Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000887.1 Hibiscus syriacus cultivar Beakdansim tig00001732_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: 662576
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:212690 original size:22 final size:22
Alignment explanation
Indices: 212665--212719 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
212655 AATAAAGCTT
212665 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
212687 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
212709 TCATCTTTGAA
1 TCATCTTTGAA
212720 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:217303 original size:19 final size:20
Alignment explanation
Indices: 217279--217326 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
217269 GACTGCCAAT
217279 TTTTTTTTCT-CTTTTTTCC
1 TTTTTTTTCTCCTTTTTTCC
*
217298 TTTTTTTTTTCCTTTTTTCC
1 TTTTTTTTCTCCTTTTTTCC
217318 TTTTGTTTT
1 TTTT-TTTT
217327 TTTTTTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTTTTCTCCTTTTTTCC
Found at i:217303 original size:20 final size:20
Alignment explanation
Indices: 217278--217328 Score: 84
Period size: 21 Copynumber: 2.5 Consensus size: 20
217268 AGACTGCCAA
217278 TTTTTTTTTCTCTTTTTTCCT
1 TTTTTTTTTC-CTTTTTTCCT
217299 TTTTTTTTTCCTTTTTTCCT
1 TTTTTTTTTCCTTTTTTCCT
217319 TTTGTTTTTT
1 TTT-TTTTTT
217329 TTTTCAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTCCTTTTTTCCT
Found at i:217326 original size:12 final size:12
Alignment explanation
Indices: 217290--217333 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
217280 TTTTTTTCTC
217290 TTTTTTCCTTTT
1 TTTTTTCCTTTT
217302 TTTTTTCCTTTT
1 TTTTTTCCTTTT
*
217314 TTCCTTTT-GTTTT
1 TT--TTTTCCTTTT
217327 TTTTTTC
1 TTTTTTC
217334 AAGTATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 4 0.14
12 14 0.50
13 6 0.21
14 4 0.14
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (12 bp):
TTTTTTCCTTTT
Found at i:222642 original size:2 final size:2
Alignment explanation
Indices: 222635--222676 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
222625 AATTTAAAGA
222635 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
222677 TTAAATAACA
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:222805 original size:114 final size:115
Alignment explanation
Indices: 222686--222892 Score: 317
Period size: 114 Copynumber: 1.8 Consensus size: 115
222676 TTTAAATAAC
* * * **
222686 ATATTTATTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTATTTTAAGACAGCTCTTTCTTTTG
1 ATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTATTTTAAGACAGCTCTTTCCTTCA
222751 ATATTAAAAAATAAATAAATAA-TAAAAAAAATTATTTTAATATAGTAAG
66 ATATTAAAAAATAAATAAATAACTAAAAAAAATTATTTTAATATAGTAAG
* * * *
222800 ATATTTATTTATTTAAAAATATTAGAAAATAGCTTCTAGTTGTTTTAAGACAGCTCTTTCCTTCA
1 ATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTATTTTAAGACAGCTCTTTCCTTCA
*
222865 ATATTTAAAAATAAATAAATAACTAAAA
66 ATATTAAAAAATAAATAAATAACTAAAA
222893 CATAATAATA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 77 0.94
115 5 0.06
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (115 bp):
ATATTTATTTATTTAAAAATATCAGAAAAGAGCTTCTAGGTATTTTAAGACAGCTCTTTCCTTCA
ATATTAAAAAATAAATAAATAACTAAAAAAAATTATTTTAATATAGTAAG
Found at i:224375 original size:14 final size:14
Alignment explanation
Indices: 224356--224405 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
224346 ATTAATTATT
224356 TAATAAATATAATA
1 TAATAAATATAATA
*
224370 TAAT-AATAATATTA
1 TAATAAAT-ATAATA
*
224384 AAATAAA-ATAATAA
1 TAATAAATATAAT-A
224398 TAATAAAT
1 TAATAAAT
224406 GAAACAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 7 0.25
14 19 0.68
15 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAAATATAATA
Found at i:224377 original size:3 final size:3
Alignment explanation
Indices: 224364--224403 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
224354 TTTAATAAAT
*
224364 ATA AT- ATA ATA ATA ATA TTA A-A ATA A-A ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
224404 ATGAAACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:224378 original size:11 final size:11
Alignment explanation
Indices: 224356--224402 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
224346 ATTAATTATT
224356 TAATA-AAT-A
1 TAATATAATAA
224365 TAATATAATAA
1 TAATATAATAA
224376 TAATATTAA-AA
1 TAATA-TAATAA
*
224387 TAAAATAATAA
1 TAATATAATAA
224398 TAATA
1 TAATA
224403 AATGAAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 5 0.16
10 6 0.19
11 18 0.56
12 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAATAA
Found at i:224389 original size:22 final size:23
Alignment explanation
Indices: 224359--224402 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
224349 AATTATTTAA
*
224359 TAAATATAATATAATAATAATAT
1 TAAATATAAAATAATAATAATAT
224382 TAAA-ATAAAATAATAATAATA
1 TAAATATAAAATAATAATAATA
224403 AATGAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TAAATATAAAATAATAATAATAT
Found at i:224393 original size:19 final size:19
Alignment explanation
Indices: 224356--224404 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
224346 ATTAATTATT
* *
224356 TAATAAATATAATATAATAA
1 TAAT-AATAAAATAAAATAA
*
224376 TAATATTAAAATAAAATAA
1 TAATAATAAAATAAAATAA
224395 TAATAATAAA
1 TAATAATAAA
224405 TGAAACAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAAAATAAAATAA
Found at i:226979 original size:29 final size:29
Alignment explanation
Indices: 226903--226979 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
226893 CTTCCCAGCA
*
226903 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
* *
226932 TAAGTCGTCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
226961 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
226980 CCTGCTCCTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:253013 original size:5 final size:5
Alignment explanation
Indices: 253003--253027 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
252993 CCACCGGATA
253003 TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC
253028 ACGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:254806 original size:31 final size:31
Alignment explanation
Indices: 254770--254828 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
254760 AACTTAAAAG
*
254770 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
254801 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
254829 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:254877 original size:22 final size:22
Alignment explanation
Indices: 254852--255193 Score: 490
Period size: 22 Copynumber: 15.6 Consensus size: 22
254842 ATAATAAATT
254852 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
254874 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** * *
254896 ATTTAAAATAAATTTTTTCACA
1 TTTTAAAATAAATCAATCCATA
*
254918 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
254940 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
254962 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
254984 TTTTAAAATAAAT-TTTCCCGTA
1 TTTTAAAATAAATCAAT-CCATA
255006 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
255028 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
255050 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
255072 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
255094 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
255116 TTTTAAAATAAA-AAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** **
255137 TTTTAAAATAAATTTTTCTTTA
1 TTTTAAAATAAATCAATCCATA
*
255159 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
255181 TTTTAAAATAAAT
1 TTTTAAAATAAAT
255194 TTTAAAATAG
Statistics
Matches: 285, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
21 20 0.07
22 264 0.93
23 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:255210 original size:11 final size:12
Alignment explanation
Indices: 255180--255219 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
255170 ATCAATCTAT
255180 ATTTTAAAATAA
1 ATTTTAAAATAA
*
255192 ATTTTAAAATAG
1 ATTTTAAAATAA
255204 A-TTT-AAAT-A
1 ATTTTAAAATAA
255213 ATTTTAA
1 ATTTTAA
255220 TTTCTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:255811 original size:21 final size:21
Alignment explanation
Indices: 255773--255812 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
255763 AAAAAATTAT
* *
255773 CTAAAATATTATTATTTTTAC
1 CTAAAACATTAATATTTTTAC
*
255794 CTAAAACATTAATGTTTTT
1 CTAAAACATTAATATTTTT
255813 TAACATTTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTAC
Found at i:256370 original size:165 final size:165
Alignment explanation
Indices: 256098--256427 Score: 482
Period size: 165 Copynumber: 2.0 Consensus size: 165
256088 ATGTTATGCC
* * * **
256098 TCGATAATGTTCATATTTCGTTGATTGAACTCCGTCCGAAAAAAGAACAGAGCATTCATCAGCTT
1 TCGATAATGTTCATATTTCGTCGATCGAACTCCGTCCGAAAAAAGAACAGAGCATTCATCAACGC
* *
256163 AAGATGACATTGAGAGATCTGCATAAGCGAATGATTCTATATCTTCAACAATCTGGTCTATATCC
66 AAAATGACATCGAGAGATCTGCATAAGCGAATGATTCTATATCTTCAACAATCTGGTCTATATCC
256228 AACCATATTTGTACGTGGCTTTAAGGTGTACCCGA
131 AACCATATTTGTACGTGGCTTTAAGGTGTACCCGA
