Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008013.1 Hibiscus syriacus cultivar Beakdansim tig00110478_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: 1461402
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1176276 original size:76 final size:76
Alignment explanation
Indices: 1175940--1177341 Score: 2600
Period size: 76 Copynumber: 18.5 Consensus size: 76
1175930 CTATTTCCCA
1175940 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176004 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1176015 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1176080 AAGCCTTCGGGT
65 AAGCCTTCGGGT
1176092 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176156 AGCCTTCGGGT
66 AGCCTTCGGGT
1176167 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176232 AGCCTTCGGGT
66 AGCCTTCGGGT
1176243 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176307 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1176318 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1176383 AAGCCTTCGGGT
65 AAGCCTTCGGGT
1176395 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176460 AGCCTTCGGGT
66 AGCCTTCGGGT
1176471 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176535 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1176546 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1176611 AGCCTTAGGGT
66 AGCCTTCGGGT
1176622 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176686 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1176697 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1176762 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
1176774 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1176839 AAGCCTTCGGGT
65 AAGCCTTCGGGT
1176851 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176916 AGCCTTCGGGT
66 AGCCTTCGGGT
1176927 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1176991 AGCCTTCGGGT
66 AGCCTTCGGGT
*
1177002 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1177067 AAGCCTTCGGGT
65 AAGCCTTCGGGT
*
1177079 CATCTGTAAGTTCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1177144 AGCTTTCGGGT
66 AGCCTTCGGGT
1177155 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1177220 AGCTTTCGGGT
66 AGCCTTCGGGT
*
1177231 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1177296 AACCTTCGGGT
66 AGCCTTCGGGT
*
1177307 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
1177342 CATTTCCATC
Statistics
Matches: 1299, Mismatches: 18, Indels: 19
0.97 0.01 0.01
Matches are distributed among these distances:
75 391 0.30
76 572 0.44
77 336 0.26
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:1177473 original size:3 final size:3
Alignment explanation
Indices: 1177467--1177570 Score: 147
Period size: 3 Copynumber: 34.0 Consensus size: 3
1177457 TTCATTTAAA
* * *
1177467 ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATT ATA ATT ATA ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
1177516 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT AT-T ATT
1177562 ATT ATT ATT
1 ATT ATT ATT
1177571 TAATAAATAA
Statistics
Matches: 91, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.02
3 80 0.88
4 9 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1178007 original size:14 final size:14
Alignment explanation
Indices: 1177988--1178014 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1177978 CAGACGGCAG
1177988 AGAACGAAAAAAAA
1 AGAACGAAAAAAAA
1178002 AGAACGAAAAAAA
1 AGAACGAAAAAAA
1178015 CAGAGGAGGA
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:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAACGAAAAAAAA
Found at i:1178292 original size:13 final size:13
Alignment explanation
Indices: 1178274--1178302 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1178264 ACCACCGTTA
1178274 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1178287 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
1178300 CGG
1 CGG
1178303 AATACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:1178908 original size:53 final size:53
Alignment explanation
Indices: 1178848--1178948 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 53
1178838 GATGATTCAG
* * * *
1178848 GTTATGTTCATAATTTTACATTTATTATTTT-ATTTATTTTTAATCATTGTTTA
1 GTTATGTT-ATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
* **
1178901 GTTATGTTTTAACTTAATTTTTATTATTTTAATATATTTTCAATCATT
1 GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATT
1178949 ACTTTAATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 17 0.43
53 23 0.57
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (53 bp):
GTTATGTTATAACTTAACATTTATTATTTTAATATATTTTCAATCATTGTTTA
Found at i:1178995 original size:35 final size:35
Alignment explanation
Indices: 1178920--1178995 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 35
1178910 TAACTTAATT
* * *
1178920 TTTATTATTTTAATATATTTTCAATCATTACTTTA
1 TTTATTATTTTAATATATTATAAATCATTACATTA
* * *
1178955 ATTATTGTTTTACTATATTATAAAT-ATATACATTA
1 TTTATTATTTTAATATATTATAAATCAT-TACATTA
1178990 TTTATT
1 TTTATT
1178996 TAACAATGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATTATTTTAATATATTATAAATCATTACATTA
Found at i:1191156 original size:74 final size:76
Alignment explanation
Indices: 1190974--1191181 Score: 244
Period size: 75 Copynumber: 2.8 Consensus size: 76
1190964 CAAAGCCAAA
* ** * **
1190974 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1191038 TTTGACTCCGAG
65 TTTGACTCCGAG
*
1191050 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
1191114 GTTG-TTCCGGG
66 -TTGACTCCGAG
* * * * *
1191125 AATTCCAGTATGCTCGGAGGGAATCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
1191182 TGTACAACGG
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
74 21 0.18
75 59 0.52
76 34 0.30
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGACTCCGAG
Found at i:1197025 original size:21 final size:21
Alignment explanation
Indices: 1196999--1197038 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1196989 CCCCCTTTGA
*
1196999 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1197020 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1197039 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1199776 original size:75 final size:75
Alignment explanation
Indices: 1199618--1199826 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 75
1199608 CAAAGCCAAA
* ** * **
1199618 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1199683 TTTGACTCCGAG
64 TTTGACTCCGAG
*
1199695 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT-
* *
1199760 TTG-TTCCGGG
65 TTGACTCCGAG
* * * * *
1199770 AATTCCAGTATGCTTGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
1199827 TGTATAACGG
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
75 81 0.70
76 9 0.08
77 25 0.22
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGACTCCGAG
Found at i:1203758 original size:369 final size:369
Alignment explanation
Indices: 1203079--1203809 Score: 1392
Period size: 369 Copynumber: 2.0 Consensus size: 369
1203069 GTCACAAAAG
1203079 TTGAAATGGCAGTTATCACTTATTTGGCTGGATGCCTGAGCTTAATTTGATCAAATAGATTTATT
1 TTGAAATGGCAGTTATCACTTATTTGGCTGGATGCCTGAGCTTAATTTGATCAAATAGATTTATT
* * *
1203144 GTTCTCCCTTTCTTCAAGATTTTTTGCCTTTTGTACCTGATAGATTCATTGTTTCTGTTGTTTCT
66 GTTCTCCCCTTCTTCAAGATTTATTACCTTTTGTACCTGATAGATTCATTGTTTCTGTTGTTTCT
*
1203209 TTTCTTCCTTTCGGATGCTTCCCCCCCTCAATTTTCCTGTTTTTAGGTCCCTTAAATTGTTTCAT
131 TTTCTTCCTTTCGGATGCTTCCCCCCCTCAATTTTCCTCTTTTTAGGTCCCTTAAATTGTTTCAT
1203274 ATTGTAATGTAAACATGCCATTGAAAGCTGTTTAAGAGTTGCATTTGCAATCCTCTTTGTTCATA
196 ATTGTAATGTAAACATGCCATTGAAAGCTGTTTAAGAGTTGCATTTGCAATCCTCTTTGTTCATA
1203339 TTAGTTTTAGTAGATATGAAAGTTGAATTGATCAAGCCATATGACACTTGAAGGACCTGGTGAGC
261 TTAGTTTTAGTAGATATGAAAGTTGAATTGATCAAGCCATATGACACTTGAAGGACCTGGTGAGC
1203404 TGTAATCTAAATTTGTTTTGTTGCACCACACTCGCTCTCTATAT
326 TGTAATCTAAATTTGTTTTGTTGCACCACACTCGCTCTCTATAT
*
1203448 TTGAAATGGCAGTTATCACTTATTTGGCTGGATGCCTGAGCTTAATTTGATTAAATAGATTTATT
