Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 133 of 173
Found at i:40506320 original size:17 final size:18
Alignment explanation
Indices: 40506294--40506327 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40506284 AAATTTGAGA
40506294 ATAAAAAAATAA-AAATC
1 ATAAAAAAATAAGAAATC
*
40506311 ATAAATAAATAAGAAAT
1 ATAAAAAAATAAGAAAT
40506328 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAAAATAAGAAATC
Found at i:40517023 original size:16 final size:16
Alignment explanation
Indices: 40516993--40517030 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
40516983 CAAAAATCTA
40516993 TAAGACAAAATAAACAG
1 TAAG-CAAAATAAACAG
40517010 -AAGCAAACATAAACAG
1 TAAGCAAA-ATAAACAG
40517026 TAAGC
1 TAAGC
40517031 CATTAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.61, C:0.16, G:0.13, T:0.11
Consensus pattern (16 bp):
TAAGCAAAATAAACAG
Found at i:40517226 original size:31 final size:31
Alignment explanation
Indices: 40517191--40517266 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
40517181 CTCGTCGAAT
40517191 GCATATAACCGAATATTGATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
* *
40517222 GCATATAACCGAGTATTTATATACATCAAGA
1 GCATATAACCGAATATTGATATACATCAAGA
*
40517253 GCATATACCCGAAT
1 GCATATAACCGAAT
40517267 GTATGTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (31 bp):
GCATATAACCGAATATTGATATACATCAAGA
Found at i:40517515 original size:31 final size:31
Alignment explanation
Indices: 40517432--40517521 Score: 81
Period size: 33 Copynumber: 2.8 Consensus size: 31
40517422 TGCTTTTAGC
* * *
40517432 CGAATGCATATACACATTAAATGTATATAAT
1 CGAATGCATATATACATCAAATATATATAAT
* ** *
40517463 CAAATGCTTATATATTTATCAAATATTTATAAT
1 CGAATGC--ATATATACATCAAATATATATAAT
*
40517496 TGAATGCATATATACATCAAAGTATA
1 CGAATGCATATATACATCAAA-TATA
40517522 GAACTGAATA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
31 18 0.41
32 3 0.07
33 23 0.52
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
CGAATGCATATATACATCAAATATATATAAT
Found at i:40528090 original size:19 final size:19
Alignment explanation
Indices: 40528053--40528090 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40528043 CGAAGCCTTT
*
40528053 TTACATTCATGCATTTGCA
1 TTACATTCATGCATATGCA
40528072 TTACATTACAT-CATATGCA
1 TTACATT-CATGCATATGCA
40528091 CTAAAGTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (19 bp):
TTACATTCATGCATATGCA
Found at i:40534497 original size:52 final size:52
Alignment explanation
Indices: 40534418--40534582 Score: 225
Period size: 52 Copynumber: 3.2 Consensus size: 52
40534408 TACTTCTGAT
*
40534418 CAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
40534471 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
**
40534523 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
40534569 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
40534583 GCTACACTTA
Statistics
Matches: 99, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
46 43 0.43
52 44 0.44
53 12 0.12
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
Found at i:40534555 original size:46 final size:44
Alignment explanation
Indices: 40534478--40534693 Score: 190
Period size: 37 Copynumber: 5.3 Consensus size: 44
40534468 TGACAAGTGA
*
40534478 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
40534524 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
40534570 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
* *
40534607 AAAGTGATAA--G-T-G---GCTACACTTATGTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
40534644 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
40534680 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
40534694 CATACGTAAG
Statistics
Matches: 158, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 87 0.55
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:40534590 original size:37 final size:37
Alignment explanation
Indices: 40534546--40534691 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
40534536 GATAGCTTTA
*
40534546 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40534583 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
40534620 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40534657 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40534692 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40536007 original size:49 final size:49
Alignment explanation
Indices: 40535946--40536138 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
40535936 ATGTGAACAT
40535946 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
40535996 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
40536045 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
40536094 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
40536139 AGAAAACGAA
Statistics
Matches: 137, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
49 133 0.97
50 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:40539343 original size:52 final size:52
Alignment explanation
Indices: 40539264--40539428 Score: 225
Period size: 52 Copynumber: 3.2 Consensus size: 52
40539254 TACTTCTGAT
*
40539264 CAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
40539317 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
**
40539369 C------AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
40539415 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
40539429 GCTACACTTA
Statistics
Matches: 99, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
46 43 0.43
52 44 0.44
53 12 0.12
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
Found at i:40539401 original size:46 final size:44
Alignment explanation
Indices: 40539324--40539539 Score: 190
Period size: 37 Copynumber: 5.3 Consensus size: 44
40539314 TGACAAGTGA
*
40539324 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTT--GCTACACTTATCTGATCAAGAGAC
40539370 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGC-TT-GCTACACTTATCTGATCAAGAGAC
*
40539416 AAAGTGATAA--G-T-G---GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
* *
40539453 AAAGTGATAA--G-T-G---GCTACACTTATGTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
*
40539490 AAAGTGAT-AG-G-T-G---GCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
40539526 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
40539540 CATACGTAAG
Statistics
Matches: 158, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
35 7 0.04
36 7 0.04
37 87 0.55
38 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 51 0.32
47 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (44 bp):
AAAGTGATAAGTGATAGCTTGCTACACTTATCTGATCAAGAGAC
Found at i:40539436 original size:37 final size:37
Alignment explanation
Indices: 40539392--40539537 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
40539382 GATAGCTTTA
*
40539392 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40539429 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
40539466 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40539503 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40539538 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40544951 original size:44 final size:44
Alignment explanation
Indices: 40544635--40544952 Score: 444
Period size: 44 Copynumber: 7.2 Consensus size: 44
40544625 AACAAACCGG
* * *
40544635 TGAAGACTATAAGCCCTAT-TCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
40544678 TGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
40544722 TGAA-AGTTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGA-TTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
* *
40544766 AGAAGATTGTAAGCCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
*
40544810 TGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
** * *
40544854 AAAAGATTGTAAGTCTTATCTCCCTGAACAGCAGTGGAATAGG-
1 TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
* * * * *
40544897 TGAAATATTGTACGTCCTATTTCCCTGAACAGAAGTGGAATAGGT
1 TG-AAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
40544942 TGAAGATTGTA
1 TGAAGATTGTA
40544953 GATCCAGTCT
Statistics
Matches: 247, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
43 16 0.06
44 228 0.92
45 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
TGAAGATTGTAAGTCCTATCTCCCTGACCAGCAGTGGAATAGGT
Found at i:40549048 original size:41 final size:41
Alignment explanation
Indices: 40548986--40549102 Score: 159
Period size: 41 Copynumber: 2.9 Consensus size: 41
40548976 GTGTGCCAAT
40548986 TTACTTC-AATTTAATT-GATGAGACACTGGGTGTCAATTTA
1 TTACTTCGAATTT-ATTCGATGAGACACTGGGTGTCAATTTA
* *
40549026 TTACTTCGAATTTATTCAATGAGATACTGGGTGTCAATTTA
1 TTACTTCGAATTTATTCGATGAGACACTGGGTGTCAATTTA
* * *
40549067 CTACTTCGAA-TTATCCGATGAGACACTGAGTGTCAA
1 TTACTTCGAATTTATTCGATGAGACACTGGGTGTCAA
40549103 ATTGGTGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 32 0.47
41 36 0.53
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (41 bp):
TTACTTCGAATTTATTCGATGAGACACTGGGTGTCAATTTA
Found at i:40553107 original size:41 final size:41
Alignment explanation
Indices: 40553035--40553142 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 41
40553025 AATTTCTAAT
