oyster.v9_M.fa.s1.2.7.7.80.10.50.500.4.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: scaffold22
Parameters: 2 7 7 80 10 50 500
Length:  1964558

Tables:   1   2   3   4   5   6   

This is table  4  of  6  ( 655 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)
1112759--1112837	31	2.5	31	81	6	79	27	12	20	39	1.89
1112791--1112855	31	2.1	30	83	8	78	27	12	16	43	1.84
1113410--1114391	437	2.2	437	97	0	1883	34	15	18	31	1.93
1117683--1117745	2	31.5	2	100	0	126	50	0	49	0	1.00
1124205--1124260	2	28.0	2	100	0	112	50	0	50	0	1.00
1130208--1130271	33	1.9	34	93	3	112	48	7	37	6	1.57
1130210--1130290	18	4.7	18	70	14	62	50	7	35	6	1.55
1130251--1130301	18	2.8	18	85	5	59	52	5	35	5	1.50
1132657--1132712	2	28.0	2	100	0	112	50	0	50	0	1.00
1133203--1133269	20	3.4	20	95	0	125	34	14	10	40	1.81
1136434--1136460	2	13.5	2	100	0	54	0	51	0	48	1.00
1136546--1136634	2	45.5	2	76	4	65	2	49	1	47	1.21
1136546--1136614	12	5.9	12	86	5	97	1	55	1	42	1.18
1141536--1141568	16	2.0	17	94	5	59	78	0	9	12	0.95
1160009--1160146	48	2.9	48	81	6	154	30	9	29	30	1.89
1162857--1162984	32	4.0	32	90	1	195	28	13	30	27	1.94
1165318--1165347	15	2.0	15	100	0	60	33	20	13	33	1.91
1171018--1171044	12	2.2	12	100	0	54	33	33	7	25	1.84
1173477--1173525	23	2.1	23	88	7	73	34	20	10	34	1.86
1177428--1177668	31	7.9	31	70	9	113	33	17	17	30	1.94
1177934--1178152	31	6.8	31	74	11	172	33	16	15	34	1.90
1177998--1178152	60	2.5	60	83	4	186	33	16	16	33	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1180367--1180745	189	2.0	188	91	3	618	35	13	12	39	1.82
1186591--1186620	2	15.0	2	100	0	60	0	50	0	50	1.00
1190384--1190445	30	2.1	29	93	3	106	33	19	12	33	1.90
1191272--1191299	14	2.0	14	100	0	56	57	7	14	21	1.61
1192185--1192415	46	5.0	46	99	0	453	17	32	12	36	1.88
1198470--1198524	2	27.5	2	88	0	83	0	43	0	56	0.99
1202023--1202059	2	18.5	2	100	0	74	0	48	0	51	1.00
1207833--1208019	80	2.3	80	93	0	311	31	16	18	33	1.93
1211351--1211396	21	2.2	21	84	7	58	32	0	17	50	1.47
1214155--1214271	24	4.9	24	80	0	135	37	16	10	35	1.82
1214151--1214271	48	2.5	48	83	0	161	38	16	9	35	1.82
1215917--1216443	166	3.2	166	92	1	864	26	24	16	32	1.96
1218574--1218621	19	2.6	18	81	12	53	27	6	25	41	1.79
1220708--1220755	2	24.0	2	100	0	96	0	50	0	50	1.00
1221278--1221317	19	2.0	20	86	13	57	47	10	12	30	1.74
1229199--1229248	24	2.1	24	100	0	100	42	18	8	32	1.79
1237335--1237393	19	3.0	20	90	7	77	44	10	10	35	1.72
1237352--1237393	19	2.2	19	100	0	84	45	9	11	33	1.73
1240227--1240306	21	3.8	21	88	4	117	26	8	23	41	1.83
1240330--1240362	10	3.3	10	91	0	57	21	12	24	42	1.86
1240511--1240544	10	3.4	10	91	0	50	23	8	26	41	1.83
1240510--1240544	15	2.3	15	90	0	52	22	8	28	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1240569--1240643	21	3.6	21	90	0	114	29	17	18	34	1.94
1240835--1240941	49	2.2	49	87	0	160	33	20	13	32	1.91
1243653--1243726	23	3.5	21	71	19	64	44	10	9	35	1.72
1243655--1243801	41	3.6	41	73	7	127	44	10	9	35	1.72
1243770--1243811	22	1.9	22	85	9	59	42	14	7	35	1.73
1257915--1258013	30	3.3	30	91	0	153	27	17	23	32	1.96
1257915--1258026	30	3.7	30	89	0	125	25	17	21	34	1.95
1258146--1258187	20	2.1	20	95	4	77	30	16	7	45	1.74
1258182--1258246	25	2.6	25	87	0	94	26	16	26	30	1.97
1262202--1262268	7	9.6	7	76	0	71	26	19	14	38	1.91
1262982--1263044	25	2.7	22	81	13	81	55	4	12	26	1.57
1267007--1267060	2	27.0	2	100	0	108	0	50	0	50	1.00
1271273--1271303	4	7.8	4	100	0	62	25	0	0	74	0.82
1273329--1273358	12	2.5	12	94	0	51	0	93	3	3	0.42
