Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_402 ID=scaffold_402-JGI_221_v2.0
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: 7522
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:122 original size:71 final size:71
Alignment explanation
Indices: 1--452 Score: 771
Period size: 71 Copynumber: 6.4 Consensus size: 71
*
1 AATTGGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
1 AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
66 ATCAAA
66 ATCAAA
* *
72 AATTAGACAGCATATAGACAACAATTTGGGCAGCATATATGTACCAAATTGAGCAGCATTTTTAC
1 AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
137 ATCAAA
66 ATCAAA
*
143 AATT-GAACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGTATTTTTA
1 AATTAG-ACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTA
207 CATCAAA
65 CATCAAA
* * * *
214 AATGAGACAGCATATAGACAACAATTTGGGTAGCATATATGTACCAAATTGAGCAGCATTTTTAC
1 AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
279 ATCAAA
66 ATCAAA
*
285 AATTGGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
1 AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
350 ATCAAA
66 ATCAAA
* *
356 AATTAGACAGCATATAAAAAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
1 AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
421 ATCAAA
66 ATCAAA
**
427 AATTAGACAGCATATATGCAACAATT
1 AATTAGACAGCATATACACAACAATT
453 AGACAGCATT
Statistics
Matches: 357, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
70 1 0.00
71 355 0.99
72 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (71 bp):
AATTAGACAGCATATACACAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTAC
ATCAAA
Found at i:438 original size:48 final size:47
Alignment explanation
Indices: 1--464 Score: 161
Period size: 48 Copynumber: 9.8 Consensus size: 47
* * * * * * *
1 AATTGGACAGCATATACACAACAATTTGGGCAGCATATATATAC-CA
1 AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACACAAA
* * * *
47 AATT-GAGCAGCATTTTTACATCAAAAATT-AGACAGCA--TATAGACAACA
1 AATTGGA-CAGCATATATACA-C-CAAATTGAG-CAGCATTTATACACAA-A
* * ** *
95 ATTTGGGCAGCATATATGTACCAAATTGAGCAGCATTTTTACATCAAA
1 AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACA-CAAA
* * * * * * * *
143 AATTGAACAGCATATACACAACAATTTGGGCAGCATATATATAC-CA
1 AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACACAAA
* * * * * *
189 AATT-GAGCAGTATTTTTACATCAAAAATGAGACAGCA--TATAGACAACA
1 AATTGGA-CAGCATATATACA-CCAAATTGAG-CAGCATTTATACACAA-A
* ** ** *
237 ATTTGGGTAGCATATATGTACCAAATTGAGCAGCATTTTTACATCAAA
1 AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACA-CAAA
* * * * * * *
285 AATTGGACAGCATATACACAACAATTTGGGCAGCATATATATAC-CA
1 AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACACAAA
* * * *
331 AATT-GAGCAGCATTTTTACATCAAAAATT-AGACAGCA--TATA-AAAAA
1 AATTGGA-CAGCATATATACA-C-CAAATTGAG-CAGCATTTATACACAAA
* * *
377 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAA
1 -AA-TTGGACAGCATATATACACCAAATTGAGCAGCATTTATACA-CAAA
* * *
427 AATTAGACAGCATATATGCAAC-AATT-AGACAGCATTTA
1 AATTGGACAGCATATATACACCAAATTGAG-CAGCATTTA
465 AGCATAAAAA
Statistics
Matches: 294, Mismatches: 90, Indels: 67
0.65 0.20 0.15
Matches are distributed among these distances:
45 6 0.02
46 87 0.30
47 37 0.13
48 149 0.51
49 12 0.04
50 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (47 bp):
AATTGGACAGCATATATACACCAAATTGAGCAGCATTTATACACAAA
Found at i:1254 original size:29 final size:29
Alignment explanation
Indices: 1188--1286 Score: 123
Period size: 28 Copynumber: 3.5 Consensus size: 29
1178 TTTAATAAGT
* *
1188 TCGCACACTTAATGC-TTA-ATAATCAAAC
1 TCGCACACTTAGTGCTTTACA-AATTAAAC
1216 TCGCACACTTAGTGCTTTACAAATTAAAC
1 TCGCACACTTAGTGCTTTACAAATTAAAC
* *
1245 TCGCACACTTAGTGCTTCAC-AATTAAAT
1 TCGCACACTTAGTGCTTTACAAATTAAAC
*
1273 TCGCACACGTAGTG
1 TCGCACACTTAGTG
1287 TCGAAAGTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 34 0.53
29 29 0.45
30 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (29 bp):
TCGCACACTTAGTGCTTTACAAATTAAAC
