genome.fa.s1.2.7.7.80.10.50.1000.3.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: 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  3  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)
937495--937533	16	2.4	16	100	0	78	30	0	5	64	1.15
938155--938184	15	2.0	15	100	0	60	66	0	0	33	0.92
938505--938760	127	2.0	127	84	4	338	37	14	12	35	1.84
939729--939766	3	12.7	3	100	0	76	65	0	0	34	0.93
940958--940996	7	5.6	7	96	0	69	30	15	0	53	1.42
942298--942356	5	11.8	5	77	13	59	61	3	0	35	1.13
947049--947090	22	1.9	22	85	9	59	66	2	9	21	1.32
953266--953292	6	4.5	6	100	0	54	33	0	29	37	1.58
960190--960224	4	8.8	4	87	0	52	45	28	2	22	1.67
960190--960245	12	4.7	12	79	0	67	39	26	8	25	1.85
963020--963054	15	2.3	15	85	0	52	60	2	5	31	1.35
981415--981450	2	18.0	2	100	0	72	50	0	0	50	1.00
983036--983072	2	18.5	2	100	0	74	48	0	0	51	1.00
986067--986108	22	1.9	22	85	0	57	35	11	28	23	1.91
994700--994729	11	2.7	11	89	0	51	50	0	3	46	1.18
1008883--1008924	18	2.3	18	84	12	50	69	9	0	21	1.17
1008974--1009033	29	2.1	29	93	0	102	53	13	10	23	1.69
1009035--1009097	30	2.1	30	90	0	99	58	14	1	25	1.45
1016576--1016616	20	2.0	20	85	4	55	36	2	7	53	1.42
1035042--1035084	20	2.2	20	84	16	54	25	0	16	58	1.38
1037114--1037145	4	8.0	4	92	0	55	28	0	21	50	1.49
1044535--1044596	28	2.2	28	85	0	79	46	8	11	33	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1047616--1047659	18	2.4	18	84	3	52	9	15	9	65	1.45
1060120--1060174	22	2.5	22	82	8	58	47	3	5	43	1.44
1067552--1067615	32	2.0	32	96	3	121	32	18	3	45	1.65
1085932--1085996	24	2.7	24	76	23	66	43	0	10	46	1.38
1087123--1087165	22	2.1	21	84	16	56	20	16	4	58	1.56
1103169--1103204	11	3.2	11	84	7	54	25	2	0	72	0.98
1103169--1103211	10	4.0	10	80	16	50	30	2	0	67	1.03
1110597--1110624	3	9.3	3	100	0	56	64	0	35	0	0.94
1110794--1110849	30	1.9	28	85	7	76	30	3	5	60	1.36
1113257--1113316	31	1.9	31	86	0	84	35	11	18	35	1.87
1115703--1115779	27	2.9	27	88	3	111	18	24	37	19	1.94
1115936--1115980	22	2.2	20	92	8	72	26	2	0	71	0.98
1116136--1116197	27	2.3	27	97	0	115	14	33	22	29	1.94
1122434--1122542	29	3.8	29	78	0	110	32	22	22	23	1.98
1123494--1123558	23	3.0	22	73	13	62	33	26	23	16	1.96
1124537--1124586	3	16.7	3	85	8	57	58	2	0	40	1.10
1124537--1124587	8	6.1	8	83	2	57	56	1	0	41	1.10
1124545--1124593	24	2.0	25	88	4	73	51	2	0	46	1.12
1125088--1125162	34	2.2	34	85	0	96	24	25	22	28	2.00
1126818--1126856	20	1.9	20	89	5	60	30	17	15	35	1.91
1126813--1126993	21	8.7	20	71	6	94	18	22	18	40	1.91
1126839--1126993	42	3.7	42	86	3	197	17	21	19	41	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1126940--1127008	21	3.3	21	74	8	68	14	24	20	40	1.90
1126837--1127014	84	2.1	84	84	2	232	17	21	19	41	1.90
1127449--1127490	2	21.0	2	100	0	84	50	0	0	50	1.00
1133008--1133049	10	3.7	11	78	15	50	28	0	0	71	0.86
1140004--1140033	3	10.0	3	100	0	60	66	0	33	0	0.92
1144802--1144836	18	1.9	18	100	0	70	40	17	11	31	1.85
1146091--1146135	25	2.0	24	83	16	60	33	4	0	62	1.15
1149253--1149312	30	2.0	30	93	0	102	31	8	11	48	1.69
1150152--1150208	28	2.0	28	86	6	80	31	0	7	61	1.23
1156849--1156894	2	23.0	2	100	0	92	50	0	0	50	1.00
1164776--1164888	60	1.9	60	85	3	156	37	4	12	46	1.62
1170877--1170995	58	2.0	58	82	4	141	26	15	6	51	1.68
1171996--1172028	3	11.0	3	100	0	66	33	0	0	66	0.92
1180262--1180323	22	2.8	22	92	0	97	24	25	14	35	1.93
1181767--1181819	27	2.0	27	85	7	72	22	5	7	64	1.41
