Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009603.1 Hibiscus syriacus cultivar Beakdansim tig00116983_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: 1462390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1308357 original size:23 final size:23
Alignment explanation
Indices: 1308331--1308395 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1308321 AGCTCATATA
1308331 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* **
1308354 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
* *
1308377 AAATGCACTGAAGTGCCAT
1 AATTGCACCGAAGTGCCAT
1308396 ATAAGGTTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:1309935 original size:21 final size:21
Alignment explanation
Indices: 1309911--1309987 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
1309901 TCAGTTGAGG
*
1309911 GGGTATCGATTCCCCTTGAAT
1 GGGTATCGATTCCCATTGAAT
*
1309932 GGGTACCGATTCCCATTGAAT
1 GGGTATCGATTCCCATTGAAT
1309953 GGGTA-CTGATTCCCATTGAAT
1 GGGTATC-GATTCCCATTGAAT
1309974 GGGTATCGATTCCC
1 GGGTATCGATTCCC
1309988 CTAGCCCAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (21 bp):
GGGTATCGATTCCCATTGAAT
Found at i:1312024 original size:18 final size:18
Alignment explanation
Indices: 1312003--1312041 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1311993 ATGTCGTTCC
1312003 TATTAAATAT-TTTTAAAA
1 TATTAAA-ATCTTTTAAAA
*
1312021 TATTAAAATCTTTTAATA
1 TATTAAAATCTTTTAAAA
1312039 TAT
1 TAT
1312042 ATAAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAAAATCTTTTAAAA
Found at i:1325953 original size:21 final size:21
Alignment explanation
Indices: 1325929--1325979 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1325919 AGATGTTGGT
1325929 GGAGGTGTTTTTGATTCATTG
1 GGAGGTGTTTTTGATTCATTG
1325950 GGAGGTGTTTTTGATTCATTG
1 GGAGGTGTTTTTGATTCATTG
*
1325971 GGAGATGTT
1 GGAGGTGTT
1325980 GGATACATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.35, T:0.45
Consensus pattern (21 bp):
GGAGGTGTTTTTGATTCATTG
Found at i:1326095 original size:17 final size:17
Alignment explanation
Indices: 1326073--1326131 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
1326063 TTTGTGTTGT
1326073 TTAATATTGTTGTAGAC
1 TTAATATTGTTGTAGAC
* *
1326090 TTAATATTG-TGTTG-T
1 TTAATATTGTTGTAGAC
1326105 TTAATATTGTTGTAGAC
1 TTAATATTGTTGTAGAC
1326122 TTAATATTGT
1 TTAATATTGT
1326132 GGTTTGAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 9 0.25
16 8 0.22
17 19 0.53
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (17 bp):
TTAATATTGTTGTAGAC
Found at i:1326105 original size:32 final size:32
Alignment explanation
Indices: 1326064--1326132 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
1326054 AATGTTTGAT
1326064 TTGTGTTGTTTAATATTGTTGTAGACTTAATA
1 TTGTGTTGTTTAATATTGTTGTAGACTTAATA
1326096 TTGTGTTGTTTAATATTGTTGTAGACTTAATA
1 TTGTGTTGTTTAATATTGTTGTAGACTTAATA
1326128 TTGTG
1 TTGTG
1326133 GTTTGAGTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (32 bp):
TTGTGTTGTTTAATATTGTTGTAGACTTAATA
Found at i:1326110 original size:15 final size:15
Alignment explanation
Indices: 1326064--1326114 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
1326054 AATGTTTGAT
1326064 TTGTGTTGTTTAATA
1 TTGTGTTGTTTAATA
* *
1326079 TTGTTGTAGACTTAATA
1 TTG-TGTTG-TTTAATA
1326096 TTGTGTTGTTTAATA
1 TTGTGTTGTTTAATA
1326111 TTGT
1 TTGT
1326115 TGTAGACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.43
16 8 0.27
17 9 0.30
ACGTcount: A:0.22, C:0.02, G:0.20, T:0.57
Consensus pattern (15 bp):
TTGTGTTGTTTAATA
Found at i:1326217 original size:40 final size:40
Alignment explanation
Indices: 1326157--1326244 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
1326147 ATTTGACACT
** * *
1326157 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
1 TTAATATTACAGTTTATTTATGGATTTTATTGTTCTAGAC
*
1326197 TTAATATTACAGTTTATTTATGGATTTTATTGTTCTAGAG
1 TTAATATTACAGTTTATTTATGGATTTTATTGTTCTAGAC
1326237 TTAATATT
1 TTAATATT
1326245 GTGGTTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (40 bp):
TTAATATTACAGTTTATTTATGGATTTTATTGTTCTAGAC
Found at i:1335782 original size:17 final size:18
Alignment explanation
Indices: 1335762--1335802 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1335752 GAATTATATT
1335762 AGTAAAAT-ATTAAATAA
1 AGTAAAATAATTAAATAA
1335779 AGTAAAATAATTAAATAA
1 AGTAAAATAATTAAATAA
*
1335797 ATTAAA
1 AGTAAA
1335803 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATAATTAAATAA
Found at i:1335859 original size:10 final size:10
Alignment explanation
Indices: 1335844--1335884 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
1335834 CTTAAACAGA
1335844 GAGAGAATTT
1 GAGAGAATTT
1335854 GAGAGAATTT
1 GAGAGAATTT
1335864 GAGAGAATTT
1 GAGAGAATTT
*
1335874 GAGAAAATTT
1 GAGAGAATTT
1335884 G
1 G
1335885 GTGTGATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1336888 original size:23 final size:23
Alignment explanation
Indices: 1336862--1336906 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1336852 CACCACAGCT
*
1336862 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1336885 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1336907 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1337127 original size:149 final size:149
Alignment explanation
Indices: 1336874--1337188 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
1336864 TATAATTGCA
1336874 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
1336938 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
1337003 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
1337023 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
1337088 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
1337152 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
1337172 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1337189 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:1337829 original size:2 final size:2
Alignment explanation
Indices: 1337822--1337846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1337812 CATGTCTATC
1337822 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 T
1337847 CCTCAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1337956 original size:2 final size:2
Alignment explanation
Indices: 1337949--1337991 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1337939 ATTATTTCTT
1337949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1337991 T
1 T
1337992 CTAATTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1338137 original size:18 final size:18
Alignment explanation
Indices: 1338116--1338150 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1338106 TCCCATCTAG
1338116 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1338134 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1338151 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1338737 original size:64 final size:63
Alignment explanation
Indices: 1338639--1338799 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
1338629 TAATGAAGGT
* *
1338639 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
1338702 GG
62 GC
*
1338704 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
1338768 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1338800 CCTTAAACAT
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:1342143 original size:23 final size:23
Alignment explanation
