Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold941
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: 27133
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:362 original size:26 final size:26
Alignment explanation
Indices: 302--362 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
292 ATTTTATTTT
302 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
** * *
329 ATAATATTAGGATTATTTAAT-TTAGG
1 ATTTTATTAGGA-TAATTAATATTAAG
355 ATTTTATT
1 ATTTTATT
363 TTAATTATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:6729 original size:6 final size:6
Alignment explanation
Indices: 6718--6792 Score: 77
Period size: 6 Copynumber: 12.7 Consensus size: 6
6708 CCAATCTTTC
* *
6718 TTTTTA TTTTTA TTTTTA TTTTTA TTTATTA -TTTT- TCTTTC TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
6765 TTTATTA TTTATTA -TTTTA -TTTTA TTTT
1 TTT-TTA TTT-TTA TTTTTA TTTTTA TTTT
6793 AGTTAAATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
5 13 0.21
6 35 0.57
7 13 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:6734 original size:7 final size:7
Alignment explanation
Indices: 6718--6782 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
6708 CCAATCTTTC
6718 TTTTTA-
1 TTTTTAT
6724 TTTTTA-
1 TTTTTAT
6730 TTTTTA-
1 TTTTTAT
6736 TTTTTAT
1 TTTTTAT
*
6743 TTATTAT
1 TTTTTAT
*
6750 TTTTCTTT
1 TTTT-TAT
6758 CTTTTTAT
1 -TTTTTAT
*
6766 TTATTAT
1 TTTTTAT
*
6773 TTATTAT
1 TTTTTAT
6780 TTT
1 TTT
6783 ATTTTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 18 0.36
7 24 0.48
8 4 0.08
9 4 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:6747 original size:10 final size:10
Alignment explanation
Indices: 6726--6792 Score: 61
Period size: 10 Copynumber: 6.8 Consensus size: 10
6716 TCTTTTTATT
6726 TTTATTTTTA
1 TTTATTTTTA
6736 TTT-TTATTTA
1 TTTATT-TTTA
*
6746 -TTATTTTTC
1 TTTATTTTTA
*
6755 TTTCTTTTTA
1 TTTATTTTTA
6765 TTTATTATTTA
1 TTTATT-TTTA
6776 -TTA-TTTTA
1 TTTATTTTTA
6784 TTTTATTTT
1 -TTTATTTT
6793 AGTTAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.09
9 8 0.17
10 27 0.59
11 7 0.15
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:6925 original size:20 final size:20
Alignment explanation
Indices: 6900--6941 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6890 ATCCATGGTA
* *
6900 CCAAACAGTTCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6920 CCAAACAATCCTATTCCAGC
1 CCAAACAATCCTATTCCAGC
6940 CC
1 CC
6942 TAGAATCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.40, G:0.07, T:0.21
Consensus pattern (20 bp):
CCAAACAATCCTATTCCAGC
Found at i:7940 original size:118 final size:118
Alignment explanation
Indices: 7720--7949 Score: 361
Period size: 118 Copynumber: 1.9 Consensus size: 118
7710 TGTTTCCATT
* * *
7720 GTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
*
7785 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTTCGCTAGCCGAG
66 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGAG
* *
7838 GTTATGAGTATAGCTCAAATCGTGACTGACTGAGTAACTGGGGCAGGGTGCTTGGGTTGTCATTC
1 GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
* ****
7903 TACTTCGCGTCAAAAGTTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
7950 ACCGGAAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (118 bp):
GTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGCAGGGTGCTTGGGTTGTCATTC
TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGAG
Found at i:8089 original size:8 final size:8
Alignment explanation
Indices: 8078--8107 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
8068 AAAATTTAAA
8078 AAAAAAAG
1 AAAAAAAG
8086 AAAAAAAG
1 AAAAAAAG
*
8094 GAAAAAAG
1 AAAAAAAG
8102 AAAAAA
1 AAAAAA
8108 TAAGTACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:8676 original size:5 final size:5
Alignment explanation
Indices: 8668--8705 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
8658 TGGAAGACTC
8668 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
8706 ATTAGGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:8777 original size:10 final size:10
Alignment explanation
Indices: 8758--8789 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
8748 TTTTAGGATT
8758 TTAT-TTTAA
1 TTATCTTTAA
8767 TTATCTTTAA
1 TTATCTTTAA
8777 TTATCTTTAA
1 TTATCTTTAA
8787 TTA
1 TTA
8790 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:11471 original size:45 final size:45
Alignment explanation
Indices: 11389--11518 Score: 134
