Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_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: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1048844 original size:593 final size:593
Alignment explanation
Indices: 1047711--1048896 Score: 2228
Period size: 593 Copynumber: 2.0 Consensus size: 593
1047701 ACTGAAAGAA
* * *
1047711 CAGTATCGATACTATAAGTTTAAATTAGAGGAAATTCGATGAACAATATCAATACTAATGCAAGT
1 CAGTACCGATACTAAAAGTTTAAATTAGAGGAAATTCGATAAACAATATCAATACTAATGCAAGT
1047776 AGTATCAATAATGTTGTGAGTATCGATACTAAGAAGAATGCATCGATACTATGGATTTCAGAATG
66 AGTATCAATAATGTTGTGAGTATCGATACTAAGAAGAATGCATCGATACTATGGATTTCAGAATG
*
1047841 TAAAAATGGTATTAATACTGAAATGAGTATCGATACCATAGTATAGAAGTATCGATATCATAGTA
131 TAAAAATGGTATTAATACTGAAAGGAGTATCGATACCATAGTATAGAAGTATCGATATCATAGTA
1047906 GGGGTATCGATACTGTTGAGCCTGGAATTTTAAGATGGATGAATTTTAATAGAAATTGAAAATAA
196 GGGGTATCGATACTGTTGAGCCTGGAATTTTAAGATGGATGAATTTTAATAGAAATTGAAAATAA
*
1047971 TAGTACTTTTTAAGTATTATCAAAAGAATAAATGTTAGAAAGTATACTAACATTTGTATGGTATG
261 TAGGACTTTTTAAGTATTATCAAAAGAATAAATGTTAGAAAGTATACTAACATTTGTATGGTATG
* * *
1048036 TGTAATAATGGATACTTGTTTAGATCGTAACCAAGCTCCAGAGTCAAGCAGGAAAAAAGGCAAAA
326 TGTAATAATAGATACTTGTATAGATCGTAACCAAGCTCCAGAGTCAAGCAAGAAAAAAGGCAAAA
*
1048101 TAAAGTAATCGAATAGCTGGACATCCTTAATGCATACTAGTGAGGCATATCATGTTAGTGCATTT
391 TAAAGTAATCGAATAGCTGGACATCCTTAATGCATACTAGTGAGACATATCATGTTAGTGCATTT
1048166 ATTGTACTTATATGAGATGAGGAAGACTTGCGATGAGTTAACCTCGAAAGTTTTGTTAAATGTAT
456 ATTGTACTTATATGAGATGAGGAAGACTTGCGATGAGTTAACCTCGAAAGTTTTGTTAAATGTAT
*
1048231 GTTTTACAGTATTTTGATATATTTTCATAATGTGTATGGGAATGTTGTTATGAATAAGTTTTAGA
521 GTTTTACAGTATTTTGATATATTTTCATAATGTGTATGGGAATGTTATTATGAATAAGTTTTAGA
1048296 GTATGAAC
586 GTATGAAC
1048304 CAGTACCGATACTAAAAGTTTAAATTAGAGGAAATTCGATAAACAATATCAATACTAATGCAAGT
1 CAGTACCGATACTAAAAGTTTAAATTAGAGGAAATTCGATAAACAATATCAATACTAATGCAAGT
*
1048369 AGTATCAATAATGTTGTGAGTATCGATACTAAGAAGAATGCATCGATACTATGGATTTCATAATG
66 AGTATCAATAATGTTGTGAGTATCGATACTAAGAAGAATGCATCGATACTATGGATTTCAGAATG
*
1048434 TAAAAATGGTATTAGTACTGAAAGGAGTATCGATACCATAGTATAGAAGTATCGATATCATAGTA
131 TAAAAATGGTATTAATACTGAAAGGAGTATCGATACCATAGTATAGAAGTATCGATATCATAGTA
1048499 GGGGTATCGATACTGTTGAGCCTGGAATTTTAAGATGGATGAATTTTAATAGAAATTGAAAATAA
196 GGGGTATCGATACTGTTGAGCCTGGAATTTTAAGATGGATGAATTTTAATAGAAATTGAAAATAA
1048564 TAGGACTTTTTAAGTATTATCAAAAGAATAAATGTTAGAAAGTATACTAACATTTGTATGGTATG
261 TAGGACTTTTTAAGTATTATCAAAAGAATAAATGTTAGAAAGTATACTAACATTTGTATGGTATG
* * *
1048629 TGTAATAATAGATGCTTGTATAGATCGTAACCAAGCTCTAGAGTCAAGCAAGAAAAAGGGCAAAA
326 TGTAATAATAGATACTTGTATAGATCGTAACCAAGCTCCAGAGTCAAGCAAGAAAAAAGGCAAAA
*
1048694 TAAAGTTATCGAATAGCTGGACATCCTTAATGCATACTAGTGAGACATATCATGTTAGTGCATTT
391 TAAAGTAATCGAATAGCTGGACATCCTTAATGCATACTAGTGAGACATATCATGTTAGTGCATTT
1048759 ATTGTACTTATATGAGATGAGGAAGACTTGCGATGAGTTAACCTCGAAAGTTTTGTTAAATGTAT
456 ATTGTACTTATATGAGATGAGGAAGACTTGCGATGAGTTAACCTCGAAAGTTTTGTTAAATGTAT
1048824 GTTTTACAGTATTTTGATATATTTTCATAATGTGTATGGGAATGTTATTATGAATAAGTTTTAGA
521 GTTTTACAGTATTTTGATATATTTTCATAATGTGTATGGGAATGTTATTATGAATAAGTTTTAGA
1048889 GTATGAAC
586 GTATGAAC
1048897 TGCTCTAAAA
Statistics
Matches: 577, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
593 577 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (593 bp):
CAGTACCGATACTAAAAGTTTAAATTAGAGGAAATTCGATAAACAATATCAATACTAATGCAAGT
AGTATCAATAATGTTGTGAGTATCGATACTAAGAAGAATGCATCGATACTATGGATTTCAGAATG
TAAAAATGGTATTAATACTGAAAGGAGTATCGATACCATAGTATAGAAGTATCGATATCATAGTA
GGGGTATCGATACTGTTGAGCCTGGAATTTTAAGATGGATGAATTTTAATAGAAATTGAAAATAA
TAGGACTTTTTAAGTATTATCAAAAGAATAAATGTTAGAAAGTATACTAACATTTGTATGGTATG
TGTAATAATAGATACTTGTATAGATCGTAACCAAGCTCCAGAGTCAAGCAAGAAAAAAGGCAAAA
TAAAGTAATCGAATAGCTGGACATCCTTAATGCATACTAGTGAGACATATCATGTTAGTGCATTT
ATTGTACTTATATGAGATGAGGAAGACTTGCGATGAGTTAACCTCGAAAGTTTTGTTAAATGTAT
GTTTTACAGTATTTTGATATATTTTCATAATGTGTATGGGAATGTTATTATGAATAAGTTTTAGA
GTATGAAC
Found at i:1053216 original size:19 final size:19
Alignment explanation
Indices: 1053183--1053227 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1053173 AAACATGCAA
1053183 TATGA-ATATTATTATCAT
1 TATGATATATTATTATCAT
* * *
1053201 TGTGATATATTGTTATTAT
1 TATGATATATTATTATCAT
1053220 TATGATAT
1 TATGATAT
1053228 TATGGTTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (19 bp):
TATGATATATTATTATCAT
Found at i:1062485 original size:528 final size:533
Alignment explanation
Indices: 1061687--1062748 Score: 2055
Period size: 528 Copynumber: 2.0 Consensus size: 533
1061677 TTTTATGGTG
1061687 CGAAGGCCCATATTAGAGGACACCAGGTGAGGAAACACTATAGAACAATCATATGGTCCGTGGGA
1 CGAAGGCCCATATTAGAGGACACCAGGTGAGGAAACACTATAGAACAATCATATGGTCCGTGGGA
1061752 ATTCTGGAGAAAGTTATTTTACGGTGGAGACGTAAAGGGAGTGGCTTGCGAGGATTTCGAAGGGA
66 ATTCTGGAGAAAGTTATTTTACGGTGGAGACGTAAAGGGAGTGGCTTGCGAGGATTTCGAAGGGA
1061817 TGCAATTACGAAGGAACCTGACCCACAGTGCATGCCCTCGAAAGAGGATGATTATGATTTTCTCA
131 TGCAATTACGAAGGAACCTGACCCACAGTGCATGCCCTCGAAAGAGGATGATTATGATTTTCTCA
1061882 AGGAGGGAAGAAAACAAACCGAGGAAAGGCTGCAGAAGGCACTTACTAGGGTAAAGTCCATGGCT
196 AGGAGGGAAGAAAACAAACCGAGGAAAGGCTGCAGAAGGCACTTACTAGGGTAAAGTCCATGGCT
1061947 CAGAATCCTGAAGGACGAGACCAATATCGAAGGCTGCTTACATTGGTTCAAGGGATTCGTGGAAA
261 CAGAATCCTGAAGGACGAGACCAATATCGAAGGCTGCTTACATTGGTTCAAGGGATTCGT-GAAA
1062012 A-CAGGTAATTGTTG-TTTCTTTTACATAGATTTCTACTTTAGTAAAGTTTACAATTCAGCAGGC
325 ACCAGGTAATTGTTGTTTTCTTTTACATAGATTTCTACTTTAGTAAAGTTTACAATTCAGCAGGC
1062075 TTCAATGATGTTAGTTAGTTACCCATGACGAGTCGATCTGT-CGAGA-TTTGTCTCCGCACCTTG
390 TTCAATGATGTTAGTTAGTTACCCATGACGAGTCGATCTGTCCGAGATTTTGTCTCCGCACCTTG
1062138 ACCTTG-TTATTTCTGTCATTCGCTGTTGCTTCATCTGGATGTTAACTAGCCAAGG-CTACTATA
455 ACCTTGATTATTTCTGTCATTCGCTGTTGCTTCATCTGGATGTTAACTAGCCAAGGCCTACTATA
1062201 ATCTGGCTAAGGTC
520 ATCTGGCTAAGGTC
1062215 CGAAGGCCCATATTAGAGGACACCAGGTGAGGAAACACTATAGAACAATCATATGGTCCGTGGGA
1 CGAAGGCCCATATTAGAGGACACCAGGTGAGGAAACACTATAGAACAATCATATGGTCCGTGGGA
1062280 ATTCTGGAGAAAGTTATTTTACGGTGGAGACGTAAAGGGAGTGGCTTGCGAGGATTTCGAAGGGA
66 ATTCTGGAGAAAGTTATTTTACGGTGGAGACGTAAAGGGAGTGGCTTGCGAGGATTTCGAAGGGA
1062345 TGCAATTACGAAGGAACCTGACCCACAGTGCATGCCCTCGAAAGAGGATGATTATGATTTTCTCA
131 TGCAATTACGAAGGAACCTGACCCACAGTGCATGCCCTCGAAAGAGGATGATTATGATTTTCTCA
1062410 AGGAGGGAAGAAAACAAACCGAGGAAAGGCTGCAGAAGGCACTTACTAGGGTAAAGTCCATGGCT
196 AGGAGGGAAGAAAACAAACCGAGGAAAGGCTGCAGAAGGCACTTACTAGGGTAAAGTCCATGGCT
1062475 CAGAATCCTGAAGGACGAGACCAATATCGAAGGCTGCTTACATTGGTTCAAGGGATTCGTGAAAA
261 CAGAATCCTGAAGGACGAGACCAATATCGAAGGCTGCTTACATTGGTTCAAGGGATTCGTGAAAA
1062540 CCAGGTAATTGTTGTTTTCTTTTACATAGATTTCTACTTTAGTAAAGTTTACAATTCAGCAGGCT
326 CCAGGTAATTGTTGTTTTCTTTTACATAGATTTCTACTTTAGTAAAGTTTACAATTCAGCAGGCT
1062605 TCAATGATGTTAGTTAGTTACCCATGACGAGTCGATCTGTCCGAGATTTTGTCTCCGCACCTTGA
391 TCAATGATGTTAGTTAGTTACCCATGACGAGTCGATCTGTCCGAGATTTTGTCTCCGCACCTTGA
*
1062670 CCTTGATTTATTTCTGTCATTCTCTGTTGCTTCATCTGGATGTTAACTAGCCAAGGCCTACTATA
456 CCTTGA-TTATTTCTGTCATTCGCTGTTGCTTCATCTGGATGTTAACTAGCCAAGGCCTACTATA
1062735 ATCTGGCTAAGGTC
520 ATCTGGCTAAGGTC
1062749 ATCTTTGATT
Statistics
Matches: 526, Mismatches: 1, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
527 5 0.01
528 333 0.63
529 90 0.17
530 5 0.01
531 23 0.04
533 48 0.09
534 22 0.04
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (533 bp):
CGAAGGCCCATATTAGAGGACACCAGGTGAGGAAACACTATAGAACAATCATATGGTCCGTGGGA
ATTCTGGAGAAAGTTATTTTACGGTGGAGACGTAAAGGGAGTGGCTTGCGAGGATTTCGAAGGGA
TGCAATTACGAAGGAACCTGACCCACAGTGCATGCCCTCGAAAGAGGATGATTATGATTTTCTCA
AGGAGGGAAGAAAACAAACCGAGGAAAGGCTGCAGAAGGCACTTACTAGGGTAAAGTCCATGGCT
CAGAATCCTGAAGGACGAGACCAATATCGAAGGCTGCTTACATTGGTTCAAGGGATTCGTGAAAA
CCAGGTAATTGTTGTTTTCTTTTACATAGATTTCTACTTTAGTAAAGTTTACAATTCAGCAGGCT
TCAATGATGTTAGTTAGTTACCCATGACGAGTCGATCTGTCCGAGATTTTGTCTCCGCACCTTGA
CCTTGATTATTTCTGTCATTCGCTGTTGCTTCATCTGGATGTTAACTAGCCAAGGCCTACTATAA
TCTGGCTAAGGTC
Found at i:1067933 original size:20 final size:20
Alignment explanation
Indices: 1067908--1067955 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1067898 TTTGGGTTAT
1067908 AGTATTGATATTGTCGATAG
1 AGTATTGATATTGTCGATAG
1067928 AGTATTGATATTGTCGATAG
1 AGTATTGATATTGTCGATAG
1067948 AGTATTGA
1 AGTATTGA
1067956 CACAGTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (20 bp):
AGTATTGATATTGTCGATAG
Found at i:1068539 original size:16 final size:16
Alignment explanation
Indices: 1068520--1068555 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1068510 TAACAAACAT
1068520 CGAGCTTAACGAGTAA
1 CGAGCTTAACGAGTAA
1068536 CGAGCTTAACGAGTAA
1 CGAGCTTAACGAGTAA
1068552 CGAG
1 CGAG
1068556 TCGAGCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (16 bp):
CGAGCTTAACGAGTAA
Found at i:1071069 original size:87 final size:86
Alignment explanation
Indices: 1070979--1071148 Score: 200
Period size: 87 Copynumber: 2.0 Consensus size: 86
1070969 TGAAATTATA
** * * *
1070979 AAAAAAATTAGAGGCCTTAATTATAAAGGCA-AAAATCGAGATTGAAAAAAA-TAAGGGTCTCAA
1 AAAAAAATTAGAACCCTCAATTAGAAAGGCAGAAAAT-GAGATT-AAAAAAACTAAGAGTCTCAA
* *
1071042 TTATAAAGTTATAATTGAGATCG
64 TTATAAAGTTAAAAGTGAGATCG
* ** *
1071065 AAAAAACTTAGAACCCTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAGAGTCTCAAT
1 AAAAAAATTAGAACCCTCAATTAGAAAGGCAGAAAATGAGATTAAAAAAAC-TAAGAGTCTCAAT
1071130 TATAAAGTTAAAAGTGAGA
65 TATAAAGTTAAAAGTGAGA
1071149 AAAAAAAAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
85 7 0.10
86 30 0.43
87 33 0.47
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (86 bp):
AAAAAAATTAGAACCCTCAATTAGAAAGGCAGAAAATGAGATTAAAAAAACTAAGAGTCTCAATT
ATAAAGTTAAAAGTGAGATCG
Found at i:1071084 original size:43 final size:43
Alignment explanation
Indices: 1071037--1071156 Score: 136
Period size: 44 Copynumber: 2.8 Consensus size: 43
