Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007968.1 Hibiscus syriacus cultivar Beakdansim tig00110403_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: 1361854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1089126 original size:10 final size:11
Alignment explanation
Indices: 1089097--1089130 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
1089087 ATAACATCTC
1089097 TTTTAAAAATA
1 TTTTAAAAATA
1089108 TTTTAAAAATA
1 TTTTAAAAATA
1089119 TTTTAAAAATA
1 TTTTAAAAATA
1089130 T
1 T
1089131 ATAACAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:1094434 original size:4 final size:4
Alignment explanation
Indices: 1094425--1094558 Score: 123
Period size: 4 Copynumber: 34.2 Consensus size: 4
1094415 CCCATTTTAG
* * *
1094425 TACA TACA T--A TACA TACA TGCA TAC- -ACA TTACA CACA TATA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA -TACA TACA TACA TACA
* * * *
1094470 CACA TATA TATA TACA TACA TACG TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * *
1094518 TACA TACA TACG TACG TACG TACG TACG TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1094559 GCACTTACAC
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
2 4 0.04
4 104 0.94
5 3 0.03
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1094448 original size:14 final size:14
Alignment explanation
Indices: 1094425--1094525 Score: 67
Period size: 14 Copynumber: 6.9 Consensus size: 14
1094415 CCCATTTTAG
*
1094425 TACATACATATACA
1 TACATACATACACA
*
1094439 TACATGCATACACA
1 TACATACATACACA
* * *
1094453 TTACACACATATATA
1 -TACATACATACACA
* * * * *
1094468 CACACATATATATA
1 TACATACATACACA
1094482 TACATACATACGTACA
1 TACATACATAC--ACA
1094498 TACATACATACATACA
1 TACATACATAC--ACA
1094514 TACATACATACA
1 TACATACATACA
1094526 TACGTACGTA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
14 32 0.46
15 10 0.14
16 28 0.40
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.27
Consensus pattern (14 bp):
TACATACATACACA
Found at i:1096044 original size:2 final size:2
Alignment explanation
Indices: 1096037--1096091 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1096027 TCATAAATTG
1096037 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
1096079 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1096092 AAATTATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1106164 original size:31 final size:34
Alignment explanation
Indices: 1106121--1106205 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 34
1106111 AAATGTTGGA
* *
1106121 ATATTATATTATTTAAATTTG-ATATTTTTAAAA-
1 ATATT-TATTATTTAAATTTGCATAATCTTAAAAT
* * * *
1106154 ATCTTT-TTATTAAAAATAGCATAATCTTAAAAT
1 ATATTTATTATTTAAATTTGCATAATCTTAAAAT
1106187 ATATTTATTATTTAAATTT
1 ATATTTATTATTTAAATTT
1106206 AATTTAAATC
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
31 10 0.26
32 11 0.28
33 9 0.23
34 9 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (34 bp):
ATATTTATTATTTAAATTTGCATAATCTTAAAAT
Found at i:1106466 original size:14 final size:14
Alignment explanation
Indices: 1106423--1106475 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1106413 AAATCTTAAG
1106423 TTAGAGTTTA-AGT
1 TTAGAGTTTATAGT
*
1106436 TTAGGGTTTAT-GAT
1 TTAGAGTTTATAG-T
*
1106450 TTAGAGATTATAGT
1 TTAGAGTTTATAGT
*
1106464 TTAGGGTTTATA
1 TTAGAGTTTATA
1106476 ATCTAGGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 10 0.31
14 21 0.66
15 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TTAGAGTTTATAGT
Found at i:1106482 original size:14 final size:14
Alignment explanation
Indices: 1106435--1106482 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1106425 AGAGTTTAAG
*
1106435 TTTAGGGTTTATGA
1 TTTAGGGTTTATAA
* * *
1106449 TTTAGAGATTATAG
1 TTTAGGGTTTATAA
1106463 TTTAGGGTTTATAA
1 TTTAGGGTTTATAA
*
1106477 TCTAGG
1 TTTAGG
1106483 ATTTTAAGTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTATAA
Found at i:1106492 original size:28 final size:29
Alignment explanation
Indices: 1106429--1106492 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
1106419 TAAGTTAGAG
* *
1106429 TTTAAGTTTAGGGTTTATGATTTAGAGAT
1 TTTAAGTTTAGGGTTTATAATCTAGAGAT
*
1106458 TAT-AGTTTAGGGTTTATAATCTAG-GAT
1 TTTAAGTTTAGGGTTTATAATCTAGAGAT
1106485 TTTAAGTT
1 TTTAAGTT
1106493 AAGAGTATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.17
28 23 0.77
29 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (29 bp):
TTTAAGTTTAGGGTTTATAATCTAGAGAT
Found at i:1119052 original size:6 final size:6
Alignment explanation
Indices: 1119033--1119064 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1119023 GCTGGAATTC
*
1119033 TCTCTG TCTATG TCTCTG TCTCTG TCTCTG TC
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TC
1119065 ACGATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.31, G:0.16, T:0.50
Consensus pattern (6 bp):
TCTCTG
Found at i:1120621 original size:43 final size:43
Alignment explanation
Indices: 1120566--1120647 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
1120556 GATTACTTAA
1120566 AAAAAAAAACTACGAAATTTGCTATAGTGTAAAGACATCACTT
1 AAAAAAAAACTACGAAATTTGCTATAGTGTAAAGACATCACTT
1120609 AAAAAAAAACTACGAAATTTGCTATAGTGTAAAGACATC
1 AAAAAAAAACTACGAAATTTGCTATAGTGTAAAGACATC
1120648 TACAGTCGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.50, C:0.13, G:0.12, T:0.24
Consensus pattern (43 bp):
AAAAAAAAACTACGAAATTTGCTATAGTGTAAAGACATCACTT
Found at i:1126702 original size:32 final size:32
Alignment explanation
Indices: 1126664--1126738 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
1126654 GGTATTGAGT
1126664 TGTTTGGAGAAAACCAATCAATTGCGTTTGCA
1 TGTTTGGAGAAAACCAATCAATTGCGTTTGCA
1126696 TGTTTGGAGAAAACCAATCAATTGCGTTTGCA
1 TGTTTGGAGAAAACCAATCAATTGCGTTTGCA
*
1126728 TGTTTAGAGAA
1 TGTTTGGAGAA
1126739 TTTGTCTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (32 bp):
TGTTTGGAGAAAACCAATCAATTGCGTTTGCA
Found at i:1129228 original size:43 final size:43
Alignment explanation
Indices: 1129167--1129324 Score: 291
Period size: 43 Copynumber: 3.7 Consensus size: 43
1129157 ATCATTTGGA
1129167 TTAATTGCAT-TATTCATACTCTTGAAAAAGTATAGCTGCTCAT
1 TTAATT-CATATATTCATACTCTTGAAAAAGTATAGCTGCTCAT
*
1129210 TTAATTCATATATTCATACTCTTGAAAAAGTATAGCTGCTTAT
1 TTAATTCATATATTCATACTCTTGAAAAAGTATAGCTGCTCAT
1129253 TTAATTCATATATTCATACTCTTGAAAAAGTATAGCTGCTCAT
1 TTAATTCATATATTCATACTCTTGAAAAAGTATAGCTGCTCAT
1129296 TTAATTCATATATTCATACTCTTGAAAAA
1 TTAATTCATATATTCATACTCTTGAAAAA
1129325 TCGCAGACAC
Statistics
Matches: 112, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
42 3 0.03
43 109 0.97
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (43 bp):
TTAATTCATATATTCATACTCTTGAAAAAGTATAGCTGCTCAT
Found at i:1133550 original size:30 final size:30
Alignment explanation
Indices: 1133488--1133598 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
1133478 GAGAAAACAA
* ** * *
1133488 AAACTTAAAGGACTAAAGTAGCTAAGACAG
1 AAACTTAAAGGACTAAAATAGAAAAAATAG
*
1133518 AAAGTTAAAGGACTAAAATAGAAAAAATAG
1 AAACTTAAAGGACTAAAATAGAAAAAATAG
*
1133548 AAACTTAAGGGACT-AAATAGTAAAAAATAG
1 AAACTTAAAGGACTAAAATAG-AAAAAATAG
* *
1133578 AATCTAAAAGGACTAAAATAG
1 AAACTTAAAGGACTAAAATAG
1133599 TAATTACAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 6 0.09
30 56 0.82
31 6 0.09
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (30 bp):
AAACTTAAAGGACTAAAATAGAAAAAATAG
Found at i:1135182 original size:18 final size:18
Alignment explanation
Indices: 1135159--1135209 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1135149 ATAAAAAAAT
*
1135159 GTAATATTAATATAATTA
1 GTAATATTAATATAATAA
*
1135177 GTAATAATAATAATAATAA
1 GTAATATTAAT-ATAATAA
*
1135196 ATAAT-TTAATATAA
1 GTAATATTAATATAA
1135210 ATAATAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.14
18 14 0.50
19 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
GTAATATTAATATAATAA
Found at i:1135205 original size:24 final size:26
Alignment explanation
Indices: 1135160--1135216 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 26
