Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015036.1 Kokia drynarioides strain JFW-HI SEQ_130080, 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: 520311
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 696 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:371266 original size:24 final size:24
Alignment explanation
Indices: 371219--371269 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
371209 AAGGTGAAGC
* *
371219 TGAAGCTGAAGTGGAGGGACATGG
1 TGAAGCAGAAGTGGAGAGACATGG
**
371243 TGAAGCAGAAGTGGAGAGTGATGG
1 TGAAGCAGAAGTGGAGAGACATGG
371267 TGA
1 TGA
371270 CCTACGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.45, T:0.18
Consensus pattern (24 bp):
TGAAGCAGAAGTGGAGAGACATGG
Found at i:377090 original size:23 final size:23
Alignment explanation
Indices: 377064--377116 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
377054 AATAATTTCA
*
377064 ATATTTCAAGTATATAAT-ATTAT
1 ATATTT-AAATATATAATAATTAT
*
377087 ATATTTAAATATTTAATAATTAT
1 ATATTTAAATATATAATAATTAT
377110 AT-TTTAA
1 ATATTTAA
377117 TGTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTAAATATATAATAATTAT
Found at i:378216 original size:20 final size:19
Alignment explanation
Indices: 378163--378217 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
378153 ATAAAAATAT
*
378163 AATATTAAATAATTTATTAA
1 AATATT-AATAATATATTAA
378183 AATATTAA-AATATATTAA
1 AATATTAATAATATATTAA
*
378201 CTATATTAATAATATAT
1 -AATATTAATAATATAT
378218 AATATTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.29
19 9 0.29
20 13 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTAATAATATATTAA
Found at i:383976 original size:29 final size:29
Alignment explanation
Indices: 383941--383996 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
383931 TAACTATTTG
*
383941 AACTAATTAATTACATTATAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
383970 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
383997 AGAGATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:414176 original size:26 final size:26
Alignment explanation
Indices: 414119--414184 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
414109 AATAAAATTG
414119 TAATATTGAATAATTTATTATATTAAT
1 TAATATT-AATAATTTATTATATTAAT
* *
414146 T-ATATTAATAATTTGTTATA-TGAT
1 TAATATTAATAATTTATTATATTAAT
*
414170 TAAATATAAATAATT
1 T-AATATTAATAATT
414185 AAATAGGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 4 0.12
25 13 0.38
26 16 0.47
27 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (26 bp):
TAATATTAATAATTTATTATATTAAT
Found at i:418491 original size:5 final size:5
Alignment explanation
Indices: 418481--418505 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
418471 CCCTAGTAAT
418481 TTCCC TTCCC TTCCC TTCCC TTCCC
1 TTCCC TTCCC TTCCC TTCCC TTCCC
418506 ATCCATCTCT
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:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TTCCC
Found at i:420886 original size:14 final size:14
Alignment explanation
Indices: 420863--420892 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
420853 TATGGATGTA
420863 ATTTTATATATTTT
1 ATTTTATATATTTT
*
420877 ATTTTCTATATTTT
1 ATTTTATATATTTT
420891 AT
1 AT
420893 AACACTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATATATTTT
Found at i:430500 original size:18 final size:18
Alignment explanation
Indices: 430477--430515 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
430467 ATAAATATAT
430477 TAAATTA-CTTGTTAATAA
1 TAAATTAGCTT-TTAATAA
*
430495 TAAATTAGCTTTTACTAA
1 TAAATTAGCTTTTAATAA
430513 TAA
1 TAA
430516 TAAATATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (18 bp):
TAAATTAGCTTTTAATAA
Found at i:430611 original size:14 final size:15
