genome.fa.s4.2.7.7.80.10.50.1000.123.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  123  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)
39544749--39544806	28	2.1	28	83	0	71	34	8	10	46	1.69
39545095--39545494	68	5.8	68	79	13	426	61	2	7	29	1.37
39545274--39545507	61	3.6	62	77	15	220	61	3	6	28	1.36
39545094--39545507	134	3.0	134	85	8	511	61	2	7	28	1.37
39545344--39545496	73	2.1	73	88	0	234	61	3	7	28	1.38
39551854--39551884	16	2.0	16	93	6	55	38	0	0	61	0.96
39551899--39551948	16	3.2	16	70	18	52	50	2	0	48	1.12
39556045--39556071	2	13.5	2	100	0	54	0	0	48	51	1.00
39557141--39557171	11	2.8	11	100	0	62	16	35	0	48	1.46
39560391--39560454	32	2.0	32	90	0	101	6	34	26	32	1.82
39561668--39561709	15	2.8	15	92	0	66	28	11	2	57	1.47
39562478--39562522	22	2.0	22	83	8	56	46	11	6	35	1.66
39563611--39563650	13	3.1	13	81	0	53	30	5	27	37	1.78
39573933--39573957	13	1.9	13	100	0	50	56	8	0	36	1.29
39588006--39588086	31	2.6	31	76	7	92	30	18	14	35	1.91
39589220--39589244	6	4.2	6	100	0	50	64	0	0	36	0.94
39591169--39591199	2	15.5	2	100	0	62	51	0	0	48	1.00
39594517--39594552	2	18.0	2	100	0	72	50	0	50	0	1.00
39596424--39596567	71	2.0	71	91	0	234	26	14	28	30	1.95
39598252--39598296	17	2.6	18	79	13	58	35	0	0	64	0.94
39606137--39606234	49	2.0	49	97	0	187	52	10	13	24	1.71
39607552--39607601	11	4.5	11	92	5	73	42	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39607552--39607601	23	2.2	23	89	3	75	42	0	0	58	0.98
39608225--39608257	6	5.5	6	100	0	66	15	0	0	84	0.61
39608804--39608839	3	11.7	3	88	5	54	30	2	0	66	1.06
39608973--39609018	23	2.0	22	83	4	56	34	8	6	50	1.59
39611175--39611221	19	2.5	19	86	6	60	27	19	8	44	1.79
39612443--39612479	17	2.1	18	90	5	58	29	24	0	45	1.53
39613230--39613283	8	6.5	8	78	16	56	85	0	11	3	0.73
39613230--39613283	25	2.2	25	89	0	81	85	0	11	3	0.73
39613230--39613290	6	10.0	6	84	8	79	83	0	13	3	0.76
39615722--39616759	100	10.8	96	90	4	1137	32	23	20	23	1.98
39616018--39616376	49	7.7	49	67	10	230	31	26	21	20	1.98
39616345--39617226	50	17.7	48	82	6	947	31	22	20	25	1.98
39616317--39617403	100	10.9	100	88	2	1166	31	22	20	25	1.98
39616317--39617361	50	20.9	50	77	6	915	31	22	21	25	1.98
39615722--39617425	100	17.4	99	87	3	825	31	23	20	23	1.98
39617650--39617765	44	2.6	44	86	2	153	33	19	18	28	1.95
39618621--39618655	16	2.2	16	89	0	52	14	0	5	80	0.89
39619331--39619396	3	21.7	3	93	3	114	31	1	0	66	1.01
39619463--39619497	2	17.5	2	87	0	52	48	0	0	51	1.00
39619549--39619593	22	2.0	22	83	8	56	33	8	6	51	1.59
39621574--39621642	26	2.7	26	88	4	104	23	27	21	27	1.99
39628435--39628478	21	2.2	20	87	4	61	72	0	2	25	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39628435--39628478	10	4.3	10	82	5	52	72	0	2	25	0.96
39632000--39632037	19	2.1	19	90	5	60	36	0	2	60	1.11
39631975--39632036	27	2.3	28	75	13	67	40	0	4	54	1.22
39637754--39637997	69	3.6	69	78	5	253	30	28	15	24	1.96
39639309--39639387	41	1.9	41	89	0	122	18	22	26	31	1.97
39639309--39639417	41	2.7	41	83	0	119	18	21	26	33	1.96
39639696--39639726	2	15.5	2	100	0	62	48	0	0	51	1.00
39640741--39640793	27	2.0	27	92	0	88	47	0	11	41	1.39
39641170--39641441	103	2.7	103	84	0	330	31	21	19	27	1.97
39648452--39648481	8	3.6	8	95	4	51	0	13	0	86	0.57
39649821--39649849	2	15.0	2	92	7	51	51	0	0	48	1.00
39654245--39654278	17	2.0	17	94	0	59	41	2	0	55	1.15
39654245--39654378	18	8.0	17	69	17	84	39	1	2	56	1.21
39654525--39654630	44	2.5	41	77	18	126	34	31	3	30	1.75
39654538--39654630	44	2.1	46	91	4	154	36	30	4	29	1.77
39654612--39654649	16	2.4	16	90	0	58	26	31	2	39	1.70
