Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398357.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1655.0, 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: 4024
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.28
Warning! 846 characters in sequence are not A, C, G, or T
Found at i:965 original size:172 final size:170
Alignment explanation
Indices: 716--1221 Score: 478
Period size: 172 Copynumber: 3.0 Consensus size: 170
706 NNNNNNNNNN
* * ** * *
716 GTAAAAAAATTCAACTTAAAATTAATTATGAGAATATAAATTTATTTAAAGTGAGTAATAAGACT
1 GTAAAAATATTCAACTTAAAATTAATTATGAGATTATAAA-CCATTTAAAGCGAGTAATAAGATT
* * * * * * ** * *
781 TTTGAAGGAATGGGTGATTACAAATGGACTTTTCTTGTTGATGAATGTCTTTTAATTCACATATC
65 TTTAAAGGAATGGGTGACTATAAATGGACTTTACTTGATAATGAATGTCTTTTTCTTCACGTTTC
**
846 TTGAGGTAGACATTCAATTATTATCTGTTTTAAAAAAAAATT
130 TAAAGGTAGACATTCAATTATTATCTGTTTTAAAAAAAAA-T
* * * *
888 GTAAACATATTCAACTTAAAATTAATTATGAGATTATAAGACCATCTAAAGCGTGTAATAAGGTT
1 GTAAAAATATTCAACTTAAAATTAATTATGAGATTATAA-ACCATTTAAAGCGAGTAATAAGATT
** * * ** *
953 TTTAAAGGAATGGGCAACTATAAATGGGCTTTCCTTGCCAATGAATGCCTTTTTCTTCACGTTTC
65 TTTAAAGGAATGGGTGACTATAAATGGACTTTACTTGATAATGAATGTCTTTTTCTTCACGTTTC
* * * * * **
1018 -ACATGGTAGACATTTAGTTATTGTCTGTTCTAACGAAAAAT
130 TA-AAGGTAGACATTCAATTATTATCTGTTTTAAAAAAAAAT
* * * * * *
1059 GTAAAAATAATCAACTTAAAATCAATTATTAGATTACAAAAGCATTTAAAGCGAGTAATAAGCCT
1 GTAAAAATATTCAACTTAAAATTAATTATGAGATTA-TAAACCATTTAAAGCGAGTAATAAG-AT
* * * * *
1124 TTTGAAA-GAATGGGTGACTATTAATGAACTTTACTT-ATCAGTGAATGTCTTTTTCTTCATGTT
64 TTTTAAAGGAATGGGTGACTATAAATGGACTTTACTTGAT-AATGAATGTCTTTTTCTTCACGTT
* * *
1187 TCTCAAGGTAAACATTCAATTATAATCTGTTTTAA
128 TCTAAAGGTAGACATTCAATTATTATCTGTTTTAA
1222 TAANNNNNNN
Statistics
Matches: 265, Mismatches: 63, Indels: 13
0.78 0.18 0.04
Matches are distributed among these distances:
171 122 0.46
172 142 0.54
173 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (170 bp):
GTAAAAATATTCAACTTAAAATTAATTATGAGATTATAAACCATTTAAAGCGAGTAATAAGATTT
TTAAAGGAATGGGTGACTATAAATGGACTTTACTTGATAATGAATGTCTTTTTCTTCACGTTTCT
AAAGGTAGACATTCAATTATTATCTGTTTTAAAAAAAAAT
Found at i:1137 original size:171 final size:170
Alignment explanation
Indices: 582--1217 Score: 526
Period size: 171 Copynumber: 3.7 Consensus size: 170
572 NNNNNNNNNN
* * ** * *
582 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAAGAATGGGAGACTATAAATAAACTTTTCATG
