Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1610090 original size:45 final size:45
Alignment explanation
Indices: 1610019--1610307 Score: 271
Period size: 45 Copynumber: 6.4 Consensus size: 45
1610009 TTTTGAATAC
* * * *
1610019 AGAGAAATCAATATTTTAGTGCTGTCTTCCTTGACTTTCTTGTGA
1 AGAGAAGTCAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCGTGA
* * * **
1610064 AGAGGAGTCAATCTTTTATTGTTGTCTTCCTTAACTTTCTCACGA
1 AGAGAAGTCAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCGTGA
* * *
1610109 AGAGAAGTCAACCTTTTATTATTGTCATT-CTTGACTTTCTCGTGA
1 AGAGAAGTCAATCTTTTAGTGTTGTC-TTCCTTGACTTTCTCGTGA
* * * * *
1610154 AGA-AGAGTCAATGTTTTAGTGTTGTCTTCTTTGAATTTTTCGCGA
1 AGAGA-AGTCAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCGTGA
* * * * *
1610199 AGAGAAGTCAATATTTTAGTGTTGTCCTACTTGACTTTCTTGTGC
1 AGAGAAGTCAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCGTGA
* * * * *
1610244 AGAGAAGTCAACCTTTCAGTGATGTTATTCC-TGACTTTCTCATGA
1 AGAGAAGTCAATCTTTTAGTGTTG-TCTTCCTTGACTTTCTCGTGA
1610289 AGATG-AGTCAATCTTTTAG
1 AGA-GAAGTCAATCTTTTAG
1610308 CAGTTTTATT
Statistics
Matches: 194, Mismatches: 44, Indels: 12
0.78 0.18 0.05
Matches are distributed among these distances:
44 3 0.02
45 184 0.95
46 7 0.04
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (45 bp):
AGAGAAGTCAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCGTGA
Found at i:1610279 original size:135 final size:135
Alignment explanation
Indices: 1610026--1610307 Score: 334
Period size: 135 Copynumber: 2.1 Consensus size: 135
1610016 TACAGAGAAA
* * * * * *
1610026 TCAATATTTTAGTGCTGTCTTCCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTTATTGTTGTCT
1 TCAATATTTTAGTGCTGTCTTCCTTGAATTTCTTGCGAAGAGAAGTCAATATTTTAGTGTTGTCC
* * * * *
1610091 TCCTTAACTTTCTCACGAAGAGAAGTCAACCTTTTATTATTGTCATTCTTGACTTTCTCGTGAAG
66 TACTTAACTTTCTCACGAAGAGAAGTCAACCTTTCATGATTGTCATTCCTGACTTTCTCATGAAG
1610156 AAGAG
131 AAGAG
* * *
1610161 TCAATGTTTTAGTGTTGTCTTCTTTGAATTT-TTCGCGAAGAGAAGTCAATATTTTAGTGTTGTC
1 TCAATATTTTAGTGCTGTCTTCCTTGAATTTCTT-GCGAAGAGAAGTCAATATTTTAGTGTTGTC
* *** * *
1610225 CTACTTGACTTTCTTGTGCAGAGAAGTCAACCTTTCAGTGA-TGTTATTCCTGACTTTCTCATGA
65 CTACTTAACTTTCTCACGAAGAGAAGTCAACCTTTCA-TGATTGTCATTCCTGACTTTCTCATGA
*
1610289 AGATGAG
129 AGAAGAG
*
1610296 TCAATCTTTTAG
1 TCAATATTTTAG
1610308 CAGTTTTATT
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
134 2 0.02
135 119 0.97
136 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (135 bp):
TCAATATTTTAGTGCTGTCTTCCTTGAATTTCTTGCGAAGAGAAGTCAATATTTTAGTGTTGTCC
TACTTAACTTTCTCACGAAGAGAAGTCAACCTTTCATGATTGTCATTCCTGACTTTCTCATGAAG
AAGAG
Found at i:1610351 original size:135 final size:135
Alignment explanation
Indices: 1610109--1610359 Score: 301
Period size: 135 Copynumber: 1.9 Consensus size: 135
1610099 TTTCTCACGA
* * * * * *
1610109 AGAGAAGTCAACCTTTTATTATTGTCATTCTTGACTTTCTCGTGAAGAAGAGTCAATGTTTTAGT
1 AGAGAAGTCAACCTTTCATGATTGTCATTCCTGACTTTCTCATGAAGAAGAGTCAATCTTTTAGA
* * * *
1610174 GTTGTCTTCTTTGAATTTTTCGCGAAGAGAAGTCAATATTTTAGTGTTGTCCTACTTGACTTTCT
66 GTTGTATTCTTTGAATTTCTCGCGAAGAGAAGTCAACATTTTAGTGATGTCCTACTTGACTTTCT
1610239 TGTGC
131 TGTGC
* *
1610244 AGAGAAGTCAACCTTTCAGTGA-TGTTATTCCTGACTTTCTCATGAAGATGAGTCAATCTTTTAG
1 AGAGAAGTCAACCTTTCA-TGATTGTCATTCCTGACTTTCTCATGAAGAAGAGTCAATCTTTTAG
* * * * *
1610308 CAGTTTTATTC-TTGAATTTCTCGGGGAA-AGGAGTTAACCTTTTAGTGATGTC
65 -AGTTGTATTCTTTGAATTTCTC-GCGAAGAGAAGTCAACATTTTAGTGATGTC
1610360 ATTCTCAACT
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
135 83 0.86
136 13 0.14
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (135 bp):
AGAGAAGTCAACCTTTCATGATTGTCATTCCTGACTTTCTCATGAAGAAGAGTCAATCTTTTAGA
GTTGTATTCTTTGAATTTCTCGCGAAGAGAAGTCAACATTTTAGTGATGTCCTACTTGACTTTCT
TGTGC
Found at i:1611622 original size:135 final size:134
Alignment explanation
Indices: 1611094--1612114 Score: 1186
Period size: 134 Copynumber: 7.6 Consensus size: 134
1611084 AAAGTGGTGG
* * *
1611094 AGTGAATCAAAATTTTCTCAAGAT-TGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTT
1 AGTGAATCAAAGTTTTCTCGAG-TCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTT
* * * * * *
1611158 TCAGATTTGGTCTTCATGAAGATCAACGAAACAAATCAAGTTCGATTCAATCTTCCTTGAAGAGC
65 TCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGC
*
1611223 AGTGA
130 AGCGA
* * * *
1611228 AGTGAATCAAATTTTTCTCGAGTTTGACCTCCTCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
* ** * * * *
1611293 CAGATTTGGTCTTCCTGAAGGGTGGCAAAGTAAATCATATTCGATTCAATCTTCCCTAAAGAGCA
66 CAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGCA
1611358 GCGA
131 GCGA
* * * * *
1611362 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAATAGTGGAACATATTATTCTTCTTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
* * * * *
1611427 CAGATTTGGTTTTCCTGAAGAGTAGCGAAGCAAATCATATTCGATTCAATCTTCCTTGAAGAGAA
66 CAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGCA
*
1611492 GCAA
131 GCGA
* * * * *
1611496 AGTGAATCAAAGTTTTCTCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCATAATCTTCTCCTTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
*
1611561 CAAGATTTGGTCTTCCTGAAGAGCACCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGC
66 C-AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGC
1611626 AGCGA
130 AGCGA
* * * *
1611631 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAATAGTAACAGAGCAGATTCTTCTCCTTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
* ** * * * *
1611696 CAAGATTTGGTCTTCCTGAAGAACAATGAAACAAATCAAAATGGATTCAATCTTCTCTGAAGAGC
66 C-AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGC
1611761 AGCGA
130 AGCGA
* * ** * *
1611766 AGTGGATCAAAATTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGTAGATTCTAT-TTCTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCT-TCTTCTT
* * * * * *
1611830 TCAGATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATTAAATTTGATTCAATCTTTCCTGAAGAGT
65 TCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGC
*
1611895 AGTGA
130 AGCGA
* * * * * * ** * * *
1611900 AGTGAATCGAAGTTTTATCAAGTCTGACCTCCCCTTAAGAGTGGC-AAATATATTATTTTTCTTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
* * * * * *
1611964 CATATTTGGTCTTCCTGAAAAGTAGCGAAGCAAATCACATTTGATTCAATCTTCCCTGAAGAGTA
66 CAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGCA
1612029 GCGA
131 GCGA
* * * * ** * *
1612033 AGTGGATCAAAATTTTCACAAGTCTGATATCCTCTAAAGAGTAGTGGAGCAGATT-TTCTTTCTT
1 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTC-TTCTT
1612097 TCAGATTTGGTCTTCCTG
65 TCAGATTTGGTCTTCCTG
1612115 TAGACATTGG
Statistics
Matches: 758, Mismatches: 123, Indels: 12
0.85 0.14 0.01
Matches are distributed among these distances:
132 1 0.00
133 110 0.15
134 408 0.54
135 238 0.31
136 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (134 bp):
AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTTT
CAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGAGCA
GCGA
Found at i:1611838 original size:269 final size:268
Alignment explanation
Indices: 1611094--1612114 Score: 1208
Period size: 269 Copynumber: 3.8 Consensus size: 268
1611084 AAAGTGGTGG
* * * * *
1611094 AGTGAATCAAAATTTTCTCAAGAT-TGATCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTTCTT
1 AGTGAATCAAAGTTTTCTCAAG-TCTGACCTCCCCTAAAGAGTAGCAGAACAGATTATTCTTCTT
* * *
1611158 TCAGATTTGGTCTTCATGAAGATCAACGAAACAAATCAAGTTCGATTCAATCTTCCTTGAAGAGC
65 TCAGATTTGGTCTTCCTGAAGAACAACGAAACAAATCAAATTCGATTCAATCTTCCTTGAAGAGC
* * * * *
1611223 AGTGAAGTGAATCAAATTTTTCTCGAGTTTGACCTCCTCTAAAGAGTAGTGGAGCAGATTCTTCT
130 AGCGAAGTGAATCAAAATTTTCTCGAGTCTGACATCCCCTAAAGAGTAGTGGAGCAGATTCTTCT
* ** * * * *
1611288 TCTTTCAGATTTGGTCTTCCTGAAGGGTGGCAAAGTAAATCATATTCGATTCAATCTTCCCTAAA
195 TCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAA
1611353 GAGCAGCGA
260 GAGCAGCGA
* * ** *
1611362 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAAGAATAGTGGAACATATTATTCTTCTTT
1 AGTGAATCAAAGTTTTCTCAAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTATTCTTCTTT
* ** * * * *
1611427 CAGATTTGGTTTTCCTGAAGAGTAGCGAAGCAAATCATATTCGATTCAATCTTCCTTGAAGAGAA
66 CAGATTTGGTCTTCCTGAAGAACAACGAAACAAATCAAATTCGATTCAATCTTCCTTGAAGAGCA
* * * * ** * * *
1611492 GCAAAGTGAATCAAAGTTTTCTCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCATAATCTTCTC
131 GCGAAGTGAATCAAAATTTTCTCGAGTCTGACATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTT
*
1611557 CTTTCAAGATTTGGTCTTCCTGAAGAGCACCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAA
196 CTTTC-AGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAA
1611622 GAGCAGCGA
260 GAGCAGCGA
* * * * * *
1611631 AGTGAATCAAAGTTTTCTCGAGTCTGACCTCCCCTAAATAGTAACAGAGCAGATTCTTCTCCTTT
1 AGTGAATCAAAGTTTTCTCAAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTATTCTTCTTT
* * *
1611696 CAAGATTTGGTCTTCCTGAAGAACAATGAAACAAATCAAAATGGATTCAATCTT-CTCTGAAGAG
66 C-AGATTTGGTCTTCCTGAAGAACAACGAAACAAATCAAATTCGATTCAATCTTCCT-TGAAGAG
* * *
1611760 CAGCGAAGTGGATCAAAATTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGTAGATTCTAT
129 CAGCGAAGTGAATCAAAATTTTCTCGAGTCTGACATCCCCTAAAGAGTAGTGGAGCAGATTCT-T
* * * * *
1611825 -TTCTTTCAGATTTGGTCTTCCTAAAGAGCAGTGAAGCAAATTAAATTTGATTCAATCTTTCCTG
193 CTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTG
* *
1611889 AAGAGTAGTGA
258 AAGAGCAGCGA
* * * * * * *
1611900 AGTGAATCGAAGTTTTATCAAGTCTGACCTCCCCTTAAGAGTGGCA-AATATATTATTTTTCTTT
1 AGTGAATCAAAGTTTTCTCAAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTATTCTTCTTT
* * * * * * * *
1611964 CATATTTGGTCTTCCTGAA-AAGTAGCGAAGCAAATCACATTTGATTCAATCTTCCCTGAAGAGT
66 CAGATTTGGTCTTCCTGAAGAA-CAACGAAACAAATCAAATTCGATTCAATCTTCCTTGAAGAGC
* * * * *
1612028 AGCGAAGTGGATCAAAATTTTCACAAGTCTGATATCCTCTAAAGAGTAGTGGAGCAGATT-TTCT
130 AGCGAAGTGAATCAAAATTTTCTCGAGTCTGACATCCCCTAAAGAGTAGTGGAGCAGATTCTTC-
1612092 TTCTTTCAGATTTGGTCTTCCTG
194 TTCTTTCAGATTTGGTCTTCCTG
1612115 TAGACATTGG
Statistics
Matches: 641, Mismatches: 103, Indels: 19
0.84 0.13 0.02
Matches are distributed among these distances:
265 1 0.00
266 3 0.00
267 127 0.20
268 184 0.29
269 218 0.34
270 107 0.17
271 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (268 bp):
AGTGAATCAAAGTTTTCTCAAGTCTGACCTCCCCTAAAGAGTAGCAGAACAGATTATTCTTCTTT
CAGATTTGGTCTTCCTGAAGAACAACGAAACAAATCAAATTCGATTCAATCTTCCTTGAAGAGCA
