Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009235.1 Hibiscus syriacus cultivar Beakdansim tig00112857_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: 1478786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:587797 original size:13 final size:13
Alignment explanation
Indices: 587776--587830 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
587766 AAGTTCGATA
*
587776 AATTCAAATACTT
1 AATTGAAATACTT
587789 AATTGAAATACTT
1 AATTGAAATACTT
* *
587802 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
587816 AATTGAAATACTT
1 AATTGAAATACTT
587829 AA
1 AA
587831 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:587861 original size:33 final size:33
Alignment explanation
Indices: 587816--587914 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
587806 AACTCAACAT
* * *
587816 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
587849 AATTCAAATACTTAAAAACTTCCAAATTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
587882 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
587914 A
1 A
587915 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:587933 original size:21 final size:21
Alignment explanation
Indices: 587909--587948 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
587899 ACTTCAAGTT
587909 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
587930 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
587949 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:602382 original size:21 final size:23
Alignment explanation
Indices: 602331--602382 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
602321 GATTCCCCTG
602331 TGGGGGGAATCGGTTCTCCTTCA
1 TGGGGGGAATCGGTTCTCCTTCA
** *
602354 AAGGGGGAATTGGTTC-CC-TCA
1 TGGGGGGAATCGGTTCTCCTTCA
602375 TGGGGGGA
1 TGGGGGGA
602383 TCGATTCCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 13 0.54
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.25
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCTCCTTCA
Found at i:606244 original size:21 final size:20
Alignment explanation
Indices: 606210--606262 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
606200 TAGTTTGTTT
*
606210 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTT-AAAAA
606231 TCATTTTTATATTTTAAAAA
1 TCATTTTTATATTTTAAAAA
*
606251 TAATTTCTTATA
1 TCATTT-TTATA
606263 ATCCGAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (20 bp):
TCATTTTTATATTTTAAAAA
Found at i:609015 original size:19 final size:19
Alignment explanation
Indices: 608974--609016 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
608964 AGTACATATT
*
608974 ATGAAATGAAATGTGAAAG
1 ATGAAATGAAATGTAAAAG
608993 -TGAATATGAAAT-TAAAAG
1 ATGAA-ATGAAATGTAAAAG
609011 ATGAAA
1 ATGAAA
609017 ATGGGATACG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (19 bp):
ATGAAATGAAATGTAAAAG
Found at i:609122 original size:38 final size:39
Alignment explanation
Indices: 609056--609137 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 39
609046 AAAAGGAATA
*
609056 TGATATGAATATTATGTATGATATTGTTTATCATGCCTT
1 TGATATGAATATTATATATGATATTGTTTATCATGCCTT
* **
609095 TGATATGACTATTA-ATATGATATTGTTTATCATGGTTT
1 TGATATGAATATTATATATGATATTGTTTATCATGCCTT
609133 TGATA
1 TGATA
609138 AAATCATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 26 0.67
39 13 0.33
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (39 bp):
TGATATGAATATTATATATGATATTGTTTATCATGCCTT
Found at i:610508 original size:24 final size:24
Alignment explanation
Indices: 610475--610528 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
610465 TAAATTGACT
610475 TTCTCCAGGGACGAAGCCATGTAGG
1 TTCT-CAGGGACGAAGCCATGTAGG
610500 TTCTCAGGGACGAAGCCATGTAGG
1 TTCTCAGGGACGAAGCCATGTAGG
610524 TTCTC
1 TTCTC
610529 GGGGGCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (24 bp):
TTCTCAGGGACGAAGCCATGTAGG
Found at i:614477 original size:29 final size:29
Alignment explanation
Indices: 614444--614501 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
614434 GCAGAGGGCC
614444 ACGTCCTGTGGAGTTCTGTGCATTATTGT
1 ACGTCCTGTGGAGTTCTGTGCATTATTGT
*
614473 ACGTCCTGTGGAGTTTTGTGCATTATTGT
1 ACGTCCTGTGGAGTTCTGTGCATTATTGT
614502 TCTGTACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.43
Consensus pattern (29 bp):
ACGTCCTGTGGAGTTCTGTGCATTATTGT
Found at i:619676 original size:101 final size:101
Alignment explanation
Indices: 619547--619730 Score: 350
Period size: 101 Copynumber: 1.8 Consensus size: 101
619537 ATAAAATTTT
*
619547 TTTTGTTCATGTTCGTTCATTAATGAATATAACTTGTTCATGTTTGTTCATTTAAATGATAAACG
1 TTTTGTTCATGTTCGTTCATTAAAGAATATAACTTGTTCATGTTTGTTCATTTAAATGATAAACG
619612 AACGAACATAAACGAACAACACAAACACAAAAACCA
66 AACGAACATAAACGAACAACACAAACACAAAAACCA
*
619648 TTTTGTTCATGTTCGTTCATTAAAGAATATAGCTTGTTCATGTTTGTTCATTTAAATGATAAACG
1 TTTTGTTCATGTTCGTTCATTAAAGAATATAACTTGTTCATGTTTGTTCATTTAAATGATAAACG
619713 AACGAACATAAACGAACA
66 AACGAACATAAACGAACA
619731 TAAGCGAACA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (101 bp):
TTTTGTTCATGTTCGTTCATTAAAGAATATAACTTGTTCATGTTTGTTCATTTAAATGATAAACG
AACGAACATAAACGAACAACACAAACACAAAAACCA
Found at i:620208 original size:9 final size:9
Alignment explanation
Indices: 620194--620219 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
620184 TAACCTTATA
620194 AATAAAATT
1 AATAAAATT
620203 AATAAAATT
1 AATAAAATT
620212 AATAAAAT
1 AATAAAAT
620220 CGTCTCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAAAATT
Found at i:620682 original size:9 final size:9
Alignment explanation
Indices: 620668--620693 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
620658 GAAATCGGTT
620668 AATTAACCG
1 AATTAACCG
620677 AATTAACCG
1 AATTAACCG
620686 AATTAACC
1 AATTAACC
620694 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:620830 original size:17 final size:17
Alignment explanation
Indices: 620808--620846 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
620798 TGAATCAAAT
620808 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
620825 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
620842 -AATTA
1 TAATTA
620847 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:626009 original size:16 final size:16
Alignment explanation
Indices: 625988--626018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
625978 TTTCTTCCTT
*
625988 AAAATATTCATTAATC
1 AAAATATTCAATAATC
626004 AAAATATTCAATAAT
1 AAAATATTCAATAAT
626019 ATCATCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATTCAATAATC
Found at i:626084 original size:3 final size:3
Alignment explanation
Indices: 626076--626106 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
626066 CAATTAATTC
626076 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
626107 CGGAAGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:627373 original size:23 final size:20
Alignment explanation
Indices: 627339--627398 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 20
627329 AAATGTAGAG
627339 AAAAAACATGTCACAAAAAC
1 AAAAAACATGTCACAAAAAC
* *
627359 AGAGATAAACGTGTCATAAAAAC
1 A-A-A-AAACATGTCACAAAAAC
627382 AAAAAACATGTCACAAA
1 AAAAAACATGTCACAAA
627399 GACATAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 13 0.39
21 2 0.06
22 2 0.06
23 16 0.48
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAAAACATGTCACAAAAAC
Found at i:628072 original size:38 final size:39
Alignment explanation
Indices: 628025--628116 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 39
628015 TTTGTATAAT
*
628025 ATTACAAATTGTAAAATATTTATAT-ATTTTTCTTTAAAAA
1 ATTA-AAATTGTAAAATATTTATATAATTTGT-TTTAAAAA
*
628065 ATT-AAATTCGT--AATATTTATATAATTTGTTTTACAAA
1 ATTAAAATT-GTAAAATATTTATATAATTTGTTTTAAAAA
*
628102 ATTAAAATTATAAAA
1 ATTAAAATTGTAAAA
628117 AATGTTTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
37 22 0.50
38 15 0.34
39 4 0.09
40 3 0.07
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (39 bp):
ATTAAAATTGTAAAATATTTATATAATTTGTTTTAAAAA
Found at i:628964 original size:59 final size:59
Alignment explanation
Indices: 628897--629016 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
628887 TCTGCAAAAT
*
628897 TTTACTCTTTATATTTTCAGTGAATTTCGTACGAATAGAGACGAACGTACAATTTTATG
1 TTTACTCTTTATATTTTCAGTGAATTCCGTACGAATAGAGACGAACGTACAATTTTATG
628956 TTTACTCTTTATATTTTCAGTGAATTCCGTACGAATAGAGACGAACGTACAATTTTATG