1 TTGAAATGGCAGTTATCACTTATTTGGCTGGATGCCTGAGCTTAATTTGATCAAATAGATTTATT
1203513 GTTCTCCCCTTCTTCAAGATTTATTACCTTTTGTACCTGATAGATTCATTGTTTCTGTTGTTTCT
66 GTTCTCCCCTTCTTCAAGATTTATTACCTTTTGTACCTGATAGATTCATTGTTTCTGTTGTTTCT
1203578 TTTCTTCCTTTCGGATGCTTCCCCCCCTCAATTTTTCC-CTTTTTAGGTCCCTTAAATTGTTTCA
131 TTTCTTCCTTTCGGATGCTTCCCCCCCTCAA-TTTTCCTCTTTTTAGGTCCCTTAAATTGTTTCA
*
1203642 TATTGTAATGTAAACATGCCATTGAAAGCTGTTTAAGAGTTGCATTTGCAATCTTCTTTGTTCAT
195 TATTGTAATGTAAACATGCCATTGAAAGCTGTTTAAGAGTTGCATTTGCAATCCTCTTTGTTCAT
1203707 ATTAGTTTTAGTAGATATGAAAGTTGAATTGATCAAGCCATATGACACTTGAAGGACCTGGTGAG
260 ATTAGTTTTAGTAGATATGAAAGTTGAATTGATCAAGCCATATGACACTTGAAGGACCTGGTGAG
1203772 CTGTAATCTAAATTTGTTTTGTTGCACCACACTCGCTC
325 CTGTAATCTAAATTTGTTTTGTTGCACCACACTCGCTC
1203810 AATAGCTTTG
Statistics
Matches: 355, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
369 349 0.98
370 6 0.02
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (369 bp):
TTGAAATGGCAGTTATCACTTATTTGGCTGGATGCCTGAGCTTAATTTGATCAAATAGATTTATT
GTTCTCCCCTTCTTCAAGATTTATTACCTTTTGTACCTGATAGATTCATTGTTTCTGTTGTTTCT
TTTCTTCCTTTCGGATGCTTCCCCCCCTCAATTTTCCTCTTTTTAGGTCCCTTAAATTGTTTCAT
ATTGTAATGTAAACATGCCATTGAAAGCTGTTTAAGAGTTGCATTTGCAATCCTCTTTGTTCATA
TTAGTTTTAGTAGATATGAAAGTTGAATTGATCAAGCCATATGACACTTGAAGGACCTGGTGAGC
TGTAATCTAAATTTGTTTTGTTGCACCACACTCGCTCTCTATAT
Found at i:1207098 original size:15 final size:16
Alignment explanation
Indices: 1207073--1207103 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1207063 TTCAGTATCA
1207073 ATTATTTATTATTTTC
1 ATTATTTATTATTTTC
1207089 ATTA-TTATTATTTTC
1 ATTATTTATTATTTTC
1207104 GCAGTCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTATTTATTATTTTC
Found at i:1210850 original size:21 final size:21
Alignment explanation
Indices: 1210824--1210865 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1210814 TTTGAGATAG
1210824 TCTCGATTTTATTCTTACTTA
1 TCTCGATTTTATTCTTACTTA
1210845 TCTCGATTTTATTCTTACTTA
1 TCTCGATTTTATTCTTACTTA
1210866 AATCTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.57
Consensus pattern (21 bp):
TCTCGATTTTATTCTTACTTA
Found at i:1213161 original size:34 final size:33
Alignment explanation
Indices: 1213116--1213296 Score: 186
Period size: 34 Copynumber: 5.3 Consensus size: 33
1213106 AATTCAGATG
* * *
1213116 TATTCATGGAAAATTTAGGCCATGGTTTTGTTT
1 TATTCATGGAAAATTTAGGTCTTGATTTTGTTT
* *
1213149 TAGTTCATGGAAAATATGGGTCTTGATTTTGTTT
1 TA-TTCATGGAAAATTTAGGTCTTGATTTTGTTT
* *
1213183 CTATTCATGGAAAATTTAAGTCTTGGTTTTGTTTT
1 -TATTCATGGAAAATTTAGGTCTTGATTTTG-TTT
* *
1213218 TATTTCATGGAAAATAT-GGATCTTGACTTTGTTTT
1 TA-TTCATGGAAAATTTAGG-TCTTGATTTTG-TTT
* *
1213253 TATTCATGGAAAAATTAGGTC-TGCTTTTGTTT
1 TATTCATGGAAAATTTAGGTCTTGATTTTGTTT
1213285 TAATTCATGGAA
1 T-ATTCATGGAA
1213297 GTACTATGCC
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
32 4 0.03
33 18 0.15
34 67 0.54
35 35 0.28
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (33 bp):
TATTCATGGAAAATTTAGGTCTTGATTTTGTTT
Found at i:1213320 original size:68 final size:68
Alignment explanation
Indices: 1213116--1213296 Score: 256
Period size: 69 Copynumber: 2.7 Consensus size: 68
1213106 AATTCAGATG
* * *
1213116 TATTCATGGAAAATTTAGGCCATGGTTTTGTTTTAGTTCATGGAAAATATGGGTCTTGATTTTGT
1 TATTCATGGAAAATTTAGGTCATGGTTTTGTTTTAATTCATGGAAAATATGGATCTTGATTTTGT
*
1213181 TTC
66 TTT
* * * *
1213184 TATTCATGGAAAATTTAAGTCTTGGTTTTGTTTTTATTTCATGGAAAATATGGATCTTGACTTTG
1 TATTCATGGAAAATTTAGGTCATGGTTTTG-TTTTAATTCATGGAAAATATGGATCTTGATTTTG
1213249 TTTT
65 TTTT
* *
1213253 TATTCATGGAAAAATTAGGTC-TGCTTTTGTTTTAATTCATGGAA
1 TATTCATGGAAAATTTAGGTCATGGTTTTGTTTTAATTCATGGAA
1213297 GTACTATGCC
Statistics
Matches: 101, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
67 14 0.14
68 34 0.34
69 53 0.52
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (68 bp):
TATTCATGGAAAATTTAGGTCATGGTTTTGTTTTAATTCATGGAAAATATGGATCTTGATTTTGT
TTT
Found at i:1216138 original size:84 final size:84
Alignment explanation
Indices: 1216029--1216197 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
1216019 AATTGAGCAC
1216029 ATGGAAATAATCAACTTAATCAAGCAAATAAAAATTAGGTGGCATTTCTGCCCCAAATCAACTTT
1 ATGGAAATAATCAACTTAATCAAGCAAATAAAAATTAGGTGGCATTTCTGCCCCAAATCAACTTT
1216094 GTGATAGGGTGAGAAGAAA
66 GTGATAGGGTGAGAAGAAA
**
1216113 ATGGAAATAATCAACTTAATCAAGCAAATAAAAATTAGGTGGCATTTCTGCCCCAAATCATTTTT
1 ATGGAAATAATCAACTTAATCAAGCAAATAAAAATTAGGTGGCATTTCTGCCCCAAATCAACTTT
1216178 GTGATAGGGTGAGAAGAAA
66 GTGATAGGGTGAGAAGAAA
1216197 A
1 A
1216198 CACTCTATCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (84 bp):
ATGGAAATAATCAACTTAATCAAGCAAATAAAAATTAGGTGGCATTTCTGCCCCAAATCAACTTT
GTGATAGGGTGAGAAGAAA
Found at i:1217237 original size:18 final size:18
Alignment explanation
Indices: 1217214--1217283 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
1217204 ACCGGTCACA
1217214 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1217232 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
1217249 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1217263 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1217281 ACC
1 ACC
1217284 GTTGACCCGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
18 33 0.73
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1217257 original size:31 final size:31
Alignment explanation
Indices: 1217218--1217298 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 31
1217208 GTCACAACCC
1217218 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1217249 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1217280 GACCGTTGACCCGTTGACC
1 GACC--CGACCCGTTGACC
1217299 GGAGTTGACC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 33 0.73
33 12 0.27
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1217283 original size:13 final size:13
Alignment explanation
Indices: 1217236--1217272 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1217226 CCGTTGACCC
1217236 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1217249 TACCCGACCCGTT
1 GACCCGACCCGTT
1217262 GACCCGACCCG
1 GACCCGACCCG
1217273 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1218637 original size:18 final size:18
Alignment explanation
Indices: 1218611--1218646 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1218601 TCGAAAGGAC
*
1218611 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1218629 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1218647 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1219879 original size:24 final size:24
Alignment explanation
Indices: 1219773--1219879 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1219763 AATATTTATC
*
1219773 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
1219797 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
1219821 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
1219845 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
1219869 TGATTTTTGAT
1 TGATTTCTGAT
1219880 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:1222029 original size:18 final size:18
Alignment explanation
Indices: 1222006--1222044 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1221996 ACCGGTCACA
1222006 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1222024 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1222042 ACC
1 ACC
1222045 GTTGACCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1223398 original size:18 final size:18
Alignment explanation
Indices: 1223372--1223407 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1223362 TCGAAAGGAC
*
1223372 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1223390 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1223408 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1224641 original size:24 final size:24
Alignment explanation
Indices: 1224535--1224641 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1224525 ATATTTTATC
*
1224535 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
