Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007731.1 Hibiscus syriacus cultivar Beakdansim tig00109983_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: 835416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:288382 original size:21 final size:20
Alignment explanation
Indices: 288338--288397 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
288328 CCCCCCCTGA
*
288338 GGGAACCGATTCCCCCTTGAAG
1 GGGAACCGATTCCCCC--CAAG
288360 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCA-AG
* *
288381 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
288398 TGGGGTTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 17 0.50
22 16 0.47
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.13
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCAAG
Found at i:292586 original size:30 final size:30
Alignment explanation
Indices: 292546--292617 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
292536 TACCCAAATC
292546 TCGATACTTTTGTGTCAGGTGTCGATACTT
1 TCGATACTTTTGTGTCAGGTGTCGATACTT
* *
292576 TCGATTCTTTTGTGTCAGGTGTCGATATTT
1 TCGATACTTTTGTGTCAGGTGTCGATACTT
292606 TCGATACGTTTT
1 TCGATAC-TTTT
292618 CATTTTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.47
Consensus pattern (30 bp):
TCGATACTTTTGTGTCAGGTGTCGATACTT
Found at i:293080 original size:173 final size:174
Alignment explanation
Indices: 292725--293083 Score: 548
Period size: 173 Copynumber: 2.1 Consensus size: 174
292715 TACTGAAACT
292725 AATTTTGTCATATTTTTACCTTCTATATTGTTATATATCGATACATATTTATAAAGTATCGATAC
1 AATTTTGTCATATTTTTACCTTCTATATTGTTATATATCGATACATATTTATAAAGTATCGATAC
* * * *
292790 TTTATAGGCGTCATTATTGTAATTCTTTTAAATTCCTAAAGTATTGATAATATCTTGCATATACT
66 TTTATAGGCGTCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATCTTACATATACT
* *
292855 TATTAAAGTATCGATACCTTCAACATATTCGGTAGCACTTTACC
131 TATTAAAGTATCGATACCTTCAACATATTCAGTAGCAATTTACC
** * *
292899 GGTTTTGTCATATTTTTACC-TCTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATA
1 AATTTTGTCATATTTTTACCTTC-TATATTGTTATATATCGATACATATTTATAAAGTATCGATA
*
292963 CTTTATAGGCG-CATTATTGCAATTATTTTAAATTCCTAAAGTATCGATATTAT-TATACATATA
65 CTTTATAGGCGTCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATCT-TACATATA
293026 CTTATTAAAGTATCGATACCTTCAACATA-TCTAGTAG-ATATTTACC
129 CTTATTAAAGTATCGATACCTTCAACATATTC-AGTAGCA-ATTTACC
293072 AATTTTGTCATA
1 AATTTTGTCATA
293084 ATGAAACCGG
Statistics
Matches: 168, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
172 4 0.02
173 96 0.57
174 68 0.40
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (174 bp):
AATTTTGTCATATTTTTACCTTCTATATTGTTATATATCGATACATATTTATAAAGTATCGATAC
TTTATAGGCGTCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATCTTACATATACT
TATTAAAGTATCGATACCTTCAACATATTCAGTAGCAATTTACC
Found at i:293291 original size:193 final size:193
Alignment explanation
Indices: 292896--293298 Score: 569
Period size: 193 Copynumber: 2.1 Consensus size: 193
292886 GTAGCACTTT
*
292896 ACCGGTTTTGTCATATTTTTACCTCTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTCATATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
* *
292961 TACTTTATAGGCGCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATATTATTATACATATA
66 TACTTTATAGGCGCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATGATACATATA
* *
293026 CTTATTAAAGTATCGATACCTTCAACATATCTAGTAGATATTTACCAATTTTGTCATAATGAA
131 CTTATTAAAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
*
293089 ACCGGTTTTGTCATATTTTTACCTGATATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTCATATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
* * ** * *
293154 TACTTTATATGCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATTTATAATATGATACTTTT
66 TACTTTATAGGCGC-ATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATGATACATAT
* * * * * ** *
293219 ACTTATTACAA-TATTGATACCTTTAACATATCCGGTAGCGCTTTACCGGTTTTGTCAT-TTG-A
130 ACTTATTA-AAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
*
293281 ACCGGGTTTTGTTATATT
1 ACC-GGTTTTGTCATATT
293299 GAACCCGGTT
Statistics
Matches: 186, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
192 4 0.02
193 91 0.49
194 89 0.48
195 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (193 bp):
ACCGGTTTTGTCATATTTTTACCTCATATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
TACTTTATAGGCGCATTATTGCAATTATTTTAAATTCCTAAAGTATCGATAATATGATACATATA
CTTATTAAAGTATCGATACCTTCAACATATCCAGTAGAGATTTACCAATTTTGTCATAATGAA
Found at i:293317 original size:20 final size:20
Alignment explanation
Indices: 293264--293318 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
293254 TAGCGCTTTA
293264 CCGGTTTTGTCAT-TTGAAC
1 CCGGTTTTGTCATATTGAAC
* *
293283 CGGGTTTTGTTATATTGAAC
1 CCGGTTTTGTCATATTGAAC
*
293303 CCGGTTTAGTCATATT
1 CCGGTTTTGTCATATT
293319 TTTACCTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (20 bp):
CCGGTTTTGTCATATTGAAC
Found at i:301955 original size:15 final size:15
Alignment explanation
Indices: 301935--301984 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
301925 AAGCATCATT
301935 GCATCAATTCAGCAA
1 GCATCAATTCAGCAA
**
301950 GCATCAATTCAGCTT
1 GCATCAATTCAGCAA
301965 GCATCAATTCAGCAA
1 GCATCAATTCAGCAA
301980 GCATC
1 GCATC
301985 CTACATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (15 bp):
GCATCAATTCAGCAA
Found at i:302114 original size:19 final size:20
Alignment explanation
Indices: 302077--302116 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
302067 AACCCTTACA
302077 AATATCAAACAGAAACAAGC
1 AATATCAAACAGAAACAAGC
302097 AATATCAAACAG-AACAAGC
1 AATATCAAACAGAAACAAGC
302116 A
1 A
302117 CCAAGTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (20 bp):
AATATCAAACAGAAACAAGC
Found at i:304764 original size:30 final size:31
Alignment explanation
Indices: 304728--304785 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
304718 GTTCGGTCTG
**
304728 GGTTTAGGTTTGAGTTAGGGTT-TGGTTTCA
1 GGTTTAGGTTCAAGTTAGGGTTATGGTTTCA
*
304758 GGTTTAGGTTCAAGTTTGGGTTATGGTT
1 GGTTTAGGTTCAAGTTAGGGTTATGGTT
304786 AAGAAGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.14, C:0.03, G:0.36, T:0.47
Consensus pattern (31 bp):
GGTTTAGGTTCAAGTTAGGGTTATGGTTTCA
Found at i:305444 original size:61 final size:60
Alignment explanation
Indices: 305363--305503 Score: 205
Period size: 61 Copynumber: 2.3 Consensus size: 60
305353 TTGTCTCCTA
*
305363 ATTTTAAATTTGTTCAATTTAGTTCAAATTTAATGATGT-AATATATTAATGTAAGCTTCAT
1 ATTTCAAATTTGTTCAATTTAGTTCAAATTTAAT-AT-TAAATATATTAATGTAAGCTTCAT
* * *
305424 ATTTCAAATTTCTTCAATTTAGTTCAAATTTAATATTACAATTTATTAATTTAAGCTTCAT
1 ATTTCAAATTTGTTCAATTTAGTTCAAATTTAATATTA-AATATATTAATGTAAGCTTCAT
305485 ATTTC-AATTTGTTCAATTT
1 ATTTCAAATTTGTTCAATTT
305504 GATCCTTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
59 1 0.01
60 15 0.21
61 57 0.78
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (60 bp):
ATTTCAAATTTGTTCAATTTAGTTCAAATTTAATATTAAATATATTAATGTAAGCTTCAT
Found at i:305591 original size:15 final size:15
Alignment explanation
Indices: 305571--305621 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
305561 ATATATGTCA
305571 TATATACTAATGAAC
1 TATATACTAATGAAC
**
305586 TATATA-TATAGTTTA-
1 TATATACTA-A-TGAAC
305601 TATATACTAATGAAC
1 TATATACTAATGAAC
305616 TATATA
1 TATATA
305622 ATGTATAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (15 bp):
TATATACTAATGAAC
Found at i:305634 original size:33 final size:31
Alignment explanation
Indices: 305570--305702 Score: 214
Period size: 33 Copynumber: 4.2 Consensus size: 31
305560 TATATATGTC
305570 ATATATACTAATGAACTATAT-ATATAGTTT
1 ATATATACTAATGAACTATATAATATAGTTT
305600 ATATATACTAATGAACTATATAATGTATAGTTT
1 ATATATACTAATGAACTATATAA--TATAGTTT
*
305633 ATATATACTAATGAACTATATAATGTTAGTTT
1 ATATATACTAATGAACTATATAAT-ATAGTTT
*
305665 ATATATACTAATGAACTATATAATATAGTAT
1 ATATATACTAATGAACTATATAATATAGTTT
305696 ATATATA
1 ATATATA
305703 TATATAGTTT
Statistics
Matches: 96, Mismatches: 3, Indels: 7
0.91 0.03 0.07
Matches are distributed among these distances:
30 21 0.22
31 14 0.15
32 30 0.31
33 31 0.32
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (31 bp):
ATATATACTAATGAACTATATAATATAGTTT
Found at i:305654 original size:17 final size:17
Alignment explanation
Indices: 305570--305621 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
305560 TATATATGTC
305570 ATATATACTAATGAACT
1 ATATATACTAATGAACT
**
305587 ATATATA-T-A-G-TTT
1 ATATATACTAATGAACT
305600 ATATATACTAATGAACT
1 ATATATACTAATGAACT
305617 ATATA
1 ATATA
305622 ATGTATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
13 8 0.30
14 2 0.07
15 2 0.07
16 2 0.07
17 13 0.48
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (17 bp):
ATATATACTAATGAACT
Found at i:305703 original size:65 final size:62
Alignment explanation
Indices: 305557--305704 Score: 210
Period size: 65 Copynumber: 2.3 Consensus size: 62
305547 TATAATAAAT
305557 TAATATA-TATGTCATATATACTAATGAACTATATATATAGTTTATATATACTAATGAACTATA
1 TAATATAGTAT-T-ATATATACTAATGAACTATATATATAGTTTATATATACTAATGAACTATA
*
305620 TAATGTATAGT-TTATATATACTAATGAACTATATAATGTTAGTTTATATATACTAATGAACTAT
1 TAA--TATAGTATTATATATACTAATGAACTATAT-AT-ATAGTTTATATATACTAATGAACTAT
305684 A
62 A
305685 TAATATAGTATATATATATA
1 TAATATAGTAT-TATATATA
305705 TATAGTTTAT
Statistics
Matches: 77, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
63 30 0.39
64 4 0.05
65 42 0.55
66 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (62 bp):
TAATATAGTATTATATATACTAATGAACTATATATATAGTTTATATATACTAATGAACTATA
Found at i:305719 original size:65 final size:64
