACATCCAAAAATT
1 AAAATTCCATTTTTAACCCCGATTTT-CCAAAAATTACCATTTTACCCCCGGACATCCAAAAATT
*
256122 CTATTTTT
65 CCATTTTT
256130 GATCTCGATT
Statistics
Matches: 156, Mismatches: 23, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
114 5 0.03
115 8 0.05
116 38 0.24
117 96 0.62
118 9 0.06
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (115 bp):
AAAATTCCATTTTTAACCCCGATTTTCCAAAAATTACCATTTTACCCCCGGACATCCAAAAATTC
CATTTTTTAACCTAAACTTCCAAAAATTACATTTACTCCCCAAACTTTCC
Found at i:256177 original size:117 final size:117
Alignment explanation
Indices: 255823--256165 Score: 283
Period size: 117 Copynumber: 2.9 Consensus size: 117
255813 AAATGAAAAA
* * * *
255823 AAAATTCCTTTTTTAACCCCGAACTTT-CAAAAAATTA-CATTTTTACCCCCCGAAGT-TCCAAA
1 AAAATTCCATTTTTAACCCCG-ATTTTACCAAAAATTACCA-TTTTA-CCCCCGAACTATCC-AA
* * * * * *
255885 AATTCCATTTTT-AACCTTGAAACTTC-CAAAAATTA-CAT-TTACTCCCCGAACTTTCC
62 AATTCCATTTTTGATCC---CAATTTCACAAAAATTACCATAATAC-CCCCAAACTGTCC
* * * * * *
255941 AAAATCCCA-TTTTGACTCCGATTTTGCCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATT
1 AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAACTATCCAAAATT
* * ** *
256005 CCATTTTTTATCCCAATTTCACCAAAATTACCATTTTACCCCCAAACTTTCC
66 CCATTTTTGATCCCAATTTCACAAAAATTACCATAATACCCCCAAACTGTCC
*
256057 AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGGAC-ATCCAAAAAT
1 AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAACTATCC-AAAAT
* * *
256121 TCTATTTTTGATCTCGATTT-ATTCTAAAAATTACCATAATACCCC
65 TCCATTTTTGATCCCAATTTCA--C-AAAAATTACCATAATACCCC
256166 GGATGTCCAA
Statistics
Matches: 186, Mismatches: 27, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
114 5 0.03
115 8 0.04
116 53 0.28
117 93 0.50
118 10 0.05
119 17 0.09
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTACCCCCGAACTATCCAAAATT
CCATTTTTGATCCCAATTTCACAAAAATTACCATAATACCCCCAAACTGTCC
Found at i:256264 original size:27 final size:28
Alignment explanation
Indices: 256203--256264 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
256193 CTAAACTTTC
*
256203 CCAAAATTACCATTTTTTGCCTCGAGAGT
1 CCAAAATTACCA-TTTTTGCCCCGAGAGT
*
256232 CTAAAATTACCA-TTTTGCCCCGAGTA-T
1 CCAAAATTACCATTTTTGCCCCGAG-AGT
256259 CCAAAA
1 CCAAAA
256265 ATCACATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 17 0.59
28 1 0.03
29 11 0.38
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTTGCCCCGAGAGT
Found at i:268580 original size:201 final size:193
Alignment explanation
Indices: 268167--268611 Score: 545
Period size: 201 Copynumber: 2.3 Consensus size: 193
268157 AAAACTAATG
** * *
268167 AGGTACAGAGAAGCGGATTGAAACAAGTAAGGCGGTCATCTTCCTGATAAGATACAGAGAAGTAT
1 AGGTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATAAGATACAAAGAACTAT
* * *
268232 ACCAACTCAATACGAACAAATCTTTGAACCTTAGCTTCTTGATGAGATACTGAGAAGCAAGGGTG
66 ACCAACTCAATACGAACAAATCTTTGAACCTCAGCTTCCTGATGAGATACTGAGAAGC-ACGGTG
* * **
268297 AAGCAATAAAAGGTTAGCTTCATGATGAGACACTGAGAAATGGACCAAATTCATCTTCCTAATG
130 AAGCAATAAAAGGTTAACTTCATGATGAAACACTGAGAAATGGACCAAATTCATCTTCCTAACA
* * *
268361 AGGTACAGAGAAGCGGATTGAAACAAACGAGGCGGTTATCTTCCTGATGAGATACAAAGAACTAT
1 AGGTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATAAGATACAAAGAACTAT
* * *
