Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014730.1 Kokia drynarioides strain JFW-HI SEQ_129769, 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: 13517
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Found at i:8665 original size:201 final size:201
Alignment explanation
Indices: 8267--9437 Score: 1988
Period size: 201 Copynumber: 5.8 Consensus size: 201
8257 TTATCCACCA
* * * *
8267 AAACGACGCGGTCCTCTTCCTGATGAGG-TACTGAGAAGAAGACCAAACCAAACCGAGGCTCAAA
1 AAACGACGCGGTCATCTTCTTGATG-GGACACCGAGAAGAAGA-C---CCAAA-CGAGGCTCAAA
*
8331 GTGAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
60 GTGAGCAGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
8396 GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATTAGATAAAGAGAA
125 GGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAA
*
8461 GCGAGTTGAAAC
190 GCGAGTTGAAAT
*
8473 AAACGATGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
8538 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
*
8603 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCTTCTTCCTGATGAGATACAGAGAAGCGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
*
8668 TGAAAC
196 TGAAAT
*
8674 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAAAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
*
8739 AGAGTCTTTGAACCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* *
8804 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTTTTCCTAATGAGATACAGAGAAGCGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
8869 TGAAAT
196 TGAAAT
8875 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
* *
8940 AGAGTCTTTGAA--CTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
9003 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
9068 TGAAAT
196 TGAAAT
9074 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
9139 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * *
9204 CTTCTTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCTTGATGAGATACAGAGAAGAGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
9269 TGAAAT
196 TGAAAT
* *
9275 AAACGACGCGATCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTAAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
* * *
9340 AAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAAGGTTA
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAAAGGTTA
* * * *
9405 GCTTCCTGACGAGTTACTAAGAAGTGAACCAAA
130 GCTTCCTGATGAGATACTGAGAAGTAAACCAAA
9438 TCCTGATGAA
Statistics
Matches: 923, Mismatches: 38, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
199 194 0.21
201 650 0.70
202 42 0.05
205 3 0.00
206 34 0.04
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (201 bp):
AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
TGAAAT
Found at i:9143 original size:400 final size:401
Alignment explanation
Indices: 8267--9437 Score: 1977
Period size: 400 Copynumber: 2.9 Consensus size: 401
8257 TTATCCACCA
* * * *
8267 AAACGACGCGGTCCTCTTCCTGATGAGG-TACTGAGAAGAAGACCAAACCAAACCGAGGCTCAAA
1 AAACGACGCGGTCATCTTCTTGATG-GGACACCGAGAAGAAGA-C---CCAAA-CGAGGCTCAAA
*
8331 GTGAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
60 GTGAGCAGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
8396 GGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATTAGATAAAGAGAA
125 GGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAA
* *
8461 GCGAGTTGAAACAAACGATGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGG
190 GCGAGTTGAAATAAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGG
8526 CTCAAAGTGAGCAGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
255 CTCAAAGTGAGCAGAGTCTTTGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
*
8591 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCTTCTTCCTGATGAGATAC
319 ATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATAC
8656 AGAGAAGCGAGTTGAAAC
384 AGAGAAGCGAGTTGAAAC
*
8674 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAAAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
*
8739 AGAGTCTTTGAACCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* *
8804 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTTTTCCTAATGAGATACAGAGAAGCGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
