Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 22
Found at i:1187086 original size:95 final size:95
Alignment explanation
Indices: 1186871--1187133 Score: 357
Period size: 95 Copynumber: 2.7 Consensus size: 95
1186861 GGCTAGCTGG
* * **
1186871 ATCCATAAAGTTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACCCAATATTGT-TGTATAGAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTT-TAT-TAT--AT
1186935 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
1186969 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCGAGCTTTATTATATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATTA
* * *
1187034 TAATCACCTTTATCATGTTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
1187064 ATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATAT-T
1187129 ATAAT
65 ATAAT
1187134 ATTATAATCT
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
95 90 0.61
96 6 0.04
97 4 0.03
98 48 0.32
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:1190991 original size:38 final size:38
Alignment explanation
Indices: 1190915--1190996 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 38
1190905 AGAAGGGACG
* *
1190915 AAAAAGTGACAAAAATAAAGAAGATAAAAACAATTAAA
1 AAAAAGTGACAAAAATAAAAAAGACAAAAACAATTAAA
* *
1190953 AAAAAGTGATACAAATAACAAAAGACAATAAA-AA-TAAA
1 AAAAAGTGACAAAAATAA-AAAAGACAA-AAACAATTAAA
*
1190991 ATAAAG
1 AAAAAG
1190997 ATAAATATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
38 25 0.68
39 9 0.24
40 3 0.08
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (38 bp):
AAAAAGTGACAAAAATAAAAAAGACAAAAACAATTAAA
Found at i:1191172 original size:25 final size:27
Alignment explanation
Indices: 1191142--1191206 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
1191132 TAAGATAATA
1191142 AAATAAAAA-AATATAT-AAAACAAAG
1 AAATAAAAATAATATATGAAAACAAAG
*
1191167 ACATAAAAAATAATATATGAAAACAAAG
1 AAAT-AAAAATAATATATGAAAACAAAG
1191195 AAATAAAAATAA
1 AAATAAAAATAA
1191207 AACATTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 3 0.09
26 5 0.14
27 15 0.43
28 12 0.34
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.17
Consensus pattern (27 bp):
AAATAAAAATAATATATGAAAACAAAG
Found at i:1191176 original size:27 final size:28
Alignment explanation
Indices: 1191146--1191208 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
1191136 ATAATAAAAT
*
1191146 AAAAAAATATAT-AAAACAAAGACATAA
1 AAAAAAATATATGAAAACAAAGAAATAA
*
1191173 AAAATAATATATGAAAACAAAGAAATAA
1 AAAAAAATATATGAAAACAAAGAAATAA
1191201 AAATAAAA
1 AAA-AAAA
1191209 CATTCACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 11 0.35
28 17 0.55
29 3 0.10
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (28 bp):
AAAAAAATATATGAAAACAAAGAAATAA
Found at i:1191307 original size:2 final size:2
Alignment explanation
Indices: 1191296--1191326 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1191286 ATAAAAAAGA
*
1191296 AT AT AC 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
1191327 CGTTAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1191420 original size:22 final size:22
Alignment explanation
Indices: 1191392--1191443 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
1191382 TAAACAAGGT
*
1191392 ATAAAAAAATAATAAGTATTAA-A
1 ATAAAAAAATAA-AA-TAATAATA
1191415 ATAAAAAAATAAAATAATAATA
1 ATAAAAAAATAAAATAATAATA
1191437 ATAAAAA
1 ATAAAAA
1191444 GGATTAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 5 0.19
22 10 0.37
23 12 0.44
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
ATAAAAAAATAAAATAATAATA
Found at i:1192781 original size:14 final size:14
Alignment explanation
Indices: 1192762--1192788 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1192752 AAAGTTGTAT
1192762 TTTATGTTCGTTTG
1 TTTATGTTCGTTTG
1192776 TTTATGTTCGTTT
1 TTTATGTTCGTTT
1192789 ATCATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67
Consensus pattern (14 bp):
TTTATGTTCGTTTG
Found at i:1196216 original size:20 final size:20
Alignment explanation
Indices: 1196191--1196268 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
1196181 GCAGCTGGAA
* *
1196191 AACCGGTTTGACCGGTTTTG
1 AACCGGTTTGACCGATTTCG
*
1196211 AACCGGTTTGACCAATTTCG
1 AACCGGTTTGACCGATTTCG
1196231 AACCGGTTTGACCGATTTCG
1 AACCGGTTTGACCGATTTCG
*
1196251 -ACCGGTTCGAACCGATTT
1 AACCGGTTTG-ACCGATTT
1196269 GACCAGTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
19 8 0.15
20 44 0.85
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTTGACCGATTTCG
Found at i:1196220 original size:10 final size:9
Alignment explanation
Indices: 1196192--1196291 Score: 65
Period size: 10 Copynumber: 10.3 Consensus size: 9
1196182 CAGCTGGAAA
1196192 ACCGGTTTG
1 ACCGGTTTG
1196201 ACCGGTTTTG
1 ACCGG-TTTG
1196211 AACCGGTTTG
1 -ACCGGTTTG
**
1196221 ACCAATTTCG
1 ACCGGTTT-G
1196231 AACCGGTTTG
1 -ACCGGTTTG
*
1196241 ACCGATTTCG
1 ACCGGTTT-G
*
1196251 ACCGGTTCG
1 ACCGGTTTG
*
1196260 AACCGATTTG
1 -ACCGGTTTG
* *
1196270 ACCAGTCTG
1 ACCGGTTTG
*
1196279 AACCGGTCTG
1 -ACCGGTTTG
1196289 ACC
1 ACC
1196292 CGACCCGACC
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
9 28 0.39
10 32 0.45
11 11 0.15
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1199205 original size:18 final size:19
Alignment explanation
Indices: 1199168--1199205 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1199158 TTGAGCAGAC
* *
1199168 CGTTACTCAGACTCCTGTA
1 CGTTACTCAGACTACAGTA
1199187 CGTT-CTCAGACTACAGTA
1 CGTTACTCAGACTACAGTA
1199205 C
1 C
1199206 AGACTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.29
Consensus pattern (19 bp):
CGTTACTCAGACTACAGTA
Found at i:1212615 original size:18 final size:17
Alignment explanation
Indices: 1212582--1212616 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1212572 TGCTCCCACT
*
1212582 TGCACCGAAATTGCATG
1 TGCACCGAAATGGCATG
1212599 TGCACCGAAAATGGCATG
1 TGCACCG-AAATGGCATG
1212617 CAATTGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (17 bp):
TGCACCGAAATGGCATG
Found at i:1221285 original size:18 final size:17
Alignment explanation
Indices: 1221252--1221286 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1221242 TGCTCCCACT
*
1221252 TGCACCGAAATTGCATG
1 TGCACCGAAATGGCATG
1221269 TGCACCGAAAATGGCATG
1 TGCACCG-AAATGGCATG
1221287 CAATTGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (17 bp):
TGCACCGAAATGGCATG
Found at i:1223137 original size:26 final size:26
Alignment explanation
Indices: 1223069--1223143 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
1223059 ACATGAATTT
* *
1223069 TTTATGACATGCAATTATGTATCATAAA
1 TTTATGACATGCATTTATG-A-CACAAA
*** *
1223097 TTTATGACGCACATTTATGACACACA
1 TTTATGACATGCATTTATGACACAAA
1223123 TTTATGACATGCATTTATGAC
1 TTTATGACATGCATTTATGAC
1223144 GTTCATTGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 22 0.58
27 1 0.03
28 15 0.39
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (26 bp):
TTTATGACATGCATTTATGACACAAA
Found at i:1223150 original size:13 final size:13
Alignment explanation
Indices: 1223096--1223143 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
1223086 TGTATCATAA
*
1223096 ATTTATGACGCAC
1 ATTTATGACACAC
1223109 ATTTATGACACAC
1 ATTTATGACACAC
**
1223122 ATTTATGACATGC
1 ATTTATGACACAC
1223135 ATTTATGAC
1 ATTTATGAC
1223144 GTTCATTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:1223236 original size:85 final size:85
Alignment explanation
Indices: 1223122--1223372 Score: 274
Period size: 85 Copynumber: 3.0 Consensus size: 85
1223112 TATGACACAC
* *
1223122 ATTTATGACAT-GCATTTATGACGTT-CATTGTGCGTCATTGAAGCCCCCGTCATAAATAAAGAT
1 ATTTATGAC-TCGCATATATGAC-TTACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGAT
*
1223185 GACACACATTTGTGTGTTATAA
64 GACACACATTTGTGTGTCATAA
* * ** **
1223207 ATTTATGACTCGCATGTATGACTTACATTGAACGTCATTGAAGCCCCCGTCATAAATCTACTTGA
1 ATTTATGACTCGCATATATGACTTACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
* *
1223272 TATACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
* * * * * * * *
1223292 ATTTTTGACACACATATATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAA-AAAGACG
1 ATTTATGACTCGCATATATGACTTACATTGAGCGTCATTGAAGCCCCCGTCA-TAAATAAAGATG
*
1223356 ACACACATTCGTGTGTC
65 ACACACATTTGTGTGTC
1223373 GTGATTGTAT
Statistics
Matches: 136, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
84 3 0.02
85 129 0.95
86 4 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (85 bp):
ATTTATGACTCGCATATATGACTTACATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
CACACATTTGTGTGTCATAA
Found at i:1224883 original size:15 final size:15
Alignment explanation
Indices: 1224854--1224895 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1224844 TTGTATTAAG
*
1224854 AAAATTAAA-AAAAC
1 AAAATAAAACAAAAC
1224868 AAAATAAAACAAAAC
1 AAAATAAAACAAAAC
*
1224883 AAAAAAAAACAAA
1 AAAATAAAACAAA
1224896 TAGTACTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAATAAAACAAAAC
Found at i:1231636 original size:58 final size:59
Alignment explanation
Indices: 1231508--1231653 Score: 249
Period size: 58 Copynumber: 2.5 Consensus size: 59
1231498 AACTTTTTTT
* * *
1231508 AGAAACTACGTCTGATTTTCAGAGGTTTCCTAATAGAGTATTTTTAAGTGAGTTTTCAA
1 AGAAACTAAGTATGCTTTTCAGAGGTTTCCTAATAGAGTATTTTTAAGTGAGTTTTCAA
*
1231567 AGAAACTAAGTATGCTTTTCAGAGGTTTCCTAATAGAGTA-TTTTAATTGAGTTTTCAA
1 AGAAACTAAGTATGCTTTTCAGAGGTTTCCTAATAGAGTATTTTTAAGTGAGTTTTCAA
1231625 AGAAACTAAGTATGCTTTTCAGAGGTTTC
1 AGAAACTAAGTATGCTTTTCAGAGGTTTC
1231654 TAGACATGAT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 46 0.55
59 37 0.45
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (59 bp):
AGAAACTAAGTATGCTTTTCAGAGGTTTCCTAATAGAGTATTTTTAAGTGAGTTTTCAA
Found at i:1232579 original size:134 final size:133
Alignment explanation
Indices: 1232340--1234165 Score: 1991
Period size: 134 Copynumber: 13.5 Consensus size: 133
1232330 AAGCAAATCG
* * *
1232340 GCCTCAATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTC-CAAGATCTGGTTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCTC-AGATCTGATTTTCCCT
** * * *
1232404 CAAGAAGAAGTGGAATAGATCCCTGTCTTTCAAGATTTGATATTCCCTGAGTAACAGTAGAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1232469 GTCT
130 GTCT
* * * *
1232473 GCCTCGATTCAATCTTCCCTAAGTGACAGTGAAATGAATCAACGTCTCGAAATATGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCTC-AGATCTGATTTTCCCT
* * * *
1232538 CAAGAAAAAGTATAACAGATCCCTCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1232603 GTCT
130 GTCT
* ** * *
1232607 GCCTCGATTCAATCTTCCCTGAGTGATAGTGGAATGAATCAATATCCACAGATCTGATTTTCCTT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * *
1232672 CATGAAGAAGCATAATAGATACCC-CTCTTTCAAGATTTGGTATTCCCTGAGTAACAGTGGAACA
65 CAAGAAGAAGCAGAACAGAT-CCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
*
1232736 AGTTT
129 AGTCT
* * *
1232741 TCCTCGATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAATGTCCTCAGATCTGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * * * * * *
1232806 CAAGAAAAAGCAAAACATATTCCTATCTTTCAATATTTGATATTCCCTGAGTAACATTGGAATAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
*
1232871 GACT
130 GTCT
* * *
1232875 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTTCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * * ** * * * *
1232940 CAAAAAAAAG-TGAAACATATCATTTTCTTTCAAAATTTGATATTTCCTAAGTAACAGTGGAACA
65 CAAGAAGAAGCAG-AACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
*
1233004 AGTTT
129 AGTCT
* * * * *
1233009 GCCTCGATTCAATCTTCCATGAGTGACAGTGGAATGAATAAACATCCTCAAATCTTATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * * *
1233074 CAACAAGAAGCGGAATAGATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1233139 GTCT
130 GTCT
* * * * *
1233143 GGCTCGATTCAATCTTCCCTGAGTGACAATGGAATGAATCAACATCCCCATATCTGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* ** * * * *
1233208 CAAGAAAAAGTGGAACAAATCCCTCTCTTTTAAGATTTGATATTCCCTGAGTAATAGTAGAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1233273 GTCT
130 GTCT
* * * * *
1233277 ACCTCGATTCAATCTTCACTTAGTGAAAGTGGAATGAATCAACGTCTTCAGATCTAATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTC-TCAGATCTGATTTTCCCT
* *
1233342 CATGAAGAAGCAGAACA-ATTCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACA
65 CAAGAAGAAGCAGAACAGA-TCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
1233406 AGTCT
129 AGTCT
* * *
1233411 GCCTCGATTCAATCTTCCTTGAGTGATAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * * * ****
1233476 CAATAAAAATG--GAACAGATCCCTCTTTTTAAATATTTGATATTCCCTGAGTAACAACACAACA
65 CAAGAAGAA-GCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
1233539 AGTCT
129 AGTCT
* * * * *
1233544 ACCTTGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCTT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCCT
* * * * *
1233609 CAAGAAAAAGCAGAGCAGATCCCTCTCTTTCACGATTTGATATTTCCTGAGTAATAGTGGAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
1233674 GTCT
130 GTCT
* * *
1233678 GCCTTGATTCAATCTTCCCTGAAG-AACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCC
1 GCCTCGATTCAATCTTCCCTG-AGTGACAGTGGAATGAATCAACGTCTC-AGATCTGATTTTCCC
* * * *
1233742 TCAAGAAGAAGCAGAACAAATCCCTATCTTTCAAGATTTGATATTCCCTAAGTAACAGTAGAACA
64 TCAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACA
1233807 AGTCT
129 AGTCT
* * * * * *
1233812 TCCTTGATTCAATCTTCCCTAAGTAACAGTGAAATGAATCAACATCTTCAGATCTGATTTTCCCT
1 GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTC-TCAGATCTGATTTTCCCT
* *
1233877 CAAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGACTAATAGTGAAACAA
65 CAAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTG------AGT--AAC-A
1233942 GTCTGCCTGAAACAAGTCT
121 G--TG---G-AACAAGTCT
* * * * * *
1233961 GCCTCGATTCAATCTTCCCTGAAG-AATAGTGGAATGAATCAACATCCTCATATATTATTTTCCC
1 GCCTCGATTCAATCTTCCCTG-AGTGACAGTGGAATGAATCAACGT-CTCAGATCTGATTTTCCC
* * * * * *
1234025 TCAAGAAGAAGTAGAACAGATCCCTCAT-TTTCAAGATTAGATCTACCCTGAGTAACAATGTAAC
64 TCAAGAAGAAGCAGAACAGATCCCTC-TCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAC
* *
1234089 AAATTT
128 AAGTCT
* * * * *
1234095 GCCTCGATTCAATCTTCCCTGAAG-AACAGTGGAATTAGTCAATGTTTCTC-GATCTGATTTACC
1 GCCTCGATTCAATCTTCCCTG-AGTGACAGTGGAATGAATCAACG--TCTCAGATCTGATTTTCC
*
1234158 CTAAAGAA
63 CTCAAGAA
1234166 ACAGTGGAGC
Statistics
Matches: 1448, Mismatches: 208, Indels: 73
0.84 0.12 0.04
Matches are distributed among these distances:
132 1 0.00
133 165 0.11
134 1142 0.79
135 14 0.01
136 1 0.00
138 2 0.00
140 4 0.00
141 3 0.00
142 3 0.00
143 5 0.00
145 1 0.00
148 1 0.00
149 102 0.07
150 4 0.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (133 bp):
GCCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACGTCTCAGATCTGATTTTCCCTC
AAGAAGAAGCAGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
TCT
Found at i:1233954 original size:15 final size:15
Alignment explanation
Indices: 1233934--1233964 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1233924 TGACTAATAG
1233934 TGAAACAAGTCTGCC
1 TGAAACAAGTCTGCC
1233949 TGAAACAAGTCTGCC
1 TGAAACAAGTCTGCC
1233964 T
1 T
1233965 CGATTCAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (15 bp):
TGAAACAAGTCTGCC
Found at i:1234074 original size:149 final size:149
Alignment explanation
Indices: 1233803--1234075 Score: 388
Period size: 149 Copynumber: 1.8 Consensus size: 149
1233793 GTAACAGTAG
* * * *
1233803 AACAAGTCTTCCTTGATTCAATCTTCCCTAAGTAACAGTGAAATGAATCAACATCTTCAGATCTG
1 AACAAGTCTGCCTCGATTCAATCTTCCCTAAGTAACAGTGAAATGAATCAACATCCTCAGATATG
* * *
1233868 ATTTTCCCTCAAGAAGAAGCGGAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGACTAATA
66 ATTTTCCCTCAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTAGATATACCCTGACTAATA
1233933 GTGAAACAAGTCTGCCTGA
131 GTGAAACAAGTCTGCCTGA
* * *
1233952 AACAAGTCTGCCTCGATTCAATCTTCCCTGAAG-AATAGTGGAATGAATCAACATCCTCATATAT
1 AACAAGTCTGCCTCGATTCAATCTTCCCT-AAGTAACAGTGAAATGAATCAACATCCTCAGATAT
* * * *
1234016 TATTTTCCCTCAAGAAGAAGTAGAACAGATCCCTCAT-TTTCAAGATTAGATCTACCCTGA
65 GATTTTCCCTCAAGAAGAAGCAGAACAGATCCATC-TCTTTCAAGATTAGATATACCCTGA
1234076 GTAACAATGT
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
149 104 0.96
150 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (149 bp):
AACAAGTCTGCCTCGATTCAATCTTCCCTAAGTAACAGTGAAATGAATCAACATCCTCAGATATG
ATTTTCCCTCAAGAAGAAGCAGAACAGATCCATCTCTTTCAAGATTAGATATACCCTGACTAATA
GTGAAACAAGTCTGCCTGA
Found at i:1235261 original size:20 final size:20
Alignment explanation
Indices: 1235236--1235283 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1235226 TTAGGAACAC
*
1235236 GGTGGCCGGAGGCGACTTGA
1 GGTGGCCGGAGGCGACTCGA
1235256 GGTGGCCGGAGGCGACTCGA
1 GGTGGCCGGAGGCGACTCGA
1235276 GGTGGCCG
1 GGTGGCCG
1235284 ACAGTGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.23, G:0.52, T:0.12
Consensus pattern (20 bp):
GGTGGCCGGAGGCGACTCGA
Found at i:1243908 original size:20 final size:20
Alignment explanation
Indices: 1243881--1243952 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1243871 CGCAAATATA
1243881 TAAA-TCGCAACACGATTTC
1 TAAATTCGCAACACGATTTC
*
1243900 TAAATTCGCAACTCGATTTC
1 TAAATTCGCAACACGATTTC
* *
1243920 TGAATTCGCAACTCGATTT-
1 TAAATTCGCAACACGATTTC
*
1243939 TCGAATTCGCAACA
1 T-AAATTCGCAACA
1243953 TGAATTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.10
20 43 0.90
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (20 bp):
TAAATTCGCAACACGATTTC
Found at i:1244163 original size:16 final size:15
Alignment explanation
Indices: 1244128--1244166 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1244118 TCCCCATCTC
*
1244128 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1244143 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1244159 TAATTTTT
1 TAATTTTT
1244167 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1247262 original size:18 final size:18
Alignment explanation
Indices: 1247239--1247274 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1247229 AAGCAAAAGG
1247239 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
1247257 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
1247275 CAACTAGATT
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:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:1247559 original size:29 final size:29
Alignment explanation
Indices: 1247486--1247559 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
1247476 AATTCGCAAC
*
1247486 GCGAAAGTCAAATTCACGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCGTTGCGATTGTT
1247515 GCGAAAGTCAAATTCGCGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCGTTGCGATTGTT
1247544 GCGAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
1247560 AAATGCGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (29 bp):
GCGAAAGTCAAATTCGCGTTGCGATTGTT
Found at i:1247568 original size:20 final size:19
Alignment explanation
Indices: 1247543--1247608 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
1247533 TTGCGATTGT
1247543 TGCGAAAGTCAAATTCGAAA
1 TGCGAAAGTCAAATTC-AAA
*
1247563 TGCGAAAGTAAAATTCACAA
1 TGCGAAAGTCAAATTCA-AA
* * *
1247583 CGCGAAAATCAAATTCCCAA
1 TGCGAAAGTCAAATT-CAAA
1247603 TGCGAA
1 TGCGAA
1247609 TTTGACTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (19 bp):
TGCGAAAGTCAAATTCAAA
Found at i:1249123 original size:21 final size:21
Alignment explanation
Indices: 1249097--1249209 Score: 118
Period size: 21 Copynumber: 5.4 Consensus size: 21
1249087 GTGAATCGGG
*
1249097 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
1249118 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
1249139 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* ** * *
1249160 CTCTTGAACGATGATAAGAGC
1 CTCTTGAACGGTGGGAGGGGC
* * *
1249181 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
1249202 CTCTTGAA
1 CTCTTGAA
1249210 TGATGACAGG
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1249156 original size:42 final size:41
Alignment explanation
Indices: 1249097--1249219 Score: 165
Period size: 42 Copynumber: 2.9 Consensus size: 41
1249087 GTGAATCGGG
*
1249097 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAGGAGC
* *
1249139 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGATAAGAGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAGGAGC
* * *
1249181 CTCTTGAACGATAGGAGAGGCCTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGACAGG
1249220 TGAATCAGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.94
43 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAGGAGC
Found at i:1249598 original size:63 final size:63
Alignment explanation
Indices: 1249509--1249630 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
1249499 CGTAGAGCAG
* * *
1249509 CTACCTCATCACGTAAAGTAGATACCTCACCACGTAAAACACCATTGTCATCGCGTAAAACAT
1 CTACCTCACCACGTAAAGTAGATACCTCACCACGCAAAACACCATTGTCATCACGTAAAACAT
* * **
1249572 CTACCTCACCACGTAAAG-ACCG-TACCTCATCACGCCATGCACCATTGTCATCACGTAAA
1 CTACCTCACCACGTAAAGTA--GATACCTCACCACGCAAAACACCATTGTCATCACGTAAA
1249631 GTACCAACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.34, C:0.34, G:0.11, T:0.21
Consensus pattern (63 bp):
CTACCTCACCACGTAAAGTAGATACCTCACCACGCAAAACACCATTGTCATCACGTAAAACAT
Found at i:1249641 original size:63 final size:63
Alignment explanation
Indices: 1249548--1249668 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
