genome.fa.s4.2.7.7.80.10.50.1000.137.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  137  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)
43612759--43612825	34	1.9	35	87	3	100	31	8	14	44	1.76
43614015--43614053	6	6.7	6	91	5	53	53	5	0	41	1.23
43614019--43614053	17	2.1	17	88	0	52	51	5	0	42	1.25
43631945--43631993	24	2.0	24	88	0	71	4	40	12	42	1.61
43631954--43631993	12	3.3	12	96	0	71	0	42	15	42	1.46
43631954--43632046	21	4.3	21	80	4	87	1	41	19	37	1.59
43634547--43634584	7	5.6	7	82	17	53	28	0	13	57	1.36
43634532--43634604	27	2.7	26	72	6	74	36	1	12	49	1.49
43634596--43634681	21	4.0	21	73	16	70	33	2	15	48	1.57
43634504--43634698	95	2.0	96	91	1	311	34	2	13	49	1.54
43634642--43634687	15	3.3	15	79	17	62	28	0	10	60	1.30
43634792--43634935	61	2.4	61	80	10	161	47	8	4	38	1.55
43634870--43634909	16	2.6	15	76	7	53	47	7	0	45	1.31
43634825--43634939	61	1.9	61	85	7	162	48	7	3	40	1.49
43634901--43634957	30	1.9	30	92	0	96	56	5	7	31	1.49
43634918--43634950	17	1.9	17	93	0	57	51	9	6	33	1.58
43637485--43637535	23	2.2	24	82	10	61	43	3	0	52	1.19
43637500--43637535	16	2.3	17	86	13	51	41	2	0	55	1.14
43637912--43637953	15	2.9	15	82	3	50	42	38	0	19	1.51
43638410--43638974	113	5.0	113	77	11	482	27	21	19	31	1.97
43638432--43638974	228	2.4	225	86	5	736	27	21	18	31	1.97
43646074--43646101	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43649093--43649162	17	4.0	18	74	22	60	55	1	21	21	1.51
43650788--43650863	37	2.1	37	100	0	152	30	7	7	53	1.58
43651714--43651878	55	3.0	55	91	0	267	24	7	16	50	1.72
43655537--43655597	26	2.3	26	80	5	70	34	22	24	18	1.96
43657569--43657712	48	3.0	48	93	0	252	41	22	11	23	1.87
43664409--43664433	13	1.9	13	100	0	50	40	0	0	60	0.97
43665751--43665862	49	2.3	49	85	0	143	24	14	32	29	1.94
43675436--43675508	26	2.9	25	84	8	85	20	23	17	38	1.93
43679267--43679302	18	2.0	18	89	10	56	30	25	0	44	1.54
43680537--43680583	14	3.4	14	79	2	51	34	10	0	55	1.35
43689562--43689586	9	2.8	9	100	0	50	40	0	36	24	1.55
43689903--43689960	24	2.4	24	82	8	73	46	0	13	39	1.44
43694300--43694344	20	2.2	20	92	0	72	31	26	11	31	1.91
43696830--43697238	84	4.8	86	82	6	406	45	11	10	32	1.74
43697030--43697489	79	5.5	87	78	11	335	39	13	14	33	1.85
43697348--43697653	160	1.9	161	80	7	354	41	12	15	31	1.84
43708660--43708688	8	3.6	8	100	0	58	24	13	27	34	1.93
43708775--43708850	23	3.3	23	96	0	143	21	21	26	31	1.98
43712047--43712392	152	2.3	151	90	0	539	31	27	15	24	1.96
43712047--43712397	101	3.5	100	80	5	323	31	27	15	24	1.96
43714376--43714439	26	2.3	27	89	7	94	28	10	10	50	1.71
43720278--43720385	54	2.0	54	100	0	216	29	14	27	27	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43734771--43734822	26	2.0	27	85	11	72	0	32	1	65	1.04
43745907--43746026	37	3.2	37	98	0	231	25	19	17	38	1.93
43745990--43746146	46	3.3	46	83	10	215	27	21	14	36	1.92
43746042--43746213	59	3.1	53	86	11	247	25	23	13	36	1.92
43753150--43753282	63	2.1	63	82	0	158	23	30	21	24	1.99
43760383--43760429	21	2.3	20	78	10	51	65	2	2	29	1.15
43760511--43760546	2	18.0	2	94	0	63	47	0	0	52	1.00
43760681--43760748	3	22.7	3	96	0	127	67	0	0	32	0.91
43765547--43765581	3	11.7	3	100	0	70	0	34	0	65	0.93
43767714--43767809	30	3.2	29	81	10	95	38	2	0	59	1.09
43767765--43767818	9	5.8	9	78	8	63	29	0	0	70	0.88
43767739--43767851	40	3.1	39	72	26	129	35	0	0	64	0.94
43767755--43767829	29	2.6	29	91	8	118	36	0	0	64	0.94
43767815--43767867	10	4.9	11	77	13	65	41	0	0	58	0.98
43767777--43767867	29	3.0	31	85	10	109	37	0	0	62	0.95
43768325--43768353	14	2.1	14	100	0	58	20	6	20	51	1.70
