Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_39 ID=scaffold_39-JGI_221_v2.0
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: 29075
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.30
Warning! 677 characters in sequence are not A, C, G, or T
Found at i:722 original size:21 final size:21
Alignment explanation
Indices: 697--748 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
687 ATGTAAGTGA
*
697 CTTTTCTTTTTATACAAGCA-T
1 CTTTTCTTTTTA-ACAAACATT
718 CTTTTCTTCTTTAACAAACATT
1 CTTTTCTT-TTTAACAAACATT
*
740 ATTTTCTTT
1 CTTTTCTTT
749 ATTGATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.23, C:0.19, G:0.02, T:0.56
Consensus pattern (21 bp):
CTTTTCTTTTTAACAAACATT
Found at i:3997 original size:14 final size:14
Alignment explanation
Indices: 3978--4026 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
3968 TCGCTGTATG
3978 AAACCAAAAAAACA
1 AAACCAAAAAAACA
3992 AAACCAAAAATAA-A
1 AAACCAAAAA-AACA
4006 AAA--AAAAAAACCAA
1 AAACCAAAAAAA-C-A
4020 AAACCAA
1 AAACCAA
4027 GCAACACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 2 0.07
12 5 0.17
14 18 0.62
15 2 0.07
16 2 0.07
ACGTcount: A:0.80, C:0.18, G:0.00, T:0.02
Consensus pattern (14 bp):
AAACCAAAAAAACA
Found at i:4009 original size:21 final size:21
Alignment explanation
Indices: 3983--4022 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3973 GTATGAAACC
*
3983 AAAAAAACAAAACCAAAAATA
1 AAAAAAAAAAAACCAAAAATA
4004 AAAAAAAAAAAACCAAAAA
1 AAAAAAAAAAAACCAAAAA
4023 CCAAGCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAAACCAAAAATA
Found at i:5008 original size:10 final size:10
Alignment explanation
Indices: 4986--5024 Score: 55
Period size: 9 Copynumber: 4.1 Consensus size: 10
4976 TTTTTTCTTG
4986 TCAATGT-TT
1 TCAATGTGTT
4995 TCAATGTGTT
1 TCAATGTGTT
*
5005 TCAAT-AGTT
1 TCAATGTGTT
5014 TCAATGTGTT
1 TCAATGTGTT
5024 T
1 T
5025 AGATACAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 15 0.58
10 11 0.42
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (10 bp):
TCAATGTGTT
Found at i:5678 original size:206 final size:206
Alignment explanation
Indices: 5321--5937 Score: 1074
Period size: 206 Copynumber: 3.0 Consensus size: 206
5311 CCAGATTCTT
** *
5321 AAAAACATCGACAAGAAAAAATACTCTTGATTCAATCAGATCTAAGCTTAAATCAAGAAGCAAGC
1 AAAAACATCGACAAGAAAAAGGACTCTTGATTCAATCAGATTTAAGCTTAAATCAAGAAGCAAGC
* * *
5386 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCCGATTGAATCAAGAATCGTTTTT
66 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCTGATTGAATCAAGAGTCTTTTTT
* * *
5451 CTTGTCGATGTTTTTAAGAGTCTGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGAAAAATGAA
131 CTTGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGAAAAATGAA
5516 AAGAAACGAAC
196 AAGAAACGAAC
*
5527 AAAAACATCGACAAGAAAAAGGACTCTTGATTCAATTAGATTTAAGCTTAAATCAAGAAGCAAGC
