Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1734
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: 26728
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1355 original size:46 final size:46
Alignment explanation
Indices: 1303--1396 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 46
1293 TAGAATTTTG
*
1303 ATTTTTA-AAAA-TAAT-TTTAATTTATTTATATTATATAAATTTTAAA
1 ATTTTTATAAAATTAATATTTAA-TAATTT-TATTATA-AAATTTTAAA
*
1349 ATTTTTATAAAATTTAATATTTTATAATTTTATTATAAAATTTTAAA
1 ATTTTTATAAAA-TTAATATTTAATAATTTTATTATAAAATTTTAAA
1396 A
1 A
1397 AATAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 7 0.17
47 15 0.36
48 7 0.17
49 9 0.21
50 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (46 bp):
ATTTTTATAAAATTAATATTTAATAATTTTATTATAAAATTTTAAA
Found at i:1359 original size:18 final size:17
Alignment explanation
Indices: 1336--1380 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1326 ATTTATATTA
1336 TATAAATTTTAAAATTTT
1 TATAAATTTTAAAA-TTT
* *
1354 TATAAAATTTAATATTT
1 TATAAATTTTAAAATTT
1371 TAT-AATTTTA
1 TATAAATTTTA
1381 TTATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
18 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAAATTTTAAAATTT
Found at i:1373 original size:17 final size:17
Alignment explanation
Indices: 1326--1375 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1316 ATTTTAATTT
*
1326 ATTT-ATATTATATAAA
1 ATTTAATATTTTATAAA
* *
1342 TTTTAAAATTTTTATAAA
1 ATTTAATA-TTTTATAAA
1360 ATTTAATATTTTATAA
1 ATTTAATATTTTATAA
1376 TTTTATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.11
17 10 0.37
18 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATATTTTATAAA
Found at i:3682 original size:21 final size:21
Alignment explanation
Indices: 3656--3742 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 21
3646 AATAATAATT
*
3656 TATTAAAATTTTAATATTTTA
1 TATTAAAATTTTAATATTTAA
3677 TATT--AATTTTATATATTTAA
1 TATTAAAATTTTA-ATATTTAA
* * *
3697 TTTTTAAAA-TTTGATATTAAA
1 -TATTAAAATTTTAATATTTAA
* *
3718 TATTTATAATTTTAAAATTT-A
1 TA-TTAAAATTTTAATATTTAA
3739 TATT
1 TATT
3743 TGTATAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
19 7 0.14
20 10 0.20
21 22 0.43
22 10 0.20
23 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
TATTAAAATTTTAATATTTAA
Found at i:3691 original size:13 final size:13
Alignment explanation
Indices: 3665--3702 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
3655 TTATTAAAAT
3665 TTTAATATTTTATA
1 TTTAAT-TTTTATA
3679 -TTAATTTTATATA
1 TTTAATTTT-TATA
3692 TTTAATTTTTA
1 TTTAATTTTTA
3703 AAATTTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 11 0.50
14 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTAATTTTTATA
Found at i:3714 original size:34 final size:35
Alignment explanation
Indices: 3664--3729 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
3654 TTTATTAAAA
* *
3664 TTTTAATATTTTATATT-AAT-TTTATATATTTAAT
1 TTTTAAAATTTGATATTAAATATTTATA-ATTTAAT
3698 TTTTAAAATTTGATATTAAATATTTATAATTT
1 TTTTAAAATTTGATATTAAATATTTATAATTT
3730 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 15 0.54
35 7 0.25
36 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (35 bp):
TTTTAAAATTTGATATTAAATATTTATAATTTAAT
Found at i:3720 original size:28 final size:28
Alignment explanation
Indices: 3689--3742 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
3679 TTAATTTTAT
*
3689 ATATTTA-ATTTTTAAAATTTGATATTAA
1 ATATTTATAATTTTAAAATTT-ATATTAA
3717 ATATTTATAATTTTAAAATTTATATT
1 ATATTTATAATTTTAAAATTTATATT
3743 TGTATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTTATAATTTTAAAATTTATATTAA
Found at i:5437 original size:15 final size:15
Alignment explanation
Indices: 5417--5448 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5407 TTCAACCTAC
5417 TATAATAGAATAGAA
1 TATAATAGAATAGAA
*
5432 TATAATAGAATATAA
1 TATAATAGAATAGAA
5447 TA
1 TA
5449 GAATTGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
TATAATAGAATAGAA
Found at i:5438 original size:10 final size:10
Alignment explanation
Indices: 5420--5452 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5410 AACCTACTAT
*
5420 AATAGAATAG
1 AATATAATAG
5430 AATATAATAG
1 AATATAATAG
5440 AATATAATAG
1 AATATAATAG
5450 AAT
1 AAT
5453 TGATTAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (10 bp):
AATATAATAG
Found at i:8598 original size:23 final size:24
Alignment explanation
Indices: 8572--8616 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
8562 ATTTATATAA
8572 ATTAAAAATTA-TTAATTATTTTT
1 ATTAAAAATTATTTAATTATTTTT
* * *
8595 ATTATAATTTATTTATTTATTT
1 ATTAAAAATTATTTAATTATTT
8617 ATTTTGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTAAAAATTATTTAATTATTTTT
Found at i:9904 original size:103 final size:103