* * **
40553035 TTACTTCGG-TTTAACCAATGAGACAGAGGGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGGGTGTCAATTTA
*
40553075 TTACTTCGGATTTATTCGATGAGACACTGGGTGTCAATTTA
1 TTACTTCGGATTTATCCGATGAGACACTGGGTGTCAATTTA
* * *
40553116 CTACTTC-GAATTATCCGATGAGGCACT
1 TTACTTCGGATTTATCCGATGAGACACT
40553143 ATGTGCCAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 26 0.45
41 32 0.55
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (41 bp):
TTACTTCGGATTTATCCGATGAGACACTGGGTGTCAATTTA
Found at i:40555788 original size:4 final size:4
Alignment explanation
Indices: 40555779--40555862 Score: 61
Period size: 4 Copynumber: 21.0 Consensus size: 4
40555769 TGTCTTTCTC
*
40555779 CTTT CTTT CTTT CCCTT -TTT C-TT -TTT CTTT CTTT CTTT CTTT C-TT
1 CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
* *
40555824 CTTT CAGTTT CATTT -TTAT CATT CTTT CTTT ATTT CTTT
1 CTTT C--TTT C-TTT CTT-T CTTT CTTT CTTT CTTT CTTT
40555863 TTATTACTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
3 11 0.17
4 42 0.66
5 7 0.11
6 4 0.06
ACGTcount: A:0.06, C:0.23, G:0.01, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:40555821 original size:22 final size:23
Alignment explanation
Indices: 40555771--40555828 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
40555761 CTTAGCCTTG
*
40555771 TCTTTCTCCTTTCTTTCTTTCCCT
1 TCTTTCT-TTTTCTTTCTTTCCCT
*
40555795 T-TTTCTTTTTCTTTCTTT-CTT
1 TCTTTCTTTTTCTTTCTTTCCCT
40555816 TCTTTCTTCTTTC
1 TCTTTCTT-TTTC
40555829 AGTTTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 17 0.57
23 9 0.30
24 1 0.03
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TCTTTCTTTTTCTTTCTTTCCCT
Found at i:40557592 original size:42 final size:42
Alignment explanation
Indices: 40557504--40557617 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
40557494 GTTTACAACC
* * * *
40557504 AAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTATAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAA
* *
40557546 AAAAACGCCGCTAAAGAACATGTTTTTTAGCGGCGCTAAGAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAA
* * * *
40557588 AAAAACTCCACTGAAGAACATGGTCTTTAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAG
40557618 TGGCATTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAA
Found at i:40557641 original size:42 final size:42
Alignment explanation
Indices: 40557601--40557917 Score: 316
Period size: 42 Copynumber: 7.5 Consensus size: 42
40557591 AACTCCACTG
* * * * *
40557601 AAGAACATGGTCTTTAGTGGCATTTTTATCTAAGCGCCACTA
1 AAGAACATGTTCTTTAGCGGCATTTTTTTATAAGCGCCGCTA
* * * *
40557643 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTG
1 AAGAACATGTTCTTTAGCGGCATTTTTTTATAAGCGCCGCTA
* *
40557685 AAGAACATGTTCTCTAGCGG-AGTTTTTTTATAAGCGCCGCTG
1 AAGAACATGTTCTTTAGCGGCA-TTTTTTTATAAGCGCCGCTA
40557727 AAGAACATGTTCTTTAGCGG-AGTTTTTTTATAAGCGCCGCTA
1 AAGAACATGTTCTTTAGCGGCA-TTTTTTTATAAGCGCCGCTA
* * *
40557769 AAGAACATGATCTTTAGTGGC-GTTTTTTATTAAGCGCCGCTA
1 AAGAACATGTTCTTTAGCGGCATTTTTTTA-TAAGCGCCGCTA
* * * * * * *
40557811 AAGAACATGTTCTTTAACGGCGTTTTGTATAAAAACACAGCTA
1 AAGAACATGTTCTTTAGCGGCATTTT-TTTATAAGCGCCGCTA
* * ** * * *
40557854 GAGATCATAATCTTTAGCGGCTCTTTTTTTACAAACGCCGCTA
1 AAGAACATGTTCTTTAGCGGC-ATTTTTTTATAAGCGCCGCTA
40557897 AAGAACATGTTCTTTAGCGGC
1 AAGAACATGTTCTTTAGCGGC
40557918 GCTTTTGTAC
Statistics
Matches: 232, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
41 7 0.03
42 162 0.70
43 56 0.24
44 7 0.03
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
AAGAACATGTTCTTTAGCGGCATTTTTTTATAAGCGCCGCTA
Found at i:40557836 original size:126 final size:127
Alignment explanation
Indices: 40557598--40557923 Score: 372
Period size: 126 Copynumber: 2.6 Consensus size: 127
40557588 AAAAACTCCA
* * * * * *
40557598 CTGAAGAACATGGTCTTTAGTGGCATTTTTATCTAAGCGCCACTAAAGAACATGGTCTTTAGCGG
1 CTGAAGAACATGATCTTTAGCGGCATTTTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGCGG
* * * * * * *
40557663 CGTTTTTTTCTAAGCGCCGCTGAAGAACATGTTCTCTAGCGGAGTTTT-TTTATAAGCGCCG
66 CGTTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTCTAACGGAGTTTTGTATAAAAACACAG
* *
40557724 CTGAAGAACATGTTCTTTAGCGG-AGTTTTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGTG
1 CTGAAGAACATGATCTTTAGCGGCA-TTTTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGCG
* *
40557788 GCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGTTCTTTAACGGCGTTTTGTATAAAAACACAG
65 GCGTTTTTT-TCTAAGCGCCGCTAAAGAACATGTTCTCTAACGGAGTTTTGTATAAAAACACAG
* * * * * *
40557851 CT-AGAGATCATAATCTTTAGCGGCTCTTTTTTTACAAACGCCGCTAAAGAACATGTTCTTTAGC
1 CTGA-AGAACATGATCTTTAGCGGC-ATTTTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGC
*
40557915 GGCGCTTTT
64 GGCGTTTTT
40557924 GTACAAAAAC
Statistics
Matches: 169, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
125 1 0.01
126 99 0.59
127 27 0.16
128 42 0.25
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (127 bp):
CTGAAGAACATGATCTTTAGCGGCATTTTTTTATAAGCGCCGCTAAAGAACATGATCTTTAGCGG
CGTTTTTTTCTAAGCGCCGCTAAAGAACATGTTCTCTAACGGAGTTTTGTATAAAAACACAG
Found at i:40557903 original size:86 final size:85
Alignment explanation
Indices: 40557551--40557933 Score: 296
Period size: 84 Copynumber: 4.5 Consensus size: 85
40557541 TATAAAAAAA
* * ** * * * **
40557551 CGCCGCTAAAGAACATGTTTTTTAGCGGCGCTAAG-AGAAAAACTCCA-CTGAAGAACATGGTCT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATAAAAAC-ACAGCTAAAGAACATAATCT
* * *
40557614 TTAGTGGCATTTTTATCT-AAG
65 TTAGCGGCGTTTTT-TTTAAAG
* * * ** * * * * ** *
40557635 CGCCACTAAAGAACATGGTCTTTAGCGGCGTTTT-TTTCTAAGCGCCGCTGAAGAACATGTTCTC
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATAAAAACACAGCTAAAGAACATAATCTT
*
40557699 TAGCGGAG-TTTTTTTATAAG
66 TAGCGGCGTTTTTTTTA-AAG
* * * * * * * *
40557719 CGCCGCTGAAGAACATGTTCTTTAGCGGAGTTTT-TTTATAAGCGCCGCTAAAGAACATGATCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATAAAAACACAGCTAAAGAACATAATCTT
*
40557783 TAGTGGCGTTTTTTATT-AAG
66 TAGCGGCGTTTTTT-TTAAAG
* * *
40557803 CGCCGCTAAAGAACATGTTCTTTAACGGCGTTTTGTATAAAAACACAGCTAGAGATCATAATCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATAAAAACACAGCTAAAGAACATAATCTT
*
40557868 TAGCGGC-TCTTTTTTTACAAA
66 TAGCGGCGT-TTTTTTTA-AAG
*
40557889 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGTACAAAAAC
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTGTATAAAAAC
40557934 GCCACTATTT
Statistics
Matches: 244, Mismatches: 44, Indels: 19
0.79 0.14 0.06
Matches are distributed among these distances:
82 2 0.01
83 5 0.02
84 153 0.63
85 38 0.16
86 33 0.14
87 13 0.05
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTGTATAAAAACACAGCTAAAGAACATAATCTT
TAGCGGCGTTTTTTTTAAAG
Found at i:40558348 original size:21 final size:21
Alignment explanation
Indices: 40558309--40558348 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40558299 TTCTTTTGAA
* *
40558309 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCACTGCAG
*
40558330 CCTCTGTTTCCCTCACTGC
1 CCTCTGCTTCCCTCACTGC
40558349 CGCGTTTGCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.45, G:0.15, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCACTGCAG
Found at i:40560133 original size:44 final size:44
Alignment explanation
Indices: 40560069--40560162 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
40560059 CTGGAAGAAG
* *
40560069 GAAGGAGGCGATTTAGGGATTTGGGATTTCAAGAAATTCGGCAA
1 GAAGGAGGCGATTTACGGATTTGGGAATTCAAGAAATTCGGCAA
*
40560113 GAAGGAGGCGATTTACGGATTTGGGAATTCAAGAAATTGGGCAA
1 GAAGGAGGCGATTTACGGATTTGGGAATTCAAGAAATTCGGCAA
40560157 GAAGGA
1 GAAGGA
40560163 CGCAAGAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.34, C:0.09, G:0.35, T:0.22
Consensus pattern (44 bp):
GAAGGAGGCGATTTACGGATTTGGGAATTCAAGAAATTCGGCAA
Found at i:40561345 original size:7 final size:7
Alignment explanation
Indices: 40561333--40561396 Score: 83
Period size: 7 Copynumber: 9.0 Consensus size: 7
40561323 ACTAAAGTAG
40561333 CCTAAAC
1 CCTAAAC
40561340 CCTAAAC
1 CCTAAAC
40561347 CCTAAAC
1 CCTAAAC
*
40561354 CCTAAAT
1 CCTAAAC
*
40561361 CTTAAAC
1 CCTAAAC
*
40561368 CCCAAAC
1 CCTAAAC
40561375 TCCTAAAC
1 -CCTAAAC
40561383 CCTAAAC
1 CCTAAAC
*
40561390 CCAAAAC
1 CCTAAAC
40561397 ACCATAACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
7 43 0.88
8 6 0.12
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:40562009 original size:114 final size:107
Alignment explanation
Indices: 40561871--40562196 Score: 312
Period size: 114 Copynumber: 3.0 Consensus size: 107
40561861 CATCTAAAAA
*
40561871 TGCGCCGCTAATAGTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCA
1 TGCGCCGCTAATAGTATA-TTTAGCGGCGTTTTCCAGTAAGCGCCACTAATTCTAATATACCTCA
40561936 AGACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTAAC
65 AGACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTT--C
* * *
40561981 TCAAAGCGCCGCTAATACTATTATTTAGCGGCGTTTTCTC-GTAAGCGCCACTAATTATAGTATA
1 T----GCGCCGCTAATAGTA-TATTTAGCGGCGTTTTC-CAGTAAGCGCCACTAATTCTAATATA
* * * *
40562045 CATCAAGACCAAAACGCTGAGTTTTGGT-TAAG-AAAT-TTAGCGGCGCTTC
60 CCTCAAGACC-AAACTCTGCGTTTTGGTGT--GCATATCTT-GCGGCGCTTC
** * * *
40562094 T----C-C-AATAGTACGCTTTAGCGGCGTTTTACAGTAAGTGCCACTAATCCTAATATACCTCA