1 TTTACTCTTTATATTTTCAGTGAATTCCGTACGAATAGAGACGAACGTACAATTTTATG
629015 TT
1 TT
629017 AAGATTAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (59 bp):
TTTACTCTTTATATTTTCAGTGAATTCCGTACGAATAGAGACGAACGTACAATTTTATG
Found at i:631363 original size:16 final size:16
Alignment explanation
Indices: 631310--631365 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
631300 ATTTAAACAT
631310 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
631327 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
631347 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
631363 ATA
1 ATA
631366 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:631380 original size:37 final size:37
Alignment explanation
Indices: 631310--631380 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
631300 ATTTAAACAT
* *
631310 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
631347 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
631381 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:633116 original size:31 final size:31
Alignment explanation
Indices: 633078--633231 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
633068 CCCGAAGGAC
* *
633078 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
633109 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
633140 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
633171 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
633202 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
633232 CCCTCGACTC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:637386 original size:31 final size:31
Alignment explanation
Indices: 637348--637501 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
637338 CCCGAAGGAC
* *
637348 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
637379 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
637410 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
637441 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
637472 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
637502 CCCTCGACTC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:639349 original size:17 final size:16
Alignment explanation
Indices: 639317--639350 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
639307 TATATATATT
639317 TAATAAATAATAATAA
1 TAATAAATAATAATAA
*
639333 TAATAATATATTAATAA
1 TAATAA-ATAATAATAA
639350 T
1 T
639351 TTATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAAATAATAATAA
Found at i:639713 original size:76 final size:76
Alignment explanation
Indices: 639479--640271 Score: 1430
Period size: 76 Copynumber: 10.5 Consensus size: 76
639469 GATGAAAATG
* * * * *
639479 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
639544 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
639556 TTTGGAAATATCATGCACTGTAGGACTTACAGATGACCCAAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639620 CCCGAAGGCTT
66 CCCGAAGGCTT
639631 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639696 CCCGAAGGCTT
66 CCCGAAGGCTT
*
639707 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639771 CCCGAAGGCTT
66 CCCGAAGGCTT
639782 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639847 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
639858 TTTGGAAACATCATGCACTATAGGACTTATAAATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639923 CCCGAAGGCTT
66 CCCGAAGGCTT
*
639934 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
639999 CCCGAAGGCTT
66 CCCGAAGGCTT
640010 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
640075 CCCGAAGGCTT
66 CCCGAAGGCTT
*
640086 TTTGGAAACATCATGCACTGTAGGACTTACAGGTGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
640151 CCCGAAGGCTT
66 CCCGAAGGCTT
*
640162 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
640226 CCCGAAGGCTT
66 CCCGAAGGCTT
640237 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
640272 TAGGAAATAG
Statistics
Matches: 694, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
75 213 0.31
76 442 0.64
77 39 0.06
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:643265 original size:22 final size:22
Alignment explanation
Indices: 643240--643316 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
643230 CATAAAGCTT
643240 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
643262 TCATCTTTAAAAAGAGAATCTT
1 TCATCTTTGAAAAGAGAATCTA
643284 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
643306 TCATTTTTGAA
1 TCATCTTTGAA
643317 GAATGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:645958 original size:114 final size:114
Alignment explanation
Indices: 645758--645986 Score: 413
Period size: 114 Copynumber: 2.0 Consensus size: 114
645748 GATTATGCAG
* *
645758 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
645823 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
645872 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
645937 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
645986 T
1 T
645987 GTGGCACTTG
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:647650 original size:32 final size:32
Alignment explanation
Indices: 647597--647658 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
647587 GAAGAAATGA
* ** *
647597 TTGTTATGCTCATCTTGTAGAGATATTTCTCG
1 TTGTTATGCTCATATCATAGAGATACTTCTCG
647629 TTGTTATGCTCATATCATAGAGATACTTCT
1 TTGTTATGCTCATATCATAGAGATACTTCT
647659 TGTGTCTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (32 bp):
TTGTTATGCTCATATCATAGAGATACTTCTCG
Found at i:648303 original size:16 final size:17
Alignment explanation
Indices: 648274--648307 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
648264 TTTTTTTTAA
648274 TTTTTATTTCTTTCCTT
1 TTTTTATTTCTTTCCTT
*
648291 TTTTTCTTT-TTTCCTT
1 TTTTTATTTCTTTCCTT
648307 T
1 T
648308 CTTTGCTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTATTTCTTTCCTT
Found at i:653953 original size:16 final size:16
Alignment explanation
Indices: 653900--653955 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
653890 ATTTAAACAT
653900 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
653917 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
653937 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
653953 ATA
1 ATA
653956 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:653970 original size:37 final size:37
Alignment explanation
Indices: 653900--653970 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
653890 ATTTAAACAT
* *
653900 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
653937 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
653971 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:655273 original size:16 final size:16
Alignment explanation
Indices: 655252--655290 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
655242 TATATATATT
655252 TAATAATAAATAATAA
1 TAATAATAAATAATAA
* * *
655268 TAATAATATATTATAT
1 TAATAATAAATAATAA
655284 TAATAAT
1 TAATAAT
655291 TTATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAAATAATAA
Found at i:671324 original size:2 final size:2
Alignment explanation
Indices: 671317--671346 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
671307 ATAAAATGAA
671317 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
671347 TTGTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:683530 original size:4 final size:4
Alignment explanation
Indices: 683521--683547 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
683511 TTATTGGACT
683521 GCAA GCAA GCAA GCAA GCAA GCAA GCA
1 GCAA GCAA GCAA GCAA GCAA GCAA GCA
683548 GGCAGGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.26, T:0.00
Consensus pattern (4 bp):
GCAA
Found at i:697422 original size:20 final size:20
Alignment explanation
Indices: 697387--697454 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
697377 AATCTGTAAA
* *
697387 TCGCAACACATAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
* * *
697407 TCACAACGCGATAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
*
697427 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCAAAAGTCAAAT
697447 TCGCAACG
1 TCGCAACG
697455 TGAATAGTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (20 bp):
TCGCAACGCAAAAGTCAAAT
Found at i:697442 original size:40 final size:41
Alignment explanation
Indices: 697384--697474 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 41
