Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 69 of 255
Found at i:20333840 original size:42 final size:42
Alignment explanation
Indices: 20333779--20333939 Score: 173
Period size: 42 Copynumber: 3.8 Consensus size: 42
20333769 TACTGTACCA
* * * *
20333779 ATGCCATATCCCATATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCAAATATGGTCTTACACGAAATCTCATATCG
* *
20333821 ATGCCA-ATAGCCAACTATGGTCTTACACGAAATCTCATATCG
1 ATGCCATAT-CCCAAATATGGTCTTACACGAAATCTCATATCG
* * * *
20333863 ATGTCATATCCCAAATATGGTCTTATAC-AATGTCTCATACCG
1 ATGCCATATCCCAAATATGGTCTTACACGAA-ATCTCATATCG
* * *
20333905 ATGCCATATCCCAGATATGATCTTACACGTAATCT
1 ATGCCATATCCCAAATATGGTCTTACACGAAATCT
20333940 TAACTAACCC
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
41 4 0.04
42 90 0.93
43 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAAATATGGTCTTACACGAAATCTCATATCG
Found at i:20340394 original size:27 final size:27
Alignment explanation
Indices: 20340324--20340520 Score: 191
Period size: 27 Copynumber: 7.3 Consensus size: 27
20340314 TACTGAAATG
** *
20340324 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * * * *
20340351 -CCTCTATTTATAGAATTACCGTTTCA
1 CCCTCGATTTACAAAATTACCATTTTA
* ***
20340377 CCCTCGACTTACAAAATTATTGTTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* *
20340404 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* * *
20340431 CCCTCAATTTACAGAATTACTATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
*
20340458 CCCTTGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCATTTTA
* *
20340485 CCCTC-AGTTTAAAAAATTACCGTTTTA
1 CCCTCGA-TTTACAAAATTACCATTTTA
20340512 CCCTCGATT
1 CCCTCGATT
20340521 GTGAAATTAC
Statistics
Matches: 140, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
26 23 0.16
27 116 0.83
28 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAAAATTACCATTTTA
Found at i:20340475 original size:81 final size:81
Alignment explanation
Indices: 20340324--20340516 Score: 237
Period size: 81 Copynumber: 2.4 Consensus size: 81
20340314 TACTGAAATG
* * * *
20340324 CCCTCGATTTGTAGAATTACCATTTTA-CCTCTATTTATAGAATTACCGTTTCACCCTCGACTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCATTTCACCCTCGACTTA
***
20340388 CAAAATTATTGTTTTA
66 CAAAATTACCATTTTA
* * * *
20340404 CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACTATTTTACCCTTGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCATTTCACCCTCGACTTA
20340469 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * *
20340485 CCCTC-AGTTTAAAAAATTACCGTTTTACCCTC
1 CCCTCGA-TTTATAGAATTACCATTTTACCCTC
20340517 GATTGTGAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
80 27 0.28
81 70 0.72
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCATTTCACCCTCGACTTA
CAAAATTACCATTTTA
Found at i:20340542 original size:27 final size:26
Alignment explanation
Indices: 20340512--20340702 Score: 129
Period size: 27 Copynumber: 7.1 Consensus size: 26
20340502 TACCGTTTTA
* **
20340512 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
20340539 CCCTG-TAGGATAGAATTACCAAAATAC
1 CCCTGAT-TG-TAAAATTACCAAAATAC
*
20340566 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
20340593 CCTTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
** * * *
20340620 CATTGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTAAAATTACCAAAATAC
*
20340646 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GA-TTGTAAAATTACCAAAATAC
20340674 CCCTGATT-TACAAAATTA-CAGAAATAC
1 CCCTGATTGT--AAAATTACCA-AAATAC
20340701 CC
1 CC
20340703 TTGACTTTCT
Statistics
Matches: 135, Mismatches: 20, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
25 2 0.01
26 8 0.06
27 118 0.87
28 6 0.04
29 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.29
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACCAAAATAC
Found at i:20340593 original size:54 final size:54
Alignment explanation
Indices: 20340519--20340674 Score: 163
Period size: 54 Copynumber: 2.9 Consensus size: 54
20340509 TTACCCTCGA
* * *
20340519 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGG-TAAAATTACCAAAATACCACTAGT
* * * ** * *
20340573 TTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
* **
20340627 TTGTGAAATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACC
1 TTGTGAAATTACCGAAATACCCCT-AGTAGGTAAAATTACCAAAATACC
20340675 CCTGATTTAC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 3 0.03
54 80 0.93
55 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
Found at i:20340689 original size:81 final size:81
Alignment explanation
Indices: 20340552--20340701 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 81
20340542 TGTAGGATAG
* * **
20340552 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCA-AA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTGAGTTTACAAAATTA-CAGAA
20340616 ATACCATTGGTTTGTGA
65 ATACCATTGGTTTGTGA
*
20340633 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCTGA-TTTACAAAATTACAGA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATA-CCCTGAGTTTACAAAATTACAGA
20340696 AATACC
64 AATACC
20340702 CTTGACTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 6 0.10
81 50 0.82
82 5 0.08
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTGAGTTTACAAAATTACAGAAA
TACCATTGGTTTGTGA
Found at i:20340690 original size:54 final size:54
Alignment explanation
Indices: 20340552--20340759 Score: 186
Period size: 54 Copynumber: 3.8 Consensus size: 54
20340542 TGTAGGATAG
* ** * * *
20340552 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATACCACTGA-TTTACAAAATTACCGAAATACCCTCAATTTGTAA
* * ***
20340606 AATTACCAAAATACCATTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCCTCAATTTGTAA
* * * * *
20340660 AATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCC-TCAATTTGT-AA
* * * *
20340716 AATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 AATTACCA-AAATACCACTGATTTACAAAATTACCGAAATACCCT
20340760 TGGTTTGTTG
Statistics
Matches: 128, Mismatches: 22, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
54 82 0.64
55 8 0.06
56 38 0.30
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCCTCAATTTGTAA
Found at i:20340753 original size:27 final size:27
Alignment explanation
Indices: 20340577--20340765 Score: 112
Period size: 27 Copynumber: 6.9 Consensus size: 27
20340567 CCTAGTTTGT
** * **
20340577 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
** * **
20340604 AAAATTACCAAAATACCATTGGTTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
* * *** **
20340631 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTGAAATACCCTTGGTTTAC
** * *
20340658 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
20340685 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
20340712 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
20340741 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
20340766 GTTGATTTAC
Statistics
Matches: 133, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
27 107 0.80
28 7 0.05
29 19 0.14
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:20341762 original size:52 final size:51
Alignment explanation
Indices: 20341684--20341806 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
20341674 GAGGAAGTGC
*
20341684 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGATTATGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGATT-TGCCCCAGTTTACCG
*
20341736 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGATTTGCCCCAGTTTACCG
20341787 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
20341807 ATTAAAGAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
50 10 0.14
51 24 0.35
52 35 0.51
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGATTTGCCCCAGTTTACCG
Found at i:20341781 original size:25 final size:26
Alignment explanation
Indices: 20341684--20341806 Score: 178
Period size: 26 Copynumber: 4.8 Consensus size: 26
20341674 GAGGAAGTGC
**
20341684 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
20341710 AAAAGGGATTATGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
20341736 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
20341762 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
20341787 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
20341807 ATTAAAGAGG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
25 33 0.38
26 54 0.62
