genome.fa.s25.2.7.7.80.10.50.1000.2.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  2  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)
137778--137839	15	4.1	15	82	15	67	61	0	0	38	0.96
137652--138165	255	2.0	255	98	0	1001	42	5	6	46	1.51
138033--138094	15	4.1	15	77	12	65	59	0	0	40	0.97
138023--138100	30	2.8	27	74	14	79	56	0	0	43	0.99
138536--138569	11	2.9	12	86	4	52	67	0	2	29	1.05
139431--139469	15	2.5	17	76	23	50	35	2	0	61	1.10
139633--139659	13	2.1	13	100	0	54	44	0	0	55	0.99
139922--139949	6	4.7	6	100	0	56	53	14	17	14	1.73
140209--140239	2	15.5	2	100	0	62	51	0	0	48	1.00
141033--141145	58	1.9	58	83	0	145	69	3	3	23	1.20
141106--141164	21	2.8	21	79	20	70	72	3	1	22	1.08
141096--141154	23	2.5	24	75	5	68	67	5	3	23	1.26
141073--141220	76	2.0	75	81	6	174	66	6	4	22	1.31
141291--141323	17	1.9	17	93	0	57	30	6	15	48	1.69
141403--141460	24	2.3	23	80	16	62	17	3	10	68	1.31
141399--141476	40	2.0	39	82	12	97	17	5	8	67	1.36
141470--141530	24	2.7	22	76	14	61	14	8	11	65	1.46
141473--141530	22	2.6	22	81	8	64	13	8	12	65	1.47
141399--141550	57	2.6	58	77	8	150	17	6	10	65	1.45
141515--141564	17	3.1	17	72	13	52	24	10	6	60	1.51
141917--141980	28	2.2	28	76	13	67	51	3	3	42	1.33
142160--142224	15	4.3	15	73	11	60	47	23	7	21	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
142149--142211	30	2.0	31	81	6	74	44	26	11	17	1.82
144136--144161	3	8.7	3	100	0	52	69	0	0	30	0.89
144581--144631	2	25.5	2	95	0	93	49	0	0	50	1.00
145127--145158	2	16.0	2	100	0	64	50	0	0	50	1.00
152245--152341	19	5.4	19	63	26	59	54	1	2	42	1.19
152467--152518	22	2.5	20	74	20	52	48	1	0	50	1.12
153200--153288	27	3.3	27	69	18	76	65	1	0	33	1.00
153239--153298	28	2.1	28	84	6	77	65	0	0	35	0.93
154168--154197	15	2.1	14	93	6	51	16	0	0	83	0.65
154168--154197	7	4.1	7	91	8	51	16	0	0	83	0.65
154386--154423	2	19.0	2	94	0	67	50	2	0	47	1.15
154658--154686	15	2.0	15	93	6	51	48	0	0	51	1.00
154722--154775	13	4.5	13	78	21	73	31	0	0	68	0.90
154708--154776	23	3.1	21	84	14	77	34	0	0	65	0.93
154713--154776	11	5.5	11	78	14	67	34	0	0	65	0.93
154961--155028	18	3.8	19	74	21	76	44	0	0	55	0.99
154966--155028	15	3.5	20	68	31	61	46	0	0	53	1.00
155521--155589	24	2.7	27	78	8	74	44	2	1	50	1.25
155760--155820	28	2.1	29	82	8	72	62	1	1	34	1.15
156295--156320	4	6.5	4	100	0	52	0	50	0	50	1.00
157961--157997	3	12.3	3	100	0	74	32	0	0	67	0.91
160153--160185	2	16.5	2	100	0	66	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)
166003--166033	5	6.2	5	92	0	53	58	19	22	0	1.40
166481--166511	3	10.3	3	100	0	62	0	32	0	67	0.91
169062--169133	22	3.3	22	78	3	74	50	2	4	43	1.36
169226--169258	2	16.5	2	100	0	66	48	0	0	51	1.00
170785--170815	16	1.9	16	93	0	53	61	9	0	29	1.28
170212--171057	417	2.0	422	88	3	1278	45	13	6	34	1.69
170970--170998	3	9.7	3	100	0	58	65	0	0	34	0.93
171464--171489	2	13.0	2	100	0	52	50	0	0	50	1.00
173555--173759	48	4.3	48	85	4	272	11	25	25	37	1.90
173555--173759	96	2.1	96	95	0	365	11	25	25	37	1.90
176780--176814	18	1.9	18	88	11	54	77	0	0	22	0.78
177946--178100	31	5.0	31	80	3	170	34	21	14	30	1.93
177945--178112	62	2.7	63	80	7	200	35	22	14	28	1.93
178701--178801	52	1.9	52	97	0	193	35	21	14	27	1.93
184545--184577	3	11.0	3	100	0	66	66	0	0	33	0.92
