Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold821
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: 30738
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:3688 original size:26 final size:27
Alignment explanation
Indices: 3654--3719 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 27
3644 ATTAATTTTA
3654 AAATTATATTTAA-TTACTATTA-AATT-
1 AAATTATA-TTAAGTTAC-ATTATAATTC
3680 AAATTATATTAAGTTACATTATAATTC
1 AAATTATATTAAGTTACATTATAATTC
*
3707 AAATGCATATTAA
1 AAAT-TATATTAA
3720 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 8 0.23
26 16 0.46
27 4 0.11
28 7 0.20
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (27 bp):
AAATTATATTAAGTTACATTATAATTC
Found at i:9642 original size:24 final size:24
Alignment explanation
Indices: 9597--9643 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9587 TTATAAGTTT
*
9597 ATATTAATTAATATGATATTATAA
1 ATATTAATTAATATAATATTATAA
*
9621 ATATT-ATTAATATTAATTTTATA
1 ATATTAATTAATA-TAATATTATA
9644 TCCTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTAATTAATATAATATTATAA
Found at i:10774 original size:83 final size:84
Alignment explanation
Indices: 10649--10804 Score: 208
Period size: 83 Copynumber: 1.9 Consensus size: 84
10639 ATGTTGTTTC
* * *
10649 ATATGTTGTTCTTTTAATTGAAAGAGAAAATTTGGAGGAAAATGTTTTCAAGATTCTTATTTTTA
1 ATATGTTGTTCTTTTAATTGAAAGAGAAAATTTGGA-GAAAATGCTCTCAAGATTCTTATTTTAA
*
10714 TTAGTATATTTTTGCTTATA
65 TTAATATATTTTTGCTTATA
* * * *
10734 ATATTTTGTTCTTTTAGTTGAGAGA-AAAATTTGGTA-AAAATGCTCTCAAGATTCTTGTTTTAA
1 ATATGTTGTTCTTTTAATTGAAAGAGAAAATTTGG-AGAAAATGCTCTCAAGATTCTTATTTTAA
10797 TTAATATA
65 TTAATATA
10805 AGTTTGCAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 30 0.48
84 9 0.15
85 23 0.37
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.47
Consensus pattern (84 bp):
ATATGTTGTTCTTTTAATTGAAAGAGAAAATTTGGAGAAAATGCTCTCAAGATTCTTATTTTAAT
TAATATATTTTTGCTTATA
Found at i:14151 original size:22 final size:22
Alignment explanation
Indices: 14123--14199 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
14113 TTTCACGTAA
14123 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* * *
14145 CATTTCAAGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
14166 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
14188 CATTTCATGCAT
1 CATTTCATGCAT
14200 TTCAAAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 9 0.21
22 21 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:14151 original size:43 final size:43
Alignment explanation
Indices: 14097--14220 Score: 187
Period size: 43 Copynumber: 2.9 Consensus size: 43
14087 CATTGCATGC
*
14097 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
*
14140 ATTTTCATTTCAAGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
14183 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
14221 TGCACTTCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 9 0.12
43 65 0.88
ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:14221 original size:5 final size:5
Alignment explanation
Indices: 14208--14298 Score: 85
Period size: 5 Copynumber: 18.2 Consensus size: 5
14198 ATTTCAAAAA
* * * *
14208 CATTT CATTG CATTG CACTT- CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTG CATTG CATTG CA-TTG CATTG CATTG CATTG CATTG CATTG CATTG
* * * * *
14258 CATTT CATTT CATTT CATTG CATTG CATTT CATTA CATTG C
1 CATTG CATTG CATTG CATTG CATTG CATTG CATTG CATTG C
14299 TTTCATGCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
4 2 0.03
5 71 0.95
6 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (5 bp):
CATTG
Found at i:14231 original size:10 final size:10
Alignment explanation
Indices: 14208--14296 Score: 97
Period size: 10 Copynumber: 8.9 Consensus size: 10
14198 ATTTCAAAAA
* *
14208 CATTTCATTG
1 CATTGCATTT
*
14218 CATTGCACTT
1 CATTGCATTT
*
14228 CATTTCATTT
1 CATTGCATTT
14238 CATTGCATTT
1 CATTGCATTT
*
14248 CATTGCATTG
1 CATTGCATTT
*
14258 CATTTCATTT
1 CATTGCATTT
* *
14268 CATTTCATTG
1 CATTGCATTT
14278 CATTGCATTT
1 CATTGCATTT
*
14288 CATTACATT
1 CATTGCATT
14297 GCTTTCATGC
