genome.fa.s25.2.7.7.80.10.50.1000.17.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  17  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)
3177980--3178019	2	20.0	2	94	0	71	47	0	0	52	1.00
3180451--3180482	2	16.0	2	100	0	64	50	0	0	50	1.00
3180787--3180818	16	2.0	16	100	0	64	62	12	0	25	1.30
3181372--3181444	26	2.8	26	78	15	80	61	0	0	38	0.96
3181401--3181448	22	2.2	23	85	14	66	64	0	0	35	0.94
3181415--3181453	18	2.2	18	90	9	62	61	0	0	38	0.96
3181397--3181451	10	6.1	9	78	21	53	65	0	0	34	0.93
3181633--3181663	13	2.5	12	90	10	53	58	0	3	38	1.15
3184322--3184360	19	2.1	19	85	9	53	38	0	2	58	1.12
3184849--3184873	2	12.5	2	100	0	50	48	0	0	52	1.00
3186072--3186120	2	24.5	2	95	0	89	48	0	2	48	1.12
3187167--3187211	2	22.5	2	95	0	81	48	0	48	2	1.13
3187481--3187523	15	2.7	16	82	10	52	39	0	0	60	0.97
3188068--3188100	13	2.5	14	90	9	52	6	15	0	78	0.93
3188212--3188278	31	2.1	33	94	5	120	56	4	0	38	1.19
3189452--3189509	28	2.1	28	100	0	116	17	24	13	44	1.85
3191942--3191968	2	13.5	2	100	0	54	51	0	0	48	1.00
3194289--3194326	2	19.0	2	100	0	76	50	0	0	50	1.00
3201333--3201381	12	3.9	12	84	12	55	48	0	2	48	1.12
3201461--3201508	22	2.0	24	84	11	64	50	0	2	47	1.12
3201471--3201515	23	2.0	23	82	8	56	51	0	0	48	1.00
3201530--3201613	42	2.0	42	90	4	134	38	4	0	57	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3201531--3201618	22	4.0	22	77	15	83	39	3	0	56	1.16
3204684--3204720	2	18.5	2	100	0	74	51	0	48	0	1.00
3206741--3206806	28	2.4	27	80	5	78	54	15	6	24	1.63
3211247--3211318	28	2.6	27	84	4	99	50	18	8	23	1.74
3214149--3214196	9	5.2	9	78	14	53	75	2	0	22	0.91
3214144--3214185	7	6.1	7	80	5	50	69	0	0	30	0.89
3214157--3214199	17	2.5	17	85	7	52	74	2	0	23	0.93
3214503--3214597	35	2.7	34	83	3	118	52	12	16	17	1.74
3215395--3215433	20	2.0	20	89	0	60	20	7	23	48	1.75
3218346--3218386	21	1.9	22	90	5	66	36	0	0	63	0.95
3218702--3218756	22	2.5	22	80	16	60	38	1	0	60	1.08
3219244--3219290	23	2.0	23	84	8	60	65	0	2	31	1.04
3221847--3221920	27	2.5	30	73	18	75	48	0	1	50	1.09
3221846--3221931	29	3.0	28	74	19	79	48	0	1	50	1.08
3221908--3221959	23	2.3	22	75	15	52	40	1	1	55	1.22
3222069--3222138	31	2.3	29	75	13	70	58	1	1	38	1.16
3222164--3222238	33	2.3	33	83	2	98	46	5	0	48	1.25
3222587--3222637	17	2.9	17	82	8	59	43	0	1	54	1.11
3222676--3222717	20	2.0	21	82	13	52	66	2	0	30	1.04
3224574--3224615	18	2.3	18	88	8	59	50	0	0	50	1.00
3224886--3224942	7	8.3	7	81	11	55	43	1	0	54	1.10
3227931--3227971	18	2.3	18	87	4	57	34	0	2	63	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3228421--3228466	3	15.3	3	100	0	92	32	0	0	67	0.91
3230948--3230986	15	2.5	16	87	4	53	38	2	2	56	1.27
3232219--3232255	3	12.7	3	94	5	67	35	0	0	64	0.94
3232221--3232257	17	2.2	17	100	0	74	35	0	0	64	0.94
3232441--3232478	2	19.0	2	100	0	76	50	0	0	50	1.00
3234159--3234199	15	2.7	15	84	3	55	41	4	0	53	1.22
3234327--3234362	16	2.2	17	90	5	56	8	8	5	77	1.11
3234740--3234786	2	23.5	2	100	0	94	51	0	0	48	1.00
3235610--3235638	2	14.5	2	100	0	58	48	0	0	51	1.00
3236249--3236283	2	17.5	2	100	0	70	48	0	0	51	1.00
3236345--3236382	3	12.7	3	100	0	76	68	0	0	31	0.90
3238584--3238619	2	18.0	2	100	0	72	50	0	0	50	1.00
3242624--3242662	15	2.5	17	80	20	57	41	0	0	58	0.98
3242885--3242943	22	2.7	22	77	12	68	45	3	0	50	1.18
3243167--3243192	2	13.0	2	100	0	52	50	0	0	50	1.00
3243424--3243475	27	2.0	26	85	11	70	50	0	0	50	1.00