Alignment explanation
Indices: 430581--430612 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
430571 GAGTTAGTAT
430581 AATTAAATATAAAAA
1 AATTAAATATAAAAA
*
430596 AATTAAATTTAAAAA
1 AATTAAATATAAAAA
430611 AA
1 AA
430613 AGACACGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATTAAATATAAAAA
Found at i:436015 original size:18 final size:20
Alignment explanation
Indices: 435992--436032 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
435982 CTCAAAATAT
435992 AAATGAATAA-AAATA-AAA
1 AAATGAATAATAAATAGAAA
*
436010 AAATGATTAATAAATAGAAA
1 AAATGAATAATAAATAGAAA
436030 AAA
1 AAA
436033 AGACGAGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 5 0.25
20 6 0.30
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATGAATAATAAATAGAAA
Found at i:442296 original size:17 final size:18
Alignment explanation
Indices: 442274--442308 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
442264 GAATGATTTA
442274 TAAAAAAAATAAA-TATT
1 TAAAAAAAATAAAGTATT
*
442291 TAAAAATAATAAAGTATT
1 TAAAAAAAATAAAGTATT
442309 ATAATATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAAAAAATAAAGTATT
Found at i:442790 original size:18 final size:17
Alignment explanation
Indices: 442765--442804 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
442755 ATTTAATTTT
442765 TAAAATTA-T-AAA-GA
1 TAAAATTATTAAAATGA
442779 TATAAATTATTAAAATGA
1 TA-AAATTATTAAAATGA
442797 TAAAATTA
1 TAAAATTA
442805 CATTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 6 0.27
16 1 0.05
17 9 0.41
18 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
TAAAATTATTAAAATGA
Found at i:444206 original size:26 final size:26
Alignment explanation
Indices: 444175--444226 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
444165 AAAATATTAA
444175 AAAGATAAAAATTGTGTTTTAAGATT
1 AAAGATAAAAATTGTGTTTTAAGATT
*
444201 AAAGATAAAGATTGTGTTTTAAGATT
1 AAAGATAAAAATTGTGTTTTAAGATT
444227 TTGGTCTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.38
Consensus pattern (26 bp):
AAAGATAAAAATTGTGTTTTAAGATT
Found at i:448609 original size:5 final size:5
Alignment explanation
Indices: 448599--448641 Score: 50
Period size: 5 Copynumber: 7.8 Consensus size: 5
448589 TATATTTAGT
448599 TTTTA TTTTA TTTTA TTTTA TATTATA GTTTTA TTTTA GTTTT
1 TTTTA TTTTA TTTTA TTTTA T-TT-TA -TTTTA TTTTA -TTTT
448642 TCTTCTATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 21 0.62
6 8 0.24
7 4 0.12
8 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:448622 original size:28 final size:29
Alignment explanation
Indices: 448586--448641 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
448576 TTCCTTAATT
448586 TTTTATATT-TAGTTTTTATTTTA-TTTTA
1 TTTTATATTATAG-TTTTATTTTAGTTTTA
448614 TTTTATATTATAGTTTTATTTTAGTTTT
1 TTTTATATTATAGTTTTATTTTAGTTTT
448642 TCTTCTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.73
Consensus pattern (29 bp):
TTTTATATTATAGTTTTATTTTAGTTTTA
Found at i:449193 original size:29 final size:27
Alignment explanation
Indices: 449112--449194 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 27
449102 ATAATGTTCC
*
449112 AAAATTTTTTAAAAAATATATAAAAATAT
1 AAAATTTTTT-AAAATTATA-AAAAATAT
*
449141 AAAATTTATTTAAAATT-TAAAAAAAATT
1 AAAATTT-TTTAAAATTATAAAAAATA-T
449169 AAAAATATTTTTAAAATTCATAAAAA
1 -AAAAT-TTTTTAAAATT-ATAAAAA
449195 CTGTAACTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
27 6 0.13
28 3 0.07
29 26 0.57
30 5 0.11
31 6 0.13
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATTTTTTAAAATTATAAAAAATAT
Found at i:449678 original size:30 final size:30
Alignment explanation
Indices: 449619--449681 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
449609 ACAGAAATTA
*
449619 TAAAAATTATTATAGTTTAAAGAAAACATG
1 TAAAAATTATTATAATTTAAAGAAAACATG
