Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 18 of 143
Found at i:5514142 original size:20 final size:20
Alignment explanation
Indices: 5514117--5514156 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5514107 ACCACATTGA
5514117 ATAGCTAATCTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
* *
5514137 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
5514157 TTAATTATAG
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:5528049 original size:29 final size:29
Alignment explanation
Indices: 5528017--5528081 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
5528007 AATAACATTG
5528017 AAGTGCAATAACAGAACAGAATGGCACCA
1 AAGTGCAATAACAGAACAGAATGGCACCA
** * * * *
5528046 AAGTGCTTTATCATAACAGAGTGGCATCA
1 AAGTGCAATAACAGAACAGAATGGCACCA
5528075 AAGTGCA
1 AAGTGCA
5528082 TCAACCGAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (29 bp):
AAGTGCAATAACAGAACAGAATGGCACCA
Found at i:5528838 original size:5 final size:5
Alignment explanation
Indices: 5528828--5528862 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
5528818 GACAAATAAG
5528828 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
5528863 ATAATTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:5529724 original size:23 final size:23
Alignment explanation
Indices: 5529681--5529724 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5529671 TTTCCCTTGA
*
5529681 TTTTTTTTATACTTAGTTTTTAT
1 TTTTTTTTATACTTAGGTTTTAT
* *
5529704 TTTTTTTTATATTTTGGTTTT
1 TTTTTTTTATACTTAGGTTTT
5529725 CTTCTAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (23 bp):
TTTTTTTTATACTTAGGTTTTAT
Found at i:5530119 original size:9 final size:8
Alignment explanation
Indices: 5530105--5530143 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
5530095 TGATGTTTCG
5530105 TTTTTTAGT
1 TTTTTTA-T
5530114 TTTTTTCAT
1 TTTTTT-AT
5530123 TTTTTTAT
1 TTTTTTAT
*
5530131 TTTGTTAT
1 TTTTTTAT
5530139 TTTTT
1 TTTTT
5530144 ACTACATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 13 0.48
9 13 0.48
10 1 0.04
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5535446 original size:23 final size:23
Alignment explanation
Indices: 5535403--5535446 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5535393 GATATTAAAT
* *
5535403 TATAATTTTTACTATAGTAAAAA
1 TATAATTTTTACAATACTAAAAA
5535426 TATAATTTTTA-AATGACTAAA
1 TATAATTTTTACAAT-ACTAAA
5535447 TCAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (23 bp):
TATAATTTTTACAATACTAAAAA
Found at i:5537091 original size:3 final size:3
Alignment explanation
Indices: 5537077--5537120 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
5537067 CTCTCTTTCG
*
5537077 TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5537121 ATATCAGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:5544206 original size:24 final size:24
Alignment explanation
Indices: 5544179--5544253 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
5544169 AGTTTGACTC
*
5544179 AAACAAGTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
5544203 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
5544227 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
5544251 AAA
1 AAA
5544254 GATTATTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:5546975 original size:25 final size:26
Alignment explanation
Indices: 5546938--5546993 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
5546928 TTTTGAAAAG
* *
5546938 TAAAAACTAAAAATAAAATAAATTTT-
1 TAAAAAATAAAAACAAAA-AAATTTTA
*
5546964 TAAAAAAT-AAAACAAAAAGATTTTA
1 TAAAAAATAAAAACAAAAAAATTTTA
5546989 TAAAA
1 TAAAA
5546994 GTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 6 0.23
25 13 0.50
26 7 0.27
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAAAAATAAAAACAAAAAAATTTTA
Found at i:5551136 original size:17 final size:17
Alignment explanation
Indices: 5551114--5551149 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5551104 TAATGAAAGC
5551114 GAAACAAGTAGAGATGT
1 GAAACAAGTAGAGATGT
5551131 GAAACAAGTAGAGATGT
1 GAAACAAGTAGAGATGT
5551148 GA
1 GA
5551150 GGTGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.31, T:0.17
Consensus pattern (17 bp):
GAAACAAGTAGAGATGT
Found at i:5558804 original size:23 final size:23
Alignment explanation
Indices: 5558743--5558804 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
5558733 AAGATTTAGT
* *
5558743 ATTTATTAGTAAAATATATTTAAC
1 ATTTATTAGT-ATATATATATAAC
* *
5558767 ATTTACTATAATATATATATATGAC
1 ATTTA-T-TAGTATATATATATAAC
5558792 ATTTATTAGTATA
1 ATTTATTAGTATA
5558805 AAAATCTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.19
24 6 0.19
25 16 0.52
26 3 0.10
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (23 bp):
ATTTATTAGTATATATATATAAC
Found at i:5565627 original size:37 final size:37
Alignment explanation
Indices: 5565577--5565652 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
5565567 AATCCATGAA
5565577 GGAATGTAGTTTGATTACTCGATCCCTATTATTACTT
1 GGAATGTAGTTTGATTACTCGATCCCTATTATTACTT
5565614 GGAATGTAGTTTGATTACTCGATCCCTATTATTACTT
1 GGAATGTAGTTTGATTACTCGATCCCTATTATTACTT
5565651 GG
1 GG
5565653 TTTAACAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (37 bp):
GGAATGTAGTTTGATTACTCGATCCCTATTATTACTT
Found at i:5569671 original size:31 final size:29
Alignment explanation
Indices: 5569627--5569732 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 29
5569617 GATTGAATTG
*
5569627 TTTTTCAATTTTTAAGGCACCCAAAAATAT
1 TTTTTCAACTTTTAAGG-ACCCAAAAATAT
* *
5569657 TTTTATCAACTTTTAAGGGATTCCAAAAAAAT
1 TTTT-TCAACTTTTAA-GGA-CCCAAAAATAT
* *
5569689 TATTTT-AACTTTTGAGGGCCC-AAAAT-T
1 T-TTTTCAACTTTTAAGGACCCAAAAATAT
5569716 TTTTTACCAACTTTTAA
1 TTTTT--CAACTTTTAA
5569733 AATACCTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
26 4 0.07
27 2 0.03
28 4 0.07
29 10 0.16
30 6 0.10
31 19 0.31
32 13 0.21
33 3 0.05
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTTTCAACTTTTAAGGACCCAAAAATAT
Found at i:5576123 original size:19 final size:16
Alignment explanation
Indices: 5576081--5576111 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5576071 TTACAATTTT
5576081 TATTA-AATTGAAAAA
1 TATTATAATTGAAAAA
5576096 TATTATAATTGAAAAA
1 TATTATAATTGAAAAA
5576112 CTATAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TATTATAATTGAAAAA
Found at i:5576373 original size:24 final size:23
Alignment explanation
Indices: 5576346--5576391 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5576336 TACACAAGAT
5576346 TATTT-TAAGATATTTTAAAAAAAA
1 TATTTGTAA-ATA-TTTAAAAAAAA
*
5576370 TATTTGTTAATATTTAAAAAAA
1 TATTTGTAAATATTTAAAAAAA
5576392 TTAACATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 8 0.40
25 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TATTTGTAAATATTTAAAAAAAA
Found at i:5576537 original size:3 final size:3
Alignment explanation
Indices: 5576529--5576585 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
5576519 AAAGCATCAC
5576529 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5576577 ATT ATT ATT
1 ATT ATT ATT
5576586 TCGTTGAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5577435 original size:18 final size:18
Alignment explanation
Indices: 5577406--5577456 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5577396 ACTTGTTCTG
*
5577406 AATTTAATTTTTTTATTTA
1 AATTT-ATTTTTTAATTTA
*
5577425 AATTTATTTTTTAATTTT
1 AATTTATTTTTTAATTTA
*
5577443 AATATATTTTTTAA
1 AATTTATTTTTTAA
5577457 ACTCTTGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
AATTTATTTTTTAATTTA
Found at i:5577443 original size:13 final size:14
Alignment explanation
Indices: 5577407--5577443 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5577397 CTTGTTCTGA
5577407 ATTTAATTTT-TTT
1 ATTTAATTTTATTT
*
5577420 ATTTAAATTTATTT
1 ATTTAATTTTATTT
5577434 -TTTAATTTTA
1 ATTTAATTTTA
5577444 ATATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 18 0.86
14 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTAATTTTATTT
Found at i:5578357 original size:20 final size:20
Alignment explanation
Indices: 5578332--5578376 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
5578322 ACATATTTTA
5578332 ATTTTAAAATTGTCAAATAT
1 ATTTTAAAATTGTCAAATAT
*
5578352 ATTTT--AATTGTCAAGTAT
1 ATTTTAAAATTGTCAAATAT
5578370 ATTTTAA
1 ATTTTAA
5578377 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 17 0.77
20 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTTAAAATTGTCAAATAT
Found at i:5578362 original size:18 final size:18
Alignment explanation
Indices: 5578339--5578378 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5578329 TTAATTTTAA
5578339 AATTGTCAAATATATTTT
1 AATTGTCAAATATATTTT
*
5578357 AATTGTCAAGTATATTTT
1 AATTGTCAAATATATTTT
5578375 AATT
1 AATT
5578379 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
AATTGTCAAATATATTTT
Found at i:5582120 original size:17 final size:17
Alignment explanation
Indices: 5582067--5582121 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
5582057 ATTGTTACTA
*
5582067 TTTTATTATTATTATTTG
1 TTTTATTATTAAT-TTTG
*
5582085 -TATATTATATAATTTTTG
1 TTTTATTAT-TAA-TTTTG
5582103 TTTTATTATTAATTTTG
1 TTTTATTATTAATTTTG
5582120 TT
1 TT
5582122 ACTATTTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 14 0.45
18 9 0.29
19 8 0.26
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATTATTAATTTTG
Found at i:5582127 original size:18 final size:17
Alignment explanation
Indices: 5582070--5582127 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
5582060 GTTACTATTT
*
5582070 TATTATTATTATTTG-TA
1 TATTATTAAT-TTTGTTA
*
5582087 TATTATATAATTTTTGTTT
1 TATTAT-TAA-TTTTGTTA
5582106 TATTATTAATTTTGTTA
1 TATTATTAATTTTGTTA
5582123 CTATT
1 -TATT
5582128 TTAGAAGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 13 0.38
18 13 0.38
19 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (17 bp):
TATTATTAATTTTGTTA
Found at i:5582437 original size:8 final size:9
Alignment explanation
Indices: 5582409--5582449 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
5582399 TATTTGGCCC
5582409 TTTAAAATT
1 TTTAAAATT
5582418 TTTAAAATT
1 TTTAAAATT
5582427 TTTAAAA-T
1 TTTAAAATT
5582435 TTT-AAATT
1 TTTAAAATT
*
5582443 ATTAAAA
1 TTTAAAA
5582450 ATAAAATTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 3 0.10
8 7 0.24
9 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAAAATT
Found at i:5582450 original size:17 final size:17
Alignment explanation
Indices: 5582409--5582451 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
5582399 TATTTGGCCC
*
5582409 TTTAAAATTTTTAAAAT
1 TTTAAAAATTTTAAAAT
*
5582426 TTTTAAAATTTT-AAAT
1 TTTAAAAATTTTAAAAT
5582442 TATTAAAAAT
1 T-TTAAAAAT
5582452 AAAATTACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAAAATTTTAAAAT
Found at i:5582639 original size:22 final size:23
Alignment explanation
Indices: 5582613--5582657 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