Alignment explanation
Indices: 305570--305702 Score: 218
Period size: 63 Copynumber: 2.1 Consensus size: 64
305560 TATATATGTC
*
305570 ATATATACTAATGAACTATAT-AT-ATAGTTTATATATACTAATGAACTATATAATGTATAGTTT
1 ATATATACTAATGAACTATATAATGTTAGTTTATATATACTAATGAACTATATAA-GTATAGTTT
*
305633 ATATATACTAATGAACTATATAATGTTAGTTTATATATACTAATGAACTATATAA-TATAGTAT
1 ATATATACTAATGAACTATATAATGTTAGTTTATATATACTAATGAACTATATAAGTATAGTTT
305696 ATATATA
1 ATATATA
305703 TATATAGTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
63 35 0.53
64 2 0.03
65 29 0.44
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (64 bp):
ATATATACTAATGAACTATATAATGTTAGTTTATATATACTAATGAACTATATAAGTATAGTTT
Found at i:305731 original size:47 final size:48
Alignment explanation
Indices: 305659--305766 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 48
305649 TATATAATGT
305659 TAGTTTATATATACTAATGAACTATATAATATAGTA-TATATATATATA
1 TAGTTTATATATACTAATGAACTATATAATATA-TAGTATATATATATA
* *
305707 TAGTTTATATATACTAAT-AACTATATAATATATAGTTTGTATATATA
1 TAGTTTATATATACTAATGAACTATATAATATATAGTATATATATATA
*
305754 TACTTTATATATA
1 TAGTTTATATATA
305767 TAGTTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
46 2 0.04
47 36 0.64
48 18 0.32
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (48 bp):
TAGTTTATATATACTAATGAACTATATAATATATAGTATATATATATA
Found at i:305779 original size:15 final size:15
Alignment explanation
Indices: 305734--305784 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 15
305724 TAACTATATA
*
305734 ATATATAGTTTGTAT
1 ATATATAGTTTTTAT
*
305749 ATATATA--CTTTAT
1 ATATATAGTTTTTAT
305762 ATATATAGTTTTT-T
1 ATATATAGTTTTTAT
305776 -TATATAGTT
1 ATATATAGTT
305785 CATAATGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 20 0.65
14 1 0.03
15 10 0.32
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (15 bp):
ATATATAGTTTTTAT
Found at i:305781 original size:2 final size:2
Alignment explanation
Indices: 305681--305768 Score: 58
Period size: 2 Copynumber: 43.0 Consensus size: 2
305671 ACTAATGAAC
*
305681 TA TA TA -A TA TA GTA TA TA TA TA TA TA TA GTT TA TA TA TA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * *
305723 -A TA -A CTA TA TA -A TA TA TA GTT TG TA TA TA TA TA CTT TA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
305763 TA TA TA
1 TA TA TA
305769 GTTTTTTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
1 4 0.06
2 57 0.83
3 8 0.12
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:306013 original size:17 final size:18
Alignment explanation
Indices: 305976--306014 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
305966 TGATTTTTCA
*
305976 TATAGTTCATATGTAAAC
1 TATAGTTCATATATAAAC
*
305994 TATAGTTCAT-TATCAAC
1 TATAGTTCATATATAAAC
306011 TATA
1 TATA
306015 TAATTTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
TATAGTTCATATATAAAC
Found at i:306068 original size:15 final size:15
Alignment explanation
Indices: 306044--306078 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
306034 AAATATCAAC
306044 TATA-AACTATAGTT
1 TATATAACTATAGTT
306058 TATATAACTATAGTT
1 TATATAACTATAGTT
306073 TATATA
1 TATATA
306079 GTTTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (15 bp):
TATATAACTATAGTT
Found at i:306089 original size:2 final size:2
Alignment explanation
Indices: 306084--306343 Score: 96
Period size: 2 Copynumber: 127.5 Consensus size: 2
306074 ATATAGTTTT
* * *
306084 TA TA TA TA CA TA T- TA AA T- TA TA CTA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * *
306126 TA TA TA -A TA TA TA GTA TA TA AA TA TA AA CTA TA GA T- 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
* * * * *
306168 TG TA GTA TA CTA TA TA AA TA GTT TA TA GT- TCA TA TG TA AA CTA
1 TA TA -TA TA -TA TA TA TA TA -TA TA TA -TA T-A TA TA TA TA -TA
* * * *
306211 TA TA GTA T- TA TA GTT TA TA CA T- TG TA TA TA TA GTT TA TGA T-
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA
* *
306252 TA -A TA TA TA -A TA TA TA GTT TA TA TA TA GTA TA TA -A TA TA AA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
* *
306293 TA TA AA CTA TA TA GTT TA TA T- TA TA TA TA T- 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
306335 TA TA TA TA T
1 TA TA TA TA T
306344 TAGTTGTTTC
Statistics
Matches: 190, Mismatches: 37, Indels: 62
0.66 0.13 0.21
Matches are distributed among these distances:
1 13 0.07
2 152 0.80
3 25 0.13
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:306166 original size:51 final size:49
Alignment explanation
Indices: 306044--306184 Score: 124
Period size: 51 Copynumber: 2.7 Consensus size: 49
306034 AAATATCAAC
* * *
306044 TATAAACTATAGTTTATATAACTATAGTTTATATAGT--TTTTATATATACA
1 TATAAACTATAGATTATAT-A-TATAGTTTATATA-TAATTATATATATAAA
* *
306094 TATTAAATTATACTATATATATATATAGTTTATATATAATATATAGTATATAAA
1 TA-TAAACTATA-GAT-TATATATATAGTTTATATATAAT-TATA-TATATAAA
* *
306148 TATAAACTATAGATTATATATGTAGTATACTATATAA
1 TATAAACTATAGATTATATATATAGTTTA-TATATAA
306185 ATAGTTTATA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
50 3 0.04
51 34 0.46
52 12 0.16
53 16 0.22
54 9 0.12
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (49 bp):
TATAAACTATAGATTATATATATAGTTTATATATAATTATATATATAAA
Found at i:306270 original size:25 final size:25
Alignment explanation
Indices: 306236--306290 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
306226 TATACATTGT
306236 ATATATAGTTTATGAT-TAATATATA
1 ATATATAGTTTAT-ATATAATATATA
*
306261 ATATATAGTTTATATATAGTATATA
1 ATATATAGTTTATATATAATATATA
306286 ATATA
1 ATATA
306291 AATATAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
ATATATAGTTTATATATAATATATA
Found at i:306277 original size:11 final size:11
Alignment explanation
Indices: 306261--306342 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
306251 TTAATATATA
*
306261 ATATATAGTTT
1 ATATATAGTAT
306272 ATATATAGTAT
1 ATATATAGTAT
*
306283 ATA-ATA-TAA
1 ATATATAGTAT
* *
306292 ATATAAACTAT
1 ATATATAGTAT
*
306303 ATAGTTTA-TATT
1 ATA-TATAGTA-T
*
306315 ATATATATTAT
1 ATATATAGTAT
306326 ATATATA-TAT
1 ATATATAGTAT
306336 ATATATA
1 ATATATA
306343 TTAGTTGTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
9 5 0.08
10 15 0.25
11 31 0.53
12 8 0.14
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (11 bp):
ATATATAGTAT
Found at i:306295 original size:38 final size:34
Alignment explanation
Indices: 306108--306342 Score: 109
Period size: 38 Copynumber: 6.4 Consensus size: 34
306098 AAATTATACT
306108 ATATATATATATAGTTTATATATAATATATAGTATATA
1 ATATATATATATAG-TTATATAT-ATATATA--ATATA
* * *
306146 A-ATATAAACTATAGATTATATATGTAGTATACTAT-
1 ATATATATA-TATAG-TTATATATATA-TATAATATA
* * * *
306181 ATAAATAGTTTATAGTTCATATGTAAACTAT-ATAGTA
1 ATATATA-TATATAGTT-ATATATATA-TATAATA-TA
* * * * * *
306218 TTATAGTTTATACATTGTATATATAGTTTATGAT-TA
1 ATATA-TATATATAGT-TATATATA-TATATAATATA
306254 ATATATAATATATAGTTTATATATAGTATATAATATAA
1 ATATAT-ATATATAG-TTATATATA-TATATAATAT-A
* *
306292 ATATAAACTATATAGTTTATATTATATATATTATATA
1 ATATATA-TATATAG-TTATA-TATATATATAATATA
306329 TATATATATATATA
1 -ATATATATATATA
306343 TTAGTTGTTT
Statistics
Matches: 149, Mismatches: 30, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
35 6 0.04
36 48 0.32
37 35 0.23
38 56 0.38
39 4 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (34 bp):
ATATATATATATAGTTATATATATATATAATATA
Found at i:307047 original size:212 final size:210
Alignment explanation
Indices: 306414--307143 Score: 1046
Period size: 212 Copynumber: 3.5 Consensus size: 210
306404 TTTTTTTTAC
* **
306414 ATTTACAATCATTTCGATTTGATCCCT--T---TGT-TGTTG-TTAATTTATTTAAAACTTTATT
1 ATTTA-AATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATT
* *
306472 TGTAATTTCGTATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCCCATACT
65 TGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCTCATACT
306537 TTACTTATTTTATATTTTTAATTAGCCCATAAC-TTTTAAATGGGTATAATTTAGTACTTTTTGT
130 TTACTTA-TTTATATTTTTAATTAGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGT
*
306601 ATTAATTTAAACCTCGCA
194 ATTAATTT-AACCTCACA
*
306619 ATTTAAAATTATTTCGATTTGACCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATT
1 ATTT-AAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATT
* * * * *
306684 T-TAATTTCATA-TTGTTCAATTTAGTCCTTAAAA-T-TATTTGCATCTAAAATAGTCTCTTAC-
65 TGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCTCATACT
*
306744 TTACTTATTTATATTTTTTAATTAGCCCATAACTTTTTAAATGGGTTTAATTTAGTACTTTTTTG
130 TTACTTATTTATA-TTTTTAATTAGCCCATAACTTTTTAAATGGGTATAATTTAGTAC-TTTTTG
*
306809 TATTAATCTAGACCTCACA
193 TATTAATTTA-ACCTCACA
*
306828 A-TTAAATTATTTCGATTTGATCCCTCATCAATGTGTGCTGTTTAATTTATTTAAATTTTTTATT
1 ATTTAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAA-TTTTTATT
306892 TGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCTCATACT
65 TGTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCTCATACT
*
306957 TATACTTA-TTATATTTTTAATT-GACCCATAACTTTTTAAATGGGTAAAATTTAGTACTTTTTG
130 T-TACTTATTTATATTTTTAATTAG-CCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTG
307020 TATTAATTTCAACCTCACA
193 TATTAATTT-AACCTCACA
*
307039 ATTTAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAA-TTATTTAAA-TTTAATTT
1 ATTTAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTT
* * * *
307102 GTAATTTTATATTTATTCAATTTAGTTCTTAAATTTATATTT
66 GTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTT
307144 TTCATAAAAT
Statistics
Matches: 473, Mismatches: 30, Indels: 40
0.87 0.06 0.07
Matches are distributed among these distances:
205 23 0.05
206 7 0.01
207 77 0.16
