genome.fa.s1.2.7.7.80.10.50.1000.4.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  4  of  52  ( 6211 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)
480220--480246	2	13.5	2	100	0	54	48	0	51	0	1.00
482105--482225	22	5.6	21	68	15	68	52	0	0	47	1.00
482139--482210	25	3.1	23	75	11	76	54	0	0	45	0.99
482163--482222	24	2.3	26	78	16	63	55	0	0	45	0.99
482147--482223	25	3.2	24	70	20	63	55	0	0	44	0.99
484495--484549	28	2.0	28	85	0	74	36	18	9	36	1.82
489787--489813	6	4.5	6	100	0	54	51	14	0	33	1.43
494974--495008	2	18.5	2	88	11	56	45	0	0	54	0.99
494974--495008	13	2.6	14	86	13	56	45	0	0	54	0.99
496331--496411	34	2.4	35	83	6	96	62	1	3	32	1.20
501531--501580	21	2.3	23	86	13	70	56	0	0	44	0.99
501531--501587	21	2.7	21	81	13	64	57	0	0	42	0.98
501659--501694	18	1.9	19	94	5	65	69	0	0	30	0.89
501746--501779	2	17.0	2	100	0	68	50	0	0	50	1.00
510280--510309	6	4.8	6	95	4	51	3	0	33	63	1.11
510433--510485	20	2.6	21	82	11	58	69	0	1	28	0.99
510981--511016	10	3.7	10	85	7	56	47	0	0	52	1.00
515646--515835	97	2.0	97	84	0	254	25	21	13	40	1.89
515665--515873	97	2.2	97	82	5	244	25	21	15	37	1.93
519157--519557	153	2.6	153	84	3	493	32	9	7	49	1.65
521522--521953	235	1.8	234	81	9	531	36	13	22	27	1.91
521507--522026	78	6.7	79	78	7	431	37	12	22	27	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
521834--522167	183	1.8	185	84	4	469	36	11	23	27	1.90
521908--522132	107	2.1	105	77	10	235	36	12	23	27	1.91
522017--522327	79	3.9	80	81	6	337	37	10	24	27	1.89
522512--522815	152	2.0	151	91	0	491	34	14	21	29	1.92
522940--523001	24	2.6	24	74	5	63	54	3	8	33	1.46
524093--524326	110	2.1	110	98	0	450	33	12	17	36	1.87
525048--525101	20	2.6	21	85	2	65	29	16	12	40	1.86
525500--526089	156	3.8	156	86	2	749	26	9	18	45	1.80
529330--529698	155	2.4	154	82	3	445	26	13	18	41	1.87
531880--531930	23	2.2	24	82	10	61	58	3	1	35	1.28
536828--536879	20	2.7	20	84	3	61	51	1	5	40	1.37
545360--545397	19	2.1	18	90	5	58	31	0	0	68	0.90
545767--545791	3	8.3	3	100	0	50	36	32	0	32	1.58
545790--545814	3	8.3	3	100	0	50	32	0	0	68	0.90
547951--547989	12	3.3	12	83	16	55	35	0	0	64	0.94
547950--547995	19	2.3	19	85	11	56	32	0	2	65	1.05
548693--548743	12	3.9	12	78	16	57	45	5	9	39	1.62
553430--553480	12	3.9	12	78	16	57	43	7	11	37	1.71
553436--553492	27	2.1	27	90	0	87	40	5	19	35	1.74
561923--561948	13	2.0	13	100	0	52	30	15	15	38	1.88
562647--562690	21	2.1	21	83	8	54	25	31	4	38	1.76
564495--564533	13	3.0	13	100	0	78	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
566591--566625	15	2.2	16	90	5	54	14	20	14	51	1.76
571064--571109	3	15.0	3	81	4	56	30	4	2	63	1.26
571353--571382	12	2.5	12	94	0	51	26	10	10	53	1.66
571795--571845	25	2.0	25	84	7	66	66	0	1	31	1.03
571822--571862	14	3.0	14	82	13	50	75	0	0	24	0.80
576436--576477	22	1.9	22	85	9	59	47	0	4	47	1.23
577317--577480	56	3.0	56	79	11	169	40	10	4	44	1.60
577403--577477	28	2.7	28	76	12	82	40	8	5	46	1.56
577527--577627	27	3.6	27	71	12	89	38	7	6	46	1.60
577522--577632	55	2.0	55	81	8	127	38	8	7	45	1.61
577738--577800	27	2.3	27	83	8	74	33	11	6	49	1.64
577757--577809	27	2.0	27	88	7	81	33	11	11	43	1.76
578814--578875	13	4.5	13	80	9	70	83	1	14	0	0.71
578815--578875	28	2.1	29	87	3	88	83	1	14	0	0.72
578962--579021	21	2.8	22	78	12	54	23	15	13	48	1.79
584059--584095	15	2.3	17	86	9	51	21	0	2	75	0.92
