Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2439
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27334
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Found at i:515 original size:37 final size:36
Alignment explanation
Indices: 473--546 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
463 AAGCCAACAA
473 ATATAT-TTATTAGTTTAAAATATAAAAATAATAAAAC
1 ATATATATTATTA-TTTAAAATATAAAAA-AATAAAAC
* * *
510 ATATATATTATTATTTATATTATAAATAAATAAAAC
1 ATATATATTATTATTTAAAATATAAAAAAATAAAAC
546 A
1 A
547 CAAATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 9 0.27
37 18 0.55
38 6 0.18
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
ATATATATTATTATTTAAAATATAAAAAAATAAAAC
Found at i:517 original size:39 final size:36
Alignment explanation
Indices: 468--563 Score: 102
Period size: 39 Copynumber: 2.5 Consensus size: 36
458 CGAACAAGCC
468 AACAAATATATTTATTAGTTTAAAATATAAAAATAATAA
1 AACAAATATA-TTATTA-TTTAAAATATAAAAA-AATAA
* * * *
507 AACATATATATTATTATTTATATTATAAATAAATAAA
1 AACAAATATATTATTATTTAAAATATAAAAAAAT-AA
544 ACACAAATTATATTATTATT
1 A-ACAAA-TATATTATTATT
564 AATTATATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
36 3 0.06
37 15 0.31
38 10 0.20
39 21 0.43
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (36 bp):
AACAAATATATTATTATTTAAAATATAAAAAAATAA
Found at i:1286 original size:23 final size:24
Alignment explanation
Indices: 1235--1297 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
1225 ATATATTTAA
* *
1235 AATTTATTA-ATTAAATTGATCTC
1 AATTTATTATATTAAATTCATATC
1258 AATTTATTATATTAAATTCA-ATC
1 AATTTATTATATTAAATTCATATC
*
1281 ATTTTATCTATAATTAA
1 AATTTAT-TAT-ATTAA
1298 TATATAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.50
24 12 0.35
25 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTTATTATATTAAATTCATATC
Found at i:2554 original size:22 final size:21
Alignment explanation
Indices: 2512--2560 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2502 TTATAAATTC
* * *
2512 ATATTTTTATAATATTATTAT
1 ATATTTTTAAAAAAATATTAT
2533 ATATTTTTAAAAAAATAGTTAT
1 ATATTTTTAAAAAAATA-TTAT
2555 A-ATTTT
1 ATATTTT
2561 ATTTTAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATTTTTAAAAAAATATTAT
Found at i:3847 original size:2 final size:2
Alignment explanation
Indices: 3783--3831 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
3773 TGACAGCCCC
* * *
3783 TA TA TA -A TA TA TC TA GA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3824 TA TA TA TA
1 TA TA TA TA
3832 GTTGAACCCC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4748 original size:20 final size:20
Alignment explanation
Indices: 4711--4748 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4701 TTATTAATAA
*
4711 TTAAATTAATATTTATTTAC
1 TTAAATTAATATTAATTTAC
4731 TTAAATTAA-ATTCAATTT
1 TTAAATTAATATT-AATTT
4749 CGATCTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATTAATATTAATTTAC
Found at i:4859 original size:2 final size:2
Alignment explanation
Indices: 4849--4881 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4839 ATAATGTGTG
*
4849 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4882 CCAGCTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5627 original size:31 final size:31
Alignment explanation
Indices: 5589--5648 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
5579 TCGAGATTTG
5589 AGAATTATTTAGTTAGTAGCTAGTAGCTTTA
1 AGAATTATTTAGTTAGTAGCTAGTAGCTTTA
5620 AGAATTATTTAGTTAGTAGCTAGTAGCTT
1 AGAATTATTTAGTTAGTAGCTAGTAGCTT
5649 CTGAGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (31 bp):
AGAATTATTTAGTTAGTAGCTAGTAGCTTTA
Found at i:7014 original size:10 final size:10
Alignment explanation
Indices: 6999--7032 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
6989 AAAAATTGAC
6999 ATAAAATATA
1 ATAAAATATA
7009 ATAAAATATA
