Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_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: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1331694 original size:32 final size:32
Alignment explanation
Indices: 1331653--1331714 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1331643 CGTCCTACTA
1331653 GATTCAAACTCCTAAAAAGGATAGAATTTTAG
1 GATTCAAACTCCTAAAAAGGATAGAATTTTAG
* *
1331685 GATTCAAACTCCTAAATATGATAGAATTTT
1 GATTCAAACTCCTAAAAAGGATAGAATTTT
1331715 GCTAGGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (32 bp):
GATTCAAACTCCTAAAAAGGATAGAATTTTAG
Found at i:1332166 original size:8 final size:8
Alignment explanation
Indices: 1332150--1332276 Score: 73
Period size: 8 Copynumber: 15.5 Consensus size: 8
1332140 TATATATATA
1332150 TTTACTTTT
1 TTTA-TTTT
1332159 TTTATTTT
1 TTTATTTT
1332167 TTTA-TTT
1 TTTATTTT
* *
1332174 TATATATT
1 TTTATTTT
*
1332182 ATTATTTT
1 TTTATTTT
1332190 ACTTT-TTATT
1 --TTTATT-TT
*
1332200 ATTATTTT
1 TTTATTTT
1332208 ATTTATTTGT
1 -TTTATTT-T
*
1332218 TTTATTTC
1 TTTATTTT
*
1332226 TATATTTT
1 TTTATTTT
*
1332234 TTT-TCTT
1 TTTATTTT
*
1332241 TTTCTTTT
1 TTTATTTT
* *
1332249 CTT-TTTC
1 TTTATTTT
1332256 TTTATTTT
1 TTTATTTT
1332264 TTTATTTAT
1 TTTATTT-T
1332273 TTTA
1 TTTA
1332277 CTTACTATTT
Statistics
Matches: 90, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
7 17 0.19
8 42 0.47
9 26 0.29
10 5 0.06
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:1332178 original size:30 final size:29
Alignment explanation
Indices: 1332144--1332275 Score: 87
Period size: 30 Copynumber: 4.5 Consensus size: 29
1332134 TATATATATA
1332144 TATATATTTACTTTTTTTATTTTTTTATTT
1 TATATATTTA-TTTTTTTATTTTTTTATTT
*
1332174 TATATA-TTATTATTTTACTTTTTATTATTAT
1 TATATATTTATTTTTTTA-TTTTT-TTATT-T
* *
1332205 T-T-TATTTATTTGTTTTATTTCTATATTT
1 TATATATTTATTT-TTTTATTTTTTTATTT
* * *
1332233 TTTTTCTTT-TTCTTTTCT-TTTTCTTTATTT
1 TATATATTTATT-TTTT-TATTTT-TTTATTT
*
1332263 T-TTTATTTATTTT
1 TATATATTTATTTT
1332276 ACTTACTATT
Statistics
Matches: 83, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
28 9 0.11
29 31 0.37
30 36 0.43
31 7 0.08
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.77
Consensus pattern (29 bp):
TATATATTTATTTTTTTATTTTTTTATTT
Found at i:1332186 original size:15 final size:15
Alignment explanation
Indices: 1332158--1332214 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
1332148 TATTTACTTT
1332158 TTTTATTT-TT-TTA
1 TTTTATTTATTATTA
*
1332171 TTTTATATATTATTA
1 TTTTATTTATTATTA
1332186 TTTTACTTTTTATTATTA
1 TTTTA---TTTATTATTA
1332204 TTTTATTTATT
1 TTTTATTTATT
1332215 TGTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 7 0.19
14 2 0.05
15 14 0.38
18 14 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTATTATTA
Found at i:1332221 original size:59 final size:58
Alignment explanation
Indices: 1332148--1332275 Score: 141
Period size: 59 Copynumber: 2.2 Consensus size: 58
1332138 TATATATATA
* *
1332148 TATTTACTTTTTTTATTTTTTTATTTTATATATTATTATTTTACTTTTT-ATTATTATTT
1 TATTTA-TTTTTTTATTTCTATATTTTATATATTATTATTTT-CTTTTTCATTATTATTT
* * * * * * *
1332207 TATTTATTTGTTTTATTTCTATATTTTTTTTCTTTTTCTTTTCTTTTTCTTTATTTTTT
1 TATTTATTT-TTTTATTTCTATATTTTATATATTATTATTTTCTTTTTCATTATTATTT
1332266 TATTTATTTT
1 TATTTATTTT
1332276 ACTTACTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
58 10 0.17
59 48 0.83
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.77
Consensus pattern (58 bp):
TATTTATTTTTTTATTTCTATATTTTATATATTATTATTTTCTTTTTCATTATTATTT
Found at i:1332250 original size:11 final size:11
Alignment explanation
Indices: 1332230--1332258 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1332220 TATTTCTATA
1332230 TTTT-TTTTCT
1 TTTTCTTTTCT
1332240 TTTTCTTTTCT
1 TTTTCTTTTCT
1332251 TTTTCTTT
1 TTTTCTTT
1332259 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1332299 original size:55 final size:57
Alignment explanation
Indices: 1332201--1332307 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 57
1332191 CTTTTTATTA
* * * *
1332201 TTATTTTATTTATTTGTTTTATTTCTATATTTTTTTTCTTTTTCTTT-TCTTTTTCT
1 TTATTTTATTTATTTATTTTATTACTATATTTTCTTTCGTTTTCTTTATCTTTTTCT
1332257 TTATTTT-TTTATTTATTTTACTTACTAT-TTTATCTTT-GTTTTCTTTATCTT
1 TTATTTTATTTATTTATTTTA-TTACTATATTT-TCTTTCGTTTTCTTTATCTT
1332308 ATCTTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
55 23 0.52
56 21 0.48
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (57 bp):
TTATTTTATTTATTTATTTTATTACTATATTTTCTTTCGTTTTCTTTATCTTTTTCT
Found at i:1332313 original size:55 final size:57
Alignment explanation
Indices: 1332201--1332323 Score: 130
Period size: 55 Copynumber: 2.2 Consensus size: 57
1332191 CTTTTTATTA
* * * * *
1332201 TTATTTTATTTATTTGTTTTATTTCTATATTTTTTTTCTTTTTCTTTTCTTTTTC-T
1 TTATTTTATTTATTTATTTTATTACTATATTTTCTTTCGTTTTCTTTTCTTTATCTT
1332257 TTATTTT-TTTATTTATTTTACTTACTAT-TTTATCTTT-GTTTTCTTTATC-TTATCTT
1 TTATTTTATTTATTTATTTTA-TTACTATATTT-TCTTTCGTTTTCTTT-TCTTTATCTT
*
1332313 TTATTTAATTT
1 TTATTTTATTT
1332324 GTTTTCTCTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
55 27 0.48
56 26 0.46
57 3 0.05
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.75
Consensus pattern (57 bp):
TTATTTTATTTATTTATTTTATTACTATATTTTCTTTCGTTTTCTTTTCTTTATCTT
Found at i:1332381 original size:15 final size:15
Alignment explanation
Indices: 1332363--1332392 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1332353 TATTTATTTC
1332363 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
1332378 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
1332393 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:1335246 original size:151 final size:148
Alignment explanation
Indices: 1334874--1335292 Score: 684
Period size: 151 Copynumber: 2.8 Consensus size: 148
1334864 GAGTCGAGGG
* * * * * * *
1334874 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* *
1334938 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
1335003 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
1335022 TCTACGCGGTCCTT--GG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1335084 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
1335149 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
*
1335167 TCTACACGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACAC
1 TCTACGCGGTCCTTCGGG--A-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACAC
1335232 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACA
63 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACA
1335293 CACTACGGTG
Statistics
Matches: 254, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
144 29 0.11
145 103 0.41
146 2 0.01
147 2 0.01
148 14 0.06
151 104 0.41
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:1335541 original size:16 final size:15
Alignment explanation
Indices: 1335520--1335559 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1335510 AAATAATTCG
1335520 ATGATAATGATAGAT
1 ATGATAATGATAGAT
* *
1335535 AATGATAATAATATAT
1 -ATGATAATGATAGAT
1335551 ATGATAATG
1 ATGATAATG
1335560 CTAAGAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (15 bp):
ATGATAATGATAGAT
Found at i:1340070 original size:21 final size:21
Alignment explanation
Indices: 1340021--1340070 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
1340011 GGCACATACT
*
1340021 TGGTCCTT-AGTATATGTATA
1 TGGTCCTTAAGGATATGTATA
* *
1340041 TGATTCTTAAGGA-ATGATATA
1 TGGTCCTTAAGGATATG-TATA
1340062 TGGTCCTTA
1 TGGTCCTTA
1340071 TGGACATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (21 bp):
TGGTCCTTAAGGATATGTATA
Found at i:1340223 original size:149 final size:149
Alignment explanation
Indices: 1339955--1340405 Score: 735
Period size: 149 Copynumber: 3.0 Consensus size: 149
1339945 GAGTCGAGGG
* * * * * * * *
1339955 TCTACGTGGTCCTTCGGGACATATGTATATTCTTTGGAACAT-TATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* * *
1340018 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATATGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
1340083 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGTAAT
*
1340102 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAATATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
**
1340167 ACTTGATCCCTAGTATATGTATATGATTCTTAAATAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
1340232 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGTAAT
*
1340251 TCTACGCGGTCCTTCTGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1340316 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
1340381 TATGGCACTACGGTTTAAT
131 TATGGCACTACGGTGTAAT
1340400 TCTACG
1 TCTACG
1340406 TGCACTTCGG
Statistics
Matches: 281, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
147 37 0.13
148 9 0.03
149 235 0.84
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGTAAT
Found at i:1343764 original size:31 final size:31
Alignment explanation
Indices: 1343726--1343787 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1343716 ATGTTGTCAC
1343726 TGCCTTTCTTGAGTGACTGGAGTTTATAGTG
1 TGCCTTTCTTGAGTGACTGGAGTTTATAGTG
1343757 TGCCTTTCTTGAGTGACTGGAGTTTATAGTG
1 TGCCTTTCTTGAGTGACTGGAGTTTATAGTG
1343788 CAGGCTGATG
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:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (31 bp):
TGCCTTTCTTGAGTGACTGGAGTTTATAGTG
Found at i:1346903 original size:41 final size:42
Alignment explanation
Indices: 1346876--1347013 Score: 142
Period size: 41 Copynumber: 3.4 Consensus size: 42
1346866 GCGAATTTGG
1346876 AAAATCGCAACGCGATACTGACTATCGCAACGCG-ATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
* * *
1346917 AAAATCGCAATGCGATACTGACTTTCGCAACGCG-ATACTTAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATA-ATAC
** * * *
1346959 --TTTCGCTACGCGATACTGACTTTCGCAACGAG-ATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
* *
1346998 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1347014 TTTCAAAGCG
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 45 0.56
42 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGAATAATAC
Found at i:1346904 original size:20 final size:20
Alignment explanation
