Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 3 of 345
Found at i:807815 original size:22 final size:23
Alignment explanation
Indices: 807771--807828 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
807761 TATTTTGAAT
807771 TTTTAAAATTTATAATATGATAA
1 TTTTAAAATTTATAATATGATAA
* *
807794 TTTTAATATTT-TAATATTATAA
1 TTTTAAAATTTATAATATGATAA
*
807816 TTTTTTAAATTTA
1 -TTTTAAAATTTA
807829 AATTTAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAAAATTTATAATATGATAA
Found at i:807829 original size:22 final size:23
Alignment explanation
Indices: 807768--807843 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 23
807758 TATTATTTTG
* *
807768 AATTTTTAAAATTTATAATATGAT
1 AATTTTTTAAATTT-TAATATTAT
807792 AA--TTTTAATATTTTAATATTAT
1 AATTTTTTAA-ATTTTAATATTAT
807814 AATTTTTTAAA-TTTAA-ATT-T
1 AATTTTTTAAATTTTAATATTAT
807834 AATATTTTTA
1 AAT-TTTTTA
807844 TTTTAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.09
21 9 0.20
22 20 0.43
23 5 0.11
24 8 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
AATTTTTTAAATTTTAATATTAT
Found at i:817449 original size:20 final size:21
Alignment explanation
Indices: 817424--817462 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
817414 TTGCTCATCT
817424 TAACAG-CAATGAAAATAACG
1 TAACAGTCAATGAAAATAACG
817444 TAACAGTCAATGAAAATAA
1 TAACAGTCAATGAAAATAA
817463 TGATGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (21 bp):
TAACAGTCAATGAAAATAACG
Found at i:840251 original size:207 final size:205
Alignment explanation
Indices: 839837--840326 Score: 564
Period size: 207 Copynumber: 2.4 Consensus size: 205
839827 TGCTCAGATT
* * *
839837 CTTCATTCTTTTTGAAGTA-CCCGTCTGACATTAGTGTTTGATACATGGATATGGAGACACGATC
1 CTTCATTCTTTTTGAAGTACCCCGTC-GACATTAGTGTTTGATACACGGATATGGAGACATGACC
* * * *
839901 TTCAAAGATCCCTTAATATATGGAAAAACTTGACAAAGTCTAATCATACCCATGTCGGGGATATT
65 TCCAAAGATCCCTTAATATATGG----ACTTGAAAAAATCTAATCATACCCATGTCGGGGATACT
* * * *
839966 CAAACCTGAGTCGAGTAACATATGAACAATGCCGATGCAACGAAGAACTAAAATGAAAAACCATC
126 CAAACCCGAGTCGAGTAAAACATGAACAATGCCGATGCAACCAAGAACTAAAATGAAAAACCATC
840031 TACCCCAATTGTTGG
191 TACCCCAATTGTTGG
*
840046 CTTCATTCTTCTTGAAGTACCCCTGTCCGACATTAGTGTTTGATACACGGATATGGAGACATGAC
1 CTTCATTCTTTTTGAAGTACCCC-GT-CGACATTAGTGTTTGATACACGGATATGGAGACATGAC
* * * * *
840111 CCCCAAAGATCCCTTAATATATGG-TTTTAAAAACATCTAATCATACTCGTGTCGGGGACT-CTC
64 CTCCAAAGATCCCTTAATATATGGACTTGAAAAA-ATCTAATCATACCCATGTCGGGGA-TACTC
* * * * *
840174 AAACCCGAGTCTACGTAAAACATG-ACAATGCCGGTGTAACCAAGAACTTACAA-GAAAAACTAT
127 AAACCCGAGTCGA-GTAAAACATGAACAATGCCGATGCAACCAAGAAC-TAAAATGAAAAACCAT
*
840237 CTGCTCCC-ATTGTTGG
190 CTAC-CCCAATTGTTGG
* * ** *
840253 CTTCATTCTTTTTGAAGCACCAC-T-GACATTAGTGTCCGATACACGGATATCGAGACATGACCT
1 CTTCATTCTTTTTGAAGTACCCCGTCGACATTAGTGTTTGATACACGGATATGGAGACATGACCT
840316 CCAAAGATCCC
66 CCAAAGATCCC
840327 CAATGTTGAG
Statistics
Matches: 243, Mismatches: 30, Indels: 22
0.82 0.10 0.07
Matches are distributed among these distances:
203 46 0.19
205 1 0.00
206 6 0.02
207 94 0.39
208 16 0.07
209 18 0.07
210 3 0.01
211 58 0.24
212 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (205 bp):
CTTCATTCTTTTTGAAGTACCCCGTCGACATTAGTGTTTGATACACGGATATGGAGACATGACCT
CCAAAGATCCCTTAATATATGGACTTGAAAAAATCTAATCATACCCATGTCGGGGATACTCAAAC
CCGAGTCGAGTAAAACATGAACAATGCCGATGCAACCAAGAACTAAAATGAAAAACCATCTACCC
CAATTGTTGG
Found at i:841462 original size:31 final size:30
Alignment explanation
Indices: 841415--841487 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 30
841405 TAACTTTTCA
* *
841415 TAGTTGGATGAGCAAAAAATAAAAAAAAATT
1 TAGTTGAATGACCAAAAAATAAAAAAAAA-T
841446 TAGTTGAATGACCAAAAAATAAAAAAAAAT
1 TAGTTGAATGACCAAAAAATAAAAAAAAAT
841476 TAGTTGAATGAC
1 TAGTTGAATGAC
841488 TACTAACGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 13 0.32
31 27 0.68
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (30 bp):
TAGTTGAATGACCAAAAAATAAAAAAAAAT
Found at i:841470 original size:30 final size:31
Alignment explanation
Indices: 841415--841487 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
841405 TAACTTTTCA
* * *
841415 TAGTTGGATGAGCAAAAAATAAAAAAAAATT
1 TAGTTGAATGACCAAAAAATAAAAAAAAAAT
841446 TAGTTGAATGACCAAAAAAT-AAAAAAAAAT
1 TAGTTGAATGACCAAAAAATAAAAAAAAAAT
841476 TAGTTGAATGAC
1 TAGTTGAATGAC
841488 TACTAACGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 21 0.54
31 18 0.46
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (31 bp):
TAGTTGAATGACCAAAAAATAAAAAAAAAAT
Found at i:846338 original size:184 final size:173
Alignment explanation
Indices: 845954--846447 Score: 660
Period size: 184 Copynumber: 2.8 Consensus size: 173
845944 TAAAACTACA
* * * *
845954 GTAAACAAT-AAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTACAACTAGGCTTTGA
1 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTAGAACTAGGCTGTAA
*
846018 AAATTCAGT-AAAAGTCATTCAACATGTAAATATGATAAAAAAAAACAAAAAAAAGGGTATTCTA
66 AAATTCAGTAAAAAGTCATTCAACATGTAAATATGAT-AAAAAAAAC-AAAAAAAGGGTATTCAA
* *
846082 AGAATTAAGCTTTATTTTTTACGAAAATACATAGAATTAAGCTGG
129 AGAATTAAGCTTTAATTTTTACGAAAATACAGAGAATTAAGCTGG
*
846127 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCTTATAAAAAAAAAGATCTATAGAACATA
1 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTC--AT----AAAAA-ATCTCTAGAAC-TA
* *
846192 GGCTGTAAAAATTCAGTAAAAAGTCATTCGACATGTAAAAATGATAAAACAAACTACAAAAAAAG
58 GGCTGTAAAAATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAA-AAA--ACAAAAAAAG
*
846257 GGTATTCAAAGAATTAAGCTTTAATTTTTATGAAAATACAGAGAATTAAGCTTGG
120 GGTATTCAAAGAATTAAGCTTTAATTTTTACGAAAATACAGAGAATTAAGC-TGG
846312 GTAAACCATAAAATACCAGG-AAAAGCTTCTGCATTCATGAAAAAATCTCTAGAACTAGGCTGTA
1 GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCAT-AAAAAATCTCTAGAACTAGGCTGTA
* * * *
846376 AAAGATTCAGGAAAAA-TCATCCAACATGTAAATATGAT-CAAAAAAC--AAAAAGGGTATTTAA
65 AAA-ATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAAAAAACAAAAAAAGGGTATTCAA
846437 AGAATTAAGCT
129 AGAATTAAGCT
846448 CGGGTAAACC
Statistics
Matches: 287, Mismatches: 19, Indels: 32
0.85 0.06 0.09
Matches are distributed among these distances:
171 25 0.09
173 10 0.03
174 27 0.09
175 3 0.01
176 4 0.01
177 31 0.11
178 21 0.07
179 5 0.02
180 5 0.02
181 9 0.03
182 23 0.08
183 28 0.10
184 71 0.25
185 25 0.09
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (173 bp):
GTAAACCATAAAATACCAGGAAAAAGCTTCTGCATTCATAAAAAATCTCTAGAACTAGGCTGTAA
AAATTCAGTAAAAAGTCATTCAACATGTAAATATGATAAAAAAAACAAAAAAAGGGTATTCAAAG
AATTAAGCTTTAATTTTTACGAAAATACAGAGAATTAAGCTGG
Found at i:846465 original size:139 final size:140
Alignment explanation
Indices: 846298--846571 Score: 430
Period size: 140 Copynumber: 2.0 Consensus size: 140
846288 GAAAATACAG
* *
846298 AGAATTAAGCTTGGGTAAACCATAAAATACCAGGAAAAGCTTCTGCATTCATGAAAAA-ATCTCT
1 AGAATTAAGCTCGGGTAAACCATAAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAGATCTCT
*
846362 AGAACTAGGCTGTAAA-AGATTCAGGAAAAATCA-TCCAACATGTAAATATGATCAAA-AAACAA
66 AGAACTAGGCTGTAAATA-ATTCAGGAAAAACCACT-CAACATGTAAATATGAT-AAAGAAACAA
846424 AAAGGGTATTTAA
128 AAAGGGTATTTAA
*
846437 AGAATTAAGCTCGGGTAAACCATGAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAGATCTCT
1 AGAATTAAGCTCGGGTAAACCATAAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAGATCTCT
* * *
846502 AGAATTAGGCTGTAAATAATTCAGTAAAAACCACTCAACATGTAAATATGATAAAGAAATAAAAA
66 AGAACTAGGCTGTAAATAATTCAGGAAAAACCACTCAACATGTAAATATGATAAAGAAACAAAAA
846567 GGGTA
131 GGGTA
846572 GAGTGAAGAT
Statistics
Matches: 124, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
139 58 0.47
140 64 0.52
141 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (140 bp):
AGAATTAAGCTCGGGTAAACCATAAAATACCAGGAAAAGCTTCTGCATTCATAAAAAAGATCTCT
AGAACTAGGCTGTAAATAATTCAGGAAAAACCACTCAACATGTAAATATGATAAAGAAACAAAAA
GGGTATTTAA
Found at i:858753 original size:33 final size:30
Alignment explanation
Indices: 858676--858755 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 30
858666 GACCCCAAAG
* * *
858676 TTTTTGAAATTTTTAGTTATATCCTTAAAT
1 TTTTTGAAATTTTTAATTATATCCCTAAAA
*
858706 TTTTCTGAAATTTTTAATTAGGTCTCCCTAAAA
1 TTTT-TGAAATTTTTAATTA--TATCCCTAAAA
858739 TTTTTGAAAATTTTTAA
1 TTTTTG-AAATTTTTAA
858756 ACATTTCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.10
31 14 0.33
32 2 0.05
33 22 0.52
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (30 bp):
TTTTTGAAATTTTTAATTATATCCCTAAAA
Found at i:858874 original size:32 final size:29
Alignment explanation
Indices: 858791--858874 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
858781 TATTTTTATT
* *
858791 TTTTTGTAAATTTTCATAAAACCTCTAAA
1 TTTTTGAAAATTTTCATAAAACCTCAAAA
* * *
858820 TTTTTGAAAGTTTTAATTAAACCTACCAAAAA
1 TTTTTGAAAATTTTCATAAAACCT--C-AAAA
858852 TTTTT-AAAATTTTCACTAAAACC
1 TTTTTGAAAATTTTCA-TAAAACC
858875 CTTGAAGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
29 20 0.47
31 9 0.21
32 14 0.33
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTTGAAAATTTTCATAAAACCTCAAAA
Found at i:862944 original size:20 final size:20
Alignment explanation
Indices: 862919--862959 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
862909 TTTATAAATT
* *
862919 TGGATTGTGCTGAGGATGGG
1 TGGATTGAGCTGAGAATGGG
862939 TGGATTGAGCTGAGAATGGG
1 TGGATTGAGCTGAGAATGGG
862959 T
1 T
862960 CAAAAAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.46, T:0.29
Consensus pattern (20 bp):
TGGATTGAGCTGAGAATGGG