GCGAAGTGAATCAAAATTTTCTCGAGTCTGACATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTT
CTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAG
AGCAGCGA
Found at i:1612220 original size:2 final size:2
Alignment explanation
Indices: 1612213--1612265 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
1612203 ATTTTTAGTT
1612213 TA TA TA TA TA TA TA TCA T- TA T- TA T- TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1612252 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1612266 ACAAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.09
2 40 0.87
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1612295 original size:9 final size:9
Alignment explanation
Indices: 1612279--1612311 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1612269 AAAAATAATT
1612279 TTAAAAAAA
1 TTAAAAAAA
*
1612288 -TGAAAAAA
1 TTAAAAAAA
1612296 TTAAAAAAA
1 TTAAAAAAA
1612305 TTAAAAA
1 TTAAAAA
1612312 CCCCTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1612301 original size:17 final size:17
Alignment explanation
Indices: 1612279--1612311 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1612269 AAAAATAATT
1612279 TTAAAAAAATGAAAAAA
1 TTAAAAAAATGAAAAAA
*
1612296 TTAAAAAAATTAAAAA
1 TTAAAAAAATGAAAAA
1612312 CCCCTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
TTAAAAAAATGAAAAAA
Found at i:1623469 original size:3 final size:3
Alignment explanation
Indices: 1623461--1623488 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1623451 TTCTCCTGTA
1623461 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1623489 TCCTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1625164 original size:20 final size:20
Alignment explanation
Indices: 1625128--1625166 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1625118 TTCAATCATT
* *
1625128 TTAAAGATTATATATATATA
1 TTAAAGATTAGACATATATA
1625148 TTAAAGATTAGACATATAT
1 TTAAAGATTAGACATATAT
1625167 TTTTAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
TTAAAGATTAGACATATATA
Found at i:1625940 original size:30 final size:29
Alignment explanation
Indices: 1625906--1625969 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
1625896 ACCCATCAAT
*
1625906 TTTTCAAAATTTACGAATTGATCTCCCAAC
1 TTTTCAAAATTTACGAAATGATCT-CCAAC
* *
1625936 TTTTCAAAATTTACGAAATGGTCTCCAAT
1 TTTTCAAAATTTACGAAATGATCTCCAAC
1625965 TTTTC
1 TTTTC
1625970 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTTCAAAATTTACGAAATGATCTCCAAC
Found at i:1630010 original size:17 final size:16
Alignment explanation
Indices: 1629986--1630029 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1629976 AAATTAAATT
*
1629986 AAAAATTTAATTATAA
1 AAAAATTTAATTACAA
*
1630002 AAAACATTTACATTACAT
1 AAAA-ATTTA-ATTACAA
1630020 AAAAATTTAA
1 AAAAATTTAA
1630030 AATTTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAAATTTAATTACAA
Found at i:1636684 original size:2 final size:2
Alignment explanation
Indices: 1636677--1636728 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
1636667 CCCAATAACT
1636677 TA TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1636717 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1636729 ATAAAGTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1637648 original size:20 final size:20
Alignment explanation
Indices: 1637623--1637695 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
1637613 GCAGCTTTGG
* *
1637623 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAGCAGGA
*
1637643 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
1637663 TGCATCGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGA
1637683 TGCATCGATGCAC
1 TGCATCGATGCAC
1637696 TAATTGCATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1639220 original size:19 final size:20
Alignment explanation
Indices: 1639185--1639222 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1639175 CAAAATTTCA
*
1639185 TTTTGATTTTTAAAATCAAC
1 TTTTGATTTTCAAAATCAAC
1639205 TTTTGA-TTTCAAAATCAA
1 TTTTGATTTTCAAAATCAA
1639223 ATTATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCAAC
Found at i:1641162 original size:20 final size:20
Alignment explanation
Indices: 1641133--1641281 Score: 217
Period size: 20 Copynumber: 7.5 Consensus size: 20
1641123 GCAGCCTTGG
* *
1641133 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGA
1641153 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
1641173 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
1641193 TGCATCGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* *
1641213 TGCATCGATACACAACAGGA
1 TGCATCGATGCACAGCAGGA
* * * *
1641233 TGCATCGATACATAACAGAA
1 TGCATCGATGCACAGCAGGA
*
1641253 TGCATCGATGCACAACAGGA
1 TGCATCGATGCACAGCAGGA
1641273 TGCATCGAT
1 TGCATCGAT
1641282 ACACTAATTT
Statistics
Matches: 120, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1641373 original size:21 final size:21
Alignment explanation
Indices: 1641324--1641404 Score: 101
Period size: 21 Copynumber: 3.8 Consensus size: 21
1641314 TGAACTACAT
*
1641324 GGTGCATCGATGCACTAGT-GG
1 GGTGCATGGATGCACT-GTAGG
1641345 CAGGTGCATGGATGCACTGTAGG
1 --GGTGCATGGATGCACTGTAGG
*
1641368 GGTGCATGGATCCACTGTAGG
1 GGTGCATGGATGCACTGTAGG
*
1641389 GGTGCATAGATGCACT
1 GGTGCATGGATGCACT
1641405 TTGACACCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
21 34 0.64
22 2 0.04
23 17 0.32
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
GGTGCATGGATGCACTGTAGG
Found at i:1647130 original size:10 final size:9
Alignment explanation
Indices: 1647102--1647137 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1647092 TTTTTGAATA
1647102 AAATATATT
1 AAATATATT
1647111 AAATAT-TT
1 AAATATATT
1647119 AAATATTATT
1 AAATA-TATT
1647129 AAATATATT
1 AAATATATT
1647138 GCATGTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AAATATATT
Found at i:1659139 original size:24 final size:23
Alignment explanation
Indices: 1659110--1659169 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
1659100 ACCACCCTAT
*
1659110 TTTGAATTCAAAACAGCCCCTTAG
1 TTTGAAATC-AAACAGCCCCTTAG
*
1659134 TTTGAAAATCAACCAGCCCCTTAG
1 TTTG-AAATCAAACAGCCCCTTAG
1659158 TTTGAAAATCAA
1 TTTG-AAATCAA
1659170 CCGGCCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (23 bp):
TTTGAAATCAAACAGCCCCTTAG
Found at i:1659145 original size:25 final size:25
Alignment explanation
Indices: 1659117--1659169 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
1659107 TATTTTGAAT
1659117 TCAAAACAGCCCCTTAGTTTGAAAA
1 TCAAAACAGCCCCTTAGTTTGAAAA
*
1659142 TC-AACCAGCCCCTTAGTTTGAAAA
1 TCAAAACAGCCCCTTAGTTTGAAAA
1659166 TCAA
1 TCAA
1659170 CCGGCCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (25 bp):
TCAAAACAGCCCCTTAGTTTGAAAA
Found at i:1659170 original size:24 final size:24
Alignment explanation
Indices: 1659123--1659171 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1659113 GAATTCAAAA
1659123 CAGCCCCTTAGTTTGAAAATCAAC
1 CAGCCCCTTAGTTTGAAAATCAAC
1659147 CAGCCCCTTAGTTTGAAAATCAAC
1 CAGCCCCTTAGTTTGAAAATCAAC
1659171 C
1 C
1659172 GGCCTTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (24 bp):
CAGCCCCTTAGTTTGAAAATCAAC
Found at i:1663818 original size:174 final size:173
Alignment explanation
Indices: 1663528--1663878 Score: 630
Period size: 174 Copynumber: 2.0 Consensus size: 173
1663518 GGATGATTTT
*
1663528 GAAGCTAATTCTAGAATTTCAACAGTCGTGGGATCGAGTCCCATGGAGGACATTTCATAATTTGG
1 GAAGCTAATTCTAGAATTTCAACAGTCATGGGATCGAGTCCCATGGAGGACATTTCATAATTTGG
*
1663593 AGGTCTCCTACGGAAGCTGCTCTCAACCTAGTGTTGGGGGCAGTATACTATCTTACCTCCCCCTT
66 AGGTCTCCTACGGAAGCTGCTCTCAACCTAGTGTTGGGGGCAGCATACTATCTTACCTCCCCCTT
*
1663658 ACCCCATTACATATGGGAACAAGGGGACAACCATTTTTCTAGGG
131 ACCCCATTACATATGGGAACAA-GAGACAACCATTTTTCTAGGG
*
1663702 GAAGCTAATTCTAGAATTTCAACAGTCATGGGATCGAGTCCCATGGAGGGCATTTCATAATTTGG
1 GAAGCTAATTCTAGAATTTCAACAGTCATGGGATCGAGTCCCATGGAGGACATTTCATAATTTGG
* * *
1663767 AGGTCTCCTACGGAAGTTGCTCTTAACCTAGTGTTGGGGGCAGCCTACTATCTTACCTCCCCCTT
66 AGGTCTCCTACGGAAGCTGCTCTCAACCTAGTGTTGGGGGCAGCATACTATCTTACCTCCCCCTT
1663832 ACCCCATTACATATGGGAACAAGAGACAACCATTTTTCTAGGG
131 ACCCCATTACATATGGGAACAAGAGACAACCATTTTTCTAGGG
1663875 GAAG
1 GAAG
1663879 ATGCATTGAG
Statistics
Matches: 170, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
173 24 0.14
174 146 0.86
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (173 bp):
GAAGCTAATTCTAGAATTTCAACAGTCATGGGATCGAGTCCCATGGAGGACATTTCATAATTTGG
AGGTCTCCTACGGAAGCTGCTCTCAACCTAGTGTTGGGGGCAGCATACTATCTTACCTCCCCCTT
ACCCCATTACATATGGGAACAAGAGACAACCATTTTTCTAGGG
Found at i:1669694 original size:21 final size:22
Alignment explanation
Indices: 1669665--1669709 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1669655 TAATATTTTT
1669665 TATATTTTTAATAAT-TAAAGAA
1 TATATTTTTAATAATATAAA-AA
1669687 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
1669708 TA
1 TA
1669710 AAAATCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:1688658 original size:81 final size:81
Alignment explanation
Indices: 1688507--1689074 Score: 816
Period size: 81 Copynumber: 7.0 Consensus size: 81
1688497 CATTTAGTAC
* * * * * * * * * ** *
1688507 TTTACCCAAAGGCATTTAGCCTTCCACCTAACTTGCATTATTGACACCTTCCTACCAAATACACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
*
1688572 GCTAGGCCATTAATAT
66 GCTAGGCCATTAATCT
* * * * * *
1688588 TTTACTCCAAGGTATTTAACCTTCCATCTAACTGGTATACTTGACATC-TTTCTATCAATTGCAC
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCAC
*
1688652 AACTAGGCCATTAATCT
65 AGCTAGGCCATTAATCT
* *
1688669 TTTACTCAAAGGTATTTAACCTTTTATCTAACTGGCATAATTGACACATTTCTGTCAAATGTACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
1688734 GCTAGGCCATTAATCT
66 GCTAGGCCATTAATCT
*
1688750 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
*
1688815 GCTAGGCCATTAATAT
66 GCTAGGCCATTAATCT
* * *
1688831 TTTACTCAGAGGTATTT-ACCTTTCATCTAACTGGCGTAATTGACACAATTCTGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
*
1688895 GCTAGGTCATTAATCT
66 GCTAGGCCATTAATCT
* *
1688911 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
1688976 GCTAGGCCATTAATCT
66 GCTAGGCCATTAATCT
* *
1688992 TTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATAATTGACACATTTTTGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
*
1689057 GCTAGGCAATTAATCT
66 GCTAGGCCATTAATCT
1689073 TT
1 TT
1689075 CATTTTAGAA
Statistics
Matches: 439, Mismatches: 45, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
