Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015001.1 Kokia drynarioides strain JFW-HI SEQ_130045, 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: 675174
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 656 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:468828 original size:17 final size:18
Alignment explanation
Indices: 468792--468829 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
468782 ACGTTATAAA
**
468792 TAAAATTAGTAAAATTAT
1 TAAAATTAGTAAAAAAAT
468810 TAAAATTA-TAAAAAAAT
1 TAAAATTAGTAAAAAAAT
468827 TAA
1 TAA
468830 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TAAAATTAGTAAAAAAAT
Found at i:468834 original size:12 final size:12
Alignment explanation
Indices: 468811--468840 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
468801 TAAAATTATT
468811 AAAATT-ATAAA
1 AAAATTAATAAA
468822 AAAATTAATAAA
1 AAAATTAATAAA
468834 AAAATTA
1 AAAATTA
468841 TTATTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATTAATAAA
Found at i:473744 original size:21 final size:22
Alignment explanation
Indices: 473711--473751 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
473701 GTCGCTTTAA
*
473711 AAATATTTGTATA-ATTTTTTG
1 AAATATTTATATATATTTTTTG
*
473732 AAATTTTTATATATATTTTT
1 AAATATTTATATATATTTTT
473752 AAGAAGAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
AAATATTTATATATATTTTTTG
Found at i:485727 original size:16 final size:14
Alignment explanation
Indices: 485698--485745 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
485688 TAAAATGATG
485698 TAAAAGTTTTTAAAAA
1 TAAAA-TTTTT-AAAA
485714 TAAAATTTTATAAAA
1 TAAAATTTT-TAAAA
* *
485729 TAAAATCTTAAAAA
1 TAAAATTTTTAAAA
485743 TAA
1 TAA
485746 TTAATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.24
15 16 0.55
16 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
TAAAATTTTTAAAA
Found at i:485728 original size:15 final size:14
Alignment explanation
Indices: 485705--485755 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
485695 ATGTAAAAGT
485705 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
485719 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
*
485734 TCTTAAAAATAATTAA
1 TTTTAAAAATAA--AA
485750 TTTTAA
1 TTTTAA
485756 TAACGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:486092 original size:15 final size:14
Alignment explanation
Indices: 486069--486119 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
486059 TGTGAAAGTT
486069 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
486083 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
*
486098 TCTTAAAAATAATTAA
1 TTTTAAAAATAA--AA
486114 TTTTAA
1 TTTTAA
486120 TAACGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:486471 original size:15 final size:15
Alignment explanation
Indices: 486448--486489 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
486438 TGTGAAAGTT
*
486448 TTTTTTAAAATAAAA
1 TTTTATAAAATAAAA
486463 TTTTATAAAATAAAA
1 TTTTATAAAATAAAA
*
486478 TCTTA-AAAATAA
1 TTTTATAAAATAA
486490 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTATAAAATAAAA
Found at i:486568 original size:380 final size:368
Alignment explanation
Indices: 485579--486600 Score: 1635
Period size: 364 Copynumber: 2.8 Consensus size: 368
485569 TCCTCAGATT
* * * *
485579 TTAAGGAGTAAAATTCAATTAGACATTTCCCAAATATAAATTATGATAGTAAATTTACATTGTAG
1 TTAAGGAGTAAAATTCAATTAGATATTTGCTAAATATAAATTATGAT-GTAAATTTACATTTTAG
* * *
485644 CCTTTTTTTTATATAATTTTTAATACTATGCCTTAATCCAT-AGCTAAAATGATGTAAAAG-TTT
