genome.fa.s9.2.7.7.80.10.50.1000.94.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  94  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)
32481730--32481792	30	2.1	30	94	5	110	57	11	3	28	1.49
32485892--32485977	45	1.9	44	81	6	102	43	6	0	50	1.29
32486902--32486940	2	19.5	2	100	0	78	51	0	0	48	1.00
32493693--32493805	37	3.1	37	78	0	118	38	23	18	19	1.93
32496311--32496370	21	2.9	21	80	7	61	55	6	3	35	1.43
32496585--32496609	12	2.1	12	100	0	50	16	0	24	60	1.36
32502087--32502134	18	2.7	18	86	0	69	16	12	41	29	1.85
32504555--32504680	44	2.9	43	75	12	114	24	18	26	30	1.98
32504558--32504713	42	3.7	41	72	19	124	25	18	25	30	1.98
32505013--32505057	17	2.6	18	76	16	51	44	0	20	35	1.51
32511055--32511093	18	2.2	18	86	9	53	35	2	12	48	1.55
32511346--32511376	2	15.5	2	100	0	62	48	0	0	51	1.00
32513397--32513453	21	2.7	21	86	5	71	21	28	17	33	1.96
32514415--32514474	23	2.5	24	76	15	70	58	1	0	40	1.08
32514418--32514475	22	2.5	23	81	10	66	58	1	0	39	1.08
32514421--32514485	22	2.8	22	75	11	60	55	3	1	40	1.25
32515720--32515786	31	2.3	28	84	7	80	28	1	2	67	1.14
32516159--32516192	7	5.0	7	89	7	52	17	0	0	82	0.67
32516159--32516185	13	2.1	13	100	0	54	14	0	0	85	0.61
32516200--32516238	19	2.0	20	90	10	62	41	0	0	58	0.98
32516201--32516245	19	2.2	20	84	11	56	40	0	2	57	1.11
32520101--32520639	70	7.7	70	80	5	515	22	17	26	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32520101--32520639	140	3.9	140	82	3	638	22	17	26	33	1.96
32520119--32520642	210	2.5	210	82	4	626	22	16	27	32	1.96
32522408--32522454	20	2.4	20	85	3	60	25	25	8	40	1.84
32535622--32535726	56	1.9	55	86	2	147	56	5	12	25	1.58
32544013--32544413	188	2.1	189	91	1	662	31	24	12	31	1.92
32545267--32545291	7	3.6	7	100	0	50	76	0	24	0	0.80
32546151--32546210	27	2.3	26	78	15	72	40	0	0	60	0.97
32546496--32546551	2	28.0	2	100	0	112	50	0	0	50	1.00
32547796--32547828	17	1.9	17	93	0	57	33	30	15	21	1.94
32555521--32555586	13	5.1	13	78	14	82	36	27	4	31	1.77
32555521--32555586	26	2.5	26	97	0	123	36	27	4	31	1.77
32560523--32560636	51	2.2	52	76	13	121	44	2	0	51	1.21
32561007--32561045	16	2.4	16	86	0	51	48	5	7	38	1.54
32560979--32561033	22	2.5	22	81	0	65	52	3	1	41	1.29
32561016--32561048	16	2.1	16	94	0	57	45	0	9	45	1.35
32561059--32561228	59	2.9	59	98	0	322	40	5	9	44	1.59
32561295--32561338	24	1.9	24	90	9	74	61	2	0	36	1.09
32563164--32563221	19	3.0	19	85	12	66	44	0	10	44	1.38
32580426--32580542	17	6.8	17	74	2	90	37	26	18	17	1.93
32580514--32580548	17	2.1	17	88	0	52	34	25	20	20	1.96
32581892--32581968	39	2.0	39	89	0	118	24	32	22	20	1.98
32586581--32586617	13	2.7	14	87	4	58	21	0	27	51	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32586581--32586629	14	3.6	13	86	8	55	22	2	24	51	1.59
32586793--32586830	14	2.7	14	84	8	51	18	0	34	47	1.49
32587189--32587226	20	1.9	20	94	0	67	34	0	7	57	1.28
32593310--32593349	21	1.9	21	89	0	62	30	12	52	5	1.60
32593348--32593373	5	5.2	5	100	0	52	42	19	38	0	1.51
32593681--32593894	86	2.5	86	86	1	277	28	18	27	26	1.98
32593681--32593872	43	4.5	43	85	1	260	29	18	28	23	1.98
32597179--32597221	17	2.5	17	84	0	50	37	30	11	20	1.89
32599106--32599252	57	2.5	61	81	10	180	25	25	21	28	1.99
32604900--32604941	21	2.0	22	90	4	68	38	26	4	30	1.77
32606085--32606130	24	1.9	24	100	0	92	34	15	4	45	1.66
32609190--32609219	2	15.0	2	100	0	60	50	0	0	50	1.00
32612088--32612253	88	1.9	89	83	3	219	36	19	9	33	1.85
32612494--32612553	20	3.0	20	73	11	61	60	3	8	28	1.42
32612741--32612792	10	5.3	10	79	4	52	34	0	1	63	1.06
