Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007930.1 Hibiscus syriacus cultivar Beakdansim tig00110338_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: 2280901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2137984 original size:3 final size:3
Alignment explanation
Indices: 2137976--2138022 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2137966 GTTTGAGTCT
2137976 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2138023 TTAACAATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2143372 original size:12 final size:12
Alignment explanation
Indices: 2143351--2143391 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2143341 ACTATATGGT
*
2143351 ATGAAGAGTACC
1 ATGAACAGTACC
2143363 ATGAACAGTA--
1 ATGAACAGTACC
2143373 ATGAACAGTACC
1 ATGAACAGTACC
*
2143385 GTGAACA
1 ATGAACA
2143392 ATACTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:2145649 original size:64 final size:64
Alignment explanation
Indices: 2145465--2145619 Score: 233
Period size: 64 Copynumber: 2.4 Consensus size: 64
2145455 CTAAGAGTGT
* * ** *
2145465 ATCGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCCCGAGTGCATCGATGCATGGTCTGTG
1 ATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CATGAGTGCATCGATGCATGGTATGTG
2145528 C
64 C
2145529 ATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGTATGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGTATGTGC
2145593 ATCGATGCATAAAATGCATTCGATGTT
1 ATCGATGCATAAAATGCATTCGATGTT
2145620 CAATTTATTC
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
64 75 0.89
65 7 0.08
66 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
ATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGTATGTGC
Found at i:2148421 original size:21 final size:20
Alignment explanation
Indices: 2148397--2148460 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 20
2148387 TCGGTGCATC
2148397 TTCATTATGTATCGATGCACT
1 TTCA-TATGTATCGATGCACT
* *
2148418 TTCAAAGGGATGCATCGATGCACT
1 TTC--A--TATGTATCGATGCACT
2148442 TTCATAGTGTATCGATGCA
1 TTCATA-TGTATCGATGCA
2148461 TTAAGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
TTCATATGTATCGATGCACT
Found at i:2148453 original size:45 final size:42
Alignment explanation
Indices: 2148337--2148460 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 42
2148327 AAAACCCGAT
** * * *
2148337 GGATGCATCGATGCATGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCATTTCATAGTGTATCGATGCACATTCAA
* *
2148379 GGAGTGCATCGGTGCATCTTCATTA-TGTATCGATGCACTTTCAAA
1 GGA-TGCATCGATGCAT-TTCA-TAGTGTATCGATGCACATTC-AA
2148424 GGGATGCATCGATGCACTTTCATAGTGTATCGATGCA
1 -GGATGCATCGATGCA-TTTCATAGTGTATCGATGCA
2148461 TTAAGCACAA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.04
43 12 0.18
44 18 0.27
45 30 0.45
46 4 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (42 bp):
GGATGCATCGATGCATTTCATAGTGTATCGATGCACATTCAA
Found at i:2149224 original size:21 final size:21
Alignment explanation
Indices: 2149180--2149224 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2149170 GATTTCTGGG
* * *
2149180 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
2149201 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
2149222 CAA
1 CAA
2149225 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:2149297 original size:23 final size:22
Alignment explanation
Indices: 2149249--2149297 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2149239 ACAGAATGTC
2149249 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
2149270 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
2149293 AAGGA
1 AAGGA
2149298 AAAATATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:2150945 original size:103 final size:102
Alignment explanation
Indices: 2150763--2151080 Score: 555
Period size: 103 Copynumber: 3.1 Consensus size: 102
2150753 GTCGAGGGTC
2150763 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2150828 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATTA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2150866 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGG-ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2150931 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
2150969 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2151034 TTGATCCCTAGTATATGTATATGATTTTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
2151072 TATATGGTC
1 TATGTGGTC
2151081 TTATGGACAT
Statistics
Matches: 205, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
102 2 0.01
103 201 0.98
104 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:2156098 original size:23 final size:23
Alignment explanation
Indices: 2156064--2156129 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
2156054 CACCACAGCT
*
2156064 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2156087 CGTAGAATTGCACCTAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
2156110 CGTAGAAATGCATCGAAGTG
1 CGTAGAAATGCACCGAAGTG
2156130 TCATATAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2156414 original size:30 final size:29
Alignment explanation
Indices: 2156361--2156419 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2156351 TGTAAACATA
* *
2156361 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
2156391 TCACATATACATGTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
2156420 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:2157260 original size:21 final size:21
Alignment explanation
Indices: 2157236--2157287 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2157226 TTATCTTTGA
*
2157236 TGCATCGGTGCAAATTGAATG
1 TGCATCGATGCAAATTGAATG
*
2157257 TGCATCGATGCACATTGAATG
1 TGCATCGATGCAAATTGAATG
*
2157278 TACATCGATG
1 TGCATCGATG
2157288 TACATAGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCAAATTGAATG
Found at i:2161000 original size:23 final size:23
Alignment explanation
Indices: 2160972--2161054 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 23
2160962 AAATGCACTA
2160972 AAGTGCCACATAGAATTTCACCT
1 AAGTGCCACATAGAATTTCACCT
* * * *
2160995 AAGTGCCGCATAGAAATGCACCG
1 AAGTGCCACATAGAATTTCACCT
* *
2161018 AAGTGCCATATA-AGATGTC-CCT
1 AAGTGCCACATAGA-ATTTCACCT
2161040 AAG-GACCACATAGAA
1 AAGTG-CCACATAGAA
2161055 AATTCCTTGA
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
21 1 0.02
22 13 0.28
23 32 0.70
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (23 bp):
AAGTGCCACATAGAATTTCACCT
Found at i:2161307 original size:30 final size:29
Alignment explanation
Indices: 2161254--2161312 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2161244 TGTAAACATA
* *
2161254 TCACATATTCATATAAACTCGTAGCTTCAT
1 TCACATATACATATAAACACGTAG-TTCAT
* *
2161284 TCACATATACATGTAATCACGTAGTTCAT
1 TCACATATACATATAAACACGTAGTTCAT
2161313 GTAAATTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (29 bp):
TCACATATACATATAAACACGTAGTTCAT
Found at i:2165125 original size:21 final size:21
Alignment explanation
Indices: 2165099--2165148 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
2165089 GGAGCGTGTG
2165099 GTGCATCGATGCATAAGGCTA
1 GTGCATCGATGCATAAGGCTA
2165120 GTGCATCGATGCATAAGGCTA
1 GTGCATCGATGCATAAGGCTA
2165141 GTGCATCG
1 GTGCATCG
2165149 GTACACTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCATAAGGCTA
Found at i:2165283 original size:64 final size:63
Alignment explanation
Indices: 2165213--2165371 Score: 230
Period size: 64 Copynumber: 2.5 Consensus size: 63
2165203 TGCACTAAGA
* * * * *
