Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold644
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: 42211
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4584 original size:23 final size:23
Alignment explanation
Indices: 4554--4663 Score: 102
Period size: 23 Copynumber: 4.8 Consensus size: 23
4544 TGATGAACAA
4554 TAAGCTCTATTGAGCTGAAATGG
1 TAAGCTCTATTGAGCTGAAATGG
*
4577 TAAGCTCTATCGAGCTGAACA--G
1 TAAGCTCTATTGAGCTGAA-ATGG
*
4599 TAAGCTC-ATACGAGCTGAAATGG
1 TAAGCTCTAT-TGAGCTGAAATGG
* * **
4622 TAAGCTCCAATGAGCTGAAAACAG
1 TAAGCTCTATTGAGCTG-AAATGG
4646 TAAGCTCT-TATGAGCTGA
1 TAAGCTCTAT-TGAGCTGA
4664 TATATCTGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
21 3 0.04
22 17 0.23
23 33 0.45
24 20 0.27
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (23 bp):
TAAGCTCTATTGAGCTGAAATGG
Found at i:4603 original size:45 final size:46
Alignment explanation
Indices: 4547--4663 Score: 152
Period size: 45 Copynumber: 2.6 Consensus size: 46
4537 CCTGAGCTGA
* *
4547 TGAACAATAAGCTCTAT-TGAGCTGAAATGGTAAGCT-CTATCGAGC
1 TGAACAGTAAGCTCTATATGAGCTGAAATGGTAAGCTCCAAT-GAGC
*
4592 TGAACAGTAAGCTC-ATACGAGCTGAAATGGTAAGCTCCAATGAGC
1 TGAACAGTAAGCTCTATATGAGCTGAAATGGTAAGCTCCAATGAGC
4637 TGAAAACAGTAAGCTCT-TATGAGCTGA
1 TG--AACAGTAAGCTCTATATGAGCTGA
4664 TATATCTGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 2 0.03
45 37 0.59
46 3 0.05
47 21 0.33
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (46 bp):
TGAACAGTAAGCTCTATATGAGCTGAAATGGTAAGCTCCAATGAGC
Found at i:9809 original size:30 final size:30
Alignment explanation
Indices: 9752--9809 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
9742 CACGGCTATG
*
9752 ACACACGGGTGTGTGGTCTACCCGTGTGTC
1 ACACACGGGTGTGTGGTCTACCAGTGTGTC
*
9782 ACACTCGGGTGTGTGGATC-ACCAGTGTG
1 ACACACGGGTGTGTGG-TCTACCAGTGTG
9810 GAACTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.26
Consensus pattern (30 bp):
ACACACGGGTGTGTGGTCTACCAGTGTGTC
Found at i:13433 original size:37 final size:37
Alignment explanation
Indices: 13383--13461 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
13373 TTATTACGAA
* * *
13383 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
13420 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
13457 GTCTT
1 GTCTT
13462 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:13718 original size:47 final size:46
Alignment explanation
Indices: 13583--14073 Score: 748
Period size: 47 Copynumber: 10.6 Consensus size: 46
13573 TTCGGGACTA
13583 TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-T
1 TCACATTCATCACATCGGCCATTAGG-CCTATCAC--ATATATACACTT
13631 TCACATTCATCACATCGGCCATTAGGCCTATCACATATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTATCAC--ATATATACACTT
13679 TCACATTCATCACATCGGCCATTAGGACCTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGG-CCTATCACATATATACACTT
13726 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCC-TATCACATATATACACTT
*
13773 TCACATTCATCACATCGACCATTAGGCCT-T-ATCA-ATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTATCA-CATATATACACTT
*
13817 TCACATTCATCACATCGGCCATTAGGCATTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGC-CTATCACATATATACACTT
*
13864 TCACATTCATCACATCGGCCATTAGGCATTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGC-CTATCACATATATACACTT
* *
13911 TCACATTCATCACATCGGCCATTAGACATTATCACATATATACACTT
