genome.fa.s1.2.7.7.80.10.50.1000.43.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  43  of  187  ( 22383 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)
13135393--13135497	49	2.1	49	85	0	138	31	7	10	50	1.65
13137923--13138000	7	11.7	7	71	17	60	42	1	1	55	1.16
13138233--13138321	46	2.0	46	86	4	128	40	23	4	31	1.75
13138310--13138354	16	2.8	16	93	0	72	20	26	4	48	1.68
13149159--13149253	47	2.0	47	100	0	190	23	18	23	34	1.96
13149824--13149850	5	5.4	5	100	0	54	37	0	22	40	1.54
13153136--13153160	2	12.5	2	100	0	50	52	0	0	48	1.00
13153599--13153636	17	2.2	18	85	4	51	31	2	2	63	1.22
13153763--13153793	14	2.2	14	94	0	53	22	0	3	74	0.96
13162983--13163035	26	2.0	26	89	7	81	39	7	16	35	1.78
13166462--13166486	2	12.5	2	100	0	50	52	0	0	48	1.00
13177406--13177470	22	2.9	22	79	2	67	36	4	32	26	1.77
13179195--13179238	16	2.8	16	78	0	52	45	0	2	52	1.13
13179227--13179278	19	2.7	20	82	11	63	38	0	3	57	1.17
13191250--13191276	7	3.9	7	100	0	54	59	0	0	40	0.98
13198633--13198663	2	15.0	2	93	6	53	48	0	3	48	1.17
13198914--13199041	64	2.0	64	93	0	220	38	2	22	36	1.67
13209530--13209835	149	2.0	151	86	5	424	42	3	10	44	1.55
13213719--13213763	22	2.0	22	100	0	90	42	13	13	31	1.82
13216114--13216156	2	21.5	2	100	0	86	51	0	0	48	1.00
13219219--13219267	21	2.3	21	92	3	80	24	4	32	38	1.74
13219230--13219275	21	2.2	21	84	0	56	26	6	32	34	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13219240--13219325	35	2.5	35	92	5	140	27	5	31	34	1.81
13221026--13221068	22	2.0	22	100	0	86	51	23	6	18	1.70
13222106--13222174	31	2.2	31	82	5	77	36	0	4	59	1.17
13222136--13222182	20	2.3	20	82	7	60	29	0	6	63	1.19
13223367--13223405	3	13.0	3	100	0	78	66	0	33	0	0.92
13237368--13237816	44	10.2	43	63	16	168	30	19	24	25	1.98
13237247--13237897	132	4.9	132	92	0	1034	31	20	23	24	1.98
13242511--13242541	9	3.4	9	90	0	53	25	12	22	38	1.90
13250154--13250215	16	3.9	16	74	17	58	46	0	0	53	1.00
13250154--13250202	15	3.1	17	77	14	59	46	0	0	53	1.00
13250153--13250219	31	2.2	30	80	15	75	47	0	0	52	1.00
13254809--13254874	22	3.0	22	93	0	105	31	15	27	25	1.95
13263064--13263344	142	2.0	142	95	0	508	37	21	4	36	1.75
13275303--13275367	28	2.3	29	76	7	71	55	1	7	35	1.38
13275667--13275721	27	2.0	28	83	13	71	50	3	7	38	1.48
13276377--13276412	11	3.3	11	92	0	54	86	0	8	5	0.72
13284710--13284743	15	2.3	15	89	0	50	17	14	8	58	1.61
13288554--13288596	14	3.0	14	86	6	59	81	4	13	0	0.84
13288554--13288597	15	3.0	15	86	3	54	81	4	13	0	0.83
13289487--13290378	50	17.9	50	69	3	508	31	22	20	25	1.98
13289487--13289779	99	2.9	100	81	3	277	32	23	19	25	1.97
13289516--13290044	249	2.1	249	90	0	824	31	22	19	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13289798--13290454	99	6.6	100	84	1	802	30	22	21	25	1.98
13289798--13290454	199	3.3	199	86	3	883	30	22	21	25	1.98
13289516--13290122	249	2.4	249	85	0	730	31	22	19	26	1.98
13289817--13290454	298	2.1	298	87	1	902	30	22	21	25	1.99
13290460--13291235	44	18.0	42	68	13	332	32	21	19	26	1.97
13290461--13291097	129	5.0	128	91	2	955	32	22	20	25	1.98
13290461--13291097	257	2.5	255	89	3	953	32	22	20	25	1.98
13290463--13291083	85	7.3	84	70	14	337	31	22	20	25	1.98
13291891--13291948	16	3.5	17	77	13	50	10	10	1	77	1.06
13292696--13292733	2	19.5	2	94	5	69	47	0	0	52	1.00
13292695--13292737	10	4.2	11	91	8	65	44	0	0	55	0.99
13293264--13293300	19	2.0	19	89	5	58	18	2	5	72	1.15
13293331--13293386	20	2.8	20	71	7	51	25	1	7	66	1.27
13294377--13294414	19	2.1	18	85	9	51	42	7	0	50	1.31
13295955--13296003	25	1.9	26	84	12	66	42	4	2	51	1.32
