genome.fa.s16.2.7.7.80.10.50.1000.30.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: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Length:  5287347

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   

This is table  30  of  35  ( 4175 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)
4313079--4313207	52	2.5	52	94	0	222	34	17	17	30	1.94
4315805--4315830	13	2.0	13	100	0	52	38	15	15	30	1.88
4315787--4315851	32	2.0	34	87	6	98	41	15	15	27	1.87
4317278--4317317	18	2.3	17	84	16	55	52	5	0	42	1.23
4319773--4319995	120	1.9	121	94	0	394	39	16	11	32	1.83
4320578--4320620	3	14.7	3	95	4	79	30	0	0	69	0.88
4320619--4320656	3	12.7	3	100	0	76	0	0	31	68	0.90
4325594--4325639	24	1.9	24	91	8	76	19	8	26	45	1.79
4330020--4330121	27	3.9	27	78	8	106	22	8	22	46	1.79
4330921--4331520	318	1.9	319	87	3	897	37	7	4	49	1.52
4331454--4331699	119	2.1	118	78	6	255	39	6	4	49	1.50
4333277--4333320	23	2.0	22	86	4	61	56	0	0	43	0.99
4333806--4333831	1	26.0	1	100	0	52	0	0	0	100	0.00
4343594--4343672	20	3.8	20	79	12	79	35	16	10	37	1.82
4348657--4348712	29	1.9	29	85	0	76	55	1	8	33	1.42
4353900--4354005	50	2.1	50	82	6	126	30	18	13	37	1.89
4356348--4356901	79	7.1	79	78	5	471	28	24	12	34	1.91
4361357--4361427	33	2.2	31	87	5	97	74	7	11	7	1.21
4363484--4363565	28	2.9	28	80	7	96	26	17	31	24	1.97
4363548--4363718	51	3.3	51	79	4	198	32	11	26	29	1.92
4363701--4363804	28	3.8	28	92	3	158	23	20	33	23	1.97
4366225--4366250	13	2.0	13	100	0	52	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4366204--4366270	33	2.0	33	88	0	98	43	16	14	25	1.86
4366290--4366357	19	3.9	18	76	23	83	38	14	11	35	1.83
4366312--4366336	13	1.9	13	100	0	50	32	16	16	36	1.90
4366293--4366355	32	2.0	32	96	0	117	36	15	12	34	1.86
4366413--4366469	21	2.7	21	97	0	105	36	19	10	33	1.86
4366474--4366521	1	48.0	1	93	0	69	4	2	0	93	0.39
4366481--4366524	22	2.0	22	100	0	88	9	4	0	86	0.70
4367117--4367574	55	8.3	55	91	4	660	20	20	29	28	1.98
4367248--4367336	29	3.2	28	64	20	69	20	19	33	26	1.96
4367163--4367307	26	5.3	26	62	21	64	20	19	32	27	1.97
4368556--4368605	1	50.0	1	79	0	55	0	4	6	90	0.57
4368556--4368604	13	3.7	13	89	5	71	0	4	6	89	0.57
4368540--4368605	15	4.4	14	78	12	69	0	9	4	86	0.70
4381007--4381088	28	2.9	28	80	7	96	26	17	31	24	1.97
4381071--4381241	51	3.3	51	79	4	198	32	11	26	29	1.92
4381224--4381327	28	3.8	28	92	3	158	23	20	33	23	1.97
4383747--4383772	13	2.0	13	100	0	52	38	15	15	30	1.88
4383726--4383792	33	2.0	33	88	0	98	43	16	14	25	1.86
4383812--4383879	19	3.9	18	76	23	83	38	14	11	35	1.83
4383834--4383858	13	1.9	13	100	0	50	32	16	16	36	1.90
4383815--4383877	32	2.0	32	96	0	117	36	15	12	34	1.86
4383935--4383991	21	2.7	21	97	0	105	36	19	10	33	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4383996--4384042	1	47.0	1	93	0	67	4	2	0	93	0.40
4384004--4384045	21	2.0	21	100	0	84	9	4	0	85	0.72
4384417--4385052	62	10.3	62	83	4	725	24	25	18	31	1.98
4391730--4392055	30	10.9	30	74	11	183	29	29	15	26	1.96
4391730--4391902	57	3.0	57	79	5	168	27	30	17	24	1.97
4391721--4391841	29	4.3	27	76	11	116	30	32	15	21	1.95
4391939--4392096	28	5.6	28	82	7	169	35	27	14	22	1.93
4391940--4392096	85	1.8	85	82	8	203	35	27	14	22	1.93
4392188--4392255	21	3.2	21	61	19	50	23	26	20	29	1.99
4392160--4392299	43	3.3	43	92	0	235	24	23	20	31	1.98
4392253--4392406	52	2.9	53	79	6	177	24	24	15	35	1.94
4393254--4393278	13	1.9	13	100	0	50	36	16	16	32	1.90
4393234--4393300	33	2.0	33	88	0	98	32	11	14	40	1.83
4393341--4393365	13	1.9	13	100	0	50	32	16	16	36	1.90