Indices: 1346879--1346993 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
1346869 AATTTGGAAA
1346879 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1346899 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1346920 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1346940 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1346960 TTCGCTACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1346980 TTCGCAACGAGATA
1 ATCGCAACGCGATA
1346994 ATACATAATC
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.77
21 14 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1347208 original size:22 final size:22
Alignment explanation
Indices: 1347180--1347223 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1347170 CACTCTCTCA
1347180 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1347202 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1347224 TATCTCCATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1347525 original size:20 final size:20
Alignment explanation
Indices: 1347502--1347544 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1347492 GATAGTCAAA
1347502 TTCGCGTTGCGATTATCATT
1 TTCGCGTTGCGATTATCATT
* *
1347522 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTATCATT
1347542 TTC
1 TTC
1347545 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTATCATT
Found at i:1347722 original size:25 final size:24
Alignment explanation
Indices: 1347668--1347722 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1347658 TGTTTATTAT
* *
1347668 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1347692 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1347718 TGTTT
1 TGTTT
1347723 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1348865 original size:18 final size:18
Alignment explanation
Indices: 1348844--1348892 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
1348834 CTCCACTTCA
1348844 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
*
1348862 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
1348880 AGAGCCATCACCT
1 AGAGCCATCACCT
1348893 GATCGACCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.45, G:0.12, T:0.14
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1349480 original size:19 final size:20
Alignment explanation
Indices: 1349437--1349481 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1349427 CGCAACACGA
*
1349437 AAATGACTATTGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
1349457 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
1349476 AAATGA
1 AAATGA
1349482 AAATCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:1349574 original size:20 final size:20
Alignment explanation
Indices: 1349521--1349626 Score: 135
Period size: 20 Copynumber: 5.3 Consensus size: 20
1349511 GCATTTTGCA
1349521 TTGCGATAG-CATTT-CGCG
1 TTGCGATAGCCATTTCCGCG
*
1349539 TTGCGATTTTGCCATTTCCGCG
1 TTGCGA--TAGCCATTTCCGCG
1349561 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
1349581 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
* *
1349601 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
1349621 TTGCGA
1 TTGCGA
1349627 AAGTAAGTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.08
20 59 0.74
21 5 0.06
22 10 0.12
ACGTcount: A:0.14, C:0.24, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:1349637 original size:20 final size:20
Alignment explanation
Indices: 1349552--1349652 Score: 94
Period size: 20 Copynumber: 5.0 Consensus size: 20
1349542 CGATTTTGCC
* * **
1349552 ATTTCCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGAAAGTA
* * *
1349572 ATTTCCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGAAAGTA
* *
1349592 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGAAAGTA
1349612 ATTTTCGCGTTGCGAAAGTA
1 ATTTTCGCGTTGCGAAAGTA
* * *
1349632 AGTTTCGTGTTGTGAAAGTA
1 ATTTTCGCGTTGCGAAAGTA
1349652 A
1 A
1349653 ACTATTCTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGAAAGTA
Found at i:1349638 original size:40 final size:40
Alignment explanation
Indices: 1349557--1349643 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
1349547 TTGCCATTTC
* * *
1349557 CGCGTTGCGATAGCCATTTCCGCGTTGCGATAGTCATTTT
1 CGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAAGTTT
* *
1349597 CGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAAGTTT
*
1349637 CGTGTTG
1 CGCGTTG
1349644 TGAAAGTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.36
Consensus pattern (40 bp):
CGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAAGTTT
Found at i:1350021 original size:21 final size:20
Alignment explanation
Indices: 1349995--1350062 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
1349985 CTGTCATCCC
1349995 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
1350016 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
1350037 TCAAGAGTCCCC-CCACCGT
1 TCAAGAGTCCCCTCCATCGT
1350056 TCAAGAG
1 TCAAGAG
1350063 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:1350074 original size:40 final size:42
Alignment explanation
Indices: 1349985--1350074 Score: 139
Period size: 40 Copynumber: 2.2 Consensus size: 42
1349975 GCCGACTCAC
* *
1349985 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
*
1350027 CTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
1350067 CTGTCATC
1 CTGTCATC
1350075 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 21 0.48
41 2 0.05
42 21 0.48
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:1351506 original size:14 final size:14
Alignment explanation
Indices: 1351472--1351510 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1351462 TTGATTGTTT
1351472 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1351486 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1351500 TGTTGATTTGT
1 AATTGATTTGT
1351511 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1351758 original size:20 final size:20
Alignment explanation
Indices: 1351733--1351788 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1351723 TCGCATTGCG
*
1351733 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
1351753 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
1351773 ATTTTCGCATTGCGAT
1 ATTTTCGCGTTGCGAT
1351789 TTCCCCGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1352027 original size:20 final size:20
Alignment explanation
Indices: 1352011--1352084 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
1352001 ATTGCGATTT
*
1352011 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
1352031 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
1352051 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
1352071 TCAGTATCGTGTTG
1 TCAGAATCGCGTTG
1352085 TGATTTTGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:1352129 original size:20 final size:20
Alignment explanation
Indices: 1352020--1352128 Score: 112
Period size: 20 Copynumber: 5.4 Consensus size: 20
1352010 TTCAGAATCT
*
1352020 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
1352040 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
1352060 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* * ** *
1352080 TGTTGTGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
*
1352101 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
1352121 CATTGCGA
1 CGTTGCGA
1352129 TTTTCCAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
19 3 0.04
20 58 0.77
21 12 0.16
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:1352162 original size:20 final size:21
Alignment explanation
Indices: 1352118--1352169 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1352108 ATAGTCAGTA
*
1352118 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1352139 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1352159 TCGCATTGCGA
1 TCGCATTGCGA
1352170 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1352944 original size:16 final size:16
Alignment explanation
Indices: 1352923--1352955 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1352913 TAAAAAATAA
*
1352923 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
1352939 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
1352955 A
1 A
1352956 AATTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:1353046 original size:16 final size:16
Alignment explanation
Indices: 1353015--1353081 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1353005 CGTTCATTTA
1353015 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
*
1353029 ATAAATGAACATGAAC
1 ATAAATGAACACGAAC
*
1353045 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
1353061 ATAAATGAATACGAAC
1 ATAAATGAACACGAAC
1353077 ATAAA
1 ATAAA
1353082 CAAACATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.13
15 2 0.04
16 38 0.83
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:1353059 original size:32 final size:32
Alignment explanation
Indices: 1353023--1353087 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1353013 TAATAAATAA
* *
1353023 ACGAACATAAATGAACATGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACAAAC
*
1353055 ACGAACATAAATGAATACGAACATAAACAAAC
1 ACGAACATAAATGAACACGAACATAAACAAAC
1353087 A
1 A
1353088 TAAACGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.12
Consensus pattern (32 bp):
ACGAACATAAATGAACACGAACATAAACAAAC
Found at i:1354205 original size:24 final size:24
Alignment explanation
Indices: 1354164--1354209 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1354154 AGATTGGGTT
* *
1354164 AAACATAAATGAATGAACATAAAC
1 AAACATAAACGAACGAACATAAAC
*
1354188 AAACATAACCGAACGAACATAA
1 AAACATAAACGAACGAACATAA
1354210 CCGAACGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.09, T:0.13
Consensus pattern (24 bp):
AAACATAAACGAACGAACATAAAC
Found at i:1354208 original size:14 final size:14
Alignment explanation
Indices: 1354189--1354240 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
1354179 AACATAAACA
1354189 AACATAACCGAACG
1 AACATAACCGAACG
1354203 AACATAACCGAACG
1 AACATAACCGAACG
1354217 AACAT-A---AACG
1 AACATAACCGAACG
1354227 AACATAACCGAACG
1 AACATAACCGAACG
1354241 TTCACGAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.52, C:0.27, G:0.13, T:0.08