3243726--3243808	22	3.8	21	74	15	78	51	12	1	34	1.47
3243723--3243820	45	2.2	45	87	7	137	50	12	2	35	1.52
3244894--3244957	32	1.9	32	87	6	92	53	0	0	46	1.00
3257032--3257070	2	19.5	2	100	0	78	51	0	48	0	1.00
3261025--3261083	22	2.6	23	81	13	68	37	3	1	57	1.25
3261988--3262040	20	2.6	19	82	8	52	37	1	5	54	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3263482--3263514	13	2.5	14	85	14	52	81	0	0	18	0.68
3263996--3264038	13	3.5	13	78	21	56	39	0	0	60	0.97
3266273--3266316	23	1.9	23	90	9	72	43	2	0	54	1.12
3267119--3267152	16	2.2	16	90	10	54	61	0	0	38	0.96
3267109--3267152	15	2.9	15	83	13	54	59	2	0	38	1.10
3267131--3267197	20	3.5	20	80	10	68	65	0	0	34	0.93
3267124--3267197	37	2.0	37	84	10	98	63	0	0	36	0.95
3267528--3267559	13	2.3	15	89	10	50	40	0	0	59	0.97
3267535--3267623	48	1.9	46	84	11	119	46	0	0	53	1.00
3267573--3267637	21	2.9	22	80	17	71	46	0	0	53	1.00
3267610--3267664	20	2.9	19	73	7	51	52	0	0	47	1.00
3268401--3268500	42	2.5	40	81	13	102	37	4	2	57	1.29
3268446--3268508	30	2.2	29	88	5	92	41	3	0	55	1.16
3269048--3269095	23	2.0	24	96	4	89	31	18	0	50	1.48
3270623--3270661	4	9.8	4	88	0	60	48	25	5	20	1.70
3270663--3270687	2	12.5	2	100	0	50	52	0	0	48	1.00
3270871--3270987	58	2.0	58	98	0	225	26	18	17	36	1.94
3272056--3272091	17	2.1	17	100	0	72	47	22	11	19	1.80
3274087--3274130	18	2.3	19	80	7	54	54	0	0	45	0.99
3280371--3280409	19	2.0	20	85	5	53	33	5	0	61	1.18
3294664--3294718	22	2.5	22	85	8	76	43	1	0	54	1.10
3295676--3295761	40	2.2	40	93	0	145	50	5	1	43	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3296160--3296203	17	2.6	17	89	7	63	72	2	0	25	0.96
3298139--3298181	22	2.0	22	95	0	77	51	4	9	34	1.55
3301513--3301550	5	7.8	5	82	5	51	78	0	2	18	0.86
3302006--3302045	21	2.0	20	90	5	62	55	0	0	45	0.99
3303226--3303276	25	2.0	25	84	3	66	39	0	7	52	1.30
3304784--3305703	310	3.0	309	96	1	1696	27	16	16	40	1.89
3306504--3306529	2	13.0	2	100	0	52	0	0	50	50	1.00
3310723--3310755	2	16.5	2	93	0	57	0	45	3	51	1.16
3311561--3311602	3	13.7	3	95	5	75	33	0	0	66	0.92
3313049--3313088	21	1.9	21	84	0	53	40	2	0	57	1.12
3314290--3314328	2	19.5	2	100	0	78	51	0	0	48	1.00
3314993--3315039	22	2.0	24	84	8	62	48	2	0	48	1.13
3315007--3315060	15	3.5	15	85	5	81	48	0	0	51	1.00
3315002--3315068	31	2.2	29	92	5	107	47	0	0	52	1.00
3315033--3315081	22	2.2	22	82	7	55	51	0	2	46	1.12
3316273--3316324	27	2.0	27	85	7	72	32	3	1	61	1.25
3317636--3317848	106	2.0	107	87	0	311	47	9	7	35	1.64
3318438--3318476	2	19.5	2	100	0	78	51	0	0	48	1.00
3320080--3320129	19	2.6	19	81	12	50	54	2	0	44	1.11
3320385--3320456	30	2.4	30	88	6	103	51	6	4	37	1.48
3320385--3320459	29	2.6	29	87	8	107	50	6	4	38	1.47
3321676--3321734	7	8.4	7	85	7	66	45	0	5	49	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3321676--3321734	14	4.2	14	85	8	75	45	0	5	49	1.24
3321676--3321734	21	2.8	21	89	0	91	45	0	5	49	1.24
3324082--3324139	29	2.0	29	86	6	82	58	8	3	29	1.44
3324790--3324861	15	5.0	15	75	8	60	62	0	1	36	1.04
3325098--3325168	23	3.0	23	75	6	70	49	1	0	49	1.09
3325096--3325168	26	2.9	26	75	19	75	49	1	0	49	1.09
3325417--3325495	24	3.5	23	70	19	67	59	1	0	39	1.06
3325425--3325498	28	2.7	28	69	19	66	60	0	0	39	0.97
3325426--3325495	15	4.9	15	77	8	74	62	0	0	37	0.95
3324457--3325707	634	2.0	627	87	5	1824	42	6	8	42	1.61

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