1071027 AAATAAGGGT
* * *
1071037 CTCAATTATAAAGTTATAATTGAGATCGAAAAAACTT-AGAACC
1 CTCAATTATAAAGTTAAAAGTGAGATCAAAAAAACTTAAG-ACC
* * **
1071080 CTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAGAGT
1 CTCAATTATAAAGTTA-AAAGTGAGATCAAAAAAACTTAAGACC
*
1071124 CTCAATTATAAAGTTAAAAGTGAGA-AAAAAAAA
1 CTCAATTATAAAGTTAAAAGTGAGATCAAAAAAA
1071157 GAATTATAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
42 7 0.11
43 24 0.36
44 33 0.50
45 2 0.03
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (43 bp):
CTCAATTATAAAGTTAAAAGTGAGATCAAAAAAACTTAAGACC
Found at i:1071128 original size:44 final size:43
Alignment explanation
Indices: 1070997--1071156 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 43
1070987 TAGAGGCCTT
** * *
1070997 AATTATAAAGGCAAAAATCGAGATTGAAAAAAA--TAAGGGTCTC
1 AATTATAAAGTTAAAAGT-GAGATT-AAAAAAACTTAAGAGTCTC
* * ** **
1071040 AATTATAAAGTTATAATTGAGATCGAAAAAACTT-AGAACCCTC
1 AATTATAAAGTTAAAAGTGAGATTAAAAAAACTTAAG-AGTCTC
*
1071083 AATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAGAGTCTC
1 AATTATAAAGTTA-AAAGTGAGATTAAAAAAACTTAAGAGTCTC
*
1071127 AATTATAAAGTTAAAAGTGAGA-AAAAAAAA
1 AATTATAAAGTTAAAAGTGAGATTAAAAAAA
1071157 GAATTATAAT
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
41 6 0.06
42 14 0.15
43 39 0.41
44 33 0.35
45 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.16, T:0.24
Consensus pattern (43 bp):
AATTATAAAGTTAAAAGTGAGATTAAAAAAACTTAAGAGTCTC
Found at i:1071353 original size:21 final size:21
Alignment explanation
Indices: 1071254--1071354 Score: 55
Period size: 20 Copynumber: 4.7 Consensus size: 21
1071244 GATTGAATAA
1071254 TATAAAGATAAAAAGACCTCAAT
1 TATAAAGATAAAAA-ACCT-AAT
* * * *
1071277 TAAAGAATAATAAATAATC-AAT
1 TATA-AA-GATAAAAAACCTAAT
* * *
1071299 TATAAAGGTAAAAATA-ATATT
1 TATAAAGATAAAAA-ACCTAAT
* *
1071320 TA-AAAAATTAAAAACCTAAT
1 TATAAAGATAAAAAACCTAAT
1071340 TATAAAGATAAAAAA
1 TATAAAGATAAAAAA
1071355 ATGAGAGCTC
Statistics
Matches: 55, Mismatches: 17, Indels: 14
0.64 0.20 0.16
Matches are distributed among these distances:
19 1 0.02
20 18 0.33
21 17 0.31
22 6 0.11
23 3 0.05
24 4 0.07
25 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (21 bp):
TATAAAGATAAAAAACCTAAT
Found at i:1071354 original size:22 final size:22
Alignment explanation
Indices: 1071254--1071355 Score: 56
Period size: 22 Copynumber: 4.7 Consensus size: 22
1071244 GATTGAATAA
*
1071254 TATAAAGATAAAAAGACCTCAA-
1 TATAAAGATAAAAAAACCT-AAT
*
1071276 T-TAAAGAATAATAAATAATC-AAT
1 TATAAAG-ATAA-AAA-AACCTAAT
* *
1071299 TATAAAGGTAAAAATAA--TATT
1 TATAAAGATAAAAA-AACCTAAT
* *
1071320 TA-AAAAAT-TAAAAACCTAAT
1 TATAAAGATAAAAAAACCTAAT
1071340 TATAAAGATAAAAAAA
1 TATAAAGATAAAAAAA
1071356 TGAGAGCTCC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 9 0.15
21 14 0.23
22 18 0.30
23 7 0.12
24 7 0.12
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (22 bp):
TATAAAGATAAAAAAACCTAAT
Found at i:1076966 original size:23 final size:23
Alignment explanation
Indices: 1076926--1076971 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1076916 CAGACTTAGC
* * *
1076926 TCGATTGAAGCTCGAACTTGAAT
1 TCGATTGAAACTCAAACTCGAAT
*
1076949 TCGATTTAAACTCAAACTCGAAT
1 TCGATTGAAACTCAAACTCGAAT
1076972 ATGAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (23 bp):
TCGATTGAAACTCAAACTCGAAT
Found at i:1077830 original size:139 final size:138
Alignment explanation
Indices: 1077564--1077906 Score: 364
Period size: 139 Copynumber: 2.5 Consensus size: 138
1077554 TACAATATTA
* * * *
1077564 TTAAAAGTTCTCCTAAATTAAAAGACTAAATATGAAATTAATCTAAAATGAAGGCTTTAATATTA
1 TTAAAA-TTCTCCTAAATTAAAAGACTAAA-GTGAAATTAAACTAAGATGAAGGCTCTAATATTA
* * ** * * *
1077629 ATCCTAATCAATTTTAACTAATTATTGGATAGACTAATTAATATGGAACTTCATGCAAAAAAGTG
64 ATCCTAACCAAATTTAACTAATTATTAAATAGACTAACTAATATGGAACATCAGGCAAAAAAGTG
1077694 AAGACCAAAT
129 AAGACCAAAT
* * * * *
1077704 TTAAAATTCTCCTAAATTAAATGTCTAAAGTGAGATTAAACTTAAGGTGAAAGCTCTAATATTAA
1 TTAAAATTCTCCTAAATTAAAAGACTAAAGTGAAATTAAAC-TAAGATGAAGGCTCTAATATTAA
* ** * * * *
1077769 TCCTAACCAAATTTAA-TAAATTATTAAATCGGGTGACTAATATGGAACATCGGGCATAAAAGTT
65 TCCTAACCAAATTTAACT-AATTATTAAATAGACTAACTAATATGGAACATCAGGCAAAAAAGTG
*
1077833 AGGACCAAAT
129 AAGACCAAAT
** * * * * *
1077843 AAAAAATTCACCTAATTTAAAGGAGTAAAGTGAAATTAACCTAAGATGAAGGCTCTAATATTAA
1 TTAAAATTCTCCTAAATTAAAAGACTAAAGTGAAATTAAACTAAGATGAAGGCTCTAATATTAA
1077907 CTTTAACTTA
Statistics
Matches: 166, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
138 31 0.19
139 129 0.78
140 6 0.04
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (138 bp):
TTAAAATTCTCCTAAATTAAAAGACTAAAGTGAAATTAAACTAAGATGAAGGCTCTAATATTAAT
CCTAACCAAATTTAACTAATTATTAAATAGACTAACTAATATGGAACATCAGGCAAAAAAGTGAA
GACCAAAT
Found at i:1078946 original size:28 final size:25
Alignment explanation
Indices: 1078902--1078962 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 25
1078892 CGTTAGTAGT
1078902 ATAAAATTTTTAAATAAA-ATGAATGTAA
1 ATAAAA-TTTTAAATAAATAT-AAT-T-A
1078930 ATAAAATTTTAAGATAAATATAATTA
1 ATAAAATTTTAA-ATAAATATAATTA
1078956 ATAAAAT
1 ATAAAAT
1078963 AAATAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 7 0.23
28 14 0.45
29 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (25 bp):
ATAAAATTTTAAATAAATATAATTA
Found at i:1078982 original size:16 final size:16
Alignment explanation
Indices: 1078949--1078982 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1078939 TAAGATAAAT
*
1078949 ATAATTAATAAAATAA
1 ATAATTAATAAAACAA
*
1078965 ATAATTAATCAAACAA
1 ATAATTAATAAAACAA
1078981 AT
1 AT
1078983 TTAATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATTAATAAAACAA
Found at i:1079737 original size:29 final size:29
Alignment explanation
Indices: 1079691--1079762 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
1079681 GGAACATATA
*
1079691 AATAGTCGAGTGACCATTTTATAACTTTT
1 AATAGTCAAGTGACCATTTTATAACTTTT
*
1079720 AATAGTCAAGTGATCATTTTATAACTTTT
1 AATAGTCAAGTGACCATTTTATAACTTTT
1079749 AATAGTCAAGTGAC
1 AATAGTCAAGTGAC
1079763 TCAACACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (29 bp):
AATAGTCAAGTGACCATTTTATAACTTTT
Found at i:1082064 original size:14 final size:13
Alignment explanation
Indices: 1082045--1082084 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1082035 ACATATTAAA
1082045 TAATAAATATAAT
1 TAATAAATATAAT
*
1082058 TATATAACTATAAT
1 TA-ATAAATATAAT
1082072 TAATAAATA-AAT
1 TAATAAATATAAT
1082084 T
1 T
1082085 TGGGGCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 12 0.50
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAAATATAAT
Found at i:1085716 original size:31 final size:32
Alignment explanation
Indices: 1085678--1085760 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 32
1085668 CTTAATCTCG
*
1085678 AAGGAAAATGAGGCAAGGGAAGATAACA-GAA
1 AAGGAAAATGAGGCAAGAGAAGATAACAGGAA
*
1085709 AAGGAAAATGAGGCAAGAGAAGATAATAGGAA
1 AAGGAAAATGAGGCAAGAGAAGATAACAGGAA
1085741 AA-GAAAATGAGGCAAGAGAA
1 AAGGAAAATGAGGCAAGAGAA
1085761 TGGAGAAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 44 0.90
32 5 0.10
ACGTcount: A:0.57, C:0.05, G:0.31, T:0.07
Consensus pattern (32 bp):
AAGGAAAATGAGGCAAGAGAAGATAACAGGAA
Found at i:1104554 original size:19 final size:19
Alignment explanation
Indices: 1104530--1104574 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1104520 TCAAACCCAG
1104530 CAACCCACCAATAGTGATC
1 CAACCCACCAATAGTGATC
1104549 CAACCCACCAATAGTGATC
1 CAACCCACCAATAGTGATC
1104568 CAACCCA
1 CAACCCA
1104575 GTAGCAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.40, G:0.09, T:0.13
Consensus pattern (19 bp):
CAACCCACCAATAGTGATC
Found at i:1116156 original size:29 final size:29
Alignment explanation
Indices: 1116124--1116224 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 29
1116114 TAAAAATTAT
1116124 ATAAAATTTTTTATGTCTAAATAAATACA
1 ATAAAATTTTTTATGTCTAAATAAATACA
* * * *
1116153 ATAAAA--TTTTAGGGTATACATATATATTAATA
1 ATAAAATTTTTTA-TGTCTA-A-ATA-AAT-ACA
*
1116185 ATATAAATTTTATTATATCTAAATAAATACA
1 ATA-AAATTTT-TTATGTCTAAATAAATACA
1116216 ATAAAATTT
1 ATAAAATTT
1116225 CAGGGTAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
27 5 0.09
28 4 0.07
29 7 0.13
30 9 0.17
31 7 0.13
32 7 0.13
33 6 0.11
34 1 0.02
35 5 0.09
36 3 0.06
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (29 bp):
ATAAAATTTTTTATGTCTAAATAAATACA
Found at i:1116206 original size:63 final size:64
Alignment explanation
Indices: 1116122--1116246 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 64
1116112 TATAAAAATT
* * * *
1116122 ATATAAAATTTTTTATGTCTAAATAAATACAATAAAATTTTAGGGTATACA-TATATATTAATA
1 ATATAAAATTTTTTATATCTAAATAAATACAATAAAATTTCAGGGTAAACACAATATATTAATA
1116185 ATAT-AAATTTTATTATATCTAAATAAATACAATAAAATTTCAGGGTAAACACAATATATTAA
1 ATATAAAATTTT-TTATATCTAAATAAATACAATAAAATTTCAGGGTAAACACAATATATTAA
1116247 GAGAAAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 7 0.12
63 40 0.71
64 9 0.16
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (64 bp):
ATATAAAATTTTTTATATCTAAATAAATACAATAAAATTTCAGGGTAAACACAATATATTAATA
Found at i:1118311 original size:14 final size:13
Alignment explanation
Indices: 1118258--1118332 Score: 59
Period size: 14 Copynumber: 5.8 Consensus size: 13
1118248 TATATTATAG
1118258 ATATTAA-TTTTA
1 ATATTAATTTTTA
1118270 ATATTAATTTTTA
1 ATATTAATTTTTA
* *
1118283 A-A-TAA-ATTAA
1 ATATTAATTTTTA
1118293 ATATTAATGTTTTA
1 ATATTAAT-TTTTA
* *
1118307 ATATTATATTATAA
1 ATATTA-ATTTTTA
1118321 ATATTTAATTTT
1 ATA-TTAATTTT
1118333 ATATCATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
10 4 0.08
11 4 0.08
12 11 0.22
13 6 0.12
14 19 0.39
15 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (13 bp):