65 CC--CTTTTTATATAATTTTTAATACTATGCCTTAATCAATGA-CTAAAATGATGTGAAAGTTTT
485707 TTAAAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAG
127 TTAAAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAG
*
485772 AATTTCTTAATTAAACTACGAAATTTATGTCAACAAATTAGGGATTTTAATTTTAAATCCGATAG
192 AATTTCTTAATTAAACTACGAAATTTATGTCAACAAATTAGGGATTTCAATTTTAAATCCGATAG
485837 GATAAAAAGATAAAATCATGAGTTGGTCATATCCAAATTATATTTTGCTTCATTTTAATTAATTG
257 GATAAAAAGATAAAATCATGAGTTGGTCATATCCAAATTATATTTTGCTTCATTTTAATTAATTG
485902 TGATAGAAATATTTTTATTCCATTTTTATGTCGGTCAACGAAAAATG
322 TGATAGAAATATTTTTATTCCATTTTTATGTCGGTCAACGAAAAATG
*
485949 TTAAGGAGTAAAATTCAATTAGATATTTG-TCAAATATAAA-T-T-AT-TAAATTTACATTTTAA
1 TTAAGGAGTAAAATTCAATTAGATATTTGCT-AAATATAAATTATGATGTAAATTTACATTTTAG
486009 CCCTTTTTATATAATTTTTAATACTATGCCTTAATCAATGACTAAAATGATGTGAAAGTTTTTTA
65 CCCTTTTTATATAATTTTTAATACTATGCCTTAATCAATGACTAAAATGATGTGAAAGTTTTTTA
486074 AAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAGAAT
130 AAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAGAAT
* *
486139 TTCTTAATTAAACTACGAAATTTATGCCAACAAATTAGGGATCTCAATTTTAAATCCGATAGGAT
195 TTCTTAATTAAACTACGAAATTTATGTCAACAAATTAGGGATTTCAATTTTAAATCCGATAGGAT
* * *
486204 AAAAGGATAAAATCATGATTTGGTCATATCTAAATTATCCAAATTATATTTTGTTTCATTTTAAT
260 AAAAAGATAAAATCATGAGTTGG-----TC---A-TATCCAAATTATATTTTGCTTCATTTTAAT
* *
486269 TAATTGTGATAGAAATTTTTTTATTTCATTTTTATGTCGGTCAACGAAAAAATG
316 TAATTGTGATAGAAATATTTTTATTCCATTTTTATGTCGGTCAACG-AAAAATG
486323 TTAAGGAGTAAAATTCAATTAGATATTTGCTAAATATAAATTATGATGGTAAATTTACATTTTAG
1 TTAAGGAGTAAAATTCAATTAGATATTTGCTAAATATAAATTATGAT-GTAAATTTACATTTTAG
* * *
486388 CCCCTTTTGTATAATTTTTAATACTATGTCTTAATCAATGACTAAAATGATGTGAAAGTTTTTTT
65 CCCTTTTTATATAATTTTTAATACTATGCCTTAATCAATGACTAAAATGATGTGAAAG-TTTTTT
*
486453 TAAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAGAA
129 AAAAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAGAA
* * *
486518 TTTCTTAATTAAATTACGAAATTAATGTCAACAAATTAAGGATTTCAATTTTAAATCCGATAGGA
194 TTTCTTAATTAAACTACGAAATTTATGTCAACAAATTAGGGATTTCAATTTTAAATCCGATAGGA
486583 TAAAAAGATAAAATCATG
259 TAAAAAGATAAAATCATG
486601 CTTATGATAT
Statistics
Matches: 605, Mismatches: 27, Indels: 30
0.91 0.04 0.05
Matches are distributed among these distances:
363 51 0.08
364 155 0.26
365 16 0.03
367 2 0.00
368 1 0.00
369 3 0.00
370 36 0.06
372 1 0.00
373 73 0.12
374 45 0.07
375 2 0.00
376 1 0.00
377 2 0.00
379 70 0.12
380 147 0.24
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (368 bp):
TTAAGGAGTAAAATTCAATTAGATATTTGCTAAATATAAATTATGATGTAAATTTACATTTTAGC
CCTTTTTATATAATTTTTAATACTATGCCTTAATCAATGACTAAAATGATGTGAAAGTTTTTTAA
AAATAAAATTTTATAAAATAAAATCTTAAAAATAATTAATTTTAATAACGAAAATAAATAGAATT
TCTTAATTAAACTACGAAATTTATGTCAACAAATTAGGGATTTCAATTTTAAATCCGATAGGATA
AAAAGATAAAATCATGAGTTGGTCATATCCAAATTATATTTTGCTTCATTTTAATTAATTGTGAT
AGAAATATTTTTATTCCATTTTTATGTCGGTCAACGAAAAATG
Found at i:489879 original size:14 final size:14
Alignment explanation
Indices: 489860--489917 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
489850 TGAATGTTTG
489860 CATGACATAGTATA
1 CATGACATAGTATA
489874 CATGACATAG-ATA
1 CATGACATAGTATA
** * *
489887 TTTGA-AT-GTTTG
1 CATGACATAGTATA
*
489899 CATAACATAGTATA
1 CATGACATAGTATA
489913 CATGA
1 CATGA
489918 GACTTCTTAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
11 1 0.03
12 5 0.16
13 8 0.26
14 17 0.55
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (14 bp):
CATGACATAGTATA