1135150 TAAAAAAATG
*
1135160 TAATATTAATATAATTAGTAATA-ATAA
1 TAATAATAATATAATTA-TAATATA-AA
1135187 TAATAATAA-ATAATT-TAATATAAA
1 TAATAATAATATAATTATAATATAAA
1135211 TAATAA
1 TAATAA
1135217 CATTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 13 0.46
25 1 0.04
26 6 0.21
27 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAATAATAATATAATTATAATATAAA
Found at i:1144808 original size:22 final size:23
Alignment explanation
Indices: 1144770--1144814 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1144760 TTCATGCATT
1144770 TTCATTGATCAAATTTTTAAGAA
1 TTCATTGATCAAATTTTTAAGAA
* *
1144793 TTCATTG-TTAAATTTTTCAGAA
1 TTCATTGATCAAATTTTTAAGAA
1144815 ATATAGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
TTCATTGATCAAATTTTTAAGAA
Found at i:1154950 original size:24 final size:23
Alignment explanation
Indices: 1154921--1154971 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
1154911 TAAACTCGTT
1154921 AATATTTTTAAACTCAAATAAA-AA
1 AATA-TTTTAAA-TCAAATAAAGAA
*
1154945 AATA-TTTAAATCAATTAAAGAA
1 AATATTTTAAATCAAATAAAGAA
1154967 AATAT
1 AATAT
1154972 AAATCCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
24 4 0.17
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (23 bp):
AATATTTTAAATCAAATAAAGAA
Found at i:1154963 original size:21 final size:23
Alignment explanation
Indices: 1154927--1154971 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1154917 CGTTAATATT
1154927 TTTAAACTCAAATAAA-AAAATA
1 TTTAAACTCAAATAAAGAAAATA
*
1154949 TTTAAA-TCAATTAAAGAAAATA
1 TTTAAACTCAAATAAAGAAAATA
1154971 T
1 T
1154972 AAATCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TTTAAACTCAAATAAAGAAAATA
Found at i:1154976 original size:20 final size:20
Alignment explanation
Indices: 1154928--1154976 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1154918 GTTAATATTT
1154928 TTAAACTCAAATAAAAAAATA
1 TTAAA-TCAAATAAAAAAATA
*
1154949 TTTAAATCAATTAAAGAAAATA
1 -TTAAATCAAATAAA-AAAATA
1154971 -TAAATC
1 TTAAATC
1154977 CTAAAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAATCAAATAAAAAAATA
Found at i:1156997 original size:27 final size:27
Alignment explanation
Indices: 1156967--1157018 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1156957 TAGTATGATA
* *
1156967 ATGTCGTGTCCTTGTATATAGAGATGG
1 ATGTAGTGTCCTTGTATATAAAGATGG
* *
1156994 ATGTAGTGTCTTTGTGTATAAAGAT
1 ATGTAGTGTCCTTGTATATAAAGAT
1157019 AGACCGAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (27 bp):
ATGTAGTGTCCTTGTATATAAAGATGG
Found at i:1157230 original size:140 final size:140
Alignment explanation
Indices: 1156973--1157252 Score: 373
Period size: 140 Copynumber: 2.0 Consensus size: 140
1156963 GATAATGTCG
* * * * *
1156973 TGTCCTTGTATATAGAGATGGATGTAGTGTCTTTGTGTATAAAGATAGACCGAAAGAGGCGAGTG
1 TGTCCTTATATATAGAGATGGATGTAGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGTA
* * *
1157038 GGATAGATCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATGTCGTGTTCTTGTGTAGA
66 GGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAGA
*
1157103 TAGATAGACC
131 TAGACAGACC
* * ** *
1157113 TGTCCTTATGTATAGAGATGGATGTCA-TGTCTTTGTGTACAGAGATAAACCGAGGGAGACGGGT
1 TGTCCTTATATATAGAGATGGATGT-AGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGT
* * * * *
1157177 AGGATGGACCGAGGAGAGATAATATGTAGTTTACCATAGTATGATAATATCGTGTCCTTGTGTAT
65 AGGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAG
1157242 ATAGACAGACC
130 ATAGACAGACC
1157253 GAGAAGTACA
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
140 119 0.99
141 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (140 bp):
TGTCCTTATATATAGAGATGGATGTAGTGTCTTTGTGTACAAAGATAAACCGAAAGAGACGAGTA
GGATAGACCGAAGAGAGACAATATGTAATTTACCATAGTATGATAATATCGTGTCCTTGTGTAGA
TAGACAGACC
Found at i:1157495 original size:52 final size:53
Alignment explanation
Indices: 1157430--1157534 Score: 151
Period size: 52 Copynumber: 2.0 Consensus size: 53
1157420 CCCTAAATTT
* *
1157430 TTATAAATTTAAATTT-ACCTTATCAAATTTAAAAAAATTCAAATTCGTCACTC
1 TTATAAATCTAAATTTGACC-TATCAAATTTAAAAAAACTCAAATTCGTCACTC
* *
1157483 TTAT-AATCTAAATTTGTCCTATGAAATTTAAAAAAACTCAAATTCGTCACTC
1 TTATAAATCTAAATTTGACCTATCAAATTTAAAAAAACTCAAATTCGTCACTC
1157535 CAACATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
52 41 0.87
53 6 0.13
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (53 bp):
TTATAAATCTAAATTTGACCTATCAAATTTAAAAAAACTCAAATTCGTCACTC
Found at i:1166594 original size:2 final size:2
Alignment explanation
Indices: 1166587--1166612 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1166577 TTCCCGTATA
1166587 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1166613 GTAGTAGTAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1171789 original size:2 final size:2
Alignment explanation
Indices: 1171784--1171808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1171774 TGTTTTTTTA
1171784 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1171809 ATTTTAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1178768 original size:59 final size:58
Alignment explanation
Indices: 1178664--1178782 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 58
1178654 CTTATTATAG
*
1178664 GATATTTATTATAGAATATTATTTTATTGAGTCATTTGATTATTAAAAGTTATAAAAT
1 GATATTTATTATAGAATATTATTTTATTGAGTCATTTGATTATTAAAAGTTAAAAAAT
* * *
1178722 GATACTTTAATTATAGTATGTTATTTT-TTGAG-GATTTCGATTATTAAAAGTTAAAAAAT
1 GATA-TTT-ATTATAGAATATTATTTTATTGAGTCATTT-GATTATTAAAAGTTAAAAAAT
1178781 GA
1 GA
1178783 ACATTTTACT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
58 8 0.15
59 30 0.56
60 16 0.30
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.46
Consensus pattern (58 bp):
GATATTTATTATAGAATATTATTTTATTGAGTCATTTGATTATTAAAAGTTAAAAAAT
Found at i:1184367 original size:22 final size:23
Alignment explanation
Indices: 1184329--1184375 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1184319 TATCACATTA
*
1184329 ATGTGATGAGTTTTAATAAAAAT
1 ATGTAATGAGTTTTAATAAAAAT
1184352 ATGTAATGA-TTTTAATAAAAAT
1 ATGTAATGAGTTTTAATAAAAAT
1184374 AT
1 AT
1184376 TTTTTATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGTAATGAGTTTTAATAAAAAT
Found at i:1184429 original size:17 final size:17
Alignment explanation
Indices: 1184404--1184437 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1184394 ATCATGATAT
1184404 AATAAATTTTAATAAAA
1 AATAAATTTTAATAAAA
* *
1184421 AATATATTTTATTAAAA
1 AATAAATTTTAATAAAA
1184438 TTTATCACTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAATTTTAATAAAA
Found at i:1187570 original size:20 final size:20
Alignment explanation
Indices: 1187545--1187582 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1187535 TGATGAATCA
1187545 TTTATTATGAAATTTATGTT
1 TTTATTATGAAATTTATGTT
1187565 TTTATTATGAAATTTATG
1 TTTATTATGAAATTTATG
1187583 AATTTATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTATTATGAAATTTATGTT
Found at i:1187588 original size:20 final size:20
Alignment explanation
Indices: 1187544--1187589 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1187534 ATGATGAATC
*
1187544 ATTTATTATGAAATTTATGT
1 ATTTATTATGAAATTTATGA
*
1187564 TTTTATTATGAAATTTATGA
1 ATTTATTATGAAATTTATGA
1187584 ATTTAT
1 ATTTAT
1187590 CTAATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTATTATGAAATTTATGA
Found at i:1188163 original size:20 final size:20
Alignment explanation
Indices: 1188138--1188185 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 20
1188128 AATTTAGATT
1188138 TTTATAAAATATCTTTAAAA
1 TTTATAAAATATCTTTAAAA
1188158 TTTAT-AAATATCTTTAAAA
1 TTTATAAAATATCTTTAAAA
1188177 TTTATAAAA
1 TTTATAAAA
1188186 CTAAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATAAAATATCTTTAAAA
Found at i:1188562 original size:2 final size:2
Alignment explanation
Indices: 1188555--1188588 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1188545 ATTGACAAAT
1188555 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
1188589 AAGTTCATGA
