Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003042.1 Kokia drynarioides strain JFW-HI SEQ_115568, 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: 109532
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:239 original size:13 final size:12
Alignment explanation
Indices: 203--235 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
193 AGAGAAGAAA
203 GAATTAGGGTTT
1 GAATTAGGGTTT
215 GAATTAGGGTTT
1 GAATTAGGGTTT
227 GAATTAGGG
1 GAATTAGGG
236 GTTTTATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (12 bp):
GAATTAGGGTTT
Found at i:462 original size:21 final size:19
Alignment explanation
Indices: 433--473 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
423 TCCTGGACAT
*
433 ATAGTAAAATAAATAAATAAA
1 ATAGAAAAAT-AA-AAATAAA
454 ATAGAAAAATAAAAATAAA
1 ATAGAAAAATAAAAATAAA
473 A
1 A
474 ATAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAGAAAAATAAAAATAAA
Found at i:475 original size:12 final size:13
Alignment explanation
Indices: 437--477 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
427 GGACATATAG
437 TAAAATA-AATAAA
1 TAAAATAGAA-AAA
450 TAAAATAGAAAAA
1 TAAAATAGAAAAA
*
463 TAAAA-ATAAAAA
1 TAAAATAGAAAAA
475 TAA
1 TAA
478 TTATAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.35
13 15 0.58
14 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (13 bp):
TAAAATAGAAAAA
Found at i:4649 original size:78 final size:78
Alignment explanation
Indices: 4551--4709 Score: 282
Period size: 78 Copynumber: 2.0 Consensus size: 78
4541 TATAATATGC
*
4551 CTAGAAGAAAATTCCAAGATCTAAGTATTATTCAAAATCCTCCAAATTCGGAAGAAACAAATAGT
1 CTAGAAGAAAATTCCAAGATCTAAGTATTATTCAAAATCCTCCAAATTCAGAAGAAACAAATAGT
4616 GATCAACAGACTA
66 GATCAACAGACTA
**
4629 CTAGAAGAAAATTCTGAGATCTAAGTATTATTCAAAATCCTCCAAATTCAGAAGAAACAAATAGT
1 CTAGAAGAAAATTCCAAGATCTAAGTATTATTCAAAATCCTCCAAATTCAGAAGAAACAAATAGT
*
4694 GATTAACAGACTA
66 GATCAACAGACTA
4707 CTA
1 CTA
4710 TTGGATCTTC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.25
Consensus pattern (78 bp):
CTAGAAGAAAATTCCAAGATCTAAGTATTATTCAAAATCCTCCAAATTCAGAAGAAACAAATAGT
GATCAACAGACTA
Found at i:7019 original size:43 final size:43
Alignment explanation
Indices: 6552--7026 Score: 458
Period size: 43 Copynumber: 11.1 Consensus size: 43
6542 TGTTAGTGGT
* * *
6552 GTTTGTGGGAAAAAG-GCCACTAAAAACCATGTTCTATAGTC-GT
1 GTTTGTGGG-AAAAGCGCCGCTAAAGACCATGTTCTATAG-CGGC
* * * * *
6595 GTTTGTGGGAAAAACACTGCTAAAGA-CATGTTCTATTGTGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
** * * * *
6637 GTTTGTGGGAAAAGCATCGTTAAAGATCATATTCTATAGCAGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* * *
6680 ATTTGTGGG-AAAGTGCCGCTAAAGACCATGTTCTATAGTGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* * ** * * **
6722 GATTGTGGAAAAAATGCCGCTAAAGACCATATTCTATAACTAC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* * * *
6765 ATTTGTGGGTAAAGCACCGCTAAAGACCATGTTCTATAGTGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* * * *
6808 GTTTGTGGAAAAAAG-GCCGCTAAAGACTATGTTCTATAGTGGA
1 GTTTGTGG-GAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* *
6851 GTTTGTGGGAAAAGCACCGCTAAAGACCATGCTCTATAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
** * *
6894 GTTTGTGGGAAAAGTTCTGCTAAAGACCATGCTT-TATAGAGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATG-TTCTATAGCGGC
* * * *
6937 GTTTGTGGGAAAAGCGCCGTTAAAGACCATGCTCTATAGCAGT
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
* * *
6980 GTTTGTGGGAAAAGCGCTGCTAAAGATCATGTTCTATAGCGGT