5582603 TTAACTGAAT
5582613 TAATTTAGTTG-AAG-TCGGTTAA
1 TAATTT-GTTGAAAGTTCGGTTAA
*
5582635 TAATTTTTTGAAAGTTCGGTTAA
1 TAATTTGTTGAAAGTTCGGTTAA
5582658 CGGTTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 3 0.15
22 9 0.45
23 8 0.40
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (23 bp):
TAATTTGTTGAAAGTTCGGTTAA
Found at i:5591375 original size:208 final size:208
Alignment explanation
Indices: 5591006--5591901 Score: 1228
Period size: 208 Copynumber: 4.3 Consensus size: 208
5590996 TGGACGAATG
* * *
5591006 AGTCTTATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTGCTTCTCTGTATCTCATCAGGAATA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* ** * *
5591071 TGACTGCCTCATTGTTTCAATCCACTTCTCTGCATCTCATTAGGAAGA-TGAATTTGGTTCACTT
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAG-ATTTGGTTCACTT
* * *
5591135 CTTTGTATCTCGTCAGGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGG
130 CTCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGG
* *
5591200 AAGACGGGGTTTGA
195 AAAACAGGGTTTGA
* *
5591214 AGTCTCATTCGTATTGAGCTTCGTTTCATTGATTTGGCCTACTTCTCTGTATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
*
5591279 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAGATTTGGTCCACTTC
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTC
* * * *
5591344 TCTGTATCTTATTAAGAAGATGA-CTGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAG
131 TCTGTATCTCATCAAGAAGATGATC-GCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGG
*
5591408 AAAATAGGGTTTGA
195 AAAACAGGGTTTGA
* * * * *
5591422 AGTCTCATTTGTATTGAGCTTCGCTTTATTGATTTGGTCTACTTTTTTATATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* * * * * *
5591487 TGACTGCCTCATTATTTCAATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTTCACTTA
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTC
* *
5591552 TTTGTATCTCATC-AGAAAGGTGATCGCTTTATTGCTTTGACCCACTT-TTCTGTATCTCATCAG
131 TCTGTATCTCATCAAG-AAGATGATCGCTTTATTGCTTTGACCCACTTCTT-TGTATCTCATCAG
*
5591615 GAAGACAGGGTTTGA
194 GAAAACAGGGTTTGA
* * * * *
5591630 AGTCTCATTTGTATTGGGCTTCGCTTCATTGATTTGATCTACTTCTCTGTATCTCATTAAGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
* *
5591695 TGACCGCCTCATTGTTTCAATCCACTTTTCTATATCTCATCAGGAAGACAGATTTGGTTCAGTTC
66 TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTC
* * * * * * * *
5591760 TCTGCATCTCGTCAGGAAGCTGACCAC-TTATTGGTTCGACCCACTTCTTTGTATCTCATCAGGA
131 TCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGA
*
5591824 AAA-TGAGGTTTGA
196 AAACAG-GGTTTGA
* *
5591837 AGTCTCATTAGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGA
1 AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
5591902 CAGATTTGGT
Statistics
Matches: 604, Mismatches: 76, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
206 1 0.00
207 104 0.17
208 496 0.82
209 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (208 bp):
AGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGA
TGACCGCCTCATTGTTTCAATCCACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTC
TCTGTATCTCATCAAGAAGATGATCGCTTTATTGCTTTGACCCACTTCTTTGTATCTCATCAGGA
AAACAGGGTTTGA
Found at i:5591389 original size:85 final size:85
Alignment explanation
Indices: 5591244--5591405 Score: 211
Period size: 85 Copynumber: 1.9 Consensus size: 85
5591234 TCGTTTCATT
* *
5591244 GATTTGGCCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTC
1 GATTTGGCCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAACCCACTTCTC
5591309 TATATCTCATCAGGAAGACA
66 TATATCTCATCAGGAAGACA
* * * * * *
5591329 GATTTGGTCC-ACTTCTCTGTATCTTATTAAGAAGATGACTGCTTTATTGCTTT-GACCCACTTC
1 GATTTGG-CCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTG-TTTCAACCCACTTC
*
5591392 TCTGTATCTCATCA
64 TCTATATCTCATCA
5591406 AGAAAATAGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
85 61 0.92
86 5 0.08
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (85 bp):
GATTTGGCCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGTTTCAACCCACTTCTC
TATATCTCATCAGGAAGACA
Found at i:5591993 original size:159 final size:159
Alignment explanation
Indices: 5591718--5592060 Score: 471
Period size: 159 Copynumber: 2.2 Consensus size: 159
5591708 GTTTCAATCC
* * * *
5591718 ACTTTTCTATATCTCATCAGGAAGACAGATTTGGTTCAGTTCTCTGCATCTCGTCAGGAAGCTGA
1 ACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGA
* * *
5591783 CCACTTATTGGTTCGACCCACTTCTTTGTATCTCATCAGGAAAATGAGGTTTGAAGTCTCA-TTA
66 CCACTTATTGGTTCGACCCACTTCTTTATATCTCATCAAGAAAATGAGGTTTGAAGTCTCACTCA
*
5591847 GTATTGAGCTT-CGCTTCATTGATTTGGTCT
131 -TATTGAG-TTGCGCTTCAATGATTTGGTCT
*
5591877 ACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTCTTTGCATCTCATC-GAGAAGATG
1 ACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAG-GAAGATG
* * * *
5591941 ACCACTTAATT-GTTCGACCCACTT-TTCTATATCTCATCAAGAAGATGGGGTTTGAATTTTCAC
65 ACCACTT-ATTGGTTCGACCCACTTCTT-TATATCTCATCAAGAAAATGAGGTTTGAAGTCTCAC
5592004 TCATATTGAGTTGCGCTTCAATGATTTGGTCT
128 TCATATTGAGTTGCGCTTCAATGATTTGGTCT
* *
5592036 ACTTCTCTGTATCTCATTAGGAAGA
1 ACTTCTCTATATCTCATCAGGAAGA
5592061 TGACCGCCTC
Statistics
Matches: 164, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
158 5 0.03
159 154 0.94
160 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (159 bp):
ACTTCTCTATATCTCATCAGGAAGACAGATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGA
CCACTTATTGGTTCGACCCACTTCTTTATATCTCATCAAGAAAATGAGGTTTGAAGTCTCACTCA
TATTGAGTTGCGCTTCAATGATTTGGTCT
Found at i:5592224 original size:39 final size:39
Alignment explanation
Indices: 5592170--5592411 Score: 225
Period size: 39 Copynumber: 6.2 Consensus size: 39
5592160 CTTCGGATAA
5592170 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
** * * *
5592209 CTGTAATCTGCCCCATGATTAGGATAAAAGA-TCGAGTGG
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGA-TGG
** * *
5592248 CTACAATCTACCCTATGATCGGGGTAAGAGATTGGATGG
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
** * * *
5592287 CTACAATCTACCCCATAATCGGGGTAAGAGATTGGATGA
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
* * * * * *
5592326 CTGCAATCTGCCACATGATCAGGGTAAAAGATCGGGTGG
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
* * ** *
5592365 TTATAATCTGCCTTATGATCGGGGTAAGAGATTAGATGATG
1 CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATG--G
5592406 CTGTAA
1 CTGTAA
5592412 CTTCACTCCA
Statistics
Matches: 161, Mismatches: 38, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
38 3 0.02
39 150 0.93
40 3 0.02
41 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (39 bp):
CTGTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
Found at i:5592382 original size:117 final size:117
Alignment explanation
Indices: 5592174--5592402 Score: 341
Period size: 117 Copynumber: 2.0 Consensus size: 117
5592164 GGATAACTGT
* * * * * *
5592174 AATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTGTAATCTGCCCCATGATTAGGATAAAAG
1 AATCTACCCCATAATCGGGGTAAGAGATTGGATGACTGCAATCTGCCACATGATCAGGATAAAAG
*
5592239 ATCGAGTGGCTACAATCTACCCTATGATCGGGGTAAGAGATTGGATGGCTAC
66 ATCGAGTGGCTACAATCTACCCTATGATCGGGGTAAGAGATTAGATGGCTAC
*
5592291 AATCTACCCCATAATCGGGGTAAGAGATTGGATGACTGCAATCTGCCACATGATCAGGGTAAAAG
1 AATCTACCCCATAATCGGGGTAAGAGATTGGATGACTGCAATCTGCCACATGATCAGGATAAAAG
* * * * *
5592356 ATCGGGTGGTTATAATCTGCCTTATGATCGGGGTAAGAGATTAGATG
66 ATCGAGTGGCTACAATCTACCCTATGATCGGGGTAAGAGATTAGATG
5592403 ATGCTGTAAC
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 99 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (117 bp):
AATCTACCCCATAATCGGGGTAAGAGATTGGATGACTGCAATCTGCCACATGATCAGGATAAAAG
ATCGAGTGGCTACAATCTACCCTATGATCGGGGTAAGAGATTAGATGGCTAC
Found at i:5592886 original size:49 final size:48
Alignment explanation
Indices: 5592666--5592887 Score: 131
Period size: 49 Copynumber: 4.5 Consensus size: 48
5592656 CGTTGCGGCT
* * * * * *
5592666 TCAACCTTTCCTTTCAAATCTTCATGGCACCAAGTTTGCCGTTATGGCC
1 TCAACCTTTCCCTTCAAAT-TTCATGGTACCGAGTTCGTCGTTATGACC
* * * * * **
5592715 TCAATCTTTCCCATCACATTTCATAGTACCGAATTCGTCGTTGCGACC
1 TCAACCTTTCCCTTCAAATTTCATGGTACCGAGTTCGTCGTTATGACC
* * ** * * * * * *
5592763 TTAATCC-TTCCCATCACGTTTTCTAAGGTATCGGGTTTGTTGTTATGACG
1 TCAA-CCTTTCCCTTCA-AATTTC-ATGGTACCGAGTTCGTCGTTATGACC
* ** * *
5592813 TCAACCTTTCCTTTCATGTCTTCATGGTACCGGGTTCGTCGTTGTGACC
1 TCAACCTTTCCCTTCAAAT-TTCATGGTACCGAGTTCGTCGTTATGACC
5592862 TCAACCTTTCCCTTCAAACTTTCATG
1 TCAACCTTTCCCTTCAAA-TTTCATG
5592888 TTTTCTTGAT
Statistics
Matches: 126, Mismatches: 41, Indels: 12
0.70 0.23 0.07
Matches are distributed among these distances:
48 32 0.25
49 64 0.51
50 30 0.24
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.37
Consensus pattern (48 bp):
TCAACCTTTCCCTTCAAATTTCATGGTACCGAGTTCGTCGTTATGACC
Found at i:5593868 original size:18 final size:18
Alignment explanation
Indices: 5593831--5593868 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5593821 CTCTCCTTTC
*
5593831 TTTTCTCTTTTTTTCCTT
1 TTTTCTCTTTTTTTACTT
5593849 TTTTCTCTTTTTTTA-TT
1 TTTTCTCTTTTTTTACTT
5593866 TTT
1 TTT
5593869 ATTTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTCTTTTTTTACTT
Found at i:5593876 original size:22 final size:23
Alignment explanation
Indices: 5593848--5593891 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5593838 TTTTTTTCCT
**
5593848 TTTTTC-TCTTTTTTTATTTTTA
1 TTTTTCTTCTTTACTTATTTTTA
5593870 TTTTTCTTCTTTACTTATTTTT
1 TTTTTCTTCTTTACTTATTTTT
5593892 CTTCATCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTCTTTACTTATTTTTA
Found at i:5599548 original size:59 final size:58
Alignment explanation
Indices: 5599431--5599629 Score: 240
Period size: 59 Copynumber: 3.4 Consensus size: 58
5599421 TTTCGAGGCA
* * * * * * *
5599431 AAAATGTAATTTTGGCAAAGTTTGAGGCTCAAAATGTAGTTTTAAAAAAGTTTAAGGGTC
1 AAAATATAATTTTGGAAAAATTTG-GGGTCAAAATGAAATTTT-GAAAAGTTTAAGGGTC
* * *
5599491 AAAATATAATTTTGGAAAAATTTGGGGATCAGAATGCAATTTTGAAAAGTTTAAGGGTT
1 AAAATATAATTTTGGAAAAATTTGGGG-TCAAAATGAAATTTTGAAAAGTTTAAGGGTC
* *
5599550 AAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGAAATTTTGAAAAGTTTAAGGGTC
1 AAAATATAATTTTGGAAAAATTT-GGGGTCAAAATGAAATTTTGAAAAGTTTAAGGGTC
5599609 AAAATATAATTTT--AAAAATTT
1 AAAATATAATTTTGGAAAAATTT
5599630 TAGGGACCTC
Statistics
Matches: 121, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
57 7 0.06
59 77 0.64
60 37 0.31
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (58 bp):
AAAATATAATTTTGGAAAAATTTGGGGTCAAAATGAAATTTTGAAAAGTTTAAGGGTC
Found at i:5599555 original size:29 final size:30
Alignment explanation
Indices: 5599431--5599621 Score: 217
Period size: 30 Copynumber: 6.4 Consensus size: 30
5599421 TTTCGAGGCA
* * *
5599431 AAAATGTAATTTTGGCAAAGTTTGAGGCTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* **
5599461 AAAATGTAGTTTTAAAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
* * *
5599491 AAAATATAATTTTGGAAAAATTT-GGGGATC