2165213 GTGCATCGATGCATGAAGTGCATTCGATGTTTCA-AACAAGCTCGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCATAA-AACCT-GAGTGCATCAATGCATGGTAT
2165277 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCAATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACCTGAGTGCATCAATGCATGGTAT
*
2165341 GTGCATCTATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
2165372 CAATTTATTC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
63 2 0.02
64 74 0.85
65 9 0.10
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACCTGAGTGCATCAATGCATGGTAT
Found at i:2165390 original size:64 final size:63
Alignment explanation
Indices: 2165213--2165419 Score: 208
Period size: 64 Copynumber: 3.2 Consensus size: 63
2165203 TGCACTAAGA
* * * *
2165213 GTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AACAAGCTCGAGTGCATCGATGCATGGTC
1 GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAA-AA-CT-GAGTGCATCGATGCATGGTA
2165276 T
63 T
* *
2165277 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCAATGCATGGTAT
1 GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAA-CTGAGTGCATCGATGCATGGTAT
* * **
2165341 GTGCATCTATGCATAAAATGCATTCGATGTTCAATTTATTCAA-TG-GTGCATCGATGCATGG-A
1 GTGCATCAATGCATAAAATGCATTCGATGTT---TTCATAAAACTGAGTGCATCGATGCATGGTA
2165403 TT
63 -T
2165405 GGTGCATCAATGCAT
1 -GTGCATCAATGCAT
2165420 GGATTGGTGC
Statistics
Matches: 125, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 92 0.74
65 24 0.19
66 2 0.02
67 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAACTGAGTGCATCGATGCATGGTAT
Found at i:2165409 original size:20 final size:20
Alignment explanation
Indices: 2165384--2165438 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2165374 ATTTATTCAA
2165384 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGATGCATGGAT
*
2165404 TGGTGCATCAATGCATGGAT
1 TGGTGCATCGATGCATGGAT
2165424 TGGTGCATCGATGCA
1 TGGTGCATCGATGCA
2165439 CTCTTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:2168265 original size:16 final size:16
Alignment explanation
Indices: 2168234--2168289 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
2168224 CACCAAGAAA
* *
2168234 ACATACATCAATACAT
1 ACATACATTAACACAT
*
2168250 ACATATATTAACACAT
1 ACATACATTAACACAT
2168266 ACATACATTAACACAT
1 ACATACATTAACACAT
2168282 ACATACAT
1 ACATACAT
2168290 GATACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (16 bp):
ACATACATTAACACAT
Found at i:2169045 original size:65 final size:66
Alignment explanation
Indices: 2168943--2169265 Score: 359
Period size: 67 Copynumber: 4.9 Consensus size: 66
2168933 ATAAACACCT
* * * *
2168943 TTGAGATTGTTTCCATC-AAACAAATTTTGTCTACCTTGAGATAGTTTCTCTTGAAACAAAAA-C
1 TTGAGATAGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATC
2169006 A
66 A
* *
2169007 TTGAGATAGTTTCCCTCGAAACAAGTTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAAAA-C
1 TTGAGATAGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATC
2169071 AA
66 -A
* * * * * *
2169073 TTGAGATTGTTTCCCTAGAAACAAAATTTTGTCTCTCTTGAGATAATTTATCTTGAAACAAAAAT
1 TTGAGATAGTTTCCCTCGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAAT
*
2169138 CT
65 CA
* * *
2169140 TTGAGTATA-TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAGAAAAAA
1 TTGAG-ATAGTTTCCCTCGAAACAAA-TTTTGTCTCCCTTGAGACAGTTTCTCTTGAA-ACAAAA
*
2169204 ATCT
63 ATCA
* * * * *
2169208 TTGAG-TATGTTTCCCTTGAAACAACTTTTGTCTCGCTTGAGACAGATTCTATTGAAAC
1 TTGAGATA-GTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
2169266 CAATTATCCC
Statistics
Matches: 226, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
64 15 0.07
65 42 0.19
66 27 0.12
67 110 0.49
68 32 0.14
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (66 bp):
TTGAGATAGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATC
A
Found at i:2169616 original size:134 final size:133
Alignment explanation
Indices: 2169268--2169616 Score: 434
Period size: 133 Copynumber: 2.6 Consensus size: 133
2169258 ATTGAAACCA
* ** * * *
2169268 ATTATCCCTAAAGATGGTC-AGCCGCCATCATCAGGTAGGAACCGTGTCATCCACCGACCAAATA
1 ATTATCCCTAAAGATGGTCAATCATCC-TCATCACGTAGGAACCGTGTCATCCACCGACCAGATC
* * * *
2169332 TCCTCATCACGTAAGAGTCACATCAACCTTAGATAACTTGTCGTCCTCATCACATAGGAACCATG
65 TCCTCATCACGTAGGAG-CACATCAACCTTAGATAACATCTCATCCTCATCACATAGGAACCATG
2169397 TTATC
129 TTATC
* * *
2169402 ATCAT-CCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
1 ATTATCCCTAAAGATGGTCAATCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* * *
2169466 CCTCATCACGTAGGAGCAACGTCAACCTTAGATAACCATCT-ATCCTCATCACGTAGGAACCGTG
66 CCTCATCACGTAGGAGC-ACATCAACCTTAGATAA-CATCTCATCCTCATCACATAGGAACCATG
2169530 TTATC
129 TTATC
* * ** *
2169535 ATTATCCCTAAAGATGGTCAATCATTCTCATCATGTAGGAATTGTGTCATCCATCGACCAGATCT
1 ATTATCCCTAAAGATGGTCAATCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
* *
2169600 CCTCATCAAGTTGGAGC
66 CCTCATCACGTAGGAGC
2169617 CGTGTCACCC
Statistics
Matches: 185, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
132 1 0.01
133 107 0.58
134 77 0.42
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (133 bp):
ATTATCCCTAAAGATGGTCAATCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGCACATCAACCTTAGATAACATCTCATCCTCATCACATAGGAACCATGTT
ATC
Found at i:2169656 original size:134 final size:133
Alignment explanation
Indices: 2169295--2169668 Score: 403
Period size: 134 Copynumber: 2.8 Consensus size: 133
2169285 TCAGCCGCCA
* * * * * *
2169295 TCATCAGGTAGGAACCGTGTCATCCACCGACCAAATATCCTCATCACGTAAGAGTC-ACATCAAC
1 TCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCAAGTAGGAG-CAACGTCAAC
*** * * *
2169359 CTTAGATAA-CTTGTCGTCCTCATCACATAGGAACCATGTTATCATCATCCTAAAGATGGCCAGT
65 CTTAGATAACCAACT-ATCCTCATCACGTAGGAACCATGTTATCATCATCCTAAAGATGGCCAAT
2169423 CATCC
129 CATCC
*
2169428 TCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCAACGTCAACC
1 TCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCAAGTAGGAGCAACGTCAACC
* * * *
2169493 TTAGATAACCATCTATCCTCATCACGTAGGAACCGTGTTATCATTATCCCTAAAGATGGTCAATC
66 TTAGATAACCAACTATCCTCATCACGTAGGAACCATGTTATCATCAT-CCTAAAGATGGCCAATC
*
2169558 ATTC
130 ATCC
* ** * * *** *
2169562 TCATCATGTAGGAATTGTGTCATCCATCGACCAGATCTCCTCATCAAGTTGGAGCCGTGTCACCC
1 TCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCAAGTAGGAGCAACGTCAACC
** * * *
2169627 TTAGATCGCCAGACT-TTCTCGTCATGTAGGAACCATGTTATC
66 TTAGATAACCA-ACTATCCTCATCACGTAGGAACCATGTTATC
2169669 TCCCAAATTT
Statistics
Matches: 206, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
132 1 0.00
133 95 0.46
134 108 0.52
135 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (133 bp):
TCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCAAGTAGGAGCAACGTCAACC
TTAGATAACCAACTATCCTCATCACGTAGGAACCATGTTATCATCATCCTAAAGATGGCCAATCA
TCC
Found at i:2169866 original size:3 final size:3
Alignment explanation
Indices: 2169858--2169916 Score: 73
Period size: 3 Copynumber: 18.7 Consensus size: 3
2169848 GTTCGGGTCT
*
2169858 TTA TTA TTA TTA TTA TTA TTAA GTTAA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TT-A -TT-A TTA TTA TTA TTA TTA TTA TTA
*
2169906 TTA TAA TTA TT
1 TTA TTA TTA TT
2169917 TTAACAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 43 0.86
4 3 0.06
5 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2170294 original size:21 final size:21
Alignment explanation
Indices: 2170268--2170320 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2170258 CCCAGTCGCG
2170268 TGAGCCGCCGTTGAGCACACT
1 TGAGCCGCCGTTGAGCACACT
2170289 TGAGCCGCCGTTGAGCACACT
1 TGAGCCGCCGTTGAGCACACT
*
2170310 CGAGCCGCCGT
