Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2022
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: 26052
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:5242 original size:81 final size:79
Alignment explanation
Indices: 5058--5292 Score: 249
Period size: 81 Copynumber: 2.9 Consensus size: 79
5048 AAAGATTTGG
* * * *
5058 TGTTTG-GGAAATAAAAATGGGGTTAGAGTATCCCCTCAAAATGGAGGGGTTGGAA-TACCCCCT
1 TGTTTGAGAAAAT-AAAATGGGGTTGGAGTATCCCCTCAAAATGGTGGGGTT-GAAGTATCCCCT
* *
5121 GAGATGAAAATTTCAG
64 GAGATGAAAAATTCAA
* ** *
5137 TGTTTGAGAAATAAAAAACAGGGTTGGAGTATCCCCTCAGAAATGGTGGGGTTGAAGTATCCCCA
1 TGTTTGAGAAA-ATAAAATGGGGTTGGAGTATCCCCTCA-AAATGGTGGGGTTGAAGTATCCCCT
*
5202 GAAATGAAGAAATTCAA
64 GAGATGAA-AAATTCAA
* * * ** *
5219 TGTTTTAGAAAATAAAATGGGGTTGGAGTATTGCCCTCAAAATGATAAGGTTGGAGTATCCCCTG
1 TGTTTGAGAAAATAAAATGGGGTTGGAGTA-TCCCCTCAAAATGGTGGGGTTGAAGTATCCCCTG
5284 AGATGAAAA
65 AGATGAAAA
5293 TTTAGGTGTT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
79 6 0.05
80 30 0.23
81 69 0.54
82 23 0.18
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (79 bp):
TGTTTGAGAAAATAAAATGGGGTTGGAGTATCCCCTCAAAATGGTGGGGTTGAAGTATCCCCTGA
GATGAAAAATTCAA
Found at i:7366 original size:21 final size:20
Alignment explanation
Indices: 7319--7372 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
7309 CATTTCAGAC
*
7319 ATGTATCAATACATTTACTT
1 ATGTATCAATACATTCACTT
*
7339 ATGTATCGATACATTCACTT
1 ATGTATCAATACATTCACTT
7359 ATTGTATCAATACA
1 A-TGTATCAATACA
7373 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:9729 original size:74 final size:72
Alignment explanation
Indices: 9546--10086 Score: 468
Period size: 74 Copynumber: 7.5 Consensus size: 72
9536 GATCAAGGAC
* * ** * *
9546 AAAAGAGATAAAAA--GTGTCACCAGCTTGTGTGGGC--TTTAAAAGAAAAAAACATCCTGCTCC
1 AAAAG-GATAAAAAGGGTGCCACCAACTTGTGTGGGCTTTTTAAAA-AGGAAAACGTCCTGCTCT
*
9607 TTGAGGACTA
64 TTGAGGA-TT
* * * * *
9617 AAAAGGATAAAAGGGGTGCCACTAGCTTATGTGGGCTTTTTTTAAAAAGGAAAACGTCATGCTCT
1 AAAAGGATAAAAAGGGTGCCACCAACTTGTGTGGGC--TTTTTAAAAAGGAAAACGTCCTGCTCT
*
9682 TTTAGGATT
64 TTGAGGATT
* * * * *
9691 AAAAGGATAAAAAGGGTGCTACCATCTTGTGTGAGC-TTTT-AAAA--AAAATGTCTTGCTCTTT
1 AAAAGGATAAAAAGGGTGCCACCAACTTGTGTGGGCTTTTTAAAAAGGAAAACGTCCTGCTCTTT
*
9752 -AAGATT
66 GAGGATT
* * * *
9758 AAAA-GAT-AAAAGGGATGCCACCAACTTGTGTGGAGCTTTTAAAAAAGGAAAGCAT-CTTCTCT
1 AAAAGGATAAAAAGGG-TGCCACCAACTTGTGTGG-GCTTTTTAAAAAGGAAAACGTCCTGCTCT
9820 TTGAGGACTCT
64 TTGAGGA-T-T
* *
9831 AAAAGGAT-AAAAGTGGTGCTACCAACTTGTGTGGGC-TTTTAAAAAGAAAAAGACGTCCTTGCT
1 AAAAGGATAAAAAG-GGTGCCACCAACTTGTGTGGGCTTTTTAAAAAG-GAAA-ACGTCC-TGCT
9894 CTTTGAGGATT
62 CTTTGAGGATT
* * * * * *
9905 GAAAGGAT-AAAGGGGT-ACACCTACTTGTGTGGGC-TTTTAAAAAGGAAAGCGTCCTACTCTTT
1 AAAAGGATAAAAAGGGTGCCACCAACTTGTGTGGGCTTTTTAAAAAGGAAAACGTCCTGCTCTTT
*
9967 GAGGACT
66 GAGGATT
* * **
9974 AAAAGGATAAAAAGGGTTTGCCACTAACTTGTGTGGGCTTTTAAAAAAGGAAAGTGTCCTGCTCT
