genome.fa.s7.2.7.7.80.10.50.1000.14.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: 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  14  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)
5451312--5451343	16	1.9	17	93	6	57	37	21	0	40	1.54
5451536--5451647	41	2.7	41	79	5	100	33	28	16	21	1.95
5454071--5454159	23	3.9	23	87	0	124	23	19	24	32	1.97
5454068--5454166	46	2.2	46	86	0	144	24	19	24	32	1.97
5457033--5457072	22	1.9	20	85	10	53	75	10	5	10	1.19
5461161--5461191	2	15.5	2	93	0	53	45	0	54	0	0.99
5463391--5463459	32	2.2	32	100	0	138	42	18	11	27	1.85
5468025--5468593	126	4.5	125	89	2	838	30	17	23	28	1.97
5471743--5471783	21	2.0	21	90	0	64	24	2	29	43	1.67
5471850--5471887	20	1.9	20	84	10	51	55	7	2	34	1.43
5472884--5472960	11	6.9	11	80	16	72	42	1	29	25	1.63
5472884--5472960	22	3.5	22	80	19	81	42	1	29	25	1.63
5472884--5472960	33	2.3	35	82	10	99	42	1	29	25	1.63
5478328--5478362	18	1.9	18	88	0	52	31	28	14	25	1.95
5481998--5482049	17	3.1	17	72	10	52	53	0	3	42	1.19
5482025--5482144	63	2.0	60	85	8	161	49	4	4	42	1.41
5485621--5485684	30	2.1	30	97	0	119	28	29	3	39	1.72
5487434--5487471	18	2.1	18	95	0	67	23	26	10	39	1.87
5490984--5491251	125	2.1	126	90	0	412	29	14	18	36	1.91
5491307--5491421	33	3.5	31	82	12	149	44	13	0	41	1.44
5491467--5491546	42	1.9	41	87	2	115	45	25	2	27	1.66
5493443--5493490	2	24.0	2	95	0	87	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5500014--5500089	40	1.9	40	94	0	134	32	28	3	34	1.76
5500074--5500123	25	2.0	25	96	0	91	28	26	8	38	1.84
5500099--5500251	46	3.3	46	92	0	252	28	24	8	38	1.85
5500000--5500215	117	1.9	106	85	7	254	30	25	7	36	1.84
5502945--5502980	3	12.0	3	93	0	63	33	2	0	63	1.08
5502945--5502989	15	3.0	15	90	6	65	33	4	0	62	1.15
5503066--5503159	41	2.3	42	83	1	118	30	24	15	28	1.96
5506612--5506644	2	16.5	2	100	0	66	51	0	0	48	1.00
5518174--5518249	22	3.5	22	87	0	107	27	15	27	28	1.96
5520651--5520697	15	3.3	15	71	17	55	14	70	0	14	1.18
5520654--5520705	27	1.9	27	96	0	95	17	67	0	15	1.24
5521468--5521507	6	6.8	6	88	5	55	0	15	0	85	0.61
5523086--5523130	15	2.9	15	80	6	54	26	4	0	68	1.08
5525694--5525727	17	1.9	18	94	5	61	55	2	0	41	1.15
5526378--5526407	9	3.3	9	95	0	51	86	0	3	10	0.67
5540196--5540233	19	2.0	20	89	5	60	5	28	0	65	1.14
5542567--5542609	21	2.0	21	86	8	61	39	0	4	55	1.20
5544107--5544145	17	2.2	18	86	13	55	48	5	0	46	1.24
5544814--5544857	22	2.0	23	81	4	54	43	4	2	50	1.35
5545163--5545187	7	3.6	7	100	0	50	76	0	0	24	0.80
5547232--5547316	39	2.2	39	97	0	161	35	16	16	31	1.91
5547952--5547993	21	2.0	22	85	4	59	57	14	4	23	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5555338--5555368	15	2.1	15	93	0	53	41	0	0	58	0.98
5557311--5557341	9	3.4	9	90	0	53	25	12	22	38	1.90
5557395--5557422	9	3.1	9	100	0	56	46	10	10	32	1.73
5563443--5563467	11	2.3	11	100	0	50	60	0	0	40	0.97
5567395--5567428	17	2.0	17	88	11	52	52	0	2	44	1.16
5567506--5567620	57	2.0	57	98	0	221	40	13	13	32	1.83
5568020--5568074	24	2.3	24	84	6	67	49	5	5	40	1.49
5568031--5568082	24	2.2	24	85	0	68	50	1	3	44	1.31
5582594--5582626	3	11.0	3	93	0	57	30	0	3	66	1.06
5591287--5591319	13	2.4	14	90	5	50	30	3	0	66	1.06
5592531--5592572	23	1.9	21	85	9	57	54	7	0	38	1.28
5592407--5592576	81	2.1	81	78	10	179	50	4	1	44	1.31
5595187--5595249	30	2.1	30	93	0	108	26	4	11	57	1.53
5605438--5605476	3	13.3	3	89	5	62	69	0	30	0	0.89
5616599--5616681	27	3.1	27	85	0	103	26	22	31	19	1.98
