Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1029
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: 26091
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:1140 original size:310 final size:308
Alignment explanation
Indices: 569--1652 Score: 1059
Period size: 310 Copynumber: 3.5 Consensus size: 308
559 GGATTGCCGG
* * * * *
569 GATACTTTTACGTCAAAGGTATACCCATAGAGGCATTTTCGTAATTTTCTAGAGCCTAGTCCTAG
1 GATACTTTTACGTCGAAGGTATACCCATAGGGGCATTTTCATAATTTCCTAGAACCTAGTCCTAG
* * * * *
634 GTTGTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCCCT-TTTCTA
66 GTTG-TCACCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTCTA
* * * * * * * *
698 ATCTTTTTAGGT-TCTTTAGGGTTTGCTGGGGTACTTTTACATC-AAAGGAT-ACTCATGGGCGC
130 GTCTTTTTAAGTCT-TTTAGGG-TTGCCGGGATACTTTTACGTCGAAAGTATCACTTA-AGG-GC
* * * * *
760 ATTTTCGTAATTTTTAGAACCTAGT-CTTGGTTGTCACCAGGT-TCGCTTTATGCCGAAAGTGGG
191 ATTTTCGTAATTTTTATAACC-AGTCCTAGGTTATCACCGGGTCTC-TTTTATGCCG-AAGTGGG
* *
823 CATTTAGGATAGGTTCATCCATTTTCTAGTCTTTTTAGGTCCTTTAAGGTTGTC-A
253 CATTTAGGATAGGTTCATCCATTTTATAGTCTTTTTAAGTCCTTTAAGGTTGTCGA
* * * *
878 GGGTACTTTTACGTCGAAGCTATACCCATAGGGGCATTTTTATAATTTCCTAGAACCTAGTCTTA
1 -GATACTTTTACGTCGAAGGTATACCCATAGGGGCATTTTCATAATTTCCTAGAACCTAGTCCTA
* *
943 GGTTGTCACCGGATCCGGTTTTATGCTGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTCTA
65 GGTTGTCACCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTCTA
* * * *
1008 GTCTTTTTAAGTCTTTTAGGG-TACCGGGATACTTTCACGTCGAAAGTATCCCTTAAGGGTATTT
130 GTCTTTTTAAGTCTTTTAGGGTTGCCGGGATACTTTTACGTCGAAAGTATCACTTAAGGGCATTT
* * * *
1072 TCGTAAGTTTTATAACCGAGTCCTAGGTTAACATCGGGTCCTCTTTTATGCCGAATGTGGGTATT
195 TCGTAATTTTTATAACC-AGTCCTAGGTTATCACCGGGT-CTCTTTTATGCCGAA-GTGGGCATT
* * * * **
1137 TAGGATAGTTTCACCCATTTTATAGTCATTTTTAAGTCCTTTAGGGGTACCGA
257 TAGGATAGGTTCATCCATTTTATAGTC-TTTTTAAGTCCTTTAAGGTTGTCGA
* * * * *
1190 GATACTTTCACATCGAAGGTGT-CCTC-TAGGAGCATTTTCATAATTTTTCCTAGAACCGAGTCC
1 GATACTTTTACGTCGAAGGTATACC-CATAGGGGCATTTTCATAA--TTTCCTAGAACCTAGTCC
* * * *
1253 TAGGTTGTCACCGGATCTGCTTTTATGCCGAAGGTAGGCATTTAGGATAGGTTCATTACCATTTC
63 TAGGTTGTCACCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTC
* * *
1318 TAGTCTTTTTAAGTCCTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTAT-ACTCGTAAGGAC
128 TAGTCTTTTTAAGTCTTTTAGGGTTGCCGGGATACTTTTACGTCGAAAGTATCACT--TAAGGGC
* * * * *
1382 ATTTTCATAATTTTTCTATAACCAATGCCTAGGTCATCACCGGGTCTGCTTTTATACTGAAGTGG
191 ATTTTCGTAA-TTTT-TATAACCAGT-CCTAGGTTATCACCGGGTCT-CTTTTATGCCGAAGTGG
* *
1447 GCATTTAGGATAGGTTCATCCCTTTTATGAGTCTTTTTAAGTCCTTTAGGGTTGTCGA
252 GCATTTAGGATAGGTTCATCCATTTTAT-AGTCTTTTTAAGTCCTTTAAGGTTGTCGA
* * * ** * **
