genome.fa.s25.2.7.7.80.10.50.1000.54.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  54  of  56  ( 6609 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)
9211582--9211607	13	2.0	13	100	0	52	38	15	15	30	1.88
9211564--9211627	32	2.0	33	87	3	94	40	17	14	28	1.88
9216151--9216217	33	2.0	33	88	0	98	40	13	11	34	1.81
9216173--9216197	13	1.9	13	100	0	50	32	16	16	36	1.90
9216848--9216892	21	2.1	22	88	8	67	55	4	17	22	1.60
9218696--9218727	15	2.1	15	94	0	55	46	15	21	15	1.83
9220772--9220809	13	2.9	13	100	0	76	31	15	15	36	1.90
9220930--9220975	21	2.2	20	81	11	58	34	19	4	41	1.71
9222583--9222655	36	2.0	36	97	0	137	36	2	23	36	1.69
9226412--9226476	13	5.0	13	94	0	112	35	15	18	30	1.92
9226412--9226475	26	2.5	26	100	0	128	34	15	18	31	1.93
9226462--9226540	20	3.7	20	78	15	77	44	15	15	25	1.85
9230383--9230427	21	2.1	21	84	8	56	22	20	4	53	1.63
9232622--9232673	19	2.7	20	85	11	72	28	13	15	42	1.85
9233545--9233570	13	2.0	13	100	0	52	38	15	15	30	1.88
9233527--9233590	32	2.0	33	87	3	94	40	17	14	28	1.88
9234346--9234410	18	3.6	17	80	15	78	53	1	0	44	1.09
9234395--9234468	40	1.9	40	83	8	100	58	1	1	39	1.15
9234396--9234469	28	2.6	31	80	16	81	59	1	1	37	1.14
9234574--9234640	16	4.2	16	73	3	55	52	17	7	22	1.70
9234642--9234694	16	3.3	17	82	10	58	52	13	0	33	1.40
9236575--9236638	28	2.2	30	83	13	89	68	4	3	23	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9236583--9236646	28	2.2	28	78	10	67	70	3	1	25	1.11
9236630--9236700	32	2.1	32	82	10	79	59	2	0	38	1.12
9236727--9236772	17	2.8	17	78	12	51	67	4	0	28	1.10
9236713--9236773	26	2.3	26	80	5	70	65	3	0	31	1.09
9240194--9240254	24	2.6	22	78	16	61	45	0	0	54	1.00
9241770--9241802	7	4.9	7	92	7	59	12	0	0	87	0.53
9241770--9241802	13	2.4	14	95	5	59	12	0	0	87	0.53
9242069--9242130	30	2.1	31	90	6	101	43	0	0	56	0.99
9242146--9242183	10	3.5	11	85	10	51	52	0	0	47	1.00
9242447--9242512	32	2.0	33	85	2	89	42	9	7	40	1.65
9245292--9245361	36	1.9	36	94	0	122	31	12	12	42	1.81
9246761--9247069	23	13.5	23	71	18	96	1	20	25	52	1.55
9246759--9247162	11	35.5	11	68	22	157	1	19	25	52	1.55
9246921--9247163	45	5.2	44	71	19	145	1	19	26	52	1.55
9246878--9247163	79	3.8	75	75	17	247	1	18	26	53	1.53
9247049--9247102	15	3.3	15	76	16	54	1	20	22	55	1.53
9246998--9247098	9	11.4	9	72	20	72	0	18	24	55	1.49
9247080--9247164	24	3.7	22	70	17	66	2	16	24	56	1.52
9247584--9247631	17	2.7	17	87	12	62	64	0	0	35	0.94
9251918--9251957	21	1.9	21	89	0	62	57	0	0	42	0.98
9256294--9256349	23	2.4	23	71	11	60	71	1	0	26	0.96
9256426--9256467	14	3.1	14	86	6	59	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)
9256428--9256476	19	2.6	18	81	9	53	67	0	0	32	0.91
9256556--9256605	17	3.0	17	72	13	50	74	4	2	20	1.08
9256728--9256800	2	35.5	2	78	8	58	45	4	6	43	1.49
9259053--9259083	15	2.1	15	93	0	53	12	0	6	80	0.89
9260041--9260082	21	2.0	22	85	4	59	47	0	0	52	1.00
9260047--9260088	22	2.0	21	85	4	57	45	0	2	52	1.13
9260000--9260263	137	1.9	138	90	2	424	54	2	1	41	1.24
9260153--9260192	22	1.9	20	90	10	62	62	0	0	37	0.95
9260183--9260225	22	2.0	22	81	9	52	48	0	0	51	1.00
9260497--9260535	2	19.5	2	100	0	78	48	0	0	51	1.00
9268075--9268122	23	2.2	24	82	17	61	43	2	2	52	1.24
9268958--9268998	16	2.6	16	88	7	57	36	0	4	58	1.20
9269288--9269344	26	2.2	27	84	12	75	40	1	0	57	1.09
9269902--9269931	16	1.9	15	93	6	51	63	0	0	36	0.95
9269906--9269975	26	2.9	24	77	10	79	47	0	0	52	1.00
9270450--9270480	2	15.5	2	93	0	53	48	3	0	48	1.17
9271707--9271742	17	2.0	19	89	10	58	41	30	0	27	1.56