268426 ACCAACTCAGGGCT-CGATGTGAGCAAATCTTTGAATCC-CATCTTCCTGATGATATACTGAGAA
66 ACCAACTCA---ATACGA----A-CAAATCTTTGAA-CCTCAGCTTCCTGATGAGATACTGAGAA
* * *
268489 GC-CGGTCGAAGCAATAAAATGGTTAACTTCCTGATGAAATACTGAGAAGTGGACCAAATTCATC
122 GCACGGT-GAAGCAATAAAA-GGTTAACTTCATGATGAAACACTGAGAAATGGACCAAATTCATC
268553 TTCCTAACA
185 TTCCTAACA
* * * *
268562 AGGTATAGGGAAGCGGATTGAAACAAGCGATGCGGTCATCTTCTTGATAA
1 AGGTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATAA
268612 TGTACTATGA
Statistics
Matches: 213, Mismatches: 27, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
194 67 0.31
196 3 0.01
197 1 0.00
199 3 0.01
200 13 0.06
201 124 0.58
202 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (193 bp):
AGGTACAGAGAAGCGGATTGAAACAAGCGAGGCGGTCATCTTCCTGATAAGATACAAAGAACTAT
ACCAACTCAATACGAACAAATCTTTGAACCTCAGCTTCCTGATGAGATACTGAGAAGCACGGTGA
AGCAATAAAAGGTTAACTTCATGATGAAACACTGAGAAATGGACCAAATTCATCTTCCTAACA
Found at i:269015 original size:11 final size:11
Alignment explanation
Indices: 268999--269024 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
268989 TTAAAGTTTA
268999 AATTTAAATTG
1 AATTTAAATTG
269010 AATTTAAATTG
1 AATTTAAATTG
269021 AATT
1 AATT
269025 AAAAAGTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:269765 original size:3 final size:3
Alignment explanation
Indices: 269757--269815 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
269747 ATAACTTATT
* *
269757 TAA TAA TAA TAA TAT TAA TAA TAT TCAA TAA TAA TTAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA
269803 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
269816 TAGTAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.86
4 5 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:270831 original size:30 final size:30
Alignment explanation
Indices: 270748--270922 Score: 114
Period size: 30 Copynumber: 5.9 Consensus size: 30
270738 CCTTAAATGT
* * * *
270748 CCCTAAACTATCCAAAAATTATA-TTTTGA
1 CCCTAAACTTTCTAAAAATTACATTTTTAA
* * *
270777 CCCCAAGCTTTCT-AAAATTCCATTTTTAA
1 CCCTAAACTTTCTAAAAATTACATTTTTAA
270806 CCCTAAACTTTCTAAAAATTACATTTTT-A
1 CCCTAAACTTTCTAAAAATTACATTTTTAA
* * *
270835 CCCTTCAAA-GTTCCAAAAATTCCATTTTTAA
1 CCC-T-AAACTTTCTAAAAATTACATTTTTAA
* *
270866 -TCTAGAAAC-TTCTAAAAATTACCA-TTTTAC
1 CCCT--AAACTTTCTAAAAATTA-CATTTTTAA
* * *
270896 CCCTGAACTTTC-CAAAATTCCATTTTT
1 CCCTAAACTTTCTAAAAATTACATTTTT
270923 GATCCCGAAT
Statistics
Matches: 113, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
28 9 0.08
29 43 0.38
30 53 0.47
31 8 0.07
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTTCTAAAAATTACATTTTTAA
Found at i:270879 original size:60 final size:59
Alignment explanation
Indices: 270790--271016 Score: 169
Period size: 59 Copynumber: 3.8 Consensus size: 59
270780 CAAGCTTTCT
*
270790 AAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTA-CATTTTTACCCTTCAAAGTTCC
1 AAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACCA-TTTTACCCCTCAAAGTTCC
* * **
270849 AAAAATTCCATTTTTAA-TCTAGAAAC-TTCTAAAAATTACCATTTTACCCCTGAACTTTCC
1 -AAAATTCCATTTTTAACCCT--AAACTTTCTAAAAATTACCATTTTACCCCTCAAAGTTCC
* * * * **
270909 AAAATTCCATTTTTGATCCC-GAA-TTCACCAAAAATTACCATTTTACCCC-CAAACATCC
1 AAAATTCCATTTTT-AACCCTAAACTT-TCTAAAAATTACCATTTTACCCCTCAAAGTTCC
