genome.fa.s29.2.7.7.80.10.50.1000.3.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: Scaffold29
Parameters: 2 7 7 80 10 50 1000
Length:  5511024

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   

This is table  3  of  34  ( 4030 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)
416317--416342	3	8.7	3	100	0	52	65	0	0	34	0.93
428255--428279	12	2.1	12	100	0	50	16	32	8	44	1.76
430365--430408	15	2.9	15	83	10	54	54	0	29	15	1.42
441242--441272	2	15.5	2	100	0	62	0	0	48	51	1.00
449602--449638	18	2.1	18	94	0	65	32	5	13	48	1.65
452040--452217	89	2.0	89	87	0	257	29	12	16	41	1.85
455219--455272	20	2.7	20	100	0	108	42	11	18	27	1.84
455311--455336	13	2.0	13	100	0	52	38	15	15	30	1.88
457554--457598	21	2.1	21	84	8	56	53	4	20	22	1.63
459402--459432	15	2.1	15	93	0	53	48	16	22	12	1.80
461439--461517	20	3.8	20	73	16	70	26	13	15	44	1.84
461506--461541	13	2.8	13	91	0	54	36	19	11	33	1.87
461662--461708	21	2.3	21	79	20	55	34	19	4	42	1.70
461664--461706	20	2.2	19	84	16	52	32	18	4	44	1.71
464067--464092	13	2.0	13	100	0	52	38	15	15	30	1.88
465412--465464	19	2.7	20	91	2	90	30	18	15	35	1.92
465563--465615	20	2.6	21	82	8	65	37	15	16	30	1.90
465657--465719	19	3.6	19	76	24	84	39	19	15	25	1.91
465675--465732	13	4.0	13	76	23	62	39	17	15	27	1.90
465657--465752	32	3.0	32	93	4	158	38	19	14	27	1.91
471216--471268	19	2.7	20	82	2	72	30	18	15	35	1.92
480115--480167	19	2.7	20	79	2	72	28	20	15	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
480212--480241	13	2.3	13	94	0	51	36	16	10	36	1.82
482210--482243	15	2.3	15	89	0	50	73	8	2	14	1.19
483231--483258	13	2.2	13	100	0	56	17	14	14	53	1.73
483655--483704	20	2.5	20	86	0	73	42	14	14	30	1.84
483737--483787	19	2.6	19	81	9	59	41	19	9	29	1.84
494127--494198	29	2.5	29	76	17	78	41	4	0	54	1.20
494253--494296	21	2.0	22	83	12	56	20	2	15	61	1.45
497049--497093	21	2.1	21	84	8	56	53	4	20	22	1.63
498897--498927	15	2.1	15	93	0	53	48	16	22	12	1.80
500994--501032	13	3.0	13	100	0	78	30	15	15	38	1.88
501153--501199	21	2.3	20	78	10	51	34	19	2	44	1.62
505112--505182	27	2.7	27	78	10	67	18	5	5	70	1.27
506643--506667	13	1.9	13	100	0	50	36	16	16	32	1.90
506624--506725	32	3.2	32	88	2	161	31	11	18	38	1.87
506600--506717	19	6.7	19	68	25	73	33	11	16	37	1.86
506770--506797	13	2.2	13	100	0	56	28	14	17	39	1.89
510010--510115	30	3.5	30	68	10	97	38	16	16	27	1.91
509977--510116	62	2.3	62	100	0	280	37	14	17	30	1.89
513441--513465	13	1.9	13	100	0	50	32	16	16	36	1.90
513420--513483	32	2.0	33	87	3	94	28	14	17	40	1.88
517341--517489	52	2.9	52	95	2	264	30	17	20	31	1.95
517478--517502	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
517543--517609	33	2.0	33	88	0	98	40	14	11	32	1.83
517565--517589	13	1.9	13	100	0	50	32	16	16	36	1.90
518361--518514	52	2.9	54	80	2	168	37	15	22	24	1.93
518533--518631	28	3.5	28	81	4	110	17	14	29	39	1.88
518630--518720	35	2.6	34	81	5	103	38	10	28	21	1.88
518699--519112	29	13.9	29	76	9	325	26	16	28	28	1.97
518583--519121	238	2.2	242	89	3	811	27	15	28	28	1.96
520492--520585	1	94.0	1	78	0	98	0	0	10	89	0.49
520492--520585	10	9.5	10	83	10	122	0	0	10	89	0.49
520492--520587	16	6.1	15	84	12	122	0	0	11	88	0.51
520492--520585	21	4.4	20	85	10	125	0	0	10	89	0.49
534425--534573	52	2.9	51	87	4	226	30	17	19	32	1.95
534562--534586	13	1.9	13	100	0	50	36	16	16	32	1.90
534627--534693	33	2.0	33	88	0	98	40	14	11	32	1.83