Found at i:863909 original size:2 final size:2
Alignment explanation
Indices: 863902--863932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
863892 TTATTAGATT
863902 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
863933 GCAGGGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:875819 original size:13 final size:14
Alignment explanation
Indices: 875791--875834 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
875781 ATATTCTAAA
875791 TAAATCTAATTTTT
1 TAAATCTAATTTTT
*
875805 TAAATTTAA-TTTT
1 TAAATCTAATTTTT
*
875818 TAAACCTAATATTTT
1 TAAATCTAAT-TTTT
875833 TA
1 TA
875835 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATCTAATTTTT
Found at i:876400 original size:10 final size:10
Alignment explanation
Indices: 876385--876419 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
876375 TAAGTCAACG
876385 TATTTTTTTT
1 TATTTTTTTT
876395 TA-TTTTTTT
1 TATTTTTTTT
876404 TATTTTTTTT
1 TATTTTTTTT
876414 TATTTT
1 TATTTT
876420 CATAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:876402 original size:9 final size:9
Alignment explanation
Indices: 876388--876419 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
876378 GTCAACGTAT
876388 TTTTTTTTA
1 TTTTTTTTA
876397 TTTTTTTTA
1 TTTTTTTTA
876406 TTTTTTTTTA
1 -TTTTTTTTA
876416 TTTT
1 TTTT
876420 CATAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:877137 original size:11 final size:10
Alignment explanation
Indices: 877122--877170 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
877112 GAAGAGAATG
877122 GAAAAAAAAA
1 GAAAAAAAAA
877132 GAAAAAAAAA
1 GAAAAAAAAA
*
877142 GAAAAGTTAAAA
1 GAAAA--AAAAA
* *
877154 GAACATAAAA
1 GAAAAAAAAA
877164 GAAAAAA
1 GAAAAAA
877171 TTAAATTACG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 25 0.76
12 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:879799 original size:20 final size:20
Alignment explanation
Indices: 879776--879823 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
879766 TTGCTATTTG
879776 AAAATTTTTATTAAG-CTCC
1 AAAATTTTTATTAAGCCTCC
*
879795 TAAAATTTTAATTAAGCCTCC
1 -AAAATTTTTATTAAGCCTCC
879816 -AAATTTTT
1 AAAATTTTT
879824 TTGGAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (20 bp):
AAAATTTTTATTAAGCCTCC
Found at i:879856 original size:30 final size:31
Alignment explanation
Indices: 879796--879869 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
879786 TTAAGCTCCT
879796 AAAATTTTAATTAAGCCTCCAAATTTTTTTG
1 AAAATTTTAATTAAGCCTCCAAATTTTTTTG
* * * *
879827 GAAATTTTCATTAAGCCTCTAGA-TTTTTTG
1 AAAATTTTAATTAAGCCTCCAAATTTTTTTG
879857 AAAATTTTAATTA
1 AAAATTTTAATTA
879870 CCCCTCCTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (31 bp):
AAAATTTTAATTAAGCCTCCAAATTTTTTTG
Found at i:886526 original size:3 final size:3
Alignment explanation
Indices: 886512--886543 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
886502 AAGTCAACAT
*
886512 ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
886544 TTAACCTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:887623 original size:14 final size:15
Alignment explanation
Indices: 887585--887626 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
887575 AAAAAATATA
*
887585 CTTATAAATTTTTAT
1 CTTATATATTTTTAT
* *
887600 CATATCTATTTTTAT
1 CTTATATATTTTTAT
887615 -TTATATATTTTT
1 CTTATATATTTTT
887627 TTATTTTCTG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (15 bp):
CTTATATATTTTTAT
Found at i:888303 original size:60 final size:60
Alignment explanation
Indices: 888230--888345 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
888220 TCACATGTTA
* * * *
888230 ATACGATATGGGTTCGCCTTTATGATGGTGCGAACCTACATCGTGTGGTCTCATAGAATT
1 ATACGATATGGGTTCACCTATATGATGGTACGAACCTACATCATGTGGTCTCATAGAATT
*
888290 ATACGATATGGGTTCACCTATATGATGGTACGAAGCTACATCATGTGGTCTCATAG
1 ATACGATATGGGTTCACCTATATGATGGTACGAACCTACATCATGTGGTCTCATAG
888346 GAGCATATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (60 bp):
ATACGATATGGGTTCACCTATATGATGGTACGAACCTACATCATGTGGTCTCATAGAATT
Found at i:890014 original size:14 final size:14
Alignment explanation
Indices: 889995--890024 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
889985 TGAATTGTAC
889995 GAACTTATGATGAT
1 GAACTTATGATGAT
890009 GAACTTATGATGAT
1 GAACTTATGATGAT
890023 GA
1 GA
890025 TGATGATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (14 bp):
GAACTTATGATGAT
Found at i:891536 original size:18 final size:18
Alignment explanation
Indices: 891513--891547 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
891503 TCGATTGACA
891513 TGAATATTATTAAGAATG
1 TGAATATTATTAAGAATG
*
891531 TGAATATTGTTAAGAAT
1 TGAATATTATTAAGAAT
891548 ATAAGTTCGA
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:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (18 bp):
TGAATATTATTAAGAATG
Found at i:891808 original size:33 final size:33
Alignment explanation
Indices: 891766--891834 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
891756 TTTCAGATCC
891766 CATTTTAGATCCAACATGAATCATAATTTTAAA
1 CATTTTAGATCCAACATGAATCATAATTTTAAA
891799 CATTTTAGATCCAACATGAATCATAATTTTAAA
1 CATTTTAGATCCAACATGAATCATAATTTTAAA
891832 CAT
1 CAT
891835 GTGAATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (33 bp):
CATTTTAGATCCAACATGAATCATAATTTTAAA
Found at i:891851 original size:20 final size:21
Alignment explanation
Indices: 891815--891857 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
891805 AGATCCAACA
*
891815 TGAATCATAATTTTAAACATG
1 TGAATCATAATTATAAACATG
*
891836 TGAATCA-AATTATAAATATG
1 TGAATCATAATTATAAACATG
891856 TG
1 TG
891858 TATTTATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAATCATAATTATAAACATG
Found at i:892853 original size:18 final size:16
Alignment explanation
Indices: 892809--892868 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 16
892799 AAAATATCAT
892809 AAATTATTTTTTAAAA
1 AAATTATTTTTTAAAA
*
892825 TAATTAAATTTTTTAAAA
1 AAATT--ATTTTTTAAAA
* *
892843 AAA-AATTATTTAAAA
1 AAATTATTTTTTAAAA
*
892858 AAATAATTTTT
1 AAATTATTTTT
892869 ATAGATATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 13 0.36
16 10 0.28
18 13 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTATTTTTTAAAA
Found at i:898169 original size:4 final size:4
Alignment explanation
Indices: 898160--898185 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
898150 ATATTTTTTA
898160 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
898186 TGTGGTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:898848 original size:19 final size:19
Alignment explanation
Indices: 898820--898859 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
898810 AAAGAAAAAG
898820 ACGGTAGAAAAGTCAGTCA
1 ACGGTAGAAAAGTCAGTCA
*
898839 ACGGTGGAAAAGTCAGTCA
1 ACGGTAGAAAAGTCAGTCA
898858 AC
1 AC
898860 CAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.28, T:0.15
Consensus pattern (19 bp):
ACGGTAGAAAAGTCAGTCA
Found at i:898867 original size:19 final size:19
Alignment explanation
Indices: 898825--898868 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
898815 AAAAGACGGT
***
898825 AGAAAAGTCAGTCAACGGT
1 AGAAAAGTCAGTCAACCAA
*
898844 GGAAAAGTCAGTCAACCAA
1 AGAAAAGTCAGTCAACCAA
898863 AGAAAA
1 AGAAAA
898869 AGACGGTAGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.23, T:0.11
Consensus pattern (19 bp):
AGAAAAGTCAGTCAACCAA
Found at i:902434 original size:4 final size:4
Alignment explanation
Indices: 902425--902454 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
902415 CTATTTATAA
902425 AATT AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
902455 CTAAGTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:904447 original size:14 final size:14
Alignment explanation
Indices: 904405--904447 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
904395 AAAATAGAGT
904405 AATTAAATTCTTAAA
1 AATTAAATTC-TAAA
* * *
904420 AATAAAAGTATAAA
1 AATTAAATTCTAAA
904434 AATTAAATTCTAAA
1 AATTAAATTCTAAA
904448 TTTAAAAAAG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (14 bp):
AATTAAATTCTAAA
Found at i:905279 original size:16 final size:16
Alignment explanation
Indices: 905257--905325 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
905247 TTTGGTTCGC
905257 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
905273 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
905289 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
905306 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
905322 TGTA
1 TGTA
905326 ATAGCTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:905303 original size:33 final size:32
Alignment explanation
Indices: 905257--905325 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
905247 TTTGGTTCGC
905257 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGGATTAGAGG
*
905289 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGGATTAGAGG
905322 TGTA
1 TGTA
905326 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.01, G:0.38, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGGATTAGAGG
Found at i:905582 original size:18 final size:17
Alignment explanation
Indices: 905561--905595 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
905551 TTATTATTAA
*
905561 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
905579 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
905596 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:905757 original size:120 final size:120