697374 TCGAATCTGT
* *
697384 AAATCGCAACACATAAGTCAAATTCACAACGCG-ATAGTCA
1 AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
* * *
697424 AATTCGCAACACAAAAGTCAAATTCGCAACGTGAATAGTAA
1 AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
697465 AAATCGCAAC
1 AAATCGCAAC
697475 GTGAATAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 29 0.66
41 15 0.34
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (41 bp):
AAATCGCAACACAAAAGTCAAATTCACAACGCGAATAGTAA
Found at i:697489 original size:20 final size:21
Alignment explanation
Indices: 697447--697495 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
697437 AAAGTCAAAT
697447 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGTAAAAA
697468 TCGCAACGTGAATAGT-AAAA
1 TCGCAACGTGAATAGTAAAAA
697488 TCGCAACG
1 TCGCAACG
697496 AATCTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
TCGCAACGTGAATAGTAAAAA
Found at i:697871 original size:21 final size:21
Alignment explanation
Indices: 697845--697896 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
697835 CAACGCGATT
697845 TTGCGA-TTTTCTAAATTCGCA
1 TTGCGATTTTTC-AAATTCGCA
*
697866 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTTCAAATTCGCA
697887 TTGCGATTTT
1 TTGCGATTTT
697897 ACTATTCACG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.46
Consensus pattern (21 bp):
TTGCGATTTTTCAAATTCGCA
Found at i:697903 original size:20 final size:20
Alignment explanation
Indices: 697866--697978 Score: 118
Period size: 21 Copynumber: 5.5 Consensus size: 20
697856 TAAATTCGCA
* * *
697866 TTGCGATTTTTCAAATTCGCG
1 TTGCGATTTTAC-TATTCACG
697887 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
697907 TTGCGATTTTACTATTCACG
1 TTGCGATTTTACTATTCACG
* * *
697927 TTACGGTTTTTACTATTTACG
1 TTGC-GATTTTACTATTCACG
* *
697948 CTGCGATTTTTACTATTCACA
1 TTGCGA-TTTTACTATTCACG
*
697969 CTGCGATTTT
1 TTGCGATTTT
697979 GGATACTGAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
20 34 0.43
21 45 0.57
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACG
Found at i:697916 original size:41 final size:41
Alignment explanation
Indices: 697866--697967 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
697856 TAAATTCGCA
* *
697866 TTGCGATTTTTCAAATTCGCGTTGC-GATTTTACTATTCACG
1 TTGCGATTTTTC-AATTCACGTTACGGATTTTACTATTCACG
* * * *
697907 TTGCGATTTTACTATTCACGTTACGGTTTTTACTATTTACG
1 TTGCGATTTTTCAATTCACGTTACGGATTTTACTATTCACG
* *
697948 CTGCGATTTTTACTATTCAC
1 TTGCGATTTTT-CAATTCAC
697968 ACTGCGATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 9 0.18
41 34 0.67
42 8 0.16
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (41 bp):
TTGCGATTTTTCAATTCACGTTACGGATTTTACTATTCACG
Found at i:699906 original size:4 final size:4
Alignment explanation
Indices: 699897--699942 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
699887 TTATCTCTAT
699897 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
699943 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:702834 original size:2 final size:2
Alignment explanation
Indices: 702827--702870 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
702817 TTCATTGGAC
* * * *
702827 AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
702869 AT
1 AT
702871 TCTTAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:710246 original size:15 final size:15
Alignment explanation
Indices: 710229--710258 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
710219 ATCTTTCTTT
710229 CCCGTTCTGGATTTTC
1 CCCG-TCTGGATTTTC
710245 CCCGTCTGGATTTT
1 CCCGTCTGGATTTT
710259 AATCTGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.30, G:0.20, T:0.43
Consensus pattern (15 bp):
CCCGTCTGGATTTTC
Found at i:711034 original size:16 final size:18
Alignment explanation
Indices: 711006--711043 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
710996 ATCGCCGACA
711006 AAATTTCACTATTCACG-
1 AAATTTCACTATTCACGT
711023 AAATTT-ACTATTCACGT
1 AAATTTCACTATTCACGT
711040 AAAT
1 AAAT
711044 AGTAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTTCACTATTCACGT
Found at i:720374 original size:36 final size:36
Alignment explanation
Indices: 720321--720406 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
720311 AATTACATCC
* *
720321 ACTTTAGC-TTAGGTAAAAGCTTAAATGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
720356 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
720392 ACTTTAGCTTTAGGT
1 ACTTTAGCTTTAGGT
720407 TAACTAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 8 0.17
36 40 0.83
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTAAAACGTAATATGA
Found at i:721939 original size:15 final size:15
Alignment explanation
Indices: 721921--721949 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
721911 TTCATTTCAA
721921 AATTTTATAAAATAC
1 AATTTTATAAAATAC
721936 AATTTTATAAAATA
1 AATTTTATAAAATA
721950 ACTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:723516 original size:36 final size:36
Alignment explanation
Indices: 723466--723717 Score: 373
Period size: 36 Copynumber: 7.0 Consensus size: 36
723456 AGTTTGCATT
*
723466 GATTCAAGTCGAACGGAGGTAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* *
723502 GATTCAAGTTGAACGGAGGAAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* *
723538 GATTCAAATCGAACGGAGGGAAGCATCGGCTCTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
*
723574 GATTCAAGTCGAACGGAGGGAAGCATTGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* *
723610 AATTCAAATCGAACGGAGGGAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
* * *
723646 GATTCAAATCGAACGAAAGGAAGCATCGGCACTTCC
1 GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
*
723682 GATTCAAGT-GAACGG-GAGGAAGCATCGACACTTCC
1 GATTCAAGTCGAACGGAG-GGAAGCATCGGCACTTCC
723717 G
1 G
723718 GTTCTAGTGT
Statistics
Matches: 196, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
35 23 0.12
36 173 0.88
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (36 bp):
GATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCC
Found at i:725533 original size:24 final size:24
Alignment explanation
Indices: 725505--725550 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
725495 GTTTGGAACA
*
725505 AAGCATTCAAAATTTGATCTTTCT
1 AAGCATTAAAAATTTGATCTTTCT
725529 AAGCATTAAAAATTTGATCTTT
1 AAGCATTAAAAATTTGATCTTT
725551 ACTACACGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (24 bp):
AAGCATTAAAAATTTGATCTTTCT
Found at i:728048 original size:15 final size:16
Alignment explanation
Indices: 728023--728057 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
728013 GCAGGCTATT
728023 CTGATTTTGCCTTAAG
1 CTGATTTTGCCTTAAG
728039 CTGA-TTTGCCTTAAG
1 CTGATTTTGCCTTAAG
728054 CTGA
1 CTGA
728058 CTGGCAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (16 bp):
CTGATTTTGCCTTAAG
Found at i:731678 original size:22 final size:21
Alignment explanation
Indices: 731649--731690 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
731639 TGATCAAATG
731649 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
731670 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
731691 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:737632 original size:2 final size:2
Alignment explanation
Indices: 737625--737651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
737615 ATCACTTGCA
737625 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
737652 CTTGCCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:746653 original size:2 final size:2
Alignment explanation
Indices: 746648--746672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
746638 AAATTAAAAT
746648 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 T
746673 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:747959 original size:81 final size:81
Alignment explanation
Indices: 747862--748024 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
747852 TAATTAAGCT
* *
747862 GGATTAAACTTAAACGTCGAGTTCGATGTAATACTCTTTCGATTTGAATATACAGAACCGAACAA
1 GGATTAAACTTAAACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAA
747927 AAACGACAAAAAGAAA
66 AAACGACAAAAAGAAA
* *
747943 GGATTAAACTTAAACGTCGAGTCCGATGTGATACTCTTTCAATTTGAATATACAGATCCGAACAA
1 GGATTAAACTTAAACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAA
*
748008 AAACGACAAAAGGAAA
66 AAACGACAAAAAGAAA
748024 G
1 G
