Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011818.1 Kokia drynarioides strain JFW-HI SEQ_126813, 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: 32200
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1509 original size:8 final size:8
Alignment explanation
Indices: 1496--1537 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
1486 CCACATAATA
1496 TTTTTTTC
1 TTTTTTTC
1504 TTTTTTTC
1 TTTTTTTC
*
1512 TTTTTCTC
1 TTTTTTTC
*
1520 ATATTTTTC
1 -TTTTTTTC
1529 TTTTTTTC
1 TTTTTTTC
1537 T
1 T
1538 CTACTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:1545 original size:19 final size:20
Alignment explanation
Indices: 1503--1546 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
1493 ATATTTTTTT
1503 CTTTTTTTCTTTTTCTCATA
1 CTTTTTTTCTTTTTCTCATA
1523 -TTTTTCTT-TTTTTCTC-TA
1 CTTTTT-TTCTTTTTCTCATA
1541 CTTTTT
1 CTTTTT
1547 ATCACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 18 0.82
20 2 0.09
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (20 bp):
CTTTTTTTCTTTTTCTCATA
Found at i:5115 original size:215 final size:214
Alignment explanation
Indices: 4292--6299 Score: 2213
Period size: 215 Copynumber: 9.4 Consensus size: 214
4282 AATCACATCA
* * * * * *
4292 CAAACTTTTACTAGTTCTTTTATAAC-TCTGATTCCTTAAAGTATTCGACACGATCCATTCTTTC
1 CAAACATTTACGAGTTCTTTTATAACTTC-GGTTCCTTAAAGTATTCAAGACGATCCATTCCTTC
* * * *** * * *
4356 GAGCAATTTTCTGAACAT-TCCATGGTGCGGGTATCACATCTTTTGGTCTAAAA-AGTTTATCAT
65 GACCAATTTTC-GAA-ATATCCATGCTCCGAAAATCGCATCATTTGGTC-AAAATAGTTTGTCAT
* * *
4419 TTTTTGAACAAGTTTTGGTCTTTGAATTAAAAATCTTATTTACGTGAGAATTGTTTCTCTCTTTG
127 TTTGTAAACAAATTTTGGTCTTTGAATTAAAAA-CTTATTTACGTGAGAATTGTTTCTCTC-TTG
*
4484 TTCTTGGATGGAA-TTCCGAACTTGT
190 TTCTTGGA-CGAACTTCCGAACTTGT
* * * * *
4509 CAAACATTTACGAGTTCTTTTATAACTTTGGTTCCTGAGAGTATTTAAGACGATCCATTCATTCG
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * *
4574 ACCAATTTTTGAACAT-TCCATTCT-CGAGAAATCGCATCATTTGGTCGAAATAGTTTGTCATTT
66 ACCAATTTTCGAA-ATATCCATGCTCCGA-AAATCGCATCATTTGGTCAAAATAGTTTGTCATTT
* * * *
4637 TGTAAACAACTTTTGGTCTTTAAATTAAAAACTTATTTACGTGAGAATTATTTATCTCTTGTTCT
129 TGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGTTCT
* *
4702 T-CATCGAACTTCCGAACTTGA
194 TGGA-CGAACTTCCGAACTTGT
* * *
4723 CAAACATTTATGAGTT-TTTTATAACGTCGGTT-CTTGAGAGTATTCAAGACGATCCATTCCTTC
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACGATCCATTCCTTC
* * * * *
4786 GACCAATTTCCTAAACATTCCATGCTCCAAAAATCGCATCATTTGGTCAAAATAGATTT-TTATT
65 GACCAATTTTCGAAATA-TCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAG-TTTGTCATT
* *
4850 TTGTAAACAACA-TTTGGTCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGAT
128 TTGTAAACAA-ATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTG-T
4914 TCTTGGACGAACTTCCGAACTTGT
191 TCTTGGACGAACTTCCGAACTTGT
* * ** * * *
4938 CAAATATTTACAAGTTCTTTTATAACTTTAGTTCCTTAAAGAATTCAAGACTATCCATTCCTTTG
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* *
5003 ACCAACTTTCGAAATATACCATGCTCCGAAAATCGCATCATTTGGTC-AAATTGTTTGTCATTTT
66 ACCAATTTTCGAAATAT-CCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTT
* * ** *
5067 GTACACAAATTTTGGTCTTTGAATTAAAAACTTATTTACATGAGAATTGTTTCAATCTTATTCTT
