genome.fa.s4.2.7.7.80.10.50.1000.3.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  3  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)
925849--925925	14	5.0	15	71	20	52	42	14	9	33	1.77
925865--925904	20	2.0	20	90	0	62	50	12	10	27	1.72
925853--925919	34	1.9	35	90	3	109	46	13	8	31	1.74
927915--927947	3	11.0	3	93	0	57	0	63	0	36	0.95
929044--929074	3	10.3	3	100	0	62	35	32	0	32	1.58
930926--930983	29	2.0	28	83	3	71	34	15	6	43	1.74
934233--934357	17	6.7	17	67	21	72	37	2	0	60	1.10
934238--934277	18	2.2	18	86	4	53	30	2	0	67	1.04
934274--934335	28	2.1	29	85	5	81	35	3	0	61	1.12
934263--934377	11	11.3	11	68	24	58	37	3	0	59	1.15
934368--934419	26	2.0	26	81	7	61	40	0	3	55	1.18
934816--934844	14	2.1	14	100	0	58	34	58	0	6	1.25
935128--935206	40	2.0	40	100	0	158	43	31	10	15	1.80
937166--937211	2	23.0	2	95	0	83	50	2	0	47	1.13
937348--937395	24	2.0	24	95	0	87	29	14	29	27	1.95
937635--937710	31	2.5	30	85	6	98	30	11	10	47	1.74
946754--946816	3	21.3	3	96	3	119	31	0	0	68	0.90
947295--947328	13	2.6	13	86	13	52	8	2	44	44	1.50
947375--947440	30	2.2	30	100	0	132	60	0	6	33	1.21
947421--947536	55	2.1	54	82	9	137	43	7	21	27	1.80
947446--947551	55	1.9	55	100	0	212	38	9	23	28	1.86
950941--951177	115	2.1	116	92	0	395	31	24	12	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
954177--954225	26	1.9	25	87	4	71	65	0	4	30	1.11
962036--962250	101	2.1	102	96	1	398	47	6	35	9	1.62
971422--971459	2	19.0	2	100	0	76	50	0	0	50	1.00
971641--971688	25	2.0	25	84	8	64	50	6	2	41	1.39
973847--974201	119	2.9	125	82	7	454	45	18	15	21	1.86
980255--980326	31	2.3	31	78	9	74	38	5	9	45	1.60
982896--982930	18	2.0	17	94	5	61	57	0	0	42	0.99
983737--983771	18	2.0	17	94	5	61	42	0	0	57	0.99
989799--989829	2	15.5	2	93	0	53	48	3	0	48	1.17
991410--991455	17	2.8	17	81	12	60	71	6	0	21	1.08
991406--991461	27	2.1	26	81	15	62	69	8	0	21	1.15
992303--992335	4	8.2	4	93	0	57	48	24	3	24	1.65
1007704--1007789	31	2.9	28	73	11	82	43	0	18	38	1.51
1012299--1012675	95	4.1	92	85	7	464	49	15	6	28	1.70
1012334--1012675	89	3.7	89	89	5	463	49	15	6	28	1.70
1013763--1013793	3	10.3	3	92	0	53	3	67	0	29	1.06
1015375--1015503	66	2.0	65	87	6	181	34	25	13	25	1.93
1015910--1015951	20	2.1	19	86	8	57	42	2	0	54	1.13
1019592--1019664	29	2.4	30	84	6	85	28	8	19	43	1.79
1019620--1019677	29	2.0	29	83	10	73	29	8	13	48	1.73
1020817--1020856	18	2.1	20	86	9	57	72	2	2	22	1.09
1024724--1024769	21	2.2	21	84	7	58	56	4	6	32	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1028168--1028203	2	18.0	2	100	0	72	50	0	0	50	1.00
1028388--1028431	23	2.0	22	86	4	61	25	4	9	61	1.45
1037956--1038019	30	2.1	32	82	8	80	31	10	10	46	1.74
1040014--1040056	21	2.0	21	86	0	59	51	4	2	41	1.35
1040033--1040084	26	2.0	26	92	0	86	48	3	1	46	1.31
1040635--1040665	15	2.0	16	93	6	55	77	0	6	16	0.97
1041158--1041199	8	5.1	8	85	5	57	42	2	0	54	1.13
1043557--1043902	173	2.0	173	95	0	629	31	16	21	30	1.95
1053334--1053412	31	2.6	31	84	6	108	26	16	13	43	1.86
1059820--1059847	6	4.7	6	100	0	56	17	46	17	17	1.85
1062740--1062809	35	2.1	33	84	10	88	35	11	15	37	1.84
1063821--1063856	2	18.0	2	94	0	63	50	2	47	0	1.15
1066063--1066087	8	3.1	8	100	0	50	76	0	0	24	0.80
1066149--1066216	27	2.5	27	82	0	91	26	33	32	7	1.84
1068139--1068177	3	13.3	3	89	5	53	61	0	33	5	1.18
1068140--1068174	11	3.1	11	91	4	52	60	0	34	5	1.21
1068168--1068219	23	2.4	21	80	6	59	65	3	23	7	1.35