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:1354250 original size:24 final size:24
Alignment explanation
Indices: 1354197--1354250 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1354187 CAAACATAAC
1354197 CGAACGAACATAACCGAACGAACA
1 CGAACGAACATAACCGAACGAACA
** **
1354221 TAAACGAACATAACCGAACGTTCA
1 CGAACGAACATAACCGAACGAACA
1354245 CGAACG
1 CGAACG
1354251 TAAATGAACG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (24 bp):
CGAACGAACATAACCGAACGAACA
Found at i:1359169 original size:5 final size:5
Alignment explanation
Indices: 1359159--1359185 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1359149 TTAGATTTTA
1359159 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1359186 TAAAATTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1360505 original size:11 final size:10
Alignment explanation
Indices: 1360486--1360512 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1360476 GATGCTCCTT
1360486 AATAAAAAAA
1 AATAAAAAAA
1360496 AATAAAAAAA
1 AATAAAAAAA
1360506 AATAAAA
1 AATAAAA
1360513 GGATTAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:1360856 original size:20 final size:20
Alignment explanation
Indices: 1360828--1360876 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1360818 AACTCCCCTC
* *
1360828 CTTCTCCCTCTTCTGTCATT
1 CTTCCCCCTCTTCGGTCATT
1360848 CTTCCCCCTCTTCGGTCATT
1 CTTCCCCCTCTTCGGTCATT
1360868 CTTCCCCCT
1 CTTCCCCCT
1360877 ATCCACTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.04, C:0.47, G:0.06, T:0.43
Consensus pattern (20 bp):
CTTCCCCCTCTTCGGTCATT
Found at i:1361894 original size:10 final size:10
Alignment explanation
Indices: 1361879--1361906 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1361869 TTGTACCTGA
1361879 AAAATAAAAC
1 AAAATAAAAC
1361889 AAAATAAAAC
1 AAAATAAAAC
1361899 AAAATAAA
1 AAAATAAA
1361907 TTAAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:1362016 original size:22 final size:21
Alignment explanation
Indices: 1361991--1362079 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 21
1361981 TATATATATT
*
1361991 ATATATTTTCAAAAAGTATAGA
1 ATATATTTTCAAAAACTATA-A
* * *
1362013 ATATGTTTTTAAAAACTATAT
1 ATATATTTTCAAAAACTATAA
* *
1362034 ATATA-TTT-AAAAACCATAT
1 ATATATTTTCAAAAACTATAA
*
1362053 ATAT-TTTTC-AAAACTATATT
1 ATATATTTTCAAAAACTATA-A
1362073 ATATATT
1 ATATATT
1362080 ATACGTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
19 25 0.45
20 8 0.14
21 6 0.11
22 17 0.30
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (21 bp):
ATATATTTTCAAAAACTATAA
Found at i:1362042 original size:19 final size:19
Alignment explanation
Indices: 1362020--1362079 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
1362010 AGAATATGTT
1362020 TTTAAAAACTATATATATA
1 TTTAAAAACTATATATATA
* *
1362039 TTTAAAAACCATATATATT
1 TTTAAAAACTATATATATA
*
1362058 TTTCAAAACTATATTATATA
1 TTTAAAAACTATA-TATATA
1362078 TT
1 TT
1362080 ATACGTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAAAACTATATATATA
Found at i:1362097 original size:24 final size:23
Alignment explanation
Indices: 1362049--1362131 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 23
1362039 TTTAAAAACC
*
1362049 ATATATAT-TTTTCAAAACTATATT
1 ATATATATATTTTCAAAAAT-TA-T
*
1362073 ATATATTATACGTTTTCCAAAATTAT
1 ATATA-TATA--TTTTCAAAAATTAT
1362099 AT-TATATATTTTCAAAAATTAT
1 ATATATATATTTTCAAAAATTAT
1362121 ATATACTATAT
1 ATATA-TATAT
1362132 ATATCTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
22 15 0.30
23 2 0.04
24 14 0.28
25 5 0.10
26 3 0.06
27 2 0.04
28 9 0.18
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATATATATTTTCAAAAATTAT
Found at i:1365337 original size:10 final size:10
Alignment explanation
Indices: 1365330--1365407 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 10
1365320 AAGAAAAAAC
1365330 AAGTAAAATA
1 AAGTAAAATA
*
1365340 AAGTAAAAGA
1 AAGTAAAATA
*
1365350 AA-TAAAAAA
1 AAGTAAAATA
*
1365359 AAG-AAAAGAA
1 AAGTAAAA-TA
*
1365369 AAGT-GAATA
1 AAGTAAAATA
*
1365378 AAAT-AAATA
1 AAGTAAAATA
*
1365387 AAAT-AAATA
1 AAGTAAAATA
1365396 AA-TAAAATA
1 AAGTAAAATA
1365405 AAG
1 AAG
1365408 ACAATAATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 1 0.02
9 38 0.67
10 18 0.32
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (10 bp):
AAGTAAAATA
Found at i:1365382 original size:5 final size:5
Alignment explanation
Indices: 1365315--1365406 Score: 54
Period size: 5 Copynumber: 19.2 Consensus size: 5
1365305 AATAAAAGTG
* * * *
1365315 AATAA AAGAA AA-AA CAAGTAA AATAA AGTAA AA-GA AATAA AA-AA AAGAA
1 AATAA AATAA AATAA -AA-TAA AATAA AATAA AATAA AATAA AATAA AATAA
* *
1365364 AAGAA AAGT-G AATAA AAT-A AATAA AAT-A AAT-A AATAA AATAA A
1 AATAA AA-TAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
1365407 GACAATAATG
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
4 22 0.31
5 44 0.63
6 2 0.03
7 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:1365396 original size:13 final size:13
Alignment explanation
Indices: 1365378--1365406 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1365368 AAAGTGAATA
1365378 AAATAAATAAAAT
1 AAATAAATAAAAT
1365391 AAATAAATAAAAT
1 AAATAAATAAAAT
1365404 AAA
1 AAA
1365407 GACAATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1365484 original size:9 final size:9
Alignment explanation
Indices: 1365449--1365572 Score: 51
Period size: 9 Copynumber: 13.2 Consensus size: 9
1365439 TAATAAATAA
1365449 AAATAAAAT
1 AAATAAAAT
* *
1365458 AAGT-AAGT
1 AAATAAAAT
1365466 AAAT-AAAT
1 AAATAAAAT
1365474 AAATAAAAT
1 AAATAAAAT
* *
1365483 AAAGATGCATAT
1 -AA-AT-AAAAT
1365495 AAATAAAAT
1 AAATAAAAT
*
1365504 ATTAAGAGAAA-
1 A--AATA-AAAT
1365515 AAATAAAAT
1 AAATAAAAT
1365524 AAAATAAAAT
1 -AAATAAAAT
**
1365534 ATGTAAAAT
1 AAATAAAAT
*
1365543 ATATAATAAT
1 AAATAA-AAT
1365553 -AATAATAAT
1 AAATAA-AAT
1365562 -AATAATAAT
1 AAATAA-AAT
1365571 AA
1 AA
1365573 TAATGAAATA
Statistics
Matches: 90, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
8 16 0.18
9 43 0.48
10 17 0.19
11 8 0.09
12 6 0.07
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.26
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1365553 original size:3 final size:3
Alignment explanation
Indices: 1365516--1365576 Score: 67
Period size: 3 Copynumber: 21.0 Consensus size: 3
1365506 TAAGAGAAAA
*
1365516 AAT AA- AAT AA- AAT AA- AAT ATGT AA- AAT ATAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT
1365559 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
1365577 GAAATATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 8 0.16
3 37 0.74
4 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1365704 original size:4 final size:4
Alignment explanation
Indices: 1365682--1365715 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1365672 ATATAATAGT
1365682 AATA AA-A AATA AA-A AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
1365716 TAATTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:1365873 original size:3 final size:3
Alignment explanation
Indices: 1365857--1365941 Score: 145
Period size: 3 Copynumber: 28.3 Consensus size: 3
1365847 AAACAAAATA
*
1365857 AAT AAT AGAA AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1365902 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1365942 CAAGGATTAC
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.03
3 74 0.95
4 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1367802 original size:14 final size:14
Alignment explanation
Indices: 1367779--1367810 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1367769 CGTTTGTGAA
*
1367779 CGTTCGATTATGTT
1 CGTTCAATTATGTT
1367793 CGTTCAATTATGTT
1 CGTTCAATTATGTT
1367807 CGTT
1 CGTT
1367811 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (14 bp):
CGTTCAATTATGTT
Found at i:1367807 original size:24 final size:24
Alignment explanation
Indices: 1367780--1367830 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1367770 GTTTGTGAAC
*
1367780 GTTCGATTATGTTCGTTCAATTAT
1 GTTCGATTATGTTCATTCAATTAT
* *
1367804 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAATTAT
1367828 GTT
1 GTT
1367831 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAATTAT
Found at i:1368588 original size:16 final size:16
Alignment explanation
Indices: 1368567--1368611 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1368557 GGGTCTCCAA
*
1368567 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTC
1368583 CGTTTATGTTCGTGTC
1 CGTTTATGTTCGTGTC
1368599 CGTTTATGTTCGT
1 CGTTTATGTTCGT
1368612 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (16 bp):
CGTTTATGTTCGTGTC
Found at i:1371941 original size:10 final size:10
Alignment explanation
Indices: 1371926--1371951 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1371916 TGGAAGACTA
1371926 AATTTATTTT
1 AATTTATTTT
1371936 AATTTATTTT
1 AATTTATTTT
1371946 AATTTA
1 AATTTA
1371952 ATATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTATTTT
Found at i:1372238 original size:29 final size:29
Alignment explanation
Indices: 1372205--1372264 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1372195 AATTATCTCA
*
1372205 TTATTTTTG-CTTTAGCTTATTAAATATTT
1 TTATTTTTGTC-TTAACTTATTAAATATTT
*
1372234 TTATTTTTGTCTTAATTTATTAAATATTT
1 TTATTTTTGTCTTAACTTATTAAATATTT
1372263 TT
1 TT
1372265 TTTATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (29 bp):
TTATTTTTGTCTTAACTTATTAAATATTT
Found at i:1372335 original size:35 final size:33
Alignment explanation
Indices: 1372256--1372354 Score: 116
Period size: 35 Copynumber: 3.0 Consensus size: 33
1372246 TAATTTATTA
1372256 AATATTTT-TT-TTATTTTAATGTAAAAA-ATAT
1 AATATTTTATTCTTATTTTAAT-TAAAAATATAT
*
1372287 -ATATTTTACTCTTATTTTAAATTAAAAAATATAT
1 AATATTTTATTCTTATTTT-AATT-AAAAATATAT
*
1372321 AATATTTTATTCTTATCTTTACTTAAAAATATAT
1 AATATTTTATTCTTAT-TTTAATTAAAAATATAT
1372355 TTTATTATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
30 7 0.12
31 1 0.02
32 8 0.14
33 8 0.14
34 14 0.24
35 17 0.29
36 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (33 bp):
AATATTTTATTCTTATTTTAATTAAAAATATAT
Found at i:1372354 original size:29 final size:30
