Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 23 of 30
Found at i:3790742 original size:41 final size:41
Alignment explanation
Indices: 3790683--3790776 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3790673 CTGCCAAGAA
*
3790683 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3790724 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3790765 ATGTATCGATAC
1 ATGTATCGATAC
3790777 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3790758 original size:21 final size:21
Alignment explanation
Indices: 3790683--3790758 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3790673 CTGCCAAGAA
* *
3790683 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3790704 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3790724 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3790745 ATGTATCGATACAT
1 ATGTATCGATACAT
3790759 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3793222 original size:13 final size:13
Alignment explanation
Indices: 3793204--3793242 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3793194 ATAATCACCC
*
3793204 TGTATCGATACAG
1 TGTATCGATACAA
3793217 TGTATCGATACAA
1 TGTATCGATACAA
3793230 TGTATCGATACAA
1 TGTATCGATACAA
3793243 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3793253 original size:20 final size:20
Alignment explanation
Indices: 3793228--3793306 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
3793218 GTATCGATAC
3793228 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3793248 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
3793273 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
3793293 CATGTATCGATACA
1 AATGTATCGATACA
3793307 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3795341 original size:15 final size:15
Alignment explanation
Indices: 3795321--3795351 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3795311 ATTTTGTTTG
*
3795321 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3795336 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3795351 G
1 G
3795352 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3799432 original size:13 final size:13
Alignment explanation
Indices: 3799414--3799439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3799404 CAATTTTTTG
3799414 TGTATCGATACAT
1 TGTATCGATACAT
3799427 TGTATCGATACAT
1 TGTATCGATACAT
3799440 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3799524 original size:20 final size:20
Alignment explanation
Indices: 3799499--3799571 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3799489 CAACTTTTTT
3799499 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3799519 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3799540 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3799560 ATGTATCGATAC
1 ATGTATCGATAC
3799572 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3799537 original size:41 final size:41
Alignment explanation
Indices: 3799478--3799571 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3799468 CTGCCAAGAA
*
3799478 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3799519 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3799560 ATGTATCGATAC
1 ATGTATCGATAC
3799572 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3799553 original size:21 final size:21
Alignment explanation
Indices: 3799478--3799553 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3799468 CTGCCAAGAA
* *
3799478 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3799499 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3799519 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3799540 ATGTATCGATACAT
1 ATGTATCGATACAT
3799554 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3802347 original size:13 final size:13
Alignment explanation
Indices: 3802329--3802355 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3802319 ACAATTGAGT
3802329 ATGTATCGATACA
1 ATGTATCGATACA
3802342 ATGTATCGATACA
1 ATGTATCGATACA
3802355 A
1 A
3802356 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3803497 original size:31 final size:32
Alignment explanation
Indices: 3803427--3803506 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 32
3803417 GATACACTGA
**
3803427 AGAATGTATCAATACATTTGGGTCAAAAAACCT
1 AGAATGTATTGATACATTTGGGTC-AAAAACCT
* *
3803460 AGAATGTATTGATACATTTGGGTC-AAATCTT
1 AGAATGTATTGATACATTTGGGTCAAAAACCT
3803491 AGAATGTATTGATACA
1 AGAATGTATTGATACA
3803507 ACTAAAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 21 0.49
33 22 0.51
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (32 bp):
AGAATGTATTGATACATTTGGGTCAAAAACCT
Found at i:3803994 original size:39 final size:39
Alignment explanation
Indices: 3803951--3804064 Score: 104
Period size: 39 Copynumber: 2.9 Consensus size: 39
3803941 GAAGTGTCTA
* *
3803951 CAAGGTCATTTTAATAATTTTATGTCAAAACTAAGTTTT
1 CAAGGTCATTTTAATAATTTTATATCAAAACCAAGTTTT
* * ** * * **
3803990 CAAGGTCGTATTAGCACTTTTATATCAAAATCGAACCTTT
1 CAAGGTCATTTTAATAATTTTATATCAAAA-CCAAGTTTT
* *
3804030 -AGGGTCATTTTAATAACTTTATATCAAAACCAAGT
1 CAAGGTCATTTTAATAATTTTATATCAAAACCAAGT
3804065 CCTTTAGGTC
Statistics
Matches: 55, Mismatches: 19, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
38 3 0.05
39 46 0.84
40 6 0.11
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (39 bp):
CAAGGTCATTTTAATAATTTTATATCAAAACCAAGTTTT
Found at i:3804083 original size:78 final size:76
Alignment explanation
Indices: 3803953--3804197 Score: 258
Period size: 78 Copynumber: 3.1 Consensus size: 76
3803943 AGTGTCTACA
*
3803953 AGGTCATTTTAATAATTTTATGTCAAAACTAAGT-TTTCAAGGTCGTATTAGCACTTTTATATCA
1 AGGTCATTTTAATAATTTTATGTCAAAACCAAGTCTTT--AGGTCGTATTAGCACTTTTATATCA
3804017 AAATCGAACCTTT
64 AAATCGAACCTTT
* * ** *
3804030 AGGGTCATTTTAATAACTTTATATCAAAACCAAGTCCTTTAGGTCGTGGTAGCACTTTTATGTCA
1 A-GGTCATTTTAATAATTTTATGTCAAAACCAAGT-CTTTAGGTCGTATTAGCACTTTTATATC-
3804095 AAAATCGAACCTTT
63 AAAATCGAACCTTT
*** ** * * * *
3804109 AAAACATTTTAATTTTTTTATGTCAAAACCAGGTCTTTATAGTCATATTAGCACTTTCATATCAA
1 AGGTCATTTTAATAATTTTATGTCAAAACCAAGTCTTTA-GGTCGTATTAGCACTTTTATATCAA
* * *
3804174 AACCAAACTTTT
65 AATCGAACCTTT
3804186 AAGGTCATTTTA
1 -AGGTCATTTTA
3804198 GCATTTTAGG
Statistics
Matches: 136, Mismatches: 26, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
77 17 0.12
78 101 0.74
79 15 0.11
80 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (76 bp):
AGGTCATTTTAATAATTTTATGTCAAAACCAAGTCTTTAGGTCGTATTAGCACTTTTATATCAAA
ATCGAACCTTT
Found at i:3804599 original size:21 final size:21
Alignment explanation
Indices: 3804573--3804617 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3804563 AAGATAACGC
3804573 ATGAATAATAGGTACCAAGTT
1 ATGAATAATAGGTACCAAGTT
*
3804594 ATGAATAATAGGTACCGAGTT
1 ATGAATAATAGGTACCAAGTT
3804615 ATG
1 ATG
3804618 CAGGCGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (21 bp):
ATGAATAATAGGTACCAAGTT
Found at i:3807990 original size:13 final size:13
Alignment explanation
Indices: 3807972--3807996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3807962 CACTAGTTTT
3807972 ATGTATCGATACA
1 ATGTATCGATACA
3807985 ATGTATCGATAC
1 ATGTATCGATAC
3807997 TGAGCGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3808023 original size:53 final size:53
Alignment explanation
Indices: 3807932--3808040 Score: 173
Period size: 53 Copynumber: 2.1 Consensus size: 53
3807922 CAATTCAAGT
* ** *
3807932 ATGTATCGATACTGAGCGAGTTTTTACTGTCACTAGTTTTATGTATCGATACA
1 ATGTATCGATACTGAGCGAGTTTTAACTACCACCAGTTTTATGTATCGATACA
*
3807985 ATGTATCGATACTGAGCGAGTTTTAACTACCACCAGTTTTATGTATTGATACA
1 ATGTATCGATACTGAGCGAGTTTTAACTACCACCAGTTTTATGTATCGATACA
3808038 ATG
1 ATG
3808041 AAGTATGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (53 bp):
ATGTATCGATACTGAGCGAGTTTTAACTACCACCAGTTTTATGTATCGATACA
Found at i:3808095 original size:20 final size:19
Alignment explanation
Indices: 3808044--3808095 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3808034 TACAATGAAG
3808044 TATGTATCAATACTAAGAA
1 TATGTATCAATACTAAGAA
* * *
3808063 CAAGTATCGATACTAAGCAA
1 TATGTATCAATACTAAG-AA
3808083 TATGTATCAATAC
1 TATGTATCAATAC
3808096 ATCTGGGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (19 bp):
TATGTATCAATACTAAGAA
Found at i:3815275 original size:15 final size:15
Alignment explanation
Indices: 3815257--3815287 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3815247 CAAGTCAACT
3815257 TCTTCATCATCATCA
1 TCTTCATCATCATCA
*
3815272 TCTTCTTCATCATCA
1 TCTTCATCATCATCA
3815287 T
1 T
3815288 TGATGGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (15 bp):
TCTTCATCATCATCA
Found at i:3817626 original size:153 final size:154
Alignment explanation
Indices: 3817346--3817633 Score: 368
Period size: 153 Copynumber: 1.9 Consensus size: 154
3817336 AAAGGGCTCG
*
3817346 AAAATAATCATAAAAAGGTGAACCTATCCTAAATGTATACTTTTGGCATAAAAGCATCTTGTTGA
1 AAAATAATCATAAAAAGGTGAACCTATCCTAAATGTACACTTTTGGCATAAAAGCATCTTGTTGA
* * * * * * * *
3817411 CTACCTAGGACTCTATTTTTGGGAAATTACAAAAATATCTCTAGACATATCTTTGACATGAAAGT
66 CTACCTAGGACTCTAGTTCTAGAAAATAACAAAAATACCTCTAAACATACCTTTGACATGAAAGT
3817476 ATCTCGGCAACTCTAAAAGACTCA
131 ATCTCGGCAACTCTAAAAGACTCA
* * * * *
3817500 AAAATAATTATAAAACGTTGAACTTATCCTAAATGTACATTTTTGGCAT-AAAGCATCTT-TGTG
1 AAAATAATCATAAAAAGGTGAACCTATCCTAAATGTACACTTTTGGCATAAAAGCATCTTGT-TG
* * *
3817563 ACTACCTAGGACT-TGGTTCTAGAAAGATAAC-AAAATGCCTCTAAAGTATACCTTTGACATGAA
65 ACTACCTAGGACTCTAGTTCTAGAAA-ATAACAAAAATACCTCTAAA-CATACCTTTGACATGAA
3817626 AGTATCTC
128 AGTATCTC
3817634 AATAACCTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
152 19 0.17
153 52 0.46
154 43 0.38
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (154 bp):
AAAATAATCATAAAAAGGTGAACCTATCCTAAATGTACACTTTTGGCATAAAAGCATCTTGTTGA
CTACCTAGGACTCTAGTTCTAGAAAATAACAAAAATACCTCTAAACATACCTTTGACATGAAAGT
ATCTCGGCAACTCTAAAAGACTCA
Found at i:3821092 original size:105 final size:105
Alignment explanation
Indices: 3820539--3821098 Score: 324