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):
TA
Found at i:1192513 original size:31 final size:32
Alignment explanation
Indices: 1192475--1192547 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
1192465 AAGTGACATT
**
1192475 ATATTATAAAAGGGACCCAATTGTTTA-TAAA
1 ATATTATAAAAGGGACCCAATTGCCTATTAAA
1192506 ATATTATAAAAGGGACCCAATTGCCTATTAAA
1 ATATTATAAAAGGGACCCAATTGCCTATTAAA
1192538 ATATTATAAA
1 ATATTATAAA
1192548 TGAAAAGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (32 bp):
ATATTATAAAAGGGACCCAATTGCCTATTAAA
Found at i:1198763 original size:21 final size:21
Alignment explanation
Indices: 1198734--1198773 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1198724 GATAATTTTA
1198734 GTGACTAAAACACAAACTTTG
1 GTGACTAAAACACAAACTTTG
* * *
1198755 GTGATTAAAATAGAAACTT
1 GTGACTAAAACACAAACTT
1198774 ATTGAACCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (21 bp):
GTGACTAAAACACAAACTTTG
Found at i:1210177 original size:13 final size:13
Alignment explanation
Indices: 1210159--1210185 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1210149 CTATTTTTAA
1210159 GCATATGAAAATT
1 GCATATGAAAATT
1210172 GCATATGAAAATT
1 GCATATGAAAATT
1210185 G
1 G
1210186 GGGATGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (13 bp):
GCATATGAAAATT
Found at i:1211355 original size:31 final size:31
Alignment explanation
Indices: 1211317--1211378 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1211307 AACATAGAGT
1211317 CGAGATCTTTAAAGAATATGCTAATTTCATC
1 CGAGATCTTTAAAGAATATGCTAATTTCATC
1211348 CGAGATCTTTAAAGAATATGCTAATTTCATC
1 CGAGATCTTTAAAGAATATGCTAATTTCATC
1211379 GTACATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (31 bp):
CGAGATCTTTAAAGAATATGCTAATTTCATC
Found at i:1223499 original size:60 final size:60
Alignment explanation
Indices: 1223426--1223539 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
1223416 CTATAGGTTA
* * * *
1223426 TTGCTTTACTAAGTCCCTTAACTATTAAAAGTTATAAAATGATCACTCGACTATAGGAAG
1 TTGCCTTACTAAGTCCCTCAACTATTAAAAGATATAAAATGATCACTCAACTATAGGAAG
* *
1223486 TTGCCTTATTAAGTCCCTCAACTATTAAAAGATATCAAATGATCACTCAACTAT
1 TTGCCTTACTAAGTCCCTCAACTATTAAAAGATATAAAATGATCACTCAACTAT
1223540 TCATTATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (60 bp):
TTGCCTTACTAAGTCCCTCAACTATTAAAAGATATAAAATGATCACTCAACTATAGGAAG
Found at i:1224591 original size:20 final size:20
Alignment explanation
Indices: 1224562--1224599 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1224552 TTTCTGTTAT
1224562 CAAAAAGATCAATCCCTTTC
1 CAAAAAGATCAATCCCTTTC
*
1224582 CAAAAGGATCAATCCCTT
1 CAAAAAGATCAATCCCTT
1224600 GACCAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (20 bp):
CAAAAAGATCAATCCCTTTC
Found at i:1224604 original size:71 final size:71
Alignment explanation
Indices: 1224512--1224651 Score: 178
Period size: 71 Copynumber: 2.0 Consensus size: 71
1224502 CATTCCCAGA
* ** * *
1224512 AAAAGGATCGATCATTCGACCAAAAGGATCGATCCCAAACTTTCTGTTAT-CAAAAAGATCAA-T
1 AAAAGGATCAATCATTCGACCAAAACCATCGACCCCAAACTTTCTATTATAC-AAAAGAT-AATT
1224575 CCCTTTCC
64 CCCTTTCC
*
1224583 AAAAGGATCAATCCCTT-GACCAAAACCATCGACCCCAAACTTTCTATTATACAAAAGATAATTC
1 AAAAGGATCAAT-CATTCGACCAAAACCATCGACCCCAAACTTTCTATTATACAAAAGATAATTC
1224647 CCTTT
65 CCTTT
1224652 TCAATAAGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
70 2 0.03
71 54 0.90
72 4 0.07
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (71 bp):
AAAAGGATCAATCATTCGACCAAAACCATCGACCCCAAACTTTCTATTATACAAAAGATAATTCC
CTTTCC
Found at i:1224607 original size:21 final size:20
Alignment explanation
Indices: 1224562--1224607 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1224552 TTTCTGTTAT
*
1224562 CAAAAAGATCAATCCCTTTC
1 CAAAAAGATCAATCCCTTAC
*
1224582 CAAAAGGATCAATCCCTTGAC
1 CAAAAAGATCAATCCCTT-AC
1224603 CAAAA
1 CAAAA
1224608 CCATCGACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.43, C:0.28, G:0.09, T:0.20
Consensus pattern (20 bp):
CAAAAAGATCAATCCCTTAC
Found at i:1240901 original size:7 final size:7
Alignment explanation
Indices: 1240864--1240888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1240854 GGAGGTTATC
1240864 TTTTTCT
1 TTTTTCT
1240871 TTTTTCT
1 TTTTTCT
1240878 TTTTTCT
1 TTTTTCT
1240885 TTTT
1 TTTT
1240889 GATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:1250796 original size:35 final size:35
Alignment explanation
Indices: 1250750--1250818 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1250740 TTATTTAAGA
1250750 AACTATTTAGTTCATGTGTTCGAACCATCAAAATC
1 AACTATTTAGTTCATGTGTTCGAACCATCAAAATC
*
1250785 AACTATTTAGTTCATGTGTTCGAACTATCAAAAT
1 AACTATTTAGTTCATGTGTTCGAACCATCAAAAT
1250819 AGGCAGAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (35 bp):
AACTATTTAGTTCATGTGTTCGAACCATCAAAATC
Found at i:1257847 original size:18 final size:18
Alignment explanation
Indices: 1257820--1257854 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1257810 GGAGGAATCC
*
1257820 AGCAGTTCAGATGAAGAT
1 AGCAGCTCAGATGAAGAT
1257838 AGCAGCTCAGATGAAGA
1 AGCAGCTCAGATGAAGA
1257855 GGAAGTAAGT
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:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (18 bp):
AGCAGCTCAGATGAAGAT
Found at i:1260955 original size:18 final size:19
Alignment explanation
Indices: 1260932--1260969 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1260922 TTATTAAAAA
1260932 AATTATAAAATA-TATTTT
1 AATTATAAAATATTATTTT
1260950 AATTATAAAATATTATTTT
1 AATTATAAAATATTATTTT
1260969 A
1 A
1260970 CTGAGTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTATAAAATATTATTTT
Found at i:1261784 original size:60 final size:60
Alignment explanation
Indices: 1261657--1261784 Score: 140
Period size: 60 Copynumber: 2.1 Consensus size: 60
1261647 CTAATCAGGT
* *
1261657 TATCATTTTATAACTTTTAATAATTAAAATATTTAATAAAATAATATTATATAATCATAAA
1 TATCATTTTATAAATTTTAATAATTAAAATATTTAATAAAATAATATTACATAAT-ATAAA
* *
1261718 -AACATTTTATAAATTTTAATAA-TAGTAAA-CTTTAATAAAATAATATCT-CATAAT-TAAGA
1 TATCATTTTATAAATTTTAATAATTA--AAATATTTAATAAAATAATAT-TACATAATATAA-A
1261777 TATCATTT
1 TATCATTT
1261785 ATGTATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
58 3 0.05
59 3 0.05
60 47 0.82
61 4 0.07
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (60 bp):
TATCATTTTATAAATTTTAATAATTAAAATATTTAATAAAATAATATTACATAATATAAA
Found at i:1261952 original size:6 final size:6
Alignment explanation
Indices: 1261915--1261951 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1261905 GGAGTCCTCT
*
1261915 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CATCTC C
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC C
1261952 ACATGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (6 bp):
CTTCTC
Found at i:1264923 original size:54 final size:54
Alignment explanation
Indices: 1264853--1264960 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
1264843 ATCTGATCAT
* * *
1264853 GTGTTAGAGTTCGTGACCTGAATATCGTTCGGCTTGGTTCTACACATATATGTA
1 GTGTTAGAGATCGTGACCTGAATATCATTCGGCTCGGTTCTACACATATATGTA
*
1264907 GTGTTAGAGATCGTGACCTGAATATCATTCGGCTCGGTTGTACACATATATGTA
1 GTGTTAGAGATCGTGACCTGAATATCATTCGGCTCGGTTCTACACATATATGTA
1264961 CCGAGAGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (54 bp):
GTGTTAGAGATCGTGACCTGAATATCATTCGGCTCGGTTCTACACATATATGTA
Found at i:1265260 original size:24 final size:24
Alignment explanation
Indices: 1265224--1265291 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
1265214 TGGCAGGAAA
** *
1265224 TGGTTGTCAAGGAAGAGATGACTG
1 TGGTTGTGGAGGAAGTGATGACTG
1265248 TGGTTGTGGAGGAAGTGATGACTG
1 TGGTTGTGGAGGAAGTGATGACTG
1265272 TGGTTGTGGAGGAAGTGATG
1 TGGTTGTGGAGGAAGTGATG
1265292 GTGCATTCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.24, C:0.04, G:0.44, T:0.28
Consensus pattern (24 bp):
TGGTTGTGGAGGAAGTGATGACTG
Found at i:1275582 original size:52 final size:50
Alignment explanation
Indices: 1275517--1275626 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
1275507 GGAACTATAT
* * *
