Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1738
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: 20326
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:3493 original size:9 final size:9
Alignment explanation
Indices: 3481--3527 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
3471 TTTATTTTAA
*
3481 TTTTAGATT
1 TTTTAAATT
* *
3490 TTTTTATTT
1 TTTTAAATT
3499 TTTTTAAATT
1 -TTTTAAATT
3509 TTTTAAATT
1 TTTTAAATT
3518 TTTT-AATT
1 TTTTAAATT
3526 TT
1 TT
3528 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
8 6 0.19
9 19 0.59
10 7 0.22
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTAAATT
Found at i:3498 original size:27 final size:26
Alignment explanation
Indices: 3460--3510 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
3450 ATTTTTTATT
*
3460 ATTTTATTATTTTTATTTTAATTTTAG
1 ATTTTATTATTTTT-TTTAAATTTTAG
*
3487 ATTTTTTTATTTTTTTTAAATTTT
1 ATTTTATTATTTTTTTTAAATTTT
3511 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (26 bp):
ATTTTATTATTTTTTTTAAATTTTAG
Found at i:3503 original size:19 final size:20
Alignment explanation
Indices: 3469--3512 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3459 TATTTTATTA
*
3469 TTTTTATTTTAATTTTAGATT
1 TTTTTATTTT-ATTTTAAATT
3490 TTTTTATTTT-TTTTAAATT
1 TTTTTATTTTATTTTAAATT
3509 TTTT
1 TTTT
3513 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
21 10 0.45
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTATTTTAAATT
Found at i:3511 original size:27 final size:28
Alignment explanation
Indices: 3460--3527 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
3450 ATTTTTTATT
* * *
3460 ATTTTATTATTTTTATTTTAA-TTTTAG
1 ATTTTTTTATTTTTATTTAAATTTTTAA
3487 ATTTTTTTATTTTT-TTTAAATTTTTTAA
1 ATTTTTTTATTTTTATTTAAA-TTTTTAA
*
3515 ATTTTTTAATTTT
1 ATTTTTTTATTTT
3528 ATATAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.14
27 13 0.37
28 17 0.49
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (28 bp):
ATTTTTTTATTTTTATTTAAATTTTTAA
Found at i:3534 original size:28 final size:28
Alignment explanation
Indices: 3481--3534 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3471 TTTATTTTAA
* * * *
3481 TTTTAGATTTTTTTATTTTTTTTAAATT
1 TTTTAAATTTTTTAATTTTATATAAATT
3509 TTTTAAATTTTTTAATTTTATATAAA
1 TTTTAAATTTTTTAATTTTATATAAA
3535 AAAAGAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTAAATTTTTTAATTTTATATAAATT
Found at i:9496 original size:82 final size:83
Alignment explanation
Indices: 9310--9659 Score: 380
Period size: 82 Copynumber: 4.3 Consensus size: 83
9300 AAAACATCAA
* *
9310 GAGGGGATACTCCAACC-CTATTTTTAC-TCCCAAAACATCAAAATTTTCATC-TTATGGGATAC
1 GAGGGGATACTCCAACCTCTATTTTTACTTCTCAAAACATCAAAATTTTCATCTTTAGGGGATAC
*
9372 TCTAACCCCACTATTTTC
66 TCTAACCCCACCATTTTC
* * * *
9390 GAAGGGATACTCCAA-CTCTATTTTTACTTCTC-AAACATTAAATTTCTTCATCTTTGGGGGATA
1 GAGGGGATACTCCAACCTCTATTTTTACTTCTCAAAACATCAAAATT-TTCATCTTTAGGGGATA
* *
9453 CTCCAACCTCACCATTTTC
65 CTCTAACCCCACCATTTTC
* * * *
9472 GAGGGGATACTCAAACCTCT-TTTTTATTTTTTAAAAACATCAAAATTTTCATC-TTAGGGGATA
