genome.fa.s4.2.7.7.80.10.50.1000.188.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  188  of  198  ( 23681 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)
58494601--58494665	29	2.2	31	88	5	98	38	7	12	41	1.71
58496936--58497161	19	11.9	19	69	21	86	44	10	11	33	1.75
58496934--58497046	17	6.4	18	71	16	60	41	9	11	37	1.74
58496936--58497161	18	11.9	18	69	18	106	44	10	11	33	1.75
58497007--58497069	17	3.6	17	77	8	63	44	7	6	41	1.59
58497056--58497124	24	2.8	25	77	14	63	50	10	11	27	1.70
58497232--58497279	22	2.2	22	88	7	71	35	6	10	47	1.63
58497158--58497507	105	3.5	97	87	9	486	44	12	12	30	1.80
58497265--58497295	16	1.9	16	93	0	53	48	16	9	25	1.76
58497258--58497305	17	2.8	17	78	9	53	45	14	10	29	1.78
58497325--58497369	20	2.2	21	88	7	67	35	13	17	33	1.89
58497376--58497410	17	2.0	17	88	5	52	45	14	11	28	1.79
58497460--58497586	17	7.2	17	71	11	69	40	10	14	34	1.79
58497439--58497586	19	8.2	19	73	15	111	39	10	14	35	1.79
58498186--58498214	15	1.9	15	100	0	58	6	20	48	24	1.74
58498317--58498372	11	4.9	12	77	16	57	3	16	1	78	0.97
58498311--58498370	17	3.5	17	78	13	70	3	15	1	80	0.93
58498296--58498373	27	2.9	27	83	9	95	3	14	2	79	0.98
58498294--58498370	34	2.3	34	84	13	97	3	12	2	80	0.95
58498294--58498359	23	2.9	22	82	8	69	3	12	3	81	0.91
58498464--58498518	21	2.7	21	78	13	62	0	34	0	65	0.93
58498670--58498717	22	2.2	22	88	0	69	6	10	12	70	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58499010--58499117	30	3.6	30	76	9	96	43	3	20	32	1.69
58499114--58499152	18	2.2	18	86	9	53	15	0	7	76	0.99
58499481--58499980	79	6.3	76	78	16	496	35	19	16	28	1.93
58499498--58499980	162	3.0	163	89	3	712	34	19	16	28	1.94
58500841--58500891	15	3.5	15	82	15	61	0	3	13	82	0.81
58511738--58511788	23	2.2	23	100	0	102	25	27	31	15	1.96
58511938--58512099	17	8.8	19	69	19	78	41	9	12	35	1.76
58511908--58512037	17	7.3	18	68	19	51	45	10	12	31	1.76
58511938--58512161	19	11.9	18	68	17	93	43	10	12	33	1.77
58512101--58512162	18	3.5	18	76	10	65	48	9	14	27	1.75
58512114--58512310	44	4.3	45	73	13	152	48	13	11	26	1.76
58512265--58512298	17	1.9	17	88	5	50	47	14	8	29	1.75
58512144--58512319	95	1.8	98	87	3	268	48	13	9	28	1.74
58512318--58512354	19	1.9	19	94	0	65	29	10	21	37	1.88
58512422--58512466	20	2.2	21	88	7	67	35	13	17	33	1.89
58512228--58512508	104	2.7	105	90	1	465	45	13	12	29	1.80
58512465--58512587	17	6.9	17	75	11	97	40	12	15	31	1.84
58512529--58512587	19	3.2	18	92	7	84	38	10	15	35	1.81
58513311--58513366	11	4.9	12	77	16	57	3	17	0	78	0.89
58513296--58513353	23	2.6	23	84	10	75	1	15	1	81	0.86
58513305--58513369	34	1.9	35	87	12	100	3	18	0	78	0.88
58513303--58513367	27	2.4	28	87	10	91	3	16	0	80	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58513306--58513369	17	3.7	18	82	15	82	3	18	0	78	0.89
58513990--58514047	30	1.9	30	89	6	91	41	0	22	36	1.54
58518095--58518705	304	2.0	304	91	0	990	36	13	23	27	1.92
58523866--58523911	19	2.5	19	80	16	60	54	0	4	41	1.20
58524919--58524968	16	3.1	16	88	11	75	62	0	30	8	1.24
58532244--58532314	20	3.6	19	77	12	72	33	11	11	43	1.76
58541608--58541666	29	2.0	31	83	6	77	38	6	10	44	1.65
58542607--58542663	29	2.0	29	86	6	82	52	14	0	33	1.41
58545382--58545507	30	4.2	30	80	9	150	32	23	5	38	1.78
58545392--58545505	59	1.9	60	87	5	169	34	22	4	38	1.74
58546022--58546090	30	2.3	29	74	13	70	73	0	23	2	0.96
58546550--58546600	17	3.1	17	81	10	54	17	0	5	76	0.98
58546574--58546600	5	5.4	5	100	0	54	18	0	0	81	0.69
58546903--58546948	17	2.6	18	80	16	60	32	13	8	45	1.73
58547005--58547231	37	6.2	36	74	14	144	31	13	10	44	1.76