* *
449649 TAAAAATTATTATCAATTTTAA-AATACATG
1 TAAAAATTATTAT-AATTTAAAGAAAACATG
449679 TAA
1 TAA
449682 TTTTTAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (30 bp):
TAAAAATTATTATAATTTAAAGAAAACATG
Found at i:449881 original size:22 final size:20
Alignment explanation
Indices: 449850--449913 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 20
449840 TTACAATAAA
449850 TTTTA-AATTTTA-AATGATTT
1 TTTTACAATTTTATAAT--TTT
449870 TTTTACTAATTTTTATAATTTT
1 TTTTAC-AA-TTTTATAATTTT
449892 TTTTACAATTTTTATAACTTTT
1 TTTTACAA-TTTTATAA-TTTT
449914 AATATTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.13
21 11 0.28
22 15 0.38
23 5 0.13
24 3 0.08
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTTACAATTTTATAATTTT
Found at i:449892 original size:21 final size:20
Alignment explanation
Indices: 449866--449913 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 20
449856 ATTTTAAATG
449866 ATTTTTTTACTAATTTTTATA
1 ATTTTTTTAC-AATTTTTATA
449887 ATTTTTTTTACAATTTTTATA
1 A-TTTTTTTACAATTTTTATA
449908 ACTTTT
1 A-TTTT
449914 AATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTTTTACAATTTTTATA
Found at i:449930 original size:106 final size:105
Alignment explanation
Indices: 449772--450098 Score: 505
Period size: 106 Copynumber: 3.1 Consensus size: 105
449762 TCTTAAGATT
* * ** *
449772 TTTTTATAATTTCTTTTACAATTTTTAGAAAAATTTAATATTTTTAAATAATATATATTTCTAGA
1 TTTTTATAATTTTTTTTACAATTTTTA-TAACTTTTAATATTTTTAAATAATATATATTTATAGA
449837 TTTTTACAATAAATTTTAAATTTTAAATGATTTTTTTACTAA
65 TTTTTA-AATAAATTTTAAATTTTAAATGATTTTTTTACTAA
449879 TTTTTATAATTTTTTTTACAATTTTTATAACTTTTAATATTTTTAAATAATATATATTTATAGAT
1 TTTTTATAATTTTTTTTACAATTTTTATAACTTTTAATATTTTTAAATAATATATATTTATAGAT
* *
449944 TTTTAAAATAAATTTTAAACTTTAAATGA-TTTTTTAATAA
66 TTTT-AAATAAATTTTAAATTTTAAATGATTTTTTTACTAA
*
449984 TTTTTATAATTTTTTTTTACAGTTTTTATAACTTTTAATATTTTTAAATAATATATATTTATAGA
1 TTTTTATAA-TTTTTTTTACAATTTTTATAACTTTTAATATTTTTAAATAATATATATTTATAGA
450049 TTTTTAAATAAATTTTAAATATTTTAAAT-ATTTTTTTACTAA
65 TTTTTAAATAAATTTT-AA-ATTTTAAATGATTTTTTTACTAA
*
450091 TTTATATA
1 TTTTTATA
450099 TATATATATA
Statistics
Matches: 204, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
105 30 0.15
106 122 0.60
107 52 0.25
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (105 bp):
TTTTTATAATTTTTTTTACAATTTTTATAACTTTTAATATTTTTAAATAATATATATTTATAGAT
TTTTAAATAAATTTTAAATTTTAAATGATTTTTTTACTAA
Found at i:449998 original size:22 final size:22
Alignment explanation
Indices: 449973--450019 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
449963 CTTTAAATGA
* *
449973 TTTTTTAATAATTTTTATAATT
1 TTTTTTAACAATTTTTATAACT
* *
449995 TTTTTTTACAGTTTTTATAACT
1 TTTTTTAACAATTTTTATAACT
450017 TTT
1 TTT
450020 AATATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTAACAATTTTTATAACT
Found at i:449999 original size:21 final size:21
Alignment explanation
Indices: 449866--449999 Score: 64
Period size: 21 Copynumber: 6.4 Consensus size: 21
449856 ATTTTAAATG
*
449866 ATTTTTTTACTAATTTTTATA
1 ATTTTTTTAATAATTTTTATA
* *
449887 ATTTTTTTTACAATTTTTATA
1 ATTTTTTTAATAATTTTTATA
*
449908 A--CTTTTAAT-ATTTTTAAATA
1 ATTTTTTTAATAATTTTT--ATA
* *
449928 ATATATATTT-ATAGATTTTTAAA
1 AT-T-TTTTTAATA-ATTTTTATA
** * ** *
449951 ATAAATTTTAA-ACTTTAAATG
1 AT-TTTTTTAATAATTTTTATA
449972 A-TTTTTTAATAATTTTTATA
1 ATTTTTTTAATAATTTTTATA
449992 ATTTTTTT
1 ATTTTTTT
450000 TTACAGTTTT
Statistics
Matches: 79, Mismatches: 23, Indels: 22
0.64 0.19 0.18
Matches are distributed among these distances:
18 6 0.08
19 11 0.14
20 11 0.14
21 30 0.38
22 4 0.05
23 8 0.10
24 3 0.04
25 6 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
ATTTTTTTAATAATTTTTATA
Found at i:450098 original size:2 final size:2
