Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold978
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: 28469
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:746 original size:36 final size:36
Alignment explanation
Indices: 699--821 Score: 108
Period size: 36 Copynumber: 3.5 Consensus size: 36
689 TTGGTTATCT
* *
699 GACTAGAGCTGGGCTCAATAATTTGTCGATTCGTTC
1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
* * * * *
735 GACTAGTGCTGGGCAGAACT-A-TCGTCGGTT-ATCC
1 GACTAGTGCTGGGCACAA-TAATTTGTCGATTCGTTC
** * * *
769 GGTTAGTGCTGAGCACAATAATTTTTCAATTCGTTC
1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
805 GACTAGTGCTGGGCACA
1 GACTAGTGCTGGGCACA
822 CCAATGATTT
Statistics
Matches: 63, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
33 1 0.02
34 17 0.27
35 12 0.19
36 32 0.51
37 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (36 bp):
GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC
Found at i:5314 original size:18 final size:18
Alignment explanation
Indices: 5286--5338 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
5276 TTGGCCAATT
*
5286 CAGTAACAGTAAACAGTG
1 CAGTAATAGTAAACAGTG
*
5304 TAGTAATAGTAAACAGTG
1 CAGTAATAGTAAACAGTG
5322 CAGT-ATCAGTAAACAGT
1 CAGTAAT-AGTAAACAGT
5339 ATGCAAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (18 bp):
CAGTAATAGTAAACAGTG
Found at i:9802 original size:24 final size:24
Alignment explanation
Indices: 9774--9825 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9764 CCCATTTTTT
*
9774 CCTCCCCTAATCTCTCCTAAAATC
1 CCTCCCCAAATCTCTCCTAAAATC
* * *
9798 CCTCCTCAAATCTCTCTTCAAATC
1 CCTCCCCAAATCTCTCCTAAAATC
9822 CCTC
1 CCTC
9826 AACTGATCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (24 bp):
CCTCCCCAAATCTCTCCTAAAATC
Found at i:9818 original size:12 final size:12
Alignment explanation
Indices: 9782--9821 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9772 TTCCTCCCCT
*
9782 AATCTCTCCTAA
1 AATCTCTCCTCA
*
9794 AATCCCTCCTCA
1 AATCTCTCCTCA
*
9806 AATCTCTCTTCA
1 AATCTCTCCTCA
9818 AATC
1 AATC
9822 CCTCAACTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.33
Consensus pattern (12 bp):
AATCTCTCCTCA
Found at i:13950 original size:13 final size:13
Alignment explanation
Indices: 13934--13967 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
13924 CACACGACCA
*
13934 TGTAACACAGCCG
1 TGTAACACAACCG
13947 TGTAACACAACCG
1 TGTAACACAACCG
13960 TGTAACAC
1 TGTAACAC
13968 GCCCATGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (13 bp):
TGTAACACAACCG
Found at i:16571 original size:46 final size:46
Alignment explanation
Indices: 16518--16654 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
16508 TATATATACG
* * * *
16518 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
16564 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
* * *
16610 TAACTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
16655 ATACATGTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:16688 original size:47 final size:47
Alignment explanation
Indices: 16628--16848 Score: 370
Period size: 47 Copynumber: 4.7 Consensus size: 47
16618 ACACATTTCG
* * * **
16628 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* *
16675 CATTGGCCATTCGGCCTTATCTCATATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
16722 CATTGGCCATTCGGCCTTAGCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
16769 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
16816 CATTGGCCATTCGGCCTTATCACACATACGCAT
1 CATTGGCCATTCGGCCTTATCACACATACGCAT
16849 CACCCAAACA
Statistics
Matches: 165, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 165 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:16771 original size:23 final size:23
Alignment explanation
Indices: 16744--16818 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
16734 GGCCTTAGCA
16744 CACATACGCATGTTCACATTCAT
1 CACATACGCATGTTCACATTCAT
** * *
16767 CACATTGGCCA--TTCGGCCTT-AT
1 CACATACG-CATGTTC-ACATTCAT
16789 CACACATACGCATGTTCACATTCAT
1 --CACATACGCATGTTCACATTCAT
16814 CACAT
1 CACAT
16819 TGGCCATTCG
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 16 0.43
24 11 0.30
25 5 0.14
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29
Consensus pattern (23 bp):
CACATACGCATGTTCACATTCAT
Found at i:20483 original size:38 final size:39
Alignment explanation
Indices: 20381--20602 Score: 256
Period size: 40 Copynumber: 5.6 Consensus size: 39
20371 TTGAATGATG
* * *
20381 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAA
*
20421 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
20461 TCCGGACTAAG-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
*
20499 TCCGGGCTAAGT-CGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
20537 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTA-AA
*
20578 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
20603 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
38 71 0.43
40 80 0.49
41 12 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:20567 original size:78 final size:79
Alignment explanation
Indices: 20381--20602 Score: 276
Period size: 78 Copynumber: 2.8 Consensus size: 79
20371 TTGAATGATG
* * *
20381 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATATCCGGGCTAAG-TCCGAAGGCAT
20444 TTGTGCGAGATACTAAA
63 TTGTGCGAGATACTAAA
*
20461 TCCGGACTAAG--CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGT-CGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA-TCCGGGCTAAGTCCGAAGGCATTT
*
20522 GTGCGAGTTACTAAA
65 GTGCGAGATACTAAA
* * * *
20537 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGT-CCGAAGGCATTT
20602 G
65 G
20603 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
76 34 0.27
77 2 0.02
78 55 0.44
79 10 0.08
80 23 0.19
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:26534 original size:39 final size:38
Alignment explanation
Indices: 26434--26643 Score: 169
Period size: 39 Copynumber: 5.4 Consensus size: 38
26424 GAGAGAGATC
* * * *
26434 CTTCGGGACATAGCCCGGTTATAGTAATTCGCAC-ACTG
1 CTTCGGGACTTAGCCCGATT-TAGTAACTCGCACAAATG
* *
26472 CTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG
1 CTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATG
* * *
26510 CCTTCGGGACTTAGCCCGAATTAGTATCTCACAC-AATG
1 -CTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATG
* *
26548 CCTTC-GGATCTTAGTCCGGATTTAGTATCTCGCACAAATG
1 -CTTCGGGA-CTTAG-CCCGATTTAGTAACTCGCACAAATG
* * * * *
26588 CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CTTCGGGA-CTTAG-CCCGATTTAGTAAC-TCGCACAAATG
26627 CTTCGGGACTTAGCCCG
1 CTTCGGGACTTAGCCCG
26644 GACATCATCA
Statistics
Matches: 145, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
37 15 0.10
38 36 0.25
39 79 0.54
40 15 0.10
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (38 bp):
CTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATG
Found at i:26631 original size:78 final size:78
Alignment explanation
Indices: 26472--26645 Score: 189
Period size: 78 Copynumber: 2.2 Consensus size: 78
26462 TCGCACACTG
*
26472 CTTCGGGACTTA-ACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTAGTA
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTAGTA
*
26536 TCTCACACAATGC
66 TCTCACACAAAGC
* * * * *
26549 CTTC-GGATCTTAGTCCGGATTTAGTATCTCGCACAAATG-CTTC-GGATCTTAGTCCGGATATG
1 CTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGAAT-TA
*
26611 GTCA-CTTAGCACAAAG-
63 GT-ATCTCA-CACAAAGC
26627 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
26646 CATCATCAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
76 6 0.07
77 22 0.27
78 44 0.54
79 10 0.12
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (78 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATTAGTA
TCTCACACAAAGC
Done.