genome.fa.s35.2.7.7.80.10.50.1000.28.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: Scaffold35
Parameters: 2 7 7 80 10 50 1000
Length:  4812169

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   

This is table  28  of  30  ( 3549 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)
4338049--4338093	22	2.0	23	82	4	56	33	20	2	44	1.63
4339780--4339805	8	3.2	8	100	0	52	30	0	46	23	1.53
4342809--4342868	30	2.0	30	93	0	102	30	3	30	36	1.74
4343977--4344002	13	2.0	13	100	0	52	38	15	15	30	1.88
4343959--4344022	32	2.0	33	90	3	103	39	18	14	28	1.90
4346236--4346280	22	2.0	23	82	4	56	33	20	2	44	1.63
4347968--4347993	8	3.2	8	100	0	52	30	0	46	23	1.53
4351150--4351190	21	2.0	21	85	9	57	39	12	9	39	1.76
4351227--4351283	21	2.8	20	81	5	69	40	15	14	29	1.87
4351271--4351407	53	2.6	53	94	1	229	37	18	17	27	1.93
4351432--4351462	10	3.1	10	90	0	53	22	29	6	41	1.78
4351555--4351593	13	3.0	13	92	0	69	30	15	17	35	1.91
4351664--4351707	20	2.2	20	83	0	52	29	9	20	40	1.83
4353946--4354043	42	2.3	42	87	0	133	15	30	18	35	1.92
4353922--4354068	42	3.5	42	77	7	127	14	26	16	42	1.87
4354057--4354107	26	1.9	27	92	4	86	9	31	11	47	1.73
4354184--4354415	126	1.8	125	82	4	297	15	30	17	37	1.91
4354077--4354448	42	8.9	43	76	8	268	14	29	17	38	1.90
4354936--4354982	24	2.0	24	87	8	69	65	0	6	27	1.16
4355312--4355387	38	2.0	38	85	12	102	43	13	30	13	1.81
4355637--4355673	16	2.3	16	90	0	56	51	16	24	8	1.71
4355811--4356090	47	6.0	47	76	7	230	29	33	19	17	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4355966--4356040	23	3.4	22	80	10	91	30	36	22	10	1.88
4355826--4356104	90	3.1	89	81	5	281	30	34	19	15	1.93
4359015--4359068	20	2.7	20	91	2	81	35	18	9	37	1.83
4362438--4362509	20	3.7	19	87	7	83	38	16	15	29	1.89
4363132--4363189	25	2.5	24	86	10	84	39	12	27	20	1.88
4363833--4363925	32	2.7	35	80	16	106	33	22	12	31	1.92
4364381--4364459	14	6.2	14	69	26	68	41	11	21	25	1.86
4364386--4364466	24	3.4	24	93	3	128	41	11	22	24	1.86
4368375--4368400	13	2.0	13	100	0	52	38	15	15	30	1.88
4370625--4370669	20	2.1	21	84	8	56	55	4	20	20	1.60
4372471--4372501	15	2.1	15	93	0	53	48	16	22	12	1.80
4374713--4374759	21	2.3	20	78	10	51	36	21	0	42	1.53
4385309--4385353	23	2.0	23	82	8	56	37	24	6	31	1.81
4385753--4385812	20	3.0	20	70	18	61	35	15	8	41	1.77
4385834--4385886	19	2.7	20	82	2	63	33	16	20	28	1.95
4385856--4385920	32	2.0	33	84	3	87	36	13	18	30	1.90
4395670--4395707	2	19.0	2	100	0	76	50	0	0	50	1.00
4400563--4400604	10	4.4	10	79	8	52	33	0	0	66	0.92
4400588--4400629	22	1.9	22	85	9	59	33	0	2	64	1.07
4401608--4401638	14	2.2	14	100	0	62	12	12	6	67	1.40
4401656--4401696	2	20.5	2	100	0	82	51	0	0	48	1.00
4401820--4401935	60	1.9	60	98	0	223	45	12	10	31	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4401921--4402047	2	63.5	2	85	0	110	48	12	0	38	1.41
4405256--4405294	16	2.3	18	83	16	57	51	7	12	28	1.67
4409422--4409459	17	2.2	17	90	0	58	18	13	31	36	1.89
4409432--4409466	17	2.1	17	94	0	61	22	17	25	34	1.96
4409733--4409793	11	5.9	10	80	12	52	77	1	18	3	0.99
4409733--4409777	11	4.0	11	91	8	65	80	0	17	2	0.82
4409733--4409777	21	2.0	23	87	12	67	80	0	17	2	0.82
4411486--4411655	89	1.9	89	91	7	283	28	28	11	31	1.91
4413174--4413217	20	2.3	19	88	7	63	38	9	11	40	1.73
4419120--4419149	2	15.0	2	100	0	60	50	0	50	0	1.00
4427608--4427651	2	22.5	2	95	4	81	50	0	0	50	1.00
4435824--4435861	18	2.1	19	85	5	51	63	7	7	21	1.47
4436830--4436869	11	3.6	11	93	6	64	47	0	5	47	1.24
4437533--4437588	20	2.8	20	83	2	69	32	14	14	39	1.86
4437638--4437662	13	1.9	13	100	0	50	36	16	16	32	1.90