1 AAAAGGATAAAAAGGG--TGCCACCAACTTGTGTGGGCTTTTTAAAAAGGAAAACGTCCTGCTCT
* *
10039 TTAAGGACT
64 TTGAGGATT
* *
10048 AAAAGGATAAAAAGGGTGCCACCAGCTTGTATGGGCTTT
1 AAAAGGATAAAAAGGGTGCCACCAACTTGTGTGGGCTTT
10087 GAAAGAGAAA
Statistics
Matches: 387, Mismatches: 57, Indels: 51
0.78 0.12 0.10
Matches are distributed among these distances:
65 7 0.02
66 18 0.05
67 11 0.03
68 18 0.05
69 24 0.06
70 29 0.07
71 19 0.05
72 74 0.19
73 28 0.07
74 117 0.30
75 23 0.06
76 19 0.05
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (72 bp):
AAAAGGATAAAAAGGGTGCCACCAACTTGTGTGGGCTTTTTAAAAAGGAAAACGTCCTGCTCTTT
GAGGATT
Found at i:10077 original size:145 final size:140
Alignment explanation
Indices: 9541--10086 Score: 520
Period size: 145 Copynumber: 3.8 Consensus size: 140
9531 GTAATGATCA
* * * * ***
9541 AGGAC-AAAAGAGATAAAAAGTGT-C-ACCAGCTTGTGTGGGCTTTAAAAGAAAAAAACATCCTG
1 AGGACTAAAAG-GATAAAAAGGGTGCTACCAACTTGTGTGGGCTTTTAAA-AAGAAAGTGTCCTG
* * * *
9603 CTCCTTGAGGACTAAAAAGGATAAAAGGGGTGCCACTAGCTTATGTGGGCTTTTTTTAAAAAGGA
64 CTCTTTAAGGACT-AAAAGGATAAAA-GGGTGCCACCAGCTTGTGTGGGC---TTTTAAAAAGGA
* * * *
9668 AAACGTCATGCTCTTTT
124 AAGCGTCCTACTCTTTG
* * * *
9685 AGGATTAAAAGGATAAAAAGGGTGCTACCATCTTGTGTGAGCTTTTAAAAA-AAA-TGTCTTGCT
1 AGGACTAAAAGGATAAAAAGGGTGCTACCAACTTGTGTGGGCTTTTAAAAAGAAAGTGTCCTGCT
* *
9748 CTTTAA-GATTAAAA-GATAAAAGGGATGCCACCAACTTGTGTGGAGCTTTTAAAAAAGGAAAGC
66 CTTTAAGGACTAAAAGGATAAAAGGG-TGCCACCAGCTTGTGTGG-GCTTTT-AAAAAGGAAAGC
* *
9811 AT-CTTCTCTTTG
128 GTCCTACTCTTTG
*
9823 AGGACTCTAAAAGGAT-AAAAGTGGTGCTACCAACTTGTGTGGGCTTTTAAAAAGAAAAAGACGT
1 AGGA--CTAAAAGGATAAAAAG-GGTGCTACCAACTTGTGTGGGCTTTTAAAAAG--AAAG-TGT
* * * * *
9887 CCTTGCTCTTTGAGGATTGAAAGGATAAAGGGGT-ACACCTA-CTTGTGTGGGCTTTTAAAAAGG
60 CC-TGCTCTTTAAGGACTAAAAGGATAAAAGGGTGCCACC-AGCTTGTGTGGGCTTTTAAAAAGG
9950 AAAGCGTCCTACTCTTTG
123 AAAGCGTCCTACTCTTTG
* *
9968 AGGACTAAAAGGATAAAAAGGGTTTGCCACTAACTTGTGTGGGCTTTTAAAAAAGGAAAGTGTCC
1 AGGACTAAAAGGATAAAAAGGG--TGCTACCAACTTGTGTGGGCTTTT-AAAAA-GAAAGTGTCC
*
10033 TGCTCTTTAAGGACTAAAAGGATAAAAAGGGTGCCACCAGCTTGTATGGGCTTT
62 TGCTCTTTAAGGACTAAAAGGAT-AAAAGGGTGCCACCAGCTTGTGTGGGCTTT
10087 GAAAGAGAAA
Statistics
Matches: 336, Mismatches: 39, Indels: 53
0.79 0.09 0.12
Matches are distributed among these distances:
138 15 0.04
139 20 0.06
140 60 0.18
141 6 0.02
142 3 0.01
143 45 0.13
144 48 0.14
145 73 0.22
146 47 0.14
147 10 0.03
148 9 0.03
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (140 bp):
AGGACTAAAAGGATAAAAAGGGTGCTACCAACTTGTGTGGGCTTTTAAAAAGAAAGTGTCCTGCT
CTTTAAGGACTAAAAGGATAAAAGGGTGCCACCAGCTTGTGTGGGCTTTTAAAAAGGAAAGCGTC
CTACTCTTTG
Found at i:11188 original size:16 final size:17
Alignment explanation
Indices: 11159--11193 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
11149 TTTGTTCTCT
*
11159 TTTTTCTTTTTTTTTTG
1 TTTTTCTTTCTTTTTTG
11176 TTTTT-TTTCTTTTTTG
1 TTTTTCTTTCTTTTTTG
11192 TT
1 TT
