Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009912.1 Kokia drynarioides strain JFW-HI SEQ_124652, 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: 61257
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:26936 original size:59 final size:57
Alignment explanation
Indices: 26859--27240 Score: 410
Period size: 59 Copynumber: 6.5 Consensus size: 57
26849 GGACATTCGG
*
26859 GGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATAAGATTTTTAGGAGTTTGA
1 GGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTT-GGAGTTT-A
* * *
26919 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGG-TCAAAATGGGATTTTTGAAAGTTTA
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTG-GAGTTTA
* * * *
26976 GGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGTTAAAAATGATATTTTTAGAAGTTTA
1 -GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTT-GGAGTTTA
* * * *
27035 GGGGTAAAATGGTAATTTTTAGAAGTTTCT-GGGTAAAAAATGGGATTTTTGGAAGTTTGG
1 -GGGTAAAATGGTAATTTTTGGAAGTTT-TGGGGTTAAAAATGAGATTTTTGG-AGTTT-A
* * * * *
27095 GGGTAAAATGGTAATTTTT-GAGAGTTTCGGGCTTAAAAATGAGATTGTTAGAGGTTCGA
1 GGGTAAAATGGTAATTTTTGGA-AGTTTTGGGGTTAAAAATGAGATTTTTGGA-GTT-TA
* * *
27154 GGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTA
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTGG-AGTTTA
*
27212 GTGGTAAAATGGTAATTTTCGGACAGTTT
1 G-GGTAAAATGGTAATTTTTGGA-AGTTT
27241 AGGGACCTTC
Statistics
Matches: 275, Mismatches: 32, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 54 0.20
59 205 0.75
60 14 0.05
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGAGATTTTTGGAGTTTA
Found at i:27131 original size:118 final size:119
Alignment explanation
Indices: 26775--27230 Score: 551
Period size: 118 Copynumber: 3.9 Consensus size: 119
26765 TTCGGAGTTA
* * *
26775 AAAAATG-GAATTTTTAGAAGTTTA-AGGGTAAAATGGTAACTTTAAG-AGTTTCGAGGTAAAAA
1 AAAAATGAG-ATTTTTAGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGT-AAAA
* **
26837 AAT-GGAGTCTTTGGACA-TTCGGGGGTAAAAATGGTAATTTTTG-GAAGTTTTGGGGTT
64 AATGGGA-TTTTTGGA-AGTTTAGGGGT-AAAATGGTAATTTTTGAGAAGTTTT-GGGTT
* * * * *
26894 AAAAATAAGATTTTTAGGAGTTT-GAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGT-CAAAA
1 AAAAATGAGATTTTTAGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGTAAAAAA
*
26957 TGGGATTTTTGAAAGTTTAGGGGTAAAATGGTAATTTTT-AGAAGTTTTGAGGTT
66 TGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAGAAGTTTTG-GGTT
*
27011 AAAAATGATATTTTTAGAAGTTTAG-GGGTAAAATGGTAATTTTTAGAAGTTTCTG-GGTAAAAA
1 AAAAATGAGATTTTTAGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTTT-TGAGGTAAAAA
* *
27074 ATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTGAG-AGTTTCGGGCTT
65 ATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAGAAGTTTTGGG-TT
* * * * *
27129 AAAAATGAGATTGTTAG-AGGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAAA
1 AAAAATGAGATTTTTAGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGTAAAAAA
*
27193 TGGGATTTTTGGAAGTTTAGTGGTAAAATGGTAATTTT
66 TGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTT
27231 CGGACAGTTT
Statistics
Matches: 295, Mismatches: 28, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
116 1 0.00
117 86 0.29
118 155 0.53
119 43 0.15
120 10 0.03
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (119 bp):
AAAAATGAGATTTTTAGAAGTTTAGAGGGTAAAATGGTAATTTTTAGAAGTTTTGAGGTAAAAAA
TGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGAGAAGTTTTGGGTT
Found at i:27242 original size:30 final size:29
Alignment explanation
Indices: 26864--27242 Score: 237
Period size: 29 Copynumber: 12.9 Consensus size: 29
26854 TTCGGGGGTA
* *
26864 AAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGTAATTTTTGGAAGTTTAGAGG-T
