Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 21
Found at i:1116950 original size:20 final size:20
Alignment explanation
Indices: 1116925--1116974 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1116915 TTTGTGTTGT
1116925 GAAATTAAAAGCTGGTTTGC
1 GAAATTAAAAGCTGGTTTGC
1116945 GAAATTAAAAGCTGGTTTGC
1 GAAATTAAAAGCTGGTTTGC
1116965 GAAATTAAAA
1 GAAATTAAAA
1116975 TTCGTGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (20 bp):
GAAATTAAAAGCTGGTTTGC
Found at i:1118477 original size:22 final size:22
Alignment explanation
Indices: 1118452--1118503 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1118442 GTATTTTAAA
*
1118452 TATTTGGGAATTATCTTTCTAT
1 TATTTAGGAATTATCTTTCTAT
1118474 TATTTAGGAATTATCTTTCTAT
1 TATTTAGGAATTATCTTTCTAT
1118496 TATTTAGG
1 TATTTAGG
1118504 TTTTTATGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (22 bp):
TATTTAGGAATTATCTTTCTAT
Found at i:1119968 original size:94 final size:94
Alignment explanation
Indices: 1119807--1119994 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 94
1119797 AAAAAAAATG
*
1119807 ATGGAGAGTCGCTATACGACTATTGGAAACGATTTAAGAAACTCTGCGCTAGCTGCCCACAACAT
1 ATGGAGAGTCACTATACGACTATTGGAAACGATTTAAGAAACTCTGCGCTAGCTGCCCACAACAT
*
1119872 GGACTGTCAGAGCATACTCTCCTCCAATA
66 GGACTGTCAGAGCATAATCTCCTCCAATA
* * * *
1119901 ATGGAGAGTCATTATATGACTATTGGGAGCGATTTAAGAAACTCTGCGCTAGCTGCCCACAACAT
1 ATGGAGAGTCACTATACGACTATTGGAAACGATTTAAGAAACTCTGCGCTAGCTGCCCACAACAT
*
1119966 GGACTGTCGGAGCATAATCTCCTCCAATA
66 GGACTGTCAGAGCATAATCTCCTCCAATA
1119995 CTTTTATGAG
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (94 bp):
ATGGAGAGTCACTATACGACTATTGGAAACGATTTAAGAAACTCTGCGCTAGCTGCCCACAACAT
GGACTGTCAGAGCATAATCTCCTCCAATA
Found at i:1120266 original size:21 final size:21
Alignment explanation
Indices: 1120240--1120283 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1120230 TATGATAAAA
*
1120240 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATTAATATTT
1120261 TTATTTAAAATATTAATATTT
1 TTATTTAAAATATTAATATTT
1120282 TT
1 TT
1120284 TAACATTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTAAAATATTAATATTT
Found at i:1122715 original size:22 final size:22
Alignment explanation
Indices: 1122687--1122764 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
1122677 TAAATGTTTG
* *
1122687 GGAATTATCTTTCTATTATTTA
1 GGAATTATCTTTATAATATTTA
1122709 GGAATTATCTTTATAATATTTA
1 GGAATTATCTTTATAATATTTA
* * *
1122731 AGATTTTAT-TTGA-ATATATTTA
1 GGA-ATTATCTTTATA-ATATTTA
1122753 GG-ATTATCTTTA
1 GGAATTATCTTTA
1122765 GGTATTTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
20 4 0.09
21 4 0.09
22 33 0.73
23 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (22 bp):
GGAATTATCTTTATAATATTTA
Found at i:1124950 original size:7 final size:7
Alignment explanation
Indices: 1124929--1124969 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
1124919 GGTAAAAAGA
1124929 GGTCAAC
1 GGTCAAC
1124936 GGTC-AC
1 GGTCAAC
1124942 GGTCAAC
1 GGTCAAC
1124949 GGTCAAC
1 GGTCAAC
*
1124956 GATCAAC
1 GGTCAAC
*
1124963 GATCAAC
1 GGTCAAC
1124970 AGTCGGGTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:1124987 original size:17 final size:17
Alignment explanation
Indices: 1124965--1124997 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1124955 CGATCAACGA
1124965 TCAACAGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
1124982 TCAACAGTCGGGTCGG
1 TCAACAGTCGGGTCGG
1124998 TCGGGTCGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (17 bp):
TCAACAGTCGGGTCGGG
Found at i:1132292 original size:19 final size:19
Alignment explanation
Indices: 1132269--1132321 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1132259 GGTCGGATCA
1132269 AACCGGTCAAATCG-TTTC
1 AACCGGTCAAATCGATTTC
* *
1132287 AGACCGGTCAAACCGATTTG
1 A-ACCGGTCAAATCGATTTC
1132307 AACCGGTCGAAATCG
1 AACCGGTC-AAATCG
1132322 GTCAAACCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 19 0.66
20 9 0.31
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (19 bp):
AACCGGTCAAATCGATTTC
Found at i:1134357 original size:22 final size:21
Alignment explanation
Indices: 1134323--1134363 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1134313 ATAATTATTT
1134323 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
1134344 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
1134364 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:1135645 original size:16 final size:16
Alignment explanation
Indices: 1135624--1135674 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1135614 AGTATTACCC
1135624 GACATGTTTTCAACCT
1 GACATGTTTTCAACCT
** *
1135640 GACATGTGATGAACCT
1 GACATGTTTTCAACCT
*
1135656 GATC-TGTTTTTAACCT
1 GA-CATGTTTTCAACCT
1135672 GAC
1 GAC
1135675 CTGTAAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (16 bp):
GACATGTTTTCAACCT
Found at i:1135719 original size:16 final size:16
Alignment explanation
Indices: 1135695--1135750 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1135685 TACGACTTGT
* *
1135695 TATTGACCTGATTTGA
1 TATTTACCTGAATTGA
*
1135711 TATTTACCTGACTTGA
1 TATTTACCTGAATTGA
* *
1135727 CATTTATCTGAATT-A
1 TATTTACCTGAATTGA
1135742 TATATTACC
1 TAT-TTACC
1135751 ATTGACGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 3 0.09
16 29 0.91
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (16 bp):
TATTTACCTGAATTGA
Found at i:1135939 original size:25 final size:22
Alignment explanation
Indices: 1135886--1135941 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
1135876 ATAGATCTAT
1135886 TATATAAAATTATTCAATAAAA
1 TATATAAAATTATTCAATAAAA
*
1135908 T-TAATAAAATTATTTGAATGTAAAA
1 TAT-ATAAAATTA-TTCAA--TAAAA
1135933 TATATAAAA
1 TATATAAAA
1135942 CATGATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
22 10 0.36
23 4 0.14
25 12 0.43
26 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
TATATAAAATTATTCAATAAAA
Found at i:1136020 original size:23 final size:24
Alignment explanation
Indices: 1135980--1136033 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1135970 CAATGATTAA
*
1135980 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAACTAATATAGTTTAATTT
1136004 ATGTAAACT-ATATAGTTTAATTT
1 ATGTAAACTAATATAGTTTAATTT
1136027 ATGTAAA
1 ATGTAAA
1136034 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
ATGTAAACTAATATAGTTTAATTT
Found at i:1136231 original size:11 final size:11
Alignment explanation
Indices: 1136215--1136253 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1136205 TGATGATGAT
1136215 AATTTAAATAA
1 AATTTAAATAA
1136226 AATTTAATATAA
1 AATTTAA-ATAA
*
1136238 AATTTGAATAA
1 AATTTAAATAA
*
1136249 CATTT
1 AATTT
1136254 GAGTTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (11 bp):
AATTTAAATAA
Found at i:1136239 original size:12 final size:12
Alignment explanation
Indices: 1136215--1136247 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1136205 TGATGATGAT
1136215 AATTTAA-ATAA
1 AATTTAATATAA
1136226 AATTTAATATAA
1 AATTTAATATAA
1136238 AATTTGAATA
1 AATTT-AATA
1136248 ACATTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 9 0.45
13 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
AATTTAATATAA
Found at i:1136927 original size:13 final size:14
Alignment explanation
Indices: 1136878--1136946 Score: 60
Period size: 14 Copynumber: 5.4 Consensus size: 14
1136868 TATTAAATAA
1136878 TAATTGCATGTTAT
1 TAATTGCATGTTAT
**
1136892 TAATT-CATG-TGG
1 TAATTGCATGTTAT
1136904 T-ATTGCATGTTAT
1 TAATTGCATGTTAT
1136917 TAATT-CATG-T-T
1 TAATTGCATGTTAT
**
1136928 GCATTGCATGTTAT
1 TAATTGCATGTTAT
1136942 TAATT
1 TAATT
1136947 TATGTTACAT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
11 7 0.17
12 11 0.27
13 11 0.27
14 12 0.29
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:1136952 original size:25 final size:25
Alignment explanation
Indices: 1136880--1136957 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
1136870 TTAAATAATA
* *
1136880 ATTGCATGTTATTAATTCATGTGGT
1 ATTGCATGTTATTAATTCATGTTGC
1136905 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTGC
* *
1136930 ATTGCATGTTATTAATTTATGTTAC
1 ATTGCATGTTATTAATTCATGTTGC
1136955 ATT
1 ATT
1136958 AGGTGTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTGC
Found at i:1137148 original size:6 final size:6
Alignment explanation
Indices: 1137137--1137239 Score: 73
Period size: 6 Copynumber: 18.3 Consensus size: 6
1137127 ACTATTTATA
1137137 ATTAAT ATTAAT A-TAA- ATTATAT ATT-AT AATTAAT ATTAAT A-T-A-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT
* * * *
1137181 ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT A-TAGT CTATAAA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT
1137226 ATTAAT ATTAAT AT
1 ATTAAT ATTAAT AT
1137240 AAATTATATT
Statistics
Matches: 77, Mismatches: 8, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 21 0.27
6 43 0.56
7 8 0.10
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:1137152 original size:29 final size:28
Alignment explanation
Indices: 1137118--1137241 Score: 108
