Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005245.1 Kokia drynarioides strain JFW-HI SEQ_119143, 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: 15566
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Found at i:1280 original size:39 final size:39
Alignment explanation
Indices: 1237--1896 Score: 148
Period size: 39 Copynumber: 17.2 Consensus size: 39
1227 CGATCATGGA
*
1237 GCAGATCATAGTCATCCGATCTTTTACCCCGAGCCTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
*** * ** ** *
1276 GCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTG-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * ** *
1314 GACATATCACCA-TCAGCTAATCTCTTACCCCGAGCCT-AGG
1 G-CAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGA-G
** * * *
1354 GCAGATTGCAG-CTATCCGATCTTTTACCTCGAGTCTGGG
1 GCAGATCACAGTC-ATCCGATCTTTTACCCCGAGCCTGAG
* * *
1393 GCAGATCACCA-TCAACCAATCTCTTACCCCGAGCCT-AG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * *
1431 GACAGATTACAGCCAT-CGAATCTTTTACCCTGAGCCTGGG
1 G-CAGATCACAGTCATCCG-ATCTTTTACCCCGAGCCTGAG
* * * * * *
1471 GTAGATCACCA-TCA-GCGAATCTCTTACCCCGGGCTTGGG
1 GCAGATCA-CAGTCATCCG-ATCTTTTACCCCGAGCCTGAG
* *** * * *
1510 GTAGATTGTAGCCATCAGATCTTTTACCCCAAGCCT-AGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGA-G
* * * * * * *
1549 GCAGATCACCA-TTAGCCAATGTCTTACCCCGAGCTTGGG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* *** *
1588 GTAGATTGTAATCATCCGATCTTTT------A----G-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * * * * * *
1616 GTAGATCACCA-TCAACCAATCTCTTACCACAAGCTTGTG
1 GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
* ** ** * * *
1655 GCAAATTGCAACCATTCGATCTTTTACCCCGAGTCTGGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * *
1694 GTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTG-G
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * * * * *
1732 AGCATATCACCA-TCAACCAAACTCTTACCCCGAGCTTGAG
1 -GCAGATCA-CAGTCATCCGATCTTTTACCCCGAGCCTGAG
*** * * *
1772 GCAGATTGTAGCCATCCGATCTTTTACCCCAAGCTTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
* ** * * *
1811 GCAGATCACA-TCAGCAAATCTCTTACCCCGAGCTTGGG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
** * ** *
1849 GCAGATTGCAGCCATTAGATCTTTTACCCCGAGTCTGAG
1 GCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTGAG
*
1888 ACAGATCAC
1 GCAGATCAC
1897 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:1303 original size:78 final size:75
Alignment explanation
Indices: 1215--1582 Score: 315
Period size: 78 Copynumber: 4.7 Consensus size: 75
1205 TGAAGATTTC
* * * * * *
1215 AATCTCTTACCCCGATCATGGAGCAGATCA-TAGTCATCCGATCTTTTACCCCGAGCCTGAGGCA
1 AATCTTTTACCCCGAGC-TGGGGCAGATCACCA-TCA-CCAATCTCTTACCCCGAGCCT-AGGCA
*
1279 GATTGTAGCCATCA
62 GATTGCAGCCATCA
** * * *
1293 AATCTTTTACCTTGAGCTTGGGACATATCACCATCAGCTAATCTCTTACCCCGAGCCTAGGGCAG
1 AATCTTTTACCCCGAGC-TGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCCTA-GGCAG
* *
1358 ATTGCAGCTATCC
63 ATTGCAGCCATCA
* *
1371 GATCTTTTACCTCGAGTCTGGGGCAGATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAG
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATC-ACCAATCTCTTACCCCGAGCCTAGG-CAG
* *
1436 ATTACAGCCATCG
63 ATTGCAGCCATCA
* * * * * * *
1449 AATCTTTTACCCTGAGCCTGGGGTAGATCACCATCAGCGAATCTCTTACCCCGGGCTTGGGGTAG
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGCCT-AGGCAG
*
1514 ATTGTAGCCATCA
63 ATTGCAGCCATCA
* * * * *
1527 GATCTTTTACCCCAAGCCTAGGGCAGATCACCATTAGCCAATGTCTTACCCCGAGC
1 AATCTTTTACCCCGAG-CTGGGGCAGATCACCATCA-CCAATCTCTTACCCCGAGC
1583 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:1510 original size:117 final size:117
Alignment explanation
Indices: 1333--1854 Score: 313
Period size: 117 Copynumber: 4.6 Consensus size: 117
1323 CCATCAGCTA
* * * ** * * *
1333 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAG-TCTGGGGCAG
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATC-ATCCGATCTCTTACCCCGAGCT-TGGGGCAG
* * *
1397 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCA-T-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTACG
* * * *
