genome.fa.s64.2.7.7.80.10.50.1000.5.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  5  of  45  ( 5312 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)
936309--936341	2	16.5	2	100	0	66	48	0	0	51	1.00
942233--942277	18	2.5	18	85	7	56	57	0	2	40	1.11
942721--942753	11	3.0	11	90	0	57	51	0	9	39	1.34
945631--946023	196	2.0	196	90	4	616	24	18	20	36	1.94
946380--946404	2	12.5	2	100	0	50	52	0	0	48	1.00
948907--948944	2	19.0	2	94	0	67	0	2	50	47	1.15
964679--964719	2	20.5	2	89	0	64	48	4	0	46	1.23
964970--965029	28	2.1	29	82	14	72	30	13	8	48	1.71
965077--965110	17	1.9	17	94	5	59	67	0	0	32	0.91
965667--965702	2	18.0	2	88	0	54	52	2	0	44	1.15
965807--965846	3	14.0	3	89	5	57	27	0	0	72	0.85
965828--965873	24	1.9	24	82	8	58	41	4	2	52	1.33
970081--970112	2	16.0	2	100	0	64	50	0	0	50	1.00
972533--972565	14	2.4	14	94	0	57	42	48	6	3	1.43
974225--974355	64	2.0	64	91	0	208	38	9	18	32	1.84
975195--975246	26	2.0	26	88	3	77	42	11	23	23	1.86
975342--975379	19	2.0	19	89	0	58	2	0	10	86	0.66
975881--975914	18	2.0	17	88	11	52	32	5	5	55	1.48
978741--979079	180	1.9	180	100	0	678	28	17	20	33	1.95
981751--981864	59	1.9	59	92	3	194	33	18	19	28	1.95
983229--983262	2	17.0	2	93	0	59	50	2	0	47	1.16
985629--985656	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
988341--988384	17	2.4	19	85	7	56	54	2	4	38	1.33
991229--991263	3	11.7	3	100	0	70	34	0	0	65	0.93
992263--992289	2	13.5	2	100	0	54	51	0	0	48	1.00
1002774--1002829	16	3.4	16	80	5	58	53	0	1	44	1.11
1002803--1002873	29	2.5	27	80	13	79	54	1	2	40	1.23
1004316--1004410	49	1.9	49	95	0	172	46	18	7	27	1.76
1007572--1007608	3	12.7	3	91	5	58	70	0	2	27	1.01
1007566--1007609	20	2.2	20	95	0	79	68	0	4	27	1.09
1009179--1009203	2	12.5	2	100	0	50	52	0	0	48	1.00
1011740--1011790	25	2.0	26	85	11	70	49	0	0	50	1.00
1011741--1011798	26	2.2	26	82	11	66	48	1	0	50	1.11
1016904--1016952	25	2.0	25	84	4	64	42	0	6	51	1.27
1018121--1018146	2	13.0	2	100	0	52	50	0	0	50	1.00
1025690--1025811	65	1.9	65	91	0	199	40	13	19	26	1.88
1029796--1029824	4	7.2	4	100	0	58	75	0	0	24	0.80
1031007--1031040	2	17.5	2	87	6	52	47	0	2	50	1.16
1031845--1031887	13	3.2	13	78	15	52	53	0	0	46	1.00
1037383--1037458	20	3.8	20	75	11	68	60	0	0	39	0.97
1037421--1037460	11	3.7	11	86	3	55	65	0	0	35	0.93
1037373--1037458	30	2.9	30	79	5	95	59	0	0	40	0.97
1038653--1038756	41	2.6	42	79	10	101	56	3	0	38	1.24
1039852--1039904	22	2.4	22	87	3	70	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1039875--1039922	17	2.7	18	75	18	55	54	0	0	45	0.99
1040004--1040090	33	2.7	32	79	13	88	43	0	0	56	0.99
1039984--1040081	17	5.5	18	67	19	62	41	1	0	57	1.05
1039980--1040101	24	5.3	23	68	18	67	39	0	0	59	1.03
1040518--1040551	2	16.5	2	87	6	50	47	2	2	47	1.32
1042086--1042117	14	2.1	16	88	11	50	37	0	0	62	0.95
1042365--1042476	32	3.5	32	71	4	100	41	28	11	17	1.85
1042352--1042476	16	7.8	16	70	16	53	43	27	12	17	1.84
1043395--1043433	16	2.4	16	82	0	51	69	0	10	20	1.17
1046721--1046833	57	2.0	57	100	0	226	47	7	5	38	1.55
1046959--1047063	40	2.6	40	82	5	115	19	24	13	42	1.87
1047305--1047354	15	3.3	14	83	13	55	50	0	2	48	1.12
1048187--1048259	31	2.4	31	90	0	110	54	4	1	39	1.28
1048156--1048300	16	8.8	16	76	12	116	54	4	2	38	1.33
1048235--1048282	23	2.1	23	92	7	80	58	0	0	41	0.98
1048219--1048297	38	2.1	39	90	7	126	56	1	0	41	1.07