1275517 TTATTATTTTATT-AGAAATTA-AGATATAATTAAAAATATTATTTTTATTTTA
1 TTATTATTATATTAAG-AATTAGAG-TAT-A-TAAAAATATTATCTTTAATTTA
*
1275569 TTATTATTATATTAAGAATTAGAGTATATCAAAATATTATCTTTAATTTA
1 TTATTATTATATTAAGAATTAGAGTATATAAAAATATTATCTTTAATTTA
1275619 TTATTATT
1 TTATTATT
1275627 TTTTATTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
50 27 0.52
51 1 0.02
52 20 0.38
53 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (50 bp):
TTATTATTATATTAAGAATTAGAGTATATAAAAATATTATCTTTAATTTA
Found at i:1276063 original size:19 final size:19
Alignment explanation
Indices: 1276039--1276075 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1276029 GCAACGTTCA
1276039 TTACTCCACTGCAATCCCT
1 TTACTCCACTGCAATCCCT
*
1276058 TTACTCCGCTGCAATCCC
1 TTACTCCACTGCAATCCC
1276076 CTATCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.43, G:0.08, T:0.30
Consensus pattern (19 bp):
TTACTCCACTGCAATCCCT
Found at i:1286137 original size:159 final size:159
Alignment explanation
Indices: 1285848--1286168 Score: 495
Period size: 159 Copynumber: 2.0 Consensus size: 159
1285838 TGATGTCCTC
1285848 TGGAATCATGTAAATAGGTAATTTATCCTTCGGATCGACCAACTTGTACATTCCTTTCCCGTGTT
1 TGGAATCATGTAAATAGGTAATTTATCCTTCGGATCGACCAACTTGTACATTCCTTTCCCGTGTT
* *
1285913 GTGTGGTCGAACTAGTAGGCAGAAAGGATAGTGTTGGCTTAAGGGACGGATTCAGGTTAGTAGAT
66 GTGTGGTCGAACTAGAAGGCAGAAAGGATAGAGTTGGCTTAAGGGACGGATTCAGGTTAGTAGAT
*
1285978 GAAGACGAAGGCTTC-GGGGTCGGTACGGA
131 GAAGACGAAGG-TTCTGGAGTCGGTACGGA
* *
1286007 TGGAATCATGTAAATAGGTAATTTATCCTTCGGATCGA-CAACCTTGTACATTCTTTTCCCTTGT
1 TGGAATCATGTAAATAGGTAATTTATCCTTCGGATCGACCAA-CTTGTACATTCCTTTCCCGTGT
* * **
1286071 TGTGTGGTCGAACTAGAAGGCAGAGAGGATAGAGTTGGCTTAGGGGTTGGATTC-GGCTTAGTAG
65 TGTGTGGTCGAACTAGAAGGCAGAAAGGATAGAGTTGGCTTAAGGGACGGATTCAGG-TTAGTAG
* *
1286135 ATGAAGACGACGGTTCTGGAGTCGGTATGGA
129 ATGAAGACGAAGGTTCTGGAGTCGGTACGGA
1286166 TGG
1 TGG
1286169 TTTAGATGGC
Statistics
Matches: 148, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
158 8 0.05
159 140 0.95
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.30
Consensus pattern (159 bp):
TGGAATCATGTAAATAGGTAATTTATCCTTCGGATCGACCAACTTGTACATTCCTTTCCCGTGTT
GTGTGGTCGAACTAGAAGGCAGAAAGGATAGAGTTGGCTTAAGGGACGGATTCAGGTTAGTAGAT
GAAGACGAAGGTTCTGGAGTCGGTACGGA
Found at i:1287408 original size:22 final size:22
Alignment explanation
Indices: 1287383--1287438 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1287373 AATTTTGATT
*
1287383 TTAACCGAATTAATCGATCGAA
1 TTAACCGAATTAACCGATCGAA
*
1287405 TTAAACGAATTAACCGATCGAA
1 TTAACCGAATTAACCGATCGAA
*
1287427 TTAACCAAATTA
1 TTAACCGAATTA
1287439 GCCAGAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.27
Consensus pattern (22 bp):
TTAACCGAATTAACCGATCGAA
Found at i:1287432 original size:13 final size:13
Alignment explanation
Indices: 1287388--1287432 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
1287378 TGATTTTAAC
*
1287388 CGAATTAATCGAT
1 CGAATTAACCGAT
1287401 CGAATTAA---A-
1 CGAATTAACCGAT
1287410 CGAATTAACCGAT
1 CGAATTAACCGAT
1287423 CGAATTAACC
1 CGAATTAACC
1287433 AAATTAGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.29
10 1 0.04
12 1 0.04
13 18 0.64
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (13 bp):
CGAATTAACCGAT
Found at i:1292670 original size:18 final size:18
Alignment explanation
Indices: 1292643--1292760 Score: 121
Period size: 18 Copynumber: 6.6 Consensus size: 18
1292633 CATAAATACC
1292643 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
* ** *
1292661 ATCGTTATCATGATCTAT
1 ATCATTATCAACATCAAT
*
1292679 ATCATTCTCAACATCAAT
1 ATCATTATCAACATCAAT
** **
1292697 ATCATTATCATGATCTCT
1 ATCATTATCAACATCAAT
1292715 ATCATTATCAACATCAAT
1 ATCATTATCAACATCAAT
**
1292733 ATCATTATC-ACGATCTCT
1 ATCATTATCAAC-ATCAAT
1292751 ATCATTATCA
1 ATCATTATCA
1292761 TGAACCCATT
Statistics
Matches: 78, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
17 2 0.03
18 76 0.97
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (18 bp):
ATCATTATCAACATCAAT
Found at i:1292690 original size:36 final size:36
Alignment explanation
Indices: 1292643--1292760 Score: 200
Period size: 36 Copynumber: 3.3 Consensus size: 36
1292633 CATAAATACC
* *
1292643 ATCATTATCAACATCAATATCGTTATCATGATCTAT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
*
1292679 ATCATTCTCAACATCAATATCATTATCATGATCTCT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
*
1292715 ATCATTATCAACATCAATATCATTATCACGATCTCT
1 ATCATTATCAACATCAATATCATTATCATGATCTCT
1292751 ATCATTATCA
1 ATCATTATCA
1292761 TGAACCCATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (36 bp):
ATCATTATCAACATCAATATCATTATCATGATCTCT
Found at i:1292759 original size:6 final size:6
Alignment explanation
Indices: 1292643--1292761 Score: 55
Period size: 6 Copynumber: 19.8 Consensus size: 6
1292633 CATAAATACC
** * * * * **
1292643 ATCATT ATCAAC ATCAAT ATCGTT ATCATG ATC-TAT ATCATT CTCAAC
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCAT-T ATCATT ATCATT
* * ** *
1292691 ATCAAT ATCATT ATCATG ATC-TCT ATCATT ATCAAC ATCAAT ATCATT
1 ATCATT ATCATT ATCATT ATCAT-T ATCATT ATCATT ATCATT ATCATT
**
1292739 ATCACG ATC-TCT ATCATT ATCAT
1 ATCATT ATCAT-T ATCATT ATCAT
1292762 GAACCCATTT
Statistics
Matches: 83, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
5 2 0.02
6 78 0.94
7 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (6 bp):
ATCATT
Found at i:1293161 original size:38 final size:38
Alignment explanation
Indices: 1293099--1293198 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 38
1293089 ATGTAAAATT
* * * * *
1293099 ATCCCGAAGGATCTCGTATATGTCTCGAATGACCTATC
1 ATCCCGAAGGATGTCATCTGTGTCTCGAAGGACCTATC
*
1293137 ATCCCGAAGGATGTCATCTGTGTCTCGTAGGACCTATC
1 ATCCCGAAGGATGTCATCTGTGTCTCGAAGGACCTATC
*
1293175 ATCCCGAAAGATGTCATCTGTGTC
1 ATCCCGAAGGATGTCATCTGTGTC
1293199 CCGTAGGATC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (38 bp):
ATCCCGAAGGATGTCATCTGTGTCTCGAAGGACCTATC
Found at i:1293204 original size:38 final size:38
Alignment explanation
Indices: 1293129--1293206 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
1293119 TGTCTCGAAT
* *
1293129 GACCTATCATCCCGAAGGATGTCATCTGTGTCTCGTAG
1 GACCTATCATCCCGAAAGATGTCATCTGTGTCCCGTAG
1293167 GACCTATCATCCCGAAAGATGTCATCTGTGTCCCGTAG
1 GACCTATCATCCCGAAAGATGTCATCTGTGTCCCGTAG
1293205 GA
1 GA
1293207 TCACTTCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (38 bp):
GACCTATCATCCCGAAAGATGTCATCTGTGTCCCGTAG
Found at i:1295605 original size:29 final size:30
Alignment explanation
Indices: 1295570--1295629 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1295560 TCCCTAAAAT
* * *
1295570 TTTCAAAGT-TTATACTTTGGTCACCAAAC
1 TTTCAAAATCTTATAATTTAGTCACCAAAC
*
1295599 TTTCAAAATCTTATAATTTAGTCACTAAAC
1 TTTCAAAATCTTATAATTTAGTCACCAAAC
1295629 T
1 T
1295630 AAATCCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTCAAAATCTTATAATTTAGTCACCAAAC
Found at i:1298331 original size:45 final size:45
Alignment explanation
Indices: 1298262--1298370 Score: 155
Period size: 45 Copynumber: 2.4 Consensus size: 45
1298252 GCACTGATTT
* * *** *
1298262 GGAAGGTTTCAGTTTAGGGCTTTGGGTACATTGGATTGGAACTTC
1 GGAAGGTTTCGGTTTAGGGATTTGGGTACATCAAATCGGAACTTC
1298307 GGAAGGTTTCGGTTTAGGGATTTGGGTACATCAAATCGGAACTTC
1 GGAAGGTTTCGGTTTAGGGATTTGGGTACATCAAATCGGAACTTC
*
1298352 GGAAGGTTTTGGTTTAGGG
1 GGAAGGTTTCGGTTTAGGG
1298371 CTTCAGGCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.21, C:0.10, G:0.35, T:0.34
Consensus pattern (45 bp):
GGAAGGTTTCGGTTTAGGGATTTGGGTACATCAAATCGGAACTTC
Found at i:1298383 original size:45 final size:45
Alignment explanation
Indices: 1298299--1298392 Score: 125
Period size: 45 Copynumber: 2.1 Consensus size: 45
1298289 ACATTGGATT
** *
1298299 GGAACTTCGGAAGGTTTCGGTTTAGGGATTTGGGTACATCAAATC
1 GGAACTTCGGAAGGTTTCGGTTTAGGGATTCAGGCACATCAAATC
* * **
1298344 GGAACTTCGGAAGGTTTTGGTTTAGGGCTTCAGGCACATCGGATC
1 GGAACTTCGGAAGGTTTCGGTTTAGGGATTCAGGCACATCAAATC
1298389 GGAA
1 GGAA