Found at i:491726 original size:2 final size:2
Alignment explanation
Indices: 491721--491745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
491711 AAAAAAAAAA
491721 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
491746 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:513972 original size:22 final size:23
Alignment explanation
Indices: 513933--513977 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
513923 AAGATTTATA
*
513933 ATTTTTAGTGATTGATTTAGTAAT
1 ATTTTTAGT-ATTAATTTAGTAAT
*
513957 ATTTTTAGT-TTAATTTGGTAA
1 ATTTTTAGTATTAATTTAGTAA
513978 ATTAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
24 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (23 bp):
ATTTTTAGTATTAATTTAGTAAT
Found at i:515009 original size:31 final size:32
Alignment explanation
Indices: 514920--515018 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
514910 TTCAGTATGA
* * *
514920 CAAGTATCAGCTAAATACTTTTTGGACAAGTT
1 CAAGTATCAACTAAATATTTTTTGAACAAGTT
* * *
514952 CACGTACCAACTAAATATTTTTTTGAACAATTT
1 CAAGTATCAACTAAATA-TTTTTTGAACAAGTT
*
514985 CAAGTATCAACTAGATA-TTTTTGAACAAGTT
1 CAAGTATCAACTAAATATTTTTTGAACAAGTT
515016 CAA
1 CAA
515019 AAGGCAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
31 16 0.29
32 14 0.25
33 26 0.46
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (32 bp):
CAAGTATCAACTAAATATTTTTTGAACAAGTT
Found at i:515454 original size:27 final size:28
Alignment explanation
Indices: 515406--515460 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
515396 TGAATTATGT
*
515406 TATTTATGTTCTCAATTATATT-ATTTA
1 TATTTATGTACTCAATTATATTAATTTA
*
515433 TATTTATGTACT-ATTTATTATTAATTTA
1 TATTTATGTACTCAATTA-TATTAATTTA
515461 AAAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 15 0.62
28 5 0.21
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (28 bp):
TATTTATGTACTCAATTATATTAATTTA
Found at i:524946 original size:22 final size:22
Alignment explanation
Indices: 524919--524960 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
524909 AAATGGATTT
524919 AATAGAAATTAAATAG-AATAAG
1 AATAG-AATTAAATAGTAATAAG
*
524941 AATAGAATTTAATAGTAATA
1 AATAGAATTAAATAGTAATA
524961 TAATTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (22 bp):
AATAGAATTAAATAGTAATAAG
Found at i:525008 original size:3 final size:3
Alignment explanation
Indices: 525000--525029 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
524990 ATTGTACCAA
525000 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
525030 GATACCAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:537530 original size:5 final size:5
Alignment explanation
Indices: 537520--537544 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
537510 ATAGATGGCT
537520 CCAAA CCAAA CCAAA CCAAA CCAAA
1 CCAAA CCAAA CCAAA CCAAA CCAAA
537545 AGAAAACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAA
Found at i:545211 original size:20 final size:21
Alignment explanation
Indices: 545188--545234 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
545178 TGCTTTAATA
545188 TTTAAAATAATAA-ACAT-TGT
1 TTTAAAATAATAATACATAT-T
*
545208 TTT-AAATATTAATACATATT
1 TTTAAAATAATAATACATATT
545228 TTTAAAA
1 TTTAAAA
545235 AAATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 8 0.35
20 11 0.48
21 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTAAAATAATAATACATATT
Found at i:549032 original size:19 final size:19
Alignment explanation
Indices: 548983--549038 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