Indices: 1342117--1342161 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1342107 CACCACAGCT
*
1342117 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1342140 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1342162 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1342382 original size:149 final size:149
Alignment explanation
Indices: 1342129--1342443 Score: 517
Period size: 149 Copynumber: 2.1 Consensus size: 149
1342119 TATAATTGCA
*
1342129 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAA
* **
1342193 TTCCTTAATAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
1342258 CCACAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
1342278 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATATCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAAT
* *
1342343 TCCTTAAGAATCATATACATATTCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
1342407 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
*
1342427 CCGAAGGATCGCGTAGA
1 CCGAAGGACCGCGTAGA
1342444 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
148 1 0.01
149 153 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:1343201 original size:2 final size:2
Alignment explanation
Indices: 1343194--1343221 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1343184 ATTATTTCTT
1343194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1343222 ATCTAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1343369 original size:18 final size:18
Alignment explanation
Indices: 1343348--1343382 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1343338 TCCCATCTAG
1343348 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1343366 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1343383 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1343972 original size:64 final size:63
Alignment explanation
Indices: 1343874--1344034 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
1343864 TAATGAAGGT
* *
1343874 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTATATTTAAAT--
*
1343937 GG
62 GC
*
1343939 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTATATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTATATTTAAATGC
* *
1344003 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1344035 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTATATTTAAATGC
Found at i:1345467 original size:17 final size:17
Alignment explanation
Indices: 1345445--1345478 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1345435 TTGTGGAATC
1345445 TTTTGCAGAAAATTGAA
1 TTTTGCAGAAAATTGAA
1345462 TTTTGCAGAAAATTGAA
1 TTTTGCAGAAAATTGAA
1345479 AGTAATTGCA
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:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
TTTTGCAGAAAATTGAA
Found at i:1348732 original size:20 final size:19
Alignment explanation
Indices: 1348709--1348745 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1348699 AGAACCCCAG
*
1348709 GGGGGTATCGATTCCCCTA
1 GGGGGAATCGATTCCCCTA
*
1348728 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
1348746 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCTA
Found at i:1353197 original size:217 final size:218
Alignment explanation
Indices: 1352815--1353251 Score: 628
Period size: 217 Copynumber: 2.0 Consensus size: 218
1352805 ATTGGAAGCA
1352815 ATATGATGTATACAATACGCCAGATATGCGTGAAGAGGCGACCACCTACTTCCCAGTCTATCAAT
1 ATATGATGTATACAATACGCCAGATATGCGTGAAGAGGCGACCACCTACTTCCCAGTCTATCAAT
* *
1352880 TGTGGCTAACAACACAGGTAAACGGTTTGATATCATACAAACCCAATCTTGAACGACAACATAGG
66 CGTGGCTAACAACACAGGTAAACAGTTTGATATCATACAAACCCAATCTTGAACGACAACATAGG
*
1352945 AACACAAATTGGAGAAAAAGAAACTCCACGTTTCCTCTAACTCATTTTTAACAATGGAAAA-ACA
131 AACACAAATTGGAGAAAAAGAAACTCCACGTTTCCTCTAAATCATTTTTAACAATGGAAAAGACA
1353009 ATAGGAAAAATGTTTCTGTCACC
196 ATAGGAAAAATGTTTCTGTCACC
*** * * * *
1353032 ATATGATGTATACAATATTTCTGATATGCGTGATGAGGCGACCATCTACTTCCCGGTCTATCAAT
1 ATATGATGTATACAATACGCCAGATATGCGTGAAGAGGCGACCACCTACTTCCCAGTCTATCAAT
* **
1353097 CGTGGCTAACAAC-CAAGGTAAACAGTTTGATATCATACAAATCCC-ATTTTGAGTGACAACATA
66 CGTGGCTAACAACAC-AGGTAAACAGTTTGATATCATACAAA-CCCAATCTTGAACGACAACATA
** * * * * * *
1353160 GGAATGCAAGTTGGAGAGAAAGAAATTTCATGTTTCCTCTAAATCATTTTTAACAATGGAAAAGG
129 GGAACACAAATTGGAGAAAAAGAAACTCCACGTTTCCTCTAAATCATTTTTAACAATGGAAAAGA
* *
1353225 CAATAGGGAAAATTTTTCTGTCACC
194 CAATAGGAAAAATGTTTCTGTCACC
1353250 AT
1 AT
1353252 CTTGTGCAAT
Statistics
Matches: 194, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
216 1 0.01
217 165 0.85
218 28 0.14
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (218 bp):
ATATGATGTATACAATACGCCAGATATGCGTGAAGAGGCGACCACCTACTTCCCAGTCTATCAAT
CGTGGCTAACAACACAGGTAAACAGTTTGATATCATACAAACCCAATCTTGAACGACAACATAGG
AACACAAATTGGAGAAAAAGAAACTCCACGTTTCCTCTAAATCATTTTTAACAATGGAAAAGACA
ATAGGAAAAATGTTTCTGTCACC
Found at i:1354078 original size:15 final size:15
Alignment explanation
Indices: 1354058--1354089 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1354048 GACGATGATA
*
1354058 TTGAGGCATTTGGGG
1 TTGAGGCATTTAGGG
1354073 TTGAGGCATTTAGGG
1 TTGAGGCATTTAGGG
1354088 TT
1 TT
1354090 TATACATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.41, T:0.38
Consensus pattern (15 bp):
TTGAGGCATTTAGGG
Found at i:1354971 original size:16 final size:17
Alignment explanation
Indices: 1354927--1354971 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1354917 ATCTCTTTTA
1354927 CAAAAACTTTTCACTGAT
1 CAAAAACTTTTCACT-AT
*
1354945 CAATAAC--TTCACT-T
1 CAAAAACTTTTCACTAT
1354959 CAAAAACTTTTCA
1 CAAAAACTTTTCA
1354972 GTGTATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 7 0.30
16 10 0.43
18 6 0.26
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (17 bp):
CAAAAACTTTTCACTAT
Found at i:1354992 original size:31 final size:31
Alignment explanation
Indices: 1354927--1355001 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
1354917 ATCTCTTTTA
1354927 CAAAAACTTTTCACTGATCAATAACTTCACTT
1 CAAAAACTTTTCACTGAT-AATAACTTCACTT
* * *
1354959 CAAAAACTTTTCAGTG-TATATCACTTCATTT
1 CAAAAACTTTTCACTGATA-ATAACTTCACTT
1354990 CAAAAATCTTTT
1 CAAAAA-CTTTT
1355002 AGATATATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 17 0.45
32 20 0.53
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (31 bp):
CAAAAACTTTTCACTGATAATAACTTCACTT
Found at i:1355119 original size:30 final size:30
Alignment explanation
Indices: 1355061--1355120 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1355051 TTAATGCACG
*
1355061 CTGACTAAAAATTAAAGAAACTCGTCATGT
1 CTGACTAAAAATTAAAGAAACTCATCATGT
* *
1355091 CTGACTAAAACTTAAA-AGAATTCATCATGT
1 CTGACTAAAAATTAAAGA-AACTCATCATGT
1355121 TGAGGTGACG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (30 bp):
CTGACTAAAAATTAAAGAAACTCATCATGT
Found at i:1360305 original size:6 final size:6
Alignment explanation
Indices: 1360294--1360324 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1360284 AGAAAATGAA
1360294 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC C
1360325 AAAGCCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CTGAGC
Found at i:1360330 original size:18 final size:18
Alignment explanation
Indices: 1360294--1360330 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1360284 AGAAAATGAA
**
1360294 CTGAGCCTGAGCCTGAGC
1 CTGAGCCTGAGCCAAAGC
1360312 CTGAGCCTGAGCCAAAGC
1 CTGAGCCTGAGCCAAAGC
1360330 C
1 C
1360331 ACTTGCCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.35, G:0.30, T:0.14
