Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011244.1 Kokia drynarioides strain JFW-HI SEQ_126222, 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: 289877
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:274820 original size:16 final size:16
Alignment explanation
Indices: 274799--274830 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
274789 AACCAGTACT
274799 TAGCTACAGTTGGATC
1 TAGCTACAGTTGGATC
*
274815 TAGCTACGGTTGGATC
1 TAGCTACAGTTGGATC
274831 AATCCCTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (16 bp):
TAGCTACAGTTGGATC
Found at i:279104 original size:29 final size:29
Alignment explanation
Indices: 279072--279254 Score: 122
Period size: 30 Copynumber: 6.2 Consensus size: 29
279062 AAGGAAAAAA
279072 GGGTTAAAATCAAATTTTTAGAAAGTTTG
1 GGGTTAAAATCAAATTTTTAGAAAGTTTG
** * **
279101 GGGTTAAAATGTAATTTTCA-AAAGTTCAC
1 GGGTTAAAATCAAATTTTTAGAAAGTT-TG
* * *
279130 AGGTCAAAATGC-AATTTTTAGAAAGTTTAA
1 GGGTTAAAAT-CAAATTTTTAGAAAGTTT-G
* * *
279160 GAGTCAAAATCAAATTTTTGGAAAGTTTGG
1 GGGTTAAAATCAAATTTTTAGAAAGTTT-G
* * * *
279190 GGGTCAAAATCAATTTTTTGGAAAGTTCGG
1 GGGTTAAAATCAAATTTTTAGAAAGTT-TG
*
279220 GGGTTAACA-CTAAATTTTT-GAGAAGTTTG
1 GGGTTAAAATC-AAATTTTTAGA-AAGTTTG
279249 AGGGTT
1 -GGGTT
279255 GAATTCGAAT
Statistics
Matches: 122, Mismatches: 23, Indels: 17
0.75 0.14 0.10
Matches are distributed among these distances:
28 6 0.05
29 37 0.30
30 79 0.65
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (29 bp):
GGGTTAAAATCAAATTTTTAGAAAGTTTG
Found at i:281082 original size:46 final size:48
Alignment explanation
Indices: 280983--281097 Score: 157
Period size: 46 Copynumber: 2.5 Consensus size: 48
280973 TCTTCTGTGA
* * *
280983 GATGGTAGCTTCAATCT-CTCCCTCTTGATTGTAAGGGTAAAAGATTT
1 GATGGTGGCTTCAATCTGCTCCCTCTTGACTGTAAGGGTAAAAGATTG
*
281030 GATGGTGGCTTCAATCTGC-CCCTCTTGACT-TAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCTCCCTCTTGACTGTAAGGGTAAAAGATTG
*
281076 GATGGTGGTTTCAATCTG-TCCC
1 GATGGTGGCTTCAATCTGCTCCC
281098 ATGATAGTGG
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
46 34 0.56
47 26 0.43
48 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (48 bp):
GATGGTGGCTTCAATCTGCTCCCTCTTGACTGTAAGGGTAAAAGATTG
Found at i:281137 original size:38 final size:37
Alignment explanation
Indices: 281085--281747 Score: 404
Period size: 38 Copynumber: 16.9 Consensus size: 37
281075 GGATGGTGGT
* * *
281085 TTCAATCTGTCCCATGATAGTGGTATGAGATTGGATGC
1 TTCAATCTGCCCCATGATCG-GGTAAGAGATTGGATGC
* *
281123 TTCAATCTACCCCATGATCGGGGTAAGAGATTAGATAATGTC
1 TTCAATCTGCCCCATGATC-GGGTAAGAGATT-G--GATG-C
* * * * *
281165 TTCTATCTGCCCTATGATTGGGGTAAAAGATCGGATGC
1 TTCAATCTGCCCCATGA-TCGGGTAAGAGATTGGATGC
* *
281203 TTCGATCTGCCTCATGATCGAGGTAAGAGATT-GATGTATC
1 TTCAATCTGCCCCATGATCG-GGTAAGAGATTGGATG---C
** *
281243 TTCAATCTGCCCTC-TGATTAAGGTAAAAGATTGGATGC
1 TTCAATCTGCCC-CATGA-TCGGGTAAGAGATTGGATGC
* *
