Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2085
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: 36841
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:6701 original size:42 final size:42
Alignment explanation
Indices: 6641--6794 Score: 202
Period size: 42 Copynumber: 3.6 Consensus size: 42
6631 CGAGACTATG
* * *
6641 TGTAAGACCATATTTGGGATATGGCATC-ATTATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGA-TACGAGATTTCA
*
6683 TGTAAGACTATATCTGGGATATGGCATCGATACGAGATTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATACGAGATTTCA
* * * **
6725 TGTAATACCATAGCTGGGCTATTGGCATCGATACGAGATCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATACGAGATTTCA
6768 TGTAAGACCATATCTGGGATATGGCAT
1 TGTAAGACCATATCTGGGATATGGCAT
6795 TGGTGTGGTA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 59 0.61
43 38 0.39
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATACGAGATTTCA
Found at i:9322 original size:79 final size:81
Alignment explanation
Indices: 9213--9395 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
9203 TACTCGTTCA
* *
9213 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
9276 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
9293 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
9356 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
9372 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9396 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:9395 original size:40 final size:40
Alignment explanation
Indices: 9192--9395 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
9182 CGGAATTTAA
** *
9192 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9232 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9272 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9311 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9351 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9391 CCGGA
1 CCGGA
9396 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:17936 original size:40 final size:39
Alignment explanation
Indices: 17852--18036 Score: 178
Period size: 40 Copynumber: 4.6 Consensus size: 39
17842 TCGAATGATG
* * * * *
17852 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
17892 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
17932 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
17971 TCC-GAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGA-CTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
* *
18012 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGACTAAGT-CCGAAGGCATTTG
18037 AATGAGTAGT
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 32 0.26
40 78 0.64
41 11 0.09
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:18059 original size:79 final size:78
Alignment explanation
Indices: 17905--18059 Score: 192
Period size: 79 Copynumber: 2.0 Consensus size: 78
17895 GGACTAAGAT
* * *
17905 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGATGAGAGTTACT-A
17970 ATCCGAGTTAAGTC
65 ATCCGAGTTAAGTC
*
17984 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAGTAGTT
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCA-TTG-ATGAG-AGTT
18048 A-T-ATCCG-GTTAA
61 ACTAATCCGAGTTAA
18060 ATTTCGAAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
78 2 0.03
79 38 0.57
80 15 0.22
81 3 0.04
82 4 0.06
83 5 0.07
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGATGAGAGTTACTAA
TCCGAGTTAAGTC
Found at i:19502 original size:26 final size:26
Alignment explanation
Indices: 19467--19518 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
19457 AATGTGAAAG
*
19467 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
19493 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
19519 TTTCATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:19573 original size:103 final size:102
Alignment explanation
Indices: 19389--19755 Score: 594
Period size: 103 Copynumber: 3.6 Consensus size: 102
19379 TGTATATAAA
** * * *
19389 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGT-ATCCACCATATCTT
*
19454 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
19492 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCT
