genome.fa.s1.2.7.7.80.10.50.1000.2.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  2  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)
457566--457784	69	3.2	69	82	2	235	28	17	17	36	1.93
457736--457784	24	2.0	24	84	7	64	32	14	14	38	1.86
475284--475407	46	2.8	45	81	9	130	45	1	6	46	1.38
475339--475407	22	3.1	22	66	22	54	49	0	7	43	1.30
489100--489138	2	19.5	2	89	0	60	46	0	53	0	1.00
503908--503958	12	4.2	12	82	5	59	23	21	27	27	1.99
515724--515816	42	2.2	41	79	9	107	21	12	35	30	1.91
515751--515812	21	3.0	21	82	0	70	24	11	35	29	1.90
515751--515851	42	2.4	42	80	3	105	24	11	37	25	1.90
515818--516082	21	12.6	21	76	6	108	22	7	44	25	1.79
515819--516025	42	4.9	42	81	3	202	21	6	45	25	1.76
515799--516025	84	2.7	84	77	1	231	21	7	45	25	1.78
515823--516037	63	3.4	62	76	3	207	21	6	45	25	1.77
515934--516046	42	2.7	42	90	2	165	21	8	43	26	1.81
515973--516109	42	3.3	41	79	6	132	21	9	40	27	1.84
515987--516094	21	5.1	21	77	4	85	23	9	39	27	1.85
516051--516118	21	3.2	21	85	4	93	26	8	38	26	1.85
516066--516130	21	3.1	21	88	4	87	24	9	38	27	1.86
516033--516118	42	2.0	42	82	4	102	26	9	37	26	1.87
516084--516142	21	2.8	21	89	0	73	20	11	40	27	1.87
516234--516309	21	3.6	21	87	0	98	30	17	38	14	1.89
516270--516349	21	3.8	21	78	3	72	27	15	40	17	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
521796--522235	223	2.0	223	93	0	745	34	24	10	30	1.89
539871--539912	15	2.8	15	82	10	50	69	0	0	30	0.89
542546--542577	3	10.7	3	100	0	64	68	0	31	0	0.90
545708--545741	6	5.7	6	92	0	59	82	0	14	2	0.79
546017--546073	27	2.0	29	86	6	82	54	0	0	45	0.99
550058--550087	15	2.0	15	93	0	51	56	0	43	0	0.99
551321--551347	2	13.5	2	100	0	54	51	0	0	48	1.00
565310--565364	16	3.4	16	72	22	60	61	5	0	32	1.19
574344--574389	2	23.0	2	100	0	92	0	50	0	50	1.00
600682--600716	2	17.5	2	87	0	52	51	0	45	2	1.16
603737--603773	8	4.9	8	80	12	51	45	16	13	24	1.83
603747--603773	14	1.9	14	100	0	54	44	18	14	22	1.86
603839--603869	1	31.0	1	93	0	53	0	96	3	0	0.21
603837--603870	11	3.2	11	91	8	61	0	91	8	0	0.43
604677--604714	20	1.9	20	84	10	51	18	10	18	52	1.73
606113--606137	2	12.5	2	100	0	50	0	52	0	48	1.00
606292--606316	2	12.5	2	100	0	50	0	52	0	48	1.00
609734--609788	30	1.9	30	85	7	78	27	3	0	69	1.05
615181--615207	6	4.5	6	100	0	54	33	0	14	51	1.43
615798--615878	35	2.3	35	81	8	94	28	0	14	56	1.39
619565--619589	4	6.2	4	100	0	50	0	76	0	24	0.80
625629--625727	48	2.1	48	98	0	189	42	14	11	32	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
657443--657579	68	2.0	68	92	0	229	26	30	14	28	1.95
660851--660895	23	2.0	23	82	8	56	44	6	0	48	1.29
660925--660976	21	2.5	19	77	20	50	34	1	7	55	1.39
661614--661639	2	13.0	2	100	0	52	50	0	0	50	1.00
693237--693302	34	1.9	34	90	0	105	7	28	15	48	1.72
705540--705775	118	2.0	118	96	0	436	27	27	20	23	1.99
706952--707017	33	2.0	33	96	0	123	31	6	31	30	1.82
707220--707270	23	2.3	23	86	6	70	23	15	17	43	1.88
724498--724528	13	2.5	12	90	10	53	41	0	3	54	1.16
732330--732367	20	2.1	19	85	14	53	18	31	10	39	1.85
736215--736508	57	5.2	57	96	3	560	25	9	28	36	1.88
736215--736508	110	2.6	114	95	4	560	25	9	28	36	1.88
759049--759131	2	41.5	2	86	13	118	48	2	0	48	1.14
763673--763937	132	2.0	132	94	0	467	43	23	12	21	1.86
775781--775820	18	2.2	18	95	0	71	50	17	10	22	1.76
778161--778188	2	14.0	2	100	0	56	50	0	0	50	1.00
