Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_pilon, whole genome shotgun sequence
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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 42
Found at i:5008616 original size:31 final size:31
Alignment explanation
Indices: 5008573--5008726 Score: 236
Period size: 31 Copynumber: 5.0 Consensus size: 31
5008563 GAGTCGAGGG
* * *
5008573 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCAGGACATATGGACTGT
*
5008604 TTACATATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCAGGACATATGGACTGT
*
5008635 TTACATATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCAGGACATATGGACTGT
5008666 TTACCTATGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCAGGACATATGGACTGT
* * *
5008697 TTACCTAGGTTCTTCGGGACCTATGGACTG
1 TTACCTATGTTCTTCAGGACATATGGACTG
5008727 GTCTTTCGGG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 115 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCAGGACATATGGACTGT
Found at i:5009390 original size:21 final size:21
Alignment explanation
Indices: 5009365--5009404 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5009355 GAAGTTACTA
5009365 TAGTAGTGCATCAGTACACTG
1 TAGTAGTGCATCAGTACACTG
*
5009386 TAGTAGTGCATCGGTACAC
1 TAGTAGTGCATCAGTACAC
5009405 AATTTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (21 bp):
TAGTAGTGCATCAGTACACTG
Found at i:5013181 original size:63 final size:63
Alignment explanation
Indices: 5013113--5013232 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
5013103 TGTGACTCTT
* * * *
5013113 AGGTAGGCTCTACGGCCCTGAGATC-ATTCTCGGATAGGCTCTGC-GGCCCTAAGATGTGTTCTC
1 AGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGATAGGCTCT-CAGGCCCTAAGATGTGTTCTC
* *
5013176 AGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 AGGTAGGCCCCACGGCCCCGAAATCTATCTCGGATAGGCTCTCAGGCCCTAAGATGT
5013233 TCCCTTAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.02
63 47 0.96
64 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.24
Consensus pattern (63 bp):
AGGTAGGCCCCACGGCCCCGAAATCTATCTCGGATAGGCTCTCAGGCCCTAAGATGTGTTCTC
Found at i:5013183 original size:32 final size:31
Alignment explanation
Indices: 5013113--5013193 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
5013103 TGTGACTCTT
*
5013113 AGGTAGGCTCTACGGCCCTGAGATCATTCTC
1 AGGTAGGCTCTACGGCCCTAAGATCATTCTC
* **
5013144 -GGATAGGCTCTGCGGCCCTAAGATGTGTTCTC
1 AGG-TAGGCTCTACGGCCCTAAGAT-CATTCTC
* *
5013176 AGGTAGGCCCCACGGCCC
1 AGGTAGGCTCTACGGCCC
5013194 CGAAATCTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 2 0.05
31 19 0.47
32 17 0.43
33 2 0.05
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.22
Consensus pattern (31 bp):
AGGTAGGCTCTACGGCCCTAAGATCATTCTC
Found at i:5013992 original size:19 final size:20
Alignment explanation
Indices: 5013960--5013999 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5013950 TACTATTTGC
5013960 ACAGTATCAGTACTATTCAT
1 ACAGTATCAGTACTATTCAT
5013980 ACAGTAT-AGTACTATTCAT
1 ACAGTATCAGTACTATTCAT
5013999 A
1 A
5014000 AAAACGTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
ACAGTATCAGTACTATTCAT
Found at i:5014304 original size:31 final size:31
Alignment explanation
Indices: 5014263--5014324 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
5014253 ATTTGCTTTT
5014263 GTCCATCCTGAAATTTTATAAGTTCAAGTTC
1 GTCCATCCTGAAATTTTATAAGTTCAAGTTC
*
5014294 GTCCTTCCTGAAATTTTATAAGTTCAAGTTC
1 GTCCATCCTGAAATTTTATAAGTTCAAGTTC
5014325 TCCCCTAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (31 bp):
GTCCATCCTGAAATTTTATAAGTTCAAGTTC
Found at i:5014455 original size:2 final size:2
Alignment explanation
Indices: 5014450--5014506 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5014440 ACAAATCATT
5014450 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5014492 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5014507 TCTTATCATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5014947 original size:108 final size:107
Alignment explanation
Indices: 5014749--5014967 Score: 321
Period size: 108 Copynumber: 2.0 Consensus size: 107
5014739 AGAGAATCCC
* *
5014749 CTCTAAGTCTTATATGAAAGATCAAGCCTAAGGTCATTATAGTTACTTGTAGATCGACCCATAAG
1 CTCTAAGTCTTATATGAAAGATCAAGCCTAAGGTCATTATAGTTACTCGTAAATCGACCCATAAG
* *
5014814 TTAACATAACAAATAGATATGATCGTCTAACAATAGATTTAA
66 TTAACATAACAAATAAATATAATCGTCTAACAATAGATTTAA
* * * *
5014856 CTCTAAGTCTTGTATGAAAAGATCAGGCCTAAGGTCATTATAGTTACTCGTAAATTGACTCATAA
1 CTCTAAGTCTTATATG-AAAGATCAAGCCTAAGGTCATTATAGTTACTCGTAAATCGACCCATAA
* ** *
5014921 GTTGACATAGTAAATAAATATAATCGTCTGACAATAGATTTAA
65 GTTAACATAACAAATAAATATAATCGTCTAACAATAGATTTAA
5014964 CTCT
1 CTCT
5014968 TAACAATCAC
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 15 0.15
108 84 0.85
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (107 bp):
CTCTAAGTCTTATATGAAAGATCAAGCCTAAGGTCATTATAGTTACTCGTAAATCGACCCATAAG
TTAACATAACAAATAAATATAATCGTCTAACAATAGATTTAA
Found at i:5028438 original size:19 final size:17
Alignment explanation
Indices: 5028414--5028458 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
5028404 TGAATTTAAA
5028414 AAAAAAACAAAAACATTAC
1 AAAAAAAC-AAAA-ATTAC
5028433 AAAAAATTACAAAAATTAC
1 AAAAAA--ACAAAAATTAC
5028452 AAAAAAA
1 AAAAAAA
5028459 AATAGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.04
19 17 0.71
20 4 0.17
21 2 0.08
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAAAAACAAAAATTAC
Found at i:5028455 original size:8 final size:9
Alignment explanation
Indices: 5028423--5028456 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
5028413 AAAAAAAACA
5028423 AAAACATTAC
1 AAAA-ATTAC
5028433 AAAAAATTAC
1 -AAAAATTAC
5028443 AAAAATTAC
1 AAAAATTAC
5028452 AAAAA
1 AAAAA
5028457 AAAATAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 5 0.22
11 4 0.17
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAAATTAC
Found at i:5028457 original size:10 final size:10
Alignment explanation
Indices: 5028420--5028457 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
5028410 TAAAAAAAAA
5028420 ACAAAAACATT
1 ACAAAAA-ATT
5028431 ACAAAAAATT
1 ACAAAAAATT
5028441 AC-AAAAATT
1 ACAAAAAATT
5028450 ACAAAAAA
1 ACAAAAAA
5028458 AAATAGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.35
10 10 0.38
11 7 0.27
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (10 bp):
ACAAAAAATT
Found at i:5031272 original size:38 final size:38
Alignment explanation
Indices: 5031221--5031299 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
5031211 ACCGGTATGG
*
5031221 AAGATACCTAGTTGCAAAATCGAGACCTTTGGAATTGT
1 AAGATACCTAGTTGCAAAATCAAGACCTTTGGAATTGT
5031259 AAGATACCTAGTTGCAAAATCAAGACCTTTGGAATTGT
1 AAGATACCTAGTTGCAAAATCAAGACCTTTGGAATTGT
5031297 AAG
1 AAG
5031300 GAATTTCTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (38 bp):
AAGATACCTAGTTGCAAAATCAAGACCTTTGGAATTGT
Found at i:5036268 original size:16 final size:15
Alignment explanation
Indices: 5036220--5036268 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5036210 ACTAAATAAA
*
5036220 ATATCAATTTTATTT
1 ATATAAATTTTATTT
* *
5036235 AAATAAATTATTAGTT
1 ATATAAATT-TTATTT
5036251 ATATAAATATTTATTT
1 ATATAAAT-TTTATTT
5036267 AT
1 AT
5036269 CAACGGAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 7 0.26
16 19 0.70
17 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
ATATAAATTTTATTT
Found at i:5044205 original size:17 final size:17
Alignment explanation
Indices: 5044183--5044216 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5044173 CGGCAGATTA
5044183 CAAATTTCCTAGTTGGT
1 CAAATTTCCTAGTTGGT
5044200 CAAATTTCCTAGTTGGT
1 CAAATTTCCTAGTTGGT
5044217 TTTCACCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
CAAATTTCCTAGTTGGT
Found at i:5045858 original size:40 final size:42
Alignment explanation
Indices: 5045813--5045896 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
5045803 TAAATATAAT
*
5045813 TTTTATTAATGAATT-TCTA-TTT-AAATCTTTTATGATATGA
1 TTTTATTAATGAATTCT-TATTTTAAAATCTTTTATGATACGA
* *
5045853 TTTTATTATTGGATTCTTATTTTAAAATCTTTTATGATACGA
1 TTTTATTAATGAATTCTTATTTTAAAATCTTTTATGATACGA
5045895 TT
1 TT
5045897 ATAGTCCTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 15 0.39
41 4 0.11
42 19 0.50
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (42 bp):
TTTTATTAATGAATTCTTATTTTAAAATCTTTTATGATACGA
Found at i:5046699 original size:16 final size:16
Alignment explanation
Indices: 5046672--5046714 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
5046662 GATATCAAGA
5046672 TGATTATATGCTTCTTG
1 TGATT-TATGCTTCTTG
5046689 TGATTTATGCTTCTTG
1 TGATTTATGCTTCTTG
5046705 TGATTTATGC
1 TGATTTATGC
5046715 GTCTATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (16 bp):
TGATTTATGCTTCTTG
Found at i:5049248 original size:64 final size:64
Alignment explanation
Indices: 5049177--5049337 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
5049167 ATTGTTCAAG
* * * * * *
5049177 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATAA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAGGCCATAA
* * * ** **
5049241 GTGTATCGATGGACAAGTAGTGCATCGATGCACCCCCTTAAGATTAAAACATCGAAGGTGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAGGCCATAA
* *
5049305 GTGTACCGATGCACAGGTAGTGCATCGATGCAC
1 GTGTATCGATGCACAAGTAGTGCATCGATGCAC
5049338 ACGTTATGGA
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 81 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAAGGCCATAA
Found at i:5049958 original size:24 final size:22
Alignment explanation
Indices: 5049887--5049947 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
5049877 CGAGGGTTAT
* *
5049887 AGTGGTCATTCGGGACATATCC
1 AGTGGTCCTTTGGGACATATCC
5049909 AGTGGTCCTTTGGGACATATCC
1 AGTGGTCCTTTGGGACATATCC
*
5049931 AGTGGTCCTTTTGGACA
1 AGTGGTCCTTTGGGACA
5049948 AATATTCAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (22 bp):
AGTGGTCCTTTGGGACATATCC
Found at i:5058927 original size:19 final size:19
Alignment explanation
Indices: 5058903--5058962 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
5058893 AAACCGAAAC
5058903 CGGTTTTTTTGGTTCGATT
1 CGGTTTTTTTGGTTCGATT
**
5058922 CGGTTTTTTT--AACGATT
1 CGGTTTTTTTGGTTCGATT
* * *
5058939 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTTGGTTCGATT
5058958 CGGTT
1 CGGTT
5058963 CGGTTTATCG
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
17 13 0.42
19 18 0.58
ACGTcount: A:0.07, C:0.13, G:0.28, T:0.52
Consensus pattern (19 bp):
CGGTTTTTTTGGTTCGATT
Found at i:5064440 original size:3 final size:3
Alignment explanation
Indices: 5064434--5064506 Score: 64
Period size: 3 Copynumber: 24.3 Consensus size: 3
5064424 CCATCATCAC
*
5064434 CTT CTT CTT CTT CTT C-T CTAT CTT -TGT CTT CTT CTT CCT CTT C-T
1 CTT CTT CTT CTT CTT CTT CT-T CTT CT-T CTT CTT CTT CTT CTT CTT
*
5064478 CTAT CTT -TGT CTT CTT CTT CCT CTT CTT C
1 CT-T CTT CT-T CTT CTT CTT CTT CTT CTT C
5064507 GTCAAACAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
2 6 0.10
3 44 0.76
4 8 0.14
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:5064475 original size:27 final size:27
Alignment explanation
Indices: 5064434--5064504 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
5064424 CCATCATCAC
*
5064434 CTTCTTCTTCTTCTTCTCTATCTTTGT
1 CTTCTTCTTCCTCTTCTCTATCTTTGT
5064461 CTTCTTCTTCCTCTTCTCTATCTTTGT
1 CTTCTTCTTCCTCTTCTCTATCTTTGT
5064488 CTTCTTCTTCCTCTTCT
1 CTTCTTCTTCCTCTTCT
5064505 TCGTCAAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.61
Consensus pattern (27 bp):
CTTCTTCTTCCTCTTCTCTATCTTTGT
Found at i:5077471 original size:24 final size:24
Alignment explanation
Indices: 5077444--5077492 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5077434 AGTTGTAAGA
*
5077444 GCATCATTCGAAGAAGAACAATTT
1 GCATCATTCGAAGAAGAAAAATTT
*
5077468 GCATCCTTCGAAGAAGAAAAATTT
1 GCATCATTCGAAGAAGAAAAATTT
5077492 G
1 G
5077493 TTCTTTTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (24 bp):
GCATCATTCGAAGAAGAAAAATTT
Found at i:5081951 original size:77 final size:75
Alignment explanation
Indices: 5081805--5081952 Score: 170
Period size: 77 Copynumber: 1.9 Consensus size: 75
5081795 ACTGATCCAT
* * * ** * *
5081805 ATTCATAGTAAAATTTGTTCATACAAGCAGCGATTTACTTTCTAATTTTTCATTCCTTGTATCAA
1 ATTCATAGTAAAATTTGTTCAAACAAACAACGAGATACATTCTAATTTTTCATTCCTAGTATCAA
5081870 ATCGATTCAC
66 ATCGATTCAC
* ** *
5081880 ATTCATAGTAAAATTTGTTCAAACAAACAACAAGAGATGCATTCTAATTTTTGGTTCCTAGTGTC
1 ATTCATAGTAAAATTTGTTCAAACAAACAAC--GAGATACATTCTAATTTTTCATTCCTAGTATC
*
5081945 ATATCGAT
64 AAATCGAT
5081953 CTACGATAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
75 28 0.47
77 31 0.53
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (75 bp):
ATTCATAGTAAAATTTGTTCAAACAAACAACGAGATACATTCTAATTTTTCATTCCTAGTATCAA
ATCGATTCAC
Found at i:5096805 original size:36 final size:36
Alignment explanation
Indices: 5096765--5096844 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
5096755 TGGCAACCAA
5096765 CTTTGAAAAA-AGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-TTTTTCAAAGTTTGGTAAATGTTT
*
5096801 CTTTGAAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
5096837 -GTTGAAAA
1 CTTTGAAAA
5096845 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
35 7 0.17
36 33 0.80
37 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:5110578 original size:2 final size:2
Alignment explanation
Indices: 5110571--5110603 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5110561 ATTTAAAAAG
5110571 TA 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 T
5110604 GAAAAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5117913 original size:43 final size:42
Alignment explanation
Indices: 5117843--5117927 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
5117833 CACATAGACC
5117843 CAGGACATATATATATGTAACTATAAGTATTTAATCAATAAA
1 CAGGACATATATATATGTAACTATAAGTATTTAATCAATAAA
* *
5117885 CAGGACATATATATTATGTAATTATAAGTATTTGATCAATAAA
1 CAGGACATATATA-TATGTAACTATAAGTATTTAATCAATAAA
5117928 TAATTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 13 0.32
43 27 0.68
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (42 bp):
CAGGACATATATATATGTAACTATAAGTATTTAATCAATAAA
Found at i:5119336 original size:19 final size:18
Alignment explanation
Indices: 5119305--5119342 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
5119295 AAAAATGAAT
5119305 AATAAATAATAATAATAA
1 AATAAATAATAATAATAA
5119323 AATAAATAAATAATAATAA
1 AATAAAT-AATAATAATAA
5119342 A
1 A
5119343 TAATGTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAATAATAATAATAA
Found at i:5120573 original size:83 final size:83
Alignment explanation
Indices: 5120375--5120646 Score: 300
Period size: 83 Copynumber: 3.3 Consensus size: 83
5120365 AGCTGAATGG
* * * * *
5120375 AATCGAACTCGACA-AT-TTTGTTGGCAGATAGCCCTTATTGCCTTGAGCTATGCTGCAAATTTG
1 AATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAA--TG
* * ** *
5120438 ATTTGCCTCT-GAGTTGAATGC
63 ATGTGCCT-TGGAGCTGAGCGT
* * * *
5120459 AATCGAACTTGAAGGTCTTTGATGACTGATAACCCTTCTTGCCTTGAGTTATGCTCCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
5120524 TGCCTTGGAGCTGAGCGT
66 TGCCTTGGAGCTGAGCGT
* * *
5120542 AGTCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
* *
5120607 TGCCCTCGAAGCTGAGCGT
66 TG-CCTTGGAGCTGAGCGT
5120626 AATCGAACTCGAAGG-CTTTGT
1 AATCGAACTCGAAGGTCTTTGT
5120647 GTTTCAAGAT
Statistics
Matches: 159, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
82 1 0.01
83 83 0.52
84 39 0.25
85 36 0.23
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (83 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
TGCCTTGGAGCTGAGCGT
Found at i:5120690 original size:29 final size:30
Alignment explanation
Indices: 5120648--5120709 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
5120638 AGGCTTTGTG
* *
5120648 TTTCAAGATAAACATTTTC-AAAGTTTTTT
1 TTTCAAGAGAAACAATTTCGAAAGTTTTTT
**
5120677 TTTCAAGAGAAACAATTTCGAGGGTTTTTT
1 TTTCAAGAGAAACAATTTCGAAAGTTTTTT
5120707 TTT
1 TTT
5120710 GTGTTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.47
Consensus pattern (30 bp):
TTTCAAGAGAAACAATTTCGAAAGTTTTTT
Found at i:5120803 original size:37 final size:36
Alignment explanation
Indices: 5120712--5120827 Score: 144
Period size: 36 Copynumber: 3.2 Consensus size: 36
5120702 TTTTTTTTGT
* * * *
5120712 GTTTCAAGAGAAACTGTCTCAATAGGGACAAAATTT
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
5120748 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
* * *
5120785 G-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATTT
1 GTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTA
5120821 GTTTCAA
1 GTTTCAA
5120828 GGAAAAGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
36 38 0.54
37 32 0.46
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:5121871 original size:32 final size:32
Alignment explanation
Indices: 5121770--5121864 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
5121760 ATTCCCAAAG
* *
5121770 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
* *
5121802 ATGTCCCAACATTTGATGTTAAATCTCAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAAA
*
5121834 ATGCCCCAACATTTAATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
5121865 GATGCCCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 50 0.91
33 5 0.09
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAAA
Found at i:5122977 original size:25 final size:25
Alignment explanation
Indices: 5122937--5122987 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
5122927 TTTTTCTTCA
5122937 ATTTTCCTTTG-TTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTCTCTTTTT
5122961 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTGC-TTTTTCTCTTTTT
5122988 GTCCTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
27 13 0.54
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGCTTTTTCTCTTTTT
Found at i:5122979 original size:14 final size:12
Alignment explanation
Indices: 5122938--5122987 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
5122928 TTTTCTTCAA
*
5122938 TTTTC-CTTTGT
1 TTTTCTCTTTTT
