genome.fa.s78.2.7.7.80.10.50.1000.11.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: Scaffold78
Parameters: 2 7 7 80 10 50 1000
Length:  2238306

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  11  of  15  ( 1751 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)
1461263--1461314	25	2.1	25	82	13	63	42	9	0	48	1.36
1463454--1463515	21	2.8	24	75	22	64	35	4	0	59	1.19
1463573--1463637	30	2.2	30	85	0	94	53	0	4	41	1.21
1463989--1464027	18	2.2	18	86	4	53	64	0	0	35	0.94
1468074--1468106	2	16.0	2	93	6	57	48	0	3	48	1.17
1472849--1472886	20	1.9	20	94	0	67	60	2	21	15	1.47
1473058--1473126	10	6.9	10	74	11	61	59	0	1	39	1.06
1473031--1473137	27	3.7	27	74	16	90	58	1	1	37	1.20
1478106--1478140	17	2.1	17	100	0	70	54	11	22	11	1.68
1480669--1480709	21	2.0	21	90	9	66	41	0	0	58	0.98
1480681--1480744	35	1.9	35	90	9	107	50	0	0	50	1.00
1480687--1480760	33	2.2	33	80	15	91	51	0	0	48	1.00
1486758--1486863	52	2.0	52	100	0	212	38	9	16	34	1.82
1490297--1490387	20	4.6	20	73	20	73	53	4	0	41	1.21
1490345--1490386	11	4.0	11	87	12	70	54	0	0	45	0.99
1490352--1490420	25	2.7	26	68	13	61	53	1	2	42	1.24
1491798--1491829	16	2.0	16	93	0	55	50	3	0	46	1.17
1492424--1492463	20	2.0	20	100	0	80	45	5	5	45	1.47
1493501--1493543	15	2.8	16	75	7	52	41	0	0	58	0.98
1496420--1496458	3	12.7	3	94	5	69	0	33	0	66	0.92
1507060--1507110	19	2.7	18	84	6	57	52	1	1	43	1.23
1507228--1507311	43	2.0	43	100	0	168	45	7	7	40	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1514168--1514242	20	3.8	20	80	3	80	40	12	13	34	1.81
1514165--1514242	40	2.0	39	87	2	111	39	12	12	34	1.82
1514770--1515602	32	27.2	32	90	5	944	18	17	33	30	1.94
1516827--1516869	13	3.4	12	87	9	59	2	2	9	86	0.76
1530875--1530949	20	3.8	20	80	3	80	40	12	13	34	1.81
1530872--1530949	40	2.0	39	87	2	111	39	12	12	34	1.82
1531978--1532039	33	1.9	32	87	9	90	27	12	16	43	1.84
1532113--1532143	10	3.1	10	95	0	53	45	19	16	19	1.86
1532314--1533059	370	2.0	370	98	0	1438	28	13	19	38	1.89
1536717--1536742	13	2.0	13	100	0	52	38	15	15	30	1.88
1538960--1539004	21	2.1	21	84	8	56	53	4	20	22	1.63
1540808--1540838	15	2.1	15	93	0	53	48	16	22	12	1.80
1542852--1542931	20	3.8	20	75	15	79	26	15	15	43	1.85
1542917--1542942	13	2.0	13	100	0	52	30	15	15	38	1.88
1543063--1543109	21	2.3	21	79	20	55	34	19	4	42	1.70
1543065--1543107	20	2.2	19	84	16	52	32	18	4	44	1.71
1545484--1545509	13	2.0	13	100	0	52	38	15	15	30	1.88
1549511--1549537	13	2.1	13	100	0	54	29	14	14	40	1.86
1549492--1549553	33	1.9	32	87	9	90	27	14	16	41	1.87
1549521--1549577	19	2.9	19	84	2	78	31	14	17	36	1.89
1549609--1549673	33	2.0	33	84	6	87	35	12	13	38	1.83
1556429--1556475	9	5.1	9	80	12	51	8	10	2	78	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1556437--1556475	18	2.0	20	90	9	64	7	12	0	79	0.93
1556510--1556551	18	2.4	17	81	18	50	50	0	0	50	1.00
1556652--1556705	26	2.0	26	89	3	81	44	1	1	51	1.22
1556797--1556848	19	2.6	20	72	9	52	55	0	0	44	0.99
1556918--1556960	10	4.2	10	80	14	52	62	0	0	37	0.95
1557093--1557170	20	3.8	20	66	10	59	42	1	1	55	1.16
1557779--1557817	17	2.5	15	84	12	51	51	0	0	48	1.00
1562837--1562895	17	3.7	17	76	21	56	32	0	1	66	1.02
1562855--1562914	24	2.6	23	81	5	75	43	0	1	55	1.10
1562829--1562895	30	2.2	29	86	5	89	34	0	1	64	1.03
1563217--1563299	23	3.4	23	70	12	60	48	1	1	49	1.16
1564420--1564491	35	2.0	35	81	7	83	51	0	1	47	1.09
1565533--1565586	11	4.9	11	78	15	58	38	0	0	61	0.96
1565485--1565601	62	1.9	60	83	13	150	37	0	0	62	0.96