Consensus pattern (18 bp):
CTGAGCCTGAGCCAAAGC
Found at i:1367697 original size:2 final size:2
Alignment explanation
Indices: 1367690--1367726 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1367680 GATAATTTTC
1367690 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 A
1367727 GGAATTGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1372433 original size:14 final size:14
Alignment explanation
Indices: 1372408--1372462 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
1372398 TTGATTTTCT
1372408 AAAAATTGAATTTTG
1 AAAAA-TGAATTTTG
*
1372423 AAAAATAAATTATT-
1 AAAAATGAATT-TTG
*
1372437 AAAAATTGAATTCTG
1 AAAAA-TGAATTTTG
1372452 AAAAATGAATT
1 AAAAATGAATT
1372463 ATATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 17 0.50
15 17 0.50
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.35
Consensus pattern (14 bp):
AAAAATGAATTTTG
Found at i:1372453 original size:29 final size:29
Alignment explanation
Indices: 1372407--1372464 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1372397 ATTGATTTTC
*
1372407 TAAAAATTGAATTTTGAAAAATAAATTAT
1 TAAAAATTGAATTCTGAAAAATAAATTAT
*
1372436 TAAAAATTGAATTCTGAAAAATGAATTAT
1 TAAAAATTGAATTCTGAAAAATAAATTAT
1372465 ATTTTTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (29 bp):
TAAAAATTGAATTCTGAAAAATAAATTAT
Found at i:1373901 original size:22 final size:22
Alignment explanation
Indices: 1373838--1373889 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1373828 CCTCTTATAT
** * *
1373838 TATTATAATATAATTGATTATTT
1 TATTATAATAT-ATAAAATATTA
1373861 TATTATAATATATAAAATATTA
1 TATTATAATATATAAAATATTA
1373883 TATTATA
1 TATTATA
1373890 TTATTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATAATATATAAAATATTA
Found at i:1374564 original size:2 final size:2
Alignment explanation
Indices: 1374557--1374600 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1374547 TAATAAAGGA
1374557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1374599 AT
1 AT
1374601 TTTTTTTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1375626 original size:183 final size:184
Alignment explanation
Indices: 1375393--1375779 Score: 629
Period size: 183 Copynumber: 2.1 Consensus size: 184
1375383 ATTAAATTTT
* *
1375393 AAATATTAAATATATTATATATAACATATGGGCTTAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAAAATATGGGCTTAACCCAAACCATTTAAAACCCAATTAATAA
*
1375458 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAA-AATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAATAATTATATAAAATTT
*
1375522 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTCT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTCTGAATTAAA
*
1375576 AAATATTAAATATATTATATATAAAATATGGGC-TAAGCCCAAACCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAAAATATGGGCTTAA-CCCAAACCATTTAAAACCCAATTAATA
** *
1375640 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAATTTTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAATAATTATATAAAATT
*
1375705 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTCTGAATTAAA
* *
1375760 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1375780 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 3 0.02
183 120 0.63
184 67 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAAAATATGGGCTTAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAATAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTCTGAATTAAA
Found at i:1375718 original size:14 final size:13
Alignment explanation
Indices: 1375685--1375709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1375675 ATTAATTAAT
1375685 TAAAATTTTTATC
1 TAAAATTTTTATC
1375698 TAAAATTTTTAT
1 TAAAATTTTTAT
1375710 TTTATAATTA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTATC
Found at i:1376628 original size:18 final size:17
Alignment explanation
Indices: 1376581--1376630 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 17
1376571 AAAGTAAATC
1376581 AAAA-TTAAATTAAAA-
1 AAAATTTAAATTAAAAG
* * *
1376596 AATATATAAAGTAAAAG
1 AAAATTTAAATTAAAAG
1376613 AAAACTTTAAATTAAAAG
1 AAAA-TTTAAATTAAAAG
1376631 GGTTTAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 3 0.12
16 9 0.35
17 3 0.12
18 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAATTTAAATTAAAAG
Found at i:1380340 original size:16 final size:16
Alignment explanation
Indices: 1380319--1380352 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1380309 AATTGAAACT
1380319 AAAGAAAATAAAATTG
1 AAAGAAAATAAAATTG
* *
1380335 AAAGAAAGTAAAGTTG
1 AAAGAAAATAAAATTG
1380351 AA
1 AA
1380353 TTAAAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (16 bp):
AAAGAAAATAAAATTG
Found at i:1380989 original size:21 final size:21
Alignment explanation
Indices: 1380941--1380995 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
1380931 TTTTAAATGA
1380941 AAAATAAGTAAAAACGAAAGAG
1 AAAA-AAGTAAAAACGAAAGAG
1380963 --AAAAGTAAAAACGAAAGAG
1 AAAAAAGTAAAAACGAAAGAG
1380982 AAAAAAGTAAAAAC
1 AAAAAAGTAAAAAC
1380996 TTTTGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 17 0.55
20 2 0.06
21 12 0.39
ACGTcount: A:0.71, C:0.05, G:0.16, T:0.07
Consensus pattern (21 bp):
AAAAAAGTAAAAACGAAAGAG
Found at i:1387495 original size:23 final size:22
Alignment explanation
Indices: 1387424--1387505 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
1387414 GCACTTAACA
1387424 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
1387448 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
1387469 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
*
1387492 GTGCATCAATGCAC
1 GTGCATCGATGCAC
1387506 AAGGCCATGC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:1389478 original size:29 final size:28
Alignment explanation
Indices: 1389446--1389503 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1389436 GGATGTTTAA
1389446 ATTTGATGGTTGT-TGGATGTTTTGAACTT
1 ATTTG-TGGTTGTATGGAT-TTTTGAACTT
* *
1389475 ATTTGTTGTTTTATGGATTTTTGAACTT
1 ATTTGTGGTTGTATGGATTTTTGAACTT
1389503 A
1 A
1389504 ATATTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.55
Consensus pattern (28 bp):
ATTTGTGGTTGTATGGATTTTTGAACTT
Found at i:1389688 original size:2 final size:2
Alignment explanation
Indices: 1389681--1389707 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1389671 TAGCTTAAGC
1389681 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 T
1389708 CAATTGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1390291 original size:65 final size:64
Alignment explanation
Indices: 1390213--1390357 Score: 152
Period size: 65 Copynumber: 2.2 Consensus size: 64
1390203 CATCGAATGC
* ** *
1390213 ATTTCATGCATCGATGC-ACATATTATGCATCGATGCACTCAGAG-TTTTATGAAAACATCGAAA
1 ATTTCATGAATCGATGCAACA-ACCATGCATCGATGCACTCAG-GCTATTATG-AAACATCGAAA
1390276 TA
63 TA
* * * *
1390278 ATTTGATGAATCGATGCAACAGCCATGCATCGATGCACTCTGGCTATTATGAAACATCG-AATGC
1 ATTTCATGAATCGATGCAACAACCATGCATCGATGCACTCAGGCTATTATGAAACATCGAAAT-A
*
1390342 ATTTCATGCATCGATG
1 ATTTCATGAATCGATG
1390358 ACACTTGATG
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
63 3 0.04
64 23 0.34
65 38 0.57
66 3 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (64 bp):
ATTTCATGAATCGATGCAACAACCATGCATCGATGCACTCAGGCTATTATGAAACATCGAAATA
Found at i:1392030 original size:69 final size:69
Alignment explanation
Indices: 1391890--1392045 Score: 179
Period size: 69 Copynumber: 2.3 Consensus size: 69
