Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3069
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: 31834
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3155 original size:26 final size:26
Alignment explanation
Indices: 3126--3301 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 26
3116 ATATTGAGCC
* *
3126 CGCACACTCAGTGCTA-TACATCAACT
1 CGCACACTTAGTGCTACTA-ATCAAAT
*
3152 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAC-TAATCAAAT
* * *
3179 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTAC-TAATCA-AAT
** * *
3207 CGCACACTTAGTGCCGC-ATGTCAATT
1 CGCACACTTAGTGCTACTA-ATCAAAT
* **
3233 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-C-TAATCAAAT
* * *
3260 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTAC-TAATCAAAT
3287 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3302 GTACAATTTA
Statistics
Matches: 122, Mismatches: 20, Indels: 15
0.78 0.13 0.10
Matches are distributed among these distances:
26 32 0.26
27 69 0.57
28 21 0.17
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (26 bp):
CGCACACTTAGTGCTACTAATCAAAT
Found at i:3183 original size:27 final size:27
Alignment explanation
Indices: 3146--3300 Score: 161
Period size: 27 Copynumber: 5.7 Consensus size: 27
3136 GTGCTATACA
* * *
3146 TCAACTCGCACACTTAGTGCCACGTAA
1 TCAAATCGCACACTTAGTGCCACATAG
*
3173 TCAAATCGCACACTTAGTGCTACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
* * *
3200 TTAGACTCGCACACTTAGTGCCGCAT-G
1 TCA-AATCGCACACTTAGTGCCACATAG
* *
3227 TCAATTCGCACACTTAGTG-CATCATAT
1 TCAAATCGCACACTTAGTGCCA-CATAG
** *
3254 TCATTTCGCACACTTAGTGCAACATAG
1 TCAAATCGCACACTTAGTGCCACATAG
*
3281 TCGAATCGCACACTTAGTGC
1 TCAAATCGCACACTTAGTGC
3301 TGTACAATTT
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.01
26 18 0.17
27 67 0.63
28 20 0.19
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
TCAAATCGCACACTTAGTGCCACATAG
Found at i:3263 original size:81 final size:80
Alignment explanation
Indices: 3146--3300 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 80
3136 GTGCTATACA
* * *
3146 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
3211 CACTTAGTGCCGCATG
65 CACTTAGTGCCGCATG
* * ** *
3227 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
3291 CACTTAGTGC
65 CACTTAGTGC
3301 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
80 20 0.31
81 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATG
Found at i:6011 original size:22 final size:22
Alignment explanation
Indices: 5960--6025 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
5950 GGTATTTGGG
* * *
5960 AATTGGTTCAAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
5981 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
6003 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
6026 TCAAAGAGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 18 0.47
22 15 0.39
23 5 0.13
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:7070 original size:52 final size:52
Alignment explanation
Indices: 7010--7120 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 52
7000 TAACATGTCA
*
7010 TAATAACTAAAATATCATGCATAATTAAGTTTGACTAGATTTAAGACCAATT
1 TAATAACTAAAATATCATGCATAATTAAGTTTGACCAGATTTAAGACCAATT
7062 TAATAACTAAAATATCATGCATAATTAAGTTTGACCAGATTTAAGACCAATT
1 TAATAACTAAAATATCATGCATAATTAAGTTTGACCAGATTTAAGACCAATT
7114 TAATAAC
1 TAATAAC
7121 GTACACTTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 58 1.00
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (52 bp):
TAATAACTAAAATATCATGCATAATTAAGTTTGACCAGATTTAAGACCAATT
Found at i:14155 original size:24 final size:23
Alignment explanation
Indices: 14127--14183 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
14117 ATACCATTTC
**
14127 ATACCATTTCGTACCAATTCCCAA
1 ATACCATTTCGTACCAA-AACCAA
***
14151 ATACCAAAACGTACCAAAACCAA
1 ATACCATTTCGTACCAAAACCAA
14174 ATACCATTTC
1 ATACCATTTC
14184 TTAATTATTC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.23
Consensus pattern (23 bp):
ATACCATTTCGTACCAAAACCAA
Found at i:15970 original size:33 final size:33
Alignment explanation
Indices: 15932--15994 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
15922 GATTACTCAC
15932 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
15965 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
15995 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:16021 original size:21 final size:21
Alignment explanation
Indices: 15992--16047 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
15982 CAAGCTCTCT
*
