genome.fa.s8.2.7.7.80.10.50.1000.14.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  14  of  190  ( 22705 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)
4115496--4115598	52	2.0	52	96	0	188	34	0	33	30	1.65
4115519--4115577	30	2.0	30	96	0	109	35	0	35	28	1.58
4115549--4115598	22	2.3	22	96	0	91	38	0	34	28	1.57
4126213--4126252	20	2.0	20	85	0	53	32	12	12	42	1.80
4127776--4127802	12	2.2	12	100	0	54	51	0	7	40	1.30
4132119--4132170	21	2.5	21	78	9	61	32	30	3	32	1.76
4132228--4132256	14	2.0	15	93	6	51	37	20	0	41	1.53
4133254--4133309	24	2.3	25	78	12	71	32	12	17	37	1.88
4134687--4134711	9	2.8	9	100	0	50	44	0	0	56	0.99
4136581--4136668	41	2.1	41	80	0	95	20	23	26	29	1.99
4136558--4136694	69	2.0	69	84	2	177	20	23	25	30	1.98
4136620--4136719	29	3.5	28	83	8	96	20	23	21	36	1.96
4136641--4136724	29	2.9	30	82	7	102	21	23	19	35	1.96
4140913--4140959	21	2.2	21	81	11	51	34	6	8	51	1.58
4141564--4141686	62	2.0	62	96	0	228	30	21	17	30	1.96
4142075--4142099	13	1.9	13	100	0	50	56	0	0	44	0.99
4142123--4142156	10	3.4	10	88	11	52	61	0	0	38	0.96
4142552--4142586	18	1.9	18	88	0	52	22	0	17	60	1.37
4149152--4149179	6	4.7	6	100	0	56	0	28	35	35	1.58
4149831--4150183	174	2.0	174	93	0	607	20	30	12	36	1.89
4150325--4150554	117	2.0	117	95	0	415	26	27	11	33	1.91
4153982--4154587	302	2.0	302	98	0	1158	35	18	16	29	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4160273--4160688	69	6.1	69	75	4	358	38	24	15	21	1.92
4160273--4160734	137	3.4	137	78	5	432	37	24	16	21	1.93
4160285--4160680	136	2.9	138	79	5	426	38	24	15	20	1.92
4160756--4160958	58	3.5	57	83	4	246	35	18	8	37	1.82
4167048--4167077	12	2.5	12	94	0	51	36	10	0	53	1.35
4172686--4172727	2	21.0	2	92	0	66	52	0	2	45	1.13
4173306--4173455	41	3.6	41	93	0	255	28	21	28	22	1.99
4173482--4173509	2	14.0	2	100	0	56	50	0	0	50	1.00
4176007--4176040	17	1.9	18	88	5	52	50	35	5	8	1.58
4180463--4180564	42	2.4	42	90	0	150	15	22	16	45	1.85
4192297--4192373	22	3.5	22	71	7	66	55	5	12	25	1.58
4192469--4192520	22	2.4	21	84	9	61	53	7	23	15	1.67
4200533--4200606	19	4.0	19	77	18	75	29	1	0	68	0.97
4200546--4200576	16	1.9	16	100	0	62	29	0	0	70	0.87
4200533--4200603	37	2.0	35	86	5	97	29	1	0	69	0.98
4203434--4203482	25	1.9	26	95	4	91	22	8	18	51	1.72
4203477--4204063	61	9.6	60	73	10	350	29	7	17	44	1.77
4203462--4204063	31	19.6	30	72	8	379	30	7	17	44	1.77
4203487--4204063	92	6.3	92	89	3	743	30	7	17	44	1.77
4208092--4208123	16	2.0	16	93	0	55	25	15	0	59	1.36
4215332--4215419	41	2.3	37	77	11	88	36	1	1	61	1.11
4222369--4222406	17	2.2	17	90	0	58	76	2	7	13	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4223914--4223939	13	2.0	13	100	0	52	30	7	15	46	1.74
4225009--4225307	50	5.9	50	80	5	264	28	21	26	23	1.99
4226860--4226923	25	2.6	25	87	2	94	29	21	29	18	1.97
4231500--4231544	19	2.4	19	88	7	65	57	2	11	28	1.45
4238455--4238560	34	3.1	34	93	0	167	41	11	16	30	1.84
4238896--4239082	98	2.0	94	93	5	322	54	9	14	20	1.68
4239297--4239359	30	2.1	31	96	3	119	20	6	12	60	1.54
4260529--4260580	16	3.3	15	86	5	68	42	1	23	32	1.65
4260753--4260904	57	2.6	59	83	10	199	53	3	0	42	1.22
4260878--4260927	24	2.1	23	82	10	57	60	2	2	36	1.20
4264219--4264302	31	2.7	31	82	10	102	58	1	1	39	1.14
4264219--4264399	41	4.4	40	87	5	247	61	0	1	36	1.10
4264219--4264399	80	2.2	81	90	4	276	61	0	1	36	1.10
4264219--4264350	11	12.9	11	71	18	90	59	0	0	38	1.08
4266322--4266355	18	1.9	17	88	5	50	23	2	2	70	1.15