1249538 CCACGTAAAA
* * * **
1249548 CACCATTGTCATCGCGTAAAACATCTACCTCACCACGTAAAG-ACCGTACCTCATCACGCCATG
1 CACCATTGTCATCACGTAAAACACCAACCTCACCACACAAAGCACCG-ACCTCATCACGCCATG
** * *
1249611 CACCATTGTCATCACGTAAAGTACCAACCTCATCACACAAAGCACTGACCTCATCACG
1 CACCATTGTCATCACGTAAAACACCAACCTCACCACACAAAGCACCGACCTCATCACG
1249669 TAACTCCCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
63 45 0.94
64 3 0.06
ACGTcount: A:0.32, C:0.36, G:0.12, T:0.20
Consensus pattern (63 bp):
CACCATTGTCATCACGTAAAACACCAACCTCACCACACAAAGCACCGACCTCATCACGCCATG
Found at i:1249643 original size:21 final size:21
Alignment explanation
Indices: 1249496--1249671 Score: 77
Period size: 21 Copynumber: 8.4 Consensus size: 21
1249486 TGAAACAATC
* * *
1249496 TCACGTAGAGCAGCTACCTCA
1 TCACGTAAAGCACCAACCTCA
* *
1249517 TCACGTAAAGTA-GATACCTCA
1 TCACGTAAAGCACCA-ACCTCA
* * ***
1249538 CCACGTAAAACACCATTGTCA
1 TCACGTAAAGCACCAACCTCA
* * * *
1249559 TCGCGTAAAACATCTACCTCA
1 TCACGTAAAGCACCAACCTCA
* *
1249580 CCACGTAAAG-ACCGTACCTCA
1 TCACGTAAAGCACC-AACCTCA
** * ***
1249601 TCACGCCATGCACCATTGTCA
1 TCACGTAAAGCACCAACCTCA
*
1249622 TCACGTAAAGTACCAACCTCA
1 TCACGTAAAGCACCAACCTCA
** **
1249643 TCACACAAAGCACTGACCTCA
1 TCACGTAAAGCACCAACCTCA
1249664 TCACGTAA
1 TCACGTAA
1249672 CTCCCCTAAC
Statistics
Matches: 107, Mismatches: 44, Indels: 8
0.67 0.28 0.05
Matches are distributed among these distances:
20 2 0.02
21 101 0.94
22 4 0.04
ACGTcount: A:0.34, C:0.34, G:0.12, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCAACCTCA
Found at i:1249866 original size:42 final size:42
Alignment explanation
Indices: 1249788--1249884 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
1249778 GATGGAATAA
* * * * *
1249788 GTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATCAG
1 GTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAG
* *
1249830 GTGATGGCTCTGGGTGTCGAGCTGTAGAATCAGCTCGATCAT
1 GTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAG
*
1249872 GTGATGACTCTCG
1 GTGATGGCTCTCG
1249885 AAGTGGGGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.30
Consensus pattern (42 bp):
GTGATGGCTCTCGGTGTCGAGCTGTAGAATCAGCTCGATCAG
Found at i:1251668 original size:22 final size:22
Alignment explanation
Indices: 1251641--1251742 Score: 159
Period size: 22 Copynumber: 4.6 Consensus size: 22
1251631 GATGGAGATA
1251641 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1251663 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1251685 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1251707 GACGGATGTCGCCAGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1251729 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1251743 TAGAGAGTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.20, C:0.19, G:0.44, T:0.18
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1260838 original size:2 final size:2
Alignment explanation
Indices: 1260831--1260872 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1260821 CACTTATGAT
1260831 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
1260873 CCGTCCATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1266710 original size:2 final size:2
Alignment explanation
Indices: 1266703--1266738 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1266693 ATTATTTTAG
1266703 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
1266739 ATTTATTAAT
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):
TA
Found at i:1267567 original size:26 final size:27
Alignment explanation
Indices: 1267529--1267580 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1267519 TAAGAGGTGA
1267529 AATTTTAAAATTTT-AAAGAA-AAAAG
1 AATTTTAAAATTTTAAAAGAACAAAAG
1267554 AATTTATAAAATTTTAAAAGAACAAAA
1 AATTT-TAAAATTTTAAAAGAACAAAA
1267581 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 5 0.21
26 9 0.38
27 6 0.25
28 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
AATTTTAAAATTTTAAAAGAACAAAAG
Found at i:1274540 original size:14 final size:15
Alignment explanation
Indices: 1274521--1274549 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1274511 TGAATAATTT
1274521 TAAAATAT-AATGAC
1 TAAAATATGAATGAC
1274535 TAAAATATGAATGAC
1 TAAAATATGAATGAC
1274550 ACGAAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.28
Consensus pattern (15 bp):
TAAAATATGAATGAC
Found at i:1276391 original size:20 final size:20
Alignment explanation
Indices: 1276368--1276429 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1276358 AGGGGGAACA
1276368 GATTCCCCCTGGGGGGTATC
1 GATTCCCCCTGGGGGGTATC
*
1276388 GATT-CCCC----GGG-AAC
1 GATTCCCCCTGGGGGGTATC
1276402 AGATTCCCCCTGGGGGGTATC
1 -GATTCCCCCTGGGGGGTATC
1276423 GATTCCC
1 GATTCCC
1276430 TCCTAAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 4 0.12
19 4 0.12
20 14 0.42
21 2 0.06
ACGTcount: A:0.15, C:0.32, G:0.31, T:0.23
Consensus pattern (20 bp):
GATTCCCCCTGGGGGGTATC
Found at i:1276407 original size:35 final size:35
Alignment explanation
Indices: 1276361--1276429 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
1276351 TATGTGCAGG
1276361 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1276396 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCC
1276430 TCCTAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:1277181 original size:31 final size:31
Alignment explanation
Indices: 1276995--1277168 Score: 303
Period size: 31 Copynumber: 5.6 Consensus size: 31
1276985 AGGGTCGAGG
*
1276995 GTTTACCTATGTTCTCCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1277026 GCTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1277057 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1277088 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1277119 GTTTACTTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1277150 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
1277169 AATCTATAGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 136 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1286112 original size:55 final size:56
Alignment explanation
Indices: 1285997--1286140 Score: 199
Period size: 55 Copynumber: 2.6 Consensus size: 56
1285987 ATTGTATGAG
*
1285997 TGTGTATC-GCTACACTGAGGAGTGT-TCGATACCCTCAAAATATCGAATGTTGTTT
1 TGTGTATCAG-TACACTGAGGAGTGTATCGATACCCTCAAAATATCGAATGTTCTTT
* * *
1286052 T-TGTATCAGTACACTGATGAGTGTATCGATACCCTTAAAATATTG-A-GTTCTATT
1 TGTGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAATATCGAATGTTCT-TT
1286106 TGTGTATCAGTACACTGAGGAGTGTATCGATACCC
1 TGTGTATCAGTACACTGAGGAGTGTATCGATACCC
1286141 CCAAGTATGA
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
53 4 0.05
54 24 0.30
55 52 0.65
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (56 bp):
TGTGTATCAGTACACTGAGGAGTGTATCGATACCCTCAAAATATCGAATGTTCTTT
Found at i:1286888 original size:21 final size:21
Alignment explanation
Indices: 1286862--1286918 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1286852 GTCGAGGGTC
*
1286862 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTTCGGGACAAT
*
1286883 TATGTGGTCCTCCGGGACAAT
1 TATGTGGTCCTTCGGGACAAT
1286904 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
1286919 TGTAACCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAT
Found at i:1286934 original size:23 final size:23
Alignment explanation
Indices: 1286904--1286969 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
1286894 CCGGGACAAT
*
1286904 TATGTGGCACTTCGGTGTAACCC
1 TATGTGGCACTTCGGTGCAACCC
*
1286927 TATGTGGCACTTCAGTGCAACCC
1 TATGTGGCACTTCGGTGCAACCC
1286950 TATGTGGCACTTCGGTGCAA
1 TATGTGGCACTTCGGTGCAA
1286970 ACTATATGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAACCC
Found at i:1291896 original size:55 final size:55
Alignment explanation
Indices: 1291816--1291956 Score: 228
Period size: 55 Copynumber: 2.6 Consensus size: 55
1291806 TATGAGTGTG
* * *
1291816 TATCGGTACACTGAGGAGTATATCGATACCCTCAAAATATTGAATGCTATTTGTA
1 TATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCTATTTGTA
* * *
1291871 TATCGGTACACTGAGAAGTGTATCGATACCCTCAAAACATCGAGTGCTATTTGTG
1 TATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCTATTTGTA
1291926 TATCGGTACACTGAGGAGTGTATCGATACCC
1 TATCGGTACACTGAGGAGTGTATCGATACCC
1291957 CCAAGTATGA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (55 bp):
TATCGGTACACTGAGGAGTGTATCGATACCCTCAAAACATCGAATGCTATTTGTA
Found at i:1292704 original size:21 final size:21
Alignment explanation
Indices: 1292677--1292732 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1292667 AGTCGATGGT
*
1292677 CTATGTGGTCCTTCGGGATAA
1 CTATGTGGTCCTTCGGGACAA
* *
1292698 TTATGTGGTCCTCCGGGACAA
1 CTATGTGGTCCTTCGGGACAA
*
1292719 CTATGTGGTACTTC
1 CTATGTGGTCCTTC
1292733 AGTGCAACCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (21 bp):
CTATGTGGTCCTTCGGGACAA
Found at i:1298233 original size:26 final size:26
Alignment explanation
Indices: 1298189--1298243 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
1298179 AATTTGAAGC
1298189 AAACATCGACGATGAATCCT-AAGGTG
1 AAACATCGACGATGAATCCTGAA-GTG
*
1298215 AAACATCGAC-AGTGGATCCTGAAGTG
1 AAACATCGACGA-TGAATCCTGAAGTG
1298241 AAA
1 AAA
1298244 GATGAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 1 0.04
26 23 0.88
27 2 0.08
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (26 bp):
AAACATCGACGATGAATCCTGAAGTG
Found at i:1299083 original size:36 final size:32
Alignment explanation
Indices: 1299005--1299090 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 32
1298995 GGTTGAGCTT
* *
1299005 AACCTAAAATGTTAATCTTTTAACATTTTTGC
1 AACCGAAAATGTTAATCTTTTAACATTTTAGC
* *
1299037 AACCTAAAATGTTAATTTTTTAACATTTCCAATAGC
1 AACCGAAAATGTTAATCTTTTAACATTT----TAGC
*
1299073 AACCGGAAATGTT-ATCTT
1 AACCGAAAATGTTAATCTT
1299091 CTTCATAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 27 0.60
35 4 0.09
36 14 0.31
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (32 bp):
AACCGAAAATGTTAATCTTTTAACATTTTAGC
Found at i:1299159 original size:34 final size:36
Alignment explanation
Indices: 1299117--1299183 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1299107 ATTACAACCC
1299117 GAAATGTTA-AAAAA-TTAACATTTTAGGTTGCTCG
1 GAAATGTTACAAAAATTTAACATTTTAGGTTGCTCG
*
1299151 GAAATGTTACAAAAATTTAACATTTTCGGTTGC
1 GAAATGTTACAAAAATTTAACATTTTAGGTTGC
1299184 ACCTTTCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 9 0.30
35 5 0.17
36 16 0.53
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (36 bp):
GAAATGTTACAAAAATTTAACATTTTAGGTTGCTCG
Found at i:1311455 original size:20 final size:17
Alignment explanation
