Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1803
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: 33608
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7559 original size:139 final size:142
Alignment explanation
Indices: 7298--7583 Score: 339
Period size: 139 Copynumber: 2.0 Consensus size: 142
7288 ATAATATAAC
* * ***
7298 ATTTAATTTTTTAATTTTTGAAAATCTCATTTCGTACCTTAATGGAGAATAAAAAAGATACAAAA
1 ATTTAATTTTTTAAGTTTTGAAAATCTCATTTCGCACCTTAAAAAAGAATAAAAAAGATACAAAA
* * *
7363 AGTTGTAAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATATTGAAAAATTAAA
66 AGTTGTAAAGATTTCTATAACCCTACGGAAAACCATAAGAATACTAGAAATACTGAAAAATTAAA
*
7428 ATAAAAATTTTT
131 ATAAAAATCTTT
**
7440 ATTTAA-TTTTTAAGTTTTGAAAAAT-TCATTTCGCACCTTAAAAAAGAA-CCAAAAGATACAAA
1 ATTTAATTTTTTAAGTTTTG-AAAATCTCATTTCGCACCTTAAAAAAGAATAAAAAAGATACAAA
* * * * * *
7502 AA-TTTTGAAGATGTT-TATAACCTTATGGAAAACCATAGGAATACTAGAAATCCTGAAAAATTA
65 AAGTTGTAAAGAT-TTCTATAACCCTACGGAAAACCATAAGAATACTAGAAATACTGAAAAATTA
** *
7565 TGATAATAATCTTT
129 AAATAAAAATCTTT
7579 ATTTA
1 ATTTA
7584 GTGATGAAAT
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
139 64 0.52
140 16 0.13
141 31 0.25
142 11 0.09
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (142 bp):
ATTTAATTTTTTAAGTTTTGAAAATCTCATTTCGCACCTTAAAAAAGAATAAAAAAGATACAAAA
AGTTGTAAAGATTTCTATAACCCTACGGAAAACCATAAGAATACTAGAAATACTGAAAAATTAAA
ATAAAAATCTTT
Found at i:9835 original size:167 final size:164
Alignment explanation
Indices: 9450--9962 Score: 645
Period size: 167 Copynumber: 3.1 Consensus size: 164
9440 TTTTAAAAAG
*
9450 TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTT
1 TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
* * * * *
9515 CATGAGCTTGTGAATTTTTTTCCTTAAAATTTTTTTATTTTCAAAATACGAAGTTTTCTACTCCG
66 CATGAGTTTTTGAATTTTTTT--TTAAAATTTTTCTATTTTCAAAAAACG-AGTTTTCTACTTCG
* * * *
9580 TAAATTTTTTTGGGGGAGATTTTTGTGGGTTTTTAATTT
128 TAAAATTTTTT--GGGAGATTTTTCTTGGTTTATAATTT
* * * * *
9619 TTAAAATCCATCAAATATTATTATCTATTTCATATTATATCAGTTTTCAAAAATTCATTCATTGT
1 TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
*
9684 CATGAGTTTTTGAATTTGTTTTTTAAAATTTCTCTATTTTCAAAAAACAGAGTTTTCTACTTCGT
66 CATGAGTTTTTGAATTT-TTTTTTAAAATTTTTCTATTTTCAAAAAAC-GAGTTTTCTACTTCGT
* *
9749 AAAATTTTTTAGGGAGATTTTTCTTAGTTTCTAATTT
129 AAAATTTTTT-GGGAGATTTTTCTTGGTTTATAATTT
* *
9786 TCAAAATTCATCAAATATTATTATTTATTTCAAATTAAATCAATTTTCAAAAATTCATTCATTTT
1 TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
* * * * * *
9851 CATGAATTTTT-TATTTTTTCTTAAAATTTTTCTGTTTTTGAAAAATCGAGTTTTCTAC-TC-TA
66 CATGAGTTTTTGAATTTTTTTTTAAAATTTTTCT-ATTTTCAAAAAACGAGTTTTCTACTTCGTA
*
9913 TAAATATTTTTGGGAGGATTTTTCTTGGTTTAAAATTT
130 -AAAT-TTTTTGGGA-GATTTTTCTTGGTTTATAATTT
*
9951 TTAAAATTCATC
1 TCAAAATTCATC
9963 CAATTTTGTA
Statistics
Matches: 302, Mismatches: 36, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
163 2 0.01
164 10 0.03
165 61 0.20
166 14 0.05
167 90 0.30
168 46 0.15
169 75 0.25