748025 AGCCACAGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (81 bp):
GGATTAAACTTAAACGTCGAGTCCGATGTAATACTCTTTCAATTTGAATATACAGAACCGAACAA
AAACGACAAAAAGAAA
Found at i:760084 original size:19 final size:18
Alignment explanation
Indices: 760050--760098 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
760040 CAAGTTTAAT
* * *
760050 TTTATATTAATTTGTATT
1 TTTATATTTATATGTATA
760068 TTGTATATTTATATGTATA
1 TT-TATATTTATATGTATA
760087 TTT-TATTTATAT
1 TTTATATTTATAT
760099 TTGGGACTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.33
18 3 0.11
19 15 0.56
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTATATTTATATGTATA
Found at i:762409 original size:103 final size:103
Alignment explanation
Indices: 762292--762495 Score: 311
Period size: 103 Copynumber: 2.0 Consensus size: 103
762282 TACGGTTAAA
* * * * *
762292 AAAATTTCATAACAGTTATAACAGTTAACCGACCGTTTAGAATAAACGATGTAGTTAACCGTCCA
1 AAAATCTCATAACAGTTATAACAGTTAACCGACCGTTTAGAAGAAACGATATAATTAACCGCCCA
762357 TGAACAACCCTAAAT-AGCATTCTAATTTTGTTTTTAGT
66 TGAACAACCCTAAATGA-CATTCTAATTTTGTTTTTAGT
* *
762395 AAAATCTCATAACAGTTATAACAGTTAACCGACCGTTTAGAAGAAACGGTATAATTAACGGCCCA
1 AAAATCTCATAACAGTTATAACAGTTAACCGACCGTTTAGAAGAAACGATATAATTAACCGCCCA
* *
762460 TGAACAGCCCTAAATGACGTTCTAATTTTGTTTTTA
66 TGAACAACCCTAAATGACATTCTAATTTTGTTTTTA
762496 ATATAATTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 90 0.99
104 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (103 bp):
AAAATCTCATAACAGTTATAACAGTTAACCGACCGTTTAGAAGAAACGATATAATTAACCGCCCA
TGAACAACCCTAAATGACATTCTAATTTTGTTTTTAGT
Found at i:762608 original size:3 final size:3
Alignment explanation
Indices: 762602--762643 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
762592 CAAAAACAAC
762602 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
762644 GGTAAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:764219 original size:2 final size:2
Alignment explanation
Indices: 764207--764246 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
764197 AAAATATTAA
*
764207 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
764247 AATTATTCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:764247 original size:6 final size:6
Alignment explanation
Indices: 764198--764249 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
764188 AAAATTACTA
* * * *
764198 AAATATT AAATAT -AATAT ATATAT ATATAT ATATAT ATATAT AAATAT
1 AAATA-T AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
764246 AAAT
1 AAAT
764250 TATTCAGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATAT
Found at i:767101 original size:31 final size:31
Alignment explanation
Indices: 767061--767138 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
767051 CAAAAAAAAC
767061 TTAATATGTGGTCACTTTCATTTCGTTTTAA
1 TTAATATGTGGTCACTTTCATTTCGTTTTAA
* *
767092 TTAAGATGTGGTCACTTTCGTTTCGTTTTAA
1 TTAATATGTGGTCACTTTCATTTCGTTTTAA
*
767123 TTAATATGTTGTCACT
1 TTAATATGTGGTCACT
767139 GAAACGTTGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (31 bp):
TTAATATGTGGTCACTTTCATTTCGTTTTAA
Found at i:772460 original size:24 final size:23
Alignment explanation
Indices: 772428--772472 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
772418 TGACATGATT
772428 TTTCCCTGCTCTTGTGGCACGCA
1 TTTCCCTGCTCTTGTGGCACGCA
772451 TTTCCTCTGCTCTTGTGGCACG
1 TTTCC-CTGCTCTTGTGGCACG
772473 ATCCTCATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.07, C:0.33, G:0.22, T:0.38
Consensus pattern (23 bp):
TTTCCCTGCTCTTGTGGCACGCA
Found at i:776525 original size:20 final size:19
Alignment explanation
Indices: 776484--776526 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
776474 ACAAAGAGTA
*
776484 AATAAAATATAATATTACT
1 AATAAAATATAATATGACT
* *
776503 AATAAATTATATATATGATT
1 AATAAAATATA-ATATGACT
776523 AATA
1 AATA
776527 TGTGATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATAAAATATAATATGACT
Found at i:777254 original size:12 final size:12
Alignment explanation
Indices: 777237--777262 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
777227 AAACCATCTT
777237 TATTTTTATATA
1 TATTTTTATATA
777249 TATTTTTATATA
1 TATTTTTATATA
777261 TA
1 TA
777263 ATCATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTTTATATA
Found at i:777308 original size:121 final size:120
Alignment explanation
Indices: 777078--777316 Score: 451
Period size: 121 Copynumber: 2.0 Consensus size: 120
777068 TAAAAGAAAA
777078 AGAAGTGAAATTTAGATTTTTATATTTTCAAACCATATTTATTTTTATATATATTTTATATATAA
1 AGAAGTGAAATTTAGATTTTTATATTTTCAAACCATATTTATTTTTATATATATTTTATATATAA
777143 TCATTAATAATTAATAATTTTAATTTTATTTAATAAATATATATATATATATAAT
66 TCATTAATAATTAATAATTTTAATTTTATTTAATAAATATATATATATATATAAT
*
777198 AGAAGTGAAATTTAGATTTTTATATTTTCAAACCATCTTTATTTTTATATATATTTTTATATATA
1 AGAAGTGAAATTTAGATTTTTATATTTTCAAACCATATTTATTTTTATATATA-TTTTATATATA
*
777263 ATCATTAATAATTAATAATTTTAATTTTATTTAATAATTATATATATATATATA
65 ATCATTAATAATTAATAATTTTAATTTTATTTAATAAATATATATATATATATA
777317 TATAATAGAG
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
120 52 0.45
121 64 0.55
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.51
Consensus pattern (120 bp):
AGAAGTGAAATTTAGATTTTTATATTTTCAAACCATATTTATTTTTATATATATTTTATATATAA
TCATTAATAATTAATAATTTTAATTTTATTTAATAAATATATATATATATATAAT
Found at i:777672 original size:21 final size:20
Alignment explanation
Indices: 777639--777677 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
777629 TATTTTAAAA
*
777639 ATAAAAATATATTTTTATAC
1 ATAAAAATATATTATTATAC
*
777659 ATAATAAATTTATTATTAT
1 ATAA-AAATATATTATTAT
777678 TTTAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAAAAATATATTATTATAC
Found at i:777689 original size:12 final size:12
Alignment explanation
Indices: 777672--777714 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
777662 ATAAATTTAT
777672 TATTATTTTAAA
1 TATTATTTTAAA
* *
777684 TATTATATTAAT
1 TATTATTTTAAA
777696 TA-TATTTTAAA
1 TATTATTTTAAA
777707 T-TTATTTT
1 TATTATTTT
777715 TTATATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATTATTTTAAA
Found at i:782042 original size:37 final size:37
Alignment explanation
Indices: 781965--782042 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
781955 TTTTTATATT
*
781965 TTTAATTTTGTAAAAAAATTTATATAAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TTATATAAAATATTATCAA
* *
782003 TTTAATTTTTTAAAGAAAA-TATAT-AAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAAATATTAT-CAA
782040 TTT
1 TTT
782043 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 8 0.23
37 10 0.29
38 13 0.37
39 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATTATATAAAATATTATCAA
Found at i:782224 original size:20 final size:20
Alignment explanation
Indices: 782188--782225 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
782178 ATCCTATTCC
**
782188 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
782208 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
782226 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:793728 original size:16 final size:18
Alignment explanation
Indices: 793707--793750 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
793697 AATTAAAATA
793707 AATATAAAAT-TTTA-AT
1 AATATAAAATATTTATAT
793723 AATAT-AAATATTTATAT
1 AATATAAAATATTTATAT
*
793740 GATATAAAATA
1 AATATAAAATA
793751 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 6 0.25
18 5 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATATAAAATATTTATAT
Found at i:793824 original size:23 final size:26
Alignment explanation
Indices: 793762--793832 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 26
793752 ATTTAAAAAA
793762 ATAATATT-AAAATTAATATCTATAAT
1 ATAATATTAAAAATTAATAT-TATAAT
793788 ATAATATTAAAAATTAATATT-TAAT
1 ATAATATTAAAAATTAATATTATAAT
*
793813 -TTAT-TTAAAAATTAATATTA
1 ATAATATTAAAAATTAATATTA
793833 AAATTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 15 0.36
24 3 0.07
25 4 0.10
26 9 0.21
27 11 0.26
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAATATTAAAAATTAATATTATAAT
Found at i:793836 original size:12 final size:12
Alignment explanation
Indices: 793758--793839 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
793748 ATAAATTTAA
*
793758 AAAAATAATATT
1 AAAATTAATATT
793770 AAAATTAATATCT
1 AAAATTAATAT-T
*
793783 ATAATATAATATT
1 AAAAT-TAATATT
793796 AAAAATTAATATT
1 -AAAATTAATATT
* *