*** * * * ** *
270967 AAAAATTATGTTTTTGATCCTGATTTTTCTAAAAATTAGCATTTTACCCC
1 -AAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACCATTTTACCCC
271017 GGATATCCAA
Statistics
Matches: 133, Mismatches: 24, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
58 10 0.08
59 70 0.53
60 46 0.35
61 7 0.05
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCTAAACTTTCTAAAAATTACCATTTTACCCCTCAAAGTTCC
Found at i:270968 original size:29 final size:29
Alignment explanation
Indices: 270879--270974 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
270869 AGAAACTTCT
** *
270879 AAAAATTACCATTTTACCCCTGAACTTTCC
1 AAAAATTACCATTTTACCCCCAAAC-ATCC
* * *
270909 -AAAATT-CCATTTTTGATCCCGAATTCA-CC
1 AAAAATTACCA-TTTT-ACCCCCAA-ACATCC
270938 AAAAATTACCATTTTACCCCCAAACATCC
1 AAAAATTACCATTTTACCCCCAAACATCC
270967 AAAAATTA
1 AAAAATTA
270975 TGTTTTTGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
28 5 0.10
29 28 0.54
30 15 0.29
31 4 0.08
ACGTcount: A:0.39, C:0.28, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCAAACATCC
Found at i:270972 original size:59 final size:57
Alignment explanation
Indices: 270815--271039 Score: 168
Period size: 59 Copynumber: 3.8 Consensus size: 57
270805 ACCCTAAACT
* ** * *
270815 TTCTAAAAATTA-CATTTTTACCCTTCAAAGTTCCAAAAATTCCATTTTTAATCTAGAAA
1 TTCTAAAAATTACCA-TTTTACCC-CCAAACATCCAAAAATTCCATTTTTGATCCAG-AA
** * *
270874 CTTCTAAAAATTACCATTTTACCCCTGAACTTTCC-AAAATTCCATTTTTGATCCCGAA
1 -TTCTAAAAATTACCATTTTACCCCCAAAC-ATCCAAAAATTCCATTTTTGATCCAGAA
* *** * *
270932 TTCACCAAAAATTACCATTTTACCCCCAAACATCCAAAAATTATGTTTTTGATCCTGATTT
1 TT--CTAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTGATCCAGA--A
* ** * *
270993 TTCTAAAAATTAGCATTTTA-CCCCGGATATCCAAAAATTTCATTTTT
1 TTCTAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTT
271040 AACCCCAAAA
Statistics
Matches: 134, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
57 2 0.01
58 26 0.19
59 78 0.58
60 24 0.18
61 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (57 bp):
TTCTAAAAATTACCATTTTACCCCCAAACATCCAAAAATTCCATTTTTGATCCAGAA
Found at i:272020 original size:20 final size:20
Alignment explanation
Indices: 271995--272035 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
271985 TTTTGTATAA
271995 TGTTCATAATATGATCCCAT
1 TGTTCATAATATGATCCCAT
* * *
272015 TGTTCATGATTTGATCTCAT
1 TGTTCATAATATGATCCCAT
272035 T
1 T
272036 ATTTTTAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (20 bp):
TGTTCATAATATGATCCCAT
Found at i:273311 original size:97 final size:96
Alignment explanation
Indices: 273131--273313 Score: 226
Period size: 97 Copynumber: 1.9 Consensus size: 96
273121 GCGAAAAAGA
* ** * *
273131 TATTTGATTATCTCGATTTGAAGAAAGGTTGCACTTAGTAAGTTAAGGCGCAATATTTCGGAATC
1 TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAATC
* * *
273196 GAAGATAAGGAAACATTGCCTCGATTAAGGG
66 GAAAAGAAAGAAACATTGCCTCGATTAAGGG
* *
273227 TATTCGATTATTTCGATTTGAAGAAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAA
1 TATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA
*
273291 CTCGAAAAGAAAG-AATATTGCCT
64 -TCGAAAAGAAAGAAACATTGCCT
273314 TGATATTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
96 22 0.30
97 42 0.58