170 4 0.01
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.50
Consensus pattern (164 bp):
TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTT
CATGAGTTTTTGAATTTTTTTTTAAAATTTTTCTATTTTCAAAAAACGAGTTTTCTACTTCGTAA
AATTTTTTGGGAGATTTTTCTTGGTTTATAATTT
Found at i:10019 original size:165 final size:167
Alignment explanation
Indices: 9450--10025 Score: 499
Period size: 165 Copynumber: 3.4 Consensus size: 167
9440 TTTTAAAAAG
* * * * * * *
9450 TCAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTT
1 TCAAAATTCATCAAATATTATAAGTAAATTCAAATTAAATCAATTTTCAAAAATTCATTCATTTT
** * * * * * *
9515 CATGAGCTTGTGAATTTTTTTCCTTAAAATTTTTTTATTTTCAAAATAC-GAAGTTTTCTACTCC
66 CATGAATTTTTGAATTTGTTT-CTTAAAATTTCTCTATTTTCAAAAAACAG-AGTTTTCTACTTC
* * * ** **
9579 GTAAATTTTTTTGGGGGAGATTTTTGTGGGTTTTTAATTT
129 GTAAAATTTTTT-AGGGAGATTTTTCTTAGTTTAAAATTT
* * * * * * * * *
9619 TTAAAATCCATCAAATATTATTA-TCTATTTCATATTATATCAGTTTTCAAAAATTCATTCATTG
1 TCAAAATTCATCAAATATTATAAGT-AAATTCAAATTAAATCAATTTTCAAAAATTCATTCATTT
* *
9683 TCATGAGTTTTTGAATTTGTTTTTTAAAATTTCTCTATTTTCAAAAAACAGAGTTTTCTACTTCG
65 TCATGAATTTTTGAATTTGTTTCTTAAAATTTCTCTATTTTCAAAAAACAGAGTTTTCTACTTCG
**
9748 TAAAATTTTTTAGGGAGATTTTTCTTAGTTTCTAATTT
130 TAAAATTTTTTAGGGAGATTTTTCTTAGTTTAAAATTT
* * * *
9786 TCAAAATTCATCAAATATTATTATTTATTTCAAATTAAATCAATTTTCAAAAATTCATTCATTTT
1 TCAAAATTCATCAAATATTATAAGTAAATTCAAATTAAATCAATTTTCAAAAATTCATTCATTTT
* * * * *
9851 CATGAATTTTT-TATTT-TTTCTTAAAATTTTTCTGTTTTTGAAAAATC-GAGTTTTCTAC-TC-
66 CATGAATTTTTGAATTTGTTTCTTAAAATTTCTCT-ATTTTCAAAAAACAGAGTTTTCTACTTCG
*
9911 TATAAATATTTTT-GGGAGGATTTTTCTTGGTTTAAAATTT
130 TA-AAAT-TTTTTAGGGA-GATTTTTCTTAGTTTAAAATTT
* * * * * * * *
9951 TTAAAATTCATCCAATTTTGTAAGTAAATT-AACATTAAATTATTTTTGAAGAATTCAAATT-A-
1 TCAAAATTCATCAAATATTATAAGTAAATTCAA-ATTAAATCAATTTTCAAAAATTC--ATTCAT
10013 TTTCATGAATTTT
63 TTTCATGAATTTT
10026 GGTTTTTTTG
Statistics
Matches: 350, Mismatches: 47, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
163 2 0.01
164 12 0.03
165 104 0.30
166 15 0.04
167 92 0.26
168 48 0.14
169 77 0.22
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (167 bp):
TCAAAATTCATCAAATATTATAAGTAAATTCAAATTAAATCAATTTTCAAAAATTCATTCATTTT
CATGAATTTTTGAATTTGTTTCTTAAAATTTCTCTATTTTCAAAAAACAGAGTTTTCTACTTCGT
AAAATTTTTTAGGGAGATTTTTCTTAGTTTAAAATTT
Found at i:10499 original size:23 final size:24
Alignment explanation
Indices: 10470--10519 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
10460 GTTTAGCTGA
*
10470 AAAGAAAGGGAGAGAAAAA-AG-AG
1 AAAGAAA-GAAGAGAAAAATAGAAG
10493 AAAGAAAGAAGAGAAAAATAGAAG
1 AAAGAAAGAAGAGAAAAATAGAAG
10517 AAA
1 AAA
10520 ATAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 10 0.42
23 9 0.38
24 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (24 bp):
AAAGAAAGAAGAGAAAAATAGAAG
Found at i:10500 original size:10 final size:9
Alignment explanation
Indices: 10480--10540 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 9
