genome.fa.s59.2.7.7.80.10.50.1000.21.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: Scaffold59
Parameters: 2 7 7 80 10 50 1000
Length:  3999109

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   

This is table  21  of  25  ( 2913 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)
3074839--3075837	507	2.0	506	93	3	1724	41	10	12	36	1.77
3079090--3079482	209	1.9	209	91	1	644	39	9	4	45	1.58
3079447--3079483	9	3.9	10	82	13	51	56	0	0	43	0.99
3079423--3079483	22	2.9	22	68	4	54	52	3	0	44	1.17
3079775--3079808	14	2.4	14	95	0	59	55	0	0	44	0.99
3080210--3080243	10	3.4	10	84	15	52	52	0	0	47	1.00
3080694--3080747	20	2.8	20	77	2	65	61	1	0	37	1.07
3081323--3081353	11	2.7	11	95	5	53	45	0	0	54	0.99
3081447--3081489	3	14.3	3	95	0	77	65	0	2	32	1.06
3081754--3081819	24	2.7	25	76	21	68	37	3	0	59	1.13
3082225--3082264	20	2.0	20	90	9	64	70	0	0	30	0.88
3082299--3082323	6	4.2	6	100	0	50	48	0	0	52	1.00
3082751--3082786	18	2.0	18	94	0	63	52	0	2	44	1.15
3082970--3083023	15	3.7	14	79	16	56	35	0	0	64	0.94
3083867--3083921	24	2.3	24	75	3	58	58	0	0	41	0.98
3084218--3084259	21	2.0	22	90	4	68	45	0	0	54	0.99
3084705--3084751	3	15.7	3	95	0	85	63	0	0	36	0.94
3084965--3085023	29	2.0	30	86	3	84	30	0	0	69	0.89
3084978--3085023	19	2.3	20	82	14	60	30	0	0	69	0.89
3085127--3085167	4	10.8	4	84	10	59	26	0	21	51	1.48
3085130--3085166	18	2.1	18	94	0	65	27	0	18	54	1.44
3090217--3090275	20	2.9	19	82	7	64	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3090233--3090278	19	2.5	19	82	3	58	60	0	0	39	0.97
3090448--3090483	10	3.7	10	85	7	56	44	0	2	52	1.15
3092126--3092161	15	2.3	16	90	4	56	44	2	0	52	1.15
3092123--3092184	17	3.7	16	75	16	54	48	3	0	48	1.17
3094111--3094146	19	1.9	18	88	5	54	66	0	0	33	0.92
3095192--3095227	2	18.0	2	100	0	72	50	0	0	50	1.00
3095499--3095555	2	30.5	2	79	13	59	45	5	0	49	1.24
3095508--3095546	15	2.6	16	84	16	64	46	5	0	48	1.24
3095508--3095547	14	2.8	15	88	11	66	45	5	0	50	1.23
3097218--3097262	20	2.2	20	84	7	56	44	0	0	55	0.99
3097368--3097400	12	2.8	12	90	4	50	30	0	0	69	0.88
3099973--3100025	14	3.6	14	80	10	52	60	0	0	39	0.97
3100069--3100127	16	3.4	17	80	17	68	37	0	0	62	0.95
3100075--3100142	25	2.7	26	75	6	68	38	0	0	61	0.96
3100074--3100142	17	4.1	16	74	17	52	37	0	0	62	0.96
3100196--3100262	16	4.1	16	70	21	50	34	2	1	61	1.20
3100667--3100767	32	3.3	29	77	15	98	48	0	0	50	1.07
3100723--3100773	13	3.0	19	65	31	51	49	0	0	50	1.00
3100667--3100772	14	7.0	14	69	20	54	49	0	0	50	1.07
3100723--3100790	32	2.1	33	88	2	102	45	0	0	54	0.99
3100780--3100826	24	2.0	22	88	8	67	29	2	0	68	1.02
3101251--3101298	22	2.2	22	84	0	60	60	2	0	37	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3101731--3101793	26	2.5	25	77	10	65	53	3	0	42	1.16
3103882--3103918	15	2.5	16	87	12	53	43	0	0	56	0.99
3103948--3103990	9	4.9	8	81	18	50	27	0	0	72	0.85
3103948--3103990	18	2.4	18	88	7	61	27	0	0	72	0.85
3104067--3104142	35	2.2	35	100	0	152	35	11	15	36	1.85
3104278--3104321	20	2.2	20	88	8	63	38	0	4	56	1.20
3104285--3104330	20	2.2	21	92	3	76	36	0	4	58	1.18
3104429--3104458	16	1.9	15	93	6	51	50	0	0	50	1.00
3104858--3104892	18	1.9	18	88	11	54	51	0	2	45	1.16
3107907--3107973	34	2.0	34	91	2	109	22	17	8	50	1.74
3112755--3112816	24	2.7	22	74	13	54	66	4	9	19	1.39
3113411--3113450	2	20.0	2	100	0	80	50	0	0	50	1.00
3114968--3115050	41	2.0	42	85	2	114	37	6	15	40	1.72
3114980--3115062	41	2.0	41	81	6	96	43	6	12	38	1.66