5122949 TTTTCTCTTTTT
1 TTTTCTCTTTTT
5122961 ATTTTCTCTTTGCTT
1 -TTTTCTCTTT--TT
5122976 TTTTCTCTTTTT
1 TTTTCTCTTTTT
5122988 GTCCTTGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
11 5 0.15
12 7 0.21
13 10 0.29
14 10 0.29
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:5126049 original size:3 final size:3
Alignment explanation
Indices: 5126043--5126079 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5126033 AAAATGAATA
5126043 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5126080 ATAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5126673 original size:37 final size:37
Alignment explanation
Indices: 5126622--5126692 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
5126612 TTCTGGATTC
5126622 TATTTTTAGAAGTTTGAATCCTAATAAAACTCTATCA
1 TATTTTTAGAAGTTTGAATCCTAATAAAACTCTATCA
* *
5126659 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGAAGTTTGAATCCTAATAAAACTCTA
5126693 ATGCTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (37 bp):
TATTTTTAGAAGTTTGAATCCTAATAAAACTCTATCA
Found at i:5128300 original size:14 final size:14
Alignment explanation
Indices: 5128283--5128331 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
5128273 AAAATGTTCG
5128283 TTTATGTTTGTTTA
1 TTTATGTTTGTTTA
* **
5128297 TTTATGTTCG-TCG
1 TTTATGTTTGTTTA
5128310 TTTATGTTTGTTTA
1 TTTATGTTTGTTTA
5128324 TTTATGTT
1 TTTATGTT
5128332 CGTCGTTTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.12, C:0.04, G:0.16, T:0.67
Consensus pattern (14 bp):
TTTATGTTTGTTTA
Found at i:5128314 original size:27 final size:27
Alignment explanation
Indices: 5128280--5128344 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
5128270 AACAAAATGT
5128280 TCGTTTATGTTTGTTTATTTATGTTCG
1 TCGTTTATGTTTGTTTATTTATGTTCG
5128307 TCGTTTATGTTTGTTTATTTATGTTCG
1 TCGTTTATGTTTGTTTATTTATGTTCG
5128334 TCGTTTATGTT
1 TCGTTTATGTT
5128345 CTCCAGACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.11, C:0.08, G:0.18, T:0.63
Consensus pattern (27 bp):
TCGTTTATGTTTGTTTATTTATGTTCG
Found at i:5128315 original size:13 final size:13
Alignment explanation
Indices: 5128297--5128345 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
5128287 TGTTTGTTTA
5128297 TTTATGTTCGTCG
1 TTTATGTTCGTCG
* **
5128310 TTTATGTTTGTTTA
1 TTTATGTTCG-TCG
5128324 TTTATGTTCGTCG
1 TTTATGTTCGTCG
5128337 TTTATGTTC
1 TTTATGTTC
5128346 TCCAGACCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.10, C:0.10, G:0.18, T:0.61
Consensus pattern (13 bp):
TTTATGTTCGTCG
Found at i:5128428 original size:16 final size:18
Alignment explanation
Indices: 5128388--5128429 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
5128378 AATTTTAACC
5128388 TTAAAC-CCATTAATATT
1 TTAAACTCCATTAATATT
5128405 TCTAAACTCCATT-A-ATT
1 T-TAAACTCCATTAATATT
5128422 TTAAACTC
1 TTAAACTC
5128430 AAATAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 6 0.26
19 5 0.22
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAACTCCATTAATATT
Found at i:5128631 original size:31 final size:29
Alignment explanation
Indices: 5128581--5128638 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
5128571 TTATCATTTA
5128581 AATGAACAAACATGAACAAGTTAAATTTCTT
1 AATGAACAAACATGAACAAG--AAATTTCTT
5128612 AATGAACAAACAT-ACACAAGAAATTTC
1 AATGAACAAACATGA-ACAAGAAATTTC
5128639 ATTTGTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
30 1 0.04
31 18 0.69
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.24
Consensus pattern (29 bp):
AATGAACAAACATGAACAAGAAATTTCTT
Found at i:5129072 original size:31 final size:30
Alignment explanation
Indices: 5129012--5129079 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
5129002 CTTTTAATTT
* **
5129012 ATTTTTTTCTAACATTTGTGTTACTGTCCA
1 ATTTTTTTCTAACATTTGTATTAAGGTCCA
5129042 ATTTTTTT-TAACATTTGTTATTAGAGGTCCA
1 ATTTTTTTCTAACATTTG-TATTA-AGGTCCA
5129073 ATTTTTT
1 ATTTTTT
5129080 CAATATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 12 0.36
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (30 bp):
ATTTTTTTCTAACATTTGTATTAAGGTCCA
Found at i:5140749 original size:2 final size:2
Alignment explanation
Indices: 5140742--5140773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5140732 TTCATACATG
5140742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5140774 CATTCGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5167647 original size:10 final size:11
Alignment explanation
Indices: 5167623--5167651 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5167613 ATAATATAAT
5167623 ATTCAAATCTG
1 ATTCAAATCTG
5167634 ATTCAAAT-TG
1 ATTCAAATCTG
5167644 ATTCAAAT
1 ATTCAAAT
5167652 GGGTTCAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (11 bp):
ATTCAAATCTG
Found at i:5171536 original size:50 final size:50
Alignment explanation
Indices: 5171419--5171524 Score: 158
Period size: 50 Copynumber: 2.1 Consensus size: 50
5171409 TTACCCGAAA
* *
5171419 CATGCTAATACATGCATCCTTATAGCACCTTGGCTCCATCAAGGTGATCT
1 CATGCTAATACATGTATCCTTATAGCACCTCGGCTCCATCAAGGTGATCT
* * *
5171469 CATGCTAATACATGTATCCTTATAGCACCTCGGTTCCATCGAGGTGGTCT
1 CATGCTAATACATGTATCCTTATAGCACCTCGGCTCCATCAAGGTGATCT
*
5171519 CGTGCT
1 CATGCT
5171525 CCATGTTGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (50 bp):
CATGCTAATACATGTATCCTTATAGCACCTCGGCTCCATCAAGGTGATCT
Found at i:5177502 original size:24 final size:24
Alignment explanation
Indices: 5177475--5177526 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5177465 CGTTCATTTA
*
5177475 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
5177499 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
5177523 CGTT
1 CGTT
5177527 TATGTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.15, G:0.27, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:5177513 original size:14 final size:14
Alignment explanation
Indices: 5177485--5177526 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
5177475 CGTTCGTGAA
5177485 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5177499 CG-T---TTATGTT
1 CGTTCGGTTATGTT
5177509 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5177523 CGTT
1 CGTT
5177527 TATGTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:5177527 original size:24 final size:24
Alignment explanation
Indices: 5177485--5177533 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5177475 CGTTCGTGAA
5177485 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
5177509 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTTATGTT
5177533 C
1 C
5177534 ATTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.08, C:0.14, G:0.24, T:0.53
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGTTTATGTT
Found at i:5177543 original size:24 final size:24
Alignment explanation
Indices: 5177491--5177546 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5177481 TGAACGTTCG
* *
5177491 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
5177515 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
5177539 TTTATGTT
1 GTTATGTT
5177547 TAACACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.11, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:5178738 original size:16 final size:16
Alignment explanation
Indices: 5178717--5178749 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5178707 AAAAAAAATT
*
5178717 TGTTCGTTTATGTTCG
1 TGTTCGTTTAAGTTCG
5178733 TGTTCGTTTAAGTTCG
1 TGTTCGTTTAAGTTCG
5178749 T
1 T
5178750 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.24, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTAAGTTCG
Found at i:5181061 original size:22 final size:19
Alignment explanation
Indices: 5181026--5181066 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 19
5181016 ATATACAAAA
5181026 TTATTTTTTATTAATATTTT
1 TTATTTTTTATTAAT-TTTT
5181046 TTATGTTTTTATTTAATTTTT
1 TTAT-TTTTTA-TTAATTTTT
5181067 AATAATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTATTTTTTATTAATTTTT
Found at i:5184989 original size:44 final size:44
Alignment explanation
Indices: 5184941--5185034 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
5184931 TTTTCTCTTC
* * * *
5184941 TACTGTGAAGGTTTTTATGGCAGGGGGTGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
5184985 TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
1 TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
5185029 TACTGT
1 TACTGT
5185035 TATTGGTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.45
Consensus pattern (44 bp):
TACTGTAAAGGCTTTTATGCCAGGGGATGTTTTTAAGTTTTATG
Found at i:5189139 original size:84 final size:84
Alignment explanation
Indices: 5189021--5189188 Score: 257
Period size: 84 Copynumber: 2.0 Consensus size: 84
5189011 TGGGGACTTC
* * *
5189021 AGTCTTGACTTCCATAAGCTGAGGTTTAACTGGCATACAG-TGGCTAACTTGTTTATAATCTTGG
1 AGTCTTCACTTCCATAAGCTGAGGTTTAACTGGCATAC-GCTGGCTAACATGTTGATAATCTTGG
5189085 TGCTGGATATCCTGAGATAT
65 TGCTGGATATCCTGAGATAT
* * * *
5189105 AGTCTTCACTTCCATAGGCTGAGGTTTAATTGGCATACGCTGGTTAACATGTTGGTAATCTTGGT
1 AGTCTTCACTTCCATAAGCTGAGGTTTAACTGGCATACGCTGGCTAACATGTTGATAATCTTGGT
