genome.fa.s4.2.7.7.80.10.50.1000.135.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  135  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)
43109832--43109873	15	2.9	15	82	10	52	47	0	0	52	1.00
43109985--43110019	18	2.0	17	88	5	52	45	0	0	54	0.99
43109816--43110132	157	2.0	157	96	0	580	47	5	3	44	1.42
43110255--43110306	16	3.2	16	94	0	86	38	32	0	28	1.57
43111663--43111703	18	2.2	18	91	4	64	14	2	2	80	0.92
43111669--43111703	18	1.9	18	100	0	70	17	0	2	80	0.84
43113170--43113308	73	1.9	74	90	1	226	28	20	16	34	1.94
43115928--43115971	23	1.9	23	85	0	61	40	15	18	25	1.90
43119289--43119788	90	5.6	89	79	9	344	25	7	14	53	1.65
43119418--43119745	90	3.6	90	88	1	478	25	7	14	52	1.69
43122420--43122515	6	17.6	5	93	4	111	22	20	0	56	1.43
43122420--43122515	49	2.0	49	89	0	147	22	20	0	56	1.43
43122510--43122567	20	2.9	21	89	7	93	20	12	0	67	1.22
43122621--43122674	17	3.1	17	75	24	58	29	12	0	57	1.36
43123011--43123092	12	6.9	11	76	14	74	24	19	1	54	1.51
43123010--43123093	18	4.7	17	73	22	66	23	19	1	55	1.49
43123088--43123145	21	2.7	21	83	2	62	24	10	1	63	1.35
43123105--43123209	22	5.2	19	68	19	61	22	9	2	64	1.36
43123208--43123285	11	6.8	11	70	13	50	26	12	1	58	1.42
43123240--43123278	18	2.2	18	90	0	60	28	10	0	61	1.28
43123183--43123285	29	3.6	29	85	3	138	27	12	0	59	1.40
43123661--43123724	22	3.0	21	65	6	56	35	1	10	51	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43127254--43127432	45	4.0	45	84	7	204	21	12	29	36	1.90
43129896--43129924	12	2.4	12	100	0	58	79	13	6	0	0.93
43139956--43139999	22	2.0	22	82	8	54	43	2	0	54	1.12
43140108--43140163	21	2.7	21	94	0	94	30	37	8	23	1.85
43146574--43146644	34	2.1	34	84	5	90	61	5	12	19	1.50
43159991--43160038	24	2.0	24	88	8	71	33	2	8	56	1.41
43161964--43162009	24	1.9	24	82	8	58	34	2	8	54	1.43
43180300--43180423	40	3.0	41	79	2	151	32	16	27	24	1.96
43181716--43181767	20	2.6	21	80	17	65	40	5	19	34	1.75
43185213--43185257	19	2.4	18	82	7	54	31	31	6	31	1.83
43185375--43185895	27	19.4	27	83	2	575	19	15	21	42	1.89
43185375--43185895	81	6.5	81	85	1	643	19	15	21	42	1.89
43190486--43190512	14	1.9	14	100	0	54	7	25	0	66	1.17
43195128--43195180	22	2.5	21	76	11	54	67	11	5	15	1.38
43196067--43196106	8	5.6	7	85	14	55	72	0	15	12	1.12
43196074--43196106	15	2.1	16	94	5	59	72	0	15	12	1.12
43197264--43198051	88	9.0	88	89	1	1134	25	23	27	23	2.00
43199404--43199443	18	2.1	20	86	9	57	45	2	0	52	1.14
43207069--43207100	2	16.0	2	100	0	64	50	0	0	50	1.00
43209165--43209202	7	5.4	7	93	0	67	44	39	0	15	1.47
43209190--43209350	80	2.0	80	93	0	277	31	16	12	39	1.86
43209416--43209444	15	1.9	15	100	0	58	68	13	10	6	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43221708--43221792	40	2.2	39	80	12	95	34	5	4	55	1.45
43227937--43228435	45	11.1	45	84	3	612	28	16	24	29	1.97
43228475--43228615	45	3.2	43	73	13	133	30	18	26	24	1.98
43228500--43228649	44	3.4	43	74	7	138	28	18	28	24	1.98
43228462--43228652	89	2.1	90	87	3	271	28	19	27	24	1.99
43230422--43230507	39	2.2	39	81	6	102	33	4	4	56	1.40
43232826--43232868	22	2.0	22	100	0	86	20	23	23	32	1.98
43237387--43237463	24	3.2	24	84	0	100	19	28	16	35	1.94
43237455--43237548	25	3.8	25	81	0	98	25	26	17	30	1.97
43241729--43241763	18	2.0	18	88	5	54	14	5	5	74	1.19
43249621--43249683	29	2.2	29	82	5	74	22	22	31	23	1.98
43261746--43261881	64	2.1	64	91	0	218	41	13	2	41	1.57
43263919--43264519	304	2.0	303	90	1	954	42	17	9	30	1.82
43267646--43267678	17	1.9	17	88	11	50	15	21	6	57	1.59
43268073--43268115	21	2.2	20	83	8	52	23	11	2	62	1.40
43272224--43272428	9	21.0	9	64	19	58	62	4	1	31	1.26
