Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold897
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: 30916
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:6887 original size:16 final size:16
Alignment explanation
Indices: 6866--6898 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6856 TCTTCCTCAA
*
6866 TACCTTAACATGACGC
1 TACCTTAACATCACGC
6882 TACCTTAACATCACGC
1 TACCTTAACATCACGC
6898 T
1 T
6899 CCAATATCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.27
Consensus pattern (16 bp):
TACCTTAACATCACGC
Found at i:14651 original size:25 final size:25
Alignment explanation
Indices: 14627--14714 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
14617 ATACATGTAT
*
14627 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTATGAATCGGTAA
* * *
14652 GCTC-TCATGAGCTATAAATTGGTAA
1 GCTCAT-ACGAGCTATGAATCGGTAA
*
14677 GCTCATACAAGC--TGAAATCGGTAA
1 GCTCATACGAGCTATG-AATCGGTAA
*
14701 GCTCATATGAGCTA
1 GCTCATACGAGCTA
14715 AAATCAGTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 1 0.02
24 19 0.40
25 27 0.56
26 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (25 bp):
GCTCATACGAGCTATGAATCGGTAA
Found at i:14713 original size:24 final size:24
Alignment explanation
Indices: 14627--14724 Score: 90
Period size: 24 Copynumber: 4.0 Consensus size: 24
14617 ATACATGTAT
* * *
14627 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATATGAGCTA-AAATCGGTAA
*
14652 GCTC-TCATGAGCTATAAATTGGTAA
1 GCTCAT-ATGAGCTA-AAATCGGTAA
** *
14677 GCTCATACAAGCTGAAATCGGTAA
1 GCTCATATGAGCTAAAATCGGTAA
*
14701 GCTCATATGAGCTAAAATCAGTAA
1 GCTCATATGAGCTAAAATCGGTAA
14725 TCCCTAATGA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
24 30 0.51
25 28 0.47
26 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (24 bp):
GCTCATATGAGCTAAAATCGGTAA
Found at i:15812 original size:28 final size:27
Alignment explanation
Indices: 15757--15868 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
15747 AGCATGGCTG
* *
15757 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
15783 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
15811 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
15838 CCTGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
15865 CCAG
1 CCAG
15869 GAAGCTTCCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.65
28 18 0.24
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:15848 original size:54 final size:54
Alignment explanation
Indices: 15757--15868 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
15747 AGCATGGCTG
* *
15757 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * * *
15811 CCAGAACAGAAATATGTGGCAGAGCCACCTGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
15865 CCAG
1 CCAG
15869 GAAGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:18798 original size:20 final size:19
Alignment explanation
Indices: 18762--18800 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
18752 AACTGCTCCA
**
18762 TTGAAAAGTATTGATACCT
1 TTGAAAAGTATCAATACCT
18781 TTGATAAAGTATCAATACCT
1 TTGA-AAAGTATCAATACCT
18801 ATTGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (19 bp):
TTGAAAAGTATCAATACCT
Found at i:19016 original size:21 final size:21
Alignment explanation
Indices: 18990--19031 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18980 TGAACAATCA
18990 CAAAAAATATCGACACCTTTT
1 CAAAAAATATCGACACCTTTT
* * *
19011 CAAAAAGTATTGATACCTTTT
1 CAAAAAATATCGACACCTTTT
19032 ACCATGTATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (21 bp):
CAAAAAATATCGACACCTTTT
Found at i:21896 original size:47 final size:47
Alignment explanation
Indices: 21841--22111 Score: 245
Period size: 47 Copynumber: 5.8 Consensus size: 47
21831 GGGTAAGGTT
21841 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAG
* * *
21888 TCGATGCCATGTCCCAAACATGGTCTTACACTGACT-ATCATCTCATAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATCTCA-AG
* * ** * *
21936 CAGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCACGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTC-AAG
