Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_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: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 26
Found at i:542037 original size:30 final size:30
Alignment explanation
Indices: 541971--542045 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
541961 TTTAAATAGT
* *
541971 TATTATTTTTATATTAATATATTTATGTAAA
1 TATTATTTTT-TATTAAAATATATATGTAAA
* *
542002 TATTATTTTTTATTAAAATA-ATATTTATA
1 TATTATTTTTTATTAAAATATATATGTAAA
*
542031 TAATTATTATTTATT
1 T-ATTATTTTTTATT
542046 TAGAATTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 7 0.18
30 21 0.55
31 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTATTTTTTATTAAAATATATATGTAAA
Found at i:542209 original size:17 final size:17
Alignment explanation
Indices: 542187--542240 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
542177 AATGTTAATA
542187 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
542204 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
542221 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
542238 TTT
1 TTT
542241 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:542777 original size:229 final size:229
Alignment explanation
Indices: 542365--542825 Score: 859
Period size: 229 Copynumber: 2.0 Consensus size: 229
542355 ATATTGCAAC
542365 AATTATAGGCGGTTGCAAACTCGAACCTGTCCTAATTTCTACACTGATTGAGAGGTGGAGGCCCG
1 AATTATAGGCGGTTGCAAACTCGAACCTGTCCTAATTTCTACACTGATTGAGAGGTGGAGGCCCG
542430 AGACACACACTTTTCACCTTCCATGTGGAGAGGCAACAATTACATTGGAGGATGTCTCTATGCAT
66 AGACACACACTTTTCACCTTCCATGTGGAGAGGCAACAATTACATTGGAGGATGTCTCTATGCAT
* *
542495 CTGGGGCTTCCCGTCGACGGAAATATGATGTGTGGTATGGCGGATGGTGATTGGCAATCAATGTG
131 CTGGGGCTTCCCGTCGACGGAAATATGATGTGTGGTATGACGGATGATGATTGGCAATCAATGTG
542560 CATTGATTATCTTGGAGCTGCTCCGCCAGAGTTT
196 CATTGATTATCTTGGAGCTGCTCCGCCAGAGTTT
* *
542594 AATTATAGGCGGTTTCAAACTCGAACCTGTCCTAATTTCTGCACTGATTGAGAGGTGGAGGCCCG
1 AATTATAGGCGGTTGCAAACTCGAACCTGTCCTAATTTCTACACTGATTGAGAGGTGGAGGCCCG
* *
542659 AGACACACACTTTTCACCTTCCATGTGGAGAGGTAACAATTATATTGGAGGATGTCTCTATGCAT
66 AGACACACACTTTTCACCTTCCATGTGGAGAGGCAACAATTACATTGGAGGATGTCTCTATGCAT
542724 CTGGGGCTTCCCGTCGACGGAAATATGATGTGTGGTATGACGGATGATGATTGGCAATCAATGTG
131 CTGGGGCTTCCCGTCGACGGAAATATGATGTGTGGTATGACGGATGATGATTGGCAATCAATGTG
*
542789 CATTGATTATCTTGGAGCTGCTCCGCTAGAGTTT
196 CATTGATTATCTTGGAGCTGCTCCGCCAGAGTTT
542823 AAT
1 AAT
542826 GGAGGTAGAA
Statistics
Matches: 225, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 225 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (229 bp):
AATTATAGGCGGTTGCAAACTCGAACCTGTCCTAATTTCTACACTGATTGAGAGGTGGAGGCCCG
AGACACACACTTTTCACCTTCCATGTGGAGAGGCAACAATTACATTGGAGGATGTCTCTATGCAT
CTGGGGCTTCCCGTCGACGGAAATATGATGTGTGGTATGACGGATGATGATTGGCAATCAATGTG
CATTGATTATCTTGGAGCTGCTCCGCCAGAGTTT
Found at i:544028 original size:21 final size:21
Alignment explanation
Indices: 543998--544045 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
543988 GCAAGGGTAC
* *
543998 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
544019 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
544040 ATGCCA
1 ATGCCA
544046 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:544075 original size:21 final size:21
Alignment explanation
Indices: 544049--544121 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
544039 TATGCCATCT
*
544049 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
544070 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
544091 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
544112 CCGCAGGGTT
1 CCGCAGGGTT
544122 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:544707 original size:33 final size:34
Alignment explanation
Indices: 544644--544740 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
544634 AAATGTTTTT
* *
544644 AAAATACAAATTATATTATTCGAAACTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
544678 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
544711 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
544741 CATTAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 27 0.50
34 27 0.50
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:544747 original size:34 final size:33
Alignment explanation
Indices: 544642--544747 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
544632 ATAAATGTTT
* *
544642 TTAAAATACAAATTATATTATTCGAAACTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAA-TTTAAA
* *
544676 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
544708 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
544743 TTAAA
1 TTAAA
544748 TTTCAACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 5 0.08
33 22 0.36
34 33 0.54
35 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:545365 original size:128 final size:128
Alignment explanation
Indices: 545132--545433 Score: 559
Period size: 128 Copynumber: 2.4 Consensus size: 128
545122 AGTTATTCAA
*
545132 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
545197 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGACTTCATATGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGACTTCATATGAATAGTGAAATAATAGGT
*
545260 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* * *
545325 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATGT
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGACTTCATATGAATAGTGAAATAATAGGT
545388 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGG
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGG
545434 GAGGACACGC
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 168 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGACTTCATATGAATAGTGAAATAATAGGT
Found at i:548644 original size:23 final size:22
Alignment explanation
Indices: 548614--548656 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
548604 TAATAATAAT
548614 AACAATAATAAT-TAAATATATA
1 AACAATAA-AATATAAATATATA
548636 AACATATAAAATATAAATATA
1 AACA-ATAAAATATAAATATA
548657 AATAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
AACAATAAAATATAAATATATA
Found at i:550028 original size:3 final size:3
Alignment explanation
Indices: 550020--550153 Score: 211
Period size: 3 Copynumber: 45.0 Consensus size: 3
550010 GTAATAGTAT
*
550020 TAA TAA TAA TAA TAA TAA TAA AAA TAA GTAA T-A TAA TAA -AA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
*
550063 TAA TAA TAA TAG TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
550109 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
550154 ACAAATGGAT
Statistics
Matches: 123, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
2 6 0.05
3 111 0.90
4 6 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:550745 original size:123 final size:123
Alignment explanation
Indices: 550518--550934 Score: 573
Period size: 119 Copynumber: 3.4 Consensus size: 123
550508 GAATTAAGGC
* * *
550518 AAGGTTGAACAAATTCTTCTTATTATGAACTTCTTC-TCCTTCTT-AGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
* *
550581 TGAACTCTTC-C-GGAAATA-TTGATGCCGATCTATCTCTTTCTGTGATAGAGTCACACAA
65 TGAACT-TTCTCTGGAAA-AGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCACACAA
** * * * *
550639 AAGGTTGAACAAGCTCTTCGCATTATGAAATTATTCTTCATCTTCAGATAAATTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
**
550704 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGC-A
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCACACAA
* *
550761 AAGGTTGAACAAGTTCTTCTCATTATG-AA--CTTCTTCCTCTTCAGATAAGTTTTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
550823 GAACTTTCTCTGGAAAAGTTGATGCTGATTTATCTCCTTCTGTGATAGAGTCACTCAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCACACAA
* *
550881 AAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTT
1 AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTT
550935 GTTGAAAACA
Statistics
Matches: 262, Mismatches: 25, Indels: 16
0.86 0.08 0.05
Matches are distributed among these distances:
119 82 0.31
120 26 0.10
121 40 0.15
122 53 0.20
123 61 0.23
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (123 bp):
AAGGTTGAACAAATTCTTCTCATTATGAAATTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCACACAA
Found at i:551297 original size:19 final size:19
Alignment explanation
Indices: 551273--551343 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
551263 AGTGCATTTG
551273 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
551292 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
551311 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
551330 ATGCATCGATGCAC
1 ATGCATCGATGCAC
551344 TCTGGCTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Found at i:558468 original size:14 final size:15
Alignment explanation
Indices: 558443--558471 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
558433 TTGATTTTGA
558443 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
558458 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
558472 AAATGTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:558525 original size:2 final size:2
Alignment explanation
Indices: 558518--558547 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
558508 TTTGAACTTA
558518 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
558548 TTGGGTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559229 original size:45 final size:44
Alignment explanation
Indices: 559174--559325 Score: 150
Period size: 45 Copynumber: 3.4 Consensus size: 44
559164 GCACCAATCC
559174 ATGCATCGATGCACTAT-GTATTAAATTGAACATCGAATGCATTTT
1 ATGCATCGATGCACTATAGTATT--ATTGAACATCGAATGCATTTT
** * * *
559219 ATGCATCGATGCAC-ATACCATTCATCGATGCACTC-AATGCATTTG
1 ATGCATCGATGCACTATAGTATT-ATTGA-ACA-TCGAATGCATTTT
* *
