oyster.v9_M.fa.s11.2.7.7.80.10.50.500.4.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold257
Parameters: 2 7 7 80 10 50 500
Length:  1615106

Tables:   1   2   3   4   5   

This is table  4  of  5  ( 556 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)
929006--929258	29	8.6	29	90	4	326	45	12	18	24	1.84
932081--932110	2	15.0	2	92	0	51	46	0	53	0	1.00
935812--935848	17	2.2	17	95	0	65	10	2	16	70	1.27
936152--936188	2	18.5	2	100	0	74	48	0	51	0	1.00
936367--936420	2	27.0	2	100	0	108	50	0	50	0	1.00
937263--937292	13	2.3	13	100	0	60	83	16	0	0	0.65
937390--937431	10	3.8	11	87	9	59	54	4	19	21	1.62
937390--937450	10	5.9	10	77	12	52	50	4	19	24	1.67
937412--937450	19	2.1	19	85	0	51	51	2	20	25	1.60
938815--938855	21	2.0	20	90	0	55	34	14	7	41	1.74
946265--946313	2	24.5	2	95	0	89	46	0	0	53	1.00
952121--952173	2	26.5	2	100	0	106	0	50	0	49	1.00
952663--952709	2	23.5	2	100	0	94	48	0	51	0	1.00
954167--954215	24	2.0	24	84	0	62	46	12	18	22	1.82
963828--963866	20	1.9	20	84	0	51	33	5	2	58	1.33
970165--970330	89	1.9	89	93	2	289	24	16	26	32	1.96
983830--983875	2	23.0	2	86	0	65	4	2	43	50	1.34
987100--987125	1	26.0	1	100	0	52	0	0	100	0	0.00
994460--994505	2	23.0	2	100	0	92	0	50	0	50	1.00
998365--998612	126	2.0	126	100	0	496	25	16	18	39	1.91
1004784--1004829	2	23.5	2	93	4	76	0	52	0	47	1.00
1015888--1015927	18	2.2	18	90	0	62	15	2	42	40	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1017987--1018056	21	3.3	21	77	0	86	18	18	24	38	1.93
1018048--1018112	21	3.0	21	73	8	67	24	20	32	23	1.98
1017987--1018077	42	2.2	42	82	4	112	18	19	27	34	1.96
1019080--1019325	130	1.9	130	96	0	456	44	14	11	29	1.81
1019721--1019810	21	4.3	21	78	0	108	17	22	25	34	1.96
1026017--1026068	21	2.5	21	87	0	77	34	15	11	38	1.83
1026408--1026457	21	2.4	22	76	10	59	36	16	12	36	1.85
1036216--1036294	32	2.5	31	80	11	90	46	16	10	26	1.78
1036878--1037098	53	4.1	53	86	3	316	45	18	20	15	1.86
1037067--1037131	33	2.0	33	90	0	103	35	24	21	18	1.96
1044368--1045174	166	4.8	166	86	2	1125	26	22	16	34	1.95
1044368--1045174	335	2.4	336	89	3	1227	26	22	16	34	1.95
1056346--1056448	51	2.0	51	96	3	181	25	15	21	36	1.93
1069949--1070001	18	2.9	18	94	0	97	26	16	16	39	1.91
1077960--1077996	3	12.3	3	100	0	74	35	32	0	32	1.58
1078163--1078199	13	3.0	13	84	11	51	67	0	8	24	1.17
1089064--1089121	2	29.0	2	100	0	116	0	50	0	50	1.00
1092475--1092501	4	6.8	4	100	0	54	22	0	0	77	0.76
1103471--1103501	2	15.5	2	100	0	62	51	0	0	48	1.00
1123363--1123429	7	9.6	7	83	0	89	35	14	22	26	1.93
1123924--1123963	2	20.0	2	100	0	80	50	0	50	0	1.00
1123961--1123989	4	7.2	4	100	0	58	51	24	24	0	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1124177--1124223	2	23.5	2	100	0	94	0	51	0	48	1.00
1126622--1126688	7	9.6	7	83	0	89	26	22	14	35	1.93
1126622--1126688	21	3.2	21	86	0	98	26	22	14	35	1.93
1152665--1152731	2	33.5	2	100	0	134	50	0	49	0	1.00
1155832--1155975	71	2.0	72	95	1	263	25	7	19	47	1.75
1164818--1164846	2	14.5	2	100	0	58	51	0	48	0	1.00
1169477--1170223	161	4.6	161	81	6	770	35	19	14	30	1.92
1169589--1170223	332	1.9	331	84	1	851	35	19	14	29	1.92
1170542--1171344	146	5.5	145	85	3	1024	31	21	18	28	1.97
1171352--1171391	12	3.3	12	85	0	53	37	25	35	2	1.69
1171351--1171385	16	2.2	16	94	0	61	40	25	34	0	1.56
1171857--1171882	12	2.2	12	100	0	52	38	11	0	50	1.39
1172329--1172379	21	2.4	21	83	6	59	17	15	33	33	1.92
1172680--1172877	100	2.0	100	94	0	351	32	23	14	29	1.94
1173681--1174166	177	2.8	175	82	5	563	33	23	16	25	1.96