1 AAAAACATCGACAAGAAAAAGGACTCTTGATTCAATCAGATTTAAGCTTAAATCAAGAAGCAAGC
*
5592 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTAAATCTGATTGAATCAAGAGTCTTTTTT
66 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCTGATTGAATCAAGAGTCTTTTTT
*
5657 CTTGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGTAAAATGAA
131 CTTGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGAAAAATGAA
5722 AAGAAACGAAC
196 AAGAAACGAAC
* * *
5733 AAAAACATCGACAAGAAAAAGGACTCTTGATCCAATCAGATTAAAGCTTAAATCAAGAACCAAGC
1 AAAAACATCGACAAGAAAAAGGACTCTTGATTCAATCAGATTTAAGCTTAAATCAAGAAGCAAGC
5798 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCTGATTGAATCAAGAGTCTTTTTT
66 CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCTGATTGAATCAAGAGTCTTTTTT
* *
5863 CTGGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAG-TAAAAATGAA
131 CTTGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGAAAAATGAA
5927 AAGAAACGAAC
196 AAGAAACGAAC
5938 GAAACACGGG
Statistics
Matches: 391, Mismatches: 20, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
205 19 0.05
206 372 0.95
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (206 bp):
AAAAACATCGACAAGAAAAAGGACTCTTGATTCAATCAGATTTAAGCTTAAATCAAGAAGCAAGC
CTCTTAATTTGAGCGGATTTCCTTTTGATTTAAGCTTGAATCTGATTGAATCAAGAGTCTTTTTT
CTTGTCAATGTTTTCAAGAGTCCGGACTCTAGATCCAATGTGTTTTTCTTCCAGCGAAAAATGAA
AAGAAACGAAC
Found at i:8045 original size:11 final size:11
Alignment explanation
Indices: 8029--8066 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
8019 TTGAAATTCA
8029 AAATTTTGAAG
1 AAATTTTGAAG
8040 AAATTTTGAAG
1 AAATTTTGAAG
**
8051 AAATTGAGAAG
1 AAATTTTGAAG
8062 AAATT
1 AAATT
8067 GCCTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (11 bp):
AAATTTTGAAG
Found at i:9642 original size:60 final size:60
Alignment explanation
Indices: 9569--9738 Score: 261
Period size: 60 Copynumber: 2.8 Consensus size: 60
9559 GCTTCTCACG
9569 TTTCCTCTCGCTTTTCCTCTCGATTTTCTTCTCACTTTTCTTCTCGCTTTTCCTCTCGCT
1 TTTCCTCTCGCTTTTCCTCTCGATTTTCTTCTCACTTTTCTTCTCGCTTTTCCTCTCGCT
*
9629 TTTCCTCTCGCTTTTCCTCTCGATTTTCTTCTCACTTTTCTTCTCGCTTTTCCTCTTGCT
1 TTTCCTCTCGCTTTTCCTCTCGATTTTCTTCTCACTTTTCTTCTCGCTTTTCCTCTCGCT
* * * * * *
9689 TTTCTTCTCGC-TTTCCTTCTCGCTTTCCTTCTCAATTTCCTTCTAGCTTT
1 TTTCCTCTCGCTTTTCC-TCTCGATTTTCTTCTCACTTTTCTTCTCGCTTT
9739 CCTTCTCAAT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 5 0.05
60 97 0.95
ACGTcount: A:0.04, C:0.35, G:0.06, T:0.54
Consensus pattern (60 bp):
TTTCCTCTCGCTTTTCCTCTCGATTTTCTTCTCACTTTTCTTCTCGCTTTTCCTCTCGCT
Found at i:9715 original size:12 final size:12
Alignment explanation
Indices: 9569--9819 Score: 201
Period size: 12 Copynumber: 20.8 Consensus size: 12
9559 GCTTCTCACG
9569 TTTCC-TCTCGC
1 TTTCCTTCTCGC
*
9580 TTTTCC-TCTCGA
1 -TTTCCTTCTCGC
* *
9592 TTTTCTTCTCAC
1 TTTCCTTCTCGC
*
9604 TTTTCTTCTCGC
1 TTTCCTTCTCGC
9616 TTTTCC-TCTCGC