5617503--5617568	28	2.4	28	85	14	100	51	0	6	42	1.26
5619009--5619033	9	2.8	9	100	0	50	32	0	0	68	0.90
5621172--5621245	29	2.5	30	73	18	73	45	12	6	35	1.68
5630152--5630205	22	2.4	22	75	6	54	51	1	0	46	1.11
5630164--5630211	21	2.2	22	88	3	71	60	0	0	39	0.97
5642462--5642492	15	2.0	15	93	6	53	58	0	19	22	1.40
5649217--5649270	28	1.9	28	85	7	74	0	33	1	64	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5649478--5649535	22	2.6	21	86	8	71	60	3	0	36	1.14
5659339--5659411	18	3.9	19	72	15	64	61	1	1	35	1.13
5659381--5659459	29	2.8	28	78	5	86	56	1	8	32	1.38
5659676--5659725	20	2.5	21	78	12	61	60	0	8	32	1.26
5661229--5661502	50	5.5	50	73	6	241	27	24	19	28	1.99
5661196--5661518	100	3.2	100	89	1	479	27	23	19	29	1.98
5661695--5661869	88	2.0	88	91	0	287	25	24	21	28	1.99
5663122--5663183	28	2.2	28	78	16	67	14	14	0	70	1.16
5663653--5663705	19	2.8	18	78	18	54	0	9	9	81	0.89
5665690--5665728	21	1.9	21	89	5	62	20	25	7	46	1.77
5667708--5667780	18	3.9	19	72	15	64	61	1	1	35	1.13
5667750--5667828	29	2.8	28	80	5	95	58	1	7	32	1.34
5679660--5679717	24	2.4	23	83	13	73	34	5	1	58	1.30
5684374--5684416	3	14.3	3	100	0	86	65	0	34	0	0.93
5686207--5686256	25	2.2	23	77	19	59	30	20	10	40	1.85
5704623--5704685	30	2.1	30	96	0	117	23	3	15	57	1.53
5708833--5708896	27	2.4	28	85	15	91	40	10	15	32	1.82
5708851--5708902	27	2.0	26	96	3	95	40	11	17	30	1.85
5728985--5729096	24	4.7	24	86	0	161	47	4	27	20	1.69
5729836--5729947	9	12.4	9	90	0	152	41	21	10	26	1.86
5729853--5729947	36	2.6	36	98	0	181	40	23	11	25	1.88
5732408--5732441	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5733287--5733337	25	2.2	25	86	10	72	66	1	0	31	1.03
5733609--5733652	13	3.4	13	81	12	54	40	4	4	50	1.43
5733601--5733652	26	2.0	26	88	0	77	36	3	7	51	1.49
5733753--5733820	26	2.5	28	88	6	106	44	7	0	48	1.30
5738543--5738732	94	2.0	93	96	1	353	24	17	33	23	1.96
5740309--5740347	14	2.7	15	84	8	53	61	5	5	28	1.39
5740321--5740349	14	2.1	14	100	0	58	55	0	6	37	1.27
5741314--5741350	17	2.2	17	100	0	74	45	8	16	29	1.76
5742655--5742694	16	2.4	16	88	12	55	5	5	5	85	0.85
5742697--5742765	28	2.5	29	93	6	117	49	0	10	40	1.37
5742771--5742796	13	2.0	13	100	0	52	23	0	0	76	0.78
5743410--5743470	10	5.5	10	74	18	50	0	31	0	68	0.89
5743375--5743458	38	2.3	38	90	8	131	1	33	0	65	1.00
5743629--5743670	17	2.4	17	88	4	57	9	2	4	83	0.88
5743638--5743671	17	2.0	17	94	0	59	8	0	5	85	0.75
5743671--5743739	27	2.5	28	93	4	115	47	1	10	40	1.46
5746417--5746468	27	2.0	27	85	11	72	0	32	3	63	1.12
5746675--5746725	13	3.9	13	77	10	59	60	1	0	37	1.08
5751800--5751879	30	2.7	30	94	3	137	26	12	13	47	1.79
5758350--5758396	17	2.8	17	78	18	53	59	0	0	40	0.97
5763108--5763161	24	2.2	24	96	0	99	35	3	7	53	1.47
5765193--5765241	24	2.0	24	96	0	89	34	20	28	16	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5765290--5765349	26	2.3	26	82	5	68	36	21	23	18	1.95
5765609--5765633	13	1.9	13	100	0	50	8	0	24	68	1.16
5766707--5766928	114	1.9	114	96	0	408	41	3	13	40	1.62
5767417--5767563	41	3.6	41	91	1	233	27	19	29	23	1.98
5769207--5769256	21	2.5	20	83	6	64	26	28	6	40	1.79
5773898--5773931	2	17.5	2	93	6	61	47	0	0	52	1.00
5782289--5782340	18	2.9	18	75	11	54	51	3	3	40	1.38
5782309--5782381	18	3.9	18	69	23	53	47	0	1	50	1.09
5782376--5782412	19	2.0	19	89	5	58	37	0	5	56	1.22
5785047--5785100	24	2.3	24	80	3	74	16	7	0	75	1.01

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