genome.fa.s40.2.7.7.80.10.50.1000.9.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  9  of  24  ( 2833 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)
1186723--1186776	27	2.0	27	88	0	81	29	14	35	20	1.93
1186743--1186899	34	4.8	34	77	10	166	32	13	35	18	1.90
1186718--1186870	62	2.5	62	88	4	220	32	13	34	19	1.90
1187864--1187899	15	2.4	15	90	0	54	0	2	11	86	0.68
1194270--1194398	52	2.5	52	94	0	222	29	17	17	35	1.93
1194474--1194571	19	5.8	18	71	28	90	36	17	12	33	1.87
1194469--1194569	32	3.1	32	97	1	184	35	17	11	34	1.87
1194493--1194549	13	3.9	13	76	24	60	33	17	14	35	1.90
1197373--1197439	26	2.6	26	97	0	125	16	10	20	52	1.73
1199460--1199492	6	5.7	6	89	3	50	0	15	0	84	0.61
1204747--1204898	65	2.4	64	79	3	162	32	21	13	31	1.93
1204710--1204901	32	6.0	32	74	16	141	33	21	12	32	1.91
1205404--1205473	20	3.6	19	72	18	63	34	18	11	35	1.87
1205424--1205492	19	3.6	19	75	11	68	34	18	10	36	1.85
1205401--1205495	39	2.4	39	91	0	154	35	17	10	35	1.85
1208326--1208359	10	3.2	10	91	8	50	61	0	2	35	1.11
1208307--1208359	21	2.5	22	78	9	56	56	0	3	39	1.17
1209824--1209923	40	2.5	38	81	13	105	39	1	0	60	1.04
1209892--1209930	13	3.1	13	81	3	53	38	0	0	61	0.96
1210150--1210306	83	1.9	85	93	2	273	50	20	15	12	1.76
1214668--1214932	143	1.8	144	89	2	417	47	11	8	32	1.70
1215853--1215908	12	4.7	12	78	8	69	0	21	0	78	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1215845--1215909	22	3.0	22	86	6	80	1	20	0	78	0.83
1215853--1215892	14	2.9	14	88	3	55	0	20	0	80	0.72
1215948--1215973	13	2.0	13	100	0	52	23	0	38	38	1.55
1216344--1216376	15	2.2	15	89	10	50	63	0	6	30	1.18
1218682--1218708	12	2.2	12	100	0	54	40	0	7	51	1.30
1219148--1219194	16	3.0	16	87	9	62	42	23	14	19	1.88
1219164--1219197	16	2.1	16	100	0	68	41	23	17	17	1.90
1220531--1220567	2	18.5	2	100	0	74	51	0	0	48	1.00
1220854--1220921	20	3.5	19	80	11	75	54	0	1	44	1.09
1220870--1220921	11	5.1	11	76	19	51	59	0	0	40	0.97
1220870--1220931	20	3.2	20	75	11	58	59	0	0	40	0.97
1223043--1223191	34	4.4	34	78	1	147	44	26	5	24	1.75
1223043--1223192	68	2.2	68	89	2	230	44	26	5	24	1.74
1223168--1223214	22	2.1	22	92	0	76	48	27	8	14	1.73
1227668--1227814	34	4.4	34	77	7	149	44	21	4	28	1.72
1227655--1227814	68	2.4	67	88	5	225	44	23	4	28	1.72
1231312--1231345	17	2.1	16	88	5	50	11	14	0	73	1.10
1232037--1232069	9	3.3	10	87	12	50	66	0	0	33	0.92
1235020--1235052	2	16.5	2	100	0	66	0	48	0	51	1.00
1235277--1235326	13	3.6	14	80	15	59	54	0	0	46	1.00
1235274--1235337	29	2.2	29	88	0	92	48	1	0	50	1.10
1236396--1236438	21	2.0	22	82	13	54	39	4	4	51	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1236306--1236633	170	2.0	166	83	6	410	45	7	6	40	1.59
1236567--1236614	18	2.7	18	74	6	53	52	0	0	47	1.00
1237334--1237499	20	7.8	20	73	14	143	30	14	13	41	1.85
1237334--1237498	40	3.8	40	77	18	188	30	14	13	41	1.85
1237324--1237549	91	2.5	92	94	1	402	28	15	13	42	1.85
1238119--1238311	20	8.7	20	71	21	127	29	15	10	44	1.80
1240148--1240611	248	1.9	248	97	0	883	26	23	14	35	1.93
1242696--1242760	24	2.9	22	74	14	62	43	0	0	56	0.99
1242812--1242896	33	2.5	32	78	17	84	42	0	0	57	0.98
1243508--1243542	17	2.1	17	94	5	63	51	0	0	48	1.00
1243511--1243549	17	2.4	17	86	4	53	51	2	2	43	1.29
1245089--1245127	2	19.5	2	94	0	69	48	0	2	48	1.15
1245614--1245666	20	2.7	20	80	13	65	32	0	5	62	1.19
1245683--1245766	18	4.5	18	71	12	62	22	7	2	67	1.26
1248728--1248837	58	1.9	58	94	0	193	36	10	24	29	1.88
