genome.fa.s4.2.7.7.80.10.50.1000.17.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  17  of  31  ( 3628 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)
3978638--3978672	6	5.7	6	86	6	52	34	0	0	65	0.93
3978638--3978676	12	3.2	13	89	7	55	33	0	0	66	0.92
3978996--3979021	13	2.0	13	100	0	52	53	0	0	46	1.00
3978976--3979032	15	4.1	14	73	24	50	52	0	0	47	1.00
3979471--3979497	7	3.9	7	100	0	54	14	29	29	25	1.95
3979977--3980010	9	3.9	9	84	7	52	29	0	0	70	0.87
3981129--3981186	26	2.2	27	87	3	82	34	5	0	60	1.19
3981779--3981817	19	2.1	17	86	13	51	66	0	0	33	0.92
3982417--3982461	18	2.3	21	74	22	60	48	0	0	51	1.00
3982429--3982463	9	3.8	9	88	3	52	51	0	0	48	1.00
3982421--3982458	18	2.1	18	95	0	67	47	0	0	52	1.00
3983573--3983622	26	1.9	26	84	8	66	40	8	20	32	1.81
3992384--3992448	27	2.5	26	71	9	62	50	1	0	47	1.10
4003738--4003777	14	2.9	14	88	0	53	45	7	0	47	1.31
4004542--4004582	15	2.7	15	96	3	73	39	21	24	14	1.91
4008152--4008189	12	3.2	12	88	7	51	60	0	7	31	1.25
4014773--4014798	3	8.7	3	100	0	52	65	0	0	34	0.93
4014809--4014841	2	16.5	2	100	0	66	0	48	0	51	1.00
4014841--4014873	2	16.5	2	100	0	66	48	0	0	51	1.00
4016038--4016088	19	2.6	19	84	3	66	64	0	0	35	0.94
4016053--4016094	19	2.4	17	84	11	50	64	0	0	35	0.94
4020432--4020472	15	2.6	16	82	14	50	48	0	2	48	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4021257--4021309	23	2.3	24	77	9	65	26	1	0	71	0.96
4021264--4021317	17	3.2	16	84	15	65	27	1	0	70	0.98
4021254--4021317	15	3.9	17	78	14	64	28	1	0	70	0.97
4021908--4021950	17	2.4	18	81	14	54	27	0	2	69	1.00
4021918--4021949	17	1.9	17	93	6	57	28	0	3	68	1.04
4021905--4021992	16	5.6	16	74	22	64	26	3	1	69	1.11
4022039--4022082	21	2.1	21	83	8	54	36	0	2	61	1.09
4024907--4024936	2	15.0	2	100	0	60	50	0	0	50	1.00
4027125--4027171	2	23.5	2	100	0	94	51	0	0	48	1.00
4028487--4028639	38	4.1	38	90	1	209	27	29	15	28	1.96
4032610--4032743	66	2.0	66	100	0	268	26	23	14	35	1.94
4033292--4033424	38	3.5	38	88	0	158	32	23	9	34	1.87
4033634--4033722	23	3.7	24	73	14	67	39	0	3	57	1.15
4033700--4033747	19	2.5	20	83	13	64	35	0	2	62	1.07
4033975--4034001	2	13.5	2	100	0	54	0	48	0	51	1.00
4035029--4035099	22	3.2	22	76	9	72	36	4	11	47	1.59
4035107--4035133	9	3.0	9	100	0	54	44	0	0	55	0.99
4036499--4036533	18	1.9	18	88	11	54	11	2	11	74	1.18
4037307--4037343	2	18.5	2	94	0	65	45	0	0	54	1.00
4039231--4039260	14	2.1	14	100	0	60	50	0	0	50	1.00
4039832--4039865	2	17.0	2	100	0	68	50	0	50	0	1.00
4040932--4040974	22	1.9	22	90	4	68	37	4	11	46	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4040931--4040980	22	2.3	22	83	10	66	32	6	10	52	1.59
4042627--4042662	16	2.2	16	95	0	63	61	0	0	38	0.96
4049400--4049437	2	19.0	2	100	0	76	50	0	0	50	1.00
4049738--4049784	18	2.5	18	86	6	58	46	0	0	53	1.00
4049750--4049786	18	2.1	18	94	0	65	40	0	0	59	0.97
4050489--4050529	2	21.0	2	95	5	75	48	0	0	51	1.00
4052945--4052985	21	2.0	21	90	0	64	46	9	9	34	1.70
4053148--4053199	19	2.7	19	81	0	68	53	0	0	46	1.00
4053184--4053218	14	2.5	15	90	9	56	40	0	0	60	0.97
4053427--4053526	43	2.3	43	91	0	155	36	9	14	41	1.77
4053536--4053647	59	2.0	53	88	10	161	26	15	17	40	1.89
4054213--4054252	3	13.3	3	100	0	80	32	0	0	67	0.91
4057820--4057928	21	5.2	21	80	6	96	51	4	4	39	1.43
4057821--4057922	42	2.5	42	83	4	127	50	3	4	41	1.42
4057821--4057927	41	2.6	41	81	11	121	51	3	4	40	1.41
4057904--4057962	31	1.9	30	82	6	73	55	1	6	35	1.36