1 AAAACCATTTAAAGCGAGTAATAA-GCTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTG
* * * * ****
647 TCAATGAATG-CATTTTTATTCATGTTTCTTGAGGTAGACATTCAATTA-TAGTATGTT-TTNNN
65 TCAATGAATGTC-TTTTTCTTCACGTTTC-TCAGGTAGACATTCAATTATTA-TCTGTTCTAAAA
******* *
709 NNNNNNNGTAAAAA-AATTCAACTTAAAATTAATTATGAGAATAT
127 AAAAATTGTAAAAATAA-TCAACTTAAAATTAATTATGAGATTAT
*** * * * * *
753 AAATTTATTTAAAGTGAGTAATAAGACTTTTGAAGGAATGGGTGATTACAAATGGACTTTTCTTG
1 AAAACCATTTAAAGCGAGTAATAAG-CTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTG
** ** * * * *
818 TTGATGAATGTCTTTTAATTCACATATCTTGAGGTAGACATTCAATTATTATCTGTTTTAAAAAA
65 TCAATGAATGTCTTTTTCTTCACGTTTC-TCAGGTAGACATTCAATTATTATCTGTTCTAAAAAA
* *
883 AAATTGTAAACATATTCAACTTAAAATTAATTATGAGATTAT
129 AAATTGTAAAAATAATCAACTTAAAATTAATTATGAGATTAT
* * * * * ** * *
925 AAGACCATCTAAAGCGTGTAATAAGGTTTTTAAAGGAATGGGCAACTATAAATGGGCTTTCCTTG
1 AAAACCATTTAAAGCGAGTAATAAGCTTTTGAAA-GAATGGGTGACTATAAATGGACTTTACTTG
* * * * * * **
990 CCAATGAATGCCTTTTTCTTCACGTTTCACATGGTAGACATTTAGTTATTGTCTGTTCTAACGAA
65 TCAATGAATGTCTTTTTCTTCACGTTTCTCA-GGTAGACATTCAATTATTATCTGTTCTAAAAAA
* * *
1055 AAA-TGTAAAAATAATCAACTTAAAATCAATTATTAGATTAC
129 AAATTGTAAAAATAATCAACTTAAAATTAATTATGAGATTAT
* * * *
1096 AAAAGCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATGGGTGACTATTAATGAACTTTACTTA
1 AAAACCATTTAAAGCGAGTAATAAG-CTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTG
* * * *
1161 TCAGTGAATGTCTTTTTCTTCATGTTTCTCAAGGTAAACATTCAATTATAATCTGTT
65 TCAATGAATGTCTTTTTCTTCACGTTTCTC-AGGTAGACATTCAATTATTATCTGTT
1218 TTAATAANNN
Statistics
Matches: 365, Mismatches: 91, Indels: 18
0.77 0.19 0.04
Matches are distributed among these distances:
170 1 0.00
171 227 0.62
172 136 0.37
173 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.36
Consensus pattern (170 bp):
AAAACCATTTAAAGCGAGTAATAAGCTTTTGAAAGAATGGGTGACTATAAATGGACTTTACTTGT
CAATGAATGTCTTTTTCTTCACGTTTCTCAGGTAGACATTCAATTATTATCTGTTCTAAAAAAAA
ATTGTAAAAATAATCAACTTAAAATTAATTATGAGATTAT
Found at i:2439 original size:171 final size:169
Alignment explanation
Indices: 2218--3140 Score: 543
Period size: 171 Copynumber: 5.4 Consensus size: 169
2208 AAGGCAAGCA
* * * *
2218 TTCAATTATAATCTGTTTCAGCTAAAAATG-AAAAAAATTTAA-TCTAAAATCTATTATGAAATT
1 TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTAACT-TAAAATCAATTATGAGATT
* *
2281 TTAAACACCATTTAAAGCGAGTTATAAGGCTTGTGAAGGAATGAGTGACTATAAATTAACTTTTT
65 ATAAA-ACCATTTAAAGCGAGTAATAAGGCTTGTGAAGGAAT-AGTGACTATAAATTAACTTTTT