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:20342010 original size:42 final size:42
Alignment explanation
Indices: 20341951--20342042 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
20341941 TAGTCTCCCT
* ** *
20341951 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
20341993 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
20342035 AAATGGGC
1 AAATGGGC
20342043 CTAAGGCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATACATTGACATTACATGTGATATTG
Found at i:20342142 original size:31 final size:31
Alignment explanation
Indices: 20342065--20342143 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
20342055 CGTTTACAGT
*
20342065 AAAA-GCTTCGGCCCAATGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
*
20342095 AAAAGGCTTCAGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGATATGATTTATG
20342126 AAAAGGCTTCGGCCCAGT
1 AAAAGGCTTCGGCCCAGT
20342144 AACCATTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:20343049 original size:28 final size:27
Alignment explanation
Indices: 20342988--20343076 Score: 133
Period size: 28 Copynumber: 3.1 Consensus size: 27
20342978 AAAGCATGAC
*
20342988 TATAAATGTGAATTGGGTCTGATGGGCCA
1 TATAAATGTG-ATTGGGCCT-ATGGGCCA
20343017 TATAAATGTGATTTGGGCCTATGGGCCA
1 TATAAATGTGA-TTGGGCCTATGGGCCA
20343045 TATAAATGTGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTA-TGGGCCA
20343073 TATA
1 TATA
20343077 CAGGTATGTG
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
27 9 0.16
28 31 0.54
29 17 0.30
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (27 bp):
TATAAATGTGATTGGGCCTATGGGCCA
Found at i:20346274 original size:31 final size:31
Alignment explanation
Indices: 20346239--20346302 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
20346229 CCTTTTCATA
20346239 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
20346270 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
20346301 TT
1 TT
20346303 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:20346570 original size:46 final size:46
Alignment explanation
Indices: 20346517--20346611 Score: 129
Period size: 46 Copynumber: 2.1 Consensus size: 46
20346507 CCTAGCTTCT
*
20346517 TTTAATAACTAGGGAAAAAAACCTTTTAATAACT-GGGCATAAGCCC
1 TTTAATAACT-GGGAAAAAAACCCTTTAATAACTGGGGCATAAGCCC
** * *
20346563 TTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGAAAAAAACCCTTTAATAACTGGGGCATAAGCCC
20346609 TTT
1 TTT
20346612 TTCACTTCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 18 0.42
46 25 0.58
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (46 bp):
TTTAATAACTGGGAAAAAAACCCTTTAATAACTGGGGCATAAGCCC
Found at i:20346577 original size:23 final size:23
Alignment explanation
Indices: 20346541--20346611 Score: 135
Period size: 23 Copynumber: 3.1 Consensus size: 23
20346531 AAAAAAACCT
20346541 TTTAATAACT-GGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
20346563 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
20346586 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
20346609 TTT
1 TTT
20346612 TTCACTTCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 10 0.21
23 38 0.79
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:20346687 original size:20 final size:20
Alignment explanation
Indices: 20346662--20346728 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
20346652 TTATGATTAC
*
20346662 ATCATGTGTATATCATACAT
1 ATCATGTGCATATCATACAT
20346682 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
20346702 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
20346722 ACCATGT
1 ATCATGT
20346729 CTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:20346797 original size:25 final size:25
Alignment explanation
Indices: 20346765--20346812 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20346755 ATACATAAAC
* * *
20346765 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
20346790 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
20346813 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:20351125 original size:25 final size:25
Alignment explanation
Indices: 20351093--20351140 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20351083 TTATAACATG
* * *
20351093 AAAATGACCTTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
20351118 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
20351141 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:20351243 original size:20 final size:20
Alignment explanation
Indices: 20351177--20351243 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
20351167 ATTTTGATAG
*
20351177 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
20351197 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
20351217 ACATGATATGTATGATATAC
1 ACATGATATGTATGATATGC
20351237 ACATGAT
1 ACATGAT
20351244 GTAATCATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:20351383 original size:24 final size:24
Alignment explanation
Indices: 20351293--20351409 Score: 134
Period size: 23 Copynumber: 5.0 Consensus size: 24
20351283 GAGGAAGTGA
*
20351293 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
20351317 -AAAGGGCTTATGCCCCAATTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
20351340 -AAAGGACTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
20351362 AAAAGGGCTTTTACCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
20351386 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
20351410 ATGATAAAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
22 9 0.11
23 41 0.52
24 18 0.23
25 11 0.14
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:20351638 original size:31 final size:31
Alignment explanation
Indices: 20351603--20351662 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20351593 CGTTTACAGT
20351603 AAAGGCTTCGGCCCAGTAATATGAAATATTA
1 AAAGGCTTCGGCCCAGTAATATGAAATATTA
**
20351634 AAAGGCTTCGGCCCAGTGTTATGAAATAT
1 AAAGGCTTCGGCCCAGTAATATGAAATAT
20351663 GAAATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATTA
Found at i:20354540 original size:29 final size:29
Alignment explanation
Indices: 20354481--20354564 Score: 125
Period size: 29 Copynumber: 2.9 Consensus size: 29
20354471 TACATGCATC
**
20354481 TGGCCCATTAGGCCC-AATCTTATTCACA
1 TGGCCCATTAGGCCCAAATCACATTCACA
**
20354509 TGGCCCATTAGGCCCAAATCACATTCGTA
1 TGGCCCATTAGGCCCAAATCACATTCACA
20354538 TGGCCCATTAGGCCCAAATCACATTCA
1 TGGCCCATTAGGCCCAAATCACATTCA
20354565 TATACATGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 15 0.30
29 35 0.70
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCACA
Found at i:20354804 original size:16 final size:16
Alignment explanation
Indices: 20354783--20354820 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
20354773 CAAACTTTCA
20354783 GCTTTTCAGCATTTTG
1 GCTTTTCAGCATTTTG
**
20354799 GCTTTTTGGCATTTTG
1 GCTTTTCAGCATTTTG
20354815 GCTTTT
1 GCTTTT
20354821 GCCTATCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.16, G:0.21, T:0.55
Consensus pattern (16 bp):
GCTTTTCAGCATTTTG
Found at i:20359052 original size:29 final size:29
Alignment explanation
Indices: 20358993--20359077 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 29
20358983 ATGCATATGA
* *
20358993 CCCACTAGGCCC-AATCTCATTCATATAG
1 CCCATTAGGCCCAAATCACATTCATATAG
* * *
20359021 CCCATTTGGCCCAAATCACATTCGTATGG
1 CCCATTAGGCCCAAATCACATTCATATAG
20359050 CCCATTAGGCCCAAATCACATTCATATA
1 CCCATTAGGCCCAAATCACATTCATATA
20359078 CATGCTTTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 10 0.21
29 38 0.79
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (29 bp):
CCCATTAGGCCCAAATCACATTCATATAG
Found at i:20360737 original size:42 final size:43
Alignment explanation
Indices: 20360678--20360770 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
20360668 GATTTAGGTA
* ** *
20360678 TAAGACCATGTCTGGGACATCGGCATCG-TATCTGAATT-CGTG
1 TAAGACCATATCTGGGACAGAGGCATCGATAT-TGAATTACATG
*
20360720 TAAGACCCTATCTGGGACAGAGGCATCGATATTGAATTACATG
1 TAAGACCATATCTGGGACAGAGGCATCGATATTGAATTACATG
20360763 TAAGACCA
1 TAAGACCA
20360771 CGTCTGAGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 30 0.70
43 13 0.30
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (43 bp):
TAAGACCATATCTGGGACAGAGGCATCGATATTGAATTACATG
Found at i:20372597 original size:21 final size:21
Alignment explanation