208 55 0.12
209 78 0.16
210 47 0.10
211 48 0.10
212 126 0.27
213 6 0.01
214 6 0.01
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (210 bp):
ATTTAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTT
GTAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTTGCATATGAAATTGGCTCATACTT
TACTTATTTATATTTTTAATTAGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTTTGTAT
TAATTTAACCTCACA
Found at i:307125 original size:28 final size:27
Alignment explanation
Indices: 307092--307147 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
307082 TAATTATTTA
*
307092 AATTTAATT-TGTAATTTTATATTTATTC
1 AATTTAATTCT-TAAATTTATATTT-TTC
*
307120 AATTTAGTTCTTAAATTTATATTTTTC
1 AATTTAATTCTTAAATTTATATTTTTC
307147 A
1 A
307148 TAAAATTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 20 0.80
29 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (27 bp):
AATTTAATTCTTAAATTTATATTTTTC
Found at i:314037 original size:16 final size:17
Alignment explanation
Indices: 314016--314048 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
314006 ATCAAAAAAA
314016 AAAAAATATGA-TTTTC
1 AAAAAATATGACTTTTC
*
314032 AAAAAATTTGACTTTTC
1 AAAAAATATGACTTTTC
314049 GGCCAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (17 bp):
AAAAAATATGACTTTTC
Found at i:314067 original size:17 final size:17
Alignment explanation
Indices: 314047--314080 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
314037 ATTTGACTTT
314047 TCGGCCAAAGTCAACGG
1 TCGGCCAAAGTCAACGG
* *
314064 TCGGTCAATGTCAACGG
1 TCGGCCAAAGTCAACGG
314081 GTCATACTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (17 bp):
TCGGCCAAAGTCAACGG
Found at i:314815 original size:9 final size:9
Alignment explanation
Indices: 314788--314840 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
314778 AACATAATGG
314788 AAAT-AAAT
1 AAATAAAAT
**
314796 AAATAGTAT
1 AAATAAAAT
314805 AAATAAAAT
1 AAATAAAAT
*
314814 AAAAAAAAT
1 AAATAAAAT
314823 AAA-AAAAT
1 AAATAAAAT
*
314831 ATATAAAAT
1 AAATAAAAT
314840 A
1 A
314841 TAAAAATGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
8 11 0.30
9 26 0.70
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:314829 original size:17 final size:17
Alignment explanation
Indices: 314803--314847 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
314793 AATAAATAGT
314803 ATAAATAAAATAAAAAAA
1 ATAAA-AAAATAAAAAAA
* *
314821 ATAAAAAAATATATAAA
1 ATAAAAAAATAAAAAAA
*
314838 ATATAAAAAT
1 ATAAAAAAAT
314848 GTATGTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
ATAAAAAAATAAAAAAA
Found at i:314841 original size:9 final size:9
Alignment explanation
Indices: 314809--314846 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
314799 TAGTATAAAT
*
314809 AAAATAAAA
1 AAAATATAA
314818 AAAATA-AA
1 AAAATATAA
*
314826 AAAATATAT
1 AAAATATAA
314835 AAAATATAA
1 AAAATATAA
314844 AAA
1 AAA
314847 TGTATGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATATAA
Found at i:315058 original size:22 final size:23
Alignment explanation
Indices: 315033--315075 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
315023 TAATATATAT
* *
315033 ATATATATATAA-TAGGAAAATA
1 ATATAAATATAAGTAAGAAAATA
315055 ATATAAATATAAGTAAGAAAA
1 ATATAAATATAAGTAAGAAAA
315076 ATGAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (23 bp):
ATATAAATATAAGTAAGAAAATA
Found at i:315076 original size:24 final size:22
Alignment explanation
Indices: 315033--315110 Score: 58
Period size: 22 Copynumber: 3.6 Consensus size: 22
315023 TAATATATAT
* *
315033 ATATATATATAATAGGAAAATA
1 ATATAAATATAATAGAAAAATA
*
315055 ATATAAATATAAGTAAGAAAAATG
1 ATATAAATATAA-T-AGAAAAATA
315079 A-A-AAA-ATAATA-AATAAATA
1 ATATAAATATAATAGAA-AAATA
315098 A-ATAAAATATAAT
1 ATAT-AAATATAAT
315111 TAAATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
18 2 0.04
19 7 0.15
20 1 0.02
21 7 0.15
22 19 0.41
23 2 0.04
24 8 0.17
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
ATATAAATATAATAGAAAAATA
Found at i:315084 original size:65 final size:63
Alignment explanation
Indices: 314966--315090 Score: 148
Period size: 65 Copynumber: 1.9 Consensus size: 63
314956 TGAAGTAAGA
* *
314966 ATATATATATATAACGTTAGGAAAATATAGTAAATAAGTAAACATAGATAAAAATAATAATATAT
1 ATATATATATATAAC--TAGGAAAATATAGTAAATAAGTAAAAAAAGATAAAAATAATAATATAT
315031 ATATATATATATAA-TAGGAAAATAATA-TAAATATAAGTAAGAAAAATGA-AAAAATAATAA
1 ATATATATATATAACTAGGAAAAT-ATAGT-AA-ATAAGTAA-AAAAA-GATAAAAATAATAA
315091 ATAAATAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
62 10 0.19
63 5 0.09
64 8 0.15
65 28 0.53
66 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (63 bp):
ATATATATATATAACTAGGAAAATATAGTAAATAAGTAAAAAAAGATAAAAATAATAATATAT
Found at i:315092 original size:15 final size:15
Alignment explanation
Indices: 315082--315138 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
315072 AAAAATGAAA
315082 AAATAATAAATAAAT
1 AAATAATAAATAAAT
*
315097 AAATAA-AATATAATT
1 AAATAATAA-ATAAAT
*
315112 AAATATATATATACATAT
1 AAATA-ATAAATA-A-AT
315130 AAATAATAA
1 AAATAATAA
315139 GGGTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 2 0.06
15 16 0.48
16 4 0.12
17 5 0.15
18 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:315575 original size:37 final size:37
Alignment explanation
Indices: 315534--315616 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
315524 ATCCTATCAC
* *
315534 TAGGAGTTTAAATAATAGTAGAACTCTATCCTATTTT
1 TAGGAGTTTAAATAATAGCAAAACTCTATCCTATTTT
* ** * *
315571 TAGGAGTTTGAATCCTAGCAAAATTCTATTCTATTTT
1 TAGGAGTTTAAATAATAGCAAAACTCTATCCTATTTT
315608 TAGGAGTTT
1 TAGGAGTTT
315617 GAATCCTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (37 bp):
TAGGAGTTTAAATAATAGCAAAACTCTATCCTATTTT
Found at i:316677 original size:106 final size:106
Alignment explanation
Indices: 316359--318051 Score: 2488
Period size: 106 Copynumber: 16.0 Consensus size: 106
316349 GCATTGTTCT
* ** * * *
316359 GAGTCCAATATCC-TC-CTTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTCATTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAC
* * *
316422 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
316465 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * * * * *
316524 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTATCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
316565 GTGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
316630 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
316671 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
316736 CCAGTGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
316777 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
316842 CCAGCGGTCCCTTCATCGTGAAGTTGAATTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
316883 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
316948 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
316989 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
317054 CCAGCGGTCCCTTTGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
317095 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
317160 CTAGCGGTCCC-TCGCCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317200 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTATGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
317265 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317306 GAGTCCAATATCCTACGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
317371 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
317412 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
317477 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317518 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
317583 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
317624 GAGTCCAATATGCTTCGCTGTGAGGTTTAAATTGGCTCTGAAATTGCGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
317689 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
317730 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
317795 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317836 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
317901 CCAGCAGTCTCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317942 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
318007 CCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
318048 GAGT
1 GAGT
318052 GGCACGATAT
Statistics
Matches: 1437, Mismatches: 140, Indels: 20
0.90 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 78 0.05
101 3 0.00
102 4 0.00
104 3 0.00
105 96 0.07
106 1248 0.87
107 3 0.00
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:318886 original size:22 final size:22
Alignment explanation
Indices: 318860--318915 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
318850 TTATGTTTGG
318860 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
318882 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
318904 TCAACGGTTTGA
1 TCAAAGGTTTGA
318916 TGGGGTAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:319608 original size:172 final size:173
Alignment explanation
Indices: 319309--319655 Score: 574
Period size: 172 Copynumber: 2.0 Consensus size: 173
319299 TAAATAGGCC
*
319309 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTA
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTA
*
319374 CTCAAAATGTATCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTATCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTCAGTAATTCGGGAATG
319439 ATTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGTGCCATTT
* *
319484 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTACT
* *
319546 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTAATTCGGGAATG
66 CAAAATG--TATCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTCAGTAATTCGGGAATG
*
319611 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATATCATAGTTTGAAGCTTGATGTGCCATTT
319656 TTTAGGGAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
170 13 0.08
172 98 0.60
174 1 0.01
175 51 0.31
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (173 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTACT
CAAAATGTATCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTCAGTAATTCGGGAATGAT
TGTGCTTGATCAATATCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:319708 original size:17 final size:18
Alignment explanation
Indices: 319688--319735 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
319678 TTTTTGTCTC
319688 TTTTTCTTTTT-GATTTT
1 TTTTTCTTTTTCGATTTT
*
319705 TTTTTCTTGTTTCTATTTT
1 TTTTTCTT-TTTCGATTTT
*
319724 TTCTTTGTTTTT
1 TT-TTTCTTTTT
319736 TTGGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 10 0.38
20 5 0.19
ACGTcount: A:0.04, C:0.08, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTTCGATTTT
Found at i:324301 original size:3 final size:3
Alignment explanation
Indices: 324293--324321 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
324283 GTTAAAAGAA
324293 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
324322 AAGAAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:324557 original size:9 final size:8
Alignment explanation
Indices: 324539--324596 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
324529 AGCATAATGA
*
324539 AAATAAAT
1 AAATATAT
324547 AAATAGTAT
1 AAATA-TAT
324556 AAATATAT
1 AAATATAT
*
324564 ATATATAT
1 AAATATAT
*
324572 ATATATAT
1 AAATATAT
*
324580 ATATATAT
1 AAATATAT
*
324588 ATATATAT
1 AAATATAT
324596 A
1 A
324597 TATGTATGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
8 40 0.85
9 7 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
AAATATAT
Found at i:324565 original size:4 final size:4
Alignment explanation
Indices: 324553--324610 Score: 89
Period size: 4 Copynumber: 14.5 Consensus size: 4
324543 AAATAAATAG
* *
324553 TATA AATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
*
324601 TATG TATA TA
1 TATA TATA TA
324611 ATAAAATACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
TATA
Found at i:324567 original size:6 final size:6
Alignment explanation
Indices: 324553--324610 Score: 89
Period size: 6 Copynumber: 9.7 Consensus size: 6
324543 AAATAAATAG
* *
324553 TATAAA TATATA TATATA TATATA TATATA TATATA TATATA TATATG
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
324601 TATGTA TATA
1 TATATA TATA
324611 ATAAAATACT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:324803 original size:29 final size:28
Alignment explanation
Indices: 324748--324811 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
324738 AACGTTAGGA
*
324748 AAATATAGTAAAAAACATAGTAAATAAGT
1 AAATATAGTAAAAAACATAATAAATAA-T
324777 AAATATAG-ATAAAAA-ATAATAATATAAT
1 AAATATAGTA-AAAAACATAATAA-ATAAT
*
324805 ATATATA
1 AAATATA
324812 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (28 bp):
AAATATAGTAAAAAACATAATAAATAAT
Found at i:324805 original size:5 final size:5
Alignment explanation
Indices: 324795--324850 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
324785 ATAAAAAATA
* *
324795 ATAAT ATAAT AT-AT ATATAT ATATAT ATAAT AGGAAA ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT A-TAAT ATAAT ATAAT
324842 ATAAT ATAA
1 ATAAT ATAA
324851 CGCAAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 14 0.32
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:325355 original size:37 final size:37
Alignment explanation
Indices: 325314--325406 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
325304 ATGCTTGTGG
* * *
325314 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
325351 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
325388 ATTCTATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
325407 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:327094 original size:57 final size:57
Alignment explanation
Indices: 327032--327139 Score: 198
Period size: 57 Copynumber: 1.9 Consensus size: 57
327022 GGTTTCCTGT
*
327032 AGTGCTTTGAACGTTATATGAAACAACTAAAATAAAATTAGATTTTCTTTTCGGGAC
1 AGTGCTTTGAACGTTATATGAAACAACTAAAATAAAATTAGATTTTATTTTCGGGAC
*
327089 AGTGCTTTGAACGTTATATGAAACAATTAAAATAAAATTAGATTTTATTTT
1 AGTGCTTTGAACGTTATATGAAACAACTAAAATAAAATTAGATTTTATTTT
327140 ATTTTCGGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (57 bp):
AGTGCTTTGAACGTTATATGAAACAACTAAAATAAAATTAGATTTTATTTTCGGGAC
Found at i:329557 original size:106 final size:106
Alignment explanation
Indices: 329411--330182 Score: 1357
Period size: 106 Copynumber: 7.3 Consensus size: 106
329401 TGCACGATTC
* *
329411 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
*
329476 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
*
329517 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAATCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
329582 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
*
329623 CCTTCGTTGTGAAGTTTTAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAG-TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCC
329688 CTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
* * * *
329730 CCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
*
329795 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
* *
329836 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
329901 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
*
329942 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
* **
330007 TTCGTCGTGAAGTTGAACATTCGTTGTCAAGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
*
330048 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
**
330112 TTCGTCGTGAAGTTGAACATGCGTTGTCAAGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
330153 CCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGA
330183 TAAAATAAGA
Statistics
Matches: 640, Mismatches: 25, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
105 91 0.14
106 446 0.70
107 103 0.16
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATAT
Found at i:330777 original size:85 final size:86
Alignment explanation
Indices: 330677--331421 Score: 946
Period size: 85 Copynumber: 8.8 Consensus size: 86
330667 TTTGCCTCTG
* * * * *
330677 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTGTAGCCTTGAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
*
330741 CTGCAAATGATGTGCCCTCGA
66 CTGCAAATGATATGCCCTCGA
* * * *
330762 AGTTGAGCGTAATCGAACTCAAAGGTC-TTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
*
330826 CTGCAAATGATATGTCCTCGA
66 CTGCAAATGATATGCCCTCGA
* ** *
330847 AGCTAAGTGTAATCGAACTCGGGGGTCTTTT-GTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* *
330911 CTGCAAATGATATG-CCTTGG
66 CTGCAAATGATATGCCCTCGA
* * * *
330931 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
*
330995 CTGCAAATGATGTGCCCTCGA
66 CTGCAAATGATATGCCCTCGA
** *
331016 AGCTGAGTGTAATCGAACTCGGGGGTCTTTT-GTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* *
331080 CTGCAAATGATATG-CCTTGG
66 CTGCAAATGATATGCCCTCGA
* * * *
331100 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
*
331164 CTGCAAATGATGTGCCCTCGA
66 CTGCAAATGATATGCCCTCGA
** *
331185 AGCTGAGTGTAATCGAACTCGGGGGTCTTTT-GTTGGCAGACAACCCTTCTAGACTTAAGTTGTG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
* *
331249 CTGCAAATGATATG-CCTTGG
66 CTGCAAATGATATGCCCTCGA
* * * *
331269 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
*
331333 CTGCAAATGATGTGCCCTCGA
66 CTGCAAATGATATGCCCTCGA
** * * * *
331354 AGCTGAGTGTAATCGAACTCGGGGGTC---T--TTGGCAGATAGCCCTTCTTGACTTAAGCTATG
1 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
331414 CTGCAAAT
66 CTGCAAAT
331422 AGTTTGTTTA
Statistics
Matches: 573, Mismatches: 77, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
81 37 0.06
83 10 0.02
84 214 0.37
85 303 0.53
86 9 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (86 bp):
AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTATG
CTGCAAATGATATGCCCTCGA
Found at i:330988 original size:169 final size:169
Alignment explanation
Indices: 330677--331421 Score: 1219
Period size: 169 Copynumber: 4.4 Consensus size: 169
330667 TTTGCCTCTG
** * * * * * * *
330677 AGCTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTGTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
* * * * * * *
330742 TGCAAATGATGTGCCCTCGAAGTTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACC
66 TGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
* * * *
330807 CTTCTAGACTTAAGTTGTGCTGCAAATGATATGTCCTCGA
130 CTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
*
330847 AGCTAAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
1 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
330912 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
330977 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
131 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
331016 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
1 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
331081 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
331146 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
131 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
331185 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
