genome.fa.s4.2.7.7.80.10.50.1000.187.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  187  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)
58177205--58177245	21	2.0	21	90	0	64	14	58	4	21	1.55
58177121--58177250	69	1.9	69	81	0	161	20	54	9	15	1.68
58185094--58185122	13	2.1	14	93	6	51	34	0	0	65	0.93
58185468--58185527	25	2.4	25	97	0	111	15	20	23	41	1.89
58185540--58185595	22	2.6	21	83	8	67	17	21	19	41	1.91
58190241--58190372	67	2.0	67	98	0	255	28	33	18	20	1.96
58192641--58192689	17	2.8	17	81	15	55	24	4	8	63	1.40
58202225--58202272	25	1.9	25	82	0	60	54	2	12	31	1.49
58203897--58204133	124	1.9	124	89	3	370	32	8	17	41	1.79
58215912--58215976	22	3.0	22	84	4	78	18	26	18	36	1.94
58220977--58221028	11	4.6	11	90	2	77	23	32	1	42	1.65
58220977--58221031	22	2.4	23	90	6	94	23	30	1	43	1.64
58220977--58221052	34	2.3	34	79	9	84	27	28	1	42	1.64
58221012--58221111	51	2.0	51	84	4	130	28	25	1	46	1.60
58221733--58221793	30	2.0	30	100	0	122	36	16	22	24	1.94
58225604--58226047	125	3.5	126	89	1	660	28	22	18	30	1.97
58226172--58226219	15	3.1	15	75	3	51	56	25	0	18	1.42
58232400--58232445	23	2.0	23	87	8	67	43	0	4	52	1.21
58241965--58241994	11	2.6	12	94	5	53	46	3	0	50	1.18
58241986--58242016	16	1.9	16	93	0	53	51	0	0	48	1.00
58256477--58256580	9	10.7	9	72	17	57	59	0	2	37	1.12
58256502--58256584	30	2.7	30	87	5	105	60	0	3	36	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58256507--58256584	10	7.9	10	75	12	72	62	0	2	34	1.09
58256479--58256581	20	5.2	20	74	9	79	60	0	2	36	1.12
58256467--58256581	10	11.8	9	75	9	68	61	0	2	35	1.10
58257227--58257293	32	2.0	33	91	5	109	32	20	1	44	1.61
58258630--58258678	24	2.0	24	92	0	80	36	14	28	20	1.92
58261308--58261483	87	2.0	87	89	0	271	33	22	21	22	1.97
58269285--58269343	31	1.9	31	89	6	93	35	8	10	45	1.68
58269285--58269355	31	2.3	31	85	4	90	35	8	11	45	1.70
58276003--58276045	18	2.4	18	85	11	61	23	2	4	69	1.18
58276163--58276208	3	15.3	3	100	0	92	32	0	0	67	0.91
58284544--58284607	22	2.9	21	73	13	56	56	1	3	39	1.25
58284941--58284997	24	2.3	25	85	8	73	73	3	8	14	1.20
58284962--58285006	24	1.9	23	86	4	63	75	2	4	17	1.07
58285209--58285278	16	4.4	16	96	0	104	31	0	35	32	1.58
58285257--58285351	45	2.1	44	90	5	147	32	6	27	33	1.82
58285511--58285545	18	2.0	17	88	5	52	54	0	0	45	0.99
58288140--58288170	2	15.5	2	100	0	62	51	0	0	48	1.00
58289688--58289789	51	2.0	51	96	0	186	41	11	25	21	1.87
58292048--58292449	149	2.7	147	81	6	436	29	17	16	35	1.93
58301019--58301043	2	12.5	2	100	0	50	48	0	0	52	1.00
58301072--58301207	44	3.1	43	80	8	150	29	7	13	49	1.70
58303024--58303063	14	2.9	14	88	0	53	37	7	15	40	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58303077--58303162	33	2.7	32	76	7	93	26	8	17	47	1.75
58305879--58305929	3	16.3	3	78	15	50	33	3	1	60	1.26
58308005--58308049	19	2.3	20	75	20	51	26	22	8	42	1.83
58312057--58312404	45	7.8	45	75	5	330	30	19	23	26	1.98
58312041--58312383	89	3.9	89	88	2	467	31	18	23	26	1.98
58312057--58312400	134	2.6	134	76	6	304	30	19	23	26	1.98
58314504--58314576	3	24.0	3	87	8	103	32	2	1	63	1.17
58315785--58315819	18	2.0	17	94	5	61	48	0	51	0	1.00
58315968--58315995	14	2.0	14	100	0	56	42	14	14	28	1.84
58318498--58318523	3	8.7	3	100	0	52	0	30	0	69	0.89
58320287--58320330	22	2.1	20	83	8	52	52	2	0	45	1.13
58323309--58323354	24	1.9	24	86	0	65	52	2	0	45	1.13
58326534--58326584	17	3.2	16	86	5	68	82	0	15	1	0.76
58326903--58327213	107	2.9	106	88	3	450	25	17	10	46	1.80
58327910--58327949	2	20.0	2	84	0	53	50	7	0	42	1.30
58327911--58327949	8	4.9	8	96	0	69	51	7	0	41	1.31
