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: chr1
Parameters: 2 7 7 80 10 50 1000
Length:  37323695

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   

This is table  3  of  93  ( 11113 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)
1105559--1105583	5	5.0	5	100	0	50	40	40	0	20	1.52
1108430--1108496	33	2.0	33	94	0	116	25	13	10	50	1.73
1118034--1118058	13	1.9	13	100	0	50	56	8	12	24	1.62
1119713--1119747	18	1.9	18	88	0	52	51	5	37	5	1.50
1129422--1129455	3	11.3	3	87	0	50	32	41	26	0	1.56
1131671--1131699	2	14.5	2	100	0	58	51	0	0	48	1.00
1143697--1143757	32	1.9	32	90	6	97	42	18	8	31	1.79
1147588--1147655	29	2.3	30	89	2	102	42	2	5	48	1.42
1152312--1152402	44	2.1	44	89	0	137	56	1	4	37	1.27
1152777--1152831	21	2.6	20	72	11	56	47	14	5	32	1.67
1158313--1158380	29	2.3	29	82	12	77	55	2	10	30	1.48
1200556--1200602	2	24.0	2	82	4	60	4	51	0	44	1.21
1204103--1204159	24	2.8	19	72	25	53	71	1	1	24	1.04
1229051--1229102	27	2.0	26	85	7	70	34	0	0	65	0.93
1234628--1234654	2	13.5	2	100	0	54	51	0	0	48	1.00
1235395--1235440	23	2.0	23	95	0	83	41	13	13	32	1.82
1241277--1241312	18	2.1	17	89	5	54	47	0	0	52	1.00
1241290--1241342	28	2.0	28	85	7	74	33	0	1	64	1.05
1241301--1241346	20	2.3	21	74	11	51	30	0	2	67	1.03
1241281--1241364	30	2.8	30	70	12	75	40	0	1	58	1.06
1241687--1241879	105	1.8	105	80	8	232	27	21	24	26	1.99
1251420--1251463	22	2.0	22	100	0	88	36	22	18	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1258554--1258582	14	2.0	15	93	6	51	58	0	0	41	0.98
1258553--1258605	23	2.3	23	84	9	65	56	1	1	39	1.21
1264732--1264772	2	21.0	2	90	5	66	53	0	0	46	1.00
1267193--1267237	2	22.5	2	100	0	90	48	0	0	51	1.00
1277513--1277578	25	2.6	25	90	0	96	43	4	0	51	1.22
1278431--1278473	15	2.9	15	77	16	54	51	0	4	44	1.22
1278520--1278573	19	2.8	19	82	2	72	55	0	0	44	0.99
1293122--1293173	15	3.7	15	77	15	65	48	0	0	51	1.00
1293118--1293169	27	2.0	27	88	7	81	48	0	0	51	1.00
1293334--1293386	27	2.0	27	88	0	79	43	1	3	50	1.30
1293396--1293501	38	2.6	38	82	11	106	33	0	1	63	1.12
1293494--1293553	26	2.3	26	88	2	84	50	1	3	45	1.28
1293644--1293696	25	2.1	25	96	0	97	41	0	0	58	0.98
1293631--1293691	32	1.9	31	83	9	79	42	0	1	55	1.09
1293650--1293703	25	2.2	25	89	0	81	46	0	0	53	1.00
1296652--1296816	87	1.9	87	93	0	285	34	18	20	26	1.95
1297255--1297321	16	4.1	15	74	20	55	58	0	0	41	0.98
1297255--1297297	18	2.2	20	80	12	54	62	0	0	37	0.95
1297257--1297304	19	2.6	19	86	3	71	60	0	0	39	0.97
1297658--1297699	16	2.7	15	85	7	66	78	0	2	19	0.86
1298520--1298571	2	26.5	2	96	3	97	51	0	0	48	1.00
1299245--1299415	59	2.9	58	79	9	186	30	12	26	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1315394--1315457	27	2.4	27	82	7	78	39	0	1	59	1.07
1315394--1315468	31	2.6	28	76	14	73	41	0	1	57	1.07
1328617--1328682	27	2.4	27	89	0	105	9	30	18	42	1.81
1329883--1330502	319	2.0	304	85	5	839	36	10	7	45	1.66
1334016--1334101	41	2.1	41	80	8	95	41	19	2	36	1.65
1336776--1336864	36	2.5	36	85	5	117	26	12	16	43	1.84
1339244--1339503	135	1.9	134	96	1	468	35	6	14	43	1.72
1340035--1340072	18	2.1	18	85	9	51	71	0	0	28	0.87
1341985--1342261	35	7.9	35	77	5	220	42	13	7	35	1.73
1342006--1342219	107	2.0	106	84	2	277	44	13	7	34	1.72
1346468--1346520	25	2.1	25	92	0	88	15	24	18	41	1.89
1347158--1347394	122	1.9	123	87	2	352	31	9	3	55	1.50
1350098--1350155	27	2.2	26	81	9	64	43	0	0	56	0.99
1354718--1354758	22	2.0	21	85	9	57	56	4	0	39	1.21
1355389--1355429	22	1.9	22	85	5	57	58	4	19	17	1.56
