Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002359.1 Hibiscus syriacus cultivar Beakdansim tig00004814_pilon, 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: 83060
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1582 original size:19 final size:19
Alignment explanation
Indices: 1558--1606 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1548 AATGTAGGGT
1558 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1577 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1596 TAATTTTGTAT
1 TAATTTTGTAT
1607 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2851 original size:200 final size:200
Alignment explanation
Indices: 1836--3204 Score: 2254
Period size: 200 Copynumber: 6.9 Consensus size: 200
1826 AATTTACAAT
*
1836 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAA-ATGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
1900 C-AAACCCATAAGTATAATGT-A-AGGTAATTTTTCAATATAACC-GTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
1961 ATGAGAGAATAGGTGCAATATATGTATCGATACTTTTTAATTTTGTGTCGATACTATTAGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2026 AATGA
196 AATGA
*
2031 ATGGCAAACAGGGTGC-ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
2095 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTAATCTAACCGGTAT-AGTATACCGTTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* *
2159 A-GA-AGATTAGGTAT-ATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
131 ATGAGAGAATAGGTGTAAT-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
2221 GAATG-
195 GAATGA
*
2226 ATGGCAAACAGGGTGCAACCATAAAGTTTCGATCCATATATAAAAGGTGTCGAT-CCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
2290 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC-GTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * * *
2354 ATGAGAGATTAGGTAT-ATATATATATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2418 AATGA
196 AATGA
* * *
2423 ATGCCAAACAGGGTGCAACCATAAAGTGTTGATCCATATATAAAATGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
2488 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC-GTATAAGTA-ACCAGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
2551 AT--GAGATTAGGTAT-ATAATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCCA
131 ATGAGAGAATAGGTGTAAT-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
2613 GAATGA
195 GAATGA
*
2619 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
2684 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGATTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
** *
2749 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGAATCGATACTATTGGTCCAA
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2814 AATGA
196 AATGA
* *
2819 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTTGATCCCAGAAATAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
2884 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* ** *
2949 ATGAGAGAATAGGTGTAATATATGTATCGACACATTTTAATTTTGAATCGATACTATTGGTCCAA
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
3014 AATGA
196 AATGA
* *
3019 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTATCGATCCCAGAAACTT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
3084 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
3149 ATGAGATAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
3205 ATTTAAATAT
Statistics
Matches: 1106, Mismatches: 50, Indels: 31
0.93 0.04 0.03
Matches are distributed among these distances:
194 32 0.03
195 135 0.12
196 314 0.28
197 85 0.08
198 106 0.10
199 4 0.00
200 428 0.39
201 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:6319 original size:184 final size:184
Alignment explanation
Indices: 6045--6542 Score: 881
Period size: 184 Copynumber: 2.7 Consensus size: 184
6035 TAACGACCTC
* *
6045 AAAAGCATCAGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATA
1 AAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATA
*
6110 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCAACACTTTTTAATATTGTGTCGCTACTTT
66 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGCTACTTT
6175 ATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGA
131 ATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGA
*
6229 AAAAACATCGGAACCCATAATTATAATGTAATAAGTAATTTTGTAATATAACCGGTATAGATATA
1 AAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATA
* * * *
6294 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGATACTTTTTGATATTGTGTTGCAACTTT
66 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGCTACTTT
* *
6359 ATGTTCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAAAAGTGTTGATTGA
131 ATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGA
*
6413 AAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATA
1 AAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATA
6478 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTC-CATACTT
66 CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGC-TACTT
6542 T
130 T
6543 TAAGTAACGC
Statistics
Matches: 297, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 1 0.00
184 296 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (184 bp):
AAAAACATCGGAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATAGATATA
CCGGTTTTATGAGAGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGCTACTTT
ATGTCCAGAATGGATGAAAAAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGA
Found at i:9554 original size:23 final size:23
Alignment explanation
Indices: 9523--9595 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
9513 ATAGATAAAA
*
