genome.fa.s4.2.7.7.80.10.50.1000.91.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   191   192   
          193   194   195   196   197   198   

This is table  91  of  198  ( 23681 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)
29127970--29128029	31	1.9	31	89	0	93	40	8	15	36	1.77
29129451--29129516	33	2.0	33	100	0	132	36	6	21	36	1.78
29132680--29132729	26	2.0	26	84	4	66	6	8	10	76	1.17
29133811--29134224	126	3.3	126	90	2	652	32	19	20	26	1.97
29137033--29137243	116	1.8	116	87	2	316	46	5	7	41	1.53
29137418--29137457	21	1.9	21	84	0	53	2	22	45	30	1.66
29137725--29137762	18	2.1	18	90	0	58	42	10	26	21	1.85
29139573--29139653	11	7.4	11	80	9	94	43	0	33	23	1.54
29139893--29139958	29	2.3	29	75	15	66	33	15	16	34	1.90
29145365--29145396	14	2.1	16	88	11	50	0	3	15	81	0.82
29149776--29149821	21	2.2	21	88	0	65	36	19	8	34	1.83
29161450--29161732	51	5.6	50	70	10	134	27	15	27	29	1.96
29161446--29161777	102	3.3	100	82	7	354	28	14	26	30	1.95
29161607--29161777	50	3.5	48	82	10	202	29	13	26	30	1.94
29172570--29172628	27	2.2	27	90	0	91	5	8	13	72	1.24
29177742--29177803	19	3.1	20	81	6	72	61	1	3	33	1.22
29178024--29178115	27	3.8	26	72	17	72	34	0	1	64	1.01
29188226--29188330	44	2.5	40	74	15	104	31	27	4	36	1.78
29188243--29188333	45	2.0	44	82	2	110	34	26	5	34	1.80
29194645--29194700	29	1.9	29	85	0	76	28	14	19	37	1.91
29194924--29194993	22	3.2	22	89	0	104	31	27	0	41	1.56
29194965--29195023	30	2.0	30	86	0	82	30	32	0	37	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29194995--29195036	22	1.9	22	90	0	66	33	33	0	33	1.58
29195068--29195132	29	2.3	28	80	17	73	36	1	1	60	1.16
29195078--29195134	29	2.0	29	89	6	89	36	0	1	61	1.07
29195080--29195141	29	2.1	29	85	5	81	37	0	1	61	1.06
29195232--29195265	15	2.3	15	90	5	52	26	0	5	67	1.13
29197402--29197493	28	3.3	28	98	0	175	44	19	1	34	1.58
29197594--29197734	23	5.2	27	78	14	118	44	24	2	28	1.68
29200940--29201207	126	2.1	127	86	2	373	30	22	16	30	1.96
29203422--29203454	16	2.1	16	100	0	66	36	6	36	21	1.78
29203741--29203792	22	2.4	21	79	17	54	55	5	0	38	1.24
29203667--29203916	119	2.1	121	93	1	432	51	4	1	42	1.30
29209834--29211515	561	3.0	555	88	3	2453	34	16	17	31	1.92
29217425--29217544	9	13.0	9	70	14	59	60	4	1	33	1.25
29218031--29218274	10	26.1	9	66	20	69	30	2	4	62	1.27
29218060--29218114	19	2.8	21	84	10	64	32	1	5	60	1.30
29218159--29218221	29	2.2	27	81	15	74	34	1	1	61	1.15
29218146--29218272	19	7.0	19	71	16	65	26	2	3	66	1.21
29222031--29222150	38	3.2	38	91	3	181	14	6	24	55	1.63
29222018--29222075	29	2.0	30	93	3	100	13	6	22	56	1.61
29222069--29222128	29	2.0	29	80	3	66	13	6	25	55	1.62
29223539--29223676	22	6.3	22	89	0	195	33	14	25	26	1.94
29223777--29223900	13	9.5	13	76	16	80	40	3	4	52	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29223809--29223909	39	2.6	39	87	1	130	39	2	3	53	1.35
29223857--29223941	27	3.1	27	80	5	100	36	3	5	54	1.42
29223815--29223909	13	7.2	13	82	7	93	38	3	4	53	1.36
29224335--29224372	19	2.0	19	100	0	76	31	21	15	31	1.94
29224337--29224379	19	2.3	19	91	0	68	37	20	13	27	1.91
29226300--29226371	33	2.2	33	97	0	135	27	8	2	61	1.39
29226405--29226441	9	4.1	9	100	0	74	35	10	43	10	1.75
29227227--29227274	25	1.9	25	100	0	96	39	4	8	47	1.53
29227345--29227378	16	2.1	16	94	0	59	50	5	2	41	1.42
29228365--29228461	25	3.9	24	80	12	99	22	21	23	31	1.98
29228362--29228477	50	2.3	50	86	5	171	23	22	23	31	1.99
29228362--29228481	25	4.8	25	74	11	93	24	22	22	30	1.99
29233607--29233760	38	4.0	38	78	3	137	34	25	22	18	1.96
29236175--29236210	19	2.0	17	89	10	54	41	22	8	27	1.82
29239168--29239290	38	3.2	38	75	4	131	34	24	21	18	1.96