1224559 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * * *
1224583 TGATTCCTAACCTGGATTCTGTTA
1 TGATTTCTGATCTGAATTATGTTT
*
1224607 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTATGTTT
*
1224631 TGATTTTTGAT
1 TGATTTCTGAT
1224642 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:1232653 original size:20 final size:20
Alignment explanation
Indices: 1232624--1232661 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1232614 CCCCTTCAAA
*
1232624 GGGGGAATCAGTTCCCTCAT
1 GGGGGAATCAATTCCCTCAT
*
1232644 GGGGGTATCAATTCCCTC
1 GGGGGAATCAATTCCCTC
1232662 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (20 bp):
GGGGGAATCAATTCCCTCAT
Found at i:1238387 original size:20 final size:20
Alignment explanation
Indices: 1238337--1238390 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1238327 GGAGTGTGGG
* *
1238337 GGGAATCGGTACCCCCTATT
1 GGGAATCGGTTCCCCCTATA
*
1238357 TGGAATCGGTTCCCCCTATA
1 GGGAATCGGTTCCCCCTATA
1238377 GGGAATCGGTTCCC
1 GGGAATCGGTTCCC
1238391 TAAGTGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (20 bp):
GGGAATCGGTTCCCCCTATA
Found at i:1251619 original size:29 final size:29
Alignment explanation
Indices: 1251580--1251687 Score: 198
Period size: 29 Copynumber: 3.7 Consensus size: 29
1251570 AGACGGTTTA
*
1251580 TCATTCATATCATTGAACTTTTAATTTCT
1 TCATTTATATCATTGAACTTTTAATTTCT
1251609 TCATTTATATCATTGAACTTTTAATTTCT
1 TCATTTATATCATTGAACTTTTAATTTCT
1251638 TCATTTATATCATTGAACTTTTAATTTCT
1 TCATTTATATCATTGAACTTTTAATTTCT
*
1251667 TCATTTATGTCATTGAACTTT
1 TCATTTATATCATTGAACTTT
1251688 ATTTTTTACT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (29 bp):
TCATTTATATCATTGAACTTTTAATTTCT
Found at i:1251973 original size:15 final size:15
Alignment explanation
Indices: 1251913--1251973 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1251903 GAACTAAGAT
*
1251913 TTTTTTAAGTTTATA
1 TTTTTTAATTTTATA
1251928 TTATTTTGAATTTTATA
1 TT-TTTT-AATTTTATA
* **
1251945 TATTTTAAAATTATA
1 TTTTTTAATTTTATA
*
1251960 TTTTTTATTTTTAT
1 TTTTTTAATTTTAT
1251974 TTAATCAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 19 0.53
16 8 0.22
17 9 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTAATTTTATA
Found at i:1251993 original size:25 final size:25
Alignment explanation
Indices: 1251972--1252028 Score: 105
Period size: 25 Copynumber: 2.2 Consensus size: 25
1251962 TTTTATTTTT
1251972 ATTTAATCAGATTTAAAATATTTCAG
1 ATTT-ATCAGATTTAAAATATTTCAG
1251998 ATTTATCAGATTTAAAATATTTCAG
1 ATTTATCAGATTTAAAATATTTCAG
1252023 ATTTAT
1 ATTTAT
1252029 TTATTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (25 bp):
ATTTATCAGATTTAAAATATTTCAG
Found at i:1251997 original size:16 final size:16
Alignment explanation
Indices: 1251978--1252027 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
1251968 TTTTATTTAA
1251978 TCAGATTTAAAATATT
1 TCAGATTTAAAATATT
1251994 TCAGA-TT----TA--
1 TCAGATTTAAAATATT
1252003 TCAGATTTAAAATATT
1 TCAGATTTAAAATATT
1252019 TCAGATTTA
1 TCAGATTTA
1252028 TTTATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
9 5 0.19
10 2 0.07
11 2 0.07
14 2 0.07
15 2 0.07
16 14 0.52
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (16 bp):
TCAGATTTAAAATATT
Found at i:1252311 original size:34 final size:35
Alignment explanation
Indices: 1252206--1252316 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
1252196 CCGAGGTCAC
* *
1252206 GTCAATAATTGTACTTCTGACATATTGAACAAGTT
1 GTCAATAATTGTATTTTTGACATATTGAACAAGTT
1252241 GTCAAT-ATCTGTATTTTTGACATATTGAACAAGTT
1 GTCAATAAT-TGTATTTTTGACATATTGAACAAGTT
* *
1252276 GTCAATAATTGTATTTTTG-CATGTTCAACAAGTT
1 GTCAATAATTGTATTTTTGACATATTGAACAAGTT
1252310 GTCAATA
1 GTCAATA
1252317 GTGGCGGGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
34 22 0.31
35 46 0.66
36 2 0.03
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (35 bp):
GTCAATAATTGTATTTTTGACATATTGAACAAGTT
Found at i:1253741 original size:40 final size:40
Alignment explanation
Indices: 1253582--1254051 Score: 441
Period size: 40 Copynumber: 11.5 Consensus size: 40
1253572 TAACGTTAGC
1253582 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
* *
1253623 GGCATTTTTATACAAAACGCTGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATAC-AAACGCCGCTATAGACTCGTACTTTA-T
* * *
1253665 GGCGTTTTTATACAAACGTCGCTATAGAGTAGTACTTT-T
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAT
* * *
1253704 -GCAGTGTTTTATACAAACGCCACTATAGACGCCTACTTTAGT
1 GGC-GT-TTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
* * *
1253746 GGC-ATTTTATATAAACGCCGCTATAGACTTGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
1253786 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
* * * * * *
1253827 GGCGTTTGTGTTTATAAACGTCGCAATAGGCTTGTACTTTAGT
1 GGCGTTT-T-TATACAAACGCCGCTATAGACTCGTACTTTA-T
* * * *
1253870 GGTG-TTTTGTACAAACGCCGCTATAGACTCTTACATTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
* * *
1253910 GCCTTTTTTTATACAAACGCCTCTATAGACTCGTACTTTAGT
1 GGC-GTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
* * * * * *
1253952 GGCGTTTATGTTTACAAATGCCACAATAGGCTTGTACTTTAGT
1 GGCGTTT-T-TATACAAACGCCGCTATAGACTCGTACTTTA-T
* *
1253995 GGCATTTTT-TACAAGCGCCGCTATAGACTCGT-CTTTAGT
1 GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTA-T
1254034 GGCGTTTTT-TACAAACGC
1 GGCGTTTTTATACAAACGC
1254052 TGCAAGTTGT
Statistics
Matches: 355, Mismatches: 61, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.01
39 26 0.07
40 104 0.29
41 79 0.22
42 79 0.22
43 65 0.18
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (40 bp):
GGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAT
Found at i:1254073 original size:125 final size:124
Alignment explanation
Indices: 1253592--1254054 Score: 530
Period size: 125 Copynumber: 3.8 Consensus size: 124
1253582 GGCGTTTTTA
* * * * *
1253592 TACAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTATACAAAACGCTGCTATAGACTCGT
1 TACAAACGCCACAATAGGCTTGTACTTTAGTGGCA-TTTTATAC-AAACGCCGCTATAGACTCGT
* * *
1253657 ACTTTAGTGGCGTTTTTATACAAACG-TCGCTATAGAGTAGTACTTT--T-GCAGTGTT-T-TA
64 ACTTTAGTGGCGTTTTTATACAAACGCT-GCTATAGACTCGTACTTTAGTGGC-GT-TTATGTT
* * *** * *
1253715 TACAAACGCCACTATAGACGCCTACTTTAGTGGCATTTTATATAAACGCCGCTATAGACTTGTAC
1 TACAAACGCCACAATAGGCTTGTACTTTAGTGGCATTTTATACAAACGCCGCTATAGACTCGTAC
* *
1253780 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTGTGTT
66 TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTACTTTAGTGGCGTTTATGTT
* * * ** * *
1253839 TATAAACGTCGCAATAGGCTTGTACTTTAGTGGTGTTTTGTACAAACGCCGCTATAGACTCTTAC
1 TACAAACGCCACAATAGGCTTGTACTTTAGTGGCATTTTATACAAACGCCGCTATAGACTCGTAC
* * *
1253904 ATTAGTGCCTTTTTTTATACAAACGCCT-CTATAGACTCGTACTTTAGTGGCGTTTATGTT
66 TTTAGTGGC-GTTTTTATACAAACG-CTGCTATAGACTCGTACTTTAGTGGCGTTTATGTT
* * *
1253964 TACAAATGCCACAATAGGCTTGTACTTTAGTGGCATTTTTTACAAGCGCCGCTATAGACTCGT-C
1 TACAAACGCCACAATAGGCTTGTACTTTAGTGGCATTTTATACAAACGCCGCTATAGACTCGTAC
1254028 TTTAGTGGCGTTTTT-TACAAACGCTGC
66 TTTAGTGGCGTTTTTATACAAACGCTGC
1254055 AAGTTGTCTC
Statistics
Matches: 290, Mismatches: 41, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
121 62 0.21
122 18 0.06
123 41 0.14
124 69 0.24
125 99 0.34
126 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (124 bp):
TACAAACGCCACAATAGGCTTGTACTTTAGTGGCATTTTATACAAACGCCGCTATAGACTCGTAC
TTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCGTACTTTAGTGGCGTTTATGTT
Found at i:1257125 original size:59 final size:59
Alignment explanation
Indices: 1257031--1257144 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
1257021 CGCCACTGAC
*
1257031 CATTTAAAACCATCTTGGTTAAATTTATAGCGAACTTTTTATTCATTACTGCTATGTAT
1 CATTTAAAACCATATTGGTTAAATTTATAGCGAACTTTTTATTCATTACTGCTATGTAT
* *
1257090 CATTTAAAACTATATTGGTTAAATTTATAGTGAACTTTTTATTCATTACTGCTAT
1 CATTTAAAACCATATTGGTTAAATTTATAGCGAACTTTTTATTCATTACTGCTAT
1257145 TCTTGTACAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (59 bp):
CATTTAAAACCATATTGGTTAAATTTATAGCGAACTTTTTATTCATTACTGCTATGTAT
