Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold730
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: 45321
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:1634 original size:28 final size:27
Alignment explanation
Indices: 1564--1634 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1554 TCGATATTTT
**
1564 GCACACTAAGTGTCATTCTCAATACTC
1 GCACACTAAGTACCATTCTCAATACTC
* *
1591 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTACCATTCTCAATA-CTC
* *
1619 GTACACTGAGTACCAT
1 GCACACTAAGTACCAT
1635 ATTTGATTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (27 bp):
GCACACTAAGTACCATTCTCAATACTC
Found at i:6602 original size:57 final size:57
Alignment explanation
Indices: 6538--6839 Score: 424
Period size: 57 Copynumber: 5.3 Consensus size: 57
6528 TGATCTCATT
** * * * *
6538 TCACACACTTAGTGCCCCAACAACCGATCTTGCACATACAGTGCTTGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * *
6595 TCACACACACAGTGCCTCAACAACTGATCTTGCACACACAGTGCTCGGTTACGAAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * * * *
6652 TCGCACACACAGTACCTCAACAACCGATCGCGCACACACAGTGTTTGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* *
6709 TCGCACACACAGTGCCTCAACAACCGATCTCGCACACAAAGTGCTCGGTTACGGAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
* * * *
6766 TCGCACACACAGTGCCTCAACAACCGGTCTCACACACACAGTGCTCGGTTACGAAAC
1 TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
6823 TCACACACACAGTGCCT
1 TCACACACACAGTGCCT
6840 ATGTTCACTT
Statistics
Matches: 220, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 220 1.00
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.18
Consensus pattern (57 bp):
TCACACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAAC
Found at i:6633 original size:29 final size:29
Alignment explanation
Indices: 6598--6809 Score: 153
Period size: 29 Copynumber: 7.4 Consensus size: 29
6588 ACGGAACTCA
* *
6598 CACACACAGTGCCTCAACAACTGATCTTG
1 CACACACAGTGCCTCAACAACCGATCTCG
**** *
6627 CACACACAGTG-CTCGGTTA-CGAAACTCG
1 CACACACAGTGCCTCAACAACCG-ATCTCG
* *
6655 CACACACAGTACCTCAACAACCGATCGCG
1 CACACACAGTGCCTCAACAACCGATCTCG
* ***** * *
6684 CACACACAGTG-TTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
6712 CACACACAGTGCCTCAACAACCGATCTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
* **** * *
6741 CACACAAAGTG-CTCGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCG
* *
6769 CACACACAGTGCCTCAACAACCGGTCTCA
1 CACACACAGTGCCTCAACAACCGATCTCG
6798 CACACACAGTGC
1 CACACACAGTGC
6810 TCGGTTACGA
Statistics
Matches: 130, Mismatches: 48, Indels: 10
0.69 0.26 0.05
Matches are distributed among these distances:
27 1 0.01
28 58 0.45
29 69 0.53
30 2 0.02
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (29 bp):
CACACACAGTGCCTCAACAACCGATCTCG
Found at i:8829 original size:26 final size:26
Alignment explanation
Indices: 8800--8859 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
8790 TCCCTTTGAA
* * *
8800 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATAGTTCGCACACTAAGTG
8826 TCATTCTCAATAGTTCGCACACTAAGTG
1 TCA-T-TCAATAGTTCGCACACTAAGTG
*
8854 CCATTC
1 TCATTC
8860 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (26 bp):
TCATTCAATAGTTCGCACACTAAGTG
Found at i:8847 original size:28 final size:28
Alignment explanation
Indices: 8814--8885 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
8804 TCGATATTTT
*
8814 GCACACTAAGTGTCATTCTCAATAGTTC
1 GCACACTAAGTGCCATTCTCAATAGTTC
*
8842 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATAGTTC
* * *
8870 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