1 TGAGCCGCCGT
2170321 CGTCAGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (21 bp):
TGAGCCGCCGTTGAGCACACT
Found at i:2172896 original size:2 final size:2
Alignment explanation
Indices: 2172889--2172913 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2172879 ATACATAACC
2172889 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 A
2172914 CAAAGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2174590 original size:28 final size:28
Alignment explanation
Indices: 2174549--2174606 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
2174539 ATGTATACAC
*
2174549 AATATATATCAGATAA-GTATACACATTT
1 AATAAATATCAGATAATG-ATACACATTT
*
2174577 AATAAATATTAGATAATGATACACATTT
1 AATAAATATCAGATAATGATACACATTT
2174605 AA
1 AA
2174607 AATGACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (28 bp):
AATAAATATCAGATAATGATACACATTT
Found at i:2176830 original size:2 final size:2
Alignment explanation
Indices: 2176823--2176858 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2176813 TTTGATTGTC
2176823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2176859 TAGAATCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2195279 original size:17 final size:17
Alignment explanation
Indices: 2195246--2195278 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2195236 TATTTTTCAG
2195246 ATTTGTATTTTACTTTT
1 ATTTGTATTTTACTTTT
2195263 ATTTGTATTTTA-TTTT
1 ATTTGTATTTTACTTTT
2195279 TTTCGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (17 bp):
ATTTGTATTTTACTTTT
Found at i:2196546 original size:11 final size:13
Alignment explanation
Indices: 2196507--2196548 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
2196497 TGTTTAATAA
2196507 AATATATATATATT
1 AATATAT-TATATT
*
2196521 AATATATTATCTT
1 AATATATTATATT
2196534 AA-A-ATTATATT
1 AATATATTATATT
2196545 AATA
1 AATA
2196549 AACTTAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
13 7 0.28
14 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATATTATATT
Found at i:2198333 original size:8 final size:8
Alignment explanation
Indices: 2198320--2198344 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2198310 CATTAACGTG
2198320 TAATTTAT
1 TAATTTAT
2198328 TAATTTAT
1 TAATTTAT
2198336 TAATTTAT
1 TAATTTAT
2198344 T
1 T
2198345 CTTTCTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTTAT
Found at i:2201490 original size:23 final size:23
Alignment explanation
Indices: 2201459--2201518 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
2201449 TATAATAAAT
* *
2201459 TATTATAAAATATATTATTTTAA
1 TATTTTAAAATATACTATTTTAA
2201482 TATTTTAAAATATACTATTTTAA
1 TATTTTAAAATATACTATTTTAA
2201505 TATTTTAAAATATA
1 TATTTTAAAATATA
2201519 ATAAATGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTTAAAATATACTATTTTAA
Found at i:2208975 original size:20 final size:21
Alignment explanation
Indices: 2208950--2209002 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2208940 GACCAACAAA
2208950 TTCGCAACGCGAACTT-CAAT
1 TTCGCAACGCGAACTTCCAAT
* **
2208970 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAACTTCCAAT
2208990 TTCGCAACGCGAA
1 TTCGCAACGCGAA
2209003 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.77
21 2 0.08
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAACTTCCAAT
Found at i:2209039 original size:40 final size:41
Alignment explanation
Indices: 2208990--2209090 Score: 138
Period size: 40 Copynumber: 2.5 Consensus size: 41
2208980 AGTTTCCAAT
*
2208990 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGTAACGCGAATA-GTCAAATTCGCAACACAGAAGTCAAA
*
2209030 TTCGTAACGCG-ATAGTCAAATTCGTAACACAGAAGTCAAA
1 TTCGTAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAA
*
2209070 TTCATAACGCGAA-AGTCAAAT
1 TTCGTAACGCGAATAGTCAAAT
2209091 GTTTTTACGC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.04
39 6 0.11
40 46 0.84
41 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (41 bp):
TTCGTAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:2209048 original size:20 final size:19
Alignment explanation
Indices: 2209021--2209090 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 19
2209011 TCGCAACACA
2209021 GAAGTCAAATTCGTAACGC
1 GAAGTCAAATTCGTAACGC
*
2209040 GATAGTCAAATTCGTAACAC
1 GA-AGTCAAATTCGTAACGC
*
2209060 AGAAGTCAAATTCATAACGC
1 -GAAGTCAAATTCGTAACGC
2209080 GAAAGTCAAAT
1 G-AAGTCAAAT
2209091 GTTTTTACGC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.07
20 40 0.89
21 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (19 bp):
GAAGTCAAATTCGTAACGC
Found at i:2213340 original size:62 final size:63
Alignment explanation
Indices: 2213239--2213379 Score: 205
Period size: 66 Copynumber: 2.2 Consensus size: 63
2213229 TTTTACATTG
*
2213239 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
* * *
2213300 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA-TTTTTT-CTTGATTAATTGATTTGT
2213365 A
63 A
2213366 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2213380 GTTTCTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
61 17 0.24
62 18 0.25
64 5 0.07
66 31 0.44
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (63 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTTGATTAATTGATTTGTA
Found at i:2213507 original size:20 final size:20
Alignment explanation
Indices: 2213482--2213524 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2213472 GATTTTCGGT
*
2213482 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCGCG
2213502 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
2213522 TTG
1 TTG
2213525 ATCGCAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:2214503 original size:20 final size:20
Alignment explanation
Indices: 2214478--2214577 Score: 77
Period size: 20 Copynumber: 5.3 Consensus size: 20
2214468 CAATTTGCAA
2214478 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
*
2214498 TTTCGCATTGTGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
* * * *
2214518 TATCACA--ACG--CTT-A-
1 TTTCGCATTGCGAATTTGAC
*
2214532 TTTCGCGTTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
* * *
2214552 TTTTGCGTTACGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
2214572 TTTCGC
1 TTTCGC
2214578 GTTGATCGCA
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 4 0.07
18 3 0.05
19 1 0.02
20 47 0.78
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTGAC
Found at i:2214579 original size:20 final size:20
Alignment explanation
Indices: 2214532--2214580 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2214522 ACAACGCTTA
*
2214532 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTACGAATTTGAC
*
2214552 TTTTGCGTTACGAATTTGAC
1 TTTCGCGTTACGAATTTGAC
2214572 TTTCGCGTT
1 TTTCGCGTT
2214581 GATCGCAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTACGAATTTGAC
Found at i:2214883 original size:18 final size:18
Alignment explanation
Indices: 2214860--2214895 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2214850 AAGCCGGTTG
*
2214860 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2214878 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2214896 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2216965 original size:3 final size:3
Alignment explanation
Indices: 2216957--2216984 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2216947 TCTTTGGGGA
2216957 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2216985 AGGGTTATAT
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2217194 original size:24 final size:23
Alignment explanation