Indices: 1311430--1311468 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1311420 TTTTTTCTTC
1311430 ATTTATTTA--TCAAAT
1 ATTTATTTATTTCAAAT
1311445 AATTTATTTATTTCAAAT
1 -ATTTATTTATTTCAAAT
1311463 ATTTAT
1 ATTTAT
1311469 ATCATGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 6 0.29
18 6 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTTATTTCAAAT
Found at i:1311550 original size:16 final size:18
Alignment explanation
Indices: 1311515--1311552 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1311505 ATTTAAAAAA
1311515 TAAATTTATAATCCATCAT
1 TAAATTTATAAT-CATCAT
1311534 TAAATTTA-AAT-ATCAT
1 TAAATTTATAATCATCAT
1311550 TAA
1 TAA
1311553 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTATAATCATCAT
Found at i:1314483 original size:15 final size:15
Alignment explanation
Indices: 1314463--1314507 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1314453 TGTCCAATTA
*
1314463 CCGAGTTAACTCAGT
1 CCGAGTCAACTCAGT
*
1314478 CCGAGTCAA-TCCGT
1 CCGAGTCAACTCAGT
*
1314492 CTGAGTCAACTCAGT
1 CCGAGTCAACTCAGT
1314507 C
1 C
1314508 TTAGTTAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (15 bp):
CCGAGTCAACTCAGT
Found at i:1315839 original size:3 final size:3
Alignment explanation
Indices: 1315833--1315879 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1315823 ATTTTAATTT
1315833 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1315880 GGTTGAAAAG
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1316287 original size:117 final size:117
Alignment explanation
Indices: 1316134--1316718 Score: 764
Period size: 117 Copynumber: 5.0 Consensus size: 117
1316124 GTGTTGATGA
* * * * * * * * *
1316134 TGATCCAACTCCTTATATGATGGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAATTTT
1 TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* *
1316199 TTCTCCCTAATCGGATGAGTTCTTCTCATTATGATCTCTCCACTGGAAATGT
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
* *
1316251 TGATCCACCTCATTCTGTGATGAAATCAAACCAAGGTTGAACAAGTTTTTCTCATTATGAACTTC
1 TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * * *
1316316 TTCTCCCTCATCGTATAAGTTCTTCTCATTATGAACTATCCATTGGAAATGT
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
1316368 TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTG---AAGTTCTTCTCATTATGAACTTC
1 TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
** * *
1316430 TTCTCCCTCATCGGATGAACTCTTCTCATTACGAACTCTCCACTTGAAATGT
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
* * * * * *
1316482 TGATCCACCTCTTTCTGTGATGGAATCAAACAAAGGATGAACAAGTTCTTCTCATTATGAACTTA
1 TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
* * ** * *
1316547 GTATCCCTCATCAAATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATAT
66 TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
* * * * *
1316599 TGATCCACCCCCTTCTATGATGGAAT-AGAACCAAAGTTGAACAAGTTCTTCTCATTGTGAACTT
1 TGATCCACCTCATTCTATGATGAAATCA-AACCAAGGTTGAACAAGTTCTTCTCATTATGAACTT
* * *
1316663 CTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGT
65 CTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
1316716 TGA
1 TGA
1316719 CTGGTTTATC
Statistics
Matches: 408, Mismatches: 56, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
114 100 0.25
116 1 0.00
117 307 0.75
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (117 bp):
TGATCCACCTCATTCTATGATGAAATCAAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTC
TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGT
Found at i:1316436 original size:231 final size:232
Alignment explanation
Indices: 1316176--1316718 Score: 775
Period size: 231 Copynumber: 2.3 Consensus size: 232
1316166 AAGGTTGAAC
* * * *
1316176 AAGTTCTTCTCATTATGAATTTTTTCTCCCTAATCGGATGAGTTCTTCTCATTATGATCTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* * * *
1316241 CTGGAAATGTTGATCCACCTCATTCTGTGATGAAATCAAACCAAGGTTGAACAAGTTTTTCTCAT
66 CTTGAAATGTTGATCCACCTCATTCTGTGATGAAATCAAACAAAGGATGAACAAGTTCTTCTCAT
** * ** * * *
1316306 TATGAACTTCTTCTCCCTCATCGTATAAGTTCTTCTCATTATGAACTATCCATTGGAAATGTTGA
131 TATGAACTTAGTATCCCTCATCAAATAAGTTCTTCTCATTATGAACTATCCACTAGAAATATTGA
* *
1316371 TCCACCTCATTCTATGATGAAATCA-AACCAAGGTTG-
196 TCCACCCCATTCTATGATGAAAT-AGAACCAAAGTTGA
** *
1316407 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAACTCTTCTCATTACGAACTCTCCA
1 AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
* *
1316472 CTTGAAATGTTGATCCACCTCTTTCTGTGATGGAATCAAACAAAGGATGAACAAGTTCTTCTCAT
66 CTTGAAATGTTGATCCACCTCATTCTGTGATGAAATCAAACAAAGGATGAACAAGTTCTTCTCAT
* *
1316537 TATGAACTTAGTATCCCTCATCAAATGAGTTCTTCTCATTATGAACTCTCCACTAGAAATATTGA
131 TATGAACTTAGTATCCCTCATCAAATAAGTTCTTCTCATTATGAACTATCCACTAGAAATATTGA
* *
1316602 TCCACCCCCTTCTATGATGGAATAGAACCAAAGTTGAA
196 TCCACCCCATTCTATGATGAAATAGAACCAAAGTTG-A
* *
1316640 CAAGTTCTTCTCATTGTGAACTTCTTCTCCCTCATCAGATGAGTTCTTCTCATTATGAACTCTCC
1 -AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCC
*
1316705 ATTTGAAATGTTGA
65 ACTTGAAATGTTGA
1316719 CTGGTTTATC
Statistics
Matches: 275, Mismatches: 33, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
230 1 0.00
231 202 0.73
234 72 0.26
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (232 bp):
AAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCA
CTTGAAATGTTGATCCACCTCATTCTGTGATGAAATCAAACAAAGGATGAACAAGTTCTTCTCAT
TATGAACTTAGTATCCCTCATCAAATAAGTTCTTCTCATTATGAACTATCCACTAGAAATATTGA
TCCACCCCATTCTATGATGAAATAGAACCAAAGTTGA
Found at i:1317180 original size:37 final size:36
Alignment explanation
Indices: 1317114--1317197 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
1317104 TTTTGGAAAC
* * * *
1317114 AATCCTAAGAATGATTCAAACGACATTCTAGACAAAT
1 AATCCTAAGAATGACTCAAACAAAATTCTA-AAAAAT
1317151 AATCCTAAGAATGACTCAAA-AAAATTTCTAAAAAAT
1 AATCCTAAGAATGACTCAAACAAAA-TTCTAAAAAAT
*
1317187 GATCCTAAGAA
1 AATCCTAAGAA
1317198 GGGAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 17 0.41
37 24 0.59
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (36 bp):
AATCCTAAGAATGACTCAAACAAAATTCTAAAAAAT
Found at i:1318463 original size:235 final size:238
Alignment explanation
Indices: 1317956--1318451 Score: 648
Period size: 235 Copynumber: 2.1 Consensus size: 238
1317946 TAACTGTATA
* *
1317956 TTAC-GAT-GCCCAAAGGACTTACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTAAAAA
1 TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTAAAAA
* *
1318019 AATAAATTTCAAAAAAAGATTTAAATAATAAAATTTGGAAATCGCTTTCTCGTTTTTCAAAAATC
66 AATAAATTT-AAAAAAAGATTTAAATAATAAAATTTGGAAATCACTTTCTCGTTTTTCAAAAATA
* * ** * *
1318084 ATGTGCAAACATCCTACCCGAAGGTCTCATAGATGGCCTGAAGGGCTTATTATCTTGCTCGAAAG
130 ATGTGAAAACATCATACCCGAAGGTCTCATAGATGGCCTGAAGAACTTATCATCTTGCTCAAAAG
*
1318149 GCTTATAGATGACCCAAAGGATTTAAGCATCATGATTAAAAGAC
195 GCTTATAGATGACCCAAAGGATTTAAGCATCATGATCAAAAGAC
* * *
1318193 TTACTGATGGCTCGAAAGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTT-TAAA
1 TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTAAAAA
* * ** * **
1318257 AA-AAA-TT-AGAAAATATTTAAATGAA-AAGTTTTGGAAATCACTTTCTCATTTTTTTGAAAAT
66 AATAAATTTAAAAAAAGATTTAAAT-AATAAAATTTGGAAATCACTTTCTC-GTTTTTCAAAAAT
* *
1318318 AATGTGAAAACATCATACCCGAAGGTCTTATAGATGG-CTCGAATAACTTATCATCTTGCTCAAA
129 AATGTGAAAACATCATACCCGAAGGTCTCATAGATGGCCT-GAAGAACTTATCATCTTGCTCAAA
* ** *
1318382 AGGCTTATAGATGACCCAAAGGATTTAAGCATCATGCTCCGAATAC
193 AGGCTTATAGATGACCCAAAGGATTTAAGCATCATGATCAAAAGAC
*
1318428 TTACTGATGGCCCGAGGGACTTAC
1 TTACTGATGGCCCGAAGGACTTAC
1318452 CAATCAAGAA
Statistics
Matches: 224, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
234 34 0.15
235 126 0.56
236 2 0.01
237 7 0.03
238 8 0.04
239 47 0.21
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (238 bp):
TTACTGATGGCCCGAAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTAAAAA
AATAAATTTAAAAAAAGATTTAAATAATAAAATTTGGAAATCACTTTCTCGTTTTTCAAAAATAA
TGTGAAAACATCATACCCGAAGGTCTCATAGATGGCCTGAAGAACTTATCATCTTGCTCAAAAGG
CTTATAGATGACCCAAAGGATTTAAGCATCATGATCAAAAGAC
Found at i:1318658 original size:56 final size:58
Alignment explanation
Indices: 1318585--1318740 Score: 158
Period size: 59 Copynumber: 2.7 Consensus size: 58
1318575 GGGAAATCAT
* *
1318585 CAAGAAACTTCTGAAAATCAGAAT-TAGCTTC-T-AAAATTCATTTGAAAATA-TCATAC
1 CAAGAAACCTCTGAAAATCAG-ATCTAGCTTCTTAAAAATTC-TTTGAAAAAAGTCATAC
* * * *
1318641 CAAGAAACCTCTAAAAATCAGATCTAGTTTCTTTAAAAATTCTTTTAAAAAAGTCATAT
1 CAAGAAACCTCTGAAAATCAGATCTAGCTTC-TTAAAAATTCTTTGAAAAAAGTCATAC
* * * * *
1318700 TAAGAAACCTCTGAAAATCAAACCTAGTTTCTTTAAAATTC
1 CAAGAAACCTCTGAAAATCAGATCTAGCTTCTTAAAAATTC
1318741 ATATCGATTG
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
55 2 0.02
56 25 0.30
58 18 0.21
59 39 0.46
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (58 bp):
CAAGAAACCTCTGAAAATCAGATCTAGCTTCTTAAAAATTCTTTGAAAAAAGTCATAC
Found at i:1320101 original size:28 final size:28
Alignment explanation
Indices: 1320038--1320101 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1320028 GATATAGGGC
*
1320038 TTAGGTTAATTTGGGAAGGTAGAGTGTT
1 TTAGGTTGATTTGGGAAGGTAGAGTGTT
* * *
1320066 TCAAGTTGATTTGGGGAGGTA-ATGTGTT
1 TTAGGTTGATTTGGGAAGGTAGA-GTGTT
1320094 TTAGGTTG
1 TTAGGTTG
1320102 GCTTCTTTGG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.22, C:0.02, G:0.36, T:0.41
Consensus pattern (28 bp):
TTAGGTTGATTTGGGAAGGTAGAGTGTT
Found at i:1320773 original size:10 final size:10
Alignment explanation
Indices: 1320760--1320822 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 10
1320750 TTTCCTTTTT
*
1320760 TTTCCCTTTC
1 TTTCTCTTTC
*
1320770 TTTCTCTCTC
1 TTTCTCTTTC
* *
1320780 TCTCTCTCTC
1 TTTCTCTTTC
*
1320790 TCTCTCTTTC
1 TTTCTCTTTC
1320800 TTTCTC-TTC
1 TTTCTCTTTC
*
1320809 TTTCAC-TTC
1 TTTCTCTTTC
1320818 TTTCT
1 TTTCT
1320823 TTCTTTTCTC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 15 0.33
10 31 0.67
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTCTCTTTC
Found at i:1320777 original size:2 final size:2
Alignment explanation
Indices: 1320772--1320806 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1320762 TCCCTTTCTT
* *
1320772 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1320807 TCTTTCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (2 bp):
TC
Found at i:1320819 original size:22 final size:22
Alignment explanation
Indices: 1320767--1320832 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 22
1320757 TTTTTTCCCT
*
1320767 TTCTTTCTCTCTCTCTCTCTCTCTC
1 TTCTTTCT-T-TCTCT-TCTCTCAC
*
1320792 TCTCTTTCTTTCTCTTCTTTCAC
1 T-TCTTTCTTTCTCTTCTCTCAC
*
1320815 TTCTTTCTTTCTTTTCTC
1 TTCTTTCTTTCTCTTCTC
1320833 ACGTTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 15 0.42
23 7 0.19