Alignment explanation
Indices: 905544--906866 Score: 2362
Period size: 120 Copynumber: 11.2 Consensus size: 120
905534 ATCATATTTA
*
905544 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
905609 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
905664 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
905729 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
905784 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
905849 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
905904 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
905969 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
906024 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
906089 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
906144 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
906209 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
906264 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
*
906329 TATTCTTATATTAATTTACTGAAATAATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
906384 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-A--AAA-----AA-AA-TAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
* *
906439 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* **
906494 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
*
906559 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
906614 AACATAATTATTATTAAATATATTTTAATTAAACTATATAA-TT--T-AAA-----AA-AATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
* *
906669 TGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
906724 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
*
906789 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
906844 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
906867 AACTTGAAAA
Statistics
Matches: 1166, Mismatches: 17, Indels: 40
0.95 0.01 0.03
Matches are distributed among these distances:
110 199 0.17
111 7 0.01
112 2 0.00
113 4 0.00
114 3 0.00
116 3 0.00
117 3 0.00
118 2 0.00
119 7 0.01
120 936 0.80
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:905822 original size:18 final size:17
Alignment explanation
Indices: 905801--905835 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
905791 TTATTATTAA
*
905801 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
905819 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
905836 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:907230 original size:24 final size:25
Alignment explanation
Indices: 907198--907251 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
907188 ACTTCTGCTG
*
907198 AACTATAAAA-ACCTCTTGAATTGC
1 AACTATAAAATACCTCTTAAATTGC
907222 AACTATAAAATACCTCTTAAATTGC
1 AACTATAAAATACCTCTTAAATTGC
907247 AACTA
1 AACTA
907252 AAGCTTTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (25 bp):
AACTATAAAATACCTCTTAAATTGC
Found at i:909928 original size:215 final size:215
Alignment explanation
Indices: 909545--910050 Score: 719
Period size: 215 Copynumber: 2.4 Consensus size: 215
909535 CGAACATAGG
* * *
909545 TACTTCAAGAAAAATGAAGAGTCTGAGCATCATAGCTTAGCATGAACTAAAACTAGGTAATGGCA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
* * * *
909610 GTGATAAAATCTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTACTCTGATTTGGGTGT
66 GTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCGGATTTGGGTGT
* * * * ***
909675 AGTTGTCCAATACTGGTAGTGTCTGACATGAGTTTAGAGGTTGTATCTCTGTATTTGTGTGTCT-
131 AGTTGTCCAATACTAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCCGTATTACAGTGT-TG
909739 GACATGAGGGTCAGACACAGA
195 GACATGAGGGTCAGACACAGA
*
909760 TACTTCAAGAAAAATGAAGAGTCCGA-CTATCATAGCTTAGCACGAACCAAAACTAGGTAATGGT
1 TACTTCAAGAAAAATGAAGAGTCCGAGC-ATCATAGCTTAGCACGAACTAAAACTAGGTAATGGT
* * * *
909824 TGTGATAAAATCGTGTTCTCTTATTTGGAAATTTACTTAGCACCTGTATTACTCGGATTTGGGTG
65 AGTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCGGATTTGGGTG
* * *
909889 TAGTTGTCCGATGCTAGTAGTGTCGGACACGATTTTAGAGGTTGTATCTCCGTATTACAGTGTTG
130 TAGTTGTCCAATACTAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCCGTATTACAGTGTTG
* *
909954 GACATGAGTGTCAGGCACAGA
195 GACATGAGGGTCAGACACAGA
* * * * *
909975 TACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGGACAAACTAAAGCTATGTAATGGTA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
910040 GTGATAAAATC
66 GTGATAAAATC
910051 TTGGAACATA
Statistics
Matches: 257, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
214 2 0.01
215 254 0.99
216 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (215 bp):
TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
GTGATAAAATCGTGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCGGATTTGGGTGT
AGTTGTCCAATACTAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCCGTATTACAGTGTTGG
ACATGAGGGTCAGACACAGA
Found at i:914339 original size:12 final size:12
Alignment explanation
Indices: 914322--914346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
914312 AAACAGGGAT
914322 TCATCATCTTCA
1 TCATCATCTTCA
914334 TCATCATCTTCA
1 TCATCATCTTCA
914346 T
1 T
914347 TCGGTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCATCATCTTCA
Found at i:915055 original size:9 final size:8
Alignment explanation
Indices: 915036--915065 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
915026 ATTATGTATT
915036 AATTTTTA
1 AATTTTTA
915044 AATTTTTA
1 AATTTTTA
*
915052 AAATTTTA
1 AATTTTTA
915060 AATTTT
1 AATTTT
915066 AGTGAAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
AATTTTTA
Found at i:916555 original size:31 final size:31
Alignment explanation
Indices: 916513--916576 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
916503 TAAAAAAATT
* *
916513 AACAGTCCAGTGATTTAAATAAAAATTTTCA
1 AACAGTCCAGTGACTTAAATAAAAACTTTCA
* *
916544 AACAGTTCAGTGACTTAAATGAAAACTTTCA
1 AACAGTCCAGTGACTTAAATAAAAACTTTCA
916575 AA
1 AA
916577 TAATTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (31 bp):
AACAGTCCAGTGACTTAAATAAAAACTTTCA
Found at i:917444 original size:16 final size:16
Alignment explanation
Indices: 917396--917446 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
917386 ATTTAAATCA
917396 TTCTAGGTTCTGATTAT
1 TTCTA-GTTCTGATTAT
*
917413 TTCTAGTTCAGATTAT
1 TTCTAGTTCTGATTAT
*
917429 TT-TGAGTTCTGGTTAT
1 TTCT-AGTTCTGATTAT
917445 TT
1 TT
917447 AATTTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.03
16 24 0.80
17 5 0.17
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55
Consensus pattern (16 bp):
TTCTAGTTCTGATTAT
Found at i:918340 original size:16 final size:16
Alignment explanation
Indices: 918319--918350 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
918309 TTGGGTCACC
*
918319 AAAAAGTAAAAAAAAA
1 AAAAAGGAAAAAAAAA
918335 AAAAAGGAAAAAAAAA
1 AAAAAGGAAAAAAAAA
918351 GAAGATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGGAAAAAAAAA
Found at i:918874 original size:24 final size:25
Alignment explanation
Indices: 918840--918889 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
918830 CAATTAATTC
* *
918840 AAACTTGAAATCA-CCAAAACAGAA
1 AAACTTAAAATAACCCAAAACAGAA
*
918864 AAACTTAAAATAACCCAAAACTGAA
1 AAACTTAAAATAACCCAAAACAGAA
918889 A
1 A
918890 CAATCCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.60, C:0.20, G:0.06, T:0.14
Consensus pattern (25 bp):
AAACTTAAAATAACCCAAAACAGAA
Found at i:924283 original size:21 final size:22
Alignment explanation
Indices: 924242--924284 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
924232 TCACATTAAC
*
924242 AAATAATTTAAAATAATTATAA
1 AAATAATTTAAAATAAATATAA
924264 AAAT-ATTT-AAATAAAATATAA
1 AAATAATTTAAAAT-AAATATAA
924285 CAAAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAATTTAAAATAAATATAA
Found at i:949955 original size:21 final size:21
Alignment explanation
Indices: 949922--949962 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
949912 TTTTATGTGA
949922 ATTAAAAATAATTATTTATTC
1 ATTAAAAATAATTATTTATTC
949943 ATTATAAAA-AATTATTTATT
1 ATTA-AAAATAATTATTTATT
949963 TAGATGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAAAAATAATTATTTATTC
Found at i:954604 original size:3 final size:3
Alignment explanation
Indices: 954596--954623 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
954586 GATGAAGGTC
954596 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
954624 TGTTAAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:955185 original size:21 final size:22
Alignment explanation
Indices: 955147--955187 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
955137 TGACTCGATG
955147 AGATTTTGACATGTTAAATAGA
1 AGATTTTGACATGTTAAATAGA
955169 AGATCTTTGA-AT-TTAAATA
1 AGAT-TTTGACATGTTAAATA
955188 TCATCATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (22 bp):
AGATTTTGACATGTTAAATAGA
Found at i:956967 original size:16 final size:15
Alignment explanation
Indices: 956946--956975 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
956936 AACTCATATT
956946 TATTCAAATCTTAAAC
1 TATTCAAAT-TTAAAC
956962 TATTCAAATTTAAA
1 TATTCAAATTTAAA
956976 ATAATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
TATTCAAATTTAAAC
Found at i:957224 original size:167 final size:168
Alignment explanation
Indices: 956997--957327 Score: 454
Period size: 167 Copynumber: 2.0 Consensus size: 168
956987 AAATATAACC
* * * *
956997 ACTTGAAATGATTAGAATAAATGAATTTAGAAATTATTTTTACACTGGGATCTGAATTTTTTTAT
1 ACTTGAAATGATTAGAATAAATGAACTTAGAAACTATTCTTACACTGGGATCTAAATTTTTTTAT