1391880 GAAAGTCGTG
* * * * *
1391890 AGGGTGAAATAGATTGAAGTGGAGATGAAACAGATGTGGGTGTTGGTAGATATGATGACAAAAGG
1 AGGGTGAAATAGATTGAAGTGGAGATAAAACAGATATGGGTGCTAGTAGAGATGATGACAAAAGG
*
1391955 TGTA
66 TATA
* * * *** *
1391959 AGGGTGAAATAAATTGAAGTGGAGATAAAACGGATATGGGTGCTAGTAGAGATTATGATGGAA-T
1 AGGGTGAAATAGATTGAAGTGGAGATAAAACAGATATGGGTGCTAGTAGAGATGATGACAAAAGG
1392023 TCATA
66 T-ATA
1392028 AGGGTGAAATAGATTGAA
1 AGGGTGAAATAGATTGAA
1392046 ATAGAGATGG
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
68 1 0.01
69 71 0.99
ACGTcount: A:0.38, C:0.03, G:0.33, T:0.25
Consensus pattern (69 bp):
AGGGTGAAATAGATTGAAGTGGAGATAAAACAGATATGGGTGCTAGTAGAGATGATGACAAAAGG
TATA
Found at i:1392053 original size:69 final size:69
Alignment explanation
Indices: 1391957--1392110 Score: 168
Period size: 69 Copynumber: 2.2 Consensus size: 69
1391947 ACAAAAGGTG
* * * * *
1391957 TAAGGGTGAAATAAATTGAAGTGGAGATAAAACGGATA-TGGGTGCT-AGTAGAGATTATGATGG
1 TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGA-AGAGGGTGCTGA-TAGAGATAATGATGG
*
1392020 AATTCA
64 AAGTCA
** *
1392026 TAAGGGTGAAATAGATTGAAATAGAGATGGAACGGAAGAGGGTGCTGATAGAGATAATGGTGGAA
1 TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGAAGAGGGTGCTGATAGAGATAATGATGGAA
*
1392091 GTCG
66 GTCA
* *
1392095 TGAGGATGAAATAGAT
1 TAAGGGTGAAATAGAT
1392111 GTTGATGTAG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
68 1 0.01
69 69 0.97
70 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.34, T:0.23
Consensus pattern (69 bp):
TAAGGGTGAAATAGATTGAAATAGAGATAAAACGGAAGAGGGTGCTGATAGAGATAATGATGGAA
GTCA
Found at i:1393561 original size:23 final size:23
Alignment explanation
Indices: 1393520--1393563 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1393510 TGCCATATAA
**
1393520 TTGTCCCGAATTACCACATAAGT
1 TTGTCCCGAAGGACCACATAAGT
*
1393543 TTGTCCCGAAGGACTACATAA
1 TTGTCCCGAAGGACCACATAA
1393564 TTTTATCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAAGT
Found at i:1393821 original size:15 final size:15
Alignment explanation
Indices: 1393801--1393842 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1393791 CATATAACAT
*
1393801 ATTCACTTAGCACAG
1 ATTCACATAGCACAG
1393816 ATTCACATAGCACA-
1 ATTCACATAGCACAG
*
1393830 TTATCACATAGCA
1 AT-TCACATAGCA
1393843 TTATCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (15 bp):
ATTCACATAGCACAG
Found at i:1394848 original size:20 final size:20
Alignment explanation
Indices: 1394815--1394863 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1394805 ATATATAGTT
* *
1394815 GTTGGTGATGTTTTAGAGCC
1 GTTGGGGATATTTTAGAGCC
*
1394835 GTTGGGGATATTTTGGAGCC
1 GTTGGGGATATTTTAGAGCC
*
1394855 GTTGAGGAT
1 GTTGGGGAT
1394864 TCATTTTCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.39, T:0.37
Consensus pattern (20 bp):
GTTGGGGATATTTTAGAGCC
Found at i:1395075 original size:20 final size:20
Alignment explanation
Indices: 1395024--1395093 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1395014 TTAGCAACGA
* * *
1395024 TACTGTTCACACAATATCGG
1 TACTATTCATACAATATCAG
* *
1395044 TACTATACATACAGTATCAG
1 TACTATTCATACAATATCAG
*
1395064 TACTATTTATACAATA-CAG
1 TACTATTCATACAATATCAG
1395083 TACTATTCATA
1 TACTATTCATA
1395094 AAACATTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.32
20 28 0.68
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCAG
Found at i:1397825 original size:20 final size:20
Alignment explanation
Indices: 1397797--1397835 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1397787 TACTGTTCAT
* *
1397797 TACTGTTCACACAGTATCGG
1 TACTATTCACACAATATCGG
*
1397817 TACTATTCATACAATATCG
1 TACTATTCACACAATATCG
1397836 ATATTATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (20 bp):
TACTATTCACACAATATCGG
Found at i:1403016 original size:23 final size:21
Alignment explanation
Indices: 1402979--1403038 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 21
1402969 ACCGAAGTGT
1402979 CACATAATTATCCCAAATGAC
1 CACATAATTATCCCAAATGAC
1403000 CACATAATTTTATCCCAAATGAC
1 CACATAA--TTATCCCAAATGAC
1403023 CACATAGGATTATCCC
1 CACATA--ATTATCCC
1403039 GTAGGACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.20
23 27 0.77
25 1 0.03
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (21 bp):
CACATAATTATCCCAAATGAC
Found at i:1403303 original size:13 final size:13
Alignment explanation
Indices: 1403262--1403315 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1403252 TATCACATAT
*
1403262 TCACATAACATT-
1 TCACATATCATTA
1403274 TCACATATCAAATTA
1 TCACATATC--ATTA
1403289 TCACATATCATTA
1 TCACATATCATTA
* *
1403302 TCAAATATTATTA
1 TCACATATCATTA
1403315 T
1 T
1403316 TATTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.22
13 16 0.44
14 3 0.08
15 9 0.25
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.39
Consensus pattern (13 bp):
TCACATATCATTA
Found at i:1407940 original size:27 final size:27
Alignment explanation
Indices: 1407910--1407992 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
1407900 ATTGAGTTAA
1407910 AACTAAAACTAAATTGATAGAATATAT
1 AACTAAAACTAAATTGATAGAATATAT
*** * * *
1407937 AACT---ACTTTTTTGAATTGAGT-TAA
1 AACTAAAACTAAATTG-ATAGAATATAT
*
1407961 AACTAAAACTAAATTGATAGAATATGT
1 AACTAAAACTAAATTGATAGAATATAT
1407988 AACTA
1 AACTA
1407993 TTGAGGACCA
Statistics
Matches: 38, Mismatches: 13, Indels: 10
0.62 0.21 0.16
Matches are distributed among these distances:
24 12 0.32
25 5 0.13
26 5 0.13
27 16 0.42
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (27 bp):
AACTAAAACTAAATTGATAGAATATAT
Found at i:1407968 original size:51 final size:51
Alignment explanation
Indices: 1407892--1407992 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
1407882 TTACTCTTTA
1407892 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
1 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
*
1407943 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATGTAACTA
1 TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTA
1407993 TTGAGGACCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (51 bp):
TTTTTTGAATTGAGTTAAAACTAAAACTAAATTGATAGAATATATAACTAC
Found at i:1413455 original size:6 final size:6
Alignment explanation
Indices: 1413446--1413474 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1413436 TCATCATAAT
1413446 CATCAC CATCAC CATCAC CATCAC CATCA
1 CATCAC CATCAC CATCAC CATCAC CATCA
1413475 TTAGTGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (6 bp):
CATCAC
Found at i:1414238 original size:3 final size:3
Alignment explanation
Indices: 1414230--1414319 Score: 180
Period size: 3 Copynumber: 30.0 Consensus size: 3
1414220 TGTCACCTAC
1414230 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1414278 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1414320 CAGTCCACAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1419797 original size:65 final size:63
Alignment explanation
Indices: 1419600--1419808 Score: 217
Period size: 65 Copynumber: 3.3 Consensus size: 63
1419590 TGGATCCTTA
* **
1419600 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATTCCATAGTGCATCGATGCATGG-TG
* * ** *
1419663 ATGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCCCAGTGCATCAATGCATGGTG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-AATTCCATAGTGCATCGATGCATGGTG
* * *
1419727 TGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGAT
1 -GTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TAATTCCATAGTGCATCGATGCATGG--