1505 GATACTTTTACGTCG-AGGTATACATAGCCCTAAGTGCATTTT-AGTAATTTTTTAGAACCAACC
1 GATACTTTTACGTCGAAGGTATAC----CCATAGGGGCATTTTCA-TAATTTCCTAGAACCTAGT
* * * * * *
1568 CCAAGGTCGT-AGTCGGGTCTGCTTTTATGCCGAATGT-GGCATTTAGGATAGGTTCATC-CT-T
61 CCTAGGTTGTCA-CCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACTAT
* *
1629 TTATGAGTCTTTTTAAGTCCTTTA
125 TTCT-AGTCTTTTTAAGTCTTTTA
1653 AGGCTATTGG
Statistics
Matches: 643, Mismatches: 101, Indels: 55
0.80 0.13 0.07
Matches are distributed among these distances:
308 38 0.06
309 68 0.11
310 144 0.22
311 39 0.06
312 100 0.16
313 25 0.04
314 23 0.04
315 91 0.14
316 58 0.09
317 41 0.06
318 2 0.00
319 14 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (308 bp):
GATACTTTTACGTCGAAGGTATACCCATAGGGGCATTTTCATAATTTCCTAGAACCTAGTCCTAG
GTTGTCACCGGATCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTCTAG
TCTTTTTAAGTCTTTTAGGGTTGCCGGGATACTTTTACGTCGAAAGTATCACTTAAGGGCATTTT
CGTAATTTTTATAACCAGTCCTAGGTTATCACCGGGTCTCTTTTATGCCGAAGTGGGCATTTAGG
ATAGGTTCATCCATTTTATAGTCTTTTTAAGTCCTTTAAGGTTGTCGA
Found at i:1449 original size:469 final size:465
Alignment explanation
Indices: 565--1652 Score: 1147
Period size: 469 Copynumber: 2.3 Consensus size: 465
555 TTTAGGATTG
* * *
565 CCGGGATACTTTTACGTCAAAGGTATACCCATAGAGGCATTTTCGTAATTTTCTAGAGCCTAGTC
1 CCGGGATACTTTCACGTCAAAGGTATACCCATAGAGGCATTTTCGTAATTTTATAGAGCCGAGTC
630 CTAGGTTGTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCCCTTTT
66 CTAGG-TGTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCCCTTTT
* * * * * * * * * * *
695 CTAATCTTTTTAGGTTCTTTAGGGTTTGCTGGGGTACTTTTACATCAAAGGATACTCATGGGCGC
130 ATAATCTTTTTAAGTCCTTTAGGGTGTACCGAGATACTTTCACATCAAAGGATACTCATAGGAGC
* * * * *
760 ATTTTCGTAATTTTTAGAACCTAGTCTTGGTTGTCACCAGGTTCGCTTTATGCCGAAAGTGGGCA
195 ATTTTCATAATTTTTAGAACCGAGTCTAGGTTGTCACCAGGATCGCTTTATGCCGAAAGTAGGCA
*
825 TTTAGGATAGGTTCATCCATTTTCTAGTCTTTTTAGGTCCTTTAAGGTTGTCAGGGTACTTTTAC
260 TTTAGGATAGGTTCATCCATTTTCTAGTCTTTTTAAGTCCTTTAAGGTTGTCAGGGTACTTTTAC
* * * * * **
890 GTCGAAGCTATACCCATAGGGGCATTTTTATAATTTCCTAGAACCTAGTCTTAGGTTGTCACCGG
325 GTCGAAGCTATACCCATAAGGACATTTTCATAATTTCCTAGAACCAAGTCCTAGGTCATCACCGG
* * *
955 ATCCGGTTTTATGCTGAAGGTGGGCATTTAGGATAGGTTCATCACTATTTCT-AGTCTTTTTAAG
390 ATCCGCTTTTATACTGAAGGTGGGCATTTAGGATAGGTTCATCACT-TTTATGAGTCTTTTTAAG
*
1019 TCTTTTAGGGTA
454 TCCTTTAGGGTA
* *
1031 CCGGGATACTTTCACGTCGAAA-GTAT-CCCTTA-AGGGTATTTTCGTAAGTTTTATA-A-CCGA
1 CCGGGATACTTTCACGTC-AAAGGTATACCCATAGA-GGCATTTTCGTAA-TTTTATAGAGCCGA
* * *
1091 GTCCTA-G-GTTAACATCGGGTCCTCTTTTATGCCGAATGTGGGTATTTAGGATAGTTTCA-CCC
63 GTCCTAGGTGTTAAC--CGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCCC
* * * *
