Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007369.1 Hibiscus syriacus cultivar Beakdansim tig00019763_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: 139234
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:30383 original size:12 final size:12
Alignment explanation
Indices: 30354--30387 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30344 CTCCTACGAT
*
30354 ACAACAATCAATC
1 ACAACAAT-AAGC
30367 ACAACAATAAGC
1 ACAACAATAAGC
30379 ACAACAATA
1 ACAACAATA
30388 GTGATCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.12
Consensus pattern (12 bp):
ACAACAATAAGC
Found at i:30906 original size:20 final size:20
Alignment explanation
Indices: 30859--30916 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
30849 AAATAACTAA
30859 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
30879 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
30899 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
30917 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:32798 original size:24 final size:24
Alignment explanation
Indices: 32788--32899 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
32778 CATAATTCAC
* * *
32788 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
32812 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
32836 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
32860 ATC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
32884 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
32900 TAAATCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:35488 original size:18 final size:18
Alignment explanation
Indices: 35465--35522 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
35455 TCGGGTCAAT
35465 GGGTCGGGTAAACAGGTC
1 GGGTCGGGTAAACAGGTC
*
35483 GGGTCGGGT---CA--AC
1 GGGTCGGGTAAACAGGTC
*
35496 GGGTCGGGTAAACGGGTC
1 GGGTCGGGTAAACAGGTC
35514 GGGTCGGGT
1 GGGTCGGGT
35523 CATGACCGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
13 10 0.31
15 2 0.06
16 1 0.03
18 19 0.59
ACGTcount: A:0.16, C:0.17, G:0.50, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTAAACAGGTC
Found at i:35488 original size:31 final size:31
Alignment explanation
Indices: 35453--35524 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
35443 CGGGTCAACT
*
35453 GGTCGGGTCAATGGGTCGGGTAAACAGGTCG
1 GGTCGGGTCAACGGGTCGGGTAAACAGGTCG
*
35484 GGTCGGGTCAACGGGTCGGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCGGGTAAACAGGTCG
35515 GGTCGGGTCA
1 GGTCGGGTCA
35525 TGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.17, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCGGGTCAACGGGTCGGGTAAACAGGTCG
Found at i:35498 original size:13 final size:13
Alignment explanation
Indices: 35443--35518 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
35433 AACGGGTTAA
*
35443 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
35456 CGGGTCAATGGGT
1 CGGGTCAACGGGT
*
35469 CGGGTAAACAGGTCGGGT
1 CGGGT---CA--ACGGGT
35487 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
35500 CGGGTAAACGGGT
1 CGGGTCAACGGGT
35513 CGGGTC
1 CGGGTC
35519 GGGTCATGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
13 38 0.75
15 2 0.04
16 2 0.04
18 9 0.18
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:35511 original size:26 final size:26
Alignment explanation
Indices: 35443--35518 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 26
35433 AACGGGTTAA
* * *
35443 CGGGTCAACTGGTCGGGTCAATGGGT
1 CGGGTAAACGGGTCGGGTCAACGGGT
35469 CGGGTAAACAGGTCGGGTCGGGTCAACGGGT
1 CGGGT-AA-A---CGGGTCGGGTCAACGGGT
35500 CGGGTAAACGGGTCGGGTC
1 CGGGTAAACGGGTCGGGTC