Indices: 20372571--20372611 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20372561 TGCATATTCT
20372571 AATTTCATAAACTAATTTACG
1 AATTTCATAAACTAATTTACG
20372592 AATTTCATAAACTAATTTAC
1 AATTTCATAAACTAATTTAC
20372612 TAAATCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTCATAAACTAATTTACG
Found at i:20402107 original size:31 final size:30
Alignment explanation
Indices: 20402014--20402118 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 30
20402004 TCTCAAAATT
* * *
20402014 ATATTTAAATTATATCTTTTTTTCTTAAATTG
1 ATATCTAAATTATA-CTTTTTATC-TAAAGTG
* *
20402046 GTATCTAAATTAT--TTTTTGTC-ACAAGTG
1 ATATCTAAATTATACTTTTTATCTA-AAGTG
20402074 ATATCTAAATTATACTTTGTTATCTAAAGTG
1 ATATCTAAATTATACTTT-TTATCTAAAGTG
20402105 ATA-CATAAATTATA
1 ATATC-TAAATTATA
20402119 TCTCGTTACC
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.02
28 16 0.26
29 7 0.11
30 4 0.07
31 21 0.34
32 12 0.20
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.49
Consensus pattern (30 bp):
ATATCTAAATTATACTTTTTATCTAAAGTG
Found at i:20411787 original size:16 final size:16
Alignment explanation
Indices: 20411766--20411796 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20411756 CCAAACTTTC
*
20411766 AGCTTTTCGGCATTTT
1 AGCTTTTCGACATTTT
20411782 AGCTTTTCGACATTT
1 AGCTTTTCGACATTT
20411797 CGACTTTTCA
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:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (16 bp):
AGCTTTTCGACATTTT
Found at i:20414280 original size:17 final size:18
Alignment explanation
Indices: 20414258--20414291 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20414248 CACATTGAAG
20414258 TGTTTT-AGTGAAAACCT
1 TGTTTTCAGTGAAAACCT
*
20414275 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
20414292 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCT
Found at i:20414727 original size:29 final size:28
Alignment explanation
Indices: 20414667--20414746 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 28
20414657 CATACATTCT
*
20414667 TATGGCCTACTAGGCCCAATCTCAATCA
1 TATGGCCTACTAGGCCCAATCACAATCA
* *
20414695 TATGGCCCAATAGGCCCAAATCAC-ATCTA
1 TATGGCCTACTAGGCCC-AATCACAATC-A
20414724 TATGGCCTACTAGGCCCAATCAC
1 TATGGCCTACTAGGCCCAATCAC
20414747 TTTTACAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 24 0.53
29 21 0.47
ACGTcount: A:0.30, C:0.33, G:0.15, T:0.23
Consensus pattern (28 bp):
TATGGCCTACTAGGCCCAATCACAATCA
Found at i:20414996 original size:16 final size:16
Alignment explanation
Indices: 20414956--20414998 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
20414946 GTAGCCAAAC
20414956 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
* *
20414972 TTTTAGCTTTTCTGCA
1 TTTCAGCTTTTCGGCA
*
20414988 TTTCGGCTTTT
1 TTTCAGCTTTT
20414999 TGGGATTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:20415788 original size:4 final size:4
Alignment explanation
Indices: 20415781--20415807 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20415771 ATATATACTA
20415781 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
20415808 AATACAAACC
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:20418743 original size:28 final size:28
Alignment explanation
Indices: 20418699--20418778 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
20418689 CAGACATGCT
* * *
20418699 TATGGCCTACTAGGCCCAATCTCAT-TCA
1 TATGGCCCACTAAGCCCAATCACATCT-A
*
20418727 TATGGCCCATTAAGCCCAAATCACATCTA
1 TATGGCCCACTAAGCCC-AATCACATCTA
*
20418756 TATGGCCCACTAGGCCCAATCAC
1 TATGGCCCACTAAGCCCAATCAC
20418779 TTTTATAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 20 0.45
29 23 0.52
30 1 0.02
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAAGCCCAATCACATCTA
Found at i:20418785 original size:28 final size:28
Alignment explanation
Indices: 20418699--20418785 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 28
20418689 CAGACATGCT
* * *
20418699 TATGGCCTACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTTA
* * *
20418727 TATGGCCCATTAAGCCCAAATCACATCTA
1 TATGGCCCACTAGGCCC-AATCACATTTA
*
20418756 TATGGCCCACTAGGCCCAATCACTTTTA
1 TATGGCCCACTAGGCCCAATCACATTTA
20418784 TA
1 TA
20418786 GTCATGCTCA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.28
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTTA
Found at i:20424303 original size:40 final size:40
Alignment explanation
Indices: 20424248--20424425 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
20424238 TGGATGATAA
** * *
20424248 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
20424288 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
20424328 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
20424368 CCTGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
20424408 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20424426 TACTTGGCTT
Statistics
Matches: 128, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 111 0.87
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:20432409 original size:39 final size:40
Alignment explanation
Indices: 20432324--20432539 Score: 305
Period size: 39 Copynumber: 5.5 Consensus size: 40
20432314 TGGATGATAA
** * *
20432324 CCGGGCTAAGTCCCGAAGGCATTTACGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
20432364 CCGGGCTAAGTCCCGAA-GCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
20432403 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
20432443 CCGGGCTAAGTCCCGAAAGCATTTGTGC-AGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
20432482 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
20432522 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
20432540 TACTTGGCTT
Statistics
Matches: 161, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
38 1 0.01
39 83 0.52
40 77 0.48
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:20432457 original size:79 final size:78
Alignment explanation
Indices: 20432324--20432538 Score: 310
Period size: 79 Copynumber: 2.7 Consensus size: 78
20432314 TGGATGATAA
* *
20432324 CCGGGCTAAGTCCCGAAGGCATTT-ACGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGA-GCGAGTAACTA-TATCCGGGCTAAGTCCCGAAGCATTT
20432387 GTGCGAGTTACTATAT
64 GTGC-AGTTACTATAT
* * *
20432403 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAAGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATATCCGGGCTAAGTCCCG-AAGCATTTG
20432468 TGCAGTTACTATAT
65 TGCAGTTACTATAT
* *
20432482 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATATCC-GGTTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATATCCGGGCTAAGTCCCGAAG
20432539 GTACTTGGCT
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
77 3 0.02
78 11 0.09
79 98 0.79
80 12 0.10
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTATATCCGGGCTAAGTCCCGAAGCATTTGT
GCAGTTACTATAT
Found at i:20444881 original size:46 final size:46
Alignment explanation
Indices: 20444831--20445040 Score: 298
Period size: 46 Copynumber: 4.6 Consensus size: 46
20444821 CCATAATGTA
* * *
20444831 TTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATC
* ** * *
20444877 TTTCAACCATGATCTTATTC-TTTCATGTCACGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
* *
20444922 TTTCAACCATTGTCTTACACATTTCATATCATGTTGCCATGATATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
20444968 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
*
20445014 TTTCAACCATGGTCTTACACCTTTCAT
1 TTTCAACCATGGTCTTACACATTTCAT
20445041 TTCAGAGAGC
Statistics
Matches: 148, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
44 4 0.03
45 35 0.24
46 109 0.74
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATC
Found at i:20444954 original size:91 final size:92
Alignment explanation
Indices: 20444831--20445040 Score: 298
Period size: 91 Copynumber: 2.3 Consensus size: 92
20444821 CCATAATGTA
* * * * *
20444831 TTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGATCTTAT
1 TTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGATATCTTTCAACCATGATCTTAC
* *
20444895 TC-TTTCATGTCACGTTGCCATGGTATC
65 ACATTTCATATCACGTTGCCATGGTATC
* *
20444922 TTTCAACCATTGTCTTACACATTTCATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACA
1 TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATCTTTCAACCATGATCTTACA
*
20444987 CATTTCATATCATGTTGCCATGGTATC
66 CATTTCATATCACGTTGCCATGGTATC
*
20445014 TTTCAACCATGGTCTTACACCTTTCAT
