Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011726.1 Corchorus olitorius cultivar O-4 contig11759, 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: 5295
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Found at i:382 original size:154 final size:154
Alignment explanation
Indices: 1--1342 Score: 1868
Period size: 154 Copynumber: 8.8 Consensus size: 154
** * * *
1 TAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTACCAAATCGAAGACGATTTAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
** * *
66 GTCACTAATGGGCCTTGATGGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
131 GGACTAATCTCACCAAAATGATTA
131 GGACTAATCTCACCAAAATGATTA
* *
155 TAGTTAGGCCATAAACAATGGAAAAAAAAAGCATTGAGGGTTGCCAAATCGAAAACGATTCAAAA
1 TAGTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * * * *
220 CAG-AACTAATGAGCCACGATAGG-CCTAAATAACAAGTGTTCCAAATGAGCTAAAAACAATCAC
65 C-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TTCAC
283 AGTGGACTAATCTCACCAAAATTG-TTA
128 AGTGGACTAATCTCACCAAAA-TGATTA
* * * *
310 TAGTTAGGCCATAAACAATGGAAATAAAAGCATTGAGGTTTACCCAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
* * * * * * *
375 GTCACTAAAGGTCCCCGATAGGCTCAAAATAACAAGTGTTCGAAATGCGCTAAAAACAAT-ACAC
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TTCACAG
* **
439 TGGACTAATCTGACCAAAATGAAAA
130 TGGACTAATCTCACCAAAATGATTA
464 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
** * * * *
529 GGAAC-AATTGCGCCCCAATAGGCCCAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAG
66 GTCACTAA-TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
*
593 TGGACTAATCTCACCAAAATTATTA
130 TGGACTAATCTCACCAAAATGATTA
* **
618 TAGTTAGGACATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATAC-AAGACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAAT-CGAAGACGATTCAAAA
* *
682 CGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTCAG
65 CGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
*
747 TGGACTAATCTCACTAAAATGATTA
130 TGGACTAATCTCACCAAAATGATTA
* *
772 TGGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGATGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
837 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
902 GGACTAATCTCACCAAAATCATTA
131 GGACTAATCTCACCAAAATGATTA
* * *
926 TAGTTAGGCCATAAA-AA--G--A-AAAA-CATTGAGGGTTGCCGAATAGAAGACGATTTAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
** * * * *
984 GGAACTAATGGGTCCTGATAGGCCCAAAAAAACAAGTGTTCCAAATGTGCTAAAAACTTCACAGT
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1049 GGACTAATCTCACCAAAATGATTA
131 GGACTAATCTCACCAAAATGATTA
* * ** * *
1073 TAGTTAGGCCATAAACAATGGAACGGAAAGCATTGAGATTTGCCAAATCGAAGATGATTCAAAAT
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
* * *
1138 GTTACTAATGGGCCCCGATAGGACGAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
1203 GGACTAATCTCACCAAAATGATTA
131 GGACTAATCTCACCAAAATGATTA
* * *
1227 TAGTTAGGCCATAAACAATGAAAAGAAAAGCA-TCAGGGTTGCCAAATCAAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
* ** * *
1291 GTCACTAATGGG-TCTTATAGGCGCAAAATAAGAAGTGTTCCAAATGAGCTAA
66 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
1343 TGATACAAAT
Statistics
Matches: 1047, Mismatches: 122, Indels: 40
0.87 0.10 0.03
Matches are distributed among these distances:
147 128 0.12
148 6 0.01
149 1 0.00
150 1 0.00
151 1 0.00
152 33 0.03
153 49 0.05
154 688 0.66
155 137 0.13
156 3 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
GGACTAATCTCACCAAAATGATTA
Found at i:677 original size:308 final size:308
Alignment explanation
Indices: 1--5295 Score: 3789
Period size: 308 Copynumber: 17.4 Consensus size: 308
** * *
1 TAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTACCAAATCGAAGACGATTTAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * *
66 GTCACTAATGGG-CCTTGATGGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
*