35519 GGGTCATGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
26 16 0.38
27 1 0.02
28 1 0.02
29 1 0.02
30 2 0.05
31 21 0.50
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (26 bp):
CGGGTAAACGGGTCGGGTCAACGGGT
Found at i:37597 original size:24 final size:24
Alignment explanation
Indices: 37587--37701 Score: 178
Period size: 24 Copynumber: 4.8 Consensus size: 24
37577 CATAATTCAC
* * *
37587 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
37611 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
37635 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
37659 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
37683 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
37702 ATCAAATCGA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:37718 original size:48 final size:48
Alignment explanation
Indices: 37563--37718 Score: 138
Period size: 48 Copynumber: 3.2 Consensus size: 48
37553 AAACGGATAT
* * * * * * * *
37563 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
37611 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
37659 GTCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
37707 ATC-GAAAATCAG
1 ATCAG-AAATCAG
37719 GTAAAATATT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 85 0.93
49 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:37718 original size:72 final size:71
Alignment explanation
Indices: 37567--37718 Score: 173
Period size: 72 Copynumber: 2.1 Consensus size: 71
37557 GGATATATCA
* * * *
37567 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
*
37632 CAAGTC
66 CAAATC
* * * *
37638 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGGTCAAGTATCAGATCAG-A
37702 AT-CAAATC
63 ATCCAAATC
37710 GAAAATCAG
1 -AAAATCAG
37719 GTAAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 58 0.87
73 5 0.07
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATC
CAAATC
Found at i:40192 original size:13 final size:13
Alignment explanation
Indices: 40174--40236 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
40164 CGCCGGTCAA
40174 CGGGTCAACGGGT
1 CGGGTCAACGGGT
40187 CGGGTCAACAGGTCGGGT
1 CGGGTC-A-A---CGGGT
40205 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
40218 CGGGTAAACGGGT
1 CGGGTCAACGGGT
40231 CGGGTC
1 CGGGTC
40237 GGGTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.26
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:40205 original size:18 final size:18
Alignment explanation
Indices: 40182--40222 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
40172 AACGGGTCAA
40182 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
40200 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
40218 CGGGT
1 CGGGT
40223 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:40209 original size:31 final size:31
Alignment explanation
Indices: 40174--40242 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
40164 CGCCGGTCAA
*
40174 CGGGTCAACGGGTCGGGTCAACAGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
*
40205 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
40236 CGGGTCA
1 CGGGTCA
40243 TGACCGGTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
Found at i:46212 original size:33 final size:33
Alignment explanation
Indices: 46175--46253 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
46165 AGTTGGCAAG
46175 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
46208 TTGGAAATTTCATCTTGGTTGGTGGCCAATTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
46241 TTGGGAATTTCAT
1 TTGGAAATTTCAT
46254 ATTTGGTGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:46262 original size:30 final size:32
