Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013003.1 Kokia drynarioides strain JFW-HI SEQ_128021, whole genome shotgun sequence
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: 2817
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.27
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:379 original size:62 final size:62
Alignment explanation
Indices: 281--528 Score: 361
Period size: 62 Copynumber: 4.0 Consensus size: 62
271 ATCGTAAAAG
** * * *
281 TTTGACAAGTTCAGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCATGTAAATCAGTT
1 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
*
343 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCCAGAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * *
405 TTTGATAAGTTTGGAAGGTCGTCCAAGAACCAAGAGAAAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * * * * *
467 TTTGATAAGTTTGGAAGTTCGTCCCAGAACCAAGAGAGAAATAATTCTTACCTAACTAAGTT
1 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
529 ATTAGTTAAC
Statistics
Matches: 169, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 169 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (62 bp):
TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:763 original size:62 final size:62
Alignment explanation
Indices: 683--809 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
673 CTAGTGAAAG
683 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
* * * * *
745 TTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
807 TTT
1 TTT
810 AATTCAAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (62 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:945 original size:277 final size:278
Alignment explanation
Indices: 405--1087 Score: 899
Period size: 278 Copynumber: 2.5 Consensus size: 278
395 TAAATAAGTT
* * * * * *
405 TTTGATAAGTTTGGAAGGTCGTCCAAGAACCAAGAGAAAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * * * * * *
470 GATAAGTTTGGAAGTTCGTCCCAGAACCAAGAGAGAAATAATTCTTACCTAACTAAGTTATTAGT
66 GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* * * * * * *
535 TAACAGTCTAAAAGTTGTTTACAAAATGACTAACTATTTTGACCAAATGGTGTGATTTCTCGAAC
131 TAACAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAAC
* * * * * * *
600 AGGGAATGTTTGGAAATTTGCTCAAAGGAATGGATCGTCTTGTATACTTTAAGGAACCTAAGTTA
196 AAGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTA
* *
665 TAAAAGAACTAGTGAAAG
261 TAAAAGAAATAGTAAAAG
683 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
* *
748 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
66 GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
*
813 TCAA-AGACCAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
131 T-AACAGACCAAAAGT-TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
* * *
875 GCAAGGAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGT
194 ACAAGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGT
*
940 TATAAAAGAAATCGTAAAAG
259 TATAAAAGAAATAGTAAAAG
* * *
960 TTTGACAAGTTC-AGATGTTCGTCCAAGAA-CAAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAA-AGAGAAACAATTCTCACGT-AAATAAGTT
* * *
1023 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
63 TTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1088 GATAAGTTCG
Statistics
Matches: 355, Mismatches: 45, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
276 5 0.01
277 156 0.44
278 192 0.54
279 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (278 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
TAACAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAAC
AAGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTA
TAAAAGAAATAGTAAAAG
Found at i:1110 original size:62 final size:62
Alignment explanation
Indices: 960--1149 Score: 256
Period size: 62 Copynumber: 3.0 Consensus size: 62
950 ATCGTAAAAG
* * * *
960 TTTGACAAGTTCAGATGTTCGTCCAAGAA-CAAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAA-AGAGAAACAATTCTCACGT-AAATAAGTT
*
1023 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
* * * * * *
1085 TTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTGTCATGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
1147 TTT
1 TTT
1150 AATTTAAAGA
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
62 67 0.59
63 43 0.38
64 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (62 bp):
TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:1624 original size:62 final size:62
Alignment explanation
Indices: 1479--1652 Score: 213
Period size: 62 Copynumber: 2.8 Consensus size: 62
1469 ATGTTCAGAT
* *
1479 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAAAATAAGTTTTTGACAACCTCGAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTTACGT-AAATAAGTTTTTGACAACCTCGAAA