1273744--1273797	21	2.6	21	75	13	58	27	16	16	38	1.90
1273733--1273807	21	3.6	21	69	15	57	24	20	14	41	1.89
1281978--1282054	13	5.7	13	75	14	57	40	19	1	38	1.60
1297622--1297664	11	3.6	12	78	12	52	34	9	9	46	1.68
1299988--1300060	38	1.9	38	94	0	128	39	8	16	35	1.78
1307132--1307168	16	2.3	16	100	0	74	54	16	5	24	1.63
1312793--1313259	42	11.1	42	85	2	580	28	17	22	31	1.96
1313666--1313891	42	5.4	42	83	3	283	28	19	21	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1313876--1313906	15	2.1	15	93	0	53	22	29	25	22	1.99
1313834--1313948	57	2.0	57	87	0	167	25	21	23	29	1.99
1313891--1314454	42	13.4	42	83	3	620	27	16	22	32	1.96
1315583--1315626	22	2.0	22	95	0	79	47	13	20	18	1.82
1318139--1318178	2	20.0	2	100	0	80	50	50	0	0	1.00
1320837--1320863	2	13.5	2	100	0	54	0	48	0	51	1.00
1321342--1321419	2	40.0	2	92	5	133	1	51	0	47	1.09
1325638--1326807	42	27.8	42	88	4	1486	32	22	17	27	1.96
1325638--1326787	126	9.1	126	90	2	1643	32	22	17	27	1.96
1328289--1328583	43	6.9	43	84	3	222	33	15	14	36	1.89
1328281--1328583	107	2.8	107	87	3	423	32	15	14	37	1.88
1328289--1328583	64	4.6	64	82	2	288	33	15	14	36	1.89
1341291--1343153	437	4.3	437	88	1	2494	30	17	15	36	1.91
1343604--1343835	115	2.0	115	94	0	410	47	16	20	15	1.82
1343604--1343829	56	4.0	56	94	3	380	46	17	21	15	1.84
1347405--1347918	130	4.0	130	93	0	895	25	25	10	38	1.87
1347401--1347918	259	2.0	259	98	0	1000	25	25	10	38	1.87
1349340--1349391	25	2.1	25	96	3	97	15	7	9	67	1.41
1363450--1363565	54	2.1	55	88	4	173	34	18	15	31	1.92
1364203--1364631	215	2.0	214	100	0	849	34	15	18	31	1.92
1365420--1365464	17	2.8	17	90	6	67	46	11	13	28	1.77
1368741--1368765	2	12.5	2	100	0	50	48	0	52	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1371597--1371628	11	2.9	11	95	0	55	71	0	15	12	1.14
1373200--1373249	10	5.0	10	75	15	50	42	2	10	46	1.49
1373200--1373259	20	3.0	20	76	13	61	40	1	11	46	1.50
1373216--1373270	25	2.2	25	86	0	74	36	3	10	49	1.56
1373256--1373299	24	1.9	23	86	9	63	38	13	9	38	1.77
1373333--1373661	15	21.6	15	67	17	128	45	11	3	38	1.58
1373398--1373466	5	13.8	5	72	11	52	43	11	2	42	1.56
1373383--1373426	20	2.2	20	91	0	70	43	13	2	40	1.57
1373338--1373446	35	3.3	35	79	11	120	43	11	4	40	1.62
1373383--1373472	20	4.8	19	71	16	62	44	12	2	41	1.54
1373397--1373470	10	7.4	10	74	6	69	45	10	2	40	1.53
1373333--1373718	15	25.2	15	67	19	97	46	11	3	38	1.57
1379052--1380138	327	3.3	326	89	2	1497	27	24	20	27	1.99
1380800--1380824	13	1.9	13	100	0	50	8	16	36	40	1.77
1382110--1382163	2	27.0	2	100	0	108	50	0	50	0	1.00
1382492--1382546	2	27.5	2	100	0	110	0	49	0	50	1.00
1383993--1384037	19	2.3	20	88	3	65	26	31	33	8	1.87
1387010--1387059	16	3.1	16	85	0	64	38	24	6	32	1.79
1388181--1388268	46	1.9	46	88	0	131	43	11	13	31	1.80
1388182--1388268	21	4.0	21	80	11	93	43	11	13	31	1.80
1388349--1388444	43	2.2	43	88	0	138	36	11	16	35	1.85
1389151--1389312	21	7.6	21	76	3	153	32	17	12	37	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1389168--1389312	43	3.4	43	85	0	193	31	17	13	37	1.88
1391611--1391668	16	3.3	18	79	15	68	0	0	17	82	0.66
1391610--1391664	27	2.0	29	89	7	87	0	0	20	80	0.72
1391627--1391675	17	2.9	17	80	14	66	0	0	18	81	0.69
1398695--1398736	12	3.5	12	83	9	50	33	28	2	35	1.70
1404996--1405025	9	3.3	9	95	0	51	3	0	16	80	0.85
1408448--1408659	107	2.0	105	87	3	300	25	25	17	31	1.97
1408551--1409002	146	3.1	146	91	1	683	28	23	17	30	1.97
1409009--1409042	12	2.8	12	100	0	68	35	26	38	0	1.57
1427259--1427322	2	32.0	2	93	0	110	1	48	0	50	1.10

Tables:   1   2   3   4   5   6