Alignment explanation
Indices: 46175--46269 Score: 113
Period size: 33 Copynumber: 3.0 Consensus size: 32
46165 AGTTGGCAAG
*
46175 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
46208 TTGGAAATTTCATCTTGGTTGGTGGCCAATTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
46241 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
46270 GTACACATCG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
30 12 0.21
32 1 0.02
33 44 0.77
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:58204 original size:29 final size:29
Alignment explanation
Indices: 58169--58250 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
58159 AAACTAAATT
*
58169 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
58198 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
58227 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
58251 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:59562 original size:15 final size:15
Alignment explanation
Indices: 59539--59568 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
59529 ACGAGGCTGG
59539 AATTACAACAATAAC
1 AATTACAACAATAAC
*
59554 AATTCCAACAATAAC
1 AATTACAACAATAAC
59569 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:62968 original size:29 final size:29
Alignment explanation
Indices: 62933--63014 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
62923 AAACTAAATT
*
62933 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
62962 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
62991 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
63015 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:71119 original size:29 final size:29
Alignment explanation
Indices: 71077--71135 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
71067 ATTTTCACCT
*
71077 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGAAATCAA
71106 AACTAAATTGATGTAAGCAATGAAATCAA
1 AACTAAATTGATGTAAGCAATGAAATCAA
71135 A
1 A
71136 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGAAATCAA
Found at i:78324 original size:38 final size:32
Alignment explanation
Indices: 78242--78307 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
78232 AGTTGGCAAG
78242 TTTA-AAATTTCATCTTGGTTGGTGGCCAACT
1 TTTAGAAATTTCATCTTGGTTGGTGGCCAACT
78273 TTTAGAAATTTCATCTTGGTTGGTGGCCAAACT
1 TTTAGAAATTTCATCTTGGTTGGTGGCC-AACT
78306 TT
1 TT
78308 GAATATGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 4 0.12
32 23 0.70
33 6 0.18
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (32 bp):
TTTAGAAATTTCATCTTGGTTGGTGGCCAACT
Found at i:81597 original size:18 final size:17
Alignment explanation
Indices: 81576--81613 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
81566 TATGTCCCAT
81576 AGGACCACTACGTCCCGA
1 AGGA-CACTACGTCCCGA
81594 AGG--ACTACGTCCCGA
1 AGGACACTACGTCCCGA
81609 AGGAC
1 AGGAC
81614 TACAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
15 15 0.83
18 3 0.17
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (17 bp):
AGGACACTACGTCCCGA
Found at i:81602 original size:15 final size:15
Alignment explanation
Indices: 81582--81616 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
81572 CCATAGGACC
81582 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
81597 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
81612 ACTAC
1 ACTAC
81617 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:88502 original size:15 final size:15
Alignment explanation
Indices: 88479--88512 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
88469 CCGTAGGACC
* *
88479 ACTAGGTCCCGAAGT
1 ACTAAGTCCCGAAGG
88494 ACTAAGTCCCGAAGG
1 ACTAAGTCCCGAAGG
88509 ACTA