15992 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
16013 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
16034 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
16048 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:16040 original size:14 final size:14
Alignment explanation
Indices: 15991--16047 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
15981 TCAAGCTCTC
15991 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
16004 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
16018 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
16032 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
16046 TT
1 TT
16048 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:16101 original size:7 final size:6
Alignment explanation
Indices: 16009--16116 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
15999 TCTTTTTTCG
* * * **
16009 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
16060 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CATTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
16108 -GTTTT CTTT
1 CTTTTT CTTT
16117 CAATTTTTTT
Statistics
Matches: 74, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
5 5 0.07
6 56 0.76
7 10 0.14
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:16107 original size:18 final size:18
Alignment explanation
Indices: 16009--16112 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
15999 TCTTTTTTCG
16009 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
16028 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* ** *
16048 CTCTCACTTTTTTGA-TTT
1 CTTTTTC-TTTTTCATTTT
* *
16066 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
16084 CTTTTTCTTTTTCATTTT
1 CTTTTTCTTTTTCATTTT
*
16102 CTTTTTGTTTT
1 CTTTTTCTTTT
16113 CTTTCAATTT
Statistics
Matches: 65, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
17 5 0.08
18 37 0.57
19 7 0.11
20 8 0.12
21 8 0.12
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:19589 original size:22 final size:23
Alignment explanation
Indices: 19558--19600 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19548 ACCTCTTTGA
*
19558 ACCATTACCAATTCGTACCAAAT
1 ACCATTACCAATTCATACCAAAT
*
19581 ACCA-TACCATTTCATACCAA
1 ACCATTACCAATTCATACCAA
19601 TTCCCAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.26
Consensus pattern (23 bp):
ACCATTACCAATTCATACCAAAT
Found at i:21328 original size:15 final size:15
Alignment explanation
Indices: 21308--21362 Score: 92
Period size: 15 Copynumber: 3.6 Consensus size: 15
21298 CTTCTTCTTC
21308 TTTTTTTCACGAATTT
1 TTTTTTTCACGAA-TT
21324 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
*
21339 TTTTTTTCACGAAAT
1 TTTTTTTCACGAATT
21354 TTTTTTTCA
1 TTTTTTTCA
21363 ACTTGATATC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 25 0.66
16 13 0.34
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:21329 original size:16 final size:16
Alignment explanation
Indices: 21308--21360 Score: 90
Period size: 16 Copynumber: 3.3 Consensus size: 16
21298 CTTCTTCTTC
21308 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
21324 TTTTTTTCACGAA-TT
1 TTTTTTTCACGAATTT
21339 TTTTTTTCACGAAATTT
1 TTTTTTTCACG-AATTT
21356 TTTTT
1 TTTTT
21361 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.37
16 15 0.43
17 7 0.20
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTTTTTCACGAATTT
Found at i:21432 original size:13 final size:13
Alignment explanation
Indices: 21404--21448 Score: 67
Period size: 12 Copynumber: 3.6 Consensus size: 13
21394 AAACCAATTG
*
21404 TTTTCTTTTC-AA
1 TTTTTTTTTCGAA
21416 TTTTTTTTT-GAA
1 TTTTTTTTTCGAA
21428 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
21441 TTTTTTTT
1 TTTTTTTT
21449 GAAGAAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:22483 original size:21 final size:23
Alignment explanation
Indices: 22438--22484 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
22428 TCACCTGCAA
* *
22438 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
22461 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
22482 TAA
1 TAA
22485 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:25232 original size:23 final size:23
Alignment explanation
Indices: 25198--25248 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
25188 AAAATGTCAT
*
25198 TAAA-ATTGGGCACAAGCAGAAA
1 TAAAGATTCGGCACAAGCAGAAA
25220 TAAAGATTCGGCACAAGCAGAAA
1 TAAAGATTCGGCACAAGCAGAAA
25243 TAAAGA
1 TAAAGA
25249 AAGAATTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (23 bp):
TAAAGATTCGGCACAAGCAGAAA
Done.