Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1542
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: 29048
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:7162 original size:13 final size:13
Alignment explanation
Indices: 7144--7169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7134 AATTTTTTGG
7144 TGTATCGATACAT
1 TGTATCGATACAT
7157 TGTATCGATACAT
1 TGTATCGATACAT
7170 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19240 original size:28 final size:28
Alignment explanation
Indices: 19184--19255 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
19174 GGAATAAAGC
** **
19184 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
19212 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
19240 CGAGGTTCGAGTATCC
1 CGGGGTTGGAGTATCC
19256 TTAATTGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:19352 original size:52 final size:51
Alignment explanation
Indices: 19266--19412 Score: 186
Period size: 51 Copynumber: 2.8 Consensus size: 51
19256 TTAATTGTGA
* * *
19266 AAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTGTCCCCGATTAAAGG
1 AAAATTGGTG-TTTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATT-AAGG
* * **
19319 AAAATTGGTGTTTTGAAAATAAAGCCGGGGTTGGAGTATCCCCGATTGTGG
1 AAAATTGGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGG
* * *
19370 AAAATCGATGATTTGGAAATAAAACCGGGGTTGGAGTATCCCC
1 AAAATTGGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCC
19413 TCGGAGATAA
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 40 0.49
52 32 0.39
53 10 0.12
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (51 bp):
AAAATTGGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAGG
Found at i:19443 original size:79 final size:80
Alignment explanation
Indices: 19344--19523 Score: 249
Period size: 80 Copynumber: 2.3 Consensus size: 80
19334 AAAATAAAGC
* * * *
19344 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATCGATGA-TTTGGAAATAAAAC-CGGGGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTATGAG-AAATCAAT-ATTTTAGAAATAAAACTAGGGGTTGGAG
*
19406 TATCCCCTCGGAGATAA
64 TATCCCCTCGAAGATAA
* * *
19423 CGGGGTTGGAGTATCTCCGATTATGAGAAATTAATATTTTAGAAATAAAGCTAGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAACTAGGGGTTGGAGTA
19488 TCCCCTCGAAGATAA
66 TCCCCTCGAAGATAA
19503 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
19524 GATTAACGGG
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 41 0.46
80 47 0.53
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (80 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAACTAGGGGTTGGAGTA
TCCCCTCGAAGATAA
Found at i:19538 original size:27 final size:26
Alignment explanation
Indices: 19476--19552 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 26
19466 AATAAAGCTA
*
19476 GGGGTTGGAGTATCCCCTCGAAGATAAC
1 GGGGTTGGAGTAT-CCC-CGATGATAAC
19504 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGA-TAAC
19531 GGGGTTGGAGTATCCCCGATGA
1 GGGGTTGGAGTATCCCCGATGA
19553 AAAATTGATG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 5 0.11
27 29 0.62
28 13 0.28
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (26 bp):
GGGGTTGGAGTATCCCCGATGATAAC
Found at i:19629 original size:51 final size:49
Alignment explanation
Indices: 19534--19651 Score: 145
Period size: 51 Copynumber: 2.4 Consensus size: 49
19524 GATTAACGGG
19534 GTTGGAGTATCCCCGA-TGAAAAATTGATGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAAAAATTGATGTTTTAGAAATAAAATCGGA
* *
19582 GTTGGAGTATCCCCGATTATAGAAAATT-AGTGTTTT-GAAAATGAAATCGGA
1 GTTGGAGTATCCCCGATT-GA-AAAATTGA-TGTTTTAG-AAATAAAATCGGA
19633 GTTGG-GATATCCCCGATTG
1 GTTGGAG-TATCCCCGATTG
19652 CGGAGAATTG
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
48 16 0.26
49 1 0.02
50 4 0.07
51 40 0.66
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (49 bp):
GTTGGAGTATCCCCGATTGAAAAATTGATGTTTTAGAAATAAAATCGGA
Found at i:21954 original size:13 final size:13
Alignment explanation
Indices: 21936--21961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21926 ACAAAGATCC
21936 ATGTATCGATACA
1 ATGTATCGATACA
21949 ATGTATCGATACA
1 ATGTATCGATACA
21962 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21957 original size:33 final size:33
Alignment explanation
Indices: 21915--21981 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
21905 AAAATTTCCA
***
21915 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
21948 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
21981 A
1 A
21982 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:22025 original size:19 final size:18
Alignment explanation
Indices: 22001--22066 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
21991 CAGTAGCTAA
22001 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
22020 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
22035 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
22052 TTATGTATCGATACA
1 TTATGTATCGATACA
22067 TTTGGAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 2 0.05
18 2 0.05
19 25 0.61
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:22041 original size:13 final size:13
Alignment explanation
Indices: 22023--22047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22013 ACAATACTTA
22023 TGTATCGATACAT
1 TGTATCGATACAT
22036 TGTATCGATACA
1 TGTATCGATACA
22048 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22045 original size:32 final size:32
Alignment explanation
Indices: 22004--22068 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
21994 TAGCTAATTA
*
22004 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
22036 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