Found at i:1258063 original size:43 final size:43
Alignment explanation
Indices: 1257994--1258280 Score: 326
Period size: 43 Copynumber: 6.7 Consensus size: 43
1257984 ATGGTAATTA
*
1257994 GCGGCGTTTGT-TCCAAAACCGCCGCTACAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTT
* *
1258036 GCGACGTTTGTATCCAAAAACGTCGCTACAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTT
* * *
1258079 GCGGCGTTTGTATCCAAAAACGCCTCTACAGATCTGACGTTTC
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTT
* * * * *
1258122 GCGGCGTTTGTATACAAAATCGTCTCTATAGATCTGACCTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACC-TTTT
* * *
1258166 GCGGCGTTTGTATACAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTT
** * * *
1258209 GCGGCGTTTGT-TTAAAAAACGCTGCTATAGATCTTGACTTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATC-TGACCTTTT
* * * *
1258252 GCGGCATTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTA
1258281 ACATTAGCGG
Statistics
Matches: 212, Mismatches: 28, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
42 28 0.13
43 133 0.63
44 38 0.18
45 13 0.06
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTT
Found at i:1258213 original size:87 final size:87
Alignment explanation
Indices: 1257994--1258280 Score: 359
Period size: 86 Copynumber: 3.3 Consensus size: 87
1257984 ATGGTAATTA
* * *
1257994 GCGGCGTTTGT-TCCAAAACCGCCGCTACAGATCTGACCTTTTGCGACGTTTGTATCCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTTGCGGCGTTTGTATACAAAAACG
* *
1258058 TCGCTACAGATCTGACC-TTTT
66 TCTCTATAGATCTGACCTTTTT
* * * *
1258079 GCGGCGTTTGTATCCAAAAACGCCTCTACAGATCTGACGTTTCGCGGCGTTTGTATACAAAATCG
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTTGCGGCGTTTGTATACAAAAACG
1258144 TCTCTATAGATCTGACCTTTTT
66 TCTCTATAGATCTGACCTTTTT
* * * *
1258166 GCGGCGTTTGTATACAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTTA-AAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTTGCGGCGTTTGTATACAAAAACG
1258230 -CTGCTATAGATCTTGA-CTTTTT
66 TCT-CTATAGATC-TGACCTTTTT
* * * *
1258252 GCGGCATTTTTATTTCACAAACGCCGCTA
1 GCGGCGTTTGTA-TCCAAAAACGCCGCTA
1258281 ACATTAGCGG
Statistics
Matches: 176, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
85 13 0.07
86 92 0.52
87 71 0.40
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (87 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTACAGATCTGACCTTTTGCGGCGTTTGTATACAAAAACG
TCTCTATAGATCTGACCTTTTT
Found at i:1258256 original size:130 final size:128
Alignment explanation
Indices: 1257994--1258256 Score: 341
Period size: 130 Copynumber: 2.0 Consensus size: 128
1257984 ATGGTAATTA
* * *
1257994 GCGGCGTTTGTTCCAAAACCGCCGCTACAGATCTGACCTTTTGCGACGTTTGTATCCAAAAACGT
1 GCGGCGTTTGTTACAAAACCGCCGCTACAGATCTGACCTTTTGCGACGTTTGTATACAAAAACGC
* *
1258059 CGCTACAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCTCTACAGATCTGACGTTTC
66 CGCTACAGATATGACCTTTTGCGGCGTTTGTATCAAAAAACGCCTCTACAGATCTGACGTTTC
* * * * *
1258122 GCGGCGTTTGTATACAAAATCGTCTCTATAGATCTGACCTTTTTGCGGCGTTTGTATACAAAAAC
1 GCGGCGTTTGT-TACAAAACCGCCGCTACAGATCTGACC-TTTTGCGACGTTTGTATACAAAAAC
* * * *
1258187 GCCGCTATAGATATGACCTTTTGCGGCGTTTGT-TTAAAAAACG-CTGCTATAGATCTTGACTTT
64 GCCGCTACAGATATGACCTTTTGCGGCGTTTGTATCAAAAAACGCCT-CTACAGATC-TGACGTT
*
1258250 TT
127 TC
1258252 GCGGC
1 GCGGC
1258257 ATTTTTATTT
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
128 13 0.11
129 38 0.33
130 65 0.56
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (128 bp):
GCGGCGTTTGTTACAAAACCGCCGCTACAGATCTGACCTTTTGCGACGTTTGTATACAAAAACGC
CGCTACAGATATGACCTTTTGCGGCGTTTGTATCAAAAAACGCCTCTACAGATCTGACGTTTC
Found at i:1262593 original size:9 final size:9
Alignment explanation
Indices: 1262581--1262652 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
1262571 TTAATATTTT
1262581 AAATAATTA
1 AAATAATTA
1262590 AAATAATATA
1 AAATAAT-TA
** * *
1262600 TTATATTTT
1 AAATAATTA
1262609 AAATAATTA
1 AAATAATTA
1262618 AAATAATATA
1 AAATAAT-TA
** * *
1262628 TTATATTTT
1 AAATAATTA
1262637 AAATAATTA
1 AAATAATTA
1262646 AAATAAT
1 AAATAAT
1262653 ATATTTTAAT
Statistics
Matches: 45, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
9 33 0.73
10 12 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATAATTA
Found at i:1262612 original size:28 final size:28
Alignment explanation
Indices: 1262563--1262657 Score: 181
Period size: 28 Copynumber: 3.4 Consensus size: 28
1262553 GAATTAGACT
1262563 ATAATATATTAATATTTTAAATAATTAAA
1 ATAATATATT-ATATTTTAAATAATTAAA
1262592 ATAATATATTATATTTTAAATAATTAAA
1 ATAATATATTATATTTTAAATAATTAAA
1262620 ATAATATATTATATTTTAAATAATTAAA
1 ATAATATATTATATTTTAAATAATTAAA
1262648 ATAATATATT
1 ATAATATATT
1262658 TTAATAGTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
28 56 0.85
29 10 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAATATATTATATTTTAAATAATTAAA
Found at i:1262670 original size:23 final size:24
Alignment explanation
Indices: 1262574--1262671 Score: 83
Period size: 28 Copynumber: 3.8 Consensus size: 24
1262564 TAATATATTA
*
1262574 ATATTTTAAATAATTAAAATAATATATT
1 ATATTTTAAATAA-TATAA-AATA-A-T
*
1262602 ATATTTTAAATAATTAAAATAATATATT
1 ATATTTTAAATAA-TATAA-AATA-A-T
1262630 ATATTTTAAATAAT-TAAAATAAT
1 ATATTTTAAATAATATAAAATAAT
*
1262653 ATATTTT-AATAGTATAAAA
1 ATATTTTAAATAATATAAAA
1262672 ATAAATTCCT
Statistics
Matches: 67, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.07
23 13 0.19
24 1 0.01
25 4 0.06
26 2 0.03
27 1 0.01
28 41 0.61
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (24 bp):
ATATTTTAAATAATATAAAATAAT
Found at i:1263692 original size:28 final size:29
Alignment explanation
Indices: 1263652--1263707 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1263642 AATACGTTAG
*
1263652 ATCAAAATTTAATAAATT-AATAAATTTTC
1 ATCAAAATATAAT-AATTAAATAAATTTTC
*
1263681 ATCAAAA-ATAATATTTAAATAAATTTT
1 ATCAAAATATAATAATTAAATAAATTTT
1263708 ATTATTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 3 0.12
28 14 0.58
29 7 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (29 bp):
ATCAAAATATAATAATTAAATAAATTTTC
Found at i:1265517 original size:2 final size:2
Alignment explanation
Indices: 1265510--1265537 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1265500 TCTATCCACA
1265510 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
1265538 GATGACAATG
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:1269132 original size:60 final size:59
Alignment explanation
Indices: 1269009--1269133 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
1268999 TGATCCCTCA
* * * ** *
1269009 ACTATAGGATATTGCTTTGTTGAGTCCTTTGACTATTAAAATTTACAAAATGGTCCCTTG
1 ACTATAGGATATTGCTTTATTGAGT-CTTTGACTATCAAAACTTACAAAATAATCCATTG
*
1269069 ACTATAGGATGTTGCTTTATTGAGT-TTCTCGACTATCAAAACTTACAAAATAAT-CATTCG
1 ACTATAGGATATTGCTTTATTGAGTCTT-T-GACTATCAAAACTTACAAAATAATCCATT-G
1269129 ACTAT
1 ACTAT
1269134 TCATTATGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
58 2 0.04
59 4 0.07
60 49 0.89
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (59 bp):
ACTATAGGATATTGCTTTATTGAGTCTTTGACTATCAAAACTTACAAAATAATCCATTG
Found at i:1271979 original size:17 final size:17
Alignment explanation
Indices: 1271957--1272011 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
1271947 CCGGTCTGAT
*
1271957 CCGACCCGGTGACCGAC
1 CCGACCCGTTGACCGAC
*
1271974 CCGACCCGTTAACCGAC
1 CCGACCCGTTGACCGAC
*
1271991 CCGACCAGTTGACTCGAC
1 CCGACCCGTTGAC-CGAC
1272009 CCG
1 CCG
1272012 TTGACCCGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 26 0.79
18 7 0.21
ACGTcount: A:0.20, C:0.45, G:0.24, T:0.11
Consensus pattern (17 bp):
CCGACCCGTTGACCGAC
Found at i:1272029 original size:13 final size:14
Alignment explanation
Indices: 1271988--1272026 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1271978 CCCGTTAACC
1271988 GACCCGA-CCAGTT
1 GACCCGACCCAGTT
*
1272001 GACTCGACCC-GTT
1 GACCCGACCCAGTT
1272014 GACCCGACCCAGT
1 GACCCGACCCAGT
1272027 GACATTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.21, C:0.41, G:0.23, T:0.15