39654816--39654885	16	4.4	16	87	0	95	34	5	34	25	1.80
39654864--39654954	45	2.0	44	87	6	130	32	5	27	34	1.80
39655099--39655166	16	4.2	16	74	20	54	54	1	0	44	1.09
39655119--39655166	18	2.8	18	74	22	50	56	0	0	43	0.99
39655108--39655149	15	2.9	15	82	10	52	52	0	0	47	1.00
39655097--39655448	120	2.9	120	93	2	582	50	4	1	42	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39655239--39655273	18	2.0	17	94	5	61	57	0	0	42	0.99
39655423--39655463	21	2.0	21	100	0	82	56	9	0	34	1.32
39661306--39661350	22	2.0	22	100	0	90	35	33	8	22	1.85
39664040--39664079	21	1.9	21	90	10	64	27	15	25	32	1.95
39667455--39667528	21	3.5	21	86	0	94	25	39	20	14	1.91
39668738--39668820	3	27.7	3	97	0	157	33	1	0	65	1.01
39668865--39668890	12	2.2	12	100	0	52	34	0	7	57	1.27
39668909--39668953	16	2.7	17	82	6	65	44	2	0	53	1.13
39668914--39668973	25	2.3	25	82	5	66	41	3	0	55	1.16
39669136--39669288	22	7.0	22	90	0	225	32	14	26	26	1.94
39672244--39672287	23	1.9	23	95	0	79	34	9	18	38	1.82
39682028--39682074	22	2.1	21	81	14	51	51	4	10	34	1.56
39692143--39692173	16	1.9	16	93	0	53	77	3	3	16	1.03
39708247--39708344	27	3.6	27	84	0	115	42	20	14	22	1.88
39708256--39708358	27	3.8	27	82	5	104	42	18	14	24	1.87
39708247--39708383	54	2.5	53	75	6	134	40	19	18	21	1.92
39709915--39710043	28	4.6	28	82	3	134	58	5	13	22	1.55
39719934--39720091	69	2.3	69	88	2	237	28	25	14	31	1.95
39722334--39722367	17	2.0	18	88	11	54	41	0	8	50	1.34
39728141--39728242	39	2.6	39	85	0	141	43	20	2	33	1.67
39730025--39730072	14	3.6	13	81	18	55	37	0	8	54	1.31
39732199--39732231	17	1.9	17	93	0	57	57	15	0	27	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39734187--39734283	30	3.3	29	84	5	90	20	24	15	39	1.91
39734186--39734373	29	6.5	29	72	16	147	22	26	13	37	1.92
39734207--39734362	57	2.7	58	76	15	178	21	29	12	35	1.91
39735582--39735903	27	12.3	26	77	9	237	19	17	21	41	1.90
39735608--39735646	19	2.1	19	95	0	69	15	17	28	38	1.91
39735610--39735653	19	2.4	19	88	3	63	18	15	20	45	1.85
39735630--39735903	81	3.4	81	82	6	279	20	17	20	41	1.90
39735628--39735903	54	5.1	53	80	8	272	20	17	20	42	1.90
39735687--39735904	107	2.0	107	83	5	271	21	16	19	42	1.89
39737310--39737342	16	2.0	17	88	5	50	18	21	12	48	1.80
39745633--39745867	49	4.7	50	80	4	210	24	26	22	27	2.00
39751550--39751599	17	3.0	17	80	11	50	16	2	14	68	1.31
39760959--39761099	74	1.9	74	95	0	255	43	6	4	45	1.51
39774946--39774999	22	2.5	22	84	6	65	25	50	9	14	1.73
39775403--39775461	3	19.7	3	100	0	118	32	0	0	67	0.91
39776745--39776769	8	3.1	8	100	0	50	64	0	12	24	1.27
39776925--39776958	16	2.1	16	94	0	59	50	5	2	41	1.42
39777364--39777422	3	19.7	3	100	0	118	33	0	0	66	0.92
39780727--39780773	21	2.2	22	88	3	69	21	17	38	23	1.93
39791055--39791141	42	2.0	43	84	2	113	32	21	13	32	1.93
39792297--39792342	23	2.0	23	91	0	74	19	2	50	28	1.60
39792690--39792728	19	2.1	18	85	4	51	76	2	5	15	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39803076--39803246	66	2.6	65	84	4	209	40	18	27	13	1.88
39803217--39803316	21	4.8	21	80	2	67	35	18	40	7	1.77
39803237--39803329	21	4.4	21	80	0	105	35	16	43	5	1.71
39803681--39803859	87	2.1	86	95	1	322	18	17	32	30	1.95
39803674--39803839	43	3.9	42	78	12	185	19	16	31	31	1.95
39803693--39803860	43	3.9	43	76	8	171	20	18	31	29	1.96
39803697--39803881	86	2.1	87	90	1	291	23	18	29	27	1.98
39805287--39805359	34	2.1	35	84	2	94	42	10	16	30	1.82
39805619--39805705	42	2.0	43	84	2	113	32	21	13	32	1.93
39807393--39807417	12	2.1	12	100	0	50	84	8	0	8	0.79

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