Indices: 2217163--2217214 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
2217153 TCACATCATC
2217163 AAAATCCGAGTATTGACCAAGAT
1 AAAATCCGAGTATTGACCAAGAT
* *
2217186 AAAAGTCCGGGTATTGACCCAGAT
1 AAAA-TCCGAGTATTGACCAAGAT
2217210 AAAAT
1 AAAAT
2217215 TTTGAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.21
Consensus pattern (23 bp):
AAAATCCGAGTATTGACCAAGAT
Found at i:2217447 original size:23 final size:23
Alignment explanation
Indices: 2217417--2217466 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2217407 AATTCTGGTG
2217417 GAACCATTAAATTTTGGGTTGAA
1 GAACCATTAAATTTTGGGTTGAA
2217440 GAACCATTAAATTTTGGGTTGAA
1 GAACCATTAAATTTTGGGTTGAA
2217463 GAAC
1 GAAC
2217467 TTACTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (23 bp):
GAACCATTAAATTTTGGGTTGAA
Found at i:2217970 original size:16 final size:16
Alignment explanation
Indices: 2217948--2217987 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2217938 GAAATCATTG
*
2217948 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
2217964 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
2217980 AAAAATTA
1 AAAAATTA
2217988 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:2218207 original size:20 final size:20
Alignment explanation
Indices: 2218159--2218212 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2218149 GAAATTAAAT
*
2218159 TCGCATTGCGAATTTGACTT
1 TCGCATTGCGAATTTGACTA
* **
2218179 TTGTGTTGCGAATTTGACTA
1 TCGCATTGCGAATTTGACTA
2218199 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2218213 GCGTTGCGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGAATTTGACTA
Found at i:2219981 original size:20 final size:20
Alignment explanation
Indices: 2219956--2220039 Score: 143
Period size: 20 Copynumber: 4.2 Consensus size: 20
2219946 GCTTGGATAG
2219956 GTGTTCTAACACTTCTTTAA
1 GTGTTCTAACACTTCTTTAA
2219976 GTGTTCTAACACTT-TTTAAA
1 GTGTTCTAACACTTCTTT-AA
2219996 GTGTTCTAACACTTCTTTAA
1 GTGTTCTAACACTTCTTTAA
*
2220016 GTGTTCTAACATTTCTTTAA
1 GTGTTCTAACACTTCTTTAA
2220036 GTGT
1 GTGT
2220040 CCTCAACTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
19 3 0.05
20 55 0.90
21 3 0.05
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (20 bp):
GTGTTCTAACACTTCTTTAA
Found at i:2223767 original size:24 final size:24
Alignment explanation
Indices: 2223740--2223798 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2223730 TACCTATAGA
* *
2223740 GTATCGATACTTCTCTTATATTTG
1 GTATCGATACCTCTCTTACATTTG
*
2223764 GTATCGATACCTCTCTTACCTTTG
1 GTATCGATACCTCTCTTACATTTG
*
2223788 GTATCGGTACC
1 GTATCGATACC
2223799 ACATGAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (24 bp):
GTATCGATACCTCTCTTACATTTG
Found at i:2224603 original size:100 final size:100
Alignment explanation
Indices: 2224479--2224691 Score: 372
Period size: 100 Copynumber: 2.1 Consensus size: 100
2224469 CAATTAAGCA
*
2224479 ATATTATATTTATTAATTGGAGTTGTTTGATCTTATATTTAATATTAGTATGTTTAATACAATAT
1 ATATTTTA-TTATTAATTGGAGTTGTTTGATCTTATATTTAATATTAGTATGTTTAATACAATAT
*
2224544 CACTCATGGGTGGATTTCGAGATTTGAAGGAACCAC
65 CACTCATAGGTGGATTTCGAGATTTGAAGGAACCAC
2224580 ATATTTTATTATTAATTGGAGTTGTTTGATCTTATATTTAATATTAGTATGTTTAATACAATATC
1 ATATTTTATTATTAATTGGAGTTGTTTGATCTTATATTTAATATTAGTATGTTTAATACAATATC
* *
2224645 ACTCATAGGTGGATTTCGATATTTGAAGTAACCAC
66 ACTCATAGGTGGATTTCGAGATTTGAAGGAACCAC
*
2224680 ATGTTTTATTAT
1 ATATTTTATTAT
2224692 GATTATGTGA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 100 0.93
101 7 0.07
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (100 bp):
ATATTTTATTATTAATTGGAGTTGTTTGATCTTATATTTAATATTAGTATGTTTAATACAATATC
ACTCATAGGTGGATTTCGAGATTTGAAGGAACCAC
Found at i:2224870 original size:17 final size:17
Alignment explanation
Indices: 2224848--2224891 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2224838 TATATATTTT
2224848 AAAATAAATAAGTAATA
1 AAAATAAATAAGTAATA
* *
2224865 AAAATAAAATTATTAATA
1 AAAAT-AAATAAGTAATA
2224883 AAATATAAA
1 AAA-ATAAA
2224892 ACAGTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATAAATAAGTAATA
Found at i:2225359 original size:2 final size:2
Alignment explanation
Indices: 2225352--2225379 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2225342 AGACGAAGAA
2225352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2225380 CGATTAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2226264 original size:23 final size:23
Alignment explanation
Indices: 2226220--2226264 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2226210 TTTTAAAATA
*
2226220 ATTTAATAAATTTAACACTTTAT
1 ATTTAATAAATTTAACAATTTAT
*
2226243 ATTTAA-AAATTCTATCAATTTA
1 ATTTAATAAATT-TAACAATTTA
2226265 GTCTTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATAAATTTAACAATTTAT
Found at i:2227655 original size:18 final size:19
Alignment explanation
Indices: 2227632--2227673 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2227622 GTAGTATTTA
2227632 AAATATTAT-TAAAACAAT
1 AAATATTATATAAAACAAT
*
2227650 AAATATTATATAAATCAAT
1 AAATATTATATAAAACAAT
2227669 AAATA
1 AAATA
2227674 ATTAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATTATATAAAACAAT
Found at i:2228922 original size:2 final size:2
Alignment explanation
Indices: 2228907--2228955 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
2228897 AAATCTTCCT
2228907 TA TA T- TA T- 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
2228947 TA TA TA TA T
1 TA TA TA TA T
2228956 GCATAGTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2229674 original size:3 final size:3
Alignment explanation
Indices: 2229662--2229720 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
2229652 GCCTGCAAAT
* * *
2229662 ATA ATAA ATA ATA TTA ATA AAA ATA ACA ATA ATA ATA ATA ATA TATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
2229709 ATA ATA ATA ATA
1 ATA ATA ATA ATA
2229721 TTTTTTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2230229 original size:129 final size:127
Alignment explanation
Indices: 2229921--2230357 Score: 395
Period size: 129 Copynumber: 3.4 Consensus size: 127
2229911 CGTCTAAAGG
* *
2229921 TGACA-AGACTCCTACATAATGAGAAGATCTAGTCAAGG-GATAACACTGCTCATACGTGATGAA
1 TGACATAG-CTCCTACATAATGAGGAGATCTAGTC-AGGTGATGACAC-GCTCATACGTGATGAA
* *
2229984 GATTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACGACTGGTTAT
63 GAGTTC-TGGCCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
2230049 CTAGGT
122 CTAGGT
* * * * *
2230055 TGACATAACTCATACATAAAGAGCAAATCTAGTCAGGTGATGACACGACTCATACGTGATGAAGA
1 TGACATAGCTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACG-CTCATACGTGATGAAGA
* * * * * ** *
2230120 GTTCTGGTCATCTAAAGGTGATAACACAGCTCATACGTGATGAAGA-GTTTTGGTTATCAAGGAT
65 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-ACTGGTTATCTAGG-T
* * *
2230184 TGACACT-GCTCCTACATAATGAGGAGATC-AGATCAGGTGATGACACGGTTCCTACGTGATGAG
1 TGACA-TAGCTCCTACATAATGAGGAGATCTAG-TCAGGTGATGACAC-GCTCATACGTGATGAA
* * * ** *
2230247 GACG-GCAGGCCATCTATAGGTGATAACACGGTTCCTACGTGATGAGGACGGGTGGTTATCTGGG
63 GA-GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGG
2230311 TT
127 -T
* *
2230313 TGACATGGCTCCTACATGATGAGGAGATC-AGGTC-GAGTGATGACA
1 TGACATAGCTCCTACATAATGAGGAGATCTA-GTCAG-GTGATGACA
2230358 AATTGATGTG
Statistics
Matches: 252, Mismatches: 38, Indels: 31
0.79 0.12 0.10
Matches are distributed among these distances:
127 1 0.00
128 40 0.16
129 138 0.55
130 5 0.02
131 2 0.01
133 11 0.04
134 54 0.21
135 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (127 bp):
