genome.fa.s4.2.7.7.80.10.50.1000.142.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  142  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)
45175296--45175351	20	2.7	21	80	5	78	50	0	41	8	1.34
45180972--45181002	12	2.6	12	94	0	53	61	19	0	19	1.35
45181281--45181319	20	2.0	21	85	10	55	66	10	0	23	1.22
45181471--45181528	27	2.1	27	83	0	71	13	29	27	29	1.94
45181569--45181622	27	2.0	27	92	0	90	33	1	9	55	1.42
45183087--45183309	89	2.5	86	84	6	295	39	21	7	30	1.81
45183371--45183486	19	6.2	19	71	17	82	64	0	1	32	1.09
45183362--45183487	29	4.5	28	79	14	127	63	0	1	34	1.10
45183371--45183518	47	3.1	48	73	13	144	61	2	3	33	1.24
45183359--45183487	9	14.0	9	71	19	72	63	0	1	34	1.09
45183360--45183495	10	14.7	9	71	19	66	62	0	1	35	1.10
45183358--45183533	56	3.1	57	80	11	161	61	1	3	32	1.24
45183757--45183844	18	4.7	19	68	19	60	39	3	1	55	1.24
45183849--45184021	88	2.0	88	87	2	249	32	8	21	38	1.83
45186060--45186097	18	2.1	18	100	0	76	26	21	23	28	1.99
45189721--45189748	2	14.0	2	100	0	56	50	0	0	50	1.00
45192265--45192298	14	2.4	14	90	9	52	32	8	0	58	1.29
45192775--45192848	29	2.5	29	84	4	94	27	13	13	45	1.81
45197457--45197487	16	1.9	16	93	0	53	61	3	16	19	1.48
45198364--45198396	17	2.1	16	88	11	50	42	0	18	39	1.50
45205711--45205737	12	2.2	12	100	0	54	48	0	0	51	1.00
45212142--45212268	24	5.3	24	69	18	68	22	29	16	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45221754--45221843	41	2.2	41	90	5	139	28	23	20	27	1.99
45223390--45223460	26	2.7	26	97	0	133	28	23	18	29	1.98
45228381--45228411	14	2.2	14	100	0	62	38	0	6	54	1.26
45230872--45230931	30	2.0	31	87	9	88	21	35	0	43	1.53
45233988--45234081	44	2.1	44	94	0	161	37	11	5	45	1.63
45234692--45234729	13	2.9	13	88	0	58	42	26	10	21	1.85
45241605--45241702	49	2.0	50	95	2	180	41	15	18	24	1.89
45244388--45244440	4	13.2	4	95	0	97	26	0	24	49	1.51
45252552--45252668	44	2.7	44	78	13	143	23	17	29	29	1.97
45258113--45258174	30	2.0	30	84	3	79	46	9	6	37	1.62
45276487--45276567	3	26.3	3	81	16	87	30	1	2	65	1.13
45276505--45276567	20	3.3	19	89	6	92	31	1	0	66	1.01
45276487--45276567	33	2.5	33	86	9	105	30	1	2	65	1.13
45276526--45276574	16	3.2	15	86	11	64	34	2	0	63	1.06
45276520--45276578	17	3.2	19	83	13	70	35	1	0	62	1.05
45277147--45277182	4	8.8	4	87	6	54	19	0	5	75	1.00
45280531--45280591	30	2.0	30	100	0	122	32	19	19	27	1.96
45284958--45284997	20	1.9	22	85	10	57	65	12	12	10	1.49
45286949--45286990	17	2.5	17	80	7	50	47	2	28	21	1.63
45287219--45287346	61	2.1	61	97	0	238	42	4	16	35	1.69
45289784--45289812	6	4.8	6	100	0	58	31	17	17	34	1.93
45295707--45295746	17	2.4	17	95	0	71	25	25	32	17	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45299391--45299444	20	2.7	20	100	0	108	5	24	25	44	1.75
45299967--45300004	19	2.1	18	90	5	58	28	5	15	50	1.66
45301145--45301195	22	2.3	22	100	0	102	52	21	5	19	1.66
45303586--45303629	22	2.0	22	100	0	88	31	13	31	22	1.93
45305243--45305294	20	2.7	19	82	14	70	38	9	0	51	1.35
45305862--45305938	33	2.3	34	86	2	111	44	27	6	22	1.77
45308245--45308300	23	2.4	23	87	0	76	48	12	21	17	1.80
45310888--45310933	22	2.1	22	88	8	67	36	2	0	60	1.09
45322067--45322139	31	2.5	29	75	14	78	65	1	1	31	1.09
45327316--45327357	9	4.6	9	82	14	50	42	0	57	0	0.99
45329619--45329647	15	1.9	15	100	0	58	79	0	20	0	0.74
45333300--45333462	42	3.9	42	81	1	166	39	19	25	16	1.92
45333325--45333392	21	3.2	21	75	4	57	39	16	27	16	1.89
45333430--45333472	21	2.0	21	86	8	61	46	16	16	20	1.84
45335853--45335897	3	16.7	3	78	21	55	62	0	0	37	0.96
45335850--45335897	5	9.6	5	82	17	64	62	0	0	37	0.95