1565533--1565595	32	2.0	32	87	6	92	36	0	0	63	0.95
1565485--1565631	58	2.5	60	80	16	148	36	0	0	63	0.94
1565491--1565620	15	8.4	16	69	21	75	36	0	0	63	0.95
1565536--1565631	32	3.0	32	78	6	86	34	0	0	65	0.93
1567499--1567540	22	1.9	22	85	0	57	57	2	0	40	1.12
1568038--1568142	18	5.9	17	71	20	72	66	0	1	30	1.09
1568089--1568144	9	6.6	8	79	16	60	71	1	0	26	0.96
1568089--1568144	17	3.3	17	80	7	69	71	1	0	26	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1568345--1568370	13	2.0	13	100	0	52	15	38	23	23	1.92
1568592--1568633	14	2.8	15	89	7	59	0	35	0	64	0.94
1568678--1568723	20	2.3	20	92	0	74	34	2	2	60	1.21
1568892--1568959	27	2.5	27	81	13	86	55	0	0	44	0.99
1569739--1569816	27	3.0	26	78	17	72	35	1	2	60	1.19
1569738--1569909	6	28.8	6	67	18	58	35	1	2	61	1.17
1569838--1569930	5	18.6	5	76	17	70	34	2	1	62	1.14
1569851--1569942	10	8.9	10	74	10	60	34	1	1	63	1.09
1569838--1569909	17	4.4	16	79	11	74	33	1	0	65	1.02
1569844--1569930	23	3.3	27	75	18	85	33	2	1	63	1.15
1570307--1570382	29	2.5	30	79	14	84	42	0	1	56	1.07
1570360--1570412	17	3.1	17	75	0	61	49	0	0	50	1.00
1573449--1573487	9	4.2	9	83	6	51	69	0	0	30	0.89
1573448--1573485	10	3.9	10	79	6	51	71	0	0	28	0.87
1577729--1577753	13	1.9	13	100	0	50	36	16	16	32	1.90
1577709--1577775	33	2.0	33	88	0	98	32	11	14	40	1.83
1577816--1577840	13	1.9	13	100	0	50	32	16	16	36	1.90
1577849--1577977	52	2.5	52	93	0	213	34	17	17	30	1.93
1582026--1582172	20	6.8	20	72	15	105	29	15	14	40	1.87
1582087--1582203	31	3.5	31	68	22	92	28	17	12	41	1.87
1582190--1582217	14	2.0	14	100	0	56	35	14	7	42	1.73
1585614--1585714	47	2.1	47	83	3	123	28	8	11	50	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1585660--1585745	29	2.9	30	70	19	90	31	8	13	46	1.73
1585660--1585760	29	3.5	29	69	17	84	31	8	11	47	1.71
1585660--1585800	58	2.4	58	86	2	194	29	8	13	48	1.71
1585700--1586011	144	2.2	145	77	2	324	28	11	10	49	1.72
1586412--1586589	77	2.3	77	76	4	178	32	11	20	35	1.89
1587506--1587543	17	2.2	18	86	13	53	55	0	0	44	0.99
1587497--1587559	29	2.3	27	81	10	74	50	0	0	49	1.00
1587694--1587859	55	3.1	51	83	10	188	50	6	5	37	1.52
1587747--1587805	31	1.9	31	82	0	73	50	5	5	38	1.46
1587716--1587859	55	2.7	54	89	4	202	49	5	5	39	1.50
1587802--1587864	31	2.0	32	87	9	94	49	4	6	39	1.49
1587892--1587928	18	2.0	19	89	5	58	56	0	0	43	0.99
1588256--1588310	14	3.9	13	80	15	65	45	1	0	52	1.11
1588264--1588310	13	3.4	13	81	16	58	40	2	0	57	1.11
1591774--1591893	62	2.0	61	83	11	156	46	1	1	50	1.21
1591927--1591970	15	2.9	15	75	3	52	50	2	2	45	1.27
1592138--1592176	19	2.1	19	85	4	53	58	0	2	38	1.12
1592705--1592769	21	3.1	21	76	8	62	40	3	0	56	1.15
1592715--1592759	9	4.8	9	80	20	56	42	0	0	57	0.98
1592899--1592952	14	3.8	15	77	18	53	50	0	3	46	1.19
1592899--1592998	21	5.0	21	73	15	77	57	0	2	41	1.10
1592911--1592957	19	2.4	18	86	13	58	48	0	2	48	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1592940--1593020	20	4.0	20	68	12	58	61	0	0	38	0.96
1592929--1593095	33	5.0	34	71	14	107	59	0	0	40	0.97
1592982--1593096	8	14.8	8	70	21	52	58	0	0	41	0.98
1593515--1593565	13	3.5	15	81	13	61	35	0	1	62	1.06
1593560--1593600	15	2.9	15	75	17	52	51	0	0	48	1.00
1593565--1593605	21	2.0	21	85	0	55	51	0	0	48	1.00
1593552--1593607	13	4.1	14	76	17	55	50	0	0	50	1.00
1593979--1594018	19	2.0	20	85	4	55	60	0	0	40	0.97
1594098--1594152	16	3.5	16	72	5	58	50	0	3	45	1.19
1594271--1594306	16	2.2	16	90	5	54	44	0	0	55	0.99

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15