1 TGCGCCGCTAATAGTA-TATTTAGCGGCGTTTTCCAGTAAGCGCCACTAATTCTAATATACCTCA
* * *
40562153 ACACCAAACTCTGCGTTTTGGTGTGCATATCTTACGGCGATTC
65 AGACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTC
40562196 T
1 T
40562197 AGAAAATCGC
Statistics
Matches: 178, Mismatches: 24, Indels: 36
0.75 0.10 0.15
Matches are distributed among these distances:
101 1 0.01
102 28 0.16
103 51 0.29
104 1 0.01
105 1 0.01
110 1 0.01
113 2 0.01
114 62 0.35
115 30 0.17
116 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (107 bp):
TGCGCCGCTAATAGTATATTTAGCGGCGTTTTCCAGTAAGCGCCACTAATTCTAATATACCTCAA
GACCAAACTCTGCGTTTTGGTGTGCATATCTTGCGGCGCTTC
Found at i:40562344 original size:55 final size:55
Alignment explanation
Indices: 40562257--40562364 Score: 135
Period size: 55 Copynumber: 2.0 Consensus size: 55
40562247 CAAATTGTAT
* * * *
40562257 TATACATCGAGACCAAATCGCTGTGTTTTGGTTAACATTTTTTGCGACGCTTTAA
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTTAA
* * * * *
40562312 TATACATCAAGATCAAAACTCTGCGTTTTGGTTATCATATTTTGTGGCGCTTT
1 TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTT
40562365 TCGTAAGCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (55 bp):
TATACATCAAGACCAAAACGCTGCGTTTTGGTTAACATATTTTGCGACGCTTTAA
Found at i:40563594 original size:40 final size:39
Alignment explanation
Indices: 40563536--40563673 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 39
40563526 ACACACCAAT
* *
40563536 TTGACACCAAGTGCCTCATTAGATAATTCGAAGTAGTAAA
1 TTGACACCCAGTGCCTCATTAGATAAATCGAAGTA-TAAA
* ** *
40563576 TTGACACCCAGTGTCTCATCGGATAAACCGAAGTA-AAA
1 TTGACACCCAGTGCCTCATTAGATAAATCGAAGTATAAA
* * *
40563614 TTGGCACTCAGTGCCTCA-TCGAATAAATCTGAAGTAATAAA
1 TTGACACCCAGTGCCTCATTAG-ATAAATC-GAAGT-ATAAA
*
40563655 TTGACACCCAGTGTCTCAT
1 TTGACACCCAGTGCCTCAT
40563674 CGACTCAAAG
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
37 1 0.01
38 24 0.31
39 5 0.06
40 30 0.38
41 18 0.23
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATTAGATAAATCGAAGTATAAA
Found at i:40563673 original size:41 final size:40
Alignment explanation
Indices: 40563564--40563676 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 40
40563554 TTAGATAATT
* *
40563564 CGAAGTAGTAAATTGACACCCAGTGTCTCATCGGATAAAC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
* * *
40563604 CGAAGT-A-AAATTGGCACTCAGTGCCTCATCGAATAAATC
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAA-C
*
40563643 TGAAGTAATAAATTGACACCCAGTGTCTCATCGA
1 CGAAGTAATAAATTGACACCCAGTGTCTCATCGA
40563677 CTCAAAGTCG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 26 0.43
39 6 0.10
40 7 0.11
41 22 0.36
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAAATTGACACCCAGTGTCTCATCGAATAAAC
Found at i:40564514 original size:4 final size:4
Alignment explanation
Indices: 40564505--40564584 Score: 62
Period size: 4 Copynumber: 20.0 Consensus size: 4
40564495 TGTCTTTCTC
*
40564505 CTTT CTTT CTTT CCCTT -TTT C-TT -TTT CTTT CTTT CTTT C-TT CTTT
1 CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
*
40564550 CTGTTT CGTTT -TTAT CTTT CTTT CTTT ATTT CTTT
1 C--TTT C-TTT CTT-T CTTT CTTT CTTT CTTT CTTT
40564585 TTATTACTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
3 11 0.17
4 39 0.62
5 9 0.14
6 4 0.06
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:40564541 original size:30 final size:29
Alignment explanation
Indices: 40564505--40564576 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
40564495 TGTCTTTCTC
* * *
40564505 CTTTCTTTCTTTCCCTTTTTCTTTTTCTTT
1 CTTTCTTTCTTTCCCTGTTTCGTTTT-TAT
**
40564535 CTTTCTTTCTTCTTTCTGTTTCGTTTTTAT
1 CTTTCTTTCTT-TCCCTGTTTCGTTTTTAT
40564565 CTTTCTTTCTTT
1 CTTTCTTTCTTT
40564577 ATTTCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.03
30 24 0.67
31 11 0.31
ACGTcount: A:0.01, C:0.24, G:0.03, T:0.72
Consensus pattern (29 bp):
CTTTCTTTCTTTCCCTGTTTCGTTTTTAT
Found at i:40566790 original size:21 final size:22
Alignment explanation
Indices: 40566766--40566806 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40566756 CCACAAGGCT
*
40566766 ATGTGACC-CTCTCACACGATC
1 ATGTGACCTATCTCACACGATC
*
40566787 ATGTGGCCTATCTCACACGA
1 ATGTGACCTATCTCACACGA
40566807 GCACGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (22 bp):
ATGTGACCTATCTCACACGATC
Found at i:40569872 original size:47 final size:47
Alignment explanation
Indices: 40569718--40569870 Score: 243
Period size: 47 Copynumber: 3.3 Consensus size: 47
40569708 GTCATAGTAA
*
40569718 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAACCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
40569765 TGCAAATAAACTACCAATAATCAAAATTGTGGATAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
* * * *
40569812 TACAGATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAAT
1 TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
*
40569859 TGTAAATAAACT
1 TGCAAATAAACT
40569871 GCTAAAAACT
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (47 bp):
TGCAAATAAACTACCAATAATCAAAATTGTGGACAAGCCACCAAAAT
Found at i:40571447 original size:13 final size:13
Alignment explanation
Indices: 40571429--40571453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40571419 CAAAAAATTA
40571429 AAAAAATATTTTC
1 AAAAAATATTTTC
40571442 AAAAAATATTTT
1 AAAAAATATTTT
40571454 TAAAGATTCT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAAATATTTTC
Found at i:40575035 original size:26 final size:26
Alignment explanation
Indices: 40575002--40575052 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40574992 AATGTGAAAA
40575002 GGGTTGCTAAGTGCTGATTCCCCAAG
1 GGGTTGCTAAGTGCTGATTCCCCAAG
*
40575028 GGGTTGCTAAGTGTTGATTCCCCAA
1 GGGTTGCTAAGTGCTGATTCCCCAA
40575053 CTCTTCGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (26 bp):
GGGTTGCTAAGTGCTGATTCCCCAAG
Found at i:40575063 original size:102 final size:102
Alignment explanation
Indices: 40574899--40575126 Score: 384
Period size: 102 Copynumber: 2.2 Consensus size: 102
40574889 AATAACAAGG
* * ** *
40574899 GGGTTGCTATGTGTTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCTTTGGTGGTT
1 GGGTTGCTAAGTGCTGATT-CCCCAAGGGGTTGCTAAGTGCTGATTCCCCAACTCTTCGGTGGTT
40574964 GCTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAA
65 GCTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAA
*
40575002 GGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGTTGATTCCCCAACTCTTCGGTGGTTG
1 GGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAACTCTTCGGTGGTTG
*
40575067 CTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAG
66 CTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAA
40575104 GGGTTGCTAAGTGCTGATTCCCC
1 GGGTTGCTAAGTGCTGATTCCCC
40575127 GAATCACTGG
Statistics
Matches: 118, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
102 101 0.86
103 17 0.14
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (102 bp):
GGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTGATTCCCCAACTCTTCGGTGGTTG
CTAAGTGCTGATTCCACCATATCCTTGAATGTGAAAA
Found at i:40575155 original size:76 final size:77
Alignment explanation
Indices: 40575025--40575239 Score: 285
Period size: 76 Copynumber: 2.8 Consensus size: 77
40575015 CTGATTCCCC
*
40575025 AAGGGGTTGCTAAGTGTTGATTCCCC-AACTC-TTCGGTGGTTGCTAAGTGCTGATTCCACCATA
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAA-TCACT-GGTGGTTGCTAAGTGCTGATTCCACCATA
*
40575088 TCCTTGAATGT-GA
64 TCCTTGAATGTAAA
* * * *
40575101 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGGTAAGTGTTGATTCTACCATATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCATATC
40575166 CTTGAATGTAAAAA
66 CTTGAATGT--AAA
* *
40575180 AAGGGGGTTACTAAGTGTTGATTCCCCGAA-CACTGGTGGTTGCTAAGTGCTGAATCCACC
1 AA-GGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACC
40575240 GATAACGGTT
Statistics
Matches: 121, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
76 64 0.53
77 3 0.02
79 29 0.24
80 25 0.21
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (77 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCATATC
CTTGAATGTAAA
Found at i:40577717 original size:22 final size:24
Alignment explanation
Indices: 40577675--40577718 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
40577665 TAACTAAGCT
40577675 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
40577699 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
40577719 TCTTGTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:40578105 original size:15 final size:15
Alignment explanation
Indices: 40578085--40578115 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40578075 GTTTCTTTCC
40578085 TGTTTTTCTTTTGTT
1 TGTTTTTCTTTTGTT
40578100 TGTTTTTCTTTTGTT
1 TGTTTTTCTTTTGTT
40578115 T
1 T
40578116 TACTTACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (15 bp):
TGTTTTTCTTTTGTT
Found at i:40578320 original size:17 final size:16
Alignment explanation
Indices: 40578297--40578354 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 16
40578287 GTTTATTTAA
40578297 TATATAATAATATAAT
1 TATATAATAATATAAT
40578313 TAATATAAT-ATATTATAT
1 T-ATATAATAATA-TA-AT
*
40578331 TATATAATAAAATAAT
1 TATATAATAATATAAT
40578347 ATATATAA
1 -TATATAA