559264 ATGCATCAATGCACTATGGCTATT-TTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTATAG-TATTATTG-AACATCGAATGCATTTT
559309 ATGCATCGATGCACTAT
1 ATGCATCGATGCACTAT
559326 TAGTGCACCG
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
44 8 0.09
45 70 0.81
46 5 0.06
47 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (44 bp):
ATGCATCGATGCACTATAGTATTATTGAACATCGAATGCATTTT
Found at i:560419 original size:22 final size:22
Alignment explanation
Indices: 560394--560477 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
560384 AAATCCAATA
* * *
560394 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
560416 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
* * *
560438 AATATATAATCTTTTAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
560460 AATCTATCATCTTTGAAG
1 AATCTATCATCTTTGAAG
560478 GTTGTAGATG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:561109 original size:18 final size:18
Alignment explanation
Indices: 561086--561123 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
561076 TATAAAAAAG
*
561086 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTCGAA
561104 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCGAA
561122 AA
1 AA
561124 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCGAA
Found at i:561484 original size:13 final size:14
Alignment explanation
Indices: 561463--561509 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
561453 TTGACCCTCC
*
561463 TTTTCTATTTTC-T
1 TTTTTTATTTTCAT
561476 TTTTTTA-TTTCAT
1 TTTTTTATTTTCAT
*
561489 TTTTTTCTTTTTCAT
1 TTTTTT-ATTTTCAT
561504 TTTTTT
1 TTTTTT
561510 CCTTCAAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.14
13 13 0.45
15 12 0.41
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTATTTTCAT
Found at i:561493 original size:15 final size:15
Alignment explanation
Indices: 561463--561510 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
561453 TTGACCCTCC
561463 TTTTCTATTTTC--TT
1 TTTTCT-TTTTCATTT
*
561477 TTTT-TATTTCATTT
1 TTTTCTTTTTCATTT
561491 TTTTCTTTTTCATTT
1 TTTTCTTTTTCATTT
561506 TTTTC
1 TTTTC
561511 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 1 0.03
14 10 0.34
15 14 0.48
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTTCATTT
Found at i:569136 original size:12 final size:12
Alignment explanation
Indices: 569119--569143 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
569109 ATACCATACT
569119 ACTTCTTTCTTC
1 ACTTCTTTCTTC
569131 ACTTCTTTCTTC
1 ACTTCTTTCTTC
569143 A
1 A
569144 TAGAAATCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (12 bp):
ACTTCTTTCTTC
Found at i:572897 original size:8 final size:8
Alignment explanation
Indices: 572886--572925 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
572876 CAATAATAAT
572886 TAAATATA
1 TAAATATA
572894 TAAATATA
1 TAAATATA
572902 TAAAT-T-
1 TAAATATA
572908 TAAA-ATA
1 TAAATATA
*
572915 TAAATAAA
1 TAAATATA
572923 TAA
1 TAA
572926 TGACTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
6 5 0.18
7 5 0.18
8 18 0.64
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAATATA
Found at i:572907 original size:21 final size:21
Alignment explanation
Indices: 572885--572925 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
572875 ACAATAATAA
*
572885 TTAAATATATAAATATATAAAT
1 TTAAA-ATATAAATAAATAAAT
572907 TTAAAATATAAATAAATAA
1 TTAAAATATAAATAAATAA
572926 TGACTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TTAAAATATAAATAAATAAAT
Found at i:573918 original size:25 final size:25
Alignment explanation
Indices: 573889--573944 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
573879 AGGGCATCGG
573889 TGGCTTTTATAGCCACCACCGGTGA
1 TGGCTTTTATAGCCACCACCGGTGA
573914 TGGCTTTTATAGCCACCACCGGTGA
1 TGGCTTTTATAGCCACCACCGGTGA
573939 TGGCTT
1 TGGCTT
573945 CAGACCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (25 bp):
TGGCTTTTATAGCCACCACCGGTGA
Found at i:574344 original size:3 final size:3
Alignment explanation
Indices: 574338--574435 Score: 92
Period size: 3 Copynumber: 32.0 Consensus size: 3
574328 TTAATATTAT
* * * *
574338 TAA TAA TAA TAA AAA TAA GTAA T-A TAA TAA AAA TTAA AAA TAA TAG
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* *
574384 TAA TAAA TAA -ATA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA AAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
574430 TAA TAA
1 TAA TAA
574436 AAAACAAATG
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.04
3 65 0.84
4 9 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:575796 original size:17 final size:18
Alignment explanation
Indices: 575774--575812 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
575764 AATTATTATG
575774 AATAAAAAAACATA-AAA
1 AATAAAAAAACATATAAA
* *
575791 AATAAATATACATATAAA
1 AATAAAAAAACATATAAA
575809 AATA
1 AATA
575813 TATATAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
AATAAAAAAACATATAAA
Found at i:575811 original size:18 final size:17
Alignment explanation
Indices: 575783--575818 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
575773 GAATAAAAAA
575783 ACATAAAAAATAAATAT
1 ACATAAAAAATAAATAT
*
575800 ACATATAAAAATATATAT
1 ACATA-AAAAATAAATAT
575818 A
1 A
575819 AGAAACAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
ACATAAAAAATAAATAT
Found at i:578448 original size:36 final size:37
Alignment explanation
Indices: 578383--578452 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
578373 TTTTTATATT
578383 TTTAATTTTGTAAAAAAAAGTATATAAATATTTTGAA
1 TTTAATTTTGTAAAAAAAAGTATATAAATATTTTGAA
* *
578420 TTTAATTTTTTAAAGAAAA-TATATAAATATTTT
1 TTTAATTTTGTAAAAAAAAGTATATAAATATTTT
578453 TCAACTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAAGTATATAAATATTTTGAA
Found at i:579325 original size:17 final size:17
Alignment explanation
Indices: 579303--579336 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
579293 TGTTAATAAG
* *
579303 TCAAATCATTTTCTTTC
1 TCAAATAATTTTATTTC
579320 TCAAATAATTTTATTTC
1 TCAAATAATTTTATTTC
579337 ATATATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (17 bp):
TCAAATAATTTTATTTC
Found at i:586479 original size:2 final size:2
Alignment explanation
Indices: 586472--586515 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
586462 TATAAGTGAC
586472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
586514 AT
1 AT
586516 GTTTACATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:586948 original size:20 final size:21
Alignment explanation
Indices: 586904--586953 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
586894 TCGAGGGTTT
586904 CATAGGTCCTTCAAGACATATA
1 CATAGGTCCTTCAAGACA-ATA
*
586926 CATAGGTCCTTCAGGAC-ATA
1 CATAGGTCCTTCAAGACAATA
586946 CATAGGTC
1 CATAGGTC
586954 ATTGAGGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (21 bp):
CATAGGTCCTTCAAGACAATA
Found at i:586961 original size:20 final size:20
Alignment explanation
Indices: 586904--586961 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
586894 TCGAGGGTTT
* *
586904 CATAGGTCCTTCAAGACATATA
1 CATAGGTCATTCAGGAC--ATA
*
586926 CATAGGTCCTTCAGGACATA
1 CATAGGTCATTCAGGACATA
*
586946 CATAGGTCATTGAGGA
1 CATAGGTCATTCAGGA
586962 TAAATTTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 17 0.52
22 16 0.48
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
CATAGGTCATTCAGGACATA
Found at i:590505 original size:44 final size:44
Alignment explanation
Indices: 590433--590528 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
590423 TTGTGCAATG
* * *
590433 TGCATAGATACACTATGAAAGTGTACCGATGCATCCCTTGAATA
1 TGCATCGACACACTATGAAAGTGCACCGATGCATCCCTTGAATA
* *
590477 TGCATCGACACACTAT-AAAGGTGCACCGATGCATGCCTTGAATG
1 TGCATCGACACACTATGAAA-GTGCACCGATGCATCCCTTGAATA
590521 TGCATCGA
1 TGCATCGA
590529 TATACTCTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (44 bp):
TGCATCGACACACTATGAAAGTGCACCGATGCATCCCTTGAATA
Found at i:592848 original size:12 final size:14
Alignment explanation
Indices: 592821--592855 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
592811 AGGGGGAGTA
592821 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
592835 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
592847 ATTTTCAAA
1 ATTTTCAAA
592856 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:593315 original size:65 final size:64
Alignment explanation
Indices: 593193--593321 Score: 161
Period size: 65 Copynumber: 2.0 Consensus size: 64
593183 AATTCAAACT
* * * * *
593193 CATTTTGTGTACAGATGCATAACCATGCATTGATGCACTCTTGATTTTATTGAAACATCAAATG
1 CATTTTATGTACAGATGCATAACCATGCATCGATGCACTCTGGATCTTATTAAAACATCAAATG
* * *
593257 CATTTTATGTACCGATGCATAGACCATGCATCGATGCACTCCTGGCTCTT-TTAAAACATCGAAT
1 CATTTTATGTACAGATGCATA-ACCATGCATCGATGCACT-CTGGATCTTATTAAAACATCAAAT
593321 G
64 G
593322 TAATTAGTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
64 19 0.35
65 30 0.55
66 6 0.11
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (64 bp):
CATTTTATGTACAGATGCATAACCATGCATCGATGCACTCTGGATCTTATTAAAACATCAAATG
Found at i:593333 original size:65 final size:65
Alignment explanation
Indices: 593199--593340 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 65
593189 AACTCATTTT
* * * * *
593199 GTGTACAGATGCATAACCATGCATTGATGCACTCTTGATTTTATTGAAACATCAAATGCATTTTA
1 GTGTACAGATGCATAACCATGCATCGATGCACTCTGGATCTTATTAAAACATCAAATGCATATTA
* * * *
593264 -TGTACCGATGCATAGACCATGCATCGATGCACTCCTGGCTCTT-TTAAAACATCGAATGTA-AT
1 GTGTACAGATGCATA-ACCATGCATCGATGCACT-CTGGATCTTATTAAAACATCAAATGCATAT
593326 TA
64 TA
*
593328 GTGTACTGATGCA
1 GTGTACAGATGCA
593341 CTAGGTCTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
64 16 0.25
65 42 0.66
66 6 0.09
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (65 bp):
GTGTACAGATGCATAACCATGCATCGATGCACTCTGGATCTTATTAAAACATCAAATGCATATTA
