genome.fa.s5.2.7.7.80.10.50.1000.23.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   207   208   

This is table  23  of  208  ( 24913 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)
6601534--6601567	18	1.9	18	88	5	52	29	0	5	64	1.17
6610041--6610086	18	2.5	19	79	13	51	58	13	0	28	1.35
6611394--6611488	41	2.3	41	88	0	136	16	17	28	36	1.92
6611512--6611676	88	1.8	90	84	6	228	20	23	30	25	1.99
6611673--6611855	73	2.5	72	85	2	240	25	23	25	25	2.00
6612103--6612195	38	2.5	37	83	1	105	21	1	39	37	1.61
6612162--6612227	29	2.2	29	79	12	73	19	0	42	37	1.52
6615036--6615165	18	6.9	18	73	17	113	45	10	0	43	1.43
6615032--6615163	39	3.3	41	81	15	129	44	10	0	43	1.44
6615036--6615165	57	2.3	56	82	15	153	45	10	0	43	1.43
6615732--6616314	9	67.8	9	66	21	188	48	18	1	31	1.58
6615732--6615914	25	7.4	25	71	16	116	47	19	2	30	1.61
6615758--6616293	34	16.1	34	65	21	160	48	18	1	31	1.57
6615772--6615949	68	2.6	68	90	1	261	44	20	2	32	1.64
6615806--6615896	43	2.1	43	83	4	112	46	19	2	31	1.62
6615738--6616310	16	34.9	16	69	19	212	49	18	1	31	1.57
6615863--6615950	41	2.1	41	89	4	133	43	21	2	32	1.65
6615936--6616209	76	3.8	74	78	16	297	51	15	0	31	1.49
6616028--6616325	25	12.6	24	76	11	169	50	17	1	30	1.55
6616038--6616200	69	2.4	67	85	7	224	53	15	0	30	1.47
6616066--6616185	21	5.4	21	80	9	98	52	15	0	32	1.43
6615926--6616204	127	2.2	128	80	11	306	51	16	0	31	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6616044--6616195	21	6.9	21	76	12	94	53	15	0	31	1.42
6621781--6621832	21	2.5	21	90	0	77	38	15	40	5	1.71
6622176--6622486	42	7.4	42	84	4	378	26	18	20	34	1.96
6622176--6622486	126	2.4	126	87	3	421	26	18	20	34	1.96
6625218--6625274	18	3.3	18	80	7	66	22	10	45	21	1.82
6628617--6628663	18	2.6	18	87	12	78	21	6	19	53	1.67
6632804--6632847	18	2.4	19	88	7	65	13	15	31	38	1.87
6634222--6634247	12	2.2	12	100	0	52	7	15	30	46	1.74
6634316--6634644	113	2.9	114	93	2	549	24	22	26	26	2.00
6634892--6634922	15	2.1	15	93	0	53	19	0	45	35	1.51
6635195--6635235	21	2.0	20	85	4	55	19	0	41	39	1.52
6639291--6639316	13	2.0	13	100	0	52	30	15	0	53	1.42
6640112--6640238	50	2.5	50	98	0	245	31	8	30	29	1.87
6641659--6641887	43	5.3	43	78	0	244	24	16	27	31	1.96
6641660--6641887	86	2.7	86	84	0	278	24	16	27	31	1.96
6646844--6646879	16	2.2	16	90	0	54	19	25	22	33	1.97
6647034--6647081	25	1.9	25	86	0	69	20	35	20	22	1.96
6647065--6647140	25	3.0	27	73	13	70	17	22	22	38	1.93
6648525--6648761	50	4.6	50	79	5	210	27	18	29	25	1.98
6648569--6648756	100	1.9	99	83	5	245	27	19	30	22	1.98
6652641--6652720	31	2.6	31	76	2	81	37	11	11	40	1.77
6660837--6660895	29	2.0	29	100	0	118	28	23	10	37	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6662766--6662795	11	2.6	11	94	5	51	36	3	0	60	1.14
6669777--6669801	8	3.1	8	100	0	50	12	24	0	64	1.27
6669756--6669842	45	1.9	46	83	6	115	29	24	1	44	1.61
6669786--6669860	39	1.9	38	84	7	98	33	22	1	42	1.62
6671068--6671097	3	10.3	3	92	7	53	66	0	0	33	0.92
6673817--6673856	18	2.2	18	95	0	71	40	20	20	20	1.92
6679715--6679765	27	1.9	26	88	4	75	23	7	50	17	1.72
6681507--6681627	23	5.3	23	69	18	99	19	9	22	47	1.78
6681494--6681652	46	3.5	46	92	0	264	21	11	20	47	1.81
6681530--6681650	23	5.3	23	69	21	65	20	11	19	47	1.80
6685420--6685457	14	2.4	17	87	12	55	52	0	0	47	1.00
6685780--6685932	22	7.0	22	90	0	225	26	26	14	32	1.94
6688416--6688734	88	3.6	89	84	2	374	28	20	17	33	1.96
6688424--6688724	133	2.3	133	81	6	335	29	20	17	32	1.96
6688416--6688724	44	7.0	44	81	4	309	28	20	17	32	1.96