8869 TGAAATAAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAA
196 TGAAATAAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAA
* *
8934 GTGAGCAGAGTCTTTGAA-CTAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAAG
261 GTGAGCAGAGTCTTTGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAG
8998 GTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAG
326 GTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAG
*
9063 CGAGTTGAAAT
391 CGAGTTGAAAC
9074 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
1 AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
9139 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
66 AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * *
9204 CTTCTTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCTTGATGAGATACAGAGAAGAGAGT
131 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
*
9269 TGAAATAAACGACGCGATCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAA
196 TGAAATAAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAA
* * * *
9334 GTAAGCAAAGTCTTTGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAA
261 GTGAGCAGAGTCTTTGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT-AAA
* * * *
9399 AGGTTAGCTTCCTGACGAGTTACTAAGAAGTGAACCAAA
324 AGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
9438 TCCTGATGAA
Statistics
Matches: 724, Mismatches: 36, Indels: 12
0.94 0.05 0.02
Matches are distributed among these distances:
400 386 0.53
402 258 0.36
403 43 0.06
406 3 0.00
407 34 0.05
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (401 bp):
AAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGC
AGAGTCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAGCGAGT
TGAAATAAACGACGCGGTCATCTTCTTGATGGGACACCGAGAAGAAGACCCAAACGAGGCTCAAA
GTGAGCAGAGTCTTTGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAG
GTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTCTTCCTGATGAGATACAGAGAAG
CGAGTTGAAAC
Found at i:9905 original size:11 final size:11
Alignment explanation
Indices: 9891--9946 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
9881 TTGTTTAAAA
9891 TTTAAATTTAT
1 TTTAAATTTAT
*
9902 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
9914 TTTAAATTAAG
1 TTTAAATTTAT
*
9925 TTTAAAATTAT
1 TTTAAATTTAT
9936 TTTCAAATTTA
1 TTT-AAATTTA
9947 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:9923 original size:5 final size:6
Alignment explanation
Indices: 9857--9955 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
9847 CTATACTCCC
* * * *
9857 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA
* * *
9902 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT TTTCAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTT-AAA
9950 TTTAAA
1 TTTAAA
9956 ATAAATAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
4 3 0.04
5 15 0.21
6 39 0.56
7 13 0.19
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:9923 original size:17 final size:17
Alignment explanation
Indices: 9857--9953 Score: 113
Period size: 17 Copynumber: 5.6 Consensus size: 17
9847 CTATACTCCC
9857 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
9874 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
9891 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
** *
9908 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
9925 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
9943 TTTAAAATTTA
1 TTT-AAATTTA
9954 AAATAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 53 0.83
18 5 0.08
19 6 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9961 original size:18 final size:18
Alignment explanation
Indices: 9888--9961 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 18
9878 AATTTGTTTA
**
9888 AAATTT-AAATTTATTTT
1 AAATTTAAAATTTAAATT
9905 AAATTT-AAATTTAAATT
1 AAATTTAAAATTTAAATT
* **
9922 AAGTTTAAAA-TTATTTT
1 AAATTTAAAATTTAAATT
*
9939 CAAATTTAAAATTTAAAAT
1 -AAATTTAAAATTTAAATT
9958 AAAT
1 AAAT
9962 AAAACTCAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
17 25 0.56
18 16 0.36
19 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
AAATTTAAAATTTAAATT
Found at i:10670 original size:9 final size:9
Alignment explanation
Indices: 10658--10739 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