Found at i:597285 original size:2 final size:2
Alignment explanation
Indices: 597278--597404 Score: 247
Period size: 2 Copynumber: 64.0 Consensus size: 2
597268 GGTATAAGTG
597278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
597320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
597362 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
597403 AT
1 AT
597405 GTTTACATAA
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 123 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:597821 original size:22 final size:20
Alignment explanation
Indices: 597793--597842 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
597783 TCGAGGGTTT
597793 CATAGGTCCTTCAAGACATATA
1 CATAGGTCCTTCAAGAC--ATA
*
597815 CATAGGTCCTTCAGGACATA
1 CATAGGTCCTTCAAGACATA
597835 CATAGGTC
1 CATAGGTC
597843 ATTGAGGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
CATAGGTCCTTCAAGACATA
Found at i:597837 original size:20 final size:20
Alignment explanation
Indices: 597793--597852 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
597783 TCGAGGGTTT
*
597793 CATAGGTCCTTCAAGACATATA
1 CATAGGTCCTTCAGGAC--ATA
597815 CATAGGTCCTTCAGGACATA
1 CATAGGTCCTTCAGGACATA
* *
597835 CATAGGTCATTGAGGACA
1 CATAGGTCCTTCAGGACA
597853 AATTTCACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 19 0.54
22 16 0.46
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
CATAGGTCCTTCAGGACATA
Found at i:604865 original size:15 final size:15
Alignment explanation
Indices: 604845--604895 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
604835 CTTAAAGTTT
604845 AAATATTAAATTAAA
1 AAATATTAAATTAAA
*
604860 AAATATATGAAATT--T
1 AAATAT-T-AAATTAAA
604875 AAATATTAAATTAAA
1 AAATATTAAATTAAA
604890 AAATAT
1 AAATAT
604896 ATGAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 18 0.60
16 1 0.03
17 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATATTAAATTAAA
Found at i:604872 original size:17 final size:17
Alignment explanation
Indices: 604847--604903 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
604837 TAAAGTTTAA
*
604847 ATATTAAATTAAAAAAT
1 ATATGAAATTAAAAAAT
*
604864 ATATGAAATT--TAAAT
1 ATATGAAATTAAAAAAT
604879 AT-T-AAATTAAAAAAT
1 ATATGAAATTAAAAAAT
604894 ATATGAAATT
1 ATATGAAATT
604904 TAAATATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 5 0.15
14 1 0.03
15 12 0.36
16 1 0.03
17 14 0.42
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (17 bp):
ATATGAAATTAAAAAAT
Found at i:604878 original size:30 final size:30
Alignment explanation
Indices: 604842--604914 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
604832 GAACTTAAAG
604842 TTTAAATATTAAATTAAAAAATATATGAAA
1 TTTAAATATTAAATTAAAAAATATATGAAA
604872 TTTAAATATTAAATTAAAAAATATATGAAA
1 TTTAAATATTAAATTAAAAAATATATGAAA
604902 TTTAAATATTAAA
1 TTTAAATATTAAA
604915 AATTAGTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTAAATATTAAATTAAAAAATATATGAAA
Found at i:604908 original size:15 final size:15
Alignment explanation
Indices: 604860--604910 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
604850 TTAAATTAAA
604860 AAATATATGAAATTT
1 AAATATATGAAATTT
*
604875 AAATAT-T-AAATTAAA
1 AAATATATGAAATT--T
604890 AAATATATGAAATTT
1 AAATATATGAAATTT
604905 AAATAT
1 AAATAT
604911 TAAAAATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 5 0.17
14 1 0.03
15 18 0.60
16 1 0.03
17 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (15 bp):
AAATATATGAAATTT
Found at i:617461 original size:30 final size:30
Alignment explanation
Indices: 617425--617485 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
617415 GGGGCATAGG
617425 GAGGAGGGTATCCCTGAGCAGGATAACCTT
1 GAGGAGGGTATCCCTGAGCAGGATAACCTT
* * *
617455 GAGGAGGGTATCCTTGAGGAGGATACCCTT
1 GAGGAGGGTATCCCTGAGCAGGATAACCTT
617485 G
1 G
617486 TGGCGGTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (30 bp):
GAGGAGGGTATCCCTGAGCAGGATAACCTT
Found at i:617469 original size:15 final size:15
Alignment explanation
Indices: 617425--617476 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
617415 GGGGCATAGG
*
617425 GAGGAGGGTATCCCT
1 GAGGAGGGTATCCTT
* * *
617440 GAGCAGGATAACCTT
1 GAGGAGGGTATCCTT
617455 GAGGAGGGTATCCTT
1 GAGGAGGGTATCCTT
617470 GAGGAGG
1 GAGGAGG
617477 ATACCCTTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.19
Consensus pattern (15 bp):
GAGGAGGGTATCCTT
Found at i:617484 original size:15 final size:15
Alignment explanation
Indices: 617425--617485 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
617415 GGGGCATAGG
*
617425 GAGGAGGGTATCCC-T
1 GAGGAGGATA-CCCTT
* *
617440 GAGCAGGATAACCTT
1 GAGGAGGATACCCTT
* *
617455 GAGGAGGGTATCCTT
1 GAGGAGGATACCCTT
617470 GAGGAGGATACCCTT
1 GAGGAGGATACCCTT
617485 G
1 G
617486 TGGCGGTAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 2 0.05
15 35 0.95
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (15 bp):
GAGGAGGATACCCTT
Found at i:618274 original size:26 final size:27
Alignment explanation
Indices: 618225--618275 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
618215 TCAAATTAAA
* *
618225 AAAATATTGATAATAAAGATAATTGAT
1 AAAATATTGAGAATAAAGACAATTGAT
*
618252 AAAAT-TTGAGAATATAGACAATTG
1 AAAATATTGAGAATAAAGACAATTG
618276 TATTCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.14, T:0.31
Consensus pattern (27 bp):
AAAATATTGAGAATAAAGACAATTGAT
Found at i:622526 original size:31 final size:31
Alignment explanation
Indices: 622488--622581 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
622478 CCCGAAGGAC
*
622488 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
622519 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
622550 CAGTCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
622581 C
1 C
622582 CCTCGACCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:623371 original size:64 final size:64
Alignment explanation
Indices: 623234--623394 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
623224 CTTTCAATGT
* * * *
623234 AAGTATGCATCGATGGACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTAC
1 AAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAA
** * * * *
623298 TGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAA
1 AAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATG-TTGTATTATTAA
*
623362 AAG-AGTGCATCGATGCACTACCAATGCATCGAT
1 AAGTA-TGCATCGATGCACTACTAATGCATCGAT
623395 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 75 0.91
65 6 0.07
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (64 bp):
AAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAA
Found at i:626883 original size:31 final size:31
Alignment explanation
Indices: 626845--626969 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
626835 CCCAAAGGAC
*
626845 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
626876 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
626907 CAGTCTATATGTCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
626938 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
626969 C
1 C
626970 CCTCTACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:627759 original size:64 final size:64
Alignment explanation
Indices: 627621--627782 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 64
627611 TCTTTTAATG
* *
627621 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTATATTATTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTATATTATTA
*** * * * *
627685 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATG-TTATATTATTA
*
627749 AAAG-AGTGCATCGATGCACTACCAATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTAATGCATCGAT
627783 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 76 0.92
65 6 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTATATTATTA
Found at i:627844 original size:21 final size:21
Alignment explanation
Indices: 627820--627872 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
627810 ACCTTGATGT
627820 ATCGATGCACTATGAATGTGC
1 ATCGATGCACTATGAATGTGC
627841 ATCGATGCACTATGAATGTGC
1 ATCGATGCACTATGAATGTGC
627862 ATCGATGCACT
1 ATCGATGCACT
627873 CTGCCCAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTATGAATGTGC
Found at i:628349 original size:3 final size:3
Alignment explanation
Indices: 628341--628370 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
628331 TCTCGTACAT
*
628341 GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
628371 AATATATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:631304 original size:19 final size:22
Alignment explanation
Indices: 631280--631324 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
631270 TATTCATAAC
631280 AAAAATC-A-AAT-TTAAAATA
1 AAAAATCGATAATATTAAAATA
*
631299 AAAAATCGATATTATTAAAATA
1 AAAAATCGATAATATTAAAATA
631321 AAAA
1 AAAA
631325 CAGAACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 2 0.09
22 12 0.55
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAATCGATAATATTAAAATA
Found at i:646397 original size:331 final size:331
Alignment explanation
Indices: 645941--646603 Score: 1269
Period size: 333 Copynumber: 2.0 Consensus size: 331
645931 TAACAAAAGT
645941 ATCATTTACTTTGTGTGAGCATTGCATAACAAGTAAGCAGCACCGGTTGAAATTCAACACGTCAA
1 ATCATTTACTTTGTGTGAGCATTGCATAACAAGTAAGCAGCACCGGTTGAAATTCAACACGTCAA
646006 ATCTAGAGGCAAAAGTGTTCTACAATTGGTTCATTCTAACGTATGGCAAGCACCGGTTACATCCC
66 ATCTAGAGGCAAAAGTGTTCTACAATTGGTTCATTCTAACGTATGGCAAGCACCGGTTACATCCC
*
646071 TAGGTGGAGCAAAAT-GTTGTCTCATTTA-TGATGACTACTCTAGGAGATGCTGAG-GTACCCTA
131 TAGGTGGAGCAAAATACTTGTCTCATTTATTGATGACTACTCTAGGAGATGCTGAGTGTACCCTA
646133 TTAAGAAGAAGTCATATGTTTTTAACTTTCAAAAACTTCAAAGCGCGGGGTGGAACTTGATTCTA
196 TTAAGAAGAAGTCATATGTTTTTAACTTTCAAAAACTTCAAAGCGC-GGGTGGAACTTGATTCTA
646198 GAAATAAGATCAAGTGTTTCATAACAGATAATGGAGGGAATACACAAGCAAAAAATTTGATGACT