6702543--6702572	12	2.5	12	88	0	51	56	0	0	43	0.99
6702544--6702591	18	2.7	18	86	0	60	54	2	2	41	1.24
6702800--6702868	12	6.0	11	79	17	61	69	0	4	26	1.07
6702811--6702843	4	8.2	4	100	0	66	75	0	0	24	0.80
6702979--6703083	8	13.8	8	71	12	60	60	0	14	25	1.35
6703974--6704000	2	13.5	2	100	0	54	48	0	0	51	1.00
6709492--6709531	20	2.0	20	90	0	62	27	17	22	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6709544--6709586	21	2.1	20	82	4	50	30	4	18	46	1.69
6723035--6723094	29	2.1	28	87	3	84	18	8	23	50	1.74
6724468--6724548	23	3.5	22	75	6	63	17	14	28	39	1.89
6725826--6726032	31	6.7	31	71	8	138	43	14	8	32	1.76
6725832--6726032	61	3.3	61	78	8	212	44	15	8	31	1.76
6726019--6726069	25	2.0	25	88	3	75	52	13	5	27	1.63
6726570--6726621	25	2.1	25	89	7	79	25	25	9	40	1.85
6729063--6729093	10	3.1	10	100	0	62	48	0	0	51	1.00
6729110--6729196	32	2.7	32	77	8	95	44	18	11	25	1.83
6729189--6729228	20	2.0	20	90	0	62	50	12	10	27	1.72
6729177--6729243	34	1.9	35	87	3	100	46	11	10	31	1.75
6729212--6729251	14	2.9	14	84	0	53	42	17	7	32	1.77
6733201--6733229	14	2.1	14	100	0	58	24	20	20	34	1.97
6733817--6733864	23	2.1	23	96	0	87	39	18	8	33	1.81
6735392--6735419	14	2.0	14	100	0	56	42	7	7	42	1.59
6741555--6741634	39	2.1	39	90	0	124	40	13	27	18	1.89
6741962--6742006	20	2.3	19	81	11	54	35	2	4	57	1.31
6741968--6742005	20	1.9	20	88	0	58	34	0	5	60	1.19
6742528--6742576	21	2.2	21	82	13	55	6	30	2	61	1.32
6743724--6743781	24	2.4	24	85	0	71	29	8	15	46	1.75
6745569--6745607	20	1.9	19	90	10	60	71	5	5	17	1.23
6749877--6750033	45	3.5	45	94	2	264	26	23	15	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6755724--6755828	53	2.0	53	86	0	147	40	9	17	33	1.82
6756014--6756043	15	1.9	16	93	6	53	40	0	0	60	0.97
6756117--6756203	38	2.2	40	86	9	119	54	5	0	40	1.25
6756335--6756375	21	2.0	21	85	9	57	43	2	0	53	1.13
6756611--6756653	12	3.3	12	78	15	50	39	4	0	55	1.20
6758407--6758436	4	7.5	4	92	0	51	23	3	0	73	0.98
6765252--6765304	27	2.0	27	100	0	106	30	22	5	41	1.77
6765397--6765429	16	1.9	18	88	11	52	51	0	3	45	1.16
6772122--6772146	13	1.9	13	100	0	50	40	0	12	48	1.40
6775176--6775226	26	2.0	26	92	0	84	37	23	21	17	1.94
6775241--6775288	25	1.9	25	82	0	60	25	18	37	18	1.94
6775266--6775305	18	2.2	18	86	0	53	27	22	35	15	1.94
6775444--6775488	16	2.8	16	82	0	54	37	24	17	20	1.93
6775481--6775573	44	2.1	44	86	4	125	30	17	33	19	1.95
6776889--6776913	11	2.3	11	100	0	50	64	0	0	36	0.94
6783015--6783074	30	2.0	29	90	3	93	31	3	25	40	1.72
6788263--6788288	13	2.0	13	100	0	52	53	15	0	30	1.42
6797018--6797082	33	2.0	32	85	11	89	21	6	9	63	1.46
6800711--6800735	11	2.3	11	100	0	50	32	8	24	36	1.84
6802146--6802307	46	3.6	46	89	2	249	30	17	24	27	1.97
6803072--6803140	28	2.5	28	95	4	124	55	8	0	36	1.31
6803461--6803507	6	7.8	6	92	0	76	2	31	31	34	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6807366--6807416	13	3.9	13	77	10	59	60	1	0	37	1.08
6808364--6808481	38	3.2	38	93	4	213	39	2	1	55	1.23
6808367--6808486	36	3.3	36	94	4	199	39	3	1	55	1.26
6808627--6808756	49	2.6	50	83	3	190	53	11	0	34	1.43
6808705--6808869	19	8.2	19	73	21	115	55	12	0	31	1.42
6808801--6808867	22	3.2	22	83	8	86	58	10	1	29	1.41
6808695--6808912	102	2.1	99	80	10	260	54	12	0	32	1.44
6809025--6809057	3	11.3	3	87	6	50	3	30	0	66	1.06
6809028--6809054	14	1.9	14	100	0	54	3	29	0	66	1.09
6809021--6809057	17	2.2	16	95	4	65	2	29	0	67	1.04

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   207   208