Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019291.1 Corchorus olitorius cultivar O-4 contig19324, 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: 9560
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:1049 original size:25 final size:24
Alignment explanation
Indices: 1013--1059 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1003 TCCTTCTATT
1013 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
1036 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
1060 AAATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:2865 original size:154 final size:154
Alignment explanation
Indices: 2396--4769 Score: 3490
Period size: 154 Copynumber: 15.4 Consensus size: 154
2386 AGAGGCCAAT
* * *
2396 AATGAGTTAAAAACTTCACAGTGGACTAATCTCACGAAAAGGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
2461 GGAAAGGAAAA-CATTGGGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCACCGA
66 GGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
*
2525 AAGGCCCAAAATAACAAGTGTTCCA
130 TAGGCCCAAAATAACAAGTGTTCCA
2550 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * ** *
2615 GGAAAGGAAAAGCATTGGGGTCTGCCAAAACGAAGACGATTCAAAACGTCACTAATGGGCACCGA
66 GGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
2680 TAGGCCCAAAATAACAAGTGTTCCA
130 TAGGCCCAAAATAACAAGTGTTCCA
* *
2705 AATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * ** *
2770 GCAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGTCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
*
2835 AGGCCTAAAATAACAAGTGTTCCA
131 AGGCCCAAAATAACAAGTGTTCCA
* * *
2859 AATGAGTTAAAAACATT-ACAGTGCACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAA
1 AATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * *
2923 TGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAATGGAACAAATGCGCCCCGA
65 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
*
2988 TAAGCCCAAAATAACAAGTGTTCCA
130 TAGGCCCAAAATAACAAGTGTTCCA
*
3013 AATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * *
3078 GGAAAGAAAAGCATTGAGGGTTGCCAAATCAAAGACGATTCAAAACAGAACTAATGGACCCTGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * *
3143 ATGCCCAAAATAACAAGTATTCAA
131 AGGCCCAAAATAACAAGTGTTCCA
* *
3167 AATGAGCAAAAAACTTCACAGTGGTCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * ** * *
3232 GGAAACAAAAGCATTGACGTTTGCCAAATCGAAGACGATTCAAAACGTCAGTAATAGGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
3297 AGGCCCAAAATAACAAGTGTTCCA
131 AGGCCCAAAATAACAAGTGTTCCA
3321 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * *
3386 GGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGCGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
*
3451 AGGCCCAAAATAAAAAGTGTTCCA
131 AGGCCCAAAATAACAAGTGTTCCA
* * * *
3475 AATTAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* **
3540 GGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
*
3605 A-GCTCAAAATAACAAGTGTTCCA
131 AGGCCCAAAATAACAAGTGTTCCA
*
3628 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * ** *
3693 GTAAAGAAAAGAATTGAGGATTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGCCCCTAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * *
3758 AGACCCAAAATAACAATTGTTTCA
131 AGGCCCAAAATAACAAGTGTTCCA
3782 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * **
3847 GGAACGAAAAGCATTAAGATTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
*
3912 A-GCTCAAAATAACAAGTGTTCCA
131 AGGCCCAAAATAACAAGTGTTCCA
* *
3935 AATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * * * * *
4000 GGAAAGAAAAGCATGGAGGGTTGCCAAATCGAAAATGATTCAAACCGGAACTAATGCGCTCTGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
4065 AGGCCCAAAATAA-ATAGTGTTCCA
131 AGGCCCAAAATAACA-AGTGTTCCA
* * *
4089 AATTAGCTAAAAACTTCACACTGGACTACTCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * ** * *
4154 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACAATTCAAAACAAAACTAGTGGGCCCCGAA
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* *
4219 AGGCCCAAAATAAGAAGTGTTCCG
131 AGGCCCAAAATAACAAGTGTTCCA
* *
4243 AATGAGCTAAAAAACTTCACAGTGGACTAATCTGACCAAAATGATTATAGTTA-GTCACTAAACA
1 AATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA-TAAACA
* *