1 TTTCAACCATGGTCTTACACATTTCAT
20445041 TTCAGAGAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
90 4 0.04
91 53 0.50
92 48 0.46
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (92 bp):
TTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGATATCTTTCAACCATGATCTTACA
CATTTCATATCACGTTGCCATGGTATC
Found at i:20448472 original size:29 final size:28
Alignment explanation
Indices: 20448413--20448492 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
20448403 TATACATGCT
*
20448413 TATGGCCTACTAGGCCCAATCTCATCCA
1 TATGGCCTACTAGGCCCAATCACATCCA
* *
20448441 TATGGCCTATTAGGCCCAAATCACATCTA
1 TATGGCCTACTAGGCCC-AATCACATCCA
**
20448470 TATGGCCCGCTAGGCCCAATCAC
1 TATGGCCTACTAGGCCCAATCAC
20448493 TTTTACAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 22 0.49
29 23 0.51
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.24
Consensus pattern (28 bp):
TATGGCCTACTAGGCCCAATCACATCCA
Found at i:20471736 original size:21 final size:22
Alignment explanation
Indices: 20471712--20471752 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20471702 AAAGCTAGAA
*
20471712 TGGAGGCTTTT-AGTTGGAATT
1 TGGAGGATTTTCAGTTGGAATT
*
20471733 TGGAGGATTTTCATTTGGAA
1 TGGAGGATTTTCAGTTGGAA
20471753 GATATTGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (22 bp):
TGGAGGATTTTCAGTTGGAATT
Found at i:20472196 original size:24 final size:24
Alignment explanation
Indices: 20472164--20472216 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
20472154 TTAACTTTTT
20472164 CTGAGGTTAAGGATGAATATTTGG
1 CTGAGGTTAAGGATGAATATTTGG
*
20472188 CTGAGGTTAAGGATGAATCTTTGG
1 CTGAGGTTAAGGATGAATATTTGG
20472212 CTGAG
1 CTGAG
20472217 TTGGTTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (24 bp):
CTGAGGTTAAGGATGAATATTTGG
Found at i:20479902 original size:20 final size:20
Alignment explanation
Indices: 20479877--20479923 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20479867 TCAGTCCTAG
*
20479877 AAATAGTGGGGTCAAGTCAT
1 AAATAGTGGAGTCAAGTCAT
*
20479897 AAATAGTGGAGTCATGTCAT
1 AAATAGTGGAGTCAAGTCAT
*
20479917 GAATAGT
1 AAATAGT
20479924 AATAATGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (20 bp):
AAATAGTGGAGTCAAGTCAT
Found at i:20485893 original size:50 final size:50
Alignment explanation
Indices: 20485813--20486010 Score: 236
Period size: 50 Copynumber: 4.0 Consensus size: 50
20485803 GACCTTGTAT
* * *
20485813 ATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGA
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
* * * *
20485863 ATATTCGGCCATGA-AGGTATGCACAAATGTGATATTATATTTGAATTTGT
1 ATATTCGGCCAT-ATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
* * * * * * * *
20485913 ATATTCGGCTATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGC
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
*
20485963 ATATTCGGCCATATAGGTATGCACATATGTGATCTTATATTTGATTTT
1 ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTT
20486011 CTATAATCGA
Statistics
Matches: 120, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 1 0.01
50 118 0.98
51 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (50 bp):
ATATTCGGCCATATAGGTATGCACATATGTGATGTTATATTTGATTTTGA
Found at i:20485985 original size:100 final size:100
Alignment explanation
Indices: 20485812--20486035 Score: 279
Period size: 100 Copynumber: 2.2 Consensus size: 100
20485802 TGACCTTGTA
* * * *
20485812 TATATTCGGCCACATAGGTATGTACATATGTGATGTTATATTGGATTTTGAATATTCGGCCATGA
1 TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
*
20485877 AGGTATGCACAAATGTGATATTATATTTGAATTTG
66 AGGTATGCACAAATGTGATATTATATTTGAATTTC
* * * * *
20485912 TATATTCGGCTATATAAGTAAGTACATATTTGATGTTAAATTTGATCTTGCATATTCGGCCAT-A
1 TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
* * *
20485976 TAGGTATGCACATATGTGATCTTATATTTGATTTTC
66 -AGGTATGCACAAATGTGATATTATATTTGAATTTC
* * *
20486012 TATAATCGACCAAATAAGTGAAGT
1 TATATTCGGCCACATAAGT-AAGT
20486036 TGGTTTATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
99 1 0.01
100 100 0.95
101 4 0.04
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (100 bp):
TATATTCGGCCACATAAGTAAGTACATATGTGATGTTAAATTGGATCTTGAATATTCGGCCATGA
AGGTATGCACAAATGTGATATTATATTTGAATTTC
Found at i:20489744 original size:68 final size:69
Alignment explanation
Indices: 20489581--20489749 Score: 207
Period size: 69 Copynumber: 2.5 Consensus size: 69
20489571 TTTAAGGTTT
* * * *
20489581 GTAGGTTTAATATCACAGCCCCCAAATAGTTAGTAAGAGTTAAAAGCTTCTAGCTGTCATTTAAA
1 GTAGGTTTAATAACACAGCCTCCAAACAGTTAGTAAGAGTTAAAAGCTTCTAGCTGTCATCTAAA
*
20489646 ACTT
66 ACTC
* * ** * *
20489650 GCAGGTTTAATACCACAATCTCCAAACAGTTAGTGAGAGTTAAAAGC-TCTTAGTTGTCA-CTAA
1 GTAGGTTTAATAACACAGCCTCCAAACAGTTAGTAAGAGTTAAAAGCTTC-TAGCTGTCATCTAA
20489713 AACTC
65 AACTC
*
20489718 GTAGGTTTAATAACGCAGCCTCCAAACAGTTA
1 GTAGGTTTAATAACACAGCCTCCAAACAGTTA
20489750 ACAAAATTCA
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
68 36 0.43
69 48 0.57
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (69 bp):
GTAGGTTTAATAACACAGCCTCCAAACAGTTAGTAAGAGTTAAAAGCTTCTAGCTGTCATCTAAA
ACTC
Found at i:20489834 original size:69 final size:70
Alignment explanation
Indices: 20489759--20489948 Score: 219
Period size: 71 Copynumber: 2.7 Consensus size: 70
20489749 AACAAAATTC
* * *
20489759 AAAAGCTC-CTAATTGTCATTCTAAGGCTCACAGGTTTAATA-CAGTAGCCCAAAATAGTTAGCG
1 AAAAGCTCTC-AACTGTCATTTTAAGGCTCACAGATTTAATACCAGTAGCCC-AAATAGTTAGCG
*
20489822 AGGGTT-
64 AGAGTTA
* * *
20489828 AAAAGCTCTCAACTGTCATTTTAAGGCTCACAAATTTAATACCA-CAACCTTCAAATAGTTAGCG
1 AAAAGCTCTCAACTGTCATTTTAAGGCTCACAGATTTAATACCAGTAGCC--CAAATAGTTAGCG
20489892 AGAGTTA
64 AGAGTTA
* * *
20489899 AAAAGCTCTCAACTATCATTTTAAGGCTCACAGTTTTAATATC-GTAGCCC
1 AAAAGCTCTCAACTGTCATTTTAAGGCTCACAGATTTAATACCAGTAGCCC
20489949 CCACACAACT
Statistics
Matches: 102, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
69 39 0.38
70 20 0.20
71 43 0.42
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (70 bp):
AAAAGCTCTCAACTGTCATTTTAAGGCTCACAGATTTAATACCAGTAGCCCAAATAGTTAGCGAG
AGTTA
Found at i:20502377 original size:9 final size:9
Alignment explanation
Indices: 20502365--20502389 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20502355 TATGGGCCGG
20502365 AATGGGCTA
1 AATGGGCTA
20502374 AATGGGCTA
1 AATGGGCTA
20502383 AATGGGC
1 AATGGGC
20502390 CCGATGGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.36, T:0.20
Consensus pattern (9 bp):
AATGGGCTA
Found at i:20502527 original size:29 final size:29
Alignment explanation
Indices: 20502495--20502577 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
20502485 CTAACGGGCG
20502495 ATATAAATGTGATTTGGGCTTAATGGACC
1 ATATAAATGTGATTTGGGCTTAATGGACC
*** * *
20502524 ATATACGGGTGATTTGGGCCTAATGGCCC
1 ATATAAATGTGATTTGGGCTTAATGGACC
* * *
20502553 ATATGAATATGA-TTGAGCTTAATGG
1 ATATAAATGTGATTTGGGCTTAATGG
20502578 GCCAGATACA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
28 11 0.26
29 31 0.74
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCTTAATGGACC
Found at i:20505712 original size:46 final size:46
Alignment explanation
Indices: 20505643--20505773 Score: 199
Period size: 46 Copynumber: 2.8 Consensus size: 46
20505633 GATATTTGGG
* *
20505643 CATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
20505689 TGTCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* *
20505735 CACCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20505774 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (46 bp):
CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:20508904 original size:51 final size:50
Alignment explanation
Indices: 20508770--20508904 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 50
20508760 GAAGCTATCT
* *
20508770 GGTACGCATAGTAGCCTGCACTTAGTACTACACACATGACCTCACCATCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACATGACCACACCATCG
** * * * * ***
20508820 AATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACATGACCACA-CCATCG
20508871 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
20508905 TGCGACCTCA
Statistics
Matches: 69, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 37 0.54
51 32 0.46
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (50 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACATGACCACACCATCG
Found at i:20513781 original size:43 final size:43
Alignment explanation
