Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3682
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: 33324
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:861 original size:48 final size:48
Alignment explanation
Indices: 790--1204 Score: 679
Period size: 48 Copynumber: 8.9 Consensus size: 48
780 CAAGATAAAT
* *
790 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
838 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATAT-AG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
883 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
*
931 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
*
979 ATATGTATATGTGGTAAAG-CGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
1026 ATATGTATATGTGGTAAAGCCAAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1074 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
*
1120 ATATGTATATGTGGTAAAGCCGAAT-GCTAATGTG-AATATGTA-GAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
* *
1165 ATATGTATATGTGGTAAA-TCGAATGGCTAGTGTGAAATAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
1205 GAAGGAGATG
Statistics
Matches: 351, Mismatches: 9, Indels: 16
0.93 0.02 0.04
Matches are distributed among these distances:
44 5 0.01
45 77 0.22
46 50 0.14
47 57 0.16
48 162 0.46
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
Found at i:1064 original size:95 final size:96
Alignment explanation
Indices: 790--1204 Score: 706
Period size: 95 Copynumber: 4.4 Consensus size: 96
780 CAAGATAAAT
* *
790 ATATATATGTGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
855 AGCCGAATGGCTAATGTGAAATA--TAT-AG
66 AGCCGAATGGCTAATGTGAAATATGTATGAG
883 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
948 AGCCGAATGGCTAATGTGAAATATGTATGAG
66 AGCCGAATGGCTAATGTGAAATATGTATGAG
*
979 ATATGTATATGTGGTAAAG-CGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
*
1043 AGCCAAATGGCTAATGTGAAATATGTATGAG
66 AGCCGAATGGCTAATGTGAAATATGTATGAG
1074 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
1137 AGCCGAAT-GCTAATGTG-AATATGTA-GAG
66 AGCCGAATGGCTAATGTGAAATATGTATGAG
* *
1165 ATATGTATATGTGGTAAA-TCGAATGGCTAGTGTGAAATAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
1205 GAAGGAGATG
Statistics
Matches: 308, Mismatches: 8, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
90 14 0.05
91 23 0.07
92 10 0.03
93 95 0.31
94 32 0.10
95 98 0.32
96 36 0.12
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (96 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:1452 original size:37 final size:37
Alignment explanation
Indices: 1353--1454 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
1343 GGAAATATAT
*
1353 TCCGGGTAAGA-CCGATGACTACGTGCGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
1389 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
1426 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
1455 GGACTATTCG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 11 0.18
37 51 0.82
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:6727 original size:46 final size:44
Alignment explanation
Indices: 6615--6786 Score: 170
Period size: 44 Copynumber: 3.8 Consensus size: 44
6605 AACCCGCCCC
* * * * *
6615 TAAGTGAACTCGGACTCAACTCAAC-AGCTCAGGCTTCGCATCCA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTC-GGATGCGCATACA
*
6659 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACA
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCGC-A--TACA
* * * *
6705 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
1 -TAAGCGAACTCGGACTCAACTCAACGAGTTCG-GATGCGCATACA
*
6750 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
6787 TCAACCATCC
Statistics
Matches: 107, Mismatches: 13, Indels: 16
0.79 0.10 0.12
Matches are distributed among these distances:
43 1 0.01
44 35 0.33
45 34 0.32
46 30 0.28
47 6 0.06
48 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
TAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCGCATACA
Found at i:6774 original size:45 final size:44
Alignment explanation
Indices: 6615--6781 Score: 189
Period size: 45 Copynumber: 3.7 Consensus size: 44
6605 AACCCGCCCC
*
6615 TAAGTGAACTCGGACTCAACTCAAC-AGCTCAGGC-TTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--GCATTCGCATCCA
* * *
6659 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCGC-A--TCCA
* *
6705 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCG-CATTCGCATCCA
6750 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
6782 GATGCTCAAC
Statistics
Matches: 103, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
43 2 0.02
44 30 0.29
45 34 0.33
46 30 0.29
47 6 0.06
48 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (44 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCGCATCCA
Found at i:6774 original size:91 final size:90
Alignment explanation
Indices: 6620--6786 Score: 291
Period size: 91 Copynumber: 1.8 Consensus size: 90
6610 GCCCCTAAGT
*
6620 GAACTCGGACTCAACTCAACAGCTCAGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACAGCTCAGACTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
6685 AGTTCGGATGCCTAGTTACATTCAC
66 AGTTCGGATGCCTAGTTACATTCAC
*
6710 GAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAC-AGCTCAGAC-TTCGCATCCATAAGTGAACTCGGACTCAACTCAA
6774 CGAGTTCGGATGC
64 CGAGTTCGGATGC
6787 TCAACCATCC
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
90 22 0.30
91 51 0.70
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (90 bp):
GAACTCGGACTCAACTCAACAGCTCAGACTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATTCAC
Found at i:13735 original size:46 final size:46
Alignment explanation
Indices: 13668--13793 Score: 182
Period size: 46 Copynumber: 2.7 Consensus size: 46
13658 AACCCGCCCC
***
13668 TAAGTGAACTCGGACTCAACTCAACGAGCT-GAGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCG-GACATTCGCATCCA
*
13714 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
* *
13760 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
13794 TGCTCAACCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 73 0.99
47 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCA
Found at i:18712 original size:13 final size:13
Alignment explanation
Indices: 18694--18718 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18684 GTATTGATCA
18694 TGTGTTCACACCT
1 TGTGTTCACACCT
18707 TGTGTTCACACC
1 TGTGTTCACACC
18719 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:20832 original size:22 final size:22
Alignment explanation
Indices: 20802--20845 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20792 TTTGGTATTT
20802 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
20824 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
20846 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:24727 original size:24 final size:25
Alignment explanation
Indices: 24700--24748 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
24690 AGAAGTGACC
* *
24700 AAAAAAAGAAAAAAAAAGTA-AAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
*
24724 AAAAGAACAAAAAAAAAGTGAAAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
24749 TATTGCGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAAGTGAAAAG
Found at i:24738 original size:16 final size:16
Alignment explanation
Indices: 24684--24738 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
24674 AAATTCAAAA
** *
24684 AAAAAAAGAAGTGACC
1 AAAAAAAGAAAAGAAC
24700 AAAAAAAGAAAA-AA-
1 AAAAAAAGAAAAGAAC
24714 AAAGTAAAAGAAAAGAAC
1 AAA--AAAAGAAAAGAAC
24732 AAAAAAA
1 AAAAAAA
24739 AAGTGAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 23 0.72
17 2 0.06
18 3 0.09
ACGTcount: A:0.78, C:0.05, G:0.13, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAC
Found at i:27570 original size:20 final size:20
Alignment explanation
Indices: 27524--27570 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27514 AGCTTGTTTC
*
27524 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
27544 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27564 CAGCTCA
1 CAGCTCA
27571 ATCTTAACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:31326 original size:12 final size:12
Alignment explanation
Indices: 31309--31347 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
31299 AAACCGTATG
31309 CAATTTTTTTTT
1 CAATTTTTTTTT
31321 CAATTTTTTTTT
1 CAATTTTTTTTT
31333 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
31348 ACGTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.54
13 2 0.08
14 1 0.04
15 8 0.33
ACGTcount: A:0.15, C:0.13, G:0.03, T:0.69
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:31675 original size:22 final size:22
Alignment explanation
Indices: 31645--31688 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31635 TTTGGTATTT
31645 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
31667 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
31689 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Done.