Found at i:7134 original size:71 final size:71
Alignment explanation
Indices: 7058--7522 Score: 648
Period size: 71 Copynumber: 6.5 Consensus size: 71
7048 CCATATACAT
* * * * * * *
7058 CAATTTGGACAGCATTTATATACCAAACT-AGGCAACATTGTTACA-CAAAAAAATAGACAGCAT
1 CAATTTGGGCAGCATATATATACCAAATTGA-GCAGCATTTTTACATC-AAAAATTGGACAGCAT
*
7121 ATATACAA
64 ATACACAA
* ** *
7129 TAATTT-GGCAGCATATGCATACCAAATTGAGCAGCATTTTTTTTTACATCTAAAATTGGACAGC
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCA----TTTTTACATCAAAAATTGGACAGC
7193 ATATACACAA
62 ATATACACAA
*
7203 CAATTTGGGCAGCATATATATAACAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
*
7268 AGACAA
66 ACACAA
* *
7274 CAATTTGGGCAGCATATATATAACAAATTGAGCAGTATTTTTACATCAAAAATTGGACAGCATAT
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
7339 ACACAA
66 ACACAA
* * *
7345 CATTTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATAAAAAATTAGACAGCATAT
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
*
7410 AGACAA
66 ACACAA
* *
7416 CAATTTGGGCAGCATATATGTACCAAATTGAGCAGTATTTTTACATCAAAAATTGGACAGCATAT
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
7481 ACACAA
66 ACACAA
*
7487 CAATTTGGGCAGCATATACATACCAAATTGAGCAGC
1 CAATTTGGGCAGCATATATATACCAAATTGAGCAGC
Statistics
Matches: 352, Mismatches: 35, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
70 22 0.06
71 270 0.77
74 32 0.09
75 28 0.08
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (71 bp):
CAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTTTACATCAAAAATTGGACAGCATAT
ACACAA
Found at i:7210 original size:23 final size:23
Alignment explanation
Indices: 7181--7516 Score: 173
Period size: 23 Copynumber: 14.3 Consensus size: 23
7171 TTTACATCTA
7181 AAATTGGACAGCATATACACAAC
1 AAATTGGACAGCATATACACAAC
* * * *
7204 AATTTGGGCAGCATATATATAAC
1 AAATTGGACAGCATATACACAAC
*
7227 AAATT-GAGCAGCATTTTTACATCAA-
1 AAATTGGA-CAGCA--TATACA-CAAC
*
7252 AAATTGGACAGCATATAGACAAC
1 AAATTGGACAGCATATACACAAC
* * * *
7275 AATTTGGGCAGCATATATATAAC
1 AAATTGGACAGCATATACACAAC
* *
7298 AAATT-GAGCAGTATTTTTACATCAA-
1 AAATTGGA-CAGCA--TATACA-CAAC
7323 AAATTGGACAGCATATACACAAC
1 AAATTGGACAGCATATACACAAC
** * * * *
7346 ATTTTGGGCAGCATATATATACC
1 AAATTGGACAGCATATACACAAC
* * *
7369 AAATT-GAGCAGCATTTTTACATAAA
1 AAATTGGA-CAGCA--TATACACAAC
* *
7394 AAATTAGACAGCATATAGACAAC
1 AAATTGGACAGCATATACACAAC
* * *** *
7417 AATTTGGGCAGCATATATGTACC
1 AAATTGGACAGCATATACACAAC
* *
7440 AAATT-GAGCAGTATTTTTACATCAA-
1 AAATTGGA-CAGCA--TATACA-CAAC
7465 AAATTGGACAGCATATACACAAC
1 AAATTGGACAGCATATACACAAC
* * * *
7488 AATTTGGGCAGCATATACATACC
1 AAATTGGACAGCATATACACAAC
7511 AAATTG
1 AAATTG
7517 AGCAGC
Statistics
Matches: 229, Mismatches: 62, Indels: 44
0.68 0.19 0.13
Matches are distributed among these distances:
22 13 0.06
23 148 0.65
25 55 0.24
26 13 0.06
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (23 bp):
AAATTGGACAGCATATACACAAC
Found at i:7286 original size:48 final size:48
Alignment explanation
Indices: 7181--7430 Score: 160
Period size: 48 Copynumber: 5.3 Consensus size: 48
7171 TTTACATCTA
* * * * *
7181 AAATTGGACAGCA-TATACA-CAACAATTTGGGCAGCATATATATAAC
1 AAATTGGGCAGCATTATACATCAACAAATTGGACAGCATATAGACAAC
* *
7227 AAATTGAGCAGCATTTTTACATCAA-AAATTGGACAGCATATAGACAAC
1 AAATTGGGCAGCA-TTATACATCAACAAATTGGACAGCATATAGACAAC
* * * * *
7275 AATTTGGGCAGCA-TATATAT-AACAAATT-GAGCAGTATTTTTACATCAA-
1 AAATTGGGCAGCATTATACATCAACAAATTGGA-CAGCA--TATAGA-CAAC
* ** * * * *
7323 AAATTGGACAGCA-TATACA-CAACATTTTGGGCAGCATATATATACC
1 AAATTGGGCAGCATTATACATCAACAAATTGGACAGCATATAGACAAC
* * * *
7369 AAATTGAGCAGCATTTTTACAT-AAAAAATTAGACAGCATATAGACAAC
1 AAATTGGGCAGCA-TTATACATCAACAAATTGGACAGCATATAGACAAC
*
7417 AATTTGGGCAGCAT
1 AAATTGGGCAGCAT
7431 ATATGTACCA
Statistics
Matches: 152, Mismatches: 38, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
45 5 0.03
46 40 0.26
47 1 0.01
48 99 0.65
49 7 0.05
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (48 bp):
AAATTGGGCAGCATTATACATCAACAAATTGGACAGCATATAGACAAC
Done.