Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008773.1 Hibiscus syriacus cultivar Beakdansim tig00111881_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: 1239499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1043455 original size:22 final size:24
Alignment explanation
Indices: 1043412--1043457 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1043402 GGTGATTGCA
1043412 TATGTTACATGATATATATGAATG
1 TATGTTACATGATATATATGAATG
*
1043436 TATGTTA-ATG-TATATGTGAATG
1 TATGTTACATGATATATATGAATG
1043458 AATATAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (24 bp):
TATGTTACATGATATATATGAATG
Found at i:1043467 original size:22 final size:22
Alignment explanation
Indices: 1043424--1043467 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1043414 TGTTACATGA
* * *
1043424 TATATATGAATGTATGTTAATG
1 TATATATGAATGAATATAAATG
*
1043446 TATATGTGAATGAATATAAATG
1 TATATATGAATGAATATAAATG
1043468 ACTTATAGGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (22 bp):
TATATATGAATGAATATAAATG
Found at i:1043676 original size:2 final size:2
Alignment explanation
Indices: 1043671--1043695 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1043661 TATATATATA
1043671 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1043696 ATTATGCTTG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1044577 original size:31 final size:31
Alignment explanation
Indices: 1044542--1044619 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
1044532 TTATATGTCC
* ** *
1044542 AAGTGACCCAAACTTAATAAAATGATAATAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
1044573 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
**
1044604 AAGTGATAAAAACTTA
1 AAGTGACCAAAACTTA
1044620 TGTCTTTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.23
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:1045006 original size:31 final size:31
Alignment explanation
Indices: 1044971--1045034 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
1044961 AAAACGTAAG
1044971 ATATGATCACTTTCGTTTTTATTTAATTAAA
1 ATATGATCACTTTCGTTTTTATTTAATTAAA
* *
1045002 ATATGGTCACTTTTGTTTTTATTTAATTAAA
1 ATATGATCACTTTCGTTTTTATTTAATTAAA
1045033 AT
1 AT
1045035 GTGGTTATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
ATATGATCACTTTCGTTTTTATTTAATTAAA
Found at i:1045182 original size:30 final size:31
Alignment explanation
Indices: 1045148--1045206 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1045138 ATAGTCATAC
*
1045148 TTTTAAATAAATTTAAC-ATAAAATATATAT
1 TTTTAAATAAAGTTAACAATAAAATATATAT
*
1045178 TTTTAAATTAAGTTAACAATAAAATATAT
1 TTTTAAATAAAGTTAACAATAAAATATAT
1045207 TTAATAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
TTTTAAATAAAGTTAACAATAAAATATATAT
Found at i:1045240 original size:22 final size:24
Alignment explanation
Indices: 1045186--1045244 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
1045176 ATTTTTAAAT
*
1045186 TAAGTTAACAATAAAATATATTTAA
1 TAAGTTAA-TATAAAATATATTTAA
*
1045211 TAAGTTAATATAAAA-ATATTT-T
1 TAAGTTAATATAAAATATATTTAA
*
1045233 TAATTTAATATA
1 TAAGTTAATATA
1045245 TATAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.35
23 6 0.19
24 6 0.19
25 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (24 bp):
TAAGTTAATATAAAATATATTTAA
Found at i:1048246 original size:18 final size:18
Alignment explanation
Indices: 1048220--1048290 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
1048210 TCAGTATTTG
1048220 TCCCGAAGGACCACTATT
1 TCCCGAAGGACCACTATT
* * *
1048238 TCCCAAAGGACTATTGATT
1 TCCCGAAGGACCACT-ATT
* * *
1048257 GTTCCGAAGAACCACTATG
1 -TCCCGAAGGACCACTATT
1048276 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
1048291 GTATATCCCT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 25 0.62
19 5 0.12
20 10 0.25
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (18 bp):
TCCCGAAGGACCACTATT
Found at i:1048876 original size:24 final size:22
Alignment explanation
Indices: 1048814--1048876 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 22
1048804 AATGAGGGTA
1048814 TGCATCGATGCACTC-T-ACAG
1 TGCATCGATGCACTCTTAACAG
* * *
1048834 TGTATCGATGCATTCCTTAACGGG
1 TGCATCGATGCACT-CTTAAC-AG
1048858 TGCATCGATGCACTACTTA
1 TGCATCGATGCACT-CTTA
1048877 TGCATCAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 12 0.36
21 1 0.03
22 1 0.03
23 2 0.06
24 17 0.52
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCACTCTTAACAG
Found at i:1048924 original size:63 final size:64
Alignment explanation