Alignment explanation
Indices: 9686--9894 Score: 312
Period size: 103 Copynumber: 2.0 Consensus size: 103
9676 AGGGTTATAA
* * *
9686 TATCCCTATTGATGACAAATAATTTTGACAAAGGAAAAGTTCAAATCTTGACAAATTTTGAAGAG
1 TATCCCCATGGATGACAAATAATTTTGACAAAGGAAAAGTTCAAATCTTGACAAATTTCGAAGAG
* **
9751 CGGGGTTGGAATATTCCCTTCAAAGGTCGGGGTTGGAG
66 CGGGGTTGGAATATCCCCTTCAAAGGTCAAGGTTGGAG
* * *
9789 TATCCCCATGGATGACAAATGATTTTGACAAAGGAAAAGTTC-AAGCTTTGACACATTTCGAAGA
1 TATCCCCATGGATGACAAATAATTTTGACAAAGGAAAAGTTCAAATC-TTGACAAATTTCGAAGA
*
9853 GCGGGGTTGGAATATCCCCTTGAAAGGTCAAGGTTGGAG
65 GCGGGGTTGGAATATCCCCTTCAAAGGTCAAGGTTGGAG
9892 TAT
1 TAT
9895 TTCTGTGGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 3 0.03
103 92 0.97
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (103 bp):
TATCCCCATGGATGACAAATAATTTTGACAAAGGAAAAGTTCAAATCTTGACAAATTTCGAAGAG
CGGGGTTGGAATATCCCCTTCAAAGGTCAAGGTTGGAG
Found at i:14752 original size:33 final size:32
Alignment explanation
Indices: 14715--14782 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
14705 CGTTACAAGC
**
14715 CAATGTATCAATACATTTTATGGTGTATCGATA
1 CAATGTATCAATACATACTAT-GTGTATCGATA
* *
14748 CAATGTATCGATACATACTGTGTGTATCGATA
1 CAATGTATCAATACATACTATGTGTATCGATA
14780 CAA
1 CAA
14783 GTTTAGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATACTATGTGTATCGATA
Found at i:14756 original size:13 final size:13
Alignment explanation
Indices: 14738--14762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14728 CATTTTATGG
14738 TGTATCGATACAA
1 TGTATCGATACAA
14751 TGTATCGATACA
1 TGTATCGATACA
14763 TACTGTGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:15525 original size:19 final size:19
Alignment explanation
Indices: 15501--15538 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
15491 TAACTATTTC
*
15501 TTTCTCCTCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
15520 TTTCTCCCCCTTAATCATA
1 TTTCTCCCCCTTAATCATA
15539 AAAAATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTCTCCCCCTTAATCATA
Found at i:16951 original size:21 final size:21
Alignment explanation
Indices: 16920--16971 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
16910 GCTGCTAGTG
*
16920 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGG-TGCCCGGTCGCGACC
16942 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
16962 TGGTGGGTGC
1 TGG-GGGTGC
16972 TGCCTAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 7 0.26
22 6 0.22
ACGTcount: A:0.04, C:0.27, G:0.50, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:17428 original size:13 final size:13
Alignment explanation
Indices: 17410--17448 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
17400 TATAAGCCCT
17410 TGTATCGATACAG
1 TGTATCGATACAG
*
17423 TGTATCGATACAA
1 TGTATCGATACAG
17436 TGTATCGATACAG
1 TGTATCGATACAG
17449 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:19029 original size:8 final size:8
Alignment explanation
Indices: 19016--19041 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19006 ATTTGATTAA
19016 ATTTTGTG
1 ATTTTGTG
19024 ATTTTGTG
1 ATTTTGTG
19032 ATTTTGTG
1 ATTTTGTG
19040 AT
1 AT
19042 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:19261 original size:13 final size:13
Alignment explanation
Indices: 19242--19278 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
19232 ACAGCATTCT
19242 CTGTATCGATACA
1 CTGTATCGATACA
*
19255 TTGTATCG--ACA
1 CTGTATCGATACA
19266 CTGTATCGATACA
1 CTGTATCGATACA
19279 AGGGGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:19745 original size:20 final size:21
Alignment explanation
Indices: 19713--19764 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
19703 CTCCTAGGCA
*
19713 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
19734 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
19755 GCAGCCCCCA
1 GCA-CCCCCA
19765 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.19, C:0.50, G:0.27, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:21193 original size:22 final size:19
Alignment explanation
Indices: 21151--21187 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21141 AGAAATTTTT
21151 TATGATTAAGGGGGAGAAA
1 TATGATTAAGGGGGAGAAA
*
21170 TATGATTAAGGAGGAGAA
1 TATGATTAAGGGGGAGAA
21188 GAAATAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (19 bp):
TATGATTAAGGGGGAGAAA
Found at i:23086 original size:24 final size:25
Alignment explanation
Indices: 23057--23103 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
23047 CAAGCAGGAA
23057 TTTTTTCTTTTTTCTTTG-GTTTTT
1 TTTTTTCTTTTTTCTTTGCGTTTTT
* *
23081 TTTTTTTTTTTTTTTTTGCGTTT
1 TTTTTTCTTTTTTCTTTGCGTTT
23104 ACGAGTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (25 bp):
TTTTTTCTTTTTTCTTTGCGTTTTT
Done.