Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2095
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: 16648
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1261 original size:162 final size:158
Alignment explanation
Indices: 1049--1510 Score: 500
Period size: 162 Copynumber: 2.8 Consensus size: 158
1039 TCCAAAACTC
* *
1049 ATAAAAATGAATGAA-TTTTGAAAACTAATTTAATATGAAATAAATAATAATATTCGATGGATTT
1 ATAAAAATGAATGAATTTTTAAAAACTAA-TTAATATGAAATAAATAATAATATT-GATGAATTT
*
1113 TAAAAACTAAAAACCAAGAAAAA-CCCATCGAAAAAAATTTACGGAGTAGAAAACTCCATTTTTG
64 TAAAAATTAAAAACCAAGAAAAATCCC-TCG-AAAAAATTTACGGAGTAGAAAACTCCATTTTTG
**
1177 AAATAAGGGAATTTCAAAAAAAATTCAAAAATGA
127 AAATAA--GAATTTCAAAAAAAATTCAAAAACCA
* * * *
1211 ATGAAAATGAATGAATTTTTCAAAACTAATATATTATGAAAT-AATAATAATAATTAATGAATTT
1 ATAAAAATGAATGAATTTTTAAAAACTAAT-TAATATGAAATAAATAATAAT-ATTGATGAATTT
* **
1275 TAAAAATTAAAAATCAAGAAAAATCTCC-CGAAAAAATTTACGAGTAGTAGAAAACTTTATTTTT
64 TAAAAATTAAAAACCAAGAAAAATC-CCTCGAAAAAATTTACG-G-AGTAGAAAACTCCATTTTT
** *
1339 CGAAAACATAAGAATTTCAAGGAAAATTCAAAAACCT
126 -G--AA-ATAAGAATTTCAAAAAAAATTCAAAAACCA
* * *
1376 ATAAAAATGAATGAATTTTTGAAAAACTGATTCAATATGTATTAAATAATAATATTTGATGAATT
1 ATAAAAATGAATGAATTTTT-AAAAACTAATT-AATATGAAATAAATAATAATA-TTGATGAATT
* * * * *
1441 TTAAAAATTTTAAACCCATGAAAAATCCCCTCGAAAATATTTACGGAATAGAAAACTCCATATTT
63 TTAAAAA-TTAAAAACCAAGAAAAAT-CCCTCGAAAAAATTTACGGAGTAGAAAACTCCAT-TTT
1506 TGAAA
125 TGAAA
1511 ATAGAAAAAT
Statistics
Matches: 252, Mismatches: 29, Indels: 36
0.79 0.09 0.11
Matches are distributed among these distances:
161 12 0.05
162 55 0.22
163 43 0.17
164 4 0.02
165 43 0.17
166 18 0.07
167 42 0.17
168 21 0.08
169 14 0.06
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (158 bp):
ATAAAAATGAATGAATTTTTAAAAACTAATTAATATGAAATAAATAATAATATTGATGAATTTTA
AAAATTAAAAACCAAGAAAAATCCCTCGAAAAAATTTACGGAGTAGAAAACTCCATTTTTGAAAT
AAGAATTTCAAAAAAAATTCAAAAACCA
Found at i:1524 original size:167 final size:162
Alignment explanation
Indices: 1049--1532 Score: 555
Period size: 167 Copynumber: 2.9 Consensus size: 162
1039 TCCAAAACTC
* *
1049 ATAAAAATGAATGAA-TTTTGAAAACTAATTTAATATGAAATAAATAATAATATTCGATGGATTT
1 ATAAAAATGAATGAATTTTTGAAAACTAA-TTAATATGAAATAAATAATAATATTTGATGAATTT
* *
1113 TAAAAACTAAAAACCAAGAAAAA-CCCATCGAAAAAAATTTACGGAGTAGAAAACTCCATTTTTG
65 TAAAAATTAAAAACCAAGAAAAATCCCCTCG-AAAAAATTTACGGAGTAGAAAACTCCATTTTTG
* * **
1177 -AAATAAGGGAATTTCAAAAAAAATTCAAAAATGA
129 AAAATAA-AGAATTTCAAAGAAAATTCAAAAACCA
* * * * *
1211 ATGAAAATGAATGAATTTTTCAAAACTAATATATTATGAAAT-AATAATAATAATTAATGAATTT
1 ATAAAAATGAATGAATTTTTGAAAACTAAT-TAATATGAAATAAATAATAATATTTGATGAATTT
* * **
1275 TAAAAATTAAAAATCAAGAAAAATCTCC-CGAAAAAATTTACGAGTAGTAGAAAACTTTATTTTT
65 TAAAAATTAAAAACCAAGAAAAATCCCCTCGAAAAAATTTACG-G-AGTAGAAAACTCCATTTTT
