Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 59 of 226
Found at i:23461827 original size:46 final size:46
Alignment explanation
Indices: 23461756--23461844 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
23461746 CCATTGCAAA
*
23461756 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAC
1 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAC
* *
23461802 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACT
1 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACT
23461845 TAGTTATAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAC
Found at i:23464269 original size:46 final size:46
Alignment explanation
Indices: 23464189--23464328 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
23464179 ACAATGCTAT
* * *
23464189 AACTAAGTATGGTTTCCTTCACTGAAATATCATACCTACTTTTCAC
1 AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* * *
23464235 AACTCAGTATGGTTTTCTTCATTTAAACACCATACCTACTTTTCAC
1 AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
23464281 AACTTAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
23464327 AA
1 AA
23464329 TTTGTCATGG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:23470419 original size:125 final size:125
Alignment explanation
Indices: 23470198--23470471 Score: 410
Period size: 125 Copynumber: 2.2 Consensus size: 125
23470188 TGTTTACTCA
* *
23470198 CTTTTGCTACT-GTAGGTCCT-GAAAAAATAATTTCTAGTTGACGTTTTTGAGCAAATAGTATAA
1 CTTTTGCTA-TAGTAGGTCCTGGAAAAAATAATTTCTAGTTGAAGTTTCTGAGCAAATAGTATAA
* * * *
23470261 AATCGCTTCTAGCAGGATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGGACCCG
65 AATCGCTTCTAACAGGATGCTATTTGAAAAGAATTTGTGAAATCGCGCCCTCGTGGACCCG
*
23470322 CTTTTGCTATAGTAGGTCCTGGAAGAAATAATTT-TGAGTTGAAGTTTCTGAGCAAATAGTATAA
1 CTTTTGCTATAGTAGGTCCTGGAAAAAATAATTTCT-AGTTGAAGTTTCTGAGCAAATAGTATAA
* * *
23470386 AATCGCTTCTAACAGGATGCTATTTGAAAAGAATTTGTGAAATCTCGCCCTCTTGGACGCG
65 AATCGCTTCTAACAGGATGCTATTTGAAAAGAATTTGTGAAATCGCGCCCTCGTGGACCCG
*
23470447 CTTTTGCTACAGTAGGTCCTGGAAA
1 CTTTTGCTATAGTAGGTCCTGGAAA
23470472 TTGAGAGGAA
Statistics
Matches: 135, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
123 1 0.01
124 19 0.14
125 115 0.85
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (125 bp):
CTTTTGCTATAGTAGGTCCTGGAAAAAATAATTTCTAGTTGAAGTTTCTGAGCAAATAGTATAAA
ATCGCTTCTAACAGGATGCTATTTGAAAAGAATTTGTGAAATCGCGCCCTCGTGGACCCG
Found at i:23472048 original size:67 final size:66
Alignment explanation
Indices: 23471940--23472073 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 66
23471930 TTTCTAATTC
23471940 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAGGCTAAAT-CCCTG
23472005 CA
65 CA
* *
23472007 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACTAGTCCAGGCTAAATCCCTGC
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAGGCTAAATCCCTGC
23472072 A
66 A
23472073 A
1 A
23472074 TGACAATTAC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 8 0.12
67 57 0.88
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAGGCTAAATCCCTGC
A
Found at i:23474163 original size:111 final size:115
Alignment explanation
Indices: 23473990--23474197 Score: 255
Period size: 112 Copynumber: 1.8 Consensus size: 115
23473980 TCCCGTCACA
* * * *
23473990 CGCCGCAAGATCTGAAGACCAAAACGCATCGTTTTGGTCTTGATGTATACAAGAATTAGTGGCG-
1 CGCCGCAAAATCTGAAGACAAAAACGCACCGTTTTGGTCTCGATGTATACAAGAATTAGTGGCGC
** * *
23474054 TTTATAGTAAA-TCGCCGCTAAAGCAATTATTAGCGGCGCAATGGCTAAAG
66 TTTA-ACAAAACACGCCGCTAAAGCAAGTATTAGCGGCGCAATGGCTAAAG
* ** **
23474104 CGCCGCAAAATCT-AA-ACAAAAACGCACCGTTTT-GTCTCGCTGTATATTAGCGTTAGTGGCGC
1 CGCCGCAAAATCTGAAGACAAAAACGCACCGTTTTGGTCTCGATGTATACAAGAATTAGTGGCGC
23474166 TTTAACAAAACACGCCGCTAAAGCAAGTATTA
66 TTTAACAAAACACGCCGCTAAAGCAAGTATTA
23474198 TGTTAACCAA
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
111 26 0.33
112 39 0.49
113 2 0.03
114 12 0.15
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (115 bp):
CGCCGCAAAATCTGAAGACAAAAACGCACCGTTTTGGTCTCGATGTATACAAGAATTAGTGGCGC
TTTAACAAAACACGCCGCTAAAGCAAGTATTAGCGGCGCAATGGCTAAAG
Found at i:23481141 original size:21 final size:21
Alignment explanation
Indices: 23481117--23481165 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
23481107 GGCAGAGAAG
*
23481117 GAAGCAGAGGCTACAGCGAGA
1 GAAGCAGAGGCCACAGCGAGA
* *
23481138 GAAGCAGATGCCGCAGCGAGA
1 GAAGCAGAGGCCACAGCGAGA
23481159 GAAGCAG
1 GAAGCAG
23481166 CGAGAGAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.39, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGGCCACAGCGAGA
Found at i:23481167 original size:12 final size:12
Alignment explanation
Indices: 23481150--23481177 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23481140 AGCAGATGCC
23481150 GCAGCGAGAGAA
1 GCAGCGAGAGAA
23481162 GCAGCGAGAGAA
1 GCAGCGAGAGAA
23481174 GCAG
1 GCAG
23481178 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:23481691 original size:85 final size:81
Alignment explanation
Indices: 23481597--23481889 Score: 360
Period size: 85 Copynumber: 3.5 Consensus size: 81
23481587 GTTTGTGAAA
** * *
23481597 TAAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAGAAGCGCCGCTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGAGC-TTTAGCGGCGTTTTT--TTAAGCGCCGCTAAAGAACATG
23481660 A-CTTTTAGAGGCGTTTTCTTCC
62 ATC-TTTAGAGGCGTTTT-TT-C
*
23481682 AAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTATTTTAAGCGCCGCTAAAGAACATGATC
1 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTT-TTTTAAGCGCCGCTAAAGAACATGATC
*
23481747 TTTAGCGGCGTTTTTTTTC
65 TTTAGAGGCG--TTTTTTC
* *
23481766 TAAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTTTTTTTAAGCGCCGCTAAAGAACATGAT
1 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCG--TTTTTTTAAGCGCCGCTAAAGAACATGAT
*
23481831 CTTTAGGGGC-TTTTTTC
64 CTTTAGAGGCGTTTTTTC
*
23481848 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTCTTTA
1 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTTTTTA
23481890 TGTAAGCGCC
Statistics
Matches: 187, Mismatches: 13, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
80 7 0.04
82 39 0.21
84 61 0.33
85 70 0.37
86 10 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (81 bp):
TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTTTTTAAGCGCCGCTAAAGAACATGATCT
TTAGAGGCGTTTTTTC
Found at i:23481700 original size:43 final size:41
Alignment explanation
Indices: 23481597--23481884 Score: 313
Period size: 42 Copynumber: 6.9 Consensus size: 41
23481587 GTTTGTGAAA
**
23481597 TAAGCGCCGCTAAAGAACACT-ACTTTTAGCGGCGTTTTTGAA
1 TAAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTT-TC
* * * *
23481639 GAAGCGCCGCTATAGAACATTACTTTTAGAGGCGTTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT-TT-C
*
23481682 AAAGCGCCGCTAAAGAACATGAGC-TTTAGCGGCGTTTATTT-
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT-TTTC
23481723 TAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG--TTTTTTC
* *
23481766 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGCGTTTTTTTT
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCG-TTTTTTC
*
23481808 TAAGCGCCGCTAAAGAACATGA-TCTTTAGGGGC-TTTTTTC
1 TAAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTC
23481848 TAAGCGCCGCTAAAGAACATGAGC-TTTAGCGGCGTTT
1 TAAGCGCCGCTAAAGAACATGA-CTTTTAGCGGCGTTT
23481885 CTTTATGTAA
Statistics
Matches: 219, Mismatches: 14, Indels: 27
0.84 0.05 0.10
Matches are distributed among these distances:
40 36 0.16
41 35 0.16
42 76 0.35
43 70 0.32
44 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
TAAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTC
Found at i:23481813 original size:126 final size:125
Alignment explanation
Indices: 23481597--23481906 Score: 387
Period size: 126 Copynumber: 2.5 Consensus size: 125
23481587 GTTTGTGAAA
* * * *
23481597 TAAGCGCCGCTAAAGAACACT-ACTTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTATAGAACATT
1 TAAGCGCCGCTAAAGAACA-TGAC-TTTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATG
23481660 ACTTTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTATTT-
64 ACTTTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGAGCTTTAGCGGC-TTT-TTTC
* *
23481723 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGA
1 TAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGA
* *** * *
23481788 -TCTTTAGGGGCGTTTT-TTTTTAAGCGCCGCTAAAGAACATGATCTTTAGGGGCTTTTTTC
65 CT-TTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCTTTTTTC
* *
23481848 TAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCGTTTCTTTATGTAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTT-TTTATATAAGCGCCGCTAAAG
23481907 TTAGCGACGT
Statistics
Matches: 162, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
124 3 0.02
125 40 0.25
126 86 0.53
127 33 0.20
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (125 bp):
TAAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTATATAAGCGCCGCTAAAGAACATGAC
TTTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGAGCTTTAGCGGCTTTTTTC
Found at i:23482378 original size:11 final size:11
Alignment explanation
Indices: 23482326--23482378 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
23482316 CTAAATAAAA
*
23482326 TAATAAAATAA
1 TAATAAAATAT
23482337 TAATAAAATAT
1 TAATAAAATAT
*
23482348 TATTTAAAA-AT
1 TA-ATAAAATAT
23482359 TAAATTAAAATAT
1 T-AA-TAAAATAT
23482372 TAATAAA
1 TAATAAA
23482379 CTAATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
11 19 0.54
12 13 0.37
13 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:23483297 original size:23 final size:23
Alignment explanation
Indices: 23483267--23483313 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
23483257 CAAACCCACA
23483267 TATTTTAAGCTTGCCCATATTAT
1 TATTTTAAGCTTGCCCATATTAT
23483290 TATTTTAAGCTTGCCCATATTAT
1 TATTTTAAGCTTGCCCATATTAT
23483313 T
1 T
23483314 TTTAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (23 bp):
TATTTTAAGCTTGCCCATATTAT
Found at i:23486540 original size:13 final size:14
Alignment explanation
Indices: 23486522--23486551 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23486512 TTTTTAACAA
23486522 TTTAAT-TTTTTCT
1 TTTAATCTTTTTCT
23486535 TTTAATCTTTTTCT
1 TTTAATCTTTTTCT
23486549 TTT
1 TTT
23486552 TTATTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTAATCTTTTTCT
Found at i:23487900 original size:25 final size:27
Alignment explanation
Indices: 23487872--23487935 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
23487862 TAAAAAAATT
23487872 AAATATTAAAATG-CAAAAA-TTATAG
1 AAATATTAAAATGACAAAAATTTATAG
* *
23487897 AAATATTATAATGACAAAAATTTATAT
1 AAATATTAAAATGACAAAAATTTATAG
23487924 AAAT-TATAAAAT
1 AAATAT-TAAAAT
23487936 ACATTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 12 0.36
26 7 0.21
27 14 0.42
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
AAATATTAAAATGACAAAAATTTATAG
Found at i:23488717 original size:19 final size:19
Alignment explanation
Indices: 23488690--23488740 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
23488680 TCATTTATAA
*
23488690 TTTTCTATATTTTGTGCAC
1 TTTTATATATTTTGTGCAC
* ** *
23488709 TTTTATATATTTTTTTTAT
1 TTTTATATATTTTGTGCAC
23488728 TTTTATATATTTT
1 TTTTATATATTTT
23488741 TTTATTTCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTATATATTTTGTGCAC
Found at i:23488740 original size:18 final size:19
Alignment explanation
Indices: 23488709--23488752 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
23488699 TTTTGTGCAC
23488709 TTTTATATATTTTTTTTAT
1 TTTTATATATTTTTTTTAT
23488728 TTTTATATA-TTTTTTTAT
1 TTTTATATATTTTTTTTAT
*
23488746 TTCTATA
1 TTTTATA
23488753 ATAATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTATATATTTTTTTTAT
Found at i:23489891 original size:32 final size:32
Alignment explanation
Indices: 23489850--23489919 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
23489840 TGGGTCCCCA
*
23489850 GACCCACCTAATCCCCGCTATACCTGCCCTGC
1 GACCCACCTAATCCCCGCTATACCCGCCCTGC
** *
23489882 GACCCACCTAATCCTTGCTATACCCGTCCTGC
1 GACCCACCTAATCCCCGCTATACCCGCCCTGC
23489914 GACCCA
1 GACCCA
23489920 TTTCATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.47, G:0.13, T:0.20
Consensus pattern (32 bp):
GACCCACCTAATCCCCGCTATACCCGCCCTGC
Found at i:23490746 original size:14 final size:15
Alignment explanation
Indices: 23490726--23490766 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
23490716 TTTGATTGCC
23490726 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
23490740 CGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
23490755 AG-AAAATGTTTT
1 AGTAAAATGTTTT
23490767 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:23490779 original size:34 final size:35
Alignment explanation
Indices: 23490735--23490801 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
23490725 CAGTAAAATG
*
23490735 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
23490769 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
23490802 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:23491447 original size:18 final size:18
Alignment explanation
Indices: 23491426--23491464 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
23491416 GTTGTATCTT
23491426 TAATTAAATTATTATCCA
1 TAATTAAATTATTATCCA
23491444 TAATTAAATTATTATCCA
1 TAATTAAATTATTATCCA
23491462 TAA
1 TAA
23491465 AGTTGGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAATTATTATCCA
Found at i:23492127 original size:14 final size:13
Alignment explanation
Indices: 23492098--23492124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23492088 AGAAGGTAAG
23492098 ACAGATACTTAAA
1 ACAGATACTTAAA
23492111 ACAGATACTTAAA
1 ACAGATACTTAAA
23492124 A
1 A
23492125 ACATGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ACAGATACTTAAA
Found at i:23493229 original size:19 final size:19
Alignment explanation
Indices: 23493205--23493244 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
23493195 AAACCAAATC
23493205 AAGGGAGAACGAAAGGGAG
1 AAGGGAGAACGAAAGGGAG
*
23493224 AAGGGAGAACGAACGGGAG
1 AAGGGAGAACGAAAGGGAG
23493243 AA
1 AA
23493245 CGAAACCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.45, T:0.00
Consensus pattern (19 bp):
AAGGGAGAACGAAAGGGAG
Found at i:23493770 original size:10 final size:9
Alignment explanation
Indices: 23493747--23493776 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
23493737 TGCAAAATAA
23493747 TAAAAATTT
1 TAAAAATTT
23493756 TAAAAATTT
1 TAAAAATTT
*
23493765 TAAAAATAT
1 TAAAAATTT
23493774 TAA
1 TAA
23493777 CTCGGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTT
Found at i:23506926 original size:15 final size:15
Alignment explanation
Indices: 23506892--23506930 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
23506882 ACACAGATCA
*
23506892 AGATGATCATGAGAT
1 AGATGATGATGAGAT
*
23506907 AGATGATGATGAGTT
1 AGATGATGATGAGAT
*
23506922 TGATGATGA
1 AGATGATGA
23506931 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (15 bp):
AGATGATGATGAGAT
Found at i:23519766 original size:4 final size:4
Alignment explanation
Indices: 23519757--23519838 Score: 137
Period size: 4 Copynumber: 20.5 Consensus size: 4
23519747 TGAAATTGCT
23519757 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
23519805 TATG TATG TATG TATG TATG CATG CATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
23519839 AATTTCTTAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:23521156 original size:25 final size:25
Alignment explanation
Indices: 23521122--23521172 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
23521112 AAGTTAAAAG
23521122 TAGCCTTTAAAAAGCATGAAGACTA
1 TAGCCTTTAAAAAGCATGAAGACTA
23521147 TAGCCTTTAAAAAGCATGAAGACTA
1 TAGCCTTTAAAAAGCATGAAGACTA
23521172 T
1 T
23521173 CTGGATGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (25 bp):
TAGCCTTTAAAAAGCATGAAGACTA
Found at i:23530084 original size:15 final size:15
Alignment explanation
Indices: 23530064--23530096 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
23530054 CTCGAGGAGA
*
23530064 AACAGAGACTTGCTG
1 AACAGAAACTTGCTG
23530079 AACAGAAACTTGCTG
1 AACAGAAACTTGCTG
23530094 AAC
1 AAC
23530097 CTGAAATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (15 bp):
AACAGAAACTTGCTG
Found at i:23539103 original size:49 final size:49
Alignment explanation
Indices: 23539011--23539104 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
23539001 ACATTTCAAG
* * *
23539011 TTCAAGTAAATTTAGATTTGGATTATTTCGGATTGTGGGTCATTTTATA
1 TTCAAATAAATTTAGATTTGGATTATTTCGGATTATGGATCATTTTATA
* *
23539060 TTCAAATAAATTTAGGTTTGGATTGTTTCAGG-TTATGGATCATTT
1 TTCAAATAAATTTAGATTTGGATTATTTC-GGATTATGGATCATTT
23539105 GAGGTTCAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 37 0.95
50 2 0.05
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.47
Consensus pattern (49 bp):
TTCAAATAAATTTAGATTTGGATTATTTCGGATTATGGATCATTTTATA
Found at i:23543139 original size:27 final size:26
Alignment explanation
Indices: 23543088--23543140 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
23543078 ACTCTCTCTT
*
23543088 TTTCTCTTTATTTTCCATTATCTTTTG
1 TTTCTCTTTATTTTCCA-TACCTTTTG
23543115 TTTCTCCTTCTATTTTCC-TACCTTTT
1 TTTCT-CTT-TATTTTCCATACCTTTT
23543141 CCATGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 3 0.13
29 8 0.35
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTCTCTTTATTTTCCATACCTTTTG
Found at i:23545129 original size:67 final size:67
Alignment explanation
Indices: 23545011--23545139 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
23545001 ATTTGAGAAA
* * * *
23545011 GAAACTATATTGCTTCGTGTAGGAATAGCAATTTCGGAATCGGAGTAATTTGCTTCATTATCAAA
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATCAAA
23545076 CG
66 CG
* * * *
23545078 GAAACTATATTGCTTTGTGTAGGAATAGCAGTTCCAGAATCTGAATCATTTGCTTCACTATC
1 GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATC
23545140 TCTCTATATC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (67 bp):