1 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
331250 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
331315 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
131 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
* * * * *
331354 AGCTGAGTGTAATCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTTGACTTAAGCTATGC
1 AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
331415 TGCAAAT
66 TGCAAAT
331422 AGTTTGTTTA
Statistics
Matches: 548, Mismatches: 27, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
165 35 0.06
166 1 0.00
169 445 0.81
170 67 0.12
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (169 bp):
AGCTGAGTGTAATCGAACTCGGGGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
Found at i:341978 original size:2 final size:2
Alignment explanation
Indices: 341971--342035 Score: 121
Period size: 2 Copynumber: 32.0 Consensus size: 2
341961 AGGTAAAATG
341971 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
342013 AT AT AT AT AT ACT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT
342036 GACTATGAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 60 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:342615 original size:23 final size:23
Alignment explanation
Indices: 342547--342607 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
342537 ACATTTTATA
342547 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
342570 CGCCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
342593 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
342608 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:343574 original size:60 final size:60
Alignment explanation
Indices: 343502--343615 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
343492 AATAGTTGGT
* *
343502 TGATCATTTTGTAACTTTTAATAGTCGGGGGACTCAACAAAGCAACACCCTATAATCGAA
1 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATAATCGAA
* *
343562 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGTATCACCCTATA
1 TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATA
343616 GTCGGAGAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (60 bp):
TGATCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACCCTATAATCGAA
Found at i:349591 original size:21 final size:22
Alignment explanation
Indices: 349549--349591 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
349539 ACTGTCAATG
*
349549 AACCGGCTAAAAACCGGTTGAA
1 AACCGGCTAAAAACCGGGTGAA
349571 AACCGG-T-AAAACCGGGGTGAA
1 AACCGGCTAAAAACC-GGGTGAA
349592 CCGTCTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 7 0.37
22 6 0.32
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.12
Consensus pattern (22 bp):
AACCGGCTAAAAACCGGGTGAA
Found at i:349601 original size:30 final size:30
Alignment explanation
Indices: 349567--349624 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
349557 AAAAACCGGT
*
349567 TGAAAACCGGTAAAACCGGGGTGAACCGTC
1 TGAAAACCGGCAAAACCGGGGTGAACCGTC
**
349597 TGAAAACCGGCAAAACCGGTTTGAACCG
1 TGAAAACCGGCAAAACCGGGGTGAACCG
349625 CCAGTTCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.28, T:0.14
Consensus pattern (30 bp):
TGAAAACCGGCAAAACCGGGGTGAACCGTC
Found at i:351280 original size:16 final size:16
Alignment explanation
Indices: 351259--351292 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
351249 ACCCAAAATT
351259 ATAATGAATGTTCACA
1 ATAATGAATGTTCACA
351275 ATAATGAATGTTCACA
1 ATAATGAATGTTCACA
351291 AT
1 AT
351293 CATAACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (16 bp):
ATAATGAATGTTCACA
Found at i:357856 original size:22 final size:22
Alignment explanation
Indices: 357831--357901 Score: 133
Period size: 22 Copynumber: 3.2 Consensus size: 22
357821 TATCACTTTA
357831 GATGTTAAAGTATCTTTCGCTC
1 GATGTTAAAGTATCTTTCGCTC
357853 GATGTTAAAGTATCTTTCGCTC
1 GATGTTAAAGTATCTTTCGCTC
357875 GATGTTAAAGTATCTTTCGCTC
1 GATGTTAAAGTATCTTTCGCTC
*
357897 AATGT
1 GATGT
357902 AAATGTCTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (22 bp):
GATGTTAAAGTATCTTTCGCTC
Found at i:360596 original size:21 final size:21
Alignment explanation
Indices: 360567--360619 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
360557 ATTCTGACTA
* *
360567 TCGCATTGCGATTTTCTAAAT
1 TCGCGTTGCGATTTTCCAAAT
360588 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
360609 TCGCGTTGCGA
1 TCGCGTTGCGA
360620 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:360629 original size:21 final size:21
Alignment explanation
Indices: 360567--360629 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
360557 ATTCTGACTA
* * *
360567 TCGCATTGCGATTTTCTAAAT
1 TCGCGTTGCGATATACTAAAT
* * *
360588 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATATACTAAAT
360609 TCGCGTTGCGA-ATACGTAAAT
1 TCGCGTTGCGATATAC-TAAAT
360630 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCGTTGCGATATACTAAAT
Found at i:360902 original size:22 final size:22
Alignment explanation
Indices: 360837--360902 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
360827 GGCGACATCC
*
360837 GTCCCCATCTCCAACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
360859 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* * *
360881 GTCTCCATCTTCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
360903 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:361301 original size:20 final size:19
Alignment explanation
Indices: 361237--361292 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
361227 GCGATTCTGT
**
361237 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
361256 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-ATTTCG
361276 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
361293 TCGTGTTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:363243 original size:20 final size:20
Alignment explanation
Indices: 363218--363375 Score: 135
Period size: 20 Copynumber: 8.6 Consensus size: 20
363208 AGAATAGTTT
363218 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
363238 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
363258 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
363274 A--ATTGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** * *
363291 AAAATCACAA--C-AACA-G
1 ACTATCGCAATGCGAAAATG
* * *
363307 A--ATCGTAACGCAAAAATG
1 ACTATCGCAATGCGAAAATG
363325 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
363345 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
363365 ACTATCGCAAT
1 ACTATCGCAAT
363376 TCTCTCGTTA
Statistics
Matches: 113, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.10
16 9 0.08
17 10 0.09
18 4 0.04
19 5 0.04
20 74 0.65
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:363420 original size:20 final size:20
Alignment explanation
Indices: 363381--363469 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
363371 GCAATTCTCT
**
363381 CGTTACGATAGTCAAATTCG
1 CGTTACGATAGTCATTTTCG
*
363401 CATTACGATAGTCATTTTCG
1 CGTTACGATAGTCATTTTCG
* * *
363421 TGTTGCAATAGTCATTTTCG
1 CGTTACGATAGTCATTTTCG
* *
363441 CGTTGCGATAGTCATTTTCA
1 CGTTACGATAGTCATTTTCG
*
363461 CGTTGCGAT
1 CGTTACGAT
363470 TTTAAGTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
CGTTACGATAGTCATTTTCG
Found at i:364037 original size:21 final size:20
Alignment explanation
Indices: 363947--364044 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
363937 ACTCACCTAT
*
363947 CATCGTTCAAGAGGCCTTCC
1 CATCGTTCAAGAGGCCCTCC
**
363967 CTATCGTTCAAGAGGCCCCTAT
1 C-ATCGTTCAAGAGG-CCCTCC
** * *
363989 CATCCCTCAAAAGTTCCCTCC
1 CATCGTTCAAGAG-GCCCTCC
* *
364010 CAGCGTTCAAGAGGCCACTGC
1 CATCGTTCAAGAGGCC-CTCC
*
364031 CATCGTTGAAGAGG
1 CATCGTTCAAGAGG
364045 TCTCTCCCAA
Statistics
Matches: 57, Mismatches: 17, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
20 3 0.05
21 50 0.88
22 4 0.07
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCTCC
Found at i:364479 original size:26 final size:26
Alignment explanation
Indices: 364449--364504 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
364439 TAATTCACTA
*
364449 ATATATGTCTTTTTTTGTAAAACAGC
1 ATATATGTCTTTTTTTGTAAAACAAC
364475 ATATATGTCTTTTTTTGTAAAACAAC
1 ATATATGTCTTTTTTTGTAAAACAAC
364501 ATAT
1 ATAT
364505 TGATGCATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (26 bp):
ATATATGTCTTTTTTTGTAAAACAAC
Found at i:366107 original size:24 final size:24
Alignment explanation
Indices: 366073--366126 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
366063 CTAAAAAATC
366073 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
366097 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
366121 ATCAAA
1 ATCAAA
366127 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:366140 original size:24 final size:24
Alignment explanation
Indices: 366073--366140 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
366063 CTAAAAAATC
* * *
366073 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
366097 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
366121 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
366141 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:366993 original size:20 final size:20
Alignment explanation
Indices: 366968--367014 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
366958 AAATTCAGTA
*
366968 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
366988 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
367008 TTGCGAT
1 TTGCGAT
367015 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:367024 original size:20 final size:20
Alignment explanation