Alignment explanation
Indices: 450093--450121 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
450083 TTTACTAATT
450093 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 T
450122 TACATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:458877 original size:24 final size:23
Alignment explanation
Indices: 458798--458886 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
458788 TTTAATGTTC
* *
458798 TCGAATATGTTCATTTAAC-TTAA
1 TCGAACATGTTCA-TGAACATTAA
*
458821 TCGAACATGTTCACGAACATTAA
1 TCGAACATGTTCATGAACATTAA
* *
458844 ACGAATATGTTCATGAACATATAA
1 TCGAACATGTTCATGAACAT-TAA
458868 TCGAACATGTTCATGAACA
1 TCGAACATGTTCATGAACA
458887 ATGTTAGTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
22 3 0.05
23 33 0.59
24 20 0.36
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (23 bp):
TCGAACATGTTCATGAACATTAA
Found at i:470165 original size:19 final size:21
Alignment explanation
Indices: 470127--470165 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
470117 CGGGAATTTT
*
470127 TTTTTGAAAAATGAATTAATC
1 TTTTTGAAAAATGAAATAATC
470148 TTTTT-AAAAAT-AAATAAT
1 TTTTTGAAAAATGAAATAAT
470166 TTTGGGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTTGAAAAATGAAATAATC
Found at i:470532 original size:20 final size:20
Alignment explanation
Indices: 470502--470544 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
470492 CAAATTTCAA
470502 TAAAATATTAAAAATATTACT
1 TAAAATATTAAAAATATTA-T
*
470523 TAAAAT-TTAATAATATTAT
1 TAAAATATTAAAAATATTAT
470542 TAA
1 TAA
470545 TGTTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 11 0.52
21 6 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATATTAAAAATATTAT
Found at i:470583 original size:17 final size:17
Alignment explanation
Indices: 470563--470596 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
470553 ATTACTATCA
470563 AAATAAAATTTTAATTT
1 AAATAAAATTTTAATTT
* *
470580 AAATAAATTTTTTATTT
1 AAATAAAATTTTAATTT
470597 TTTGAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATAAAATTTTAATTT
Found at i:472350 original size:34 final size:34
Alignment explanation
Indices: 472308--472377 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
472298 CTTACTTGCG
472308 AAAAATCTATTGGAGTGATAGAGAAAATATAGTA
1 AAAAATCTATTGGAGTGATAGAGAAAATATAGTA
472342 AAAAATCTATTGGAGTGATAGAGAAAATATAGTA
1 AAAAATCTATTGGAGTGATAGAGAAAATATAGTA
472376 AA
1 AA
472378 GAGGAAGGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.26
Consensus pattern (34 bp):
AAAAATCTATTGGAGTGATAGAGAAAATATAGTA
Found at i:476750 original size:12 final size:13
Alignment explanation
Indices: 476720--476755 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
476710 TGAAATTATC
476720 TTATAATTCAAGA
1 TTATAATTCAAGA
476733 --ATAATTCAA-A
1 TTATAATTCAAGA
476743 TTATAATTCAAGA
1 TTATAATTCAAGA
476756 ACCGATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.05
11 9 0.45
12 9 0.45
13 1 0.05
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (13 bp):
TTATAATTCAAGA
Found at i:477570 original size:20 final size:20
Alignment explanation
Indices: 477523--477580 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
477513 AAATTTAGTA
477523 CCAAAAATTAATATATTTTAATT
1 CCAAAAATT-A-AT-TTTTAATT
* *
477546 TCAAAAATTAATTTTTCATT
1 CCAAAAATTAATTTTTAATT
*
477566 CCAAAACTT-ATTTTT
1 CCAAAAATTAATTTTT
477581 GAAAGCATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 6 0.19
20 14 0.45
21 2 0.06
22 1 0.03
23 8 0.26
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (20 bp):
CCAAAAATTAATTTTTAATT
Found at i:477854 original size:11 final size:11
Alignment explanation
Indices: 477838--477908 Score: 55
Period size: 10 Copynumber: 6.9 Consensus size: 11
477828 AAAGGAATAC
477838 AAAAAATTATG