Period size: 105 Copynumber: 5.3 Consensus size: 105
3820529 CCGTACAACC
** * ** * * * *
3820539 AGGTTGAGTGGGATGAAACCATACGAGTTAAC-AAAAAGTGATCGAGGCAGAACCTAGGTCGAAA
1 AGGTTGACAGGGATGAAACCATACGAGTCAACGAAGGA-TGACCAAGGCAGAACCTAAGTCAAAA
* *
3820603 AGGAGTTGGCCTA-GATGAAACCATACAA-TGAACAAGTTTAA
65 AAGAGTTGGTC-AGGATGAAACCATACAACT-AACAAGTTTAA
* ** * * ** * * * * **
3820644 AAGTTGACCA-CAAGGAAACTATACGAGTCAGTGGAA-GATAACCATGGCAAAACATAAGTTGAA
1 AGGTTGA-CAGGGATGAAACCATACGAGTCA-ACGAAGGATGACCAAGGCAGAACCTAAGTCAAA
* * *
3820707 AATGAGTTGGTCAGGAT-AAAGCAATACAACCAACAAGTTTAA
64 AAAGAGTTGGTCAGGATGAAA-CCATACAACTAACAAGTTTAA
* * * * * * *
3820749 AGGTTGATTA-GGATGAAACCATACAAGTTAACAAAAGG-TTAGCAAGGC-GAAACCTAAGTCAT
1 AGGTTGA-CAGGGATGAAACCATACGAGTCAAC-GAAGGATGACCAAGGCAG-AACCTAAGTCAA
** * ** *
3820811 AATGGAGTTAGTCAGGACAAAACCATACAACCAACAAGTTTAA
63 AAAAGAGTTGGTCAGGATGAAACCATACAACTAACAAGTTTAA
* ** * * * **
3820854 A-GTTAACAAAGATAAAATCCTATA--AGTCAACGAAGGATGACCATGGTTA-AACCTAAGT-TG
1 AGGTTGACAGGGATGAAA-CC-ATACGAGTCAACGAAGGATGACCAAGG-CAGAACCTAAGTCAA
** * *
3820914 AAAAGAAGTT-CACTAGAATGAGACCATACAACTAACAAGTTTAA
63 AAAAG-AGTTGGTC-AGGATGAAACCATACAACTAACAAGTTTAA
* * * ** *
3820958 AGGTTGACCGAGAT-AAAGCCACATAAGTCAATGAAGGATGACCAAGGCAGAACCTAAGTCAAAA
1 AGGTTGACAGGGATGAAA-CCATACGAGTCAACGAAGGATGACCAAGGCAGAACCTAAGTCAAAA
* *
3821022 AAGAGTTGGTCAGGATGAAACCATATAACTAATAAGTTTAA
65 AAGAGTTGGTCAGGATGAAACCATACAACTAACAAGTTTAA
*
3821063 AGGTTTACAGGGATGAAACCATACGAGTCAACGAAG
1 AGGTTGACAGGGATGAAACCATACGAGTCAACGAAG
3821099 AGCAGCCGAA
Statistics
Matches: 338, Mismatches: 92, Indels: 50
0.70 0.19 0.10
Matches are distributed among these distances:
103 11 0.03
104 71 0.21
105 237 0.70
106 17 0.05
107 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (105 bp):
AGGTTGACAGGGATGAAACCATACGAGTCAACGAAGGATGACCAAGGCAGAACCTAAGTCAAAAA
AGAGTTGGTCAGGATGAAACCATACAACTAACAAGTTTAA
Found at i:3821166 original size:86 final size:87
Alignment explanation
Indices: 3821019--3821185 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 87
3821009 ACCTAAGTCA
* * * * *
3821019 AAAAAGAGTTGGTCAGGATGAAACCATATAACTAATAAGTTTAAAGGTTTACAGGGATGAAACCA
1 AAAAAGAGTTGGCCAGGATGAAACCA-ATAACCAACAAGTTTAAAGGTTGACAGAGATGAAACCA
*
3821084 TACGAGTCAACGAAGAGCAGCCG
65 TACGAGTCAACAAAGAGCAGCCG
**
3821107 AAAAAGAGTTGGCC-GAGATGAAACC-ATAACCAACAAGTTTAAAGGTTGACCA-AGATGAAATT
1 AAAAAGAGTTGGCCAG-GATGAAACCAATAACCAACAAGTTTAAAGGTTGA-CAGAGATGAAACC
*
3821169 ATATGAGTCAACAAAGA
64 ATACGAGTCAACAAAGA
3821186 ATGACCAAGG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 43 0.63
87 3 0.04
88 22 0.32
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (87 bp):
AAAAAGAGTTGGCCAGGATGAAACCAATAACCAACAAGTTTAAAGGTTGACAGAGATGAAACCAT
ACGAGTCAACAAAGAGCAGCCG
Found at i:3821479 original size:105 final size:104
Alignment explanation
Indices: 3821105--3821572 Score: 323
Period size: 105 Copynumber: 4.5 Consensus size: 104
3821095 GAAGAGCAGC
* ** *
3821105 CGAAAAAGAGTTGGCCGAGATGAAACCAT--AACCAACAAGTTTAAAGGTTGACCA-AGATGAAA
1 CGAAAAAGAGTTGGCTGAGACAAAACCATACAACCAACAAGTTTAAAGGTTAACCAGAGA--AAA
* *
3821167 -TTATATGAGTCAACAAAGAATGACCAAGGTGAAACCTAAGT
64 CCT-TATGAGTCAACAAAGGATGACCAAGGTGAAACCTAAGT
* * * *
3821208 --AAAAAGGGATTGGTTGAGACAAAACCATACAACCAACAAGTTTAAAGGTTGAGCAGA-AAGAA
1 CGAAAAAGAG-TTGGCTGAGACAAAACCATACAACCAACAAGTTTAAAGGTTAACCAGAGAA-AA
* * * * *
3821270 CCATATAAGTCACCGAAAGG--GACCAAGATGGAACCTAAGT
64 CCTTATGAGTCAAC-AAAGGATGACCAAGGTGAAACCTAAGT
* * ** * * * * * *
3821310 CAAAAAAGAGTTGG-TCAAGATGAAACCATACAACTAAAAAGTTTAAAGATTAGCTAGGACAAAA
1 CGAAAAAGAGTTGGCT-GAGACAAAACCATACAACCAACAAGTTTAAAGGTTAACCA-GAGAAAA
* * *
3821374 CCTTATGAGTCAATAAAGGATGACCAAGGCGAAACTTAAGT
64 CCTTATGAGTCAACAAAGGATGACCAAGGTGAAACCTAAGT
* * **
3821415 CGAAAAAGAGTTGGCTGAGACAAAACCATAAAACCAATAAGTTTAAAGGTTAATTATGAGAAAAC
1 CGAAAAAGAGTTGGCTGAGACAAAACCATACAACCAACAAGTTTAAAGGTTAACCA-GAGAAAAC
* * ** * * * * *
3821480 CATACGAGTTGACAAAAGG-TGACTAGGGAGGAACCTAAAT
65 CTTATGAGTCAAC-AAAGGATGACCAAGGTGAAACCTAAGT
* * * * *
3821520 TGAAAAGGAGTTGG-TCGAGATAAAATCC-TAAAACTAACAAGTTTAAAGGTTAA
1 CGAAAAAGAGTTGGCT-GAGACAAAA-CCATACAACCAACAAGTTTAAAGGTTAA
3821573 TCGGGACAAA
Statistics
Matches: 287, Mismatches: 60, Indels: 34
0.75 0.16 0.09
Matches are distributed among these distances:
101 7 0.02
102 35 0.12
103 50 0.17
104 51 0.18
105 136 0.47
106 8 0.03
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (104 bp):
CGAAAAAGAGTTGGCTGAGACAAAACCATACAACCAACAAGTTTAAAGGTTAACCAGAGAAAACC
TTATGAGTCAACAAAGGATGACCAAGGTGAAACCTAAGT
Found at i:3821583 original size:210 final size:207
Alignment explanation
Indices: 3821170--3821567 Score: 464
Period size: 210 Copynumber: 1.9 Consensus size: 207
3821160 GATGAAATTA
* * *
3821170 TATGAGTCAACAAAGAATGACCAAGGTGAAACCTAAGTAAAAAGGGATTGGTTGAGACAAAACCA
1 TATGAGTCAACAAAGAATGACCAAGGCGAAACCTAAGTAAAAAGAGATTGGCTGAGACAAAACCA
* * * *
3821235 TACAACCAACAAGTTTAAAGGTTGAGCAGAAAGAACCATATAAGTCACCGAAAGGGACCAAGATG
66 TAAAACCAACAAGTTTAAAGGTTAAGCAGAAAGAACCATACAAGTCACCAAAAGGGACCAAGATG
* * *
3821300 GAACCTAAGTCAAAAAAGAGTTGGTCAAGATGAAACCATACAACTAAAAAGTTTAAAGATTAGCT
131 GAACCTAAATCAAAAAAGAGTTGGTCAAGATAAAACCATAAAACTAAAAAGTTTAAAGATTAGCT
3821365 AGGACAAAACCT
196 AGGACAAAACCT
* * *
3821377 TATGAGTCAATAAAGGATGACCAAGGCGAAACTTAAGTCGAAAAAGAG-TTGGCTGAGACAAAAC
1 TATGAGTCAACAAAGAATGACCAAGGCGAAACCTAAGT--AAAAAGAGATTGGCTGAGACAAAAC
* ** * * *
3821441 CATAAAACCAATAAGTTTAAAGGTTAATTATGAGAA-AACCATACGAGTTGA-CAAAAGGTGACT
64 CATAAAACCAACAAGTTTAAAGGTTAAGCA-GA-AAGAACCATACAAG-TCACCAAAAGG-GACC
* ** * * *
3821504 AGGGA-GGAACCTAAATTGAAAAGGAGTTGGTCGAGATAAAATCC-TAAAACTAACAAGTTTAAA
125 A-AGATGGAACCTAAATCAAAAAAGAGTTGGTCAAGATAAAA-CCATAAAACTAAAAAGTTTAAA
3821567 G
188 G
3821568 GTTAATCGGG
Statistics
Matches: 158, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
207 34 0.22
208 40 0.25
209 24 0.15
210 56 0.35
211 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (207 bp):
TATGAGTCAACAAAGAATGACCAAGGCGAAACCTAAGTAAAAAGAGATTGGCTGAGACAAAACCA
TAAAACCAACAAGTTTAAAGGTTAAGCAGAAAGAACCATACAAGTCACCAAAAGGGACCAAGATG
GAACCTAAATCAAAAAAGAGTTGGTCAAGATAAAACCATAAAACTAAAAAGTTTAAAGATTAGCT
AGGACAAAACCT
Found at i:3827239 original size:153 final size:154
Alignment explanation
Indices: 3826949--3827271 Score: 366
Period size: 153 Copynumber: 2.1 Consensus size: 154
3826939 ATAACCTTAG
* *
3826949 AAGACTCAAAAATAATCATAAAAGGGTGAACCTACCCTAAATGTACACCTTTGGCATAAAGCATC
1 AAGACTCAAAAATAATCATAAAAGGGTGAACCTACCCTAAATGTACACCTTTGACATAAAGAATC
* * * * * ** * * *
3827014 CCGGTGACTATCTAAGACTCAGTTTTAAAGAAATTACCAAAATACCTTTGAGATATACCTTCAAT
66 CCAGTGACTACCTAAGACTCAATTCTAAAGAAATTAACAAAATACCACTGAAAAATACCTTCAAC
*
3827079 ATGAAAGTATCCT-GGCAACCCAAA
131 ATGAAAGTA-CCTCAGCAACCCAAA
* *
3827103 AAGACTCAAAAATAATCATAAAA-GGTGAACCTATCCTAAATGTACACTTTTGACATAAAAGAAT
1 AAGACTCAAAAATAATCATAAAAGGGTGAACCTACCCTAAATGTACACCTTTGACAT-AAAGAAT
* * * * * *
3827167 CCTAGTGCCTACCTAGGACTCAATTCT-AAGAAAATTAACAAAATGCCACT-AAAAATATCTTCG
65 CCCAGTGACTACCTAAGACTCAATTCTAAAG-AAATTAACAAAATACCACTGAAAAATACCTTCA
* *
3827230 ACATGAAAGTACCTCAGTAACCCTAA
129 ACATGAAAGTACCTCAGCAACCCAAA
* *
3827256 AGGACTAAAAAATAAT
1 AAGACTCAAAAATAAT
3827272 ATAGAATGAC
Statistics
Matches: 141, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
152 3 0.02
153 74 0.52
154 64 0.45
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (154 bp):
AAGACTCAAAAATAATCATAAAAGGGTGAACCTACCCTAAATGTACACCTTTGACATAAAGAATC
CCAGTGACTACCTAAGACTCAATTCTAAAGAAATTAACAAAATACCACTGAAAAATACCTTCAAC
ATGAAAGTACCTCAGCAACCCAAA
Found at i:3827881 original size:21 final size:22
Alignment explanation
Indices: 3827856--3827902 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3827846 TTAAAATTAC
*
3827856 AAATGGTCCTCAAA-ATG-TTAA
1 AAATGG-CCTAAAACATGTTTAA
3827877 AAAT-GCCTAAAACATGTTTAA
1 AAATGGCCTAAAACATGTTTAA
3827898 AAATG
1 AAATG
3827903 CATCAAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 12 0.55
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (22 bp):
AAATGGCCTAAAACATGTTTAA
Found at i:3827910 original size:21 final size:20
Alignment explanation
Indices: 3827865--3827911 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
3827855 CAAATGGTCC
*
3827865 TCAAA-ATGTTAAAAATGCC
1 TCAAACATGTTAAAAATGCA
*
3827884 TAAAACATGTTTAAAAATGCA
1 TCAAACATG-TTAAAAATGCA
3827905 TCAAACA
1 TCAAACA
3827912 CACTTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 16 0.70
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (20 bp):
TCAAACATGTTAAAAATGCA
Found at i:3829659 original size:20 final size:20
Alignment explanation
Indices: 3829634--3829689 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3829624 AAATAAGCTC
*
3829634 TCTTTTT-TCTTTTTTTTTT
1 TCTTTTTATCTTTTTTCTTT
3829653 ATCTTTTTTATCTTTTTTCTTT
1 -TC-TTTTTATCTTTTTTCTTT
*
3829675 TCTTTTTCTCTTTTT
1 TCTTTTTATCTTTTT
3829690 CTATGGAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
21 7 0.22
22 11 0.34
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (20 bp):
TCTTTTTATCTTTTTTCTTT
Found at i:3829680 original size:29 final size:29
Alignment explanation
Indices: 3829634--3829689 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3829624 AAATAAGCTC
*
3829634 TCTTTTTTCTTTTTTTTTTATCTTTTTTA
1 TCTTTTTTCTTTTCTTTTTATCTTTTTTA
*
3829663 TCTTTTTTCTTTTCTTTTTCTCTTTTT
1 TCTTTTTTCTTTTCTTTTTATCTTTTT
3829690 CTATGGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (29 bp):
TCTTTTTTCTTTTCTTTTTATCTTTTTTA
Found at i:3833909 original size:25 final size:25
Alignment explanation
Indices: 3833875--3833924 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3833865 AAAGCCATAT
*
3833875 TGTATTAATGCATGCCTATTGTATC
1 TGTATCAATGCATGCCTATTGTATC
3833900 TGTATCAATGCATGCCTATTGTATC
1 TGTATCAATGCATGCCTATTGTATC
3833925 GATATAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TGTATCAATGCATGCCTATTGTATC
Found at i:3834671 original size:12 final size:12
Alignment explanation