8886 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATAGTTC
Found at i:13838 original size:29 final size:29
Alignment explanation
Indices: 13753--13843 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 29
13743 TACTTGTATC
* * * *
13753 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCAATTAGGCCCAAATCACATTTATA
* * *
13781 TGGCCAATTAGGCCCAAGTCACCTATATA
1 TGGCCAATTAGGCCCAAATCACATTTATA
* *
13810 GGGCCTATTAGGCCCAAATCACATTTATA
1 TGGCCAATTAGGCCCAAATCACATTTATA
13839 TGGCC
1 TGGCC
13844 CGATAGGCCC
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
28 13 0.27
29 36 0.73
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (29 bp):
TGGCCAATTAGGCCCAAATCACATTTATA
Found at i:27364 original size:25 final size:25
Alignment explanation
Indices: 27336--27383 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27326 TTATAATATG
* * *
27336 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
27361 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
27384 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:27446 original size:11 final size:11
Alignment explanation
Indices: 27430--27467 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
27420 ACACGATTGG
27430 ACATGATATGC
1 ACATGATATGC
27441 ACATGATATG-
1 ACATGATATGC
*
27451 -TATGATATGC
1 ACATGATATGC
27461 ACATGAT
1 ACATGAT
27468 GTATTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (11 bp):
ACATGATATGC
Found at i:27553 original size:24 final size:25
Alignment explanation
Indices: 27515--27584 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
27505 GAGGAAGTGC
* *
27515 AAAAGGGTTTTTGCCCCAGTTTACCG
1 AAAAGGG-CTTTGCCCCAGTTTACCA
* *
27541 AAAA-GGCTTTGCCCCAATTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
27565 AAAAGGGCTTTGGCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
27585 ATTAAAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 18 0.49
25 15 0.41
26 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:27586 original size:24 final size:24
Alignment explanation
Indices: 27524--27597 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
27514 CAAAAGGGTT
* *
27524 TTTGCCCC-AGTTTACCGAAAAGGC
1 TTTGCCCCAAG-TTATCAAAAAGGC
*
27548 TTTGCCCCAATTTATCAAAAAGGGC
1 TTTGCCCCAAGTTATCAAAAA-GGC
* *
27573 TTTGGCCC-AGTTATTAAAAGAGGC
1 TTTGCCCCAAGTTATCAAAA-AGGC
27597 T
1 T
27598 AGGCCTCCAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
24 29 0.71
25 12 0.29
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (24 bp):
TTTGCCCCAAGTTATCAAAAAGGC
Found at i:27870 original size:31 final size:30
Alignment explanation
Indices: 27803--27872 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
27793 ACCGTTTACA
* *
27803 GTAAAGGCTTCGGCCCAGTGATATGATAAT
1 GTAAAGGCTTCAGCCCAGTGACATGATAAT
* *
27833 GAAAAGGCTTCAGCCTAGTGACATGAATAAT
1 GTAAAGGCTTCAGCCCAGTGACATG-ATAAT
27864 GTAAAGGCT
1 GTAAAGGCT
27873 GATATTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 21 0.62
31 13 0.38
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (30 bp):
GTAAAGGCTTCAGCCCAGTGACATGATAAT
Found at i:31100 original size:38 final size:39
Alignment explanation
Indices: 31058--31287 Score: 226
Period size: 38 Copynumber: 6.2 Consensus size: 39
31048 TTGCGAATAA
* *
31058 CCGGGCTAAGTCCCGAA-GCATTTGTGCTAGTGCTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATA-T
*
31096 CCGGGCTAAGT-CCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
31135 CCGGGCTAAGT---G--GGCATTTG-GC-A-T--TATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
*
31164 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