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 66 1.00
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.49
Consensus pattern (10 bp):
CATTGCATTT
Found at i:14231 original size:20 final size:20
Alignment explanation
Indices: 14208--14298 Score: 137
Period size: 20 Copynumber: 4.5 Consensus size: 20
14198 ATTTCAAAAA
*
14208 CATTTCATTGCATTGCACTT
1 CATTTCATTGCATTGCATTT
*
14228 CATTTCATTTCATTGCATTT
1 CATTTCATTGCATTGCATTT
* *
14248 CATTGCATTGCATTTCATTT
1 CATTTCATTGCATTGCATTT
14268 CATTTCATTGCATTGCATTT
1 CATTTCATTGCATTGCATTT
*
14288 CATTACATTGC
1 CATTTCATTGC
14299 TTTCATGCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (20 bp):
CATTTCATTGCATTGCATTT
Found at i:14638 original size:20 final size:19
Alignment explanation
Indices: 14613--14653 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
14603 TAGGTTCCAG
*
14613 CATCCATTCCAGCAGCCTTC
1 CATCCATACCAGCAG-CTTC
*
14633 CATCCATAGCAGCAGCTTC
1 CATCCATACCAGCAGCTTC
14652 CA
1 CA
14654 GCGTCTGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.24, C:0.41, G:0.12, T:0.22
Consensus pattern (19 bp):
CATCCATACCAGCAGCTTC
Found at i:18991 original size:52 final size:52
Alignment explanation
Indices: 18842--18966 Score: 241
Period size: 52 Copynumber: 2.4 Consensus size: 52
18832 CGAAATATGA
18842 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
18894 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
18946 AAATTTGCCTGCATGTATCGA
1 AAATTTGCCTGCATGTATCGA
18967 CACAAAGATC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:19059 original size:19 final size:19
Alignment explanation
Indices: 19035--19097 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
19025 GCTTATATTA
19035 TATCGATACAAAACTTATG
1 TATCGATACAAAACTTATG
19054 TATCGATAC---A--T-TG
1 TATCGATACAAAACTTATG
**
19067 TATCGATACAGCACTTATG
1 TATCGATACAAAACTTATG
19086 TATCGATACAAA
1 TATCGATACAAA
19098 TCGTTGAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (19 bp):
TATCGATACAAAACTTATG
Found at i:19070 original size:13 final size:13
Alignment explanation
Indices: 19052--19076 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19042 ACAAAACTTA
19052 TGTATCGATACAT
1 TGTATCGATACAT
19065 TGTATCGATACA
1 TGTATCGATACA
19077 GCACTTATGT
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:19076 original size:32 final size:32
Alignment explanation
Indices: 19035--19095 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
19025 GCTTATATTA
19035 TATCGATACAAAACTTATGTATCGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTG
**
19067 TATCGATACAGCACTTATGTATCGATACA
1 TATCGATACAAAACTTATGTATCGATACA
19096 AATCGTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTG
Found at i:23808 original size:28 final size:28
Alignment explanation
Indices: 23728--23824 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 28
23718 TTTGATAACT
*
23728 TAAATTAAT-TTTAATTATTATTTTAATA-A
1 TAAA-TAATATTTAA-TATTA-TTAAATATA
23757 TAAA-AATAATTTAATATTAATTAAAATATA
1 TAAATAAT-ATTTAATATT-ATT-AAATATA
23787 TAAATAATATTTAATATT-TTAAATAGTA
1 TAAATAATATTTAATATTATTAAATA-TA
23815 -AAATAA-ATTT
1 TAAATAATATTT
23825 TAAATCAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 17
0.77 0.01 0.22
Matches are distributed among these distances:
26 4 0.07
27 14 0.23
28 10 0.17
29 14 0.23
30 15 0.25
31 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAATAATATTTAATATTATTAAATATA
Found at i:23818 original size:27 final size:28
Alignment explanation
Indices: 23728--23824 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
23718 TTTGATAACT
* **
23728 TAAATTAATTTTAATTATTATTTTAATA-A
1 TAAA-TAAATTTAA-TATTATTAAAATATA
*
23757 TAAAAATAATTTAATATTAATTAAAATATA
1 TAAATA-AATTTAATATT-ATTAAAATATA
23787 TAAATAATATTTAATATT-TT-AAATAGTA
1 TAAATAA-ATTTAATATTATTAAAATA-TA
23815 -AAATAAATTT
1 TAAATAAATTT
23825 TAAATCAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.07
27 11 0.19
28 9 0.16
29 18 0.31
30 16 0.28
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAAATAAATTTAATATTATTAAAATATA
Found at i:24201 original size:27 final size:27
Alignment explanation
