genome.fa.s13.2.7.7.80.10.50.1000.165.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  165  of  199  ( 23770 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)
48487620--48487668	8	6.4	8	79	9	57	53	0	2	44	1.12
48487620--48487679	30	2.0	30	100	0	120	53	0	3	43	1.17
48487622--48487687	30	2.2	30	94	2	114	57	0	3	39	1.14
48487678--48487748	31	2.3	28	78	21	72	50	11	1	36	1.47
48488198--48488242	21	2.1	21	83	0	54	26	15	24	33	1.95
48490402--48490434	3	11.3	3	87	6	50	0	30	0	69	0.88
48493446--48493531	32	2.7	31	80	3	100	40	11	8	39	1.71
48494116--48494141	12	2.2	12	100	0	52	30	0	30	38	1.58
48495745--48495811	32	2.2	30	82	12	84	35	0	0	64	0.94
48495745--48495804	32	1.9	32	86	6	88	38	0	0	61	0.96
48496104--48496149	24	1.9	24	81	0	56	47	6	4	41	1.49
48506593--48506683	45	2.0	45	85	2	121	37	28	6	27	1.82
48506664--48506699	16	2.2	16	100	0	72	38	36	0	25	1.56
48506825--48506880	27	2.1	27	100	0	112	30	26	17	25	1.97
48512748--48512791	19	2.3	20	84	7	56	27	20	11	40	1.86
48517044--48518077	132	7.9	132	91	2	1505	28	19	24	27	1.98
48517044--48518077	263	3.9	264	89	2	1509	28	19	24	27	1.98
48519653--48519698	24	1.9	24	82	8	58	28	4	2	65	1.23
48520780--48520828	3	16.3	3	82	0	62	61	2	0	36	1.08
48521325--48521351	4	6.8	4	100	0	54	22	0	0	77	0.76
48521801--48521902	6	17.0	6	89	0	114	26	8	0	63	1.30
48526029--48526112	8	10.0	8	71	19	64	79	0	20	0	0.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48526028--48526112	11	7.6	11	74	11	57	80	0	20	0	0.72
48526032--48526100	19	3.5	19	84	11	95	78	0	21	0	0.76
48526028--48526109	37	2.2	36	83	10	112	80	0	19	0	0.71
48527334--48527646	132	2.4	132	84	1	376	30	19	23	26	1.98
48527659--48528817	99	11.7	99	84	3	1334	31	20	21	27	1.98
48527651--48528817	297	3.9	297	86	3	1474	31	20	21	26	1.98
48527669--48528825	50	23.4	50	68	7	410	31	20	20	26	1.98
48528847--48529469	44	14.4	44	68	13	251	30	20	21	27	1.98
48528841--48528999	85	1.9	85	84	2	212	31	23	21	23	1.98
48528885--48529385	129	3.9	129	89	1	691	30	21	21	26	1.98
48529015--48529478	85	5.4	86	71	10	279	29	18	22	28	1.98
48528847--48529425	129	4.5	127	85	5	664	30	20	21	26	1.98
48529184--48529569	173	2.2	174	81	5	444	31	18	22	28	1.97
48531061--48531104	6	7.3	6	92	0	52	45	0	0	54	0.99
48531082--48531159	3	26.0	3	78	0	84	30	6	2	60	1.35
48531327--48531356	14	2.1	14	93	0	51	43	10	0	46	1.37
48531366--48531416	18	2.5	20	75	18	61	43	5	5	45	1.52
48534168--48534268	44	2.3	44	87	0	148	27	22	12	36	1.91
48534249--48534634	44	8.8	44	82	1	342	30	20	16	31	1.95
48534201--48534684	132	3.7	132	80	4	447	29	20	15	33	1.94
48534246--48534684	88	5.0	88	81	2	414	30	20	15	33	1.94
48541412--48541525	41	2.8	41	94	1	203	28	21	22	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48541823--48541976	75	2.1	75	82	2	184	40	20	7	31	1.81
48549866--48549912	21	2.2	21	84	0	67	23	38	29	8	1.84
48556525--48556564	20	2.0	20	85	0	53	52	0	0	47	1.00
48556546--48556580	17	2.0	17	88	5	52	71	0	2	25	1.00
48560057--48560219	89	1.8	88	82	12	208	24	12	11	52	1.71
48560376--48560416	18	2.2	18	86	4	55	34	2	2	60	1.23
48561957--48562006	20	2.5	20	86	0	73	18	6	34	42	1.74
48562799--48563037	127	1.9	127	79	5	268	35	12	17	35	1.87
48563704--48563753	18	2.7	19	75	9	50	68	2	6	24	1.23
48564696--48564807	53	2.1	53	98	0	215	16	16	14	53	1.73
48564838--48564953	56	2.1	56	100	0	232	10	10	32	46	1.72
48565256--48565407	41	3.6	41	75	8	162	31	24	19	24	1.98
48565257--48565450	85	2.3	85	94	1	354	30	23	19	26	1.98
48565293--48565450	44	3.7	44	74	8	171	30	23	18	27	1.98
48565511--48565919	45	9.1	44	81	8	475	31	24	15	28	1.95