10648 CAATAACAGC
10658 AATAATATT
1 AATAATATT
*
10667 AATAATAAT
1 AATAATATT
10676 AATAAATATTACT
1 AAT-AATA-T--T
*
10689 AATAACATT
1 AATAATATT
*
10698 AGTAATATT
1 AATAATATT
* * *
10707 AATGACAGT
1 AATAATATT
10716 AATAATAATT
1 AATAAT-ATT
*
10726 ATTAATATT
1 AATAATATT
10735 AATAA
1 AATAA
10740 ATGCTATTAA
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
9 35 0.65
10 11 0.20
11 1 0.02
12 3 0.06
13 4 0.07
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (9 bp):
AATAATATT
Found at i:10693 original size:40 final size:43
Alignment explanation
Indices: 10649--10729 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 43
10639 TTATAATAAC
10649 AATAACAGCAATAATATTAAT-A-A-TAATAATAAATATTACT
1 AATAACAGCAATAATATTAATGACAGTAATAATAAATATTACT
** * *
10689 AATAACATTAGTAATATTAATGACAGTAATAATAATTATTA
1 AATAACAGCAATAATATTAATGACAGTAATAATAAATATTA
10730 ATATTAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 18 0.53
41 1 0.03
42 1 0.03
43 14 0.41
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (43 bp):
AATAACAGCAATAATATTAATGACAGTAATAATAAATATTACT
Found at i:11806 original size:30 final size:29
Alignment explanation
Indices: 11772--12180 Score: 305
Period size: 30 Copynumber: 13.9 Consensus size: 29
11762 TATACCCCCG
11772 AACTTCCAAAAATCCCATTTTCGACCCCAA
1 AACTTCCAAAAATCCCATTTT-GACCCCAA
* *
11802 AACTTCCAAAAATTCCAATTTT-ACCCCCA
1 AACTTCCAAAAA-TCCCATTTTGACCCCAA
*
11831 AACTTCCAAAAATCCCATTTTCGACCCTAA
1 AACTTCCAAAAATCCCATTTT-GACCCCAA
* * *
11861 AACTTCCAAAAATTCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTGACCCCAA
* *
11890 AACTTTCAAAAATCTCATTTTCGACCCCAA
1 AACTTCCAAAAATCCCATTTT-GACCCCAA
** *
11920 AACTTCCAAAAATTACATTTTTACCCTC-A
1 AACTTCCAAAAATCCCATTTTGACCC-CAA
* * *
11949 AACTTCCAAAAGTCCCATTTTTTACCCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCCAA
*
11979 AACTTCCAAAAATTACCATTTT-ACACCC-A
1 AACTTCCAAAAA-TCCCATTTTGAC-CCCAA
* **
12008 AACTTCCCAAAATCCCATTTTTGACCCTGA
1 AACTTCCAAAAATCCCA-TTTTGACCCCAA
*
12038 AACTTCCAAAAATAACCA-TTT-ACCCTC-A
1 AACTTCCAAAAAT-CCCATTTTGACCC-CAA
* * * * *
12066 AATTTCCAAAAGTCCTATTTTTAACCCTAA
1 AACTTCCAAAAATCCCA-TTTTGACCCCAA
* * * * *
12096 AACTTCTAAAAATTCCATTTTTAGCCTC-G
1 AACTTCCAAAAATCCCATTTTGA-CCCCAA
* * * *
12125 AACTTCCCAAAATTCCATTTTTGACTCCGA
1 AACTTCCAAAAATCCCA-TTTTGACCCCAA
* *
12155 AACTTCCTAAAATTACCATTTT-ACCC
1 AACTTCC-AAAAATCCCATTTTGACCC
12181 TCGGATGTCC
Statistics
Matches: 304, Mismatches: 53, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 28 0.09
29 112 0.37
30 140 0.46
31 22 0.07
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTGACCCCAA
Found at i:11839 original size:59 final size:58
Alignment explanation
Indices: 11741--12180 Score: 486
Period size: 59 Copynumber: 7.4 Consensus size: 58
11731 GGAGGTCCCT
* * * *
11741 AAACTGTCCAAACATTTCATTTATACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACT-TCCAAAAATTCCATTT-TACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* *
11801 AAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCTA
1 AAACTTCCAAAAATTCC-ATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
11860 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCTCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * *
11919 AAACTTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAGTCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * **
11978 AAACTTCCAAAAATTACCATTTTACACCCAAACTTCCCAAAATCCCATTTTTGACCCTG
1 AAACTTCCAAAAATT-CCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * * * *
12037 AAACTTCCAAAAATAACCA-TTTACCCTCAAATTTCCAAAAGTCCTATTTTTAACCCTA
1 AAACTTCCAAAAAT-TCCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * * * * *
12095 AAACTTCTAAAAATTCCATTTTTAGCCTCGAACTTCCCAAAATTCCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
*
12154 AAACTTCCTAAAATTACCATTTTACCC
1 AAACTTCCAAAAATT-CCATTTTACCC
12181 TCGGATGTCC
Statistics
Matches: 326, Mismatches: 47, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
57 3 0.01
58 45 0.14
59 264 0.81
60 14 0.04
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:11945 original size:118 final size:118
Alignment explanation
Indices: 11737--12208 Score: 544
Period size: 118 Copynumber: 4.0 Consensus size: 118
