genome.fa.s6.2.7.7.80.10.50.1000.17.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  17  of  168  ( 20060 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)
4668225--4668631	9	46.2	9	71	14	262	45	17	1	35	1.57
4668219--4668578	16	22.1	16	74	16	235	46	17	1	34	1.56
4668231--4668578	25	14.0	25	72	15	194	46	18	1	33	1.56
4668219--4668588	34	10.8	34	76	12	287	46	17	1	34	1.56
4668294--4668609	110	2.9	109	82	9	324	45	16	1	36	1.55
4670638--4670725	21	4.2	21	88	0	122	31	18	46	3	1.65
4671086--4671289	86	2.4	85	84	2	257	25	22	20	32	1.98
4671086--4671289	42	4.8	42	83	4	212	25	22	20	32	1.98
4671260--4671361	43	2.4	42	86	1	150	34	21	21	22	1.97
4671260--4671373	42	2.7	43	83	6	151	32	22	21	22	1.98
4680504--4680553	20	2.6	19	84	6	64	50	8	0	42	1.32
4680493--4680562	19	3.5	19	81	11	79	51	5	0	42	1.25
4689409--4689534	43	2.9	43	78	9	139	30	29	19	20	1.97
4690417--4690467	27	2.0	27	92	7	88	43	5	0	50	1.26
4709614--4709642	3	10.0	3	92	7	51	68	0	0	31	0.89
4709659--4709688	15	1.9	16	93	6	53	43	0	0	56	0.99
4715402--4715440	3	13.0	3	89	10	62	66	0	2	30	1.05
4715408--4715457	9	5.7	9	88	9	52	64	0	8	28	1.22
4716769--4716815	18	2.8	16	87	12	76	34	8	40	17	1.79
4717024--4717062	15	2.7	14	88	11	53	46	2	0	51	1.14
4717165--4717200	18	2.1	18	89	5	56	61	0	0	38	0.96
4717027--4717322	120	2.5	120	93	3	490	49	5	2	43	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4717338--4717474	73	1.9	73	92	0	229	45	3	2	48	1.35
4717339--4717452	34	3.2	34	71	16	104	42	4	3	49	1.39
4717434--4717574	44	3.1	44	72	16	153	49	2	2	45	1.28
4717388--4717617	91	2.5	91	94	0	397	46	3	3	46	1.38
4717388--4717617	47	5.0	46	69	17	165	46	3	3	46	1.38
4724245--4724299	2	27.5	2	75	14	51	43	7	0	49	1.30
4726904--4726942	20	2.0	20	90	10	62	23	0	12	64	1.28
4726912--4726949	14	2.8	13	88	11	58	21	0	13	65	1.26
4730122--4730178	9	6.1	9	80	8	69	82	14	1	1	0.83
4730125--4730165	7	5.9	7	85	8	57	85	14	0	0	0.60
4730123--4730167	20	2.3	19	88	7	72	86	13	0	0	0.57
4730122--4730178	19	2.9	18	80	19	62	82	14	1	1	0.83
4730595--4730629	13	2.8	12	91	8	52	80	0	14	5	0.89
4731570--4732032	50	9.3	50	67	2	158	29	22	23	25	1.99
4731507--4732029	100	5.2	100	87	1	742	29	21	23	25	1.99
4732075--4732512	127	3.4	126	89	3	617	32	22	20	25	1.98
4732169--4732347	43	4.2	43	70	16	131	31	22	20	25	1.98
4732918--4732956	20	2.0	20	89	0	60	17	48	15	17	1.81
4734009--4734069	3	20.0	3	83	3	77	34	3	1	60	1.23
4734230--4734263	13	2.6	13	95	0	59	32	5	0	61	1.20
4735418--4735468	21	2.5	19	84	9	66	54	1	3	39	1.30
4736612--4736705	48	2.0	48	100	0	188	53	10	14	21	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4738933--4738972	16	2.5	16	88	8	55	27	2	2	67	1.16
4739186--4739244	2	29.5	2	100	0	118	49	0	0	50	1.00
4739579--4739724	10	15.0	9	73	14	71	59	2	4	34	1.28
4739590--4739668	30	2.7	29	81	13	97	56	0	3	39	1.17
4739616--4739714	19	5.1	19	67	17	60	60	2	4	33	1.27
4747685--4747725	21	2.0	21	95	0	73	43	14	19	21	1.87
4749427--4749468	16	2.6	16	78	17	50	57	0	7	35	1.26
4755996--4756097	52	1.9	53	92	5	172	33	4	1	59	1.30
4756851--4757389	105	5.0	113	76	12	432	32	18	17	31	1.94
4757132--4757421	105	2.7	110	77	6	315	32	19	16	31	1.94
4756866--4757482	325	1.9	321	81	6	749	31	18	17	31	1.94
4757487--4757669	100	1.8	98	91	2	303	37	22	16	23	1.94
4758080--4758505	109	3.9	110	87	3	591	36	18	15	29	1.92
4758640--4758719	4	19.5	4	74	14	65	71	5	3	20	1.21
4764663--4764692	12	2.5	12	88	0	51	90	0	10	0	0.47
