genome.fa.s3.2.7.7.80.10.50.1000.4.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  4  of  32  ( 3795 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)
349931--349977	15	3.2	15	79	8	53	59	0	0	40	0.97
351554--351599	24	1.9	24	86	8	67	52	0	0	47	1.00
352161--352241	32	2.5	32	86	4	101	51	0	3	44	1.19
352190--352255	16	4.1	16	72	16	57	50	0	1	48	1.10
352243--352294	25	2.1	24	89	7	77	65	0	0	34	0.93
352244--352296	16	3.5	15	79	10	63	66	0	0	33	0.92
352257--352296	21	1.9	21	89	0	62	67	0	0	32	0.91
357540--357582	19	2.1	21	83	8	54	51	0	2	46	1.13
358613--358668	22	2.6	23	83	8	64	58	1	0	39	1.08
358728--358753	2	13.0	2	100	0	52	50	0	0	50	1.00
358870--358911	3	14.0	3	100	0	84	66	0	0	33	0.92
359486--359536	5	10.2	5	75	8	50	70	0	0	29	0.87
359606--359702	36	2.5	37	75	12	99	57	0	1	41	1.05
359667--359709	16	2.7	15	82	7	50	60	0	0	39	0.97
360719--360776	19	3.1	18	78	16	55	31	0	0	68	0.89
361268--361301	2	16.5	2	93	6	59	50	0	2	47	1.16
361301--361344	2	22.0	2	100	0	88	50	0	50	0	1.00
362051--362188	38	3.6	38	87	0	177	33	13	24	28	1.93
362046--362186	76	1.9	76	86	0	201	32	12	25	29	1.93
362044--362212	38	4.4	38	85	0	176	30	13	27	28	1.94
366758--366935	38	4.7	38	86	3	205	29	15	29	26	1.96
367537--367604	30	2.3	29	79	13	77	44	4	7	44	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
367721--367779	26	2.3	27	80	14	70	44	0	1	54	1.10
368362--368405	16	2.5	17	82	14	54	56	0	6	36	1.26
370909--370980	34	2.1	35	82	15	87	47	0	0	52	1.00
371467--371605	38	3.7	38	83	1	163	31	26	10	30	1.90
371451--371605	76	2.0	76	83	2	195	30	28	10	29	1.91
379209--379233	13	1.9	13	100	0	50	32	16	16	36	1.90
379189--379256	33	2.1	33	91	2	111	35	16	14	33	1.89
385739--385776	20	1.9	20	94	0	67	42	13	15	28	1.85
386232--386486	127	2.0	128	99	0	503	29	21	18	30	1.97
387287--387434	74	2.0	74	94	0	260	37	16	14	31	1.89
394513--394550	18	2.1	18	85	9	51	23	5	2	68	1.23
398917--398953	3	12.3	3	100	0	74	64	0	0	35	0.94
399640--399673	17	2.1	16	89	10	52	58	0	0	41	0.98
400843--400896	18	3.1	18	77	20	60	33	1	0	64	1.04
402356--402385	7	4.3	7	100	0	60	40	0	0	60	0.97
403319--403378	19	3.6	16	82	10	61	40	0	8	51	1.32
403367--403400	13	2.7	13	86	4	52	29	2	0	67	1.05
403364--403400	18	2.1	18	90	10	58	32	2	0	64	1.07
403808--403855	17	2.7	17	78	15	53	54	0	0	45	0.99
404301--404342	3	14.0	3	100	0	84	66	0	0	33	0.92
404550--404613	26	2.3	28	89	7	96	56	1	0	42	1.09
406170--406196	2	13.5	2	100	0	54	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)
406259--406298	11	3.9	11	81	15	50	57	0	2	40	1.12
406259--406298	15	2.6	15	88	4	62	57	0	2	40	1.12
407538--407590	28	1.9	27	88	3	79	37	0	0	62	0.96
412864--412937	12	6.0	12	69	13	53	50	4	1	44	1.29
412921--412991	15	4.5	17	76	16	64	56	0	0	43	0.99
412928--412970	22	2.0	21	86	4	59	55	0	0	44	0.99
412917--412991	17	4.7	17	67	18	54	57	0	0	42	0.98
413965--414018	21	2.6	21	83	13	60	53	0	0	46	1.00
415477--415515	2	19.5	2	100	0	78	48	0	0	51	1.00
415704--415737	16	2.1	17	88	5	52	55	17	2	23	1.55
416705--416806	16	6.4	16	74	12	84	33	5	3	56	1.42
416725--416794	31	2.2	30	80	14	79	35	5	2	55	1.38
416699--416815	16	7.3	16	72	10	71	34	5	5	54	1.47
417830--417868	15	2.5	15	87	4	51	46	2	2	48	1.29
417887--417914	14	2.0	14	100	0	56	50	7	0	42	1.30