1 TCACATTCATCACATCGGCCATTAGGC-CTATCACATATATACACTT
* *
13958 TCACATTCAT--CATCGGCCATTAGGCTTATCACAGATATACACTT
1 TCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACTT
14002 TCACATTCATCACATCGGCCATTAGGCCTTATCA-ATATAT--ACTT
1 TCACATTCATCACATCGGCCATTAGGCC-TATCACATATATACACTT
14046 TCACATTCATCACATCGGCCATTAGGCC
1 TCACATTCATCACATCGGCCATTAGGCC
14074 ATACTATCAT
Statistics
Matches: 424, Mismatches: 8, Indels: 26
0.93 0.02 0.06
Matches are distributed among these distances:
44 97 0.23
45 18 0.04
46 26 0.06
47 222 0.52
48 53 0.12
49 8 0.02
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (46 bp):
TCACATTCATCACATCGGCCATTAGGCCTATCACATATATACACTT
Found at i:13850 original size:22 final size:23
Alignment explanation
Indices: 13820--13900 Score: 67
Period size: 22 Copynumber: 3.5 Consensus size: 23
13810 TACACTTTCA
13820 CATTCATCACATCGGCCATTAGG
1 CATTCATCACATCGGCCATTAGG
**** ***
13843 CATT-ATCACATATATACACTTTCA
1 CATTCATCACAT-CGGCCA-TTAGG
13867 CATTCATCACATCGGCCATTAGG
1 CATTCATCACATCGGCCATTAGG
13890 CATT-ATCACAT
1 CATTCATCACAT
13901 ATATACACTT
Statistics
Matches: 41, Mismatches: 14, Indels: 7
0.66 0.23 0.11
Matches are distributed among these distances:
22 14 0.34
23 12 0.29
24 8 0.20
25 7 0.17
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (23 bp):
CATTCATCACATCGGCCATTAGG
Found at i:13855 original size:138 final size:140
Alignment explanation
Indices: 13583--14073 Score: 779
Period size: 138 Copynumber: 3.5 Consensus size: 140
13573 TTCGGGACTA
*
13583 TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-TTCACATTCATCACATC
1 TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATC
*
13647 GGCCATTAGGCC-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-ACCTA
64 GGCCATTAGGCCTTAT-AC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCA-TTA
13710 TCACATATATACACTT
125 TCACATATATACACTT
*
13726 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGA
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
13791 CCATTAGGCCTTAT-CA-ATATACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACAT
66 CCATTAGGCCTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACAT
13854 ATATACACTT
131 ATATACACTT
*
13864 TCACATTCATCACATCGGCCATTAGGCATTATCACATATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
* *
13929 CCATTAGACATTATCACATATATACACTTTCACATTCAT--CATCGGCCATTAGGC-TTATCACA
66 CCATTAGGCCTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACA
*
13991 GATATACACTT
130 TATATACACTT
14002 TCACATTCATCACATCGGCCATTAGGCCTTATCA-ATATAT--ACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
14064 CCATTAGGCC
66 CCATTAGGCC
14074 ATACTATCAT
Statistics
Matches: 331, Mismatches: 11, Indels: 20
0.91 0.03 0.06
Matches are distributed among these distances:
135 30 0.09
137 6 0.02
138 180 0.54
139 17 0.05
140 2 0.01
141 31 0.09
142 28 0.08
143 37 0.11
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (140 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CCATTAGGCCTTATACATATATACACTTTCACATTCATCACATCGGCCATTAGGCATTATCACAT
ATATACACTT
Found at i:13900 original size:185 final size:187
Alignment explanation
Indices: 13583--14072 Score: 768
Period size: 185 Copynumber: 2.6 Consensus size: 187
13573 TTCGGGACTA
* *
13583 TCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC-TTCACATTCATCACATC
1 TCACATTCATCACATCGGCCATTAGGCCTTAT-AC--AGATATACACTTTCACATTCATCACATC