4393354--4393502	52	2.9	52	95	2	264	31	20	17	30	1.95
4407343--4407374	14	2.4	13	94	5	55	90	9	0	0	0.45
4408824--4409149	30	10.9	30	75	11	199	28	29	15	26	1.96
4408815--4408935	29	4.3	27	78	11	125	30	33	15	20	1.94
4408974--4409065	35	2.7	36	80	8	111	20	29	11	38	1.89
4409039--4409190	28	5.3	28	84	5	173	36	27	15	20	1.93
4409212--4409429	43	4.5	52	77	14	166	23	24	20	31	1.98
4409254--4409393	43	3.3	43	93	0	235	23	24	21	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4409347--4409500	52	2.9	53	79	6	177	24	24	15	35	1.94
4410348--4410372	13	1.9	13	100	0	50	36	16	16	32	1.90
4410328--4410394	33	2.0	33	88	0	98	32	11	14	40	1.83
4414235--4414346	50	2.2	50	90	0	170	29	16	11	42	1.83
4414248--4414362	50	2.3	50	87	3	151	28	16	13	41	1.86
4415413--4415472	30	2.0	30	100	0	120	26	23	10	40	1.86
4416771--4417108	79	4.3	79	77	8	273	28	22	11	36	1.89
4416771--4417108	158	2.2	155	76	6	342	28	22	11	36	1.89
4420454--4420495	22	1.9	22	85	0	57	30	28	19	21	1.97
4424757--4424801	18	2.3	20	85	11	67	64	4	0	31	1.13
4425088--4425134	8	5.8	8	78	14	51	44	0	4	51	1.21
4425149--4425185	18	2.2	18	90	9	60	27	0	0	72	0.84
4425233--4425272	21	1.9	21	94	0	71	37	2	0	60	1.11
4426772--4426804	16	2.0	17	94	5	59	66	0	0	33	0.92
4434415--4434479	24	2.7	24	84	11	87	20	1	4	73	1.08
4436717--4436755	2	19.5	2	100	0	78	48	0	0	51	1.00
4436885--4436914	2	15.0	2	100	0	60	50	0	0	50	1.00
4438888--4439091	80	2.5	81	79	9	211	16	20	13	49	1.80
4438974--4439085	40	2.8	39	74	5	107	16	20	14	49	1.80
4439274--4439415	65	2.2	65	87	3	198	19	23	15	40	1.90
4439291--4439434	65	2.2	65	83	4	175	21	25	14	38	1.92
4439385--4439540	64	2.4	65	78	11	171	16	23	18	41	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4440771--4440816	24	1.9	24	86	0	65	21	2	2	73	1.04
4443299--4443354	20	2.8	20	83	8	78	41	17	10	30	1.84
4444123--4444189	33	2.0	33	86	11	93	31	19	13	35	1.90
4446694--4446735	13	3.2	13	89	0	66	38	14	14	33	1.86
4450542--4450576	9	3.9	9	85	14	54	25	31	0	42	1.55
4452168--4452199	13	2.5	13	94	0	55	37	12	15	34	1.85
4452244--4452299	19	2.9	19	86	2	67	37	17	12	32	1.88
4453828--4453867	16	2.4	17	95	4	73	62	5	5	27	1.37
4454295--4454345	19	2.6	20	84	3	68	29	15	13	41	1.86
4454909--4455008	35	2.9	35	87	1	148	33	10	22	35	1.87
4457123--4457166	19	2.3	19	88	4	61	43	11	13	31	1.80
4457123--4457173	20	2.6	19	84	3	66	43	11	13	31	1.80
4464303--4464401	52	1.9	52	91	4	164	38	14	18	29	1.90
4464387--4464414	13	2.2	13	100	0	56	39	17	14	28	1.89
4464459--4464510	13	3.5	13	73	26	50	34	19	13	32	1.90
4464467--4464529	19	3.6	19	74	24	75	33	19	14	33	1.91
4464459--4464529	32	2.2	32	97	0	133	33	19	14	32	1.92
4465677--4465784	52	2.1	52	82	0	126	34	16	17	31	1.93
4466193--4466259	35	1.9	34	93	3	116	32	10	23	32	1.89
4469370--4469410	22	2.0	21	85	9	57	36	7	12	43	1.70
4477902--4477965	33	2.0	32	87	3	92	42	17	15	25	1.88
4481220--4481257	16	2.3	17	86	4	51	44	7	15	31	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4483028--4483088	23	2.6	23	76	5	59	42	11	9	36	1.74
4487094--4487131	20	1.9	20	94	0	67	34	15	7	42	1.76
4487699--4487747	23	2.1	24	81	11	57	57	4	4	34	1.37
4489296--4489412	40	3.1	37	69	10	101	42	12	14	29	1.83
4491290--4491420	27	4.8	26	68	20	63	46	6	9	36	1.64
4491349--4491422	26	2.8	27	81	4	87	43	8	10	37	1.69
4491493--4491549	30	1.9	29	85	3	78	33	12	10	43	1.76
4491493--4491555	29	2.1	30	82	2	74	34	11	11	42	1.76
4493176--4493212	2	20.0	2	84	15	53	45	0	0	54	1.00
4497083--4497135	3	17.7	3	100	0	106	33	0	0	66	0.92

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