genome.fa.s5.2.7.7.80.10.50.1000.3.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   199   200   201   202   203   204   205   206   207   208   

This is table  3  of  208  ( 24913 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)
905312--905351	14	2.9	14	84	0	53	32	7	17	42	1.77
905320--905386	35	1.9	35	87	3	100	31	10	13	44	1.77
905335--905374	20	2.0	20	85	0	53	27	12	12	47	1.77
908085--908133	24	2.0	24	100	0	98	34	4	48	12	1.59
909050--909088	18	2.2	17	86	13	53	33	0	20	46	1.51
909314--909388	23	3.3	23	92	0	123	21	21	24	33	1.97
910687--910783	40	2.5	39	77	6	108	24	17	27	29	1.97
932950--933011	29	2.2	29	94	2	108	48	0	4	46	1.23
934051--934087	19	1.9	19	88	0	56	67	0	2	29	1.04
934435--934503	31	2.2	30	80	10	77	46	4	13	36	1.62
946805--946850	15	2.8	16	83	12	58	58	0	0	41	0.98
946804--946850	17	2.8	17	84	15	71	57	0	0	42	0.98
949555--949638	44	1.9	44	82	0	105	16	15	28	39	1.89
952247--952946	236	3.0	236	90	3	1039	33	17	18	30	1.94
957299--957337	18	2.0	20	85	9	55	43	0	0	56	0.99
957337--957401	29	2.1	32	83	8	82	35	4	0	60	1.18
959855--959924	14	5.1	14	89	3	99	47	8	7	37	1.62
959862--959929	27	2.5	27	85	4	84	51	8	7	32	1.61
959853--959929	13	5.8	13	83	7	84	49	7	7	35	1.61
959853--959929	40	1.9	39	92	2	127	49	7	7	35	1.61
961626--961762	49	2.7	51	88	4	190	29	12	28	29	1.93
963006--963075	28	2.4	28	81	9	79	57	1	2	38	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
962976--963068	40	2.5	37	87	8	134	55	1	4	38	1.26
965397--965868	236	2.0	236	86	2	653	33	15	19	30	1.93
968631--968666	18	2.0	18	89	10	56	36	0	0	63	0.94
970228--970924	236	3.0	233	90	2	1052	35	16	17	31	1.92
973314--973417	51	2.0	51	92	3	174	43	20	18	18	1.89
974809--974858	9	5.6	9	75	15	50	52	2	0	46	1.12
978903--978947	18	2.5	18	85	0	63	40	48	11	0	1.39
978904--978944	14	2.9	14	85	0	55	36	51	12	0	1.40
980846--980893	24	2.0	25	92	8	82	29	29	14	27	1.95
985442--985479	6	6.3	6	100	0	76	50	18	0	31	1.47
1004895--1004939	19	2.3	20	77	11	58	62	0	2	35	1.08
1004897--1004946	19	2.6	19	81	6	57	62	0	2	36	1.07
1004915--1005027	38	3.0	38	75	6	104	60	1	2	35	1.21
1010324--1010398	23	3.3	23	90	3	116	17	21	29	32	1.96
1011417--1011442	2	13.0	2	100	0	52	50	0	0	50	1.00
1014439--1014482	18	2.6	16	80	16	52	38	2	0	59	1.10
1014558--1014598	17	2.5	16	92	4	64	63	4	0	31	1.15
1014575--1014622	22	2.1	23	85	11	64	62	4	2	31	1.26
1023333--1023407	10	7.6	10	79	7	73	30	1	1	66	1.08
1023405--1023451	19	2.4	21	82	13	64	25	8	0	65	1.20
1023576--1023635	9	6.7	9	77	7	59	26	0	5	68	1.10
1023588--1023645	28	2.1	27	81	9	64	36	0	3	60	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1033618--1033649	3	10.7	3	93	0	55	31	3	0	65	1.08
1036997--1037036	14	2.9	14	84	0	53	32	7	17	42	1.77
1037005--1037071	35	1.9	35	87	3	100	31	10	13	44	1.77
1037020--1037059	20	2.0	20	85	0	53	27	12	12	47	1.77
1038416--1038485	27	2.6	27	80	8	79	50	21	2	25	1.63
1042985--1043038	6	9.0	6	79	0	63	64	22	12	0	1.27
1042985--1043038	24	2.2	24	96	0	99	64	22	12	0	1.27
1045443--1045468	1	26.0	1	100	0	52	100	0	0	0	0.00
1050580--1050629	21	2.4	22	80	6	59	42	2	0	56	1.11
1050993--1051021	12	2.5	12	94	5	51	48	0	0	51	1.00
1054749--1054800	21	2.5	21	84	3	70	26	19	1	51	1.57
1067569--1068592	518	2.0	517	95	1	1829	24	13	16	46	1.82
1071371--1071404	14	2.5	14	95	4	61	14	0	35	50	1.44
1071531--1071580	24	2.0	25	88	3	75	62	6	6	26	1.42
1073338--1073362	13	1.9	13	100	0	50	24	24	16	36	1.94
1076477--1076527	21	2.4	22	80	3	59	45	0	7	47	1.32
