genome.fa.s1947.2.7.7.80.10.50.1000.4.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: scaffold189
Parameters: 2 7 7 80 10 50 1000
Length:  1445563

Tables:   1   2   3   4   

This is table  4  of  4  ( 480 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)
1126324--1126586	45	5.9	45	88	0	350	33	25	15	25	1.95
1131706--1131928	45	5.0	45	83	1	272	33	22	15	28	1.95
1137929--1138296	185	2.0	185	91	1	594	41	16	13	28	1.87
1151613--1151742	26	4.8	26	67	21	88	37	13	4	44	1.64
1151573--1151745	84	2.1	84	98	0	337	39	13	3	42	1.62
1156489--1156529	16	2.5	17	84	15	59	60	4	0	34	1.18
1156499--1156536	16	2.4	16	86	8	51	60	5	2	31	1.33
1162612--1163056	225	2.0	225	100	0	890	46	5	6	40	1.54
1167578--1167608	11	2.8	11	95	0	53	54	22	9	12	1.67
1168058--1168095	18	2.1	18	85	9	51	34	21	21	23	1.97
1168066--1168119	27	2.0	27	88	0	81	27	18	20	33	1.96
1169165--1169217	4	13.2	4	80	7	63	30	0	24	45	1.54
1169156--1169202	25	1.9	24	91	4	76	31	2	23	42	1.66
1171466--1171668	13	15.2	13	67	11	90	41	3	18	36	1.67
1171583--1171644	27	2.3	27	88	5	90	48	3	14	33	1.60
1173301--1173650	175	2.0	175	98	1	684	26	16	25	30	1.97
1174067--1174151	27	3.1	27	89	0	134	41	22	16	20	1.90
1174106--1174187	27	3.0	27	81	10	80	36	20	17	25	1.94
1176324--1176362	20	2.0	19	90	5	60	15	10	15	58	1.62
1190716--1190791	24	3.2	24	82	0	98	19	26	30	23	1.98
1193515--1193559	23	2.0	23	82	8	56	40	26	2	31	1.68
1197095--1197204	42	2.6	42	79	4	132	22	30	23	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1199895--1199936	12	3.5	12	81	12	59	7	42	23	26	1.80
1199893--1199946	24	2.2	24	100	0	108	7	44	22	25	1.79
1199893--1199946	12	4.5	12	77	13	58	7	44	22	25	1.79
1200716--1200745	14	2.1	15	93	6	53	40	13	6	40	1.71
1203291--1203375	37	2.3	37	91	0	134	36	28	1	34	1.65
1204245--1204276	12	2.6	13	85	14	50	37	0	6	56	1.25
1207842--1207937	49	1.9	50	93	2	167	28	13	25	33	1.93
1209664--1209695	12	2.6	13	85	14	50	37	0	6	56	1.25
1221241--1221299	23	2.6	23	81	7	66	50	25	11	11	1.73
1225550--1225593	22	2.0	22	100	0	88	40	9	13	36	1.76
1229531--1229653	53	2.3	54	83	4	151	18	30	26	25	1.98
1229554--1229663	54	2.1	53	85	1	148	20	30	25	23	1.99
1231472--1232050	287	2.0	287	97	0	1095	42	18	11	28	1.84
1232382--1232414	12	2.8	12	100	0	66	57	0	0	42	0.98
1232650--1232738	38	2.3	38	92	0	151	30	32	23	13	1.93
1232651--1232713	22	3.1	22	63	32	59	25	34	26	12	1.92
1232655--1232721	16	3.8	16	71	21	62	25	31	28	14	1.95
1232722--1232750	15	1.9	15	100	0	58	41	34	13	10	1.79
1232737--1232811	38	2.0	38	84	5	98	38	30	14	16	1.88
1232650--1232815	91	1.8	91	84	0	224	33	31	19	15	1.93
1243028--1243066	18	2.3	16	86	8	51	17	15	10	56	1.66
1243027--1243082	17	3.2	16	85	10	58	19	12	12	55	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1243397--1243464	18	3.8	18	68	14	59	23	7	4	64	1.37
1255372--1255438	18	3.7	18	90	4	100	17	26	19	35	1.94
1255369--1255438	36	1.9	36	91	5	115	18	25	20	35	1.95
1255450--1255523	29	2.5	30	86	2	105	12	24	21	41	1.87
1258180--1258297	43	2.7	43	80	7	141	32	27	19	20	1.97
1260734--1260816	28	3.0	27	76	3	67	15	30	20	33	1.94
1260747--1260828	28	2.9	28	79	0	83	15	28	20	35	1.94
1262337--1262436	48	2.1	48	94	0	173	44	15	19	22	1.87
1262593--1262622	14	2.1	14	100	0	60	33	20	0	46	1.51
1265936--1265985	25	2.0	25	88	0	73	24	24	4	48	1.68
1271162--1271188	14	1.9	14	100	0	54	59	7	0	33	1.25
1273370--1273402	17	2.0	17	94	5	59	12	0	15	72	1.12
1275243--1275276	13	2.8	12	86	8	50	0	11	14	73	1.10
1290375--1290423	20	2.3	22	75	10	57	32	2	2	63	1.17