548973 TTTCCATCTC
* *
548983 AAAAATTTATAAAAAAACT
1 AAAAAATTATAAATAAACT
*
549002 AAAGAATGTAT-AATAAACTT
1 AAAAAAT-TATAAATAAAC-T
549022 AAAAAATTATAAATAAA
1 AAAAAATTATAAATAAA
549039 AAAAAACTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAATAAACT
Found at i:566399 original size:13 final size:13
Alignment explanation
Indices: 566381--566406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
566371 TCGAAATTAA
566381 ATTATAATTTTAT
1 ATTATAATTTTAT
566394 ATTATAATTTTAT
1 ATTATAATTTTAT
566407 GATAGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATAATTTTAT
Found at i:569102 original size:48 final size:48
Alignment explanation
Indices: 569038--569151 Score: 140
Period size: 48 Copynumber: 2.4 Consensus size: 48
569028 AAAAGTACCG
* * **
569038 AAGTACTTAACAGAGGGCACA-TAAGTGCTGGGTAACAAAGGGCACACA
1 AAGTACTAAACAGAGGGCACACGAAGTGCT-AATAACAAAGGGCACACA
* * *
569086 AAGTGCTAATCAGAGGGCACACGAAGTGCTAATAACAGAGGGCACACA
1 AAGTACTAAACAGAGGGCACACGAAGTGCTAATAACAAAGGGCACACA
*
569134 CAGTACTAAACAGAGGGC
1 AAGTACTAAACAGAGGGC
569152 GCGCTAGTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 48 0.87
49 7 0.13
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.13
Consensus pattern (48 bp):
AAGTACTAAACAGAGGGCACACGAAGTGCTAATAACAAAGGGCACACA
Found at i:569130 original size:25 final size:25
Alignment explanation
Indices: 569045--569151 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 25
569035 CCGAAGTACT
* **
569045 TAACAGAGGGCACA-TAAGTGCTGGG
1 TAACAGAGGGCACACAAAGTGCT-AA
*
569070 TAACAAAGGGCACACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
569095 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
* *
569118 TAACAGAGGGCACACACAGTACT-A
1 TAACAGAGGGCACACAAAGTGCTAA
569142 -AACAGAGGGC
1 TAACAGAGGGC
569152 GCGCTAGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
23 31 0.44
24 1 0.01
25 31 0.44
26 7 0.10
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:573938 original size:16 final size:17
Alignment explanation
Indices: 573919--573986 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 17
573909 TAAATTTTAA
*
573919 TATTTTAAT-ATTTTTT
1 TATTTTTATAATTTTTT
* *
573935 TATTTTTATAATTGTTA
1 TATTTTTATAATTTTTT
573952 TA-TTTTATAATTTTTGT
1 TATTTTTATAATTTTT-T
* *
573969 AATTTTTAT-TTTTTTT
1 TATTTTTATAATTTTTT
573985 TA
1 TA
573987 AAAATTTGCG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
16 22 0.54
17 13 0.32
18 6 0.15
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTTATAATTTTTT
Found at i:573952 original size:9 final size:9
Alignment explanation
Indices: 573911--573977 Score: 54
Period size: 8 Copynumber: 8.0 Consensus size: 9
573901 TGTGGTAATA
*
573911 AATTTTAAT
1 AATTTTTAT
*
573920 -ATTTTAAT
1 AATTTTTAT
573928 -ATTTTT-T
1 AATTTTTAT
*
573935 TATTTTTAT
1 AATTTTTAT
*
573944 AATTGTTAT
1 AATTTTTAT
573953 -A-TTTTAT
1 AATTTTTAT
*
573960 AATTTTTGT
1 AATTTTTAT
573969 AATTTTTAT
1 AATTTTTAT
573978 TTTTTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 6 0.12
8 21 0.44
9 21 0.44
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
AATTTTTAT
Found at i:573954 original size:25 final size:25
Alignment explanation
Indices: 573926--573986 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
573916 TAATATTTTA
573926 ATATTTTTTTATTTTTATAATTGTT
1 ATATTTTTTTATTTTTATAATTGTT
* * * *
573951 ATATTTTATAATTTTTGTAATTTTT
1 ATATTTTTTTATTTTTATAATTGTT
*
573976 ATTTTTTTTTA
1 ATATTTTTTTA
