genome.fa.s4.2.7.7.80.10.50.1000.3.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: chr4
Parameters: 2 7 7 80 10 50 1000
Length:  31929104

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   

This is table  3  of  82  ( 9773 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)
546179--546216	18	2.1	18	85	9	51	55	23	10	10	1.65
568743--568806	30	2.1	30	91	0	101	31	10	9	48	1.70
578204--578232	12	2.5	12	94	5	51	86	0	0	13	0.58
591118--591148	12	2.5	13	94	5	55	0	16	0	83	0.64
591513--591565	23	2.4	21	77	20	54	47	5	1	45	1.37
591655--591685	15	2.1	15	93	0	53	41	0	9	48	1.36
591742--591800	31	1.9	31	86	6	84	50	1	1	45	1.21
598753--598826	2	37.5	2	81	8	89	44	1	4	50	1.29
616541--616586	1	46.0	1	86	0	65	2	93	0	4	0.41
616599--616624	1	26.0	1	100	0	52	0	100	0	0	0.00
617947--617994	25	1.9	26	83	8	64	37	2	14	45	1.57
622181--622205	5	5.0	5	100	0	50	20	0	0	80	0.72
622902--622958	29	2.0	29	86	3	80	36	1	0	61	1.07
632831--632856	9	2.9	9	100	0	52	0	23	7	69	1.14
638592--638629	18	2.1	19	90	5	60	50	10	5	34	1.59
638566--638623	27	2.0	30	87	9	86	46	15	6	31	1.72
638620--638690	35	2.0	36	86	2	99	54	1	0	43	1.08
641294--641336	3	14.3	3	85	0	59	58	2	39	0	1.11
641302--641340	12	3.2	12	92	0	60	58	2	38	0	1.12
652262--652330	30	2.3	31	80	9	79	65	2	1	30	1.16
652595--652623	12	2.3	13	94	5	51	79	0	0	20	0.74
652592--652631	21	2.0	19	90	9	62	77	0	0	22	0.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
652928--652954	11	2.5	11	100	0	54	25	0	0	74	0.83
657862--657980	59	2.0	59	91	0	193	29	19	11	39	1.87
659611--659656	18	2.6	18	89	0	74	21	10	19	47	1.80
661566--661621	21	2.7	21	85	0	76	21	14	17	46	1.84
664870--664904	2	17.5	2	93	0	61	51	0	48	0	1.00
665143--665167	2	12.5	2	100	0	50	0	48	0	52	1.00
667555--667604	24	2.1	24	96	0	91	20	16	30	34	1.94
678060--678126	25	2.7	25	95	2	118	17	34	2	44	1.64
679772--679834	33	1.9	33	90	0	99	36	11	9	42	1.73
679880--679929	3	18.3	3	76	19	56	66	0	2	32	1.03
679882--679955	31	2.4	31	86	4	96	63	0	1	35	1.03
680022--680070	3	18.3	3	76	23	56	69	0	0	30	0.89
680022--680070	5	9.2	6	82	17	56	69	0	0	30	0.89
680091--680159	30	2.3	30	90	5	104	50	7	13	28	1.67
680103--680190	30	3.0	29	80	6	88	53	6	10	29	1.60
687796--687828	2	16.5	2	87	12	50	48	3	0	48	1.17
688543--688569	3	9.0	3	100	0	54	33	0	0	66	0.92
694362--694415	19	3.2	16	80	16	65	25	0	0	74	0.83
696086--696158	33	2.2	33	87	0	101	65	1	5	27	1.22
704115--704156	18	2.3	18	87	0	57	19	0	2	78	0.86
707077--707159	23	3.6	23	77	9	89	38	3	21	36	1.71
707073--707179	46	2.3	47	82	7	130	36	7	20	35	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
709494--709617	61	2.0	62	93	4	216	29	24	4	41	1.75
711150--711871	280	2.6	278	83	3	923	31	22	17	28	1.96
714503--714685	2	97.5	2	79	16	178	49	0	1	45	1.13
714500--714686	97	2.0	94	89	6	247	49	1	1	45	1.16
721688--721741	19	2.8	19	85	0	72	42	7	11	38	1.68
724781--724854	26	3.1	25	77	14	77	45	1	1	51	1.18
727184--727214	2	15.5	2	100	0	62	48	0	0	51	1.00
728256--728282	7	3.9	7	100	0	54	14	11	0	74	1.08
732931--733104	91	1.9	92	85	3	244	41	9	22	26	1.84
740069--740188	41	3.0	41	85	7	158	31	19	20	28	1.97
740076--740196	38	3.1	39	85	7	156	29	19	22	28	1.98
743106--743166	30	2.1	29	87	3	86	34	6	4	54	1.48
743437--743502	28	2.4	26	87	7	87	63	3	1	31	1.19
749059--749139	40	1.9	43	83	14	107	59	7	7	25	1.51