281281 -TCTAATTTGCCCCATGATCGAGGTAAGAGATTGGACGGC
1 TTC-AATCTGCCCCATGATCG-GGTAAGAGATTGGA-TGC
* * * *
281320 TGCAATTTGCCTCATGATTAGGGTAAGAGATTGGATGATGTC
1 TTCAATCTGCCCCATGA-TCGGGTAAGAGATT-G--GATG-C
* * * * *
281362 TTCAATCTACTCCATGATTAGGGTAAAAGATCGGATGC
1 TTCAATCTGCCCCATGA-TCGGGTAAGAGATTGGATGC
* * *
281400 TTTAATCTGCCTCATGATTGGGATAAGAGATTTGATGATGTC
1 TTCAATCTGCCCCATGATCGGG-TAAGAGA-TTG--GATG-C
* * * *
281442 TTCAATCTGCCTCATTATCGGGGTAAGAGATCGGATGT
1 TTCAATCTGCCCCATGATC-GGGTAAGAGATTGGATGC
*
281480 TTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCCATGATC-GGGTAAGAGATTGG-ATG-C
** * * * *
281520 TTCAATCTGCCCTTTGATTAGGGTAAAAGATCGGATAC
1 TTCAATCTGCCCCATGA-TCGGGTAAGAGATTGGATGC
* * *
281558 TTCAATTTGCCTCATGATCGGGGTAAGAGATTGGTGTGTC
1 TTCAATCTGCCCCATGATC-GGGTAAGAGATTGG-ATG-C
* * *
281598 TTCAATTTGCCCTC-TGATTAGGGTAAAAGATTGGATGC
1 TTCAATCTGCCC-CATGA-TCGGGTAAGAGATTGGATGC
*
281636 TTCAATCTGCCCCATGATCGGGGTATGAGATTAAGG-TGTC
1 TTCAATCTGCCCCATGATC-GGGTAAGAGATT--GGATG-C
* * * *
281676 TTCAATCTTCCCTC-TAATTAGGGTAAAAGATAT-GATGC
1 TTCAATCTGCCC-CATGA-TCGGGTAAGAGAT-TGGATGC
*
281714 TTCAATATGCCCCATGATCGTGGTAAGAGATTGG
1 TTCAATCTGCCCCATGATCG-GGTAAGAGATTGG
281748 TGTGTAGCTT
Statistics
Matches: 486, Mismatches: 90, Indels: 98
0.72 0.13 0.15
Matches are distributed among these distances:
37 21 0.04
38 201 0.41
39 51 0.10
40 108 0.22
41 24 0.05
42 77 0.16
43 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (37 bp):
TTCAATCTGCCCCATGATCGGGTAAGAGATTGGATGC
Found at i:281182 original size:80 final size:78
Alignment explanation
Indices: 281085--281313 Score: 257
Period size: 78 Copynumber: 2.9 Consensus size: 78
281075 GGATGGTGGT
* ** * *
281085 TTCAATCTGTCCC-ATGATAGTGGTATGAGATTGGATGCTTCAATCTACCCCATGATCGGGGTAA
1 TTCAATCTG-CCCTATGATAGAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAA
*
281149 GAGATTAGATAATGTC
65 GAGATT-GAT-ATATC
* * * * * *
281165 TTCTATCTGCCCTATGATTGGGGTAAAAGATCGGATGCTTCGATCTGCCTCATGATCGAGGTAAG
1 TTCAATCTGCCCTATGATAGAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAG
*
281230 AGATTGATGTATC
66 AGATTGATATATC
* *
281243 TTCAATCTGCCCTCTGATTA-AGGTAAAAGATTGGATGC-TCTAATTTGCCCCATGATCGAGGTA
1 TTCAATCTGCCCTATGA-TAGAGGTAAAAGATTGGATGCTTC-AATCTGCCCCATGATCGAGGTA
281306 AGAGATTG
64 AGAGATTG
281314 GACGGCTGCA
Statistics
Matches: 126, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
77 2 0.02
78 61 0.48
79 7 0.06
80 56 0.44
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (78 bp):
TTCAATCTGCCCTATGATAGAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAG
AGATTGATATATC
Found at i:281272 original size:78 final size:79
Alignment explanation
Indices: 281112--281313 Score: 264
Period size: 78 Copynumber: 2.6 Consensus size: 79
281102 TAGTGGTATG
* * * *
281112 AGATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTAGATAATGTCTTCTATCTGCCC
1 AGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATT-GATAATATCTTCAATCTGCCC