GAAACTATATTGCTTCGTGTAGGAATAGCAATTCCAGAATCGGAATAATTTGCTTCACTATCAAA
CG
Found at i:23547498 original size:26 final size:27
Alignment explanation
Indices: 23547462--23547516 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
23547452 TGAATATTCA
23547462 AATTTTAAGAAGT-AGAGTCAGTTATT
1 AATTTTAAGAAGTAAGAGTCAGTTATT
*
23547488 AATTTTGAGAAGTAGAGAGTCAGTTATT
1 AATTTTAAGAAGTA-AGAGTCAGTTATT
23547516 A
1 A
23547517 TTTCCTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
28 14 0.54
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (27 bp):
AATTTTAAGAAGTAAGAGTCAGTTATT
Found at i:23551358 original size:35 final size:37
Alignment explanation
Indices: 23551318--23551392 Score: 93
Period size: 35 Copynumber: 2.1 Consensus size: 37
23551308 TTTTTAATAA
*
23551318 TATTTAA-GATTTTAATATATTTTATT-TTATA-AATT
1 TATTTAATGATTTTAAT-TAATTTATTATTATATAATT
*
23551353 TATTTAATTATTTTAATTAATTTATTAATTATATAATT
1 TATTTAATGATTTTAATTAATTTATT-ATTATATAATT
23551391 TA
1 TA
23551393 AAAATCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 15 0.44
36 8 0.24
37 5 0.15
38 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (37 bp):
TATTTAATGATTTTAATTAATTTATTATTATATAATT
Found at i:23551365 original size:21 final size:21
Alignment explanation
Indices: 23551339--23551384 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
23551329 TTAATATATT
23551339 TTATTTT-ATAAATTTATTTAA
1 TTATTTTAATAAATTTA-TTAA
*
23551360 TTATTTTAATTAATTTATTAA
1 TTATTTTAATAAATTTATTAA
23551381 TTAT
1 TTAT
23551385 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTAATAAATTTATTAA
Found at i:23551370 original size:18 final size:18
Alignment explanation
Indices: 23551326--23551376 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
23551316 AATATTTAAG
* *
23551326 ATTTTAATATATTTTATT
1 ATTTTAATTTATTTAATT
*
23551344 -TTATAAATTTATTTAATT
1 ATT-TTAATTTATTTAATT
*
23551362 ATTTTAATTAATTTA
1 ATTTTAATTTATTTA
23551377 TTAATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAATTTATTTAATT
Found at i:23551412 original size:29 final size:28
Alignment explanation
Indices: 23551375--23551431 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
23551365 TTAATTAATT
* *
23551375 TATTAATTATATAATTTAAAAATCTCTTTA
1 TATTAATTAAATAACTT-AAAAT-TCTTTA
23551405 TATT-ATTAAATAACTTAAAATTCTTTA
1 TATTAATTAAATAACTTAAAATTCTTTA
23551432 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 5 0.20
29 10 0.40
30 4 0.16
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTAATTAAATAACTTAAAATTCTTTA
Found at i:23552357 original size:15 final size:15
Alignment explanation
Indices: 23552337--23552370 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23552327 TATGGTAGGA
23552337 TAAAATTTAAAATTT
1 TAAAATTTAAAATTT
**
23552352 TAAAATTTATGATTT
1 TAAAATTTAAAATTT
23552367 TAAA
1 TAAA
23552371 GAAAGGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TAAAATTTAAAATTT
Found at i:23552890 original size:9 final size:10
Alignment explanation
Indices: 23552872--23552922 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
23552862 TTTAATATTT
*
23552872 AAAATTTTAA
1 AAAATATTAA
23552882 AAAA-ATTAA
1 AAAATATTAA
23552891 AAAATATT-A
1 AAAATATTAA
* *
23552900 ACATTATTAA
1 AAAATATTAA
23552910 AAAATATATAA
1 AAAATAT-TAA
23552921 AA
1 AA
23552923 GTTTTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
9 15 0.45
10 13 0.39
11 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATATTAA
Found at i:23552929 original size:20 final size:19
Alignment explanation
Indices: 23552872--23552931 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
23552862 TTTAATATTT
* **
23552872 AAAATTTTAAAAAAATTAA
1 AAAATATTAAAATTATTAA
*
23552891 AAAATATTAACATTATTAA
1 AAAATATTAAAATTATTAA
23552910 AAAATATATAAAAGTT-TTAA
1 AAAATAT-TAAAA-TTATTAA
23552930 AA
1 AA
23552932 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 22 0.65
20 10 0.29
21 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATATTAAAATTATTAA
Found at i:23556547 original size:33 final size:33
Alignment explanation
Indices: 23556510--23556683 Score: 226
Period size: 33 Copynumber: 5.3 Consensus size: 33
23556500 CTTTACTTTT
* *
23556510 CTCACCTGCTTTTTTAATGGATTCACC-TTCTCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTC-CC
*
23556543 CTCACCTGGATTTTCAATGGATTCACC-TTCTCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTC-CC
*
23556576 CTCACCTGGATTTTCAATGGATTCACCTTTCCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTCCC
* * *
23556609 CTCACCTGCTTTTTCAGTGGATTCACGTTTCCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTCCC
* * *
23556642 CTCGCCTGGATTTTCAATGGGTTCACCTTTCCC
1 CTCACCTGCATTTTCAATGGATTCACCTTTCCC
23556675 CTCACCTGC
1 CTCACCTGC
23556684 TGCTACAGGT
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
33 122 0.98
34 3 0.02
ACGTcount: A:0.15, C:0.34, G:0.13, T:0.37
Consensus pattern (33 bp):
CTCACCTGCATTTTCAATGGATTCACCTTTCCC
Found at i:23562539 original size:20 final size:20
Alignment explanation
Indices: 23562501--23562539 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23562491 GTCACAGTTG
* *
23562501 TCCTTCAATTCTCTATATTT
1 TCCTTCAAATCGCTATATTT
*
23562521 TCCTTCAAATCGCTTTATT
1 TCCTTCAAATCGCTATATT
23562540 CCAACTGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.51
Consensus pattern (20 bp):
TCCTTCAAATCGCTATATTT
Found at i:23562584 original size:14 final size:14
Alignment explanation
Indices: 23562565--23562594 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23562555 CCTTCTCCCT
*
23562565 TTCGTTTCGTTTCC
1 TTCGTTTCATTTCC
23562579 TTCGTTTCATTTCC
1 TTCGTTTCATTTCC
23562593 TT
1 TT
23562595 TCCATAGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.27, G:0.10, T:0.60
Consensus pattern (14 bp):
TTCGTTTCATTTCC
Found at i:23567502 original size:41 final size:41
Alignment explanation
Indices: 23567451--23567589 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
23567441 CAACGGCACA
* *
23567451 TAGCCCGCTAGACTTATAGCCTGATTCAGATCACCGACACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGACACG
* ** *
23567492 TAACCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACG
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGACACG
** **
23567533 TAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGACAAT
1 TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGACACG
23567574 TAGCCTGCTAGACTTA
1 TAGCCTGCTAGACTTA
23567590 AAGTCTGAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (41 bp):
TAGCCTGCTAGACTTATAACCTGATTCAGATCACCGACACG
Found at i:23571487 original size:43 final size:43
Alignment explanation
Indices: 23571362--23571487 Score: 180
Period size: 43 Copynumber: 2.9 Consensus size: 43
23571352 GCGCCTCTAA
* * * *
23571362 GTCATGTTCTTTAGCGGCGTTTGTGGGGACAGTGCCACTAAAG
1 GTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG
** * *
23571405 GTCATGTTCTATAGCGGCGTTTGTGAAAAAAGCGTCGCTAAAG
1 GTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG
23571448 GTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTA
1 GTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTA
23571488 TAGCGCCGCT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 71 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
GTCATGTTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAG
Found at i:23574712 original size:43 final size:43
Alignment explanation
Indices: 23574631--23574840 Score: 226
Period size: 43 Copynumber: 4.9 Consensus size: 43
23574621 ATTTTCGATA
* *
23574631 TGTGATTT-CGTGTAAGACCACGTCTAGGACGTTGGCATCAACT
1 TGTG-TTTACGTGTAAGACCACATCTGGGACGTTGGCATCAACT
* * *
23574674 TGTGTTTACGTGTAAGACCACATCTGGGACATTTGCATCGACT
1 TGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCATCAACT
* *
23574717 TATGTTTATGTGTAAGACCACATCTGGGACGTTGGCATCAACT
1 TGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCATCAACT
** * * *
23574760 TGTGTTTACGTGTAAGACCATGTCTAGGACAG-TGGCATCGATT
1 TGTGTTTACGTGTAAGACCACATCTGGGAC-GTTGGCATCAACT
*** * * *
23574803 TGTAAATACATGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCAT
23574841 TGTACGAGCT
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
42 4 0.03
43 137 0.96
44 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCATCAACT
Found at i:23574790 original size:86 final size:85
Alignment explanation
Indices: 23574639--23574840 Score: 280
Period size: 86 Copynumber: 2.4 Consensus size: 85
23574629 TATGTGATTT
*
23574639 CGTGTAAGACCACGTCTAGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACATCTGGGAC
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACATCTAGGAC
* * *
23574704 ATTTGCATCGACTTATGT-TTA
66 AGTGGCATCGA-TT-TGTAATA
* * * **
23574725 TGTGTAAGACCACATCTGGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCATGTCTAGGAC
1 CGTGTAAGACCACGTCTAGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACATCTAGGAC
23574790 AGTGGCATCGATTTGTAAATA
66 AGTGGCATCGATTTGT-AATA