573987 AAAATTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (25 bp):
ATATTTTTTTATTTTTATAATTGTT
Found at i:579859 original size:15 final size:16
Alignment explanation
Indices: 579818--579859 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
579808 GCTTGTACTG
*
579818 AAATTATTTTATTCTT
1 AAATTATTTTATCCTT
**
579834 AAATTCGTTTATCCTT
1 AAATTATTTTATCCTT
579850 -AATTATTTTA
1 AAATTATTTTA
579860 ATCTGTCTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (16 bp):
AAATTATTTTATCCTT
Found at i:585934 original size:40 final size:39
Alignment explanation
Indices: 585879--585957 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
585869 ATTTCTCCCA
585879 AGTATTACTGCATTACTGCTTTTTTTTGTGTGTGTGTGT
1 AGTATTACTGCATTACTGCTTTTTTTTGTGTGTGTGTGT
* * *
585918 NAGTATTACTGCATTACTGTTTTTTTTTTTTTGTGTGTGT
1 -AGTATTACTGCATTACTGCTTTTTTTTGTGTGTGTGTGT
585958 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.57
Consensus pattern (39 bp):
AGTATTACTGCATTACTGCTTTTTTTTGTGTGTGTGTGT
Found at i:592544 original size:6 final size:6
Alignment explanation
Indices: 592535--592566 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
592525 GCTTCTGCTC
*
592535 CCTCTG CCTCTG CCTCTG CCTCTG TCTCTG CC
1 CCTCTG CCTCTG CCTCTG CCTCTG CCTCTG CC
592567 CCAGTCTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
CCTCTG
Found at i:600676 original size:5 final size:5
Alignment explanation
Indices: 600668--600692 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
600658 TTTTATTATG
600668 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
600693 ACCTTCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:604793 original size:95 final size:95
Alignment explanation
Indices: 604681--604865 Score: 280
Period size: 95 Copynumber: 1.9 Consensus size: 95
604671 AGCAAATATA
* * * *
604681 TATACATGTAACAACTTAAATAACAACTAAAGGAGGATTAAAATGAAAGAACGAGAACTTATATG
1 TATACATGTAACAACTTAAATAAAAAATAAAGGAGGACTAAAATGAAAGAACGAGAACTTATAGG
* *
604746 GGATGAAATGTGATTGCAACTAATGGAGGG
66 GGATGAAATATGATTGCAACCAATGGAGGG
* * * *
604776 TATATATGTAATAACTTAAATAAAAAATAATGGAGGACTAAAATGAAAGAACGATAACTTATAGG
1 TATACATGTAACAACTTAAATAAAAAATAAAGGAGGACTAAAATGAAAGAACGAGAACTTATAGG
604841 GGATGAAATATGATTGCAACCAATG
66 GGATGAAATATGATTGCAACCAATG
604866 CCAAAAAGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (95 bp):
TATACATGTAACAACTTAAATAAAAAATAAAGGAGGACTAAAATGAAAGAACGAGAACTTATAGG
GGATGAAATATGATTGCAACCAATGGAGGG
Found at i:604884 original size:46 final size:46
Alignment explanation
Indices: 604834--604928 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
604824 GAACGATAAC
604834 TTATAGGGGATGAAATATGATTGCAACCAATGCCAAAAAGATAATG
1 TTATAGGGGATGAAATATGATTGCAACCAATGCCAAAAAGATAATG
604880 TTATAGGGGATGAAATATGATTGCAACCAATGCCAAAAAGATAATG
1 TTATAGGGGATGAAATATGATTGCAACCAATGCCAAAAAGATAATG
604926 TTA
1 TTA
604929 CCAAGAAAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (46 bp):
TTATAGGGGATGAAATATGATTGCAACCAATGCCAAAAAGATAATG
Found at i:607538 original size:70 final size:70
Alignment explanation
Indices: 607450--607589 Score: 264
Period size: 71 Copynumber: 2.0 Consensus size: 70
607440 AGGGCAACAT
607450 GATGCCTCCATTTCTCC-TTTTTTTTTTTTCAAATGATCGTGGCAAAATGATGGGTGAATTTTTT
1 GATGCCTCCATTTCTCCTTTTTTTTTTTTTCAAATGATCGTGGCAAAATGATGGGTGAATTTTTT
607514 ATGTC
66 ATGTC
607519 NGATGCCTCCATTTCTCCTTTTTTTTTTTTTCAAATGATCGTGGCAAAATGATGGGTGAATTTTT
1 -GATGCCTCCATTTCTCCTTTTTTTTTTTTTCAAATGATCGTGGCAAAATGATGGGTGAATTTTT
607584 TATGTC
65 TATGTC