1419791 TG
62 TG
* *
1419793 GTGCATTGGTGCATCA
1 GTGCATCGATGCATCA
1419809 CTTTGAAAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
63 31 0.26
64 26 0.22
65 60 0.50
66 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAATTCCATAGTGCATCGATGCATGGTG
Found at i:1422488 original size:21 final size:20
Alignment explanation
Indices: 1422458--1422522 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1422448 TATGCATTGG
*
1422458 TGCACCTTCATGGTGTATCGA
1 TGCACATTCA-GGTGTATCGA
*
1422479 TGCACATTCAAGGATGCATCGA
1 TGCACATTC-AGG-TGTATCGA
*
1422501 TGCACTATT-AGGTGTATTGA
1 TGCAC-ATTCAGGTGTATCGA
1422521 TG
1 TG
1422523 TATTAAGCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 8 0.22
21 13 0.35
22 13 0.35
23 3 0.08
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TGCACATTCAGGTGTATCGA
Found at i:1428390 original size:56 final size:57
Alignment explanation
Indices: 1428318--1428429 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
1428308 AAGAGTGCAT
* *
1428318 TGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGC
1 TGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCCACAGTGCATCGATGCATGGC
* *
1428374 TGATGCATCAAATGCATTCGATGTTTTCATAAAATCCCCAGTGCATCGATGCATGG
1 TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGG
1428430 TGTGTGCATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 22 0.44
57 25 0.50
58 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (57 bp):
TGATGCATCAAATGCATTCGATGTTTTCATAAAAGCCACAGTGCATCGATGCATGGC
Found at i:1429641 original size:7 final size:7
Alignment explanation
Indices: 1429629--1429654 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1429619 TTAACTAAAA
1429629 AATATAT
1 AATATAT
1429636 AATATAT
1 AATATAT
1429643 AATATAT
1 AATATAT
1429650 AATAT
1 AATAT
1429655 TTATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Found at i:1429694 original size:17 final size:17
Alignment explanation
Indices: 1429668--1429702 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1429658 TTTATAAATT
*
1429668 TCGATTAATTCGGTTAA
1 TCGATCAATTCGGTTAA
*
1429685 TCGATCAATTTGGTTAA
1 TCGATCAATTCGGTTAA
1429702 T
1 T
1429703 TCGGTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (17 bp):
TCGATCAATTCGGTTAA
Found at i:1436278 original size:13 final size:13
Alignment explanation
Indices: 1436257--1436316 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
1436247 ATTTTGTTAG
1436257 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
1436270 TATTGTA-TTATT
1 TATTTTATTTAAT
1436282 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
1436294 TATTTTATTTAAT
1 TATTTTATTTAAT
1436307 TATTTTATTT
1 TATTTTATTT
1436317 TTTCACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:1436282 original size:21 final size:20
Alignment explanation
Indices: 1436257--1436311 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1436247 ATTTTGTTAG
1436257 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
1436278 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
1436294 TATTTTATTTAATTATTT
1 TATTTTATTTAATTATTT
1436312 TATTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 2 0.07
19 2 0.07
20 9 0.32
21 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:1436303 original size:16 final size:16
Alignment explanation
Indices: 1436261--1436303 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1436251 TGTTAGTATT
* *
1436261 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
1436277 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
1436293 TTATTTTATTT
1 TTATTTAATTT
1436304 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:1436312 original size:21 final size:20
Alignment explanation
Indices: 1436277--1436319 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1436267 AATTATTGTA
*
1436277 TTATTTAATTTTTTTATTATT
1 TTATTTAATTATTTTATT-TT
1436298 TTATTTAATTATTTTATTTT
1 TTATTTAATTATTTTATTTT
1436318 TT
1 TT
1436320 CACAGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTATTTAATTATTTTATTTT
Found at i:1437049 original size:24 final size:24
Alignment explanation
Indices: 1437019--1437070 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1437009 AGTTCGATTA
1437019 AAGCCTAAAATTTGAGCTCAATTG
1 AAGCCTAAAATTTGAGCTCAATTG
1437043 AAGCCTAAAATTTGAGCTCAATTG
1 AAGCCTAAAATTTGAGCTCAATTG
1437067 AAGC
1 AAGC
1437071 GAAAGAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (24 bp):
AAGCCTAAAATTTGAGCTCAATTG
Found at i:1438931 original size:7 final size:7
Alignment explanation
Indices: 1438921--1438987 Score: 116
Period size: 7 Copynumber: 9.6 Consensus size: 7
1438911 ACGAGAAAGC
1438921 AAGCATG
1 AAGCATG
1438928 AAGCATG
1 AAGCATG
*
1438935 AAACATG
1 AAGCATG
1438942 AAGCATG
1 AAGCATG
*
1438949 AAACATG
1 AAGCATG
1438956 AAGCATG
1 AAGCATG
1438963 AAGCATG
1 AAGCATG
1438970 AAGCATG
1 AAGCATG
1438977 AAGCATG
1 AAGCATG
1438984 AAGC
1 AAGC
1438988 CCAGCATCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.46, C:0.15, G:0.25, T:0.13
Consensus pattern (7 bp):
AAGCATG
Found at i:1440192 original size:314 final size:314
Alignment explanation
Indices: 1439619--1440252 Score: 1216
Period size: 314 Copynumber: 2.0 Consensus size: 314
1439609 TAGTGATTTT
1439619 CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
1 CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
*
1439684 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTGAAGGGATTTATTTTTAAAAATATTGTT
66 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTGAAGGGATCTATTTTTAAAAATATTGTT
1439749 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCAAAAGTATGGTA
131 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCAAAAGTATGGTA
*
1439814 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAACTCGAAAA
196 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAAATCGAAAA
*
1439879 TATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGTAAATTAAGTATGAG
261 TATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGGAAATTAAGTATGAG
1439933 CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
1 CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
*
1439998 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTGAAGGGGTCTATTTTTAAAAATATTGTT
66 GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTGAAGGGATCTATTTTTAAAAATATTGTT
*
1440063 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCGAAAGTATGGTA
131 AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCAAAAGTATGGTA
1440128 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAAATCGAAAA
196 ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAAATCGAAAA
1440193 TATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGGAAATTAAGTATGAG
261 TATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGGAAATTAAGTATGAG
1440247 -CCATCA
1 CCCATCA
1440253 CTTATCTTCT
Statistics
Matches: 315, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
313 6 0.02
314 309 0.98
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (314 bp):
CCCATCATGATAATATTTATTACGTGTATACCAAAGCCCCCAAATGATTACTATAATTTTAACAT
GTTTAGAGGAATCAGGGCCGCCTAAGGCCCCAAGTTTGAAGGGATCTATTTTTAAAAATATTGTT
AAGTTTAATAATTAAAAAATATTTTTAAACGTATTTTTTTATTTTAAACACTCAAAAGTATGGTA
ATTCAGTTAGCTCCAATAATTAAAAAATATTGTTAAACATCATTTTTTATTAAAAAAATCGAAAA
TATGGTGATCTAATGGGTCTCATTTTAATGATTGGAAGGGAAATTAAGTATGAG
Found at i:1441817 original size:54 final size:54
Alignment explanation