24 5 0.14
25 2 0.06
26 7 0.19
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (22 bp):
TTCTTTCTTTCTCTTCTCTCAC
Found at i:1321120 original size:2 final size:2
Alignment explanation
Indices: 1321113--1321140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1321103 ACAAAAAGGG
1321113 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
1321141 CTTTTTTATA
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:1326143 original size:18 final size:19
Alignment explanation
Indices: 1326112--1326147 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1326102 GGTTTTGGTT
*
1326112 TGGGTATTGGGTTTGTAAA
1 TGGGTATTGAGTTTGTAAA
1326131 TGGGT-TTGAGTTTGTAA
1 TGGGTATTGAGTTTGTAA
1326148 TAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.44
Consensus pattern (19 bp):
TGGGTATTGAGTTTGTAAA
Found at i:1326166 original size:3 final size:3
Alignment explanation
Indices: 1326158--1326215 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
1326148 TAAATAAATA
*
1326158 AAT AAT AAT -TT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1326204 AGT AAT AAT AAT
1 AAT AAT AAT AAT
1326216 GGTTGAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 3 0.06
3 46 0.94
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1326577 original size:19 final size:20
Alignment explanation
Indices: 1326545--1326604 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1326535 TGACATATAT
*
1326545 TATTTTATTATTTTATATGA
1 TATTTTAATATTTTATATGA
* *
1326565 TA-TTTCATATTTT-TATTAA
1 TATTTTAATATTTTATA-TGA
*
1326584 TATTTTAATATTATATATGA
1 TATTTTAATATTTTATATGA
1326604 T
1 T
1326605 TATAATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 14 0.45
21 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTTAATATTTTATATGA
Found at i:1326720 original size:26 final size:26
Alignment explanation
Indices: 1326685--1326759 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
1326675 AAATCAATAA
1326685 TCTCAAGGCAACACCTTCTTCTCATC
1 TCTCAAGGCAACACCTTCTTCTCATC
*
1326711 TCTCACGGCAACACCTTCTTCTCATC
1 TCTCAAGGCAACACCTTCTTCTCATC
*
1326737 TCTCATGGCAACACCTTC-TCTCA
1 TCTCAAGGCAACACCTTCTTCTCA
1326760 AGTTATTCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 5 0.11
26 42 0.89
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (26 bp):
TCTCAAGGCAACACCTTCTTCTCATC
Found at i:1333774 original size:23 final size:23
Alignment explanation
Indices: 1333729--1333777 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1333719 ATAAAGAACC
*
1333729 AAAATAAACTTAAATATATCATT
1 AAAATAAACTTAAATACATCATT
*
1333752 AAAATAAAGTTAAA-ACATCCATT
1 AAAATAAACTTAAATACAT-CATT
1333775 AAA
1 AAA
1333778 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTTAAATACATCATT
Found at i:1339384 original size:23 final size:23
Alignment explanation
Indices: 1339340--1339388 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1339330 ATAAAGAACC
*
1339340 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
1339363 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
1339386 AAA
1 AAA
1339389 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:1343292 original size:18 final size:16
Alignment explanation
Indices: 1343264--1343303 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 16
1343254 TTAAATCTTT
1343264 TTTTCTTTCGGTTCGTCTC
1 TTTT-TTTCGGTT-GT-TC
1343283 TTTTTTTCGGTTGTTC
1 TTTTTTTCGGTTGTTC
1343299 TTTTT
1 TTTTT
1343304 CCTCCCCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 8 0.38
19 4 0.19
ACGTcount: A:0.00, C:0.17, G:0.15, T:0.68
Consensus pattern (16 bp):
TTTTTTTCGGTTGTTC
Found at i:1344062 original size:18 final size:19
Alignment explanation
Indices: 1344026--1344068 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1344016 TTTAATATTT
1344026 AAAAATAATTAAGAATATA
1 AAAAATAATTAAGAATATA
* *
1344045 AGAAATTATTAA-AATATA
1 AAAAATAATTAAGAATATA
1344063 AAAAAT
1 AAAAAT
1344069 GTTAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATAATTAAGAATATA
Found at i:1344160 original size:24 final size:22
Alignment explanation
Indices: 1344123--1344180 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1344113 AAAAAGGAGT
**
1344123 AAAATTATGGAATTGAAAATATTA
1 AAAATTATTAAATT-AAAA-ATTA
*
1344147 AAAATTATTAAATTATAAATTA
1 AAAATTATTAAATTAAAAATTA
*
1344169 TAAATTATTAAA
1 AAAATTATTAAA
1344181 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 15 0.50
23 3 0.10
24 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
AAAATTATTAAATTAAAAATTA
Found at i:1344180 original size:15 final size:14
Alignment explanation
Indices: 1344143--1344176 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1344133 AATTGAAAAT
*
1344143 ATTAAAAATTATTAA
1 ATTATAAATTA-TAA
1344158 ATTATAAATTATAA
1 ATTATAAATTATAA
1344172 ATTAT
1 ATTAT
1344177 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATAAATTATAA
Found at i:1344190 original size:7 final size:7
Alignment explanation
Indices: 1344143--1344176 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1344133 AATTGAAAAT
*
1344143 ATTAAAA
1 ATTATAA
1344150 ATTATTAA
1 ATTA-TAA
1344158 ATTATAA
1 ATTATAA
1344165 ATTATAA
1 ATTATAA
1344172 ATTAT
1 ATTAT
1344177 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTATAA
Found at i:1347809 original size:6 final size:6
Alignment explanation
Indices: 1347800--1347836 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1347790 CGCCGCCGTC
1347800 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1347837 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1347970 original size:21 final size:21
Alignment explanation
Indices: 1347945--1348015 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
1347935 AATTTGGAAA
1347945 ATCGCAACGACACTGTACACT
1 ATCGCAACGACACTGTACACT
* * *
1347966 ATCGCAATGCGAGA-TGGA-A-A
1 ATCGCAA--CGACACTGTACACT
*
1347986 ATCGCAATGACACTGTACACT
1 ATCGCAACGACACTGTACACT
1348007 ATCGCAACG
1 ATCGCAACG
1348016 CGATTTTCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 8 0.22
21 16 0.43
22 3 0.08
23 4 0.11
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGACACTGTACACT
Found at i:1347985 original size:41 final size:41
Alignment explanation
Indices: 1347939--1348018 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
1347929 ACGACGAATT
*
1347939 TGGAAAATCGCAACGACACTGTACACTATCGCAATGCGAGA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAGA
*
1347980 TGGAAAATCGCAATGACACTGTACACTATCGCAACGCGA
1 TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGA
1348019 TTTTCAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGACACTGTACACTATCGCAACGCGAGA
Found at i:1348045 original size:62 final size:62
Alignment explanation
Indices: 1347963--1348238 Score: 306
Period size: 62 Copynumber: 4.3 Consensus size: 62
1347953 GACACTGTAC
* * *
1347963 ACTATCGCAATGCGAGATGGAAAATCGCAATGACACTGTACACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
1348025 ACTATCGCAACGCGAAATGGAAAATCGCAACGATCGCAATGACACTGTACACTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGC-A--A---C---GACACTGTACACTATCGCAACGCGA
1348090 TTTTCA
57 TTTTCA
* ** **
1348096 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
* * ** *
1348158 A-AATCGCAA--CGACACTGTAGACTATCGCAACGACACTGTAGACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGA-AATG--GAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
1348220 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
1348239 CAACGCGAAT
Statistics
Matches: 181, Mismatches: 18, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
59 3 0.02
60 3 0.02
61 7 0.04
62 91 0.50
63 8 0.04
64 3 0.02
65 5 0.03
68 1 0.01
70 1 0.01
71 59 0.33
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTACACTATCGCAACGCGATTTTCA
Found at i:1348102 original size:71 final size:71
Alignment explanation
Indices: 1347986--1348128 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
1347976 GAGATGGAAA
1347986 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1348051 GCAACG
66 GCAACG
1348057 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1 ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
1348122 GCAACG
66 GCAACG
1348128 A
1 A
1348129 CACTGTAGAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (71 bp):
ATCGCAATGACACTGTACACTATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATC
GCAACG
Found at i:1348124 original size:20 final size:20
Alignment explanation
Indices: 1348099--1348168 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1348089 ATTTTCAACT
1348099 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
1348119 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
1348140 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1348160 ATCGCAACG
1 ATCGCAACG
1348169 ACACTGTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 18 0.46
21 9 0.23
22 3 0.08
23 3 0.08
ACGTcount: A:0.40, C:0.24, G:0.23, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1348125 original size:41 final size:41
Alignment explanation
Indices: 1348096--1348189 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1348086 GCGATTTTCA
1348096 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1348137 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1348178 ACTATCGCAACG
1 ACTATCGCAACG
1348190 ACACTGTAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:1348145 original size:21 final size:21
Alignment explanation
Indices: 1348119--1348210 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
1348109 GAAATGGAAA
1348119 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
1348140 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
1348160 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1348181 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
1348202 ATCGCAACG
1 ATCGCAACG
1348211 CGATTTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.05
20 12 0.20
21 42 0.70
22 3 0.05
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:1348242 original size:21 final size:21
Alignment explanation
Indices: 1348075--1348242 Score: 82
Period size: 21 Copynumber: 8.1 Consensus size: 21
1348065 GACACTGTAC
** *
1348075 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
1348096 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
1348117 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
*
1348136 GACTATCGCAACGCGAAATGGA
1 -ACTATCGCAACGCGAAATGCA
* * *
1348158 A-AATCGCAA--CGACACTGTA
1 ACTATCGCAACGCGA-AATGCA
* *
1348177 GACTATCGCAA--CGACACTGTA
1 -ACTATCGCAACGCGA-AATGCA
** *
1348198 GACTATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGCA
1348220 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1348241 AC
