genome.fa.s196.2.7.7.80.10.50.1000.9.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: Scaffold196
Parameters: 2 7 7 80 10 50 1000
Length:  7488280

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   

This is table  9  of  47  ( 5587 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)
1188199--1188249	14	3.4	15	78	15	52	76	0	21	1	0.88
1188196--1188251	17	3.3	17	74	0	58	78	0	19	1	0.84
1190944--1190995	17	3.1	17	72	10	52	42	0	1	55	1.10
1191907--1191974	27	2.5	27	90	0	100	26	5	20	47	1.73
1193780--1193868	27	3.1	28	82	4	99	30	31	16	21	1.96
1193782--1194222	58	7.5	58	75	10	312	29	29	17	24	1.97
1193966--1194187	88	2.6	87	94	3	385	33	28	18	20	1.96
1193782--1194224	30	15.1	30	77	12	343	29	29	16	24	1.97
1194228--1194317	43	2.1	43	91	0	144	26	25	17	30	1.98
1194271--1194424	52	2.9	53	80	4	184	24	24	16	35	1.95
1195256--1195280	13	1.9	13	100	0	50	36	16	16	32	1.90
1195236--1195302	33	2.0	33	88	0	98	32	11	14	40	1.83
1195344--1195368	13	1.9	13	100	0	50	32	16	16	36	1.90
1195377--1195557	52	3.5	52	97	0	335	34	18	17	28	1.94
1202492--1202556	27	2.4	27	89	0	94	26	6	23	44	1.76
1203909--1203964	13	4.2	14	80	17	57	46	1	0	51	1.11
1203920--1203965	13	3.4	14	85	5	60	45	0	0	54	0.99
1204203--1204231	14	2.1	14	100	0	58	41	0	0	58	0.98
1204307--1204355	18	2.6	19	87	9	66	69	0	0	30	0.89
1204313--1204353	12	3.5	12	87	12	59	68	0	0	31	0.90
1204304--1204352	23	2.1	24	85	11	66	71	0	0	28	0.86
1204866--1204988	49	2.5	49	94	0	210	32	15	28	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1205111--1205573	43	10.1	43	82	12	548	31	18	24	25	1.97
1205067--1205568	92	5.4	92	95	1	851	31	18	23	26	1.97
1205609--1205664	27	2.1	27	86	0	76	39	14	25	21	1.91
1205634--1206232	34	17.8	34	79	9	631	33	12	33	20	1.90
1205635--1206232	100	5.9	101	83	7	661	33	12	33	20	1.90
1205634--1206232	66	8.9	65	79	10	543	33	12	33	20	1.90
1205634--1206177	205	2.7	203	87	3	724	34	12	33	20	1.89
1206212--1206385	31	5.7	31	85	6	203	27	17	30	25	1.97
1207339--1207395	1	57.0	1	75	0	51	0	0	12	87	0.54
1207339--1207392	6	8.7	6	85	6	72	0	0	12	87	0.56
1213697--1213745	22	2.2	22	96	0	89	69	8	8	14	1.36
1214664--1214738	20	3.8	20	80	3	80	40	12	13	34	1.81
1214661--1214738	40	2.0	39	87	2	111	39	12	12	34	1.82
1218209--1218337	52	2.5	52	93	0	213	31	17	16	35	1.92
1218209--1218357	52	2.9	51	87	4	201	32	16	16	34	1.92
1218346--1218383	13	2.9	13	100	0	76	36	15	15	31	1.90
1218447--1218471	13	1.9	13	100	0	50	32	16	16	36	1.90
1218425--1218491	33	2.0	33	88	0	98	38	14	13	32	1.86
1220928--1220977	24	2.1	22	85	10	64	54	2	0	44	1.11
1220932--1220975	14	3.4	14	70	23	51	52	2	0	45	1.13
1220973--1221017	19	2.5	17	82	7	54	42	2	0	55	1.12
1222255--1222287	17	1.9	17	93	0	57	36	0	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1222258--1222303	23	2.0	23	88	12	69	32	0	2	65	1.05
1222470--1223295	72	11.5	72	78	5	719	31	2	10	55	1.46
1222470--1223295	142	5.7	144	81	5	782	31	2	10	55	1.46
1222434--1223274	430	1.9	433	81	5	1020	32	2	9	55	1.45
1223076--1223367	143	2.0	141	81	7	331	28	4	11	55	1.55
1226756--1227037	90	3.1	90	77	8	270	38	16	4	41	1.68
1227896--1227929	2	17.0	2	100	0	68	50	0	0	50	1.00
1228192--1228224	17	1.9	17	88	11	50	45	0	0	54	0.99
1228664--1228719	16	3.4	17	76	18	55	32	0	3	64	1.11
1228725--1228800	24	3.5	21	76	16	66	61	0	0	38	0.96
1228756--1228810	15	4.1	14	75	25	57	56	0	0	43	0.99
1228740--1228802	24	2.4	27	79	15	80	60	0	0	39	0.97
1230020--1230076	20	2.8	20	78	10	53	70	1	0	28	0.98