11194 GTTGTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (17 bp):
TTTTTCTTTCTTTTTTG
Found at i:11195 original size:19 final size:20
Alignment explanation
Indices: 11158--11196 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
11148 GTTTGTTCTC
*
11158 TTTTTTCTTTTTTTTTTGTT
1 TTTTTTCTTTTTTTGTTGTT
11178 TTTTTTC-TTTTTTGTTGTT
1 TTTTTTCTTTTTTTGTTGTT
11197 GTTGTTGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (20 bp):
TTTTTTCTTTTTTTGTTGTT
Found at i:11409 original size:20 final size:20
Alignment explanation
Indices: 11382--11419 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11372 TCACATTTTG
11382 TCTAAATGTATC-ATACATT
1 TCTAAATGTATCGATACATT
11401 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
11420 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:13731 original size:24 final size:26
Alignment explanation
Indices: 13704--13755 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
13694 ATCAAAATTT
13704 CATTCAT-C-GGGGACACTCCAACCC
1 CATTCATCCAGGGGACACTCCAACCC
*
13728 CATTCCTCCGAGGGGACACTCCAACCC
1 CATTCATCC-AGGGGACACTCCAACCC
13755 C
1 C
13756 GTTTTCAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 1 0.04
27 17 0.71
ACGTcount: A:0.23, C:0.44, G:0.17, T:0.15
Consensus pattern (26 bp):
CATTCATCCAGGGGACACTCCAACCC
Found at i:25448 original size:9 final size:8
Alignment explanation
Indices: 25431--25465 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
25421 GAGAGACAAA
25431 AAAAAAAC
1 AAAAAAAC
25439 AAACAAAAC
1 AAA-AAAAC
*
25448 AAAAAAAG
1 AAAAAAAC
25456 AAAAAAAC
1 AAAAAAAC
25464 AA
1 AA
25466 CAACAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:25452 original size:21 final size:22
Alignment explanation
Indices: 25426--25474 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
25416 AAAAAGAGAG
*
25426 ACAAAAAAA-AAACAAACAA-A
1 ACAAAAAAAGAAAAAAACAACA
25446 ACAAAAAAAGAAAAAAACAACA
1 ACAAAAAAAGAAAAAAACAACA
25468 ACAAAAA
1 ACAAAAA
25475 GGGTCCGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (22 bp):
ACAAAAAAAGAAAAAAACAACA
Found at i:25462 original size:16 final size:17
Alignment explanation
Indices: 25431--25465 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25421 GAGAGACAAA
25431 AAAAAAACAAACAAAAC
1 AAAAAAACAAACAAAAC
*
25448 AAAAAAAGAAA-AAAAC
1 AAAAAAACAAACAAAAC
25464 AA
1 AA
25466 CAACAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAACAAAAC
Found at i:25475 original size:20 final size:20
Alignment explanation
Indices: 25426--25475 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
25416 AAAAAGAGAG
*
25426 ACAAAAAAAAAACAAACAAA
1 ACAAAAAGAAAACAAACAAA
25446 ACAAAAAAAGAAAA-AAACAACA
1 AC--AAAAAGAAAACAAACAA-A
25468 ACAAAAAG
1 ACAAAAAG
25476 GGTCCGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 8 0.31
21 6 0.23
22 12 0.46
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (20 bp):
ACAAAAAGAAAACAAACAAA
Done.