Period size: 29 Copynumber: 4.2 Consensus size: 28
1137108 TATATAATTT
1137118 ATATAATAAACTATTTATAATTAATATTA
1 ATATAATAAA-TATTTATAATTAATATTA
*
1137147 ATATAA-ATTATATATTATAATTAATATTA
1 ATATAATA-AATAT-TTATAATTAATATTA
*
1137176 ATATAATTAATATTAATATTAACTT-ATATTA
1 ATATAATAAATATT--TA-TAA-TTAATATTA
* * * *
1137207 ATATAATATAGTCTATAAAATTAATATTA
1 ATATAATA-AATATTTATAATTAATATTA
1137236 ATATAA
1 ATATAA
1137242 ATTATATTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
28 7 0.09
29 46 0.59
30 4 0.05
31 16 0.21
32 5 0.06
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATAATAAATATTTATAATTAATATTA
Found at i:1137262 original size:29 final size:30
Alignment explanation
Indices: 1137131--1137336 Score: 142
Period size: 29 Copynumber: 7.0 Consensus size: 30
1137121 TAATAAACTA
1137131 TTTAT-AATTAATATTAATATAAATTATAT
1 TTTATAAATTAATATTAATATAAATTATAT
*
1137160 ATTAT-AATTAATATTAATAT-AATTAATAT
1 TTTATAAATTAATATTAATATAAATT-ATAT
* * *
1137189 TAATATTAACTT-ATATTAATAT-AA-TATAG
1 T-TTA-TAAATTAATATTAATATAAATTATAT
*
1137218 TCTATAAAATTAATATTAATATAAATTATAT
1 TTTAT-AAATTAATATTAATATAAATTATAT
* ** *
1137249 TTTATAAATT-ATA-TAGTATAGTTTATAA
1 TTTATAAATTAATATTAATATAAATTATAT
** * * *
1137277 ACTATATACT-ATATTAATATAAATTATAG
1 TTTATAAATTAATATTAATATAAATTATAT
* * * *
1137306 TTAAGATAATTAACATTAATATAAACTATAT
1 TTTATA-AATTAATATTAATATAAATTATAT
1137337 AGTACATTAA
Statistics
Matches: 136, Mismatches: 30, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 30 0.22
29 53 0.39
30 12 0.09
31 37 0.27
32 3 0.02
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTATAAATTAATATTAATATAAATTATAT
Found at i:1137268 original size:21 final size:21
Alignment explanation
Indices: 1137244--1137304 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1137234 TAATATAAAT
*
1137244 TATATTTTATAAATTATATAG
1 TATATTTTATAAATTATATAC
* *
1137265 TATAGTTTATAAACTATATAC
1 TATATTTTATAAATTATATAC
*
1137286 TATATTAATATAAATTATA
1 TATATT-TTATAAATTATA
1137305 GTTAAGATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (21 bp):
TATATTTTATAAATTATATAC
Found at i:1137324 original size:117 final size:110
Alignment explanation
Indices: 1137170--1137400 Score: 243
Period size: 110 Copynumber: 2.0 Consensus size: 110
1137160 ATTATAATTA
* * * *
1137170 ATATTAATATAATTAATATTAATATTAACTTATATTAATATAATATAGTCTATAAAATTAATATT
1 ATATTAATATAATTAATATTAAGATTAACTTACATTAATAT-A-A-A--CTAT-AAAGT-ACATT
* * * * *
1137235 AATATAAATTATATTTTATAAATTATATAGTATAGTTTATAAACTATATACT
59 AATATAAACTATAGTTTATAAATTATATACTATAGATTATAAACTATAAACT
*
1137287 ATATTAATATAAATT-ATAGTTAAGA-TAA-TTAACATTAATATAAACTATATAGTACATTAATA
1 ATATTAATAT-AATTAATA-TTAAGATTAACTT-ACATTAATATAAACTATAAAGTACATTAATA
* *
1137349 TAAACTATAGTTTATAAATTATATACTATCGATTATAAAGTATAAACT
63 TAAACTATAGTTTATAAATTATATACTATAGATTATAAACTATAAACT
1137397 ATAT
1 ATAT
1137401 AGTACACTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
110 53 0.54
111 3 0.03
112 4 0.04
114 1 0.01
115 1 0.01
116 3 0.03
117 25 0.25
118 9 0.09
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (110 bp):
ATATTAATATAATTAATATTAAGATTAACTTACATTAATATAAACTATAAAGTACATTAATATAA
ACTATAGTTTATAAATTATATACTATAGATTATAAACTATAAACT
Found at i:1137359 original size:20 final size:21
Alignment explanation
Indices: 1137318--1137359 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1137308 AAGATAATTA
1137318 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
1137340 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
1137360 TTATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:1137376 original size:21 final size:21
Alignment explanation
Indices: 1137347--1137399 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1137337 AGTACATTAA
* *
1137347 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGATTATAAAG
* *
1137368 TATATACTATCGATTATAAAG
1 TATAAACTATAGATTATAAAG
1137389 TATAAACTATA
1 TATAAACTATA
1137400 TAGTACACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGATTATAAAG
Found at i:1137607 original size:24 final size:24
Alignment explanation
Indices: 1137579--1137640 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1137569 CGTTCGTGAA
1137579 CGTTCAGTTATGTTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* * *
1137603 TGTTCGGTTATATTCGTTTATGTT
1 CGTTCAGTTATGTTCGTTTATGTT
* *
1137627 CATTCATTTATGTT
1 CGTTCAGTTATGTT
1137641 TAAGCCAATC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.11, G:0.18, T:0.56
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATGTT
Found at i:1138316 original size:16 final size:15
Alignment explanation
Indices: 1138295--1138345 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
1138285 GGTCTCAATG
1138295 TTTATGTTCGTGTTCA
1 TTTATGTTCGT-TTCA
*
1138311 TTTATGTTCGTATTCG
1 TTTATGTTCGT-TTCA
1138327 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
1138341 TTTAT
1 TTTAT
1138346 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:1138427 original size:15 final size:16
Alignment explanation
Indices: 1138407--1138438 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1138397 AAAAACATTT
1138407 TGTTCGTTTAT-TTCG
1 TGTTCGTTTATGTTCG
1138422 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1138438 T
1 T
1138439 TTATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1138565 original size:20 final size:21
Alignment explanation
Indices: 1138535--1138661 Score: 106
Period size: 20 Copynumber: 6.2 Consensus size: 21
1138525 AACTATACGT
1138535 TACATAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
*
1138554 -ACATATAAATAGATTGTATATA
1 TACATATACATAG-TT-TATATA
* * *
1138576 TAAATATGCTATAGGTTATATA
1 TACATATAC-ATAGTTTATATA
*
1138598 T--ATATATATAGTTTATATA
1 TACATATACATAGTTTATATA
* *
1138617 TA-TTATACATAGTTTATACA
1 TACATATACATAGTTTATATA
*
1138637 TAC-TATACATAGTTTATACA
1 TACATATACATAGTTTATATA
1138657 TACAT
1 TACAT
1138662 GTACTATAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.07
19 12 0.13
20 45 0.51
21 3 0.03
22 13 0.15
23 6 0.07
24 4 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
TACATATACATAGTTTATATA
Found at i:1138633 original size:11 final size:11
Alignment explanation
Indices: 1138600--1138658 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
1138590 GTTATATATA
*
1138600 TATATATAGTT
1 TATACATAGTT
*
1138611 TATATATA--T
1 TATACATAGTT
1138620 TATACATAGTT
1 TATACATAGTT
*
1138631 TATACATA--C
1 TATACATAGTT
1138640 TATACATAGTT
1 TATACATAGTT
1138651 TATACATA
1 TATACATA
1138659 CATGTACTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
9 16 0.39
11 25 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (11 bp):
TATACATAGTT
Found at i:1138684 original size:35 final size:36
Alignment explanation
Indices: 1138645--1138718 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
1138635 CATACTATAC
*
1138645 ATAGTTTATA-CATACATGTACTATAAGTTACATAT
1 ATAGTTTATAGCATACATATACTATAAGTTACATAT
* *
1138680 ATAGTTTATATGTATACATATACTATAGGTTACATAT
1 ATAGTTTATA-GCATACATATACTATAAGTTACATAT
1138717 AT
1 AT
1138719 TAACTATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.42
Consensus pattern (36 bp):
ATAGTTTATAGCATACATATACTATAAGTTACATAT
Found at i:1138932 original size:2 final size:2
Alignment explanation
Indices: 1138925--1139003 Score: 62
Period size: 2 Copynumber: 41.5 Consensus size: 2
1138915 TTCTATAAAC
* *
1138925 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
1138965 TA TA T- TA GT- TA TA CA TA CA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1139004 TAATATAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
1 6 0.10
2 53 0.87
3 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1139057 original size:13 final size:13
Alignment explanation
Indices: 1139039--1139065 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1139029 ATATATTTTA
1139039 TATAGTTTATACG
1 TATAGTTTATACG
1139052 TATAGTTTATACG
1 TATAGTTTATACG
1139065 T
1 T
1139066 GTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TATAGTTTATACG
Found at i:1139335 original size:19 final size:19
Alignment explanation
Indices: 1139295--1139358 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
1139285 AAATTTTCTA
*
1139295 TTCCTTCTAAATTTCTCAAT
1 TTCCCTCTAAA-TTCTCAAT
*
1139315 TTCCCTCTAAATTCCCAAT
1 TTCCCTCTAAATTCTCAAT
*
1139334 TTCCCTATAAATTCTCAAT
1 TTCCCTCTAAATTCTCAAT
1139353 TTCCCT
1 TTCCCT
1139359 ATATTCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCCCTCTAAATTCTCAAT
Found at i:1139359 original size:19 final size:19
Alignment explanation
Indices: 1139302--1139361 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
1139292 CTATTCCTTC
*
1139302 TAAATTTCTCAATTTCCCTC
1 TAAA-TTCTCAATTTCCCTA
*
1139322 TAAATTCCCAATTTCCCTA
1 TAAATTCTCAATTTCCCTA
1139341 TAAATTCTCAATTTCCCTA
1 TAAATTCTCAATTTCCCTA
1139360 TA
1 TA
1139362 TTCTCAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 33 0.89
20 4 0.11
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATTCTCAATTTCCCTA
Found at i:1139374 original size:19 final size:18