* * *
21982 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA-G
* * * * *
22028 CCGATTCCATGTCCCAGAAATGGTCTTACACTAGCTCTCATAATGT--GG
1 CCGATGCCATGTCCCAGACATGGTCTTACACT-G-GCTCAT-ATCTCAAG
* *
22076 CTGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA
22112 CACACAAATG
Statistics
Matches: 183, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
44 4 0.02
45 1 0.01
46 71 0.39
47 80 0.44
48 21 0.11
50 4 0.02
51 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAG
Found at i:22100 original size:140 final size:141
Alignment explanation
Indices: 21841--22105 Score: 369
Period size: 140 Copynumber: 1.9 Consensus size: 141
21831 GGGTAAGGTT
* *
21841 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAAA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGCCGATGCCATGTCCCAAA
*
21906 CATGGTCTTACACTGACTATCATCTCATAGCAGATGCATGTCCCAGACATGTCTTACACTGGCTT
66 CATGGTCTTACACTGACTATCATATCATAGCAGATGCATGTCCCAGACATGTCTTACACTGGCTT
21971 ACGTCACGAGG
131 ACGTCACGAGG
* * *
21982 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTCTCAATGCCGATTCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAA-GCCGATGCCATGTCCCA-
* * * *
22045 AA-ATGGTCTTACACT-AGCTCTCATAAT-GTGGCTGATGCATGTCCCAGACATGTCTTACACT
64 AACATGGTCTTACACTGA-CTATCAT-ATCATAGCAGATGCATGTCCCAGACATGTCTTACACT
22106 AGCTCACACA
Statistics
Matches: 110, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
139 22 0.20
140 79 0.72
141 9 0.08
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (141 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGCCGATGCCATGTCCCAAA
CATGGTCTTACACTGACTATCATATCATAGCAGATGCATGTCCCAGACATGTCTTACACTGGCTT
ACGTCACGAGG
Found at i:26620 original size:34 final size:34
Alignment explanation
Indices: 26582--26652 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
26572 AGTCCAATGT
26582 ACTGTTAGTCTAGTCAAACACATCTACTTCACTA
1 ACTGTTAGTCTAGTCAAACACATCTACTTCACTA
*
26616 ACTGTTAGTCTAGTCAGACACATCTACTTCACTA
1 ACTGTTAGTCTAGTCAAACACATCTACTTCACTA
26650 ACT
1 ACT
26653 TTTGGAGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.27, G:0.10, T:0.32
Consensus pattern (34 bp):
ACTGTTAGTCTAGTCAAACACATCTACTTCACTA
Found at i:29044 original size:49 final size:50
Alignment explanation
Indices: 28970--29158 Score: 193
Period size: 50 Copynumber: 3.8 Consensus size: 50
28960 TAGCTGAAGC
* * *
28970 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCACAA
* * *
29018 TAGTCTGGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCAC
1 TA-TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCACAA
* ** * * *
29069 CATCTAATACACGTAGTAGCCTGCACGTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCACA-A
* * * * *
29120 TTTCAGGTACGCATAGTAGCCTGTACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
29159 TGCCACCTCA
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
48 2 0.02
49 38 0.33
50 42 0.37
51 33 0.29
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (50 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCACAA
Found at i:29167 original size:101 final size:99
Alignment explanation
Indices: 28983--29169 Score: 239
Period size: 101 Copynumber: 1.9 Consensus size: 99
28973 CTGGTACGCA
* * * **
28983 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATAGTCTGGTACATGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACGTAGTACTACACACGTGACCAATAGTCAGGTACACATAGTAGCCTGCACTTA
**
29048 GTACTACACACGTGACCTCACCATCTAATACACG
66 GTACTACACACGCCACCTCACCATCTAATACACG
* ** * *
29082 TAGTAGCCTGCACGTAGTACTACACACGTGATCACAGTTTTCAGGTACGCATAGTAGCCTGTACT
1 TAGTAGCCTGCACGTAGTACTACACACGTGA-C-CAATAGTCAGGTACACATAGTAGCCTGCACT
*
29147 TAGTACTACACATGCCACCTCAC
64 TAGTACTACACACGCCACCTCAC
29170 AATAGATCAT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 29 0.40
100 1 0.01
101 43 0.59
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACGTAGTACTACACACGTGACCAATAGTCAGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCCACCTCACCATCTAATACACG
Done.