98 9 0.12
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAATC
GAAAAGAAAGAAACATTGCCTCGATTAAGGG
Found at i:273656 original size:29 final size:29
Alignment explanation
Indices: 273618--274046 Score: 520
Period size: 30 Copynumber: 14.6 Consensus size: 29
273608 GAAAAATTTA
*
273618 GGGTCAAAAATGGGATTTTTAGAAGTTTGG
1 GGGT-AAAAATGGGATTTTTGGAAGTTTGG
* *
273648 GGGTAAAAAT-GGACCTTTTGAAAGTTTTGG
1 GGGTAAAAATGGGA-TTTTTGGAAG-TTTGG
* * *
273678 GGTTAAAAATGGGATTTTTGGTAGTTTCGA
1 GGGTAAAAATGGGATTTTTGGAAGTTT-GG
* *
273708 GGGTAAAAATGGGATTTTTGGTAGTTTAG
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
* * * * *
273737 GGTTAAAAGTGGGATTTTTAGAGGTTCGG
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
**
273766 GGGTAAAAATGTAATTTTTGGAAGTTTTGG
1 GGGTAAAAATGGGATTTTTGGAAG-TTTGG
*
273796 GGTTAAAAATGGGATTTTTGGAAGTTTGG
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
*
273825 GGGTAAAAATGGGATTTTTGGAAGTTTTAG
1 GGGTAAAAATGGGATTTTTGGAAG-TTTGG
* *
273855 GGTTAAAAATGGGATTTTTAGAAGTTTGG
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
* *
273884 GGGTAAAAATGGTATTTTTAGAAGTTTAGG
1 GGGTAAAAATGGGATTTTTGGAAGTTT-GG
273914 GGGTAAAAATGGGATTTTTGGAAGTTTGG
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
273943 GGGTAAAAATGGGATTTTTGGAAGTTTTGG
1 GGGTAAAAATGGGATTTTTGGAAG-TTTGG
* * * *
273973 GGTTAAAAATGGG-TTTTTAGAAGTTCGA
1 GGGTAAAAATGGGATTTTTGGAAGTTTGG
*
274001 GGGTAAAAATGAGATTTTTGGAAGTTTCGG
1 GGGTAAAAATGGGATTTTTGGAAGTTT-GG
*
274031 GGTTAAAAATGGGATT
1 GGGTAAAAATGGGATT
274047 GTTGAACAAT
Statistics
Matches: 341, Mismatches: 48, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
28 17 0.05
29 159 0.47
30 162 0.48
31 3 0.01
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGGGATTTTTGGAAGTTTGG
Found at i:273690 original size:59 final size:58
Alignment explanation
Indices: 273618--274046 Score: 583
Period size: 59 Copynumber: 7.3 Consensus size: 58
273608 GAAAAATTTA
* * *
273618 GGGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGACCTTTTGAAAGTTTTG
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGA-TTTTTGGAAGTTTTG
* * * * *
273677 GGGTTAAAAATGGGATTTTTGGTAGTTTCGAGGGTAAAAATGGGATTTTTGGTAG-TTTA
1 GGGTTAAAAATGGGATTTTTAGAAGTTT-GGGGGTAAAAAT-GGATTTTTGGAAGTTTTG
* * * *
273736 GGGTTAAAAGTGGGATTTTTAGAGGTTCGGGGGTAAAAATGTAATTTTTGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATG-GATTTTTGGAAGTTTTG
* *
273795 GGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAAT-GGATTTTTGGAAGTTTTG
* *
273854 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGTATTTTTAGAAGTTTAG
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGG-ATTTTTGGAAGTTTTG
* *
273913 GGGGTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATGGGATTTTTGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAAT-GGATTTTTGGAAGTTTTG
* * *
273972 GGGTTAAAAATGGG-TTTTTAGAAGTTCGAGGGTAAAAATGAGATTTTTGGAAGTTTCG
1 GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATG-GATTTTTGGAAGTTTTG
274030 GGGTTAAAAATGGGATT
1 GGGTTAAAAATGGGATT
274047 GTTGAACAAT
Statistics
Matches: 325, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.01
58 75 0.23
59 224 0.69
60 21 0.06
61 3 0.01
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (58 bp):
GGGTTAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGATTTTTGGAAGTTTTG
Found at i:275155 original size:19 final size:20
Alignment explanation
Indices: 275127--275165 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
275117 CAGTGTCACT
*
275127 ATTATTATTATT-AATATTA
1 ATTATGATTATTAAATATTA
275146 ATTATGATTATTAAATATTA
1 ATTATGATTATTAAATATTA
275166 TTAATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTATGATTATTAAATATTA
Found at i:275914 original size:6 final size:6
Alignment explanation
Indices: 275900--275958 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
275890 AATTTGATAA
* * * *
275900 TAAATT TAAACT TAAATT TAAATT TAAA-A TACATT TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
275946 TAAATT TAAATT T
1 TAAATT TAAATT T
275959 TTAAACAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 7 0.16
6 36 0.84
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:275937 original size:17 final size:17
Alignment explanation
Indices: 275900--275990 Score: 112
Period size: 17 Copynumber: 5.2 Consensus size: 17
275890 AATTTGATAA
*
275900 TAAATTTAAACTTAAATT
1 TAAATTTAAA-ATAAATT
*
275918 TAAATTTAAAATACATT
1 TAAATTTAAAATAAATT
275935 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
* *
275952 TAAATTTTTAAACAAATT
1 TAAA-TTTAAAATAAATT
275970 T-AATCTTAAAATAAATT
1 TAAAT-TTAAAATAAATT
275987 TAAA
1 TAAA
275991 GGGGAGCTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
16 1 0.02
17 38 0.60
18 24 0.38
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:275971 original size:35 final size:34
Alignment explanation
Indices: 275900--275990 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 34
275890 AATTTGATAA
* * *
275900 TAAATTTAAACTTAAATTTAAATTTAAAATACATT
1 TAAATTTAAA-ATAAATTTAAATTTAAAACAAATT
*
275935 TAAATTTAAAATAAATTTAAATTTTTAAACAAATT
1 TAAATTTAAAATAAATTTAAA-TTTAAAACAAATT
275970 T-AATCTTAAAATAAATTTAAA
1 TAAAT-TTAAAATAAATTTAAA
275991 GGGGAGCTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 13 0.26
35 37 0.74
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAAATTTAAAACAAATT
Found at i:277112 original size:217 final size:218
Alignment explanation
Indices: 276734--277498 Score: 1295
Period size: 217 Copynumber: 3.5 Consensus size: 218
276724 NNNNNNNNNN
* *
276734 ACGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGATCATGGGTTTG
1 ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
*
276799 GTTTGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTC
66 GTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTC
* * *
276864 TATATCTCATCAGGAAAACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCAGGAA
131 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
* *
276929 GCCAACCGTTTTATTAGTTCTGC
196 GCTAACCGTTTTATTACTTCTGC
* *
276952 AC-CTTCTCAGTATCTCATCAGGAAGTTATGGTTCGAAGATTTGCTCACATCGAGCATGGATTTG
1 ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
* * *
277016 GTTCGGTCTTCTTCTTAGTATCTCATCGGGAAGATGACTGCGTCGTTTATTTCAATTCACTTCTC
66 GTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTC
277081 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
131 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
*
277146 GCTAATCGTTTTATTACTTC-GAC
