genome.fa.s1.2.7.7.80.10.50.1000.140.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  140  of  187  ( 22383 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)
41876421--41876481	3	20.3	3	75	0	59	31	3	3	62	1.27
41881132--41881183	23	2.2	24	86	10	72	73	7	0	19	1.07
41881142--41881186	19	2.3	20	88	3	65	77	4	0	17	0.92
41881190--41881233	6	7.0	6	80	19	54	81	0	18	0	0.68
41881190--41881228	21	1.9	20	94	5	69	82	0	17	0	0.68
41881192--41881223	15	2.2	15	94	5	57	84	0	15	0	0.63
41881198--41881233	17	2.1	17	90	10	56	83	0	16	0	0.65
41881193--41881233	11	3.8	11	78	15	50	82	0	17	0	0.66
41883436--41883701	44	6.0	44	89	3	387	29	16	25	28	1.97
41883684--41884180	45	11.3	44	60	9	118	27	19	24	27	1.99
41883672--41884769	88	12.5	88	88	1	1551	27	20	24	27	1.99
41883801--41884735	43	21.2	44	60	10	174	27	20	24	27	1.99
41886330--41886387	3	19.3	3	74	0	53	32	3	5	58	1.37
41900294--41900412	63	1.9	61	84	3	157	43	14	8	33	1.75
41902913--41902944	16	2.1	16	94	5	57	43	18	0	37	1.51
41915940--41916224	50	5.7	50	84	5	353	21	29	21	27	1.99
41915981--41916224	102	2.4	100	90	2	373	21	30	21	26	1.98
41921136--41921282	25	6.4	23	70	21	105	21	23	16	39	1.92
41921137--41921218	43	1.9	43	92	0	137	20	20	17	41	1.90
41921136--41921282	69	2.1	68	87	6	208	21	23	16	39	1.92
41923082--41923208	50	2.5	50	85	8	152	26	15	26	30	1.96
41923214--41923308	45	2.1	45	90	0	154	25	20	24	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41929912--41929973	21	3.0	21	81	9	72	14	17	17	50	1.79
41933031--41933055	12	2.1	12	100	0	50	60	0	24	16	1.36
41937977--41938106	28	4.7	28	74	6	113	35	13	20	30	1.91
41940375--41940563	37	5.1	36	81	5	177	37	28	13	20	1.91
41940387--41940563	74	2.4	74	81	1	221	36	28	14	20	1.91
41941501--41941678	86	2.1	86	95	1	322	28	10	20	39	1.86
41944803--41945181	189	2.0	189	98	0	731	35	12	20	32	1.89
41946746--41946830	40	2.1	40	91	0	134	47	29	14	9	1.75
41960194--41960225	9	3.7	9	95	4	57	34	9	0	56	1.32
41962830--41962905	26	2.9	26	86	0	89	38	26	22	13	1.91
41963081--41963462	27	14.2	26	84	4	469	18	20	17	43	1.88
41963081--41963462	81	4.7	81	86	3	520	18	20	17	43	1.88
41969451--41969493	23	1.9	22	85	4	59	20	6	6	65	1.41
41969448--41969500	22	2.4	22	81	12	63	22	5	5	66	1.35
41972433--41972498	29	2.3	29	83	0	78	34	22	21	21	1.96
41981747--41981806	29	2.1	29	96	0	111	40	8	5	46	1.56
41986445--41986761	160	2.0	160	94	0	553	14	22	15	47	1.82
41993042--41993082	21	2.0	21	100	0	82	34	0	9	56	1.32
41993066--41993249	38	4.7	37	66	19	97	42	1	4	50	1.33
41993057--41993287	120	1.9	120	94	1	410	43	1	4	51	1.30
41993389--41993462	15	5.1	15	72	20	52	41	1	1	55	1.17
41993404--41993622	102	2.1	102	100	0	438	43	1	4	49	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41993606--41993640	18	2.0	17	88	5	52	45	0	0	54	0.99
41993797--41993893	45	2.2	45	88	5	144	34	28	5	31	1.79
41993873--41993919	16	2.9	16	87	0	67	17	31	6	44	1.73
41994672--41994704	3	11.0	3	100	0	66	66	0	0	33	0.92
41996274--41996325	13	3.8	14	75	10	54	30	0	5	63	1.18
41996302--41996335	17	2.0	17	88	0	50	32	2	2	61	1.26
42007045--42007071	7	3.9	7	100	0	54	44	25	0	29	1.54
42007631--42007655	2	12.5	2	100	0	50	52	0	0	48	1.00
42008019--42008052	2	17.0	2	100	0	68	50	0	0	50	1.00
42011101--42011175	36	2.1	36	87	0	105	37	14	13	34	1.85
42019695--42019841	41	3.6	41	83	5	190	25	19	21	33	1.97
42020242--42020315	35	2.1	35	82	0	85	36	8	16	39	1.78
42022140--42022184	19	2.2	20	88	11	65	0	35	0	64	0.94
42027744--42027818	28	2.7	28	78	12	82	33	16	26	24	1.95
42027822--42027867	23	2.0	23	95	0	83	50	8	28	13	1.70