80 75 0.17
81 363 0.83
82 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACA
GCTAGGCCATTAATCT
Found at i:1688979 original size:242 final size:243
Alignment explanation
Indices: 1688507--1689070 Score: 828
Period size: 242 Copynumber: 2.3 Consensus size: 243
1688497 CATTTAGTAC
* * * * * * * * ** ** *
1688507 TTTACCCAAAGGCATTTAGCCTTCCACCTAACTTGCATTATTGACACCTTCCTACCAAATACACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
* * *
1688572 GCTAGGCCATTAATATTTTACTCCAAGGTATTTAACCTTCCATCTAACTGGTATACTTGACATCT
66 GCTAGGCCATTAATATTTTACTCCAAGGTATTTAACCTTCCATCTAACTGGCATAATTGACATCA
* *
1688637 TTCTATCAATTGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTTATCTAACT
131 TTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT
* *
1688702 GGCATAATTGACACATTTCTGTCAAATGTACAGCTAGGCCATTAATCT
196 GGCATAATTGACACATTTCTATCAAATGCACAGCTAGGCCATTAATCT
1688750 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
* *
1688815 GCTAGGCCATTAATATTTTACT-CAGAGGTATTT-ACCTTTCATCTAACTGGCGTAATTGACA-C
66 GCTAGGCCATTAATATTTTACTCCA-AGGTATTTAACCTTCCATCTAACTGGCATAATTGACATC
* * *
1688877 AATTCTGTCAAATGCACAGCTAGGTCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
130 -ATTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
*
1688942 CTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCATTAATCT
194 CTGGCATAATTGACACATTTCTATCAAATGCACAGCTAGGCCATTAATCT
* *
1688992 TTTACTCAAAGGTATTTAACCTTTAATCTAACTGGCATAATTGACACATTTTTGTCAAATGCACA
1 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
*
1689057 GCTAGGCAATTAAT
66 GCTAGGCCATTAAT
1689071 CTTTCATTTT
Statistics
Matches: 290, Mismatches: 29, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
241 1 0.00
242 207 0.71
243 82 0.28
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (243 bp):
TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACA
GCTAGGCCATTAATATTTTACTCCAAGGTATTTAACCTTCCATCTAACTGGCATAATTGACATCA
TTCTATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT
GGCATAATTGACACATTTCTATCAAATGCACAGCTAGGCCATTAATCT
Found at i:1693634 original size:30 final size:30
Alignment explanation
Indices: 1693593--1693713 Score: 206
Period size: 30 Copynumber: 4.0 Consensus size: 30
1693583 CACTAATGAA
*
1693593 AGCTCAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
*
1693623 AGCTGAACTTAGCTGGAGGAGCTAGCATAT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1693653 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
* *
1693683 AGCTAAACTTAGCTAGAGGAGCTAGCATGT
1 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1693713 A
1 A
1693714 ACTAAAGGTA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
AGCTGAACTTAGCTGGAGGAGCTAGCATGT
Found at i:1693719 original size:30 final size:30
Alignment explanation
Indices: 1693593--1693729 Score: 202
Period size: 30 Copynumber: 4.6 Consensus size: 30
1693583 CACTAATGAA
*
1693593 AGCTCAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTAAACTTAGCTGGAGGAGCTAGCATGT
* *
1693623 AGCTGAACTTAGCTGGAGGAGCTAGCATAT
1 AGCTAAACTTAGCTGGAGGAGCTAGCATGT
*
1693653 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTAAACTTAGCTGGAGGAGCTAGCATGT
*
1693683 AGCTAAACTTAGCTAGAGGAGCTAGCATGT
1 AGCTAAACTTAGCTGGAGGAGCTAGCATGT
* **
1693713 AACTAAAGGTAGCTGGA
1 AGCTAAACTTAGCTGGA
1693730 AGTAGCTGGG
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (30 bp):
AGCTAAACTTAGCTGGAGGAGCTAGCATGT
Found at i:1696237 original size:23 final size:22
Alignment explanation
Indices: 1696195--1696237 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
1696185 TCCACAAGAT
*
1696195 ATGTCCTTTGACATTGCAAATG
1 ATGTCCTTTGAAATTGCAAATG
1696217 ATGTACCTCTTGAAATT-CAAA
1 ATGT-CCT-TTGAAATTGCAAA
1696238 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGTCCTTTGAAATTGCAAATG
Found at i:1696884 original size:22 final size:22
Alignment explanation
Indices: 1696859--1696903 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1696849 AACAGTGAAC
1696859 AGTGGGGGAATCGATTCCATGT
1 AGTGGGGGAATCGATTCCATGT
1696881 AGTGGGGGAATCGATTCCATGT
1 AGTGGGGGAATCGATTCCATGT
1696903 A
1 A
1696904 TCAGGGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.13, G:0.36, T:0.27
Consensus pattern (22 bp):
AGTGGGGGAATCGATTCCATGT
Found at i:1696910 original size:22 final size:22
Alignment explanation
Indices: 1696863--1696913 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1696853 GTGAACAGTG
*
1696863 GGGGAATCGATTCCATGTAGTG
1 GGGGAATCGATTCCATGTAGTA
1696885 GGGGAATCGATTCCATGTA-TCA
1 GGGGAATCGATTCCATGTAGT-A
1696907 GGGGAAT
1 GGGGAAT
1696914 TGGTACCCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGAATCGATTCCATGTAGTA
Found at i:1698368 original size:29 final size:30
Alignment explanation
Indices: 1698330--1698392 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
1698320 AATCCCTCCA
* * *
1698330 TTTTCCAAAATTTACGAATTGATCTCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
*
1698360 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
1698389 TTTT
1 TTTT
1698393 TTAAGGCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:1700475 original size:30 final size:30
Alignment explanation
Indices: 1700441--1700521 Score: 153
Period size: 30 Copynumber: 2.7 Consensus size: 30
1700431 CACTAAGGAA
1700441 AGCTGAACTTAGTTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGTTGGAGGAGCTAGCATGT
*
1700471 AGCTGAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAGTTGGAGGAGCTAGCATGT
1700501 AGCTGAACTTAGTTGGAGGAG
1 AGCTGAACTTAGTTGGAGGAG
1700522 AGTTTTGGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.25
Consensus pattern (30 bp):
AGCTGAACTTAGTTGGAGGAGCTAGCATGT
Found at i:1707858 original size:16 final size:16
Alignment explanation
Indices: 1707837--1707870 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1707827 ACTTGATGGG
1707837 CTTCGCTCCCAATCTT
1 CTTCGCTCCCAATCTT
1707853 CTTCGCTCCCAATCTT
1 CTTCGCTCCCAATCTT
1707869 CT
1 CT
1707871 ACCCCATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.06, T:0.38
Consensus pattern (16 bp):
CTTCGCTCCCAATCTT
Found at i:1710208 original size:36 final size:36
Alignment explanation
Indices: 1710161--1710235 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1710151 CATGGAGGAG
*
1710161 TTTATACACGACTCTGATTGAGTTGTGTGATGGTTT
1 TTTATACACGACTCTGATTGAGTTGCGTGATGGTTT
1710197 TTTATACACGACTCTGATTGAGTTGCGTGATGGTTT
1 TTTATACACGACTCTGATTGAGTTGCGTGATGGTTT
1710233 TTT
1 TTT
1710236 CCTGATGGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (36 bp):
TTTATACACGACTCTGATTGAGTTGCGTGATGGTTT
Found at i:1711282 original size:23 final size:23
Alignment explanation
Indices: 1711252--1711299 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1711242 AACTGAGGTC
*
1711252 AATCCTCCGATTCAATTTGTCTG
1 AATCCTCCGATTCAATTAGTCTG
*
1711275 AATCCTCCGATTCTATTAGTCTG
1 AATCCTCCGATTCAATTAGTCTG
1711298 AA
1 AA
1711300 GCTCGACAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (23 bp):
AATCCTCCGATTCAATTAGTCTG
Found at i:1722311 original size:2 final size:2
Alignment explanation
Indices: 1722304--1722338 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1722294 TAGGAGGTAC
1722304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1722339 GTTGTAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1723374 original size:5 final size:5
Alignment explanation
Indices: 1723361--1723408 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
1723351 ACAAAAATTA
* *
1723361 AAAAA AAAAT AAAAT AAAAT AAAAT -AAAT AATA- AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
1723409 GAACGATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 7 0.19
5 25 0.68
6 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1723374 original size:9 final size:9
Alignment explanation
Indices: 1723362--1723403 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
1723352 CAAAAATTAA
1723362 AAAAAAAAT
1 AAAAAAAAT
1723371 AAAATAAAAT
1 AAAA-AAAAT
*
1723381 AAAATAAAT
1 AAAAAAAAT
*
1723390 AATAAAAAT
1 AAAAAAAAT
1723399 AAAAA
1 AAAAA
1723404 TAAAAGAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1723376 original size:29 final size:28
Alignment explanation
Indices: 1723336--1723408 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
1723326 TATCAATTGC
1723336 AAAATATAAATAAAGACAAAAATTAAA-AA-A
1 AAAATA-AAATAAA-A-AAAAA-TAAATAATA
*
1723366 AAAATAAAATAAAATAAAATAAATAATA
1 AAAATAAAATAAAAAAAAATAAATAATA
1723394 AAAATAAAAATAAAA
1 AAAAT-AAAATAAAA
1723409 GAACGATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 4 0.10
27 6 0.15
28 7 0.18
29 16 0.41
30 6 0.15
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.18
Consensus pattern (28 bp):
AAAATAAAATAAAAAAAAATAAATAATA
Found at i:1723381 original size:34 final size:35
Alignment explanation
Indices: 1723336--1723408 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
1723326 TATCAATTGC
1723336 AAAATATAAATAAAGACAAA-AATTAAAAA-AAAAAT
1 AAAATATAAATAAA-ACAAATAA-TAAAAATAAAAAT
*
1723371 AAAATA-AAATAAAATAAATAATAAAAATAAAAAT
1 AAAATATAAATAAAACAAATAATAAAAATAAAAAT
1723405 AAAA
1 AAAA
1723409 GAACGATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
33 10 0.29
34 19 0.54
35 6 0.17
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.18
Consensus pattern (35 bp):
AAAATATAAATAAAACAAATAATAAAAATAAAAAT
Found at i:1724588 original size:14 final size:13
Alignment explanation
Indices: 1724539--1724589 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1724529 AACTTAGGTC
*
1724539 GGGTCGGTTTGCT
1 GGGTCGGCTTGCT
*
1724552 GGGTC--CTTAGCC
1 GGGTCGGCTT-GCT
1724564 GGGTCGGCTTGCT
1 GGGTCGGCTTGCT
1724577 GGGTCAGGCTTGC
1 GGGTC-GGCTTGC
1724590 CCGCCCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 2 0.06
12 7 0.23
13 12 0.39
14 10 0.32
ACGTcount: A:0.04, C:0.24, G:0.43, T:0.29
Consensus pattern (13 bp):
GGGTCGGCTTGCT
Found at i:1724768 original size:18 final size:18
Alignment explanation
Indices: 1724747--1724782 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1724737 TATAATATTT
* *
1724747 AAATATATTTTTTTAAAA
1 AAATATATATTTTCAAAA
1724765 AAATATATATTTTCAAAA
1 AAATATATATTTTCAAAA
1724783 TATTTTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATATATTTTCAAAA
Found at i:1724787 original size:11 final size:11
Alignment explanation
Indices: 1724771--1724830 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 11
