Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2134
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: 35034
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:6525 original size:40 final size:40
Alignment explanation
Indices: 6467--6675 Score: 255
Period size: 40 Copynumber: 5.3 Consensus size: 40
6457 TTCGAATGAT
*
6467 ATCCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
6507 ATTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * * * *
6547 TTCTGGGCTAAG-CCCGAAGGCACTGGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* *
6586 ATCCGGGTTAAGTCCCGAAGACATTTGTACGAGTTACTATA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * * *
6627 A-CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTAT
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAA
6666 ATCC-GGTTAA
1 ATCCGGGTTAA
6676 ATTACAAAGG
Statistics
Matches: 142, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
39 41 0.29
40 99 0.70
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:6674 original size:79 final size:79
Alignment explanation
Indices: 6469--6675 Score: 249
Period size: 79 Copynumber: 2.6 Consensus size: 79
6459 CGAATGATAT
* * * *
6469 CCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTACTAAATTCGGGTTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA-TCCGGTTAAGTCCCGAAGACATTTG
* *
6534 TGCGAGTTACTAATT
65 TACGAGTTACTAATA
* * *
6549 CTGGGCTAAG-CCCGAAGGCACTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGACATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC-GGTTAAGTCCCGAAGACATTTG
6613 TACGAGTTACT-ATAA
65 TACGAGTTACTAAT-A
* * *
6628 CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGGTTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGTTAA
6676 ATTACAAAGG
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
78 4 0.04
79 73 0.68
80 31 0.29
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGACATTTGT
ACGAGTTACTAATA
Found at i:11188 original size:48 final size:48
Alignment explanation
Indices: 11024--11248 Score: 168
Period size: 48 Copynumber: 4.9 Consensus size: 48
11014 CACATAGTAA
* * * *
11024 GATGCCAATGCCATATCCTAGATATGGTCTTACATGGGATCACAAATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGAGATCACATATC
* * ** * *
11072 GA----AGT-CGATGGCCCAGCTATGGTCTTACACGATG-TCTCATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGA-GATCACATATC
* *
11115 GATGCC-ATG-----TCCCAGACATGGTCTTACACGAAATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGAGATCACATATC
* * *
11157 GATGCCAGTGCCATATCCCAGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGAGATCACATATC
* * * * * *
11205 AATGCCAATGCCATGTCCCAGACATGGCCTTACATGGGATCACA
1 GATGCCAATGCCATATCCCAGATATGGTCTTACACGAGATCACA
11249 CATAACCCTA
Statistics
Matches: 138, Mismatches: 26, Indels: 26
0.73 0.14 0.14
Matches are distributed among these distances:
42 33 0.24
43 31 0.22
44 3 0.02
46 1 0.01
48 70 0.51
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGATATGGTCTTACACGAGATCACATATC
Found at i:15470 original size:43 final size:43
Alignment explanation
Indices: 15413--15610 Score: 134
Period size: 43 Copynumber: 4.6 Consensus size: 43
15403 CAGTGCCATA
* * * * * * *
15413 TCCCAGATATGGTCTTAGATGTTATCACTTATCGATGCCACTG
1 TCCCAAATAGGGTCTTACATGTAATCAATTAACGATGCCAATG
15456 TCCCAAATAGGGTCTTACATGTAATCAATTAACGATGCCAATG
1 TCCCAAATAGGGTCTTACATGTAATCAATTAACGATGCCAATG
* * * * * * * *
15499 TCTCAGACATGGTCATACACGTAATC-GTATAATGATGCCAATG
1 TCCCAAATAGGGTCTTACATGTAATCAAT-TAACGATGCCAATG
** * *
15542 TCCCAGACATA--GTCTTACACATAATCACAAT-ACAATGCCAATG
1 TCCCA-A-ATAGGGTCTTACATGTAATCA-ATTAACGATGCCAATG
* * *
15585 TCCCAGACATGGTCTTACATGTAATC
1 TCCCAAATAGGGTCTTACATGTAATC
15611 TCATCTCATT
Statistics
Matches: 120, Mismatches: 28, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 114 0.95
44 1 0.01
45 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
TCCCAAATAGGGTCTTACATGTAATCAATTAACGATGCCAATG
Found at i:15567 original size:86 final size:85
Alignment explanation
Indices: 15446--15610 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 85
15436 ATCACTTATC
* ** * * *
15446 GATGCCACTGTCCCAAATAGGGTCTTACATGTAATCA-ATTAACGATGCCAATGTCTCAGACATG
1 GATGCCAATGTCCCAAATA-GGTCTTACACATAATCACAAT-ACAATGCCAATGTCCCAGACATG
15510 GTCATACACGTAATCGTATAAT
64 GTCATACACGTAATCGTATAAT
15532 GATGCCAATGTCCCAGACATA-GTCTTACACATAATCACAATACAATGCCAATGTCCCAGACATG
1 GATGCCAATGTCCCA-A-ATAGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGACATG
* *
15596 GTCTTACATGTAATC
64 GTCATACACGTAATC
15611 TCATCTCATT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
86 62 0.91
87 3 0.04
88 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (85 bp):
GATGCCAATGTCCCAAATAGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGACATGGT
CATACACGTAATCGTATAAT
Found at i:17564 original size:27 final size:27
Alignment explanation
Indices: 17534--17711 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
17524 ATATTGAGCC
* * *
17534 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
17561 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
17588 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
17616 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
17643 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
17670 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
17697 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17712 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:17627 original size:55 final size:55
Alignment explanation
Indices: 17534--17711 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
17524 ATATTGAGCC
* * *