1 AC
1348243 GCGAATTTGC
Statistics
Matches: 116, Mismatches: 21, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.05
19 8 0.07
20 16 0.14
21 74 0.64
22 6 0.05
23 6 0.05
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1349080 original size:45 final size:45
Alignment explanation
Indices: 1349031--1349333 Score: 295
Period size: 45 Copynumber: 6.7 Consensus size: 45
1349021 ACTATAACAT
* * * * *
1349031 CTTTTGTGTTGATAATGCACCCATATGCCTTTCAACTATTGTATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
* * * * *
1349076 CTTTTATGTTGATGATGTACCCATATACATCTCAAC-CATAGTATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTC-TAGCATA
* * * *
1349121 CATTTTTTGTTGAGAATGTACCCATATACATTTCAACTCTAGCATA
1 C-TTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
* * * * *
1349167 CTTTTCTATTAATAATGCACCCATGTGCATTTCAACTCTAGTATA
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
* * *
1349212 TTTTTATGTTGATAATGCACCCATATGCATTTTAACTCT-GACATC
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAG-CATA
* ** * *
1349257 CTTTCATGCCGATAATGCACCCATATGCATTTCAACTCTGGCATC
1 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
* **
1349302 CTTTCATGCCGATAATGCACCCATATGCATTT
1 CTTTTATGTTGATAATGCACCCATATGCATTT
1349334 TTTTCTTTTA
Statistics
Matches: 219, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.00
45 178 0.81
46 39 0.18
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (45 bp):
CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
Found at i:1349916 original size:95 final size:95
Alignment explanation
Indices: 1349795--1349974 Score: 263
Period size: 95 Copynumber: 1.9 Consensus size: 95
1349785 CTATTAGGGT
* * *
1349795 ATTGATACCTCCTTAATGTATCGATACCTAAATTAGCTTCGATATAGATTGGTATCGATACCCTC
1 ATTGATACCTCCTTAAGGTATCGATACCTAAATTAGATTCGATATAGACTGGTATCGATACCCTC
**
1349860 ACCATGGTATTGATACCCCTATACTATGGA
66 ACCATGGTATCAATACCCCTATACTATGGA
* **
1349890 ATTGATACCTCCTCT-AGGTATTGATACCTAAATTAGATTCGATATTTACTGGTATCGATACCCT
1 ATTGATACCTCCT-TAAGGTATCGATACCTAAATTAGATTCGATATAGACTGGTATCGATACCCT
*
1349954 TACCATGGTATCAATACCCCT
65 CACCATGGTATCAATACCCCT
1349975 TTGCTTGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
95 74 0.99
96 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (95 bp):
ATTGATACCTCCTTAAGGTATCGATACCTAAATTAGATTCGATATAGACTGGTATCGATACCCTC
ACCATGGTATCAATACCCCTATACTATGGA
Found at i:1351379 original size:20 final size:22
Alignment explanation
Indices: 1351334--1351380 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1351324 GATCTGAGGC
1351334 TATCTTCATATTACTCTGTACA
1 TATCTTCATATTACTCTGTACA
* *
1351356 -ATCTTCAT-TTTCTCT-TCCA
1 TATCTTCATATTACTCTGTACA
1351375 TATCTT
1 TATCTT
1351381 TCATCAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (22 bp):
TATCTTCATATTACTCTGTACA
Found at i:1355446 original size:21 final size:22
Alignment explanation
Indices: 1355407--1355448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1355397 ACATAATGAT
* *
1355407 AACATTATCATTATTAACATTC
1 AACATCATCATTAGTAACATTC
1355429 AACATCATC-TTAGTAACATT
1 AACATCATCATTAGTAACATT
1355449 ATCATCAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (22 bp):
AACATCATCATTAGTAACATTC
Found at i:1356158 original size:45 final size:46
Alignment explanation
Indices: 1356091--1356391 Score: 256
Period size: 45 Copynumber: 6.7 Consensus size: 46
1356081 TATAACATCG
* *
1356091 TTTATGTTGATAATGCAGCCATATGCATTTCAACTATTA-TATACT
1 TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
* * * * * *
1356136 TTTATGTTGATGATGTACCCATATACATCTCAACCA-TAGTATACAT
1 TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATAC-T
* * * * * * * *
1356182 TTTCTGTTGAGAATGTACTCATATACATTTCGACT-CTAGCAAACT
1 TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
* * *
1356227 TTTCTGTTGATAATGCACCCATATGCATTTCAACT-CTAGTATACT
1 TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
* * * *
1356272 TTTCTGTTGATAATGCAACCATATGCATTTCAACT-CTGGCAT-CT
1 TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
*** * * *
1356316 TTTCATGCCAATAATGTACCCATATGCATTTCAACTA-TGGCATCCT
1 TTT-ATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
* *
1356362 TTCATGTCGATAATGCACCCATATGCATTT
1 TTTATGTTGATAATGCACCCATATGCATTT
1356392 TTTTCTTTTT
Statistics
Matches: 215, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
44 7 0.03
45 169 0.79
46 39 0.18
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (46 bp):
TTTATGTTGATAATGCACCCATATGCATTTCAACTATTAGCATACT
Found at i:1356228 original size:91 final size:90
Alignment explanation
Indices: 1356095--1356308 Score: 236
Period size: 91 Copynumber: 2.4 Consensus size: 90
1356085 ACATCGTTTA
* * * * * * * *
1356095 TGTTGATAATGCAGCCATATGCATTTCAACTATTA-TATACTTTTATGTTGATGATGTACCCATA
1 TGTTGAGAATGCAACCATATACATTTCAACT-CTAGCAAACTTTTATGTTGATAATGCACCCATA
1356159 TACATCTCAAC-CATAGTATACATTTTC
65 TACATCTCAACTC-TAGTATAC-TTTTC
* * *
1356186 TGTTGAGAATG-TACTCATATACATTTCGACTCTAGCAAACTTTTCTGTTGATAATGCACCCATA
1 TGTTGAGAATGCAAC-CATATACATTTCAACTCTAGCAAACTTTTATGTTGATAATGCACCCATA
* *
1356250 TGCATTTCAACTCTAGTATACTTTTC
65 TACATCTCAACTCTAGTATACTTTTC
* *
1356276 TGTTGATAATGCAACCATATGCATTTCAACTCT
1 TGTTGAGAATGCAACCATATACATTTCAACTCT
1356309 GGCATCTTTT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
90 34 0.33
91 67 0.66
92 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (90 bp):
TGTTGAGAATGCAACCATATACATTTCAACTCTAGCAAACTTTTATGTTGATAATGCACCCATAT
ACATCTCAACTCTAGTATACTTTTC
Found at i:1356330 original size:90 final size:90
Alignment explanation
Indices: 1356095--1356391 Score: 291
Period size: 90 Copynumber: 3.3 Consensus size: 90
1356085 ACATCGTTTA
* * * *
1356095 TGTTGATAATGCAGCCATATGCATTTCAACTATTA-TATACTTTT-ATGTTGATGATGTACCCAT
1 TGTTGATAATGCAACCATATGCATTTCAACT-CTAGCAT-CTTTTCATGTTGATAATGTACCCAT
* *
1356158 ATACATCTCAAC-CATAGTATACATTTTC
64 ATGCATTTCAACTC-TAGTATAC-TTTTC
* * * * * *
1356186 TGTTGAGAATG-TACTCATATACATTTCGACTCTAGCAAACTTTTC-TGTTGATAATGCACCCAT
1 TGTTGATAATGCAAC-CATATGCATTTCAACTCTAGC-ATCTTTTCATGTTGATAATGTACCCAT
1356249 ATGCATTTCAACTCTAGTATACTTTTC
64 ATGCATTTCAACTCTAGTATACTTTTC
* ***
1356276 TGTTGATAATGCAACCATATGCATTTCAACTCTGGCATCTTTTCATGCCAATAATGTACCCATAT
1 TGTTGATAATGCAACCATATGCATTTCAACTCTAGCATCTTTTCATGTTGATAATGTACCCATAT
* * * *
1356341 GCATTTCAACTATGGCAT-CCTTTC
66 GCATTTCAACTCTAGTATACTTTTC
* *
1356365 ATGTCGATAATGCACCCATATGCATTT
1 -TGTTGATAATGCAACCATATGCATTT
1356392 TTTTCTTTTT
Statistics
Matches: 170, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
89 12 0.07
90 91 0.54
91 65 0.38
92 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (90 bp):
TGTTGATAATGCAACCATATGCATTTCAACTCTAGCATCTTTTCATGTTGATAATGTACCCATAT
GCATTTCAACTCTAGTATACTTTTC
Found at i:1357225 original size:209 final size:209
Alignment explanation
Indices: 1356847--1357287 Score: 792
Period size: 209 Copynumber: 2.1 Consensus size: 209
1356837 ATCCTATTAG
* *
1356847 GGTATCGATACCCACTTAATATATCGATACCTAAATTAGCTTCAATATAGATTGGTATCGATACC
1 GGTATCGATA-CCTC-TGATATATCGATACCTAAATTAGCTTCAATATAGATTGGTATCGATACC
*
1356912 CTCACCATGGTATCGATACCCCTATGCTAACATACTGATACCTTCTCTAGGTATCGATACCCAAA
64 CTCACCATGGTATCGATACCCCTATGCTAACATACTGATACCTCCTCTAGGTATCGATACCCAAA
1356977 TTAGATTCGATATTTACTGATATCGATACCTTCACCATGGTATCGATACCCCTTTGCTTGGGTAC
129 TTAGATTCGATATTTACTGATATCGATACCTTCACCATGGTATCGATACCCCTTTGCTTGGGTAC
*
1357042 TGATACTGGTTGAATA
194 TGATACTAGTTGAATA
* *
1357058 GGTATCGATACCTCTGATATATCGATACCTAAATTAGCTTCATTATAGATTGGTATTGATACCCT
1 GGTATCGATACCTCTGATATATCGATACCTAAATTAGCTTCAATATAGATTGGTATCGATACCCT
1357123 CACCATGGTATCGATACCCCTATGCTAACATACTGATACCTCCTCTAGGTATCGATACCCAAATT
66 CACCATGGTATCGATACCCCTATGCTAACATACTGATACCTCCTCTAGGTATCGATACCCAAATT
*
1357188 AGATTCGATATTTACTGGTATCGATACCTTCACCATGGTATCGATACCCCTTTGCTTGGGTACTG
131 AGATTCGATATTTACTGATATCGATACCTTCACCATGGTATCGATACCCCTTTGCTTGGGTACTG
1357253 ATACTAGTTGAATA
196 ATACTAGTTGAATA
*
1357267 GGTATTGATACCTCTGATATA
1 GGTATCGATACCTCTGATATA
1357288 ATTTAGCCTA
Statistics
Matches: 222, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
209 209 0.94
210 3 0.01
211 10 0.05
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (209 bp):
GGTATCGATACCTCTGATATATCGATACCTAAATTAGCTTCAATATAGATTGGTATCGATACCCT
CACCATGGTATCGATACCCCTATGCTAACATACTGATACCTCCTCTAGGTATCGATACCCAAATT
AGATTCGATATTTACTGATATCGATACCTTCACCATGGTATCGATACCCCTTTGCTTGGGTACTG
ATACTAGTTGAATA
Found at i:1359475 original size:23 final size:23
Alignment explanation
Indices: 1359409--1359468 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1359399 GAAAATAAAT
1359409 CTCCCCTTCCCCAACCTTTCTCC
1 CTCCCCTTCCCCAACCTTTCTCC
*
1359432 CTCCCCTTCCCCGACCTTTCTCC
1 CTCCCCTTCCCCAACCTTTCTCC
1359455 CTCCCCTTCCCCAA
1 CTCCCCTTCCCCAA
1359469 TTTTTCTGGT
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:0.08, C:0.62, G:0.02, T:0.28
Consensus pattern (23 bp):
CTCCCCTTCCCCAACCTTTCTCC
Found at i:1370550 original size:39 final size:38
Alignment explanation
Indices: 1370492--1370571 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 38
1370482 CAAGAAGAAC
* * *
1370492 AATAATCCACTATATATGTAGAGATTACAAAAGATACA
1 AATAATCCACTATAGATGTAAAGATCACAAAAGATACA
* *
1370530 AATATATCCATTATAGATGTAAAGATCACAAAGGATACA
1 AATA-ATCCACTATAGATGTAAAGATCACAAAAGATACA
1370569 AAT
1 AAT
1370572 GTAACCCCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.26
Consensus pattern (38 bp):
AATAATCCACTATAGATGTAAAGATCACAAAAGATACA
Found at i:1372186 original size:28 final size:28
Alignment explanation
Indices: 1372128--1372286 Score: 228
Period size: 28 Copynumber: 5.6 Consensus size: 28
1372118 CATATTCGAA
* *
1372128 AATTCCCAAAATGTCAATTTTTTAAAAAT
1 AATTCCCAAAATGTC-ACTTTTTCAAAAT
* *
1372157 AATTCCCAGAATGCCACTTTTTCAAAAT
1 AATTCCCAAAATGTCACTTTTTCAAAAT
* *
1372185 AATTTCCAGAATGTCACTTTTTCAAAAT
1 AATTCCCAAAATGTCACTTTTTCAAAAT
1372213 AATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCA-CTTTTTCAAAAT
*
1372242 AATTCTCAAAATGTCACTTTTTCAAAAT
1 AATTCCCAAAATGTCACTTTTTCAAAAT
*
1372270 AATTCCCAGAATGTCAC
1 AATTCCCAAAATGTCAC
1372287 CTGGTCGGGT
Statistics
Matches: 118, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
28 78 0.66
29 40 0.34
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (28 bp):
AATTCCCAAAATGTCACTTTTTCAAAAT
Found at i:1372228 original size:85 final size:85
Alignment explanation
Indices: 1372128--1372286 Score: 255
Period size: 85 Copynumber: 1.9 Consensus size: 85
1372118 CATATTCGAA
* * *
1372128 AATTCCCAAAATGTCAATTTTTTAAAAATAATTCCCAGAATGCCACTTTTTCAAAATAATTTCCA
1 AATTCCCAAAATGTCAACTTTTTAAAAATAATTCCCAAAATGCCACTTTTTCAAAATAATTCCCA