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
7023 GTTT
1 GTTT
7027 TCTCACATAA
Statistics
Matches: 348, Mismatches: 76, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
42 75 0.22
43 268 0.77
44 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (43 bp):
GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTATAGCGGC
Found at i:18989 original size:31 final size:31
Alignment explanation
Indices: 18954--19016 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
18944 CTCAAACGAT
18954 TCACCTGTCACCATCGAAGCAAATTCCTTGG
1 TCACCTGTCACCATCGAAGCAAATTCCTTGG
*
18985 TCACCTGTCACCATCGAAGCAGATTCCTTGG
1 TCACCTGTCACCATCGAAGCAAATTCCTTGG
19016 T
1 T
19017 AAACAATTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (31 bp):
TCACCTGTCACCATCGAAGCAAATTCCTTGG
Found at i:26747 original size:22 final size:22
Alignment explanation
Indices: 26719--26765 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
26709 TGAACCATTC
26719 AACATCTCAATATTCTAGTTTA
1 AACATCTCAATATTCTAGTTTA
26741 AACATCTCAATATTCTAGTTTA
1 AACATCTCAATATTCTAGTTTA
26763 AAC
1 AAC
26766 CTATGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (22 bp):
AACATCTCAATATTCTAGTTTA
Found at i:28228 original size:24 final size:24
Alignment explanation
Indices: 28196--28244 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
28186 ATCTAAATAT
28196 AATTTAACTTAATTAACATCCAAA
1 AATTTAACTTAATTAACATCCAAA
28220 AATTTAACTTAATTAACATCCAAA
1 AATTTAACTTAATTAACATCCAAA
28244 A
1 A
28245 TGTGCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTTAACTTAATTAACATCCAAA
Found at i:29186 original size:24 final size:24
Alignment explanation
Indices: 29147--29209 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29137 TAAACTAATA
* * *
29147 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
29171 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
29195 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
29210 TTTATTTCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:54296 original size:11 final size:11
Alignment explanation
Indices: 54282--54326 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
54272 CTATATAATG
54282 TTATTTTTATA
1 TTATTTTTATA
*
54293 TTATTTTTATC
1 TTATTTTTATA
*
54304 GT-TTTTTAT-
1 TTATTTTTATA
54313 TT-TTTTTATA
1 TTATTTTTATA
54323 TTAT
1 TTAT
54327 CATTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.28
10 9 0.31
11 12 0.41
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:55452 original size:47 final size:47
Alignment explanation
Indices: 55399--55540 Score: 266
Period size: 47 Copynumber: 3.0 Consensus size: 47
55389 TCCATTTAAG
*
55399 TCTGATGCTAATGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
1 TCTGATGCTAACGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
55446 TCTGATGCTAACGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
1 TCTGATGCTAACGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
*
55493 TCTGATGCTAACGTTTGTGGTTGCAATTCATCCACATGCATCAACTT
1 TCTGATGCTAACGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
55540 T
1 T
55541 TGCTACATAT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 93 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (47 bp):
TCTGATGCTAACGTTTGTGGTTGCAATTCATCCAAATGCATCAACTT
Found at i:63378 original size:29 final size:29
Alignment explanation
Indices: 63343--63409 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
63333 TCAATCTCTA
** *
63343 AAATTATTTTAATTGATTTGAAATTGAAT
1 AAATTATTCAAATTGATTTGAAATTAAAT
* *