4307 ATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGG-CCCG
64 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
* ** *
4371 AAAGGCCCAAAATATGAAGTGTTCCG
129 ATAGGCCCAAAATAACAAGTGTTCCA
* *
4397 AATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACGAA
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AA
* * * * *
4462 TGGAAAGAAAAGCTTTGAGGTTTGTCAAATCGATGTCGATTCAAAACGGATCTAATGGGCCCCGA
65 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* *
4527 AAGGCCCAAAATAAGAAGTGTTTCCA
130 TAGGCCCAAAATAACAAGTG-TTCCA
4553 AATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
1 AATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * *
4617 TGTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGTCCCCGA
65 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
*
4682 AAGGCCCAAAATAACAAGTGTTCCA
130 TAGGCCCAAAATAACAAGTGTTCCA
* * *
4707 AATGACCTAAAAACTTTACAGTGGAC-ATATCTCACCAAAATGATTACT-GTTAGGCCGTAAACA
1 AATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTA-TAGTTAGGCCATAAACA
4770 TATCTCACCA
Statistics
Matches: 2024, Mismatches: 181, Indels: 30
0.91 0.08 0.01
Matches are distributed among these distances:
153 325 0.16
154 1285 0.63
155 352 0.17
156 62 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCA
Found at i:3086 original size:308 final size:308
Alignment explanation
Indices: 2396--5835 Score: 4040
Period size: 308 Copynumber: 11.1 Consensus size: 308
2386 AGAGGCCAAT
* * *
2396 AATGAGTTAAAAACTTCACAGTGGACTAATCTCACGAAAAGGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
2461 GGAAAGGAAAA-CATTGGGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCACCGA
66 GGAAA-GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
*
2525 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
130 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* *
2590 TGATTATAGTTAGGCCATAAACAATGGAAAGGAAAAGCA-TTGGGGTCTGCCAAAACGAAGACGA
195 TGATTATAGTTAGGCCATAAACAATGGAAA-GAAAAGCATTTAGGGT-TGCCAAATCGAAGACGA
* *
2654 TTCAAAACGTCACTAATGGGCACCGATAGGCCCAAAATAACAAGTGTTCCA
258 TTCAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
* *
2705 AATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * ** *
2770 GCAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGTCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * * *
2835 AGGCCTAAAATAACAAGTGTTCCAAATGAGTTAAAAACATT-ACAGTGCACTAATCTGACCAAAA
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAA
2899 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATT
195 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATT
* ** * *
2964 CAAAATGGAACAAATGCGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
260 CAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
*
3013 AATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * *
3078 GGAAAGAAAAGCATTGAGGGTTGCCAAATCAAAGACGATTCAAAACAGAACTAATGGACCCTGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * * * *
3143 ATGCCCAAAATAACAAGTATTCAAAATGAGCAAAAAACTTCACAGTGGTCTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * * *
3208 GATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATTGACGTTTGCCAAATCGAAGACGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTC
* * *
3273 AAAACGTCAGTAATAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
261 AAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
3321 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * *
3386 GGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGCGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * * *
3451 AGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* *
3516 AATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTC
*
3581 AAAACGTCACTAATGGGCCCCGAT-AGCTCAAAATAACAAGTGTTCCA
261 AAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
*
3628 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * ** *
3693 GTAAAGAAAAGAATTGAGGATTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGCCCCTAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * *
3758 AGACCCAAAATAACAATTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * **
3823 GATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTAAGATTTGCCAAATCGAAGACGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTC
*
3888 AAAACGTCACTAATGGGCCCCGAT-AGCTCAAAATAACAAGTGTTCCA
261 AAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
* *
3935 AATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACGAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * * * * * *
4000 GGAAAGAAAAGCATGGAGGGTTGCCAAATCGAAAATGATTCAAACCGGAACTAATGCGCTCTGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
* * *
4065 AGGCCCAAAATAA-ATAGTGTTCCAAATTAGCTAAAAACTTCACACTGGACTACTCTCACCAAAA
131 AGGCCCAAAATAACA-AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* *
4129 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-TTTGAGGTTTGCCAAATCGAAGACAAT
195 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTT-AGGGTTGCCAAATCGAAGACGAT
*** * * *
4193 TCAAAACAAAACTAGTGGGCCCCGA-AAGGCCCAAAATAAGAAGTGTTCCG
259 TCAAAACGTCACTAATGGGCCCCGATAA-GCCCAAAATAACAAGTGTTCCA
* *
4243 AATGAGCTAAAAAACTTCACAGTGGACTAATCTGACCAAAATGATTATAGTTA-GTCACTAAACA
1 AATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA-TAAACA
* *
4307 ATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGG-CCCG
64 ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
* ** * *
4371 AAAGGCCCAAAATATGAAGTGTTCCGAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAA
129 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* * * * *
4436 ATGATTATAGTTAGTCCATAAACGAATGGAAAGAAAAGC-TTTGAGGTTTGTCAAATCGATGTCG
194 ATGATTATAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTT-AGGGTTGCCAAATCGAAGACG
* *
4500 ATTCAAAACG-GATCTAATGGGCCCCGA-AAGGCCCAAAATAAGAAGTGTTTCCA
257 ATTCAAAACGTCA-CTAATGGGCCCCGATAA-GCCCAAAATAACAAGTG-TTCCA
4553 AATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
1 AATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * *
4617 TGTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGTCCCCGA
65 TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* * *
4682 AAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAACTTTACAGTGGAC-ATATCTCACCAAA
130 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAA
* *** ** **
4746 ATGATTACT-GTTAGGCCGTAAACATATCTCACCAAAATG-A-TTATTGTTAGGCC--AT--AA-
194 ATGATTA-TAGTTAGGCCATAAACA-ATGGAAAGAAAA-GCATTTAGGGTT--GCCAAATCGAAG
* * * ** * ** * **
4803 ACAACTTAAAGAAAAG-CTTTGA-GGTTTG-CCAAATTGAAGACGATTCAAAGCGGAACTAA-TA
254 ACGA-TT-CA-AAACGTCACTAATGG---GCCCCGA-T-AAG-C---CCAAA--ATAAC-AAGT-
**
4864 GGCCCCGA
303 -GTTCC-A
** * * ** * * * *
4872 AA-G-GCCCAAAA--TAAGAAGTGTTCTAA-ATGAGCTAAAA--ACTTCACAG-T-GGACACATC
1 AATGAGCTAAAAACTTCA-CAGTGGACTAATCTCA-CCAAAATGA-TT-ATAGTTAGG-C-CA--
* * * * ** *** * ** ** * *
4928 TAACCAAAAT-GATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GATTTGCCAAAT
58 TAA--ACAATGGA-AAGAA--AAG-CATTGAGGTTTGCCA-AATCG-A-AGACGA-TT--CAAAA
* ** * * ** *
4991 CGAACACGATTCAAAACGTCACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGA
111 CGGA-AC---T--AATGGGCCCCGAT----------AGGCCCAAAATAACAAGTGTTCCAAATGA
*
5056 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAA
160 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * *
5121 GAAAAGCA-TTGGGGTTTGCCAAATCGAAGAAGATTCAAAACGTCACTAATGGGACCCGATAGGC
225 GAAAAGCATTTAGGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAAGC
*
5185 CGAAAATAACAAGTGTTCCA
289 CCAAAATAACAAGTGTTCCA
* *
5205 AATGAGCTAAAGATTTCACAGTGGACTAATCTCACCAAAATGATTA-A-TT--G--------AA-
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
*
5257 --AAA-AAAA-TATTGAGGTTTGCCAAATCGAAGACGAATTCAAAACGGAACTAATGGGCCCCGA
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGA
* *
5318 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAATCTCACCAAAA
130 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* *
5383 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
195 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATT
** * *
5448 CAAAACGGAACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCA
260 CAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
5497 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
5562 GGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCCGAT
66 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
5627 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA-
* * *
