genome.fa.s53.2.7.7.80.10.50.1000.25.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: Scaffold53
Parameters: 2 7 7 80 10 50 1000
Length:  4419549

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   

This is table  25  of  28  ( 3325 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)
3883915--3884790	28	30.3	31	79	11	173	29	30	16	23	1.96
3885688--3885885	51	3.9	51	93	0	324	27	17	13	41	1.86
3886746--3886786	21	2.0	22	85	9	59	21	19	9	48	1.77
3889831--3889900	15	4.8	15	74	11	65	31	12	21	34	1.91
3889831--3889900	29	2.4	29	82	2	77	31	12	21	34	1.91
3896930--3896978	25	1.9	26	84	12	66	28	4	4	63	1.31
3898896--3898924	14	2.1	14	100	0	58	41	20	6	31	1.79
3899064--3899094	15	2.1	15	100	0	62	38	6	6	48	1.55
3899358--3899405	14	3.4	14	75	11	53	75	0	0	25	0.81
3903438--3903483	24	1.9	24	90	0	74	8	21	32	36	1.84
3903452--3903497	21	2.2	21	84	7	58	8	19	36	34	1.83
3903486--3903580	31	3.0	31	80	10	104	25	16	35	22	1.95
3904118--3904183	31	2.1	31	94	0	114	16	27	19	36	1.93
3904778--3906697	42	45.9	42	76	7	1081	39	17	29	14	1.88
3905385--3905516	71	1.9	71	87	3	194	45	15	24	15	1.84
3905343--3905558	113	1.9	113	86	1	308	43	16	25	14	1.86
3905304--3905600	155	1.9	155	84	0	396	42	16	26	13	1.86
3905502--3905767	145	1.8	145	82	1	345	40	18	27	13	1.88
3906535--3906592	30	1.9	30	89	6	91	32	22	29	15	1.95
3906505--3906638	72	1.9	72	84	3	180	34	17	32	15	1.91
3906451--3907159	126	6.0	114	72	11	364	37	17	30	15	1.91
3906692--3907041	42	8.3	42	77	5	260	37	16	29	16	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3906623--3906763	69	2.0	70	82	4	169	41	14	29	14	1.85
3906692--3907041	84	4.2	84	81	1	315	37	16	29	16	1.91
3906602--3906808	111	1.9	111	82	4	265	41	14	28	15	1.87
3906692--3907390	126	5.6	126	76	8	563	38	16	29	16	1.90
3907013--3907073	32	1.9	32	93	0	104	37	21	26	14	1.92
3907044--3907385	42	8.1	41	80	3	306	38	14	29	16	1.89
3907056--3907391	84	4.0	84	80	0	368	38	15	30	16	1.90
3920098--3920145	13	3.7	13	79	20	64	22	2	0	75	0.91
3920102--3920153	23	2.2	24	79	6	61	26	1	0	71	0.97
3921029--3921089	24	2.8	21	79	13	77	4	19	37	37	1.74
3921084--3921174	31	2.9	31	86	3	121	27	20	34	17	1.95
3921726--3921784	31	1.9	31	96	0	109	20	28	16	33	1.95
3926011--3926189	67	2.8	66	79	8	167	27	13	18	40	1.88
3926041--3926189	67	2.3	65	82	6	176	27	13	19	39	1.89
3926231--3926407	68	2.6	68	87	4	250	25	12	21	39	1.89
3932332--3932460	65	2.0	62	96	3	222	34	9	22	34	1.86
3932441--3932474	2	17.0	2	100	0	68	50	0	0	50	1.00
3933495--3933525	2	15.5	2	100	0	62	48	0	0	51	1.00
3934150--3934178	15	2.0	15	93	6	51	68	0	0	31	0.89
3935726--3935769	2	22.0	2	100	0	88	50	0	0	50	1.00
3936036--3936076	2	20.5	2	100	0	82	48	0	0	51	1.00
3936667--3936738	16	4.5	16	76	0	81	13	12	23	50	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3936696--3936749	16	3.4	16	78	0	63	11	14	24	50	1.75
3936688--3936756	32	2.2	32	86	0	93	14	14	24	46	1.82
3937229--3937255	14	1.9	14	100	0	54	81	0	3	14	0.82
3937227--3937261	14	2.4	14	85	4	52	77	2	2	17	1.02
3943075--3943105	14	2.1	15	94	5	55	58	16	0	25	1.38
3945281--3945349	28	2.5	27	76	2	66	33	18	8	39	1.82
3951170--3951195	13	2.0	13	100	0	52	38	15	15	30	1.88
3951219--3951293	20	3.7	20	76	13	62	36	12	12	40	1.79
3953803--3953852	25	2.0	24	85	14	66	26	20	4	50	1.66
3961480--3962380	31	28.0	31	73	9	470	26	20	12	41	1.87
3961480--3962380	66	14.0	62	72	11	479	26	20	12	41	1.87
3961568--3961930	159	2.3	157	82	5	428	25	20	11	41	1.86
3961480--3961895	61	6.6	62	75	8	259	27	20	11	40	1.87
3961495--3961997	225	2.3	220	81	4	557	27	20	11	40	1.87
