genome.fa.s112.2.7.7.80.10.50.1000.10.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: Scaffold112
Parameters: 2 7 7 80 10 50 1000
Length:  1714866

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  10  of  11  ( 1240 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)
1405156--1405239	37	2.3	35	78	13	89	51	1	2	45	1.22
1412658--1412732	6	12.7	6	72	20	52	41	0	1	57	1.07
1414247--1414283	2	18.5	2	100	0	74	48	0	0	51	1.00
1422490--1422518	12	2.4	12	100	0	58	27	17	0	55	1.42
1424435--1424489	20	2.9	20	78	7	62	49	0	0	50	1.00
1427339--1427383	20	2.2	21	84	4	56	48	2	2	46	1.26
1427475--1427513	21	1.9	20	84	5	51	23	2	2	71	1.10
1428070--1428155	43	2.0	43	95	0	154	31	17	17	33	1.93
1437486--1438044	171	3.3	171	93	3	941	36	14	24	24	1.93
1437964--1438145	49	3.8	49	88	5	241	31	17	25	26	1.97
1437900--1438145	98	2.5	93	82	8	253	32	16	25	26	1.96
1438161--1438612	30	15.5	29	76	11	336	23	17	29	29	1.97
1438145--1438399	88	2.9	86	89	6	363	19	18	29	32	1.96
1438145--1438399	58	4.4	58	84	7	311	19	18	29	32	1.96
1438436--1438608	29	5.9	29	80	6	161	24	18	30	26	1.98
1440051--1440152	1	102.0	1	76	0	69	1	3	8	85	0.80
1440051--1440153	34	3.0	32	80	14	107	1	3	9	84	0.82
1449843--1449869	10	2.7	10	100	0	54	77	22	0	0	0.76
1454248--1454318	20	3.6	20	90	3	108	46	14	2	36	1.59
1454334--1454374	20	2.0	20	90	0	64	53	17	2	26	1.56
1457513--1457543	13	2.4	13	94	0	53	38	0	0	61	0.96
1457579--1457612	18	2.0	17	88	11	52	61	2	0	35	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1458594--1458754	11	16.0	11	67	21	52	58	0	1	39	1.14
1458643--1458690	17	3.0	16	74	20	55	56	2	0	41	1.11
1458684--1458766	30	2.9	30	76	16	86	56	0	1	42	1.07
1458649--1458744	15	6.2	15	70	22	65	58	1	0	40	1.05
1463187--1463221	15	2.3	15	95	0	61	48	22	5	22	1.72
1466875--1466919	15	3.1	15	87	6	67	26	0	0	73	0.84
1469424--1469466	3	14.7	3	80	4	52	34	0	0	65	0.93
1473380--1473435	28	2.0	28	86	6	78	17	28	32	21	1.96
1473839--1473883	2	22.5	2	95	0	81	48	0	2	48	1.13
1474650--1474674	2	12.5	2	100	0	50	52	48	0	0	1.00
1476312--1476338	2	13.5	2	100	0	54	0	0	51	48	1.00
1476613--1476680	8	8.5	8	88	0	82	36	4	0	58	1.18
1478742--1478798	28	2.1	27	86	3	69	56	0	0	43	0.99
1480004--1480042	3	13.0	3	100	0	78	66	0	0	33	0.92
1480390--1480426	17	2.2	17	95	0	65	54	8	5	32	1.53
1491183--1491217	2	17.5	2	100	0	70	48	0	0	51	1.00
1499225--1499268	21	2.0	22	86	4	63	43	6	4	45	1.51
1502426--1502460	2	17.5	2	93	0	61	45	0	0	54	0.99
1504519--1504552	15	2.2	16	89	5	52	52	0	0	47	1.00
1504569--1504624	22	2.5	22	82	2	58	58	0	1	39	1.08
1505422--1505467	3	15.3	3	100	0	92	32	0	0	67	0.91
1506950--1506982	14	2.2	16	89	10	52	54	0	9	36	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1507753--1507780	2	14.0	2	100	0	56	50	0	0	50	1.00
1508628--1508659	17	2.0	17	88	11	50	56	0	0	43	0.99
1508651--1508685	7	4.9	7	89	3	52	82	0	2	14	0.77
1508651--1508707	15	3.9	15	81	4	62	75	0	1	22	0.90
1509238--1509278	3	13.7	3	94	0	73	63	2	34	0	1.08
1513494--1513527	2	17.0	2	100	0	68	50	0	0	50	1.00
1516140--1516164	2	12.5	2	100	0	50	48	0	0	52	1.00
1516472--1516518	20	2.4	19	83	13	60	31	0	8	59	1.27
1517539--1517601	23	3.0	21	79	9	67	49	0	0	50	1.00
1533741--1533789	20	2.5	19	77	9	53	38	0	2	59	1.09
1535855--1535893	2	19.5	2	94	0	69	0	46	0	53	1.00
1536565--1536596	2	16.0	2	100	0	64	50	0	0	50	1.00
1542085--1542128	16	2.8	16	80	10	54	45	2	0	52	1.13
1542357--1542410	22	2.3	24	81	9	67	64	1	3	29	1.21
