Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold108
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: 2128633
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 114048 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1932259 original size:7 final size:6
Alignment explanation
Indices: 1932233--1932276 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1932223 CCCAAAGTAG
* *
1932233 AGAAAA GGAAAA GGAAAA AGAACAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA AGAAAA A
1932277 TGGAAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:1933509 original size:26 final size:25
Alignment explanation
Indices: 1933480--1933528 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1933470 GCTTTCTGCT
* *
1933480 ATTCTCTTCTTTTTTTTTCCTTTTTG
1 ATTCT-TTATTTTTTCTTCCTTTTTG
*
1933506 ATTCTTTATTTTTTCTTCGTTTT
1 ATTCTTTATTTTTTCTTCCTTTT
1933529 AATCACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.73
Consensus pattern (25 bp):
ATTCTTTATTTTTTCTTCCTTTTTG
Found at i:1950576 original size:51 final size:51
Alignment explanation
Indices: 1950521--1950617 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
1950511 CCAGGCCGTT
* *
1950521 TAACACACTGTTCATCGAATTCAAACCACACGTGCAAGGGACACGTGTGTG
1 TAACACACTGTTCATCGAATTCAAACCACACGGGCAAGCGACACGTGTGTG
* * *
1950572 TAACACATTGTTCATTGAATTCAAACCACACGGGCAATCGACACGT
1 TAACACACTGTTCATCGAATTCAAACCACACGGGCAAGCGACACGT
1950618 ACGTGTGTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (51 bp):
TAACACACTGTTCATCGAATTCAAACCACACGGGCAAGCGACACGTGTGTG
Found at i:1957441 original size:37 final size:38
Alignment explanation
Indices: 1957385--1957460 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
1957375 AAACTGAATG
* * *
1957385 TGAAAGCTCAAACTGAAACCGAAGTT-AAAATTCCAAAC
1 TGAAAACTCAAACTAAAACCGAAGTTGAAAA-CCCAAAC
*
1957423 TGAAAACT-AAACTAAAACCTAAGTTGAAAACCCAAAC
1 TGAAAACTCAAACTAAAACCGAAGTTGAAAACCCAAAC
1957460 T
1 T
1957461 TAAGGCTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 22 0.67
38 11 0.33
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (38 bp):
TGAAAACTCAAACTAAAACCGAAGTTGAAAACCCAAAC
Found at i:1957550 original size:732 final size:724
Alignment explanation
Indices: 1956148--1958442 Score: 3068
Period size: 732 Copynumber: 3.1 Consensus size: 724
1956138 GTTTCAATAA
* * * * * * * *
1956148 TAGATGAACTAAGCTCTCGAAGTAGCCTACTTGAAACAAAAAACTTAGAAATTTTGGGTAAATTG
1 TAGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAGAAACCTAGAAATTCTGAGCAAATTG
* * * * * * *
1956213 TGACGATTTTCAATGTTTTGAGCCCCAAAATCTTAAGCTTTTGGTAAATGTTTTTTGATAAAACG
66 TGACGATTTTCAATATTTTGAGCCCCAAAATCTTAAGCTTTTGGTGATTGGTTTCT-ATGAAATG
* * * * * * *
1956278 TAAGTTCTAGTTTTAGAATTACATTTTACCTTTAAATTACTATTCTTAAAACCACAAAATATTTG
130 AAATTTCTAGTTTTAGAATCACATTTCACCTTTAAAATAATATTCTTAAAACCAAAAAATATTTG
* *
1956343 AACGAGCATAGAGTTTTAATGGCTT-AAACGAGCCAAAAAGTCATGAAAATTCTTAAATATAAAA
195 AACGAGCATAGAGTTTTGATGGCTTAAAACGAGCCAAAAA-TCATGAAAATTCTAAAATATAAAA
* *
1956407 TACAAAAAAATTTCAATTTTATTTCATTTAATATTTATTGTTATCCAAATTATGTTTTGTTAAAT
259 T---AAAAAATTT-TATTTTATTTCATTTAATA-TTATTGTTATCCAAATTATGTTTTATTAAAT
* *
1956472 TAAACATAATATTAAATTAATTTTCAAAATTTTTTGTTGAATTTTTTATTTAAATATATTACAAA
319 TAAA-ATCATATTAAATTAATTTTCAAAATTTTTAGTTGAATTTTTTATTT--ATATATTACAAA
* * * * * *
1956537 TTTTTAGAATTACCACACGTGTTAAGGTACTCGATAAGTTATCGCACTACCAAAATGCCTTGGAA
381 ATTGTAGAATTATCACACGTGTTAAGTTACTCGGTAAGTTATCGCACAACCAAAATGCCTTGGAA
* * ** *
1956602 TCGAAATCTCAAACCGAAACCAAAT-C--A-AAAACCCAAAACCCAAACTGAAAGTGAAAGCCCA
446 TCGAAACCCCAAATAGAAACCAAATCCAAACAAAACCCAAAACCGAAACTGAAAGTGAAAGCCCA
* * * * *
1956663 AAC-CAACACCGAATCTAAAGCTCCAAACTGGAAACTAAACTAAAACCTAAATCGAAAACCCAAA
511 AACTGAA-ACCGAATCTAAAACTCCAAACTGAAAACTAAACTAAAACCTAAGTTGAAAACCCAAA
* *
1956727 CTTAGGGGTTTCAACATATTTGGTAACTACATTTAAGGCTTTTTAAAACCATCTATTGTTTCTCT
575 CTTAAGGCTTTCAACATATTTGGTAACTACATTTAAGGCTTTTTAAAACCATCTATTGTTTCT-T
* *
1956792 -TTCTAGTCGAACTTTAAATGATTTCTGCTGTACGAAATGTGATATTTCCATTGGTTTGTTTTTC
639 ATTCTAGTCGAACTTTAAATGATTTCTGTTGTATGAAATGTGATATTTCCATTGGTTTGTTTTTC
* *
1956856 TAGCCAAATTGAATTTTGTCT
704 TAGCCAAATTGAGTTATGTCT
* *
1956877 TTGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAGAAACCTAGAAATTCTAAGCAAATTG
1 TAGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAGAAACCTAGAAATTCTGAGCAAATTG
* * *
1956942 TGACCATTTGT-AATATTTTGAGCCCCAAAATCTTAAACTTTTGGTGATTGGTTTCTATGGAATG
66 TGACGATTT-TCAATATTTTGAGCCCCAAAATCTTAAGCTTTTGGTGATTGGTTTCTATGAAATG
1957006 AAATTTCTAGTTTTAGAATCACATTTCACCTTTAAAATAATATTCTTAAAACCAAAAAAATATTT
130 AAATTTCTAGTTTTAGAATCACATTTCACCTTTAAAATAATATTCTTAAAACC-AAAAAATATTT
1957071 GAACGAGCATAGAGTTTTGATGGCTTAAAACGAGCCAAATAATCATGAAAATTCTAAAATATAAA
194 GAACGAGCATAGAGTTTTGATGGCTTAAAACGAGCCAAA-AATCATGAAAATTCTAAAATATAAA
* *
1957136 ATAAAATAATTTTATTTTATTTCTTTTTAATATTATTGTTATCTAAATTATGTTTTATTAAATTA
258 ATAAAA-AATTTTATTTTATTTC-ATTTAATATTATTGTTATCCAAATTATGTTTTATTAAATTA
* * * *
1957201 AAATCATATTACATTGATTTTCAAAAATTTTAGTTGAATTTTTTACTTTATATAATACAAAATTG
321 AAATCATATTAAATTAATTTTCAAAATTTTTAGTTGAATTTTTTA-TTTATATATTACAAAATTG
* * *
1957266 TAGAATTATCACACGTGTTAAGTTAC-CGGGTAAGTTTTTGCACAACCAAAATGCCTTGAAATC-
385 TAGAATTATCACACGTGTTAAGTTACTC-GGTAAGTTATCGCACAACCAAAATGCCTTGGAATCG
* *
1957329 AAAGCCCCAAATAGAAACCAAATCCAAAACCCAAAACCCAAAACCGAAACTGAATGTGAAAGCTC
449 AAA-CCCCAAATAGAAACCAAATCC-AAA--CAAAACCCAAAACCGAAACTGAAAGTGAAAGCCC
*
1957394 AAACTGAAACCGAAGT-TAAAATTCCAAACTGAAAACTAAACTAAAACCTAAGTTGAAAACCCAA
510 AAACTGAAACCGAA-TCTAAAACTCCAAACTGAAAACTAAACTAAAACCTAAGTTGAAAACCCAA
1957458 ACTTAAGGCTTTCAACATA-TTGAGTAACTACATTTAAGG-TGTTTTAAAACCATCTATTGTTTC
574 ACTTAAGGCTTTCAACATATTTG-GTAACTACATTTAAGGCT-TTTTAAAACCATCTATTGTTTC
* *
1957521 TTATTCTAGTCGAACTTTAAATGATTTCTGTTGTATGAAATGCGATCTTTCCATTGGTTTGTTTT
637 TTATTCTAGTCGAACTTTAAATGATTTCTGTTGTATGAAATGTGATATTTCCATTGGTTTGTTTT
* *
1957586 TCTAGCCAAATTGAGTTCTATCT
702 TCTAGCCAAATTGAGTTATGTCT
* * *
1957609 TAGATGAACTAAGCTCCCAAATTAGCCTAATTGAAACAGGAAACCTAGAAATTTTGAGCAAATTG
1 TAGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAGAAACCTAGAAATTCTGAGCAAATTG
* * * *
1957674 CGACGATTTGT-AATATTTTGAGCACCAAAATCTTAGGCTTTTGGTGATTGGTTTCCATGAAATG
66 TGACGATTT-TCAATATTTTGAGCCCCAAAATCTTAAGCTTTTGGTGATTGGTTTCTATGAAATG
* * *
1957738 GAATTTCTAGTTTTAGAATCACATTTGACCTTTAAAATAATATTCTTAAAA-CTAAAAATATTTG
130 AAATTTCTAGTTTTAGAATCACATTTCACCTTTAAAATAATATTCTTAAAACCAAAAAATATTTG
* * * *
1957802 AATGAGCATAGAGTTTTGATGGCTTAAAATGAGCCAAAAAATCATGAAAATTTTGAAATATAAAA
195 AACGAGCATAGAGTTTTGATGGCTTAAAACGAGCC-AAAAATCATGAAAATTCTAAAATATAAAA
* *
1957867 TACAAAATTTTTTGATTTTATTTCAGTTTCATATTATTGTTATCCAAATTATGTTTTATTAAATT