63372 AATTTATTCAAATTGATTTTAAATTAAAT
1 AAATTATTCAAATTGATTTGAAATTAAAT
63401 AAATTATTC
1 AAATTATTC
63410 CATATTCTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (29 bp):
AAATTATTCAAATTGATTTGAAATTAAAT
Found at i:67348 original size:3 final size:3
Alignment explanation
Indices: 67342--67379 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
67332 TTATTATCAC
* *
67342 ATT ATT ATT ATT ATT ATT ATT ATC ATT AAT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
67380 AATTTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:69499 original size:24 final size:24
Alignment explanation
Indices: 69462--69511 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
69452 TTTGTCCCAC
*
69462 ACGAGCCTAAAATGGTTAGCTCTT
1 ACGAGCCTAAAATGGTTAACTCTT
* *
69486 ACGAGTCTAGAATGGTTAACTCTT
1 ACGAGCCTAAAATGGTTAACTCTT
69510 AC
1 AC
69512 TAGCTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (24 bp):
ACGAGCCTAAAATGGTTAACTCTT
Found at i:72172 original size:56 final size:55
Alignment explanation
Indices: 72100--72215 Score: 178
Period size: 56 Copynumber: 2.1 Consensus size: 55
72090 CCTTTAATAG
* * * *
72100 CAAAACAGTATCCACACATGGTTTGACACACGCCCGTGTGTCTGGCCAGTGTACCT
1 CAAAACAGAATACACACATGGTATGACACACGCCCGTGTGTCTGCCCA-TGTACCT
*
72156 CAAAACAGAATACACACATGGTATGACACACGCCTGTGTGTCTGCCCATGTACCT
1 CAAAACAGAATACACACATGGTATGACACACGCCCGTGTGTCTGCCCATGTACCT
72211 CAAAA
1 CAAAA
72216 TAGTATGCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 12 0.22
56 43 0.78
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (55 bp):
CAAAACAGAATACACACATGGTATGACACACGCCCGTGTGTCTGCCCATGTACCT
Found at i:73101 original size:13 final size:13
Alignment explanation
Indices: 73083--73108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73073 TAAAAACATT
73083 TAGCTTTTCTCTC
1 TAGCTTTTCTCTC
73096 TAGCTTTTCTCTC
1 TAGCTTTTCTCTC
73109 CTCTCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.54
Consensus pattern (13 bp):
TAGCTTTTCTCTC
Found at i:77652 original size:29 final size:28
Alignment explanation
Indices: 77607--77694 Score: 98
Period size: 29 Copynumber: 3.3 Consensus size: 28
77597 TCAATCCCTA
77607 AAATTATTCTATTTGATTTTAAATTGAAT
1 AAATTATTCTA-TTGATTTTAAATTGAAT
* *
77636 AAATTATTC---TGA--GT-GATTGAAT
1 AAATTATTCTATTGATTTTAAATTGAAT
77658 AAATTATTCTTATTGATTTTAAATTGAAT
1 AAATTATTC-TATTGATTTTAAATTGAAT
77687 AAATTATT
1 AAATTATT
77695 TCATATTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
22 16 0.33
23 1 0.02
25 3 0.06
26 3 0.06
28 1 0.02
29 24 0.50
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (28 bp):
AAATTATTCTATTGATTTTAAATTGAAT
Found at i:80774 original size:16 final size:16
Alignment explanation
Indices: 80755--80801 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
80745 AAATTTCAAT
80755 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
80771 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
80787 AAATAAAACAATATA
1 AAATAAAA-AATATA
80802 AATATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:80783 original size:28 final size:28
Alignment explanation
Indices: 80735--80827 Score: 64
Period size: 28 Copynumber: 3.1 Consensus size: 28
80725 TGTTAAAACG
* *
80735 AATATATAAAA-AATTTCAATAAATAAAA
1 AATATATAAAATTA-TTAAATAAATAAAA
80763 AATATATAAAATTATTAAATATTAAAATAAAA
1 AATATATAAAATTATT-AA-A-T-AAATAAAA
* * *
80795 CAATATA-AATATTTTTTAAAAAAATAAAA
1 -AATATATAA-AATTATTAAATAAATAAAA
80824 AATA
1 AATA
80828 ATATGGGCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
28 17 0.32
