genome.fa.s3.2.7.7.80.10.50.1000.136.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  136  of  150  ( 17918 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)
40916417--40916666	114	2.2	114	89	2	369	32	38	5	24	1.77
40918589--40918666	33	2.4	33	79	12	88	28	26	15	29	1.96
40920753--40920819	34	1.9	35	87	3	100	31	8	14	44	1.76
40922709--40922747	17	2.3	17	90	0	60	35	2	17	43	1.63
40924705--40924731	5	5.4	5	100	0	54	0	18	18	62	1.32
40945821--40945874	22	2.5	22	74	17	58	57	0	3	38	1.17
40946360--40946396	9	4.1	9	89	0	56	32	10	10	45	1.74
40950372--40950511	40	3.5	40	75	8	117	31	23	17	27	1.97
40950643--40950695	19	2.7	19	72	13	54	52	11	0	35	1.37
40951387--40951454	11	6.2	11	78	13	68	1	17	2	77	0.96
40951387--40951452	4	16.8	4	77	14	50	1	18	3	77	0.98
40954380--40954413	17	2.0	17	94	0	59	70	2	0	26	1.01
40955152--40955184	16	2.0	17	88	5	50	51	0	21	27	1.48
40955253--40955324	36	2.0	36	86	5	101	45	0	23	30	1.53
40955524--40955633	23	5.0	22	82	5	127	19	21	24	34	1.96
40960046--40960161	57	2.0	58	86	1	162	47	8	4	39	1.54
40967275--40967321	9	5.2	9	84	7	51	59	4	2	34	1.29
40968930--40968973	19	2.4	18	85	11	54	50	0	6	43	1.29
40971084--40971124	4	10.2	4	94	0	73	46	26	2	24	1.65
40971805--40971868	32	2.0	32	87	0	92	26	3	29	40	1.71
40985084--40985108	11	2.3	11	100	0	50	68	0	0	32	0.90
40990153--40990205	27	2.0	27	88	0	79	18	15	28	37	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40990179--40990253	35	2.1	36	82	2	89	20	9	29	41	1.83
40991682--40991850	81	2.1	81	96	0	311	32	15	12	39	1.85
40991871--40991908	20	1.9	19	89	5	58	36	7	7	47	1.62
41000329--41000376	25	2.0	24	87	4	69	31	2	0	66	1.03
41003969--41003998	16	1.9	15	93	6	51	53	6	33	6	1.53
41006229--41006259	2	15.5	2	100	0	62	48	0	0	51	1.00
41010236--41010275	20	2.0	20	85	5	53	50	7	22	20	1.73
41010879--41010910	2	16.0	2	100	0	64	50	0	0	50	1.00
41023453--41023484	17	1.9	16	93	6	55	12	6	0	81	0.87
41024122--41024159	3	12.7	3	89	10	60	28	2	0	68	1.03
41024467--41024506	20	2.0	20	100	0	80	30	5	10	55	1.54
41029113--41029147	2	17.5	2	100	0	70	51	0	0	48	1.00
41039745--41039795	15	3.3	15	81	8	57	52	13	1	31	1.51
41046294--41046340	3	15.7	3	100	0	94	65	0	0	34	0.93
41046605--41046666	27	2.6	22	70	29	56	16	20	0	62	1.32
41049271--41049343	38	1.9	38	91	0	119	34	30	10	24	1.90
41049623--41049675	21	2.6	21	82	14	58	66	0	7	26	1.18
41050852--41050989	67	2.0	68	87	1	197	55	1	6	36	1.35
41063172--41063205	17	2.0	17	88	0	50	26	23	17	32	1.97
41066783--41066817	14	2.5	14	95	0	61	34	20	5	40	1.76
41068021--41068184	62	2.6	62	94	0	292	47	10	6	35	1.64
41069490--41069536	20	2.3	21	88	7	78	51	19	6	23	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41074078--41074113	18	2.0	18	94	0	63	0	25	2	72	0.98
41077183--41077255	34	2.1	34	94	0	128	32	10	24	31	1.90
41090280--41090306	14	1.9	14	100	0	54	25	0	0	74	0.83
41091948--41091972	2	12.5	2	100	0	50	52	0	0	48	1.00
41095263--41095290	2	14.0	2	100	0	56	0	50	0	50	1.00
41098309--41098421	51	2.2	51	93	3	192	34	15	21	29	1.93
41098996--41099029	14	2.4	14	90	0	50	14	0	38	47	1.45
41109298--41109331	14	2.4	14	90	0	50	47	38	0	14	1.45
41109968--41110030	33	1.9	33	93	0	108	31	17	17	33	1.93
41115544--41115572	15	1.9	15	100	0	58	13	34	17	34	1.89
41117619--41117687	25	2.7	26	77	4	77	30	4	4	60	1.35
41123898--41123926	15	1.9	15	100	0	58	13	34	17	34	1.89
41124743--41124812	33	2.1	33	82	10	81	61	12	1	24	1.40
41125426--41125494	16	4.2	16	96	3	129	24	0	37	37	1.56
41125426--41125494	33	2.1	32	97	2	129	24	0	37	37	1.56