260 GAAATAAGATCAAGTGTTTCATAACAGATAATGGAGGGAATACACAAGCAAAAAA-TTGATGACT
646263 TTTGCAAG
324 TTTGCAAG
646271 ATCATTTACTTTGTGTGAGCATTGCATAACAAGTAAGCAGCACCGGTTGAAATTCAACACGTCAA
1 ATCATTTACTTTGTGTGAGCATTGCATAACAAGTAAGCAGCACCGGTTGAAATTCAACACGTCAA
646336 ATTCTAGAGGCAAAAGTGTTCTACAATTGGTTCATTCTAACGTATGGCAAGCACCGGTTACATCC
66 A-TCTAGAGGCAAAAGTGTTCTACAATTGGTTCATTCTAACGTATGGCAAGCACCGGTTACATCC
646401 CTAGGTGGAGCAAAATACTTGTCTCATTTATTGATGACTACTCTAGGAGATGCTGAGTGTACCCT
130 CTAGGTGGAGCAAAATACTTGTCTCATTTATTGATGACTACTCTAGGAGATGCTGAGTGTACCCT
646466 ATTAAGAAGAAGTCATATGTTTTTAACTTTCAAAAACTTCAAAGCGCGGGTGGAACTTGATTCTA
195 ATTAAGAAGAAGTCATATGTTTTTAACTTTCAAAAACTTCAAAGCGCGGGTGGAACTTGATTCTA
646531 GAAATAAGATCAAGTGTTTCATAACAGATAATGGAGGGAATACACAAGCAAAAAATTGATGACTT
260 GAAATAAGATCAAGTGTTTCATAACAGATAATGGAGGGAATACACAAGCAAAAAATTGATGACTT
646596 TTGCAAG
325 TTGCAAG
646603 A
1 A
646604 AAGAAGGCAT
Statistics
Matches: 328, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
330 66 0.20
331 79 0.24
332 30 0.09
333 99 0.30
334 54 0.16
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (331 bp):
ATCATTTACTTTGTGTGAGCATTGCATAACAAGTAAGCAGCACCGGTTGAAATTCAACACGTCAA
ATCTAGAGGCAAAAGTGTTCTACAATTGGTTCATTCTAACGTATGGCAAGCACCGGTTACATCCC
TAGGTGGAGCAAAATACTTGTCTCATTTATTGATGACTACTCTAGGAGATGCTGAGTGTACCCTA
TTAAGAAGAAGTCATATGTTTTTAACTTTCAAAAACTTCAAAGCGCGGGTGGAACTTGATTCTAG
AAATAAGATCAAGTGTTTCATAACAGATAATGGAGGGAATACACAAGCAAAAAATTGATGACTTT
TGCAAG
Found at i:663308 original size:82 final size:83
Alignment explanation
Indices: 663156--663327 Score: 292
Period size: 82 Copynumber: 2.1 Consensus size: 83
663146 GAAATGTTAA
* * *
663156 AATAATAGTATATATGTTATCTGTATATGTTAAAAAAATTTAAATGATACTGAGTCTAGAAATAA
1 AATAATAGTATATATATTATCTGTATATGTTAAAAAAATTCAAATGATACCGAGTCTAGAAATAA
663221 AACGACAAGAACTTATCT
66 AACGACAAGAACTTATCT
*
663239 AATAATAGTATATATATTATCTGTATATGTT-AAAAAATTCCAATGATACCGAGTCTAGAAATAA
1 AATAATAGTATATATATTATCTGTATATGTTAAAAAAATTCAAATGATACCGAGTCTAGAAATAA
*
663303 AACGACAAGAACTTATGT
66 AACGACAAGAACTTATCT
663321 AATAATA
1 AATAATA
663328 AAAGTAATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 54 0.64
83 30 0.36
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (83 bp):
AATAATAGTATATATATTATCTGTATATGTTAAAAAAATTCAAATGATACCGAGTCTAGAAATAA
AACGACAAGAACTTATCT
Found at i:668000 original size:24 final size:24
Alignment explanation
Indices: 667973--668022 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
667963 ATAAAGAACC
667973 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
667997 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
668021 AA
1 AA
668023 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:669178 original size:9 final size:9
Alignment explanation
Indices: 669164--669206 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
669154 TAGTACACAT
669164 TTTTTTTTC
1 TTTTTTTTC
669173 TTTTTTTTC
1 TTTTTTTTC
669182 TTTTTTTTC
1 TTTTTTTTC
**
669191 -ACTTTTTC
1 TTTTTTTTC
669199 TTTTTTTT
1 TTTTTTTT
669207 ACGCTGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 6 0.21
9 23 0.79
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:669185 original size:17 final size:18
Alignment explanation
Indices: 669164--669206 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
669154 TAGTACACAT
**
669164 TTTTTTTTCTTTTTTTTC
1 TTTTTTTTCTACTTTTTC
669182 TTTTTTTTC-ACTTTTTC
1 TTTTTTTTCTACTTTTTC
669199 TTTTTTTT
1 TTTTTTTT
669207 ACGCTGCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTCTACTTTTTC
Found at i:673582 original size:24 final size:24
Alignment explanation
Indices: 673555--673603 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
673545 AATAAGAACC
673555 AAATAAA-CTTAAACATACCATTAA
1 AAATAAAGCTTAAACAT-CCATTAA
*
673579 AAATAAAGTTTAAACATCCATTAA
1 AAATAAAGCTTAAACATCCATTAA
673603 A
1 A
673604 CCAACCACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATAAAGCTTAAACATCCATTAA
Found at i:688368 original size:21 final size:20
Alignment explanation
Indices: 688333--688385 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
688323 ATTAATATCG
688333 GTACCCCCTGGGGGGAATCT
1 GTACCCCCTGGGGGGAATCT
*
688353 GTTCCCCCTGGAGGGGAATCT
1 GTACCCCCTGG-GGGGAATCT
*
688374 GTACCTCCTGGG
1 GTACCCCCTGGG
688386 TAATCTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.13, C:0.30, G:0.34, T:0.23
Consensus pattern (20 bp):
GTACCCCCTGGGGGGAATCT
Found at i:688660 original size:95 final size:95
Alignment explanation
Indices: 688466--688660 Score: 347
Period size: 95 Copynumber: 2.1 Consensus size: 95
688456 TAAAATTGTT
688466 TTAAAATAGTTTAAGTATAAAACACAATTTTACACTTTAGTAAGGATTAAATGAACTTTGAAAGA
1 TTAAAATAGTTTAAGTATAAAACACAATTTTACACTTTAGTAAGGATTAAATGAACTTTGAAAGA
* **
688531 CTTGGAGTAATATTTTGATATTCGATTGTT
66 CTTGGAGTAATATTTTGATATTCGAATGAA
688561 TTAAAATAGTTTAAGTATAAAACACAATTTTACACTTTAGTAAGGATTAAAATGAACTTTGAAAG
1 TTAAAATAGTTTAAGTATAAAACACAATTTTACACTTTAGTAAGGATT-AAATGAACTTTGAAAG
688626 ACTTGGAGTAATATTTTGATATTCGAAT-AA
65 ACTTGGAGTAATATTTTGATATTCGAATGAA
688656 TTAAA
1 TTAAA
688661 TCGAATATAC
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
95 53 0.55
96 43 0.45
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (95 bp):
TTAAAATAGTTTAAGTATAAAACACAATTTTACACTTTAGTAAGGATTAAATGAACTTTGAAAGA
CTTGGAGTAATATTTTGATATTCGAATGAA
Found at i:691021 original size:20 final size:21
Alignment explanation
Indices: 690964--691026 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
690954 CCGTTAGACA
*
690964 GGGGGAATATGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
690985 GGGGGAATTTGTTCCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
691006 GGGGG-ATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
691026 G
1 G
691027 TAATCTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.13, C:0.25, G:0.40, T:0.22
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:692007 original size:2 final size:2
Alignment explanation
Indices: 692000--692027 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
691990 TGTTTGCACA
692000 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
692028 TTGTTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:694755 original size:18 final size:19
Alignment explanation
Indices: 694720--694756 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
694710 CACGGAATGT
694720 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
694740 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
694757 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:699973 original size:49 final size:49
Alignment explanation
Indices: 699911--700004 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
699901 AAATTAGAAT
* * *
699911 AACACCCCAATACCAAAGGAACAATTTAAATAAGAGGCCACAAACAAAA
1 AACACCCCAATACCAAAGAAACAATATAAATAAGAGACCACAAACAAAA
* *
699960 AACACCCCCATACCGAAGAAACAATATAAATAAGAGACCACAAAC
1 AACACCCCAATACCAAAGAAACAATATAAATAAGAGACCACAAAC
700005 GATTAAGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.54, C:0.27, G:0.10, T:0.10
Consensus pattern (49 bp):
AACACCCCAATACCAAAGAAACAATATAAATAAGAGACCACAAACAAAA
Found at i:702107 original size:22 final size:22
Alignment explanation
Indices: 702075--702118 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
702065 CGATGTACCG
*
702075 AATCGCGATTTTGAAACGATCC
1 AATCGCAATTTTGAAACGATCC
702097 AATCGCAATTTTGAAACGATCC
1 AATCGCAATTTTGAAACGATCC
702119 GAACGCGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (22 bp):
AATCGCAATTTTGAAACGATCC
Found at i:712106 original size:2 final size:2
Alignment explanation
Indices: 712099--712143 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
712089 ATTGGTGTTT
712099 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
712141 TA T
1 TA T
712144 GCATATTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:715196 original size:29 final size:30
Alignment explanation
Indices: 715158--715214 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
715148 TGCATTTACA
715158 TTTACATTTGCATTCACATCTTT-GCATTT
1 TTTACATTTGCATTCACATCTTTCGCATTT
* * * *
715187 TTTACGTTTGTATTTACATTTTTCGCAT
1 TTTACATTTGCATTCACATCTTTCGCAT
715215 CTTTGTATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.19, C:0.18, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTACATTTGCATTCACATCTTTCGCATTT
Found at i:720235 original size:40 final size:40
Alignment explanation
Indices: 720184--720317 Score: 223
Period size: 40 Copynumber: 3.4 Consensus size: 40
720174 ATTTAATAAC
* *
720184 GAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAATA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
* *
720224 GAAGATATTATCTCATTCAAGATTGTTTTTCCTTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
*
720264 GAAGATTTTATCTCACTCAAGATTGTTTTTCATTGAAACA
1 GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
720304 GAAGATTTTATCTC
1 GAAGATTTTATCTC
720318 GCTTTAGATA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (40 bp):
GAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
Found at i:720407 original size:36 final size:36
Alignment explanation
Indices: 720323--720415 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
720313 ATCTCGCTTT
* *
720323 AGATAGTTTCCCTCGAAACAAATTTTGTCTCCCTTG
1 AGATAGTTTCCCTTGAAACAAATTTTGTCTCCATTG
**
720359 AGACGGTTTCCCTTGAAACAAATTTTGTCTCCATTG
1 AGATAGTTTCCCTTGAAACAAATTTTGTCTCCATTG
* *
720395 AGATAGTCTCCCTTGAGACAA
1 AGATAGTTTCCCTTGAAACAA
720416 TTTCACTTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (36 bp):
AGATAGTTTCCCTTGAAACAAATTTTGTCTCCATTG
Found at i:720464 original size:54 final size:51
Alignment explanation
Indices: 720349--720464 Score: 117
Period size: 51 Copynumber: 2.2 Consensus size: 51
720339 AACAAATTTT
* ** * *
