genome.fa.s3.2.7.7.80.10.50.1000.43.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: 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  43  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)
12082945--12082993	15	3.4	14	83	13	64	16	0	48	34	1.46
12082941--12082991	22	2.3	22	83	10	68	17	0	47	35	1.48
12082945--12082993	21	2.3	21	83	13	64	16	0	48	34	1.46
12083366--12083400	15	2.2	17	90	10	56	77	0	2	20	0.90
12084024--12084056	2	16.5	2	93	0	57	48	3	0	48	1.17
12084157--12084553	194	2.0	194	83	2	494	27	13	18	40	1.88
12086052--12086324	43	6.4	43	86	0	354	19	16	28	34	1.94
12086372--12086432	25	2.4	25	97	0	113	16	26	26	31	1.96
12086435--12086477	22	2.0	22	90	0	68	48	27	13	9	1.73
12087832--12087877	18	2.3	21	85	10	62	23	2	2	71	1.08
12087832--12087877	10	4.7	10	76	13	51	23	2	2	71	1.08
12087893--12087937	19	2.3	20	88	11	76	40	0	4	55	1.20
12087893--12087943	19	2.7	19	87	0	75	41	0	3	54	1.19
12088696--12088732	11	3.0	13	76	15	51	45	16	29	8	1.76
12090406--12090436	15	2.1	15	93	0	53	48	29	0	22	1.51
12104270--12104318	20	2.5	20	77	12	64	46	20	24	8	1.77
12128778--12128826	20	2.5	20	86	6	64	38	22	28	10	1.87
12128790--12128839	20	2.5	20	83	0	64	40	18	26	16	1.90
12148211--12148320	55	2.0	55	100	0	220	36	5	20	38	1.75
12150357--12150598	50	4.9	50	81	2	256	22	28	21	28	1.99
12160632--12160788	43	3.7	43	77	7	133	24	19	26	29	1.98
12160629--12160788	85	1.9	86	84	8	220	23	19	26	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12165889--12165913	13	1.9	13	100	0	50	8	20	0	72	1.10
12168931--12168984	26	2.1	26	96	0	99	12	11	24	51	1.72
12169872--12169914	23	1.9	22	90	4	68	37	2	2	58	1.24
12171112--12171180	16	4.3	16	96	0	102	31	0	36	31	1.58
12171160--12171254	44	2.1	45	86	1	129	33	6	27	32	1.82
12171395--12171436	15	2.7	16	82	14	52	52	2	0	45	1.13
12171404--12171445	15	2.9	15	82	10	52	52	0	0	47	1.00
12173307--12173333	11	2.5	11	100	0	54	51	18	7	22	1.70
12176738--12176775	18	2.1	18	95	5	67	0	57	0	42	0.98
12176744--12176775	6	5.3	6	92	0	55	0	59	0	40	0.97
12179902--12180068	26	6.8	25	67	22	88	43	1	2	52	1.21
12179875--12180073	59	3.3	59	73	14	210	41	1	3	54	1.22
12179858--12180095	120	2.0	120	97	0	449	42	1	3	52	1.28
12180023--12180078	15	4.0	15	73	17	57	44	0	0	55	0.99
12180049--12180102	23	2.4	22	82	14	65	38	3	1	55	1.28
12180295--12180347	21	2.5	21	90	0	79	32	37	9	20	1.85
12182992--12183159	84	2.0	84	97	0	318	31	16	18	33	1.93
12185476--12185512	17	2.3	17	86	9	51	51	13	2	32	1.55
12186005--12186038	18	1.9	18	94	5	61	29	0	0	70	0.87
12186005--12186078	10	7.6	10	76	19	59	36	4	0	59	1.16
12186012--12186099	18	4.7	18	71	25	58	37	3	0	59	1.15
12188841--12188876	16	2.2	16	100	0	72	25	0	36	38	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12188857--12188947	45	2.0	45	85	2	121	27	6	28	37	1.82
12189112--12189146	18	2.0	17	88	5	52	54	0	0	45	0.99
12188999--12189469	156	3.0	156	94	0	798	42	3	6	47	1.46
12189268--12189302	18	2.0	17	88	5	52	54	0	0	45	0.99
12198033--12198127	25	3.8	25	86	4	129	32	16	10	40	1.83
12200295--12200422	43	3.0	43	87	3	168	48	3	23	25	1.65
12209371--12209412	16	2.7	15	85	7	57	45	2	0	52	1.13
12209950--12209999	20	2.5	21	78	18	61	30	10	0	60	1.30
12213657--12213701	21	2.1	21	84	8	56	26	4	22	46	1.70
12221925--12221964	21	1.9	21	90	10	64	27	5	20	47	1.70
12223819--12224025	48	4.3	49	85	3	233	22	28	21	27	1.99
12223831--12224006	96	1.8	96	87	0	262	20	29	22	27	1.99
12236465--12236550	30	2.8	30	77	8	86	38	8	17	36	1.79
12236923--12236977	22	2.5	21	82	8	65	45	1	3	49	1.30
12236929--12236976	23	2.1	22	88	3	69	45	0	4	50	1.21