Alignment explanation
Indices: 1139307--1139368 Score: 81
Period size: 19 Copynumber: 3.4 Consensus size: 18
1139297 CCTTCTAAAT
*
1139307 TTCTCAATTTCCCTCTAAA
1 TTCTCAATTTCCCTAT-AA
*
1139326 TTCCCAATTTCCCTATAAA
1 TTCTCAATTTCCCTAT-AA
1139345 TTCTCAATTTCCCTAT-A
1 TTCTCAATTTCCCTATAA
1139362 TTCTCAA
1 TTCTCAA
1139369 ATTTTCTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.20
19 32 0.80
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (18 bp):
TTCTCAATTTCCCTATAA
Found at i:1139375 original size:27 final size:29
Alignment explanation
Indices: 1139345--1139399 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1139335 TCCCTATAAA
* *
1139345 TTCTCAA-TTTCC-CTATATTCTCAAATT
1 TTCTCAATTTTCCTCTAAATTCCCAAATT
1139372 TTCTCAATTTTCCTCTAAATTCCCAAAT
1 TTCTCAATTTTCCTCTAAATTCCCAAAT
1139400 AAAATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.29
28 5 0.21
29 12 0.50
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (29 bp):
TTCTCAATTTTCCTCTAAATTCCCAAATT
Found at i:1141357 original size:15 final size:16
Alignment explanation
Indices: 1141337--1141373 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1141327 ATTTTGTTAG
1141337 TAATTTATTTAA-ATT
1 TAATTTATTTAATATT
1141352 TAATTT-TTTAATATT
1 TAATTTATTTAATATT
*
1141367 TTATTTA
1 TAATTTA
1141374 ATAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTTATTTAATATT
Found at i:1141374 original size:26 final size:28
Alignment explanation
Indices: 1141308--1141374 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 28
1141298 TGTTTAAGGT
*
1141308 ATATTTTA-TTATATTTAGTATTTTGTTA
1 ATATTTTATTTAAATTTAG-ATTTTGTTA
* *
1141336 GTAATTTATTTAAATTTA-ATTTT-TTA
1 ATATTTTATTTAAATTTAGATTTTGTTA
1141362 ATATTTTATTTAA
1 ATATTTTATTTAA
1141375 TAATTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 14 0.42
27 5 0.15
28 6 0.18
29 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
ATATTTTATTTAAATTTAGATTTTGTTA
Found at i:1141375 original size:12 final size:12
Alignment explanation
Indices: 1141337--1141385 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
1141327 ATTTTGTTAG
1141337 TAATTTATTTAAA
1 TAATTTATTT-AA
1141350 TTTAATTT-TTTAA
1 --TAATTTATTTAA
*
1141363 TATTTTATTTAA
1 TAATTTATTTAA
1141375 TAATTTATTTA
1 TAATTTATTTA
1141386 CAGATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 2 0.06
14 3 0.10
15 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TAATTTATTTAA
Found at i:1143047 original size:24 final size:21
Alignment explanation
Indices: 1143021--1143064 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1143011 CTTCAGCTGC
*
1143021 ACCAGCAGGACCTTTACAGCA
1 ACCACCAGGACCTTTACAGCA
*
1143042 ACCACCAGGACCTTTACATCA
1 ACCACCAGGACCTTTACAGCA
1143063 AC
1 AC
1143065 TACCGTCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.36, G:0.14, T:0.16
Consensus pattern (21 bp):
ACCACCAGGACCTTTACAGCA
Found at i:1143388 original size:13 final size:14
Alignment explanation
Indices: 1143370--1143417 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1143360 ATTTACTCAT
*
1143370 TGAGAGA-AATATG
1 TGAGAGAGAAGATG
1143383 TGAGAGAGGAAGATG
1 TGAGAGA-GAAGATG
*
1143398 TGAGAGAGGAAGGTG
1 TGAGAGA-GAAGATG
1143413 TGAGA
1 TGAGA
1143418 TAGTTTACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 7 0.23
15 24 0.77
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.17
Consensus pattern (14 bp):
TGAGAGAGAAGATG
Found at i:1143398 original size:15 final size:15
Alignment explanation
Indices: 1143380--1143417 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1143370 TGAGAGAAAT
1143380 ATGTGAGAGAGGAAG
1 ATGTGAGAGAGGAAG
1143395 ATGTGAGAGAGGAAG
1 ATGTGAGAGAGGAAG
*
1143410 GTGTGAGA
1 ATGTGAGA
1143418 TAGTTTACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (15 bp):
ATGTGAGAGAGGAAG
Found at i:1148095 original size:16 final size:16
Alignment explanation
Indices: 1148074--1148116 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1148064 ACTCAAATTA
1148074 TTGACTTTGATCAGA-G
1 TTGACTTTGATCA-ACG
*
1148090 TTGACTTTGATTAACG
1 TTGACTTTGATCAACG
1148106 TTGACTTTGAT
1 TTGACTTTGAT
1148117 AAAAAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (16 bp):
TTGACTTTGATCAACG
Found at i:1148425 original size:21 final size:21
Alignment explanation
Indices: 1148399--1148451 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1148389 GTTATATGAC
*
1148399 TGATTTATCTATTTTGAAATA
1 TGATTTATATATTTTGAAATA
*
1148420 TGATTTATATGTTTTGAAATA
1 TGATTTATATATTTTGAAATA
1148441 TGATTTGATAT
1 TGATTT-ATAT
1148452 CTGAATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (21 bp):
TGATTTATATATTTTGAAATA
Found at i:1149217 original size:13 final size:14
Alignment explanation
Indices: 1149195--1149224 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1149185 CATGTTTTGT
1149195 TATCATTTTGGATA
1 TATCATTTTGGATA
1149209 TATCA-TTTGGATA
1 TATCATTTTGGATA
1149222 TAT
1 TAT
1149225 TATGATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
TATCATTTTGGATA
Found at i:1150138 original size:18 final size:19
Alignment explanation
Indices: 1150115--1150166 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
1150105 AATGTATTAT
1150115 TAAAATTGTATATAATA-A
1 TAAAATTGTATATAATAGA
1150133 TAAAATAT-T-T-TAATTAGA
1 TAAAAT-TGTATATAA-TAGA
1150151 TAAAATTGTA-ATAATA
1 TAAAATTGTATATAATA
1150167 TTGAAATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
16 3 0.11
17 4 0.14
18 17 0.61
19 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TAAAATTGTATATAATAGA
Found at i:1153590 original size:17 final size:17
Alignment explanation
Indices: 1153568--1153614 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1153558 GCTTCACTTA
1153568 ATTTTTTTA-TTATTTAT
1 ATTTTTTTATTTATTT-T
1153585 ATTTTTTTATTTTATTTT
1 ATTTTTTTA-TTTATTTT
*
1153603 ATTTTTTAATTT
1 ATTTTTTTATTT
1153615 TAAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 12 0.44
18 9 0.33
19 6 0.22
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTTTATTTATTTT
Found at i:1153592 original size:18 final size:18
Alignment explanation
Indices: 1153569--1153609 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1153559 CTTCACTTAA
1153569 TTTTTT-TATTATTTATAT
1 TTTTTTATATTATTT-TAT
*
1153587 TTTTTTATTTTATTTTAT
1 TTTTTTATATTATTTTAT
1153605 TTTTT
1 TTTTT
1153610 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTATATTATTTTAT
Found at i:1153614 original size:18 final size:19
Alignment explanation
Indices: 1153577--1153616 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1153567 AATTTTTTTA
*
1153577 TTATTTATATTTTTTTATT
1 TTATTTATATTTTTTAATT
1153596 TTATTT-TATTTTTTAATT
1 TTATTTATATTTTTTAATT
1153614 TTA
1 TTA
1153617 AAAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (19 bp):
TTATTTATATTTTTTAATT
Found at i:1153934 original size:15 final size:15
Alignment explanation
Indices: 1153914--1153944 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1153904 CAAATTGAGT
1153914 TCAAAGAAGATTATA
1 TCAAAGAAGATTATA
1153929 TCAAAGAAGATTATA
1 TCAAAGAAGATTATA
1153944 T
1 T
1153945 GTTTTTGTCC
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:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (15 bp):
TCAAAGAAGATTATA
Found at i:1155378 original size:54 final size:54
Alignment explanation
Indices: 1155312--1155761 Score: 533
Period size: 54 Copynumber: 8.4 Consensus size: 54
1155302 TCTTTTGAGG
* * * * * * *
1155312 TGCACACGTAGTGCCGATACGGTCCTTTATAAACATATTATGAATTTCGTGGGC
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * * *
1155366 TGCACACTTAGTGTCGATACAGTCGTTTATCAATATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * * *
1155420 TGCACACTTAGTGT-GATACGGTCGTTCATAAATACATTATGAATTTCATGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* *
1155473 TGCACACTTAGTGTTGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * *
1155527 TGCACACTTAGTGTCGATACGTTCGTTCATCAACATATGATGAATTCCATGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * *
1155581 TGCACACTTAGTGTCGATACGGTCGTTCATAAACACATTATGATTTCTGTGGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * * *
1155635 TACACACTTAGTGCCGATATGGTCGTTCATCAACATATGATGAATTCCGTGAGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* * * * * * *
1155689 TACACACTTAGTGTCAATACAGTCGGTCATCAACATATGATGAATTTCGTAGGT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
* *
1155743 TACACACTTAGTGCCGATA
1 TGCACACTTAGTGTCGATA
1155762 GAAAACATAG
Statistics
Matches: 344, Mismatches: 51, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
53 47 0.14
54 297 0.86
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATGATGAATTCCGTGGGT
Found at i:1155672 original size:162 final size:162
Alignment explanation
Indices: 1155314--1155761 Score: 632
Period size: 162 Copynumber: 2.8 Consensus size: 162
1155304 TTTTGAGGTG
* * * * * * *
1155314 CACACGTAGTGCCGATACGGTCCTTTATAAACATATTATGAATTTCGTGGGCTGCACACTTAGTG
1 CACACTTAGTGCCGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
* * *