5189170 GCTGGATATCCTGAGATAT
66 GCTGGATATCCTGAGATAT
5189189 GTGAGGTTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 75 0.99
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (84 bp):
AGTCTTCACTTCCATAAGCTGAGGTTTAACTGGCATACGCTGGCTAACATGTTGATAATCTTGGT
GCTGGATATCCTGAGATAT
Found at i:5191990 original size:17 final size:17
Alignment explanation
Indices: 5191960--5191992 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5191950 TCATCAAAGC
5191960 TATATAGAAATAATGAT
1 TATATAGAAATAATGAT
5191977 TATAT-GAAATTAATGA
1 TATATAGAAA-TAATGA
5191993 CAGGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
TATATAGAAATAATGAT
Found at i:5192081 original size:13 final size:13
Alignment explanation
Indices: 5192063--5192096 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5192053 AAGGATCATC
5192063 ACATACATCTCCA
1 ACATACATCTCCA
*
5192076 ACATACATCTCCC
1 ACATACATCTCCA
5192089 ACATACAT
1 ACATACAT
5192097 GGATTCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (13 bp):
ACATACATCTCCA
Found at i:5194639 original size:32 final size:31
Alignment explanation
Indices: 5194569--5194654 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
5194559 TTAAATTTTA
*
5194569 AAAT-TATTTCTTTATTTTTGTTTTAACTTATT
1 AAATATATTT-TTT-TTTTTTTTTTAACTTATT
* *
5194601 AAATAT-TTTTTTTTTTTTTCTTAATTTATT
1 AAATATATTTTTTTTTTTTTTTTAACTTATT
* *
5194631 AAATATATTTTATTTTTATTTTTA
1 AAATATATTTTTTTTTTTTTTTTA
5194655 TATAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 21 0.46
31 17 0.37
32 7 0.15
33 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (31 bp):
AAATATATTTTTTTTTTTTTTTTAACTTATT
Found at i:5194772 original size:36 final size:36
Alignment explanation
Indices: 5194732--5194802 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
5194722 TATTTAAATA
5194732 TTTTACTATTAATTTAATATAAA-ATAT-ATTTTTTAT
1 TTTTACTATTAATTTAA-A-AAATATATAATTTTTTAT
* * *
5194768 TTTTATTTTTTATTTAAAAAATATATAATTTTTTA
1 TTTTACTATTAATTTAAAAAATATATAATTTTTTA
5194803 ATATATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
34 3 0.10
35 5 0.17
36 22 0.73
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (36 bp):
TTTTACTATTAATTTAAAAAATATATAATTTTTTAT
Found at i:5194776 original size:13 final size:13
Alignment explanation
Indices: 5194758--5194782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5194748 ATATAAAATA
5194758 TATTTTTTATTTT
1 TATTTTTTATTTT
5194771 TATTTTTTATTT
1 TATTTTTTATTT
5194783 AAAAAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:5194857 original size:34 final size:33
Alignment explanation
Indices: 5194810--5194927 Score: 88
Period size: 34 Copynumber: 3.6 Consensus size: 33
5194800 TTAATATATT
5194810 TTTAAAAGTTAAGATAATAATAAATTATATTTTTAA
1 TTTAAAA--TAAGATAA-AATAAATTATATTTTTAA
* *
5194846 TTTAAAATAAG---AATTCAA-T-TATTTTTAA
1 TTTAAAATAAGATAAAATAAATTATATTTTTAA
* *
5194874 -GTAAAGATAAGAATAAAAT-ATTATATATTTTTAA
1 TTTAAA-ATAAG-ATAAAATAAAT-TATATTTTTAA
5194908 TTTAAAATAAGAGTAAAATA
1 TTTAAAATAAGA-TAAAATA
5194928 TATATTTTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
27 4 0.06
28 14 0.22
29 1 0.02
30 4 0.06
31 2 0.03
32 3 0.05
33 2 0.03
34 24 0.37
35 4 0.06
36 7 0.11
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.41
Consensus pattern (33 bp):
TTTAAAATAAGATAAAATAAATTATATTTTTAA
Found at i:5194928 original size:34 final size:33
Alignment explanation
Indices: 5194865--5194936 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 33
5194855 AGAATTCAAT
5194865 TATTTTTAAGTAAAGATAAGAATAAAATATTATA
1 TATTTTTAAGTAAAGATAAGAATAAAATA-TATA
* *
5194899 TATTTTTAATTTAAA-ATAAGAGTAAAATATATA
1 TATTTTTAA-GTAAAGATAAGAATAAAATATATA
5194932 T-TTTT
1 TATTTT
5194937 ATATTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.11
33 5 0.14
34 22 0.63
35 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (33 bp):
TATTTTTAAGTAAAGATAAGAATAAAATATATA
Found at i:5195089 original size:29 final size:29
Alignment explanation
Indices: 5195048--5195123 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
5195038 ATAATTTTAC
* *
5195048 ATTAAAATAAAAACAAAATATATTTAATAA
1 ATTAAAACAAAAATAAAA-ATATTTAATAA
*
5195078 ATTAAGACAAAAATAAAAATATTTAATAA
1 ATTAAAACAAAAATAAAAATATTTAATAA
*
5195107 GTTAAAACAAAAATAAA
1 ATTAAAACAAAAATAAA
5195124 GAGATAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 26 0.63
30 15 0.37
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (29 bp):
ATTAAAACAAAAATAAAAATATTTAATAA
Found at i:5197386 original size:4 final size:4
Alignment explanation
Indices: 5197379--5197420 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
5197369 AGAATGCATA
*
5197379 TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
5197421 AGAAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:5197692 original size:104 final size:103
Alignment explanation
Indices: 5197403--5197722 Score: 408
Period size: 109 Copynumber: 3.0 Consensus size: 103
5197393 TGTATGTATG
* *
5197403 TATGTATGTATGCATGTAAGAAAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGTATGAAGA
1 TATGTATGCACGCATGTAAGAAAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGTATGAAGA
* *
5197468 AGACTGCCAAAAACAAGCATATCCCTCCTAAAATGATA
66 AGACTGCCAAAAACAAGCATAGCCCTCCTACAATGATA
* * * * * *
5197506 CATGTATGCATGCATGCGTGTATGTATGTAAA-AAACTTGCTTTGGTTTGATAACATAAAGAAGT
1 TATGTATGCA--C--GCATGTAAG-A--AAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGT
* * * * *
5197570 ATGAATAAGACTGTCAAAAACAAGCATAGACTTACTACAATGATA
59 ATGAAGAAGACTGCCAAAAACAAGCATAGCCCTCCTACAATGATA
*
5197615 TATGTATGCACGTATGTAAAGAAAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGTATGAAG
1 TATGTATGCACGCATGT-AAGAAAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGTATGAAG
*
5197680 AAGACAGCCAAAAACAAGCATAGCCCTCCTACAATGATA
65 AAGACTGCCAAAAACAAGCATAGCCCTCCTACAATGATA
5197719 TATG
1 TATG
5197723 CAATTCCCAG
Statistics
Matches: 180, Mismatches: 28, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
103 11 0.06
104 73 0.41
105 5 0.03
106 2 0.01
107 8 0.04
108 1 0.01
109 77 0.43
110 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (103 bp):
TATGTATGCACGCATGTAAGAAAAAGAAACTTGCCTTGGCTTGATAACATAAAGAAGTATGAAGA
AGACTGCCAAAAACAAGCATAGCCCTCCTACAATGATA
Found at i:5203020 original size:29 final size:31
Alignment explanation
Indices: 5202994--5203050 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
5202984 CGTTTATATA
5202994 ATTAAAC-TTGTAATTT-TA-TCAATTATAAC
1 ATTAAACGTT-TAATTTATATTCAATTATAAC
*
5203023 ATTGAACGTTTAATTTATATTCAATTAT
1 ATTAAACGTTTAATTTATATTCAATTAT
5203051 GATACCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.50
30 4 0.17
31 8 0.33
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTAAACGTTTAATTTATATTCAATTATAAC
Found at i:5203671 original size:19 final size:19
Alignment explanation
Indices: 5203649--5203747 Score: 78
Period size: 19 Copynumber: 5.0 Consensus size: 19
5203639 AATAAATTTT
5203649 GTAATTTTATTAAATAAAA
1 GTAATTTTATTAAATAAAA
5203668 GTAATATATTTATTAAA-AAATA
1 GT-A-AT-TTTATTAAATAAA-A
*
5203690 TTAATTTTATTAAATAAAA
1 GTAATTTTATTAAATAAAA
5203709 -TAATATATTTATTAAA-AAAA
1 GT-A-AT-TTTATTAAATAAAA
* * *
5203729 TTATTTTTATTTAATAAAA
1 GTAATTTTATTAAATAAAA
5203748 ATAGGGATTT
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
18 9 0.13
19 18 0.27
20 13 0.19
21 16 0.24
22 11 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
GTAATTTTATTAAATAAAA
Found at i:5203679 original size:22 final size:20
Alignment explanation
Indices: 5203654--5203750 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 20
5203644 ATTTTGTAAT
5203654 TTTATTAAATAAAAGTAATATA
1 TTTATTAAA-AAAA-TAATATA
*
5203676 TTTATT-AAAAAATATTA-A
1 TTTATTAAAAAAATAATATA
5203694 TTTTATTAAATAAAATAATATA
1 -TTTATTAAA-AAAATAATATA
*
5203716 TTTATTAAAAAAAT--TATT
1 TTTATTAAAAAAATAATATA
5203734 TTTATTTAATAAAAATA
1 TTTA-TTAA-AAAAATA
5203751 GGGATTTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
18 8 0.12
19 14 0.22
20 17 0.26
21 19 0.29
22 7 0.11
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
TTTATTAAAAAAATAATATA
Found at i:5203724 original size:40 final size:40
Alignment explanation
Indices: 5203650--5203747 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
5203640 ATAAATTTTG
5203650 TAATTTTATTAAATAAAAGTAATATATTTATTAAAAAATAT
1 TAATTTTATTAAATAAAAGTAATATATTTATTAAAAAA-AT
5203691 TAATTTTATTAAATAAAA-TAATATATTTATTAAAAAAAT
1 TAATTTTATTAAATAAAAGTAATATATTTATTAAAAAAAT
* *
5203730 TATTTTTATTTAATAAAA
1 TAATTTTATTAAATAAAA
5203748 ATAGGGATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
39 18 0.33
40 19 0.35
41 18 0.33
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (40 bp):
TAATTTTATTAAATAAAAGTAATATATTTATTAAAAAAAT
Found at i:5207069 original size:17 final size:17
Alignment explanation
Indices: 5207047--5207081 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5207037 GCCTAGGACT
* *
5207047 CTAAGTTTGGAGGGGCC
1 CTAAGTTTAGAGGAGCC
5207064 CTAAGTTTAGAGGAGCC
1 CTAAGTTTAGAGGAGCC
5207081 C
1 C