1 AAAATGTAATTTTGGAAAAGTTTAAGGG-TC
* * *
5599521 AGAATGCAATTTT-GAAAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
*
5599550 AAAATGTAATTTTGGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
*
5599580 AAAATGAAATTTT-GAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAAGGGTC
*
5599609 AAAATATAATTTT
1 AAAATGTAATTTT
5599622 AAAAATTTTA
Statistics
Matches: 132, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
29 49 0.37
30 83 0.63
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAAGGGTC
Found at i:5599569 original size:89 final size:89
Alignment explanation
Indices: 5599433--5599597 Score: 217
Period size: 89 Copynumber: 1.9 Consensus size: 89
5599423 TCGAGGCAAA
* * * *
5599433 AATGTAATTTTGGCAAAGTTTGAGGCTCAAAATGTAGTTTTAAAAAAGTTTAAGGGTCAAAAT-A
1 AATGCAATTTTGGAAAAGTTTAAGGCTCAAAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATGA
5599497 TAATTTTGGAAAAATTTGGGGATCAG
66 -AATTTT-GAAAAATTTGGGGATCAG
* * ** *
5599523 AATGCAATTTT-GAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGA
1 AATGCAATTTTGGAAAAGTTTAAGGCTCAAAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATGA
5599587 AATTTTGAAAA
66 AATTTTGAAAA
5599598 GTTTAAGGGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
88 5 0.08
89 49 0.75
90 11 0.17
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (89 bp):
AATGCAATTTTGGAAAAGTTTAAGGCTCAAAATGTAATTTTAAAAAAGTTTAAGGGTCAAAATGA
AATTTTGAAAAATTTGGGGATCAG
Found at i:5608152 original size:24 final size:24
Alignment explanation
Indices: 5608124--5608174 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5608114 ATTTTGAAAG
5608124 AGTAAATAAATTGAAAATTAACTA
1 AGTAAATAAATTGAAAATTAACTA
5608148 AGTAAATAAATTGAAAATTAACTA
1 AGTAAATAAATTGAAAATTAACTA
5608172 AGT
1 AGT
5608175 TTCCAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.10, T:0.29
Consensus pattern (24 bp):
AGTAAATAAATTGAAAATTAACTA
Found at i:5612377 original size:12 final size:12
Alignment explanation
Indices: 5612360--5612425 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
5612350 TTATTTTCCT
*
5612360 TCATTTAGTTTA
1 TCATTTACTTTA
* *
5612372 TCATTTAATTTT
1 TCATTTACTTTA
* *
5612384 TCGTACTTAGTTTA
1 TC--ATTTACTTTA
*
5612398 TCATGTACTTTA
1 TCATTTACTTTA
5612410 TCATTTACTTT-
1 TCATTTACTTTA
5612421 TCATT
1 TCATT
5612426 GTCTTTTATT
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
11 5 0.12
12 29 0.67
14 9 0.21
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.58
Consensus pattern (12 bp):
TCATTTACTTTA
Found at i:5622859 original size:37 final size:37
Alignment explanation
Indices: 5622809--5623099 Score: 352
Period size: 37 Copynumber: 7.9 Consensus size: 37
5622799 TTGTATAATA
*
5622809 TTCAGCCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * *
5622846 TTCAGGCTATGTGCCTAGTAAGCTTTGTGCCAGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * *
5622883 TTCAGGCTATGTGCTTAGTAGGCTTCGTGCCGGTATA
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* *
5622920 TTCAGGGTATGTGCCTAGTAGGCTTTGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* *
5622957 TTCAGGCTATGTGCCTAGTAGGCTTCATGCCGGTGTA
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * * *
5622994 TTCAGGCTATGTGCCTAGTAAGCTTTGCGCTGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* **
5623031 TGT-AGGCTATATGCCTAGTAGGCTTCGTGTTGGTGTAT
1 T-TCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT-T
* * * *
5623069 TT-GGGCTATGTGCTTAGCAGGCTTTGTGCCG
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCG
5623100 ATGATCCAAG
Statistics
Matches: 215, Mismatches: 37, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
37 212 0.99
38 3 0.01
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
Found at i:5622931 original size:74 final size:74
Alignment explanation
Indices: 5622809--5623099 Score: 404
Period size: 74 Copynumber: 3.9 Consensus size: 74
5622799 TTGTATAATA
* *
5622809 TTCAGCCTATGTGCCTAGTAGGCTTCGTGCCGGTGTTTTCAGGCTATGTGCCTAGTAAGCTTTGT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTGT
*
5622874 GCCAGTGTT
66 GCCGGTGTT
* * * *
5622883 TTCAGGCTATGTGCTTAGTAGGCTTCGTGCCGGTATATTCAGGGTATGTGCCTAGTAGGCTTTGT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTGT
5622948 GCCGGTGTT
66 GCCGGTGTT
* *
5622957 TTCAGGCTATGTGCCTAGTAGGCTTCATGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTGC
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTGT
*
5623022 GCTGGTGTT
66 GCCGGTGTT
* ** ** * * *
5623031 TGT-AGGCTATATGCCTAGTAGGCTTCGTGTTGGTGTATTTGGGCTATGTGCTTAGCAGGCTTTG
1 T-TCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTG
5623095 TGCCG
65 TGCCG
5623100 ATGATCCAAG
Statistics
Matches: 191, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 190 0.99
75 1 0.01
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (74 bp):
TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCCTAGTAAGCTTTGT
GCCGGTGTT
Found at i:5623008 original size:21 final size:21
Alignment explanation
Indices: 5622939--5623008 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 21
5622929 TGTGCCTAGT
* *
5622939 AGGCTTTGTGCCGGTGTTTTC
1 AGGCTATGTGCCGGTGTATTC
*
5622960 AGGCTATGTGCC----TAGT-
1 AGGCTATGTGCCGGTGTATTC
*
5622976 AGGCT-TCATGCCGGTGTATTC
1 AGGCTAT-GTGCCGGTGTATTC
5622997 AGGCTATGTGCC
1 AGGCTATGTGCC
5623009 TAGTAAGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
15 1 0.03
16 9 0.25
17 2 0.06
20 3 0.08
21 20 0.56
22 1 0.03
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.34
Consensus pattern (21 bp):
AGGCTATGTGCCGGTGTATTC
Found at i:5625256 original size:870 final size:870
Alignment explanation
Indices: 5623577--5625318 Score: 3297
Period size: 870 Copynumber: 2.0 Consensus size: 870
5623567 ATGTTTTATG
*
5623577 AATAGAAAAGAGACTTGAGTGAAGTTAGAATTAAATTTTTAGCAATAGTTTGTGTTGTGCTGGTA
1 AATAGAAAAGAGACTTGAGTGAAGTTAGAATTAAATTTTTAGCAATAGTTTGTGTTGTGCTAGTA
5623642 CTTTGTTGCTTAGTATCGATAGAAGTGCAGGGGATTTGAAACTTTAGTTACTGACTTATTTAGTT
66 CTTTGTTGCTTAGTATCGATAGAAGTGCAGGGGATTTGAAACTTTAGTTACTGACTTATTTAGTT
*
5623707 AAAGTACACAAAATGAACGGAGAACTTAAAGGCCCGAAAATGTTGCACCGGATGCATTCCTCCAA
131 AAAGTACACAAAATGAACGGAGAACTCAAAGGCCCGAAAATGTTGCACCGGATGCATTCCTCCAA
* *
5623772 ATGATGCAGGATATGTATGACGCATACTTAAAGGTAAACGTATCAAACCGACCTACTCCTTCCCT
196 ATGATGCAGGACATGTATGACGCATACTAAAAGGTAAACGTATCAAACCGACCTACTCCTTCCCT
*
5623837 ACGACCTGAAGGATCGTCTAACCGTGATAATCGTAAAATCTCTATCGATAAAGTGAGGAAATGTG
261 ACGACCTGAAGGATCGTCTAACCATGATAATCGTAAAATCTCTATCGATAAAGTGAGGAAATGTG
5623902 GAGCGATGGAATTTAGTGGGAATGTTGATGATGATCCTACCAAAGCTGAGTATTGGTTAGAATAT
326 GAGCGATGGAATTTAGTGGGAATGTTGATGATGATCCTACCAAAGCTGAGTATTGGTTAGAATAT
*
5623967 ACTCAAAGGATACTTGATGAGATGTTGTGCCCTTCCGAAGATTGCTTACATTGTACTGTATCACT
391 ACTCAAAGGATACTTAATGAGATGTTGTGCCCTTCCGAAGATTGCTTACATTGTACTGTATCACT
5624032 ATTGAAGGAAGAAGCTTTCCACTGGTGGTCCACTCTAACATCAATGGTACCGAAAGCAAGGGTCA
456 ATTGAAGGAAGAAGCTTTCCACTGGTGGTCCACTCTAACATCAATGGTACCGAAAGCAAGGGTCA
*
5624097 ATTGGAATTCTTTAAACCCGAGTTTCGTAAGAAGTATGTGAGCAAGTGGTATTTAGAGCGGAAGA
521 ATTGGAATTCTTTAAACCCGAGTTTCGTAAGAAGTATGTGAGCAAGTGGTATTTAGAGCGAAAGA
5624162 AGAAAGAGTTTCTTAAACTGAAGCAAGAAAACAAGTCCGTGGCAGAGTACGAGAAACAGTTTGTT
586 AGAAAGAGTTTCTTAAACTGAAGCAAGAAAACAAGTCCGTGGCAGAGTACGAGAAACAGTTTGTT
5624227 CAACTTAGTAAGTATGCTCGCGAGATTGTGCCCACAGAAGAGGCCTTATGCATATGTTTTGAAGA
651 CAACTTAGTAAGTATGCTCGCGAGATTGTGCCCACAGAAGAGGCCTTATGCATATGTTTTGAAGA
* *
5624292 TGGACTGAATGACGAAATTTGAATGCTAGTCGGAGCTTTAGAGATTCGGGAGCTGGTAATACTGT
716 TGGAATGAATGACGAAATTTGAATGCTAGTCGGAGCTTTAGAGATTCGAGAGCTGGTAATACTGT
5624357 TGGATCGGGCACAGAAGATGGAAGAAACTTGTTCTATCAAAAGGAGAAATGAGGCAAGGACTCTT
781 TGGATCGGGCACAGAAGATGGAAGAAACTTGTTCTATCAAAAGGAGAAATGAGGCAAGGACTCTT
5624422 TATTTTGGCAAACGCTTCGGGACAA
846 TATTTTGGCAAACGCTTCGGGACAA
*
5624447 AATAGAAAAGAGACTTGAGTGAAGTTAGAATTGAATTTTTAGCAATAGTTTGTGTTGTG-TCAGT
1 AATAGAAAAGAGACTTGAGTGAAGTTAGAATTAAATTTTTAGCAATAGTTTGTGTTGTGCT-AGT
5624511 ACTTTGTTGCTTAGTATCGATAGAAGTGCAGGGGATTTGAAACTTTAGTTACTGACTTATTTAGT
65 ACTTTGTTGCTTAGTATCGATAGAAGTGCAGGGGATTTGAAACTTTAGTTACTGACTTATTTAGT
5624576 TAAAGTACACAAAATGAACGGAGAACTCAAAGGCCCGAAAATGTTGCACCGGATGCATTCCTCCA
130 TAAAGTACACAAAATGAACGGAGAACTCAAAGGCCCGAAAATGTTGCACCGGATGCATTCCTCCA
* *
5624641 AATGATGTAGGACATGTATGATGCATACTAAAAGGTAAACGTATCAAACCGACCTACTCCTTCCC
195 AATGATGCAGGACATGTATGACGCATACTAAAAGGTAAACGTATCAAACCGACCTACTCCTTCCC
5624706 TACGACCTGAAGGATCGTCTAACCATGATAATCGTAAAATCTCTATCGATAAAGTGAGGAAATGT
260 TACGACCTGAAGGATCGTCTAACCATGATAATCGTAAAATCTCTATCGATAAAGTGAGGAAATGT
5624771 GGAGCGATGGAATTTAGTGGGAATGTTGATGATGATCCTACCAAAGCTGAGTATTGGTTAGAATA
325 GGAGCGATGGAATTTAGTGGGAATGTTGATGATGATCCTACCAAAGCTGAGTATTGGTTAGAATA
* *
5624836 TACTTAAAGGATACTTAATGAGATGTTGTGCCTTTCCGAAGATTGCTTACATTGTACTGTATCAC
390 TACTCAAAGGATACTTAATGAGATGTTGTGCCCTTCCGAAGATTGCTTACATTGTACTGTATCAC
5624901 TATTGAAGGAAGAAGCTTTCCACTGGTGGTCCACTCTAACATCAATGGTACCGAAAGCAAGGGTC
455 TATTGAAGGAAGAAGCTTTCCACTGGTGGTCCACTCTAACATCAATGGTACCGAAAGCAAGGGTC
5624966 AATTGGAATTCTTTAAACCCGAGTTTCGTAAGAAGTATGTGAGCAAGTGGTATTTAGAGCGAAAG
520 AATTGGAATTCTTTAAACCCGAGTTTCGTAAGAAGTATGTGAGCAAGTGGTATTTAGAGCGAAAG
* *
5625031 AAGAAAGAGTTTCTTGAACTGAAGCAAGAAAACAAGTCCGTGGTAGAGTACGAGAAACAGTTTGT
585 AAGAAAGAGTTTCTTAAACTGAAGCAAGAAAACAAGTCCGTGGCAGAGTACGAGAAACAGTTTGT
*
5625096 TCAACTTAGTAAGTATGCTCGTGAGATTGTGCCCACAGAAGAGGCCTTATGCATATGTTTTGAAG
650 TCAACTTAGTAAGTATGCTCGCGAGATTGTGCCCACAGAAGAGGCCTTATGCATATGTTTTGAAG
5625161 ATGGAATGAATGACGAAATTTGAATGCTAGTCGGAGCTTTAGAGATTCGAGAGCTGGTAATACTG
715 ATGGAATGAATGACGAAATTTGAATGCTAGTCGGAGCTTTAGAGATTCGAGAGCTGGTAATACTG
* *
5625226 TTGGATCGGGCATAGAAGATGGAAGAAACTTGTTCTATCAAAAGGAGAAATGAGGCGAGGACTCT
780 TTGGATCGGGCACAGAAGATGGAAGAAACTTGTTCTATCAAAAGGAGAAATGAGGCAAGGACTCT
5625291 TTATTTTGGCAAACGCTTCGGGACAA
845 TTATTTTGGCAAACGCTTCGGGACAA
5625317 AA
1 AA
5625319 AGTTTTCCGG
Statistics
Matches: 852, Mismatches: 19, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
869 1 0.00
870 851 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (870 bp):
AATAGAAAAGAGACTTGAGTGAAGTTAGAATTAAATTTTTAGCAATAGTTTGTGTTGTGCTAGTA
CTTTGTTGCTTAGTATCGATAGAAGTGCAGGGGATTTGAAACTTTAGTTACTGACTTATTTAGTT
AAAGTACACAAAATGAACGGAGAACTCAAAGGCCCGAAAATGTTGCACCGGATGCATTCCTCCAA
ATGATGCAGGACATGTATGACGCATACTAAAAGGTAAACGTATCAAACCGACCTACTCCTTCCCT
ACGACCTGAAGGATCGTCTAACCATGATAATCGTAAAATCTCTATCGATAAAGTGAGGAAATGTG
GAGCGATGGAATTTAGTGGGAATGTTGATGATGATCCTACCAAAGCTGAGTATTGGTTAGAATAT
ACTCAAAGGATACTTAATGAGATGTTGTGCCCTTCCGAAGATTGCTTACATTGTACTGTATCACT
ATTGAAGGAAGAAGCTTTCCACTGGTGGTCCACTCTAACATCAATGGTACCGAAAGCAAGGGTCA
ATTGGAATTCTTTAAACCCGAGTTTCGTAAGAAGTATGTGAGCAAGTGGTATTTAGAGCGAAAGA
AGAAAGAGTTTCTTAAACTGAAGCAAGAAAACAAGTCCGTGGCAGAGTACGAGAAACAGTTTGTT
CAACTTAGTAAGTATGCTCGCGAGATTGTGCCCACAGAAGAGGCCTTATGCATATGTTTTGAAGA
TGGAATGAATGACGAAATTTGAATGCTAGTCGGAGCTTTAGAGATTCGAGAGCTGGTAATACTGT
TGGATCGGGCACAGAAGATGGAAGAAACTTGTTCTATCAAAAGGAGAAATGAGGCAAGGACTCTT
