genome.fa.s4.2.7.7.80.10.50.1000.35.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  35  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)
10359545--10359712	91	1.8	91	87	0	246	45	20	10	23	1.81
10359589--10359839	69	3.6	69	90	0	367	45	21	10	22	1.83
10360500--10360585	42	2.0	43	82	6	104	32	23	17	26	1.96
10366139--10366213	30	2.5	30	82	0	96	21	24	10	44	1.84
10366224--10366304	30	2.7	29	79	9	92	24	30	13	30	1.94
10368594--10368650	28	2.0	28	96	0	105	15	14	22	47	1.82
10374513--10374840	162	2.0	162	87	1	469	36	17	22	23	1.94
10381855--10381899	16	2.7	17	86	6	65	17	0	11	71	1.14
10382862--10383085	112	2.0	112	97	0	421	33	20	16	29	1.95
10383237--10383341	28	3.8	28	77	7	99	27	27	18	26	1.98
10383634--10383669	18	1.9	19	88	5	56	41	47	0	11	1.39
10383815--10383881	9	7.4	9	81	0	71	29	7	19	43	1.78
10394143--10394241	40	2.4	43	77	9	109	34	5	3	57	1.36
10397339--10397433	30	3.0	30	80	10	84	58	2	2	36	1.21
10397360--10397419	11	5.6	11	74	25	58	58	0	1	40	1.08
10397352--10397432	30	2.6	31	82	9	103	58	1	1	39	1.14
10398034--10398164	71	1.9	69	88	4	201	30	8	11	49	1.68
10398825--10398977	22	7.0	22	90	0	225	26	26	14	32	1.94
10401970--10402884	299	3.1	293	78	9	895	34	13	10	40	1.79
10405307--10405335	3	9.7	3	100	0	58	31	0	0	68	0.89
10416578--10416633	14	4.0	14	79	6	60	32	1	1	64	1.14
10430455--10430982	44	11.9	44	79	6	444	28	21	18	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10430323--10430982	88	7.4	88	75	10	468	28	21	18	31	1.97
10431620--10431670	26	2.0	26	92	0	84	13	27	9	49	1.74
10439503--10439543	20	2.1	20	86	13	59	48	9	17	24	1.76
10444608--10444645	18	2.1	18	85	9	51	44	26	2	26	1.67
10445873--10445923	25	2.0	25	92	0	84	33	23	7	35	1.84
10455453--10455507	16	3.4	16	75	5	58	34	21	5	38	1.77
10460167--10460203	2	19.0	2	94	5	67	51	0	0	48	1.00
10461276--10461314	20	2.0	20	90	10	62	35	2	5	56	1.35
10461357--10461402	10	4.3	11	76	15	51	34	0	2	63	1.07
10461601--10461644	21	2.1	21	87	8	63	25	0	0	75	0.81
10462013--10462087	32	2.3	32	93	2	123	26	0	12	61	1.31
10462150--10462413	100	2.6	101	85	1	341	28	1	13	56	1.47
10462088--10462437	100	3.4	110	77	13	318	26	2	14	57	1.48
10477848--10477872	13	1.9	13	100	0	50	36	16	0	48	1.46
10478965--10479065	23	4.4	23	78	9	89	36	18	24	19	1.95
10479271--10479364	49	1.9	49	91	0	152	42	18	1	38	1.57
10497916--10497957	21	2.0	21	86	9	59	52	0	4	42	1.22
10498228--10498290	19	3.3	19	77	4	65	42	0	0	57	0.99
10498400--10498442	13	2.9	15	86	10	54	51	2	0	46	1.13
10498474--10498530	15	3.5	15	73	17	60	50	1	0	47	1.11
10519154--10519201	24	2.0	24	87	0	69	54	2	2	41	1.24
10537372--10537557	92	2.0	92	92	0	309	33	16	20	29	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10539499--10539544	22	2.1	22	87	0	65	58	30	0	10	1.32
10544297--10544321	13	1.9	13	100	0	50	20	0	0	80	0.72
10544763--10544989	110	2.1	107	79	9	235	34	16	15	33	1.91
10550497--10550521	5	5.0	5	100	0	50	80	0	0	20	0.72
10550754--10550794	21	2.0	21	90	9	66	36	2	0	60	1.10
10554191--10554247	28	2.0	29	93	3	98	43	14	28	14	1.83
10570016--10570083	33	2.1	33	91	0	109	20	19	13	47	1.82
10575543--10575585	11	4.1	10	82	8	50	25	2	23	48	1.62
10576490--10576554	11	5.8	12	77	15	68	26	32	1	40	1.65
10581781--10582201	125	3.4	125	85	2	576	31	22	17	28	1.96
10594524--10594566	2	21.5	2	100	0	86	48	0	0	51	1.00
10597442--10597495	21	2.6	21	81	0	63	31	7	31	29	1.85
10619681--10619722	19	2.2	20	86	4	59	16	54	11	16	1.70
10620674--10620715	6	6.8	6	82	15	50	42	7	0	50	1.30
10621395--10621564	85	2.0	85	98	0	331	36	16	12	34	1.86