1050177--1050208	3	10.7	3	100	0	64	34	0	0	65	0.93
1054868--1054892	2	12.5	2	100	0	50	0	0	48	52	1.00
1054895--1054922	2	14.0	2	100	0	56	50	0	0	50	1.00
1055649--1055679	3	10.3	3	92	0	53	0	29	0	70	0.87
1061789--1061832	18	2.2	20	84	11	56	63	0	0	36	0.95
1064802--1064840	2	19.5	2	100	0	78	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)
1068104--1068137	2	17.0	2	100	0	68	50	0	0	50	1.00
1069377--1069416	20	2.0	20	85	4	55	55	0	0	45	0.99
1069346--1069423	18	4.1	18	69	18	50	44	0	3	51	1.19
1071611--1071639	2	14.5	2	100	0	58	51	0	0	48	1.00
1075017--1075162	79	1.8	79	95	0	265	39	8	15	36	1.77
1076295--1076344	3	16.7	3	100	0	100	34	0	0	66	0.92
1076978--1077033	23	2.6	21	86	8	76	41	7	1	50	1.40
1077381--1077412	3	10.7	3	100	0	64	65	0	0	34	0.93
1082694--1082759	33	2.0	33	100	0	132	48	15	18	18	1.81
1083262--1083292	2	15.5	2	100	0	62	51	0	48	0	1.00
1086023--1086170	65	2.3	65	86	0	206	31	34	18	16	1.93
1086021--1086347	65	5.3	63	70	18	204	29	31	18	19	1.96
1085963--1086344	178	2.1	179	88	1	561	30	32	18	18	1.95
1086088--1086314	113	2.0	116	84	5	300	28	33	18	19	1.95
1086151--1086245	51	1.9	48	85	6	127	29	34	15	20	1.93
1086201--1086347	66	2.2	65	82	5	181	28	29	19	21	1.98
1090172--1090248	21	3.5	22	74	15	70	32	2	0	64	1.07
1090191--1090259	24	3.0	23	78	15	72	31	1	0	66	1.00
1091024--1091052	2	14.5	2	100	0	58	51	0	0	48	1.00
1091180--1091220	21	1.9	22	85	5	57	26	14	4	53	1.61
1093839--1093879	22	1.9	22	90	5	66	56	0	0	43	0.99
1098865--1098901	18	2.1	17	90	5	56	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1102271--1102480	105	2.0	105	100	0	420	30	19	17	33	1.94
1103788--1103893	54	2.0	54	88	0	158	35	13	16	33	1.88
1106810--1106847	11	3.3	12	82	10	53	73	0	2	23	0.95
1106807--1106839	12	2.8	12	86	4	50	69	0	6	24	1.10
1107200--1107256	25	2.3	25	78	6	62	61	1	0	36	1.07
1107272--1107346	38	2.0	38	91	0	123	49	6	0	44	1.28
1108334--1108366	3	11.0	3	100	0	66	66	0	0	33	0.92
1115475--1115536	30	2.1	30	84	0	79	32	17	16	33	1.92
1115947--1116003	8	7.1	8	77	15	55	43	0	0	56	0.99
1116066--1116114	17	2.9	16	93	6	71	38	0	2	59	1.09
1116065--1116122	17	3.0	20	75	17	59	37	0	1	60	1.07
1116076--1116122	10	5.0	10	78	21	57	38	0	0	61	0.96
1116078--1116136	20	3.1	20	85	7	70	40	0	0	59	0.97
1116194--1116228	13	2.5	15	86	13	56	65	2	0	31	1.07
1116253--1116293	13	2.8	15	82	14	50	53	0	0	46	1.00
1116257--1116298	22	1.9	22	85	9	59	47	2	0	50	1.14
1121524--1121588	26	2.4	27	84	7	78	38	0	1	60	1.07
1124478--1124534	29	2.0	29	89	0	87	22	19	17	40	1.91
1126639--1126674	2	18.0	2	94	0	63	47	0	52	0	1.00
1127021--1127189	65	2.6	63	76	10	169	44	0	4	50	1.25
1127324--1127353	8	3.8	8	95	0	51	13	0	0	86	0.57
1128002--1128031	7	4.3	7	100	0	60	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1128051--1128103	27	2.0	26	81	3	61	56	3	0	39	1.17
1130213--1130241	2	14.5	2	100	0	58	51	48	0	0	1.00
1130241--1130276	2	18.0	2	100	0	72	50	0	0	50	1.00
1138967--1139016	18	2.7	19	76	17	52	30	0	4	66	1.10
1138975--1139015	15	2.6	16	78	17	50	26	0	2	70	0.99
1144322--1144353	2	16.0	2	100	0	64	50	0	0	50	1.00
1146104--1146155	18	2.8	18	80	11	52	44	1	0	53	1.11
1148044--1148074	14	2.1	15	94	5	55	25	0	0	74	0.82
1149033--1149061	2	14.5	2	100	0	58	51	0	0	48	1.00
1149493--1149539	12	3.9	12	77	0	58	34	14	0	51	1.43

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