11727 CCCCGGAGGT
* * * *
11737 CCCT-AAACTGTCCAAACATTTCATTTATACCCCCGAACTTCCAAAAATCCCATTTTCGACCCCA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCCA
* * **
11801 AAACTTCCAAAAATT-CCAATTTTACCCCCAAACTTCCAAAAATCCCATTTTCGA
65 AAACTTCCAAAAATTACC-ATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTAA
* *
11855 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTTCAAAAATCTCATTTTCGACCCCAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCCAA
*
11920 AACTTCCAAAAATTA-CATTTTTACCCTCAAACTTCCAAAAGTCCCATTTTTTA
66 AACTTCCAAAAATTACCA-TTTTACCCTCAAACTTCCAAAAGTCCCATTTTTAA
** * * * **
11973 CCCCGAAACTTCCAAAAATTACCA-TTTTACACCCAAACTTCCCAAAATCCCATTTTTGACCCTG
1 CCCTAAAACTTCCAAAAATT-CCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCCA
* * *
12037 AAACTTCCAAAAATAACCA-TTTACCCTCAAATTTCCAAAAGTCCTATTTTTAA
65 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTAA
* * * * * * * * *
12090 CCCTAAAACTTCTAAAAATTCCATTTTTAGCCTCGAACTTCCCAAAATTCCATTTTTGACTCCGA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCCAA
* **
12155 AACTTCCTAAAATTACCATTTTACCCTCGGA-TGTCCAAAAAGT-CCATTTTTAA
66 AACTTCCAAAAATTACCATTTTACCCTCAAACT-TCC-AAAAGTCCCATTTTTAA
12208 C
1 C
12209 ACCGAATTTT
Statistics
Matches: 307, Mismatches: 38, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
116 3 0.01
117 100 0.33
118 188 0.61
119 16 0.05
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (118 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTCGACCCCAA
AACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAGTCCCATTTTTAA
Found at i:12145 original size:29 final size:29
Alignment explanation
Indices: 11737--12206 Score: 372
Period size: 29 Copynumber: 16.0 Consensus size: 29
11727 CCCCGGAGGT
* * *
11737 CCCT-AAACTGTCCAAACATTTCATTTATA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
* * * *
11766 CCCCCGAACTTCCAAAAATCCCATTTTCGA
1 CCCTCAAACTTCCAAAAATTCCATTTT-TA
*
11796 CCC-CAAAACTTCCAAAAATTCCAATTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * *
11825 CCCCCAAACTTCCAAAAATCCCATTTTCGA
1 CCCTCAAACTTCCAAAAATTCCATTTT-TA
*
11855 CCCTAAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * *
11884 CCCCCAAACTTTCAAAAA-TCTCATTTTCGA
1 CCCTCAAACTTCCAAAAATTC-CATTTT-TA
*
11914 CCC-CAAAACTTCCAAAAATTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* *
11943 CCCTCAAACTTCCAAAAGTCCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTCCA-TTTTTA
11973 CCC-CGAAACTTCCAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATT-CCATTTTTA
* *
12002 CACC-CAAACTTCCCAAAATCCCATTTTTGA
1 C-CCTCAAACTTCCAAAAATTCCATTTTT-A
* *
12032 CCCTGAAACTTCCAAAAATAACCA--TTTA
1 CCCTCAAACTTCCAAAAAT-TCCATTTTTA
* *
12060 CCCTCAAATTTCC-AAAAGTCCTATTTTTAA
1 CCCTCAAACTTCCAAAAATTCC-ATTTTT-A
* *
12090 CCCTAAAACTTCTAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * *
12119 GCCTCGAACTTCCCAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
* *
12149 CTCC-GAAACTTCCTAAAATTACCA-TTTTA
1 C-CCTCAAACTTCCAAAAATT-CCATTTTTA
** *
12178 CCCTCGGA-TGTCCAAAAAGTCCATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTA
12207 ACACCGAATT
Statistics
Matches: 355, Mismatches: 57, Indels: 58
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.01
27 5 0.01
28 23 0.06
29 155 0.44
30 151 0.43
31 19 0.05
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:12254 original size:29 final size:30
Alignment explanation
Indices: 12220--12279 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
12210 CCGAATTTTC
*
12220 CCAAAATTATC-GTTTTGCCCCCCGAGAAT
1 CCAAAATTATCAGTTTTGCCCCCCAAGAAT
* *
12249 CCAAAATTATCATTTTTGTCCCCCAAGAAT
1 CCAAAATTATCAGTTTTGCCCCCCAAGAAT
12279 C
1 C
12280 TGAAAAGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (30 bp):
CCAAAATTATCAGTTTTGCCCCCCAAGAAT
Found at i:12293 original size:31 final size:30
Alignment explanation
Indices: 12232--12295 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
12222 AAAATTATCG
* *
12232 TTTTGCCCCCCGAGAATCCAAAATTATCAT
1 TTTTGCCCCCCAAGAATCCAAAAGTATCAT
* * *
12262 TTTTGTCCCCCAAGAATCTGAAAAGTCTCAT
1 TTTTGCCCCCCAAGAATC-CAAAAGTATCAT
12293 TTT
1 TTT
12296 GAACTCTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (30 bp):
TTTTGCCCCCCAAGAATCCAAAAGTATCAT
Done.