Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 128 of 205
Found at i:38616152 original size:50 final size:50
Alignment explanation
Indices: 38616028--38616268 Score: 281
Period size: 50 Copynumber: 4.8 Consensus size: 50
38616018 GATAATAACA
* * ** * *
38616028 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** *
38616077 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
38616127 TGCCCATGCCATGTCCCAAACATGGTCTTAC-TGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCGG
* * * *
38616177 TGCCAACGCCATGTCCCAAACATGGTCTTACATGTGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
38616227 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38616269 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
48 1 0.01
49 40 0.24
50 123 0.75
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:38623557 original size:50 final size:50
Alignment explanation
Indices: 38623415--38623647 Score: 236
Period size: 50 Copynumber: 4.7 Consensus size: 50
38623405 GATAATAACA
* ** * *
38623415 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * * **
38623464 TACCAATGTCATATCCCTGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
38623514 TGCCTATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * * * *
38623564 TGCCAACGCCACGTCCCAGACATGGTCTTACATGAGACCTCTCGTCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
38623614 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
38623648 TGATCTCTTT
Statistics
Matches: 148, Mismatches: 34, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 1 0.01
49 37 0.25
50 110 0.74
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:38625218 original size:11 final size:10
Alignment explanation
Indices: 38625191--38625216 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38625181 GCATTTTTAG
38625191 AAAAAATTCA
1 AAAAAATTCA
38625201 AAAAAATTCA
1 AAAAAATTCA
38625211 AAAAAA
1 AAAAAA
38625217 ATCGTTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTCA
Found at i:38630609 original size:9 final size:9
Alignment explanation
Indices: 38630595--38630620 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
38630585 CAATCAAATA
38630595 TTTTTTTTC
1 TTTTTTTTC
38630604 TTTTTTTTC
1 TTTTTTTTC
38630613 TTTTTTTT
1 TTTTTTTT
38630621 AGAACAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:38635896 original size:31 final size:35
Alignment explanation
Indices: 38635858--38635934 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
38635848 AATATTAAAT
*
38635858 TTAATTTAATACTTATC-T-T-AAT-AATATTTTA
1 TTAATTTAATACTTATCTTGTAAATAAATATTCTA
*
38635889 TTAATTTAATATTTATCTTGTAAATAAATATTCTA
1 TTAATTTAATACTTATCTTGTAAATAAATATTCTA
*
38635924 TTATTTTAATA
1 TTAATTTAATA
38635935 AGATTTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 16 0.41
32 1 0.03
33 1 0.03
34 3 0.08
35 18 0.46
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (35 bp):
TTAATTTAATACTTATCTTGTAAATAAATATTCTA
Found at i:38639522 original size:25 final size:25
Alignment explanation
Indices: 38639476--38639523 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38639466 TTTGAGTGAT
* *
38639476 TTAAATTGGTCTTACTTTAGACAAA
1 TTAAATTGGTCTTACATCAGACAAA
*
38639501 TTAAATTGGTCTTAGATCAGACA
1 TTAAATTGGTCTTACATCAGACA
38639524 CTTTAATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (25 bp):
TTAAATTGGTCTTACATCAGACAAA
Found at i:38639529 original size:25 final size:25
Alignment explanation
Indices: 38639474--38639537 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
38639464 TTTTTGAGTG
* *
38639474 ATTTAAATTGGTCTTACTTTAGACA
1 ATTTAAATTGGTCTTACATCAGACA
* *
38639499 AATTAAATTGGTCTTAGATCAGACA
1 ATTTAAATTGGTCTTACATCAGACA
*
38639524 CTTT-AATTGTGTCT
1 ATTTAAATTG-GTCT
38639538 ATTGTTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAAATTGGTCTTACATCAGACA
Found at i:38641739 original size:54 final size:54
Alignment explanation
Indices: 38641657--38641760 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
38641647 GTTAAGGATT
** * *
38641657 CAAATGTCTAATGATTTTTTGAGCAGAGATCTATATCGTGATTCCTATTCGAGC
1 CAAATGTCTAATGATTTCCTGAGAAGAGATCTATATCGAGATTCCTATTCGAGC
38641711 CAAATGTCTAATGATTTCCTGAGAAGAGATCTATATCGAGATTCCTATTC
1 CAAATGTCTAATGATTTCCTGAGAAGAGATCTATATCGAGATTCCTATTC
38641761 ATCAAGGAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (54 bp):
CAAATGTCTAATGATTTCCTGAGAAGAGATCTATATCGAGATTCCTATTCGAGC
Found at i:38642479 original size:23 final size:23
Alignment explanation
Indices: 38642448--38642492 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
38642438 ATCGAGAAAA
*
38642448 GTAAGATCAGAAATGAAATTAAG
1 GTAACATCAGAAATGAAATTAAG
38642471 GTAACATCAGAAATGAAATTAA
1 GTAACATCAGAAATGAAATTAA
38642493 TCTACAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (23 bp):
GTAACATCAGAAATGAAATTAAG
Found at i:38643041 original size:35 final size:35
Alignment explanation
Indices: 38642995--38643064 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
38642985 GAGAAGGTAA
38642995 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
1 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
38643030 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
1 GACCAACTTATAACTCCTACTCTGACATTGGTTTC
38643065 TGCATTCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (35 bp):
GACCAACTTATAACTCCTACTCTGACATTGGTTTC
Found at i:38643751 original size:25 final size:25
Alignment explanation
Indices: 38643723--38643803 Score: 101
Period size: 25 Copynumber: 3.2 Consensus size: 25
38643713 ATTGAGTGAT
*
38643723 TTAAATTGGTCTTAGTTTAGACAAA
1 TTAAATTGGTCTTAGTTCAGACAAA
*
38643748 TTAAATTGGTCTTAGTTCAGAC-AC
1 TTAAATTGGTCTTAGTTCAGACAAA
* *
38643772 TTTAATTGTGTCTATTGTTCAGACAAA
1 TTAAATTG-GTCT-TAGTTCAGACAAA
38643799 TTAAA
1 TTAAA
38643804 GTGAGTCTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.17
25 25 0.53
26 9 0.19
27 5 0.11
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (25 bp):
TTAAATTGGTCTTAGTTCAGACAAA
Found at i:38647209 original size:19 final size:18
Alignment explanation
Indices: 38647182--38647224 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
38647172 AATTAGAATG
*
38647182 TAAAAATTAAATTAAAAA
1 TAAAAATTAAAGTAAAAA
38647200 TAAAATATTAAAGTAAAAA
1 TAAAA-ATTAAAGTAAAAA
38647219 TAAAAA
1 TAAAAA
38647225 AAGGCTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAATTAAAGTAAAAA
Found at i:38650599 original size:137 final size:137
Alignment explanation
Indices: 38650353--38650627 Score: 541
Period size: 137 Copynumber: 2.0 Consensus size: 137
38650343 CCTAAATTCA
38650353 ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGATATGAGTTT
1 ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGATATGAGTTT
38650418 GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
66 GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
38650483 ATGGCAG
131 ATGGCAG
*
38650490 ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGCTATGAGTTT
1 ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGATATGAGTTT
38650555 GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
66 GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
38650620 ATGGCAG
131 ATGGCAG
38650627 A
1 A
38650628 AAGGACCTAG
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (137 bp):
ATTTTCTCTCTCCTCCAACACGAGCACTAGTTGATTCTACAAGAAATTAAGCTTGATATGAGTTT
GTTCTATTGATTTCACTAAAATTTTAAGAAAGAAATTGAAGAAATCAAGCTTGAGATGATTAAAT
ATGGCAG
Found at i:38651052 original size:18 final size:17
Alignment explanation
Indices: 38651029--38651071 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
38651019 TTTTAATTAA
38651029 ATAAATATCG-TTTTATAT
1 ATAAATAT-GATTTTAT-T
38651047 ATAAATATGATTTTATT
1 ATAAATATGATTTTATT
*
38651064 TTAAATAT
1 ATAAATAT
38651072 AATAATTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
ATAAATATGATTTTATT
Found at i:38655208 original size:203 final size:205
Alignment explanation
Indices: 38654965--38655372 Score: 714
Period size: 203 Copynumber: 2.0 Consensus size: 205
38654955 CTTGAGATTG
* *
38654965 GTTAAATGATTAAATTTTATACAATTAATTAATTCTTTTATATTTAAAAAAATTTAATCTAAACC
1 GTTAAATGATAAAATTTTATACAATTAATTAATACTTTTATATTTAAAAAAATTTAATCTAAACC
*
38655030 ATTTGATATATTTAAATATTAGTTTAAATAGAATTAATAAATAAGTT-AAAAAA-TAATAGATTC
66 ATTTGATATATTTAAATATTAGTTTAAATAGAATTAATAAATAAATTAAAAAAAGTAATAGATTC
* * *
38655093 ATATGGATATTTAGGTATAATTATTTATTTTGGAGAGGA-TCAAATTATAAGAAATAAAATTAAA
131 ATATGGATATTTAAGTATAATTATTTATTTTAGAAAGGACT-AAATTATAAGAAATAAAATTAAA
38655157 ATACAAAAATA
195 ATACAAAAATA
*
38655168 GTTAAATGATAAAATTTTATACAATTAATTAATACTTTTATATTTAAAAAAATTTAATCTAAAGC
1 GTTAAATGATAAAATTTTATACAATTAATTAATACTTTTATATTTAAAAAAATTTAATCTAAACC
38655233 ATTTGATATATTTAAATATTAGTTTAAATAGAATTAATAAATAAATTAAAAAAAGTAATAGATTC
66 ATTTGATATATTTAAATATTAGTTTAAATAGAATTAATAAATAAATTAAAAAAAGTAATAGATTC
*
38655298 ATATGGATATTTAAGTATAATTATTTATTTTAGAAATGACTAAATTATAAGAAATAAAATTAAAA
131 ATATGGATATTTAAGTATAATTATTTATTTTAGAAAGGACTAAATTATAAGAAATAAAATTAAAA
38655363 TACAAAAATA
196 TACAAAAATA
38655373 AAATGATTTT
Statistics
Matches: 194, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
203 108 0.56
204 6 0.03
205 79 0.41
206 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.39
Consensus pattern (205 bp):
GTTAAATGATAAAATTTTATACAATTAATTAATACTTTTATATTTAAAAAAATTTAATCTAAACC
ATTTGATATATTTAAATATTAGTTTAAATAGAATTAATAAATAAATTAAAAAAAGTAATAGATTC
ATATGGATATTTAAGTATAATTATTTATTTTAGAAAGGACTAAATTATAAGAAATAAAATTAAAA
TACAAAAATA
Found at i:38656673 original size:39 final size:39
Alignment explanation
Indices: 38656628--38656706 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
38656618 CTAAATGCAA
* *
38656628 ACATGTTATGATGCATGGGCCTATGGTATAAATTCTATG
1 ACATGTTATGATGCATAGGCCTATGGTATAAATTCAATG
* *
38656667 ACATGTTATGATGGATAGGCCTTTGGTATAAATTCAATG
1 ACATGTTATGATGCATAGGCCTATGGTATAAATTCAATG
38656706 A
1 A
38656707 TTGCCAGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.35
Consensus pattern (39 bp):
ACATGTTATGATGCATAGGCCTATGGTATAAATTCAATG
Found at i:38659107 original size:43 final size:43
Alignment explanation
Indices: 38658962--38659269 Score: 214
Period size: 43 Copynumber: 7.2 Consensus size: 43
38658952 AGGTTTGTTT
* * ** * * * *
38658962 TATAGTGGCGTTTGTGAGAAAAGCATCGTTAAAGGTCCTGAGC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
* * * * * * *
38659005 TATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
*** * * *
38659048 TATAATAGCATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
* *
38659091 TATAGCGGCGTCTGTGGGAAAAGCGTCGCT-AAAGTTCTTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-TCTTGATC
* * * * *** *
38659134 TACAGCGACGTTTAT-GTAAAAGCGTAACTAAAGGT-TTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
38659175 TATAGCGGCGTTTGT-GGAAAATGCGCCGCTAAAAGTCCTT-ATC
1 TATAGCGGCGTTTGTGGGAAAA-GCGCCGCTAAAAGT-CTTGATC
* * * * *
38659218 TATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAGGT-TATGATT
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCT-TGATC
38659261 TATAGCGGC
1 TATAGCGGC
38659270 ATTTATTTCT
Statistics
Matches: 212, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
41 24 0.11
42 26 0.12
43 154 0.73
44 8 0.04
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
Found at i:38659166 original size:42 final size:41
Alignment explanation