** * * * **
1542 GTTCATCCAAGAACTGAGAGAGAAACAATACTTACGTGAATAAGTTTTTGTCAATTTCGAAA
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTGACAACCTCGAAA
* * * * *
1604 GTTCATCCGAGATCCAAGAGAGAACCAATTCTCATGTAAATAAGTTTTT
1 GTTCATCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTT
1653 AATTCAGCGA
Statistics
Matches: 93, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
62 61 0.66
63 32 0.34
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (62 bp):
GTTCATCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTTGACAACCTCGAAA
Found at i:1889 original size:62 final size:62
Alignment explanation
Indices: 1820--1989 Score: 295
Period size: 62 Copynumber: 2.7 Consensus size: 62
1810 AAGTACGGAT
*
1820 GTTCGTCCAAGAACCAAGAGAGAAAAAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAA
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAA
*
1882 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGATAAGTTTGGAA
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAA
* * *
1944 GTTCGTCCCAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTT
1 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
1990 ATTAATTAAC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 103 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (62 bp):
GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTGACAAGTTTGGAA
Found at i:2069 original size:340 final size:340
Alignment explanation
Indices: 1324--2269 Score: 1202
Period size: 340 Copynumber: 2.8 Consensus size: 340
1314 NNNNNNNNNN
* * *
1324 AAAACTTGTTTACAAAAAGAAAAACTATTTAGACTAAATTATGTGATTTC-CAAAGCATGGAATG
1 AAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGTGATTTCTC-GAGCATGGAATG
* * **
1388 GTCAAAAAATTGCTCAAAGGAATGGATCCTCTTGAATACTTTCGGGAACCAAAGTTATAAAATAA
65 TTCAAAAAATTTCTCAAAGGAATGGATCCTCTTGAATACTTTAAGGAACCAAAGTTATAAAATAA
* * * *
1453 ATCGTAAAAGTTTGACATGTTCAGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACATAA
130 ATCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-A
** * ** * * *
1518 AATAAGTTTTTGACAACCTCGAAAGTTCATCCAAGAACTGAGAGAGAAACAATACTTACGTGAAT
194 AATAAGTTTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* * * *
1583 AAGTTTTTGTCAATTTCGAAAGTTCATCCGAGATCCAAGAGAGAACCAATTCTCATGTAAATAAG
259 AAGTTTTTGTCAATTTCGAAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1648 TTTTTAATTCAGCGACC
324 TTATTAATTCAACGACC
*
1665 AAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGCGATTTCTCGAGCATGGAATGT
1 AAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGTGATTTCTCGAGCATGGAATGT
* * * *
1730 TCAAAAAATTTCTCAAAGGAATTGATCCTCTTGAATACTTTTAGGAACAAAAGTTATAGAATAAA
66 TCAAAAAATTTCTCAAAGGAATGGATCCTCTTGAATACTTTAAGGAACCAAAGTTATAAAATAAA
* * *
1795 TCGTAAAAGTTTGAAAAGTACGGATGTTCGTCCAAGAACCAAGAGAGAAAAAATTCTCACGTAAA
131 TCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAA
* *
1860 TAAGTTTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
196 TAAGTTTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
* * * *
1925 GTTTTTGAT-AAGTTT-GGAAGTTCGTCCCAGAACCAAGAGAGAAACAATTCTTACGTAACTAAG
261 GTTTTTG-TCAA-TTTCGAAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1988 TTATTAATT-AACAGTCG
324 TTATTAATTCAAC-GACC
* * * * ** *
2005 AAAAGTTGTTTACAAAATGACAAATTATTTTGACCAAATGGTGTGATTTCTCGAGCACGGAATGT
1 AAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGTGATTTCTCGAGCATGGAATGT
*** * * * * * *
2070 T-TGGAAATTTGTTCAAAGGAATGGAT-GTTTTGTATACTTTAAGGAACCTAAGTTATAAAAGAA
66 TCAAAAAATTT-CTCAAAGGAATGGATCCTCTTGAATACTTTAAGGAACCAAAGTTATAAAATAA
* * * * * *
2133 CTAGTGAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAA
130 ATCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAA
* * *
2198 ATAAGTTTTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATA
195 ATAAGTTTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
2263 AGTTTTT
260 AGTTTTT
2270 AATTCAAAGA
Statistics
Matches: 526, Mismatches: 74, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
339 161 0.31
340 188 0.36
341 176 0.33
342 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (340 bp):
AAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGTGATTTCTCGAGCATGGAATGT
TCAAAAAATTTCTCAAAGGAATGGATCCTCTTGAATACTTTAAGGAACCAAAGTTATAAAATAAA
TCGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAA
TAAGTTTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTGTCAATTTCGAAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
ATTAATTCAACGACC
Found at i:2189 original size:277 final size:277
Alignment explanation
Indices: 1866--2544 Score: 927
Period size: 277 Copynumber: 2.4 Consensus size: 277
1856 TAAATAAGTT
* * *