ATATTAATTTTTA
Found at i:1118327 original size:21 final size:21
Alignment explanation
Indices: 1118303--1118388 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
1118293 ATATTAATGT
1118303 TTTAATATTATATTATAAATA
1 TTTAATATTATATTATAAATA
*
1118324 TTTAATTTTATATCATATAAATTA
1 TTTAATATTATAT--TATAAA-TA
1118348 TTT--TA-TATATTATTAAA-A
1 TTTAATATTATATTA-TAAATA
* * *
1118366 TTTTATATT-TATTTTAATTA
1 TTTAATATTATATTATAAATA
1118386 TTT
1 TTT
1118389 TGATTTAAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
18 4 0.08
19 5 0.09
20 14 0.26
21 18 0.34
22 1 0.02
23 6 0.11
24 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATATTATATTATAAATA
Found at i:1118388 original size:20 final size:19
Alignment explanation
Indices: 1118328--1118389 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1118318 TAAATATTTA
*
1118328 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1118347 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1118365 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1118385 ATTTT
1 ATTTT
1118390 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1119283 original size:22 final size:22
Alignment explanation
Indices: 1119253--1119296 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1119243 ATTTATTCAG
*
1119253 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
1119275 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
1119297 AAAATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1119358 original size:31 final size:31
Alignment explanation
Indices: 1119321--1119379 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1119311 AGTTGTATGG
*
1119321 ATTATTTAAATGTCAGTATTGTAAAACTAAA
1 ATTATTTAAATGTCAGTATTGCAAAACTAAA
*
1119352 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATGTCAGTATTGCAAAACT
1119380 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATGTCAGTATTGCAAAACTAAA
Found at i:1120262 original size:31 final size:31
Alignment explanation
Indices: 1120227--1120313 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
1120217 TCAATAAAGT
1120227 TTAAAAAAATATAAAATAATTATTAAATTTA
1 TTAAAAAAATATAAAATAATTATTAAATTTA
* * * *
1120258 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAAATATAAAATAATTATTAAATTTA
* *
1120289 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAAATATAAAATAATTATTA
1120314 TATTATCGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 46 0.98
32 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAAAATATAAAATAATTATTAAATTTA
Found at i:1123140 original size:18 final size:18
Alignment explanation
Indices: 1123113--1123156 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1123103 ATGGCTCGGC
1123113 TTGG-TCAATGGTTTAGT
1 TTGGATCAATGGTTTAGT
1123130 TTGGATCAATGGTTTAGT
1 TTGGATCAATGGTTTAGT
*
1123148 TCGGATCAA
1 TTGGATCAA
1123157 CGGCTTAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (18 bp):
TTGGATCAATGGTTTAGT
Found at i:1123164 original size:18 final size:18
Alignment explanation
Indices: 1123125--1123175 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1123115 GGTCAATGGT
* * *
1123125 TTAGTTTGGATCAATGGT
1 TTAGTTCGGATCAACGGC
1123143 TTAGTTCGGATCAACGGC
1 TTAGTTCGGATCAACGGC
* *
1123161 TTAGCTCGGCTCAAC
1 TTAGTTCGGATCAAC
1123176 AGTTTGGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (18 bp):
TTAGTTCGGATCAACGGC
Found at i:1125895 original size:2 final size:2
Alignment explanation
Indices: 1125890--1125935 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1125880 TTAAAAAATA
1125890 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
1125932 AT AT
1 AT AT
1125936 TCAAAAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1126772 original size:22 final size:22
Alignment explanation
Indices: 1126747--1126796 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1126737 ACGTTTTCAG
*
1126747 AAGCTATTA-TTTTCCTATTCGA
1 AAGCAATTATTTTTCC-ATTCGA
1126769 AAGCAATTATTTTTCCATTCGA
1 AAGCAATTATTTTTCCATTCGA
1126791 AAGCAA
1 AAGCAA
1126797 AAAAACACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (22 bp):
AAGCAATTATTTTTCCATTCGA
Found at i:1127973 original size:20 final size:20
Alignment explanation
Indices: 1127948--1128043 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
1127938 GTGATTTTCC
*
1127948 TAAATCGCAACGCGAATACG
1 TAAATCGCAATGCGAATACG
*
1127968 TAAATCGCAACGCGAATACG
1 TAAATCGCAATGCGAATACG
*
1127988 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAA-TACG
*
1128009 AAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
1128029 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
1128044 TTTACATAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 52 0.74
21 18 0.26
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:1128026 original size:41 final size:40
Alignment explanation
Indices: 1127948--1128043 Score: 147
Period size: 41 Copynumber: 2.4 Consensus size: 40
1127938 GTGATTTTCC
* *
1127948 TAAATCGCAACGCGAATACGTAAATCGCAACGCGAATACG
1 TAAATCGCAATGCGAATACGAAAATCGCAACGCGAATACG
* *
1127988 TAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAA-TACGAAAATCGCAACGCGAATACG
1128029 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
1128044 TTTACATAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 15 0.29
41 36 0.71
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (40 bp):
TAAATCGCAATGCGAATACGAAAATCGCAACGCGAATACG
Found at i:1128637 original size:21 final size:21
Alignment explanation
Indices: 1128576--1128653 Score: 83
Period size: 20 Copynumber: 3.9 Consensus size: 21
1128566 TTCTAAACTT
* *
1128576 AAAATCCCAAC-ATGAAAATG
1 AAAATCGCAACGACGAAAATG
1128596 AAAATCGCAAC-ACGAAAATG
1 AAAATCGCAACGACGAAAATG
**
1128616 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAACGACGA-AAATG
1128637 AAAATCGCAACG-CGAAA
1 AAAATCGCAACGACGAAA
1128654 CCAAAATCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 31 0.63
21 18 0.37
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGACGAAAATG
Found at i:1128687 original size:19 final size:19
Alignment explanation
Indices: 1128665--1128805 Score: 115
Period size: 20 Copynumber: 7.8 Consensus size: 19
1128655 CAAAATCGCA
*
1128665 TTGCGATTTTCATTTCTTG
1 TTGCGATTTTCATTTCTCG
1128684 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
*
1128698 TTGCGCTTTTCATTT-TGCG
1 TTGCGATTTTCATTTCT-CG
1128717 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
*
1128731 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
** *
1128750 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCTCG
*
1128770 TTGTGATTTTCATTCTCTCG
1 TTGCGATTTTCATT-TCTCG
1128790 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1128806 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 32 0.33
20 33 0.34
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:1128708 original size:33 final size:33
Alignment explanation
Indices: 1128665--1128797 Score: 142
Period size: 33 Copynumber: 3.8 Consensus size: 33
1128655 CAAAATCGCA
*
1128665 TTGCGATTTTCATTTCTTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCTCGTTGCGATTCTCTCG
*
1128698 TTGCGCTTTTCATTT-TGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCT-CGTTGCGATTCTCTCG
* *
1128731 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCATTTCTCGTTGCGAT--TC----TCTCG
*
1128770 TTGTGATTTTCATTCTCTCGTTGCGATT
1 TTGCGATTTTCATT-TCTCGTTGCGATT
1128798 TTCATTTCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
32 1 0.01
33 52 0.62
35 2 0.02
38 1 0.01
39 17 0.20
40 11 0.13
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCTCGTTGCGATTCTCTCG
Found at i:1130577 original size:12 final size:12
Alignment explanation
Indices: 1130560--1130585 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1130550 GAAGTTAGTA
1130560 TTTGTCTTTTGT
1 TTTGTCTTTTGT
1130572 TTTGTCTTTTGT
1 TTTGTCTTTTGT
1130584 TT
1 TT
1130586 GAAGTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTGTCTTTTGT
Found at i:1130687 original size:94 final size:93
Alignment explanation
Indices: 1130498--1130873 Score: 618
Period size: 94 Copynumber: 4.1 Consensus size: 93
1130488 TAGATTGCTT
*
1130498 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
*
1130558 TATTTGTCTTTTGTTTTGTCTTTTGTTTGA
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
1130588 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1130653 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1130682 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1130747 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
1130776 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1130841 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1130869 AGTAA
1 AGTAA
1130874 TGCAATCCAT
Statistics
Matches: 274, Mismatches: 6, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
90 35 0.13
93 25 0.09
94 213 0.78
95 1 0.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1130989 original size:16 final size:17
Alignment explanation
Indices: 1130968--1131015 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
1130958 TGGTTGTAAT
*
1130968 GAAAATCGCAACGAGA-
1 GAAAATCGCAACGAAAC
1130984 GAAAATCGCAACGCGAAAC
1 GAAAATCGCAA--CGAAAC
1131003 GAAAATCGCAACG
1 GAAAATCGCAACG
1131016 CGAAACGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 11 0.39
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (17 bp):
GAAAATCGCAACGAAAC
Found at i:1131053 original size:19 final size:19
Alignment explanation
Indices: 1130985--1131044 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 19
1130975 GCAACGAGAG
*
1130985 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAACA
1131004 AAAATCGCAACGCGAAACGCAAA
1 AAAATCGCAACGCGAAA--C--A
1131027 AAAATCGCAACGCGAAAC