**
281177 TATGATTGGGGTAAA
65 TATGATTAAGGTAAA
* * * *
281192 AGATCGGATGCTTCGATCTGCCTCATGATCGAGGTAAGAGATTGAT-GTATCTTCAATCTGCCCT
1 AGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGATAATATCTTCAATCTGCCCT
*
281256 CTGATTAAGGTAAA
66 ATGATTAAGGTAAA
*
281270 AGATTGGATGC-TCTAATTTGCCCCATGATCGAGGTAAGAGATTG
1 AGATTGGATGCTTC-AATCTGCCCCATGATCGAGGTAAGAGATTG
281314 GACGGCTGCA
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 2 0.02
78 63 0.59
79 3 0.03
80 38 0.36
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (79 bp):
AGATTGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGATAATATCTTCAATCTGCCCT
ATGATTAAGGTAAA
Found at i:281388 original size:197 final size:199
Alignment explanation
Indices: 281086--281513 Score: 510
Period size: 197 Copynumber: 2.2 Consensus size: 199
281076 GATGGTGGTT
* * * * * * * * * **
281086 TCAATCTGTCCCATGATAGTGGTATGAGATTGGA-TGCTTCAATCTACCCCATGATCGGGGTAAG
1 TCAATCTGCCCCATGATCGAGGTAAGAGATTGGACGGCTGCAATTTGCCTCATGATTAGGGTAAG
* * * *
281150 AGATTAGATAATGTCTTCTATCTGCCCTATGATTGGGGTAAAAGATCGGATGCTTCGATCTGCCT
66 AGATTAGATAATGTCTTCAATCTACCCTATGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCT
* *
281215 CATGATCGAGG-TAAGAGA-TTGATG-TATCTTCAATCTGCCCTC-TGATTAAGGTAAAAGATTG
131 CATGATCG-GGATAAGAGATTTGATGATATCTTCAATCTG-CCTCATGATCAAGGTAAAAGATCG
281276 GATG-C
194 GATGTC
*
281281 TCTAATTTGCCCCATGATCGAGGTAAGAGATTGGACGGCTGCAATTTGCCTCATGATTAGGGTAA
1 TC-AATCTGCCCCATGATCGAGGTAAGAGATTGGACGGCTGCAATTTGCCTCATGATTAGGGTAA
* * *
281346 GAGATTGGATGATGTCTTCAATCTACTCC-ATGATTAGGGTAAAAGATCGGATGCTTTAATCTGC
65 GAGATTAGATAATGTCTTCAATCTAC-CCTATGATTAGGGTAAAAGATCGGATGCTTCAATCTGC
* * * ** *
281410 CTCATGATTGGGATAAGAGATTTGATGATGTCTTCAATCTGCCTCATTATCGGGGTAAGAGATCG
129 CTCATGATCGGGATAAGAGATTTGATGATATCTTCAATCTGCCTCATGATCAAGGTAAAAGATCG
*
281475 GATGTT
194 GATGTC
*
281481 TCAATCTGCCCCATGATCGGGGTAAGAGATTGG
1 TCAATCTGCCCCATGATCGAGGTAAGAGATTGG
281514 TGTGTCTTCA
Statistics
Matches: 195, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
195 2 0.01
196 29 0.15
197 92 0.47
198 12 0.06
199 58 0.30
200 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (199 bp):
TCAATCTGCCCCATGATCGAGGTAAGAGATTGGACGGCTGCAATTTGCCTCATGATTAGGGTAAG
AGATTAGATAATGTCTTCAATCTACCCTATGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCT
CATGATCGGGATAAGAGATTTGATGATATCTTCAATCTGCCTCATGATCAAGGTAAAAGATCGGA
TGTC
Found at i:281562 original size:78 final size:78
Alignment explanation
Indices: 281322--281752 Score: 508
Period size: 78 Copynumber: 5.5 Consensus size: 78
281312 TGGACGGCTG
* * ** * *
281322 CAATTTGCCTCATGATTAGGGTAAGAGATTGGATGATGTCTTCAATCTACTCC-ATGATTAGGGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGG-TG-TGTCTTCAATCTGC-CCTCTGATTAGGGT
281386 AAAAGATCGGATGCTT
63 AAAAGATCGGATGCTT
* * * * * * **
281402 TAATCTGCCTCATGATTGGGATAAGAGATTTGATGATGTCTTCAATCTG-CCTCATTATCGGGGT