607590 ATTTTCCCCA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 17 0.25
71 52 0.75
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.46
Consensus pattern (70 bp):
GATGCCTCCATTTCTCCTTTTTTTTTTTTTCAAATGATCGTGGCAAAATGATGGGTGAATTTTTT
ATGTC
Found at i:608682 original size:16 final size:16
Alignment explanation
Indices: 608641--608683 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
608631 TTAAATCGAG
*
608641 ATAAAAATATTTAATAA
1 ATAAAAAT-TTTAAAAA
* *
608658 ATTATAATTTTAAAAA
1 ATAAAAATTTTAAAAA
608674 ATAAAAATTT
1 ATAAAAATTT
608684 GTTTATTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAAATTTTAAAAA
Found at i:609480 original size:20 final size:20
Alignment explanation
Indices: 609455--609495 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
609445 TTAATGAGAT
609455 TGTATCATATATGACGACTA
1 TGTATCATATATGACGACTA
609475 TGTATCATATATGACGACTA
1 TGTATCATATATGACGACTA
609495 T
1 T
609496 CTTTGAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCATATATGACGACTA
Found at i:613757 original size:19 final size:18
Alignment explanation
Indices: 613708--613759 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
613698 TGAAAAATAT
*
613708 AAAAATATAGAAATTATAA
1 AAAAATATA-AAATGATAA
* *
613727 GAAATTATTAAAATGATAAA
1 AAAAATA-TAAAATGAT-AA
613747 AAAAATATAAAAT
1 AAAAATATAAAAT
613760 TATTATAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AAAAATATAAAATGATAA
Found at i:614275 original size:20 final size:21
Alignment explanation
Indices: 614244--614291 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
614234 TTGTTTATGT
614244 TTTTAATA-TTTTAATAA-AA
1 TTTTAATATTTTTAATAATAA
*
614263 TTTTAATATTTTTCATAATAA
1 TTTTAATATTTTTAATAATAA
614284 -TTTAATAT
1 TTTTAATAT
614292 ATAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 16 0.62
21 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATATTTTTAATAATAA
Found at i:617690 original size:6 final size:6
Alignment explanation
Indices: 617679--617705 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
617669 GTGCTTGAGG
617679 CGGCGT CGGCGT CGGCGT CGGCGT CGG
1 CGGCGT CGGCGT CGGCGT CGGCGT CGG
617706 ATGAGAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.52, T:0.15
Consensus pattern (6 bp):
CGGCGT
Found at i:638788 original size:2 final size:2
Alignment explanation
Indices: 638783--638815 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
638773 TCTCTCTGTC
638783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
638816 GCCCTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:641758 original size:35 final size:34
Alignment explanation
Indices: 641680--641758 Score: 81
Period size: 35 Copynumber: 2.3 Consensus size: 34
641670 AAAGATTAGA
* * *
641680 TTATAAATTTATCAAAGTGTACATTTTAAATTTT
1 TTATAAATTTATCAAAATGTACATTATAAATTAT
*
641714 TTA-ATAATTTAGTCAAAAT-TTCATTCATAAATTAT
1 TTATA-AATTTA-TCAAAATGTACATT-ATAAATTAT
641749 TTATAAATTT
1 TTATAAATTT
641759 CAAACCCTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.03
34 14 0.38
35 21 0.57
36 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (34 bp):
TTATAAATTTATCAAAATGTACATTATAAATTAT
Found at i:658668 original size:217 final size:218
Alignment explanation
Indices: 658242--658678 Score: 621
Period size: 217 Copynumber: 2.0 Consensus size: 218
658232 ATTTATATTG
* * *
658242 TACTTTGGTTGTATTTTTCTCGTAACACTTTTTAAAAAAAATATAGAATGCCATGAGTTAACTTG
1 TACTTTGGTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTG
* * *