TGACATAGCTCCTACATAATGAGGAGATCTAGTCAGGTGATGACACGCTCATACGTGATGAAGAG
TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAGGT
Found at i:2230710 original size:117 final size:115
Alignment explanation
Indices: 2230568--2230779 Score: 334
Period size: 117 Copynumber: 1.8 Consensus size: 115
2230558 AATGTTAATG
** *
2230568 CAAGGTTGAATGAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGATGAGTTCTTCTCATTA
1 CAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATGAGTTCTTCTCATTA
2230633 TGAACTCTCCACTGAAAATGTTGGTCCACCTCTTTCTGTGATGGAATCAAAC
66 TG-AC-CTCCACTGAAAATGTTGGTCCACCTCTTTCTGTGATGGAATCAAAC
*
2230685 CAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATGAGTTCTTCTCATTA
** * *
2230750 TGACCTCTTCTGGAAATGTTGGTTCACCTC
66 TGACCTCCACTGAAAATGTTGGTCCACCTC
2230780 CTTATGCGGT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
115 22 0.25
116 2 0.02
117 63 0.72
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (115 bp):
CAAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTAGATGAGTTCTTCTCATTA
TGACCTCCACTGAAAATGTTGGTCCACCTCTTTCTGTGATGGAATCAAAC
Found at i:2231039 original size:136 final size:135
Alignment explanation
Indices: 2230809--2231142 Score: 500
Period size: 136 Copynumber: 2.5 Consensus size: 135
2230799 AGGAACAAAT
* * *
2230809 TCTTCTCATTATGAAC-T-TTCT--C-CTGTAGGACGAGTTCTTCTCATTATGAACTCT-TTTGG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCATTGG
* * * *
2230868 AAATATTAATCCCTCAAGCGAGGCGTCACTAATTCGAAATGTCGTGAATCGAGTGATAGGTCGAA
66 AAATATCAATCCCTAAAGCGAGGCATCACTAATTCGAAATGTCGTGAATCAAGTGATAGGTCGAA
2230933 CAAGC
131 CAAGC
2230938 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCAATTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTC-ATTG
* * * *
2231003 GAAATGTCAATCCCTAAAGTGAGGTATCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCGA
65 GAAATATCAATCCCTAAAGCGAGGCATCACTAATTCGAAATGTCGTGAATCAAGTGATAGGTCGA
2231068 ACAAGC
130 ACAAGC
*
2231074 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCT-CATTG
2231139 GAAA
65 GAAA
2231143 CACTGATGTG
Statistics
Matches: 185, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
129 16 0.09
130 1 0.01
131 4 0.02
133 1 0.01
134 30 0.16
136 132 0.71
137 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (135 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCATTGG
AAATATCAATCCCTAAAGCGAGGCATCACTAATTCGAAATGTCGTGAATCAAGTGATAGGTCGAA
CAAGC
Found at i:2231262 original size:227 final size:227
Alignment explanation
Indices: 2230928--2231361 Score: 656
Period size: 227 Copynumber: 1.9 Consensus size: 227
2230918 GAGTGATAGG
*
2230928 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAA
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAA
* * * * *
2230993 CTCTCAATTGGAAATGTCAATCCCTAAAGTGAGGTATCACTGATTCGAAATGTCGTGAATCAAGT
66 CTCTCAACTGAAAATGTCAATCCCTAAAGCGAGGCATCACTGATTCGAAATGCCGTGAATCAAGT
*
2231058 GATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCAT
131 GATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TATCGGATGAGTTCTTCTCAT
2231123 TATGAACTCTCCACTGGAAACACTGATGTGAGA
195 TATGAACTCTCCACTGGAAACACTGATGTGAGA
* * *
2231156 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCT-TATTGGATGAGTTCTTCTCATTATGAA
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAA
** * * * * *
2231220 CTCTTC-ACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACTGATTCGAAATGCCTTGAATCGAG
66 CTC-TCAACTGAAAATGTCAATCCCTAAAGCGAGGCATCACTGATTCGAAATGCCGTGAATCAAG
* * *
2231284 TGATGGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTTATTGGATGAGTTCTTCTCAT
130 TGATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCAT
2231349 TATGAACTCTCCA
195 TATGAACTCTCCA
2231362 TTGAGAATGT
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
226 32 0.17
227 116 0.63
228 37 0.20
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (227 bp):
TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAA
CTCTCAACTGAAAATGTCAATCCCTAAAGCGAGGCATCACTGATTCGAAATGCCGTGAATCAAGT
GATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAGTTCTTCTCATT
ATGAACTCTCCACTGGAAACACTGATGTGAGA
Found at i:2231823 original size:74 final size:73
Alignment explanation
Indices: 2231742--2231898 Score: 215
Period size: 74 Copynumber: 2.1 Consensus size: 73
2231732 CTCAAGCGAG
* *
2231742 ACTGTCTCAAGCAAAATGAAGTAGGTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTT
1 ACTGTCTCAAGCAAAACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTT
2231807 CAAGATAAA
66 CAAGA-AAA
* * * * * *
2231816 ACTGTCTCAAGCGAGACGAAGTTGATTTTAAGAAAAACCATTTTAAGGGAGATAAAACTTTGTTT
1 ACTGTCTCAAGCAAAACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTT
*
2231881 CAAGAGAA
66 CAAGAAAA
*
2231889 ATTGTCTCAA
1 ACTGTCTCAA
2231899 AAACTTGTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 11 0.15
74 62 0.85
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (73 bp):
ACTGTCTCAAGCAAAACGAAGTAGATTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTTGTTT
CAAGAAAA
Found at i:2231824 original size:38 final size:37
Alignment explanation
Indices: 2231766--2231898 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
2231756 AATGAAGTAG
* **
2231766 GTTTTAAGAAAAACCATCTCAAGGGAGACAAAACTTT
1 GTTTCAAGAAAAACTGTCTCAAGGGAGACAAAACTTT
* * *
2231803 GTTTCAAGATAAAACTGTCTCAAGCGAGAC-GAA-GTT
1 GTTTCAAGA-AAAACTGTCTCAAGGGAGACAAAACTTT
* ** * * *
2231839 GATTTTAAGAAAAACCATTTTAAGGGAGATAAAACTTT
1 G-TTTCAAGAAAAACTGTCTCAAGGGAGACAAAACTTT
* *
2231877 GTTTCAAGAGAAATTGTCTCAA
1 GTTTCAAGAAAAACTGTCTCAA
2231899 AAACTTGTTA
Statistics
Matches: 70, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
36 17 0.24
37 33 0.47
38 20 0.29
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28
Consensus pattern (37 bp):
GTTTCAAGAAAAACTGTCTCAAGGGAGACAAAACTTT
Found at i:2231992 original size:66 final size:65
Alignment explanation
Indices: 2231860--2232029 Score: 207
Period size: 66 Copynumber: 2.6 Consensus size: 65
2231850 AAACCATTTT
* *
2231860 AAGGGAGATAAAACTTTGTTTCAAGAGAAATTGTCTCAAAAACTTGTTACCAAAAGAAACTATCT
1 AAGGGAGACAAAA-TTTGTTTCAAGGGAAATTGTCTCAAAAACTTGTTACCAAAAGAAACTATCT
2231925 C
65 C
* ** ** *
2231926 AAGGGAGACAAAATTCGTTTCAAGGGAAA-TGTTCTCAAAATTTTGTGTTTCAAGAGAAACTATC
1 AAGGGAGACAAAATTTGTTTCAAGGGAAATTG-TCTCAAAAACTTGT-TACCAAAAGAAACTATC
2231990 TC
64 TC
* * *
2231992 AAGGGAGACAAAATTTGTTTTAAGGGAAACTATCTCAA
1 AAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAA
2232030 GCGAGATAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.02
65 26 0.29
66 61 0.68
67 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (65 bp):
AAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAAAACTTGTTACCAAAAGAAACTATCTC
Found at i:2232021 original size:36 final size:37
Alignment explanation
Indices: 2231961--2232089 Score: 143
Period size: 39 Copynumber: 3.4 Consensus size: 37
2231951 GAAATGTTCT
* *
2231961 CAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGA
1 CAAAATTTTGT-TTT-AAGGGAAACTATCTCAAGCGAGA
2232000 CAAAA-TTTGTTTTAAGGGAAACTATCTCAAGCGAGA
1 CAAAATTTTGTTTTAAGGGAAACTATCTCAAGCGAGA
* **
2232036 TAAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 -CAAA-ATTTTGTTTTAAGGGAAACTATCTCAAGCGAGA
*
2232075 TAAAATCTTTTGTTT
1 CAAAA--TTTTGTTT
2232090 CAAGAAAAAC
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
36 21 0.27
37 7 0.09
38 9 0.11
39 42 0.53
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (37 bp):
CAAAATTTTGTTTTAAGGGAAACTATCTCAAGCGAGA
Found at i:2232059 original size:39 final size:39
Alignment explanation