Indices: 3834629--3834672 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
3834619 AACAAAAAGC
3834629 AAAAAGAGAATAA
1 AAAAAGA-AATAA
3834642 AAAAGAGAAA-AA
1 AAAA-AGAAATAA
3834654 AGAAAAGAAATAA
1 A-AAAAGAAATAA
3834667 AAAAAG
1 AAAAAG
3834673 TGAGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 13 0.46
13 12 0.43
14 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (12 bp):
AAAAAGAAATAA
Found at i:3834864 original size:61 final size:62
Alignment explanation
Indices: 3834769--3834894 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 62
3834759 TTTATAAAAG
* * *
3834769 CTTGATCATCCTAAAACATGTTTAGGGAGTGATAGCTTTAAGATTCTGCTTAAG-TTGTTTT
1 CTTGATCATCCTAAAACATGTTTAGGGAGTGATAGCTTCAAGATTCTACCTAAGATTGTTTT
* * *
3834830 CTTGATGATCTTAAAACATGTTTAGGGAGTGATAGCTTCAAGATTCTACCTGAGATTGTTTT
1 CTTGATCATCCTAAAACATGTTTAGGGAGTGATAGCTTCAAGATTCTACCTAAGATTGTTTT
3834892 CTT
1 CTT
3834895 CATCCTCTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
61 48 0.83
62 10 0.17
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (62 bp):
CTTGATCATCCTAAAACATGTTTAGGGAGTGATAGCTTCAAGATTCTACCTAAGATTGTTTT
Found at i:3835721 original size:58 final size:58
Alignment explanation
Indices: 3835648--3835866 Score: 253
Period size: 58 Copynumber: 3.8 Consensus size: 58
3835638 TACTTTCATC
* * ** ** * **
3835648 ACTTTTATGTCATTTTATGAATGCTGACACCATTTAAGTCATTTTAGATGACTTAGGG
1 ACTTTGATGTAATTTTATGAATTTTGACGTCATTTAGGTCATTTTCCATGACTTAGGG
* * *
3835706 ACTTTGATGTAATTTTATGAATTTTTACGTCATTTAGGTTATTTTCCATGATTTAGGG
1 ACTTTGATGTAATTTTATGAATTTTGACGTCATTTAGGTCATTTTCCATGACTTAGGG
* * *
3835764 ACTTTGAAGCAATTTTATGAATTTTGATGTCATTTTAGGTCATTTTCCAT-ATCTTAGGG
1 ACTTTGATGTAATTTTATGAATTTTGACGTCA-TTTAGGTCATTTTCCATGA-CTTAGGG
* *
3835823 AC-TTGATGTAATTTTATGAATTTTGATGTCATTTAGGTTATTTT
1 ACTTTGATGTAATTTTATGAATTTTGACGTCATTTAGGTCATTTT
3835867 TCGTAATCTA
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
57 12 0.09
58 102 0.74
59 24 0.17
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (58 bp):
ACTTTGATGTAATTTTATGAATTTTGACGTCATTTAGGTCATTTTCCATGACTTAGGG
Found at i:3835868 original size:58 final size:59
Alignment explanation
Indices: 3835695--3835866 Score: 262
Period size: 58 Copynumber: 3.0 Consensus size: 59
3835685 GTCATTTTAG
* *
3835695 ATGA-CTTAGGGACTTTGATGTAATTTTATGAATTTTTACGTCATTTAGGTTATTTTCC
1 ATGATCTTAGGGACTTTGATGTAATTTTATGAATTTTGATGTCATTTAGGTTATTTTCC
* * *
3835753 ATGAT-TTAGGGACTTTGAAGCAATTTTATGAATTTTGATGTCATTTTAGGTCATTTTCC
1 ATGATCTTAGGGACTTTGATGTAATTTTATGAATTTTGATGTCA-TTTAGGTTATTTTCC
3835812 AT-ATCTTAGGGAC-TTGATGTAATTTTATGAATTTTGATGTCATTTAGGTTATTTT
1 ATGATCTTAGGGACTTTGATGTAATTTTATGAATTTTGATGTCATTTAGGTTATTTT
3835867 TCGTAATCTA
Statistics
Matches: 103, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
57 12 0.12
58 67 0.65
59 24 0.23
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (59 bp):
ATGATCTTAGGGACTTTGATGTAATTTTATGAATTTTGATGTCATTTAGGTTATTTTCC
Found at i:3842833 original size:21 final size:20
Alignment explanation
Indices: 3842807--3842857 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3842797 AATGTGCTTA
3842807 AAAAGAAAGAAGAAGAATTAG
1 AAAAGAAAGAAG-AGAATTAG
* *
3842828 AAAAGAAAATAAGTGAATTAG
1 AAAAG-AAAGAAGAGAATTAG
3842849 AAAA-AAAGA
1 AAAAGAAAGA
3842858 TAATTGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
21 16 0.62
22 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.12
Consensus pattern (20 bp):
AAAAGAAAGAAGAGAATTAG
Found at i:3842860 original size:21 final size:21
Alignment explanation
Indices: 3842821--3842867 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3842811 GAAAGAAGAA
3842821 GAATTAGAAAAGAAAATAAGT
1 GAATTAGAAAAGAAAATAAGT
*
3842842 GAATTAGAAAA-AAAGATAATT
1 GAATTAGAAAAGAAA-ATAAGT
3842863 GAATT
1 GAATT
3842868 GCAAGATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (21 bp):
GAATTAGAAAAGAAAATAAGT
Found at i:3842908 original size:21 final size:20
Alignment explanation
Indices: 3842882--3842932 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3842872 GATAGTAATA
3842882 AAGAATTTGCTAATGAA-AAC
1 AAGAATTTGCTAA-GAAGAAC
*
3842902 AACGAATTGGCTAAGAAGAAC
1 AA-GAATTTGCTAAGAAGAAC
*
3842923 AAGAACTTGC
1 AAGAATTTGC
3842933 ATGATTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGAATTTGCTAAGAAGAAC
Found at i:3848506 original size:16 final size:16
Alignment explanation
Indices: 3848485--3848520 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3848475 ACTTTTGTTT
**
3848485 CTTTGCTTGTTTTTAA
1 CTTTGCTTGTACTTAA
3848501 CTTTGCTTGTACTTAA
1 CTTTGCTTGTACTTAA
3848517 CTTT
1 CTTT
3848521 CCTTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.58
Consensus pattern (16 bp):
CTTTGCTTGTACTTAA
Found at i:3849464 original size:13 final size:13
Alignment explanation
Indices: 3849446--3849470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3849436 TATATTGCTT
3849446 TGTATCGATACAG
1 TGTATCGATACAG
3849459 TGTATCGATACA
1 TGTATCGATACA
3849471 CGATCTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3851132 original size:14 final size:14
Alignment explanation
Indices: 3851111--3851172 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 14
3851101 TTGATACTTT
3851111 ACTGTTCATGTATC
1 ACTGTTCATGTATC
*
3851125 ATTGTTC----ATC
1 ACTGTTCATGTATC
3851135 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3851149 ACTGTTC----ATC
1 ACTGTTCATGTATC
3851159 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3851173 GATACATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
10 19 0.50
14 19 0.50
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (14 bp):
ACTGTTCATGTATC
Found at i:3851138 original size:24 final size:24
Alignment explanation
Indices: 3851111--3851172 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
3851101 TTGATACTTT
*
3851111 ACTGTTCATGTATCATTGTTCATC
1 ACTGTTCATGTATCACTGTTCATC
3851135 ACTGTTCATGTATCACTGTTCATC
1 ACTGTTCATGTATCACTGTTCATC
3851159 ACTGTTCATGTATC
1 ACTGTTCATGTATC
3851173 GATACATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (24 bp):
ACTGTTCATGTATCACTGTTCATC
Found at i:3851198 original size:11 final size:13
Alignment explanation
Indices: 3851169--3851195 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3851159 ACTGTTCATG
3851169 TATCGATACATTA
1 TATCGATACATTA
3851182 TATCGATACATTA
1 TATCGATACATTA
3851195 T
1 T
3851196 CGAAGCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:3851387 original size:13 final size:13
Alignment explanation
Indices: 3851365--3851421 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
3851355 TTTTACAATT
3851365 TGTATCGATACAA
1 TGTATCGATACAA
*
3851378 TGTATGGATACATAA
1 TGTATCGATAC--AA
3851393 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
3851410 TGTATCGATACA
1 TGTATCGATACA
3851422 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3851399 original size:32 final size:32
Alignment explanation
Indices: 3851363--3851440 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
3851353 ATTTTTACAA
*
3851363 TTTGTATCGATACAATGTATGGATACATAAGT
1 TTTGTATCGATACAATGTATCGATACATAAGT
3851395 TTTGTATCGATACAATGTATCGATACATAAGT
1 TTTGTATCGATACAATGTATCGATACATAAGT
3851427 TTTGTATCGATACA
1 TTTGTATCGATACA
3851441 TTGAATAATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (32 bp):
TTTGTATCGATACAATGTATCGATACATAAGT
Found at i:3851406 original size:19 final size:19
Alignment explanation
Indices: 3851378--3851441 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
3851368 ATCGATACAA
*
3851378 TGTATGGATACATAAGTTT
1 TGTATCGATACATAAGTTT
3851397 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTTT
3851410 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTTT
3851429 TGTATCGATACAT
1 TGTATCGATACAT
3851442 TGAATAATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATAAGTTT
Found at i:3851454 original size:20 final size:21
Alignment explanation
Indices: 3851408--3851507 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 21
3851398 GTATCGATAC
3851408 AATGTATCGATACA-T-AAGT
1 AATGTATCGATACATTGAAGT
**
3851427 TTTGTATCGATACATTGAA-T
1 AATGTATCGATACATTGAAGT
*
3851447 AATGTATCGATACATACATGCAAATT
1 AATGTATCGATACAT---TG--AAGT
3851473 AATGTATCGATACATTGAA-T
1 AATGTATCGATACATTGAAGT
3851493 AATGTATCGATACAT
1 AATGTATCGATACAT
3851508 GCAGGCAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
19 12 0.17
20 31 0.45
21 4 0.06
23 4 0.06
25 2 0.03
26 16 0.23
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTGAAGT
Found at i:3851477 original size:26 final size:25
Alignment explanation
Indices: 3851446--3851518 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 25
3851436 ATACATTGAA
3851446 TAATGTATCGATACATACATGCAAAT
1 TAATGTATCGATACAT-CATGCAAAT
3851472 TAATGTATCGATACAT--TG--AA-
1 TAATGTATCGATACATCATGCAAAT
*
3851492 TAATGTATCGATACATGCAGGCAAAT
1 TAATGTATCGATACAT-CATGCAAAT
3851518 T
1 T
3851519 TTCACACTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
20 16 0.40
21 2 0.05
23 3 0.08
25 2 0.05
26 17 0.43
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (25 bp):
TAATGTATCGATACATCATGCAAAT
Found at i:3851481 original size:46 final size:46
Alignment explanation
Indices: 3851429--3851518 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
3851419 ACATAAGTTT
*
3851429 TGTATCGATACATTGAATAATGTATCGATACATACATGCAAATTAA
1 TGTATCGATACATTGAATAATGTATCGATACATACAGGCAAATTAA
*
3851475 TGTATCGATACATTGAATAATGTATCGATACATGCAGGCAAATT
1 TGTATCGATACATTGAATAATGTATCGATACATACAGGCAAATT
3851519 TTCACACTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (46 bp):
TGTATCGATACATTGAATAATGTATCGATACATACAGGCAAATTAA
Found at i:3857725 original size:13 final size:13
Alignment explanation
Indices: 3857707--3857732 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3857697 TCACTGTTCA
3857707 TGTATCGATACAT
1 TGTATCGATACAT
3857720 TGTATCGATACAT
1 TGTATCGATACAT
3857733 GTTGAGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3858558 original size:372 final size:372