*
26894 AAAAAT--AAGATTTTTAGG-AGTTT-GAGGGT
1 -AAAATGGTA-ATTTTT-GGAAGTTTAGA-GGT
* *
26923 AAAATGGTAATTTTTGGAAGTTTTGGGGT
1 AAAATGGTAATTTTTGGAAGTTTAGAGGT
* * *
26952 CAAAATGG-GATTTTTGAAAGTTTAGGGGT
1 -AAAATGGTAATTTTTGGAAGTTTAGAGGT
* *
26981 AAAATGGTAATTTTTAGAAGTTTTGAGGTT
1 AAAATGGTAATTTTTGGAAGTTTAGAGG-T
* * *
27011 AAAAATGAT-ATTTTTAGAAGTTTAGGGGT
1 -AAAATGGTAATTTTTGGAAGTTTAGAGGT
* *
27040 AAAATGGTAATTTTTAGAAGTTTCTG-GGT
1 AAAATGGTAATTTTTGGAAGTTT-AGAGGT
* * *
27069 AAAAAATGG-GATTTTTGGAAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTAGAGGT
*
27099 AAAATGGTAATTTTT-GAGAGTTTCG-GGCTT
1 AAAATGGTAATTTTTGGA-AGTTTAGAGG--T
* * * *
27129 AAAAAT-G-AGATTGTTAG-AGGTTCGAGGGT
1 -AAAATGGTA-ATTTTTGGAAGTTTAGA-GGT
*
27158 AAAATGGTAATTTTTGGAAGTTTTGAGGT
1 AAAATGGTAATTTTTGGAAGTTTAGAGGT
* *
27187 CAAAAATGG-GATTTTTGGAAGTTTAGTGGT
1 --AAAATGGTAATTTTTGGAAGTTTAGAGGT
*
27217 AAAATGGTAATTTTCGGACAGTTTAG
1 AAAATGGTAATTTTTGGA-AGTTTAG
27243 GGACCTTCGG
Statistics
Matches: 283, Mismatches: 33, Indels: 65
0.74 0.09 0.17
Matches are distributed among these distances:
28 44 0.16
29 107 0.38
30 96 0.34
31 36 0.13
ACGTcount: A:0.32, C:0.02, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTAGAGGT
Found at i:29005 original size:6 final size:6
Alignment explanation
Indices: 28996--29057 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
28986 AATTTTGAAG
*
28996 TTAAAT TTAAA- TTAAAT TTAAAT TCAAGA- TT-AAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT
*
29042 TTAAA- TCAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
29058 ATAAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 1 0.02
5 12 0.26
6 33 0.70
7 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:29012 original size:11 final size:11
Alignment explanation
Indices: 28996--29047 Score: 61
Period size: 11 Copynumber: 4.5 Consensus size: 11
28986 AATTTTGAAG
28996 TTAAATTTAAA
1 TTAAATTTAAA
29007 TTAAATTTAAA
1 TTAAATTTAAA
*
29018 TTCAAGA-TTAAT
1 TT-AA-ATTTAAA
29030 TTAAATTTAAA
1 TTAAATTTAAA
29041 TTTAAAT
1 -TTAAAT
29048 CAAATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
10 1 0.03
11 19 0.54
12 14 0.40
13 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:29018 original size:17 final size:17
Alignment explanation
Indices: 28996--29064 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
28986 AATTTTGAAG
28996 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
*
29013 TTAAATTCAAGATT-AAT
1 TTAAATTTAA-ATTAAAT
29030 TTAAATTTAAATTTAAA-
1 TTAAATTTAAA-TTAAAT
* *
29047 TCAAATTTAAAATAAAT
1 TTAAATTTAAATTAAAT
29064 T
1 T
29065 AAAAAGGGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 5 0.11
17 34 0.77
18 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:29053 original size:23 final size:23
Alignment explanation
Indices: 29003--29057 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28993 AAGTTAAATT
29003 TAAA-TTAAATTTAAATTCAAGA
1 TAAATTTAAATTTAAATTCAAGA
* *
29025 TTAATTTAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAATTCAAGA
29047 TCAAATTTAAA
1 T-AAATTTAAA
29058 ATAAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTCAAGA
Found at i:29288 original size:30 final size:28
Alignment explanation
Indices: 29254--29345 Score: 73
Period size: 30 Copynumber: 3.2 Consensus size: 28
29244 AAATAGTGTT
29254 AAAATCAAAATTTTGAAAAGTTTAGGGGTC
1 AAAATC-AAATTTT-AAAAGTTTAGGGGTC
** *
29284 AAAATGCATTTTTTAAAAAGTTT-GGGGTT
1 AAAAT-CAAATTTT-AAAAGTTTAGGGGTC
*
29313 AAAATTC-AATTTTAGAAAGTTTA-TGGTC
1 AAAA-TCAAATTTTA-AAAGTTTAGGGGTC
29341 AAAAT
1 AAAAT
29346 TTAATTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
27 2 0.04
28 18 0.36
29 10 0.20