1 CAATCTGCCCCATGATCGGGGTAAGAGA-TTGGTG-TGTCTTCAATCTGCCCTC-TGATTAGGGT
* *
281466 AAGAGATCGGATGTTT
63 AAAAGATCGGATGCTT
*
281482 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTTTGATTAGGGTAAA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAA
*
281547 AGATCGGATACTT
66 AGATCGGATGCTT
* * *
281560 CAATTTGCCTCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATTTGCCCTCTGATTAGGGTAAA
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAA
*
281625 AGATTGGATGCTT
66 AGATCGGATGCTT
* * * *
281638 CAATCTGCCCCATGATCGGGGTATGAGATTAAG-GTGTCTTCAATCTTCCCTCTAATTAGGGTAA
1 CAATCTGCCCCATGATCGGGGTAAGAGATT-GGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAA
**
281702 AAGATATGATGCTT
65 AAGATCGGATGCTT
* *
281716 CAATATGCCCCATGATCGTGGTAAGAGATTGGTGTGT
1 CAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
281753 AGCTTCGCTT
Statistics
Matches: 302, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
77 1 0.00
78 205 0.68
79 9 0.03
80 84 0.28
81 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (78 bp):
CAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGATTAGGGTAAA
AGATCGGATGCTT
Found at i:281567 original size:277 final size:278
Alignment explanation
Indices: 281049--281634 Score: 747
Period size: 277 Copynumber: 2.1 Consensus size: 278
281039 TTCAATCTGC
* * **
281049 CCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGTTTCAATCTGTCCCATGATAGTGGTATGAG
1 CCCTC-TGA-TTA-GGGTAAAAGATTGGATGATGGTTTCAATCTCTCCCATGATAGTGGTAAAAG
* * *
281114 ATTGGATGCTTCAATCTACCCCATGATCGGGGTAAGAGATTAGATAATGTCTTCTATCTGCCCTA
63 ATCGGATGCTTCAATCTACCCCATGATCGGGATAAGAGATTAGATAATGTCTTCAATCTGCCCTA
* * *
281179 TGATTGGGGTAAAAGATCGGATGCTTCGATCTGCCTCATGATCGAGGTAAGAGATTGATGTATCT
128 TGATCGGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGATGTATCT
* *
281244 TCAATCTGCCCTCTGATTAAGGTAAAAGATTGGATGCTCTAATTTGCCCCATGATCGAGGTAAGA
193 TCAATCTGCCCTCTGATTAAGGTAAAAGATCGGATACTCTAATTTGCCCCATGATCGAGGTAAGA
281309 GATTGGACG-G-CTGCAATTTG
258 GATTGG-CGTGTCTGCAATTTG
*
281329 -CCTCATGATTAGGGTAAGAGATTGGATGAT-GTCTTCAATCTACT-CCATGATTAG-GGTAAAA
1 CCCTC-TGATTAGGGTAAAAGATTGGATGATGGT-TTCAATCT-CTCCCATGA-TAGTGGTAAAA
* * * * * *
281390 GATCGGATGCTTTAATCTGCCTCATGATTGGGATAAGAGATTTGATGATGTCTTCAATCTG-CCT
62 GATCGGATGCTTCAATCTACCCCATGATCGGGATAAGAGATTAGATAATGTCTTCAATCTGCCCT
* * * * * *
281454 CATTATCGGGGTAAGAGATCGGATGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
127 -ATGATCGGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGATGTAT
* * * *
281519 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATCGGATACT-TCAATTTGCCTCATGATCGGGGTA
191 CTTCAATCTGCCCTCTGATTAAGGTAAAAGATCGGATACTCT-AATTTGCCCCATGATCGAGGTA
* *
281583 AGAGATTGGTGTGTCTTCAATTTG
255 AGAGATTGGCGTGTCTGCAATTTG
281607 CCCTCTGATTAGGGTAAAAGATTGGATG
1 CCCTCTGATTAGGGTAAAAGATTGGATG
281635 CTTCAATCTG
Statistics
Matches: 265, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