45335853--45335897	19	2.4	19	96	3	83	62	0	0	37	0.96
45338770--45338833	32	2.0	32	100	0	128	34	9	15	40	1.80
45339236--45339309	13	5.7	13	81	0	94	37	28	6	27	1.82
45343258--45343294	2	18.5	2	100	0	74	51	0	0	48	1.00
45347269--45347319	26	2.0	26	85	14	70	7	27	0	64	1.21
45349642--45349676	17	1.9	19	88	11	56	22	2	0	74	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45352488--45352542	27	2.0	27	100	0	110	40	27	3	29	1.73
45353250--45353320	25	2.9	25	79	4	74	38	18	21	22	1.94
45353284--45353372	45	1.9	47	84	4	119	41	15	19	23	1.89
45353417--45353469	25	2.2	24	83	10	63	39	20	20	18	1.92
45359774--45359825	18	3.1	17	77	5	52	34	0	1	63	1.06
45362509--45362590	44	1.9	44	85	9	116	17	4	23	54	1.61
45365643--45365683	18	2.2	19	83	12	50	70	7	0	21	1.11
45373781--45373865	30	2.9	30	77	10	77	43	2	24	29	1.67
45376900--45377002	34	3.0	35	76	8	120	19	24	25	31	1.98
45376821--45377003	74	2.6	72	78	7	169	20	20	23	35	1.96
45379955--45379996	21	2.0	21	90	9	68	23	9	4	61	1.45
45388359--45388413	25	2.2	25	83	0	65	32	23	25	18	1.97
45392769--45392814	6	7.7	6	77	18	51	67	2	0	30	1.03
45392773--45392821	16	3.3	15	82	5	55	65	2	0	32	1.04
45395354--45395382	15	1.9	15	100	0	58	27	0	17	55	1.42
45395868--45396088	110	2.0	110	97	0	415	36	11	16	36	1.84
45408130--45408173	22	2.0	23	86	4	63	54	25	13	6	1.63
45410050--45410099	22	2.3	22	75	0	55	24	4	4	68	1.24
45415645--45415744	32	3.3	31	79	10	100	68	1	0	31	0.97
45415645--45415718	16	4.7	14	73	23	51	66	0	0	33	0.92
45415673--45415744	31	2.4	29	80	8	81	69	1	0	29	0.97
45428664--45428732	22	3.2	21	78	13	77	33	5	2	57	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45432410--45432438	7	4.3	7	95	4	51	86	0	0	13	0.58
45437483--45437617	67	2.0	67	89	2	209	20	16	32	30	1.95
45438614--45438653	3	13.3	3	94	0	71	35	0	0	65	0.93
45438763--45438810	23	2.0	25	88	8	73	39	0	10	50	1.37
45440350--45440386	16	2.3	16	100	0	74	24	13	32	29	1.93
45440490--45440522	2	16.5	2	93	0	57	51	0	0	48	1.00
45445530--45445605	23	3.3	23	88	0	125	30	27	21	21	1.98
45446215--45446259	21	2.1	21	100	0	90	22	24	8	44	1.81
45447258--45447301	3	14.7	3	100	0	88	68	0	0	31	0.90
45447501--45447528	2	14.0	2	100	0	56	50	0	0	50	1.00
45449052--45449135	43	1.9	44	83	7	109	23	28	19	28	1.98
45449056--45449181	44	2.9	43	73	12	105	26	26	19	27	1.99
45449304--45449524	44	5.0	44	80	4	237	27	21	21	29	1.98
45449631--45449875	129	1.9	128	83	4	316	30	21	17	31	1.96
45449888--45450269	44	8.7	44	71	9	226	25	24	19	30	1.98
45449863--45450298	132	3.3	132	91	0	685	24	24	21	30	1.99
45449913--45450269	88	4.1	88	70	9	251	25	24	19	29	1.98
45459983--45460051	23	3.0	23	66	8	68	43	10	2	43	1.53
45459959--45460051	46	2.0	47	97	2	179	44	10	4	40	1.59
45460136--45460202	13	5.3	12	75	16	57	71	4	22	1	1.12
45460136--45460202	25	2.6	25	79	11	66	71	4	22	1	1.12
45468033--45468194	50	3.2	50	74	0	162	23	19	22	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
45468033--45468219	100	1.9	100	85	0	257	23	20	24	31	1.98
45468209--45468297	43	2.0	45	82	4	110	22	22	23	31	1.98
45468405--45468804	132	3.0	132	91	1	642	25	24	19	31	1.98
45471677--45471740	8	7.8	8	75	6	56	71	9	4	14	1.27
45471677--45471741	12	5.2	12	78	7	76	70	9	4	15	1.29
45471934--45471969	4	8.8	4	87	6	54	75	0	2	22	0.94
45471932--45471969	17	2.2	17	95	0	67	73	0	2	23	0.95
45473178--45473232	21	2.7	19	81	10	56	0	18	10	70	1.15
45483245--45483280	18	2.0	18	88	0	54	66	0	5	27	1.13
45485415--45485464	3	16.7	3	79	8	57	60	4	0	36	1.16

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