1153 ATTTTATAGTCATTTTTAAGTCCTTTAGGG-GTACCGAGATACTTTCACATCGAAGGTGTCCTC-
126 -TTTTATAATC-TTTTTAAGTCCTTTAGGGTGTACCGAGATACTTTCACATCAAAGG-ATACTCA
1216 TAGGAGCATTTTCATAATTTTTCCTAGAACCGAGTCCTAGGTTGTCACC-GGATCTGCTTTTATG
188 TAGGAGCATTTTCATAA-TTTT--TAGAACCGAGT-CTAGGTTGTCACCAGGATC-GC-TTTATG
* *
1280 CCGAAGGTAGGCATTTAGGATAGGTTCATTACCA-TTTCTAGTCTTTTTAAGTCCTTTAGGGTTG
247 CCGAAAGTAGGCATTTAGGATAGGTTCA-T-CCATTTTCTAGTCTTTTTAAGTCCTTTAAGGTTG
* * * * * *
1344 -CCGGGATACTTTTACGTCGAAGGTATACTCGTAAGGACATTTTCATAATTTTTCTATAACCAA-
310 TCAGGG-TACTTTTACGTCGAAGCTATACCCATAAGGACATTTTCATAA-TTTCCTAGAACCAAG
* * *
1407 TGCCTAGGTCATCACCGGGTCTGCTTTTATACTGAA-GTGGGCATTTAGGATAGGTTCATCCCTT
373 T-CCTAGGTCATCACCGGATCCGCTTTTATACTGAAGGTGGGCATTTAGGATAGGTTCATCACTT
*
1471 TTATGAGTCTTTTTAAGTCCTTTAGGGTTG
437 TTATGAGTCTTTTTAAGTCCTTTAGGG-TA
* * * * * * * *
1501 TCGAGATACTTTTACGTC-GAGGTATACATAGCCCTA-AGTGCATTTTAGTAATTTTTTAGAACC
1 CCGGGATACTTTCACGTCAAAGGTATAC----CCATAGAG-GCATTTTCGTAATTTTATAGAGCC
* ** * ** **
1564 AACCCCAAGGTCG-TAGTCGGGTCTGCTTTTATGCCGAATGT-GGCATTTAGGATAGGTTCAT-C
61 GAGTCCTAGGT-GTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCC
*
1626 CTTTTATGAGTCTTTTTAAGTCCTTTA
125 CTTTTAT-AATCTTTTTAAGTCCTTTA
1653 AGGCTATTGG
Statistics
Matches: 517, Mismatches: 70, Indels: 63
0.80 0.11 0.10
Matches are distributed among these distances:
461 6 0.01
462 3 0.01
463 83 0.16
464 34 0.07
465 18 0.03
466 41 0.08
467 17 0.03
468 41 0.08
469 117 0.23
470 58 0.11
473 28 0.05
474 39 0.08
475 28 0.05
476 1 0.00
477 2 0.00
478 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (465 bp):
CCGGGATACTTTCACGTCAAAGGTATACCCATAGAGGCATTTTCGTAATTTTATAGAGCCGAGTC
CTAGGTGTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGGTTCATCCCTTTTA
TAATCTTTTTAAGTCCTTTAGGGTGTACCGAGATACTTTCACATCAAAGGATACTCATAGGAGCA
TTTTCATAATTTTTAGAACCGAGTCTAGGTTGTCACCAGGATCGCTTTATGCCGAAAGTAGGCAT
TTAGGATAGGTTCATCCATTTTCTAGTCTTTTTAAGTCCTTTAAGGTTGTCAGGGTACTTTTACG
TCGAAGCTATACCCATAAGGACATTTTCATAATTTCCTAGAACCAAGTCCTAGGTCATCACCGGA
TCCGCTTTTATACTGAAGGTGGGCATTTAGGATAGGTTCATCACTTTTATGAGTCTTTTTAAGTC
CTTTAGGGTA
Found at i:1498 original size:157 final size:156
Alignment explanation
Indices: 554--1652 Score: 1036
Period size: 158 Copynumber: 7.0 Consensus size: 156
544 TATTTTGTAT
* * * *
554 CTTTAGGATTGCCGGGATACTTTTACGTCAAAGGTATACCCAT-AGAGGCATTTTCGTAATTTTC
1 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAG-GGCATTTTCATAATTTTC
* * ** *
618 TAGAGCCTAGTCCTAGGTTGTTAACCGGGTCCACTTTTATGCCGAATGTGGGCATTTAGGATAGG
65 TAGAACCTAGTCCTAGGTTG-TCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGG
* * *
683 TTCATCCCTTTTCTAATCTTTTTAGGTT