778606--778670	2	31.5	2	80	6	67	46	4	3	46	1.39
778612--778670	23	2.6	23	86	5	75	45	5	3	45	1.42
782601--782631	2	15.5	2	93	0	53	48	0	51	0	1.00
827959--828023	13	4.7	13	71	19	51	50	0	0	49	1.00
827930--828004	24	3.1	24	75	11	64	50	0	1	48	1.09
827968--828023	26	2.2	26	81	12	62	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
829574--829616	2	21.5	2	100	0	86	51	0	0	48	1.00
830264--830298	10	3.7	10	85	14	56	40	0	11	48	1.39
830264--830298	18	1.9	18	100	0	70	40	0	11	48	1.39
832343--832733	174	2.2	174	90	1	611	19	26	21	33	1.97
833638--833675	20	1.9	20	84	10	51	65	13	21	0	1.26
834483--834523	21	2.0	21	85	9	57	48	0	41	9	1.36
844700--844729	15	2.0	15	100	0	60	60	26	6	6	1.47
915755--915868	56	2.0	56	89	0	174	31	27	8	32	1.87
916019--916084	33	2.0	33	90	0	105	31	1	19	46	1.59
918320--918422	51	2.0	51	90	0	161	16	17	30	35	1.92
928420--928455	17	2.1	18	89	5	56	50	13	5	30	1.65
929971--930000	9	3.3	9	90	0	51	26	10	20	43	1.83
943623--943684	24	2.6	24	94	0	106	48	17	30	3	1.63
943623--943698	24	3.2	24	74	20	70	48	18	30	2	1.62
945278--945378	53	1.9	53	81	0	121	30	8	8	51	1.64
945752--945790	14	2.9	14	84	3	53	43	0	0	56	0.99
945752--945785	7	5.0	7	85	7	52	47	0	0	52	1.00
946129--946183	23	2.3	24	81	9	67	41	0	3	54	1.18
956525--956580	3	18.7	3	78	14	62	60	3	35	0	1.14
959209--959267	29	2.0	29	96	0	109	32	28	11	27	1.92
960997--961024	2	14.0	2	100	0	56	50	0	0	50	1.00
998223--998267	23	1.9	24	90	4	74	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1006640--1006677	18	2.1	19	90	5	60	68	5	23	2	1.23
1038405--1038440	19	1.9	19	88	5	56	25	0	0	75	0.81
1038552--1038600	16	3.1	16	82	5	55	34	0	2	63	1.06
1038765--1038847	18	4.8	17	74	20	66	37	1	0	61	1.04
1038819--1038847	15	1.9	15	100	0	58	31	0	0	68	0.89
1046397--1046449	4	13.2	4	85	0	61	54	16	0	28	1.43
1046435--1046498	2	35.0	2	75	17	59	48	1	0	50	1.10
1046435--1046498	9	7.0	10	71	20	59	48	1	0	50	1.10
1046423--1046495	20	3.5	20	77	14	60	50	4	0	45	1.20
1046456--1046499	5	9.0	5	80	14	56	43	0	0	56	0.99
1046437--1046505	17	4.0	17	76	10	68	46	1	0	52	1.09
1048393--1048442	2	25.0	2	100	0	100	50	0	0	50	1.00
1059268--1059405	69	2.0	69	83	5	172	57	6	7	28	1.51
1059670--1059696	3	9.0	3	100	0	54	33	0	0	66	0.92
1059861--1060177	106	3.0	106	95	1	553	33	31	16	19	1.93
1062363--1062391	2	15.0	2	92	7	51	51	0	48	0	1.00
1063280--1063439	27	6.0	27	67	17	84	53	4	1	40	1.32
1063253--1063449	106	1.9	106	86	4	281	55	3	1	39	1.26
1063409--1063537	33	4.0	31	74	12	100	59	1	0	37	1.12
1063484--1063534	15	3.3	16	78	8	61	54	0	1	43	1.11
1066014--1066060	6	7.8	6	90	0	67	2	8	68	21	1.27
1066014--1066063	18	2.8	18	90	0	82	4	8	68	20	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1066465--1066494	3	10.0	3	100	0	60	33	0	66	0	0.92
1072872--1072945	19	4.1	18	72	18	55	2	24	4	68	1.19
1072872--1072934	19	3.5	17	76	18	56	3	23	3	69	1.17
1098235--1098346	45	2.5	45	89	0	170	29	19	17	33	1.95
1098339--1098584	45	5.4	45	73	5	183	31	19	15	32	1.94
1098237--1098449	111	1.9	112	83	2	277	32	19	15	32	1.93
1098364--1098589	91	2.5	90	82	2	256	30	19	16	34	1.93
1098574--1098627	21	2.6	21	93	0	90	40	25	11	22	1.87
1098629--1098687	24	2.5	24	88	0	82	30	8	16	44	1.78
1100479--1100521	22	1.9	22	85	4	59	34	4	0	60	1.17

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