19557 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
19596 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TATCCACCATATCTT
*
19661 TGAAAT-AAAAAGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
19698 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCA
19756 ATAACGGCTA
Statistics
Matches: 252, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
101 8 0.03
102 78 0.31
103 93 0.37
104 72 0.29
105 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTATCCACCATATCTTT
GAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:19713 original size:27 final size:27
Alignment explanation
Indices: 19671--19722 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
19661 TGAAATAAAA
*
19671 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
19698 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
19723 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:27074 original size:26 final size:26
Alignment explanation
Indices: 27039--27089 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
27029 AATGTGAAAG
*
27039 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
27065 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
27090 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:27263 original size:26 final size:26
Alignment explanation
Indices: 27227--27279 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
27217 ATGAAATAAA
*
27227 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
27253 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
27279 A
1 A
27280 TTCAGTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:27274 original size:88 final size:95
Alignment explanation
Indices: 26961--27311 Score: 378
Period size: 103 Copynumber: 3.6 Consensus size: 95
26951 GTTGTATAAA
** * * *
26961 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATT--CCGATTCATTGGTGGTGCTAAGT-CGAT-ATCCACCATA---
*
27025 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
59 TTGAAA--TGAAAAGGGGTTGCTATGTGCTGATTCCCCG
*
27064 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATT--CCGATTCATTGGTGGTGCTAAGT-CGATATCCACCATA---T
*
27129 TGAAATGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
60 TGAAATGAAAAGGGGTTGCTATGTGCTGATT-CCCCG
27166 AGGGGTTGCTAAGTGC-GATTCC-ATT-ATT-GT-GTGCTAAGT-GATATCCACCATA-TGAAAT
1 AGGGGTTGCTAAGTGCTGATTCCGATTCATTGGTGGTGCTAAGTCGATATCCACCATATTGAAAT
27224 -AAAAGGGGTTGCTATGTGCTGATTCCCCG
66 GAAAAGGGGTTGCTATGTGCTGATTCCCCG
* *
27253 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATT--CCGATTCATTGGTGGTGCTAAGT-CGATATCCACCA
27312 ATAACGGTTA
Statistics
Matches: 227, Mismatches: 10, Indels: 29
0.85 0.04 0.11
Matches are distributed among these distances:
87 21 0.09
88 27 0.12
89 6 0.03
90 2 0.01
91 3 0.01
92 2 0.01
93 15 0.07
94 9 0.04
95 9 0.04
96 12 0.05
97 3 0.01
98 2 0.01
99 2 0.01
101 30 0.13
102 21 0.09
103 62 0.27
104 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.30
Consensus pattern (95 bp):
AGGGGTTGCTAAGTGCTGATTCCGATTCATTGGTGGTGCTAAGTCGATATCCACCATATTGAAAT
GAAAAGGGGTTGCTATGTGCTGATTCCCCG
Found at i:34831 original size:100 final size:99
Alignment explanation
Indices: 34641--34870 Score: 262
Period size: 100 Copynumber: 2.3 Consensus size: 99
34631 GAATGTGAAA
*
34641 GGGGTT-CTATGTGCTGATT--CCGAGGGGTTTGCTAAGTGCTGATTCCCGATTTCATGGTGGTG
1 GGGGTTGCTAGGTGCTGATTCCCCGAGGGG--TGCTAAGTGCTGATTCCCGATTT-ATGGTGGTG
*
34703 CTAAGTGCGATATCACCATATCTTTGAAATGAAAAGG
63 CTAAGTGCGATATCACCATATCTTTGAAATAAAAAGG
34740 GGGGTTGC-AGGGTTGTCTGATTCCCCGAGGGGTGCTAAGTG-TGGATT-CCGA-TTATTGGTGG
1 GGGGTTGCTA-GG-TG-CTGATTCCCCGAGGGGTGCTAAGTGCT-GATTCCCGATTTA-TGGTGG
34801 TGCTAA-TGCGATATCCACCAATATC-TTGAAATAAAAAGG
61 TGCTAAGTGCGATAT-CACC-ATATCTTTGAAATAAAAAGG
** *
34840 GGTTTTGCTATGTGCTGATTCCCCGAGGGGT
1 GGGGTTGCTAGGTGCTGATTCCCCGAGGGGT
34871 TCCTAGATGC
Statistics
Matches: 115, Mismatches: 5, Indels: 23
0.80 0.03 0.16
Matches are distributed among these distances:
98 17 0.15
99 18 0.16
100 40 0.35
101 13 0.11
102 19 0.17
104 8 0.07
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (99 bp):
GGGGTTGCTAGGTGCTGATTCCCCGAGGGGTGCTAAGTGCTGATTCCCGATTTATGGTGGTGCTA
AGTGCGATATCACCATATCTTTGAAATAAAAAGG
Done.