1 GAGGGGATACTCCAACCTCTATTTTTA-CTTCTCAAAACATCAAAATTTTCATCTTTAGGGGATA
* * *
9535 TTCAAACCCCATCA-TTTC
65 CTCTAACCCCACCATTTTC
* * ** * * *
9553 TAAAGGGATACTCCAA-CTCCGTTTTTATTTTTCAAAACATCAAAATTTTCAT-TTCAGGGGATA
1 -GAGGGGATACTCCAACCTCTATTTTTACTTCTCAAAACATCAAAATTTTCATCTTTAGGGGATA
9616 CTCTAACCCCACCATTTTC
65 CTCTAACCCCACCATTTTC
9635 GAGGGGATACTCCAACC-CTGATTTT
1 GAGGGGATACTCCAACCTCT-ATTTT
9660 CACCAAAAAA
Statistics
Matches: 223, Mismatches: 34, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
79 1 0.00
80 35 0.16
81 74 0.33
82 89 0.40
83 13 0.06
84 11 0.05
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (83 bp):
GAGGGGATACTCCAACCTCTATTTTTACTTCTCAAAACATCAAAATTTTCATCTTTAGGGGATAC
TCTAACCCCACCATTTTC
Found at i:9517 original size:164 final size:163
Alignment explanation
Indices: 9341--9651 Score: 430
Period size: 164 Copynumber: 1.9 Consensus size: 163
9331 TTTTACTCCC
* * *
9341 AAAACATCAAAATTTTCATCTTATGGGATACTCTAACCCCA-CTATTT-TCGAAGGGATACTCCA
1 AAAACATCAAAATTTTCATCTTAGGGGATACTCAAACCCCATC-ATTTCT-AAAGGGATACTCCA
* * * ** *
9404 ACTCTATTTTTACTTCTC-AAACATTAAATTTCTTCATCTTTGGGGGATACTCCAACCTCACCAT
64 ACTCCATTTTTACTTCTCAAAACATCAAAATT-TTCAT-TTCAGGGGATACTCCAACCCCACCAT
9468 TTTCGAGGGGATACTCAAACCTCTTTTTTATTTTTTA
127 TTTCGAGGGGATACTCAAACCTCTTTTTTATTTTTTA
*
9505 AAAACATCAAAATTTTCATCTTAGGGGATATTCAAACCCCATCATTTCTAAAGGGATACTCCAAC
1 AAAACATCAAAATTTTCATCTTAGGGGATACTCAAACCCCATCATTTCTAAAGGGATACTCCAAC
* * * *
9570 TCCGTTTTTATTTTTCAAAACATCAAAATTTTCATTTCAGGGGATACTCTAACCCCACCATTTTC
66 TCCATTTTTACTTCTCAAAACATCAAAATTTTCATTTCAGGGGATACTCCAACCCCACCATTTTC
*
9635 GAGGGGATACTCCAACC
131 GAGGGGATACTCAAACC
9652 CTGATTTTCA
Statistics
Matches: 129, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
163 42 0.33
164 74 0.57
165 13 0.10
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (163 bp):
AAAACATCAAAATTTTCATCTTAGGGGATACTCAAACCCCATCATTTCTAAAGGGATACTCCAAC
TCCATTTTTACTTCTCAAAACATCAAAATTTTCATTTCAGGGGATACTCCAACCCCACCATTTTC
GAGGGGATACTCAAACCTCTTTTTTATTTTTTA
Found at i:12518 original size:102 final size:102
Alignment explanation
Indices: 12337--12669 Score: 357
Period size: 102 Copynumber: 3.3 Consensus size: 102
12327 TTGTAGTTGG
* *** * *
12337 AAAGGCAGGGTTGGAGTATCCTTGTGGGTGA-TGAATAATTTTGACAAAGGAAATA-TTCAAATC
1 AAAGGCGGGGTTGGAGTATCCCCATGGATGACT-AATGATTTTGACAAAGGAAA-AGTTCAAATC
* *
12400 TTAATAAATTTTGAAGAGCAGGGTTGGAGTATCCCCTCA
64 TTGACAAATTTTGAAGAGCAGGGTTGGAGTATCCCCTCA
* * *
12439 AAAGGCCGGGTTGGAGTATCCCCATGGATGACTAATGATTTTGATAAAGGAAAAGTTCAAATTTT
1 AAAGGCGGGGTTGGAGTATCCCCATGGATGACTAATGATTTTGACAAAGGAAAAGTTCAAATCTT
* * * *
12504 GACAAATTTGGAAGAGC-GACGTTGGAATATCCCTTCGA
66 GACAAATTTTGAAGAGCAG-GGTTGGAGTATCCCCTC-A
* * * * *
12542 AATGTCGGGGTTGGAGTATCCCCATGGATGACCAATGATTTTGACAAAAGAAATGTTCAAATCTT
1 AAAGGCGGGGTTGGAGTATCCCCATGGATGACTAATGATTTTGACAAAGGAAAAGTTCAAATCTT
* * ** * *
12607 GACATATTTTGAAGAGCAAGGTCAGAGTATTCCCTCG
66 GACAAATTTTGAAGAGCAGGGTTGGAGTATCCCCTCA
* *
12644 GAAGGTGGGGTTGGAGTATCCCCATG
1 AAAGGCGGGGTTGGAGTATCCCCATG
12670 AATAAAAATT
Statistics