22068 T
1 T
22069 TGGAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:22831 original size:55 final size:54
Alignment explanation
Indices: 22748--23462 Score: 716
Period size: 55 Copynumber: 12.4 Consensus size: 54
22738 ATAAAGTGTA
* * *
22748 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
22803 TCCTGCTCTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGACTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
22858 TCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
22913 TCCTGCTTTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
** * *
22968 TCCTATTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTTGAAAGGTGAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAA---G----GCG
*
23030 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAAATCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G-G-----CG
*
23092 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
23147 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
23202 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
*
23262 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** *
23321 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACATGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
** *
23380 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGACG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
23440 TCCTGCTCTTTGAGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
23463 ATGGAAGGAG
Statistics
Matches: 582, Mismatches: 49, Indels: 53
0.85 0.07 0.08
Matches are distributed among these distances:
54 8 0.01
55 263 0.45
56 12 0.02
57 1 0.00
58 4 0.01
59 135 0.23
60 56 0.10
61 1 0.00
62 102 0.18
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:22941 original size:110 final size:111
Alignment explanation
Indices: 22748--23465 Score: 801
Period size: 110 Copynumber: 6.2 Consensus size: 111
22738 ATAAAGTGTA
* * **
22748 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCATCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* *
22812 TTGAGGACTGAAAGGTGCCACTAACTTGTGTGGACTTT-AAGAGGTG
65 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
* *
22858 TCCTGCTCTTTGAGGACTGGAAAATGTCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTTTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
*
22923 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
** *
22968 TCCTATTCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTTGAAAGGTGAAAAGCATCC
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT-----G--TCC
* *
23033 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAG-GTGAAAATCA
59 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAG-G----T-G
23092 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* **
23157 TGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAG-GG-G
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGAGGTG
*
23202 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGAAAAG-GCATCCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG----GTG--TCCT
*
23266 GCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
60 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGTG
** * *
23321 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACATGTGTGGGCTTTAAAAGAAAAGGCGTCCTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTGTCCTG
*
23385 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGACG
61 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-GAG--G-TG
*
23440 TCCTGCTCTTTGAGGACTGAAAAATG
1 TCCTGCTCTTTGAGGACTGGAAAATG
23466 GAAGGAGAAG
Statistics
Matches: 534, Mismatches: 33, Indels: 72
0.84 0.05 0.11
Matches are distributed among these distances:
110 197 0.37
111 4 0.01
113 1 0.00
114 31 0.06
115 19 0.04
116 6 0.01
117 87 0.16
118 82 0.15
119 45 0.08
120 5 0.01
122 1 0.00
123 5 0.01
124 51 0.10
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (111 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGTG
Found at i:23071 original size:62 final size:62
Alignment explanation
Indices: 22974--23465 Score: 579
Period size: 59 Copynumber: 8.3 Consensus size: 62
22964 GGTGTCCTAT
* *
22974 TCTTTGAGGACTGGAAAATACCACCAACTTGTGTGGGCTTTGAAAGGTGAAAAGCATCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
* *
23036 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAAATCATCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
*
23098 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G-G---TG--TCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
**
23153 TCTTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG-G----G--TCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
* *
23208 TCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA-GA-AAAGGCATCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
* *
23268 TCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTT-AAA--AGAAAAGGCGTCCTGC
1 TCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAA-GCATCCTGC
** * *
23327 TCTTTGAGGACT-GAAGGTGCCACCAACATGTGTGGGCTTT-AAA--AGAAAAGGCGTCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAA-GCATCCTGC
** * * *
23386 TCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGA-CGTCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
*
23446 TCTTTGAGGACTGAAAAATG
1 TCTTTGAGGACTGGAAAATG
23466 GAAGGAGAAG
Statistics
Matches: 394, Mismatches: 20, Indels: 33
0.88 0.04 0.07
Matches are distributed among these distances:
54 1 0.00
55 98 0.25
56 2 0.01
57 1 0.00
58 10 0.03
59 124 0.31
60 43 0.11
61 5 0.01
62 110 0.28
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (62 bp):
TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAAAAGCATCCTGC
Done.