9523 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
9546 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
9569 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
9592 ATAT
1 ATAT
9596 TGTAAATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:10544 original size:85 final size:87
Alignment explanation
Indices: 10451--10611 Score: 281
Period size: 85 Copynumber: 1.9 Consensus size: 87
10441 AAAATAGGTC
10451 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGAT-A-ATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
10514 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
** *
10536 ATATAAGCGCTATGTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
10601 CCGGTTAAATA
66 CCGGTTAAATA
10612 ATACATAACC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
85 55 0.77
86 1 0.01
87 15 0.21
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:38433 original size:59 final size:58
Alignment explanation
Indices: 38311--38445 Score: 146
Period size: 59 Copynumber: 2.3 Consensus size: 58
38301 AACATAATGA
* * *
38311 ATAGTCGGGTGACCATTTTATAACTTTTAATAGTCAAATGACTCTACAAAATAACATCCT
1 ATAGT-GGG-GACCATTTTATAACTTTTAATAATCAAATGACTCAACAAAATAACATACT
* * * * * *
38371 ATAGTTGAGGGACCATTTTTTAAC-TTTAATAATCGAATGACTCAACAAAGTGATATATT
1 ATAG-TG-GGGACCATTTTATAACTTTTAATAATCAAATGACTCAACAAAATAACATACT
38430 ATAGTGGGGACCATTT
1 ATAGTGGGGACCATTT
38446 GTGTACTTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
57 10 0.16
58 2 0.03
59 31 0.48
60 18 0.28
61 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (58 bp):
ATAGTGGGGACCATTTTATAACTTTTAATAATCAAATGACTCAACAAAATAACATACT
Found at i:40964 original size:34 final size:35
Alignment explanation
Indices: 40899--40968 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
40889 GTTAAAAACT
* * * * *
40899 ATATTAATATATTAAATTAAAAGCAGGGCCCATAA
1 ATATTAATAAACTAAATAAAAAACAGAGCCCATAA
40934 ATATTAATAAACTAAATAAAAAACA-AGCCCATAA
1 ATATTAATAAACTAAATAAAAAACAGAGCCCATAA
40968 A
1 A
40969 CTTATTTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.24
Consensus pattern (35 bp):
ATATTAATAAACTAAATAAAAAACAGAGCCCATAA
Found at i:42276 original size:229 final size:229
Alignment explanation
Indices: 41871--42358 Score: 888
Period size: 229 Copynumber: 2.1 Consensus size: 229
41861 GTAAATTATC
* * *
41871 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
41936 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
42001 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
42066 -AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAAACATAAATTACATAACTTTCAAAAAAGTATA
*
42099 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
42164 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
42229 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
42294 GAAAACATAAATTACATAACTTTCAAAAAAGTATA
195 GAAAACATAAATTACATAACTTTCAAAAAAGTATA
42329 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
42359 AAAAGTAGGT
Statistics
Matches: 250, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
228 36 0.14
229 151 0.60
230 63 0.25
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (229 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:42658 original size:20 final size:19
Alignment explanation
Indices: 42635--42681 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
42625 CGATATACCA
42635 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
42655 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
42675 GGTAAAA
1 GGTAAAA
42682 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:42721 original size:181 final size:182
Alignment explanation
Indices: 42424--42844 Score: 596
Period size: 181 Copynumber: 2.3 Consensus size: 182
42414 GATCCAAATT
* * * *
42424 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGA-CAAACCGGTATAGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-AAAAATGATA
* * * *
42488 AAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
65 AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
42553 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTT-TA
130 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAA
*
42605 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAA-AAAATGATA
* * *
42670 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** * *
42734 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTTGATACTTTAAA
130 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAA
* * *
42787 AAAATATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTAAAA
1 AAAA-ATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAA
42845 TGATACCGGA
Statistics
Matches: 213, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
181 103 0.48
182 63 0.30
183 47 0.22
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAAATGATAA
AACCGGTAAAACGCTACCGGATACATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAA
Found at i:45094 original size:21 final size:21
Alignment explanation
Indices: 45067--45131 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
45057 AAGACAATAA
*
45067 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
45088 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
45109 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
45130 AG
1 AG
45132 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:45207 original size:33 final size:33
Alignment explanation
Indices: 45165--45230 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
45155 AAATAGATGG
*
45165 AGTGGTGAAAGAAGTACAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTACAGGTGTTAAGGGGTGA
***
45198 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTACAGGTGTTAAGGGGTGA
45231 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTACAGGTGTTAAGGGGTGA
Found at i:47055 original size:18 final size:19
Alignment explanation
Indices: 47011--47058 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
47001 AATGTAGGGT
47011 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
47030 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
47049 T-ATTTTGTAT
1 TAATTTTGTAT
47059 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:47670 original size:198 final size:199
Alignment explanation
Indices: 47177--47945 Score: 1432
Period size: 199 Copynumber: 3.9 Consensus size: 199
47167 CAATATGGCC
* * *
47177 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
* *
47242 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
47307 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
*
47372 TAGAA
195 TGGAA
*
47377 AACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
47442 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
47507 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
47571 GGAA
196 GGAA
47575 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
47640 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
47705 AATATGTCTAAATAATGTGTTGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
47770 GGAA
196 GGAA
*
47774 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCAAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
47839 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAT
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
47904 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTC
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTC
47946 TTCACATTCC
Statistics
Matches: 556, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
198 195 0.35
199 303 0.54
200 58 0.10
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAA
Found at i:47911 original size:397 final size:398
Alignment explanation
Indices: 47177--47945 Score: 1441
Period size: 397 Copynumber: 1.9 Consensus size: 398
47167 CAATATGGCC
47177 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
*
47242 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
47307 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
47372 TAGAAAACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
196 TAGAAAACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
*
47437 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
261 AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
47502 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
326 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
47567 GAATGGAA
391 GAATGGAA
* * *
47575 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
*
47639 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
47704 GAATATGTCTAAATAATGTGTTGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
* *
47769 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
196 TAGAAAACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
47834 AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
261 AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
*
47899 GAGATAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTC
326 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTC
47946 TTCACATTCC
Statistics
Matches: 361, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
397 302 0.84
398 59 0.16
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
TAGAAAACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
AAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
GAATGGAA
Found at i:48373 original size:25 final size:25
Alignment explanation
Indices: 48345--48409 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
48335 TTATCATTAA
48345 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
48370 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
48395 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
48410 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:48785 original size:23 final size:23
Alignment explanation
Indices: 48754--48826 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
48744 ATAGGTAAAC
*
48754 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
48777 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
48800 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
48823 ATAT
1 ATAT
48827 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:49258 original size:24 final size:25
Alignment explanation
Indices: 49231--49285 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
49221 TTTCAAATTC
*
49231 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
49255 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
49279 ATTTCAA
1 ATTTCAA
49286 TATATATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:49271 original size:18 final size:18
Alignment explanation
Indices: 49250--49286 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49240 GTAATTGGAG
49250 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
49268 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
49286 T
1 T
49287 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:49587 original size:39 final size:39
Alignment explanation
Indices: 49544--49630 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
49534 TTCCGAGCTC
*
49544 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
49583 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
49622 ATCAAAATC
1 ATCAAAATC
49631 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:50078 original size:23 final size:23