TATTTTGGCAAACGCTTCGGGACAA
Found at i:5626437 original size:17 final size:18
Alignment explanation
Indices: 5626415--5626450 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5626405 TAAATGAGTT
5626415 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5626432 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5626450 A
1 A
5626451 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5632996 original size:37 final size:37
Alignment explanation
Indices: 5632946--5633081 Score: 200
Period size: 37 Copynumber: 3.7 Consensus size: 37
5632936 TTGTATAATA
*
5632946 TTCAGCCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * *
5632983 TTCAGGCTATGTGCCTAGTAAGCTTTGTGCCAGTGTT
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
* * *
5633020 TTCAGGCTATGTGCTTAGTAGGCTTCGTGCCGGTATA
1 TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
*
5633057 TTCAGGGTATGTGCCTAGTAGGCTT
1 TTCAGGCTATGTGCCTAGTAGGCTT
5633082 TATGTTAAGT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 87 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (37 bp):
TTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGTT
Found at i:5633955 original size:37 final size:37
Alignment explanation
Indices: 5633895--5634193 Score: 334
Period size: 37 Copynumber: 8.1 Consensus size: 37
5633885 TATATATGTC
* *
5633895 GTGCCGGTGGTTTT-AGGATATGTGCCTAGTAGGCTTT
1 GTGCCAGT-GTTTTCAGGCTATGTGCCTAGTAGGCTTT
*
5633932 GTGCCAGTGTTTTCAGGCGATGTGCCTAGTAGGCTTT
1 GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
* *
5633969 GTGTC-GATGTTTTTAGGCTATGTGCCTAGTAGGCTTT
1 GTGCCAG-TGTTTTCAGGCTATGTGCCTAGTAGGCTTT
* *
5634006 GTGTCGGT-TTATTCAGGCTATGTGCCTAGTAGGCTTT
1 GTGCCAGTGTT-TTCAGGCTATGTGCCTAGTAGGCTTT
* * *
5634043 GTGCTAGTATTTTCAAGCTATGTGCCTAGTAGGCTTT
1 GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
*** * *
5634080 GTGTTGGTGTATTCAAGCTATGTGCCTAGTAGGCTTT
1 GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
* * * * *
5634117 GTACAAGTGTTTGCAGGCTATATGCCTAGTAGGCTTC
1 GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
* * **
5634154 GTGCCAGTGTGTTCGGGCTATGTGCCTACCAGGCTTT
1 GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
5634191 GTG
1 GTG
5634194 TCGATGATCC
Statistics
Matches: 224, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
36 8 0.04
37 213 0.95
38 3 0.01
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (37 bp):
GTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTT
Found at i:5634051 original size:15 final size:16
Alignment explanation
Indices: 5633982--5634051 Score: 52
Period size: 16 Copynumber: 4.1 Consensus size: 16
5633972 TCGATGTTTT
5633982 TAGGCTATGTGCCTAG
1 TAGGCTATGTGCCTAG
* * *
5633998 TAGGCTTTGTGTCGGTTTAT
1 TAGGCTATGTG-C---CTAG
5634018 TCAGGCTATGTGCCTAG
1 T-AGGCTATGTGCCTAG
*
5634035 TAGGCTTTGTG-CTAG
1 TAGGCTATGTGCCTAG
5634050 TA
1 TA
5634052 TTTTCAAGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
15 6 0.14
16 19 0.45
17 4 0.10
20 4 0.10
21 9 0.21
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.39
Consensus pattern (16 bp):
TAGGCTATGTGCCTAG
Found at i:5634107 original size:111 final size:111
Alignment explanation
Indices: 5633913--5634199 Score: 380
Period size: 111 Copynumber: 2.6 Consensus size: 111
5633903 GGTTTTAGGA
*
5633913 TATGTGCCTAGTAGGCTTTGTGCCAGTGTTTTCAGGCGATGTGCCTAGTAGGCTTTGTGTCGATG
1 TATGTGCCTAGTAGGCTTTGTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGATG
* * * * * *
5633978 TTTTTAGGCTATGTGCCTAGTAGGCTTTGTGTC-GGT-TTATTCAGGC
66 TATTCAAGCTATGTGCCTAGTAGGCTTTGT-ACAAGTGTT-TGCAGGC
* * * * *
5634024 TATGTGCCTAGTAGGCTTTGTGCTAGTATTTTCAAGCTATGTGCCTAGTAGGCTTTGTGTTGGTG
1 TATGTGCCTAGTAGGCTTTGTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGATG
5634089 TATTCAAGCTATGTGCCTAGTAGGCTTTGTACAAGTGTTTGCAGGC
66 TATTCAAGCTATGTGCCTAGTAGGCTTTGTACAAGTGTTTGCAGGC
* * * * **
5634135 TATATGCCTAGTAGGCTTCGTGCCAGTGTGTTCGGGCTATGTGCCTACCAGGCTTTGTGTCGATG
1 TATGTGCCTAGTAGGCTTTGTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGATG
5634200 ATCCAAGAAC
Statistics
Matches: 151, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
110 1 0.01
111 148 0.98
112 2 0.01
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.38
Consensus pattern (111 bp):
TATGTGCCTAGTAGGCTTTGTGCCAGTGTTTTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGATG
TATTCAAGCTATGTGCCTAGTAGGCTTTGTACAAGTGTTTGCAGGC
Found at i:5635428 original size:34 final size:34
Alignment explanation
Indices: 5635390--5635462 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
5635380 TTAGTTAAAG
* * *
5635390 GCATATTAAATGCTACTATATTGATA-TGTTATGT
1 GCATATTAAATGCTACCAT-TTGAAATTGTTATGA
*
5635424 GCATATTAATTGCTACCATTTGAAATTGTTATGA
1 GCATATTAAATGCTACCATTTGAAATTGTTATGA
5635458 GCATA
1 GCATA
5635463 CCATAATGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 5 0.15
34 29 0.85
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (34 bp):
GCATATTAAATGCTACCATTTGAAATTGTTATGA
Found at i:5636936 original size:45 final size:45
Alignment explanation
Indices: 5636868--5636976 Score: 110
Period size: 45 Copynumber: 2.4 Consensus size: 45
5636858 TCTGCAATGT
* * ** *
5636868 TGAGTGGTTCATCCGCATGGTATTAAAAACTTTAATCTACACCAA
1 TGAGTGGTTTATCCACACCGTATTAAAAACTTTAATCTACAACAA
** ** * *
5636913 TGAGTGGTTTATCCACACCGTATTAGCAACTTTTCTTTGCAACAA
1 TGAGTGGTTTATCCACACCGTATTAAAAACTTTAATCTACAACAA
*
5636958 TGAGTGATTTATCCACACC
1 TGAGTGGTTTATCCACACC
5636977 ATACTCGCAG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
TGAGTGGTTTATCCACACCGTATTAAAAACTTTAATCTACAACAA
Found at i:5638118 original size:61 final size:61
Alignment explanation
Indices: 5638016--5638133 Score: 218
Period size: 61 Copynumber: 1.9 Consensus size: 61
5638006 GAAAACCTTG
5638016 CAATTGAATATCTATATGTATGTATATATTAAATATATTAGATTAATGTATTTGATTTTTC
1 CAATTGAATATCTATATGTATGTATATATTAAATATATTAGATTAATGTATTTGATTTTTC
* *
5638077 CAATTGAATATCTATATGTATGTATATATTAGATATTTTAGATTAATGTATTTGATT
1 CAATTGAATATCTATATGTATGTATATATTAAATATATTAGATTAATGTATTTGATT
5638134 GGGTTGATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (61 bp):
CAATTGAATATCTATATGTATGTATATATTAAATATATTAGATTAATGTATTTGATTTTTC
Found at i:5641698 original size:91 final size:91
Alignment explanation
Indices: 5641543--5641725 Score: 339
Period size: 91 Copynumber: 2.0 Consensus size: 91
5641533 AAGATTCTAA
*
5641543 TGTGATAAACTATATAATTTAGCAGTTTCTCATAAAAATATCAAAGTTCGACAAAACCAACCAAA
1 TGTGATAAACTATATAATTTAGCAGTTTCTCATAAAAATATCAAAGTCCGACAAAACCAACCAAA
5641608 CCGATAAATAAAGTCCAAAATAGTTT
66 CCGATAAATAAAGTCCAAAATAGTTT
* *
5641634 TGTGATAAACTGTATAATTTAGCAGTTTCTGATAAAAATATCAAAGTCCGACAAAACCAACCAAA
1 TGTGATAAACTATATAATTTAGCAGTTTCTCATAAAAATATCAAAGTCCGACAAAACCAACCAAA
5641699 CCGATAAATAAAGTCCAAAATAGTTT
66 CCGATAAATAAAGTCCAAAATAGTTT
5641725 T
1 T
5641726 ACAGTTCAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.27
Consensus pattern (91 bp):
TGTGATAAACTATATAATTTAGCAGTTTCTCATAAAAATATCAAAGTCCGACAAAACCAACCAAA
CCGATAAATAAAGTCCAAAATAGTTT
Found at i:5642668 original size:29 final size:29
Alignment explanation
Indices: 5642625--5642709 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
5642615 CATGTGGCCT
* * *
5642625 ACATGACCTGGCACACGATCGTATGGCTC
1 ACATGATCTAGCACACGATCGTATGGCAC
* * *
5642654 ATA-GAGTCTAGCACACGACCGTGTGGCAC
1 ACATGA-TCTAGCACACGATCGTATGGCAC
5642683 ACATGATCTAGCACAC-AGTCGTATGGC
1 ACATGATCTAGCACACGA-TCGTATGGC
5642710 GTCAAAAGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.07
29 39 0.89
30 2 0.05
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (29 bp):
ACATGATCTAGCACACGATCGTATGGCAC
Found at i:5647934 original size:30 final size:30
Alignment explanation
Indices: 5647900--5648032 Score: 107
Period size: 30 Copynumber: 4.5 Consensus size: 30
5647890 TGAAGGTCCC
5647900 TAAACTTTTCCAAAATTATATTTTAACCCT
1 TAAACTTTTCCAAAATTATATTTTAACCCT
* * *
5647930 TAAACTTCTCTAAAATTCTATTTTTAACCCT
1 TAAACTTTTCCAAAATTATA-TTTTAACCCT
* * *
5647961 TAAAC-TTTCAAAAATTACCATTTT-ACCCC
1 TAAACTTTTCCAAAATTA-TATTTTAACCCT
* *
5647990 CAAAC-TTTCTAAAATTCCAT-TTTTAACCC-
1 TAAACTTTTCCAAAATT--ATATTTTAACCCT
*
5648019 T-AATTTTTCCAAAA
1 TAAACTTTTCCAAAA
5648033 GTTACCATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.02
29 30 0.36
30 34 0.41
31 17 0.20
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTATATTTTAACCCT
Found at i:5647994 original size:29 final size:29
Alignment explanation
Indices: 5647962--5648225 Score: 133
Period size: 29 Copynumber: 8.9 Consensus size: 29
5647952 TTTAACCCTT
5647962 AAACTTTCAAAAATTACCATTTTACCCCC
1 AAACTTTCAAAAATTACCATTTTACCCCC
* * *
5647991 AAACTTTCTAAAATT-CCATTTTTAACCCT
1 AAACTTTCAAAAATTACCA-TTTTACCCCC
** * **
5648020 AATTTTTCCAAAAGTTACCATTTTACCTTC
1 AAACTTT-CAAAAATTACCATTTTACCCCC
* *
5648050 GAACTTTCAAAAATT-CCATTTTTGACCCCG
1 AAACTTTCAAAAATTACCA-TTTT-ACCCCC
***
5648080 ATTTTTTTCAAAAATTACCATTTTACCCCC
1 A-AACTTTCAAAAATTACCATTTTACCCCC
* * * ** *
5648110 GAACTTCCCAAAATT-CCATTTTTAATCCT
1 AAACTTTCAAAAATTACCA-TTTTACCCCC
* ** * *
5648139 GATTTTTCAAAAAACTACCATTTTACCCTC
1 AAACTTTC-AAAAATTACCATTTTACCCCC
** * *
5648169 GTA-TTTCCAAAAATT-CCATTTTTAACCCT
1 AAACTTT-CAAAAATTACCA-TTTTACCCCC
* *
5648198 AAATTTTCCTAAAATTACCATTTTACCC
1 AAACTTT-CAAAAATTACCATTTTACCC
5648226 TCGAGTATCC
Statistics
Matches: 170, Mismatches: 51, Indels: 27
0.69 0.21 0.11
Matches are distributed among these distances:
28 12 0.07
29 76 0.45
30 55 0.32
31 24 0.14
32 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.39
Consensus pattern (29 bp):
AAACTTTCAAAAATTACCATTTTACCCCC
Found at i:5648108 original size:119 final size:118
Alignment explanation
Indices: 5647941--5648225 Score: 358
Period size: 119 Copynumber: 2.4 Consensus size: 118
5647931 AAACTTCTCT
* * * * *
5647941 AAAATTCTATTTTTAACCCTTAAA-CTTTCAAAAATTACCATTTTACCCCCAAACTTTCTAAAAT
1 AAAATTCCATTTTTAACCC-GAAATTTTTCAAAAATTACCATTTTACCCCCAAACTTCCCAAAAT
* ** *
5648005 TCCATTTTTAACCCTAATTTTTCCAAAAGTTACCATTTTACCTTCGAACTTT-CA
65 TCCATTTTTAACCCTAATTTTTCAAAAAACTACCATTTTACCCTCGAA-TTTCCA
* ** *
5648059 AAAATTCCATTTTTGACCCCGATTTTTTTCAAAAATTACCATTTTACCCCCGAACTTCCCAAAAT
1 AAAATTCCATTTTT-AACCCGAAATTTTTCAAAAATTACCATTTTACCCCCAAACTTCCCAAAAT
* * *
5648124 TCCATTTTTAATCCTGATTTTTCAAAAAACTACCATTTTACCCTCGTATTTCCA
65 TCCATTTTTAACCCTAATTTTTCAAAAAACTACCATTTTACCCTCGAATTTCCA
* * *
5648178 AAAATTCCATTTTTAACCCTAAATTTTCCTAAAATTACCATTTTACCC
1 AAAATTCCATTTTTAACCCGAAATTTTTCAAAAATTACCATTTTACCC
5648226 TCGAGTATCC
Statistics
Matches: 142, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
118 45 0.32
119 97 0.68
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (118 bp):
AAAATTCCATTTTTAACCCGAAATTTTTCAAAAATTACCATTTTACCCCCAAACTTCCCAAAATT
CCATTTTTAACCCTAATTTTTCAAAAAACTACCATTTTACCCTCGAATTTCCA
Found at i:5648249 original size:59 final size:59
Alignment explanation