1298393 GCTTTGTTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (45 bp):
GGAACTTCGGAAGGTTTCGGTTTAGGGATTCAGGCACATCAAATC
Found at i:1303702 original size:104 final size:98
Alignment explanation
Indices: 1303536--1303910 Score: 322
Period size: 104 Copynumber: 3.8 Consensus size: 98
1303526 ACATGGATCA
* * *
1303536 TATATTCGAGTATCTTCCACCTTTTTCCATGTTTCTATGATCCCATAGTGTTATAACTTATGTTA
1 TATATACGAGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTATAACTTATGTTA
* *
1303601 CTCGATTTCATGTGCAAGTGCCAGTATCGATATATATCC
66 CTCAATTTC--GTGCAAGTGCCAG--T-GACAT-TATCC
* *
1303640 TATATACGAGTATCTTCCACTTTTTTCCAAGTTTCTATTATCCCATAGTGTTCTAACTTATGTTA
1 TATATACGAGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTATAACTTATGTTA
*
1303705 CTCAATTTCG-G---GTGCAAGTGACATTATCC
66 CTCAATTTCGTGCAAGTGCCAGTGACATTATCC
* * * * *
1303734 --GATACAAGTATCTTCCAACTTTTTTTCCAAGTTCCTATGATCCCATGGTGTTTTAACTTATGT
1 TATATACGAGTATCTTCC-AC-TTTTTTCCAAGTTTCTATGATCCCATAGTGTTATAACTTATGT
* *
1303797 TACTCAATTTCGGGTACAAGTGCCACAT-A-AGTCTGCATCC
64 TACTCAATTTC--GTGCAAGTGCCA-GTGACA-T-T--ATCC
* * * * * * *
1303837 -A-ATACAAGCACCTTCTTC-CTTTTTTCCAAGTTTCTAAGATCCCATAATGTTTTAACTTATGC
1 TATATACGAGTATCTTC--CACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTATAACTTATGT
1303899 TACTCAATTTCG
64 TACTCAATTTCG
1303911 GGTACAAGAA
Statistics
Matches: 231, Mismatches: 24, Indels: 36
0.79 0.08 0.12
Matches are distributed among these distances:
92 14 0.06
93 2 0.01
94 55 0.24
95 4 0.02
96 2 0.01
98 6 0.03
99 1 0.00
100 8 0.03
101 3 0.01
102 50 0.22
103 17 0.07
104 68 0.29
105 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (98 bp):
TATATACGAGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTATAACTTATGTTA
CTCAATTTCGTGCAAGTGCCAGTGACATTATCC
Found at i:1303796 original size:94 final size:97
Alignment explanation
Indices: 1303544--1303990 Score: 368
Period size: 102 Copynumber: 4.5 Consensus size: 97
1303534 CATATATTCG
* * * *
1303544 AGTATCTTCCACCTTTTTCCATGTTTCTATGATCCCATAGTGTTATAACTTATGTTACTCGATTT
1 AGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTTTAACTTATGTTACTCAATTT
** * * * *
1303609 CATGTGCAAGTGC-CAGTATCGATATATATCCTATATACG
66 CGGGTACAAGTGCACA--A--G-TCT-CATCC-A-ATACA
* *
1303648 AGTATCTTCCACTTTTTTCCAAGTTTCTATTATCCCATAGTGTTCTAACTTATGTTACTCAATTT
1 AGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTTTAACTTATGTTACTCAATTT
* *
1303713 CGGGTGCAAGTG-AC-A-T-T-ATCCGATACA
66 CGGGTACAAGTGCACAAGTCTCATCCAATACA
* *
1303740 AGTATCTTCCAACTTTTTTTCCAAGTTCCTATGATCCCATGGTGTTTTAACTTATGTTACTCAAT
1 AGTATCTTCC-AC-TTTTTTCCAAGTTTCTATGATCCCATAGTGTTTTAACTTATGTTACTCAAT
1303805 TTCGGGTACAAGTGCCACATAAGTCTGCATCCAATACA
64 TTCGGGTACAAGTG-CAC--AAGTCT-CATCCAATACA
* * * * *
1303843 AGCACCTTCTTC-CTTTTTTCCAAGTTTCTAAGATCCCATAATGTTTTAACTTATGCTACTCAAT
1 AGTATCTTC--CACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTTTAACTTATGTTACTCAAT
** * * *
1303907 TTCGGGTACAAGAACCACATAAGTATGTATCGAATACA
64 TTCGGGTACAAG-TGCAC--AAGTCT-CATCCAATACA
* * * * *
1303945 AGTATCTTCTAACTTTTTTTCCAAGTTTATGTGATTCCATAATGTT
1 AGTATCTTC-CAC-TTTTTTCCAAGTTTCTATGATCCCATAGTGTT
1303991 CTTTCTTTCT
Statistics
Matches: 292, Mismatches: 34, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
92 14 0.05
93 2 0.01
94 64 0.22
96 3 0.01
97 1 0.00
99 1 0.00
100 1 0.00
101 3 0.01
102 86 0.29
103 45 0.15
104 71 0.24
105 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (97 bp):
AGTATCTTCCACTTTTTTCCAAGTTTCTATGATCCCATAGTGTTTTAACTTATGTTACTCAATTT
CGGGTACAAGTGCACAAGTCTCATCCAATACA
Found at i:1310837 original size:29 final size:29
Alignment explanation
Indices: 1310778--1310842 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1310768 TGAGTCATTT
* *
1310778 GACTATTAAAAGTTACAAAATGGTCCCTC
1 GACTATTAAAAGCTACAAAATGGTCCATC
* **
1310807 GACTATTAAAAGCTACAAAATGTTGTATC
1 GACTATTAAAAGCTACAAAATGGTCCATC
1310836 GACTATT
1 GACTATT
1310843 CATTATGTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (29 bp):
GACTATTAAAAGCTACAAAATGGTCCATC
Found at i:1311863 original size:20 final size:20
Alignment explanation
Indices: 1311838--1311883 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1311828 TGCGATTTTC
1311838 CAAATTCACAACAC-ATAAGT
1 CAAATTCACAACACGA-AAGT
* *
1311858 CAAATTCGCAACGCGAAAGT
1 CAAATTCACAACACGAAAGT
1311878 CAAATT
1 CAAATT
1311884 TCCAACGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.20
Consensus pattern (20 bp):
CAAATTCACAACACGAAAGT
Found at i:1311905 original size:22 final size:21
Alignment explanation
Indices: 1311883--1311923 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1311873 AAAGTCAAAT
1311883 TTCCAACGTAAATAGTAAAAA
1 TTCCAACGTAAATAGTAAAAA
* * *
1311904 TTGCAACGTGAATATTAAAA
1 TTCCAACGTAAATAGTAAAA
1311924 TCGCAACGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCCAACGTAAATAGTAAAAA
Found at i:1311911 original size:21 final size:20
Alignment explanation
Indices: 1311886--1311951 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1311876 GTCAAATTTC
* *
1311886 CAACGTAAATAGTAAAAATTG
1 CAACGTGAATAGT-AAAATCG
*
1311907 CAACGTGAATATTAAAATCG
1 CAACGTGAATAGTAAAATCG
*
1311927 CAACGTGAATGGTAAAATCG
1 CAACGTGAATAGTAAAATCG
1311947 CAACG
1 CAACG
1311952 AATCTATATG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 29 0.73
21 11 0.28
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (20 bp):
CAACGTGAATAGTAAAATCG
Found at i:1312352 original size:21 final size:20
Alignment explanation
Indices: 1312301--1312351 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1312291 CAACGCGATT
* *
1312301 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTC-CAATTCACG
1312322 TTGCGATTTTCCAATTCACG
1 TTGCGATTTTCCAATTCACG
1312342 TTGCGATTTT
1 TTGCGATTTT
1312352 TACTATTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCCAATTCACG
Found at i:1312359 original size:21 final size:21
Alignment explanation
Indices: 1312301--1312368 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1312291 CAACGCGATT
*
1312301 TTGCGATTTTCTA-AATTCGCG
1 TTGCGATTTT-TACAATTCACG
*
1312322 TTGCGA-TTTTCCAATTCACG
1 TTGCGATTTTTACAATTCACG
* *
1312342 TTGCGATTTTTACTATTCACA
1 TTGCGATTTTTACAATTCACG
1312363 TTGCGA
1 TTGCGA
1312369 AATTGGAGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.40
21 23 0.57
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTTACAATTCACG
Found at i:1313353 original size:59 final size:58
Alignment explanation
Indices: 1313292--1313474 Score: 156
Period size: 60 Copynumber: 3.1 Consensus size: 58
1313282 GGATGAAATT
* * *
1313292 GGGATGAAATTGAAATATCTAAAAGTTTAGAGATC-AATTTAGAATGACATTCATAGTTTG
1 GGGATGAAATTGAAATATCTAAAAG-TTA-AGAACGAATTTAGAATGACAGTCATA-TTTA
* * *
1313352 GGGATGAAATTCAAAT-GCTCAAAAGTTAAGAACGAATTTAGAATGAGAGTCATATTGTA
1 GGGATGAAATTGAAATATCT-AAAAGTTAAGAACGAATTTAGAATGACAGTCATATT-TA
* * * * * * *
1313411 AGGATGAAATTGGAATATTTAAAAGCTTAAGGACTAATTT-GAAATGAGAGTTATAGTTTA
1 GGGATGAAATTGAAATATCTAAAAG-TTAAGAACGAATTTAG-AATGACAGTCATA-TTTA
1313471 GGGA
1 GGGA
1313475 CATATGATGC
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
58 6 0.06
59 43 0.43
60 50 0.50
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (58 bp):
GGGATGAAATTGAAATATCTAAAAGTTAAGAACGAATTTAGAATGACAGTCATATTTA
Found at i:1313361 original size:60 final size:59
Alignment explanation
Indices: 1313292--1313450 Score: 153
Period size: 59 Copynumber: 2.7 Consensus size: 59
1313282 GGATGAAATT
* * *
1313292 GGGATGAAATTGAAATATCTAAAAGTTTAGAGATC-AATTTAGAATGACATTCATAGTT-TG
1 GGGATGAAATTGAAATATCTAAAAG-TTA-AGAACGAATTTAGAATGACAGTCATA-TTGTA
* * *
1313352 GGGATGAAATTCAAAT-GCTCAAAAGTTAAGAACGAATTTAGAATGAGAGTCATATTGTA
1 GGGATGAAATTGAAATATCT-AAAAGTTAAGAACGAATTTAGAATGACAGTCATATTGTA
* * * * *
1313411 AGGATGAAATTGGAATATTTAAAAGCTTAAGGACTAATTT
1 GGGATGAAATTGAAATATCTAAAAG-TTAAGAACGAATTT
1313451 GAAATGAGAG
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
58 6 0.07
59 42 0.52
60 33 0.41
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.31
