Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014115.1 Kokia drynarioides strain JFW-HI SEQ_129148, 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: 337767
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 396 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:275221 original size:20 final size:19
Alignment explanation
Indices: 275176--275213 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
275166 GAGGGGGAGA
*
275176 GCGAGGGGGGTCATTAGGT
1 GCGAAGGGGGTCATTAGGT
275195 GCGAAGGGGGTCATTAGGT
1 GCGAAGGGGGTCATTAGGT
275214 TGTTAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.50, T:0.21
Consensus pattern (19 bp):
GCGAAGGGGGTCATTAGGT
Found at i:276370 original size:31 final size:32
Alignment explanation
Indices: 276318--276441 Score: 96
Period size: 31 Copynumber: 4.0 Consensus size: 32
276308 ATTTGGTGTC
276318 TATATTTTTGGCTCAATTTGATACCTAAACTT
1 TATATTTTTGGCTCAATTTGATACCTAAACTT
* * *
276350 TATATTTTT-TCTTAATTTGATACTTAAAC-T
1 TATATTTTTGGCTCAATTTGATACCTAAACTT
* * * *
276380 T-T-TTTTGGGCACAATTTGATACTTGAACTT
1 TATATTTTTGGCTCAATTTGATACCTAAACTT
* * ** * *
276410 GACATTTTTTCCT-AATTTGGTACCTAAGCTT
1 TATATTTTTGGCTCAATTTGATACCTAAACTT
276441 T
1 T
276442 TTTTAGGTTC
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
28 4 0.06
29 17 0.25
30 3 0.04
31 31 0.45
32 14 0.20
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (32 bp):
TATATTTTTGGCTCAATTTGATACCTAAACTT
Found at i:276409 original size:60 final size:59
Alignment explanation
Indices: 276322--276460 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
276312 GGTGTCTATA
* * * *
276322 TTTTTGGCTCAATTTGATACCTAAACTTTATATTTTTTCTTAATTTGATACTTAAACTT
1 TTTTTGGCTCAATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACCTAAACTT
* * * * *
276381 TTTTTGGGCACAATTTGATACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAGCTT
1 TTTTT-GGCTCAATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACCTAAACTT
*
276441 TTTTTAGGTTCAATTTGATA
1 TTTTT-GGCTCAATTTGATA
276461 TTTAAAATTA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 5 0.07
60 62 0.93
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.50
Consensus pattern (59 bp):
TTTTTGGCTCAATTTGATACCTAAACTTGACATTTTTTCCTAATTTGATACCTAAACTT
Found at i:276977 original size:32 final size:31
Alignment explanation
Indices: 276897--276978 Score: 74
Period size: 32 Copynumber: 2.6 Consensus size: 31
276887 GGACCCCAAA
* * *
276897 AAGTTTAAATACCAACTTAAGAAATAGTGTT
1 AAGTTTAAATACCAAATTAAGAAAAAGTGTC
* ** * **
276928 AAGTTCAGGTACTAAATTTCGAAAAAAGTGTC
1 AAGTTTAAATACCAAATTAAG-AAAAAGTGTC
276960 AAGTTTAAATACCAAATTA
1 AAGTTTAAATACCAAATTA
276979 GATTAAAAAA
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
31 14 0.39
32 22 0.61
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (31 bp):
AAGTTTAAATACCAAATTAAGAAAAAGTGTC
Found at i:277458 original size:13 final size:14
Alignment explanation
Indices: 277440--277468 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
277430 TTTGATCTTG
277440 TTTTATTT-TTTAT
