genome.fa.s8.2.7.7.80.10.50.1000.43.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  43  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)
11958867--11959083	55	3.9	55	87	1	310	26	7	15	51	1.69
11960236--11960359	62	2.0	62	96	0	230	42	8	12	35	1.75
11966357--11966472	30	3.7	29	68	20	81	25	18	27	28	1.98
11967803--11967856	26	2.1	25	90	10	83	44	7	18	29	1.77
11973103--11973287	51	3.7	50	79	6	178	24	17	25	31	1.97
11973103--11973287	101	1.8	102	88	3	284	24	17	25	31	1.97
11973513--11973544	16	2.0	16	93	0	55	59	0	15	25	1.36
11976526--11976672	65	2.3	65	89	2	215	38	10	13	36	1.80
11976591--11977531	132	7.1	132	83	2	994	36	14	16	32	1.89
11976828--11977043	67	3.2	68	69	12	196	37	9	17	35	1.82
11976596--11977536	396	2.4	393	83	4	1151	36	14	16	32	1.89
11977467--11977597	67	2.0	67	83	3	165	34	17	15	32	1.91
11985155--11985190	13	2.7	13	91	4	54	30	2	50	16	1.60
11986490--11986516	13	2.1	13	100	0	54	33	29	7	29	1.85
11991916--11992031	58	2.0	58	100	0	232	46	5	6	41	1.53
11991946--11992031	28	2.9	30	68	13	88	47	5	5	40	1.51
11991918--11992009	28	3.2	28	70	11	96	46	4	6	42	1.49
11999718--11999796	31	2.5	32	85	2	106	35	5	15	44	1.68
12000780--12000861	34	2.4	34	82	8	96	36	6	10	46	1.64
12000781--12000884	17	6.2	16	73	15	61	34	7	10	47	1.67
12000800--12000880	34	2.4	32	82	14	83	34	9	9	45	1.71
12006848--12006880	17	1.9	17	100	0	66	57	12	12	18	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12017714--12017782	32	2.2	32	86	5	95	40	24	4	30	1.74
12017871--12017902	17	1.9	16	93	6	55	59	9	0	31	1.29
12019262--12019367	49	2.1	50	84	1	142	26	23	30	19	1.98
12019271--12019385	49	2.3	50	81	1	133	27	26	26	20	1.99
12019656--12019694	12	3.2	12	85	0	51	56	5	20	17	1.60
12028893--12029013	59	2.1	59	100	0	242	30	4	28	35	1.79
12031713--12031758	19	2.4	18	85	10	56	71	0	2	26	0.97
12036798--12037024	114	2.0	114	95	0	409	43	5	10	40	1.62
12036973--12037085	61	1.9	60	90	5	185	51	4	3	40	1.39
12038279--12038361	41	2.0	41	97	0	157	39	14	15	30	1.87
12047386--12047420	18	1.9	18	88	0	52	71	8	11	8	1.31
12048700--12048870	27	6.4	27	81	1	182	19	18	19	42	1.90
12057190--12057231	12	3.2	13	83	13	50	76	2	4	16	1.07
12063670--12063786	44	2.6	45	84	1	164	45	13	17	23	1.84
12066246--12066282	19	1.9	19	94	0	65	13	35	13	37	1.84
12069630--12069725	50	1.9	49	85	2	129	25	26	30	18	1.98
12070022--12070060	12	3.2	12	88	0	60	56	7	20	15	1.63
12077035--12077160	50	2.5	50	83	2	146	27	19	30	23	1.98
12084671--12084734	25	2.5	24	80	9	65	31	17	28	23	1.97
12084837--12084918	26	3.3	26	73	11	73	31	18	29	20	1.96
12096715--12096981	42	6.4	42	90	1	405	28	19	22	28	1.98
12096715--12097024	84	3.7	84	89	3	425	29	19	22	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12096715--12097024	42	7.5	41	85	5	367	29	19	22	28	1.98
12098304--12098347	23	1.9	22	82	17	54	36	25	0	38	1.56
12098489--12098617	51	2.5	51	82	8	147	34	25	15	24	1.95
12102601--12102667	32	2.1	32	97	0	125	37	14	8	38	1.78
12105996--12106086	25	3.7	25	71	7	60	34	16	24	25	1.95
12106162--12106228	26	2.7	25	77	6	75	35	17	23	22	1.95
12107702--12107756	11	5.2	11	84	8	78	38	7	0	54	1.28
12107702--12107756	21	2.6	21	91	2	83	38	7	0	54	1.28
12111986--12112060	37	2.0	37	97	0	141	24	30	13	32	1.93
12119706--12120166	237	1.9	237	86	2	649	38	22	13	26	1.90
12123940--12124034	25	3.8	25	78	1	82	35	27	11	25	1.90
12130191--12130233	24	1.9	24	86	13	65	30	13	20	34	1.92
12130654--12130687	17	2.0	17	88	11	52	5	17	0	76	0.98
12130652--12130699	22	2.2	21	85	14	62	8	16	0	75	1.04
12137159--12137311	62	2.5	61	82	3	171	23	21	29	25	1.99