5692 TGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATT
195 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATT
* * *
5757 CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAGAAGCGTTCCA
260 CAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
5806 AATGAGCTAAAAACTTCACAGTGGACTAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAAT
5836 GATTGAGCCA
Statistics
Matches: 2678, Mismatches: 331, Indels: 244
0.82 0.10 0.08
Matches are distributed among these distances:
292 206 0.08
293 4 0.00
294 2 0.00
296 1 0.00
302 6 0.00
304 3 0.00
306 5 0.00
307 566 0.21
308 822 0.31
309 664 0.25
310 111 0.04
311 9 0.00
312 9 0.00
314 4 0.00
315 12 0.00
316 18 0.01
317 11 0.00
318 9 0.00
319 5 0.00
320 9 0.00
322 2 0.00
323 6 0.00
324 3 0.00
325 3 0.00
326 3 0.00
328 7 0.00
329 2 0.00
332 1 0.00
333 3 0.00
334 12 0.00
335 9 0.00
336 18 0.01
337 6 0.00
338 4 0.00
341 1 0.00
342 6 0.00
343 14 0.01
344 89 0.03
345 5 0.00
346 6 0.00
347 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (308 bp):
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTC
AAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCA
Found at i:3301 original size:462 final size:461
Alignment explanation
Indices: 2396--5835 Score: 4619
Period size: 462 Copynumber: 7.4 Consensus size: 461
2386 AGAGGCCAAT
* * *
2396 AATGAGTTAAAAACTTCACAGTGGACTAATCTCACGAAAAGGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* *
2461 GGAAAGGAAAA-CA-TTGGGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCACCG
66 GGAAA-GAAAAGCATTTAGGG-TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
2524 AAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
129 AAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
*
2589 ATGATTATAGTTAGGCCATAAACAATGGAAAGGAAAAGCATTG-GGGTCTGCCAAAACGAAGACG
194 ATGATTATAGTTAGGCCATAAACAATGGAAA-GAAAAGCATTGAGGGT-TGCCAAATCGAAGACG
* * *
2653 ATTCAAAACGTCACTAATGGGCACCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAA
257 ATTCAAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* *
2718 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGCAAAGAAAAGCA
321 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * *
2783 TTGAGGTTTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGTCCCGATAGGCCTAAAATAA
386 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
2848 CAAGTGTTCCA
451 CAAGTGTTCCA
* * *
2859 AATGAGTTAAAAACATT-ACAGTGCACTAATCTGACCAAAATGATTATAGTTAGGCCATAAACAA
1 AATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
2923 TGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAATGGAACAAATGCGCCCCGA
65 TGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
*
2988 TAA-GCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
130 -AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
*
3052 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCAAAGACGAT
194 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
* * * * * *
3117 TCAAAACAGAACTAATGGACCCTGATATGCCCAAAATAACAAGTATTCAAAATGAGCAAAAAACT
259 TCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACT
* *
3182 TCACAGTGGTCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATT
323 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
* * *
3247 GACGTTTGCCAAATCGAAGACGATTCAAAACGTCAGTAATAGGCCCCGATAGGCCCAAAATAACA
388 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACA
3312 AGTGTTCCA
453 AGTGTTCCA
3321 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * * *
3386 GGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACAAATGCGCCCCGAT
66 GGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
* * * *
3451 AGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAACCTTCATAGTGGACTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
3516 AATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC
* *
3581 AAAACGTCACTAATGGGCCCCGATA-GCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
261 AAAACG-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* * *
3645 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGTAAAGAAAAGAATTGA
325 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
* * * * *
3710 GGATTGCCAAATCGAAGACCATTCAAAACGTCACTAATGGGCCCCTATAGACCCAAAATAACAAT