Indices: 1048855--1048998 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 64
1048845 ATTCCTTAAC
*
1048855 GGGTGCATCGATGCACTACTTATGCATC-AGTTCA-TGAATCACATTCGATGTTTGTATTTAAT-
1 GGGTGCATCGATGCACTACTTATGCATCGA-TGCACT-AATCACATTCGATGTTTGTATTTAATC
*
1048917 G
64 A
* ** * *
1048918 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTTTATTTTATCA
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTTAATCA
*
1048982 GAGTGCATCGATGCACT
1 GGGTGCATCGATGCACT
1048999 TCATGTGCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
63 52 0.74
64 18 0.26
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTTAATCA
Found at i:1051185 original size:80 final size:80
Alignment explanation
Indices: 1051051--1051420 Score: 600
Period size: 80 Copynumber: 4.6 Consensus size: 80
1051041 TGTAAGTCCT
* * *
1051051 TACGGACCTAAGGATATCTTAGGTAGG-CCCAAGGCATATCCTTAAGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1051115 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
1051130 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1051195 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
*
1051210 TACGGACCTAAGGATATATTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1051275 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
*
1051290 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
* * *
1051355 TTCTTAAGGTAACCT
66 TGCATAAGGTAACCC
* * * * *
1051370 TACGTATCTAAGGATGTCCTTAGGTAGAT-CCAAGGTATATCCTTAGGTTGG
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
1051421 CTCCTTTTTT
Statistics
Matches: 274, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
79 26 0.09
80 240 0.88
81 8 0.03
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:1056586 original size:80 final size:80
Alignment explanation
Indices: 1056449--1056818 Score: 609
Period size: 80 Copynumber: 4.6 Consensus size: 80
1056439 TGTAAGTCCT
* * * *
1056449 TACGGACCTAAGGATATCTTAGGTA-GCCCCAAGGCATATACTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1056513 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
1056528 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1056593 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
1056608 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1056673 TGCATAAGGTAACCC
66 TGCATAAGGTAACCC
*
1056688 TACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
* *
1056753 TTCTTAAGGTAACCC
66 TGCATAAGGTAACCC
* * * * *
1056768 TACGTATCTAAGGATGTCCTTAGGTAGAT-CCAAGGTATATCCTTAGGTTGG
1 TACGGACCTAAGGATAT-CTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGG
1056819 CTCCTTTTTT
Statistics
Matches: 276, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
79 24 0.09
80 244 0.88
81 8 0.03
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:1059742 original size:2 final size:2
Alignment explanation
Indices: 1059737--1059762 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1059727 GATAAACACC
1059737 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1059763 AACTGTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1061836 original size:18 final size:18
Alignment explanation
Indices: 1061815--1061855 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1061805 CCCAACTTAA
1061815 AAATTAAAAATTGAAGTT
1 AAATTAAAAATTGAAGTT
1061833 AAATTAAAAATTGAAGTT
1 AAATTAAAAATTGAAGTT
1061851 AAATT
1 AAATT
1061856 CAAGCTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (18 bp):
AAATTAAAAATTGAAGTT
Found at i:1063479 original size:59 final size:59
Alignment explanation
Indices: 1063378--1063506 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
1063368 TGTAGTGCTA
* **
1063378 TCCCGAATATGACACATAAGGTCGTGCCCACAATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACAATATACACTAGGTATCCTTAAGTACAG
* * ** *
1063437 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACAATATACACTAGGTATCCTTAAGTACAG
1063496 TCCCGAATATG
1 TCCCGAATATG
1063507 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACAATATACACTAGGTATCCTTAAGTACAG
Found at i:1068182 original size:14 final size:14
Alignment explanation
Indices: 1068160--1068189 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1068150 AGAAAACTTG
1068160 ATAAATTTATAGCA
1 ATAAATTTATAGCA
*
1068174 ATAACTTTATAGCA
1 ATAAATTTATAGCA
1068188 AT
1 AT
1068190 TAATGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
ATAAATTTATAGCA
Found at i:1073590 original size:18 final size:18
Alignment explanation
Indices: 1073563--1073598 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1073553 GCCAAACGAC