3962906--3962958	20	2.6	20	84	3	70	20	15	30	33	1.93
3967065--3967095	15	2.1	15	100	0	62	32	12	35	19	1.90
3967394--3967510	51	2.3	51	90	0	189	35	14	22	28	1.93
3967493--3967569	28	2.7	30	86	7	108	25	22	31	20	1.98
3967561--3967668	51	2.1	51	79	6	121	34	13	22	29	1.93
3967965--3968071	20	5.7	20	72	22	97	42	12	15	29	1.84
3967985--3968056	33	2.2	33	94	0	126	41	12	16	29	1.85
3968998--3969246	111	2.2	114	84	8	312	27	21	24	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3968937--3969244	57	5.3	56	79	8	293	27	21	24	26	1.99
3969169--3969340	94	1.8	93	91	1	281	25	21	27	25	1.99
3969262--3969817	55	9.5	59	84	8	592	26	20	26	26	1.99
3969633--3969717	29	3.0	29	61	22	72	23	21	27	28	1.99
3969264--3969813	294	1.9	295	89	1	870	26	20	26	26	1.99
3976056--3976174	51	2.3	51	89	0	193	31	14	26	27	1.95
3976159--3976230	28	2.6	28	93	0	117	26	20	30	22	1.98
3976218--3976446	51	4.5	51	82	1	237	35	11	24	28	1.90
3978756--3978860	20	5.6	19	79	17	114	41	13	17	27	1.86
3978756--3978825	33	2.1	33	100	0	140	40	14	18	27	1.89
3978775--3978805	13	2.4	13	100	0	62	38	16	16	29	1.90
3983726--3983776	27	2.0	25	85	14	68	41	0	0	58	0.98
3983761--3983802	13	3.1	14	80	13	52	52	0	0	47	1.00
3994494--3994536	15	3.1	14	80	9	52	62	0	0	37	0.95
3999449--3999545	26	3.8	26	68	18	78	46	1	0	52	1.07
3999466--3999515	22	2.3	21	83	6	64	42	0	0	58	0.98
3999459--3999573	48	2.6	42	81	12	115	47	0	0	52	1.00
3999501--3999596	41	2.3	42	81	13	117	52	0	0	47	1.00
3999688--3999739	24	2.2	24	89	0	77	40	1	7	50	1.42
4000241--4000291	23	2.3	23	79	3	59	33	1	0	64	1.05
4000908--4001125	74	3.0	73	78	8	191	31	1	11	54	1.47
4001167--4001245	8	9.9	8	75	14	74	81	1	16	1	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4001177--4001244	7	8.9	7	77	22	66	80	1	16	1	0.85
4001168--4001245	15	4.9	15	80	14	86	80	1	16	1	0.84
4001452--4001879	139	3.0	141	80	10	501	32	6	13	48	1.68
4002257--4002323	30	2.3	30	84	2	91	17	16	16	49	1.80
4002282--4002399	60	2.0	60	83	3	148	18	19	16	45	1.85
4003338--4003393	21	2.7	21	89	8	80	39	14	14	32	1.86
4003453--4003516	32	2.0	33	87	3	94	39	15	14	31	1.87
4003616--4003658	21	2.0	22	90	4	70	37	9	9	44	1.69
4003621--4003664	22	2.0	22	86	8	63	38	11	9	40	1.73
4004337--4004375	21	1.9	21	89	5	62	33	30	0	35	1.58
4004622--4004656	18	1.9	18	88	0	52	42	25	5	25	1.77
4010101--4010229	52	2.5	52	92	0	213	30	18	15	35	1.92
4010101--4010249	52	2.9	51	86	4	201	31	18	16	34	1.93
4010238--4010262	13	1.9	13	100	0	50	36	16	16	32	1.90
4010305--4010371	33	2.0	33	85	0	89	40	13	11	34	1.81
4014280--4014322	3	14.3	3	90	9	70	30	34	0	34	1.58
4016895--4017025	64	2.0	64	83	0	163	19	21	12	46	1.83
4016942--4017030	31	2.8	32	78	11	101	17	21	13	47	1.82
4016905--4017180	31	8.7	31	67	14	98	21	20	12	45	1.84
4016831--4017172	159	2.2	158	81	4	377	19	21	13	45	1.85
4016969--4017417	94	4.8	94	74	6	327	20	20	13	45	1.85
4016956--4017417	189	2.4	190	78	4	479	20	20	14	45	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4017246--4017316	33	2.2	32	85	9	92	16	22	15	45	1.85
4017130--4017371	31	7.7	31	66	15	77	21	20	14	43	1.87
4018821--4018886	27	2.4	28	78	19	75	40	6	4	48	1.48
4022789--4022877	46	1.9	46	93	0	151	16	26	28	28	1.97
4025868--4025945	28	2.8	28	83	9	81	42	1	0	56	1.07
4026470--4026519	16	2.9	17	88	5	75	38	0	0	62	0.96
4026493--4026540	22	2.2	22	85	7	62	31	0	0	68	0.90
4026466--4026525	16	3.6	16	74	17	59	35	0	0	65	0.93
4026453--4026539	18	5.0	18	79	14	78	35	0	1	63	1.02
4026950--4026995	19	2.5	19	82	3	58	47	0	4	47	1.21

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