1 AAAAAATTATG
477849 AAAAAA-TATG
1 AAAAAATTATG
*
477859 -AAAAA-TACG
1 AAAAAATTATG
477868 AAAAAATTAT-
1 AAAAAATTATG
* *
477878 TAAAAATGAT-
1 AAAAAATTATG
*
477888 AAGAAAA-TATT
1 AA-AAAATTATG
477899 AAAAAATTAT
1 AAAAAATTAT
477909 ATTTAGTGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
9 8 0.16
10 24 0.49
11 17 0.35
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.25
Consensus pattern (11 bp):
AAAAAATTATG
Found at i:484631 original size:6 final size:6
Alignment explanation
Indices: 484622--484659 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
484612 ACACACACAC
484622 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT AT
484660 ATGTGCGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:485101 original size:2 final size:2
Alignment explanation
Indices: 485094--485125 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
485084 ACACTGCGTG
485094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
485126 TCTTGCTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:487885 original size:28 final size:27
Alignment explanation
Indices: 487849--487904 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 27
487839 ATTTATTTTG
*
487849 ATTATTTATATTTTCAGTTGTGATATAT
1 ATTATTTATATCTTCAGTTGTGAT-TAT
487877 ATTATTTATATCTTCAGTTGTGATTAT
1 ATTATTTATATCTTCAGTTGTGATTAT
487904 A
1 A
487905 ACTATAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (27 bp):
ATTATTTATATCTTCAGTTGTGATTAT
Found at i:488152 original size:18 final size:18
Alignment explanation
Indices: 488129--488174 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
488119 GAATAGGGCT
488129 TTAATTAAATAAACTT-AA
1 TTAATTAAA-AAACTTAAA
**
488147 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAACTTAAA
488165 TTAATTAAAA
1 TTAATTAAAA
488175 CTAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAATTAAAAAACTTAAA
Found at i:489256 original size:23 final size:23
Alignment explanation
Indices: 489230--489275 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
489220 TTTTTCTTTT
*
489230 TCTTTTTCTTTTTC-ATTCTAATA
1 TCTTTTTCCTTTTCTATT-TAATA
489253 TCTTTTTCCTTTTCTATTTAATA
1 TCTTTTTCCTTTTCTATTTAATA
489276 ATTTTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.65
Consensus pattern (23 bp):
TCTTTTTCCTTTTCTATTTAATA
Found at i:490376 original size:22 final size:22
Alignment explanation
Indices: 490320--490377 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 22
490310 TTTAGATTGA
* *
490320 TTAAATAA-AATACTGAGAATT
1 TTAAAAAATAATAATGAGAATT
490341 TATATAAAACATAATAATGAGAATT
1 T-TA-AAAA-ATAATAATGAGAATT
490366 TTAAAAAATAAT
1 TTAAAAAATAAT
490378 TTTATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
22 7 0.23
23 7 0.23
24 3 0.10
25 13 0.42
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (22 bp):
TTAAAAAATAATAATGAGAATT
Found at i:492154 original size:6 final size:6
Alignment explanation
Indices: 492138--492175 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
492128 ATATCTTGCT
* *
492138 CTCCCA GTCCCA CTCCCA CTTCCA CTCCCA CTCCCA CT
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CT
492176 GCTACCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.16, C:0.61, G:0.03, T:0.21
Consensus pattern (6 bp):
CTCCCA
Found at i:495688 original size:89 final size:89
Alignment explanation
Indices: 495537--495715 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
495527 CAATCACTAA
*
495537 AACTTCAAATACTGACAACCAACCACACAATTACAATGAAAAATAAGGATTATTGCTCCAACCTT
1 AACTTCAAATACTGACAACCAACCACACAATTACAATGAAAAATAAGGATTATTGCCCCAACCTT
495602 TCCTAAGAAAGAAAAATACTTTCT
66 TCCTAAGAAAGAAAAATACTTTCT
495626 AACTTCAAATACTGACAACCAACCACACAATTACAATGAAAAATAAGGATTATTGCCCCAACCTT
1 AACTTCAAATACTGACAACCAACCACACAATTACAATGAAAAATAAGGATTATTGCCCCAACCTT
