Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_193 ID=scaffold_193-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: 9562
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1131 original size:2 final size:2
Alignment explanation
Indices: 1124--1152 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1114 TTATTTTGTA
1124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1153 CACATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6995 original size:44 final size:43
Alignment explanation
Indices: 6906--7545 Score: 534
Period size: 44 Copynumber: 14.5 Consensus size: 43
6896 GCAGATCAGT
* * *
6906 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* *
6950 GAAGATGCAGATCTTGTCTTCTCATATTGGTGGCGGAGTAGATC
1 GAAGATGCAGATCTTGTCTTC-CATATTGGTAGCGAAGTAGATC
* * **
6994 GAAGAAAGTAGATCTTGTCTT-CAT-TTATTAGCGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCATATTGGTAGC--GAAGTAGATC
* * *
7038 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAATAGATC
1 GAAGAT-GCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* * *
7082 AAAGATGCAGATCTTGTCTT-CATGTATTGGCA-TGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCA--TATTGGTAGCGAAGTAGATC
* *
7125 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* *
7170 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTT-CCATATTGGTAGCGAAGTAGATC
* *
7214 GAAGAAAGCAGATCTTGTCTT-CATGTATTGGT-GTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCA--TATTGGTAGCGAAGTAGATC
* * * *
7258 AAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* *
7302 GAAGATGCAGATCTTATCTTCCTATATTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* * *
7346 GAAGAAAGCAGATCTTGTCTT-CATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCA--TATTGGTAGCGAAGTAGATC
* * * *
7390 GAAAATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCC-ATATTGGTAGCGAAGTAGATC
* * *
7434 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGATGCAGATCTTGTCTT-CCATATTGGTAGCGAAGTAGATC
* * *
7478 GAAGAAAGCAGATCTTGTCTT-CATGTATTGGCA-TGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCA--TATTGGTAGCGAAGTAGATC
* * *
7522 GAAAATAGCAAATCTTGCCTTCCA
1 GAAGAT-GCAGATCTTGTCTTCCA
7546 GCACCGACAG
Statistics
Matches: 487, Mismatches: 70, Indels: 77
0.77 0.11 0.12
Matches are distributed among these distances:
41 1 0.00
42 6 0.01
43 110 0.23
44 260 0.53
45 100 0.21
46 5 0.01
47 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (43 bp):
GAAGATGCAGATCTTGTCTTCCATATTGGTAGCGAAGTAGATC
Found at i:7164 original size:132 final size:132
Alignment explanation
Indices: 6906--7531 Score: 807
Period size: 132 Copynumber: 4.7 Consensus size: 132
6896 GCAGATCAGT
* * * * *
6906 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
* * * * * * * * *
6969 TC-TCATATTGGTGGCGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATTTATTAGCGT--GAA
65 TCAT-GTATTGG-CGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATT-G-GTAGGAA
*
7031 GTAGATC
126 GTGGATC
* * * * * *
7038 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAATAGATCAAAG-ATGCAGATCTTGTCT
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCT
*
7101 TCATGTATTGGCATGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTG
65 TCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTG
7166 GATC
129 GATC
* *
7170 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * *
7235 CATGTATTGGTGTGAAGTAGATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
7300 TC
131 TC
*
7302 GAAGATGCAGATCTTATCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * *
7367 CATGTATTGGCGTGAAGTAGATCGAAAATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
7432 TC
131 TC
* * *
7434 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* *
7499 CATGTATTGGCATGAAGTAGATCGAAAATAGCA
66 CATGTATTGGCGTGAAGTAGATCGAAGATAGCA
7532 AATCTTGCCT
Statistics
Matches: 448, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
129 2 0.00
130 1 0.00
131 55 0.12
132 321 0.72
133 69 0.15
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (132 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
CATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGA
TC
Found at i:7287 original size:220 final size:220
Alignment explanation
Indices: 6906--7543 Score: 791
Period size: 220 Copynumber: 2.9 Consensus size: 220
6896 GCAGATCAGT
*
6906 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * * * * *
6971 TCATATTGGTGGCGGAGTAGATCGAAGAAAGTAGATCTTGTCTTCATTTATTAGCGTGAAGTAGA
66 CCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTGTGAAGTAGA
*
7036 TCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAATAGATCAAAGATGCAGATCTTGTCT
131 TCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGATGCAGATCTTGTCT
* *
7101 TCATGTATTGG-CATGAAGTAGATC
196 TCATATATTGGTCACGAAGTAGATC
7125 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
7190 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAG
65 CCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTGTGAAGTAG
* * * *
7255 ATCAAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTATC
130 ATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGATGCAGATCTTGTC
* **
7320 TTCCTATATTGGTGGCGAAGTAGATC
195 TTCATATATTGGTCACGAAGTAGATC
* * * * * * * * *
7346 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAAATAGTAGGTCTTGTCT
1 GAAGATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAGATCTTGTCT
* * * * ** *
7410 TCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGT
64 TCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGT-GTGAAGT
* * * * * * * *
7473 AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAA-ATAGCAAATCT
128 AGATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATC-AAAGAT-GCAGATCT
*
7537 TGCCTTC
191 TGTCTTC
7544 CAGCACCGAC
Statistics
Matches: 363, Mismatches: 50, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
219 55 0.15
220 235 0.65
221 73 0.20
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (220 bp):
GAAGATAGCAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTGTGAAGTAGA
TCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTAGATCAAAGATGCAGATCTTGTCT
TCATATATTGGTCACGAAGTAGATC
Found at i:7765 original size:44 final size:43
Alignment explanation
Indices: 7669--8159 Score: 158
Period size: 44 Copynumber: 11.2 Consensus size: 43
7659 ACCTCAGCCC
* * * * *
7669 TATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGT-GAATT
1 TATCTCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAG-ATT
* *
7712 CTA-CTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCT
1 -TATC-TCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAGAT-T
* ** * * * **
7757 TATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
1 TATCTCCCTGGA-CAACAGTGGAGTAGATTGAAGATTGTAGA-TT
* *** * ***
7801 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA-ATT
1 TATCTCCCTG-GACAACAGTGGAGTAGATTGAAGATTGTAGATT
*
7844 CTA-CTTCCCTGGACAACAGTGGAATAGATTGAAGATT-TCAGATCT
1 -TATC-TCCCTGGACAACAGTGGAGTAGATTGAAGATTGT-AGAT-T
* ** * * *
7889 TATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGTAGATTT
1 TATCTCCCTGGA-CAACAGTGGAGTAGATTGAAGATTGTAGA-TT
* *** * * ***
7933 TACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA-ATT
1 TATCTCCCTG-GACAACAGTGGAGTAGATTGAAGATTGTAGATT
* * *
7976 CTA-CTTCTCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCT
1 -TATC-TCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAGAT-T
** ** * * *
8021 TATCTCCCTAAACAGTAGTGGAGCAGATTGAAGATGGTGGATTT
1 TATCTCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAGA-TT
* *** * * ***
8065 TACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA-ATT
1 TATCTCCCTG-GACAACAGTGGAGTAGATTGAAGATTGTAGATT
* * *
8108 CTA-CTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTTAGATCT
1 -TATC-TCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAGAT-T
8153 TATCTCC
1 TATCTCC
8160 GTAAGCAGTA
Statistics
Matches: 316, Mismatches: 100, Indels: 62
0.66 0.21 0.13
Matches are distributed among these distances:
42 1 0.00
43 70 0.22
44 181 0.57
45 64 0.20
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
TATCTCCCTGGACAACAGTGGAGTAGATTGAAGATTGTAGATT
Found at i:8307 original size:132 final size:132
Alignment explanation
Indices: 7708--8292 Score: 976
Period size: 132 Copynumber: 4.4 Consensus size: 132
7698 AAAGATTGTG
7708 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
1 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
*
7773 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
7838 GT
131 GT
*
7840 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
* *
7905 AGTGGAGCAGATCGAAGATGGTAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
7970 GT
131 GT
* *
7972 AATTCTACTTCTCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAACAGT
1 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
* ** *
8037 AGTGGAGCAGATTGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
8102 GT
131 GT
* *
8104 AATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCGTAAGCAGT
1 AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
*
8169 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCA
66 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
8234 GT
131 GT
* * * * * *
8236 AATTCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGGTATAAG-TCTTATCTCCCT
1 AATTCTACT-TCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCT
8293 GAAGTTGCAG
Statistics
Matches: 427, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
131 12 0.03
132 415 0.97
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
AATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
GT
Found at i:8514 original size:4 final size:4
Alignment explanation
Indices: 8505--8535 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
8495 CCATGCAGAT
8505 TAAA TAAA TAAA TAAA TAAA -AAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
8536 ACCAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:8530 original size:11 final size:11
Alignment explanation
Indices: 8505--8536 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
8495 CCATGCAGAT
8505 TAAATAAATAAA
1 TAAATAAA-AAA
8517 TAAATAAAAAA
1 TAAATAAAAAA
8528 TAAATAAAA
1 TAAATAAAA
8537 CCAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
TAAATAAAAAA
Done.