Indices: 5647905--5648229 Score: 341
Period size: 59 Copynumber: 5.5 Consensus size: 59
5647895 GTCCCTAAAC
* ** * * *
5647905 TTTTCC-AAAATTA-TATTTTAACCCTTAAACTTCTCTAAAATTCTATTTTTAACCCTTAAA
1 TTTTCCAAAAATTACCATTTT-ACCCTCGAACTTC-CAAAAATTCCATTTTTAACCC-TAAT
* * * * *
5647965 CTTT-CAAAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCTAAT
1 TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
* * * * * *
5648023 TTTTCCAAAAGTTACCATTTTACCTTCGAACTTTCAAAAATTCCATTTTTGACCCCGATT
1 TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTT-AACCCTAAT
* * * * *
5648083 TTTTTCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTTAATCCTGAT
1 TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
* * * * *
5648142 TTTTCAAAAAACTACCATTTTACCCTCGTATTTCCAAAAATTCCATTTTTAACCCTAAA
1 TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
*
5648201 TTTTCCTAAAATTACCATTTTACCCTCGA
1 TTTTCCAAAAATTACCATTTTACCCTCGA
5648230 GTATCCGAAA
Statistics
Matches: 220, Mismatches: 41, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
58 6 0.03
59 139 0.63
60 70 0.32
61 5 0.02
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.40
Consensus pattern (59 bp):
TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAAT
Found at i:5653752 original size:38 final size:38
Alignment explanation
Indices: 5653708--5653784 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
5653698 GTATTAATGA
*
5653708 TAGTTTTTCTTATATTTTAACTCTTTTGAGACCTAAAT
1 TAGTTTTTCTTATATTTTAAATCTTTTGAGACCTAAAT
5653746 TAGTTTTTCTTATATTTTAAATCTTTTGAGACCTAAAT
1 TAGTTTTTCTTATATTTTAAATCTTTTGAGACCTAAAT
5653784 T
1 T
5653785 GGAAAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (38 bp):
TAGTTTTTCTTATATTTTAAATCTTTTGAGACCTAAAT
Found at i:5654234 original size:40 final size:40
Alignment explanation
Indices: 5654179--5654270 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
5654169 GTTGGAATAT
5654179 TGGGTATAATCTCAATACAATTAATTCTTACATTTATTTA
1 TGGGTATAATCTCAATACAATTAATTCTTACATTTATTTA
*
5654219 TGGGTGTAATCTCAATACAATTAATTCTTACATTTATTTA
1 TGGGTATAATCTCAATACAATTAATTCTTACATTTATTTA
5654259 TGGGTATAATCT
1 TGGGTATAATCT
5654271 TAAATTTGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (40 bp):
TGGGTATAATCTCAATACAATTAATTCTTACATTTATTTA
Found at i:5665354 original size:151 final size:151
Alignment explanation
Indices: 5665080--5665384 Score: 601
Period size: 151 Copynumber: 2.0 Consensus size: 151
5665070 CACACTCTCC
5665080 AAAAATGACGTATTTCCTTAATTTTCAAAAAAAATAAAAATAAAGGCCAATTAAAAATGGCATAT
1 AAAAATGACGTATTTCCTTAATTTTCAAAAAAAATAAAAATAAAGGCCAATTAAAAATGGCATAT
5665145 ATGACTAATTTAGCCTAAGATTATATCAAAATTAATCATTATAAAGCTTGACCTAAATGAGAATA
66 ATGACTAATTTAGCCTAAGATTATATCAAAATTAATCATTATAAAGCTTGACCTAAATGAGAATA
5665210 TATGCATATCTAAACTAAAAT
131 TATGCATATCTAAACTAAAAT
5665231 AAAAATGACGTATTTCCTTAATTTTCAAAAAAAATAAAAATAAAGGCCAATTAAAAATGGCATAT
1 AAAAATGACGTATTTCCTTAATTTTCAAAAAAAATAAAAATAAAGGCCAATTAAAAATGGCATAT
5665296 ATGACTAATTTAGCCTAAGATTATATCAAAATTAATCATTATAAAGCTTGACCTAAATGAGAATA
66 ATGACTAATTTAGCCTAAGATTATATCAAAATTAATCATTATAAAGCTTGACCTAAATGAGAATA
*
5665361 TATGCATATCTAAACTAGAAT
131 TATGCATATCTAAACTAAAAT
5665382 AAA
1 AAA
5665385 TGTATACAAC
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 153 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.30
Consensus pattern (151 bp):
AAAAATGACGTATTTCCTTAATTTTCAAAAAAAATAAAAATAAAGGCCAATTAAAAATGGCATAT
ATGACTAATTTAGCCTAAGATTATATCAAAATTAATCATTATAAAGCTTGACCTAAATGAGAATA
TATGCATATCTAAACTAAAAT
Found at i:5665825 original size:6 final size:6
Alignment explanation
Indices: 5665814--5665847 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5665804 ATTAAGTATA
5665814 AATTTT AATTTT AATTTT AATTTT AATTTT AATT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATT
5665848 GAAGTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:5668698 original size:21 final size:20
Alignment explanation
Indices: 5668672--5668717 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
5668662 GTGGTGGGGG
5668672 TGGGGGTGGGGGTAGGTCTGC
1 TGGGGGTGGGGG-AGGTCTGC
5668693 TGGGGGTGGGGGAGGTCTGC
1 TGGGGGTGGGGGAGGTCTGC
5668713 TGGGG
1 TGGGG
5668718 ATTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.04, C:0.09, G:0.65, T:0.22
Consensus pattern (20 bp):
TGGGGGTGGGGGAGGTCTGC
Found at i:5672676 original size:95 final size:96
Alignment explanation
Indices: 5672513--5672704 Score: 350
Period size: 95 Copynumber: 2.0 Consensus size: 96
5672503 TGGCCTGCTG
* *
5672513 ACATCTGTGTCCCATTGAAGCAGTATCCATTTAACGGGAGTGGGGGGAGCTCGAGTTTATGATAT
1 ACATCTCTGTCACATTGAAGCAGTATCCATTTAACGGGAGTGGGGGGAGCTCGAGTTTATGATAT
5672578 AAGTTAATAATTTAAGATG-TTTCCAGGGAA
66 AAGTTAATAATTTAAGATGTTTTCCAGGGAA
*
5672608 ACATCTCTGTCACATTGAAGCAGTATCCATTTAACGGGAGTGGGGGGGGCTCGAGTTTATGATAT
1 ACATCTCTGTCACATTGAAGCAGTATCCATTTAACGGGAGTGGGGGGAGCTCGAGTTTATGATAT
5672673 AAGTTAATAATTTAAGATGTTTTCCAGGGAA
66 AAGTTAATAATTTAAGATGTTTTCCAGGGAA
5672704 A
1 A
5672705 TCATTGGATT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
95 81 0.87
96 12 0.13
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (96 bp):
ACATCTCTGTCACATTGAAGCAGTATCCATTTAACGGGAGTGGGGGGAGCTCGAGTTTATGATAT
AAGTTAATAATTTAAGATGTTTTCCAGGGAA
Found at i:5681534 original size:7 final size:7
Alignment explanation
Indices: 5681524--5681562 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
5681514 AGGATTGATG
5681524 ATTGAAA
1 ATTGAAA
5681531 ATTGAAA
1 ATTGAAA
5681538 ATTGAAA
1 ATTGAAA
5681545 ATT-AAA
1 ATTGAAA
5681551 ATTGAAA
1 ATTGAAA
5681558 ATTGA
1 ATTGA
5681563 GAATATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (7 bp):
ATTGAAA
Found at i:5681553 original size:13 final size:14
Alignment explanation
Indices: 5681524--5681562 Score: 71
Period size: 13 Copynumber: 2.9 Consensus size: 14
5681514 AGGATTGATG
5681524 ATTGAAAATTGAAA
1 ATTGAAAATTGAAA
5681538 ATTGAAAATT-AAA
1 ATTGAAAATTGAAA
5681551 ATTGAAAATTGA
1 ATTGAAAATTGA
5681563 GAATATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (14 bp):
ATTGAAAATTGAAA
Found at i:5685446 original size:13 final size:14
Alignment explanation
Indices: 5685428--5685464 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5685418 TATATTATCA
5685428 ATTAAA-ATTTAAT
1 ATTAAATATTTAAT
5685441 ATTAAATATTTAAT
1 ATTAAATATTTAAT
*
5685455 -CTAAATATTT
1 ATTAAATATTT
5685465 GTTTAGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTAAATATTTAAT
Found at i:5698922 original size:11 final size:11
Alignment explanation
Indices: 5698906--5699000 Score: 97
Period size: 11 Copynumber: 8.5 Consensus size: 11
5698896 TACTTTGAAA
*
5698906 TTAAATTTATT
1 TTAAATTTAAT
5698917 TTAAATTTTAAT
1 TTAAA-TTTAAT
5698929 TT-AATTTAAT
1 TTAAATTTAAT
5698939 TTAAATTT-AT
1 TTAAATTTAAT
5698949 TTAAATTTAAT
1 TTAAATTTAAT
*
5698960 TTAAGTTTGAAT
1 TTAAATTT-AAT
5698972 TT-AATTTAAAT
1 TTAAATTT-AAT
*
5698983 TTAATTTGTAAGT
1 TTAAATT-TAA-T
5698996 TTAAA
1 TTAAA
5699001 ATAAATAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
10 18 0.25
11 30 0.42
12 17 0.24
13 6 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5698931 original size:5 final size:5
Alignment explanation
Indices: 5698904--5698989 Score: 84
Period size: 5 Copynumber: 16.0 Consensus size: 5
5698894 TTTACTTTGA
* *
5698904 AATTA AATTT ATTTT AAATTTT AATTT AATTT AATTT AAATTT -ATTT
1 AATTT AATTT AATTT -AA-TTT AATTT AATTT AATTT -AATTT AATTT
5698951 AAATTT AATTT AAGTTT GAATTT AATTT AAATTT AATTT
1 -AATTT AATTT AA-TTT -AATTT AATTT -AATTT AATTT
5698990 GTAAGTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 4 0.06
5 38 0.54
6 23 0.33
7 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:5699781 original size:19 final size:20
Alignment explanation
Indices: 5699759--5699802 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5699749 TTAATAACTG
* *
5699759 TAATAAATATTTATGATT-A
1 TAATAAATATTAATAATTAA
*
5699778 TAATTAATATTAATAATTAA
1 TAATAAATATTAATAATTAA
5699798 TAATA
1 TAATA
5699803 TCAACCATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TAATAAATATTAATAATTAA
Found at i:5700502 original size:31 final size:30
Alignment explanation
Indices: 5700450--5700512 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 30
5700440 GGAAAATGGG
*
5700450 TTATTTGTTCAATTGGTCC-TTTCGCATTT
1 TTATTTGTTCAATTAGTCCTTTTCGCATTT
*
5700479 TTATTTGCTTCAATTTAGTCCTTTTTGCATTT
1 TTATTTG-TTCAA-TTAGTCCTTTTCGCATTT
5700511 TT
1 TT
5700513 TAATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 5 0.17
31 6 0.21
32 11 0.38
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.59
Consensus pattern (30 bp):
TTATTTGTTCAATTAGTCCTTTTCGCATTT
Found at i:5700734 original size:161 final size:162
Alignment explanation
Indices: 5700560--5700874 Score: 551
Period size: 161 Copynumber: 2.0 Consensus size: 162
5700550 TTCAATTTCA
*
5700560 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCTTATTTATGCATGTA
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
5700625 GTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCT-AATCAACTTTTATTTAATTATAAAATT
66 GTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTATAAAATT
* *
5700689 GGCCCGAGAATTTTTCAAGGTTTATAAATCAG
131 GGCCCAAGAATTTTTCAAGATTTATAAATCAG
* *
5700721 TCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTTA
1 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
* *
5700786 TTCCCTGACATTTTTAATTTGTTTTTATTTAATCCCTAAATCAACTTTTATTTAATTATAAAATT
66 GTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTATAAAATT
*
5700851 TGCCCAAGAATTTTTCAAGATTTA
131 GGCCCAAGAATTTTTCAAGATTTA
5700875 CAATTTAATC
Statistics
Matches: 145, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
161 97 0.67
162 48 0.33
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (162 bp):
TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
GTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTATAAAATT
GGCCCAAGAATTTTTCAAGATTTATAAATCAG
Found at i:5700912 original size:161 final size:161
Alignment explanation
Indices: 5700559--5700923 Score: 518
Period size: 161 Copynumber: 2.3 Consensus size: 161
5700549 TTTCAATTTC
* * * * *
5700559 ATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCTTATTTATGCATGT
1 ATCCCTTGACTGCTGGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGT
5700624 AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAATCAACTTTTATTTAATTATAAAATT
66 AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAATCAACTTTTATTTAATTATAAAATT
* * *
5700689 GGCCCGAGAATTTTTCAAGGTTTATAAATCA
131 GGCCCAAGAATTTTTCAAGATTTACAAATCA
* * * * *
5700720 GTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTT
1 ATCCCTTGACTGCTGGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGT
* *
5700785 ATTCCCTGACATTTTTAATTTGTTTTTATTTAATCCCTAAATCAACTTTTATTTAATTATAAAAT
66 AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCT-AATCAACTTTTATTTAATTATAAAAT