1372193 GAATGTCACTTTTTCAAAAT
66 GAATGTCACTTTTTCAAAAT
* * * *
1372213 AATTCCCAAAATGTCACCTTTTTCAAAATAATTCTCAAAATGTCACTTTTTCAAAATAATTCCCA
1 AATTCCCAAAATGTCAACTTTTTAAAAATAATTCCCAAAATGCCACTTTTTCAAAATAATTCCCA
1372278 GAATGTCAC
66 GAATGTCAC
1372287 CTGGTCGGGT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (85 bp):
AATTCCCAAAATGTCAACTTTTTAAAAATAATTCCCAAAATGCCACTTTTTCAAAATAATTCCCA
GAATGTCACTTTTTCAAAAT
Found at i:1372235 original size:57 final size:57
Alignment explanation
Indices: 1372128--1372288 Score: 236
Period size: 57 Copynumber: 2.8 Consensus size: 57
1372118 CATATTCGAA
* * * *
1372128 AATTCCCAAAATGTCAATTTTTTAAAAATAATTCCCAGAATGCCA-CTTTTTCAAAAT
1 AATTTCCAAAATGTC-ACTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
* *
1372185 AATTTCCAGAATGTCACTTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAAT
1 AATTTCCAAAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
1372242 AA-TTCTCAAAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACCT
1 AATTTC-CAAAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACCT
1372289 GGTCGGGTCG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
56 28 0.30
57 66 0.70
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (57 bp):
AATTTCCAAAATGTCACTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:1372311 original size:17 final size:17
Alignment explanation
Indices: 1372289--1372328 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1372279 AATGTCACCT
1372289 GGTCGGGTCGGGT-AACG
1 GGTCGGGTC-GGTCAACG
1372306 GGTCGGGTCGGTCAACG
1 GGTCGGGTCGGTCAACG
1372323 GGTCGG
1 GGTCGG
1372329 TCAATGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.10, C:0.20, G:0.53, T:0.17
Consensus pattern (17 bp):
GGTCGGGTCGGTCAACG
Found at i:1372324 original size:12 final size:12
Alignment explanation
Indices: 1372309--1372340 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1372299 GGTAACGGGT
1372309 CGGGTCGGTCAA
1 CGGGTCGGTCAA
1372321 CGGGTCGGTCAA
1 CGGGTCGGTCAA
*
1372333 TGGGTCGG
1 CGGGTCGG
1372341 ATCGGACCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (12 bp):
CGGGTCGGTCAA
Found at i:1376623 original size:20 final size:19
Alignment explanation
Indices: 1376585--1376623 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1376575 CAAAACATGG
*
1376585 CCATTTCTCCTTCGGTATC
1 CCATTTCTCATTCGGTATC
*
1376604 CCATTTCTTCATTTGGTATC
1 CCATTTC-TCATTCGGTATC
1376624 TGTTTGGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.13, C:0.31, G:0.10, T:0.46
Consensus pattern (19 bp):
CCATTTCTCATTCGGTATC
Found at i:1379740 original size:22 final size:25
Alignment explanation
Indices: 1379683--1379734 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1379673 TCTTAATTTA
1379683 TTATGAG-AAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
1379707 TTATGAGAAAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
1379732 TTA
1 TTA
1379735 GAAAAATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:1384426 original size:3 final size:3
Alignment explanation
Indices: 1384420--1384475 Score: 69
Period size: 3 Copynumber: 18.0 Consensus size: 3
1384410 CTGCAAAAAA
*
1384420 AAT AAT AATT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AA-T AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT
1384467 AAT AAT AAT
1 AAT AAT AAT
1384476 TAAAATTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 1 0.02
3 39 0.83
4 7 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1386722 original size:18 final size:18
Alignment explanation
Indices: 1386699--1386735 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1386689 TTGGCCATGT
1386699 TTGGACACTGAGTGTGAA
1 TTGGACACTGAGTGTGAA
1386717 TTGGACACTGAGTGTGAA
1 TTGGACACTGAGTGTGAA
1386735 T
1 T
1386736 GTGTGTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (18 bp):
TTGGACACTGAGTGTGAA
Found at i:1392644 original size:2 final size:2
Alignment explanation
Indices: 1392637--1392664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1392627 ATAAACTTAA
1392637 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
1392665 TTTCCTTATT
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:1392944 original size:3 final size:3
Alignment explanation
Indices: 1392936--1392971 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1392926 TCCCGACACC
1392936 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1392972 TTGTTGCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1394012 original size:108 final size:107
Alignment explanation
Indices: 1393833--1394051 Score: 302
Period size: 108 Copynumber: 2.0 Consensus size: 107
1393823 TTTAGTGCGG
* * *
1393833 TTTTGCATGTTAGTCACCTATAAGAAACGAACTTGTTATTTCCCCTTTTTTATGCATGCTATATA
1 TTTTGCAAGTTAGTCACCTATAAGAAACGAAATTGTTATTTCCCCTTTCTTATGCATGCTATATA
1393898 TTTTTGGGATATTTTTTGTTTAGTCCCCCATAGTTTA-GCGTGT
66 TTTTTGGGATATTTTTT-TTTAGTCCCCCATA-TTTAGGCGTGT
* *
1393941 TTTTGCAAGTTGGTCACCTATAAG-GACTGAAATTGTTA-TTCACCCGTTTCTTATGCAT-CTAT
1 TTTTGCAAGTTAGTCACCTATAAGAAAC-GAAATTGTTATTTC-CCC-TTTCTTATGCATGCTAT
* *
1394003 GTATTTTTGGGATATTTTTTTTTAGTCCCCCTTATTTAGGCGTGT
63 ATATTTTTGGGATATTTTTTTTTAGTCCCCCATATTTAGGCGTGT
1394048 TTTT
1 TTTT
1394052 ATATTTTGAT
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
106 4 0.04
107 28 0.28
108 57 0.57
109 11 0.11
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (107 bp):
TTTTGCAAGTTAGTCACCTATAAGAAACGAAATTGTTATTTCCCCTTTCTTATGCATGCTATATA
TTTTTGGGATATTTTTTTTTAGTCCCCCATATTTAGGCGTGT
Found at i:1399125 original size:6 final size:6
Alignment explanation
Indices: 1399116--1399461 Score: 578
Period size: 6 Copynumber: 58.3 Consensus size: 6
1399106 CCAGTTGAAG
* *
1399116 ATGTAT ATGTAT ATATAT ATATAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
* * *
1399164 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGCAT ATGCAT ATGCAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1399212 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTATAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG--TAT ATGTAT ATGTAT
1399262 ATGTAT ATG--T ATGTAT ATG--T ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1399306 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1399354 ATGTAT A--TAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1399400 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
*
1399448 ATGCAT ATGTAT AT
1 ATGTAT ATGTAT AT
1399462 CTATGATGAC
Statistics
Matches: 326, Mismatches: 6, Indels: 16
0.94 0.02 0.05
Matches are distributed among these distances:
4 12 0.04
6 308 0.94
8 6 0.02
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (6 bp):
ATGTAT
Found at i:1408473 original size:43 final size:42
Alignment explanation
Indices: 1408424--1408776 Score: 350
Period size: 43 Copynumber: 8.2 Consensus size: 42
1408414 TGAGAACAAA
* * * *
1408424 AAACGCCGTAATAGGTCAATATCTATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTC-ATACCTA-TAGCGGCGTTTTTGGAAC
* * *
1408467 AAACGCCGCAAAAGGTCGATATCTATAGCGGTGTTTTTGGAAT
1 AAACGCCGCAAAAGGTC-ATACCTATAGCGGCGTTTTTGGAAC
* * * *
1408510 AAACGCCGCAAAAAGTTATGCTATATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATAC-CTATAGCGGCGTTTTTGGA-AC
* * *
1408554 AAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCATACCTATAGCGGCGTTTTTGGA-AC
* * * *
1408597 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTCATACCTATAGC-GGCGTTTTTGGAAC
* * *
1408639 AAACGTCGTAAAAGGTCATACCTATAGTGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCATACCTATAGCGGCGTTTTTGGA-AC
* * * *
1408682 AAACGCCGCAAAATGTCATACCTATAACGGCATTTTTGAACAC
1 AAACGCCGCAAAAGGTCATACCTATAGCGGCGTTTTTGGA-AC
* * *
1408725 AAACGACGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATACCTATAGCGGCGTTTTTGGA-AC
1408768 AAACGCCGC
1 AAACGCCGC
1408777 TAATTACCTT
Statistics
Matches: 256, Mismatches: 48, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
42 38 0.15
43 201 0.79
44 17 0.07
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATACCTATAGCGGCGTTTTTGGAAC
Found at i:1408689 original size:128 final size:129
Alignment explanation
Indices: 1408533--1408772 Score: 333
Period size: 128 Copynumber: 1.9 Consensus size: 129
1408523 AGTTATGCTA
* * ** * *
1408533 TATAGCGGCGTTTTTGGATACAAACGCCGTAAAAGGTCAGACCTATAGTGGCGTTTTTGGACACA
1 TATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTGAACACA
*
1408598 AACGCCGC-AAAAGATAAGACCTATA-CTGGCGTTTTTAGA-ACAAACGTCGTAAAAGGTCATAC
66 AACGACGCAAAAAG-TAAGACCTATAGC-GGCGTTTTTAGATACAAACGTCGTAAAAGGTCATAC
1408660 C
129 C
* * *
1408661 TATAGTGGCGTTTTTGGACACAAACGCCGCAAAATGTCATACCTATAACGGCATTTTTGAACACA
1 TATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTGAACACA
* *
1408726 AACGACGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAACG
66 AACGACGCAAAAAGTAAGACCTATAGCGGCGTTTTTAGATACAAACG
1408773 CCGCTAATTA
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
128 84 0.87
129 13 0.13
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (129 bp):
TATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGGTCAGACCTATAACGGCATTTTTGAACACA
AACGACGCAAAAAGTAAGACCTATAGCGGCGTTTTTAGATACAAACGTCGTAAAAGGTCATACC
Found at i:1409510 original size:80 final size:80
Alignment explanation
Indices: 1409423--1409583 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
1409413 ATATTCTACA
1409423 TAAGAATGTAAAAAATGTCATCATAAAGAAAAAATTTAATAATGTATTGGTTGCCATCTTACTTT
1 TAAGAATGTAAAAAATGTCATCATAAAGAAAAAATTTAATAATGTATTGGTTGCCATCTTACTTT
1409488 TAGAAGTTAGAATTC
66 TAGAAGTTAGAATTC
1409503 TAAGAATGTAAAAAATGTCATCATAAAGAAAAAATTTAATAATGTATTGGTTGCCATCTTACTTT
1 TAAGAATGTAAAAAATGTCATCATAAAGAAAAAATTTAATAATGTATTGGTTGCCATCTTACTTT
1409568 TAGAAGTTAGAATTC
66 TAGAAGTTAGAATTC
1409583 T
1 T
1409584 TACCCCAAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (80 bp):
TAAGAATGTAAAAAATGTCATCATAAAGAAAAAATTTAATAATGTATTGGTTGCCATCTTACTTT
TAGAAGTTAGAATTC
Found at i:1412774 original size:41 final size:41
Alignment explanation
Indices: 1412681--1413039 Score: 337
Period size: 41 Copynumber: 8.6 Consensus size: 41
1412671 TTGTAAACTT
* * * * *
1412681 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
** * * * * *
1412724 ATGACGTTTGAATAAAAATGCCACTAAAGTATGCGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
1412765 GCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1412806 GCGGCGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
1412847 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* * * *
1412890 ACGGCGTTTGTATAAAAACGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1412931 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