129 TTCATCCCTTTTCTAGTCTTTTTAAGTC
* * * * * *
711 CTTTAGGGTTTGCTGGGGTACTTTTACATCAAAGG-ATACTCAT-GGGCGCATTTTCGTAATTTT
1 CTTTAGGG-TTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAGG-GCATTTTCATAATTTT
* * *
774 -TAGAACCTAGT-CTTGGTTGTCACCAGGT-TCGC-TTTATGCCGAAAGTGGGCATTTAGGATAG
64 CTAGAACCTAGTCCTAGGTTGTCACCGGGTCT-GCTTTTATGCCGAAGGTGGGCATTTAGGATAG
* *
835 GTTCATCCATTTTCTAGTCTTTTTAGGTC
128 GTTCATCCCTTTTCTAGTCTTTTTAAGTC
* * * * * * *
864 CTTTAAGGTTGTCAGGG-TACTTTTACGTCGAAGCTATACCCATAGGGGCATTTTTATAATTTCC
1 CTTTAGGGTTG-CCGGGATACTTTTACGTCGAAGGTATACTCATAAGGGCATTTTCATAATTTTC
* * * * *
928 TAGAACCTAGTCTTAGGTTGTCACCGGATCCGGTTTTATGCTGAAGGTGGGCATTTAGGATAGGT
65 TAGAACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGT
*
993 TCATCACTATTTCTAGTCTTTTTAAGTC
130 TCATCCCT-TTTCTAGTCTTTTTAAGTC
* * * * * * * * *
1021 TTTTAGGG-TACCGGGATACTTTCACGTCGAAAGTAT-CCCTTAAGGGTATTTTCGTAAGTTT-T
1 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAGGGCATTTTCATAATTTTCT
* * ** * * * *
1083 ATAACCGAGTCCTAGGTTAACATCGGGTCCT-CTTTTATGCCGAATGTGGGTATTTAGGATAGTT
66 AGAACCTAGTCCTAGGTTGTCACCGGGT-CTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGT
*
1147 TCA-CCCATTTTATAGTCATTTTTAAGTC
130 TCATCCC-TTTTCTAGTC-TTTTTAAGTC
* * * * * * *
1175 CTTTAGGGGTACCGAGATACTTTCACATCGAAGGTGTCCTC-T-AGGAGCATTTTCATAATTTTT
1 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAGG-GCATTTTCATAA-TTTT
* * *
1238 CCTAGAACCGAGTCCTAGGTTGTCACCGGATCTGCTTTTATGCCGAAGGTAGGCATTTAGGATAG
64 -CTAGAACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAG
* *
1303 GTTCATTACCATTTCTAGTCTTTTTAAGTC
128 GTTCA-TCCCTTTTCTAGTCTTTTTAAGTC
* *
1333 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCGTAAGGACATTTTCATAATTTTTC
1 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAGGGCATTTTCATAA-TTTTC
* * ** * *
1398 TATAACC-AATGCCTAGGTCATCACCGGGTCTGCTTTTATACTGAA-GTGGGCATTTAGGATAGG
65 TAGAACCTAGT-CCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGG
*
1461 TTCATCCCTTTTATGAGTCTTTTTAAGTC
129 TTCATCCCTTTTCT-AGTCTTTTTAAGTC
* * * *
1490 CTTTAGGGTTGTCGAGATACTTTTACGTCG-AGGTATACATAGCCCTAAGTGCATTTT-AGTAAT
1 CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATAC-T---CATAAGGGCATTTTCA-TAAT
* * ** * * * *
1553 TTTTTAGAACCAACCCCAAGGTCGT-AGTCGGGTCTGCTTTTATGCCGAATGT-GGCATTTAGGA
61 TTTCTAGAACCTAGTCCTAGGTTGTCA-CCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGA
*
1616 TAGGTTCAT-CCTTTTATGAGTCTTTTTAAGTC
125 TAGGTTCATCCCTTTTCT-AGTCTTTTTAAGTC
1648 CTTTA
1 CTTTA
1653 AGGCTATTGG
Statistics
Matches: 787, Mismatches: 119, Indels: 71
0.81 0.12 0.07
Matches are distributed among these distances:
152 17 0.02
153 95 0.12
154 96 0.12