Alignment explanation
Indices: 3857873--3858607 Score: 1434
Period size: 372 Copynumber: 2.0 Consensus size: 372
3857863 AATCATAATG
*
3857873 TCTCCAACGGATACATCCTTGATCAAGCCTATAAATACAGCATTCCAAGCAAGAAATTAAGAACA
1 TCTCCAACGAATACATCCTTGATCAAGCCTATAAATACAGCATTCCAAGCAAGAAATTAAGAACA
*
3857938 AGAAGTGCAAAATCAAGCTTATTCATCTATACAAAAATTCAAGAGCTTAGTATTAAGTTTTCTAT
66 AGAAGTGCAAAATCAAGCTTATTCATCCATACAAAAATTCAAGAGCTTAGTATTAAGTTTTCTAT
*
3858003 TGTTGTTTTTCTATAAAAGCTTTTTCATTCATTCCTTATACTAAAACTTCCACAAACACCAGCCT
131 TGTTGTTTTTCTATAAAAGCTCTTTCATTCATTCCTTATACTAAAACTTCCACAAACACCAGCCT
3858068 CGTAGAGGTCTATTGAGTTTGTAATTCTTTATTTCATTGTGTAAGATTGTATTCAACCTTGTTTG
196 CGTAGAGGTCTATTGAGTTTGTAATTCTTTATTTCATTGTGTAAGATTGTATTCAACCTTGTTTG
3858133 CAATCACTTGAGAATTCAGAGTATAATTCTCTAAGTGATTGAGAGGTTTTATCTTAGCCTTTGAA
261 CAATCACTTGAGAATTCAGAGTATAATTCTCTAAGTGATTGAGAGGTTTTATCTTAGCCTTTGAA
3858198 AAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAATAGAACCTC
326 AAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAATAGAACCTC
3858245 TCTCCAACGAATACATCCTTGATCAAGCCTATAAATACAGCATTCCAAGCAAGAAATTAAGAACA
1 TCTCCAACGAATACATCCTTGATCAAGCCTATAAATACAGCATTCCAAGCAAGAAATTAAGAACA
3858310 AGAAGTGCAAAATCAAGCTTATTCATCCATACAAAAATTCAAGAGCTTAGTATTAAGTTTTCTAT
66 AGAAGTGCAAAATCAAGCTTATTCATCCATACAAAAATTCAAGAGCTTAGTATTAAGTTTTCTAT
3858375 TGTTGTTTTTCTATAAAAGCTCTTTCATTCATTCCTTATACTAAAACTTCCACAAACACCAGCCT
131 TGTTGTTTTTCTATAAAAGCTCTTTCATTCATTCCTTATACTAAAACTTCCACAAACACCAGCCT
*
3858440 CGTAGAGGTCTATTGAGTTTGTAATTCTTTATTTCATTGTGTAAGGTTGTATTCAACCTTGTTTG
196 CGTAGAGGTCTATTGAGTTTGTAATTCTTTATTTCATTGTGTAAGATTGTATTCAACCTTGTTTG
3858505 CAATCACTTGAGAATTCAGAGTATAATTCTCTAAGTGATTGAGAGGTTTTATCTTAGCCTTTGAA
261 CAATCACTTGAGAATTCAGAGTATAATTCTCTAAGTGATTGAGAGGTTTTATCTTAGCCTTTGAA
3858570 AAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAA
326 AAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAA
3858608 GATAGGGAGG
Statistics
Matches: 359, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
372 359 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (372 bp):
TCTCCAACGAATACATCCTTGATCAAGCCTATAAATACAGCATTCCAAGCAAGAAATTAAGAACA
AGAAGTGCAAAATCAAGCTTATTCATCCATACAAAAATTCAAGAGCTTAGTATTAAGTTTTCTAT
TGTTGTTTTTCTATAAAAGCTCTTTCATTCATTCCTTATACTAAAACTTCCACAAACACCAGCCT
CGTAGAGGTCTATTGAGTTTGTAATTCTTTATTTCATTGTGTAAGATTGTATTCAACCTTGTTTG
CAATCACTTGAGAATTCAGAGTATAATTCTCTAAGTGATTGAGAGGTTTTATCTTAGCCTTTGAA
AAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAATAGAACCTC
Found at i:3858615 original size:35 final size:36
Alignment explanation
Indices: 3858545--3858699 Score: 164
Period size: 36 Copynumber: 4.5 Consensus size: 36
3858535 CTAAGTGATT
* **
3858545 GAGAGGTTTTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
*
3858581 GAGAGGTTCTATTTTAGCCCGTG-AAAAGATA-GG-
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
* ** *
3858614 GAG-GTTTCTATCTTAGCCTTTGAAAAAGATAAGGA
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
*
3858649 GAGAGGTTCTATTTTAGCCCGTG-AAAAGATA-GG-
1 GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
*
3858682 GAG-GTTTCTATCTTAGCC
1 GAGAGGTTCTATCTTAGCC
3858700 TTGAAAGATA
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
32 28 0.28
33 14 0.14
34 6 0.06
35 19 0.19
36 34 0.34
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCCGTGAAAAAGATAGGGA
Found at i:3858630 original size:32 final size:34
Alignment explanation
Indices: 3858545--3858699 Score: 167
Period size: 32 Copynumber: 4.6 Consensus size: 34
3858535 CTAAGTGATT
**
3858545 GAGAGGTTT-TATCTTAGCCTTTGAAAAAGATAGG
1 GAGAGGTTTCTATCTTAGCCCGTGAAAAAGATA-G
* *
3858579 GAGAGAGGTTCTATTTTAGCCCGTG-AAAAGATAG
1 GAGAG-GTTTCTATCTTAGCCCGTGAAAAAGATAG
**
3858613 G-GAGGTTTCTATCTTAGCCTTTGAAAAAGATAAG
1 GAGAGGTTTCTATCTTAGCCCGTGAAAAAGAT-AG
* *
3858647 GAGAGAGGTTCTATTTTAGCCCGTG-AAAAGATAG
1 GAGAG-GTTTCTATCTTAGCCCGTGAAAAAGATAG
3858681 G-GAGGTTTCTATCTTAGCC
1 GAGAGGTTTCTATCTTAGCC
3858700 TTGAAAGATA
Statistics
Matches: 101, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
32 28 0.28
33 13 0.13
34 13 0.13
35 21 0.21
36 26 0.26
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (34 bp):
GAGAGGTTTCTATCTTAGCCCGTGAAAAAGATAG
Found at i:3858663 original size:68 final size:68
Alignment explanation
Indices: 3858547--3858705 Score: 295
Period size: 68 Copynumber: 2.4 Consensus size: 68
3858537 AAGTGATTGA
*
3858547 GAGGTTT-TATCTTAGCCTTTGAAAAAGATAGGGAGAGAGGTTCTATTTTAGCCCGTGAAAAGAT
1 GAGGTTTCTATCTTAGCCTTTGAAAAAGATAAGGAGAGAGGTTCTATTTTAGCCCGTGAAAAGAT
3858611 AGG
66 AGG
3858614 GAGGTTTCTATCTTAGCCTTTGAAAAAGATAAGGAGAGAGGTTCTATTTTAGCCCGTGAAAAGAT
1 GAGGTTTCTATCTTAGCCTTTGAAAAAGATAAGGAGAGAGGTTCTATTTTAGCCCGTGAAAAGAT
3858679 AGG
66 AGG
3858682 GAGGTTTCTATCTTAGCC-TTGAAA
1 GAGGTTTCTATCTTAGCCTTTGAAA
3858706 GATAGTGTTG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
67 13 0.14
68 77 0.86
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (68 bp):
GAGGTTTCTATCTTAGCCTTTGAAAAAGATAAGGAGAGAGGTTCTATTTTAGCCCGTGAAAAGAT
AGG
Found at i:3860958 original size:16 final size:15
Alignment explanation
Indices: 3860907--3860959 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
3860897 AATAACTCAA
3860907 ATTCAAAACAACTTCT
1 ATTCAAAACAACTT-T
* * *
3860923 ATTTAATAGAACTCTT
1 ATTCAAAACAACT-TT
3860939 ATTCAAAACAACTTT
1 ATTCAAAACAACTTT
3860954 AATTCA
1 -ATTCA
3860960 TACAATCCCC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 26 0.90
17 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (15 bp):
ATTCAAAACAACTTT
Found at i:3869770 original size:206 final size:207
Alignment explanation
Indices: 3869392--3869798 Score: 807
Period size: 206 Copynumber: 2.0 Consensus size: 207
3869382 CTCAACGAGA
3869392 TGATGAGCGTGAGGAACAGCAAGCTATGGAAGCATGAGTTGTTGACTTTGATCCAAGGAATTCTC
1 TGATGAGCGTGAGGAACAGCAAGCTATGGAAGCATGAGTTGTTGACTTTGATCCAAGGAATTCTC
3869457 ACACTCATTACACAACATTTAGACACCTTGGATAAGCGGTTTACCACAATCGAGAATTACATCCG
66 ACACTCATTACACAACATTTAGACACCTTGGATAAGCGGTTTACCACAATCGAGAATTACATCCG
3869522 ACGTGATTTGACTAACTCTAGTGATGATGAGTGATAGGATTAGTCTTGGTGGTCTTTGTAATAGG
131 ACGTGATTTGACTAACTCTAGTGATGATGAGTGATAGGATTAGTCTTGGTGGTCTTTGTAATAGG
3869587 AGTTGTTGACTT
196 AGTTGTTGACTT
3869599 TGATGAGCGTGAGGAACAGCAAGCTATGGAAGCATGAGTTGTTGACTTTGATCCAAGGAATTCTC
1 TGATGAGCGTGAGGAACAGCAAGCTATGGAAGCATGAGTTGTTGACTTTGATCCAAGGAATTCTC
3869664 ACACTCATTACACAACATTTA-ACACCTTGGATAAGCGGTTTACCACAATCGAGAATTACATCCG
66 ACACTCATTACACAACATTTAGACACCTTGGATAAGCGGTTTACCACAATCGAGAATTACATCCG
3869728 ACGTGATTTGACTAACTCTAGTGATGATGAGTGATAGGATTAGTCTTGGTGGTCTTTGTAATAGG
131 ACGTGATTTGACTAACTCTAGTGATGATGAGTGATAGGATTAGTCTTGGTGGTCTTTGTAATAGG
3869793 AGTTGT
196 AGTTGT
3869799 CGTATTTATT
Statistics
Matches: 200, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 114 0.57
207 86 0.43
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (207 bp):
TGATGAGCGTGAGGAACAGCAAGCTATGGAAGCATGAGTTGTTGACTTTGATCCAAGGAATTCTC
ACACTCATTACACAACATTTAGACACCTTGGATAAGCGGTTTACCACAATCGAGAATTACATCCG
ACGTGATTTGACTAACTCTAGTGATGATGAGTGATAGGATTAGTCTTGGTGGTCTTTGTAATAGG
AGTTGTTGACTT
Found at i:3870028 original size:24 final size:25
Alignment explanation
Indices: 3869996--3870045 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3869986 AATGAGAAAT
3869996 GTTTTAAATAAA-TTTTTTTATAAA
1 GTTTTAAATAAATTTTTTTTATAAA
3870020 GTTTTAAATAAATTTTTTTTATAAA
1 GTTTTAAATAAATTTTTTTTATAAA
3870045 G
1 G
3870046 GGGGAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (25 bp):
GTTTTAAATAAATTTTTTTTATAAA
Found at i:3870682 original size:13 final size:13
Alignment explanation
Indices: 3870664--3870690 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3870654 ACATTATGCT
3870664 TTGTATCGATACA
1 TTGTATCGATACA
3870677 TTGTATCGATACA
1 TTGTATCGATACA
3870690 T
1 T
3870691 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3870724 original size:20 final size:19
Alignment explanation
Indices: 3870675--3870728 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
3870665 TGTATCGATA
***
3870675 CATTGTATCGATACATGTT
1 CATTGTATCGATACACACT
*
3870694 CATTATATCGATACACACT
1 CATTGTATCGATACACACT
3870713 CAATTGTATCGATACA
1 C-ATTGTATCGATACA
3870729 TGAAACTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACACACT
Found at i:3876024 original size:20 final size:20
Alignment explanation
Indices: 3875987--3876025 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3875977 CTTTAATTGA
*
3875987 AATTTTTAATTAAGCTTTTC
1 AATTTTTAATTAAACTTTTC
3876007 AATTTTT-ATTAAAACTTTT
1 AATTTTTAATT-AAACTTTT
3876026 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTTAATTAAACTTTTC
Found at i:3876878 original size:153 final size:153
Alignment explanation
Indices: 3876549--3877054 Score: 585
Period size: 149 Copynumber: 3.4 Consensus size: 153
3876539 TTTTTCTTTG
* * * * * * * *
3876549 ATTTAAAGCTTGATGATCCTAAGCTTAAGTTTAAGCGATTGCATAGGCTAAAGGTTTTCAATCTT
1 ATTTAAAGCTTGATGATCCTAACCTTAAGCTTATGTGATTGCTTAAGCTAAAGGTTTTCAAGCAT
* * * *
3876614 TTTTAATGCCCAAGCATGAGAAAAATTTCTCCT-CTCAATGTTCTTG----TTTATTCAATTTAT
66 TTTTAATGGCCAAGCATGAGCAAAATTTCT-CTATTCAATGTTCTTGTTAATTTATTTAATTTAT
*
3876674 TCTTATATTTACTTTAAAGTTGTA
130 TGTTATATTTACTTTAAAGTTGTA
* * * * *
3876698 ATTTAAAGCTTGATGATCCCAAGCTTAAGCTTATTTGATTGCTTAAGCTGAAGATTTTCAAGCAT
1 ATTTAAAGCTTGATGATCCTAACCTTAAGCTTATGTGATTGCTTAAGCTAAAGGTTTTCAAGCAT
*
3876763 TTTTAGTGGCCAAGCATGAGCAAAATTTCTCTATTCAATGTTCTTGTTAATTTATTTAATTTATT
66 TTTTAATGGCCAAGCATGAGCAAAATTTCTCTATTCAATGTTCTTGTTAATTTATTTAATTTATT
* *
3876828 GTTTTATTTACTTTGAAGTTGTA
131 GTTATATTTACTTTAAAGTTGTA
* * * *
3876851 ATTTAAATCTTGATGATCATAACCTTAAGCTT-TG-G--TG----AGCTAAAGGTTTTTAAGCCT
1 ATTTAAAGCTTGATGATCCTAACCTTAAGCTTATGTGATTGCTTAAGCTAAAGGTTTTCAAGCAT
* *
3876908 TTTTAATGGCCAAGCATGAGCAAAATTTC-C-ATTTTAATATTCTTGTTAATTTATTTAATTTAT
66 TTTTAATGGCCAAGCATGAGCAAAATTTCTCTA-TTCAATGTTCTTGTTAATTTATTTAATTTAT
** *
3876971 TGTTGCATTTA-TTTCAAGTTGTA
130 TGTTATATTTACTTTAAAGTTGTA