184693--184752	4	15.0	4	92	0	102	1	26	0	71	0.95
184855--184884	2	15.0	2	92	0	51	46	0	3	50	1.18
184937--184982	24	1.9	24	86	0	65	63	2	6	28	1.31
185464--185501	2	19.0	2	100	0	76	50	0	0	50	1.00
185563--185592	2	15.0	2	92	0	51	46	0	0	53	1.00
187065--187095	3	10.3	3	100	0	62	64	0	0	35	0.94
187319--187358	2	20.0	2	100	0	80	50	0	50	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
188589--188629	21	2.0	21	90	0	64	4	68	4	21	1.28
190330--190368	2	20.5	2	84	10	55	56	0	43	0	0.99
191582--191619	15	2.5	15	84	12	51	47	2	2	47	1.30
192479--192515	2	18.5	2	100	0	74	51	0	0	48	1.00
193803--193858	6	9.3	6	88	0	76	55	1	0	42	1.10
193802--193855	14	4.0	14	83	9	58	57	1	0	40	1.09
193803--193858	4	14.0	4	86	0	76	55	1	0	42	1.10
194417--194454	2	19.0	2	100	0	76	50	0	0	50	1.00
195419--195447	14	2.0	15	93	6	51	41	6	0	51	1.28
195407--195455	21	2.3	21	89	3	71	42	6	0	51	1.27
199873--199932	24	2.5	24	76	15	61	45	1	0	53	1.10
200168--200216	18	2.6	18	80	9	53	57	0	0	42	0.99
200168--200213	21	2.2	21	88	0	65	56	0	0	43	0.99
206203--206236	2	17.5	2	87	6	52	50	2	0	47	1.16
214183--214231	20	2.4	21	80	13	57	32	2	14	51	1.54
214314--214357	19	2.3	19	88	0	61	40	0	2	56	1.11
219833--219861	3	9.7	3	100	0	58	34	0	0	65	0.93
221087--221118	2	16.5	2	93	6	57	50	0	0	50	1.00
230015--230041	5	5.4	5	100	0	54	22	0	0	77	0.76
230252--230281	3	10.0	3	100	0	60	66	0	0	33	0.92
234254--234283	3	10.0	3	100	0	60	33	0	0	66	0.92
239213--239256	13	3.3	13	81	6	52	40	0	13	45	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
239679--239719	19	2.1	20	86	4	57	34	2	19	43	1.64
239889--239967	6	12.2	6	72	20	54	73	1	2	22	1.03
247270--247393	44	2.8	44	97	0	230	25	7	37	29	1.83
256946--256977	2	16.0	2	100	0	64	0	50	0	50	1.00
259185--259262	34	2.3	34	97	2	147	23	8	17	50	1.75
267436--267468	3	10.7	3	93	6	57	30	0	0	69	0.88
267887--267969	32	2.6	32	84	1	105	61	0	1	37	1.04
267966--267990	7	3.6	7	100	0	50	48	0	0	52	1.00
267907--267983	31	2.6	29	79	16	95	55	0	1	42	1.07
275404--275434	8	3.9	8	91	0	53	90	9	0	0	0.46
280863--280914	3	17.7	3	88	4	79	63	0	0	36	0.95
281071--281113	2	21.5	2	100	0	86	48	0	51	0	1.00
283809--283887	40	2.0	40	92	0	131	59	15	13	11	1.61
286806--286845	15	2.5	17	76	19	50	60	0	0	40	0.97
293940--293965	1	26.0	1	100	0	52	100	0	0	0	0.00
294619--294657	2	19.5	2	83	0	51	48	7	0	43	1.31
294619--294657	16	2.4	16	95	0	69	48	7	0	43	1.31
294613--294657	12	3.9	12	80	11	58	46	8	2	42	1.47
295467--295556	46	2.0	46	93	0	153	35	17	18	27	1.94
298112--298171	30	2.0	31	87	9	88	15	3	10	71	1.25
302129--302167	18	2.0	20	85	9	55	25	0	2	71	0.98
303757--303791	18	1.9	18	88	0	52	42	8	2	45	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
305192--305229	18	2.1	19	85	5	51	44	2	5	47	1.39
308310--308354	2	22.5	2	100	0	90	51	0	0	48	1.00
310100--310124	11	2.3	11	100	0	50	8	24	20	48	1.76
310599--310631	3	11.0	3	100	0	66	0	33	0	66	0.92
310877--310919	22	2.0	22	100	0	86	23	4	25	46	1.71
318028--318179	74	2.1	74	98	0	295	17	24	15	42	1.88
322243--322278	2	18.5	2	88	5	56	52	0	0	47	1.00
322452--322479	14	2.0	14	100	0	56	42	14	21	21	1.88
325743--325776	2	17.0	2	100	0	68	50	0	0	50	1.00
328435--329125	345	2.0	345	97	0	1319	31	14	27	26	1.95

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