genome.fa.s13.2.7.7.80.10.50.1000.42.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   

This is table  42  of  199  ( 23770 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12125994--12126077	21	4.0	21	87	0	123	46	17	21	14	1.84
12128326--12128353	13	2.2	13	100	0	56	32	0	21	46	1.52
12130812--12130841	9	3.3	9	90	0	51	36	0	10	53	1.35
12135767--12135807	18	2.4	18	84	15	61	24	4	0	70	1.06
12140942--12141009	34	2.0	35	82	8	86	22	25	22	30	1.99
12150749--12150810	26	2.4	26	94	0	106	33	12	14	38	1.84
12159208--12159339	42	3.1	42	91	0	201	21	31	25	21	1.98
12161296--12161351	9	6.0	9	77	10	51	73	21	1	3	1.08
12176394--12176547	14	11.6	13	71	17	88	56	0	0	42	1.04
12176413--12176505	12	8.3	11	72	18	50	53	0	0	46	1.00
12176455--12176578	11	11.6	11	68	21	77	58	0	1	40	1.08
12176425--12176619	39	4.7	40	76	13	139	58	0	2	39	1.10
12176519--12176587	31	2.2	31	100	0	138	62	0	2	34	1.10
12183041--12183071	16	1.9	16	93	0	53	61	9	16	12	1.56
12184383--12184879	23	21.2	23	78	5	469	42	17	12	27	1.86
12184383--12184877	46	10.5	46	84	4	591	42	17	12	28	1.85
12184420--12184890	93	5.1	93	90	1	730	42	16	12	28	1.85
12185232--12185256	2	12.5	2	100	0	50	52	0	0	48	1.00
12185248--12185295	15	3.1	15	82	8	53	47	18	0	33	1.49
12185799--12185911	43	2.6	43	81	10	124	30	30	18	20	1.96
12191841--12191911	28	2.5	28	86	0	97	30	12	25	30	1.93
12193952--12194078	28	4.5	28	87	2	164	30	11	25	33	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12193952--12194079	57	2.3	56	84	1	166	31	10	25	32	1.90
12194919--12195151	23	10.0	23	68	17	122	25	12	18	42	1.86
12194920--12195169	46	5.3	46	77	7	270	25	12	19	42	1.86
12194890--12195262	94	3.9	94	91	1	575	26	12	18	41	1.86
12200649--12201462	94	8.6	94	94	0	1376	26	12	19	42	1.86
12200682--12201322	23	27.3	22	69	16	168	25	12	19	42	1.86
12203341--12203765	93	4.6	93	88	3	516	41	16	14	27	1.87
12203344--12203761	139	3.0	139	86	2	552	40	16	15	27	1.88
12203341--12203765	46	9.1	46	82	3	485	41	16	14	27	1.87
12204644--12204755	43	2.6	43	81	13	140	29	28	19	22	1.98
12210569--12210761	50	3.7	52	81	6	214	26	20	28	24	1.99
12210575--12210761	100	1.8	102	82	6	243	26	19	29	24	1.99
12216442--12216504	30	2.1	30	96	0	117	57	15	3	23	1.53
12217901--12218027	43	3.0	42	81	2	155	24	17	27	30	1.97
12217909--12218043	43	3.1	43	77	4	130	25	17	25	31	1.97
12224335--12224372	20	1.9	20	88	0	58	44	0	15	39	1.47
12224411--12224679	75	3.6	75	81	2	306	21	21	22	34	1.97
12230007--12230117	53	2.1	51	91	8	188	27	12	21	37	1.90
12231823--12231880	16	3.5	16	72	9	62	32	0	5	62	1.18
12232213--12232262	25	2.1	23	85	7	64	50	2	0	48	1.12
12239880--12239914	16	2.1	17	89	5	54	31	2	11	54	1.51
12241333--12241364	14	2.3	14	94	0	55	50	9	18	21	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12252153--12252215	29	2.1	29	82	8	74	46	7	9	36	1.66
12254215--12254340	28	4.5	28	87	2	173	30	12	25	30	1.93
12254214--12254341	56	2.3	56	87	4	195	32	12	25	30	1.92
12255039--12255803	23	33.0	22	75	15	602	28	14	17	39	1.89
12255033--12255825	93	8.5	93	91	3	1240	28	14	17	39	1.89
12267047--12267140	24	3.9	24	74	12	68	56	8	7	27	1.56
12269404--12269429	5	5.2	5	100	0	52	19	19	19	42	1.90
12269623--12269784	81	2.0	81	98	0	315	32	10	24	32	1.89
12269729--12269913	63	2.9	63	79	1	210	25	6	33	34	1.82
12271864--12271929	27	2.5	27	85	4	82	37	3	19	39	1.67
12273519--12273563	7	6.4	7	97	0	81	53	0	15	31	1.43
12274934--12274968	18	1.9	18	88	0	52	51	2	0	45	1.16
12281555--12281635	30	2.6	31	84	3	110	40	11	13	34	1.80
12285405--12285455	24	2.1	24	88	0	75	23	25	17	33	1.96
12285527--12285648	44	2.7	45	79	13	144	26	25	18	29	1.98