793809 -TAATTTAT-TT
1 AAAATTAATATT
793819 AAAAATTAATATT
1 -AAAATTAATATT
793832 AAAATTAA
1 AAAATTAA
793840 AATCAAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 24 0.42
13 15 0.26
14 10 0.18
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:793859 original size:17 final size:18
Alignment explanation
Indices: 793826--793870 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
793816 TTTAAAAATT
793826 AATATTAAAATTAAAATCA
1 AATA-TAAAATTAAAATCA
*
793845 AATATAAAA-TAAAATTA
1 AATATAAAATTAAAATCA
793862 AATATAAAA
1 AATATAAAA
793871 CCTCTTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAAATTAAAATCA
Found at i:793868 original size:12 final size:11
Alignment explanation
Indices: 793820--793870 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
793810 AATTTATTTA
*
793820 AAAATTAATATT
1 AAAATTAA-AAT
793832 AAAATTAAAAT
1 AAAATTAAAAT
*
793843 CAAATATAAAAT
1 AAAAT-TAAAAT
793855 AAAATTAAATAT
1 AAAATTAAA-AT
793867 AAAA
1 AAAA
793871 CCTCTTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.29
12 24 0.71
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:796209 original size:63 final size:63
Alignment explanation
Indices: 796124--796258 Score: 263
Period size: 63 Copynumber: 2.2 Consensus size: 63
796114 TTATTTAGGG
796124 ATAATTATAATAATAATCTTCTATATATATTCTTTTTCAATTAGATCTCTATATACTCGAAAA
1 ATAATTATAATAATAATCTTCTATATATATTCTTTTTCAATTAGATCTCTATATACTCGAAAA
796187 ATAATTATAATAATAATCTTCTATATATATTCTTTTTCAATTAGATCTCTATATACTCGAAAA
1 ATAATTATAATAATAATCTTCTATATATATTCTTTTTCAATTAGATCTCTATATACTCGAAAA
796250 ATAA-TATAA
1 ATAATTATAA
796259 ATTTATCTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 5 0.07
63 67 0.93
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (63 bp):
ATAATTATAATAATAATCTTCTATATATATTCTTTTTCAATTAGATCTCTATATACTCGAAAA
Found at i:799068 original size:30 final size:31
Alignment explanation
Indices: 798988--799068 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
798978 GAAAATAATT
* * *
798988 GATCGGATATGACTTGACCCGAAAATTAACC
1 GATCTGATATGACTAGACCCGAAAATCAACC
* * *
799019 GATCTAATTTGA-TCCGACCCG-AAATCAACC
1 GATCTGATATGACT-AGACCCGAAAATCAACC
799049 GATCTGATATGACTAGACCC
1 GATCTGATATGACTAGACCC
799069 AATACCCGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
30 24 0.60
31 16 0.40
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (31 bp):
GATCTGATATGACTAGACCCGAAAATCAACC
Found at i:801766 original size:2 final size:2
Alignment explanation
Indices: 801759--801787 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
801749 ATGCATTTCG
801759 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
801788 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:801792 original size:2 final size:2
Alignment explanation
Indices: 801787--801823 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
801777 TCTCTCTCTC
*
801787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
801824 TCGATTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:810762 original size:71 final size:71
Alignment explanation
Indices: 810687--810951 Score: 322
Period size: 71 Copynumber: 3.7 Consensus size: 71
810677 ATTATATGCC
* *
810687 GATCTTTCT-AGTTTGTCATAACACATATGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATC
1 GATCTTTCTAAG-TTGTCGTAACACTTATGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATC
810751 ATATGAT
65 ATATGAT
* ** * *
810758 GATCTTTTTAAGTTGTCGTAATGCTTATGTGCTTTTATGATCTTTTAATAAGTGAATTAGAATCA
1 GATCTTTCTAAGTTGTCGTAACACTTATGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCA
*
810823 TATGAC
66 TATGAT
* * * * **
810829 GATC-TGCTTAAGTTGTCCTAACAC--GTGTGTTTTTAATGATCTTTTAAGAAGTCTATTAGGAT
1 GATCTTTC-TAAGTTGTCGTAACACTTATGTGCTTTT-ATGATCTTTTAAGAAGTGAATTAGGAT
*
810891 CATACGAT
64 CATATGAT
**
810899 GATCTTTCTAAGTTGTCGTAATGCTTATGTGCTTTTATGATCTTTTAAGAAGT
1 GATCTTTCTAAGTTGTCGTAACACTTATGTGCTTTTATGATCTTTTAAGAAGT
810952 TATTCGGTTT
Statistics
Matches: 161, Mismatches: 27, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
69 8 0.05
70 47 0.29
71 96 0.60
72 10 0.06
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (71 bp):
GATCTTTCTAAGTTGTCGTAACACTTATGTGCTTTTATGATCTTTTAAGAAGTGAATTAGGATCA
TATGAT
Found at i:812868 original size:14 final size:14
Alignment explanation
Indices: 812849--812882 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
812839 ATTTGAAATC
812849 TCAATCACCCTATT
1 TCAATCACCCTATT
812863 TCAATCACCCTATT
1 TCAATCACCCTATT
*
812877 ACAATC
1 TCAATC
812883 GTTGCTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (14 bp):
TCAATCACCCTATT
Found at i:819971 original size:19 final size:19
Alignment explanation
Indices: 819927--819965 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
819917 TTTGTTAGTG
819927 TAGAGGAAAGATAAAACAA
1 TAGAGGAAAGATAAAACAA
* *
819946 TAGAGGAAAGTTATAACAA
1 TAGAGGAAAGATAAAACAA
819965 T
1 T
819966 GAAGGATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (19 bp):
TAGAGGAAAGATAAAACAA
Found at i:821293 original size:15 final size:16
Alignment explanation
Indices: 821273--821314 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
821263 CTAATCAAAA
*
821273 CAAAGAGAAAAGA-AG
1 CAAAGAGAAAAAAGAG
821288 CAAAGA-AAAAAAGAG
1 CAAAGAGAAAAAAGAG
821303 CAAA-AGAAAAAA
1 CAAAGAGAAAAAA
821315 AGAAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (16 bp):
CAAAGAGAAAAAAGAG
Found at i:821296 original size:24 final size:24
Alignment explanation
Indices: 821269--821322 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
821259 AGATCTAATC
**
821269 AAAACAAAGAG-AAAAGAAGCAAAG
1 AAAA-AAAGAGCAAAAGAAAAAAAG
821293 AAAAAAAGAGCAAAAGAAAAAAAG
1 AAAAAAAGAGCAAAAGAAAAAAAG
821317 AAAAAA
1 AAAAAA
821323 GAGGATACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAGCAAAAGAAAAAAAG
Found at i:821300 original size:8 final size:8
Alignment explanation
Indices: 821289--821322 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
821279 GAAAAGAAGC
821289 AAAGAAAA
1 AAAGAAAA
**
821297 AAAGAGCA
1 AAAGAAAA
821305 AAAGAAAA
1 AAAGAAAA
821313 AAAGAAAA
1 AAAGAAAA
821321 AA
1 AA
821323 GAGGATACGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:821301 original size:16 final size:17
Alignment explanation
Indices: 821280--821318 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
821270 AAACAAAGAG
821280 AAAAGAAGC-AAAGAAA
1 AAAAGAAGCAAAAGAAA
821296 AAAAG-AGCAAAAGAAA
1 AAAAGAAGCAAAAGAAA
821312 AAAAGAA
1 AAAAGAA
821319 AAAAGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 17 0.81
17 1 0.05
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAAGCAAAAGAAA
Found at i:822553 original size:38 final size:37
Alignment explanation
Indices: 822510--822601 Score: 87
Period size: 37 Copynumber: 2.5 Consensus size: 37
822500 CTTTGAGATT
* *
822510 GTTTCTCTCGAAACAAAATGTTGTCTCGCTAGAGACA
1 GTTTCTCTAGAAACAAAATGTTGTCTCGCTAGAAACA
* * * * * *
822547 GTTTTCTTTAAAAAC-AAGTTTTGTCTCTCTTGAAACA
1 G-TTTCTCTAGAAACAAAATGTTGTCTCGCTAGAAACA
*
822584 GTTTCTCTTGAAACAAAA
1 GTTTCTCTAGAAACAAAA
822602 GTCCTTGAGT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
36 10 0.24
37 21 0.51
38 10 0.24
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (37 bp):
GTTTCTCTAGAAACAAAATGTTGTCTCGCTAGAAACA
Found at i:822766 original size:66 final size:65
Alignment explanation
Indices: 822558--822860 Score: 294
Period size: 66 Copynumber: 4.6 Consensus size: 65
822548 TTTTCTTTAA
* * * * *
822558 AAACAAGTTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAAGTC-CTTGAGTC-TGTTGCTC
1 AAACAATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTC-TGAGTCAT-TT-CCC
822621 TTG
63 TTG
* * * *
822624 AAACAAAATTTTGTCTCTCTTGAGATAGTTTTTCTTG---GAAAAATCTTTGAGT-ATGTTTCCC
1 AAAC-AATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCA--TTTCCC
822685 TTG
63 TTG
* * *
822688 AAACAAGTTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
1 AAACAATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
* * *** * *
822753 AAACGAATTTTTGTCTCTCTTGTGATAGTTTCTATTGAAACACCCATCTTTGAGATCGTTTCCCT
1 AAAC-AATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAG-TCATTTCCCT
822818 TG
64 TG
* * *
822820 AAACAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 AAACAATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
822861 TCATCTTTAA
Statistics
Matches: 197, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
