genome.fa.s1.2.7.7.80.10.50.1000.131.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  131  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)
39711426--39711645	102	2.2	102	95	0	395	40	1	5	52	1.33
39711361--39711544	56	3.1	58	72	16	196	41	1	5	51	1.32
39711511--39711608	29	3.1	29	75	21	83	39	1	5	54	1.30
39718498--39718532	17	2.1	17	89	10	54	74	2	22	0	0.95
39723741--39723801	26	2.3	26	86	10	81	47	11	11	29	1.75
39738476--39738530	5	10.2	6	80	11	50	61	0	0	38	0.96
39738477--39738530	16	3.4	17	80	10	69	61	0	0	38	0.96
39738709--39738760	25	2.1	25	81	0	59	55	9	7	26	1.59
39740119--39740175	22	2.6	22	97	0	105	43	17	21	17	1.88
39741866--39741908	21	2.0	22	86	13	63	51	4	0	44	1.22
39742071--39742133	3	21.0	3	100	0	126	66	0	0	33	0.92
39743451--39743505	26	2.1	27	83	10	69	61	1	7	29	1.33
39743456--39743511	26	2.2	25	81	9	60	60	1	8	28	1.37
39754451--39754478	3	9.3	3	100	0	56	32	32	35	0	1.58
39758402--39758434	7	4.9	7	92	3	50	72	15	0	12	1.12
39770120--39770170	16	3.2	16	83	5	59	43	0	23	33	1.54
39770379--39770471	21	4.0	23	73	23	72	51	2	0	46	1.13
39770343--39770469	55	2.2	57	86	5	168	50	1	1	46	1.20
39778396--39778438	19	2.4	19	84	7	54	6	2	6	83	0.88
39785819--39785849	12	2.6	12	94	0	53	38	0	0	61	0.96
39794428--39794459	3	10.7	3	100	0	64	0	0	34	65	0.93
39796933--39796963	9	3.4	9	90	0	53	25	12	22	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39798540--39798598	29	2.0	29	90	0	91	15	30	20	33	1.93
39798540--39798621	29	2.9	29	83	1	76	14	28	21	35	1.93
39798631--39798704	28	2.6	29	86	4	114	13	25	20	40	1.89
39798549--39798728	79	2.3	79	85	0	234	14	26	19	39	1.90
39801015--39801058	3	14.7	3	100	0	88	31	0	0	68	0.90
39803714--39803751	3	12.7	3	100	0	76	34	31	0	34	1.58
39809370--39809419	21	2.4	21	80	10	57	30	2	0	68	1.01
39810189--39810219	13	2.4	13	94	0	53	45	6	22	25	1.76
39815421--39815474	21	2.5	21	76	8	56	14	24	1	59	1.46
39816618--39816648	2	15.5	2	100	0	62	48	0	0	51	1.00
39825949--39825983	18	1.9	18	94	0	61	42	5	20	31	1.75
39829227--39829296	31	2.3	31	90	7	108	18	35	34	11	1.87
39832144--39832201	12	4.8	12	86	0	80	27	36	36	0	1.57
39832151--39832197	6	7.8	6	92	0	58	27	38	34	0	1.57
39834746--39834802	28	2.0	28	100	0	114	22	14	31	31	1.93
39835900--39835930	13	2.3	14	94	5	55	0	32	0	67	0.91
39835900--39835939	18	2.2	18	90	0	62	0	37	0	62	0.95
39836005--39836079	27	2.8	27	81	0	96	22	25	26	25	2.00
39837367--39837410	16	2.8	16	83	13	63	38	2	0	59	1.10
39837714--39837748	18	1.9	18	94	0	61	28	11	0	60	1.32
39837748--39837777	13	2.4	13	94	5	53	46	0	6	46	1.29
39843008--39843069	31	2.1	30	82	17	76	29	17	8	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39843222--39843333	25	4.5	25	72	12	79	29	18	23	28	1.98
39844300--39844343	12	3.8	12	85	14	65	29	29	0	40	1.57
39844509--39844540	15	2.1	15	94	0	55	28	0	6	65	1.16
39846663--39846836	25	7.2	25	78	9	191	42	0	13	43	1.44
39846616--39846864	95	2.6	95	91	1	403	39	0	12	46	1.45
39852964--39853007	18	2.5	17	82	10	52	43	0	6	50	1.29
39852977--39853038	19	3.3	19	81	2	72	41	1	4	51	1.33
39854693--39854811	49	2.4	49	78	0	139	21	40	18	20	1.92
39857929--39857965	3	12.3	3	100	0	74	67	0	32	0	0.91
39861024--39861122	39	2.6	39	85	3	130	36	6	8	49	1.57
39863552--39863807	125	2.1	124	89	2	388	30	15	22	31	1.95
39867092--39867436	29	12.7	27	75	14	155	31	1	24	43	1.63
39867089--39867581	28	18.3	28	81	12	507	32	1	21	44	1.60
39870695--39870728	15	2.3	15	90	5	52	67	5	0	26	1.13
39870827--39870887	29	2.1	29	90	6	97	60	1	0	37	1.07
