genome.fa.s40.2.7.7.80.10.50.1000.23.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  23  of  24  ( 2833 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)
3076244--3076277	2	17.0	2	100	0	68	50	0	0	50	1.00
3076548--3076582	2	17.5	2	100	0	70	48	0	0	51	1.00
3076731--3076773	13	3.4	12	84	9	50	44	0	2	53	1.13
3076895--3076931	3	12.3	3	100	0	74	32	0	0	67	0.91
3077299--3077498	50	4.0	50	84	5	262	34	18	18	30	1.94
3077299--3077498	100	2.0	100	88	0	292	34	18	18	30	1.94
3077996--3078076	33	2.4	35	91	6	132	66	4	2	25	1.24
3084926--3085212	50	5.7	50	91	1	423	32	20	18	28	1.96
3086559--3086585	2	13.5	2	100	0	54	51	0	0	48	1.00
3094345--3094390	20	2.3	20	84	0	56	32	4	52	10	1.56
3094484--3094537	27	2.0	27	85	3	72	50	18	1	29	1.58
3094973--3095033	26	2.4	25	78	8	68	32	0	1	65	1.02
3094994--3095032	13	3.0	13	80	0	51	38	0	2	58	1.12
3095118--3095149	3	10.7	3	100	0	64	31	0	0	68	0.90
3096002--3096040	21	1.9	20	85	15	53	43	0	7	48	1.31
3096355--3096448	31	3.0	31	86	7	102	58	2	3	36	1.26
3096379--3096448	31	2.2	32	92	5	115	62	1	0	35	1.04
3098232--3098273	21	2.1	19	83	16	50	52	0	0	47	1.00
3098593--3098629	12	3.2	12	85	11	51	29	0	0	70	0.88
3101746--3101779	2	17.0	2	100	0	68	50	0	0	50	1.00
3102270--3102304	3	11.7	3	100	0	70	31	0	0	68	0.90
3103948--3103985	18	2.1	19	90	5	60	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3104386--3104705	34	9.5	34	85	5	425	39	27	8	24	1.83
3104386--3104705	102	3.2	102	95	1	556	39	27	8	24	1.83
3108771--3108833	19	3.3	19	90	0	90	34	19	17	28	1.94
3109135--3109452	34	9.4	34	84	5	403	39	27	8	25	1.84
3109135--3109452	102	3.1	102	93	1	534	39	27	8	25	1.84
3109921--3109969	24	2.1	24	85	7	66	46	0	0	53	1.00
3109911--3109984	29	2.6	29	77	14	80	47	0	0	52	1.00
3109932--3109979	22	2.1	24	81	14	57	52	0	0	47	1.00
3110936--3110998	27	2.4	26	77	15	76	58	0	0	41	0.98
3115615--3115640	6	4.3	6	100	0	52	34	30	34	0	1.58
3116164--3116199	17	2.1	17	100	0	72	44	5	16	33	1.71
3117049--3117080	2	16.0	2	100	0	64	50	0	0	50	1.00
3120071--3120112	2	21.5	2	95	4	77	50	0	0	50	1.00
3120945--3120978	3	11.3	3	93	0	59	32	0	2	64	1.08
3121357--3121390	15	2.3	15	89	0	50	50	0	0	50	1.00
3130640--3130680	2	20.5	2	94	0	73	48	2	0	48	1.14
3132014--3132062	26	1.9	25	83	4	62	71	6	4	18	1.23
3132567--3132594	5	5.6	5	100	0	56	17	0	0	82	0.68
3149327--3149383	28	2.0	28	100	0	114	47	24	10	17	1.79
3151513--3151591	26	3.0	27	73	15	67	58	0	0	41	0.98
3156788--3156812	6	4.2	6	100	0	50	0	52	0	48	1.00
3160438--3160488	24	2.1	25	88	3	77	68	0	7	23	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3161438--3161472	3	11.7	3	93	0	61	28	2	0	68	1.04
3162715--3162745	5	6.2	5	100	0	62	61	0	0	38	0.96
3164511--3164557	17	2.7	18	77	12	53	48	0	0	51	1.00
3165908--3165932	4	6.2	4	100	0	50	48	0	0	52	1.00
3166374--3166428	20	2.8	20	75	13	60	67	1	0	30	1.01
3168017--3168054	2	19.0	2	100	0	76	50	0	0	50	1.00
3177055--3177120	32	2.1	32	86	8	91	53	1	1	43	1.19
3177833--3177886	23	2.2	26	81	18	71	22	0	20	57	1.41
3177836--3177886	27	2.0	27	85	14	74	19	0	19	60	1.36
3178441--3178473	15	2.2	15	94	0	57	18	3	48	30	1.63
3180236--3180390	82	1.9	82	86	0	220	43	3	9	43	1.52
3181047--3181076	15	2.0	15	100	0	60	20	13	20	46	1.83
3184208--3184249	11	3.7	11	79	17	50	66	0	0	33	0.92
3190019--3190052	17	2.0	17	88	0	50	44	2	0	52	1.16
3190762--3190794	17	2.0	17	88	5	50	45	0	0	54	0.99
