genome.fa.s9.2.7.7.80.10.50.1000.175.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  175  of  226  ( 27023 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)
55965242--55965269	2	14.0	2	100	0	56	0	50	0	50	1.00
55965802--55965835	3	11.3	3	100	0	68	67	0	0	32	0.91
55968096--55968143	4	12.0	4	100	0	96	25	0	0	75	0.81
55969489--55969518	13	2.3	13	94	0	51	30	6	6	56	1.51
55978201--55978254	25	2.1	27	83	16	71	31	3	3	61	1.31
55985187--55985222	17	2.1	17	100	0	72	30	16	16	36	1.91
55985941--55985974	11	2.8	13	91	8	54	44	11	8	35	1.72
55986648--55986697	26	1.9	26	95	0	91	16	24	32	28	1.96
55986570--55986834	102	2.6	102	87	1	406	18	20	30	30	1.96
55989741--55989787	22	2.2	22	85	11	62	40	4	0	55	1.19
55990002--55990039	2	19.5	2	89	5	60	50	2	0	47	1.15
55998235--55998365	50	2.6	50	85	0	163	26	22	29	21	1.99
55998248--55998427	50	3.6	49	79	8	154	27	21	28	22	1.99
55998518--55998605	44	2.0	44	100	0	176	43	6	25	25	1.79
55999134--55999336	101	2.0	101	97	0	379	46	6	17	29	1.73
56006524--56006571	25	1.9	25	95	0	87	14	10	20	54	1.70
56022512--56022575	31	2.1	31	100	0	128	23	3	21	51	1.62
56024755--56024790	12	3.1	12	92	4	56	22	25	0	52	1.47
56027475--56027505	15	2.0	16	93	6	55	58	3	0	38	1.15
56028731--56028823	43	2.2	43	84	3	116	35	2	11	50	1.51
56030102--56030131	15	1.9	16	93	6	53	56	10	0	33	1.32
56031551--56031604	19	2.8	19	81	8	56	55	7	0	37	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56033380--56033418	2	19.5	2	100	0	78	48	0	51	0	1.00
56033566--56033602	2	18.5	2	100	0	74	0	48	0	51	1.00
56037473--56038050	86	6.7	86	81	8	559	32	14	10	42	1.79
56037473--56038050	174	3.3	173	82	8	596	32	14	10	42	1.79
56040824--56040848	12	2.1	12	100	0	50	32	8	16	44	1.76
56044468--56045323	44	19.7	44	71	7	408	27	25	19	28	1.99
56044369--56044914	264	2.1	265	89	1	835	27	24	18	29	1.98
56044634--56045370	217	3.4	217	93	1	1244	26	25	19	28	1.99
56046600--56046697	51	1.9	51	85	2	135	14	25	18	41	1.88
56047543--56047573	15	2.0	16	93	6	55	3	19	0	77	0.90
56047563--56047601	11	3.5	11	92	3	60	7	5	5	82	0.96
56047553--56047601	11	4.4	11	87	5	53	6	8	4	81	0.97
56047576--56047629	28	1.9	28	88	7	83	9	5	5	79	1.04
56047605--56047649	20	2.2	20	84	7	56	15	6	4	73	1.21
56047674--56047724	23	2.2	23	82	6	59	11	7	7	72	1.28
56047540--56047731	107	1.8	103	79	14	223	9	10	5	74	1.21
56054712--56054763	24	2.2	24	89	0	77	53	7	3	34	1.48
56056727--56056778	24	2.2	24	85	0	68	59	7	0	32	1.26
56063206--56063409	27	7.6	27	82	0	237	43	18	16	21	1.88
56063206--56063406	81	2.5	81	88	0	285	43	18	16	21	1.88
56065659--56065718	29	2.1	29	100	0	120	23	13	23	40	1.90
56080171--56080213	3	14.3	3	100	0	86	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56081953--56082009	26	2.2	26	81	12	64	54	0	1	43	1.10
56084342--56084544	68	3.2	60	74	18	171	47	3	3	44	1.40
56084444--56084498	25	2.2	25	81	12	60	49	5	1	43	1.36
56084402--56084546	68	2.1	71	82	10	174	50	2	2	44	1.31
56086122--56086153	15	2.1	15	94	0	55	65	6	9	18	1.42
56088812--56088851	19	2.1	19	90	0	62	30	0	7	62	1.23
56093623--56093660	2	19.0	2	100	0	76	50	0	0	50	1.00
56101637--56101788	60	2.5	60	81	5	157	22	21	19	37	1.94
56101799--56101945	58	2.5	60	83	8	183	41	17	20	20	1.90
56127451--56127488	21	1.9	19	85	15	51	47	15	2	34	1.60
56146142--56146199	20	3.0	20	75	25	61	60	0	0	39	0.97
56146380--56146413	2	17.0	2	100	0	68	50	0	0	50	1.00
56146474--56146506	17	1.9	17	88	11	50	57	9	0	33	1.30
56148186--56148233	17	2.9	17	90	3	71	27	0	18	54	1.44
56149094--56149272	46	3.9	46	90	0	277	33	11	25	29	1.91
56155714--56155955	101	2.4	100	84	4	299	30	26	17	25	1.97