259 TA-AAAA-ATTTT-ATTTTATTTCA-TTTAATATTATTGTTATCCAAATTATGTTTTATTAAATT
1957932 AAAAGTCATATTAAATTAATTTTCAAAATTTTTAGTTGAATTTTTTATTTATATATTACAAAATT
320 AAAA-TCATATTAAATTAATTTTCAAAATTTTTAGTTGAATTTTTTATTTATATATTACAAAATT
* * * * * *
1957997 GAAAAATTATCACACGTGTTAAGTTACTCGGTAGGTTATCGCACAATCGAAATACCTTGGAATCG
384 GTAGAATTATCACACGTGTTAAGTTACTCGGTAAGTTATCGCACAACCAAAATGCCTTGGAATCG
* * **
1958062 AAACCCCAAATGGAAACCAAATCCAAAC----CCTAAAATTGAATA-TGAAAGTGAAAGCCCAAA
449 AAACCCCAAATAGAAACCAAATCCAAACAAAACCCAAAACCGAA-ACTGAAAGTGAAAGCCCAAA
* * *
1958122 -TCGACACCGAATCTAAAACTCCAAACCGAAAACTAAACTGAAACCTAAGTTGAAAACCCAAACT
513 CT-GAAACCGAATCTAAAACTCCAAACTGAAAACTAAACTAAAACCTAAGTTGAAAACCCAAACT
*
1958186 TAAGGCTTTCAACATATTTGGATAACTACATTTAAGGCTTTTTAAAACCATCTATTGTTTCTCAT
577 TAAGGCTTTCAACATATTTGG-TAACTACATTTAAGGCTTTTTAAAACCATCTATTGTTTCTTAT
* *
1958251 TCTCGTCGAACTTTAAATGATTTTTGTTGTATGAAATGTGATATTTCCATTGGTTTGTTTTTCTA
641 TCTAGTCGAACTTTAAATGATTTCTGTTGTATGAAATGTGATATTTCCATTGGTTTGTTTTTCTA
1958316 GCCAAATTGAGTTATGTCT
706 GCCAAATTGAGTTATGTCT
** * * *
1958335 TAGATGAACTAATTTCCCAAAGTAGCCTATTTGAAAC-AGAAAACTTAGAAATTCTGAGCAAGTT
1 TAGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAG-AAACCTAGAAATTCTGAGCAAATT
* * * ** * *
1958399 CTGACAATTTTCAATGTTTTGATTCCCAAAATCATAGGCTTTTG
65 GTGACGATTTTCAATATTTTGAGCCCCAAAATCTTAAGCTTTTG
1958443 TTAGAATTGT
Statistics
Matches: 1390, Mismatches: 139, Indels: 77
0.87 0.09 0.05
Matches are distributed among these distances:
724 6 0.00
725 182 0.13
726 249 0.18
727 51 0.04
728 64 0.05
729 139 0.10
730 108 0.08
731 21 0.02
732 524 0.38
733 46 0.03
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (724 bp):
TAGATGAACTAAGCTCCCAAAGTAGCCTAATTGAAACAAGAAACCTAGAAATTCTGAGCAAATTG
TGACGATTTTCAATATTTTGAGCCCCAAAATCTTAAGCTTTTGGTGATTGGTTTCTATGAAATGA
AATTTCTAGTTTTAGAATCACATTTCACCTTTAAAATAATATTCTTAAAACCAAAAAATATTTGA
ACGAGCATAGAGTTTTGATGGCTTAAAACGAGCCAAAAATCATGAAAATTCTAAAATATAAAATA
AAAAATTTTATTTTATTTCATTTAATATTATTGTTATCCAAATTATGTTTTATTAAATTAAAATC
ATATTAAATTAATTTTCAAAATTTTTAGTTGAATTTTTTATTTATATATTACAAAATTGTAGAAT
TATCACACGTGTTAAGTTACTCGGTAAGTTATCGCACAACCAAAATGCCTTGGAATCGAAACCCC
AAATAGAAACCAAATCCAAACAAAACCCAAAACCGAAACTGAAAGTGAAAGCCCAAACTGAAACC
GAATCTAAAACTCCAAACTGAAAACTAAACTAAAACCTAAGTTGAAAACCCAAACTTAAGGCTTT
CAACATATTTGGTAACTACATTTAAGGCTTTTTAAAACCATCTATTGTTTCTTATTCTAGTCGAA
CTTTAAATGATTTCTGTTGTATGAAATGTGATATTTCCATTGGTTTGTTTTTCTAGCCAAATTGA
GTTATGTCT
Found at i:1961349 original size:29 final size:30
Alignment explanation
Indices: 1961293--1961404 Score: 84
Period size: 31 Copynumber: 3.7 Consensus size: 30
1961283 AATCTCAAAA
* *
1961293 TTATACATGAACTTTGATTTAATGTGCAATT
1 TTATACATGAACTTTAATTT-AGGTGCAATT
*
1961324 TTATGCATGAACTTTAATTT-GGTGCAATT
1 TTATACATGAACTTTAATTTAGGTGCAATT
* * * * *
1961353 ATACACGTGAAACTTTAATTGT-GGTTCAAAT
1 TTATACATG-AACTTTAATT-TAGGTGCAATT
* *
1961384 GTATACTTGAAACTTTAATTT
1 TTATACATG-AACTTTAATTT
1961405 TGATTTAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 13 0.19
30 11 0.16
31 43 0.64
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (30 bp):
TTATACATGAACTTTAATTTAGGTGCAATT
Found at i:1961398 original size:31 final size:30
Alignment explanation
Indices: 1961333--1961404 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 30
1961323 TTTATGCATG
*
1961333 AACTTTAATTTGGTGCAATTATACACGTGA
1 AACTTTAATTTGGTGCAAATATACACGTGA
* * * *
1961363 AACTTTAATTGTGGTTCAAATGTATACTTGA
1 AACTTTAATT-TGGTGCAAATATACACGTGA
1961394 AACTTTAATTT
1 AACTTTAATTT
1961405 TGATTTAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATACACGTGA
Found at i:1964908 original size:27 final size:26
Alignment explanation
Indices: 1964888--1965134 Score: 289
Period size: 27 Copynumber: 9.0 Consensus size: 26
1964878 GGGTATAATA
1964888 GTCATTTTACCCTATAGGGGTATTTC
1 GTCATTTTACCCTATAGGGGTATTTC
1964914 GATCATTTTACCCTATAGGGGTATTTC
1 G-TCATTTTACCCTATAGGGGTATTTC
* *
1964941 GGTCATTTTACCCTAAAAGGGTATTTC
1 -GTCATTTTACCCTATAGGGGTATTTC
*
1964968 GATCATTTTACCCTATGGGGGTATTTC
1 G-TCATTTTACCCTATAGGGGTATTTC
* * *
1964995 GTTTATTTTACCCTATGGGGGTATTTTG
1 G-TCATTTTACCCTATAGGGGTA-TTTC
1965023 GTCATTTTACCCTATAGGGGTATTTC
1 GTCATTTTACCCTATAGGGGTATTTC
1965049 TGTCATTTTACCCTAT-GAGGGTATTTC
1 -GTCATTTTACCCTATAG-GGGTATTTC
* * *
1965076 GATCATTTTACCTTATGGGGGTATTTTA
1 G-TCATTTTACCCTATAGGGGTA-TTTC
1965104 GTCATTTTACCTACCCTATAGGGGTATTTC
1 GTCA-TTT---TACCCTATAGGGGTATTTC
1965134 G
1 G
1965135 ATTATATTAC
Statistics
Matches: 192, Mismatches: 16, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.04
27 155 0.81
28 13 0.07
30 4 0.02
31 13 0.07
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCCTATAGGGGTATTTC
Found at i:1965003 original size:81 final size:81
Alignment explanation
Indices: 1964888--1965114 Score: 348
Period size: 81 Copynumber: 2.8 Consensus size: 81
1964878 GGGTATAATA
* * *
1964888 GTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACC
1964953 CTAAAAGGGTATTTC-
66 CTAAAAGGGTATTTCT
* *
1964968 GATCATTTTACCCTATGGGGGTATTTCGTTTATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
1 G-TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTAC
* *
1965033 CCTATAGGGGTATTTCT
65 CCTAAAAGGGTATTTCT
* * *
1965050 GTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCTTATGGGGGTATTTTAGTCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACC
1965115 TACCCTATAG
Statistics
Matches: 133, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.01
81 131 0.98
82 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (81 bp):
GTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACC
CTAAAAGGGTATTTCT
Found at i:1969771 original size:88 final size:89
Alignment explanation
Indices: 1969595--1969764 Score: 245
Period size: 88 Copynumber: 1.9 Consensus size: 89
1969585 TAGTGTCGTA
1969595 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
1 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
** * *
1969660 TTGATCTCGATAACTAGGATCATT
66 TTGATCTAAATAAATAAGATCATT
* * * *
1969684 GTAGTAGAGTCGAAC-AATCCTAAGCTTTAGCTTTTCCTTTATTTAAGT-TCGATTGTGGTTTAT
1 GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCT-GATTGTGGTTTAT
1969747 CTTGATCTAAATAAATAA
65 CTTGATCTAAATAAATAA
1969765 TTTCATTTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
87 1 0.01
88 56 0.78
89 15 0.21
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (89 bp):
GTAGTAGAGTCGAACTAATCCGAAGCTTTAACTTTTCCTTGAATTAAGTCTGATTGTGGTTTATC
TTGATCTAAATAAATAAGATCATT
Found at i:1970483 original size:27 final size:27
Alignment explanation
Indices: 1970436--1970663 Score: 216
Period size: 27 Copynumber: 8.4 Consensus size: 27
