Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001830.1 Kokia drynarioides strain JFW-HI SEQ_113574, 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: 14669
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1332 original size:17 final size:17
Alignment explanation
Indices: 1298--1338 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1288 AAAAAAAGGG
1298 AAAAG-AAAAGAAGAAA
1 AAAAGAAAAAGAAGAAA
1314 AAAAGAAAAAGGAAG-AA
1 AAAAGAAAAA-GAAGAAA
1331 AAAAGAAA
1 AAAAGAAA
1339 GCAAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAA
Found at i:2222 original size:15 final size:14
Alignment explanation
Indices: 2202--2259 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 14
2192 TAATAAATTA
2202 AAAAAAGAAGAAAAG
1 AAAAAA-AAGAAAAG
2217 AAAAAAAAGGAAAGAG
1 AAAAAAAA-GAAA-AG
*
2233 AAGAANAAA-AAAA-
1 AA-AAAAAAGAAAAG
2246 AAAAAAAA-AAAAG
1 AAAAAAAAGAAAAG
2259 A
1 A
2260 GAGGTTGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 9 0.24
13 3 0.08
14 3 0.08
15 13 0.35
16 4 0.11
17 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:2231 original size:19 final size:17
Alignment explanation
Indices: 2201--2259 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 17
2191 GTAATAAATT
2201 AAAAAAAGAAGAAAAGA
1 AAAAAAAGAAGAAAAGA
*
2218 AAAAAAAGGAAAGAGAAGA
1 AAAAAAA-G-AAGAAAAGA
*
2237 ANAAAAA-AA-AAAA-A
1 AAAAAAAGAAGAAAAGA
2251 AAAAAAAGA
1 AAAAAAAGA
2260 GAGGTTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 7 0.20
15 4 0.11
16 2 0.06
17 7 0.20
18 1 0.03
19 14 0.40
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAGAAAAGA
Found at i:3518 original size:39 final size:39
Alignment explanation
Indices: 3475--4134 Score: 148
Period size: 39 Copynumber: 17.2 Consensus size: 39
3465 CGATCATGGA
*
3475 GCAGATCATAGTCATCCGATCTTTTACCCCGAGCCTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
*** * ** ** *
3514 GCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTG-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * ** *
3552 GACATATCACCA-TCAGCTAATCTCTTACCCCGAGCCT-AGG
1 G-CAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGA-G
** * * *
3592 GCAGATTGCAG-CTATCCGATCTTTTACCTCGAGTCTGGG
1 GCAGATCACAGTC-ATCCGATCTTTTACCCCGAGCCTGAG
* * *
3631 GCAGATCACCA-TCAACCAATCTCTTACCCCGAGCCT-AG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * *
3669 GACAGATTACAGCCAT-CGAATCTTTTACCCTGAGCCTGGG
1 G-CAGATCACAGTCATCCG-ATCTTTTACCCCGAGCCTGAG
* * * * * *
3709 GTAGATCACCA-TCA-GCGAATCTCTTACCCCGGGCTTGGG
1 GCAGATCA-CAGTCATCCG-ATCTTTTACCCCGAGCCTGAG
* *** * * *
3748 GTAGATTGTAGCCATCAGATCTTTTACCCCAAGCCT-AGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGA-G
* * * * * * *
3787 GCAGATCACCA-TTAGCCAATGTCTTACCCCGAGCTTGGG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* *** *
3826 GTAGATTGTAATCATCCGATCTTTT------A----G-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * * * * * *
3854 GTAGATCACCA-TCAACCAATCTCTTACCACAAGCTTGTG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* ** ** * * *
3893 GCAAATTGCAACCATTCGATCTTTTACCCCGAGTCTGGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * *
3932 GTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTG-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * * * *
3970 AGCATATCACCA-TCAACCAAACTCTTACCCCGAGCTTGAG
1 -GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
*** * * *
4010 GCAGATTGTAGCCATCCGATCTTTTACCCCAAGCTTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* ** * * *
4049 GCAGATCACA-TCAGCAAATCTCTTACCCCGAGCTTGGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
** * ** *
4087 GCAGATTGCAGCCATTAGATCTTTTACCCCGAGTCTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
*
4126 ACAGATCAC
1 GCAGATCAC
4135 CATCAGCTAA
Statistics
Matches: 429, Mismatches: 153, Indels: 78
0.65 0.23 0.12
Matches are distributed among these distances:
28 18 0.04
29 2 0.00
33 1 0.00
34 1 0.00
38 46 0.11
39 346 0.81
40 15 0.03
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (39 bp):
GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