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAAGCATTGAGGG
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAAGAAAAGCATTGAGGG
* * * * *
195 TTGCCAAATCGAAAACGATTCAAAACAGAACTAATGAGCCACGATAGG-CCTAAATAACAAGTGT
194 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* *
259 TCCAAATGAGCTAAAAACAATCACAGTGGACTAATCTCACCAAAATTGTTA
259 TCCAAATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAATTATTA
* * *
310 TAGTTAGGCCATAAACAATGGAAATAAAAGCATTGAGGTTTACCCAATCGAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * * * * * *
375 GTCACTAAAGGTCCCCGATAGGCTCAAAATAACAAGTGTTCGAAATGCGCTAAAAACAAT-ACAC
66 GTCACTAAGGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TTCACAG
* **
439 TGGACTAATCTGACCAAAATGAAAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
* * *
504 TGCCAAATCGAAGACGATTCAAAACGGAAC-AATTGCGCCCCAATAGGCCCAAAATAAAAAGTGT
195 TGCCAAATCGAAGACGATTCAAAACGGAACTAA-TGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
568 TCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
259 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* *
618 TAGTTAGGACATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATAC-AAGACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAAT-CGAAGACGATTCAAAA
*
682 CGTCACTAATGGG--CCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCTC
65 CGTCACTAA-GGGTCCCT-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
* *
745 AGTGGACTAATCTCACTAAAATGATTATGGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
128 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* **
810 GTTGCCAAATCGAAGATGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
193 GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
*
875 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATCATTA
258 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* * * *
926 TAGTTAGGCCATAAA-AA--G--A-AAAA-CATTGAGGGTTGCCGAATAGAAGACGATTTAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
** * *
984 GGAACTAATGGGT-CCTGATAGGCCCAAAAAAACAAGTGTTCCAAATGTGCTAAAAACTTCACAG
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * **
1048 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGGAAAGCATTGAGATT
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
* * ** * *
1113 TGCCAAATCGAAGATGATTCAAAATGTTACTAATGGGCCCCGATAGGACGAAAATAACAAGTGTT
195 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
*
1178 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
260 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* * * *
1227 TAGTTAGGCCATAAACAATGAAAAGAAAAGCA-TCAGGGTTGCCAAATCAAAGACGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * * **
1291 GTCACTAATGGGT--CTTATAGGCGCAAAATAAGAAGTGTTCCAAATGAGCTAATGATACAAATC
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA--A-A-ACTTC
* * * ** * * * * * *
1354 -TAGTTGTATTAGAT-TCA--AATCTAGCCTTGAATA-TCTA--ACA-AAGTCGACTTGAACTTG
126 ACAG-TGGACTA-ATCTCACCAAAAT-G-ATT--ATAGT-TAGGCCATAA-AC-AATGGAA--AG
** * * * ** * * * * * * *** ** *
1411 CTCAA-C-TTCTA-GATGTG-TATGTCGATGAC-CTTCACAA-GGTTATTACTCTTCTTTCG-TC
180 -AAAAGCATT-GAGGGT-TGCCAAATCGAAGACGATTCAAAACGG-AACTAATGGGC-CCCGATA
* * ** * * * * * ** *
1469 GGTCCAAAGTCTCCAATTAG-ACCTGCAAT-TG-T--CAAC-TCA-AGAAGACAAGAT-TCA-CA
240 GGCCCAAAAT-AACAAGT-GTTCC--AAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCA
*
1525 ACTTAATTGTT-
300 A---AATTATTA
* * ** ** ** * * * * * ** *
1536 T-GCTAGGAC-TCTACAA--GATTGAAGAA-CCCTAAGTTTTGCTCAAACTAGAACAAGAAGC-T
1 TAGTTAGGCCATAAACAATGGAAAGAA-AAGCATTGAGGTTTGC-CAAA-TCGAAGACGATTCAA
* * *** *** * *
1595 AA-G--A-TAA---TCACT--TTGGGTGAAAACCTCAA-T-TT-----T-A-TTAATCAACTTCA
63 AACGTCACTAAGGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA-AAACTTCA
*
1642 CAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
127 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
* * *
1707 GTTTCCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGTCCAAAATAACAAG
192 GGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAG
* *
1771 TGTTCCAAATGAGCTAAAAA-TATCACAGTGGACTAATCTCATCAAAAATGATTA
256 TGTTCCAAATGAGCTAAAAACT-TCACAGTGGACTAATCTCA-CCAAAATTATTA
* * * *
1825 TAGTTAGGCCATAAAC-ATTGAAAGAAAAGCGATCGAGGGTTGCCAAATCGAATACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGC-ATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
** * * *
1889 CGGAACTAATGGG-CCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
65 CGTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* **
1953 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAG-AAAGCATCAAGGG
129 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG
** * ** * * *
2017 TTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGG-TCTTATAGACGCAAAATAAGAAGTG
194 TTGCCAAATCGAA-GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
** * * * ***
2080 TTCCAAATGAGCTAATGATACAAATC-TAGTTGTATTAGAT-T---C-AAATCTAGCC
258 TTCCAAATGAGCTAA--A-A-ACTTCACAG-TGGACTA-ATCTCACCAAAAT-TATTA
* * * * * * * ** * * * * ** *
2132 TTGAATA-TCTATCAAAGTCGACTTGAACTTGCTCAA-C-TTCTAGATGTG-TATGTCGATGAC-
1 TAG-TTAGGCCAT-AAA--C-AATGGAA--AG-AAAAGCATT-GAGGTTTGCCAAATCGAAGACG
* * * * * **** ** * * * ** * * * * *
2192 CTTCACAAGGTTATTACTCTTCTTTCG-TCGGTCCAAAGTCTCCAATTAGACCTGCAATTGTCAA
57 ATTCAAAACGTCACTAAGGGTCCCT-GATAGGCCCAAAAT-AACAAGT-G--TTCCAAATG--AG
*** * * ** * * * * * **
2256 CTCAAGAAGACAAGATTCACA-AACAATCAAGTATCA-CAACTTAATTGTTTGCTAGGAC-TCTA
115 CT-AA-AA-AC----TTCACAGTGGACT-AA-TCTCACCAAAATGATT-ATAGTTAGGCCATAAA
** ** * ** * **
2318 CAA--GATTGAAGAA-CCCTAAGTTTTGCTCAAA-C-TAGA--A--C--AA--GAAGCTAA-GAT
170 CAATGGAAAGAA-AAGCATTGAGGGTTGC-CAAATCGAAGACGATTCAAAACGGAA-CTAATGGG
*** * * *** *** * *
2369 AATCAATTTGGGTGAAAACCTCAA-T-TT-----T-A-TTAATCAACTTCACAGTGGACTAATCT
232 CCCCGA-TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA-AAACTTCACAGTGGACTAATCT
*
2425 CACCAAAATGATTA
295 CACCAAAATTATTA
* *
2439 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTGAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * *
2504 GACATTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAACTTCACA
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAAACTTCACA
* * *
2568 GTGGACTAATACTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAGAAGCATTTAGG
129 GTGGACTAAT-CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * * ** *
2633 ATTTCCAAATCGTAA-ACGATTCAAAAAGTCACTAAAGGGCCCCGATAGGCCCAAAATAACAAGT
193 GTTGCCAAATCG-AAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
* ** *
2697 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTTAGTAAAATGATTA
257 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* *
2749 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CTCAAATCGAAAACGATTTAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC-CAAATCGAAGACGATTCAAAA
** * *
2813 CAACACTAATGGG-CCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
65 CGTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* *
2877 GTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAGAAAAGCATCGAGGG
129 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG
* *
2942 TTGCCAAATCGAAGACGATTCAAAACGGAACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGT
194 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* * * * *
3006 TCCAAATGAGCTAAAAACATGACAGTGGACTAATCTCACGAAAATGATAA
259 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
*
3056 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TT-CTCAAATCAAAGACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGC-CAAATCGAAGACGATTCAAAA
* * * * *
3119 CGACACTAATGGG-CCCCGATTA-GCCC-AACTTAGAAGTGTTCCAAATGAGCTAAAAACTTCAC
65 CGTCACTAA-GGGTCCCTGA-TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
**
3181 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCAAGG
128 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