1 TTTTATTTATTTAT
277453 TTTTATTTATTTAT
1 TTTTATTTATTTAT
277467 TT
1 TT
277469 ATTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:278749 original size:35 final size:36
Alignment explanation
Indices: 278698--278774 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
278688 CCTCTTATAT
* *
278698 TTTATTTATTTATTTAATTTGCATGATTTT-ATTTA
1 TTTAATTAGTTATTTAATTTGCATGATTTTAATTTA
*
278733 TTTAATTAGTTATTTAATTTGCATGATTTTAATTTG
1 TTTAATTAGTTATTTAATTTGCATGATTTTAATTTA
278769 TTTAAT
1 TTTAAT
278775 CTGCATGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 28 0.74
36 10 0.26
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (36 bp):
TTTAATTAGTTATTTAATTTGCATGATTTTAATTTA
Found at i:278779 original size:24 final size:24
Alignment explanation
Indices: 278745--278790 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
278735 TAATTAGTTA
*
278745 TTTAATTTGCATGATTTTAATTTG
1 TTTAATCTGCATGATTTTAATTTG
278769 TTTAATCTGCATGATTTTAATT
1 TTTAATCTGCATGATTTTAATT
278791 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.57
Consensus pattern (24 bp):
TTTAATCTGCATGATTTTAATTTG
Found at i:284556 original size:21 final size:21
Alignment explanation
Indices: 284532--284580 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
284522 ACTATGACAG
* * *
284532 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
* *
284553 TTCTGCCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
284574 TTCTACC
1 TTCTACC
284581 AGTACTAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:293497 original size:18 final size:18
Alignment explanation
Indices: 293474--293509 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
293464 GGAGTGCAAC
293474 AATTTTCATGGGTACACA
1 AATTTTCATGGGTACACA
293492 AATTTTCATGGGTACACA
1 AATTTTCATGGGTACACA
293510 TCAGGCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (18 bp):
AATTTTCATGGGTACACA
Found at i:294549 original size:50 final size:49
Alignment explanation
Indices: 294495--294733 Score: 140
Period size: 51 Copynumber: 4.8 Consensus size: 49
294485 GAGTGAAGTT
**
294495 ACGAAACCAAATTCTATATCCCTGAAGTTACAGTGGACCAGATTGAAGCC
1 ACGAAACCAAATTCTATATCCCTGAAGTTGTAGTGGACCAGA-TGAAGCC
** * ** * *
294545 ACGAAGGCAAA-TCTTTATCTCTCTGAAGTTGTAGTAAAGCAGGATGAAGCT
1 ACGAAACCAAATTCTATATC-C-CTGAAGTTGTAGTGGACCA-GATGAAGCC
* * * * ** * * *
294596 ACAAAACCAAATCCTATACCCCTGAAGTTATAGTGGGTCGGATTAAAGTC
1 ACGAAACCAAATTCTATATCCCTGAAGTTGTAGTGGACCAGA-TGAAGCC
* * * * * *
294646 ATGAAAGCAAATCTTTATCTCCCTGAAGTTGTAGTGGAGCAAGATGAAGCT
1 ACGAAACCAAAT-TCTATATCCCTGAAGTTGTAGTGGA-CCAGATGAAGCC
* * * *
294697 ACAAAACCAAATCCTATA-CCACTGCAGTTGCAGTGGA
1 ACGAAACCAAATTCTATATCC-CTGAAGTTGTAGTGGA
294734 TTGGATTAAA
Statistics
Matches: 134, Mismatches: 47, Indels: 16
0.68 0.24 0.08
Matches are distributed among these distances:
49 11 0.08
50 53 0.40
51 61 0.46
52 9 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (49 bp):
ACGAAACCAAATTCTATATCCCTGAAGTTGTAGTGGACCAGATGAAGCC
Found at i:294607 original size:51 final size:50
Alignment explanation
Indices: 294469--294709 Score: 147
