genome.fa.s6.2.7.7.80.10.50.1000.4.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  4  of  109  ( 13028 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)
1136559--1136638	31	2.5	32	80	8	92	48	16	7	27	1.72
1143531--1143624	47	2.0	47	97	0	179	37	12	11	38	1.80
1147100--1147581	246	2.0	246	100	0	964	26	23	19	30	1.98
1150091--1150127	18	2.1	18	100	0	74	35	27	16	21	1.94
1158521--1158547	6	4.5	6	100	0	54	0	14	0	85	0.61
1158600--1158677	19	3.9	20	75	17	81	35	0	2	61	1.10
1158598--1158685	41	2.1	42	95	4	162	36	0	2	61	1.09
1158637--1158691	25	2.2	25	77	6	58	41	0	1	56	1.10
1178331--1178398	26	2.6	26	97	2	127	29	8	23	38	1.85
1180390--1180446	28	2.0	28	96	0	105	22	12	17	47	1.81
1187186--1187213	10	2.8	10	100	0	56	82	10	7	0	0.85
1187660--1187706	4	11.8	4	86	0	58	44	25	4	25	1.72
1191218--1191406	94	2.0	95	96	1	353	43	17	16	22	1.88
1191642--1191671	2	15.0	2	100	0	60	50	0	0	50	1.00
1207723--1207752	13	2.3	13	94	0	51	46	16	16	20	1.84
1209294--1209326	17	1.9	17	88	11	50	45	0	0	54	0.99
1214814--1214850	9	4.1	9	85	0	56	29	8	13	48	1.71
1214904--1214934	9	3.4	9	90	0	53	38	22	12	25	1.90
1216931--1216955	10	2.5	10	100	0	50	80	0	12	8	0.92
1223789--1223853	32	2.0	32	96	0	121	16	9	21	52	1.72
1224761--1224788	2	14.0	2	100	0	56	50	0	0	50	1.00
1224791--1224928	67	2.0	68	98	1	269	19	18	18	43	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1226847--1226901	20	2.8	20	70	26	53	56	1	7	34	1.38
1230631--1230672	18	2.3	19	84	12	52	45	14	4	35	1.66
1238259--1238318	27	2.2	27	79	5	68	16	31	25	26	1.96
1238342--1238378	16	2.3	16	90	9	58	64	8	0	27	1.21
1238355--1238606	99	2.5	102	85	6	314	57	13	0	27	1.42
1238593--1238636	12	3.7	12	82	8	54	65	13	0	20	1.26
1246692--1247040	173	2.0	174	98	1	673	39	16	6	36	1.76
1248171--1248280	54	2.0	54	94	0	193	40	24	12	21	1.88
1249734--1249870	68	2.0	68	98	0	265	39	8	27	24	1.85
1250371--1250450	27	3.2	24	76	11	79	18	28	20	32	1.96
1250478--1250549	24	3.0	24	78	11	76	20	26	20	31	1.98
1256193--1256226	17	2.0	17	88	0	50	44	14	0	41	1.45
1259038--1259094	30	1.9	28	82	10	69	21	33	31	14	1.92
1259643--1259682	11	3.5	11	86	3	53	75	2	2	20	1.04
1262790--1262830	22	2.0	21	86	13	59	2	14	24	58	1.49
1269134--1269189	22	2.6	22	81	10	62	50	5	1	42	1.35
1269667--1269712	24	2.0	23	83	8	58	65	4	6	23	1.35
1270937--1270962	2	13.0	2	100	0	52	50	0	0	50	1.00
1278735--1279525	50	15.8	50	75	3	633	24	22	22	30	1.99
1278743--1279589	100	8.5	100	90	0	1246	25	22	22	30	1.99
1279722--1279762	16	2.7	15	85	7	64	31	2	21	43	1.66
1280506--1280532	13	2.1	13	100	0	54	7	7	0	85	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1280972--1281017	5	9.4	5	86	13	60	0	4	15	80	0.86
1283730--1283782	24	2.2	25	86	3	72	47	7	18	26	1.75
1291039--1291199	25	6.6	25	81	5	177	35	19	26	18	1.95
1291039--1291199	74	2.2	73	85	3	216	35	19	26	18	1.95
1301987--1302026	19	2.1	19	95	0	71	50	10	12	27	1.72
1302339--1302373	15	2.4	15	90	4	54	48	0	8	42	1.33
1302368--1302411	18	2.4	18	85	7	54	34	0	6	59	1.24
1302396--1302425	10	3.0	10	100	0	60	30	0	0	70	0.88
1305167--1305197	3	10.3	3	100	0	62	32	0	0	67	0.91
1311330--1311469	69	2.0	69	100	0	280	44	7	22	25	1.78
1331118--1331179	24	2.6	24	94	0	106	37	6	25	30	1.81
1336450--1336503	26	2.1	26	96	0	99	35	7	18	38	1.79
1349551--1349576	13	2.0	13	100	0	52	38	23	15	23	1.92
1350680--1350724	11	3.8	12	80	13	58	31	0	2	66	1.04
1355315--1355363	17	2.8	19	79	17	61	71	2	2	24	1.07