12285732--12285780	24	2.0	24	92	0	80	22	24	20	32	1.98
12285853--12286411	44	12.7	44	74	12	325	27	22	19	30	1.98
12285853--12286490	44	14.6	44	74	14	305	27	22	19	29	1.98
12285397--12286057	324	2.0	325	92	0	1092	28	20	20	31	1.97
12285754--12286497	217	3.4	217	87	3	1089	28	22	19	30	1.98
12286027--12286410	177	2.2	178	86	5	528	27	24	19	28	1.99
12297825--12297867	22	2.0	21	91	8	70	60	0	4	34	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12297835--12297900	21	3.1	21	84	6	71	63	0	4	31	1.14
12301581--12301610	11	2.6	11	94	5	51	60	0	3	36	1.14
12301568--12301648	33	2.5	32	82	11	103	60	0	3	35	1.15
12301579--12301648	33	2.1	33	92	5	115	62	0	2	34	1.10
12301832--12301908	29	2.5	31	87	4	104	25	14	12	46	1.80
12302031--12302073	20	2.2	20	82	0	50	11	6	2	79	1.02
12302234--12302277	21	2.1	21	100	0	88	31	4	13	50	1.62
12304450--12304540	40	2.3	40	78	1	103	37	2	17	42	1.62
12304935--12304980	22	2.1	22	95	0	83	67	2	4	26	1.21
12304984--12305034	22	2.4	21	81	9	59	58	1	1	37	1.20
12305040--12305085	23	2.0	23	87	8	67	36	8	4	50	1.53
12305474--12305512	18	2.3	17	86	8	53	43	15	7	33	1.75
12305975--12306170	99	2.0	99	91	0	320	23	18	19	38	1.93
12306369--12306418	26	2.0	25	84	4	64	24	0	16	60	1.36
12309195--12309239	14	2.9	16	77	16	58	44	2	6	46	1.42
12309285--12309412	65	2.0	65	92	4	213	53	3	8	35	1.48
12309647--12309675	14	2.1	14	100	0	58	27	20	20	31	1.98
12312275--12312315	15	2.7	15	80	0	55	63	29	2	4	1.28
12312397--12312432	16	2.1	18	90	10	58	66	0	33	0	0.92
12312493--12312521	5	5.8	5	100	0	58	20	79	0	0	0.74
12319279--12319334	30	1.9	28	85	7	76	55	1	3	39	1.28
12323593--12323634	10	4.2	10	82	11	59	9	9	2	78	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12324443--12324486	21	2.1	21	95	0	79	45	11	9	34	1.72
12328390--12328450	3	20.3	3	100	0	122	67	0	32	0	0.91
12330203--12330411	40	5.2	40	83	1	249	21	27	16	33	1.95
12344987--12345023	17	2.2	17	95	0	65	21	18	8	51	1.72
12349051--12349084	17	1.9	18	88	5	52	32	14	11	41	1.82
12350755--12350860	55	1.9	55	92	0	176	35	4	17	41	1.71
12350755--12350873	55	2.2	55	87	3	168	35	5	16	42	1.70
12357796--12357860	32	2.0	32	100	0	130	18	9	27	44	1.80
12359387--12359442	3	18.7	3	100	0	112	67	0	32	0	0.91
12365970--12366086	38	3.1	37	67	26	100	43	16	6	33	1.74
12365970--12366124	76	2.0	76	94	0	274	43	16	6	33	1.73
12375187--12375300	56	2.0	56	94	0	201	23	27	6	42	1.77
12386852--12387096	29	8.4	29	91	3	368	18	29	11	39	1.87
12386841--12387095	87	2.9	86	91	2	420	19	29	12	38	1.89
12404510--12404569	25	2.4	25	88	0	93	46	28	16	8	1.76
12406788--12406832	21	2.1	22	84	12	58	20	2	20	57	1.51
12413850--12413973	54	2.3	54	85	2	160	26	26	26	20	1.99
12413895--12414005	54	2.1	54	80	0	123	26	27	27	18	1.98
12417892--12417922	4	8.0	4	92	7	55	74	0	0	25	0.82
12418228--12418323	31	3.1	31	95	3	174	45	13	9	31	1.75
12423307--12423358	15	3.3	15	75	19	61	0	13	11	75	1.06
12423322--12423390	22	3.1	21	75	19	61	1	14	10	73	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12423328--12423379	21	2.3	23	87	9	72	1	17	11	69	1.27
12423342--12423391	21	2.5	20	90	9	75	2	14	12	72	1.22
12423362--12423399	10	3.9	10	82	3	51	0	10	10	78	0.95
12423615--12423645	4	8.0	4	92	7	55	74	0	0	25	0.82
12428053--12428125	34	2.1	34	87	0	101	43	15	16	24	1.86
12430017--12430070	21	2.5	21	84	6	63	25	25	5	42	1.77
12434578--12434638	26	2.3	27	83	13	83	36	1	3	59	1.24
12436081--12436127	24	2.0	24	91	0	76	29	27	14	27	1.96
12438123--12438332	106	2.0	106	93	0	357	29	18	13	39	1.89
12439170--12439269	35	2.9	35	86	0	137	17	12	28	43	1.84

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199