Indices: 20513731--20513879 Score: 174
Period size: 43 Copynumber: 3.7 Consensus size: 43
20513721 ATCTCATATT
* * *
20513731 GATGCCAATATCCCATACATGGTTTTATACGAAATCATATAAC
1 GATGCCAATATCCCAAACATGGTCTTACACGAAATCATATAAC
*
20513774 GATGCCAATGTCCCAAACATGGTCTTACACGAAATCATATAAC
1 GATGCCAATATCCCAAACATGGTCTTACACGAAATCATATAAC
20513817 GATG--------CC--ACATGGTCTTACACGAAATCATATAAC
1 GATGCCAATATCCCAAACATGGTCTTACACGAAATCATATAAC
* *
20513850 GATGCCAATGTCCCAGACATGGTCTTACAC
1 GATGCCAATATCCCAAACATGGTCTTACAC
20513880 ATAATCACAA
Statistics
Matches: 92, Mismatches: 4, Indels: 20
0.79 0.03 0.17
Matches are distributed among these distances:
33 31 0.34
35 2 0.02
41 2 0.02
43 57 0.62
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
GATGCCAATATCCCAAACATGGTCTTACACGAAATCATATAAC
Found at i:20513832 original size:33 final size:33
Alignment explanation
Indices: 20513790--20513856 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
20513780 AATGTCCCAA
20513790 ACATGGTCTTACACGAAATCATATAACGATGCC
1 ACATGGTCTTACACGAAATCATATAACGATGCC
20513823 ACATGGTCTTACACGAAATCATATAACGATGCC
1 ACATGGTCTTACACGAAATCATATAACGATGCC
20513856 A
1 A
20513857 ATGTCCCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (33 bp):
ACATGGTCTTACACGAAATCATATAACGATGCC
Found at i:20513886 original size:43 final size:43
Alignment explanation
Indices: 20513823--20513921 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
20513813 TAACGATGCC
*
20513823 ACATGGTCTTACACGAAATCA-TATAACGAT-GCCAATGTCCCAG
1 ACATGGTCTTACACGAAATCACAAT-AC-ATAGCCAATGTCCCAG
* *
20513866 ACATGGTCTTACAC-ATAATCACAATACATAGCTAATGTCCTAG
1 ACATGGTCTTACACGA-AATCACAATACATAGCCAATGTCCCAG
*
20513909 ATATGGTCTTACA
1 ACATGGTCTTACA
20513922 TGTAATCTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.06
43 44 0.90
44 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (43 bp):
ACATGGTCTTACACGAAATCACAATACATAGCCAATGTCCCAG
Found at i:20516672 original size:28 final size:28
Alignment explanation
Indices: 20516632--20516701 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
20516622 GCAATCAAAT
* * * *
20516632 ATGGTACTCAGTGTATGAAATGTTGAGA
1 ATGGAACTTAGTGTACGAAATATTGAGA
* * *
20516660 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGAACTTAGTGTACGAAATATTGAGA
*
20516688 ATGAAACTTAGTGT
1 ATGGAACTTAGTGT
20516702 GAAAAATATC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (28 bp):
ATGGAACTTAGTGTACGAAATATTGAGA
Found at i:20516710 original size:28 final size:28
Alignment explanation
Indices: 20516649--20516710 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
20516639 TCAGTGTATG
* ** **
20516649 AAATGTTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAGAATGAAACTTAGTGTGAA
*
20516677 AGATATTGAGAATGAAACTTAGTGTGAA
1 AAATATTGAGAATGAAACTTAGTGTGAA
20516705 AAATAT
1 AAATAT
20516711 CGAATGATTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGAAACTTAGTGTGAA
Found at i:20519028 original size:41 final size:41
Alignment explanation
Indices: 20518970--20519117 Score: 176
Period size: 41 Copynumber: 3.6 Consensus size: 41
20518960 GAGCTTGGTC
20518970 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
20519011 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
20519051 CCGAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
20519092 TCGAAGGGCTTTTGAGCCAGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
20519118 GAATCGGGCT
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
39 4 0.04
40 35 0.39
41 48 0.53
43 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:20527638 original size:11 final size:11
Alignment explanation
Indices: 20527622--20527646 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20527612 TTATATATAC
20527622 TAATAAAATAA
1 TAATAAAATAA
20527633 TAATAAAATAA
1 TAATAAAATAA
20527644 TAA
1 TAA
20527647 AATATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:20541240 original size:40 final size:40
Alignment explanation
Indices: 20541195--20541276 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
20541185 TATGAAATTG
* *
20541195 CCTTAGATTATGAATTAGAAGGTATTGGAGAGCAATTTTC
1 CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
*
20541235 CCTTAGATTAAGAATTAGAAAGTCTTGGAGAGCAATTTTC
1 CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
20541275 CC
1 CC
20541277 AAATTCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (40 bp):
CCTTAGATTAAGAATTAGAAAGTATTGGAGAGCAATTTTC
Found at i:20543002 original size:49 final size:49
Alignment explanation
Indices: 20542930--20543028 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
20542920 GTATAAAGAC
20542930 TCTGTTTATTTTGTTCAATGGCATGTATAGTATTTTGAGTATTTTGTTA
1 TCTGTTTATTTTGTTCAATGGCATGTATAGTATTTTGAGTATTTTGTTA
20542979 TCTGTTTATTTTGTTCAATGGCATGTATAGTATTTTGAGTATTTTGTTA
1 TCTGTTTATTTTGTTCAATGGCATGTATAGTATTTTGAGTATTTTGTTA
20543028 T
1 T
20543029 ATGTGTCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.20, C:0.06, G:0.18, T:0.56
Consensus pattern (49 bp):
TCTGTTTATTTTGTTCAATGGCATGTATAGTATTTTGAGTATTTTGTTA
Found at i:20560807 original size:9 final size:9
Alignment explanation
Indices: 20560793--20560824 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20560783 TGGTATCAGA
20560793 TTTTGGGCG
1 TTTTGGGCG
*
20560802 TTTTGGACG
1 TTTTGGGCG
20560811 TTTTGGGCG
1 TTTTGGGCG
20560820 TTTTG
1 TTTTG
20560825 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.03, C:0.09, G:0.38, T:0.50
Consensus pattern (9 bp):
TTTTGGGCG
Found at i:20565347 original size:13 final size:13
Alignment explanation
Indices: 20565329--20565354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20565319 ACCTGAAAGC
20565329 AATTTAATTCATA
1 AATTTAATTCATA
20565342 AATTTAATTCATA
1 AATTTAATTCATA
20565355 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:20565769 original size:20 final size:21
Alignment explanation
Indices: 20565744--20565782 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
20565734 TCAAACAAGC
20565744 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
20565764 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
20565783 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:20567056 original size:17 final size:17
Alignment explanation
Indices: 20567036--20567089 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
20567026 CTTCACTCGT
20567036 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
20567053 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
20567071 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
20567087 TTT
1 TTT
20567090 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:20567079 original size:18 final size:18
Alignment explanation
Indices: 20567058--20567109 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
20567048 CTCTCTTTCT
20567058 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
20567076 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
20567093 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
20567110 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:20567123 original size:6 final size:6
Alignment explanation
Indices: 20567114--20567212 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
20567104 CATTTTCATA
* * * **
20567114 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * **
20567165 GTTTTC GTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
20567213 GAATTCATTA
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:20568097 original size:20 final size:20
Alignment explanation
Indices: 20568051--20568097 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20568041 AGCTCGTTTC
*
20568051 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20568071 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20568091 CAGCTCA
1 CAGCTCA
20568098 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:20569944 original size:20 final size:20
Alignment explanation
Indices: 20569921--20569967 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20569911 GGGTTAAAAT
*
20569921 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
20569941 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
20569961 TGAGCTG
1 TGAGCTG
20569968 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:20571693 original size:48 final size:48
Alignment explanation
Indices: 20571638--20571743 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