3190785--3190819	17	1.9	18	88	11	54	71	0	0	28	0.86
3191082--3191120	19	1.9	19	85	10	51	64	0	0	35	0.94
3191120--3191167	16	2.9	17	81	9	55	52	0	0	47	1.00
3191083--3191164	25	3.2	25	69	17	62	58	0	0	41	0.98
3193870--3193895	2	13.0	2	100	0	52	50	0	0	50	1.00
3195770--3195796	2	13.5	2	100	0	54	48	0	0	51	1.00
3195794--3195826	4	8.2	4	93	0	57	24	3	24	48	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3198878--3198918	2	20.5	2	94	0	73	53	46	0	0	1.00
3199553--3199581	2	14.5	2	100	0	58	0	48	0	51	1.00
3199581--3199613	2	16.5	2	100	0	66	48	0	0	51	1.00
3200656--3200720	21	3.1	21	76	10	62	49	0	0	50	1.00
3208776--3208804	2	14.5	2	100	0	58	48	0	51	0	1.00
3208893--3208923	2	15.5	2	100	0	62	48	0	0	51	1.00
3209116--3209170	25	2.2	25	96	0	101	40	1	23	34	1.66
3210080--3210116	19	1.9	19	88	0	56	32	2	2	62	1.23
3210092--3210153	27	2.1	31	88	11	96	35	0	0	64	0.94
3210099--3210143	16	2.8	16	79	3	54	33	0	0	66	0.92
3210100--3210163	27	2.3	28	79	12	71	39	0	0	60	0.97
3212983--3213033	20	2.6	19	78	9	57	33	0	0	66	0.92
3213553--3213579	2	13.5	2	100	0	54	48	0	0	51	1.00
3214215--3214248	17	2.0	17	88	0	50	58	0	0	41	0.98
3214631--3214668	14	2.7	15	88	12	62	42	0	0	57	0.98
3214599--3214660	25	2.5	24	80	17	65	43	4	0	51	1.23
3214868--3214907	21	2.0	20	85	5	53	30	0	0	70	0.88
3216248--3216283	15	2.3	16	95	4	65	52	0	0	47	1.00
3216955--3217008	17	3.2	17	75	19	67	57	0	0	42	0.98
3216971--3217003	9	3.7	9	92	8	50	60	0	0	39	0.97
3216944--3216997	24	2.4	21	75	21	56	61	0	1	37	1.07
3216955--3217022	34	2.1	32	91	5	109	57	1	0	41	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3218060--3218100	16	2.6	16	88	0	64	46	0	0	53	1.00
3218283--3218317	16	2.3	15	90	5	52	37	2	0	60	1.12
3224277--3224310	2	17.0	2	100	0	68	50	0	0	50	1.00
3229235--3229330	9	10.7	9	75	17	76	66	3	0	30	1.07
3229247--3229295	11	4.5	11	74	23	50	69	4	0	26	1.06
3229237--3229336	20	5.4	19	73	17	77	65	3	0	32	1.08
3231433--3231462	9	3.4	9	90	9	53	76	0	0	23	0.78
3232839--3232872	2	17.5	2	93	6	61	52	0	0	47	1.00
3238230--3238261	13	2.5	13	94	0	55	71	0	0	28	0.86
3238623--3238647	9	2.8	9	100	0	50	60	0	0	40	0.97
3245772--3245848	38	2.0	38	100	0	154	35	12	18	33	1.89
3247256--3247283	2	14.0	2	100	0	56	50	0	0	50	1.00
3247357--3247393	2	18.5	2	94	0	65	48	0	0	51	1.00
3249858--3249885	2	14.0	2	100	0	56	50	0	0	50	1.00
3259663--3259721	26	2.3	26	85	11	77	42	0	0	57	0.98
3259935--3259964	2	15.0	2	100	0	60	50	0	0	50	1.00
3259964--3259992	2	14.5	2	100	0	58	51	0	48	0	1.00
3260312--3260400	11	8.5	11	69	18	64	60	0	5	33	1.20
3260317--3260408	21	4.6	19	71	25	73	61	0	4	33	1.15
3260385--3260461	31	2.4	31	79	12	93	55	1	1	41	1.16
3261910--3261936	14	1.9	14	100	0	54	25	0	0	74	0.83
3264013--3264042	5	6.0	5	96	0	51	76	0	3	20	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3264868--3264895	2	14.0	2	100	0	56	50	0	0	50	1.00
3265146--3265226	20	4.1	21	75	12	82	43	0	0	56	0.99
3265187--3265235	18	2.7	19	82	14	52	46	0	0	53	1.00
3271457--3271498	20	2.0	20	86	4	57	42	0	2	54	1.13
3274103--3274148	14	3.1	16	76	17	55	47	4	0	47	1.21
3282333--3282366	2	17.0	2	93	0	59	50	2	0	47	1.16
3283704--3283801	11	8.6	11	79	10	99	31	0	1	67	0.98
3283707--3283800	23	4.0	24	86	6	113	29	0	1	69	0.96
3283707--3283802	33	2.8	34	82	4	122	31	0	1	67	0.97
3286387--3286413	2	13.5	2	100	0	54	48	0	0	51	1.00

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