Found at i:3541 original size:78 final size:75
Alignment explanation
Indices: 3453--3820 Score: 315
Period size: 78 Copynumber: 4.7 Consensus size: 75
3443 TGAAGATTTC
* * * * * *
3453 AATCTCTTACCCCGATCATGGAGCAGATCA-TAGTCATCCGATCTTTTACCCCGAGCCTGAGGCA
1 AATCTTTTACCCCGAGC-TGGGGCAGATCACCA-TCA-CCAATCTCTTACCCCGAGCCT-AGGCA
*
3517 GATTGTAGCCATCA
62 GATTGCAGCCATCA
** * * *
3531 AATCTTTTACCTTGAGCTTGGGACATATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGCAG
1 AATCTTTTACCCCGAGC-TGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCCTA-GGCAG
* *
3596 ATTGCAGCTATCC
63 ATTGCAGCCATCA
* *
3609 GATCTTTTACCTCGAGTCTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAG
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATC-ACCAATCTCTTACCCCGAGCCTAGG-CAG
* *
3674 ATTACAGCCATCG
63 ATTGCAGCCATCA
* * * * * * *
3687 AATCTTTTACCCTGAGCCTGGGGTAGATCACCATCAGCGAATCTCTTACCCCGGGCTTGGGGTAG
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCCT-AGGCAG
*
3752 ATTGTAGCCATCA
63 ATTGCAGCCATCA
* * * * *
3765 GATCTTTTACCCCAAGCCTAGGGCAGATCACCATTAGCCAATGTCTTACCCCGAGC
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGC
3821 TTGGGGTAGA
Statistics
Matches: 237, Mismatches: 46, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
77 4 0.02
78 228 0.96
79 5 0.02
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (75 bp):
AATCTTTTACCCCGAGCTGGGGCAGATCACCATCACCAATCTCTTACCCCGAGCCTAGGCAGATT
GCAGCCATCA
Found at i:3748 original size:117 final size:117
Alignment explanation
Indices: 3571--4092 Score: 313
Period size: 117 Copynumber: 4.6 Consensus size: 117
3561 CCATCAGCTA
* * * ** * * *
3571 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAG-TCTGGGGCAG
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATC-ATCCGATCTCTTACCCCGAGCT-TGGGGCAG
* * *
3635 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCA-T-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTACG
* * * *
3687 AATCTTTTACCCTGAGCCTGGGGTAGATCACCATCA-GCGAATCTCTTACCCCGGGCTTGGGGTA
1 -ATCTTTTACCCCGAGCCTGGGGTAGATCA-CATCATCCG-ATCTCTTACCCCGAGCTTGGGGCA
* * * *
3751 GATTGTAGCCATC-A--GATCTTTTACCCCAAGCCTAGGGCAGA-T-CA-CCATTAGCCA
63 GA-T-CA-CCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTA--CG
* * * * * *
3805 ATGTCTTACCCCGAGCTTGGGGTAGATTGTA-ATCATCCGA--TCTT---------TTAGGGTAG
1 ATCTTTTACCCCGAGCCTGGGGTAGA-T-CACATCATCCGATCTCTTACCCCGAGCTTGGGGCAG
* * * *
3858 ATCACCATCAACCAATCTCTTACCACAAG-CTTGTGGCAAATTGCAACCATT-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * *
3911 ATCTTTTACCCCGAGTCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTGGAGCATA
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACA-TCATCCGATCTCTTACCCCGAGCTTGGGGCAGA
* * * * *
3976 TCACCATCAACCAAACTCTTACCCCGAG-CTTGAGGCAGATTGTAGCCA-TCCG
65 TCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * * **
4028 ATCTTTTACCCCAAGCTTGAGGCAGATCACATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGAT
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATCATCCGATCTCTTACCCCGAGCTTGGGGCAGAT
4093 TGCAGCCATT
Statistics
Matches: 311, Mismatches: 60, Indels: 69
0.71 0.14 0.16
Matches are distributed among these distances:
103 5 0.02
104 4 0.01
105 6 0.02
106 58 0.19
107 1 0.00
108 5 0.02
109 5 0.02
114 3 0.01
115 7 0.02
116 32 0.10
117 168 0.54
118 9 0.03
119 3 0.01
120 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (117 bp):
ATCTTTTACCCCGAGCCTGGGGTAGATCACATCATCCGATCTCTTACCCCGAGCTTGGGGCAGAT
CACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTACG
Found at i:3823 original size:78 final size:78
Alignment explanation
Indices: 3493--3851 Score: 387
Period size: 78 Copynumber: 4.6 Consensus size: 78
3483 TAGTCATCCG
* * * ** * * *
3493 ATCTTTTACCCCGAGCCTGAGGCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTGGGACATA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
3558 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * * * *
3571 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAGTCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
3636 TCACCATCAACCA
66 TCACCATCAGCCA