1724761 AAAAAAATAT
*
1724771 ATATTTTCAAA
1 ATATTTTTAAA
*
1724782 ATATTTTCAAAA
1 ATATTTT-TAAA
*
1724794 ACTATTTATTATAT
1 A-TATTT-TTA-AA
1724808 ATATTTTTAAA
1 ATATTTTTAAA
1724819 ATATTTTTAAA
1 ATATTTTTAAA
1724830 A
1 A
1724831 CTATATATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 20 0.49
12 7 0.17
13 11 0.27
14 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:1724906 original size:2 final size:2
Alignment explanation
Indices: 1724895--1724924 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1724885 TTCTAAAACA
1724895 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1724925 ATGTTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1725027 original size:42 final size:39
Alignment explanation
Indices: 1724950--1725060 Score: 161
Period size: 42 Copynumber: 2.8 Consensus size: 39
1724940 ATATATTATA
*
1724950 TTTCAAAATATTTTTAAAAACTATATATTATATATATGT
1 TTTCAAAATATTTTTAAAAACTATATATTACATATATGT
1724989 TTTCAAAACGTATTTTTAGAAAACTATATATTACATATATGT
1 TTTCAAAA--TATTTTTA-AAAACTATATATTACATATATGT
*
1725031 TTTCAAAAT-TTTATAAAAAACTATATATTA
1 TTTCAAAATATTT-TTAAAAACTATATATTA
1725061 TACACTATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
39 25 0.38
40 3 0.05
41 8 0.12
42 30 0.45
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (39 bp):
TTTCAAAATATTTTTAAAAACTATATATTACATATATGT
Found at i:1725733 original size:202 final size:202
Alignment explanation
Indices: 1725378--1725762 Score: 504
Period size: 202 Copynumber: 1.9 Consensus size: 202
1725368 AAGGTGACTT
* * *
1725378 CTTGTTGCCAAATCCTAGTCAACCTTGGTCTTCTTCTCAGTTTAAAGACCTCGGTTTGAAAATTC
1 CTTGTTGCCAAATCCTAGCCAACATTGGTCTTCTTCTCAGCTTAAAGACCTCGGTTTGAAAATTC
* * ** * *
1725443 AACCGGAAAGTAGTTCCTCGATGCTACCATATGGTTGATATACCCTTGAGCTGAACGGAATCAAA
66 AACAGGAAAGTAGTTCATCGATGCTACCATATGACTGATACACCCTTGAGCTGAACGAAATCAAA
* *** * *
1725508 CTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTGAATTAGGTTAGGAG
131 CTCGAAAGTTTTCACTAACAGATAACCCTTCTCGCCTTGAGCAATGCTGTGAATTAGGTTAGGAG
1725573 ATAGTTC
196 ATAGTTC
* * *
1725580 CTTGTTGCTAAATCGTAGCCAACATTGGTCTTCTTCT-AGGCTTAAAGACCTTGGTTT-AAAATT
1 CTTGTTGCCAAATCCTAGCCAACATTGGTCTTCTTCTCA-GCTTAAAGACCTCGGTTTGAAAA-T
* * ** * *
1725643 TCAACAGGAAAGTAGTTCATCGTTGCTACCATGTGACTGATACGTCCTTGAGCTGAATGAAATCG
64 TCAACAGGAAAGTAGTTCATCGATGCTACCATATGACTGATACACCCTTGAGCTGAACGAAATCA
* *
1725708 AACTCGAAAGTTTTCACTAACAGATAATCCTTCTCGCCTTGAGCAATGTTGTGAA
129 AACTCGAAAGTTTTCACTAACAGATAACCCTTCTCGCCTTGAGCAATGCTGTGAA
1725763 CGGTTCCTCT
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
201 5 0.03
202 150 0.97
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (202 bp):
CTTGTTGCCAAATCCTAGCCAACATTGGTCTTCTTCTCAGCTTAAAGACCTCGGTTTGAAAATTC
AACAGGAAAGTAGTTCATCGATGCTACCATATGACTGATACACCCTTGAGCTGAACGAAATCAAA
CTCGAAAGTTTTCACTAACAGATAACCCTTCTCGCCTTGAGCAATGCTGTGAATTAGGTTAGGAG
ATAGTTC
Found at i:1730767 original size:21 final size:19
Alignment explanation
Indices: 1730739--1730784 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1730729 TCATTGAATC
1730739 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1730759 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1730778 ACTTAGT
1 A-TTAGT
1730785 AGGATTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1730809 original size:180 final size:172
Alignment explanation
Indices: 1730481--1730830 Score: 628
Period size: 180 Copynumber: 2.0 Consensus size: 172
1730471 TTGTTTGCAT
1730481 TATTTAATACAATACGTTGTTTTGTTTTATCTGTCTGCATATTTTCTTTTCTCAACCACACTTGT
1 TATTTAATACAATACGTTGTTTTGTTTTATCTGTCTGCATATTTTCTTTTCTCAACCACACTTGT
1730546 CTGCAATCATTGAATCATTATTCTTAGCTCCTAATTAGTTCTTAGCTTTAATACTTAGTAGGATT
66 CTGCAATCATTGAATCATTATTCTTAGCTCCTAATTAGTTCTTAGCTTTAATACTTAGTAGGATT
1730611 GATTTGTGGCATTAGCTCTAGTTGTGGTGAAAAGATATTTTA
131 GATTTGTGGCATTAGCTCTAGTTGTGGTGAAAAGATATTTTA
1730653 TATTTAATACAATACTTGTTTTGTTTTGTTTTATCTGTCTGCATATTTTCTTTTTCTCAACCACA
1 TATTTAATACAATAC--G--TTGTTTTGTTTTATCTGTCTGCATATTTTC-TTTTCTCAACCACA
1730718 CTTGTCTGCAATCATTGAATCATTATTCTTAGCTCCTTAATATTAGTTCTTAGCTTTAATACTTA
61 CTTGTCTGCAATCATTGAATCATTATTCTTAGCTCC-T-A-ATTAGTTCTTAGCTTTAATACTTA
1730783 GTAGGATTGATTTGTGGCATTAGCTCTAGTTGTGGTGAAAAGATATTT
123 GTAGGATTGATTTGTGGCATTAGCTCTAGTTGTGGTGAAAAGATATTT
1730831 CTAATCCAAT
Statistics
Matches: 170, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
172 15 0.09
174 1 0.01
176 30 0.18
177 50 0.29
178 1 0.01
179 1 0.01
180 72 0.42
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (172 bp):
TATTTAATACAATACGTTGTTTTGTTTTATCTGTCTGCATATTTTCTTTTCTCAACCACACTTGT
CTGCAATCATTGAATCATTATTCTTAGCTCCTAATTAGTTCTTAGCTTTAATACTTAGTAGGATT
GATTTGTGGCATTAGCTCTAGTTGTGGTGAAAAGATATTTTA
Found at i:1736093 original size:30 final size:29
Alignment explanation
Indices: 1736020--1736102 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
1736010 ATTTATTTAA
* *
1736020 TGACCAAATTATAAATTTGGTAAAGTTTGG
1 TGACCAAAATATAAATTTGG-AAAGTTAGG
* *
1736050 TGATCAAAGTATAAACTTTGGAAAGTTCAGG
1 TGACCAAAATATAAA-TTTGGAAAGTT-AGG
*
1736081 -GACCAAAATATAATTTTGGAAA
1 TGACCAAAATATAAATTTGGAAA
1736103 AATTACAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.18
30 30 0.67
31 7 0.16
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (29 bp):
TGACCAAAATATAAATTTGGAAAGTTAGG
Found at i:1738403 original size:45 final size:45
Alignment explanation
Indices: 1738313--1738514 Score: 343
Period size: 45 Copynumber: 4.5 Consensus size: 45
1738303 GGTAAGTATG
*
1738313 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1738357 AAAATAAGATTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
* *
1738402 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGCTCGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1738447 AAAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1738492 AAAATAAGCTTACAAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
1738515 GATTAAATTG
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
44 25 0.17
45 122 0.83
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
Found at i:1749541 original size:14 final size:14
Alignment explanation
Indices: 1749518--1749555 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1749508 TCTGTATATA
*
1749518 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
1749531 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
1749546 TGCAGGGATT
1 TGCAGGGATT
1749556 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:1749794 original size:3 final size:3
Alignment explanation
Indices: 1749786--1749815 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1749776 GAATTGGGTT
1749786 TTG TTG TTG TTG TTG TTG TTG TTG TCTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG T-TG TT
1749816 TCCAACCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.03, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1749850 original size:27 final size:27
Alignment explanation
Indices: 1749812--1749889 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
1749802 TGTTGTTGTC
*
1749812 TGTTTCCAACCCTTTATTTCCCAATTT
1 TGTTTCCAACCCTTTCTTTCCCAATTT
1749839 TGTTTCCAACCCTTTCTTTCCCAA--T
1 TGTTTCCAACCCTTTCTTTCCCAATTT
** *
1749864 TCCTTCCAACCTTTTCTTTCCCAATT
1 TGTTTCCAACCCTTTCTTTCCCAATT
1749890 CCTTCCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 22 0.49
27 23 0.51
ACGTcount: A:0.17, C:0.35, G:0.03, T:0.46
Consensus pattern (27 bp):
TGTTTCCAACCCTTTCTTTCCCAATTT
Found at i:1749879 original size:25 final size:25
Alignment explanation
Indices: 1749815--1749900 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
1749805 TGTTGTCTGT
* **
1749815 TTCCAACCCTTTATTTCCCAATTTTGT
1 TTCCAACCCTTTCTTTCCCAA--TTCC
1749842 TTCCAACCCTTTCTTTCCCAATTCC
1 TTCCAACCCTTTCTTTCCCAATTCC
*
1749867 TTCCAACCTTTTCTTTCCCAATTCC
1 TTCCAACCCTTTCTTTCCCAATTCC
1749892 TTCCAACCC
1 TTCCAACCC
1749901 CTTCCCTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
25 34 0.63
27 20 0.37
ACGTcount: A:0.17, C:0.40, G:0.01, T:0.42
Consensus pattern (25 bp):
TTCCAACCCTTTCTTTCCCAATTCC
Found at i:1749905 original size:21 final size:22
Alignment explanation
Indices: 1749856--1749906 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
1749846 AACCCTTTCT
*
1749856 TTCCCAATTCCTTCCAACCTTTTCT
1 TTCCCAATTCCTTCCAACC---TCC
1749881 TTCCCAATTCCTTCCAACC-CC
1 TTCCCAATTCCTTCCAACCTCC
1749902 TTCCC
1 TTCCC
1749907 TTTGGGCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
25 19 0.76
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.37
Consensus pattern (22 bp):
TTCCCAATTCCTTCCAACCTCC
Found at i:1754629 original size:20 final size:21
Alignment explanation
Indices: 1754596--1754636 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1754586 TTTACCAAAG
*
1754596 AAAGAAAAACGAAAAATAAAT
1 AAAGAAAAACGAAAAAGAAAT
1754617 AAAGAAAAA-GAAAAAGAAAT
1 AAAGAAAAACGAAAAAGAAAT
1754637 TGAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.07
Consensus pattern (21 bp):
AAAGAAAAACGAAAAAGAAAT
Found at i:1754666 original size:7 final size:7
Alignment explanation
Indices: 1754640--1754713 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
1754630 AAGAAATTGA
*
1754640 ATAAAAT
1 ATAATAT
* *
1754647 ATAGTAA
1 ATAATAT
1754654 ATAATAT
1 ATAATAT
1754661 ATAATACT
1 ATAATA-T
*
1754669 ATACTAT
1 ATAATAT
1754676 ATAATAT
1 ATAATAT
1754683 ATAA-AT
1 ATAATAT
** *
1754689 ATTTTTT
1 ATAATAT
*
1754696 AAAACTAT
1 ATAA-TAT
1754704 ATAATAT
1 ATAATAT
1754711 ATA
1 ATA
1754714 TATTTTCAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
6 4 0.08
7 34 0.69
8 11 0.22
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:1754711 original size:26 final size:26
Alignment explanation
Indices: 1754671--1754750 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 26
1754661 ATAATACTAT
**
1754671 ACTATATAATATATAAATATTTTTTAAA
1 ACTATATAATATAT--ATATTTTCAAAA
1754699 ACTATATAATATATATATTTTCAAAA
1 ACTATATAATATATATATTTTCAAAA
*
1754725 ACTATATATTATATATATTTTCAAAA
1 ACTATATAATATATATATTTTCAAAA
1754751 CATTTTCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 35 0.71
28 14 0.29
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (26 bp):
ACTATATAATATATATATTTTCAAAA
Found at i:1754742 original size:37 final size:37
Alignment explanation
Indices: 1754713--1755043 Score: 387
