genome.fa.s64.2.7.7.80.10.50.1000.24.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  24  of  45  ( 5312 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)
4338320--4338371	26	2.0	27	88	3	79	59	0	3	36	1.16
4338383--4338436	16	3.3	16	82	5	63	61	0	0	38	0.96
4338383--4338444	16	3.8	16	81	12	56	56	1	0	41	1.09
4338664--4338702	20	2.0	19	85	5	51	64	10	0	25	1.25
4339222--4339306	38	2.2	37	81	8	89	49	4	0	45	1.23
4339655--4339714	20	2.9	21	74	20	63	53	0	1	45	1.10
4339711--4339741	16	1.9	16	93	0	53	67	0	0	32	0.91
4341821--4341865	19	2.3	20	92	3	74	68	0	4	26	1.08
4343788--4343838	2	25.5	2	100	0	102	49	0	0	50	1.00
4344259--4344332	16	4.6	16	77	3	67	62	4	0	33	1.14
4344257--4344332	11	7.1	10	70	12	53	63	3	0	32	1.13
4345180--4345417	50	4.8	50	90	2	370	30	21	16	31	1.96
4349797--4350032	50	4.8	50	85	2	341	30	20	16	32	1.94
4349797--4350032	98	2.4	100	86	2	350	30	20	16	32	1.94
4350818--4350873	21	2.7	21	75	8	60	32	3	3	60	1.31
4352119--4352177	21	2.8	21	81	2	73	52	5	6	35	1.50
4352961--4353002	2	21.5	2	85	4	59	45	2	2	50	1.27
4355590--4355660	29	2.5	28	80	14	83	36	5	2	54	1.38
4355819--4355869	19	2.7	18	85	11	59	43	0	0	56	0.99
4356609--4356637	7	4.1	7	100	0	58	86	0	0	13	0.58
4358557--4358594	2	19.0	2	88	0	58	44	0	2	52	1.14
4359012--4359060	16	3.1	16	80	13	50	51	2	2	44	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4359024--4359069	23	2.0	24	86	4	67	54	0	0	45	0.99
4359052--4359091	22	1.9	20	90	10	62	47	2	0	50	1.14
4360739--4360786	24	1.9	26	91	8	82	45	0	2	52	1.12
4361888--4361954	21	3.1	21	76	16	75	55	10	4	29	1.53
4361892--4361958	11	6.3	11	72	17	52	58	8	4	28	1.48
4362157--4362241	30	2.9	28	74	10	80	36	14	2	47	1.57
4363295--4363459	84	2.0	84	91	0	267	27	26	20	25	1.99
4367804--4367837	2	17.0	2	93	0	59	52	0	47	0	1.00
4369852--4369894	22	2.0	22	90	9	70	60	0	0	39	0.97
4370245--4370269	13	1.9	13	100	0	50	24	0	0	76	0.80
4371828--4371870	2	21.5	2	100	0	86	0	48	0	51	1.00
4376017--4376049	2	16.5	2	100	0	66	51	0	0	48	1.00
4379508--4379537	2	15.0	2	100	0	60	50	0	50	0	1.00
4383925--4383958	10	3.4	10	87	0	50	50	8	0	41	1.34
4384215--4384251	2	18.5	2	100	0	74	48	0	0	51	1.00
4386287--4386329	23	2.0	21	86	9	59	37	2	0	60	1.10
4386665--4386689	2	12.5	2	100	0	50	52	0	0	48	1.00
4389679--4389714	2	18.0	2	88	0	54	50	5	0	44	1.25
4389679--4389714	10	3.6	10	92	0	63	50	5	0	44	1.25
4389962--4390020	17	3.6	17	73	15	52	71	0	0	28	0.87
4391499--4391527	3	9.7	3	100	0	58	31	0	0	68	0.89
4392808--4392873	29	2.4	26	80	16	71	69	3	0	27	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4393284--4393340	17	3.4	17	75	2	62	31	1	1	64	1.13
4393233--4393334	28	3.6	28	71	13	68	36	2	1	58	1.24
4395277--4395327	19	2.8	17	82	8	57	50	0	0	49	1.00
4395277--4395310	17	1.9	18	88	5	52	55	0	0	44	0.99
4395296--4395393	13	7.5	13	73	20	62	46	2	0	51	1.12
4395302--4395342	21	1.9	22	95	5	75	41	0	0	58	0.98
4395315--4395360	15	3.1	15	87	6	58	50	0	0	50	1.00
4395322--4395363	14	2.9	14	86	6	57	52	0	0	47	1.00
4395674--4395712	17	2.2	18	86	4	53	46	5	2	46	1.38
4395697--4395736	22	1.9	21	85	10	55	47	0	5	47	1.24
4395686--4395737	22	2.6	19	77	14	52	50	0	3	46	1.20
4395758--4395827	29	2.4	28	83	7	77	52	0	2	44	1.15
4395784--4395871	36	2.6	34	63	21	60	53	0	4	42	1.21
4396630--4396668	20	2.0	20	84	0	51	20	15	10	53	1.70
4400174--4400209	2	18.0	2	94	0	63	50	2	0	47	1.15
4407063--4407128	18	3.6	18	72	25	50	45	1	0	53	1.09