* *
2346 TGCAAATGAGCACCTTTTTCTTCATATTTCCCAAGGTAAACT
128 TGCAAATGAACATCTTTTTCTTCATATTTCCCAAGGTAAACT
* * * *
2388 TTCAATTATAGTGTGTTTTAACTAAAAATGTAAAACAGTTTAACTTAAAATCAATTATGAGATTA
1 TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTA
********** * * * * * **
2453 TANNNNNNNNNNAAGCGAGTAACAAGGCTTTTGAAGGAATAAGTGATTTTGAATGGACTTTTCTT
66 TAAAACCATTTAAAGCGAGTAATAAGGCTTGTGAAGGAAT-AGTGACTATAAATTAACTTTT-TT
* * * *
2518 GCCAATGAATATCTTTTTCTTCACATTTCTCCAA-GTAGA-T
129 GCAAATGAACATCTTTTTCTTCATATTTC-CCAAGGTAAACT
* * ** ** * *
2558 ATTCAATTATAATCTATTTTGACCCAAAATGTTAAAAAAAATAAAAACTTAAAATCAATTTTTAG
1 -TTCAATTATAATCTGTTTTAACTAAAAATG-T-AAAAAAAT-TTAACTTAAAATCAATTATGAG
* * * * *
2623 ATTATAAAATCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTTACTATAAATTAACTTT
62 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTGTGAAGGAATA-GTGACTATAAATTAAC-TT
* * * ***
2688 TTTTACAAATGAACGTCTTTTTCTTCATGTTTCTTGAGGTAAACT
125 TTTTGCAAATGAACATCTTTTTCTTCATATTTCCCAAGGTAAACT
* * ** ******
2733 TTCAATTATAGTGTGTTTTAACTAAAAATGTAAAAACGTTTAACTTAAAATCAATTATGNNNNNN
1 TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTA
**** * * * ** *
2798 NNNNACCATTTAAAGCGACTAATAAGGCTT-TCGAAGGAATAAGTGATTTTAAATGGAC-TTTTC
66 TAAAACCATTTAAAGCGAGTAATAAGGCTTGT-GAAGGAAT-AGTGACTATAAATTAACTTTTTT
* * * * * * *
2861 ACCAATG-A-ATGCCTTTTATTCATATTTCTCAAGGTAGACA
129 GCAAATGAACAT-CTTTTTCTTCATATTTCCCAAGGTAAACT
* * ** ** * *
2901 TTCATTTATAATCTGTTTTGACCCAAAATGTAAAAAAAAAAATAAAAACTTAAAATCAATTTTTA
1 TTCAATTATAATCTGTTTTAACTAAAAATGT----AAAAAAAT-TTAACTTAAAATCAATTATGA
* * * * * *********
2966 GATTATAAAACCGTTTAGAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGACTANNNNNNNNNNT
61 GATTATAAAACCATTTAAAGCGAGTAATAAGGCTTGTGAAGGAAT-AGTGACTA-TAAATTAACT
* * * ** * *
3031 TTTTTGCCAATG-A-ATGCTTTTTTCTTCATGTCTCTAAAGGTAGACA
124 TTTTTGCAAATGAACAT-C-TTTTTCTTCATATTTCCCAAGGTAAACT
* * * * *
3077 TTCAATTATAGTCTGTTTTAACTAAAAATATAAAACAATTCAAATTAAAATCAATTATGAGATT
1 TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATT
3141 CTANNNNNNN
Statistics
Matches: 553, Mismatches: 176, Indels: 47
0.71 0.23 0.06
Matches are distributed among these distances:
167 1 0.00
168 48 0.09
169 10 0.02
170 69 0.12
171 159 0.29
172 26 0.05
173 60 0.11
174 112 0.20
175 20 0.04
176 48 0.09
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.35
Consensus pattern (169 bp):
TTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAGGCTTGTGAAGGAATAGTGACTATAAATTAACTTTTTTGC
AAATGAACATCTTTTTCTTCATATTTCCCAAGGTAAACT
Found at i:2664 original size:174 final size:172
Alignment explanation
Indices: 2469--3010 Score: 493
Period size: 174 Copynumber: 3.1 Consensus size: 172
2459 NNNNNNAAGC
* * *
2469 GAGTAACAAGGCTTTTGAAGGAATAAGTGATTTTGAATGGACTTTTCTTGCCAATGAATATCTTT
1 GAGTAATAAGGCTTTTGAAGGAATAAGTGATTTTAAATGGACTTTTCTTACCAATGAAT-TCTTT
* *
2534 TTCTTCACATTTCTCCAAGTAGATATTCAATTATAATCTATTTTGACCCAAAATGTTAAAAAAAA
65 TTCTTCATATTTCT-CAAGTAGATATTCAATTATAATCTGTTTTGACCCAAAATGTTAAAAAAAA
*
2599 TAAAAACTTAAAATCAATTTTTAGATTATAAAATCGTTTAAAGG
129 TAAAAACTTAAAATCAATTTTTAGATTATAAAACCGTTTAAAGG
** * * * * ** * * *
2643 GAGTAATAAGGCTCGTGAAGGAATAGGTTACTATAAATTAACTTTTTTTACAAATGAACGTCTTT
1 GAGTAATAAGGCTTTTGAAGGAATAAGTGATTTTAAATGGACTTTTCTTACCAATGAA-TTCTTT
* * * * * * * ** *
2708 TTCTTCATGTTTCTTGAGGTAAACT-TTCAATTATAGTGTGTTTTAACTAAAAATG-T-AAAAAC
65 TTCTTCATATTTC-TCAAGTAGA-TATTCAATTATAATCTGTTTTGACCCAAAATGTTAAAAAAA
* ** * *********** * *
2770 GT-TTAACTTAAAATCAATTATGNNNNNNNNNNACCATTTAAAGC
128 ATAAAAACTTAAAATCAATTTTTAGATTATAAAACCGTTTAAAGG
* * * *
2814 GACTAATAAGGCTTTCGAAGGAATAAGTGATTTTAAATGGACTTTTC--ACCAATGAATGCCTTT
1 GAGTAATAAGGCTTTTGAAGGAATAAGTGATTTTAAATGGACTTTTCTTACCAATGAATTCTTTT
* * * *
2877 TATTCATATTTCTCAAGGTAGACATTCATTTATAATCTGTTTTGACCCAAAATGTAAAAAAAAAA
66 TCTTCATATTTCTCAA-GTAGATATTCAATTATAATCTGTTTTGACCCAAAATGT--TAAAAAAA
*
2942 ATAAAAACTTAAAATCAATTTTTAGATTATAAAACCGTTTAGAGG
128 ATAAAAACTTAAAATCAATTTTTAGATTATAAAACCGTTTAAAGG
2987 GAGTAATAAGGCTTTTGAAGGAAT
1 GAGTAATAAGGCTTTTGAAGGAAT
3011 GGGTGACTAN
Statistics
Matches: 265, Mismatches: 93, Indels: 21
0.70 0.25 0.06
Matches are distributed among these distances:
167 2 0.01
168 42 0.16
169 8 0.03
171 61 0.23
172 12 0.05
173 48 0.18
174 90 0.34
175 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.35
Consensus pattern (172 bp):
GAGTAATAAGGCTTTTGAAGGAATAAGTGATTTTAAATGGACTTTTCTTACCAATGAATTCTTTT
TCTTCATATTTCTCAAGTAGATATTCAATTATAATCTGTTTTGACCCAAAATGTTAAAAAAAATA
AAAACTTAAAATCAATTTTTAGATTATAAAACCGTTTAAAGG
Found at i:2764 original size:345 final size:338
Alignment explanation
Indices: 2282--3140 Score: 952
Period size: 344 Copynumber: 2.5 Consensus size: 338
2272 TATGAAATTT
* * *
2282 TAAACACCATTTAAAGCGAGTTATAAGGCTTGTGAAGGAATGAGTGACTATAAATTAACTTTTTT
1 TAAA-ACCGTTTAAAGGGAGTAATAAGGCTTGTGAAGGAATG-GTGACTATAAATTAACTTTTTT