276 7 0.03
277 209 0.79
278 38 0.14
279 11 0.04
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (278 bp):
CCCTCTGATTAGGGTAAAAGATTGGATGATGGTTTCAATCTCTCCCATGATAGTGGTAAAAGATC
GGATGCTTCAATCTACCCCATGATCGGGATAAGAGATTAGATAATGTCTTCAATCTGCCCTATGA
TCGGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGAGGTAAGAGATTGATGTATCTTCA
ATCTGCCCTCTGATTAAGGTAAAAGATCGGATACTCTAATTTGCCCCATGATCGAGGTAAGAGAT
TGGCGTGTCTGCAATTTG
Found at i:282415 original size:49 final size:49
Alignment explanation
Indices: 281952--282421 Score: 363
Period size: 49 Copynumber: 9.6 Consensus size: 49
281942 CTTTGCAGCC
* * * ** * *
281952 TCAATCTTTCCCTTAATATCTCTAAGGTATAAGGTTCATCATTGCAGCT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * * *
282001 TCAACCTTTCCCTTAACAT-TTTC-ATGGTACACGATTCGCCGTTGCGGCT
1 TCAACCTTTCCCTT--CATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * * * * * * *
282050 GCAATCTTT-CATATCACATCTTTAAGGTACAAGGTTCGCCATTGCAGTT
1 TCAACCTTTCCCT-TCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * * *
282099 TCAACCTTTCCCTACATATCTCCATGGTACAAGATTCGCCGTTGCGGCT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * ** ** * * ** *
282148 ACAATCTTTCCCACCACGTCTCTAAGGTACAAGGTTCGTCATTATGACT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * * *
282197 TCAACCTTT-CCTTCCATATCTCCATGGTACAAGATTCGCTGTTGCGGCT
1 TCAACCTTTCCCTT-CATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * ** *
282246 TCAATCTTTCCCATCACGTCTTTAAGGTACAAGGTTCGCCGTTGCGGCT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * * * ** *
282295 TCAACCTTTCCCTCCATATCTCCATGGTACAAGATTCATCGTTACGGCT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
* * ** * *
282344 TCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCGTTACGGCT
1 TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
*
282393 TCAACCTTTCCCTTCATATCTCTAGGGTA
1 TCAACCTTTCCCTTCATATCTCTAAGGTA
282422 TTAGATTTTC
Statistics
Matches: 314, Mismatches: 99, Indels: 16
0.73 0.23 0.04
Matches are distributed among these distances:
47 2 0.01
48 6 0.02
49 296 0.94
50 8 0.03
51 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.34
Consensus pattern (49 bp):
TCAACCTTTCCCTTCATATCTCTAAGGTACAAGGTTCGCCGTTGCGGCT
Found at i:282428 original size:98 final size:98
Alignment explanation
Indices: 281934--282414 Score: 577
Period size: 98 Copynumber: 4.9 Consensus size: 98
281924 TTAGGGTATG
* * * * * ** * * *
281934 AGATTCACCTTTGCAGCCTCAATCTTTCCCTTAATATCTCTAAGGTATAAGGTTCATCATTGCAG
1 AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
* * * *
281999 CTTCAACCTTTCCCTTAACATTTTCATGGTACA
66 CTTCAACCTTTCCCTTCATATCTCCATGGTACA
* * * ** * * * *
282032 CGATTCGCCGTTGCGGCTGCAATCTTTCATATCACATCTTTAAGGTACAAGGTTCGCCATTGCAG
1 AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
* *
282097 TTTCAACCTTTCCCTACATATCTCCATGGTACA
66 CTTCAACCTTTCCCTTCATATCTCCATGGTACA
* * * ** *