*
495691 TCCTAGGAAAGAAAAATACTTTCT
66 TCCTAAGAAAGAAAAATACTTTCT
495715 A
1 A
495716 TAACTAACAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (89 bp):
AACTTCAAATACTGACAACCAACCACACAATTACAATGAAAAATAAGGATTATTGCCCCAACCTT
TCCTAAGAAAGAAAAATACTTTCT
Found at i:495869 original size:3 final size:3
Alignment explanation
Indices: 495861--495907 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
495851 ATAGAGATGA
*
495861 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
495908 CCTTTTTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:501122 original size:23 final size:22
Alignment explanation
Indices: 501087--501210 Score: 95
Period size: 23 Copynumber: 5.5 Consensus size: 22
501077 GCTGGGGAAA
*
501087 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
* *
501109 CCAGTAGGCGCACATAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
501132 CAGTAGGCACACATAGCGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
* * *
501155 CAGTAGGCACACAAAGTGTGAAA
1 CAGTAGGCACACACAGTG-CAAT
* * *
501178 CAGTAAGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
*
501201 CAGTAAGCAC
1 CAGTAGGCAC
501211 GCTAGCGTTC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
22 17 0.20
23 70 0.80
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:501182 original size:68 final size:69
Alignment explanation
Indices: 501083--501210 Score: 152
Period size: 68 Copynumber: 1.9 Consensus size: 69
501073 AAGTGCTGGG
* * * * * * *
501083 GAAACAGTAAGCACACACAGTGCAATCCAGTAGGCGCACATAGTGC-AATCAGTAGGCACACATA
1 GAAACAGTAAGCACACAAAGTGCAATACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACATA
501147 GCGC
66 GCGC
* *
501151 GAAACAGTAGGCACACAAAGTGTGAA-ACAGTAAGCACACAAAGTGCGAAACAGTAAGCAC
1 GAAACAGTAAGCACACAAAGTG-CAATACAGTAAGCACACAAAGTGCGAAACAGTAAGCAC
501211 GCTAGCGTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
68 36 0.73
69 13 0.27
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (69 bp):
GAAACAGTAAGCACACAAAGTGCAATACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACATA
GCGC
Found at i:508241 original size:23 final size:22
Alignment explanation
Indices: 508209--508304 Score: 111
Period size: 23 Copynumber: 4.2 Consensus size: 22
508199 GCTGGGGAAA
*
508209 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
508231 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
508254 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
* *
508277 CAGTAGGCACACAAAGTGCGAAA
1 CAGTAGGCACACACAGTGC-AAT
508300 CAGTA
1 CAGTA
508305 AGCGCGCTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 16 0.25
23 47 0.75
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:511108 original size:45 final size:45
Alignment explanation
Indices: 511029--511128 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
511019 GTTGTTGTTG
* * **
511029 GGATATTATTATGCGATATTATTTTTTAGTAATTT-AATTTTAAT
1 GGATATTATTATGCGATATTATCTCTTAACAATTTGAATTTTAAT
* *
511073 AGGATATTATTATGGGATATTATCTCTTAACAATTTGATTTTTAAT
1 -GGATATTATTATGCGATATTATCTCTTAACAATTTGAATTTTAAT
511119 GAGATATTAT
1 G-GATATTAT
511129 ATGATAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 31 0.66
46 16 0.34
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (45 bp):
GGATATTATTATGCGATATTATCTCTTAACAATTTGAATTTTAAT
Found at i:511201 original size:116 final size:112
Alignment explanation
Indices: 511076--511284 Score: 269
Period size: 116 Copynumber: 1.8 Consensus size: 112
511066 TTTTAATAGG
* * * *
511076 ATATTATTATGGGATATTATCTCTTAACAATTTGATTTTTAAT-GAGATATTATATGATAAATAC
1 ATATTATTATGAGATATTATCTCTTAACAATTTGATTCTTAATAG-GACATTATAAGAT--AT--
*
511140 TATTATGAG-ATATTATCTTTTATCAATTTGATTACTAATGGGATATTATAAC