12138602--12138639	14	2.8	13	92	7	67	36	10	5	47	1.61
12138804--12139010	69	3.0	68	81	2	243	20	22	15	41	1.90
12138804--12139010	34	6.0	34	85	1	225	20	22	15	41	1.90
12138823--12139010	103	1.8	103	90	0	304	20	23	14	40	1.90
12141814--12141858	21	2.1	22	84	12	58	15	6	6	71	1.29
12141890--12141932	21	2.0	23	81	9	54	32	11	11	44	1.77
12142657--12142685	6	4.8	6	100	0	58	0	17	0	82	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12144220--12144257	20	1.9	20	88	0	58	31	5	13	50	1.63
12145434--12145583	41	3.7	41	88	0	201	17	19	26	36	1.94
12160950--12160979	8	3.9	8	95	4	53	13	0	10	76	1.01
12161098--12161141	21	2.1	21	82	0	52	61	2	2	34	1.21
12161763--12161799	10	3.5	11	82	10	51	62	0	37	0	0.96
12182507--12182550	19	2.3	19	84	7	54	15	34	47	2	1.58
12186225--12186273	2	24.5	2	100	0	98	51	0	0	48	1.00
12186465--12186503	14	2.7	14	80	4	51	66	2	2	28	1.18
12186465--12186524	30	2.0	29	81	9	68	63	5	3	28	1.31
12190034--12190060	12	2.2	12	100	0	54	14	40	0	44	1.46
12192353--12192560	91	2.3	91	91	0	326	45	3	3	47	1.37
12192393--12192535	44	3.2	43	70	20	130	46	2	2	48	1.28
12192666--12192712	18	2.6	18	80	19	62	51	2	4	42	1.33
12192819--12192870	15	3.6	15	80	12	56	44	0	1	53	1.11
12192579--12192981	120	3.4	119	92	3	656	42	2	5	49	1.39
12192943--12192984	15	2.7	15	82	10	50	45	0	2	52	1.13
12193198--12193251	16	3.4	16	89	0	81	27	33	1	37	1.68
12193961--12194022	26	2.4	26	97	0	115	41	11	0	46	1.39
12194027--12194057	11	2.8	11	90	0	53	87	12	0	0	0.55
12194085--12194144	27	2.2	27	90	0	93	26	23	33	16	1.96
12194096--12194160	27	2.4	27	89	0	94	23	26	32	18	1.97
12194241--12194282	11	3.9	11	78	6	50	69	0	28	2	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12194306--12194344	19	2.0	21	85	10	55	17	0	12	69	1.19
12194400--12194491	3	30.7	3	95	0	166	33	0	1	65	1.00
12195274--12195318	18	2.5	18	96	0	81	28	4	51	15	1.63
12199178--12199202	12	2.1	12	100	0	50	24	36	24	16	1.94
12199357--12199423	9	7.4	9	86	0	80	43	25	8	22	1.82
12199496--12199573	39	2.1	36	81	11	88	19	2	28	50	1.61
12200421--12200894	160	3.0	154	69	13	373	30	11	8	49	1.69
12200949--12201004	27	2.1	27	93	0	94	8	32	14	44	1.76
12201172--12201201	16	1.9	15	93	6	51	26	3	0	70	1.03
12201721--12201895	39	4.7	37	76	13	146	0	32	0	67	0.91
12201734--12201873	26	5.3	26	68	22	89	0	33	0	66	0.92
12201781--12201932	4	38.0	4	74	19	97	0	30	0	69	0.94
12201789--12201927	33	4.2	32	75	17	126	0	30	0	69	0.94
12201749--12201929	39	4.6	40	81	11	196	0	30	0	68	0.94
12201774--12201888	10	11.7	10	65	27	52	0	31	0	68	0.90
12201748--12201941	80	2.4	80	86	6	248	0	31	0	67	0.95
12201977--12202055	27	2.9	27	86	0	104	15	32	22	29	1.95
12202112--12202175	28	2.4	28	94	5	114	48	0	10	40	1.38
12203421--12203452	15	2.1	15	100	0	64	31	21	12	34	1.91
12205523--12205728	103	2.0	103	97	0	385	32	11	14	42	1.81
12211092--12211137	16	2.9	16	75	21	51	58	4	2	34	1.30
12216992--12217103	42	2.7	43	80	6	140	46	16	19	17	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12216992--12217118	42	3.0	41	78	4	137	44	17	19	18	1.87
12222962--12223071	51	2.2	51	85	6	143	33	11	11	42	1.78
12232797--12232830	17	2.0	17	94	0	59	44	2	0	52	1.16
12233316--12233385	28	2.4	29	82	15	92	41	2	0	55	1.14
12235125--12235191	34	1.9	35	84	3	91	47	1	0	50	1.10
12240130--12240629	168	3.0	166	85	2	660	38	17	21	23	1.93
12244049--12244088	21	2.0	20	90	5	62	62	17	5	15	1.49
12245816--12245942	63	2.0	63	85	0	173	25	22	22	28	1.99
12249138--12249188	18	2.8	18	78	3	57	39	47	1	11	1.52
12249291--12249366	9	8.4	9	77	11	84	27	13	21	38	1.90

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