* * * * *
256263 TCGATAATGTTCATATCTT-GTCGATCGAACTCTGTCCGGAAGAAGAACATAGCATTCGTCAACG
1 TCGATAATGTTCATAT-TTCGTCGATCGAACTCCGTCCGAAAAAAGAACAGAGCATTCATCAACG
* ** * *
256327 CAAAATGACATCGAGAGATTTGCATAAGCGGGTGATTCTATATCTTCAGCAATCTGGTCTATATT
65 CAAAATGACATCGAGAGATCTGCATAAGCGAATGATTCTATATCTTCAACAATCTGGTCTATATC
*
256392 CAACCATATTTGTATGTGGCTTTAAGGTGTACCCGA
130 CAACCATATTTGTACGTGGCTTTAAGGTGTACCCGA
256428 CGTTGATTTC
Statistics
Matches: 146, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
165 144 0.99
166 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (165 bp):
TCGATAATGTTCATATTTCGTCGATCGAACTCCGTCCGAAAAAAGAACAGAGCATTCATCAACGC
AAAATGACATCGAGAGATCTGCATAAGCGAATGATTCTATATCTTCAACAATCTGGTCTATATCC
AACCATATTTGTACGTGGCTTTAAGGTGTACCCGA
Found at i:261710 original size:8 final size:8
Alignment explanation
Indices: 261700--261741 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
261690 TAAAAGTTAG
*
261700 TAAAATAG
1 TAAAATAA
261708 TAAAATAA
1 TAAAATAA
261716 TAAAATAA
1 TAAAATAA
261724 TAAAATAAAA
1 TAAAAT--AA
261734 TAAAATAA
1 TAAAATAA
261742 AAGGACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 23 0.74
10 8 0.26
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (8 bp):
TAAAATAA
Found at i:261721 original size:16 final size:16
Alignment explanation
Indices: 261651--261741 Score: 60
Period size: 16 Copynumber: 5.6 Consensus size: 16
261641 AAATATTAAT
*
261651 ATAATAATAATAAAAAA
1 ATAA-AATAATAAAATA
**
261668 ATAAAATAGATACCA-A
1 ATAAAATA-ATAAAATA
* **
261684 AGAAAATAA-AAGTTA
1 ATAAAATAATAAAATA
* *
261699 GTAAAATAGTAAAATA
1 ATAAAATAATAAAATA
261715 ATAAAATAATAAAATAAA
1 ATAAAATAATAAAAT--A
261733 ATAAAATAA
1 ATAAAATAA
261742 AAGGACCAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
14 1 0.02
15 8 0.14
16 29 0.52
17 8 0.14
18 10 0.18
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.22
Consensus pattern (16 bp):
ATAAAATAATAAAATA
Found at i:261732 original size:13 final size:13
Alignment explanation
Indices: 261708--261741 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
261698 AGTAAAATAG
261708 TAAAATAATAAAA
1 TAAAATAATAAAA
261721 TAATAA-AATAAAA
1 TAA-AATAATAAAA
261734 TAAAATAA
1 TAAAATAA
261742 AAGGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.11
13 15 0.79
14 2 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:263105 original size:17 final size:18
Alignment explanation
Indices: 263073--263107 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
263063 CAGCTACCCC
263073 TCTTTGCTCTATTGTCGT
1 TCTTTGCTCTATTGTCGT
263091 TCTTTGCTC-ATTGTCGT
1 TCTTTGCTCTATTGTCGT
263108 GTAACGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.06, C:0.23, G:0.17, T:0.54
Consensus pattern (18 bp):
TCTTTGCTCTATTGTCGT
Found at i:263835 original size:106 final size:105
Alignment explanation
Indices: 263525--264050 Score: 659
Period size: 106 Copynumber: 5.0 Consensus size: 105
263515 GTATTGTTCC
* * * * *
263525 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAA
* *
263590 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTC
65 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
263631 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-AA-T-GAAA-T-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGAAATTGTTTGTTGACAAT
* *
263691 CAGCCACCCATTCG-TCGTGAAGTTGAGCTTGTGTTGTCTT
66 CAGCCGCCCCTTCGCT-GTGAAGTTGAGCTTGTGTTGTCTT
* * * * * * *
263731 GGGTCCAATATCCTTCGTTGGGAAGTTGAAATTGGCTATGAAATTAGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAA
**
263796 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTACTGTCTT
65 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
* * *
263837 GAGCCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAACTGGAAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGG-AAATTGTTTGTTGACAA
* * * *
263902 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
*
263943 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GGAAATTGTTTGTTGACAA
* * * * *
264008 ACAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCTT
65 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
264049 GA
1 GA
264051 ATGGCACGAT
Statistics
Matches: 367, Mismatches: 43, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
99 1 0.00
100 80 0.22
101 3 0.01
102 5 0.01
104 4 0.01
105 5 0.01
106 266 0.72
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGAAATTGTTTGTTGACAAT
CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:264435 original size:36 final size:36
Alignment explanation
Indices: 264387--264455 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
264377 AAAGTTTATT
* *
264387 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
1 TTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTG
*
264423 TTTCAAGGGAAACTATCTCAAGCGAGACAAAAT
1 TTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
264456 CTTCTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (36 bp):
TTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTG
Found at i:265990 original size:23 final size:22
Alignment explanation
Indices: 265959--266019 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 22
265949 TTCTTTTTGA
265959 TTTCTTTTTC-CTTTTGTTCTTG
1 TTTCTTTTTCTCTTTT-TTCTTG
265981 TTTCTCTTTTCTCTTTTTTCTT-
1 TTTCT-TTTTCTCTTTTTTCTTG
266003 TTT-TTTTTGCTTCTTTT
1 TTTCTTTTT-C-TCTTTT
266020 CTTTTTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
20 4 0.11
21 2 0.06
22 14 0.40
23 10 0.29
24 5 0.14
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTCTTTTTCTCTTTTTTCTTG
Found at i:266006 original size:7 final size:7
Alignment explanation
Indices: 265959--266026 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 7
265949 TTCTTTTTGA
265959 TTTCTTT
1 TTTCTTT
*
265966 TTCCTTT
1 TTTCTTT
265973 TGTTCTTGT
1 T-TTCTT-T
265982 TTCTCTTT
1 TT-TCTTT
*
265990 TCTCTTT
1 TTTCTTT
265997 TTTC-TT
1 TTTCTTT
266003 TTT-TTT
1 TTTCTTT
*
266009 TTGCTTCT
1 TTTCTT-T
266017 TTTCTTT
1 TTTCTTT
266024 TTT
1 TTT
266027 GTTCTTGATT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
6 9 0.18
7 21 0.43
8 13 0.27
9 6 0.12
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:266016 original size:15 final size:15
Alignment explanation
Indices: 265985--266032 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
265975 TTCTTGTTTC
*
265985 TCTTTTCTCTTTT-T
1 TCTTTTCTTTTTTGT
265999 TCTTTT-TTTTTTGCT
1 TCTTTTCTTTTTTG-T
266014 TCTTTTCTTTTTTGT
1 TCTTTTCTTTTTTGT
266029 TCTT
1 TCTT
266033 GATTGGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 12 0.40
16 7 0.23
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (15 bp):
TCTTTTCTTTTTTGT
Found at i:269087 original size:8 final size:8
Alignment explanation
Indices: 269058--269158 Score: 51
Period size: 8 Copynumber: 11.8 Consensus size: 8
269048 AAAAAGAGAC
*
269058 AAATATTA
1 AAATAATA
*
269066 ATATAATA
1 AAATAATA
269074 ATAATAATA
1 A-AATAATA
269083 AAATAA-A
1 AAATAATA
**
269090 ATAGATACCA
1 A-A-ATAATA
*
269100 AAGAAAATA
1 AA-ATAATA
*
269109 AAAGTTAGTA
1 AAA--TAATA
* *
269119 AAAGAGTA
1 AAATAATA
269127 AAATAATA
1 AAATAATA
269135 AAATAATA
1 AAATAATA
269143 AAATAAAATA
1 AAAT--AATA
269153 AAATAA
1 AAATAA
269159 AAGGACCAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
7 2 0.03
8 38 0.52
9 17 0.23
10 16 0.22
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:269149 original size:13 final size:13
Alignment explanation
Indices: 269125--269158 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
269115 AGTAAAAGAG
269125 TAAAATAATAAAA
1 TAAAATAATAAAA
269138 TAATAA-AATAAAA
1 TAA-AATAATAAAA
269151 TAAAATAA
1 TAAAATAA
269159 AAGGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.11
13 15 0.79
14 2 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:271407 original size:2 final size:2
Alignment explanation
Indices: 271400--271428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
271390 GAACATACGC
271400 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 A
271429 ACAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:271465 original size:12 final size:11
Alignment explanation
Indices: 271437--271477 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
271427 TAACAAAATA
* *
271437 AATAATATAAA
1 AATAATACAAG
271448 AATAATACAAG
1 AATAATACAAG
271459 TAATAATACAAG
1 -AATAATACAAG
271471 AATAATA
1 AATAATA
271478 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:271582 original size:12 final size:12
Alignment explanation
Indices: 271560--271604 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
271550 GAATAAAAGG
271560 AAAATATAATAGT
1 AAAA-ATAATAGT
*
271573 AAAAATAATAAT
1 AAAAATAATAGT
*
271585 AAATATAATAGT
1 AAAAATAATAGT
*
271597 AATAATAA
1 AAAAATAA
271605 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:272202 original size:37 final size:37
Alignment explanation
Indices: 272161--272265 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
272151 GTGCTTGTGG
* *
272161 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
272198 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