1177532--1177556	11	2.3	11	100	0	50	56	8	20	16	1.65
1178311--1178346	4	9.0	4	87	0	54	2	44	25	27	1.68
1178320--1178354	12	2.9	12	86	0	52	0	40	25	34	1.56
1178312--1178363	8	6.5	8	88	0	59	1	38	25	34	1.67
1178324--1178362	12	3.2	12	85	0	51	0	35	25	38	1.56
1178772--1178802	14	2.2	14	100	0	62	51	0	12	35	1.40
1178771--1178827	22	2.8	21	89	7	82	47	0	14	38	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1180304--1180381	31	2.4	32	93	4	131	26	28	19	25	1.99
1180304--1180407	31	3.2	32	86	2	120	24	27	20	27	1.99
1186819--1186851	17	1.9	17	100	0	66	24	21	24	30	1.99
1190740--1190779	15	2.7	15	88	7	55	15	30	20	35	1.93
1193861--1193891	15	2.1	15	93	0	53	9	29	19	41	1.83
1194812--1194845	4	8.5	4	93	0	59	29	23	47	0	1.52
1194808--1194845	12	3.2	12	92	0	67	31	23	44	0	1.54
1198715--1199449	166	4.5	164	78	9	709	34	14	22	28	1.93
1199038--1199066	15	2.0	15	93	6	51	62	6	0	31	1.22
1201250--1201279	15	2.0	15	93	0	51	10	26	33	30	1.89
1201910--1201940	15	2.1	15	100	0	62	38	12	0	48	1.42
1203488--1204026	166	3.2	164	86	4	751	25	25	14	33	1.95
1205832--1205857	11	2.4	11	100	0	52	30	19	15	34	1.93
1234772--1234808	13	2.8	13	91	0	56	18	2	0	78	0.87
1264817--1264856	11	3.7	11	86	3	55	35	10	30	25	1.88
1264926--1264965	11	3.7	11	90	3	64	27	25	10	37	1.88
1264958--1265018	22	2.8	22	78	9	70	18	24	14	42	1.88
1265347--1265388	2	21.0	2	100	0	84	0	50	0	50	1.00
1265603--1265825	112	2.0	112	98	0	428	32	18	18	29	1.95
1266837--1266978	11	12.9	11	78	12	150	28	10	33	27	1.90
1266856--1267027	88	2.0	85	86	13	235	29	11	30	27	1.91
1267033--1267073	11	3.7	11	80	0	55	21	26	9	41	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1267082--1267113	11	2.9	11	95	0	55	34	9	28	28	1.88
1267118--1267157	21	1.9	21	94	0	71	27	20	10	42	1.83
1267118--1267157	11	3.7	11	86	6	64	27	20	10	42	1.83
1272054--1272310	27	9.4	27	67	6	113	37	31	12	18	1.88
1272049--1272362	54	5.7	53	75	7	288	38	31	11	18	1.86
1272039--1272415	110	3.4	110	94	0	637	38	31	11	18	1.86
1275055--1275093	2	19.5	2	100	0	78	0	48	0	51	1.00
1275454--1275488	18	1.9	18	88	0	52	42	14	8	34	1.76
1276848--1276882	13	2.7	13	95	0	61	51	0	8	40	1.33
1277811--1277856	22	2.1	22	100	0	92	34	13	4	47	1.62
1283873--1283898	13	2.0	13	100	0	52	46	7	15	30	1.74
1283927--1283959	17	1.9	17	100	0	66	30	24	21	24	1.99
1285844--1285869	1	26.0	1	100	0	52	0	0	100	0	0.00
1286223--1286431	105	2.0	100	92	4	346	34	9	13	41	1.78
1286677--1286719	2	21.5	2	95	0	77	0	53	0	46	1.00
1287200--1287419	42	5.2	42	93	0	359	18	32	22	26	1.97
1287346--1287414	22	3.2	22	64	15	63	21	31	21	24	1.98
1287399--1287450	22	2.4	21	77	3	68	9	28	26	34	1.88
1303698--1303744	11	4.0	12	83	10	62	8	17	23	51	1.72
1303699--1303745	22	2.0	24	88	8	71	8	14	23	53	1.69
1303756--1303806	22	2.3	22	86	0	66	11	15	29	43	1.82
1304029--1304062	11	3.1	11	86	0	50	44	26	17	11	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1306931--1306965	4	9.0	4	87	6	54	0	48	25	25	1.51
1307269--1307796	163	3.3	163	77	8	470	33	13	22	30	1.93
1309075--1309125	5	10.4	5	83	12	70	60	0	3	35	1.15
1309078--1309125	20	2.5	19	93	3	78	62	0	4	33	1.14
1309466--1309512	5	9.4	5	90	9	78	59	0	2	38	1.09
1310161--1311175	165	6.1	164	81	8	969	32	15	24	27	1.96
1310178--1311175	336	3.0	322	79	9	908	32	15	24	27	1.96
1317490--1317521	4	8.0	4	100	0	64	0	25	25	50	1.50
1317610--1317649	4	9.5	4	84	10	53	2	30	20	47	1.63
1317610--1317655	22	2.1	22	95	0	83	2	32	17	47	1.60

Tables:   1   2   3   4   5