Consensus pattern (14 bp):
GACCCGACCCAGTT
Found at i:1272075 original size:29 final size:29
Alignment explanation
Indices: 1272024--1272215 Score: 242
Period size: 29 Copynumber: 6.6 Consensus size: 29
1272014 GACCCGACCC
* *
1272024 AGTGACATTCTGGGAATTTTTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* * *
1272053 GGTGACATTTTGGTAATCATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* *
1272082 TGTGGCATTCTT-GGAATTATTTTGAAAAA
1 AGTGACATT-TTGGGAATTATTTTGAAAAA
* *
1272111 AGTGAAATTATGGGAATTATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
* * *
1272140 AGTGATATTCTGGGAAGTATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
*
1272169 TGTGACATTTTGGGAATTATTTTGAAAAA
1 AGTGACATTTTGGGAATTATTTTGAAAAA
*
1272198 GGTGACATTTTGGGAATT
1 AGTGACATTTTGGGAATT
1272216 TTCGAATGTG
Statistics
Matches: 140, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
28 1 0.01
29 137 0.98
30 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (29 bp):
AGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:1279539 original size:29 final size:29
Alignment explanation
Indices: 1279489--1279676 Score: 254
Period size: 29 Copynumber: 6.6 Consensus size: 29
1279479 CCCGACCCGT
*
1279489 TGACATTTTGGGAATTATTTTGAAAAAGG
1 TGACATTCTGGGAATTATTTTGAAAAAGG
*
1279518 TGATATTCTGGGAATTATTTTGAAAAAGG
1 TGACATTCTGGGAATTATTTTGAAAAAGG
* * *
1279547 TGACATTTTGGGAATCATTTTGAAAAA-A
1 TGACATTCTGGGAATTATTTTGAAAAAGG
* *
1279575 TGGCATTCTGGGAATTATTTTGAAAAATG
1 TGACATTCTGGGAATTATTTTGAAAAAGG
* *
1279604 TGACATTTTGGGAATTATTTTGAAAAAGA
1 TGACATTCTGGGAATTATTTTGAAAAAGG
*
1279633 TGACATTCT-GGAATTATTTTGAAAAATG
1 TGACATTCTGGGAATTATTTTGAAAAAGG
* *
1279661 TGATATTTTGGGAATT
1 TGACATTCTGGGAATT
1279677 TTCGAATGTG
Statistics
Matches: 138, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
28 48 0.35
29 90 0.65
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.39
Consensus pattern (29 bp):
TGACATTCTGGGAATTATTTTGAAAAAGG
Found at i:1279607 original size:57 final size:58
Alignment explanation
Indices: 1279489--1279676 Score: 308
Period size: 57 Copynumber: 3.3 Consensus size: 58
1279479 CCCGACCCGT
* * *
1279489 TGACATTTTGGGAATTATTTTGAAAAAGGTGATATTCTGGGAATTATTTTGAAAAAGG
1 TGACATTTTGGGAATTATTTTGAAAAAGATGACATTCTGGGAATTATTTTGAAAAATG
* *
1279547 TGACATTTTGGGAATCATTTTGAAAAA-ATGGCATTCTGGGAATTATTTTGAAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAAGATGACATTCTGGGAATTATTTTGAAAAATG
1279604 TGACATTTTGGGAATTATTTTGAAAAAGATGACATTCT-GGAATTATTTTGAAAAATG
1 TGACATTTTGGGAATTATTTTGAAAAAGATGACATTCTGGGAATTATTTTGAAAAATG
*
1279661 TGATATTTTGGGAATT
1 TGACATTTTGGGAATT
1279677 TTCGAATGTG
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
57 86 0.71
58 35 0.29
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.39
Consensus pattern (58 bp):
TGACATTTTGGGAATTATTTTGAAAAAGATGACATTCTGGGAATTATTTTGAAAAATG
Found at i:1279673 original size:86 final size:86
Alignment explanation
Indices: 1279492--1279676 Score: 266
Period size: 86 Copynumber: 2.2 Consensus size: 86
1279482 GACCCGTTGA
* * *
1279492 CATTTTGGGAATTATTTTGAAAAAGGTGATATTCTGGGAATTATTTTGAAAAAGGTGACATTTTG
1 CATTTTGGGAATTATTTTGAAAAAGGTGACATTCTGGGAATTATTTTGAAAAAGATGACATTCTG
1279557 GGAATCATTTTGAAAAAATGG
66 GGAATCATTTTGAAAAAATGG
* * *
1279578 CATTCTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAAGATGACATTCT-
1 CATTTTGGGAATTATTTTGAAAAAGGTGACATTCTGGGAATTATTTTGAAAAAGATGACATTCTG
*
1279642 GGAATTATTTTG-AAAAATGTG
66 GGAATCATTTTGAAAAAATG-G
*
1279663 ATATTTTGGGAATT
1 -CATTTTGGGAATT
1279677 TTCGAATGTG
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 7 0.08
85 12 0.14
86 69 0.78
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.39
Consensus pattern (86 bp):
CATTTTGGGAATTATTTTGAAAAAGGTGACATTCTGGGAATTATTTTGAAAAAGATGACATTCTG
GGAATCATTTTGAAAAAATGG
Found at i:1285879 original size:23 final size:22
Alignment explanation
Indices: 1285845--1285893 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1285835 ATGACACATT
*
1285845 TTTCTCTACCTTTATGGCACGC
1 TTTCTCTACCTTTATGACACGC
* *
1285867 TTTCTTCTTCCTTTATGACACGT
1 TTTC-TCTACCTTTATGACACGC
1285890 TTTC
1 TTTC
1285894 AATCGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.12, C:0.29, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTCTCTACCTTTATGACACGC
Found at i:1286863 original size:23 final size:24
Alignment explanation
Indices: 1286810--1286864 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1286800 AACCTTCACG
*
1286810 AACAAATTCATTTATATGTTCAGT
1 AACATATTCATTTATATGTTCAGT
* *
1286834 AATATATTCATTTA-ATGTTCATT
1 AACATATTCATTTATATGTTCAGT
*
1286857 GACATATT
1 AACATATT
1286865 TGTTTATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (24 bp):
AACATATTCATTTATATGTTCAGT
Found at i:1296788 original size:61 final size:61
Alignment explanation
Indices: 1296711--1296831 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
1296701 TATTATCAGC
* *
1296711 TAGGCCAAACATTATTTCTAAAGTTTC-CAAGGGTCTTATAGGATTATTTATCATCTAAATT
1 TAGGCCAAACAATATTTCTAAAG-TTCACAAGGGTCTTATAGGATCATTTATCATCTAAATT
1296772 TAGGCCAAACAATATTTCTAAAGTTCACAAGGGTCTTATAGGATCATTTATCATCTAAAT
1 TAGGCCAAACAATATTTCTAAAGTTCACAAGGGTCTTATAGGATCATTTATCATCTAAAT
1296832 ATCCTATGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 3 0.05
61 54 0.95
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (61 bp):
TAGGCCAAACAATATTTCTAAAGTTCACAAGGGTCTTATAGGATCATTTATCATCTAAATT
Found at i:1309754 original size:18 final size:18
Alignment explanation
Indices: 1309731--1309769 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1309721 ATTATTGGGT
1309731 CACCTCATAAAATAAAGG
1 CACCTCATAAAATAAAGG
1309749 CACCTCATAAAATAAAGG
1 CACCTCATAAAATAAAGG
1309767 CAC
1 CAC
1309770 GTTACAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (18 bp):
CACCTCATAAAATAAAGG
Found at i:1310712 original size:12 final size:12
Alignment explanation
Indices: 1310697--1310727 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1310687 GTTATTTAAA
1310697 CGGGTATCGGGC
1 CGGGTATCGGGC
1310709 CGGGTATCGGGC
1 CGGGTATCGGGC
*
1310721 TGGGTAT
1 CGGGTAT
1310728 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:1310748 original size:17 final size:17
Alignment explanation
Indices: 1310726--1310775 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1310716 CGGGCTGGGT
1310726 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
*
1310743 ATATATA---AATATTAT
1 ATATATATTTAA-ATTAA
*
1310758 ATATATATTTTAATTAA
1 ATATATATTTAAATTAA
1310775 A
1 A
1310776 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
17 12 0.46
18 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:1310788 original size:32 final size:32
Alignment explanation
Indices: 1310725--1310786 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1310715 TCGGGCTGGG
1310725 TATATATATTTAAATTAAATATATAAATATTA
1 TATATATATTTAAATTAAATATATAAATATTA
*
1310757 TATATATATTTTAATTAAA-AT-TAAA-ATTA
1 TATATATATTTAAATTAAATATATAAATATTA
1310786 T
1 T
1310787 TAAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.17
30 4 0.14
31 2 0.07
32 18 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TATATATATTTAAATTAAATATATAAATATTA
Found at i:1320088 original size:22 final size:23
Alignment explanation
Indices: 1320045--1320099 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
1320035 ATTAATAATC
* *
1320045 AATAATTTAATTGATATCATTAA
1 AATAATTTAATTAATATAATTAA
*
1320068 AATAA-TTAATTAATCTAATTAA
1 AATAATTTAATTAATATAATTAA
* *
1320090 TAGAATTTAA
1 AATAATTTAA
1320100 AAATTAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (23 bp):
AATAATTTAATTAATATAATTAA
Found at i:1322822 original size:20 final size:21
Alignment explanation
Indices: 1322789--1322836 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1322779 TTATCAGAAA
*
1322789 TATTATTATTTTTATC-TGTTT
1 TATTATTATTTTTA-CAAGTTT
1322810 TATTATT-TTTTTACAAGTTT
1 TATTATTATTTTTACAAGTTT
1322830 TATTATT
1 TATTATT
1322837 GTTTGACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TATTATTATTTTTACAAGTTT
