genome.fa.s8.2.7.7.80.10.50.1000.127.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  127  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)
37817000--37817049	22	2.3	22	92	0	82	32	12	4	52	1.57
37818805--37818842	2	19.5	2	94	5	69	47	0	0	52	1.00
37828193--37828973	393	2.0	391	90	3	1241	30	11	23	34	1.90
37835141--37835325	46	4.0	46	94	0	325	34	9	27	28	1.88
37839506--37839559	26	2.1	26	100	0	108	40	18	9	31	1.82
37846156--37846287	43	3.1	43	78	1	140	32	21	16	28	1.96
37848639--37848686	21	2.2	21	88	3	69	62	0	6	31	1.20
37857567--37857637	36	2.0	36	83	5	90	42	12	22	22	1.87
37861479--37861524	2	23.0	2	95	0	83	47	0	2	50	1.13
37862090--37862262	43	4.0	43	76	12	185	31	25	19	23	1.98
37862764--37862910	22	6.7	22	90	0	213	26	25	14	33	1.94
37863170--37863324	73	2.1	73	87	2	222	30	21	23	24	1.99
37863226--37863819	114	5.2	113	86	4	770	25	21	25	27	1.99
37863754--37863826	37	1.9	38	88	2	112	23	20	23	32	1.98
37864055--37864102	22	2.2	21	81	3	60	20	0	31	47	1.50
37864055--37864163	57	1.9	58	83	5	141	21	0	34	43	1.59
37864476--37864537	14	4.3	15	73	15	51	20	1	40	37	1.63
37864713--37864737	7	3.6	7	100	0	50	28	0	24	48	1.52
37865787--37865814	12	2.3	12	100	0	56	14	0	10	75	1.06
37868457--37868614	43	3.7	43	95	1	273	20	18	29	31	1.97
37880491--37880520	2	15.0	2	100	0	60	50	0	0	50	1.00
37881110--37881136	6	4.5	6	100	0	54	14	0	0	85	0.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37881845--37881870	4	6.5	4	100	0	52	76	0	0	23	0.78
37882174--37882264	25	3.5	25	69	16	69	42	10	1	45	1.46
37882415--37882451	2	17.5	2	89	10	56	48	2	2	45	1.30
37882411--37882451	13	3.2	13	90	10	66	46	4	2	46	1.37
37892591--37892641	27	1.9	26	84	11	68	54	13	9	21	1.67
37892903--37892947	23	2.0	23	81	0	54	60	4	4	31	1.37
37894494--37894539	23	2.0	23	100	0	92	60	0	8	30	1.26
37897320--37897370	25	2.1	25	88	3	77	29	0	7	62	1.23
37898907--37898943	2	18.5	2	100	0	74	51	0	0	48	1.00
37912778--37912833	29	1.9	29	85	0	76	51	8	14	25	1.70
37916073--37916107	2	17.5	2	100	0	70	51	0	0	48	1.00
37917543--37917581	21	1.9	20	94	5	69	33	10	25	30	1.89
37923414--37923459	24	1.9	24	86	0	65	19	32	19	28	1.96
37926296--37926325	3	10.0	3	100	0	60	66	0	0	33	0.92
37929489--37929527	16	2.3	18	86	8	55	30	20	17	30	1.96
37931196--37931483	143	2.0	143	81	4	339	45	12	8	33	1.72
37933787--37933837	23	2.2	24	82	3	59	41	7	1	49	1.43
37943275--37943310	14	2.3	17	86	13	51	69	11	0	19	1.18
37943278--37943354	22	3.6	22	75	8	79	68	11	2	16	1.30
37946120--37946149	16	1.9	15	93	6	51	60	0	10	30	1.30
37948301--37948525	45	5.0	45	81	3	256	29	24	15	30	1.95
37948301--37948523	89	2.5	90	80	3	245	30	25	15	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37948534--37948928	132	3.0	132	89	3	616	27	25	18	28	1.98
37948922--37949702	50	15.6	49	68	6	445	25	24	20	29	1.99
37948938--37949706	100	7.7	100	93	0	1261	25	24	20	29	1.99
37949740--37949835	44	2.2	44	81	3	104	25	28	23	22	2.00
37951108--37951199	45	2.0	45	91	0	148	11	25	16	46	1.81
37951114--37951211	45	2.2	45	84	1	124	13	25	15	45	1.82
37955464--37955493	16	1.9	15	93	6	51	60	0	10	30	1.30
37965940--37966441	125	4.0	124	84	4	657	30	16	22	30	1.96
37965940--37966441	251	2.0	250	90	1	801	30	16	22	30	1.96
37969623--37970577	65	14.7	65	84	3	933	24	0	30	44	1.59
37969624--37970577	43	22.0	44	86	3	1051	24	0	30	44	1.58
37969624--37970577	22	44.0	22	81	3	1051	24	0	30	44	1.58
37971154--37971193	18	2.2	18	90	0	62	42	7	30	20	1.79
37974656--37974714	4	14.8	4	100	0	118	50	25	0	23	1.49
37975404--37975437	14	2.2	16	90	10	54	52	0	2	44	1.16