Indices: 367001--367114 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
366991 CGATAGTCAG
*
367001 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
367021 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
367041 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
* * **
367061 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
367082 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
367102 ATTCGCATTGCGA
1 ATTCGCATTGCGA
367115 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 66 0.82
21 14 0.17
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:367032 original size:40 final size:38
Alignment explanation
Indices: 366988--367114 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 38
366978 CAGAATCTCG
366988 TTGCGATAGTCAGATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCA
* * * *
367028 TTGCGATTTACGTATTCGCATTGCGATTTATGTAATCGCA
1 TTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCA
*
367068 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCGCA
367109 TTGCGA
1 TTGCGA
367115 ATTAGGAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 37 0.51
41 30 0.41
42 2 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (38 bp):
TTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCA
Found at i:367135 original size:21 final size:21
Alignment explanation
Indices: 367111--367151 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
367101 TATTCGCATT
367111 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
*
367132 GCGAATTTGGAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
367152 TGTGATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:367505 original size:36 final size:36
Alignment explanation
Indices: 367451--367707 Score: 227
Period size: 36 Copynumber: 7.4 Consensus size: 36
367441 TTTTAAAAAA
367451 TATATAATATATAGTTTTTAAAACATTTTGAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTGAAAACT
* * *
367487 TAAATAATATATAATTTTTTAAAACATTTTGAAAAAAT
1 TATATAATATAT-AGTTTTTAAAACATTTTG-AAAACT
*
367525 ATATATAATATATAGTTTTTAAAACAGTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAACATTTTGAAAACT
* *
367562 TATATAATATATAGTTTTTAAAACATTTTTAAAA-A
1 TATATAATATATAGTTTTTAAAACATTTTGAAAACT
* * *
367597 TATATTAA-A-ACA-TTTTGAAAA-A---T--ATA--
1 TATA-TAATATATAGTTTTTAAAACATTTTGAAAACT
**
367623 TATATAATATATAGTTTTTAAAACATTTT-AAAAAA
1 TATATAATATATAGTTTTTAAAACATTTTGAAAACT
* * *
367658 TATATAATATAT-GGTTTTAGAAATATTTTGAAAAAT
1 TATATAATATATAGTTTTTA-AAACATTTTGAAAACT
*
367694 AAATATAATATATA
1 -TATATAATATATA
367708 TATATATTTA
Statistics
Matches: 183, Mismatches: 20, Indels: 34
0.77 0.08 0.14
Matches are distributed among these distances:
25 3 0.02
26 5 0.03
27 4 0.02
28 8 0.04
29 2 0.01
32 2 0.01
33 10 0.05
34 8 0.04
35 25 0.14
36 51 0.28
37 33 0.18
38 21 0.11
39 11 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAACT
Found at i:367541 original size:75 final size:73
Alignment explanation
Indices: 367440--367707 Score: 262
Period size: 75 Copynumber: 3.8 Consensus size: 73
367430 ATTTTTTTCG
* * *
367440 TTTTTAAAAA-ATATATAATATATAGTTTTTAAAACATTTTGAAAACTTAAATAATATATAATTT
1 TTTTAAAAAATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTAAATAATATAT-AGTT
367504 TTTAAAACA
65 TTTAAAACA
*
367513 TTTTGAAAAAATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTATATAATATATAGTT
1 TTTT-AAAAAATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTAAATAATATATAGTT
367578 TTTAAAACA
65 TTTAAAACA
* * * * *
367587 TTTTTAAAAATATAT-TAA-A-ACA-TTTTGAAAA-A---T--ATA--TATATAATATATAGTTT
1 TTTTAAAAAATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTAAATAATATATAGTTT
367640 TTAAAACA
66 TTAAAACA
* * * * *
367648 TTTT-AAAAA-ATATATAATATAT-GGTTTTAGAAATATTTTGAAAAATAAATATAATATATA
1 TTTTAAAAAATATATATAATATATAGTTTTTA-AAACAGTTTGAAAACTTAA-ATAATATATA
367708 TATATATTTA
Statistics
Matches: 165, Mismatches: 14, Indels: 33
0.78 0.07 0.16
Matches are distributed among these distances:
59 4 0.02
60 8 0.05
61 30 0.18
62 5 0.03
63 5 0.03
64 1 0.01
65 1 0.01
67 1 0.01
68 1 0.01
69 10 0.06
70 2 0.01
71 2 0.01
72 13 0.08
73 14 0.08
74 21 0.13
75 47 0.28
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (73 bp):
TTTTAAAAAATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTAAATAATATATAGTTT
TTAAAACA
Found at i:367592 original size:11 final size:11
Alignment explanation
Indices: 367576--367617 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
367566 TAATATATAG
367576 TTTTTAAAACA
1 TTTTTAAAACA
367587 TTTTTAAAA-A
1 TTTTTAAAACA
*
367597 TATATTAAAACA
1 T-TTTTAAAACA
*
367609 TTTTGAAAA
1 TTTTTAAAA
367618 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (11 bp):
TTTTTAAAACA
Found at i:367605 original size:22 final size:22
Alignment explanation
Indices: 367579--367623 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
367569 TATATAGTTT
*
367579 TTAAAACATTTTTAAAAATATA
1 TTAAAACATTTTGAAAAATATA
367601 TTAAAACATTTTGAAAAATATA
1 TTAAAACATTTTGAAAAATATA
367623 T
1 T
367624 ATATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAACATTTTGAAAAATATA
Found at i:367615 original size:96 final size:96
Alignment explanation
Indices: 367505--367694 Score: 294
Period size: 96 Copynumber: 2.0 Consensus size: 96
367495 ATATAATTTT
**
367505 TTAAAACATTTTGAAAAA-ATATATATAATATATAGTTTTTAAAACAGTTTGAAAACTTATATAA
1 TTAAAACATTTTGAAAAATATATATATAATATATAGTTTTTAAAACA-TTTGAAAAAATATATAA
* *
367569 TATATAGTTTTTA-AAACATTTTTAAAAATATA
65 TATAT-GGTTTTAGAAACATTTTGAAAAATATA
*
367601 TTAAAACATTTTGAAAAATATATATATAATATATAGTTTTTAAAACATTTTAAAAAATATATAAT
1 TTAAAACATTTTGAAAAATATATATATAATATATAGTTTTTAAAACATTTGAAAAAATATATAAT
*
367666 ATATGGTTTTAGAAATATTTTGAAAAATA
66 ATATGGTTTTAGAAACATTTTGAAAAATA
367695 AATATAATAT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
95 6 0.07
96 52 0.60
97 28 0.33
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (96 bp):
TTAAAACATTTTGAAAAATATATATATAATATATAGTTTTTAAAACATTTGAAAAAATATATAAT
ATATGGTTTTAGAAACATTTTGAAAAATATA
Found at i:367635 original size:35 final size:35
Alignment explanation
Indices: 367596--367708 Score: 108
Period size: 35 Copynumber: 3.2 Consensus size: 35
367586 ATTTTTAAAA
367596 ATATATTAAAACATTTTGAAAAATATATATATAAT
1 ATATATTAAAACATTTTGAAAAATATATATATAAT
*
367631 ATATAGTTTTTAAAACATTTTAAAAAATATATA-AT-AT
1 ATATA----TTAAAACATTTTGAAAAATATATATATAAT
* * *
367668 ATGGTTTTAGAAATATTTTGAAAAATA-A-ATATAAT
1 AT-ATATTA-AAACATTTTGAAAAATATATATATAAT
367703 ATATAT
1 ATATAT
367709 ATATATTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
33 1 0.02
34 8 0.13
35 24 0.38
37 4 0.06
38 3 0.05
39 23 0.37
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (35 bp):
ATATATTAAAACATTTTGAAAAATATATATATAAT
Found at i:367774 original size:3 final size:3
Alignment explanation
Indices: 367722--367755 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
367712 TATTTATTTA
367722 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
367756 CTGTTTTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:370994 original size:24 final size:22
Alignment explanation
Indices: 370941--370983 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
370931 ACTGCCAACG
*
370941 TGATATTTTTTTAATGATGACA
1 TGATATTATTTTAATGATGACA
*
370963 TGACATTATTTT-ATGATGACA
1 TGATATTATTTTAATGATGACA
370984 CATTGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (22 bp):
TGATATTATTTTAATGATGACA
Found at i:378852 original size:22 final size:21
Alignment explanation
Indices: 378819--378861 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
378809 GATTACAAGA
*
378819 TATAAGCCATGTGATGTGAAT
1 TATAAGCCATGTGATATGAAT
*
378840 TATATGCCTATGTGATATGAAT
1 TATAAGCC-ATGTGATATGAAT
378862 ATGTGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (21 bp):
TATAAGCCATGTGATATGAAT
Found at i:379946 original size:22 final size:22
Alignment explanation
Indices: 379908--379956 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
379898 GATATGATAA
*
379908 TATAAGGAGTATGTTGTCT-TGT
1 TATAAGGAATATGTTGT-TATGT
379930 TATAA-GAATATGATTGTTATGT
1 TATAAGGAATATG-TTGTTATGT
379952 TATAA
1 TATAA
379957 TAGAAGTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (22 bp):
TATAAGGAATATGTTGTTATGT
Found at i:383164 original size:23 final size:23
Alignment explanation
Indices: 383118--383166 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
383108 TCGAAGGTTC
* *
383118 TATGTGGTCCTTCAGCACATTTT
1 TATGTGGTCCTTCAGAACAATTT
* *
383141 TATGTGGTTCTTCGGAACAATTT
1 TATGTGGTCCTTCAGAACAATTT
383164 TAT
1 TAT
383167 ATGCTCCTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (23 bp):
TATGTGGTCCTTCAGAACAATTT
Found at i:386051 original size:39 final size:39
Alignment explanation
Indices: 385992--386078 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
385982 GTATGAGGGT
385992 TGTCTGATGTTATGTGGGCCAGACACCATGTCACTCTAC
1 TGTCTGATGTTATGTGGGCCAGACACCATGTCACTCTAC
* * *
386031 TGTCGGATGTTATGTGGGCCAGACGCCATGTCACTTTAC
1 TGTCTGATGTTATGTGGGCCAGACACCATGTCACTCTAC
386070 TGTCTGATG
1 TGTCTGATG
386079 CCCTGTGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.32
Consensus pattern (39 bp):
TGTCTGATGTTATGTGGGCCAGACACCATGTCACTCTAC
Found at i:386086 original size:39 final size:39
Alignment explanation
Indices: 386003--386096 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
385993 GTCTGATGTT
**
386003 ATGTGGGCCAGACACCATGTCACTCTACTGTCGGATGTT
1 ATGTGGGCCAGACACCATGTCACTCTACTGTCGGATGCC
* * *
386042 ATGTGGGCCAGACGCCATGTCACTTTACTGTCTGATGCC
1 ATGTGGGCCAGACACCATGTCACTCTACTGTCGGATGCC
* **
386081 CTGTGGATCAGACACC
