Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009467.1 Kokia drynarioides strain JFW-HI SEQ_124174, 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: 24968
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 95 characters in sequence are not A, C, G, or T
Found at i:729 original size:14 final size:14
Alignment explanation
Indices: 706--739 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
696 AATTTACATC
*
706 ATTTTATTATTATT
1 ATTTTGTTATTATT
720 ATTTTGTTATTATT
1 ATTTTGTTATTATT
734 ATTTTG
1 ATTTTG
740 GTTTTGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
ATTTTGTTATTATT
Found at i:833 original size:13 final size:14
Alignment explanation
Indices: 811--843 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
801 ATTTTACATC
*
811 ATTTTATTATTATT
1 ATTTTGTTATTATT
825 -TTTTGTTATTATT
1 ATTTTGTTATTATT
838 ATTTTG
1 ATTTTG
844 GTTTTGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
ATTTTGTTATTATT
Found at i:15210 original size:15 final size:16
Alignment explanation
Indices: 15186--15234 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 16
15176 TTTCACCAAA
15186 AAAAAGAGAAGAAAA-G
1 AAAAA-AGAAGAAAAGG
15202 AAAAAAGAA-AAAAGG
1 AAAAAAGAAGAAAAGG
15217 AAAAAAGAAGAAAGAGG
1 AAAAAAGAAGAAA-AGG
15234 A
1 A
15235 GGTCGAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.13
15 14 0.47
16 8 0.27
17 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAAAGG
Found at i:15212 original size:6 final size:7
Alignment explanation
Indices: 15186--15231 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
15176 TTTCACCAAA
15186 AAAAAGAG
1 AAAAA-AG
15194 AAGAAAAG
1 AA-AAAAG
15202 AAAAAAG
1 AAAAAAG
15209 AAAAAAGG
1 AAAAAA-G
15217 AAAAAAG
1 AAAAAAG
*
15224 AAGAAAG
1 AAAAAAG
15231 A
1 A
15232 GGAGGTCGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
7 19 0.54
8 13 0.37
9 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:15540 original size:20 final size:20
Alignment explanation
Indices: 15512--15549 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15502 TTGATTAATG
*
15512 TTTGTTATTTTATACCAACA
1 TTTGCTATTTTATACCAACA
*
15532 TTTGCTATTTTTTACCAA
1 TTTGCTATTTTATACCAA
15550 TTTTTACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTGCTATTTTATACCAACA
Found at i:16645 original size:42 final size:41
Alignment explanation
Indices: 16415--17086 Score: 519
Period size: 42 Copynumber: 16.7 Consensus size: 41
16405 AGTAAAGCAA
** * * *
16415 ATTGAAGACACA-CTGATCTCTTACCCAGATCATAGGGCAA
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
* ** * *
16455 ATTGAAG---CATCCAATCTTTTACCCTAAT-AAGAGGGCAA
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATG-GGGCAG
* * * *
16493 ATTGAAGACACA-CCAATCACTTATCACGATCATGGGGCAA
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
* ** *
16533 ATTG-A-A-ACATCCAATCTTTTACCCTAATCA-GAGGGCAA
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATG-GGGCAG
* *
16571 ATTGAAGACACA-CCGATCTCTTACCCCTATCATGGGGCAG
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
* * *
16611 ATTGAAGACATTATCCAATCTCTTACCTCGATCATGGGGCAA
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
* * * * *
16653 ATTGAAG-CAC--CCAATCTTTTTCCCTGATCATGAGGTAG
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
* ** * * *