** * ** * *
3246 GTTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGG-TCTTATAGGCGCAAAATAAGAAGT
193 GTTGCCAAATCGAA-GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
** * * *
3309 GTTCCAAATGAGCTAATGATACAAATC-TAGTTGTATTAGAT-T---C-AAATCTAGCCTTGAA
257 GTTCCAAATGAGCTAA--A-A-ACTTCACAG-TGGACTA-ATCTCACCAAAAT-TA---TT--A
* * * * * ** * * * * ** * *
3367 TA-TCTA--ACA-AAGTCGACTTGAACTTGCTCAA-C-TTCTAGATGTG-TATGTCGATGAC-CT
1 TAGT-TAGGCCATAA-AC-AATGGAA--AG-AAAAGCATT-GAGGTTTGCCAAATCGAAGACGAT
* * * * **** ** * * * ** * * * *
3424 TCACAAGGTTATTACTCTTCTTTCG-TCGGTCCAAAGTCTCCAATTAG-ACCTGCAAT-TG-T--
59 TCAAAACGTCACTAAGGGTCCCT-GATAGGCCCAAAAT-AACAAGT-GTTCC--AAATGAGCTAA
* ** * ** * * * * * ** **
3483 CAAC-TCA-AGAAGACAAGAT-TCA-CAACTTAATTGTTTGCTAGGAC-TCTACAA--GATTGAA
119 AAACTTCACAGTGGACTA-ATCTCACCAAAATGATT-ATAGTTAGGCCATAAACAATGGAAAGAA
** * ** * ***** * * *
3541 GAA-CCCTAAGTTTTGCTCAAA-C-TAGA--A--C--AA--GAAGCTAA-GATAATCAATTTGGG
182 -AAGCATTGAGGGTTGC-CAAATCGAAGACGATTCAAAACGGAA-CTAATGGGCCCCGA-TAGGC
** *** * * * *
3594 TGAAAACCTCAA-T-TT-----T-A-TTAATCAACTTCACAGTGGACTAATCTCACTAAAATGAT
243 CCAAAATAACAAGTGTTCCAAATGAGCTAA-AAACTTCACAGTGGACTAATCTCACCAAAATTAT
3650 TA
307 TA
** * *
3652 TAGTTAGGCCATAAACAATGGAAAGAAAAATATTGAGGTTTACCAAATCGAAGACGATTTAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * *
3717 GTCACTAATGGG-CCTTGATGGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * * **
3781 TGGACTAATCTCACCAAAATGATTATAGCTAGGCCATACACAATGGAAATAAAAGCATCAAGGGT
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
* * *
3846 TGCCAAATCGAATACGATTCAAAACGGAACTAAT-GG-CCCGAAAGGCCTAAAATAACAAGTGTT
195 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* * *
3909 TCAAATGAGCTAAAAACTTCACAGTGGACTAATCACACCAAAATGATTA
260 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* * ** * * *
3958 TAGTTAGGCCATAAACAATTGAAATAAAAGCATCAAGGGTTGCCAAATCGATGGCGATTCAAAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * *
4023 GACACT-AGTGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
66 GTCACTAAG-GGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* *
4087 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGAT
130 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
* * * ** * * *
4152 TTCCAAATCGTAGACGATTCAAAAAGTCACTAAAGGGCCCCGATAGACCCAAAATAACAAGTGGT
195 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTT
* *
4217 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTA
260 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
* *
4266 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGATTT-CCAAATCGTAGACGATTCAAAA
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAA
*
4330 -GTCACTAAAGGG-CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
65 CGTCACT-AAGGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* * *
4393 GTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGCATCGAGGG
129 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG
* * *
4458 TTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAATAACAAGTGT
194 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
*
4523 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
259 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
** * *
4573 TAGTTAGGCCATAAACAATGG-AAG-AAAGCATCAAGGGTTGCCAAATCGATGACGATTC-AAAC
1 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * *
4635 GTCACTAATGGGT-CTTGATACGCCC-AAATAACAAGTGTTCCAAATGAG-TTAAAACTTACACA
66 GTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACA
* *
4697 GTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGG-AAG-AAAGTAATTGAGG
129 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-CATTGAGG
**
4760 GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAAGCCCCGATAGGCCCAAAATAACAAGTG
193 GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTG
* * * *
4825 TTCCAAATTAGCAAAAAACTTCACATTGGACTAATCTCACCAAAATGATTA
