genome.fa.s13.2.7.7.80.10.50.1000.18.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  18  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)
5445816--5445870	23	2.4	23	87	0	74	23	20	21	34	1.97
5445852--5445912	21	2.8	21	90	5	95	13	27	27	31	1.94
5448429--5448453	13	1.9	13	100	0	50	36	16	0	48	1.46
5449009--5449035	2	13.5	2	100	0	54	48	0	0	51	1.00
5449633--5449735	23	4.4	22	71	20	75	33	20	25	21	1.97
5453584--5453673	45	2.0	45	91	0	144	24	22	20	33	1.97
5461571--5461602	12	2.6	12	95	5	55	53	0	3	43	1.16
5461756--5461798	22	2.0	22	86	9	61	55	2	0	41	1.12
5465155--5465272	62	1.9	62	96	0	218	24	16	11	47	1.80
5467601--5467637	2	18.5	2	94	0	65	54	0	0	45	1.00
5469040--5469073	17	1.9	18	88	5	52	50	0	2	47	1.16
5471062--5471107	5	9.4	5	81	15	53	41	0	2	56	1.11
5481927--5481952	3	8.7	3	100	0	52	65	0	0	34	0.93
5484826--5484956	66	2.0	66	83	5	167	12	22	18	45	1.83
5491284--5491333	26	1.9	26	87	0	73	52	0	14	34	1.42
5491297--5491361	24	2.6	24	78	9	60	52	0	10	36	1.37
5491475--5491548	3	24.7	3	94	0	130	63	2	0	33	1.09
5491551--5491606	30	2.0	27	82	10	67	48	10	12	28	1.74
5492725--5492789	23	2.9	22	69	17	53	36	7	10	44	1.68
5495767--5495897	70	1.9	70	91	0	217	29	20	12	38	1.89
5501999--5502136	67	2.1	67	97	0	258	57	21	5	15	1.58
5510209--5510254	9	5.1	9	94	0	83	30	10	13	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5511751--5511868	63	1.9	60	86	5	164	42	2	4	50	1.35
5515313--5515464	53	2.9	53	85	2	207	35	8	14	41	1.76
5519961--5519998	18	2.2	18	90	4	60	84	0	15	0	0.63
5525005--5525043	19	2.0	20	90	5	62	51	20	7	20	1.72
5525058--5525136	29	2.6	30	76	5	79	32	12	17	36	1.88
5531219--5531250	16	1.9	17	93	6	57	21	9	0	68	1.17
5535277--5535511	41	5.8	38	80	10	218	22	22	25	29	1.99
5535296--5535511	82	2.6	81	81	5	247	24	22	25	27	2.00
5535278--5535511	123	1.9	123	82	6	296	22	22	25	29	1.99
5536217--5536247	15	2.1	15	93	0	53	22	0	32	45	1.53
5536616--5536650	17	2.1	17	100	0	70	48	0	5	45	1.26
5536699--5536736	13	2.8	14	88	8	60	57	0	5	36	1.21
5540922--5540962	15	2.7	15	88	3	55	48	2	2	46	1.28
5546947--5547064	27	4.4	26	75	15	98	38	19	20	21	1.93
5547082--5547137	24	2.3	24	81	0	76	32	5	19	42	1.74
5547339--5547446	32	3.4	32	76	10	130	18	21	24	36	1.95
5547339--5547461	32	3.8	32	70	12	99	19	20	23	36	1.95
5547340--5547462	64	1.9	64	88	3	185	19	19	23	37	1.94
5547469--5547534	22	3.0	21	80	4	69	16	21	18	43	1.87
5550466--5550552	24	3.6	24	75	4	77	28	9	17	44	1.79
5550724--5550844	32	3.8	32	81	9	149	20	21	22	35	1.96
5550850--5550899	22	2.3	22	78	0	55	22	16	14	48	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5555490--5555544	25	2.2	25	86	0	74	32	18	10	38	1.85
5555490--5555555	25	2.6	24	79	9	69	33	15	12	39	1.84
5555874--5555916	18	2.4	16	82	17	50	41	13	0	44	1.44
5557296--5557328	16	1.9	17	88	11	50	30	30	0	39	1.57
5561144--5561244	53	1.9	53	97	0	193	24	4	24	45	1.73
5562512--5562554	22	2.0	21	86	13	61	55	9	11	23	1.64
5568057--5568097	20	2.0	22	90	9	68	51	0	4	43	1.23
5568992--5569018	2	13.5	2	100	0	54	51	0	0	48	1.00
5569628--5569673	24	1.9	24	86	0	65	23	41	15	19	1.89
5570584--5570638	27	2.0	27	86	6	76	54	1	3	40	1.28
5580803--5580835	7	4.7	7	96	0	57	48	30	0	21	1.50
5581398--5581476	40	2.0	39	92	2	131	39	1	0	59	1.06
5581409--5581472	17	3.4	17	71	21	56	39	1	0	59	1.07
5581416--5581476	11	5.9	11	71	21	51	42	1	0	55	1.09
5584897--5584948	16	3.2	16	75	0	59	48	3	5	42	1.45
5584899--5584976	31	2.5	32	85	2	95	50	6	5	38	1.50