5207082 ATTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (17 bp):
CTAAGTTTAGAGGAGCC
Found at i:5207231 original size:73 final size:73
Alignment explanation
Indices: 5207106--5207252 Score: 213
Period size: 73 Copynumber: 2.0 Consensus size: 73
5207096 TTTTAAGTTT
* ** * * *
5207106 AATAATTAAAAATTATTTTTAAACATGTTTTTTTATTTCAAATATTCAAAAATATGGTAATTTAG
1 AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCAAAAATATGGTAATTTAG
*
5207171 TGGGTCCC
66 TGGGCCCC
* *
5207179 AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCGAAAATATGGTTATTTAG
1 AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCAAAAATATGGTAATTTAG
5207244 TGGGCCCC
66 TGGGCCCC
5207252 A
1 A
5207253 TTTTAATGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (73 bp):
AATAATTAAAAAATATTTTTAAACATCATTTTTTATTTAAAAAACTCAAAAATATGGTAATTTAG
TGGGCCCC
Found at i:5207989 original size:28 final size:29
Alignment explanation
Indices: 5207946--5208012 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
5207936 TGTTTATTTT
*
5207946 AATTTTAAATATTAAAA-TCTAAAACCCTA
1 AATTTTAAATAGTAAAATTCTAAAA-CCTA
*
5207975 AATTTT-AATAGTAAAATTCTAAAATCTA
1 AATTTTAAATAGTAAAATTCTAAAACCTA
*
5208003 AATTATAAAT
1 AATTTTAAAT
5208013 CTTATAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.37
Consensus pattern (29 bp):
AATTTTAAATAGTAAAATTCTAAAACCTA
Found at i:5211601 original size:21 final size:21
Alignment explanation
Indices: 5211575--5211614 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5211565 GTAAATGTTA
*
5211575 AAAAATATTAATATTTTAATT
1 AAAAATAATAATATTTTAATT
5211596 AAAAATAATAATATTTTAA
1 AAAAATAATAATATTTTAA
5211615 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATAATAATATTTTAATT
Found at i:5212886 original size:17 final size:17
Alignment explanation
Indices: 5212861--5212897 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5212851 CTCTTCAACT
5212861 TTTAAATTTTCTTTATA
1 TTTAAATTTTCTTTATA
* *
5212878 TTTAGATTTTTTTTATA
1 TTTAAATTTTCTTTATA
5212895 TTT
1 TTT
5212898 TCTATTGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTAAATTTTCTTTATA
Found at i:5221790 original size:455 final size:457
Alignment explanation
Indices: 5220903--5221814 Score: 1783
Period size: 455 Copynumber: 2.0 Consensus size: 457
5220893 GATCAAAGGT
5220903 GAAAGCTTTGGTTTAGTTTCAGTTTATTTCTTTAAACCAAGGAAATGAGTTAATTCAGTATCTTT
1 GAAAGCTTTGGTTTAGTTTCAGTTTATTTCTTTAAACCAAGGAAATGAGTTAATTCAGTATCTTT
5220968 AGAGCTTTCTTTTAAATCCCCAACATCACCATCTCACCATGGGAGCTAAGAACGAGTTTTGTGGG
66 AGAGCTTTCTTTTAAATCCCCAACATCACCATCTCACCATGGGAGCTAAGAACGAGTTTTGTGGG
5221033 GTTTAAGAGTTTTCAAGATTTCAGCCCGTTTTCAATAATCCATAGGTTTTGGAAGTGTTCTTATT
131 GTTTAAGAGTTTTCAAGATTTCAGCCCGTTTTCAATAATCCATAGGTTTTGGAAGTGTTCTTATT
5221098 ACCTTCTTAACCATTTTTTTTCCAGCTAGTAATCTATCCCTTGATGTTTGTCTAGTGAGAGAGAT
196 ACCTTCTTAACCATTTTTTTTCCAGCTAGTAATCTATCCCTTGATGTTTGTCTAGTGAGAGAGAT
5221163 TGGAGAAAACTCCAAAGCTAAAAGGAAGGAGAAACTCACCCTTGGTTGAGCATTGAGTGTTTTCA
261 TGGAGAAAACTCCAAAGCTAAAAGGAAGGAGAAACTCACCCTTGGTTGAGCATTGAGTGTTTTCA
5221228 GAAGTTTAGTATCAAAGGTAACTCACTCTTAACTCAACTATACCATATGTAAGTCATTTAGATGA
326 GAAGTTTAGTATCAAAGGTAACTCACTCTTAACTCAACTATACCATATGTAAGTCATTTAGATGA
5221293 AATGTAGTAGGTTGCATAAGCTTGAAGCACTCCCATGTTAGATTTCATGTTTTAGAGTTATGTTT
391 AATGTAGTAGGTTGCATAAGCTTGAAGCACTCCCATGTTAGATTTCATGTTTTAGAGTTATGTTT
5221358 AA
456 AA
5221360 GAAAGCTTTGGTTTAGTTTCAGTTTATTTCTTTAAACCAAGGAAATGAGTTAATTCAGTATCTTT
1 GAAAGCTTTGGTTTAGTTTCAGTTTATTTCTTTAAACCAAGGAAATGAGTTAATTCAGTATCTTT
*
5221425 AGAGCTTTCTTTTAAATCCCCAACTTCACCATCTCACCATGGGAGCTAAGAACGAGTTTTGTGGG
66 AGAGCTTTCTTTTAAATCCCCAACATCACCATCTCACCATGGGAGCTAAGAACGAGTTTTGTGGG
5221490 GTTTAAGAGTTTTCAAGATTTCAGCCCGTTTTCAATAATCCATAGGTTTTGGAAGTGTTCTTATT
131 GTTTAAGAGTTTTCAAGATTTCAGCCCGTTTTCAATAATCCATAGGTTTTGGAAGTGTTCTTATT
5221555 ACCTTCTTAACCA-TTTTTTT-CAGCTAGTAATCTATCCCTTGATGTTTGTCTAGTGAGAGAGAT
196 ACCTTCTTAACCATTTTTTTTCCAGCTAGTAATCTATCCCTTGATGTTTGTCTAGTGAGAGAGAT
*
5221618 TGGAGAAAACTCCAAAGCTAAAGGGAAGGAGAAACTCACCCTTGGTTGAGCATTGAGTGTTTTCA
261 TGGAGAAAACTCCAAAGCTAAAAGGAAGGAGAAACTCACCCTTGGTTGAGCATTGAGTGTTTTCA
*
5221683 GCAGTTTAGTATCAAAGGTAACTCACTCTTAACTCAACTATACCATATGTAAGTCATTTAGATGA
326 GAAGTTTAGTATCAAAGGTAACTCACTCTTAACTCAACTATACCATATGTAAGTCATTTAGATGA
5221748 AATGTAGTAGGTTGCATAAGCTTGAAGCACTCCCATGTTAGATTTCATGTTTTAGAGTTATGTTT
391 AATGTAGTAGGTTGCATAAGCTTGAAGCACTCCCATGTTAGATTTCATGTTTTAGAGTTATGTTT
5221813 AA
456 AA
5221815 AGCCCTATTT
Statistics
Matches: 452, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
455 238 0.53
456 7 0.02
457 207 0.46
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (457 bp):
GAAAGCTTTGGTTTAGTTTCAGTTTATTTCTTTAAACCAAGGAAATGAGTTAATTCAGTATCTTT
AGAGCTTTCTTTTAAATCCCCAACATCACCATCTCACCATGGGAGCTAAGAACGAGTTTTGTGGG
GTTTAAGAGTTTTCAAGATTTCAGCCCGTTTTCAATAATCCATAGGTTTTGGAAGTGTTCTTATT
ACCTTCTTAACCATTTTTTTTCCAGCTAGTAATCTATCCCTTGATGTTTGTCTAGTGAGAGAGAT
TGGAGAAAACTCCAAAGCTAAAAGGAAGGAGAAACTCACCCTTGGTTGAGCATTGAGTGTTTTCA
GAAGTTTAGTATCAAAGGTAACTCACTCTTAACTCAACTATACCATATGTAAGTCATTTAGATGA
AATGTAGTAGGTTGCATAAGCTTGAAGCACTCCCATGTTAGATTTCATGTTTTAGAGTTATGTTT
AA
Found at i:5224750 original size:20 final size:20
Alignment explanation
Indices: 5224716--5224812 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
5224706 ATCAGTTTCC
*
5224716 AAAATCGCAACGCGATTCTG
1 AAAATCGCAACGCGATTATG
*
5224736 AAAATCGCAATGCGA-TA-G
1 AAAATCGCAACGCGATTATG
** * *
5224754 TACAAATTCGCATTGCGATTTTC
1 -A-AAA-TCGCAACGCGATTATG
*
5224777 AAGAATCGCAACGCGAATATG
1 AA-AATCGCAACGCGATTATG
5224798 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
5224813 ACACATAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 2 0.03
20 30 0.49
21 24 0.39
22 4 0.07
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTATG
Found at i:5224813 original size:20 final size:20
Alignment explanation
Indices: 5224780--5224975 Score: 191
Period size: 20 Copynumber: 9.8 Consensus size: 20
5224770 GATTTTCAAG
* **
5224780 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGAA
*
5224800 AATCGCAACGCG-AACAC-ATA
1 AATCGCAACGCGTATC-CGA-A
* *
5224820 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGAA
* *
5224840 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGAA
*
5224860 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
5224880 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
5224900 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
* *
5224920 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCG-AA
*
5224941 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGAA
5224961 AATCGCAACGCGTAT
1 AATCGCAACGCGTAT
5224976 TTTATTTTCA
Statistics
Matches: 150, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.01
20 130 0.87
21 18 0.12
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGAA
Found at i:5224863 original size:60 final size:60
Alignment explanation
Indices: 5224780--5224975 Score: 252
Period size: 60 Copynumber: 3.2 Consensus size: 60
5224770 GATTTTCAAG
* ** * * *
5224780 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
* * *
5224840 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTAAATCGCAACGCGTATCCGTA
* *
5224900 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAACACGT-AAATCGCAACGCGTATCCGTA
5224961 AATCGCAACGCGTAT
1 AATCGCAACGCGTAT
5224976 TTTATTTTCA
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 79 0.68
61 37 0.32
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTAAATCGCAACGCGTATCCGTA
Found at i:5225356 original size:31 final size:33
Alignment explanation
Indices: 5225319--5225384 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 33
5225309 TTCACTTAGA
5225319 TTTCATTTCGCGTTACGA-T-TCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
5225350 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
5225383 TT
1 TT
5225385 CAAGTTAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 16 0.52
32 1 0.03
33 14 0.45
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:5225492 original size:21 final size:20
Alignment explanation
Indices: 5225466--5225539 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
5225456 TGCAGAAGAG
5225466 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
5225487 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
5225507 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
5225529 TCGCAACGAGA
1 TCGCAACGAGA
5225540 GAATCGCAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.22
21 25 0.56
22 10 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:5225584 original size:19 final size:19
Alignment explanation
Indices: 5225562--5225688 Score: 69
Period size: 19 Copynumber: 7.1 Consensus size: 19
5225552 GAAACCAAAA
*
5225562 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
5225581 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
5225595 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
5225614 TCACGTTGCGA---TC---
1 TCGCGTTGCGATTTTCATT
*
5225627 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
5225647 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