Consensus pattern (59 bp):
GGGATGAAATTGAAATATCTAAAAGTTAAGAACGAATTTAGAATGACAGTCATATTGTA
Found at i:1318846 original size:20 final size:22
Alignment explanation
Indices: 1318821--1318860 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1318811 AATAATTTTA
1318821 TGATTT-A-TATTTTATTTAAT
1 TGATTTGAGTATTTTATTTAAT
*
1318841 TGATTTGAGTATTTTTTTTA
1 TGATTTGAGTATTTTATTTA
1318861 TTTGGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (22 bp):
TGATTTGAGTATTTTATTTAAT
Found at i:1320869 original size:20 final size:21
Alignment explanation
Indices: 1320829--1320869 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1320819 TAAGTGTTAA
*
1320829 AATTATTAAAACTGATAATTT
1 AATTACTAAAACTGATAATTT
*
1320850 AATTACTAAAATTG-TAATTT
1 AATTACTAAAACTGATAATTT
1320870 CAACCTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTACTAAAACTGATAATTT
Found at i:1321040 original size:20 final size:21
Alignment explanation
Indices: 1321000--1321040 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1320990 TAAGTGTTAA
*
1321000 AATTATTAAAACTGATAATTT
1 AATTACTAAAACTGATAATTT
*
1321021 AATTACTAAAATTG-TAATTT
1 AATTACTAAAACTGATAATTT
1321041 CAACCTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
AATTACTAAAACTGATAATTT
Found at i:1321058 original size:171 final size:170
Alignment explanation
Indices: 1320718--1321058 Score: 664
Period size: 171 Copynumber: 2.0 Consensus size: 170
1320708 ATTAAATTTT
1320718 GAACTAAGTATTAAAATGAAATGAAGACTAAAGTTTTTATCGATATGATATTAAAATGAAACAAA
1 GAACTAAGTATTAAAATGAAATGAAGACTAAAGTTTTTATCGATATGATATTAAAATGAAACAAA
1320783 AATTAAATTTTAGGTATTTTTTTAAAATTAAAAGTTTAAGTGTTAAAATTATTAAAACTGATAAT
66 AATTAAATTTTAGGTATTTTTTTAAAATTAAAAGTTTAAGTGTTAAAATTATTAAAACTGATAAT
1320848 TTAATTACTAAAATTGTAATTTCAACCTATAGTAATTTGC
131 TTAATTACTAAAATTGTAATTTCAACCTATAGTAATTTGC
1320888 GAACTAAGTATTAAAATGAAATGAAGACTAAAGTTTTTATCGATATGATATTAAAATGAAACAAA
1 GAACTAAGTATTAAAATGAAATGAAGACTAAAGTTTTTATCGATATGATATTAAAATGAAACAAA
*
1320953 AATTAAATTTTAGGTATTTTTTTTTAAATTAAAAGTTTAAGTGTTAAAATTATTAAAACTGATAA
66 AATTAAATTTTAGGTA-TTTTTTTAAAATTAAAAGTTTAAGTGTTAAAATTATTAAAACTGATAA
1321018 TTTAATTACTAAAATTGTAATTTCAACCTATAGTAATTTGC
130 TTTAATTACTAAAATTGTAATTTCAACCTATAGTAATTTGC
1321059 AATGGCTGTG
Statistics
Matches: 169, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
170 81 0.48
171 88 0.52
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.39
Consensus pattern (170 bp):
GAACTAAGTATTAAAATGAAATGAAGACTAAAGTTTTTATCGATATGATATTAAAATGAAACAAA
AATTAAATTTTAGGTATTTTTTTAAAATTAAAAGTTTAAGTGTTAAAATTATTAAAACTGATAAT
TTAATTACTAAAATTGTAATTTCAACCTATAGTAATTTGC
Found at i:1326170 original size:59 final size:60
Alignment explanation
Indices: 1326077--1326192 Score: 166
Period size: 59 Copynumber: 1.9 Consensus size: 60
1326067 TTAGTTTGGC
*
1326077 GATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTT-AGAACGAGAGTCATAATTTTGA
1 GATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTTGA-AACGAGAATCATAATTTTGA
* *
1326137 GATGAAATTGG-ATGATT-AAAAGTTTAAGGACTAATTTGAAATGAGAATCATAATTT
1 GATGAAATTGGAATG-TTCAAAAGTTTAAAGACTAATTTGAAACGAGAATCATAATTT
1326193 GAGGACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
59 37 0.73
60 14 0.27
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (60 bp):
GATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTTGAAACGAGAATCATAATTTTGA
Found at i:1327182 original size:5 final size:5
Alignment explanation
Indices: 1327172--1327206 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1327162 GTTCTCCTAA
1327172 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1327207 CCTTTCTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1337003 original size:22 final size:23
Alignment explanation
Indices: 1336975--1337020 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1336965 CTTTGTTTTT
1336975 TTTTG-AATGAATATT-CATAAAA
1 TTTTGAAATG-ATATTGCATAAAA
*
1336997 TTTTGAAATGTTATTGCATAAAA
1 TTTTGAAATGATATTGCATAAAA
1337020 T
1 T
1337021 AATAAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
TTTTGAAATGATATTGCATAAAA
Found at i:1340338 original size:21 final size:20
Alignment explanation
Indices: 1340311--1340408 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1340301 AAACAGTGTC
1340311 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
1340332 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* ** *
1340352 CAAATTCGCATTGCTATTTT
1 CAAAATCGCAACGCGATTTT
* *
1340372 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1340393 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1340409 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
20 30 0.51
21 29 0.49
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1340418 original size:20 final size:20
Alignment explanation
Indices: 1340395--1340565 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
1340385 GCGAATATGA
1340395 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
1340415 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1340435 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
1340455 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1340475 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
1340495 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
1340515 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
1340535 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
1340555 AAATCGCAACG
1 AAATCGCAACG
1340566 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:1340460 original size:60 final size:58
Alignment explanation
Indices: 1340375--1340584 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
1340365 CTATTTTCCA
* ** * *
1340375 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
1340435 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
1340495 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
1340555 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
1340585 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:1340566 original size:20 final size:20
Alignment explanation
Indices: 1340429--1340584 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
1340419 CGCAATGCGT
*
1340429 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
1340449 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
1340469 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
1340489 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
1340509 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
1340529 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
1340549 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
1340569 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
1340585 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:1340566 original size:40 final size:40
Alignment explanation
Indices: 1340395--1340584 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
1340385 GCGAATATGA
* *
1340395 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
1340435 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
1340475 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
1340515 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
1340555 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
1340585 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:1341503 original size:12 final size:12
Alignment explanation
Indices: 1341486--1341510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1341476 ATATAATCCT
1341486 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1341498 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1341510 G
1 G
1341511 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1343806 original size:19 final size:19
Alignment explanation
Indices: 1343784--1344057 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
1343774 CGGAAAATAC
*