20571628 TTGTCTTTTC
*
20571638 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
20571686 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
20571734 TTTCTTTTTC
1 TTTCTTTTTC
20571744 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:20572785 original size:10 final size:9
Alignment explanation
Indices: 20572772--20572807 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
20572762 TTTTCACTTT
20572772 TTTTTTGTTC
1 TTTTTT-TTC
20572782 TTTTTTTTAC
1 TTTTTTTT-C
20572792 TTTTTTTTC
1 TTTTTTTTC
20572801 TTTTTTT
1 TTTTTTT
20572808 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:20576122 original size:37 final size:37
Alignment explanation
Indices: 20576072--20576150 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
20576062 TTATTACGAA
* *
20576072 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
20576109 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
20576146 GTCTT
1 GTCTT
20576151 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:20576347 original size:47 final size:47
Alignment explanation
Indices: 20576269--20576761 Score: 824
Period size: 47 Copynumber: 10.4 Consensus size: 47
20576259 CCCTTCGAAA
* * * * * * *
20576269 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20576316 CCTGTCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576363 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20576410 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576457 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20576504 CTTATCACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTAT--CACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20576553 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576600 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20576647 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576694 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20576743 CTTATCACATATATACACT
1 CTTATCACATATATACACT
20576762 GTCTTGGCTG
Statistics
Matches: 422, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
47 330 0.78
49 92 0.22
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20576595 original size:190 final size:190
Alignment explanation
Indices: 20576269--20576761 Score: 837
Period size: 190 Copynumber: 2.6 Consensus size: 190
20576259 CCCTTCGAAA
* * * * * * * * *
20576269 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGT--CACATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATAC
*
20576332 CCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
20576397 TTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576457 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTTGGCCTTATCACACATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATAC
20576522 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
20576587 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
20576647 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATAC
*
20576712 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
20576762 GTCTTGGCTG
Statistics
Matches: 288, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 43 0.15
190 245 0.85
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (190 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:20589358 original size:43 final size:42
Alignment explanation
Indices: 20589309--20589405 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
20589299 CCAGATGTGC
**
20589309 TCTTACATGTAATCGAATATCGATG-CCACTATCCCAGACAGGG
1 TCTTACATGTAATAAAATA-CGATGTCCA-TATCCCAGACAGGG
* * * *
20589352 TCTTACATGAAATAAAATACGATGTCGATGTCCCAGACATGG
1 TCTTACATGTAATAAAATACGATGTCCATATCCCAGACAGGG
*
20589394 TCTTACACGTAA
1 TCTTACATGTAA
20589406 ATAATAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
42 27 0.60
43 18 0.40
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
TCTTACATGTAATAAAATACGATGTCCATATCCCAGACAGGG
Found at i:20593175 original size:16 final size:16
Alignment explanation
Indices: 20593156--20593202 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
20593146 TTGAACCAGG
*
20593156 CCGTGCATGAATCTTC
1 CCGTTCATGAATCTTC
20593172 CCGTTCATTGAA-CTTTC
1 CCGTTCA-TGAATC-TTC
*
20593189 CCGTTCATGCATCT
1 CCGTTCATGAATCT
20593203 CTTCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.17, C:0.32, G:0.15, T:0.36
Consensus pattern (16 bp):
CCGTTCATGAATCTTC
Found at i:20596690 original size:18 final size:18
Alignment explanation
Indices: 20596669--20596707 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
20596659 GATTGCGAGT
* *
20596669 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
20596687 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
20596705 GAA
1 GAA
20596708 GTTGAAGAAA
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:0.62, C:0.03, G:0.23, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:20599946 original size:18 final size:19
Alignment explanation
Indices: 20599923--20599961 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
20599913 TTTATCTCAA
*
20599923 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
20599941 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
20599960 TT
1 TT
20599962 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:20599977 original size:48 final size:49
Alignment explanation
Indices: 20599925--20600028 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
20599915 TATCTCAATT
* * *
20599925 TCTTTTTCCACTCT-TTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTCTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
20599973 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
20600021 TCTTTTTC
1 TCTTTTTC
20600029 TTTTTCTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.12, C:0.28, G:0.01, T:0.59
Consensus pattern (49 bp):
TCTTTTTCCACTCTCTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:20600000 original size:18 final size:18
Alignment explanation
Indices: 20599979--20600028 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
20599969 AAACTCTTTT
20599979 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
20599997 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
20600015 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
20600029 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:20600018 original size:24 final size:24
Alignment explanation
Indices: 20599954--20600035 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
20599944 CTTGTTCACA
*
20599954 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
20599978 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
20600002 TTCTTTTTCACTCTCAATCTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
20600026 TTCTTTTTCT
1 TTCTTTTTCT
20600036 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:20603491 original size:10 final size:10
Alignment explanation
Indices: 20603476--20603513 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20603466 GCTCGTTTCC
*
20603476 AGCTCACTCG
1 AGCTCAATCG
20603486 AGCTCAAGTC-
1 AGCTCAA-TCG
20603496 AGCTCAATCG
1 AGCTCAATCG
20603506 AGCTCAAT
1 AGCTCAAT
20603514 TTAGCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:20603519 original size:20 final size:20
Alignment explanation
Indices: 20603475--20603512 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20603465 AGCTCGTTTC
*
20603475 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
20603495 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
20603513 TTTAGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:20606331 original size:20 final size:20
Alignment explanation
Indices: 20606308--20606354 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20606298 GGGTTAAAAT
**
20606308 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
20606328 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
20606348 TGAGCTG
1 TGAGCTG
20606355 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:20608080 original size:48 final size:48
Alignment explanation
Indices: 20608025--20608130 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
20608015 TTGTCTTTTC
*
20608025 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
20608073 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
20608121 TTTCTTTTTC
1 TTTCTTTTTC
