Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008466.1 Hibiscus syriacus cultivar Beakdansim tig00111280_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: 685270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:587362 original size:35 final size:35
Alignment explanation
Indices: 587316--587391 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
587306 AAAACAATCC
* *
587316 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
587351 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
587386 TCAATT
1 TCAATT
587392 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:587941 original size:130 final size:130
Alignment explanation
Indices: 587788--588035 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
587778 TATTTATATA
* **
587788 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
587853 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATACATCAT
66 TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTATTTATACATCAT
587918 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
587983 TTAACACATGATCATGATATATGTTATTGGCGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTA
588036 CAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTATTTATACATCAT
Found at i:588066 original size:130 final size:129
Alignment explanation
Indices: 587802--588066 Score: 293
Period size: 130 Copynumber: 2.0 Consensus size: 129
587792 ATTTGGTCCT
* ** *
587802 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * ** * * * **** *
587867 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATACATCATATCAATTTGGTCCT
66 TGACACATGTCATTGGCGACACATGTCACCACCTAATTATCAAAAAATAATATCAAAGAAGT-CA
587932 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
587997 TGATATATGTTATTGGCGACACATGTCACCACCTAATTA-CAAGAAAATTAAGT-TACAAAGAAG
66 TGACACATGTCATTGGCGACACATGTCACCACCTAATTATCAA-AAAA-TAA-TAT-CAAAGAAG
588060 T-A
127 TCA
588062 AAATT
1 AAATT
588067 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
129 1 0.01
130 102 0.91
131 3 0.03
132 6 0.05
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGCGACACATGTCACCACCTAATTATCAAAAAATAATATCAAAGAAGTCA
Found at i:588391 original size:28 final size:27
Alignment explanation
Indices: 588360--588422 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
588350 AGTTGATACA
*
588360 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
588388 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
588416 ATATTTT
1 ATATTTT
588423 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:588524 original size:16 final size:18
Alignment explanation
Indices: 588503--588536 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
588493 ATTTCTTATT
588503 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
588519 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
588537 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:590398 original size:23 final size:23
Alignment explanation
Indices: 590364--590442 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
590354 TAGTCGAAGG
*
590364 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
590387 TTCTACGTGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * * *
590410 TACTATGTGGTCCTTCGAGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
590433 TTCTATGTGG
1 TTCTACGTGG
590443 CACTTCGATG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:590448 original size:23 final size:23
Alignment explanation
Indices: 590372--590450 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
590362 GGTTCTACGC
* *
590372 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGAGACAATTCTATGT
* *
590395 GGTCCTTCGGGACAATACTATGT
1 GGTCCTTCGAGACAATTCTATGT
*
590418 GGTCCTTCGAGACATTTCTATGT
1 GGTCCTTCGAGACAATTCTATGT
590441 GG-CACTTCGA
1 GGTC-CTTCGA
590451 TGTATATTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 1 0.02
23 49 0.98
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGAGACAATTCTATGT
Found at i:592208 original size:12 final size:11
Alignment explanation
Indices: 592184--592223 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
592174 GAAAAAGGCC
*
592184 AAAAAAAGAAA
1 AAAAAAAGCAA
592195 AAGAAAAAGCAA
1 AA-AAAAAGCAA
592207 AAAAAAAGTCAA
1 AAAAAAAG-CAA
592219 AAAAA
1 AAAAA
592224 TGGAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAAAGCAA
Found at i:592213 original size:23 final size:24
Alignment explanation
Indices: 592159--592214 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
592149 TATTTTTTTA
*
592159 AAAAAAAAAGAAGAAGAAAAAGGC
1 AAAAAAAAAGAAAAAGAAAAAGGC
*
592183 -CAAAAAAAGAAAAAGAAAAA-GC
1 AAAAAAAAAGAAAAAGAAAAAGGC
592205 AAAAAAAAAG
1 AAAAAAAAAG
592215 TCAAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAGAAAAAGAAAAAGGC
Found at i:595856 original size:12 final size:11
Alignment explanation
Indices: 595827--595860 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
595817 ATTTTTTATA
595827 TATCTTGTTTT
1 TATCTTGTTTT
*
595838 AATCTTGTTTCT
1 TATCTTGTTT-T
595850 TATCTTGTTTT
1 TATCTTGTTTT