1970426 TTGGTCTAGT
* *
1970436 GGTAGAATGA-CTAAAACACCCTCATAG
1 GGTAAAATGACCT-AAATACCCTCATAG
1970463 GGTAAAATGACCTAAATACCCTCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
* *
1970490 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
*
1970517 GGTAAAATGA-CTGAAATACCCCCATAG
1 GGTAAAATGACCT-AAATACCCTCATAG
* * *
1970544 GATAAAATGAACGAAATACCC-CAATAG
1 GGTAAAATGACCTAAATACCCTC-ATAG
* *
1970571 GGTAAAAATGA-TTGAAGTAACCCT-ATAG
1 GGT-AAAATGACCT-AAAT-ACCCTCATAG
* *
1970599 GGTAAAATTACCAAAATACCCTCATAG
1 GGTAAAATGACCTAAATACCCTCATAG
* *
1970626 GGTAAAATGATCGAAATACCC-CTATAG
1 GGTAAAATGACCTAAATACCCTC-ATAG
*
1970653 AGTAAAATGAC
1 GGTAAAATGAC
1970664 TGTTATACCC
Statistics
Matches: 170, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
26 8 0.05
27 138 0.81
28 20 0.12
29 4 0.02
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCTAAATACCCTCATAG
Found at i:1970625 original size:82 final size:81
Alignment explanation
Indices: 1970436--1970663 Score: 253
Period size: 82 Copynumber: 2.8 Consensus size: 81
1970426 TTGGTCTAGT
* * * * *
1970436 GGTAGAATGACTAAAACACCCTCATAGGGTAAAATGACCTAAATACCCTCATAGGGT-AAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCC-CATAGGGTAAAAATGA
*
1970500 CCAAAATACCCCCATAG
65 CCAAAATAACCCCATAG
** * *
1970517 GGTAAAATGACTGAAATACCCCCATAGGATAAAATGAACGAAATACCCCAATAGGGTAAAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCC-ATAGGGTAAAAATGA
*** * *
1970582 TTGAAGTAACCCTATAG
65 CCAAAATAACCCCATAG
* * *
1970599 GGTAAAATTACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAGAGT-AAAATGA
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCC-ATAGGGTAAAAATGA
1970663 C
65 C
1970664 TGTTATACCC
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 55 0.45
82 67 0.54
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (81 bp):
GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGAACGAAATACCCCATAGGGTAAAAATGAC
CAAAATAACCCCATAG
Found at i:1970671 original size:27 final size:27
Alignment explanation
Indices: 1970641--1970696 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1970631 AATGATCGAA
1970641 ATACCCCTATAGAG-TAAAATGACTGTT
1 ATACCCCTA-AGAGATAAAATGACTGTT
* *
1970668 ATACCCCTAGGAGATGAAATGACTGTT
1 ATACCCCTAAGAGATAAAATGACTGTT
1970695 AT
1 AT
1970697 GGCTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
ATACCCCTAAGAGATAAAATGACTGTT
Found at i:1970673 original size:54 final size:54
Alignment explanation
Indices: 1970436--1970663 Score: 264
Period size: 54 Copynumber: 4.2 Consensus size: 54
1970426 TTGGTCTAGT
* * * * *
1970436 GGTAGAATGACTAAAACACCCTCATAGGGTAAAATGACCTAAATA-CCCTCATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCT-ATAG
* *
1970490 GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGA-CTGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATC-GAAATACCCCTATAG
* * * * * *
1970544 GATAAAATGAACGAAATACCC-CAATAGGGTAAAAATGATTGAAGTAACCCTATAG
1 GGTAAAATGACCAAAATACCCTC-ATAGGGT-AAAATGATCGAAATACCCCTATAG
*
1970599 GGTAAAATTACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
*
1970653 AGTAAAATGAC
1 GGTAAAATGAC
1970664 TGTTATACCC
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
53 2 0.01
54 97 0.66
55 46 0.32
56 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (54 bp):
GGTAAAATGACCAAAATACCCTCATAGGGTAAAATGATCGAAATACCCCTATAG
Found at i:1975123 original size:13 final size:12
Alignment explanation
Indices: 1975078--1975125 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1975068 ATTTCATGTT
1975078 ATTTAAAAAAAA
1 ATTTAAAAAAAA
* *
1975090 ATTGAAAAAAAC
1 ATTTAAAAAAAA
* *
1975102 TTTTGAAAAGAAA
1 ATTT-AAAAAAAA
1975115 ATTTAAAAAAA
1 ATTTAAAAAAA
1975126 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (12 bp):
ATTTAAAAAAAA
Found at i:1976596 original size:19 final size:19
Alignment explanation
Indices: 1976554--1976596 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1976544 ACTTTGTTCT
*
1976554 CTAAAAAAAAGAAAAAAAA
1 CTAATAAAAAGAAAAAAAA
* *
1976573 C-AATAAAAAGGAGAAAAA
1 CTAATAAAAAGAAAAAAAA
1976591 CTAATA
1 CTAATA
1976597 TTTTTTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (19 bp):
CTAATAAAAAGAAAAAAAA
Found at i:1980085 original size:21 final size:20
Alignment explanation
Indices: 1980040--1980085 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1980030 TTGTTGGAAT
1980040 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
1980059 GATTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
1980080 GGTTGA
1 GGTTGA
1980086 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:1990902 original size:18 final size:19
Alignment explanation
Indices: 1990874--1990910 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1990864 GCATTCACAT
1990874 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
1990893 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
1990911 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:1991195 original size:21 final size:20
Alignment explanation
Indices: 1991150--1991195 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1991140 TTGTTGGAAT
1991150 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
1991169 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
1991190 GGTTGA
1 GGTTGA
1991196 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:2003392 original size:44 final size:45
Alignment explanation
Indices: 2003328--2003420 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 45
2003318 GGTAACCCAC
* *
2003328 TAACAAAATCCATCGTTACACACTTTCCCTTCCACTGGGGAATCT
1 TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
2003373 TAAC-AAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
1 TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
2003417 TAAC
1 TAAC
2003421 TGGTTGAAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 42 0.91
45 4 0.09
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.29
Consensus pattern (45 bp):
TAACAAAATCCATCGTTACACACTTTCACTTCCACTAGGGAATCT
Found at i:2009278 original size:50 final size:49
Alignment explanation
Indices: 2009217--2009464 Score: 289
Period size: 50 Copynumber: 4.9 Consensus size: 49
2009207 ACATGAGAGT
* * * *
2009217 TCTCATATCGGTGCCCATGCCATGTCCTAGACATGGTCTTACGAGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACG-GGGACC
* ***
2009267 TCTCATCTCGGTAACAATGCCATGTCATGGACATGGTCTTACGGGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTAC-GGGGACC
2009317 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGAACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGG-ACC
* *
2009367 TCTCATCTCGGTACCAACGCCATGTCCCAGACATGGTCTTACTTGGGACC