Alignment explanation
Indices: 1372322--1372386 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
1372312 AAAATATATA
* **
1372322 ATATTTTATTCTTATCTTTAC-TTAAAAAT
1 ATATTTTATTATTATCTCAACTTTAAAAAT
1372351 ATATTTTATTATTATCTCAACTTTTAAAAAT
1 ATATTTTATTATTATCTCAAC-TTTAAAAAT
1372382 ATATT
1 ATATT
1372387 AAAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.58
31 13 0.42
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTTTATTATTATCTCAACTTTAAAAAT
Found at i:1372363 original size:32 final size:32
Alignment explanation
Indices: 1372266--1372363 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
1372256 AATATTTTTT
* *
1372266 TTATTTT-AATGTAAAAAATATATATTTTACTC
1 TTATTTTAAAT-TAAAAAATATATTTTTTATTC
1372298 TTATTTTAAATTAAAAAATATATAATATTTTATTC
1 TTATTTTAAATTAAAAAATATAT--T-TTTTATTC
*
1372333 TTATCTTT-ACTT-AAAAATATATTTTATTATT
1 TTAT-TTTAAATTAAAAAATATATTTT-TTATT
1372364 ATCTCAACTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
31 2 0.04
32 25 0.44
33 3 0.05
34 10 0.18
35 14 0.25
36 3 0.05
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (32 bp):
TTATTTTAAATTAAAAAATATATTTTTTATTC
Found at i:1372583 original size:29 final size:29
Alignment explanation
Indices: 1372545--1372605 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1372535 TTAAGATAAA
1372545 AAAAATATTTAATAAATTAAAACAAAAAT
1 AAAAATATTTAATAAATTAAAACAAAAAT
*
1372574 AAAAATATTTAATAAGTTAAAACAAAAAT
1 AAAAATATTTAATAAATTAAAACAAAAAT
1372603 AAA
1 AAA
1372606 GAGATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (29 bp):
AAAAATATTTAATAAATTAAAACAAAAAT
Found at i:1372795 original size:30 final size:30
Alignment explanation
Indices: 1372759--1372817 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1372749 TTTCAAAGTG
*
1372759 TCCTATG-TTCATATCCCCATATTTGCTTTT
1 TCCTATGTTTCA-ATCCCCATACTTGCTTTT
*
1372789 TCCTATGTTTGAATCCCCATACTTGCTTT
1 TCCTATGTTTCAATCCCCATACTTGCTTT
1372818 ATTTGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.47
Consensus pattern (30 bp):
TCCTATGTTTCAATCCCCATACTTGCTTTT
Found at i:1373271 original size:11 final size:11
Alignment explanation
Indices: 1373257--1373281 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1373247 TTTTTTACTA
1373257 CTGTAATATTG
1 CTGTAATATTG
1373268 CTGTAATATTG
1 CTGTAATATTG
1373279 CTG
1 CTG
1373282 AATCACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (11 bp):
CTGTAATATTG
Found at i:1375583 original size:29 final size:29
Alignment explanation
Indices: 1375548--1375622 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
1375538 AAGTCTCTCT
* *
1375548 ACTATAAAAAATTATAAAATAATCATTTG
1 ACTATAAAAAATTACAAAATAATCAATTG
* *
1375577 ACTATAAAAAGTTACAAAATAGTCAATTG
1 ACTATAAAAAATTACAAAATAATCAATTG
*
1375606 ACTATAAAAAGTTACAA
1 ACTATAAAAAATTACAA
1375623 GTCACTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (29 bp):
ACTATAAAAAATTACAAAATAATCAATTG
Found at i:1375710 original size:23 final size:22
Alignment explanation
Indices: 1375641--1375710 Score: 104
Period size: 23 Copynumber: 3.1 Consensus size: 22
1375631 ATAATCTATC
*
1375641 TAAAATAATTTTTGATTATTTTT
1 TAAAATAATTTTTTATTA-TTTT
*
1375664 TAAAATAACTTTTTATTATTTT
1 TAAAATAATTTTTTATTATTTT
1375686 TAAAATAAATTTTTTATTATTTT
1 TAAAAT-AATTTTTTATTATTTT
1375709 TA
1 TA
1375711 TTGAAATTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 10 0.23
23 33 0.77
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (22 bp):
TAAAATAATTTTTTATTATTTT
Found at i:1377044 original size:22 final size:22
Alignment explanation
Indices: 1377019--1377068 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1377009 AGTCAACCTG
* *
1377019 TTGACCGGTCTGACCGTGGACT
1 TTGACAGGTCAGACCGTGGACT
* *
1377041 TTGACATGTCAGACCGTTGACT
1 TTGACAGGTCAGACCGTGGACT
1377063 TTGACA
1 TTGACA
1377069 AAAAAGTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (22 bp):
TTGACAGGTCAGACCGTGGACT
Found at i:1381766 original size:29 final size:29
Alignment explanation
Indices: 1381731--1381805 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
1381721 AAGTCTCTCT
* *
1381731 ACTATAAAAAGTTATAAAATAATCATTTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
* *
1381760 ACTATAAAAAATTACAAAATAGTCAATTG
1 ACTATAAAAAGTTACAAAATAATCAATTG
1381789 ACTATAAAAAGTTACAA
1 ACTATAAAAAGTTACAA
1381806 GTCACTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (29 bp):
ACTATAAAAAGTTACAAAATAATCAATTG
Found at i:1381847 original size:11 final size:11
Alignment explanation
Indices: 1381831--1381915 Score: 59
Period size: 12 Copynumber: 7.7 Consensus size: 11
1381821 ATCTTAAATA
1381831 ATTTTTATATT
1 ATTTTTATATT
* *
1381842 ATTTTTAAAATA
1 ATTTTT-ATATT
1381854 ATTTTT-TATT
1 ATTTTTATATT
*
1381864 ATTTTTATAATA
1 ATTTTTAT-ATT
* *
1381876 ATTTGT-GATT
1 ATTTTTATATT
* *
1381886 ATTTTTAAAATA
1 ATTTTT-ATATT
1381898 ATTTTT-TATT
1 ATTTTTATATT
1381908 ATTTTTAT
1 ATTTTTAT
1381916 TGAAATTGCT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
10 23 0.42
11 8 0.15
12 24 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1381922 original size:22 final size:22
Alignment explanation
Indices: 1381826--1381914 Score: 142
Period size: 22 Copynumber: 4.0 Consensus size: 22
1381816 AATCTATCTT
1381826 AAATAATTTTTATATTATTTTTA
1 AAATAATTTTT-TATTATTTTTA
1381849 AAATAATTTTTTATTATTTTTA
1 AAATAATTTTTTATTATTTTTA
* * *
1381871 TAATAATTTGTGATTATTTTTA
1 AAATAATTTTTTATTATTTTTA
1381893 AAATAATTTTTTATTATTTTTA
1 AAATAATTTTTTATTATTTTTA
1381915 TTGAAATTGC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
22 49 0.82
23 11 0.18
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
AAATAATTTTTTATTATTTTTA
Found at i:1383193 original size:13 final size:13
Alignment explanation
Indices: 1383175--1383212 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
1383165 CCTGACTCAG
1383175 TCACTGAGTCAAC
1 TCACTGAGTCAAC
1383188 TCACTGAGTCAAC
1 TCACTGAGTCAAC
1383201 TCACTGAGTCAA
1 TCACTGAGTCAA
1383213 TTCATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (13 bp):
TCACTGAGTCAAC
Found at i:1385082 original size:66 final size:66
Alignment explanation
Indices: 1384956--1385085 Score: 154
Period size: 66 Copynumber: 2.0 Consensus size: 66
1384946 GGGATGAAGA
** * ** *
1384956 CTCTAACAGGTTCAGTCGCTGATGGTTATTCCTTGTATAGGTTCAGTATCGGCTGATAATTCCTA
1 CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATCGACTGATAATTCCTA
1385021 T
66 T
* * * *
1385022 CTCTAGCAGGTTTAGTCGCTGCTGGCAATTCCTTGTATAGATTCAACA-CTGACTGGTAATTCCT
1 CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATC-GACTGATAATTCCT
1385086 TATGGACCTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (66 bp):
CTCTAACAGGTTCAGTCGCTGATGGCAATTCCTTGTATAGATTCAACATCGACTGATAATTCCTA
T
Found at i:1386741 original size:15 final size:16
Alignment explanation
Indices: 1386701--1386745 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1386691 ACCTGACATA
1386701 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* *
1386718 TGAGTACCCGAAAA-C
1 CGGGTACCCGAAAATC
1386733 CGGGTACCCGAAA
1 CGGGTACCCGAAA
1386746 CATTCGAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 4 0.17
17 8 0.33
ACGTcount: A:0.33, C:0.31, G:0.24, T:0.11
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:1395799 original size:147 final size:146
Alignment explanation
Indices: 1395598--1396046 Score: 551
Period size: 147 Copynumber: 3.0 Consensus size: 146
1395588 TGTATCGTTA
* * * * *
1395598 ATTTACGACGTTTGTTACTAAAACGCCGCTATGTGTGCAACCTATTGTGGCATTTTTGTTAAAAC
1 ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTG-AACCTATTGCGGCATTTTTGTCAAAAC
** ** ** *
1395663 GCTACTAAAGTACTAATTTATTGCAGTATTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATG
65 GCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATG
1395728 ACGTTTAAATAAAAAAC
130 ACGTTTAAATAAAAAAC
* * * *
1395745 ATTTGCGGCGTTTGTTACCAAAACACCGCTATATGTGAACCCTATTACGACATTTTTGTCAAAAC
1 ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTGAA-CCTATTGCGGCATTTTTGTCAAAAC
* * *
1395810 ACCGCTAAACTACTAATTTGTTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATG
65 GCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATG
1395875 ACGTTTAAATAAAAAAC
130 ACGTTTAAATAAAAAAC
* * ** * * * * *
1395892 ATTTGCGATGTTTTTTGTCTAAACGCCACTA-ATGTACGAATC-ATTTGCGGCGTTTGTTATCAA
1 ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGT--GAACCTA-TTGCGGCATTT-TTGTCAA
*
1395955 AACGCCGCTAAAGTACTAATCTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTA
62 AACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTA
*
1396020 ATAACGTTTAAATAAAAAAAC
127 ATGACGTTTAAAT-AAAAAAC
1396041 ATTTGC
1 ATTTGC
1396047 AGCATTTTCT
Statistics
Matches: 259, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
146 7 0.03
147 157 0.61
148 82 0.32
149 13 0.05
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (146 bp):
ATTTGCGACGTTTGTTACCAAAACGCCGCTATATGTGAACCTATTGCGGCATTTTTGTCAAAACG
CCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGA
CGTTTAAATAAAAAAC
Found at i:1396002 original size:41 final size:42
Alignment explanation
Indices: 1395912--1396005 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
1395902 TTTTTTGTCT
* * * *
1395912 AAACGCCACTAATGTACGAATCATTTGCGGCGTTTGTTATCA
1 AAACGCCGCTAAAGTACGAATCATTTGCGGCGTTTATTATAA
* *
1395954 AAACGCCGCTAAAGTACTAATC-TATTGTGGCGTTTATTA-AA
1 AAACGCCGCTAAAGTACGAATCAT-TTGCGGCGTTTATTATAA
1395995 AAACGCCGCTA
1 AAACGCCGCTA
1396006 TATGTCTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 13 0.29
42 32 0.71
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (42 bp):
AAACGCCGCTAAAGTACGAATCATTTGCGGCGTTTATTATAA
Found at i:1396013 original size:148 final size:146
Alignment explanation
Indices: 1395658--1396113 Score: 540
Period size: 147 Copynumber: 3.1 Consensus size: 146
1395648 CATTTTTGTT
** ** **
1395658 AAAACGCTACTAAAGTACTAATTTATTGCAGTATTTATTAAAAAACGCCGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* * * * * * * *
1395723 AAATGACGTTTAAATAAAAAACATTTGCGGCGTTTGTTACCAAAACACCGCTATATGT-GAACCC
66 TAATGACGTTTAAATAAAAAACATTTGC-GAGTTTTTTATCAAAACGCCACTA-ATGTCGAATCA
* * * *
1395787 TATTACGACATTT-TTGTC
129 T-TTGCGGCGTTTGTTATC
* * *