1 ACTA
88513 CAATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (15 bp):
ACTAAGTCCCGAAGG
Found at i:94620 original size:24 final size:24
Alignment explanation
Indices: 94588--94635 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
94578 GAAGGATAGT
94588 AGACGTTGAAGGAGAAGTTACTTG
1 AGACGTTGAAGGAGAAGTTACTTG
*
94612 AGACTTTGAAGGAGAAGTTACTTG
1 AGACGTTGAAGGAGAAGTTACTTG
94636 GGTGGCTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.27
Consensus pattern (24 bp):
AGACGTTGAAGGAGAAGTTACTTG
Found at i:119736 original size:13 final size:13
Alignment explanation
Indices: 119718--119747 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
119708 AAAATCGTGC
119718 AAAGGAAAGGAAG
1 AAAGGAAAGGAAG
119731 AAAGGAAAGGAAG
1 AAAGGAAAGGAAG
119744 AAAG
1 AAAG
119748 AGAGATTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
AAAGGAAAGGAAG
Found at i:123475 original size:2 final size:2
Alignment explanation
Indices: 123468--123501 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
123458 TTTCCAATAA
123468 AT AT AT 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
123502 CCCTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123782 original size:6 final size:6
Alignment explanation
Indices: 123762--123841 Score: 58
Period size: 6 Copynumber: 13.2 Consensus size: 6
123752 AATATAGCAA
* * *
123762 AAAAAG AGAAAG AAAATG AAAAAG AAAAAG AAAAA- ATAGAAAG AGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A-A-AAAG AAAAAG
* *
123811 AAAAAA AAAGAAG CAAAAA- ATAAA- AAAAAG A
1 AAAAAG AAA-AAG -AAAAAG AAAAAG AAAAAG A
123842 GAGAAAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 9 0.16
6 38 0.66
7 7 0.12
8 4 0.07
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:123783 original size:20 final size:18
Alignment explanation
Indices: 123760--123843 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 18
123750 AAAATATAGC
123760 AAAAAAAGAGAAAGAAAA
1 AAAAAAAGAGAAAGAAAA
** *
123778 TGAAAAAGAAAAAGAAAA
1 AAAAAAAGAGAAAGAAAA
*
123796 AATAGAAAGAGAAAGAAAA
1 AA-AAAAAGAGAAAGAAAA
*
123815 AAAAAGAAGCA-AAA-AATA
1 AAAAA-AAG-AGAAAGAAAA
123833 AAAAAAAGAGA
1 AAAAAAAGAGA
123844 GAAAATAAGG
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
16 1 0.02
17 4 0.08
18 25 0.47
19 22 0.42
20 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.04
Consensus pattern (18 bp):
AAAAAAAGAGAAAGAAAA
Found at i:123796 original size:31 final size:33
Alignment explanation
Indices: 123739--123830 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 33
123729 GATAATACAG
* * *
123739 AGAGAAAGAAGAAAATA-TAGCAAAAAAAGAGAA
1 AGAGAAAGAAAAAAAAAGAAGC-AAAAAAGAGAA
* *
123772 AGA-AAATGAAAAAGAAA-AAG-AAAAAATAGAA
1 AGAGAAA-GAAAAAAAAAGAAGCAAAAAAGAGAA
123803 AGAGAAAGAAAAAAAAAGAAGCAAAAAA
1 AGAGAAAGAAAAAAAAAGAAGCAAAAAA
123831 TAAAAAAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
31 22 0.45
32 9 0.18
33 18 0.37
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.04
Consensus pattern (33 bp):
AGAGAAAGAAAAAAAAAGAAGCAAAAAAGAGAA
Found at i:123809 original size:33 final size:33
Alignment explanation
Indices: 123757--123832 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
123747 AAGAAAATAT
*
123757 AGCAAAAAA-AGAGAAAGAAAATGAAAAAGAAA-A
1 AGCAAAAAATAGAGAAAG-AAA-GAAAAAAAAAGA
123790 AG-AAAAAATAGA-AAGAGAAAGAAAAAAAAAGA
1 AGCAAAAAATAGAGAA-AGAAAGAAAAAAAAAGA
123822 AGCAAAAAATA
1 AGCAAAAAATA
123833 AAAAAAAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
31 9 0.24
32 14 0.37
33 15 0.39
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (33 bp):
AGCAAAAAATAGAGAAAGAAAGAAAAAAAAAGA
Found at i:130084 original size:22 final size:22