1155379 TCGATACAGTCGTTTATCAATATATTATGAATTCCGTGGGTTGCACACTTAGTGT-GATACGGTC
66 TCGATACAGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGGTC
* *
1155443 GTTCATAAATACATTATGAATTTCATGGGTTG
131 GTTCATAAACACATTATGAATTTCATGGGTTA
**
1155475 CACACTTAGTGTTGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
1 CACACTTAGTGCCGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
*
1155540 TCGATAC-GTTCGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGTGTCGATACGGT
66 TCGATACAG-TCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGGT
*
1155604 CGTTCATAAACACATTATG-ATTTCTGTGGGTTA
130 CGTTCATAAACACATTATGAATTTC-ATGGGTTA
* * *
1155637 CACACTTAGTGCCGATATGGTCGTTCATCAACATATGATGAATTCCGTGAGTTACACACTTAGTG
1 CACACTTAGTGCCGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
* * * * * *
1155702 TCAATACAGTCGGTCATCAACATATGATGAATTTCGTAGGTTACACACTTAGTGCCGATA
66 TCGATACAGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTCGATA
1155762 GAAAACATAG
Statistics
Matches: 255, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
160 1 0.00
161 110 0.43
162 143 0.56
163 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (162 bp):
CACACTTAGTGCCGATATGGTCGTTCATAAACATATGATGAATTCCGTGGGTTGCACACTTAGTG
TCGATACAGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTCGATACGGTC
GTTCATAAACACATTATGAATTTCATGGGTTA
Found at i:1157544 original size:9 final size:10
Alignment explanation
Indices: 1157528--1157553 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1157518 TTATGCCTTT
1157528 GTTTTTTTGA
1 GTTTTTTTGA
1157538 GTTTTTTTGA
1 GTTTTTTTGA
1157548 GTTTTT
1 GTTTTT
1157554 GACTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.19, T:0.73
Consensus pattern (10 bp):
GTTTTTTTGA
Found at i:1160212 original size:29 final size:30
Alignment explanation
Indices: 1160147--1160219 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
1160137 CTATGACTCT
* * * *
1160147 CATTCTAAATTAATCCTTAAATTTTTTGAA
1 CATTCTAATTTTATCCCTAAACTTTTTGAA
*
1160177 CATTCTATTTTTATCCCTAAACTTTTT-AA
1 CATTCTAATTTTATCCCTAAACTTTTTGAA
*
1160206 TATTCTAATTTTAT
1 CATTCTAATTTTAT
1160220 TCCCAAATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.32, C:0.15, G:0.01, T:0.52
Consensus pattern (30 bp):
CATTCTAATTTTATCCCTAAACTTTTTGAA
Found at i:1161313 original size:19 final size:20
Alignment explanation
Indices: 1161274--1161313 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1161264 TATATTTTTT
*
1161274 ATTAAGATTTCATTTTATTA
1 ATTAAGATTTCATTATATTA
*
1161294 ATTAATATTT-ATTATATTA
1 ATTAAGATTTCATTATATTA
1161313 A
1 A
1161314 ATATACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTAAGATTTCATTATATTA
Found at i:1162550 original size:2 final size:2
Alignment explanation
Indices: 1162543--1162574 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1162533 TCCTTCAGTG
*
1162543 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1162575 AAGAGAGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1171485 original size:20 final size:20
Alignment explanation
Indices: 1171460--1171498 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1171450 AATAATGAAA
1171460 AGATAATTCATAAAAATAAG
1 AGATAATTCATAAAAATAAG
* *
1171480 AGATAATTCCTAAAGATAA
1 AGATAATTCATAAAAATAA
1171499 TTATTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (20 bp):
AGATAATTCATAAAAATAAG
Found at i:1172556 original size:13 final size:13
Alignment explanation
Indices: 1172540--1172564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1172530 AAACAAATAT
1172540 AATAAACGAACAC
1 AATAAACGAACAC
1172553 AATAAACGAACA
1 AATAAACGAACA
1172565 ACACAAACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAACGAACAC
Found at i:1180803 original size:25 final size:26
Alignment explanation
Indices: 1180769--1180824 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
1180759 TTTTAAATTT
1180769 CAATACTGATTCAAATAAT-AAATAAA
1 CAATACTGATT-AAATAATAAAATAAA
*
1180795 CAATA-TGATTAAATTATAAAATAAA
1 CAATACTGATTAAATAATAAAATAAA
*
1180820 AAATA
1 CAATA
1180825 AATTTATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 6 0.22
25 16 0.59
26 5 0.19
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.29
Consensus pattern (26 bp):
CAATACTGATTAAATAATAAAATAAA
Found at i:1191006 original size:111 final size:111
Alignment explanation
Indices: 1190799--1191017 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 111
1190789 GATTGAAAGT
1190799 AAATTATAGGACAATTTTGGGACATGTAGGACTTTATCAAAGGAGAAATTTTCTACTAATTTAAC
1 AAATTATAGGACAATTTTGGGACATGTAGGACTTTATCAAAGGAGAAATTTTCTACTAATTTAAC
*
1190864 TCTTCCAATTCCATCACCAGTGAGTAAGATCCATCAGCTATGCGGA
66 TCTTCCAATTCCATCACCAGTGAGAAAGATCCATCAGCTATGCGGA
* * ** * * *
1190910 AAATTATAGGATAATTTTGGGACTTGTAGGACTTTATCAGTGGAGAAATTTTTTGCTAATTTTAC
1 AAATTATAGGACAATTTTGGGACATGTAGGACTTTATCAAAGGAGAAATTTTCTACTAATTTAAC
1190975 TCTTCCAATTCCATCCACCAGT-A-AAAGGATCCATCAGCTATGC
66 TCTTCCAATTCCAT-CACCAGTGAGAAA-GATCCATCAGCTATGC
1191018 AGATTCGGGA
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
110 2 0.02
111 89 0.91
112 7 0.07
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (111 bp):
AAATTATAGGACAATTTTGGGACATGTAGGACTTTATCAAAGGAGAAATTTTCTACTAATTTAAC
TCTTCCAATTCCATCACCAGTGAGAAAGATCCATCAGCTATGCGGA
Found at i:1206026 original size:36 final size:36
Alignment explanation
Indices: 1205979--1206051 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1205969 CAACAATGGG
* *
1205979 AGCCACATTAGCAACCTCCTCTCTACTCTTGGCCAC
1 AGCCACATTAGCAAACTCCACTCTACTCTTGGCCAC
1206015 AGCCACATTAGCAAACTCCACTCTACTCTTGGCCAC
1 AGCCACATTAGCAAACTCCACTCTACTCTTGGCCAC
1206051 A
1 A
1206052 TCTGGTTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.23
Consensus pattern (36 bp):
AGCCACATTAGCAAACTCCACTCTACTCTTGGCCAC
Found at i:1212605 original size:110 final size:109
Alignment explanation
Indices: 1212451--1212679 Score: 381
Period size: 110 Copynumber: 2.1 Consensus size: 109
1212441 ATATAACACT
* *
1212451 AATTTATTTTATTAGATAAAAAAAGTAATCATTTTATTTTTTTCAAAATTATTATTTTTAAATAT
1 AATTTATTTTATTACATAAAAAAAGTAATCATTTTATTTGTTTCAAAATTATTATTTTTAAATAT
*
1212516 TTTAAAAAA-TTTGAAATTTATCCAATAAAAAAAAACATAAAATG
66 TTTAAAAAATTTTGAAATTTATCCAAT-AAAAAAAACATAAAATA
1212560 AATTTATTTTATTACATAAAAAAAAGTAATCATTTT-TATTGTTTCAAAATTATTATTTTTAAAT
1 AATTTATTTTATTACAT-AAAAAAAGTAATCATTTTAT-TTGTTTCAAAATTATTATTTTTAAAT
*
1212624 ATTTTAAAAAATTTTGAAATTTATCCAATATAAAAAACATAAAATA
64 ATTTTAAAAAATTTTGAAATTTATCCAATAAAAAAAACATAAAATA
1212670 AATTTATTTT
1 AATTTATTTT
1212680 CAAAGTAAAA
Statistics
Matches: 113, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
109 17 0.15
110 79 0.70
111 17 0.15
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (109 bp):
AATTTATTTTATTACATAAAAAAAGTAATCATTTTATTTGTTTCAAAATTATTATTTTTAAATAT
TTTAAAAAATTTTGAAATTTATCCAATAAAAAAAACATAAAATA
Found at i:1213598 original size:34 final size:34
Alignment explanation
Indices: 1213555--1213622 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1213545 GTCGCCCTTG
* *
1213555 TTCTAGTCATTGCCATTTGAAGTATCTGGAGATT
1 TTCTAGTCATTGCCATTCGAAGCATCTGGAGATT
*
1213589 TTCTAGTCATTGCCATTCGAAGCATTTGGAGATT
1 TTCTAGTCATTGCCATTCGAAGCATCTGGAGATT
1213623 GATCCACTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (34 bp):
TTCTAGTCATTGCCATTCGAAGCATCTGGAGATT
Found at i:1214298 original size:178 final size:181
Alignment explanation
Indices: 1214043--1214369 Score: 511
Period size: 178 Copynumber: 1.8 Consensus size: 181
1214033 CCAGATGAAT
*
1214043 ATTTAGGAGTTCCGAACTCCAAGAACTATGAATGGATAGTTCAGAGAGAACTAAAAAAACTCCCA
1 ATTTAGGAGTTCCGAACTCCAAGAACCATGAATGGATAGTTCAGAGAGAACT-AAAAAACTCCCA
** * * *
1214108 TTTTTAATATAAGCATCACTCAGATTCTCTTTACCCACCATAATTGGGCAAGAGTGAAGTAATA-
65 ACTTTAATATAAGCATCACTCAGATCCTCTTTACCCACCATAACTGGGCAAGAGTGAAATAATAG
1214172 CCGATGCTAAAAAAATGCGGTCAAATAAAACAACTATATCTATATTCAAGAA
130 CCGATGCTAAAAAAATGCGGTCAAATAAAACAACTATATCTATATTCAAGAA
*
1214224 ATTTAGGAGTTCCCGAACTCC-AGAACCATGAAT-GA-AGATTCAGAGAGAACT-AAAAACTCCG
1 ATTTAGGAGTT-CCGAACTCCAAGAACCATGAATGGATAG-TTCAGAGAGAACTAAAAAACTCCC
*
1214285 AACTTTAATATAAGCATCATTCAGATCCTCTTTACCCACCATAACTGGGCAAGAGTGAAATAATA
64 AACTTTAATATAAGCATCACTCAGATCCTCTTTACCCACCATAACTGGGCAAGAGTGAAATAATA
*
1214350 GCCGATGCTAAAAAATTGCG
129 GCCGATGCTAAAAAAATGCG
1214370 CTAAAATGAA
Statistics
Matches: 134, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
178 68 0.51
179 20 0.15
180 15 0.11
181 22 0.16
182 9 0.07
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (181 bp):
ATTTAGGAGTTCCGAACTCCAAGAACCATGAATGGATAGTTCAGAGAGAACTAAAAAACTCCCAA
CTTTAATATAAGCATCACTCAGATCCTCTTTACCCACCATAACTGGGCAAGAGTGAAATAATAGC
CGATGCTAAAAAAATGCGGTCAAATAAAACAACTATATCTATATTCAAGAA
Found at i:1231740 original size:21 final size:22
Alignment explanation
Indices: 1231700--1231741 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1231690 AAACATTTAT
* *
1231700 TTTATTATTACTATAAATCGTA
1 TTTAATATTACTAAAAATCGTA
1231722 TTTAATATTAC-AAAAATCGT
1 TTTAATATTACTAAAAATCGT
1231742 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTAATATTACTAAAAATCGTA
Found at i:1237276 original size:15 final size:15
Alignment explanation
Indices: 1237256--1237290 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1237246 TGTTCATCAT
*
1237256 TCGAACAAACTCTAC
1 TCGAACAAACACTAC
*
1237271 TCGAACAAGCACTAC
1 TCGAACAAACACTAC
1237286 TCGAA
1 TCGAA
1237291 GAGCCTCGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.17
Consensus pattern (15 bp):
TCGAACAAACACTAC
Found at i:1239022 original size:19 final size:19
Alignment explanation
Indices: 1238994--1239048 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1238984 GATCGGGTTA
*
1238994 GACCGCTCAAACCGGTTCG
1 GACCGGTCAAACCGGTTCG
*
1239013 GACCGGTCAAACCAGTTCG
1 GACCGGTCAAACCGGTTCG
*
1239032 AACCGGTCGAAACCGGT
1 GACCGGTC-AAACCGGT
1239049 CATAACCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 24 0.77
20 7 0.23
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.15
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCG
Found at i:1239035 original size:29 final size:31
Alignment explanation
Indices: 1239002--1239077 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
1238992 TAGACCGCTC
*
1239002 AAACCGGTTCG-GACCGGTCA-AACCAGTTCG
1 AAACCGGTTCGAAACCGGTCATAACCAG-TCG
1239032 -AACCGG-TCGAAACCGGTCATAACCAGTCG
1 AAACCGGTTCGAAACCGGTCATAACCAGTCG
1239061 AAACCGG-TC-AAACCGGT
1 AAACCGGTTCGAAACCGGT
1239078 TTCCAGCCCT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 3 0.07
29 25 0.60
30 14 0.33
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.14
Consensus pattern (31 bp):
AAACCGGTTCGAAACCGGTCATAACCAGTCG
Found at i:1239045 original size:10 final size:9
Alignment explanation
Indices: 1238995--1239077 Score: 67
Period size: 10 Copynumber: 8.7 Consensus size: 9
1238985 ATCGGGTTAG
*
1238995 ACCGCTCAA
1 ACCGGTCAA
**
1239004 ACCGGTTCGG
1 ACCGG-TCAA
1239014 ACCGGTCAA
1 ACCGGTCAA
* *
1239023 ACCAGTTCGA
1 ACC-GGTCAA
1239033 ACCGGTCGAA
1 ACCGGTC-AA
1239043 ACCGGTCATA
1 ACCGGTCA-A
*
1239053 ACCAGTCGAA
1 ACCGGTC-AA
1239063 ACCGGTCAA
1 ACCGGTCAA
1239072 ACCGGT
1 ACCGGT
1239078 TTCCAGCCCT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.36
10 36 0.62
11 1 0.02
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1239055 original size:20 final size:19
Alignment explanation
Indices: 1239014--1239077 Score: 76
Period size: 20 Copynumber: 3.3 Consensus size: 19
1239004 ACCGGTTCGG
* *
1239014 ACCGGTC-AAACCAGTTCGA
1 ACCGGTCGAAACC-GGTCAA
1239033 ACCGGTCGAAACCGGTCATA
1 ACCGGTCGAAACCGGTCA-A
*
1239053 ACCAGTCGAAACCGGTCAA
1 ACCGGTCGAAACCGGTCAA
1239072 ACCGGT
1 ACCGGT
1239078 TTCCAGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 16 0.41
20 23 0.59
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.14
Consensus pattern (19 bp):
ACCGGTCGAAACCGGTCAA
Found at i:1246250 original size:9 final size:9
Alignment explanation
Indices: 1246238--1246307 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
1246228 AGTCGGATCG
*
1246238 GGTCAGACC
1 GGTCAAACC
1246247 GGTCAAACC
1 GGTCAAACC
*
1246256 GGTTCGAACC
1 GG-TCAAACC
**
1246266 AATCAAACC
1 GGTCAAACC
1246275 GGTCATAACC
1 GGTCA-AACC
*
1246285 GGTTGAACACC
1 GG-TCAA-ACC
1246296 GGTCAAACC
1 GGTCAAACC
1246305 GGT
1 GGT
1246308 TTCCAGCCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 25 0.52
10 16 0.33
11 7 0.15
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1247665 original size:2 final size:2
Alignment explanation
Indices: 1247658--1247754 Score: 64
Period size: 2 Copynumber: 52.0 Consensus size: 2
1247648 AAATAATTAT
* * * * *
1247658 TA TA TA TA TA TA TA TA AA TA T- TA -A TA AA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1247697 T- TA -A TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1247735 TT TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1247755 CCCGGCCCGA
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
1 7 0.10
2 63 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1271650 original size:6 final size:6
Alignment explanation
Indices: 1271639--1271664 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1271629 GCAATAGGTA
1271639 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
1271665 AAAAAACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:1274533 original size:17 final size:18
Alignment explanation
Indices: 1274511--1274572 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 18
1274501 ATTGTTCGAC
1274511 TTGTTTTTATTA-TTTAG
1 TTGTTTTTATTATTTTAG
1274528 TTGTTTTTATTATTTTAG
1 TTGTTTTTATTATTTTAG
*
1274546 TTGTATCGTTTTATTTTTTTAG
1 TTG--T--TTTTATTATTTTAG
1274568 TTGTT
1 TTGTT
1274573 CGAATTGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 12 0.31
18 9 0.23
20 2 0.05
22 16 0.41
ACGTcount: A:0.15, C:0.02, G:0.13, T:0.71
Consensus pattern (18 bp):
TTGTTTTTATTATTTTAG
Found at i:1274543 original size:26 final size:25
Alignment explanation
Indices: 1274466--1274588 Score: 65
Period size: 26 Copynumber: 4.8 Consensus size: 25
1274456 TATGGACTTT
*
1274466 TTATTTATCTTGTTTCTTAATTTTTTTA
1 TTATTTA-ATTGTTT-TT-ATTTTTTTA
**
1274494 TTATTTAATTG-TTCGACTTGTTTTTA
1 TTATTTAATTGTTTTTA-TT-TTTTTA
* *
1274520 TTATTTAGTTGTTTTTATTATTTTA
1 TTATTTAATTGTTTTTATTTTTTTA
* * *
1274545 GT-TGT-ATCG-TTTTATTTTTTTA
1 TTATTTAATTGTTTTTATTTTTTTA
* *
1274567 GTTGTTCGAATTGTTTTTATTT
1 -TTATT-TAATTGTTTTTATTT
1274589 AATTCTTAAG
Statistics
Matches: 71, Mismatches: 16, Indels: 17
0.68 0.15 0.16
Matches are distributed among these distances:
22 12 0.17
23 3 0.04
24 4 0.06
25 8 0.11
26 23 0.32
27 14 0.20
28 7 0.10
ACGTcount: A:0.17, C:0.05, G:0.11, T:0.67
Consensus pattern (25 bp):
TTATTTAATTGTTTTTATTTTTTTA
Found at i:1274583 original size:21 final size:22
Alignment explanation
Indices: 1274534--1274584 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1274524 TTAGTTGTTT
* **
1274534 TTATTATTTTAGTTGTATCGTT
1 TTATTTTTTTAGTTGTATCGAA
1274556 TTATTTTTTTAGTTGT-TCGAA
1 TTATTTTTTTAGTTGTATCGAA
*
1274577 TTGTTTTT
1 TTATTTTT
1274585 ATTTAATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.67
Consensus pattern (22 bp):
TTATTTTTTTAGTTGTATCGAA
Found at i:1279418 original size:29 final size:28
Alignment explanation
Indices: 1279369--1279426 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1279359 AGAAAAAAGT
*
1279369 ATTTGAAAATATTAACCGAACCAAATTA
1 ATTTAAAAATATTAACCGAACCAAATTA
* *
1279397 ATTTAAAAATTATTAACTGAACCGAATTA
1 ATTTAAAAA-TATTAACCGAACCAAATTA
1279426 A
1 A
1279427 CTAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (28 bp):
ATTTAAAAATATTAACCGAACCAAATTA
Found at i:1279435 original size:137 final size:137
Alignment explanation
Indices: 1279266--1279577 Score: 375
Period size: 137 Copynumber: 2.3 Consensus size: 137
1279256 AATACGATTG
* * * * **
1279266 AAAATTATTAACCAACTGAATTAACCGATTTTTTTTTAAAAAATTTAATTGAATTAATCGAAGC-
1 AAAATTATTAACGAACCGAATTAA-CTAATTTTTTTTAAAAAA-TTAATCAAATTAATCGAAGCA
1279330 AAAATTCGGTTTAATTCAGTTCGGTTAATAGAA-AAAA-GTATTTGAAAA-TATTAACCGAACCA
64 AAAATTCGG-TTAATTCAGTTCGGTTAATAGAACAAAATGTATTTGAAAATTATTAACCGAACCA
1279392 AATTAATTTA
128 AATTAATTTA
**
1279402 AAAATTATTAACTGAACCGAATTAACTAA--TTTTTTAAATTATTAATCAAATTAATCGAAGCAA
1 AAAATTATTAAC-GAACCGAATTAACTAATTTTTTTTAAAAAATTAATCAAATTAATCGAAGCAA
* * * * * *
1279465 AAATTTGGTTAATTCAGTTTGGTTAATCGAACTAAAATTTATTTGAAAATTATTAACTGAACCGA
65 AAATTCGGTTAATTCAGTTCGGTTAATAGAAC-AAAATGTATTTGAAAATTATTAACCGAACCAA
*
1279530 ATTAATTTG
129 ATTAATTTA
* *
1279539 AAAATTATTAACCGAATCGAATTAACTAAATTTTTTTAA
1 AAAATTATTAA-CGAACCGAATTAACTAATTTTTTTTAA
1279578 CCATTAATCG
Statistics
Matches: 151, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
133 39 0.26
134 18 0.12
135 4 0.03
136 24 0.16
137 57 0.38
138 1 0.01
139 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (137 bp):
AAAATTATTAACGAACCGAATTAACTAATTTTTTTTAAAAAATTAATCAAATTAATCGAAGCAAA
AATTCGGTTAATTCAGTTCGGTTAATAGAACAAAATGTATTTGAAAATTATTAACCGAACCAAAT
TAATTTA
Found at i:1279542 original size:29 final size:29
Alignment explanation
Indices: 1279500--1279563 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1279490 ATCGAACTAA
* *
1279500 AATTTATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
1279529 AATTAATTTGAAAATTATTAACCGAATCG
1 AATTAATTTGAAAATTATTAACCGAACCG
1279558 AATTAA
1 AATTAA
1279564 CTAAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:1285072 original size:122 final size:122
Alignment explanation
Indices: 1284773--1285212 Score: 627
Period size: 122 Copynumber: 3.6 Consensus size: 122
1284763 ATTTAAAAAA
* * *
1284773 ATTAATTCAATTAT-AGTAATTGATTCCCTAAACACAACTAGGGAGTTACTTTATTCATTAATTA
1 ATTATTTCAATTATAAG-AAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTA
* * **
1284837 AAAATAAACAAATTGTATCATATTTTTTTTAAAAAAAAAT-TATAAAGATATAGAAATGTCAAT
65 AAAATAAACAAATTGTGTCATA----TTTTAAAAAAAATTGTA-AAAG-TATAGAAATACCAAT
1284900 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
*
1284965 AAATAAAGAAATTGTGTCATATTTTAAAAAAAATTGTAAAAGTATAGAAATACCAAT
66 AAATAAACAAATTGTGTCATATTTTAAAAAAAATTGTAAAAGTATAGAAATACCAAT