* * *
3876994 ATTTAAAGCTTGATGATCCTAACCTTAAGCTTAGGTAATAGCTTAAGCTAAAGGTTTTCAA
1 ATTTAAAGCTTGATGATCCTAACCTTAAGCTTATGTGATTGCTTAAGCTAAAGGTTTTCAA
3877055 ACCTTTTAAG
Statistics
Matches: 303, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
143 42 0.14
144 40 0.13
145 44 0.15
147 1 0.00
148 2 0.01
149 95 0.31
151 16 0.05
152 1 0.00
153 62 0.20
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (153 bp):
ATTTAAAGCTTGATGATCCTAACCTTAAGCTTATGTGATTGCTTAAGCTAAAGGTTTTCAAGCAT
TTTTAATGGCCAAGCATGAGCAAAATTTCTCTATTCAATGTTCTTGTTAATTTATTTAATTTATT
GTTATATTTACTTTAAAGTTGTA
Found at i:3876965 original size:21 final size:21
Alignment explanation
Indices: 3876940--3876984 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3876930 AAATTTCCAT
*
3876940 TTTAATATTCTTGTT-AATTTA
1 TTTAAT-TTATTGTTGAATTTA
*
3876961 TTTAATTTATTGTTGCATTTA
1 TTTAATTTATTGTTGAATTTA
3876982 TTT
1 TTT
3876985 CAAGTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTAATTTATTGTTGAATTTA
Found at i:3877635 original size:20 final size:21
Alignment explanation
Indices: 3877585--3877636 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3877575 TTCTACAATT
*
3877585 TGTATCGATACAACAAGTTAA
1 TGTATCGATACAACAAGTGAA
* * *
3877606 TGTGTTGATAC-ATAAGTGAA
1 TGTATCGATACAACAAGTGAA
3877626 TGTATCGATAC
1 TGTATCGATAC
3877637 TGGACCTTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:3877751 original size:52 final size:52
Alignment explanation
Indices: 3877672--3877815 Score: 175
Period size: 52 Copynumber: 2.7 Consensus size: 52
3877662 ATTCTAGACA
* *
3877672 AAAAATGTAGCGATACATTTTTTATTGTATCGATACATTCTGGATTTTTGAC-C
1 AAAAA-GTATCGATACA-TTTTTATTGTATTGATACATTCTGGATTTTTGACTC
* * *
3877725 AAAAAGTATCGATACATGTTTCATTGTATTGATACATTTTGGGTTTTTGACTC
1 AAAAAGTATCGATACAT-TTTTATTGTATTGATACATTCTGGATTTTTGACTC
* *
3877778 -AAATGTATCGATACATTCTTTAATGTATTGATACATTC
1 AAAAAGTATCGATACATT-TTTATTGTATTGATACATTC
3877816 GGTTAAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
51 2 0.03
52 71 0.90
53 6 0.08
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (52 bp):
AAAAAGTATCGATACATTTTTATTGTATTGATACATTCTGGATTTTTGACTC
Found at i:3879775 original size:78 final size:78
Alignment explanation
Indices: 3879676--3879876 Score: 226
Period size: 79 Copynumber: 2.6 Consensus size: 78
3879666 AATAACAGGG
* * * * *
3879676 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
3879739 GAAAAAAAATCGGGA
64 GAAAAAAAACCGGGA
* *
3879754 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * *
3879819 GAATAAAGCCGGGG
65 AAAAAAAACCGGGA
* * *
3879833 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
3879877 GAAATAACGA
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 7 0.07
78 45 0.43
79 52 0.50
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (78 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCGGGA
Found at i:3879868 original size:28 final size:28
Alignment explanation
Indices: 3879828--3879899 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
3879818 GGAATAAAGC
** *
3879828 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3879856 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3879884 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3879900 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:3879957 original size:52 final size:52
Alignment explanation
Indices: 3879888--3880224 Score: 176
Period size: 52 Copynumber: 6.4 Consensus size: 52
3879878 AAATAACGAG
*
3879888 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
3879940 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
3879993 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* * **** * * *
3880044 GTTGGAGTATCCCC--TCG-AAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
3880099 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
3880153 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* * *
3880204 GTTAGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
3880225 GAGAATTGAT
Statistics
Matches: 214, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 3 0.01
49 2 0.01
50 2 0.01
51 38 0.18
52 79 0.37
53 33 0.15
54 28 0.13
55 18 0.08
56 2 0.01
57 4 0.02
58 4 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:3880076 original size:28 final size:28
Alignment explanation
Indices: 3880031--3880112 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
3880021 AGTGTTTTAG
* *
3880031 CGATAAA-ACCGGAGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
3880058 TCGA-AAATAACGGGGTTGGAGTAT-CCC
1 -CGATAAATAACGGGGTTGGAGTATCCCC
* *
3880085 CGATGATTAACGGGGTTGGAGTATCCCC
1 CGATAAATAACGGGGTTGGAGTATCCCC
3880113 GATTGTGAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.06
27 24 0.51
28 20 0.43
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
CGATAAATAACGGGGTTGGAGTATCCCC
Found at i:3880127 original size:107 final size:105
Alignment explanation
Indices: 3879774--3880166 Score: 332
Period size: 107 Copynumber: 3.7 Consensus size: 105
3879764 CCTTCGAAAA
* * * * * * * *
3879774 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
* *
3879839 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * *
3879881 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
3879946 GTAT-CCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * * *
3879983 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTTG-GAATAAAACCGGAGTT
3880047 GGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
3880092 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTTGG-AATAAAACCGGAGTTG
3880157 GAGTATCCCC
63 GAGTATCCCC
3880167 GATTATAGAA
Statistics
Matches: 220, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 46 0.21
105 20 0.09
106 19 0.09
107 71 0.32
108 32 0.15
109 27 0.12
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTTGGAATAAAACCGGAGTTGGAG
TATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:3880180 original size:212 final size:212
Alignment explanation
Indices: 3879821--3880226 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
3879811 TATTTTGGGA
* * * *
3879821 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
3879886 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
3879951 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTAGAATATCCCCGATTGTGGA
3880015 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
3880033 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
3880097 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
3880162 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGG
3880226 A
194 A
3880227 GAATTGATAA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 32 0.18
212 104 0.59
213 39 0.22
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:3880199 original size:51 final size:53
Alignment explanation
Indices: 3880103--3880221 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
3880093 AACGGGGTTG
* * *
3880103 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
3880157 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
3880208 GAATATCCTCGATT
1 GAGTATCCCCGATT
3880222 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:3883572 original size:28 final size:29
Alignment explanation
Indices: 3883544--3883626 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 29
3883534 GGAGTAAAAA
3883544 GTGCCACCAACTCGTGTGGGCTTTGAAAG
1 GTGCCACCAACTCGTGTGGGCTTTGAAAG
* * *
3883573 GTG--TCCTACTC-TTTGAGGAC--TGAAAG
1 GTGCCACCAACTCGTGTG-GG-CTTTGAAAG
*
3883599 GTGCCACCAACTTGTGTGGGCTTTGAAA
1 GTGCCACCAACTCGTGTGGGCTTTGAAA
3883627 ACAAAAAACA
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
26 12 0.30
27 9 0.22
28 8 0.20
29 11 0.28
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (29 bp):
GTGCCACCAACTCGTGTGGGCTTTGAAAG
Found at i:3883616 original size:55 final size:55
Alignment explanation
Indices: 3883521--3886137 Score: 3613
Period size: 55 Copynumber: 47.3 Consensus size: 55
3883511 ATAAAGTGTA
* * * * * *
3883521 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * ****
3883576 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAACAAAAAACA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT------AAGAGGTG
** * * * *
3883637 TCCTGCTCTTTGAGGACTGAAAAATGCCATCAACCTGTATGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * * *
3883692 CCCTGCTCTTTAAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3883747 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
3883802 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3883857 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
3883912 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3883967 TCCTGCTC-TTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884021 CCCTGCTCTTTGAGGACTGGAAA--TACCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * * **
3884075 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
** * *
3884136 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
3884191 TCCTGCTCTTTGAGGATTGGAAA-AAGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884246 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884301 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* ** *
3884356 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTAGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884411 TCCTGCTCTTTGGGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884466 CCCTGCTCTTTGAGGACTGGAAA--TACCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * * **
3884520 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT---AAG---AGGTG
** * *
3884581 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884636 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
3884691 TCCTGCTCTTTGAGGACTGGAAGGCGCGACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
3884746 TCCTGCTCTTTGAGGACTGGAAGACGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3884801 TCCTTCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3884856 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