272235 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
272266 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:272874 original size:41 final size:42
Alignment explanation
Indices: 272776--273156 Score: 366
Period size: 41 Copynumber: 9.2 Consensus size: 42
272766 GGTTTATAGC
* * * * * *
272776 GGCGTTTTTAGAACAAACGTCGCAAAACACTTGAACTTTAAT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* *
272818 GGCGTTTTT-GGACAAACGCCGCTAAAGAAT-GTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* * * *
272858 GACGTTTTTAGAACAAATGCCGCAAAAAACTAGTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* *
272900 GGCGTTTTTA-TACAAACGCCGCCAAAGACT-GTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* * * *
272940 GGCGTGTTTATAA-AAACGCTGCTATAGACTAGTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* * *
272981 AGCTTTTTTA-TACAAACGCCGC-AATAGACTAGTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAA-AGACTAGTACTTTAGT
* * * * *
273022 GGCGTTTTTTGAACAAATGCCGCTATAGAATCGTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
* * * *
273064 GGCGTTTGTA-TACAAACGTCGTTAAAGACTCA-TAACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACT-AGT-ACTTTAGT
* * **
273106 GGCGTTTTTAGAACAAACGCCGCTATAGAGTCTTACTTTAGT
1 GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
273148 GGCGTTTTT
1 GGCGTTTTT
273157 GTTTACAGAC
Statistics
Matches: 274, Mismatches: 53, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
40 51 0.19
41 112 0.41
42 94 0.34
43 17 0.06
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (42 bp):
GGCGTTTTTAGAACAAACGCCGCTAAAGACTAGTACTTTAGT
Found at i:272884 original size:82 final size:83
Alignment explanation
Indices: 272776--273156 Score: 403
Period size: 82 Copynumber: 4.6 Consensus size: 83
272766 GGTTTATAGC
* * * * * **
272776 GGCGTTTTTAGAACAAACGTCGCAAAACACTTGAACTTTAATGGCGTTTTTGGACAAACGCCGCT
1 GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
*
272841 AAAGAAT-GTACTTTAGT
66 AAAGACTAGTACTTTAGT
* * * *
272858 GACGTTTTTAGAACAAATGCCGCAAAAAACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCC
1 GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
272923 AAAGACT-GTACTTTAGT
66 AAAGACTAGTACTTTAGT
* * * * * * *
272940 GGCGTGTTTATAA-AAACGCTGCTATAGACTAGTACTTTAGTAGCTTTTTTATACAAACGCCGC-
1 GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
273003 AATAGACTAGTACTTTAGT
66 AA-AGACTAGTACTTTAGT
* * * * * * * * *
273022 GGCGTTTTTTGAACAAATGCCGCTATAGAATCGTACTTTAGTGGCGTTTGTATACAAACGTCGTT
1 GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
273087 AAAGACTCA-TAACTTTAGT
66 AAAGACT-AGT-ACTTTAGT
* * * **
273106 GGCGTTTTTAGAACAAACGCCGCTATAGAGTCTTACTTTAGTGGCGTTTTT
1 GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTT
273157 GTTTACAGAC
Statistics
Matches: 255, Mismatches: 38, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.01
81 48 0.19
82 101 0.40
83 47 0.18
84 57 0.22
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (83 bp):
GGCGTTTTTAGAACAAACGCCGCAAAAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCT
AAAGACTAGTACTTTAGT
Found at i:273258 original size:19 final size:18
Alignment explanation
Indices: 273215--273256 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
273205 ACCCTTTTTC
*
273215 ATTTTTCTCACATCACCT
1 ATTTTTCCCACATCACCT
*
273233 ATTTTTCCCACTTCACCT
1 ATTTTTCCCACATCACCT
273251 ATTTTT
1 ATTTTT
273257 TCATTCTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTTCCCACATCACCT
Found at i:276600 original size:42 final size:42
Alignment explanation
Indices: 276538--276786 Score: 257
Period size: 42 Copynumber: 5.9 Consensus size: 42
276528 TTGTTTTAAA
*
276538 AAAAACACCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
* * * *
276580 AAAAATGCCGCTATATATCTGACATTTTACGGCGTTTGTTCG
1 AAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
** * * * * * *
276622 GGAAACACCGCTATATAACTAACATTTTACGGTGTTTGTTCC
1 AAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
** *
276664 AAAAACGCCGCTATAGATCTGACCCTTTGCGGCGTTTGTTAC
1 AAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
* * * * *
276706 AAAAATGTCGCTATAGGTATC-GACCTTTTGCTGCGTTTGTTAC
1 AAAAACGCCGCTATA-G-ATCTGACATTTTGCGGCGTTTGTTCC
* *
276749 AAAAACGCCGCTATAGATCTTGACCTATTGCGGCGTTT
1 AAAAACGCCGCTATAGATC-TGACATTTTGCGGCGTTT
276787 TTTGTTCTCA
Statistics
Matches: 171, Mismatches: 32, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
41 3 0.02
42 116 0.68
43 49 0.29
44 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
AAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTTCC
Found at i:288816 original size:340 final size:338
Alignment explanation
Indices: 288147--288825 Score: 1260
Period size: 340 Copynumber: 2.0 Consensus size: 338
288137 ATTGAAATTT
288147 TCCAAAATTTAATATATATATTATGTTTACATTAAGAGTGTTTAAACTTTGATTTTAACTAAATT
1 TCCAAAATTTAATATATATATTATGTTTACATTAAGAGTGTTTAAACTTTGATTTTAACTAAATT
288212 CACCGACCAAATTAACCAAAATTATTTAATATATAATATATTATTTATAAATTTCGGTTATCGAG
66 CACCGACCAAATTAACCAAAATTATTTAATATATAATATATTATTTATAAATTTCGGTTATCGAG
288277 CGATTAACCAAACTTAGTTTGGTTCGGTTAATTATTTTTGAAAAAAAATTCCGGTTTGATTAACA
131 CGATTAACCAAACTTAGTTTGGTTCGGTTAATTATTTTTGAAAAAAAATTCCGGTTTGATTAACA
288342 ATTAAAGAGAAAAATTTTGGTTAATGAAATTTTAGAAGTTTGCTTCGGTCGATTAAACGAACCAA
196 ATTAAAGAGAAAAATTTTGGTTAATGAAATTTTAGAAGTTTGCTTCGGTCGATTAAACGAACCAA
288407 CCGATTGAACACCCCTAACAATTATGAGTGTATTTCCTAATTTAACTCATTTTCTCATATATAAA
261 CCGATTGAACACCCCTAACAATTATGAGTGTATTTCCTAATTTAACTCATTTTCTCATATATAAA
288472 AAATA-TGTTCTC
326 AAATATTGTTCTC
288484 TCCAAAATTTAATATTATATATATTATGTTTACATTAAGAGTGTTTAAACTTTGATTTTAACTAA
1 TCCAAAATTT-A-A-TATATATATTATGTTTACATTAAGAGTGTTTAAACTTTGATTTTAACTAA
288549 ATTCACCGACCAAATTAACCAAAATTATTTAATATA-AATATATATATTTATAAATTTCGGTTAA
63 ATTCACCGACCAAATTAACCAAAATTATTTAATATATAATATAT-TATTTATAAATTTCGGTT-A
288613 TCGAGCGATTAACC-AACTTAGTTTGGTTCGGTTAATTATTTTTG-AAAAAAATTCCGGTTTGAT
126 TCGAGCGATTAACCAAACTTAGTTTGGTTCGGTTAATTATTTTTGAAAAAAAATTCCGGTTTGAT
288676 TAACAATTAAAGAGAAAAATTTTGGTTAATGAAATTTTAGAAGTTTGCTTCGGTCGATTAAACGA
191 TAACAATTAAAGAGAAAAATTTTGGTTAATGAAATTTTAGAAGTTTGCTTCGGTCGATTAAACGA
288741 ACCAACCGATTGAACACCCCTAACAATTATGAGTGTAATTTTCCTAATTTAACTCATTTTCTCAT
256 ACCAACCGATTGAACACCCCTAACAATTATGAGTGT-A-TTTCCTAATTTAACTCATTTTCTCAT
288806 ATAT-AAAAATATTGTTCTC
319 ATATAAAAAATATTGTTCTC
288825 T
1 T
288826 ATAAAGAATT
Statistics
Matches: 334, Mismatches: 0, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
337 10 0.03
338 1 0.00
339 128 0.38
340 142 0.43
341 53 0.16
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (338 bp):
TCCAAAATTTAATATATATATTATGTTTACATTAAGAGTGTTTAAACTTTGATTTTAACTAAATT
CACCGACCAAATTAACCAAAATTATTTAATATATAATATATTATTTATAAATTTCGGTTATCGAG
CGATTAACCAAACTTAGTTTGGTTCGGTTAATTATTTTTGAAAAAAAATTCCGGTTTGATTAACA
ATTAAAGAGAAAAATTTTGGTTAATGAAATTTTAGAAGTTTGCTTCGGTCGATTAAACGAACCAA
CCGATTGAACACCCCTAACAATTATGAGTGTATTTCCTAATTTAACTCATTTTCTCATATATAAA
AAATATTGTTCTC
Found at i:289419 original size:2 final size:2
Alignment explanation
Indices: 289412--289444 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
289402 CCTACTTCTT
289412 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
289445 ACTAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:291217 original size:41 final size:41
Alignment explanation
Indices: 291115--291207 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
291105 TTGTGGTAGA
291115 AAATATACTTTTTCTCTCTTTT-A-ATAGATTCTGTTATAC
1 AAATATACTTTTTCTCTCTTTTAATATAGATTCTGTTATAC
291154 AAATATACTTTTTCTCTCTTTTAATATAGATTCTGTTATAC
1 AAATATACTTTTTCTCTCTTTTAATATAGATTCTGTTATAC
291195 AAATA-ACATTTTT
1 AAATATAC-TTTTT
291208 TTACCTTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
39 22 0.43
40 3 0.06
41 26 0.51
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (41 bp):
AAATATACTTTTTCTCTCTTTTAATATAGATTCTGTTATAC
Found at i:303345 original size:96 final size:96
Alignment explanation
Indices: 303181--303567 Score: 729
Period size: 96 Copynumber: 4.0 Consensus size: 96
303171 AAGTTCTGCA
*
303181 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCATCGAGACATGAAATTGTTATCCTTC
1 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
303246 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
66 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
303277 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
1 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
*
303342 ACTGATTCTGCAGATCAGAGGTACTGGCCTG
66 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
*
303373 ATTGAGGTATCCATTTTATTCAGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
1 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
303438 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
66 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
303469 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
1 ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
* *
303534 ACTGATTCTGCACATCAGAGATACTGGCTTG
66 ACTGATTCTGCAGATCAGAGGTACTGGCTTG
303565 ATT
1 ATT
303568 CATGGTACCG
Statistics
