Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold654
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: 13276
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.29
Warning! 749 characters in sequence are not A, C, G, or T
Found at i:2747 original size:21 final size:21
Alignment explanation
Indices: 2721--2770 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2711 AACAACTCAC
*
2721 TTAGTTTAATGAATAAAAAGT
1 TTAGTTTAATCAATAAAAAGT
2742 TTAGTTTAATCAATAAAAAGT
1 TTAGTTTAATCAATAAAAAGT
2763 TTAGTTTA
1 TTAGTTTA
2771 GTTTAGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (21 bp):
TTAGTTTAATCAATAAAAAGT
Found at i:2768 original size:5 final size:5
Alignment explanation
Indices: 2760--2793 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2750 ATCAATAAAA
2760 AGTTT AGTTT AGTTT AGTTT AGTTT AGTTT AGTT
1 AGTTT AGTTT AGTTT AGTTT AGTTT AGTTT AGTT
2794 GTGTGGCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
AGTTT
Found at i:3159 original size:25 final size:25
Alignment explanation
Indices: 3126--3219 Score: 134
Period size: 25 Copynumber: 3.7 Consensus size: 25
3116 CCAACACACC
* *
3126 AATATCGCAGCAAAGCTACCAGAAT
1 AATAACGCAGCAAAGCTGCCAGAAT
*
3151 AATAACGCAACAAAGCTGCCAGAAT
1 AATAACGCAGCAAAGCTGCCAGAAT
*
3176 AATAACGCAGCAAAGCTGCCAGTAAC
1 AATAACGCAGCAAAGCTGCCAG-AAT
*
3202 AGTAACGCAGCAAAGCTG
1 AATAACGCAGCAAAGCTG
3220 TCGGTAACAG
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 43 0.69
26 19 0.31
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (25 bp):
AATAACGCAGCAAAGCTGCCAGAAT
Found at i:3226 original size:26 final size:26
Alignment explanation
Indices: 3131--3231 Score: 116
Period size: 25 Copynumber: 4.0 Consensus size: 26
3121 ACACCAATAT
* * *
3131 CGCAGCAAAGCTACCAG-AATAATAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* * *
3156 CGCAACAAAGCTGCCAG-AATAATAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
3181 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTGCCAGTAACAGTAA
* *
3207 CGCAGCAAAGCTGTCGGTAACAGTA
1 CGCAGCAAAGCTGCCAGTAACAGTA
3232 TATGTCGCAA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
25 39 0.57
26 29 0.43
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.13
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTAACAGTAA
Found at i:3428 original size:27 final size:27
Alignment explanation
Indices: 3397--3635 Score: 236
Period size: 27 Copynumber: 8.9 Consensus size: 27
3387 TCAACTCCTA
** *
3397 AGGGTATAACAGTCATTTTACCCTTTG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * *
3424 GGGGTATTTCGGTCATTTTACACATT-G
1 AGGGTATTTCAGTCATTTTAC-CCTTCG
* *
3451 GGGGTATTTC-GATCATTTTACTCTTCG
1 AGGGTATTTCAG-TCATTTTACCCTTCG
3478 AGGGTATTTCAGTCATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTCG
* * *
3505 AGGGTATTTTATTCATTTTACCCTTGG
1 AGGGTATTTCAGTCATTTTACCCTTCG
3532 AGGGTATTTC-GATCATTTTACCCTTCG
1 AGGGTATTTCAG-TCATTTTACCCTTCG
*
3559 AGGGTATTTCAGT-TTTTTCACCCTTCG
1 AGGGTATTTCAGTCATTTT-ACCCTTCG
* * * * *
3586 AGCGTATTTCGGTTATTTTAACCTTCA
1 AGGGTATTTCAGTCATTTTACCCTTCG
*
3613 AGGGTATTT-TGATCATTTTACCC
1 AGGGTATTTCAG-TCATTTTACCC
3636 ACAAATCGCA
Statistics
Matches: 178, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.04
27 161 0.90
28 9 0.05
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTTTACCCTTCG
Found at i:3537 original size:81 final size:81
Alignment explanation
Indices: 3397--3635 Score: 295
Period size: 81 Copynumber: 3.0 Consensus size: 81
3387 TCAACTCCTA
** * * * *
3397 AGGGTATAACAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTACACATTGG-GGGTATTTC