595861 CAGCACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.12, G:0.09, T:0.68
Consensus pattern (11 bp):
TATCTTGTTTT
Found at i:598601 original size:2 final size:2
Alignment explanation
Indices: 598594--598625 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
598584 TGGTTCGTCT
598594 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
598626 ACCGTTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:603047 original size:28 final size:28
Alignment explanation
Indices: 603015--603069 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
603005 TTGGCTAATG
603015 GCCAATACATGTTACTAATGTAACATTA
1 GCCAATACATGTTACTAATGTAACATTA
603043 GCCAATACATGTTACTAATGTAACATT
1 GCCAATACATGTTACTAATGTAACATT
603070 TTTACATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (28 bp):
GCCAATACATGTTACTAATGTAACATTA
Found at i:604777 original size:17 final size:18
Alignment explanation
Indices: 604755--604791 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
604745 CAAAATGGAT
604755 TAACTTTT-AATTAAAAA
1 TAACTTTTAAATTAAAAA
*
604772 TAACTTTTAAATTAATAA
1 TAACTTTTAAATTAAAAA
604790 TA
1 TA
604792 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TAACTTTTAAATTAAAAA
Found at i:605872 original size:3 final size:3
Alignment explanation
Indices: 605864--605917 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
605854 GATTATTCAA
605864 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
605912 AAT AAT
1 AAT AAT
605918 GGTTGACTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:607997 original size:19 final size:19
Alignment explanation
Indices: 607973--608009 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
607963 CAATCGTTTG
607973 ATTGCAATGAGAAGAACAT
1 ATTGCAATGAGAAGAACAT
607992 ATTGCAATGAGAAGAACA
1 ATTGCAATGAGAAGAACA
608010 GGAGTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
ATTGCAATGAGAAGAACAT
Found at i:609485 original size:16 final size:16
Alignment explanation
Indices: 609460--609504 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
609450 TAATAAATAA
*
609460 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
609476 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
609492 ACGAACATAAACG
1 ACGAACATAAACG
609505 TTGGAGACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:612602 original size:2 final size:2
Alignment explanation
Indices: 612589--612628 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
612579 TGAATAAAAT
612589 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
612629 TCTGTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:614496 original size:10 final size:10
Alignment explanation
Indices: 614481--614550 Score: 52
Period size: 10 Copynumber: 6.5 Consensus size: 10
614471 GTTTGATCTG
614481 TTTTCTTTCT
1 TTTTCTTTCT
614491 TTTTCTTT-T
1 TTTTCTTTCT
*
614500 CCTTTCTTTCT
1 -TTTTCTTTCT
614511 TTTTCTTTTCT
1 TTTTC-TTTCT
* *
614522 ATTGCTTTCTAT
1 TTTTCTTTC--T
614534 TTTTCTCTCTCT
1 TTTTCT-T-TCT
614546 TTTTC
1 TTTTC
614551 CCCTTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
9 1 0.02
10 23 0.49
11 9 0.19
12 11 0.23
13 1 0.02
14 2 0.04
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.73
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:614507 original size:20 final size:20
Alignment explanation
Indices: 614482--614520 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
614472 TTTGATCTGT
614482 TTTCTTTCTTTTTCTTTTCC
1 TTTCTTTCTTTTTCTTTTCC
614502 TTTCTTTCTTTTTCTTTTC
1 TTTCTTTCTTTTTCTTTTC
614521 TATTGCTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCTTTCTTTTTCTTTTCC
Found at i:614565 original size:19 final size:17
Alignment explanation
Indices: 614541--614585 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
614531 TATTTTTCTC
614541 TCTCTTTTTCCCCTTTTTT
1 TCTCTTTTT--CCTTTTTT
*
614560 TCTCTTCTTCCTTTTTT
1 TCTCTTTTTCCTTTTTT
*
614577 TCTGTTTTT
1 TCTCTTTTT
614586 TTGTGTTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
19 8 0.35
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (17 bp):
TCTCTTTTTCCTTTTTT
Found at i:615982 original size:2 final size:2
Alignment explanation
Indices: 615975--616002 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
615965 AAATGCATGG
615975 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
616003 GATTGGTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:620544 original size:24 final size:24
Alignment explanation
Indices: 620514--620618 Score: 84
Period size: 24 Copynumber: 4.4 Consensus size: 24
620504 TGAATATTTT
** *
620514 ATATGATTTCTGATTTGAATTCTG
1 ATATGATACCTGATATGAATTCTG
* *
620538 TTATGATACCTGATATGGATTCTG
1 ATATGATACCTGATATGAATTCTG
* ** *
620562 ATATGATACTTGACCTGGATTCTG
1 ATATGATACCTGATATGAATTCTG
** ** *
620586 ATCCGATATTTGACATGAATTCTG
1 ATATGATACCTGATATGAATTCTG
620610 ATATGATAC
1 ATATGATAC
620619 TTGACCTGAA
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (24 bp):
ATATGATACCTGATATGAATTCTG
Found at i:620640 original size:24 final size:24
Alignment explanation