* * * *
1285022 ATTATTTCAATGATAAGAAATGATTTCCTAAACACAGCTACGGAGTTACTTTCTTCATTAATTAA
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
***
1285087 AAATAAACAAATTGTGTCATATTTT--TTTAAATTGTAAAAGTATAGAAATACCAAT
66 AAATAAACAAATTGTGTCATATTTTAAAAAAAATTGTAAAAGTATAGAAATACCAAT
* * *
1285142 ATTATTTCAATTATAAGAAATGATTCCCTAAACATAGCTAGGGAGTTACTTTCTTCATTAATTAG
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
1285207 AAATAA
66 AAATAA
1285213 TAATAGACAT
Statistics
Matches: 290, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
120 93 0.32
122 98 0.34
123 17 0.06
124 2 0.01
127 78 0.27
128 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (122 bp):
ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
AAATAAACAAATTGTGTCATATTTTAAAAAAAATTGTAAAAGTATAGAAATACCAAT
Found at i:1285233 original size:120 final size:118
Alignment explanation
Indices: 1284773--1285212 Score: 551
Period size: 120 Copynumber: 3.6 Consensus size: 118
1284763 ATTTAAAAAA
* * * *
1284773 ATTAATTCAATTAT-AGTAATTGATTCCCTAAACACAACTAGGGAGTTACTTTATTCATTAATTA
1 ATTATTTCAATTATAAG-AAATGATTCCCTAAACACAGCTAGGGAGTTACTTTCTTCATTAATTA
* * * **
1284837 AAAATAAACAAATTGTATCATATTTTTTTTAAAAAAAAAT-TATAAAGATATAGAAATGTCAAT
65 AAAATAAAGAAATTGTGTC--A--TTTTTT----AAAATTGTA-AAAG-TATAGAAATACCAAT
*
1284900 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAACTAGGGAGTTACTTTCTTCATTAATTAA
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAGCTAGGGAGTTACTTTCTTCATTAATTAA
*
1284965 AAATAAAGAAATTGTGTCATATTTTAAAAAAAATTGTAAAAGTATAGAAATACCAAT
66 AAATAAAGAAATTGTGTCAT-TTTT---TAAAATTGTAAAAGTATAGAAATACCAAT
* * *
1285022 ATTATTTCAATGATAAGAAATGATTTCCTAAACACAGCTACGGAGTTACTTTCTTCATTAATTAA
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAGCTAGGGAGTTACTTTCTTCATTAATTAA
* *
1285087 AAATAAACAAATTGTGTCATATTTTTTTAAATTGTAAAAGTATAGAAATACCAAT
66 AAATAAAGAAATTGTGTC--ATTTTTTAAAATTGTAAAAGTATAGAAATACCAAT
* *
1285142 ATTATTTCAATTATAAGAAATGATTCCCTAAACATAGCTAGGGAGTTACTTTCTTCATTAATTAG
1 ATTATTTCAATTATAAGAAATGATTCCCTAAACACAGCTAGGGAGTTACTTTCTTCATTAATTAA
1285207 AAATAA
66 AAATAA
1285213 TAATAGACAT
Statistics
Matches: 284, Mismatches: 21, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
120 93 0.33
122 91 0.32
123 14 0.05
124 8 0.03
125 1 0.00
127 75 0.26
128 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (118 bp):
ATTATTTCAATTATAAGAAATGATTCCCTAAACACAGCTAGGGAGTTACTTTCTTCATTAATTAA
AAATAAAGAAATTGTGTCATTTTTTAAAATTGTAAAAGTATAGAAATACCAAT
Found at i:1285941 original size:4 final size:4
Alignment explanation
Indices: 1285932--1285957 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1285922 AAGAGATGAG
1285932 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
1285958 AATTAAAATG
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1290331 original size:16 final size:16
Alignment explanation
Indices: 1290310--1290342 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1290300 CCCATTTATC
1290310 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1290326 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1290342 A
1 A
1290343 AAACACTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:1292654 original size:21 final size:23
Alignment explanation
Indices: 1292603--1292654 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1292593 GATTCCCCTG
1292603 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
1292626 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
1292647 TGGGGGGA
1 TGGGGGGA
1292655 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:1301831 original size:5 final size:5
Alignment explanation
Indices: 1301821--1301848 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1301811 TTAATATTAT
1301821 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
1301849 ATAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:1302060 original size:20 final size:20
Alignment explanation
Indices: 1302035--1302072 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1302025 TTTGGTTCAC
*
1302035 GGAATATAAGATTATCAGTG
1 GGAATAAAAGATTATCAGTG
1302055 GGAATAAAAGATTATCAG
1 GGAATAAAAGATTATCAG
1302073 ATAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (20 bp):
GGAATAAAAGATTATCAGTG
Found at i:1306033 original size:31 final size:30
Alignment explanation
Indices: 1305997--1306073 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
1305987 TATCACACTT
1305997 AAAATAACCTGACCCGAACCCAAAATTTTTA
1 AAAATAACC-GACCCGAACCCAAAATTTTTA
* * *
1306028 AAAATATCCGACCCGATCCCAAAA-TTTAA
1 AAAATAACCGACCCGAACCCAAAATTTTTA
* *
1306057 AAAAAAAACGACCCGAA
1 AAAATAACCGACCCGAA
1306074 TACTAAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 17 0.44
30 14 0.36
31 8 0.21
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.17
Consensus pattern (30 bp):
AAAATAACCGACCCGAACCCAAAATTTTTA
Found at i:1306041 original size:30 final size:31
Alignment explanation
Indices: 1305997--1306054 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1305987 TATCACACTT
1305997 AAAATAACCTGACCCGAACCCAAAATTTTTA
1 AAAATAACCTGACCCGAACCCAAAATTTTTA
* *
1306028 AAAATATCC-GACCCGATCCCAAAATTT
1 AAAATAACCTGACCCGAACCCAAAATTT
1306055 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (31 bp):
AAAATAACCTGACCCGAACCCAAAATTTTTA
Found at i:1306061 original size:30 final size:31
Alignment explanation
Indices: 1305997--1306073 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 31
1305987 TATCACACTT
**
1305997 AAAATAACCTGACCCGAACCCAAAATTTTTA
1 AAAATAACCTGACCCGAACCCAAAATTTAAA
* *
1306028 AAAATATCC-GACCCGATCCCAAAATTTAAA
1 AAAATAACCTGACCCGAACCCAAAATTTAAA
*
1306058 AAAA-AAAC-GACCCGAA
1 AAAATAACCTGACCCGAA
1306074 TACTAAAAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 9 0.23
30 22 0.56
31 8 0.21
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.17
Consensus pattern (31 bp):
AAAATAACCTGACCCGAACCCAAAATTTAAA
Found at i:1306630 original size:12 final size:12
Alignment explanation
Indices: 1306620--1306666 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
1306610 AAGTCCGCCT
*
1306620 CCTCCTCCGCCG
1 CCTCCTCCTCCG
*
1306632 CCTCCGCCTCCG
1 CCTCCTCCTCCG
* *
1306644 CCTCCACCTCCA
1 CCTCCTCCTCCG
1306656 CCTCCTCCTCC
1 CCTCCTCCTCC
1306667 CCCACCACCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.04, C:0.68, G:0.09, T:0.19
Consensus pattern (12 bp):
CCTCCTCCTCCG
Found at i:1306634 original size:15 final size:15
Alignment explanation
Indices: 1306614--1306645 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1306604 TAACACAAGT
*
1306614 CCGCCTCCTCCTCCG
1 CCGCCTCCGCCTCCG
1306629 CCGCCTCCGCCTCCG
1 CCGCCTCCGCCTCCG
1306644 CC
1 CC
1306646 TCCACCTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.69, G:0.16, T:0.16
Consensus pattern (15 bp):
CCGCCTCCGCCTCCG
Found at i:1306638 original size:6 final size:6
Alignment explanation
Indices: 1306613--1306666 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1306603 CTAACACAAG
* * *
1306613 TCCGCC TCCTCC TCCG-- -CCGCC TCCGCC TCCGCC TCCACC TCCACC
1 TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC
*
1306658 TCCTCC TCC
1 TCCGCC TCC
1306667 CCCACCACCG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.07
6 38 0.93
ACGTcount: A:0.04, C:0.67, G:0.09, T:0.20
Consensus pattern (6 bp):
TCCGCC
Found at i:1312857 original size:101 final size:102
Alignment explanation
Indices: 1312684--1312991 Score: 331
Period size: 101 Copynumber: 3.0 Consensus size: 102
1312674 CTGTCTCAGC
**
1312684 TGAGATAAAATTTTGTTTTGAGTGAAACAATTTCAAAATTTGCGTTTCAAGGGAAAACTATCTCA
1 TGAGATAAAATTTTGTTTCAAGTGAAACAATTTCAAAATTT-CGTTTCAAGGGAAAACTATCTCA
* *
1312749 AGCGAGAC-ATAATTTATTTTTAGGAAAACAATCTCAAG
65 AGCGAGACGA-AATTTAGTTTTAGGAAAACAATCTCAAA
* * * *
1312787 TGAGAT-AAATTTTGTTTCAAGTGAAACATTTTCACAATTAT-GTTTCAAGGGAAAATTGTCTCA
1 TGAGATAAAATTTTGTTTCAAGTGAAACAATTTCAAAATT-TCGTTTCAAGGGAAAACTATCTCA
* *
1312850 AGTGAGACGAAATTTGGTTTTAGGAAAACAATCTCAAA
65 AGCGAGACGAAATTTAGTTTTAGGAAAACAATCTCAAA
* * * * * *
1312888 TGAGATCAATTTCTTGTTTCAAGTGAAACAACTTT-GAAATTTGGGCTTCAAGGG-AAACTGTCT
1 TGAGATAAAATT-TTGTTTCAAGTGAAACAA-TTTCAAAATTT-CGTTTCAAGGGAAAACTATCT
* * *
1312951 CAAGCGAGATGAAACTTT-GTTTCAAGAGAAACAATCTCAAA
63 CAAGCGAGACGAAA-TTTAGTTTTAGGA-AAACAATCTCAAA
1312992 GGTTTATATT
Statistics
Matches: 176, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
101 58 0.33
102 35 0.20
103 55 0.31
104 28 0.16
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (102 bp):
TGAGATAAAATTTTGTTTCAAGTGAAACAATTTCAAAATTTCGTTTCAAGGGAAAACTATCTCAA
GCGAGACGAAATTTAGTTTTAGGAAAACAATCTCAAA
Found at i:1313006 original size:30 final size:30
Alignment explanation
Indices: 1312968--1313144 Score: 106
Period size: 30 Copynumber: 5.5 Consensus size: 30
1312958 GATGAAACTT
1312968 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* * *** *
1312998 TATTTCAAGATAAATTGTCTCAAGCAAGACGAAATT-
1 TGTTTCAAGAGAAACAATCTC-A--AAG--G--TTTA
1313034 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* * * **