* **
2347 GCAAATGAGCAC-CTTTTTCTTCATATTTCCCAAGGTAAACTTTCAATTATAGTGTGTTTTAACT
64 GCAAATGA--ACGCTTTTTCTTCATGTTTCTAAAGGTAAACTTTCAATTATAGTGTGTTTTAACT
******** *
2411 AAAAATGTAAAACAGTTTAACTTAAAATCAATTATGAGATTATANNNNNNNNNNAAGCGAGTAAC
127 AAAAATGTAAAACAGTTTAACTTAAAATCAATTATGAGATTATA--ACCATTTAAAGCGACTAAC
* * * * * *
2476 AAGGCTTTTGAAGGAATAAGTGATTTTGAATGGACTTTTCTTGCCAATGAATATCTTTTTCTTCA
190 AAGGCTTTCGAAGGAATAAGTGATTTTAAATGGACTTTTC--ACCAATGAAT-GCCTTTTATTCA
* *
2541 CATTTCTCCAA-GTAGATATTCAATTATAATCTATTTTGACCCAAAATGT-TAAAAAAAATAAAA
252 CATTTCT-CAAGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGTAAAAAAAAAATAAAA
2604 ACTTAAAATCAATTTTTAGATTA
316 ACTTAAAATCAATTTTTAGATTA
* * *
2627 TAAAATCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTTACTATAAATTAACTTTTTTT
1 TAAAACCGTTTAAAGGGAGTAATAAGGCTTGTGAAGGAAT-GGTGACTATAAATTAAC-TTTTTT
* **
2692 ACAAATGAACGTCTTTTTCTTCATGTTTCTTGAGGTAAACTTTCAATTATAGTGTGTTTTAACTA
64 GCAAATGAACG-CTTTTTCTTCATGTTTCTAAAGGTAAACTTTCAATTATAGTGTGTTTTAACTA
******** *
2757 AAAATGTAAAA-ACGTTTAACTTAAAATCAATTATGNNNNNNNNNNACCATTTAAAGCGACTAAT
128 AAAATGTAAAACA-GTTTAACTTAAAATCAATTATG--AGATTATAACCATTTAAAGCGACTAAC
*
2821 AAGGCTTTCGAAGGAATAAGTGATTTTAAATGGACTTTTCACCAATGAATGCCTTTTATTCATAT
190 AAGGCTTTCGAAGGAATAAGTGATTTTAAATGGACTTTTCACCAATGAATGCCTTTTATTCACAT
* *
2886 TTCTCAAGGTAGACATTCATTTATAATCTGTTTTGACCCAAAATGTAAAAAAAAAAATAAAAACT
255 TTCTCAAGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGT-AAAAAAAAAATAAAAACT
2951 TAAAATCAATTTTTAGATTA
319 TAAAATCAATTTTTAGATTA
* * *********
2971 TAAAACCGTTTAGAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGACTANNNNNNNNNNTTTTTT
1 TAAAACCGTTTAAAGGGAGTAATAAGGCTTGTGAAGGAAT-GGTGACTA-TAAATTAACTTTTTT
* * * * * *
3036 GCCAATGAATGCTTTTTTCTTCATGTCTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAACTA
64 GCAAATGAACGC-TTTTTCTTCATGTTTCTAAAGGTAAACTTTCAATTATAGTGTGTTTTAACTA
* * * *
3101 AAAATATAAAACAATTCAAATTAAAATCAATTATGAGATT
128 AAAATGTAAAACAGTTTAACTTAAAATCAATTATGAGATT
3141 CTANNNNNNN
Statistics
Matches: 428, Mismatches: 73, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
341 3 0.01
342 50 0.12
343 12 0.03
344 215 0.50
345 148 0.35
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.35
Consensus pattern (338 bp):
TAAAACCGTTTAAAGGGAGTAATAAGGCTTGTGAAGGAATGGTGACTATAAATTAACTTTTTTGC
AAATGAACGCTTTTTCTTCATGTTTCTAAAGGTAAACTTTCAATTATAGTGTGTTTTAACTAAAA