16691 ATTGAAGATATCATTTAATCTCTTACCCCGACCATGAGGCGG
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
* *
16733 ATTGAAGACATCATCCAATCTCTTACCTCGATCATGGGGAAG
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
** ** *
16775 ATTGAAG---CATCCAATCTAGTACCCTAATCA-GAGGGAAG
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATG-GGGCAG
* * * **
16813 ATTAAAGACATCATCCAATCTCTTACCTCGATCATGAGGTTG
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
* *
16855 ATTGAAGACATCATTCAATCTCTTACCCCGACCATGGGGCAG
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
*
16897 ATTGAAG-C-CATCCAATCTCTTACCCCAATCATGGGGCAG
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
* ** *
16936 ATTGAAG---CATCCAATCTTTTACCCTAATCA-GAGAGCAG
1 ATTGAAGACACATCCAATCTCTTACCCCGATCATG-GGGCAG
*
16974 ATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAG
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
* * * * *
17016 ATTAAAGACATCATCCAATCTCTTACCTCAATTATGGGGCAT
1 ATTGAAGACA-CATCCAATCTCTTACCCCGATCATGGGGCAG
* *
17058 ATTGAAGTCACTATCCAATCTTTTACCCC
1 ATTGAAGACAC-ATCCAATCTCTTACCCC
17087 TAAATCAAGA
Statistics
Matches: 504, Mismatches: 97, Indels: 60
0.76 0.15 0.09
Matches are distributed among these distances:
37 9 0.02
38 142 0.28
39 38 0.08
40 62 0.12
41 13 0.03
42 238 0.47
43 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (41 bp):
ATTGAAGACACATCCAATCTCTTACCCCGATCATGGGGCAG
Found at i:16682 original size:38 final size:39
Alignment explanation
Indices: 16411--16698 Score: 187
Period size: 38 Copynumber: 7.3 Consensus size: 39
16401 TTGTAGTAAA
** * * * *
16411 GCAAATTGAAGACACACTGATCTCTTACCCAGATCATAGG
1 GCAAATTGAAGACAC-CCAATCTTTTTCCCTGATCATGGG
* * * *
16451 GCAAATTGAAG-CATCCAATCTTTTACCCTAAT-AAGAGG
1 GCAAATTGAAGACACCCAATCTTTTTCCCTGATCATG-GG
* * *
16489 GCAAATTGAAGACACACCAATCACTTATCAC-GATCATGGG
1 GCAAATTGAAGACAC-CCAATC-TTTTTCCCTGATCATGGG
* * *
16529 GCAAATTGAA-ACATCCAATCTTTTACCCTAATCA-GAGG
1 GCAAATTGAAGACACCCAATCTTTTTCCCTGATCATG-GG
* **
16567 GCAAATTGAAGACACACCGATCTCTTACCCCT-ATCATGGG
1 GCAAATTGAAGACAC-CCAATCT-TTTTCCCTGATCATGGG
* * * *
16607 GCAGATTGAAGACATTATCCAATC-TCTTACCTCGATCATGGG
1 GCAAATTGAAGAC---ACCCAATCTTTTTCCCT-GATCATGGG
*
16649 GCAAATTGAAG-CACCCAATCTTTTTCCCTGATCATGAG
1 GCAAATTGAAGACACCCAATCTTTTTCCCTGATCATGGG
* *
16687 GTAGATTGAAGA
1 GCAAATTGAAGA
16699 TATCATTTAA
Statistics
Matches: 191, Mismatches: 39, Indels: 37
0.72 0.15 0.14
Matches are distributed among these distances:
37 6 0.03
38 72 0.38
39 16 0.08
40 59 0.31
41 14 0.07
42 23 0.12
43 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (39 bp):
GCAAATTGAAGACACCCAATCTTTTTCCCTGATCATGGG
Found at i:16713 original size:80 final size:82
Alignment explanation
Indices: 16411--17088 Score: 402
Period size: 80 Copynumber: 8.4 Consensus size: 82
16401 TTGTAGTAAA
** ** *
16411 GCAAATTGAAGACACACTGATCTCTTACCCAGATCAT-AGGGCAAATTGAAG----CATCCAATC
1 GCAAATTGAAGACACACCAATCTCTTACCCCTATCATGA-GGCAGATTGAAGACATCATCCAATC
* * ** *
16471 TTTTA-CCCTAATAAGAGG
65 TCTTACCCCGACCATG-GG
* * * * * *
16489 GCAAATTGAAGACACACCAATCACTTATCACGATCATGGGGCAAATTG-A-A-A-CATCCAATCT
1 GCAAATTGAAGACACACCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAATCT
* ** *
16550 TTTACCCTAATCA-GAGG
66 CTTACCCCGACCATG-GG
* * *
16567 GCAAATTGAAGACACACCGATCTCTTACCCCTATCATGGGGCAGATTGAAGACATTATCCAATCT
1 GCAAATTGAAGACACACCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAATCT
* *
16632 CTTACCTCGATCATGGG
66 CTTACCCCGACCATGGG
** * * **
16649 GCAAATTGAAG-CAC-CCAATCT-TTTTCCCTGATCATGAGGTAGATTGAAGATATCATTTAATC
1 GCAAATTGAAGACACACCAATCTCTTACCCCT-ATCATGAGGCAGATTGAAGACATCATCCAATC
*
16711 TCTTACCCCGACCATGAG
65 TCTTACCCCGACCATGGG
** * * * *
16729 GCGGATTGAAGACATCATCCAATCTCTTACCTCGATCATGGGGAAGATTGAAG----CATCCAAT
1 GCAAATTGAAGACA-CA-CCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAAT
** ** *
16790 CTAGTACCCTAATCA-GAGG
64 CTCTTACCCCGACCATG-GG
* * * ** *
16809 G-AAGATTAAAGACATCATCCAATCTCTTACCTCGATCATGAGGTTGATTGAAGACATCATTCAA
1 GCAA-ATTGAAGACA-CA-CCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAA
16873 TCTCTTACCCCGACCATGGG
63 TCTCTTACCCCGACCATGGG
* * *
16893 GCAGATTGAAG-C-CATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAG----CATCCAATC
1 GCAAATTGAAGACACA-CCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAATC
* ** * *
16952 TTTTACCCTAATCA-GAGA
65 TCTTACCCCGACCATG-GG
* * * * *
16970 GCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAGATTAAAGACATCATCCAAT
1 GCAAATTGAAGACA-CA-CCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAAT
* * **
17035 CTCTTACCTCAATTATGGG
64 CTCTTACCCCGACCATGGG
* * *
17054 GCATATTGAAGTCACTATCCAATCTTTTACCCCTA
1 GCAAATTGAAGACAC-A-CCAATCTCTTACCCCTA
17089 AATCAAGAGG
Statistics
Matches: 480, Mismatches: 87, Indels: 60
0.77 0.14 0.10
Matches are distributed among these distances:
76 1 0.00
77 31 0.06
78 101 0.21
79 12 0.03
80 155 0.32
81 39 0.08
82 32 0.07
83 3 0.01
84 99 0.21
85 7 0.01
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (82 bp):
GCAAATTGAAGACACACCAATCTCTTACCCCTATCATGAGGCAGATTGAAGACATCATCCAATCT
CTTACCCCGACCATGGG
Found at i:16758 original size:122 final size:121
Alignment explanation
Indices: 16430--17012 Score: 593
Period size: 122 Copynumber: 4.9 Consensus size: 121
16420 AGACACACTG
* * * * ** *
16430 ATCTCTTACCC-AGATCATAGGGCAAATTGAAG---CATCCAATCTTTTACCCTAAT-AAGAGGG
1 ATCTTTTACCCTA-ATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGA-GG
* * * * *
16490 CAAATTGAAGACA-CA-CCAATCACTTATCACGATCATGGGGCAAATTGAAACATCCA
64 CAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCA
* * * *
16546 ATCTTTTACCCTAATCAGAGGGCAAATTGAAGACACA-CCGATCTCTTACCCCTATCATGGGGCA
1 ATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAGGCA
* * *
16610 GATTGAAGACATTATCCAATCTCTTACCTCGATCATGGGGCAAATTGAAGCACCCA
66 GATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCA
* * * * ** *
16666 ATCTTTTTCCCTGATCATGA-GGTAGATTGAAGATATCATTTAATCTCTTACCCCGACCATGAGG
1 ATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGATCATGAGG
* *
16730 CGGATTGAAGACATCATCCAATCTCTTACCTCGATCATGGGG-AAGATTGAAGCATCCA
64 CAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAA-ATTGAAGCATCCA
** * * * *
16788 ATCTAGTACCCTAATCAGAGGGAAGATTAAAGACATCATCCAATCTCTTACCTCGATCATGAGGT
1 ATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGATCATGAGGC
* * * *
16853 TGATTGAAGACATCATTCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCA
65 AGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAG-CATCCA
* * * **
16911 ATCTCTTACCCCAATCATG-GGGCAGATTGAAG---CATCCAATCTTTTACCCTAATCA-GAGAG
1 ATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAG-G
