Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold208
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: 20502
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:914 original size:26 final size:26
Alignment explanation
Indices: 793--915 Score: 84
Period size: 23 Copynumber: 5.0 Consensus size: 26
783 ACTTCAATGG
** *
793 CCTCGATTTGTAG-ATTACCATTTTA
1 CCTCGATTTACAGAATTACCGTTTTA
* * *
818 CC-CG-TTT-TAGAATTACCGGTTCA
1 CCTCGATTTACAGAATTACCGTTTTA
841 CCCTC-ATTTACA-AA-T-CCGTTTTA
1 -CCTCGATTTACAGAATTACCGTTTTA
* *
864 CCTCGATTTATAGAATTACCATTTTA
1 CCTCGATTTACAGAATTACCGTTTTA
*
890 CCTCG-TTTACAGAAATTATCGTTTTA
1 CCTCGATTTACAG-AATTACCGTTTTA
916 TAACCCTGAT
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
22 7 0.09
23 24 0.31
24 7 0.09
25 15 0.19
26 24 0.31
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.41
Consensus pattern (26 bp):
CCTCGATTTACAGAATTACCGTTTTA
Found at i:3467 original size:22 final size:22
Alignment explanation
Indices: 3439--3560 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
3429 TTCCACATCC
3439 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
3461 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
3485 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
3508 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
3532 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
3555 ATCACA
1 ATCACA
3561 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:3474 original size:47 final size:47
Alignment explanation
Indices: 3411--4049 Score: 986
Period size: 47 Copynumber: 13.6 Consensus size: 47
3401 CCCTTCGGGA
* * *
3411 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
3458 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
3505 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
3552 CTTATCACACATACACA-TGTTCACATTCATCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACA-T--TCATCACATTGGCCATTCGGC
* *
3602 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
3649 CTTATCAC--ATATACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
3694 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
3741 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
3788 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
3835 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
3882 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
3929 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
3976 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
4023 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
4050 TATTCAAATA
Statistics
Matches: 569, Mismatches: 16, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
45 44 0.08
46 1 0.00
47 475 0.83
48 2 0.00
49 1 0.00
50 46 0.08
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:5440 original size:85 final size:85
Alignment explanation
Indices: 5311--5489 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
5301 TATTTTATTG
*
5311 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
5376 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
5396 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
5461 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
5481 CCCATGCTC
1 CCCATGCTC
5490 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:6789 original size:40 final size:40
Alignment explanation
Indices: 6744--7099 Score: 553
Period size: 39 Copynumber: 9.1 Consensus size: 40
6734 CGAATACACG
* * * *
6744 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * * *
6784 ACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* *
6823 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
6863 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
6903 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
6943 TCACTAGCACGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
6982 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
7021 TCACTAGCATGAATGCTCTTC-GGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
7060 TCACTAGCATGAATGCTCTTCGGGACTTAG-CCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
7098 TC
1 TC
7100 GTCGAGACCT
Statistics
Matches: 298, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
38 4 0.01
39 155 0.52
40 139 0.47
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:7222 original size:38 final size:38
Alignment explanation
Indices: 7153--7227 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
7143 GAATTTTAAT
*
7153 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
7191 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
7228 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:9717 original size:47 final size:47
Alignment explanation
Indices: 9654--10175 Score: 804
Period size: 47 Copynumber: 11.1 Consensus size: 47
9644 CCCTTCGGGA
* * *
9654 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
9701 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
9748 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
9795 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
9842 CTTATCAC--ACATACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
9887 CTTATCACATATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
9934 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
9981 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
10028 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
10075 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
10124 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
10171 CTTAT
1 CTTAT