*
1073563 ATTCGTCGATAAGCGAAG
1 ATTCGCCGATAAGCGAAG
1073581 ATTCGCCGATAAGCGAAG
1 ATTCGCCGATAAGCGAAG
1073599 GTACCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (18 bp):
ATTCGCCGATAAGCGAAG
Found at i:1077167 original size:11 final size:10
Alignment explanation
Indices: 1077141--1077172 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
1077131 CTGGTTCACT
1077141 GGTTCAACCG
1 GGTTCAACCG
1077151 GGTTCAACCG
1 GGTTCAACCG
1077161 CGGTTCAACCG
1 -GGTTCAACCG
1077172 G
1 G
1077173 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:1081799 original size:17 final size:17
Alignment explanation
Indices: 1081777--1081821 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
1081767 GAATATGGCA
1081777 AGGATTAAATTTGGTAT
1 AGGATTAAATTTGGTAT
*
1081794 AGGATTGTAATTTGGTAT
1 AGGATT-AAATTTGGTAT
1081812 AGGATTAAAT
1 AGGATTAAAT
1081822 CGCAAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (17 bp):
AGGATTAAATTTGGTAT
Found at i:1083187 original size:18 final size:18
Alignment explanation
Indices: 1083164--1083198 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1083154 AGGGATTATC
*
1083164 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
1083182 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGAGACA
1083199 AATATTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:1086421 original size:31 final size:32
Alignment explanation
Indices: 1086385--1086445 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1086375 AGTTAAGTTT
*
1086385 TTTCGAGCTCGAGTCGAGCTT-CAATTTTTTA
1 TTTCGAGCTCGAGTCAAGCTTACAATTTTTTA
*
1086416 TTTCGATCTCGAGTCAAGCTTGACAATTTT
1 TTTCGAGCTCGAGTCAAGCTT-ACAATTTT
1086446 ACTTTTGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 19 0.73
33 7 0.27
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (32 bp):
TTTCGAGCTCGAGTCAAGCTTACAATTTTTTA
Found at i:1088560 original size:18 final size:19
Alignment explanation
Indices: 1088506--1088554 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
1088496 TGTTATATAC
1088506 ATATAATAAAATTATTTAT
1 ATATAATAAAATTATTTAT
* *
1088525 ATATTCAAATGACATTATTTAT
1 ATA-T--AATAAAATTATTTAT
1088547 ATATAATA
1 ATATAATA
1088555 TATTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 1 0.04
22 16 0.67
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATAATAAAATTATTTAT
Found at i:1090127 original size:2 final size:2
Alignment explanation
Indices: 1090122--1090155 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1090112 AAACCATGAA
1090122 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
1090156 TCTTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1096585 original size:22 final size:22
Alignment explanation
Indices: 1096557--1096604 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1096547 CTTTCAGGTT
1096557 GTACTAGTTGGAAATTAAACGA
1 GTACTAGTTGGAAATTAAACGA
* *
1096579 GTACTAGTTGGGAATTCAACGA
1 GTACTAGTTGGAAATTAAACGA
1096601 GTAC
1 GTAC
1096605 GAGTAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (22 bp):
GTACTAGTTGGAAATTAAACGA
Found at i:1100717 original size:16 final size:17
Alignment explanation
Indices: 1100686--1100719 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1100676 TGTATCGCCG
*
1100686 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
1100703 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
1100719 A
1 A
1100720 TATGAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:1118988 original size:141 final size:142
Alignment explanation
Indices: 1118770--1119055 Score: 531
Period size: 141 Copynumber: 2.0 Consensus size: 142
1118760 TCGCATTGTC
1118770 ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGTT
1 ATCAAGTAGAAGACTTAATAAGTTGGTCA-GTTTCCTATAGAACTTGGAATGACACCAGTAAGTT
1118835 ATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAG
65 ATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAG
1118900 AGAGGTAATTACT
130 AGAGGTAATTACT
1118913 ATCAAGTAGAAGACTTAATAAGTTGGTCA-TTTCCTATAGAACTTGGAATGACA-CAGTAAGATT
1 ATCAAGTAGAAGACTTAATAAGTTGGTCAGTTTCCTATAGAACTTGGAATGACACCAGTAAG-TT
*
1118976 ATTTTCCAACAACTGTAATGTGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAG
65 ATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAG
1119041 AGAGGTAATTACT
130 AGAGGTAATTACT
1119054 AT
1 AT
1119056 AAAAATAAAG
Statistics
Matches: 141, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
140 7 0.05
141 105 0.74
143 29 0.21
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (142 bp):