Indices: 620529--620630 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
620519 ATTTCTGATT
* * **
620529 TGAATTCTGTTATGATACCTGATA
1 TGAATTCTGATATGATACTTGACC
*
620553 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACC
* ** * *
620577 TGGATTCTGATCCGATATTTGACA
1 TGAATTCTGATATGATACTTGACC
620601 TGAATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACC
620625 TGAATT
1 TGAATT
620631 ATGTTTTGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACC
Found at i:625045 original size:51 final size:49
Alignment explanation
Indices: 624976--625090 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 49
624966 GCATAAAATA
*
624976 AAATAAAAGTGACTAAAATGCAAGAAAATAAAAGT-TAGTAGTTAAATAAG
1 AAATAAAAGTGACCAAAATGCAA-AAAATAAAA-TATAGTAGTTAAATAAG
* *
625026 AAATAAATAGTGACCAAAATGCAAAAATTAAAATAATAGTAGTTAAATCAG
1 AAATAAA-AGTGACCAAAATGCAAAAAATAAAAT-ATAGTAGTTAAATAAG
*
625077 AAATTAACAGTGAC
1 AAA-TAAAAGTGAC
625091 TAAATTAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
49 1 0.02
50 15 0.26
51 38 0.67
52 3 0.05
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.23
Consensus pattern (49 bp):
AAATAAAAGTGACCAAAATGCAAAAAATAAAATATAGTAGTTAAATAAG
Found at i:626492 original size:2 final size:2
Alignment explanation
Indices: 626485--626521 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
626475 GTCATTCAAT
626485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
626522 GAATTCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:627178 original size:20 final size:21
Alignment explanation
Indices: 627142--627180 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
627132 GAATTAAAAG
627142 GTTAAAACCATTTGATGAAGA
1 GTTAAAACCATTTGATGAAGA
627163 GTTAAAACCA-TTGATGAA
1 GTTAAAACCATTTGATGAA
627181 AAGAATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (21 bp):
GTTAAAACCATTTGATGAAGA
Found at i:627724 original size:23 final size:24
Alignment explanation
Indices: 627694--627740 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
627684 AAATGAAAAT
627694 AAATTATC-AAAAAATAAAATAAA
1 AAATTATCTAAAAAATAAAATAAA
* *
627717 AAATTATCTAAAATATATAATAAA
1 AAATTATCTAAAAAATAAAATAAA
627741 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATTATCTAAAAAATAAAATAAA
Found at i:630569 original size:33 final size:33
Alignment explanation
Indices: 630532--630606 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
630522 AATGTTAGTA
*
630532 AGTTGAATTTGAAGCTGAATTTGACTTGTCATC
1 AGTTGAATTTGAAACTGAATTTGACTTGTCATC
630565 AGTTGAATTTGAAACTGAATTTGACTTGTCATC
1 AGTTGAATTTGAAACTGAATTTGACTTGTCATC
*
630598 AGTTAAATT
1 AGTTGAATT
630607 AAGAAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (33 bp):
AGTTGAATTTGAAACTGAATTTGACTTGTCATC
Found at i:632080 original size:16 final size:16
Alignment explanation
Indices: 632059--632091 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
632049 TATAAGAAAG
*
632059 GATATATGTGTTATAT
1 GATATATGTGATATAT
632075 GATATATGTGATATAT
1 GATATATGTGATATAT
632091 G
1 G
632092 TGGTATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (16 bp):
GATATATGTGATATAT
Found at i:632099 original size:11 final size:9
Alignment explanation
Indices: 632059--632100 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
632049 TATAAGAAAG
632059 GATATATGT
1 GATATATGT
*
632068 G-T-TATAT
1 GATATATGT
632075 GATATATGT
1 GATATATGT
632084 GATATATGT
1 GATATATGT
*
632093 GGTATATG
1 GATATATG
632101 AGAAACATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
7 5 0.18
8 2 0.07
9 21 0.75
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (9 bp):
GATATATGT
Found at i:632362 original size:21 final size:23
Alignment explanation
Indices: 632314--632374 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
632304 GGTTACCTAT
632314 GTCCTTCGGGACAT--ATGGACA
1 GTCCTTCGGGACATAGATGGACA
632335 GGTCCTTCGGGACATAGAT-GAC-
1 -GTCCTTCGGGACATAGATGGACA
632357 GTCCTTCGGGACATAGAT
1 GTCCTTCGGGACATAGAT
632375 TTCGCATGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 3 0.08
24 2 0.05
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (23 bp):
GTCCTTCGGGACATAGATGGACA
Found at i:636667 original size:18 final size:18
Alignment explanation
Indices: 636646--636689 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
636636 GGGTATATTA
*
636646 GTCATTCGGGATATAGTG
1 GTCATTCGGGACATAGTG
636664 GTCATTCGGGACATAGTG
1 GTCATTCGGGACATAGTG
*
636682 GTCCTTCG
1 GTCATTCG
636690 TGACGTATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.32
Consensus pattern (18 bp):
GTCATTCGGGACATAGTG
Found at i:636707 original size:22 final size:22
Alignment explanation
Indices: 636678--636759 Score: 128
Period size: 22 Copynumber: 3.7 Consensus size: 22
636668 TTCGGGACAT
*
636678 AGTGGTCCTTCGTGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
* *
636700 TGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGGGACGTATCC
636722 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
636744 AGTGGTCATTCGGGAC
1 AGTGGTCCTTCGGGAC
636760 AAATACTGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.15, C:0.26, G:0.30, T:0.29