1313064 TGTTTCAAAAGAAACTATTTCAAGCGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG----GTTTA
*
1313100 TGTTTCAAGAGAAACAATCTCAAAGTTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1313130 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1313145 TGTCTCAATC
Statistics
Matches: 109, Mismatches: 22, Indels: 32
0.67 0.13 0.20
Matches are distributed among these distances:
29 4 0.04
30 51 0.47
31 2 0.02
33 10 0.09
35 2 0.02
36 36 0.33
37 4 0.04
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:1313055 original size:36 final size:36
Alignment explanation
Indices: 1313015--1313122 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
1313005 AGATAAATTG
1313015 TCTCAAGCAAGACGAAATTTGTTTCAAGAGAAACAA
1 TCTCAAGCAAGACGAAATTTGTTTCAAGAGAAACAA
* * *
1313051 TCTC-A--AAG--G--TTTATGTTTCAAAAGAAACTA
1 TCTCAAGCAAGACGAAATT-TGTTTCAAGAGAAACAA
* * *
1313081 TTTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAA
1 TCTCAAGCAAGACGAAATTTGTTTCAAGAGAAACAA
1313117 TCTCAA
1 TCTCAA
1313123 AGTTTTATGT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
29 2 0.04
30 18 0.33
31 2 0.04
33 5 0.09
35 1 0.02
36 24 0.44
37 2 0.04
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.27
Consensus pattern (36 bp):
TCTCAAGCAAGACGAAATTTGTTTCAAGAGAAACAA
Found at i:1313170 original size:36 final size:36
Alignment explanation
Indices: 1313064--1313198 Score: 122
Period size: 36 Copynumber: 3.9 Consensus size: 36
1313054 CAAAGGTTTA
* *
1313064 TGTTTCAAAAGAAACTATTTCAAGCGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* **
1313100 TGTTTCAAGAGAAACAATCTCAA---AG----TTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* *
1313129 ATGTTTCAAGAGAAACTGTCTCAATCGAGACAAAATT
1 -TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* * *
1313166 TGTTTCAAGAGAAAATGTCTCAAGGGAGACAAA
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAA
1313199 CAATCTATTC
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
29 2 0.03
30 21 0.27
33 4 0.05
36 50 0.63
37 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
Found at i:1313188 original size:66 final size:66
Alignment explanation
Indices: 1312934--1313179 Score: 366
Period size: 66 Copynumber: 3.7 Consensus size: 66
1312924 AAATTTGGGC
* * *
1312934 TTCAAGGGAAACTGTCTCAAGCGAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGA-CAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
*
1312999 AT
65 GT
* * * *
1313001 TTCAAGATAAATTGTCTCAAGCAAGACGAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATG
1 TTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATG
1313066 T
66 T
* * * *
1313067 TTCAAAAGAAACTATTTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGTTTTATG
1 TTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATG
1313132 T
66 T
*
1313133 TTCAAGAGAAACTGTCTCAATCGAGACAAAATTTGTTTCAAGAGAAA
1 TTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAA
1313180 ATGTCTCAAG
Statistics
Matches: 159, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 137 0.86
67 22 0.14
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (66 bp):
TTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATG
T
Found at i:1314145 original size:65 final size:65
Alignment explanation
Indices: 1314069--1314221 Score: 182
Period size: 65 Copynumber: 2.4 Consensus size: 65
1314059 CACACCCATT
* * * *
1314069 TCGAATACATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCATTCGTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATACATCGATACACTCGTGAATATTTTGAAAC
1314133 A
65 A
* * ** *
1314134 TCGAATGCATTTTGTGTACCAATGCACAGACCATACATCGATACACTCTTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATACATCGATACACTCGTGAATATTTTGAAACA
* * *
1314199 TCGAATGTAATTAGTGTACCGAT
1 TCGAATGCATTTTGTGTACCGAT
1314222 ACACCCCTAG
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 73 0.99
66 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATACATCGATACACTCGTGAATATTTTGAAACA
Found at i:1320050 original size:23 final size:22
Alignment explanation
Indices: 1320020--1320099 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
1320010 ACACTAGACA
1320020 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* *
1320043 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
* *
1320063 GATGCACCAATGCATTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
1320087 GTGCATCGATGCA
1 GTGCATCGATGCA
1320100 CTCTGCTGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 1 0.02
23 28 0.62
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1334740 original size:65 final size:65
Alignment explanation
Indices: 1334652--1334808 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
1334642 CACACCTATT
*
1334652 TCGAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATACACTCTTGAATATTTTGAAAC
1334716 A
65 A
* * ** *
1334717 TCGAATGCATTTTTTGTATCGATGCACAGACCATGCATCGATACACTCTTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATACACTCTTGAATATTTTGAAACA
* * * * *
1334782 TTGAATGTAATTAGTGTAGCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
1334809 CCTAGTGTAC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 78 0.99
66 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATACACTCTTGAATATTTTGAAACA
Found at i:1339975 original size:15 final size:16
Alignment explanation
Indices: 1339955--1339988 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1339945 AACCTTTAAA
1339955 TCAAAACTTTC-TTTT
1 TCAAAACTTTCATTTT
*
1339970 TCAAAATTTTCATTTT
1 TCAAAACTTTCATTTT
1339986 TCA
1 TCA
1339989 TTTTTTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (16 bp):
TCAAAACTTTCATTTT
Found at i:1340046 original size:21 final size:20
Alignment explanation
Indices: 1340009--1340048 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1339999 CTCTAAATCG
**
1340009 TTTTTCAAAATTTCTTTTTT
1 TTTTTCAAAATAACTTTTTT
1340029 TTTTTCAAAATCAACTTTTT
1 TTTTTCAAAAT-AACTTTTT
1340049 CTTTCAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTCAAAATAACTTTTTT
Found at i:1340737 original size:90 final size:90
Alignment explanation
Indices: 1340584--1340764 Score: 319
Period size: 90 Copynumber: 2.0 Consensus size: 90
1340574 CAGAGGTGGA
1340584 AACCATCTTTTCGGTTATGTAGAAAATGGATATAGTTTCTTCAAATATCATCTCAAGGTTGTTAG
1 AACCATCTTTTCGGTTATGTAGAAAATGGATATAGTTTCTTCAAATATCATCTCAAGGTTGTTAG
*
1340649 ACCTTCTAATGAGTCAAACTATGAT
66 ACCTTATAATGAGTCAAACTATGAT
* *
1340674 AACCATCTTTTCGGTTGTGTCA-AAAATGGATATAGTTTCTTCAAATATCGTCTCAAGGTTGTTA
1 AACCATCTTTTCGGTTATGT-AGAAAATGGATATAGTTTCTTCAAATATCATCTCAAGGTTGTTA
1340738 GACCTTATAATGAGTCAAACTATGAT
65 GACCTTATAATGAGTCAAACTATGAT
1340764 A
1 A
1340765 CAAATTGTTG
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
90 86 0.99
91 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (90 bp):
AACCATCTTTTCGGTTATGTAGAAAATGGATATAGTTTCTTCAAATATCATCTCAAGGTTGTTAG
ACCTTATAATGAGTCAAACTATGAT
Found at i:1341159 original size:15 final size:17
Alignment explanation
Indices: 1341133--1341167 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1341123 AACGTCATTT
1341133 AAATCAATTTTAAGA-A
1 AAATCAATTTTAAGACA
1341149 AAATC-ATTTTAAGACA
1 AAATCAATTTTAAGACA
1341165 AAA
1 AAA
1341168 AATGGTCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (17 bp):
AAATCAATTTTAAGACA
Found at i:1343928 original size:41 final size:41
Alignment explanation
Indices: 1343868--1343947 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
1343858 CAAATAACAA
** *
1343868 AAACTTGAACCATAATAATTATGTGAAATATGGATCATACT
1 AAACTTGAACCATAATAATTACATGAAACATGGATCATACT
*
1343909 AAACTTGAACCATAGTAATTACATGAAACATGGATCATA
1 AAACTTGAACCATAATAATTACATGAAACATGGATCATA
1343948 GATTTAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (41 bp):
AAACTTGAACCATAATAATTACATGAAACATGGATCATACT
Found at i:1345851 original size:23 final size:21
Alignment explanation
Indices: 1345813--1345855 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1345803 TTAATTATTT
1345813 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
1345834 AAAAACATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
1345855 A
1 A
1345856 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:1350158 original size:2 final size:2
Alignment explanation
Indices: 1350153--1350183 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1350143 ATAAAAATGC
1350153 TA TA TA 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 TA TA TA T
1350184 GAGGACTAAA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1354010 original size:17 final size:17
Alignment explanation
Indices: 1353988--1354023 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1353978 CAAGGCTTCC
1353988 TTGTAACTATTAGATTT
1 TTGTAACTATTAGATTT
1354005 TTGTAACTATTAGATTT
1 TTGTAACTATTAGATTT
1354022 TT
1 TT
1354024 CTAAAGCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (17 bp):
TTGTAACTATTAGATTT
Found at i:1356110 original size:27 final size:28
Alignment explanation
Indices: 1356080--1356140 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
1356070 AAAGCCCCAT
*
1356080 ACCCCACACCATG-TTGCCCACGTGAAG-