12236995--12237019	11	2.3	11	100	0	50	48	8	16	28	1.74
12237401--12237493	44	2.1	44	86	9	127	35	27	4	32	1.77
12237475--12237512	16	2.4	16	90	0	58	26	31	2	39	1.70
12243621--12243649	12	2.3	13	94	5	51	20	6	6	65	1.40
12256206--12256234	15	1.9	15	100	0	58	27	27	13	31	1.94
12257328--12257367	14	2.9	14	85	3	55	40	5	2	52	1.37
12270550--12271163	306	2.0	306	96	0	1129	22	31	18	27	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12271341--12271404	26	2.5	26	73	14	60	23	6	4	65	1.35
12274722--12274775	28	2.0	27	82	17	67	53	0	11	35	1.36
12281464--12281689	24	9.6	23	74	6	166	40	17	15	26	1.89
12281431--12281642	70	3.0	71	89	3	313	40	18	12	28	1.87
12281561--12281699	47	2.9	47	86	6	174	38	17	16	27	1.91
12283696--12283757	31	2.0	31	84	12	83	38	6	0	54	1.26
12289181--12289331	71	2.1	70	81	6	171	41	17	11	29	1.84
12289236--12289295	23	2.6	23	91	0	93	41	16	16	25	1.89
12289236--12289331	23	4.1	23	77	7	88	42	16	13	27	1.86
12289922--12290143	37	6.0	37	76	6	173	37	17	16	28	1.91
12289921--12290140	75	3.0	74	81	4	223	37	17	16	28	1.91
12289944--12290203	112	2.3	112	83	1	315	37	17	16	28	1.92
12292846--12292886	18	2.3	18	88	12	59	43	19	0	36	1.51
12299964--12300016	23	2.3	23	84	12	81	32	26	20	20	1.98
12307691--12307733	3	14.3	3	100	0	86	67	0	0	32	0.91
12308456--12308505	10	5.2	10	78	9	59	62	0	0	38	0.96
12308460--12308496	18	2.1	18	100	0	74	64	0	0	35	0.94
12309743--12309791	9	5.4	9	92	0	80	44	22	8	24	1.79
12322283--12322376	37	2.5	38	79	5	111	38	19	14	27	1.91
12326814--12327048	48	4.9	48	95	0	425	28	18	24	28	1.98
12329831--12329863	17	1.9	18	88	11	52	45	0	12	42	1.41
12334113--12334166	25	2.3	23	81	12	56	66	20	7	5	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12335202--12335229	3	9.3	3	100	0	56	32	0	0	67	0.91
12335312--12335364	11	4.6	11	76	15	54	28	5	5	60	1.42
12339999--12340033	15	2.3	15	100	0	70	82	5	0	11	0.82
12342359--12342743	44	8.3	44	66	19	158	32	19	21	25	1.97
12342363--12342791	142	3.0	142	95	0	777	32	19	20	26	1.97
12342886--12343078	50	3.9	50	73	0	170	35	26	15	22	1.94
12342869--12343078	100	2.1	100	84	0	267	35	26	15	22	1.94
12349434--12349547	44	2.6	44	76	4	104	27	25	16	30	1.97
12349459--12350082	132	4.8	132	89	3	888	25	24	19	31	1.98
12349459--12350082	257	2.4	258	87	4	867	25	24	19	31	1.98
12349848--12350070	44	5.1	44	70	8	139	26	25	18	30	1.98
12363190--12363222	14	2.4	14	94	0	57	21	18	27	33	1.96
12364897--12364927	14	2.2	14	94	0	53	38	0	41	19	1.51
12365680--12365750	31	2.2	32	85	7	92	26	26	29	16	1.97
12365810--12365912	27	3.8	28	80	5	122	32	18	25	24	1.97
12365810--12365929	27	4.4	27	76	8	93	32	17	25	25	1.97
12369297--12369343	21	2.2	21	80	0	58	17	29	21	31	1.96
12382579--12382611	14	2.2	16	89	10	52	57	0	42	0	0.98
12384217--12384243	12	2.2	12	100	0	54	7	74	18	0	1.05
12384702--12384728	13	2.1	13	100	0	54	62	7	0	29	1.22
12385650--12385844	98	2.0	98	95	0	354	36	24	10	28	1.88
12386511--12386558	25	2.0	25	87	4	71	54	4	8	33	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12387185--12387313	19	6.8	19	92	0	213	36	14	10	37	1.82
12387162--12387313	38	3.9	38	90	3	223	38	14	9	37	1.79
12387543--12388191	132	4.9	132	89	2	903	29	23	18	27	1.98
12387649--12387980	44	7.5	44	63	16	123	29	23	17	29	1.97
12389536--12389602	1	67.0	1	78	0	71	0	0	10	89	0.48
12389539--12389600	7	8.9	7	89	7	83	0	0	11	88	0.51
12389538--12389599	8	7.9	8	87	12	85	0	0	11	88	0.51
12389536--12389602	21	3.1	22	83	14	95	0	0	10	89	0.48
12393670--12393864	98	2.0	98	94	0	345	36	23	10	29	1.88
12394522--12394574	24	2.3	23	87	6	72	56	3	7	32	1.45

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