43272296--43272368	20	3.7	21	87	10	84	64	5	0	30	1.16
43272311--43272428	51	2.3	51	73	9	116	61	4	2	31	1.28
43272312--43272370	21	2.8	22	85	10	79	62	5	0	32	1.17
43272871--43272908	11	3.6	11	79	13	53	36	5	0	57	1.21
43272863--43273055	20	9.9	18	70	18	79	36	2	3	58	1.25
43272863--43272918	20	2.8	20	94	2	96	35	3	0	60	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43272884--43272927	9	4.7	9	78	10	52	31	2	0	65	1.05
43273256--43273302	23	1.9	26	83	12	64	25	8	2	63	1.34
43274774--43274856	25	3.4	25	73	8	80	31	21	27	19	1.97
43277363--43277413	25	2.0	25	96	0	93	37	19	5	37	1.76
43277811--43277885	23	3.4	21	80	10	78	29	24	28	18	1.98
43277869--43277929	23	2.7	23	86	0	86	37	18	19	24	1.94
43277827--43277885	23	2.6	23	94	0	100	28	25	28	16	1.97
43279233--43279276	23	1.9	23	90	0	70	43	9	4	43	1.56
43280964--43281163	50	3.9	52	76	8	169	28	19	28	24	1.98
43280971--43281202	50	4.5	50	77	5	155	28	20	27	24	1.99
43281415--43281453	20	2.0	20	90	10	62	56	5	23	15	1.59
43287720--43287781	25	2.5	25	86	0	70	30	22	22	24	1.99
43287737--43287793	25	2.3	25	87	0	78	28	24	26	21	1.99
43288351--43288392	21	2.0	21	85	0	57	42	21	2	33	1.66
43292833--43292868	19	1.9	19	88	5	56	61	0	2	36	1.11
43294807--43294837	3	10.7	3	93	6	55	0	32	0	67	0.91
43295128--43295195	27	2.5	27	80	0	73	42	23	8	25	1.82
43295313--43295353	21	2.0	21	90	9	66	34	29	14	21	1.93
43299344--43299416	32	2.3	33	81	13	91	39	1	0	58	1.06
43301221--43301284	21	2.9	22	79	9	76	37	3	4	54	1.37
43302346--43302399	23	2.3	23	81	6	65	40	14	11	33	1.82
43302533--43302604	20	3.7	19	88	7	101	56	8	0	34	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43302533--43302609	19	4.1	19	88	6	88	55	7	0	36	1.29
43302600--43302672	28	2.5	30	80	6	80	53	2	2	41	1.29
43302568--43302656	45	2.0	44	80	12	101	50	5	1	42	1.33
43318277--43318322	23	2.0	24	87	12	69	13	8	4	73	1.21
43319025--43319052	5	5.6	5	100	0	56	17	0	17	64	1.30
43320439--43320484	23	2.0	24	87	12	69	13	8	4	73	1.21
43322598--43322643	23	2.0	24	87	12	69	13	8	4	73	1.21
43334051--43334103	26	2.0	26	88	0	79	22	16	32	28	1.96
43334080--43334302	42	5.3	42	74	9	195	22	16	24	36	1.94
43334079--43334313	85	2.8	84	88	1	328	22	17	24	35	1.95
43337271--43338369	44	25.0	43	64	10	351	21	26	26	25	1.99
43337202--43338515	88	14.9	88	85	1	1637	21	26	26	26	2.00
43345884--43345981	3	33.7	3	69	15	55	60	4	5	30	1.37
43345886--43345981	15	6.6	15	73	15	69	59	4	5	31	1.38
43346609--43346647	15	2.6	15	84	8	53	79	5	15	0	0.90
43349559--43349746	43	4.5	42	80	6	202	22	15	27	34	1.95
43349562--43349754	85	2.3	84	94	0	332	22	17	25	34	1.96
43356808--43356836	11	2.6	11	100	0	58	48	0	0	51	1.00
43357241--43357277	5	7.4	5	100	0	74	0	18	0	81	0.70
43361259--43361327	20	3.3	20	67	25	61	31	5	15	46	1.70
43365697--43365773	39	2.0	39	92	0	127	22	23	22	32	1.98
43379765--43379804	19	2.1	19	100	0	80	30	15	10	45	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43384180--43384417	31	7.7	32	76	7	195	41	16	13	28	1.86
43384177--43384408	62	3.8	60	84	3	293	40	16	14	28	1.88
43389305--43389835	125	4.2	126	85	1	739	29	18	22	29	1.97
43389305--43389835	250	2.1	250	92	0	891	29	18	22	29	1.97
43390184--43390243	29	2.1	29	93	0	102	20	16	38	25	1.93
43393075--43393427	22	16.3	21	74	11	216	17	0	31	49	1.53
43393068--43393170	7	14.4	7	70	20	54	16	0	32	51	1.45
43393047--43393099	15	3.6	15	75	12	56	20	0	30	49	1.50
43393043--43393184	29	5.0	29	68	22	95	20	0	31	47	1.50
43393068--43393427	44	8.3	43	79	8	345	17	0	31	49	1.53

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