1395805 AAAACACCGCTAAACTACTAATTTGTTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* *
1395870 TAATGACGTTTAAATAAAAAACATTTGCGATGTTTTTTGTCTAAACGCCACTAATGTACGAATCA
66 TAATGACGTTTAAATAAAAAACATTTGCGA-GTTTTTTATCAAAACGCCACTAATGT-CGAATCA
1395935 TTTGCGGCGTTTGTTATC
129 TTTGCGGCGTTTGTTATC
*
1395953 AAAACGCCGCTAAAGTACTAATCTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
1 AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
* * * *
1396018 TAATAACGTTTAAATAAAAAAACATTTGC-AGCATTTTCTATCAAAAGGCCACTAAAGTCCGAAT
66 TAATGACGTTTAAAT-AAAAAACATTTGCGAG--TTTTTTATCAAAACGCCACTAATGT-CGAAT
* *
1396082 CATTTGCGGCGTTTGATACC
127 CATTTGCGGCGTTTGTTATC
1396102 AAAACGCCGCTA
1 AAAACGCCGCTA
1396114 TATGTTAACC
Statistics
Matches: 266, Mismatches: 36, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
146 5 0.02
147 108 0.41
148 85 0.32
149 68 0.26
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (146 bp):
AAAACGCCGCTAAAGTACTAATTTATTGTGGCGTTTATTAAAAAACGCCGCTATATGTCTAAAGT
TAATGACGTTTAAATAAAAAACATTTGCGAGTTTTTTATCAAAACGCCACTAATGTCGAATCATT
TGCGGCGTTTGTTATC
Found at i:1396128 original size:149 final size:146
Alignment explanation
Indices: 1395691--1396113 Score: 451
Period size: 148 Copynumber: 2.9 Consensus size: 146
1395681 TATTGCAGTA
* * *
1395691 TTTATTAAAAAACGCCGCTATATGTCTAAAGTAAATGACGTTTAAATAAAAAACATTTGCGGCGT
1 TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATAACGTTTAAATAAAAAACATTTGC-GAGT
* * * * * * * * * * ** *
1395756 TTGT-TACCAAAACACCGCTATATGT--GAACCCTATTACGACATTT-TTGTCAAAACACCGCTA
65 TT-TCTATCAAAACGCCACTA-AAGTACGAATCAT-TTGCGGCGTTTGATACCAAAACGCCGCTA
* ** *
1395817 AACTACTAATTTGTTGTGGCG
127 AAGTA-TAACCTATTGTGGCG
*
1395838 TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTGCGATGT
1 TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATAACGTTTAAATAAAAAACATTTGCGA-GT
* * * * * *
1395903 TTTTTGTCTAAACGCCACTAATGTACGAATCATTTGCGGCGTTTGTTATCAAAACGCCGCTAAAG
65 TTTCTATCAAAACGCCACTAAAGTACGAATCATTTGCGGCGTTTGATACCAAAACGCCGCTAAAG
*
1395968 TACTAATCTATTGTGGCG
130 TA-TAACCTATTGTGGCG
1395986 TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATAACGTTTAAATAAAAAAACATTTGC-AGC
1 TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATAACGTTTAAAT-AAAAAACATTTGCGAG-
* *
1396050 ATTTTCTATCAAAAGGCCACTAAAGTCCGAATCATTTGCGGCGTTTGATACCAAAACGCCGCTA
64 -TTTTCTATCAAAACGCCACTAAAGTACGAATCATTTGCGGCGTTTGATACCAAAACGCCGCTA
1396114 TATGTTAACC
Statistics
Matches: 242, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
146 6 0.02
147 83 0.34
148 85 0.35
149 68 0.28
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (146 bp):
TTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATAACGTTTAAATAAAAAACATTTGCGAGTT
TTCTATCAAAACGCCACTAAAGTACGAATCATTTGCGGCGTTTGATACCAAAACGCCGCTAAAGT
ATAACCTATTGTGGCG
Found at i:1401110 original size:15 final size:16
Alignment explanation
Indices: 1401063--1401111 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
1401053 AATAAGTTTG
1401063 AAAGTTAGAGTAATT-
1 AAAGTTAGAGTAATTA
1401078 AAA-TTAAGAGTAATTTA
1 AAAGTT-AGAGTAA-TTA
1401095 AAAGTTA-AGTAATTA
1 AAAGTTAGAGTAATTA
1401110 AA
1 AA
1401112 CTAAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.07
15 15 0.50
16 7 0.23
17 4 0.13
18 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (16 bp):
AAAGTTAGAGTAATTA
Found at i:1401124 original size:31 final size:32
Alignment explanation
Indices: 1401063--1401126 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
1401053 AATAAGTTTG
* * **
1401063 AAAGTTAGAGTAATTAAATTAAGAGTAATTTA
1 AAAGTTAGAGTAATTAAACTAAAAACAATTTA
1401095 AAAGTTA-AGTAATTAAACTAAAAACAATTTA
1 AAAGTTAGAGTAATTAAACTAAAAACAATTTA
1401126 A
1 A
1401127 CTTTAGTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.31
Consensus pattern (32 bp):
AAAGTTAGAGTAATTAAACTAAAAACAATTTA
Found at i:1409132 original size:21 final size:21
Alignment explanation
Indices: 1409018--1409160 Score: 154
Period size: 21 Copynumber: 6.8 Consensus size: 21
1409008 TTGTACCAAG
*
1409018 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
1409039 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
1409060 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
1409081 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
1409102 GACGAGAAGACCTTTCAT-AA
1 GACGAGAAGACCATTCATCAA
1409122 CGACGAGAAGACC-TTCAT-AA
1 -GACGAGAAGACCATTCATCAA
1409142 CGAC-ATGAAGACCACTTCA
1 -GACGA-GAAGACCA-TTCA
1409161 CATTGGAGGT
Statistics
Matches: 112, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.01
20 21 0.19
21 85 0.76
22 5 0.04
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:1414246 original size:36 final size:36
Alignment explanation
Indices: 1414014--1414279 Score: 311
Period size: 36 Copynumber: 7.4 Consensus size: 36
1414004 AGCAAAGTCA
* * *
1414014 ATCTTTAGCCTTCACCGAAGAGA-AGTGAAGAAAACC
1 ATCTTAAGCCTTCACCGGAGA-ATAGTGAAGCAAACC
* *
1414050 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
1414086 ATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
1414122 ATCTGAAGCCTTCACCGGAGAATAGGGAAGCAATCA
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
1414158 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
1414194 ATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * *
1414230 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTTAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACC
*
1414267 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
1414280 TCAGAAGAGT
Statistics
Matches: 199, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
35 3 0.02
36 182 0.91
37 14 0.07
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:1414260 original size:108 final size:108
Alignment explanation
Indices: 1414014--1414279 Score: 345
Period size: 108 Copynumber: 2.5 Consensus size: 108
1414004 AGCAAAGTCA
* * * * * *
1414014 ATCTTTAGCCTTCACCGAAGAGAAGTGAAGAAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAA
* *
1414079 GCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
66 GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * * *
1414122 ATCTGAAGCCTTCACCGGAGAA-TAGGGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGA
1 ATCTTAAGCCTTCACC-GAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGA
* *
1414186 AGCAAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
65 AGCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * * *
1414230 ATCTTAAGTCTTCACCAAAAAGTAGTGAAGCAGATCCATTTTAAGCCTTC
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCA-ATCCATCTGAAGCCTTC
1414280 TCAGAAGAGT
Statistics
Matches: 133, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
107 3 0.02
108 113 0.85
109 17 0.13
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
Found at i:1414784 original size:51 final size:51
Alignment explanation
Indices: 1414649--1415083 Score: 560
Period size: 51 Copynumber: 8.5 Consensus size: 51
1414639 GTGAAGCAAA
* * *
1414649 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGAGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1414700 TGAAGATG--CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * *
1414749 TGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTG
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * *
1414800 TG-AGATATCCGAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* *
1414850 TGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCAG-T
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTT
*
1414901 TGAAGATGTTCAAGTTCTATACTCCTTAAAGAAAGAAGGGAGCGAACCCAG-T
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCC-GTT
1414953 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * *
1415004 TGAAGAGATGTTCGAGTTCTATACTCC-TAGAGAAATAGGGAGCGAACCCATTTGT
1 TG-A-AGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC--GT-T
1415059 TGAAGATTGTTCGAG-TCTTATACTC
1 TGAAGA-TGTTCGAGTTC-TATACTC
1415084 TCTGAAGAAA
Statistics
Matches: 343, Mismatches: 28, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
49 48 0.14
50 44 0.13
51 133 0.39
52 71 0.21
53 27 0.08
54 17 0.05
55 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (51 bp):
TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
Found at i:1414967 original size:103 final size:102
Alignment explanation
Indices: 1414649--1415083 Score: 560
Period size: 101 Copynumber: 4.2 Consensus size: 102
1414639 GTGAAGCAAA
* * *
1414649 TGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAGGAGAGAACCCGTTTGAAGATG--CGAG
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAG
1414712 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
66 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * * * * * *
1414749 TGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTG-AGATATCCGAG
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAG
* *
1414813 TTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTT
66 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
* * *
1414850 TGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCAG-TTGAAGATGTTCAA
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTCGA
1414914 GTTCTATACTCCTTAAAGAAAGAAGGGAGCGAACCCAG-T
65 GTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCC-GTT
1414953 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTTCG
1 TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTCG
* * * *
1415018 AGTTCTATACTCC-TAGAGAAATAGGGAGCGAACCCATTTGT
64 AGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC--GT-T
1415059 TGAAGATTGTTCGAG-TCTTATACTC
1 TGAAGA-TGTTCGAGTTC-TATACTC
1415084 TCTGAAGAAA
Statistics
Matches: 290, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
99 4 0.01
100 45 0.16
101 83 0.29
102 31 0.11
103 72 0.25
104 10 0.03
105 21 0.07
106 9 0.03
107 15 0.05
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (102 bp):
TGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAG
TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTT
Found at i:1415097 original size:55 final size:54
Alignment explanation
Indices: 1414849--1415391 Score: 362
Period size: 55 Copynumber: 10.1 Consensus size: 54
1414839 GCGAACCCGT
* * * * *
1414849 TTGAAGATGTTCGAGT-TCTATACTCTTTAAAGAGAGAAGGAGCGAACCCA---G
