genome.fa.s4.2.7.7.80.10.50.1000.155.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  155  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)
49035397--49035518	60	2.0	60	85	3	165	31	0	13	53	1.46
49038594--49038657	22	3.0	22	93	2	103	0	32	3	64	1.10
49038599--49038664	22	3.3	18	78	19	69	1	31	3	63	1.19
49038745--49038853	27	4.0	27	93	0	182	22	37	22	17	1.94
49052892--49052972	36	2.2	37	84	2	101	41	20	7	29	1.80
49053177--49053304	43	3.0	43	80	11	154	31	27	17	23	1.97
49053678--49053711	14	2.4	14	95	0	59	14	29	11	44	1.81
49054034--49054079	25	1.9	23	83	16	58	39	13	0	47	1.42
49054892--49054936	23	2.0	23	90	0	72	31	8	4	55	1.51
49058330--49058575	101	2.4	101	89	0	384	29	25	14	30	1.95
49058375--49058538	35	4.8	34	68	8	109	28	28	15	28	1.96
49062660--49062723	22	2.9	22	78	0	83	15	26	20	37	1.92
49062639--49062723	44	1.9	44	88	4	127	15	28	18	37	1.91
49064309--49064365	13	4.5	13	72	18	57	64	0	3	31	1.10
49065045--49065102	22	2.6	22	81	7	64	41	17	5	36	1.72
49065363--49065397	18	1.9	18	88	0	52	31	5	17	45	1.71
49065453--49065511	21	2.8	21	86	0	82	35	16	22	25	1.95
49067162--49067229	31	2.4	27	83	11	75	26	1	2	69	1.12
49067288--49067471	90	2.0	92	84	2	237	34	20	9	35	1.84
49067472--49067526	26	2.0	29	86	13	80	63	0	1	34	1.05
49067498--49067544	10	4.9	10	74	10	53	57	0	0	42	0.98
49067516--49067559	19	2.3	20	80	11	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49067807--49067903	10	10.3	9	71	13	54	27	3	3	65	1.22
49067823--49067921	29	3.4	28	72	17	85	32	2	3	62	1.22
49067853--49067904	19	2.7	20	88	5	81	26	3	1	67	1.18
49067989--49068199	89	2.4	89	78	7	239	33	8	18	39	1.81
49072796--49072825	2	15.0	2	100	0	60	0	50	0	50	1.00
49085709--49085743	16	2.2	16	90	10	54	45	2	14	37	1.59
49092940--49092996	19	3.1	19	82	14	66	36	0	5	57	1.21
49098816--49099220	110	3.7	110	91	2	629	33	19	16	31	1.93
49099868--49099901	3	11.3	3	93	0	59	67	2	0	29	1.05
49105362--49105413	19	2.7	19	76	8	52	57	3	0	38	1.17
49108744--49108803	30	2.0	30	100	0	120	30	20	16	33	1.94
49110758--49110924	46	3.6	46	87	1	237	27	23	16	32	1.96
49112651--49112715	23	2.8	23	76	2	67	43	16	10	29	1.82
49120751--49120792	15	2.9	15	82	10	52	47	0	0	52	1.00
49123831--49123879	25	2.0	25	84	8	64	24	6	6	63	1.41
49126576--49127029	32	14.2	32	80	6	458	31	10	16	41	1.82
49126576--49127018	64	6.9	64	88	2	622	31	10	16	41	1.83
49129990--49130020	16	1.9	16	100	0	62	45	0	9	45	1.36
49131430--49131467	19	2.1	19	85	5	51	26	10	2	60	1.43
49138594--49138646	21	2.5	21	81	3	61	11	20	16	50	1.76
49138625--49138772	42	3.5	42	82	8	176	14	22	16	45	1.85
49138669--49138775	21	5.1	21	64	8	65	14	25	17	42	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49146225--49146251	6	4.5	6	100	0	54	0	14	0	85	0.61
49147946--49147989	19	2.4	18	81	7	54	34	0	2	63	1.07
49149903--49149948	25	1.9	24	86	8	67	60	10	0	28	1.30
49151105--49151142	9	4.2	9	89	0	58	34	10	0	55	1.34
49151108--49151146	12	3.2	12	88	0	60	33	7	0	58	1.26
49151108--49151146	3	13.0	3	88	0	51	33	7	0	58	1.26
49151473--49151503	2	15.5	2	100	0	62	48	0	0	51	1.00
49163224--49163263	16	2.5	16	91	0	71	35	5	32	27	1.79
49163474--49163875	120	3.3	120	95	0	725	51	3	0	43	1.24
49165167--49165270	49	2.1	49	90	0	163	49	10	8	31	1.68
49167407--49167478	27	2.6	28	78	20	71	45	2	5	45	1.41
49180304--49180447	48	3.0	48	97	0	270	30	28	12	28	1.93
49186094--49186173	31	2.6	31	90	2	117	20	10	21	48	1.78
49195974--49196005	2	16.0	2	100	0	64	0	50	0	50	1.00
49208428--49208585	70	2.3	69	78	1	172	34	17	10	37	1.84
49208185--49208495	140	2.2	140	82	3	367	35	19	9	35	1.85