1 ATAAAATATA
*
7019 A-AAAATAAA
1 ATAAAATATA
7028 ATAAA
1 ATAAA
7033 CATAATACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAAATATA
Found at i:11931 original size:13 final size:14
Alignment explanation
Indices: 11905--11938 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
11895 TTTGAAAACT
11905 TTTTAAAAATATAA
1 TTTTAAAAATATAA
11919 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
11932 TTATTAA
1 TT-TTAA
11939 GAACAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:14141 original size:25 final size:23
Alignment explanation
Indices: 14116--14158 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14106 GATGATGATG
14116 ATGA-TACATATATATCATCAGC
1 ATGATTACATATATATCATCAGC
*
14138 ATGATTCCATATATATCATCA
1 ATGATTACATATATATCATCA
14159 TCATCATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (23 bp):
ATGATTACATATATATCATCAGC
Found at i:14190 original size:3 final size:3
Alignment explanation
Indices: 14152--14176 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14142 TTCCATATAT
14152 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
14177 ATTTTTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:14769 original size:2 final size:2
Alignment explanation
Indices: 14764--14805 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14754 GGTCTCTCTC
14764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14806 CATTGGATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16949 original size:8 final size:8
Alignment explanation
Indices: 16938--16991 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
16928 ATATAAATAT
16938 AATATAAA
1 AATATAAA
16946 AATATAAA
1 AATATAAA
*
16954 AATA-AAC
1 AATATAAA
16961 AATATAAA
1 AATATAAA
* *
16969 TATTTTAAA
1 -AATATAAA
*
16978 AATATATA
1 AATATAAA
16986 AATATA
1 AATATA
16992 TTAACATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 6 0.16
8 25 0.68
9 6 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AATATAAA
Found at i:16995 original size:19 final size:18
Alignment explanation
Indices: 16928--16995 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
16918 AAATTATATT
*
16928 ATATAAATATAATATAAAA
1 ATATAAATATATTA-AAAA
*
16947 ATATAAA-A-A-TAAACA
1 ATATAAATATATTAAAAA
*
16962 ATATAAATATTTTAAAAA
1 ATATAAATATATTAAAAA
16980 TATATAAATATATTAA
1 -ATATAAATATATTAA
16996 CATTTATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.24
16 3 0.07
17 1 0.02
18 6 0.15
19 21 0.51
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAATATATTAAAAA
Found at i:17367 original size:23 final size:22
Alignment explanation
Indices: 17317--17372 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
17307 TTACTATATT
* *
17317 AATTAAAAAATTTTAAAAATAT
1 AATTTAAAAATTTTAAAAATAA
* *
17339 ATTTTAAAAATTTTAAAATTTAA
1 AATTTAAAAATTTTAAAA-ATAA
*
17362 AATTTATAAAT
1 AATTTAAAAAT
17373 CTTATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAAAAATTTTAAAAATAA
Found at i:18626 original size:29 final size:29
Alignment explanation
Indices: 18593--18650 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
18583 CAAACGTCAA
18593 ATGCAAATAATGGTATTATCACTAACAAT
1 ATGCAAATAATGGTATTATCACTAACAAT
*
18622 ATGCAAATGATGGTATTATCACTAACAAT
1 ATGCAAATAATGGTATTATCACTAACAAT
18651 CTAATTTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (29 bp):
ATGCAAATAATGGTATTATCACTAACAAT
Found at i:19366 original size:20 final size:20
Alignment explanation
Indices: 19321--19364 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
19311 TTTCGTCGTG
*
19321 TTTTTAAAATATTATTTTAT
1 TTTTTAAAATATTATTATAT
19341 TTTTTAAAATATT-TTATAT
1 TTTTTAAAATATTATTATAT
19360 TTTTT
1 TTTTT
19365 TATATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAAAATATTATTATAT
Found at i:21078 original size:32 final size:32
Alignment explanation