130 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGTTCTT
* * *
5132 CGACGAACTTTCGAACTCGT
195 GGACGAACTTCCGAACTTGT
* * * * * * *
5152 CAGATATTAACGAGTTCTTTTATAACTTTGGTT-TTTAAGAGTATTCAAGATGATCGATTCCTTC
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAA-AGTATTCAAGACGATCCATTCCTTC
* * * * *
5216 GACCAATTTTCTGAACAT-TCAATGCTCGGGAAATCGCATCAATTT-GTCTAAATAGTTTTTCAT
65 GACCAATTTTC-GAA-ATATCCATGCTCCGAAAATCGCATC-ATTTGGTCAAAATAGTTTGTCAT
* *
5279 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTTTCTTGGT
127 TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GT
*
5344 TCTTGGACGAACTTTCGAACTTGT
191 TCTTGGACGAACTTCCGAACTTGT
* * * * *
5368 CAAATATTTATGAGTTCTTTTATAACGTCAGTT-CTTGAGAGTATTCAAGACGATCCATTCCTTC
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTT-AAAGTATTCAAGACGATCCATTCCTTC
* * * * *
5432 TACCAATTTCCTAAACATTCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTTTCATTT
65 GACCAATTTTCGAAATA-TCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTGTCATTT
5497 TGTAAACAACA-TTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT-TCT-TT
129 TGTAAACAA-ATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT-TGTT
* *
5559 CTTGGATGAACTTCCGAAATTGT
192 CTTGGACGAACTTCCGAACTTGT
* * * * *
5582 TAAACATTTACGAGTTCTTTTCTGACTTCGGTTCCTTAAAGTATTCAAGACGATCCATACCTTTG
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* * * *
5647 ACTAATTTTCGGAACATA-CCATGCT-CGAGAAATCGTATCATTTGGTCAAATTA-TTTATCATT
66 ACCAATTTTC-GAA-ATATCCATGCTCCGA-AAATCGCATCATTTGGTCAAAATAGTTTGTCATT
** **
5709 TTGTAAACAACA-TTTGGTCTTTGAATTAAAAACTTAAATATTTGAGAATTGTTTCTCTCTTGGT
128 TTGTAAACAA-ATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTT-GT
* *
5773 TATTGGATGAACTT-CGAAACTTGT
191 TCTTGGACGAACTTCCG-AACTTGT
* * *
5797 -AAATTATTTA-GAGTTCTTTTATAACTTCGGTTCC-TAAGAGTATTGAAGACGATCCATTCATT
1 CAAA-CATTTACGAGTTCTTTTATAACTTCGGTTCCTTAA-AGTATTCAAGACGATCCATTCCTT
* * ** *
5859 CGACCAATTTTCCGAACAT-TCCTTTCTCAAAAAATCGCATCATTTGGTAAAAATAGTTTGTCAT
64 CGACCAATTTT-CGAA-ATATCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTGTCAT
* *
5923 TTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTAGTTACGTGAGAATTGTTTCTCTCTTGTT
127 TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGTT
*
5988 CTTCGACGAACTTCCGAACTTGT
192 CTTGGACGAACTTCCGAACTTGT
* * * *
6011 GAAACATTTACAAGTTCTTTTATAACTTCGATTCCTGAAAGTATTCAAGACGATCCATTCCTTCG
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
* ** * ** *
6076 ACCAATTTTCCGAACAT-TCCATTCTTGGGAAATCTTATCATTTGGTCAAAATAGTTTTTCATTT
66 ACCAATTTT-CGAA-ATATCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTGTCATTT
* * * * ** *
6140 TATAAGCAACTTTTGGTCTTTGAATTAAAAACTAATTTACAAGACAATTGTTTCTCTCTTGTTCT
129 TGTAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGTTCT
* ** * *
6205 TCGACGTGCTTCAGAACTTAT
194 TGGACGAACTTCCGAACTTGT
* * *
6226 CAAACATTTACAAGTTCTTTAAT-ACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTTG
1 CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
*
6290 ACCAACTTTC
66 ACCAATTTTC
6300 AGAATATACC
Statistics
Matches: 1539, Mismatches: 204, Indels: 100
0.84 0.11 0.05
Matches are distributed among these distances:
212 3 0.00
213 129 0.08
214 503 0.33
215 513 0.33
216 325 0.21
217 65 0.04
218 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (214 bp):
CAAACATTTACGAGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAAGACGATCCATTCCTTCG
ACCAATTTTCGAAATATCCATGCTCCGAAAATCGCATCATTTGGTCAAAATAGTTTGTCATTTTG
TAAACAAATTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGTTCTTG
GACGAACTTCCGAACTTGT
Found at i:6430 original size:5 final size:5
Alignment explanation
Indices: 6420--6458 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
6410 AGGATAATTT
6420 TTTTC TTTTC TTTTTC TTTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC -TTTTC -TTTTC TTTTC TTTTC TTTTC TT
6459 GTTTGAACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:6435 original size:11 final size:11
Alignment explanation
Indices: 6419--6455 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
6409 GAGGATAATT
6419 TTTTTCTTTTC
1 TTTTTCTTTTC
6430 TTTTTCTTTT-
1 TTTTTCTTTTC
6440 TCTTTTCTTTTC
1 T-TTTTCTTTTC
6452 TTTT
1 TTTT
6456 CTTGTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:16232 original size:23 final size:24
Alignment explanation
Indices: 16189--16233 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16179 ACTAGCCTTC
16189 TTTTTTTTATACTTTCGAAACTCT
1 TTTTTTTTATACTTTCGAAACTCT
16213 TTTTTTTTAATA-TTTC-AAACT
1 TTTTTTTT-ATACTTTCGAAACT
16234 TTGCACTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTTTTATACTTTCGAAACTCT
Found at i:16300 original size:14 final size:15
Alignment explanation
Indices: 16268--16304 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
16258 ATTCTCTCTC
*
16268 TTTTTCATGAATTAT
1 TTTTTCACGAATTAT
16283 TTTTTCACGAATTAT
1 TTTTTCACGAATTAT
16298 TTTTTCA
1 TTTTTCA
16305 AGAACTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTTTCACGAATTAT
Found at i:20128 original size:41 final size:41
Alignment explanation
Indices: 20077--20160 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
20067 TTAAATAGGG
*
20077 TTTTAGTGTGTCATAGTTTGATACATATTTAATAGTTGTTT
1 TTTTAATGTGTCATAGTTTGATACATATTTAATAGTTGTTT
* *
20118 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTGTTT
1 TTTTAATGTGTCATAGTTTGATACATATTTAATAGTTGTTT
20159 TT
1 TT
20161 AAGGTGTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (41 bp):
TTTTAATGTGTCATAGTTTGATACATATTTAATAGTTGTTT
Found at i:20177 original size:39 final size:40
Alignment explanation
Indices: 20091--20177 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 40
20081 AGTGTGTCAT
* *
20091 AGTTTGATACATATTTAATAGTTGTTTTTTTAATGTGTCTT
1 AGTTTGATACATATTTAATAGTTG-TTTTTTAAGGTGTCTA
*
20132 ATTTTGATACATATTTAATAGTTG-TTTTTAAGGTGTCTA
1 AGTTTGATACATATTTAATAGTTGTTTTTTAAGGTGTCTA
20171 AGTTTGA
1 AGTTTGA
20178 GACAAATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 19 0.45
41 23 0.55
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (40 bp):
AGTTTGATACATATTTAATAGTTGTTTTTTAAGGTGTCTA
Found at i:23438 original size:50 final size:49
Alignment explanation
Indices: 23355--23482 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 49
23345 TGCATGACTT
*
23355 GATTTAATGATGC-ATTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAATTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * *
23404 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCA-ATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
23454 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGC-AATTTAACTAA-CATG
23483 AGAGTTAATG
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
48 7 0.10
49 6 0.09
50 50 0.74
51 5 0.07
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (49 bp):
GATTTATGATGCAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:24225 original size:69 final size:69
Alignment explanation
Indices: 24107--24242 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 69
24097 CGATACTCTG
* * * * * *
24107 AACTTGTCAAACATTTACGATTTTTTTTATAACTTCGGTTCTTGTGAGTATTCAAGATGATCCAT
1 AACTTGTCAAACATTCACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
24172 TCCA
66 TCCA
** *
24176 AACTTGTCAATTATTCACGAGTTCTTTTATAACTTCTGTTCCTGAGAGTATTCAAGACGATCCAT
1 AACTTGTCAAACATTCACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
24241 TC
66 TC
24243 TTTCGACCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (69 bp):
AACTTGTCAAACATTCACGAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATCCAT
TCCA
Found at i:24400 original size:285 final size:285
Alignment explanation
Indices: 23890--24459 Score: 854
Period size: 285 Copynumber: 2.0 Consensus size: 285
23880 ACGAACTTCT
* **
23890 AAACTTGTCAATTATTTACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATTGA
1 AAACTTGTCAATTATTCACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCCA
** **
23955 TTCCTTCGACAAATTTTCTAAATATTTCCTGATAGGGAAATCGTATCATTTGGTCCAAAAAGTTT
66 TTCCTTCGACAAATTTTCTAAATATTTCCTGATAGGGAAATCCCAAAATTTGGTCCAAAAAGTTT
* *
24020 GCCATTTTGTAAAAAACTTTTGGTCTTCGAATTAAAAACTTATTTACATGAGAATTGTTTCTCTC
131 GCCATTTTATAAAAAACTTTTGGTCTTCGAATTAAAAACTTATTTACATGAGAATTGTTTCTATC
* * * * *
24085 TTGCATCTTGGACGATACTCTGAACTTGTCAAACATTTACGATTTTTTTTATAACTTCGGTTCTT
196 TTGCATCTTGGACGAAACTCTAAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGATTCCT
*
24150 GTGAGTATTCAAGATGATCCATTCC
261 GTGAGTAGTCAAGATGATCCATTCC
*
24175 AAACTTGTCAATTATTCACGAGTTCTTTTATAACTTCTGTTCCTGAGAGTATTCAAGACGATCCA
1 AAACTTGTCAATTATTCACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCCA
* * * * * *
24240 TTCTTTCGACCAATTTT-TCGAATATTTCTTGCTAGGGAAATCCCAAAATTTGGTCTAAAAAGTT
66 TTCCTTCGACAAATTTTCT-AAATATTTCCTGATAGGGAAATCCCAAAATTTGGTCCAAAAAGTT
* * * *
24304 TTCCATTTTATAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGATAATTGTTTCTAT
130 TGCCATTTTATAAAAAACTTTTGGTCTTCGAATTAAAAACTTATTTACATGAGAATTGTTTCTAT
* * *
24369 CTTGCTTCTTGGATGAAATTCTAAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGATTCC
195 CTTGCATCTTGGACGAAACTCTAAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGATTCC
*
24434 TGTGAGTAGTCAAGATGTTCCATTCC
260 TGTGAGTAGTCAAGATGATCCATTCC
24460 TTAAACAAAT
Statistics
Matches: 254, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
284 1 0.00
285 253 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (285 bp):
AAACTTGTCAATTATTCACGAGTTCTTTTATAACTTCAGTTCCTGAGAGTATTCAAGACGATCCA
TTCCTTCGACAAATTTTCTAAATATTTCCTGATAGGGAAATCCCAAAATTTGGTCCAAAAAGTTT
