genome.fa.s13.2.7.7.80.10.50.1000.16.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  16  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)
4942541--4942573	16	2.1	16	94	0	57	63	3	12	21	1.41
4944453--4944894	45	9.9	44	73	5	350	26	24	19	30	1.98
4944426--4944894	89	5.2	89	91	1	681	26	23	20	30	1.98
4952963--4953002	20	2.0	20	100	0	80	30	15	25	30	1.95
4956738--4956769	15	2.1	15	100	0	64	62	0	12	25	1.30
4957774--4957801	5	5.6	5	100	0	56	78	0	0	21	0.75
4960517--4960549	17	2.0	17	88	5	50	63	6	0	30	1.18
4967314--4967478	86	1.9	86	82	4	210	35	4	12	46	1.63
4974618--4974708	31	2.9	31	75	18	91	12	36	20	30	1.89
4979396--4979457	25	2.5	25	83	0	88	20	20	24	33	1.97
4982593--4982771	50	3.7	48	80	12	206	26	19	32	21	1.97
4982592--4982817	50	4.7	47	80	7	188	27	19	30	22	1.98
4982827--4982943	53	2.2	52	79	7	128	37	18	23	19	1.94
4983311--4983402	47	2.0	47	97	0	175	38	9	10	41	1.73
4985964--4986001	18	2.2	18	90	4	60	55	5	5	34	1.45
4989434--4989495	20	3.0	20	81	9	63	58	9	1	30	1.40
4989463--4989500	19	2.1	18	90	5	58	57	7	0	34	1.28
4992828--4992859	15	2.1	15	100	0	64	31	0	12	56	1.37
5002045--5002228	43	4.3	43	80	6	201	28	27	17	26	1.98
5002068--5002228	86	1.9	87	88	1	243	27	26	18	27	1.98
5002300--5002333	16	2.1	16	88	0	50	55	8	0	35	1.31
5004810--5004847	14	2.7	15	84	12	53	42	28	0	28	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5005120--5005163	17	2.7	17	89	6	65	43	27	0	29	1.55
5004638--5005241	315	1.9	308	84	8	790	41	27	2	28	1.68
5008852--5008877	12	2.2	12	100	0	52	46	30	15	7	1.74
5011563--5011690	50	2.6	50	81	1	159	19	38	19	22	1.94
5013995--5014023	15	2.0	15	93	6	51	58	6	13	20	1.58
5020014--5020071	2	29.0	2	100	0	116	50	0	0	50	1.00
5021726--5021927	84	2.4	84	95	0	359	29	21	19	29	1.98
5041332--5041360	8	3.8	8	95	4	51	55	0	0	44	0.99
5042516--5042557	10	4.2	10	79	8	50	59	0	0	40	0.97
5043374--5043428	2	28.0	2	87	10	78	49	3	0	47	1.19
5047874--5047911	17	2.2	18	85	4	51	31	7	0	60	1.25
5052342--5052636	145	2.0	145	98	0	563	23	18	20	37	1.94
5057738--5057764	5	5.4	5	100	0	54	18	0	0	81	0.69
5060554--5060607	24	2.3	22	76	17	54	55	3	1	38	1.28
5060563--5060614	24	2.1	24	85	3	68	51	0	3	44	1.19
5061997--5062039	18	2.4	18	92	7	70	51	0	0	48	1.00
5077565--5077594	15	2.0	15	93	0	51	56	6	13	23	1.60
5082138--5082217	38	2.1	38	88	0	115	16	18	28	36	1.93
5082171--5082217	19	2.5	20	79	10	53	17	19	29	34	1.94
5084393--5084452	30	2.0	30	84	9	79	45	3	21	30	1.68
5084662--5084692	13	2.4	13	94	0	53	32	0	12	54	1.38
5084785--5084934	50	2.8	54	86	6	209	28	22	28	20	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5091113--5091143	13	2.4	13	94	0	53	32	0	12	54	1.38
5091238--5091479	50	4.7	50	86	3	286	27	23	28	19	1.99
5091238--5091487	100	2.4	103	87	5	353	26	23	28	20	1.99
5096879--5097051	27	6.4	27	80	2	195	45	20	15	18	1.85
5096875--5097051	81	2.2	81	88	0	264	45	20	15	18	1.85
5105044--5105101	26	2.2	26	87	6	82	27	15	13	43	1.85
5108155--5108211	27	2.1	27	81	12	64	45	10	0	43	1.38
5116089--5116193	19	5.2	21	66	16	71	62	0	1	35	1.06
5116131--5116249	38	3.5	32	74	16	80	62	0	2	35	1.09
5116132--5116310	39	4.6	38	82	8	218	62	0	2	34	1.10
5116100--5116310	78	2.7	79	84	8	270	61	0	2	35	1.11
5116184--5116300	12	9.5	12	68	18	71	60	0	3	35	1.13
5116086--5116308	77	2.9	77	84	8	265	60	0	2	36	1.11
5116241--5116312	18	3.7	19	68	17	58	61	0	2	36	1.11
5116750--5116802	23	2.3	23	81	18	74	24	18	26	30	1.98
