genome.fa.s7.2.7.7.80.10.50.1000.15.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   199   200   201   202   203   204   

This is table  15  of  204  ( 24458 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)
5786074--5786120	17	2.8	17	75	15	53	29	4	0	65	1.11
5787464--5787489	4	6.5	4	100	0	52	76	23	0	0	0.78
5793533--5793586	21	2.5	21	75	3	54	62	3	0	33	1.12
5795226--5795254	2	15.0	2	92	7	51	51	0	0	48	1.00
5796463--5796497	2	18.0	2	88	5	54	45	0	0	54	0.99
5813877--5813932	19	2.8	20	75	17	55	44	1	1	51	1.22
5819975--5820011	19	2.0	19	89	5	58	40	5	0	54	1.24
5825012--5825079	24	2.7	25	81	6	66	42	1	5	50	1.35
5833257--5833295	14	2.8	13	85	14	51	17	0	5	76	0.96
5839688--5839721	15	2.3	15	94	0	59	64	11	0	23	1.26
5839728--5839764	13	2.7	14	84	16	51	67	5	5	21	1.31
5840258--5840310	15	3.5	15	89	0	52	62	7	0	30	1.23
5840273--5840313	3	13.7	3	94	0	73	65	2	0	31	1.05
5841488--5842399	132	6.9	132	95	0	1592	29	23	18	28	1.98
5847259--5847599	47	7.3	47	92	1	479	44	19	12	24	1.85
5847218--5847599	94	4.1	94	87	2	466	43	18	13	24	1.85
5847238--5847599	25	15.5	22	70	18	173	44	18	12	23	1.85
5847389--5847603	24	9.3	22	68	19	134	44	20	12	22	1.85
5851229--5851262	15	2.3	15	94	0	59	64	11	0	23	1.26
5851269--5851305	13	2.7	14	84	16	51	67	5	5	21	1.31
5851806--5851838	3	11.0	3	100	0	66	66	0	0	33	0.92
5855894--5855946	27	2.0	27	96	0	97	20	32	18	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5873097--5873133	14	2.6	15	83	12	51	43	8	0	48	1.32
5873148--5873335	61	3.1	61	69	14	190	42	2	6	48	1.40
5873209--5873254	16	2.9	16	78	12	51	45	0	2	52	1.13
5873104--5873372	120	2.2	120	94	2	470	42	2	5	50	1.37
5873149--5873332	57	3.1	59	66	25	150	42	2	6	48	1.41
5873329--5873370	15	2.7	16	82	14	52	45	0	2	52	1.13
5873320--5873361	15	2.9	15	82	10	52	47	0	0	52	1.00
5873584--5873616	16	2.1	16	94	0	57	18	36	9	36	1.82
5878114--5878154	19	2.1	20	90	4	66	36	2	0	60	1.10
5880998--5881161	82	2.0	82	95	0	292	39	11	10	37	1.77
5883903--5883931	10	2.7	11	89	10	51	34	0	0	65	0.93
5885315--5885355	19	2.1	20	86	4	57	34	4	0	60	1.18
5887251--5887317	29	2.3	29	81	2	80	28	16	16	38	1.90
5890085--5890229	19	8.1	17	70	17	89	44	9	10	35	1.71
5890096--5890233	17	7.8	17	69	18	70	46	8	9	35	1.67
5890100--5890269	37	4.6	36	73	13	98	45	8	10	35	1.69
5890237--5890346	55	2.0	54	82	3	132	45	10	9	35	1.69
5891132--5891180	12	4.2	11	80	19	55	0	20	2	77	0.87
5891131--5891180	18	2.8	17	88	8	73	0	20	2	78	0.86
5891133--5891183	24	2.1	25	89	10	79	0	21	1	76	0.88
5892136--5892185	24	2.1	23	85	3	64	46	0	0	54	1.00
5893311--5893354	18	2.4	18	100	0	88	4	20	22	52	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5893792--5893837	24	1.9	24	86	0	65	45	0	2	52	1.13
5894555--5894599	21	2.1	22	84	12	58	40	15	6	37	1.74
5898248--5898307	22	2.7	22	81	2	66	51	6	28	13	1.66
5900006--5900036	3	10.7	3	93	6	55	0	29	0	70	0.87
5902563--5902626	33	1.9	33	87	0	92	15	9	46	28	1.77
5908201--5908270	30	2.3	30	97	2	131	38	18	8	34	1.81
5930264--5930301	18	2.2	17	86	13	51	68	5	5	21	1.29
5941558--5941595	10	3.9	10	82	6	51	47	0	0	52	1.00
5943102--5943160	27	2.2	28	78	9	68	44	30	1	23	1.64
5949235--5949331	9	10.4	9	69	18	65	64	2	4	28	1.23
5949217--5949267	20	2.5	19	81	12	57	70	1	3	23	1.14
5949235--5949340	28	3.8	27	75	9	88	63	1	3	31	1.23
5949234--5949401	20	8.8	19	69	15	91	61	2	5	30	1.33
5949599--5949633	18	1.9	18	94	0	61	42	0	0	57	0.99
5949680--5949855	90	2.0	87	84	8	230	32	9	21	36	1.85