17534 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
17588 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
17643 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
17697 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17712 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:17673 original size:82 final size:81
Alignment explanation
Indices: 17555--17710 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
17545 TGCTATACAA
* * *
17555 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
17620 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
17637 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
17701 CACTTAGTGC
65 CACTTAGTGC
17711 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:25467 original size:27 final size:27
Alignment explanation
Indices: 25437--25614 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
25427 ATATTGAGCC
* * *
25437 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
25464 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
25491 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
25519 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
25546 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
25573 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
25600 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25615 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:25530 original size:55 final size:55
Alignment explanation
Indices: 25437--25614 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
25427 ATATTGAGCC
* * *
25437 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
25491 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
25546 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
25600 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
25615 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:25576 original size:82 final size:81
Alignment explanation
Indices: 25458--25613 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
25448 TGCTATACAA
* * *
25458 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
25523 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
25540 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
25604 CACTTAGTGC
65 CACTTAGTGC
25614 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28658 original size:27 final size:27
Alignment explanation
Indices: 28606--28761 Score: 138
Period size: 27 Copynumber: 5.7 Consensus size: 27
28596 AAATTGTACA
*
28606 GCACTAAGTGTGGCG-ATTCGACTATGTT
1 GCACTAAGTGT-GCGAATT-GAATATGTT
* *
28634 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGAATATGTT
** **
28661 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGAATATGTT
* *
28688 GCACTAAGTGTGCGAGTCT-AACTATGTA
1 GCACTAAGTGTGCGAAT-TGAA-TATGTT
* * *
28716 GCACTAAGTGTGCGATTTGATTACG-T
1 GCACTAAGTGTGCGAATTGAATATGTT
*
28742 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
28762 TTGTATATGC
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
26 19 0.18
27 53 0.50
28 34 0.32
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGAATATGTT
Found at i:28774 original size:54 final size:53
Alignment explanation
Indices: 28605--28783 Score: 155
Period size: 54 Copynumber: 3.3 Consensus size: 53
28595 TAAATTGTAC
* * * ** *
28605 AGCACTAAGTGTGGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGT-GCGATTTGAATACG-TGCACTAAGTGTGCGAGTTGATTAT-AT
* * * * *
28661 -GCACTAAGTGTGCGAATTGACCATGCG-GCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGATTTGA--ATACGTGCACTAAGTGTGCGAGT-TGATTATAT
* *
28715 AGCACTAAGTGTGCGATTTGATTACGTGCACTAAGTGTGCGAGTTGATTGTAT
1 AGCACTAAGTGTGCGATTTGAATACGTGCACTAAGTGTGCGAGTTGATTATAT
*
28768 ATGCACTGAGTGTGCG
1 A-GCACTAAGTGTGCG
28784 GGCTCAATAT
Statistics
Matches: 99, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
53 9 0.09
54 53 0.54
55 35 0.35
56 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (53 bp):
AGCACTAAGTGTGCGATTTGAATACGTGCACTAAGTGTGCGAGTTGATTATAT
Found at i:28774 original size:82 final size:81
Alignment explanation
Indices: 28598--28783 Score: 194
Period size: 82 Copynumber: 2.3 Consensus size: 81
28588 GCGGGATTAA
* * * * *
28598 ATTGTACAGCACTAAGTGTGGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGC
1 ATTGTATAGCACTAAGTGT-GCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGC
28663 ACTAAGTGTGCGAATTG
65 ACTAAGTGTGCGAATTG
*** *** ** *
28680 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGC
1 ATTGTATAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGATGC
*
28744 ACTAAGTGTGCGAGTTG
65 ACTAAGTGTGCGAATTG
*
28761 ATTGTATATGCACTGAGTGTGCG
1 ATTGTATA-GCACTAAGTGTGCG
28784 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
81 27 0.33
82 55 0.67
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
ATTGTATAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:28781 original size:28 final size:26
Alignment explanation
Indices: 28633--28783 Score: 90
Period size: 27 Copynumber: 5.6 Consensus size: 26
28623 TCGACTATGT
** * *
28633 TGCACTAAGTGTGCGAAATGAATATGA
1 TGCACTAAGTGTGCGAGTTGATTA-CA
* *
28660 TGCACTAAGTGTGCGAATTGA--CCA
1 TGCACTAAGTGTGCGAGTTGATTACA
* * **
28684 TGCGGCACTAAGTGTGCGAGTCTAACTATG
1 T---GCACTAAGTGTGCGAGT-TGATTACA
* *
28714 TAGCACTAAGTGTGCGATTTGATTACG
1 T-GCACTAAGTGTGCGAGTTGATTACA
*
28741 TGCACTAAGTGTGCGAGTTGATTGTATA
1 TGCACTAAGTGTGCGAGTTGA-T-TACA
*
28769 TGCACTGAGTGTGCG
1 TGCACTAAGTGTGCG
28784 GGCTCAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
24 2 0.02
26 19 0.19
27 43 0.43
28 34 0.34
30 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
TGCACTAAGTGTGCGAGTTGATTACA
Done.