5119605--5119634	15	2.0	15	93	0	51	50	0	0	50	1.00
5123545--5123598	27	2.0	27	100	0	108	33	7	25	33	1.84
5127458--5127723	115	2.4	105	80	11	336	56	14	1	27	1.48
5127833--5127885	22	2.4	22	84	9	63	0	37	0	62	0.96
5127833--5127885	11	4.7	11	77	9	54	0	37	0	62	0.96
5132985--5133061	29	2.6	29	83	4	91	49	15	11	23	1.77
5133978--5134042	27	2.3	30	81	7	82	63	1	4	30	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5134039--5134075	9	4.2	9	83	16	51	56	0	0	43	0.99
5133999--5134213	10	22.4	9	68	17	96	60	3	1	33	1.25
5134019--5134213	19	10.2	18	72	19	89	60	4	2	33	1.27
5134102--5134197	21	4.8	21	78	14	87	60	3	2	34	1.24
5134634--5134690	20	2.8	20	81	5	62	29	0	5	64	1.15
5134757--5134824	10	7.3	9	71	14	50	27	4	2	64	1.27
5135184--5135232	25	2.0	25	84	4	64	59	2	4	34	1.28
5135360--5135397	17	2.3	16	86	8	58	34	0	2	63	1.09
5144792--5144817	6	4.3	6	100	0	52	84	15	0	0	0.62
5147494--5147567	35	2.1	34	85	2	94	32	9	13	44	1.76
5151631--5151722	42	2.2	41	83	7	107	25	23	33	17	1.96
5155822--5155882	17	3.4	17	68	12	50	32	3	13	50	1.57
5155818--5155891	37	2.0	37	97	0	139	33	5	14	45	1.68
5155890--5155947	9	6.4	10	79	15	56	29	12	18	39	1.87
5155885--5155947	27	2.3	27	81	8	74	28	12	19	39	1.88
5160689--5160755	35	1.9	35	82	14	86	7	28	10	53	1.62
5161375--5161555	27	6.7	27	81	7	197	43	18	19	19	1.89
5161378--5161555	54	3.3	53	84	7	225	43	17	19	19	1.89
5161382--5161555	81	2.1	81	85	2	233	43	18	18	19	1.89
5161691--5161771	26	3.1	26	71	7	74	18	22	24	34	1.96
5164312--5164366	16	3.4	16	92	0	92	29	25	7	38	1.83
5165435--5165492	28	2.1	28	96	0	107	15	22	32	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5167057--5167098	21	2.0	22	90	4	68	35	9	0	54	1.33
5167053--5167105	22	2.5	22	84	6	74	33	7	0	58	1.26
5167192--5167257	21	3.2	20	78	16	64	21	4	3	71	1.18
5168350--5168441	43	2.1	43	82	10	105	33	4	23	38	1.75
5169892--5169974	42	2.0	42	85	0	112	37	14	8	39	1.76
5172378--5173143	267	2.9	266	84	5	943	41	16	18	23	1.90
5172308--5173204	134	6.8	131	78	7	782	41	17	18	23	1.90
5175751--5175815	31	2.1	31	86	11	89	44	4	0	50	1.22
5176213--5176275	27	2.4	27	94	2	110	41	11	0	47	1.39
5184755--5184795	17	2.5	17	88	4	57	26	26	0	46	1.53
5190161--5190215	27	2.0	27	82	10	67	47	0	3	49	1.19
5190161--5190219	26	2.2	27	85	8	77	49	0	3	47	1.18
5190288--5190352	27	2.4	27	92	0	103	30	23	30	15	1.95
5190478--5190528	14	3.8	13	82	15	59	62	0	37	0	0.95
5190490--5190522	3	11.3	3	87	6	50	63	0	36	0	0.95
5190798--5190936	22	5.9	22	83	15	179	30	0	13	56	1.38
5190790--5190940	49	3.1	49	91	1	250	31	0	13	54	1.39
5190678--5190893	19	11.5	19	67	23	118	30	0	13	55	1.45
5191033--5191060	12	2.3	12	100	0	56	28	7	17	46	1.75
5193966--5194007	13	3.5	13	75	18	54	0	38	2	59	1.10
5196213--5196238	2	13.0	2	100	0	52	50	0	0	50	1.00
5197792--5197816	2	12.5	2	100	0	50	0	48	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5203076--5203116	14	3.0	14	80	16	50	34	0	4	60	1.18
5212038--5212080	23	1.9	22	86	13	61	65	4	2	27	1.25
5214115--5214150	17	2.1	17	100	0	72	55	5	0	38	1.23
5218147--5218181	5	7.0	5	90	9	54	80	2	0	17	0.84
5219874--5219983	54	2.0	54	92	0	184	10	8	35	45	1.69
5224133--5224196	2	32.5	2	90	9	105	51	1	0	46	1.10
5225479--5225528	26	1.9	26	84	8	66	50	8	14	28	1.70
5227314--5227614	44	6.7	44	74	15	170	27	20	19	32	1.97
5227313--5227482	44	3.8	45	81	7	177	27	21	18	32	1.97
5227823--5228424	88	6.8	88	81	2	555	27	21	20	30	1.98

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