48565506--48565919	90	4.6	90	91	0	639	31	24	15	28	1.95
48566037--48566592	50	11.2	50	64	5	196	26	23	20	29	1.99
48565926--48566630	99	7.1	98	83	2	777	26	22	20	30	1.98
48565930--48566630	198	3.5	198	87	1	951	26	22	20	30	1.98
48567487--48567544	18	3.2	18	81	13	75	1	10	3	84	0.81
48567506--48567535	14	2.2	14	94	5	53	0	13	0	86	0.57
48573107--48573156	18	2.7	19	75	9	50	68	2	6	24	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48578409--48578444	18	1.9	18	88	5	54	44	0	0	55	0.99
48578426--48578478	14	3.9	14	80	7	65	50	1	0	47	1.12
48580044--48580100	20	2.8	19	75	19	53	43	1	0	54	1.10
48580039--48580102	24	2.8	24	81	11	71	45	1	0	53	1.10
48580031--48580102	22	3.4	22	74	21	73	44	1	0	54	1.08
48581421--48581494	29	2.5	29	86	4	94	50	14	14	20	1.78
48585253--48585299	14	3.3	14	75	16	51	65	4	2	27	1.22
48585743--48585908	81	2.0	81	98	0	323	31	20	12	35	1.89
48586682--48586710	15	1.9	15	100	0	58	65	0	0	34	0.93
48586679--48586749	26	2.7	26	73	6	63	53	1	0	45	1.09
48591933--48591997	34	1.9	34	87	0	94	32	16	23	27	1.96
48595154--48595196	22	2.1	20	87	12	61	32	0	0	67	0.91
48595235--48595276	19	2.2	19	95	0	75	35	0	0	64	0.94
48606218--48606252	18	2.1	17	89	10	54	48	0	0	51	1.00
48608121--48608169	26	2.0	24	84	8	62	57	0	10	32	1.32
48608456--48608504	24	2.0	24	84	7	64	61	8	0	30	1.25
48609125--48609158	16	2.1	16	88	0	50	50	2	0	47	1.16
48609508--48609573	20	3.5	20	69	12	66	62	16	6	15	1.52
48609496--48609590	37	2.6	37	96	0	172	58	15	7	17	1.59
48609495--48609599	17	5.8	17	70	12	66	56	16	6	20	1.63
48609761--48609800	8	5.2	8	88	11	66	12	12	50	25	1.75
48609761--48609799	14	2.6	14	92	8	60	10	12	51	25	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48609765--48609822	22	2.7	22	84	5	66	12	8	51	27	1.68
48610744--48610819	27	2.8	27	89	0	125	17	23	38	21	1.93
48610836--48610876	19	2.2	19	95	0	73	31	0	17	51	1.46
48610843--48611324	241	2.0	245	97	1	909	46	10	3	39	1.56
48611283--48611339	27	2.1	27	90	0	87	49	14	1	35	1.53
48611380--48611466	22	3.7	22	82	14	120	32	1	13	52	1.48
48611375--48611474	49	2.0	49	94	0	173	33	1	13	53	1.46
48611456--48611527	8	8.4	8	71	14	54	36	1	15	47	1.54
48611670--48611727	27	2.1	27	83	3	71	24	25	13	36	1.92
48611682--48611748	27	2.5	27	95	0	116	14	31	20	32	1.93
48613703--48613743	4	10.2	4	100	0	82	24	0	24	51	1.49
48620100--48620158	31	1.9	30	83	10	75	23	8	0	67	1.17
48623538--48623576	15	2.6	15	91	0	60	33	35	15	15	1.89
48625631--48625672	21	2.0	22	85	4	59	61	28	4	4	1.36
48629465--48629491	2	13.5	2	100	0	54	48	0	0	51	1.00
48632820--48632869	20	2.5	21	83	9	68	50	0	2	48	1.12
48632919--48632961	3	14.7	3	85	4	61	34	4	0	60	1.17
48635472--48635594	64	1.9	65	83	5	160	52	6	8	32	1.56
48645349--48645517	30	5.7	30	78	8	159	33	21	5	39	1.76
48645356--48645497	29	4.8	27	75	14	86	36	22	2	38	1.69
48645356--48645468	59	1.9	59	85	7	158	38	22	2	37	1.68
48645992--48646052	4	16.5	4	83	16	71	73	0	26	0	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48645993--48646052	23	2.8	22	87	10	88	73	0	26	0	0.84
48645993--48646054	7	8.6	7	84	12	81	72	0	27	0	0.85
48646365--48646409	23	2.0	22	91	4	72	80	0	20	0	0.72
48646574--48646611	5	7.8	5	82	5	51	26	0	0	73	0.83
48646872--48647061	17	10.7	17	69	13	89	33	13	8	44	1.74
48646872--48647182	18	17.3	18	66	19	89	31	11	10	45	1.75
48646938--48646977	16	2.4	17	87	4	55	47	10	2	40	1.50
48646955--48647011	16	3.4	16	75	15	53	36	12	8	42	1.74
48646956--48647048	34	2.7	33	86	8	116	31	15	8	45	1.76
48647057--48647100	20	2.1	21	88	12	65	52	11	11	25	1.70

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