13302709--13302741	17	1.9	17	93	0	57	15	6	12	66	1.42
13304755--13305230	233	2.0	235	91	5	762	36	13	13	36	1.83
13305611--13305641	14	2.2	14	94	0	53	29	19	12	38	1.89
13307153--13307203	26	2.0	26	96	0	93	78	7	7	5	1.09
13309329--13309368	19	2.1	19	90	0	62	30	20	0	50	1.49
13309556--13309746	45	4.2	45	90	1	267	41	19	18	20	1.91
13309949--13310030	40	2.0	40	83	4	103	40	20	7	31	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13314296--13314351	20	2.8	20	83	0	76	44	3	7	44	1.48
13314296--13314358	20	3.2	19	82	8	72	41	3	9	46	1.52
13315853--13315892	13	2.6	16	74	25	50	65	0	0	35	0.93
13328276--13328300	3	8.3	3	100	0	50	64	0	0	36	0.94
13330751--13330802	22	2.4	23	81	12	65	40	0	30	28	1.57
13330746--13330803	22	2.8	20	78	7	62	36	1	29	32	1.68
13344877--13344933	21	2.7	21	78	7	62	19	21	14	45	1.85
13344899--13344949	21	2.4	21	83	6	59	21	19	11	47	1.81
13344939--13345027	42	2.1	42	85	4	117	13	21	20	44	1.85
13347762--13347845	25	3.2	25	67	18	71	52	13	5	28	1.63
13347718--13347855	54	2.5	54	91	1	222	52	13	5	28	1.61
13347832--13347879	24	2.0	24	95	0	87	50	10	6	33	1.62
13348388--13348432	5	9.0	5	97	0	81	60	2	0	37	1.09
13352907--13353189	140	2.0	141	90	6	446	31	19	21	28	1.97
13353796--13353834	18	2.3	16	86	8	51	28	5	0	66	1.12
13353585--13353949	156	2.4	156	92	2	601	29	11	7	50	1.66
13353975--13354205	116	2.0	116	88	5	346	51	5	9	32	1.57
13354087--13354455	153	2.4	149	83	4	470	54	5	7	32	1.50
13354449--13354498	14	3.7	14	75	20	52	26	0	8	66	1.19
13373633--13373705	36	2.0	36	100	0	146	43	19	16	20	1.88
13376738--13376940	104	2.0	101	83	2	253	33	17	21	27	1.96
13376839--13377078	125	1.9	126	88	1	365	30	18	22	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13380289--13380588	22	13.9	22	85	4	360	23	0	31	45	1.56
13380284--13380588	65	4.7	65	86	4	402	23	0	31	44	1.56
13380289--13380588	43	6.9	44	82	4	360	23	0	31	45	1.56
13383103--13383146	11	3.8	12	80	19	58	43	0	31	25	1.55
13389087--13389172	25	3.5	24	81	9	84	27	12	30	29	1.93
13391812--13391851	21	1.9	21	89	0	62	25	15	10	50	1.74
13394159--13394256	27	3.6	28	72	9	78	36	19	25	18	1.94
13410863--13410930	30	2.2	31	86	2	93	41	0	5	52	1.25
13418760--13418915	46	3.4	46	97	0	287	30	19	16	33	1.94
13419642--13419667	12	2.2	12	100	0	52	53	11	7	26	1.63
13425173--13425209	9	4.1	9	92	0	65	45	13	10	29	1.77
13425636--13425683	21	2.3	20	82	13	53	66	14	0	18	1.25
13432069--13432121	21	2.5	21	75	0	52	16	7	30	45	1.75
13432810--13432841	16	2.0	16	93	0	55	40	0	0	59	0.97
13432857--13432931	27	2.6	29	93	6	127	40	0	0	60	0.97
13432864--13432915	10	5.5	10	77	13	65	42	0	0	57	0.98
13432902--13432956	20	2.6	22	83	11	62	43	0	1	54	1.10
13453105--13453144	11	3.5	11	83	12	53	45	2	2	50	1.28
13455214--13455248	17	2.1	17	88	0	52	65	0	0	34	0.93
13455420--13455467	13	3.7	13	78	8	53	33	0	2	64	1.05
13455419--13455470	14	3.9	14	80	7	54	34	0	1	63	1.06
13461726--13461996	143	1.9	143	89	0	425	19	16	21	42	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13466686--13466756	3	24.7	3	74	8	67	30	2	4	61	1.29
13466789--13466910	38	3.3	38	78	13	112	39	9	2	48	1.50
13466789--13466912	36	3.4	36	80	12	121	39	9	2	48	1.49
13467085--13467115	3	10.3	3	100	0	62	32	0	0	67	0.91
13467504--13467826	107	3.0	106	93	1	538	30	17	18	34	1.94
13471864--13471937	19	3.7	19	80	8	76	35	0	6	58	1.25
13471909--13471948	11	3.5	11	89	3	53	27	0	5	67	1.11
13473875--13473993	25	4.8	25	72	6	82	31	20	26	21	1.98
13473937--13474018	25	3.3	24	75	11	85	35	21	25	17	1.95
13475616--13475643	8	3.5	8	100	0	56	42	0	28	28	1.56

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