1543402--1543443	19	2.2	19	86	0	57	11	4	9	73	1.22
1546440--1546492	22	2.5	22	81	3	63	62	3	1	32	1.24
1547142--1547183	2	21.5	2	95	4	77	52	0	0	47	1.00
1547375--1547427	16	3.3	16	80	17	65	32	3	5	58	1.39
1547361--1547427	31	2.1	32	83	2	82	34	4	5	55	1.45
1547361--1547441	32	2.6	30	78	9	81	30	3	8	56	1.47
1547749--1547788	19	2.2	18	86	13	55	60	0	0	40	0.97
1548422--1548495	32	2.3	32	81	4	87	27	12	16	44	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1548486--1548522	16	2.3	16	95	0	65	37	0	2	59	1.12
1549434--1549464	3	10.3	3	100	0	62	0	35	0	64	0.94
1550688--1550723	2	18.0	2	94	0	63	2	0	47	50	1.15
1555410--1555443	5	6.8	5	86	0	50	38	0	23	38	1.55
1557200--1557231	2	16.0	2	100	0	64	50	0	0	50	1.00
1559811--1559840	2	15.0	2	92	0	51	46	0	3	50	1.18
1564047--1564116	28	2.4	28	86	9	88	47	1	0	51	1.09
1564111--1564170	29	2.1	29	84	12	79	43	0	0	56	0.99
1564105--1564152	25	2.0	23	84	15	62	45	0	0	54	0.99
1564574--1564605	12	2.6	13	85	14	50	59	0	0	40	0.97
1564644--1564698	28	2.0	28	85	7	76	50	1	1	45	1.22
1564730--1564757	3	9.3	3	100	0	56	32	0	0	67	0.91
1566942--1566979	19	2.0	19	100	0	76	21	10	10	57	1.61
1568659--1568692	2	17.0	2	100	0	68	50	0	0	50	1.00
1572612--1572666	7	8.0	7	97	2	103	41	14	29	14	1.85
1573158--1573190	2	17.0	2	93	6	59	48	0	0	51	1.00
1573453--1573496	23	1.9	23	90	0	70	47	0	6	45	1.29
1573452--1573503	23	2.3	23	82	0	68	44	0	5	50	1.26
1574213--1574237	2	12.5	2	100	0	50	52	0	0	48	1.00
1578587--1578618	2	16.0	2	93	0	55	0	53	0	46	1.00
1584913--1584939	3	9.0	3	100	0	54	33	0	0	66	0.92
1596259--1596309	2	26.0	2	88	4	77	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1596729--1596757	6	4.8	6	100	0	58	17	34	17	31	1.93
1596929--1596964	2	18.0	2	100	0	72	50	0	50	0	1.00
1599132--1599160	2	14.5	2	100	0	58	48	0	0	51	1.00
1604062--1604094	14	2.3	15	89	5	50	21	9	15	54	1.68
1604549--1604584	2	18.0	2	100	0	72	50	0	0	50	1.00
1605263--1605296	3	11.3	3	93	0	59	64	2	0	32	1.08
1605338--1605369	15	2.1	16	94	5	57	31	0	0	68	0.90
1605339--1605380	20	2.1	20	86	8	59	33	0	2	64	1.07
1605833--1605872	22	1.9	20	90	10	62	37	0	0	62	0.95
1605845--1605930	35	2.5	35	81	9	97	51	0	0	48	1.00
1607961--1608049	45	2.0	45	95	0	160	17	25	12	43	1.84
1630281--1630307	2	13.5	2	100	0	54	51	0	0	48	1.00
1632515--1632642	64	2.0	64	98	0	247	35	18	13	32	1.90
1634413--1634449	15	2.5	15	90	0	56	37	0	32	29	1.58
1634516--1634545	7	4.4	7	95	4	53	0	23	63	13	1.29
1635830--1635874	2	22.5	2	95	0	81	51	0	0	48	1.00
1639198--1639255	23	2.6	23	84	13	68	74	1	0	24	0.92
1639207--1639342	18	7.2	18	69	21	57	66	2	2	29	1.16
1639205--1639279	6	12.5	6	71	20	59	66	1	1	30	1.08
1640144--1640170	2	13.5	2	100	0	54	48	0	0	51	1.00
1640183--1640228	4	11.5	4	86	9	67	54	0	45	0	0.99
1640786--1640828	5	8.6	5	97	0	77	23	18	37	20	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1641048--1641091	2	22.0	2	95	0	79	47	2	0	50	1.13
1644826--1644860	2	17.5	2	100	0	70	48	0	0	51	1.00
1645672--1645705	2	17.0	2	100	0	68	0	50	0	50	1.00
1647369--1647446	37	2.1	37	100	0	156	39	15	2	42	1.61
1647453--1647505	22	2.5	20	82	14	54	49	5	0	45	1.26
1648771--1648849	26	3.2	24	66	28	58	44	2	1	51	1.23
1648804--1648853	26	1.9	26	84	8	66	46	0	0	54	1.00
1649151--1649201	25	2.0	26	82	17	63	60	1	5	31	1.31
1649514--1649547	2	17.0	2	87	0	50	47	2	0	50	1.16
1650962--1651017	29	1.9	29	100	0	112	25	8	23	42	1.82

Tables:   1   2   3   4   5   6   7   8   9   10   11