658307 TCAACTTACAAATTTTTGCTTAATTTGTTGGTAATATCTGTAAATTTTGAATTTAGCCCCTTACT
66 TCAACTTACAAATTTTTGCTTAACTTGTTGGTAATATCTATAAATTTTAAATTTAGCCCCTTACT
* * * * *
658372 TTTATTTCAAGAATTTAACACCTTCATTTTTCAAATTTAAAGATGTAAGTTCAATTATTAACACC
131 TTTATTTCAAGAATTTAACACATCCACTTTTCAAATTTAAAAATGTAACTTCAATTATTAACACC
*
658437 ATTTTTTGTTAATTTTAGTTCAT
196 ATTTTTTGTTAATTTTAATTCAT
* *
658460 TACTTTGGTTGTATTGTACTCGTAACACTTTTT-AAAAAAATATGGAACGGCATGAGTTAACTTG
1 TACTTTGGTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTG
*
658524 TCAACTTACAAATTTTTGCTTAACTTGTTGGTAATATCTATAAATTTTAAATTTAGCCTCC-TAT
66 TCAACTTACAAATTTTTGCTTAACTTGTTGGTAATATCTATAAATTTTAAATTTAGCC-CCTTAC
* *** * *
658588 TTTTATTTTAAGGAATTTTGTACATCCACTTTTCAAATTTAAAAATGTAACTTCAATTGTTAATA
130 TTTTATTTCAA-GAATTTAACACATCCACTTTTCAAATTTAAAAATGTAACTTCAATTATTAACA
*
658653 -TATATTTTT-TTAATTTTAATTCAT
194 CCAT-TTTTTGTTAATTTTAATTCAT
658677 TA
1 TA
658679 TGATATTTTT
Statistics
Matches: 194, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
217 113 0.58
218 81 0.42
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (218 bp):
TACTTTGGTTGTATTGTACTCGTAACACTTTTTAAAAAAAATATAGAACGCCATGAGTTAACTTG
TCAACTTACAAATTTTTGCTTAACTTGTTGGTAATATCTATAAATTTTAAATTTAGCCCCTTACT
TTTATTTCAAGAATTTAACACATCCACTTTTCAAATTTAAAAATGTAACTTCAATTATTAACACC
ATTTTTTGTTAATTTTAATTCAT
Found at i:664798 original size:22 final size:23
Alignment explanation
Indices: 664771--664826 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
664761 TTCGTACTTC
664771 GTGTGCCTACT-GATTGCACTGT
1 GTGTGCCTACTGGATTGCACTGT
664793 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACTGGATTGCACTGT
*
664816 GTGTGCTTACT
1 GTGTGCCTACT
664827 ATTTCCCAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (23 bp):
GTGTGCCTACTGGATTGCACTGT
Found at i:664871 original size:22 final size:22
Alignment explanation
Indices: 664846--664898 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
664836 CACTTGTGTG
664846 CTTACTGTTAAGTACTTCAGTA
1 CTTACTGTTAAGTACTTCAGTA
664868 CTTACTGTTAAGTACTTCAGTA
1 CTTACTGTTAAGTACTTCAGTA
*
664890 CTTTCTGTT
1 CTTACTGTT
664899 TCGTTTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (22 bp):
CTTACTGTTAAGTACTTCAGTA
Found at i:667434 original size:26 final size:26
Alignment explanation
Indices: 667399--667452 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
667389 TAAAAATCTA
667399 AAAGCATTGTATCAACTTTATATTTT
1 AAAGCATTGTATCAACTTTATATTTT
667425 AAAGCATTGTATCAACTTTATATTTT
1 AAAGCATTGTATCAACTTTATATTTT
667451 AA
1 AA
667453 TTATAGTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (26 bp):
AAAGCATTGTATCAACTTTATATTTT
Found at i:668952 original size:18 final size:21
Alignment explanation
Indices: 668917--668957 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
668907 TTCTCCAGAA
668917 TAATCAAGCAATTGAGAAATT
1 TAATCAAGCAATTGAGAAATT
668938 TAAT-AAGCAA-T-AGAAATT
1 TAATCAAGCAATTGAGAAATT
668956 TA
1 TA
668958 TTGTTTAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 6 0.30
21 4 0.20
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
TAATCAAGCAATTGAGAAATT
Found at i:671503 original size:7 final size:7
Alignment explanation
Indices: 671491--671523 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
671481 GAATTTAGAG
671491 ATAGGGA
1 ATAGGGA
671498 ATAGGGA
1 ATAGGGA
671505 ATAGGGA
1 ATAGGGA
671512 ATAGGGA
1 ATAGGGA
671519 ATAGG
1 ATAGG
671524 TTAACATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.42, T:0.15
Consensus pattern (7 bp):
ATAGGGA
Done.