258 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
*
4876 TAGTTAGGCCGTAAACAAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
1 TAGTTAGGCCATAAAC-AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
** * *
4941 CGGAACTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACA
65 CGTCACTAA-GGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
* * *
5005 GTGGACTAGTCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGG
129 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG
* * * *
5070 TTGCCAAATCGAATACGATTCAAAACAGAACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGT
194 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT
* * *
5134 TCCAAATGAGCT-AAAACTTCATAGTGGACTAATCTCATCAAAATGGA--A
259 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT-TATTA
* * * * * * *
5182 CTA-ATAGGCCATAAACACCT-TAAAGAAAAGCTTTGAGGTTTACCAAATCGAATATGATTCAAA
1 -TAGTTAGGCCATAAACA-ATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAA
** * *
5245 ACGGAACTAATAGG-CCCCGATACGGCCCAAAATAACAAGTGTTCCAAATGA
64 ACGTCACTAA-GGGTCCCTGATA-GGCCCAAAATAACAAGTGTTCCAAATGA
Statistics
Matches: 3897, Mismatches: 782, Indels: 617
0.74 0.15 0.12
Matches are distributed among these distances:
283 10 0.00
284 13 0.00
285 49 0.01
286 59 0.02
287 35 0.01
288 25 0.01
289 30 0.01
290 27 0.01
291 44 0.01
292 41 0.01
293 15 0.00
294 12 0.00
295 5 0.00
296 6 0.00
297 13 0.00
298 16 0.00
299 35 0.01
300 8 0.00
301 291 0.07
302 43 0.01
303 179 0.05
304 99 0.03
305 286 0.07
306 415 0.11
307 533 0.14
308 778 0.20
309 369 0.09
310 193 0.05
311 82 0.02
312 59 0.02
313 22 0.01
314 13 0.00
315 17 0.00
316 10 0.00
317 3 0.00
318 3 0.00
319 2 0.00
320 3 0.00
322 5 0.00
323 13 0.00
324 26 0.01
325 10 0.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (308 bp):
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
GTCACTAAGGGTCCCTGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT
GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
CAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTA
Found at i:1920 original size:155 final size:153
Alignment explanation
Indices: 1635--2094 Score: 653
Period size: 155 Copynumber: 3.0 Consensus size: 153
1625 TTTATTAATC
*
1635 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * *
1700 CATTGAGGTTTCCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGTCCAAAA
66 CATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGA-ACTAATGGGCCCCGATAGG-CCAAAA
1764 TAACAAGTGTTCCAAATGAGCTAAA
129 TAACAAGTGTTCCAAATGAGCTAAA
* *
1789 AA-TATCACAGTGGACTAATCTCATCAAAAATGATTATAGTTAGGCCATAAAC-ATTGAAAGAAA
1 AACT-TCACAGTGGACTAATCTCA-CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
*
1852 AGCGATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAA
64 AGC-ATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC-AA
1917 AATAACAAGTGTTCCAAATGAGCTAAA
127 AATAACAAGTGTTCCAAATGAGCTAAA
*
1944 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAG-AAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* ** * ** *
2008 CATCAAGGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGG-TCTTATAGACGCAAAA
66 CATCGAGGGTTGCCAAATCGAAT-ACGATTCAAAACGGAACTAATGGGCCCCGATAGGC-CAAAA
*
2071 TAAGAAGTGTTCCAAATGAGCTAA
129 TAACAAGTGTTCCAAATGAGCTAA
2095 TGATACAAAT
Statistics
Matches: 277, Mismatches: 20, Indels: 20
0.87 0.06 0.06
Matches are distributed among these distances:
152 35 0.13
153 41 0.15
154 66 0.24
155 132 0.48
156 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (153 bp):
AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCAAAATA
ACAAGTGTTCCAAATGAGCTAAA
Found at i:3051 original size:153 final size:153
Alignment explanation
Indices: 2404--3324 Score: 1329
Period size: 154 Copynumber: 6.0 Consensus size: 153
2394 TTTATTAATC
2404 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