1 ACCCCACACCATGCTT-CCCACATGAAGC
**
1356107 ACCCCATGCCATGCTTCCCACATGAAGC
1 ACCCCACACCATGCTTCCCACATGAAGC
1356135 ACCCCA
1 ACCCCA
1356141 ACTGAGTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.15
Consensus pattern (28 bp):
ACCCCACACCATGCTTCCCACATGAAGC
Found at i:1362700 original size:76 final size:76
Alignment explanation
Indices: 1362607--1362776 Score: 211
Period size: 76 Copynumber: 2.2 Consensus size: 76
1362597 AGGATTTATC
* * *
1362607 TCACTTAAGATTGTTTTTCTTAAAAC-AGAATTTGTCTCACTTGAGATAG-TTTTTACTCGAATC
1 TCACTCAAGATTGTTTTTCTTAAAACAAG-ATTAGTCTCACTTGAGA-AGATTTTTACTCGAAAC
*
1362670 AAGAAGATGT-ATT
64 AAG-ACATGTCATT
* * *
1362683 TCACTCAAGATTGTTTTTCTTAAAACAAGATTAGTCTCGCTTGAGACGATTTTTACTCGAAAGAA
1 TCACTCAAGATTGTTTTTCTTAAAACAAGATTAGTCTCACTTGAGAAGATTTTTACTCGAAACAA
*
1362748 GACATTTCATT
66 GACATGTCATT
*
1362759 TTACTCAAGATTGTTTTT
1 TCACTCAAGATTGTTTTT
1362777 ACAGAAAATT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
75 5 0.06
76 75 0.91
77 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (76 bp):
TCACTCAAGATTGTTTTTCTTAAAACAAGATTAGTCTCACTTGAGAAGATTTTTACTCGAAACAA
GACATGTCATT
Found at i:1362833 original size:39 final size:39
Alignment explanation
Indices: 1362777--1363124 Score: 510
Period size: 39 Copynumber: 9.1 Consensus size: 39
1362767 GATTGTTTTT
* *
1362777 ACAGAAAATTTTGTCTCGCTTGAGATAGTTTCCCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
*
1362816 ACAGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
*
1362855 ACAGAAGATTTTATCTCGCTTGAGGTAGTTTCCCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
* * *
1362894 ACAAAAGATTTTACCTCGCTTGAGATAGTTTCCCTCGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
* *
1362933 ACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
* *
1362972 ACAGAAGATTTTATCTCGTTTGAGATAGTTTCCCTCGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
1363011 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
* * *
1363050 AC--AA-ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
* *
1363086 AC--AAG-TTTTATCTCCCTTGAGATAGTTTCTCTTGAA
1 ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
1363122 ACA
1 ACA
1363125 CAAAACTTTG
Statistics
Matches: 288, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
36 62 0.22
37 2 0.01
39 224 0.78
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.36
Consensus pattern (39 bp):
ACAGAAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAA
Found at i:1363185 original size:15 final size:15
Alignment explanation
Indices: 1363161--1363214 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1363151 AACAAATTTT
1363161 GTTTCCCTTGAGACA
1 GTTTCCCTTGAGACA
* *
1363176 GTTTCTCTTGAAACAA
1 GTTTCCCTTGAGAC-A
1363192 GTTT--C-TGAGACA
1 GTTTCCCTTGAGACA
1363204 GTTTCCCTTGA
1 GTTTCCCTTGA
1363215 AACAAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 2 0.06
15 15 0.47
16 5 0.16
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (15 bp):
GTTTCCCTTGAGACA
Found at i:1363186 original size:36 final size:36
Alignment explanation
Indices: 1363144--1363255 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 36
1363134 GAGAACATTC
* * *
1363144 CCCTTGAAACAAATTTTGTTTCCCTTGAGACAGTTT
1 CCCTTGAAACAAATTTTATCTCCCTTGAGATAGTTT
* * *
1363180 CTCTTGAAAC-AA--GT-T-T--C-TGAGACAGTTT
1 CCCTTGAAACAAATTTTATCTCCCTTGAGATAGTTT
* *
1363208 CCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTT
1 CCCTTGAAAC-AAATTTTATCTCCCTTGAGATAGTTT
*
1363245 CTCTTGAAACA
1 CCCTTGAAACA
1363256 TAAACTTTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
28 20 0.32
29 1 0.02
30 2 0.03
31 1 0.02
32 2 0.03
33 2 0.03
34 1 0.02
35 2 0.03
36 11 0.18
37 20 0.32
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (36 bp):
CCCTTGAAACAAATTTTATCTCCCTTGAGATAGTTT
Found at i:1363239 original size:65 final size:63
Alignment explanation
Indices: 1363066--1363280 Score: 263
Period size: 66 Copynumber: 3.3 Consensus size: 63
1363056 TTTGTCTCTC
* * *
1363066 TTGAGACAGTTTCCCTTGAAACAAGTTTTATCTCCCTTGAGATAGTTTCTCTTGAAACACAAAAC
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-AC-AAAC
1363131 T
63 T
* * **
1363132 TTGAGAACA-TTCCCCTTGAAACAAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACAAGTT
1 TTGAG-ACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAACT
1363195 TCTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 T-TGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC--AAA
1363260 CT
62 CT
*
1363262 TTGA-AAATGTTTCCCTTGA
1 TTGAGACA-GTTTCCCTTGA
1363281 GACACAAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
63 7 0.05
64 18 0.14
65 39 0.30
66 59 0.45
67 7 0.05
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (63 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAACT
Found at i:1363279 original size:29 final size:30
Alignment explanation
Indices: 1363241--1363316 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
1363231 CCTTGAGACA
*
1363241 GTTTCTCTTGAAACATAAA-CTTTGAAAAT
1 GTTTCCCTTGAAACATAAATCTTTGAAAAT
* *
1363270 GTTTCCCTTGAGACACA-AAATCTTTGAGATT
1 GTTTCCCTTGA-A-ACATAAATCTTTGAAAAT
1363301 GTTTCCCTTGAAACAT
1 GTTTCCCTTGAAACAT
1363317 GTTTTATCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 13 0.32
30 5 0.12
31 22 0.55
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (30 bp):
GTTTCCCTTGAAACATAAATCTTTGAAAAT
Found at i:1363312 original size:97 final size:97
Alignment explanation
Indices: 1363204--1363425 Score: 279
Period size: 96 Copynumber: 2.3 Consensus size: 97
1363194 TTCTGAGACA
* *
1363204 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAACTTTGA-A
1 GTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTATCTTGAAACACTAAACTTTGAGA
* *
1363267 AATGTTTCCCTTGAGACACAAAATCTTTGAGATT
66 AA-GTTTCCCTTGAAACAC-AAACCTTTGAGATT
** * *
1363301 GTTTCCCTTGAAAC-ATGTTTTATCTCTCTTGAGACAGTTTATCTTGAAACACTAACCTTTGAGA
1 GTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTATCTTGAAACACTAAACTTTGAGA
* * *
1363365 CAGTTTCTCTTGAAACACCAACCTTTGAGATT
66 AAGTTTCCCTTGAAACACAAACCTTTGAGATT
*
1363397 ATTTCCCTTGAAACAAGAAATTTTATCTC
1 GTTTCCCTTGAAAC-A-AAATTTTATCTC
1363426 ACTCGAGAGA
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
96 57 0.54
97 37 0.35
98 2 0.02
99 10 0.09
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (97 bp):
GTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTATCTTGAAACACTAAACTTTGAGA
AAGTTTCCCTTGAAACACAAACCTTTGAGATT
Found at i:1363365 original size:30 final size:30
Alignment explanation
Indices: 1363329--1363394 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
1363319 TTTATCTCTC
*
1363329 TTGAGACAGTTTATCTTGAAACACTAACCT
1 TTGAGACAGTTTATCTTGAAACACCAACCT
*
1363359 TTGAGACAGTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTATCTTGAAACACCAACCT
1363389 TTGAGA
1 TTGAGA
1363395 TTATTTCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (30 bp):
TTGAGACAGTTTATCTTGAAACACCAACCT
Found at i:1363407 original size:30 final size:30
Alignment explanation
Indices: 1363329--1363411 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
1363319 TTTATCTCTC
** *
1363329 TTGAGACAGTTTATCTTGAAACACTAACCT
1 TTGAGACAGTTTCCCTTGAAACACCAACCT
*
1363359 TTGAGACAGTTTCTCTTGAAACACCAACCT
1 TTGAGACAGTTTCCCTTGAAACACCAACCT
*
1363389 TTGAGATTA-TTTCCCTTGAAACA
1 TTGAGA-CAGTTTCCCTTGAAACA
1363412 AGAAATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 47 0.98
31 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (30 bp):
TTGAGACAGTTTCCCTTGAAACACCAACCT
Found at i:1363869 original size:91 final size:91
Alignment explanation
Indices: 1363709--1364069 Score: 551
Period size: 91 Copynumber: 4.0 Consensus size: 91
1363699 GATAAACCGA
* * * * * *
1363709 TCAACATTTCCAGTGAAGAGTTTACAATGAGAAGAACTCGTCCAACGAGGGAAAAAAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1363774 ATGAGAAGAACTTGTTCAGCCTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
*
1363800 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
1363865 ATGAGAAGAACTTGTTCAACCTTAGC
66 ATGAGAAGAACTTGTTCAACCTTGGT
* * ** * *
1363891 TCAGCATTTGCAACGGAGAGTTCATAATGAGAAGAACTTATCCAACGAGGGAGAATAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1363956 ATGAGAAGAACTTGTTCAACCTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
1363982 TCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1364047 ATGAGAAGAACTTCTTCAACCTT
66 ATGAGAAGAACTTGTTCAACCTT
1364070 ATATCATCAT
Statistics
Matches: 242, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 242 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGT
Found at i:1364383 original size:27 final size:27
Alignment explanation
Indices: 1364353--1364406 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1364343 AAAGCCCCAT
1364353 ACCCCACACCATGCTGCCCACGTGAAG
1 ACCCCACACCATGCTGCCCACGTGAAG
** *
1364380 ACCCCATTCCATGCTTCCCACGTGAAG
1 ACCCCACACCATGCTGCCCACGTGAAG
1364407 CGCCCCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.43, G:0.17, T:0.17
Consensus pattern (27 bp):
ACCCCACACCATGCTGCCCACGTGAAG
Done.