* * ** * *
3649 ATCTCTTACCCCGAGCCTAGGACAGATTACAGCCATC-GAATCTTTTACCCTGAGCCTGGGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAG-ATCTTTTACCCCGAGCCTGGGGCAG
*
3713 ATCACCATCAGCGA
65 ATCACCATCAGCCA
* * * * *
3727 ATCTCTTACCCCGGGCTTGGGGTAGATTGTAGCCATCAGATCTTTTACCCCAAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
3792 TCACCATTAGCCA
66 TCACCATCAGCCA
* * * ** *
3805 ATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCTTTTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTA
3852 GGGTAGATCA
Statistics
Matches: 238, Mismatches: 41, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
77 1 0.00
78 236 0.99
79 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:3913 original size:67 final size:67
Alignment explanation
Indices: 3783--3918 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
3773 ACCCCAAGCC
* * * * * * * * *
3783 TAGGGCAGATCACCATTAGCCAATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
3848 TT
66 TT
* * *
3850 TAGGGTAGATCACCATCAACCAATCTCTTACCACAAGCTTGTGGCAAATTGCAACCATTCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
3915 TT
66 TT
3917 TA
1 TA
3919 CCCCGAGTCT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (67 bp):
TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
TT
Found at i:4094 original size:77 final size:78
Alignment explanation
Indices: 3911--4206 Score: 311
Period size: 77 Copynumber: 3.8 Consensus size: 78
3901 CAACCATTCG
* * * * *
3911 ATCTTTTACCCCGAG-TCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTG-GAGCA
1 ATCTCTTACCCCGAGCT-TGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAG-GCA
* *
3974 TATCACCATCAACCAA
64 GATCACCATC-AGCAA
* *
3990 A-CTCTTACCCCGAGCTTGAGGCAGATTGTAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
4054 TCA-CATCAGCAA
66 TCACCATCAGCAA
** * *
4066 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTAGATCTTTTACCCCGAG-TCTGAGACAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCT-TGAGGCAG
*
4130 ATCACCATCAGCTA
65 ATCACCATCAGCAA
* * * * * * *
4144 ATCTCTTA-CCCAAGCCT-GGGCAGAATGCAACCGTCCGATCTCTTACCCCAAGCTT-AGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
4206 T
66 T
4207 TGCAACCATC
Statistics
Matches: 184, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
75 6 0.03
76 35 0.19
77 70 0.38
78 70 0.38
79 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
TCACCATCAGCAA
Found at i:4153 original size:39 final size:38
Alignment explanation
Indices: 3950--4154 Score: 154
Period size: 39 Copynumber: 5.3 Consensus size: 38
3940 CAGTCATCCG
* * *
3950 ATCTTTTACCCCGAGCTTG-GAGCATATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAG-GCAGATCACCATC-AGCA
* * *
3989 AACTCTTACCCCGAGCTTGAGGCAGATTGTAGCCATC--CG
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCA
* *
4028 ATCTTTTACCCCAAGCTTGAGGCAGATCA-CATCAGCAA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGC-A
* *
4066 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTAG--
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCA
* *
4105 ATCTTTTACCCCGAG-TCTGAGACAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCT-TGAGGCAGATCACCATCAGC-A
4144 ATCTCTTACCC
1 ATCTCTTACCC
4155 AAGCCTGGGC
Statistics
Matches: 132, Mismatches: 19, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
35 4 0.03
36 6 0.05
37 4 0.03
38 26 0.20
39 77 0.58
40 4 0.03
41 1 0.01
42 10 0.08
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCA
Found at i:4211 original size:38 final size:38
Alignment explanation
Indices: 4144--4232 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
4134 CCATCAGCTA
* *
4144 ATCTCTTA-CCCAAGCCTGGGCAGAATGCAACCGTCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
* * *
4181 ATCTCTTACCCCAAGCTTAGGTAGATTGCAACCATCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
*
4219 ATCTTTTACCCCAA
1 ATCTCTTACCCCAA
4233 TCATGGGGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
37 8 0.18
38 37 0.82
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.25
Consensus pattern (38 bp):
ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