196 GCTAACCGTTTTATTACTTCTG-C
277169 ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
1 ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
* * * *
277234 GTTCGGTCTTCTTCTCAGTATCTCATCAGGAATATGACTGCGTCGTTTGTTTCAATTCACTTCTT
66 GTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTC
277299 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
131 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
*
277364 GCTAGCCGTTTT-TTACTT-TGGC
196 GCTAACCGTTTTATTACTTCT-GC
*
277386 ACGCTTCTCAGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
1 ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
*
277451 GCTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTT
66 GTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTT
277499 TGTGGATAAT
Statistics
Matches: 515, Mismatches: 28, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
216 1 0.00
217 316 0.61
218 198 0.38
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (218 bp):
ACGCTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAGATTTGCTCACATCGAGCATGGGTTTG
GTTCGGTCTTCTTCTCAGTATCTCATCGGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTC
TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCGTACCTCATCAGGAAGATGGTCCGGAA
GCTAACCGTTTTATTACTTCTGC
Found at i:277999 original size:27 final size:27
Alignment explanation
Indices: 277962--278019 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
277952 TCAAAAATTT
*
277962 AAAGGAGACAAAATTAAGAAA-AGGATC
1 AAAGGAAACAAAATTAA-AAAGAGGATC
* *
277989 AAAGGAAACAATATTAAAAAGAGGGTC
1 AAAGGAAACAAAATTAAAAAGAGGATC
278016 AAAG
1 AAAG
278020 AAAGCAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (27 bp):
AAAGGAAACAAAATTAAAAAGAGGATC
Found at i:278027 original size:27 final size:28
Alignment explanation
Indices: 277974--278033 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
277964 AGGAGACAAA
277974 ATTAAGAAAAGGATCAAAGGAAACAAT-
1 ATTAAGAAAAGGATCAAAGGAAACAATC
*
278001 ATTAA-AAAGAGGGTCAAA-GAAAGCAATC
1 ATTAAGAAA-AGGATCAAAGGAAA-CAATC
278029 ATTAA
1 ATTAA
278034 TTGAAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 17 0.59
28 5 0.17
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (28 bp):
ATTAAGAAAAGGATCAAAGGAAACAATC
Found at i:286849 original size:27 final size:27
Alignment explanation
Indices: 286812--286869 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
286802 TCAAAAATTT
*
286812 AAAGGAGACAAAATTAAGAAA-AGGATC
1 AAAGGAAACAAAATTAA-AAAGAGGATC
* *
286839 AAAGGAAACAATATTAAAAAGAGGGTC
1 AAAGGAAACAAAATTAAAAAGAGGATC
286866 AAAG
1 AAAG
286870 AAAGCAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (27 bp):
AAAGGAAACAAAATTAAAAAGAGGATC
Found at i:286877 original size:27 final size:28
Alignment explanation
Indices: 286824--286883 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
286814 AGGAGACAAA
286824 ATTAAGAAAAGGATCAAAGGAAACAAT-
1 ATTAAGAAAAGGATCAAAGGAAACAATC
*
286851 ATTAA-AAAGAGGGTCAAA-GAAAGCAATC
1 ATTAAGAAA-AGGATCAAAGGAAA-CAATC
286879 ATTAA
1 ATTAA
286884 TTGAAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.24
27 17 0.59
28 5 0.17
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.17
Consensus pattern (28 bp):
ATTAAGAAAAGGATCAAAGGAAACAATC
Done.