720349 GTCTCCCTTGAGACGGTTTCCCTTGAAACAAATTTTGTCTCCATTGAGATA
1 GTCTCACTTGAGACAATTTCACTTGAAACAAATTTTATCTCCATTGAGATA
* *
720400 GTCTCCCTTGAGACAATTTCACTTGAAACAGAAGATTTTATCTCGC-TTGAGATT
1 GTCTCACTTGAGACAATTTCACTTGAAAC--AA-ATTTTATCTC-CATTGAGATA
*
720454 GTTTCACTTGA
1 GTCTCACTTGA
720465 AACATAAGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
51 26 0.48
53 2 0.04
54 25 0.46
55 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (51 bp):
GTCTCACTTGAGACAATTTCACTTGAAACAAATTTTATCTCCATTGAGATA
Found at i:720491 original size:39 final size:39
Alignment explanation
Indices: 720401--720497 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
720391 ATTGAGATAG
* * *
720401 TCTCCCTTGAGACAATTTCACTTGAAACAGAAGATTTTA
1 TCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTA
* *
720440 TCTCGCTTGAGATTGTTTCACTTGAAACATAAGATTTTA
1 TCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTA
720479 TCTCGCTTGAGATAGTTTC
1 TCTCGCTTGAGATAGTTTC
720498 GCTCGACAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (39 bp):
TCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTTA
Found at i:720564 original size:43 final size:43
Alignment explanation
Indices: 720511--720728 Score: 249
Period size: 43 Copynumber: 4.8 Consensus size: 43
720501 CGACAATATT
*
720511 TTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
1 TTGAGGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
720554 TTGAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAATTTGATGAAAAGC
1 TTGAGGAACCATCGTGATATGTAGGGG----TT--T--C----TTGATGAAAAGC
* * *
720609 TTGAAGGACCATCGTGATATGTAGGGG-TTCTTTGATGACAAGC
1 TTGAGGAACCATCGTGATATGTAGGGGTTTC-TTGATGAAAAGC
* *
720652 TTCAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
1 TTGAGGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
*
720695 TTGAGGAACCATCGTGATATGTAGGGGTTCCTTG
1 TTGAGGAACCATCGTGATATGTAGGGGTTTCTTG
720729 GTGATAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 26
0.80 0.06 0.14
Matches are distributed among these distances:
43 103 0.69
44 3 0.02
46 1 0.01
47 2 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 1 0.01
55 37 0.25
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (43 bp):
TTGAGGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
Found at i:720626 original size:55 final size:55
Alignment explanation
Indices: 720542--720649 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
720532 TAGGGGTTTC
720542 TTGATGAAAAGCTTGAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAAT
1 TTGATGAAAAGCTTGAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAAT
*
720597 TTGATGAAAAGCTTGAAGG-ACCATCGTGATATGTAGGGGTTCTTTGATGACAA
1 TTGATGAAAAGCTTG-AGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAA
720650 GCTTCAGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
55 48 0.94
56 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30
Consensus pattern (55 bp):
TTGATGAAAAGCTTGAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAAT
Found at i:720986 original size:89 final size:90
Alignment explanation
Indices: 720736--721058 Score: 472
Period size: 90 Copynumber: 3.6 Consensus size: 90
720726 TTGGTGATAA
* *
720736 TTAAGAAACTAAACCTTCGGGGGTTTCTT-AGTTTTTAAGTCCTTCGGACCATCCATAAGACCTT
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACCTT
*
720800 CAGTGCAAGATGTTTTCAAATGACAA-
65 CAGTGCAGGATGTTTTCAAATGA-AAT
*
720826 TTAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
* *
720891 AGTGCAGGATATTTTCAAATGAGAT
66 AGTGCAGGATGTTTTCAAATGAAAT
* * * *
720916 TTAAGAAACTGAGCCTTCGGGGGTTT-TTGATTTCTAAGTCCTTCGGGTCATCCATAAGACCATC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
720980 AGTGCAGGATGTTTTCAAATGAAATT
66 AGTGCAGGATGTTTTCAAATGAAA-T
* * * *
721006 TTAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTTTAAATCCTTTGGGTCATC
1 TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATC
721059 TGTAAGCCTT
Statistics
Matches: 213, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
89 58 0.27
90 131 0.62
91 24 0.11
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (90 bp):
TTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
AGTGCAGGATGTTTTCAAATGAAAT
Found at i:725326 original size:24 final size:24
Alignment explanation
Indices: 725294--725339 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
725284 AACCAAAGGA
725294 AAATAATAATATACCAAAGAAGAG
1 AAATAATAATATACCAAAGAAGAG
725318 AAATAATAATATACCAAAGAAG
1 AAATAATAATATACCAAAGAAG
725340 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (24 bp):
AAATAATAATATACCAAAGAAGAG
Found at i:725345 original size:24 final size:23
Alignment explanation
Indices: 725280--725345 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
725270 AGTGCTAAAA
*
725280 AATAAACCAAAG--GAAAATAAT
1 AATATACCAAAGAAGAAAATAAT
725301 AATATACCAAAGAAGAGAAATAAT
1 AATATACCAAAGAAGA-AAATAAT
725325 AATATACCAAAGAAGTAAAAT
1 AATATACCAAAGAAG-AAAAT
725346 TAAAATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 11 0.28
23 2 0.05
24 26 0.65
25 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.17
Consensus pattern (23 bp):
AATATACCAAAGAAGAAAATAAT
Found at i:726466 original size:3 final size:3
Alignment explanation
Indices: 726458--726496 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
726448 AATAAATAGG
726458 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
726497 TATATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:726479 original size:17 final size:17
Alignment explanation
Indices: 726459--726493 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
726449 ATAAATAGGA
726459 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
726476 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
726493 A
1 A
726494 ATATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:726481 original size:20 final size:20
Alignment explanation
Indices: 726458--726503 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 20
726448 AATAAATAGG
726458 AATAATAATAATAATAATAT
1 AATAATAATAATAATAATAT
726478 AATAATAATAATAATAATAT
1 AATAATAATAATAATAATAT
726498 ATATAA
1 A-ATAA
726504 AATTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAATAATAATAATAATAT
Found at i:726525 original size:24 final size:24
Alignment explanation
Indices: 726494--726564 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
726484 AATAATAATA
726494 ATAT-ATATAAAATTTTCAAAAAC
1 ATATAATATAAAATTTTCAAAAAC
* ***
726517 ATATAATAT-AACTTTTCAAATGT
1 ATATAATATAAAATTTTCAAAAAC
726540 ATTATAATATAAATATTTTCAAAAA
1 A-TATAATATAAA-ATTTTCAAAAA
726565 TGTTTTCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 15 0.41
24 12 0.32
25 2 0.05
26 8 0.22
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (24 bp):
ATATAATATAAAATTTTCAAAAAC
Found at i:726583 original size:28 final size:27
Alignment explanation
Indices: 726552--726645 Score: 66
Period size: 31 Copynumber: 3.2 Consensus size: 27
726542 TATAATATAA
726552 ATATTTTCAAAAATGTTTTCAAAACTATATAT
1 ATATTTTC-AAAATGTTTTCAAAAC----TAT
726584 ATAATTTTC-AAATG-TTTCAAAACTAT
1 AT-ATTTTCAAAATGTTTTCAAAACTAT
**
726610 ATTTAATTTTCAAAATGTTTAAAAAAACTAT
1 A--T-ATTTTCAAAATGTTT-TCAAAACTAT
726641 ATATT
1 ATATT
726646 ATATATTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
26 4 0.07
28 11 0.20
29 6 0.11
30 11 0.20
31 14 0.26
32 2 0.04
33 6 0.11
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (27 bp):
ATATTTTCAAAATGTTTTCAAAACTAT
Found at i:726619 original size:61 final size:58
Alignment explanation
Indices: 726506--726653 Score: 147
Period size: 61 Copynumber: 2.4 Consensus size: 58
726496 ATATATAAAA
*
726506 TTTTCAAAAAC-ATATAATATAACTTTTCAAATGTATTATAATATAAATATTTTCAAAAATG
1 TTTTC-AAAACTATAT-ATATAA-TTTTCAAATGTATTAAAATATAAATATTTTC-AAAATG
**
726567 TTTTCAAAACTATATATATAATTTTCAAATGT-TTCAAAACTATATTTAATTTTCAAAATG
1 TTTTCAAAACTATATATATAATTTTCAAATGTATT-AAAA-TATAAAT-ATTTTCAAAATG
**
726627 TTTAAAAAAACTATATATTATATATTT
1 TTT-TCAAAACTATATA-TATA-ATTT
726654 ATTTTCAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
58 2 0.03
59 14 0.19
60 25 0.33
61 26 0.35
62 4 0.05
63 4 0.05
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (58 bp):
TTTTCAAAACTATATATATAATTTTCAAATGTATTAAAATATAAATATTTTCAAAATG
Found at i:726676 original size:70 final size:70
Alignment explanation
Indices: 726552--726793 Score: 265
Period size: 70 Copynumber: 3.5 Consensus size: 70
726542 TATAATATAA
* *
726552 ATATTTTCAAAAATGTTTTCAAAAC--TATA-TATATA---ATTTTC-AAATGTTT--CAAAACT
1 ATATTTTC-AAAATGTTTTGAAAACTATATATTATATATTTATTTTCAAAATGTTTAAAAAAACT
726608 ATATTT
65 ATATTT
**
726614 A-ATTTTCAAAATGTTTAAAAAAACTATATATTATATATTTATTTTCAAAATGTTTAAAAAAACT
1 ATATTTTCAAAATGTTT-TGAAAACTATATATTATATATTTATTTTCAAAATGTTTAAAAAAACT
726678 ATATATAT
65 ATAT-T-T
726686 ATATGTTTTCAAAATGTTTTGAAAACTATATATTATATA-TT-TTTTCAAAATGTTTTAAAAAAA
1 ATA--TTTTCAAAATGTTTTGAAAACTATATATTATATATTTATTTTCAAAATG-TTTAAAAAAA
*
726749 CTATAATAT
63 CTAT-ATTT
* *
726758 ATATATTCAAAAGGTTTTGAAAACTATATATTATAT
1 ATATTTTCAAAATGTTTTGAAAACTATATATTATAT
726794 TTTTGTAAAA
Statistics
Matches: 155, Mismatches: 8, Indels: 26
0.82 0.04 0.14
Matches are distributed among these distances:
60 9 0.06
61 11 0.07
62 1 0.01
63 4 0.03
64 6 0.04
67 6 0.04
68 8 0.05
70 41 0.26
71 1 0.01
72 17 0.11
73 17 0.11
74 20 0.13
75 14 0.09
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (70 bp):
ATATTTTCAAAATGTTTTGAAAACTATATATTATATATTTATTTTCAAAATGTTTAAAAAAACTA
TATTT
Found at i:726695 original size:36 final size:34
Alignment explanation
Indices: 726546--726879 Score: 250
Period size: 36 Copynumber: 9.7 Consensus size: 34
726536 ATGTATTATA
* **
726546 ATATAAATA-TTTTCAAAAATGTTTTCAAAACTAT
1 ATATATATATTTTTC-AAAATGTTTAAAAAACTAT
*
726580 ATATATA-A-TTTTC-AAATGTTT-CAAAACTAT