Indices: 2231962--2232563 Score: 599
Period size: 40 Copynumber: 15.2 Consensus size: 39
2231952 AAATGTTCTC
* * *
2231962 AAAAT-TTTGTGTTTCAA-GAGAAACTATCTCAAGGGAGAC
1 AAAATCTTT-TGTTTCAAGGA-AAACAATCTCAAGTGAGAT
* * * *
2232001 AAAA---TTTGTTTTAAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTTTGTTTCAAGGAAAACAATCTCAAGTGAGAT
* * * * *
2232037 AAAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTTTGTTTCAAGGAAAACAATCTCAAGTGAGAT
* **
2232076 AAAATCTTTTGTTTCAAGAAAAACCAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGGAAAA-CAATCTCAAGTGAGAT
**
2232116 AAAATCTTTTGTTTCAAGGAAAAGCAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGGAAAA-CAATCTCAAGTGAGAT
*
2232156 AAAATCTTTTGTTTCAAGGAAAAACAATCTTGAA-TGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATC-TCAAGTGAGAT
* **
2232196 AAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
* *
2232236 AAAATCTTTTGTTTCAAGGAAAAACAATCTTGAA-TGAAAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATC-TCAAGTGAGAT
* * **
2232276 AAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
* * * *
2232316 AAAATCTTCTGTTTCAAGGAAAAACAATCTTGAA-TAAAAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATC-TCAAGTGAGAT
**
2232356 AAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
* **
2232396 AAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
* **
2232436 AAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
**
2232476 AAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTGAGAT
* **
2232516 AAAATCTTCTGTTTCAAGGAAAAGCAATCTTGAGTGAGAT
1 AAAATCTTTTGTTTCAAGGAAAA-CAATCTCAAGTGAGAT
2232556 AAAATCTT
1 AAAATCTT
2232564 CTGTATTAAA
Statistics
Matches: 507, Mismatches: 43, Indels: 25
0.88 0.07 0.04
Matches are distributed among these distances:
36 28 0.06
37 3 0.01
39 63 0.12
40 403 0.79
41 10 0.02
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (39 bp):
AAAATCTTTTGTTTCAAGGAAAACAATCTCAAGTGAGAT
Found at i:2232119 original size:40 final size:40
Alignment explanation
Indices: 2232071--2232567 Score: 843
Period size: 40 Copynumber: 12.4 Consensus size: 40
2232061 TATCTCAAGC
*
2232071 GAGATAAAATCTTTTGTTTCAA-GAAAAACCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAA-CAATCTTGAGT
* *
2232111 GAGATAAAATCTTTTGTTTCAAGGAAAAGCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
2232151 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2232191 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
2232231 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
2232271 GAAATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2232311 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
2232351 AAAATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2232391 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2232431 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2232471 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
2232511 GAGATAAAATCTTCTGTTTCAAGGAAAAGCAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
2232551 GAGATAAAATCTTCTGT
1 GAGATAAAATCTTCTGT
2232568 ATTAAATGAG
Statistics
Matches: 432, Mismatches: 24, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
40 427 0.99
41 5 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:2232339 original size:20 final size:20
Alignment explanation
Indices: 2232276--2232339 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
2232266 TGAATGAAAT
2232276 AAAATCTTCTGTTTCAAGGA
1 AAAATCTTCTGTTTCAAGGA
** ** *
2232296 AAAATAATCTTGAGT-GA-GA
1 AAAATCTTC-TGTTTCAAGGA
2232315 TAAAATCTTCTGTTTCAAGGA
1 -AAAATCTTCTGTTTCAAGGA
2232336 AAAA
1 AAAA
2232340 CAATCTTGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 5 0.17
20 20 0.67
21 5 0.17
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
AAAATCTTCTGTTTCAAGGA
Found at i:2235458 original size:1 final size:1
Alignment explanation
Indices: 2235452--2235494 Score: 77
Period size: 1 Copynumber: 43.0 Consensus size: 1
2235442 ATTTAATTTC
*
2235452 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2235495 CTTTCTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:2235499 original size:4 final size:4
Alignment explanation
Indices: 2235481--2235544 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
2235471 TTTTTTTTTT
* *
2235481 TTTC TTT- TTTT TTTC TTTC TTTC TTTC TTTC TTTC --TC TTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
2235526 -TTC TTT- TTTCC TTT- TTTC T
1 TTTC TTTC TTT-C TTTC TTTC T
2235545 CTGATGGATG
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
2 2 0.04
3 12 0.24
4 33 0.66
5 3 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:2239055 original size:20 final size:19
Alignment explanation
Indices: 2239032--2239086 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2239022 GATGATTATG
2239032 CAAATGCGAAGATGC-AAATA
1 CAAATGC-AA-ATGCAAAATA
2239052 CAAATGCAAATGCGAAAATA
1 CAAATGCAAATGC-AAAATA
*
2239072 CAAATACAAATGCAA
1 CAAATGCAAATGCAA
2239087 TAGAGTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 24 0.75
ACGTcount: A:0.55, C:0.16, G:0.15, T:0.15
Consensus pattern (19 bp):
CAAATGCAAATGCAAAATA
Found at i:2239065 original size:26 final size:26
Alignment explanation
Indices: 2239029--2239086 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
2239019 CATGATGATT
* *
2239029 ATGCAAATGCGAAGATGCAAATACAA
1 ATGCAAATGCGAAAATACAAATACAA
2239055 ATGCAAATGCGAAAATACAAATACAA
1 ATGCAAATGCGAAAATACAAATACAA
2239081 ATGCAA
1 ATGCAA
2239087 TAGAGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (26 bp):
ATGCAAATGCGAAAATACAAATACAA
Found at i:2240704 original size:18 final size:19
Alignment explanation
Indices: 2240681--2240722 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2240671 GTAGTATTTA
2240681 AAATATTAT-TAAAACAAT
1 AAATATTATATAAAACAAT
*
2240699 AAATATTATATAAATCAAT
1 AAATATTATATAAAACAAT
2240718 AAATA
1 AAATA
2240723 ATTAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATTATATAAAACAAT
Found at i:2241971 original size:2 final size:2
Alignment explanation
Indices: 2241956--2241998 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
2241946 AAACCTTCCT
2241956 TA TA T- TA T- 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
2241996 TA T
1 TA T
2241999 GCATAGTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2242746 original size:3 final size:3
Alignment explanation
Indices: 2242712--2242766 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
2242702 CCTGCAAATG
* * *
2242712 TAA TAAA TAA TAT TAA TAA AAA TAA CAA TAA TAA TAA TAA TATA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
2242759 TAA TAA TA
1 TAA TAA TA
2242767 TTTTTTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2244548 original size:5 final size:5
Alignment explanation
Indices: 2244538--2244591 Score: 67
Period size: 5 Copynumber: 11.2 Consensus size: 5
2244528 ATATCGAATA
* * *
2244538 ATAAT ATAAT ATAAT ATAAT ATAAT GTAAT GTAAT GTAAT ATAAT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2244587 A-AAT A
1 ATAAT A
2244592 ATACTATACT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
4 8 0.17
5 39 0.83
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:2244760 original size:22 final size:21
Alignment explanation
Indices: 2244714--2244767 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2244704 AAAGCCATAT
* * *
2244714 ATATTATATGTTTTCAAAATG
1 ATATAATATATTTTCAAAATC
2244735 ATATAATATATTTTCAAAAATC
1 ATATAATATATTTTC-AAAATC
*
2244757 ATATATTATAT
1 ATATAATATAT