1866 TTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * * *
1931 GATAAGTTTGGAAGTTCGTCCCAGAACCAAGAGAGAAACAATTCTTACGTAACTAAGTTATTAAT
66 GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTATTAAT
* * * * * * *
1996 T-AACAGTCGAAAAGT-TGTTTACAAAATGACAAATTATTTTGACCAAATGGTGTGATTTCTCGA
131 TCAA-AGACCAAAA-TAT-TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
* * * * * ** * *
2059 GCACGGAATGTTTGGAAATTTGTTCAAAGGAATGGAT-GTTTTGTATACTTTAAGGAACCTAAGT
193 GCAAGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGT
* *
2123 TATAAAAGAACTAGTGAAAG
258 TATAAAAGAAATAGTAAAAG
2143 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
* * *
2208 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
66 GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTATTAAT
*
2273 TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
131 TCAAAGACCAAAATATTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
* *
2338 AGGAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGTTAT
196 AGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTAT
*
2403 AAAAGAAATCGTAAAAG
261 AAAAGAAATAGTAAAAG
* * *
2420 TTTGACAAGTTC-AGATGTTCGTCCAAGAA-CAAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAA-AGAGAAACAATTCTCACGT-AAATAAGTT
* * *
2483 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
63 TTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
2545 TTTGATAAGT
Statistics
Matches: 356, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
276 77 0.22
277 211 0.59
278 68 0.19
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (277 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
GATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTATTAAT
TCAAAGACCAAAATATTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
AGGAAGGTTTGGAAAATAGCTCAAAGGAATGGATCGTCATGAATACTTTAAGGAACCGAAGTTAT
AAAAGAAATAGTAAAAG
Found at i:2243 original size:62 final size:62
Alignment explanation
Indices: 2143--2269 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
2133 CTAGTGAAAG
2143 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
* * * * *
2205 TTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
2267 TTT
1 TTT
2270 AATTCAAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (62 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:2548 original size:340 final size:340
Alignment explanation
Indices: 2143--2815 Score: 1240
Period size: 340 Copynumber: 2.0 Consensus size: 340
2133 CTAGTGAAAG
2143 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
2208 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
66 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
*
2273 TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
131 TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATCATGCGATTTCCCGAGCA
*
2338 AGGAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGTTAT
196 AGAAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGTTAT
2403 AAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAAAC-AATTC
261 AAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAG-AACTAATTC
2467 TTACATAAAATAAGTT
325 TTACATAAAATAAGTT
2483 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
2548 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
66 GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
**
2613 TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATCATGCGATTTTTCGAGCA
131 TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATCATGCGATTTCCCGAGCA
* *
2678 AGAAAGGTTTGGAGAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAATCGAAGTTAT
196 AGAAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGTTAT
* * *
2743 AAAAGTAATTGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACCAAGAGAGAACTAATTCT
261 AAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAACTAATTCT
*
2808 TACGTAAA
326 TACATAAA
2816 TA
Statistics
Matches: 322, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
339 3 0.01
340 319 0.99
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (340 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
GATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAAT
TCAAAGACCAAAATATTTTTCAAAATGACAAACTATTTAGACCAAATCATGCGATTTCCCGAGCA
AGAAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGTTAT
AAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAACTAATTCT
TACATAAAATAAGTT
Found at i:2570 original size:62 final size:62
Alignment explanation
Indices: 2420--2609 Score: 274
Period size: 62 Copynumber: 3.0 Consensus size: 62
2410 ATCGTAAAAG
* * * *
2420 TTTGACAAGTTCAGATGTTCGTCCAAGAA-CAAAGAGAGAAACAATTCTTACATAAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAA-AGAGAAACAATTCTCACGT-AAATAAGTT