Found at i:1323407 original size:126 final size:126
Alignment explanation
Indices: 1323181--1323435 Score: 474
Period size: 126 Copynumber: 2.0 Consensus size: 126
1323171 GCGTTGTCCC
1323181 TTAACCCTACTGTTGCTTTTATTTTGTTTAGGGTTAATTCTAATGCGGGATTCAAAAATATTTTT
1 TTAACCCTACTGTTGCTTTTATTTTGTTTAGGGTTAATTCTAATGCGGGATTCAAAAATATTTTT
* *
1323246 GATGGTGGATATTATATGTTAACAATAAAATTTTTCGTATAAGATAAATATAAATAAAATT
66 GATGGTGGATATTATATATTAACAATAAAAATTTTCGTATAAGATAAATATAAATAAAATT
* *
1323307 TTAACTCTATTGTTGCTTTTATTTTGTTTAGGGTTAATTCTAATGCGGGATTCAAAAATATTTTT
1 TTAACCCTACTGTTGCTTTTATTTTGTTTAGGGTTAATTCTAATGCGGGATTCAAAAATATTTTT
1323372 GATGGTGGATATTATATATTAACAATAAAAATTTTCGTATAAGATAAATATAAATAAAATT
66 GATGGTGGATATTATATATTAACAATAAAAATTTTCGTATAAGATAAATATAAATAAAATT
1323433 TTA
1 TTA
1323436 TGGTGAACAT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (126 bp):
TTAACCCTACTGTTGCTTTTATTTTGTTTAGGGTTAATTCTAATGCGGGATTCAAAAATATTTTT
GATGGTGGATATTATATATTAACAATAAAAATTTTCGTATAAGATAAATATAAATAAAATT
Found at i:1327497 original size:74 final size:74
Alignment explanation
Indices: 1327413--1327561 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
1327403 TGAGTTGGTC
*
1327413 GCTTTGACAAGAGAGTAAGAGAAGTCGTATGAGTGATTAATCTCAAGTGGTAGTTCACCACATTC
1 GCTTTGACAAGAGAGTAAGAGAAGTCCTATGAGTGATTAATCTCAAGTGGTAGTTCACCACATTC
1327478 CTTATGAAG
66 CTTATGAAG
1327487 GCTTTGACAAGAGAGTAAGAGAAGTCCTATGAGTGATTAATCTCAAGTGGTAGTTCACCACATTC
1 GCTTTGACAAGAGAGTAAGAGAAGTCCTATGAGTGATTAATCTCAAGTGGTAGTTCACCACATTC
1327552 CTTATGAAG
66 CTTATGAAG
1327561 G
1 G
1327562 TTAAAGCTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (74 bp):
GCTTTGACAAGAGAGTAAGAGAAGTCCTATGAGTGATTAATCTCAAGTGGTAGTTCACCACATTC
CTTATGAAG
Found at i:1336198 original size:78 final size:78
Alignment explanation
Indices: 1336069--1336221 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
1336059 CACGTACACC
*
1336069 AACATTACCTTGACTGTTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
1 AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
1336134 TACCAGTAGCGCT
66 TACCAGTAGCGCT
* *
1336147 AACATTACCTTGACTGCTATTGGAAGCACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACCCT
1 AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
1336212 TACCAGTAGC
66 TACCAGTAGC
1336222 ACTAGTATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (78 bp):
AACATTACCTTGACTGCTATTGGAAGAACTGACGTCGCCACTTCCTCTAGTTTTAGCTTCACACT
TACCAGTAGCGCT
Found at i:1337595 original size:96 final size:94
Alignment explanation
Indices: 1337495--1337832 Score: 367
Period size: 96 Copynumber: 3.6 Consensus size: 94
1337485 TGTCGGTAGA
** * * * *
1337495 ACTAGCACCACCATGTCCACCAACTGTAGCTTGACTATTGCTACAATCACTAACACCGCCT-TCT
1 ACTAG-ACCACCACCTCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCT-T
1337559 CCACTAACAATAGCTTGACCATGGCCAGAAGC
64 CCAC-AACAATAGCTTGACCATGGCCAGAAGC
* * *
1337591 ACTAG---------TGCCACCAACTTTAACTTGACTATTTCTAGAAGCATTAGCACCGCCTCTTC
1 ACTAGACCACCACCT-CCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTC
*
1337647 CACCAACAATAGCTTGACAATGAG-CAGAAGC
65 CA-CAACAATAGCTTGACCATG-GCCAGAAGC
*
1337678 ACTAGAGCCACCACCTCCACCAATTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTC
1 ACTAGA-CCACCACCTCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTC
* *
1337743 CAGCAACAATAGTTTGACCATGGCCATAAGC
65 CA-CAACAATAGCTTGACCATGGCCAGAAGC
* *
1337774 ACTAG-CGCTACCACCTCCACTAACTTTAGCTTGATTATTGCTAGAAGCACTAGCACCGC
1 ACTAGAC-C-ACCACCTCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGC
1337833 TAAGGATTAT
Statistics
Matches: 206, Mismatches: 19, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
86 1 0.00
87 71 0.34
88 3 0.01
94 1 0.00
95 2 0.01
96 127 0.62
97 1 0.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (94 bp):
ACTAGACCACCACCTCCACCAACTTTAGCTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCC
ACAACAATAGCTTGACCATGGCCAGAAGC
Found at i:1337663 original size:48 final size:48
Alignment explanation
Indices: 1337611--1337832 Score: 187
Period size: 48 Copynumber: 4.6 Consensus size: 48
1337601 CCAACTTTAA
* *
1337611 CTTGACTATTTCTAGAAGCATTAGCACCGCCTCTTCCACCAACAATAG
1 CTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACCAACAATAG
* * * * * ***
1337659 CTTGACAATGAGC-AGAAGCACTAG-AGCCACCACCTCCACCAATTTTAG
1 CTTGACTAT-TGCTAGAAGCACTAGCA-CCGCCTCTTCCACCAACAATAG
*
1337707 CTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCAGCAACAATAG
1 CTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACCAACAATAG
* * * * * * ** * * * **
1337755 TTTGACCATGGCCATAAGCACTAGCGCTACCACCTCCACTAACTTTAG
1 CTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACCAACAATAG
*
1337803 CTTGATTATTGCTAGAAGCACTAGCACCGC
1 CTTGACTATTGCTAGAAGCACTAGCACCGC
1337833 TAAGGATTAT
Statistics
Matches: 128, Mismatches: 42, Indels: 8
0.72 0.24 0.04
Matches are distributed among these distances:
47 3 0.02
48 123 0.96
49 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (48 bp):
CTTGACTATTGCTAGAAGCACTAGCACCGCCTCTTCCACCAACAATAG
Found at i:1342079 original size:90 final size:90
Alignment explanation
Indices: 1341950--1342169 Score: 235
Period size: 90 Copynumber: 2.4 Consensus size: 90
1341940 CGGGCACTCG
* * * * * * *
1341950 CACCACCCCCACCTTCTCCTCTTGCCCCACCAGCTACACCAAAACTAGCACCAGAACCTGCAACT
1 CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCAAAACCAACACCAGAACCGGCAACT
*
1342015 CCTGATCCACCAACACCACCACTTG
66 CCTGATCCACCAACACCACCACTTA
* * *** * * * *
1342040 CACTACCTCCACCATGTCCTTTTGCCCCACCAGCAACACCTCCACCAACACTAGTACCGGTAGCT
1 CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCAAAACCAACACCAGAACCGGCAACT
* * *
1342105 CCTGATCCACCAATACCGCTACTTA
66 CCTGATCCACCAACACCACCACTTA
*
1342130 CACCACCTCCACCTTG-CCATCTTGCCCCACCAGCAACACC
1 CACCACCTCCACCATGTCC-TCTTGCCCCACCAGCAACACC
1342170 TCCACCTCCG
Statistics
Matches: 106, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
89 2 0.02
90 104 0.98
ACGTcount: A:0.26, C:0.48, G:0.09, T:0.18
Consensus pattern (90 bp):
CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCAAAACCAACACCAGAACCGGCAACT
CCTGATCCACCAACACCACCACTTA
Found at i:1342202 original size:90 final size:90
Alignment explanation
Indices: 1341950--1342202 Score: 195
Period size: 90 Copynumber: 2.8 Consensus size: 90
1341940 CGGGCACTCG
* * * * *** * * * *
1341950 CACCACCCCCACCTTCTCCTCTTGCCCCACCAGCTACACCAAAACTAGCACCAGA-ACCTGCAAC
1 CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCTCCACCAACACCA-ACACCGGCACC
* * *
1342014 TCCTGATCCACCAACACCACCACTTG
65 GCCAGATCCACCAACACCACCACTTA
* * * ** * * *
1342040 CACTACCTCCACCATGTCCTTTTGCCCCACCAGCAACACCTCCACCAACACTAGTACCGGTAGCT
1 CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCTCCACCAACACCAACACCGGCACCG
* * * *
1342105 CCTGATCCACCAATACCGCTACTTA
66 CCAGATCCACCAACACCACCACTTA
* ** *
1342130 CACCACCTCCACCTTG-CCATCTTGCCCCACCAGCAACACCTCCACCTCCGCCAACACCGGCACC
1 CACCACCTCCACCATGTCC-TCTTGCCCCACCAGCAACACCTCCACCAACACCAACACCGGCACC
*
1342194 GGCAGATCC
65 GCCAGATCC
1342203 TGATCCACCA
Statistics
Matches: 127, Mismatches: 34, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
89 2 0.02
90 125 0.98
ACGTcount: A:0.25, C:0.48, G:0.10, T:0.17
Consensus pattern (90 bp):
CACCACCTCCACCATGTCCTCTTGCCCCACCAGCAACACCTCCACCAACACCAACACCGGCACCG
CCAGATCCACCAACACCACCACTTA
Found at i:1342309 original size:18 final size:18
Alignment explanation
Indices: 1342286--1342332 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1342276 CGTCCTCCAA
*
1342286 CTCCACCTCCAAAACTAG
1 CTCCACCTCCAAAACCAG
1342304 CTCCACCTCCAAAACCAG
1 CTCCACCTCCAAAACCAG
*
1342322 CTCCAGCTCCA
1 CTCCACCTCCA
1342333 CCTCCAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.49, G:0.06, T:0.15
Consensus pattern (18 bp):
CTCCACCTCCAAAACCAG
Found at i:1345401 original size:18 final size:18
Alignment explanation
Indices: 1345380--1345460 Score: 99
Period size: 18 Copynumber: 4.5 Consensus size: 18
1345370 AACTCCACCT
* *
1345380 CCTCCATGACCACCTGCA
