genome.fa.s4.2.7.7.80.10.50.1000.37.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  37  of  198  ( 23681 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)
11153603--11153683	19	4.4	19	68	16	53	74	2	2	20	1.06
11153610--11153682	38	1.9	38	83	5	94	75	2	2	19	1.05
11153584--11153671	28	3.0	29	75	11	72	72	3	2	21	1.10
11153940--11153986	18	2.4	20	79	10	53	25	6	2	65	1.27
11154550--11154584	18	1.9	18	88	0	52	68	2	2	25	1.17
11154886--11154928	22	2.0	22	95	0	77	9	20	27	41	1.83
11160514--11160915	82	4.9	82	83	3	439	32	26	25	16	1.96
11160596--11160915	41	7.7	41	90	0	433	32	27	25	15	1.95
11160793--11160902	23	5.2	23	60	27	64	30	29	25	15	1.96
11161204--11161371	88	1.9	88	89	4	259	44	5	7	42	1.54
11162144--11162418	41	6.7	41	90	2	428	21	21	27	30	1.98
11162857--11162915	7	8.6	7	76	10	50	18	1	40	38	1.61
11162955--11162999	7	6.4	7	84	0	63	15	0	48	35	1.45
11162955--11163008	21	2.6	21	78	0	63	18	0	46	35	1.50
11167600--11167647	22	2.0	23	84	11	62	54	2	2	41	1.24
11167692--11167919	43	5.3	43	86	2	289	23	16	30	28	1.96
11167672--11167919	129	1.9	128	84	4	329	22	16	30	30	1.96
11167961--11168003	22	2.0	22	95	0	77	41	27	20	9	1.83
11168685--11168719	6	5.8	6	100	0	70	51	14	0	34	1.42
11168678--11168717	18	2.2	18	90	0	62	50	17	0	32	1.47
11169401--11169506	41	2.6	41	86	0	122	33	22	18	24	1.97
11169431--11169533	41	2.5	41	91	0	161	33	23	16	26	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11169431--11169548	41	2.9	41	87	0	110	33	23	17	24	1.96
11171421--11171469	20	2.5	20	90	6	75	34	12	16	36	1.86
11176661--11176720	20	2.9	21	65	22	54	23	31	16	28	1.96
11176661--11176743	41	2.0	41	86	4	114	20	30	16	32	1.95
11183388--11183587	103	1.9	103	88	2	303	19	27	18	35	1.95
11187665--11187698	11	3.0	11	91	4	50	70	0	0	29	0.87
11194087--11194226	41	3.4	41	88	2	185	40	11	23	25	1.88
11196522--11196556	18	1.9	18	94	0	61	45	14	11	28	1.79
11203052--11203100	6	7.7	6	82	13	62	83	12	2	2	0.82
11203047--11203108	27	2.3	26	91	8	99	82	9	1	6	0.91
11203052--11203094	21	2.1	20	91	4	68	83	11	2	2	0.83
11205986--11206015	14	2.1	14	93	0	51	83	0	0	16	0.65
11207804--11207989	93	2.0	93	90	0	291	33	23	13	29	1.93
11207960--11208581	27	23.0	27	83	0	679	19	17	20	41	1.90
11213573--11213689	62	1.9	60	84	5	155	48	3	5	42	1.42
11215368--11215399	15	2.1	15	94	0	55	68	9	6	15	1.36
11221982--11222012	15	2.1	15	93	0	53	35	3	0	61	1.12
11224331--11224405	25	3.0	25	88	0	114	20	28	14	37	1.92
11224331--11224436	50	2.1	49	82	1	122	24	25	15	34	1.94
11231580--11231673	25	3.7	25	81	4	91	20	27	12	39	1.89
11231567--11231673	50	2.1	50	86	3	144	20	27	14	38	1.91
11240092--11240196	40	2.6	40	93	1	183	20	19	24	35	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11243196--11243234	18	2.2	18	90	9	62	20	15	5	58	1.55
11243908--11244530	130	4.8	130	85	2	747	31	16	13	38	1.88
11250790--11250826	19	1.9	19	94	0	65	24	5	0	70	1.08
11257348--11257421	38	1.9	38	91	0	121	45	14	5	33	1.68
11259441--11259475	17	2.1	17	100	0	70	42	5	17	34	1.73
11260515--11260541	12	2.2	12	100	0	54	62	11	0	25	1.28
11262800--11262959	21	7.6	21	74	8	128	45	16	21	17	1.86
11262803--11262959	42	3.7	42	78	9	160	45	15	21	17	1.86
11267731--11267765	18	2.0	17	88	5	52	22	0	5	71	1.07
11268145--11268191	2	23.5	2	95	0	85	46	0	0	53	1.00
11270492--11270535	23	1.9	24	90	9	74	54	0	20	25	1.45
11270845--11270936	36	2.5	36	80	13	98	45	1	21	31	1.59
11271966--11272014	18	2.8	17	81	9	53	36	0	0	63	0.95
11275107--11275150	2	22.0	2	100	0	88	50	0	0	50	1.00
11275805--11275842	18	2.1	18	85	9	51	36	2	0	60	1.11
