genome.fa.s48.2.7.7.80.10.50.1000.9.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: Scaffold48
Parameters: 2 7 7 80 10 50 1000
Length:  4619657

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   

This is table  9  of  27  ( 3212 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)
1180960--1180992	15	2.2	15	89	10	50	48	9	6	36	1.60
1184915--1184949	1	35.0	1	88	0	52	5	94	0	0	0.32
1187578--1187609	6	5.3	6	100	0	64	53	0	31	15	1.43
1187940--1187988	21	2.3	21	86	6	64	32	0	14	53	1.41
1188282--1188329	25	1.9	25	87	8	71	37	0	2	60	1.09
1189586--1189636	20	2.5	20	77	0	57	49	0	1	49	1.12
1190294--1190345	17	2.9	17	80	11	59	30	1	0	67	1.02
1190988--1191016	13	2.1	14	93	6	51	27	0	3	68	1.05
1190982--1191030	24	2.1	24	84	3	64	36	0	2	61	1.08
1191451--1191497	18	2.5	19	79	6	51	31	2	2	63	1.18
1196995--1197063	28	2.5	28	90	0	111	42	7	20	30	1.79
1197355--1197391	20	1.9	18	89	10	56	70	5	0	24	1.08
1201895--1201943	15	3.1	16	75	18	57	57	0	0	42	0.99
1202832--1202887	19	2.8	20	81	10	71	57	0	1	41	1.09
1207849--1207884	2	18.0	2	100	0	72	50	0	0	50	1.00
1209667--1209700	16	2.1	16	88	5	50	41	0	0	58	0.98
1209747--1209802	20	2.8	20	73	10	60	48	0	0	51	1.00
1209761--1209830	36	1.9	37	83	16	94	51	0	0	48	1.00
1209782--1209836	18	3.1	17	77	12	58	54	0	0	45	0.99
1210141--1210166	11	2.4	11	100	0	52	65	0	0	34	0.93
1210336--1210387	18	2.8	19	82	8	54	44	0	0	55	0.99
1210317--1210383	29	2.3	31	75	19	72	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1211268--1211339	31	2.2	32	81	13	78	59	4	0	36	1.17
1211624--1211649	12	2.2	12	100	0	52	38	0	0	61	0.96
1211778--1211809	2	16.0	2	93	0	55	46	0	0	53	1.00
1214202--1214237	2	18.0	2	100	0	72	50	0	0	50	1.00
1214887--1214964	33	2.4	31	85	6	93	66	1	1	30	1.07
1214879--1214964	21	4.0	21	74	16	70	66	1	2	30	1.12
1214910--1214956	12	4.0	12	83	10	53	72	2	0	25	0.96
1237028--1237057	13	2.4	12	94	5	51	20	0	0	80	0.72
1237028--1237057	6	4.8	6	92	8	51	20	0	0	80	0.72
1237229--1237260	13	2.5	13	95	5	57	46	0	12	40	1.42
1246265--1246314	25	2.0	25	100	0	100	40	16	4	40	1.67
1263291--1263362	36	2.0	36	97	0	135	40	11	20	27	1.87
1269449--1269505	30	2.0	28	83	10	71	63	1	0	35	1.05
1271547--1271617	14	5.2	13	81	10	63	56	1	0	42	1.08
1271979--1272036	19	2.9	19	85	10	64	68	1	0	29	0.99
1272078--1272129	24	2.1	24	82	13	61	55	0	0	44	0.99
1272328--1272371	12	3.6	12	82	14	54	63	2	2	31	1.19
1272937--1272965	14	2.0	15	93	6	51	44	13	0	41	1.44
1273021--1273047	2	13.5	2	100	0	54	51	0	0	48	1.00
1273281--1273306	11	2.4	11	100	0	52	80	0	0	19	0.71
1275707--1275740	3	11.3	3	100	0	68	67	0	0	32	0.91
1283025--1283061	2	18.5	2	100	0	74	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1283238--1283267	2	15.0	2	100	0	60	50	0	0	50	1.00
1286321--1286345	2	12.5	2	100	0	50	52	0	0	48	1.00
1286689--1286720	15	2.1	15	94	0	55	53	0	0	46	1.00
1288656--1288715	22	2.7	22	71	21	52	36	3	6	53	1.44
1288703--1288772	22	2.9	25	74	18	67	41	1	5	51	1.34
1288658--1288772	46	2.5	46	81	5	126	40	2	6	50	1.41
1289057--1289108	20	2.5	20	75	3	59	34	0	0	65	0.93
1289915--1289972	24	2.5	22	76	13	55	51	3	0	44	1.18
1290482--1290521	21	1.9	20	85	10	53	47	0	0	52	1.00
1290794--1290846	18	3.1	18	70	30	53	64	0	0	35	0.94
1290807--1290858	19	2.8	18	77	5	59	63	0	0	36	0.95
1290811--1290858	18	2.7	17	75	9	51	64	0	0	35	0.94
1290968--1291040	29	2.4	31	71	15	71	52	4	0	43	1.20
1291026--1291060	12	2.8	13	86	8	54	71	0	0	28	0.86