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:642982 original size:65 final size:64
Alignment explanation
Indices: 642903--643064 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 64
642893 TTGTTGAAGG
*
642903 TGCATCGATGCATAAGGAGTGCATCGATGCACTCAT-TTAAATTA-ATGAACATCGAAT-GCCAT
1 TGCATCGATGCATAAGGAGTGCATCGATGCAC-CATCTTAAAATACA--AACATCGAATAG-CAT
642965 TAA
62 TAA
* * *
642968 TGCATCGATGCATAAGGAGTGCATCGATGCACCTTCTTAAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACCATCTTAAAATACAAACATCGAATAGCATTAA
* *
643032 TGCAACGATGCAT-GGGTAGTGCATCGATGCACC
1 TGCATCGATGCATAAGG-AGTGCATCGATGCACC
643065 CGTCAAGGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 2 0.02
64 44 0.51
65 40 0.46
66 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACCATCTTAAAATACAAACATCGAATAGCATTAA
Found at i:643653 original size:22 final size:22
Alignment explanation
Indices: 643612--643729 Score: 138
Period size: 22 Copynumber: 5.5 Consensus size: 22
643602 GGGTATATTA
643612 GTCCTTCGGGAC--AT--AGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
643630 GTCCTTTGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
643652 GT-CTTCCGGGACGTATCCAGTG
1 GTCCTT-CGGGACGTATCCAGTG
*
643674 GTCATTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
643696 GTCATTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
643718 GTCCTTCAGGAC
1 GTCCTTCGGGAC
643730 ATAGTGGTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.13
20 2 0.02
21 3 0.03
22 68 0.79
23 2 0.02
ACGTcount: A:0.16, C:0.23, G:0.31, T:0.30
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:643685 original size:44 final size:44
Alignment explanation
Indices: 643626--643747 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 44
643616 TTCGGGACAT
* *
643626 AGTGGTCCTTTGGGACGTATCTAGTGGTC-TTCCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCCAGTGGTCATT-CGGGACGTATCC
* *
643670 AGTGGTCATTCGGGACGTATCCAGTGGTCATTCGGGATGTATCC
1 AGTGGTCCTTCGGGACGTATCCAGTGGTCATTCGGGACGTATCC
*
643714 AGTGGTCCTTCAGGAC--AT--AGTGGTCATTCGGGAC
1 AGTGGTCCTTCGGGACGTATCCAGTGGTCATTCGGGAC
643748 AAATACTGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
40 15 0.21
42 2 0.03
44 51 0.73
45 2 0.03
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (44 bp):
AGTGGTCCTTCGGGACGTATCCAGTGGTCATTCGGGACGTATCC
Found at i:643718 original size:66 final size:62
Alignment explanation
Indices: 643626--643747 Score: 147
Period size: 66 Copynumber: 1.9 Consensus size: 62
643616 TTCGGGACAT
* * * *
643626 AGTGGTCCTTTGGGACGTATCTAGTGGT-CTTCCGGGACGTATCCAGTGGTCATTCGGGACGTAT
1 AGTGGTCATTCGGGACGTATCCAGTGGTCCTT-CAGGAC--AT--AGTGGTCATTCGGGACGTAT
643690 CC
61 CC
*
643692 AGTGGTCATTCGGGATGTATCCAGTGGTCCTTCAGGACATAGTGGTCATTCGGGAC
1 AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCAGGACATAGTGGTCATTCGGGAC
643748 AAATACTGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
62 16 0.32
64 2 0.04
66 29 0.58
67 3 0.06
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (62 bp):
AGTGGTCATTCGGGACGTATCCAGTGGTCCTTCAGGACATAGTGGTCATTCGGGACGTATCC
Found at i:646068 original size:74 final size:74
Alignment explanation
Indices: 645910--646072 Score: 186
Period size: 74 Copynumber: 2.2 Consensus size: 74
645900 CTCATAGGGT
* * * * **
645910 GTACTGATACCCCTATGCCAAATTTTTGCTCCGAGAAAATAGATTGTCCAATGGGTACTGATACC
1 GTACTGATACCCCTATGCCAAATTTTGGCTCCGAGAAAACAGAATGCCCAATGGGTACCAATACC
645975 CTACATAGG
66 CTACATAGG
** * *
645984 GTACCAATACCCCTATG-CAAGTTTTGGCTCCGAGAAAAACAGAATGCCCTATGGGTACCAATAC
1 GTACTGATACCCCTATGCCAAATTTTGGCTCCGAG-AAAACAGAATGCCCAATGGGTACCAATAC
* *
646048 CC-CCTTAGAG
65 CCTACATAG-G
646058 GTACTGATACCCCTA
1 GTACTGATACCCCTA
646073 GTCATTTAAC
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
73 19 0.26
74 54 0.74
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (74 bp):
GTACTGATACCCCTATGCCAAATTTTGGCTCCGAGAAAACAGAATGCCCAATGGGTACCAATACC
CTACATAGG
Found at i:651310 original size:23 final size:23
Alignment explanation
Indices: 651257--651339 Score: 116
Period size: 24 Copynumber: 3.7 Consensus size: 23
651247 TGTGCATTAG
* *
651257 GTATCGATA-CCCC-TTCAACGT
1 GTATCGATACCCCCTTTGAATGT
651278 GTATCGATACCCCCTTTGAATGT
1 GTATCGATACCCCCTTTGAATGT
*
651301 GTATCAATACCCCCCTTTGAATGT
1 GTATCGATA-CCCCCTTTGAATGT
651325 GTATCGATACCCCCT
1 GTATCGATACCCCCT
651340 AAGGGTACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
21 9 0.16
22 4 0.07
23 20 0.36
24 22 0.40
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (23 bp):
GTATCGATACCCCCTTTGAATGT
Found at i:653782 original size:74 final size:77
Alignment explanation
Indices: 653641--653800 Score: 227
Period size: 74 Copynumber: 2.1 Consensus size: 77
653631 AGGGAGGAAT
* * * *
653641 CGATACCCCTCATAGGGTGTACCGATACCCCTATGCCAAATTTTGGCTCTGAGAAAAATAGATTG
1 CGATACCCCACATAGGGTGTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATG
653706 CCCAATGGGTAC
66 CCCAATGGGTAC
**
653718 CGATACCCCACATA-GG-GTACCGATACCCCTATG-CAGGTTTTGGCTCCGAGAAAAACAGAATG
1 CGATACCCCACATAGGGTGTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATG
*
653780 CCCTATGGGTAC
66 CCCAATGGGTAC
*
653792 TGATACCCC
1 CGATACCCC
653801 TAGTCATTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
74 43 0.57
75 17 0.23
76 2 0.03
77 13 0.17
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (77 bp):
CGATACCCCACATAGGGTGTACCGATACCCCTATGCCAAATTTTGGCTCCGAGAAAAACAGAATG
CCCAATGGGTAC
Found at i:655585 original size:18 final size:18
Alignment explanation
Indices: 655562--655597 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
655552 ATATAACACA
655562 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
655580 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
655598 ATATAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:655593 original size:46 final size:46
Alignment explanation
Indices: 655515--655641 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
655505 GCGTAGAATT
*
655515 TGTCCCAAATGACCACTTAGATGTCCCGAAGGACCACATATAACACATA
1 TGTCCCAAAGGACCAC-T--ATGTCCCGAAGGACCACATATAACACATA
*
655564 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
*
655610 TGTCCCAAAGGACCACTATGTCCCGAAAGACC
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACC
655642 GCGTATACCC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
46 59 0.80
48 1 0.01
49 14 0.19
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.18
Consensus pattern (46 bp):
TGTCCCAAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
Found at i:660335 original size:21 final size:20
Alignment explanation
Indices: 660311--660349 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
660301 TAAGGTATTA
*
660311 AACATCATAAACAAAACAAAT
1 AACAACATAAA-AAAACAAAT
*
660332 AACAACATACAAAAACAA
1 AACAACATAAAAAAACAA
660350 CCATATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAT
Found at i:661206 original size:20 final size:20
Alignment explanation
Indices: 661177--661215 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
661167 TTTTCACCAC
*
661177 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
661197 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
661216 TATGAGCTCT
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:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:662816 original size:59 final size:59
Alignment explanation
Indices: 662745--663154 Score: 730
Period size: 59 Copynumber: 6.9 Consensus size: 59
662735 TAAATTCAAT
* *
662745 TGGAAATTCATACAATTAGTACGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
662804 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGTCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
662863 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTATCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
662922 TAGAAATTCATACAATTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
662981 TAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
663040 TGAAAATTCATACACTTAGTATGATTTTCTTACTATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
663099 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
663155 TTGGTAATTC
Statistics
Matches: 335, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 335 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:663519 original size:22 final size:20
Alignment explanation
Indices: 663476--663530 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
663466 TGGCCCTTCA
663476 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
**
663496 GTATCGATACTACCCTACTTTG
1 GTATCGATAC--CCCTACCATG
663518 GTATCGATACCCC
1 GTATCGATACCCC
663531 CCATCCAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 18 0.58
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:663600 original size:20 final size:20
Alignment explanation
Indices: 663572--663697 Score: 70
Period size: 20 Copynumber: 6.5 Consensus size: 20
663562 ATGTGACACA
*
663572 GTATGGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
* *
663592 GTATCGATACTACTATACTATG
1 GTATCGATAC-CCT-TACCATG
* *
663614 GTATTGATA-CCTCTA-TATG
1 GTATCGATACCCT-TACCATG
*** **
663633 GTATCGATACCAAAATTA-G
1 GTATCGATACCCTTACCATG
*
663652 GT-TCGAT---GTTACC-TG
1 GTATCGATACCCTTACCATG
663667 GTATCGATACCCTTACCATG
1 GTATCGATACCCTTACCATG
663687 GTATCGATACC
1 GTATCGATACC
663698 ACTTCGTTAG
Statistics
Matches: 80, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
15 4 0.05
16 5 0.06
18 5 0.06
19 21 0.26
20 29 0.36
21 2 0.03
22 14 0.17
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
GTATCGATACCCTTACCATG
Found at i:663615 original size:22 final size:19
Alignment explanation
Indices: 663589--663643 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
663579 TACCCTTACC
663589 ATGGTATCGATACTACTATACT
1 ATGGTATCGATAC--CTATA-T
* *
663611 ATGGTATTGATACCTCTAT
1 ATGGTATCGATACCTATAT
663630 ATGGTATCGATACC
1 ATGGTATCGATACC
663644 AAAATTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
22 12 0.40
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGGTATCGATACCTATAT
Found at i:663685 original size:95 final size:96
Alignment explanation
Indices: 663474--663696 Score: 279
Period size: 95 Copynumber: 2.3 Consensus size: 96
663464 TCTGGCCCTT
* * * *
663474 CAGTATCGATACCCCTACCATGGTATCGATACTACCCTACTTTGGTATCGATACCCCCCATCCAG
1 CAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCCATACAG
663539 TATCAATACCAAAATTAGATTCAATGTGACA
66 TATCAATACCAAAATTAGATTCAATGTGACA
* * * * * **
663570 CAGTATGGATACCCTTACCATGGTATCGATACTACTATACTATGGTATTGATA-CCTCTATATGG
1 CAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCCATACAG
* * * *
663634 TATCGATACCAAAATTAGGTTCGATGTTAC-
66 TATCAATACCAAAATTAGATTCAATGTGACA
*
663664 CTGGTATCGATACCCTTACCATGGTATCGATAC
1 C-AGTATCGATACCCTTACCATGGTATCGATAC
663697 CACTTCGTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
94 1 0.01
95 61 0.56
96 47 0.43
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (96 bp):
CAGTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCCATACAG
TATCAATACCAAAATTAGATTCAATGTGACA
Found at i:664291 original size:13 final size:13
Alignment explanation
Indices: 664273--664297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
664263 TATGGGGGAA
664273 AGAGAAAGAAAAG
1 AGAGAAAGAAAAG
664286 AGAGAAAGAAAA
1 AGAGAAAGAAAA
664298 CTTTATAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AGAGAAAGAAAAG
Found at i:673915 original size:30 final size:30
Alignment explanation
Indices: 673876--673941 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
673866 ACCTGAGACT
673876 CTCCC-CCTCTCGAAAATCACCAACCCCAG
1 CTCCCTCCTCTCGAAAATCACCAACCCCAG
673905 CTCCCTCCTCTCGAAAATCACCAACCCCAG
1 CTCCCTCCTCTCGAAAATCACCAACCCCAG
673935 CTCCCTC
1 CTCCCTC
673942 ATCTGGTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.24, C:0.53, G:0.06, T:0.17
Consensus pattern (30 bp):
CTCCCTCCTCTCGAAAATCACCAACCCCAG
Found at i:674262 original size:3 final size:3
Alignment explanation
Indices: 674256--674305 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
674246 ATAATAGACA
*
674256 AAT AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
674302 AAT A
1 AAT A
674306 TTAAATTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:675557 original size:42 final size:39
Alignment explanation
Indices: 675470--675557 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
675460 TTTTATCTTT
* * **
675470 TCTGTTATGCTCACATAACTAAATTTTCTTCTTCTTGAA
1 TCTGTTATGCCCACAAAACTAAATTTTCTTCTTCTCAAA
675509 TCTGTTATGCCCACAAAACTAAACTCCCTTT-TTCTTCTCAAA
1 TCTGTTATGCCCACAAAACTAAA-T---TTTCTTCTTCTCAAA
675551 TCTGTTA
1 TCTGTTA
675558 GGACCACAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 21 0.51
40 1 0.02
42 16 0.39
43 3 0.07
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (39 bp):
TCTGTTATGCCCACAAAACTAAATTTTCTTCTTCTCAAA
Found at i:676562 original size:25 final size:25
Alignment explanation
Indices: 676528--676582 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
676518 CTTCCTCCTC
676528 TTTCTTTCAAAATTCCATGGCCAAA
1 TTTCTTTCAAAATTCCATGGCCAAA
676553 TTTCTTTCAAAATTCCATGGCCAAA
1 TTTCTTTCAAAATTCCATGGCCAAA
676578 TTTCT
1 TTTCT
676583 CCCTTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (25 bp):
TTTCTTTCAAAATTCCATGGCCAAA
Found at i:678152 original size:2 final size:2
Alignment explanation
Indices: 678147--678175 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
678137 GTGTGTGTGT
678147 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
678176 TTGAGAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:678254 original size:18 final size:17
Alignment explanation
Indices: 678223--678258 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
678213 GAGGATGTAT
*
678223 AAATAAATATATTATAA
1 AAATAAATAAATTATAA
678240 AAATATAATAAATTATAA
1 AAATA-AATAAATTATAA
678258 A
1 A
678259 TCTCGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATAAATTATAA
Found at i:678453 original size:28 final size:28
Alignment explanation
Indices: 678415--678480 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
678405 ACCCTTGTGT
678415 GAGAGTGAGAGAGAGAAAGAGAAAGAGA
1 GAGAGTGAGAGAGAGAAAGAGAAAGAGA
* * *
678443 GAGAGTGAGAGAGAGAATGAGAGAGAGT
1 GAGAGTGAGAGAGAGAAAGAGAAAGAGA
678471 GAGAGTGAGA
1 GAGAGTGAGA
678481 ACCAAGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.45, T:0.08
Consensus pattern (28 bp):
GAGAGTGAGAGAGAGAAAGAGAAAGAGA
Found at i:678473 original size:10 final size:10
Alignment explanation
Indices: 678415--678475 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
678405 ACCCTTGTGT
678415 GAGAGTGAGA
1 GAGAGTGAGA
*
678425 GAGA--GAAA
1 GAGAGTGAGA
**
678433 GAGAAAGAGA
1 GAGAGTGAGA
678443 GAGAGTGAGA
1 GAGAGTGAGA
678453 GAGAGAATGAGA
1 GAGAG--TGAGA
678465 GAGAGTGAGA
1 GAGAGTGAGA
678475 G
1 G
678476 TGAGAACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 7 0.16
10 26 0.60
12 10 0.23
ACGTcount: A:0.48, C:0.00, G:0.46, T:0.07
Consensus pattern (10 bp):
GAGAGTGAGA
Found at i:678475 original size:22 final size:22
Alignment explanation
Indices: 678416--678481 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