1 TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTAC-GGGGACC
** *
2009417 TCTCATAACCTCAATAATGCCAATGCCATGTCCCAGATATGGTCTTAC
1 TCTCAT---CTCGGT-A--CCAATGCCATGTCCCAGACATGGTCTTAC
2009465 ATAGGGTCTC
Statistics
Matches: 173, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
49 4 0.02
50 133 0.77
51 4 0.02
53 4 0.02
54 1 0.01
56 27 0.16
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (49 bp):
TCTCATCTCGGTACCAATGCCATGTCCCAGACATGGTCTTACGGGGACC
Found at i:2012048 original size:22 final size:22
Alignment explanation
Indices: 2011980--2012048 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
2011970 AAATTCCAAC
*
2011980 AAAGTAAAAAG-AAGGAAAAAGGA
1 AAAG-AAAAAGAAAGG-AAAGGGA
**
2012003 AAAGAAAAAGAAA-GAAAGAAA
1 AAAGAAAAAGAAAGGAAAGGGA
* *
2012024 AAATAAAAATAAAGGAAAGGGA
1 AAAGAAAAAGAAAGGAAAGGGA
2012046 AAA
1 AAA
2012049 AAAGAATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.41
22 16 0.43
23 6 0.16
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (22 bp):
AAAGAAAAAGAAAGGAAAGGGA
Found at i:2012819 original size:19 final size:20
Alignment explanation
Indices: 2012783--2012820 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2012773 CTACGGTGAT
*
2012783 ACCTTTAGAAACACTCGATC
1 ACCTATAGAAACACTCGATC
2012803 ACCTATAGAAA-ACTCGAT
1 ACCTATAGAAACACTCGAT
2012821 ATCTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (20 bp):
ACCTATAGAAACACTCGATC
Found at i:2020016 original size:24 final size:24
Alignment explanation
Indices: 2019988--2020039 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2019978 TTCCAAGAAG
*
2019988 ATTTAGTATTTATTA-CTATAATAT
1 ATTTAGCATTTATTAGC-ATAATAT
*
2020012 ATTTAGCATTTATTAGCATAATCT
1 ATTTAGCATTTATTAGCATAATAT
2020036 ATTT
1 ATTT
2020040 GACCTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:2020888 original size:13 final size:13
Alignment explanation
Indices: 2020870--2020894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2020860 TAAAGACCGA
2020870 GCATTAGCGGCGG
1 GCATTAGCGGCGG
2020883 GCATTAGCGGCG
1 GCATTAGCGGCG
2020895 TTTTTCGAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GCATTAGCGGCGG
Found at i:2021549 original size:105 final size:105
Alignment explanation
Indices: 2021461--2021650 Score: 260
Period size: 105 Copynumber: 1.8 Consensus size: 105
2021451 TGTGATTTAG
* * *
2021461 GGGTTAAGGG-TTAGGGGTTAGGGATT-TGGGTTAGAG-TTTAGGGTTTAGATTAATTAGTATTT
1 GGGTTAAGGGTTTA-GGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTA-TT
2021523 TTTTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
64 TTTTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
** * *
2021565 GGGTTTGGGGTTTAGGGTTAGGGGTTAAGAGTTAGTGATTTAAGGTTTAGATTAATTAGTATTTT
1 GGGTTAAGGGTTTAGGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTATTTT
* *
2021630 TTAATTTATATATTAATTAAG
66 TTAATTTACATATTAAATAAG
2021651 TTCTTATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
104 19 0.26
105 33 0.45
106 22 0.30
ACGTcount: A:0.28, C:0.01, G:0.28, T:0.44
Consensus pattern (105 bp):
GGGTTAAGGGTTTAGGGTTAGGGATTAAGAGTTAGAGATTTAAGGTTTAGATTAATTAGTATTTT
TTAATTTACATATTAAATAAGGTTTAGGGTTAGTAGTTAA
Found at i:2021598 original size:14 final size:14
Alignment explanation
Indices: 2021545--2021599 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
2021535 TATTAAATAA
* *
2021545 GGTTTAGGGTTAGT
1 GGTTAAGGGTTAGG
* *
2021559 AGTTAAGGGTTTGG
1 GGTTAAGGGTTAGG
*
2021573 GGTTTAGGGTTAGG
1 GGTTAAGGGTTAGG
*
2021587 GGTTAAGAGTTAG
1 GGTTAAGGGTTAG
2021600 TGATTTAAGG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (14 bp):
GGTTAAGGGTTAGG
Found at i:2021606 original size:28 final size:28
Alignment explanation
Indices: 2021547--2021611 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
2021537 TTAAATAAGG
* * * *
2021547 TTTAGGGTTAGTAGTTAAGGGTTTGGGG
1 TTTAGGGTTAGGAGTTAAGAGTTAGGGA
* *
2021575 TTTAGGGTTAGGGGTTAAGAGTTAGTGA
1 TTTAGGGTTAGGAGTTAAGAGTTAGGGA
*
2021603 TTTAAGGTT
1 TTTAGGGTT
2021612 TAGATTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (28 bp):
TTTAGGGTTAGGAGTTAAGAGTTAGGGA
Found at i:2024047 original size:31 final size:31
Alignment explanation
Indices: 2024009--2024070 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2023999 TATGTGATAG
* *
2024009 AGTCTCGTTTGTGTTTGTTTTTAGCCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
2024040 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
1 AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
2024071 GCTTTTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (31 bp):
AGTCTCGTCTGTGTTTGTTTTTAACCCAGGT
Found at i:2027077 original size:43 final size:43
Alignment explanation
Indices: 2026981--2027244 Score: 282
Period size: 43 Copynumber: 6.2 Consensus size: 43
2026971 AGATTATGTT
* ** * * *
2026981 TTTAGCGGCGTTTTTGCTAGAAGCGCCACTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* ** * *
2027023 TTTAGTGGCGTTTGTGATAAAAGCGCTGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* *
2027066 TTTAGTGGCGTTTGTGGGAGAAGTGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
* *
2027109 TTTAGCGGCCTTTGTGGGAAAAGCGCCGCTAAAGGTCAG-GGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC-GTGGTC
* * * * *
2027152 TATCGCGACGTTTGTGGGAGAAGCGTCGCTAAAGGTCAG-CGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTC-GTGGTC
* * *
2027195 TTTAGCAGCGTTTGTAGGAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
2027238 TTTAGCG
1 TTTAGCG
2027245 CCGCTAAAGA
Statistics
Matches: 186, Mismatches: 33, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
42 30 0.16
43 155 0.83
44 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCGTGGTC
Found at i:2028590 original size:24 final size:24
Alignment explanation
Indices: 2028563--2028614 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2028553 TTTCTAAAAG
*
2028563 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
2028587 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
2028611 ATTT
1 ATTT
2028615 GACCTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:2031677 original size:18 final size:16
Alignment explanation
Indices: 2031654--2031698 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
2031644 TCATTTCATA
2031654 TTCCATTTCACATCTCCT
1 TTCCATTTCACA--TCCT
*
2031672 TTCCATTTCTCATCCT
1 TTCCATTTCACATCCT
2031688 TTACCATTTCA
1 TT-CCATTTCA
2031699 ATATCAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 7 0.29
18 11 0.46
ACGTcount: A:0.18, C:0.36, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCCATTTCACATCCT
Found at i:2033440 original size:23 final size:23
Alignment explanation
Indices: 2033409--2033453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2033399 TGAGATGAAG