155 79 0.10
156 84 0.11
157 123 0.16
158 188 0.24
159 83 0.11
160 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (156 bp):
CTTTAGGGTTGCCGGGATACTTTTACGTCGAAGGTATACTCATAAGGGCATTTTCATAATTTTCT
AGAACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTT
CATCCCTTTTCTAGTCTTTTTAAGTC
Found at i:3961 original size:29 final size:28
Alignment explanation
Indices: 3872--3960 Score: 133
Period size: 28 Copynumber: 3.1 Consensus size: 28
3862 TGAAATTCCC
* *
3872 TTTTCGTACTAAATGAGTCCGGGGTGAT
1 TTTTCATACTAAATGAGTCGGGGGTGAT
*
3900 TTTTCATACTAAATGACTCGGTGGGTGAT
1 TTTTCATACTAAATGAGTCGG-GGGTGAT
*
3929 TTTTCATACTAAATGAGTCGGGGGTGTT
1 TTTTCATACTAAATGAGTCGGGGGTGAT
3957 TTTT
1 TTTT
3961 TTCAAAATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
28 28 0.51
29 27 0.49
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (28 bp):
TTTTCATACTAAATGAGTCGGGGGTGAT
Found at i:9324 original size:13 final size:13
Alignment explanation
Indices: 9306--9331 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9296 CAATTTTTTG
9306 TGTATCGATACAT
1 TGTATCGATACAT
9319 TGTATCGATACAT
1 TGTATCGATACAT
9332 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10078 original size:21 final size:21
Alignment explanation
Indices: 10037--10078 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
10027 TCCCCTTTTA
* *
10037 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
10058 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
10079 ATCATATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:11905 original size:13 final size:13
Alignment explanation
Indices: 11887--11925 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
11877 ATAATCACCC
11887 TGTATCGATACAA
1 TGTATCGATACAA
11900 TGTATCGATACAA
1 TGTATCGATACAA
11913 TGTATCGATACAA
1 TGTATCGATACAA
11926 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:15885 original size:21 final size:21
Alignment explanation
Indices: 15838--15882 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
15828 AAGTTTTCAT
15838 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
15858 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
15880 TTT
1 TTT
15883 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:18084 original size:13 final size:13
Alignment explanation
Indices: 18066--18091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18056 CAATTTTTTG
18066 TGTATCGATACAT
1 TGTATCGATACAT
18079 TGTATCGATACAT
1 TGTATCGATACAT
18092 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19989 original size:76 final size:79
Alignment explanation
Indices: 19902--20103 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