Alignment explanation
Indices: 130059--130103 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
130049 CTAGGTATCG
130059 ATACCATCCTTGAATGGGTACC
1 ATACCATCCTTGAATGGGTACC
130081 ATACCATCCTTGAATGGGTACC
1 ATACCATCCTTGAATGGGTACC
130103 A
1 A
130104 CCCCCCCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (22 bp):
ATACCATCCTTGAATGGGTACC
Found at i:133237 original size:10 final size:9
Alignment explanation
Indices: 133207--133274 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 9
133197 AGTCGGGTCA
*
133207 GGTCAGACC
1 GGTCAAACC
133216 GGTCAAACC
1 GGTCAAACC
*
133225 GGTTCATACC
1 GG-TCAAACC
133235 GGTCAAACC
1 GGTCAAACC
*
133244 GGTTCGAACC
1 GG-TCAAACC
133254 GGTCGAAACC
1 GGTC-AAACC
*
133264 GATCAGAACC
1 GGTCA-AACC
133274 G
1 G
133275 ATTGAAAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
9 21 0.43
10 28 0.57
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:133237 original size:19 final size:19
Alignment explanation
Indices: 133213--133264 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
133203 GTCAGGTCAG
133213 ACCGGTCAAACCGGTTC-A
1 ACCGGTCAAACCGGTTCGA
133231 TACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
133251 ACCGGTCGAAACCG
1 ACCGGTC-AAACCG
133265 ATCAGAACCG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.15
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:133272 original size:20 final size:20
Alignment explanation
Indices: 133232--133296 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
133222 ACCGGTTCAT
*
133232 ACCGGTC-AAACCGGTTC-GA
1 ACCGGTCGAAACC-GATCAGA
133251 ACCGGTCGAAACCGATCAGA
1 ACCGGTCGAAACCGATCAGA
* *
133271 ACCGATTGAAAACCGATCA-A
1 ACCGGTCG-AAACCGATCAGA
133291 ACCGGT
1 ACCGGT
133297 TTCCAGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 10 0.26
20 19 0.49
21 10 0.26
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (20 bp):
ACCGGTCGAAACCGATCAGA
Found at i:135039 original size:18 final size:19
Alignment explanation
Indices: 135011--135051 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
135001 AAAACGATTG
*
135011 CCCAGATGGTACAGGTACC
1 CCCAGATGGTACAGATACC
*
135030 CCCA-ATGGTACCGATACC
1 CCCAGATGGTACAGATACC
135048 CCCA
1 CCCA
135052 TGCCAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.27, C:0.39, G:0.20, T:0.15
Consensus pattern (19 bp):
CCCAGATGGTACAGATACC
Found at i:136232 original size:28 final size:28
Alignment explanation
Indices: 136191--136267 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
136181 CCAAAGCCAA
*
136191 CTGAAACACATTACCTCCCTAAATTAAC
1 CTGAAACACATTACCTCCCCAAATTAAC
** *
136219 CTGAAACATGTTACTTCCCCAAATTAAC
1 CTGAAACACATTACCTCCCCAAATTAAC
* *
136247 CTG-AACGCATTACCTTCCCAA
1 CTGAAACACATTACCTCCCCAA
136268 GTCAGCCTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 13 0.32
28 27 0.68
ACGTcount: A:0.35, C:0.32, G:0.06, T:0.26
Consensus pattern (28 bp):
CTGAAACACATTACCTCCCCAAATTAAC
Found at i:137833 original size:54 final size:55
Alignment explanation
Indices: 137538--138647 Score: 772
Period size: 54 Copynumber: 20.6 Consensus size: 55
137528 TTTTTTTAGG
* *
137538 AACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTTTAAAATGAG-TTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--AT-G-A--TTTTCAAATGAGTTTTCAAAGA
* * *
137598 AACTAAGTCTAATTTTCAGAGGTTTCTTGACATGGTATTTTTAAAATGAGTTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--AT-G-A-TTTTCAAATGAGTTTTCAAAGA
* * *
137658 AACTAAGTCTTATTTTCA-AAGTTTC-TGCTTATTTT-AAATGAGTTTTC-AAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* *