2033409 AACAATAAGCTC-TATCGAGCTGA
1 AACAATAAGCTCATA-CGAGCTGA
*
2033432 AACAGTAAGCTCATACGAGCTG
1 AACAATAAGCTCATACGAGCTG
2033454 TGGTGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (23 bp):
AACAATAAGCTCATACGAGCTGA
Found at i:2037333 original size:25 final size:26
Alignment explanation
Indices: 2037304--2037372 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
2037294 TCACATCCCA
*
2037304 ATTTTACTCC-AATAAAACTTTGACG
1 ATTTTACCCCTAATAAAACTTTGACG
* * *
2037329 ATTTTACCCCTATTAAAATTTTGATG
1 ATTTTACCCCTAATAAAACTTTGACG
*
2037355 ATTTTACCCCTAGTAAAA
1 ATTTTACCCCTAATAAAA
2037373 TTTCAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 9 0.24
26 29 0.76
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCTAATAAAACTTTGACG
Found at i:2037351 original size:26 final size:26
Alignment explanation
Indices: 2037316--2037375 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
2037306 TTTACTCCAA
* *
2037316 TAAAACTTTGACGATTTTACCCCTAT
1 TAAAATTTTGACGATTTTACCCCTAG
*
2037342 TAAAATTTTGATGATTTTACCCCTAG
1 TAAAATTTTGACGATTTTACCCCTAG
2037368 TAAAATTT
1 TAAAATTT
2037376 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACCCCTAG
Found at i:2051518 original size:14 final size:14
Alignment explanation
Indices: 2051499--2051525 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2051489 GTGGTCCAGT
2051499 TGAACTGAACCGAG
1 TGAACTGAACCGAG
2051513 TGAACTGAACCGA
1 TGAACTGAACCGA
2051526 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:2054957 original size:16 final size:18
Alignment explanation
Indices: 2054931--2054964 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2054921 ATATACATCA
2054931 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
2054948 TAAA-TAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
2054965 CTGGTTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:2055086 original size:37 final size:37
Alignment explanation
Indices: 2055041--2055114 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2055031 ATTTTCTACG
2055041 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
1 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
2055078 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
1 TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
2055115 GTTTTTGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (37 bp):
TTCAACAAATTCACCATGACCAATTAATTTAATTTCA
Found at i:2062606 original size:27 final size:27
Alignment explanation
Indices: 2062564--2063114 Score: 520
Period size: 27 Copynumber: 20.3 Consensus size: 27
2062554 AGAGGTCAAT
2062564 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * **
2062591 AAAT-AACAAAACTACCTTCATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
* **
2062618 GAATGACCGAAATACCTTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
2062645 GAATGACCGAAATAGCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
2062672 AATTGACCGAAATA-CCCCATTGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
2062698 AAATAACTGAAATGCCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
2062725 GAATGACTGAAACAGCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
2062752 AAATGATCGAAATACCTCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
2062779 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
2062806 AAATGATCGAAATACCCCCATTGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
2062833 AAATGATCGAAATA-CACTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
2062859 AATTGACCGAAATA-CCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
2062885 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
2062912 GAATGACCGAAATACCTCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
2062939 GAATGATCGAAATACCTCTATACCCTTACAGGGTA
1 AAATGACCGAAATA-C-C----CCC--ATAGGGTA
* * *
2062974 AAATG-GCTAAAGTACCCCTATAGGGTA
1 AAATGACCGAAA-TACCCCCATAGGGTA
*
2063001 AAATGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
**
2063028 AAATGAATGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * * *
2063055 GAATGATCGAAATA-CACTATAGGTTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
2063081 AATTGACCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
2063108 AAATGAC
1 AAATGAC
2063115 TGTTATACCC
Statistics
Matches: 429, Mismatches: 80, Indels: 30
0.80 0.15 0.06
Matches are distributed among these distances:
26 87 0.20
27 309 0.72
28 10 0.02
29 3 0.01
33 3 0.01
34 5 0.01
35 12 0.03
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:2062742 original size:80 final size:81
Alignment explanation
Indices: 2062564--2063114 Score: 519
Period size: 80 Copynumber: 6.8 Consensus size: 81
2062554 AGAGGTCAAT
* * * * *
2062564 AAATGACCGAAATACCCCCATAGGGTAAAAT-AACAAAACTACCTTCATAGGGTAGAATGACCGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAA-TACCTCCATAGGATAAAATGACCGA
*
2062628 AATACCTTCATAGGGTA
65 AATACCCTCATAGGGTA
* * * * * *
2062645 GAATGACCGAAATAGCCCCATAGGGTAAATTGACCGAAATACC-CCATTGGATAAAATAACTGAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCATAGGATAAAATGACCGAA
*
2062709 ATGCCCTCATAGGGTA
66 ATACCCTCATAGGGTA
* * * * * * *
2062725 GAATGACTGAAACAGCCCCATAGGGTAAAATGATCGAAATACCTCCATAGGGTAAAATGACCAAA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCATAGGATAAAATGACCGAA
2062790 ATACCCTCATAGGGTA
66 ATACCCTCATAGGGTA
* * * * *
2062806 AAATGATCGAAATACCCCCATTGGGTAAAATGATCGAAATACACT--ATAGGTTAAATTGACCGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATAC-CTCCATAGGATAAAATGACCGA
2062869 AATACCC-CATAGGGTA
65 AATACCCTCATAGGGTA
* * *
2062885 AAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAATACCTCCATAAGG-TAGAATGATCGA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCAT-AGGATAAAATGACCGA
*
2062949 AATACCTCTATACCCTTACAGGGTA
65 AATACC-C--T---C--ATAGGGTA
* * * * **
2062974 AAATG-GCTAAAGTACCCCTATAGGGTAAAATGACCGAAATACC-CCTATAGGGTAAAATGAATG
1 AAATGACCGAAA-TACCCCCATAGGGTAAAATGACCGAAATACCTCC-ATAGGATAAAATGACCG
*
2063037 AAATACCCCCATAGGGTA
64 AAATACCCTCATAGGGTA
* * * * * * *
2063055 GAATGATCGAAATA-CACTATAGGTTAAATTGACCGAAATACC-CCTATAGGGTAAAATGAC
1 AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCC-ATAGGATAAAATGAC
2063115 TGTTATACCC
Statistics
Matches: 395, Mismatches: 56, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.01
79 47 0.12
80 149 0.38
81 116 0.29
82 11 0.03
83 1 0.00
87 1 0.00
88 10 0.03
89 58 0.15
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (81 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCATAGGATAAAATGACCGAA
ATACCCTCATAGGGTA
Found at i:2062749 original size:107 final size:104
Alignment explanation