1 -TTTCCTTCTCGC
9628 TTTTCC-TCTCGC
1 -TTTCCTTCTCGC
*
9640 TTTTCC-TCTCGA
1 -TTTCCTTCTCGC
* *
9652 TTTTCTTCTCAC
1 TTTCCTTCTCGC
*
9664 TTTTCTTCTCGC
1 TTTCCTTCTCGC
*
9676 TTTTCC-TCTTGC
1 -TTTCCTTCTCGC
*
9688 TTTTCTTCTCGC
1 TTTCCTTCTCGC
9700 TTTCCTTCTCGC
1 TTTCCTTCTCGC
**
9712 TTTCCTTCTCAA
1 TTTCCTTCTCGC
*
9724 TTTCCTTCTAGC
1 TTTCCTTCTCGC
**
9736 TTTCCTTCTCAA
1 TTTCCTTCTCGC
**
9748 TTTCCTTCTCAA
1 TTTCCTTCTCGC
9760 TTTCCTTCTCGC
1 TTTCCTTCTCGC
9772 TTTCCTTCTCAAGC
1 TTTCCTTCTC--GC
**
9786 TTTCCATT-TCAA
1 TTTCC-TTCTCGC
9798 TTTCCTTCTCGC
1 TTTCCTTCTCGC
*
9810 TTTCCCTCTC
1 TTTCCTTCTC
9820 ACTGTTTTAC
Statistics
Matches: 199, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
11 14 0.07
12 166 0.83
13 8 0.04
14 9 0.05
15 2 0.01
ACGTcount: A:0.06, C:0.36, G:0.06, T:0.52
Consensus pattern (12 bp):
TTTCCTTCTCGC
Found at i:9914 original size:14 final size:14
Alignment explanation
Indices: 9897--9936 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9887 CCATGTCTCT
9897 TCTTTTCTCTCCTC
1 TCTTTTCTCTCCTC
* *
9911 TCTTCTCTCTTCTC
1 TCTTTTCTCTCCTC
9925 TCTTTTCT-TCCT
1 TCTTTTCTCTCCT
9937 GTTCTTTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (14 bp):
TCTTTTCTCTCCTC
Found at i:12634 original size:11 final size:11
Alignment explanation
Indices: 12620--12646 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12610 TGTTTGTTTG
12620 TTTTTGTTTTT
1 TTTTTGTTTTT
12631 TTTTTGTTTTT
1 TTTTTGTTTTT
12642 TTTTT
1 TTTTT
12647 TATGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:12638 original size:17 final size:16
Alignment explanation
Indices: 12616--12647 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12606 TTAGTGTTTG
12616 TTTGTTTTTGTTTTTTT
1 TTTGTTTTT-TTTTTTT
12633 TTTGTTTTTTTTTTT
1 TTTGTTTTTTTTTTT
12648 ATGAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (16 bp):
TTTGTTTTTTTTTTTT
Found at i:12645 original size:10 final size:10
Alignment explanation
Indices: 12612--12645 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12602 AAGTTTAGTG
*
12612 TTTGTTTGTT
1 TTTGTTTTTT
12622 TTTGTTTTTTT
1 TTTG-TTTTTT
12633 TTTGTTTTTT
1 TTTGTTTTTT
12643 TTT
1 TTT
12646 TTATGAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:13345 original size:1 final size:1
Alignment explanation
Indices: 13339--13365 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
13329 TTACTTTGCA
13339 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
13366 CTTTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16764 original size:150 final size:150
Alignment explanation
Indices: 16481--16778 Score: 488
Period size: 150 Copynumber: 2.0 Consensus size: 150
16471 TTGCTACCTG
*
16481 GAGAAATATGTGTTTGAAGTCTCAAAATTACACGGATCTTTATGGCGGAAAGAAAGTTCAAACTG
1 GAGAAATATGTGTTTGAAGTCTCAAAATTACACGGATCCTTATGGCGGAAAGAAAGTTCAAACTG
* * *