4765943--4766501	50	11.2	50	72	2	413	29	20	24	25	1.99
4765921--4766501	100	5.8	100	90	1	878	29	20	24	26	1.99
4768219--4768287	33	1.9	37	83	16	92	31	4	1	62	1.24
4773297--4773353	29	2.0	29	82	6	71	38	8	10	42	1.71
4775505--4775611	36	2.9	35	75	12	90	54	5	0	39	1.30
4775578--4775624	20	2.4	19	82	10	58	61	2	6	29	1.32
4781686--4781715	13	2.3	13	94	0	51	6	10	16	66	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4784563--4784660	49	2.0	49	90	4	153	31	7	11	50	1.65
4784693--4784883	61	3.2	61	73	11	221	42	1	4	51	1.30
4784646--4784918	120	2.3	120	98	0	519	42	1	3	52	1.26
4785012--4785207	98	2.0	98	97	0	374	29	20	7	42	1.80
4785156--4785247	44	2.1	45	86	10	127	35	27	4	32	1.77
4785236--4785284	16	3.1	16	93	0	89	24	34	4	36	1.75
4785857--4785975	7	17.0	7	84	0	112	28	31	0	38	1.63
4785857--4785974	14	8.4	14	82	0	128	28	32	0	38	1.63
4792830--4792871	22	1.9	22	100	0	84	33	4	7	54	1.49
4793195--4793219	13	1.9	13	100	0	50	24	20	40	16	1.91
4794702--4794743	14	2.9	14	80	16	50	7	0	11	80	0.88
4798593--4798617	13	1.9	13	100	0	50	56	0	4	40	1.18
4798698--4798737	3	13.3	3	100	0	80	67	0	0	32	0.91
4798773--4798825	18	2.9	18	78	10	63	56	3	11	28	1.51
4798778--4798820	9	4.8	9	82	5	52	53	2	11	32	1.50
4799900--4799936	16	2.3	16	100	0	74	37	5	35	21	1.77
4799918--4800012	44	2.1	45	86	5	131	32	5	29	32	1.80
4800170--4800203	18	1.9	18	88	5	52	52	0	0	47	1.00
4800195--4800224	15	1.9	16	93	6	53	50	6	0	43	1.28
4800526--4800562	16	2.2	17	86	13	51	54	0	2	43	1.14
4800155--4800563	120	3.4	120	96	1	741	48	4	2	43	1.38
4800545--4800785	47	5.3	46	69	20	166	47	3	2	45	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4800502--4800785	91	3.0	98	85	8	294	48	3	2	45	1.33
4800605--4800647	13	3.2	13	78	15	52	58	0	0	41	0.98
4800262--4800664	54	7.2	55	66	21	192	49	4	2	44	1.35
4800604--4800746	44	3.2	44	69	21	125	49	2	2	45	1.28
4800570--4800785	91	2.4	91	92	1	353	47	4	2	45	1.36
4807458--4807497	21	1.9	21	89	0	62	32	12	27	27	1.93
4809108--4809142	2	17.5	2	100	0	70	48	0	0	51	1.00
4809144--4809583	184	2.4	184	86	1	587	42	20	8	27	1.81
4815523--4816035	144	3.6	143	79	7	520	30	18	13	38	1.89
4826257--4826390	63	2.1	63	84	0	169	29	7	29	34	1.85
4828054--4828144	7	13.0	7	77	0	74	43	2	25	28	1.66
4828047--4828120	28	2.6	28	86	0	103	50	0	21	28	1.49
4848800--4848829	15	2.1	14	93	6	51	73	3	0	23	0.98
4851254--4851295	21	2.0	22	81	13	52	69	4	2	23	1.20
4851661--4851778	23	5.2	22	76	8	103	58	2	4	34	1.31
4851669--4851775	46	2.3	47	85	3	146	57	1	4	35	1.30
4852982--4853017	16	2.3	16	90	4	56	19	0	8	72	1.10
4853264--4853293	15	2.0	15	100	0	60	13	26	13	46	1.80
4853315--4853403	46	1.9	46	88	4	135	33	24	16	24	1.96
4853274--4853532	118	2.2	118	85	1	367	28	25	14	30	1.95
4853413--4854043	97	6.5	97	90	0	861	31	23	15	29	1.95
4853413--4854043	291	2.2	291	90	1	969	31	23	15	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4856282--4856325	11	3.9	11	83	13	54	2	13	2	81	0.88
4856281--4856324	18	2.6	16	89	7	61	2	13	2	81	0.88
4856282--4856327	23	2.0	23	87	8	67	2	15	2	80	0.91
4856287--4856338	24	2.2	24	82	6	61	3	13	1	80	0.93
4860259--4860302	21	2.0	22	91	4	72	38	15	22	22	1.92
4864777--4864834	29	2.0	29	86	6	82	39	12	10	37	1.77
4865665--4865707	2	21.5	2	100	0	86	48	0	0	51	1.00
4867465--4867534	18	3.9	18	74	10	63	52	5	0	41	1.25
4867524--4867567	20	2.3	19	84	11	54	65	2	6	25	1.28
4867521--4867568	21	2.4	18	77	16	51	64	2	6	27	1.28

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