genome.fa.s4.2.7.7.80.10.50.1000.143.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  143  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)
45492362--45492395	17	1.9	18	88	5	52	35	23	0	41	1.55
45492851--45492875	2	12.5	2	100	0	50	48	0	0	52	1.00
45493080--45493122	13	3.3	13	83	9	61	60	0	0	39	0.97
45493499--45493542	18	2.6	18	86	13	58	70	4	11	13	1.31
45493590--45493628	16	2.4	16	87	8	53	33	7	0	58	1.26
45494132--45494171	13	3.1	13	82	10	55	32	0	0	67	0.91
45505353--45505571	46	4.8	46	94	2	377	28	23	9	37	1.86
45512994--45513044	21	2.4	21	80	6	59	49	0	13	37	1.43
45515719--45515803	9	9.4	9	74	5	82	44	17	8	29	1.78
45516108--45516150	18	2.4	18	84	0	50	11	2	44	41	1.53
45517984--45518054	2	35.5	2	97	0	133	50	47	0	1	1.09
45521495--45521542	20	2.4	20	82	6	53	31	2	6	60	1.33
45521511--45521553	22	2.0	21	82	13	52	39	2	4	53	1.34
45529396--45529472	39	2.0	39	97	0	145	29	25	14	29	1.95
45532869--45532903	18	1.9	18	88	11	54	34	5	0	60	1.21
45539426--45539470	21	2.1	21	84	8	56	22	4	4	68	1.25
45539786--45539813	2	14.0	2	100	0	56	50	0	0	50	1.00
45547424--45547528	41	2.6	41	84	3	122	28	23	25	21	1.99
45552494--45552531	14	2.6	15	87	4	51	44	2	0	52	1.14
45552922--45552972	27	1.9	26	84	11	68	49	3	5	41	1.45
45558640--45558711	28	2.6	28	86	4	92	31	13	25	29	1.94
45563315--45563380	2	34.0	2	90	6	109	50	0	1	48	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45563676--45563710	2	17.5	2	87	0	52	51	0	0	48	1.00
45566377--45566521	41	3.5	41	91	0	218	26	20	28	24	1.99
45566553--45566577	2	12.5	2	100	0	50	52	0	0	48	1.00
45570554--45570582	15	1.9	15	100	0	58	20	27	6	44	1.77
45572677--45572733	27	2.1	27	96	0	105	45	10	15	28	1.79
45574379--45574403	13	1.9	13	100	0	50	8	32	8	52	1.60
45577626--45577667	15	2.9	15	82	10	52	47	0	0	52	1.00
45581631--45581672	11	3.8	11	93	0	75	19	21	7	52	1.69
45583471--45583506	18	2.0	18	94	0	63	25	27	8	38	1.84
45584028--45584214	23	8.2	23	76	12	179	50	23	0	26	1.50
45584052--45584160	45	2.4	45	92	1	184	50	23	0	25	1.49
45584075--45584181	45	2.4	45	90	3	162	47	28	0	24	1.52
45584024--45584206	68	2.7	68	85	5	246	49	25	0	25	1.51
45591555--45591589	17	2.1	17	89	10	54	0	25	0	74	0.82
45591555--45591589	13	2.6	14	91	8	56	0	25	0	74	0.82
45591603--45591639	2	19.0	2	88	5	58	54	0	0	45	1.00
45594633--45594657	3	8.3	3	100	0	50	32	36	0	32	1.58
45599971--45600008	19	2.0	19	85	10	51	31	7	7	52	1.59
45601989--45602067	38	2.1	38	82	2	95	41	16	22	18	1.90
45607768--45607822	28	2.0	28	85	0	74	36	0	0	63	0.95
45607995--45608113	41	2.9	41	88	5	177	36	23	16	23	1.95
45608470--45608515	2	24.0	2	86	8	69	50	2	0	47	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45608952--45608997	14	3.3	14	93	0	83	41	0	2	56	1.11
45609113--45609165	3	17.7	3	100	0	106	33	0	0	66	0.92
45610331--45610415	21	4.0	22	84	7	95	16	23	25	34	1.95
45610344--45610417	21	3.5	21	87	5	96	14	22	27	35	1.94
45613821--45615123	75	17.1	75	86	2	1613	27	18	20	34	1.95
45613821--45615119	228	5.7	226	88	1	1722	26	18	20	34	1.95
45613823--45615123	303	4.3	305	86	3	1755	27	18	20	34	1.95
45616011--45616066	16	3.5	15	78	9	58	69	1	28	0	0.98
45616034--45616064	13	2.3	14	94	5	55	80	0	19	0	0.71
45622527--45622579	3	17.7	3	100	0	106	66	0	0	33	0.92
45622683--45622716	3	11.3	3	100	0	68	67	0	0	32	0.91
45623645--45623798	76	2.0	76	100	0	308	49	7	3	38	1.50
45623973--45624088	58	2.0	58	100	0	232	37	8	15	37	1.78
45629698--45630266	126	4.5	125	85	3	748	30	17	22	29	1.97
45633385--45633775	22	18.1	21	83	5	433	25	0	30	43	1.55
45633388--45633775	43	9.0	42	83	8	442	25	0	30	43	1.55
