Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3574
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: 16268
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Found at i:11409 original size:43 final size:43
Alignment explanation
Indices: 11286--12354 Score: 946
Period size: 43 Copynumber: 24.7 Consensus size: 43
11276 ATAGGTCCTA
* * *
11286 TCTTCCTATATTGGTAG-GAAGTGGATCAAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * *
11329 TCTTCCCATATTGGTGGCGAAGTAGATCGAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGA-AGAGCAGATCTTG
* * *
11373 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGTAGCAGATC-TA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG-AGCAGATCTTG
* *
11415 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * *
11458 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG-AGCAGATCTTG
* *
11501 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * *
11544 TCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAGCAGATCTTG
* * * *
11587 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG-AGCAGATCTTG
* *
11630 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * *
11673 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCG-A-AGAGCAGATCTTG
* * * *
11718 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAG-TCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG--AGCAGATCTTG
* *
11761 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * * *
11804 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCG-A-AGAGCAGATCTTG
* * * *
11849 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAA-G-AGCAGATCTTG
11893 TCTTCCTATATTGG-CGTGAAGTAGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * *
11936 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGAGCAGATCCTA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAGCAGATCTTG
* *
11978 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * ** *
12021 TCTTCCCATATTGGTGGCAAAGT--ATCGCAGAAAG-AGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCG-A-AGAGCAGATCTTG
* * * *
12063 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG--AGCAGATCTTG
* * *
12107 TCTTCCTATATTGGTAG-GAAGTGGATCGACGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * * *
12150 TCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG--AGCAGATCTTG
* * * *
12195 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAG--AGCAGATCTTG
* * * *
12239 TCTTCCTATATCGGTAG-GAAGTGGATCGACGATGCAGATCTTG
1 TCTTCCTATATTGGTCGTGAAGTAGATCGAAGA-GCAGATCTTG
* * *
12282 TCTTCCCATACTGGT-G-GCAAGTAGATCGAAGAAAGCAGATCTTA
1 TCTTCCTATATTGGTCGTG-AAGTAGATCGAAG--AGCAGATCTTG
* *
12326 TCTTCATGTATTGG-CGTGAAGTAGATCGA
1 TCTTCCTATATTGGTCGTGAAGTAGATCGA
12355 GGATTGTAGA
Statistics
Matches: 835, Mismatches: 141, Indels: 99
0.78 0.13 0.09
Matches are distributed among these distances:
41 8 0.01
42 121 0.14
43 369 0.44
44 263 0.31
45 69 0.08
46 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TCTTCCTATATTGGTCGTGAAGTAGATCGAAGAGCAGATCTTG
Found at i:12172 original size:477 final size:475
Alignment explanation
Indices: 11278--12354 Score: 1896
Period size: 477 Copynumber: 2.3 Consensus size: 475
11268 AGGCGTAAAT
*
11278 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
*
11343 TGGCGAAGTAGATCGAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGC
66 TGGCGAAGTAGATCGAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGC
*
11408 AGATCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCATGTATTGGC
131 AGATCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTGTCTTCATGTATTGGC
11473 GTGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAG
196 GTGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAG
* *
11538 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAGCAGATCTTGTCTTCATGTATTGGCG
261 ATCTTGTCTTCCCATATTGGTGGCAAAGTA-ATCGAAAAGCAGATCTTGTCTTCATGTATTGGCG
11603 TGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGA
325 TGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGA
* *
11668 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
390 TCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGC
11733 GTGAAGTAGATCGAAGATAGC
455 GTGAAGTAGATCGAAGATAGC
11754 A-GTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
11818 TGGCGAAGTAGATCGCAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGGTA
66 TGGCGAAGTAGATCG-AGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAA-GTA
*
11883 GCAGATCCTATCTTCCTATATTGG-CGTGAAGTAGATCGAAGATGCAGATCTTGTCTTCATGTAT
129 GCAGAT-CTATCTTCCTATATTGGTAG-GAAGTAGATCGAAGATGCAGATCTTGTCTTCATGTAT
11947 TGGCGTGAAGTAGATCGAAG-AGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
192 TGGCGTGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT
12011 GCAGATCTTGTCTTCCCATATTGGTGGCAAAGT-ATCGCAGAAAG-AGATCTTGTCTTCATGTAT
257 GCAGATCTTGTCTTCCCATATTGGTGGCAAAGTAATCG-A-AAAGCAGATCTTGTCTTCATGTAT
* * *
12074 TGGCGTGAAGTAGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGACGA
320 TGGCGTGAAGTAGATCGAAG-TAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGA
