genome.fa.s1.2.7.7.80.10.50.1000.47.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  47  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)
14200202--14200234	17	1.9	17	100	0	66	24	3	12	60	1.46
14201866--14201892	5	5.4	5	100	0	54	18	0	0	81	0.69
14203514--14203637	44	2.8	44	81	3	135	20	14	33	30	1.93
14203511--14203648	43	3.2	43	79	6	143	20	15	34	30	1.93
14204245--14204341	40	2.4	38	77	9	104	39	24	19	16	1.92
14204411--14205064	114	5.8	114	81	4	671	31	19	23	25	1.98
14204411--14205064	227	2.9	228	82	4	723	31	19	23	25	1.98
14205477--14205541	22	3.0	22	88	2	87	15	0	38	46	1.46
14211429--14211515	25	3.5	25	90	0	138	39	22	12	25	1.90
14211410--14211515	50	2.1	50	84	3	133	37	21	13	27	1.91
14213782--14213845	33	1.9	33	87	0	92	21	14	25	39	1.91
14216557--14216652	49	2.0	49	85	4	131	42	11	20	25	1.85
14222462--14222501	10	3.9	10	80	6	53	62	0	2	35	1.09
14222463--14222579	21	5.7	19	72	16	67	64	1	5	28	1.24
14222504--14222579	20	3.8	20	76	10	66	65	2	5	26	1.27
14222828--14222930	10	10.2	10	66	17	52	36	1	1	59	1.20
14222808--14222873	29	2.3	28	80	10	71	31	6	4	57	1.43
14222831--14222930	41	2.5	41	75	16	100	38	2	2	58	1.21
14223735--14223767	3	11.0	3	100	0	66	33	0	0	66	0.92
14228078--14228297	75	2.9	75	92	0	352	45	15	4	34	1.65
14232025--14232243	99	2.1	103	84	5	275	27	23	27	21	1.99
14232025--14232243	50	4.3	50	87	4	260	27	23	27	21	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14235118--14235159	18	2.3	19	79	4	50	33	0	4	61	1.17
14235116--14235158	19	2.2	20	84	12	54	30	0	4	65	1.13
14238444--14238480	18	2.0	19	89	5	58	48	0	5	45	1.25
14239142--14239195	23	2.4	22	81	9	63	62	0	1	35	1.06
14244857--14244884	11	2.5	11	100	0	56	0	10	0	89	0.49
14252275--14252307	3	11.0	3	93	0	57	30	0	3	66	1.06
14253552--14253605	26	2.1	25	83	13	65	55	1	1	40	1.21
14253627--14253696	33	2.1	33	89	0	104	52	4	4	38	1.41
14261388--14261469	22	3.7	22	86	0	119	28	15	26	29	1.96
14264361--14264425	32	2.0	32	90	0	103	32	18	10	38	1.85
14269010--14269082	32	2.3	32	95	2	130	32	17	10	38	1.85
14276508--14276546	6	6.5	6	90	0	60	5	0	25	69	1.09
14276513--14276553	18	2.3	18	86	0	55	2	2	24	70	1.11
14276508--14276546	12	3.2	12	92	0	69	5	0	25	69	1.09
14276804--14276869	35	1.9	34	90	6	107	34	7	10	46	1.67
14276956--14276994	20	2.0	20	94	0	69	48	2	0	48	1.15
14279373--14279398	11	2.4	11	100	0	52	61	15	0	23	1.33
14279695--14279739	18	2.4	19	92	3	74	44	0	55	0	0.99
14279695--14279745	6	8.2	6	82	4	57	43	0	56	0	0.99
14280432--14280468	3	12.3	3	100	0	74	67	0	0	32	0.91
14290534--14290559	7	3.7	7	100	0	52	42	0	0	57	0.98
14296579--14296650	30	2.4	30	81	4	83	45	13	11	29	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14317487--14317529	21	2.0	22	86	4	61	37	2	4	55	1.33
14327974--14328144	86	2.0	86	91	0	279	36	11	17	35	1.85
14331013--14331069	28	2.0	28	86	6	80	14	24	14	47	1.80
14334827--14334895	26	2.6	26	88	2	102	37	13	23	26	1.91
14334827--14334904	26	3.0	26	78	16	81	39	12	23	24	1.89
14335794--14335820	13	2.1	13	100	0	54	29	7	7	55	1.55
14336983--14337174	45	4.3	45	91	0	285	21	19	18	40	1.92
14338911--14338935	4	6.2	4	100	0	50	76	0	0	24	0.80
14339279--14339350	3	24.3	3	85	2	101	63	2	2	30	1.22
14344044--14344104	30	2.0	30	96	0	113	55	16	3	24	1.56
14344143--14344181	11	3.5	11	82	0	51	58	2	12	25	1.47
14347799--14347847	24	2.0	24	85	14	66	51	0	6	42	1.27
14347796--14347844	16	3.1	16	77	14	57	48	0	8	42	1.32
14353377--14353420	22	2.0	22	86	0	61	52	0	0	47	1.00
14353420--14353458	18	2.2	18	86	9	53	41	2	2	53	1.28
14353444--14353480	16	2.3	16	86	13	58	59	0	0	40	0.97