1 TTGAAGATGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCGAACCCATTTG
* * *
1414900 TTGAAGATGTTCAAGT-TCTATACTC-CTTAAAGAAAGAAGGGAGCGAACCCA---G
1 TTGAAGATGTTCGAGTCT-TATACTCTC-TGAAGAAA-TAGGGAGCGAACCCATTTG
* * * *
1414952 TTGAAGATGTTCGAGT-TCTATACTC-CTTAAAGAAAGAAGGAGCGAACCCGTTTG
1 TTGAAGATGTTCGAGTCT-TATACTCTC-TGAAGAAATAGGGAGCGAACCCATTTG
**
1415006 AAG-AGATGTTCGAGT-TCTATACTC-CT-AGAGAAATAGGGAGCGAACCCATTTG
1 TTGAAGATGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCGAACCCATTTG
* * * *
1415058 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATAG
1 TTGAAGA-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACCCATTTG
* * * * ** *
1415113 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGATATAGGGGGC-AGACACGGTCG
1 TTGAAGA-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACCCATTTG
* ** *
1415168 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGA-TTG
1 TTGAAGA-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-GAACCCATTTG
* * * * * * *
1415223 ATG-AGA--TACGGGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCG
1 TTGAAGATGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACCCATTTG
* *
1415274 TTGAAGATTGTTCGAGTCTTATACTCT-TGAAGAAATAGGGGGC-AGA-CAAGTTTG
1 TTGAAGA-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACCCA-TTTG
* * *
1415328 TTGAAGATGATTCAAGTCTTATACCCTCTGAAGAAATAGGGAGCGAACCCATTTT
1 TTGAAGATG-TTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATTTG
1415383 TCTGAAGAT
1 T-TGAAGAT
1415392 TATTGAATTC
Statistics
Matches: 412, Mismatches: 54, Indels: 47
0.80 0.11 0.09
Matches are distributed among these distances:
49 1 0.00
50 1 0.00
51 80 0.19
52 74 0.18
53 28 0.07
54 65 0.16
55 151 0.37
56 11 0.03
57 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (54 bp):
TTGAAGATGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATTTG
Found at i:1415240 original size:161 final size:160
Alignment explanation
Indices: 1415073--1415368 Score: 495
Period size: 161 Copynumber: 1.8 Consensus size: 160
1415063 GATTGTTCGA
*
1415073 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGGGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
* * * *
1415138 CTCTGAAGATATAGGGGGCAGACACGGTCGTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGA
66 CT-TGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGA-TGATTCAAGTCTTATACCCTCTGAAGA
1415202 AATAGGGGGCAGATGCGATTGATGAGATACGG
129 AATAGGGGGCAGATGCGATTGATGAGATACGG
*
1415234 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
* *
1415299 CTTGAAGAAATAGGGGGCAGACAAGTTTGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAAA
66 CTTGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAAA
1415364 TAGGG
131 TAGGG
1415369 AGCGAACCCA
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
159 2 0.02
160 59 0.47
161 65 0.52
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (160 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATTGTTCGAGTCTTATACT
CTTGAAGAAATAGGGGGCAGACAAGGTCGTTGAAGATGATTCAAGTCTTATACCCTCTGAAGAAA
TAGGGGGCAGATGCGATTGATGAGATACGG
Found at i:1415283 original size:106 final size:108
Alignment explanation
Indices: 1415057--1415320 Score: 408
Period size: 106 Copynumber: 2.5 Consensus size: 108
1415047 GAACCCATTT
*
1415057 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGATGAAGA-T
* * **
1415122 GTTCGGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGGTC
65 -TACGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
* * *
1415167 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATG-AGA-T
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGATGAAGATT
*
1415230 ACGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
66 ACGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
1415273 GTTGAAGATTGTTCGAGTCTTATACTCT-TGAAGAAATAGGGGGCAGAC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
1415321 AAGTTTGTTG
Statistics
Matches: 144, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
105 19 0.13
106 67 0.47
109 3 0.02
110 55 0.38
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATAGATGAAGATT
ACGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACAATC
Found at i:1418979 original size:18 final size:18
Alignment explanation
Indices: 1418956--1419028 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 18
1418946 AGGGTTATAC
1418956 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1418974 AGTGGTCCTTCGGGACATATAT
1 AGTGGTCCTTCGGGAC----AT
* *
1418996 AATGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1419014 AGTGGTCATTCGGGA
1 AGTGGTCCTTCGGGA
1419029 TAAATATTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 30 0.65
22 16 0.35
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1420724 original size:2 final size:2
Alignment explanation
Indices: 1420717--1420755 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1420707 GGAAAATGAG
1420717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1420756 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1420760 original size:2 final size:2
Alignment explanation
Indices: 1420755--1420811 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1420745 ATATATATAT
1420755 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1420797 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
1420812 CCAAATCTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1423953 original size:3 final size:3
Alignment explanation
Indices: 1423928--1423984 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
1423918 CTACAAAAAC
1423928 ATT A-T ATT A-T ATT A-T ATTT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT A-TT
*
1423972 ATTT ATT TTT ATT
1 A-TT ATT ATT ATT
1423985 TTTGTAGGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 6 0.13
3 32 0.68
4 9 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1424153 original size:34 final size:33
Alignment explanation
Indices: 1424038--1424153 Score: 135
Period size: 33 Copynumber: 3.5 Consensus size: 33
1424028 GAAAATAAAT
* *
1424038 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACATATTTGAGTCCTATTAAAACACTAAAAA
* * *
1424071 CAACATATTTGAGTCATATTAAAATACTAAAAT
1 CAACATATTTGAGTCCTATTAAAACACTAAAAA
* * *
1424104 CAACGTATATGAGTCCTATTGAAACACTAAAAA
1 CAACATATTTGAGTCCTATTAAAACACTAAAAA
1424137 CGAAGCAT-TTTGAGTCC
1 C-AA-CATATTTGAGTCC
1424154 AAGTAGGACT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
33 57 0.83
34 10 0.14
35 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.28
Consensus pattern (33 bp):
CAACATATTTGAGTCCTATTAAAACACTAAAAA
Found at i:1431374 original size:13 final size:13
Alignment explanation
Indices: 1431353--1431387 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1431343 CCCGCTTACT
1431353 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
1431366 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
1431379 TTTCACTTT
1 TTTCACTTT
1431388 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:1434010 original size:20 final size:20
Alignment explanation
Indices: 1433985--1434027 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1433975 TCTAAGAGCC
*
1433985 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
1434005 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1434025 CAT
1 CAT
1434028 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1436388 original size:7 final size:7
Alignment explanation
Indices: 1436376--1436404 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1436366 CTCGAATATT
1436376 TCATGCA
1 TCATGCA
1436383 TCATGCA
1 TCATGCA
1436390 TCATGCA
1 TCATGCA
1436397 TCATGCA
1 TCATGCA
1436404 T
1 T
1436405 TCTTGCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (7 bp):
TCATGCA
Found at i:1438458 original size:110 final size:110
Alignment explanation
Indices: 1438293--1439078 Score: 1285
Period size: 110 Copynumber: 7.2 Consensus size: 110
1438283 GATGGTGGTT
1438293 GCTCAACTTCACAGCGAA-GGG-G-C-GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1438354 AATTTCAATTTCACAGCGAAGGATATTGGACTCGAGACAAAACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
1438399 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTA
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* ** *
1438464 AATTTCAACTTCAC-GACAAAATATATTGGACTTGAGACAACACAA
66 AATTTCAACTTCACAG-CGAAGGATATTGGACTCGAGACAACACAA
*
1438509 GCTCAACTTCACAGCGAAGAGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1438574 AATTTCAACTTCAAAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
1438619 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1438684 AATTTCAACTTCACAACGAAGGATATTGGACTTGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1438729 GCTCAACTTCACAGTGAATGGGCGACTGACTGTCAACAAATAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1438794 AATTTCAACTTCACAGTGAAGGATATTGGACTCGAGATAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
1438839 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1438904 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1438949 GCTTAACTTCACAGCGAATGGGCGACTGACTATCAACAAACAACTTTCCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1439014 AATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
1439059 GCTCAACTTCACAGCAAAGG
1 GCTCAACTTCACAGCGAAGG
1439079 ATATTAGACT
Statistics
Matches: 632, Mismatches: 42, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
106 18 0.03
107 3 0.00
108 1 0.00
109 2 0.00
110 607 0.96
111 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1439081 original size:43 final size:43
Alignment explanation
Indices: 1439020--1439121 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
1439010 AGTCAATTTT
* *
1439020 AACTTCACAACGAAGGATATTAGACTCGAGACAACACAAGCTC
1 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
1439063 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
1 AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
*
1439106 AACTTCATAGCAAAGG
1 AACTTCACAGCAAAGG
1439122 GGCGACTGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (43 bp):
AACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTC
Found at i:1439112 original size:153 final size:153
Alignment explanation