20608131 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:20609172 original size:10 final size:9
Alignment explanation
Indices: 20609159--20609194 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
20609149 TTTTCACTTT
20609159 TTTTTTGTTC
1 TTTTTT-TTC
20609169 TTTTTTTTAC
1 TTTTTTTT-C
20609179 TTTTTTTTC
1 TTTTTTTTC
20609188 TTTTTTT
1 TTTTTTT
20609195 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:20610756 original size:20 final size:20
Alignment explanation
Indices: 20610733--20610779 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
20610723 GGGTTAAAAT
**
20610733 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCAAG
* *
20610753 TGAGTTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
20610773 TGAGCTG
1 TGAGCTG
20610780 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:20611987 original size:20 final size:19
Alignment explanation
Indices: 20611940--20611987 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
20611930 AGTAAGCTCG
20611940 GTTGAGCTCAAATGAGCTA
1 GTTGAGCTCAAATGAGCTA
***
20611959 GAACAAGCTCAAATGAGCTGA
1 G-TTGAGCTCAAATGAGCT-A
20611980 GTTGAGCT
1 GTTGAGCT
20611988 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 3
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.86
21 2 0.10
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (19 bp):
GTTGAGCTCAAATGAGCTA
Found at i:20612639 original size:15 final size:15
Alignment explanation
Indices: 20612619--20612666 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
20612609 TCAAAGGTGG
20612619 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
20612634 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
20612649 -TTTATGGATATAAA
1 GTTTATGGATATGAA
20612663 GTTT
1 GTTT
20612667 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:20618774 original size:15 final size:15
Alignment explanation
Indices: 20618754--20618801 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
20618744 TCAAAGGTGG
20618754 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
20618769 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
20618784 -TTTATGGATATAAA
1 GTTTATGGATATGAA
20618798 GTTT
1 GTTT
20618802 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:20623655 original size:9 final size:9
Alignment explanation
Indices: 20623641--20623665 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20623631 TGGTATCAGA
20623641 TTTTGGGCG
1 TTTTGGGCG
20623650 TTTTGGGCG
1 TTTTGGGCG
20623659 TTTTGGG
1 TTTTGGG
20623666 TGTTATTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.44, T:0.48
Consensus pattern (9 bp):
TTTTGGGCG
Found at i:20626145 original size:18 final size:17
Alignment explanation
Indices: 20626122--20626225 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 17
20626112 AACAAGTGAG
20626122 GAAAAAGAAAAAGAGAAT
1 GAAAAAGAAAAAGA-AAT
*
20626140 GAAAAAGAGCAAAAAGAGATT
1 G-AAAA-AG-AAAAAGA-AAT
* **
20626161 GAGAGTGAAAAAGAAATT
1 GAAAAAGAAAAAGAAA-T
*
20626179 GAAGAAAG-AAGAGAAAAT
1 GAA-AAAGAAAAAG-AAAT
**
20626197 GAATTAGAAAAAGAAAT
1 GAAAAAGAAAAAGAAAT
20626214 --AAAAGAAAAAGA
1 GAAAAAGAAAAAGA
20626226 CGTGGAAAAG
Statistics
Matches: 65, Mismatches: 14, Indels: 17
0.68 0.15 0.18
Matches are distributed among these distances:
15 10 0.15
17 7 0.11
18 23 0.35
19 10 0.15
20 4 0.06
21 11 0.17
ACGTcount: A:0.66, C:0.01, G:0.23, T:0.10
Consensus pattern (17 bp):
GAAAAAGAAAAAGAAAT
Found at i:20633432 original size:19 final size:18
Alignment explanation
Indices: 20633399--20633442 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
20633389 AATACTATAT
20633399 ATAAATATAAAATAAAAA
1 ATAAATATAAAATAAAAA
** *
20633417 AGTAAATATACGATAAATA
1 A-TAAATATAAAATAAAAA
20633436 ATAAATA
1 ATAAATA
20633443 AAAGGCCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (18 bp):
ATAAATATAAAATAAAAA
Found at i:20634194 original size:32 final size:32
Alignment explanation
Indices: 20634158--20634219 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
20634148 AGCTTTTGGT
20634158 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
20634190 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
20634220 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:20639156 original size:10 final size:10
Alignment explanation
Indices: 20639143--20639188 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
20639133 AGCTCACTTG
20639143 AGCTCGTTTT
1 AGCTCGTTTT
*
20639153 AGCTCGTTTG
1 AGCTCGTTTT
*
20639163 AGCTCGAATTT
1 AGCTCG-TTTT
*
20639174 AGCTCGTTTC
1 AGCTCGTTTT
20639184 AGCTC
1 AGCTC
20639189 ATTCCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:20639176 original size:21 final size:20
Alignment explanation
Indices: 20639140--20639188 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
20639130 ATCAGCTCAC
*
20639140 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGATTTAGCTCGT
20639160 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
20639181 TTCAGCTC
1 TTGAGCTC
20639189 ATTCCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:20640460 original size:12 final size:12
Alignment explanation
Indices: 20640442--20640475 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20640432 TCCCTCATTT
20640442 CTTTTCACTCAC
1 CTTTTCACTCAC
* *
20640454 TTTTTCACACAC
1 CTTTTCACTCAC
20640466 CTTTTCACTC
1 CTTTTCACTC
20640476 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTTTCACTCAC
Found at i:20640483 original size:38 final size:36
Alignment explanation
Indices: 20640404--20640483 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 36
20640394 TTGATCTTTA
* * *
20640404 TTCTTTTCTCTCATTTTTACAACTTGTTTCCCTCAT
1 TTCTTTTCACTCATTTTTACAACCTGTTTCACTCAT
*
20640440 TTCTTTTCACTCACTTTTTCACACACCT-TTTCACTCTT
1 TTCTTTTCACTCA-TTTTT-ACA-ACCTGTTTCACTCAT
20640478 TTCTTT
1 TTCTTT
20640484 CTTTCCATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 12 0.32
37 5 0.14
38 17 0.46
39 3 0.08
ACGTcount: A:0.14, C:0.30, G:0.01, T:0.55
Consensus pattern (36 bp):
TTCTTTTCACTCATTTTTACAACCTGTTTCACTCAT
Found at i:20642610 original size:11 final size:11
Alignment explanation
Indices: 20642584--20642626 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
20642574 AATTACCTCT
*
20642584 ATTTTTTTTAT
1 ATTTTTTTTAA
*
20642595 TTTTTTTTTAA
1 ATTTTTTTTAA
**
20642606 ATTTTTTTCGA
1 ATTTTTTTTAA
20642617 ATTTTTTTTA
1 ATTTTTTTTA
20642627 TAATATACTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
ATTTTTTTTAA
Found at i:20643215 original size:14 final size:14
Alignment explanation
Indices: 20643168--20643215 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
20643158 GTACGAATGG
*
20643168 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
20643182 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
20643196 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
20643210 ATTGGT
1 AATGGT
20643216 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:20652827 original size:23 final size:22
Alignment explanation
Indices: 20652775--20652827 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
20652765 TCCACGTCTT
*
20652775 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
20652797 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
20652820 TTTCTTTT
1 TTTCTTTT
20652828 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:20657433 original size:30 final size:30
Alignment explanation
Indices: 20657353--20657434 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
20657343 CACTTTCAAG
*
20657353 TCACGAGCTAAACCTTAGCTCAACTTCAGC
1 TCACGAGCTAAAGCTTAGCTCAACTTCAGC
* * ** * *
20657383 TTAGGAG-TTTAGCCTCAGCTCAACTTTAGC
1 TCACGAGCTAAAG-CTTAGCTCAACTTCAGC
20657413 TCACGAGCTAAAGCTTAGCTCA
1 TCACGAGCTAAAGCTTAGCTCA
20657435 TTTTAGTTTA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 33 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (30 bp):
TCACGAGCTAAAGCTTAGCTCAACTTCAGC
Found at i:20660438 original size:23 final size:21
Alignment explanation
Indices: 20660388--20660438 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
20660378 CCTTTCCACG
*
20660388 TCTTTTGTTTCTTTTTCTAAT
1 TCTTTTCTTTCTTTTTCTAAT
20660409 TCATTTTCTCTTCTTTCTTC-AATT
1 TC-TTTTCT-TTCTTT-TTCTAA-T
20660433 TCTTTT
1 TCTTTT
20660439 TCACTCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 12 0.48
24 6 0.24
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.69