3884911 TCCTGCTTTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
3884966 TCGTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
3885021 TCCTGCTCTTTGGGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885076 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGC-TTT-AAGAGGTG
*
3885132 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
3885187 TCCTGCTTTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885242 TCGTGCTCTTTG-GGGCTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885296 TCCTGCTCTTTAAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885351 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885406 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3885461 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885516 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885571 TCGTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885626 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
3885681 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885736 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885791 TCGTGCTCTTTG-GGGCTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885845 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
3885900 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
3885955 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
3886010 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
3886065 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
3886120 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
3886138 AAAAAGCGGA
Statistics
Matches: 2320, Mismatches: 178, Indels: 128
0.88 0.07 0.05
Matches are distributed among these distances:
53 8 0.00
54 287 0.12
55 1768 0.76
56 111 0.05
57 6 0.00
58 4 0.00
60 2 0.00
61 134 0.06
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:3885481 original size:26 final size:26
Alignment explanation
Indices: 3885452--3885541 Score: 85
Period size: 26 Copynumber: 3.3 Consensus size: 26
3885442 GGGTGGGCTT
3885452 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
3885478 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
3885505 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
3885533 TGAAAGGTG
1 TGAAAGGTG
3885542 CCACCAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 9 0.18
28 9 0.18
29 8 0.16
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:3886030 original size:26 final size:26
Alignment explanation
Indices: 3886001--3886090 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
3885991 GGGTGGGCTT
3886001 TGAAAGGTGTCCTGCTCTTTGGGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
3886027 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
* *
3886054 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
3886082 TGAAAGGTG
1 TGAAAGGTG
3886091 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 8 0.17
28 9 0.19
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:3887156 original size:23 final size:23
Alignment explanation
Indices: 3887130--3887173 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3887120 TTTTTCTTTG
3887130 TTTTGTTTTTTTG-TTTTTTTTCC
1 TTTT-TTTTTTTGCTTTTTTTTCC
3887153 TTTTTTTTTTTGCTTTTTTTT
1 TTTTTTTTTTTGCTTTTTTTT
3887174 TTGAAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTTTGCTTTTTTTTCC
Found at i:3887173 original size:14 final size:14
Alignment explanation
Indices: 3887137--3887175 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3887127 TTGTTTTGTT
*
3887137 TTTTTGTTTTTTTTC
1 TTTTT-TTTTTTTGC
*
3887152 CTTTTTTTTTTTGC
1 TTTTTTTTTTTTGC
3887166 TTTTTTTTTT
1 TTTTTTTTTT
3887176 GAAGAGAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTTTGC
Found at i:3887176 original size:12 final size:13
Alignment explanation
Indices: 3887143--3887175 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3887133 TGTTTTTTTG
*
3887143 TTTTTTTTCCTTT
1 TTTTTTTTGCTTT
3887156 TTTTTTTTGCTTT
1 TTTTTTTTGCTTT
3887169 TTTTTTT
1 TTTTTTT
3887176 GAAGAGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTGCTTT
Found at i:3899696 original size:78 final size:78
Alignment explanation
Indices: 3899597--3899797 Score: 226
Period size: 79 Copynumber: 2.6 Consensus size: 78
3899587 AATAACAGGG
* * * * *
3899597 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
3899660 GAAAAAAAATCGGGA
64 GAAAAAAAACCGGGA
* *
3899675 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTCG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * *
3899740 GAATAAAGCCGGGG
65 AAAAAAAACCGGGA
* * *
3899754 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
3899798 GAAATAACGA
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 7 0.07
78 45 0.43
79 52 0.50
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (78 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCGGGA
Found at i:3899782 original size:28 final size:28
Alignment explanation
Indices: 3899749--3899820 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
3899739 GGAATAAAGC
** *
3899749 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3899777 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
3899805 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3899821 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:3899878 original size:52 final size:52
Alignment explanation
Indices: 3899809--3900145 Score: 176
Period size: 52 Copynumber: 6.4 Consensus size: 52
3899799 AAATAACGAG
*
3899809 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
3899861 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
* * * *
3899914 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* * **** * * *
3899965 GTTGGAGTAT-CCC-ATCG-AAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
3900020 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
* * * * *
3900074 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* * *
3900125 GTTAGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
3900146 GAGAATTGAT
Statistics
Matches: 214, Mismatches: 44, Indels: 54
0.69 0.14 0.17
Matches are distributed among these distances:
48 3 0.01
49 2 0.01
50 3 0.01
51 41 0.19
52 75 0.35
53 33 0.15
54 28 0.13
55 14 0.07
56 5 0.02
57 5 0.02
58 4 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:3899997 original size:28 final size:27
Alignment explanation
Indices: 3899952--3900036 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
3899942 AGTGTTTTAG
* *
3899952 CGATAAA-ACCGGAGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
3899978 ATCGA-AAATAACGGGGTTGGAGTATCCC
1 --CGATAAATAACGGGGTTGGAGTATCCC
* *
3900006 CGATGATTAACGGGGTTGGAGTATCCC
1 CGATAAATAACGGGGTTGGAGTATCCC
3900033 CGAT
1 CGAT
3900037 TGTGAAGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 3 0.06
27 28 0.55
28 20 0.39
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (27 bp):
CGATAAATAACGGGGTTGGAGTATCCC
Found at i:3900048 original size:107 final size:104
Alignment explanation
Indices: 3899695--3900086 Score: 310
Period size: 107 Copynumber: 3.7 Consensus size: 104
3899685 CCTTCGAAAA
* * * * * * * *
3899695 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTCGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGGAATAAAACCGGAGTTGGAG
* *
3899760 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
66 TAT-CCCTC-GAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * * *
3899802 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGG-AATAAAACCGGAGTTGGA
* * ** * ** **
3899867 GTATCCC-CG-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
65 GTATCCCTCGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * *
3899904 AAAACCAGGATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTATTTTAG-GAATAAAACCGGAGTT
3899968 GGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATGAT
62 GGAGTATCCC-TCG-AAATAACGGGGTTGGAGTATCCCCGATGAT
* * * * *
3900013 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGT-ATTTTAGG-AATAAAACCGGAGTTG
3900078 GAGTATCCC
63 GAGTATCCC
3900087 CGATTATAGA
Statistics
Matches: 219, Mismatches: 48, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 49 0.22
105 17 0.08
106 19 0.09
107 71 0.32
108 32 0.15
109 26 0.12
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (104 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGGAATAAAACCGGAGTTGGAG
TATCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:3900101 original size:212 final size:212
Alignment explanation
Indices: 3899742--3900147 Score: 611
Period size: 212 Copynumber: 1.9 Consensus size: 212
3899732 TATTTTCGGA
* * * * *
3899742 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
3899807 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATC
66 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
* * *
3899872 CCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGA
131 CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTAGAATATCCCCGATTGTGGA
3899936 AAAATTAGTGTTTTAGCG
195 AAAATTAGTGTTTTAGCG
*
3899954 ATAAAACCGGAGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACG
1 ATAAAACCGGAGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
* *
3900018 GGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTA
66 AGGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTAGAGTA
* * * *
3900083 TCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTAGAATATCCTCGATTGTGG
129 TCCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGG
3900147 A
194 A
3900148 GAATTGATAA
Statistics
Matches: 174, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
211 32 0.18
212 103 0.59
213 39 0.22
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATGAAATAACG
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATC
CCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTAGCG
Found at i:3900120 original size:51 final size:53
Alignment explanation
Indices: 3900024--3900142 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
3900014 AACGGGGTTG
