Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_828
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: 45293
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2426 original size:42 final size:42
Alignment explanation
Indices: 2310--2427 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
2300 TGAGATTATG
* * * **
2310 TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTTA
1 TGTAAGACCATATCTGGGATATTGCATAGGTATGAGACTCCA
* * *
2352 TGTAAGA-CATAGCTTGGCTATTGGCATAGGTATGAGA-TCCCA
1 TGTAAGACCATATCTGGGATATT-GCATAGGTATGAGACT-CCA
*
2394 TGTAAGACCATATCTGGGATATTGCATTGGTATG
1 TGTAAGACCATATCTGGGATATTGCATAGGTATG
2428 GCACTATGTG
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 12 0.20
42 37 0.61
43 12 0.20
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATTGCATAGGTATGAGACTCCA
Found at i:2531 original size:20 final size:20
Alignment explanation
Indices: 2503--2549 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2493 CGATAAAGTT
2503 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
2523 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
2543 TAAGTTG
1 TAAGTTG
2550 CAAGTTGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:5347 original size:39 final size:39
Alignment explanation
Indices: 5288--5364 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
5278 AGTGGCAGTC
*
5288 TGACAATGTGAGAAAATTATATAAAGGAGGAGGTTTCGA
1 TGACAATGTGAGAAAATTATATAAAGGAGGAGGGTTCGA
*
5327 TGACGATGTGAGAAAATTATATAAAGGAGGAGGGTTCG
1 TGACAATGTGAGAAAATTATATAAAGGAGGAGGGTTCG
5365 GTCACCAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.39, C:0.05, G:0.31, T:0.25
Consensus pattern (39 bp):
TGACAATGTGAGAAAATTATATAAAGGAGGAGGGTTCGA
Found at i:7299 original size:23 final size:23
Alignment explanation
Indices: 7272--7321 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
7262 AAGAGAGCAG
7272 AAGGATTGATCAAAGAAGAAATT
1 AAGGATTGATCAAAGAAGAAATT
* * *
7295 AAGGATTGATTAGATAAGAAATT
1 AAGGATTGATCAAAGAAGAAATT
7318 AAGG
1 AAGG
7322 TTTCTGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24
Consensus pattern (23 bp):
AAGGATTGATCAAAGAAGAAATT
Found at i:8616 original size:27 final size:27
Alignment explanation
Indices: 8585--8643 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
8575 TAGGTGTAAG
*
8585 TGATTTTGACAAGCAACTAAGTGTATA
1 TGATTTTGACAAGCAACTAACTGTATA
* *
8612 TGATTTTGATAAGCAACTAACTGTATG
1 TGATTTTGACAAGCAACTAACTGTATA
8639 TGATT
1 TGATT
8644 CGGATTCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
TGATTTTGACAAGCAACTAACTGTATA
Found at i:12273 original size:39 final size:39
Alignment explanation
Indices: 12152--12332 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 39
12142 GCTACTCGTT
*
12152 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAG-CCGGATT-TAGTAACTCGCA
*
12192 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGC-CGGATTTAGTAACTCGCA
* *
12232 CAAATGCCTTCGGG-CTTAGCCAGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCC-GGATTTAGTAACTCGCA
* * * *
12271 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCGGATTTAGTAAC-TCGCA
12312 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
12333 CGGACATCAT
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
38 3 0.02
39 34 0.28
40 70 0.57
41 15 0.12
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCGGATTTAGTAACTCGCA
Found at i:12297 original size:79 final size:81
Alignment explanation
Indices: 12152--12332 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 81
12142 GCTACTCGTT
* * *
12152 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGG
1 CAAATGCCTTCGGGACTTAGCCAGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGG
* *
12217 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* *
12232 CAAATGCCTTCGGG-CTTAGCCAGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTT-AGTC
1 CAAATGCCTTCGGGACTTAGCCAGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACT-
* *
12293 CGGATATGGTCACTTAGCA
63 CGGATATAGTAACTTAGCA
12312 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
12333 CGGACATCAT
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
78 6 0.07
79 52 0.60
80 29 0.33
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCAGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGG
ATATAGTAACTTAGCA
Found at i:24384 original size:37 final size:37
Alignment explanation
Indices: 24334--24412 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
24324 TTATTACGAA
* * *
24334 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
24371 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
24408 GTCTT
1 GTCTT
24413 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:24609 original size:47 final size:47
Alignment explanation
Indices: 24531--24894 Score: 595
Period size: 47 Copynumber: 7.7 Consensus size: 47
24521 CCCTTCGGGA
* * * * * *
24531 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24578 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24625 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
24672 CTTATCACATATATACACTTTCACATTGATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24719 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24766 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24813 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24860 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
