Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4808
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: 13348
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Found at i:302 original size:40 final size:38
Alignment explanation
Indices: 270--521 Score: 234
Period size: 40 Copynumber: 6.7 Consensus size: 38
260 CCAGCATGAT
* * *
270 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCA--AA
* * **
310 TGCTCTTCGGAACTTAGTCCGGATACCTCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCA--AA
* *
350 TGCTCTTC-GGAATTAGCCCGGATA-CTCACTAGCAAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCAAA
* *
386 TGCTCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAA
1 TGCTCTTCGGGACTTAGCCCGGATATATC-ACTAGCA-AA
* * *
426 TTGC-CTTCGGGTCTTAGCCCGGATATAACGC-A-CAAA
1 -TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCAAA
* *
462 TGC-CTTCGGGTCTTAG-CCGGATA-ATCACTAGCAAT
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCAAA
497 TGC-CTTCGGGACTTAGCCCGGATAT
1 TGCTCTTCGGGACTTAGCCCGGATAT
522 CATTCAAATA
Statistics
Matches: 182, Mismatches: 21, Indels: 21
0.81 0.09 0.09
Matches are distributed among these distances:
33 3 0.02
34 8 0.04
35 34 0.19
36 19 0.10
37 16 0.09
38 12 0.07
39 20 0.11
40 67 0.37
41 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (38 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCAAA
Found at i:402 original size:76 final size:72
Alignment explanation
Indices: 274--521 Score: 243
Period size: 76 Copynumber: 3.3 Consensus size: 72
264 CATGATTGCT
* * ** *
274 CTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGAACTTAGTCCGGATACCTC
1 CTTCGGGACTTAGCCCGGATAT-A-A-C-GCACAAATGCTCTTCGGGTCTTAG-CCGGATA-ATC
339 ACTAGCACGAATGC
60 ACTAGCAC-AATGC
* * *
353 TCTTC-GGAATTAGCCCGGATACTCAC-TAGCAAATGCTCTTCGGGTCTTAGCCCGGATATATCA
1 -CTTCGGGACTTAGCCCGGATA-TAACGCA-CAAATGCTCTTCGGGTCTTAG-CCGGATA-ATC-
*
416 ACTTGCACAATTGC
60 ACTAGCACAA-TGC
*
430 CTTCGGGTCTTAGCCCGGATATAACGCACAAATGC-CTTCGGGTCTTAGCCGGATAATCACTAGC
1 CTTCGGGACTTAGCCCGGATATAACGCACAAATGCTCTTCGGGTCTTAGCCGGATAATCACTAGC
*
494 A-ATTGC
66 ACAATGC
500 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
522 CATTCAAATA
Statistics
Matches: 144, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
70 24 0.17
71 1 0.01
72 6 0.04
73 3 0.02
74 7 0.05
75 14 0.10
76 43 0.30
77 26 0.18
78 1 0.01
79 14 0.10
80 5 0.03
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (72 bp):
CTTCGGGACTTAGCCCGGATATAACGCACAAATGCTCTTCGGGTCTTAGCCGGATAATCACTAGC
ACAATGC
Found at i:466 original size:35 final size:35
Alignment explanation
Indices: 382--521 Score: 149
Period size: 35 Copynumber: 3.8 Consensus size: 35
372 TACTCACTAG
382 CAAATGCTCTTCGGGTCTTAGCCCGGATATATCAACTTGCA
1 CAAATGC-CTTCGGGTCTTAGCCCGG--ATAT-AAC--GCA
*
423 CAATTGCCTTCGGGTCTTAGCCCGGATATAACGCA
1 CAAATGCCTTCGGGTCTTAGCCCGGATATAACGCA
* *
458 CAAATGCCTTCGGGTCTTAG-CCGGATAATCAC-TA
1 CAAATGCCTTCGGGTCTTAGCCCGGAT-ATAACGCA
* *
492 GCAATTGCCTTCGGGACTTAGCCCGGATAT
1 -CAAATGCCTTCGGGTCTTAGCCCGGATAT
522 CATTCAAATA
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.08
35 46 0.51
36 6 0.07
37 3 0.03
38 4 0.04
40 18 0.20
41 6 0.07
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (35 bp):
CAAATGCCTTCGGGTCTTAGCCCGGATATAACGCA
Found at i:850 original size:29 final size:29
Alignment explanation
Indices: 811--889 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
801 CTTAATAATC
*
811 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
841 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
870 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
890 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:932 original size:43 final size:43
Alignment explanation
Indices: 871--1058 Score: 369
Period size: 43 Copynumber: 4.4 Consensus size: 43
861 TGCATTTCAA
871 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
914 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
957 GCCCGCACACTTAGTGCCAATCTCA-AACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
999 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1042 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
1059 TGAAAACCAA
Statistics
Matches: 144, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
42 42 0.29
43 102 0.71
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:1015 original size:85 final size:86
Alignment explanation
Indices: 871--1058 Score: 369
Period size: 85 Copynumber: 2.2 Consensus size: 86
861 TGCATTTCAA
871 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
936 TCACAACCGTGAACACTTATT
66 TCACAACCGTGAACACTTATT
957 GCCCGCACACTTAGTGCCAATCTCA-AACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
1021 TCACAACCGTGAACACTTATT
66 TCACAACCGTGAACACTTATT
1042 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
1059 TGAAAACCAA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 77 0.75
86 25 0.25
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (86 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATTGCCCGCACACTTAGTGCCAATC
TCACAACCGTGAACACTTATT
Found at i:3250 original size:46 final size:48
Alignment explanation
Indices: 3040--3318 Score: 370
Period size: 48 Copynumber: 5.8 Consensus size: 48
3030 ATCACATTTA
* * * * * * *
3040 ACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAT
*
3089 ACACTTCCACATTCATCACCATCGGCCATTAGGCCTTATCAC-ATATAT
1 ACACTTTCACATTCATCA-CATCGGCCATTAGGCCTTATCACAATATAT
*
3137 ACACTTTCACATTCATCACATCGGCCCATTA-GCCCTATACACCAATATATT
1 ACACTTTCACATTCATCACATCGG-CCATTAGGCCTTAT-CA-CAATATA-T
*
3188 ACACTTTCACATTCATCACATCGGCCATTAGTCCTTATCAC-ATATAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATAT
3235 ACAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAT
3283 ACACTTTCACATTCATCACA-CGGCCATTAGGCCTTA
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
3319 CATCATTCAT
Statistics
Matches: 207, Mismatches: 13, Indels: 21
0.86 0.05 0.09
Matches are distributed among these distances:
46 35 0.17
47 17 0.08
48 62 0.30
49 33 0.16
50 30 0.14
51 30 0.14
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (48 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATAT
Found at i:9293 original size:26 final size:26
Alignment explanation
Indices: 9264--9320 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
9254 GTTTATGTAG
9264 TACATGCATGAAAAACA-TGAAGATAA
1 TACATGCA-GAAAAACATTGAAGATAA
* *
9290 TACATGCAGAACAGCATTGAAGATAA
1 TACATGCAGAAAAACATTGAAGATAA
*
9316 AACAT
1 TACAT
9321 ACAGCATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (26 bp):
TACATGCAGAAAAACATTGAAGATAA
Done.