1 AAAATCGCAACGCGAAAC
1131045 TATAATCGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 17 0.47
21 2 0.06
23 17 0.47
ACGTcount: A:0.50, C:0.27, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1131070 original size:14 final size:14
Alignment explanation
Indices: 1131053--1131109 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1131043 ACTATAATCG
1131053 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1131067 CGTTGCGATTTTTATTTCG
1 CGTTGCGA----T-TCTCT
1131086 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1131100 CGTTGCGATT
1 CGTTGCGATT
1131110 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
15 1 0.03
18 1 0.03
19 11 0.32
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1131091 original size:19 final size:19
Alignment explanation
Indices: 1131067--1131190 Score: 114
Period size: 19 Copynumber: 6.6 Consensus size: 19
1131057 GCGATTCTCT
*
1131067 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
*
1131086 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
1131100 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
1131119 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
*
1131139 CATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
1131158 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
1131179 CGTTGCGATTTT
1 CGTTGCGATTTT
1131191 AAGTTCCAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 14
0.76 0.12 0.13
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 2 0.02
19 38 0.45
20 17 0.20
21 14 0.17
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1131092 original size:33 final size:33
Alignment explanation
Indices: 1131050--1131166 Score: 153
Period size: 33 Copynumber: 3.4 Consensus size: 33
1131040 GAAACTATAA
*
1131050 TCGCGTTGCGATTCTCTCGTTGCGATTTTTATT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
1131083 TCGCGTTGCGATTCTCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
1131116 TCGCGTTGCGATTTTCATTCTCTCATTGCGATTTTCATT
1 TCGCGTTGCG------ATTCTCTCGTTGCGATTTTCATT
1131155 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1131167 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
33 43 0.58
39 31 0.42
ACGTcount: A:0.09, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1131173 original size:39 final size:38
Alignment explanation
Indices: 1131060--1131190 Score: 130
Period size: 39 Copynumber: 3.5 Consensus size: 38
1131050 TCGCGTTGCG
* *
1131060 ATTCTCTCGTTGCGATTTTTATTTCGCGTTGC---G--
1 ATTCTCTCATTGCGATTTTCATTTCGCGTTGCGATGTC
* * *
1131093 ATTCTCTCGTTGCGATTTTCGTTTCGCGTTGCGATTTTC
1 ATTCTCTCATTGCGATTTTCATTTCGCGTTGCGA-TGTC
1131132 ATTCTCTCATTGCGATTTTCATTTCGCGTTGCGATAGTC
1 ATTCTCTCATTGCGATTTTCATTTCGCGTTGCGAT-GTC
*
1131171 ATT-TTTCACGTTGCGATTTT
1 ATTCTCTCA--TTGCGATTTT
1131191 AAGTTCCAGA
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
33 30 0.37
38 5 0.06
39 37 0.45
40 10 0.12
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.48
Consensus pattern (38 bp):
ATTCTCTCATTGCGATTTTCATTTCGCGTTGCGATGTC
Found at i:1131667 original size:21 final size:21
Alignment explanation
Indices: 1131643--1131709 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1131633 TCATTCCTCG
1131643 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1131664 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1131685 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1131706 AGAG
1 AGAG
1131710 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1131667 original size:42 final size:42
Alignment explanation
Indices: 1131591--1131709 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1131581 GACTCGCCTG
* * * * * * *
1131591 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1131633 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1131675 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1131710 CTCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1133081 original size:14 final size:14
Alignment explanation
Indices: 1133062--1133097 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1133052 ATTGTTTAAT
1133062 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1133076 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1133090 TGATTTGT
1 TGATTTGT
1133098 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1133265 original size:19 final size:19
Alignment explanation
Indices: 1133243--1133313 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1133233 CGAAACTAAA
*
1133243 TTCGCGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1133262 TTCGCTTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1133281 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1133300 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1133314 AGACATTAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 35 0.78
20 10 0.22
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1133312 original size:20 final size:19
Alignment explanation
Indices: 1133258--1133320 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
1133248 GTTACGATTT
* **
1133258 TCATTTCGCTTTGCGATTT
1 TCATTTCGCATTGCGATAG
1133277 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
*
1133296 TCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
*
1133316 ACATT
1 TCATT
1133321 AAGATGATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1135861 original size:24 final size:24
Alignment explanation
Indices: 1135827--1135880 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1135817 CTGAAAAATC
*
1135827 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGGATTGACCAAG
* *
1135851 ATCAAAGTCCGGGGATTGACCAAG
1 ATCAAAATCCGAGGATTGACCAAG
1135875 ATCAAA
1 ATCAAA
1135881 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (24 bp):
ATCAAAATCCGAGGATTGACCAAG
Found at i:1136829 original size:41 final size:40
Alignment explanation
Indices: 1136743--1136854 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 40
1136733 AGAATCTCGT
* *
1136743 TGCGATTTAC-TAAATCGCAATGCGATTTACTAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGAATTACAAAATCGCAA
*
1136783 TGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTA-CAAAATCGCAA
1136824 TGCGATTACGTAAATCGCAATGCG-ATTACAA
1 TGCGATTACGTAAATCGCAATGCGAATTACAA
1136855 GAAATGGAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
39 6 0.09
40 27 0.41
41 33 0.50
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (40 bp):
TGCGATTACGTAAATCGCAATGCGAATTACAAAATCGCAA
Found at i:1136851 original size:20 final size:20
Alignment explanation
Indices: 1136743--1136852 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
1136733 AGAATCTCGT
1136743 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
1136763 TGCGATTTAC-TAAATCGCAA
1 TGCGA-TTACGTAAATCGCAA
1136783 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
* *
1136803 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTACGTAAATCGCAA
1136824 TGCGATTACGTAAATCGCAA
1 TGCGATTACGTAAATCGCAA
1136844 TGCGATTAC
1 TGCGATTAC
1136853 AAGAAATGGA
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.05
20 62 0.74
21 18 0.21
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (20 bp):
TGCGATTACGTAAATCGCAA
Found at i:1139065 original size:3 final size:3
Alignment explanation
Indices: 1139059--1139124 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
1139049 TATAATAACA
1139059 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1139107 AAT AAT -AT AAT TAT AAT A
1 AAT AAT AAT AAT AAT AAT A
1139125 TTTTTAAAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1139390 original size:43 final size:43
Alignment explanation
Indices: 1139335--1139665 Score: 196
Period size: 43 Copynumber: 7.6 Consensus size: 43
1139325 AATAACACGA
* * * *
1139335 TTCCTACATGATGAGGACGGCTGGTTATCTAAGGTTGACACGG
1 TTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACATGG
* * * *
1139378 CTCCTACGTGATGAGGA-GATCTGG---TCGAGGGATGACATAG
1 TTCCTACGTGATGAGGACGA-CTGGTTATCTAGGGTTGACATGG
* ** * * *
1139418 TTCCTACGTGATGAGGATGAC-GGACCATCATTAGGGATGATAACACGA
1 TTCCTACGTGATGAGGACGACTGG-TTATC--TAGGG-T--TGACATGG
* * *
1139466 TTACTACGTGATGAGGACGATTGGTTATCTAAGGTTGACATGG
1 TTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACATGG
* * * * *
1139509 CTCCTACGTGATGAGGA-GA-T--TTGGTCGAGGGATGACATAG
1 TTCCTACGTGATGAGGACGACTGGTT-ATCTAGGGTTGACATGG
* * ** * *
1139549 TTCCTACGTGATGAGGACGTCAGGCCATCATTAGGGATGATAACACGG
1 TTCCTACGTGATGAGGACGACTGGTTATC--TAGGG-T--TGACATGG
* *
1139597 TTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGA
1 TTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACATGG
1139640 TTCCTACGTGATGAGGA-GATCTGGTT
1 TTCCTACGTGATGAGGACGA-CTGGTT
1139666 GAGGGATGAC
Statistics
Matches: 215, Mismatches: 50, Indels: 46
0.69 0.16 0.15
Matches are distributed among these distances:
39 4 0.02
40 56 0.26
41 4 0.02
42 5 0.02
43 71 0.33
45 10 0.05
46 8 0.04
48 55 0.26
49 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
TTCCTACGTGATGAGGACGACTGGTTATCTAGGGTTGACATGG
Found at i:1139560 original size:131 final size:131
Alignment explanation
Indices: 1139321--1139724 Score: 614
Period size: 131 Copynumber: 3.1 Consensus size: 131
1139311 GTTCGTCAAA
* * * *
1139321 GGATAATAACACGATTCCTACATGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACG
1 GGATGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGGCTCCTACG
1139386 TGATGAGGAGATCTGGTCGAGGGATGACATAGTTCCTACGTGATGAGGATGAC-GGACCATCATT
66 TGATGAGGAGATCTGGTCGAGGGATGACATAGTTCCTACGTGATGAGGATGACAGG-CCATCATT
1139450 AG
130 AG
* *
1139452 GGATGATAACACGATTACTACGTGATGAGGACGATTGGTTATCTAAGGTTGACATGGCTCCTACG
1 GGATGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGGCTCCTACG
* * *