43768680--43768726	19	2.5	19	82	0	58	57	2	4	36	1.30
43797475--43797534	20	3.0	20	90	7	88	30	18	38	13	1.89
43797523--43797621	40	2.5	40	75	6	110	36	19	28	16	1.93
43806015--43806219	69	3.0	69	91	0	313	35	17	22	24	1.95
43806016--43806245	69	3.3	69	87	3	304	35	18	23	23	1.95
43809812--43809869	25	2.3	25	81	0	71	22	32	34	10	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43814731--43814824	49	1.9	49	88	0	143	41	7	27	23	1.81
43816151--43816222	25	2.9	25	76	15	85	25	22	19	33	1.97
43816137--43816248	50	2.2	51	85	3	147	25	20	21	33	1.97
43823769--43823826	29	2.0	30	83	10	75	44	0	31	24	1.54
43825394--43825576	90	2.0	90	95	0	330	21	26	14	36	1.93
43825510--43825642	66	2.0	66	100	0	266	25	25	16	32	1.96
43831369--43831482	51	2.2	51	93	0	201	30	17	12	39	1.86
43832817--43832876	31	2.0	31	84	9	81	50	10	1	38	1.46
43833179--43833216	19	2.0	19	89	0	58	44	7	2	44	1.47
43834004--43834219	108	2.0	108	94	0	378	31	19	14	34	1.92
43835353--43835409	10	5.2	11	74	21	57	21	35	0	43	1.52
43835370--43835425	22	2.5	22	97	2	103	28	32	0	39	1.57
43835397--43835512	51	2.3	51	93	0	196	27	24	0	47	1.58
43836653--43836677	7	3.6	7	100	0	50	28	0	12	60	1.32
43837929--43837957	12	2.3	13	94	5	51	37	48	0	13	1.43
43837948--43838534	23	25.3	23	73	18	454	46	24	1	28	1.60
43837952--43838534	45	12.6	44	77	16	422	46	24	1	28	1.60
43837948--43838531	68	8.4	67	77	16	482	46	24	1	28	1.60
43838124--43838534	186	2.2	185	96	0	768	45	24	1	28	1.63
43838544--43838763	118	1.9	118	91	1	363	38	10	9	41	1.71
43838739--43838780	17	2.4	18	80	4	50	42	9	2	45	1.49
43841793--43842142	125	2.8	124	88	2	533	32	21	15	30	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43845157--43845275	27	4.4	27	73	8	107	24	25	18	31	1.97
43845157--43845223	26	2.5	26	90	2	98	22	26	19	31	1.98
43845133--43845303	81	2.1	80	89	3	254	26	22	19	32	1.97
43846692--43846738	5	9.4	5	100	0	94	59	0	0	40	0.97
43847301--43847329	14	2.1	14	100	0	58	55	13	6	24	1.63
43847358--43847397	21	1.9	21	90	10	64	55	15	20	10	1.68
43852752--43852889	40	3.5	40	73	6	129	31	23	17	27	1.97
43853769--43853793	12	2.1	12	100	0	50	0	32	0	68	0.90
43853784--43853841	25	2.2	26	81	6	64	1	22	3	72	1.09
43853799--43853860	30	2.0	31	84	3	81	6	14	4	74	1.19
43860176--43860247	24	3.2	24	62	22	66	47	6	5	40	1.54
43860171--43860324	42	3.7	42	94	0	263	46	5	6	41	1.52
43860169--43860352	42	4.5	40	89	4	187	46	4	5	44	1.46
43862980--43863011	9	3.4	9	91	8	55	65	3	0	31	1.08
43867022--43867176	44	3.5	44	91	0	265	32	16	21	29	1.95
43870699--43870750	18	2.8	18	75	13	52	67	0	25	7	1.17
43876125--43876157	15	2.3	15	89	5	50	45	0	0	54	0.99
43876222--43876356	58	2.3	58	83	8	157	41	3	4	50	1.40
43883941--43884431	245	2.0	245	96	0	901	24	20	15	39	1.91
43902692--43902761	31	2.3	30	85	4	88	48	14	12	24	1.78
43924942--43925013	28	2.6	28	82	2	83	33	13	25	27	1.94
43927663--43927850	20	9.4	20	68	8	96	35	21	32	11	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43927681--43927807	40	3.2	40	71	14	118	34	19	33	12	1.90
43927678--43927850	80	2.2	80	81	4	215	35	21	31	11	1.89
43933964--43934007	23	2.0	23	86	4	63	38	4	18	38	1.71
43933952--43934021	22	3.3	22	76	11	65	32	5	18	42	1.74
43934382--43934421	20	2.0	21	85	14	57	67	7	15	10	1.41
43940304--43940438	43	3.2	42	75	5	128	28	21	24	25	1.99
43943118--43943147	14	2.1	14	93	0	51	30	6	20	43	1.77
43943316--43943358	20	2.2	20	91	0	68	67	4	0	27	1.10
43943365--43943416	24	2.1	24	82	10	61	55	0	3	40	1.18
43943399--43943459	10	6.7	9	76	14	54	63	1	1	32	1.13

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