30 19 0.38
31 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (28 bp):
AAAATCAAATTTTAAAAGTTTAGGGGTC
Found at i:29346 original size:28 final size:28
Alignment explanation
Indices: 29262--29358 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
29252 TTAAAATCAA
*
29262 AATTTT-GAAAAGTTTAGGGGTCAAAATGC
1 AATTTTAG-AAAGTTTA-GGGTCAAAATTC
* * * *
29291 ATTTTTTAAAAAGTTTGGGGTTAAAATTC
1 A-ATTTTAGAAAGTTTAGGGTCAAAATTC
* *
29320 AATTTTAGAAAGTTTATGGTCAAAATTT
1 AATTTTAGAAAGTTTAGGGTCAAAATTC
29348 AATTTTTAGAA
1 AA-TTTTAGAA
29359 TGGTCAAAGG
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
28 23 0.43
29 20 0.37
30 11 0.20
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (28 bp):
AATTTTAGAAAGTTTAGGGTCAAAATTC
Found at i:31300 original size:91 final size:91
Alignment explanation
Indices: 31145--31323 Score: 349
Period size: 91 Copynumber: 2.0 Consensus size: 91
31135 ATCAATATCG
31145 AGTCTAGTGGTATTAAGGTGTCTCGTGGGGCCCTAGTTTTGTTAAAATGTAAAAGGATCGATAGT
1 AGTCTAGTGGTATTAAGGTGTCTCGTGGGGCCCTAGTTTTGTTAAAATGTAAAAGGATCGATAGT
31210 CTTTATATTCTGGAAGGTTCTACTAA
66 CTTTATATTCTGGAAGGTTCTACTAA
31236 AGTCTAGTGGTATTAAGGTGTCTCGTGGGGCCCTAGTTTTGTTAAAATGTAAAAGGATCGATAGT
1 AGTCTAGTGGTATTAAGGTGTCTCGTGGGGCCCTAGTTTTGTTAAAATGTAAAAGGATCGATAGT
*
31301 CTTTATATTTTGGAAGGTTCTAC
66 CTTTATATTCTGGAAGGTTCTAC
31324 AATGACCGGT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (91 bp):
AGTCTAGTGGTATTAAGGTGTCTCGTGGGGCCCTAGTTTTGTTAAAATGTAAAAGGATCGATAGT
CTTTATATTCTGGAAGGTTCTACTAA
Found at i:46290 original size:17 final size:17
Alignment explanation
Indices: 46242--46290 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
46232 GTTTGGCCCA
*
46242 ATAAACTTAAGTTTATT
1 ATAAAATTAAGTTTATT
* *
46259 TTAAAATTGAGTTTATT
1 ATAAAATTAAGTTTATT
* *
46276 ATAAATTTAATTTTA
1 ATAAAATTAAGTTTA
46291 AAATTTATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (17 bp):
ATAAAATTAAGTTTATT
Found at i:46935 original size:3 final size:3
Alignment explanation
Indices: 46929--46957 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46919 AATAGCTGTT
46929 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
46958 GCATTAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48153 original size:59 final size:59
Alignment explanation
Indices: 48052--48431 Score: 453
Period size: 59 Copynumber: 6.4 Consensus size: 59
48042 GTAGGTCCCT
* * ** * * *
48052 AAACTGTCCGAAAATTACCATTTTATCCCCGAACTTCAAAAAATCCCAATTTTCACCCCG
1 AAACT-TCCAAAAATTACCATTTTAACCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
48112 AAACTTCCAAAAATTACCATTTTAACCATAAACTTCCAAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATTACCATTTTAACCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
48171 AAACTTCCAAAAATTACCATTTT-ACCCTCAAACTTCTAAAAATCCCATTTTTTAACCCCA
1 AAACTTCCAAAAATTACCATTTTAACCCT-AAACTTCCAAAAATCCCA-TTTTTGACCCCG
* * *
48231 AAACTTCAAAAAATTACCATTTT-ACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTAACCC-TAAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
48290 AAACTTCTAAAAAATGCCATTTTACCCCTAAAC-TCCTAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTAACCCTAAACTTCC-AAAAATCCCATTTTTGACCCCG
* * * * *
48349 ATACTTCCAAAAATTACCATTTTATA-CCTGAACTTCTAAAAATCTCATTTTTGACCCTG
1 AAACTTCCAAAAATTACCATTTTA-ACCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
48408 AAACTTCCAAAAATTACCATTTTA
1 AAACTTCCAAAAATTACCATTTTA
48432 CTCCCGGATG
Statistics
Matches: 279, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
58 7 0.03
59 210 0.75
60 61 0.22
61 1 0.00
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTAACCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:48361 original size:178 final size:176