*
23574811 CATGTAAGACCACGTCTAGGACGTTGGCAT
1 CGTGTAAGACCACGTCTAGGACGTTGGCAT
23574841 TGTACGAGCT
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
84 3 0.03
85 2 0.02
86 96 0.95
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (85 bp):
CGTGTAAGACCACGTCTAGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACATCTAGGAC
AGTGGCATCGATTTGTAATA
Found at i:23575842 original size:42 final size:42
Alignment explanation
Indices: 23575771--23576075 Score: 452
Period size: 42 Copynumber: 7.2 Consensus size: 42
23575761 CTAACTTTTT
* * *
23575771 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGGTCATATTCTTTA
1 GCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTTCTTTA
23575815 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
*
23575857 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* *
23575899 GCGGCGCTAAGAAAAAAACGCCACTAAAGATCATGTTATTTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* * *
23575941 ACGGCGCTAAGAAAAAAACGCCACTAAAGATCATGTGC-TTA
1 GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
* *
23575982 GCGGCGCTTGTGAAAAAAACGCCACTAAAGATCGTGTTCTTTA
1 GCGGCGCTT-AGAAAAAAACGCCACTAAAGATCATGTTCTTTA
*
23576025 GCGGCGCTTGGGAAAAAAA-GCCACTAAAGATCATGTTCTTTA
1 GCGGCGCTT-AGAAAAAAACGCCACTAAAGATCATGTTCTTTA
23576067 GCGGCGCTT
1 GCGGCGCTT
23576076 TATCTACAAA
Statistics
Matches: 242, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
41 10 0.04
42 202 0.83
43 21 0.09
44 9 0.04
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTA
Found at i:23576550 original size:12 final size:12
Alignment explanation
Indices: 23576533--23576560 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23576523 TTTTGAACCT
23576533 CTGCTTCTCTCG
1 CTGCTTCTCTCG
23576545 CTGCTTCTCTCG
1 CTGCTTCTCTCG
23576557 CTGC
1 CTGC
23576561 GGCATATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.18, T:0.39
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:23576607 original size:21 final size:21
Alignment explanation
Indices: 23576545--23576610 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
23576535 GCTTCTCTCG
* *
23576545 CTGCTTCTCTCGCTGCGGCAT
1 CTGCTTCTCTCGCTGCAGCCT
* *
23576566 ATGCTTCTCTCGTTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
23576587 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
23576608 CTG
1 CTG
23576611 TTTTAAGTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.05, C:0.41, G:0.21, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:23578927 original size:9 final size:9
Alignment explanation
Indices: 23578913--23579051 Score: 83
Period size: 9 Copynumber: 15.8 Consensus size: 9
23578903 TTTTTATGTA
23578913 TTATGTAAG
1 TTATGTAAG
*
23578922 TTATGTAAC
1 TTATGTAAG
**
23578931 TTACATAAG
1 TTATGTAAG
** *
23578940 TTA-CCAAA
1 TTATGTAAG
*
23578948 TTAATGTATG
1 TT-ATGTAAG
23578958 TTATGTAAG
1 TTATGTAAG
23578967 -T-TGTAAG
1 TTATGTAAG
*
23578974 TTAT-TATG
1 TTATGTAAG
*
23578982 TATTATGTAGG
1 --TTATGTAAG
23578993 TTATGTAAG
1 TTATGTAAG
*
23579002 TTGTGTAAG
1 TTATGTAAG
* *
23579011 ATATTTAAG
1 TTATGTAAG
23579020 TTATGTAAG
1 TTATGTAAG
* *
23579029 TTTTG-CA-
1 TTATGTAAG
23579036 TTATGTAAG
1 TTATGTAAG
23579045 TTATGTA
1 TTATGTA
23579052 TGCTATGTAT
Statistics
Matches: 96, Mismatches: 25, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
7 10 0.10
8 11 0.11
9 65 0.68
10 7 0.07
11 3 0.03
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:23578927 original size:16 final size:16
Alignment explanation
Indices: 23578906--23579236 Score: 77
Period size: 16 Copynumber: 20.4 Consensus size: 16
23578896 TGATATATTT
23578906 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
**
23578922 TTATGTAACTTACATAAG
1 TTATGT-A-TTATGTAAG
*** *
23578940 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
*
23578958 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
*
23578974 TTATTATGTATTATGTAGG
1 -T--TATGTATTATGTAAG
*
23578993 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
23579011 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* *
23579029 TTTTGCATTATGTAAG
1 TTATGTATTATGTAAG
23579045 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
23579061 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
23579073 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
23579089 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
* *
23579101 TAACGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
23579117 TTTATATAAAAATTTTATATAAG
1 -TTATGT----A--TTATGTAAG
23579140 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
** *
23579156 ----GTAACATATAAG
1 TTATGTATTATGTAAG
23579168 TTATG-A--ATGTAAG
1 TTATGTATTATGTAAG
23579181 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
23579197 TTATTTAAATTATTTAAG
1 TTATGT--ATTATGTAAG
* *
23579215 TTGTGTATTATATAAG
1 TTATGTATTATGTAAG
*
23579231 TCATGT
1 TTATGT
23579237 TGCTATGTGT
Statistics
Matches: 228, Mismatches: 49, Indels: 76
0.65 0.14 0.22
Matches are distributed among these distances:
11 2 0.01
12 25 0.11
13 12 0.05
14 2 0.01
15 4 0.02
16 83 0.36
17 10 0.04
18 66 0.29
19 10 0.04
21 1 0.00
22 5 0.02
23 8 0.04
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:23579191 original size:20 final size:21
Alignment explanation
Indices: 23579136--23579196 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
23579126 AAATTTTATA
23579136 TAAGTTATGTATTATGTAAGG
1 TAAGTTATGTATTATGTAAGG
** * *
23579157 TAACATAT-AAGTTATG-AATG
1 TAAGTTATGTA-TTATGTAAGG
23579177 TAAGTTATGTATTATGTAAG
1 TAAGTTATGTATTATGTAAG
23579197 TTATTTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.38, C:0.02, G:0.20, T:0.41
Consensus pattern (21 bp):
TAAGTTATGTATTATGTAAGG
Found at i:23580271 original size:12 final size:12
Alignment explanation
Indices: 23580251--23580293 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
23580241 AAACTAAAAT
*
23580251 TGAACATATATA
1 TGAATATATATA
23580263 TGAATATATATA
1 TGAATATATATA
23580275 T--ATATATATA
1 TGAATATATATA
23580285 TGAATATAT
1 TGAATATAT
23580294 GTTGAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 10 0.36
12 18 0.64
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (12 bp):
TGAATATATATA
Found at i:23580746 original size:19 final size:19
Alignment explanation
Indices: 23580722--23580763 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
23580712 AAATTGAATT
23580722 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
23580741 TTCTGTTTTCATTTGCATC
1 TTCTGTTTTCATTTGCATC
23580760 TTCT
1 TTCT
23580764 AATTTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTGTTTTCATTTGCATC
Found at i:23580769 original size:19 final size:19
Alignment explanation
Indices: 23580728--23580769 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
23580718 AATTTTCTGT
**
23580728 TTTCATTTGCATCTTCTGT
1 TTTCATTTGCATCTTCTAA
23580747 TTTCATTTGCATCTTCTAA
1 TTTCATTTGCATCTTCTAA
23580766 TTTC
1 TTTC
23580770 TAATTTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTCATTTGCATCTTCTAA
Found at i:23582591 original size:7 final size:7
Alignment explanation
Indices: 23582579--23582709 Score: 61
Period size: 7 Copynumber: 18.0 Consensus size: 7
23582569 CTTAATTGAC
23582579 ACCCTAA
1 ACCCTAA
23582586 ACCCTAA
1 ACCCTAA
23582593 ATCCCT-A
1 A-CCCTAA
23582600 ACCCTTAA
1 ACCC-TAA
*
23582608 CCCCTAA
1 ACCCTAA
*
23582615 ATCTCCTAG
1 A-C-CCTAA
*
23582624 TCCCTAA
1 ACCCTAA
**
23582631 ATTTCTAA
1 A-CCCTAA
*
23582639 CCCCT-A
1 ACCCTAA
23582645 ACTCCTAA
1 AC-CCTAA
*
23582653 CCCCTAA
1 ACCCTAA
23582660 ATCCCTAA
1 A-CCCTAA
*
23582668 CCCCTAA
1 ACCCTAA
*
23582675 GCCCTAA
1 ACCCTAA
*
23582682 CCCCTAA
1 ACCCTAA
*
23582689 ACCTTATA
1 ACCCTA-A
*
23582697 TCCC-AA
1 ACCCTAA
23582703 ACCCTAA
1 ACCCTAA
23582710 TAATCATATA
Statistics
Matches: 91, Mismatches: 22, Indels: 22
0.67 0.16 0.16
Matches are distributed among these distances:
6 9 0.10
7 53 0.58
8 25 0.27
9 4 0.04
ACGTcount: A:0.33, C:0.43, G:0.02, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Found at i:23582604 original size:14 final size:15
Alignment explanation
Indices: 23582580--23582689 Score: 95
Period size: 14 Copynumber: 7.5 Consensus size: 15
23582570 TTAATTGACA
*
23582580 CCCTAAA-CCCTAAAT
1 CCCTAAATCCCT-AAC
23582595 CCCT-AA-CCCTTAAC
1 CCCTAAATCCC-TAAC
**
23582609 CCCTAAATCTCCTAGT
1 CCCTAAATC-CCTAAC
**
23582625 CCCTAAATTTCTAAC
1 CCCTAAATCCCTAAC
*
23582640 CCCTAACT-CCTAAC
1 CCCTAAATCCCTAAC
23582654 CCCTAAATCCCTAAC
1 CCCTAAATCCCTAAC
*
23582669 CCCT-AAGCCCTAAC
1 CCCTAAATCCCTAAC
23582683 CCCTAAA
1 CCCTAAA
23582690 CCTTATATCC
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
14 36 0.46
15 29 0.37
16 11 0.14
17 2 0.03
ACGTcount: A:0.32, C:0.44, G:0.02, T:0.23
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:23582657 original size:29 final size:30
Alignment explanation
Indices: 23582605--23582689 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 30