4057967--4058012	21	2.2	21	84	3	58	52	4	6	36	1.47
4057821--4058012	42	4.6	42	71	11	119	52	3	5	38	1.43
4058067--4058142	21	3.6	21	68	18	59	43	11	7	36	1.71
4058130--4058232	21	4.9	21	77	9	84	53	10	4	31	1.56
4058503--4058538	12	3.0	12	100	0	72	58	0	0	41	0.98
4058503--4058565	24	2.5	26	82	10	69	50	1	0	47	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4058863--4058965	21	4.8	21	76	10	93	52	4	0	41	1.29
4059126--4059177	22	2.5	20	76	11	50	53	5	7	32	1.53
4059243--4059379	21	6.5	21	79	12	111	56	7	1	34	1.36
4059256--4059379	42	3.0	40	83	8	149	56	7	1	34	1.37
4059243--4059364	63	1.9	63	83	9	160	58	6	1	33	1.34
4059283--4059398	42	2.8	42	81	6	121	53	9	3	33	1.50
4059965--4060010	19	2.3	20	78	14	51	58	0	4	36	1.18
4062943--4062996	14	3.8	15	78	11	60	46	0	0	53	1.00
4062920--4063000	27	3.0	28	76	20	82	50	0	0	49	1.00
4062913--4063000	14	5.9	15	70	20	53	48	1	0	50	1.08
4065993--4066026	2	17.5	2	93	6	61	50	0	0	50	1.00
4066135--4066210	28	2.8	26	79	15	75	36	2	0	60	1.11
4066145--4066257	30	3.8	30	79	10	124	37	7	1	53	1.38
4066766--4066797	2	16.0	2	100	0	64	50	0	0	50	1.00
4067377--4067406	15	1.9	16	93	6	53	40	0	16	43	1.48
4067898--4067941	22	1.9	24	90	9	74	29	0	0	70	0.88
4068803--4068835	2	16.5	2	100	0	66	51	0	0	48	1.00
4069205--4069260	21	2.8	21	76	18	64	39	0	0	60	0.97
4069207--4069259	27	2.0	27	85	14	74	37	0	0	62	0.96
4069246--4069309	30	2.2	29	86	8	85	40	3	0	56	1.15
4071609--4071649	11	3.8	11	75	18	50	65	0	0	34	0.93
4073271--4073299	3	9.7	3	100	0	58	31	0	0	68	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4073610--4073634	13	1.9	13	100	0	50	92	0	8	0	0.40
4073881--4073908	5	5.6	5	100	0	56	57	0	42	0	0.99
4074211--4074244	17	1.9	17	88	5	50	61	2	8	26	1.40
4077116--4077258	57	2.5	57	82	11	161	51	5	20	21	1.68
4077156--4077313	77	2.1	77	80	4	176	52	5	20	22	1.65
4077253--4077336	20	4.3	20	73	8	66	53	5	17	22	1.65
4077228--4077372	57	2.5	57	80	4	166	51	6	18	23	1.70
4077106--4077412	134	2.3	134	87	5	433	50	6	20	22	1.71
4077253--4077392	57	2.4	58	79	8	135	52	6	18	22	1.68
4078613--4078641	13	2.1	14	93	6	51	51	0	0	48	1.00
4078997--4079036	3	13.0	3	94	5	71	65	0	2	32	1.06
4080756--4080786	14	2.2	14	100	0	62	54	12	19	12	1.70
4087115--4087155	20	2.0	20	86	9	57	31	0	2	65	1.05
4087382--4087421	21	1.9	21	90	10	64	42	0	0	57	0.98
4087744--4087869	17	7.3	17	70	18	64	37	1	2	58	1.20
4087757--4087857	27	4.0	26	72	25	72	39	0	1	57	1.17
4088770--4088829	16	3.8	16	73	18	54	56	1	3	38	1.26
4089629--4089653	2	12.5	2	100	0	50	52	0	0	48	1.00
4090780--4090821	2	21.0	2	100	0	84	50	0	0	50	1.00
4091679--4091715	16	2.2	18	85	9	51	2	8	2	86	0.76
4093532--4093573	6	7.0	6	94	0	57	57	0	30	11	1.35
4099107--4099138	16	2.1	16	88	11	50	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4099129--4099168	14	2.9	14	81	3	55	62	0	0	37	0.95
4099129--4099182	26	2.0	26	86	13	74	64	0	0	35	0.94
4105728--4105838	34	3.2	34	77	13	111	43	2	0	54	1.14
4114147--4114176	13	2.3	13	100	0	60	33	0	6	60	1.23
4114152--4114189	13	3.4	11	89	10	51	36	0	5	57	1.21
4114448--4114487	12	3.3	13	76	16	50	45	0	0	55	0.99
4114444--4114507	29	2.3	28	79	15	71	46	0	0	53	1.00
4114757--4114790	2	17.0	2	100	0	68	50	0	0	50	1.00
4115418--4115453	3	12.0	3	93	0	63	66	2	0	30	1.06
4119009--4119054	2	23.5	2	95	4	85	50	0	0	50	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   25   26   27   28   29   30   31