Indices: 1441716--1442142 Score: 579
Period size: 54 Copynumber: 7.9 Consensus size: 54
1441706 AATATGGTCG
** * * ** ** * *
1441716 TTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTGTCAATACGTAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
1441770 TTCATAAACTCATTATGAATTTCTTAAGTTGTACATACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
1441824 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
** * *
1441876 TTCATAAACTTATTATGAATTTCTTAAGTTGCAGGCACATTGCCAATACAGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
1441930 TTCATAAACTTATTATGATTTTCTTAAGTTGCACACACACAGTGCAAATATGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTG--CACACACAGTGCCAATACGGAAA
1441986 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * * *
1442040 TTCATAAATTTATTATGAATTTCTTAAGTTACACACATAGTGCCAATACGAAAA
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
* * *
1442094 TTTATAAACTTATTATGAATTTCTTAAGTTGCACATACAATGCCAATAC
1 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
1442143 ATACATTAAG
Statistics
Matches: 332, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
52 51 0.15
54 234 0.70
56 47 0.14
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (54 bp):
TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGGAAA
Found at i:1442030 original size:110 final size:109
Alignment explanation
Indices: 1441754--1442143 Score: 572
Period size: 110 Copynumber: 3.6 Consensus size: 109
1441744 TTGCACACTT
* * * * *
1441754 AGTGTCAATACGTAAATTCATAAACTCATTATGAATTTCTTAAGTTGTACATACAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
*
1441819 GGAAATTCATAAACTTATTATGAATTTCTTAAGTTG---CACAC
66 AGAAATTCATAAACTTATTATGAATTTCTTAAGTTGACACACAC
** *
1441860 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCAGGCACATTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
*
1441925 AGAAATTCATAAACTTATTATGATTTTCTTAAGTTGCACACACAC
66 AGAAATTCATAAACTTATTATGAATTTCTTAAGTTG-ACACACAC
* *
1441970 AGTGCAAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
* * *
1442035 GGAAATTCATAAATTTATTATGAATTTCTTAAGTT-ACACACAT
66 AGAAATTCATAAACTTATTATGAATTTCTTAAGTTGACACACAC
* * * *
1442078 AGTGCCAATACGAAAATTTATAAACTTATTATGAATTTCTTAAGTTGCACATACAATGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
1442143 A
66 A
1442144 TACATTAAGC
Statistics
Matches: 254, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
106 91 0.36
108 66 0.26
110 97 0.38
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (109 bp):
AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC
AGAAATTCATAAACTTATTATGAATTTCTTAAGTTGACACACAC
Found at i:1445619 original size:30 final size:30
Alignment explanation
Indices: 1445585--1445650 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
1445575 AAAACCGATA
1445585 GAACCGACTGAAAACCGGT-AAAACCGGGGT
1 GAACCGACTGAAAACC-GTCAAAACCGGGGT
* **
1445615 GAACCGGCTGAAAACCGTCAAAACCGGTTT
1 GAACCGACTGAAAACCGTCAAAACCGGGGT
1445645 GAACCG
1 GAACCG
1445651 CCGGTTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.35, C:0.26, G:0.27, T:0.12
Consensus pattern (30 bp):
GAACCGACTGAAAACCGTCAAAACCGGGGT
Found at i:1449223 original size:2 final size:2
Alignment explanation
Indices: 1449216--1449257 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1449206 CTTAACATTA
1449216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1449258 TCTTATCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449294 original size:23 final size:23
Alignment explanation
Indices: 1449252--1449348 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 23
1449242 ATATATATAT
1449252 ATATATTCTTATCTTAACTTAAAA
1 ATATATT-TTATCTTAACTTAAAA
* * *
1449276 GTATATTTTATTTTCACTTAAAA
1 ATATATTTTATCTTAACTTAAAA
*
1449299 ATATATTTAATATTTTATTAACTTAAAA
1 ATATATTT--TA---TCTTAACTTAAAA
* *
1449327 ATATAATTTATTCTTACCTTAA
1 ATATATTTTA-TCTTAACTTAA
1449349 CTTAAATATT
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
23 21 0.36
24 16 0.27
25 2 0.03
26 2 0.03
28 18 0.31
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATATTTTATCTTAACTTAAAA
Found at i:1449371 original size:31 final size:29
Alignment explanation
Indices: 1449246--1449373 Score: 85
Period size: 29 Copynumber: 4.6 Consensus size: 29
1449236 ATATATATAT
* *
1449246 ATATATATATATTCTTATCTTAACTTAAAA
1 ATATA-ATTTATTCTTACCTTAACTTAAAA
* *
1449276 GTATATTTTATT-TT--C---ACTTAAAA
1 ATATAATTTATTCTTACCTTAACTTAAAA
*
1449299 ATAT-ATTTAATATTTTA--TTAACTTAAAA
1 ATATAATTT-AT-TCTTACCTTAACTTAAAA
1449327 ATATAATTTATTCTTACCTTAACTTAAATA
1 ATATAATTTATTCTTACCTTAACTTAAA-A
* *
1449357 TTTATATTTTATTCTTA
1 -ATATAATTTATTCTTA
1449374 TAATATTTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
22 3 0.04
23 13 0.17
24 1 0.01
25 2 0.03
26 1 0.01
27 4 0.05
28 16 0.21
29 19 0.24
30 5 0.06
31 14 0.18
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.52
Consensus pattern (29 bp):
ATATAATTTATTCTTACCTTAACTTAAAA
Found at i:1449538 original size:27 final size:27
Alignment explanation
Indices: 1449498--1449566 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
1449488 TTATATTTAA
* * *
1449498 TAATTTAAGGTAAGACTAGAATATATT
1 TAATTTAAGTTAAGAATAGAATATATG
*
1449525 TAATTTAAGTTAAGAATATAATATATG
1 TAATTTAAGTTAAGAATAGAATATATG
1449552 TAA--TAAGTTAA-AATA
1 TAATTTAAGTTAAGAATA
1449567 AAAATAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 4 0.11
25 8 0.21
27 26 0.68
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (27 bp):
TAATTTAAGTTAAGAATAGAATATATG
Found at i:1449619 original size:29 final size:29
Alignment explanation
Indices: 1449556--1449664 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
1449546 TATATGTAAT
*
1449556 AAGTTAAAATAAAAATAAGATATATTTTTAA
1 AAGTTAAAATAAAAATAA-A-ATATTTTTTA
*
1449587 AAGTTAAGATAAAAATAAAATATTTTTTA
1 AAGTTAAAATAAAAATAAAATATTTTTTA
* * * * * *
1449616 AAGTTGAGATAAGATTAAAATATATTTTC
1 AAGTTAAAATAAAAATAAAATATTTTTTA
1449645 AAGTTAAAATAAAAATAAAA
1 AAGTTAAAATAAAAATAAAA
1449665 ATAAAATATA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 49 0.73
30 1 0.01
31 17 0.25
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (29 bp):
AAGTTAAAATAAAAATAAAATATTTTTTA
Found at i:1449638 original size:95 final size:92
Alignment explanation
Indices: 1449530--1449700 Score: 204
Period size: 95 Copynumber: 1.8 Consensus size: 92
1449520 ATATTTAATT
* * *
1449530 TAAGTTAAGAATATAATAT-ATG-TAATAAGTTAAAATAAAAATAAGATATATTTTTAAAAGTTA
1 TAAGTTAAGAATATAATATCAAGTTAA-AA-TAAAAATAAAAATAAAATATATTTTT--AAGTT-
*
1449593 AGATAAAAATAAAATATTTTTTAAAGTTGAGA
61 AGACAAAAATAAAATATTTTTTAAAGTTGAGA
* * *
1449625 TAAGATTAA-AATATATTTTCAAGTTAAAATAAAAATAAAAATAAAATATATTTTTAGGTTAGAC
1 TAAG-TTAAGAATATAATATCAAGTTAAAATAAAAATAAAAATAAAATATATTTTTAAGTTAGAC
1449689 AAAAATAAAATA
65 AAAAATAAAATA
1449701 GATTTAATAC
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
92 15 0.23
93 4 0.06
95 36 0.55
96 8 0.12
97 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.35
Consensus pattern (92 bp):
TAAGTTAAGAATATAATATCAAGTTAAAATAAAAATAAAAATAAAATATATTTTTAAGTTAGACA
AAAATAAAATATTTTTTAAAGTTGAGA
Found at i:1449744 original size:29 final size:29
Alignment explanation
Indices: 1449375--1449744 Score: 94
Period size: 30 Copynumber: 12.7 Consensus size: 29
1449365 TTATTCTTAT
* *
1449375 AATAT-TTTAAAAT-TTAAGATAAAATAA
1 AATATATTTATAATGTTAAAATAAAATAA
* * *
1449402 AACATATTT-TCAA-ATTAAAA-AATA-AA
1 AATATATTTAT-AATGTTAAAATAAAATAA
* * *