1449 AATCTTTTACCCTGAGCCTGGGGTAGATCACCATCA-GCGAATCTCTTACCCCGGGCTTGGGGTA
1 -ATCTTTTACCCCGAGCCTGGGGTAGATCA-CATCATCCG-ATCTCTTACCCCGAGCTTGGGGCA
* * * *
1513 GATTGTAGCCATC-A--GATCTTTTACCCCAAGCCTAGGGCAGA-T-CA-CCATTAGCCA
63 GA-T-CA-CCATCAACCAATCTCTTACCCCAAGCCTAGGGCAGATTGCAGCCATTA--CG
* * * * * *
1567 ATGTCTTACCCCGAGCTTGGGGTAGATTGTA-ATCATCCGA--TCTT---------TTAGGGTAG
1 ATCTTTTACCCCGAGCCTGGGGTAGA-T-CACATCATCCGATCTCTTACCCCGAGCTTGGGGCAG
* * * *
1620 ATCACCATCAACCAATCTCTTACCACAAG-CTTGTGGCAAATTGCAACCATT-CG
64 ATCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * *
1673 ATCTTTTACCCCGAGTCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTGGAGCATA
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACA-TCATCCGATCTCTTACCCCGAGCTTGGGGCAGA
* * * * *
1738 TCACCATCAACCAAACTCTTACCCCGAG-CTTGAGGCAGATTGTAGCCA-TCCG
65 TCACCATCAACCAATCTCTTACCCCAAGCCTAG-GGCAGATTGCAGCCATTACG
* * * * * **
1790 ATCTTTTACCCCAAGCTTGAGGCAGATCACATCAGCAAATCTCTTACCCCGAGCTTGGGGCAGAT
1 ATCTTTTACCCCGAGCCTGGGGTAGATCACATCATCCGATCTCTTACCCCGAGCTTGGGGCAGAT
1855 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:1585 original size:78 final size:78
Alignment explanation
Indices: 1255--1613 Score: 387
Period size: 78 Copynumber: 4.6 Consensus size: 78
1245 TAGTCATCCG
* * * ** * * *
1255 ATCTTTTACCCCGAGCCTGAGGCAGATTGTAGCCATCAAATCTTTTACCTTGAGCTTGGGACATA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
1320 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * * * *
1333 ATCTCTTACCCCGAGCCTAGGGCAGATTGCAGCTATCCGATCTTTTACCTCGAGTCTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
1398 TCACCATCAACCA
66 TCACCATCAGCCA
* * ** * *
1411 ATCTCTTACCCCGAGCCTAGGACAGATTACAGCCATC-GAATCTTTTACCCTGAGCCTGGGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAG-ATCTTTTACCCCGAGCCTGGGGCAG
*
1475 ATCACCATCAGCGA
65 ATCACCATCAGCCA
* * * * *
1489 ATCTCTTACCCCGGGCTTGGGGTAGATTGTAGCCATCAGATCTTTTACCCCAAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTACCCCGAGCCTGGGGCAGA
*
1554 TCACCATTAGCCA
66 TCACCATCAGCCA
* * * ** *
1567 ATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCTTTTA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGCCATCAGATCTTTTA
1614 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:1675 original size:67 final size:67
Alignment explanation
Indices: 1545--1680 Score: 164
Period size: 67 Copynumber: 2.0 Consensus size: 67
1535 ACCCCAAGCC
* * * * * * * * *
1545 TAGGGCAGATCACCATTAGCCAATGTCTTACCCCGAGCTTGGGGTAGATTGTAATCATCCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
1610 TT
66 TT
* * *
1612 TAGGGTAGATCACCATCAACCAATCTCTTACCACAAGCTTGTGGCAAATTGCAACCATTCGATCT
1 TAGGGCAGATCACCATCAACCAATCTCTTACCACAAGCTTGGGGCAAATTGCAACCATCCGATCT
1677 TT
66 TT
1679 TA
1 TA
1681 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:1856 original size:77 final size:78
Alignment explanation
Indices: 1673--1968 Score: 311
Period size: 77 Copynumber: 3.8 Consensus size: 78
1663 CAACCATTCG
* * * * *
1673 ATCTTTTACCCCGAG-TCTGGGGTAGATTACAGTCATCCGATCTTTTACCCCGAGCTTG-GAGCA
1 ATCTCTTACCCCGAGCT-TGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAG-GCA
* *
1736 TATCACCATCAACCAA
64 GATCACCATC-AGCAA
* *
1752 A-CTCTTACCCCGAGCTTGAGGCAGATTGTAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
1816 TCA-CATCAGCAA
66 TCACCATCAGCAA
** * *
1828 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTAGATCTTTTACCCCGAG-TCTGAGACAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCT-TGAGGCAG
*
1892 ATCACCATCAGCTA
65 ATCACCATCAGCAA
* * * * * * *
1906 ATCTCTTA-CCCAAGCCT-GGGCAGAATGCAACCGTCCGATCTCTTACCCCAAGCTT-AGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCAAGCTTGAGGCAGA
1968 T
66 T
1969 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:1915 original size:39 final size:38
Alignment explanation
Indices: 1712--1916 Score: 154
Period size: 39 Copynumber: 5.3 Consensus size: 38
1702 CAGTCATCCG
* * *
1712 ATCTTTTACCCCGAGCTTG-GAGCATATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAG-GCAGATCACCATC-AGCA
* * *
1751 AACTCTTACCCCGAGCTTGAGGCAGATTGTAGCCATC--CG
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCA
* *