Period size: 51 Copynumber: 4.8 Consensus size: 50
294459 ATCTCCATTA
* * * * *
294469 AAGTTGTAGTG-GAATGGAGTGAAGTTACGAAACCAAAT-TCTATATCCCTG
1 AAGTTGTAGTGAGCA-GGA-TGAAGCTACAAAACCAAATCTTTATCTCCCTG
** * * * ** *
294519 AAGTTACAGTGGACCA-GATTGAAGCCACGAAGGCAAATCTTTATCTCTCTG
1 AAGTTGTAGT-GAGCAGGA-TGAAGCTACAAAACCAAATCTTTATCTCCCTG
* *
294570 AAGTTGTAGTAAAGCAGGATGAAGCTACAAAACCAAATC-CTATAC-CCCTG
1 AAGTTGTAGT-GAGCAGGATGAAGCTACAAAACCAAATCTTTAT-CTCCCTG
* * * *
294620 AAGTTATAGTGGGTC-GGATTAAAG-T-CATGAAAGCAAATCTTTATCTCCCTG
1 AAGTTGTAGTGAG-CAGGA-TGAAGCTACA--AAACCAAATCTTTATCTCCCTG
*
294671 AAGTTGTAGTGGAGCAAGATGAAGCTACAAAACCAAATC
1 AAGTTGTAGT-GAGCAGGATGAAGCTACAAAACCAAATC
294710 CTATACCACT
Statistics
Matches: 142, Mismatches: 34, Indels: 29
0.69 0.17 0.14
Matches are distributed among these distances:
48 2 0.01
49 5 0.04
50 56 0.39
51 69 0.49
52 8 0.06
53 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (50 bp):
AAGTTGTAGTGAGCAGGATGAAGCTACAAAACCAAATCTTTATCTCCCTG
Found at i:294656 original size:101 final size:101
Alignment explanation
Indices: 294488--294840 Score: 420
Period size: 101 Copynumber: 3.5 Consensus size: 101
294478 TGGAATGGAG
* * * * * * * * * *
294488 TGAAGTTACGAAACCAAATTCTATATCCCTGAAGTTACAGTGGACCAGATTGAAGCCACGAAGGC
1 TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTACAGTGGATCGGATTAAAGTCATGAAAGC
** *
294553 AAATCTTTATCTCTCTGAAGTTGTAGTAAAGCAGGA
66 AAATCTTTATCTCTCTGAAGTTGTAGTGGAGCAAGA
* *
294589 TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTATAGTGGGTCGGATTAAAGTCATGAAAGC
1 TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTACAGTGGATCGGATTAAAGTCATGAAAGC
*
294654 AAATCTTTATCTCCCTGAAGTTGTAGTGGAGCAAGA
66 AAATCTTTATCTCTCTGAAGTTGTAGTGGAGCAAGA
* * * * *
294690 TGAAGCTACAAAACCAAATCCTATACCACTGCAGTTGCAGTGGATTGGATTAAAGTCAT-AAAGT
1 TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTACAGTGGATCGGATTAAAGTCATGAAAGC
* * *
294754 AAATTTTTATCTCTCTGAAGCTGCAGTGGAGCAAGA
66 AAATCTTTATCTCTCTGAAGTTGTAGTGGAGCAAGA
* * * * * * *
294790 TGAAGCTACAACATCAAATCCTATATCCCTAAAGTTTCAATGGATTGGATT
1 TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTACAGTGGATCGGATT
294841 GAGTCTACAT
Statistics
Matches: 217, Mismatches: 35, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
100 79 0.36
101 138 0.64
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (101 bp):
TGAAGCTACAAAACCAAATCCTATACCCCTGAAGTTACAGTGGATCGGATTAAAGTCATGAAAGC
AAATCTTTATCTCTCTGAAGTTGTAGTGGAGCAAGA
Found at i:295303 original size:14 final size:14
Alignment explanation
Indices: 295284--295310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
295274 TTTATTATTT
295284 AATAAATATAAAAA
1 AATAAATATAAAAA
295298 AATAAATATAAAA
1 AATAAATATAAAA
295311 CAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATATAAAAA
Found at i:296538 original size:35 final size:36
Alignment explanation
Indices: 296473--296547 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 36
296463 CCTCTTATAT
* *
296473 TTTATTTATTTATTTATTTTACATGATTTT-ATTTA
1 TTTATTTAGTTATTTAATTTACATGATTTTAATTTA