Indices: 38659109--38659187 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
38659099 CGTCTGTGGG
** *
38659109 AAAAGCGTCGCTAAAGTTCTTGATCTACAGCGACGTTTATGT
1 AAAAGCGTAACTAAAGGT-TTGATCTACAGCGACGTTTATGT
* *
38659151 AAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTTT
1 AAAAGCGTAACTAAAGGTTTGATCTACAGCGACGTTT
38659188 GTGGAAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.53
42 15 0.47
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
AAAAGCGTAACTAAAGGTTTGATCTACAGCGACGTTTATGT
Found at i:38659982 original size:43 final size:43
Alignment explanation
Indices: 38659837--38660144 Score: 214
Period size: 43 Copynumber: 7.2 Consensus size: 43
38659827 AGGTTTGTTT
* * ** * * * *
38659837 TATAGTGGCGTTTGTGAGAAAAGCATCGTTAAAGGTCCTGAGC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
* * * * * * *
38659880 TATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
*** * * *
38659923 TATAATAGCATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
* *
38659966 TATAGCGGCGTCTGTGGGAAAAGCGTCGCT-AAAGTTCTTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAG-TCTTGATC
* * * * *** *
38660009 TACAGCGACGTTTAT-GTAAAAGCGTAACTAAAGGT-TTGATC
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
38660050 TATAGCGGCGTTTGT-GGAAAATGCGCCGCTAAAAGTCCTT-ATC
1 TATAGCGGCGTTTGTGGGAAAA-GCGCCGCTAAAAGT-CTTGATC
* * * * *
38660093 TATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAGGT-TATGATT
1 TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCT-TGATC
38660136 TATAGCGGC
1 TATAGCGGC
38660145 ATTTATTTCT
Statistics
Matches: 212, Mismatches: 45, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
41 24 0.11
42 26 0.12
43 154 0.73
44 8 0.04
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
TATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCTTGATC
Found at i:38660041 original size:42 final size:41
Alignment explanation
Indices: 38659984--38660062 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
38659974 CGTCTGTGGG
** *
38659984 AAAAGCGTCGCTAAAGTTCTTGATCTACAGCGACGTTTATGT
1 AAAAGCGTAACTAAAGGT-TTGATCTACAGCGACGTTTATGT
* *
38660026 AAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTTT
1 AAAAGCGTAACTAAAGGTTTGATCTACAGCGACGTTT
38660063 GTGGAAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.53
42 15 0.47
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
AAAAGCGTAACTAAAGGTTTGATCTACAGCGACGTTTATGT
Found at i:38660617 original size:875 final size:875
Alignment explanation
Indices: 38658927--38660676 Score: 3500
Period size: 875 Copynumber: 2.0 Consensus size: 875
38658917 GTTTTTAGTG
38658927 ACGTTTTTTTGAGAAGCGTTGCTAAAGGTTTGTTTTATAGTGGCGTTTGTGAGAAAAGCATCGTT
1 ACGTTTTTTTGAGAAGCGTTGCTAAAGGTTTGTTTTATAGTGGCGTTTGTGAGAAAAGCATCGTT
38658992 AAAGGTCCTGAGCTATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGCTATAATAGC
66 AAAGGTCCTGAGCTATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGCTATAATAGC
38659057 ATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATCTATAGCGGCGTCTGTGGGAAAAGCGTCGCTA
131 ATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATCTATAGCGGCGTCTGTGGGAAAAGCGTCGCTA
38659122 AAGTTCTTGATCTACAGCGACGTTTATGTAAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTT
196 AAGTTCTTGATCTACAGCGACGTTTATGTAAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTT
38659187 TGTGGAAAATGCGCCGCTAAAAGTCCTTATCTATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAG
261 TGTGGAAAATGCGCCGCTAAAAGTCCTTATCTATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAG
38659252 GTTATGATTTATAGCGGCATTTATTTCTAAAAATGCCACAAATGTTTGCAGCGTTGACAACAGCG
326 GTTATGATTTATAGCGGCATTTATTTCTAAAAATGCCACAAATGTTTGCAGCGTTGACAACAGCG
38659317 GTGTTTTTTGCGGCGCTTTCAAAAAAGCCGCTAAAGGCTTAAAAAAGCGCCGCTAAAAGCCTGTT
391 GTGTTTTTTGCGGCGCTTTCAAAAAAGCCGCTAAAGGCTTAAAAAAGCGCCGCTAAAAGCCTGTT
38659382 TTGGTGTAGTGATTAAAAGGATGGATTTCCCATAATTCCTTAAATATATATACAAAACATACTCC
456 TTGGTGTAGTGATTAAAAGGATGGATTTCCCATAATTCCTTAAATATATATACAAAACATACTCC
38659447 ATATGCAAAGACATAATTTGATATCAAACTTTCTCAAAACATATTATATATAAATATACCAAAAC
521 ATATGCAAAGACATAATTTGATATCAAACTTTCTCAAAACATATTATATATAAATATACCAAAAC
38659512 ATAATTCGAGTGGCATAAATATACCAAAAGCATAGTTTGCACATAATCAAATTTAAGTATAAAAA
586 ATAATTCGAGTGGCATAAATATACCAAAAGCATAGTTTGCACATAATCAAATTTAAGTATAAAAA
38659577 GATACAAACAACAACCTCCTGACCTAGAAACAAAAGTATTATGTTATAGCATAAGAGTTTTGGTT
651 GATACAAACAACAACCTCCTGACCTAGAAACAAAAGTATTATGTTATAGCATAAGAGTTTTGGTT
38659642 CAATCCCAAGCAACCCCATTCCCTATCCCCAATTATCAAAAAAGAAAAAAACATAGAAAAATAGA
716 CAATCCCAAGCAACCCCATTCCCTATCCCCAATTATCAAAAAAGAAAAAAACATAGAAAAATAGA
38659707 ACACTTAGATAATTCAAAATTTTACATTGCAAAATTTAAAACTATATTAGCATGTCTAAACCAAT
781 ACACTTAGATAATTCAAAATTTTACATTGCAAAATTTAAAACTATATTAGCATGTCTAAACCAAT
38659772 TTTCAAAACATGGACAAAATATATCAAATA
846 TTTCAAAACATGGACAAAATATATCAAATA
38659802 ACGTTTTTTTGAGAAGCGTTGCTAAAGGTTTGTTTTATAGTGGCGTTTGTGAGAAAAGCATCGTT
1 ACGTTTTTTTGAGAAGCGTTGCTAAAGGTTTGTTTTATAGTGGCGTTTGTGAGAAAAGCATCGTT
38659867 AAAGGTCCTGAGCTATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGCTATAATAGC
66 AAAGGTCCTGAGCTATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGCTATAATAGC
38659932 ATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATCTATAGCGGCGTCTGTGGGAAAAGCGTCGCTA
131 ATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATCTATAGCGGCGTCTGTGGGAAAAGCGTCGCTA
38659997 AAGTTCTTGATCTACAGCGACGTTTATGTAAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTT
196 AAGTTCTTGATCTACAGCGACGTTTATGTAAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTT
38660062 TGTGGAAAATGCGCCGCTAAAAGTCCTTATCTATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAG
261 TGTGGAAAATGCGCCGCTAAAAGTCCTTATCTATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAG
38660127 GTTATGATTTATAGCGGCATTTATTTCTAAAAATGCCACAAATGTTTGCAGCGTTGACAACAGCG
326 GTTATGATTTATAGCGGCATTTATTTCTAAAAATGCCACAAATGTTTGCAGCGTTGACAACAGCG
38660192 GTGTTTTTTGCGGCGCTTTCAAAAAAGCCGCTAAAGGCTTAAAAAAGCGCCGCTAAAAGCCTGTT
391 GTGTTTTTTGCGGCGCTTTCAAAAAAGCCGCTAAAGGCTTAAAAAAGCGCCGCTAAAAGCCTGTT
38660257 TTGGTGTAGTGATTAAAAGGATGGATTTCCCATAATTCCTTAAATATATATACAAAACATACTCC
456 TTGGTGTAGTGATTAAAAGGATGGATTTCCCATAATTCCTTAAATATATATACAAAACATACTCC
38660322 ATATGCAAAGACATAATTTGATATCAAACTTTCTCAAAACATATTATATATAAATATACCAAAAC
521 ATATGCAAAGACATAATTTGATATCAAACTTTCTCAAAACATATTATATATAAATATACCAAAAC
38660387 ATAATTCGAGTGGCATAAATATACCAAAAGCATAGTTTGCACATAATCAAATTTAAGTATAAAAA
586 ATAATTCGAGTGGCATAAATATACCAAAAGCATAGTTTGCACATAATCAAATTTAAGTATAAAAA
38660452 GATACAAACAACAACCTCCTGACCTAGAAACAAAAGTATTATGTTATAGCATAAGAGTTTTGGTT
651 GATACAAACAACAACCTCCTGACCTAGAAACAAAAGTATTATGTTATAGCATAAGAGTTTTGGTT
38660517 CAATCCCAAGCAACCCCATTCCCTATCCCCAATTATCAAAAAAGAAAAAAACATAGAAAAATAGA
716 CAATCCCAAGCAACCCCATTCCCTATCCCCAATTATCAAAAAAGAAAAAAACATAGAAAAATAGA
38660582 ACACTTAGATAATTCAAAATTTTACATTGCAAAATTTAAAACTATATTAGCATGTCTAAACCAAT
781 ACACTTAGATAATTCAAAATTTTACATTGCAAAATTTAAAACTATATTAGCATGTCTAAACCAAT
38660647 TTTCAAAACATGGACAAAATATATCAAATA
846 TTTCAAAACATGGACAAAATATATCAAATA
38660677 TTGCTTAACC
Statistics
Matches: 875, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
875 875 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (875 bp):
ACGTTTTTTTGAGAAGCGTTGCTAAAGGTTTGTTTTATAGTGGCGTTTGTGAGAAAAGCATCGTT
AAAGGTCCTGAGCTATGGTGGCGTTTGTGAGATAAGCGCCGTTAAAGGTCTTGAGCTATAATAGC
ATTTGTGGGAAAAGTGCCGCTAAAACTCTTGATCTATAGCGGCGTCTGTGGGAAAAGCGTCGCTA
AAGTTCTTGATCTACAGCGACGTTTATGTAAAAGCGTAACTAAAGGTTTGATCTATAGCGGCGTT
TGTGGAAAATGCGCCGCTAAAAGTCCTTATCTATAGCGGCATTTTTGGGAAAAGTGCCGCTAAAG
GTTATGATTTATAGCGGCATTTATTTCTAAAAATGCCACAAATGTTTGCAGCGTTGACAACAGCG
GTGTTTTTTGCGGCGCTTTCAAAAAAGCCGCTAAAGGCTTAAAAAAGCGCCGCTAAAAGCCTGTT
TTGGTGTAGTGATTAAAAGGATGGATTTCCCATAATTCCTTAAATATATATACAAAACATACTCC
ATATGCAAAGACATAATTTGATATCAAACTTTCTCAAAACATATTATATATAAATATACCAAAAC
ATAATTCGAGTGGCATAAATATACCAAAAGCATAGTTTGCACATAATCAAATTTAAGTATAAAAA
GATACAAACAACAACCTCCTGACCTAGAAACAAAAGTATTATGTTATAGCATAAGAGTTTTGGTT
CAATCCCAAGCAACCCCATTCCCTATCCCCAATTATCAAAAAAGAAAAAAACATAGAAAAATAGA
ACACTTAGATAATTCAAAATTTTACATTGCAAAATTTAAAACTATATTAGCATGTCTAAACCAAT
TTTCAAAACATGGACAAAATATATCAAATA
Found at i:38661028 original size:24 final size:24
Alignment explanation
Indices: 38660996--38661042 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
38660986 AATGAGGGAC
38660996 CAATTAAGGTAGGAATCCGATGGG
1 CAATTAAGGTAGGAATCCGATGGG
*
38661020 CAATTAAGGTAGGAATTCGATGG
1 CAATTAAGGTAGGAATCCGATGG
38661043 AGGGTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.23
Consensus pattern (24 bp):
CAATTAAGGTAGGAATCCGATGGG
Found at i:38671698 original size:15 final size:15
Alignment explanation
Indices: 38671674--38671703 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38671664 GAATTTAGTG
*
38671674 TTTAGGGTTTATGGT
1 TTTAGAGTTTATGGT
38671689 TTTAGAGTTTATGGT
1 TTTAGAGTTTATGGT
38671704 ATATGGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (15 bp):
TTTAGAGTTTATGGT
Found at i:38671698 original size:22 final size:22
Alignment explanation
Indices: 38671667--38671711 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38671657 TGATTTGGAA
* *
38671667 TTTAGTGTTTAGGGTTTATGGT
1 TTTAGAGTTTAGGGTATATGGT
*
38671689 TTTAGAGTTTATGGTATATGGT
1 TTTAGAGTTTAGGGTATATGGT
38671711 T
1 T
38671712 AATATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (22 bp):
TTTAGAGTTTAGGGTATATGGT
Found at i:38672358 original size:40 final size:40
Alignment explanation
Indices: 38672275--38672368 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
38672265 TTTATGAGAA
* * * **
38672275 AAACACCGCAAAAGGTAAGCATTAGCGGCGTTTTTATTGT
1 AAACACCGCAAAAGGTAAGCAATAGCGGCATTTTAATCAT
*
38672315 AAACGCCGCAAAAGGTAAGCAATAGCGGCATTTTAATCAT
1 AAACACCGCAAAAGGTAAGCAATAGCGGCATTTTAATCAT
*
38672355 AAACACGGCAAAAG
1 AAACACCGCAAAAG
38672369 ATCATTTTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (40 bp):
AAACACCGCAAAAGGTAAGCAATAGCGGCATTTTAATCAT
Found at i:38675236 original size:17 final size:17
Alignment explanation
Indices: 38675197--38675230 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38675187 TATTATTAAA
*
38675197 TATATTTTAATTAAAAT
1 TATAATTTAATTAAAAT
38675214 TATAATTTAA-TAAAAT
1 TATAATTTAATTAAAAT
38675230 T
1 T
38675231 CTTAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATTTAATTAAAAT
Found at i:38675336 original size:18 final size:17
Alignment explanation
Indices: 38675315--38675349 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38675305 TTATTATTAA
*
38675315 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38675333 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38675350 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38675463 original size:14 final size:15
Alignment explanation
Indices: 38675414--38675465 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
38675404 GTAAAATATA
38675414 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
38675429 TATTAAATATATTAT
1 AATTAAATATATTAT
38675444 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
38675457 AATTTAATA
1 AATTAAATA
38675466 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:38675721 original size:120 final size:120
Alignment explanation
Indices: 38675179--38675710 Score: 937
Period size: 120 Copynumber: 4.4 Consensus size: 120
38675169 ATCATATTTA