1301961--1301985	2	12.5	2	100	0	50	52	0	48	0	1.00
1302402--1302445	21	2.0	22	86	4	63	40	0	0	59	0.98
1302613--1302659	16	3.3	16	67	32	52	48	0	0	51	1.00
1302616--1302661	12	3.3	15	71	22	55	45	0	0	54	0.99
1302613--1302681	26	2.7	26	91	6	106	47	0	0	52	1.00
1302672--1302727	5	11.2	5	81	7	51	33	0	0	66	0.92
1302616--1302723	26	4.0	28	82	10	95	41	0	0	58	0.98
1302668--1302745	12	6.2	12	76	12	68	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1303084--1303156	22	3.3	22	78	16	78	35	0	0	64	0.94
1303102--1303172	12	6.0	12	73	18	60	38	0	0	61	0.96
1303084--1303156	23	3.3	22	77	12	69	35	0	0	64	0.94
1303116--1303167	23	2.2	24	83	10	63	34	0	0	65	0.93
1303253--1303299	11	4.2	11	79	15	51	57	0	2	40	1.11
1303373--1303424	26	2.0	27	88	3	79	30	1	0	67	1.02
1303428--1303466	18	2.0	20	90	9	64	51	0	0	48	1.00
1304505--1304534	2	15.0	2	92	0	51	53	0	0	46	1.00
1305118--1305183	27	2.6	24	73	9	60	63	0	0	36	0.95
1305186--1305220	19	1.9	18	88	11	54	42	0	0	57	0.99
1306334--1306417	8	10.9	8	75	10	59	42	0	1	55	1.07
1306365--1306427	30	2.1	30	82	5	74	46	0	0	53	1.00
1306378--1306476	33	2.9	35	77	13	98	43	0	0	56	0.99
1306383--1306476	35	2.8	32	75	15	91	42	0	0	57	0.98
1320858--1320889	16	1.9	17	93	6	57	31	0	0	68	0.90
1320869--1320904	19	1.9	18	88	5	54	27	0	2	69	1.02
1320963--1320998	19	1.9	18	88	5	54	61	0	0	38	0.96
1321725--1321777	23	2.2	25	83	12	67	77	1	5	15	1.04
1323034--1323070	14	2.5	15	86	8	58	56	2	0	40	1.13
1324965--1325047	22	4.0	21	75	17	75	50	0	1	48	1.08
1324996--1325051	17	3.1	18	82	7	69	57	0	0	42	0.99
1324961--1325008	2	24.5	2	80	4	53	50	0	2	47	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1324989--1325059	18	3.7	18	71	16	54	54	0	0	45	0.99
1325954--1325987	17	1.9	17	88	5	50	61	0	2	35	1.11
1326569--1326610	21	2.0	22	85	4	59	61	9	2	26	1.39
1332934--1333008	28	2.7	27	86	12	98	57	0	1	41	1.07
1333764--1333851	40	2.2	41	82	10	101	43	1	3	52	1.25
1333783--1333877	41	2.4	39	82	10	111	45	0	2	52	1.12
1333864--1333920	21	2.9	21	80	17	68	61	0	1	36	1.07
1333904--1333993	33	2.8	30	78	11	90	62	0	4	33	1.15
1333933--1333985	15	3.5	15	78	17	56	69	0	3	26	1.05
1333973--1334044	25	2.9	25	87	4	92	56	0	0	43	0.99
1334382--1334431	19	2.5	20	77	3	57	62	0	0	38	0.96
1334382--1334437	19	2.9	19	71	10	51	60	0	0	39	0.97
1334472--1334502	16	1.9	16	93	0	53	51	0	0	48	1.00
1334892--1334943	20	2.6	19	82	11	59	30	0	1	67	1.02
1335254--1335324	24	3.0	24	76	13	74	50	0	0	49	1.00
1335247--1335281	18	2.0	18	88	5	54	51	2	0	45	1.16
1335421--1335480	24	2.3	26	75	21	63	63	0	0	36	0.95
1341441--1341474	1	34.0	1	100	0	68	0	0	0	100	0.00
1343186--1343227	21	2.0	22	95	4	77	76	0	11	11	1.03
1343530--1343570	20	2.0	20	95	0	73	4	7	31	56	1.48
1345371--1345418	24	2.0	24	91	0	78	10	29	20	39	1.86
1347246--1347354	54	2.0	54	98	0	209	31	11	19	38	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1351451--1351486	2	18.0	2	100	0	72	50	0	0	50	1.00
1351490--1351529	2	20.0	2	100	0	80	50	0	50	0	1.00
1351933--1351965	3	11.0	3	100	0	66	33	0	0	66	0.92
1355795--1356162	150	2.5	150	82	5	408	43	17	13	25	1.86
1362462--1362529	32	2.2	32	86	2	93	69	4	0	26	1.07
1362932--1362985	27	1.9	29	85	7	76	40	0	0	59	0.98
1364545--1364635	41	2.1	44	82	11	109	46	0	2	51	1.13
1364585--1364662	30	2.6	29	82	13	95	46	0	1	52	1.08
1364585--1364662	16	5.1	16	71	20	60	46	0	1	52	1.08
1364590--1364693	23	4.5	23	67	21	56	46	0	0	52	1.07

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