40578355 AACATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 6 0.17
17 25 0.69
18 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATAATAATATAAT
Found at i:40578321 original size:5 final size:5
Alignment explanation
Indices: 40578294--40578354 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
40578284 TTGGTTTATT
*
40578294 TAATA T-ATAA TAATA TAAT- TAATA TAATA TATTATA TTATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TA--ATA TAATA TAATA
40578340 -AA-A TAATA T-ATA TAA
1 TAATA TAATA TAATA TAA
40578355 AACATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
3 1 0.02
4 14 0.30
5 25 0.54
6 2 0.04
7 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:40581114 original size:46 final size:46
Alignment explanation
Indices: 40581054--40581151 Score: 187
Period size: 46 Copynumber: 2.1 Consensus size: 46
40581044 TTTAATTGAG
*
40581054 TCAATTTATTCGAAGTAGAATTAAGTTAAGTGGTCGTAATAATTGT
1 TCAACTTATTCGAAGTAGAATTAAGTTAAGTGGTCGTAATAATTGT
40581100 TCAACTTATTCGAAGTAGAATTAAGTTAAGTGGTCGTAATAATTGT
1 TCAACTTATTCGAAGTAGAATTAAGTTAAGTGGTCGTAATAATTGT
40581146 TCAACT
1 TCAACT
40581152 AGATAATTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (46 bp):
TCAACTTATTCGAAGTAGAATTAAGTTAAGTGGTCGTAATAATTGT
Found at i:40581821 original size:62 final size:59
Alignment explanation
Indices: 40581748--40581864 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
40581738 AATGATTATC
* * * *
40581748 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAACATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TA-ATAAACATTATATTAATTTAATAAGAT
*
40581810 TTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATA
40581865 TTAAAATGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
60 2 0.04
61 1 0.02
62 27 0.54
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTAATAAACATTATATTAATTTAATAAGAT
Found at i:40590998 original size:17 final size:16
Alignment explanation
Indices: 40590965--40591005 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
40590955 AAAATGACCC
*
40590965 AAAAATAAATAATTAT
1 AAAAATAAATAAGTAT
*
40590981 AAAAATAACTCAAGTAT
1 AAAAATAAAT-AAGTAT
40590998 AAAAATAA
1 AAAAATAA
40591006 TTATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATAAATAAGTAT
Found at i:40591146 original size:90 final size:90
Alignment explanation
Indices: 40591064--40591233 Score: 234
Period size: 90 Copynumber: 1.9 Consensus size: 90
40591054 GGCATGTATA
* * * *** *
40591064 ACCTTAATTTTTGACCAAATTATTACCTTATAATTGTGTCAGGCTTAAAATTTTTAATTTTTTGG
1 ACCTTAATTTTTGACCAAATAATCACCTGATAATTGTGTCAGGCTTAAAAAAATTAAATTTTTGG
40591129 GTT-GGGGGACTTAACGGCCGACACC
66 GTTGGGGGGACTTAACGGCCGACA-C
* * *
40591154 ACCTTGATTTTTGACCCAATAATCATCTGATAATTGTGTCAGGCTTAAAAAAATTAAATTTTTGG
1 ACCTTAATTTTTGACCAAATAATCACCTGATAATTGTGTCAGGCTTAAAAAAATTAAATTTTTGG
40591219 GTTGGGGGGACTTAA
66 GTTGGGGGGACTTAA
40591234 GGCTATTTGA
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
90 58 0.84
91 11 0.16
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (90 bp):
ACCTTAATTTTTGACCAAATAATCACCTGATAATTGTGTCAGGCTTAAAAAAATTAAATTTTTGG
GTTGGGGGGACTTAACGGCCGACAC
Found at i:40593515 original size:42 final size:41
Alignment explanation
Indices: 40593469--40593599 Score: 149
Period size: 42 Copynumber: 3.1 Consensus size: 41
40593459 CACGAACTTT
* *
40593469 TGTTTAACTCATATGAGTTTCCT-TTCAGCT-TTATTGAGCTTC
1 TGTTTAACCCTTATG-GTTT-CTGTTCAGCTCTTA-TGAGCTTC
* *
40593511 TGTTTAACCCTTATGGTTTCTGTTCAACTCTTACGAGCTTC
1 TGTTTAACCCTTATGGTTTCTGTTCAGCTCTTATGAGCTTC
* * *
40593552 TGTTCAACCCTTATGGGTTTCTGTTTAGCTCTCATGAGCTTC
1 TGTTTAACCCTTAT-GGTTTCTGTTCAGCTCTTATGAGCTTC
40593594 TGTTTA
1 TGTTTA
40593600 GCCTTTGAGC
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
40 2 0.03
41 30 0.39
42 44 0.58
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (41 bp):
TGTTTAACCCTTATGGTTTCTGTTCAGCTCTTATGAGCTTC
Found at i:40593554 original size:21 final size:21
Alignment explanation
Indices: 40593503--40593614 Score: 95
Period size: 21 Copynumber: 5.5 Consensus size: 21
40593493 TCAGCTTTAT
*
40593503 TGAGCTTCTGTTTAACCCTTA
1 TGAGCTTCTGTTCAACCCTTA
* *
40593524 TG-GTTTCTGTTCAACTCTTA
1 TGAGCTTCTGTTCAACCCTTA
*
40593544 CGAGCTTCTGTTCAACCCTTA
1 TGAGCTTCTGTTCAACCCTTA
* * * * * *
40593565 TGGGTTTCTGTTTAGCTCTCA
1 TGAGCTTCTGTTCAACCCTTA
* *
40593586 TGAGCTTCTGTT-TAGCCTT-
1 TGAGCTTCTGTTCAACCCTTA
40593605 TGAGCTTCTG
1 TGAGCTTCTG
40593615 ATAACGATAT
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
19 10 0.14
20 18 0.26
21 42 0.60
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (21 bp):
TGAGCTTCTGTTCAACCCTTA
Found at i:40600508 original size:21 final size:21
Alignment explanation
Indices: 40600363--40600511 Score: 63
Period size: 21 Copynumber: 7.1 Consensus size: 21
40600353 TTACTTTCCA
* *
40600363 TTTATCTCTCACGAGCTTCTG
1 TTTAACTCTCATGAGCTTCTG
** *
40600384 TTTAACTCAT-ATGAATTTCCG
1 TTTAACTC-TCATGAGCTTCTG
* *
40600405 TTCAGCTCT-ATTGAGCTTCTG
1 TTTAACTCTCA-TGAGCTTCTG
* * * *
40600426 TTTAAC-CTTTATGGGTTTCCG
1 TTTAACTC-TCATGAGCTTCTG
* * * *
40600447 TTTAGCTCTTACGAGCTTCCG
1 TTTAACTCTCATGAGCTTCTG
* * *
40600468 TTCAACCCTTC-TGAGTTTCTG
1 TTTAACTC-TCATGAGCTTCTG
*
40600489 TTTAGCTCTCATGAGCTTCTG
1 TTTAACTCTCATGAGCTTCTG
40600510 TT
1 TT
40600512 CAGCCTTCGG
Statistics
Matches: 91, Mismatches: 30, Indels: 14
0.67 0.22 0.10
Matches are distributed among these distances:
20 5 0.05
21 82 0.90
22 4 0.04
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (21 bp):
TTTAACTCTCATGAGCTTCTG
Found at i:40600510 original size:84 final size:84
Alignment explanation
Indices: 40600357--40600511 Score: 195
Period size: 84 Copynumber: 1.8 Consensus size: 84
40600347 TCGTGTTTAC
* * * *
40600357 TTTCCATTTATCTCTCACGAGCTTCTGTTTAACTCATATGAATTTCCGTTCAGCTCTATTGAGCT
1 TTTCCATTTAGCTCTCACGAGCTTCCGTTCAACCCATATGAATTTCCGTTCAGCTCTATTGAGCT
40600422 TCTGTTTAACCTTTATGGG
66 TCTGTTTAACCTTTATGGG
* * * * * * *
40600441 TTTCCGTTTAGCTCTTACGAGCTTCCGTTCAACCCTTCTGAGTTTCTGTTTAGCTCTCA-TGAGC
1 TTTCCATTTAGCTCTCACGAGCTTCCGTTCAACCCATATGAATTTCCGTTCAGCTCT-ATTGAGC
40600505 TTCTGTT
65 TTCTGTT
40600512 CAGCCTTCGG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
84 58 0.98
85 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.15, T:0.44
Consensus pattern (84 bp):
TTTCCATTTAGCTCTCACGAGCTTCCGTTCAACCCATATGAATTTCCGTTCAGCTCTATTGAGCT
TCTGTTTAACCTTTATGGG
Found at i:40600513 original size:42 final size:42
Alignment explanation
Indices: 40600357--40600513 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 42
40600347 TCGTGTTTAC
* * * * * *
40600357 TTTCCATTTATCTCTCACGAGCTTCTGTTTAACTCATATGAA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
* * * * *
40600399 TTTCCGTTCAGCTCT-ATTGAGCTTCTGTTTAACCTTTATGGG
1 TTTCCGTTTAGCTCTCA-CGAGCTTCTGTTCAACCCTTATGAG
* * *
40600441 TTTCCGTTTAGCTCTTACGAGCTTCCGTTCAACCCTTCTGAG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
* *
40600483 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTCA
40600514 GCCTTCGGGC
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
41 1 0.01
42 91 0.98
43 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTCACGAGCTTCTGTTCAACCCTTATGAG
Found at i:40602954 original size:47 final size:47
Alignment explanation
Indices: 40602901--40603048 Score: 242
Period size: 47 Copynumber: 3.1 Consensus size: 47
40602891 AAATGTTTTA
40602901 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
* *
40602948 AATAAATAAATTATTAAGATATTATATAGTGTAAAATAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
* * *
40602995 AATAAATAAATTGTAAAGTTATTAAATAGTGTAAAGTAAAATAATTT
1 AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
40603042 AAATAAA
1 -AATAAA
40603049 ATATTAATAC
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 87 0.94
48 6 0.06
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (47 bp):
AATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
Found at i:40603069 original size:94 final size:94
Alignment explanation
Indices: 40602883--40603057 Score: 246
Period size: 94 Copynumber: 1.9 Consensus size: 94
40602873 TCATGATTAT
** * *
40602883 TGTAAAATAAATGTTTTAAATAAATAAATTATTAAGTTATTATATAGTGTAAAGTAAAATAATTT
1 TGTAAAATAAATAATTTAAATAAATAAATTATAAAGTTATTAAATAGTGTAAAGTAAAATAATTT
* *
40602948 AATAAATAAATTATTAAGATATTATATAG
66 AATAAATAAATTAATAACATATTATATAG
*
40602977 TGTAAAATAAAATAATTT-AATAAATAAATTGTAAAGTTATTAAATAGTGTAAAGTAAAATAATT
1 TGTAAAAT-AAATAATTTAAATAAATAAATTATAAAGTTATTAAATAGTGTAAAGTAAAATAATT
*
40603041 TAAATAAA-ATATTAATA
65 T-AATAAATAAATTAATA
40603058 CATTTAAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 59 0.82
95 13 0.18
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (94 bp):
TGTAAAATAAATAATTTAAATAAATAAATTATAAAGTTATTAAATAGTGTAAAGTAAAATAATTT
AATAAATAAATTAATAACATATTATATAG
Found at i:40603077 original size:23 final size:21
Alignment explanation
Indices: 40603044--40603090 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
40603034 AATAATTTAA
*
40603044 ATAAAATATTAATACATTTAAAT
1 ATAAAAAATT-AT-CATTTAAAT
*
40603067 ATAAAAAATTATTATTTAAAT
1 ATAAAAAATTATCATTTAAAT
40603088 ATA
1 ATA
