genome.fa.s25.2.7.7.80.10.50.1000.7.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  7  of  56  ( 6609 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)
1325970--1326013	17	2.6	18	86	10	58	59	0	0	40	0.98
1326173--1326214	22	2.0	21	85	4	57	61	0	2	35	1.09
1328732--1328798	29	2.3	30	80	12	79	61	0	1	37	1.05
1328897--1328955	15	4.0	14	75	16	57	54	1	0	44	1.10
1329653--1329685	9	3.6	9	95	4	57	48	24	0	27	1.51
1330915--1330947	5	6.6	5	93	6	50	84	0	15	0	0.61
1335437--1335712	136	2.0	139	88	6	420	48	5	6	40	1.50
1339340--1339451	58	1.9	58	88	0	170	35	8	24	32	1.84
1348770--1348965	88	2.2	88	91	3	317	46	21	5	27	1.72
1353719--1353751	16	2.0	17	88	5	50	57	3	0	39	1.14
1353781--1353835	19	2.8	19	83	10	58	40	0	0	60	0.97
1362937--1362973	9	4.0	9	89	3	56	56	2	0	40	1.13
1363130--1363192	16	3.8	17	73	10	51	38	0	1	60	1.07
1363149--1363196	23	2.1	23	84	0	60	33	0	0	66	0.92
1369815--1369892	23	3.1	24	78	12	70	51	0	0	48	1.00
1370213--1370237	8	3.1	8	100	0	50	12	0	0	88	0.53
1373721--1373813	45	2.1	46	83	4	118	48	0	0	51	1.00
1373772--1373807	18	2.0	18	89	10	56	63	0	0	36	0.94
1374466--1374490	2	12.5	2	100	0	50	52	0	0	48	1.00
1375011--1375126	11	10.7	11	67	16	55	36	0	0	62	1.01
1375006--1375073	22	3.1	22	75	12	77	39	0	1	58	1.07
1375054--1375118	17	4.1	16	79	16	66	30	0	0	69	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1375060--1375103	19	2.2	20	88	11	65	29	0	0	70	0.88
1375054--1375124	28	2.6	27	82	14	85	30	0	0	69	0.89
1377175--1377207	16	2.1	16	100	0	66	24	15	24	36	1.93
1379218--1379255	2	19.0	2	100	0	76	50	0	0	50	1.00
1394274--1394333	30	2.0	29	96	3	111	30	23	15	31	1.95
1399158--1399237	8	10.8	8	67	23	50	48	2	0	48	1.14
1399839--1399962	6	21.2	6	69	14	57	58	0	0	41	0.98
1399835--1399965	29	4.8	27	69	18	92	58	0	0	41	0.98
1399865--1399913	17	3.0	17	72	27	52	59	0	0	40	0.98
1399837--1399978	32	4.3	34	68	19	95	58	0	0	41	0.98
1399837--1399969	23	6.1	22	71	14	82	58	0	0	41	0.98
1399843--1399972	34	4.2	31	68	21	87	58	0	0	41	0.98
1399877--1399972	27	3.8	24	69	22	65	57	0	0	42	0.98
1399835--1399983	7	21.3	7	70	22	50	58	0	0	41	0.98
1399839--1399983	14	9.9	15	69	22	71	58	0	0	41	0.98
1403974--1404008	18	1.9	18	88	0	52	28	2	5	62	1.32
1404579--1404618	20	2.0	20	95	0	71	25	37	15	22	1.93
1406315--1406359	2	22.5	2	86	0	63	53	2	2	42	1.25
1406882--1406948	20	3.5	19	75	20	68	55	0	1	43	1.09
1407025--1407050	2	13.0	2	100	0	52	50	0	0	50	1.00
1407050--1407085	2	18.0	2	100	0	72	50	0	50	0	1.00
1408245--1408290	21	2.2	21	84	7	58	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1408974--1409077	30	3.4	30	76	6	102	42	8	0	48	1.40
1408957--1409069	31	3.7	29	75	12	93	37	7	1	53	1.38
1409110--1409180	30	2.3	32	83	9	103	64	0	1	33	1.02
1413994--1414033	21	1.9	21	84	0	53	40	0	2	57	1.12
1414188--1414239	19	2.8	18	77	11	61	65	1	0	32	1.04
1414211--1414291	14	5.6	14	70	20	51	53	1	1	44	1.16
1414188--1414291	29	3.6	28	72	12	77	56	0	0	41	1.12
1414258--1414300	18	2.3	18	84	11	52	58	0	0	41	0.98
1414661--1414721	22	2.7	23	94	5	106	36	0	13	50	1.41
1414661--1414731	22	3.1	22	87	4	88	30	0	15	53	1.42
1422363--1422397	2	17.5	2	100	0	70	51	0	0	48	1.00
1423604--1423634	2	16.0	2	93	6	55	48	0	0	51	1.00
1426538--1426568	2	15.5	2	93	0	53	51	0	0	48	1.00
1427078--1427115	17	2.2	18	85	4	51	60	0	5	34	1.19
1427058--1427120	28	2.2	28	76	13	67	60	0	3	36	1.13
1427082--1427192	40	2.6	41	73	22	104	53	0	2	43	1.21