23582595 CCCTAACCCT
* ** **
23582605 TAACCCCTAAATCTCCTAGTCCCTAAATTTC
1 TAACCCCT-AAGCTCCTAACCCCTAAATCCC
23582636 TAACCCCTAA-CTCCTAACCCCTAAATCCC
1 TAACCCCTAAGCTCCTAACCCCTAAATCCC
23582665 TAACCCCTAAGC-CCTAACCCCTAAA
1 TAACCCCTAAGCTCCTAACCCCTAAA
23582690 CCTTATATCC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 38 0.78
30 3 0.06
31 8 0.16
ACGTcount: A:0.32, C:0.42, G:0.02, T:0.24
Consensus pattern (30 bp):
TAACCCCTAAGCTCCTAACCCCTAAATCCC
Found at i:23583506 original size:40 final size:41
Alignment explanation
Indices: 23583462--23583630 Score: 143
Period size: 41 Copynumber: 4.1 Consensus size: 41
23583452 ATGTTTTTTT
*
23583462 GCGGCGCTTCA-ACAAAAACGCCGCTAAAACCTTAACATTA
1 GCGGCGCTTCACATAAAAACGCCGCTAAAACCTTAACATTA
* * *
23583502 GCGGCG-TTTATCATAAAAACGCCGCTAAAAATCTTAACTTTA
1 GCGGCGCTTCA-CATAAAAACGCCGCT-AAAACCTTAACATTA
* * * * *
23583544 GCGTCGCTT-ACATAAAAACGCCGGCTAAGACC-AAATATTC
1 GCGGCGCTTCACATAAAAACGCC-GCTAAAACCTTAACATTA
* * *
23583584 GCAGCGCTTCA-A-AGAAATCGCCGCTAAATACCTTAACTTTA
1 GCGGCGCTTCACATA-AAAACGCCGCTAAA-ACCTTAACATTA
23583625 GCGGCG
1 GCGGCG
23583631 GTTGATTAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
39 9 0.09
40 28 0.28
41 39 0.39
42 22 0.22
43 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTCACATAAAAACGCCGCTAAAACCTTAACATTA
Found at i:23583521 original size:41 final size:41
Alignment explanation
Indices: 23583475--23583655 Score: 133
Period size: 41 Copynumber: 4.4 Consensus size: 41
23583465 GCGCTTCAAC
23583475 AAAAACGCCGCTAAAACCTTAACATTAGCGGCGTTTATCAT
1 AAAAACGCCGCTAAAACCTTAACATTAGCGGCGTTTATCAT
* * * *
23583516 AAAAACGCCGCTAAAAATCTTAACTTTAGCGTCGCTTA-CAT
1 AAAAACGCCGCT-AAAACCTTAACATTAGCGGCGTTTATCAT
* * * * * *
23583557 AAAAACGCCGGCTAAGACC-AAATATTCGCAGCG-CT-TCA-
1 AAAAACGCC-GCTAAAACCTTAACATTAGCGGCGTTTATCAT
* *
23583595 AAGAAATCGCCGCTAAATACCTTAACTTTAGCGGCGGTTGAT--T
1 AA-AAA-CGCCGCTAAA-ACCTTAACATTAGCGGC-GTTTATCAT
* *
23583638 AAAAACGCCACGAAAACC
1 AAAAACGCCGCTAAAACC
23583656 CCCGACCATT
Statistics
Matches: 106, Mismatches: 23, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
38 2 0.02
39 11 0.10
40 18 0.17
41 44 0.42
42 28 0.26
43 2 0.02
44 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACCTTAACATTAGCGGCGTTTATCAT
Found at i:23588508 original size:31 final size:30
Alignment explanation
Indices: 23588473--23588537 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
23588463 TTTATTGTTA
* * *
23588473 AATTTGACTCTTAATTTTTTAAAAAGAGTCG
1 AATTT-ACTATTAACTTTTTAAAAAAAGTCG
* *
23588504 AATTTAGTATTAACTTTTTAAAAAAAGTTG
1 AATTTACTATTAACTTTTTAAAAAAAGTCG
23588534 AATT
1 AATT
23588538 GTTATTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (30 bp):
AATTTACTATTAACTTTTTAAAAAAAGTCG
Found at i:23589791 original size:26 final size:28
Alignment explanation
Indices: 23589757--23589810 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
23589747 TTTATGTGTC
23589757 TTTTCGTTA-CTTT-TGTCAATTTTTAG
1 TTTTCGTTAGCTTTATGTCAATTTTTAG
* * *
23589783 TTTTTGTTAGTTTTATGTCATTTTTTAG
1 TTTTCGTTAGCTTTATGTCAATTTTTAG
23589811 ACCCAAATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
28 12 0.52
ACGTcount: A:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (28 bp):
TTTTCGTTAGCTTTATGTCAATTTTTAG
Found at i:23603095 original size:52 final size:52
Alignment explanation
Indices: 23603024--23603178 Score: 292
Period size: 52 Copynumber: 3.0 Consensus size: 52
23603014 CTAAGAACTT
* *
23603024 TGTCTTTCACTTTGTAAAAGTAGATTCCCTCTTATCTGCTCGTTTAACTTTA
1 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTA
23603076 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTA
1 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTA
23603128 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
1 TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
23603179 TATCCCCTAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 101 1.00
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (52 bp):
TGTCTTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTA
Found at i:23604262 original size:29 final size:28
Alignment explanation
Indices: 23604228--23604324 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 28
23604218 ACAAAAATAA
23604228 AAAATTACATTTTGACCCCTAAAATTTTT
1 AAAATTACATTTT-ACCCCTAAAATTTTT
* * * *
23604257 GAAATTTCACTTTAACCCCTCAAATTTTT
1 AAAATTACA-TTTTACCCCTAAAATTTTT
*
23604286 AAAATTACATTTTAACCCTAAAATTTTCT
1 AAAATTACATTTTACCCCTAAAATTTT-T
23604315 CAAAATTACA
1 -AAAATTACA
23604325 CTTTGGCCCT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 15 0.27
29 29 0.52
30 12 0.21
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAATTACATTTTACCCCTAAAATTTTT
Found at i:23604700 original size:22 final size:22
Alignment explanation
Indices: 23604670--23604724 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
23604660 CAAAAAAGTA
*
23604670 AAAAG-AAAATAGCAAACAAAG
1 AAAAGAAAAAGAGCAAACAAAG
*
23604691 AAGAA-AAAAAGAGCAAAGAAAG
1 AA-AAGAAAAAGAGCAAACAAAG
23604713 AAAAGAAAAAGA
1 AAAAGAAAAAGA
23604725 AGAAAATAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 25 0.86
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02
Consensus pattern (22 bp):
AAAAGAAAAAGAGCAAACAAAG
Found at i:23604723 original size:15 final size:16
Alignment explanation
Indices: 23604691--23604730 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
23604681 GCAAACAAAG
*
23604691 AAGAAA-AAAAGAGCA
1 AAGAAAGAAAAGAGAA
23604706 AAGAAAGAAAAGA-AA
1 AAGAAAGAAAAGAGAA
23604721 AAG-AAGAAAA
1 AAGAAAGAAAA
23604731 TAGGGGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAGAAAAGAGAA
Found at i:23604817 original size:4 final size:4
Alignment explanation
Indices: 23604808--23604866 Score: 65
Period size: 4 Copynumber: 15.8 Consensus size: 4
23604798 GCTGATCGGC
*
23604808 AAAG AAAG AAAGG AAGG AAAG -AAG -AAG AAAG AAAG -AAG AAAG -AAG
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
23604853 AAAG AAAG -AAG AAA
1 AAAG AAAG AAAG AAA
23604867 AGGGGAAGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 15 0.31
4 30 0.62
5 3 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:23604843 original size:11 final size:11
Alignment explanation
Indices: 23604809--23604866 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
23604799 CTGATCGGCA
23604809 AAGAAAGAAAG
1 AAGAAAGAAAG
*
23604820 --GAAGGAAAG
1 AAGAAAGAAAG
23604829 AAG-AAGAAAG
1 AAGAAAGAAAG
23604839 AA-AGAAGAAAG
1 AAGA-AAGAAAG
23604850 AAGAAAGAAAG
1 AAGAAAGAAAG
23604861 AAGAAA
1 AAGAAA
23604867 AGGGGAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 8 0.20
10 8 0.20
11 23 0.57
12 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:23604866 original size:7 final size:7
Alignment explanation
Indices: 23604808--23604858 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
23604798 GCTGATCGGC
23604808 AAAGAAAG
1 AAAG-AAG
23604816 AAAGGAAGG
1 AAA-GAA-G
23604825 AAAGAAG
1 AAAGAAG
23604832 -AAGAAAG
1 AAAG-AAG
23604839 AAAGAAG
1 AAAGAAG
23604846 AAAGAAG
1 AAAGAAG
23604853 AAAGAA
1 AAAGAA
23604859 AGAAGAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
6 3 0.08
7 20 0.51
8 11 0.28
9 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:23604875 original size:18 final size:19
Alignment explanation
Indices: 23604809--23604895 Score: 81
Period size: 18 Copynumber: 4.5 Consensus size: 19
23604799 CTGATCGGCA
23604809 AAGAAAGAAAGGAAGGAAAGAAG
1 AAGAAAGAAA-GAA-G-AA-AAG
23604832 AAGAAAGAAAGAAG-AAAG
1 AAGAAAGAAAGAAGAAAAG
23604850 AAGAAAGAAAGAAGAAAAG
1 AAGAAAGAAAGAAGAAAAG
* * *
23604869 -GGGAAGAAGGAAGAAAA-
1 AAGAAAGAAAGAAGAAAAG
*
23604886 AAAAAAGAAA
1 AAGAAAGAAA
23604896 ATATTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
18 36 0.65
19 5 0.09
21 1 0.02
22 3 0.05
23 10 0.18
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAAGAAGAAAAG
Found at i:23605158 original size:26 final size:23
Alignment explanation
Indices: 23605117--23605169 Score: 61
Period size: 26 Copynumber: 2.2 Consensus size: 23
23605107 GCAGGCCTGT
23605117 AGCAGCCCAGTCCCCAGCAGCCC
1 AGCAGCCCAGTCCCCAGCAGCCC
**
23605140 AGCAGGCCCAGTTCGCCCATTAGCCC
1 AGCA-GCCCAG-TC-CCCAGCAGCCC
23605166 AGCA
1 AGCA
23605170 AAAAAAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 6 0.24
25 2 0.08
26 13 0.52
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.09
Consensus pattern (23 bp):
AGCAGCCCAGTCCCCAGCAGCCC
Found at i:23605189 original size:14 final size:13
Alignment explanation
Indices: 23605169--23605224 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 13
23605159 TTAGCCCAGC
*
23605169 AAAAAAAAAGGAG
1 AAAAAAAAAGAAG
23605182 AGAAAAAAAAGAAG
1 A-AAAAAAAAGAAG
*
23605196 AAAAAGAAAAGAAA
1 AAAAA-AAAAGAAG
*
23605210 AAAGAAAAAAAAAG
1 AAA-AAAAAAGAAG
23605224 A
1 A
23605225 GGTTCAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 5 0.14
14 29 0.81
15 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:23605199 original size:11 final size:11