38675179 AACATAATTATTATTAAATATATTTTAATTAAAAT-TATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
38675243 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
38675298 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38675363 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
38675418 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
38675483 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
38675538 AACATAACTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
38675603 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* *
38675658 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
38675711 TAAAATAATT
Statistics
Matches: 400, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
119 42 0.10
120 356 0.89
121 2 0.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTACATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:38675797 original size:24 final size:25
Alignment explanation
Indices: 38675751--38675798 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
38675741 TATGAATTTG
38675751 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
38675777 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
38675799 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:38675802 original size:92 final size:92
Alignment explanation
Indices: 38675706--38675934 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
38675696 TGATTTAATA
* * *
38675706 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
38675768 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
38675798 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
38675863 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
38675888 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
38675935 CTAAAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:38679019 original size:33 final size:33
Alignment explanation
Indices: 38678980--38679055 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
38678970 ATTATAAAGC
*
38678980 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
38679013 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
38679046 ATGTATAATT
1 ATGTATAATT
38679056 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:38679153 original size:37 final size:37
Alignment explanation
Indices: 38679098--38679184 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
38679088 GTATAAATAT
* * *
38679098 ATTGATTAGTTCATTAAAGCATGTTCAAAGTCCT-CAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGT-CTGAAC
*
38679135 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTCTGAAC
38679172 ATTGATTAGTTTA
1 ATTGATTAGTTTA
38679185 TTTATTTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.02
37 44 0.98
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTCTGAAC
Found at i:38682002 original size:14 final size:14
Alignment explanation
Indices: 38681978--38682027 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
38681968 TACTCTGTTA
*
38681978 AATTATATTTTTAT
1 AATTTTATTTTTAT
*
38681992 CATTTTATTTTTTAT
1 AATTTTA-TTTTTAT
**
38682007 TTTTTTATTTTTAT
1 AATTTTATTTTTAT
38682021 AATTTTA
1 AATTTTA
38682028 AATTTAGCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (14 bp):
AATTTTATTTTTAT
Found at i:38682294 original size:27 final size:27
Alignment explanation
Indices: 38682262--38682362 Score: 112
Period size: 27 Copynumber: 3.5 Consensus size: 27
38682252 AATCAATTTA
38682262 CATAACTTACATAAATATATATCATAT
1 CATAACTTACATAAATATATATCATAT
38682289 CATAACTTACATGATACATAAATATGTATCATAT
1 CATAACTTACAT-A-A-AT--ATA--TATCATAT
* * *
38682323 TATAACTTCCATAAATATATATCATAC
1 CATAACTTACATAAATATATATCATAT
38682350 CATAACTTACATA
1 CATAACTTACATA
38682363 CAACTTTGGA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
27 30 0.48
28 1 0.02
29 4 0.06
30 2 0.03
31 2 0.03
32 4 0.06
33 1 0.02
34 18 0.29
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.36
Consensus pattern (27 bp):
CATAACTTACATAAATATATATCATAT
Found at i:38682308 original size:34 final size:32
Alignment explanation
Indices: 38682268--38682361 Score: 108
Period size: 34 Copynumber: 3.0 Consensus size: 32
38682258 TTTACATAAC
38682268 TTACATAAATATATATCATATCATAACTTACA
1 TTACATAAATATATATCATATCATAACTTACA
* *
38682300 TGATACATAAATATGTATCATATTATAACTT-C-
1 T--TACATAAATATATATCATATCATAACTTACA
*
38682332 ---CATAAATATATATCATACCATAACTTACA
1 TTACATAAATATATATCATATCATAACTTACA
38682361 T
1 T
38682362 ACAACTTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
27 23 0.44
28 1 0.02
32 1 0.02
33 1 0.02
34 26 0.50
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (32 bp):
TTACATAAATATATATCATATCATAACTTACA
Found at i:38688664 original size:20 final size:20
Alignment explanation
Indices: 38688641--38688679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38688631 ATTCAAACAA
* *
38688641 TATTACTTGAATAGTTATAG
1 TATTACATGAATAATTATAG
*
38688661 TATTAGATGAATAATTATA
1 TATTACATGAATAATTATA
38688680 TATCTTTTTA
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:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (20 bp):
TATTACATGAATAATTATAG
Found at i:38702179 original size:26 final size:26
Alignment explanation
Indices: 38702149--38702208 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
38702139 AAACATAAAA
38702149 TCAAACATTAAAA-CAAATATAACATC
1 TCAAACATTAAAACCAAATATAA-ATC
* *
38702175 TCAAA-ATTAAAATCCAAATGTAAGTC
1 TCAAACATTAAAA-CCAAATATAAATC
38702201 TCAAACAT
1 TCAAACAT
38702209 CTATTACGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 7 0.24
26 12 0.41
27 10 0.34
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.25
Consensus pattern (26 bp):
TCAAACATTAAAACCAAATATAAATC
Found at i:38704207 original size:25 final size:25
Alignment explanation
Indices: 38704179--38704229 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
38704169 AGTGAGGAGG
38704179 CTGTAGTGTTTTCGAACTGAAGAAC
1 CTGTAGTGTTTTCGAACTGAAGAAC
38704204 CTGTAGTGTTTTCGAACTGAAGAAC
1 CTGTAGTGTTTTCGAACTGAAGAAC
38704229 C
1 C
38704230 CCCACTTGAT
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:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (25 bp):
CTGTAGTGTTTTCGAACTGAAGAAC
Found at i:38709590 original size:23 final size:24
Alignment explanation
Indices: 38709553--38709599 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
38709543 AGCAATATGT
*
38709553 AGAAAATTCTGCCAGTAAAAATGC
1 AGAAAAGTCTGCCAGTAAAAATGC
38709577 AGAAAAGT-TGCCAGTAAAAATGC
1 AGAAAAGTCTGCCAGTAAAAATGC
38709600 GATAAATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (24 bp):
AGAAAAGTCTGCCAGTAAAAATGC
Found at i:38715912 original size:14 final size:15
Alignment explanation
Indices: 38715888--38715920 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
38715878 CTACATCATG
38715888 ACATGGGTCTTAACC
1 ACATGGGTCTTAACC
*
38715903 ACAT-GGTCTTACCC
1 ACATGGGTCTTAACC
38715917 ACAT
1 ACAT
38715921 TCATGTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (15 bp):
ACATGGGTCTTAACC
Found at i:38732885 original size:23 final size:23
Alignment explanation
Indices: 38732856--38732902 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
38732846 GTTCAATTAT
* *
38732856 ATGTTCATGAACATGTTTGTTTA
1 ATGTTCACGAACATGTTCGTTTA
*
38732879 ATGTTCACGAATATGTTCGTTTA
1 ATGTTCACGAACATGTTCGTTTA
38732902 A
1 A
38732903 CTTAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (23 bp):
ATGTTCACGAACATGTTCGTTTA
Found at i:38735920 original size:31 final size:31
Alignment explanation
Indices: 38735885--38735950 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
38735875 CATATTTGAT
38735885 CATGCTTGCTAAAAAATTATT-CATTTTGCCA
1 CATGCTTGCTAAAAAATTATTCCA-TTTGCCA
*
38735916 CATGCTTGCTCAAAAATTATTCCATTTGCCA
1 CATGCTTGCTAAAAAATTATTCCATTTGCCA
38735947 CATG
1 CATG
38735951 TATCTATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (31 bp):
CATGCTTGCTAAAAAATTATTCCATTTGCCA
Found at i:38761961 original size:8 final size:8
Alignment explanation
Indices: 38761951--38761993 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
38761941 ATTGTACTAC
*
38761951 AATTTTAC
1 AATTTTAA
38761959 AATTTTAA
1 AATTTTAA
*
38761967 AATTTTGA
1 AATTTTAA
38761975 AATTTTAA
1 AATTTTAA
38761983 AATTTTAA
1 AATTTTAA
38761991 AAT
1 AAT
38761994 AAAGAGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (8 bp):
AATTTTAA
Found at i:38770422 original size:50 final size:50
Alignment explanation
Indices: 38770364--38771204 Score: 410
Period size: 50 Copynumber: 16.5 Consensus size: 50
38770354 GATTCACCAT
* * * * *
38770364 CTTCAATCTGTTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGTAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
** ** ** * * * ** *
38770414 CTTCAATCTGGTCCTCTGCACCGCCAGGGAAGTAAGATTTGCTATTGTAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * *
38770464 CTTCAATCTACTT-AACTTCAATGTCGGGGAAAAAAGATTCGCCGTCGTAG
1 CTTCAATCTA-TTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * **** * * *
38770514 CTTCAATCTGTTCCATTACACCACCAGGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * *
38770564 CTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * ** * * * *
38770614 CTTTAATCTGTTCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * *
38770664 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGCAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * * *
38770714 CTTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGG
1 CTTCAATCTATT----CA-ACTG-CA---ATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * *
38770773 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGCAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * * *
38770823 CTTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGG
1 CTTCAATCTATT----CA-ACTG-CA---ATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * *
38770882 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGCCATAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * * * * *
38770932 CTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * *
38770982 CTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGA-TCTGCCGTCGTAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTC-GCCGTCGTAG
* * * * * * ** ** *
38771032 GTTTAATCTATTCCACTAC-ATCTCTAGGGAAGTAAGATTCATCGTTATGG
1 CTTCAATCTATTCAACTGCAATGTC-AGGGAAATAAGATTCGCCGTCGTAG
* * ** * * *
38771082 CTTCAATCTATTTAAATGCAATGTTGGGGAAACATGATCCGCCGTCGTAG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* * * * * * * * *
38771132 CTTCAATCTGTCCCACTACATTGCCAGGGAAGTAAGATTCGCCGTTGTGG
1 CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
* *
38771182 CTTCAATCTATTCCACTGTAATG
1 CTTCAATCTATTCAACTGCAATG
38771205 CCAAAGAGAT
Statistics
Matches: 547, Mismatches: 220, Indels: 48
0.67 0.27 0.06
Matches are distributed among these distances:
49 8 0.01
50 445 0.81
51 6 0.01
53 4 0.01
54 10 0.02
55 10 0.02
56 4 0.01
59 60 0.11
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (50 bp):
CTTCAATCTATTCAACTGCAATGTCAGGGAAATAAGATTCGCCGTCGTAG
Found at i:38770492 original size:100 final size:100
Alignment explanation
Indices: 38770364--38771193 Score: 987
Period size: 100 Copynumber: 8.1 Consensus size: 100
38770354 GATTCACCAT
* * * *
38770364 CTTCAATCTGTTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGGTCCT
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * * *
38770429 CTGCACCGCCAGGGAAGTAAGATTTGCTATTGTAG
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
* * *
38770464 CTTCAATCTACTTAACTTCAATGTCGGGGAAAAAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
38770529 TTACACCACCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
* * *
38770564 CTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTTAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
*
38770629 CTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
* * *
38770664 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGCAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
38770729 CCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGG
66 CTACACCGCC---------AGGGAAGTAAGATTCGCCATTGTGG
* * *
38770773 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGCAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
38770838 CCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGG
66 CTACACCGCC---------AGGGAAGTAAGATTCGCCATTGTGG
* * *
38770882 GTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGCCATAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
* * *
38770947 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
* * * *
38770982 CTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGA-TCTGCCGTCGTAGGTTTAATCTATTCC
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC-GCCGTCGTAGCTTCAATCTGTTCC
* * * ** * *
38771046 ACTACATCTCTAGGGAAGTAAGATTCATCGTTATGG
65 ACTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
* * * * *
38771082 CTTCAATCTATTTAAATGCAATGTTGGGGAAACATGATCCGCCGTCGTAGCTTCAATCTGTCCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
** *
38771147 CTACATTGCCAGGGAAGTAAGATTCGCCGTTGTGG
66 CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
38771182 CTTCAATCTATT
1 CTTCAATCTATT
38771194 CCACTGTAAT
Statistics
Matches: 654, Mismatches: 65, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
99 2 0.00
100 449 0.69
101 1 0.00
109 202 0.31
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGGAAGTAAGATTCGCCATTGTGG
Found at i:38770778 original size:59 final size:59
Alignment explanation
Indices: 38770715--38770890 Score: 172
Period size: 59 Copynumber: 3.1 Consensus size: 59
38770705 TCGTCGCAGC
38770715 TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
1 TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
* * ** ** ** * * ** *
38770774 TTCAATCTATT----TA-ACTG-CA---ATGTCGGGGAAACAAGATTCGTCGTCGCAGC
1 TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
38770824 TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
1 TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
38770883 TTCAATCT
1 TTCAATCT
38770891 ATTTAACTGC
Statistics
Matches: 82, Mismatches: 26, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
50 30 0.37
53 2 0.02
54 5 0.06
55 5 0.06
56 2 0.02
59 38 0.46
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (59 bp):
TTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGG
Found at i:38770830 original size:109 final size:109
Alignment explanation
Indices: 38770639--38771167 Score: 673
Period size: 109 Copynumber: 5.0 Consensus size: 109
38770629 CTACACCGCC
*
38770639 AGGGAAGTAAGATTCGCCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
1 AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * *
38770704 GTCGTCGCAGCTTCAATCTGTTCCACCACACTGCCAGGGATGTA
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
*
38770748 AGGGAAGTAAGATTCACCATTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
1 AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * *
38770813 GTCGTCGCAGCTTCAATCTGTTCCACCACACTGCCAGGGATGTA
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
*
38770857 AGGGAAGTAAGATTCACCATTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
1 AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* *
38770922 GCCGCCATAGCTTCAATCTGTTCCACTACACTGCC---------
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
* *
38770957 AGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGA-TC
1 AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * * *
38771021 TGCCGTCGTAGGTTTAATCTATTCCACTACA-T--C-----TCT-
66 -GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
* * * * * * *
38771057 AGGGAAGTAAGATTCATCGTTATGGCTTCAATCTATTTAAATGCAATGTTGGGGAAACATGATCC
1 AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
* * *
38771122 GCCGTCGTAGCTTCAATCTGTCCCACTACATTGCCAGGGAAGTA
66 GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
38771166 AG
1 AG
38771168 ATTCGCCGTT
Statistics
Matches: 378, Mismatches: 28, Indels: 28
0.87 0.06 0.06
Matches are distributed among these distances:
97 1 0.00
99 3 0.01
100 166 0.44
101 2 0.01
103 1 0.00
108 1 0.00
109 204 0.54
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (109 bp):
AGGGAAGTAAGATTCACCGTTGTGGGTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTC
GCCGTCGTAGCTTCAATCTGTTCCACTACACTGCCAGGGATGTA
Found at i:38771136 original size:418 final size:409
Alignment explanation
Indices: 38770365--38771167 Score: 1104
Period size: 418 Copynumber: 1.9 Consensus size: 409
38770355 ATTCACCATC
* * *
38770365 TTCAATCTGTTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGGTCCTC
1 TTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGGTCCAC
** ** * *
38770430 TGCACCGCCAGGGAAGTAAGATTTGCTATTGTAGCTTCAATCTACTTAACTTCAATGTCGGGGAA
66 CACACCGCCAGGGAAGTAAGATTCACCATTGTAGCTTCAATCTACTTAACTGCAATGTCGGGGAA
* * * *
38770495 AAAAGATTCGCCGTCGTAGCTTCAATCTGTTCCATTACACCACCAGGGAAGTAAGATTCGCCGTT
131 AAAAGATTCGCCGCCATAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCACCGTT
*
38770560 GTGGCTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTTAATCTGT
196 GTGGCTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTTAATCTAT
* * * *
38770625 TCCACTACACCGCCAGGGAAGTAAGATTCGCCGTTGTGGGTTCAATCTATTTAACTGCAATGTCG
261 TCCACTACACCGCCAGGGAAGTAAGATTCACCGTTATGGCTTCAATCTATTTAAATGCAATGTCG
* * * *
38770690 GGGAAACAAGATTCGTCGTCGCAGCTTCAATCTGTTCCACCACACTGCCAGGGATGTAAGGGAAG
326 GGGAAACAAGATCCGCCGTCGCAGCTTCAATCTGTCCCACCACACTGCCAGGGAAGTAAGGGAAG
38770755 TAAGATTCACCATTGTGGG
391 TAAGATTCACCATTGTGGG
* * *
38770774 TTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGTCGTCGCAGCTTCAATCTGTTCCAC
1 TTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGGTCCAC
* * * *
38770839 CACACTGCCAGGGATGTAAGGGAAGTAAGATTCACCATTGTGGGTTCAATCTATTTAACTGCAAT
66 CACACCGCC---------AGGGAAGTAAGATTCACCATTGTAGCTTCAATCTACTTAACTGCAAT
* **
38770904 GTCGGGGAAACAAGATTCGCCGCCATAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGA
122 GTCGGGGAAAAAAGATTCGCCGCCATAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGA
* * * *
38770969 TTCACCGTTGTGGCTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGA-TCTGCCGTCGTAGG
187 TTCACCGTTGTGGCTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTC-GCCGTCGTAGC
* * * *
38771033 TTTAATCTATTCCACTACATCTCTAGGGAAGTAAGATTCATCGTTATGGCTTCAATCTATTTAAA
251 TTTAATCTATTCCACTACACCGCCAGGGAAGTAAGATTCACCGTTATGGCTTCAATCTATTTAAA
* * * * *
38771098 TGCAATGTTGGGGAAACATGATCCGCCGTCGTAGCTTCAATCTGTCCCACTACATTGCCAGGGAA
316 TGCAATGTCGGGGAAACAAGATCCGCCGTCGCAGCTTCAATCTGTCCCACCACACTGCCAGGGAA
38771163 GTAAG
381 GTAAG
38771168 ATTCGCCGTT
Statistics
Matches: 339, Mismatches: 45, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
409 65 0.19
417 2 0.01
418 272 0.80
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (409 bp):
TTCAATCTATTTAACTACAATGTCGGGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGGTCCAC
CACACCGCCAGGGAAGTAAGATTCACCATTGTAGCTTCAATCTACTTAACTGCAATGTCGGGGAA
AAAAGATTCGCCGCCATAGCTTCAATCTGTTCCACTACACCACCAGGGAAGTAAGATTCACCGTT
GTGGCTCCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTCGTAGCTTTAATCTAT
TCCACTACACCGCCAGGGAAGTAAGATTCACCGTTATGGCTTCAATCTATTTAAATGCAATGTCG
GGGAAACAAGATCCGCCGTCGCAGCTTCAATCTGTCCCACCACACTGCCAGGGAAGTAAGGGAAG
TAAGATTCACCATTGTGGG
Found at i:38772708 original size:15 final size:15
Alignment explanation
Indices: 38772683--38772737 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
38772673 CACATTAGCC
*
38772683 TTTCCAATTTT-ACTT
1 TTTCCATTTTTCA-TT
38772698 TTTCCATTTTTCATT
1 TTTCCATTTTTCATT
38772713 TTT-CATTTTTCATT
1 TTTCCATTTTTCATT
*
38772727 TTTTCATTTTT
1 TTTCCATTTTT
38772738 TTCATTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 14 0.38
15 22 0.59
16 1 0.03
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTCCATTTTTCATT
Found at i:38772714 original size:6 final size:7
Alignment explanation
Indices: 38772696--38772737 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
38772686 CCAATTTTAC
38772696 TTTTTCCA
1 TTTTT-CA
38772704 TTTTTCA
1 TTTTTCA
38772711 TTTTTCA
1 TTTTTCA
38772718 TTTTTCA
1 TTTTTCA
38772725 TTTTTTCA
1 -TTTTTCA
38772733 TTTTT
1 TTTTT
38772738 TTCATTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
7 21 0.64
8 12 0.36
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:38772714 original size:14 final size:14
Alignment explanation
Indices: 38772683--38772728 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
38772673 CACATTAGCC
* *
38772683 TTTCCAATTTTACTT
1 TTTCC-ATTTTTCAT
38772698 TTTCCATTTTTCAT
1 TTTCCATTTTTCAT
*
38772712 TTTTCATTTTTCAT
1 TTTCCATTTTTCAT
38772726 TTT
1 TTT
38772729 TTCATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 23 0.82
15 5 0.18
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTCCATTTTTCAT
Found at i:38772738 original size:8 final size:8
Alignment explanation
Indices: 38772704--38772744 Score: 59
Period size: 7 Copynumber: 5.2 Consensus size: 8
38772694 ACTTTTTCCA
38772704 TTTTTCA-
1 TTTTTCAT
38772711 TTTTTCA-
1 TTTTTCAT
38772718 TTTTTCAT
1 TTTTTCAT
38772726 TTTTTCATT
1 TTTTTCA-T
38772735 TTTTTCAT
1 TTTTTCAT
38772743 TT
1 TT
38772745 CATTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 14 0.44
8 10 0.31
9 8 0.25
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCAT
Found at i:38772745 original size:22 final size:21
Alignment explanation
Indices: 38772704--38772752 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
38772694 ACTTTTTCCA
38772704 TTTTTCATTTTTCATTTTTCAT
1 TTTTTCATTTTTCA-TTTTCAT
38772726 TTTTTCATTTTTTTCA-TTTCAT
1 TTTTTCA--TTTTTCATTTTCAT
38772748 TTTTT
1 TTTTT
38772753 TACGACTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 18 0.72
24 7 0.28
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTCATTTTTCATTTTCAT
Found at i:38776313 original size:40 final size:40
Alignment explanation
Indices: 38776269--38776455 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
38776259 GCTCCTCGTT
*
38776269 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
38776309 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
38776349 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAT-TCGCA
* *** * *
38776389 CAAATGCCTTC-GGATCTTAGTCCGGATACGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AATTCGCA
38776430 CAAA-GCCTTCGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAGCCCGGAT
38776456 ATCATTCAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.03
40 111 0.86
41 13 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Found at i:38778164 original size:14 final size:14
Alignment explanation
Indices: 38778131--38778175 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