1082798--1082925	7	17.7	7	65	20	50	41	2	3	52	1.33
1082746--1082961	101	2.2	101	94	1	391	44	3	4	47	1.39
1082765--1082925	26	6.2	26	69	18	95	42	1	3	52	1.28
1083239--1083327	46	2.0	46	84	4	119	35	29	3	31	1.74
1083309--1083361	16	3.3	15	82	10	61	24	30	3	41	1.72
1083316--1083362	16	2.9	16	83	0	67	25	31	2	40	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1085425--1085466	18	2.3	18	91	0	66	28	14	21	35	1.92
1085708--1085773	31	2.2	31	97	2	125	31	16	6	45	1.72
1085854--1085901	24	2.0	24	84	8	62	56	4	4	35	1.38
1094319--1094383	32	2.0	32	93	0	112	33	18	12	35	1.88
1104814--1104882	35	2.0	35	83	11	88	44	4	4	46	1.43
1111106--1111140	17	2.0	18	94	5	63	65	0	34	0	0.93
1115823--1115899	31	2.5	32	80	6	86	41	1	6	50	1.36
1116355--1116401	23	2.0	23	100	0	94	34	21	8	36	1.84
1116575--1116878	162	1.9	163	88	2	459	43	15	7	33	1.74
1123983--1124016	2	17.5	2	93	6	61	50	0	0	50	1.00
1127255--1127316	31	2.0	31	90	6	99	45	4	9	40	1.58
1131428--1131502	39	1.9	39	100	0	150	34	18	21	25	1.96
1135340--1135370	15	2.1	15	100	0	62	25	22	0	51	1.48
1142844--1143258	207	2.0	207	100	0	830	32	12	16	38	1.87
1146332--1146373	22	1.9	22	100	0	84	47	0	14	38	1.44
1147362--1147386	13	1.9	13	100	0	50	56	8	12	24	1.62
1156342--1156523	59	3.2	57	81	8	199	35	14	12	37	1.84
1157743--1157792	27	1.9	27	84	15	70	48	0	20	32	1.50
1157739--1157796	25	2.4	23	76	23	57	46	0	18	34	1.50
1166178--1166207	14	2.1	14	100	0	60	20	13	6	60	1.55
1168189--1168758	60	9.6	60	82	4	575	23	18	18	38	1.93
1176761--1176803	16	2.8	15	78	3	50	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1186154--1186187	17	1.9	18	94	5	61	58	0	0	41	0.98
1191817--1191880	29	2.1	31	85	5	87	29	14	9	46	1.75
1192394--1192474	41	2.0	41	95	4	146	34	14	19	30	1.92
1200407--1200845	89	4.8	90	78	7	400	47	18	6	27	1.74
1200490--1200827	182	1.9	181	86	0	487	46	17	7	28	1.75
1202298--1202345	24	2.0	24	87	4	69	33	10	14	41	1.80
1202657--1202710	27	2.0	27	82	7	65	37	9	0	53	1.33
1207927--1208021	44	2.1	44	94	1	163	28	13	9	48	1.74
1211359--1211406	22	2.2	22	85	7	62	58	4	0	37	1.18
1219024--1219089	31	2.1	31	94	0	114	43	10	9	36	1.71
1220431--1220457	2	13.5	2	100	0	54	48	0	0	51	1.00
1233802--1233835	13	2.4	14	90	9	52	20	0	0	79	0.73
1240055--1240088	17	2.0	17	94	0	59	29	14	14	41	1.86
1240982--1241023	21	2.0	21	85	0	57	42	0	16	40	1.48
1241483--1241548	26	2.6	25	79	11	71	16	24	24	34	1.95
1241586--1241644	24	2.5	24	82	0	82	18	28	18	33	1.95
1243825--1243896	36	2.0	36	97	0	135	25	12	29	33	1.92
1246087--1246112	11	2.4	11	100	0	52	61	0	0	38	0.96
1246789--1246823	18	2.1	18	89	10	56	25	0	0	74	0.82
1250992--1251027	18	2.0	18	88	0	54	50	0	5	44	1.25
1251284--1251390	39	2.8	38	87	5	128	37	2	0	59	1.12
1251293--1251364	27	2.5	28	91	8	110	36	4	0	59	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1251304--1251406	39	2.6	39	90	4	154	36	2	0	60	1.12
1251378--1251426	22	2.2	21	86	10	71	36	0	4	59	1.17
1268443--1268476	17	2.0	17	88	0	50	29	5	8	55	1.54
1291532--1291803	129	2.1	127	82	5	314	33	22	20	23	1.98
1295973--1296008	17	2.1	17	94	0	63	25	0	19	55	1.43
1296721--1296764	21	2.1	21	100	0	88	38	4	9	47	1.56
1301174--1301216	19	2.2	20	88	12	63	25	4	0	69	1.07
1303179--1303249	30	2.4	30	95	0	124	30	16	0	52	1.45
1305349--1305391	17	2.3	20	88	11	65	30	4	0	65	1.13
1312930--1312964	6	5.5	6	87	12	52	65	0	20	14	1.26

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   199   200   201   202   203   204   205   206   207   208