Period size: 37 Copynumber: 8.7 Consensus size: 37
1754703 TATAATATAT
1754713 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
* *
1754750 ACATTTTCAAAAACTATATATTATACATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
1754787 ATATTTTCAAAAACTATATATTATTTATATATATTCAAA
1 ATATTTTCAAAAACTATATATTA--TATATATTTTCAAA
* * *
1754826 ATGTTTTCAAAAATTATATACTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
* * *
1754863 ATATTTTCAAAAACAATAAATTATATATATATTTTTAAA
1 ATATTTTCAAAAACTATATA-T-TATATATATTTTCAAA
* *
1754902 ATGTTTTCAAAAATTATATATTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
1754939 ATAATTTT-AAAAACTATATATTATATATGTTTTCAAAA
1 AT-ATTTTCAAAAACTATATATTATATATATTTTC-AAA
* * * *
1754977 CATCTTTTTAGAAAACTATATACTACATATATGTTTTCAAA
1 -ATATTTTCA-AAAACTATATA-T-TATATATATTTTCAAA
*
1755018 AT-TTTATAAAAAAACTATATATTATA
1 ATATTT-T-CAAAAACTATATATTATA
1755044 CATTATATAT
Statistics
Matches: 254, Mismatches: 27, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
37 127 0.50
38 15 0.06
39 70 0.28
40 25 0.10
41 5 0.02
42 12 0.05
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (37 bp):
ATATTTTCAAAAACTATATATTATATATATTTTCAAA
Found at i:1754790 original size:11 final size:11
Alignment explanation
Indices: 1754739--1754798 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
1754729 TATATTATAT
1754739 ATATTTTCAAA
1 ATATTTTCAAA
*
1754750 ACATTTTCAAAA
1 ATATTTTC-AAA
*
1754762 ACTATATATT-ATAC
1 A-TAT-T-TTCA-AA
1754776 ATATTTTCAAA
1 ATATTTTCAAA
1754787 ATATTTTCAAA
1 ATATTTTCAAA
1754798 A
1 A
1754799 ACTATATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 22 0.56
12 6 0.15
13 6 0.15
14 3 0.08
15 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:1754838 original size:76 final size:75
Alignment explanation
Indices: 1754713--1755042 Score: 398
Period size: 76 Copynumber: 4.3 Consensus size: 75
1754703 TATAATATAT
** *
1754713 ATATTTTCAAAAACTATATATTA-TATATATTTTCAAAACATTTTCAAAAACTATATATTATACA
1 ATATTTTCAAAAACTATATATTATTATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
1754777 TATTTTCAAA
66 TATTTTCAAA
* * *
1754787 ATATTTTCAAAAACTATATATTATTTATATATATTCAAAATGTTTTCAAAAATTATATACTATAT
1 ATATTTTCAAAAACTATATATTA-TTATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
1754852 ATATTTTCAAA
65 ATATTTTCAAA
* * * *
1754863 ATATTTTCAAAAACAATAAATTATATATATATTTTTAAAATGTTTTCAAAAATTATATATTATAT
1 ATATTTTCAAAAACTATATATTAT-TATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
1754928 ATATTTTCAAA
65 ATATTTTCAAA
* * *
1754939 ATAATTTT-AAAAACTATATATTA-TATATGTTTTCAAAACATCTTTTTAGAAAACTATATACTA
1 AT-ATTTTCAAAAACTATATATTATTATATATTTTC-AAA-ATGTTTTCA-AAAACTATATA-T-
* *
1755002 CATATATGTTTTCAAA
60 TATATATATTTTCAAA
*
1755018 AT-TTTATAAAAAAACTATATATTAT
1 ATATTT-T-CAAAAACTATATATTAT
1755043 ACATTATATA
Statistics
Matches: 223, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
74 32 0.14
75 4 0.02
76 136 0.61
77 18 0.08
78 2 0.01
79 16 0.07
80 15 0.07
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (75 bp):
ATATTTTCAAAAACTATATATTATTATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
TATTTTCAAA
Found at i:1754851 original size:113 final size:114
Alignment explanation
Indices: 1754715--1755042 Score: 405
Period size: 113 Copynumber: 2.9 Consensus size: 114
1754705 TAATATATAT
*
1754715 ATTTTCAAAAACTATATATTATATATATTTTCAAAACATTTTCAAAAACTATATA-T-TATACAT
1 ATTTTCAAAAACTATATATTATATATATTTTCAAAACATTTTCAAAAACTATATACTATATATAT
1754778 ATTTTCAAAATATTTTCAAAAACTATATATTATTTATATATATTCAAAAT-
66 ATTTTCAAAAT-TTTTCAAAAACTATATATTA-TTATATATATTCAAAATA
* * * * * * *
1754828 GTTTTCAAAAATTATATACTATATATATTTTCAAAATATTTTCAAAAACAATAAATTATATATAT
1 ATTTTCAAAAACTATATATTATATATATTTTCAAAACATTTTCAAAAACTATATACTATATATAT
* * *
1754893 ATTTTTAAAATGTTTTCAAAAATTATATATTA-TATATATTTTCAAAATA
66 ATTTTCAAAAT-TTTTCAAAAACTATATATTATTATATATATTCAAAATA
* * *
1754942 ATTTT-AAAAACTATATATTATATATGTTTTCAAAACATCTTTTTAGAAAACTATATACTACATA
1 ATTTTCAAAAACTATATATTATATATATTTTCAAAACA--TTTTCA-AAAACTATATACTATATA
* *
1755006 TATGTTTTCAAAATTTTATAAAAAAACTATATATTAT
63 TATATTTTCAAAATTTT-T-CAAAAACTATATATTAT
1755043 ACATTATATA
Statistics
Matches: 181, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
113 92 0.51
114 5 0.03
115 43 0.24
116 27 0.15
117 14 0.08
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (114 bp):
ATTTTCAAAAACTATATATTATATATATTTTCAAAACATTTTCAAAAACTATATACTATATATAT
ATTTTCAAAATTTTTCAAAAACTATATATTATTATATATATTCAAAATA
Found at i:1760261 original size:28 final size:29
Alignment explanation
Indices: 1760176--1760277 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
1760166 TTTCATTTAA
* * * *
1760176 GTACCTAAAGTATTATGTGGTCAAAATAA
1 GTACCTAAAGTATTTTATAGTCAAAATAG
* * *
1760205 ATACCTAAAGTTATCTTTTTAGTTAAAATAG
1 GTACCTAAAG-TAT-TTTATAGTCAAAATAG
1760236 GTACCTAAAGTATTTTAT-GTCAAAATAG
1 GTACCTAAAGTATTTTATAGTCAAAATAG
*
1760264 GTACCTAAACTATT
1 GTACCTAAAGTATT
1760278 CAATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
28 22 0.36
29 13 0.21
30 6 0.10
31 20 0.33
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (29 bp):
GTACCTAAAGTATTTTATAGTCAAAATAG
Found at i:1760416 original size:28 final size:28
Alignment explanation
Indices: 1760359--1760415 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1760349 ATGAAAATTG
* *
1760359 AATATTTTAGGCACCTATTTTGACCAAA
1 AATACTTTAGGCACCTATTTTAACCAAA
*
1760387 AATACTTTAGGTA-CTATTTTAACCAAA
1 AATACTTTAGGCACCTATTTTAACCAAA
1760414 AA
1 AA
1760416 AAGATAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (28 bp):
AATACTTTAGGCACCTATTTTAACCAAA
Found at i:1760904 original size:51 final size:51
Alignment explanation
Indices: 1760849--1760945 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
1760839 TGGAAGTGGA
1760849 TTATATTTTTTAAAATTAAATTATTTATATTATTTTATGAATATAAGGGTT
1 TTATATTTTTTAAAATTAAATTATTTATATTATTTTATGAATATAAGGGTT
*
1760900 TTATATTTTTTAAAATTAAATTATTTATATTATTTTATTAATATAA
1 TTATATTTTTTAAAATTAAATTATTTATATTATTTTATGAATATAA
1760946 TCTTATGTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (51 bp):
TTATATTTTTTAAAATTAAATTATTTATATTATTTTATGAATATAAGGGTT
Found at i:1760926 original size:24 final size:25
Alignment explanation
Indices: 1760849--1760936 Score: 101
Period size: 24 Copynumber: 3.5 Consensus size: 25
1760839 TGGAAGTGGA
1760849 TTATATT-TTTTAAAATTAAATTAT
1 TTATATTATTTTAAAATTAAATTAT
* **
1760873 TTATATTATTTTATGAATATAAGGGT-T
1 TTATATTATTTTA-AAAT-TAA-ATTAT
1760900 TTATATT-TTTTAAAATTAAATTAT
1 TTATATTATTTTAAAATTAAATTAT
1760924 TTATATTATTTTA
1 TTATATTATTTTA
1760937 TTAATATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 1 0.02
24 18 0.35
25 13 0.25
26 8 0.15
27 11 0.21
28 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (25 bp):
TTATATTATTTTAAAATTAAATTAT
Found at i:1760951 original size:24 final size:23
Alignment explanation
Indices: 1760863--1760951 Score: 58
Period size: 24 Copynumber: 3.7 Consensus size: 23
1760853 ATTTTTTAAA
*
1760863 ATTAA-ATTATTTATATTATTTT
1 ATTAATATAATTTATATTATTTT
*
1760885 ATGAATATAAGGGTTTTATATT-TTTT
1 ATTAATATAA----TTTATATTATTTT
*
1760911 AAAATTAA-ATTATTTATATTATTTT
1 ---ATTAATATAATTTATATTATTTT
1760936 ATTAATATAATCTTAT
1 ATTAATATAAT-TTAT
1760952 GTCATGAGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 20
0.67 0.07 0.26
Matches are distributed among these distances:
22 9 0.18
23 7 0.14
24 12 0.24
25 4 0.08
26 4 0.08
27 8 0.16
28 3 0.06
29 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTAATATAATTTATATTATTTT
Found at i:1762619 original size:23 final size:23
Alignment explanation
Indices: 1762589--1762663 Score: 105
Period size: 23 Copynumber: 3.3 Consensus size: 23
1762579 TAGTCGATGG
1762589 TTCTACGCGGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTTGGGACAT
*
1762612 TTCTACGCGGTCCTTTGAGACAT
1 TTCTACGCGGTCCTTTGGGACAT
* * * *
1762635 ATCTATGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTTGGGACAT
1762658 TTCTAC
1 TTCTAC
1762664 ATGGCACTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCCTTTGGGACAT
Found at i:1772647 original size:35 final size:36
Alignment explanation
Indices: 1772600--1772687 Score: 144
Period size: 35 Copynumber: 2.5 Consensus size: 36
1772590 TCACTAGAAT
*
1772600 AGTATCGATACTGAATGAGTAGCTTCGATACTAAGG
1 AGTATCGATACTGAATGAGTAGCATCGATACTAAGG
1772636 -GTATCGATACTGAATGAGTAGCATCGATACTAAGG
1 AGTATCGATACTGAATGAGTAGCATCGATACTAAGG
1772671 TAGTATCGATACT-AATG
1 -AGTATCGATACTGAATG
1772688 GACAAGTATC
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
35 34 0.69
36 4 0.08
37 11 0.22
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (36 bp):
AGTATCGATACTGAATGAGTAGCATCGATACTAAGG
Found at i:1772678 original size:17 final size:19
Alignment explanation
Indices: 1772599--1772687 Score: 93
Period size: 20 Copynumber: 4.9 Consensus size: 19
1772589 ATCACTAGAA
1772599 TAGTATCGATACTGAATGAG
1 TAGTATCGATACT-AATGAG
1772619 TAGCT-TCGATACTAA-G-G
1 TAG-TATCGATACTAATGAG
1772636 --GTATCGATACTGAATGAG
1 TAGTATCGATACT-AATGAG
*
1772654 TAGCATCGATACTAA-G-G
1 TAGTATCGATACTAATGAG
1772671 TAGTATCGATACTAATG
1 TAGTATCGATACTAATG
1772688 GACAAGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
16 2 0.03
17 17 0.29
18 4 0.07
19 4 0.07
20 21 0.36
21 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (19 bp):
TAGTATCGATACTAATGAG
Found at i:1773358 original size:23 final size:23
Alignment explanation
Indices: 1773323--1773367 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1773313 GAGTCGAGGG
*
1773323 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGCAGTCCTTCGAGACAA
**
1773346 TTCTACGTGGTCCTTCGAGACA
1 TTCTACGCAGTCCTTCGAGACA
1773368 TATATATGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (23 bp):
TTCTACGCAGTCCTTCGAGACAA
Found at i:1773407 original size:23 final size:23
Alignment explanation
Indices: 1773381--1773450 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
1773371 ATATGCGATC
1773381 CTTCGGGATATTTCTATGTGGCA
1 CTTCGGGATATTTCTATGTGGCA
* *
1773404 CTTCGGTGCATA-TTCTATGCGACA
1 CTTCGG-G-ATATTTCTATGTGGCA
* *
1773428 CTTCGGTACAATTT-TATGTGGCA
1 CTTCGGGA-TATTTCTATGTGGCA
1773451 GTTTCGACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
22 1 0.03
23 14 0.38
24 19 0.51
25 3 0.08
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (23 bp):
CTTCGGGATATTTCTATGTGGCA
Found at i:1773421 original size:24 final size:23