ATCAAGTAGAAGACTTAATAAGTTGGTCAGTTTCCTATAGAACTTGGAATGACACCAGTAAGTTA
TTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGA
GAGGTAATTACT
Found at i:1132462 original size:36 final size:31
Alignment explanation
Indices: 1132370--1132459 Score: 180
Period size: 31 Copynumber: 2.9 Consensus size: 31
1132360 AGGGTCGGGT
1132370 TTTTTTAAGTGTGATATTCGGGTCGGGTTAA
1 TTTTTTAAGTGTGATATTCGGGTCGGGTTAA
1132401 TTTTTTAAGTGTGATATTCGGGTCGGGTTAA
1 TTTTTTAAGTGTGATATTCGGGTCGGGTTAA
1132432 TTTTTTAAGTGTGATATTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGGT
1132460 CGGATTCGGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.18, C:0.07, G:0.30, T:0.46
Consensus pattern (31 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTTAA
Found at i:1133090 original size:18 final size:17
Alignment explanation
Indices: 1133036--1133099 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
1133026 TATGGAATTG
1133036 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
1133053 GATTCTAATTCCTGACA
1 GATTCCAATTCCTGACA
*
1133070 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
1133088 GATTCCAATTCC
1 GATTCCAATTCC
1133100 CTCAAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 27 0.63
18 16 0.37
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:1133975 original size:46 final size:44
Alignment explanation
Indices: 1133877--1133979 Score: 109
Period size: 46 Copynumber: 2.3 Consensus size: 44
1133867 CACATTCAAT
* * *
1133877 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTA
1 GTGTATCGATGCACCCTTAAAAGAAGAAACATCGAAGGCAATTA
* ** *
1133921 GTGCATCGATGCACCCCCTTAAAATGAA-AAACATCGAAGGTGATTG
1 GTGTATCGATGCA--CCCTTAAAA-GAAGAAACATCGAAGGCAATTA
1133967 GTGTATCGATGCA
1 GTGTATCGATGCA
1133980 TGGGTAGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 12 0.25
46 33 0.69
47 3 0.06
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (44 bp):
GTGTATCGATGCACCCTTAAAAGAAGAAACATCGAAGGCAATTA
Found at i:1135023 original size:20 final size:20
Alignment explanation
Indices: 1134993--1135048 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1134983 TTTTACACTT
*
1134993 AGGGA-ACCGATTCCTCATG
1 AGGGATACCGATTCCCCATG
*
1135012 AGGGGTACCGATTCCCCATG
1 AGGGATACCGATTCCCCATG
1135032 AGGGATACCGATTCCCC
1 AGGGATACCGATTCCCC
1135049 CCACGCTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (20 bp):
AGGGATACCGATTCCCCATG
Found at i:1137185 original size:167 final size:166
Alignment explanation
Indices: 1136973--1137308 Score: 606
Period size: 170 Copynumber: 2.0 Consensus size: 166
1136963 TTTGCAAATC
1136973 AACTAGAAGAGTTGAAAAGAAAATTCGATTTGCAAATTTACTTTCAAAGGTCAATGATGATCATC
1 AACTAGAAGAGTTGAAAAGAAAATTCGATTTGCAAATTTACTTTCAAAGGTCAATGATGATCATC
1137038 AAAAGAAAA-T-TGATCTTAAAGCTTCTTTTGATAAAGTTGGAACAAAACGTTTTAAAAAATGAG
66 AAAAGAAAATTATGATCTTAAAGCTTCTTTTGATAAAGTTGGAACAAAACGTTTTAAAAAATGAG
1137101 -AAATTCAAAATCCAACATTGTTAGAAAAAGTTTTA
131 AAAATTCAAAATCCAACATTGTTAGAAAAAGTTTTA
1137136 AACTAGAAGAGTTTGAAAAGAAAAATTCGGATTTGCAAAATTTACTTTCAAAGGTCAATGATGAT
1 AACTAGAAGAG-TTGAAAAG-AAAATTC-GATTTGC-AAATTTACTTTCAAAGGTCAATGATGAT
1137201 CATCAAAAGAAAATTGATGATCTTAAAGCTTCTTTTGATAAAGTTGGAACAAAACGTTTTAAAAA
62 CATCAAAAGAAAATT-ATGATCTTAAAGCTTCTTTTGATAAAGTTGGAACAAAACGTTTTAAAAA
1137266 ATGAGAAAATTCAAAATCCAACATTGTTAGAAAAAGTTTTA
126 ATGAGAAAATTCAAAATCCAACATTGTTAGAAAAAGTTTTA
1137307 AA
1 AA
1137309 AACTACAATC
Statistics
Matches: 165, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
163 11 0.07
164 8 0.05
165 7 0.04
166 7 0.04
167 41 0.25
168 1 0.01
170 53 0.32
171 37 0.22
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (166 bp):
AACTAGAAGAGTTGAAAAGAAAATTCGATTTGCAAATTTACTTTCAAAGGTCAATGATGATCATC
AAAAGAAAATTATGATCTTAAAGCTTCTTTTGATAAAGTTGGAACAAAACGTTTTAAAAAATGAG
AAAATTCAAAATCCAACATTGTTAGAAAAAGTTTTA
Found at i:1146885 original size:78 final size:78
Alignment explanation
Indices: 1146793--1147020 Score: 361
Period size: 76 Copynumber: 2.9 Consensus size: 78
1146783 TTTTCACGGG
1146793 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
1146858 GATCCAACACAGT
66 GATCCAACACAGT
* *
1146871 TATACTTTTCTCATTAGGATATGGATAATAG-T-TGTCTCATATGAATAGACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
* *
1146934 AATCCAACACGGT
66 GATCCAACACAGT
* * * *
1146947 TATACTTTTCCCATTAGGATATGAATAATAATTATGTTTTATATGAATAGACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
*
1147012 GGTCCAACA
66 GATCCAACA
1147021 ATTATAGTAT
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