1449428 AATACATTTTTAA-GTAAAAATAATAATAA
1 AATATATTTATAATGTTAAAATAA-AATAA
* *
1449457 AATATAGATTT-T-ATGTTACAATAAGGATAA
1 AATAT--ATTTATAATGTTAAAATAA-AATAA
* ** * *
1449487 ATTATATTTAATAAT-TTAAGGTAAGACTAG
1 AATATATTT-ATAATGTTAAAATAA-AATAA
** *
1449517 AATATA-TT-TAAT-TTAAGTTAAGAATAT
1 AATATATTTATAATGTTAAAATAA-AATAA
*
1449544 AATATATGTAATAA-GTTAAAATAAAAATAA
1 AATATAT-TTATAATGTTAAAAT-AAAATAA
* * * *
1449574 GATATATTTTTAAAAGTTAAGATAAAAATAA
1 AATATATTTAT-AATGTTAAAAT-AAAATAA
* * * * *
1449605 AATAT-TTTTTAAAGTTGAGATAAGATTAA
1 AATATATTTATAATGTTAAAATAA-AATAA
1449634 AATATATTT-TCAA-GTTAAAATAAAAATAAA
1 AATATATTTAT-AATGTTAAAAT-AAAAT-AA
* * * *
1449664 AATAAAATATATTTTTAGGTTAGACA-AAAATAA
1 AAT---ATAT-TTATAATGTTA-AAATAAAATAA
* *
1449697 AATAGATTTAATACT-TTAAAATAAAATAA
1 AATATATTT-ATAATGTTAAAATAAAATAA
*
1449726 AAAATATTTATAATGTTAA
1 AATATATTTATAATGTTAA
1449745 TATGTAAATT
Statistics
Matches: 258, Mismatches: 50, Indels: 68
0.69 0.13 0.18
Matches are distributed among these distances:
26 16 0.06
27 32 0.12
28 23 0.09
29 63 0.24
30 73 0.28
31 27 0.10
33 9 0.03
34 8 0.03
35 5 0.02
36 2 0.01
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
AATATATTTATAATGTTAAAATAAAATAA
Found at i:1450752 original size:138 final size:140
Alignment explanation
Indices: 1450486--1450767 Score: 514
Period size: 138 Copynumber: 2.0 Consensus size: 140
1450476 TTTTTAATAT
*
1450486 ATAATTTAACATTTAATATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
1 ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
1450551 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
66 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
1450616 CGAATG-AAG
131 CGAATGAAAG
* *
1450625 ATAATTTAACATTTAACATATTAATTACATACAAATCTATATATAATTATACTAATATATTAT-A
1 ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
*
1450689 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAG
66 AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
1450754 CGAATGAAAG
131 CGAATGAAAG
1450764 ATAA
1 ATAA
1450768 AACAGGGAGG
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
138 71 0.51
139 67 0.49
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (140 bp):
ATAATTTAACATTTAACATATTAATTACACACAAATCTATATATAATTATAATAATATATTATAA
AAAATAAAATTTAATTCATTGATATTTTTATAAATTATATACCATCATTATATCAGATATATAAA
CGAATGAAAG
Found at i:1451163 original size:20 final size:20
Alignment explanation
Indices: 1451138--1451230 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
1451128 TTTTCCCAAT
*
1451138 TCGCAATGTGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1451158 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1451179 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1451199 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1451220 TCGCAATGCGA
1 TCGCAATGCGA
1451231 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1451181 original size:21 final size:21
Alignment explanation
Indices: 1451155--1451230 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1451145 GTGAATAAGT
1451155 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1451176 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1451196 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1451217 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1451231 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1451195 original size:41 final size:41
Alignment explanation
Indices: 1451138--1451230 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1451128 TTTTCCCAAT
*
1451138 TCGCAATGTGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1451179 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1451220 TCGCAATGCGA
1 TCGCAATGCGA
1451231 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1451243 original size:41 final size:41
Alignment explanation
Indices: 1451157--1451291 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
1451147 GAATAAGTAA
* *
1451157 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
1451198 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
1451239 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
1451280 TTCGCAACGCGA
1 ATCGCAACGCGA
1451292 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:1451244 original size:20 final size:20
Alignment explanation
Indices: 1451219--1451313 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1451209 AATTGGGAAA
*
1451219 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1451239 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1451260 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1451280 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1451300 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1451314 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1451529 original size:22 final size:22
Alignment explanation
Indices: 1451501--1451544 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1451491 CACTCTCTCA
1451501 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1451523 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1451545 TATCTAAATC
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:1453178 original size:18 final size:18
Alignment explanation
Indices: 1453157--1453201 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1453147 TCCACTTCGG
* *
1453157 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCCA
*
1453175 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1453193 GAGCCATCA
1 GAGCCATCA
1453202 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1453737 original size:19 final size:20
Alignment explanation
Indices: 1453683--1453749 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1453673 TAGTTTACTT
* *
1453683 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1453703 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* * **
1453723 TCGTAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1453742 TCGCAACG
1 TCGCAACG
1453750 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 13 0.35
20 24 0.65
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1453873 original size:19 final size:19
Alignment explanation
Indices: 1453810--1453916 Score: 109
Period size: 19 Copynumber: 5.9 Consensus size: 19
1453800 GCGATTTGTG
1453810 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
1453828 TTTCGCGTTGCGATTTT-A
1 TTTCGCGTTGCGATTTTCA
1453846 --T--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
1453861 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
1453880 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
1453900 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1453917 ATGTTTCGTG
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.16
15 1 0.01
16 1 0.01
17 1 0.01
18 14 0.19
19 28 0.38
20 17 0.23
ACGTcount: A:0.13, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1453893 original size:20 final size:19
Alignment explanation
Indices: 1453859--1453913 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1453849 TTGCGATTTT
*
1453859 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1453878 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1453898 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1453914 TTTATGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1453930 original size:39 final size:37
Alignment explanation
Indices: 1453810--1453932 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 37