1 CCTCCATGAGCACCGGCA
*
1345398 CCTCCATGAGCACCGGCT
1 CCTCCATGAGCACCGGCA
* *
1345416 CCTCCATGGGCACCTGCA
1 CCTCCATGAGCACCGGCA
* *
1345434 CCCCCCTGAGCACCGGCA
1 CCTCCATGAGCACCGGCA
1345452 CCTCCATGA
1 CCTCCATGA
1345461 ATCCTCCTCC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.19, C:0.48, G:0.19, T:0.15
Consensus pattern (18 bp):
CCTCCATGAGCACCGGCA
Found at i:1345418 original size:36 final size:36
Alignment explanation
Indices: 1345378--1345460 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
1345368 CCAACTCCAC
*
1345378 CTCCTCCATGACCACCTGCACCTCCATGAGCACCGG
1 CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
** *
1345414 CTCCTCCATGGGCACCTGCACCCCCCTGAGCACCGG
1 CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
*
1345450 CACCTCCATGA
1 CTCCTCCATGA
1345461 ATCCTCCTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.18, C:0.48, G:0.18, T:0.16
Consensus pattern (36 bp):
CTCCTCCATGACCACCTGCACCCCCATGAGCACCGG
Found at i:1347158 original size:2 final size:2
Alignment explanation
Indices: 1347147--1347229 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
1347137 GGAAATATTA
1347147 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1347186 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1347228 AT
1 AT
1347230 TTAAAGCTCA
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 75 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1347623 original size:25 final size:27
Alignment explanation
Indices: 1347582--1347632 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
1347572 TTATTTATCC
*
1347582 AAAATAAATATATAAA-G-TATTATTA
1 AAAATAAATATAAAAAGGATATTATTA
1347607 AAAAT-AATATTAAAAAGGATATTATT
1 AAAATAAATA-TAAAAAGGATATTATT
1347633 TCATAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 1 0.05
27 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAATAAATATAAAAAGGATATTATTA
Found at i:1357873 original size:22 final size:21
Alignment explanation
Indices: 1357833--1357873 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1357823 GCATGGCAAA
*
1357833 GATCAGGGTTATGCACAAAAT
1 GATCAGGGTTATCCACAAAAT
*
1357854 GATCATGGGTTATCCTCAAA
1 GATCA-GGGTTATCCACAAA
1357874 TAAATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (21 bp):
GATCAGGGTTATCCACAAAAT
Found at i:1359988 original size:51 final size:51
Alignment explanation
Indices: 1359929--1360029 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
1359919 TCAGGGGGAG
* *
1359929 AGTTACAAGGAATTTCAGCCTGCTCAAACCGATATTTCTTTACAGTCTATT
1 AGTTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTATT
*
1359980 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
1 AGTTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTAT
1360030 CCTTTCCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGCTCAAACCGATATTTCTTTACAGCCTATT
Found at i:1362271 original size:14 final size:14
Alignment explanation
Indices: 1362252--1362295 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
1362242 TAACAGACTT
1362252 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1362266 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
1362282 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1362296 ACTGGATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:1362284 original size:16 final size:16
Alignment explanation
Indices: 1362252--1362295 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1362242 TAACAGACTT
1362252 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
1362266 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
1362282 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
1362296 ACTGGATGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:1378692 original size:27 final size:27
Alignment explanation
Indices: 1378654--1378709 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1378644 CTAATATATG
1378654 AATTTGCAACCTCCTCACAACCACCAA
1 AATTTGCAACCTCCTCACAACCACCAA
1378681 AATTTGCAACCTCCTCACAACCACCAA
1 AATTTGCAACCTCCTCACAACCACCAA
1378708 AA
1 AA
1378710 CAAGGTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.39, G:0.04, T:0.18
Consensus pattern (27 bp):
AATTTGCAACCTCCTCACAACCACCAA
Found at i:1382059 original size:64 final size:64
Alignment explanation
Indices: 1381974--1382130 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 64
1381964 TTCAGTGTGT
* * * * *
1381974 ATCGATACACAGGAAGTGCATCGATGCACCCCTTAAAAATGGAAATATCGAATGCAATTAGTGC
1 ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
* * * * *** * *
1382038 ATCGATGCATAGGGAGTGCATCGATACACCCCTTTAATATTAAAACATCGAATGTGCTTTGTGT
1 ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
*
1382102 ATTGATGCAT-GGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGG-AGTGCATCGATGCAC
1382131 ATGTTAAGGG
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 3 0.04
64 73 0.96
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGGAGTGCATCGATGCACCCCTTAAAAATGAAAACATCGAATGCAATTAGTGC
Found at i:1388221 original size:23 final size:23
Alignment explanation
Indices: 1388187--1388244 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1388177 TTTTATATGC
1388187 CACTTCGGTGCAATTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
* * *
1388210 CACTTCGATGCAATTCTATGTGG
1 CACTTCGGTGCAATTCTACGCGG
1388233 CACTTCGGTGCA
1 CACTTCGGTGCA
1388245 TTTATACGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:1390576 original size:30 final size:31
Alignment explanation
Indices: 1390532--1390590 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1390522 AGGTATAAAT
*
1390532 AGAAAAAGTGATAATTCTTATGGACAAATCG
1 AGAAAAAGTGATAATTCTTAAGGACAAATCG
*
1390563 AGAAAAA-TGATAATTCTTAAGGATAAAT
1 AGAAAAAGTGATAATTCTTAAGGACAAAT
1390591 TAAGAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (31 bp):
AGAAAAAGTGATAATTCTTAAGGACAAATCG
Found at i:1390793 original size:16 final size:16
Alignment explanation
Indices: 1390762--1390803 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1390752 TTTTTTAGAT
1390762 TTTAAGTTTAAGTTTAAA
1 TTTAA-TTT-AGTTTAAA
1390780 TTTAATTTAGTTTAAA
1 TTTAATTTAGTTTAAA
1390796 TTT-ATTTA
1 TTTAATTTA
1390804 TGTGTGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 3 0.12
18 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTAATTTAGTTTAAA
Found at i:1391216 original size:12 final size:12
Alignment explanation
Indices: 1391189--1391236 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
1391179 ATATGATATA
1391189 ATATTTGAATAATT
1 ATATTT-AA-AATT
1391203 ATATTTAAAATT
1 ATATTTAAAATT
1391215 ATAATTTAAAA-T
1 AT-ATTTAAAATT
*
1391227 ATAATTAAAA
1 ATATTTAAAA
1391237 ATTAAGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 7 0.22
12 9 0.28
13 10 0.31
14 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATATTTAAAATT
Found at i:1392072 original size:16 final size:16
Alignment explanation
Indices: 1392051--1392086 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1392041 TTTGGAGCTG
*
1392051 TTTTGACTTCTGGGTA
1 TTTTGACTTCGGGGTA
1392067 TTTTGACTTCGGGGTA
1 TTTTGACTTCGGGGTA
1392083 TTTT
1 TTTT
1392087 TCCTTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.25, T:0.53
Consensus pattern (16 bp):
TTTTGACTTCGGGGTA
Found at i:1397066 original size:15 final size:15
Alignment explanation
Indices: 1397043--1397072 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1397033 TATCTTGTCT
1397043 GTTCCGTCTCCCAAA
1 GTTCCGTCTCCCAAA
*
1397058 GTTCTGTCTCCCAAA
1 GTTCCGTCTCCCAAA
1397073 CACTGCATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (15 bp):
GTTCCGTCTCCCAAA
Found at i:1432894 original size:32 final size:31
Alignment explanation
Indices: 1432857--1432917 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
1432847 TATGTTATTA
* * *
1432857 TTTTTGTGATGTGATGTATATTTCATCATCAT
1 TTTTTGTGACGTGATATATATAT-ATCATCAT
1432889 TTTTTGTGACGTGATATATATATATCATC
1 TTTTTGTGACGTGATATATATATATCATC
1432918 TTTAGATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.51
Consensus pattern (31 bp):
TTTTTGTGACGTGATATATATATATCATCAT