1 ATATATATATTTTTCAAAATGTTTAAAAAACTAT
726610 AT-T-TA-A-TTTTCAAAATGTTTAAAAAAACTAT
1 ATATATATATTTTTCAAAATGTTT-AAAAAACTAT
726641 ATATTATATATTTATTTTCAAAATGTTTAAAAAAACTAT
1 ATA-TATATA--T-TTTTCAAAATGTTT-AAAAAACTAT
**
726680 ATATATATATGTTTTCAAAATGTTTTGAAAACTAT
1 ATATATATAT-TTTTCAAAATGTTTAAAAAACTAT
726715 ATATTATATATTTTTTCAAAATGTTTTAAAAAAACTAT
1 ATA-TATATA-TTTTTCAAAATG-TTT-AAAAAACTAT
* * **
726753 A-ATATATA-TATTCAAAAGGTTTTGAAAACTAT
1 ATATATATATTTTTCAAAATGTTTAAAAAACTAT
* * *
726785 ATAT-TATATTTTTGTAAAAAACGTTTTAAACAAATTAT
1 ATATATATA-TTTT-T-CAAAATG-TTTAAA-AAACTAT
*
726823 ATATATATAAATGTTTTCAAAATGTTT-CAAAACTAT
1 ATATATAT--AT-TTTTCAAAATGTTTAAAAAACTAT
726859 AT-TATATA-TTTTC-AAATGTTT
1 ATATATATATTTTTCAAAATGTTT
726880 TCGAAAATAT
Statistics
Matches: 253, Mismatches: 21, Indels: 56
0.77 0.06 0.17
Matches are distributed among these distances:
28 8 0.03
29 9 0.04
30 19 0.08
31 23 0.09
32 13 0.05
33 13 0.05
34 19 0.08
35 18 0.07
36 51 0.20
37 10 0.04
38 28 0.11
39 36 0.14
40 2 0.01
41 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (34 bp):
ATATATATATTTTTCAAAATGTTTAAAAAACTAT
Found at i:726716 original size:74 final size:74
Alignment explanation
Indices: 726616--726870 Score: 312
Period size: 70 Copynumber: 3.5 Consensus size: 74
726606 CTATATTTAA
**
726616 TTTTCAAAATGTTTAAAAAAACTATATATTATATATTTATTTTCAAAATG-TTTAAAAAAACTAT
1 TTTTCAAAATGTTT-TGAAAACTATATATTATATATTT-TTTTCAAAATGTTTTAAAAAAACTAT
726680 ATATATATATG
64 ATATATATATG
726691 TTTTCAAAATGTTTTGAAAACTATATATTATATA-TTTTTTCAAAATGTTTTAAAAAAACTATA-
1 TTTTCAAAATGTTTTGAAAACTATATATTATATATTTTTTTCAAAATGTTTTAAAAAAACTATAT
726754 ATATATA--
66 ATATATATG
* * * ** * * *
726761 TATTCAAAAGGTTTTGAAAACTATATATTATAT-TTTTGTAAAAAACGTTTTAAACAAATTATAT
1 TTTTCAAAATGTTTTGAAAACTATATATTATATATTTTTTTCAAAATGTTTTAAAAAAACTATAT
726825 ATATATAAATG
66 ATATAT--ATG
*
726836 TTTTCAAAATG-TTTCAAAAC--TATATTATATATTTT
1 TTTTCAAAATGTTTTGAAAACTATATATTATATATTTT
726871 CAAATGTTTT
Statistics
Matches: 159, Mismatches: 13, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
70 54 0.34
71 6 0.04
72 28 0.18
73 22 0.14
74 26 0.16
75 23 0.14
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (74 bp):
TTTTCAAAATGTTTTGAAAACTATATATTATATATTTTTTTCAAAATGTTTTAAAAAAACTATAT
ATATATATG
Found at i:727714 original size:163 final size:163
Alignment explanation
Indices: 727393--728194 Score: 913
Period size: 162 Copynumber: 5.0 Consensus size: 163
727383 TATTGACAAA
* * * * * * * *
727393 AACCTTTCTCGCCATGAGTTATGTTGTAAATGATATGACTCGAAGTTGAGTGTAATCAAACTCG-
1 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCCGAAGCTGAGTGTAATCGAACTCGA
* *
727457 -GG---CTTGGCAGAT-AGCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGA
66 AGGTTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA-GTGCCTTGGAGCTGA
*
727517 GCGTAGTCGAACTCAAAGGTCTTTGGTCACAGAT
130 GCGTAGTCGAACTCAAAGGTCTTTGGTGACAGAT
* *
727551 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCCGAAGCTGAGTGTAATCAAACTCGA
1 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCCGAAGCTGAGTGTAATCGAACTCGA
* * * * *
727616 AGGTTTTGTTGGCAGACAACCCTTCTAGACTTAAGCTGTGCCGCAAATGA-TGCCTTGGAGCTGA
66 AGG-TTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAGTGCCTTGGAGCTGA
*
727680 GCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
130 GCGTAGTCGAACTCAAAGGTCTTTGGTGACAGAT
* *
727714 AA-CCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-T
1 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCC-CGAAGCTGAGTGTAATCGAACTCG
*
727777 AAGGGTCTT-TAGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAGTGCCTTGGAG
65 AA-GGT-TTCT--TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAGTGCCTTGGAG
*
727841 CTGAGCGTAGTCGAACTCAAA-GTCTTT-GTTAGCAGAT
126 CTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGA-CAGAT
* * * * * * * * ** *
727878 AACCCTTCTTGACTTAAGTTATACTGCAAATGATGTACCTTCGAAGCTGAACGTAGTCGAACTCG
1 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCC-CCGAAGCTGAGTGTAATCGAACTCG
* * * *
727943 AGGGTCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTG
65 AAGGTTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA-GTGCCTTGGAGCTG
* *
728007 AGCGTAGTCG-ACTCAAAGGTCTTTGCTAACAGAT
129 AGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGAT
* * *
728041 AACCCTTC-AGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-T
1 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCC-CGAAGCTGAGTGTAATCGAACTCG
* * * * * *
728104 AAGG-GTCTTGGCAGATAGCTCTTCT-AAATTAAGCTATACTGCAAATGATGTGCCTTGGAGCTG
65 AAGGTTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA-GTGCCTTGGAGCTG
*
728167 AGCGTAGTCGAACTCGAAGGTC-TTGGTG
129 AGCGTAGTCGAACTCAAAGGTCTTTGGTG
728195 GGCATAGCCT
Statistics
Matches: 550, Mismatches: 71, Indels: 44
0.83 0.11 0.07
Matches are distributed among these distances:
158 56 0.10
160 52 0.09
161 30 0.05
162 125 0.23
163 118 0.21
164 61 0.11
165 107 0.19
166 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (163 bp):
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCCGAAGCTGAGTGTAATCGAACTCGA
AGGTTTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAGTGCCTTGGAGCTGAG
CGTAGTCGAACTCAAAGGTCTTTGGTGACAGAT
Found at i:728081 original size:327 final size:324
Alignment explanation
Indices: 727393--728190 Score: 1035
Period size: 327 Copynumber: 2.5 Consensus size: 324
727383 TATTGACAAA
* * * * * * *
727393 AACCTTTCTCGCCATGAGTTATGTTGTAAATGATATG-ACTCGAAGTTGAGTGTAATCAAAC-T-
1 AACC-TTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTA
* * *
727455 CGGG-CTTGGCAGAT-AGCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAG
65 AGGGTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* * * *
727518 CGTAGTCGAACTCAAAGGTCTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
130 CGTAGTCGAACTCAAA-GTCTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATG
* ** * *
727583 ATGTGCCCCGAAGCTGAGTGTAATCAAACTCGAAGGTTTTGTTGGCAGACAACCCTTCTAGACTT
194 ATGTACCCCGAAGCTGAACGTAATCAAACTCGAAGGGTCTGTTGGCAGACAACCCTTCTAGACTT
* * * *
727648 AAGCTGTGCCGCAAATGATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
259 AAGCTATGCCGCAAATGATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGA
727713 T
324 T
727714 AACCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAA
1 AACCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAA
*
727779 GGGTCTTTAGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA-GTGCCTTGGAGCT
66 GGGTC--T--TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* *
727843 GAGCGTAGTCGAACTCAAAGTCTTT-GTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAA
127 GAGCGTAGTCGAACTCAAAGTCTTTGGTCA-CAGATAACCCTTCTAGACTTAAGTTATACTGCAA
* * * * * *
727907 ATGATGTACCTTCGAAGCTGAACGTAGTCGAACTCG-AGGGTCT-TTGGCAGATAGCCCTTCTCG
191 ATGATGTACC-CCGAAGCTGAACGTAATCAAACTCGAAGGGTCTGTTGGCAGACAACCCTTCTAG
* *
727970 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG-ACTCAAAGGTCTTTGCT
255 ACTTAAGCTATGCCGCAAATGA--TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCT
728034 AACAGAT
318 AACAGAT
*
728041 AACCCTTC-AGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTA
1 AA-CCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTA
* * * * *
728105 AGGGTCTTGGCAGATAGCTCTTCT-AAATTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAG
65 AGGGTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
*
728169 CGTAGTCGAACTCGAAGGTCTT
130 CGTAGTCGAACTC-AAAGTCTT
728191 GGTGGGCATA
Statistics
Matches: 419, Mismatches: 42, Indels: 29
0.86 0.09 0.06
Matches are distributed among these distances:
320 29 0.07
321 24 0.06
322 20 0.05
323 47 0.11
324 8 0.02
325 1 0.00
326 40 0.10
327 133 0.32
328 88 0.21
329 29 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (324 bp):
AACCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAA
GGGTCTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGTCTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGAT
GTACCCCGAAGCTGAACGTAATCAAACTCGAAGGGTCTGTTGGCAGACAACCCTTCTAGACTTAA
GCTATGCCGCAAATGATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGAT
Found at i:728090 original size:245 final size:241
Alignment explanation
Indices: 727460--728229 Score: 846
Period size: 245 Copynumber: 3.2 Consensus size: 241
727450 AAACTCGGGC
*
727460 TTGGCAGATAGCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTC
1 TTGGCAGATAGCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
727525 GAACTCAAAGGTCTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCC
66 GAACTCAAAGGTCTTT-GTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG-TATGCC
* * * *
727590 C-CGAAGCTGAGTGTAATCAAACTCGAAGGT-TTTGTTGGCAGACAACCCTTCTAGACTTAAGCT
129 CTTGAAGCTGAGTGTAATCGAACTC-AAGGTCTTTGTT-GCAGATAACCCTTCTTGACTTAAGCT
* * *
727653 GTGCCGCAAATGATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
192 ATACTGCAAATGATGTCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * * * * *
727702 TTGGTGACAGATAACCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGT
1 TT-G-G-CAGATAGCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
* * * ** * * * *
727767 AATCGAACTTAAGGGTCTTTAGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG-AG
62 AGTCGAACTCAAAGGTCTTT-GTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTA-
* * * *
727831 TG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGTCTTTGTTAGCAGATAACCCTTCTTGACTTAA
125 TGCCCTTGAAGCTGAGTGTAATCGAACTCAAGGTCTTTGTT-GCAGATAACCCTTCTTGACTTAA
* * * *
727895 GTTATACTGCAAATGATGTACCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCT
189 GCTATACTGCAAATGATGT-CCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTCT
*
727950 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAG-CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