1139517 TGATGAGGAGATTTGGTCGAGGGATGACATAGTTCCTACGTGATGAGGACGTCAGGCCATCATTA
66 TGATGAGGAGATCTGGTCGAGGGATGACATAGTTCCTACGTGATGAGGATGACAGGCCATCATTA
1139582 G
131 G
* **
1139583 GGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGATTCCTACG
1 GGATGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGGCTCCTACG
* * ** * *
1139648 TGATGAGGAGATCTGGTTGAGGGATGACA-CGATTCCTATATGATGAGGATGGCAGGCCATCTTT
66 TGATGAGGAGATCTGGTCGAGGGATGACATAG-TTCCTACGTGATGAGGATGACAGGCCATCATT
1139712 AG
130 AG
1139714 GGATGATAACA
1 GGATGATAACA
1139725 TAATTTCAAA
Statistics
Matches: 249, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
130 1 0.00
131 246 0.99
132 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (131 bp):
GGATGATAACACGATTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTGACATGGCTCCTACG
TGATGAGGAGATCTGGTCGAGGGATGACATAGTTCCTACGTGATGAGGATGACAGGCCATCATTA
G
Found at i:1139839 original size:33 final size:34
Alignment explanation
Indices: 1139802--1139917 Score: 119
Period size: 33 Copynumber: 3.4 Consensus size: 34
1139792 GTTTCAAGGA
*
1139802 AAACGATCTCAAA-TATCTTTGTTGTTTCATGAG
1 AAACGATCTCAAAGTATATTTGTTGTTTCATGAG
* * ** *
1139835 AAACGATCTCAAAGAAAATAGGATTTGTTTCAAGAG
1 AAACGATCTCAAAGTATATTTG--TTGTTTCATGAG
* **
1139871 AAAC-ATCTCAAAGTTTGGTTGTTGTTTCATGAG
1 AAACGATCTCAAAGTATATTTGTTGTTTCATGAG
1139904 AAACGATCTCAAAG
1 AAACGATCTCAAAG
1139918 AAAATAAGAT
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
33 28 0.43
34 12 0.18
35 10 0.15
36 15 0.23
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (34 bp):
AAACGATCTCAAAGTATATTTGTTGTTTCATGAG
Found at i:1139872 original size:36 final size:35
Alignment explanation
Indices: 1139823--1139952 Score: 140
Period size: 36 Copynumber: 3.7 Consensus size: 35
1139813 AATATCTTTG
*
1139823 TTGTTTCATGAGAAACGATCTCAAAGAAAATAGGAT
1 TTGTTTCAAGAGAAAC-ATCTCAAAGAAAATAGGAT
* * *
1139859 TTGTTTCAAGAGAAACATCTCAAAG---TTTGGTT
1 TTGTTTCAAGAGAAACATCTCAAAGAAAATAGGAT
* *
1139891 GTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGAT
1 -TTGTTTCAAGAGAAAC-ATCTCAAAGAAAATAGGAT
* *
1139928 TTGTGTCAAAAGAAACATCTCAAAG
1 TTGTTTCAAGAGAAACATCTCAAAG
1139953 TTTGGTTGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
32 4 0.05
33 15 0.19
34 9 0.12
35 18 0.23
36 28 0.36
37 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACATCTCAAAGAAAATAGGAT
Found at i:1139893 original size:69 final size:69
Alignment explanation
Indices: 1139820--1139962 Score: 259
Period size: 69 Copynumber: 2.1 Consensus size: 69
1139810 TCAAATATCT
* * *
1139820 TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAGGATTTGTTTCAAGAGAAACATCTCAAAGT
1 TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGATTTGTGTCAAAAGAAACATCTCAAAGT
1139885 TTGG
66 TTGG
1139889 TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGATTTGTGTCAAAAGAAACATCTCAAAGT
1 TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGATTTGTGTCAAAAGAAACATCTCAAAGT
1139954 TTGG
66 TTGG
1139958 TTGTT
1 TTGTT
1139963 TCATAAGAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (69 bp):
TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGATTTGTGTCAAAAGAAACATCTCAAAGT
TTGG
Found at i:1140008 original size:36 final size:36
Alignment explanation
Indices: 1139958--1140101 Score: 137
Period size: 36 Copynumber: 4.0 Consensus size: 36
1139948 CAAAGTTTGG
*
1139958 TTGTTTCATA-AGAAAATGTCTCGAGGGAGACAAAAT
1 TTGTTTCA-AGAGAAAATGTCTCAAGGGAGACAAAAT
* * * *
1139994 TTGTTCCAAGAGAAACTGTATCGAGGGAGACAAAAT
1 TTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAAT
* ** * * *
1140030 TTGTTTTAAGAGAAACCGACTTAAGTGAGACAAAAT
1 TTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAAT
* * **
1140066 ATGTTTCAAGGGAAAATGTCTCAAAAGAGACAAAAT
1 TTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAAT
1140102 ATATTTTAAG
Statistics
Matches: 87, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
35 1 0.01
36 86 0.99
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (36 bp):
TTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAAT
Found at i:1140008 original size:66 final size:67
Alignment explanation
Indices: 1139821--1140009 Score: 195
Period size: 69 Copynumber: 2.8 Consensus size: 67
1139811 CAAATATCTT
* * **
1139821 TGTTGTTTCATGAGAAACGATCTCAAAGAAAATAGGATTTGTTTCAAGAGAAACATCTCAAAGTT
1 TGTTGTTTCATAAGAAACGATCTCAAAGAAAACAAAATTTG-TTCAAGAGAAACATCTCAAAGTT
1139886 TGG
65 TGG
* * * *
1139889 TTGTTGTTTCATGAGAAACGATCTCAAAGAAAATAAGATTTGTGTCAAAAGAAACATCTCAAAGT
1 -TGTTGTTTCATAAGAAACGATCTCAAAGAAAACAAAATTTGT-TCAAGAGAAACATCTCAAAGT
1139954 TT-G
64 TTGG
* * * * *
1139957 -GTTGTTTCATAAGAAAATG-TCTCGAGGGAGACAAAATTTGTTCCAAGAGAAAC
1 TGTTGTTTCATAAG-AAACGATCTCAAAGAAAACAAAATTTGTT-CAAGAGAAAC
1140010 TGTATCGAGG
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
65 1 0.01
66 37 0.35
67 4 0.04
68 2 0.02
69 62 0.58
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (67 bp):
TGTTGTTTCATAAGAAACGATCTCAAAGAAAACAAAATTTGTTCAAGAGAAACATCTCAAAGTTT
GG
Found at i:1140060 original size:72 final size:72
Alignment explanation
Indices: 1139984--1140117 Score: 169
Period size: 72 Copynumber: 1.9 Consensus size: 72
1139974 TGTCTCGAGG
* * * ** * *
1139984 GAGACAAAATTTGTTCCAAGAGAAACTGTATCGAGGGAGACAAAATTTGTTTTAAGAGAAACCGA
1 GAGACAAAATATGTTCCAAGAGAAAATGTATCAAAAGAGACAAAATATATTTTAAGAGAAACCGA
1140049 CTTAAGT
66 CTTAAGT
* * * *
1140056 GAGACAAAATATGTTTCAAGGGAAAATGTCTCAAAAGAGACAAAATATATTTTAAGGGAAAC
1 GAGACAAAATATGTTCCAAGAGAAAATGTATCAAAAGAGACAAAATATATTTTAAGAGAAAC
1140118 AATCTCAATG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 51 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (72 bp):
GAGACAAAATATGTTCCAAGAGAAAATGTATCAAAAGAGACAAAATATATTTTAAGAGAAACCGA
CTTAAGT
Found at i:1140124 original size:36 final size:36
Alignment explanation
Indices: 1140056--1140125 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1140046 CGACTTAAGT
* *
1140056 GAGACAAAATATGTTTCAAGGGAAAATGTCTCAAAA
1 GAGACAAAATATATTTCAAGGGAAAATATCTCAAAA
*
1140092 GAGACAAAATATATTTTAAGGGAAACA-ATCTCAA
1 GAGACAAAATATATTTCAAGGGAAA-ATATCTCAA
1140126 TGTTTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (36 bp):
GAGACAAAATATATTTCAAGGGAAAATATCTCAAAA
Found at i:1140184 original size:67 final size:67
Alignment explanation
Indices: 1140065--1140192 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
1140055 TGAGACAAAA
* * * * *
1140065 TATGTTTCAAGGGAAAATGTCTCAAAAGAGACAAAATATATTTTAAGGGAAACAATCTCAATGTT
1 TATGTTTCAAGAGAAAATATCTCAAAAGAGACAAAATATATTTCAAGAGAAACAACCTCAATGTT
1140130 TT
66 TT
* * * * *
1140132 TATGTTTCAAGAGAAACTATCTCAACAGAGACAAAATTTGTTTCGAGAGAAACAACCTCAA
1 TATGTTTCAAGAGAAAATATCTCAAAAGAGACAAAATATATTTCAAGAGAAACAACCTCAA
1140193 AGGAATTAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 51 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (67 bp):
TATGTTTCAAGAGAAAATATCTCAAAAGAGACAAAATATATTTCAAGAGAAACAACCTCAATGTT
TT
Found at i:1140383 original size:37 final size:36
Alignment explanation
Indices: 1140314--1140383 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1140304 GGAAGATCTG
* *
1140314 TCTCAAGTGAGACAAATTTTGTTTTGATAGAAATTT
1 TCTCAAGCGAGACAAATTTTGTTTTCATAGAAATTT
*
1140350 TCTCAAGCGAGGCAAAATTTTGATTTTCA-AGAAA
1 TCTCAAGCGAGAC-AAATTTTG-TTTTCATAGAAA
1140384 AGTTATCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 11 0.38
37 13 0.45
38 5 0.17
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTCATAGAAATTT
Found at i:1140539 original size:32 final size:32
Alignment explanation
Indices: 1140502--1140590 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
1140492 TTCGCATCAG
* * *
1140502 GATGTTGAATCCCCAAAGATGCCGTAATATTCT
1 GATGTTGAATCTCCAAAGATGCCCTAACATT-T
1140535 -ATGTTGAATCTCCAAAGATGCCCTAACATTT
1 GATGTTGAATCTCCAAAGATGCCCTAACATTT
*
1140566 GATGTTGAATCTTCAAAGATGCCCT
1 GATGTTGAATCTCCAAAGATGCCCT
1140591 CTATTGCTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 1 0.02
32 50 0.98
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCTAACATTT
Found at i:1142362 original size:24 final size:24
Alignment explanation
Indices: 1142335--1142391 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 24
1142325 TTCCATATGT
1142335 TTAAAATCTA-TAATTCTTGAAGAA
1 TTAAAAT-TATTAATTCTTGAAGAA
1142359 TTAAAAGAATTATTAATTCTTGAAGAA
1 TT--AA-AATTATTAATTCTTGAAGAA
1142386 TTAAAA
1 TTAAAA
1142392 GAATTCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 4 0.14
25 2 0.07
26 4 0.14
27 19 0.66
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (24 bp):
TTAAAATTATTAATTCTTGAAGAA
Found at i:1142375 original size:27 final size:27
Alignment explanation
Indices: 1142345--1142404 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
1142335 TTAAAATCTA
1142345 TAATTCTTGAAGAATTAAAAGAATTAT
1 TAATTCTTGAAGAATTAAAAGAATTAT
*
1142372 TAATTCTTGAAGAATTAAAAGAATTCT
1 TAATTCTTGAAGAATTAAAAGAATTAT
1142399 TAATTC
1 TAATTC
1142405 ATTTAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (27 bp):
TAATTCTTGAAGAATTAAAAGAATTAT
Found at i:1145931 original size:3 final size:3
Alignment explanation
Indices: 1145925--1145958 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1145915 TAACAACAAT
1145925 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1145959 TTTAAAGTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1150596 original size:24 final size:23
Alignment explanation
Indices: 1150568--1150651 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 23
1150558 ATTATAAATA
1150568 TTAAATATTATAAATAATATTATT
1 TTAAATATTATAAATAATATTA-T
*
1150592 TTAAAAATATTA-GAATAAT-TTAT
1 TT--AAATATTATAAATAATATTAT
*
1150615 TT-AATATTATTTATATCAATATTAT
1 TTAAATATTA--TAAAT-AATATTAT
*
1150640 TAAAATATTATA