63 28 0.14
64 20 0.10
65 15 0.08
66 90 0.46
67 44 0.22
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (65 bp):
AAACAATTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAAATCTCTGAGTCATTTCCCTTG
Found at i:822849 original size:132 final size:130
Alignment explanation
Indices: 822558--822891 Score: 392
Period size: 132 Copynumber: 2.6 Consensus size: 130
822548 TTTTCTTTAA
* * *
822558 AAACAAGTTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAAAGTCCTTGAGTCTGTTGCTCTT
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCCTTGAGTCTGTTGCCCTT
* *
822623 GAAACAAAATTTTGTCTCTCTTGAGATAGTTTTTCTTGGAAAAATCTTTGAGTATGTTTCCCTTG
66 GAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAAAATCTTTGAGTATGTTTCCCTTG
* * *
822688 AAACAAGTTTTGTCTCCCTTAAGATAGTTTCTCTTGAAACAAAAAT-CTCTGAGTCAT-TT-CCC
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCCT-TGAGTC-TGTTGCCC
* * *
822750 TTGAAACGAATTTTTGTCTCTCTTGTGATAGTTTCTATT-GAAACACCCATCTTTGAG-ATCGTT
64 TTGAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAA-A---ATCTTTGAGTAT-GTT
822813 TCCCTTG
124 TCCCTTG
* * * ** * * *
822820 AAACAATTTTTTTCTCTCTTGAGACAGTTTCCCTTGAAAC-ATCATCTTTAAGTCTGTTTCCCTT
1 AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCCTTGAGTCTGTTGCCCTT
822884 GAAACAAA
66 GAAACAAA
822892 TCCCTAAAGA
Statistics
Matches: 172, Mismatches: 22, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
128 4 0.02
129 39 0.23
130 50 0.29
131 13 0.08
132 66 0.38
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (130 bp):
AAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAAATCCTTGAGTCTGTTGCCCTT
GAAACAAAATTTTGTCTCTCTTGAGATAGTTTCTATTGGAAAAATCTTTGAGTATGTTTCCCTTG
Found at i:826356 original size:22 final size:22
Alignment explanation
Indices: 826290--826406 Score: 155
Period size: 22 Copynumber: 5.2 Consensus size: 22
826280 GGGGAATCAG
* *
826290 TTCCTCTTCAAAGGGGGAATC-A
1 TTCCCCTTC-AAGGGGGTATCGA
* *
826312 GTTCCCCTTTAAAGGGGGGATCGA
1 -TTCCCC-TTCAAGGGGGTATCGA
*
826336 TTCCCCTTCAATGGGGTATCGA
1 TTCCCCTTCAAGGGGGTATCGA
826358 TTCCCCTTCAAGGGGGTATCGA
1 TTCCCCTTCAAGGGGGTATCGA
826380 TTCCCCTTCAAGGGGGTATCGA
1 TTCCCCTTCAAGGGGGTATCGA
826402 TTCCC
1 TTCCC
826407 TTTGTCTTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
22 61 0.72
23 21 0.25
24 3 0.04
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGTATCGA
Found at i:832688 original size:131 final size:132
Alignment explanation
Indices: 832467--832798 Score: 450
Period size: 131 Copynumber: 2.5 Consensus size: 132
832457 ATCGTCTTTT
* * * * *
832467 TCACGTATGAACCATGCCATCCCCCGACCAGACCTCCTCACCACGTAGGAGTCGTGTCACCCCTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
*
832532 GATAAACAGTCGTCCTCATCACGTAGGAACAATGTTATCA-TCCCTAAAGATGGCATGTCATCCT
66 GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCACTCCCTAAAGATGGCATGTCATCCT
832596 CA
131 CA
** * * * *
832598 TCACGTAGGAACTGTGTCATCCCCTGACCAGACCTTCTCATCACTTAGGAGCCGTTTCACCCCTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
* * * **
832663 GATAATCAGTCATCCTTATCGCGTAGGAACCGTGTTATCACCCTCCCTAAAGATGGCATGTCATC
66 GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCA--CTCCCTAAAGATGGCATGTCATC
832728 CTCA
129 CTCA
* * * *
832732 TCGCGTAGGAACCATGTCATCCCCTGACCAGATCTCCTCATCGCGTAGGAGACGTGTCACCCTTA
1 TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
832797 GA
66 GA
832799 CGACCAAAAC
Statistics
Matches: 172, Mismatches: 26, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
131 89 0.52
134 83 0.48
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (132 bp):
TCACGTAGGAACCATGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGACGTGTCACCCCTA
GATAAACAGTCATCCTCATCACGTAGGAACAATGTTATCACTCCCTAAAGATGGCATGTCATCCT
CA
Found at i:833480 original size:2 final size:2
Alignment explanation
Indices: 833475--833513 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
833465 AATATCAAAC
*
833475 TA TA TA TA CA 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 TA T
833514 TTATGCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:834925 original size:43 final size:43
Alignment explanation
Indices: 834865--834950 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
834855 ATCCTACCTC
834865 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
1 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
* * * *
834908 CCCCTTACCCCATTACATATGGGAATATGGTCAGCTAATTTTT
1 CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
834951 TTTTATATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (43 bp):
CCCCTTACCCAATTACATATGGGAATAAGGTCAACCAATTTTT
Found at i:836758 original size:12 final size:12
Alignment explanation
Indices: 836741--836765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
836731 GAAGTATATC
836741 ATAATTGATTAA
1 ATAATTGATTAA
836753 ATAATTGATTAA
1 ATAATTGATTAA
836765 A
1 A
836766 CTTTCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATAATTGATTAA
Found at i:847396 original size:38 final size:36
Alignment explanation
Indices: 847354--847527 Score: 141
Period size: 38 Copynumber: 4.8 Consensus size: 36
847344 TTTGAAACGT
*
847354 TTTTGAAAACTTATGTACAATATATAAGTTTT-AAAACA
1 TTTTGAAAA--TATGTATAATATAT-AGTTTTGAAAACA
* *
847392 TTTTGAAAAT-TGTATAGTATATAGTTTTGAAATCA
1 TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
*
847427 TTTTGAAAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTG--AAAATATGTATAATATATAGTTTTGAAAACA
* * *
847465 TTTTTTG-AAATCT-TAT-ATA-ATA-TTTTTAAATCA
1 --TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
847498 TTTTTGAAAACTA--TATAATATATAGTTTTG
1 -TTTTGAAAA-TATGTATAATATATAGTTTTG
847528 TAATTTTTTT
Statistics
Matches: 114, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
32 6 0.05
33 15 0.13
34 13 0.11
35 26 0.23
36 8 0.07
37 10 0.09
38 31 0.27
40 5 0.04
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATGTATAATATATAGTTTTGAAAACA
Found at i:847500 original size:33 final size:31
Alignment explanation
Indices: 847446--847518 Score: 85
Period size: 33 Copynumber: 2.3 Consensus size: 31
847436 AATATATATA
*
847446 ATAT-ATAGTTTTGAAAACATTTTTTGAAATCTT
1 ATATAATA-TTTTGAAAACA-TTTTTGAAAAC-T
* *
847479 ATATAATATTTTTAAATCATTTTTGAAAACT
1 ATATAATATTTTGAAAACATTTTTGAAAACT
847510 ATATAATAT
1 ATATAATAT
847519 ATAGTTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 10 0.28
32 10 0.28
33 13 0.36
34 3 0.08
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (31 bp):
ATATAATATTTTGAAAACATTTTTGAAAACT
Found at i:847514 original size:73 final size:72
Alignment explanation
Indices: 847334--847519 Score: 190
Period size: 73 Copynumber: 2.6 Consensus size: 72
847324 TTTTTTGAAA
* * *
847334 TATATAAT-TTTTTGAAA-CGTTTTTGAAAACT-TATGTACAATATATAAGTTTTAAAACATTTT
1 TATATAATATTTTT-AAATCATTTTTGAAAACTATATATATAATATATAAGTTTTAAAACATTTT
847396 GAAAATTG
65 GAAAATTG
* *
847404 TATAGTATATAGTTTTGAAATCA-TTTTGAAAA-AATATATATAATATAT-AGTTTTGAAAACAT
1 TATA-TA-ATA-TTTTTAAATCATTTTTGAAAACTATATATATAATATATAAGTTTT-AAAACA-
847466 TTTTTG-AAATCT-
61 -TTTTGAAAAT-TG
847478 TATATAATATTTTTAAATCATTTTTGAAAACTATATAATATA
1 TATATAATATTTTTAAATCATTTTTGAAAACTATAT-ATATA
847520 TAGTTTTGTA
Statistics
Matches: 96, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
70 4 0.04
71 12 0.12
72 20 0.21
73 36 0.38
74 18 0.19
75 6 0.06
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (72 bp):
TATATAATATTTTTAAATCATTTTTGAAAACTATATATATAATATATAAGTTTTAAAACATTTTG
AAAATTG
Found at i:847650 original size:19 final size:19
Alignment explanation
Indices: 847610--847650 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
847600 ATATTATTAT
*
847610 TTTCATTTCATTTTATTCA
1 TTTCATTTCATTTTAATCA
847629 TTTCATTTCA-TTTAATCGA
1 TTTCATTTCATTTTAATC-A
847648 TTT
1 TTT
847651 TTTTTTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTCATTTCATTTTAATCA
Found at i:848958 original size:12 final size:13
Alignment explanation
Indices: 848941--848972 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
848931 TCAAATCGAA
848941 TAATTTTAA-TTT
1 TAATTTTAATTTT
848953 TAATTTTAATTTT
1 TAATTTTAATTTT
848966 TAATTTT
1 TAATTTT
848973 CGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:848968 original size:7 final size:6
Alignment explanation
Indices: 848941--848972 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