29 10 0.19
30 1 0.02
31 2 0.04
32 12 0.23
33 11 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
AATATATAAAATTATTAAATAAATAAAA
Found at i:85089 original size:19 final size:19
Alignment explanation
Indices: 85065--85146 Score: 119
Period size: 19 Copynumber: 4.3 Consensus size: 19
85055 TAGAGAGAAT
85065 AGCAATACTGGCTCGTAAG
1 AGCAATACTGGCTCGTAAG
*
85084 AGCAATATTGGCTCGTAAG
1 AGCAATACTGGCTCGTAAG
* * *
85103 AGTAATACTAGCTCATAAG
1 AGCAATACTGGCTCGTAAG
*
85122 AGCAATATTGGCTCGTAAG
1 AGCAATACTGGCTCGTAAG
85141 AGCAAT
1 AGCAAT
85147 GTTGAATCGC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (19 bp):
AGCAATACTGGCTCGTAAG
Found at i:85111 original size:38 final size:38
Alignment explanation
Indices: 85068--85142 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
85058 AGAGAATAGC
* *
85068 AATACTGGCTCGTAAGAGCAATATTGGCTCGTAAGAGT
1 AATACTAGCTCATAAGAGCAATATTGGCTCGTAAGAGT
85106 AATACTAGCTCATAAGAGCAATATTGGCTCGTAAGAG
1 AATACTAGCTCATAAGAGCAATATTGGCTCGTAAGAG
85143 CAATGTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (38 bp):
AATACTAGCTCATAAGAGCAATATTGGCTCGTAAGAGT
Found at i:89252 original size:29 final size:29
Alignment explanation
Indices: 89210--89271 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
89200 AAGGATTCCT
89210 TTGGGATGCACAATAGACTTGTCCGCCTA
1 TTGGGATGCACAATAGACTTGTCCGCCTA
*
89239 TTGGGATGCACAATAGACTTGTTCGCCTA
1 TTGGGATGCACAATAGACTTGTCCGCCTA
89268 TTGG
1 TTGG
89272 ATGATAACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (29 bp):
TTGGGATGCACAATAGACTTGTCCGCCTA
Found at i:93150 original size:101 final size:100
Alignment explanation
Indices: 93010--93752 Score: 923
Period size: 101 Copynumber: 7.4 Consensus size: 100
93000 AACGACGTGA
93010 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
** *
93075 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAG
66 CCTGTAACTTCAGGGATATAGGATTTG-GGTTGTAG
* * *
93111 CTTCATTTTGCTCCACTACAACTTCAGGGAGATAAAGATTT-TCCACTGTTAGTTTTAAT-TCGA
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGT-CACTGTTAGTTTTAATCT-GA
* *
93174 TCCTTGTAACTTTAGGGATAT-GAGATTTGGTGTTGTAG
64 TCCCTGTAACTTCAGGGATATAG-GATTTGG-GTTGTAG
* ** * * *
93212 CTTTATCTTTATCTACTGCAACTTC-A-GAGAGAAAGATTTGTCACTCTTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
* * * *
93275 TCTATAACTTCAAGGATATAGGATTTGAGGTTGCAG
66 CCTGTAACTTCAGGGATATAGGATTTG-GGTTGTAG
* *
93311 CTTCATCTTGCTCCACTACAACTTCAAAGAGATAAAGAATTT-TCACTGTTAGTTTTAATCTGAT
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAG-ATTTGTCACTGTTAGTTTTAATCTGAT
* * * *
93375 CCATATAACTTTAGGGATAT-GAGATTTGCTGTTGTAG
65 CCCTGTAACTTCAGGGATATAG-GATTTG-GGTTGTAG
* * * *
93412 CTTCATCTTGCTCCATTGTAACTTTAAGGAGATAAAGATTTGTCACTATTAG-TTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
* * * *
93476 CTTGTAACTTTAGGGATATATGATTTGGGGTTATAG
66 CCTGTAACTTCAGGGATATAGGATTT-GGGTTGTAG
* * * * * *
93512 CTTCATCTTGCTCCATTGTAACTTC-AGG-GAGAAAGATTTGCCATTGTTAGTTTTAATCCGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
93575 CCTGTAACTTCAGGGATATAGGATTTGGTGTTGTAG
66 CCTGTAACTTCAGGGATATAGGATTTGG-GTTGTAG
*
93611 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
* * *
93676 CCTGCAACTTCAAGGATATAGGATTTGGTTTGTAG
66 CCTGTAACTTCAGGGATATAGGATTTGGGTTGTAG
93711 CTTCATCTTGCTCCACTGCAACTTC-AGAGAGATAAAGATTTG
1 CTTCATCTTGCTCCACTGCAACTTCAAG-GAGATAAAGATTTG
93753 CTATTGTTTT
Statistics
Matches: 554, Mismatches: 68, Indels: 41
0.84 0.10 0.06
Matches are distributed among these distances:
98 20 0.04