1 TTAAATATTATA
1150652 TCTATATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
20 7 0.15
23 5 0.10
24 10 0.21
25 11 0.23
26 15 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
TTAAATATTATAAATAATATTAT
Found at i:1150602 original size:14 final size:15
Alignment explanation
Indices: 1150556--1150603 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
1150546 TTAATTTTTT
*
1150556 TTATTATAAATATTAA
1 TTATTATAAATAAT-A
*
1150572 ATATTATAAATAATA
1 TTATTATAAATAATA
*
1150587 TTATTTTAAA-AATA
1 TTATTATAAATAATA
1150601 TTA
1 TTA
1150604 GAATAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATTATAAATAATA
Found at i:1150652 original size:22 final size:22
Alignment explanation
Indices: 1150625--1150692 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1150615 TTAATATTAT
1150625 TTATATCAATATTATTAAAATA
1 TTATATCAATATTATTAAAATA
* *
1150647 TTATATCTATATTTTTATAAATAA
1 TTATATCAATATTATTA-AAAT-A
** * *
1150671 AAATATTAAGATTATTAAAATA
1 TTATATCAATATTATTAAAATA
1150693 AAATTATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 16 0.44
23 8 0.22
24 12 0.33
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (22 bp):
TTATATCAATATTATTAAAATA
Found at i:1150811 original size:14 final size:14
Alignment explanation
Indices: 1150781--1150821 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1150771 ATATTGTTAA
*
1150781 AATATTAAAAATTAT
1 AATATT-AAAATAAT
1150796 AATATTAAAATAAT
1 AATATTAAAATAAT
*
1150810 AATATTATAATA
1 AATATTAAAATA
1150822 TATTTTAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATTAAAATAAT
Found at i:1150822 original size:37 final size:38
Alignment explanation
Indices: 1150681--1150822 Score: 130
Period size: 37 Copynumber: 3.7 Consensus size: 38
1150671 AAATATTAAG
*
1150681 ATTATTAAAATAA-AATTATTATAA-ATTATATTAATTA-
1 ATTATTAAAATAATAA-TATTATAATATTA-ATAAATTAT
* * *
1150718 ATTATTAAAATAAGAATAATATATTATTAATTAAATTAATT
1 ATTATTAAAATAATAATATTATAATATTAA-TAAATT-A-T
* * * *
1150759 TTTATTAAAATAATATTGTTAAAATATTAA-AAATTAT
1 ATTATTAAAATAATAATATTATAATATTAATAAATTAT
*
1150796 AATATTAAAATAATAATATTATAATAT
1 ATTATTAAAATAATAATATTATAATAT
1150823 ATTTTAAGGA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
37 43 0.51
38 12 0.14
39 6 0.07
41 23 0.27
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
ATTATTAAAATAATAATATTATAATATTAATAAATTAT
Found at i:1150969 original size:29 final size:29
Alignment explanation
Indices: 1150911--1150969 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1150901 TTAATAATTT
* *
1150911 ATTATATATTATTGAAATAAAAGTATAAC
1 ATTATATATTATTAAAATAAAAGTAGAAC
* *
1150940 ATTATATATTA-TAATAATATAATTAGAAC
1 ATTATATATTATTAA-AATAAAAGTAGAAC
1150969 A
1 A
1150970 ATAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (29 bp):
ATTATATATTATTAAAATAAAAGTAGAAC
Found at i:1151056 original size:28 final size:28
Alignment explanation
Indices: 1151017--1151094 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 28
1151007 AATATAATTT
1151017 AATAATTAATATTTTTATTAAAATGATACTAA
1 AATAA-TAATATTTTTATTAAAAT-ATA-T-A
**
1151049 AATAAT-ATATTAATATT-AAATATATGA
1 AATAATAATATTTTTATTAAAATATAT-A
1151076 AATAATAATATTTTTATTA
1 AATAATAATATTTTTATTA
1151095 TTTATGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 8 0.21
28 12 0.31
29 4 0.10
30 9 0.23
31 1 0.03
32 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (28 bp):
AATAATAATATTTTTATTAAAATATATA
Found at i:1151062 original size:43 final size:44
Alignment explanation
Indices: 1150974--1151067 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
1150964 AGAACAATAA
*
1150974 AATA-TAATATTATATTATTAAAATTATCAAAAAAATATAATTT
1 AATATTAATATTATATTATTAAAATGATCAAAAAAATATAATTT
*
1151017 AATAATTAATATT-T-TTATTAAAATGATACTAAAATAATAT-A-TT
1 AAT-ATTAATATTATATTATTAAAATGAT-C-AAAAAAATATAATTT
1151060 AATATTAA
1 AATATTAA
1151068 ATATATGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
42 5 0.11
43 20 0.44
44 4 0.09
45 16 0.36
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (44 bp):
AATATTAATATTATATTATTAAAATGATCAAAAAAATATAATTT
Found at i:1152451 original size:3 final size:3
Alignment explanation
Indices: 1152443--1152529 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
1152433 TAGTTTACCC
1152443 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
1152491 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
1152530 GAATAGAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1157152 original size:3 final size:3
Alignment explanation
Indices: 1157080--1157141 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
1157070 TTTTACTTAA
* * * *
1157080 ATT ATT ATT ATT ATA ATT ATA AAT ATA ATT ATT ATT A-T ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
1157127 ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
1157142 AATAATTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 6 0.13
3 38 0.81
4 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:1158393 original size:19 final size:20
Alignment explanation
Indices: 1158355--1158393 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1158345 AATTATTATC
* *
1158355 TTTATTTTTAATACTTTTTA
1 TTTAGTTTTAATAATTTTTA
1158375 TTTAGTTTT-ATAATTTTTA
1 TTTAGTTTTAATAATTTTTA
1158394 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTAGTTTTAATAATTTTTA
Found at i:1159343 original size:27 final size:27
Alignment explanation
Indices: 1159305--1159366 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1159295 AAGTGTAATT
1159305 ATTTAATAGTTGATGTACTATGCTAGA
1 ATTTAATAGTTGATGTACTATGCTAGA
1159332 ATTTAATAGTTGATGTACTATGCTAGA
1 ATTTAATAGTTGATGTACTATGCTAGA
1159359 ATTTAATA
1 ATTTAATA
1159367 ATAGAATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (27 bp):
ATTTAATAGTTGATGTACTATGCTAGA
Found at i:1177354 original size:18 final size:18
Alignment explanation
Indices: 1177333--1177369 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1177323 AATATTTATA
*
1177333 TGATAATTTATGTTGTTT
1 TGATAATTTATATTGTTT
*
1177351 TGATTATTTATATTGTTT
1 TGATAATTTATATTGTTT
1177369 T
1 T
1177370 CATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (18 bp):
TGATAATTTATATTGTTT
Found at i:1177378 original size:18 final size:18
Alignment explanation
Indices: 1177338--1177376 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1177328 TTATATGATA
* *
1177338 ATTTATGTTGTTTTGATT
1 ATTTATATTGTTTTCATT
1177356 ATTTATATTGTTTTCA-T
1 ATTTATATTGTTTTCATT
1177373 ATTT
1 ATTT
1177377 TAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (18 bp):
ATTTATATTGTTTTCATT
Found at i:1178728 original size:14 final size:14
Alignment explanation
Indices: 1178661--1178727 Score: 107
Period size: 14 Copynumber: 4.8 Consensus size: 14
1178651 ATAATATGTC
*
1178661 CGTTTATGTTTGTT
1 CGTTTATGTTCGTT
*
1178675 CATTTATGTTCGTT
1 CGTTTATGTTCGTT
1178689 CGTTTATGTTCGTT
1 CGTTTATGTTCGTT
*
1178703 CGTTTATGTTCATT
1 CGTTTATGTTCGTT
1178717 CGTTTATGTTC
1 CGTTTATGTTC
1178728 AATTATGTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 49 1.00
ACGTcount: A:0.10, C:0.13, G:0.18, T:0.58
Consensus pattern (14 bp):
CGTTTATGTTCGTT
Found at i:1179192 original size:23 final size:23
Alignment explanation
Indices: 1179164--1179227 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1179154 TTTGTTTTCT
*
1179164 TTCGTTTATATTCATTTATTATG
1 TTCGTTTATATCCATTTATTATG
*
1179187 TTCGTTTATGTCCATTTATTATG
1 TTCGTTTATATCCATTTATTATG
* *
1179210 TTCGTTTATGTCCGTTTA
1 TTCGTTTATATCCATTTA
1179228 CGTTCGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.58
Consensus pattern (23 bp):
TTCGTTTATATCCATTTATTATG
Found at i:1179316 original size:24 final size:25
Alignment explanation
Indices: 1179261--1179323 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
1179251 ACATTTGTTT
1179261 ATTGTGTTCGTTTATGTTCATTTAC
1 ATTGTGTTCGTTTATGTTCATTTAC
1179286 ATCTGT-TT-GTTTATGTTC-TTT-C
1 AT-TGTGTTCGTTTATGTTCATTTAC
1179308 ATTTGTGTTCGTTTAT
1 A-TTGTGTTCGTTTAT
1179324 CATTTAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
22 5 0.15
23 6 0.18
24 16 0.47
25 4 0.12
26 3 0.09
ACGTcount: A:0.13, C:0.11, G:0.16, T:0.60
Consensus pattern (25 bp):
ATTGTGTTCGTTTATGTTCATTTAC
Found at i:1181958 original size:14 final size:14
Alignment explanation
Indices: 1181939--1181971 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1181929 ATAAATAAGT
*
1181939 ATATATATATATAG
1 ATATATAGATATAG
1181953 ATATATAGATATAG
1 ATATATAGATATAG
1181967 ATATA
1 ATATA
1181972 CATAAAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (14 bp):
ATATATAGATATAG
Found at i:1183166 original size:37 final size:37
Alignment explanation
Indices: 1183119--1183193 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
1183109 CTGAACCTAT
* * *
1183119 ATAAGGAATTACCATCTTGATCAGAACTGAACATGCA
1 ATAAGGAATTACCAGCTTGACCAGAAATGAACATGCA
*
1183156 ATAAGGAATTACCAGCTTGACCAGAAATGAACCTGCA
1 ATAAGGAATTACCAGCTTGACCAGAAATGAACATGCA
1183193 A
1 A
1183194 AGACTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (37 bp):
ATAAGGAATTACCAGCTTGACCAGAAATGAACATGCA
Found at i:1187813 original size:2 final size:2
Alignment explanation
Indices: 1187806--1187838 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1187796 TCACCCATTA
1187806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1187839 AATTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1188187 original size:17 final size:17
Alignment explanation
Indices: 1188138--1188187 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1188128 TTGTTCATGT
1188138 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
1188155 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
1188169 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