137709 AACTAAGTTTGATTTTCAGAGGTTT-TTGACATGAAATTTTTCAAAATGAG-TTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--ATG--A-TTTTC-AAATGAGTTTTCAAAGA
* * *
137768 AACAAATTCTGATTTTCATAAGTTTCTTGATGATTTT-AAATGAGTTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * *
137822 AACTAAGTCTGATTTTTAGGAGTTTGTTGATTA-TTTCTAAATGAGATTTT-AAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTC-AAATGAG-TTTTCAAAGA
* * ** * *
137877 AACTAAGTATGATTTTCAGAAGTTTTTTGACAATTTTTAAATGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * *
137932 AACTAAGTCTGATTTTTAGAAGTTTCTTGACGATTTTCAAGTGAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * * *
137987 AATTAAGTCTGATTTTCA-AAGTTTCTTAATTATTTTTAAATGAGCTTTC-AAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * *
138040 AACTAAGTTTGATTTTTAGATGTTTCTTGACGATTTTCAAATGAGTTTT-AAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * **
138094 AACTAAGCCTGGTCTTCAGAAGTTTCTTGATGATTTT-AAATGAACTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * ** * *
138148 AATTAAGCCTAATTTGT-AGGGGTTTCTTAATG-TTTTCAAATGA-ATTTCAAAGA
1 AACTAAGTCTGATTT-TCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* *
138201 AACTAAGTCAT-ATTTTCATAAG-TTCTTGACGATTTTCAAATGAGCTTTT-AAAGA
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAG-TTTTCAAAGA
* * * *
138255 AACTAAGTCCGA-TTTCATAAGTTTCTTGATTA-TTT-AAATGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* ** * * * *
138307 AATTAAGTCTGATTTTCAGTGGTTTCTTAAT--TTTTCCATATGA--ATT-AAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTT-CAAATGAGTTTTCAAAGA
* ** * *
138358 AACTAAGTCTAATTTT-AGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * ** * *
138410 AGA-TAAGCCTAATTTTTAGGGGTTTCTTGAT-ATTTTCAAATGA--ATT-AAAAA
1 A-ACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * * *
138461 AAGCTAAG-CAT-AATTTAAG-GGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AA-CTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * * * ** * * *
138513 AGCTAAGCCTAATTTTTAGGGGTTTCTTAATG--TTTC-AATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
* * ** * * * *
138564 AGCTAAGCCT-ATTTTCAGGGGTTTCTTGACG-TTTTCAAATGA-ATTTGAAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
*
138616 AACTAAGTCT-ATTTTCAG-GGTTTCTTGATGAT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGAT
138648 AATTTTCAAT
Statistics
Matches: 878, Mismatches: 119, Indels: 114
0.79 0.11 0.10
Matches are distributed among these distances:
50 59 0.07
51 107 0.12
52 125 0.14
53 142 0.16
54 185 0.21
55 122 0.14
56 10 0.01
57 4 0.00
58 9 0.01
59 50 0.06
60 65 0.07
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (55 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAGTTTTCAAAGA
Found at i:137939 original size:110 final size:107
Alignment explanation
Indices: 137538--138334 Score: 690
Period size: 110 Copynumber: 7.3 Consensus size: 107
137528 TTTTTTTAGG
*
137538 AACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTTTAAAATGAG-TTTCAAAGAAACT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGAC---G-A-TTTTT-AAATGAGCTTTCAAAGAAACT
* *
137602 AAGTCTAATTTTCAGAGGTTTCTTGACATGGTATTTTTAAAATGAGTTTTCAAAGA
60 AAGTCTGATTTTTAGA-GTTTCTTG--AT--TA-TTTT-AAATGAGTTTT-AAAGA
* * * *
137658 AACTAAGTCTTATTTTCA-AAGTTTC-TG-C-TTATTTTAAATGAGTTTTC-AAGAAACTAAGTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGAT-TTTTAAATGAGCTTTCAAAGAAACTAAGTC
* * *
137718 TGATTTTCAGAGGTTT-TTGACATGAAATTTTTCAAAATGAGTTTCAAAGA
65 TGATTTTTAGA-GTTTCTTG--AT--TA-TTTT--AAATGAGTTTTAAAGA
* * * * *
137768 AACAAATTCTGATTTTCATAAGTTTCTTGATGA-TTTTAAATGAGTTTTCAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
*
137832 GATTTTTAGGAGTTTGTTGATTATTTCTAAATGAGATTTTAAAGA