Indices: 2062564--2063114 Score: 497
Period size: 107 Copynumber: 5.1 Consensus size: 104
2062554 AGAGGTCAAT
* * *
2062564 AAATGACCGAAATACCCCCATAGGGTAAAATAAC-AAAACTACCTTCATAGGGTAGAATGACCGA
1 AAATGACCGAAATA-CCCCATAGGGTAAAATAACTGAAA-TACCCTCATAGGGTAGAATGACTGA
*
2062628 AATACCTTCATAGGGTAGAATGACCGAAATAGCCCCATAGGGTA
64 AATACC-CCATAGGGTA-AATGACCGAAATA-CCCCATAGGGTA
* * * *
2062672 AATTGACCGAAATACCCCATTGGATAAAATAACTGAAATGCCCTCATAGGGTAGAATGACTGAAA
1 AAATGACCGAAATACCCCATAGGGTAAAATAACTGAAATACCCTCATAGGGTAGAATGACTGAAA
* *
2062737 CAGCCCCATAGGGTAAAATGATCGAAATACCTCCATAGGGTA
66 TA-CCCCATAGGGT-AAATGACCGAAATACC-CCATAGGGTA
* * * * *
2062779 AAATGACCAAAATACCCTCATAGGGTAAAATGA-TCGAAATACCCCCATTGGGTAAAATGA-TCG
1 AAATGACCGAAATACCC-CATAGGGTAAAATAACT-GAAATACCCTCATAGGGTAGAATGACT-G
* * *
2062842 AAATACACTATAGGTTAAATTGACCGAAATACCCCATAGGGTA
63 AAATACCCCATAGGGTAAA-TGACCGAAATACCCCATAGGGTA
* * * *
2062885 AAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAATA-CCTCCATAAGGTAGAATGA-TCG
1 AAATGACCGAAATA-CCCCATAGGGTAAAATAACTGAAATACCCT-CATAGGGTAGAATGACT-G
* * *
2062948 AAATACCTCTATACCCTTACAGGGTAAAATG-GCTAAAGTACCCCTATAGGGTA
63 AAATA---C----CCC--ATAGGGT-AAATGACCGAAA-TACCCC-ATAGGGTA
*
2063001 AAATGACCGAAATACCCCTATAGGGTAAAATGAA-TGAAATACCCCCATAGGGTAGAATGA-TCG
1 AAATGACCGAAATACCCC-ATAGGGTAAAAT-AACTGAAATACCCTCATAGGGTAGAATGACT-G
* * *
2063064 AAATACACTATAGGTTAAATTGACCGAAATACCCCTATAGGGTA
63 AAATACCCCATAGGGTAAA-TGACCGAAATACCCC-ATAGGGTA
2063108 AAATGAC
1 AAATGAC
2063115 TGTTATACCC
Statistics
Matches: 367, Mismatches: 48, Indels: 57
0.78 0.10 0.12
Matches are distributed among these distances:
105 2 0.01
106 71 0.19
107 141 0.38
108 61 0.17
109 2 0.01
113 2 0.01
114 4 0.01
115 17 0.05
116 64 0.17
117 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (104 bp):
AAATGACCGAAATACCCCATAGGGTAAAATAACTGAAATACCCTCATAGGGTAGAATGACTGAAA
TACCCCATAGGGTAAATGACCGAAATACCCCATAGGGTA
Found at i:2063033 original size:89 final size:89
Alignment explanation
Indices: 2062879--2063043 Score: 228
Period size: 89 Copynumber: 1.9 Consensus size: 89
2062869 AATACCCCAT
* *
2062879 AGGGTAAAATGACCGAAATACCCCCATAGGGTAGAATGACCGAAATACCTCCATAAGGTAGAATG
1 AGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATG
2062944 -ATCGAAATACCTCTATACCCTTAC
66 AAT-GAAATACCTCTATACCCTTAC
* * * *
2062968 AGGGTAAAATG-GCTAAAGTACCCCTATAGGGTAAAATGACCGAAATACC-CCTATAGGGTAAAA
1 AGGGTAAAATGACCGAAA-TACCCCCATAGGGTAAAATGACCGAAATACCTCC-ATAAGGTAAAA
2063031 TGAATGAAATACC
64 TGAATGAAATACC
2063044 CCCATAGGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
88 6 0.09
89 59 0.88
90 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (89 bp):
AGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCTCCATAAGGTAAAATG
AATGAAATACCTCTATACCCTTAC
Found at i:2066324 original size:27 final size:27
Alignment explanation
Indices: 2066263--2066324 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2066253 TTGAGATCTT
* *
2066263 CATGTTTAGTGTCCCGACGAACTATTC
1 CATGTTTAGTGTCCCAACGAACTATCC
*
2066290 CATATTTAGTGTCCCAAC-AGACTATCC
1 CATGTTTAGTGTCCCAACGA-ACTATCC
*
2066317 CGTGTTTA
1 CATGTTTA
2066325 ATATTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 1 0.03
27 28 0.97
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (27 bp):
CATGTTTAGTGTCCCAACGAACTATCC
Found at i:2066640 original size:45 final size:45
Alignment explanation
Indices: 2066536--2066640 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
2066526 TTCAACCAGG
* * *
2066536 GTCTTACTTATTTCCAAAATGATGTCATAGCATCTTTCAGTTATT
1 GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
* ** *
2066581 ATCTTACTCATTTCTATCATGATGTCATAGAATCTTTTAGTTATT
1 GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
2066626 GTCTTACTCATTTCT
1 GTCTTACTCATTTCT
2066641 GGCATATAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.48
Consensus pattern (45 bp):
GTCTTACTCATTTCTAAAATGATGTCATAGAATCTTTCAGTTATT
Found at i:2069607 original size:20 final size:20
Alignment explanation
Indices: 2069582--2069632 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2069572 ATCGTAAAAC
*
2069582 GGTATCGATACCAGGATAAA
1 GGTATCGATACCAGAATAAA
* *
2069602 GGTATCGATACTATAATAAA
1 GGTATCGATACCAGAATAAA
*
2069622 GGTATCAATAC
1 GGTATCGATAC
2069633 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCAGAATAAA
Found at i:2069633 original size:20 final size:20
Alignment explanation
Indices: 2069597--2069646 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2069587 CGATACCAGG
*
2069597 ATAAAGGTATCGATACTATA
1 ATAAAGGTATCAATACTATA
*
2069617 ATAAAGGTATCAATACTTTA
1 ATAAAGGTATCAATACTATA
*
2069637 ATAAAAGTAT
1 ATAAAGGTAT
2069647 TAAAACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (20 bp):
ATAAAGGTATCAATACTATA
Found at i:2069654 original size:20 final size:20
Alignment explanation
Indices: 2069615--2069655 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2069605 ATCGATACTA
* *
2069615 TAATAAAGGTATCAATACTT
1 TAATAAAAGTATCAAAACTT
*
2069635 TAATAAAAGTATTAAAACTT
1 TAATAAAAGTATCAAAACTT
2069655 T
1 T
2069656 GAGAAAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
TAATAAAAGTATCAAAACTT
Found at i:2069691 original size:20 final size:20
Alignment explanation
Indices: 2069629--2069695 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
2069619 AAAGGTATCA
* * *
2069629 ATACTTTAATAAAAGTATTA
1 ATACTTTGAGAAAAGTATTG
* * *
2069649 AAACTTTGAGAAAAGCATCG
1 ATACTTTGAGAAAAGTATTG
2069669 ATACTTTGAGAAAAGTATTG
1 ATACTTTGAGAAAAGTATTG
2069689 ATACTTT
1 ATACTTT
2069696 AAGGAATGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (20 bp):
ATACTTTGAGAAAAGTATTG
Found at i:2073323 original size:11 final size:10
Alignment explanation
Indices: 2073292--2073360 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
2073282 TATTTATGAG
*
2073292 TTTTATGAAT
1 TTTTATAAAT
*
2073302 TTTTATGAAT
1 TTTTATAAAT
*
2073312 TTTTATAAAA
1 TTTTATAAAT
2073322 TTTTA-AATAT
1 TTTTATAA-AT
*
2073332 GTTTTATTAA-
1 -TTTTATAAAT
*
2073342 TTTTATAATTT
1 TTTTATAA-AT
2073353 TTTTATAA
1 TTTTATAA
2073361 TTTATTAGAC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
9 9 0.19
10 24 0.50
11 14 0.29
12 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:2073326 original size:10 final size:10
Alignment explanation
Indices: 2073261--2073317 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
2073251 TTATATATAT
2073261 AATTTATTA-G
1 AATTT-TTATG
2073271 AATTTTTAT-
1 AATTTTTATG
2073280 -ATTATTTATG
1 AATT-TTTATG
*
2073290 -AGTTTTATG
1 AATTTTTATG
2073299 AATTTTTATG
1 AATTTTTATG
2073309 AATTTTTAT
1 AATTTTTAT
2073318 AAAATTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 3 0.07