16971 CAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
64 CAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
17013 TAGATTAAAG
Statistics
Matches: 392, Mismatches: 59, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
116 28 0.07
117 1 0.00
118 31 0.08
119 63 0.16
120 63 0.16
121 8 0.02
122 165 0.42
123 32 0.08
124 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (121 bp):
ATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCATGAGGCA
GATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCA
Found at i:16965 original size:161 final size:160
Alignment explanation
Indices: 16415--17086 Score: 672
Period size: 161 Copynumber: 4.2 Consensus size: 160
16405 AGTAAAGCAA
** * *
16415 ATTGAAGACACA-CTGATCTCTTA-CCCAGATCATAGGGCAAATTGAAGCATCCAATCTTTTACC
1 ATTGAAGACACATCCAATCTCTTACCCCA-ATCATGGGGCAGATTGAAGCATCCAATCTTTTACC
* * * * * *
16478 CTAATAAGAGGGCAAATTGAAGACACACCAATCACTTATCACGATCATGGGGCAAATTGAA-ACA
65 CTAATCAGAGGGCAAATTGAAGACACACCAATCTCTTA-CCCGATCATGAGGTAGATTGAAGACA
* * * *
16542 TC---CAATCTTTTACCCTAATCA-GAGGGCAA
129 TCATTCAATCTCTTACCCCAACCATG-GGGCAG
* * *
16571 ATTGAAGACACA-CCGATCTCTTACCCCTATCATGGGGCAGATTGAAGACATTATCCAATCTCTT
1 ATTGAAGACACATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAG-C---ATCCAATCTTTT
* * *
16635 A-CCTCGATCATG-GGGCAAATTGAAG-CAC-CCAATCTTTTTCCCTGATCATGAGGTAGATTGA
62 ACCCT-AATCA-GAGGGCAAATTGAAGACACACCAATCTCTTACCC-GATCATGAGGTAGATTGA
* * * * *
16696 AGATATCATTTAATCTCTTACCCCGACCATGAGGCGG
124 AGACATCATTCAATCTCTTACCCCAACCATGGGGCAG
* * * **
16733 ATTGAAGACATCATCCAATCTCTTACCTCGATCATGGGGAAGATTGAAGCATCCAATCTAGTACC
1 ATTGAAGACA-CATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACC
* *
16798 CTAATCAGAGGG-AAGATTAAAGACATCATCCAATCTCTTACCTCGATCATGAGGTTGATTGAAG
65 CTAATCAGAGGGCAA-ATTGAAGACA-CA-CCAATCTCTTACC-CGATCATGAGGTAGATTGAAG
*
16862 ACATCATTCAATCTCTTACCCCGACCATGGGGCAG
126 ACATCATTCAATCTCTTACCCCAACCATGGGGCAG
16897 ATTGAAG-C-CATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCC
1 ATTGAAGACACATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCC
* * * *
16960 TAATCAGAGAGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAGATTAAAGAC
66 TAATCAGAGGGCAAATTGAAGACA-CA-CCAATCTCTTA-CCCGATCATGAGGTAGATTGAAGAC
* * ** *
17025 ATCATCCAATCTCTTACCTCAATTATGGGGCAT
128 ATCATTCAATCTCTTACCCCAACCATGGGGCAG
* *
17058 ATTGAAGTCACTATCCAATCTTTTACCCC
1 ATTGAAGACAC-ATCCAATCTCTTACCCC
17087 TAAATCAAGA
Statistics
Matches: 432, Mismatches: 56, Indels: 48
0.81 0.10 0.09
Matches are distributed among these distances:
156 39 0.09
157 6 0.01
158 24 0.06
159 13 0.03
160 52 0.12
161 144 0.33
162 32 0.07
163 6 0.01
164 115 0.27
165 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (160 bp):
ATTGAAGACACATCCAATCTCTTACCCCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCC
TAATCAGAGGGCAAATTGAAGACACACCAATCTCTTACCCGATCATGAGGTAGATTGAAGACATC
ATTCAATCTCTTACCCCAACCATGGGGCAG
Found at i:19379 original size:3 final size:3
Alignment explanation
Indices: 19371--19395 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19361 ACCTCATTGC
19371 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19396 TTGTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23207 original size:20 final size:21
Alignment explanation