Alignment explanation
Indices: 50047--50119 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
50037 ATAGGTAAAC
*
50047 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
50070 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
50093 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
50116 ATAT
1 ATAT
50120 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:50147 original size:20 final size:20
Alignment explanation
Indices: 50122--50160 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50112 GGTTATATTG
* *
50122 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
50142 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
50161 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:50506 original size:23 final size:23
Alignment explanation
Indices: 50475--50547 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
50465 ATAGGTAAAA
*
50475 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
50498 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
50521 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
50544 ATAT
1 ATAT
50548 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:50752 original size:30 final size:29
Alignment explanation
Indices: 50693--50759 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
50683 GTTACGATAT
* *
50693 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
50723 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
50753 ATTTTTT
1 ATATTTT
50760 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:50797 original size:430 final size:430
Alignment explanation
Indices: 49860--51319 Score: 2645
Period size: 430 Copynumber: 3.4 Consensus size: 430
49850 TTTAAATTAT
* *
49860 AATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTA
1 AATAATATTTTATAAAATATCAAAA-AATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTA
* *
49925 ATATTGTAGGTGGAAAATATGAAACACTGTT-AAAAAAATTGAAACATAAATTACATAACTTTTA
65 ATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAAC-TTTA
* * *
49989 AAAAAAATATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGAT
129 AAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGAT
*
50054 GTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAATAGGTAGTGGTTATA
194 GTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATA
50119 TTGTAAAGTGTCTATCCTTTTTAT-AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTT
259 TTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTT
50183 AAGGTTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATT
324 AAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATT
50247 TTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
389 TTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
*
50289 AATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
1 AATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
50354 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
66 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
* *
50419 AGAAGTATCGATCCTTTTTATAAGAAGTATGGACATTTTCAATATAATAGGTAAAAATATGATGT
131 AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
50484 AATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATT
196 AATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATT
50549 GTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
261 GTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
50614 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
326 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
*
50679 TTATGTTACGATATATATTATTATTAAATTAAAAATTCTA
391 TTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
50719 AATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
1 AATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
* *
50784 TATTATAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTACA
66 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
*
50849 AGAAGTATCGATACTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
131 AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
*
50914 AATAAGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATT
196 AATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATT
50979 GTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
261 GTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
*
51044 GGTTATCTTTTGAGTAAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
326 GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
51109 TTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
391 TTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
*
51149 AATAATATTTTATAAAATATC---AAAT---AT--TTTTTTGTGCAAATGAAATTAATAAATTAA
1 AATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
51206 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
66 TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
* *
51271 ATAAGTATCGATCCTTTTTATAAAAAGTATTGACACTTTCAATATAATA
131 AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
51320 TAATGTAATA
Statistics
Matches: 1001, Mismatches: 27, Indels: 13
0.96 0.03 0.01
Matches are distributed among these distances:
422 138 0.14
424 2 0.00
427 4 0.00
428 219 0.22
429 100 0.10
430 538 0.54
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (430 bp):
AATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAA
TATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAA
AGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGT
AATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATT
GTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAA
GGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTT
TTACGTTACGATATATATTATTATTAAATTAAAAATTCTA
Found at i:50931 original size:23 final size:23
Alignment explanation
Indices: 50905--50977 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
50895 ATAGGTAAAA
* *
50905 ATATGATGTAATAAGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
50928 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
50951 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
50974 ATAT
1 ATAT
50978 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:52008 original size:2 final size:2
Alignment explanation
Indices: 52001--52060 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
51991 AATAATCATT
52001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52043 TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
52061 TCCATTTTAG
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52736 original size:32 final size:32
Alignment explanation
Indices: 52695--52758 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
52685 GCACCGAAAG
*
52695 TTTCTTTGGCCATTTGTTGGCTGGCTTTTCAA
1 TTTCTTTGGCCATTTGTTGGCTAGCTTTTCAA
*
52727 TTTCTTTGGCCATTTGTTGGTTAGCTTTTCAA
1 TTTCTTTGGCCATTTGTTGGCTAGCTTTTCAA
52759 CAATCTCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.52
Consensus pattern (32 bp):
TTTCTTTGGCCATTTGTTGGCTAGCTTTTCAA
Found at i:56265 original size:32 final size:32
Alignment explanation
Indices: 56224--56287 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
56214 GCACCGAAAG
*
56224 TTTCTTTGGCCATTTGTTGGTTGGCTTTTCAA
1 TTTCTTTGGCCATTTGTTGGTTAGCTTTTCAA
56256 TTTCTTTGGCCATTTGTTGGTTAGCTTTTCAA
1 TTTCTTTGGCCATTTGTTGGTTAGCTTTTCAA
56288 CAATCTCACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.53
Consensus pattern (32 bp):
TTTCTTTGGCCATTTGTTGGTTAGCTTTTCAA
Found at i:60805 original size:158 final size:158
Alignment explanation
Indices: 60512--60814 Score: 570
Period size: 158 Copynumber: 1.9 Consensus size: 158
60502 AAAGAGACAA
60512 AAAACTTACGTGAAAAATCCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTAGAAGAATTT
1 AAAACTTACGTGAAAAATCCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTAGAAGAATTT
60577 CACTATGAGAAAATAGGAATTACAACCTCTCTCGATCTACCAAAGAGAAAACAATGATAATTCTA
66 CACTATGAGAAAATAGGAATTACAACCTCTCTCGATCTACCAAAGAGAAAACAATGATAATTCTA
60642 TCTTGATAAAAAAAAAACAACTCTCAAG
131 TCTTGATAAAAAAAAAACAACTCTCAAG
* *
60670 AAAATTTACGTGGAAAATCCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTAGAAGAATTT
1 AAAACTTACGTGAAAAATCCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTAGAAGAATTT
* *
60735 CACTATGAGAAAATAGGAATTACAACCTCTCTCGATCTACCAAGGAGAAAACAATGATAATTCTC
66 CACTATGAGAAAATAGGAATTACAACCTCTCTCGATCTACCAAAGAGAAAACAATGATAATTCTA
60800 TCTTGATAAAAAAAA
131 TCTTGATAAAAAAAA
60815 GGAGACAAAC
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 141 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (158 bp):
AAAACTTACGTGAAAAATCCCTAAATAATATAGGGTAAAAACCACGGGCAACGGTAGAAGAATTT
CACTATGAGAAAATAGGAATTACAACCTCTCTCGATCTACCAAAGAGAAAACAATGATAATTCTA
TCTTGATAAAAAAAAAACAACTCTCAAG
Found at i:66469 original size:20 final size:20
Alignment explanation
Indices: 66440--66477 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
66430 TTTCAAAGTG
66440 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
66460 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
66478 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:66546 original size:45 final size:46
Alignment explanation
Indices: 66497--66587 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
66487 AAACATCGAA
* * * *
66497 TGCATTTTATGCATCGATGCAC-ATACCATGCATCTATTCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
66542 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
66588 GTTTTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:72238 original size:20 final size:22
Alignment explanation
Indices: 72213--72265 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
72203 GTGTGCTTCA
72213 TGCATCGATACA-C-TTAACAG
1 TGCATCGATACATCTTTAACAG
*
72233 TGCATCGATGCATTCCTTTAACAG
1 TGCATCGATACA-T-CTTTAACAG
72257 TGCATCGAT
1 TGCATCGAT
72266 GCATTCCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 11 0.39
23 1 0.04
24 16 0.57
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (22 bp):
TGCATCGATACATCTTTAACAG
Found at i:72325 original size:24 final size:24
Alignment explanation
Indices: 72232--72360 Score: 135
Period size: 24 Copynumber: 5.5 Consensus size: 24
72222 ACACTTAACA
*
72232 GTGCATCGATGCATTCCTTT-AACA
1 GTGCATCGATGCATTCCTTTGAA-T
72256 GTGCATCGATGCATTCCTTTGAAT
1 GTGCATCGATGCATTCCTTTGAAT
*
72280 GTGCATCAATGCATTCCTTTGAAT
1 GTGCATCGATGCATTCCTTTGAAT
* *
72304 GTGCATCGATTCA-TCATGTTG-A-
1 GTGCATCGATGCATTCCT-TTGAAT
* **
72326 -TGCACCGATGCACGCC-TTGAAT
1 GTGCATCGATGCATTCCTTTGAAT
72348 GTGCATCGATGCA
1 GTGCATCGATGCA
72361 CGGGGTCATG
Statistics
Matches: 89, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.03
21 11 0.12
22 1 0.01
23 15 0.17
24 57 0.64
25 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATTCCTTTGAAT
Found at i:75152 original size:45 final size:46
Alignment explanation
Indices: 75103--75193 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
75093 AAACATCAAA
* * *
75103 TGCATTTTATGCATCGATGCACATG-CCTTGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
75148 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
75194 GTTTTTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 23 0.55
46 19 0.45
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:80087 original size:43 final size:43