848931 TCAAATCGAA
848941 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
848973 CGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:849565 original size:2 final size:2
Alignment explanation
Indices: 849558--849582 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
849548 AGAATTTTTC
849558 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
849583 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:849801 original size:18 final size:18
Alignment explanation
Indices: 849764--849802 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
849754 GAGATAAATA
*
849764 TAATATATATATTTAGTT
1 TAATATATATATTTACTT
* *
849782 TAATATATTTATTTTCTT
1 TAATATATATATTTACTT
849800 TAA
1 TAA
849803 AATAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TAATATATATATTTACTT
Found at i:851152 original size:21 final size:20
Alignment explanation
Indices: 851078--851153 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
851068 TACCCCATCT
851078 ATATATTATTTTCTTTCAATTAA
1 ATAT-TTATTTT-TTTCAA-TAA
* * *
851101 ATCTCTATTTTTATTGAATAA
1 ATATTTATTTTT-TTCAATAA
* *
851122 AAATTATATTTTTTTTAATAA
1 ATATT-TATTTTTTTCAATAA
851143 ATATATTATTT
1 ATAT-TTATTT
851154 CAGGTCTGGT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
21 21 0.50
22 18 0.43
23 3 0.07
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (20 bp):
ATATTTATTTTTTTCAATAA
Found at i:852781 original size:58 final size:58
Alignment explanation
Indices: 852718--852868 Score: 216
Period size: 58 Copynumber: 2.6 Consensus size: 58
852708 ATCATATATA
* *
852718 AAATAAATCGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTT-ATAAAAGT
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGATAAAA-C
* * *
852776 TAATAAATTGTTAAATTTATTTTCTTGAGAATATTAAATGATTCTATTTTGTTAAAAC
1 AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGATAAAAC
*
852834 AAATAAATTGTTAAATTTATTTCCTTG-GAAATCTT
1 AAATAAATTGTTAAATTTATTTTCTTGAG-AATCTT
852869 GAATAAATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
57 1 0.01
58 77 0.93
59 5 0.06
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (58 bp):
AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGATAAAAC
Found at i:852942 original size:43 final size:43
Alignment explanation
Indices: 852834--852945 Score: 188
Period size: 43 Copynumber: 2.6 Consensus size: 43
852824 TTGTTAAAAC
* * *
852834 AAATAAATTGTTAAATTTATTTCCTTGGAAATCTTGAATAAAT
1 AAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAATAAAG
*
852877 AAATAAATTGTTGAATTTATTTTCTTGGGAATCTTGAATAAAG
1 AAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAATAAAG
852920 AAATAAATTGTTGAATTTATTTTCTT
1 AAATAAATTGTTGAATTTATTTTCTT
852946 ATATGATTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (43 bp):
AAATAAATTGTTGAATTTATTTTCTTGGAAATCTTGAATAAAG
Found at i:853016 original size:39 final size:39
Alignment explanation
Indices: 852961--853069 Score: 146
Period size: 39 Copynumber: 2.7 Consensus size: 39
852951 ATTCTATTTT
*
852961 AAAATGAAATAGATCGTTGAATTTATTTTCATGTTTTGTA
1 AAAAT-AAATAAATCGTTGAATTTATTTTCATGTTTTGTA
*
853001 AAAATAAATAAATCGTTAAATTTATTTTCATGTTTTGTA
1 AAAATAAATAAATCGTTGAATTTATTTTCATGTTTTGTA
** **
853040 AAAGGAAATAAATTATTGAATTTTATTTTC
1 AAAATAAATAAATCGTTGAA-TTTATTTTC
853070 CTTAGAATCT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 47 0.77
40 14 0.23
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (39 bp):
AAAATAAATAAATCGTTGAATTTATTTTCATGTTTTGTA
Found at i:853147 original size:39 final size:38
Alignment explanation
Indices: 853093--853166 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
853083 ATGATTATAA
* *
853093 TTTGTAAAAGGAAATAAAT-CGTAGAATTTAGTTTTCTAT
1 TTTGAAAAAGAAAATAAATACGTA-AATTTA-TTTTCTAT
*
853132 TTTGAAAAAGAAAATAAATATGTAAATTTATTTTC
1 TTTGAAAAAGAAAATAAATACGTAAATTTATTTTC
853167 CTAAGAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 5 0.16
39 23 0.74
40 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (38 bp):
TTTGAAAAAGAAAATAAATACGTAAATTTATTTTCTAT
Found at i:853256 original size:97 final size:95
Alignment explanation
Indices: 852997--853263 Score: 291
Period size: 97 Copynumber: 2.7 Consensus size: 95
852987 TTTCATGTTT
** * * * * *
852997 TGTAAAAATAAATAAATCGTTAAATTTATTTTCATGTTTTGTAAAAGGAAATAAATTATTGAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTATTTTC-TATTTTGAAAAAGGAAATAAA-TA-TAAAAT
* *
853062 TTATTTTCCTTAGAATCTCACATGATTATAATT
63 TTATTTTCCTAAGAATCTCACATGATTATAATA
* * *
853095 TGTAAAAGGAAATAAATCGTAGAATTTAGTTTTCTATTTTGAAAAAGAAAATAAATATGTAAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCTATTTTGAAAAAGGAAATAAATAT-AAAATT
*** * *
853160 TATTTTCCTAAGAATCTTGTATGATTCTGATA
64 TATTTTCCTAAGAATCTCACATGATTATAATA
* *
853192 TGTAAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATT
1 TGTAAAAGGAAATAAATCGTTGAATTTA-TTTTCTATTTTGAAAAAGGAAATAAAT-ATAAAATT
*
853257 TAGTTTC
64 TATTTTC
853264 ATGGTTTGTA
Statistics
Matches: 143, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
96 1 0.01
97 93 0.65
98 44 0.31
99 5 0.03
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (95 bp):
TGTAAAAGGAAATAAATCGTTGAATTTATTTTCTATTTTGAAAAAGGAAATAAATATAAAATTTA
TTTTCCTAAGAATCTCACATGATTATAATA
Found at i:853333 original size:40 final size:40
Alignment explanation
Indices: 853195--853367 Score: 185
Period size: 39 Copynumber: 4.4 Consensus size: 40
853185 TCTGATATGT
* *
853195 AAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTG-A
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
* ** *
853234 AAAAGGAAATAAATCATAAAATTTA-GTTTC-ATGGTTTGTA
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTAT--TTTGTA
*
853274 AAAA-GAAATAAATCGTTGGATTTATTTTTCTATTTTGTA
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
* * * *
853313 AAAAGGAAATAAATCGTTGGATATAGTTTCCTATTTTGT-
1 AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
*
853352 AAAATGAAATAAATCG
1 AAAAGGAAATAAATCG
853368 AAACAAATCG
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.02
38 4 0.03
39 67 0.58
40 40 0.35
41 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (40 bp):
AAAAGGAAATAAATCGTTGAATTTATTTTTCTATTTTGTA
Found at i:853342 original size:79 final size:78
Alignment explanation
Indices: 853192--853367 Score: 226
Period size: 79 Copynumber: 2.2 Consensus size: 78
853182 GATTCTGATA
* * * *
853192 TGTAAAAGGAATTAAATCATTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATT
1 TGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATA
*
853257 TAGTTTCATGGTT
66 TAGTTTCATAGTT
* * ***
853270 TGTAAAAAGAAATAAATCGTTGGATTTATTTTTCTATTTTGTAAAAAGGAAATAAATCGTTGGAT
1 TGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTATTTTG-AAAAAGGAAATAAATCATAAAAT
* *
853335 ATAGTTTCCTATTT
65 ATAGTTTCATAGTT
*
853349 TGTAAAATGAAATAAATCG
1 TGTAAAAAGAAATAAATCG
853368 AAACAAATCG
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 37 0.44
79 47 0.56
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (78 bp):
TGTAAAAAGAAATAAATCGTTGAATTTATTTTTCTATTTTGAAAAAGGAAATAAATCATAAAATA
TAGTTTCATAGTT
Found at i:853379 original size:49 final size:49
Alignment explanation
Indices: 853318--853415 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
853308 TTGTAAAAAG
*
853318 GAAATAAATCGTTGGATATAGTTTCCTATTTTGTAAAA-TGAAATAAATC
1 GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGT-AAATAAATC
* * * *
853367 GAAACAAATCGTTTGATTTATTTTTCTATTTTGTAAAAGTAAATAAATC
1 GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGTAAATAAATC
853416 TTTGAATTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 42 0.98
50 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (49 bp):
GAAACAAATCGTTGGATATAGTTTCCTATTTTGTAAAAGTAAATAAATC
Found at i:854538 original size:3 final size:3
Alignment explanation
Indices: 854530--854599 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
854520 AGATTCTTAG
854530 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
854578 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
854600 ATAAAAGGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:858113 original size:11 final size:11
Alignment explanation
Indices: 858099--858124 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
858089 TGTGGGGCGA
858099 GCGGATGCGGG
1 GCGGATGCGGG
858110 GCGGATGCGGG
1 GCGGATGCGGG
858121 GCGG
1 GCGG
858125 GTAATGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.19, G:0.65, T:0.08