41125475--41125565	45	2.0	45	85	6	123	27	5	28	38	1.79
41127564--41127605	18	2.3	18	100	0	84	21	14	21	42	1.88
41130806--41130870	32	2.0	32	100	0	130	20	18	12	49	1.79
41136220--41136258	16	2.5	15	84	12	51	53	7	2	35	1.43
41139024--41139062	18	2.2	18	90	0	60	46	0	12	41	1.42
41139618--41139669	27	1.9	27	92	7	88	15	32	23	28	1.95
41139620--41139678	27	2.2	27	84	6	75	15	28	27	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41139731--41139797	26	2.5	27	97	2	127	47	0	11	40	1.40
41154110--41154322	42	4.9	42	85	8	273	14	24	19	41	1.88
41154110--41154163	21	2.6	21	72	0	54	12	20	22	44	1.85
41154167--41154339	21	8.3	21	72	3	145	14	26	17	41	1.88
41156671--41156728	28	2.0	31	83	12	79	50	0	1	48	1.11
41166643--41166709	34	2.0	34	87	0	98	38	2	1	56	1.24
41171881--41171926	18	2.6	17	86	10	65	26	6	4	63	1.38
41172751--41172784	2	17.0	2	93	0	59	47	0	0	52	1.00
41174541--41174570	7	4.3	7	91	0	51	50	0	0	50	1.00
41187860--41187924	34	1.9	34	87	12	98	40	7	4	47	1.53
41188006--41188041	17	2.1	17	94	0	63	66	2	0	30	1.06
41190650--41190674	2	12.5	2	100	0	50	0	52	0	48	1.00
41194881--41194920	2	20.0	2	100	0	80	0	50	0	50	1.00
41213214--41213248	7	5.3	7	90	10	56	25	0	0	74	0.82
41213208--41213250	6	7.0	6	84	10	52	30	0	0	69	0.88
41214866--41214921	2	28.0	2	100	0	112	50	0	0	50	1.00
41215264--41215329	3	22.0	3	100	0	132	33	0	0	66	0.92
41215335--41215384	8	6.0	8	88	6	55	42	0	0	58	0.98
41215343--41215386	8	5.5	8	94	0	79	40	0	0	59	0.98
41215947--41215996	2	24.5	2	84	11	66	44	6	0	50	1.26
41219823--41219860	11	3.5	11	100	0	76	42	0	0	57	0.98
41220470--41220511	21	2.0	20	86	4	57	42	16	2	38	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41221600--41221639	19	2.0	20	95	4	73	37	0	0	62	0.95
41221604--41221646	20	2.2	19	87	4	59	34	0	4	60	1.17
41227396--41227447	18	2.7	20	80	17	65	80	7	0	11	0.89
41227396--41227460	21	3.2	20	82	8	69	81	7	1	9	0.93
41228013--41228053	14	2.7	16	77	14	50	53	24	0	21	1.46
41235528--41235560	17	2.0	17	88	5	50	33	12	21	33	1.90
41247579--41247635	14	4.0	14	81	2	69	63	3	1	31	1.22
41249289--41249347	6	9.5	6	80	7	64	13	5	5	76	1.13
41249374--41249416	3	14.3	3	100	0	86	32	0	0	67	0.91
41250886--41250915	7	4.3	7	100	0	60	13	13	30	43	1.82
41251458--41251500	12	3.7	12	87	3	52	44	0	0	55	0.99
41252602--41252626	7	3.6	7	100	0	50	28	0	12	60	1.32
41253790--41254254	68	6.8	68	77	13	338	48	25	0	26	1.53
41253794--41254254	23	20.2	23	76	12	407	48	24	0	26	1.53
41253890--41254246	91	3.9	91	86	6	442	49	25	0	25	1.51
41254249--41254492	116	2.1	116	93	1	418	38	9	6	45	1.63
41257535--41257907	124	3.0	125	90	2	563	33	22	15	28	1.94
41271648--41271694	12	4.0	12	78	13	53	51	2	0	46	1.13
41274461--41274498	14	2.7	15	88	8	53	65	0	2	31	1.06
41275303--41275362	9	6.3	9	72	16	50	60	3	1	35	1.23
41275312--41275383	9	7.4	9	73	18	56	62	4	0	33	1.14
41275312--41275362	19	2.7	19	79	11	61	62	3	0	33	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41275303--41275385	10	8.4	10	72	24	52	60	3	1	34	1.22
41275442--41275519	16	4.5	15	75	21	57	66	0	7	25	1.18
41275503--41275564	20	3.2	20	84	9	74	66	0	6	27	1.16
41275442--41275557	54	2.2	53	82	6	135	64	0	7	27	1.21
41275512--41275567	19	2.9	20	84	7	80	60	0	8	30	1.27
41275677--41275714	18	2.1	18	90	0	58	63	0	5	31	1.17
41276098--41276143	21	2.4	19	85	10	58	28	2	2	67	1.14
41276098--41276143	20	2.4	19	85	10	58	28	2	2	67	1.14
41280060--41280132	11	6.3	11	74	12	56	24	1	9	64	1.32
41280180--41280212	12	2.8	12	90	9	50	36	0	0	63	0.95

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