9 14 0.34
10 24 0.59
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (10 bp):
AATTTTTATG
Found at i:2073343 original size:20 final size:19
Alignment explanation
Indices: 2073291--2073363 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
2073281 TTATTTATGA
2073291 GTTTTATGAATTTTTATGAATT
1 GTTTTAT-AA-TTTTAT-AATT
*
2073313 -TTTATAAAATTTTA-AATAT
1 GTTT-TATAATTTTATAAT-T
2073332 GTTTTATTAATTTTATAATT
1 GTTTTA-TAATTTTATAATT
*
2073352 TTTTTATAATTT
1 GTTTTATAATTT
2073364 ATTAGACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.07
19 9 0.21
20 21 0.49
21 8 0.19
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
GTTTTATAATTTTATAATT
Found at i:2074808 original size:17 final size:14
Alignment explanation
Indices: 2074774--2074804 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2074764 TAGCTATTAC
2074774 TATAACTATTAATA
1 TATAACTATTAATA
*
2074788 TATAACTATTATTA
1 TATAACTATTAATA
2074802 TAT
1 TAT
2074805 TATAGATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAACTATTAATA
Found at i:2076891 original size:15 final size:16
Alignment explanation
Indices: 2076873--2076903 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2076863 CAATAAATAA
2076873 TGAAATG-ATAAAAAT
1 TGAAATGTATAAAAAT
2076888 TGAAATGTATAAAAAT
1 TGAAATGTATAAAAAT
2076904 ATTAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (16 bp):
TGAAATGTATAAAAAT
Found at i:2077234 original size:15 final size:15
Alignment explanation
Indices: 2077214--2077257 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2077204 ATGAATTACT
2077214 AAATTTAAAATTAAA
1 AAATTTAAAATTAAA
* *
2077229 ATATTTATAATCTAAA
1 AAATTTAAAAT-TAAA
*
2077245 AAATTCAAAATTA
1 AAATTTAAAATTA
2077258 TTTGAATGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTTAAAATTAAA
Found at i:2078775 original size:26 final size:26
Alignment explanation
Indices: 2078746--2078797 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2078736 AATATTGACA
*
2078746 TAAACAATATTTATCTTAATGATAAT
1 TAAACAATATTTATATTAATGATAAT
* *
2078772 TAAATAATATTTATATTTATGATAAT
1 TAAACAATATTTATATTAATGATAAT
2078798 ATTATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAACAATATTTATATTAATGATAAT
Found at i:2078817 original size:21 final size:21
Alignment explanation
Indices: 2078774--2078830 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2078764 ATGATAATTA
* * **
2078774 AATAATATTTATATTTATGAT
1 AATATTATTTATTTTTACAAT
2078795 AATATTATTTATTTTTACAAT
1 AATATTATTTATTTTTACAAT
* *
2078816 AATTTTATATATTTT
1 AATATTATTTATTTT
2078831 CATATTCTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
AATATTATTTATTTTTACAAT
Found at i:2079525 original size:23 final size:23
Alignment explanation
Indices: 2079499--2079578 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
2079489 AGTTAAAAAA
2079499 AATTTTATTATCTGAAAAAACAT
1 AATTTTATTATCTGAAAAAACAT
2079522 AATTTTATTTTTATCT-ATTTAAAAA-A-
1 AATTTTA---TTATCTGA---AAAAACAT
2079548 AA-TTTATTATCTGAAAAAACAT
1 AATTTTATTATCTGAAAAAACAT
2079570 AATTTTATT
1 AATTTTATT
2079579 TTTATCTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 20
0.70 0.00 0.30
Matches are distributed among these distances:
20 5 0.11
21 1 0.02
22 8 0.17
23 14 0.30
25 5 0.11
26 8 0.17
27 1 0.02
28 5 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (23 bp):
AATTTTATTATCTGAAAAAACAT
Found at i:2079551 original size:26 final size:26
Alignment explanation
Indices: 2079522--2079609 Score: 64
Period size: 26 Copynumber: 3.5 Consensus size: 26
2079512 GAAAAAACAT
2079522 AATTTTATTTTTATCTATTTAAAAAA
1 AATTTTATTTTTATCTATTTAAAAAA
2079548 AA-TTTA---TTATCTGA---AAAAACA
1 AATTTTATTTTTATCT-ATTTAAAAA-A
* **
2079569 TAATTTTATTTTTATCTATTTATAATT
1 -AATTTTATTTTTATCTATTTAAAAAA
2079596 AATTTTAATTTTTA
1 AATTTT-ATTTTTA
2079610 AGGTGTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 21
0.67 0.04 0.29
Matches are distributed among these distances:
20 5 0.10
21 1 0.02
22 8 0.17
23 5 0.10
25 5 0.10
26 14 0.29
27 7 0.15
28 3 0.06
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (26 bp):
AATTTTATTTTTATCTATTTAAAAAA
Found at i:2079555 original size:48 final size:49
Alignment explanation
Indices: 2079491--2079590 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 49
2079481 AGAATATAAG
2079491 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
1 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
2079540 TTAAAAAAAA-TTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
1 TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
2079588 TTA
1 TTA
2079591 TAATTAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 41 0.80
49 10 0.20
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (49 bp):
TTAAAAAAAATTTTATTATCTGAAAAAACATAATTTTATTTTTATCTAT
Found at i:2084349 original size:28 final size:28
Alignment explanation
Indices: 2084312--2084366 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2084302 TAATAGTGTG
* * *
2084312 TGGGCTTTAGCCTAATGTAGTAACAGTC
1 TGGGCCTTAGCCCAATATAGTAACAGTC
2084340 TGGGCCTTAGCCCAATATAGTAACAGT
1 TGGGCCTTAGCCCAATATAGTAACAGT
2084367 ACAATGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATATAGTAACAGTC
Found at i:2084502 original size:26 final size:26
Alignment explanation
Indices: 2084473--2084569 Score: 97
Period size: 26 Copynumber: 3.7 Consensus size: 26
2084463 CACCAATATC
*
2084473 GCAGCAAAGTTGTCAGTAATAGTGAT
1 GCAGCAAAGTTGCCAGTAATAGTGAT
*
2084499 GCAGCAATGTTGCCAGTAATAGTGAT
1 GCAGCAAAGTTGCCAGTAATAGTGAT
* * * * *
2084525 GCAGTAATA-CTGCCAGTAACAGTAAC
1 GCAGCAA-AGTTGCCAGTAATAGTGAT
* *
2084551 ACAGCAAAGCTGCCAGTAA
1 GCAGCAAAGTTGCCAGTAA
2084570 CAGTATATGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
25 1 0.02
26 58 0.98
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
GCAGCAAAGTTGCCAGTAATAGTGAT
Found at i:2084531 original size:14 final size:14
Alignment explanation
Indices: 2084486--2084533 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
2084476 GCAAAGTTGT
2084486 CAGTAATAGTGATG
1 CAGTAATAGTGATG
*
2084500 CAGCAAT-GT--TG
1 CAGTAATAGTGATG
2084511 CCAGTAATAGTGATG
1 -CAGTAATAGTGATG
2084526 CAGTAATA
1 CAGTAATA
2084534 CTGCCAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.07
12 6 0.21
13 4 0.14
14 14 0.50
15 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (14 bp):
CAGTAATAGTGATG
Found at i:2084817 original size:27 final size:27
Alignment explanation
Indices: 2084757--2084926 Score: 161
Period size: 27 Copynumber: 6.3 Consensus size: 27
2084747 GGGTATAACA
* *
2084757 ATCATTTTACCCTTCG-GGAGT-TTTCG
1 ATCATTTTACCTTTCGAGG-GTATTTTG
*
2084783 ATCATTTTATCTTTCGAGGGTATTTTG