5225667 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
5225687 TC
1 TC
5225689 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
13 10 0.12
14 10 0.12
16 7 0.08
17 3 0.04
19 22 0.26
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5225634 original size:32 final size:33
Alignment explanation
Indices: 5225567--5225689 Score: 149
Period size: 33 Copynumber: 3.5 Consensus size: 33
5225557 CAAAATCGCA
*
5225567 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
5225600 TTGCGATTTTCATTTCACGTTGCGA-TCTCTCG
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
*
5225632 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCACGTT--G-C-G--ATTCTCTCG
5225673 TTGCGATTTTCATTTCA
1 TTGCGATTTTCATTTCA
5225690 ACCAAAAGAC
Statistics
Matches: 78, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
32 19 0.24
33 26 0.33
34 6 0.08
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.03
40 3 0.04
41 19 0.24
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCG
Found at i:5225651 original size:21 final size:21
Alignment explanation
Indices: 5225625--5225688 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
5225615 CACGTTGCGA
5225625 TCTCTCGTTGCGATTTTCATT
1 TCTCTCGTTGCGATTTTCATT
***
5225646 TCTCTCGTTGCGACAGTCA-T
1 TCTCTCGTTGCGATTTTCATT
5225666 TCTCTCGTTGCGATTTTCATT
1 TCTCTCGTTGCGATTTTCATT
5225687 TC
1 TC
5225689 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.11, C:0.27, G:0.16, T:0.47
Consensus pattern (21 bp):
TCTCTCGTTGCGATTTTCATT
Found at i:5227503 original size:93 final size:93
Alignment explanation
Indices: 5227331--5227548 Score: 413
Period size: 93 Copynumber: 2.4 Consensus size: 93
5227321 TAGATTGCTT
*
5227331 AGTAAATTTATTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5227395 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5227423 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
5227488 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
5227516 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAA
5227549 CTAATACCCT
Statistics
Matches: 124, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
92 42 0.34
93 82 0.66
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:5227683 original size:13 final size:13
Alignment explanation
Indices: 5227665--5227694 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5227655 ACGAAACTTA
5227665 AAATCGCAACGAG
1 AAATCGCAACGAG
*
5227678 AAATCGCAACGCG
1 AAATCGCAACGAG
5227691 AAAT
1 AAAT
5227695 GAAAATCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (13 bp):
AAATCGCAACGAG
Found at i:5227693 original size:33 final size:33
Alignment explanation
Indices: 5227648--5227767 Score: 156
Period size: 33 Copynumber: 3.7 Consensus size: 33
5227638 TAGTTTACTT
* * *
5227648 TCGCAACACGAAACTTAAAATCGCAACGAGAAA
1 TCGCAACGCGAAACTCAAAATCGCAACGAAAAA
* *
5227681 TCGCAACGCGAAA-TGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACTCAAAATCGCAACGA-AAAA
5227714 TCGCAACGCGAAAC-CAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACTCAAAATCGCAACGA-AAAA
5227747 TCGCAACGCGAAAC-CAAAATC
1 TCGCAACGCGAAACTCAAAATC
5227768 CATTGCGATT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 14 0.18
33 65 0.82
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACTCAAAATCGCAACGAAAAA
Found at i:5227702 original size:19 final size:18
Alignment explanation
Indices: 5227678--5227759 Score: 63
Period size: 14 Copynumber: 4.9 Consensus size: 18
5227668 TCGCAACGAG
5227678 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAA-GA
*
5227697 AAATCGCAA--CGACAG-
1 AAATCGCAACGCGAAAGA
*
5227712 -AATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAA-GA
*
5227730 AAATCGCAA--CG--ACA
1 AAATCGCAACGCGAAAGA
5227744 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
5227760 CCAAAATCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
14 19 0.37
15 1 0.02
16 7 0.14
17 6 0.12
18 1 0.02
19 17 0.33
ACGTcount: A:0.48, C:0.27, G:0.18, T:0.07
Consensus pattern (18 bp):
AAATCGCAACGCGAAAGA
Found at i:5227717 original size:14 final size:14
Alignment explanation
Indices: 5227696--5227754 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
5227686 ACGCGAAATG
5227696 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5227710 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
5227729 AAAATCGCAACGAC
1 AAAATCGCAACGAC
5227743 AAAATCGCAACG
1 AAAATCGCAACG
5227755 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5227766 original size:19 final size:18
Alignment explanation
Indices: 5227678--5227767 Score: 79
Period size: 19 Copynumber: 5.3 Consensus size: 18
5227668 TCGCAACGAG
*
5227678 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAA-CA
5227697 AAATCGCAA--CG--ACA
1 AAATCGCAACGCGAAACA
*
5227711 GAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAA-CA
5227730 AAATCGCAA--CG--ACA
1 AAATCGCAACGCGAAACA
5227744 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAA-CA
5227763 AAATC
1 AAATC
5227768 CATTGCGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 26 0.45
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AAATCGCAACGCGAAACA
Found at i:5227812 original size:33 final size:32
Alignment explanation
Indices: 5227770--5227861 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
5227760 CCAAAATCCA
5227770 TTGCGATTTTTCATTTCGCGTTGCGATCTCTCG
1 TTGCGA-TTTTCATTTCGCGTTGCGATCTCTCG
* * *
5227803 TTGCGATTTTCATTTCGCATTGTGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TCTCTCG
*
5227836 TTGCGATTTTCATTTCACGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
5227862 TTGGGTTTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
32 18 0.35
33 34 0.65
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATCTCTCG
Found at i:5227858 original size:19 final size:19
Alignment explanation
Indices: 5227770--5227922 Score: 103
Period size: 19 Copynumber: 8.5 Consensus size: 19
5227760 CCAAAATCCA
5227770 TTGCGATTTTTCATTTCGCG
1 TTGCGA-TTTTCATTTCGCG
*
5227790 TTGCGA---TC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
5227803 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
* *
5227822 TTGTGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
*
5227836 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGCG
***
5227855 TTGCGATTTGGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
** *
5227874 TTGCGATTTTGGTTTCCTCG
1 TTGCGATTTTCATTT-CGCG
*
5227894 TTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
5227913 TTGCGATTTT
1 TTGCGATTTT
5227923 AAGTTTCGTT
Statistics
Matches: 102, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
13 10 0.10
14 6 0.06
16 9 0.09
17 5 0.05
19 51 0.50
20 21 0.21
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:5229899 original size:19 final size:18
Alignment explanation
Indices: 5229869--5229971 Score: 100
Period size: 19 Copynumber: 6.1 Consensus size: 18
5229859 GCATTATGTT
5229869 GAAATGAAATCGCAATGC
1 GAAATGAAATCGCAATGC
5229887 GAAATGAAAATCGCAA--C
1 GAAATG-AAATCGCAATGC
5229904 G--A-G-AATCGCAATGC
1 GAAATGAAATCGCAATGC
5229918 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAATGC
5229937 GGAAATGAAATCGCAA--C
1 -GAAATGAAATCGCAATGC
*
5229954 GAGA-G-AATCGCAATGC
1 GAAATGAAATCGCAATGC
5229970 GA
1 GA
5229972 TTTTCATTTC
Statistics
Matches: 73, Mismatches: 1, Indels: 24
0.74 0.01 0.24
Matches are distributed among these distances:
12 8 0.11
14 11 0.15
15 2 0.03
16 7 0.10
17 4 0.05
18 6 0.08
19 29 0.40
20 6 0.08
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (18 bp):
GAAATGAAATCGCAATGC
Found at i:5229948 original size:50 final size:50
Alignment explanation
Indices: 5229869--5229971 Score: 165
Period size: 50 Copynumber: 2.0 Consensus size: 50
5229859 GCATTATGTT
5229869 GAAATGAAATCGCAATGCGAAATGAAAATCGCAAC-GAGAATCGCAATGC
1 GAAATGAAATCGCAATGCGAAATGAAAATCGCAACAGAGAATCGCAATGC
5229918 GAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGAATCGCAATGC
1 GAAATG-AAATCGCAATGC-GAAATGAAAATCGCAAC-AGAGAATCGCAATGC
5229970 GA
1 GA
5229972 TTTTCATTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
49 6 0.12
50 22 0.44
51 6 0.12
52 16 0.32
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (50 bp):
GAAATGAAATCGCAATGCGAAATGAAAATCGCAACAGAGAATCGCAATGC
Found at i:5229989 original size:19 final size:19
Alignment explanation
Indices: 5229961--5230219 Score: 301
Period size: 19 Copynumber: 14.7 Consensus size: 19
5229951 AACGAGAGAA
*
5229961 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5229980 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5229999 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
5230016 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230033 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
5230051 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
5230067 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230084 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
5230103 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