1251784--1251820	2	18.5	2	100	0	74	51	0	0	48	1.00
1252568--1252611	16	2.8	16	85	0	61	54	0	0	45	0.99
1253051--1253210	80	2.0	80	96	2	295	43	3	26	25	1.71
1253171--1253289	20	5.9	20	73	13	66	68	0	28	3	1.06
1253168--1253292	25	5.0	24	69	12	67	68	0	28	3	1.05
1253220--1253251	11	2.9	11	95	0	55	59	0	40	0	0.97
1253235--1253290	16	3.6	15	81	13	60	76	0	21	1	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1253414--1253451	13	3.0	13	88	3	60	26	0	0	73	0.83
1253546--1253585	21	1.9	21	84	0	53	37	0	2	60	1.11
1253557--1253608	28	2.0	26	85	11	70	36	1	0	61	1.07
1253556--1253602	15	3.2	15	73	14	53	34	0	0	65	0.93
1254105--1254145	2	20.5	2	100	0	82	51	0	0	48	1.00
1256132--1256167	17	2.2	16	90	5	54	27	2	0	69	1.02
1256154--1256199	21	2.2	20	82	14	58	30	2	4	63	1.26
1256675--1256730	16	3.6	16	75	2	60	35	5	5	53	1.47
1257259--1257298	15	2.7	15	82	17	57	35	0	0	65	0.93
1257318--1257454	73	1.9	74	90	1	222	43	2	11	42	1.56
1259857--1259897	12	3.0	14	79	17	50	34	0	0	65	0.93
1259972--1260020	25	2.2	23	80	20	59	65	0	0	34	0.93
1260674--1260716	22	2.0	22	86	9	61	41	2	0	55	1.12
1260893--1260924	16	1.9	17	93	6	57	56	0	0	43	0.99
1261985--1262026	23	1.9	22	85	9	59	28	4	16	50	1.66
1263557--1263604	24	2.1	24	84	7	64	43	0	0	56	0.99
1299137--1299167	15	2.1	15	100	0	62	19	16	19	45	1.86
1303510--1303544	16	2.2	16	90	5	54	31	0	0	68	0.90
1308156--1308273	39	3.1	39	83	2	175	44	11	13	30	1.78
1308151--1308264	38	2.9	39	84	2	167	45	11	12	30	1.77
1308509--1308552	17	2.6	16	82	10	52	65	0	0	34	0.93
1308509--1308555	16	2.8	17	83	6	60	63	0	0	36	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1309586--1309614	2	14.5	2	100	0	58	51	0	0	48	1.00
1310289--1310320	16	2.0	16	93	0	55	53	0	6	40	1.26
1310376--1310421	21	2.2	22	80	11	60	36	6	0	56	1.25
1310380--1310428	20	2.5	20	86	6	64	32	4	0	63	1.13
1311277--1311335	15	4.1	14	77	20	59	44	1	0	54	1.10
1311282--1311335	14	3.7	15	81	16	69	42	0	0	57	0.98
1311286--1311344	28	2.1	28	81	6	66	44	0	0	55	0.99
1312221--1312248	14	2.0	14	100	0	56	64	0	0	35	0.94
1312806--1312844	19	2.2	18	90	9	62	51	0	2	46	1.14
1312877--1312909	15	2.1	16	88	5	50	51	0	0	48	1.00
1312913--1312965	25	2.1	26	82	10	65	43	1	3	50	1.30
1313017--1313053	17	2.2	17	90	0	56	21	0	0	78	0.75
1313105--1313137	16	2.0	17	88	5	50	42	0	0	57	0.98
1313239--1313278	17	2.4	16	84	8	53	30	0	0	70	0.88
1313248--1313290	17	2.5	17	88	11	70	32	0	0	67	0.91
1314651--1314693	2	21.5	2	100	0	86	0	48	0	51	1.00
1314693--1314718	2	13.0	2	100	0	52	50	0	0	50	1.00
1315246--1315287	13	3.2	13	76	10	50	2	16	2	78	0.96
1315480--1315544	28	2.3	28	83	0	76	36	3	1	58	1.23
1315519--1315579	30	2.0	32	83	6	81	37	3	3	55	1.32
1315848--1315909	16	3.9	16	72	10	56	56	4	3	35	1.37
1315853--1315959	29	3.6	29	78	5	99	56	6	1	35	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1317047--1317132	43	2.0	43	100	0	172	20	13	25	39	1.90
1322187--1322248	30	2.1	30	84	6	81	53	0	0	46	1.00
1322288--1322319	2	16.0	2	100	0	64	50	0	0	50	1.00
1328361--1328390	15	1.9	16	93	6	53	83	16	0	0	0.65
1331628--1331739	57	2.0	56	92	1	188	48	21	8	22	1.76
1335155--1335204	17	2.7	19	75	12	50	40	4	0	56	1.18
1335151--1335215	18	3.7	19	76	13	59	36	3	0	60	1.13
1335165--1335215	16	3.2	16	75	22	54	37	1	0	60	1.08
1335174--1335223	19	2.6	19	81	6	57	38	0	0	62	0.96
1335419--1335469	21	2.4	21	81	12	59	49	0	9	41	1.36

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