Matches: 284, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 284 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (96 bp):
ATTGAGGTATCCATTTTATTCGGTCAATATTTAGTGAGCGTCGAGACATGAAATTGTTATCCTTC
ACTGATTCTGCAGATCAGAGGTACTGGCTTG
Found at i:305670 original size:29 final size:29
Alignment explanation
Indices: 305637--305694 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
305627 TGTCGAACTC
*
305637 AAGTGATTATA-TTAGAATTATTATTCTTT
1 AAGTGATTATAGTGA-AATTATTATTCTTT
*
305666 AAGTGATTTTAGTGAAATTATTATTCTTT
1 AAGTGATTATAGTGAAATTATTATTCTTT
305695 CTCATGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (29 bp):
AAGTGATTATAGTGAAATTATTATTCTTT
Found at i:313927 original size:25 final size:26
Alignment explanation
Indices: 313875--313927 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
313865 GATTAAGAAC
*
313875 TATCAAATGAAAGAAACAGAAAACAAA
1 TATCAAA-GAAAGAAAAAGAAAACAAA
313902 TATCAAA-AAAGAAAAAAGAAAA-AAA
1 TATCAAAGAAAG-AAAAAGAAAACAAA
313927 T
1 T
313928 TGAAGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
26 9 0.38
27 7 0.29
ACGTcount: A:0.72, C:0.08, G:0.09, T:0.11
Consensus pattern (26 bp):
TATCAAAGAAAGAAAAAGAAAACAAA
Found at i:315357 original size:2 final size:2
Alignment explanation
Indices: 315350--315379 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
315340 TAGTCTGGCC
315350 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
315380 CTTATATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:315654 original size:5 final size:5
Alignment explanation
Indices: 315645--315674 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
315635 TGGGGAACAA
*
315645 CAAAG TAAAG CAAAG CAAAG CAAAG CAAAG
1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG
315675 GCATGCGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.60, C:0.17, G:0.20, T:0.03
Consensus pattern (5 bp):
CAAAG
Found at i:315895 original size:20 final size:20
Alignment explanation
Indices: 315848--316201 Score: 305
Period size: 20 Copynumber: 17.2 Consensus size: 20
315838 AATGACCAAC
315848 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
315867 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
315887 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
315907 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
315929 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
315949 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
315971 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
315991 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
316011 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
316033 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
316053 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
316075 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
316095 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
316115 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
316135 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
316155 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
316177 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
316197 AAAAT
1 AAAAT
316202 GAGTAAATTC
Statistics
Matches: 280, Mismatches: 29, Indels: 51
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.00
19 28 0.10
20 159 0.57
21 6 0.02
22 79 0.28
23 7 0.03
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:315956 original size:42 final size:40
Alignment explanation
Indices: 315931--316193 Score: 345
Period size: 42 Copynumber: 6.4 Consensus size: 40
315921 ATCTTCCAAG
* * *
315931 AATCGCAATGCGATT-CATAAAATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-CAGAA
*
315973 AATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCAGAA
316013 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAA
316055 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAA
316097 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAA
*
316137 AATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGA--TT-CAGAA
316179 AATCGCAACGCGATT
1 AATCGCAACGCGATT
316194 AAGAAAATGA
Statistics
Matches: 209, Mismatches: 5, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
39 2 0.01
40 76 0.36
42 127 0.61
43 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAA
Found at i:315997 original size:62 final size:60
Alignment explanation
Indices: 315931--316201 Score: 343
Period size: 62 Copynumber: 4.4 Consensus size: 60
315921 ATCTTCCAAG
* *
315931 AATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAA
315993 AATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAA
* * *
316055 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATT-CAGAA
*
316117 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGA--TT-CAGAA
*
316179 AATCGCAACGCGATTAAGAAAAT
1 AATCGCAACGCGATTCAGAAAAT
316202 GAGTAAATTC
Statistics
Matches: 192, Mismatches: 8, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
59 2 0.01
60 32 0.17
61 4 0.02
62 134 0.70
63 2 0.01
64 16 0.08
65 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAGAA
Found at i:316308 original size:6 final size:6
Alignment explanation
Indices: 316297--316406 Score: 204
Period size: 6 Copynumber: 18.5 Consensus size: 6
316287 GACACGTATT
316297 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
316345 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
316393 ACCATG ACC-CG ACC
1 ACCACG ACCACG ACC
316407 CGAGACGAGA
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
5 4 0.04
6 98 0.96
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:317012 original size:6 final size:6
Alignment explanation
Indices: 316986--317034 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
316976 TCTCGTCTCG
316986 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
317031 GGTC
1 GGTC
317035 ATACGTGTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.35
6 28 0.65
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:317185 original size:20 final size:20
Alignment explanation
Indices: 317137--317296 Score: 166
Period size: 20 Copynumber: 7.7 Consensus size: 20
317127 TCATTTTCTT
317137 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
317157 AAGATCGCGTTGCGATTCTTGG
1 -A-ATCGCGTTGCGATTCTTGG
317179 AATCGCGTTGCGATTTTCTT--
1 AATCGCGTTGCGA--TTCTTGG
*
317199 AATCGCGTTGCGATT-TTCTG
1 AATCGCGTTGCGATTCTT-GG
317219 AATCGCGTTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
317239 AAGATCGCGTTGCGATT-TTATG
1 -A-ATCGCGTTGCGATTCTT-GG
*
317261 AATCGCATTGCGATTCTTGG
1 AATCGCGTTGCGATTCTTGG
*
317281 AAGATCGTGTTGCGAT
1 -A-ATCGCGTTGCGAT
317297 CTTCTTTTCA
Statistics
Matches: 120, Mismatches: 6, Indels: 25
0.79 0.04 0.17
Matches are distributed among these distances:
17 2 0.02
18 2 0.02
20 55 0.46
21 11 0.09
22 50 0.42
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTTGG
Found at i:317189 original size:42 final size:42
Alignment explanation
Indices: 317137--317296 Score: 227
Period size: 42 Copynumber: 3.9 Consensus size: 42
317127 TCATTTTCTT
*
317137 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTT-GG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTATG
*** *
317179 AATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
317219 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
* *
317261 AATCGCATTGCGATTCTTGGAAGATCGTGTTGCGAT
1 AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAT
317297 CTTCTTTTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.02
40 30 0.29
41 6 0.06
42 67 0.64
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (42 bp):
AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATG
Found at i:317204 original size:62 final size:60
Alignment explanation
Indices: 317129--317356 Score: 237
Period size: 62 Copynumber: 3.7 Consensus size: 60
317119 GAATTTACTC
317129 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGG-AGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
317191 ATTTTCTTAATCGCGTTGCGATTTTCTGA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTTT-GGAGATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * * * **** *
317253 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGTGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATTTTCTTAATCGCGTTGCGATT-TTGG-AGATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * * *
317315 CTTTTCTAAATCGCGTTGCGGTTTT-GATATCGCGTTGCGATT
1 ATTTTCTTAATCGCGTTGCGATTTTGGAGATCGCGTTGCGATT
317357 TTGTTGGTCA
Statistics
Matches: 140, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
59 12 0.09
60 21 0.15
61 8 0.06
62 81 0.58
63 7 0.05
64 11 0.08
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (60 bp):
ATTTTCTTAATCGCGTTGCGATTTTGGAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:317331 original size:20 final size:20
Alignment explanation
Indices: 317129--317358 Score: 160
Period size: 20 Copynumber: 11.2 Consensus size: 20
317119 GAATTTACTC
*
317129 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
317149 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
**
317171 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