5230120 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230137 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230156 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230175 TCGCATTGCGA-TTTC--T
1 TCGCATTGCGATTTTCATT
*
5230191 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
5230207 TCGCATTGCGATT
1 TCGCATTGCGATT
5230220 CTCTCGTTGC
Statistics
Matches: 208, Mismatches: 9, Indels: 46
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.02
14 22 0.11
15 1 0.00
16 21 0.10
17 20 0.10
18 28 0.13
19 91 0.44
20 20 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5230030 original size:53 final size:52
Alignment explanation
Indices: 5229967--5230233 Score: 407
Period size: 53 Copynumber: 5.1 Consensus size: 52
5229957 AGAATCGCAA
5229967 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
5230020 TGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
5230071 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
5230124 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * *** *
5230174 TTCGCA-TTGCGATTTCTTGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
5230227 TGCGATT
1 TGCGATT
5230234 GTAATTTCCG
Statistics
Matches: 198, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
50 9 0.05
51 76 0.38
52 30 0.15
53 83 0.42
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:5230096 original size:104 final size:103
Alignment explanation
Indices: 5229967--5230233 Score: 414
Period size: 104 Copynumber: 2.6 Consensus size: 103
5229957 AGAATCGCAA
5229967 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
5230032 TTCGCATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCAT
5230071 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
5230136 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAT
* * *** *
5230174 TTCGCA-TTGCGATTTCTTGTTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCG-ATTTTC-ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
5230234 GTAATTTCCG
Statistics
Matches: 153, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
103 35 0.23
104 98 0.64
105 20 0.13
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (103 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAT
Found at i:5233404 original size:20 final size:20
Alignment explanation
Indices: 5233376--5233604 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
5233366 AAATTTCAGT
* * *
5233376 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5233396 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
** *
5233416 GTTGCGATTTATAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
5233436 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
5233456 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
5233476 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
5233496 GTTGCTATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
5233516 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
5233536 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
5233556 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
5233576 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
5233596 GTTGCGATT
1 GTTGCGATT
5233605 CTTGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:5233657 original size:21 final size:20
Alignment explanation
Indices: 5233572--5233669 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
5233562 ATTTATGTGT
* *
5233572 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
5233592 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
5233613 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
5233634 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
5233655 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
5233670 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:5233665 original size:42 final size:43
Alignment explanation
Indices: 5233572--5233670 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
5233562 ATTTATGTGT
* *
5233572 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
5233613 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
5233655 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
5233671 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:5238144 original size:55 final size:55
Alignment explanation
Indices: 5238071--5238175 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
5238061 TTACATACCG
*
5238071 ATGGATCTAAATTAAGTTTAAAACTGAACATGTTTTATTATGAAATTTAATACTA
1 ATGGATCTAAATTAAGTTTAAAACTGAACACGTTTTATTATGAAATTTAATACTA
** *
5238126 ATGGATCTAGGTTAAGTTTAAAGCTGAACACGTTTTATTATGAAATTTAA
1 ATGGATCTAAATTAAGTTTAAAACTGAACACGTTTTATTATGAAATTTAA
5238176 AAGTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (55 bp):
ATGGATCTAAATTAAGTTTAAAACTGAACACGTTTTATTATGAAATTTAATACTA
Found at i:5239178 original size:205 final size:205
Alignment explanation
Indices: 5238826--5239236 Score: 822
Period size: 205 Copynumber: 2.0 Consensus size: 205
5238816 ATTCGCCGGA
5238826 GACTCTGAATCAACAAGGTAACGCAACTGATCAGCCTAGAGTGTTTTCGTGTAACTATTGCCAAA
1 GACTCTGAATCAACAAGGTAACGCAACTGATCAGCCTAGAGTGTTTTCGTGTAACTATTGCCAAA
5238891 GGAAGTTTTTTAGCTCACAGGCCTTGGGTGGGCACCAAAATGCTCATAAACGAGAAAGGACACTA
66 GGAAGTTTTTTAGCTCACAGGCCTTGGGTGGGCACCAAAATGCTCATAAACGAGAAAGGACACTA
5238956 GCCAAACGAGGGCATCAAAGAATCAGTGCCGGTGCGGCGGCATCCTTCGTGGCGTTTGGTAGATA
131 GCCAAACGAGGGCATCAAAGAATCAGTGCCGGTGCGGCGGCATCCTTCGTGGCGTTTGGTAGATA
5239021 TTTGACCATG
196 TTTGACCATG
5239031 GACTCTGAATCAACAAGGTAACGCAACTGATCAGCCTAGAGTGTTTTCGTGTAACTATTGCCAAA
1 GACTCTGAATCAACAAGGTAACGCAACTGATCAGCCTAGAGTGTTTTCGTGTAACTATTGCCAAA
5239096 GGAAGTTTTTTAGCTCACAGGCCTTGGGTGGGCACCAAAATGCTCATAAACGAGAAAGGACACTA
66 GGAAGTTTTTTAGCTCACAGGCCTTGGGTGGGCACCAAAATGCTCATAAACGAGAAAGGACACTA
5239161 GCCAAACGAGGGCATCAAAGAATCAGTGCCGGTGCGGCGGCATCCTTCGTGGCGTTTGGTAGATA
131 GCCAAACGAGGGCATCAAAGAATCAGTGCCGGTGCGGCGGCATCCTTCGTGGCGTTTGGTAGATA
5239226 TTTGACCATG
196 TTTGACCATG
5239236 G
1 G
5239237 CCTCGCTTCC
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 206 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (205 bp):
GACTCTGAATCAACAAGGTAACGCAACTGATCAGCCTAGAGTGTTTTCGTGTAACTATTGCCAAA
GGAAGTTTTTTAGCTCACAGGCCTTGGGTGGGCACCAAAATGCTCATAAACGAGAAAGGACACTA
GCCAAACGAGGGCATCAAAGAATCAGTGCCGGTGCGGCGGCATCCTTCGTGGCGTTTGGTAGATA
TTTGACCATG
Found at i:5244443 original size:79 final size:79
Alignment explanation
Indices: 5244274--5244534 Score: 407
Period size: 79 Copynumber: 3.3 Consensus size: 79
5244264 GGGGCCTATG
* * * *
5244274 GGCCTACTCAAGGATATCCTTATATCCGTAAGGTTACCTTAAGCACACAACAAAAGGGAACCAAC
1 GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAAC-AAAGGGAACCAAC
*
5244339 CTAAGGATATACCTT
65 CTAAGGATATGCCTT
* * *
5244354 GGCTTACCCAAGGACATCCTTAGATCCGTAGGGTTGCCTTATGCACACAACAAAGGGAACCAACC
1 GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAACAAAGGGAACCAACC
5244419 TAAGGATATGCCTT
66 TAAGGATATGCCTT
* *
5244433 GGCCTACCCAAGGATATCATTAGATCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACC
1 GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAACAAAGGGAACCAACC
5244498 TAAGGATATGCCTT
66 TAAGGATATGCCTT
5244512 GGGCCTACCCAA-GATATCCTTAG
1 -GGCCTACCCAAGGATATCCTTAG
5244535 GTCCTTAAGG
Statistics
Matches: 166, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
79 111 0.67
80 55 0.33
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (79 bp):
GGCCTACCCAAGGATATCCTTAGATCCGTAGGGTTACCTTATGCACACAACAAAGGGAACCAACC
TAAGGATATGCCTT
Found at i:5249177 original size:20 final size:20
Alignment explanation
Indices: 5249152--5249200 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5249142 GAGGGCTGGA
*
5249152 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACC-GATTTC
5249172 AACCGGTTCTGACCGATTTC
1 AACCGGTTCTGACCGATTTC
*
5249192 TACCGGTTC
1 AACCGGTTC
5249201 AAACCGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (20 bp):
AACCGGTTCTGACCGATTTC
Found at i:5249206 original size:20 final size:20
Alignment explanation
Indices: 5249168--5249206 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5249158 TTTGACCGGT
**
5249168 TTTCAACCGGTTCTGACCGA
1 TTTCAACCGGTTCAAACCGA
*
5249188 TTTCTACCGGTTCAAACCG
1 TTTCAACCGGTTCAAACCG
5249207 GTTTGACCGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.31, G:0.18, T:0.31
Consensus pattern (20 bp):
TTTCAACCGGTTCAAACCGA
Found at i:5249230 original size:5 final size:5
Alignment explanation
Indices: 5249220--5249266 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
5249210 TGACCGGTCT
* * *
5249220 GACCC GACCC GA-CT GACCC GACCT GACCC GA-CT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
5249267 GTTGACCGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 6 0.18
5 28 0.82
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:5249235 original size:14 final size:14
Alignment explanation
Indices: 5249218--5249265 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
5249208 TTTGACCGGT
5249218 CTGACCCGACCCGA
1 CTGACCCGACCCGA
5249232 CTGACCCGACCTGACCCGA
1 CTGA--C--CC-GACCCGA
5249251 CTGACCCGACCCGA
1 CTGACCCGACCCGA