Alignment explanation
Indices: 1773392--1773450 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
1773382 TTCGGGATAT
*
1773392 TTCTATGTGGCACTTCGGTGCATA
1 TTCTATGTGGCACTTCGGTACA-A
* *
1773416 TTCTATGCGACACTTCGGTACAA
1 TTCTATGTGGCACTTCGGTACAA
*
1773439 TTTTATGTGGCA
1 TTCTATGTGGCA
1773451 GTTTCGACTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGCACTTCGGTACAA
Found at i:1788200 original size:22 final size:22
Alignment explanation
Indices: 1788156--1788200 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1788146 AATATTTTAA
* * * *
1788156 AATTAATATTATTTCAAATAAT
1 AATTAATATAAATTAAAAAAAT
1788178 AATTAATATAAATTAAAAAAAT
1 AATTAATATAAATTAAAAAAAT
1788200 A
1 A
1788201 GTCTTTTAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTAATATAAATTAAAAAAAT
Found at i:1790115 original size:102 final size:102
Alignment explanation
Indices: 1789899--1790104 Score: 331
Period size: 102 Copynumber: 2.0 Consensus size: 102
1789889 TTTGTTAAAA
* * * *
1789899 TCAATTAGGAATAAAATTAGAGACTCCATTTTAGGTTTAATTTAACTTTAGTCCCTTAATTTAGG
1 TCAATTATGATTAAAATTAGAGACTCCATTTTAGATTTAATTTAACTTTAGTCCCTTAATTCAGG
* *
1789964 GAGTATTCAATTTGTCCCTCGCCTTAATGCCCGAGGG
66 GAGTATTCAATTTGGCCCTCGCCTTAATGCCCAAGGG
* *
1790001 TCAATTATGATTAAAATTAGAGCCTCCATTTTAGATTTGATTTAACTTTAGTCCCTTAATTCAGG
1 TCAATTATGATTAAAATTAGAGACTCCATTTTAGATTTAATTTAACTTTAGTCCCTTAATTCAGG
*
1790066 GAGTATTCAATTTGGCCCTCTCCTTAATGCCCAAGGG
66 GAGTATTCAATTTGGCCCTCGCCTTAATGCCCAAGGG
1790103 TC
1 TC
1790105 TATTTCGATT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (102 bp):
TCAATTATGATTAAAATTAGAGACTCCATTTTAGATTTAATTTAACTTTAGTCCCTTAATTCAGG
GAGTATTCAATTTGGCCCTCGCCTTAATGCCCAAGGG
Found at i:1797856 original size:24 final size:25
Alignment explanation
Indices: 1797827--1797903 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 25
1797817 TTTTAATCAT
*
1797827 TTATTACTAATTATTATTATTATT-
1 TTATTACTAATTAATATTATTATTA
* * *
1797851 TTATTA-TTATCACTATTATTATTA
1 TTATTACTAATTAATATTATTATTA
* * *
1797875 TTATTCCTAA-TAATACTATTATTG
1 TTATTACTAATTAATATTATTATTA
1797899 TTATT
1 TTATT
1797904 TTCAGGTTAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
23 14 0.33
24 26 0.62
25 2 0.05
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.58
Consensus pattern (25 bp):
TTATTACTAATTAATATTATTATTA
Found at i:1797897 original size:3 final size:3
Alignment explanation
Indices: 1797836--1797879 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1797826 TTTATTACTA
* *
1797836 ATT ATT ATT ATT ATT -TT ATT ATT ATC ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1797880 CCTAATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1803223 original size:47 final size:46
Alignment explanation
Indices: 1803172--1803264 Score: 109
Period size: 47 Copynumber: 2.0 Consensus size: 46
1803162 ATGCAAAGTG
1803172 CAAAGATCAAAAGAA-AAAAAACAAAGAAAGAAG-AGAACAAAGAAAAA
1 CAAAGA-CAAAAGAACAAAAAA-AAAG-AAGAAGAAGAACAAAGAAAAA
* * *
1803219 CAAAGAGAAAAGAAGCAAAAAAGAAGAAGAAGAAGAAGAAAGAAAA
1 CAAAGACAAAAGAA-CAAAAAAAAAGAAGAAGAAGAACAAAGAAAA
1803265 CGAATGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
46 13 0.32
47 21 0.52
48 6 0.15
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.01
Consensus pattern (46 bp):
CAAAGACAAAAGAACAAAAAAAAAGAAGAAGAAGAACAAAGAAAAA
Found at i:1804112 original size:24 final size:23
Alignment explanation
Indices: 1804072--1804128 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 23
1804062 GGGGCAATAT
*
1804072 TTTTTTCCAAAAAA-TTTGATTAAA
1 TTTTTT-CAAAAAATTTTAATT-AA
*
1804096 TTTTTTCAAAATTATTTTAATTAA
1 TTTTTTCAAAA-AATTTTAATTAA
1804120 -TTTTTCAAA
1 TTTTTTCAAA
1804129 TTTTTTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 14 0.48
24 9 0.31
25 6 0.21
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTTCAAAAAATTTTAATTAA
Found at i:1806492 original size:24 final size:24
Alignment explanation
Indices: 1806447--1806497 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1806437 TGGTGGTTGG
1806447 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
1806471 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
1806495 TTT
1 TTT
1806498 GTTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:1813193 original size:36 final size:36
Alignment explanation
Indices: 1813087--1813238 Score: 153
Period size: 36 Copynumber: 4.2 Consensus size: 36
1813077 TGTTTCTCCC
* * *
1813087 AAAACAAAGTTTCGTCTCGTTTGAGACAATTTTTCTT
1 AAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTCTT
* * * *** *
1813124 GAAACAAA-ATTGATCTCACTTGAGATTGTTTTCTCTA
1 AAAACAAATTTTG-TCTCGCTTGAGA-CAATTTCTCTT
*
1813161 AAAACAAATTTTGTCTCGCTTGAGACCATTTCTCTT
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTT
* *
1813197 GAAACAAATTTTGTCTCGCTTGAGATAATTTCTCTT
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTT
1813233 AAAACA
1 AAAACA
1813239 TAAATACTTG
Statistics
Matches: 91, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
35 2 0.02
36 55 0.60
37 31 0.34
38 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTT
Found at i:1813218 original size:21 final size:21
Alignment explanation
Indices: 1813162--1813219 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1813152 TTTTCTCTAA
1813162 AAACAAATTTTGTCTCGCTTG
1 AAACAAATTTTGTCTCGCTTG
* *
1813183 AGAC-CA--TT-TCT--CTTG
1 AAACAAATTTTGTCTCGCTTG
1813198 AAACAAATTTTGTCTCGCTTG
1 AAACAAATTTTGTCTCGCTTG
1813219 A
1 A
1813220 GATAATTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 12
0.63 0.09 0.28
Matches are distributed among these distances:
15 7 0.26
16 1 0.04
17 3 0.11
18 4 0.15
19 3 0.11
20 1 0.04
21 8 0.30
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (21 bp):
AAACAAATTTTGTCTCGCTTG
Found at i:1813236 original size:73 final size:74
Alignment explanation
Indices: 1813087--1813238 Score: 193
Period size: 73 Copynumber: 2.1 Consensus size: 74
1813077 TGTTTCTCCC
* * **
1813087 AAAACAAAGTTTCGTCTCGTTTGAGACAATTTTTCTTGAAACAAAATTGATCTCACTTGAGATTG
1 AAAACAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAAACAAAATTGATCTCACTTGAGATAA
1813152 TTTTCTCTA
66 TTTTCTCTA
* * * *
1813161 AAAACAAA-TTTTGTCTCGCTTGAGACCATTTCTCTTGAAACAAATTTTG-TCTCGCTTGAGATA
1 AAAACAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAAACAAA-ATTGATCTCACTTGAGATA
*
1813224 A-TTTCTCTT
65 ATTTTCTCTA
1813233 AAAACA
1 AAAACA
1813239 TAAATACTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 13 0.19
73 44 0.65
74 11 0.16
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (74 bp):
AAAACAAAGTTTCGTCTCGCTTGAGACAATTTCTCTTGAAACAAAATTGATCTCACTTGAGATAA
TTTTCTCTA
Found at i:1818418 original size:2 final size:2
Alignment explanation
Indices: 1818411--1818510 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
1818401 TGAATAGATG
1818411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1818453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1818495 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
1818511 AATTATCATC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1825756 original size:31 final size:31
Alignment explanation
Indices: 1825678--1825813 Score: 170
Period size: 31 Copynumber: 4.5 Consensus size: 31
1825668 TAAAAAATTA
*
1825678 AAAAAT-AAATATATA-TTTTAAATAAAAAT
1 AAAAATAAAATATACATTTTTAAATAAAAAT
* *
1825707 AAAAAT-AAATGTACATTTTTCAATAAAAAT
1 AAAAATAAAATATACATTTTTAAATAAAAAT
* *
1825737 AAAAATAAAATATACATTTTTAAATTAAATT
1 AAAAATAAAATATACATTTTTAAATAAAAAT
* *
1825768 AAAAATAAAATATACCTTTTTAAGTTAAAAAT
1 AAAAATAAAATATACATTTTTAA-ATAAAAAT
*
1825800 AAGAATAAAATATA
1 AAAAATAAAATATA
1825814 TTTTATGTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
29 13 0.14
30 19 0.21
31 42 0.46
32 18 0.20
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (31 bp):
AAAAATAAAATATACATTTTTAAATAAAAAT
Found at i:1825872 original size:30 final size:30
Alignment explanation
Indices: 1825788--1826004 Score: 126
Period size: 29 Copynumber: 7.3 Consensus size: 30
1825778 TATACCTTTT
* *
1825788 TAAGTTAAAAATAAGAATAAAATATATTT--
1 TAAGTT-AAAGTAAGATTAAAATATATTTAA
* * **
1825817 TATGTTAAAATAAAGA-TAAGTTATATTTAA
1 TAAGTTAAAGT-AAGATTAAAATATATTTAA
* *
1825847 TAAATTAAAGTAAGATTAGAATATATTTAA
1 TAAGTTAAAGTAAGATTAAAATATATTTAA
* * * * *
1825877 TAA-TTTAAGTTAAGAATATAATATATGTGA
1 TAAGTTAAAG-TAAGATTAAAATATATTTAA
* * * * *
1825907 TAAGTTAAAATAAAAATAAGATATTTTTTTAA
1 TAAGTTAAAGTAAGATTAA-A-ATATATTTAA
* *
1825939 -AAGTTAAAATAA-ATATAAAATATATTT-T
1 TAAGTTAAAGTAAGAT-TAAAATATATTTAA
* *
1825967 TAAGTTAAGGTAAGATTAAAATATATTT-T
1 TAAGTTAAAGTAAGATTAAAATATATTTAA
1825996 TAAGTTAAA
1 TAAGTTAAA
1826005 ATAAAATAAT
Statistics
Matches: 148, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
28 15 0.10
29 55 0.37
30 52 0.35
31 20 0.14
32 6 0.04
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (30 bp):
TAAGTTAAAGTAAGATTAAAATATATTTAA
Found at i:1825969 original size:24 final size:24
Alignment explanation
Indices: 1825942--1826021 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 24
1825932 TTTTTAAAAG
1825942 TTAAAATAAATATAAAATATATTT
1 TTAAAATAAATATAAAATATATTT
1825966 TTAAGTTAAGGTAAGAT-TAAAATATATTT
1 TTAA---AA--TAA-ATATAAAATATATTT
**
1825995 TTAAGTTAAA-ATAAAATAATATTT
1 TTAAAATAAATATAAAAT-ATATTT
1826019 TTA
1 TTA
1826022 GGTTAAGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
23 7 0.15
24 16 0.35
27 2 0.04
29 19 0.41
30 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TTAAAATAAATATAAAATATATTT
Found at i:1826026 original size:24 final size:24
Alignment explanation
Indices: 1825948--1826037 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
1825938 AAAGTTAAAA
1825948 TAAATATAAAAT-ATATTTTTAAGT
1 TAAA-ATAAAATAATATTTTTAAGT
1825972 TAAGGTAAGATTAAAAT-ATATTTTTAAGT
1 T-A---AA-A-TAAAATAATATTTTTAAGT
*
1826001 TAAAATAAAATAATATTTTTAGGT
1 TAAAATAAAATAATATTTTTAAGT
*
1826025 TAAGATAAAATAA
1 TAAAATAAAATAA
1826038 AATAGATTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 6 0.11
24 25 0.44
25 3 0.05
28 4 0.07
29 19 0.33
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (24 bp):
TAAAATAAAATAATATTTTTAAGT
Found at i:1826062 original size:53 final size:52
Alignment explanation
Indices: 1825950--1826063 Score: 140
Period size: 53 Copynumber: 2.2 Consensus size: 52
1825940 AGTTAAAATA
* * * *
1825950 AATATAAAATATATTTTTAAGTTAAGGTAAGATTAAAATATATTTTTAAGTT