678406 CCCTTGTGTG
* * *
678416 AGAGTGAGAGAGAGAAAGAGAA
1 AGAGAGAGAGTGAGAGAGAGAA
678438 AGAGAGAGAGTGAGAGAGAGAA
1 AGAGAGAGAGTGAGAGAGAGAA
* *
678460 TGAGAGAGAGTGAGAGTGAGAA
1 AGAGAGAGAGTGAGAGAGAGAA
678482 CCAAGATTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (22 bp):
AGAGAGAGAGTGAGAGAGAGAA
Found at i:678480 original size:12 final size:12
Alignment explanation
Indices: 678415--678469 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
678405 ACCCTTGTGT
* *
678415 GAGAGTGAGAGA
1 GAGAGAGAGTGA
* **
678427 GAGAAAGAGAAA
1 GAGAGAGAGTGA
678439 GAGAGAGAGTGA
1 GAGAGAGAGTGA
*
678451 GAGAGAGAATGA
1 GAGAGAGAGTGA
678463 GAGAGAG
1 GAGAGAG
678470 TGAGAGTGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.49, C:0.00, G:0.45, T:0.05
Consensus pattern (12 bp):
GAGAGAGAGTGA
Found at i:678540 original size:18 final size:17
Alignment explanation
Indices: 678509--678544 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
678499 GAGGATGTAT
*
678509 AAATAAATATATTATAA
1 AAATAAATAAATTATAA
678526 AAATATAATAAATTATAA
1 AAATA-AATAAATTATAA
678544 A
1 A
678545 TCTTGGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAATAAATTATAA
Found at i:681949 original size:20 final size:20
Alignment explanation
Indices: 681924--681997 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
681914 TTTTCCCAAT
*
681924 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
681944 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
681965 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
*
681985 TCGTAACGCGAAT
1 TCGCAACGCGAAT
681998 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:681967 original size:21 final size:21
Alignment explanation
Indices: 681941--682037 Score: 124
Period size: 21 Copynumber: 4.7 Consensus size: 21
681931 GCGAATAAGT
681941 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
681962 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
681982 AAATCGTAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
682003 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
682024 AAATCGCAATGCGA
1 AAATCGCAACGCGA
682038 TACTTACTAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 15 0.24
21 47 0.76
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:681969 original size:41 final size:41
Alignment explanation
Indices: 681924--682011 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
681914 TTTTCCCAAT
681924 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
681965 TCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
682006 TCGCAA
1 TCGCAA
682012 CACGAATTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:681975 original size:62 final size:63
Alignment explanation
Indices: 681919--682039 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 63
681909 TGCGATTTTC
* * * *
681919 CCAATTCGCAATGCGAA-TAAGTAAATCGCAACGCGAATTGGGAAAATCGCAATGCGA-ATAA
1 CCAAATCGCAACGCGAATTAAGAAAATCGCAACACGAATTGGGAAAATCGCAATGCGATATAA
** * **
681980 GTAAATCGTAACGCGAATTGGGAAAATCGCAACACGAATTGGGAAAATCGCAATGCGATA
1 CCAAATCGCAACGCGAATTAAGAAAATCGCAACACGAATTGGGAAAATCGCAATGCGATA
682040 CTTACTATCG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 12 0.24
62 36 0.73
63 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.18
Consensus pattern (63 bp):
CCAAATCGCAACGCGAATTAAGAAAATCGCAACACGAATTGGGAAAATCGCAATGCGATATAA
Found at i:682051 original size:20 final size:20
Alignment explanation
Indices: 682026--682119 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
682016 AATTGGGAAA
*
682026 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
682046 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
682067 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
682087 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
* *
682107 TTCGTAACGCGAT
1 ATCGCAACGCGAT
682120 TTACATAATC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 43 0.70
21 12 0.20
22 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:682068 original size:41 final size:41
Alignment explanation
Indices: 682023--682100 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
682013 ACGAATTGGG
* * *
682023 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
682064 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
682101 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:682068 original size:62 final size:62
Alignment explanation
Indices: 681941--682074 Score: 155
Period size: 62 Copynumber: 2.2 Consensus size: 62
681931 GCGAATAAGT
* * * **
681941 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTAAATCGTAACGCGAATTGGGA
1 AAATCGCAACACGAATTGGGAAAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGACA
** * *
682003 AAATCGCAACACGAATTGGGAAAATCGCAATGCG-ATACTTACTATCGCAATGCGATAAT-ACA
1 AAATCGCAACACGAATTGGGAAAATCGCAATGCGAATAAGTA-AATCGCAACGCGA-AATGACA
682065 AAATCGCAAC
1 AAATCGCAAC
682075 GAGATACTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
61 5 0.08
62 54 0.89
63 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (62 bp):