Found at i:1434353 original size:27 final size:29
Alignment explanation
Indices: 1434323--1434392 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 29
1434313 AAAATATAAA
*
1434323 GATGAATTTAGAATGTTAAAAA-TTT-TG
1 GATGAATTTAGAATGTTAAAAAGTTTGAG
*
1434350 GATGAAATT-GAAATGTTAAAAAGTTTGAG
1 GATGAATTTAG-AATGTTAAAAAGTTTGAG
*
1434379 GATTAATTTAGAAT
1 GATGAATTTAGAAT
1434393 AAAAATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 3 0.09
29 11 0.31
30 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (29 bp):
GATGAATTTAGAATGTTAAAAAGTTTGAG
Found at i:1438535 original size:16 final size:16
Alignment explanation
Indices: 1438494--1438536 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1438484 TGAATATTAA
*
1438494 ATTAATTAT-TAAAAT
1 ATTAAATATATAAAAT
*
1438509 GTTAAAT-TATAAAAT
1 ATTAAATATATAAAAT
1438524 ATTAAATATATAA
1 ATTAAATATATAA
1438537 TTATAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 17 0.74
16 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTAAATATATAAAAT
Found at i:1439046 original size:16 final size:17
Alignment explanation
Indices: 1439014--1439054 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1439004 TATAAAACTA
1439014 ATATTTT-ATAAATATT
1 ATATTTTAATAAATATT
*
1439030 ATATTTTAATTAA-ATT
1 ATATTTTAATAAATATT
*
1439046 ACATTTTAA
1 ATATTTTAA
1439055 ATTTTAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTTAATAAATATT
Found at i:1440519 original size:22 final size:22
Alignment explanation
Indices: 1440494--1440551 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1440484 TCTACGGGAC
1440494 ATCCGTCCTCATCTCCGACGAA
1 ATCCGTCCTCATCTCCGACGAA
*
1440516 ATCCGTCCTCATCTCCGGCGAA
1 ATCCGTCCTCATCTCCGACGAA
1440538 ATCCGT-CT-ATCTCC
1 ATCCGTCCTCATCTCC
1440552 ATCTCTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 6 0.17
21 2 0.06
22 27 0.77
ACGTcount: A:0.19, C:0.41, G:0.14, T:0.26
Consensus pattern (22 bp):
ATCCGTCCTCATCTCCGACGAA
Found at i:1440957 original size:14 final size:14
Alignment explanation
Indices: 1440940--1440971 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1440930 GCGATTTTAG
1440940 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
1440954 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
1440968 TTTC
1 TTTC
1440972 ATTTCGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:1441002 original size:20 final size:20
Alignment explanation
Indices: 1440960--1441029 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1440950 CGATTTTCTC
*
1440960 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
1440979 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1440999 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
1441019 GTTGAGATTTT
1 GTTGCGATTTT
1441030 AAGTTTCAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 11 0.25
20 33 0.75
ACGTcount: A:0.13, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1441036 original size:20 final size:20
Alignment explanation
Indices: 1440993--1441036 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1440983 CGATAGTCAT
* * *
1440993 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGAGATTTTAAG
1441013 TTTCGTGTTGAGATTTTAAG
1 TTTCGTGTTGAGATTTTAAG
1441033 TTTC
1 TTTC
1441037 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGAGATTTTAAG
Found at i:1448069 original size:20 final size:20
Alignment explanation
Indices: 1448044--1448081 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1448034 TTTTGGTGCA
*
1448044 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
1448064 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
1448082 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1448110 original size:18 final size:18
Alignment explanation
Indices: 1448087--1448126 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1448077 CCCCCTTTGA
*
1448087 AGGGGAACCGATTCCCAT
1 AGGGGAACCGATACCCAT
* *
1448105 AGGGGAATCGATACCCCT
1 AGGGGAACCGATACCCAT
1448123 AGGG
1 AGGG
1448127 TTCTGGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.33, T:0.15
Consensus pattern (18 bp):
AGGGGAACCGATACCCAT
Found at i:1452149 original size:14 final size:14
Alignment explanation
Indices: 1452130--1452163 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1452120 TTGTTTAATT
1452130 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1452144 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
1452158 ATTTGT
1 ATTTGT
1452164 TTAATTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:1452320 original size:20 final size:20
Alignment explanation
Indices: 1452295--1452357 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1452285 AACGCTAAAC
1452295 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
1452315 TCAAAATCGCAATACGAAAG
1 TCAAAATCGCAATGCGAAAG
* *
1452335 -CCAAATCGCAACGCGAAAG
1 TCAAAATCGCAATGCGAAAG
1452354 TCAA
1 TCAA
1452358 TTTGCATTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:1452422 original size:20 final size:20
Alignment explanation
Indices: 1452397--1452505 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
1452387 GATTTTCTCT
*
1452397 TTGCGATAGTCAAATTCCCG
1 TTGCGATAGTCAAATTCGCG
*
1452417 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
1452437 TTGCGAT--T----TTTGCA
1 TTGCGATAGTCAAATTCGCG
1452451 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
1452471 TTGCGATAGTCAAATTCGC-
1 TTGCGATAGTCAAATTCGCG
*
1452490 TATGCGATATTCAAAT
1 T-TGCGATAGTCAAAT
1452506 GAATGTGTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
14 11 0.15
16 1 0.01
18 1 0.01
19 1 0.01
20 61 0.81
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:1452444 original size:54 final size:53
Alignment explanation
Indices: 1452364--1452497 Score: 189
Period size: 54 Copynumber: 2.5 Consensus size: 53
1452354 TCAATTTGCA
* * *
1452364 TTGCGATAGTCTAATACGCTTGCGATTTTCT-CTTTGCGATAGTCAAATTCCCG
1 TTGCGATAGTCAAATTCGCTTGCGATTTT-TGCATTGCGATAGTCAAATTCCCG
* *
1452417 TTGCGATAATCAAATTCGCGTTGCGATTTTTGCATTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGC-TTGCGATTTTTGCATTGCGATAGTCAAATTCCCG
1452471 TTGCGATAGTCAAATTCGCTATGCGAT
1 TTGCGATAGTCAAATTCGCT-TGCGAT
1452498 ATTCAAATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
53 18 0.25
54 54 0.75
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (53 bp):
TTGCGATAGTCAAATTCGCTTGCGATTTTTGCATTGCGATAGTCAAATTCCCG
Found at i:1452696 original size:18 final size:18
Alignment explanation
Indices: 1452673--1452707 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1452663 AAGCCGGTTA
*
1452673 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1452691 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1452708 GTCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1454985 original size:24 final size:24
Alignment explanation
Indices: 1454958--1455011 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1454948 TTGAAACATC
1454958 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
1454982 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
1455006 ATCAAA
1 ATCAAA
1455012 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:1455848 original size:20 final size:20
Alignment explanation
Indices: 1455823--1455886 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1455813 TTCAGTGTTA
*
1455823 CGATAGTTAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
**
1455843 CGATAGTCAGAATCGTATTG
1 CGATAGTCAGAATCGCGTTG
1455863 CGATAGTCAGAATCGCGTTG
1 CGATAGTCAGAATCGCGTTG
1455883 CGAT
1 CGAT
1455887 TTACATATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
CGATAGTCAGAATCGCGTTG
Found at i:1458291 original size:15 final size:15
Alignment explanation
Indices: 1458271--1458304 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1458261 GAAACATGAT
1458271 TACATCAAGCAGGGG
1 TACATCAAGCAGGGG
1458286 TACATCAAGCAGGGG
1 TACATCAAGCAGGGG
1458301 TACA
1 TACA
1458305 AAAGGGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.29, T:0.15
Consensus pattern (15 bp):
TACATCAAGCAGGGG
Done.