Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1778
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: 12821
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Found at i:1473 original size:27 final size:28
Alignment explanation
Indices: 1430--1489 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
1420 GACATTTATC
* *
1430 ACCTTCAAAAGTCCACAAGTCAGTGGCA
1 ACCTTCAAAAGCCCACAAATCAGTGGCA
1458 ACCTTC-AAAGCCCACAAATCAGTGGCA
1 ACCTTCAAAAGCCCACAAATCAGTGGCA
*
1485 CCCTT
1 ACCTT
1490 TTTTTCGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.18
Consensus pattern (28 bp):
ACCTTCAAAAGCCCACAAATCAGTGGCA
Found at i:1652 original size:29 final size:29
Alignment explanation
Indices: 1560--1662 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 29
1550 TTTTCTTTTT
* *
1560 AAGCCC-CAAGTTAGTGGCACCCTTTTCA
1 AAGCCCACAAGTTAGTGGCAACCTTTTAA
* *
1588 AAGCCCAC-AGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTT-AA
1617 AAGCCCACAAGTTAGTGGCAACC-TTTAA
1 AAGCCCACAAGTTAGTGGCAACCTTTTAA
*
1645 AAGCCCCACAAGTCAGTG
1 AAG-CCCACAAGTTAGTG
1663 ATGCAAACCT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
28 28 0.42
29 26 0.39
30 12 0.18
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCAACCTTTTAA
Found at i:1777 original size:48 final size:47
Alignment explanation
Indices: 1715--1933 Score: 209
Period size: 48 Copynumber: 4.7 Consensus size: 47
1705 CTTTTAAAGC
*
1715 CCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTGCCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CCTTTAAGT
* * *
1763 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATATTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC--CTTTAAGT
* * *
1812 CCAATGTAGCTGACCTTGAATCAGCA-CTTGGCA----CC-TTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCTTTAAGT
* *
1853 CCAATATAGCTGGCCTTGAATAATCATA-TGGCACCTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-C--CTTTAAGT
* * * *
1903 TCAATGTAGCTCGCCTTGAATCAGCACATTG
1 CCAATATAGCTGGCCTTGAATCAGCATATTG
1934 ACATCCTTTT
Statistics
Matches: 137, Mismatches: 21, Indels: 23
0.76 0.12 0.13
Matches are distributed among these distances:
41 33 0.24
44 1 0.01
47 2 0.01
48 41 0.30
49 30 0.22
50 28 0.20
51 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (47 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCCTTTAAGT
Found at i:1885 original size:41 final size:41
Alignment explanation
Indices: 1806--1889 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
1796 ACCTTCATAT
* *
1806 TTAAGTCCAATGTAGCTGACCTTGAATCAGCACTTGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATAAGCACTTGGCACC
* *
1847 TTAAGTCCAATATAGCTGGCCTTGAATAATCA-TATGGCACC
1 TTAAGTCCAATATAGCTGACCTTGAATAAGCACT-TGGCACC
1888 TT
1 TT
1890 TCCATCTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (41 bp):
TTAAGTCCAATATAGCTGACCTTGAATAAGCACTTGGCACC
Found at i:1925 original size:91 final size:90
Alignment explanation
Indices: 1757--1929 Score: 251
Period size: 91 Copynumber: 1.9 Consensus size: 90
1747 CACCTTGCCT
* *
1757 TTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTCATATTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTAAATAAGCATATTGGCACCTTCATATTTAAGTCCAATGTAGC
1822 TGACCTTGAATCAGCACTTGGCACC
66 TGACCTTGAATCAGCACTTGGCACC
* * * *
1847 TTAAGTCCAATATAGCTGGCCTTGAATAATCATA-TGGCACCTTTCCATCTTTAAGTTCAATGTA
1 TTAAGTCCAATATAGCTGGCCTTAAATAAGCATATTGGCACC-TT-CATATTTAAGTCCAATGTA
1911 GCTCG-CCTTGAATCAGCAC
64 GCT-GACCTTGAATCAGCAC
1930 ATTGACATCC
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
89 7 0.09
90 32 0.43
91 34 0.46
92 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (90 bp):
TTAAGTCCAATATAGCTGGCCTTAAATAAGCATATTGGCACCTTCATATTTAAGTCCAATGTAGC