Alignment explanation
Indices: 48062--48437 Score: 504
Period size: 178 Copynumber: 2.1 Consensus size: 176
48052 AAACTGTCCG
* *
48062 AAAATTACCATTTTATCCCCGAACTTCAAAAAATCCCAATTTTCACCCCGAAACTTCCAAAAATT
1 AAAATTACCATTTTA-CCCCGAACTTCAAAAAATCCCAATTTTCACCCCAAAACTTCCAAAAAAT
* *
48127 ACCATTTTAACCATAAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTACCATT
65 ACCATTTTAACCATAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTACCATT
*
48192 TTA-CCCTCAAACTTCTAAAAATCCCATTTTTTAACCCCAAAACTTCAA
130 TTATACCT-AAACTTCTAAAAATCCCA-TTTTTAACCCCAAAACTTCAA
* * * * *
48240 AAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCTAAAAAAT
1 AAAATTACCATTTTACCC-CGAACTTCAAAAAATCCCAATTTTCACCCCAAAACTTCCAAAAAAT
* * * *
48305 GCCATTTTACCCCTAAAC-TCCTAAAAATCCCATTTTTGACCCCGATACTTCCAAAAATTACCAT
65 ACCATTTTAACCATAAACTTCC-AAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTACCAT
* * * ** *
48369 TTTATACCTGAACTTCTAAAAATCTCATTTTTGACCCTGAAACTTCCA
129 TTTATACCTAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCAA
48417 AAAATTACCATTTTACTCCCG
1 AAAATTACCATTTTAC-CCCG
48438 GATGTTCGAA
Statistics
Matches: 173, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
177 40 0.23
178 130 0.75
179 3 0.02
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (176 bp):
AAAATTACCATTTTACCCCGAACTTCAAAAAATCCCAATTTTCACCCCAAAACTTCCAAAAAATA
CCATTTTAACCATAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTT
TATACCTAAACTTCTAAAAATCCCATTTTTAACCCCAAAACTTCAA
Found at i:59892 original size:191 final size:191
Alignment explanation
Indices: 59597--59948 Score: 623
Period size: 191 Copynumber: 1.8 Consensus size: 191
59587 CACGCTTGAT
*
59597 ACGAACAAATCCTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGGTCAAAGCCATAAAAG
1 ACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTAAGAAGCAGGTCAAAGCCATAAAAG
*
59662 GTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
66 GTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
*
59727 CGAATTGAAACAAATGACGCGGTCATCTTCCTGATACTGAGAAGAAGACCAGATCAAACTC
131 CGAATTGAAACAAATGACGCAGTCATCTTCCTGATACTGAGAAGAAGACCAGATCAAACTC
* **
59788 ACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTGAGAAGCAGGTTGAAGCCATAAAAG
1 ACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTAAGAAGCAGGTCAAAGCCATAAAAG
* * *
59853 GTTAGCTTCCTGATAAGATATGGAGAAGTGGACCAAATTCGTTTTCCTGATGAGATACAGAGAAA
66 GTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
59918 CGAATTGAAACAAATGACGCAGTCATCTTCC
131 CGAATTGAAACAAATGACGCAGTCATCTTCC
59949 CGATGAGATA
Statistics
Matches: 152, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
191 152 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (191 bp):
ACGAACAAATCCTCGAACCCCAACTTCCTGATGAGACACTAAGAAGCAGGTCAAAGCCATAAAAG
GTTAGCTTCCTGATAAGATACGAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAA
CGAATTGAAACAAATGACGCAGTCATCTTCCTGATACTGAGAAGAAGACCAGATCAAACTC
Found at i:60533 original size:13 final size:12
Alignment explanation
Indices: 60495--60540 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
60485 TAAACTTAAG
60495 TTTATTTTAAAA
1 TTTATTTTAAAA
* *
60507 TTGAGTTTATAAA
1 TTTATTTTA-AAA
60520 TTTAATTTTAAAA
1 TTT-ATTTTAAAA
60533 TTTATTTT
1 TTTATTTT
60541 GAATGTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 12 0.43
13 11 0.39
14 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (12 bp):
TTTATTTTAAAA
Found at i:61174 original size:3 final size:3
Alignment explanation
Indices: 61168--61214 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
61158 AATAGCTGTT
61168 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
61215 GCAATAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.