76 68 0.50
77 2 0.01
78 67 0.49
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (78 bp):
TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
GATCCAACACAGT
Found at i:1149730 original size:401 final size:401
Alignment explanation
Indices: 1148966--1149768 Score: 1286
Period size: 401 Copynumber: 2.0 Consensus size: 401
1148956 GTAAACTTTC
* * *
1148966 AAGTATCTTCAATCGAGCACATATCGAATAGTTTAGAGTATATGATCATTGTGAAGGGTATACTT
1 AAGTATCTTCAATCGAGCACATATCGAATAGTTTAGAGCATAGGATCATTGTGAAGGGTATACTC
* * *
1149031 GTAAGCGATAAAAAGTATCACGTGAATAACATGATAAAGGAATCGTGCACTATGTAAACGTCAAT
66 GTAAGCGAGAAAAAGAATCACATGAATAACATGATAAAGGAATCGTGCACTATGTAAACGTCAAT
* * * * *
1149096 AAATCGAGGATGTACAAGTCATCCCTCCAATTTAAGGCTGGATTGAATGGAAATCTGATAACAAT
131 AAACCAAGGATGTACAAGTCATCCCTACAATTCAAGGCTGGATTGAATGGAAATCCGATAACAAT
* * * *
1149161 GACTAGAGCATCGCTACCAAGTAACAAACCCGAGTCGAACGTCAGGCTAGCAAATAATGCATTAA
196 GACTAGAACATCGCTACCAAGAAACAAACCCGAGTCGAACATCAGGCTAGCAAATAATACATTAA
* *
1149226 GTTAGCATTGATAACATTGATTATCGTAGAATCAAAAAACACTTAGAGACCTCCTAAGAGACATA
261 GGTAGCATTGATAACATTGATTATCGTAGAATCAAAAAACACTTAGAGACATCCTAAGAGACATA
1149291 AATGACTATTGAGTGTAACAAACTATGCAGTACATATCTAAGCTACTTTAGTTGTCCTGGTAGGG
326 AATGACTATTGAGTGTAACAAACTATGCAGTACATATCTAAGCTACTTTAGTTGTCCTGGTAGGG
1149356 AATTGATTGTT
391 AATTGATTGTT
*
1149367 AAGTATCTTCAATCGAGCACATATCGAATAGTTTAGAGCATAGGATCATTGTGAAGGGTATGCTC
1 AAGTATCTTCAATCGAGCACATATCGAATAGTTTAGAGCATAGGATCATTGTGAAGGGTATACTC
* * *
1149432 GTAAGCGAGAAGAAGAATCACATGAATAACATGATAGAGGAATCGTGCACTATGTGAACGTCAAT
66 GTAAGCGAGAAAAAGAATCACATGAATAACATGATAAAGGAATCGTGCACTATGTAAACGTCAAT
* * *
1149497 AAACCAAGGATGTTCAAGTCATCCCTATAATTCAAGGTTGGATTGAA-GGAAAATCCGATAACAA
131 AAACCAAGGATGTACAAGTCATCCCTACAATTCAAGGCTGGATTGAATGG-AAATCCGATAACAA
*
1149561 TGACTAGAACATCGCTACCAAGAAACAAACCCTAGTCGAACATCAGGCTAGCAAATAATACATTA
195 TGACTAGAACATCGCTACCAAGAAACAAACCCGAGTCGAACATCAGGCTAGCAAATAATACATTA
* *
1149626 AGGTATCATTGATAACATTGATTATCGTAGAAT-AAAAAACACTTAGAGACATCCTTAGAGACAT
260 AGGTAGCATTGATAACATTGATTATCGTAGAATCAAAAAACACTTAGAGACATCCTAAGAGACAT
* ** * *
1149690 AAATGACTCTTGAGTGTAATGAACTATGCCAGTGCATATCTAAGCTACTTTAGTTGTCCTTGTAG
325 AAATGACTATTGAGTGTAACAAACTATG-CAGTACATATCTAAGCTACTTTAGTTGTCCTGGTAG
1149755 GGAATTGATTGTT
389 GGAATTGATTGTT
1149768 A
1 A
1149769 TGTGTAGCCT
Statistics
Matches: 368, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
400 56 0.15
401 312 0.85
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (401 bp):
AAGTATCTTCAATCGAGCACATATCGAATAGTTTAGAGCATAGGATCATTGTGAAGGGTATACTC
GTAAGCGAGAAAAAGAATCACATGAATAACATGATAAAGGAATCGTGCACTATGTAAACGTCAAT
AAACCAAGGATGTACAAGTCATCCCTACAATTCAAGGCTGGATTGAATGGAAATCCGATAACAAT
GACTAGAACATCGCTACCAAGAAACAAACCCGAGTCGAACATCAGGCTAGCAAATAATACATTAA
GGTAGCATTGATAACATTGATTATCGTAGAATCAAAAAACACTTAGAGACATCCTAAGAGACATA
AATGACTATTGAGTGTAACAAACTATGCAGTACATATCTAAGCTACTTTAGTTGTCCTGGTAGGG
AATTGATTGTT
Found at i:1152408 original size:22 final size:23
Alignment explanation
Indices: 1152366--1152408 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1152356 CTTAGTCCTT
1152366 TTTACACAATAAAGGTATTTTTG
1 TTTACACAATAAAGGTATTTTTG
*
1152389 TTTACACAATAAGGGT-TTTT
1 TTTACACAATAAAGGTATTTT
1152409 AGACAATTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (23 bp):
TTTACACAATAAAGGTATTTTTG
Found at i:1155667 original size:15 final size:15
Alignment explanation
Indices: 1155644--1155689 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1155634 TCAAATGAAA
*
1155644 TTATTTATATATTAT
1 TTATATATATATTAT
1155659 TTATATATA-ATATAT
1 TTATATATATAT-TAT
1155674 TTATATATATA-TAT
1 TTATATATATATTAT
1155688 TT
1 TT
1155690 TAATTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 20 0.71
16 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATATATATTAT
Found at i:1155866 original size:15 final size:15
Alignment explanation
Indices: 1155846--1155875 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1155836 GGAATGTTGT
1155846 TTGTTCTAGTTTGAA
1 TTGTTCTAGTTTGAA
1155861 TTGTTCTAGTTTGAA
1 TTGTTCTAGTTTGAA
1155876 AATGTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
TTGTTCTAGTTTGAA
Found at i:1156131 original size:27 final size:26
Alignment explanation
Indices: 1156081--1156131 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1156071 GTCTTGGTTA
*
1156081 GTGCATAATTTTTTCATGATTGTTTT
1 GTGCATAATTTTTTCATGAATGTTTT
*
1156107 GTGCATAATTTTTTTTATGAATGTT
1 GTGCATAA-TTTTTTCATGAATGTT