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTCGTTCATTTTAC-CCTTGGAGGGTATTTC
*
3461 GATCATTTTACTCTTCG
65 GATCATTTTACCCTTCG
**
3478 AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTATTCATTTTACCCTTGGAGGGTATTTCG
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTCGTTCATTTTACCCTTGGAGGGTATTTCG
3543 ATCATTTTACCCTTCG
66 ATCATTTTACCCTTCG
* * * **
3559 AGGGTATTTCAGT-TTTTTCACCCTTCGAGCGTATTTCGGTT-ATTTTAACCTTCAAGGGTATTT
1 AGGGTATTTCAGTCATTTT-ACCCTTCGAGGGTATTTC-GTTCATTTTACCCTTGGAGGGTATTT
*
3622 TGATCATTTTACCC
64 CGATCATTTTACCC
3636 ACAAATCGCA
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
80 9 0.07
81 127 0.92
82 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (81 bp):
AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTCGTTCATTTTACCCTTGGAGGGTATTTCG
ATCATTTTACCCTTCG
Found at i:4525 original size:18 final size:18
Alignment explanation
Indices: 4491--4525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4481 AACAAGAAGA
*
4491 GAAAAAAAAGAATAAAAG
1 GAAAAAAAAGAAAAAAAG
*
4509 GAAAAGAAAGAAAAAAA
1 GAAAAAAAAGAAAAAAA
4526 TAAGCAAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
GAAAAAAAAGAAAAAAAG
Found at i:6671 original size:45 final size:44
Alignment explanation
Indices: 6611--6775 Score: 150
Period size: 45 Copynumber: 3.6 Consensus size: 44
6601 TAAATCTATC
* * *
6611 ACCCACCAAATACAACCAATTTACCCTCCAAACACAACAAAACAT
1 ACCCTCCAAACACAACCAATTTACCCTCCGAACACAAC-AAACAT
* * * **
6656 AGCCTCCAAACACAACTAATTTACCCTTCGAACACAACCAAATGT
1 ACCCTCCAAACACAACCAATTTACCCTCCGAACACAA-CAAACAT
* * * *
6701 ACCCTCAAAACAAAACCATATATATAACCTCCGAACACAACCAACTAT
1 ACCCTCCAAACACAACCA-AT-T-TACCCTCCGAACACAACAAAC-AT
* *
6749 ACCCTCCAAACACAATCAATATACCCT
1 ACCCTCCAAACACAACCAATTTACCCT
6776 TCAACATATC
Statistics
Matches: 93, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
45 54 0.58
46 3 0.03
47 6 0.06
48 30 0.32
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.17
Consensus pattern (44 bp):
ACCCTCCAAACACAACCAATTTACCCTCCGAACACAACAAACAT
Found at i:6712 original size:23 final size:23
Alignment explanation
Indices: 6611--6775 Score: 138
Period size: 23 Copynumber: 7.2 Consensus size: 23
6601 TAAATCTATC
* * *
6611 ACCCACCAAATACAACC-AATTT
1 ACCCTCCAAACACAACCAAATAT
* *
6633 ACCCTCCAAACACAACAAAACAT
1 ACCCTCCAAACACAACCAAATAT
* * *
6656 AGCCTCCAAACACAA-CTAATTT
1 ACCCTCCAAACACAACCAAATAT
* * *
6678 ACCCTTCGAACACAACCAAATGT
1 ACCCTCCAAACACAACCAAATAT
* *
6701 ACCCTCAAAACAAAACCATATATAT
1 ACCCTCCAAACACAACCA-A-ATAT
* * *
6726 AACCTCCGAACACAACCAACTAT
1 ACCCTCCAAACACAACCAAATAT
*
6749 ACCCTCCAAACACAATC-AATAT
1 ACCCTCCAAACACAACCAAATAT
6771 ACCCT
1 ACCCT
6776 TCAACATATC
Statistics
Matches: 110, Mismatches: 29, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
22 38 0.35
23 53 0.48
24 2 0.02
25 17 0.15
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.17
Consensus pattern (23 bp):
ACCCTCCAAACACAACCAAATAT
Found at i:10986 original size:22 final size:21
Alignment explanation
Indices: 10956--11341 Score: 169
Period size: 23 Copynumber: 16.7 Consensus size: 21
10946 CTATCACCCC
10956 CCAAACACAACCAATTTACTCT
1 CCAAACACAACCAATTTAC-CT
* *
10978 CGAAACACAGCCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
11000 CCAAACACAACCATATATATAACCT
1 CCAAACACAACCA-AT-T-T-ACCT
* *
11025 CCGAACACAACCAAGTATACCTT
1 CCAAACACAACCAA-TTTACC-T
11048 CCAAACACAACCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
*** * * *
11070 TTGAACATAACCAAATGTACTT
1 CCAAACACAACC-AATTTACCT
* *
11092 GCAAAACACCACCATATATATAACCT
1 -CCAAACACAACCA-AT-T-T-ACCT
* *
11118 CCGAACACAACCAACTATACCCT
1 CCAAACACAACCAA-TTTA-CCT