* * * * * *
957062 -CAAAGTCA-AACTCGGAACTTTGTAATTATTTCTACATTGAGGTTTGAATTTTTTTC-AAATTA
66 CCAAA-TCAGAAC-CGGAACTATGCAATTATTTCCACATTGAGGCTTAAATTTTTTTCTAAAATA
957124 ATCTTTGATATTTCCTTCAAAATCTTAAAGTTTAGGAACA
129 ATCTTTGATATTTCCTTCAAAATCTTAAAGTTTAGGAACA
* * * *
957164 ACTTGAAATGATTCGAATAAATGAACTTGGTAACTATTCTTATA-TCGGGATCTAAATTTTTTTA
1 ACTTGAAATGATTAGAATAAATGAACTTAGAAACTATTCTTACACT-GGGATCTAAATTTTTTTA
* * *
957228 TCCAAATTAGAACCTGAACTATGCAATTATTTCCATATTGAGGCTTAAATTTTTTTCTAAAATAA
65 TCCAAATCAGAACCGGAACTATGCAATTATTTCCACATTGAGGCTTAAATTTTTTTCTAAAATAA
957293 TCTTTGATATTTCCTTCAAAATCTTAAAGTTTAGG
130 TCTTTGATATTTCCTTCAAAATCTTAAAGTTTAGG
957328 GCTTAATATA
Statistics
Matches: 143, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
166 1 0.01
167 94 0.66
168 48 0.34
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (168 bp):
ACTTGAAATGATTAGAATAAATGAACTTAGAAACTATTCTTACACTGGGATCTAAATTTTTTTAT
CCAAATCAGAACCGGAACTATGCAATTATTTCCACATTGAGGCTTAAATTTTTTTCTAAAATAAT
CTTTGATATTTCCTTCAAAATCTTAAAGTTTAGGAACA
Found at i:966497 original size:2 final size:2
Alignment explanation
Indices: 966490--966524 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
966480 GGGCTGTATA
966490 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
966525 ATTTGCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:972019 original size:22 final size:22
Alignment explanation
Indices: 971991--972112 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
971981 TTCCACATCC
971991 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
972013 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
972037 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
972060 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
972084 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
972107 ATCACA
1 ATCACA
972113 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:972026 original size:47 final size:47
Alignment explanation
Indices: 971963--972266 Score: 425
Period size: 47 Copynumber: 6.4 Consensus size: 47
971953 CCCTTCGGGA
* * *
971963 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
972010 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
972057 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
972104 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
972151 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
972198 CTTATCACGCATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCA--CATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
972247 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
972267 GTACATCAAT
Statistics
Matches: 239, Mismatches: 14, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 197 0.82
49 40 0.17
50 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:977115 original size:43 final size:43
Alignment explanation
Indices: 977054--977144 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
977044 TAATATCTCT
977054 TAATTATGCATAAAATAAATTTATTTGGATTCTTGTAACCTAA
1 TAATTATGCATAAAATAAATTTATTTGGATTCTTGTAACCTAA
977097 TAATTATGCATAAAATAAATTTATTTGGATTCTTGTAACCTAA
1 TAATTATGCATAAAATAAATTTATTTGGATTCTTGTAACCTAA
977140 TAATT
1 TAATT
977145 TTGTTTTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (43 bp):
TAATTATGCATAAAATAAATTTATTTGGATTCTTGTAACCTAA
Found at i:977460 original size:14 final size:14
Alignment explanation
Indices: 977441--977472 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
977431 TCTTGTTGTA
*
977441 TTTTCTTTTATGTT
1 TTTTCTTTTATCTT
977455 TTTTCTTTTATCTT
1 TTTTCTTTTATCTT
977469 TTTT
1 TTTT
977473 TGTAAGAAAT
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:0.09, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTATCTT
Found at i:978243 original size:31 final size:31
Alignment explanation
Indices: 978200--978260 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
978190 ATGACTTAAA
978200 TAAAAAAAAACTTTTAAATAATTCAATGATT
1 TAAAAAAAAACTTTTAAATAATTCAATGATT
* *
978231 TAAATAAAAACTTTTAAATAGTTCAATGAT
1 TAAAAAAAAACTTTTAAATAATTCAATGAT
978261 CATTTTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (31 bp):
TAAAAAAAAACTTTTAAATAATTCAATGATT
Found at i:997314 original size:26 final size:26
Alignment explanation
Indices: 997258--997317 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
997248 AAAAAACAAA
*
997258 TTAATTTTT-CTGTTAAAAATTTCAT
1 TTAATTTTTACTGTTAAAAATTGCAT
*
997283 CT-ATTTTTACTGTTAAAAATTGGC-T
1 TTAATTTTTACTGTTAAAAATT-GCAT
997308 TTAATTTTTA
1 TTAATTTTTA
997318 ATAGTGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 6 0.21
25 15 0.52
26 8 0.28
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (26 bp):
TTAATTTTTACTGTTAAAAATTGCAT
Found at i:1001721 original size:123 final size:124
Alignment explanation
Indices: 1001448--1001812 Score: 420
Period size: 124 Copynumber: 3.0 Consensus size: 124
1001438 TACAAATATA
* * * **
1001448 TATAGTATTTACAGCATTTAGGTGCAAGCAATCC-CATATTCTATCAATTGAAAGGCAAATCATA
1 TATAGTATTTACAGCATTTAGATGCAAGAAAACCTCATATTCTATCAATTCTAAGGCAAATCATA
* * * *
1001512 CATAAGCAACTATGGGTCAACTAATTATTCATTGACATAACTGCAGTGTATACAT-ATACG
66 AATAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCA--ATATACATAATACG
* * *
1001572 TCTAGTATTTACAGCATGTAGATGCAA-AAAACCTCATATTTTATCAATTCTAAGGCAAATCATA
1 TATAGTATTTACAGCATTTAGATGCAAGAAAACCTCATATTCTATCAATTCTAAGGCAAATCATA
* * * * *
1001636 AATCAGCAACTA-GGGTCAACTTGTCATTCATTGGCATAACAGCAACATACATACATACAG
66 AATAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACATA-ATAC-G
* * * * *
1001696 -ATAGTATTTGCAGTATTTAGATGCAATAAAA-CTCATATTCTATCAATTCTGAGGCAAATAATA
1 TATAGTATTTACAGCATTTAGATGCAAGAAAACCTCATATTCTATCAATTCTAAGGCAAATCATA
* *
1001759 AATAAGCATCTATGGGTCAA-TTAATCATTCAGTGACATAACTGCAATATACATA
66 AATAAGCAACTATGGGTCAACTT-ATCATTCATTGACATAACTGCAATATACATA
1001813 TACATGCATA
Statistics
Matches: 203, Mismatches: 31, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
121 6 0.03
123 98 0.48
124 99 0.49
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (124 bp):
TATAGTATTTACAGCATTTAGATGCAAGAAAACCTCATATTCTATCAATTCTAAGGCAAATCATA
AATAAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACATAATACG
Found at i:1001883 original size:154 final size:145
Alignment explanation
Indices: 1001680--1002248 Score: 532
Period size: 154 Copynumber: 3.9 Consensus size: 145
1001670 CATAACAGCA
* * * *
1001680 ACATACATACATACAGATAGTATTTGCAGTATTTAGATGCAATAAAACTCATATTCTATCAATTC
1 ACATACAT-CATACATATAGTATTTACAGCATTTAGATGCAA-GAAACTCATATTCTATCAATTC
* * * * * *
1001745 TGAGGCAAATAATAAATAAGCATCTATGGGTCAATTAATCATTCAGTGACATAACTGCAATATAC
64 TAAGGCAAATAATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATAC
1001810 ATATACATGCATACATATC-T
129 ATATAC-T--ATACATA-CAT
* * *
1001830 ACATATCTACATCCATACATATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTCA
1 AC--A--TACAT-CATACATATAGTATTTACAGCATTTAGATGCAAGA-AACTCATATTCTATCA
* * * * *
1001895 GTTCTAAGGCAAATCATAAAAAACCAACTATGGGTCAACTAGTCATTCATTAACATAATTGCAAT
60 ATTCTAAGGCAAATAATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAAT
*
1001960 ATACATATACTATACATGCAT
125 ATACATATACTATACATACAT
1001981 ACATACA-CAT--ATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTATCAATTCT
1 ACATACATCATACATATAGTATTTACAGCATTTAGATGCAAGAAA-CTCATATTCTATCAATTCT
* * * * * *
1002043 AAGGCATATTATAAAGAAACCAACTATGGGTCAACTAATAATTGATTGACATAAC--CTACATAC
65 AAGGCAAATAATAAA-AAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATAC
1002106 --ATAC-ATACATACAT
129 ATATACTATACATACAT
* * ** * * *
1002120 ACATATAT-ATATATACT-GTATCCAAAGTATTTAGATGCAATAAAACTCATATTCTATCAATTC
1 ACATACATCATACATA-TAGTATTTACAGCATTTAGATGCAA-GAAACTCATATTCTATCAATTC
* * * * * * *
1002183 TAAGGCTAATTATTGAAAAACCAACTATGGGTCAAGTAACCA-TCAACTGACATAACTACATATA
64 TAAGGC-AAATAATAAAAAACCAACTATGGGTCAACTAATCATTC-ATTGACATAACTGCA-ATA
1002247 TA
126 TA
1002249 GAGAATCTAC
Statistics
Matches: 349, Mismatches: 52, Indels: 42
0.79 0.12 0.09
Matches are distributed among these distances:
139 17 0.05
140 5 0.01
141 78 0.22
142 17 0.05
143 59 0.17
144 38 0.11
145 3 0.01
147 4 0.01
149 1 0.00
150 3 0.01
151 9 0.03
152 1 0.00
153 2 0.01
154 112 0.32
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (145 bp):
ACATACATCATACATATAGTATTTACAGCATTTAGATGCAAGAAACTCATATTCTATCAATTCTA
AGGCAAATAATAAAAAACCAACTATGGGTCAACTAATCATTCATTGACATAACTGCAATATACAT
ATACTATACATACAT
Found at i:1002000 original size:143 final size:137
Alignment explanation
Indices: 1001848--1002217 Score: 425
Period size: 141 Copynumber: 2.6 Consensus size: 137
1001838 ACATCCATAC
* * * * *
1001848 ATATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTCAGTTCTAAGGCAAATCATA
1 ATATAGTATTTACAGCATTTAGATGCAAGA-AACTCATATTCTATCAATTCTAAGGCAAATTATA
* * * * *
1001913 AAAAACCAACTATGGGTCAACTAGTCATTCATTAACATAATTGCAATATACATATACTATACATG
65 AAAAACCAACTATGGGTCAACTAATAATTCATTAACATAA--CCAACATAC--ATAC-ATACATA
1001978 CATACATACACAT
125 CATACATACACAT
*
1001991 ATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTATCAATTCTAAGGCATATTATA
1 ATATAGTATTTACAGCATTTAGATGCAAGAAA-CTCATATTCTATCAATTCTAAGGCAAATTATA
* * *
1002056 AAGAAACCAACTATGGGTCAACTAATAATTGATTGACATAACCTACATACATACATACATACATA
65 AA-AAACCAACTATGGGTCAACTAATAATTCATTAACATAACCAACATACATACATACATACATA
* *
1002121 CATATATAT
129 CATACACAT
** * * * *
1002130 ATATACTGTATCCAAAGTATTTAGATGCAATAAAACTCATATTCTATCAATTCTAAGGCTAATTA