1453800 GCGATTTGTG
1453810 TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTA-
1 TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTAT
* ***
1453846 --T--CGTTGCGATTTTCATTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTCATTTCGCGTTGCGAT-TTTAT
* *
1453881 TTCCGCGTTGCGATAGTCATTTCGCGTTGCGATTTTAT
1 TTTCGCGTTGCGAT-TTCATTTCGCGTTGCGATTTTAT
*
1453919 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
1453933 AAGTAAACTA
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
32 8 0.12
33 18 0.27
34 2 0.03
38 3 0.05
39 35 0.53
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTCATTTCGCGTTGCGATTTTAT
Found at i:1455938 original size:33 final size:34
Alignment explanation
Indices: 1455893--1456041 Score: 132
Period size: 33 Copynumber: 4.4 Consensus size: 34
1455883 AAAACAGACT
* ***
1455893 ATCGCAACGCGAAATGGCTATCGCAACGA-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
1455926 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAA
1455964 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAA
*
1455997 ATCGCAATGTGAAATGAAAATCGCAACGA-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
1456030 ATCGCAATGCGA
1 ATCGCAATGCGA
1456042 TTTTCATTTC
Statistics
Matches: 100, Mismatches: 6, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
33 67 0.67
34 2 0.02
35 3 0.03
36 4 0.04
37 2 0.02
38 22 0.22
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
Found at i:1455944 original size:19 final size:19
Alignment explanation
Indices: 1455922--1456041 Score: 161
Period size: 19 Copynumber: 6.8 Consensus size: 19
1455912 ATCGCAACGA
1455922 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1455941 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1455960 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1455974 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
1455993 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
1456012 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1456026 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1456042 TTTTCATTTC
Statistics
Matches: 91, Mismatches: 2, Indels: 18
0.82 0.02 0.16
Matches are distributed among these distances:
14 22 0.24
15 2 0.02
16 4 0.04
17 3 0.03
18 1 0.01
19 59 0.65
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1456054 original size:52 final size:52
Alignment explanation
Indices: 1455893--1456041 Score: 253
Period size: 52 Copynumber: 2.9 Consensus size: 52
1455883 AAAACAGACT
* ***
1455893 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1455945 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
1455997 ATCGCAATGTGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1456042 TTTTCATTTC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1456117 original size:20 final size:20
Alignment explanation
Indices: 1456060--1456117 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
1456050 TCGCATTGCG
* *
1456060 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1456080 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1456100 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1456118 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1457198 original size:24 final size:24
Alignment explanation
Indices: 1457171--1457224 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1457161 GTATTCGAAA
* *
1457171 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1457195 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1457219 TTTGAT
1 TTTGAT
1457225 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1457416 original size:12 final size:12
Alignment explanation
Indices: 1457399--1457423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1457389 ATATAATCCT
1457399 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1457411 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1457423 G
1 G
1457424 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1459750 original size:33 final size:33
Alignment explanation
Indices: 1459706--1459828 Score: 178
Period size: 33 Copynumber: 3.7 Consensus size: 33
1459696 ATTACTATCA
*
1459706 CAATGCAAAATGAAAATCGCAACGAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCG
** *
1459739 CAATGCGAAATGAAAATCGCAACGCTA-ATTTCG
1 CAATGCGAAATGAAAATCGCAACGAGAGA-ATCG
1459772 CAATGCGAAATGAAAATCGCAACGACG-GAATCG
1 CAATGCGAAATGAAAATCGCAACGA-GAGAATCG
1459805 CAATGCGAAATGAAAATCGCAACG
1 CAATGCGAAATGAAAATCGCAACG
1459829 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCG
Found at i:1459758 original size:19 final size:19
Alignment explanation
Indices: 1459706--1459832 Score: 77
Period size: 19 Copynumber: 7.5 Consensus size: 19
1459696 ATTACTATCA
*
1459706 CAATGCAAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
1459725 CAA--CG--A-GAGAATCG
1 CAATGCGAAATGAAAATCG
1459739 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
* **
1459758 CAA--CG--CT-AATTTCG
1 CAATGCGAAATGAAAATCG
1459772 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
* *
1459791 CAA--CG--ACG-GAATCG
1 CAATGCGAAATGAAAATCG
1459805 CAATGCGAAATGAAAATCG
1 CAATGCGAAATGAAAATCG
*
1459824 CAACGCGAA
1 CAATGCGAA
1459833 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 14, Indels: 30
0.64 0.11 0.24
Matches are distributed among these distances:
14 26 0.33
15 4 0.05
16 6 0.08
17 5 0.06
18 4 0.05
19 34 0.43
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
CAATGCGAAATGAAAATCG
Found at i:1459812 original size:66 final size:66
Alignment explanation
Indices: 1459706--1459835 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
1459696 ATTACTATCA
*
1459706 CAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTC
1 CAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
1459771 G
66 G
*
1459772 CAATGCGAAATGAAAATCGCAACGACG-GAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 CAATGCAAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1459836 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 60 0.98
67 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (66 bp):
CAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
G
Found at i:1460030 original size:14 final size:14
Alignment explanation
Indices: 1460011--1460047 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1460001 CATCAATTAA
1460011 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1460025 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1460039 ACAAATCAA
1 ACAAATCAA
1460048 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1461459 original size:21 final size:21
Alignment explanation
Indices: 1461393--1461459 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1461383 TGTAATCGGG
*
1461393 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1461413 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1461435 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1461456 CTCT
1 CTCT
1461460 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1461478 original size:42 final size:41
Alignment explanation
Indices: 1461393--1461515 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1461383 TGTAATCGGG
* * * * *
1461393 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1461435 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1461477 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1461516 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Done.