99 145 0.26
100 126 0.23
101 259 0.47
102 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (100 bp):
CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
CCTGTAACTTCAGGGATATAGGATTTGGGTTGTAG
Found at i:93386 original size:200 final size:201
Alignment explanation
Indices: 93010--93751 Score: 1032
Period size: 200 Copynumber: 3.7 Consensus size: 201
93000 AACGACGTGA
*
93010 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
* *
93075 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATTTTGCTCCACTACAACTTCAGGG
66 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGAG
*
93140 AGATAAAGATTTTCCACTGTTAGTTTTAAT-TCGATCCTTGTAACTTTAGGGATATGAGATTTGG
131 AGATAAAGATTTT-CACTGTTAGTTTTAATCT-GATCCATGTAACTTTAGGGATATGAGATTTGG
93204 TGTTGTAG
194 TGTTGTAG
* ** * * *
93212 CTTTATCTTTATCTACTGCAACTTC-A-GAGAGAAAGATTTGTCACTCTTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
* * * *
93275 TCTATAACTTCAAGGATATAGGATTTGAGGTTGCAGCTTCATCTTGCTCCACTACAACTTCAAAG
66 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGAG
* *
93340 AGATAAAGAATTTTCACTGTTAGTTTTAATCTGATCCATATAACTTTAGGGATATGAGATTTGCT
131 AGATAAAG-ATTTTCACTGTTAGTTTTAATCTGATCCATGTAACTTTAGGGATATGAGATTTGGT
93405 GTTGTAG
195 GTTGTAG
* * *
93412 CTTCATCTTGCTCCATTGTAACTTTAAGGAGATAAAGATTTGTCACTATTAG-TTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
* ** * * * * * * **
93476 CTTGTAACTTTAGGGATATATGATTTGGGGTTATAGCTTCATCTTGCTCCATTGTAACTTCAG-G
66 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGAG
* * * * * *
93540 -GAGAAAGATTTGCCATTGTTAGTTTTAATCCGATCCCTGTAACTTCAGGGATAT-AGGATTTGG
131 AGATAAAGATTT-TCACTGTTAGTTTTAATCTGATCCATGTAACTTTAGGGATATGA-GATTTGG
93603 TGTTGTAG
194 TGTTGTAG
93611 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
* * *
93676 CCTGCAACTTCAAGGATATAGGATTTG-GTTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAG
66 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGAG
93740 AGATAAAGATTT
131 AGATAAAGATTT
93752 GCTATTGTTT
Statistics
Matches: 473, Mismatches: 58, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
198 5 0.01
199 136 0.29
200 209 0.44
201 80 0.17
202 43 0.09
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (201 bp):
CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATCTTGCTCCACTACAACTTCAGAG
AGATAAAGATTTTCACTGTTAGTTTTAATCTGATCCATGTAACTTTAGGGATATGAGATTTGGTG
TTGTAG
Found at i:93434 original size:50 final size:49
Alignment explanation
Indices: 93380--93652 Score: 187
Period size: 50 Copynumber: 5.4 Consensus size: 49
93370 CTGATCCATA
93380 TAACTTTAGGGATATGAGATTTGCTGTTGTAGCTTCATCTTGCTCCATTG
1 TAACTTTAGGGATAT-AGATTTGCTGTTGTAGCTTCATCTTGCTCCATTG
* ** * * *
93430 TAACTTTAAGGAGATAAAGATTTGTCACTAT-TAGTTTAATC-TGATCC-TTG
1 TAACTTT-AGG-GATATAGATTTG-CTGT-TGTAGCTTCATCTTGCTCCATTG
** *
93480 TAACTTTAGGGATATATGATTTGGGGTTATAGCTTCATCTTGCTCCATTG
1 TAACTTTAGGGATATA-GATTTGCTGTTGTAGCTTCATCTTGCTCCATTG
* * * ** * * * * *
93530 TAACTTCAGGGAGAAAGATTTGCCATTGTTAGTTTTAATC-CGATCC-CTG
1 TAACTTTAGGGATATAGATTTGCTGTTG-TAG-CTTCATCTTGCTCCATTG
* * *
93579 TAACTTCAGGGATATAGGATTTGGTGTTGTAGCTTCATCTTGCTCCACTG
1 TAACTTTAGGGATATA-GATTTGCTGTTGTAGCTTCATCTTGCTCCATTG
* * *
93629 CAACTTCAAGGAGATAAAGATTTG
1 TAACTT-TAGG-GATATAGATTTG
93653 TCACTATTAG
Statistics
Matches: 171, Mismatches: 37, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
47 1 0.01
48 19 0.11
49 45 0.26
50 57 0.33
51 29 0.17
52 19 0.11
53 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (49 bp):
TAACTTTAGGGATATAGATTTGCTGTTGTAGCTTCATCTTGCTCCATTG