390 GGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
*
3775 TGTTTCA
455 TGTTCCA
3782 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * ** ** *
3847 GGAACGAAAAGCATTAAGATTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAT
66 GGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
* *
3912 A-GCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAAAAT
131 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * * *
3976 GATTATAGTTAGGCCATAAACGATGGAAAGAAAAGCATGGAGGGTTGCCAAATCGAAAATGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC
* * * * *
4041 AAACCGGAACTAATGCGCTCTGATAGGCCCAAAATAA-ATAGTGTTCCAAATTAGCTAAAAACTT
261 AAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACA-AGTGTTCCAAATGAGCTAAAAACTT
* * *
4105 CACACTGGACTACTCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTG
324 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* *** * * *
4170 AGGTTTGCCAAATCGAAGACAATTCAAAACAAAACTAGTGGGCCCCGAAAGGCCCAAAATAAGAA
389 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA
*
4235 GTGTTCCG
454 GTGTTCCA
* *
4243 AATGAGCTAAAAAACTTCACAGTGGACTAATCTGACCAAAATGATTATAGTTA-GTCACTAAACA
1 AATGAGCT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA-TAAACA
* *
4307 ATGGAAAGAAAAGC-TTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGG-CCC
64 ATGGAAAGAAAAGCATTT-AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
** * *
4370 GAAAGGCCCAAAATATGAAGTGTTCCGAATGAGCTAAAAACTTCATAGTGGACTAATCTCACCAA
128 GAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * * * * *
4435 AATGATTATAGTTAGTCCATAAACGAATGGAAAGAAAAGCTTTGAGGTTTGTCAAATCGATGTCG
193 AATGATTATAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
* * *
4500 ATTCAAAACGGATCTAATGGGCCCCGAAAGGCCCAAAATAAGAAGTGTTTCCAAATGAGCTAAAA
257 ATTCAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG-TTCCAAATGAGCTAAAA
*
4565 ACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAG
320 ACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * ** * *
4629 CTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGTCCCCGAAAGGCCCAAAAT
384 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAAT
4694 AACAAGTGTTCCA
449 AACAAGTGTTCCA
* * *
4707 AATGACCTAAAAACTTTACAGTGGAC-ATATCTCACCAAAATGATTACT-GTTAGGCCGTAAACA
1 AATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTA-TAGTTAGGCCATAAACA
*** ** ** * *
4770 TATCTCACCAAAATG-A-TTATTGTTAGGCCATAAACAACTTAAAGAAAAGCTTTGAGGTTTGCC
64 -ATGGAAAGAAAA-GCATTTAGGGTT--GCC----A-AA--T--CGAAGA-C---GA---TT--C
** * * ** * * *
4833 AAATTGAAGACGATTCAAAGCGG-AACTAATAGGCCCCGAAAGGCCCAAAATAAGAAGTGTTCTA
107 AAAACG--GA--ACT-AATG-GGCCCCGAA-A-G---------GCCCAAAATAACAAGTGTTCCA
* *
4897 AATGAGCTAAAAACTTCACAGTGGAC-ACATCTAACCAAAATGATTATAATTAGGCCATAAACAA
155 AATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
** * *
4961 TGGAAAGAAAAGCATTGAGATTTGCCAAATCGAACACGATTCAAAACGTCACTAATGGGCCCCGA
219 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGA
* *
5026 AATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
283 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* * *
5091 GGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGGTTTGCCAAATCGAAGAAGATT
348 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
* *
5156 CAAAACGTCACTAATGGGACCCGATAGGCCGAAAATAACAAGTGTTCCA
413 CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* *
5205 AATGAGCTAAAGATTTCACAGTGGACTAATCTCACCAAAATGATTA-A-TT--G--------AA-
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
* * *
5257 --AAA-AAAA-TATTGAGGTTTGCCAAATCGAAGACGAATTCAAAACGGAACTAATGGGCCCCGA
66 GGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGA
*
5318 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAATCTCACCAAAA
130 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
*
5383 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT
195 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATT
*
5448 CAAAACGGAACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAAATGAGCTAAAAACTT
260 CAAAAC-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
5513 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
324 CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG
* * **