* *
296508 TTTATTTAGTTATTTAATTTGCAT-ACTTTTAATTTG
1 TTTATTTAGTTATTTAATTTACATGA-TTTTAATTTA
296544 TTTA
1 TTTA
296548 ATTTGCATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.03
35 25 0.74
36 8 0.24
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.65
Consensus pattern (36 bp):
TTTATTTAGTTATTTAATTTACATGATTTTAATTTA
Found at i:296547 original size:24 final size:24
Alignment explanation
Indices: 296520--296565 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
296510 TATTTAGTTA
296520 TTTAATTTGCAT-ACTTTTAATTTG
1 TTTAATTTGCATGA-TTTTAATTTG
296544 TTTAATTTGCATGATTTTAATT
1 TTTAATTTGCATGATTTTAATT
296566 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.59
Consensus pattern (24 bp):
TTTAATTTGCATGATTTTAATTTG
Found at i:296795 original size:30 final size:29
Alignment explanation
Indices: 296747--296842 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
296737 CGATTGACAT
*
296747 TTATTGTCA-TTA-TTATTTTATTGTGTTA
1 TTATTGT-ATTTATTTATTTTATTTTGTTA
* *
296775 TTAATTGTATTTATTTATTTTATTTTATTCT
1 TT-ATTGTATTTATTTATTTTATTTTGTT-A
* *
296806 TGTATTGTTTTTATTTA-TTTATTTTGTCA
1 T-TATTGTATTTATTTATTTTATTTTGTTA
296835 TTATTGTA
1 TTATTGTA
296843 AATTATGTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.16
29 9 0.16
30 22 0.40
31 14 0.25
32 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (29 bp):
TTATTGTATTTATTTATTTTATTTTGTTA
Found at i:296798 original size:35 final size:35
Alignment explanation
Indices: 296745--296830 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
296735 ATCGATTGAC
*
296745 ATTTATTGTCATTATTATTTTATT-GTGTTATTAATTGT
1 ATTTATT-T-ATT-TTATTTTATTCTTG-TATTAATTGT
** *
296783 ATTTATTTATTTTATTTTATTCTTGTATTGTTTTT
1 ATTTATTTATTTTATTTTATTCTTGTATTAATTGT
296818 ATTTATTTATTTT
1 ATTTATTTATTTT
296831 GTCATTATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
35 30 0.70
36 5 0.12
37 1 0.02
38 7 0.16
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (35 bp):
ATTTATTTATTTTATTTTATTCTTGTATTAATTGT
Found at i:296830 original size:13 final size:13
Alignment explanation
Indices: 296763--296829 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
296753 TCATTATTAT
*
296763 TTTATTGT-GTTA
1 TTTATTGTATTTA
*
296775 TTAATTGTATTTA
1 TTTATTGTATTTA
*
296788 TTTATTTTATTT-
1 TTTATTGTATTTA
* *
296800 TATTCTTGTATTGTT
1 T-TTATTGTATT-TA
296815 TTTATT-TATTTA
1 TTTATTGTATTTA
296827 TTT
1 TTT
296830 TGTCATTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
12 12 0.28
13 25 0.58
14 5 0.12
15 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTATTGTATTTA
Found at i:299134 original size:10 final size:10
Alignment explanation
Indices: 299119--299151 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
299109 AATCACACCA
299119 TCTATATCAT
1 TCTATATCAT
299129 TCTATATCAT
1 TCTATATCAT
299139 TCTATATCAT
1 TCTATATCAT
299149 TCT
1 TCT
299152 TTTGGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.27, C:0.21, G:0.00, T:0.52
Consensus pattern (10 bp):
TCTATATCAT
Found at i:303844 original size:42 final size:40