Consensus pattern (21 bp):
TCTTTTCTTTCTTTTTCTAAT
Found at i:20664705 original size:13 final size:12
Alignment explanation
Indices: 20664701--20664747 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
20664691 AAATTCAGAA
20664701 AAAAAAAAATTC
1 AAAAAAAAATTC
*
20664713 GAAAAAAAATTC
1 AAAAAAAAATTC
*
20664725 AAAAAAAAGTTTC
1 AAAAAAAA-ATTC
20664738 AAAAAAAAAT
1 AAAAAAAAAT
20664748 GATTTGTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAAAAAAATTC
Found at i:20664708 original size:16 final size:15
Alignment explanation
Indices: 20664687--20664721 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
20664677 ATACAAGTAT
20664687 AAAAAAATTCAGAAAA
1 AAAAAAATTC-GAAAA
20664703 AAAAAAATTCGAAAA
1 AAAAAAATTCGAAAA
20664718 AAAA
1 AAAA
20664722 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAAAATTCGAAAA
Found at i:20665497 original size:30 final size:31
Alignment explanation
Indices: 20665463--20665559 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
20665453 AGCTCACTCC
*
20665463 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
20665493 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
20665523 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
20665553 TAGCTCA
1 TAGCTCA
20665560 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:20666449 original size:22 final size:20
Alignment explanation
Indices: 20666417--20666465 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
20666407 GCCAAATTTA
20666417 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
20666440 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
20666460 TGAACA
1 TGAACA
20666466 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:20667352 original size:12 final size:12
Alignment explanation
Indices: 20667335--20667379 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
20667325 TTATACAAGT
20667335 AAAAAAAATTCG
1 AAAAAAAATTCG
20667347 AAAAAAAATTC-
1 AAAAAAAATTCG
*
20667358 AAAAAAATTTTCG
1 AAAAAAA-ATTCG
20667371 AAAAGAAAA
1 AAAA-AAAA
20667380 AAAATGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 7 0.25
12 14 0.50
13 4 0.14
14 3 0.11
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:20667362 original size:42 final size:39
Alignment explanation
Indices: 20667315--20667393 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 39
20667305 CAATATAGTA
* *
20667315 CAAAAAAAATTTATACAAGTAAAAAAAATTCGAAAAAAAATT
1 CAAAAAAAATTTAGAAAAG-AAAAAAAA-T-GAAAAAAAATT
* *
20667357 CAAAAAAATTTTCGAAAAGAAAAAAAATGAAAAAAAA
1 CAAAAAAAATTTAGAAAAGAAAAAAAATGAAAAAAAA
20667394 GTGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 9 0.27
40 1 0.03
41 8 0.24
42 15 0.45
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (39 bp):
CAAAAAAAATTTAGAAAAGAAAAAAAATGAAAAAAAATT
Found at i:20668403 original size:12 final size:12
Alignment explanation
Indices: 20668395--20668419 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20668385 TTTGAAAAGC
20668395 AAAAAGAAAATG
1 AAAAAGAAAATG
20668407 AAAAAGAAAATG
1 AAAAAGAAAATG
20668419 A
1 A
20668420 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:20668416 original size:18 final size:18
Alignment explanation
Indices: 20668389--20668444 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
20668379 AAAGCCTTTG
20668389 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
20668408 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
20668426 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
20668443 AA
1 AA
20668445 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:20668429 original size:30 final size:31
Alignment explanation
Indices: 20668395--20668476 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
20668385 TTTGAAAAGC
*
20668395 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
20668425 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
20668455 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
20668477 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:20670272 original size:30 final size:30
Alignment explanation
Indices: 20670186--20670283 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
20670176 TTAAACTAAA
* *
20670186 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
20670216 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
20670246 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
20670276 ATGAGCTA
1 ATGAGCTA
20670284 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:20672020 original size:20 final size:19
Alignment explanation
Indices: 20671997--20672061 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
20671987 AAGCTCAAAC
20671997 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
20672017 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * *
20672037 AAGCTCATGTGAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
20672057 GAGCT
1 GAGCT
20672062 GGGAAAAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 31 0.84
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:20672021 original size:10 final size:10
Alignment explanation
Indices: 20671997--20672061 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
20671987 AAGCTCAAAC
*
20671997 GAGCTAAAGT
1 GAGCTAAATT
*
20672007 AAGCTAAATT
1 GAGCTAAATT
*
20672017 GAGCTCAAA-C
1 GAGCT-AAATT
20672027 GAGCTAAATT
1 GAGCTAAATT
* *
20672037 AAGCT-CATGT
1 GAGCTAAAT-T
20672047 GAGCTAAATT
1 GAGCTAAATT
20672057 GAGCT
1 GAGCT
20672062 GGGAAAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
9 5 0.12
10 32 0.76
11 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (10 bp):
GAGCTAAATT
Found at i:20673867 original size:33 final size:33
Alignment explanation
Indices: 20673829--20673891 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
20673819 GATTACTCAC
20673829 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
20673862 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
20673892 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:20673918 original size:27 final size:27
Alignment explanation
Indices: 20673888--20673973 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
20673878 TCAAGCTCTC
*
20673888 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
*
20673915 TTTCAATTT-TTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
20673943 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
20673970 TTTC
1 TTTC
20673974 TCTCACTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.08
27 21 0.41
28 16 0.31
29 5 0.10
30 5 0.10
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:20673948 original size:12 final size:12
Alignment explanation
Indices: 20673909--20673997 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 12
20673899 TTTTTCGCTT
20673909 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
20673921 TTTTTTTCATTCTCAA
1 -TTTCTT--TT-TCAA
20673937 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
20673949 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
20673964 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
20673976 TCACTTTTTCGA
1 TTTCTTTTTCAA
20673988 TTTCTTTTTC
1 TTTCTTTTTC
20673998 TTTTGCAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
12 23 0.39
13 14 0.24
14 7 0.12
15 11 0.19
16 4 0.07
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.67
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:20673949 original size:28 final size:27
Alignment explanation
Indices: 20673909--20673973 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
20673899 TTTTTCGCTT
*
20673909 TTTCTTTTTCAATTTTTTTCATTC-TCAA
1 TTTCTTTTTCAATTTTCTT--TTCTTCAA
*
20673937 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
20673964 TTTCTTTTTC
1 TTTCTTTTTC
20673974 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 3 0.09
27 13 0.38
28 18 0.53
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:20674000 original size:18 final size:18
Alignment explanation
Indices: 20673979--20674037 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
20673969 TTTTCTCTCA
20673979 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
20673997 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
20674015 CTTTTTTGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
20674033 GTTTT
1 CTTTT
20674038 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Done.