* * *
1339 CGAAAACATAAGAATTTCAAGGAAAATTCAAAAACCT
128 -GAAAATA-AAGAATTTCAAAGAAAATTCAAAAACCA
* * *
1376 ATAAAAATGAATGAATTTTTGAAAAACTGATTCAATATGTATTAAATAATAATATTTGATGAATT
1 ATAAAAATGAATGAATTTTTG-AAAACTAATT-AATATGAAATAAATAATAATATTTGATGAATT
* * * * *
1441 TTAAAAATTTTAAACCCATGAAAAATCCCCTCGAAAATATTTACGGAATAGAAAACTCCATATTT
64 TTAAAAA-TTAAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCCAT-TTT
*
1506 TGAAAATAGAAAAATTTCAAAGAAAAT
127 TGAAAATA-AAGAATTTCAAAGAAAAT
1533 CAATAACTCG
Statistics
Matches: 267, Mismatches: 41, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
161 12 0.04
162 57 0.21
163 41 0.15
164 1 0.00
165 45 0.17
166 16 0.06
167 60 0.22
168 22 0.08
169 13 0.05
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (162 bp):
ATAAAAATGAATGAATTTTTGAAAACTAATTAATATGAAATAAATAATAATATTTGATGAATTTT
AAAAATTAAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGTAGAAAACTCCATTTTTGAA
AATAAAGAATTTCAAAGAAAATTCAAAAACCA
Found at i:1639 original size:331 final size:325
Alignment explanation
Indices: 1049--1650 Score: 702
Period size: 330 Copynumber: 1.8 Consensus size: 325
1039 TCCAAAACTC
* *
1049 ATAAAAATGAATGAATTTTGAAAACTAATTTAATATGAAATAAATAATAATATTCGATGGATTTT
1 ATAAAAATGAATGAATTTTGAAAACTAATTCAATATGAAATAAATAATAATATTCGATGAATTTT
*
1114 AAAAACTAAAAACCAAGAAAAACCCATCGAAAAAAATTTACGGAGTAGAAAACTCCATTTTTGAA
66 AAAAACTAAAAACCAAGAAAAACCCATCGAAAAAAATTTACGGAATAGAAAACTCCATTTTTGAA
** * *
1179 ATAAGGGAATTTCAAAAAAAATTCAAAAATGAATGAAAATGAATGAATTTTTCAAAACTAATATA
131 ATAAGAAAATTTCAAAAAAAATTCAAAAATG-ATGAAAATGAAGGAAATTTTCAAAACTAATATA
*
1244 TTATGAAATAATAATAATAATTAATGAATTTTAAAAATTAAAAATCAAGAAAAATCTCCCGAAAA
195 TGATGAAATAATAATAATAATTAATGAATTTTAAAAATTAAAAATCAAGAAAAATCTCCCG-AAA
*
1309 AATTTACGAGTAGTAGAAAACTTTATTTTTCGAAAACATAAGAATTTCAAGGAAAATTCAAAAAC
259 AATGTACGAGTAGTAGAAAACTTTATTTTTCGAAAACATAAGAATTTCAAGGAAAATTCAAAAAC
1374 CT
324 CT
* * * *
1376 ATAAAAATGAATGAATTTTTGAAAAACTGATTCAATATGTATTAAATAATAATATTTGATGAATT
1 ATAAAAATGAATGAA-TTTTG-AAAACTAATTCAATATGAAATAAATAATAATATTCGATGAATT
* * * * * *
1441 TTAAAAATTTTAAACCCATGAAAAATCCCCTCG-AAAATATTTACGGAATAGAAAACTCCATATT
64 TTAAAAA-CTAAAAACCAAGAAAAA-CCCATCGAAAAAAATTTACGGAATAGAAAACTCCAT-TT
* *
1505 TTGAAA-ATAGAAAAATTTCAAAGAAAA-TCAATAACTCG-T-AAAATAGAAGGAAAATTTT-AA
126 TTGAAATA-AG-AAAATTTCAAAAAAAATTCAA-AAAT-GATGAAAAT-GAAGG-AAATTTTCAA
* * * * * * * **
1565 AACTGATTTAATGATG-ATTAAATGATAATATTTAA-GAAATTTT-GAAATTAAAACTTGAGAAA
185 AACTAATAT-ATGATGAAAT-AATAATAATAATTAATG-AATTTTAAAAATTAAAAATCAAGAAA
*
1627 ATTC-CACCGAAAAATGTACGAGTA
247 AATCTC-CCGAAAAATGTACGAGTA
1651 AAGAAAAGCT
Statistics
Matches: 229, Mismatches: 31, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
327 15 0.07
328 5 0.02
329 44 0.19
330 60 0.26
331 58 0.25
332 46 0.20