19892 ACCCTAATGA
* * * * ***
19902 ACATATATTGACATGAAAGCTCCCACATGACCGT-A-GACTTGGTTTTAAGG-TAA-TATTACCT
1 ACATATTTTGACATGAAAGTTCTCACATGACCATAAGGACTCAATTTT-AGGATAAGTATTACCT
*
19963 AAATACCCTTAAAAG
65 AAATACCCCTAAAAG
* * *
19978 ACATATTTTGACAT-AAGAGTTCTCATATGATCATAAGGACTCAATTTTTGGATAAGTATTACCT
1 ACATATTTTGACATGAA-AGTTCTCACATGACCATAAGGACTCAATTTTAGGATAAGTATTACCT
*
20042 AAATACCCCTAATAG
65 AAATACCCCTAAAAG
*
20057 ACATATTTTGACATGAAAGTTCTCACATGATCC-TAAAGACTCAATTT
1 ACATATTTTGACATGAAAGTTCTCACATGA-CCATAAGGACTCAATTT
20104 GAGGTGATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
75 2 0.02
76 25 0.24
77 3 0.03
78 11 0.11
79 60 0.58
80 3 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (79 bp):
ACATATTTTGACATGAAAGTTCTCACATGACCATAAGGACTCAATTTTAGGATAAGTATTACCTA
AATACCCCTAAAAG
Found at i:20046 original size:79 final size:79
Alignment explanation
Indices: 19955--20103 Score: 237
Period size: 79 Copynumber: 1.9 Consensus size: 79
19945 TTTAAGGTAA
* * *
19955 TATTACCTAAATACCCTTAAAAGACATATTTTGACAT-AAGAGTTCTCATATGATCATAAGGACT
1 TATTACCTAAATACCCCTAAAAGACATATTTTGACATGAA-AGTTCTCACATGATCATAAAGACT
20019 CAATTTTTGGATAAG
65 CAATTTTTGGATAAG
* *
20034 TATTACCTAAATACCCCTAATAGACATATTTTGACATGAAAGTTCTCACATGATCCTAAAGACTC
1 TATTACCTAAATACCCCTAAAAGACATATTTTGACATGAAAGTTCTCACATGATCATAAAGACTC
20099 AATTT
66 AATTT
20104 GAGGTGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 62 0.97
80 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (79 bp):
TATTACCTAAATACCCCTAAAAGACATATTTTGACATGAAAGTTCTCACATGATCATAAAGACTC
AATTTTTGGATAAG
Found at i:22985 original size:102 final size:103
Alignment explanation
Indices: 22826--23072 Score: 243
Period size: 103 Copynumber: 2.4 Consensus size: 103
22816 AATTATTTCT
* * * ** **
22826 TTTAAATTCAAATAAATTA-AAAATTACATATTTAAATAGGGAAAGTTTATTTTTTTTAAAAT-C
1 TTTAAATTTAAATAAATTATAAAATTACATATTTAAACA-GAAAACATTATTAATTTTAAAATAC
* * *** *
22889 ATTTAATGTCTTGTAGGCTTTA-TTTCAAATATTTACAAA
65 A-TCAATATCACATAGACTTTATTTTCAAATATTTACAAA
*
22928 TTTAAATTTAAATAAATTATAAAATTATATATTTAAACA-AACAACATTATTAATTTTAAAATAC
1 TTTAAATTTAAATAAATTATAAAATTACATATTTAAACAGAA-AACATTATTAATTTTAAAATAC
* **
22992 ATCAATATCACATAGACTTTATTTTTAAATATTTATTAA
65 ATCAATATCACATAGACTTTATTTTCAAATATTTACAAA
* * *
23031 TTAAAATTTAAATAAAGTAATAAAATTACAT-TTTAAATAGAA
1 TTTAAATTTAAATAAA-TTATAAAATTACATATTTAAACAGAA
23073 TAAATTTGTT
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
101 1 0.01
102 48 0.41
103 55 0.47
104 14 0.12
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (103 bp):
TTTAAATTTAAATAAATTATAAAATTACATATTTAAACAGAAAACATTATTAATTTTAAAATACA
TCAATATCACATAGACTTTATTTTCAAATATTTACAAA
Done.