38778121 ATACATGGTT
* *
38778131 ATAATAATATTAAA
1 ATAATAATAATACA
*
38778145 AAAATAATAATACA
1 ATAATAATAATACA
*
38778159 ATAATAATGATACA
1 ATAATAATAATACA
38778173 ATA
1 ATA
38778176 TAACAGTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (14 bp):
ATAATAATAATACA
Found at i:38779216 original size:9 final size:9
Alignment explanation
Indices: 38779202--38779244 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
38779192 AGGGTTTCTG
38779202 TTTGGGCCA
1 TTTGGGCCA
*
38779211 TTTGGGTTACA
1 TTTGGG--CCA
38779222 TTTGGGCCA
1 TTTGGGCCA
38779231 TTTGGGCCA
1 TTTGGGCCA
*
38779240 CTTGG
1 TTTGG
38779245 TGTTTTAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 21 0.72
11 8 0.28
ACGTcount: A:0.12, C:0.19, G:0.33, T:0.37
Consensus pattern (9 bp):
TTTGGGCCA
Found at i:38779986 original size:50 final size:50
Alignment explanation
Indices: 38779906--38780372 Score: 394
Period size: 50 Copynumber: 9.3 Consensus size: 50
38779896 GATTCGCCAT
* ** * * * *
38779906 CTTCAATCTGTTTAACTGTAATGTCGGGGAAACAAGATTCGCCATCGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
* ** ** ** ** *
38779956 CTTCAATCTATTCCTCTGCACCGTCAGGGAAGTAAGATTTGCTATTGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
* ** * **
38780006 CTTTAATCTATTTAACTTCAATGTTGGGGAAACAAGATTCACCGTCGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
* * * * ** * *
38780056 CTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
** * *
38780106 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
* * * * ** * *
38780156 CTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
** * *
38780206 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
* * * * ** * *
38780256 CTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
** * *
38780306 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAG
1 CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
*
38780356 CTTCAATCTGTTCCACT
1 CTTCAATCTATTCCACT
38780373 ACACTGCCAG
Statistics
Matches: 312, Mismatches: 105, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
50 312 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
CTTCAATCTATTCCACTGCAATGTCAGGGAAACAAGATTCACCGTCGTAG
Found at i:38780039 original size:100 final size:100
Alignment explanation
Indices: 38779906--38780383 Score: 785
Period size: 100 Copynumber: 4.8 Consensus size: 100
38779896 GATTCGCCAT
* * * * * * *
38779906 CTTCAATCTGTTTAACTGTAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTATTCCT
1 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
* * * ** ** *
38779971 CTGCACCGTCAGGGAAGTAAGATTTGCTATTGTAG
66 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
* * * *
38780006 CTTTAATCTATTTAACTTCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
38780071 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
38780106 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
38780171 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
38780206 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
38780271 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
38780306 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
38780371 CTACACTGCCAGG
66 CTACACTGCCAGG
38780384 CCGTCATCGT
Statistics
Matches: 357, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 357 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (100 bp):
CTTCAATCTATTTAACTGCAATATCGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
CTACACTGCCAGGGAAGTAAGATTCACCGTTGTGG
Found at i:38793774 original size:25 final size:25
Alignment explanation
Indices: 38793728--38793793 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
38793718 AGGCCTATTT
* *
38793728 TTCACAGCTCATATGAGAATTCTAA
1 TTCACAGCTCGTGTGAGAATTCTAA
* *
38793753 TTCACAGCTCGTGTGTGCATTCTAA
1 TTCACAGCTCGTGTGAGAATTCTAA
*
38793778 TT-ACAACTCGTGTGAG
1 TTCACAGCTCGTGTGAG
38793794 TAGACATGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 12 0.34
25 23 0.66
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGAATTCTAA
Found at i:38803720 original size:20 final size:20
Alignment explanation
Indices: 38803697--38803734 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
38803687 CATTAATGCT
38803697 GACAAGCTACCAGTAATGTA
1 GACAAGCTACCAGTAATGTA
38803717 GACAAGCTACCAGTAATG
1 GACAAGCTACCAGTAATG
38803735 CAGATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
GACAAGCTACCAGTAATGTA
Found at i:38804242 original size:22 final size:22
Alignment explanation
Indices: 38804175--38804242 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
38804165 GGGGTTTGCG
*
38804175 CTACAGTGCCTACTGGTTCGCA
1 CTACAGTGCCTACTGATTCGCA
* * * * *
38804197 ATATAGTGCATACTTATTTGCA
1 CTACAGTGCCTACTGATTCGCA
*
38804219 CTACAGTGCCTACTGATTCACA
1 CTACAGTGCCTACTGATTCGCA
38804241 CT
1 CT
38804243 TTGATGCCTA
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (22 bp):
CTACAGTGCCTACTGATTCGCA
Found at i:38806919 original size:21 final size:22
Alignment explanation
Indices: 38806895--38806963 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 22
38806885 TTTTTTCAGT
* **
38806895 AACTTCTTCTTCTT-TAGTGAC
1 AACTTCTTCTTCTTGCAGCAAC
*
38806916 AACTTCTTATT-TTGCAGCAAC
1 AACTTCTTCTTCTTGCAGCAAC
*
38806937 AACTTCTTCTTC-TGCAGCATC
1 AACTTCTTCTTCTTGCAGCAAC
38806958 AACTTC
1 AACTTC
38806964 CATTTTTCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 2 0.05
21 38 0.95
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.41
Consensus pattern (22 bp):
AACTTCTTCTTCTTGCAGCAAC
Found at i:38818414 original size:23 final size:23
Alignment explanation
Indices: 38818379--38818423 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
38818369 AATGAGTGTT
*
38818379 GATGTATAATTGGTATTAAATGG
1 GATGAATAATTGGTATTAAATGG
*
38818402 GATGAATATTTGGTATTAAATG
1 GATGAATAATTGGTATTAAATG
38818424 TTTATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (23 bp):
GATGAATAATTGGTATTAAATGG
Found at i:38820375 original size:80 final size:81
Alignment explanation
Indices: 38820228--38820564 Score: 403
Period size: 80 Copynumber: 4.2 Consensus size: 81
38820218 AAATCGTCTT
* * * * * * *
38820228 ATAGGGTAGAATGACCAAAATATCCCCACAAGGTAAAATGACCGAAATACCCTCACAGGATAGAA
1 ATAGGGTAAAATGACCGAAATATCCCCATAAGGTAAAATGACCGAATTACCCTCATAGGGTAAAA
38820293 TGACCGAAATACCCCC
66 TGACCGAAATACCCCC
* * * *
38820309 ATAGGGTAAAATGACCGAATTA-CCCCATAAGGTAAAATGACTGAATTACCCCCATAGGCTAAAA
1 ATAGGGTAAAATGACCGAAATATCCCCATAAGGTAAAATGACCGAATTACCCTCATAGGGTAAAA
*
38820373 TGACC-AAATTACCCTC
66 TGACCGAAA-TACCCCC
* * * *
38820389 ATAGGGTAAAATGATCGAATTA-CCCCAT-AGGATAAAATTACTGAATTACCCTCATAGGGTAAA
1 ATAGGGTAAAATGACCGAAATATCCCCATAAGG-TAAAATGACCGAATTACCCTCATAGGGTAAA
* *
38820452 ATGACCAAAATACCCTC
65 ATGACCGAAATACCCCC
* * * *
38820469 ATAGGGTAAAATGACTGAAATATCCCTATAGGGTAAAATGACCAAATTACCCTCATAGGGTAAAA
1 ATAGGGTAAAATGACCGAAATATCCCCATAAGGTAAAATGACCGAATTACCCTCATAGGGTAAAA
* * *
38820534 TGACCGAATTACCTCT
66 TGACCGAAATACCCCC
38820550 ATAGGGTAAAATGAC
1 ATAGGGTAAAATGAC
38820565 TGTTATACCC
Statistics
Matches: 223, Mismatches: 28, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
79 6 0.03
80 133 0.60
81 82 0.37
82 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (81 bp):
ATAGGGTAAAATGACCGAAATATCCCCATAAGGTAAAATGACCGAATTACCCTCATAGGGTAAAA
TGACCGAAATACCCCC
Found at i:38820552 original size:54 final size:52
Alignment explanation
Indices: 38820227--38820564 Score: 372
Period size: 54 Copynumber: 6.3 Consensus size: 52
38820217 GAAATCGTCT
* * * * *
38820227 TATAGGGTAGAATGACCAAAATATCCCCACAAGGTAAAATGACCGAAATACCC
1 TATAGGGTAAAATGACCAAATTA-CCCCATAGGGTAAAATGACCGAATTACCC
* * *
38820280 TCACAGGATAGAATGACCGAAA-TACCCCCATAGGGTAAAATGACCGAATTACCC
1 T-ATAGGGTAAAATGACC-AAATTA-CCCCATAGGGTAAAATGACCGAATTACCC
* * ** * *
38820334 CATAAGGTAAAATGACTGAATTACCCCCATAGGCTAAAATGACCAAATTACCC
1 TATAGGGTAAAATGACCAAATTA-CCCCATAGGGTAAAATGACCGAATTACCC
* * * * *
38820387 TCATAGGGTAAAATGATCGAATTACCCCATAGGATAAAATTACTGAATTACCC
1 T-ATAGGGTAAAATGACCAAATTACCCCATAGGGTAAAATGACCGAATTACCC
* * *
38820440 TCATAGGGTAAAATGACCAAAATACCCTCATAGGGTAAAATGACTGAAATATCCC
1 T-ATAGGGTAAAATGACCAAATTACCC-CATAGGGTAAAATGACCGAATTA-CCC
38820495 TATAGGGTAAAATGACCAAATTACCCTCATAGGGTAAAATGACCGAATTACCTC
1 TATAGGGTAAAATGACCAAATTACCC-CATAGGGTAAAATGACCGAATTACC-C
38820549 TATAGGGTAAAATGAC
1 TATAGGGTAAAATGAC
38820565 TGTTATACCC
Statistics
Matches: 246, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.01
53 93 0.38
54 144 0.59
55 7 0.03
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (52 bp):
TATAGGGTAAAATGACCAAATTACCCCATAGGGTAAAATGACCGAATTACCC
Found at i:38820573 original size:27 final size:26
Alignment explanation
Indices: 38820205--38820564 Score: 321
Period size: 27 Copynumber: 13.4 Consensus size: 26
38820195 CCTCAAAATA
* *
38820205 GGTAAAATGACTGAAAT-CGTCTTATAG
1 GGTAAAATGACCGAAATAC--CCTATAG
* * * * *
38820232 GGTAGAATGACCAAAATATCCCCACAA
1 GGTAAAATGACCGAAATA-CCCTATAG
*
38820259 GGTAAAATGACCGAAATACCCTCACAG
1 GGTAAAATGACCGAAATACCCT-ATAG
* * *
38820286 GATAGAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCTATAG
* * *
38820313 GGTAAAATGACCGAATTACCCCATAA
1 GGTAAAATGACCGAAATACCCTATAG
* * *
38820339 GGTAAAATGACTGAATTACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCTATAG
*
38820366 GCTAAAATGACC-AAATTACCCTCATAG
1 GGTAAAATGACCGAAA-TACCCT-ATAG
* * *
38820393 GGTAAAATGATCGAATTACCCCATAG
1 GGTAAAATGACCGAAATACCCTATAG
* * * *
38820419 GATAAAATTACTGAATTACCCTCATAG
1 GGTAAAATGACCGAAATACCCT-ATAG
*
38820446 GGTAAAATGACCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCCT-ATAG
*
38820473 GGTAAAATGACTGAAATATCCCTATAG
1 GGTAAAATGACCGAAATA-CCCTATAG
38820500 GGTAAAATGACC-AAATTACCCTCATAG
1 GGTAAAATGACCGAAA-TACCCT-ATAG
*
38820527 GGTAAAATGACCGAATTACCTCTATAG
1 GGTAAAATGACCGAAATACC-CTATAG
38820554 GGTAAAATGAC
1 GGTAAAATGAC
38820565 TGTTATACCC
Statistics
Matches: 276, Mismatches: 43, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
26 60 0.22
27 202 0.73
28 13 0.05
29 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCTATAG
Found at i:38820745 original size:26 final size:26
Alignment explanation
Indices: 38820716--38820792 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
38820706 AGAAGTATAT
38820716 TGTTACTGGCAGCTTTGCTGCGATAC
1 TGTTACTGGCAGCTTTGCTGCGATAC
* * **
38820742 TGTTACTGACAGCTTCGCTATGATAC
1 TGTTACTGGCAGCTTTGCTGCGATAC
* *
38820768 TATTACTAGCAGCTTTGCTGCGATA
1 TGTTACTGGCAGCTTTGCTGCGATA
38820793 TTGGTGTGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (26 bp):
TGTTACTGGCAGCTTTGCTGCGATAC
Found at i:38820938 original size:28 final size:28
Alignment explanation
Indices: 38820902--38821484 Score: 842
Period size: 28 Copynumber: 20.8 Consensus size: 28
38820892 GTATGAATAT
38820902 TGTATTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38820930 TGTACTGGGCTAAGGCCCATATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* * * *
38820958 TTTATTGGGCTAAGGGCCACGTTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38820986 TGCATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38821014 TGCACTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38821042 TGTATTAGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38821070 TGTATTGGGCAAAGGCCTACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* * *