37978235--37978506	131	2.1	131	90	0	418	36	13	12	37	1.84
37979688--37979728	19	2.2	19	86	8	57	78	2	7	12	1.06
37980084--37980209	44	2.9	46	79	12	131	30	23	18	27	1.98
37980279--37980398	45	2.6	45	92	5	186	28	21	20	30	1.98
37980357--37980710	136	2.6	136	88	4	507	29	21	18	31	1.97
37980606--37980842	89	2.7	89	83	3	293	28	22	19	29	1.98
37980142--37980844	44	15.6	45	71	12	329	28	21	19	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
37981728--37981767	17	2.3	18	87	8	57	5	10	5	80	1.02
37986395--37986669	131	2.1	131	88	1	408	35	14	12	37	1.84
37986963--37987011	3	16.3	3	100	0	98	65	0	0	34	0.93
37987889--37987929	19	2.2	19	86	8	57	78	2	7	12	1.06
37987884--37987930	24	2.0	24	83	8	60	76	4	6	12	1.12
37992595--37992738	72	2.0	72	97	0	270	34	12	17	35	1.87
37998243--37998309	29	2.3	28	82	7	80	41	17	16	23	1.89
38006832--38006879	23	2.1	23	84	0	60	39	18	14	27	1.90
38008772--38008807	17	2.1	18	89	5	56	44	5	0	50	1.25
38009911--38009965	6	9.0	6	86	11	76	50	0	0	49	1.00
38013558--38013595	2	19.0	2	94	0	67	47	0	2	50	1.15
38019785--38019921	54	2.4	54	80	8	150	26	17	24	31	1.97
38021248--38021282	10	3.5	10	88	0	52	17	22	0	60	1.37
38022989--38023050	27	2.3	28	81	10	76	25	20	11	41	1.86
38024359--38024396	15	2.4	16	91	4	60	76	0	23	0	0.79
38027504--38027665	85	1.9	85	81	0	198	30	16	16	37	1.91
38028013--38028051	14	2.8	14	96	0	69	51	17	15	15	1.77
38036302--38036372	31	2.3	32	85	7	101	45	4	8	42	1.54
38037962--38038274	109	2.9	109	94	0	527	43	20	16	19	1.88
38037962--38038376	109	3.8	109	87	1	514	44	20	15	20	1.87
38042781--38042837	25	2.3	26	85	8	75	14	3	15	66	1.38
38043220--38043337	31	3.8	32	69	10	84	38	5	14	42	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38045985--38046142	79	2.0	79	90	1	246	32	10	11	46	1.73
38046096--38046233	58	2.5	54	76	18	151	48	7	10	33	1.66
38046103--38046218	58	2.0	59	88	8	175	49	7	9	33	1.64
38047065--38047104	19	2.0	20	85	14	55	47	0	0	52	1.00
38051479--38051522	20	2.2	20	91	0	70	36	0	2	61	1.09
38051461--38051528	31	2.2	30	78	5	66	36	1	1	60	1.15
38052719--38052752	16	2.2	16	89	5	52	20	2	0	76	0.92
38053026--38053057	14	2.3	14	100	0	64	43	12	6	37	1.68
38054189--38054238	22	2.2	22	82	10	57	48	6	10	36	1.61
38055565--38055592	9	3.1	9	100	0	56	32	10	10	46	1.73
38056122--38056165	19	2.3	19	84	7	54	59	0	4	36	1.18
38056195--38056254	22	2.8	21	76	18	61	43	1	1	53	1.20
38056247--38056299	11	5.0	10	78	13	61	22	5	0	71	1.06
38056247--38056299	22	2.5	21	96	3	97	22	5	0	71	1.06
38061159--38061225	29	2.3	29	81	0	80	38	22	16	22	1.92
38063749--38063800	16	3.3	16	76	12	63	17	21	0	61	1.34
38065440--38065474	14	2.6	13	91	8	61	20	0	28	51	1.47
38065601--38065649	24	2.0	25	84	4	64	63	6	4	26	1.36
38065888--38065936	24	2.0	25	88	8	73	18	0	12	69	1.19
38065891--38065947	26	2.3	24	78	6	60	21	3	10	64	1.39
38067731--38067813	29	2.8	29	76	5	78	40	20	1	37	1.60
38071329--38071422	43	2.2	43	94	0	161	29	17	8	44	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38072539--38072568	10	2.8	11	90	10	53	10	6	6	76	1.15
38073138--38073176	12	3.2	12	82	13	53	35	10	0	53	1.35
38073815--38073861	12	3.8	12	83	8	51	34	4	8	53	1.51
38075613--38075658	19	2.4	18	82	10	56	21	19	10	47	1.80
38079843--38080729	132	6.7	132	88	2	1305	27	19	24	27	1.99
38079843--38080722	264	3.3	264	96	0	1591	27	19	24	27	1.99
38085544--38085603	29	2.0	30	83	3	77	41	3	8	46	1.50
38089019--38089052	16	2.1	16	88	0	50	50	11	11	26	1.73
38090730--38090772	20	2.1	21	86	4	61	62	2	9	25	1.37
38101785--38101864	31	2.7	29	84	9	92	40	10	10	40	1.72

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