1068504--1068536	14	2.4	14	94	0	57	21	0	27	51	1.48
1069068--1069096	15	1.9	15	100	0	58	34	37	0	27	1.57
1078555--1078609	28	1.9	29	88	3	85	29	1	0	69	0.99
1078546--1078616	28	2.4	30	79	9	83	33	1	0	64	1.02
1080649--1080705	4	14.2	4	96	0	96	24	0	28	47	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1084665--1084767	31	3.4	30	75	4	98	40	16	3	38	1.67
1085105--1085134	3	10.0	3	92	0	51	66	30	3	0	1.07
1087750--1087811	28	2.3	28	81	8	76	41	0	0	58	0.98
1089169--1089283	57	2.0	58	86	5	162	47	5	18	28	1.70
1090606--1090636	16	1.9	16	100	0	62	35	6	6	51	1.53
1094926--1094976	25	2.0	25	100	0	102	19	15	3	60	1.50
1097357--1097471	62	1.9	61	82	8	146	25	8	10	55	1.62
1097407--1097468	29	2.2	29	83	11	76	25	8	9	56	1.59
1098785--1098819	19	1.9	17	88	11	52	20	8	11	60	1.57
1098785--1098825	18	2.2	19	83	12	50	21	9	9	58	1.59
1100167--1100199	18	1.9	17	88	11	50	45	0	3	51	1.16
1100711--1100751	19	2.0	21	86	9	59	21	9	31	36	1.86
1103097--1103157	20	2.9	22	83	7	65	70	6	9	13	1.33
1108595--1108624	7	4.3	7	91	0	51	13	0	36	50	1.42
1108417--1108884	96	4.8	102	86	8	623	40	1	18	39	1.60
1108417--1108884	97	4.8	97	89	4	683	40	1	18	39	1.60
1108883--1109173	126	2.3	126	85	3	424	32	17	20	29	1.95
1110063--1110088	7	3.7	7	100	0	52	57	15	0	26	1.38
1114088--1114117	13	2.3	13	94	0	51	36	43	3	16	1.65
1114256--1114314	9	6.4	9	81	11	75	22	10	27	40	1.85
1118351--1118715	162	2.3	162	87	3	522	31	9	28	29	1.89
1118475--1118715	57	4.4	56	74	14	180	30	10	29	29	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1118532--1118750	105	2.1	105	81	3	253	32	11	28	27	1.92
1118554--1118769	105	2.1	105	84	3	274	32	12	28	26	1.93
1125306--1125714	206	2.0	206	96	0	746	32	16	18	33	1.93
1125512--1126166	230	2.9	227	88	2	963	34	15	16	33	1.91
1127109--1127151	2	21.5	2	100	0	86	48	0	0	51	1.00
1137512--1137555	23	2.0	22	86	13	63	45	2	2	50	1.27
1154545--1154745	93	2.2	93	80	3	217	27	18	26	27	1.98
1154664--1154895	75	3.1	75	89	1	313	30	20	27	21	1.98
1161476--1161507	2	16.0	2	100	0	64	50	0	0	50	1.00
1163887--1163935	21	2.4	21	79	3	55	34	26	10	28	1.89
1166049--1166115	29	2.3	29	82	7	82	41	16	7	34	1.76
1166178--1166283	53	2.0	53	100	0	212	35	11	9	43	1.73
1174178--1174205	7	4.0	7	100	0	56	0	0	57	42	0.99
1176126--1176161	4	9.5	4	88	11	58	50	0	0	50	1.00
1176665--1176691	10	2.7	10	100	0	54	29	11	51	7	1.64
1178913--1178945	16	2.0	17	88	5	50	51	0	0	48	1.00
1186638--1186850	26	8.2	24	74	15	133	60	5	7	27	1.46
1186762--1186827	28	2.3	28	89	7	98	59	1	7	31	1.35
1190280--1190315	17	2.1	17	100	0	72	41	16	11	30	1.83
1192546--1192878	97	3.3	105	79	8	379	42	2	15	39	1.59
1193977--1194342	154	2.4	152	83	8	462	53	4	9	32	1.53
1195449--1195514	11	5.5	12	76	8	64	63	0	1	34	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1195432--1195498	18	3.4	18	78	21	73	64	0	1	34	1.03
1204421--1204482	28	2.2	28	100	0	124	46	20	14	17	1.83
1210407--1210449	20	2.2	20	91	0	68	62	0	0	37	0.95
1227829--1227891	31	2.0	31	81	6	74	31	15	12	39	1.85
1231039--1231070	2	16.0	2	100	0	64	50	0	0	50	1.00
1231180--1231211	2	16.0	2	100	0	64	50	0	0	50	1.00
1240635--1240685	24	2.1	24	85	0	66	31	5	19	43	1.75
1244031--1244079	11	4.5	11	97	0	89	42	6	0	51	1.27
1247821--1247869	26	1.9	26	83	4	64	44	0	10	44	1.37
1250712--1250743	2	16.0	2	100	0	64	50	0	0	50	1.00

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