333 1 0.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (325 bp):
ATAAAAATGAATGAATTTTGAAAACTAATTCAATATGAAATAAATAATAATATTCGATGAATTTT
AAAAACTAAAAACCAAGAAAAACCCATCGAAAAAAATTTACGGAATAGAAAACTCCATTTTTGAA
ATAAGAAAATTTCAAAAAAAATTCAAAAATGATGAAAATGAAGGAAATTTTCAAAACTAATATAT
GATGAAATAATAATAATAATTAATGAATTTTAAAAATTAAAAATCAAGAAAAATCTCCCGAAAAA
TGTACGAGTAGTAGAAAACTTTATTTTTCGAAAACATAAGAATTTCAAGGAAAATTCAAAAACCT
Found at i:5834 original size:29 final size:28
Alignment explanation
Indices: 5743--5842 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 28
5733 CTAAAATGGT
* * * *
5743 TTTAAAATATATGAAATTGCATAGAAATC
1 TTTAAAAT-CATGAAATTGAATAAAAATA
* * * *
5772 CTTAAAA-CATGAAAATGATTAAAATTA
1 TTTAAAATCATGAAATTGAATAAAAATA
5799 TCTTAAAATGCATGAAATTGAATAAAAATA
1 T-TTAAAAT-CATGAAATTGAATAAAAATA
5829 TTTAAAAT-ATGAAA
1 TTTAAAATCATGAAA
5843 AATGGTTAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
27 19 0.34
28 6 0.11
29 13 0.23
30 18 0.32
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (28 bp):
TTTAAAATCATGAAATTGAATAAAAATA
Found at i:5862 original size:29 final size:27
Alignment explanation
Indices: 5772--5865 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 27
5762 CATAGAAATC
*
5772 CTTAAAACATGAAAATGATTAAAATTAT
1 CTTAAAATATGAAAATGATTAAAA-TAT
* *
5800 CTTAAAATGCATGAAATTGAATAAAAATAT
1 CTTAAAAT--ATGAAAATG-ATTAAAATAT
*
5830 -TTAAAATATGAAAAATGGTTAAAATGAT
1 CTTAAAATATG-AAAATGATTAAAAT-AT
5858 CTTAAAAT
1 CTTAAAAT
5866 GAATGAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
27 9 0.17
28 14 0.26
29 14 0.26
30 11 0.20
31 6 0.11
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (27 bp):
CTTAAAATATGAAAATGATTAAAATAT
Found at i:5864 original size:58 final size:58
Alignment explanation
Indices: 5717--5936 Score: 227
Period size: 57 Copynumber: 3.9 Consensus size: 58
5707 TAATAGTTCC
* * ** * *
5717 TAAAACAT-AAAAATGACTAAAATGGTTTTAAAATATATGAAATTGCATAGAAATCCT
1 TAAAACATGAAAAATGACTAAAATGATCTTAAAATGCATGAAATTGCATAAAAATCTT
* * * *
5774 TAAAACATG-AAAATGATTAAAATTATCTTAAAATGCATGAAATTGAATAAAAATATT
1 TAAAACATGAAAAATGACTAAAATGATCTTAAAATGCATGAAATTGCATAAAAATCTT
* ** * *
5831 TAAAATATGAAAAATGGTTAAAATGATCTTAAAATGAATGAAATTGCATAAAAACCTT
1 TAAAACATGAAAAATGACTAAAATGATCTTAAAATGCATGAAATTGCATAAAAATCTT
* ** *
5889 T----TATGGCAAATTACTAAAATGATCTTAAAATGCATGAAATTGCATAAA
1 TAAAACATGAAAAATGACTAAAATGATCTTAAAATGCATGAAATTGCATAAA
5937 TGGTCATAAA
Statistics
Matches: 138, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
54 41 0.30
57 54 0.39
58 43 0.31
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (58 bp):
TAAAACATGAAAAATGACTAAAATGATCTTAAAATGCATGAAATTGCATAAAAATCTT
Found at i:5874 original size:29 final size:27
Alignment explanation
Indices: 5784--5874 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 27