Alignment explanation
Indices: 23605171--23605224 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 11
23605161 AGCCCAGCAA
23605171 AAAAAAAGGAGAG
1 AAAAAAA-GA-AG
23605184 AAAAAAAAGAAG
1 -AAAAAAAGAAG
23605196 AAAAAGAA-AAG
1 AAAAA-AAGAAG
23605207 -AAAAAAGAA-
1 AAAAAAAGAAG
23605216 AAAAAAAGA
1 AAAAAAAGA
23605225 GGTTCAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.05
10 14 0.38
11 8 0.22
12 4 0.11
13 2 0.05
14 7 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:23605203 original size:18 final size:18
Alignment explanation
Indices: 23605182--23605224 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
23605172 AAAAAAGGAG
23605182 AGAAAA-AAAAGAAGAAAA
1 AGAAAAGAAAA-AAGAAAA
23605200 AGAAAAGAAAAAAGAAAA
1 AGAAAAGAAAAAAGAAAA
23605218 A-AAAAGA
1 AGAAAAGA
23605225 GGTTCAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAAAAAGAAAA
Found at i:23605213 original size:12 final size:12
Alignment explanation
Indices: 23605172--23605222 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
23605162 GCCCAGCAAA
* *
23605172 AAAAAAGGAGAG
1 AAAAAAGAAAAG
23605184 AAAAAA-AAGAAG
1 AAAAAAGAA-AAG
23605196 -AAAAAGAAAAG
1 AAAAAAGAAAAG
23605207 AAAAAAGAAAA-
1 AAAAAAGAAAAG
23605218 AAAAA
1 AAAAA
23605223 GAGGTTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 14 0.41
12 20 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:23605356 original size:26 final size:25
Alignment explanation
Indices: 23605327--23605392 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
23605317 TATGCTATTT
23605327 CATTTTAATATTATTAGTACTTCATA
1 CATTTTAATATTATTAGTA-TTCATA
* * * *
23605353 CATTTTTATATTTTTTGTATTTATA
1 CATTTTAATATTATTAGTATTCATA
* *
23605378 TATTTTAATTTTATT
1 CATTTTAATATTATT
23605393 TTATTTTATT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
25 16 0.50
26 16 0.50
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (25 bp):
CATTTTAATATTATTAGTATTCATA
Found at i:23605601 original size:21 final size:20
Alignment explanation
Indices: 23605569--23605610 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
23605559 TCGGGTTTTG
23605569 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
23605589 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
23605610 A
1 A
23605611 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:23605611 original size:19 final size:19
Alignment explanation
Indices: 23605569--23605610 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
23605559 TCGGGTTTTG
23605569 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
23605589 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
23605609 AA
1 AA
23605611 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:23605737 original size:18 final size:17
Alignment explanation
Indices: 23605714--23605876 Score: 98
Period size: 18 Copynumber: 9.2 Consensus size: 17
23605704 ATAAAATCGG
23605714 AAAATTTTTCGTGTTTTC
1 AAAA-TTTTCGTGTTTTC
*
23605732 AAAATTCTCGTG-TTTC
1 AAAATTTTCGTGTTTTC
* *
23605748 AAAAAGTTTCATGTTTTC
1 -AAAATTTTCGTGTTTTC
* *
23605766 AAAAATTCTCGTGTTTTAA
1 -AAAATTTTCGTGTTTT-C
**
23605785 AAAAAATTCGTG-TTTC
1 AAAATTTTCGTGTTTTC
** *
23605801 AAAAATCCTCATGATTTTC
1 -AAAATTTTCGTG-TTTTC
**
23605820 TAAAAAGTTC-TGTGTTTC
1 -AAAATTTTCGTGT-TTTC
* *
23605838 AAAAATTTCGGTGTTTTG
1 AAAATTTTC-GTGTTTTC
23605856 AAAATTTTCGTGTTTTC
1 AAAATTTTCGTGTTTTC
23605873 AAAA
1 AAAA
23605877 AAAATCACGT
Statistics
Matches: 112, Mismatches: 24, Indels: 19
0.72 0.15 0.12
Matches are distributed among these distances:
16 4 0.04
17 47 0.42
18 48 0.43
19 13 0.12
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTC
Found at i:23605744 original size:17 final size:18
Alignment explanation
Indices: 23605722--23605963 Score: 139
Period size: 17 Copynumber: 13.5 Consensus size: 18
23605712 GGAAAATTTT
23605722 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTC
23605739 TCGTG-TTTCAAAAAGTT-
1 TCGTGTTTTCAAAAA-TTC
*
23605756 TCATGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* *
23605774 TCGTGTTTTAAAAAAAAT-
1 TCGTGTTTT-CAAAAATTC
*
23605792 TCGTG-TTTCAAAAATCC
1 TCGTGTTTTCAAAAATTC
*
23605809 TCATGATTTTCTAAAAAGTTC
1 TCGTG-TTTTC-AAAAA-TTC
23605830 T-GTG-TTTCAAAAATT-
1 TCGTGTTTTCAAAAATTC
* *
23605845 TCGGTGTTTT-GAAAATTT
1 TC-GTGTTTTCAAAAATTC
*
23605863 TCGTGTTTTCAAAAAAAATC
1 TCGTGTTTTC--AAAAATTC
* * *
23605883 ACGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTC
* * ***
23605900 TCGTTTTTTTTGTAAAAAAAA
1 TCG--TGTTTT-CAAAAATTC
* *
23605921 TTGTG-TTTCTAAAATTC
1 TCGTGTTTTCAAAAATTC
23605938 TCGTGTTTT-AAAAATTC
1 TCGTGTTTTCAAAAATTC
23605955 TCGTGTTTT
1 TCGTGTTTT
23605964 AATCGGATCA
Statistics
Matches: 169, Mismatches: 34, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
15 1 0.01
16 11 0.07
17 74 0.44
18 39 0.23
19 16 0.09
20 19 0.11
21 9 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:23605777 original size:35 final size:36
Alignment explanation
Indices: 23605720--23605877 Score: 159
Period size: 35 Copynumber: 4.5 Consensus size: 36
23605710 TCGGAAAATT
23605720 TTTCGTGTTTTC-AAAATTCTCGTG-TTTCAAAAAG
1 TTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAAG
* * *
23605754 TTTCATGTTTTCAAAAATTCTCGTGTTTTAAAAAAA
1 TTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAAG
* * *
23605790 ATTCGTG-TTTCAAAAATCCTCATGATTTTCTAAAAAG
1 TTTCGTGTTTTCAAAAATTCTCGTG-TTTTC-AAAAAG
* *
23605827 -TTC-TGTGTTTCAAAAATT-TCGGTGTTTT-GAAAAT
1 TTTCGTGT-TTTCAAAAATTCTC-GTGTTTTCAAAAAG
23605861 TTTCGTGTTTTCAAAAA
1 TTTCGTGTTTTCAAAAA
23605878 AAATCACGTG
Statistics
Matches: 102, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
34 15 0.15
35 41 0.40
36 29 0.28
37 17 0.17
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (36 bp):
TTTCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAAG
Found at i:23606414 original size:52 final size:52
Alignment explanation
Indices: 23606335--23606437 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
23606325 ATAGGGGATA
* *
23606335 AAAGCTAAACAAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGACAT
1 AAAGCTAAACAAGCAGATAAGAAGGAATCTACTTTTACAAAGTGAAAGACAT
*
23606387 AAAGCTAAACGAGCAGATAAGAAGGAATCTACTTTTACAAAGTGAAAGACA
1 AAAGCTAAACAAGCAGATAAGAAGGAATCTACTTTTACAAAGTGAAAGACA
23606438 ATTATTCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (52 bp):
AAAGCTAAACAAGCAGATAAGAAGGAATCTACTTTTACAAAGTGAAAGACAT
Found at i:23612944 original size:18 final size:18
Alignment explanation
Indices: 23612921--23612957 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
23612911 AATATTGTGT
* *
23612921 TTTAGTTTTGTTTGTGCA
1 TTTAGTGTTGTTTATGCA
23612939 TTTAGTGTTGTTTATGCA
1 TTTAGTGTTGTTTATGCA
23612957 T
1 T
23612958 GTTTTGCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.22, T:0.59
Consensus pattern (18 bp):
TTTAGTGTTGTTTATGCA
Found at i:23614729 original size:89 final size:92
Alignment explanation
Indices: 23614615--23614793 Score: 256
Period size: 89 Copynumber: 2.0 Consensus size: 92
23614605 GCTCCTGCTT
23614615 TTTTTTTTCCACTCATTTGAATACTTAAACTTTCAAAATGCA-TAAAAAAACCCTCAAACCTT-A
1 TTTTTTTTCCACTCATTTGAATACTTAAACTTTCAAAATGCATTAAAAAAACCCTCAAACCTTAA
*
23614678 AAAAAA-AAAAGCAATTAAGCCCTTAC
66 AAAAAAGAAAAGAAATTAAGCCCTTAC
* ** * * * *
23614704 TTTTTTTTGCACTCATTTGGGTACTTGAACTTTCAAAATGCATTAAAAAGACTCTCAAACTTTAA
1 TTTTTTTTCCACTCATTTGAATACTTAAACTTTCAAAATGCATTAAAAAAACCCTCAAACCTTAA
*
23614769 AAAAAAGAAAAGAAATTAAGTCCTT
66 AAAAAAGAAAAGAAATTAAGCCCTT
23614794 TATTTTATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 38 0.49
90 17 0.22
91 7 0.09
92 16 0.21
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (92 bp):
TTTTTTTTCCACTCATTTGAATACTTAAACTTTCAAAATGCATTAAAAAAACCCTCAAACCTTAA
AAAAAAGAAAAGAAATTAAGCCCTTAC
Found at i:23614907 original size:10 final size:10
Alignment explanation
Indices: 23614876--23614963 Score: 51
Period size: 10 Copynumber: 9.1 Consensus size: 10
23614866 ATAGAAAATT
*
23614876 AAAATATTAA
1 AAAATATAAA
*
23614886 AAGAT-TAGAA
1 AAAATATA-AA
23614896 AAAATAT-AA
1 AAAATATAAA
23614905 AAAATAT-AA
1 AAAATATAAA
*
23614914 AAAATCGTAAA
1 AAAAT-ATAAA
*
23614925 AAAAT-T-AT
1 AAAATATAAA
*
23614933 AAAATATATA
1 AAAATATAAA
* *
23614943 GATATATAAA
1 AAAATATAAA
*
23614953 AAATTATAAA
1 AAAATATAAA
23614963 A
1 A
23614964 TTTTATAAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
8 6 0.10
9 19 0.32
10 26 0.44
11 8 0.14
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (10 bp):
AAAATATAAA
Found at i:23614907 original size:20 final size:19
Alignment explanation
Indices: 23614876--23615010 Score: 73
Period size: 20 Copynumber: 7.1 Consensus size: 19
23614866 ATAGAAAATT
* *
23614876 AAAATATTAAAAGATTAGAA
1 AAAATA-TAAAAAATTATAA
23614896 AAAATATAAAAAA-TATAA
1 AAAATATAAAAAATTATAA
*
23614914 AAAATCGTAAAAAAATTATAA
1 AAAAT-AT-AAAAAATTATAA
* * *
23614935 AATATAT-AGATA-TATAA
1 AAAATATAAAAAATTATAA