49208392--49208731	69	4.9	69	72	3	227	32	17	11	39	1.84
49210962--49210992	2	15.5	2	100	0	62	48	0	0	51	1.00
49215994--49216048	25	2.2	25	81	12	60	18	21	25	34	1.96
49216003--49216064	25	2.5	24	77	15	63	20	19	22	37	1.95
49218102--49218768	44	15.0	45	68	13	324	28	23	24	23	1.99
49218102--49218967	89	9.8	88	82	4	827	28	23	23	24	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49219761--49219785	7	3.6	7	100	0	50	48	12	16	24	1.79
49220512--49220605	9	10.4	9	77	0	80	29	6	2	61	1.32
49220512--49220605	6	15.7	6	77	0	80	29	6	2	61	1.32
49220512--49220592	30	2.7	30	86	3	101	32	7	2	58	1.39
49220546--49220600	21	2.6	21	88	0	74	30	3	1	63	1.22
49226109--49226191	43	2.0	42	80	7	96	49	16	20	13	1.79
49227588--49229507	89	21.6	89	82	3	1922	28	25	22	23	1.99
49229118--49229360	44	5.5	42	67	13	130	28	26	23	20	1.99
49231068--49231180	6	18.8	6	85	0	118	29	6	0	63	1.24
49231068--49231180	9	12.6	9	82	0	118	29	6	0	63	1.24
49231150--49231178	15	1.9	15	100	0	58	20	0	3	75	0.94
49235497--49235531	17	2.1	16	89	5	52	51	0	0	48	1.00
49241461--49242161	81	8.7	81	86	1	796	42	17	28	11	1.84
49241659--49241884	36	5.8	36	70	19	157	44	16	27	11	1.82
49241897--49242121	36	5.8	36	69	17	117	43	16	27	13	1.85
49244680--49244716	13	2.8	13	83	0	56	24	45	21	8	1.78
49245813--49245892	39	2.1	39	100	0	160	28	15	7	48	1.71
49250383--49250417	15	2.4	15	95	4	63	40	5	17	37	1.73
49251437--49251468	13	2.5	13	94	0	55	31	0	12	56	1.37
49251563--49251911	50	6.8	50	91	2	500	26	22	30	21	1.99
49264619--49264685	29	2.3	29	92	0	107	19	25	35	19	1.95
49268059--49268090	16	2.0	16	100	0	64	12	12	12	62	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49272485--49272587	41	2.5	40	89	4	154	51	5	22	20	1.68
49272553--49272598	24	1.9	24	90	0	74	56	6	23	13	1.60
49279361--49279521	46	3.6	45	94	3	272	32	15	23	28	1.95
49280103--49280248	73	2.0	73	100	0	292	28	16	24	30	1.96
49280739--49280794	19	2.8	19	91	5	85	37	10	14	37	1.81
49281021--49281065	23	2.0	23	81	0	54	22	0	15	62	1.33
49281359--49281435	37	2.1	37	80	11	86	37	9	1	51	1.42
49296632--49296664	10	3.0	11	86	13	50	18	36	0	45	1.49
49296654--49296701	22	2.2	22	92	0	78	25	33	0	41	1.55
49296727--49296777	22	2.3	22	89	0	84	25	31	1	41	1.67
49296647--49296813	73	2.3	73	92	1	273	26	28	1	44	1.62
49297951--49297976	7	3.7	7	100	0	52	26	0	15	57	1.38
49298623--49298658	18	2.0	18	94	0	63	22	30	5	41	1.76
49299161--49299328	29	5.7	29	91	2	255	45	30	0	23	1.53
49299335--49299629	37	8.0	37	97	0	554	40	12	0	46	1.47
49303962--49304002	3	13.7	3	100	0	82	68	0	0	31	0.90
49311041--49311114	21	3.5	21	80	10	89	21	33	12	32	1.90
49316212--49316271	32	2.0	31	81	18	74	48	0	0	51	1.00
49316722--49316780	23	2.4	24	83	8	66	40	6	6	45	1.57
49325072--49325100	9	3.2	9	100	0	58	68	0	0	31	0.89
49325521--49325581	30	2.1	30	84	3	79	39	0	40	19	1.52
49325712--49325742	9	3.4	9	90	0	53	38	22	12	25	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49333401--49333461	27	2.3	27	100	0	122	18	40	9	31	1.83
49339404--49339436	14	2.4	14	90	5	50	33	3	0	63	1.10
49340128--49340165	18	2.0	20	90	10	62	36	0	2	60	1.11
49343772--49343801	5	5.8	5	96	4	51	80	3	0	16	0.85
49346413--49346450	16	2.4	16	90	0	58	31	0	34	34	1.58
49346684--49346718	18	2.0	17	88	5	52	54	0	0	45	0.99
49346783--49346823	15	2.8	15	82	10	50	53	2	0	43	1.13
49346924--49346958	18	2.0	17	88	5	52	54	0	0	45	0.99
49346880--49347077	59	3.3	58	69	21	167	50	4	3	42	1.36
49346662--49347079	120	3.5	120	95	1	748	49	5	2	43	1.37

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