*
31202 CCGGGCTAAGTCCCGAAGGCA-TTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
31241 CCGGGCT-AGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATAT
31280 CC-GGCTAA
1 CCGGGCTAA
31288 ACTCCGAAGG
Statistics
Matches: 165, Mismatches: 9, Indels: 35
0.79 0.04 0.17
Matches are distributed among these distances:
29 16 0.10
31 1 0.01
32 1 0.01
33 4 0.02
34 8 0.05
35 8 0.05
37 7 0.04
38 76 0.46
39 43 0.26
40 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:31243 original size:106 final size:106
Alignment explanation
Indices: 31058--31248 Score: 287
Period size: 106 Copynumber: 1.8 Consensus size: 106
31048 TTGCGAATAA
* * *
31058 CCGGGCTAAGTCCCGAAGCATTTGTGCTAGTGCTAATTCCGGGCTAAGTCCGAAGGCATTCGTGC
1 CCGGGCTAAGTCCCGAAGCATTTGTGCGAGTGATAATACCGGGCTAAGTCCGAAGGCATTCGTGC
*
31123 GAGCTACTATATCCGGGCTAAGTGGGCATTTGGCATTATAT
66 AAGCTACTATATCCGGGCTAAGTGGGCATTTGGCATTATAT
* *
31164 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTATTATACCGGGCTAAGTCCCGAAGGCATT-GT
1 CCGGGCTAAGTCCCGAA-GCATTTGTGCGAGTGATAATACCGGGCTAAGT-CCGAAGGCATTCGT
*
31227 GCAAGTTACTATATCCGGGCTA
64 GCAAGCTACTATATCCGGGCTA
31249 GTCCCGAAGG
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
106 62 0.82
107 14 0.18
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (106 bp):
CCGGGCTAAGTCCCGAAGCATTTGTGCGAGTGATAATACCGGGCTAAGTCCGAAGGCATTCGTGC
AAGCTACTATATCCGGGCTAAGTGGGCATTTGGCATTATAT
Found at i:39216 original size:75 final size:75
Alignment explanation
Indices: 39053--39266 Score: 251
Period size: 75 Copynumber: 2.9 Consensus size: 75
39043 TGTTCGGATG
*
39053 ATAACCGGGCTAAGTCCCGAA-GCATTTGTGCTAGTGCTA-AT-TCCGGGCTAAGT-CCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGC-TTTGTGC--GAGCTATATATCCGGGCTAAGTCCCGAAGGC
*
39114 ATTCGTGTGAGCT
63 ATTCGTGCGAGCT
* * *
39127 AT-ATCAGGCTAAGTCCCGAAGGCTTTGTACGAGCTATTATATCCGGGCTAAGTCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCTTTGTGCGAGCTA-TATATCCGGGCTAAGTCCCGAAGGCAT
*
39191 T-GTGCGAGTT
65 TCGTGCGAGCT
* * * *
39201 ATAACCGGGCTAAGTCCCGAAGGCATTGTGCAAGTTACTATAACCGGGCTAAGTCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCTTTGTGCGAGCTA-TATATCCGGGCTAAGTCCCGAAGGCAT
39266 T
65 T
39267 TGAGCTAGTG
Statistics
Matches: 120, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
71 5 0.04
73 24 0.20
74 25 0.21
75 66 0.55
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (75 bp):
ATAACCGGGCTAAGTCCCGAAGGCTTTGTGCGAGCTATATATCCGGGCTAAGTCCCGAAGGCATT
CGTGCGAGCT
Found at i:39290 original size:39 final size:38
Alignment explanation
Indices: 39057--39291 Score: 227
Period size: 39 Copynumber: 6.2 Consensus size: 38
39047 CGGATGATAA
39057 CCGGGCTAAGTCCCGAA-GCATTTGTGCTAGTGCTA-ATT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGTGCTATA-T
*
39095 CCGGGCTAAGT-CCGAAGGCATTCGTG-T-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATT-GTGCTAGTGCTATAT
* * * * **
39131 -CAGGCTAAGTCCCGAAGGCTTTGTACGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCTAG-TGCTATAT
* *
39169 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGT--TATAA
1 CCGGGCTAAGTCCCGAAGGCATTGTGCTAGTGCTATAT
* * *
39205 CCGGGCTAAGTCCCGAAGGCATTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTGTGCTAG-TGCTATAT
*
39244 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCTAGT-GCTATAT
39284 CC-GGCTAA
1 CCGGGCTAA
39292 ACTCCGAAGG
Statistics
Matches: 167, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
35 11 0.07
36 49 0.29
37 11 0.07
38 23 0.14
39 59 0.35
40 14 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCTAGTGCTATAT
Done.