10176 TATATATTCA
Statistics
Matches: 453, Mismatches: 16, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
45 43 0.09
46 1 0.00
47 361 0.80
48 1 0.00
49 47 0.10
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:10061 original size:233 final size:233
Alignment explanation
Indices: 9654--10175 Score: 784
Period size: 233 Copynumber: 2.2 Consensus size: 233
9644 CCCTTCGGGA
* *
9654 CTTATCACATTTATACAC-TTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACA
1 CTTATCACA--TATACACATTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
* *
9718 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACAT
64 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACAT
* * *
9783 TGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATC
129 TGGCCATTAGGCCTTATCACACATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATC
* *
9848 AC-ACATACA-TGTTCACATTCATCACATTGGCCATTCGGC
194 ACAACATACACT-TTCACATTCATCACATCGGCCATTAGGC
9887 CTTATCACATATACACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACAT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACAC
9952 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCATCACAT
65 TTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCACAT
* *
10016 TGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCACATCGGCCATTAGGCCTTAT
129 TGGCCATTAGGCCTTATCACACATACACA-TGTTCACATTCATCACATCGGCCATTAGGCCTTAT
*
10080 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
193 CAC--A-ACATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
10124 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
1 CTTATCACATATACACA-TTTCACATTCATCACATTGGCCATTCGGCCTTAT
10176 TATATATTCA
Statistics
Matches: 264, Mismatches: 15, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
231 7 0.03
232 1 0.00
233 173 0.66
234 2 0.01
237 79 0.30
238 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (233 bp):
CTTATCACATATACACATTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT
TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTG
GCCATTAGGCCTTATCACACATACACATGTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
AACATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11564 original size:85 final size:85
Alignment explanation
Indices: 11459--11636 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
11449 TATTTTATTG
11459 CCCATGC-CTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
11523 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
11543 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
11608 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
11628 CCCATGCTC
1 CCCATGCTC
11637 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 7 0.08
85 86 0.92
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:17982 original size:31 final size:30
Alignment explanation
Indices: 17930--17987 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17920 AACCAAGTAC
*
17930 CTTCGGAATTTAGCCGATATAGCTACTCAAG
1 CTTCGGAACTTAGCCGATATAG-TACTCAAG
*
17961 CTTCGG-ACTTAGCCGGTTATAGTACTC
1 CTTCGGAACTTAGCC-GATATAGTACTC
17988 GCCAAATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (30 bp):
CTTCGGAACTTAGCCGATATAGTACTCAAG
Found at i:18119 original size:38 final size:40
Alignment explanation
Indices: 17961--18248 Score: 426
Period size: 39 Copynumber: 7.5 Consensus size: 40
17951 GCTACTCAAG
17961 CTTC-GGACTTAG-CCGGTTATAGT-ACTCGC-CAAATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
17997 CTTC-GGACTTAG-CCGG--ATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
18033 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
*
18072 CTTCGGGACTTAGCCCGGATATAGTAACT-GCACAAATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
18111 CTTC-GGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
18150 CTTCGGGACTTAG-CCGG-TATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
* * *
18188 CTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGC
18227 CTTCGGGACTTAGCCCGGTTAT
1 CTTCGGGACTTAGCCCGGTTAT
18249 CATCCGAATA
Statistics
Matches: 233, Mismatches: 6, Indels: 22
0.89 0.02 0.08
Matches are distributed among these distances:
34 5 0.02
35 6 0.03
36 27 0.12
37 13 0.06
38 64 0.27
39 84 0.36
40 33 0.14
41 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGC
Found at i:18124 original size:77 final size:77
Alignment explanation
Indices: 17961--18241 Score: 434
Period size: 77 Copynumber: 3.7 Consensus size: 77
17951 GCTACTCAAG
17961 CTTCGGACTTAG-CCGGTTATAGT-ACTCGC-CAAATGCCTTC-GGACTTAGCCGG-ATAGTAAC
1 CTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGTATAGTAAC
18021 TCGCACAAATGC
66 TCGCACAAATGC
18033 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAGCCCGGATATAGT
1 CTTC-GGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAG-CCGG-TATAGT
18097 AACT-GCACAAATGC
63 AACTCGCACAAATGC
18111 CTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGTATAGTAAC
1 CTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGTATAGTAAC
18176 TCGCACAAATGC
66 TCGCACAAATGC
* * * *
18188 CTTCGGGCTTAGCCCGG-AATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCC
1 CTTCGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
18242 CGGTTATCAT
Statistics
Matches: 194, Mismatches: 4, Indels: 17
0.90 0.02 0.08
Matches are distributed among these distances:
72 4 0.02
73 8 0.04
74 11 0.06
75 15 0.08
76 20 0.10
77 95 0.49
78 32 0.16
79 9 0.05
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (77 bp):
CTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGTATAGTAAC
TCGCACAAATGC
Done.