40603091 GATTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 2 0.09
23 9 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAAAATTATCATTTAAAT
Found at i:40603204 original size:24 final size:23
Alignment explanation
Indices: 40603172--40603234 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 23
40603162 ATTATATACA
40603172 ATAAAGTAAATAAATTATTCAATT
1 ATAAAGTAAATAAATTATTC-ATT
40603196 ATAAAGTAAATAAATTATTCATT
1 ATAAAGTAAATAAATTATTCATT
*
40603219 TTAAAGATTAAATAAA
1 ATAAAG--TAAATAAA
40603235 AAACTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 8 0.22
24 20 0.56
25 8 0.22
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (23 bp):
ATAAAGTAAATAAATTATTCATT
Found at i:40605292 original size:21 final size:22
Alignment explanation
Indices: 40605251--40605292 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40605241 AAAACTAATT
*
40605251 TACGAAAATATTTATAATTTATA
1 TACGAAAATA-TTAAAATTTATA
40605274 TACGAAAATA-TAAAATTTA
1 TACGAAAATATTAAAATTTA
40605293 ACCAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (22 bp):
TACGAAAATATTAAAATTTATA
Found at i:40606260 original size:30 final size:30
Alignment explanation
Indices: 40606226--40606287 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
40606216 ACTTATTTCA
40606226 TTGTTAATTTTGTTACTATTTTAAAGACAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
* * *
40606256 TTGTTAATTTTGTTATTATTTTATAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGACAT
40606286 TT
1 TT
40606288 TCTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGACAT
Found at i:40610469 original size:37 final size:34
Alignment explanation
Indices: 40610382--40610484 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 34
40610372 ATCACTAACT
* *
40610382 AATACTAATGTAATATTAATAGAATAGAATAGAATAG
1 AATACTAATCTAATA-TAATAGAATAGAA-A-AATAA
40610419 AATACTAATCTAATACTAATAGAATAGAAAAATAA
1 AATACTAATCTAATA-TAATAGAATAGAAAAATAA
40610454 AATA-TAAAATACTAATATAATAGAA-AGAAAA
1 AATACT--AAT-CTAATATAATAGAATAGAAAA
40610485 TAACTATGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
34 1 0.02
35 14 0.23
36 12 0.20
37 33 0.55
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (34 bp):
AATACTAATCTAATATAATAGAATAGAAAAATAA
Found at i:40611862 original size:22 final size:23
Alignment explanation
Indices: 40611828--40611870 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40611818 ATATGATATG
40611828 TAATATTAGAAGATATGATTTTA
1 TAATATTAGAAGATATGATTTTA
* *
40611851 TAATCTTA-AAGATTTGATTT
1 TAATATTAGAAGATATGATTT
40611871 GTAGATAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (23 bp):
TAATATTAGAAGATATGATTTTA
Found at i:40620203 original size:12 final size:12
Alignment explanation
Indices: 40620188--40620227 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
40620178 AAAAATAGAA
40620188 ATAATAATATAT
1 ATAATAATATAT
40620200 ATAATAATATAT
1 ATAATAATATAT
*
40620212 A-AAAAATGATAT
1 ATAATAAT-ATAT
40620224 ATAA
1 ATAA
40620228 ATATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 5 0.20
12 18 0.72
13 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:40620213 original size:22 final size:20
Alignment explanation
Indices: 40620188--40620238 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40620178 AAAAATAGAA
40620188 ATAATAATAT-ATATAATAATAT
1 ATAA-AATATGATAT-ATAA-AT
*
40620210 ATAAAAAATGATATATAAAT
1 ATAAAATATGATATATAAAT
40620230 ATAAAATAT
1 ATAAAATAT
40620239 TTAGAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 10 0.38
21 8 0.31
22 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAAAATATGATATATAAAT
Found at i:40620272 original size:26 final size:26
Alignment explanation
Indices: 40620220--40620283 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
40620210 ATAAAAAATG
* * **
40620220 ATATATAAATATAAAATATTTAGAAT
1 ATATAAAAAAATAAAATAGATAGAAT
*
40620246 ATATAAAAAAATAAAATAGATATAAT
1 ATATAAAAAAATAAAATAGATAGAAT
*
40620272 ATATAAATAAAT
1 ATATAAAAAAAT
40620284 TGAATATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (26 bp):
ATATAAAAAAATAAAATAGATAGAAT
Found at i:40620292 original size:22 final size:23
Alignment explanation
Indices: 40620203--40620301 Score: 79
Period size: 22 Copynumber: 4.6 Consensus size: 23
40620193 AATATATATA
*
40620203 ATAATATATAAA-AAA-TGATAT
1 ATAATATATAAATAAATTGAGAT
* *
40620224 ATAA-ATATAAA-ATATTTAGA-
1 ATAATATATAAATAAATTGAGAT
* * *
40620244 ATATATAAAAAAATAAAAT-AGAT
1 ATA-ATATATAAATAAATTGAGAT
40620267 ATAATATATAAATAAATTGA-AT
1 ATAATATATAAATAAATTGAGAT
40620289 ATAATAT-TAAATA
1 ATAATATATAAATA
40620302 TATAAATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 12 0.19
21 14 0.23
22 29 0.47
23 7 0.11
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
ATAATATATAAATAAATTGAGAT
Found at i:40620314 original size:17 final size:17
Alignment explanation
Indices: 40620225--40620316 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
40620215 AAATGATATA
*
40620225 TAAATATA-AAAT-ATT
1 TAAATATATAAATAAAT
*
40620240 TAGAATATATAAAAAAAT
1 TA-AATATATAAATAAAT
* * *
40620258 AAAATAGATATAATATA-
1 TAAATATATA-AATAAAT
*
40620275 TAAATAAATTGAATATAATAT
1 TAAATATA-T-AA-ATAA-AT
40620296 TAAATATATAAATAAAT
1 TAAATATATAAATAAAT
40620313 TAAA
1 TAAA
40620317 CCAAAAGAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
15 2 0.03
16 6 0.10
17 22 0.38
18 13 0.22
19 6 0.10
20 2 0.03
21 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAATATATAAATAAAT
Found at i:40625045 original size:13 final size:13
Alignment explanation
Indices: 40625029--40625053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40625019 CTTTTAGCTG
40625029 TTACTTTAATTTA
1 TTACTTTAATTTA
40625042 TTACTTTAATTT
1 TTACTTTAATTT
40625054 CATTTATCCT
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TTACTTTAATTTA
Found at i:40631599 original size:12 final size:12
Alignment explanation
Indices: 40631582--40631660 Score: 58
Period size: 12 Copynumber: 6.6 Consensus size: 12
40631572 CTTTATTTTC
40631582 TTTATTTTATTT
1 TTTATTTTATTT
40631594 TTTA--TTATTT
1 TTTATTTTATTT
* *
40631604 GTTATATTATTT
1 TTTATTTTATTT
*
40631616 ATATATATTTGATTT
1 -T-T-TATTTTATTT
*
40631631 GTTT-CTTTATTT
1 -TTTATTTTATTT
40631643 TTTATTTTA-TT
1 TTTATTTTATTT
40631654 TTTATTT
1 TTTATTT
40631661 ATGCTTAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
10 9 0.17
11 12 0.23
12 20 0.38
13 1 0.02
14 2 0.04
15 9 0.17
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:40631790 original size:6 final size:6
Alignment explanation
Indices: 40631759--40631813 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
40631749 ATTGAGTTTA
* * * * *
40631759 TTTC-T TTTCTT TTTCGT TTCCAT TTTCGT TTTCTT TTTCGT TTTCTT
1 TTTCGT TTTCGT TTTCGT TTTCGT TTTCGT TTTCGT TTTCGT TTTCGT
40631806 TTTC-T TTT
1 TTTCGT TTT
40631814 AGCTTTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 8 0.20
6 33 0.80
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTCGT
Found at i:40631802 original size:12 final size:12
Alignment explanation
Indices: 40631759--40631813 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
40631749 ATTGAGTTTA
40631759 TTTC-TTTTCTT
1 TTTCGTTTTCTT
* *
40631770 TTTCGTTTCCAT
1 TTTCGTTTTCTT
40631782 TTTCGTTTTCTT
1 TTTCGTTTTCTT
40631794 TTTCGTTTTCTT
1 TTTCGTTTTCTT
40631806 TTTC-TTTT
1 TTTCGTTTT
40631814 AGCTTTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 8 0.21
12 31 0.79
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTCGTTTTCTT
Found at i:40632859 original size:20 final size:21
Alignment explanation
Indices: 40632812--40632859 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
40632802 TGCTGAATTA
*
40632812 TTTAAATTCATGTTTCTATAC
1 TTTAAAATCATGTTTCTATAC
40632833 TTTAAAATCATGTTTCTATAC
1 TTTAAAATCATGTTTCTATAC
40632854 -TTAAAA
1 TTTAAAA
40632860 GAGCATTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.35, C:0.12, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTAAAATCATGTTTCTATAC
Found at i:40635269 original size:51 final size:51
Alignment explanation
Indices: 40635197--40635301 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
40635187 TAATTAAAAT
* * * *
40635197 AAAATAATTAATTAAAGGATAAATTATATTTAAAGCAAAAAATTTAAATTA
1 AAAATAATCAACTAAAGGATAAATCATATTTAAAACAAAAAATTTAAATTA
* * *
40635248 AAAATAATCAACTAAATGATAAATCATATTTAAAACAATAAATTTCAATTA
1 AAAATAATCAACTAAAGGATAAATCATATTTAAAACAAAAAATTTAAATTA
40635299 AAA
1 AAA
40635302 TAAAATAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (51 bp):
AAAATAATCAACTAAAGGATAAATCATATTTAAAACAAAAAATTTAAATTA
Found at i:40635300 original size:70 final size:70
Alignment explanation
Indices: 40635226--40635371 Score: 195
Period size: 70 Copynumber: 2.1 Consensus size: 70
40635216 TAAATTATAT
* *
40635226 TTAAAGCAAAA-AATTTAAATTAAAAATAATCAACTAAATGATAAATCATATTTAAAACAATAAA
1 TTAAAACAAAATAATTTAAA-TAAAAATAATCAACTAAAGGATAAATCATATTTAAAACAATAAA
*
40635290 TTTCAA
65 TTTAAA
* * * * * *
40635296 TTAAAATAAAATAATTTAAATAAAAATAATTAAGTATAGGATAAATTATATTTAAAGCAATAAAT
1 TTAAAACAAAATAATTTAAATAAAAATAATCAACTAAAGGATAAATCATATTTAAAACAATAAAT
40635361 TTAAA
66 TTAAA
40635366 TTAAAA
1 TTAAAA
40635372 ATAATAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
