genome.fa.s5.2.7.7.80.10.50.1000.22.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  22  of  208  ( 24913 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)
6392609--6392733	33	3.5	33	72	17	97	20	15	28	36	1.92
6392605--6392815	75	2.8	73	85	5	287	22	18	27	32	1.97
6394867--6394904	19	2.0	19	89	0	58	34	5	26	34	1.79
6397014--6397054	10	4.2	10	84	6	57	26	2	2	68	1.15
6398363--6398397	2	17.5	2	93	0	61	48	2	0	48	1.16
6402310--6402392	25	3.3	25	91	0	130	15	22	22	38	1.92
6402381--6402438	22	2.6	22	75	0	62	17	27	17	37	1.92
6403361--6403414	28	1.9	27	82	14	65	44	3	16	35	1.66
6406786--6406903	41	2.9	41	94	0	200	23	20	24	31	1.98
6407082--6407257	41	4.3	41	86	0	226	30	16	27	25	1.97
6410086--6410432	173	2.0	173	100	0	694	40	13	20	25	1.89
6417359--6417913	44	12.6	44	82	4	591	32	16	20	30	1.94
6417370--6417880	177	2.9	176	83	2	673	33	15	20	30	1.94
6420500--6420552	28	2.0	26	85	7	70	33	13	1	50	1.52
6424598--6424623	6	4.3	6	100	0	52	15	15	0	69	1.20
6426356--6426392	16	2.3	16	90	0	56	27	13	2	56	1.50
6430118--6430210	46	2.0	46	97	0	177	58	12	15	13	1.64
6444974--6445023	18	2.7	18	84	6	55	46	2	2	50	1.24
6445531--6445663	61	2.2	60	84	1	167	37	6	15	40	1.72
6446877--6446905	14	2.1	14	100	0	58	75	0	0	24	0.80
6446872--6446953	42	1.9	42	87	7	121	63	0	1	35	1.02
6446876--6446965	41	2.2	41	80	9	103	64	0	1	34	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6447681--6447729	19	2.5	20	80	6	64	24	4	0	71	1.03
6468718--6468771	28	2.0	27	85	10	74	29	20	1	48	1.60
6478923--6479069	77	1.9	77	81	2	179	24	28	12	34	1.92
6479089--6479113	8	3.1	8	100	0	50	24	0	28	48	1.52
6479148--6479181	11	2.8	12	86	13	52	17	2	0	79	0.86
6480026--6480086	30	2.1	29	87	3	86	32	8	4	54	1.52
6480026--6480086	29	2.1	30	84	9	81	32	8	4	54	1.52
6482595--6483230	318	2.0	318	99	0	1254	27	20	20	32	1.97
6483518--6483591	28	2.7	27	83	6	105	45	6	0	47	1.29
6483647--6483723	27	2.9	27	90	0	118	28	29	27	14	1.95
6483639--6483739	27	3.7	25	76	15	94	26	27	28	16	1.97
6483873--6483911	19	2.0	21	85	10	55	23	0	10	66	1.22
6483978--6484003	3	8.7	3	100	0	52	0	0	30	69	0.89
6489644--6489673	16	1.9	15	93	6	51	26	3	0	70	1.03
6505719--6505878	86	1.9	85	83	8	209	29	25	19	26	1.98
6506520--6506547	14	2.0	14	100	0	56	50	21	0	28	1.49
6508237--6508272	2	18.5	2	94	5	65	50	0	0	50	1.00
6519329--6519392	26	2.5	25	82	5	74	70	3	6	20	1.23
6520009--6520033	8	3.1	8	100	0	50	12	0	0	88	0.53
6520739--6520790	24	2.2	24	85	0	68	53	0	5	40	1.25
6521033--6521376	178	1.9	177	89	2	530	36	12	10	40	1.78
6522001--6522096	42	2.3	42	94	0	165	25	22	18	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6522085--6522111	13	2.1	13	100	0	54	37	33	22	7	1.82
6522043--6522150	55	2.0	55	85	3	146	28	24	20	26	1.99
6521999--6522195	97	2.0	97	80	1	216	27	21	21	28	1.99
6522096--6522308	42	5.0	42	72	6	164	28	19	20	30	1.97
6522685--6522733	21	2.3	21	82	6	64	4	46	16	32	1.65
6525070--6525422	9	38.3	9	72	15	231	35	1	16	45	1.58
6525187--6525273	25	3.4	25	75	12	104	34	1	22	41	1.62
6525176--6525342	52	3.2	52	87	3	219	34	0	18	46	1.54
6525374--6525428	18	3.1	18	87	7	69	36	1	14	47	1.55
6525532--6525570	17	2.2	17	86	4	51	56	0	5	38	1.22
6528279--6528324	14	3.3	14	81	0	56	43	34	0	21	1.53
6528506--6528554	21	2.3	22	85	3	64	36	40	2	20	1.64
6528623--6528655	14	2.4	14	89	0	57	51	27	0	21	1.48
6528595--6528687	39	2.4	40	83	5	127	48	22	2	26	1.62
6530054--6530115	3	20.7	3	100	0	124	67	0	0	32	0.91