5578 AGGGTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
389 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAA
5643 GTGTTCCA
454 GTGTTCCA
5651 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTGATTATAGTTAGGCCATAAACAA
1 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA-TGATTATAGTTAGGCCATAAACAA
* * * **
5716 TGGAAGGAAAAGCATTGAGAGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGA
65 TGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* * *
5781 TAGGCCCAAAATAAGAAGCGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
130 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
5836 GATTGAGCCA
Statistics
Matches: 2635, Mismatches: 250, Indels: 184
0.86 0.08 0.06
Matches are distributed among these distances:
446 344 0.13
447 8 0.00
448 1 0.00
449 2 0.00
451 1 0.00
455 1 0.00
456 3 0.00
457 6 0.00
458 2 0.00
459 2 0.00
460 140 0.05
461 458 0.17
462 666 0.25
463 399 0.15
464 199 0.08
465 4 0.00
466 1 0.00
467 1 0.00
469 2 0.00
470 6 0.00
472 2 0.00
474 5 0.00
475 2 0.00
478 2 0.00
479 3 0.00
480 1 0.00
481 10 0.00
482 1 0.00
483 5 0.00
485 3 0.00
486 1 0.00
487 2 0.00
488 3 0.00
489 5 0.00
490 1 0.00
491 1 0.00
494 1 0.00
496 2 0.00
498 186 0.07
499 78 0.03
500 75 0.03
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (461 bp):
AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT
GGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAA
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC
AAAACGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
GTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
GTTCCA
Found at i:4772 original size:36 final size:36
Alignment explanation
Indices: 4731--4805 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
4721 TTTACAGTGG
*
4731 ACATATCTCACCAAAATGATTACTGTTAGGCCGTAA
1 ACATATCTCACCAAAATGATTACTGTTAGGCCATAA
*
4767 ACATATCTCACCAAAATGATTATTGTTAGGCCATAA
1 ACATATCTCACCAAAATGATTACTGTTAGGCCATAA
4803 ACA
1 ACA
4806 ACTTAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (36 bp):
ACATATCTCACCAAAATGATTACTGTTAGGCCATAA
Found at i:4909 original size:190 final size:190
Alignment explanation
Indices: 4577--4959 Score: 610
Period size: 190 Copynumber: 2.0 Consensus size: 190
4567 TTCACAGTGG
4577 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAGCTTTGAGGTTTGC
1 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAGCTTTGAGGTTTGC
*
4642 CAAATCGAAGTCGATTCAAAACGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
* * * * *
4707 AATGACCTAAAAACTTTACAGTGGACATATCTCACCAAAATGATTACT-GTTAGGCCGTAA
131 AATGACCTAAAAACTTCACAGTGGACACATCTAACCAAAATGATTA-TAATTAGGCCATAA
*
4767 ACATATCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTG
1 ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGTAAAGAAAAGCTTTGAGGTTTG
* * *
4831 CCAAATTGAAGACGATTCAAAGCGGAACTAATAGG-CCCCGAAAGGCCCAAAATAAGAAGTGTTC
65 CCAAATCGAAGACGATTCAAAACGGAACTAAT-GGTCCCCGAAAGGCCCAAAATAACAAGTGTTC
* *
4895 TAAATGAGCTAAAAACTTCACAGTGGACACATCTAACCAAAATGATTATAATTAGGCCATAA
129 CAAATGACCTAAAAACTTCACAGTGGACACATCTAACCAAAATGATTATAATTAGGCCATAA
4957 ACA
1 ACA
4960 ATGGAAAGAA
Statistics
Matches: 178, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
189 1 0.01
190 174 0.98
191 3 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (190 bp):
ACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAGAAAAGCTTTGAGGTTTGC
CAAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGTGTTCCA
AATGACCTAAAAACTTCACAGTGGACACATCTAACCAAAATGATTATAATTAGGCCATAA
Found at i:5056 original size:154 final size:154
Alignment explanation
Indices: 4771--5835 Score: 1612
Period size: 154 Copynumber: 7.0 Consensus size: 154
4761 CCGTAAACAT
* * *
4771 ATCTCACCAAAATGATTATTGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * * * *
4835 ATTGAAGACGATTCAAAGCGGAACTAATAGGCCCCGAAAGGCCCAAAATAAGAAGTGTTCTAAAT
65 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
4900 GAGCTAAAAACTTCACAGTGGAC-A
130 GAGCTAAAAACTTCACAGTGGACTA
* * *
4924 CATCTAACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAA
1 -ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* ** * *
4989 ATCGAACACGATTCAAAACGTCACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAAT
65 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
5054 GAGCTAAAAACTTCACAGTGGACTA
130 GAGCTAAAAACTTCACAGTGGACTA
* *
5079 ATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* ** * *
5144 TCGAAGAAGATTCAAAACGTCACTAATGGGACCCGATAGGCCGAAAATAACAAGTGTTCCAAATG
66 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
5209 AGCTAAAGATTTCACAGTGGACTA
131 AGCTAAAAACTTCACAGTGGACTA
*
5233 ATCTCACCAAAATGATTA-A-TT--G--------AA---AAA-AAAA-TATTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
*
5281 TCGAAGACGAATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
66 TCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
*
5346 GAGCTAAACACTTCACAGTGGACTA
130 GAGCTAAAAACTTCACAGTGGACTA
5371 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
*
5436 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAAATG
66 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
5501 AGCTAAAAACTTCACAGTGGACTA
131 AGCTAAAAACTTCACAGTGGACTA
*
5525 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAA
1 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
*
5590 TCGAAAACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
66 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
5655 AGCTAAAAACTTCACAGTGGACTA
131 AGCTAAAAACTTCACAGTGGACTA
*
5679 ATCTCACCAAAATTGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGAG-TTGCCA
1 ATCTCACCAAAA-TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG-GTTTGCCA
** * *
5743 AATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAGAAGCGTTCCAAA
64 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
5808 TGAGCTAAAAACTTCACAGTGGACTA
129 TGAGCTAAAAACTTCACAGTGGACTA
5834 AT
1 AT
5836 GATTGAGCCA
Statistics
Matches: 837, Mismatches: 52, Indels: 43
0.90 0.06 0.05
Matches are distributed among these distances:
137 23 0.03
138 95 0.11
139 4 0.00
140 2 0.00
142 3 0.00
150 3 0.00
152 2 0.00
153 5 0.01
154 537 0.64
155 162 0.19
156 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTA
Found at i:5678 original size:446 final size:454
Alignment explanation
Indices: 4811--5835 Score: 1581
Period size: 446 Copynumber: 2.3 Consensus size: 454
4801 AAACAACTTA
* * * *
4811 AAGAAAAGCTTTGAGGTTTGCCAAATTGAAGACGATTCAAAGCGGAACTAATAGGCCCCGAAAGG
1 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGG
*
4876 CCCAAAATAAGAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGAC-ACATCTAACCAAAATGA
66 CCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTAACCAAAATGA
4940 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAACACGATTCAA
130 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAACACGATTCAA
** *
5005 AACGTCACTAATGGGCCCCGAAATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
195 AACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
5070 AGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGG
260 AGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGG
** *
5135 TTTGCCAAATCGAAGAAGATTCAAAACGTCACTAATGGGACCCGATAGGCCGAAAATAACAAGTG
325 TTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGACCCGATAGGCCCAAAATAACAAGTG
* *
5200 TTCCAAATGAGCTAAAGATTTCACAGTGGACTAATCTCACCAAAA-TGATTA-A-TT-G-A-AA-
390 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTGATTATAGTTAGAACAAG
*
5258 AA-AAAA-TATTGAGGTTTGCCAAATCGAAGACGAATTCAAAACGGAACTAATGGGCCCCGAAAG
1 AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGAAAG
* * *
5321 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCACAGTGGACTAATCTCACCAAAATGA
65 GCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGA
* * *
5386 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
130 TTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAACACGATTCAA
* *
5451 AACGGAACTAATGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
195 AACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
5516 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
260 AGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTG-GG
*
5581 G-TTGCCAAATCGAA-AACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
324 GTTTGCCAAATCGAAGAA-GATTCAAAACGGAACTAATGGGACCCGATAGGCCCAAAATAACAAG
5644 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTGATTATAGTTAGGCCA
388 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTGATTATAGTTA-G---
5709 TAAACAATGG
449 --AACAA--G
** *
5719 AAGGAAAAGCATTGAGAG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATA
1 AA-GAAAAGCATTGAG-GTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
*
5783 GGCCCAAAATAAGAAGCGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
64 GGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
5836 GATTGAGCCA
Statistics
Matches: 524, Mismatches: 31, Indels: 30
0.90 0.05 0.05
Matches are distributed among these distances:
445 25 0.05
446 374 0.71
447 12 0.02
448 1 0.00
449 2 0.00
451 1 0.00
457 1 0.00
458 2 0.00
461 2 0.00
463 80 0.15
464 23 0.04
465 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (454 bp):
AAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGG
CCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGAT
TATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAACACGATTCAAA
ACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
GTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGGGGT
TTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGACCCGATAGGCCCAAAATAACAAGTGT
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTGATTATAGTTAGAACAAG
Found at i:7890 original size:154 final size:154
Alignment explanation
Indices: 7610--8326 Score: 1182
Period size: 154 Copynumber: 4.7 Consensus size: 154
7600 CGACCGATCA
*
7610 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
* * *
7675 CAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
7740 AATGAGCTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
*
7764 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
7829 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
*
7894 AATGAGCTAAAAACTTCAAAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
*
7918 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAGGAAAAGCATTGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
* ** * * **
7983 CAAATCGAAAATAATTCAAAACGGAACTAATGGGCCCCGTTAGGCCCAAAATAAAAAGTGTTTTA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
8048 AATGAGCTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
* * *
8072 ACTAATCTCACCAAAGTGATTATAGTTAGGCCATGAACAATGGAAAGAAAAGCATTAAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
* * * * * *
8137 CAAATCTAAGACGATTCAAAACGGAACTAATGGACCCTGATATGCCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
*
8202 AATGAGTTAAAAACTTCACAGTGG
131 AATGAGCTAAAAACTTCACAGTGG
* *
8226 ACTAATCTCACCAAAATGATTATAGTTTGGCCATGAACAATGGAAAGAAAAGCATTGAGGGTTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
* *
8291 CAAATCTAAGACGATTCAAAACGTCACTAATGGGCC
66 CAAATCGAAGACGATTCAAAACGGCACTAATGGGCC
8327 TGTCTTCATT
Statistics
Matches: 525, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 525 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
CAAATCGAAGACGATTCAAAACGGCACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCA
AATGAGCTAAAAACTTCACAGTGG
Found at i:8942 original size:45 final size:42
Alignment explanation
Indices: 8893--8986 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
8883 GCAAACAATT
* *
8893 AATATTAGTTTTATTTTGATGAATTATCTAAAGATAGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAAAGAT---GGAGTAG
*
8938 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAAAGATGGAGTAG
8980 AAT-TTAG
1 AATATTAG
8987 GTAATGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
45 32 0.70
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.39
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAAAGATGGAGTAG
Found at i:9332 original size:60 final size:61
Alignment explanation
Indices: 9220--9336 Score: 218
Period size: 60 Copynumber: 1.9 Consensus size: 61
9210 TGGCGATATT
9220 TCATAATTATTTTTAGTATTTAAAAAAAAAACATAACATGGCATGCCAAAATAGCTTTAAC
1 TCATAATTATTTTTAGTATTTAAAAAAAAAACATAACATGGCATGCCAAAATAGCTTTAAC
*
9281 TCATAATTATTTTTAGTATTT-ATAAAAAAACATAACATGGCATGCCAAAATAGCTT
1 TCATAATTATTTTTAGTATTTAAAAAAAAAACATAACATGGCATGCCAAAATAGCTT
9337 GAACAAGTAT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
60 34 0.62
61 21 0.38
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (61 bp):
TCATAATTATTTTTAGTATTTAAAAAAAAAACATAACATGGCATGCCAAAATAGCTTTAAC
Done.