genome.fa.s3.2.7.7.80.10.50.1000.4.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  4  of  150  ( 17918 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)
1075943--1076018	27	2.8	27	87	0	98	19	27	36	15	1.93
1075940--1076029	27	3.3	27	83	4	92	17	27	36	17	1.93
1081386--1081435	12	4.2	12	84	0	55	16	46	2	36	1.58
1081389--1081429	15	2.7	15	84	0	55	17	43	2	36	1.62
1081781--1081817	15	2.5	15	86	0	56	16	40	0	43	1.48
1083161--1083213	26	2.2	24	90	10	81	43	5	0	50	1.25
1083278--1083344	27	2.5	27	92	0	107	28	26	28	16	1.97
1083389--1083447	23	2.6	24	83	5	70	71	0	28	0	0.87
1083434--1083486	16	3.3	16	76	7	63	66	1	32	0	1.03
1083395--1083512	38	3.2	39	83	10	151	68	0	30	0	0.95
1083519--1083555	18	2.1	19	90	10	60	35	0	0	64	0.94
1084127--1084258	65	2.1	65	88	5	200	46	9	4	40	1.56
1084237--1084299	27	2.4	27	94	2	110	44	11	0	44	1.39
1084338--1084400	27	2.3	27	91	0	99	25	23	36	14	1.93
1084772--1084801	16	1.9	15	93	6	51	70	0	0	30	0.88
1087621--1087650	16	1.9	15	93	6	51	26	3	0	70	1.03
1088017--1088077	27	2.3	27	88	0	86	16	37	21	24	1.93
1088117--1088181	28	2.4	28	86	2	87	41	0	10	47	1.38
1088920--1089017	3	34.3	3	69	15	57	0	32	0	67	0.91
1088896--1089088	41	4.8	40	79	14	188	0	31	0	68	0.90
1088953--1089099	5	29.6	5	71	19	53	0	31	0	68	0.90
1088951--1089095	63	2.4	62	77	10	147	0	31	0	68	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1088888--1089071	82	2.2	81	89	3	269	0	30	0	69	0.89
1088955--1089094	36	3.8	37	76	18	114	0	31	0	68	0.90
1088905--1089082	85	2.2	83	84	10	235	0	33	0	66	0.92
1088888--1089098	82	2.6	81	79	14	242	0	31	0	68	0.90
1089497--1089528	2	16.5	2	93	6	57	46	0	0	53	1.00
1095414--1095457	20	2.3	20	88	7	65	45	9	0	45	1.35
1102642--1102691	26	1.9	26	84	8	66	32	8	2	58	1.39
1104467--1104532	31	2.1	31	86	10	91	42	9	12	36	1.74
1114164--1114477	159	2.0	158	86	3	436	21	26	25	26	2.00
1121487--1121790	156	2.0	153	83	5	382	27	23	26	22	2.00
1121792--1121827	12	3.0	12	95	0	63	8	19	50	22	1.74
1126518--1126552	17	2.0	18	88	5	54	68	11	8	11	1.39
1130281--1130466	83	2.4	72	86	12	237	40	22	15	21	1.91
1132910--1132955	24	1.9	24	82	8	58	73	0	19	6	1.04
1134817--1134847	2	15.5	2	100	0	62	48	0	0	51	1.00
1137552--1137607	19	2.8	20	78	10	53	50	1	1	46	1.22
1150406--1150440	2	17.5	2	100	0	70	51	0	0	48	1.00
1155050--1155075	10	2.6	10	100	0	52	30	0	19	50	1.48
1164323--1164377	27	2.0	28	89	3	85	50	5	10	32	1.60
1169856--1169884	14	2.0	15	93	6	51	68	6	0	24	1.13
1169849--1169918	22	3.2	20	72	20	52	67	7	2	22	1.29
1170339--1170386	21	2.3	21	100	0	96	10	12	12	64	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1181619--1182406	263	3.0	262	88	4	1188	24	17	18	39	1.92
1181896--1182395	254	2.0	250	91	1	804	24	18	18	40	1.91
1191073--1191212	70	2.0	70	100	0	280	24	25	21	28	1.99
1191300--1192494	263	4.6	262	89	3	1843	25	17	18	38	1.92
1191307--1192494	523	2.3	524	92	1	1956	25	17	18	38	1.92
1197387--1197465	39	2.0	39	100	0	158	39	22	20	17	1.92
1198189--1198292	51	2.0	51	86	0	145	40	17	19	23	1.91
1198090--1198292	45	4.4	46	73	9	162	39	18	20	21	1.92
1201258--1201419	73	2.2	73	87	2	236	26	7	3	62	1.39
1201623--1201671	12	3.9	12	78	7	53	20	6	0	73	1.04
1202030--1202095	32	2.1	32	94	0	114	25	22	13	37	1.91
1205454--1205493	5	8.0	5	100	0	80	60	0	0	40	0.97
1206108--1206172	33	2.0	32	85	11	87	52	0	13	33	1.41
1206813--1206923	23	5.1	21	75	9	107	20	19	20	38	1.93
1209548--1209584	9	4.1	9	89	0	56	48	13	8	29	1.71