Consensus pattern (11 bp):
GCGGATGCGGG
Found at i:861093 original size:18 final size:17
Alignment explanation
Indices: 861068--861111 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
861058 ATTAATTTTG
861068 TTTTATTA-AATAATATA
1 TTTTATTATAATAAT-TA
*
861085 TTTTGATTATAATTATTA
1 TTTT-ATTATAATAATTA
861103 TTTTATTAT
1 TTTTATTAT
861112 CTCGGATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTTATTATAATAATTA
Found at i:862678 original size:82 final size:83
Alignment explanation
Indices: 862305--862704 Score: 367
Period size: 83 Copynumber: 4.8 Consensus size: 83
862295 TGAATATAAT
* * * * * * *
862305 AGTGATCCAT-CCATCCGAAATGAAAGACGCATTTC-GGGAGAAGCATTTTCCATTATTATTCAG
1 AGTGTTCCATCCCATCTGAAATGAAAGGCACGTTTCGGGGA-AAGCGTTTTCCATTATTATTTAG
* * *
862368 AGAATCTCTGTCATGTCAG
65 AGAATCTATGCCATGTCAA
* * * * **
862387 AGTGTTACATCCTATTTGAAATGAAAGGTACGTTTCGGGGAAAGTATTTTTCCATTATTATTTAG
1 AGTGTTCCATCCCATCTGAAATGAAAGGCACGTTTCGGGGAAAG-CGTTTTCCATTATTATTTAG
*
862452 AGAATCTCTGCCATGTCAA
65 AGAATCTATGCCATGTCAA
** * * *
862471 AGTGTTCCATCATATCTAAAATGAAAGGCACGGTTT-AGGGAAAGCGTTTTCCATTATTATTCAG
1 AGTGTTCCATCCCATCTGAAATGAAAGGCAC-GTTTCGGGGAAAGCGTTTTCCATTATTATTTAG
* * *
862535 AGAATCTTTGCCATATCAG
65 AGAATCTATGCCATGTCAA
* * ** * * *
862554 AGTGTTACATCCCATCTGAAATGAAATGCACAATCCGGGGAAAGCGTTTT-TATTATTATTTATA
1 AGTGTTCCATCCCATCTGAAATGAAAGGCACGTTTCGGGGAAAGCGTTTTCCATTATTATTTAGA
* * **
862618 TAATATATATCATGTCAA
66 GAATCTATGCCATGTCAA
* * * * * *
862636 ACTATTCCATCCCATCCGAAATGAAAGGCACGTTTCGAGGAAAGTGTTTTCCATTATTATTCAGA
1 AGTGTTCCATCCCATCTGAAATGAAAGGCACGTTTCGGGGAAAGCGTTTTCCATTATTATTTAGA
862701 GAAT
66 GAAT
862705 TTTTGTCACT
Statistics
Matches: 253, Mismatches: 59, Indels: 11
0.78 0.18 0.03
Matches are distributed among these distances:
82 71 0.28
83 107 0.42
84 71 0.28
85 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (83 bp):
AGTGTTCCATCCCATCTGAAATGAAAGGCACGTTTCGGGGAAAGCGTTTTCCATTATTATTTAGA
GAATCTATGCCATGTCAA
Found at i:862699 original size:165 final size:165
Alignment explanation
Indices: 862310--862709 Score: 471
Period size: 167 Copynumber: 2.4 Consensus size: 165
862300 ATAATAGTGA
* * * *
862310 TCCAT-CCATCCGAAATGAAAGACGCATTTCGGGAGAAGCATTTTCCATTATTATTCAGAGAATC
1 TCCATCCCATCCGAAATGAAAGGCACGTTTCGGGA-AAGCGTTTTCCATTATTATTCAGAGAATC
* * * * * * ** * *
862374 TCTGTCATGTCAGAGTGTTACATCCTATTTGAAATGAAAGGTACGTTTCGGGGAAAGTATTTTTC
65 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTT-
* * * * *
862439 CATTATTATTTAGAGAATCTCTGCCATGTCAAAGTGT
129 CATTATTATTTAGAGAATATATACCATGTCAAACTAT
** ** *
862476 TCCATCATATCTAAAATGAAAGGCACGGTTTAGGGAAAGCGTTTTCCATTATTATTCAGAGAATC
1 TCCATCCCATCCGAAATGAAAGGCAC-GTTTCGGGAAAGCGTTTTCCATTATTATTCAGAGAATC
* *
862541 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAATGCACAATCCGGGGAAAGCGTTTTT-
65 TTTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTTC
* * *
862605 ATTATTATTTATATAATATATATCATGTCAAACTAT
130 ATTATTATTTAGAGAATATATACCATGTCAAACTAT
* *
862641 TCCATCCCATCCGAAATGAAAGGCACGTTTCGAGGAAAGTGTTTTCCATTATTATTCAGAGAATT
1 TCCATCCCATCCGAAATGAAAGGCACGTTTCG-GGAAAGCGTTTTCCATTATTATTCAGAGAATC
862706 TTTG
65 TTTG
862710 TCACTTCACA
Statistics
Matches: 195, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
164 5 0.03
165 84 0.43
166 5 0.03
167 94 0.48
168 7 0.04
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (165 bp):
TCCATCCCATCCGAAATGAAAGGCACGTTTCGGGAAAGCGTTTTCCATTATTATTCAGAGAATCT
TTGCCATATCAGAGTGTTACATCCCATCTGAAATGAAAGGCACAATCCGGGGAAAGCATTTTTCA
TTATTATTTAGAGAATATATACCATGTCAAACTAT
Found at i:871874 original size:2 final size:2
Alignment explanation
Indices: 871867--871953 Score: 158
Period size: 2 Copynumber: 44.0 Consensus size: 2
871857 AATCAAATGT
871867 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
*
871908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
871950 TA TA
1 TA TA
871954 ATGTATCCAT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:881121 original size:21 final size:20
Alignment explanation
Indices: 881097--881135 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
881087 AAAAATCTTA
881097 TCAAATCGACTTAAATAAAGT
1 TCAAATCGA-TTAAATAAAGT
* *
881118 TCAATTCGATTCAATAAA
1 TCAAATCGATTAAATAAA
881136 TTTATAGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (20 bp):
TCAAATCGATTAAATAAAGT
Found at i:883774 original size:156 final size:156
Alignment explanation
Indices: 883490--883810 Score: 615
Period size: 156 Copynumber: 2.1 Consensus size: 156
883480 ATCAAGTGAA
883490 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
1 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
*
883555 TTACGAGGAAGCTGCCGGAGCGGGAACCACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
66 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
883620 CTGCAACCGAAGTGGAAACAGAGCAG
131 CTGCAACCGAAGTGGAAACAGAGCAG
*
883646 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGGCGGATAAACCAAGTCCAGT
1 GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
883711 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
66 TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
883776 CTGCAACCGAAGTGGAAACAGAGCAG
131 CTGCAACCGAAGTGGAAACAGAGCAG
*
883802 GTTCAAAAT
1 GGTCAAAAT
883811 CAGGATAAAG
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 162 1.00
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.15
Consensus pattern (156 bp):
GGTCAAAATACAACCAAGCAAGAATCGGCAATGGATTATGGAAAGACGGATAAACCAAGTCCAGT
TTACGAGGAAGCTGCCGGAGCGGGAACAACCGTCATGTCGAAGGTACACGGTCCTGGCTCTGGAA
CTGCAACCGAAGTGGAAACAGAGCAG
Found at i:884985 original size:14 final size:14
Alignment explanation
Indices: 884966--884995 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
884956 AAATTGAATT
884966 TTATATAAATTTTA
1 TTATATAAATTTTA
*
884980 TTATATAACTTTTA
1 TTATATAAATTTTA
884994 TT
1 TT
884996 TATTTATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:885124 original size:10 final size:10
Alignment explanation
Indices: 885094--885125 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
885084 TTCATCATGC
885094 TATTAAAATT
1 TATTAAAATT
*
885104 CATTAAAATT
1 TATTAAAATT
885114 TATTAAAATT
1 TATTAAAATT
885124 TA
1 TA
885126 ATAGTTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
TATTAAAATT
Found at i:885629 original size:22 final size:23
Alignment explanation
Indices: 885588--885640 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
885578 AACTTATTAA
885588 AAAAATAAAAAATGTCATAAA-AT
1 AAAAAT-AAAAATGTCATAAAGAT
* * *
885611 ATAAATAAATATGTTATAAAGAT
1 AAAAATAAAAATGTCATAAAGAT
885634 AAAAATA
1 AAAAATA
885641 TTTGGATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (23 bp):
AAAAATAAAAATGTCATAAAGAT
Found at i:890042 original size:12 final size:12
Alignment explanation
Indices: 890027--890148 Score: 120
Period size: 12 Copynumber: 9.9 Consensus size: 12
890017 CAGAAATCAT
*
890027 TTCTTTTCTTCC
1 TTCTTCTCTTCC
*
890039 TTCTTCTCTTCT
1 TTCTTCTCTTCC
* * *
890051 TTCTTTTCCTCT
1 TTCTTCTCTTCC
890063 TTCTTCTCTTCC
1 TTCTTCTCTTCC
890075 TTCTTCTCCTCTTTCC
1 TTC-T-T-CTC-TTCC
*
890091 -TCTTCTCCTCC
1 TTCTTCTCTTCC
* *
890102 TTCTTCTCCTCT
1 TTCTTCTCTTCC
*
890114 TTCTTTTCTTCC
1 TTCTTCTCTTCC
890126 TTCTTCTCTTCC
1 TTCTTCTCTTCC
890138 TTCTTCTCTTC
1 TTCTTCTCTTC
890149 TTTAGCAGGT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
11 3 0.03
12 76 0.83
13 2 0.02
14 2 0.02
15 5 0.05
16 4 0.04
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTTCTCTTCC
Found at i:890073 original size:36 final size:36
Alignment explanation
Indices: 890026--890151 Score: 153
Period size: 36 Copynumber: 3.8 Consensus size: 36
890016 ACAGAAATCA
*
890026 TTTCTTTTCTTCCTTCTTCTCTTCTTTCTTTTCCTC
1 TTTCTTCTCTTCCTTCTTCTCTTCTTTCTTTTCCTC
890062 TTTCTTCTCTTCCTTCTTCTC--C--TC-TTTCCTC
1 TTTCTTCTCTTCCTTCTTCTCTTCTTTCTTTTCCTC
* *
890093 -TTC-TC-C-TCCTTCTTCTCCTCTTTCTTTTCTTC
1 TTTCTTCTCTTCCTTCTTCTCTTCTTTCTTTTCCTC
*
890125 CTTCTTCTCTTCCTTCTTCTCTTCTTT
1 TTTCTTCTCTTCCTTCTTCTCTTCTTT
890152 AGCAGGTCCG
Statistics
Matches: 78, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
27 11 0.14
28 1 0.01
29 3 0.04
30 3 0.04
31 9 0.12
32 8 0.10
33 3 0.04
34 3 0.04
35 1 0.01
36 36 0.46
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (36 bp):
TTTCTTCTCTTCCTTCTTCTCTTCTTTCTTTTCCTC
Done.