1 ATATA--GTATTTACAGCATTTAGATGCAA-GAAACTCATATTCTATCAATTCTAAGGCAAATTA
*
1002195 TTGAAAAACCAACTATGGGTCAA
63 -TAAAAAACCAACTATGGGTCAA
1002218 GTAACCATCA
Statistics
Matches: 197, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
139 22 0.11
140 4 0.02
141 65 0.33
142 14 0.07
143 58 0.29
144 34 0.17
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (137 bp):
ATATAGTATTTACAGCATTTAGATGCAAGAAACTCATATTCTATCAATTCTAAGGCAAATTATAA
AAAACCAACTATGGGTCAACTAATAATTCATTAACATAACCAACATACATACATACATACATACA
TACACAT
Found at i:1002106 original size:4 final size:4
Alignment explanation
Indices: 1002099--1002124 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1002089 TGACATAACC
1002099 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
1002125 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1005556 original size:20 final size:21
Alignment explanation
Indices: 1005522--1005571 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1005512 TTAATAACAC
* *
1005522 AATAACTTAATTTATTAAA-AA
1 AATAA-TTAAATTATAAAATAA
*
1005543 AATTATTAAATTATAAAATAA
1 AATAATTAAATTATAAAATAA
1005564 AATAATTA
1 AATAATTA
1005572 TAACTAAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATTAAATTATAAAATAA
Found at i:1006653 original size:24 final size:24
Alignment explanation
Indices: 1006608--1006653 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1006598 TTTTTTAGAA
* **
1006608 TTGAGTTAAATCAAAAGGAATTGT
1 TTGAGCTAAATCAAAAAAAATTGT
*
1006632 TTGAGCTAAATTAAAAAAAATT
1 TTGAGCTAAATCAAAAAAAATT
1006654 AAACATGTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (24 bp):
TTGAGCTAAATCAAAAAAAATTGT
Found at i:1006836 original size:8 final size:8
Alignment explanation
Indices: 1006823--1006870 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
1006813 CGAATTATTA
1006823 TTTTTAAT
1 TTTTTAAT
1006831 TTTTTAAT
1 TTTTTAAT
1006839 TTTTTATAT
1 TTTTTA-AT
1006848 ATTCTTTAGA-
1 -TT-TTTA-AT
1006858 TTTTTAAT
1 TTTTTAAT
1006866 TTTTT
1 TTTTT
1006871 TTAAAAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 1 0.03
8 23 0.66
9 4 0.11
10 2 0.06
11 5 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTAAT
Found at i:1006855 original size:27 final size:25
Alignment explanation
Indices: 1006817--1006870 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
1006807 GTCCTACGAA
1006817 TTATTATTTTTA-ATTTTTTAATTTT
1 TTATTATTTTTAGA-TTTTTAATTTT
1006842 TTATATATTCTTTAGATTTTTAATTTT
1 TTAT-TATT-TTTAGATTTTTAATTTT
1006869 TT
1 TT
1006871 TTAAAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 4 0.15
27 17 0.65
28 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (25 bp):
TTATTATTTTTAGATTTTTAATTTT
Found at i:1013120 original size:21 final size:22
Alignment explanation
Indices: 1013096--1013148 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1013086 AATTTATCTC
1013096 TATTTTTTTTAAATTTTC-TAG
1 TATTTTTTTTAAATTTTCTTAG
* **
1013117 TATTTTATTT-CTTTTTCTTAG
1 TATTTTTTTTAAATTTTCTTAG
*
1013138 TAATTTTTTTA
1 TATTTTTTTTA
1013149 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.70
Consensus pattern (22 bp):
TATTTTTTTTAAATTTTCTTAG
Found at i:1018433 original size:54 final size:54
Alignment explanation
Indices: 1018367--1018475 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
1018357 TAATTGAGTC
*
1018367 ATATCCTTAAACGGAAATAAAAGTTCTTCTAATGTTATTTTATTCGTACATAAA
1 ATATCCTTAAACGAAAATAAAAGTTCTTCTAATGTTATTTTATTCGTACATAAA
1018421 ATATCCTTAAACGAAAATAAAAGTTCTTCTAATGTTATTTTATTCGTACATAAA
1 ATATCCTTAAACGAAAATAAAAGTTCTTCTAATGTTATTTTATTCGTACATAAA
1018475 A
1 A
1018476 CTTGAAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (54 bp):
ATATCCTTAAACGAAAATAAAAGTTCTTCTAATGTTATTTTATTCGTACATAAA
Found at i:1027517 original size:16 final size:16
Alignment explanation
Indices: 1027498--1027556 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
1027488 CTCCAACCGA
*
1027498 AAATGATTTGAATCCG
1 AAATGATCTGAATCCG
**
1027514 AAATGATCT--ATCTA
1 AAATGATCTGAATCCG
1027528 AAATGATCTGAATCCG
1 AAATGATCTGAATCCG
*
1027544 AAATTATCTGAAT
1 AAATGATCTGAAT
1027557 TTAAGTGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 12 0.34
16 23 0.66
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (16 bp):
AAATGATCTGAATCCG
Found at i:1028705 original size:40 final size:40
Alignment explanation
Indices: 1028658--1028738 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
1028648 AGAGATTAAA
1028658 TGCAAGTCTTAGAACAATAAAGAACACAAGAAAGAGAAAC
1 TGCAAGTCTTAGAACAATAAAGAACACAAGAAAGAGAAAC
1028698 TGCAAGTCTTAGAACAATAAAGAACACAAGAAAGAGAAAC
1 TGCAAGTCTTAGAACAATAAAGAACACAAGAAAGAGAAAC
1028738 T
1 T
1028739 TACTCGTGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.14
Consensus pattern (40 bp):
TGCAAGTCTTAGAACAATAAAGAACACAAGAAAGAGAAAC
Found at i:1029384 original size:31 final size:32
Alignment explanation
Indices: 1029328--1029389 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1029318 ACTTTATTAC
**
1029328 TTGATTTTTTTGTTCCAATTAAATACTTGAGT
1 TTGATTTTCATGTTCCAATTAAATACTTGAGT
*
1029360 TTGATTTTCATGTT-CAATTTAATACTTGAG
1 TTGATTTTCATGTTCCAATTAAATACTTGAG
1029390 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.52
Consensus pattern (32 bp):
TTGATTTTCATGTTCCAATTAAATACTTGAGT
Found at i:1031917 original size:83 final size:84
Alignment explanation
Indices: 1031763--1031952 Score: 222
Period size: 83 Copynumber: 2.3 Consensus size: 84
1031753 GCTGTCTCTA
* * * * * *
1031763 AGATGTTTGATAAAATGTTTGTGTTGGGCCAAATCGAGTTGTAGAAGAAATATTAGTGACCCAAA
1 AGATGTTTGATAATATGTTTGTGTTGAGACAAATCGAGTTGTAGAAGAAAAATGAATGACCCAAA
*
1031828 GTCAAATTAGATGCCTTTC
66 GACAAATTAGATGCCTTTC
* * * *
1031847 AGATGTTTGATAATATG-TTGTGTT-AGACTAATTGAAGTTTTAGAAGAAAAATGAATGACGCAA
1 AGATGTTTGATAATATGTTTGTGTTGAGACAAATCG-AGTTGTAGAAGAAAAATGAATGACCCAA
* **
1031910 AGACAAATTAGTTGTTTTTC
65 AGACAAATTAGATGCCTTTC
*
1031930 AGATGTTTGATAATATATTTGTG
1 AGATGTTTGATAATATGTTTGTG
1031953 CGGATAAATG
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
82 6 0.07
83 62 0.70
84 21 0.24
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.36
Consensus pattern (84 bp):
AGATGTTTGATAATATGTTTGTGTTGAGACAAATCGAGTTGTAGAAGAAAAATGAATGACCCAAA
GACAAATTAGATGCCTTTC
Found at i:1041183 original size:17 final size:16
Alignment explanation
Indices: 1041161--1041198 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
1041151 TATGATAAGT
1041161 AGTGAATTGATTACAG
1 AGTGAATTGATTACAG
1041177 AAGTGAATTGATTACAG
1 -AGTGAATTGATTACAG
1041194 AGTGA
1 AGTGA
1041199 TATTAAGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (16 bp):
AGTGAATTGATTACAG
Found at i:1059332 original size:137 final size:137
Alignment explanation
Indices: 1059118--1059364 Score: 356
Period size: 137 Copynumber: 1.8 Consensus size: 137
1059108 CAAAGTAGTT
1059118 GATAAGCTCAATGATAAAACAAGTTAAAAATAAATTGACATAAATATTTATTTTATGTAATTTAA
1 GATAAGCTCAATGATAAAACAAGTTAAAAATAAATTGACATAAATATTTATTTTATGTAATTTAA
* *
1059183 CCACATTATGAAAATGATGGTGAAATTAATAAAATCCTTTAAAAGATTTAAATATAAGATGCCAA
66 CCACATTATGAAAATGATGGCGAAATAAATAAAATCCTTTAAAAGATTTAAATATAAGATGCCAA
1059248 CAAAGTA
131 CAAAGTA
* * * *
1059255 GATAAGTTCAATGATATAACACA-TT-AAAGTAAACTT-ACATAAATATTTCTTTTAATGTAATT
1 GATAAGCTCAATGATAAAACA-AGTTAAAAATAAA-TTGACATAAATATTTATTTT-ATGTAATT
* * * *
1059317 TACCCACATTTTGAAAATGATGGCGGAATAAATAAAATCCTTTGAAAG
63 TAACCACATTATGAAAATGATGGCGAAATAAATAAAATCCTTTAAAAG
1059365 TAATTGTGGT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
136 23 0.24
137 73 0.75
138 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (137 bp):
GATAAGCTCAATGATAAAACAAGTTAAAAATAAATTGACATAAATATTTATTTTATGTAATTTAA
CCACATTATGAAAATGATGGCGAAATAAATAAAATCCTTTAAAAGATTTAAATATAAGATGCCAA
CAAAGTA
Found at i:1060472 original size:12 final size:12
Alignment explanation
Indices: 1060457--1060505 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
1060447 TTTGAGTTCG
1060457 AATTTAATATTT
1 AATTTAATATTT
1060469 AATTTAATATTT
1 AATTTAATATTT
* *
1060481 ATATTAAATAAATT
1 A-ATTTAAT-ATTT
1060495 AA-TTAATATTT
1 AATTTAATATTT
1060506 GACACGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 3 0.10
12 17 0.55
13 7 0.23
14 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATATTT
Found at i:1061923 original size:8 final size:8
Alignment explanation
Indices: 1061910--1061937 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1061900 TTATGCACCT
1061910 TATAAAAA
1 TATAAAAA
1061918 TATAAAAA
1 TATAAAAA
1061926 TATAAAAA
1 TATAAAAA
1061934 TATA
1 TATA
1061938 TTATAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TATAAAAA
Found at i:1073610 original size:23 final size:23
Alignment explanation
Indices: 1073582--1073625 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1073572 AATTTTTGAA
*
1073582 TTTAAGTATATAAAT-TATAATCG
1 TTTAAGTA-AAAAATATATAATCG
1073605 TTTAAGTAAAAAATATATAAT
1 TTTAAGTAAAAAATATATAAT
1073626 TTATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
TTTAAGTAAAAAATATATAATCG
Found at i:1077323 original size:19 final size:20
Alignment explanation
Indices: 1077278--1077325 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1077268 AGTCCAAACA
1077278 AATTTCAATTAAAATTGAATT
1 AATTT-AATTAAAATTGAATT
* *
1077299 AA-TTAATTAAATTTGTA-T
1 AATTTAATTAAAATTGAATT
1077317 AATTTAATT
1 AATTTAATT
1077326 GACTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 2 0.08
21 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTTAATTAAAATTGAATT
Found at i:1077332 original size:24 final size:23
Alignment explanation
Indices: 1077297--1077349 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1077287 TAAAATTGAA
*
1077297 TTAATTAATTAAATT-TGTATAAT
1 TTAATTAATTAAATTCGGT-TAAT
*
1077320 TTAATTGACTTAAATTCGGTTAAT
1 TTAATT-AATTAAATTCGGTTAAT
1077344 TTAATT
1 TTAATT
1077350 TTAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 18 0.69
25 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (23 bp):
TTAATTAATTAAATTCGGTTAAT
Found at i:1079783 original size:38 final size:34
Alignment explanation
Indices: 1079713--1079783 Score: 81
Period size: 39 Copynumber: 2.0 Consensus size: 34
1079703 TCATTGGAAT
*
1079713 ATGTTTTTTTATATATATAATTAAGATATTTTTA
1 ATGTTTTTTTATATATATAATTAAAATATTTTTA
1079747 ATGTTTATTTTATGATATATGAGAATTAAAAT-TTTTT
1 ATGTTT-TTTTAT-ATATAT---AATTAAAATATTTTT
1079784 GAGTTTGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
34 6 0.19
35 6 0.19
36 6 0.19
38 5 0.16
39 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (34 bp):
ATGTTTTTTTATATATATAATTAAAATATTTTTA
Found at i:1080364 original size:24 final size:24
Alignment explanation
Indices: 1080315--1080366 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1080305 AAAGTTCCGG
*
1080315 ATAGACCAAAATCAACATCCTTTT
1 ATAGACCAAAATCAACATCCTATT
1080339 ATAGACCAAAAT--ACAATCCGTATT
1 ATAGACCAAAATCAAC-ATCC-TATT
1080363 ATAG
1 ATAG
1080367 TATAAAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 4 0.16
24 19 0.76
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (24 bp):
ATAGACCAAAATCAACATCCTATT
Found at i:1092235 original size:34 final size:34
Alignment explanation
Indices: 1092192--1092259 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1092182 TTTTACTAAG
1092192 TGTATTTGGGTGAGGATGCAATTATTCAAGAGTT
1 TGTATTTGGGTGAGGATGCAATTATTCAAGAGTT
1092226 TGTATTTGGGTGAGGATGCAATTATTCAAGAGTT
1 TGTATTTGGGTGAGGATGCAATTATTCAAGAGTT
1092260 AAGATAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (34 bp):
TGTATTTGGGTGAGGATGCAATTATTCAAGAGTT
Found at i:1096218 original size:31 final size:31
Alignment explanation
Indices: 1096175--1096240 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1096165 CTTAACTACC
* * *
1096175 CAGTGATTTAAATAAAAACTTTTGAATAGTT
1 CAGTAATTTAAATAAAAACTTTTAAATAATT
*
1096206 CAGTAATTTAAATGAAAACTTTTAAATAATT
1 CAGTAATTTAAATAAAAACTTTTAAATAATT
1096237 CAGT
1 CAGT
1096241 GATCAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (31 bp):
CAGTAATTTAAATAAAAACTTTTAAATAATT
Found at i:1097829 original size:20 final size:22
Alignment explanation
Indices: 1097790--1097829 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
1097780 CTTTTTAAAT
*
1097790 TTTTTATTATAAATTTTTATGA
1 TTTTTATTATAAAATTTTATGA
1097812 TTTTT-TTA-AAAATTTTAT
1 TTTTTATTATAAAATTTTAT
1097830 CAAGTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTTTATTATAAAATTTTATGA
Found at i:1097872 original size:31 final size:31
Alignment explanation
Indices: 1097834--1097898 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1097824 TTTTATCAAG
1097834 TACATTATGATTATGACATGGACTATCACAT
1 TACATTATGATTATGACATGGACTATCACAT
*
1097865 TACATTATGATTATTACATGGACTATCACAT
1 TACATTATGATTATGACATGGACTATCACAT
1097896 TAC
1 TAC
1097899 TAGTATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (31 bp):
TACATTATGATTATGACATGGACTATCACAT
Found at i:1098024 original size:3 final size:3
Alignment explanation
Indices: 1098018--1098062 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
1098008 AAAAAAAAAA
** *
1098018 TAT TAT TAT GCT TAT TAT TAT TAT TAT TGT TAT TAT TAT TCAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TA
1098063 ATTTTCATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1101955 original size:30 final size:31
Alignment explanation
Indices: 1101887--1101974 Score: 83
Period size: 30 Copynumber: 2.9 Consensus size: 31
1101877 AAATTATAAA
* * *
1101887 TTAATAAATGATTAAATTATATTTTAGTCCTC
1 TTAA-AAATGATAAAATTATAATTTAATCCTC
*
1101919 TT-AAAATGATAAAATTTTAATTTAATCCT-
1 TTAAAAATGATAAAATTATAATTTAATCCTC
* *
1101948 TTAAAAATTATAAAGA-TATAAGTTAAT
1 TTAAAAATGATAAA-ATTATAATTTAAT
1101975 ATAATTATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.04
30 41 0.87
31 2 0.04
32 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (31 bp):
TTAAAAATGATAAAATTATAATTTAATCCTC
Found at i:1105722 original size:12 final size:12
Alignment explanation
Indices: 1105705--1105750 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1105695 AACAGATCGA
1105705 TCGGTTGGCTAT
1 TCGGTTGGCTAT
1105717 TCGGTTGGCTAT
1 TCGGTTGGCTAT
* *
1105729 T-TGAT--CTAT
1 TCGGTTGGCTAT
1105738 TCGGTTGGCTAT
1 TCGGTTGGCTAT
1105750 T
1 T
1105751 TGATCTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.19
10 2 0.07
11 2 0.07
12 18 0.67
ACGTcount: A:0.11, C:0.15, G:0.28, T:0.46
Consensus pattern (12 bp):
TCGGTTGGCTAT
Found at i:1105739 original size:21 final size:21
Alignment explanation
Indices: 1105713--1105757 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1105703 GATCGGTTGG
1105713 CTATTCGGTTGGCTATTTGAT
1 CTATTCGGTTGGCTATTTGAT
1105734 CTATTCGGTTGGCTATTTGAT
1 CTATTCGGTTGGCTATTTGAT
1105755 CTA
1 CTA
1105758 ATAGAAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.47
Consensus pattern (21 bp):
CTATTCGGTTGGCTATTTGAT
Found at i:1108481 original size:38 final size:38
Alignment explanation
Indices: 1108422--1108527 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
1108412 TATTTTTAAG
*
1108422 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
1108459 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
1108497 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
1108528 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:1109666 original size:5 final size:5
Alignment explanation
Indices: 1109656--1109684 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1109646 GATTTGCAAT
1109656 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1109685 CTATGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1110672 original size:97 final size:95
Alignment explanation
Indices: 1110434--1110758 Score: 614
Period size: 95 Copynumber: 3.4 Consensus size: 95
1110424 AAGATCTGTA
1110434 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1110499 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
1110529 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1110594 TAGTCACATGGAGGTAAAATCTGCCATCTTCG
66 TAGT--CAGGGAGGTAAAATCTGCCATCTTCG
1110626 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
1110691 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
1110721 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
1110759 GATCTGTTTT
Statistics
Matches: 225, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
95 131 0.58
97 94 0.42
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCG
Found at i:1110806 original size:95 final size:94
Alignment explanation
Indices: 1110434--1110819 Score: 431
Period size: 95 Copynumber: 4.0 Consensus size: 94
1110424 AAGATCTGTA
** **
1110434 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* *
1110499 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
** **
1110529 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
*
1110594 TAGTCACATGG-AGGTAAAATCTGCCATCTTCG
65 TAGT--CA-GGAAGGCAAAATCTGCCATCTTCG
** **
1110626 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* * *
1110691 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
**
1110721 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG-G-ATCTGTTTTTCAATCCACTTCCTA
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATC-G-GCTTCAATCCAC-TCC-A
** *
1110784 CCAATA-T-AGGAAGGCAGGATCTGCTATCTTCG
62 -CAATAGTCAGGAAGGCAAAATCTGCCATCTTCG
1110816 ATCT
1 ATCT
1110820 ACTTCACACC
Statistics
Matches: 269, Mismatches: 13, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
92 3 0.01
93 1 0.00
94 11 0.04
95 155 0.58
96 2 0.01
97 95 0.35
98 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (94 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATCGGCTTCAATCCACTCCACAAT
AGTCAGGAAGGCAAAATCTGCCATCTTCG
Found at i:1110831 original size:44 final size:44
Alignment explanation
Indices: 1110783--1111335 Score: 494
Period size: 44 Copynumber: 12.6 Consensus size: 44
1110773 TCCACTTCCT
* *
1110783 ACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCAC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * *
1110827 ACCAATATATGAATACAAGATCTGCTTTCTTCGATCTACTTCACC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-C
* * * * *
1110872 ACCAGTATGGGAAGACAAGATCTGC-GTCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
1110914 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCA-
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
1110958 AGCCAATACATGAAGACAAAATCTGCTTTCTGCGATCTACTTCGCC
1 A-CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
1111004 ACCAATATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
1111046 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
1111091 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
1111136 ACCAATATGGGAAGACAAGATCTGC-ATCTTGGATCCACTTC-C
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
1111178 TATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC
1 -ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * * * *
1111223 GCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCC
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-AC
* * *
1111268 ACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCAT
1 ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
* * * *
1111311 GCCAATACATG-AGACAAGATATGCT
1 ACCAATATAGGAAGACAAGATCTGCT
1111336 TTAATGACTT
Statistics
Matches: 398, Mismatches: 95, Indels: 33
0.76 0.18 0.06
Matches are distributed among these distances:
42 15 0.04
43 67 0.17
44 227 0.57
45 88 0.22
46 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC
Found at i:1111317 original size:132 final size:132
Alignment explanation
Indices: 1110772--1111308 Score: 948
Period size: 132 Copynumber: 4.1 Consensus size: 132
1110762 CTGTTTTTCA
* ** * * *
1110772 ATCCACTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTCACACCAATATAT
1 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * *
1110837 GAATACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCGTCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1110902 GG
131 GG
*
1110904 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAAGCCAATACAT
1 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
1110969 GAAGACAAAATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1111034 GG
131 GG
1111036 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1111101 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
1111166 GG
131 GG
1111168 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1111233 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
*
1111298 CG
131 GG
1111300 ATCCACTTC
1 ATCCACTTC
1111309 ATGCCAATAC
Statistics
Matches: 389, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 389 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (132 bp):
ATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
GG
Found at i:1122069 original size:22 final size:22
Alignment explanation
Indices: 1122041--1122083 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1122031 AACAATAACA
1122041 ATAACAATAAAATAATAGTAAT
1 ATAACAATAAAATAATAGTAAT
* *
1122063 ATAACAATGAAATGATAGTAA
1 ATAACAATAAAATAATAGTAA
1122084 AACAGTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAACAATAAAATAATAGTAAT
Found at i:1130170 original size:59 final size:56
Alignment explanation
Indices: 1130105--1130290 Score: 144
Period size: 59 Copynumber: 3.1 Consensus size: 56
1130095 ATGATAAATT
*
1130105 ATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATT
1 ATATATTTTTATTAA--TATATTTAATAATAATTAT-TTAAATTATATTTTATAGTATC
* * * * * *
1130164 ATATATTATGATT-TTAAAAAATTCATATAAGAA-TATTTAATATTAAGAATTTTATTA-AATC
1 ATATATT-T--TTATTAATATATTTA-ATAATAATTATTTAA-ATT-A-TATTTTA-TAGTATC
* *
1130225 ATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGTATC
1 ATATATTTTTATT--AATATATTTAATAATAATTATTT-AAATTATATTTTATAGTATC
1130284 ATATATT
1 ATATATT
1130291 ATGATTTGAG
Statistics
Matches: 98, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
58 7 0.07
59 36 0.37
60 15 0.15
61 34 0.35
62 6 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (56 bp):
ATATATTTTTATTAATATATTTAATAATAATTATTTAAATTATATTTTATAGTATC
Found at i:1130216 original size:61 final size:61
Alignment explanation
Indices: 1130151--1130338 Score: 165
Period size: 61 Copynumber: 3.1 Consensus size: 61
1130141 GTTAAATTAT
*
1130151 ATTTTATAGTATTATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGA
* * * * * *
1130212 ATTTTATTA-AATCATATATT-TTA-ATTAAAATATATTTAATATTA-ATTATTTCAA-ATT-A-
1 ATTTTA-TAGTATCATATATTATGATTTTAAAA-A-A-TTCATATAAGAATATTT-AATATTAAG
*
1130270 T
61 A
* ** * *
1130271 ATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGA
1130332 ATTTTAT
1 ATTTTAT
1130339 TATAAATTAT
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
58 10 0.11
59 31 0.33
60 8 0.08
61 35 0.37
62 11 0.12
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGA
Found at i:1130312 original size:120 final size:122
Alignment explanation
Indices: 1130098--1130388 Score: 453
Period size: 120 Copynumber: 2.4 Consensus size: 122
1130088 TAGTATGATG
* **
1130098 ATAAATTATATATTTTTATTAACTTATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
* * *
1130163 TATATATTATGATTTTAAAAAATTCATATAAGAATATTTAATATTAAGAATTTTA-T
66 CATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
* *
1130219 -TAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTA
** *
1130282 TCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATT
65 TCATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
1130340 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1130389 ATATGATTAA
Statistics
Matches: 153, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
119 2 0.01
120 105 0.69
121 1 0.01
122 43 0.28
123 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (122 bp):
ATAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTAT
CATATATTATGATTTGAAAAAATTCATATAAGAATATTGAATATTAAGAATTTTATT
Found at i:1130367 original size:18 final size:19
Alignment explanation
Indices: 1130332--1130368 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1130322 ATTATTAAGA
1130332 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
1130351 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
1130369 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:1130598 original size:44 final size:45
Alignment explanation
Indices: 1130533--1130623 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1130523 ACCTCTATTC
* * *
1130533 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1130577 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1130622 CA
1 CA
1130624 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1130625 original size:16 final size:16
Alignment explanation
Indices: 1130604--1130674 Score: 133
Period size: 16 Copynumber: 4.4 Consensus size: 16
1130594 GATTAGCTAT
1130604 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1130620 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1130637 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1130653 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1130669 TACACC
1 TACACC
1130675 GAACCAAACG
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 38 0.70
17 16 0.30
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1130646 original size:33 final size:32
Alignment explanation
Indices: 1130604--1130674 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 32
1130594 GATTAGCTAT
1130604 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
1130637 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1130669 TACACC
1 TACACC
1130675 GAACCAAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 10 0.26
33 28 0.74
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1133450 original size:17 final size:17
Alignment explanation
Indices: 1133428--1133461 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1133418 TGTGAAAATT
1133428 AAAATTTCAA-AACTTAA
1 AAAATTT-AATAACTTAA
1133445 AAAATTTAATAACTTAA
1 AAAATTTAATAACTTAA
1133462 CATATTCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATTTAATAACTTAA
Found at i:1135526 original size:17 final size:16
Alignment explanation
Indices: 1135483--1135527 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1135473 TGAGTACTCG
1135483 AAAAATAGGTTTGAGT
1 AAAAATAGGTTTGAGT
**
1135499 AAAAATAAGGTTTGTTT
1 AAAAAT-AGGTTTGAGT
1135516 AGAAAATAGGTT
1 A-AAAATAGGTT
1135528 AAGCAATGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (16 bp):
AAAAATAGGTTTGAGT
Found at i:1135625 original size:21 final size:21
Alignment explanation
Indices: 1135589--1135640 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1135579 AAATTTGCTA
* *
1135589 TTTTTTTTACTGTTTTATTAC
1 TTTTTTTTTCTATTTTATTAC
* **
1135610 TTTTTTTTTCTATTTTGTTGT
1 TTTTTTTTTCTATTTTATTAC
1135631 TTTTTTTTTC
1 TTTTTTTTTC
1135641 ACTATTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTCTATTTTATTAC
Found at i:1135841 original size:18 final size:18
Alignment explanation
Indices: 1135820--1135854 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1135810 GGGAAACATT
1135820 TATTTTTAATGTTTTTAG
1 TATTTTTAATGTTTTTAG
* *
1135838 TATTTTTGATTTTTTTA
1 TATTTTTAATGTTTTTA
1135855 AAAAAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (18 bp):
TATTTTTAATGTTTTTAG
Found at i:1137866 original size:3 final size:3
Alignment explanation
Indices: 1137858--1137904 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
1137848 AAGCACATAC
1137858 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TCAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
1137903 TA
1 TA
1137905 TGAAAATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1139506 original size:75 final size:75
Alignment explanation
Indices: 1139412--1139982 Score: 652
Period size: 73 Copynumber: 7.5 Consensus size: 75
1139402 ACGTGAGCTA
**
1139412 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACATTAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAATACCTCA
* *
1139477 GCGTGCCCCG
66 GCGTGTCCTG
* *
1139487 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAATAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAATACCTCA
* *
1139550 ACGTGTCATG
66 GCGTGTCCTG
* **
1139560 AGGCTCAACTCACATCTCGCAACGTGAGTTGATCTTTTTG-AAAAAACAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAAACAGAAATTGAAAATACCT
* *
1139624 CGGCGTGTGACCCG
64 CAGCGTGT--CCTG
* ** * *
