genome.fa.s13.2.7.7.80.10.50.1000.3.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  3  of  199  ( 23770 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)
963913--963944	2	16.0	2	100	0	64	50	0	0	50	1.00
977358--978062	142	5.0	141	89	2	1049	43	16	14	25	1.86
977359--978062	281	2.5	279	89	4	1108	43	16	14	25	1.86
978117--978143	10	2.7	10	100	0	54	37	33	18	11	1.86
979020--979085	29	2.3	28	82	15	73	59	3	1	36	1.22
1009737--1009775	7	5.4	7	96	3	69	58	0	0	41	0.98
1011188--1011249	25	2.5	25	79	7	65	70	0	1	27	0.96
1012127--1012178	27	1.9	27	96	0	95	34	7	23	34	1.83
1012337--1012409	36	2.0	36	94	0	128	39	9	12	38	1.76
1018444--1018495	14	3.7	14	78	0	59	61	9	21	7	1.51
1022127--1022176	26	1.9	26	100	0	100	56	0	12	32	1.36
1022135--1022190	14	4.1	14	72	9	62	62	0	5	32	1.18
1027264--1027349	35	2.5	35	81	9	106	45	0	4	50	1.22
1027291--1027351	24	2.5	23	80	15	61	45	0	4	49	1.23
1052529--1052566	20	1.9	20	88	0	58	44	0	0	55	0.99
1056841--1056887	15	3.1	16	72	9	53	55	4	19	21	1.60
1058957--1059102	51	2.8	50	77	12	136	39	6	17	36	1.74
1060028--1060073	24	1.9	24	91	8	76	36	0	2	60	1.09
1060170--1060197	9	3.1	9	100	0	56	57	10	0	32	1.33
1060140--1060349	68	3.1	68	97	1	388	45	9	4	40	1.57
1060238--1060265	9	3.1	9	100	0	56	57	10	0	32	1.33
1060338--1060379	16	2.6	16	92	0	66	42	7	2	47	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1060353--1060414	23	2.7	23	82	2	72	48	1	1	48	1.21
1070286--1070325	2	20.0	2	100	0	80	50	0	0	50	1.00
1080565--1080599	2	17.5	2	100	0	70	48	0	0	51	1.00
1083209--1083235	6	4.5	6	100	0	54	85	0	0	14	0.61
1083717--1083774	26	2.3	26	81	3	73	36	13	1	48	1.53
1090028--1090319	98	3.0	98	82	2	361	33	11	11	43	1.77
1090520--1090565	22	2.0	23	83	4	58	47	4	8	39	1.54
1099300--1099336	17	2.1	19	90	10	60	48	10	2	37	1.52
1107599--1107658	25	2.4	25	86	8	79	23	5	6	65	1.37
1108113--1108162	23	2.0	25	85	11	68	50	2	0	48	1.12
1110919--1111008	43	2.1	44	95	2	164	30	13	27	28	1.94
1112316--1112340	2	12.5	2	100	0	50	52	0	0	48	1.00
1115533--1115558	2	13.0	2	100	0	52	50	0	0	50	1.00
1117916--1117958	22	2.0	22	90	0	68	11	11	18	58	1.63
1125327--1125360	17	2.0	17	88	0	50	79	0	14	5	0.91
1127736--1127774	18	2.2	18	86	9	53	23	0	17	58	1.38
1128719--1128759	7	5.9	7	100	0	82	26	0	0	73	0.84
1142141--1142184	23	1.9	23	95	0	79	54	11	13	20	1.69
1144200--1144279	31	2.6	30	86	5	99	32	3	13	50	1.60
1144221--1144279	29	2.0	29	90	3	91	30	3	13	52	1.57
1149872--1150249	19	18.3	19	66	26	134	30	0	12	55	1.41
1149990--1150053	8	7.2	8	74	19	56	28	1	14	56	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1149976--1150075	27	4.0	27	74	19	99	32	2	13	53	1.51
1149976--1150089	46	2.5	46	94	0	192	32	1	13	52	1.50
1150049--1150398	80	4.3	80	90	5	556	30	0	11	57	1.34
1150223--1150513	88	3.3	87	79	10	290	29	0	12	58	1.34
1150314--1150419	34	3.3	32	69	17	96	32	0	10	57	1.32
1150350--1150446	27	3.3	27	67	18	77	27	0	12	59	1.33
1150448--1150649	8	23.1	8	70	21	113	30	0	13	55	1.38
1150438--1150686	19	13.2	19	72	20	134	30	0	14	55	1.39
1150438--1150649	27	8.0	27	89	4	342	30	0	13	56	1.38
1150910--1150946	16	2.4	16	86	13	51	32	2	8	56	1.43
1151255--1151279	13	1.9	13	100	0	50	32	8	12	48	1.69
1157966--1158005	19	2.1	19	86	9	55	40	0	0	60	0.97
1158474--1158541	34	2.0	34	100	0	136	26	11	5	55	1.58
1158474--1158525	16	3.1	17	72	10	61	25	13	7	53	1.65
1158862--1158887	6	4.3	6	100	0	52	0	0	15	84	0.62