1343784 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1343803 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1343817 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1343837 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1343851 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1343870 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1343889 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1343903 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1343922 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1343941 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1343960 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1343979 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
1343998 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1344012 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1344031 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1344050 AATCGCAA
1 AATCGCAA
1344058 CGAGATAATC
Statistics
Matches: 224, Mismatches: 10, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 13 0.06
17 12 0.05
18 2 0.01
19 145 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1343983 original size:109 final size:104
Alignment explanation
Indices: 1343812--1344079 Score: 437
Period size: 109 Copynumber: 2.5 Consensus size: 104
1343802 AAATCCCAAC
*
1343812 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
* *
1343877 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1343917 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
1343982 CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1344026 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
1344080 TATAAACGCA
Statistics
Matches: 152, Mismatches: 6, Indels: 11
0.90 0.04 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.11
106 2 0.01
107 2 0.01
108 1 0.01
109 97 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1344095 original size:52 final size:52
Alignment explanation
Indices: 1343812--1344079 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
1343802 AAATCCCAAC
1343812 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1343865 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1343917 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
* *
1343974 ATGAAAATCGCAATGCGAAATAAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1344026 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1344078 AT
1 AT
1344080 TATAAACGCA
Statistics
Matches: 199, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
52 132 0.66
53 17 0.09
54 2 0.01
55 2 0.01
56 1 0.01
57 45 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1344095 original size:71 final size:73
Alignment explanation
Indices: 1343778--1344079 Score: 345
Period size: 71 Copynumber: 4.3 Consensus size: 73
1343768 GCAACACGGA
* *
1343778 AAATACAATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAA
1 AAATA-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAA
1343838 ATCGCAA-CG
64 ATCGCAAGCG
* * *
1343847 AGA-GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AAT
1 AAATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1343906 CGCAATGCG
66 CGCAA-GCG
1343915 AAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 AAA-T-AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1343980 ATCGCAATGCG
64 ATCGCAA-GCG
1343991 AAATAAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 AAAT--AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1344051 ATCGCAA-CG
64 ATCGCAAGCG
*
1344060 AGAT-AATCGCAATGCGAAAT
1 AAATAAATCGCAATGCGAAAT
1344080 TATAAACGCA
Statistics
Matches: 205, Mismatches: 9, Indels: 38
0.81 0.04 0.15
Matches are distributed among these distances:
66 16 0.08
67 25 0.12
68 10 0.05
69 11 0.05
70 1 0.00
71 92 0.45
72 13 0.06
73 5 0.02
74 6 0.03
75 1 0.00
76 25 0.12
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (73 bp):
AAATAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
CGCAAGCG
Found at i:1344195 original size:19 final size:19
Alignment explanation
Indices: 1344086--1344187 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1344076 AAATTATAAA
1344086 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1344105 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1344125 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1344141 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1344158 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1344177 CGCATTGCGAT
1 CGCATTGCGAT
1344188 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1344313 original size:14 final size:14
Alignment explanation
Indices: 1344294--1344330 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1344284 CATCAATTAC
1344294 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1344308 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1344322 ACAAATCAA
1 ACAAATCAA
1344331 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1346305 original size:14 final size:14
Alignment explanation
Indices: 1346286--1346342 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1346276 GCGAAATGAA
*
1346286 AATCGCAACGACAG
1 AATCGCAACGAAAG
1346300 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1346317 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1346333 AATCGCAACG
1 AATCGCAACG
1346343 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1346313 original size:33 final size:33
Alignment explanation
Indices: 1346267--1346359 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1346257 GCGAAACCAA
*
1346267 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1346300 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1346333 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1346360 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1346324 original size:19 final size:19
Alignment explanation
Indices: 1346230--1346364 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1346220 TAGTTTACTT
* *
1346230 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1346250 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1346269 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1346288 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1346302 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1346321 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1346335 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1346354 TCGCAATGCGA
1 TCGCAACGCGA
1346365 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1346382 original size:19 final size:19
Alignment explanation
Indices: 1346360--1346488 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1346350 AAAATCGCAA
1346360 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1346379 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1346393 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1346412 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1346426 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1346445 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1346464 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1346484 TGCGA
1 TGCGA
1346489 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1346402 original size:33 final size:33
Alignment explanation
Indices: 1346360--1346451 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1346350 AAAATCGCAA
1346360 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1346393 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1346426 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1346452 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1346702 original size:92 final size:93
Alignment explanation
Indices: 1346532--1347002 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
1346522 TTGAATGGAT
1346532 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1346597 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1346625 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1346689 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1346717 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1346781 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1346809 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1346873 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1346901 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1346966 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1346994 AAATTTACT