12139 TGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
384 TGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
12204 ATTGGCGTGAAGTAGATCGAAGATAGC
449 ATTGGCGTGAAGTAGATCGAAGATAGC
* * * *
12231 AGGTCCTGTCTTCCTATATCGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCCATACTGG
1 AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
12296 TGGC-AAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGA
66 TGGCGAAGTAGATCG-AGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGA
12355 GGATTGTAGA
Statistics
Matches: 577, Mismatches: 16, Indels: 15
0.95 0.03 0.02
Matches are distributed among these distances:
475 81 0.14
476 85 0.15
477 275 0.48
478 136 0.24
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (475 bp):
AGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGG
TGGCGAAGTAGATCGAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGC
AGATCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGATGCAGATCTTGTCTTCATGTATTGGC
GTGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAG
ATCTTGTCTTCCCATATTGGTGGCAAAGTAATCGAAAAGCAGATCTTGTCTTCATGTATTGGCGT
GAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
CTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCG
TGAAGTAGATCGAAGATAGC
Found at i:12478 original size:45 final size:45
Alignment explanation
Indices: 12427--12579 Score: 121
Period size: 45 Copynumber: 3.2 Consensus size: 45
12417 CTCCCTGACT
*
12427 ACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTG
1 ACAGTGGAGTACATTGAAGCAGATAACTCTATCTCCCTGCATTTG
* ** * * * * *
12472 ACAGTGGAATGGATTGAAGATCAAAGATGGCAGATTTTACCTCCCTGTGA-CT-
1 ACAGTGGAGTACATTGAAG--C--AGAT---A-ACTCTATCTCCCTG-CATTTG
*
12524 ACAGTGGAGTACATTGAAGCTGATAACTCTATCTCCCTGCATTTG
1 ACAGTGGAGTACATTGAAGCAGATAACTCTATCTCCCTGCATTTG
12569 ACAGTGGAGTA
1 ACAGTGGAGTA
12580 GATCGGAGAT
Statistics
Matches: 79, Mismatches: 18, Indels: 22
0.66 0.15 0.18
Matches are distributed among these distances:
43 1 0.01
44 12 0.15
45 28 0.35
47 1 0.01
48 3 0.04
49 3 0.04
50 1 0.01
52 17 0.22
53 12 0.15
54 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGTGGAGTACATTGAAGCAGATAACTCTATCTCCCTGCATTTG
Found at i:12558 original size:97 final size:95
Alignment explanation
Indices: 12394--12576 Score: 330
Period size: 97 Copynumber: 1.9 Consensus size: 95
12384 ACAGCGAAGC
*
12394 AGATCGAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
12459 CTCCCTGCATTTGACAGTGGAATGGATTGA
66 CTCCCTGCATTTGACAGTGGAATGGATTGA
*
12489 AGATCAAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCTGATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCCC--TGACTACAGTGGAGTACATTGAAGCCGATAACTCT
12554 ATCTCCCTGCATTTGACAGTGGA
64 ATCTCCCTGCATTTGACAGTGGA
12577 GTAGATCGGA
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
95 27 0.32
97 57 0.68
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGCATTTGACAGTGGAATGGATTGA
Found at i:14063 original size:3 final size:3
Alignment explanation
Indices: 14045--14095 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
14035 TCAAATACCC
* * * * *
14045 TTA TTA TT- TTA ATA TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14092 TTA T
1 TTA T
14096 GTGCTAGTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:14223 original size:3 final size:3
Alignment explanation
Indices: 14215--14252 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
14205 TATTCCAATG
14215 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14253 GTTTATGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:14258 original size:17 final size:17
Alignment explanation
Indices: 14219--14252 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14209 CCAATGTTAT
14219 TATTATTATTATTATTA
1 TATTATTATTATTATTA
14236 TATTATTATTATTATTA
1 TATTATTATTATTATTA
14253 GTTTATGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:15677 original size:44 final size:45
Alignment explanation
Indices: 15595--15679 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
15585 ACCACACTAG
15595 TAGGCACCGAAGTGCTTAAACAATAGGCACCAAAGTGCTGAGCAA
1 TAGGCACCGAAGTGCTTAAACAATAGGCACCAAAGTGCTGAGCAA
* * * * *
15640 TAGGCACGGAAGTG-TTAGACAGTGGGCACCGAAGTGCTGA
1 TAGGCACCGAAGTGCTTAAACAATAGGCACCAAAGTGCTGA
15680 ACAGTAGGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 22 0.63
45 13 0.37
ACGTcount: A:0.33, C:0.20, G:0.31, T:0.16
Consensus pattern (45 bp):
TAGGCACCGAAGTGCTTAAACAATAGGCACCAAAGTGCTGAGCAA
Found at i:15683 original size:22 final size:22
Alignment explanation
Indices: 15595--15687 Score: 89
Period size: 22 Copynumber: 4.2 Consensus size: 22
15585 ACCACACTAG
*
15595 TAGGCACCGAAGTGCTTAAACAA
1 TAGGCACCGAAGTGC-TGAACAA
* *
15618 TAGGCACCAAAGTGCTGAGCAA
1 TAGGCACCGAAGTGCTGAACAA
* * *
15640 TAGGCACGGAAGTG-TTAGACAG
1 TAGGCACCGAAGTGCTGA-ACAA
* *
15662 TGGGCACCGAAGTGCTGAACAG
1 TAGGCACCGAAGTGCTGAACAA
15684 TAGG
1 TAGG
15688 TATCCTAGTG
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.04
22 38 0.68
23 16 0.29
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.16
Consensus pattern (22 bp):
TAGGCACCGAAGTGCTGAACAA
Done.