1230104--1230368	114	2.3	115	85	2	345	43	14	13	27	1.83
1235318--1235377	29	2.1	28	87	3	84	55	0	0	45	0.99
1235553--1235596	20	2.1	21	91	4	72	40	0	0	59	0.98
1237324--1237383	29	2.1	28	85	11	79	53	0	0	46	1.00
1237307--1237384	14	5.7	14	68	14	56	52	0	0	47	1.00
1237418--1237478	11	5.4	12	79	13	58	62	0	4	32	1.17
1237516--1237590	32	2.4	31	80	8	80	49	1	1	48	1.18
1238461--1238534	19	3.9	19	80	5	71	4	28	1	66	1.18
1239051--1239107	20	2.6	22	81	13	73	64	1	0	33	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1239153--1239194	16	2.6	16	88	7	59	0	19	0	80	0.70
1239478--1239529	19	2.8	18	80	11	61	44	0	0	55	0.99
1239491--1239543	23	2.3	25	78	18	69	47	0	0	52	1.00
1239528--1239587	23	2.6	22	73	17	59	58	0	0	41	0.98
1239528--1239595	24	2.9	23	71	16	59	58	0	0	41	0.98
1239580--1239665	11	8.2	11	71	20	60	65	2	0	32	1.06
1239604--1239697	27	3.5	26	79	15	100	67	0	0	32	0.91
1239604--1239694	28	3.3	27	74	17	89	65	0	0	34	0.93
1248006--1248086	41	2.0	41	87	0	117	38	2	4	54	1.35
1248093--1248130	15	2.5	16	83	12	53	39	0	0	60	0.97
1248182--1248284	50	2.0	49	85	9	134	52	0	0	46	1.07
1248213--1248310	49	2.0	49	80	11	112	57	3	0	39	1.14
1254073--1254112	3	13.3	3	100	0	80	67	0	0	32	0.91
1254540--1254567	2	14.0	2	100	0	56	50	0	0	50	1.00
1256940--1256973	3	11.3	3	100	0	68	67	0	0	32	0.91
1258130--1258216	32	2.7	32	81	0	84	21	6	28	42	1.79
1259359--1259414	28	2.0	28	82	3	67	46	0	0	53	1.00
1259699--1259775	16	4.6	17	69	12	52	46	0	3	49	1.20
1259751--1259807	23	2.6	21	74	17	53	47	1	1	49	1.22
1259901--1259939	21	1.9	20	89	5	60	38	0	0	61	0.96
1260019--1260091	15	4.7	16	73	22	66	61	0	0	38	0.96
1261419--1261448	2	15.0	2	100	0	60	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1263006--1263036	2	15.5	2	100	0	62	48	0	0	51	1.00
1269103--1269134	3	10.7	3	100	0	64	31	0	0	68	0.90
1269669--1269751	11	7.5	11	79	15	100	57	1	0	40	1.06
1269689--1269751	20	3.1	20	88	4	99	58	1	0	39	1.07
1269689--1269744	9	5.7	9	76	19	58	57	1	0	41	1.09
1269670--1269760	41	2.1	44	84	11	118	59	1	1	38	1.12
1269670--1269763	20	4.3	21	78	14	93	59	1	1	38	1.11
1269696--1269766	21	3.4	20	76	16	65	61	1	1	35	1.13
1272996--1273027	6	5.3	6	100	0	64	34	0	0	65	0.93
1273246--1273312	16	4.2	16	90	0	98	53	0	4	41	1.21
1273265--1273310	22	2.1	22	84	8	58	54	0	4	41	1.20
1278289--1278333	21	2.1	21	84	8	56	37	4	4	53	1.41
1282666--1282703	2	19.0	2	94	0	67	52	47	0	0	1.00
1282722--1282746	2	12.5	2	100	0	50	0	0	48	52	1.00
1284715--1284755	2	20.5	2	100	0	82	48	0	0	51	1.00
1286979--1287033	18	3.1	18	83	0	65	49	3	3	43	1.37
1286960--1287123	84	1.9	84	88	3	249	46	5	6	42	1.52
1287063--1287118	18	3.1	18	76	2	58	51	3	3	41	1.36
1289660--1289733	18	4.1	18	82	6	96	47	9	5	37	1.59
1289660--1289827	36	4.9	36	70	14	122	42	10	8	38	1.70
1289763--1289828	18	3.7	18	74	6	64	40	10	7	40	1.68
1289714--1289835	16	7.3	16	69	15	61	41	9	9	39	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1291276--1291347	20	3.6	20	76	0	81	36	13	9	40	1.78
1291273--1291350	40	2.0	39	89	2	120	35	12	11	39	1.80
1292258--1292313	22	2.5	23	94	5	105	17	10	8	62	1.52
1292266--1292320	22	2.6	21	88	5	58	20	9	9	61	1.52
1305379--1305434	12	4.8	12	86	6	71	87	10	1	0	0.62
1305378--1305429	22	2.4	22	93	6	88	86	13	0	0	0.57
1305379--1305436	1	58.0	1	75	0	53	87	10	1	0	0.60
1305381--1305436	22	2.7	20	83	5	67	87	10	1	0	0.62
1306668--1307612	28	32.9	29	88	3	1314	28	31	17	22	1.96
1306668--1307612	86	11.0	86	87	4	1302	28	31	17	22	1.96

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