genome.fa.s9.2.7.7.80.10.50.1000.115.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  115  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)
39322169--39322264	22	4.3	22	88	4	122	48	11	12	27	1.75
39327569--39327616	4	12.0	4	81	0	51	22	4	4	68	1.24
39327727--39327754	2	14.0	2	100	0	56	50	0	0	50	1.00
39327856--39327909	26	2.1	26	89	0	81	42	9	0	48	1.35
39329952--39329976	9	2.8	9	100	0	50	68	8	0	24	1.16
39331707--39332336	132	4.8	132	92	0	1055	29	23	17	29	1.97
39331827--39332125	44	6.8	43	63	15	103	29	24	17	29	1.97
39334215--39334279	1	65.0	1	75	0	58	0	1	10	87	0.61
39334215--39334278	10	6.5	10	80	8	69	0	1	10	87	0.61
39334215--39334279	19	3.5	18	85	6	85	0	1	10	87	0.61
39334215--39334272	19	3.1	19	92	2	91	0	1	10	87	0.60
39338281--39338468	98	1.9	98	94	2	333	36	25	9	28	1.87
39338754--39338778	9	2.8	9	100	0	50	68	8	0	24	1.16
39339768--39339825	22	2.6	22	84	7	73	43	17	3	36	1.66
39341395--39341424	2	15.0	2	92	0	51	50	3	0	46	1.18
39345462--39345660	100	2.0	100	90	2	310	27	9	26	36	1.88
39351197--39351392	100	2.0	100	90	0	311	27	12	26	33	1.93
39359165--39359203	12	3.3	11	80	19	51	17	0	5	76	0.96
39365627--39365680	13	4.2	13	71	19	51	16	5	3	74	1.16
39367389--39367426	11	3.4	11	92	3	58	10	5	2	81	0.94
39367389--39367450	23	2.6	24	80	10	65	16	3	4	75	1.10
39367389--39367457	12	6.0	11	83	6	66	17	2	5	73	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39367407--39367457	11	4.5	11	79	16	50	21	0	5	72	1.05
39369771--39369841	3	23.7	3	91	0	115	35	29	0	35	1.58
39369840--39369885	3	15.3	3	100	0	92	65	0	0	34	0.93
39373686--39373731	16	2.9	16	81	12	60	43	0	2	54	1.12
39373677--39373736	16	4.0	15	78	8	52	43	0	3	53	1.17
39373855--39373958	44	2.5	39	82	14	145	35	27	3	32	1.75
39373872--39374005	44	3.0	44	93	3	216	35	27	5	31	1.79
39382558--39382608	23	2.3	21	76	23	59	49	0	3	47	1.20
39382562--39382607	24	1.9	25	91	8	78	50	0	4	45	1.21
39384262--39384304	12	3.6	12	83	0	50	25	4	2	67	1.22
39384362--39384450	3	29.3	3	76	6	72	31	5	2	60	1.32
39384380--39384453	30	2.5	30	82	8	80	33	6	1	58	1.33
39384816--39384869	24	2.3	23	81	9	65	33	9	5	51	1.57
39388131--39388193	11	5.6	11	71	3	54	80	14	1	3	0.90
39388624--39388673	5	10.0	5	79	16	59	80	0	18	2	0.82
39388635--39388675	6	6.8	6	79	20	50	80	0	19	0	0.71
39388624--39388675	11	5.1	11	82	15	67	78	0	19	1	0.84
39388637--39388673	19	1.9	19	100	0	74	81	0	18	0	0.70
39389587--39390165	44	13.3	44	67	11	190	27	20	25	25	1.99
39389589--39390160	131	4.4	131	88	2	805	28	20	25	25	1.99
39390109--39390433	129	2.5	128	84	4	375	31	19	19	29	1.97
39390147--39390432	44	6.7	43	69	11	120	31	19	18	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39391955--39392023	23	2.9	24	69	16	63	33	4	7	55	1.47
39393506--39393535	11	2.7	11	100	0	60	63	0	20	16	1.31
39410017--39410139	65	1.9	64	85	6	169	53	17	4	23	1.63
39419667--39419915	129	1.9	129	82	1	311	18	13	14	53	1.72
39423538--39423579	12	3.7	12	75	12	52	52	2	2	42	1.27
39424568--39424643	26	3.0	25	86	5	107	34	17	9	39	1.81
39431824--39431892	26	2.7	26	76	0	84	24	28	23	23	1.99
39441929--39441960	12	2.7	12	90	0	55	15	15	34	34	1.90
39443223--39443260	20	2.0	20	84	5	51	42	21	5	31	1.75
39444047--39444123	30	2.6	30	85	0	100	29	22	25	22	1.99
39444231--39444333	26	4.0	26	79	9	120	39	25	20	14	1.90
39444479--39444592	27	4.2	27	79	4	122	23	16	21	37	1.93
39444478--39444847	54	6.9	53	82	4	341	25	16	19	38	1.92
39444492--39444847	27	13.2	25	79	9	244	25	16	18	39	1.91
39444478--39444847	81	4.6	79	81	5	348	25	16	19	38	1.92
39447157--39447212	26	2.2	26	90	3	87	33	25	17	23	1.96
