genome.fa.s7.2.7.7.80.10.50.1000.8.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  8  of  204  ( 24458 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)
3199180--3199702	173	3.0	174	96	0	967	38	14	19	28	1.90
3200213--3200259	9	5.0	9	76	19	51	44	0	0	55	0.99
3200213--3200259	19	2.5	19	82	6	60	44	0	0	55	0.99
3207256--3207298	16	2.8	15	77	19	52	60	6	6	25	1.48
3207256--3207292	15	2.4	17	82	17	53	59	8	5	27	1.48
3209021--3209066	23	2.0	23	83	8	58	17	19	30	32	1.95
3210051--3210099	21	2.2	21	82	10	53	26	0	14	59	1.36
3213053--3213104	24	2.3	22	80	6	59	67	3	13	15	1.37
3214346--3214422	31	2.5	31	82	4	102	42	6	11	38	1.67
3216838--3216877	21	1.9	21	85	10	55	55	0	0	45	0.99
3227192--3227251	31	1.9	31	86	6	86	36	6	6	50	1.55
3227191--3227258	31	2.2	30	82	12	84	35	5	8	50	1.58
3227505--3227584	31	2.6	31	78	5	83	46	7	6	40	1.57
3229363--3229397	17	2.1	16	89	5	52	57	2	0	40	1.14
3232995--3233029	15	2.2	17	90	10	56	42	0	0	57	0.99
3233355--3233385	3	10.7	3	93	6	55	70	0	0	29	0.87
3233353--3233385	17	1.9	17	100	0	66	72	0	0	27	0.85
3233358--3233387	14	2.1	14	100	0	60	73	0	0	26	0.84
3233366--3233511	68	2.1	69	93	2	258	47	10	6	36	1.63
3233498--3233541	9	5.1	9	83	10	65	54	11	0	34	1.36
3233507--3233544	16	2.4	16	90	0	58	52	10	0	36	1.36
3233604--3233674	23	3.0	23	83	8	81	50	1	1	46	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3235400--3235503	29	3.7	29	65	14	90	37	12	13	36	1.83
3238635--3238703	31	2.2	31	81	0	84	44	7	10	37	1.66
3252084--3252134	19	2.6	19	84	3	66	31	1	7	58	1.37
3252123--3252162	13	2.9	14	81	11	55	12	0	10	77	0.99
3254785--3254883	23	4.3	23	92	0	171	23	21	25	30	1.99
3255254--3255287	9	3.8	9	88	0	50	38	23	8	29	1.85
3255453--3255482	13	2.3	13	100	0	60	16	0	43	40	1.48
3260730--3260936	112	1.8	112	94	2	371	48	11	15	25	1.78
3275967--3276006	6	6.7	6	100	0	80	15	0	35	50	1.44
3284992--3285068	38	2.0	38	92	0	127	27	18	14	40	1.89
3301500--3301690	43	4.4	43	88	0	265	34	24	15	25	1.95
3301808--3302081	31	8.7	31	85	5	327	41	16	10	31	1.81
3303554--3303853	46	6.6	46	94	1	462	29	22	13	34	1.92
3305612--3305643	12	2.6	13	85	14	50	56	6	0	37	1.25
3308705--3308745	21	1.9	22	90	5	66	48	2	0	48	1.14
3309321--3309363	23	1.9	22	90	4	68	27	0	0	72	0.85
3312863--3312887	12	2.1	12	100	0	50	52	0	8	40	1.31
3317111--3317200	45	2.0	45	93	2	155	45	13	7	33	1.72
3323475--3323535	27	2.4	24	75	19	61	32	6	1	59	1.33
3323644--3323669	9	2.9	9	100	0	52	69	0	0	30	0.89
3324670--3324839	59	2.9	59	95	0	295	44	10	5	40	1.60
3324719--3324810	29	3.1	29	64	14	71	43	7	6	42	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3324850--3324884	16	2.2	16	94	0	61	48	8	0	42	1.33
3324759--3324881	66	1.9	60	80	16	133	47	9	3	39	1.53
3326341--3326378	20	2.0	20	89	5	60	36	0	5	57	1.21
3326807--3326879	26	2.9	25	81	4	85	32	0	4	63	1.14
3327122--3327176	23	2.4	23	93	0	92	41	16	16	25	1.88
3331238--3331287	24	2.1	24	88	0	73	38	30	2	30	1.69
3331254--3331321	32	2.3	28	75	18	73	33	38	1	26	1.66
3331263--3331323	32	1.9	32	93	0	104	31	36	1	31	1.68
3335140--3335193	2	26.5	2	89	10	83	48	1	1	48	1.23
3340376--3340411	11	3.2	11	84	7	54	80	0	19	0	0.71
3365902--3365978	37	2.1	37	92	0	127	50	10	6	32	1.62
3367183--3367370	102	1.8	102	98	0	367	30	12	15	40	1.84
3373894--3373925	15	2.1	15	94	0	55	65	0	12	21	1.25
3378049--3378243	98	2.0	97	91	1	318	37	21	9	31	1.86
3378526--3378550	9	2.8	9	100	0	50	68	8	0	24	1.16