4407079--4407161	33	2.5	31	83	14	96	44	3	0	51	1.18
4407145--4407217	5	14.4	5	77	17	55	31	1	0	67	1.00
4407145--4407219	11	6.8	11	77	22	86	32	1	0	66	1.00
4407145--4407219	21	3.4	21	76	23	82	32	1	0	66	1.00
4409917--4409951	12	2.9	12	91	0	52	65	0	8	25	1.21
4410084--4410160	28	2.8	28	79	16	81	57	0	1	41	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4410084--4410156	18	4.0	17	74	20	67	57	0	1	41	1.07
4410087--4410162	27	2.7	28	80	15	86	56	0	1	42	1.07
4410167--4410219	19	2.8	20	85	8	74	58	0	0	41	0.98
4410217--4410262	14	3.3	14	80	14	51	34	0	0	65	0.93
4411988--4412028	13	3.2	13	80	13	57	26	0	0	73	0.84
4438069--4438098	2	15.0	2	100	0	60	50	0	0	50	1.00
4439509--4439569	30	2.0	30	90	6	97	36	0	0	63	0.94
4439554--4439600	14	3.4	14	76	8	51	57	2	0	40	1.11
4439547--4439603	16	3.9	15	75	17	57	54	1	0	43	1.10
4439620--4439662	2	22.0	2	80	4	52	51	4	0	44	1.22
4439956--4439988	14	2.4	14	90	5	50	39	0	3	57	1.14
4441543--4441583	2	20.5	2	100	0	82	51	0	48	0	1.00
4442623--4442681	26	2.3	26	83	11	70	55	0	0	44	0.99
4443594--4443638	19	2.3	19	85	11	56	46	2	2	48	1.26
4443625--4443708	13	6.8	13	68	12	52	48	1	1	48	1.16
4444200--4444238	16	2.4	16	87	8	53	58	0	0	41	0.98
4444278--4444360	36	2.4	33	82	11	103	55	2	0	42	1.13
4444876--4444919	23	1.9	23	86	9	63	54	0	0	45	0.99
4444876--4444923	24	2.0	23	84	4	60	56	0	0	43	0.99
4448917--4448947	14	2.1	15	94	5	55	6	29	0	64	1.18
4452714--4452772	19	3.2	19	90	2	93	50	8	0	40	1.33
4453478--4453538	30	2.0	30	87	6	88	50	18	1	29	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4453478--4453529	15	3.5	15	79	7	61	51	17	0	30	1.45
4453480--4453539	15	4.0	15	78	4	59	51	16	1	30	1.54
4455291--4455338	25	2.0	25	91	4	80	25	0	4	70	1.04
4456041--4456221	91	2.0	91	98	0	353	30	6	12	50	1.66
4458890--4458922	16	2.0	17	94	5	59	42	0	0	57	0.98
4459901--4459962	13	4.6	14	73	20	53	40	1	0	58	1.08
4459901--4459937	14	2.6	15	83	12	51	40	0	0	59	0.97
4460602--4460643	21	2.0	21	90	0	66	42	0	0	57	0.99
4460634--4460665	3	11.3	3	87	12	50	28	0	0	71	0.86
4461941--4461996	26	2.2	26	96	0	103	35	30	3	30	1.75
4461953--4462007	26	2.1	26	83	6	67	34	29	3	32	1.75
4462184--4462226	22	1.9	22	85	4	59	51	0	0	48	1.00
4462911--4462976	17	3.6	17	76	17	62	59	0	3	37	1.13
4462951--4463073	11	10.3	12	68	22	64	59	0	1	38	1.13
4462988--4463067	31	2.6	30	84	11	108	56	1	1	41	1.15
4462993--4463067	32	2.5	29	83	12	89	57	1	0	41	1.07
4462913--4463060	10	15.3	10	65	24	52	58	0	2	39	1.15
4463016--4463111	27	3.7	26	77	12	83	57	0	3	39	1.15
4464186--4464220	18	2.1	18	89	10	56	34	0	0	65	0.93
4464821--4464916	39	2.5	37	80	14	113	48	3	8	39	1.49
4470287--4470330	23	2.0	22	95	4	79	34	9	22	34	1.86
4474986--4475025	2	20.0	2	84	0	53	45	2	0	52	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4475349--4475398	18	2.8	17	81	9	55	40	0	0	60	0.97
4475373--4475417	23	2.0	22	86	8	63	40	0	0	60	0.97
4475389--4475452	28	2.2	29	83	8	78	35	0	0	64	0.94
4477103--4477145	22	2.0	21	86	13	61	65	2	0	32	1.06
4477112--4477165	9	6.0	9	80	8	65	64	0	1	33	1.04
4481701--4481726	3	8.7	3	100	0	52	30	0	0	69	0.89
4488300--4488336	17	2.1	19	85	10	51	18	35	0	45	1.50
4489207--4489633	214	2.0	214	97	0	800	29	17	21	31	1.96
4490229--4490254	1	26.0	1	100	0	52	0	100	0	0	0.00
4494881--4494921	2	20.5	2	100	0	82	48	0	0	51	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   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45