5585884--5585929	24	1.9	24	86	0	65	23	41	15	19	1.89
5590026--5590092	9	7.4	9	91	0	98	23	7	20	47	1.75
5590244--5590268	12	2.1	12	100	0	50	16	24	36	24	1.94
5591403--5591447	14	3.3	14	84	3	56	40	33	6	20	1.78
5591864--5591902	14	2.8	14	80	0	51	46	33	0	20	1.51
5591943--5592029	27	3.2	28	73	15	76	48	27	4	19	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5592494--5592522	14	2.1	14	93	6	51	55	34	0	10	1.34
5592777--5592829	15	3.7	15	71	21	51	60	20	0	18	1.36
5592766--5592830	27	2.4	28	84	10	89	56	23	0	20	1.42
5592890--5592940	13	3.6	14	76	7	50	58	25	0	15	1.37
5592890--5592996	7	15.3	7	74	13	60	51	29	0	17	1.52
5593139--5593176	14	2.7	15	84	12	53	50	23	0	26	1.50
5593252--5593294	14	3.1	14	79	0	50	51	27	0	20	1.48
5593377--5593427	21	2.5	20	81	6	59	45	27	0	27	1.54
5597299--5597395	49	2.0	50	87	6	144	22	23	19	34	1.97
5605296--5605329	4	8.5	4	87	12	52	23	2	0	73	0.97
5605296--5605410	15	7.7	15	68	24	57	22	5	1	70	1.17
5605294--5605410	16	7.1	16	70	12	76	22	5	1	70	1.15
5613949--5613987	20	2.0	20	94	0	69	46	7	2	43	1.46
5614253--5614301	24	2.0	24	100	0	98	51	4	8	36	1.51
5615237--5615856	159	3.9	159	92	2	992	28	10	40	20	1.86
5617309--5617337	15	1.9	15	100	0	58	10	6	0	82	0.83
5617479--5617512	17	2.0	17	88	0	50	52	32	0	14	1.42
5618505--5618530	11	2.4	11	100	0	52	84	0	0	15	0.62
5621076--5621104	10	2.9	10	100	0	58	72	0	10	17	1.11
5622943--5622989	19	2.5	19	96	0	85	14	4	42	38	1.66
5623140--5623180	20	2.1	19	90	4	64	75	0	2	21	0.92
5623139--5623194	16	3.2	16	83	16	60	76	0	3	19	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5623143--5623192	20	2.4	21	83	9	59	78	0	4	18	0.91
5624575--5624653	34	2.4	33	80	4	95	24	8	25	41	1.83
5626991--5627021	12	2.6	12	94	0	53	51	9	0	38	1.35
5627409--5627438	11	2.6	12	94	5	53	40	0	16	43	1.48
5628578--5628635	26	2.3	25	80	11	64	25	3	3	67	1.22
5629095--5629258	9	17.4	9	67	18	59	63	3	4	28	1.30
5629130--5629258	19	6.7	19	67	15	59	61	3	4	31	1.32
5629129--5629200	28	2.5	29	82	8	85	62	1	2	33	1.18
5629131--5629200	29	2.4	29	83	2	88	62	1	2	32	1.18
5629131--5629209	29	2.8	28	78	3	86	60	3	3	31	1.32
5629160--5629279	29	4.1	29	70	11	77	64	4	5	25	1.35
5629550--5629617	30	2.3	31	92	5	113	36	0	0	63	0.95
5629532--5629631	10	10.4	10	73	10	75	33	0	3	64	1.09
5630314--5630356	22	2.0	22	90	0	68	9	13	27	48	1.73
5630447--5630655	43	5.0	41	86	6	235	32	21	20	25	1.97
5630433--5630654	84	2.6	86	83	8	249	31	21	21	25	1.98
5631073--5631112	12	3.3	12	92	0	53	2	37	17	42	1.63
5631097--5631165	21	3.3	21	89	0	102	1	43	20	34	1.61
5633545--5633593	23	2.2	22	85	10	64	40	6	6	46	1.53
5636454--5636515	5	12.4	5	100	0	124	59	0	0	40	0.97
5650103--5650144	20	2.1	20	90	0	66	33	7	7	52	1.56
5650109--5650152	20	2.2	20	87	0	61	31	6	11	50	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5650821--5651439	87	7.2	87	85	4	702	30	14	10	44	1.78
5650821--5651437	173	3.6	174	83	3	705	30	13	10	44	1.78
5657432--5657763	113	3.0	113	78	8	331	23	22	23	30	1.99
5658113--5658161	18	2.5	21	80	9	59	61	10	2	26	1.39
5658736--5658775	14	2.9	13	85	10	53	2	0	50	47	1.14
5658710--5658772	21	3.0	21	75	9	58	6	0	49	44	1.28
5659454--5660005	231	2.4	229	88	2	813	29	16	19	33	1.94
5659454--5660114	231	2.9	228	82	5	778	28	17	20	33	1.95
5660390--5660433	19	2.3	19	80	0	52	31	38	2	27	1.69
5665376--5665443	21	3.2	21	85	8	93	33	19	44	2	1.66

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