2469 CATTGAGGTTTTCCAAATCGAAGACGATTGAAAACGACATTAATGGGCCCCGATAGGCCCAAAAT
66 CATTGAGGGTTTCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGG-CCAAAAT
2534 AACAAGTGTTCCAAATGAGCTAAAA
130 AACAAGTGTTCCAAATGAGCT-AAA
* *
2559 AACTTCACAGTGGACTAATACTGACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAGAA
1 AACTTCACAGTGGACTAAT-CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * * * *
2624 GCATTTAGGATTTCCAAATCGTAA-ACGATTCAAAAAGTCACTAAAGGGCCCCGATAGGCCCAAA
65 GCATTGAGGGTTTCCAAATCG-AAGACGATTCAAAACGACACTAATGGGCCCCGATAGG-CCAAA
2688 ATAACAAGTGTTCCAAATGAGCTAAA
128 ATAACAAGTGTTCCAAATGAGCTAAA
* **
2714 AACTTCACAGTGGACTAATCTTAGTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
2779 CATTGA-GGTTTCTCAAATCGAAAACGATTTAAAACAACACTAATGGGCCCCGATAGGCCTAAAA
66 CATTGAGGGTTTC-CAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCC-AAAA
2843 TAACAAGTGTTCCAAATGAGCTAAA
129 TAACAAGTGTTCCAAATGAGCTAAA
*
2868 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
2933 CATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAA
66 CATTGAGGGTTTCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGCC-AAAA
2996 TAACAAGTGTTCCAAATGAGCTAAA
129 TAACAAGTGTTCCAAATGAGCTAAA
* * * *
3021 AACATGACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
3086 CATTGA-GG-TTCTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATTA-GCCCAAC
66 CATTGAGGGTTTC-CAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGA-TAGGCCAAAA
* *
3148 TTAGAAGTGTTCCAAATGAGCTAAA
129 TAACAAGTGTTCCAAATGAGCTAAA
3173 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * * * **
3238 CATCAAGGGTTGCCAAATC-AATGACGATTCAAAACGTCACTAATGGG-TCTTATAGGCGCAAAA
66 CATTGAGGGTTTCCAAATCGAA-GACGATTCAAAACGACACTAATGGGCCCCGATAGGC-CAAAA
*
3301 TAAGAAGTGTTCCAAATGAGCTAA
129 TAACAAGTGTTCCAAATGAGCTAA
3325 TGATACAAAT
Statistics
Matches: 693, Mismatches: 57, Indels: 34
0.88 0.07 0.04
Matches are distributed among these distances:
151 6 0.01
152 125 0.18
153 186 0.27
154 207 0.30
155 47 0.07
156 120 0.17
157 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGGTTTCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCAAAATA
ACAAGTGTTCCAAATGAGCTAAA
Found at i:4112 original size:154 final size:154
Alignment explanation
Indices: 3617--5295 Score: 2297
Period size: 154 Copynumber: 11.0 Consensus size: 154
3607 TTTATTAATC
* *
3617 AACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * * ** ** * *
3682 TATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAAT
66 CATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
3747 AACAAGTGTTCCAAATGAGCTAAA
131 AACAAGTGTTCCAAATGAGCTAAA
* * *
3771 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGGCCATACACAATGGAAATAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * *
3836 CATCAAGGGTTGCCAAATCGAAT-ACGATTCAAAACGGAACTAAT-GG-CCCGAAAGGCCTAAAA
66 CATTGAGGGTTGCCAAATCG-ATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
*
3898 TAACAAGTGTTTCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* * *
3923 AACTTCACAGTGGACTAATCACACCAAAATGATTATAGTTAGGCCATAAACAATTGAAATAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** * *
3988 CATCAAGGGTTGCCAAATCGATGGCGATTCAAAAC-GACACTAGTGGGCCCCGATAGGCCCAAAA
66 CATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAAA
4052 TAACAAGTGTTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
4077 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * * ** * *
4142 CATTTAGGATTTCCAAATCG-TAGACGATTCAAAAAGTCACTAAAGGGCCCCGATAGACCCAAAA
66 CATTGAGGGTTGCCAAATCGAT-GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
*
4206 TAACAAGTGGTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
*
4231 AACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * ** *
4296 CATTTAGGATTTCCAAATCG-TAGACGATTCAAAA-GTCACTAAAGGGCCCCGATAGGCCCAAAA
66 CATTGAGGGTTGCCAAATCGAT-GACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