10623713--10623746	17	2.0	17	88	0	50	41	14	0	44	1.45
10629377--10629409	12	2.8	12	95	0	57	57	0	3	39	1.14
10633193--10633221	14	2.0	15	93	6	51	55	3	0	41	1.17
10634282--10634328	14	3.3	14	85	5	58	44	2	10	42	1.51
10634271--10634328	29	2.0	30	86	3	82	41	3	13	41	1.62
10638642--10638691	26	1.9	26	91	4	75	56	0	0	44	0.99
10638804--10638850	16	3.0	16	78	12	53	46	0	2	51	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10638722--10638966	119	2.0	121	96	1	449	42	2	5	49	1.38
10638923--10638964	15	2.7	16	82	14	52	45	0	2	52	1.13
10638914--10638955	15	2.9	15	82	10	52	47	0	0	52	1.00
10644254--10644316	26	2.4	26	100	0	126	22	19	26	31	1.97
10647763--10648185	141	3.0	141	95	0	767	32	5	23	38	1.77
10659649--10659862	51	4.3	50	80	5	245	41	18	19	21	1.90
10659648--10659862	101	2.1	100	90	2	333	41	18	19	20	1.91
10659883--10659908	6	4.3	6	100	0	52	84	0	0	15	0.62
10661137--10661173	3	12.3	3	100	0	74	67	0	0	32	0.91
10664662--10664690	13	2.1	14	93	6	51	0	24	0	75	0.80
10665345--10665379	19	1.9	17	88	11	52	37	22	0	40	1.55
10666264--10666312	20	2.6	19	80	6	55	36	8	2	53	1.43
10667263--10667292	5	5.8	5	96	4	51	3	60	36	0	1.14
10668330--10668416	21	4.0	22	78	14	72	43	1	3	51	1.26
10668359--10668416	21	2.8	21	86	7	82	48	0	1	50	1.11
10672496--10672539	22	1.9	22	86	9	61	40	13	2	43	1.57
10681042--10681066	7	3.6	7	100	0	50	60	28	0	12	1.32
10682554--10682605	26	2.0	26	85	3	70	61	1	0	36	1.07
10684377--10684410	14	2.3	15	90	5	52	14	8	0	76	1.01
10688255--10688296	15	2.7	16	82	14	52	52	2	0	45	1.13
10688264--10688305	15	2.9	15	82	10	52	52	0	0	47	1.00
10688566--10688626	28	2.2	28	85	5	81	50	3	0	45	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10688573--10688716	47	3.1	46	65	23	113	49	4	2	43	1.35
10688541--10688745	91	2.2	91	92	0	329	46	4	3	45	1.41
10688566--10688708	44	3.2	43	68	16	119	48	4	2	45	1.33
10688591--10688729	47	3.0	47	68	17	137	49	5	2	43	1.36
10690143--10690169	11	2.5	11	100	0	54	51	18	7	22	1.70
10691726--10691788	33	1.9	33	100	0	126	36	6	15	41	1.73
10691983--10692071	37	2.4	37	94	0	160	33	7	14	43	1.74
10694068--10694106	19	2.1	19	100	0	78	41	20	28	10	1.85
10694085--10694170	33	2.7	31	76	13	102	50	13	29	6	1.68
10706797--10706824	6	4.7	6	100	0	56	17	28	0	53	1.44
10711819--10711865	24	1.9	24	86	4	67	36	0	38	25	1.56
10712556--10712840	27	10.6	27	85	3	333	43	18	16	21	1.88
10712556--10712840	81	3.5	81	83	5	371	43	18	16	21	1.88
10717445--10717492	16	3.0	16	81	0	60	45	25	6	22	1.75
10717504--10717572	16	4.3	16	75	14	61	42	28	4	24	1.74
10717726--10717833	52	2.1	53	82	5	130	37	18	12	31	1.87
10721183--10721238	22	2.5	22	85	8	78	44	21	25	8	1.81
10747912--10748073	37	4.6	36	75	16	160	6	24	12	55	1.61
10747938--10748010	31	2.3	32	90	6	123	8	21	10	58	1.58
10747972--10748066	38	2.5	38	81	10	122	6	24	12	56	1.59
10750075--10750138	26	2.5	26	92	2	112	46	9	20	23	1.79
10750325--10750398	23	3.3	23	66	11	64	47	2	4	45	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10750319--10750424	43	2.5	41	83	9	133	49	4	2	43	1.38
10754350--10754410	28	2.3	26	82	5	68	44	0	3	52	1.17
10754229--10754437	91	2.3	91	89	0	319	44	2	4	47	1.39
10754717--10754758	15	2.7	16	82	14	52	45	0	2	52	1.13
10754708--10754749	15	2.9	15	82	10	52	47	0	0	52	1.00
10754972--10755025	16	3.4	16	92	0	90	27	35	1	35	1.68
10757189--10757260	30	2.4	30	83	4	92	33	33	20	12	1.90
10758934--10759007	25	3.0	25	91	0	130	29	22	17	29	1.97
10760942--10761013	3	24.3	3	75	8	67	30	4	4	61	1.34
10760946--10761002	16	3.7	15	81	11	62	31	5	1	61	1.28

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