728015 CG-ACTCAAAGGTCTTTGCTAACAGATAACCCTTC-AGCCTTGAGTTATGCTGTAAATGTTATGC
65 CGAACTCAAAGGTCTTTG-TAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG-TATGC
* * * * *
728078 CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTG--GCAGATAGCTCTTC-TAAATTAAGCT
128 CCTTGAAGCTGAGTGTAATCGAACTCAA-GGTCTTTGTTGCAGATAACCCTTCTTGACTTAAGCT
728139 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
192 ATACTGCAAATGATGT-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * *
728190 TGGTGG--GCATAGCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 T--TGGCAG-ATAGCCTTCTCGACTTAAGCTATGCTGCAAAT
728230 AGTTTGTTTA
Statistics
Matches: 434, Mismatches: 75, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
240 52 0.12
241 32 0.07
242 17 0.04
243 21 0.05
244 35 0.08
245 146 0.34
246 97 0.22
247 5 0.01
248 29 0.07
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (241 bp):
TTGGCAGATAGCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCAAAGGTCTTTGTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTATGCCCT
TGAAGCTGAGTGTAATCGAACTCAAGGTCTTTGTTGCAGATAACCCTTCTTGACTTAAGCTATAC
TGCAAATGATGTCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
Found at i:731492 original size:18 final size:19
Alignment explanation
Indices: 731451--731495 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
731441 AGTTAATGTG
731451 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
731470 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
731488 AATGCAAA
1 AATGCAAA
731496 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:733228 original size:21 final size:22
Alignment explanation
Indices: 733204--733265 Score: 56
Period size: 25 Copynumber: 2.7 Consensus size: 22
733194 AAATAGTGCT
733204 AAAAAATAAACCAAAGGAA-AG
1 AAAAAATAAACCAAAGGAAGAG
733225 AAAATAATAATATACCAAA-GAAGAG
1 AAAA-AAT-A-A-ACCAAAGGAAGAG
* *
733250 AAATAATATACCAAAG
1 AAAAAATAAACCAAAG
733266 AAGTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
21 10 0.30
22 3 0.09
23 2 0.06
24 7 0.21
25 11 0.33
ACGTcount: A:0.66, C:0.10, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAAATAAACCAAAGGAAGAG
Found at i:733241 original size:25 final size:22
Alignment explanation
Indices: 733204--733274 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
733194 AAATAGTGCT
*
733204 AAAA-AATAAACCAAAGGAAAGAA
1 AAAATAATATACCAAAGG-AAG-A
733227 AATAATAATATACCAAA-GAAGA
1 AA-AATAATATACCAAAGGAAGA
* *
733249 GAAATAATATACCAAA-GAAGT
1 AAAATAATATACCAAAGGAAGA
733270 AAAAT
1 AAAAT
733275 TAAAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 22 0.52
22 2 0.05
23 5 0.12
24 3 0.07
25 10 0.24
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAATAATATACCAAAGGAAGA
Found at i:734476 original size:3 final size:3
Alignment explanation
Indices: 734457--734514 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
734447 AAGAAAAATA
734457 AAT AAT AAAT AGA- AAT AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
734504 AA- AAT AAT AAT
1 AAT AAT AAT AAT
734515 CTATATAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 3 0.06
3 40 0.80
4 7 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:734478 original size:16 final size:15
Alignment explanation
Indices: 734451--734510 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
734441 AGAGAAAAGA
734451 AAAATAAATAATAAAT
1 AAAAT-AATAATAAAT
*
734467 AGAAATAATAATATAT
1 A-AAATAATAATAAAT
734483 AATAATAATAAT-AAT
1 AA-AATAATAATAAAT
734498 AATAATAA-AATAA
1 AA-AATAATAATAA
734511 TAATCTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.08
15 12 0.31
16 20 0.51
17 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAATAATAATAAAT
Found at i:734509 original size:23 final size:24
Alignment explanation
Indices: 734454--734514 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 24
734444 GAAAAGAAAA
734454 ATAAATAATAAATAGAAATAATAAT
1 ATAAATAAT-AATAGAAATAATAAT
734479 ATATAATAATAATA-ATAATAATAAT
1 ATA-AATAATAATAGA-AATAATAAT
734504 A-AAATAATAAT
1 ATAAATAATAAT
734515 CTATATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.26
24 2 0.06
25 17 0.50
26 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
ATAAATAATAATAGAAATAATAAT
Found at i:734557 original size:32 final size:30
Alignment explanation
Indices: 734521--734658 Score: 92
Period size: 32 Copynumber: 4.4 Consensus size: 30
734511 TAATCTATAT
734521 AAAATTTTCAAAACATATAATTATAACTTTTC
1 AAAATTTTCAAAAC-TATAATTATAA-TTTTC
*
734553 AAAATGTCTT--ATA-TAT-A-TA-AATATTTC
1 AAAAT-T-TTCAAAACTATAATTATAAT-TTTC
*
734580 AAAAATGTTTTC-AAACTATTATTATAATTTTC
1 -AAAA--TTTTCAAAACTATAATTATAATTTTC
734612 AAAATGTTTTCAAAACTATATATTATAATTTTC
1 AAAA--TTTTCAAAACTATA-ATTATAATTTTC
*
734645 AAAATGTTTAAAAA
1 AAAAT-TTTCAAAA
734659 AAAACTATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 28
0.73 0.03 0.23
Matches are distributed among these distances:
26 1 0.01
27 6 0.07
28 8 0.09
29 4 0.05
30 7 0.08
31 13 0.15
32 27 0.31
33 20 0.23
34 2 0.02
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (30 bp):
AAAATTTTCAAAACTATAATTATAATTTTC
Found at i:734686 original size:38 final size:38
Alignment explanation
Indices: 734606--734811 Score: 191
Period size: 38 Copynumber: 5.6 Consensus size: 38
734596 TATTATTATA
* * *
734606 ATTTTCAAAATGTTTT---CAAAACTATA-TAT-TATA
1 ATTTTCAAAATGTTTTAAAAAAAACTATATTATATTTT
*
734639 ATTTTCAAAATGTTTAAAAAAAAACTATATTATATTTT
1 ATTTTCAAAATGTTTTAAAAAAAACTATATTATATTTT
* *
734677 ATTTTCAAAATGTTTTAAAAAAAA-TATTATAATATATAT
1 ATTTTCAAAATGTTTTAAAAAAAACTA-TATTATAT-TTT
*
734716 ATTTTCAAAAATGTTTT---GAAAACTATATTATATATTT
1 ATTTTC-AAAATGTTTTAAAAAAAACTATATTATAT-TTT
* *
734753 A-TTTCAAAATGTTTTAAAAAAAACTATATAATA-TAT
1 ATTTTCAAAATGTTTTAAAAAAAACTATATTATATTTT
*
734789 ATATTTCAAAAATGTTTTGAAAA
1 AT-TTTC-AAAATGTTTTAAAAA
734812 CTATATATTT
Statistics
Matches: 144, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
33 15 0.10
35 10 0.07
36 16 0.11
37 20 0.14
38 51 0.35
39 22 0.15
40 10 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (38 bp):
ATTTTCAAAATGTTTTAAAAAAAACTATATTATATTTT
Found at i:734819 original size:38 final size:36
Alignment explanation
Indices: 734562--734891 Score: 239
Period size: 36 Copynumber: 9.2 Consensus size: 36
734552 CAAAATGTCT
* *
734562 TATATATATAAATATTTCAAAAATGTTTT-CAAACTA
1 TATATATATATATATTTC-AAAATGTTTTAAAAACTA
*
734598 T-TAT-TATA-AT-TTTCAAAATGTTTTCAAAACTA
1 TATATATATATATATTTCAAAATGTTTTAAAAACTA
*
734630 TATAT-TATA-AT-TTTCAAAATGTTTAAAAAAAAACTA
1 TATATATATATATATTTCAAAATGTTT---TAAAAACTA
* **
734666 TAT-TATAT-TTTATTTTCAAAATGTTTTAAAAAAAA
1 TATATATATATATA-TTTCAAAATGTTTTAAAAACTA
*
734701 TATTATAATATATATATTTTCAAAAATGTTTTGAAAACTA
1 TA-TAT-ATATATATA-TTTC-AAAATGTTTTAAAAACTA
*
734741 TAT-TATATATTTATTTCAAAATGTTTTAAAAAAAACTA
1 TATATATATATATATTTCAAAATGTTTT---AAAAACTA
*
734779 TATA-ATATATATATTTCAAAAATGTTTTGAAAACTA
1 TATATATATATATATTTC-AAAATGTTTTAAAAACTA
* * * *
734815 TATAT-T-T-T-T-TGTAAAAACGTTTTAAACAATTA
1 TATATATATATATATTTCAAAATGTTTTAAA-AACTA
* *
734847 TATA-ATATCA-ATGTTTTCAAAATGTTTCAAAAACTA
1 TATATATAT-ATAT-ATTTCAAAATGTTTTAAAAACTA
734883 TATATATAT
1 TATATATAT
734892 TTTCAAAATG
Statistics
Matches: 240, Mismatches: 25, Indels: 57
0.75 0.08 0.18
Matches are distributed among these distances:
31 21 0.09
32 22 0.09
33 26 0.11
34 5 0.02
35 24 0.10
36 40 0.17
37 26 0.11
38 40 0.17
39 19 0.08
40 17 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATATATATATTTCAAAATGTTTTAAAAACTA
Found at i:734871 original size:68 final size:72
Alignment explanation
Indices: 734659--734893 Score: 241
Period size: 68 Copynumber: 3.2 Consensus size: 72
734649 TGTTTAAAAA
* * * *
734659 AAAACTATAT-TATATTTTATTTTCAAAATGTTTTAAAAAAAATATTATAATATATATATTTTCA
1 AAAACTATATATATA-TTTA-TGTAAAAACGTTTTAAAAAAACTA-TATAATATATAT-TTTTCA
734723 AAAATGTTTTG
62 AAAATGTTTTG
* * * *
734734 AAAACTATATTATATATTTATTTCAAAATGTTTTAAAAAAAACTATATAATATATATATTTCAAA
1 AAAACTATA-TATATATTTATGTAAAAACGTTTT-AAAAAAACTATATAATATATATTTTTCAAA
734799 AATGTTTTG
64 AATGTTTTG
* *
734808 AAAACTATATAT-T-TTT-TGTAAAAACGTTTT-AAACAATTATATAATATCA-ATGTTTTC-AA
1 AAAACTATATATATATTTATGTAAAAACGTTTTAAAAAAACTATATAATAT-ATAT-TTTTCAAA
**
734867 AATGTTTCA
64 AATGTTTTG
734876 AAAACTATATATATATTT
1 AAAACTATATATATATTT
734894 TCAAAATGTT
Statistics
Matches: 143, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
68 38 0.27
69 6 0.04
70 14 0.10
71 3 0.02
72 1 0.01
73 3 0.02
74 25 0.17
75 35 0.24
76 14 0.10
77 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (72 bp):
AAAACTATATATATATTTATGTAAAAACGTTTTAAAAAAACTATATAATATATATTTTTCAAAAA
TGTTTTG
Found at i:742267 original size:19 final size:22
Alignment explanation
Indices: 742224--742268 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 22
742214 CATGATCTTA
742224 AAAACAAAAATAATTGAGTGAAT
1 AAAACAAAAATAATTGAG-GAAT
742247 AAAAC-AAAATAA-TGA-GAAT
1 AAAACAAAAATAATTGAGGAAT
742266 AAA
1 AAA
742269 TGGATGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.32
21 3 0.14
22 7 0.32
23 5 0.23
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAACAAAAATAATTGAGGAAT
Found at i:743381 original size:27 final size:27
Alignment explanation
Indices: 743321--743375 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
743311 GTCATTTGTC
*
743321 AAATAAATGCTATAAAGATTGTATATT
1 AAATAAATGCTACAAAGATTGTATATT
*
743348 AAATAAATGTTACAAAG-TTCGTATATT
1 AAATAAATGCTACAAAGATT-GTATATT
743375 A
1 A
743376 TTTAAAGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (27 bp):
AAATAAATGCTACAAAGATTGTATATT
Found at i:749541 original size:2 final size:2
Alignment explanation
Indices: 749534--749564 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
749524 ATCTTATCCC
749534 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