5774 TAAAACATGA
5784 AAATGATTAAAATTATCTTAAAATGCATG
1 AAATGATTAAAA-TATCTTAAAATG-ATG
*
5813 AAATTGAATAAAAATAT-TTAAAAT-ATG
1 AAA-TG-ATTAAAATATCTTAAAATGATG
*
5840 AAAAATGGTTAAAATGATCTTAAAATGAATG
1 --AAATGATTAAAAT-ATCTTAAAATG-ATG
5871 AAAT
1 AAAT
5875 TGCATAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
27 9 0.18
28 4 0.08
29 24 0.47
30 5 0.10
31 9 0.18
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (27 bp):
AAATGATTAAAATATCTTAAAATGATG
Found at i:6044 original size:58 final size:57
Alignment explanation
Indices: 5891--6027 Score: 168
Period size: 58 Copynumber: 2.4 Consensus size: 57
5881 AAAACCTTTT
* *
5891 ATGGCAAATTACTAAAATGATCTTAAAATGCATGAAATTGCATAAATGGTCATAAAAC
1 ATGGCAAATTACTAAAATGATC-TAAAATGCATGAAATGGCATAAAGGGTCATAAAAC
* * * * * *
5949 ATAGCATATTATTAGAATAACTTTAAAATGCATGAAATGGCATAAAGGGT-ATTAAAAC
1 ATGGCAAATTACTAAAATGA-TCTAAAATGCATGAAATGGCATAAAGGGTCA-TAAAAC
6007 ATGGCAAATTACTAAAATGAT
1 ATGGCAAATTACTAAAATGAT
6028 GCAAAAATAC
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
57 2 0.03
58 61 0.95
59 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (57 bp):
ATGGCAAATTACTAAAATGATCTAAAATGCATGAAATGGCATAAAGGGTCATAAAAC
Found at i:6120 original size:58 final size:57
Alignment explanation
Indices: 6057--6215 Score: 169
Period size: 58 Copynumber: 2.8 Consensus size: 57
6047 CTTAATAACC
*
6057 TCTAAATCATGAAAAATTACTAAAATGACCTTAAAGTATATGAGAATGCATAAATGG
1 TCTAAATCATGAAAAATTACTAAAATGACCTTAAAGTATATGAAAATGCATAAATGG
** * ** * *
6114 TACTAAAGGAAGGCAAATTACTAAAGTGACCTTAAAATATATGAAAATGCATAAATGG
1 T-CTAAATCATGAAAAATTACTAAAATGACCTTAAAGTATATGAAAATGCATAAATGG
* * * *
6172 TC-ATAATCATGAAAATTTATTAAAAT-AGCATTAAAGTGTATGAA
1 TCTA-AATCATGAAAAATTACTAAAATGA-CCTTAAAGTATATGAA
6216 TGAAATAATA
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
56 2 0.03
57 29 0.36
58 49 0.61
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.28
Consensus pattern (57 bp):
TCTAAATCATGAAAAATTACTAAAATGACCTTAAAGTATATGAAAATGCATAAATGG
Found at i:10387 original size:14 final size:14
Alignment explanation
Indices: 10368--10409 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
10358 AGATTTGAAT
10368 ATACTAAAAGAAAA
1 ATACTAAAAGAAAA
*
10382 ATACTAAAACAAAA
1 ATACTAAAAGAAAA
**
10396 A-AAAAAAAGAAAA
1 ATACTAAAAGAAAA
10409 A
1 A
10410 ATATAGAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.10
Consensus pattern (14 bp):
ATACTAAAAGAAAA
Found at i:12484 original size:17 final size:17
Alignment explanation
Indices: 12462--12496 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12452 TATCCACAAT
12462 ATTCACTATATTTATGC
1 ATTCACTATATTTATGC
12479 ATTCACTATATTTATGC
1 ATTCACTATATTTATGC
12496 A
1 A
12497 CAATGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (17 bp):
ATTCACTATATTTATGC
Done.