317191 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
*
317211 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
317231 ATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* * *
317253 ATTTTATGAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
** *
317273 ATTCTTGGAAGATCGTGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* ** *
317295 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
*
317315 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
317335 GTTTT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
317354 ATTTT
1 ATTTT
317359 GTTGGTCATT
Statistics
Matches: 166, Mismatches: 35, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
19 20 0.12
20 86 0.52
21 18 0.11
22 42 0.25
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:319093 original size:25 final size:26
Alignment explanation
Indices: 319063--319127 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
319053 AAAAATTAGG
319063 ATTTTTAATAAATTAATTAAT-TTTTT
1 ATTTTTAATAAATTAA-TAATATTTTT
319089 ATTTTTAATTAAA--AATAATATTTTT
1 ATTTTTAA-TAAATTAATAATATTTTT
* *
319114 ATTATTAAAAAATT
1 ATTTTTAATAAATT
319128 TAAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
24 7 0.21
25 14 0.42
26 8 0.24
27 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTTTTAATAAATTAATAATATTTTT
Found at i:319201 original size:26 final size:26
Alignment explanation
Indices: 319165--319228 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
319155 ATGTATAATC
319165 GAGAAAATTCTAGGCACTTATTTCTA
1 GAGAAAATTCTAGGCACTTATTTCTA
319191 GAGAAAATTCTAGGCACTTATTTCTA
1 GAGAAAATTCTAGGCACTTATTTCTA
*
319217 GCGAAAAATTCT
1 GAG-AAAATTCT
319229 TTAGACACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 28 0.78
27 8 0.22
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (26 bp):
GAGAAAATTCTAGGCACTTATTTCTA
Found at i:319643 original size:99 final size:99
Alignment explanation
Indices: 319467--320894 Score: 1872
Period size: 99 Copynumber: 14.3 Consensus size: 99
319457 AAATATTTTA
* * *
319467 CAAATCTTC-AAAGGAAATTGTATAAAATATTTTGAATAGATATATTTGTCACTCACAATTTTCT
1 CAAATCTTCAAAAGG-AATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCT
*
319531 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTT
65 TGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* *
319566 CAAATCTTCAAATGGAATTGTGTAAAATATTTTAAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * * * *
319631 GAATAAATTTTCTCAAGTCAAAATCTGATACTGT
66 GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * *
319665 AAAATCTTCAAAAGGAATTGTATAAAGTATTTTGAATAGATATGTTTGTCACTCATGATTTTGTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTT-CT
* * * *
319730 TTAGTAAGGTTTCTTAGGTCAAAATTTGATACTTT
65 TGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
319765 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * *
319830 GAGTAAAGTTTCTCAAGCCAAAATATGATTCTTT
66 GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* *
319864 CAAATCTTCAAAAAGAATTGTATAAAATA-TTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTC--
* *
319928 TTCCCGAGTAAAGTTTCTCAGGACAAAATTTGATACTTT
64 TT---GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
319967 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTC--
320032 TTCTCGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
64 -T-T-GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
320071 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * *
320136 GAGTAAAGTTTCTCAGGTCAAAATCTAATGCTTT
66 GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
320170 CAAATCTTCAAAAGGAATTGTGT-AAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * * *
320234 GAGTAAAATTTCTTAAGTCAAAATTTGATACTTT
66 GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * *
320268 CAAATCTTCAAAAGAAATTGTGTAAAATATTTTGAATAGATATGATTGTCACTCACGGTTTTTTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
*
320333 GAGTAAGGTTTCTCAGGTCAAAATATGATACTTT
66 GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * *
320367 CAAATC-TCTAAAATGAAATGTGTAAAATATTTTGAAT-GTATATGTTTGTCACTAACAATTTTT
1 CAAATCTTC-AAAAGGAATTGTGTAAAATATTTTGAATAG-ATATGTTTGTCACTCACGATTTTC
*
320430 TTGAGTAAAGTTTCTCAGGTCAAAATCTGATACTTT
64 TTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * *
320466 CAAATCTTCAAAAAAAAAAAAAAGAATTGTGTAAAATATTTTGAATAGATATGCTTGTCACTCGC
1 CAAATCTTC---------AAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCAC
* *
320531 AATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATATGATACTTT
57 GATTTTCTTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * * *
320574 CAAATGTTCAAAAGGAATTTTG-ATAAATATTTTGGACATATATGTTTGTTACTCACGATTTTCT
1 CAAATCTTCAAAAGGAATTGTGTA-AAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCT
* *
320638 TGAGTAGAGTTTCTCAGGTCAAAATCTGATACTTT
65 TGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * *
320673 CAAATCTTTAAAAGGAATTCTGTAAAGGTA--TTGAATATATA-GGTTGTCACTCACGATTTTCT
1 CAAATCTTCAAAAGGAATTGTGTAAA-ATATTTTGAATAGATATGTTTGTCACTCACGATTTTCT
* *
320735 TGAGTAAAGTTTCTCAAGTCAAAATATGACACTTT
65 TGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * **
320770 CAAATATT-AAAAGGAAATGTGTAAAATATTTTGAAT-GTATATGTTTGTCACTCATAATTTT-T
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAG-ATATGTTTGTCACTCACGATTTTCT
*
320832 TCGAGTAAAGTTTCTCAGGTCAAAATCTGATACTTT
65 T-GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * *
320868 CAAATATTTAAAAGGATTTGTGTAAAA
1 CAAATCTTCAAAAGGAATTGTGTAAAA
320895 AGAGATGCAC
Statistics
Matches: 1177, Mismatches: 120, Indels: 64
0.86 0.09 0.05
Matches are distributed among these distances:
95 2 0.00
96 15 0.01
97 68 0.06
98 192 0.16
99 522 0.44
100 98 0.08
101 1 0.00
103 57 0.05
104 129 0.11
105 3 0.00
106 1 0.00
108 88 0.07
109 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (99 bp):
CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
Found at i:320120 original size:306 final size:299
Alignment explanation
Indices: 319467--320894 Score: 1900
Period size: 306 Copynumber: 4.8 Consensus size: 299
319457 AAATATTTTA
* * *
319467 CAAATCTTC-AAAGGAAATTGTATAAAATATTTTGAATAGATATATTTGTCACTCACAATTTTCT
1 CAAATCTTCAAAAGG-AATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCT
*
319531 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAATGGAATTGTGTAAAATAT
65 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATAT
* * *
319596 TTTAAATAGATATGTTTGTCACTCACGATTTTCTTGAATAAATTTTCTCAAGTCAAAATCTGATA
130 TTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATCTGATA
* * * * *
319661 CTGTAAAATCTTCAAAAGGAATTGTATAAAGTATTTTGAATAGATATGTTTGTCACTCATGATTT
195 CTTTCAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTT
* * * *
319726 TGTTTT-AGTAAGGTTTCTTAGGTCAAAATTTGATACTTT
260 TTTTTTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
319765 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * * *
319830 GAGTAAAGTTTCTCAAGCCAAAATATGATTCTTTCAAATCTTCAAAAAGAATTGTATAAAATA-T
66 GAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATT
* * *
319894 TTGAATAGATATGTTTGTCACTCACGATTTTCTTTTCCCGAGTAAAGTTTCTCAGGACAAAATTT
131 TTGAATAGATATGTTTGTCACTCACGATTTTC--TT---GAGTAAAGTTTCTCAAGTCAAAATCT
319959 GATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACG
191 GATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACG
320024 ATTTTCTTTTCTCGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
256 ATTTT-TTTT-T-GAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
320071 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
* * * *
320136 GAGTAAAGTTTCTCAGGTCAAAATCTAATGCTTTCAAATCTTCAAAAGGAATTGTGT-AAATATT
66 GAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATT
* * *
320200 TTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAATTTCTTAAGTCAAAATTTGATAC
131 TTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATCTGATAC
* * *
320265 TTTCAAATCTTCAAAAGAAATTGTGTAAAATATTTTGAATAGATATGATTGTCACTCACG--GTT
196 TTTCAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTT
*
320328 TTTTTGAGTAAGGTTTCTCAGGTCAAAATATGATACTTT
261 TTTTTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * *
320367 CAAATC-TCTAAAATGAAATGTGTAAAATATTTTGAAT-GTATATGTTTGTCACTAACAATTTTT
1 CAAATCTTC-AAAAGGAATTGTGTAAAATATTTTGAATAG-ATATGTTTGTCACTCACGATTTTC
* * *
320430 TTGAGTAAAGTTTCTCAGGTCAAAATCTGATACTTTCAAATCTTCAAAAAAAAAAAAAAGAATTG
64 TTGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTC---------AAAAGGAATTG
* * *
320495 TGTAAAATATTTTGAATAGATATGCTTGTCACTCGCAATTTTCTTGAGTAAAGTTTCTCAAGTCA
120 TGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAAGTCA
* * * * * * *
320560 AAATATGATACTTTCAAATGTTCAAAAGGAATTTTG-ATAAATATTTTGGACATATATGTTTGTT
185 AAATCTGATACTTTCAAATCTTCAAAAGGAATTGTGTA-AAATATTTTGAATAGATATGTTTGTC
* * *
320624 ACTCACGA--TTTTCTTGAGTAGAGTTTCTCAGGTCAAAATCTGATACTTT
249 ACTCACGATTTTTTTTTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
* * * * *
320673 CAAATCTTTAAAAGGAATTCTGTAAAGGTA--TTGAATATATA-GGTTGTCACTCACGATTTTCT
1 CAAATCTTCAAAAGGAATTGTGTAAA-ATATTTTGAATAGATATGTTTGTCACTCACGATTTTCT
* * *