39870925--39870966	22	1.9	22	90	0	66	33	0	33	33	1.58
39870938--39870996	30	2.0	30	96	0	109	32	0	35	32	1.58
39870916--39871018	52	2.0	51	84	5	136	33	0	32	33	1.65
39870967--39871037	22	3.2	22	90	7	108	36	1	28	33	1.66
39880949--39881050	47	2.2	46	85	5	134	25	22	16	35	1.95
39880949--39881067	46	2.6	47	82	6	143	26	21	15	35	1.94
39882173--39882207	3	11.7	3	100	0	70	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39882439--39882469	2	15.5	2	100	0	62	48	0	0	51	1.00
39885860--39885904	18	2.5	18	96	0	81	53	26	0	20	1.46
39891226--39891268	9	4.9	9	80	2	52	48	4	2	44	1.36
39891226--39891282	17	3.3	17	82	4	69	47	7	1	43	1.40
39891226--39891268	18	2.5	17	88	3	59	48	4	2	44	1.36
39891491--39891519	14	2.0	15	93	6	51	27	0	20	51	1.47
39891711--39891767	28	2.0	28	90	6	89	56	0	5	38	1.22
39892720--39892762	21	2.0	22	86	13	63	44	0	13	41	1.44
39892720--39892763	20	2.1	21	84	12	56	45	0	13	40	1.44
39893153--39893308	41	3.8	41	80	7	165	20	19	27	32	1.97
39903684--39903741	17	3.5	17	74	9	57	51	1	1	44	1.21
39905420--39905451	15	2.1	15	94	0	55	71	6	6	15	1.26
39909749--39909800	24	2.2	24	85	0	68	50	7	3	38	1.50
39913995--39914046	24	2.2	24	85	0	68	50	7	3	38	1.50
39915586--39915625	20	2.0	20	100	0	80	65	10	0	25	1.24
39916173--39916251	39	2.0	39	85	0	104	36	20	11	31	1.88
39917486--39917894	204	2.0	205	98	0	784	37	8	4	49	1.54
39918108--39918188	14	5.6	14	74	10	65	35	34	1	28	1.65
39918111--39918195	29	3.0	28	73	14	84	34	36	1	28	1.65
39918149--39918252	7	14.6	7	74	7	66	35	37	0	26	1.57
39918197--39918252	14	3.9	14	93	4	94	33	37	0	28	1.58
39918193--39918255	29	2.2	29	88	2	101	36	36	0	26	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39918466--39918521	14	4.0	14	79	6	60	37	44	0	17	1.49
39918531--39918562	15	2.1	15	94	0	55	40	34	0	25	1.56
39918914--39919055	42	3.5	42	78	4	146	32	31	18	17	1.94
39918912--39919070	40	3.9	41	80	4	196	31	33	17	17	1.94
39919114--39919239	40	3.1	41	82	4	168	22	21	19	37	1.94
39921992--39922108	52	2.2	52	80	8	123	18	18	14	47	1.82
39922138--39922193	26	2.2	26	87	6	78	16	0	21	62	1.32
39924479--39924505	5	5.4	5	100	0	54	18	0	0	81	0.69
39924667--39924697	9	3.6	9	95	4	55	22	0	6	70	1.09
39924660--39924710	12	4.2	12	82	7	59	21	1	9	66	1.31
39926350--39926408	29	2.0	30	86	3	84	45	15	11	27	1.81
39927108--39927169	31	2.0	31	84	9	83	48	17	8	25	1.75
39927211--39927252	21	2.0	21	95	0	75	23	16	28	30	1.96
39927313--39927373	29	2.1	31	85	14	85	34	14	4	45	1.67
39927808--39927841	3	11.7	3	93	6	61	70	0	29	0	0.87
39927806--39927841	14	2.5	14	95	4	63	72	0	27	0	0.85
39927803--39927838	17	2.1	17	94	0	63	75	0	25	0	0.81
39928003--39928033	3	10.3	3	100	0	62	0	32	0	67	0.91
39944071--39944122	21	2.5	20	78	9	61	46	0	1	51	1.12
39947098--39947141	11	3.7	11	80	16	52	27	0	2	70	0.99
39948301--39948331	9	3.4	9	90	0	53	25	12	22	38	1.90
39948971--39948996	5	5.2	5	100	0	52	19	19	19	42	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39953737--39953793	29	2.0	28	82	3	69	38	3	1	56	1.27
39956838--39956873	14	2.6	14	86	0	54	8	8	0	83	0.82
39957292--39957325	5	6.8	5	87	12	52	79	0	2	17	0.86
39970323--39970364	22	1.9	22	90	9	68	42	2	0	54	1.13
39977348--39977382	16	2.2	16	100	0	70	31	0	20	48	1.50
39980602--39980642	18	2.3	18	86	0	55	31	0	46	21	1.52
39981566--39981603	14	2.8	14	92	4	60	55	0	0	44	0.99
39984380--39984412	16	2.1	16	94	0	57	60	0	0	39	0.97
40001523--40001626	2	51.5	2	81	5	120	4	47	0	48	1.23
40003682--40003968	43	6.7	43	83	3	303	31	30	16	22	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