282130 AGATTCGCCGTTGCGGCTACAATCTTTCCCACCACGTCTCTAAGGTACAAGGTTCGTCATTATGA
1 AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
282195 CTTCAACCTTT-CCTTCCATATCTCCATGGTACA
66 CTTCAACCTTTCCCTT-CATATCTCCATGGTACA
* * * * *
282228 AGATTCGCTGTTGCGGCTTCAATCTTTCCCATCACGTCTTTAAGGTACAAGGTTCGCCGTTGCGG
1 AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
*
282293 CTTCAACCTTTCCCTCCATATCTCCATGGTACA
66 CTTCAACCTTTCCCTTCATATCTCCATGGTACA
* * * *
282326 AGATTCATCGTTACGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCGTTACGG
1 AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
282391 CTTCAACCTTTCCCTTCATATCTC
66 CTTCAACCTTTCCCTTCATATCTC
282415 TAGGGTATTA
Statistics
Matches: 328, Mismatches: 53, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
97 3 0.01
98 322 0.98
99 3 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (98 bp):
AGATTCACCGTTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTACAAGGTTCGTCATTGCGG
CTTCAACCTTTCCCTTCATATCTCCATGGTACA
Found at i:283382 original size:7 final size:7
Alignment explanation
Indices: 283370--283435 Score: 55
Period size: 7 Copynumber: 8.9 Consensus size: 7
283360 TGACCTCTCA
283370 TTTTTTC
1 TTTTTTC
283377 TTTTTTC
1 TTTTTTC
283384 TTCTCTTT-
1 TT-T-TTTC
283392 TCTTTTTC
1 T-TTTTTC
283400 -TTTTTC
1 TTTTTTC
283406 TTTTTTC
1 TTTTTTC
283413 TTTCTTTCCC
1 TTT-TTT--C
*
283423 TTTTTTA
1 TTTTTTC
283430 TTTTTT
1 TTTTTT
283436 TGGGTGAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
6 6 0.12
7 27 0.54
8 6 0.12
9 7 0.14
10 4 0.08
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTTC
Found at i:283407 original size:17 final size:17
Alignment explanation
Indices: 283372--283426 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
283362 ACCTCTCATT
283372 TTTTCTTTTT-TCTTCTC
1 TTTTCTTTTTCT-TTCTC
*
283389 TTTTCTTTTTCTTTTTC
1 TTTTCTTTTTCTTTCTC
*
283406 TTTT-TTCTTTCTTTCCC
1 TTTTCTT-TTTCTTTCTC
283423 TTTT
1 TTTT
283427 TTATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 2 0.06
17 30 0.91
18 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTTCTC
Found at i:283433 original size:29 final size:29
Alignment explanation
Indices: 283371--283427 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
283361 GACCTCTCAT
*
283371 TTTTTCTTTTTTCTTCTCTTTTCTTTTTC
1 TTTTTCTTTTTTCTTCTCTTTCCTTTTTC
283400 TTTTTCTTTTTTCTT-TCTTTCCCTTTTT
1 TTTTTCTTTTTTCTTCTCTTT-CCTTTTT
283428 TATTTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTTTCTTTTTTCTTCTCTTTCCTTTTTC
Found at i:284337 original size:16 final size:18
Alignment explanation
Indices: 284301--284343 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
284291 CTTGACTTTC
284301 TTCTTTCTTCCTTTGTCTT
1 TTCTTT-TTCCTTTGTCTT
284320 TTCTTTTT-CTTT-TCTT
1 TTCTTTTTCCTTTGTCTT
284336 TTCTTTTT
1 TTCTTTTT
284344 TTAAAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.50
17 4 0.17
18 2 0.08
19 6 0.25
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (18 bp):