Found at i:93626 original size:300 final size:302
Alignment explanation
Indices: 93010--93752 Score: 1038
Period size: 300 Copynumber: 2.5 Consensus size: 302
93000 AACGACGTGA
93010 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
* * * * *
93075 CCTACAACTTCAAGGATATAGGATTTGAGGTTGTAGCTTCATTTTGCTCCACTACAACTTCAGGG
66 CCTACAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAGG
*
93140 AGATAAAGATTT-TCCACTGTTAGTTTTAATTCGATCCTTGTAACTTTAGGGATATGAGATTTGG
131 AGATAAAGATTTGTCCACTATTAGTTTTAATTCGATCCTTGTAACTTTAGGGATATGAGATTTGG
* * * * * *
93204 TGTTGTAGCTTTATCTTTATCTACTGCAACTTCAGAGAGAAAGATTTGTCACTCTTAGTTTTAAT
196 GGTTATAGCTTCATCTTGATCCACTGCAACTTCAGAGAGAAAGATTTGCCACTCTTAGTTTTAAT
* *
93269 CTGATCTCTATAACTTCAAGGATATAGGATTTGAGGTTGCAG
261 CCGATCCCTATAACTTCAAGGATATAGGATTTGAGGTTGCAG
* *
93311 CTTCATCTTGCTCCACTACAACTTCAAAGAGATAAAGAATTT-TCACTGTTAGTTTTAATCTGAT
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAG-ATTTGTCACTGTTAGTTTTAATCTGAT
* * * * * * *
93375 CCATATAACTTTAGGGATAT-GAGATTTGCTGTTGTAGCTTCATCTTGCTCCATTGTAACTTTAA
65 CCCTACAACTTCAAGGATATAG-GATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTTAA
93439 GGAGATAAAGATTTGT-CACTATTAG-TTTAA-TCTGATCCTTGTAACTTTAGGGATAT-ATGAT
129 GGAGATAAAGATTTGTCCACTATTAGTTTTAATTC-GATCCTTGTAACTTTAGGGATATGA-GAT
* * * * * *
93500 TTGGGGTTATAGCTTCATCTTGCTCCATTGTAACTTCAGGGAGAAAGATTTGCCATTGTTAGTTT
192 TTGGGGTTATAGCTTCATCTTGATCCACTGCAACTTCAGAGAGAAAGATTTGCCACTCTTAGTTT
* * *
93565 TAATCCGATCCCTGTAACTTCAGGGATATAGGATTTG-GTGTTGTAG
257 TAATCCGATCCCTATAACTTCAAGGATATAGGATTTGAG-GTTGCAG
*
93611 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTATTAGTTTTAATCTGATC
1 CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
* * *
93676 CCTGCAACTTCAAGGATATAGGATTTGGT-TTGTAGCTTCATCTTGCTCCACTGCAAC-TTCAGA
66 CCTACAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAG-
93739 GAGATAAAGATTTG
130 GAGATAAAGATTTG
93753 CTATTGTTTT
Statistics
Matches: 389, Mismatches: 44, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
298 4 0.01
299 48 0.12
300 202 0.52
301 130 0.33
302 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (302 bp):
CTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGTCACTGTTAGTTTTAATCTGATC
CCTACAACTTCAAGGATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAACTTTAAGG
AGATAAAGATTTGTCCACTATTAGTTTTAATTCGATCCTTGTAACTTTAGGGATATGAGATTTGG
GGTTATAGCTTCATCTTGATCCACTGCAACTTCAGAGAGAAAGATTTGCCACTCTTAGTTTTAAT
CCGATCCCTATAACTTCAAGGATATAGGATTTGAGGTTGCAG
Found at i:98101 original size:13 final size:14
Alignment explanation
Indices: 98072--98101 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
98062 TTTAGTACAT
98072 TGACATTTAACCTC
1 TGACATTTAACCTC
98086 TGACATTTAA-CTC
1 TGACATTTAACCTC
98099 TGA
1 TGA
98102 TTGTGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:107144 original size:2 final size:2
Alignment explanation
Indices: 107139--107165 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
107129 CCTTTATATA
107139 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
107166 ACCTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:109457 original size:21 final size:21
Alignment explanation
Indices: 109424--109464 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
109414 AATATATATA
109424 TAAAAATACATAAATAAATTTT
1 TAAAAATACAT-AATAAATTTT
*
109446 TAAAAAT-GATAATAAATTT
1 TAAAAATACATAATAAATTT
109465 AAAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAAATACATAATAAATTTT
Done.