584057--584094	20	1.9	20	84	10	51	21	0	2	76	0.91
588070--588119	12	4.4	12	72	23	54	76	2	0	22	0.89
588065--588110	23	2.0	23	83	8	58	73	4	0	21	1.00
588098--588349	19	13.3	18	67	21	72	67	4	1	26	1.20
588086--588235	40	3.8	39	78	15	166	69	3	1	26	1.12
588107--588245	30	4.8	28	70	16	88	68	2	1	27	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
588065--588237	76	2.3	74	81	14	210	69	3	1	26	1.11
588165--588211	16	2.8	16	77	20	51	72	2	0	25	0.96
588173--588372	9	21.4	9	69	15	61	67	5	1	26	1.20
588084--588245	39	4.2	38	78	13	161	69	3	1	26	1.11
588084--588322	58	4.1	57	76	11	191	67	4	1	26	1.17
588325--588354	16	1.9	15	93	6	51	76	0	3	20	0.92
588271--588374	9	11.8	9	73	22	71	65	3	2	27	1.24
588450--588715	8	30.6	8	73	16	117	28	1	2	67	1.11
588447--588715	9	30.7	9	71	22	159	28	1	2	67	1.11
589336--589360	13	1.9	13	100	0	50	32	16	16	36	1.90
589431--589500	19	3.6	19	94	5	115	40	17	15	27	1.90
597436--597487	19	2.7	20	84	6	70	40	17	13	28	1.87
599694--599736	22	1.9	22	85	4	59	46	6	11	34	1.67
603674--603712	13	3.0	13	96	0	69	30	17	15	35	1.91
606220--606271	19	2.7	20	84	6	70	40	17	13	28	1.87
612091--612210	59	2.0	59	96	0	222	41	3	26	28	1.71
612896--612963	33	2.1	32	91	2	109	33	16	17	32	1.92
616089--616151	28	2.3	26	76	7	72	39	12	6	41	1.69
619197--619222	3	8.7	3	100	0	52	30	0	0	69	0.89
619574--619612	21	1.9	21	89	5	62	66	0	2	30	1.05
619604--619629	12	2.2	12	100	0	52	61	7	0	30	1.24
619621--619663	19	2.3	19	92	8	70	65	6	2	25	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
619552--619719	47	3.5	45	74	11	138	64	5	2	26	1.28
619675--619749	28	2.6	29	78	14	75	66	1	2	29	1.13
619692--619751	21	2.9	21	75	9	68	66	0	1	31	1.01
619796--619958	17	10.1	15	69	25	93	25	0	3	70	1.06
619797--620008	34	6.5	32	74	18	138	26	0	3	68	1.09
619791--620040	8	27.7	9	73	21	152	29	0	3	67	1.09
619794--620036	68	3.7	66	78	15	213	28	0	3	67	1.09
619821--620019	18	11.6	17	67	16	70	29	0	3	66	1.12
620243--620276	16	2.1	17	88	5	52	35	0	5	58	1.22
620489--620513	7	3.6	7	100	0	50	0	0	12	88	0.53
621832--621860	2	14.5	2	100	0	58	0	0	51	48	1.00
626919--626968	19	2.5	20	81	15	68	38	0	0	62	0.96
626970--627012	15	2.8	15	85	3	50	55	2	0	41	1.12
626967--627036	26	2.7	26	79	16	74	48	2	0	48	1.16
626967--627053	31	2.8	31	83	1	102	49	2	0	48	1.13
628946--629726	157	5.0	157	77	7	676	39	18	14	27	1.89
629815--630556	165	4.5	166	82	5	796	43	12	9	33	1.76
629815--630556	332	2.2	330	82	5	865	43	12	9	33	1.76
632138--632193	28	1.9	29	82	7	69	51	3	3	41	1.36
632121--632444	153	2.1	151	85	4	459	52	6	7	33	1.55
635889--635986	51	1.9	51	87	4	144	29	28	10	31	1.90
635921--636179	79	3.3	78	79	6	274	28	27	13	31	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
636050--636304	139	1.8	139	88	1	386	27	27	14	30	1.95
636191--636702	79	6.5	79	80	2	431	29	24	12	33	1.92
635958--636385	218	2.0	216	84	6	571	27	26	13	31	1.94
636191--636678	158	3.1	157	83	2	557	28	25	12	34	1.92
640730--640879	60	2.5	60	82	0	174	28	15	21	35	1.93
642905--642931	13	2.1	13	100	0	54	29	14	14	40	1.86
642885--642952	34	2.0	32	86	13	93	29	17	13	39	1.88
648232--648274	20	2.2	20	87	4	61	16	13	2	67	1.33
648231--648283	21	2.5	21	78	9	63	13	13	3	69	1.31
649798--650132	79	4.2	79	86	2	415	32	15	25	25	1.95

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