Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2617
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: 43874
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:3245 original size:12 final size:12
Alignment explanation
Indices: 3228--3273 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
3218 AGCTCTCTTC
3228 TTTTTCAATTTT
1 TTTTTCAATTTT
3240 TTTTTCACAATTTTT
1 TTTTT--CAA-TTTT
*
3255 TTTTTCAAATTT
1 TTTTTCAATTTT
3267 TTTTTCA
1 TTTTTCA
3274 CACTTGATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 15 0.50
13 3 0.10
14 3 0.10
15 9 0.30
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTCAATTTT
Found at i:3252 original size:14 final size:14
Alignment explanation
Indices: 3233--3275 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
3223 TCTTCTTTTT
3233 CAATTTTTTTTTCA
1 CAATTTTTTTTTCA
3247 CAATTTTTTTTTTCA
1 CAA-TTTTTTTTTCA
3262 -AA-TTTTTTTTCA
1 CAATTTTTTTTTCA
3274 CA
1 CA
3276 CTTGATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 5 0.19
15 11 0.41
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (14 bp):
CAATTTTTTTTTCA
Found at i:3256 original size:15 final size:14
Alignment explanation
Indices: 3228--3271 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
3218 AGCTCTCTTC
3228 TTTTTC-AA-TTTT
1 TTTTTCAAATTTTT
3240 TTTTTCACAATTTTT
1 TTTTTCA-AATTTTT
3255 TTTTTCAAATTTTT
1 TTTTTCAAATTTTT
3269 TTT
1 TTT
3272 CACACTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.21
14 12 0.41
15 11 0.38
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTCAAATTTTT
Found at i:8449 original size:20 final size:22
Alignment explanation
Indices: 8426--8470 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
8416 GTGGTTCAAA
8426 CTCAATTC-GAGCTCAAGT-AG
1 CTCAATTCTGAGCTCAAGTCAG
*
8446 CTC-ATTCTGTGCTCAAGTCAG
1 CTCAATTCTGAGCTCAAGTCAG
8467 CTCA
1 CTCA
8471 TTGTCAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (22 bp):
CTCAATTCTGAGCTCAAGTCAG
Found at i:11023 original size:20 final size:21
Alignment explanation
Indices: 10981--11023 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10971 ATGAGCTCAA
10981 AATCAGCTCAATTTTAGCGTC
1 AATCAGCTCAATTTTAGCGTC
*
11002 AATCAGCTCATTTTTAGC-TC
1 AATCAGCTCAATTTTAGCGTC
11022 AA
1 AA
11024 AACTTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (21 bp):
AATCAGCTCAATTTTAGCGTC
Found at i:12742 original size:16 final size:17
Alignment explanation
Indices: 12721--12757 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12711 GGTAACGGTT
*
12721 AAAAAAATTGAAA-AAA
1 AAAAAAATCGAAAGAAA
12737 AAAAAAATCGAAAGAAA
1 AAAAAAATCGAAAGAAA
12754 AAAA
1 AAAA
12758 TTTGAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAATCGAAAGAAA
Found at i:12768 original size:16 final size:15
Alignment explanation
Indices: 12721--12775 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
12711 GGTAACGGTT
*
12721 AAAAAAA-TTGAAAAA
1 AAAAAAATTTG-AAAG
* *
12736 AAAAAAAATCGAAAG
1 AAAAAAATTTGAAAG
12751 AAAAAAATTTGAACAG
1 AAAAAAATTTGAA-AG
12767 AAAAAAATT
1 AAAAAAATT
12776 GTATACGGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.15
Consensus pattern (15 bp):
AAAAAAATTTGAAAG
Found at i:16080 original size:13 final size:14
Alignment explanation
Indices: 16059--16097 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
16049 ATAGTAGTTC
*
16059 TCAAAAAAAAAAAT
1 TCAAAAAAAAAATT
16073 TCAAAAAAAAAATT
1 TCAAAAAAAAAATT
*
16087 TGAAAAAAAAA
1 TCAAAAAAAAA
16098 CTAGTTTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (14 bp):
TCAAAAAAAAAATT
Found at i:16155 original size:12 final size:12
Alignment explanation
Indices: 16138--16183 Score: 74
Period size: 12 Copynumber: 3.7 Consensus size: 12
16128 TATCAAGTTG
16138 TGAAAAAAAATT
1 TGAAAAAAAATT
16150 TGAAAAAAAATT
1 TGAAAAAAAATT
16162 GTGAAAAAAAAATT
1 -TG-AAAAAAAATT
16176 TGAAAAAA
1 TGAAAAAA
16184 GAGAGAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 18 0.56
13 4 0.12
14 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (12 bp):
TGAAAAAAAATT
Found at i:16163 original size:25 final size:26
Alignment explanation
Indices: 16135--16183 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
16125 GGATATCAAG
16135 TTGTG-AAAAAAAATTTGAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAA
16160 TTGTGAAAAAAAAATTTGAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAA
16184 GAGAGAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (26 bp):
TTGTGAAAAAAAAATTTGAAAAAAAA
Found at i:26226 original size:22 final size:22
Alignment explanation
Indices: 26198--26241 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26188 TTTTGAACCA
26198 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
26220 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
26242 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:26572 original size:13 final size:12
Alignment explanation
Indices: 26556--26587 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
26546 AAAGAGTTCG
26556 AAAAAAAAATTGA
1 AAAAAAAAATT-A
26569 AAAAAAAAATTA
1 AAAAAAAAATTA
26581 AAAAAAA
1 AAAAAAA
26588 TTGCATACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:28790 original size:22 final size:22
Alignment explanation
Indices: 28763--28810 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28753 CAATCTTTGG
*
28763 AGAATTTGAAAGA-ACTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
* *
28784 AGAAATTGAGAGAGAGTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
28806 AGAAA
1 AGAAA
28811 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AGAAATTGAAAGAGACTGAAAA
Found at i:28832 original size:26 final size:26
Alignment explanation
Indices: 28799--28849 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
28789 TTGAGAGAGA
28799 GTGAAAAAGAAAAGAAAAATGATTCC
1 GTGAAAAAGAAAAGAAAAATGATTCC
28825 GTGAAAAAGAAAAGAAAAATGATTC
1 GTGAAAAAGAAAAGAAAAATGATTC
28850 AAAAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.20, T:0.16
Consensus pattern (26 bp):
GTGAAAAAGAAAAGAAAAATGATTCC
Found at i:28858 original size:26 final size:26
Alignment explanation
Indices: 28801--28862 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
28791 GAGAGAGAGT
***
28801 GAAAAAGAAAAGAAAAATGATTCCGT
1 GAAAAAGAAAAGAAAAATGATTCAAA
28827 GAAAAAGAAAAGAAAAATGATTCAAA
1 GAAAAAGAAAAGAAAAATGATTCAAA
28853 -AGAAAAGAAA
1 GA-AAAAGAAA
28863 GAAGAGAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.66, C:0.05, G:0.18, T:0.11
Consensus pattern (26 bp):
GAAAAAGAAAAGAAAAATGATTCAAA
Found at i:28885 original size:20 final size:20
Alignment explanation
Indices: 28860--28901 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
28850 AAAAGAAAAG
28860 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
28880 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
28900 AA
1 AA
28902 CACAAGAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.31, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:32111 original size:22 final size:22
Alignment explanation
Indices: 32083--32126 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
32073 TTTTGAACCA
32083 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
32105 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
32127 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:36498 original size:40 final size:40
Alignment explanation
Indices: 36349--36534 Score: 200
Period size: 40 Copynumber: 4.7 Consensus size: 40
36339 TTGAATGATG
* * * * *
36349 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
36389 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
36429 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
36469 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
36510 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
36535 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 117 0.91
41 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:36552 original size:80 final size:79
Alignment explanation
Indices: 36402--36567 Score: 178
Period size: 80 Copynumber: 2.1 Consensus size: 79
36392 GGACTAAGAT
** *
36402 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTA
*
36467 AATCCGGGTTAAGTC
66 AATCC-GGTTAAATC
* * *
36482 CCGAAGGCATTTGTGCGA-ATTACTATAA-CTGGGCTATG-TCCCGAAGGCATTTGAACGAG-GA
1 CCGAAGGCATTTGTGCGAGA-TACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTGA
* *
36543 GCTATATCCGGTTAAATT
63 -CTAAATCCGGTTAAATC
36561 CCGAAGG
1 CCGAAGG
36568 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
79 17 0.23
80 54 0.74
81 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTA
AATCCGGTTAAATC
Done.