Period size: 45 Copynumber: 2.9 Consensus size: 45
11379 ACCAGGAGTG
* * * * * *
11389 AGTAAGACCATAGCTGAAACATACTATGCCATAATGATGATAATA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * *
11434 AGTAAGACCATAGCTGAAAGATGCTACGATATCATGATAAAAATG
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
* * * * *
11479 AGTAAGACAATAGTTGAAAGACGCTATGGCATAATGATAA
1 AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAA
11519 GGGTGAGTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGATGCTACGACATAATGATAAAAATA
Found at i:12564 original size:17 final size:17
Alignment explanation
Indices: 12542--12585 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
12532 TCTGATACCA
* *
12542 ATGGCGGATACCTATCT
1 ATGGCGAATACCTATCC
12559 ATGGCGAATACCTATCC
1 ATGGCGAATACCTATCC
12576 ATGGCGAATA
1 ATGGCGAATA
12586 GTTTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (17 bp):
ATGGCGAATACCTATCC
Found at i:21812 original size:35 final size:35
Alignment explanation
Indices: 21766--21836 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
21756 TTTAACCTTA
*
21766 AAAAAAAACTTTTAGAACACCCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
*
21801 AAAAAAAACTTTTAAAACACTCAAAAATTTAAAGC
1 AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
21836 A
1 A
21837 TCACCCTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.59, C:0.15, G:0.04, T:0.21
Consensus pattern (35 bp):
AAAAAAAACTTTTAAAACACCCAAAAATTTAAAGC
Found at i:22813 original size:3 final size:3
Alignment explanation
Indices: 22802--22942 Score: 98
Period size: 3 Copynumber: 47.7 Consensus size: 3
22792 TGATGATAGC
* * *
22802 AAT AGT AAT AAT -AT AAT AAT AA- AGT AGAA AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * * * *
22846 AAT AAT AAT ACGTT AAT AAG AAT AAT AAT AGT -AT ATT AAT AAT AAC
1 AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
22892 AAT AAT AGA- AAGT AAT GAT AA- AAT AAT AA- AAA AAT AAT AAT AAT
1 AAT AAT A-AT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22936 AA- AAT AA
1 AAT AAT AA
22943 AGAATAGTGC
Statistics
Matches: 107, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
2 11 0.10
3 90 0.84
4 4 0.04
5 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:22864 original size:20 final size:20
Alignment explanation
Indices: 22838--22936 Score: 76
Period size: 20 Copynumber: 4.9 Consensus size: 20
22828 GAAAATAATA
22838 ATAATAATAATAATAATACGT
1 ATAATAATAATAATAATA-GT
*
22859 -TAATAAGAATAATAATAGT
1 ATAATAATAATAATAATAGT
* * *
22878 ATATTAATAATAACAATAAT
1 ATAATAATAATAATAATAGT
* * *
22898 AGAAAGTAATGATAA-AATAAT
1 A-TAA-TAATAATAATAATAGT
* *
22919 AAAAAAATAATAATAATA
1 ATAATAATAATAATAATA
22937 AAATAAAGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
19 9 0.14
20 39 0.61
21 8 0.12
22 8 0.12
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (20 bp):
ATAATAATAATAATAATAGT
Found at i:22869 original size:23 final size:23
Alignment explanation
Indices: 22836--22942 Score: 87
Period size: 23 Copynumber: 4.8 Consensus size: 23
22826 TAGAAAATAA
*
22836 TAATAATAATAATAATAATACGT
1 TAATAATAATAATAATAATACAT
* * *
22859 TAATAAGAATAATAATAGTATAT
1 TAATAATAATAATAATAATACAT
* *
22882 TAATAATAACAATAATAGA-A-AG
1 TAATAATAATAATAATA-ATACAT
* * * *
22904 TAATGATAA-AATAATAAAAAAA
1 TAATAATAATAATAATAATACAT
22926 TAATAATAATAA-AATAA
1 TAATAATAATAATAATAA
22943 AGAATAGTGC
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.01
21 8 0.12
22 23 0.33
23 37 0.54
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
TAATAATAATAATAATAATACAT
Found at i:22929 original size:22 final size:23
Alignment explanation
Indices: 22882--22943 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
22872 AATAGTATAT
* *
22882 TAATAATAACAATAAT-AGAAAG
1 TAATAATAACAATAATAAAAAAA
*
22904 TAATGATAA-AATAATAAAAAAA
1 TAATAATAACAATAATAAAAAAA
*
22926 TAATAATAATAA-AATAAA
1 TAATAATAACAATAATAAA
22944 GAATAGTGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.18
22 26 0.76
23 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (23 bp):
TAATAATAACAATAATAAAAAAA
Found at i:22932 original size:14 final size:14
Alignment explanation
Indices: 22913--22942 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22903 GTAATGATAA
22913 AATAATAAAAAAAT
1 AATAATAAAAAAAT
*
22927 AATAATAATAAAAT
1 AATAATAAAAAAAT
22941 AA
1 AA
22943 AGAATAGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATAAAAAAAT
Done.