1360739--1360812	37	2.0	37	84	12	98	32	13	8	45	1.73
1368963--1369014	2	25.5	2	96	3	95	48	0	1	50	1.12
1370751--1370784	16	2.1	16	88	0	50	26	11	14	47	1.79
1378544--1378623	3	26.0	3	76	16	58	27	2	0	70	1.01
1378553--1378634	29	2.9	28	80	14	98	23	2	0	74	0.94
1378544--1378638	32	3.0	31	79	10	102	25	2	0	72	0.95
1378544--1378628	24	3.5	23	76	19	82	25	2	0	71	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1378544--1378638	8	11.6	8	73	20	63	25	2	0	72	0.95
1378544--1378638	50	1.9	49	83	10	122	25	2	0	72	0.95
1379227--1379349	39	3.1	39	83	5	167	8	45	9	35	1.69
1379295--1379350	20	2.9	19	69	10	51	12	44	7	35	1.70
1379580--1379655	4	18.0	4	76	20	50	27	0	0	72	0.85
1379579--1379655	10	7.9	10	71	18	56	27	0	0	72	0.85
1379578--1379654	9	8.4	9	78	13	77	27	0	0	72	0.85
1379578--1379655	23	3.0	24	83	14	86	28	0	0	71	0.86
1382858--1382899	2	21.0	2	100	0	84	0	50	0	50	1.00
1397231--1397307	38	2.1	38	90	7	122	32	12	7	46	1.71
1415709--1415758	19	2.6	19	83	3	64	48	2	2	48	1.24
1419844--1419899	15	3.5	16	76	23	64	53	0	0	46	1.00
1420467--1420530	17	4.2	16	70	26	50	57	1	35	4	1.29
1443111--1443185	33	2.3	33	85	0	105	40	6	5	48	1.52
1444447--1444483	18	2.1	18	90	10	58	27	37	27	8	1.84
1473326--1473362	17	2.2	17	100	0	74	29	10	21	37	1.88
1492142--1492169	5	5.6	5	100	0	56	0	0	35	64	0.94
1511260--1511306	23	2.1	22	88	4	67	68	2	0	29	1.02
1511292--1511330	21	1.9	20	89	5	60	48	7	0	43	1.31
1513754--1513804	15	3.4	15	77	0	66	35	5	5	52	1.50
1513763--1513812	15	3.3	15	77	0	64	36	10	4	50	1.55
1530609--1530636	13	2.2	13	100	0	56	64	0	7	28	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1534101--1534231	64	2.1	63	94	4	228	22	32	13	31	1.93
1548172--1548206	18	1.9	18	88	11	54	0	17	2	80	0.84
1552323--1552347	13	1.9	13	100	0	50	12	0	0	88	0.53
1578628--1578792	76	2.2	74	89	2	249	26	7	26	40	1.81
1578776--1578809	8	4.1	8	85	7	50	20	0	38	41	1.53
1580333--1580420	35	2.5	36	74	18	87	39	2	0	57	1.11
1580333--1580389	19	3.4	17	80	15	57	42	0	0	57	0.98
1581257--1581305	21	2.3	21	85	0	62	0	30	36	32	1.58
1581316--1581368	23	2.3	23	83	6	63	54	0	41	3	1.18
1594179--1594217	19	2.1	19	85	9	53	25	30	2	41	1.69
1595799--1596054	123	2.1	123	86	5	351	49	5	7	38	1.52
1595922--1596265	182	1.9	183	82	6	435	47	3	6	42	1.45
1608022--1608081	26	2.3	26	85	0	84	50	3	5	41	1.41
1608088--1608231	57	2.6	56	77	11	150	48	6	14	30	1.68
1608136--1608446	94	3.3	92	84	3	370	44	8	16	31	1.76
1612472--1612563	45	2.1	44	84	6	116	48	2	4	44	1.34
1612591--1612663	23	3.3	21	75	17	76	52	2	2	42	1.30
1614952--1615043	44	2.1	44	91	0	148	31	17	15	35	1.91
1616810--1616840	16	1.9	16	93	0	53	6	12	29	51	1.65
1620223--1620264	19	2.2	19	87	12	59	57	4	0	38	1.20
1620639--1620712	20	3.8	20	79	16	93	55	0	0	44	0.99
1623527--1623629	29	3.5	29	74	13	79	33	9	5	50	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1633721--1633790	2	34.0	2	79	11	70	44	5	45	2	1.42
1637852--1637908	6	9.5	6	78	0	51	1	15	33	49	1.55
1638168--1638206	12	3.1	12	79	13	51	53	2	41	2	1.28
1654863--1654907	2	22.5	2	100	0	90	48	0	0	51	1.00
1658402--1658439	19	2.0	20	85	15	53	2	34	2	60	1.24
1666273--1666308	13	2.7	13	86	4	54	41	11	0	47	1.39
1672818--1672842	13	1.9	13	100	0	50	64	0	0	36	0.94
1691609--1691655	18	2.6	18	89	0	76	25	36	21	17	1.94
1693521--1694070	278	2.0	272	91	3	888	35	19	17	28	1.94
1703650--1703724	24	3.1	24	98	0	141	34	33	10	21	1.88

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