Indices: 1438908--1439231 Score: 531
Period size: 153 Copynumber: 2.1 Consensus size: 153
1438898 AGAGTCAATT
* * * *
1438908 TCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTTAACTTCACAGCGAATGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
* *
1438973 ACTGACTATCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGAT
66 ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
1439038 ATTAGACTCGAGACAACACAAGC
131 ATTAGACTCGAGACAACACAAGC
*
1439061 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCATAGCAAAGGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
* * **
1439126 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
66 ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
* *
1439191 ATTGGACTCTAGACAACACAAGC
131 ATTAGACTCGAGACAACACAAGC
1439214 TCAACTTCACAGCAAAGG
1 TCAACTTCACAGCAAAGG
1439232 GGCGATTGGC
Statistics
Matches: 158, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 158 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (153 bp):
TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
ACTGACTATCAACAAACAACTTTCCAGTTCCATTCAGAGTCAATTTCAACTTCACAACGAAGGAT
ATTAGACTCGAGACAACACAAGC
Found at i:1439162 original size:263 final size:259
Alignment explanation
Indices: 1438798--1439317 Score: 788
Period size: 263 Copynumber: 2.0 Consensus size: 259
1438788 AGAGTCAATT
** * * *
1438798 TCAACTTCACAGTGAAGGATATTGGACTCGAGATAACACAAGCTCAACTTCACAGCGAAGGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
* *
1438863 ACTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
66 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * *
1438928 ATTAGACTCGAGACAACACAAGCTTAACTTCACAGCGAATGGGCGACTGACTATCAACAAACAAC
131 ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
* *
1438993 TTTCCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCGAGACAACACA
196 TTTCCAG--T--TTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCAAAACAACACA
1439058 AGC
257 AGC
*
1439061 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCATAGCAAAGGGGCG
1 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
*
1439126 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGTGAAGGAT
66 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
* * * * * *
1439191 ATTGGACTCTAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGATTGGCTATTAACAAATAAC
131 ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
** * *
1439256 TTTCCAGTTTCAGAGTCAATTTTAACTTCACGGCGAAGGATATTGGCCTCAAAACAACACAA
196 TTTCCAGTTTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCAAAACAACACAA
1439318 ATATTTGTCT
Statistics
Matches: 233, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
259 48 0.21
261 1 0.00
263 184 0.79
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (259 bp):
TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATTTCAACTTCACAGCGAAGGAT
ATTAGACTCGAGACAACACAAGCTCAACTTCACAGCAAAGGGGCGACTGACTATCAACAAACAAC
TTTCCAGTTTCAGAGTCAATTTTAACTTCACAACGAAGGATATTAGACTCAAAACAACACAAGC
Found at i:1439257 original size:110 final size:106
Alignment explanation
Indices: 1439061--1439317 Score: 334
Period size: 110 Copynumber: 2.4 Consensus size: 106
1439051 CAACACAAGC
* * * *
1439061 TCAACTTCACAGCAAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCATAGCAAAGGGGCG
1 TCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
* *
1439126 ACTGACTGTCAACAAACAACTTTTCAGTTCCATTCAGAGTCAATT
66 ACTGACTATCAACAAACAACTTTCCAG-T---TTCAGAGTCAATT
* *
1439171 TCAACTTCACAGTGAAGGATATTGGACTCTAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
1 TCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
* * * *
1439236 ATTGGCTATTAACAAATAACTTTCCAGTTTCAGAGTCAATT
66 ACTGACTATCAACAAACAACTTTCCAGTTTCAGAGTCAATT
* * * *
1439277 TTAACTTCACGGCGAAGGATATTGGCCTCAAAACAACACAA
1 TCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAA
1439318 ATATTTGTCT
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
106 48 0.37
109 1 0.01
110 81 0.62
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (106 bp):
TCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAGCAAAGGGGCG
ACTGACTATCAACAAACAACTTTCCAGTTTCAGAGTCAATT
Found at i:1439486 original size:84 final size:84
Alignment explanation
Indices: 1439351--1439943 Score: 480
Period size: 84 Copynumber: 7.1 Consensus size: 84
1439341 AAGGGAATCG
* * * * * * * *
1439351 TGCCCACCAAA-AGCCTTCCAGTTTGACTACGCTCAACTCCAAGGTATATCATTTGTAGCATAAC
1 TGCCAACCAAAGA-CCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
1439415 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
** * * ** *
1439435 TGCCAATTAAAGACCTTCGAGTTCGATTATGCTCAGCTCCAAGACACATCATTTGCAATATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
1439500 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGTTATC
* * * * * * * *
1439519 TG----CCAAAGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGCGCATCATTTACTGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAAC
* * *
1439580 TCAAGGCTAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * * * * * * * *
1439600 TGTC-ACCAAAATACCTTTGAGTTTGACTACGCTCAGCTCTAAGGCATAGCATTTGTAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
1439664 CTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * ** * ** *
1439684 TGCCAACCAAAGACATTCAAGTTCGATTATACTCATCTCCGGGGGCACAACATTTGCAGCATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCC-AAGGCACATCATTTGCAGCATAAC
* * *
1439749 TCAAGGCTAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * *
1439769 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* *
1439833 TAAGTCAAGAAGGGCTATC
66 TAAGTCGAGAAGGGTTATC
* * * * * * * * * *
1439852 TGTCAAACCAAAGACCTTCAAGTTCGACTCCACTCAACTCAAAGGAACCATCATTTGCAGTATAG
1 TG-CCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAA
* * * *
1439917 CTCAAGGCAAGAAAGGTTATC
64 CTTAAGTCGAGAAGGGTTATC
1439938 TGCCAA
1 TGCCAA
1439944 AGACCTTCGA
Statistics
Matches: 397, Mismatches: 101, Indels: 21
0.76 0.19 0.04
Matches are distributed among these distances:
80 25 0.06
81 36 0.09
83 38 0.10
84 159 0.40
85 104 0.26
86 35 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGTTATC
Found at i:1439766 original size:169 final size:167
Alignment explanation
Indices: 1439400--1439956 Score: 588
Period size: 169 Copynumber: 3.3 Consensus size: 167
1439390 CAAGGTATAT
* * * * * * *
1439400 CATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAATTAAAGACCTTCGAGTTCGATTAT
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
* * **
1439465 GCTCAGCTCCAAGACACATCATTTGCAATATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAG
65 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCAACCAAAG
* * * * * *
1439527 ACCCTCGAGTTCAATTACACTCAGCTTCGAGGGCGCAT
130 ACCTTCAAGTTCGATTACACTCAGCTCCGAGGGCACAA
* * * * * * *
1439565 CATTTACTGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAATACCTTTGAGTTTGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* * * * * * *
1439630 GCTCAGCTCTAAGGCATAGCATTTGTAGCATAACCTAAGTCGAGAAGGGTTATCTGCCAACCAAA
65 GCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CAACCAAA
* * * *
1439695 GACATTCAAGTTCGATTATACTCATCTCCGGGGGCACAA
129 GACCTTCAAGTTCGATTACACTCAGCTCCGAGGGCACAA
1439734 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
1439799 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGTCAAACCAAA
66 CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-AACCAAA
* * * * * * *
1439864 GACCTTCAAGTTCGACTCCACTCAACT-CAAAGGAACCAT
129 GACCTTCAAGTTCGATTACACTCAGCTCCGAGGGCA-CAA
* * * *
1439903 CATTTGCAGTATAGCTCAAGGCAAGAAAGGTTATCTG-C--CAAAGACCTTCGAGTT
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTT
1439957 TGATTCCATT
Statistics
Matches: 321, Mismatches: 64, Indels: 13
0.81 0.16 0.03
Matches are distributed among these distances:
165 96 0.30
166 16 0.05
168 73 0.23
169 136 0.42
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (167 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCAACCAAAGA
CCTTCAAGTTCGATTACACTCAGCTCCGAGGGCACAA
Found at i:1440313 original size:26 final size:26
Alignment explanation
Indices: 1440286--1440338 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
1440276 AAAAACATTT
1440286 TATTA-TATTA-TATTTATTTATTTATT
1 TATTATTATTATTA-TTA-TTATTTATT
1440312 TATTATTATTATTATTATTATTTATT
1 TATTATTATTATTATTATTATTTATT
1440338 T
1 T
1440339 TTGTAGGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.60
27 8 0.32
28 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
TATTATTATTATTATTATTATTTATT
Found at i:1440802 original size:2 final size:2
Alignment explanation
Indices: 1440795--1440827 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1440785 TTTTTACATT
1440795 TA 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 TA T
1440828 TTCATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1440984 original size:12 final size:12
Alignment explanation
Indices: 1440967--1440993 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1440957 GAATTGAATT
1440967 TTTAAATTCTAA
1 TTTAAATTCTAA
1440979 TTTAAATTCTAA
1 TTTAAATTCTAA
1440991 TTT
1 TTT
1440994 TCGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTCTAA
Found at i:1444575 original size:27 final size:28
Alignment explanation
Indices: 1444527--1444602 Score: 136
Period size: 28 Copynumber: 2.8 Consensus size: 28
1444517 ATCCGTTTTA
1444527 ATACTTAAATTTTTAATTTTTTAAAATC
1 ATACTTAAATTTTTAATTTTTTAAAATC
1444555 ATACTTAAATTTTTAATTTTTTAAAATC
1 ATACTTAAATTTTTAATTTTTTAAAATC
*
1444583 ATACTTAAA-GTTTAATTTTT
1 ATACTTAAATTTTTAATTTTT
1444603 GTTTCATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 10 0.21
28 37 0.79
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (28 bp):
ATACTTAAATTTTTAATTTTTTAAAATC
Found at i:1446156 original size:76 final size:76
Alignment explanation
Indices: 1446065--1446210 Score: 251
Period size: 76 Copynumber: 1.9 Consensus size: 76
1446055 GTTCTAGAAC
*
1446065 GATCCAGTATAAAATAAAAATATTTTAATA-GTTTTTTTAATAATGAT-AATGTGATATCATAAA
1 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTTAATAATGATCAATGTG--ATCATAAA
1446128 ATATTATATGAAT
64 ATATTATATGAAT
1446141 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTTAATAATGATCAATGTGATCATAAAAT
