genome.fa.s4.2.7.7.80.10.50.1000.103.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  103  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)
33075168--33075267	39	2.6	39	80	0	110	32	7	20	41	1.79
33076046--33076086	20	2.0	20	86	9	57	26	24	19	29	1.98
33080339--33080651	27	11.6	27	86	3	427	44	20	18	17	1.87
33080864--33080913	26	1.9	26	95	0	91	16	20	24	40	1.91
33081603--33081666	33	1.9	33	100	0	128	26	9	9	54	1.62
33082113--33082159	23	2.0	23	95	0	85	40	23	21	14	1.90
33082867--33082961	48	2.0	48	93	0	163	40	26	17	15	1.90
33097284--33097316	12	2.8	12	95	0	57	27	15	12	45	1.81
33099147--33099288	29	4.9	29	79	5	153	37	15	28	19	1.92
33106111--33106189	26	3.0	26	81	3	97	44	21	17	16	1.87
33106360--33106465	27	3.9	27	87	4	160	20	14	22	42	1.88
33107142--33107186	15	3.0	14	78	15	54	64	2	33	0	1.06
33107136--33107186	19	2.6	20	81	12	61	62	1	35	0	1.06
33107136--33107186	10	4.8	11	81	16	63	62	1	35	0	1.06
33108135--33108272	72	2.0	68	87	11	199	40	3	5	50	1.42
33111768--33111798	13	2.4	13	100	0	62	48	12	0	38	1.42
33112484--33112540	10	5.2	11	74	21	57	21	35	0	43	1.52
33112501--33112556	22	2.5	22	97	2	103	28	32	0	39	1.57
33112528--33112643	51	2.3	51	93	3	198	27	26	0	45	1.54
33113781--33113805	7	3.6	7	100	0	50	28	0	12	60	1.32
33114445--33114479	18	1.9	18	94	0	61	25	31	8	34	1.86
33114878--33114976	44	2.2	44	85	7	130	38	0	11	50	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33114890--33114976	44	2.0	45	88	6	133	36	0	11	51	1.38
33114982--33115505	23	21.7	23	76	18	455	45	24	1	27	1.63
33114995--33115455	73	6.4	71	84	9	578	45	24	1	28	1.62
33115468--33115509	22	2.0	20	90	9	66	45	30	0	23	1.53
33115511--33115728	116	1.9	116	96	0	400	38	9	9	42	1.69
33115704--33115745	17	2.4	18	80	4	50	42	9	2	45	1.49
33118757--33119108	126	2.8	125	85	2	483	33	21	15	29	1.94
33119515--33119562	24	2.0	24	84	8	62	54	6	31	8	1.55
33123136--33123178	3	14.3	3	100	0	86	67	0	0	32	0.91
33140535--33140571	17	2.2	17	95	0	65	75	0	0	24	0.80
33140535--33140586	21	2.8	17	74	20	50	75	1	0	23	0.91
33146758--33146819	20	3.1	20	83	4	72	33	9	9	46	1.69
33154500--33154547	20	2.4	20	79	6	53	29	14	14	41	1.85
33154948--33154998	23	2.3	23	90	6	79	23	5	0	70	1.09
33171808--33171952	68	2.1	67	87	1	200	35	18	22	23	1.96
33175695--33175747	24	2.2	24	83	6	63	32	32	0	35	1.58
33175705--33175807	24	4.1	24	82	16	129	32	32	0	35	1.58
33175711--33175791	30	3.0	27	89	10	114	28	33	0	38	1.57
33175766--33175816	22	2.3	22	90	6	77	31	33	0	35	1.58
33175850--33175916	31	2.2	31	91	0	107	31	1	0	67	1.00
33178792--33179088	123	2.4	124	93	2	510	31	22	17	28	1.97
33197083--33197188	54	2.0	54	86	0	149	35	21	19	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33198463--33198658	107	1.8	107	82	2	250	23	23	20	32	1.98
33205119--33205161	14	2.8	16	86	10	54	30	2	4	62	1.28
33210977--33211045	21	3.2	21	81	2	75	24	34	14	26	1.94
33226035--33226077	22	2.0	22	100	0	86	23	25	13	37	1.92
33226094--33226188	3	31.7	3	91	0	154	1	29	0	69	0.95
33228929--33228962	13	2.6	13	86	13	52	41	5	14	38	1.70
33230026--33230200	50	3.5	50	94	0	287	23	22	22	31	1.98
33230026--33230200	25	7.0	25	76	14	182	23	22	22	31	1.98
33230867--33231043	43	4.1	43	88	0	237	32	29	15	22	1.95
33230867--33231100	43	5.5	42	83	1	130	32	26	14	25	1.95
33234864--33234901	13	2.8	14	88	8	60	36	5	0	57	1.21
33235237--33235275	7	5.6	7	84	0	51	28	51	0	20	1.48
33236107--33236264	41	3.8	42	82	8	182	34	23	20	21	1.97
33236988--33237017	12	2.5	12	94	0	51	23	40	30	6	1.80
33237183--33237240	30	1.9	30	96	0	107	20	37	25	15	1.92