4359 TAACAAGTGTTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* *
4384 AACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
4449 CATCGAGGGTTGCCAAATCGAAT-ACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAA
66 CATTGAGGGTTGCCAAATCG-ATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
4513 TAACAAGTGTTCCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
4538 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG-AAG-AAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
** ** * ** *
4601 CATCAAGGGTTGCCAAATCGATGACGATTC-AAACGTCACTAATGGGTCTTGATACGCCC-AAAT
66 CATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
*
4664 AACAAGTGTTCCAAATGAG-TTAA
131 AACAAGTGTTCCAAATGAGCTAAA
*
4687 AACTTACACAGTGGACTAATCTCACCAAAATAATTATAGTTAGGCCATAAACAATGG-AAG-AAA
1 AACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* * **
4750 GTAATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAAGCCCCGATAGGCCCAAA
65 G-CATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
* *
4815 ATAACAAGTGTTCCAAATTAGCAAAA
129 ATAACAAGTGTTCCAAATGAGCTAAA
* *
4841 AACTTCACATTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAATGGAAAGAAAA
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AATGGAAAGAAAA
* *
4906 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
65 GCATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
*
4971 TAACAAGTGTTTCAAATGAGCTAAA
130 TAACAAGTGTTCCAAATGAGCTAAA
* *
4996 AACTTCACAGTGGACTAGTCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAACAAAAG
1 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * *
5061 CATCGAGGGTTGCCAAATCGAAT-ACGATTCAAAACAGAACTAAT-GGCCCCGAAAGGCCTAAAA
66 CATTGAGGGTTGCCAAATCG-ATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAA
5124 TAACAAGTGTTCCAAATGAGCT-AA
130 TAACAAGTGTTCCAAATGAGCTAAA
* * * * *
5148 AACTTCATAGTGGACTAATCTCATCAAAATGGA--ACTA-ATAGGCCATAAACACCT-TAAAGAA
1 AACTTCACAGTGGACTAATCTCACCAAAAT-GATTA-TAGTTAGGCCATAAACA-ATGGAAAGAA
* * * * *
5209 AAGCTTTGAGGTTTACCAAATCGAAT-ATGATTCAAAACGGAACTAATAGGCCCCGATACGGCCC
63 AAGCATTGAGGGTTGCCAAATCG-ATGACGATTCAAAACGGAACTAATGGGCCCCGATA-GGCCC
5273 AAAATAACAAGTGTTCCAAATGA
126 AAAATAACAAGTGTTCCAAATGA
Statistics
Matches: 1378, Mismatches: 122, Indels: 51
0.89 0.08 0.03
Matches are distributed among these distances:
149 8 0.01
150 80 0.06
151 113 0.08
152 223 0.16
153 283 0.21
154 531 0.39
155 136 0.10
156 4 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGGTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
AACAAGTGTTCCAAATGAGCTAAA
Found at i:5090 original size:765 final size:764
Alignment explanation
Indices: 3617--5295 Score: 2418
Period size: 765 Copynumber: 2.2 Consensus size: 764
3607 TTTATTAATC
* *
3617 AACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAA
1 AACTTCACAGTGGACTAATCTCAC-AAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAG
* * * ** ** **
3682 TATTGAGGTTTACCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTTGATGGGCACAAAAT
65 CATTGAGGTTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGC-CAAAAT
3747 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTA
129 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTA
*
3812 GGCCATACACAATGGAAATAAAAGCATCAAGGGTTGCCAAATCGAATACGATTCAAAACGGAACT
194 GGCCATAAACAATGGAAATAAAAGCATCAAGGGTTGCCAAATCGAATACGATTCAAAACGGAACT
* *
3877 AATGGCCCGAAAGGCCTAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAAT
259 AATGGCCCGAAACGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* *
3942 CACACCAAAATGATTATAGTTAGGCCATAAACAATTGAAATAAAAGCATCAAGGGTTGCCAAATC
324 CACACCAAAATAATTATAGTTAGGCCATAAACAATTGAAATAAAAGAATCAAGGGTTGCCAAATC
* * * **
4007 GATGGCGATTCAAAACGACACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
389 GAAGACGATTCAAAACGACACTAATAAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG
*
4072 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
