genome.fa.s2.2.7.7.80.10.50.1000.22.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   205   206   

This is table  22  of  206  ( 24623 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)
6535210--6535243	8	4.2	8	84	0	50	50	11	0	38	1.39
6537505--6537556	20	2.8	18	78	21	63	51	3	1	42	1.31
6539807--6540035	48	4.7	49	80	7	234	21	28	21	27	1.99
6539807--6540043	50	4.8	50	81	4	241	21	29	21	27	1.99
6539807--6540046	98	2.4	99	80	5	263	22	29	21	27	1.99
6546221--6546390	85	2.0	85	91	0	277	36	24	21	17	1.94
6550794--6550865	22	3.3	22	94	0	117	30	16	27	25	1.97
6552560--6552626	29	2.3	29	76	0	80	50	4	2	41	1.37
6552935--6552973	18	2.2	18	100	0	78	69	10	0	20	1.17
6552935--6553006	18	3.9	17	83	5	63	62	11	0	26	1.28
6555071--6555114	21	2.1	21	87	8	63	27	6	2	63	1.31
6555414--6555469	27	2.1	27	96	0	103	35	12	17	33	1.88
6556283--6556345	23	2.6	24	71	19	58	30	1	4	63	1.24
6556630--6556667	19	2.0	19	100	0	76	21	15	15	47	1.82
6557476--6557525	2	25.0	2	100	0	100	50	0	0	50	1.00
6558453--6558686	41	5.7	41	92	1	369	21	28	21	28	1.99
6561316--6561380	21	3.0	21	71	8	58	35	1	6	56	1.33
6561681--6561709	10	2.9	10	100	0	58	48	20	10	20	1.79
6567488--6567522	15	2.3	15	85	0	52	62	11	0	25	1.28
6567784--6567820	11	3.5	11	85	14	51	75	0	2	21	0.92
6567857--6567919	26	2.6	24	83	11	83	61	3	4	30	1.32
6567923--6567967	21	2.1	21	92	8	74	53	6	4	35	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6571944--6572055	20	5.6	19	68	17	59	56	3	1	38	1.27
6574837--6574910	27	2.8	26	84	11	105	28	17	13	40	1.87
6574837--6574910	26	2.8	27	86	11	109	28	17	13	40	1.87
6586479--6586513	16	2.1	17	89	5	54	62	5	0	31	1.18
6590881--6590938	30	1.9	31	82	6	75	32	10	3	53	1.52
6592709--6592751	19	2.3	19	79	0	50	69	4	0	25	1.07
6592706--6592730	5	5.0	5	100	0	50	80	0	0	20	0.72
6611122--6611181	7	8.4	7	81	3	75	36	0	3	60	1.14
6611122--6611208	36	2.3	38	94	5	151	34	0	5	59	1.21
6612779--6612826	18	2.8	18	74	22	50	43	0	0	56	0.99
6612779--6612843	16	4.0	16	74	20	55	44	0	0	55	0.99
6612682--6612868	59	3.1	59	66	15	150	43	3	3	49	1.38
6612990--6613023	18	1.9	17	88	5	50	44	0	0	55	0.99
6619675--6619739	3	21.7	3	96	0	121	33	1	0	64	1.03
6619791--6619845	29	2.0	27	82	13	67	20	5	3	70	1.22
6624452--6624476	13	1.9	13	100	0	50	32	0	4	64	1.12
6626092--6626265	94	1.9	94	87	0	258	34	20	6	38	1.79
6626335--6626490	77	2.0	76	86	6	217	33	19	7	38	1.81
6626593--6626629	19	1.9	19	100	0	74	37	10	13	37	1.80
6634123--6634169	24	2.0	24	83	8	60	17	34	0	48	1.47
6635515--6635552	18	2.1	18	85	9	51	0	10	7	81	0.87
6636077--6636208	45	3.0	44	77	5	140	30	23	16	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6636310--6636426	44	2.8	42	72	11	105	29	19	19	31	1.97
6636455--6636632	44	4.0	44	78	2	142	28	22	17	32	1.96
6636990--6637340	50	7.0	50	76	0	342	26	19	21	32	1.97
6636909--6637340	100	4.3	100	88	0	598	27	19	20	32	1.97
6643583--6643610	14	2.0	14	100	0	56	35	21	0	42	1.53
6656753--6657176	214	2.0	214	97	0	803	35	9	16	38	1.82
6661233--6661301	24	2.8	24	82	2	84	18	21	18	40	1.91
6661425--6661506	24	3.4	23	77	9	67	17	18	23	41	1.90
6661862--6661899	19	2.0	19	100	0	76	15	5	21	57	1.57
6662622--6662802	73	2.5	73	93	0	308	18	26	28	27	1.98
6664639--6664889	27	9.3	27	81	7	278	42	19	19	19	1.89
6665246--6665337	28	3.2	28	84	7	130	25	23	22	28	2.00
6665250--6665334	30	2.9	30	87	3	129	25	24	22	27	2.00
6683953--6684107	84	1.8	84	84	2	213	49	9	9	30	1.68
6684069--6684331	86	3.0	87	84	3	334	41	11	12	33	1.79