39448690--39448723	17	2.1	17	94	5	61	47	0	11	41	1.40
39454289--39454326	18	2.1	18	95	0	67	31	28	21	18	1.97
39458091--39458115	5	5.0	5	100	0	50	60	0	0	40	0.97
39463019--39463058	18	2.2	18	100	0	80	40	5	30	25	1.77
39464860--39464957	51	1.9	51	85	8	137	48	4	20	26	1.67
39474717--39474758	20	2.0	20	86	9	57	40	4	21	33	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39482681--39482722	2	21.0	2	100	0	84	50	0	0	50	1.00
39483657--39483696	20	2.0	20	90	0	62	60	15	0	25	1.35
39485947--39486103	41	3.8	41	89	1	235	17	19	30	31	1.95
39487879--39487916	14	2.7	14	91	0	58	21	0	44	34	1.52
39487885--39487934	21	2.3	21	82	3	64	24	0	44	32	1.54
39490837--39490921	43	2.0	43	88	0	125	35	7	11	45	1.68
39491170--39491299	43	3.1	40	82	5	143	26	13	27	31	1.94
39491192--39491428	129	1.8	128	81	2	296	29	16	27	27	1.97
39491184--39491436	43	5.9	43	79	3	251	28	16	28	26	1.97
39491171--39491451	129	2.2	127	78	3	285	28	15	27	28	1.96
39491522--39491567	21	2.2	21	96	0	83	23	32	21	21	1.98
39498202--39498465	130	2.0	130	94	1	458	26	15	10	46	1.78
39507569--39507691	43	2.9	42	77	13	135	26	16	24	32	1.96
39513801--39513854	25	2.2	25	81	15	60	16	9	22	51	1.72
39514239--39514744	250	2.0	251	89	2	768	23	18	27	31	1.97
39521702--39521781	30	2.7	30	84	0	115	22	27	11	38	1.88
39521735--39521930	60	3.3	58	73	10	173	24	23	14	37	1.92
39521768--39521921	30	5.2	30	72	12	113	25	22	13	38	1.91
39521760--39521870	30	3.7	29	82	5	132	25	21	14	38	1.91
39521735--39521936	59	3.4	58	72	10	167	24	23	13	37	1.92
39525024--39525101	25	3.1	25	78	10	88	28	19	25	26	1.99
39529023--39529075	28	1.9	28	84	3	72	43	7	1	47	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39531180--39531371	50	3.8	50	91	0	303	23	22	33	20	1.97
39532108--39532150	16	2.6	16	77	3	50	51	2	9	37	1.47
39538208--39538278	30	2.4	30	76	9	83	35	12	19	32	1.90
39538616--39538850	50	4.7	50	87	0	317	25	22	30	20	1.98
39541076--39541114	19	2.1	19	100	0	78	20	10	25	43	1.83
39541440--39541494	20	2.7	20	80	2	56	5	40	0	54	1.23
39542173--39542369	27	7.3	27	73	10	161	43	19	18	18	1.88
39542173--39542351	54	3.3	54	87	0	241	43	20	18	17	1.88
39542188--39542365	81	2.2	81	84	3	225	43	19	18	18	1.89
39542517--39542619	26	4.0	26	79	2	100	16	23	24	35	1.95
39542729--39542813	30	2.9	30	85	3	111	25	23	22	28	1.99
39543608--39543643	17	2.1	17	89	0	54	47	11	27	13	1.77
39547080--39547147	27	2.5	27	81	9	77	27	10	10	51	1.68
39548377--39548424	20	2.5	20	78	21	57	33	10	8	47	1.68
39549366--39549421	18	3.1	18	82	15	71	69	0	19	10	1.17
39549377--39549429	18	3.0	18	86	8	65	71	0	18	9	1.12
39553931--39554493	138	4.1	138	88	1	833	46	6	7	40	1.57
39553931--39554493	275	2.0	276	91	1	903	46	6	7	40	1.57
39555856--39556052	51	3.9	50	76	6	191	25	17	27	29	1.97
39559552--39559728	77	2.3	76	86	6	241	35	7	7	49	1.61
39559552--39559751	77	2.6	77	82	8	214	33	8	8	50	1.62
39562732--39562775	22	1.9	24	86	9	65	47	2	9	40	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39566708--39566734	3	9.0	3	100	0	54	33	0	33	33	1.58
39567768--39567820	20	2.7	20	90	0	88	47	9	7	35	1.64
39569876--39569919	22	1.9	24	86	9	65	50	0	9	40	1.34
39572731--39572764	16	2.1	16	88	0	50	44	0	0	55	0.99
39578222--39578281	24	2.5	24	83	0	75	13	21	41	23	1.88
39578244--39578280	12	3.1	12	88	0	56	16	27	35	21	1.94
39583035--39583086	27	1.9	27	84	0	68	57	9	25	7	1.57
39591200--39591316	25	4.8	25	68	7	78	34	21	23	20	1.97
39591382--39591430	26	1.9	26	83	4	64	34	20	24	20	1.96
39599362--39599555	101	1.9	102	88	3	293	26	17	26	29	1.97

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