1 ATGTGGGCCAGACACC
386097 TTGTTGTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.27
Consensus pattern (39 bp):
ATGTGGGCCAGACACCATGTCACTCTACTGTCGGATGCC
Found at i:387200 original size:15 final size:15
Alignment explanation
Indices: 387179--387213 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
387169 TAATAGAAAC
387179 ATTATCTTTCAAGTA
1 ATTATCTTTCAAGTA
*
387194 GTTATCTTTCAAGTA
1 ATTATCTTTCAAGTA
387209 ATTAT
1 ATTAT
387214 AACTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (15 bp):
ATTATCTTTCAAGTA
Found at i:387962 original size:110 final size:110
Alignment explanation
Indices: 387824--388043 Score: 368
Period size: 110 Copynumber: 2.0 Consensus size: 110
387814 AAACAATTTA
* * *
387824 CAAGCAAATTTATTTAATTTTACTTGTTTTTATGATTTAATTTTTTCGATAATTGTTATTAGAGA
1 CAAGAAAATTTATTGAATTTTACATGTTTTTATGATTTAATTTTTTCGATAATTGTTATTAGAGA
* * * *
387889 CCTAATTTCTGTGTTCTTCTTAGGCTAGTAAAATCTCAGAAGCGG
66 CCTAATTTCTATATTCTCCTCAGGCTAGTAAAATCTCAGAAGCGG
*
387934 CAAGAAAATTTATTGAATTTTACATGTTTTTATGATTTAATTTTTTTGATAATTGTTATTAGAGA
1 CAAGAAAATTTATTGAATTTTACATGTTTTTATGATTTAATTTTTTCGATAATTGTTATTAGAGA
387999 CCTAATTTCTATATTCTCCTCAGGCTAGTAAAATCTCAGAAGCGG
66 CCTAATTTCTATATTCTCCTCAGGCTAGTAAAATCTCAGAAGCGG
388044 GCCTGAAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (110 bp):
CAAGAAAATTTATTGAATTTTACATGTTTTTATGATTTAATTTTTTCGATAATTGTTATTAGAGA
CCTAATTTCTATATTCTCCTCAGGCTAGTAAAATCTCAGAAGCGG
Found at i:392639 original size:2 final size:2
Alignment explanation
Indices: 392632--392658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
392622 TACATCATAA
392632 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 A
392659 AAGTCAACAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:393277 original size:2 final size:2
Alignment explanation
Indices: 393235--393259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
393225 CTTTATACCA
393235 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
393260 AGTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:394297 original size:31 final size:32
Alignment explanation
Indices: 394221--394297 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
394211 TTGGGGCTTG
* * *
394221 AGAGCCTACCCAAGACAATTATCGGGGCCACCT
1 AGAGTCTACCCAAGAAAAATATCGGGGCCA-CT
* *
394254 AGACT-TACCCAAGAAAAATCTCGGGGCCA-T
1 AGAGTCTACCCAAGAAAAATATCGGGGCCACT
394284 AGAGTCTACCCAAG
1 AGAGTCTACCCAAG
394298 GGTCGCCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 5 0.14
31 8 0.22
32 21 0.57
33 3 0.08
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.16
Consensus pattern (32 bp):
AGAGTCTACCCAAGAAAAATATCGGGGCCACT
Found at i:404917 original size:11 final size:10
Alignment explanation
Indices: 404903--404952 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
404893 TTTTTTTTGT
404903 TTTTTTATATA
1 TTTTTTAT-TA
*
404914 TTTTCTATTA
1 TTTTTTATTA
404924 TTTTATTATTA
1 TTTT-TTATTA
404935 TTTTTTGATTAA
1 TTTTTT-ATT-A
404947 TTTTTT
1 TTTTTT
404953 TGTAATTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 8 0.24
11 19 0.56
12 7 0.21
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:404945 original size:22 final size:20
Alignment explanation
Indices: 404895--404950 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
404885 TATGACACTT
*
404895 TTTTTTG-TTTTTTTATATA
1 TTTTTTGATTATTTTATATA
*
404914 TTTTCT-ATTATTTTATTATTA
1 TTTTTTGATTATTTTA-TA-TA
404935 TTTTTTGATTAATTTT
1 TTTTTTGATT-ATTTT
404951 TTTGTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 12 0.41
20 2 0.07
21 7 0.24
22 3 0.10
23 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTTGATTATTTTATATA
Found at i:410581 original size:17 final size:16
Alignment explanation
Indices: 410551--410610 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 16
410541 ATTAGGGATT
410551 TATATATATA-TA-TA
1 TATATATATATTATTA
410565 TATATA-ATATTATTA
1 TATATATATATTATTA
*
410580 TATATTTA-ATTATTA
1 TATATATATATTATTA
410595 -ATA-ATATATTATTA
1 TATATATATATTATTA
410609 TA
1 TA
410611 AATTTGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.13
14 18 0.46
15 15 0.38
16 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATATATTATTA
Found at i:410601 original size:19 final size:17
Alignment explanation
Indices: 410548--410604 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
410538 CCGATTAGGG
410548 ATTT-ATATATATATATAT
1 ATTTAATAT-TATA-ATAT
* *
410566 ATATAATATTATTATAT
1 ATTTAATATTATAATAT
410583 ATTTAATTATTAATAATAT
1 ATTTAA-TATT-ATAATAT
410602 ATT
1 ATT
410605 ATTATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 9 0.28
18 10 0.31
19 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTAATATTATAATAT
Found at i:412468 original size:13 final size:13
Alignment explanation
Indices: 412450--412494 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
412440 TGACCCAGTT
412450 TTGACCCGACCCG
1 TTGACCCGACCCG
*
412463 TTGACCC-AGCCTG
1 TTGACCCGA-CCCG
*
412476 TTGACCTGACCCG
1 TTGACCCGACCCG
412489 TTGACC
1 TTGACC
412495 GTTGACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 1 0.04
13 25 0.93
14 1 0.04
ACGTcount: A:0.16, C:0.40, G:0.22, T:0.22
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:412507 original size:26 final size:25
Alignment explanation
Indices: 412439--412494 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
412429 TTGGGGCAAT
*
412439 TTGACCCAG-TTTTGACCCGACCCG
1 TTGACCCAGACTTTGACCCGACCCG
* *
412463 TTGACCCAGCCTGTTGACCTGACCCG
1 TTGACCCAGACT-TTGACCCGACCCG
412489 TTGACC
1 TTGACC
412495 GTTGACTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.32
25 1 0.04
26 18 0.64
ACGTcount: A:0.16, C:0.38, G:0.21, T:0.25
Consensus pattern (25 bp):
TTGACCCAGACTTTGACCCGACCCG
Found at i:415547 original size:25 final size:26
Alignment explanation
Indices: 415512--415569 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
415502 TTGTATTTTG
415512 TTTTATATCTG-AGT-CTGA-AAATCTA
1 TTTTATATCTGTA-TACTGATAAATC-A
*
415537 TTTTATTTCTGTATACTGATAAATCA
1 TTTTATATCTGTATACTGATAAATCA
415563 TTTTATA
1 TTTTATA
415570 AGTTTACATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 11 0.39
26 12 0.43
27 5 0.18
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (26 bp):
TTTTATATCTGTATACTGATAAATCA
Found at i:417160 original size:36 final size:36
Alignment explanation
Indices: 417090--417265 Score: 198
Period size: 36 Copynumber: 5.0 Consensus size: 36
417080 AAAGATGAAC
* * *
417090 ACTTGAATCGAAAGTG-CGACGCCTCATTCTGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
*
417125 ACTTGAATCGAAAGAGTCGATGCTTCATTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* * * *
417161 ACTTGAATCGAAAGTGCCGATGTTTCCTTCCTTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* * *
417197 ACTTGAATCGAAAGTGTTGATGCTTCCTTCTGTTC-
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* *
417232 ACTTGAATCG-AAGTG-CTGATGCTTCCTTTCGTTC
1 ACTTGAATCGAAAGTGTC-GATGCTTCATTCCGTTC
417266 TTCTTATTCA
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
34 20 0.16
35 25 0.20
36 77 0.63
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
Found at i:417238 original size:71 final size:71
Alignment explanation
Indices: 417089--417259 Score: 222
Period size: 72 Copynumber: 2.4 Consensus size: 71
417079 AAAAGATGAA
* * *
417089 CACTTGAATCGAAAGTG-CGACGCCTCATTCTGTTCGACTTGAATCGAAAGAGTCGATGCTTCAT
1 CACTTGAATCGAAAGTGCCGATGCTTCCTTCTGTTCGACTTGAATCGAAAGAGTCGATGCTTCAT
417153 TCCGTT
66 TCCGTT
* * *
417159 CGACTTGAATCGAAAGTGCCGATGTTTCCTTCCT-TTCGACTTGAATCGAAAGTGTTGATGCTTC
1 C-ACTTGAATCGAAAGTGCCGATGCTTCCTT-CTGTTCGACTTGAATCGAAAGAGTCGATGCTTC
* *
417223 CTTCTGTT
64 ATTCCGTT
*
417231 CACTTGAATCG-AAGTGCTGATGCTTCCTT
1 CACTTGAATCGAAAGTGCCGATGCTTCCTT
417260 TCGTTCTTCT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
70 17 0.19
71 26 0.30
72 43 0.49
73 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (71 bp):
CACTTGAATCGAAAGTGCCGATGCTTCCTTCTGTTCGACTTGAATCGAAAGAGTCGATGCTTCAT
TCCGTT
Found at i:417912 original size:15 final size:13
Alignment explanation
Indices: 417881--417911 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
417871 CATCATTGTT
417881 ACACAATCCATTG
1 ACACAATCCATTG
417894 ACACAATCCATTG
1 ACACAATCCATTG
*
417907 GCACA
1 ACACA
417912 CCTAAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.32, G:0.10, T:0.19
Consensus pattern (13 bp):
ACACAATCCATTG
Found at i:418655 original size:17 final size:17
Alignment explanation
Indices: 418632--418676 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
418622 TAAATTAAAA
418632 ATATATATATATAATATT
1 ATATATATATATAAT-TT
418650 -TATATAT-T-TAATTT
1 ATATATATATATAATTT
*
418664 AAATATATATATA
1 ATATATATATATA
418677 CCCAGCCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.09
15 10 0.43
16 2 0.09
17 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATATAATTT
Found at i:420040 original size:15 final size:16
Alignment explanation
Indices: 420011--420040 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
420001 ATATAAATCT
420011 TTTAAAACAATAATTG
1 TTTAAAACAATAATTG
420027 TTTAAAAC-ATAATT
1 TTTAAAACAATAATT
420041 TCAAAACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAAACAATAATTG
Found at i:427531 original size:15 final size:15
Alignment explanation
Indices: 427495--427541 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
427485 TTTCTGCCTA
* * *
427495 TTTACTTTTCAGTAG
1 TTTAATTTTCAGAAT
427510 TTT-ATTTTCAGAAT
1 TTTAATTTTCAGAAT
427524 TTTAATTTTCAGCAAT
1 TTTAATTTTCAG-AAT
427540 TT
1 TT
427542 ATCTTTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 11 0.41
