genome.fa.s64.2.7.7.80.10.50.1000.23.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  23  of  45  ( 5312 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)
4200292--4200326	17	2.1	17	94	0	61	34	5	8	51	1.56
4202818--4202850	2	16.5	2	100	0	66	0	48	0	51	1.00
4211098--4211140	18	2.4	18	88	0	59	79	0	20	0	0.74
4211952--4212001	23	2.1	25	81	7	59	54	2	0	44	1.11
4212184--4212273	35	3.0	29	72	20	76	46	2	0	51	1.13
4212240--4212281	22	1.9	23	85	9	61	45	2	0	52	1.13
4212812--4212869	24	2.4	23	80	11	71	32	0	3	63	1.11
4213367--4213406	14	2.6	16	88	11	57	52	0	5	42	1.23
4214230--4214265	13	2.8	13	95	0	63	38	11	16	33	1.84
4214456--4214500	20	2.1	22	88	8	67	33	11	8	46	1.70
4217076--4217101	12	2.2	12	100	0	52	34	15	15	34	1.89
4220200--4220239	20	2.0	20	100	0	80	30	10	10	50	1.69
4223107--4223185	33	2.4	33	95	0	149	36	16	10	36	1.82
4223597--4223661	34	1.9	34	83	0	85	44	9	1	44	1.45
4224527--4224559	15	2.1	16	88	11	50	24	0	0	75	0.80
4225081--4225134	28	2.0	28	85	3	74	35	1	5	57	1.33
4225246--4225287	16	2.6	16	84	0	57	50	0	0	50	1.00
4225467--4225525	24	2.5	23	76	13	57	37	0	3	59	1.14
4225710--4225811	22	4.4	24	65	15	61	54	0	2	41	1.22
4225791--4225848	18	3.2	18	72	13	57	56	0	0	43	0.99
4225830--4225881	21	2.4	22	78	21	56	65	0	0	34	0.93
4225890--4225918	14	2.0	15	93	6	51	62	0	0	37	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4228142--4228551	79	5.2	79	84	4	542	31	15	26	26	1.95
4228135--4228551	155	2.7	155	86	4	597	32	14	26	26	1.95
4228487--4228653	51	3.3	50	86	5	210	31	13	26	28	1.93
4231031--4231055	13	1.9	13	100	0	50	32	20	16	32	1.94
4236584--4236615	5	6.6	5	92	7	57	40	0	0	59	0.97
4237067--4237141	16	4.9	16	68	14	50	50	0	4	45	1.20
4237587--4237642	12	4.6	12	75	18	53	37	0	0	62	0.95
4237586--4237653	27	2.4	28	87	4	93	36	0	0	63	0.95
4237581--4237640	13	4.5	13	82	12	68	40	0	0	60	0.97
4237610--4237700	21	4.2	22	72	15	64	42	1	0	56	1.06
4237586--4237668	29	3.0	27	85	7	94	38	0	0	61	0.96
4237615--4237668	22	2.6	20	82	5	63	38	0	0	61	0.96
4237560--4237674	44	2.6	46	75	12	105	43	0	0	56	0.99
4237673--4237740	27	2.4	29	80	14	79	54	1	0	44	1.09
4237713--4237774	22	2.9	22	75	15	67	58	0	0	41	0.98
4237756--4237813	24	2.4	24	82	5	73	46	0	0	53	1.00
4237772--4237844	40	1.9	38	83	10	96	47	0	0	52	1.00
4237779--4237838	21	3.0	21	74	13	63	50	0	0	50	1.00
4237859--4237886	2	14.0	2	100	0	56	50	0	0	50	1.00
4238950--4239010	21	3.0	21	79	15	65	34	0	1	63	1.04
4240944--4240984	21	2.0	21	86	9	59	53	2	2	41	1.27
4241517--4241550	18	1.9	18	88	5	52	47	2	2	47	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4242516--4242559	23	2.0	22	86	13	63	68	0	0	31	0.90
4242509--4242571	21	3.1	21	77	6	60	66	0	0	33	0.92
4242630--4242665	2	18.0	2	94	0	63	47	2	0	50	1.15
4246468--4246542	20	3.9	20	68	20	61	41	0	0	58	0.98
4246476--4246545	16	4.1	17	71	16	56	41	0	0	58	0.98
4246427--4246592	89	1.9	84	79	15	178	46	0	0	52	1.04
4246504--4246630	18	7.3	18	65	22	58	44	0	0	55	1.05
4246461--4246610	27	5.3	28	71	18	98	44	0	0	54	1.04
4251495--4251581	32	2.5	37	85	12	121	51	0	0	48	1.00
4251527--4251581	18	2.8	20	72	25	55	50	0	0	49	1.00
4261747--4261890	71	2.0	71	89	0	216	22	18	20	38	1.94
4267819--4267859	18	2.2	19	83	12	50	19	17	0	63	1.31
4268480--4268515	16	2.2	16	100	0	72	44	0	11	44	1.39
4268517--4268578	32	1.9	32	90	0	97	24	22	22	30	1.99
4268766--4268829	30	2.2	29	78	10	78	64	0	1	34	1.03