* * *
3900024 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
3900078 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
3900129 GAATATCCTCGATT
1 GAGTATCCCCGATT
3900143 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:3902551 original size:33 final size:33
Alignment explanation
Indices: 3902493--3902559 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3902483 AAAATTTCCA
***
3902493 AATGTATCGATACAAAGATCCATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
* *
3902526 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
3902559 A
1 A
3902560 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:3902603 original size:19 final size:18
Alignment explanation
Indices: 3902579--3902646 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3902569 CAGTAGCTAA
3902579 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3902598 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3902613 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3902630 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3902647 TCATTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3902619 original size:13 final size:13
Alignment explanation
Indices: 3902601--3902625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3902591 ACAATACTTA
3902601 TGTATCGATACAT
1 TGTATCGATACAT
3902614 TGTATCGATACA
1 TGTATCGATACA
3902626 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3902623 original size:32 final size:32
Alignment explanation
Indices: 3902582--3902644 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3902572 TAGCTAATTA
*
3902582 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3902614 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3902645 AATCATTGAA
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3903024 original size:12 final size:12
Alignment explanation
Indices: 3903007--3903036 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3902997 ATTTATGTTT
3903007 TGTCATGATCCA
1 TGTCATGATCCA
3903019 TGTCATGATCCA
1 TGTCATGATCCA
*
3903031 TCTCAT
1 TGTCAT
3903037 AAACATGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (12 bp):
TGTCATGATCCA
Found at i:3906103 original size:16 final size:16
Alignment explanation
Indices: 3906082--3906115 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3906072 CCTAAACTAA
3906082 ACCTCTAAGGTTACTT
1 ACCTCTAAGGTTACTT
3906098 ACCTCTAAGGTTACTT
1 ACCTCTAAGGTTACTT
3906114 AC
1 AC
3906116 TTTTTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (16 bp):
ACCTCTAAGGTTACTT
Found at i:3912685 original size:29 final size:29
Alignment explanation
Indices: 3912593--3913490 Score: 1092
Period size: 28 Copynumber: 31.1 Consensus size: 29
3912583 TTTTTTTTAA
* *
3912593 AAAAG-GTGCCACTAACTTATGTAGGCTTTG
1 AAAAGAGTGCCACTGAC-T-TGTGGGCTTTG
*
3912623 AAAAGAGTTGCCACCGACTTGTGTGGGCTTTG
1 AAAAGAG-TGCCACTGAC-T-TGTGGGCTTTG
* * *
3912655 AAAAGAATGCCACTGGCCTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3912684 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3912713 -AAAGGGTGCCATTGACTTGTGGGTTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* ***
3912741 -AAAG-GTTGCCATTGACTTGTCCTCTTTG
1 AAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * *
3912769 AAAAGAGTGCCACTAACCTGTGAGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3912798 -AAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3912826 AAATAG-GTTGCCACCGACTTGTGTGGGCTTTG
1 AAA-AGAG-TGCCACTGAC-T-TGTGGGCTTTG
* * *
3912858 AAATGGGTTGCCACTGACTTGTGTGCTTTG
1 AAAAGAG-TGCCACTGACTTGTGGGCTTTG
* *
3912888 AAAGGAATGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3912917 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3912945 -AAAGGGTGCCATTGACTTGTGGGGTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3912973 AAAAG-GTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913001 AAAAGA-TGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3913029 AAAATAGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3913058 AAAATAGTGCCACTAATTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
3913087 -AAAGGGTGCCACTGACTTGTAGACTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913115 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913143 AAAAGAGTGCCACTAACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
3913172 AAAAATAGTGCCACTAACTTGTGGGCTTTG
1 -AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913202 AAAAGAGTGCCACTGATTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913231 -AAAGGGTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGAGTGCCACTGACTT--GTGGGCTTTG
3913261 AAAAG-GTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3913289 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913318 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913346 AAAGGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3913375 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
*
3913404 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
3913432 AAAGGA-AGCCACTAACTTATGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3913460 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGAGTGCCACTGACTTGTGGGCTTTG
3913489 AA
1 AA
3913491 GAGATGAACA
Statistics
Matches: 769, Mismatches: 76, Indels: 47
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.00
28 332 0.43
29 288 0.37
30 81 0.11
31 16 0.02
32 51 0.07
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
AAAAGAGTGCCACTGACTTGTGGGCTTTG
Found at i:3912741 original size:57 final size:57
Alignment explanation
Indices: 3912597--3913490 Score: 1050
Period size: 57 Copynumber: 15.5 Consensus size: 57
3912587 TTTTAAAAAA
* * *
3912597 GGTGCCACTAACTTATGTAGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTG-AAAG
** * *
3912660 AATGCCACTGGCCTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * ***
3912717 GGTGCCATTGACTTGTGGGTTTTG-AAAG-GTTGCCATTGACTTGTCCTCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG-AAAG
* * * * * *
3912774 AGTGCCACTAACCTGTGAGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAATAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AA-AG
* * * * *
3912832 GTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGCTTTGAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAG
* *
3912892 GAATGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
1 G-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3912949 GGTGCCATTGACTTGTGGGGTTTGAAAAG-GTGCCACTAACTTGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
3913005 GATGCCACTAACTTGTGGGCTTTGAAAATAGTGCCACTAACTTGTGGGCTTTGAAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG
* * * * * *
3913063 AGTGCCACTAATTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTAGACTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* *
3913119 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAAT
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG--AAAG
* * *
3913178 AGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
3913235 GGTGCCACTGACTTGCGTGGGCTTTGAAAAG-GTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
3913294 AGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
3913350 GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
1 G-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
3913408 GGTGCCACTGACTTGTGGGCTTTGAAAGGA-AGCCACTAACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG
*
3913465 AGTGCCACTGACTTGTGGGCTTTGAA
1 GGTGCCACTGACTTGTGGGCTTTGAA
3913491 GAGATGAACA
Statistics
Matches: 724, Mismatches: 85, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
55 1 0.00
56 142 0.20
57 296 0.41
58 105 0.15
59 96 0.13
60 23 0.03
61 33 0.05
62 20 0.03
63 8 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (57 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:3914749 original size:11 final size:11
Alignment explanation
Indices: 3914735--3914784 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
3914725 TCTTTTCTTG
3914735 GTTTTTTTGTT
1 GTTTTTTTGTT
*
3914746 GTTTTGTTTTTT
1 GTTTT-TTTGTT
3914758 GTTTTTTTGTT
1 GTTTTTTTGTT
*
3914769 TTTTTTTTGTT
1 GTTTTTTTGTT
3914780 -TTTTT
1 GTTTTT
3914785 GTGTAAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 5 0.14
11 20 0.57
12 10 0.29
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
GTTTTTTTGTT
Found at i:3914752 original size:8 final size:8
Alignment explanation
Indices: 3914739--3914786 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
3914729 TTCTTGGTTT
3914739 TTTTGTTG
1 TTTTGTTG
3914747 TTTTGTT-
1 TTTTGTTG
*
3914754 TTTTGTTT
1 TTTTGTTG
*
3914762 TTTTGTTT
1 TTTTGTTG
*
3914770 TTTTTTTG
1 TTTTGTTG
*
3914778 TTTTTTTG
1 TTTTGTTG
3914786 T
1 T
3914787 GTAAAGGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 7 0.19
8 30 0.81
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (8 bp):
TTTTGTTG
Found at i:3914757 original size:15 final size:15
Alignment explanation
Indices: 3914737--3914772 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3914727 TTTTCTTGGT
3914737 TTTTTTGTTGTTTTG
1 TTTTTTGTTGTTTTG
*
3914752 TTTTTTGTTTTTTTG
1 TTTTTTGTTGTTTTG
3914767 TTTTTT
1 TTTTTT
3914773 TTTTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (15 bp):
TTTTTTGTTGTTTTG
Found at i:3914759 original size:7 final size:7
Alignment explanation
Indices: 3914737--3914783 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
3914727 TTTTCTTGGT
3914737 TTTTTTG
1 TTTTTTG
3914744 TTGTTTTG
1 TT-TTTTG
3914752 TTTTTTG
1 TTTTTTG
3914759 TTTTTT-
1 TTTTTTG
*
3914765 TGTTTT-
1 TTTTTTG
3914771 TTTTTTG
1 TTTTTTG
3914778 TTTTTT
1 TTTTTT
3914784 TGTGTAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 10 0.28
7 19 0.53
8 7 0.19
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:3928526 original size:20 final size:20
Alignment explanation
Indices: 3928501--3928577 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
3928491 GTAAAAAGAT
*
3928501 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTAA
*
3928521 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATT-AA
** *
3928542 A-CTTGTTTCGATACATTAA
1 AGAATGTATCGATACATTAA
*
3928561 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
3928578 CTAGGTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.93
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:3929838 original size:20 final size:20
Alignment explanation
Indices: 3929801--3929838 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3929791 TGGATTTAGT
*
3929801 GTTTTTGGGTAATTGTTTGG
1 GTTTTTGGGTAATGGTTTGG
3929821 GTTTATTGGGT-ATGGTTT
1 GTTT-TTGGGTAATGGTTT
3929839 AATTTGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (20 bp):
GTTTTTGGGTAATGGTTTGG
Found at i:3931453 original size:12 final size:13
Alignment explanation
Indices: 3931428--3931457 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3931418 TTACTTTATC
3931428 ATGTATCGATACA
1 ATGTATCGATACA
3931441 ATGTATC-ATACA
1 ATGTATCGATACA
3931453 ATGTA
1 ATGTA
3931458 CTATGTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3931546 original size:19 final size:19
Alignment explanation
Indices: 3931501--3931557 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
3931491 ACTGCTAGTT
**
3931501 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATAA
3931520 TCCATGTATCGATACAATAA
1 T-CATGTATCGATACAATAA
3931540 TCATGTATCGATACAATA
1 TCATGTATCGATACAATA
3931558 TATCGAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TCATGTATCGATACAATAA
Found at i:3938047 original size:10 final size:10
Alignment explanation
Indices: 3938032--3938056 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3938022 ATCAATTTGT
3938032 ATTTCGATTA
1 ATTTCGATTA
3938042 ATTTCGATTA
1 ATTTCGATTA
3938052 ATTTC
1 ATTTC
3938057 TTTTCTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (10 bp):
ATTTCGATTA
Found at i:3940253 original size:13 final size:13
Alignment explanation
Indices: 3940235--3940265 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3940225 TTACTTCATC
*
3940235 ATGTATCGATATA
1 ATGTATCGATACA
3940248 ATGTATCGATACA
1 ATGTATCGATACA
3940261 ATGTA
1 ATGTA
3940266 CTATGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3941883 original size:15 final size:15
Alignment explanation
Indices: 3941863--3941893 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3941853 CTTCTCTTAG
3941863 TTTGAGAATTATACC
1 TTTGAGAATTATACC
3941878 TTTGAGAATTATACC
1 TTTGAGAATTATACC
3941893 T
1 T
3941894 CAAATTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTTGAGAATTATACC
Found at i:3942440 original size:33 final size:33
Alignment explanation
Indices: 3942397--3942461 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
3942387 CATTTTATGG
* *
3942397 TGTATTGATACAAAGCAATTTGTATCGATACAA
1 TGTATCGATACAAAGCAATATGTATCGATACAA
**
3942430 TGTATCGATACTTAGCAATATGTATCGATACA
1 TGTATCGATACAAAGCAATATGTATCGATACA
3942462 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATATGTATCGATACAA
Found at i:3943648 original size:10 final size:10
Alignment explanation
Indices: 3943635--3943668 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3943625 AAACATAAAT
3943635 ATAATATGTA
1 ATAATATGTA
*
3943645 ATAAT-TTTA
1 ATAATATGTA
3943654 ATAATATGTA
1 ATAATATGTA
3943664 ATAAT
1 ATAAT
3943669 TTTAAAATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (10 bp):
ATAATATGTA
Found at i:3943659 original size:19 final size:19
Alignment explanation
Indices: 3943635--3943673 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3943625 AAACATAAAT
3943635 ATAATATGTAATAATTTTA
1 ATAATATGTAATAATTTTA
3943654 ATAATATGTAATAATTTTA
1 ATAATATGTAATAATTTTA
3943673 A
1 A
3943674 AATCCGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
ATAATATGTAATAATTTTA
Found at i:3944178 original size:18 final size:19
Alignment explanation
Indices: 3944144--3944189 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3944134 CTCTCTTCCT
3944144 TTTCTATTTTTTGTTTAGA
1 TTTCTATTTTTTGTTTAGA
*
3944163 TTTCT-TTTTTAT-TTTATA
1 TTTCTATTTTT-TGTTTAGA
3944181 TTTCTATTT
1 TTTCTATTT
3944190 AAAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTCTATTTTTTGTTTAGA
Found at i:3949446 original size:2 final size:2
Alignment explanation
Indices: 3949439--3949469 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3949429 GTTGGGATGT
3949439 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3949470 GGACTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3951361 original size:20 final size:20
Alignment explanation
Indices: 3951338--3951377 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3951328 TAAATATAAA
*
3951338 CATAATAATTATATTAAAAT
1 CATAATAATAATATTAAAAT
*
3951358 CATATTAATAATATTAAAAT
1 CATAATAATAATATTAAAAT
3951378 ATTTATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
CATAATAATAATATTAAAAT
Found at i:3951388 original size:17 final size:19
Alignment explanation
Indices: 3951343--3951399 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
3951333 ATAAACATAA
3951343 TAATTATATTAAAATCATAT
1 TAATTATATTAAAAT-ATAT
*
3951363 TAATAATATTAAAATAT-T
1 TAATTATATTAAAATATAT
*
3951381 T-ATTATATTATAATATAT
1 TAATTATATTAAAATATAT
3951399 T
1 T
3951400 GTTATTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 13 0.39
18 4 0.12
19 2 0.06
20 14 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTATATTAAAATATAT
Found at i:3951469 original size:15 final size:15
Alignment explanation
Indices: 3951434--3951471 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3951424 AATTTTACAG
* *
3951434 TTAAATAACATTAAT
1 TTAAATAAAAATAAT
3951449 TT-AATAAAAATAAT
1 TTAAATAAAAATAAT
3951463 TTAAATAAA
1 TTAAATAAA
3951472 TTTATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATAAAAATAAT
Found at i:3952350 original size:21 final size:21
Alignment explanation
Indices: 3952320--3952363 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3952310 TTTAATTGAT
*
3952320 AGTAAATTTGATAT-TTTTTA
1 AGTAAATTTGATATATTTGTA
3952340 AGTAATATTTGATATATTTGTA
1 AGTAA-ATTTGATATATTTGTA
3952362 AG
1 AG
3952364 ATCAATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (21 bp):
AGTAAATTTGATATATTTGTA
Found at i:3956224 original size:2 final size:2
Alignment explanation
Indices: 3956217--3956257 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3956207 CGCATCAATT
*
3956217 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3956258 GAAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3957337 original size:13 final size:13
Alignment explanation
Indices: 3957319--3957369 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
3957309 CATTATGCTT
3957319 TGTATCGATACAA
1 TGTATCGATACAA
* **
3957332 TGTATCGATGCTT
1 TGTATCGATACAA
*
3957345 TTTATCGATACAA
1 TGTATCGATACAA
3957358 TGTATCGATACA
1 TGTATCGATACA
3957370 CACTCAATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3957350 original size:26 final size:26
Alignment explanation
Indices: 3957313--3957366 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3957303 TCGATACATT
3957313 ATGCTTTGTATCGATACAATGTATCG
1 ATGCTTTGTATCGATACAATGTATCG
*
3957339 ATGCTTTTTATCGATACAATGTATCG
1 ATGCTTTGTATCGATACAATGTATCG
3957365 AT
1 AT
3957367 ACACACTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (26 bp):
ATGCTTTGTATCGATACAATGTATCG
Found at i:3957903 original size:23 final size:23
Alignment explanation
Indices: 3957868--3957911 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3957858 GCATCCAACC
*
3957868 TTGGGTTACAATTTCTT-AAGAAT
1 TTGGGGTACAA-TTCTTGAAGAAT
*
3957891 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTACAATTCTTGAAGA
3957912 GATTGAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTACAATTCTTGAAGAAT
Found at i:3959058 original size:3 final size:3
Alignment explanation
Indices: 3959052--3959086 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3959042 AATCATCAAA
*
3959052 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3959087 ACTTGACTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:3961428 original size:19 final size:19
Alignment explanation
Indices: 3961404--3961499 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
3961394 TTTCAACAAT
3961404 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3961423 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
3961437 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
3961455 TTGTATCGATAC--AA--G
1 TTGTATCGATACATAAGTG
* *
3961470 --GTATCAATACATAAGTT
1 TTGTATCGATACATAAGTG
3961487 TTGTATCGATACA
1 TTGTATCGATACA
3961500 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
13 20 0.32
15 5 0.08
17 4 0.06
19 33 0.53
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:3961442 original size:13 final size:13
Alignment explanation
Indices: 3961424--3961448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3961414 ACATAAGTGT
3961424 TGTATCGATACAA
1 TGTATCGATACAA
3961437 TGTATCGATACA
1 TGTATCGATACA
3961449 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3961442 original size:32 final size:32
Alignment explanation
Indices: 3961405--3961507 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
3961395 TTCAACAATT
3961405 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3961437 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* * *
3961469 GGTATCAATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3961501 TGTATCG
1 TGTATCG
3961508 CTACGAAGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3961629 original size:52 final size:52
Alignment explanation
Indices: 3961585--3961713 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
3961575 CACTGATCTT
*
3961585 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
3961637 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATATACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3961689 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
3961714 TCATATTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Done.