1 AATATAAAATATATTTTTAAGTTAAGATAAGAATAAAATAGATTTATAAGTT
* * *
1826002 AAAATAAAATAATATTTTTAGGTTAAGATAA-AATAAAATAGATTTAATAATTT
1 AATATAAAAT-ATATTTTTAAGTTAAGATAAGAATAAAATAGATTT-ATAAGTT
1826055 AATATAAAA
1 AATATAAAA
1826064 ATAAAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
52 21 0.40
53 31 0.60
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (52 bp):
AATATAAAATATATTTTTAAGTTAAGATAAGAATAAAATAGATTTATAAGTT
Found at i:1826088 original size:29 final size:29
Alignment explanation
Indices: 1825678--1826085 Score: 260
Period size: 30 Copynumber: 13.9 Consensus size: 29
1825668 TAAAAAATTA
* *
1825678 AAAAAT-AAATATATATTTTAAATAAAAAT
1 AAAAATAAAATATAT-TTTTAAGTTAAAAT
* * *
1825707 AAAAATAAATGTACATTTTTCAA-TAAAAAT
1 AAAAATAAA-ATATATTTTT-AAGTTAAAAT
* *
1825737 AAAAATAAAATATACATTTTTAAATTAAATT
1 AAAAATAAAATAT--ATTTTTAAGTTAAAAT
1825768 AAAAATAAAATATACCTTTTTAAGTTAAAAAT
1 AAAAATAAAATATA--TTTTTAAGTT-AAAAT
* *
1825800 AAGAATAAAATATA-TTTTATGTTAAAAT
1 AAAAATAAAATATATTTTTAAGTTAAAAT
* ** * * *
1825828 AAAGATAAGTTATATTTAATAAATTAAAGT
1 AAAAATAAAATATATTT-TTAAGTTAAAAT
* * * * * **
1825858 AAGATTAGAATATATTTAATAATTTAAGTT
1 AAAAATAAAATATATTT-TTAAGTTAAAAT
* * **
1825888 AAGAATATAATATATGTGATAAGTTAAAAT
1 AAAAATAAAATATAT-TTTTAAGTTAAAAT
* *
1825918 AAAAATAAGATATTTTTTTAAAAGTTAAAAT
1 AAAAATAAAATATATTTTT--AAGTTAAAAT
* **
1825949 AAATATAAAATATATTTTTAAGTTAAGGT
1 AAAAATAAAATATATTTTTAAGTTAAAAT
* *
1825978 AAGATTAAAATATATTTTTAAGTTAAAAT
1 AAAAATAAAATATATTTTTAAGTTAAAAT
* *
1826007 -AAAAT---A-ATATTTTTAGGTTAAGAT
1 AAAAATAAAATATATTTTTAAGTTAAAAT
* * * *
1826031 -AAAATAAAATAGATTTAATAATTTAATAT
1 AAAAATAAAATATATTT-TTAAGTTAAAAT
1826060 AAAAATAAAA-ATATTTTTAATGTTAA
1 AAAAATAAAATATATTTTTAA-GTTAA
1826086 TATTTAAATT
Statistics
Matches: 297, Mismatches: 61, Indels: 42
0.74 0.15 0.10
Matches are distributed among these distances:
24 21 0.07
25 1 0.00
27 1 0.00
28 26 0.09
29 70 0.24
30 95 0.32
31 66 0.22
32 17 0.06
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAAATAAAATATATTTTTAAGTTAAAAT
Found at i:1839543 original size:111 final size:112
Alignment explanation
Indices: 1839419--1839648 Score: 318
Period size: 112 Copynumber: 2.1 Consensus size: 112
1839409 GTTATACGTG
* * * * * * *
1839419 CATTTCAACATACTTTGTATATGATAG-TGTCGATCGATTTTGTTTAATGCATAACCGTGCATTT
1 CATTTCGACATACTTCGTATATGAAAGTTATCGATCAATTTTGCTTAATGCATAACAGTGCATTT
* * *
1839483 TCGGCATAAAATGTGTCACCCATGATATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAGGTGCCACCAATGATATTCATAATGAGGTGAATTAC
* * *
1839530 CATTTCGACATACTTCGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACAGTTCTTTT
1 CATTTCGACATACTTCGTATATGAAAGTTATCGATCAATTTTGCTTAATGCATAACAGTGCATTT
* *
1839595 TCGGTATAAAAGGTGCCACCAATGGTATTCATAATGAGGTGAATTAC
66 TCGGCATAAAAGGTGCCACCAATGATATTCATAATGAGGTGAATTAC
1839642 CATTTCG
1 CATTTCG
1839649 GCACTTCGAT
Statistics
Matches: 103, Mismatches: 15, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
111 23 0.22
112 80 0.78
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (112 bp):
CATTTCGACATACTTCGTATATGAAAGTTATCGATCAATTTTGCTTAATGCATAACAGTGCATTT
TCGGCATAAAAGGTGCCACCAATGATATTCATAATGAGGTGAATTAC
Found at i:1846412 original size:112 final size:112
Alignment explanation
Indices: 1846214--1846443 Score: 327
Period size: 112 Copynumber: 2.1 Consensus size: 112
1846204 AGTTATAGGT
* * * * *
1846214 GCATTTCGACATACTTTGTGTATGATAGTATTGATCAATTTTGTTTAATGCATAACGGTGCATTT
1 GCATTTCGACATACTTCGTGTATGAAAGTATTGATCAATTTTGCTTAACGCATAAAGGTGCATTT
* *
1846279 TTCGGCATAAAAGGTGACACCCATTGTATTCATAATGAGGTGAATTA
66 TTCGACATAAAAGGTGACACCCATGGTATTCATAATGAGGTGAATTA
* * * *
1846326 TCATTTCGTCATACTTCGTGTATGAAAGTTATTGATCGATTTTGCTTAACGTATAAAGGTGCA-T
1 GCATTTCGACATACTTCGTGTATGAAAG-TATTGATCAATTTTGCTTAACGCATAAAGGTGCATT
* *
1846390 TTTCGACATAAAAGGTGCCACCCATGGTATTCATAATGAGTTGAATTA
65 TTTCGACATAAAAGGTGACACCCATGGTATTCATAATGAGGTGAATTA
1846438 GCATTT
1 GCATTT
1846444 TGGTGCAACA
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
112 74 0.72
113 29 0.28
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.37
Consensus pattern (112 bp):
GCATTTCGACATACTTCGTGTATGAAAGTATTGATCAATTTTGCTTAACGCATAAAGGTGCATTT
TTCGACATAAAAGGTGACACCCATGGTATTCATAATGAGGTGAATTA
Found at i:1848898 original size:19 final size:19
Alignment explanation
Indices: 1848870--1848906 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1848860 CATGTTTCAG
*
1848870 AGGAAGAAAAATAGATGGA
1 AGGAAAAAAAATAGATGGA
*
1848889 AGGAAAAAAAATGGATGG
1 AGGAAAAAAAATAGATGG
1848907 TAATAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.32, T:0.11
Consensus pattern (19 bp):
AGGAAAAAAAATAGATGGA
Found at i:1849059 original size:26 final size:26
Alignment explanation
Indices: 1849030--1849081 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1849020 AAGTAACCTA
1849030 GAACTAAAGAAATGTGGGATAACTTC
1 GAACTAAAGAAATGTGGGATAACTTC
1849056 GAACTAAAGAAATGTGGGATAACTTC
1 GAACTAAAGAAATGTGGGATAACTTC
1849082 ACATACTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (26 bp):
GAACTAAAGAAATGTGGGATAACTTC
Found at i:1853646 original size:30 final size:30
Alignment explanation
Indices: 1853610--1853695 Score: 154
Period size: 30 Copynumber: 2.9 Consensus size: 30
1853600 CCTGTTAGAT
*
1853610 ATGCTTGCTCAGTAAATAAATATTTCTAAC
1 ATGCTTGCTCAGTAAATATATATTTCTAAC
1853640 ATGCTTGCTCAGTAAATATATATTTCTAAC
1 ATGCTTGCTCAGTAAATATATATTTCTAAC
*
1853670 ATGCTTGCTCAATAAATATATATTTC
1 ATGCTTGCTCAGTAAATATATATTTC
1853696 GAACGGAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (30 bp):
ATGCTTGCTCAGTAAATATATATTTCTAAC
Found at i:1855808 original size:14 final size:15
Alignment explanation
Indices: 1855782--1855820 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1855772 TTTTCATGAT
*
1855782 CATATATATATATATA
1 CATATACATATATA-A
1855798 CATATACATATATAA
1 CATATACATATATAA
1855813 CA-ATACAT
1 CATATACAT
1855821 TCATGTGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 3 0.14
16 13 0.59
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (15 bp):
CATATACATATATAA
Found at i:1858460 original size:13 final size:13
Alignment explanation
Indices: 1858427--1858471 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1858417 TTTAAATACT
1858427 TTTTAAAAAT-TA
1 TTTTAAAAATATA
* *
1858439 ATTTGAAAATATA
1 TTTTAAAAATATA
*
1858452 TTTTAAAAATATT
1 TTTTAAAAATATA
1858465 TTTTAAA
1 TTTTAAA
1858472 TATTTATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:1858613 original size:37 final size:39
Alignment explanation
Indices: 1858549--1858632 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 39
1858539 ACACAATAAG
* * *
1858549 ATATAAAT-TTTTTAAAACTCATAATAAA-GTATTAATT
1 ATATAAATATTTTTAAAACTAATAATAAATCTATAAATT
1858586 ATATAAATATTTTTAATAA-TAAT-ATAAATCTATAAATT
1 ATATAAATATTTTTAA-AACTAATAATAAATCTATAAATT
*
1858624 ATAAAAATA
1 ATATAAATA
1858633 AGGATGAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 13 0.32
38 25 0.62
39 2 0.05
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (39 bp):
ATATAAATATTTTTAAAACTAATAATAAATCTATAAATT
Found at i:1860488 original size:23 final size:24
Alignment explanation
Indices: 1860457--1860512 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1860447 TTCAATTTTT
* **
1860457 TATTCTTATCTTAGCTTTAAAA-TA
1 TATT-TTATCTTAACTGCAAAAGTA
*
1860481 TATTTTATTTTAACTGCAAAAGTA
1 TATTTTATCTTAACTGCAAAAGTA
1860505 TATTTTAT
1 TATTTTAT
1860513 TTTTGTCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (24 bp):
TATTTTATCTTAACTGCAAAAGTA
Found at i:1860525 original size:30 final size:31
Alignment explanation
Indices: 1860478--1860555 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
1860468 TAGCTTTAAA
* * *
1860478 ATATATTTTATTTTAACTGC-AAAAGTATATT
1 ATAT-TTTTATCTTAACTACAAAAAATATATT
* *
1860509 TTATTTTTGTCTTAACTACAAAAAAATATATT
1 ATATTTTTATCTTAACTAC-AAAAAATATATT
1860541 ATATTTTTATCTTAA
1 ATATTTTTATCTTAA
1860556 ATTTAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 12 0.32
31 3 0.08
32 23 0.61
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (31 bp):
ATATTTTTATCTTAACTACAAAAAATATATT
Found at i:1860628 original size:30 final size:30
Alignment explanation
Indices: 1860573--1860747 Score: 146
Period size: 30 Copynumber: 5.9 Consensus size: 30
1860563 ATATTATCAT
* * *
1860573 AATAAAATATAAATATTTAAGTTAAGATAAT
1 AATAAAATAT-ATTTTTTAAGTTAAGATAAG
* *
1860604 AATAAATTATATTTTTTAATTTAAGATAAG
1 AATAAAATATATTTTTTAAGTTAAGATAAG
* * * *
1860634 ATTAAAATATATATTTTAAATTAAAATAAG
1 AATAAAATATATTTTTTAAGTTAAGATAAG
* * *
1860664 AAT-AAATATA-TTTTTAGGTTACA-AAAAT
1 AATAAAATATATTTTTTAAGTTA-AGATAAG
**
1860692 AATAAAATATATTTAATAAGTTAAGATAA-
1 AATAAAATATATTTTTTAAGTTAAGATAAG
1860721 AA-AAAAT-TATTTTTTTAATGTTAAGAT
1 AATAAAATATA-TTTTTTAA-GTTAAGAT
1860748 GTAAAATTAA
Statistics
Matches: 116, Mismatches: 22, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
27 2 0.02
28 25 0.22
29 26 0.22
30 54 0.47
31 9 0.08
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.41
Consensus pattern (30 bp):
AATAAAATATATTTTTTAAGTTAAGATAAG
Found at i:1860977 original size:20 final size:20
Alignment explanation
Indices: 1860954--1861003 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1860944 GAATATGTAA
1860954 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1860974 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1860994 GTCGCAACGC
1 ATCGCAACGC
1861004 TGAATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1864064 original size:18 final size:18
Alignment explanation
Indices: 1864041--1864075 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1864031 AGAAAAAGGC
*
1864041 AATCAAAATCGCAATCAA
1 AATCAAAATCACAATCAA
1864059 AATCAAAATCACAATCA
1 AATCAAAATCACAATCA
1864076 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCACAATCAA
Found at i:1864386 original size:140 final size:140
Alignment explanation
Indices: 1864133--1864556 Score: 794
Period size: 140 Copynumber: 3.0 Consensus size: 140
1864123 GCAAATGTTG
1864133 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1864198 TTGAACATTGCTATGATCTGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1864263 CGAATTTGAC
131 CGAATTTGAC
*
1864273 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAATAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