1209939--1209999	17	3.4	18	78	15	72	22	26	0	50	1.49
1210612--1210639	5	5.6	5	100	0	56	21	17	21	39	1.93
1211305--1211401	23	4.2	23	87	0	140	32	23	21	21	1.98
1217681--1217746	32	2.1	32	82	5	80	36	12	9	42	1.74
1220894--1221075	9	19.2	9	66	16	57	32	4	2	60	1.31
1220986--1221065	18	4.4	17	77	12	70	33	3	2	60	1.28
1220965--1221035	18	3.9	17	80	12	72	32	5	1	60	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1220987--1221044	19	3.1	18	78	11	55	32	3	1	62	1.22
1220958--1221044	37	2.3	38	77	14	101	34	4	1	59	1.25
1221385--1221483	46	2.2	45	87	5	137	15	4	21	59	1.52
1225310--1225337	13	2.2	13	100	0	56	64	0	14	21	1.29
1230637--1230669	8	4.1	8	85	14	50	45	0	0	54	0.99
1233793--1234095	164	1.8	164	89	0	471	29	17	14	37	1.90
1234623--1234653	16	1.9	16	93	0	53	74	3	0	22	0.96
1240173--1240482	77	4.0	77	91	1	487	30	7	22	39	1.81
1245857--1245885	2	15.0	2	92	7	51	51	0	0	48	1.00
1247798--1247841	23	1.9	23	86	9	63	45	18	11	25	1.82
1248357--1248403	24	1.9	25	82	4	60	19	4	12	63	1.44
1257203--1257300	3	32.7	3	84	8	128	64	2	1	32	1.12
1258624--1259384	100	7.6	100	92	1	1215	25	23	20	30	1.98
1259622--1259947	44	7.3	44	77	6	327	28	25	14	31	1.94
1259648--1259971	45	7.3	44	75	4	310	29	24	15	30	1.96
1259622--1259971	89	3.9	89	89	1	506	29	25	15	30	1.95
1263838--1263924	39	2.2	39	100	0	174	45	14	8	31	1.74
1270208--1270384	85	2.1	84	87	2	266	32	7	34	25	1.84
1273577--1273612	2	18.5	2	94	5	65	52	0	0	47	1.00
1273592--1273637	24	1.9	24	81	0	56	54	0	8	36	1.32
1273711--1273740	2	15.0	2	100	0	60	50	0	0	50	1.00
1275415--1275627	44	4.8	44	68	2	122	27	24	17	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1275356--1276149	132	6.0	132	83	4	960	26	24	19	29	1.99
1275443--1275642	44	4.5	44	66	7	136	26	26	19	28	1.98
1275356--1276161	265	3.0	265	87	3	1090	26	24	19	29	1.99
1275355--1276148	397	2.0	397	85	4	1077	26	24	19	29	1.99
1275966--1276446	220	2.2	220	93	0	809	24	24	22	28	2.00
1277673--1277709	19	1.9	20	94	5	67	13	13	0	72	1.11
1282579--1282603	2	12.5	2	100	0	50	52	0	0	48	1.00
1285382--1285414	15	2.2	15	100	0	66	54	12	6	27	1.60
1302369--1302500	62	2.1	62	80	5	142	21	20	29	28	1.98
1309821--1309877	27	2.2	25	87	9	80	54	17	8	19	1.68
1313359--1313450	31	3.0	31	75	9	80	25	8	15	51	1.71
1314491--1314519	14	2.0	15	93	6	51	27	3	0	68	1.05
1316794--1316862	29	2.3	30	75	7	70	42	15	8	33	1.78
1321374--1321439	29	2.4	27	78	16	73	34	13	4	46	1.64
1326871--1326915	9	5.1	9	84	10	58	75	2	2	20	1.01
1326871--1326915	17	2.6	17	80	16	56	75	2	2	20	1.01
1331808--1331836	15	2.0	15	93	6	51	62	0	37	0	0.96
1331880--1331912	5	6.6	5	92	0	57	75	0	24	0	0.80
1339283--1339317	14	2.5	14	100	0	70	42	0	28	28	1.56
1341513--1341583	26	2.7	27	84	4	99	36	22	26	14	1.92
1342863--1342893	14	2.2	14	94	0	53	48	12	0	38	1.42
1344604--1344645	5	9.2	5	89	10	56	0	21	0	78	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1344604--1344645	9	4.6	10	85	14	56	0	21	0	78	0.75
1345617--1345677	6	10.5	6	89	3	90	80	3	0	16	0.84
1349883--1349953	36	2.0	36	85	0	97	42	19	7	30	1.78
1354586--1354616	14	2.2	14	94	0	53	48	12	0	38	1.42
1362150--1362217	26	2.6	27	78	2	75	39	22	23	14	1.91
1366427--1366455	15	1.9	15	100	0	58	37	0	0	62	0.96
1366925--1366949	2	12.5	2	100	0	50	52	0	0	48	1.00
1376169--1376299	67	2.0	66	84	4	174	46	6	13	33	1.68
1381950--1381995	17	2.6	18	82	6	58	76	2	0	21	0.90
1381950--1382001	19	2.8	20	75	19	58	75	1	0	23	0.91

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