Alignment explanation
Indices: 80040--80166 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 43
80030 AGAAGTAGCA
*
80040 TCATCCTTAAATAACCAGACGTCCTCATCATGAAGGAACAATG
1 TCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACAATG
*** * **
80083 TCATCCACCGATCAA--A-AC-TCCTCATCACGAA-GAAGCAACA
1 TCATCCTTAGAT-AACCAGACGTCCTCATCATGAAGGAA-CAATG
* * *
80123 TCATCATTAGATAACCAGATGTCCTCATCATGAAGGAACCATG
1 TCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACAATG
80166 T
1 T
80167 TATTTTAAAT
Statistics
Matches: 61, Mismatches: 16, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
39 5 0.08
40 23 0.38
41 3 0.05
42 2 0.03
43 23 0.38
44 5 0.08
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (43 bp):
TCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACAATG
Found at i:80117 original size:86 final size:83
Alignment explanation
Indices: 79972--80166 Score: 255
Period size: 86 Copynumber: 2.3 Consensus size: 83
79962 AGATGGCCAA
** * * * *
79972 ACGTCCTCATCACAAAGGAACAATGACATCCACTAATTAGAACTCCTCATCACGAAGAAGAAGTA
1 ACGTCCTCATCATGAAGGAACAATGTCATCCACCAATCAAAACTCCTCATCACGAAGAAGAA--A
*
80037 GCATCATCCTTAAATAACCAG
64 -CATCATCATTAAATAACCAG
* *
80058 ACGTCCTCATCATGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACGAAGAAGCAACA
1 ACGTCCTCATCATGAAGGAACAATGTCATCCACCAATCAAAACTCCTCATCACGAAGAAGAAACA
*
80123 TCATCATTAGATAACCAG
66 TCATCATTAAATAACCAG
* *
80141 ATGTCCTCATCATGAAGGAACCATGT
1 ACGTCCTCATCATGAAGGAACAATGT
80167 TATTTTAAAT
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
83 42 0.43
84 1 0.01
86 54 0.56
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (83 bp):
ACGTCCTCATCATGAAGGAACAATGTCATCCACCAATCAAAACTCCTCATCACGAAGAAGAAACA
TCATCATTAAATAACCAG
Found at i:80398 original size:136 final size:136
Alignment explanation
Indices: 80056--80495 Score: 648
Period size: 137 Copynumber: 3.2 Consensus size: 136
80046 TTAAATAACC
* *
80056 AGACGTCCTCATCATGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACGAAGAAGCAA
1 AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGAAGCAA
* * * *
80121 CATCATCATTAGATAACCAGATGTCCTCATCATGAAGGAACCATGTTATTTTAAATATCTTTAAA
66 CATCATCATTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTA-TCTCAATATCTTTAAA
80186 GATGGCT
130 GATGGCT
* * * *
80193 AAACGTCCTCATCATGAAGGAATAATGTCATCCACCGATCAGAACTCCTCATCACGAAGAAGCAT
1 AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGAAGCAA
* *
80258 CATCATCATTAGATAACTAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAATATCTTTAAAG
66 CATCATCATTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAATATCTTTAAAG
80323 ATGGCT
131 ATGGCT
** * * ** *
80329 AGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATTAGAATTCCTCATCATAAAGGAGCAA
1 AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGAAGCAA
* * *
80394 CATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTTAAA
66 CATCATCATTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTC-AATATCTTTAAA
80459 GATGGCT
130 GATGGCT
*
80466 AGACGTCCTCATAAC-AAGGAACAATGTCAT
1 AGACGTCCTCATCACGAAGGAACAATGTCAT
80496 ACACTAGTTT
Statistics
Matches: 275, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
136 137 0.50
137 138 0.50
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (136 bp):
AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGAAGCAA
CATCATCATTAGATAACCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAATATCTTTAAAG
ATGGCT
Found at i:80432 original size:43 final size:41
Alignment explanation
Indices: 80333--80434 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 41
80323 ATGGCTAGAC
**
80333 GTCCTCATCACGAAGGAACAATGTCATCCATTGATTAGAAT
1 GTCCTCATCACGAAGGAACAACATCATCCATTGATTAGAAT
** *
80374 -TCCTCATCATAAAGGAGCAACATCATCC-TTAGA-TAGCCAGAT
1 GTCCTCATCACGAAGGAACAACATCATCCATT-GATTAG--A-AT
80416 GTCCTCATCACGAAGGAAC
1 GTCCTCATCACGAAGGAAC
80435 CGAGTTATCT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
39 5 0.10
40 25 0.52
41 1 0.02
42 2 0.04
43 15 0.31
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
GTCCTCATCACGAAGGAACAACATCATCCATTGATTAGAAT
Found at i:80689 original size:20 final size:21
Alignment explanation
Indices: 80655--80694 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
80645 TTATTTTTTC
**
80655 TATTATTATTTATA-TATTAT
1 TATTATTATAAATATTATTAT
80675 TATTATTATAAATATTATTA
1 TATTATTATAAATATTATTA
80695 ATAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTATAAATATTATTAT
Found at i:80721 original size:19 final size:19
Alignment explanation
Indices: 80668--80713 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
80658 TATTATTTAT
* *
80668 ATATTATT-ATTATTATAA
1 ATATTATTAATAAATATAA
80686 ATATTATTAATAAATATAA
1 ATATTATTAATAAATATAA
*
80705 ATTTTATTA
1 ATATTATTA
80714 GTAGATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTATTAATAAATATAA
Found at i:80825 original size:17 final size:18
Alignment explanation
Indices: 80785--80827 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
80775 AAAATGATCC
*
80785 AGGCCCAAATAACCCAGT
1 AGGCCCAAATAACCCAGA
*
80803 AGGCCCAAATAA-CCTGA
1 AGGCCCAAATAACCCAGA
80820 AGGCCCAA
1 AGGCCCAA
80828 CAAGACCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.40, C:0.33, G:0.19, T:0.09
Consensus pattern (18 bp):
AGGCCCAAATAACCCAGA
Found at i:82089 original size:2 final size:2
Alignment explanation
Indices: 82078--82110 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
82068 ACACATTAAG
82078 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82111 GAAAAATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.