1 AAATTTACT
1347003 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 15 0.04
92 243 0.65
93 114 0.31
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1348725 original size:14 final size:14
Alignment explanation
Indices: 1348706--1348795 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1348696 TTGAAATGAA
1348706 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1348720 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1348737 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1348753 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1348772 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1348786 AATCGCAACG
1 AATCGCAACG
1348796 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1348743 original size:33 final size:33
Alignment explanation
Indices: 1348698--1348812 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1348688 TCTTTTGGTT
1348698 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1348731 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1348764 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1348797 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1348813 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1348744 original size:19 final size:18
Alignment explanation
Indices: 1348705--1348817 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1348695 GTTGAAATGA
1348705 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1348720 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1348737 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1348753 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1348770 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1348786 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1348803 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1348818 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1348848 original size:14 final size:14
Alignment explanation
Indices: 1348829--1348883 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1348819 TTTGGTTTCG
1348829 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1348843 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1348862 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1348876 CGTTGCGA
1 CGTTGCGA
1348884 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1348861 original size:33 final size:33
Alignment explanation
Indices: 1348813--1348883 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1348803 AAAATCGCAA
**
1348813 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1348846 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1348879 TGCGA
1 TGCGA
1348884 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1348891 original size:33 final size:33
Alignment explanation
Indices: 1348824--1348905 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1348814 GCGATTTTGG
***
1348824 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1348857 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1348890 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1348906 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1348910 original size:20 final size:20
Alignment explanation
Indices: 1348836--1348924 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1348826 TCGCGTTGCG
1348836 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1348856 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1348869 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1348889 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1348909 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1348925 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1349046 original size:33 final size:33
Alignment explanation
Indices: 1349004--1349074 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1348994 AATACTAACT
*
1349004 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1349037 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1349070 TGAAA
1 TGAAA
1349075 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1349308 original size:22 final size:22
Alignment explanation
Indices: 1349256--1349310 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1349246 TGGTTGTGAG
**
1349256 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1349278 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1349300 GGATTTCTTCG
1 GGATTTCTTCG
1349311 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1349440 original size:20 final size:20
Alignment explanation
Indices: 1349415--1349607 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1349405 CTTTAAATAT
1349415 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1349435 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1349457 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1349476 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1349496 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1349516 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1349536 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1349556 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1349576 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1349596 CGCGTTGCGATT
1 CGCGTTGCGATT
1349608 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1349602 original size:60 final size:60
Alignment explanation
Indices: 1349415--1349607 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1349405 CTTTAAATAT
**
1349415 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1349476 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1349536 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1349596 CGCGTTGCGATT
1 CGCGTTGCGATT
1349608 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1349688 original size:20 final size:20
Alignment explanation
Indices: 1349663--1349714 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1349653 AAGAATCGCG
*
1349663 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1349683 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1349703 TTGCGATTCTGG
1 TTGCGATTCTGG
1349715 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1357248 original size:143 final size:144
Alignment explanation
Indices: 1356989--1357270 Score: 503
Period size: 143 Copynumber: 2.0 Consensus size: 144
1356979 AGAAATTTGA
*
1356989 TTTCTGTAGAATAGCTTGATGGAGAAAGATATAATACAACTTTTTTCAGGCTGTGAATGGAAGAT
1 TTTCTGTAGAATAGCTTGATAGAGAAAGATATAATACAACTTTTTTCAGGCTGTGAATGGAAGAT
*
1357054 TACCAAAGGAGCACTCATCATTGCTCGTGGTAAGAAGACTGATACTCTCTATGTAACCTCAAACT
66 TACCAAAGGAGCACTCATCATTGCTCGTGATAAGAAGACTGATACTCTCTATGTAACCTCAAACT
1357119 TAGAGAATACAACT
131 TAGAGAATACAACT
* *
1357133 TTTCTGTAGGATAGCTTGATAGAGAAGGATATAATACAAC-TTTTTCAGGCTGTGAATGGAAGAT
1 TTTCTGTAGAATAGCTTGATAGAGAAAGATATAATACAACTTTTTTCAGGCTGTGAATGGAAGAT
* *
1357197 TACCAAAGGAGCACTCGTCATTGCTCGTGATAAGAAGATTGATACTCTCTATGTAACCTCAAACT
66 TACCAAAGGAGCACTCATCATTGCTCGTGATAAGAAGACTGATACTCTCTATGTAACCTCAAACT
1357262 TAGAGAATA
131 TAGAGAATA
1357271 TCATTGCAGT
Statistics
Matches: 132, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
143 95 0.72
144 37 0.28
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (144 bp):
TTTCTGTAGAATAGCTTGATAGAGAAAGATATAATACAACTTTTTTCAGGCTGTGAATGGAAGAT
TACCAAAGGAGCACTCATCATTGCTCGTGATAAGAAGACTGATACTCTCTATGTAACCTCAAACT
TAGAGAATACAACT
Found at i:1359649 original size:2 final size:2
Alignment explanation
Indices: 1359642--1359672 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1359632 GACACGTGGT
1359642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1359673 CAAAGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.