454 CAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * **
4137 AAAAGCATTTAGGATTTCCAAATCGTAGACGATTCAAAAAGTCACTAAAGGGCCCCGATAGACCC
519 AAAAGCATTGAGGATTTCCAAATCGAAGACGATTCAAAAAGGAACTAAAGGGCCCCGATAGACCC
*
4202 AAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTAT
584 AAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* ** * *
4267 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGATTTCCAAATCGTAGACGATTC-AAA-A
649 AGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACA
* *
4330 GTCACTAAAGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
714 G-AACT-AAGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AA
4384 AACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAG
1 AACTTCACAGTGGACTAATCTCA-CAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAG
* * *
4449 CATCGAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCTAAAAT
65 CATTGAGGTTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCC-AAAAT
*
4514 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
129 AACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTA
* **
4579 GGCCATAAACAATGG-AA-GAAAGCATCAAGGGTTGCCAAATCG-ATGACGATTC-AAACGTCAC
194 GGCCATAAACAATGGAAATAAAAGCATCAAGGGTTGCCAAATCGAAT-ACGATTCAAAACGGAAC
** * * *
4640 TAATGGGTCTTGATACGCC-CAAATAACAAGTGTTCCAAATGAG-TTAAAACTTACACAGTGGAC
258 TAAT-GG-CCCGAAACGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGAC
* * * **
4703 TAATCTCACCAAAATAATTATAGTTAGGCCATAAACAA-TGGAA-GAAAGTAATTGAGGGTTGCC
320 TAATCACACCAAAATAATTATAGTTAGGCCATAAACAATTGAAATAAAAG-AATCAAGGGTTGCC
4766 AAATCGAAGACGATTCAAAACGGA-ACTAATAAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
384 AAATCGAAGACGATTCAAAAC-GACACTAATAAGCCCCGATAGGCCCAAAATAACAAGTGTTCCA
* * *
4830 AATTAGCAAAAAACTTCACATTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAAA
448 AATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-AA
* *
4895 TGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
512 TGGAAAGAAAAGCATTGAGGATTT-CCAAATCGAAGACGATTCAAAAAGGAACTAAAGGGCCCCG
* * * *
4959 ATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAACTTCACAGTGGACTAGTCTCACCAAA
576 ATAGACCCAAAATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* *
5024 ATGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGAT
641 ATGATTATAGTTAGGCCATAAACAATGGAAACAAAAGCATCGAGGATTGCCAAATCGAAGACGAT
* *
5089 TCAAAACAGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAA
706 TCAAAACAGAACTAAGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* * *
5148 AACTTCATAGTGGACTAATCTCATCAAAATGGA--ACTA-ATAGGCCATAAACACCTT-AAAGAA
1 AACTTCACAGTGGACTAATCTCA-CAAAAT-GATTA-TAGTTAGGCCATAAACA-ATTGAAAGAA
* * * *
5209 AAGCTTTGAGGTTTACCAAATCGAATATGATTCAAAACGGAACTAATAGGCCCCGATACGGCCCA
62 AAGCATTGAGGTTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGA-AAGG-CCA
5274 AAATAACAAGTGTTCCAAATGA
125 AAATAACAAGTGTTCCAAATGA
Statistics
Matches: 820, Mismatches: 75, Indels: 37
0.88 0.08 0.04
Matches are distributed among these distances:
763 74 0.09
764 213 0.26
765 324 0.40
766 16 0.02
767 192 0.23
768 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (764 bp):
AACTTCACAGTGGACTAATCTCACAAAATGATTATAGTTAGGCCATAAACAATTGAAAGAAAAGC
ATTGAGGTTTACCAAATCGAATACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGG
CCATAAACAATGGAAATAAAAGCATCAAGGGTTGCCAAATCGAATACGATTCAAAACGGAACTAA
TGGCCCGAAACGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCA
CACCAAAATAATTATAGTTAGGCCATAAACAATTGAAATAAAAGAATCAAGGGTTGCCAAATCGA
AGACGATTCAAAACGACACTAATAAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCA
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGATTTCCAAATCGAAGACGATTCAAAAAGGAACTAAAGGGCCCCGATAGACCCAA
AATAACAAGTGGTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
TTAGGCCATAAACAATGGAAACAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACAGA
ACTAAGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
Done.