70 58 0.88
71 8 0.12
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (70 bp):
TTAAAACAAAATAATTTAAATAAAAATAATCAACTAAAGGATAAATCATATTTAAAACAATAAAT
TTAAA
Found at i:40635311 original size:14 final size:15
Alignment explanation
Indices: 40635294--40635328 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
40635284 AATAAATTTC
40635294 AATTAAAAT-AAAAT
1 AATTAAAATAAAAAT
*
40635308 AATTTAAATAAAAAT
1 AATTAAAATAAAAAT
40635323 AATTAA
1 AATTAA
40635329 GTATAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAAATAAAAAT
Found at i:40635358 original size:19 final size:19
Alignment explanation
Indices: 40635336--40635413 Score: 93
Period size: 19 Copynumber: 4.1 Consensus size: 19
40635326 TAAGTATAGG
**
40635336 ATAAATTATATTTAAAGCA
1 ATAAATTATATTTAAAATA
* *
40635355 ATAAATTTAAATTAAAAATA
1 ATAAA-TTATATTTAAAATA
40635375 ATAAATTATATTTAAAATA
1 ATAAATTATATTTAAAATA
* *
40635394 ATAAATTTTAATTAAAATA
1 ATAAATTATATTTAAAATA
40635413 A
1 A
40635414 AATAATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 35 0.70
20 15 0.30
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
ATAAATTATATTTAAAATA
Found at i:40635379 original size:20 final size:20
Alignment explanation
Indices: 40635354--40635434 Score: 96
Period size: 19 Copynumber: 4.2 Consensus size: 20
40635344 TATTTAAAGC
40635354 AATAAATTTAAATTAAAAAT
1 AATAAATTTAAATTAAAAAT
* *
40635374 AATAAA-TTATATTTAAAAT
1 AATAAATTTAAATTAAAAAT
*
40635393 AATAAATTTTAATT-AAAAT
1 AATAAATTTAAATTAAAAAT
*
40635412 AAAATAATTTAAA-TAAAAAT
1 AATA-AATTTAAATTAAAAAT
40635432 AAT
1 AAT
40635435 TAAGTATAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 26 0.51
20 25 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAATTTAAATTAAAAAT
Found at i:40635381 original size:39 final size:39
Alignment explanation
Indices: 40635336--40635490 Score: 141
Period size: 39 Copynumber: 4.2 Consensus size: 39
40635326 TAAGTATAGG
40635336 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
** *
40635375 ATAAATTATATTTAAAATAATAAATTTTAATT-AAAAT-
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
* **
40635412 A-AAA-TA-ATTTAAA-TAA-AAA--T-AATTAAGTATA
1 ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
* *
40635443 GGATAAATCATATTTAAAGCAATAAATTTAAATTAGAAATA
1 --ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
*
40635484 ATTAATT
1 ATAAATT
40635491 GAATGATAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
29 4 0.04
30 4 0.04
32 3 0.03
33 4 0.04
34 10 0.11
35 3 0.03
36 10 0.11
37 3 0.03
38 8 0.09
39 34 0.37
40 1 0.01
41 8 0.09
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (39 bp):
ATAAATTATATTTAAAGCAATAAATTTAAATTAAAAATA
Found at i:40635399 original size:109 final size:109
Alignment explanation
Indices: 40635261--40635490 Score: 397
Period size: 109 Copynumber: 2.1 Consensus size: 109
40635251 ATAATCAACT
* *
40635261 AAATGATAAATCATATTTAAAACAATAAATTTCAATTAAAATAAAATAATTTAAATAAAAATAAT
1 AAATAATAAATTATATTTAAAACAATAAATTTCAATTAAAATAAAATAATTTAAATAAAAATAAT
*
40635326 TAAGTATAGGATAAATTATATTTAAAGCAATAAATTTAAATTAA
66 TAAGTATAGGATAAATCATATTTAAAGCAATAAATTTAAATTAA
* *
40635370 AAATAATAAATTATATTTAAAATAATAAATTTTAATTAAAATAAAATAATTTAAATAAAAATAAT
1 AAATAATAAATTATATTTAAAACAATAAATTTCAATTAAAATAAAATAATTTAAATAAAAATAAT
*
40635435 TAAGTATAGGATAAATCATATTTAAAGCAATAAATTTAAATTAG
66 TAAGTATAGGATAAATCATATTTAAAGCAATAAATTTAAATTAA
*
40635479 AAATAATTAATT
1 AAATAATAAATT
40635491 GAATGATAAA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 114 1.00
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (109 bp):
AAATAATAAATTATATTTAAAACAATAAATTTCAATTAAAATAAAATAATTTAAATAAAAATAAT
TAAGTATAGGATAAATCATATTTAAAGCAATAAATTTAAATTAA
Found at i:40635419 original size:14 final size:15
Alignment explanation
Indices: 40635402--40635437 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40635392 TAATAAATTT
40635402 TAATTAAAAT-AAAA
1 TAATTAAAATAAAAA
*
40635416 TAATTTAAATAAAAA
1 TAATTAAAATAAAAA
40635431 TAATTAA
1 TAATTAA
40635438 GTATAGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATTAAAATAAAAA
Found at i:40635423 original size:15 final size:15
Alignment explanation
Indices: 40635402--40635435 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
40635392 TAATAAATTT
*
40635402 TAATTAAAAT-AAAA
1 TAATTTAAATAAAAA
40635416 TAATTTAAATAAAAA
1 TAATTTAAATAAAAA
40635431 TAATT
1 TAATT
40635436 AAGTATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATTTAAATAAAAA
Found at i:40635551 original size:17 final size:17
Alignment explanation
Indices: 40635526--40635559 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40635516 AATTATATTA
*
40635526 TAATTAAAGGATAAATT
1 TAATGAAAGGATAAATT
*
40635543 TAATGAAAGGCTAAATT
1 TAATGAAAGGATAAATT
40635560 AGATTTTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (17 bp):
TAATGAAAGGATAAATT
Found at i:40636451 original size:12 final size:14
Alignment explanation
Indices: 40636421--40636455 Score: 56
Period size: 12 Copynumber: 2.6 Consensus size: 14
40636411 ACAACCATGA
40636421 TTTTAATTACTTGT
1 TTTTAATTACTTGT
40636435 TTTTAATTA-TT-T
1 TTTTAATTACTTGT
40636447 TTTTAATTA
1 TTTTAATTA
40636456 GAATTATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 9 0.43
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTAATTACTTGT
Found at i:40636971 original size:24 final size:23
Alignment explanation
Indices: 40636944--40636989 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
40636934 AAATACATCA
40636944 TGTGAAAAAAAAGAAGGAAAAAAT
1 TGTGAAAAAAAA-AAGGAAAAAAT
*
40636968 TGTGAAAAAAAAAATGAAAAAA
1 TGTGAAAAAAAAAAGGAAAAAA
40636990 ATGGACCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (23 bp):
TGTGAAAAAAAAAAGGAAAAAAT
Found at i:40646417 original size:27 final size:27
Alignment explanation
Indices: 40646379--40646430 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
40646369 TATTAAAGTT
*
40646379 ATTGAAGGGAGGTCAACTCCATCAAAA
1 ATTGAAGGGAGGTCAACTACATCAAAA
40646406 ATTGAAGGGAGGTCAACTACATCAA
1 ATTGAAGGGAGGTCAACTACATCAA
40646431 GAGAAACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (27 bp):
ATTGAAGGGAGGTCAACTACATCAAAA
Found at i:40655445 original size:16 final size:16
Alignment explanation
Indices: 40655426--40655457 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40655416 AAAATAACCC
40655426 AAATTTAAAACGATTT
1 AAATTTAAAACGATTT
*
40655442 AAATTTAAAATGATTT
1 AAATTTAAAACGATTT
40655458 GGATAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTTAAAACGATTT
Found at i:40664980 original size:18 final size:18
Alignment explanation
Indices: 40664939--40664980 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40664929 GATAAGATAG
*
40664939 AATTTTGAAATTTTTTGT
1 AATTTTAAAATTTTTTGT
*
40664957 ATTTTTAAAATATTTTT-T
1 AATTTTAAAAT-TTTTTGT
40664975 AATTTT
1 AATTTT
40664981 TTAATTTTAA
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:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
AATTTTAAAATTTTTTGT
Found at i:40681663 original size:14 final size:15
Alignment explanation
Indices: 40681644--40681673 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40681634 GTGATTCAGC
40681644 ATTCAA-TCAACAAT
1 ATTCAACTCAACAAT
40681658 ATTCAACTCAACAAT
1 ATTCAACTCAACAAT
40681673 A
1 A
40681674 CTTATATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (15 bp):
ATTCAACTCAACAAT
Found at i:40682221 original size:47 final size:47
Alignment explanation
Indices: 40682168--40682265 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
40682158 GCATACAAAA
*
40682168 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGT
1 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGC
*
40682215 ACATTGAATGATTTATGGGATGGGATGGTGAAATATGAGGAAAGGGC
1 ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGC
40682262 ACAT
1 ACAT
40682266 CACATTAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.27
Consensus pattern (47 bp):
ACATTGAATGATTTATAGGATGGGATGGTGAAATATGAGGAAAGGGC
Found at i:40682586 original size:16 final size:16
Alignment explanation
Indices: 40682565--40682595 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40682555 GACTTAAAAG
40682565 TTAAAACTAATTGTTT
1 TTAAAACTAATTGTTT
*
40682581 TTAAAATTAATTGTT
1 TTAAAACTAATTGTT
40682596 ATTGAATTTA
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:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TTAAAACTAATTGTTT
Found at i:40682698 original size:25 final size:25
Alignment explanation
Indices: 40682670--40682717 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
40682660 AAGATTACTT
40682670 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
40682695 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
40682718 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:40685956 original size:13 final size:13
Alignment explanation
Indices: 40685938--40686071 Score: 103
Period size: 13 Copynumber: 10.2 Consensus size: 13
40685928 AATTTAAAAG
*
40685938 TTAAAACATTATA
1 TTAAAACAGTATA
*
40685951 TTAAAACAATATAA
1 TTAAAACAGTAT-A
*
40685965 TTATAACAGTATA
1 TTAAAACAGTATA
*
40685978 TTAAAACAATATA
1 TTAAAACAGTATA
*
40685991 TTAAAAAAGTATA
1 TTAAAACAGTATA