* * *
23614952 AAAAT-TATAAAATTTTAT
1 AAAATATAAAAAATTATAA
* *
23614970 AAAGTCATAAGAAAATTATAC
1 AAAAT-ATAA-AAAATTATAA
*
23614991 AAAATGTAAAGAAA-TATAA
1 AAAATATAAA-AAATTATAA
23615010 A
1 A
23615011 TTTTGTAAAA
Statistics
Matches: 86, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
16 1 0.01
17 11 0.13
18 19 0.22
19 13 0.15
20 21 0.24
21 21 0.24
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
AAAATATAAAAAATTATAA
Found at i:23614914 original size:28 final size:28
Alignment explanation
Indices: 23614876--23614963 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
23614866 ATAGAAAATT
23614876 AAAATATTAAAAGAT-TAGAAAAAATATAA
1 AAAATA-TAAAAGATATA-AAAAAATATAA
* * *
23614905 AAAATATAAAAAATCGTAAAAAAAT-TAT
1 AAAATATAAAAGAT-ATAAAAAAATATAA
*
23614933 AAAATAT-ATAGATATATAAAAAATTATAA
1 AAAATATAAAAGATATA-AAAAAA-TATAA
23614962 AA
1 AA
23614964 TTTTATAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.04
27 10 0.21
28 17 0.35
29 17 0.35
30 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (28 bp):
AAAATATAAAAGATATAAAAAAATATAA
Found at i:23614935 original size:11 final size:9
Alignment explanation
Indices: 23614894--23614963 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
23614884 AAAAGATTAG
23614894 AAAAAATAT
1 AAAAAATAT
23614903 AAAAAATAT
1 AAAAAATAT
*
23614912 AAAAAATCGT
1 AAAAAAT-AT
23614922 AAAAAA-ATT
1 AAAAAATA-T
*
23614931 ATAAAATAT
1 AAAAAATAT
* *
23614940 ATAGATATAT
1 A-AAAAATAT
23614950 AAAAAATTAT
1 AAAAAA-TAT
23614960 AAAA
1 AAAA
23614964 TTTTATAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 27 0.56
10 21 0.44
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAAAATAT
Found at i:23615223 original size:37 final size:36
Alignment explanation
Indices: 23615169--23615242 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
23615159 GAGGTCATTA
* **
23615169 ATTTTTTTATGATTTTTATAAAATTTTAAAATTTTT
1 ATTTTTTTACGATTTTTATAAAAAATTAAAATTTTT
*
23615205 ATTTCTTTTACGATTTTTATAAAAAATTATAATTTTT
1 ATTT-TTTTACGATTTTTATAAAAAATTAAAATTTTT
23615242 A
1 A
23615243 GTAAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (36 bp):
ATTTTTTTACGATTTTTATAAAAAATTAAAATTTTT
Found at i:23615492 original size:85 final size:86
Alignment explanation
Indices: 23615331--23615501 Score: 240
Period size: 85 Copynumber: 2.0 Consensus size: 86
23615321 TTAATAAGAG
* *
23615331 CAGGGGCTTAATTGCTTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAG
1 CAGGGGCTTAAGTGCTTTTTTTGAAAAATTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAG
*
23615396 TACCCAGTTGAGTG-AAAAAA
66 TACCCAATTGAGTGCAAAAAA
*
23615416 CAGGGGCTTAAGTGCTTTTTTT-AAGAAA-TTTGAGGGCCTTTTTTTATGCATTTTGAAAGTTCA
1 CAGGGGCTTAAGTGCTTTTTTTGAA-AAATTTTGAGGGCC-TTTTTGATGCATTTTGAAAGTTCA
***
23615479 AGTGTTCAATTGAGTGCAAAAAA
64 AGTACCCAATTGAGTGCAAAAAA
23615502 AGAGAGGAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 11 0.14
85 59 0.78
86 6 0.08
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (86 bp):
CAGGGGCTTAAGTGCTTTTTTTGAAAAATTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAG
TACCCAATTGAGTGCAAAAAA
Found at i:23618103 original size:13 final size:13
Alignment explanation
Indices: 23618085--23618109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23618075 CTATATTTTA
23618085 AAATTTTAAATAT
1 AAATTTTAAATAT
23618098 AAATTTTAAATA
1 AAATTTTAAATA
23618110 ACTAGAGATG
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:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTTAAATAT
Found at i:23619163 original size:3 final size:3
Alignment explanation
Indices: 23619155--23619209 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
23619145 TTCACTATCG
23619155 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
23619203 TCT TCT T
1 TCT TCT T
23619210 TACATTCGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:23628222 original size:45 final size:46
Alignment explanation
Indices: 23628155--23628278 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
23628145 CATATGACCT
* *
23628155 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTATCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23628198 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23628244 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
23628279 CACTTATCAC
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 20 0.27
46 41 0.56
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:23628504 original size:37 final size:37
Alignment explanation
Indices: 23628396--23628505 Score: 184
Period size: 38 Copynumber: 2.9 Consensus size: 37
23628386 NNNNNNNNNN
*
23628396 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAACCA
1 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCA
23628433 CTTATCACTTTGTTTTCTTGATCAGATAAGTGTAGCCA
1 CTTATCACTTTG-TTTCTTGATCAGATAAGTGTAGCCA
**
23628471 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
23628506 TAAAACTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
37 33 0.48
38 36 0.52
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCCA
Found at i:23631341 original size:23 final size:23
Alignment explanation
Indices: 23631315--23631390 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
23631305 ATAAGTGCCA
23631315 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
23631338 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
23631361 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
23631384 CACTGAT
1 CACTGAT
23631391 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:23631490 original size:8 final size:8
Alignment explanation
Indices: 23631477--23631505 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
23631467 ACCCGGGACT
23631477 CACTGTAA
1 CACTGTAA
23631485 CACTGTAA
1 CACTGTAA
23631493 CACTGTAA
1 CACTGTAA
23631501 CACTG
1 CACTG
23631506 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:23631636 original size:18 final size:17
Alignment explanation
Indices: 23631610--23631648 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
23631600 ATTTTCCTTC
23631610 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
23631627 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
23631645 CACA
1 CACA
23631649 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:23638190 original size:13 final size:13
Alignment explanation
Indices: 23638172--23638198 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23638162 ACCTAAACTT
23638172 ACTAAATCACTAA
1 ACTAAATCACTAA
23638185 ACTAAATCACTAA
1 ACTAAATCACTAA
23638198 A
1 A
23638199 TTAAGTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
ACTAAATCACTAA
Found at i:23639321 original size:19 final size:21
Alignment explanation
Indices: 23639283--23639321 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
23639273 GTTTAAATTT
23639283 TATTTTCTTTACAATTTAATC
1 TATTTTCTTTACAATTTAATC
*
23639304 TATTTT-TTT-CATTTTAAT
1 TATTTTCTTTACAATTTAAT
23639322 ATCGCACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTCTTTACAATTTAATC
Found at i:23651981 original size:175 final size:175
Alignment explanation
Indices: 23651690--23652040 Score: 684
Period size: 175 Copynumber: 2.0 Consensus size: 175
23651680 CCCAATATTT
23651690 ATAACAGAAAAAGTTCCAGTATTCAAAATAAAGCAAAACATATATAAAGGAGTTCAACAGTTGGC
1 ATAACAGAAAAAGTTCCAGTATTCAAAATAAAGCAAAACATATATAAAGGAGTTCAACAGTTGGC
23651755 ATGAACCACACTGAATCCTAACGTCCGTTACCTTAGAAGGAACCTTAAACATTTGGGATGTTTCC
66 ATGAACCACACTGAATCCTAACGTCCGTTACCTTAGAAGGAACCTTAAACATTTGGGATGTTTCC
23651820 CATCAAACAAAACAAGCTTAGAAAGGGAAATGATAAAGAATTGGG
131 CATCAAACAAAACAAGCTTAGAAAGGGAAATGATAAAGAATTGGG
*
23651865 ATAACAGAAAAAGTTCCAGTATTCAAAATAAAGCAAAACATATATAAAGGAGTTGAACAGTTGGC
1 ATAACAGAAAAAGTTCCAGTATTCAAAATAAAGCAAAACATATATAAAGGAGTTCAACAGTTGGC
*
23651930 ATGAACCACACTGAATCCTAATGTCCGTTACCTTAGAAGGAACCTTAAACATTTGGGATGTTTCC
66 ATGAACCACACTGAATCCTAACGTCCGTTACCTTAGAAGGAACCTTAAACATTTGGGATGTTTCC
23651995 CATCAAACAAAACAAGCTTAGAAAGGGAAATGATAAAGAATTGGG
131 CATCAAACAAAACAAGCTTAGAAAGGGAAATGATAAAGAATTGGG
23652040 A
1 A
23652041 CTAGAATCGG
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.23
Consensus pattern (175 bp):
ATAACAGAAAAAGTTCCAGTATTCAAAATAAAGCAAAACATATATAAAGGAGTTCAACAGTTGGC
ATGAACCACACTGAATCCTAACGTCCGTTACCTTAGAAGGAACCTTAAACATTTGGGATGTTTCC
CATCAAACAAAACAAGCTTAGAAAGGGAAATGATAAAGAATTGGG
Found at i:23656233 original size:3 final size:3
Alignment explanation
Indices: 23656225--23656250 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23656215 GAGTTTGATC
23656225 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
23656251 ATCAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23666465 original size:25 final size:25
Alignment explanation
Indices: 23666418--23666466 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
23666408 AAAATTTTGA
*
23666418 TTAATTATAAAAATAACTCATTTTT
1 TTAATTATAAAAATAAATCATTTTT
* * *
23666443 TTAATTATACACATAAATGATTTT