751447--752014	286	2.0	286	93	2	971	40	8	16	35	1.79
767780--767828	25	2.0	24	84	4	62	8	34	28	28	1.86
771326--771486	29	5.8	29	73	14	117	39	14	13	32	1.85
771435--771525	28	3.2	28	80	7	69	36	13	8	41	1.75
773921--773983	31	2.0	31	100	0	126	33	19	9	38	1.84
775219--775243	12	2.1	12	100	0	50	40	0	0	60	0.97
775241--775289	18	2.7	19	78	12	59	24	4	0	71	1.03
778136--778247	36	3.1	36	92	2	154	33	34	10	21	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
779272--779317	10	4.6	10	80	17	51	73	0	26	0	0.83
783138--783219	30	2.7	30	80	9	96	32	9	9	47	1.69
783090--783218	60	2.2	60	82	2	152	32	10	9	47	1.70
784734--784871	51	2.7	51	87	4	192	39	14	13	31	1.85
784734--784884	25	6.0	26	72	4	112	40	14	14	30	1.86
789064--789098	16	2.2	16	90	5	54	14	14	17	54	1.72
789646--789688	23	1.9	23	85	4	61	69	0	13	16	1.19
792305--792366	15	4.1	15	72	12	56	50	1	1	46	1.20
797065--797128	15	4.1	16	76	4	51	68	6	0	25	1.12
799406--799441	2	18.0	2	94	0	63	47	0	2	50	1.15
800954--800992	19	2.1	19	90	0	60	46	7	2	43	1.46
802768--802835	30	2.3	30	84	5	84	39	13	5	41	1.68
808635--808768	67	2.0	66	94	1	232	30	12	34	22	1.91
809676--809763	42	2.1	42	95	0	158	29	15	15	38	1.89
810187--810231	19	2.4	19	80	0	54	26	20	28	24	1.99
818028--818062	2	17.5	2	100	0	70	48	0	0	51	1.00
821615--821725	55	2.0	55	94	0	195	40	16	23	19	1.91
822818--823113	145	2.0	145	91	0	477	53	7	4	35	1.49
830509--830543	2	17.5	2	100	0	70	0	48	0	51	1.00
843998--844039	18	2.3	18	84	8	50	35	0	0	64	0.94
844010--844053	18	2.5	17	81	7	52	31	0	0	68	0.90
851873--851902	9	3.4	9	95	4	53	0	16	0	83	0.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
858539--858614	30	2.6	29	82	12	93	59	2	1	36	1.20
859790--859814	6	4.2	6	100	0	50	84	0	16	0	0.63
871888--871950	30	2.1	31	93	3	110	60	15	9	14	1.59
878916--878948	15	2.2	15	89	10	50	66	0	33	0	0.92
878916--878948	7	4.4	8	85	14	52	66	0	33	0	0.92
880063--880155	39	2.4	39	83	0	114	25	13	36	23	1.92
882328--882366	20	2.0	20	94	0	69	38	20	10	30	1.86
885890--885936	15	3.1	15	87	0	58	36	4	29	29	1.77
886221--886329	30	3.7	27	72	20	78	27	5	0	66	1.20
889702--889735	1	34.0	1	87	0	50	2	94	0	0	0.23
889702--889735	16	2.1	16	94	0	59	2	94	0	0	0.23
893653--893696	22	2.0	22	100	0	88	31	18	13	36	1.90
898914--898951	20	1.9	20	94	0	67	71	5	0	23	1.07
898985--899020	2	18.0	2	94	0	54	50	5	0	44	1.25
903458--903503	22	2.0	23	87	4	67	21	6	19	52	1.69
912156--912231	29	2.6	30	81	6	84	34	6	5	53	1.49
912287--912336	25	2.0	26	88	11	77	30	8	28	34	1.86
916325--916376	2	26.0	2	100	0	104	50	0	0	50	1.00
916572--916621	24	2.0	25	88	3	75	54	0	2	44	1.11
925497--925524	3	9.3	3	100	0	56	67	0	0	32	0.91
934731--934808	40	2.0	40	92	0	129	23	12	15	48	1.79
962687--962725	21	2.0	20	85	14	55	43	15	10	30	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
964627--964665	11	3.6	11	82	6	53	43	2	2	51	1.29
967425--967691	137	2.0	136	98	0	507	45	6	7	39	1.60
967632--967694	33	1.9	33	83	0	81	55	3	1	39	1.25
967984--968014	14	2.2	14	94	0	53	16	3	0	80	0.83
969176--969235	31	1.9	31	93	0	102	30	6	5	58	1.45
980092--980166	2	38.5	2	84	10	84	46	1	0	46	1.11
984822--984852	2	16.0	2	93	6	55	51	0	0	48	1.00
998530--998766	129	1.8	130	85	6	336	33	12	18	35	1.89
999671--999700	3	10.3	3	92	7	53	30	0	0	70	0.88
1000842--1000891	24	2.1	24	84	0	64	44	8	14	34	1.74

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