genome.fa.s13.2.7.7.80.10.50.1000.9.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  9  of  199  ( 23770 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)
2911473--2911542	19	3.7	19	76	3	79	35	10	1	52	1.44
2911765--2911834	19	3.7	19	78	3	88	38	8	0	52	1.32
2911782--2911840	18	3.2	18	76	4	73	42	6	0	50	1.28
2911770--2911840	37	1.9	37	100	0	142	42	8	0	49	1.33
2912113--2912178	19	3.6	19	81	6	82	53	0	10	36	1.36
2912113--2912178	18	3.6	19	81	6	91	53	0	10	36	1.36
2912113--2912187	19	3.9	19	80	5	62	52	0	12	36	1.39
2912255--2912332	27	2.9	27	85	7	106	17	29	23	29	1.97
2912256--2912341	27	3.2	26	85	4	102	18	26	23	31	1.97
2912825--2912888	31	2.1	31	100	0	128	15	15	9	59	1.60
2916950--2916974	6	4.2	6	100	0	50	0	0	16	84	0.63
2918238--2918300	27	2.3	27	82	12	76	52	0	1	46	1.10
2918238--2918302	26	2.4	28	82	5	80	52	0	1	46	1.10
2918520--2918620	48	2.1	49	83	5	125	27	6	2	62	1.36
2918567--2918674	19	5.5	19	73	9	76	27	4	1	65	1.22
2918567--2918658	20	4.7	20	71	9	73	27	4	2	66	1.22
2918567--2918674	39	2.8	39	70	13	96	27	4	1	65	1.22
2918752--2918973	85	2.6	85	84	6	259	33	9	19	36	1.85
2924396--2924450	9	5.6	10	75	12	51	69	1	1	27	1.09
2924534--2924558	3	8.3	3	100	0	50	32	0	0	68	0.90
2925011--2925049	18	2.1	19	85	4	53	58	0	2	38	1.12
2939358--2939407	21	2.4	21	93	0	82	32	36	8	24	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2949101--2949186	42	2.1	41	93	4	147	24	17	13	44	1.85
2951924--2951958	18	1.9	18	88	0	52	54	0	0	45	0.99
2951952--2952009	24	2.5	22	78	8	62	51	0	0	48	1.00
2953368--2953425	29	2.0	29	100	0	116	31	6	31	31	1.84
2954626--2954913	144	2.0	145	92	1	479	23	14	17	44	1.85
2956002--2956070	27	2.4	27	77	18	68	43	1	2	52	1.25
2956059--2956101	22	1.9	23	85	4	61	39	2	2	55	1.25
2956059--2956102	23	2.0	22	83	16	56	40	2	2	54	1.25
2958915--2958941	13	2.1	13	100	0	54	33	0	22	44	1.53
2966896--2966951	24	2.3	24	100	0	112	17	30	14	37	1.90
2980768--2980811	16	2.9	15	90	6	70	72	0	0	27	0.85
2980788--2980812	13	1.9	13	100	0	50	76	0	0	24	0.80
2991970--2992096	60	2.1	60	85	2	166	42	11	6	40	1.66
2992823--2992939	60	2.0	60	84	1	155	38	5	11	44	1.64
2996780--2996816	18	2.1	18	89	0	56	8	8	59	24	1.53
2996785--2996840	21	2.8	20	84	7	62	10	7	55	26	1.60
2996851--2996903	3	17.7	3	88	0	79	5	0	60	33	1.20
3000409--3000450	21	2.0	21	81	9	50	30	4	16	47	1.67
3001412--3001497	42	2.0	42	100	0	172	38	13	6	40	1.72
3008796--3008841	20	2.2	20	96	3	83	36	23	17	21	1.94
3014128--3014168	20	2.0	20	86	9	57	48	41	0	9	1.36
3018605--3018647	19	2.3	18	81	18	52	23	0	30	46	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3022630--3022720	35	2.6	35	70	16	80	45	0	3	51	1.17
3023973--3024002	3	10.0	3	100	0	60	33	0	0	66	0.92
3024024--3024063	14	2.9	14	84	0	53	32	7	17	42	1.77
3024047--3024086	20	2.0	20	90	0	62	27	10	12	50	1.72
3024032--3024098	34	1.9	35	90	3	109	31	8	13	46	1.74
3024026--3024102	14	5.0	15	71	20	52	32	9	15	42	1.78
3025426--3025494	35	1.9	36	94	2	122	52	17	4	26	1.63
3025462--3025531	27	2.5	28	81	6	81	52	20	4	22	1.63
3028667--3028692	7	3.7	7	100	0	52	61	15	11	11	1.57
3038459--3038498	21	1.9	20	85	10	53	55	2	10	32	1.47
3038487--3038602	60	1.9	60	81	6	137	43	7	10	37	1.68
3038538--3038603	30	2.2	30	83	0	87	45	9	12	33	1.73
3044909--3044986	34	2.4	34	82	8	90	48	1	0	50	1.09
3045797--3045857	24	2.6	23	75	14	63	60	0	3	36	1.13
3048741--3048787	15	2.9	17	85	14	57	25	0	0	74	0.82
