Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2135
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: 36425
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:6310 original size:83 final size:84
Alignment explanation
Indices: 6181--6425 Score: 272
Period size: 83 Copynumber: 3.0 Consensus size: 84
6171 ATTCCCTTTG
* * * * *
6181 GAGAAATAGGGTTGGAGTATCCCTGAGAATTTAAATAT-ATGATTTTTTTTGTAAG-AAAAACGA
1 GAGAAATAAGGTTGGAGTATCCTTGAGAATGTAAAT-TCAAGATTTTTTTTGTAAGAAAAAAAGA
*
6244 GGTTGGAGTATCCTCTTTTA
65 GGTTGGAGTATCCTCTCTTA
* *
6264 GAGAAATAAGGTTGTAGTATCCTTGAGAATGTAAATTCAAGA--TTTTTTGTAAGAAAAAAAAAG
1 GAGAAATAAGGTTGGAGTATCCTTGAGAATGTAAATTCAAGATTTTTTTTGTAAGAAAAAAAGA-
*
6327 GGTTTGAGTAT-CTC-CTTA
65 GGTTGGAGTATCCTCTCTTA
* * * * *
6345 GAGAGATGAA-GTTGGAGTACCTCTTAATAATGTAAATTCAAGATTTTTTTTGTAAGAAAAAATG
1 GAGAAAT-AAGGTTGGAGTATC-CTTGAGAATGTAAATTCAAGATTTTTTTTGTAAGAAAAAAAG
6409 -GGTTGGAGTATCCTCTC
64 AGGTTGGAGTATCCTCTC
6426 AAAGTGGTGG
Statistics
Matches: 136, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
81 29 0.21
82 41 0.30
83 48 0.35
84 18 0.13
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (84 bp):
GAGAAATAAGGTTGGAGTATCCTTGAGAATGTAAATTCAAGATTTTTTTTGTAAGAAAAAAAGAG
GTTGGAGTATCCTCTCTTA
Found at i:6441 original size:82 final size:81
Alignment explanation
Indices: 6291--6447 Score: 192
Period size: 82 Copynumber: 1.9 Consensus size: 81
6281 TATCCTTGAG
* * *
6291 AATGTAAATTCAAGATTTTTTGTAAGAAAAAAAAAGGGTTTGAGTATCTCCTTAGAGAGATGAAG
1 AATGTAAATTCAAGATTTTTTGTAAG-AAAAAAAAGGGTTGGAGTATCTCCTCAAAGAGATGAAG
6356 TTGGAGTACCTCTTAAT
65 TTGGAGTACCTCTTAAT
* * * *
6373 AATGTAAATTCAAGATTTTTTTTGTAAG-AAAAAATGGGTTGGAGTATC-CTCTCAAAGTGGTGG
1 AATGTAAATTCAAGA--TTTTTTGTAAGAAAAAAAAGGGTTGGAGTATCTC-CTCAAAGAGATGA
*
6436 GGTTGGAGTACC
63 AGTTGGAGTACC
6448 CCTAAAGGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 1 0.02
82 52 0.81
84 11 0.17
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (81 bp):
AATGTAAATTCAAGATTTTTTGTAAGAAAAAAAAGGGTTGGAGTATCTCCTCAAAGAGATGAAGT
TGGAGTACCTCTTAAT
Found at i:10495 original size:32 final size:33
Alignment explanation
Indices: 10437--10498 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
10427 CACACCCAGA
*
10437 TGTATCGATACGTATTACTTGGTATCGATATAT
1 TGTATCGATACATATTACTTGGTATCGATATAT
*
10470 TGTATCGATACATGTT-CTTGGTATCGATA
1 TGTATCGATACATATTACTTGGTATCGATA
10499 CATATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTACTTGGTATCGATATAT
Found at i:10587 original size:20 final size:20
Alignment explanation
Indices: 10564--10614 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
10554 TGATACAATG
10564 TATCGATACATGATGAATTA
1 TATCGATACATGATGAATTA
* *
10584 TATCGATACATGGTGAATTG
1 TATCGATACATGATGAATTA
*
10604 TATTGATACAT
1 TATCGATACAT
10615 TCAGCCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATACATGATGAATTA
Found at i:16576 original size:20 final size:20
Alignment explanation
Indices: 16551--16601 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
16541 ACTTAGATGC
*
16551 ATCGATACATTTTTCAATGT
1 ATCGATACATTTATCAATGT
* *
16571 ATCGATACATGTATGAATGT
1 ATCGATACATTTATCAATGT
16591 ATCGATACATT
1 ATCGATACATT
16602 CTGTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
ATCGATACATTTATCAATGT
Found at i:16652 original size:31 final size:32
Alignment explanation
Indices: 16587--16661 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
16577 ACATGTATGA
16587 ATGTATCGATACATTCTGTCTTTTTTACCTAG
1 ATGTATCGATACATTCTGTCTTTTTTACCTAG
16619 ATGTATCGATACATTCTGTC-TTTTTATCC-AG
1 ATGTATCGATACATTCTGTCTTTTTTA-CCTAG
16650 ATGTATCGATAC
1 ATGTATCGATAC
16662 TTTTTTCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
31 20 0.48
32 22 0.52
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (32 bp):
ATGTATCGATACATTCTGTCTTTTTTACCTAG
Found at i:16675 original size:20 final size:20
Alignment explanation
Indices: 16650--16703 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
16640 TTTTATCCAG
* * *
16650 ATGTATCGATACTTTTTTCA
1 ATGTATCGATACATGTATCA
* *
16670 ATGTATCGACACATGTATGA
1 ATGTATCGATACATGTATCA
16690 ATGTATCGATACAT
1 ATGTATCGATACAT
16704 TCTATCTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:16744 original size:71 final size:71
Alignment explanation
Indices: 16619--16754 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 71
16609 TTTTACCTAG
* * * ***
16619 ATGTATCGATACATTCTGTCTTTTTATCCAGATGTATCGATACTTTTTTCAATGTATCGACACAT
1 ATGTATCGATACATTCTATCTTTTTACCCAGATGTATCAATACTTGAATCAATGTATCGACACAT