33237182--33237250	30	2.3	30	87	0	102	18	33	30	17	1.94
33237330--33237367	14	2.7	14	95	0	67	36	5	18	39	1.73
33243730--33243826	49	2.0	48	87	2	140	42	21	14	21	1.88
33244019--33244082	17	3.6	17	74	15	67	46	14	12	26	1.79
33244037--33244090	17	2.9	19	71	20	60	46	16	12	24	1.82
33244020--33244090	36	2.0	36	97	0	133	46	15	12	25	1.81
33248860--33248956	49	2.0	48	87	2	140	42	20	14	22	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33249167--33249220	17	2.9	19	71	20	60	46	14	12	25	1.81
33249150--33249220	36	2.0	36	94	0	124	46	14	12	26	1.80
33249149--33249212	17	3.6	17	72	15	58	46	12	12	28	1.78
33252571--33252603	15	2.1	16	88	5	50	36	0	36	27	1.57
33259793--33259834	20	2.0	21	86	13	61	73	14	2	9	1.18
33262514--33262622	37	3.0	37	91	2	177	25	22	15	36	1.93
33262586--33262755	46	3.6	46	81	12	209	27	22	13	36	1.92
33262586--33262749	52	3.2	52	80	14	207	26	22	13	37	1.91
33264202--33264235	17	2.0	17	100	0	68	58	11	17	11	1.62
33271228--33271450	43	5.2	43	82	5	238	26	30	17	25	1.98
33271231--33271409	85	2.1	86	88	3	263	27	29	17	25	1.97
33271579--33271619	21	2.0	21	100	0	82	63	4	2	29	1.28
33271748--33271838	43	2.1	43	87	2	130	43	9	10	35	1.73
33278169--33278220	19	2.7	19	79	5	61	63	1	0	34	1.06
33279546--33279576	2	15.5	2	93	0	53	51	3	0	45	1.17
33279935--33279979	23	2.0	23	86	4	65	37	6	17	37	1.76
33283338--33283370	15	2.1	16	88	5	50	30	6	0	63	1.18
33287395--33287449	21	2.6	21	97	0	101	54	16	5	23	1.63
33290720--33290749	15	2.0	15	93	0	51	83	13	3	0	0.77
33290848--33290880	17	2.1	16	88	11	50	15	15	57	12	1.65
33291414--33291469	29	2.0	28	85	3	76	41	1	3	53	1.29
33294251--33294283	2	16.5	2	93	0	57	3	0	45	51	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33294325--33294371	23	2.0	23	100	0	94	25	21	4	48	1.68
33299477--33299506	10	2.9	10	95	5	51	0	13	0	86	0.57
33301120--33301149	2	14.5	2	93	6	51	46	0	3	50	1.18
33306371--33306419	6	7.8	6	82	11	55	18	16	14	51	1.77
33306285--33306391	46	2.4	45	87	4	153	21	18	17	42	1.90
33307492--33307542	26	2.0	26	88	7	77	56	1	0	41	1.10
33307492--33307549	27	2.2	26	84	9	73	56	1	1	39	1.19
33307578--33307628	22	2.3	21	83	9	66	33	0	33	33	1.58
33307633--33307701	22	3.1	22	89	0	102	39	0	28	31	1.57
33318407--33318448	19	2.2	20	95	4	77	50	23	11	14	1.76
33320270--33320294	7	3.6	7	100	0	50	32	0	0	68	0.90
33326204--33326247	23	1.9	22	82	17	54	36	25	0	38	1.56
33326337--33326478	50	2.8	50	83	3	178	30	28	17	22	1.97
33328857--33328926	36	1.9	36	88	0	104	18	21	21	38	1.93
33330776--33330811	14	2.5	15	86	9	56	36	38	2	22	1.69
33333143--33333232	44	2.0	44	84	0	117	50	3	6	40	1.45
33334060--33334089	13	2.4	13	94	5	53	30	0	6	63	1.20
33336513--33336569	25	2.3	26	82	11	66	61	0	3	35	1.13
33339654--33339706	26	2.0	26	96	0	97	18	22	33	24	1.97
33339683--33339833	42	3.6	43	79	7	157	22	18	24	34	1.96
33346983--33347037	20	2.8	20	85	0	74	20	25	1	52	1.56
33347749--33347825	40	1.9	40	81	5	93	35	15	31	18	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33347763--33347920	40	4.0	40	81	8	128	35	16	31	17	1.92
33347763--33347942	80	2.2	80	82	7	215	35	16	31	17	1.92
33347818--33347883	20	3.3	19	68	16	53	34	15	34	15	1.88
33347828--33347922	20	4.8	19	69	8	64	38	15	30	14	1.88
33347811--33347942	40	3.3	40	86	2	185	35	15	31	17	1.92
33350103--33350165	28	2.2	28	91	5	101	41	6	20	31	1.77
33353020--33353069	25	2.0	25	92	0	82	40	16	12	32	1.84
33353314--33353355	17	2.5	17	84	7	59	71	9	7	11	1.31
33358847--33358875	6	4.8	6	100	0	58	0	51	31	17	1.45
33362719--33362771	27	2.0	27	84	0	70	20	20	20	37	1.94

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