GCCATTTTATAAAAAACTTTTGGTCTTCGAATTAAAAACTTATTTACATGAGAATTGTTTCTATC
TTGCATCTTGGACGAAACTCTAAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGATTCCT
GTGAGTAGTCAAGATGATCCATTCC
Found at i:24550 original size:216 final size:212
Alignment explanation
Indices: 24170--24798 Score: 672
Period size: 216 Copynumber: 2.9 Consensus size: 212
24160 AAGATGATCC
** * * *
24170 ATTCCAAACTTGTCAATTATTCACGAGTTCTTTTATAACTTCTGTTCCTGAGAGTATTCAAGACG
1 ATTCCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTC-GTTCCTGTGAGTATTCAAGATG
* * * * * **
24235 ATCCATTCTTTCGACCAATTTTTCGAATATTTCTTGCTAGGGAAATCCCAAAATTTGGTCTAAA-
65 ATCCATTCCTTCGACCAATTTTT-GAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAAT
* * * * *
24299 AAGTTTTCCATTTTATAAAAAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGATAATTGTT
129 AA-TTTTTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATT
* * *
24364 TCTATCTTGCTTCTTGGATGAA
193 TC--TCTCGATTCTTGGACGAA
* * *
24386 ATTCTAAACTTGTCAAACATTTACGATTTCTTTTATAACTTCGATTCCTGTGAGTAGTCAAGATG
1 ATTCCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCG-TTCCTGTGAGTATTCAAGATG
* ** * * *
24451 TTCCATTCCTTAAACAAATTTTCTGAACATTCCATGATCGGGAAATCGCATCATTTGGTCTAAAT
65 ATCCATTCCTTCGACCAATTTT-TGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAAT
* *
24516 AATTTTTCATTTTGGAAACAACTTTTGTTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTT
129 AATTTTTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTT
*
24581 CTCTCGATTTTTGGACGAA
194 CTCTCGATTCTTGGACGAA
* * * *
24600 CTTCCGAACTTGTCAAAATTCAAAATTTTACAAGTTCTTTTATAACTTAGGTT--TGTAAGAGTA
1 ATTCCAAACTTGTC-AAA--C---A-TTTACGAGTTCTTTTATAACTT-CGTTCCTGT--GAGTA
* * *
24663 TTCAAGATGATCCATTCCTTCGACCAATTTTTTGAACTTTCCATGCTTGAGAAATCGCATCAATT
56 TTCAAGATGATCCATTCCTTCGACCAA-TTTTTGAACATTCCATGCTAGGGAAATCGCATC-ATT
* * * *
24728 T-GTCTAAATAGTTTGTCATTTTGTAAACAACTTTTGGTATTTGAATTAAAAACTTATTTACATG
119 TGGTCTAAATAATTTTTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTG
24792 AGAATTA
184 AGAATTA
24799 AAGCTCAGAA
Statistics
Matches: 345, Mismatches: 53, Indels: 25
0.82 0.13 0.06
Matches are distributed among these distances:
214 25 0.07
215 4 0.01
216 161 0.47
217 4 0.01
219 3 0.01
220 1 0.00
221 138 0.40
222 9 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (212 bp):
ATTCCAAACTTGTCAAACATTTACGAGTTCTTTTATAACTTCGTTCCTGTGAGTATTCAAGATGA
TCCATTCCTTCGACCAATTTTTGAACATTCCATGCTAGGGAAATCGCATCATTTGGTCTAAATAA
TTTTTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTCT
CTCGATTCTTGGACGAA
Found at i:27582 original size:15 final size:15
Alignment explanation
Indices: 27564--27602 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27554 TGGAAGATGT
27564 GAGCACTGGTGTTAC
1 GAGCACTGGTGTTAC
**
27579 GAGCACTCATGTTAC
1 GAGCACTGGTGTTAC
*
27594 GAACACTGG
1 GAGCACTGG
27603 AGCTACGAAC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (15 bp):
GAGCACTGGTGTTAC
Found at i:31930 original size:3 final size:3
Alignment explanation
Indices: 31924--31951 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31914 AAAAATTCAA
31924 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
31952 GCTAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.