1356794--1357050	51	5.3	49	73	17	236	30	16	18	34	1.93
1356823--1357220	45	8.6	45	76	12	301	29	20	16	34	1.94
1356763--1357185	95	4.5	92	83	5	435	29	19	16	34	1.94
1356725--1357215	95	5.3	91	80	7	406	28	20	15	34	1.94
1364576--1365063	256	1.9	253	92	5	824	59	9	11	20	1.58
1370044--1370073	2	14.5	2	93	6	51	46	0	3	50	1.18
1384610--1384642	17	1.9	17	100	0	66	48	27	12	12	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1391681--1391711	2	15.0	2	93	6	53	48	3	0	48	1.17
1392694--1392726	2	16.0	2	93	6	57	48	3	0	48	1.17
1393239--1393265	13	2.1	13	100	0	54	48	0	7	44	1.31
1398021--1398053	2	16.0	2	93	6	57	48	3	0	48	1.17
1398156--1398190	17	2.0	18	88	5	54	54	0	5	40	1.24
1398028--1398306	132	2.1	134	95	2	517	45	4	15	33	1.67
1398698--1398724	13	2.1	13	100	0	54	48	0	7	44	1.31
1399582--1399705	59	2.1	60	93	3	223	50	13	7	29	1.69
1403908--1403936	2	14.5	2	100	0	58	48	0	0	51	1.00
1405541--1405567	3	9.0	3	100	0	54	66	0	33	0	0.92
1405765--1405844	14	5.8	14	76	12	85	18	40	30	11	1.86
1405749--1405877	56	2.2	58	86	9	183	20	40	28	10	1.85
1405752--1405844	28	3.3	28	100	0	186	18	39	29	12	1.88
1405925--1405976	14	3.9	14	80	10	63	80	0	19	0	0.71
1405926--1406037	28	3.9	28	78	14	122	77	0	21	0	0.82
1405948--1406037	10	9.1	10	80	4	76	78	0	20	1	0.81
1405927--1406027	38	2.7	38	86	6	125	79	0	20	0	0.74
1405925--1406038	18	6.6	17	75	19	87	77	0	21	0	0.83
1406339--1406363	13	1.9	13	100	0	50	48	0	12	40	1.40
1411298--1411330	2	17.0	2	93	6	59	48	0	0	51	1.00
1411916--1411944	2	14.5	2	100	0	58	51	0	0	48	1.00
1425075--1425110	14	2.6	14	95	0	63	19	44	5	30	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1433399--1433431	16	2.0	17	88	5	50	63	0	12	24	1.28
1433739--1433847	19	5.7	19	88	0	164	37	13	11	37	1.81
1433975--1434339	182	2.0	183	99	0	723	38	11	12	37	1.80
1440790--1440835	20	2.2	21	96	3	85	34	10	8	45	1.70
1440882--1440942	27	2.3	27	97	0	113	40	8	0	50	1.32
1441012--1441076	27	2.4	27	89	0	94	29	20	32	18	1.96
1447992--1448061	22	3.2	21	69	26	56	38	11	1	48	1.48
1448705--1448743	14	2.8	14	100	0	78	56	7	7	28	1.55
1449584--1449610	11	2.5	11	100	0	54	44	7	18	29	1.77
1453158--1453259	52	2.0	52	86	5	145	30	10	22	36	1.88
1453966--1453996	6	5.0	6	92	7	53	19	16	16	48	1.81
1455432--1455478	20	2.3	20	96	0	85	46	12	10	29	1.76
1455462--1455499	14	2.7	14	88	8	51	39	15	5	39	1.70
1456306--1456333	9	3.1	9	100	0	56	57	10	0	32	1.33
1456276--1456413	68	2.1	66	94	2	240	44	8	5	41	1.57
1456406--1456447	16	2.6	16	92	0	66	42	4	2	50	1.36
1462627--1462670	23	1.9	23	85	0	61	45	2	9	43	1.48
1471839--1471878	9	4.4	9	84	12	55	40	22	10	27	1.86
1473875--1473907	17	2.0	17	88	5	50	48	0	0	51	1.00
1474492--1474522	16	1.9	16	93	0	53	48	0	0	51	1.00
1475578--1475622	21	2.1	22	83	4	56	35	8	13	42	1.75
1487623--1487908	142	2.0	143	97	1	538	38	13	13	34	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1488541--1488592	17	3.0	17	77	2	59	50	11	0	38	1.39
1490611--1490788	51	3.6	50	74	11	163	36	13	19	30	1.90
1490643--1490830	44	4.1	43	73	11	142	35	14	18	30	1.91
1490611--1490830	95	2.3	95	84	3	291	36	14	19	29	1.92
1491347--1491410	26	2.4	26	80	10	76	35	6	1	56	1.34
1491453--1491504	17	3.0	17	77	2	59	50	11	0	38	1.39
1492595--1492678	30	2.8	31	87	5	127	25	22	7	45	1.77
1492595--1492671	15	5.1	15	65	12	50	25	20	7	45	1.78
1494794--1494837	23	1.9	24	90	9	74	54	0	20	25	1.45
1496150--1496202	2	26.5	2	100	0	106	0	0	49	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