* *
40686004 TTTATAATAGTATA
1 -TTAAAACAGTATA
*
40686018 TTAAAATAGTATA
1 TTAAAACAGTATA
* * *
40686031 TTATAA-ATTTTA
1 TTAAAACAGTATA
*
40686043 -TAACAATA-TATTA
1 TTAA-AACAGTA-TA
40686056 TTAAAACAGTATA
1 TTAAAACAGTATA
40686069 TTA
1 TTA
40686072 CATTTAAAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
11 2 0.02
12 7 0.07
13 62 0.63
14 27 0.28
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:40685972 original size:27 final size:27
Alignment explanation
Indices: 40685906--40686005 Score: 105
Period size: 27 Copynumber: 3.7 Consensus size: 27
40685896 AAATTAAATG
* **
40685906 TATATTTATAACAGTATATTAAAA-TT
1 TATAATTATAACAGTATATTAAAACAA
* * *
40685932 TAAAAGTTAAAACATTATATTAAAACAA
1 TATAA-TTATAACAGTATATTAAAACAA
40685960 TATAATTATAACAGTATATTAAAACAA
1 TATAATTATAACAGTATATTAAAACAA
* *
40685987 TAT-ATTAAAAAAGTATATT
1 TATAATTATAACAGTATATT
40686006 TATAATAGTA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
26 17 0.28
27 40 0.66
28 4 0.07
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (27 bp):
TATAATTATAACAGTATATTAAAACAA
Found at i:40685983 original size:40 final size:40
Alignment explanation
Indices: 40685938--40686033 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
40685928 AATTTAAAAG
*
40685938 TTAAAACATTATATTAAAACAA-TATAATTATAACAGTATA
1 TTAAAACAATATATTAAAA-AAGTATAATTATAACAGTATA
* *
40685978 TTAAAACAATATATTAAAAAAGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAAAAGTATAATTATAACAGTATA
* *
40686018 TTAAAATAGTATATTA
1 TTAAAACAATATATTA
40686034 TAAATTTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 2 0.04
40 48 0.96
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (40 bp):
TTAAAACAATATATTAAAAAAGTATAATTATAACAGTATA
Found at i:40686299 original size:7 final size:7
Alignment explanation
Indices: 40686287--40686311 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40686277 TATAAAAATA
40686287 AATACAT
1 AATACAT
40686294 AATACAT
1 AATACAT
40686301 AATACAT
1 AATACAT
40686308 AATA
1 AATA
40686312 GTATAATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACAT
Found at i:40687785 original size:38 final size:39
Alignment explanation
Indices: 40687734--40687813 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
40687724 AATAAAAAAC
*
40687734 ACAACCATTAACAGCAAAATCAAAATCAGAACACCATTA
1 ACAACCATTAACAGAAAAATCAAAATCAGAACACCATTA
40687773 ACAA-CATTAACAGAAAAATCAAAATCAGAACACCATTA
1 ACAACCATTAACAGAAAAATCAAAATCAGAACACCATTA
40687811 ACA
1 ACA
40687814 GCAAAAATCA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 36 0.90
39 4 0.10
ACGTcount: A:0.56, C:0.24, G:0.05, T:0.15
Consensus pattern (39 bp):
ACAACCATTAACAGAAAAATCAAAATCAGAACACCATTA
Found at i:40687809 original size:29 final size:30
Alignment explanation
Indices: 40687772--40687839 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
40687762 GAACACCATT
40687772 AACAACATTAACAG-AAAAATCAAAATCAG
1 AACAACATTAACAGCAAAAATCAAAATCAG
* *
40687801 AACACCATTAACAGCAAAAATCAAAATCAC
1 AACAACATTAACAGCAAAAATCAAAATCAG
40687831 AACCAACAT
1 AA-CAACAT
40687840 CAAAAAGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 13 0.38
30 16 0.47
31 5 0.15
ACGTcount: A:0.59, C:0.24, G:0.04, T:0.13
Consensus pattern (30 bp):
AACAACATTAACAGCAAAAATCAAAATCAG
Found at i:40697740 original size:16 final size:18
Alignment explanation
Indices: 40697713--40697747 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40697703 CACTACCTCA
40697713 AAATTAACAAGATT-TGG
1 AAATTAACAAGATTATGG
40697730 AAATT-ACAAGATTATGG
1 AAATTAACAAGATTATGG
40697747 A
1 A
40697748 TATCACGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.29
Consensus pattern (18 bp):
AAATTAACAAGATTATGG
Found at i:40709545 original size:12 final size:12
Alignment explanation
Indices: 40709528--40709561 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
40709518 TGGCCTACCC
40709528 ATATTAATTTTT
1 ATATTAATTTTT
*
40709540 ATATTATTTTTT
1 ATATTAATTTTT
40709552 ATA-TAATTTT
1 ATATTAATTTT
40709562 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:40722598 original size:37 final size:37
Alignment explanation
Indices: 40722535--40722624 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
40722525 ATTCCAAAAA
*
40722535 TAATATTATTTTAATAGTTTTATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTTATATTAAATTAATATT
*
40722571 TAATACTTATCTTAATAGTATTT-TATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTTATATTAAATTAATATT
*
40722609 AAAGTAATTATCTTAA
1 TAA-T-ATTATCTTAA
40722625 AATTAAATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
36 5 0.11
37 22 0.48
38 8 0.17
39 10 0.22
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTTATATTAAATTAATATT
Found at i:40724611 original size:40 final size:41
Alignment explanation
Indices: 40724531--40724630 Score: 166
Period size: 40 Copynumber: 2.4 Consensus size: 41
40724521 TGATTCTGTA
*
40724531 CACCGGCATTAAGCCTGCTATAGATGTATAGTATGAATATTT
1 CACCGGCATTAAGCCTGC-ATAGACGTATAGTATGAATATTT
*
40724573 CACCGGCATTAAGCCTGC-TAGACGTATAGTCTGAATATTT
1 CACCGGCATTAAGCCTGCATAGACGTATAGTATGAATATTT
40724613 CACCGGCATTAAGCCTGC
1 CACCGGCATTAAGCCTGC
40724631 CAGGCACAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 38 0.68
42 18 0.32
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCATAGACGTATAGTATGAATATTT
Found at i:40727713 original size:21 final size:22
Alignment explanation
Indices: 40727689--40727735 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
40727679 AGTAGAGGAG
*
40727689 ACACGGT-CGTGTGGTTGAGAT
1 ACACGGTCCGTGTGGCTGAGAT
40727710 ACAC-GTCCGTGTGGCTGAGAT
1 ACACGGTCCGTGTGGCTGAGAT
40727731 ACACG
1 ACACG
40727736 ACCATGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.23
Consensus pattern (22 bp):
ACACGGTCCGTGTGGCTGAGAT
Found at i:40727743 original size:21 final size:21
Alignment explanation
Indices: 40727698--40727743 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40727688 GACACGGTCG
* * *
40727698 TGTGGTTGAGATACACGTCCG
1 TGTGGCTGAGATACACGACCA
40727719 TGTGGCTGAGATACACGACCA
1 TGTGGCTGAGATACACGACCA
40727740 TGTG
1 TGTG
40727744 TACAGGCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.26
Consensus pattern (21 bp):
TGTGGCTGAGATACACGACCA
Found at i:40731602 original size:50 final size:50
Alignment explanation
Indices: 40731487--40731679 Score: 278
Period size: 50 Copynumber: 3.8 Consensus size: 50
40731477 GATAAGAACA
* ** *
40731487 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* *
40731538 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
40731588 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
40731638 TGCCAATACCATATCCCAGACATGGTCTTACATGAGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40731680 TTACCCAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 93 0.73
51 34 0.27
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40732051 original size:30 final size:30
Alignment explanation
Indices: 40732017--40732074 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
40732007 CATCGACTTT
40732017 AACTTTGGA-AAAATTATGATTTTGCCCCTA
1 AACTTT-GACAAAATTATGATTTTGCCCCTA
* * *
40732047 AACTTTTACATAATTATGCTTTTGCCCC
1 AACTTTGACAAAATTATGATTTTGCCCC
40732075 AAAGTTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (30 bp):
AACTTTGACAAAATTATGATTTTGCCCCTA
Found at i:40736214 original size:15 final size:16
Alignment explanation
Indices: 40736184--40736216 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40736174 TTTTCCCTTA
40736184 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
*
40736200 TTATT-ATTTTTAAAT
1 TTATTCATTTTCAAAT
40736215 TT
1 TT
40736217 GTTTACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:40738871 original size:42 final size:42
Alignment explanation
Indices: 40738818--40739043 Score: 184
Period size: 43 Copynumber: 5.3 Consensus size: 42
40738808 TTTTAGAAAT
* *
40738818 AAACGCCGCTAAATATCATGACCTTTAACGGCGCTTTTCCAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCAA
* * * * *
40738860 AAACGCTGCTAAAGATCCTAATCTTTAGCGGCGCTTCTCCAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCAA
* * * *
40738902 CAAACGCCACTAAAGACCATGACCTTTAGCGGCACTTTTCCCAC
1 -AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-CCAA
* * * * * * *
40738946 AAACGCCGCTATAGCTAAAGACCTTTAGCAGCACTTTTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-CCAA
* * * * * *
40738989 AAACGCCACTATAGAACA-AACCTTTAGCGACGCTTCTTGCAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTT-TTCCAA
*
40739031 AAACGCCACTAAA
1 AAACGCCGCTAAA
40739044 AACATAACAT
Statistics
Matches: 146, Mismatches: 35, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
42 62 0.42
43 81 0.55
44 3 0.02
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTCCAA
Found at i:40745855 original size:16 final size:17
Alignment explanation
Indices: 40745819--40745860 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
40745809 CACTATAATC
40745819 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
40745837 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
40745853 ATTATTTA
1 ATTATTTA
40745861 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:40746014 original size:14 final size:14