Indices: 23167--23207 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23157 TAAATCCACT
*
23167 AAATCTACCCTTAAAATTTTC
1 AAATCTACCCTTAAAAGTTTC
*
23188 AAATCT-CCCTTGAAAGTTTC
1 AAATCTACCCTTAAAAGTTTC
23208 GACCTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (21 bp):
AAATCTACCCTTAAAAGTTTC
Found at i:23349 original size:18 final size:18
Alignment explanation
Indices: 23318--23352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23308 TGGTTCATTT
* *
23318 AATATTTATTTGAAATAG
1 AATATATATATGAAATAG
23336 AATATATATATGAAATA
1 AATATATATATGAAATA
23353 TGTATATAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
AATATATATATGAAATAG
Found at i:24403 original size:39 final size:39
Alignment explanation
Indices: 24358--24640 Score: 216
Period size: 39 Copynumber: 7.2 Consensus size: 39
24348 ATCGGATGGT
* *
24358 CTTCAATTTGCTCTCTAGTTAGGGTAAAAGATTGGATTG
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
** * * * ** *
24397 CTTCAATCTGCCCAAT-GGTCGAGGTAAGAGATAAGATGG
1 CTTCAATCTGCCCTCTAGTTAG-GGTAAAAGATTGGATTG
24436 TCTAT-AATCTGCCCTCT-GTTTAGGGTAAAAGATTGGATTG
1 -CT-TCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGGATTG
* * ** * *
24476 CTTCAATCTGCCCTATGGTCGGGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
* * *
24515 TCTTCAATCTGCACTCTGGTTAGGGTAAAAGATTGGATTT
1 -CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
* * * * * *
24555 CTTCAATTTGTCC-C-ATGGTCGAGGTAAGAGATTGGATGG
1 CTTCAATCTGCCCTCTA-GTTAG-GGTAAAAGATTGGATTG
* *
24594 TCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
24634 CTTCAAT
1 CTTCAAT
24641 TGGCCCCATG
Statistics
Matches: 185, Mismatches: 47, Indels: 24
0.72 0.18 0.09
Matches are distributed among these distances:
38 8 0.04
39 86 0.46
40 85 0.46
41 6 0.03
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (39 bp):
CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATTG
Found at i:24435 original size:79 final size:78
Alignment explanation
Indices: 24313--24660 Score: 477
Period size: 79 Copynumber: 4.4 Consensus size: 78
24303 TAAATAATTA
* * * * *
24313 GATTGCTTCAATCTGTCCCATGATCG-GGATAAGAGATCGGATGGTCTTCAATTTGCTCTCTAGT
1 GATTGCTTCAATCTG-CCCATGGTCGAGG-TAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGT
24377 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
** *
24392 GATTGCTTCAATCTGCCCAATGGTCGAGGTAAGAGATAAGATGGTCTAT-AATCTGCCCTCTGTT
1 GATTGCTTCAATCTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCT-TCAATCTGCCCTCTGGT
24456 TAGGGTAAAAGATTG
64 TAGGGTAAAAGATTG
* *
24471 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTGGATGGTCTTCAATCTGCACTCTGGTT
1 GATTGCTTCAATCTGCCC-ATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
24536 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
* * *
24550 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGGTT
1 GATTGCTTCAATCTG-CCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTT
24615 AGGGTAAAAGATTG
65 AGGGTAAAAGATTG
*
24629 GATTGCTTCAAT-TGGCCCCATGGTCGGGGTAA
1 GATTGCTTCAATCT-G-CCCATGGTCGAGGTAA
24661 AATACTCGGG
Statistics
Matches: 242, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
78 5 0.02
79 231 0.95
80 6 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (78 bp):
GATTGCTTCAATCTGCCCATGGTCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTCTGGTTA
GGGTAAAAGATTG
Found at i:24463 original size:40 final size:40
Alignment explanation
Indices: 24346--24640 Score: 273
Period size: 40 Copynumber: 7.5 Consensus size: 40
24336 TCGGGATAAG
* * * *
24346 AGATCGGATGGTCTTCAATTTGCTCTCTAGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* ** * *
24386 AGATTGGATTG-CTTCAATCTGCCCAATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAG-GGTAAA
** *
24425 AGATAAGATGGTCTAT-AATCTGCCCTCTGTTTAGGGTAAA
1 AGATTGGATGGTCT-TCAATCTGCCCTCTGGTTAGGGTAAA
* * ** *
24465 AGATTGGATTG-CTTCAATCTGCCCTATGGTCGGGGTAAG
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
24504 AGATTGGATGGTCTTCAATCTGCACTCTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
* * * * *
24544 AGATTGGAT-TTCTTCAATTTGTCCC-ATGG-TCGAGGTAAG
1 AGATTGGATGGTCTTCAATCTG-CCCTCTGGTTAG-GGTAAA
*
24583 AGATTGGATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAA
1 AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
*
24623 AGATTGGATTG-CTTCAAT
1 AGATTGGATGGTCTTCAAT
24641 TGGCCCCATG
Statistics
Matches: 201, Mismatches: 43, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
38 5 0.02
39 94 0.47
40 97 0.48
41 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
AGATTGGATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
Found at i:24659 original size:39 final size:39
Alignment explanation
Indices: 24313--24662 Score: 260
Period size: 40 Copynumber: 8.9 Consensus size: 39
24303 TAAATAATTA
* * * * *
24313 GATTGCTTCAATCTGTCCCATGATCGGGATAAGAGATCG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * * * **
24352 GATGGTCTTCAATTTGCTCTC-TAGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * **
24392 GATTGCTTCAATCTGCCCAATGGTCGAGGTAAGAGATAA
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
24431 GATGGTCTAT-AATCTGCCCTC-TGTTTAGGGTAAAAGATTG
1 GATTG-CT-TCAATCTGCCC-CATGGTCGGGGTAAAAGATTG
* *
24471 GATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* * **
24510 GATGGTCTTCAATCTGCACTC-TGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGC-CCCATGGTCGGGGTAAAAGATTG
* * * * *
24550 GATTTCTTCAATTTGTCCCATGGTCGAGGTAAGAGATTG
1 GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
* ** **
24589 GATGGTCTTCAATCTGCCCTTTGGTTAGGGTAAAAGATTG
1 GATTG-CTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
24629 GATTGCTTCAAT-TGGCCCCATGGTCGGGGTAAAA
1 GATTGCTTCAATCT-GCCCCATGGTCGGGGTAAAA
24663 TACTCGGGGT
Statistics
Matches: 231, Mismatches: 67, Indels: 26
0.71 0.21 0.08
Matches are distributed among these distances:
38 5 0.02
39 110 0.48
40 112 0.48
41 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (39 bp):
GATTGCTTCAATCTGCCCCATGGTCGGGGTAAAAGATTG
Found at i:24862 original size:50 final size:50
Alignment explanation
Indices: 24735--24865 Score: 165
Period size: 50 Copynumber: 2.6 Consensus size: 50
24725 TTAATATGCT
* * *
24735 CCTCTACAGCTTTAGGTGAATGAGATTCGTCATTGCGGCTTCAATCTGCC
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* * **
24785 CCTTTACAGCTTTAGGTGTATGAGATTTTTCATTGCAGCTTCAATCTGTT
1 CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
* *
24835 TCTCTACAGCTTTAGGGGTAT-AGGATTTGTC
1 CCTCTACAGCTTTAGGTGTATGA-GATTTGTC
24866 GTTCTATTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (50 bp):
CCTCTACAGCTTTAGGTGTATGAGATTTGTCATTGCAGCTTCAATCTGCC
Done.