38821098 TGTATTTGGCTAAGGCGCACAATATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* *
38821126 TGTATTGGGCTAAGGCCCATATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* * * *
38821154 TGCATTAGGCTAAGGCCCACGTTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821182 TGCATTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821210 TGTATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
38821238 TGTATTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821266 TGTATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821294 TGTATTGGGCTAAGGACCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* * *
38821322 TGTATTAGGCTAAGGCCAACAATATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
38821350 TGTATTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821378 TGTATTGGGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
* * * *
38821406 TTTATTGGGCTAAGGGCCACGTTGTTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
*
38821434 TGCATTGGGCTAAGGCCCACATTATTAC
1 TGTATTGGGCTAAGGCCCACATTATTAC
38821462 TGTATTGGGCTAAGGCCCACATT
1 TGTATTGGGCTAAGGCCCACATT
38821485 GTACTATTAC
Statistics
Matches: 493, Mismatches: 62, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 493 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACATTATTAC
Found at i:38829530 original size:19 final size:17
Alignment explanation
Indices: 38829506--38829549 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
38829496 AAATGCATCA
*
38829506 AATAATTATACATATTACC
1 AATAATAATACAT-TT-CC
*
38829525 AATAATAATTCATTTCC
1 AATAATAATACATTTCC
38829542 AATAATAA
1 AATAATAA
38829550 AACACACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATACATTTCC
Found at i:38832528 original size:49 final size:49
Alignment explanation
Indices: 38832473--38832573 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 49
38832463 CTCGTTTTCT
*
38832473 CGATGCCATAGTCCAACTATGGT-CT-TACATGTAATCACATATCA-TGTAC
1 CGATGCCATAGCCCAACTATGGTCCTATACA-G-AATCACATATCACT-TAC
*
38832522 CGATGCCATAGCCCAGCTATGGTCCTATACAGAATCACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCCTATACAGAATCACATATCACTTAC
38832571 CGA
1 CGA
38832574 AAGTACTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
49 39 0.83
50 4 0.09
51 4 0.09
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (49 bp):
CGATGCCATAGCCCAACTATGGTCCTATACAGAATCACATATCACTTAC
Found at i:38844024 original size:16 final size:17
Alignment explanation
Indices: 38844003--38844035 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38843993 TTGAGAGAGA
38844003 GGATGA-GAGATGAGGG
1 GGATGATGAGATGAGGG
38844019 GGATGATGAGATGAGGG
1 GGATGATGAGATGAGGG
38844036 ATGATTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.30, C:0.00, G:0.55, T:0.15
Consensus pattern (17 bp):
GGATGATGAGATGAGGG
Found at i:38846231 original size:16 final size:16
Alignment explanation
Indices: 38846207--38846240 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38846197 ATTAAGTCCT
38846207 AATTACTAAAGAAATA
1 AATTACTAAAGAAATA
*
38846223 AATTCCTAAAGAAATA
1 AATTACTAAAGAAATA
38846239 AA
1 AA
38846241 AAACAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (16 bp):
AATTACTAAAGAAATA
Found at i:38849885 original size:12 final size:13
Alignment explanation
Indices: 38849861--38849889 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
38849851 GGGCTATAAC
38849861 TATTGCATTTATT
1 TATTGCATTTATT
38849874 TATTGC-TTTATT
1 TATTGCATTTATT
38849886 TATT
1 TATT
38849890 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:38878090 original size:17 final size:18
Alignment explanation
Indices: 38878057--38878090 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38878047 TATAAATACC
*
38878057 CCATTCACCTATTCATTT
1 CCATACACCTATTCATTT
38878075 CCATACACCT-TTCATT
1 CCATACACCTATTCATT
38878091 CCACACATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (18 bp):
CCATACACCTATTCATTT
Found at i:38882311 original size:16 final size:16
Alignment explanation
Indices: 38882290--38882328 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
38882280 GTTGTTAATA
38882290 ATTAATATATAAT-TAT
1 ATTAAT-TATAATGTAT
38882306 ATTAATTATAATGTAT
1 ATTAATTATAATGTAT
38882322 ATTAATT
1 ATTAATT
38882329 TTATGAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTAATTATAATGTAT
Found at i:38888407 original size:16 final size:17
Alignment explanation
Indices: 38888375--38888415 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
38888365 ATTCCCCCTT
38888375 CACCTATTCATTTCCACA
1 CACCT-TTCATTTCCACA
38888393 CACCTTTCA-TTCCACA
1 CACCTTTCATTTCCACA
*
38888409 CATCTTT
1 CACCTTT
38888416 TTCCTTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.59
17 4 0.18
18 5 0.23
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (17 bp):
CACCTTTCATTTCCACA
Found at i:38893208 original size:49 final size:48
Alignment explanation
Indices: 38893089--38894099 Score: 1629
Period size: 49 Copynumber: 20.8 Consensus size: 48
38893079 TTAGGATTCT
* * * *
38893089 ATGTGATGGATGTGAACA-TG-CATATATGTGATAAGGCCTAATGGCCA
1 ATGTGATGAATGTGAA-AGTGATATATATGTGATAAGACCTAATGGCCG
*
38893136 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGACCTAATGGCCG
* * *
38893183 ATATGTGATGAATGTGAAAGTGTATATATATCTGATAAGGCCTAATGCCCG
1 --ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
*
38893234 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCCCG
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGACCTAATGG--CCG
38893283 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893332 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893381 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893430 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893479 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893528 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893577 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893626 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893675 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893724 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893773 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893822 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893871 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893920 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
38893969 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGACCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGACCTAATGGCCG
* * * * * *
38894018 ATGTGATGAATGTGAAAGTG-TATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGACCTAATGGCCG
* * *
38894065 ACGTGATGGATGTGAAAGTG-TATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAG
38894100 TCCCGAAGGG
Statistics
Matches: 936, Mismatches: 19, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
46 1 0.00
47 115 0.12
49 772 0.82
51 48 0.05
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (48 bp):
ATGTGATGAATGTGAAAGTGATATATATGTGATAAGACCTAATGGCCG
Found at i:38894276 original size:37 final size:37
Alignment explanation
Indices: 38894218--38894296 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
38894208 CCGAGCTCTA
* * *
38894218 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
* *
38894255 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
38894292 AAGAC
1 AAGAC
38894297 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
Found at i:38903972 original size:32 final size:31
Alignment explanation
Indices: 38903931--38903993 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 31
38903921 ATCAAACTCT
38903931 TTCCCTTGTACTAGTACCCTTTCCCATGTAG
1 TTCCCTTGTACTAGTACCCTTTCCCATGTAG
38903962 NTTCCCTTGTACTAGTACCCTTTCCCATGTAG
1 -TTCCCTTGTACTAGTACCCTTTCCCATGTAG
38903994 CACCCTTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.16, C:0.32, G:0.13, T:0.38
Consensus pattern (31 bp):
TTCCCTTGTACTAGTACCCTTTCCCATGTAG
Found at i:38905338 original size:25 final size:25
Alignment explanation
Indices: 38905304--38905359 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
38905294 AATAGAAGAA
*
38905304 ATTTCAGCTGGTTATCGACACTTTG
1 ATTTGAGCTGGTTATCGACACTTTG
38905329 ATTTGAGCTGGTTATCGACACTTTG
1 ATTTGAGCTGGTTATCGACACTTTG
38905354 ATTTGA
1 ATTTGA
38905360 CGTTATTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (25 bp):
ATTTGAGCTGGTTATCGACACTTTG
Found at i:38906366 original size:41 final size:41
Alignment explanation
Indices: 38906317--38906526 Score: 215
Period size: 41 Copynumber: 5.1 Consensus size: 41
38906307 ACTAGAGTGT
* * * *
38906317 AAACAAGGGCACGTATTTGAAATTCAAGGGTACCGAAGCAC
1 AAACAAGGGCACGTATGTGCAATTCAAGGGTACCAAAGTAC
* * * *
38906358 AAAAAAGGGCACGTATATGCAATTCAGGGGTACTAAAGTAC
1 AAACAAGGGCACGTATGTGCAATTCAAGGGTACCAAAGTAC
*
38906399 AAACAGGGGCACGTATGTGCAATTC-AGAGGTACCAAAGTAC
1 AAACAAGGGCACGTATGTGCAATTCAAG-GGTACCAAAGTAC
* * * * *
38906440 AAACAGGGGCACATATGTGCAATTTAGGGGTACCGAAGTAC
1 AAACAAGGGCACGTATGTGCAATTCAAGGGTACCAAAGTAC
* * * * * * *
38906481 AAATAGGGGTATGTATGTGCAATTTAGGGGTACCAAAGTAT
1 AAACAAGGGCACGTATGTGCAATTCAAGGGTACCAAAGTAC
38906522 AAACA
1 AAACA
38906527 GGTAATCACA
Statistics
Matches: 144, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
40 1 0.01
41 142 0.99
42 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (41 bp):
AAACAAGGGCACGTATGTGCAATTCAAGGGTACCAAAGTAC
Found at i:38906405 original size:20 final size:20
Alignment explanation
Indices: 38906382--38906448 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
38906372 ATATGCAATT
38906382 CAGGGGTACTAAAGTACAAA
1 CAGGGGTACTAAAGTACAAA
* * * *
38906402 CAGGGGCACGT-ATGTGCAATT
1 CAGGGGTAC-TAAAGTACAA-A
* *
38906423 CAGAGGTACCAAAGTACAAA
1 CAGGGGTACTAAAGTACAAA
38906443 CAGGGG
1 CAGGGG
38906449 CACATATGTG
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (20 bp):
CAGGGGTACTAAAGTACAAA
Found at i:38906450 original size:82 final size:82
Alignment explanation
Indices: 38906317--38906528 Score: 246
Period size: 82 Copynumber: 2.6 Consensus size: 82
38906307 ACTAGAGTGT
* * * * * * * *
38906317 AAACAAGGGCACGTATTTGAAATTCA-AGGGTACCGAAGCACAAAAAAGGGCACGTATATGCAAT
1 AAACAGGGGCACGTATGTGCAATTCAGA-GGTACCAAAGTACAAACAGGGGCACATATATGCAAT
*
38906381 TCAGGGGTACTAAAGTAC
65 TCAGGGGTACCAAAGTAC
*
38906399 AAACAGGGGCACGTATGTGCAATTCAGAGGTACCAAAGTACAAACAGGGGCACATATGTGCAATT
1 AAACAGGGGCACGTATGTGCAATTCAGAGGTACCAAAGTACAAACAGGGGCACATATATGCAATT
* *
38906464 TAGGGGTACCGAAGTAC
66 CAGGGGTACCAAAGTAC
* * * * * *
38906481 AAATAGGGGTATGTATGTGCAATTTAGGGGTACCAAAGTATAAACAGG
1 AAACAGGGGCACGTATGTGCAATTCAGAGGTACCAAAGTACAAACAGG
38906529 TAATCACATA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
82 110 0.99
83 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (82 bp):
AAACAGGGGCACGTATGTGCAATTCAGAGGTACCAAAGTACAAACAGGGGCACATATATGCAATT
CAGGGGTACCAAAGTAC
Found at i:38906510 original size:21 final size:22
Alignment explanation
Indices: 38906453--38906514 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 22
38906443 CAGGGGCACA
38906453 TATGTGCAATTTAGGGGTACCG
1 TATGTGCAATTTAGGGGTACCG
* * * *
38906475 -AAGTACAA-ATAGGGGTA-TG
1 TATGTGCAATTTAGGGGTACCG
38906494 TATGTGCAATTTAGGGGTACC
1 TATGTGCAATTTAGGGGTACC
38906515 AAAGTATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 14 0.48
