Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold921
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: 4223
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.30
Warning! 608 characters in sequence are not A, C, G, or T
Found at i:132 original size:40 final size:41
Alignment explanation
Indices: 77--221 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 41
67 GTCTACTCCG
77 CTACTGCTTAGGGAGATAAGACTTGATGT-GATCTGCTTCA
1 CTACTGCTTAGGGAGATAAGACTTGATGTAGATCTGCTTCA
* * *
117 CTACTGCTTAGGGAGATAGGAC-TGGTAGCTTAAATCTGCTTCA
1 CTACTGCTTAGGGAGATAAGACTTGAT-G--TAGATCTGCTTCA
* * * * **
160 CTACTGTTTAGGAAGATAAGA-TTCGCCATTTTCGATCTGCCCCA
1 CTACTGCTTAGGGAGATAAGACTT-G--A-TGTAGATCTGCTTCA
204 CTACTGCTTAGGGAGATA
1 CTACTGCTTAGGGAGATA
222 GGATCTACCA
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
39 3 0.04
40 22 0.27
42 1 0.01
43 29 0.35
44 26 0.32
47 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
CTACTGCTTAGGGAGATAAGACTTGATGTAGATCTGCTTCA
Found at i:249 original size:44 final size:44
Alignment explanation
Indices: 105--249 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
95 AGACTTGATG
* ** *
105 TGATCTGCTTCACTACTGCTTAGGGAGATAGGA-CTGGTAGCTT
1 TGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGCCATCTT
** * * * *
148 AAATCTGCTTCACTACTGTTTAGGAAGATAAGAT-TCGCCAT-TT
1 TGATCTGCTCCACTACTGCTTAGGGAGATAGGATCT-GCCATCTT
* *
191 TCGATCTGCCCCACTACTGCTTAGGGAGATAGGATCTACCATCTT
1 T-GATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGCCATCTT
*
236 TGACCTGCTCCACT
1 TGATCTGCTCCACT
250 GTAACCTCAG
Statistics
Matches: 79, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
43 31 0.39
44 44 0.56
45 4 0.05
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (44 bp):
TGATCTGCTCCACTACTGCTTAGGGAGATAGGATCTGCCATCTT
Found at i:302 original size:46 final size:46
Alignment explanation
Indices: 243--358 Score: 205
Period size: 46 Copynumber: 2.5 Consensus size: 46
233 CTTTGACCTG
*
243 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTTTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGGTTTA
**
289 CTCCACTGTAACCTCAGGGAGATAAGACCTGATGTTCTTCGGTTTA
1 CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGGTTTA
335 CTCCACTGTAACCTCAGGGAGATA
1 CTCCACTGTAACCTCAGGGAGATA
359 CTAATCCGCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (46 bp):
CTCCACTGTAACCTCAGGGAGATAAGACCTGAAATTCTTCGGTTTA
Found at i:520 original size:90 final size:90
Alignment explanation
Indices: 416--704 Score: 345
Period size: 90 Copynumber: 3.2 Consensus size: 90
406 ATCTGCTCTT
416 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
*
481 AAACTTGCATATTCAACCTGCCCCA
66 AGACTTGCATATTCAACCTGCCCCA
* * * * * ** *
506 CTGTAA-CTTCAGGGAGATAAGGTTTG---TGGCTTCGATCTGCTCTTCTGTAATCTCAGGGAGA
1 CTGTAATC-TCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGA
** **** * * **
567 TAAGGTTTGTGGCTTCAATCTGCTCTT
64 TAAGACTTGCATATTCAACCTGCCCCA
594 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
1 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
659 AGACTTGCATATTCAACCTGCCCCA
66 AGACTTGCATATTCAACCTGCCCCA
684 CTGTAA-CTTCAGGGAGATAAG
1 CTGTAATC-TCAGGGAGATAAG
705 GGTTTATGTG
Statistics
Matches: 155, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
87 1 0.01
88 65 0.42
89 3 0.02
90 85 0.55
91 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (90 bp):
CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATA
AGACTTGCATATTCAACCTGCCCCA
Found at i:679 original size:178 final size:177
Alignment explanation
Indices: 366--1095 Score: 762
Period size: 175 Copynumber: 4.2 Consensus size: 177
356 ATACTAATCC
* *
366 GCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCTTCTGTAATCTCAGGGA
1 GCTCCTCTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCCTCTGTAATCTCAGGGA
* *
431 GATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAAACTTGCATATTC
66 GATAAGATCT--AATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTC
495 AACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCT
129 AACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCT
* *
544 GCTCTTCTGTAA-TCTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCTTCTGTAATCTCAGGG
1 GCTCCTCTGTAACT-TCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCCTCTGTAATCTCAGGG
*