TTCTTTTTCCTTTGTCTT
Found at i:284343 original size:11 final size:11
Alignment explanation
Indices: 284297--284342 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
284287 TCATCTTGAC
284297 TTTCTTCTTTC-
1 TTTCTT-TTTCT
* *
284308 TTCCTTTGTCT
1 TTTCTTTTTCT
284319 TTTCTTTTTCT
1 TTTCTTTTTCT
284330 TTTC-TTTTCT
1 TTTCTTTTTCT
284340 TTT
1 TTT
284343 TTTAAAAGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 12 0.40
11 18 0.60
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:284398 original size:74 final size:79
Alignment explanation
Indices: 284267--284416 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 79
284257 ATAGATTTTC
* *
284267 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTCTTTCTTCCTTTGTCTTTTCTTTTTCTTT
1 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTC-TTCTTCCTTTGTCTTTTCTTCTTCTTC
284332 TCTTTTCTTTTTTTAA
65 TCTTTT-TTTTTTTAA
284348 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTT-TTC-T-TT-C-TT-TCTTTTCTTCTTCTTCT
1 AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTCTTCTTCCTTTGTCTTTTCTTCTTCTTCT
284407 CTTTTTTTTT
66 CTTTTTTTTT
284417 ATCTTCTCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
73 5 0.07
74 20 0.30
75 2 0.03
76 1 0.01
77 2 0.03
78 1 0.01
80 3 0.04
81 33 0.49
ACGTcount: A:0.08, C:0.21, G:0.10, T:0.61
Consensus pattern (79 bp):
AAGATGCCCTTTGCGGGTTTTCATCTTGACTTTCTTCTTCTTCCTTTGTCTTTTCTTCTTCTTCT
CTTTTTTTTTTTAA
Found at i:286683 original size:24 final size:24
Alignment explanation
Indices: 286645--286722 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
286635 ATTCAAAATA
* *
286645 AATAAGTCAGTATGATTAATACAGG
1 AATAAGT-AATATGATTAATACAAG
* *
286670 AATAATTAATATGATTAATACAAT
1 AATAAGTAATATGATTAATACAAG
*
286694 AATAAGTAGTATGATTAATACAAG
1 AATAAGTAATATGATTAATACAAG
286718 AATAA
1 AATAA
286723 AACTTGAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 40 0.87
25 6 0.13
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (24 bp):
AATAAGTAATATGATTAATACAAG
Found at i:288940 original size:29 final size:29
Alignment explanation
Indices: 288874--288940 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
288864 GAAATTTTGG
* * * * *
288874 AAAGTTTGGGGTTAACATGTATTTTTTAA
1 AAAGTTTAGGATTAAAATGTAATTTTCAA
288903 AAAGTTTTAGGATTAAAATGTAATTTTCAA
1 AAAG-TTTAGGATTAAAATGTAATTTTCAA
288933 AAAGTTTA
1 AAAGTTTA
288941 CAGGTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (29 bp):
AAAGTTTAGGATTAAAATGTAATTTTCAA
Found at i:288951 original size:30 final size:31
Alignment explanation
Indices: 288890--288970 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 31
288880 TGGGGTTAAC
* * *
288890 ATGTATTTTTTAAAAAGTTT-TAGGATTAAA
1 ATGTAATTTTTAAAAAGTTTACAGGATAAAA
*
288920 ATGTAATTTTCAAAAAGTTTACAGG-TAAAA
1 ATGTAATTTTTAAAAAGTTTACAGGATAAAA
** *
288950 ATGCGATTTTTAGAAAGTTTA
1 ATGTAATTTTTAAAAAGTTTA
288971 AGTGTCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (31 bp):