* * *
5700850 TTGCCCAAGAATTTTTCAAGATTTACAATTTA
130 TGGCCCAAGAATTTTTCAAGATTTACAAATCA
**
5700882 ATCCCTTGACTGCTGGA-TGC-CTGTGGGGCTGCCACGTGTCAC
1 ATCCCTTGACTGCTGGACTGCAC-CAGGGGCTGCCACGTGTCAC
5700924 CCACTCTTTG
Statistics
Matches: 184, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
160 1 0.01
161 118 0.64
162 65 0.35
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (161 bp):
ATCCCTTGACTGCTGGACTGCACCAGGGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGT
AGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAATCAACTTTTATTTAATTATAAAATT
GGCCCAAGAATTTTTCAAGATTTACAAATCA
Found at i:5701057 original size:59 final size:58
Alignment explanation
Indices: 5700965--5701217 Score: 319
Period size: 59 Copynumber: 4.3 Consensus size: 58
5700955 CGAAACTTCC
* * * *
5700965 AAAATTACCATTTTACCCCCGAACTTTTCAAAATTCCACTTTTAACCTCAATTTCATCA
1 AAAATTACCATTTTACCCCCAAACTTTT-AAAATTCCATTTTTAACCCCGATTTCATCA
* *
5701024 AAAATTACTATTTTACCCCCAAACCTTTTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAA-CTTTTAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
5701083 AAAATTACCATTTTACCCTCAAACTTTCCAAGATTCCATTTTTAACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCCAAACTTT-TAAAATTCCATTTTTAACCCCGATTTCATCA
* * * ** * *
5701142 AAAATTACCATTTTACCCTCGAAGCCTCAAAAATTCCATTTTTAACCTCGATTTCA-CC
1 AAAATTACCATTTTACCC-CCAAACTTTTAAAATTCCATTTTTAACCCCGATTTCATCA
5701200 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
5701218 TCGGGTATCC
Statistics
Matches: 171, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
58 23 0.13
59 139 0.81
60 9 0.05
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAACTTTTAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:5701171 original size:29 final size:29
Alignment explanation
Indices: 5701139--5701220 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
5701129 CCCGATTTCA
5701139 TCAAAAATTACCATTTTACCCTCGAAGCC
1 TCAAAAATTACCATTTTACCCTCGAAGCC
* ***
5701168 TCAAAAATT-CCATTTTTAACCTCGATTTC
1 TCAAAAATTACCA-TTTTACCCTCGAAGCC
* *
5701197 ACCAAAATTACCATTTTACCCTCG
1 TCAAAAATTACCATTTTACCCTCG
5701221 GGTATCCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
TCAAAAATTACCATTTTACCCTCGAAGCC
Found at i:5701175 original size:118 final size:117
Alignment explanation
Indices: 5700963--5701219 Score: 372
Period size: 118 Copynumber: 2.2 Consensus size: 117
5700953 CCCGAAACTT
* * * *
5700963 CCAAAATTACCATTTTACCCCCGAACTTTTCAAAATTCCACTTTTAACCTCAATTTCATCAAAAA
1 CCAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCACTTTTAACCCCAATTTCATCAAAAA
* **
5701028 TTACTATTTTACCCCCAAACCTTTTAAAATTCCATTTTTAACCCCGATTTCA
66 TTACCATTTTACCCCCAAACCTTCAAAAATTCCATTTTTAACCCCGATTTCA
* * *
5701080 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAGATTCCATTTTTAACCCCGATTTCATCAAAA
1 CC-AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCACTTTTAACCCCAATTTCATCAAAA
* * *
5701145 ATTACCATTTTACCCTCGAAGCC-TCAAAAATTCCATTTTTAACCTCGATTTCA
65 ATTACCATTTTACCC-CCAAACCTTCAAAAATTCCATTTTTAACCCCGATTTCA
5701198 CCAAAATTACCATTTTACCCTC
1 CCAAAATTACCATTTTACCCTC
5701220 GGGTATCCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 22 0.18
118 98 0.78
119 5 0.04
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (117 bp):
CCAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCACTTTTAACCCCAATTTCATCAAAAA
TTACCATTTTACCCCCAAACCTTCAAAAATTCCATTTTTAACCCCGATTTCA
Found at i:5701239 original size:58 final size:57
Alignment explanation
Indices: 5700963--5701255 Score: 255
Period size: 59 Copynumber: 5.0 Consensus size: 57
5700953 CCCGAAACTT
* * * * * * *
5700963 CCAAAATTACCATTTTACCCCCGAACTTTTCAAAATTCCACTTTTAACCTCAATTTCA
1 CCAAAATTACCATTTTACCCTCG-AGTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * * **
5701021 TCAAAAATTACTATTTTACCCCCAAACCT-TTTAAAATTCCATTTTTAACCCCGATTTCA
1 -CCAAAATTACCATTTTACCCTC-GA-GTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
5701080 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAGATTCCATTTTTAACCCCGATTTCA
1 CC-AAAATTACCATTTTACCCTC-GAGTATCCAAAATTCCATTTTTAACCCCGATTTCA
* ** * *
5701139 TCAAAAATTACCATTTTACCCTCGAAGCCTCAAAAATTCCATTTTTAACCTCGATTTCA
1 -CCAAAATTACCATTTTACCCTCG-AGTATCCAAAATTCCATTTTTAACCCCGATTTCA
* * **
5701198 CCAAAATTACCATTTTACCCTCGGGTATCCAAAAGTCCCATTTTCCACCCCGATTTCA
1 CCAAAATTACCATTTTACCCTCGAGTATCCAAAA-TTCCATTTTTAACCCCGATTTCA
5701256 TTGTTTCTTA
Statistics
Matches: 197, Mismatches: 30, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
57 7 0.04
58 44 0.22
59 143 0.73
60 3 0.02
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (57 bp):
CCAAAATTACCATTTTACCCTCGAGTATCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:5713655 original size:161 final size:162
Alignment explanation
Indices: 5713482--5713790 Score: 539
Period size: 161 Copynumber: 1.9 Consensus size: 162
5713472 TTCAATTTCA
*
5713482 TCCTTTGACTGTTTGACTGCACCAAAGGCTGCCACGTGTCATTTTTTGGCTTATTTATGCATGTA
1 TCCTTTGACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
*
5713547 ATCCCTGACATTTTTAATTTATTTTAGTTTAATCCCT-AATCAACTTTTATTTAATTACAAAATT
66 ATCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAAAATT
*
5713611 GGCCCGAGAATTTTTCAAGGTTTATAAATCAG
131 GGCCCAAGAATTTTTCAAGGTTTATAAATCAG
* *
5713643 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTTA
1 TCCTTTGACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
* *
5713708 TTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAAAATT
66 ATCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAAAATT
*
5713773 GGCCCAAGATTTTTTCAA
131 GGCCCAAGAATTTTTCAA
5713791 TATTTACAAT
Statistics
Matches: 139, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
161 96 0.69
162 43 0.31
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (162 bp):
TCCTTTGACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTA
ATCCCTGACATTTTTAATTTATTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAAAATT
GGCCCAAGAATTTTTCAAGGTTTATAAATCAG
Found at i:5713836 original size:161 final size:161
Alignment explanation
Indices: 5713496--5713845 Score: 479
Period size: 161 Copynumber: 2.2 Consensus size: 161
5713486 TTGACTGTTT
* *
5713496 GACTGCACCAAAGGCTGCCACGTGTCATTTTTTGGCTTATTTATGCATGTAATCCCTGACATTTT
1 GACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTAATCCCTGACATTTT
* *
5713561 TAATTTATTTTAGTTTAATCCCTAATCAACTTTTATTTAATTACAAAATTGGCCCGAGAATTTTT
66 TAATTTATTTTAATTTAATCCCTAATCAACTTTTATTTAATTACAAAATTGGCCCAAGAATTTTT
* * * * ** *
5713626 CAAGGTTTATAAATCAGTCCTTTGACTGTTT
131 CAAGATTTACAAATCAATCCCTTGACTACTG
* *
5713657 GACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTTATTCCCTGACATTTT
1 GACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTAATCCCTGACATTTT
* *
5713722 TAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAAAATTGGCCCAAGATTTTT
66 TAATTTATTTTAATTTAATCCCT-AATCAACTTTTATTTAATTACAAAATTGGCCCAAGAATTTT
* * *
5713787 TCAATATTTACAATTTAATCCCTTGACTACTG
130 TCAAGATTTACAAATCAATCCCTTGACTACTG
** *
5713819 GA-TGC-CTGTGGGGCTGCCACGTGTCAC
1 GACTGCAC-CAGAGGCTGCCACGTGTCAC
5713846 CCACTCTTTG
Statistics
Matches: 166, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
160 1 0.01
161 102 0.61
162 63 0.38
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (161 bp):
GACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATGTAATCCCTGACATTTT
TAATTTATTTTAATTTAATCCCTAATCAACTTTTATTTAATTACAAAATTGGCCCAAGAATTTTT
CAAGATTTACAAATCAATCCCTTGACTACTG
Found at i:5713915 original size:29 final size:29
Alignment explanation
Indices: 5713874--5714134 Score: 199
Period size: 29 Copynumber: 8.9 Consensus size: 29
5713864 GGTTATAGGT
*
5713874 CCCCGAAAC-TTCCAAAATTACCATTTTAC
1 CCCCG-AACTTTCCAAAATTACCATTTTAA
5713903 CCCCGAACTTTCCAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAA
* *
5713932 CCCCG-A-TTTCACCAAAAATTACTATTTTAC
1 CCCCGAACTTT--CC-AAAATTACCATTTTAA
*
5713962 CCCCGAACTTTCTAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAA
*
5713991 CCCCG-A-TTTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTT--CC-AAAATTACCATTTTAA
*
5714021 CCCCAAACTTTCCAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAA
* *
5714050 CCCC-TA-TTTCACCAAAAATTACCA-TTTAC
1 CCCCGAACTTT--CC-AAAATTACCATTTTAA
*
5714079 CCCCAAACTTTCCAAAATT-CCATTTTTAA
1 CCCCGAACTTTCCAAAATTACCA-TTTTAA
5714108 CCCCG-A-TTTCACCAAAATTACCATTTT
1 CCCCGAACTTT--CCAAAATTACCATTTT
5714135 GCCCTCGGGT
Statistics
Matches: 190, Mismatches: 15, Indels: 54
0.73 0.06 0.21
Matches are distributed among these distances:
27 15 0.08
28 21 0.11
29 91 0.48
30 44 0.23
31 13 0.07
32 6 0.03
ACGTcount: A:0.33, C:0.32, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCCGAACTTTCCAAAATTACCATTTTAA
Found at i:5714106 original size:58 final size:59
Alignment explanation
Indices: 5713887--5714134 Score: 437
Period size: 59 Copynumber: 4.2 Consensus size: 59
5713877 CGAAACTTCC
*
5713887 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
5713946 AAAATTACTATTTTACCCCCGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
5714005 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCTATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
5714064 AAAATTACCA-TTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC-
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
5714121 AAAATTACCATTTT
1 AAAATTACCATTTT
5714135 GCCCTCGGGT
Statistics
Matches: 181, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
57 10 0.06
58 49 0.27
59 122 0.67
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:5721738 original size:27 final size:28
Alignment explanation
Indices: 5721680--5721738 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
5721670 GATTAATGGG
* * *
5721680 TTTTGTTTGTTATGTTAATTTTTTAGGG
1 TTTTATTTGTGATGTTAATTTTTTAGGC
*
5721708 TTTTATTTGTGATGTTAGTTTTTT-GGC
1 TTTTATTTGTGATGTTAATTTTTTAGGC
5721735 TTTT
1 TTTT
5721739 TTTTAATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.12, C:0.02, G:0.20, T:0.66
Consensus pattern (28 bp):
TTTTATTTGTGATGTTAATTTTTTAGGC
Found at i:5721739 original size:28 final size:28
Alignment explanation
Indices: 5721677--5721731 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
5721667 ATGGATTAAT
* *
5721677 GGGTTTTGTTTGTTATGTTAATTTTTTA
1 GGGTTTTATTTGTGATGTTAATTTTTTA
*
5721705 GGGTTTTATTTGTGATGTTAGTTTTTT
1 GGGTTTTATTTGTGATGTTAATTTTTT
5721732 GGCTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.64
Consensus pattern (28 bp):
GGGTTTTATTTGTGATGTTAATTTTTTA
Found at i:5721948 original size:13 final size:14
Alignment explanation
Indices: 5721926--5721965 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
5721916 ATCAAACTTC
*
5721926 AAAGGAAAAAAAAG
1 AAAGGGAAAAAAAG
5721940 -AAGGGAAAAAAAG
1 AAAGGGAAAAAAAG
5721953 AAAGGGAAAAAAA
1 AAAGGGAAAAAAA
5721966 ATTGTAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAAGGGAAAAAAAG
Found at i:5722327 original size:20 final size:21
Alignment explanation
Indices: 5722301--5722341 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5722291 TTAGAAGTGC
*
5722301 TATATAACACTCGATTTAAACA
1 TATA-AACAATCGATTTAAACA
*
5722323 TATAAATAATCGATTTAAA
1 TATAAACAATCGATTTAAA
5722342 AGAAACAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (21 bp):
TATAAACAATCGATTTAAACA
Found at i:5724783 original size:14 final size:15
Alignment explanation
Indices: 5724764--5724792 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5724754 GCATGAAGTA
5724764 AAACTTA-GATGCTT
1 AAACTTATGATGCTT
5724778 AAACTTATGATGCTT
1 AAACTTATGATGCTT
5724793 GTAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
AAACTTATGATGCTT
Found at i:5726551 original size:2 final size:2
Alignment explanation
Indices: 5726544--5726594 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5726534 TATAAAAATA
5726544 AT AT AT AT AT 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 AT AT AT AT AT
5726586 AT AT AT AT A
1 AT AT AT AT A
5726595 AAGAGAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5730441 original size:2 final size:2
Alignment explanation
Indices: 5730434--5730476 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5730424 GAGCTTGTCA
5730434 AT AT AT AT AT 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 AT AT AT AT AT
5730476 A
1 A
5730477 CAGCCAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5735047 original size:14 final size:14
Alignment explanation
Indices: 5735028--5735055 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5735018 ATTGTTAATA
5735028 TTATTAAATTTATT
1 TTATTAAATTTATT
5735042 TTATTAAATTTATT
1 TTATTAAATTTATT
5735056 AATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTAAATTTATT
Found at i:5735882 original size:44 final size:44
Alignment explanation
Indices: 5735819--5735904 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
5735809 AGCGTGCTTG
*
5735819 AGTTAAAAAGCTTAATTGTTTTGCTCATCGGACTATTTCAAATC
1 AGTTAAAAAGCTTAATTGTTTGGCTCATCGGACTATTTCAAATC
5735863 AGTTAAAAAGCTTAATTGTTTGGCTCATCGGACTATTTCAAA
1 AGTTAAAAAGCTTAATTGTTTGGCTCATCGGACTATTTCAAA
5735905 CAACAGGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (44 bp):
AGTTAAAAAGCTTAATTGTTTGGCTCATCGGACTATTTCAAATC
Found at i:5747295 original size:98 final size:98
Alignment explanation
Indices: 5747126--5747323 Score: 378
Period size: 98 Copynumber: 2.0 Consensus size: 98
5747116 AGTAAAAAAA
5747126 CTTTTGCATGGAAGATGTAGTCCTGTTCCTTACCTCTTTTTCTTTAATACGGATGAACATTGTTA
1 CTTTTGCATGGAAGATGTAGTCCTGTTCCTTACCTCTTTTTCTTTAATACGGATGAACATTGTTA
5747191 GTGATTAATGTTTTTGATGTATGACACTGCTTC
66 GTGATTAATGTTTTTGATGTATGACACTGCTTC
*
5747224 CTTTTGCATGGAAGATGTAGTCCTGTTCCTTACCTCTTTTTCTTTAATACGGATGAACATTGTTG
1 CTTTTGCATGGAAGATGTAGTCCTGTTCCTTACCTCTTTTTCTTTAATACGGATGAACATTGTTA
*
5747289 GTGATTAATGTTTTTGATGTATGCCACTGCTTC
66 GTGATTAATGTTTTTGATGTATGACACTGCTTC
5747322 CT
1 CT
5747324 GTTCCTAGCT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (98 bp):
CTTTTGCATGGAAGATGTAGTCCTGTTCCTTACCTCTTTTTCTTTAATACGGATGAACATTGTTA
GTGATTAATGTTTTTGATGTATGACACTGCTTC
Found at i:5753957 original size:20 final size:20
Alignment explanation
Indices: 5753932--5754009 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
5753922 CTAGACCATG
*
5753932 TCTGGTATTGCTCGATGCTC
1 TCTGATATTGCTCGATGCTC
* *
5753952 TCTGGTACTGCTCGATGCT-
1 TCTGATATTGCTCGATGCTC
*
5753971 TCTTGATGTTGCTCGATGCTC
1 TC-TGATATTGCTCGATGCTC
* *
5753992 CCTGATGTTGCTCGATGC
1 TCTGATATTGCTCGATGC
5754010 ATGCTGGTGT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 2 0.04
20 48 0.94
21 1 0.02
ACGTcount: A:0.10, C:0.26, G:0.26, T:0.38
Consensus pattern (20 bp):
TCTGATATTGCTCGATGCTC
Found at i:5759421 original size:30 final size:30
Alignment explanation
Indices: 5759380--5759438 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5759370 AAATAATAGG
5759380 ATTTGTTAACTCGACTT-AACTTGACTCGAA
1 ATTTGTTAACTCGA-TTCAACTTGACTCGAA
* *
5759410 ATTTTTTAACTCGATTCGACTTGACTCGA
1 ATTTGTTAACTCGATTCAACTTGACTCGA
5759439 TCGAATACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (30 bp):
ATTTGTTAACTCGATTCAACTTGACTCGAA
Found at i:5762382 original size:59 final size:59
Alignment explanation
Indices: 5762298--5762604 Score: 399
Period size: 59 Copynumber: 5.2 Consensus size: 59
5762288 TCGAGGGGCA
* * * * **
5762298 AAAAT-GTAA-TTTTGGGAAAATTTGAGGTTAAAAATGGGATTTTAGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTAAAA-TTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * ** *
5762356 AAAATGGTAATTTTTAGTGAAATTGAGGTTAAAAAT-GAGATTTCAGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGGA-ATTTTGGAAAGTTTAGGGGT
* * *
5762415 AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGT-AAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
5762475 AAAATGGTAATTTTTGGTGAAACTG-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
5762533 AAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
5762592 AAAATGGT-ATTTT
1 AAAATGGTAATTTT
5762605 AGAAAGTTTG
Statistics
Matches: 222, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
58 65 0.29
59 98 0.44
60 57 0.26
61 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:5762480 original size:28 final size:28
Alignment explanation
Indices: 5762447--5762633 Score: 166
Period size: 28 Copynumber: 6.5 Consensus size: 28
5762437 ACTGAGGTTA
5762447 AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAAGTTTGGGGGT
* *
5762475 AAAATGGTAATTTTTGGTGAAA--CT-GGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTTGGGGGT
*
5762504 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* * * *
5762533 AAAATGGTAATTTTTGGTAAA-ATCGAGGTT
1 AAAATGG-AA-TTTTGG-AAAGTTTGGGGGT
*
5762563 AAAAATGGAATTTTGGAAAGTTTAGGGGT
1 -AAAATGGAATTTTGGAAAGTTTGGGGGT
* *
5762592 AAAATGGTATTTTAGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAAGTTTGGGGGT
5762620 AAAATGGTAATTTT
1 AAAATGG-AATTTT
5762634 TGGTGAAACC
Statistics
Matches: 127, Mismatches: 18, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.03
27 1 0.01
28 54 0.43
29 29 0.23
30 24 0.19
31 11 0.09
32 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTGGGGGT
Found at i:5762604 original size:87 final size:86
Alignment explanation
Indices: 5762505--5762676 Score: 263
Period size: 87 Copynumber: 2.0 Consensus size: 86
5762495 AACTGGGTTA
* *
5762505 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATG
1 AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAACCGAGGTTAAAAATG
5762570 GAATTTTGGAAAGTTTAGGGGT
66 GAATTTTGGAAAGTTT-GGGGT
* * * *
5762592 AAAATGGTATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATG
1 AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAACCGAGGTTAAAAATG
* *
5762657 TAATTTTGGTAAGTTTGGGG
66 GAATTTTGGAAAGTTTGGGG
5762677 ACTAGAGAGC
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 4 0.05
87 73 0.95
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (86 bp):
AAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAACCGAGGTTAAAAATG
GAATTTTGGAAAGTTTGGGGT
Found at i:5762636 original size:117 final size:117
Alignment explanation
Indices: 5762298--5762604 Score: 372
Period size: 119 Copynumber: 2.6 Consensus size: 117
5762288 TCGAGGGGCA
* ** * * * **
5762298 AAAATG-TAA-TTTTGGGAAAATTTGAGGTTAAAAATGGGATTTTAGAAGGTTCGGGGGTAAAAT
1 AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAT
* * * **
5762361 GGTAATTTTTAGTGAAATTGAGGTTAAAAAT-GAGATTTCAGAAAGTTCAGGGGT
66 GGTAATTTTT-GAGAAACTG-GGGTAAAAATGGA-ATTTTGGAAAGTTCAGGGGT
*
5762415 AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAT
1 AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAT
* * *
5762480 GGTAATTTTTGGTGAAACTGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 GGTAATTTTT-GAGAAACTGGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGT
* *
5762533 AAAATGGTAATTTTTGGTAAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAT
1 AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAT
5762597 GGT-ATTTT
66 GGTAATTTT
5762605 AGAAAGTTTG
Statistics
Matches: 172, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
116 5 0.03
117 48 0.28
118 52 0.30
119 67 0.39
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (117 bp):
AAAATGATAATTTTTGGTAAAAACTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAT
GGTAATTTTTGAGAAACTGGGGTAAAAATGGAATTTTGGAAAGTTCAGGGGT
Found at i:5764559 original size:13 final size:13
Alignment explanation
Indices: 5764541--5764587 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
5764531 CAATTTGGGC
5764541 TTGTAAATGGACT
1 TTGTAAATGGACT
*
5764554 TTGTAATTGGACT
1 TTGTAAATGGACT
* *
5764567 TTGTAATTGGGC-
1 TTGTAAATGGACT
5764579 TTGTAAATG
1 TTGTAAATG
5764588 AACAAACAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (13 bp):
TTGTAAATGGACT
Found at i:5764584 original size:12 final size:12
Alignment explanation
Indices: 5764517--5764584 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
5764507 TTGGGTTAAT
5764517 TTGTAATTGGGC
1 TTGTAATTGGGC
* *
5764529 CT-CAATTTGGGC
1 TTGTAA-TTGGGC
* *
5764541 TTGTAAATGGAC
1 TTGTAATTGGGC
*
5764553 TTTGTAATTGGAC
1 -TTGTAATTGGGC
5764566 TTTGTAATTGGGC
1 -TTGTAATTGGGC
5764579 TTGTAA
1 TTGTAA
5764585 ATGAACAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
11 2 0.04
12 18 0.40
13 25 0.56
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.41
Consensus pattern (12 bp):
TTGTAATTGGGC
Found at i:5765233 original size:152 final size:147
Alignment explanation
Indices: 5765016--5765339 Score: 495
Period size: 152 Copynumber: 2.2 Consensus size: 147
5765006 CTTCGACCTG
* * * * *
5765016 CTTCTCAATATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTGAGCGCTGAGCTGGTAT
1 CTTCTCTATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCACGTTGAGCGCTGAGCTAGTAT
5765081 TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCC
66 TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTG---T--TTCGCTTCTCTGGATCTCC
5765146 GCAGGAAGACGAATCTGGTCCA
126 GCAGGAAGACGAATCTGGTCCA
* * * * *
5765168 CTTCTCTGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCATGTTGAGTGTTGAGTTAGTAT
1 CTTCTCTATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCACGTTGAGCGCTGAGCTAGTAT
* *
5765233 TCTTTTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGCTTCTCTGGATCTCCTCAGG
66 TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGCTTCTCTGGATCTCCGCAGG
5765298 AAGACGAATCTGGTCCA
131 AAGACGAATCTGGTCCA
5765315 CTTCTCTATGTCTCATCAGGAAGCT
1 CTTCTCTATGTCTCATCAGGAAGCT
5765340 AACCTTTTTA
Statistics
Matches: 159, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
147 64 0.40
149 1 0.01
152 94 0.59
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (147 bp):
CTTCTCTATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCACGTTGAGCGCTGAGCTAGTAT
TCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGCTTCTCTGGATCTCCGCAGG
AAGACGAATCTGGTCCA
Found at i:5777241 original size:15 final size:15
Alignment explanation
Indices: 5777217--5777247 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5777207 TATTTAACAG
*
5777217 ATGAATGTTTTTTTT
1 ATGAAAGTTTTTTTT
5777232 ATGAAAGTTTTTTTT
1 ATGAAAGTTTTTTTT
5777247 A
1 A
5777248 CATAAAAAAA
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:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (15 bp):
ATGAAAGTTTTTTTT
Found at i:5778299 original size:13 final size:13
Alignment explanation
Indices: 5778249--5778299 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
5778239 AAAAAGTTCT
*
5778249 AATAATATTTTGG
1 AATAATATTTTGA
5778262 AATAATATTTT--
1 AATAATATTTTGA
5778273 -ATAA-AGTTTTGA
1 AATAATA-TTTTGA
5778285 AATAATATTTTGA
1 AATAATATTTTGA
5778298 AA
1 AA
5778300 CATTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
13 23 0.70
14 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (13 bp):
AATAATATTTTGA
Found at i:5778383 original size:18 final size:20
Alignment explanation
Indices: 5778360--5778399 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5778350 TTTCTATTAT
5778360 AAAT-AAAAT-TAATTTTAA
1 AAATAAAAATATAATTTTAA
*
5778378 AAATAAAAATATTATTTTAA
1 AAATAAAAATATAATTTTAA
5778398 AA
1 AA
5778400 TATTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAAAAATATAATTTTAA
Found at i:5784103 original size:4 final size:4
Alignment explanation
Indices: 5784096--5784142 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
5784086 AAAAAAAAAT
*
5784096 AAAG AAAG AAAG TAAG AAAG -AAG -AAG -AAG -AAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
5784140 AAA
1 AAA
5784143 TCTTGTTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 12 0.30
4 28 0.70
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:5786682 original size:34 final size:35
Alignment explanation
Indices: 5786611--5786682 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 35
5786601 TTTTATGTTA
* * *
5786611 ATTTTATTATTATATATTTTTTTTACTTTTAAGTT
1 ATTTTATTATTATATATTTTTTATAATTTTAAATT
*
5786646 ATTTTATTGTTA-ATA-TTTTTATAATTATTAAATT
1 ATTTTATTATTATATATTTTTTATAATT-TTAAATT
5786680 ATT
1 ATT
5786683 ATTGACATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 9 0.28
34 12 0.38
35 11 0.34
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (35 bp):
ATTTTATTATTATATATTTTTTATAATTTTAAATT
Found at i:5789051 original size:105 final size:105
Alignment explanation
Indices: 5788869--5789074 Score: 367
Period size: 105 Copynumber: 2.0 Consensus size: 105
5788859 CAAAACTGCT
* * *
5788869 AAATCATTTGGGATGAATAGATCGACAGCTTATACCGGCATGTATGGTCTACTAAAAAACATGCC
1 AAATCATTTGGGATGAACAGATCGACAGCTTATACCAGCATGTATAGTCTACTAAAAAACATGCC
5788934 AGAACCAAGGATTTAAATAGCAGTCCAATAGCGGAACTGA
66 AGAACCAAGGATTTAAATAGCAGTCCAATAGCGGAACTGA
5788974 AAATCATTTGGGATGAACAGATCGACAGCTTATACCAGCATGTATAGTCTACTAAAAAACATGCC
1 AAATCATTTGGGATGAACAGATCGACAGCTTATACCAGCATGTATAGTCTACTAAAAAACATGCC
* *
5789039 AGAACCAGGGATTTAAATAGCAGTCCGATAGCGGAA
66 AGAACCAAGGATTTAAATAGCAGTCCAATAGCGGAA
5789075 TAGCGGCCGC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 96 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22
Consensus pattern (105 bp):
AAATCATTTGGGATGAACAGATCGACAGCTTATACCAGCATGTATAGTCTACTAAAAAACATGCC
AGAACCAAGGATTTAAATAGCAGTCCAATAGCGGAACTGA
Found at i:5796320 original size:34 final size:34
Alignment explanation
Indices: 5796281--5796356 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
5796271 CACATTTTCA
*
5796281 TGCATCATTTTAAACATCATATTTGGTTTCATAT
1 TGCATCATTTTAAACATCATATCTGGTTTCATAT
* * * *
5796315 TGCATCATTTTAGATATCATATCTGGTTTCCTTT
1 TGCATCATTTTAAACATCATATCTGGTTTCATAT
5796349 TGCATCAT
1 TGCATCAT
5796357 AATGCAGTCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (34 bp):
TGCATCATTTTAAACATCATATCTGGTTTCATAT
Found at i:5798964 original size:4 final size:4
Alignment explanation
Indices: 5798955--5798981 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5798945 TGAATCTTCT
5798955 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
5798982 GAACACTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:5803212 original size:28 final size:28
Alignment explanation
Indices: 5803181--5803261 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
5803171 ATTCTATTAT
5803181 TTTGATTTTGCATTTTTAATTTGAGAAG
1 TTTGATTTTGCATTTTTAATTTGAGAAG
* *
5803209 TTTGATTTTCCATTTTTAATTTGAGTAG
1 TTTGATTTTGCATTTTTAATTTGAGAAG
* *
5803237 GTTGATTTTGCATTTTCTATTTTGA
1 TTTGATTTTGCATTTT-TAATTTGA
5803262 ACATTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 40 0.85
29 7 0.15
ACGTcount: A:0.21, C:0.06, G:0.16, T:0.57
Consensus pattern (28 bp):
TTTGATTTTGCATTTTTAATTTGAGAAG
Found at i:5808865 original size:34 final size:34
Alignment explanation
Indices: 5808826--5808904 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
5808816 ACTCATTTTC
*
5808826 ATGCATCATTTTAAACATCATATTTGGTTTCATA
1 ATGCATCATTTTAAACATCATATCTGGTTTCATA
* * * * *
5808860 ATGCATCACTGTAGACATCATATCTGGTTTCCTT
1 ATGCATCATTTTAAACATCATATCTGGTTTCATA
*
5808894 TTGCATCATTT
1 ATGCATCATTT
5808905 GGTTTTGTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (34 bp):
ATGCATCATTTTAAACATCATATCTGGTTTCATA
Found at i:5825908 original size:19 final size:21
Alignment explanation
Indices: 5825864--5825924 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
5825854 AAATAATTTC
5825864 AATAATTTTAAATTAATTTT---
1 AATAATTTT-AA-TAATTTTAAA
5825884 AATAATTTT-AT-ATTTTAAA
1 AATAATTTTAATAATTTTAAA
5825903 AATAATTTTAATAATTTTAAA
1 AATAATTTTAATAATTTTAAA
5825924 A
1 A
5825925 TCATTTGCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.14
17 1 0.03
18 1 0.03
19 9 0.25
20 11 0.31
21 9 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATTTTAATAATTTTAAA
Found at i:5825916 original size:28 final size:27
Alignment explanation
Indices: 5825868--5825921 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
5825858 AATTTCAATA
*
5825868 ATTTTAAATTAATTTTAATAATTTTAT
1 ATTTTAAAATAATTTTAATAATTTTAT
5825895 ATTTTAAAAATAATTTTAATAATTTTA
1 ATTTT-AAAATAATTTTAATAATTTTA
5825922 AAATCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTAAAATAATTTTAATAATTTTAT
Found at i:5825920 original size:9 final size:9
Alignment explanation
Indices: 5825855--5825922 Score: 68
Period size: 9 Copynumber: 7.2 Consensus size: 9
5825845 ATTTCAAAAA
*
5825855 AATAATTTC
1 AATAATTTT
5825864 AATAATTTT
1 AATAATTTT
5825873 AAATTAATTTT
1 -AA-TAATTTT
5825884 AATAATTTT
1 AATAATTTT
5825893 -AT-ATTTT
1 AATAATTTT
5825900 AAAAATAATTTT
1 ---AATAATTTT
5825912 AATAATTTT
1 AATAATTTT
5825921 AA
1 AA
5825923 AATCATTTGC
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 26 0.51
10 4 0.08
11 9 0.18
12 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:5829695 original size:29 final size:29
Alignment explanation
Indices: 5829647--5829710 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
5829637 ATTTGGTATT
*
5829647 TAAA-TTTTTTTGGATCCAATTTGATACC
1 TAAATTTTTTTTAGATCCAATTTGATACC
* *
5829675 TAAATTTTTTTTAGATTCAATTTGGTACC
1 TAAATTTTTTTTAGATCCAATTTGATACC
5829704 TAAATTT
1 TAAATTT
5829711 ATTAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (29 bp):
TAAATTTTTTTTAGATCCAATTTGATACC
Found at i:5833060 original size:14 final size:14
Alignment explanation
Indices: 5833041--5833074 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5833031 TTTTAGGGTT
*
5833041 TAAGAAAAGGAAAA
1 TAAGAAAAGAAAAA
5833055 TAAGAAAAGAAAAA
1 TAAGAAAAGAAAAA
*
5833069 GAAGAA
1 TAAGAA
5833075 GCAGCCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
TAAGAAAAGAAAAA
Found at i:5834219 original size:34 final size:34
Alignment explanation
Indices: 5834171--5834238 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
5834161 CGTGAATCAA
5834171 ACGTATTGTAATTTTTAGTTGAAATAATAAAATT
1 ACGTATTGTAATTTTTAGTTGAAATAATAAAATT
*
5834205 ACGTATTGTTATTTTTAGTTGAAATAATAAAATT
1 ACGTATTGTAATTTTTAGTTGAAATAATAAAATT
5834239 GAGGTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.46
Consensus pattern (34 bp):
ACGTATTGTAATTTTTAGTTGAAATAATAAAATT
Found at i:5834710 original size:24 final size:24
Alignment explanation
Indices: 5834679--5834725 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5834669 AATTTTCAAT
5834679 AAATAAAAAAATTATAAA-ATATTA
1 AAATAAAAAAA-TATAAATATATTA
*
5834703 AAATAAAACAATATAAATATATT
1 AAATAAAAAAATATAAATATATT
5834726 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATAAAAAAATATAAATATATTA
Found at i:5845780 original size:22 final size:22
Alignment explanation
Indices: 5845748--5845816 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
5845738 GAAATTTTAT
*
5845748 AAATAATATAGATGATATATATA
1 AAATAA-ATAGATAATATATATA
*
5845771 AAATAAATAGA-AAAATGATATA
1 AAATAAATAGATAATAT-ATATA
*
5845793 ATAATAAATACATACATATATATA
1 A-AATAAATAGATA-ATATATATA
5845817 TATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.08
22 11 0.29
23 15 0.39
24 6 0.16
25 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (22 bp):
AAATAAATAGATAATATATATA
Found at i:5846796 original size:22 final size:23
Alignment explanation
Indices: 5846748--5846798 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
5846738 ATTGAATTGT
* *
5846748 AATTTTTATAATAGTAAAAATAT
1 AATTTTTATAATAATAAAAATAA
* *
5846771 AATTTTTA-AATAATTAAATTAA
1 AATTTTTATAATAATAAAAATAA
5846793 AATTTT
1 AATTTT
5846799 ATTATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTTTATAATAATAAAAATAA
Found at i:5847860 original size:12 final size:12
Alignment explanation
Indices: 5847845--5847869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5847835 CATGGAATAC
5847845 AAAGAATTTCTA
1 AAAGAATTTCTA
5847857 AAAGAATTTCTA
1 AAAGAATTTCTA
5847869 A
1 A
5847870 TTGATTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAGAATTTCTA
Found at i:5848041 original size:6 final size:6
Alignment explanation
Indices: 5848030--5848060 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
5848020 TTGGAAACTT
5848030 ATAAGA ATAAGA ATAAGA ATAAGA ATAAGA A
1 ATAAGA ATAAGA ATAAGA ATAAGA ATAAGA A
5848061 AGGGCGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATAAGA
Found at i:5865951 original size:47 final size:47
Alignment explanation
Indices: 5865882--5865976 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
5865872 CACTTCCCTG
*
5865882 TCCTGCGTTGCTTTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGA
1 TCCTGCGTTGCCTTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGA
*
5865929 TCCTGCGTTGCCTTTATTGTGTCGCTTGCACCCTTTGTGTTTCTCGA
1 TCCTGCGTTGCCTTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGA
5865976 T
1 T
5865977 AGTGAGGCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.06, C:0.27, G:0.21, T:0.45
Consensus pattern (47 bp):
TCCTGCGTTGCCTTTATTGTGTCGCTTGCACCCTTCGTGTTTCTCGA
Done.