ATGTAAAACAGTTTAACTTAAAATCAATTATGAGATTATAACCATTTAAAGCGACTAACAAGGCT
TTCGAAGGAATAAGTGATTTTAAATGGACTTTTCACCAATGAATGCCTTTTATTCACATTTCTCA
AGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGTAAAAAAAAAATAAAAACTTAAAATC
AATTTTTAGATTA
Found at i:3204 original size:344 final size:342
Alignment explanation
Indices: 2282--3251 Score: 779
Period size: 344 Copynumber: 2.8 Consensus size: 342
2272 TATGAAATTT
* * * *
2282 TAAACACCATTTAAAGCGAGTTATAAGGCTTGTGAAGGAAT-GAGTGACTATAAATTAAC-TTTT
1 TAAA-ACCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAG-GTGACTATAAATTAACTTTTT
* * ** * * ** * *
2345 TTGCAAATGAGCACCTTTTTCTTCATATTTCCCAAGGTAAACTTTCAATTATAGTGTGTTTTAAC
64 TTACAAATGAACGTCTTTTTCTTCATGTCTCTAAAGGTAAACATTCAATTATAGTCTGTTTTAAC
* * * * ******** *
2410 TAAAAATGT-AAAACAGTTTAACTTAAAATCAATTATGAGATTATANNNNNNNNNNAAGCGAGTA
129 TAAAAATATAAAAACA-TTCAAATTAAAATCAATTATGAGATTCTA--ACCATTTAAAGCGACTA
* * * ** * * * ** * *
2474 ACAAGGCTTTTGAAGGAATAAGTGATTTTGAATGGACTTTTCTTGCCAATGAAT-ATCTTTTTCT
191 ATAAGGCTTTCGAAAGAATAAGAAACTATAAATACACTTTTC-AGCCAATGAATGCTC-TTTTCT
* * *
2538 TCACATTTCTCCAA-GTAGATATTCAATTATAATCTATTTTGACCCAAAATGTTAAAAAAAATAA
254 TCATATTTCT-CAAGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGTAAAAAAAAATAA
2602 AAACTTAAAATCAATTTTTAGATTA
318 AAACTTAAAATCAATTTTTAGATTA
* *
2627 TAAAATCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTTACTATAAATTAACTTTTTTT
1 TAAAACCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTGACTATAAATTAACTTTTTTT
* ** * *
2692 ACAAATGAACGTCTTTTTCTTCATGTTTCTTGAGGTAAACTTTCAATTATAGTGTGTTTTAACTA
66 ACAAATGAACGTCTTTTTCTTCATGTCTCTAAAGGTAAACATTCAATTATAGTCTGTTTTAACTA
* * * * ********
2757 AAAATGTAAAAACGTTTAACTTAAAATCAATTATGNNNNNNNNNNACCATTTAAAGCGACTAATA
131 AAAATATAAAAACATTCAAATTAAAATCAATTATG--AGATTCTAACCATTTAAAGCGACTAATA
* ** * * ** *
2822 AGGCTTTCGAAGGAATAAGTGATTTTAAATGGACTTTTCA-CCAATGAATGC-CTTTTATTCATA
194 AGGCTTTCGAAAGAATAAGAAACTATAAATACACTTTTCAGCCAATGAATGCTCTTTTCTTCATA
* *
2885 TTTCTCAAGGTAGACATTCATTTATAATCTGTTTTGACCCAAAATGTAAAAAAAAAAATAAAAAC
259 TTTCTCAAGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGT--AAAAAAAAATAAAAAC
2950 TTAAAATCAATTTTTAGATTA
322 TTAAAATCAATTTTTAGATTA
* ** * **********
2971 TAAAACCGTTTAGAGGGAGTAATAAGGCTTTTGAAGGAATGGGTGACTANNNNNNNNNNTTTTTT
1 TAAAACCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTGACTATAAATTAACTTTTTTT
* * * *
3036 GCCAATGAATG-CTTTTTTCTTCATGTCTCTAAAGGTAGACATTCAATTATAGTCTGTTTTAACT