1188926--1188959	7	4.9	7	88	0	50	20	0	0	79	0.73
1194842--1194882	16	2.5	16	88	4	55	24	0	19	56	1.42
1200716--1200770	25	2.2	25	87	6	76	47	0	0	52	1.00
1200734--1200766	10	3.3	10	88	12	50	48	0	0	51	1.00
1202848--1202918	27	2.5	28	81	6	81	18	39	5	36	1.74
1202845--1202925	12	6.8	12	75	0	54	17	38	4	39	1.71
1204679--1204707	11	2.6	11	100	0	58	79	0	0	20	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1207897--1207941	18	2.4	19	77	3	56	55	0	2	42	1.12
1207906--1207970	26	2.6	25	90	4	103	60	0	3	36	1.13
1207907--1207970	25	2.6	25	90	5	103	60	0	3	35	1.12
1209033--1209064	15	2.1	15	100	0	64	34	6	6	53	1.51
1214208--1214250	22	2.0	22	85	0	59	58	2	0	39	1.11
1217731--1217844	54	2.1	54	93	1	194	42	6	9	41	1.62
1218059--1218148	47	1.9	47	86	0	126	36	21	10	32	1.86
1220609--1220671	33	2.0	33	87	6	94	36	1	3	58	1.23
1222723--1223020	153	1.9	153	95	1	535	32	17	14	34	1.90
1227067--1227132	31	2.1	31	88	0	96	42	18	10	28	1.83
1228121--1228159	21	1.9	20	89	5	60	53	2	2	41	1.28
1231626--1231664	2	19.5	2	100	0	78	51	0	0	48	1.00
1232894--1232929	10	3.7	10	85	7	56	19	0	0	80	0.71
1238263--1238287	10	2.5	10	100	0	50	28	0	8	64	1.22
1239975--1240073	51	1.9	51	83	4	128	36	15	6	42	1.71
1242575--1242624	24	2.1	23	85	3	64	32	4	2	62	1.25
1260672--1260708	19	1.9	19	89	10	58	70	18	8	2	1.25
1265569--1265620	26	2.0	26	85	7	70	30	0	5	63	1.18
1266865--1266899	18	1.9	18	100	0	70	11	28	0	60	1.32
1269863--1270056	61	3.2	61	71	11	191	43	2	5	48	1.38
1269821--1270087	120	2.2	120	93	0	453	43	1	4	49	1.34
1270031--1270065	18	2.0	17	88	5	52	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1270229--1270319	45	2.0	45	85	2	121	37	28	6	27	1.82
1270300--1270352	16	3.2	16	94	5	97	37	37	0	24	1.56
1271191--1271229	13	2.9	14	88	7	55	38	0	0	61	0.96
1281170--1281599	214	2.0	214	97	0	815	31	19	19	30	1.96
1283603--1283629	8	3.4	8	100	0	54	0	22	22	55	1.44
1301249--1301320	3	24.0	3	100	0	144	33	0	0	66	0.92
1311253--1311298	2	23.0	2	100	0	92	50	0	0	50	1.00
1316247--1316379	11	12.9	11	67	22	67	60	0	2	36	1.09
1316247--1316409	41	4.0	40	92	7	249	60	0	3	36	1.12
1316247--1316410	81	2.1	76	83	16	207	60	0	3	36	1.12
1316352--1316417	30	2.2	30	94	0	114	62	0	4	33	1.16
1319520--1319558	19	2.1	19	100	0	78	35	15	12	35	1.86
1322020--1322077	29	2.0	29	86	0	80	24	15	18	41	1.89
1324003--1324058	29	1.9	29	88	0	85	33	8	21	35	1.85
1324014--1324079	29	2.2	29	83	5	78	36	10	22	30	1.88
1326980--1327070	28	3.1	28	77	13	103	34	3	0	62	1.11
1326980--1327090	31	3.7	31	75	17	101	33	3	0	63	1.12
1327015--1327109	40	2.6	38	82	15	119	36	3	0	60	1.13
1334856--1334884	14	2.1	14	100	0	58	20	6	0	72	1.07
1341618--1341657	20	2.0	20	90	9	64	30	15	20	35	1.93
1341619--1341664	20	2.3	20	85	7	58	30	17	21	30	1.96
1342499--1342543	16	2.6	17	79	6	56	42	2	2	53	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1342499--1342544	17	2.7	18	76	10	60	41	2	2	54	1.25
1350712--1350771	24	2.5	24	82	15	79	30	5	13	51	1.62
1353518--1353584	34	1.9	35	84	3	91	44	13	8	32	1.75
1360949--1360973	13	1.9	13	100	0	50	32	8	0	60	1.26
1361783--1361828	20	2.2	22	88	7	69	23	10	13	52	1.71
1362370--1362432	5	12.8	5	73	21	53	36	0	4	58	1.19
1363585--1363741	25	6.5	24	86	5	194	16	21	21	40	1.91
1365509--1365590	40	2.1	40	88	4	132	63	0	2	34	1.08
1365565--1365596	16	2.0	16	100	0	64	68	0	0	31	0.90
1383288--1383452	81	2.0	81	92	0	276	45	4	12	37	1.63

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