32612741--32612792	19	2.7	20	78	3	61	34	0	1	63	1.06
32612775--32612881	29	3.7	29	77	7	92	29	1	0	67	1.08
32612775--32612880	28	3.7	29	76	12	94	30	1	0	66	1.08
32612767--32612847	37	2.2	39	80	8	96	35	1	1	61	1.12
32613048--32613227	87	2.1	85	82	6	218	35	9	11	43	1.73
32615205--32615264	26	2.4	25	83	5	84	26	11	16	45	1.82
32617661--32617720	27	2.3	26	83	11	77	55	6	8	30	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32622654--32622692	18	2.2	17	86	4	51	10	5	7	76	1.13
32624112--32624157	24	1.9	24	86	0	65	52	2	0	45	1.13
32624326--32624357	11	2.8	11	95	4	55	56	0	0	43	0.99
32628381--32628446	3	22.0	3	100	0	132	33	0	0	66	0.92
32632108--32632169	27	2.3	27	86	2	81	64	1	0	33	1.03
32632177--32632210	14	2.4	14	90	0	50	79	0	0	20	0.73
32632516--32632580	30	2.2	30	83	5	78	24	1	10	63	1.36
32632787--32632836	23	2.2	23	89	7	75	14	24	8	54	1.66
32633910--32633943	15	2.3	15	100	0	68	38	23	14	23	1.92
32638269--32638310	15	2.8	16	82	10	52	4	7	14	73	1.21
32638853--32638880	14	2.0	14	100	0	56	7	28	0	64	1.20
32638833--32638877	19	2.5	18	83	16	58	6	26	0	66	1.16
32640637--32640699	29	2.2	29	80	5	74	46	6	12	34	1.68
32642041--32642086	16	2.9	16	84	9	51	39	2	4	54	1.32
32642415--32642456	15	2.9	15	82	10	52	47	0	0	52	1.00
32642679--32642732	16	3.4	16	84	0	72	27	33	1	37	1.68
32653733--32653845	56	2.0	56	83	8	140	28	18	8	44	1.80
32653847--32653871	10	2.5	10	100	0	50	12	20	8	60	1.57
32663801--32664078	41	6.8	41	83	1	333	17	19	32	29	1.96
32664728--32664756	15	1.9	15	100	0	58	20	0	34	44	1.52
32664789--32664825	7	5.1	7	87	6	56	18	2	51	27	1.60
32668960--32669245	43	6.6	43	85	4	362	20	16	27	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32668960--32669245	87	3.3	83	84	7	347	20	16	27	34	1.95
32670736--32671026	50	5.8	50	85	0	341	21	27	21	28	1.99
32675563--32675588	12	2.2	12	100	0	52	15	23	34	26	1.94
32686511--32686542	14	2.2	15	94	5	57	78	0	3	18	0.89
32687574--32688575	100	10.1	100	85	2	1284	23	20	22	32	1.98
32687574--32688575	299	3.4	296	85	4	1316	23	20	22	32	1.98
32687558--32688576	50	20.4	50	71	4	604	23	21	22	32	1.98
32688602--32688754	45	3.4	45	73	8	150	25	23	25	25	2.00
32688609--32688812	89	2.3	89	87	2	302	23	24	25	27	2.00
32690016--32690048	16	2.1	16	88	11	50	3	21	0	75	0.93
32690013--32690064	26	2.0	27	88	3	79	1	19	0	78	0.84
32690015--32690064	19	2.5	19	81	18	66	2	20	0	78	0.86
32695138--32695201	3	21.0	3	79	3	56	54	1	4	39	1.31
32695138--32695201	24	2.6	24	82	7	76	54	1	4	39	1.31
32701598--32701659	3	20.7	3	100	0	124	66	0	0	33	0.92
32703638--32703678	16	2.7	16	85	7	59	65	4	12	17	1.42
32704654--32704709	25	2.2	25	87	0	85	21	23	26	28	1.99
32713014--32713041	10	2.8	10	100	0	56	0	53	39	7	1.28
32713043--32713104	27	2.3	27	88	2	90	62	1	0	35	1.05
32717843--32717969	36	3.5	36	79	2	103	25	12	35	25	1.92
32719247--32719325	34	2.3	34	82	0	95	26	18	21	32	1.97
32726245--32726279	14	2.4	15	90	4	54	17	14	0	68	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32726783--32726815	17	2.0	17	88	5	50	3	9	6	81	0.95
32731258--32731289	6	5.3	6	100	0	64	84	0	0	15	0.63
32752502--32752593	37	2.4	36	81	15	98	40	3	4	52	1.38
32757177--32757218	10	4.2	10	100	0	84	9	9	19	61	1.53
32757177--32757233	15	3.8	15	83	0	69	8	10	19	61	1.54
32757178--32757255	15	5.2	15	79	0	66	7	12	17	61	1.54
32757198--32757251	25	2.2	25	83	6	65	7	11	18	62	1.50
32757253--32757293	20	2.0	20	85	0	55	12	24	7	56	1.61
32766713--32766737	13	1.9	13	100	0	50	40	8	8	44	1.63
32768833--32768866	17	2.0	17	94	0	59	14	17	55	11	1.68

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