6530498--6530539	21	2.0	21	85	0	57	66	7	2	23	1.28
6535570--6535595	8	3.2	8	100	0	52	38	0	11	50	1.39
6535780--6535848	26	2.6	27	75	18	74	56	5	7	30	1.50
6535780--6535861	26	3.2	26	71	22	73	57	4	7	30	1.47
6535882--6535929	3	16.0	3	100	0	96	66	0	0	33	0.92
6541073--6541125	3	17.7	3	100	0	106	32	0	0	67	0.91
6541131--6541164	12	2.8	12	87	12	52	23	5	0	70	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6542254--6542291	10	3.7	10	92	3	58	92	5	2	0	0.47
6542254--6542291	11	3.5	11	92	7	60	92	5	2	0	0.47
6542251--6542291	20	2.0	20	90	9	66	90	7	2	0	0.54
6544264--6544513	44	5.8	44	72	10	178	27	21	22	29	1.99
6544264--6544511	128	1.9	129	81	7	299	27	21	22	29	1.99
6544555--6544746	44	4.4	44	70	10	158	27	23	19	29	1.98
6544582--6544775	44	4.4	44	68	10	128	26	24	18	30	1.97
6544415--6544686	150	1.8	150	80	3	332	25	24	19	30	1.98
6544560--6544855	132	2.2	131	92	2	486	27	24	19	29	1.98
6544845--6545158	44	7.1	44	84	1	439	29	26	14	29	1.95
6544834--6545158	89	3.7	86	85	5	418	29	25	14	29	1.95
6544834--6545158	133	2.4	133	94	0	569	29	25	14	29	1.95
6546320--6546371	8	7.3	7	81	14	54	11	17	0	71	1.15
6546333--6546380	21	2.2	21	85	10	62	14	14	0	70	1.16
6547268--6547306	17	2.2	17	86	4	51	66	7	15	10	1.43
6549255--6549280	13	2.0	13	100	0	52	46	15	7	30	1.74
6551324--6551392	26	2.6	27	75	18	74	56	5	7	30	1.50
6551324--6551405	26	3.2	26	71	22	73	57	4	7	30	1.47
6551426--6551480	3	18.3	3	100	0	110	67	0	0	32	0.91
6552046--6552096	16	3.2	15	76	20	50	78	1	9	9	1.04
6553544--6553586	21	2.0	21	100	0	86	48	27	4	18	1.68
6580301--6580492	63	3.0	62	92	1	303	36	13	16	33	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6585513--6585553	2	20.5	2	100	0	82	48	0	0	51	1.00
6585867--6585917	22	2.3	23	80	16	63	39	45	0	15	1.47
6585888--6585934	17	2.9	16	87	12	69	34	48	0	17	1.47
6586191--6586586	118	3.4	116	88	3	564	26	25	20	27	1.99
6586687--6587625	115	8.1	115	87	3	1260	26	25	21	26	1.99
6586687--6587887	231	5.1	229	81	7	1293	26	25	21	26	2.00
6586687--6587887	346	3.4	345	83	7	1358	26	25	21	26	2.00
6587538--6587768	72	3.2	72	83	2	293	25	25	21	26	2.00
6587669--6587886	118	1.9	115	90	2	346	26	27	21	25	1.99
6587407--6588013	262	2.3	260	84	4	756	24	26	21	27	1.99
6587784--6588089	147	2.1	148	86	4	422	23	24	23	28	2.00
6587784--6588106	73	4.4	74	87	2	427	23	25	23	27	2.00
6588136--6588161	12	2.2	12	100	0	52	46	30	15	7	1.74
6588706--6588735	14	2.1	14	93	0	51	70	0	6	23	1.11
6588904--6589000	23	4.4	21	71	18	58	54	5	4	36	1.42
6588889--6588995	45	2.3	45	81	13	112	56	4	3	35	1.38
6588904--6589000	45	2.2	46	82	15	116	54	5	4	36	1.42
6588920--6588995	21	3.4	21	72	22	59	53	6	2	36	1.41
6589122--6589179	3	19.3	3	100	0	116	67	0	0	32	0.91
6589205--6589230	6	4.3	6	100	0	52	84	0	0	15	0.62
6589121--6589230	18	6.1	18	81	0	76	67	0	3	28	1.14
6589411--6589474	3	21.3	3	95	0	110	68	0	1	29	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6589498--6589545	6	7.5	6	84	9	51	75	8	2	14	1.13
6590755--6590792	20	2.0	20	90	10	62	18	0	5	76	0.97
6591790--6591836	25	1.9	24	83	12	60	42	6	4	46	1.48
6596021--6596049	15	1.9	15	100	0	58	62	0	6	31	1.22
6596064--6596119	17	3.3	16	74	16	51	78	5	1	14	1.00
6599243--6599318	10	7.9	9	75	16	64	60	0	2	36	1.11
6599638--6599681	9	4.6	10	77	11	56	63	0	4	31	1.14
6599638--6599681	19	2.3	19	84	7	63	63	0	4	31	1.14
6600319--6600351	16	2.1	16	94	0	57	27	27	0	45	1.54
6600274--6600392	48	2.4	50	84	4	143	25	34	0	39	1.62

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