320735 TGAGTAAAGTTTCTCAAGTCAAAATATGACACTTTCAAATATT-AAAAGGAAATGTGTAAAATAT
65 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATAT
** *
320799 TTTGAAT-GTATATGTTTGTCACTCATAATTTT-TTCGAGTAAAGTTTCTCAGGTCAAAATCTGA
130 TTTGAATAG-ATATGTTTGTCACTCACGATTTTCTT-GAGTAAAGTTTCTCAAGTCAAAATCTGA
* * *
320862 TACTTTCAAATATTTAAAAGGATTTGTGTAAAA
193 TACTTTCAAATCTTCAAAAGGAATTGTGTAAAA
320895 AGAGATGCAC
Statistics
Matches: 1010, Mismatches: 89, Indels: 66
0.87 0.08 0.06
Matches are distributed among these distances:
293 3 0.00
294 99 0.10
295 4 0.00
296 129 0.13
297 33 0.03
298 118 0.12
299 9 0.01
301 85 0.08
302 86 0.09
303 3 0.00
304 59 0.06
305 28 0.03
306 351 0.35
307 3 0.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (299 bp):
CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
GAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATT
TTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATCTGATAC
TTTCAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTT
TTTTTGAGTAAAGTTTCTCAGGTCAAAATATGATACTTT
Found at i:320546 original size:503 final size:496
Alignment explanation
Indices: 319467--320872 Score: 1961
Period size: 503 Copynumber: 2.8 Consensus size: 496
319457 AAATATTTTA
* * *
319467 CAAATCTTC-AAAGGAAATTGTATAAAATATTTTGAATAGATATATTTGTCACTCACAATTTTCT
1 CAAATCTTCAAAAAG-AATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACAATTTTCT
*
319531 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAATGGAATTGTGTAAAATAT
65 TGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATAT
* * * *
319596 TTTAAATAGATATGTTTGTCACTCACGATTTTCTTGAATAAATTTTCTCAAGTCAAAATCTGATA
130 TTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAGGTCAAAATCTGATA
* * * *
319661 CTGTAAAATCTTCAAAAGGAATTGTATAAAGTATTTTGAATAGATATGTTTGTCACTCATGATTT
195 CTTTCAAATCTTCAAAAGGAATTGTGTAAA-TATTTTGAATAGATATGTTTGTCACTCACGATTT
* * * * *
319726 TGTTTTAGTAAGGTTTCTTAGGTCAAAATTTGATACTTTCAAATCTTCAAAAGGAATTGTGTAAA
259 T-CTTGAGTAAAGTTTCTTAAGTCAAAATTTGATACTTTCAAATCTTCAAAAGAAATTGTGTAAA
* * *
319791 ATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAAGCCAAAATAT
323 ATATTTTGAATAGATATGTTTGTCACTCACGATTTTTTTGAGTAAAGTTTCTCAGGTCAAAATAT
* * *
319856 GATTCTTTCAAATCTTCAAAAAGAATTGTATAAAATATTTGAATAGATATGTTTGTCACTCACGA
388 GATACTTTCAAATCTTCAAAAAGAAATGTATAAAATATTTGAATAGATATGTTTGTCACTAACGA
* *
319921 TTTTCTTTTCCCGAGTAAAGTTTCTCAGGACAAAATTTGATACTTT
453 ATTTCTTTT--CGAGTAAAGTTTCTCAGGACAAAATCTGATACTTT
* *
319967 CAAATCTTCAAAAGGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTT
1 CAAATCTTCAAAAAGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACAATTTTC--
*
320032 TTCTCGAGTAAAGTTTCTCAGGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAA
64 -T-T-GAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAA
320097 ATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAGGTCAAAATCT
126 ATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAGGTCAAAATCT
* *
320162 AATGCTTTCAAATCTTCAAAAGGAATTGTGTAAATATTTTGAATAGATATGTTTGTCACTCACGA
191 GATACTTTCAAATCTTCAAAAGGAATTGTGTAAATATTTTGAATAGATATGTTTGTCACTCACGA
*
320227 TTTTCTTGAGTAAAATTTCTTAAGTCAAAATTTGATACTTTCAAATCTTCAAAAGAAATTGTGTA
256 TTTTCTTGAGTAAAGTTTCTTAAGTCAAAATTTGATACTTTCAAATCTTCAAAAGAAATTGTGTA
* * *
320292 AAATATTTTGAATAGATATGATTGTCACTCACGGTTTTTTTGAGTAAGGTTTCTCAGGTCAAAAT
321 AAATATTTTGAATAGATATGTTTGTCACTCACGATTTTTTTGAGTAAAGTTTCTCAGGTCAAAAT
* *
320357 ATGATACTTTCAAATC-TCTAAAATGAAATGTGTAAAATATTTTGAAT-GTATATGTTTGTCACT
386 ATGATACTTTCAAATCTTC-AAAAAGAAATGTATAAAATA-TTTGAATAG-ATATGTTTGTCACT
*
320420 AAC-AATTT-TTTT-GAGTAAAGTTTCTCAGGTCAAAATCTGATACTTT
448 AACGAATTTCTTTTCGAGTAAAGTTTCTCAGGACAAAATCTGATACTTT
* *
320466 CAAATCTTCAAAAAAAAAAAAAAGAATTGTGTAAAATATTTTGAATAGATATGCTTGTCACTCGC
1 CAAATCTTC---------AAAAAGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCAC
* *
320531 AATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATGTTCAAAAGGAATTTTG
57 AATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTG
* * * * *
320596 -ATAAATATTTTGGACATATATGTTTGTTACTCACGATTTTCTTGAGTAGAGTTTCTCAGGTCAA
122 TA-AAATATTTTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAGGTCAA
* * ** * * *
320660 AATCTGATACTTTCAAATCTTTAAAAGGAATTCTGTAAAGGTATTGAATATATA-GGTTGTCACT
186 AATCTGATACTTTCAAATCTTCAAAAGGAATTGTGTAAATATTTTGAATAGATATGTTTGTCACT
* * * *
320724 CACGATTTTCTTGAGTAAAGTTTCTCAAGTCAAAATATGACACTTTCAAATATT-AAAAGGAAA-
251 CACGATTTTCTTGAGTAAAGTTTCTTAAGTCAAAATTTGATACTTTCAAATCTTCAAAA-GAAAT
** *
320787 TGTGTAAAATATTTTGAAT-GTATATGTTTGTCACTCATAATTTTTTCGAGTAAAGTTTCTCAGG
315 TGTGTAAAATATTTTGAATAG-ATATGTTTGTCACTCACGATTTTTTTGAGTAAAGTTTCTCAGG
*
320851 TCAAAATCTGATACTTTCAAAT
379 TCAAAATATGATACTTTCAAAT
320873 ATTTAAAAGG
Statistics
Matches: 817, Mismatches: 68, Indels: 41
0.88 0.07 0.04
Matches are distributed among these distances:
499 41 0.05
500 55 0.07
501 86 0.11
502 69 0.08
503 308 0.38
504 59 0.07
505 149 0.18
508 50 0.06
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (496 bp):
CAAATCTTCAAAAAGAATTGTGTAAAATATTTTGAATAGATATGTTTGTCACTCACAATTTTCTT
GAGTAAAGTTTCTCAAGTCAAAATATGATACTTTCAAATCTTCAAAAGGAATTGTGTAAAATATT
TTGAATAGATATGTTTGTCACTCACGATTTTCTTGAGTAAAGTTTCTCAGGTCAAAATCTGATAC
TTTCAAATCTTCAAAAGGAATTGTGTAAATATTTTGAATAGATATGTTTGTCACTCACGATTTTC
TTGAGTAAAGTTTCTTAAGTCAAAATTTGATACTTTCAAATCTTCAAAAGAAATTGTGTAAAATA
TTTTGAATAGATATGTTTGTCACTCACGATTTTTTTGAGTAAAGTTTCTCAGGTCAAAATATGAT
ACTTTCAAATCTTCAAAAAGAAATGTATAAAATATTTGAATAGATATGTTTGTCACTAACGAATT
TCTTTTCGAGTAAAGTTTCTCAGGACAAAATCTGATACTTT
Found at i:325812 original size:34 final size:32
Alignment explanation
Indices: 325750--325819 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
325740 CCTTACAAAC
* *
325750 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
325782 TCCCTAGCTTTTACACGGGATAAGCTAGAACTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
325816 TCCC
1 TCCC
325820 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:326058 original size:20 final size:22
Alignment explanation
Indices: 326033--326072 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
326023 AGTTGTATAT
326033 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
326053 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
326073 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:326124 original size:21 final size:21
Alignment explanation
Indices: 326100--326142 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
326090 CCCAGAATAG
*
326100 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
*
326121 AGGGAATCGATATCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
326142 A
1 A
326143 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:326204 original size:21 final size:21
Alignment explanation
Indices: 326178--326220 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
326168 CTGTTGAACA
326178 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
326199 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
326220 G
1 G
326221 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:326279 original size:21 final size:20
Alignment explanation
Indices: 326254--326331 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
326244 AAAACCTGCA
326254 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
326275 GGGGGTATCTGTA-CCC---
1 GGGGGTATCTGTACCCCTGG
326291 -GGGGTATCTGTACCCCTGG
1 GGGGGTATCTGTACCCCTGG
* *
326310 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
326331 G
1 G
326332 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
16 3 0.06
19 3 0.06
20 10 0.20
21 21 0.43
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCTGG
Found at i:326296 original size:15 final size:15
Alignment explanation
Indices: 326276--326305 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
326266 ACCCCCTGGG
326276 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
326291 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
326306 CTGGGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:326314 original size:35 final size:36
Alignment explanation
Indices: 326255--326325 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
326245 AAACCTGCAG
* *
326255 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
326291 GGGGTATCTGTA-CCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
326326 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:326453 original size:29 final size:31
Alignment explanation
Indices: 326421--326479 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
326411 AAACTGTGAA
*
326421 TAAATTCAATT-AAGTCTAAAAA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
326450 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
326480 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:329128 original size:34 final size:32
Alignment explanation
Indices: 329066--329135 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
329056 TACAAACTCC
* *
329066 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
329098 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
329132 TCCC
1 TCCC
329136 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:329443 original size:21 final size:21