1864338 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATTGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1864403 CGAATTTGAC
131 CGAATTTGAC
*
1864413 TATTATGTGTATTTTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1864478 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1864543 CGAATTTGAC
131 CGAATTTGAC
1864553 TATT
1 TATT
1864557 GCAACGCAAA
Statistics
Matches: 275, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 275 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1864551 original size:20 final size:20
Alignment explanation
Indices: 1864526--1864780 Score: 266
Period size: 20 Copynumber: 13.4 Consensus size: 20
1864516 TTACACATTC
*
1864526 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864546 ATTTGACTATTGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1864565 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864580 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1864600 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864620 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
1864639 A----A-AATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864654 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864674 ATTCGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1864694 ATTCGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1864714 ATTCGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
1864734 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* **
1864754 A-TTGACTTTCGCATTGCGA
1 ATTTGACTATCGCAACGCGA
*
1864773 TTTTGACT
1 ATTTGACT
1864781 TTCACATTGT
Statistics
Matches: 201, Mismatches: 21, Indels: 26
0.81 0.08 0.10
Matches are distributed among these distances:
14 18 0.09
15 6 0.03
19 20 0.10
20 157 0.78
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1864616 original size:74 final size:74
Alignment explanation
Indices: 1864526--1864780 Score: 314
Period size: 74 Copynumber: 3.4 Consensus size: 74
1864516 TTACACATTC
* * *
1864526 ATTTGAATATCGCAACGCGAATTTGACTATTGCAACGCAAAAATCGCAACGCGAATATGACTATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATC
1864591 GCAACGCGA
66 GCAACGCGA
* *
1864600 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGCAAAAATCACAACGCGAATTTGACTATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATC
*
1864665 ACAACGCGA
66 GCAACGCGA
* * * *
1864674 ATTCGACTATCGCAACGCGAATTCGACTATCGCAACGCGAATTCGACTATCGCAACGTGAATTTG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-AATCGCAACGCGAATTTG
*
1864739 ATTATCGCAACGCGA
60 ACTATCGCAACGCGA
* ** *
1864754 A-TTGACTTTCGCATTGCGATTTTGACT
1 ATTTGACTATCGCAACGCGAATTTGACT
1864781 TTCACATTGT
Statistics
Matches: 155, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
74 103 0.66
75 2 0.01
79 21 0.14
80 29 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCGAATTTGACTATC
GCAACGCGA
Found at i:1864781 original size:20 final size:20
Alignment explanation
Indices: 1864755--1864798 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1864745 GCAACGCGAA
*
1864755 TTGACTTTCGCATTGCGATT
1 TTGACTTTCACATTGCGATT
*
1864775 TTGACTTTCACATTGTGATT
1 TTGACTTTCACATTGCGATT
1864795 TTGA
1 TTGA
1864799 GTTTAGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.48
Consensus pattern (20 bp):
TTGACTTTCACATTGCGATT
Found at i:1866357 original size:21 final size:21
Alignment explanation
Indices: 1866333--1866402 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
1866323 ATGAATCGGA
1866333 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * * ** *
1866354 CTCTTCAACGATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGAC
1866375 CTCTTGAATGGTGGGAGGGGA-
1 CTCTTGAATGGTGGGA-GGGAC
1866396 CTCTTGA
1 CTCTTGA
1866403 GGGATAATAG
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:1866392 original size:42 final size:42
Alignment explanation
Indices: 1866333--1866451 Score: 143
Period size: 42 Copynumber: 2.8 Consensus size: 42
1866323 ATGAATCGGA
*
1866333 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTGAACGATGATAGGGGC
** *
1866375 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATAATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTGAACGATGATAGGGGC
* * *
1866417 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGA
1 CTCTTGAATGGTGGGAG-GGACCTCTTGAACGATGA
1866452 CAGGTGTGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 59 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTGAACGATGATAGGGGC
Found at i:1866429 original size:21 final size:21
Alignment explanation
Indices: 1866347--1866449 Score: 80
Period size: 21 Copynumber: 4.9 Consensus size: 21
1866337 TGAATGGTGG
* * *
1866347 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTGAACGATAA
* * * **
1866368 TAGGGGCCTCTTGAATGGTGG
1 GAGGGGCCTCTTGAACGATAA
* **
1866389 GAGGGGACTCTTGAGGGATAA
1 GAGGGGCCTCTTGAACGATAA
* *
1866410 TAGGGGCCTCTTGAACGATAG
1 GAGGGGCCTCTTGAACGATAA
*
1866431 GAGAGGCCTCTTGAACGAT
1 GAGGGGCCTCTTGAACGAT
1866450 GACAGGTGTG
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (21 bp):
GAGGGGCCTCTTGAACGATAA
Found at i:1866962 original size:20 final size:21
Alignment explanation
Indices: 1866937--1866981 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1866927 AATAGTTTCT
1866937 GAAACTT-AAAATAGCAACAC
1 GAAACTTAAAAATAGCAACAC
* *
1866957 GAAACTTAAAAATCGCAACGC
1 GAAACTTAAAAATAGCAACAC
1866978 GAAA
1 GAAA
1866982 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.53, C:0.20, G:0.13, T:0.13
Consensus pattern (21 bp):
GAAACTTAAAAATAGCAACAC
Found at i:1866993 original size:20 final size:20
Alignment explanation
Indices: 1866968--1867036 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
1866958 AAACTTAAAA
1866968 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1866988 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1867008 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1867028 ATCGCAACG
1 ATCGCAACG
1867037 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1867109 original size:20 final size:20
Alignment explanation
Indices: 1867080--1867117 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1867070 CGAAACTAAA
* *
1867080 TTCGCGTTGCGTTTTTCATT
1 TTCGCATTGCGATTTTCATT
1867100 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
1867118 CGTTGCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.50
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:1867139 original size:33 final size:35
Alignment explanation
Indices: 1867084--1867159 Score: 122
Period size: 33 Copynumber: 2.3 Consensus size: 35
1867074 ACTAAATTCG
*
1867084 CGTTGCG-TTTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTTCATTTTCGCATTGCGATTATCA
1867118 CGTTGCGATTTTT-A-TTTCGCATTGCGATTATCA
1 CGTTGCGATTTTTCATTTTCGCATTGCGATTATCA
1867151 CGTTGCGAT
1 CGTTGCGAT
1867160 AGTCAAATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 27 0.68
34 8 0.20
35 5 0.12
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (35 bp):
CGTTGCGATTTTTCATTTTCGCATTGCGATTATCA
Found at i:1867176 original size:20 final size:20
Alignment explanation
Indices: 1867151--1867199 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1867141 GCGATTATCA
1867151 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1867171 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1867191 CGTTGCGAT
1 CGTTGCGAT
1867200 TTTTATGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1867229 original size:20 final size:21
Alignment explanation
Indices: 1867186--1867230 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1867176 CGATAGTCAT
*
1867186 TTTCGCGTTGCGATTTTTATG
1 TTTCGCGTTGCGATTTTTAAG
*
1867207 TTTCGTGTTGCGA-TTTTAAG
1 TTTCGCGTTGCGATTTTTAAG
1867227 TTTC
1 TTTC
1867231 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.53
Consensus pattern (21 bp):
TTTCGCGTTGCGATTTTTAAG
Found at i:1869172 original size:20 final size:20
Alignment explanation
Indices: 1869149--1869186 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1869139 ATCACAGCGC
1869149 GAAAATGAAAATCGCAACAT
1 GAAAATGAAAATCGCAACAT
**
1869169 GAAAATGATTATCGCAAC
1 GAAAATGAAAATCGCAAC
1869187 GCGAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAT
Found at i:1869201 original size:20 final size:19
Alignment explanation
Indices: 1869171--1869275 Score: 76
Period size: 20 Copynumber: 5.6 Consensus size: 19
1869161 CGCAACATGA
*
1869171 AAATGATTATCGCAACGCG
1 AAATGACTATCGCAACGCG
* *
1869190 AATTTGACTATCGCAACGAG
1 AA-ATGACTATCGCAACGCG
1869210 -AA--A--ATCGCAACGCG
1 AAATGACTATCGCAACGCG
** *
1869224 AAATGAAAATCGCAACACG
1 AAATGACTATCGCAACGCG
*
1869243 AAAATGACTATCGCAATGCG
1 -AAATGACTATCGCAACGCG
*
1869263 AATTTGACTATCG
1 AA-ATGACTATCG
1869276 TTGCGATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 1 0.01
17 1 0.01
19 15 0.22
20 38 0.57
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:1869237 original size:53 final size:54
Alignment explanation
Indices: 1869155--1869258 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 54
1869145 GCGCGAAAAT
* ** * **
1869155 GAAAATCGCAACATGAAAATGATTATCGCAACGCGAATTTGACTATCGCAACGA
1 GAAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGA
*
1869209 GAAAATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAA
1 GAAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAA
1869259 TGCGAATTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 30 0.70
54 13 0.30
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.16
Consensus pattern (54 bp):
GAAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGA
Found at i:1869256 original size:73 final size:74
Alignment explanation
Indices: 1869136--1869275 Score: 228
Period size: 73 Copynumber: 1.9 Consensus size: 74
1869126 TCTAAAACTT
* * *
1869136 AAAATCACAGCGCGAAAATGAAAATCGCAACATGAAAATGATTATCGCAACGCGAATTTGACTAT
1 AAAATCACAACGCGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1869201 CGCAACGAG
66 CGCAACGAG
* *
1869210 AAAATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AAAATCACAACGCGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1869274 CG
66 CG
1869276 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 49 0.80
74 12 0.20
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.18
Consensus pattern (74 bp):
AAAATCACAACGCGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
CGCAACGAG
Done.