1 ATCATTTTACCTTTCGAGGGTATTTTG
2084810 ATCATTTTA-CTCTTCGAGGGTATTTT-
1 ATCATTTTACCT-TTCGAGGGTATTTTG
**
2084836 AGTCATTTTACCCTTT-GAGGGTATTTCC
1 A-TCATTTTA-CCTTTCGAGGGTATTTTG
* * *
2084864 ATCATTTTACCCTTCGGGGGTATTTCG
1 ATCATTTTACCTTTCGAGGGTATTTTG
* *
2084891 ATCATTCTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCTTTCGAGGGTATTTTG
* *
2084918 GTTATTTTA
1 ATCATTTTA
2084927 GGCCCATTAC
Statistics
Matches: 123, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
26 23 0.19
27 95 0.77
28 3 0.02
29 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (27 bp):
ATCATTTTACCTTTCGAGGGTATTTTG
Found at i:2084858 original size:54 final size:54
Alignment explanation
Indices: 2084757--2084926 Score: 186
Period size: 54 Copynumber: 3.2 Consensus size: 54
2084747 GGGTATAACA
* *
2084757 ATCATTTTACCCTTCG-GGAGT-TTTCGATCATTTTA-TCTTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGAGG-GTATTTAGATCATTTTACCCTTT-GAGGGTATTTTG
* **
2084810 ATCATTTTACTCTTCGAGGGTATTTTAG-TCATTTTACCCTTTGAGGGTATTTCC
1 ATCATTTTACCCTTCGAGGGTA-TTTAGATCATTTTACCCTTTGAGGGTATTTTG
* * * *
2084864 ATCATTTTACCCTTCGGGGGTATTTCGATCATTCTACCCTTCGAGGGTATTTTG
1 ATCATTTTACCCTTCGAGGGTATTTAGATCATTTTACCCTTTGAGGGTATTTTG
* *
2084918 GTTATTTTA
1 ATCATTTTA
2084927 GGCCCATTAC
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
53 21 0.21
54 69 0.70
55 8 0.08
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (54 bp):
ATCATTTTACCCTTCGAGGGTATTTAGATCATTTTACCCTTTGAGGGTATTTTG
Found at i:2084906 original size:81 final size:80
Alignment explanation
Indices: 2084758--2084926 Score: 223
Period size: 81 Copynumber: 2.1 Consensus size: 80
2084748 GGTATAACAA
* * * * * *
2084758 TCATTTTACCCTTCGGGAGTTTTCGATCATTTTATCTTTCGAGGGTATTTTGATCATTTTACTCT
1 TCATTTTACCCTTCGGGAGTTTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACCCT
2084823 TCGAGGGTATTTTAG
66 TCGAGGGTATTTTAG
* *
2084838 TCATTTTACCCTTTGAGG-GTATTTCCATCATTTTACCCTTCGGGGGTATTTCGATCATTCTACC
1 TCATTTTACCCTTCG-GGAGT-TTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACC
*
2084902 CTTCGAGGGTATTTTGG
64 CTTCGAGGGTATTTTAG
*
2084919 TTATTTTA
1 TCATTTTA
2084927 GGCCCATTAC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 16 0.21
81 61 0.79
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (80 bp):
TCATTTTACCCTTCGGGAGTTTTCCATCATTTTACCCTTCGAGGGTATTTCGATCATTCTACCCT
TCGAGGGTATTTTAG
Found at i:2093721 original size:43 final size:42
Alignment explanation
Indices: 2093663--2093859 Score: 279
Period size: 43 Copynumber: 4.6 Consensus size: 42
2093653 CAATGCCTAC
* * *
2093663 GTCCCAGACGA-GGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGAC-ATGGTCTTACACGTAATCATATA-CGATGCCAAT
* *
2093706 GTCCCAGACAGGGTCTTATACGTAAATCATATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGT-AATCATATACGATGCCAAT
*
2093749 GTCCCAGACATGGTCTTACACGTAAATCTTATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGT-AATCATATACGATGCCAAT
2093792 GTCCCAGACATGGTCTTACACGTAACTCATATACGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAA-TCATATACGATGCCAAT
*
2093835 GTCCTAGACATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
2093860 ATCTCAAATC
Statistics
Matches: 142, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
42 3 0.02
43 131 0.92
44 8 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGTAATCATATACGATGCCAAT
Found at i:2093786 original size:86 final size:87
Alignment explanation
Indices: 2093663--2093895 Score: 307
Period size: 86 Copynumber: 2.7 Consensus size: 87
2093653 CAATGCCTAC
* * * *
2093663 GTCCCAGACGA-GGTCTTACATGT-AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTATA
1 GTCCCAGAC-ATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACA
2093726 CGTAAATCATATACGATGCCAAT
65 CGTAAATCATATACGATGCCAAT
* *
2093749 GTCCCAGACATGGTCTTACACGTAAATCTTATA-CGATGCCAATGTCCCAGACATGGTCTTACAC
1 GTCCCAGACATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACAC
*
2093813 GTAACTCATATACGATGCCAAT
66 GTAAATCATATACGATGCCAAT
* *
2093835 GTCCTAGACATGGTCTTACACGTAAATCTCAA-ATCAATGCC-ATCGTCCCAGAC-GTGGTCTT
1 GTCCCAGACATGGTCTTACACGTAAATCT-AATATCGATGCCAAT-GTCCCAGACAG-GGTCTT
2093896 TCTCAATATT
Statistics
Matches: 130, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
85 1 0.01
86 100 0.77
87 29 0.22
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (87 bp):
GTCCCAGACATGGTCTTACACGTAAATCTAATATCGATGCCAATGTCCCAGACAGGGTCTTACAC
GTAAATCATATACGATGCCAAT
Found at i:2101658 original size:24 final size:21
Alignment explanation
Indices: 2101575--2101672 Score: 121
Period size: 21 Copynumber: 4.7 Consensus size: 21
2101565 TCTTCAAGGA
*
2101575 TATGTAATCTTAGATATGA--
1 TATGCAATCTTAGATATGATT
*
2101594 TATGCAATCTTAGATATGATA
1 TATGCAATCTTAGATATGATT
2101615 TATGCAATCTTAGATATGATT
1 TATGCAATCTTAGATATGATT
2101636 TATGCAATCTTAGAAGATATGATT
1 TATGCAATCTT---AGATATGATT
*
2101660 T-TGTAATCTTAGA
1 TATGCAATCTTAGA
2101673 GATTTAATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
19 18 0.25
20 3 0.04
21 31 0.44
23 8 0.11
24 11 0.15
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (21 bp):
TATGCAATCTTAGATATGATT
Found at i:2114842 original size:6 final size:6
Alignment explanation
Indices: 2114831--2114867 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
2114821 AGTATACTTT
*
2114831 TATACA TATACA TATACA TATTCA TATACA TATACA T
1 TATACA TATACA TATACA TATACA TATACA TATACA T
2114868 CTGCATGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (6 bp):
TATACA
Found at i:2116765 original size:12 final size:12
Alignment explanation
Indices: 2116748--2116776 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2116738 TTCTTTTCGG
2116748 TTTTAGTTTTTA
1 TTTTAGTTTTTA
2116760 TTTTAGTTTTTA
1 TTTTAGTTTTTA
2116772 TTTTA
1 TTTTA
2116777 CCAGGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTAGTTTTTA
Found at i:2121465 original size:26 final size:26
Alignment explanation
Indices: 2121436--2121486 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2121426 GATGTCCCAT
* *
2121436 AAGATAGTCCTTGGCGAACTTTCCAA
1 AAGATAGTCCATGACGAACTTTCCAA
*
2121462 AAGATAGTCCATGACGGACTTTCCA
1 AAGATAGTCCATGACGAACTTTCCA
2121487 GATATGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (26 bp):
AAGATAGTCCATGACGAACTTTCCAA
Found at i:2122832 original size:22 final size:23
Alignment explanation
Indices: 2122797--2122840 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2122787 TTATTATATA
*
2122797 AAATAAAATTAATTATTATGTAGG
1 AAATAAAA-TAATTATAATGTAGG
2122821 AAATAAAA-AATTATAATGTA
1 AAATAAAATAATTATAATGTA
2122841 TAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AAATAAAATAATTATAATGTAGG
Done.