Alignment explanation
Indices: 329404--329446 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
329394 CCCAGAATAG
*
329404 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
* *
329425 AGGGAATCGATATCTCTTCAT
1 AGGGAATCGATACCCCTTCAT
329446 A
1 A
329447 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:329523 original size:22 final size:21
Alignment explanation
Indices: 329482--329521 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
329472 CTGTTGAACA
329482 GGGGGGGAATCGGTACCCCTT
1 GGGGGGGAATCGGTACCCCTT
329503 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
329522 CTGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCTT
Found at i:329584 original size:21 final size:20
Alignment explanation
Indices: 329559--329636 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
329549 AAAACCTGCA
329559 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
329580 GGGGGTATCTGTA-CCC---
1 GGGGGTATCTGTACCCCTGG
329596 -GGGGTATCTGTACCCCTGG
1 GGGGGTATCTGTACCCCTGG
* *
329615 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
329636 G
1 G
329637 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.24
16 3 0.06
19 3 0.06
20 10 0.20
21 21 0.43
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCTGG
Found at i:329601 original size:15 final size:15
Alignment explanation
Indices: 329581--329610 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
329571 ACCCCCTGGG
329581 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
329596 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
329611 CTGGGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:329619 original size:35 final size:36
Alignment explanation
Indices: 329560--329630 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
329550 AAACCTGCAG
* *
329560 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
329596 GGGGTATCTGTA-CCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
329631 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 21 0.64
36 12 0.36
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:329748 original size:29 final size:30
Alignment explanation
Indices: 329713--329783 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
329703 TGAAACCTTT
329713 TAAAAAC-TTTGAATAAATTCAATT-AAGTC
1 TAAAAACATTT-AATAAATTCAATTCAAGTC
**
329742 TAAAAACATTTTTTAAATTCAATTCAAGTC
1 TAAAAACATTTAATAAATTCAATTCAAGTC
*
329772 CAAAAACCATTT
1 TAAAAA-CATTT
329784 TGCCTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.50
30 13 0.36
31 5 0.14
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAAACATTTAATAAATTCAATTCAAGTC
Found at i:329777 original size:30 final size:30
Alignment explanation
Indices: 329726--329784 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
329716 AAACTTTGAA
*
329726 TAAATTCAATTAAGTCTAAAAA-CATTTTT
1 TAAATTCAATTAAGTCCAAAAACCATTTTT
329755 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
329785 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTT
Found at i:329784 original size:29 final size:28
Alignment explanation
Indices: 329726--329784 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
329716 AAACTTTGAA
*
329726 TAAATTCAATTAAGTCTAAAAACATTTTT
1 TAAATTCAATTAAGTCCAAAAACA-TTTT
329755 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAA-CATTTT
329785 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.37
Consensus pattern (28 bp):
TAAATTCAATTAAGTCCAAAAACATTTT
Found at i:335983 original size:10 final size:10
Alignment explanation
Indices: 335944--335981 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
335934 AGACCTGCTG
335944 AAAACCGGAA
1 AAAACCGGAA
335954 AAAACCGGAA
1 AAAACCGGAA
* *
335964 AAAATCGGGA
1 AAAACCGGAA
335974 AAAACCGG
1 AAAACCGG
335982 GATTTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.55, C:0.18, G:0.24, T:0.03
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:337478 original size:20 final size:20
Alignment explanation
Indices: 337377--337605 Score: 178
Period size: 20 Copynumber: 11.4 Consensus size: 20
337367 GATTTTCCAG
* ** *
337377 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
337397 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* ** *
337417 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
337437 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
337457 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
337477 AACCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
337497 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
337517 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
337537 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
337557 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
337577 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
337597 AATCACAAC
1 AATCGCAAC
337606 ACTGAAATTT
Statistics
Matches: 167, Mismatches: 34, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.02
20 161 0.96
21 3 0.02
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:337484 original size:40 final size:39
Alignment explanation
Indices: 337377--337605 Score: 215
Period size: 40 Copynumber: 5.7 Consensus size: 39
337367 GATTTTCCAG
* *
337377 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAAC-CATA
* *
337417 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAAC-CATA
* * * * * *
337457 AATCGCAACGCGTATCCGTAAACCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCG-AACCATA
* * * ** *
337497 TATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAA-CCATA
* ** *
337537 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAA-CCATA
* *
337577 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGAATCTGTAAATCGCAAC
337606 ACTGAAATTT
Statistics
Matches: 168, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 165 0.98
41 2 0.01
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.17
Consensus pattern (39 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGCGAACCATA
Found at i:338332 original size:24 final size:24
Alignment explanation
Indices: 338293--338339 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
338283 AAATTTGGTC
338293 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
338317 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
338340 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:340000 original size:31 final size:32
Alignment explanation
Indices: 339976--340038 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
339966 TTTATATATT
339976 TTACTAAGTATG-TTATTTAAATTTACAGGAA
1 TTACTAAGTATGTTTATTTAAATTTACAGGAA
340007 TTACTAAGTATGTTTATTTAAATTTACAGGAA
1 TTACTAAGTATGTTTATTTAAATTTACAGGAA
340039 CATTGGAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (32 bp):
TTACTAAGTATGTTTATTTAAATTTACAGGAA
Found at i:340911 original size:19 final size:19
Alignment explanation
Indices: 340842--341102 Score: 278
Period size: 19 Copynumber: 14.7 Consensus size: 19
340832 TCGCAACGAG
340842 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
340861 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
340875 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
340895 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
340914 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
340933 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
340947 AATCACAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
340966 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
340985 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
340999 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
341019 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
341038 AATCG-AA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
341051 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
341071 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
341090 AATCGCATTGCGA
1 AATCGCAATGCGA
341103 TTCTCTCGTT
Statistics
Matches: 205, Mismatches: 11, Indels: 52
0.76 0.04 0.19
Matches are distributed among these distances:
13 7 0.03
14 34 0.17
15 2 0.01
16 6 0.03
17 8 0.04
18 8 0.04
19 97 0.47
20 43 0.21
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:340959 original size:72 final size:71
Alignment explanation
Indices: 340842--340992 Score: 250
Period size: 72 Copynumber: 2.1 Consensus size: 71
340832 TCGCAACGAG
*
340842 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCACAATGCGGAAATG-AAATCGCAATGCG
340907 AAATGAA
65 AAATGAA
* *
340914 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCACAATGCGGAAATGAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCACAATGCGGAAATGAAATCGCAATGCG
340978 AAATGAA
65 AAATGAA
340985 AATCGCAA
1 AATCGCAA
340993 CGAGAGAATC
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
71 28 0.37
72 46 0.61
73 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCACAATGCGGAAATGAAATCGCAATGCGA
AATGAA
Found at i:340978 original size:52 final size:53
Alignment explanation
Indices: 340830--341096 Score: 376
Period size: 52 Copynumber: 5.1 Consensus size: 53