56157175--56157262	43	2.0	43	86	0	122	37	9	15	37	1.80
56157973--56158026	9	6.0	9	79	16	67	22	31	0	46	1.52
56157950--56158024	36	2.1	35	82	9	89	24	32	1	42	1.63
56157974--56158024	18	2.8	18	93	0	93	23	31	0	45	1.53
56165355--56165398	23	1.9	23	90	0	70	43	6	38	11	1.67
56171601--56171629	15	1.9	15	100	0	58	55	0	27	17	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56180152--56180228	39	2.0	39	100	0	154	27	0	23	49	1.50
56187582--56187720	43	3.3	43	77	9	142	27	24	16	31	1.96
56187864--56188501	31	20.8	31	69	10	308	43	15	6	35	1.72
56187871--56188536	92	7.2	92	92	0	1071	43	14	7	34	1.73
56197706--56197750	15	2.6	17	80	20	58	55	0	2	42	1.12
56198710--56199099	194	2.0	194	90	2	622	32	16	16	33	1.92
56199334--56199385	3	17.3	3	100	0	104	32	0	0	67	0.91
56199924--56200001	39	2.0	38	85	2	102	37	14	6	42	1.71
56203883--56203934	16	3.2	16	86	0	77	42	1	25	30	1.66
56204101--56204269	61	2.6	63	81	16	204	56	1	1	41	1.15
56204253--56204303	25	2.1	25	86	13	72	62	0	1	35	1.06
56209680--56209966	27	10.7	27	80	7	273	41	18	16	23	1.89
56209680--56209966	54	5.3	54	81	5	305	41	18	16	23	1.89
56209691--56209982	81	3.6	81	81	4	317	40	18	17	23	1.91
56212359--56212420	24	2.6	25	79	7	74	27	14	27	30	1.95
56214821--56214868	26	2.0	22	84	15	60	39	10	8	41	1.69
56214976--56215102	62	2.1	58	84	5	155	49	2	4	43	1.36
56218113--56218167	26	2.1	26	96	0	101	34	16	20	29	1.94
56222900--56223013	62	1.9	59	85	8	158	50	4	4	40	1.42
56225623--56225710	31	2.8	31	82	3	106	37	18	21	22	1.94
56225854--56225903	26	1.9	26	91	0	82	46	12	16	26	1.81
56225889--56225954	29	2.3	28	87	5	96	34	21	15	28	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56230463--56230513	26	2.0	26	96	0	93	33	23	15	27	1.95
56231564--56231619	16	3.5	16	82	0	76	30	16	10	42	1.82
56231552--56231636	32	2.7	32	80	14	120	32	20	8	38	1.82
56232162--56232380	40	5.5	40	81	4	248	34	14	27	23	1.94
56232162--56232380	79	2.8	78	88	4	298	34	14	27	23	1.94
56232767--56232807	20	2.0	20	85	4	55	39	26	2	31	1.70
56234340--56234371	14	2.1	16	88	11	50	34	6	28	31	1.82
56238553--56238603	21	2.5	20	77	3	57	31	1	5	60	1.31
56239495--56239531	19	1.9	20	94	5	67	27	5	18	48	1.70
56241407--56241547	54	2.4	59	76	13	150	36	17	19	26	1.94
56241407--56241569	54	2.8	56	75	15	145	36	17	19	25	1.94
56241407--56241679	29	9.5	29	69	13	145	36	17	19	26	1.94
56241434--56241679	85	2.9	84	83	4	280	36	17	19	26	1.94
56241407--56241694	30	10.0	30	71	13	192	36	17	19	26	1.94
56242338--56242656	159	2.0	159	100	0	638	41	10	23	24	1.85
56246952--56247022	31	2.3	32	76	11	76	43	22	8	25	1.81
56247127--56247163	19	1.9	19	100	0	74	37	0	0	62	0.96
56247108--56247160	10	5.5	10	77	8	56	28	0	1	69	0.99
56248067--56248097	6	5.3	6	96	3	55	48	16	16	19	1.81
56260771--56260807	18	2.1	18	100	0	74	29	21	21	27	1.99
56263592--56263713	54	2.3	54	80	8	133	19	27	27	25	1.99
56263621--56263726	54	2.0	54	84	3	142	16	30	26	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56276579--56276741	72	2.3	72	83	0	191	28	8	23	39	1.84
56276989--56277026	20	1.9	20	94	0	67	18	10	21	50	1.76
56280006--56280118	33	3.4	32	79	6	127	19	23	10	46	1.81
56279992--56280129	33	4.2	32	76	5	114	21	23	10	44	1.83
56290447--56290515	36	1.9	36	82	5	86	21	20	23	34	1.96
56296819--56296891	23	3.2	23	78	3	85	34	26	16	23	1.95
56297343--56297404	30	2.1	30	84	0	79	35	24	4	35	1.77
56299217--56299283	9	7.4	9	78	6	73	41	19	10	28	1.84
56299323--56299347	11	2.3	11	100	0	50	16	0	16	68	1.22
56300498--56300579	42	2.0	42	82	4	103	30	23	14	31	1.94

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   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226