58328598--58328630	15	2.2	15	100	0	66	18	12	6	63	1.48
58334254--58334311	16	4.1	14	68	27	50	46	1	1	50	1.22
58334249--58334321	22	3.4	21	74	20	71	49	1	2	46	1.24
58335287--58335394	37	2.7	40	80	9	114	25	14	24	36	1.93
58340401--58340447	25	1.9	25	86	4	69	14	27	21	36	1.93
58345143--58345320	37	4.5	41	84	11	146	28	19	15	36	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58345170--58345318	37	4.0	37	93	0	217	27	20	14	37	1.91
58346987--58347471	242	2.0	242	96	1	891	34	21	14	30	1.92
58353459--58353510	21	2.7	18	72	18	50	38	1	3	55	1.29
58354424--58354473	23	2.2	23	85	7	66	54	0	2	44	1.11
58354458--58354514	21	2.8	21	73	23	59	50	8	5	35	1.56
58355971--58356007	3	12.3	3	100	0	74	67	0	0	32	0.91
58380038--58380102	19	3.3	18	74	18	51	55	0	1	43	1.09
58389593--58389628	7	5.1	7	100	0	72	55	0	0	44	0.99
58393979--58394047	23	2.9	23	85	10	77	30	1	1	66	1.09
58404873--58404911	19	2.0	19	85	5	51	56	0	0	43	0.99
58405647--58405689	21	2.0	21	100	0	86	23	13	25	37	1.92
58406849--58407024	40	4.4	40	87	3	196	36	21	22	20	1.95
58407064--58407336	41	6.7	41	89	2	388	19	21	27	31	1.97
58407361--58407400	15	2.9	14	86	13	57	47	5	0	47	1.24
58407744--58407811	29	2.4	27	76	11	64	19	1	32	47	1.58
58407744--58407813	15	4.8	15	79	8	65	20	1	31	47	1.59
58412072--58412237	43	3.9	43	87	0	235	25	17	28	27	1.98
58412026--58412237	43	5.0	43	82	4	232	27	16	28	27	1.97
58424866--58424899	13	2.6	13	95	0	59	11	2	44	41	1.56
58428571--58428623	19	2.7	19	77	11	63	35	11	9	43	1.73
58428650--58428697	22	2.0	22	88	11	69	39	8	2	50	1.44
58429893--58429955	30	2.1	30	90	0	99	25	3	14	57	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58430327--58430386	29	2.1	29	93	6	106	41	0	6	51	1.28
58439897--58439930	15	2.2	16	89	5	52	32	0	2	64	1.08
58442727--58442751	6	4.2	6	100	0	50	52	0	0	48	1.00
58446865--58446964	50	2.0	50	90	0	155	28	19	12	41	1.86
58447841--58447896	17	3.2	18	78	12	55	69	0	1	28	0.98
58448514--58448552	19	2.1	19	85	9	53	38	0	2	58	1.12
58448520--58448594	16	4.5	15	73	18	53	40	0	2	57	1.13
58453124--58453163	21	1.9	21	94	0	71	42	22	5	30	1.75
58456930--58456968	19	2.0	19	85	5	51	56	0	0	43	0.99
58476721--58476782	31	2.1	29	90	6	97	38	4	9	46	1.58
58476726--58476790	29	2.2	31	83	5	80	38	7	12	41	1.71
58479672--58479719	16	3.2	16	77	22	59	43	0	2	54	1.12
58479668--58479712	12	3.4	12	78	21	54	46	0	2	51	1.13
58482706--58482802	30	3.2	30	81	7	99	31	15	4	48	1.64
58483347--58483419	11	6.6	11	79	14	53	79	0	20	0	0.73
58483362--58483423	22	2.9	21	83	9	81	85	0	14	0	0.60
58483372--58483442	8	9.0	8	80	10	58	83	0	11	5	0.81
58483359--58483423	18	3.6	18	85	8	87	84	0	15	0	0.62
58483766--58483808	15	2.8	16	76	16	54	79	0	20	0	0.74
58484261--58484311	18	2.8	18	76	8	59	31	13	11	43	1.80
58484438--58484570	17	7.6	18	69	18	68	27	15	8	48	1.73
58484445--58484523	35	2.2	37	78	14	96	21	15	10	53	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58484488--58484570	17	4.8	17	75	5	69	31	14	8	45	1.74
58490801--58492216	78	18.3	78	86	5	1615	27	16	20	34	1.95
58492353--58492469	59	2.0	59	84	3	155	25	19	5	49	1.69
58492350--58492473	29	4.2	29	79	3	149	28	18	4	48	1.68
58493922--58493963	22	2.0	21	86	9	59	40	7	9	42	1.65
58494031--58494070	18	2.2	18	86	8	55	22	12	12	52	1.72
58494049--58494106	27	2.2	26	81	3	62	24	15	6	53	1.66
58493974--58494135	61	2.6	62	83	6	195	28	12	9	48	1.73
58494091--58494171	17	4.6	18	72	17	71	30	12	11	45	1.76
58494593--58494657	29	2.2	28	89	10	96	40	4	9	46	1.57

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