45634327--45634361	18	1.9	18	88	0	52	42	8	28	20	1.81
45634982--45635021	7	5.7	7	87	0	62	55	12	2	30	1.50
45636219--45636295	11	6.9	11	75	21	72	44	1	27	27	1.62
45636219--45636295	22	3.4	23	77	19	83	44	1	27	27	1.62
45650889--45650956	34	2.0	34	100	0	136	32	2	2	61	1.26
45650892--45650960	12	6.0	11	74	15	68	28	1	2	66	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45652427--45652459	16	2.1	16	94	0	57	12	33	0	54	1.37
45653055--45653092	18	2.1	18	100	0	76	21	5	21	52	1.66
45654577--45654616	20	2.0	20	85	0	53	50	15	10	25	1.74
45668268--45668948	44	15.7	44	70	12	327	27	23	20	28	1.99
45668490--45668818	172	1.9	173	81	6	400	27	21	20	30	1.98
45668268--45668948	217	3.1	217	91	1	1141	27	23	20	28	1.99
45680846--45680892	17	2.8	17	80	6	51	76	6	0	17	0.98
45685450--45685529	41	2.0	41	100	0	160	33	3	22	40	1.72
45687905--45687983	39	2.0	39	95	0	140	44	13	11	30	1.80
45707538--45707725	38	4.9	38	78	0	196	13	20	31	34	1.91
45713626--45713663	2	19.0	2	100	0	76	50	0	0	50	1.00
45714094--45714224	46	2.8	46	89	0	190	28	25	20	25	1.99
45722355--45722406	26	2.0	26	96	0	95	28	3	17	50	1.64
45724577--45724728	25	6.1	25	93	1	252	20	29	15	34	1.94
45728998--45729051	27	2.0	28	88	3	83	48	20	14	16	1.81
45734519--45734613	20	4.8	20	78	7	79	38	16	28	15	1.90
45734507--45734622	40	2.9	42	76	12	100	37	16	29	17	1.91
45745085--45745217	41	3.2	40	86	4	131	30	23	19	26	1.98
45745115--45745217	41	2.5	41	95	0	179	31	23	18	27	1.97
45745842--45745873	2	16.0	2	100	0	64	50	0	0	50	1.00
45757077--45757124	25	1.9	25	86	0	69	29	20	20	29	1.98
45763511--45763560	19	2.5	21	87	12	86	36	14	12	38	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45765693--45765960	30	9.0	30	75	8	226	23	25	12	38	1.90
45765699--45765957	59	4.4	59	76	9	267	23	26	11	38	1.89
45765708--45765984	89	3.1	89	87	2	412	24	24	12	38	1.90
45765731--45765984	59	4.3	58	74	10	226	24	25	12	38	1.90
45772653--45772792	49	2.9	49	90	0	217	32	26	15	26	1.95
45773972--45774045	23	3.2	23	86	0	112	27	29	18	24	1.98
45775508--45775746	121	2.0	121	97	0	451	41	15	15	26	1.87
45785516--45785588	18	3.9	18	70	16	51	39	8	1	50	1.41
45799991--45800023	2	16.5	2	100	0	66	51	0	0	48	1.00
45800219--45800379	41	3.9	41	98	0	304	27	24	22	25	2.00
45801423--45801452	2	15.0	2	92	0	51	46	0	3	50	1.18
45802154--45802205	28	1.9	26	92	7	86	46	7	0	46	1.31
45804569--45804986	41	10.2	41	86	2	527	21	22	23	32	1.98
45806040--45806084	23	2.0	23	87	8	67	24	15	6	53	1.66
45810675--45811024	86	4.1	85	80	5	219	22	16	30	30	1.96
45810736--45811024	43	6.7	43	83	3	350	21	17	31	29	1.96
45810740--45811028	129	2.2	128	85	3	393	20	17	31	30	1.96
45816663--45816717	25	2.2	25	87	3	76	23	27	16	32	1.96
45833336--45833612	68	4.1	68	82	5	317	38	16	19	24	1.92
45838091--45838115	12	2.1	12	100	0	50	24	36	24	16	1.94
45838274--45838349	9	8.4	9	81	5	91	44	19	7	27	1.78
45838273--45838342	27	2.6	27	86	0	104	45	18	8	27	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45840469--45840873	202	2.0	202	94	0	704	25	14	20	39	1.91
45842299--45842351	23	2.3	23	84	12	74	56	5	0	37	1.23
45845992--45846129	40	3.5	40	74	11	135	30	22	18	28	1.97
45847014--45847046	10	3.2	11	87	12	52	0	21	0	78	0.75
45847013--45847059	20	2.3	20	81	0	58	0	23	4	72	1.02
45847114--45847210	43	2.3	42	78	8	106	46	3	1	49	1.24
45861517--45861559	18	2.4	18	88	0	59	44	9	27	18	1.80
45863390--45863432	22	2.0	22	81	9	52	48	0	25	25	1.51
45865949--45866171	81	2.8	81	88	3	326	21	19	30	29	1.97
45865949--45866171	40	5.5	41	91	1	326	21	19	30	29	1.97

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