16546 ACTTTTTGAAGCTTACAAATTGAAATTTGAGAGGGAATTTTTCACAAAATATGCACTTAGGATAG
66 ACTTTTTGAAGCTTAAAAATTGAAATTTGAGAGGGAATTTTTCACAAAATATGCACTAAGCATAG
16611 TTTTACTTGAAATCATTATC
131 TTTTACTTGAAATCATTATC
* **
16631 GAGAAATATGTGTTTGAAGTCTCAAAATTACACGGATCCTTATGGCGGAATGAAAGTTTGAACTG
1 GAGAAATATGTGTTTGAAGTCTCAAAATTACACGGATCCTTATGGCGGAAAGAAAGTTCAAACTG
* * * * *
16696 ACTTTTTGAAGCTTAAAAATTGAAATTTGGGAGGGAATTTTTCACAGAATATGCAGTAAGCCTGG
66 ACTTTTTGAAGCTTAAAAATTGAAATTTGAGAGGGAATTTTTCACAAAATATGCACTAAGCATAG
16761 TTTTACTTGAAATCATTA
131 TTTTACTTGAAATCATTA
16779 AAATCTCAAC
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
150 136 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (150 bp):
GAGAAATATGTGTTTGAAGTCTCAAAATTACACGGATCCTTATGGCGGAAAGAAAGTTCAAACTG
ACTTTTTGAAGCTTAAAAATTGAAATTTGAGAGGGAATTTTTCACAAAATATGCACTAAGCATAG
TTTTACTTGAAATCATTATC
Found at i:18159 original size:17 final size:17
Alignment explanation
Indices: 18137--18176 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
18127 CTACTCAACA
18137 CATTTTCTGTCATACTT
1 CATTTTCTGTCATACTT
*
18154 CATTTTCTGTTATACTT
1 CATTTTCTGTCATACTT
18171 CATTTT
1 CATTTT
18177 TTCTCGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.57
Consensus pattern (17 bp):
CATTTTCTGTCATACTT
Found at i:19385 original size:20 final size:20
Alignment explanation
Indices: 19355--19415 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
19345 AAATTTTAAT
*
19355 AATAAAGTACCGAACACGAA
1 AATATAGTACCGAACACGAA
*
19375 AATTTAGTACCGAACACGAA
1 AATATAGTACCGAACACGAA
*
19395 AGTATAGTACCGAACACGAA
1 AATATAGTACCGAACACGAA
19415 A
1 A
19416 CTACACTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.15
Consensus pattern (20 bp):
AATATAGTACCGAACACGAA
Found at i:24201 original size:22 final size:22
Alignment explanation
Indices: 24175--24226 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
24165 TTGGTACACA
*
24175 CAACCGAATTATTCGGTCTGTT
1 CAACCGAATTATTCGGTCTGTG
* *
24197 CAACCGAATTGTTCGGTTTGTG
1 CAACCGAATTATTCGGTCTGTG
24219 CAACCGAA
1 CAACCGAA
24227 CCATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (22 bp):
CAACCGAATTATTCGGTCTGTG
Found at i:26577 original size:12 final size:12
Alignment explanation
Indices: 26556--26596 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
26546 GAAGAAGCGC
26556 GAGAGGGAGAGA
1 GAGAGGGAGAGA
*
26568 GAGGGGGAGAGA
1 GAGAGGGAGAGA
26580 GAGAGGGAGAGA
1 GAGAGGGAGAGA
26592 GAGAG
1 GAGAG
26597 AATGATATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (12 bp):
GAGAGGGAGAGA
Found at i:26581 original size:14 final size:14
Alignment explanation
Indices: 26562--26597 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
26552 GCGCGAGAGG
*
26562 GAGAGAGAGGGGGA
1 GAGAGAGAGGGAGA
26576 GAGAGAGAGGGAGA
1 GAGAGAGAGGGAGA
26590 GAGAGAGA
1 GAGAGAGA
26598 ATGATATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGGGAGA
Done.