Alignment explanation
Indices: 303773--303851 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 40
303763 TTTCTAAACC
303773 TAGGAACATGCCTTTTCTGTACAACTTAGCCAACTTAACT
1 TAGGAACATGCCTTTTCTGTACAACTTAGCCAACTTAACT
*
303813 TAGGAACATGCCTGTTTTTTGTACAACTTAGCCAACTTA
1 TAGGAACATGCC--TTTTCTGTACAACTTAGCCAACTTA
303852 TACCTTACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 12 0.33
42 24 0.67
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (40 bp):
TAGGAACATGCCTTTTCTGTACAACTTAGCCAACTTAACT
Found at i:310962 original size:130 final size:130
Alignment explanation
Indices: 310729--310988 Score: 520
Period size: 130 Copynumber: 2.0 Consensus size: 130
310719 CGGCTGAAGA
310729 TGCCTCTAAAAGGGTTTCAGAAATAGCTGCTGCTGCTGCTTCTTTCAGGCTTTGGTCCATTTGAA
1 TGCCTCTAAAAGGGTTTCAGAAATAGCTGCTGCTGCTGCTTCTTTCAGGCTTTGGTCCATTTGAA
310794 GATGAGAGGTATGGAGAAGATAATACCATCATCTAGGAATAAAGAGAACAGTAGAACACCCAGCC
66 GATGAGAGGTATGGAGAAGATAATACCATCATCTAGGAATAAAGAGAACAGTAGAACACCCAGCC
310859 TGCCTCTAAAAGGGTTTCAGAAATAGCTGCTGCTGCTGCTTCTTTCAGGCTTTGGTCCATTTGAA
1 TGCCTCTAAAAGGGTTTCAGAAATAGCTGCTGCTGCTGCTTCTTTCAGGCTTTGGTCCATTTGAA
310924 GATGAGAGGTATGGAGAAGATAATACCATCATCTAGGAATAAAGAGAACAGTAGAACACCCAGCC
66 GATGAGAGGTATGGAGAAGATAATACCATCATCTAGGAATAAAGAGAACAGTAGAACACCCAGCC
310989 ACAGATTGAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 130 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (130 bp):
TGCCTCTAAAAGGGTTTCAGAAATAGCTGCTGCTGCTGCTTCTTTCAGGCTTTGGTCCATTTGAA
GATGAGAGGTATGGAGAAGATAATACCATCATCTAGGAATAAAGAGAACAGTAGAACACCCAGCC
Found at i:312534 original size:18 final size:17
Alignment explanation
Indices: 312486--312536 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
312476 CCCCAAAAAA
*
312486 AATTTAAAAGTTTTTTTT
1 AATTTAAAA-TATTTTTT
* *
312504 AATTTTAATTATTTTTT
1 AATTTAAAATATTTTTT
312521 AAGTTTAAAATATTTT
1 AA-TTTAAAATATTTT
312537 GCTAATGTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
AATTTAAAATATTTTTT
Found at i:312843 original size:27 final size:28
Alignment explanation
Indices: 312783--312843 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
312773 TTATTATAAG
* *
312783 ATAAAA-TTTAATTTCATTAACATTTTT
1 ATAAAATTTTAATTACATTAACATTTTC
* *
312810 AT-TAATTTTAATTACTTTAA-ATTTTC
1 ATAAAATTTTAATTACATTAACATTTTC
312836 ATAAAATT
1 ATAAAATT
312844 ATTTTATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAAAATTTTAATTACATTAACATTTTC
Found at i:334354 original size:6 final size:6
Alignment explanation
Indices: 334345--334385 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
334335 GTTTTGTGAT
334345 TGTGCC TGTGCC TGTGCC TGTGCC TGTGCC TGTGCC TGTGC
1 TGTGCC TGTGCC TGTGCC TGTGCC TGTGCC TGTGCC TGTGC
334386 ATGAATGCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.34, T:0.34
Consensus pattern (6 bp):
TGTGCC
Found at i:337743 original size:2 final size:2
Alignment explanation
Indices: 337738--337767 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
337728 TAAAAAAAAT
337738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.