6684077--6684361	86	3.3	85	79	9	297	41	10	12	34	1.78
6684293--6684596	79	3.8	79	85	2	389	42	12	14	30	1.83
6684531--6684701	89	2.0	86	82	3	207	40	13	15	30	1.86
6687181--6687352	69	2.5	69	81	3	186	29	23	26	20	1.99
6687193--6687351	35	4.6	35	71	5	110	30	23	25	20	1.98
6692150--6692180	2	15.5	2	100	0	62	48	0	0	51	1.00
6695757--6695800	23	1.9	23	85	0	61	43	20	6	29	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6706306--6706343	19	2.0	19	94	0	67	23	21	13	42	1.88
6708566--6709008	84	5.2	83	90	3	629	46	12	10	30	1.76
6708498--6709008	168	3.0	167	86	5	647	45	11	11	31	1.76
6709014--6709269	79	3.2	77	80	6	280	40	11	17	30	1.84
6709050--6709268	80	2.8	79	86	1	312	40	11	16	31	1.84
6709050--6709296	79	3.1	79	84	2	325	38	11	17	32	1.85
6709546--6709585	18	2.3	18	86	4	55	45	0	7	47	1.31
6711239--6711319	31	2.6	31	83	9	105	38	8	14	38	1.77
6714151--6714203	16	3.2	16	82	12	54	52	1	1	43	1.23
6715398--6715424	12	2.2	12	100	0	54	14	14	25	44	1.84
6715749--6715773	11	2.3	11	100	0	50	56	24	0	20	1.43
6716650--6716955	70	4.4	70	84	3	373	31	23	21	24	1.99
6716734--6716925	35	5.5	34	62	20	83	32	23	20	22	1.98
6716650--6716955	140	2.2	140	85	1	416	31	23	21	24	1.99
6719388--6719510	12	9.8	12	71	11	77	50	8	14	26	1.71
6719388--6719510	25	4.9	25	74	14	101	50	8	14	26	1.71
6719505--6719542	18	2.1	18	85	9	51	60	7	15	15	1.57
6724709--6724826	25	4.7	24	75	12	94	51	8	14	25	1.70
6724709--6724833	12	9.8	12	67	13	63	50	8	14	26	1.72
6724821--6724858	18	2.1	18	85	9	51	60	7	15	15	1.57
6728275--6728304	12	2.5	12	100	0	60	26	40	26	6	1.81
6744660--6744705	23	2.0	22	91	4	74	45	0	4	50	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6744674--6744719	16	2.8	17	78	15	53	45	0	4	50	1.21
6746707--6746831	63	2.0	63	85	0	169	28	21	27	22	1.99
6748582--6749198	61	10.1	60	73	11	403	43	16	6	33	1.74
6748678--6748920	31	8.1	27	71	18	96	43	18	5	32	1.72
6748680--6749221	214	2.5	215	87	4	774	43	17	5	33	1.73
6748609--6749191	92	6.3	92	80	5	454	43	16	6	33	1.74
6748833--6749191	184	2.0	183	87	3	526	44	17	5	32	1.72
6748673--6749191	92	5.6	91	80	6	466	43	16	5	33	1.73
6761622--6761657	17	2.2	16	90	5	54	8	8	2	80	0.99
6761635--6761674	15	2.6	16	80	11	57	7	12	5	75	1.18
6761635--6761678	14	3.0	14	90	6	61	11	13	6	68	1.39
6766250--6766387	50	2.8	50	83	2	170	21	26	23	27	1.99
6772014--6772082	21	3.3	20	80	6	77	18	7	17	56	1.63
6772014--6772105	20	4.5	20	75	4	76	20	7	16	55	1.65
6774933--6774958	4	6.5	4	100	0	52	0	26	0	73	0.84
6774968--6774996	13	2.2	13	100	0	58	37	0	10	51	1.36
6781279--6781321	21	2.1	21	86	4	61	46	2	6	44	1.43
6781355--6781410	29	1.9	29	85	7	78	46	7	8	37	1.63
6784567--6784625	29	2.1	29	96	3	111	45	13	6	33	1.70
6788070--6788381	43	7.4	42	72	9	213	35	24	16	24	1.95
6788062--6788382	85	3.8	85	84	2	385	34	23	17	23	1.95
6788062--6788382	170	1.9	169	85	0	444	34	23	17	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6792065--6792104	20	2.0	20	86	13	57	40	5	17	37	1.72
6792352--6792392	2	21.0	2	95	5	75	51	0	0	48	1.00
6797792--6797832	21	2.0	21	85	0	55	39	7	26	26	1.82
6798677--6798710	17	2.1	17	88	5	52	50	0	17	32	1.47
6812139--6812243	39	2.7	37	82	5	138	55	0	3	40	1.18
6812158--6812214	10	5.9	10	71	21	50	54	0	3	42	1.17
6812154--6812243	37	2.3	39	90	5	139	54	0	4	41	1.20
6812139--6812243	37	2.8	38	81	12	128	55	0	3	40	1.18
6812139--6812271	39	3.6	37	79	11	125	57	0	3	39	1.14
6816921--6816978	2	29.5	2	96	3	109	50	0	0	50	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   205   206