749565 TTTCTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:750541 original size:30 final size:30
Alignment explanation
Indices: 750507--750574 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
750497 GTATATATTT
*
750507 GATA-CAAATGGGACATAACCCAATAGTTTA
1 GATACCAAA-GGGAAATAACCCAATAGTTTA
*
750537 GATACCAAAGTGAAATAACCCAATAGTTTA
1 GATACCAAAGGGAAATAACCCAATAGTTTA
*
750567 GGTACCAA
1 GATACCAA
750575 CGAAACATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (30 bp):
GATACCAAAGGGAAATAACCCAATAGTTTA
Found at i:750627 original size:26 final size:27
Alignment explanation
Indices: 750558--750627 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 27
750548 GAAATAACCC
750558 AATAGTTTAGGTACCAACGAAACATATTTT
1 AATAGTTTAGGTACCAACGAAACATA---T
* * *
750588 GATAGTTTAAGTACCAATGAAACATA-
1 AATAGTTTAGGTACCAACGAAACATAT
750614 AATAGTTTAGGTAC
1 AATAGTTTAGGTAC
750628 TAACATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 12 0.34
30 23 0.66
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (27 bp):
AATAGTTTAGGTACCAACGAAACATAT
Found at i:753972 original size:50 final size:50
Alignment explanation
Indices: 753893--754019 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 50
753883 GTAGCAGTAA
* * *
753893 AGCGCGCCCCCTGACCCGCGCTATATGCTGATTTGGTGACACGTGGGGTAT
1 AGCGCGCCCCCTGA-CCGCGCTATATGCTGACTGGGTGACACGTGGGATAT
* * *
753944 AGCGCG-CCCCTGCACCGCACTATTTGCTGACTGGGTTACACGTGGGATAT
1 AGCGCGCCCCCTG-ACCGCGCTATATGCTGACTGGGTGACACGTGGGATAT
753994 AGCGCGCCCCCTGAACCGCGCTATAT
1 AGCGCGCCCCCTG-ACCGCGCTATAT
754020 CTGTGTATCT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 42 0.65
51 23 0.35
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCCTGACCGCGCTATATGCTGACTGGGTGACACGTGGGATAT
Found at i:757714 original size:26 final size:24
Alignment explanation
Indices: 757685--757755 Score: 60
Period size: 26 Copynumber: 2.9 Consensus size: 24
757675 AAAATCCAAC
757685 AAATGTAACAAAATAAAGTAAGTATT
1 AAATGTAACAAAATAAAGTAA--ATT
757711 AAATG-AGA-AATAATAAA--AAATT
1 AAATGTA-ACAA-AATAAAGTAAATT
*
757733 ACAATTTAACAAAATAAAGTAAA
1 A-AATGTAACAAAATAAAGTAAA
757756 CACAAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 15
0.70 0.02 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 6 0.16
26 12 0.32
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (24 bp):
AAATGTAACAAAATAAAGTAAATT
Found at i:759972 original size:17 final size:18
Alignment explanation
Indices: 759952--759992 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
759942 AAATTATATT
759952 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
759969 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
759987 ATTAAA
1 AGTAAA
759993 TAAATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:761596 original size:19 final size:19
Alignment explanation
Indices: 761572--761610 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
761562 ATGACCAACA
*
761572 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
761591 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
761610 A
1 A
761611 GTATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:761657 original size:20 final size:20
Alignment explanation
Indices: 761634--761705 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
761624 GTTTCCAGAT
*
761634 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
** * *
761654 TCGCATTGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
*
761674 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
761694 TCGCAACGCGAT
1 TCGCAACGCGAT
761706 AATACAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:762389 original size:20 final size:19
Alignment explanation
Indices: 762282--762386 Score: 85
Period size: 20 Copynumber: 5.7 Consensus size: 19
762272 GATAGTTTAA
* *
762282 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATATTCA-T
* *
762302 TTCGTATTGCGATTTTCAT
1 TTCGTGTTGCGATATTCAT
*
762321 TTCGCGTTGC-A-ATT-AT
1 TTCGTGTTGCGATATTCAT
* *
762337 CTC--GTTGCGATAGTCAT
1 TTCGTGTTGCGATATTCAT
*
762354 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATATTCA-T
762374 TTCGTGTTGCGAT
1 TTCGTGTTGCGAT
762387 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
14 5 0.07
15 1 0.01
16 6 0.09
17 6 0.09
18 1 0.01
19 20 0.30
20 28 0.42
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (19 bp):
TTCGTGTTGCGATATTCAT
Found at i:762396 original size:20 final size:20
Alignment explanation
Indices: 762353--762396 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
762343 GCGATAGTCA
* *
762353 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
762373 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
762393 TTTC
1 TTTC
762397 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:764330 original size:20 final size:20
Alignment explanation
Indices: 764301--764369 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
764291 AAACTTAAAA
764301 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
764321 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* * *
764341 ATCGTAACGCGGAAATGATT
1 ATCGCAACGCGAAAATGACT
764361 ATCGCAACG
1 ATCGCAACG
764370 GGATAATCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:764422 original size:14 final size:14
Alignment explanation
Indices: 764390--764423 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
764380 AATGCGAAAT
764390 AAAAATTGCAACGC
1 AAAAATTGCAACGC
* *
764404 GAAAATTGCAATGC
1 AAAAATTGCAACGC
764418 AAAAAT
1 AAAAAT
764424 GACTATCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.18
Consensus pattern (14 bp):
AAAAATTGCAACGC
Found at i:764490 original size:20 final size:20
Alignment explanation
Indices: 764465--764533 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
764455 GCGATTATCC
*
764465 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
764485 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
764505 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
764525 CGTTGCGAT
1 CGTTGCGAT
764534 TTAAGTTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:764490 original size:34 final size:37
Alignment explanation
Indices: 764447--764534 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 37
764437 CGAATTTAGT
*
764447 TTCGCGTTGCGATT-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCATTCCGCGTTGCAATAGTCAAA
**
764481 TTCGCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATT
1 TTCGCGTTGCGAT--TCA-TTCCGCGTTGCAATAGTCAAA
764521 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
764535 TAAGTTTCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
34 13 0.29
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.07
40 26 0.58
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (37 bp):
TTCGCGTTGCGATTCATTCCGCGTTGCAATAGTCAAA
Found at i:764548 original size:19 final size:20
Alignment explanation
Indices: 764520--764562 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
764510 CAATAGTCAT
764520 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
764539 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
764559 TTTC
1 TTTC
764563 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:765109 original size:42 final size:42
Alignment explanation
Indices: 765063--765156 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
765053 CCTCTCCTTT
765063 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCTCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTC-CCTCCCAC
* ** *
765105 CGTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
*
765147 CATTCAAGAG
1 CGTTCAAGAG
765157 CCCGATTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 43 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:765111 original size:21 final size:20
Alignment explanation
Indices: 765087--765156 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
765077 CTATCATCCC
765087 TCAAGAGTCTCCTCCCACCGT
1 TCAAGAGTC-CCTCCCACCGT
* ** *
765108 TCAAGAGGCCCCTGTCATCGT
1 TCAAGA-GTCCCTCCCACCGT
* *
765129 TGAAGAGGTCCCTCCCACCAT
1 TCAAGA-GTCCCTCCCACCGT
765150 TCAAGAG
1 TCAAGAG
765157 CCCGATTCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 34 0.92
22 2 0.05
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (20 bp):
TCAAGAGTCCCTCCCACCGT
Found at i:766607 original size:36 final size:35
Alignment explanation
Indices: 766559--766671 Score: 116
Period size: 36 Copynumber: 3.4 Consensus size: 35
766549 TAAAAGTTGA
766559 TTTGTTTAATTGATGTGTAAATAATTCTTATTTGT
1 TTTGTTTAATTGATGTGTAAATAATTCTTATTTGT
* * *
766594 TATTGTTTAATTGATTTGT--A-AA-----AGTTGA
1 T-TTGTTTAATTGATGTGTAAATAATTCTTATTTGT
766622 TTTGTTTAATTGATGTGTAAATAATTCTTATTTGT
1 TTTGTTTAATTGATGTGTAAATAATTCTTATTTGT
*
766657 GTTTATTTAATTGAT
1 -TTTGTTTAATTGAT
766672 TGAAATGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
27 16 0.26
28 5 0.08
29 1 0.02
30 2 0.03
33 2 0.03
34 1 0.02
35 5 0.08
36 29 0.48
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (35 bp):
TTTGTTTAATTGATGTGTAAATAATTCTTATTTGT
Found at i:766611 original size:63 final size:63
Alignment explanation
Indices: 766533--766694 Score: 263
Period size: 63 Copynumber: 2.5 Consensus size: 63
766523 AATTTTTTGC
766533 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGT-T
1 TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGT
766595 ATTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGT
1 -TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGT
*
766659 TTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
766695 GATTTCAATC
Statistics
Matches: 93, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
63 74 0.80
64 1 0.01
67 18 0.19
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.53
Consensus pattern (63 bp):
TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTGTGT
Done.