1790 ATCTTTTACCCCAAGCTTGAGGCAGATCA-CATCAGCAA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGC-A
* *
1828 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTAG--
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCA
* *
1867 ATCTTTTACCCCGAG-TCTGAGACAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCT-TGAGGCAGATCACCATCAGC-A
1906 ATCTCTTACCC
1 ATCTCTTACCC
1917 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:1973 original size:38 final size:38
Alignment explanation
Indices: 1906--1994 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
1896 CCATCAGCTA
* *
1906 ATCTCTTA-CCCAAGCCTGGGCAGAATGCAACCGTCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
* * *
1943 ATCTCTTACCCCAAGCTTAGGTAGATTGCAACCATCCG
1 ATCTCTTACCCCAAGCCTAGGCAGAATGCAACCATCCG
*
1981 ATCTTTTACCCCAA
1 ATCTCTTACCCCAA
1995 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:2215 original size:28 final size:29
Alignment explanation
Indices: 2178--2246 Score: 104
Period size: 28 Copynumber: 2.4 Consensus size: 29
2168 ATCATTTAAC
2178 CCCTAAACTTTTATAAAATTACA-ACTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
* **
2206 CCCTAAACTTTTCTAAAATTACATTTTAA
1 CCCTAAACTTTTATAAAATTACATACTAA
2235 CCCTAAACTTTT
1 CCCTAAACTTTT
2247 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:2403 original size:28 final size:29
Alignment explanation
Indices: 2172--2429 Score: 245
Period size: 29 Copynumber: 8.9 Consensus size: 29
2162 ATCATCATCA
**
2172 TTTAACCCCTAAACTTTTATAAAATTACA-
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
** *
2201 ACTAACCCTAAACTTTTCTAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
2230 TTTAACCCTAAACTTTTCCAAAAATATAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* *
2259 TTTAACCCCTAAACTTCTCCAAAATCACAT
1 TTTAA-CCCTAAACTTTTCCAAAATTACAT
* *
2289 TTTAAACCCTAAAATCTTCCAAAATTACAT
1 TTT-AACCCTAAACTTTTCCAAAATTACAT
* * * *
2319 TTT-TCTCTAAAC-TTTCTTAAAATCACAT
1 TTTAACCCTAAACTTTTC-CAAAATTACAT
* * *
2347 TTTGACCCTAAACTTCTCCAAAATCACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
*
2376 TTTAACCC-AAATTTTTCCAAAATTACAT
1 TTTAACCCTAAACTTTTCCAAAATTACAT
* * * *
2404 TTTACCCCCAAATTTTTCTAAAATTA
1 TTTAACCCTAAACTTTTCCAAAATTA
2430 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:3831 original size:26 final size:25
Alignment explanation
Indices: 3769--3829 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
3759 TCTTTTTAAA
*
3769 AATTT-AATTTATTTGTTTAACAAT
1 AATTTAAATTTATTTGTTTAAGAAT
3793 AATTTAAACTTTATTTGTTTAAGAAT
1 AATTTAAA-TTTATTTGTTTAAGAAT
3819 AATTTAAATTT
1 AATTTAAATTT
3830 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:5266 original size:30 final size:30
Alignment explanation
Indices: 5179--5486 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 30
5169 TCTTTAAATT
* *
5179 TTACATTTTGACCACT-AACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
5208 TTACATTTTAACCCC-AAATTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
5237 TTGCATTTTTACCCCTTAAACTTTTCAAAAA
1 TTACATTTTAACCCC-TAAACTTTTCCAAAA
* *
5268 TTGCATTTTAACCTCTAAACTTTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
*
5298 TTACATTTTAACCCCTAAACTTCTT-TAAAA
1 TTACATTTTAACCCCTAAACTT-TTCCAAAA
* * * * *
5328 TCACATTTTAAACCTTAAAATCTTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
5358 CTACATTTTATCCCCCAAACATTCTT--AAAA
1 TTACATTTTAACCCCTAAAC-TT-TTCCAAAA
* * *
5388 TCACATTTTGA-CCC-AAACTTCTCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
5416 TTACATTTTGA-CCC-ACACTTTGCCAAAA
1 TTACATTTTAACCCCTAAACTTTTCCAAAA
* * *
5444 TTACATTTTTACCCCTAAATTTTTTCTAAAA
1 TTACATTTTAACCCCTAAA-CTTTTCCAAAA
**
5475 TTATGTTTTAAC
1 TTACATTTTAAC
5487 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:7054 original size:31 final size:34
Alignment explanation
Indices: 6982--7056 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
6972 ATATATACCA
*
6982 ATATATATACGTTTATTTATTTTTTTATACTGCAT
1 ATATATATACGTTTATTTATTTTTCTATACTG-AT
* *
7017 ACATATATTCGTTTA-TTATTTTTCTATAC-G-T
1 ATATATATACGTTTATTTATTTTTCTATACTGAT
7048 ATATATATA
1 ATATATATA
7057 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.