10470 AAAGAAAGGG
10480 AGAGAAAAA
1 AGAGAAAAA
10489 AGAGAAAGAA
1 AGAGAAA-AA
10499 AGAAGAGAAAA
1 AG-AGA-AAAA
*
10510 ATAGAAGAAA
1 AGAGAA-AAA
*
10520 ATAGAAAAA
1 AGAGAAAAA
10529 AGTAGAGAAAA
1 AG-AGA-AAAA
10540 A
1 A
10541 TAAGCTAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 12 0.27
10 19 0.43
11 11 0.25
12 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (9 bp):
AGAGAAAAA
Found at i:10537 original size:30 final size:30
Alignment explanation
Indices: 10482--10542 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
10472 AGAAAGGGAG
10482 AGAAAAAAGAGAAAGAAAGAAGAGAAAAAT
1 AGAAAAAAGAGAAAGAAAGAAGAGAAAAAT
* *
10512 AGAAGAAAATAGAAA-AAAGTAGAGAAAAAT
1 AGAA-AAAAGAGAAAGAAAGAAGAGAAAAAT
10542 A
1 A
10543 AGCTAGTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (30 bp):
AGAAAAAAGAGAAAGAAAGAAGAGAAAAAT
Found at i:11578 original size:162 final size:162
Alignment explanation
Indices: 11311--11603 Score: 428
Period size: 162 Copynumber: 1.8 Consensus size: 162
11301 TATTTTCATA
*
11311 TTAATCATTTTTTAATCTTTTATATTCCTATGACCATCCGTAGGAGTATAAAAGATTTCAAAAAC
1 TTAATCAATTTTTAATCTTTTATATTCCTATGACCA-CCGTAGGAGTATAAAAGATTTCAAAAAC
* * *
11376 TTTTCGTATCTCTTTAGGCTTCCATTAAGGTACAAAATGGTATTT-CAGAAATAAATTAAATTAA
65 TTTTCGTATCTCTTTAGGCATCCATTAAGGTACAAAATGGTATTTACAAAAATAAATAAAATTAA
11440 ACTAAATTAACACTTTCATAACCAAGACAAATT
130 ACTAAATTAACACTTTCATAACCAAGACAAATT
* * *
11473 TTAATCAATTTTTAATCTTTTATATTCTTATGGAGGC-CCGTAGGGGTATAAAAGATTTCAAAAA
1 TTAATCAATTTTTAATCTTTTATATTCCTAT-GA-CCACCGTAGGAGTATAAAAGATTTCAAAAA
* * * * **
11537 CTTTTCGTTTCTTTTTGGGCATCCATTAAGTTATGAAATGGTATTTACAAAAATAAATAAAATTA
64 CTTTTCGTATCTCTTTAGGCATCCATTAAGGTACAAAATGGTATTTACAAAAATAAATAAAATTA
11602 AA
129 AA
11604 TTAGACTAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
162 94 0.82
163 20 0.17
164 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.38
Consensus pattern (162 bp):
TTAATCAATTTTTAATCTTTTATATTCCTATGACCACCGTAGGAGTATAAAAGATTTCAAAAACT
TTTCGTATCTCTTTAGGCATCCATTAAGGTACAAAATGGTATTTACAAAAATAAATAAAATTAAA
CTAAATTAACACTTTCATAACCAAGACAAATT
Found at i:12764 original size:21 final size:22
Alignment explanation
Indices: 12740--12780 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12730 TTTCCGAGAT
*
12740 GAAAAGGCGAA-GGAAAGAAGA
1 GAAAAGGAGAAGGGAAAGAAGA
*
12761 GAAAATGAGAAGGGAAAGAA
1 GAAAAGGAGAAGGGAAAGAA
12781 CACTGGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.59, C:0.02, G:0.37, T:0.02
Consensus pattern (22 bp):
GAAAAGGAGAAGGGAAAGAAGA
Found at i:19654 original size:12 final size:12
Alignment explanation
Indices: 19637--19672 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
19627 GTAAAAAGAT
19637 AGAATGTATCGA
1 AGAATGTATCGA
19649 AGAATGTATCGA
1 AGAATGTATCGA
19661 AGAATGTATCGA
1 AGAATGTATCGA
19673 TCATTCATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (12 bp):
AGAATGTATCGA
Found at i:20916 original size:29 final size:28
Alignment explanation
Indices: 20716--21276 Score: 507