14353513--14353570	15	3.6	15	74	17	62	50	1	0	48	1.11
14355240--14355311	6	12.0	6	98	0	135	34	0	15	50	1.44
14355347--14355400	2	28.0	2	78	14	51	53	0	3	42	1.18
14355370--14355429	8	7.5	8	79	7	59	55	0	8	36	1.30
14355349--14355465	37	3.3	35	72	16	89	55	0	8	35	1.36
14355385--14355566	60	3.0	62	89	7	273	57	1	8	32	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14355696--14355799	4	26.8	4	68	9	54	46	2	7	43	1.47
14355696--14355799	6	17.8	6	72	9	54	46	2	7	43	1.47
14355907--14355961	12	4.7	12	77	11	60	54	0	5	40	1.23
14357705--14357747	20	2.2	20	91	0	68	25	18	25	30	1.98
14358440--14358496	3	20.3	3	81	13	68	0	33	0	66	0.92
14358440--14358496	29	2.0	28	83	6	71	0	33	0	66	0.92
14359987--14360333	113	3.1	112	80	6	396	33	17	21	27	1.96
14360234--14360392	73	2.2	74	85	3	205	28	15	23	31	1.96
14360121--14360904	208	4.1	186	83	8	966	33	16	21	29	1.95
14360307--14360575	114	2.4	112	80	6	310	34	16	20	28	1.95
14360650--14360788	74	1.9	75	86	1	199	30	17	23	29	1.97
14360650--14360808	74	2.1	74	81	6	187	33	16	21	27	1.95
14360576--14360918	188	1.8	188	95	0	623	32	15	22	29	1.95
14360182--14360934	396	1.9	394	97	1	1427	33	15	21	29	1.94
14360725--14360961	114	2.1	114	81	5	266	32	16	23	27	1.96
14366318--14366429	53	2.1	54	89	3	181	37	10	5	46	1.62
14366542--14366696	13	11.8	13	69	13	75	40	10	4	45	1.59
14366561--14366963	53	7.6	53	70	14	260	39	10	4	45	1.60
14366808--14366859	13	4.0	13	87	9	70	44	9	3	42	1.55
14366318--14366996	266	2.5	267	98	0	1297	39	10	5	45	1.60
14373668--14373894	42	5.3	42	83	9	257	25	22	22	30	1.99
14373668--14373894	85	2.7	86	85	7	286	25	22	22	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14376489--14376574	43	2.0	41	88	4	127	36	3	11	48	1.57
14376590--14376635	25	1.9	23	82	8	56	52	2	6	39	1.40
14382151--14382214	32	2.0	32	96	0	119	26	43	10	18	1.83
14383744--14383833	41	2.2	41	91	0	144	16	24	34	24	1.95
14386878--14386920	22	1.9	23	86	13	63	62	2	0	34	1.08
14393724--14393771	24	2.0	24	100	0	96	33	8	0	58	1.28
14393772--14393801	14	2.1	14	93	0	51	63	20	6	10	1.47
14393948--14393988	11	3.9	11	87	12	68	70	0	29	0	0.87
14394012--14394050	19	2.0	21	85	10	55	23	0	10	66	1.22
14395001--14395038	18	2.1	18	90	0	58	36	7	44	10	1.68
14397832--14398290	159	2.9	156	69	14	380	32	11	6	49	1.66
14399130--14399263	18	7.1	18	69	18	69	0	29	0	69	0.99
14399117--14399242	44	3.2	40	73	17	120	0	31	0	67	0.96
14399172--14399221	15	3.1	16	77	22	52	0	28	0	72	0.86
14399162--14399218	26	2.3	23	82	11	69	0	29	0	70	0.88
14399159--14399258	34	2.9	34	80	8	94	0	29	1	70	0.94
14399180--14399233	16	3.2	16	78	5	54	0	25	0	74	0.83
14399172--14399219	16	3.1	15	82	11	53	0	29	0	70	0.87
14399241--14399267	14	1.9	14	100	0	54	0	22	7	70	1.12
14401116--14401165	11	4.7	11	75	9	50	42	0	0	58	0.98
14401137--14401194	25	2.4	25	82	5	66	36	3	0	60	1.14
14401113--14401177	31	2.1	31	100	0	130	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
14401151--14401210	19	3.1	19	72	13	59	38	3	0	58	1.15
14401151--14401212	20	3.1	20	73	13	65	38	3	0	58	1.15
14401113--14401262	31	4.1	37	74	20	122	40	2	1	55	1.22
14403805--14403917	56	2.0	56	96	0	208	43	4	29	23	1.73
14405537--14405579	2	21.5	2	100	0	86	51	0	0	48	1.00
14405793--14405932	44	3.2	44	87	4	194	40	22	4	32	1.73
14406666--14406773	44	2.5	44	83	3	121	27	28	19	24	1.98
14423023--14423785	417	1.8	415	84	5	1047	36	19	17	26	1.93
14427462--14427496	11	3.0	11	91	8	52	77	5	0	17	0.96
14429164--14429223	25	2.4	25	83	5	68	33	5	1	60	1.29

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