66 GATTTTTA-GAGTTTCTTGATTATTT-TAAATGAG-TTTTAAAGA
* * *
137877 AACTAAGTATGATTTTCAGAAGTTTTTTGACAATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
** *
137942 GATTTTTAGAAGTTTCTTGACGATTTTCAAGTGAGTTTTTAAAGA
66 GATTTTTAG-AGTTTCTTGATTATTTT-AAATGAG-TTTTAAAGA
* * ** *
137987 AATTAAGTCTGATTTTCA-AAGTTTCTTAATTATTTTTAAATGAGCTTTC-AAGAAACTAAGTTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
**
138050 GATTTTTAGATGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
66 GATTTTTAGA-GTTTCTTGATTATTTT-AAATGAGTTTTAAAGA
* * * * * * *
138094 AACTAAGCCTGGTCTTCAGAAGTTTCTTGATGA-TTTTAAATGAACTTTCAAAGAAATTAAGCCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
* * * * * * *
138158 AATTTGTAGGGGTTTCTTAATGT-TTTCAAATGAATTTCAAAGA
66 GATTTTTA-GAGTTTCTTGAT-TATTTTAAATGAGTTTTAAAGA
* * *
138201 AACTAAGTCAT-ATTTTCATAAG-TTCTTGACGATTTTCAAATGAGCTTTTAAAGAAACTAAGTC
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTC
* * *
138264 CGATTTCATA-AGTTTCTTGATTA-TTTAAATGAGCTTTCAAAGA
65 TGATTT-TTAGAGTTTCTTGATTATTTTAAATGAG-TTTTAAAGA
* **
138307 AATTAAGTCTGATTTTCAGTGGTTTCTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTT
138335 AATTTTTCCA
Statistics
Matches: 572, Mismatches: 78, Indels: 67
0.80 0.11 0.09
Matches are distributed among these distances:
105 10 0.02
106 43 0.08
107 103 0.18
108 95 0.17
109 67 0.12
110 118 0.21
111 53 0.09
112 28 0.05
113 24 0.04
114 5 0.01
117 1 0.00
118 2 0.00
119 6 0.01
120 17 0.03
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (107 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
GATTTTTAGAGTTTCTTGATTATTTTAAATGAGTTTTAAAGA
Found at i:138373 original size:51 final size:53
Alignment explanation
Indices: 138318--138694 Score: 370
Period size: 51 Copynumber: 7.2 Consensus size: 53
138308 ATTAAGTCTG
* * *
138318 ATTTTCAGTGGTTTCTTAAT-TTTTCCATATGAA-TT-AAAAAAACTAAGTCTA
1 ATTTTCAGGGGTTTCTTAATGTTTT-CAAATGAATTTGAAAAAAACTAAGCCTA
* *
138369 ATTTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGA-TAAGCCTA
1 ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAA-AAAACTAAGCCTA
* * * *
138421 ATTTTTAGGGGTTTCTTGATATTTTCAAATGAA-TT-AAAAAAAGCTAAGCATA
1 ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAAAAAA-CTAAGCCTA
* * * *
138473 A-TTT-AAGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTA
1 ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAAAAAACTAAGCCTA
* * *
138524 ATTTTTAGGGGTTTCTTAATG-TTTC-AATGAATTTGAAAGAAGCTAAGCCT-
1 ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAAAAAACTAAGCCTA
* * *
138574 ATTTTCAGGGGTTTCTTGACGTTTTCAAATGAATTTGAAAAAAACTAAGTCT-
1 ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAAAAAACTAAGCCTA
* * *
138626 ATTTTCA-GGGTTTCTTGATGATAATTTTC-AATGAATTTTAAAAGAAGCTAAGCCTA
1 ATTTTCAGGGGTTTCTT-A--AT-GTTTTCAAATGAATTTGAAAA-AAACTAAGCCTA
*
138682 ATTTTTAGGGGTT
1 ATTTTCAGGGGTT
138695 CCTTGACAAT
Statistics
Matches: 278, Mismatches: 28, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
50 65 0.23
51 66 0.24
52 66 0.24
53 42 0.15
54 14 0.05
55 14 0.05
56 6 0.02
57 5 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (53 bp):
ATTTTCAGGGGTTTCTTAATGTTTTCAAATGAATTTGAAAAAAACTAAGCCTA
Found at i:138387 original size:103 final size:100
Alignment explanation
Indices: 138061--138700 Score: 436
Period size: 103 Copynumber: 6.1 Consensus size: 100
138051 ATTTTTAGAT
* * * ** * ** *
138061 GTTTCTTGACGATTTTCAAATGAGTTTTAAAGAAACTAAGCCTGGTCTTCAGAAGTTTCTTGATG
1 GTTTCTTGATG-TTTTCAAATGAATTTGAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAAT-
* * *
138126 ATTTTAAATGAACTTTCAAAGAAATTAAGCCTAATTTGTAGGG
64 -TTTTCAATGAA--TT-AAAAAAACTAAG-CTAATTT-TAGGG