1298018--1298072	24	2.3	24	90	3	85	21	16	12	49	1.79
1300583--1300616	15	2.3	15	89	0	50	20	0	5	73	1.04
1300622--1300731	23	4.7	23	82	3	105	28	13	18	40	1.88
1302611--1302646	18	2.0	18	100	0	72	27	0	11	61	1.30
1307727--1307826	23	4.3	23	76	9	87	41	26	15	18	1.89
1311112--1311162	10	5.1	10	75	17	52	27	15	31	25	1.96
1311114--1311162	20	2.5	20	89	0	80	26	16	32	24	1.96
1313808--1313837	15	1.9	16	93	6	53	20	6	0	73	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1315255--1315306	26	2.0	26	100	0	104	34	23	26	15	1.94
1321929--1322109	43	4.3	43	85	1	231	23	30	18	27	1.98
1321935--1322109	86	2.1	84	91	2	278	22	30	18	27	1.98
1323380--1323419	21	1.9	21	94	0	71	40	27	5	27	1.77
1325160--1325216	29	2.0	29	85	0	78	43	15	14	26	1.85
1325975--1326008	17	2.1	17	94	5	61	41	35	0	23	1.55
1326484--1326516	16	2.1	16	100	0	66	30	0	36	33	1.58
1326738--1326772	18	2.0	17	88	5	52	54	0	0	45	0.99
1331514--1331658	77	1.9	77	94	2	256	31	11	8	47	1.71
1331648--1331917	138	2.0	137	92	2	452	25	14	14	44	1.84
1332399--1332427	15	1.9	15	100	0	58	34	51	0	13	1.42
1332447--1332488	14	2.9	14	89	6	66	35	38	0	26	1.57
1332443--1332489	15	3.3	15	88	8	71	40	34	0	25	1.56
1332654--1332688	15	2.4	15	90	4	54	40	40	0	20	1.52
1332875--1332907	14	2.4	14	90	10	50	30	45	0	24	1.53
1332887--1332930	23	2.0	22	86	4	61	31	50	0	18	1.47
1332954--1332980	14	1.9	14	100	0	54	37	37	0	25	1.57
1333156--1333400	72	3.4	73	93	3	415	27	25	20	26	1.99
1335697--1335733	19	1.9	19	89	10	58	64	0	5	29	1.15
1338562--1338597	18	2.1	18	89	5	56	19	0	25	55	1.43
1338561--1338597	17	2.1	19	80	15	51	18	0	24	56	1.41
1339750--1339793	22	2.0	23	95	4	81	40	18	18	22	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1341782--1341831	24	2.1	24	92	0	82	40	20	2	38	1.64
1344635--1344670	18	1.9	19	94	5	65	5	13	8	72	1.27
1349522--1349573	11	4.7	11	73	0	50	9	13	50	26	1.72
1356577--1356619	18	2.3	19	92	4	70	53	0	25	20	1.46
1357787--1357812	7	3.7	7	100	0	52	30	11	42	15	1.82
1357879--1357972	49	1.9	49	93	0	161	41	6	25	26	1.79
1360640--1360732	44	2.1	46	91	4	154	29	4	30	36	1.77
1360635--1360745	44	2.6	41	79	18	136	28	3	31	36	1.75
1364350--1364412	32	2.0	32	100	0	126	36	9	12	41	1.76
1365706--1365939	130	1.8	130	99	0	459	38	16	11	33	1.85
1368506--1368536	2	15.5	2	93	0	53	3	48	0	48	1.17
1373432--1373571	70	2.0	70	97	0	262	24	11	19	45	1.83
1379948--1379979	16	2.0	16	93	0	55	0	21	0	78	0.76
1379948--1379976	10	2.7	11	94	5	51	0	20	0	79	0.74
1382508--1382537	15	2.0	15	93	0	51	26	0	36	36	1.57
1382602--1382642	18	2.2	19	86	4	57	36	4	4	53	1.44
1383667--1383724	21	2.7	22	78	7	75	44	0	3	51	1.18
1394939--1394968	2	15.0	2	100	0	60	50	0	0	50	1.00
1398060--1398186	35	3.6	35	76	3	112	14	13	31	40	1.84
1398776--1398814	21	1.9	20	84	5	51	20	5	23	51	1.67
1400450--1400482	17	1.9	17	100	0	66	27	24	12	36	1.91
1402428--1402505	36	2.1	36	97	2	147	21	12	33	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1403422--1403480	18	3.3	18	85	0	91	40	20	8	30	1.82
1403667--1403699	17	2.1	16	88	11	50	51	6	3	39	1.42
1405220--1405271	22	2.3	22	75	21	54	34	7	0	57	1.27
1405222--1405288	32	2.1	31	83	8	82	38	7	0	53	1.29
1405650--1405818	87	1.9	87	90	0	266	42	14	14	29	1.85
1409316--1409529	90	2.4	90	84	3	279	30	17	18	32	1.95
1409316--1409529	45	4.8	45	85	0	248	30	17	18	32	1.95
1413212--1413241	13	2.2	14	94	5	53	50	16	0	33	1.46
1414117--1414152	11	3.2	11	92	4	54	30	13	16	38	1.88
1433702--1433741	19	2.1	19	85	0	53	32	2	5	60	1.32

Tables:   1   2   3   4

The End!