16684 GTATGA
66 GTATGA
*
16690 ATGTATCGATACATTCTATCTTTTTACCCAGATGTATCAATACATTGAAT-AATGTATCGATACA
1 ATGTATCGATACATTCTATCTTTTTACCCAGATGTATCAATAC-TTGAATCAATGTATCGACACA
16754 T
65 T
16755 ATAGTTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 54 0.95
72 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (71 bp):
ATGTATCGATACATTCTATCTTTTTACCCAGATGTATCAATACTTGAATCAATGTATCGACACAT
GTATGA
Found at i:21732 original size:43 final size:43
Alignment explanation
Indices: 21666--21755 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
21656 TCCTCATCAT
*
21666 CTTTAAGTCCAATGTAGCGGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCGGGCCTTGAATCAGCACATTGGCAC
** *
21709 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCGGGCCTTGAATCAGCACATTGGCAC
21752 CTTT
1 CTTT
21756 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCGGGCCTTGAATCAGCACATTGGCAC
Found at i:21844 original size:55 final size:55
Alignment explanation
Indices: 21709--22081 Score: 185
Period size: 52 Copynumber: 6.7 Consensus size: 55
21699 ACATTGGCAC
* * * * * *
21709 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTGACATCCTTTTTCTCAT
** * * * *
21761 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTGACATCCTTTTTCTCAT
* * * *
21816 CTTTAAGCCTAATATTGTTGGTCGTGAATCAACATATTGGCATCTTTATCATTTTTCTCACCTTC
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATT-G-A-C---ATC-CTTTT-T---C-TC
21881 AT
54 AT
* * * * * * *
21883 CTTTAAGTCCAATATTGCTGTCCTTGAATCAGCATATTGGCA-CC---TTCATCAT
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTGACATCCTTTTTC-TCAT
* * *
21935 CTTTAAAACCCAATGTTGTTGG-CGTTGAATCAGCACATT-AGCA---TTTTTCTCAT
1 CTTT-AAGCCCAATATTGTTGGCCG-TGAATCAACACATTGA-CATCCTTTTTCTCAT
* * * * * * * *
21988 CTTCAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTGACATCCTTTTTCTCAT
* * *
22043 CTTTAAACCCAATATCGTTGGCCGTGAATCAACATATTG
1 CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTG
22082 GTCCTTTTAT
Statistics
Matches: 245, Mismatches: 50, Indels: 49
0.71 0.15 0.14
Matches are distributed among these distances:
52 73 0.30
53 39 0.16
54 8 0.03
55 73 0.30
56 2 0.01
57 1 0.00
58 1 0.00
60 1 0.00
61 4 0.02
62 4 0.02
63 1 0.00
64 1 0.00
66 2 0.01
67 35 0.14
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGCCCAATATTGTTGGCCGTGAATCAACACATTGACATCCTTTTTCTCAT
Found at i:22780 original size:19 final size:19
Alignment explanation
Indices: 22718--22802 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
22708 ATTTCAACGA
22718 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACAT-AAGT
*
22738 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
22753 --TGTACCGATACATAAGT
1 TTTGTATCGATACATAAGT
22770 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
22789 TTTGTATCGATACA
1 TTTGTATCGATACA
22803 ATGTAAGCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
19 30 0.54
20 12 0.21
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:22780 original size:32 final size:33
Alignment explanation
Indices: 22720--22783 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
22710 TTCAACGATT
*
22720 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTACCGATACATAAAGTGTTGTATCGATACAA
*
22753 TGTACCGATACAT-AAGTTTTGTATCGATACA
1 TGTACCGATACATAAAGTGTTGTATCGATACA
22784 TAAGTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTACCGATACATAAAGTGTTGTATCGATACAA
Found at i:22867 original size:34 final size:34
Alignment explanation
Indices: 22824--22903 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
22814 TACCAAAAAA
22824 TGTATCGATACATTACTCAAATGTATCGATACGT
1 TGTATCGATACATTACTCAAATGTATCGATACGT
22858 TGTATCGATACATTACTCAAATGTATCGATACGT
1 TGTATCGATACATTACTCAAATGTATCGATACGT
22892 TGTATCGATACA
1 TGTATCGATACA
22904 CTGATCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACGT
Found at i:22957 original size:52 final size:52
Alignment explanation
Indices: 22892--23037 Score: 233
Period size: 52 Copynumber: 2.8 Consensus size: 52
22882 ATCGATACGT
**
22892 TGTATCGATACACTGAT-CTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATAAATTGTATCGATACATGCAGGCAAATTTGCCCAGA
*
22944 TGTATCGATACACTATAAATTGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATAAATTGTATCGATACATGCAGGCAAATTTGCCCAGA
22996 TGTATCGATACACTATGAAA-TGTATCGATACATGCAGGCAAA
1 TGTATCGATACACTAT-AAATTGTATCGATACATGCAGGCAAA
23038 ATTTCATATT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.94
53 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACACTATAAATTGTATCGATACATGCAGGCAAATTTGCCCAGA
Done.