42031431--42031474	18	2.4	19	81	14	56	50	0	2	47	1.13
42036625--42036650	2	13.0	2	100	0	52	50	0	0	50	1.00
42037479--42037551	38	1.9	37	86	8	103	31	21	1	45	1.61
42037539--42037582	23	1.9	22	82	17	54	38	22	0	38	1.55
42037684--42037756	23	3.2	23	90	0	119	31	21	21	24	1.98
42037982--42038023	18	2.4	17	81	18	50	40	19	2	38	1.64
42044753--42044800	24	1.9	25	84	16	64	58	0	2	39	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42048215--42048276	32	1.9	32	96	0	115	29	8	33	29	1.86
42052542--42052623	41	2.0	41	86	9	114	35	8	7	48	1.61
42061242--42061341	11	9.4	11	67	13	57	45	3	28	24	1.68
42061277--42061338	22	2.8	23	80	7	74	45	3	25	25	1.69
42071721--42071783	27	2.4	26	80	12	76	63	11	3	22	1.41
42082738--42082769	10	3.4	10	87	12	50	0	15	0	84	0.63
42083561--42083587	2	13.5	2	100	0	54	48	0	0	51	1.00
42090189--42090758	132	4.3	132	86	3	772	27	17	24	30	1.97
42090484--42090688	44	4.7	44	70	10	132	27	19	22	30	1.98
42098541--42098575	18	1.9	18	94	0	61	65	14	5	14	1.44
42103452--42103530	29	2.8	28	75	13	72	48	0	1	50	1.08
42103467--42103533	28	2.3	28	85	10	82	46	0	1	52	1.09
42104591--42104632	22	1.9	22	90	0	66	26	21	35	16	1.94
42105701--42105749	19	2.5	20	81	18	68	59	0	0	40	0.98
42105690--42105751	17	3.4	19	80	14	69	53	0	0	46	1.00
42110190--42110369	48	3.8	48	91	3	283	40	18	8	32	1.81
42113784--42113873	42	2.1	42	81	4	110	20	18	17	43	1.88
42117401--42117429	15	1.9	15	100	0	58	31	13	27	27	1.94
42118629--42118658	14	2.1	14	93	0	51	43	23	3	30	1.70
42120299--42120327	2	14.5	2	100	0	58	48	0	0	51	1.00
42121351--42121394	6	7.2	6	89	5	70	38	0	45	15	1.47
42121351--42121394	19	2.4	19	92	3	72	38	0	45	15	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42121373--42121558	58	3.2	59	77	13	190	32	3	51	12	1.56
42121576--42121765	62	3.1	62	88	3	260	51	1	9	37	1.44
42121576--42121765	31	6.2	30	84	6	229	51	1	9	37	1.44
42121935--42121989	21	2.6	21	88	0	83	30	38	7	23	1.82
42123332--42123383	25	2.0	26	85	3	70	38	11	9	40	1.74
42123616--42123688	19	3.9	19	74	13	62	53	4	2	39	1.34
42125285--42125316	15	2.1	15	94	0	55	68	9	6	15	1.36
42127847--42127891	2	22.5	2	100	0	90	51	0	0	48	1.00
42128146--42128183	2	18.5	2	94	5	67	47	0	2	50	1.15
42128248--42128293	20	2.3	20	82	10	60	21	0	8	69	1.15
42128256--42128300	21	2.1	21	87	0	63	17	0	11	71	1.14
42131751--42131814	25	2.5	25	84	5	74	20	26	26	26	1.99
42138346--42138560	30	7.2	30	76	4	175	33	25	14	26	1.95
42138346--42138548	15	13.7	15	77	4	151	33	25	14	26	1.95
42143957--42144090	50	2.7	50	75	2	135	26	19	22	32	1.97
42144291--42144539	46	5.6	45	71	12	176	29	19	19	31	1.96
42144160--42144666	44	11.7	44	68	12	244	28	20	18	32	1.96
42144129--42144674	175	3.1	173	91	3	853	28	19	18	32	1.96
42152074--42152127	26	2.1	26	100	0	108	40	11	11	37	1.76
42153093--42153135	3	14.3	3	100	0	86	67	0	0	32	0.91
42157176--42157205	14	2.1	14	93	0	51	16	16	46	20	1.84
42157344--42157377	15	2.3	15	89	0	50	23	5	29	41	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42163331--42163382	26	2.0	26	100	0	104	19	15	30	34	1.93
42174331--42174372	18	2.3	18	91	0	66	35	0	7	57	1.26
42174925--42175389	114	4.1	111	80	7	470	33	19	22	24	1.97
42174941--42175362	229	1.8	228	82	4	544	34	20	21	23	1.96
42175002--42175425	113	3.7	114	79	6	317	34	20	21	24	1.97
42176132--42176174	22	2.0	22	90	4	70	18	0	30	51	1.47
42176265--42176329	28	2.3	28	83	0	76	20	4	26	49	1.68
42176455--42176484	15	2.0	15	93	0	51	63	0	3	33	1.11
42176692--42176733	21	2.0	21	90	0	66	33	0	9	57	1.31
42177517--42177551	18	1.9	18	94	0	61	14	28	17	40	1.88

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