TGACCTTGAATCAGCACTTGGCACC
Found at i:2918 original size:12 final size:12
Alignment explanation
Indices: 2881--2925 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
2871 TGCCAAAAAC
2881 TGTATCGATACA
1 TGTATCGATACA
2893 T-TACTC-A-A-A
1 TGTA-TCGATACA
2902 TGTATCGATACA
1 TGTATCGATACA
2914 TGTATCGATACA
1 TGTATCGATACA
2926 CTGATCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.14
10 4 0.14
11 4 0.14
12 16 0.57
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:2977 original size:52 final size:50
Alignment explanation
Indices: 2913--3056 Score: 168
Period size: 50 Copynumber: 2.8 Consensus size: 50
2903 GTATCGATAC
*
2913 ATGTATCGATACACTGATCTTTGTATCGATACATGCCAGGC-AATTTGCCCAG
1 ATGTATCGATACACT-AT-TATGTATCGATACATGCCA-GCAAATTTGCCCAG
* *
2965 ATGTATCGATACATTATAAAATGTATCGATACATG-CAGCAAATTTGCCCAG
1 ATGTATCGATACACTAT--TATGTATCGATACATGCCAGCAAATTTGCCCAG
*
3016 A-GTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 ATGTATCGATACACTATT--ATGTATCGATACATGCCAGCAA
3057 CTTTTCATAT
Statistics
Matches: 80, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
50 31 0.39
51 21 0.26
52 28 0.35
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACACTATTATGTATCGATACATGCCAGCAAATTTGCCCAG
Found at i:3056 original size:51 final size:52
Alignment explanation
Indices: 2934--3056 Score: 189
Period size: 50 Copynumber: 2.4 Consensus size: 52
2924 CACTGATCTT
* *
2934 TGTATCGATACATGCCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATG-CAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2986 TGTATCGATACATGC-AGCAAATTTGCCCAGA-GTATCGATACACTATTAAA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3036 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAAGCAA
3057 CTTTTCATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
50 34 0.52
51 18 0.27
52 14 0.21
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3938 original size:21 final size:21
Alignment explanation
Indices: 3905--3944 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3895 TCATGTTAAC
3905 AAGCCATGATTCATGCATTTT
1 AAGCCATGATTCATGCATTTT
* *
3926 AAGCTATGCTTCATGCATT
1 AAGCCATGATTCATGCATT
3945 ATGGACATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (21 bp):
AAGCCATGATTCATGCATTTT
Found at i:8063 original size:4 final size:4
Alignment explanation
Indices: 8056--8080 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8046 AAACAGATAT
8056 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
8081 CACCTCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:10247 original size:28 final size:29
Alignment explanation
Indices: 10202--10256 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
10192 CGATGATTAG
*
10202 AAAAAAAATGGGGATTGGAGTATCCCCTC
1 AAAAAAAACGGGGATTGGAGTATCCCCTC
*
10231 AAAAATAACGGGG-TTGGAGTATCCCC
1 AAAAAAAACGGGGATTGGAGTATCCCC
10257 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (29 bp):
AAAAAAAACGGGGATTGGAGTATCCCCTC
Found at i:10330 original size:28 final size:28
Alignment explanation
Indices: 10290--10361 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
10280 GGAATAAAGC
** *
10290 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
10318 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
10346 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
10362 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:10344 original size:107 final size:108
Alignment explanation
Indices: 10211--10412 Score: 255
Period size: 107 Copynumber: 1.9 Consensus size: 108
10201 GAAAAAAAAT
* *
10211 GGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 GGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
10276 TTTGGGAATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAAC
66 TTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAAC
* * * * * ***
10319 GGGG-TTGGAGTATCCCC-GATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTA
1 GGGGATTGGAGTATCCCCTCA-AAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATA
*
10382 TTTTGGAAATAAAATCGGAGTTGGAGTATCC
65 TTTTGGAAATAAAACCGGAGTTGGAGTATCC
10413 TCGATTAAAG
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
106 1 0.01
107 74 0.94
108 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (108 bp):
GGGGATTGGAGTATCCCCTCAAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTTGGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAAGTAAC
Found at i:10413 original size:51 final size:50
Alignment explanation
Indices: 10349--10618 Score: 283
Period size: 51 Copynumber: 5.3 Consensus size: 50
10339 GAAATAACGA
* * *
10349 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGG
1 GGTTGGAGTATCC-CGATTATGAAAAATTAGTATTTTGAAAATAAAATCGG
* * * * * *
10400 AGTTGGAGTATCCTCGATTAAAGGAAAATTGGT-GTTTGAAAATAAAACCGG
1 GGTTGGAGTATCC-CGATT-ATGAAAAATTAGTATTTTGAAAATAAAATCGG
** * *
10451 GGTTGGAGTATCCCCGATTGCGGAAAAATTAGTGTTTT-AGCAATAAAATCGG
1 GGTTGGAGTAT-CCCGATT-ATGAAAAATTAGTATTTTGA-AAATAAAATCGG
* * *
10503 GGTTGGAGTATCCCTGATTATGAAAAATCAATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCC-GATTATGAAAAATTAGTATTTTGAAAATAAAATCGG
* * *
10554 GGTTGGAGTATCCCTGATTATGAAAAATCAATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCC-GATTATGAAAAATTAGTATTTTGAAAATAAAATCGG
10605 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
10619 CGATGATTAA
Statistics
Matches: 190, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
51 149 0.78
52 41 0.22
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (50 bp):
GGTTGGAGTATCCCGATTATGAAAAATTAGTATTTTGAAAATAAAATCGG
Found at i:10502 original size:103 final size:102
Alignment explanation
Indices: 10349--10618 Score: 285
Period size: 103 Copynumber: 2.6 Consensus size: 102
10339 GAAATAACGA
* * * *
10349 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGAGTTGGAGTAT-CC
1 GGTTGGAGTATCCCCGATTGGGAAAAATTAGTATTTTAGAAATAAAATCGGAGTTGGAGTATCCC
* ***
10413 TCGATTAAAGGAAAATTGGT-GTTTGAAAATAAAACCGG
66 T-GATT-AAGAAAAATCAATAGTTTGAAAATAAAACCGG
* * *
10451 GGTTGGAGTATCCCCGATTGCGGAAAAATTAGTGTTTTAGCAATAAAATCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTG-GGAAAAATTAGTATTTTAGAAATAAAATCGGAGTTGGAGTATCC
* * **
10516 CTGATTATGAAAAATCAATATTTTGAAAATAAAGTCGG
65 CTGATTAAGAAAAATCAATAGTTTGAAAATAAAACCGG
* ** * * * *
10554 GGTTGGAGTATCCCTGATTATGAAAAATCAATATTTT-GAAAATAAAGTCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGGGAAAAATTAGTATTTTAG-AAATAAAATCGGAGTTGGAGTATCC
10618 C
65 C
10619 CGATGATTAA
Statistics
Matches: 141, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
101 1 0.01
102 64 0.45
103 73 0.52
104 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (102 bp):
GGTTGGAGTATCCCCGATTGGGAAAAATTAGTATTTTAGAAATAAAATCGGAGTTGGAGTATCCC
TGATTAAGAAAAATCAATAGTTTGAAAATAAAACCGG
Found at i:10736 original size:51 final size:52
Alignment explanation
Indices: 10632--10756 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 52
10622 TGATTAACGG
* *
10632 GTTGGAGTATCCCCGATTGCGA-AGAAATTGGTGGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATT---ATAGAAATTAGTGGTTTTTGAAAATAAAATCGGA
10686 GTTGGAGTATCCCCGATTATAGAAAATTAGT-G-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAG-AAATTAGTGGTTTTTGAAAATAAAATCGGA
*
10737 GTTGGAATATCCCCGATTAT
1 GTTGGAGTATCCCCGATTAT
10757 GGAGAATTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
51 38 0.58
52 3 0.05
53 7 0.11
54 18 0.27
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAAATTAGTGGTTTTTGAAAATAAAATCGGA
Done.