1156132 GATGTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.57
Consensus pattern (26 bp):
GTGCATAATTTTTTCATGAATGTTTT
Found at i:1159567 original size:3 final size:3
Alignment explanation
Indices: 1159543--1159593 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
1159533 CTATAAAAGC
* * *
1159543 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1159589 AAT AA
1 AAT AA
1159594 CGGGATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1162926 original size:18 final size:18
Alignment explanation
Indices: 1162903--1162937 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1162893 TAGCCGCAAG
*
1162903 ATTTGAGTTATTCAAGTT
1 ATTTGAGTTATTAAAGTT
1162921 ATTTGAGTTATTAAAGT
1 ATTTGAGTTATTAAAGT
1162938 GTTGCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (18 bp):
ATTTGAGTTATTAAAGTT
Found at i:1163065 original size:38 final size:37
Alignment explanation
Indices: 1163026--1163100 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 37
1163016 GAGATGATTG
* *
1163026 TTTGTTTCCATTTATACTTTTCAAGTGGTATTTGTTTGTT
1 TTTGTTTCC-TTCA-ACTTTTCAAGCGGTATTTGTTTG-T
* *
1163066 TTTTTTTCCTTCAATTTTTCAAGCGGTATTTGTTT
1 TTTGTTTCCTTCAACTTTTCAAGCGGTATTTGTTT
1163101 TTTATGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 20 0.65
39 3 0.10
40 8 0.26
ACGTcount: A:0.15, C:0.12, G:0.13, T:0.60
Consensus pattern (37 bp):
TTTGTTTCCTTCAACTTTTCAAGCGGTATTTGTTTGT
Found at i:1171893 original size:17 final size:19
Alignment explanation
Indices: 1171854--1171900 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1171844 ATAGCCTGAG
1171854 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1171873 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
1171890 TGCATTCGATG
1 TGCA-TCGATG
1171901 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1171944 original size:65 final size:64
Alignment explanation
Indices: 1171805--1171950 Score: 197
Period size: 64 Copynumber: 2.3 Consensus size: 64
1171795 CGGTGCACCA
* * *
1171805 AGAATGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGAATGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAGCCTGAATGCATCGATGCATGG
*
1171869 AGAATGCATCGGTGCATGAAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCAT
1 AGAATGCATCGGTGCATGAAATGCATTCGATGTTTCAA--AATAGC-CTGAATGCATCGATGCAT
1171932 GG
63 GG
* *
1171934 TGGATGCATCGGTGCAT
1 AGAATGCATCGGTGCAT
1171951 CACCTCAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
64 36 0.49
65 32 0.44
66 5 0.07
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (64 bp):
AGAATGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAGCCTGAATGCATCGATGCATGG
Found at i:1172143 original size:20 final size:21
Alignment explanation
Indices: 1172120--1172159 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1172110 GAATCGAATA
1172120 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1172140 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1172160 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1180438 original size:17 final size:19
Alignment explanation
Indices: 1180399--1180445 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1180389 ATAACCTGAG
1180399 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1180418 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
1180435 TGCATTCGATG
1 TGCA-TCGATG
1180446 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1180489 original size:65 final size:64
Alignment explanation
Indices: 1180354--1180495 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 64
1180344 ACACCAAGTG
* * *
1180354 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCTGAGTGCATCGATGCATGGAGAA
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAACCTGAATGCATCGATGCATGGAGAA
* *
1180418 TGCATCGGTGCATGAAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCATGGTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAA--AATAAC-CTGAATGCATCGATGCATGGAG
*
1180481 GA
63 AA
1180483 TGCATCGGTGCAT
1 TGCATCGGTGCAT
1180496 CACCTCAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 32 0.46
65 32 0.46
66 5 0.07
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATAACCTGAATGCATCGATGCATGGAGAA
Found at i:1180688 original size:20 final size:21
Alignment explanation
Indices: 1180665--1180704 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1180655 GAATCGAATA
1180665 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1180685 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1180705 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1181912 original size:26 final size:25