5950590--5950619	14	2.1	15	93	6	53	66	3	0	30	1.07
5951089--5951128	16	2.4	16	91	4	62	50	0	0	50	1.00
5951098--5951130	16	2.1	16	100	0	66	42	0	0	57	0.98
5951117--5951196	11	7.5	11	73	17	62	37	2	0	60	1.11
5951101--5951204	41	2.6	40	83	6	140	39	1	0	58	1.09
5951858--5951892	18	1.9	18	88	0	52	37	5	5	51	1.50
5952060--5952118	16	3.5	16	77	15	57	38	0	8	52	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5952597--5952653	20	2.8	21	77	17	57	45	0	3	50	1.18
5966069--5966133	33	2.0	33	81	6	78	16	6	1	75	1.08
5970960--5971006	23	2.0	23	87	0	67	34	6	17	42	1.74
6000300--6000335	2	18.0	2	100	0	72	50	0	0	50	1.00
6007753--6007960	59	3.5	59	83	5	251	35	6	8	49	1.60
6010855--6010973	41	2.9	41	93	0	193	34	25	17	22	1.96
6011973--6012119	41	3.6	41	87	1	215	23	29	19	27	1.98
6013506--6013562	28	2.0	28	90	6	89	38	5	0	56	1.22
6013754--6013782	14	2.0	15	93	6	51	51	20	0	27	1.47
6014500--6014527	9	3.1	9	100	0	56	57	10	0	32	1.33
6014462--6014710	68	3.7	68	95	2	441	46	8	4	40	1.56
6014568--6014595	9	3.1	9	100	0	56	57	10	0	32	1.33
6014462--6014710	134	1.8	136	93	3	441	46	8	4	40	1.56
6015670--6015797	40	3.2	40	64	12	107	23	25	19	32	1.98
6015647--6015811	82	2.0	82	98	0	321	24	24	20	30	1.98
6016114--6016179	29	2.2	29	83	2	78	27	21	3	48	1.64
6037978--6038003	7	3.7	7	100	0	52	0	11	0	88	0.52
6046219--6046263	20	2.3	20	81	14	58	46	0	0	53	1.00
6046572--6046604	17	1.9	17	93	0	57	39	6	0	54	1.25
6054680--6054773	29	3.1	29	64	14	73	38	23	10	27	1.88
6054683--6054780	32	3.2	32	64	14	87	36	23	11	28	1.89
6061420--6061448	3	9.7	3	100	0	58	68	0	0	31	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6061615--6061691	13	5.8	13	79	1	64	28	7	25	37	1.84
6061615--6061688	26	2.8	25	78	8	85	25	8	27	39	1.84
6062156--6062251	15	6.5	15	81	13	128	37	0	9	53	1.34
6062162--6062242	29	2.8	29	100	0	162	38	0	9	51	1.35
6062177--6062227	14	3.6	14	80	15	68	37	0	11	50	1.39
6062156--6062251	44	2.2	44	85	10	126	37	0	9	53	1.34
6063539--6063960	211	2.0	211	99	0	826	30	16	16	35	1.92
6068398--6068451	16	3.4	16	84	0	72	42	1	24	31	1.65
6071588--6071722	25	5.6	24	79	15	113	22	22	15	38	1.92
6071612--6071722	47	2.3	49	73	26	114	20	22	17	39	1.92
6076239--6076315	30	2.5	31	77	6	77	50	3	2	42	1.34
6076274--6076338	30	2.2	31	83	10	82	53	1	3	41	1.25
6076388--6076441	16	3.1	16	72	23	54	51	0	1	46	1.11
6076378--6076454	37	2.1	37	87	4	111	50	2	2	44	1.29
6076999--6077085	42	2.0	43	91	2	140	50	3	4	41	1.40
6090049--6090089	21	2.0	21	100	0	82	31	14	19	34	1.92
6096283--6096569	96	3.0	95	94	2	495	22	22	18	36	1.95
6115615--6115680	33	2.0	33	100	0	132	39	18	12	30	1.87
6118999--6119056	30	1.9	31	85	3	82	50	0	6	43	1.29
6121643--6121668	3	8.7	3	100	0	52	69	0	0	30	0.89
6128689--6128719	16	1.9	16	100	0	62	45	3	0	51	1.17
6128867--6128951	40	2.2	39	85	10	111	24	2	3	69	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6131961--6132149	51	3.7	51	81	5	213	32	24	15	26	1.96
6131960--6132149	102	1.9	102	86	4	276	32	25	15	26	1.96
6134559--6134660	50	2.0	50	86	0	141	30	13	16	39	1.88
6135589--6135656	21	3.5	20	78	7	59	38	10	16	35	1.82
6139524--6139581	30	1.9	30	89	0	89	41	3	24	31	1.71
6139794--6139824	13	2.4	13	94	0	53	32	0	12	54	1.38
6139919--6140161	50	4.8	50	91	0	387	25	22	31	20	1.98
6147508--6147799	50	5.8	50	92	0	460	26	22	30	20	1.98
6150796--6150867	21	3.4	21	74	0	72	19	22	19	38	1.93
6153268--6153302	2	17.5	2	100	0	70	48	0	0	51	1.00

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   199   200   201   202   203   204