24895 AGAATCCTAA
Statistics
Matches: 299, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 1 0.00
47 298 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26552 original size:56 final size:56
Alignment explanation
Indices: 26485--26641 Score: 305
Period size: 56 Copynumber: 2.8 Consensus size: 56
26475 TATTAGTTTA
26485 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
26541 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
26597 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTT
26642 TGCCCATCAT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 100 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:30854 original size:22 final size:22
Alignment explanation
Indices: 30829--30870 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30819 TTTATTAAAT
30829 CACCACTAC-AAAACCACCATAC
1 CACCAC-ACTAAAACCACCATAC
*
30851 CACCACACTAACACCACCAT
1 CACCACACTAAAACCACCAT
30871 TTCTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.43, C:0.48, G:0.00, T:0.10
Consensus pattern (22 bp):
CACCACACTAAAACCACCATAC
Found at i:32513 original size:40 final size:40
Alignment explanation
Indices: 32454--32671 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
32444 CGGATGATAA
* *
32454 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
32494 CCGAGCTAAGTCCCGAAGGCA-TTGTTGCGAGTTACTA-ACT
1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATA-T
*
32534 CCGGGCTAAGTCCCGAAGGCATTTGTGGGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
32574 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
32614 CCGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
32654 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
32672 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 19 0.12
40 137 0.86
41 4 0.03
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39862 original size:40 final size:40
Alignment explanation
Indices: 39755--39967 Score: 240
Period size: 40 Copynumber: 5.4 Consensus size: 40
39745 TGATAACCGA
* *
39755 GCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGG
39795 GCTAAGT-CCGAAGGCA-TTGTTGCGAGTTACTA-ATTCCGG
1 GCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATA-TCCGG
*
39834 GCTAAGTCCCGAAGGCATTTGTGGGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* ** *
39874 GCTAAGTCCCGAAGGAATTTGTGCGAACTACTTTATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* * *
39914 GCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTAGATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
* *
39953 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
39968 TACTTGGTTT
Statistics
Matches: 152, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 3 0.02
39 49 0.32
40 96 0.63
41 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:39952 original size:80 final size:79
Alignment explanation
Indices: 39755--39967 Score: 231
Period size: 79 Copynumber: 2.7 Consensus size: 79
39745 TGATAACCGA
* *
39755 GCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTAATTCCGGGCTAAGT-CCGAAGGCATTGTTGC
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTAG-CTAA-TCCGGGCTAAGTCCCGAAGGAATTGTTGC
**
39818 GAGTTACTAATTCCGG
64 GAACTACTAATTCCGG
*
39834 GCTAAGTCCCGAAGGCATTTGTGGGAGTTA-CTATATCCGGGCTAAGTCCCGAAGGAATT-TGTG
1 GCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTA-ATCCGGGCTAAGTCCCGAAGGAATTGT-TG
*
39897 CGAACTACT-TTATCCGG
63 CGAACTACTAAT-TCCGG
* * * *
39914 GCTAAGTCCCGAAGGCATTCGAGCGAGTAGCTAGATCC-GGTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTA-ATCCGGGCTAAGTCCCGAAGG
39968 TACTTGGTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
79 58 0.50
80 57 0.50
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTAATCCGGGCTAAGTCCCGAAGGAATTGTTGCGA
ACTACTAATTCCGG
Found at i:41409 original size:46 final size:47
Alignment explanation
Indices: 41328--41431 Score: 140
Period size: 46 Copynumber: 2.2 Consensus size: 47
41318 ATTAATTTAT
* * *
41328 AAATTTGGTGGTTTATCCATAACCTACATGTTTTAGTAGTTTGTCTGA
1 AAATTTGGTGGTTTATCCACAACCTACATGTTTTAGCAGCTTG-CTGA
* *
41376 AAATTTGGTGG-TTATCC-CAAGCTACATGTTTTAGCAGCTTGCTGC
1 AAATTTGGTGGTTTATCCACAACCTACATGTTTTAGCAGCTTGCTGA
41421 AAATTTGGTGG
1 AAATTTGGTGG
41432 CTTCGTCCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
45 14 0.27
46 20 0.39
47 6 0.12
48 11 0.22
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (47 bp):
AAATTTGGTGGTTTATCCACAACCTACATGTTTTAGCAGCTTGCTGA
Found at i:42820 original size:45 final size:43
Alignment explanation
Indices: 42769--42860 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 43
42759 ACATAAATAC
42769 ACATTCATGCAAAATTCACTCATATCC-ATATTAGAAAATATATTT
1 ACATTCATGCAAAATTCACTCATA-CCTATATTAG--AATATATTT
42814 ACATTCATGCAAAATTCACTCATACCTATATTAGAATATATTT
1 ACATTCATGCAAAATTCACTCATACCTATATTAGAATATATTT
42857 ACAT
1 ACAT
42861 GAATGCTACC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
43 13 0.28
44 2 0.04
45 31 0.67
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.36
Consensus pattern (43 bp):
ACATTCATGCAAAATTCACTCATACCTATATTAGAATATATTT
Done.