5249265 C
1 C
5249266 CGTTGACCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 12 0.41
15 2 0.07
16 1 0.03
17 1 0.03
18 2 0.07
19 11 0.38
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.08
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:5249237 original size:9 final size:9
Alignment explanation
Indices: 5249225--5249260 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
5249215 GGTCTGACCC
5249225 GACCCGACT
1 GACCCGACT
5249234 GACCCGACCT
1 GACCCGA-CT
5249244 GACCCGACT
1 GACCCGACT
5249253 GACCCGAC
1 GACCCGAC
5249261 CCGACCGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.22, C:0.47, G:0.22, T:0.08
Consensus pattern (9 bp):
GACCCGACT
Found at i:5249247 original size:19 final size:19
Alignment explanation
Indices: 5249220--5249266 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
5249210 TGACCGGTCT
5249220 GACCCGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
*
5249239 GACCTGACCCGACTGACCC
1 GACCCGACCCGACTGACCC
5249258 GACCCGACC
1 GACCCGACC
5249267 GTTGACCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.21, C:0.51, G:0.21, T:0.06
Consensus pattern (19 bp):
GACCCGACCCGACTGACCC
Found at i:5256475 original size:6 final size:7
Alignment explanation
Indices: 5256451--5256480 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5256441 GACCCGACCC
5256451 GACCGTT
1 GACCGTT
5256458 GACCGTT
1 GACCGTT
5256465 GACCG-T
1 GACCGTT
5256471 GACCGTT
1 GACCGTT
5256478 GAC
1 GAC
5256481 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:5256475 original size:13 final size:14
Alignment explanation
Indices: 5256451--5256480 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5256441 GACCCGACCC
5256451 GACCGTTGACCGTT
1 GACCGTTGACCGTT
5256465 GACCG-TGACCGTT
1 GACCGTTGACCGTT
5256478 GAC
1 GAC
5256481 TTCCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:5258944 original size:19 final size:19
Alignment explanation
Indices: 5258913--5258950 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5258903 GGTATTTTCC
*
5258913 CGCAACATGTTTGCTATTT
1 CGCAACATGTTTGATATTT
5258932 CGCAACA-GATTTGATATTT
1 CGCAACATG-TTTGATATTT
5258951 AGCAGCGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (19 bp):
CGCAACATGTTTGATATTT
Found at i:5259414 original size:21 final size:21
Alignment explanation
Indices: 5259388--5259427 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5259378 ATGCTACTTT
*
5259388 TCTCTCTGTTTCTCTCGCTGC
1 TCTCTCTGCTTCTCTCGCTGC
5259409 TCTCTCTGCTTCTCTCGCT
1 TCTCTCTGCTTCTCTCGCT
5259428 TCAGCTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.40, G:0.12, T:0.47
Consensus pattern (21 bp):
TCTCTCTGCTTCTCTCGCTGC
Found at i:5264366 original size:31 final size:30
Alignment explanation
Indices: 5264284--5264428 Score: 182
Period size: 30 Copynumber: 4.8 Consensus size: 30
5264274 TTTAACGTCA
* * * *
5264284 AATAATATTTTCGGTCATTTTTTAACGCAT
1 AATAATGTTTTCGGTTATTTTTTAGCGCCT
* *
5264314 AATAATGTTGTCGGTTATTTTTTAGTGCCT
1 AATAATGTTTTCGGTTATTTTTTAGCGCCT
*
5264344 AATAATGTTTTTGGTTATTTTTTAGCGCCT
1 AATAATGTTTTCGGTTATTTTTTAGCGCCT
*
5264374 AATAATGTTTTCGGTTATTTGTTTAGCACCT
1 AATAATGTTTTCGGTTATTT-TTTAGCGCCT
* * *
5264405 AATTATGTTTCCAGTTATTTTTTA
1 AATAATGTTTTCGGTTATTTTTTA
5264429 CATGTTTTTT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 74 0.74
31 26 0.26
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (30 bp):
AATAATGTTTTCGGTTATTTTTTAGCGCCT
Found at i:5264822 original size:82 final size:83
Alignment explanation
Indices: 5264722--5264873 Score: 209
Period size: 82 Copynumber: 1.8 Consensus size: 83
5264712 AAAAACGTCA
*
5264722 CTAAAGTACTACTCTGTTGCGGCGTTTGTTGTAAA-AAAACCACTATATATGAACCCCATTGCGG
1 CTAAAGTACTACTCTGTTGCGGCATTTGTTG-AAACAAAACCACTATATATGAACCCCATTGCGG
5264786 CATTTTTATACAAACACCG
65 CATTTTTATACAAACACCG
* * ** **
5264805 CTAAAGTACT-CTTTGTTGTGGCATTTGTTGAAACAATGCCACTATATATGAACCTTATTGCGGC
1 CTAAAGTACTACTCTGTTGCGGCATTTGTTGAAACAAAACCACTATATATGAACCCCATTGCGGC
*
5264869 GTTTT
66 ATTTT
5264874 GAATTGAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 3 0.05
82 47 0.78
83 10 0.17
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (83 bp):
CTAAAGTACTACTCTGTTGCGGCATTTGTTGAAACAAAACCACTATATATGAACCCCATTGCGGC
ATTTTTATACAAACACCG
Found at i:5271444 original size:21 final size:21
Alignment explanation
Indices: 5271402--5271444 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5271392 TTTTCGGGCT
* * *
5271402 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
5271423 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
5271444 A
1 A
5271445 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:5272263 original size:149 final size:149
Alignment explanation
Indices: 5271988--5272291 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
5271978 GGGTAGAGGG
* * *
5271988 TCTATGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
5272053 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
5272118 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5272137 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
5272202 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
5272267 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5272286 TCTACG
1 TCTACG
5272292 GGGCACTTCG
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:5278399 original size:21 final size:21
Alignment explanation
Indices: 5278357--5278399 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5278347 TTTTCGGGCT
* *
5278357 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
5278378 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
5278399 A
1 A
5278400 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:5278451 original size:20 final size:20
Alignment explanation
Indices: 5278426--5278463 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5278416 GAATGCTAGA
5278426 GGGGAACCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
5278446 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
5278464 TGAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.37, G:0.32, T:0.08
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:5279105 original size:149 final size:149
Alignment explanation
Indices: 5278917--5279211 Score: 545
Period size: 149 Copynumber: 2.0 Consensus size: 149
5278907 GGGTAGAGGG
* *
5278917 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
5278982 ACTTGATCCCTAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
5279047 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
5279066 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
5279131 ACTTGATCCATAGTTTATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
5279196 TATGGCACTACGGTGC
131 TATGGCACTACGGTGC
5279212 TACGGGGCAC
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 141 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATATATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:5280069 original size:51 final size:51
Alignment explanation
Indices: 5279993--5280095 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
5279983 TGTCATTAGG
5279993 TAATTGATTGGTAATTTCTTGGTCAGCTTCATTCGAGTGCCCCACATTGTC
1 TAATTGATTGGTAATTTCTTGGTCAGCTTCATTCGAGTGCCCCACATTGTC
5280044 TAATTGATTGGTAATTTCTTGGTCAGCTTCATTCGAGTGCCCCACATTGTC
1 TAATTGATTGGTAATTTCTTGGTCAGCTTCATTCGAGTGCCCCACATTGTC
5280095 T
1 T
5280096 GAAGTTGAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (51 bp):
TAATTGATTGGTAATTTCTTGGTCAGCTTCATTCGAGTGCCCCACATTGTC
Found at i:5285689 original size:25 final size:24
Alignment explanation
Indices: 5285639--5285689 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
5285629 AAATTGTCGT
*
5285639 AACGTTTTTATTTTTCAAAATGAA
1 AACGTTTTTATTTTTCAAAATAAA
5285663 AACGATTTTTATTTTT-AAAAGTAAA
1 AACG-TTTTTATTTTTCAAAA-TAAA
5285688 AA
1 AA
5285690 TTTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (24 bp):
AACGTTTTTATTTTTCAAAATAAA
Found at i:5286836 original size:21 final size:22
Alignment explanation
Indices: 5286805--5286857 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
5286795 AAAATCTAAT
*
5286805 GAATTAAAAAAG-AAACTTAAAA
1 GAATAAAAAAAGTAAA-TTAAAA
5286827 -AATAAAAAAAGTAAATTAAAA
1 GAATAAAAAAAGTAAATTAAAA
*
5286848 GTATAAAAAA
1 GAATAAAAAA
5286858 TAAAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.72, C:0.02, G:0.08, T:0.19
Consensus pattern (22 bp):
GAATAAAAAAAGTAAATTAAAA
Found at i:5286861 original size:20 final size:20
Alignment explanation
Indices: 5286809--5286904 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 20
5286799 TCTAATGAAT
* *
5286809 TAAAAAAGAAACTTAAAA-AA
1 TAAAAAATAAA-TTAAAAGTA
5286829 TAAAAAAAGTAAATTAAAAGTA
1 T-AAAAAA-TAAATTAAAAGTA
* **
5286851 TAAAAAATAAAATGTAAGTAA
1 TAAAAAATAAATTAAAAGT-A
* *
5286872 GTAAGAAAT-AATTAACAAGCA
1 -TAAAAAATAAATTAA-AAGTA
5286893 TAAAAAATAAAT
1 TAAAAAATAAAT
5286905 ATATACTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
20 17 0.29
21 26 0.45
22 15 0.26
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (20 bp):
TAAAAAATAAATTAAAAGTA
Done.