* * * ***
138169 GTTTCTTAATGTTTTCAAATGAATTTCAAAGAAACTAAGTC-ATATTTTCATAAG-TTCTTGACG
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAGCCTA-ATTTTCAGGGGTTTCTT-A--
* * ** * ***
138232 A-TTTTCAAATGAGCTTTTAAAGAAACTAAGTCCGATTTCATAA
62 ATTTTTC-AATGA---ATTAAAAAAACTAAG-CTAATTTTAGGG
* * * * * *
138275 GTTTCTTGAT-TATTT-AAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCAGTGGTTTCTTAAT
1 GTTTCTTGATGT-TTTCAAATGA-ATTTGAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAAT
138338 TTTTCCATATGAATTAAAAAAACTAAGTCTAATTTTAGGG
64 TTTT-CA-ATGAATTAAAAAAACTAAG-CTAATTTTAGGG
* *
138378 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGA-TAAGCCTAATTTTTAGGGGTTTCTTGATA
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAA-ACTAAGCCTAATTTTCAGGGGTTTCTTAAT-
*
138442 TTTTCAAATGAATTAAAAAAAGCTAAGCATAA-TTTAAGG
64 TTTTC-AATGAATTAAAAAAA-CTAAGC-TAATTTTAGGG
* * *
138481 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATGT
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAATTT
* *
138546 TTCAATGAATTTGAAAGAAGCTAAGCCT-ATTTTCAGGG
66 TTCAATGAA-TT-AAAAAAACTAAG-CTAATTTT-AGGG
* * *
138584 GTTTCTTGACGTTTTCAAATGAATTTGAAAAAAACTAAGTCT-ATTTTCA-GGGTTTCTTGATGA
1 GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTT-A--A
*
138647 TAATTTTCAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGG
63 T--TTTTCAATGAA--TTAAAA-AAACTAAG-CTAA-TTTTAGGG
*
138692 GTTCCTTGA
1 GTTTCTTGA
138701 CAATTAAGAA
Statistics
Matches: 438, Mismatches: 57, Indels: 74
0.77 0.10 0.13
Matches are distributed among these distances:
101 16 0.04
102 22 0.05
103 194 0.44
104 24 0.05
105 12 0.03
106 66 0.15
107 75 0.17
108 24 0.05
109 5 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (100 bp):
GTTTCTTGATGTTTTCAAATGAATTTGAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAATTT
TTCAATGAATTAAAAAAACTAAGCTAATTTTAGGG
Found at i:138600 original size:206 final size:207
Alignment explanation
Indices: 138275--138685 Score: 491
Period size: 206 Copynumber: 2.0 Consensus size: 207
138265 GATTTCATAA
* * * * * *
138275 GTTTCTTGATTATTTAAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCAGTGGTTTCTTAATTT
1 GTTTCTTGATTATTTAAATGAGATTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAATGT
* *
138340 TTCCATATGAATTAAAAAAACTAAGTCTAATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTG
66 TTCCATATGAATTAAAAAAACTAAGCCTAATTTTAGGGGTTTCTTGACGTTTTCAAATGAATTTG
* *
138405 AAAGAAGA-TAAGCCTAATTTTTAGGGGTTTC-T-TGAT-ATTTTCAAATGAA-TTAAAAAAAGC
131 AAA-AAAACTAAGCCT-ATTTTCA-GGGTTTCTTATGATAATTTTC-AATGAATTTAAAAAAAGC
138465 TAAGCATAATTTAAGG
192 TAAGCATAATTTAAGG
* * *
138481 GTTTCTTGATGT-TTTCAAATGA-ATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAAT
1 GTTTCTTGAT-TATTT-AAATGAGATTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAAT
* *
138544 GTTT-CA-ATGAATTTGAAAGAAGCTAAGCCT-ATTTTCAGGGGTTTCTTGACGTTTTCAAATGA
64 GTTTCCATATGAA-TT-AAAAAAACTAAGCCTAATTTT-AGGGGTTTCTTGACGTTTTCAAATGA
* *
138606 ATTTGAAAAAAACTAAGTCTATTTTCAGGGTTTCTTGATGATAATTTTCAATGAATTTTAAAAGA
126 ATTTGAAAAAAACTAAGCCTATTTTCAGGGTTTCTT-ATGATAATTTTCAATGAA-TTTAAAAAA
*
138671 AGCTAAGCCTAATTT
189 AGCTAAGCATAATTT
138686 TTAGGGGTTC
Statistics
Matches: 175, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
204 12 0.07
205 19 0.11
206 100 0.57
207 17 0.10
208 6 0.03
209 21 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (207 bp):
GTTTCTTGATTATTTAAATGAGATTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTAATGT
TTCCATATGAATTAAAAAAACTAAGCCTAATTTTAGGGGTTTCTTGACGTTTTCAAATGAATTTG
AAAAAAACTAAGCCTATTTTCAGGGTTTCTTATGATAATTTTCAATGAATTTAAAAAAAGCTAAG
CATAATTTAAGG
Done.