1188186 TT
1 TT
1188188 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:1188380 original size:11 final size:11
Alignment explanation
Indices: 1188361--1188391 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1188351 GAAGCTCCAC
*
1188361 CCGACCCATCT
1 CCGATCCATCT
1188372 CCGATCCATCT
1 CCGATCCATCT
1188383 CCGATCCAT
1 CCGATCCAT
1188392 TGCTAGCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.10, T:0.23
Consensus pattern (11 bp):
CCGATCCATCT
Found at i:1193734 original size:20 final size:21
Alignment explanation
Indices: 1193685--1193735 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1193675 ATTATCTCAA
1193685 TATCGATACTGACCCTCTGAG
1 TATCGATACTGACCCTCTGAG
* *
1193706 TATCAATACTGGACCC-C-GAT
1 TATCGATACT-GACCCTCTGAG
1193726 TATCGATACT
1 TATCGATACT
1193736 CCTTGAAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.42
21 10 0.38
22 5 0.19
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (21 bp):
TATCGATACTGACCCTCTGAG
Found at i:1196783 original size:18 final size:19
Alignment explanation
Indices: 1196749--1196784 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1196739 CACGGAATGT
1196749 AAGATTACCAGGGGAATAA
1 AAGATTACCAGGGGAATAA
1196768 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1196785 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.47, C:0.11, G:0.25, T:0.17
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1197889 original size:16 final size:15
Alignment explanation
Indices: 1197864--1197895 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1197854 TTTATATTTT
1197864 ATAATTTTTATTTAA
1 ATAATTTTTATTTAA
1197879 ATAATTATTTATTTAA
1 ATAATT-TTTATTTAA
1197895 A
1 A
1197896 AAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAATTTTTATTTAA
Found at i:1201045 original size:37 final size:37
Alignment explanation
Indices: 1200969--1201045 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1200959 TTTTTATATT
*
1200969 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1201006 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1201043 TTT
1 TTT
1201046 GAAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1204205 original size:2 final size:2
Alignment explanation
Indices: 1204198--1204222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1204188 TAACTAAAAT
1204198 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1204223 TAAGGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1209466 original size:2 final size:2
Alignment explanation
Indices: 1209459--1209505 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
1209449 CACCTCAGAT
* *
1209459 TA TA TA TA TA TA TA TA TA TA TG CA -A TGA GTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA
1209502 TA TA
1 TA TA
1209506 CATGCAATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 1 0.03
2 35 0.90
3 2 0.05
4 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1209495 original size:29 final size:29
Alignment explanation
Indices: 1209459--1209516 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1209449 CACCTCAGAT
*
1209459 TATATATATATATATATATATGCAATGAG
1 TATATATATATATATATACATGCAATGAG
1209488 TATATATATATATATATACATGCAATGAG
1 TATATATATATATATATACATGCAATGAG
1209517 GGGTTATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (29 bp):
TATATATATATATATATACATGCAATGAG
Found at i:1209794 original size:43 final size:43
Alignment explanation
Indices: 1209706--1209934 Score: 121
Period size: 43 Copynumber: 5.3 Consensus size: 43
1209696 TTTTGCAGAA
** * * * **
1209706 AAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGC-AGAC
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTT-TCTTCAC
* *
1209749 AAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTCAC
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
* * * * * *
1209792 AAACGCCGCAGTAGATGTTTATTTTTACCGGCATTTT-TCCTAC
1 AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTC-AC
* * * *** *
1209835 AAACACCGCAGA-AGATGTTGATATTTAGCGATGTTTTCCT-AC
1 AAACGCCGCA-ATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
* *
1209877 AAACGCCGCAGAATATGTC-TTGA-GATTTAGCGGCATTTTCGTCGA-
1 AAACGCCGC--AATA-GACGTTGATG-TTTAGCGGCATTTTCTTC-AC
1209922 AAACGCCGCAATA
1 AAACGCCGCAATA
1209935 TGTCTTGAGA
Statistics
Matches: 142, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
42 13 0.09
43 99 0.70
44 19 0.13
45 10 0.07
46 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAATAGACGTTGATGTTTAGCGGCATTTTCTTCAC
Found at i:1209837 original size:86 final size:85
Alignment explanation
Indices: 1209706--1209914 Score: 195
Period size: 86 Copynumber: 2.4 Consensus size: 85
1209696 TTTTGCAGAA
* * * *
1209706 AAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAGACAAACGCCGCA-ATAGGCGTTGA
1 AAACGCCGCAGTAGATGTTGATATTTAACGGCATTTGGCAGACAAACACCGCAGA-AGACGTTGA
* * *
1209770 TGTTTAGCGGCGTTTTCTTCAC
65 TATTTAGCGACGTTTTCCT-AC
* * * ** ** *
1209792 AAACGCCGCAGTAGATGTTTATTTTTACCGGCATTTTTCCTACAAACACCGCAGAAGATGTTGAT
1 AAACGCCGCAGTAGATGTTGATATTTAACGGCATTTGGCAGACAAACACCGCAGAAGACGTTGAT
*
1209857 ATTTAGCGATGTTTTCCTAC
66 ATTTAGCGACGTTTTCCTAC
* * * *
1209877 AAACGCCGCAGAATATGTCTTGAGATTTAGCGGCATTT
1 AAACGCCGCAGTAGATG--TTGATATTTAACGGCATTT
1209915 TCGTCGAAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
85 17 0.17
86 65 0.66
87 16 0.16
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (85 bp):
AAACGCCGCAGTAGATGTTGATATTTAACGGCATTTGGCAGACAAACACCGCAGAAGACGTTGAT
ATTTAGCGACGTTTTCCTAC
Found at i:1209886 original size:42 final size:42
Alignment explanation
Indices: 1209747--1209908 Score: 139
Period size: 43 Copynumber: 3.8 Consensus size: 42
1209737 CATTTGGCAG
** * ** *
1209747 ACAAACGCCGCA-ATAGGCGTTGATGTTTAGCGGCGTTTTCTT
1 ACAAACGCCGCAGA-AGATGTTGATATTTAGCGATGTTTTCCT
* * * *
1209789 CACAAACGCCGCAGTAGATGTTTATTTTTACCGGCAT-TTTTCCT
1 -ACAAACGCCGCAGAAGATGTTGATATTTAGC-G-ATGTTTTCCT
*
1209833 ACAAACACCGCAGAAGATGTTGATATTTAGCGATGTTTTCCT
1 ACAAACGCCGCAGAAGATGTTGATATTTAGCGATGTTTTCCT
* *
1209875 ACAAACGCCGCAGAATATGTCTTGAGATTTAGCG
1 ACAAACGCCGCAGAAGATG--TTGATATTTAGCG
1209909 GCATTTTCGT
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 25 0.26
43 50 0.52
44 19 0.20
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
ACAAACGCCGCAGAAGATGTTGATATTTAGCGATGTTTTCCT
Found at i:1209969 original size:43 final size:45
Alignment explanation
Indices: 1209875--1209978 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 45
1209865 ATGTTTTCCT
*
1209875 ACAAACGCCGCAGAATATGTCTTGAGATTTAGCGGCATTTTCGTCG
1 ACAAACGCCGCA-AATATGTCTTGAGATTTAGCGGCATTTTCATCG
* * * *
1209921 A-AAACGCCGC-AATATGTCTTGAGATTTTGTGGCGTTTTTATC-
1 ACAAACGCCGCAAATATGTCTTGAGATTTAGCGGCATTTTCATCG
1209963 ACAAACGCCGCTAAAT
1 ACAAACGCCGC-AAAT
1209979 GTATGGTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 1 0.02
43 36 0.72
45 12 0.24
46 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (45 bp):
ACAAACGCCGCAAATATGTCTTGAGATTTAGCGGCATTTTCATCG
Found at i:1210338 original size:21 final size:21
Alignment explanation
Indices: 1210314--1210375 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1210304 ATATATTACT
1210314 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTTCTGCCGCTGCC
* * *
1210335 TCTCTCTGTACTGCCACTGCT
1 TCTCTCTGTTCTGCCGCTGCC
*
1210356 TCTCTCT-TTGCTTCCGCTGC
1 TCTCTCTGTT-CTGCCGCTGC
1210376 TGCTCTAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.03, C:0.40, G:0.16, T:0.40
Consensus pattern (21 bp):
TCTCTCTGTTCTGCCGCTGCC
Found at i:1210376 original size:21 final size:20
Alignment explanation
Indices: 1210312--1210381 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
1210302 TGATATATTA
1210312 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCT-TTCTGCCGCTG
* * *
1210333 CCTCTCTCTGTACTGCCACTG
1 CTTCTCTCT-TTCTGCCGCTG
*
1210354 CTTCTCTCTTTGCTTCCGCTG
1 CTTCTCTCTTT-CTGCCGCTG
*
1210375 CTGCTCT
1 CTTCTCT
1210382 AGCTGCTTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.03, C:0.40, G:0.16, T:0.41
Consensus pattern (20 bp):
CTTCTCTCTTTCTGCCGCTG
Found at i:1210409 original size:21 final size:21
Alignment explanation
Indices: 1210363--1210411 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1210353 GCTTCTCTCT
* *
1210363 TTGCTTCCGCTGCTGCTCTAG
1 TTGCTTCCACTGCTGCTCCAG
*
1210384 CTGCTTCCACTGCTGCTTCCA-
1 TTGCTTCCACTGCTGC-TCCAG
1210405 TTGCTTC
1 TTGCTTC
1210412 ATTTTCCGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.06, C:0.37, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGCTTCCACTGCTGCTCCAG
Found at i:1219494 original size:81 final size:81
Alignment explanation
Indices: 1219407--1219680 Score: 383
Period size: 81 Copynumber: 3.4 Consensus size: 81
1219397 TGTTAAATCA
* * * *
1219407 ATTGCGGCGTTTACAGAAAAATGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGTGTTTCTTGTAAAACGC
1219472 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* *
1219488 ATTGCGGCATTTATATAAAAAGGCCACTAATGTACGACCCATTTGCGGTGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGTGTTTCTTGTAAAACGC
1219553 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* * * * *
1219569 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACTACTC-TATTGCGGTATTT-TTTTAGAAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTACGACCCAT-TTGCGGTGTTTCTTGT--AAA
1219631 ACGCCACTATAAACAACTCT
62 ACGCCACTATAAACAACTCT
*
1219651 ATTGCGGCGTTTATATAAAAACGCCGCTAA
1 ATTGCGGCGTTTATATAAAAACGCCACTAA
1219681 ATTACCACCC
Statistics
Matches: 177, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
80 4 0.02
81 119 0.67
82 54 0.31
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (81 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGTGTTTCTTGTAAAACGC
CACTATAAACAACTCT
Found at i:1219615 original size:41 final size:41
Alignment explanation
Indices: 1219407--1219703 Score: 204
Period size: 41 Copynumber: 7.3 Consensus size: 41
1219397 TGTTAAATCA
* * * * *
1219407 ATTGCGGCGTTTACAGAAAAATGCCACT-AATGTACGAC-CC
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAT-TACAACTCT
* *
1219447 ATTTGCGGCGTTTCT-TGTAAAACGCCACTATAA--ACAACTCT
1 A-TTGCGGCGTTTATAT-AAAAACGCCACTA-AATTACAACTCT
* * * *
1219488 ATTGCGGCATTTATATAAAAAGGCCACT-AATGTACGAC-CC
1 ATTGCGGCGTTTATATAAAAACGCCACTAAAT-TACAACTCT
* * *
1219528 ATTTGCGGTGTTTCT-TGTAAAACGCCACTATAA--ACAACTCT
1 A-TTGCGGCGTTTATAT-AAAAACGCCACTA-AATTACAACTCT
* *
1219569 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
** * *
1219610 ATTGCGGTATTTTTTTAGAAAACGCCACTATAA--ACAACTCT
1 ATTGCGGCGTTTATATA-AAAACGCCACTA-AATTACAACTCT
* * *
1219651 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCCT
1 ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
*
1219692 ATTACGGCGTTT
1 ATTGCGGCGTTT
1219704 GTTGAAAAAA
Statistics
Matches: 197, Mismatches: 39, Indels: 41
0.71 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
39 4 0.02
40 66 0.34
41 108 0.55
42 11 0.06
43 6 0.03
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (41 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAAATTACAACTCT
Found at i:1219657 original size:82 final size:80
Alignment explanation
Indices: 1219407--1219717 Score: 349
Period size: 81 Copynumber: 3.8 Consensus size: 80
1219397 TGTTAAATCA
* * * * * * *
1219407 ATTGCGGCGTTTACAGAAAAATGCCACT-AATGTACGACCCATTTGCGGCGTTTCTTGTAAAACG
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACCACCTA-TTGCGGTGTTTCTTGTAAAACG
1219471 CCACTATAAACAACTCT
64 CCACTATAAACAACTCT
* * * * *
1219488 ATTGCGGCATTTATATAAAAAGGCCACT-AATGTACGACCCATTTGCGGTGTTTCTTGTAAAACG
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACCACCTA-TTGCGGTGTTTCTTGTAAAACG
1219552 CCACTATAAACAACTCT
64 CCACTATAAACAACTCT
* * *
1219569 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTATTGCGGTATTT-TTTTAGAAAAC
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCAC-CTATTGCGGTGTTTCTTGT--AAAAC
1219633 GCCACTATAAACAACTCT
63 GCCACTATAAACAACTCT
* * * *
1219651 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCCTATTACGGCGTTTGTTGAAAAAACG
1 ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCA-CCTATTGCGGTGTTTCTTG-TAAAACG
1219716 CC
64 CC
1219718 GCTAAAGTTT
Statistics
Matches: 205, Mismatches: 18, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
80 3 0.01
81 116 0.57
82 83 0.40
83 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (80 bp):
ATTGCGGCGTTTATATAAAAACGCCGCTAAATTACCACCTATTGCGGTGTTTCTTGTAAAACGCC
ACTATAAACAACTCT
Found at i:1222453 original size:23 final size:23
Alignment explanation
Indices: 1222427--1222470 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1222417 AATTAGGCTC
* *
1222427 GGGTTGGCTTGTATCTGGGTCTT
1 GGGTTGGCTTGCATATGGGTCTT
1222450 GGGTTGGCTTGCATATGGGTC
1 GGGTTGGCTTGCATATGGGTC
1222471 GGGTTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.39
Consensus pattern (23 bp):
GGGTTGGCTTGCATATGGGTCTT
Found at i:1224443 original size:24 final size:24
Alignment explanation
Indices: 1224411--1224466 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1224401 CTATTCTTTC
1224411 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1224435 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
1224459 GCTTCAAT
1 GCTTCAAT
1224467 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:1224725 original size:30 final size:30
Alignment explanation
Indices: 1224689--1224754 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
1224679 AGTGAACCGG
* *
1224689 CGGTTCAAACCGGTTTTGTCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTCTCGATTTTCAGC
**
1224719 CGGTTCACCCCGGTTTTCTCGATTTTCAGC
1 CGGTTCAAACCGGTTTTCTCGATTTTCAGC
1224749 CGGTTC
1 CGGTTC
1224755 TTCCGGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.29, G:0.24, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTCTCGATTTTCAGC
Found at i:1225281 original size:39 final size:39
Alignment explanation
Indices: 1225215--1225289 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1225205 TTATTCATAA
*
1225215 TTCTCAAATTATTTCACTCCAATATTCTAAAATTTTAAT
1 TTCTCAAATTATTTCACTCCAACATTCTAAAATTTTAAT
* *
1225254 TTCTCAAATTATTTCAACT-TAACATTCTAAATTTTT
1 TTCTCAAATTATTTC-ACTCCAACATTCTAAAATTTT
1225290 TGAGATGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 29 0.91
40 3 0.09
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (39 bp):
TTCTCAAATTATTTCACTCCAACATTCTAAAATTTTAAT
Found at i:1228362 original size:14 final size:13
Alignment explanation
Indices: 1228337--1228382 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
1228327 TAACTTTTTG
1228337 GTCAACGGTCAAA
1 GTCAACGGTCAAA
1228350 GTCAACTGGTCAAA
1 GTCAAC-GGTCAAA
*
1228364 GTCGACGGATCAAA
1 GTCAACGG-TCAAA
1228378 GTCAA
1 GTCAA
1228383 TGGGTTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:1240721 original size:31 final size:31
Alignment explanation
Indices: 1240680--1240751 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1240670 AAAACATAAG
*
1240680 ATATGATCACTTTTGTTTTTATTTAATTAAA
1 ATATGATCACTTTCGTTTTTATTTAATTAAA
* *
1240711 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGTTTTTATTTAATTAAA
*
1240742 ATGTGATCAC
1 ATATGATCAC
1240752 CCCGAGTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAA
Found at i:1241571 original size:27 final size:25
Alignment explanation
Indices: 1241512--1241598 Score: 78
Period size: 25 Copynumber: 3.5 Consensus size: 25
1241502 TTTATATGTA
*
1241512 TTAACTTAAAATATTTT-TATATCAAC
1 TTAA-TTAAAATATTTTAT-TATTAAC
1241538 TT-ATTAAACATATTTTATTATTAAC
1 TTAATTAAA-ATATTTTATTATTAAC
1241563 TTAATTTAAAAATATTTTATT-TTAA-
1 TTAA-TT-AAAATATTTTATTATTAAC
1241588 TT--TTAAAATAT
1 TTAATTAAAATAT
1241599 AATTTATTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
21 7 0.13
22 2 0.04
24 5 0.09
25 18 0.33
26 8 0.15
27 12 0.22
28 3 0.05
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATTAAAATATTTTATTATTAAC
Found at i:1241608 original size:23 final size:22
Alignment explanation
Indices: 1241563--1241613 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1241553 TATTATTAAC
*
1241563 TTAA-TTTAAAAATATTTTATT
1 TTAATTTTAAAAATAATTTATT
1241584 TTAATTTTAAAATATAATTTATT
1 TTAATTTTAAAA-ATAATTTATT
1241607 TTAATTT
1 TTAATTT
1241614 CTTAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 7 0.26
23 16 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAATTTTAAAAATAATTTATT
Found at i:1242285 original size:18 final size:18
Alignment explanation
Indices: 1242262--1242296 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1242252 ATTTTTATTA
1242262 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
1242280 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
1242297 GAGTCAGGTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:1242391 original size:38 final size:38
Alignment explanation
Indices: 1242343--1242416 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
1242333 AAACCGGATT
* *
1242343 GAGTTTAGGTCAGGTGGAAAATATATATTTTTCGGGTG
1 GAGTTCAGGTCAGGTGGAAAATATATAATTTTCGGGTG
** *
1242381 GAGTTCAGGTCAGGTGGAGGATTTATAATTTTCGGG
1 GAGTTCAGGTCAGGTGGAAAATATATAATTTTCGGG
1242417 ACGGGTAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.35
Consensus pattern (38 bp):
GAGTTCAGGTCAGGTGGAAAATATATAATTTTCGGGTG
Found at i:1242691 original size:11 final size:11
Alignment explanation
Indices: 1242675--1242730 Score: 103
Period size: 11 Copynumber: 5.1 Consensus size: 11
1242665 CTAAACAATA
1242675 TGAATCAAATG
1 TGAATCAAATG
*
1242686 TGAATCAAATA
1 TGAATCAAATG
1242697 TGAATCAAATG
1 TGAATCAAATG
1242708 TGAATCAAATG
1 TGAATCAAATG
1242719 TGAATCAAATG
1 TGAATCAAATG
1242730 T
1 T
1242731 TTATCTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (11 bp):
TGAATCAAATG
Found at i:1264063 original size:9 final size:9
Alignment explanation
Indices: 1264049--1264073 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1264039 AATTTCTCTT
1264049 TTTCTTTAC
1 TTTCTTTAC
1264058 TTTCTTTAC
1 TTTCTTTAC
1264067 TTTCTTT
1 TTTCTTT
1264074 TAAGTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTCTTTAC
Found at i:1276988 original size:101 final size:101
Alignment explanation
Indices: 1276775--1276958 Score: 350
Period size: 101 Copynumber: 1.8 Consensus size: 101
1276765 AAGAGAGTTA
1276775 TTTACATATATGAAACAACTGAAAAGACTAATGGACCATTATGTCCAAATATCCAGAAGAAGATG
1 TTTACATATATGAAACAACTGAAAAGACTAATGGACCATTATGTCCAAATATCCAGAAGAAGATG
*
1276840 AACATTATAATTGAACAAGCAACTAGGTAACTAATG
66 AACATTACAATTGAACAAGCAACTAGGTAACTAATG
1276876 TTTACATATATGAAACAACTGAAAAGACTAATGGACCATTATGTCCAAATATCCAGAAGAAGATG
1 TTTACATATATGAAACAACTGAAAAGACTAATGGACCATTATGTCCAAATATCCAGAAGAAGATG
1276941 AACATTACAATTAGAACA
66 AACATTACAATT-GAACA
1276959 TTATTGTCAT
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 76 0.94
102 5 0.06
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24
Consensus pattern (101 bp):
TTTACATATATGAAACAACTGAAAAGACTAATGGACCATTATGTCCAAATATCCAGAAGAAGATG
AACATTACAATTGAACAAGCAACTAGGTAACTAATG
Found at i:1289814 original size:30 final size:30
Alignment explanation
Indices: 1289780--1289853 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
1289770 GTCACTTAAT
* *
1289780 CCACCTACAACAGTTCGTTGGATGATGCCA
1 CCACCTACAACAGTTCATTGGATGATGACA
* *
1289810 CCACCTACAACAATTTATTGGATGATGACA
1 CCACCTACAACAGTTCATTGGATGATGACA
*
1289840 CCTCCTACAACAGT
1 CCACCTACAACAGT
1289854 CCATGCGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (30 bp):
CCACCTACAACAGTTCATTGGATGATGACA
Done.