Alignment explanation
Indices: 1181877--1181928 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 25
1181867 CAAAGGTCAT
1181877 CCAAAATTCAACGTTTAGTACAACC
1 CCAAAATTCAACGTTTAGTACAACC
1181902 CCAAATATTCAACGTTTAGTACAACC
1 CCAAA-ATTCAACGTTTAGTACAACC
1181928 C
1 C
1181929 TCTCTCGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.25
Consensus pattern (25 bp):
CCAAAATTCAACGTTTAGTACAACC
Found at i:1197135 original size:17 final size:17
Alignment explanation
Indices: 1197109--1197154 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
1197099 TATGGAATTG
1197109 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
1197126 GATTCTAATTCCTGACA
1 GATTCCAATTCCTGACA
1197143 GATTCCAATTCC
1 GATTCCAATTCC
1197155 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:1197986 original size:44 final size:45
Alignment explanation
Indices: 1197937--1198038 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
1197927 CACATTCAAT
* * *
1197937 GTGTATCGATGCA-CTCTTTAAAGAAG-AAACATCGAATGCAATTA
1 GTGTATCGATGCACCCCCTTAAA-AAGAAAACATCGAAGGCAATTA
* ** *
1197981 GTGTATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCACCCCCTTAAAAAGAAAACATCGAAGGCAATTA
1198026 GTGTATCGATGCA
1 GTGTATCGATGCA
1198039 TGAGTAGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 15 0.31
45 34 0.69
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (45 bp):
GTGTATCGATGCACCCCCTTAAAAAGAAAACATCGAAGGCAATTA
Found at i:1199109 original size:20 final size:20
Alignment explanation
Indices: 1199084--1199134 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1199074 CACTTAGAGA
* *
1199084 ACCGATTCCTCATGAGGGGT
1 ACCGATTCCCCATGAGGGAT
1199104 ACCGATTCCCCATGAGGGAT
1 ACCGATTCCCCATGAGGGAT
1199124 ACCGATTCCCC
1 ACCGATTCCCC
1199135 CCCACGCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.33, G:0.24, T:0.22
Consensus pattern (20 bp):
ACCGATTCCCCATGAGGGAT
Found at i:1210968 original size:78 final size:78
Alignment explanation
Indices: 1210875--1211182 Score: 546
Period size: 78 Copynumber: 3.9 Consensus size: 78
1210865 TTTCCATGGG
*
1210875 TATAC-TTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAACC
1210939 GATCCAACACGGT
66 GATCCAACACGGT
*
1210952 TATACTTTTCTCATTAGAATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAACC
1211017 GATCCAACACGGT
66 GATCCAACACGGT
* *
1211030 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTTATATGAATAAACATGTAAACTAACC
1 TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAACC
*
1211095 AATCCAACACGGT
66 GATCCAACACGGT
*
1211108 TATACTTTTTCTCATTAGGATATGGATAATAGTTGTGTTTCATATGAATAGACATGTAAACTAAC
1 TATAC-TTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAAC
1211173 CGATCCAACA
65 CGATCCAACA
1211183 ATTATAGTTT
Statistics
Matches: 219, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
77 5 0.02
78 149 0.68
79 65 0.30
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (78 bp):
TATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAACTAACC
GATCCAACACGGT
Found at i:1219221 original size:12 final size:12
Alignment explanation
Indices: 1219200--1219229 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1219190 GTTCTCCTTC
*
1219200 CTCTCCCCCTCT
1 CTCTCGCCCTCT
1219212 CTCTCGCCCTCT
1 CTCTCGCCCTCT
1219224 CTCTCG
1 CTCTCG
1219230 ACCTTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.60, G:0.07, T:0.33
Consensus pattern (12 bp):
CTCTCGCCCTCT
Found at i:1221237 original size:54 final size:53
Alignment explanation
Indices: 1220867--1221696 Score: 1158
Period size: 53 Copynumber: 15.7 Consensus size: 53
1220857 TTCTTGGGCT
*
1220867 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATCATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
*** * * * * *
1220920 TATTATCTCTTCCTTCAAGGAGTAGAACTCGAACAATAATCTTCTTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
** * * *
1220973 TACTCTCTCTTCCTTCAAGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
* * * *
1221026 TGCTCTCTTTTTCTTCAAGGAGTAAAACTCGAACAATCATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
** * * * * *
1221079 TACTATCTCTTCCTTCAAGGAGTAGAATTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
** * * *
1221132 TACTCTCTCTTCCTTCAAGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
*
1221185 TGCTCTCTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTC
*
1221239 CGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTC
*
1221293 CGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTC
1221347 CGCTCTCTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTC
1221401 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
* *
1221454 CACTCTTTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1221507 CGC-C-CTATTTTCTTCAGGGAGTAGAACTCGAAC---AATCTTCCTACGGG-C
1 CGCTCTCT-TTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
* *
1221555 TCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACCGGTC
1 -CGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTC
* *
1221610 CAC-C-CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
1 CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
*
1221661 CGC-C-CTATTTTCTTTAGGGAGTAGAACTCGAACAAT
1 CGCTCTCT-TTTTCTTCAGGGAGTAGAACTCGAACAAT
1221697 CTTCTGTTGC
Statistics
Matches: 722, Mismatches: 44, Indels: 23
0.92 0.06 0.03
Matches are distributed among these distances:
48 1 0.00
49 17 0.02
50 15 0.02
51 48 0.07
52 71 0.10
53 342 0.47
54 227 0.31
55 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (53 bp):
CGCTCTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC
Found at i:1223064 original size:29 final size:28
Alignment explanation
Indices: 1223024--1223099 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
1223014 TTTTGTTTTA
* *
1223024 TTTTTTT-ATTTTCTTCATTTTCTTCGTT
1 TTTTTTTCATTTTTTTCATTTT-TTCATT
1223052 TTTTTTTCATTTTTTTTTCA-TTTTTCATT
1 TTTTTTTCA--TTTTTTTCATTTTTTCATT
*
1223081 TTTTTTTCCTTTTTTTCAT
1 TTTTTTTCATTTTTTTCAT
1223100 CTCCAAGCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 9 0.22
28 7 0.17
29 14 0.34
30 3 0.07
31 8 0.20
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (28 bp):
TTTTTTTCATTTTTTTCATTTTTTCATT
Found at i:1223065 original size:12 final size:11
Alignment explanation
Indices: 1223050--1223096 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
1223040 ATTTTCTTCG
1223050 TTTTTTTTTCA
1 TTTTTTTTTCA
1223061 TTTTTTTTTCA
1 TTTTTTTTTCA
1223072 ----TTTTTCA
1 TTTTTTTTTCA
*
1223079 TTTTTTTTTCC
1 TTTTTTTTTCA
1223090 TTTTTTT
1 TTTTTTT
1223097 CATCTCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
7 7 0.23
11 24 0.77
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:1223077 original size:18 final size:18
Alignment explanation
Indices: 1223054--1223094 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1223044 TCTTCGTTTT
1223054 TTTTTCATTTTTTTTTCA
1 TTTTTCATTTTTTTTTCA
*
1223072 TTTTTCATTTTTTTTTCC
1 TTTTTCATTTTTTTTTCA
1223090 TTTTT
1 TTTTT
1223095 TTCATCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCATTTTTTTTTCA
Found at i:1228541 original size:20 final size:21
Alignment explanation
Indices: 1228516--1228567 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
1228506 GCGATGTGGA
1228516 CTTCTCGTCTTTACGAA-GGT
1 CTTCTCGTCTTTACGAAGGGT
*
1228536 CTTCTCGTCTTTATGAAGGGT
1 CTTCTCGTCTTTACGAAGGGT
1228557 CTTCTCGTCTT
1 CTTCTCGTCTT
1228568 GATGAATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (21 bp):
CTTCTCGTCTTTACGAAGGGT
Found at i:1228559 original size:21 final size:21
Alignment explanation
Indices: 1228516--1228604 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
1228506 GCGATGTGGA
*
1228516 CTTCTCGTCTTTACGAA-GGT
1 CTTCTCGTCTTTATGAAGGGT
1228536 CTTCTCGTCTTTATGAAGGGT
1 CTTCTCGTCTTTATGAAGGGT
* **
1228557 CTTCTCGTCTTGATGAATGGAA
1 CTTCTCGTCTTTATGAA-GGGT
* *
1228579 C-TCTCGTCTTTATGAATGCT
1 CTTCTCGTCTTTATGAAGGGT
1228599 CTTCTC
1 CTTCTC
1228605 ATCCTTGGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
20 18 0.31
21 37 0.64
22 3 0.05
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.42
Consensus pattern (21 bp):
CTTCTCGTCTTTATGAAGGGT
Found at i:1234739 original size:22 final size:22
Alignment explanation
Indices: 1234709--1234772 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
1234699 GGCATGTAAA
*
1234709 ATTTATCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* * *
1234731 ATTTGTCCCAAAGGACCTCTGT
1 ATTTGTCCCGAATGACCTATGT
*
1234753 ATATGTCCCGAATGACCTAT
1 ATTTGTCCCGAATGACCTAT
1234773 ATAACCCTTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:1236151 original size:30 final size:31
Alignment explanation
Indices: 1236094--1236154 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1236084 CAATCATTCA
* *
1236094 TAACTTTTCCAAAATTGCCAAATTGGTCCCC
1 TAACTTTTCAAAAATTGACAAATTGGTCCCC
1236125 TAACTTTTCAAAAATT-ACATAA-TGGTCCCC
1 TAACTTTTCAAAAATTGACA-AATTGGTCCCC
1236155 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (31 bp):
TAACTTTTCAAAAATTGACAAATTGGTCCCC
Done.