29243826--29243904	42	1.9	42	82	7	99	40	11	3	44	1.58
29243836--29243926	42	2.2	41	80	11	96	36	10	3	49	1.55
29244744--29244802	24	2.5	24	94	0	100	57	0	30	11	1.35
29254417--29254461	4	11.2	4	85	0	63	24	2	26	46	1.64
29260227--29260257	9	3.6	9	91	8	55	35	9	22	32	1.87
29261405--29261445	13	3.2	13	100	0	82	21	7	21	48	1.74
29261667--29261701	18	1.9	18	88	0	52	57	5	0	37	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29262000--29262036	19	1.9	19	94	0	65	43	21	0	35	1.53
29265396--29265425	15	1.9	16	93	6	53	43	0	6	50	1.28
29265417--29265451	18	2.0	17	88	5	52	45	0	0	54	0.99
29265417--29265470	15	3.4	16	80	19	53	46	0	0	53	1.00
29265536--29265569	17	2.0	17	100	0	68	41	0	0	58	0.98
29265585--29265609	11	2.3	11	100	0	50	52	0	0	48	1.00
29265520--29265611	26	3.5	26	67	21	66	45	0	2	52	1.13
29265322--29265589	120	2.2	120	97	1	504	44	0	4	51	1.26
29267093--29267150	29	2.0	30	89	3	91	15	5	20	58	1.56
29267106--29267194	38	2.3	38	88	0	133	17	7	21	52	1.70
29268898--29268992	39	2.4	40	87	1	129	37	4	4	53	1.40
29268926--29269024	27	3.7	27	80	6	105	37	4	5	53	1.42
29268860--29268992	13	10.2	13	76	12	103	39	3	4	52	1.40
29271430--29271457	9	3.1	9	100	0	56	35	10	42	10	1.74
29272244--29272291	25	1.9	25	100	0	96	39	4	8	47	1.53
29272362--29272395	16	2.1	16	94	0	59	50	5	2	41	1.42
29274461--29274507	19	2.5	19	82	6	60	40	4	4	51	1.41
29281209--29281264	22	2.5	23	82	2	69	51	1	1	44	1.22
29281240--29281279	16	2.5	16	91	0	62	47	2	7	42	1.45
29281290--29281459	59	2.9	59	97	0	313	40	5	9	45	1.59
29281528--29281572	21	2.2	20	84	11	56	55	0	0	44	0.99
29284449--29284746	44	6.6	44	69	16	166	28	21	19	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29284476--29284762	142	2.0	142	97	0	538	26	21	18	32	1.97
29284674--29284764	44	2.1	44	89	0	137	25	23	20	30	1.98
29301783--29301880	25	4.0	25	76	12	96	22	24	22	30	1.99
29301786--29301895	50	2.2	49	85	4	150	23	23	21	30	1.99
29302334--29302368	17	2.1	17	88	0	52	25	17	25	31	1.97
29308177--29308208	12	2.6	13	85	14	50	56	6	0	37	1.25
29310959--29310983	12	2.1	12	100	0	50	76	0	0	24	0.80
29315136--29315244	34	3.4	34	69	20	115	30	13	19	36	1.90
29315111--29315247	62	2.2	62	96	3	249	30	14	18	35	1.91
29324836--29324943	57	1.9	57	88	0	162	26	18	19	35	1.95
29324842--29324933	29	3.2	29	69	14	73	27	19	18	34	1.95
29329996--29330037	21	2.0	21	100	0	84	52	28	0	19	1.46
29330530--29330625	35	2.7	34	82	6	120	38	33	13	14	1.85
29334315--29334364	19	2.4	22	83	12	70	64	2	0	34	1.05
29334316--29334374	19	3.0	18	78	14	55	62	3	0	33	1.12
29338733--29338765	17	1.9	17	93	0	57	66	3	6	24	1.28
29338729--29338839	29	3.8	29	72	17	97	63	0	4	30	1.20
29338760--29338831	9	7.5	10	72	13	53	61	0	4	34	1.16
29338851--29338905	19	2.8	19	75	2	56	56	1	3	38	1.28
29338851--29338954	10	10.4	10	66	22	58	55	1	1	40	1.22
29338977--29339003	3	9.0	3	100	0	54	0	33	0	66	0.92
29350729--29350870	56	2.8	50	83	14	166	25	26	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29351521--29351581	22	2.7	22	87	2	77	49	1	1	47	1.21
29351557--29351596	16	2.5	16	91	0	62	47	2	7	42	1.45
29351669--29351696	9	3.1	9	100	0	56	32	0	10	57	1.33
29351585--29351794	68	3.1	68	97	1	388	40	4	9	45	1.57
29351737--29351764	9	3.1	9	100	0	56	32	0	10	57	1.33
29351861--29351907	24	1.9	25	91	4	78	61	2	0	36	1.08
29357737--29358033	50	5.8	50	79	6	222	23	28	21	26	1.99
29365670--29365704	17	2.1	17	100	0	70	20	34	11	34	1.88
29365852--29365926	27	2.8	28	86	11	104	29	29	12	29	1.92
29365959--29366083	27	4.6	27	76	11	121	25	27	15	32	1.95

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   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   191   192   
          193   194   195   196   197   198