Indices: 21039--21117 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
21029 AATTATGTGA
* *
21039 ATATAATAAAAATTAAAAATATTTTAAAATTT
1 ATATAATAAAAATTAAAAACATATTAAAATTT
* ** *
21071 ATATAATATAAATTAGTAACGTATTAAAATTT
1 ATATAATAAAAATTAAAAACATATTAAAATTT
21103 ATATAAATATAAAAT
1 ATAT-AATA-AAAAT
21118 ATTTTAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 30 0.79
33 4 0.11
34 4 0.11
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (32 bp):
ATATAATAAAAATTAAAAACATATTAAAATTT
Found at i:21082 original size:27 final size:26
Alignment explanation
Indices: 21052--21125 Score: 67
Period size: 32 Copynumber: 2.6 Consensus size: 26
21042 TAATAAAAAT
21052 TAAAAATATTTTAAAATTTATATAATA
1 TAAAAATATTTTAAAATTTATATAA-A
* *
21079 TAAATTAGTAACGTATTAAAATTTATATAAA
1 TAAA--AAT-A--TTTTAAAATTTATATAAA
21110 TATAAAATATTTTAAA
1 TA-AAAATATTTTAAA
21126 TATGATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
27 10 0.27
29 3 0.08
30 3 0.08
31 3 0.08
32 18 0.49
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAAAATATTTTAAAATTTATATAAA
Found at i:22111 original size:27 final size:25
Alignment explanation
Indices: 22081--22151 Score: 76
Period size: 24 Copynumber: 2.8 Consensus size: 25
22071 AGTGGGTTGT
*
22081 TTTTATCAAATAAAAAATGACAAGTTA-
1 TTTT-TCAAATAAAAAA-GA-AAATTAG
22108 TTTTTCAAA-AAAAAAGAAAATTAG
1 TTTTTCAAATAAAAAAGAAAATTAG
*
22132 TTTTTTAAAT-AAAAAGAAAA
1 TTTTTCAAATAAAAAAGAAAA
22152 ATCAGATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.12
24 20 0.50
25 6 0.15
26 5 0.12
27 4 0.10
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.32
Consensus pattern (25 bp):
TTTTTCAAATAAAAAAGAAAATTAG
Found at i:23806 original size:17 final size:16
Alignment explanation
Indices: 23784--23827 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
23774 CATAAATTAT
23784 ATATATATATTAAAATC
1 ATATATATATT-AAATC
* *
23801 ATATATAGATT-AATG
1 ATATATATATTAAATC
23816 ATATATATATTA
1 ATATATATATTA
23828 CATATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
ATATATATATTAAATC
Found at i:24471 original size:2 final size:2
Alignment explanation
Indices: 24464--24504 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
24454 TGTTTTCACA
24464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24505 CACATGAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24865 original size:25 final size:26
Alignment explanation
Indices: 24835--24884 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
24825 AAAAAATAAT
24835 TGATAAATGTACAT-AAAAGAAAAGA
1 TGATAAATGTACATCAAAAGAAAAGA
*
24860 TGATAAATGTACATCAAAATAAAAG
1 TGATAAATGTACATCAAAAGAAAAG
24885 GTAAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22
Consensus pattern (26 bp):
TGATAAATGTACATCAAAAGAAAAGA
Found at i:26849 original size:12 final size:12
Alignment explanation
Indices: 26822--26861 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
26812 TTAAATTATC
26822 TTATTTATAT-A
1 TTATTTATATAA
26833 TTATTTATATAA
1 TTATTTATATAA
* *
26845 TTATTTTTAAAA
1 TTATTTATATAA
26857 TTATT
1 TTATT
26862 AAATTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATTTATATAA
Found at i:27073 original size:18 final size:18
Alignment explanation
Indices: 27050--27084 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27040 AATTAACCAG
27050 TTTTATTATTTT-ATTTTA
1 TTTTATT-TTTTAATTTTA
27068 TTTTATTTTTTAATTTT
1 TTTTATTTTTTAATTTT
27085 TTATTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTTAATTTTA
Found at i:27141 original size:18 final size:17
Alignment explanation
Indices: 27118--27151 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27108 TCATTTCACT
*
27118 TTATTTTTATCTTTTTTG
1 TTATTTTGAT-TTTTTTG
27136 TTATTTTGATTTTTTT
1 TTATTTTGATTTTTTT
27152 ATTTCCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (17 bp):
TTATTTTGATTTTTTTG
Done.