58547001--58547228	17	12.5	18	71	15	157	30	13	10	45	1.76
58547253--58547317	22	3.2	21	80	12	64	43	6	9	41	1.61
58554769--58555140	77	4.8	74	83	9	453	28	15	20	35	1.93
58554769--58555140	160	2.4	149	81	11	464	28	15	20	35	1.93
58555335--58555460	30	4.2	30	78	11	134	30	23	5	40	1.77
58555342--58555458	59	2.0	60	86	5	166	32	23	4	39	1.74
58555822--58555871	24	2.1	23	92	3	82	74	16	10	0	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58555995--58556063	23	3.0	21	75	17	66	75	0	21	2	0.93
58555992--58556061	30	2.4	29	75	13	72	74	0	22	2	0.95
58556583--58556634	18	3.1	17	81	8	54	17	0	5	76	0.97
58556608--58556634	5	5.4	5	100	0	54	18	0	0	81	0.69
58556936--58556981	17	2.6	18	80	16	60	32	13	8	45	1.73
58557030--58557242	17	11.8	17	68	15	106	30	13	10	45	1.77
58557022--58557168	54	2.7	54	74	13	149	30	14	10	44	1.78
58557020--58557260	37	6.6	37	75	11	187	31	13	10	43	1.78
58557308--58557366	19	3.4	17	74	9	57	44	5	10	40	1.60
58557341--58557384	23	2.0	23	86	8	65	50	6	11	31	1.65
58557265--58557398	56	2.4	56	81	7	146	39	5	10	44	1.63
58558469--58558502	2	17.0	2	100	0	68	50	0	0	50	1.00
58558733--58558771	20	1.9	20	84	5	51	71	5	7	15	1.26
58559792--58559848	28	2.0	29	93	3	98	12	22	26	38	1.89
58560986--58561052	27	2.5	27	97	0	125	31	20	32	14	1.93
58561233--58561314	19	4.6	19	64	20	59	51	10	1	36	1.45
58561233--58561315	22	3.1	27	71	25	95	51	10	1	36	1.45
58561648--58561688	19	2.2	19	95	0	73	51	17	0	31	1.46
58561705--58561779	27	2.8	27	93	0	132	22	37	22	17	1.94
58567104--58567186	41	2.0	41	100	0	166	34	16	12	36	1.86
58569000--58569307	106	2.9	105	85	2	418	37	20	15	27	1.92
58574388--58574448	26	2.3	26	86	5	79	14	22	24	37	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58574490--58574551	24	2.5	24	84	7	72	19	25	19	35	1.95
58574536--58574606	24	2.9	24	73	10	63	21	21	19	38	1.94
58575716--58575761	20	2.3	20	96	0	83	36	4	6	52	1.47
58576540--58576591	19	2.7	19	77	14	54	71	3	0	25	1.03
58581913--58581954	21	2.0	21	85	0	57	54	2	2	40	1.26
58584416--58584449	2	17.0	2	100	0	68	50	0	0	50	1.00
58586603--58586667	30	2.1	31	82	2	78	44	16	4	33	1.69
58586877--58586930	19	2.8	19	94	0	90	40	11	14	33	1.82
58587796--58588045	24	10.7	24	70	15	148	33	5	4	56	1.44
58587794--58587968	70	2.5	69	75	12	178	32	5	5	57	1.44
58587755--58588036	69	4.1	67	73	15	195	34	5	5	54	1.46
58598101--58598135	2	18.0	2	94	5	63	51	0	0	48	1.00
58598665--58598728	31	2.1	31	87	0	92	32	12	10	43	1.77
58599224--58599283	27	2.2	28	84	3	77	33	13	0	53	1.40
58610225--58610257	2	16.5	2	100	0	66	51	0	0	48	1.00
58611991--58612031	2	20.5	2	100	0	82	51	0	0	48	1.00
58616934--58616999	31	2.1	31	85	0	87	33	9	12	45	1.73
58618442--58618490	2	24.5	2	95	0	89	46	0	2	51	1.12
58627301--58627384	18	4.8	18	73	15	86	44	11	11	32	1.78
58627310--58627385	35	2.1	37	83	11	95	40	10	11	36	1.76
58627877--58627927	10	4.9	10	76	23	52	0	15	0	84	0.63
58627872--58627927	21	2.8	20	82	15	78	0	17	0	82	0.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58627877--58627925	16	3.1	15	85	5	62	0	16	0	83	0.64
58627869--58627916	25	1.9	25	87	8	71	0	22	0	77	0.78
58628221--58628314	7	14.8	6	75	18	68	0	26	0	73	0.84
58628222--58628322	31	3.3	31	74	12	100	0	26	0	73	0.84
58628221--58628331	24	4.5	25	80	14	117	0	27	0	72	0.84
58628408--58628447	15	2.7	16	85	11	50	0	20	2	77	0.88
58628414--58628468	22	2.5	21	85	8	74	0	16	7	76	1.00
58628758--58628841	29	3.0	28	77	5	98	41	3	21	33	1.70
58629027--58630267	78	16.0	79	86	7	1662	35	21	17	25	1.95
58629026--58630267	241	5.3	235	87	7	1670	35	21	17	25	1.95

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