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (22 bp):
TATGTGCAATTTAGGGGTACCG
Found at i:38912169 original size:23 final size:23
Alignment explanation
Indices: 38912139--38912188 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
38912129 TGGAAGCTTG
38912139 TTGGAGATAAATCACACTATCCA
1 TTGGAGATAAATCACACTATCCA
38912162 TTGGAGATAAATCACACTATCCA
1 TTGGAGATAAATCACACTATCCA
38912185 TTGG
1 TTGG
38912189 CTCTTTTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (23 bp):
TTGGAGATAAATCACACTATCCA
Found at i:38916703 original size:41 final size:41
Alignment explanation
Indices: 38916645--38916812 Score: 149
Period size: 41 Copynumber: 4.1 Consensus size: 41
38916635 ATTGAAGTGT
* * *
38916645 AAATAGGGGCACATATATGTAATTCAGGCGTACTGAACTAC
1 AAATAGGGGCACGTATATGAAATTCAGGCGTACCGAACTAC
* * *
38916686 AAATAGGGGCACGTATATGAAATTTAGGGGTACCGAAGTAC
1 AAATAGGGGCACGTATATGAAATTCAGGCGTACCGAACTAC
* * * * * * *
38916727 AAGTAGGGGCACGTATGTGCAATTCAGGGGCACCTAAGTAC
1 AAATAGGGGCACGTATATGAAATTCAGGCGTACCGAACTAC
* * * * *
38916768 AAACAAGGGGCACGCATCT-ACAATTCAGGGGTACCGAAGTAC
1 AAA-TAGGGGCACGTATATGA-AATTCAGGCGTACCGAACTAC
38916810 AAA
1 AAA
38916813 CAGGTAATCA
Statistics
Matches: 106, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
41 72 0.68
42 34 0.32
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (41 bp):
AAATAGGGGCACGTATATGAAATTCAGGCGTACCGAACTAC
Found at i:38916792 original size:42 final size:42
Alignment explanation
Indices: 38916706--38916814 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
38916696 ACGTATATGA
* * ** * * *
38916706 AATTTAGGGGTACCGAAGTAC-AAGTAGGGGCACGTATGTGC
1 AATTCAGGGGCACCGAAGTACAAACAAGGGGCACGCATCTAC
*
38916747 AATTCAGGGGCACCTAAGTACAAACAAGGGGCACGCATCTAC
1 AATTCAGGGGCACCGAAGTACAAACAAGGGGCACGCATCTAC
*
38916789 AATTCAGGGGTACCGAAGTACAAACA
1 AATTCAGGGGCACCGAAGTACAAACA
38916815 GGTAATCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 18 0.32
42 39 0.68
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (42 bp):
AATTCAGGGGCACCGAAGTACAAACAAGGGGCACGCATCTAC
Found at i:38916810 original size:21 final size:21
Alignment explanation
Indices: 38916706--38916811 Score: 67
Period size: 21 Copynumber: 5.1 Consensus size: 21
38916696 ACGTATATGA
* *
38916706 AATTTAGGGGTACCGAAGTAC
1 AATTCAGGGGCACCGAAGTAC
* * *
38916727 AAGT-AGGGGCA-CGTATGTGC
1 AATTCAGGGGCACCG-AAGTAC
*
38916747 AATTCAGGGGCACCTAAGTAC
1 AATTCAGGGGCACCGAAGTAC
* **
38916768 AA-ACAAGGGGCA-CGCATCTAC
1 AATTC-AGGGGCACCG-AAGTAC
*
38916789 AATTCAGGGGTACCGAAGTAC
1 AATTCAGGGGCACCGAAGTAC
38916810 AA
1 AA
38916812 ACAGGTAATC
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
19 2 0.03
20 15 0.24
21 41 0.66
22 4 0.06
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (21 bp):
AATTCAGGGGCACCGAAGTAC
Found at i:38918188 original size:21 final size:21
Alignment explanation
Indices: 38918164--38918205 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38918154 ATATTTAATG
*
38918164 CATCAT-TTTTATCATTTTTGC
1 CATCATGTTTTA-CATGTTTGC
38918185 CATCATGTTTTACATGTTTGC
1 CATCATGTTTTACATGTTTGC
38918206 TAATACCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (21 bp):
CATCATGTTTTACATGTTTGC
Found at i:38923048 original size:50 final size:50
Alignment explanation
Indices: 38922968--38923260 Score: 388
Period size: 50 Copynumber: 5.8 Consensus size: 50
38922958 ATTTGGGTAA
* *
38922968 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
38923018 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
38923068 AGAGCCCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *
38923118 AGAGGTCTTATGTAAGACCATGTCTGGGACATGGCGTTGTCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** *** *
38923168 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCAAGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * *
38923218 AGAACATCTCATGTAATACCATGTCTGGGACATAGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
38923261 TGTTATTATC
Statistics
Matches: 210, Mismatches: 32, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
50 180 0.86
51 30 0.14
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:38931584 original size:42 final size:42
Alignment explanation
Indices: 38931464--38931679 Score: 199
Period size: 42 Copynumber: 5.1 Consensus size: 42
38931454 TAGGATTCTG
* * *
38931464 GTATGTGATTACGTGTAAGACCAC-GTCTGGGACGTTGGCA-T
1 GTATATGATTTCGTGTAAGACC-CTGTCTGGGACATTGGCATT
** * * *
38931505 CAATTTGAGATTTACGTGTAAGACCATGTCT-AGACATTGGCATT
1 GTATAT--GATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATT
*
38931549 GTATATGATTTCGTGTAAGACCCTTTCTGGGACATTGGCATT
1 GTATATGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATT
* *
38931591 GTATATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATC
1 GTATATGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATT
* * * *
38931633 GATATTTGATTACATGTAAGACCAC-GTCTGGGATGA-TGGCATT
1 G-TATATGATTTCGTGTAAGACC-CTGTCTGGGA-CATTGGCATT
38931676 GTAT
1 GTAT
38931680 GAGTTGTTGA
Statistics
Matches: 145, Mismatches: 21, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
41 18 0.12
42 60 0.41
43 46 0.32
44 21 0.14
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (42 bp):
GTATATGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATT
Found at i:38931663 original size:85 final size:85
Alignment explanation
Indices: 38931464--38931679 Score: 226
Period size: 85 Copynumber: 2.5 Consensus size: 85
38931454 TAGGATTCTG
* * ** *
38931464 GTATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA-TCAATTTGAGATTTACGTGTAAGA
1 GTATATGATTACGTGTAAGACCACGTCTGGGACATTGGCATTGTATAT-AGATTTACGTGTAAGA
* *
38931528 CCATGTCTAGACATTGGCATT
65 CCATGTCTAGACAGTGGCATC
* *
38931549 GTATATGATTTCGTGTAAGACC-CTTTCTGGGACATTGGCATTGTATAT-GATTT-CGTGTAAGA
1 GTATATGATTACGTGTAAGACCAC-GTCTGGGACATTGGCATTGTATATAGATTTACGTGTAAGA
* *
38931611 CCCTGTCTGGGACAGTGGCATC
65 CCATGTCT-AGACAGTGGCATC
* * *
38931633 GATATTTGATTACATGTAAGACCACGTCTGGGATGA-TGGCATTGTAT
1 G-TATATGATTACGTGTAAGACCACGTCTGGGA-CATTGGCATTGTAT
38931680 GAGTTGTTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
83 16 0.15
84 17 0.16
85 70 0.64
86 6 0.06
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (85 bp):
GTATATGATTACGTGTAAGACCACGTCTGGGACATTGGCATTGTATATAGATTTACGTGTAAGAC
CATGTCTAGACAGTGGCATC
Found at i:38938203 original size:25 final size:25
Alignment explanation
Indices: 38938150--38938203 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
38938140 AATTTAAGTT
* *
38938150 AATTATCTAATTTTTCAATTTATTG
1 AATTATCTAATTTTTCAATTAATTA
38938175 AATTAT-TAATATTTT-ATATTAATTA
1 AATTATCTAAT-TTTTCA-ATTAATTA
38938200 AATT
1 AATT
38938204 TTTGAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATCTAATTTTTCAATTAATTA
Found at i:38940790 original size:40 final size:40
Alignment explanation
Indices: 38940707--38940891 Score: 124
Period size: 40 Copynumber: 4.6 Consensus size: 40
38940697 TTGAATGCTG
* * * * *
38940707 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGACTAAGTCCCGAAGGCATTCGTGCGAGA-T-ATTAAA
* *
38940747 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATATTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTCGTGCGAGATATTAAA
** * *
38940787 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGACTAAGTCCCGAAGGCATTCGTGCGAGATATTAAA
** * * * * *
38940827 TCCGGGTTATGTCCCGAAGGCATTGTGTGTGAGTTACTAAA
1 TCCGGACTAAGTCCCGAAGGCATT-CGTGCGAGATATTAAA
* * *
38940868 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGACTAAGTCCCGAAGGCATT
38940892 TGAACGAGGA
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 77 0.63
41 44 0.36
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTCGTGCGAGATATTAAA
Found at i:38940873 original size:41 final size:40
Alignment explanation
Indices: 38940760--38940893 Score: 178
Period size: 40 Copynumber: 3.3 Consensus size: 40
38940750 GGACTAAGAT
* * *
38940760 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAAATCCGGGTTATGTC
* *
38940800 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGTTATTAAATCCGGGTTATGTC
* * * *
38940840 CCGAAGGCATTGTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATT-TGTGCGAGTTATTAAATCCGGGTTATGTC
38940881 CCGAAGGCATTTG
1 CCGAAGGCATTTG
38940894 AACGAGGAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 48 0.59
41 34 0.41
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAAATCCGGGTTATGTC
Found at i:38946482 original size:103 final size:104
Alignment explanation
Indices: 38946303--38946567 Score: 424
Period size: 103 Copynumber: 2.6 Consensus size: 104
38946293 AACCGTTATT
* * * * *
38946303 GGTGGATCTCGCACTTAGCACCACTACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
38946368 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
38946406 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
38946471 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* *
38946510 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACATAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
38946568 TTATGTACAA
Statistics
Matches: 149, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 82 0.55
104 67 0.45
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:38946929 original size:30 final size:29
Alignment explanation
Indices: 38946895--38946959 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
38946885 TAATCCACCA
38946895 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
38946925 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
38946955 CCCAA
1 CCCAA
38946960 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:38946933 original size:31 final size:30
Alignment explanation
Indices: 38946902--38946959 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
38946892 CCACCCAACT
38946902 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
38946932 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
38946960 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:38956638 original size:19 final size:19
Alignment explanation
Indices: 38956611--38956654 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
38956601 AATGTATGTT
*
38956611 TTTACTTAGTTTTAATATG
1 TTTATTTAGTTTTAATATG
38956630 TTTATTTAGTTTTAATATG
1 TTTATTTAGTTTTAATATG
38956649 TTTATT
1 TTTATT
38956655 GCTATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (19 bp):
TTTATTTAGTTTTAATATG
Found at i:38959211 original size:18 final size:18
Alignment explanation
Indices: 38959188--38959222 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
38959178 GGGTTTGATG
38959188 AACAAAATCTTCAGACCT
1 AACAAAATCTTCAGACCT
38959206 AACAAAATCTTCAGACC
1 AACAAAATCTTCAGACC
38959223 GTATTTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.29, G:0.06, T:0.20
Consensus pattern (18 bp):
AACAAAATCTTCAGACCT
Found at i:38962008 original size:22 final size:22
Alignment explanation
Indices: 38961983--38962028 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
38961973 GCCAAAACAA
38961983 TATCAAAATAATATGGTTCATT
1 TATCAAAATAATATGGTTCATT
38962005 TATCAAAATAATATGGTTCATT
1 TATCAAAATAATATGGTTCATT
38962027 TA
1 TA
38962029 CCATAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
TATCAAAATAATATGGTTCATT
Found at i:38964493 original size:25 final size:25
Alignment explanation
Indices: 38964459--38964573 Score: 115