1158887--1158918	2	16.0	2	93	0	55	46	0	0	53	1.00
1159024--1159083	31	1.9	31	83	6	77	31	13	10	45	1.76
1160211--1160325	60	1.9	60	85	0	158	36	13	18	31	1.90
1160862--1161250	61	6.4	61	88	1	539	30	9	17	42	1.81
1160862--1161250	31	12.7	31	87	3	504	30	9	17	42	1.81
1160862--1161250	92	4.2	92	89	1	552	30	9	17	42	1.81
1162594--1162630	19	1.9	19	89	10	58	51	2	0	45	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1162641--1162682	20	2.2	19	86	4	57	42	0	9	47	1.36
1174454--1174512	17	3.3	18	76	23	52	33	0	1	64	1.04
1174454--1174512	9	6.6	9	73	21	52	33	0	1	64	1.04
1177675--1177741	31	2.2	31	83	5	82	31	17	25	25	1.97
1177725--1177890	88	1.9	88	79	9	187	34	20	23	21	1.96
1180158--1180204	2	23.5	2	95	0	85	48	2	0	48	1.13
1197522--1197569	9	5.3	9	75	9	53	29	0	0	70	0.87
1197520--1197584	27	2.4	27	94	0	112	35	1	0	63	1.04
1204148--1204235	30	2.9	31	70	10	81	20	7	18	53	1.69
1204333--1204482	58	2.6	57	77	11	148	45	15	16	22	1.85
1208290--1208319	14	2.1	14	100	0	60	43	13	0	43	1.43
1212081--1212130	26	2.0	25	84	4	64	56	2	20	22	1.53
1217100--1217134	17	2.1	17	89	10	54	71	2	0	25	1.00
1219975--1220039	2	34.5	2	85	11	93	46	0	53	0	1.00
1223261--1223324	6	10.7	6	100	0	128	15	0	0	84	0.63
1223249--1223324	6	12.5	6	95	2	53	13	2	0	84	0.73
1223691--1223764	31	2.4	31	84	6	89	43	8	18	29	1.79
1227001--1227036	7	5.0	7	86	6	54	69	0	11	19	1.18
1226998--1227035	11	3.5	11	79	13	51	71	0	7	21	1.11
1229477--1229502	11	2.4	11	100	0	52	46	11	34	7	1.69
1229653--1229701	24	2.0	24	100	0	98	51	16	20	12	1.76
1234358--1234417	24	2.4	26	78	18	65	48	3	0	48	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1241291--1241339	2	24.5	2	91	0	80	46	0	4	48	1.20
1243324--1243360	6	5.8	6	90	9	56	81	2	0	16	0.81
1243324--1243360	19	1.9	19	94	0	65	81	2	0	16	0.81
1243324--1243360	13	2.9	12	92	8	56	81	2	0	16	0.81
1245575--1245628	28	2.0	27	82	10	65	64	7	14	12	1.47
1252345--1252379	14	2.4	15	90	4	54	34	2	0	62	1.10
1254298--1254358	29	2.1	28	87	3	86	60	4	3	31	1.34
1254366--1254421	23	2.3	24	88	11	80	57	0	1	41	1.09
1259936--1260029	47	2.0	47	97	0	179	40	11	8	39	1.72
1261154--1261187	16	2.1	16	100	0	68	35	23	5	35	1.79
1261157--1261197	16	2.5	16	88	4	55	29	19	4	46	1.71
1265710--1265762	9	5.8	9	80	4	61	35	1	41	20	1.64
1265923--1265994	29	2.5	28	80	6	72	37	19	11	31	1.87
1265941--1266001	29	2.1	29	81	6	70	39	19	13	27	1.89
1266422--1266461	22	1.9	22	85	10	57	42	7	7	42	1.61
1270898--1270964	30	2.2	31	84	7	84	38	10	10	40	1.74
1273417--1273453	9	4.1	9	92	0	65	45	13	10	29	1.77
1273489--1273531	21	2.0	21	82	8	52	20	41	0	37	1.53
1273508--1273568	29	2.1	29	84	6	79	21	54	0	24	1.45
1275263--1275298	12	2.9	12	91	4	54	27	2	0	69	1.02
1282912--1283102	44	4.1	47	84	15	254	26	25	17	31	1.97
1288305--1288406	31	3.3	30	76	5	105	34	18	21	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1292269--1292306	13	2.9	13	77	14	51	31	5	26	36	1.79
1293927--1293983	30	1.9	30	82	10	73	26	10	15	47	1.78
1302655--1302690	2	18.0	2	100	0	72	50	0	0	50	1.00
1303674--1303715	21	2.0	21	100	0	84	52	23	4	19	1.65
1304961--1305040	26	3.2	24	75	10	70	63	2	1	32	1.15
1304979--1305045	26	2.6	27	83	9	86	64	1	0	34	1.03
1308837--1308894	18	3.4	18	76	6	59	44	3	0	51	1.18
1311903--1311928	12	2.2	12	100	0	52	15	0	0	84	0.62
1312579--1312608	3	9.7	3	92	7	51	30	0	0	70	0.88
1312712--1312758	4	11.8	4	91	8	78	23	0	0	76	0.78

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