66 ACAAATGAACGTC-TTTTTCTTCATGTCTCTAAAGGTAAACATTCAATTATAGTCTGTTTTAACT
******** * *
3100 AAAAATAT-AAAACAATTCAAATTAAAATCAATTATGAGATTCTANNNNNNNNNNAAGTGAGTAA
130 AAAAATATAAAAAC-ATTCAAATTAAAATCAATTATGAGATTCTA--ACCATTTAAAGCGACTAA
* * * *
3164 TAAGGCTTTTGAAAGAATGAGAAACTATAAATACACTTTTCATGTCAATGAATGCTTTTTTCTTC
192 TAAGGCTTTCGAAAGAATAAGAAACTATAAATACACTTTTCA-GCCAATGAATGCTCTTTTCTTC
* *
3229 ATGTTTCTCGAGGTAGACATTCA
256 ATATTTCTCAAGGTAGACATTCA
3252 NNNNNNNNNN
Statistics
Matches: 505, Mismatches: 104, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
341 3 0.01
342 49 0.10
343 16 0.03
344 251 0.50
345 143 0.28
346 15 0.03
347 28 0.06
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (342 bp):
TAAAACCGTTTAAAGGGAGTAATAAGGCTCGTGAAGGAATAGGTGACTATAAATTAACTTTTTTT
ACAAATGAACGTCTTTTTCTTCATGTCTCTAAAGGTAAACATTCAATTATAGTCTGTTTTAACTA
AAAATATAAAAACATTCAAATTAAAATCAATTATGAGATTCTAACCATTTAAAGCGACTAATAAG
GCTTTCGAAAGAATAAGAAACTATAAATACACTTTTCAGCCAATGAATGCTCTTTTCTTCATATT
TCTCAAGGTAGACATTCAATTATAATCTATTTTGACCCAAAATGTAAAAAAAAATAAAAACTTAA
AATCAATTTTTAGATTA
Found at i:3515 original size:168 final size:159
Alignment explanation
Indices: 3341--3654 Score: 333
Period size: 168 Copynumber: 1.9 Consensus size: 159
3331 GTGATAAGGC
* * ** * *
3341 TTTTGAAGGAATGAGTGATTACAAATGGACTTTTCTTGTCAACGAATGCCTTTTTCTTTACGTAT
1 TTTTGAAGGAATGAGTGACTACAAATAGACTTTTCTTCCCAACGAATGCATTTTTCTTCACGTAT
* * * * *
3406 CTCGTGGTACACATTCAATTATTGTCTCTTTT-AAAAAATGTAAAAATATTCAACTTAAAATTAA
66 CACATAGTACACATTCAATTATTGTCTCTTTTAAAAAAATGTAAAAATAATCAACTTAAAATCAA
3470 TTATGAGATTATAAGACCATCNNNNNNNNNNAATAAGAT
131 TTATGAGATTATAAGACCATC----------AATAAGAT
* * * * *
3509 TTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTCCCAATGAATGCATTTTTCTTCATGTTT
1 TTTTGAAGGAATGAGTGACTACAAATAGACTTTTCTTCCCAACGAATGCATTTTTCTTCACGTAT
* * *
3574 CACATAGTAGACATTCAGTTATTGTCTGTTTTAACAAAAAATGTAAAAATAATCAACTTAAAATC
66 CACATAGTACACATTCAATTATTGTCTCTTTT-A-AAAAAATGTAAAAATAATCAACTTAAAATC
*
3639 AATTATTAGATTATAA
129 AATTATGAGATTATAA
3655 AANNNNNNNN
Statistics
Matches: 123, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
168 80 0.65
171 43 0.35
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.37
Consensus pattern (159 bp):
TTTTGAAGGAATGAGTGACTACAAATAGACTTTTCTTCCCAACGAATGCATTTTTCTTCACGTAT
CACATAGTACACATTCAATTATTGTCTCTTTTAAAAAAATGTAAAAATAATCAACTTAAAATCAA
TTATGAGATTATAAGACCATCAATAAGAT
Done.