1 TTAATTATAAAAATAAATCATTTT
23666467 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (25 bp):
TTAATTATAAAAATAAATCATTTTT
Found at i:23670693 original size:6 final size:6
Alignment explanation
Indices: 23670682--23670712 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
23670672 TATTGAATTC
23670682 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
23670713 TATTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:23673094 original size:2 final size:2
Alignment explanation
Indices: 23673087--23673132 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
23673077 TATTGAGGAT
23673087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23673129 TA TA
1 TA TA
23673133 CACACTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23673781 original size:20 final size:20
Alignment explanation
Indices: 23673758--23673798 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
23673748 ATAAAAAATT
23673758 AAAATTAGAAAAAAAT-TAAA
1 AAAATT-GAAAAAAATATAAA
*
23673778 AAAATTGTAAAAAATATAAA
1 AAAATTGAAAAAAATATAAA
23673798 A
1 A
23673799 GATATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (20 bp):
AAAATTGAAAAAAATATAAA
Found at i:23673798 original size:17 final size:18
Alignment explanation
Indices: 23673749--23673798 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
23673739 TAATTTTTAA
23673749 TAAAAAAT-TAAAATTAG
1 TAAAAAATATAAAATTAG
* *
23673766 AAAAAAATTAAAAAAATT-G
1 TAAAAAA-T-ATAAAATTAG
23673785 TAAAAAATATAAAA
1 TAAAAAATATAAAA
23673799 GATATAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
17 11 0.42
18 2 0.08
19 7 0.27
20 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (18 bp):
TAAAAAATATAAAATTAG
Found at i:23674084 original size:10 final size:10
Alignment explanation
Indices: 23674071--23674117 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
23674061 TTTTGATACA
23674071 TTTTTATAAT
1 TTTTTATAAT
23674081 TTTTTATTCTAAT
1 TTTTTA---TAAT
*
23674094 TTTTAAT-AT
1 TTTTTATAAT
23674103 TTTTTATAAT
1 TTTTTATAAT
23674113 TTTTT
1 TTTTT
23674118 GCCACATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 8 0.26
10 14 0.45
13 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:23676930 original size:171 final size:171
Alignment explanation
Indices: 23676645--23676976 Score: 664
Period size: 171 Copynumber: 1.9 Consensus size: 171
23676635 AATTAAAAGG
23676645 ACAAACAACCAGAAAAATCTGGTGAAGCTGATGTTGTAGAAGACTATAGTGATGGTGAACTTCTA
1 ACAAACAACCAGAAAAATCTGGTGAAGCTGATGTTGTAGAAGACTATAGTGATGGTGAACTTCTA
23676710 GTCACTTCTGTCAATAATTGTAAAGTGAGCGAAGAGTGGATCCTTGATTCAGGCTGCACCTTCCA
66 GTCACTTCTGTCAATAATTGTAAAGTGAGCGAAGAGTGGATCCTTGATTCAGGCTGCACCTTCCA
23676775 CATGTGTCCCAATCGGGATTGGTTTACAACTGGATTGGTTT
131 CATGTGTCCCAATCGGGATTGGTTTACAACTGGATTGGTTT
23676816 ACAAACAACCAGAAAAATCTGGTGAAGCTGATGTTGTAGAAGACTATAGTGATGGTGAACTTCTA
1 ACAAACAACCAGAAAAATCTGGTGAAGCTGATGTTGTAGAAGACTATAGTGATGGTGAACTTCTA
23676881 GTCACTTCTGTCAATAATTGTAAAGTGAGCGAAGAGTGGATCCTTGATTCAGGCTGCACCTTCCA
66 GTCACTTCTGTCAATAATTGTAAAGTGAGCGAAGAGTGGATCCTTGATTCAGGCTGCACCTTCCA
23676946 CATGTGTCCCAATCGGGATTGGTTTACAACT
131 CATGTGTCCCAATCGGGATTGGTTTACAACT
23676977 TACGAAACAA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 161 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (171 bp):
ACAAACAACCAGAAAAATCTGGTGAAGCTGATGTTGTAGAAGACTATAGTGATGGTGAACTTCTA
GTCACTTCTGTCAATAATTGTAAAGTGAGCGAAGAGTGGATCCTTGATTCAGGCTGCACCTTCCA
CATGTGTCCCAATCGGGATTGGTTTACAACTGGATTGGTTT
Found at i:23680382 original size:15 final size:16
Alignment explanation
Indices: 23680356--23680385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23680346 CCAAATTTTC
23680356 CCTTTCTTCTTTCTTT
1 CCTTTCTTCTTTCTTT
23680372 CCTTT-TTCTTTCTT
1 CCTTTCTTCTTTCTT
23680386 GCTCTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
CCTTTCTTCTTTCTTT
Found at i:23680622 original size:30 final size:29
Alignment explanation
Indices: 23680588--23680644 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
23680578 TTATCAAATA
23680588 AATAAA-ATCTTTTAATATAATAATTTAATT
1 AATAAATATCTTTTAAT-TAA-AATTTAATT
* *
23680618 AATAAATTTCTTTTACTTAAAATTTAA
1 AATAAATATCTTTTAATTAAAATTTAA
23680645 GAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
AATAAATATCTTTTAATTAAAATTTAATT
Found at i:23680767 original size:17 final size:16
Alignment explanation
Indices: 23680736--23680779 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
23680726 GATTTATTTA
23680736 ATAATATAATATCATT
1 ATAATATAATATCATT
*
23680752 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
23680769 AATTATATAAT
1 -ATAATATAAT
23680780 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:23683072 original size:27 final size:27
Alignment explanation
Indices: 23683034--23683091 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
23683024 ACTTGTAGTT
*
23683034 TTTTTCCAAAAGGGTTTTCACGTAAAA
1 TTTTCCCAAAAGGGTTTTCACGTAAAA
23683061 TTTTCCCAAAAGGGTTTTCACGTAAAA
1 TTTTCCCAAAAGGGTTTTCACGTAAAA
23683088 TTTT
1 TTTT
23683092 GTGTCTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (27 bp):
TTTTCCCAAAAGGGTTTTCACGTAAAA
Found at i:23689953 original size:17 final size:17
Alignment explanation
Indices: 23689931--23689967 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
23689921 GAATTGGTTA
23689931 TGGTCCTCCATATGTTG
1 TGGTCCTCCATATGTTG
23689948 TGGTCCTCCATATGTTG
1 TGGTCCTCCATATGTTG
23689965 TGG
1 TGG
23689968 ACACACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.41
Consensus pattern (17 bp):
TGGTCCTCCATATGTTG
Found at i:23690063 original size:25 final size:25
Alignment explanation
Indices: 23690009--23690068 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
23689999 TTAGCTCTTA
*
23690009 TGAGCATCCCGATATATGGCTCTCT
1 TGAGCTTCCCGATATATGGCTCTCT
*
23690034 TGAGCTTCCCGTTATATGG-T-TCT
1 TGAGCTTCCCGATATATGGCTCTCT
23690057 TGCGAGCTTCCC
1 T--GAGCTTCCC
23690069 ATTAATAGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
25 26 0.84
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGATATATGGCTCTCT
Found at i:23694086 original size:3 final size:3
Alignment explanation
Indices: 23694080--23694104 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23694070 TTATGATGAT
23694080 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
23694105 TCAATGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23694983 original size:3 final size:3
Alignment explanation
Indices: 23694975--23694999 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23694965 TAATAAAACA
23694975 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
23695000 TGCCAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23695404 original size:14 final size:14
Alignment explanation
Indices: 23695385--23695411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23695375 ATTAAATTCT
23695385 TGAAAATTAAAATG
1 TGAAAATTAAAATG
23695399 TGAAAATTAAAAT
1 TGAAAATTAAAAT
23695412 ATTTGTGGTT
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:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (14 bp):
TGAAAATTAAAATG
Found at i:23696710 original size:26 final size:26
Alignment explanation
Indices: 23696666--23696718 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
23696656 TTATACAAAC
*
23696666 AATACTTTAAGTTAGTT-AATTGAAAT
1 AATACTTTAAGTAAGTTAAATT-AAAT
* *
23696692 AATATTTTAAGTAATTTAAATTAAAT
1 AATACTTTAAGTAAGTTAAATTAAAT
23696718 A
1 A
23696719 TATAAGTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
AATACTTTAAGTAAGTTAAATTAAAT
Found at i:23696798 original size:24 final size:24
Alignment explanation
Indices: 23696731--23696804 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
23696721 TAAGTCATAT
23696731 ATTAGATATTA-ATAATATAATAACA
1 ATTA-ATATTACA-AATATAATAACA
* **
23696756 ATTACTATTAC-TTTGATAATAACA
1 ATTAATATTACAAAT-ATAATAACA
23696780 ATTAATATTACAAATATAAT-ACA
1 ATTAATATTACAAATATAATAACA
23696803 AT
1 AT
23696805 ACAGTGTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 6 0.15
24 29 0.73
25 5 0.12
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (24 bp):
ATTAATATTACAAATATAATAACA
Found at i:23699575 original size:21 final size:21
Alignment explanation
Indices: 23699537--23699587 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
23699527 GGTCTAAACA
*
23699537 CCCATGTGAAGGCCACACATG
1 CCCATGTGAAGGCCACACACG
* **
23699558 CCCATGTGGAGGGGACACACG
1 CCCATGTGAAGGCCACACACG
*
23699579 CCCGTGTGA
1 CCCATGTGA
23699588 GTAGCCCGTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.31, T:0.14
Consensus pattern (21 bp):
CCCATGTGAAGGCCACACACG
Found at i:23701661 original size:2 final size:2
Alignment explanation
Indices: 23701654--23701701 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
23701644 GGTCACTCAA
23701654 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23701696 CT CT CT
1 CT CT CT
23701702 ATATATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.