1139638 AGGCTCAATTCACCTCTCGCAACGTGAGTTGATCTTTTTAAAAAAATAGAAATTGAAAATACCTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTGAAAAAAACAGAAATTGAAAATACCTC
* *
1139703 GGCGTGTCCTA
65 AGCGTGTCCTG
*
1139714 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAATACCTCA
*
1139777 GCGTGTCTTG
66 GCGTGTCCTG
* * *
1139787 AGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACATAAATTGAACAGGAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG----A-A-AAA---AACAGAAATTGAA
* * *
1139852 AATACCTCAACGTGTCTTA
57 AATACCTCAGCGTGTCCTG
* *
1139871 AGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTCTTG--AAAAGCAGAAATTGAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAAAACAGAAATTGAAAATACCT
** *
1139934 CAATGTGTCTTG
64 CAGCGTGTCCTG
1139946 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1139983 TTGAAATGGA
Statistics
Matches: 430, Mismatches: 46, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
73 124 0.29
74 3 0.01
75 107 0.25
76 60 0.14
77 4 0.01
78 66 0.15
81 3 0.01
84 58 0.13
85 3 0.01
86 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACAGAAATTGAAAATACCTCA
GCGTGTCCTG
Found at i:1139742 original size:227 final size:225
Alignment explanation
Indices: 1139411--1139982 Score: 713
Period size: 227 Copynumber: 2.5 Consensus size: 225
1139401 CACGTGAGCT
* * **
1139411 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAACATTAATTGAAAATACCTC
1 AAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAACAGAAATTGAAAATACCTC
* * *
1139476 AGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAA
66 AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
* * *
1139541 ATTACCTCAACGTGTCATGAGGCTCAACTCACATCTCGCAACGTGAGTTGATCTTTTTG-A-AAA
131 ATTACCTCAACGTGTCATGAGCCTCAACTCACATCTCGCAACATGAGTTGA--TTTTCGAATAAA
**
1139604 -AACAGAAATTGAAAATACCTCGGCGTGTGACCC
194 TAACAGAAATTGAAAATACCTCAACGTGT--CCC
* ** *
1139637 GAGGCTCAATTCACCTCTCGCAACGTGAGTTGATCTTTTTAAAAAAATAGAAATTGAAAATACCT
1 AAGGCTCAATTCACCTCTCGCAATATGAGTTGAT-TTTTTAAAAAAACAGAAATTGAAAATACCT
* *
1139702 CGGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
65 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGA
* * * *
1139767 AATTACCTCAGCGTGTCTTGAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACA
130 AATTACCTCAACGTGTCATGAGCCTCAACTCACATCTCGCAACATGAGTTGATTTTCG----A-A
* **
1139832 TAAATTGAACAGGAATTGAAAATACCTCAACGTGTCTT
190 TAAA-T-AACAGAAATTGAAAATACCTCAACGTGTCCC
* *
1139870 AAGGCTCAACTT-ACCTCTCGCAATATGAGTTGATTTTCTT-GAAAAGCAGAAATTGAAAATACC
1 AAGGCTCAA-TTCACCTCTCGCAATATGAGTTGATTTT-TTAAAAAAACAGAAATTGAAAATACC
** *
1139933 TCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
64 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1139983 TTGAAATGGA
Statistics
Matches: 297, Mismatches: 36, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
225 5 0.02
226 30 0.10
227 132 0.44
231 1 0.00
232 71 0.24
233 31 0.10
234 2 0.01
235 25 0.08
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (225 bp):
AAGGCTCAATTCACCTCTCGCAATATGAGTTGATTTTTTAAAAAAACAGAAATTGAAAATACCTC
AGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
ATTACCTCAACGTGTCATGAGCCTCAACTCACATCTCGCAACATGAGTTGATTTTCGAATAAATA
ACAGAAATTGAAAATACCTCAACGTGTCCC
Found at i:1139975 original size:159 final size:149
Alignment explanation
Indices: 1139410--1139981 Score: 666
Period size: 159 Copynumber: 3.8 Consensus size: 149
1139400 GCACGTGAGC
**
1139410 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAAACATTAATTGAAAATACC
1 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG--AAAAACAGAAATTGAAAATACC
* * ** **
1139474 TCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--TGAAAAATAGAAAT
64 TCAGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAAATAGAAAT
*
1139537 TGAAATTACCTCAACGTGTCA
129 TGAAAATACCTCAACGTGTCA
* * **
1139558 TGAGGCTCAACTCACATCTCGCAACGTGAGTTGATCTTTTTGAAAAAACAGAAATTGAAAATACC
1 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTG-AAAAACAGAAATTGAAAATACC
* * ** * ** **
1139623 TCGGCGTGTGACCCGAGGCTCAATTCACCTCTCGCAACGTGAGTTGATCTTTTTAAAAAAATAGA
64 TC--AGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTAAAAAAAAATAGA
** *
1139688 AATTGAAAATACCTCGGCGTGTCC
126 AATTGAAAATACCTCAACGTGTCA
*
1139712 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTC
1 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTC
* *
1139776 AGCGTGTCTTGAGCCTCAACTCACCTCTCGCAATATGAGTTGATTTTCGAAAAACATAAATTGAA
66 AGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--AAAAA-A-AAA-T---
* *
1139841 CAGGAATTGAAAATACCTCAACGTGTCT
123 -AGAAATTGAAAATACCTCAACGTGTCA
* *
1139869 TAAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCT
1 TAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAAACAGAAATTGAAAATACCT
*
1139934 CAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
65 CAGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1139982 TTTGAAATGG
Statistics
Matches: 362, Mismatches: 44, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
148 33 0.09
149 58 0.16
150 9 0.02
151 62 0.17
152 12 0.03
153 1 0.00
154 59 0.16
157 56 0.15
158 3 0.01
159 69 0.19
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (149 bp):
TAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTC
AGTGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAAATAGAAATTG
AAAATACCTCAACGTGTCA
Found at i:1139987 original size:75 final size:75
Alignment explanation
Indices: 1139839--1139988 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 75
1139829 ACATAAATTG
* * * * *
1139839 AACAGGAATTGAAAATACCTCAACGTGTCTTAAGGCTCAACTTACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
1139904 TTTCTTGAAA
66 TTTTTTGAAA
* ** *
1139914 AGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1139979 TTTTTTGAAA
66 TTTTTTGAAA
1139989 TGGAAATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGAAA
Found at i:1152359 original size:23 final size:18
Alignment explanation
Indices: 1152312--1152356 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
1152302 AAAAACATAT
1152312 TAATATTAATAATAATAC
1 TAATATTAATAATAATAC
1152330 TAATATTACATAAATATATAC
1 TAATATTA-AT-AATA-ATAC
*
1152351 TTATAT
1 TAATAT
1152357 ATTTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 2 0.09
20 4 0.17
21 9 0.39
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATATTAATAATAATAC
Found at i:1152713 original size:8 final size:8
Alignment explanation
Indices: 1152700--1152737 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1152690 CTATACGTAA
*
1152700 ATATATAT
1 ATATATAC
1152708 ATATATAC
1 ATATATAC
1152716 ATATATAC
1 ATATATAC
*
1152724 ATA-AAAC
1 ATATATAC
1152731 ATATATA
1 ATATATA
1152738 AACATTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATATAC
Found at i:1152754 original size:3 final size:3
Alignment explanation
Indices: 1152746--1152800 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1152736 TAAACATTGG
1152746 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1152794 TAA TAA T
1 TAA TAA T
1152801 GTTGAAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1152914 original size:3 final size:3
Alignment explanation
Indices: 1152906--1152959 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1152896 ACAAAAGAAC
1152906 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1152954 ATA ATA
1 ATA ATA
1152960 TGAAAATAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1161600 original size:19 final size:19
Alignment explanation
Indices: 1161576--1161612 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1161566 AAACTCATGA
1161576 TAATCTCCTAAGAAATCAT
1 TAATCTCCTAAGAAATCAT
1161595 TAATCTCCTAAGAAATCA
1 TAATCTCCTAAGAAATCA
1161613 ACTGGGAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (19 bp):
TAATCTCCTAAGAAATCAT
Found at i:1163151 original size:30 final size:30
Alignment explanation
Indices: 1163115--1163176 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1163105 TGTGCATGTA
1163115 TCACTTTAAGTATTTGATTAAAAAATTATG
1 TCACTTTAAGTATTTGATTAAAAAATTATG
1163145 TCACTTTAAGTATTTGATTAAAAAATTATG
1 TCACTTTAAGTATTTGATTAAAAAATTATG
1163175 TC
1 TC
1163177 TTTTCATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (30 bp):
TCACTTTAAGTATTTGATTAAAAAATTATG
Found at i:1164235 original size:15 final size:15
Alignment explanation
Indices: 1164215--1164245 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1164205 GTCATGTAAG
1164215 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
1164230 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
1164245 T
1 T
1164246 ATATTGTTTT
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:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:1164435 original size:17 final size:17
Alignment explanation
Indices: 1164402--1164440 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1164392 TAAGCTTTTG
1164402 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
1164419 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
1164436 ATTTT
1 ATTTT
1164441 CCACAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:1168589 original size:15 final size:15
Alignment explanation
Indices: 1168569--1168599 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1168559 GTCATGTAAG
1168569 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
1168584 TGAAAGGTCTAGAGT
1 TGAAAGGTCAAGAGT
1168599 T
1 T
1168600 ATATTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Done.