1412972 GCGGTGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTC-TTTA
*
1413014 -CGGCATTTGT-TGAAAAAACGCCACTA
1 GCGGCGTTTGTAT--AAAAACGCCACTA
1413040 TAGATGAACC
Statistics
Matches: 260, Mismatches: 49, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.00
41 199 0.77
42 21 0.08
43 39 0.15
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:1412909 original size:125 final size:123
Alignment explanation
Indices: 1412770--1413003 Score: 360
Period size: 125 Copynumber: 1.9 Consensus size: 123
1412760 CTTTAGCGGA
** *
1412770 GTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* *
1412835 TATGAGTCTTTCGCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGC
66 TACGAGTCTTTCGCGGCGTTTGTAAA-A-AAACGCCACTAAAGTACATGTGTATAACGGC
* *
1412895 GTTTGTATAAAAACGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAT
1 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
* * *
1412960 TACGAGTCTTTTGCGGTGTTTGTATAAAAACGCCACTAAAGTAC
66 TACGAGTCTTTCGCGGCGTTTGTAAAAAAACGCCACTAAAGTAC
1413004 TACTCTTTTA
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 16 0.16
124 1 0.01
125 82 0.83
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (123 bp):
GTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAT
TACGAGTCTTTCGCGGCGTTTGTAAAAAAACGCCACTAAAGTACATGTGTATAACGGC
Found at i:1412956 original size:166 final size:166
Alignment explanation
Indices: 1412681--1412999 Score: 494
Period size: 166 Copynumber: 1.9 Consensus size: 166
1412671 TTGTAAACTT
* *
1412681 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAATGACGTTTGAATAAAAATGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
*** * *
1412746 ACTAAAGTATGCGTCTTTAGCGGAGTTTGTATAAAAACGCCACTAAAGTATGAGTCTTTAGCGGC
66 ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
1412811 GTTTGTATAAAAACGCCACTAAATTATGAGTCTTTC
131 GTTTGTATAAAAACGCCACTAAATTATGAGTCTTTC
* * *
1412847 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
* * * * * *
1412912 ACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTTGCGGT
66 ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
1412977 GTTTGTATAAAAACGCCACTAAA
131 GTTTGTATAAAAACGCCACTAAA
1413000 GTACTACTCT
Statistics
Matches: 137, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
166 137 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (166 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGACGTTTGAATAAAAACGCC
ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGC
GTTTGTATAAAAACGCCACTAAATTATGAGTCTTTC
Found at i:1414363 original size:134 final size:131
Alignment explanation
Indices: 1413928--1414412 Score: 463
Period size: 134 Copynumber: 3.6 Consensus size: 131
1413918 AATCAAACTT
*
1413928 GATTCAATCTTCCCTGAGTGACAATAGAATGAATCAACGTCCTCAGATCTGATTTTTCCTCAAGA
1 GATTCAATCTTCCCTGAGTGACAATAGAATGAATCAACGTCCCCAGATCTGATTTTTCCTCAAGA
* * *
1413993 AGAAGCGAACCAAATCCTCCTTTTTCATGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
66 AGAAG-GAAACAAAT-C-CCTTTTTCAAGATTTGATATTCACTGAGTAACAGTGGAACAAGTCTG
1414058 CCTC
128 CCTC
* * * * * *
1414062 GATTCGATC-TCCTCTGAATGACAATGGAATGAACCAACATCCCCAGATCTGATTTTTCCTAAAG
1 GATTCAATCTTCC-CTGAGTGACAATAGAATGAATCAACGTCCCCAGATCTGATTTTTCCTCAAG
* * * *
1414126 AAGAAGCAGAACATATCCTTCTTTTTCAAGATTTGATATTCTCTGAGTAACAGTGGAACAAGTCC
65 AAGAAGGA-AACAAATCC--CTTTTTCAAGATTTGATATTCACTGAGTAACAGTGGAACAAGTCT
*
1414191 ACCTC
127 GCCTC
* * * * * * ** *
1414196 GATTTAATCTTCCTTAAGTGATAGT-GTAATGAATCAACGTCCCCATAAATGATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAGTGACAATAG-AATGAATCAACGTCCCCAGATCTGATTTTTCCTCAAG
* * * * * * *
1414260 AAAAAGTGAAACAGATCCCTGTATTCCAAGATTTGATATTCACTAAGTAATAGAGGAACAAATCT
65 AAGAAG-GAAACAAATCCCT-T-TTTCAAGATTTGATATTCACTGAGTAACAGTGGAACAAGTCT
1414325 GCCTC
127 GCCTC
* * * * * ** * *
1414330 AATCCAATCTTCCCTGAGTTACAGTAGAATGAATCAAAGTCCTTAGATCTAATTTTCCCTCAA-A
1 GATTCAATCTTCCCTGAGTGACAATAGAATGAATCAACGTCCCCAGATCTGATTTTTCCTCAAGA
* *
1414394 AAAAGCGGAACAAATCCCT
66 AGAAG-GAAACAAATCCCT
1414413 CATCATATTC
Statistics
Matches: 285, Mismatches: 56, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
132 3 0.01
133 24 0.08
134 253 0.89
135 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (131 bp):
GATTCAATCTTCCCTGAGTGACAATAGAATGAATCAACGTCCCCAGATCTGATTTTTCCTCAAGA
AGAAGGAAACAAATCCCTTTTTCAAGATTTGATATTCACTGAGTAACAGTGGAACAAGTCTGCCT
C
Found at i:1414543 original size:3 final size:3
Alignment explanation
Indices: 1414537--1414576 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1414527 TTTGTCCCGC
*
1414537 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1414577 AATACATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1416824 original size:131 final size:130
Alignment explanation
Indices: 1416674--1417041 Score: 459
Period size: 131 Copynumber: 2.8 Consensus size: 130
1416664 TCGATATTGA
* * *
1416674 AAATAGTAATATCTTTTCATTTCGGTTAGATTAATAAATG-TCTGCTTTAAGGCAGGAGAGGTCA
1 AAATAGTAATATCTCTTCATTTCGATTAGATTAATAAATGAT-TG-TTTAAGGCACGAGAGGTCA
* * * * *
1416738 TTTATTCTCGATTGGAAATAATTTGATATTGTCGTTTTCTCTTGAATTAATATTGATTTTTAAGA
64 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCAATATTGAATTTTAAGA
*
1416803 TG
129 CG
* * * * * * * *
1416805 GAATAGTGATATCTCTTCATTTCGATTGGATCAATAAATGATTGTTTTAAGGTATGAGAGATAAT
1 AAATAGTAATATCTCTTCATTTCGATTAGATTAATAAATGATTG-TTTAAGGCACGAGAGGTCAT
* *
1416870 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCGATATTGAATTTTAAGAC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCAATATTGAATTTTAAGAC
1416935 G
130 G
* * * ** * *
1416936 AAATACTAATATCTCTTTATTTCAATTAGGGTAATAAATGATTGTTTCAATGCACGAAAGGTCAT
1 AAATAGTAATATCTCTTCATTTCGATTAGATTAATAAATGATTGTTT-AAGGCACGAGAGGTCAT
1417001 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACT
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACT
1417042 CTTAAAACTA
Statistics
Matches: 200, Mismatches: 35, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
130 3 0.01
131 196 0.98
132 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (130 bp):
AAATAGTAATATCTCTTCATTTCGATTAGATTAATAAATGATTGTTTAAGGCACGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTTGAATCAATATTGAATTTTAAGACG
Found at i:1418548 original size:29 final size:28
Alignment explanation
Indices: 1418513--1418583 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
1418503 TCGCTTGAAG
1418513 AAAGAAAAAGAAAAAT-AAATAAAAGAAA
1 AAAGAAAAAGAAAAATGAAA-AAAAGAAA
* *
1418541 AAATGAAAAGGAAAAATGAAAAAAAGAGA
1 AAA-GAAAAAGAAAAATGAAAAAAAGAAA
*
1418570 TAA-AAAAAGAAAAA
1 AAAGAAAAAGAAAAA
1418584 AAAAGGGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 10 0.27
28 3 0.08
29 21 0.57
30 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (28 bp):
AAAGAAAAAGAAAAATGAAAAAAAGAAA
Found at i:1418555 original size:13 final size:13
Alignment explanation
Indices: 1418529--1418562 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1418519 AAAGAAAAAT
1418529 AAAT-AAAAGAAA
1 AAATGAAAAGAAA
*
1418541 AAATGAAAAGGAA
1 AAATGAAAAGAAA
1418554 AAATGAAAA
1 AAATGAAAA
1418563 AAAGAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAATGAAAAGAAA
Found at i:1418587 original size:13 final size:13
Alignment explanation
Indices: 1418517--1418587 Score: 54
Period size: 15 Copynumber: 5.2 Consensus size: 13
1418507 TTGAAGAAAG
1418517 AAAAAGAAAAATAA
1 AAAAAGAAAAA-AA
*
1418531 ATAAAAGAAAAAATG
1 A-AAAAGAAAAAA-A
*
1418546 AAAAGGAAAAATGAA
1 AAAAAGAAAAA--AA
* *
1418561 AAAAAG-AGATAA
1 AAAAAGAAAAAAA
1418573 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
1418586 AA
1 AA
1418588 GGGAAAAGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
12 8 0.18
13 6 0.14
14 13 0.30
15 16 0.36
16 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:1418594 original size:10 final size:10
Alignment explanation
Indices: 1418510--1418588 Score: 61
Period size: 10 Copynumber: 7.3 Consensus size: 10
1418500 ACTTCGCTTG
*
1418510 AAGAAAGAAA
1 AAGAAAAAAA
1418520 AAGAAAAATAA
1 AAGAAAAA-AA
1418531 ATA-AAAGAAAA
1 A-AGAAA-AAAA
1418542 AATGAAAAGGAAA
1 AA-GAAAA--AAA
1418555 AATGAAAAAAA
1 AA-GAAAAAAA
* *
1418566 GAGATAAAAA
1 AAGAAAAAAA
1418576 AAGAAAAAAA
1 AAGAAAAAAA
1418586 AAG
1 AAG
1418589 GGAAAAGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
10 26 0.46
11 14 0.25
12 6 0.11
13 11 0.19
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.06
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:1418611 original size:22 final size:22
Alignment explanation
Indices: 1418559--1418612 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1418549 AGGAAAAATG
* *
1418559 AAAAAAAGAGATAAAAAAAGAA
1 AAAAAAAGGGATAAAAAAACAA
1418581 AAAAAAAGGGA-AAAGAAAACAA
1 AAAAAAAGGGATAAA-AAAACAA
*
1418603 ATAAAAAGGG
1 AAAAAAAGGG
1418613 GTTTAAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (22 bp):
AAAAAAAGGGATAAAAAAACAA
Found at i:1420157 original size:132 final size:131
Alignment explanation
Indices: 1419892--1420325 Score: 460
Period size: 132 Copynumber: 3.3 Consensus size: 131
1419882 ATCGATCTTC
* * * * * * *
1419892 ATTCAATCTTCCCTAAAGAATAGGGGAATGAATCAACTTTTCCAGATCTGATTTACCTTGAAGAA
1 ATTCAATCTTCCCTAAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTCCCTGAAGAA
* * * * *
1419957 GTAGCAGAGCATATCCCCTTTTTCCAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTTCC
66 GTAGCAGAACAGAT--CCTCTTTCAAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCC
1420022 TCA
129 TCA
* * * * *
1420025 ATTCAATCTTCACTGAAGAACAGTGGAACGAATCAACGTCTCCAAATTTGATTTTCCCTAAAGAA
1 ATTCAATCTTCCCTAAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTCCCTGAAGAA
* * *
1420090 GCAGCAGAACAGATCCATCTTTCTAGATTTGATCTTCCCTAAGTAGCAGTGGAACAAGTCTGCCT
66 GTAGCAGAACAGATCC-TCTTTCAAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCT
1420155 CA
130 CA
* * * ** * * * *
1420157 ATTGAATCTTCTCTAAAAAACAGTGGAATAAATCAATGCCTCTAGATCTGATTTTCCCTGAACAA
1 ATTCAATCTTCCCTAAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTCCCTGAAGAA
* * * * *
1420222 GTAGC-GTAACAGATCTCTCTTTCAATATTTGATCTT-CCTGGAGTAACTGTTGAACAAGTATGC
66 GTAGCAG-AACAGATC-CTCTTTCAAGATTTGATCTTCCCT-GAGTAGCAGTGGAACAAGTCTGC
*
1420285 CTCG
128 CTCA
*
1420289 ATTCAATCTTCCCTAAAGAACAATGGAATC-AATCAAC
1 ATTCAATCTTCCCTAAAGAACAGTGGAA-CGAATCAAC
1420326 ACTTCCATAT
Statistics
Matches: 249, Mismatches: 47, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
131 6 0.02
132 178 0.71
133 65 0.26
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (131 bp):
ATTCAATCTTCCCTAAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTCCCTGAAGAA
GTAGCAGAACAGATCCTCTTTCAAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTGCCTC
A
Done.