1 GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTTAATAATGATCAATGTGATCATAAAAT
1446206 ATTAT
66 ATTAT
1446211 GTTCATAAAT
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
76 44 0.66
77 17 0.25
78 6 0.09
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (76 bp):
GATCAAGTATAAAATAAAAATATTTTAATAGGTTTTTTTAATAATGATCAATGTGATCATAAAAT
ATTATATGAAT
Found at i:1447610 original size:30 final size:30
Alignment explanation
Indices: 1447574--1447632 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
1447564 TTGTACCATA
1447574 AAGTTCTCCTATTTTAATATATATTATATC
1 AAGTTCTCCTATTTTAATATATATTATATC
1447604 AAGTTCTCCTATTTTAATATATATTATAT
1 AAGTTCTCCTATTTTAATATATATTATAT
1447633 AATAAAGGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (30 bp):
AAGTTCTCCTATTTTAATATATATTATATC
Found at i:1448855 original size:26 final size:26
Alignment explanation
Indices: 1448826--1448879 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1448816 ATGATCCTAA
*
1448826 AGATAATAAGGACTTTAAGATCTTAT
1 AGATAATAAAGACTTTAAGATCTTAT
1448852 AGATAATAAAGACTTTAAGATCTTAT
1 AGATAATAAAGACTTTAAGATCTTAT
1448878 AG
1 AG
1448880 TTTATTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (26 bp):
AGATAATAAAGACTTTAAGATCTTAT
Found at i:1449061 original size:56 final size:56
Alignment explanation
Indices: 1448987--1449136 Score: 210
Period size: 56 Copynumber: 2.7 Consensus size: 56
1448977 TAAAATTTTC
* * * * * *
1448987 TAGATTTAGAGATCTTTAATGAGGCATTTTTCCTTAATGTATTCTTTTCTTTTATA
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
* * *
1449043 TAGGTTTAGAGATATTTAACGAGACATTCTTCTTTAATATATTTTTTTCTTTCATA
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
*
1449099 TAGATTTAGAGATTTTTAACGAGACATTTTTCTTTAAT
1 TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAAT
1449137 CAATACTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 82 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (56 bp):
TAGATTTAGAGATATTTAACGAGACATTTTTCTTTAATATATTCTTTTCTTTCATA
Found at i:1453453 original size:31 final size:31
Alignment explanation
Indices: 1453418--1453508 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
1453408 TTTGAACGGT
1453418 TACAAAATAATCATTAAATTTATCAAACTAG
1 TACAAAATAATCATTAAATTTATCAAACTAG
* * *
1453449 TACAAAATAGTCGTTAGAATTTATCAGAA--AT
1 TACAAAATAATCATTA-AATTTATCA-AACTAG
* * *
1453480 TACGAAATTATCATTAAGTTTATCAAACT
1 TACAAAATAATCATTAAATTTATCAAACT
1453509 TTTAGAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
29 2 0.04
30 8 0.17
31 27 0.56
32 9 0.19
33 2 0.04
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (31 bp):
TACAAAATAATCATTAAATTTATCAAACTAG
Found at i:1458541 original size:17 final size:17
Alignment explanation
Indices: 1458519--1458552 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1458509 GATTGCATAA
1458519 CTGATATAAAGGCAGGG
1 CTGATATAAAGGCAGGG
1458536 CTGATATAAAGGCAGGG
1 CTGATATAAAGGCAGGG
1458553 GTTGATTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (17 bp):
CTGATATAAAGGCAGGG
Found at i:1460586 original size:65 final size:65
Alignment explanation
Indices: 1460388--1460588 Score: 234
Period size: 65 Copynumber: 3.1 Consensus size: 65
1460378 TACACTAAGA
* * * *
1460388 GTGCATCGATGCATGAAATACATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
* * * *
1460452 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAT-C-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-ATATATCCATGAGTGCATCGATGCATGGT
1460515 AT-
64 -TG
*
1460517 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-TCCATGAGTGCATCGATGCATGG-T
1460580 TG
64 TG
1460582 GTGCATC
1 GTGCATC
1460589 ACTCTGAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
62 2 0.02
63 5 0.04
64 44 0.38
65 61 0.52
66 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
Found at i:1462514 original size:23 final size:23
Alignment explanation
Indices: 1462488--1462538 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1462478 GGTGGAGGAG
*
1462488 GAACGTGATTAGGAGGTTGGTTT
1 GAACGGGATTAGGAGGTTGGTTT
1462511 GAACGGGATTAGGAGGTTGGTTT
1 GAACGGGATTAGGAGGTTGGTTT
1462534 GAACG
1 GAACG
1462539 AGAATGACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.06, G:0.41, T:0.29
Consensus pattern (23 bp):
GAACGGGATTAGGAGGTTGGTTT
Found at i:1462810 original size:13 final size:13
Alignment explanation
Indices: 1462792--1462816 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1462782 ATCAAAAAAC
1462792 ATCAAATTTAGAA
1 ATCAAATTTAGAA
1462805 ATCAAATTTAGA
1 ATCAAATTTAGA
1462817 TTTTTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:1463301 original size:21 final size:22
Alignment explanation
Indices: 1463240--1463320 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
1463230 CATGGCCTTG
1463240 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* *
1463263 TGCATCGGTGCATC-TTCATGG-
1 TGCATCGATGCA-CATTCAAGGA
*
1463284 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
1463308 TGCATCGATGCAC
1 TGCATCGATGCAC
1463321 TGTTAAGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 13 0.28
22 1 0.02
23 19 0.40
24 13 0.28
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1463334 original size:44 final size:44
Alignment explanation
Indices: 1463243--1463339 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
1463233 GGCCTTGTGC
* * *
1463243 ATCGATGCACATTCAAGGCATGCATCGGTGCATCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCATCTTCATAGTCT
* *
1463287 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTA-AGTCT
1 ATCGATGCACATTC-AAGGCATGCATCGATGCATCT-TCATAGTCT
1463331 ATCGATGCA
1 ATCGATGCA
1463340 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 28 0.61
45 18 0.39
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCATCTTCATAGTCT
Found at i:1469330 original size:65 final size:65
Alignment explanation
Indices: 1469132--1469332 Score: 243
Period size: 65 Copynumber: 3.1 Consensus size: 65
1469122 TACACTAAGA
* * *
1469132 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
* * * *
1469196 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAAT-C-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCA-ATATATCCATGAGTGCATCGATGCATGGT
1469259 AT-
64 -TG
*
1469261 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATA-TCCATGAGTGCATCGATGCATGG-T
1469324 TG
64 TG
1469326 GTGCATC
1 GTGCATC
1469333 ACTCTGAAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 17
0.81 0.07 0.12
Matches are distributed among these distances:
62 2 0.02
63 5 0.04
64 45 0.38
65 61 0.52
66 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATATATCCATGAGTGCATCGATGCATGGTTG
Found at i:1470010 original size:29 final size:30
Alignment explanation
Indices: 1469972--1470034 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1469962 TTTCTTAAAT
* * *
1469972 ATTTTAGGACTAAATTG-AATTTTGATTAC
1 ATTTTAGGACCAAAGTGAAATTTTGATTAA
*
1470001 ATTTTGGGACCAAAGTGAAATTTTGATTAA
1 ATTTTAGGACCAAAGTGAAATTTTGATTAA
1470031 ATTT
1 ATTT
1470035 GGATCCAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
ATTTTAGGACCAAAGTGAAATTTTGATTAA
Found at i:1471758 original size:4 final size:4
Alignment explanation
Indices: 1471749--1472777 Score: 2044
Period size: 4 Copynumber: 257.8 Consensus size: 4
1471739 ATTTAAATTA
1471749 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1471797 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1471845 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1471893 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1471941 TCAT TCAT TCAT TCAT TCAT TCAT TCA- TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1471988 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472036 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472084 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472132 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472180 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCA- TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472227 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472275 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472323 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472371 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472419 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472467 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472515 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472563 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472611 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472659 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472707 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
1472755 TCAT TCAT TCAT TCAT TCAT TCA
1 TCAT TCAT TCAT TCAT TCAT TCA
1472778 AAATATTTAA
Statistics
Matches: 1023, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
3 6 0.01
4 1017 0.99
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TCAT
Found at i:1473052 original size:26 final size:26
Alignment explanation
Indices: 1473016--1473069 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1473006 ATGGTCCTAA
1473016 AGATAATAAGGACTTTAAGATCTTAT
1 AGATAATAAGGACTTTAAGATCTTAT
1473042 AGATAATAAGGACTTTAAGATCTTAT
1 AGATAATAAGGACTTTAAGATCTTAT
1473068 AG
1 AG
1473070 TTTATTGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (26 bp):
AGATAATAAGGACTTTAAGATCTTAT
Found at i:1473248 original size:56 final size:56
Alignment explanation
Indices: 1473174--1473315 Score: 200
Period size: 56 Copynumber: 2.6 Consensus size: 56
1473164 TAAAGATCTC
*
1473174 TAGATTTAGATAA-CTTTAACGAGACATTCTTCCTTAATATACTCTTTTCTTTTATA
1 TAGATTTAGA-AATCTTTAACGAGACATTCTTCCTTAATATACTCTTTTCTTTCATA
* *
1473230 TATG-TTTAGAGATCTTTAACGAGACATTCTTCCTTAATATACTGTTTTCTTTCATA
1 TA-GATTTAGAAATCTTTAACGAGACATTCTTCCTTAATATACTCTTTTCTTTCATA
* *
1473286 TAGATTTATAAATCTTTAAC-ATACATTCTT
1 TAGATTTAGAAATCTTTAACGAGACATTCTT
1473316 TTTTAATCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
55 11 0.14
56 65 0.84
57 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.46
Consensus pattern (56 bp):
TAGATTTAGAAATCTTTAACGAGACATTCTTCCTTAATATACTCTTTTCTTTCATA
Done.