3118732--3118793	20	3.1	18	78	17	61	40	6	0	53	1.27
3118746--3118800	18	2.9	18	84	10	58	40	5	0	54	1.23
3119480--3119548	15	4.2	16	83	9	86	57	0	1	40	1.07
3119480--3119540	31	1.9	32	90	3	97	59	0	1	39	1.08
3119567--3119614	18	2.9	16	79	11	60	54	4	0	41	1.20
3119762--3119811	16	3.5	15	79	17	61	46	0	0	54	1.00
3120167--3120199	17	1.9	17	93	0	57	45	0	0	54	0.99
3120164--3120208	17	2.6	17	79	6	56	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3120199--3120270	27	2.6	28	76	14	69	36	0	2	61	1.11
3120141--3120254	27	4.3	26	71	17	74	37	0	1	59	1.14
3120176--3120255	17	4.7	17	74	9	74	36	0	2	61	1.10
3120223--3120267	17	2.6	18	82	7	56	35	0	0	64	0.94
3120233--3120270	12	3.5	11	82	10	51	36	0	0	63	0.95
3126479--3126517	18	2.2	17	86	13	53	64	0	15	20	1.30
3129634--3129715	32	2.5	32	77	13	87	41	3	4	50	1.41
3130829--3130872	13	3.3	13	87	3	61	22	2	4	70	1.17
3134959--3135001	17	2.3	17	84	15	50	62	0	4	32	1.15
3135733--3135780	25	1.9	25	86	0	69	68	2	2	27	1.11
3136067--3136110	22	2.0	22	100	0	88	50	9	18	22	1.75
3136147--3136202	24	2.2	24	84	9	67	51	0	5	42	1.24
3136157--3136213	24	2.4	24	81	0	69	50	0	3	45	1.18
3136658--3136683	2	13.0	2	100	0	52	50	0	0	50	1.00
3137092--3137434	89	3.9	89	81	2	280	33	12	11	41	1.80
3137712--3137825	7	16.6	7	76	17	100	42	1	2	53	1.25
3137706--3137826	2	66.0	2	73	19	104	42	1	2	52	1.24
3137723--3137825	11	9.6	11	79	14	126	42	1	1	53	1.23
3137696--3137825	17	8.0	17	76	16	107	41	2	3	53	1.29
3137706--3137826	43	2.9	42	78	12	133	42	1	2	52	1.24
3144616--3144645	2	15.0	2	92	0	51	50	3	46	0	1.18
3145022--3145048	2	13.5	2	100	0	54	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3145968--3145996	5	5.8	5	100	0	58	62	20	0	17	1.33
3146492--3146523	2	16.0	2	100	0	64	50	0	0	50	1.00
3146524--3146549	2	13.0	2	100	0	52	0	0	50	50	1.00
3148623--3148653	15	2.1	15	100	0	62	38	0	19	41	1.51
3153204--3153271	27	2.5	27	100	0	136	16	13	41	29	1.86
3155477--3155521	20	2.2	20	88	0	63	44	11	13	31	1.78
3160440--3160566	62	2.0	63	87	6	186	38	0	29	31	1.58
3160652--3160707	11	5.0	11	74	18	53	78	0	16	5	0.92
3160653--3160720	31	2.2	31	81	5	75	79	0	13	7	0.93
3160651--3160708	29	2.0	28	83	12	73	77	0	15	6	0.97
3165398--3165438	16	2.5	16	84	4	55	43	0	0	56	0.99
3166066--3166109	23	1.9	23	86	9	63	65	0	2	31	1.05
3168985--3169062	26	3.0	26	82	0	102	26	19	23	30	1.98
3169308--3169371	34	1.9	33	84	15	87	40	0	0	59	0.97
3169316--3169372	17	3.0	19	75	12	55	40	0	0	59	0.97
3169906--3169939	13	2.6	13	85	0	50	44	8	14	32	1.76
3171004--3171042	20	1.9	21	84	5	53	38	2	0	58	1.12
3171071--3171146	24	3.2	25	81	12	79	48	1	1	48	1.18
3172967--3173004	3	12.7	3	100	0	76	34	0	0	65	0.93
3176491--3176659	89	1.9	89	97	1	322	26	20	14	37	1.92
3176740--3176799	31	1.9	31	100	0	120	40	21	15	23	1.91
3177916--3177999	39	2.2	39	89	2	125	47	9	3	39	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3180175--3180233	9	6.6	9	70	14	50	35	0	1	62	1.05
3180156--3180215	28	2.1	29	87	3	86	33	0	5	61	1.17
3180165--3180230	10	6.7	10	75	15	57	34	0	3	62	1.11
3180179--3180219	16	2.4	18	88	8	59	39	0	2	58	1.11
3180179--3180227	20	2.6	19	84	9	64	38	0	2	59	1.09
3180853--3180886	10	3.4	10	87	0	50	32	0	0	67	0.91
3180841--3180930	28	3.2	28	74	12	94	36	0	1	62	1.03
3181818--3181862	18	2.6	17	82	6	54	31	2	2	64	1.18
3182301--3182331	8	3.9	8	91	0	53	29	0	0	70	0.87
3184043--3184102	25	2.4	24	89	10	93	16	10	21	51	1.73

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