15 11 0.41
16 5 0.19
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (15 bp):
TTTAATTTTCAGAAT
Found at i:427792 original size:2 final size:2
Alignment explanation
Indices: 427712--427775 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
427702 ACTAATTTGT
427712 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
427754 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
427776 CACACACAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:433196 original size:27 final size:27
Alignment explanation
Indices: 433164--433225 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
433154 AGGTACTTTA
*
433164 GGTCATTTTACACTTTAGGGGCATTTT
1 GGTCATTTTACACTTCAGGGGCATTTT
*
433191 GGTCATTTTATACTTCAGGGGCATTTT
1 GGTCATTTTACACTTCAGGGGCATTTT
433218 GGTCATTT
1 GGTCATTT
433226 CCTTCATTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.45
Consensus pattern (27 bp):
GGTCATTTTACACTTCAGGGGCATTTT
Found at i:433752 original size:21 final size:21
Alignment explanation
Indices: 433701--433753 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
433691 ATTATTACTA
433701 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
433722 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
433743 TCGCAATGCGA
1 TCGCAATGCGA
433754 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:433768 original size:20 final size:21
Alignment explanation
Indices: 433743--433794 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
433733 TTTTCCCAAT
*
433743 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
433763 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
433784 TCGCAATGCGA
1 TCGCAATGCGA
433795 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:433773 original size:41 final size:41
Alignment explanation
Indices: 433728--433959 Score: 123
Period size: 41 Copynumber: 5.7 Consensus size: 41
433718 AATTTCGCGT
*
433728 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
433769 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
433810 CGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * *
433851 TGCGATTTTCATAATTCGTAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
433892 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
433933 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
433960 CTGACTATCG
Statistics
Matches: 142, Mismatches: 42, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
39 2 0.01
40 25 0.18
41 113 0.80
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:433838 original size:21 final size:21
Alignment explanation
Indices: 433814--433868 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
433804 TCGCAACGCA
*
433814 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
433835 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
433855 ATTTTCATAATTCG
1 ATTTTCATAATTCG
433869 TAATGCGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:433958 original size:20 final size:20
Alignment explanation
Indices: 433870--433959 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
433860 CATAATTCGT
433870 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
* * *
433890 AACGCGATTAAGTAAATCGC
1 AATGCGAATACGTAAATCGC
* *
433910 AATGCGAATTAGGAAAATCGC
1 AATGCGAA-TACGTAAATCGC
433931 AATGCGAATACGTAAATCGC
1 AATGCGAATACGTAAATCGC
433951 AATGCGAAT
1 AATGCGAAT
433960 CTGACTATCG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
20 42 0.70
21 18 0.30
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGC
Found at i:434568 original size:19 final size:19
Alignment explanation
Indices: 434544--434591 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
434534 GCAACGAGAG
*
434544 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
434563 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
434582 AATTGCAACG
1 AATCGCAACG
434592 AGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:434591 original size:52 final size:53
Alignment explanation
Indices: 434504--434621 Score: 157
Period size: 52 Copynumber: 2.2 Consensus size: 53
434494 TAGTTTCGAG
* * **
434504 AATGACAATCGCAACGCGGAAATGATTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAGAGAATCGCAACGCGA
* *
434557 AATGAAAATCGCAACGC-GAAATAAAAATTGCAACGAGATAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAGAGAATCGCAACGCGA
**
434609 AACCAAAATCGCA
1 AATGAAAATCGCA
434622 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 41 0.72
53 16 0.28
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (53 bp):
AATGAAAATCGCAACGCGGAAATAAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:434700 original size:52 final size:52
Alignment explanation
Indices: 434617--434754 Score: 213
Period size: 52 Copynumber: 2.6 Consensus size: 52
434607 GAAACCAAAA
* **
434617 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
434669 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
* *
434721 TCCGCGTTGTGATTTTCATTCTCTCGTTGCGATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATT
434755 TTCATTTCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 50 0.63
53 17 0.22
54 12 0.15
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:434739 original size:20 final size:19
Alignment explanation
Indices: 434617--434762 Score: 141
Period size: 19 Copynumber: 8.1 Consensus size: 19
434607 GAAACCAAAA
*
434617 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
434636 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
434650 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
434669 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
434688 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
434702 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
434721 TCCGCGTTGTGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
434741 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
434761 TC
1 TC
434763 AACTAAAAGA
Statistics
Matches: 104, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.19
16 5 0.05
17 6 0.06
19 42 0.40
20 30 0.29
21 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:436666 original size:92 final size:94
Alignment explanation
Indices: 436455--436757 Score: 485
Period size: 92 Copynumber: 3.3 Consensus size: 94
436445 TAGATTGCTT
* * *
436455 AGTAAATTTATTCGGTTGCTGCCAATACTACTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
436516 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
436545 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
436610 ATTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
436638 AGTAAA-TTGTTCGGTTGCTGCTAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
436702 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
436731 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
436758 GAAACTATTC
Statistics
Matches: 199, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
90 34 0.17
92 85 0.43
93 36 0.18
94 44 0.22
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:437226 original size:21 final size:20
Alignment explanation
Indices: 437202--437268 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
437192 TCATTCCTCG
437202 AGAGTTCCCTCCCACCGTTCA
1 AGAG-TCCCTCCCACCGTTCA
* ** * *
437223 AGAGGCCACTATCATCGTTGA
1 AGAGTCC-CTCCCACCGTTCA
*
437244 AGAGGTCCCTCCCACCATTCA
1 AGA-GTCCCTCCCACCGTTCA
437265 AGAG
1 AGAG
437269 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 11, Indels: 5
0.67 0.22 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.21
Consensus pattern (20 bp):
AGAGTCCCTCCCACCGTTCA
Found at i:437227 original size:42 final size:42
Alignment explanation
Indices: 437150--437268 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
437140 GACTTGCCTG
* * * *
437150 TCATCCCTC-AAGA-GTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
437192 TCATTCCTCG-AGAGTTCCCTCCCACCGTTCAAGAGGCCACTA
1 TCA-TCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
* * *
437234 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAG
437269 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 4 0.06
42 56 0.88
43 4 0.06
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:438640 original size:14 final size:14
Alignment explanation
Indices: 438621--438656 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
438611 ATTGTTTAAT
438621 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
438635 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
438649 TGATTTGT
1 TGATTTGT
438657 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:438838 original size:19 final size:19
Alignment explanation
Indices: 438763--438828 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
438753 AAAAATGACT
*
438763 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
438782 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
438796 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
438815 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
438829 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:438882 original size:33 final size:33
Alignment explanation
Indices: 438840--438964 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 33
438830 TAAATTCGCG
* * *
438840 TTGCGATTTTCATTTTGCTTTGCGATTCCCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
* *
438873 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
* ** *
438906 TTGCAATTTTCATTTCGCATTATGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
438939 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
438965 AGTCATTTCC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
Done.