4441724--4441895	79	2.2	80	82	7	217	34	13	23	29	1.93
4441840--4441920	28	3.0	28	80	10	98	30	20	27	20	1.98
4441840--4442041	109	1.9	109	91	0	332	33	17	25	23	1.96
4441956--4442029	28	2.6	28	89	4	105	25	22	31	20	1.98
4442016--4442133	51	2.3	51	82	2	139	32	11	26	29	1.92
4444417--4444483	17	3.9	16	79	13	62	41	13	16	28	1.86
4448817--4448843	13	2.1	13	100	0	54	29	14	14	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4450675--4450700	13	2.0	13	100	0	52	30	15	15	38	1.88
4453074--4453120	21	2.3	21	76	23	55	42	4	19	34	1.70
4453241--4453279	13	3.0	13	96	0	69	35	15	17	30	1.91
4453265--4453343	20	3.7	20	78	15	77	44	15	15	25	1.85
4455350--4455380	15	2.1	15	93	0	53	12	22	16	48	1.80
4457184--4457228	21	2.1	21	84	8	56	22	20	4	53	1.63
4459447--4459472	13	2.0	13	100	0	52	30	15	15	38	1.88
4460191--4460231	18	2.3	18	86	0	55	58	7	12	21	1.58
4461591--4461977	164	2.3	163	87	3	544	31	11	8	49	1.68
4463232--4463269	20	1.9	20	88	0	58	39	13	15	31	1.86
4469230--4469378	77	1.9	78	86	1	210	28	26	13	32	1.94
4471948--4471977	13	2.3	13	94	0	51	36	16	13	33	1.88
4478743--4478778	13	2.8	13	86	0	54	33	13	16	36	1.89
4479752--4479785	18	1.9	17	88	5	50	32	29	11	26	1.92
4481192--4481216	13	1.9	13	100	0	50	32	16	16	36	1.90
4481296--4481363	33	2.1	33	89	8	104	36	16	14	32	1.89
4481936--4481987	21	2.6	20	93	6	88	46	15	11	26	1.80
4488145--4488169	13	1.9	13	100	0	50	32	20	16	32	1.94
4490701--4490765	21	3.6	19	73	26	70	44	15	12	27	1.82
4490719--4490744	13	2.0	13	100	0	52	38	15	15	30	1.88
4490701--4490765	34	2.0	33	93	6	114	44	15	12	27	1.82
4496323--4496363	19	2.0	21	90	9	68	41	9	19	29	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4496392--4496430	13	3.0	13	92	0	69	30	17	15	35	1.91
4497254--4497815	280	2.0	280	97	0	1070	28	29	15	26	1.96
4500284--4500740	162	2.8	162	92	0	743	41	14	12	32	1.82
4503920--4504055	50	2.7	50	88	4	186	38	13	13	34	1.83
4504019--4504074	20	2.8	20	86	0	76	35	8	10	44	1.71
4504981--4505006	13	2.0	13	100	0	52	38	15	15	30	1.88
4505055--4505081	13	2.1	13	100	0	54	40	14	14	29	1.86
4512992--4513107	19	6.7	19	77	22	139	33	12	18	35	1.88
4513012--4513036	13	1.9	13	100	0	50	36	16	16	32	1.90
4512993--4513056	32	2.0	32	100	0	128	34	12	18	34	1.89
4512992--4513106	51	2.3	51	98	0	221	33	12	19	34	1.89
4513044--4513121	32	2.4	32	93	0	138	35	12	17	33	1.88
4513063--4513120	13	4.0	13	72	23	53	34	13	17	34	1.89
4513136--4513202	20	3.7	20	74	25	85	37	17	11	32	1.87
4513155--4513215	13	5.2	13	77	22	80	37	18	13	31	1.88
4513136--4513235	33	3.0	33	94	2	166	35	17	13	35	1.88
4513203--4513338	51	2.7	51	93	2	229	29	18	16	36	1.92
4514188--4514233	21	2.2	20	82	14	58	26	17	15	41	1.88
4516602--4516730	52	2.5	52	89	0	204	36	17	17	29	1.92
4539455--4539503	9	5.8	8	80	7	53	85	12	0	2	0.68
4539454--4539503	17	2.9	17	88	5	66	84	12	0	4	0.76
4540782--4541330	119	4.6	116	79	10	504	29	30	17	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4540758--4541313	89	6.3	88	84	7	532	28	29	18	23	1.97
4540841--4541342	208	2.4	207	89	3	751	28	30	17	22	1.97
4541319--4541367	25	2.0	25	87	0	71	30	30	22	16	1.96
4541444--4541609	48	3.5	48	85	2	203	19	25	19	34	1.96
4544635--4544691	17	3.4	17	75	0	60	1	21	0	77	0.86
4545772--4545962	20	8.5	20	70	21	121	29	15	14	41	1.86
4545707--4545962	71	3.6	70	80	7	259	28	16	14	41	1.87
4545720--4545913	91	2.1	91	85	1	255	29	15	15	39	1.88
4549172--4549223	19	2.7	19	84	3	59	38	15	13	32	1.86
4553155--4553186	16	2.0	17	88	11	50	15	21	12	50	1.77

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