AAATCGCAACACGAATTGGGAAAATCGCAATGCGAATAAGTAAATCGCAACGCGAAATGACA
Found at i:682335 original size:22 final size:22
Alignment explanation
Indices: 682307--682350 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
682297 CACTCTCTCA
682307 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
682329 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
682351 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:682636 original size:20 final size:20
Alignment explanation
Indices: 682611--682648 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
682601 CGATTCTCTC
682611 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
682631 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
682649 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:683977 original size:18 final size:18
Alignment explanation
Indices: 683951--683995 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
683941 TCCACTTCGG
* *
683951 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
683969 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
683987 GAGCCATCA
1 GAGCCATCA
683996 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:684515 original size:19 final size:19
Alignment explanation
Indices: 684464--684527 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
684454 TAGTTTACTT
*
684464 TCGCAACACG-AATGACTA
1 TCGCAACGCGAAATGACTA
* *
684482 TCGCAACGCGGAATGGCTA
1 TCGCAACGCGAAATGACTA
* **
684501 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
684520 TCGCAACG
1 TCGCAACG
684528 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
18 9 0.24
19 28 0.76
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:684558 original size:32 final size:33
Alignment explanation
Indices: 684500--684590 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
684490 CGGAATGGCT
*
684500 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
684533 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
684565 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
684591 GCGATTTGTG
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:684584 original size:19 final size:18
Alignment explanation
Indices: 684500--684594 Score: 82
Period size: 14 Copynumber: 5.6 Consensus size: 18
684490 CGGAATGGCT
684500 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
684519 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
684533 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
684551 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
684565 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
684584 ATCGCAAGCGA
1 ATCGCAAGCGA
684595 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 23
0.69 0.05 0.26
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 15 0.25
19 17 0.28
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:684625 original size:14 final size:14
Alignment explanation
Indices: 684606--684663 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
684596 TTGTGTTTCG
684606 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
684620 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
684636 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
684652 CGTTGCGATTTT
1 CGTTGCGATTTT
684664 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:684639 original size:32 final size:33
Alignment explanation
Indices: 684601--684671 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 33
684591 GCGATTTGTG
684601 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
684633 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
684666 TTTCGC
1 TTTCGC
684672 ATTACGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 27 0.71
33 11 0.29
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:684686 original size:19 final size:19
Alignment explanation
Indices: 684664--684710 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
684654 TTGCGATTTT
684664 CATTTCGCATTACGATAGC
1 CATTTCGCATTACGATAGC
* * *
684683 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTACGATAGC
684703 CATTTCGC
1 CATTTCGC
684711 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (19 bp):
CATTTCGCATTACGATAGC
Found at i:684713 original size:19 final size:19
Alignment explanation
Indices: 684652--684718 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
684642 GCGATTTTGT
**
684652 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
684671 CATTACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
684691 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
684710 CGTTGCGAT
1 CGTTGCGAT
684719 TTAAGTTTCG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:684898 original size:17 final size:17
Alignment explanation
Indices: 684876--684914 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
684866 GCTAGTTTGA
684876 AATATTTGTCTTTGTTT
1 AATATTTGTCTTTGTTT
684893 AATATTTGTCTTTGTTT
1 AATATTTGTCTTTGTTT
684910 AATAT
1 AATAT
684915 CATGTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (17 bp):
AATATTTGTCTTTGTTT
Done.