11281676--11281736	26	2.3	26	80	5	70	31	4	3	60	1.34
11281675--11281737	27	2.4	25	77	12	65	33	4	3	58	1.35
11284725--11284786	21	3.1	18	72	19	52	41	1	4	51	1.33
11284725--11284826	41	2.5	41	81	16	106	42	3	3	50	1.39
11285870--11285914	20	2.2	20	88	7	65	28	0	2	68	1.01
11286356--11286383	5	5.6	5	100	0	56	60	21	17	0	1.36
11286823--11286855	17	1.9	17	100	0	66	36	18	9	36	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11287817--11287851	17	2.0	17	88	5	52	65	2	0	31	1.07
11287826--11287858	17	2.0	17	88	5	50	63	3	0	33	1.10
11288371--11288746	124	3.0	125	88	1	533	30	15	22	31	1.95
11290456--11290921	23	20.8	23	85	8	525	26	0	24	48	1.55
11290456--11290921	69	6.9	67	88	5	611	26	0	24	48	1.55
11290462--11290921	205	2.3	197	86	6	627	26	0	24	48	1.55
11290952--11290988	9	4.2	9	96	3	67	59	10	0	29	1.31
11290991--11291108	25	4.9	25	75	14	131	44	13	0	41	1.44
11290985--11291118	70	1.9	70	100	0	268	47	12	0	39	1.42
11291538--11291577	18	2.2	18	95	0	71	40	7	30	22	1.81
11292224--11292248	7	3.6	7	100	0	50	60	12	0	28	1.32
11292419--11292456	20	1.9	20	89	10	60	55	5	2	36	1.37
11293351--11293392	12	3.5	12	83	0	57	61	0	7	30	1.22
11293460--11293499	11	3.6	11	93	6	64	42	0	35	22	1.54
11301800--11301833	17	1.9	18	94	5	61	55	26	0	17	1.42
11304456--11304493	19	2.0	19	94	0	67	39	13	0	47	1.42
11308642--11308701	30	2.0	29	93	3	102	38	18	15	28	1.91
11322741--11322791	26	1.9	26	88	4	75	13	9	3	72	1.24
11326759--11326785	2	13.5	2	100	0	54	48	0	0	51	1.00
11332121--11332188	18	3.9	17	72	16	59	64	2	1	30	1.17
11332120--11332161	9	4.7	9	80	8	50	59	2	0	38	1.10
11332120--11332196	19	4.4	17	69	18	59	63	2	1	32	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11332103--11332205	27	3.8	26	71	18	86	64	1	1	32	1.16
11333824--11333918	49	1.9	50	86	2	138	27	21	32	18	1.97
11333823--11333928	49	2.1	50	82	1	133	28	19	32	19	1.97
11347636--11347690	9	6.1	9	84	0	74	30	9	12	47	1.73
11347636--11347690	18	3.1	18	91	0	83	30	9	12	47	1.73
11347842--11347904	24	2.6	24	76	0	72	49	22	11	17	1.78
11347911--11347983	30	2.5	29	80	6	85	38	26	13	21	1.91
11350645--11350711	9	7.4	9	86	0	80	25	7	25	41	1.81
11350645--11350712	18	3.8	18	84	7	93	25	7	25	42	1.80
11356277--11356324	25	1.9	25	91	0	78	33	6	25	35	1.81
11361550--11361574	2	12.5	2	100	0	50	52	48	0	0	1.00
11362822--11362915	20	4.9	19	69	20	61	60	4	1	34	1.23
11363694--11363770	9	8.4	9	68	18	52	40	0	1	58	1.06
11363675--11363785	19	5.8	19	70	18	70	36	0	4	58	1.18
11363694--11363770	36	2.1	37	81	11	88	40	0	1	58	1.06
11363632--11363787	10	16.6	9	71	15	86	37	0	3	58	1.21
11363806--11363832	14	1.9	14	100	0	54	14	7	0	77	0.97
11363806--11363851	17	2.9	16	82	17	53	21	4	0	73	1.00
11364425--11364482	19	2.9	19	85	10	64	53	6	0	39	1.28
11372353--11372399	7	6.7	7	100	0	94	29	42	14	12	1.83
11372396--11372451	18	3.0	19	78	5	69	46	33	0	19	1.50
11372423--11372578	78	2.0	78	100	0	312	39	26	5	28	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11377118--11377151	16	2.1	16	88	0	50	8	11	5	73	1.24
11377471--11377521	22	2.3	22	89	3	75	39	29	1	29	1.68
11383528--11383637	12	8.9	12	67	16	55	50	9	15	24	1.72
11383605--11383654	14	3.6	14	81	5	57	60	10	14	16	1.59
11383518--11383648	12	10.2	13	66	20	53	52	9	14	23	1.70
11391846--11391895	14	3.6	14	84	15	68	54	6	8	32	1.54
11391850--11391995	13	11.5	12	69	20	66	53	8	11	26	1.65
11391953--11392019	14	4.6	14	76	10	55	58	10	8	22	1.59
11391954--11392006	27	1.9	28	84	3	72	58	9	9	22	1.58
11394409--11394443	18	1.9	18	88	0	52	60	8	8	22	1.54

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