2244768 ATATATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
ATATAATATATTTTCAAAATC
Found at i:2244773 original size:11 final size:11
Alignment explanation
Indices: 2244757--2244807 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2244747 TTCAAAAATC
2244757 ATATATTATAT
1 ATATATTATAT
* *
2244768 ATATATTTTGAA
1 ATATATTAT-AT
*
2244780 AT-TATTTTAT
1 ATATATTATAT
2244790 ATATATTATAT
1 ATATATTATAT
2244801 ACTATAT
1 A-TATAT
2244808 AAATATTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 3 0.09
11 22 0.67
12 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
ATATATTATAT
Found at i:2258720 original size:16 final size:15
Alignment explanation
Indices: 2258697--2258741 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
2258687 AAGATAAAAA
2258697 TAAAATAAAACAAAG
1 TAAAATAAAACAAAG
*
2258712 TAGAAATAAAACGAAG
1 TA-AAATAAAACAAAG
2258728 TAAAA-AAAATCAAA
1 TAAAATAAAA-CAAA
2258742 ACAAAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 14 0.54
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (15 bp):
TAAAATAAAACAAAG
Found at i:2258930 original size:2 final size:2
Alignment explanation
Indices: 2258923--2258984 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
2258913 TATGTAAATA
2258923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2258965 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2258985 GCGCATAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2259254 original size:17 final size:17
Alignment explanation
Indices: 2259223--2259281 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 17
2259213 AAAAGACTGG
**
2259223 AATAAAATGCAGAAAAA
1 AATAAAATGTTGAAAAA
2259240 AATAAAATGTTG--AAA
1 AATAAAATGTTGAAAAA
**
2259255 TTTAAAATGTTAGAAAATA
1 AATAAAATGTT-GAAAA-A
2259274 AATAAAAT
1 AATAAAAT
2259282 AAAAAACAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 12 0.38
16 1 0.03
17 10 0.31
18 2 0.06
19 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (17 bp):
AATAAAATGTTGAAAAA
Found at i:2259742 original size:99 final size:98
Alignment explanation
Indices: 2259572--2259753 Score: 265
Period size: 99 Copynumber: 1.8 Consensus size: 98
2259562 TATAAAAACA
* * * * *
2259572 AAATAAATAAAAAAAGGTTTGTATTTAGCAAAGTCCGAACCATAATAATGTGGATTTTACCCCGG
1 AAATAAATAAAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCGG
*
2259637 ATCGGGTCACCGCAAGGTTGAATCGAATAATGC
66 ATCGGGTCACCACAAGGTTGAATCGAATAATGC
* * * *
2259670 AAATAAATATAAAAAAAGTTAGTGGTTAGCATAGTCCGAACAATAATAATGTGGGTCTTACCTCG
1 AAATAAATA-AAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCG
2259735 GATCGGGTCACCACAAGGT
65 GATCGGGTCACCACAAGGT
2259754 CGAGTAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 9 0.12
99 64 0.88
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (98 bp):
AAATAAATAAAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCGG
ATCGGGTCACCACAAGGTTGAATCGAATAATGC
Found at i:2260868 original size:16 final size:17
Alignment explanation
Indices: 2260847--2260891 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2260837 ATTACAAGAG
2260847 AAAATGATAAAAAT-AA
1 AAAATGATAAAAATAAA
*
2260863 AAAATG-TTAAAATAAA
1 AAAATGATAAAAATAAA
2260879 AAAATGA-AAAAAT
1 AAAATGATAAAAAT
2260892 GTTAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAATGATAAAAATAAA
Found at i:2260905 original size:24 final size:23
Alignment explanation
Indices: 2260847--2260896 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
2260837 ATTACAAGAG
2260847 AAAATGATAAAAATAAAAAATGTT
1 AAAAT-ATAAAAATAAAAAATGTT
*
2260871 AAAATAAAAAAATGAAAAAATGTT
1 AAAATATAAAAAT-AAAAAATGTT
2260895 AA
1 AA
2260897 TTTCTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (23 bp):
AAAATATAAAAATAAAAAATGTT
Found at i:2262058 original size:18 final size:17
Alignment explanation
Indices: 2262016--2262048 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2262006 AATAAACATA
2262016 ATATAA-AT-AAAAACT
1 ATATAATATAAAAAACT
2262031 ATATAATATAAAAAACT
1 ATATAATATAAAAAACT
2262048 A
1 A
2262049 ATATTGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATAATATAAAAAACT
Found at i:2262096 original size:37 final size:35
Alignment explanation
Indices: 2262042--2262251 Score: 191
Period size: 37 Copynumber: 5.8 Consensus size: 35
2262032 TATAATATAA
2262042 AAAACTA-ATATTGTATATATTTTCGAAAAAATGTTTTC
1 AAAACTATATA-T-TATATATTTTC--AAAAATGTTTTC
* *
2262080 CAAATTATATATTATATATATTTTTTCAAAACA--TTTT-
1 AAAACTATATA-T-TATATA--TTTTCAAAA-ATGTTTTC
*
2262117 AAAACTAT-TATTATATATATTTTCAAAAATGGTTTC
1 AAAACTATATA-T-TATATATTTTCAAAAATGTTTTC
2262153 AAAAACTATATATTATATATATTTTC-AAAATGTTTTC
1 -AAAACTATATA-T-TATATATTTTCAAAAATGTTTTC
*
2262190 AAACACTATATATTATATTTTTTC-AAAATGTTTTC
1 AAA-ACTATATATTATATATTTTCAAAAATGTTTTC
*
2262225 AAAACTATATAGTATATATTTTCAAAA
1 AAAACTATATATTATATATTTTCAAAA
2262252 TTGATTTTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 25
0.81 0.05 0.13
Matches are distributed among these distances:
33 1 0.01
34 27 0.18
35 30 0.20
36 15 0.10
37 32 0.21
38 25 0.17
39 15 0.10
40 1 0.01
41 5 0.03
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (35 bp):
AAAACTATATATTATATATTTTCAAAAATGTTTTC
Found at i:2262134 original size:36 final size:36
Alignment explanation
Indices: 2262087--2262246 Score: 165
Period size: 35 Copynumber: 4.5 Consensus size: 36
2262077 TTCCAAATTA
*
2262087 TATATTATATATATTTTTTCAAAACATTTT-AAAAC
1 TATATTATATATATTTTTTCAAAATATTTTCAAAAC
2262122 TATTATTATATATA--TTTTCAAAA-ATGGTTTCAAAAAC
1 TA-TATTATATATATTTTTTCAAAATAT--TTTC-AAAAC
* *
2262159 TATA-TATTATATATATTTTCAAAATGTTTTCAAACAC
1 TATATTA-TATATATTTTTTCAAAATATTTTCAAA-AC
*
2262196 TATA-TAT-TATATTTTTTCAAAATGTTTTCAAAAC
1 TATATTATATATATTTTTTCAAAATATTTTCAAAAC
2262230 TATA-TAGTATATATTTT
1 TATATTA-TATATATTTT
2262247 CAAAATTGAT
Statistics
Matches: 111, Mismatches: 2, Indels: 23
0.82 0.01 0.17
Matches are distributed among these distances:
33 2 0.02
34 17 0.15
35 32 0.29
36 31 0.28
37 19 0.17
38 9 0.08
39 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (36 bp):
TATATTATATATATTTTTTCAAAATATTTTCAAAAC
Found at i:2263865 original size:22 final size:21
Alignment explanation
Indices: 2263819--2263891 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
2263809 TGTAAGGGAT
*
2263819 GTATCGATACC-TGTTGAGAGTG
1 GTATCGATACCTTGATG-GAG-G
2263841 GTATCGATACCTTGATGGATGG
1 GTATCGATACCTTGATGGA-GG
*
2263863 GTATCGGTACCTT-A-GG-GG
1 GTATCGATACCTTGATGGAGG
2263881 GTATCGATACC
1 GTATCGATACC
2263892 CTTAAAACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 12 0.26
20 2 0.04
21 1 0.02
22 26 0.57
23 5 0.11
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (21 bp):
GTATCGATACCTTGATGGAGG
Found at i:2264027 original size:21 final size:21
Alignment explanation
Indices: 2263987--2264040 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2263977 TACATGCGTC
2263987 GGTATCGATACCCCTGAGGGGT
1 GGTATCGATACCCCTGA-GGGT
* *
2264009 GGTATCGGTA-CCCTTAGGGT
1 GGTATCGATACCCCTGAGGGT
*
2264029 GGTACCGATACC
1 GGTATCGATACC
2264041 TCTAAGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.44
21 6 0.22
22 9 0.33
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (21 bp):
GGTATCGATACCCCTGAGGGT
Found at i:2264392 original size:21 final size:21
Alignment explanation
Indices: 2264351--2264400 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2264341 GTGTTATGAA
*
2264351 AATATGAACCTTGAATAAGTG
1 AATATGAACCTTGAACAAGTG
*
2264372 AATATGAA-CTTCGAACCAGTG
1 AATATGAACCTT-GAACAAGTG
*
2264393 AATGTGAA
1 AATATGAA