11141 CCAAACACAACCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
** * * *
11163 CTGAACATAACCAAATGTACTT
1 CCAAACACAACC-AATTTACCT
* *
11185 GCAAAACACCACCATATATATAACCT
1 -CCAAACACAACCA-AT-T-T-ACCT
* *
11211 CCGAACACAACCAAGTATACCTT
1 CCAAACACAACCAA-TTTACC-T
11234 CCAAACACAACCAATTTACCCT
1 CCAAACACAACCAATTTA-CCT
** * * *
11256 CTGAACATAACCAAATGTACTT
1 CCAAACACAACC-AATTTACCT
* *
11278 GCAAAACACCACCATATATATAACCT
1 -CCAAACACAACCA-AT-T-T-ACCT
* *
11304 CCGAACACAACCAACTATACCCT
1 CCAAACACAACCAA-TTTA-CCT
11327 CCAAACACAACCAAT
1 CCAAACACAACCAAT
11342 ATACTCTTTA
Statistics
Matches: 271, Mismatches: 60, Indels: 66
0.68 0.15 0.17
Matches are distributed among these distances:
22 88 0.32
23 115 0.42
24 5 0.02
25 53 0.20
26 10 0.04
ACGTcount: A:0.42, C:0.34, G:0.04, T:0.19
Consensus pattern (21 bp):
CCAAACACAACCAATTTACCT
Found at i:11114 original size:93 final size:93
Alignment explanation
Indices: 10946--11341 Score: 627
Period size: 93 Copynumber: 4.3 Consensus size: 93
10936 TAGCATAAAG
* * * * * * *
10946 CTATCACCCCCCAAACACAACCAATTTACTCTC-GAAACACAGCC-AATTTACCCT-CCAAACAC
1 CTAT-ACCCTCCAAACACAACCAATTTACCCTCTG-AACATAACCAAATGTA-CTTGCAAAACAC
*
11008 AACCATATATATAACCTCCGAACACAACCAA
63 CACCATATATATAACCTCCGAACACAACCAA
* * *
11039 GTATACCTTCCAAACACAACCAATTTACCCTTTGAACATAACCAAATGTACTTGCAAAACACCAC
1 CTATACCCTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
11104 CATATATATAACCTCCGAACACAACCAA
66 CATATATATAACCTCCGAACACAACCAA
11132 CTATACCCTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
1 CTATACCCTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
11197 CATATATATAACCTCCGAACACAACCAA
66 CATATATATAACCTCCGAACACAACCAA
* *
11225 GTATACCTTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
1 CTATACCCTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
11290 CATATATATAACCTCCGAACACAACCAA
66 CATATATATAACCTCCGAACACAACCAA
11318 CTATACCCTCCAAACACAACCAAT
1 CTATACCCTCCAAACACAACCAAT
11342 ATACTCTTTA
Statistics
Matches: 282, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
92 33 0.12
93 249 0.88
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (93 bp):
CTATACCCTCCAAACACAACCAATTTACCCTCTGAACATAACCAAATGTACTTGCAAAACACCAC
CATATATATAACCTCCGAACACAACCAA
Found at i:11844 original size:20 final size:21
Alignment explanation
Indices: 11802--11846 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
11792 AATTACTTTA
11802 AAAACACATTATAAATAACCT
1 AAAACACATTATAAATAACCT
* *
11823 AAAACACATT-TAAATCATCT
1 AAAACACATTATAAATAACCT
11843 AAAA
1 AAAA
11847 ACTGCATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAACACATTATAAATAACCT
Found at i:11847 original size:21 final size:22
Alignment explanation
Indices: 11800--11848 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11790 TTAATTACTT
11800 TAAAAACACATTATAAATAACC
1 TAAAAACACATTATAAATAACC
* *
11822 T-AAAACACATT-TAAATCATC
1 TAAAAACACATTATAAATAACC
11842 TAAAAAC
1 TAAAAAC
11849 TGCATACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAACACATTATAAATAACC
Found at i:12489 original size:65 final size:65
Alignment explanation
Indices: 12408--12537 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
12398 TTCCTCAAAT
*
12408 TTGAAAAGAAATTTTGCGTTTAAAGAGCTTAGGAATAAACATGGATGAACTAATTTTGAAAGAAA
1 TTGAAAAGAAATTTTGCGCTTAAAGAGCTTAGGAATAAACATGGATGAACTAATTTTGAAAGAAA
12473 TTGAAAAGAAATTTTGCGCTTAAAGAGCTTAGGAATAAACATGGATGAACTAATTTTGAAAGAAA
1 TTGAAAAGAAATTTTGCGCTTAAAGAGCTTAGGAATAAACATGGATGAACTAATTTTGAAAGAAA
12538 AACTTTAATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (65 bp):
TTGAAAAGAAATTTTGCGCTTAAAGAGCTTAGGAATAAACATGGATGAACTAATTTTGAAAGAAA
Done.