61 TATTATG-GTATATTATCTTTTAGCAATTTGATTACTAATGGGATATTATAAC
* **
511192 ATATTATTATGAGATATTATCTTTTAGTAATTTGATTCTTAATAGGACATTATAAGATATTATTA
1 ATATTATTATGAGATATTATCTCTTAACAATTTGATTCTTAATAGGACATTATAAGATATTATTA
*
511257 TGGTATATTATTTTTTAGCAATTTGATT
66 TGGTATATTATCTTTTAGCAATTTGATT
511285 TTTACGTAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
111 1 0.01
112 29 0.35
114 2 0.02
116 49 0.60
117 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (112 bp):
ATATTATTATGAGATATTATCTCTTAACAATTTGATTCTTAATAGGACATTATAAGATATTATTA
TGGTATATTATCTTTTAGCAATTTGATTACTAATGGGATATTATAAC
Found at i:511224 original size:56 final size:55
Alignment explanation
Indices: 511076--511284 Score: 222
Period size: 56 Copynumber: 3.7 Consensus size: 55
511066 TTTTAATAGG
* * * * *
511076 ATATTATTATGGGATATTATCTCTTAACAATTTGATTTTTAATGAGATATTATATGATAA
1 ATATTATTATGAGATATTATCTTTTAGCAATTTGA-TTCTAATGGGATA-T-TAT-A-AA
* * *
511136 ATACTATTATGAGATATTATCTTTTATCAATTTGATTACTAATGGGATATTATAAC
1 ATATTATTATGAGATATTATCTTTTAGCAATTTGATT-CTAATGGGATATTATAAA
* * * *
511192 ATATTATTATGAGATATTATCTTTTAGTAATTTGATTCTTAATAGGACATTATAAG
1 ATATTATTATGAGATATTATCTTTTAGCAATTTGATTC-TAATGGGATATTATAAA
*
511248 ATATTATTATG-GTATATTATTTTTTAGCAATTTGATT
1 ATATTATTATGAG-ATATTATCTTTTAGCAATTTGATT
511285 TTTACGTAAC
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
55 2 0.02
56 82 0.63
57 1 0.01
58 3 0.02
59 3 0.02
60 40 0.31
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (55 bp):
ATATTATTATGAGATATTATCTTTTAGCAATTTGATTCTAATGGGATATTATAAA
Found at i:514892 original size:2 final size:2
Alignment explanation
Indices: 514885--514919 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
514875 ATTAAGCATG
514885 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
514920 CATATTCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:518379 original size:10 final size:10
Alignment explanation
Indices: 518364--518397 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
518354 TGAATTATGC
518364 AAAAAAAGAA
1 AAAAAAAGAA
518374 AAAAAAAGAAA
1 AAAAAAAG-AA
518385 AAAAAAAGAA
1 AAAAAAAGAA
518395 AAA
1 AAA
518398 GATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:518380 original size:11 final size:11
Alignment explanation
Indices: 518364--518397 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
518354 TGAATTATGC
518364 AAAAAAAG-AA
1 AAAAAAAGAAA
518374 AAAAAAAGAAA
1 AAAAAAAGAAA
518385 AAAAAAAGAAA
1 AAAAAAAGAAA
518396 AA
1 AA
518398 GATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:520163 original size:4 final size:4
Alignment explanation
Indices: 520154--520235 Score: 78
Period size: 4 Copynumber: 20.0 Consensus size: 4
520144 AAATAAACGG
*
520154 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA G-AA GAAGA GGAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA GAAA
* * *
520204 GAAG GAGAG GAAA TAAA G-AA GAAA GAAA GAAA
1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
520236 TGTAATGTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
3 6 0.09
4 48 0.72
5 10 0.15
6 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:520176 original size:17 final size:16
Alignment explanation
Indices: 520154--520235 Score: 78
Period size: 17 Copynumber: 5.0 Consensus size: 16
520144 AAATAAACGG
520154 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAG-AAA
*
520171 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGAAA
520187 G-AAGAAGAGGAAAGAAA
1 GAAAGAA-A-GAAAGAAA
* * *
520204 GAAGGAGAGGAAATAAA
1 GAAAGA-AAGAAAGAAA
520221 G-AAGAAAGAAAGAAA
1 GAAAGAAAGAAAGAAA
520236 TGTAATGTGT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.25
16 7 0.13
17 29 0.55
18 3 0.06
19 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (16 bp):
GAAAGAAAGAAAGAAA
Done.