4268824--4268869	18	2.6	17	83	10	56	56	2	0	41	1.11
4268828--4268887	15	3.8	16	77	16	63	55	1	0	43	1.10
4268842--4268894	26	2.0	27	81	7	63	56	1	0	41	1.10
4268770--4268883	15	7.6	16	70	21	54	59	0	0	38	1.09
4269045--4269069	12	2.1	12	100	0	50	56	0	0	44	0.99
4269087--4269119	16	2.1	16	94	0	57	36	3	0	60	1.12
4269118--4269167	19	2.6	20	78	15	61	44	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4269118--4269169	20	2.8	19	82	11	63	44	0	0	55	0.99
4269895--4269923	4	7.2	4	100	0	58	27	0	0	72	0.85
4270727--4270762	19	1.9	20	88	11	58	50	2	0	47	1.15
4270765--4270806	21	2.1	19	86	13	57	64	0	0	35	0.94
4272759--4272797	21	1.9	20	89	5	60	38	0	7	53	1.30
4273464--4273544	39	2.0	40	83	2	101	39	11	2	46	1.53
4274073--4274187	11	11.5	11	70	15	54	36	1	1	60	1.18
4274093--4274155	19	3.3	18	78	6	63	31	1	3	63	1.19
4274987--4275012	9	2.9	9	100	0	52	30	0	0	69	0.89
4275236--4275331	48	2.0	49	91	2	158	45	6	9	38	1.62
4275574--4275637	29	2.2	28	81	8	76	50	0	0	50	1.00
4284248--4284291	19	2.3	20	88	7	65	75	2	0	22	0.92
4285295--4285320	13	2.0	13	100	0	52	30	0	0	69	0.89
4286761--4286791	2	15.5	2	100	0	62	51	0	0	48	1.00
4290586--4290611	2	13.0	2	100	0	52	50	0	0	50	1.00
4291664--4291748	39	2.3	37	76	17	88	47	1	0	51	1.08
4291672--4291739	23	2.9	23	71	28	63	44	1	0	54	1.09
4294400--4294428	2	14.5	2	100	0	58	48	0	0	51	1.00
4294706--4294746	22	1.9	22	90	5	66	58	0	0	41	0.98
4296518--4296556	21	1.9	21	89	5	62	43	0	0	56	0.99
4296817--4296887	30	2.3	32	73	9	76	43	1	1	53	1.18
4297572--4297616	2	22.5	2	100	0	90	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4302016--4302064	26	1.9	25	87	4	71	65	2	0	32	1.04
4302087--4302134	15	3.1	15	90	3	69	60	0	0	39	0.97
4302154--4302188	15	2.3	15	90	0	52	74	0	0	25	0.82
4302469--4302501	17	1.9	17	93	0	57	27	3	0	69	1.03
4304575--4304624	15	3.5	15	75	10	59	42	0	0	58	0.98
4304957--4304988	2	16.0	2	100	0	64	50	0	0	50	1.00
4305117--4305150	17	2.0	17	88	0	50	47	0	8	44	1.34
4309131--4309176	21	2.2	20	81	7	56	63	0	0	36	0.95
4310179--4310237	31	1.9	31	86	6	84	23	1	5	69	1.18
4310791--4310826	17	2.2	16	90	9	56	30	5	11	52	1.59
4310781--4310826	15	2.8	17	80	12	60	34	4	8	52	1.52
4312470--4312513	23	1.9	23	86	9	63	45	4	0	50	1.22
4312811--4312853	22	2.0	22	85	0	59	51	2	4	41	1.35
4313120--4313158	3	13.3	3	89	5	62	30	0	2	66	1.05
4313119--4313158	20	2.0	20	95	0	71	30	0	2	67	1.04
4313123--4313156	17	2.0	17	94	0	59	29	0	2	67	1.05
4314710--4314748	17	2.4	16	84	12	53	51	7	0	41	1.31
4315432--4315469	3	13.0	3	94	5	69	68	0	0	31	0.90
4316486--4316525	21	2.0	20	90	5	62	62	0	0	37	0.95
4316881--4316910	13	2.3	13	94	0	51	60	0	3	36	1.14
4316894--4316985	17	5.0	17	70	17	67	51	2	0	46	1.13
4316907--4316957	19	2.5	20	81	15	61	47	1	0	50	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4329294--4329338	20	2.2	20	88	0	63	42	6	22	28	1.79
4331061--4331109	20	2.4	20	79	3	53	38	8	22	30	1.83
4333162--4333232	24	3.0	25	70	14	69	43	0	0	56	0.99
4333987--4334019	16	2.0	17	88	5	50	54	0	0	45	0.99
4334073--4334121	20	2.5	19	81	15	55	46	2	10	40	1.49
4334853--4335796	246	3.9	248	90	3	1393	39	10	13	36	1.79
4334853--4335796	489	1.9	487	88	4	1438	39	10	13	36	1.79
4336255--4336299	16	2.8	16	82	3	54	60	0	0	40	0.97
4337083--4337135	16	3.1	17	84	15	65	43	0	0	56	0.99
4337539--4337568	12	2.6	11	90	10	51	70	0	0	30	0.88

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