3048761--3048787	5	5.4	5	100	0	54	22	0	0	77	0.76
3048798--3048840	17	2.6	17	81	3	52	25	0	9	65	1.22
3054975--3055018	20	2.2	19	84	15	54	20	4	9	65	1.38
3055671--3055710	13	3.1	13	88	0	62	40	22	7	30	1.81
3056118--3056151	15	2.2	16	89	5	52	50	5	14	29	1.67
3093077--3093116	21	1.9	21	84	0	53	37	20	7	35	1.81
3114538--3114571	17	2.0	17	88	0	50	61	2	2	32	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3115519--3115568	21	2.4	22	83	10	68	34	30	8	28	1.86
3125788--3125860	23	3.2	23	82	0	92	31	20	19	28	1.97
3127738--3127779	21	2.0	21	85	0	57	45	11	4	38	1.62
3129743--3129785	21	2.0	21	82	8	52	34	2	4	58	1.32
3130687--3130721	2	17.5	2	100	0	70	51	0	48	0	1.00
3130983--3131014	2	16.0	2	100	0	64	50	0	0	50	1.00
3143512--3143572	30	2.0	30	83	0	77	39	6	24	29	1.80
3143965--3144158	50	3.9	50	77	3	178	29	21	26	21	1.99
3150761--3150789	2	14.5	2	100	0	58	51	48	0	0	1.00
3152543--3152592	20	2.5	20	78	9	50	38	0	8	54	1.30
3153561--3153634	31	2.3	33	76	9	80	50	2	4	43	1.35
3154432--3154471	21	1.9	21	85	10	55	70	2	5	22	1.19
3155394--3155443	26	1.9	26	83	0	64	34	10	6	50	1.60
3157117--3157189	36	2.0	36	91	0	119	35	20	4	39	1.72
3159375--3159433	29	2.0	29	100	0	118	54	6	6	32	1.53
3159896--3159925	14	2.1	14	93	0	51	33	16	6	43	1.74
3161945--3162009	16	4.1	16	88	7	105	35	6	35	23	1.80
3161989--3162078	45	2.0	44	89	6	137	32	5	28	33	1.80
3162223--3162264	15	2.7	16	82	14	52	52	2	0	45	1.13
3162232--3162273	15	2.9	15	82	10	52	52	0	0	47	1.00
3162258--3162445	61	3.1	61	70	14	199	49	6	1	42	1.36
3162226--3162518	120	2.4	121	94	1	509	50	5	2	42	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3162226--3162522	59	5.0	59	67	17	184	50	5	2	42	1.35
3162342--3162393	15	3.6	15	80	12	56	53	1	0	44	1.11
3162500--3162666	47	3.6	46	71	12	146	47	4	2	45	1.35
3162559--3162630	28	2.6	28	84	8	85	51	4	0	44	1.20
3162799--3162843	22	2.0	22	100	0	90	42	13	0	44	1.43
3177386--3177434	17	3.0	16	80	19	57	42	2	2	53	1.24
3177392--3177441	17	2.9	17	82	11	50	42	2	2	54	1.23
3179793--3180108	170	1.9	171	88	2	483	46	14	14	24	1.82
3181439--3181708	143	1.9	143	82	1	344	27	21	14	35	1.93
3192446--3192502	27	2.1	29	83	9	75	52	35	3	8	1.50
3192814--3192861	12	4.3	11	82	10	53	16	2	2	79	0.93
3192813--3192861	17	2.8	17	84	3	53	16	2	2	79	0.92
3192824--3192861	11	3.2	12	85	11	51	15	0	2	81	0.80
3193559--3193693	3	45.3	3	79	10	125	31	4	2	60	1.31
3193984--3194008	2	12.5	2	100	0	50	48	0	0	52	1.00
3197066--3197118	24	2.2	24	96	3	99	43	13	11	32	1.79
3198973--3198997	2	12.5	2	100	0	50	48	0	0	52	1.00
3209146--3209190	21	2.2	20	80	11	54	48	0	0	51	1.00
3213087--3213116	16	1.9	15	93	6	51	46	0	30	23	1.52
3213200--3213258	30	2.0	29	83	6	73	42	0	37	20	1.52
3213472--3213508	9	4.1	9	92	0	65	29	10	13	45	1.77
3213875--3213909	19	1.9	17	88	11	52	34	2	28	34	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3216548--3216664	61	1.9	59	89	6	182	52	2	4	41	1.35
3225325--3225360	3	12.0	3	93	0	63	30	0	33	36	1.58
3233122--3233212	40	2.3	40	82	1	103	26	29	23	20	1.99
3234417--3234498	24	3.4	24	82	0	101	28	18	4	48	1.68
3235332--3235358	14	1.9	14	100	0	54	48	29	0	22	1.51
3236395--3236423	2	14.5	2	100	0	58	51	0	0	48	1.00
3237858--3237888	15	2.1	15	100	0	62	41	12	12	32	1.81
3244132--3244276	72	2.0	72	91	2	236	35	18	16	28	1.93
3244505--3244529	13	1.9	13	100	0	50	80	0	0	20	0.72
3244681--3244751	26	3.2	21	71	19	63	59	1	4	35	1.26

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