Period size: 28 Copynumber: 19.6 Consensus size: 28
20706 CACCAACTTG
* * **
20716 TGTGGGCTTTAGAGAAAGTTGCCACCAACT
1 TGTGGGCTTT-GA-AAGGGTGCCACTGACT
* * * * *
20746 TGTGGGCTTTAAAAGGATACCACTAATT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
20774 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
20802 TGTGGGCTTCAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
20830 TGTGGGCTTTGAATGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
20858 TGTGGGCTTTGAGAGAGGTTGCCAGC-GACTT
1 TGTGGGCTTTGA-A-AGGGTGCCA-CTGAC-T
20889 GTGTGGGC-TT-AAAGGGGTGCCACTGACT
1 -TGTGGGCTTTGAAA-GGGTGCCACTGACT
*
20917 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
* * *
20946 TGTGGGCTTTGAGAAAGATGCCATTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
*
20975 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
* * **
21004 CGTGGGCTTTAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
21032 TGTGGGATTTGAAAGGATGCCACTAACA
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
21060 TGTGGGCTTTGAAAGGGTGGCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
21088 TGTGGGCTTTGAAAGGATGCCACTTACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
21116 TGTGGACTTTGAAAAGATGCCACTTACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** *
21144 TGTGGTCTTTGAAAGAATGACACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
21172 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * ** *
21200 TTTGGGCGTTGAGAAGAATGCCACGGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
*
21229 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGGTGCCACTGACT
* *
21258 TGTGGACTCTGAAAAGGGT
1 TGTGGGCTTTG-AAAGGGT
21277 CGTATTGACA
Statistics
Matches: 447, Mismatches: 72, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
27 7 0.02
28 263 0.59
29 143 0.32
30 23 0.05
31 4 0.01
32 7 0.02
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:21300 original size:14 final size:14
Alignment explanation
Indices: 21281--21368 Score: 67
Period size: 14 Copynumber: 6.6 Consensus size: 14
21271 AAGGGTCGTA
21281 TTGACAAAAATTTC
1 TTGACAAAAATTTC
*
21295 TTGAC-AAAGTTTC
1 TTGACAAAAATTTC
* *
21308 -TGAGAAACA-TTC
1 TTGACAAAAATTTC
*
21320 TTGAC-AAAAGTTC
1 TTGACAAAAATTTC
** *
21333 TTGATGATAATTTC
1 TTGACAAAAATTTC
**
21347 TTGACAACCATTTC
1 TTGACAAAAATTTC
21361 TTGACAAA
1 TTGACAAA
21369 TGGCGAATTG
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
12 9 0.16
13 19 0.34
14 28 0.50
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (14 bp):
TTGACAAAAATTTC
Found at i:28400 original size:15 final size:15
Alignment explanation
Indices: 28389--28419 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28379 TTATGGTAGG
28389 TAATTTGGTGGTGGA
1 TAATTTGGTGGTGGA
*
28404 TAATTTTGTGGTGGA
1 TAATTTGGTGGTGGA
28419 T
1 T
28420 TTGGCGGAAT
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:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (15 bp):
TAATTTGGTGGTGGA
Done.