*
2483 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
* * * *
2545 TTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTT
1 TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
2607 TTT
1 TTT
2610 AATTCAAAGA
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
62 69 0.59
63 43 0.37
64 4 0.03
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (62 bp):
TTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTT
Found at i:2726 original size:617 final size:617
Alignment explanation
Indices: 1526--2817 Score: 1704
Period size: 617 Copynumber: 2.1 Consensus size: 617
1516 AAAATAAGTT
** * ** * *
1526 TTTGACAACCTCGAAAGTTCATCCAAGAACTGAGAGAGAAACAATACTTACGTGAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTT
* * * * *
1591 GTCAATTTCGAAAGTTCATCCGAGATCCAAGAGAGAACCAATTCTCATGTAAATAAGTTTTTAAT
66 GTCAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
** * *
1656 TCAGCGACCAAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATTATGCGATTTCTCGAGC
131 TCAAAGACCAAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGC
* * ** * * *
1721 ATGGAATGTTCAAAAAATTTCTCAAAGGAATTGATCCTCTTGAATACTTTTAGGAACAAAAGTTA
196 AAGGAAGGTTCAAAAAATAGCTCAAAGGAATGGATCCTCATGAATACTTTCAGGAACAAAAGTTA
* * * *
1786 TAGAATAAATCGTAAAAGTTTGAAAAGTACGGATGTTCGTCCAAGAACCAAGAGAGAAAAAATTC
261 TAAAAGAAATCGTAAAAGTTTGAAAAGTACAGATGTTCGTCCAAGAACAAAGAGAGAAAAAATTC
* * * *
1851 TCACGTAAATAAGTTTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
326 TCACATAAATAAGTTTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCA
* * *
1916 CGTAAATAAGTTTTTGATAAGTTTGGAAGTTCGTCCCAGAACCAAGAGAGAAACAATTCTTACGT
391 CGTAAATAAGTTTTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT
* * * * * **
1981 AACTAAGTTATTAATTAACAGTCGAAAAGTTGTTTACAAAATGACAAATTATTTTGACCAAATGG
456 AAATAAGTTATTAATTAACAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATCA
* * * * * * ** *
2046 TGTGATTTCTCGAGCACGGAATGTTTGGAAATTTGTTCAAAGGAATGGATGTTTTGTATACTTTA
521 TGCGATTTCTCGAGCAAGAAAGGTTTGGAAATTAGCTCAAAGGAATGGATGTCATGAATACTTTA
* *
2111 AGGAACCTAAGTTATAAAAG-AACTAGTGAAAG
586 AGGAACCGAAGTTATAAAAGTAA-TAGTAAAAG
* *
2143 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCACGTAAATAAGTTTTT
1 TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTT
* * *
2208 GAT-AAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCACGTAAATAAGTTTTTAA
66 G-TCAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA
* *
2272 TTCAAAGACCAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
130 TTCAAAGACCAAAACT-TGTTTACAAAAAGACAAACTATTTAGACCAAATGATGCGATTTCCCGA
*** * * **
2335 GCAAGGAAGGTTTGGAAAATAGCTCGAAGGAATGGATCGTCATGAATACTTTCAGGAACCGAAGT
194 GCAAGGAAGGTTCAAAAAATAGCTCAAAGGAATGGATCCTCATGAATACTTTCAGGAACAAAAGT
* * *
2400 TATAAAAGAAATCGTAAAAGTTTGACAAGTTCAGATGTTCGTCCAAGAACAAAGAGAGAAACAAT
259 TATAAAAGAAATCGTAAAAGTTTGAAAAGTACAGATGTTCGTCCAAGAACAAAGAGAGAAAAAAT
*
2465 TCTTACATAAAATAAGTTTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTC
324 TCTCACAT-AAATAAGTTTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTC
* *
2530 TCACGTAAATAAGTTTTTGATAAGTTCGGAAGTTCTTCCAAGAACCAAGAGAGAAACAGTTCTCA
388 TCACGTAAATAAGTTTTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCA
* *
2595 CGTAAATAAGTTTTTAATTCAA-AGACCAAAA-TAT-TTTTCAAAATGACAAACTATTTAGACCA
453 CGTAAATAAGTTATTAATT-AACAGACCAAAAGT-TGTTTACAAAATGACAAACTATTTAGACCA
* *
2657 AATCATGCGATTTTTCGAGCAAGAAAGGTTTGGAGAA-TAGCTCGAAGGAATGGATCGTCATGAA
516 AATCATGCGATTTCTCGAGCAAGAAAGGTTTGGA-AATTAGCTCAAAGGAATGGAT-GTCATGAA
* * *
2721 TACTTTCAGGAATCGAAGTTATAAAAGTAATTGTAAAAG
579 TACTTTAAGGAACCGAAGTTATAAAAGTAATAGTAAAAG
*
2760 TTTGACAAGTTC-AGATGTTCGTCCAAGAACCAAGAGAG-AACTAATTCTTACGTAAATA
1 TTTGACAAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAAC-AATTCTTACGTAAATA
Statistics
Matches: 583, Mismatches: 82, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
616 230 0.39
617 348 0.60
618 5 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (617 bp):
TTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTTACGTAAATAAGTTTTT
GTCAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
TCAAAGACCAAAACTTGTTTACAAAAAGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGC
AAGGAAGGTTCAAAAAATAGCTCAAAGGAATGGATCCTCATGAATACTTTCAGGAACAAAAGTTA
TAAAAGAAATCGTAAAAGTTTGAAAAGTACAGATGTTCGTCCAAGAACAAAGAGAGAAAAAATTC
TCACATAAATAAGTTTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAACAATTCTCA
CGTAAATAAGTTTTTGATAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT
AAATAAGTTATTAATTAACAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATCA
TGCGATTTCTCGAGCAAGAAAGGTTTGGAAATTAGCTCAAAGGAATGGATGTCATGAATACTTTA
AGGAACCGAAGTTATAAAAGTAATAGTAAAAG
Done.