2264401 TATACTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (21 bp):
AATATGAACCTTGAACAAGTG
Found at i:2270487 original size:21 final size:22
Alignment explanation
Indices: 2270462--2270511 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2270452 ATGTTATGAA
2270462 AATATGAACCTT-GAACAAGTG
1 AATATGAACCTTCGAACAAGTG
* *
2270483 AATATG-ATCTTCGAACCAGTG
1 AATATGAACCTTCGAACAAGTG
*
2270504 AATGTGAA
1 AATATGAA
2270512 TATACTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (22 bp):
AATATGAACCTTCGAACAAGTG
Found at i:2270717 original size:23 final size:23
Alignment explanation
Indices: 2270691--2270761 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
2270681 GACAAATATA
2270691 TGGCACTTTGGTGCAACCCTATG
1 TGGCACTTTGGTGCAACCCTATG
**
2270714 TGGCACTTCAGTGCAACCCTATG
1 TGGCACTTTGGTGCAACCCTATG
* *
2270737 TGGTACTTTGGTGCAA-ACTATG
1 TGGCACTTTGGTGCAACCCTATG
2270759 TGG
1 TGG
2270762 TCATTCGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 8 0.19
23 34 0.81
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTTTGGTGCAACCCTATG
Found at i:2270801 original size:22 final size:22
Alignment explanation
Indices: 2270683--2270801 Score: 84
Period size: 23 Copynumber: 5.4 Consensus size: 22
2270673 TCCTCTGGGA
* *
2270683 CAAA-TATATGGCACTTTGGTG
1 CAAACTATGTGGCACTTCGGTG
* *
2270704 CAACCCTATGTGGCACTTCAGTG
1 CAA-ACTATGTGGCACTTCGGTG
* * *
2270727 CAACCCTATGTGGTACTTTGGTG
1 CAA-ACTATGTGGCACTTCGGTG
2270750 CAAACTATGTGGTCA-TTCGG-G
1 CAAACTATGTGG-CACTTCGGTG
*
2270771 -ACAATTATGTGGCACTTCGGTG
1 CA-AACTATGTGGCACTTCGGTG
* *
2270793 TAAATTATG
1 CAAACTATG
2270802 AGTTGTGGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
20 3 0.04
21 18 0.22
22 20 0.25
23 39 0.49
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (22 bp):
CAAACTATGTGGCACTTCGGTG
Found at i:2272082 original size:201 final size:201
Alignment explanation
Indices: 2271422--2272078 Score: 886
Period size: 201 Copynumber: 3.3 Consensus size: 201
2271412 GGGTGTTACA
* ** *
2271422 GCTACAATGCGGTTGATACACCCTCGAGCTGAATGGAATC-AACTCAAAAGTGGTCATTGAGAGA
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTTCATTGATAGA
* *
2271486 TAACCCTTATCGCATTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTATTGCTAAATCG
66 TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCG
* * *
2271551 CATCCAAACCGGGTCTTCTTCTGGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTTC
131 CATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
**
2271616 CTCTTT
196 CTCGCT
* *
2271622 GCTACAATGCGGTTGATACACCCTCAAGATT-AATGGAATCGAACTCGAAAGTCTTCATTGATAG
1 GCTACAATGCGGTTGATACACCCTCGAG-TTGAATGGAATCGAACTCAAAAGTCTTCATTGATAG
* * * * *
2271686 ATATCCTTTATCGCCTTGAGCTATGCTATGAATTTGGCTGGGATATAGTTCATTGTTTCTAAATC
65 ATAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATC
* * * * *
2271751 GCATCCAACCCGGGTCTTTTTTTCGACTTAAATACCTCAGTTTAAACTTCACCCGGAAAGTAGTT
130 GCATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTT
*
2271816 CCTTGCT
195 CCTCGCT
* * * * ** **
2271823 GCTACAATGCAGTTGATACACCATCGAGTTGAATGGAATCAAATTTGAAAGTCTTTGTTGATAGA
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTTCATTGATAGA
* * **
2271888 TAACCCTTATCTCCTTGAGCTATGCTGTGAATTTAGCTGAAATATAGTTCCTTGTTGCTAAATCG
66 TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCG
* ** * * *
2271953 CAGCCAACCCAAGTATTCTTCTAGACTTAAAGACCTCAATTTAAACTTCAACAGGAAAGTAGTTC
131 CATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
*
2272018 ATCGCT
196 CTCGCT
* *
2272024 ACTACAATACGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTT
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTT
2272079 TGTTAACAGA
Statistics
Matches: 393, Mismatches: 61, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
200 38 0.10
201 355 0.90
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (201 bp):
GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTTCATTGATAGA
TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTGTTGCTAAATCG
CATCCAACCCGGGTCTTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
CTCGCT
Found at i:2276948 original size:15 final size:16
Alignment explanation
Indices: 2276919--2276954 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2276909 ATAGAGTCAG
*
2276919 AAATGAAAATTATAAA
1 AAATGAAAATCATAAA
2276935 AAATG-AAATCATAAA
1 AAATGAAAATCATAAA
2276950 AAATG
1 AAATG
2276955 TTAGTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (16 bp):
AAATGAAAATCATAAA
Found at i:2277891 original size:54 final size:54
Alignment explanation
Indices: 2277792--2278181 Score: 520
Period size: 54 Copynumber: 7.3 Consensus size: 54
2277782 TTCCTTGTTT
* * *
2277792 TGCAC-CTATAGTGCC-AAATGGTTATTCATCCACGTTGGATGAATTCCGTGAAA
1 TGCACACT-TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
2277845 TGCACACTTAGTGCCGAGACGGTTATTCATCTATATAGGATGAATTCCGTGAAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * **
2277899 TGCACAATTAGTGTCGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
2277953 TGCACACTTAGTGCCGAAATGG-T-TTCATCCACATATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** *
2278005 TGCACACTTAGTTTCGAAACGGTTATTTCATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTA-TTCATCCACATAGGATGAATTCCGTGAAA
* * *
2278060 TGCACACTTAGTGCCGAAACGGTTATTTATCCACATATGATG-ATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* **
2278113 TGCACACTTAGTGCTGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
2278167 TGTACACTTAGTGCC
1 TGCACACTTAGTGCC
2278182 TATTTGATAA
Statistics
Matches: 293, Mismatches: 38, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
52 47 0.16
53 62 0.21
54 134 0.46
55 50 0.17
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:2277942 original size:108 final size:108
Alignment explanation
Indices: 2277813--2278181 Score: 548
Period size: 107 Copynumber: 3.4 Consensus size: 108
2277803 TGCCAAATGG
* * * *
2277813 TTATTCATCCACGTTGGATGAATTCCGTGAAATGCACACTTAGTGCCGAGACGGTTATTCATCTA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
* * * *
2277878 TATAGGATGAATTCCGTGAAGTGCACAATTAGTGTCGAAACAA
66 CATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAA
*
2277921 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAATGG-T-TTCATCCA
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
* **
2277984 CATATGATGAATTCCGTGAAATGCACACTTAGTTTCGAAACGG
66 CATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAA
* *
2278027 TTATTTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTATTTATCC
1 TTA-TTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCC
*
2278092 ACATATGATG-ATTCCATGAAATGCACACTTAGTG-CTGAAACAA
65 ACATATGATGAATTCCGTGAAATGCACACTTAGTGTC-GAAACAA
*
2278135 TTATTCATCCACATAGGATGAATTCCGTGAAATGTACACTTAGTGCC
1 TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCC
2278182 TATTTGATAA
Statistics
Matches: 236, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
106 46 0.19
107 93 0.39
108 81 0.34
109 16 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (108 bp):
TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCA
CATATGATGAATTCCGTGAAATGCACACTTAGTGTCGAAACAA
Found at i:2278542 original size:22 final size:22
Alignment explanation
Indices: 2278508--2278553 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2278498 TCAGTATCGA
*
2278508 TACCATACCATGGTATCGATAC
1 TACCATACCATGGTACCGATAC
* *
2278530 TACCATTCTATGGTACCGATAC
1 TACCATACCATGGTACCGATAC
2278552 TA
1 TA
2278554 TGCTATGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (22 bp):
TACCATACCATGGTACCGATAC
Done.