9272707--9272739	13	2.3	15	90	10	52	78	0	0	21	0.75
9273137--9273172	2	18.0	2	100	0	72	50	0	0	50	1.00
9275174--9275220	22	2.1	21	81	14	51	68	0	0	31	0.90
9276522--9276594	30	2.4	31	84	6	105	24	28	15	31	1.95
9276718--9276914	67	2.9	67	96	0	358	15	26	9	48	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9276734--9276914	35	5.4	34	61	19	83	16	27	9	46	1.77
9276862--9277295	41	10.5	40	76	8	228	18	28	13	39	1.89
9276869--9277216	125	2.8	125	84	3	438	19	29	14	37	1.91
9276869--9277378	84	6.2	83	79	6	387	18	28	13	39	1.88
9276869--9277295	125	3.4	123	77	9	388	18	28	13	38	1.89
9276948--9277378	209	2.1	209	82	5	514	18	27	13	40	1.88
9277231--9277409	83	2.2	82	79	7	182	18	26	10	44	1.82
9277538--9278084	31	17.7	31	77	4	498	25	28	26	19	1.98
9277533--9278096	93	6.1	93	83	1	567	26	28	26	19	1.99
9278816--9278867	20	2.6	20	87	0	68	38	15	13	32	1.86
9282620--9282670	21	2.5	21	81	9	61	27	15	17	39	1.90
9283240--9283282	22	2.0	23	90	9	72	37	30	0	32	1.58
9285139--9285176	13	2.9	13	92	0	58	34	15	15	34	1.90
9287790--9287819	16	1.9	16	93	6	53	50	16	0	33	1.46
9291404--9291456	20	2.6	21	76	8	56	30	16	15	37	1.90
9293579--9293604	13	2.0	13	100	0	52	38	15	15	30	1.88
9295823--9295867	21	2.1	21	84	8	56	53	4	20	22	1.63
9297671--9297701	15	2.1	15	93	0	53	48	16	22	12	1.80
9299779--9299815	13	2.8	13	91	0	65	29	10	16	43	1.82
9302367--9302392	13	2.0	13	100	0	52	38	15	15	30	1.88
9307341--9307424	29	2.9	29	76	5	89	23	26	16	33	1.96
9307489--9307587	41	2.4	42	75	14	116	18	23	13	45	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9307595--9308001	41	9.8	41	69	6	183	19	24	14	41	1.89
9307595--9307873	84	3.3	83	82	6	337	19	25	13	41	1.88
9307725--9307999	126	2.2	122	82	7	331	19	23	15	41	1.89
9307807--9308116	82	3.7	84	78	6	274	17	24	13	44	1.85
9307850--9308116	85	3.2	85	78	6	292	16	23	13	46	1.83
9308144--9308225	36	2.2	37	86	4	121	19	30	12	37	1.88
9308319--9309521	31	38.8	31	75	3	876	28	27	25	18	1.98
9308319--9309521	62	19.4	62	77	2	966	28	27	25	18	1.98
9313863--9313889	13	2.1	13	100	0	54	29	14	14	40	1.86
9313844--9313908	32	2.0	32	90	3	103	26	16	16	40	1.90
9313874--9313930	19	2.9	19	89	5	78	29	17	17	35	1.93
9313960--9314012	20	2.7	19	88	11	72	37	13	18	30	1.89
9320563--9320601	20	1.9	21	84	5	53	15	35	28	20	1.93
9321988--9322061	35	2.1	36	94	2	132	32	2	33	31	1.72
9321988--9322061	17	4.2	18	73	11	64	32	2	33	31	1.72
9321997--9322062	17	3.8	18	74	18	68	31	1	34	31	1.67
9322585--9322649	32	2.0	33	87	3	96	26	15	16	41	1.88
9322716--9322746	13	2.4	13	94	0	53	35	16	12	35	1.87
9322700--9322766	33	2.0	32	88	11	100	35	13	17	32	1.89
9324757--9324782	13	2.0	13	100	0	52	38	15	15	30	1.88
9326997--9327041	21	2.1	21	84	8	56	53	4	20	22	1.63
9328846--9328876	15	2.1	15	93	0	53	48	16	22	12	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9330947--9330985	13	3.0	13	100	0	78	30	15	15	38	1.88
9333509--9333567	28	2.1	29	90	3	93	40	15	11	32	1.83
9339192--9339242	19	2.7	19	84	9	68	39	15	15	29	1.89
9342796--9342924	52	2.5	52	96	0	240	29	17	17	34	1.94
9342933--9342957	13	1.9	13	100	0	50	36	16	16	32	1.90
9343000--9343064	33	2.0	33	87	3	96	38	12	12	36	1.80
9343937--9344257	49	6.7	49	82	10	398	31	17	24	26	1.97
9343937--9344257	92	3.4	93	85	10	370	31	17	24	26	1.97
9344144--9344211	22	3.1	22	62	19	52	30	17	25	26	1.97
9343937--9344262	141	2.3	143	92	3	541	31	17	25	26	1.97

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   46   47   48   
          49   50   51   52   53   54   55   56