*
13647 GGCCATTAGGCCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG-ACCTAT
63 GGCCATTAGGCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCACCTAT
* *
13711 CACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
126 CACATATATACACTTTCACATTCATCACATCGGCCATTAGACATTATCACATATATACACTT
*
13773 TCACATTCATCACATCGACCATTAGGCCTTAT-CA-ATATACACTTTCACATTCATCACATCGGC
1 TCACATTCATCACATCGGCCATTAGGCCTTATACAGATATACACTTTCACATTCATCACATCGGC
*
13836 CATTAGGCATTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCA-TTATCACA
66 CATTAGGC-TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCACCTATCACA
13900 TATATACACTTTCACATTCATCACATCGGCCATTAGACATTATCACATATATACACTT
130 TATATACACTTTCACATTCATCACATCGGCCATTAGACATTATCACATATATACACTT
13958 TCACATTCAT--CATCGGCCATTAGG-CTTATCACAGATATACACTTTCACATTCATCACATCGG
1 TCACATTCATCACATCGGCCATTAGGCCTTAT-ACAGATATACACTTTCACATTCATCACATCGG
14020 CCATTAGGCCTTATCA-ATATAT--ACTTTCACATTCATCACATCGGCCATTAGGC
65 CCATTAGG-CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
14073 CATACTATCA
Statistics
Matches: 286, Mismatches: 7, Indels: 22
0.91 0.02 0.07
Matches are distributed among these distances:
182 36 0.13
183 13 0.05
184 8 0.03
185 161 0.56
186 31 0.11
187 6 0.02
188 1 0.00
190 30 0.10
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (187 bp):
TCACATTCATCACATCGGCCATTAGGCCTTATACAGATATACACTTTCACATTCATCACATCGGC
CATTAGGCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCACCTATCACAT
ATATACACTTTCACATTCATCACATCGGCCATTAGACATTATCACATATATACACTT
Found at i:19382 original size:13 final size:13
Alignment explanation
Indices: 19364--19389 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19354 TGGAAAAATT
19364 TTCGAAAATTTCG
1 TTCGAAAATTTCG
19377 TTCGAAAATTTCG
1 TTCGAAAATTTCG
19390 AACGTTTGGG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTCGAAAATTTCG
Found at i:20624 original size:103 final size:101
Alignment explanation
Indices: 20445--20662 Score: 261
Period size: 103 Copynumber: 2.1 Consensus size: 101
20435 GTATTATAAA
** * *
20445 AGGGTTGCTGTGTG-CTGATTCCCCGATTTATGGGTGGTGCATGTGCGTGATCCACCAATCTTTG
1 AGGGTTGCTAAGTGCCTGATTCCCCGATTCATGGGTGGTGCAAGTGCGTGATCCACCAATCTTTG
20509 AAAATGTGAAAGG-GGGTTGC-ATGTGCTGATTCCCCCG
66 AAAATGTGAAAGGCGGGTT-CTATGTGCTGATT--CCCG
* *
20546 AGGGGTTGCTAAGTGCCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCG-GATATCC-CCATAT
1 A-GGGTTGCTAAGTGCCTGATTCCCCGATTCATGGGTGGTGC-AAGTGCGTG--ATCCACCA-AT
20609 CTTTG-AAATG-GAAAGGCGGGTTCTATGTGCTGATTCCCG
61 CTTTGAAAATGTGAAAGGCGGGTTCTATGTGCTGATTCCCG
20648 AGGGTTGCTAAGTGC
1 AGGGTTGCTAAGTGC
20663 GATATCCATT
Statistics
Matches: 103, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
101 15 0.15
102 16 0.16
103 31 0.30
104 30 0.29
105 11 0.11
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (101 bp):
AGGGTTGCTAAGTGCCTGATTCCCCGATTCATGGGTGGTGCAAGTGCGTGATCCACCAATCTTTG
AAAATGTGAAAGGCGGGTTCTATGTGCTGATTCCCG
Found at i:27630 original size:29 final size:29
Alignment explanation
Indices: 27575--27638 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
27565 TAATTCCGGC
* * *
27575 TTGGGACAAAAGTGTAATTTATGAAAAGT
1 TTGGGGCAAAAGTGTAATTTATAAAAAGG
*
27604 TTGGGGCAAAATTGTAATTT-TCAAAAAGG
1 TTGGGGCAAAAGTGTAATTTAT-AAAAAGG
27633 TTGGGG
1 TTGGGG
27639 TGGTGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (29 bp):
TTGGGGCAAAAGTGTAATTTATAAAAAGG
Done.