Alignment explanation
Indices: 40745997--40746045 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
40745987 CCATAACTCT
*
40745997 TAACCCTCAACCCC
1 TAACCCTAAACCCC
*
40746011 TAACCCTTAACCCC
1 TAACCCTAAACCCC
*
40746025 TAAACCTTAAACCCC
1 T-AACCCTAAACCCC
40746040 -AACCCT
1 TAACCCT
40746046 TAATCTATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 14 0.47
15 11 0.37
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (14 bp):
TAACCCTAAACCCC
Found at i:40746014 original size:21 final size:21
Alignment explanation
Indices: 40745984--40746023 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40745974 CTAAATCTTA
*
40745984 AACCCATAACTCTTAACCCTC
1 AACCCATAACCCTTAACCCTC
*
40746005 AACCCCTAACCCTTAACCC
1 AACCCATAACCCTTAACCC
40746024 CTAAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCATAACCCTTAACCCTC
Found at i:40746046 original size:14 final size:15
Alignment explanation
Indices: 40746005--40746048 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
40745995 CTTAACCCTC
40746005 AACCCCTAACCCTT-
1 AACCCCTAACCCTTA
*
40746019 AACCCCTAAACCTTA
1 AACCCCTAACCCTTA
40746034 AACCCC-AACCCTTA
1 AACCCCTAACCCTTA
40746048 A
1 A
40746049 TCTATACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (15 bp):
AACCCCTAACCCTTA
Found at i:40746071 original size:7 final size:7
Alignment explanation
Indices: 40746059--40746147 Score: 70
Period size: 7 Copynumber: 12.6 Consensus size: 7
40746049 TCTATACCCT
40746059 TAAACCA
1 TAAACCA
*
40746066 TAAACCG
1 TAAACCA
* *
40746073 TAATCCT
1 TAAACCA
*
40746080 TAAACCC
1 TAAACCA
* *
40746087 TAAATCT
1 TAAACCA
40746094 TAAACCA
1 TAAACCA
*
40746101 TAAACTA
1 TAAACCA
40746108 TAAACCA
1 TAAACCA
* *
40746115 TAACCCC
1 TAAACCA
40746122 TAAACTCA
1 TAAAC-CA
*
40746130 TAATCCA
1 TAAACCA
*
40746137 TAAACCT
1 TAAACCA
40746144 TAAA
1 TAAA
40746148 ATAGTAACTC
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
7 58 0.92
8 5 0.08
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (7 bp):
TAAACCA
Found at i:40746080 original size:21 final size:21
Alignment explanation
Indices: 40746056--40746147 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
40746046 TAATCTATAC
* *
40746056 CCTTAAACCATAAACCGTAAT
1 CCTTAAACCATAAACCATAAA
* * *
40746077 CCTTAAACCCTAAATCTTAAA
1 CCTTAAACCATAAACCATAAA
* * *
40746098 CCATAAACTATAAACCATAAC
1 CCTTAAACCATAAACCATAAA
* *
40746119 CCCTAAACTCATAATCCATAAA
1 CCTTAAAC-CATAAACCATAAA
40746141 CCTTAAA
1 CCTTAAA
40746148 ATAGTAACTC
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
21 39 0.71
22 16 0.29
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAAACCATAAA
Found at i:40746147 original size:22 final size:23
Alignment explanation
Indices: 40746122--40746172 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
40746112 CCATAACCCC
40746122 TAAACTCA-TAA-TCCATAAACCT
1 TAAACTCAGTAACTCC-TAAACCT
*
40746144 TAAAAT-AGTAACTCCTAAACCT
1 TAAACTCAGTAACTCCTAAACCT
40746166 TAAACTC
1 TAAACTC
40746173 TAAATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 1 0.04
22 20 0.83
23 3 0.12
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAACTCAGTAACTCCTAAACCT
Found at i:40746582 original size:41 final size:41
Alignment explanation
Indices: 40746527--40746762 Score: 323
Period size: 41 Copynumber: 5.8 Consensus size: 41
40746517 GTGGCACTTT
* * *
40746527 CCCAAAAATGCCGCTAAAGACTAGAGCATTAGCGGCGCTTT
1 CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
* *
40746568 TCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTTC
1 CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
* *
40746609 TCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTTC
1 CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
*
40746650 CCCAAAAACACCGCTAAAGACCAGAGCATTAGCGGCGCTTC
1 CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
* * * *
40746691 CCCAAAAACGCCGCTAAAAACCAAAGCATTAGCAGCTCTT-
1 CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
* *
40746731 TCCAAAAACGCCGCTAAA-ACCCTGAGCATTAG
1 CCCAAAAACGCCGCTAAAGA-CCAGAGCATTAG
40746763 TGACGTTTTA
Statistics
Matches: 178, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 27 0.15
41 150 0.84
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.15
Consensus pattern (41 bp):
CCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTC
Found at i:40748368 original size:14 final size:15
Alignment explanation
Indices: 40748346--40748422 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40748336 CAATCAAACA
40748346 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
40748360 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
40748375 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
40748395 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
40748409 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
40748423 ACTGGCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:40748387 original size:20 final size:20
Alignment explanation
Indices: 40748362--40748401 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40748352 AATATTTTCC
*
40748362 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40748382 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40748402 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40748407 original size:34 final size:35
Alignment explanation
Indices: 40748350--40748416 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40748340 CAAACACCAG
*
40748350 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40748385 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40748417 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40755276 original size:23 final size:23
Alignment explanation
Indices: 40755246--40755294 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
40755236 CTAAATCAGG
40755246 CTCAATTAA-TGACGTTGAATTTA
1 CTCAATTAATTG-CGTTGAATTTA
40755269 CTCAATTAATTGCGTTGAATTTA
1 CTCAATTAATTGCGTTGAATTTA
40755292 CTC
1 CTC
40755295 TTTTTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (23 bp):
CTCAATTAATTGCGTTGAATTTA
Found at i:40756033 original size:12 final size:12
Alignment explanation
Indices: 40756016--40756069 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
40756006 AACTAATCCT
40756016 CTCTCAAATTTC
1 CTCTCAAATTTC
*
40756028 CTCTC-AATTTG
1 CTCTCAAATTTC
40756039 CTCTC-AATTTC
1 CTCTCAAATTTC
40756050 CT-TCCAAATTT-
1 CTCT-CAAATTTC
40756061 CTCTCAAAT
1 CTCTCAAAT
40756070 CCATATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
10 1 0.03
11 25 0.68
12 11 0.30
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:40756042 original size:11 final size:11
Alignment explanation
Indices: 40756016--40756104 Score: 55
Period size: 11 Copynumber: 8.4 Consensus size: 11
40756006 AACTAATCCT
40756016 CTCTCAAATTTC
1 CTCTC-AATTTC
*
40756028 CTCTCAATTTG
1 CTCTCAATTTC
40756039 CTCTCAATTTC
1 CTCTCAATTTC
40756050 CT-TCCAAATTT-
1 CTCT-C-AATTTC
*
40756061 CTCTCAA-ATC
1 CTCTCAATTTC
* *
40756071 C-AT--ATTTA
1 CTCTCAATTTC
* *
40756079 ATCTCAATTTG
1 CTCTCAATTTC
40756090 CTCTCAATTTC
1 CTCTCAATTTC
40756101 CTCT
1 CTCT
40756105 TAAATTTCTC
Statistics
Matches: 58, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.07
11 38 0.66
12 11 0.19
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40756089 original size:51 final size:51
Alignment explanation
Indices: 40756029--40756128 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
40756019 TCAAATTTCC
40756029 TCTCAATTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * *
40756080 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
40756129 TAAAATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:40756139 original size:51 final size:51
Alignment explanation
Indices: 40756031--40756139 Score: 141
Period size: 51 Copynumber: 2.1 Consensus size: 51
40756021 AAATTTCCTC
**
40756031 TCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAATC
1 TCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAAAA
* * *
40756082 TCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCCTATTTTAAAA
1 TCAATTTGCTCTCAATTTCCTTC-CAAATTTCTCTCAAATCCATA-TTTAAAA
40756134 T-AATTT
1 TCAATTT
40756140 TTTTTAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.04
51 43 0.84
52 6 0.12
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAAAA
Found at i:40756146 original size:15 final size:15
Alignment explanation
Indices: 40756126--40756161 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
40756116 TAAATCCCTA
40756126 TTTTAAAATAAT-TTT
1 TTTTAAAA-AATATTT
40756141 TTTTAAAAAATATTT
1 TTTTAAAAAATATTT
40756156 TTTTAA
1 TTTTAA
40756162 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAAAAAATATTT
Found at i:40758571 original size:22 final size:22
Alignment explanation
Indices: 40758545--40758596 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
40758535 CCTAAACCCT
** *
40758545 AACCCTTAACTTCGAAACCTTA
1 AACCCTTAACTTAAAAACCATA
40758567 AACCCTTAACTTAAAAACCATA
1 AACCCTTAACTTAAAAACCATA
40758589 AA-CCTTAA
1 AACCCTTAA
40758597 ACTCTAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.25
Consensus pattern (22 bp):
AACCCTTAACTTAAAAACCATA
Done.