ATGTAATTTTTAAAAAGTTTACAGGATAAAA
Found at i:288981 original size:30 final size:30
Alignment explanation
Indices: 288924--289030 Score: 82
Period size: 30 Copynumber: 3.6 Consensus size: 30
288914 ATTAAAATGT
* *
288924 AATTTTCAAAAAGTTTACAGGTAAAAA-TG
1 AATTTTTAGAAAGTTTACAGGTAAAAATTG
* *
288953 CGATTTTTAGAAAGTTTA-AGTGTCAAAATTG
1 -AATTTTTAGAAAGTTTACAG-GTAAAAATTG
288984 AATTTTTAGAAAG-TT-CGAGGGCT-AAAATTG
1 AATTTTTAGAAAGTTTAC-A-GG-TAAAAATTG
289014 AATTTTT-GAAAAGTTTA
1 AATTTTTAG-AAAGTTTA
289031 GGGGTCGAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
29 5 0.08
30 52 0.83
31 6 0.10
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTACAGGTAAAAATTG
Found at i:289033 original size:29 final size:30
Alignment explanation
Indices: 288955--289024 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
288945 TAAAAATGCG
** *
288955 ATTTTTAGAAAGTTTAAGTG-TCAAAATTGA
1 ATTTTTAGAAAGTTCGAGGGCT-AAAATTGA
288985 ATTTTTAGAAAGTTCGAGGGCTAAAATTGA
1 ATTTTTAGAAAGTTCGAGGGCTAAAATTGA
289015 ATTTTT-GAAA
1 ATTTTTAGAAA
289025 AGTTTAGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.11
30 31 0.86
31 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (30 bp):
ATTTTTAGAAAGTTCGAGGGCTAAAATTGA
Found at i:289480 original size:10 final size:10
Alignment explanation
Indices: 289467--289506 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
289457 TATATGCAAA
289467 TATATATATG
1 TATATATATG
289477 TATATACATATG
1 TATAT--ATATG
289489 TATATATATG
1 TATATATATG
289499 TATATATA
1 TATATATA
289507 AATGCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 18 0.64
12 10 0.36
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (10 bp):
TATATATATG
Found at i:289481 original size:12 final size:12
Alignment explanation
Indices: 289466--289506 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
289456 ATATATGCAA
289466 ATATATATATGT
1 ATATATATATGT
*
289478 ATATACATATG-
1 ATATATATATGT
289489 -TATATATATGT
1 ATATATATATGT
289500 ATATATA
1 ATATATA
289507 AATGCTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (12 bp):
ATATATATATGT
Found at i:289517 original size:22 final size:22
Alignment explanation
Indices: 289467--289518 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
289457 TATATGCAAA
*
289467 TATATATATGTATATACATATG
1 TATATATATGTATATACAAATG
*
289489 TATATATATGTATATATAAATG
1 TATATATATGTATATACAAATG
289511 CTA-ATATA
1 -TATATATA
289519 CCTTGCACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (22 bp):
TATATATATGTATATACAAATG
Found at i:289835 original size:2 final size:2
Alignment explanation
Indices: 289830--289877 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
289820 ATATATGCGA
* * * *
289830 AT AT AT AT AT TT AT AT AC AT AT GT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
289872 AT AT AT
1 AT AT AT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Done.