Matches: 190, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
101 2 0.01
102 103 0.54
103 85 0.45
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (102 bp):
AAAGGCGGGGTTGGAGTATCCCCATGGATGACTAATGATTTTGACAAAGGAAAAGTTCAAATCTT
GACAAATTTTGAAGAGCAGGGTTGGAGTATCCCCTCA
Found at i:12600 original size:103 final size:101
Alignment explanation
Indices: 12374--12669 Score: 353
Period size: 103 Copynumber: 2.9 Consensus size: 101
12364 GTGATGAATA
* * *
12374 ATTTTGACAAAGGAAATATTCAAATCTTAATAAATTTTGAAGAGCAGGGTTGGAGTATCCCCTC-
1 ATTTTGACAAAGGAAATGTTCAAATCTTGACAAATTTTGAAGAGCA-GGTTGGAGTAT-CCCTCG
* * *
12438 AAAAGGCCGGGTTGGAGTATCCCCATGGATGACTAATG
64 AAAAGTCGGGGTTGGAGTATCCCCATGGATGACCAATG
* * * * * *
12476 ATTTTGATAAAGGAAAAGTTCAAATTTTGACAAATTTGGAAGAGCGACGTTGGAATATCCCTTCG
1 ATTTTGACAAAGGAAATGTTCAAATCTTGACAAATTTTGAAGAGC-AGGTTGGAGTATCCC-TCG
*
12541 AAATGTCGGGGTTGGAGTATCCCCATGGATGACCAATG
64 AAAAGTCGGGGTTGGAGTATCCCCATGGATGACCAATG
* * **
12579 ATTTTGACAAAAGAAATGTTCAAATCTTGACATATTTTGAAGAGCAAGGTCAGAGTATTCCCTCG
1 ATTTTGACAAAGGAAATGTTCAAATCTTGACAAATTTTGAAGAGC-AGGTTGGAGTA-TCCCTCG
* *
12644 GAAGGT-GGGGTTGGAGTATCCCCATG
64 AAAAGTCGGGGTTGGAGTATCCCCATG
12670 AATAAAAATT
Statistics
Matches: 164, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
101 3 0.02
102 69 0.42
103 88 0.54
104 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (101 bp):
ATTTTGACAAAGGAAATGTTCAAATCTTGACAAATTTTGAAGAGCAGGTTGGAGTATCCCTCGAA
AAGTCGGGGTTGGAGTATCCCCATGGATGACCAATG
Found at i:14138 original size:13 final size:13
Alignment explanation
Indices: 14122--14152 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14112 GCAATTCATC
14122 ATGTATCGATACA
1 ATGTATCGATACA
14135 ATGTATCGATACA
1 ATGTATCGATACA
*
14148 TTGTA
1 ATGTA
14153 CCATGTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14251 original size:19 final size:19
Alignment explanation
Indices: 14197--14251 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
14187 CTGCCAATCT
**
14197 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
14217 CATG-ATCGATACAATGAA
1 CATGTATCGATACAATGAA
14235 CATGTATCGATACAATG
1 CATGTATCGATACAATG
14252 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 6 0.19
19 22 0.69
20 4 0.12
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:14254 original size:13 final size:13
Alignment explanation
Indices: 14236--14262 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14226 TACAATGAAC
14236 ATGTATCGATACA
1 ATGTATCGATACA
14249 ATGTATCGATACA
1 ATGTATCGATACA
14262 A
1 A
14263 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14868 original size:21 final size:21
Alignment explanation
Indices: 14806--14857 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
14796 AGTTTTCGTT
* *
14806 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCTTTAA-TAAAAAA
14828 TTTCTCCCCTTTAATAAAAAA
1 TTTCTCCCCTTTAATAAAAAA
14849 TTTCTCCCC
1 TTTCTCCCC
14858 GTTTGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.29, C:0.31, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTCTCCCCTTTAATAAAAAA
Done.