Found at i:4453 original size:28 final size:29
Alignment explanation
Indices: 4416--4484 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
4406 ATCATTTAAC
4416 CCCTAAACTTTTATAAAATTACA-ACTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
* **
4444 CCCTAAACTTTTCTAAAATTACATTTTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
4473 CCCTAAACTTTT
1 CCCTAAACTTTT
4485 CCAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTATAAAATTACATACTAA
Found at i:4641 original size:28 final size:29
Alignment explanation
Indices: 4410--4667 Score: 245
Period size: 29 Copynumber: 8.9 Consensus size: 29
4400 ATCATCATCA
**
4410 TTTAACCCCTAAACTTTTATAAAATTACA-
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
** *
4439 ACTAACCCTAAACTTTTCTAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
4468 TTTAACCCTAAACTTTTCCAAAAATATAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
4497 TTTAACCCCTAAACTTCTCCAAAATCACAT
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
* *
4527 TTTAAACCCTAAAATCTTCCAAAATTACAT
1 TTT-AACCCTAAACTTTTCCAAAATTACAT
* * * *
4557 TTT-TCTCTAAAC-TTTCTTAAAATCACAT
1 TTTAACCCTAAACTTTTC-CAAAATTACAT
* * *
4585 TTTGACCCTAAACTTCTCCAAAATCACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
*
4614 TTTAACCC-AAATTTTTCCAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* * * *
4642 TTTACCCCCAAATTTTTCTAAAATTA
1 TTTAACCCTAAACTTTTCCAAAATTA
4668 TGTTTTCACA
Statistics
Matches: 190, Mismatches: 32, Indels: 14
0.81 0.14 0.06
Matches are distributed among these distances:
27 3 0.02
28 64 0.34
29 72 0.38
30 49 0.26
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.37
Consensus pattern (29 bp):
TTTAACCCTAAACTTTTCCAAAATTACAT
Found at i:6069 original size:26 final size:25
Alignment explanation
Indices: 6007--6067 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
5997 TCTTTTTAAA
*
6007 AATTT-AATTTATTTGTTTAACAAT
1 AATTTAAATTTATTTGTTTAAGAAT
6031 AATTTAAACTTTATTTGTTTAAGAAT
1 AATTTAAA-TTTATTTGTTTAAGAAT
6057 AATTTAAATTT
1 AATTTAAATTT
6068 TAGTTTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 5 0.15
25 5 0.15
26 24 0.71
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (25 bp):
AATTTAAATTTATTTGTTTAAGAAT
Found at i:7504 original size:30 final size:30
Alignment explanation
Indices: 7417--7724 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 30
7407 TCTTTAAATT
* *
7417 TTACATTTTGACCACT-AACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
7446 TTACATTTTAACCCC-AAATTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
7475 TTGCATTTTTACCCCTTAAACTTTTCAAAAA
1 TTACATTTTAACCCC-TAAACTTTTCCAAAA
* *
7506 TTGCATTTTAACCTCTAAACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
7536 TTACATTTTAACCCCTAAACTTCTT-TAAAA
1 TTACATTTTAACCCCTAAACTT-TTCCAAAA
* * * * *
7566 TCACATTTTAAACCTTAAAATCTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
7596 CTACATTTTATCCCCCAAACATTCTT--AAAA
1 TTACATTTTAACCCCTAAAC-TT-TTCCAAAA
* * *
7626 TCACATTTTGA-CCC-AAACTTCTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
7654 TTACATTTTGA-CCC-ACACTTTGCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
7682 TTACATTTTTACCCCTAAATTTTTTCTAAAA
1 TTACATTTTAACCCCTAAA-CTTTTCCAAAA
**
7713 TTATGTTTTAAC
1 TTACATTTTAAC
7725 AACGTATTAT
Statistics
Matches: 223, Mismatches: 44, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 42 0.19
29 46 0.21
30 85 0.38
31 45 0.20
32 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
TTACATTTTAACCCCTAAACTTTTCCAAAA
Found at i:9292 original size:31 final size:34
Alignment explanation
Indices: 9220--9294 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
9210 ATATATACCA
*
9220 ATATATATACGTTTATTTATTTTTTTATACTGCAT
1 ATATATATACGTTTATTTATTTTTCTATACTG-AT
* *
9255 ACATATATTCGTTTA-TTATTTTTCTATAC-G-T
1 ATATATATACGTTTATTTATTTTTCTATACTGAT
9286 ATATATATA
1 ATATATATA
9295 GACATATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 8 0.23
33 1 0.03
34 13 0.37
35 13 0.37
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (34 bp):
ATATATATACGTTTATTTATTTTTCTATACTGAT
Done.