Indices: 24169--24236 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
24159 ATAAGCCATA
*
24169 ATTTTTGATAAACAAAAAGGAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
* * *
24196 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGGAACCACC
*
24223 ATTGTTGACAAACA
1 ATTTTTGACAAACA
24237 CATGGTGGCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCACC
Found at i:24255 original size:24 final size:25
Alignment explanation
Indices: 24224--24281 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
24214 GTAACCACCA
*
24224 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
24248 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
24274 TTGTTGAC
1 TTGTTGAC
24282 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:26171 original size:21 final size:22
Alignment explanation
Indices: 26145--26190 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
26135 ATCTGTTGAA
* *
26145 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
26166 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
26188 ACT
1 ACT
26191 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:28668 original size:20 final size:20
Alignment explanation
Indices: 28643--28688 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
28633 AAGAATTGAA
*
28643 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
* **
28663 GAGGGATGCTTGAGAAGGAG
1 GAGGGATACAAGAGAAGGAG
28683 GAGGGA
1 GAGGGA
28689 GCCTCCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:28762 original size:24 final size:24
Alignment explanation
Indices: 28735--28804 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
28725 AATAAAAATT
*
28735 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAAAA
* *
28759 AGCCA-TAATTTTTGATAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
28783 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
28805 TACAAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 1 0.03
27 12 0.34
28 1 0.03
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:28798 original size:27 final size:27
Alignment explanation
Indices: 28737--28831 Score: 88
Period size: 27 Copynumber: 3.6 Consensus size: 27
28727 TAAAAATTAG
* *
28737 CCACCAATTTTGACAAACAATAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
** *
28761 CCATAATTTTTGATAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
28788 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
28815 CCACCATTGTTGACAAA
1 CCACCATTTTTGACAAA
28832 TACATGGTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
24 18 0.32
25 1 0.02
27 37 0.66
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:28832 original size:27 final size:27
Alignment explanation
Indices: 28781--28835 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
28771 TGATAAACAA
*
28781 AAAGGAACCACCATTTTTGACAAATAC
1 AAAGGAACCACCATTGTTGACAAATAC
*
28808 AAAGTAACCACCATTGTTGACAAATAC
1 AAAGGAACCACCATTGTTGACAAATAC
28835 A
1 A
28836 TGGTGACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (27 bp):
AAAGGAACCACCATTGTTGACAAATAC
Found at i:29229 original size:32 final size:32
Alignment explanation
Indices: 29143--29242 Score: 114
Period size: 34 Copynumber: 3.1 Consensus size: 32
29133 TCAAACATTA
* *
29143 ATATATAAATATTGCAATTAACGGGAAAAATAT
1 ATATATAAATATTGCAATTAA-TGGAAAAAAAT
* **
29176 ATTTATAAATATATTATAATTAATGGAAAAAAAT
1 ATATAT-AA-ATATTGCAATTAATGGAAAAAAAT
29210 ATATATAAATATTGCAATTAAT-G-AAAAAAT
1 ATATATAAATATTGCAATTAATGGAAAAAAAT
29240 ATA
1 ATA
29243 CTAGAATAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
30 10 0.18
31 1 0.02
32 12 0.21
33 7 0.12
34 16 0.28
35 11 0.19
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (32 bp):
ATATATAAATATTGCAATTAATGGAAAAAAAT
Found at i:29665 original size:22 final size:22
Alignment explanation
Indices: 29623--29665 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29613 TAATGTTATC
* *
29623 ATAATTTATATATTTACATACG
1 ATAATTTATATATTAAAATACG
29645 ATAATTTATATATTAAAATAC
1 ATAATTTATATATTAAAATAC
29666 ATATTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTATATATTAAAATACG
Done.