Period size: 25 Copynumber: 4.6 Consensus size: 25
38964449 TGCTCCACAT
*
38964459 CTCGTGAGAGCATATTGATTTATAG
1 CTCGTGAGAGCATACTGATTTATAG
* * *
38964484 CTCGTGAGAGTATACCGAATTATAG
1 CTCGTGAGAGCATACTGATTTATAG
* * *
38964509 CTCGTAAGAGCATACTAATCTATAG
1 CTCGTGAGAGCATACTGATTTATAG
* * * *
38964534 CTCGAGTGAGCATACTGATTCACAG
1 CTCGTGAGAGCATACTGATTTATAG
38964559 CTCGT-ATGAGCATAC
1 CTCGTGA-GAGCATAC
38964574 ATGTACATGA
Statistics
Matches: 70, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (25 bp):
CTCGTGAGAGCATACTGATTTATAG
Found at i:38969991 original size:12 final size:12
Alignment explanation
Indices: 38969966--38970030 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 12
38969956 TGTTACTTTT
38969966 AAAAA-TTG-AA
1 AAAAATTTGAAA
38969976 AAAAATTTGAAAA
1 AAAAATTTG-AAA
***
38969989 AAAAGAAAAGAAA
1 AAAA-ATTTGAAA
*
38970002 AAATATTTGAAA
1 AAAAATTTGAAA
38970014 AAAAATTTCGAAA
1 AAAAATTT-GAAA
38970027 AAAA
1 AAAA
38970031 TTCAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
10 5 0.12
11 3 0.07
12 12 0.29
13 20 0.48
14 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (12 bp):
AAAAATTTGAAA
Found at i:38970038 original size:11 final size:12
Alignment explanation
Indices: 38969999--38970040 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
38969989 AAAAGAAAAG
* *
38969999 AAAAAATATTTG
1 AAAAAAAATTTC
38970011 AAAAAAAATTTC
1 AAAAAAAATTTC
*
38970023 GAAAAAAA-TTC
1 AAAAAAAATTTC
38970034 AAAAAAA
1 AAAAAAA
38970041 GGGGTCCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (12 bp):
AAAAAAAATTTC
Found at i:38970501 original size:21 final size:19
Alignment explanation
Indices: 38970475--38970511 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38970465 TATATATTTA
*
38970475 TATATTTTTTTATTTTCTT
1 TATATATTTTTATTTTCTT
*
38970494 TATTTATTTTTATTTTCT
1 TATATATTTTTATTTTCT
38970512 AGATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.78
Consensus pattern (19 bp):
TATATATTTTTATTTTCTT
Found at i:38970517 original size:19 final size:19
Alignment explanation
Indices: 38970481--38970519 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38970471 TTTATATATT
**
38970481 TTTTTATTTTCTTTATTTA
1 TTTTTATTTTCTAGATTTA
38970500 TTTTTATTTTCTAGATTTA
1 TTTTTATTTTCTAGATTTA
38970519 T
1 T
38970520 ATATTTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTCTAGATTTA
Found at i:38972366 original size:171 final size:171
Alignment explanation
Indices: 38972081--38972388 Score: 526
Period size: 171 Copynumber: 1.8 Consensus size: 171
38972071 TAGACACGCT
*
38972081 CGTGTGGACATTCGAAATAGGAGCACATGGTCGTGTCCCAGCCCATGTCCTACCCCGTGTAACTC
1 CGTGTGGACATTCGAAATAAGAGCACATGGTCGTGTCCCAGCCCATGTCCTACCCCGTGTAACTC
* * * * *
38972146 TCTGACTTGGGTCACACGACCAACACACACACCTGTTTGGCTGGCCCGTGTGCCCTAAAAATGTC
66 TCTGACTTGGGTCACACAACCAACACACACACCCGTGTGGCTAGCCCGTGTGCCCTAAAAATGGC
38972211 CATAAACGCGCGTGTGCCAGGAACACGCCCGTGTCATAGGC
131 CATAAACGCGCGTGTGCCAGGAACACGCCCGTGTCATAGGC
* *
38972252 CGTGTGGACATTCGAAATAAGAGCACATGGTCGTGTCCTAGCCCATGTTCTACCCCGTGTAACTC
1 CGTGTGGACATTCGAAATAAGAGCACATGGTCGTGTCCCAGCCCATGTCCTACCCCGTGTAACTC
* *
38972317 TTTGACTTGGGTCACACAACCAATACACACACCCGTGTGGCTAGCCCGTGTGCCCTAAAAATGGC
66 TCTGACTTGGGTCACACAACCAACACACACACCCGTGTGGCTAGCCCGTGTGCCCTAAAAATGGC
38972382 CATAAAC
131 CATAAAC
38972389 ACTCATGTGT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 127 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (171 bp):
CGTGTGGACATTCGAAATAAGAGCACATGGTCGTGTCCCAGCCCATGTCCTACCCCGTGTAACTC
TCTGACTTGGGTCACACAACCAACACACACACCCGTGTGGCTAGCCCGTGTGCCCTAAAAATGGC
CATAAACGCGCGTGTGCCAGGAACACGCCCGTGTCATAGGC
Found at i:38973718 original size:24 final size:24
Alignment explanation
Indices: 38973691--38973754 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
38973681 TAAAACGATT
* *
38973691 AGCTCTAACAAGCTGAAAACAGTA
1 AGCTCTTACAAGCTGAAAACAGAA
**
38973715 AGCTCTTACAAGCTGGTAACAGAA
1 AGCTCTTACAAGCTGAAAACAGAA
*
38973739 AGCTCTTACGAGCTGA
1 AGCTCTTACAAGCTGA
38973755 TATATCGGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (24 bp):
AGCTCTTACAAGCTGAAAACAGAA
Found at i:38975838 original size:36 final size:36
Alignment explanation
Indices: 38975798--38975916 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
38975788 TGGTACACCC
*
38975798 GAAACACACCAGATGCACATAAAAGCTAATCTATCT
1 GAAACACACCAGATGCACATAAAAGCTAATCCATCT
*
38975834 GAAACACACCAAATG-ATCATAAAAGCTAATCCATCT
1 GAAACACACCAGATGCA-CATAAAAGCTAATCCATCT
* * * * *
38975870 GAAACACACCAGATGCTCATAAGAGTTAATACAACT
1 GAAACACACCAGATGCACATAAAAGCTAATCCATCT
*
38975906 AAAACACACCA
1 GAAACACACCA
38975917 AAAACTGGGA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
35 1 0.01
36 71 0.99
ACGTcount: A:0.47, C:0.25, G:0.10, T:0.18
Consensus pattern (36 bp):
GAAACACACCAGATGCACATAAAAGCTAATCCATCT
Found at i:38986719 original size:16 final size:16
Alignment explanation
Indices: 38986698--38986729 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38986688 TTGTGTCGTA
*
38986698 ATTTACGAATTTCTTC
1 ATTTACGAAGTTCTTC
38986714 ATTTACGAAGTTCTTC
1 ATTTACGAAGTTCTTC
38986730 GTAAAAGCCC
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:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (16 bp):
ATTTACGAAGTTCTTC
Found at i:38992953 original size:39 final size:40
Alignment explanation
Indices: 38992848--38993110 Score: 301
Period size: 39 Copynumber: 6.7 Consensus size: 40
38992838 TTGAATGTTG
* *
38992848 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* * *
38992887 ATCCGGACTAAGAT-CTGAAGGCATTTGTGCAAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
38992928 TCCGGGCTAAG-CCCGAAGGCGTTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
38992967 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
** *
38993006 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGATTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
38993045 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
38993084 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
38993111 AACGAGGAGC
Statistics
Matches: 197, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
39 109 0.55
40 75 0.38
41 12 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:38993132 original size:79 final size:79
Alignment explanation
Indices: 38992903--38993143 Score: 242
Period size: 78 Copynumber: 3.1 Consensus size: 79
38992893 ACTAAGATCT
* * * ** * *
38992903 GAAGGCATTTGTGCAAGATACTAATTCCGGGCTAAGCCCGAAGGCGTTTGTGCGA-GATACTAAT
1 GAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATG-GACTAAA
*
38992967 TCCGGGCTAAG-CCC
65 TCCGGGTTAAGTCCC
* ** **
38992981 GAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGATTTACTAAAT
1 GAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAAAT
38993046 CCGGGTTAAGTCCC
66 CCGGGTTAAGTCCC
*
38993060 GAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGA-GGAGCT
1 GAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGATGGA-CT
* * *
38993122 ATATCC-GGTTAAATTCC
62 AAATCCGGGTTAAGTCCC
38993139 GAAGG
1 GAAGG
38993144 TACGTGATTT
Statistics
Matches: 143, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
78 72 0.50
79 47 0.33
80 24 0.17
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
GAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGATGGACTAAAT
CCGGGTTAAGTCCC
Found at i:39000827 original size:28 final size:28
Alignment explanation
Indices: 39000795--39000889 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 28
39000785 GAAAATTCAT
39000795 AAATTAAAGGAAAAATTGGAATATTGCA
1 AAATTAAAGGAAAAATTGGAATATTGCA
** ** * *
39000823 AAATTAACTAAATAAAAAGCAGGAAAATT-AA
1 AAATT-A--AAGGAAAAA-TTGGAATATTGCA
*
39000854 TAAATTAAGGGAAAAATTGGAATATTGCA
1 -AAATTAAAGGAAAAATTGGAATATTGCA
39000883 AAATTAA
1 AAATTAA
39000890 CTAAATAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
28 19 0.40
29 8 0.17
31 9 0.19
32 12 0.25
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (28 bp):
AAATTAAAGGAAAAATTGGAATATTGCA
Found at i:39000851 original size:60 final size:60
Alignment explanation
Indices: 39000780--39000899 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
39000770 GCATGAAATC
*
39000780 AGCAGGAAAATTCATAAATTAAAGGAAAAATTGGAATATTGCAAAATTAACTAAATAAAA
1 AGCAGGAAAATTAATAAATTAAAGGAAAAATTGGAATATTGCAAAATTAACTAAATAAAA
*
39000840 AGCAGGAAAATTAATAAATTAAGGGAAAAATTGGAATATTGCAAAATTAACTAAATAAAA
1 AGCAGGAAAATTAATAAATTAAAGGAAAAATTGGAATATTGCAAAATTAACTAAATAAAA
39000900 CTAGGACTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.23
Consensus pattern (60 bp):
AGCAGGAAAATTAATAAATTAAAGGAAAAATTGGAATATTGCAAAATTAACTAAATAAAA
Found at i:39002318 original size:32 final size:32
Alignment explanation
Indices: 39002277--39002339 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
39002267 ATAAAAAGGG
*
39002277 GAAGAAATCCCGGTTGAATGAAAGGAAAATTT
1 GAAGAAATCCCGGTTGAATAAAAGGAAAATTT
39002309 GAAGAAATCCCGGTTGAATAAAAGGAAAATT
1 GAAGAAATCCCGGTTGAATAAAAGGAAAATT
39002340 CGATGGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.21
Consensus pattern (32 bp):
GAAGAAATCCCGGTTGAATAAAAGGAAAATTT
Found at i:39003219 original size:23 final size:23
Alignment explanation
Indices: 39003193--39003237 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39003183 TGGGTATGTG
*
39003193 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
39003216 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
39003238 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:39008723 original size:49 final size:50
Alignment explanation
Indices: 39008666--39008764 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 50
39008656 GCATGAAATC
* *
39008666 AGCAGGAAAATTGATAAATTAAGGG-CAAATTGGAATATTGCAAAATTAA
1 AGCAGGAAAATTAATAAATTAAGGGAAAAATTGGAATATTGCAAAATTAA
39008715 AGCAGGAAAATTAATAAATTAAGGGAAAAATTGGAATATTGCAAAATTAA
1 AGCAGGAAAATTAATAAATTAAGGGAAAAATTGGAATATTGCAAAATTAA
39008765 CTAAATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 24 0.51
50 23 0.49
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (50 bp):
AGCAGGAAAATTAATAAATTAAGGGAAAAATTGGAATATTGCAAAATTAA
Found at i:39011220 original size:40 final size:40
Alignment explanation
Indices: 39011137--39011341 Score: 245
Period size: 40 Copynumber: 5.1 Consensus size: 40
39011127 TTGAATGATG
* * *
39011137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
39011177 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAGA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* *
39011217 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* *
39011257 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * **
39011297 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
39011337 TCCGG
1 TCCGG
39011342 TTAAATTCCG
Statistics
Matches: 144, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.02
40 133 0.92
41 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:39011504 original size:28 final size:28
Alignment explanation
Indices: 39011464--39011519 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
39011454 GTTCACCCCT
39011464 TACAAAGAAGTATTCGCTCAGTTGATAA
1 TACAAAGAAGTATTCGCTCAGTTGATAA
*
39011492 TACAAATAAGTATTCGCTCAGTTGATAA
1 TACAAAGAAGTATTCGCTCAGTTGATAA
39011520 ACGAGCTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (28 bp):
TACAAAGAAGTATTCGCTCAGTTGATAA
Done.