417932--417997	21	3.2	21	79	12	75	59	1	0	39	1.07
417921--417977	20	2.6	22	75	16	64	57	1	0	40	1.09
417933--418003	20	3.5	19	78	16	72	56	1	0	42	1.08
418111--418188	30	2.5	30	81	8	77	50	2	1	46	1.23
418162--418220	31	1.9	30	83	16	59	52	1	3	42	1.28
425359--425460	20	5.1	20	72	5	73	32	8	18	40	1.82
425397--425460	19	3.3	19	78	4	83	31	6	20	42	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
425373--425460	39	2.3	39	93	0	149	30	9	20	39	1.83
427421--427469	20	2.6	19	77	6	55	44	0	2	53	1.12
428189--428250	23	2.5	24	82	15	74	61	0	0	38	0.96
428670--428701	6	5.3	6	96	0	55	46	34	18	0	1.49
433543--433585	18	2.4	18	85	11	54	55	4	4	34	1.41
434534--434579	22	2.1	21	84	11	58	50	4	2	43	1.34
443433--443465	16	2.2	15	89	10	50	21	0	72	6	1.05
455551--455579	2	15.0	2	92	7	51	51	0	0	48	1.00
459181--459213	13	2.4	14	90	5	50	42	6	3	48	1.43
459691--459753	4	15.8	4	93	0	72	44	26	6	22	1.76
464573--464606	13	2.5	14	95	4	61	29	26	29	14	1.95
464573--464606	7	5.0	7	92	7	61	29	26	29	14	1.95
465986--466066	34	2.4	34	81	10	94	55	1	0	43	1.07
465988--466061	20	4.1	19	72	25	70	56	1	0	41	1.07
465994--466065	18	4.0	18	76	23	71	56	0	0	43	0.99
467779--467872	37	2.4	39	82	14	120	62	11	6	19	1.49
468409--468437	2	15.0	2	92	7	51	51	0	0	48	1.00
468343--468473	66	2.0	66	93	0	226	38	9	16	35	1.80
471233--471277	15	2.9	15	86	3	63	40	2	0	57	1.11
471561--471595	2	17.5	2	100	0	70	48	0	0	51	1.00
474161--474235	31	2.4	31	95	0	123	52	2	8	37	1.45
484980--485022	22	2.0	22	90	0	68	34	9	2	53	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
485477--485518	21	2.0	20	86	4	57	47	0	0	52	1.00
487268--487303	18	1.9	19	94	5	65	33	0	5	61	1.19
487934--487993	28	2.1	28	82	11	70	40	0	3	56	1.16
490658--490757	49	2.0	49	82	3	121	42	4	10	44	1.56
492356--492389	17	1.9	18	88	5	52	85	2	11	0	0.71
496058--496103	24	1.9	24	86	0	65	34	6	26	32	1.82
496082--496123	18	2.4	18	88	4	59	40	2	26	30	1.69
498490--498532	9	4.8	9	80	8	52	44	0	0	55	0.99
498496--498550	9	5.7	10	79	14	53	38	0	0	61	0.96
499132--499176	18	2.3	20	85	7	58	31	0	2	66	1.04
499571--499657	28	3.0	29	76	15	83	56	0	0	43	0.99
499593--499647	23	2.5	22	80	8	67	54	0	0	45	0.99
499582--499682	28	3.6	27	70	12	69	57	0	0	42	0.98
500002--500069	28	2.5	28	85	7	86	45	0	0	54	0.99
500006--500039	18	1.9	17	88	5	50	55	0	0	44	0.99
500228--500256	15	1.9	15	100	0	58	62	0	10	27	1.28
500243--500290	23	2.1	22	85	11	62	64	0	2	33	1.05
501258--501310	16	3.2	16	80	15	56	33	0	0	66	0.92
501258--501310	18	3.2	16	84	10	63	33	0	0	66	0.92
504381--504444	22	3.0	22	84	11	71	64	0	0	35	0.94
504381--504432	11	4.6	11	79	11	52	65	0	0	34	0.93
504390--504464	27	2.8	27	82	11	91	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
504398--504446	11	4.6	11	85	7	57	63	0	0	36	0.95
504386--504446	20	3.0	20	85	9	70	63	0	0	36	0.94
504428--504501	32	2.3	32	86	4	96	52	1	0	45	1.09
504404--504551	20	7.7	19	69	23	71	56	1	0	41	1.07
504503--504573	30	2.4	29	82	11	83	61	5	1	30	1.27
504842--504872	2	15.5	2	100	0	62	51	0	0	48	1.00
506014--506113	50	2.0	50	96	3	184	44	18	12	26	1.84
506176--506392	34	6.4	34	83	2	258	25	7	25	41	1.82
506176--506391	102	2.1	102	87	0	317	25	7	25	41	1.82
510805--511023	34	6.5	34	84	2	271	26	7	25	40	1.82

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