534649--534673	13	1.9	13	100	0	50	32	16	16	36	1.90
536210--536252	20	2.1	20	82	4	50	9	27	44	18	1.80
536684--536721	13	2.9	13	92	0	58	34	15	15	34	1.90
542860--542924	20	3.6	20	73	26	81	27	12	15	44	1.82
542880--542938	13	4.0	13	73	26	55	28	13	15	42	1.85
542860--542956	33	3.0	33	95	1	169	27	13	15	43	1.84
545432--545500	36	1.9	36	96	0	129	31	23	10	34	1.88
546423--546472	20	2.5	20	96	0	91	40	22	18	20	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
547610--547697	45	2.0	44	81	2	104	35	7	19	37	1.81
548560--548593	16	2.1	16	88	0	50	29	2	0	67	1.05
548636--548746	32	3.4	32	70	16	86	36	0	1	61	1.07
548566--548741	74	2.4	73	86	4	230	38	0	1	60	1.07
548699--548742	18	2.4	19	81	11	56	38	0	0	61	0.96
548854--548887	14	2.4	14	90	0	50	61	2	0	35	1.11
551654--551706	21	2.8	18	76	20	54	35	0	5	58	1.22
551715--551758	3	14.7	3	100	0	88	68	0	0	31	0.90
551819--551858	16	2.6	16	88	4	55	67	2	0	30	1.04
551883--551934	22	2.2	22	83	10	59	44	3	0	51	1.19
553846--553934	43	2.0	44	82	6	110	55	1	5	38	1.31
558079--558186	37	2.9	39	86	9	140	37	9	10	42	1.71
558108--558169	18	3.4	19	77	6	74	37	9	11	41	1.74
558110--558204	18	5.3	18	73	10	72	36	9	9	44	1.70
558128--558186	18	3.2	18	80	2	73	38	5	8	47	1.56
558106--558203	37	2.7	36	86	10	114	36	8	10	44	1.68
560968--561022	16	3.1	18	79	7	51	45	7	12	34	1.70
561254--561301	18	2.6	18	83	3	60	27	10	8	54	1.63
563178--563390	81	2.7	80	75	10	220	32	9	25	31	1.89
564867--565005	51	2.7	51	85	7	176	41	11	15	31	1.83
567011--567061	20	2.5	20	90	0	84	43	11	11	33	1.78
570197--570315	52	2.3	51	89	4	177	31	15	19	33	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
571015--571680	49	13.7	49	83	5	838	30	17	26	25	1.97
571015--571680	98	6.9	98	92	4	1009	30	17	26	25	1.97
571006--571685	92	7.1	93	88	8	904	31	17	26	25	1.97
571680--571749	33	2.1	35	94	5	126	20	17	37	25	1.94
571734--572319	71	8.6	70	74	13	476	34	11	33	20	1.89
571734--572288	35	15.3	36	81	12	595	34	11	33	20	1.89
571827--572062	121	1.9	124	89	6	374	33	13	34	19	1.90
572268--572422	31	5.0	31	89	4	199	27	16	31	25	1.96
580641--580770	52	2.5	51	91	3	199	31	16	19	33	1.94
580641--580790	52	2.9	50	83	12	171	32	16	19	32	1.93
580779--580803	13	1.9	13	100	0	50	36	16	16	32	1.90
580865--580889	13	1.9	13	100	0	50	32	16	16	36	1.90
580844--580909	32	2.0	33	88	2	98	39	13	12	34	1.82
583741--583942	78	2.6	76	77	9	192	31	20	9	37	1.86
583741--584013	79	3.5	77	77	6	226	31	20	10	38	1.86
584894--584919	13	2.0	13	100	0	52	38	15	15	30	1.88
587137--587181	21	2.1	21	84	8	56	53	4	20	22	1.63
588985--589015	15	2.1	15	93	0	53	48	16	22	12	1.80
591242--591287	21	2.2	20	81	11	58	32	19	4	43	1.71
593665--593690	13	2.0	13	100	0	52	38	15	15	30	1.88
595200--595262	21	3.0	21	71	0	54	41	15	3	39	1.64
595210--595270	21	2.9	20	71	9	50	37	13	4	44	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
596170--596216	19	2.5	20	79	10	62	46	23	0	29	1.52
599474--599624	71	2.2	69	85	2	194	30	16	9	43	1.81
611151--611183	12	2.8	12	90	9	50	84	9	0	6	0.76
612467--612830	28	12.6	28	80	8	340	30	31	17	21	1.96
612471--612830	60	6.2	59	83	6	389	30	31	17	20	1.96
613821--613898	20	3.9	20	80	6	86	29	14	15	41	1.86
617058--617198	52	2.7	52	91	2	230	31	17	17	33	1.94
617187--617211	13	1.9	13	100	0	50	36	16	16	32	1.90
617278--617302	13	1.9	13	100	0	50	32	16	16	36	1.90
618192--618349	49	3.1	49	76	7	147	35	15	24	24	1.94

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