1427482--1427522	2	21.0	2	95	5	75	51	0	0	48	1.00
1427853--1427879	2	13.5	2	100	0	54	51	0	0	48	1.00
1429306--1429340	2	17.5	2	100	0	70	51	0	0	48	1.00
1432730--1432768	14	2.8	14	84	0	51	10	28	0	61	1.28
1435884--1435910	3	9.0	3	100	0	54	66	0	0	33	0.92
1437306--1437344	2	20.0	2	94	5	71	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)
1438594--1438627	3	11.3	3	100	0	68	67	0	32	0	0.91
1441786--1441853	27	2.5	27	83	4	84	30	35	16	17	1.92
1445262--1445305	21	2.1	20	87	8	61	34	0	0	65	0.93
1446506--1446539	2	17.0	2	100	0	68	50	0	0	50	1.00
1447757--1447829	33	2.2	33	95	0	128	54	2	0	42	1.14
1448350--1448374	13	1.9	13	100	0	50	64	4	0	32	1.12
1448364--1448399	17	2.1	18	89	5	56	55	0	0	44	0.99
1448374--1448438	28	2.3	28	84	12	89	41	0	1	56	1.08
1451521--1451596	20	3.8	21	73	15	72	61	0	0	38	0.96
1451493--1451605	27	4.2	28	77	14	105	64	0	0	34	1.00
1454916--1454971	21	2.5	24	77	11	73	42	0	0	57	0.99
1455328--1455357	15	1.9	16	93	6	53	70	0	0	30	0.88
1455907--1455950	3	14.7	3	95	0	79	29	0	2	68	1.02
1456494--1456540	24	2.0	23	88	8	69	61	10	0	27	1.29
1465015--1465052	10	3.9	10	79	6	51	65	0	0	34	0.93
1465918--1465942	2	12.5	2	100	0	50	48	0	0	52	1.00
1468431--1468473	17	2.3	19	88	11	63	51	0	2	46	1.13
1468521--1468572	14	3.5	15	74	10	54	44	0	0	55	0.99
1468511--1468579	27	2.5	29	77	13	74	43	0	0	56	0.99
1476010--1476059	22	2.3	22	79	6	57	40	2	4	54	1.31
1480219--1480248	2	15.0	2	100	0	60	50	0	50	0	1.00
1486166--1486205	17	2.4	17	95	4	73	30	20	20	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1487858--1487898	18	2.2	19	95	4	75	24	0	4	70	1.06
1488533--1488587	26	2.1	26	83	12	69	50	1	0	47	1.11
1489296--1489350	23	2.5	23	76	5	60	52	0	0	47	1.00
1493981--1494028	24	2.0	24	84	8	62	62	0	0	37	0.95
1497007--1497042	2	18.0	2	100	0	72	50	0	0	50	1.00
1498724--1498783	2	30.0	2	100	0	120	50	0	0	50	1.00
1504647--1504693	14	3.4	14	79	8	51	57	0	0	42	0.98
1509216--1509267	17	3.1	17	73	15	54	36	1	0	61	1.07
1514195--1514242	2	24.0	2	100	0	96	0	50	0	50	1.00
1515655--1515694	14	2.9	14	85	14	57	35	0	0	65	0.93
1516546--1516595	20	2.4	21	87	9	68	50	0	0	50	1.00
1516573--1516622	18	2.8	19	72	22	54	40	0	0	60	0.97
1517464--1517527	18	3.5	19	75	12	53	50	0	0	50	1.00
1517474--1517569	33	3.0	32	77	10	83	47	0	1	51	1.07
1519221--1519264	19	2.4	18	84	3	52	43	2	0	54	1.12
1519287--1519341	19	2.8	20	78	13	51	47	1	1	49	1.23
1519451--1519506	2	28.0	2	100	0	112	50	0	0	50	1.00
1520581--1520621	18	2.2	20	87	12	61	26	0	0	73	0.84
1521941--1522013	32	2.4	29	79	20	80	45	1	4	49	1.29
1530564--1530620	12	4.8	12	80	8	53	33	1	1	63	1.15
1532417--1532447	2	15.5	2	100	0	62	51	0	0	48	1.00
1532990--1533097	53	2.0	53	96	0	198	10	28	13	47	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1536603--1536687	20	4.3	20	70	20	72	49	1	1	48	1.16
1537182--1537315	70	1.9	70	84	3	180	48	1	6	43	1.38
1537182--1537333	70	2.2	69	82	6	175	48	1	5	44	1.35
1537662--1537701	18	2.2	18	86	8	55	52	0	0	47	1.00
1537676--1537715	20	2.0	20	85	9	55	57	0	0	42	0.98
1537721--1537774	11	4.8	11	73	13	56	38	1	0	59	1.08
1537966--1538013	19	2.3	21	79	13	55	33	0	4	62	1.14
1538327--1538358	16	1.9	17	93	6	57	50	9	6	34	1.60
1544601--1544634	2	17.0	2	100	0	68	0	50	0	50	1.00
1546129--1546166	17	2.3	17	90	4	60	60	0	0	39	0.97

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   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56