3379552--3379617	23	3.0	23	75	18	68	39	16	6	37	1.74
3379575--3379649	19	3.8	19	89	3	114	36	16	10	37	1.83
3379552--3379649	38	2.4	40	85	10	119	37	16	9	36	1.80
3380154--3380193	15	2.5	16	84	8	55	62	0	2	35	1.09
3380125--3380180	25	2.2	24	81	12	60	58	0	0	41	0.98
3381849--3381920	37	1.9	36	86	10	101	58	0	2	38	1.13
3387611--3387658	16	3.1	16	72	3	53	8	10	0	81	0.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3388645--3388689	14	2.8	17	74	22	51	57	2	0	40	1.11
3389448--3389498	21	2.4	21	74	6	50	27	5	0	66	1.14
3389587--3389626	18	2.2	19	86	4	55	30	0	2	67	1.04
3396024--3396066	21	2.0	22	82	13	54	16	6	2	74	1.14
3402491--3402634	41	3.5	41	88	0	216	24	18	24	33	1.97
3402484--3402675	82	2.3	83	79	5	212	25	18	23	32	1.97
3403086--3403242	71	2.2	70	81	4	190	32	10	14	42	1.79
3406205--3406238	14	2.3	15	90	10	52	38	2	0	58	1.13
3408200--3408238	20	1.9	21	84	5	53	43	2	5	48	1.38
3412246--3412283	2	19.0	2	94	0	67	50	47	2	0	1.15
3413287--3413363	31	2.8	26	73	19	75	58	1	0	40	1.06
3413296--3413356	31	2.0	32	84	12	83	57	1	0	40	1.08
3413719--3413743	7	3.6	7	100	0	50	0	40	16	44	1.47
3413714--3413784	33	2.2	32	80	9	92	1	32	18	47	1.57
3413799--3413864	25	2.8	23	84	8	78	3	28	18	50	1.62
3413791--3413868	23	3.2	25	83	10	90	2	32	16	48	1.60
3416597--3416657	19	3.1	19	81	9	70	47	1	0	50	1.10
3423939--3423997	29	2.0	30	86	3	84	28	5	13	52	1.61
3424170--3424248	31	2.6	30	80	6	79	46	11	5	36	1.62
3424184--3424251	29	2.4	27	74	13	64	48	11	2	36	1.55
3447314--3447353	21	1.9	21	84	0	53	40	2	0	57	1.12
3450393--3450425	17	1.9	17	88	11	50	39	0	3	57	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3450416--3450449	11	3.0	12	87	12	54	17	0	0	82	0.67
3450397--3450490	41	2.3	42	90	7	156	29	0	2	68	1.02
3450428--3450483	29	2.0	28	92	3	94	32	0	1	66	1.03
3450415--3450492	12	6.2	12	77	16	77	29	0	1	69	0.97
3450395--3450499	41	2.5	42	86	7	153	35	0	1	62	1.06
3450553--3450641	27	3.3	27	98	0	169	29	21	33	15	1.94
3450798--3450856	22	2.6	22	84	10	75	67	0	1	30	1.00
3451108--3451145	19	2.0	19	94	0	67	50	5	7	36	1.54
3451241--3451304	27	2.4	27	89	2	94	51	10	1	35	1.47
3451345--3451508	27	6.8	24	71	24	123	32	1	13	51	1.51
3451345--3451458	27	4.6	27	79	15	131	34	1	12	51	1.50
3451345--3451506	49	3.3	49	84	6	215	32	1	13	51	1.52
3451814--3451890	27	2.9	27	88	3	111	19	37	24	18	1.94
3470194--3470270	14	5.0	15	70	20	52	44	12	7	35	1.72
3470198--3470264	34	1.9	35	96	3	127	47	11	7	32	1.68
3470233--3470272	14	2.9	14	82	14	55	45	12	5	37	1.64
3470535--3470618	26	3.2	26	83	9	100	21	1	14	63	1.37
3474252--3474278	2	13.5	2	100	0	54	48	0	0	51	1.00
3480024--3480604	290	2.0	290	99	0	1153	33	20	17	28	1.95
3480738--3480835	28	3.5	28	91	2	153	35	14	0	50	1.43
3481272--3481347	37	2.1	37	97	0	143	48	0	11	39	1.40
3481272--3481347	19	4.1	18	74	5	62	48	0	11	39	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3481283--3481351	19	3.7	19	78	5	88	52	0	8	39	1.33
3481522--3481632	27	4.1	27	97	1	206	17	27	30	24	1.97
3481651--3481692	6	6.8	6	82	12	50	0	2	16	80	0.81
3481652--3481692	13	3.2	13	77	16	50	0	2	14	82	0.76
3481655--3481699	23	2.0	23	82	8	56	4	2	13	80	0.97
3481698--3481790	27	3.4	28	91	7	147	48	0	13	37	1.43
3490929--3490954	5	5.2	5	100	0	52	80	0	0	19	0.71
3495613--3495641	8	3.6	8	100	0	58	24	13	27	34	1.93
3495728--3495803	23	3.3	23	94	0	134	22	21	25	31	1.98
3499970--3500092	64	1.9	64	88	3	185	20	19	24	35	1.95

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