608 AGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATT
65 AGATAAGATCT--AATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATT
* *
672 CAACCTGCCCCACTGTAACTTCAGGGAGATAAGGGTTTAT-G--T-GACCT
128 CAACCTGCCCCACTGTAACTTCAGGGAGATAA-GGTTTGTGGCTTCGATCT
* ** * * * *
719 GCT-CTGCTGTAACTTCAGAGAGAT-AGGATCCTT-T-ATTTTAATCCGCTCCACTATAA-CTTC
1 GCTCCT-CTGTAACTTCAGGGAGATAAGG-T--TTGTGGCTTCAATCTGCTCCTCTGTAATC-TC
* * * * * * *
779 AGGGAGATAGGA--TAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAAATAAGATCTCTG-G
61 AGGGAGATAAGATCTAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGA-CT-TGCA
* * * * * * *** ** *
841 T-GTCAATCTGCTCCATTGTAACCTCAGGGAGATAAGATCTT-TTATTTTAATCC
124 TATTCAACCTGCCCCACTGTAACTTCAGGGAGATAAGGT-TTGTGGCTTCGATCT
* * * * * * *
894 GCTCCACTGTAACTTCAGAGAGAT-AGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCTCTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCCTCTGTAATCTCAGGGA
* * * *
958 GATAAGATCT-CTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCTA
66 GATAAGATCTAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAA
*
1022 CCTGCCCCACTGTAACTTCAGGGAGATAAAGTTTGTGGCTTCGATCT
131 CCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCT
1069 GCTCCTCTGTAA-TCTCAGGGAGATAAG
1 GCTCCTCTGTAACT-TCAGGGAGATAAG
1096 ATCTGAAATT
Statistics
Matches: 458, Mismatches: 67, Indels: 56
0.79 0.12 0.10
Matches are distributed among these distances:
171 5 0.01
172 65 0.14
173 7 0.02
174 42 0.09
175 167 0.36
176 7 0.02
177 3 0.01
178 156 0.34
179 6 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (177 bp):
GCTCCTCTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCCTCTGTAATCTCAGGGA
GATAAGATCTAATGTCTTCGATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAA
CCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCT
Found at i:852 original size:131 final size:131
Alignment explanation
Indices: 360--1142 Score: 617
Period size: 131 Copynumber: 5.9 Consensus size: 131
350 AGGGAGATAC
* * * * **
360 TAATCCGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCTTCTGTAATCT
1 TAATCCGCTCCACTGTAACTTCAGGGAGAT-AGGATAGTGTCTTCGATCTGCTCCGCTGTAATCT
* * ** * *
425 CAGGGAGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAA-A-ACTT
65 CAGGGAGATAAGATCT---CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTT
*
487 GCATATT
127 -TAT-TT
* * * * * **
494 CAA-CCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTCGATCTGCTCTTCTGTAATC
1 TAATCC-GCTCCACTGTAACTTCAGGGAGAT-AGGATAGTGTCTTCGATCTGCTCCGCTGTAATC
* * * ** * **
558 TCAGGGAGATAAGGTTTGTGGCTTCAATCTGCTCTTCTGTAATCTCAGGGAGATAAGAT-CTGAA
64 TCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCT-TT
622 ATTCT
128 ATT-T
** ** * * * ** * * * * *
627 TCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTCAACCTGCCCCACTGTAA-C
1 T-AATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAATC
* * * * * ** * * *
691 TTCAGGGAGATAAGGGTTTAT-G--T-GACCTGCTCTGCTGTAACTTCAGAGAGATAGGATCCTT
64 -TCAGGGAGATAA-GATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTT
752 TATTT
127 TATTT
*
757 TAATCCGCTCCACTATAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
1 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
* * *
822 AGGGAAATAAGATCTCTGG-TGTCAATCTGCTCCATTGTAACCTCAGGGAGATAAGATCTTTTAT
66 AGGGAGATAAGATCTCTGGCT-TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTTTAT
886 TT
130 TT
*
888 TAATCCGCTCCACTGTAACTTCAGAGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
1 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
*
953 AGGGAGATAAGATCTCTGGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGA--CTTGCAT
66 AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTT---T
*
1016 ATTC
128 ATTT
* * * * * *
1020 T-A-CCTGCCCCACTGTAACTTCAGGGAGATAAAGTTTGTGGCTTCGATCTGCTCCTCTGTAATC
1 TAATCC-GCTCCACTGTAACTTCAGGGAGAT-AGGATAGTGTCTTCGATCTGCTCCGCTGTAATC
* * ** *
1083 TCAGGGAGATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA
64 TCAGGGAGATAAGATCT---CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA
1143 CNNNNNNNNN
Statistics
Matches: 534, Mismatches: 89, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
127 4 0.01
128 31 0.06
129 29 0.05
130 5 0.01
131 202 0.38
132 84 0.16
133 11 0.02
134 160 0.30
135 8 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (131 bp):
TAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCTTTATT
T
Found at i:1079 original size:44 final size:44
Alignment explanation
Indices: 361--1142 Score: 407
Period size: 44 Copynumber: 17.8 Consensus size: 44
351 GGGAGATACT
* *
361 AATCCGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
** * *
405 AATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTGAAAT-TCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTG---TGGCTTC
** * * * * ****
451 GGTCTACTCCACTGTAACCTCAGGGAGATAAAACTTGCATATTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* * *
495 AACCTGCCCCACTGTAACTTCAGGGAGATAAGGTTTGTGGCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* ** *
539 GATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGGTTTGTGGCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTGTGGCTTC
** * *
583 AATCTGCTCTTCTGTAA-TCTCAGGGAGATAAGATCTGAAAT-TCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTG---TGGCTTC
** * * * ****
629 GGTCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* * * *
673 AACCTGCCCCACTGTAACTTCAGGGAGATAAGGGTTTAT-G--T-
1 AATCTGCTCCACTGTAACTTCAGGGAGATAA-GATTTGTGGCTTC
* * ** * * ** *
714 GACCTGCTCTGCTGTAACTTCAGAGAGATAGGATCCTT-T-ATTTT
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGAT--TTGTGGCTTC
* * * * *
758 AATCCGCTCCACTATAACTTCAGGGAGATAGGA-TAGTGTCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* * * * *
801 GATCTGCTCCGCTGTAA-TCTCAGGGAAATAAGATCTCTGG-TGTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTGTGGCT-TC
* * *** *
845 AATCTGCTCCATTGTAACCTCAGGGAGATAAGATCTT-TTATTTT
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGAT-TTGTGGCTTC
* * * * *
889 AATCCGCTCCACTGTAACTTCAGAGAGATAGGA-TAGTGTCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* * * *
932 GATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTGTGGCTTC
* * * ****
976 AATCTACTCCACTGTAACCTCAGGGAGATAAGACTTGCATATTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
* * *
1020 TACCTGCCCCACTGTAACTTCAGGGAGATAA-AGTTTGTGGCTTC
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TTTGTGGCTTC
* * * *
1064 GATCTGCTCCTCTGTAA-TCTCAGGGAGATAAGATCTGAAAT-TCTTC
1 AATCTGCTCCACTGTAACT-TCAGGGAGATAAGATTTG---TGGCTTC
** * *
1110 GGTCTACTCCACTGTAACCTCAGGGAGATAAGA
1 AATCTGCTCCACTGTAACTTCAGGGAGATAAGA
1143 CNNNNNNNNN
Statistics
Matches: 553, Mismatches: 148, Indels: 72
0.72 0.19 0.09
Matches are distributed among these distances:
40 2 0.00
41 27 0.05
42 7 0.01
43 62 0.11
44 351 0.63
45 6 0.01
46 95 0.17
47 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTGGCTTC
Found at i:2588 original size:14 final size:13
Alignment explanation
Indices: 2569--2629 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
2559 TTAGCCTCTC
*
2569 CATTTTTTATCTTT
1 CATTTTTCAT-TTT
2583 CATTTTTCATTTT
1 CATTTTTCATTTT
* *
2596 CCTTTTTCCTTTT
1 CATTTTTCATTTT
* * *
2609 TAATTCTCATTTTT
1 CATTTTTCA-TTTT
2623 CATTTTT
1 CATTTTT
2630 TTTCAGAGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
13 18 0.51
14 17 0.49
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:2592 original size:7 final size:7
Alignment explanation
Indices: 2569--2629 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
2559 TTAGCCTCTC
2569 CATTTTT
1 CATTTTT
* *
2576 TATCTTT
1 CATTTTT
2583 CATTTTT
1 CATTTTT
2590 CA-TTTT
1 CATTTTT
*
2596 CCTTTTT
1 CATTTTT
*
2603 CCTTTTT
1 CATTTTT
* *
2610 -AATTCT
1 CATTTTT
2616 CATTTTT
1 CATTTTT
2623 CATTTTT
1 CATTTTT
2630 TTTCAGAGTG
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 8 0.19
7 34 0.81
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:2603 original size:20 final size:20
Alignment explanation
Indices: 2580--2629 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2570 ATTTTTTATC
* * *
2580 TTTCATTTTTCATTTTCCTT
1 TTTCATTTTTAATTCTCATT
*
2600 TTTCCTTTTTAATTCTCATT
1 TTTCATTTTTAATTCTCATT
2620 TTTCATTTTT
1 TTTCATTTTT
2630 TTTCAGAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTCATTTTTAATTCTCATT
Found at i:3570 original size:6 final size:6
Alignment explanation
Indices: 3565--3599 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3555 TCTCAGTTTC
*
3565 ATTTTC ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
3600 TTTCCTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.03, G:0.11, T:0.69
Consensus pattern (6 bp):
ATTTTG
Done.