4266737--4266777	11	3.6	11	83	6	55	41	2	0	56	1.13
4269424--4269505	43	1.9	43	80	9	96	21	18	29	30	1.97
4270470--4270510	22	1.9	21	90	5	64	19	2	24	53	1.57
4272529--4272581	24	2.1	25	86	10	72	56	0	0	43	0.99
4272537--4272568	16	2.1	16	94	5	57	59	0	0	40	0.97
4272539--4272596	24	2.4	22	78	16	53	55	0	1	43	1.10
4272540--4272598	28	2.1	27	81	12	66	54	0	1	44	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4273736--4273822	21	4.0	21	78	11	70	19	22	22	34	1.97
4273869--4273922	26	2.1	26	96	0	81	12	14	33	38	1.85
4278432--4278511	8	10.0	8	94	0	124	30	12	32	25	1.92
4278432--4278509	24	3.2	24	96	0	138	30	12	30	25	1.93
4286928--4286966	21	1.9	19	85	10	51	48	5	0	46	1.24
4287161--4287204	14	3.1	14	76	0	52	70	2	4	22	1.17
4287635--4287703	17	4.1	16	76	14	59	44	1	0	53	1.09
4288227--4288270	2	22.0	2	95	0	79	52	0	0	47	1.00
4292190--4292232	21	2.0	22	86	4	61	65	6	4	23	1.37
4305260--4305318	27	2.2	27	100	0	118	28	6	18	45	1.75
4306346--4306392	23	2.1	21	81	14	51	48	25	2	23	1.62
4308698--4308877	45	4.0	45	88	4	258	22	16	26	34	1.95
4311530--4311600	30	2.4	30	83	4	90	25	22	11	40	1.87
4311586--4311787	30	6.8	30	78	6	162	20	26	13	39	1.90
4311557--4311746	60	3.2	60	75	5	186	20	27	13	38	1.90
4311613--4311776	90	1.8	88	81	11	199	20	28	12	38	1.89
4318645--4318681	20	1.9	18	89	10	56	37	2	5	54	1.38
4324042--4324084	21	2.0	21	86	0	59	20	27	0	51	1.48
4324036--4324086	26	2.0	25	84	3	66	21	27	0	50	1.48
4329219--4329282	3	21.3	3	100	0	128	67	0	0	32	0.91
4331194--4331238	23	2.0	23	86	0	63	31	31	8	28	1.88
4341429--4341467	20	2.0	20	84	0	51	46	7	0	46	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4346675--4346717	17	2.5	17	79	20	54	25	13	20	39	1.90
4346775--4346816	16	2.6	16	81	7	50	33	14	14	38	1.86
4348765--4348820	21	2.7	21	88	0	85	26	8	35	28	1.87
4350687--4350877	97	2.0	97	93	0	328	40	7	18	33	1.79
4352522--4352581	25	2.3	26	82	5	77	13	10	8	68	1.39
4357390--4357430	20	2.0	20	100	0	82	26	24	4	43	1.74
4360881--4360914	6	5.7	6	100	0	68	0	32	0	67	0.91
4365029--4365084	15	3.6	15	79	9	58	32	17	14	35	1.90
4367285--4367329	19	2.2	21	80	11	58	62	4	2	31	1.27
4367311--4367355	23	1.9	24	82	13	58	57	0	4	37	1.19
4367693--4367777	43	1.9	44	92	7	145	27	11	18	42	1.85
4367777--4367810	9	3.8	9	96	0	59	44	17	11	26	1.83
4367911--4367935	5	5.0	5	100	0	50	0	80	0	20	0.72
4369310--4369373	32	2.0	32	84	6	85	21	9	12	56	1.64
4372712--4372736	10	2.5	10	100	0	50	44	0	0	56	0.99
4374321--4374389	33	2.1	33	94	0	120	40	13	18	27	1.88
4378516--4378566	6	8.5	6	82	8	50	45	35	0	19	1.51
4378516--4378565	18	2.8	18	81	0	64	44	36	0	20	1.52
4380837--4380906	19	3.8	19	76	16	58	15	7	2	74	1.16
4380944--4381015	23	3.2	22	76	7	74	40	0	5	54	1.24
4380977--4381019	21	2.0	23	90	9	72	41	0	0	58	0.98
4381011--4381054	21	2.2	20	87	4	61	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4381116--4381144	14	2.1	14	100	0	58	51	0	0	48	1.00
4380989--4381228	33	6.8	33	71	20	134	44	2	1	52	1.20
4381209--4381271	21	3.1	21	75	8	69	46	0	0	53	1.00
4381230--4381259	13	2.3	13	100	0	60	46	0	0	53	1.00
4381334--4381372	13	3.3	11	83	16	51	61	2	0	35	1.10
4381529--4381613	40	2.1	41	93	2	145	55	3	5	35	1.41
4381540--4381604	20	3.2	20	67	16	62	53	3	6	36	1.41
4381548--4381611	20	3.2	20	68	16	60	57	3	6	32	1.39
4382044--4382098	20	2.7	20	80	8	67	34	3	0	61	1.13
4382100--4382143	19	2.2	20	92	4	72	47	6	0	45	1.29

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