Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold331
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: 1394875
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 8 of 8
Found at i:1369285 original size:260 final size:260
Alignment explanation
Indices: 1368745--1369353 Score: 840
Period size: 260 Copynumber: 2.4 Consensus size: 260
1368735 ACGTTCATCT
* * *
1368745 CTTT-AAAGCCCACAAGTCAGT-GCAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTT
* * * *
1368803 CAAGGTCCACAAGTCAGTGGCACTATTTCAAAGACCACAAGCTAGTGGTAACTCTTTTCAAAGCC
66 CAAAGCCCACAAGTTAGTGGCACTATTTCAAAGACCACAAGCTAGTGGCAACTCTTTTCAAAGCC
* * *
1368868 CACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCTCACAAGTCA
131 CACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
*
1368933 GTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
196 GTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGGCACC
* * * *
1368998 CTTTCATAGCTCACAAATCAGTGGCACTCTTTTCAAAGCCCACACGACTCGGTGGCAACTCTTTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTT
* * *
1369063 CAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACGAG-TCAGTGGCAACTCTTTTCAAAG
66 CAAAGCCCACAAGTTAGTGGCACT-ATTTCAAAGACCACAAGCT-AGTGGCAACTCTTTTCAAAG
* *
1369126 CCCACAACTGAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
129 CCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
* * * * *
1369191 CAGTGGCATTCTTTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAACCCATAAGTCAGTGGTA
194 CAGTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGGCA
1369256 CC
259 CC
* * * *
1369258 CTTTCAAAGCCCACAAGTTAATGGCACTCTTTTTCAAAGCCTACACGAGTCGGTGGCAACTATTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTC-TTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTT
*
1369323 TCAAAGCCCACACAAGTTAGTGGCACCATTT
65 TCAAAG-CC-CACAAGTTAGTGGCACTATTT
1369354 TTTTTTAAAA
Statistics
Matches: 308, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
253 4 0.01
254 14 0.05
255 4 0.01
256 15 0.05
258 8 0.03
259 4 0.01
260 201 0.65
261 38 0.12
262 2 0.01
263 18 0.06
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (260 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTT
CAAAGCCCACAAGTTAGTGGCACTATTTCAAAGACCACAAGCTAGTGGCAACTCTTTTCAAAGCC
CACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
GTGACACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGTCAGTGGCACC
Found at i:1370204 original size:20 final size:20
Alignment explanation
Indices: 1370181--1370306 Score: 108
Period size: 20 Copynumber: 5.7 Consensus size: 20
1370171 AAGTACCCAG
1370181 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1370201 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1370221 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1370241 ATGTAATCGATACATTCTATCTTTTTACCTA
1 ATGT-ATCGAT--A--C-A--TTTTT--C-A
1370272 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1370293 ATGTATCGATACAT
1 ATGTATCGATACAT
1370307 CTAGTTAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 51 0.59
21 7 0.08
22 1 0.01
23 1 0.01
24 5 0.06
25 1 0.01
26 2 0.02
27 1 0.01
28 4 0.05
29 1 0.01
30 1 0.01
31 7 0.08
32 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1375085 original size:21 final size:22
Alignment explanation
Indices: 1375046--1375088 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1375036 ATGATTTCGA
* *
1375046 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1375068 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1375089 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1375376 original size:18 final size:20
Alignment explanation
Indices: 1375335--1375387 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1375325 CTATAGACCC
1375335 TAATTCACATCAAACAAGCA
1 TAATTCACATCAAACAAGCA
1375355 TAATTCA-AT-AACACAA-CA
1 TAATTCACATCAA-ACAAGCA
*
1375373 TAATTAAACATCAAA
1 TAATT-CACATCAAA
1375388 TTCATCTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 10 0.36
21 2 0.07
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.23
Consensus pattern (20 bp):
TAATTCACATCAAACAAGCA
Found at i:1379169 original size:52 final size:52
Alignment explanation
Indices: 1379021--1379149 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1379011 CGAAATATGA
* *
1379021 AAATTTGCCTGCATGTATCAATACATTTCATAGTGTATCAATACATCTGGAC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
* *
1379073 AAATTTGCCTTCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
1379125 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1379150 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGAC
Found at i:1379176 original size:13 final size:13
Alignment explanation
Indices: 1379158--1379182 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1379148 CAAAGATCAG
1379158 TGTATCGATACAA
1 TGTATCGATACAA
1379171 TGTATCGATACA
1 TGTATCGATACA
1379183 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1379258 original size:18 final size:19
Alignment explanation
Indices: 1379235--1379283 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1379225 AGCGATACAT
1379235 TGTATCGATACAA-ACTTA
1 TGTATCGATACAACACTTA
1379253 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1379272 TGTATCGATACA
1 TGTATCGATACA
1379284 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1379290 original size:13 final size:13
Alignment explanation
Indices: 1379272--1379296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1379262 ACAACACTTA
1379272 TGTATCGATACAT
1 TGTATCGATACAT
1379285 TGTATCGATACA
1 TGTATCGATACA
1379297 ATATTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1380875 original size:15 final size:17
Alignment explanation
Indices: 1380857--1380888 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1380847 TGTACATCAA
1380857 CTTC-TTTTGGA-ACTT
1 CTTCATTTTGGACACTT
1380872 CTTCATTTTGGACACTT
1 CTTCATTTTGGACACTT
1380889 TCATCTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (17 bp):
CTTCATTTTGGACACTT
Found at i:1385564 original size:15 final size:15
Alignment explanation
Indices: 1385544--1385574 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1385534 TAAAAATGTC
*
1385544 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1385559 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1385574 C
1 C
1385575 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1387628 original size:13 final size:13
Alignment explanation
Indices: 1387610--1387645 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1387600 TTTTTCTTTG
1387610 TATCGATACAATA
1 TATCGATACAATA
* *
1387623 TATCGATACACTG
1 TATCGATACAATA
1387636 TATCGATACA
1 TATCGATACA
1387646 GGGAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:1387800 original size:20 final size:20
Alignment explanation
Indices: 1387757--1387802 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1387747 AAATCTTTTG
1387757 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1387778 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1387798 CAAAA
1 CAAAA
1387803 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1388871 original size:15 final size:17
Alignment explanation
Indices: 1388841--1388873 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1388831 CAACTCGGCA
1388841 ATTCTTCATGGGATGAT
1 ATTCTTCATGGGATGAT
1388858 ATTC-TCAT-GGATGAT
1 ATTCTTCATGGGATGAT
1388873 A
1 A
1388874 CTTAGCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.39
Consensus pattern (17 bp):
ATTCTTCATGGGATGAT
Found at i:1390230 original size:13 final size:13
Alignment explanation
Indices: 1390212--1390237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1390202 TACACAAAGT
1390212 ATGTATCGATACA
1 ATGTATCGATACA
1390225 ATGTATCGATACA
1 ATGTATCGATACA
1390238 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1390235 original size:32 final size:33
Alignment explanation
Indices: 1390194--1390257 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1390184 TAGCCAAACT
**
1390194 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1390226 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1390258 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1392814 original size:20 final size:20
Alignment explanation
Indices: 1392754--1392816 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
1392744 GTTTGAAGCA
1392754 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1392774 ATGTA-CGATAC-AT-T--C
1 ATGTATCGATACAATGTGCC
1392789 ---TATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
1392806 ATGTATCGATA
1 ATGTATCGATA
1392817 AAACAATGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 2 0.06
15 2 0.06
17 2 0.06
18 2 0.06
19 6 0.17
20 13 0.37
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Done.