340820 CGGAAATTAC
*
340830 AATCGCAAC--GAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
340875 AATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
*
340933 AATCGCAACGAGAGAATCACAATGCGGAAATG-AAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
340985 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
341038 AATCG-AACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
341090 AATCGCA
1 AATCGCA
341097 TTGCGATTCT
Statistics
Matches: 201, Mismatches: 5, Indels: 24
0.87 0.02 0.10
Matches are distributed among these distances:
45 8 0.04
47 1 0.00
52 115 0.57
53 61 0.30
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
Found at i:341015 original size:105 final size:104
Alignment explanation
Indices: 340895--341096 Score: 370
Period size: 105 Copynumber: 1.9 Consensus size: 104
340885 CGGAAATGAA
340895 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG-AACGAGAGAATCACAATGCGG
340960 AAATG-AAATCGCAATGCGAAATGAAAATCGCAACGAGAG
65 AAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
340999 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCGCAATGCGG
1 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCACAATGCGG
341064 AAATGAAAATCGCAATGCGAAATGAAAATCGCA
65 AAATGAAAATCGCAATGCGAAATGAAAATCGCA
341097 TTGCGATTCT
Statistics
Matches: 95, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
104 36 0.38
105 59 0.62
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (104 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGAACGAGAGAATCACAATGCGGA
AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:341080 original size:124 final size:123
Alignment explanation
Indices: 340811--341102 Score: 344
Period size: 124 Copynumber: 2.4 Consensus size: 123
340801 TGCATTGACT
* * * * *
340811 ATCGCAACACGGAAATTACAAT-CGCAACGAGAATCGCAATGCGAAATGAAAATCCCAACATGAA
1 ATCGCAACA-GAAAATCACAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCCCAACATGAA
* *
340875 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
65 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAATGAAA
* *
340934 ATCGCAACGAGAGAATCACAATGCGGAAATG-AAATCGCAATGCGAAATGAAAATCGCAACGA-G
1 ATCGCAAC-AGAAAATCACAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCCCAAC-ATG
* *
340997 AGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCG-AACGAGAGAATCG-CA
63 AAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA-AAT-GAAA
* * *
341058 ATGCGGAA-ATGAAAATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AT-CGCAACA-GAAAATCACAATGCGAAATGAAAATCGCAATGCGA
341103 TTCTCTCGTT
Statistics
Matches: 145, Mismatches: 15, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
123 29 0.20
124 106 0.73
125 10 0.07
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (123 bp):
ATCGCAACAGAAAATCACAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCCCAACATGAAA
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAATGAAA
Found at i:341135 original size:52 final size:52
Alignment explanation
Indices: 341073--341187 Score: 151
Period size: 52 Copynumber: 2.2 Consensus size: 52
341063 GAAATGAAAA
*
341073 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
341124 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
341177 TCGCATTGCGA
1 TCGCATTGCGA
341188 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
51 1 0.02
52 46 0.84
53 8 0.15
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:341188 original size:52 final size:52
Alignment explanation
Indices: 341092--341207 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
341082 GAAATGAAAA
341092 TCGCATTGCGATTCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
341144 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTCATT
341196 TCGCATTGCGAT
1 TCGCATTGCGAT
341208 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 55 0.87
53 8 0.13
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTCATTTCCGCATTGCGATTTTCATT
Found at i:341215 original size:19 final size:19
Alignment explanation
Indices: 341111--341207 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
341101 GATTCTCTCG
341111 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
341130 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
341149 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
341163 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
341182 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
341201 TTGCGAT
1 TTGCGAT
341208 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 42 0.60
20 8 0.11
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:341349 original size:13 final size:14
Alignment explanation
Indices: 341314--341349 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
341304 CATCAATTAC
341314 ACAAATCAACTTTT
1 ACAAATCAACTTTT
341328 ACAAATCAACTTTT
1 ACAAATCAACTTTT
341342 AC-AATCAA
1 ACAAATCAA
341350 TTAAACAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:341359 original size:12 final size:12
Alignment explanation
Indices: 341342--341378 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
341332 ATCAACTTTT
341342 ACAATCAATTAA
1 ACAATCAATTAA
*
341354 ACAATCAA-AAA
1 ACAATCAATTAA
341365 ACAATCAATTAA
1 ACAATCAATTAA
341377 AC
1 AC
341379 TATTGAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ACAATCAATTAA
Found at i:343228 original size:19 final size:19
Alignment explanation
Indices: 343186--343357 Score: 123
Period size: 19 Copynumber: 9.6 Consensus size: 19
343176 ATAGTTACTT
* *
343186 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
343206 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
343225 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* **
343244 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
343263 TCGCAACGCAAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
343282 CCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
343296 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
343315 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
343329 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
343347 TCGCAATGCGA
1 TCGCAACGCGA
343358 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 21, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.14
15 1 0.01
16 7 0.06
17 6 0.05
18 13 0.11
19 65 0.54
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:343299 original size:33 final size:33
Alignment explanation
Indices: 343261--343346 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
343251 GCGAAACCAA
*
343261 AATCGCAACGCAAAATGAAAACCGCAACGACAG
1 AATCGCAACGCGAAATGAAAACCGCAACGACAG
* * *
343294 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAACCGCAACGACAG
343327 AATCGCAACGCGAAATGAAA
1 AATCGCAACGCGAAATGAAA
343347 TCGCAATGCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAACCGCAACGACAG
Found at i:343388 original size:14 final size:14
Alignment explanation
Indices: 343369--343426 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
343359 TTTGGTTTCG
343369 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
343383 CGTTGCGATTTGGTTT
1 CGTTGCGATTT--TGT
*
343399 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
343415 CGTTGCGATTTT
1 CGTTGCGATTTT
343427 CATTTGTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:343398 original size:32 final size:32
Alignment explanation
Indices: 343353--343425 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 32
343343 GAAATCGCAA
*
343353 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGA-TTTGGTTTCGCGTTGCGATTCTGTCGT
343386 TGCGATTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTGGTTTCGCGTTGCGATTCTGTCGT
343418 TGCGATTT
1 TGCGATTT
343426 TCATTTGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 34 0.87
33 5 0.13
ACGTcount: A:0.07, C:0.16, G:0.30, T:0.47
Consensus pattern (32 bp):
TGCGATTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:343406 original size:18 final size:18
Alignment explanation
Indices: 343353--343410 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
343343 GAAATCGCAA
343353 TGCGATTTTGGTTTCGCGT
1 TGCGA-TTTGGTTTCGCGT
*
343372 TGCGATTT--TGT--CGT
1 TGCGATTTGGTTTCGCGT
343386 TGCGATTTGGTTTCGCGT
1 TGCGATTTGGTTTCGCGT
343404 TGCGATT
1 TGCGATT
343411 CTGTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
16 4 0.12
18 13 0.39
19 5 0.15
ACGTcount: A:0.07, C:0.16, G:0.31, T:0.47
Consensus pattern (18 bp):
TGCGATTTGGTTTCGCGT
Found at i:343438 original size:32 final size:32
Alignment explanation
Indices: 343364--343440 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
343354 GCGATTTTGG
* **
343364 TTTCGCGTTGCGATTTTGTCGTTGCGATTTGG
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTCA
343396 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGA-TTTCA
*
343429 TTT-GTGTTGCGA
1 TTTCGCGTTGCGA
343441 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 34 0.85
33 6 0.15
ACGTcount: A:0.08, C:0.17, G:0.29, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTCTGTCGTTGCGATTTCA
Found at i:343690 original size:92 final size:92
Alignment explanation
Indices: 343539--343754 Score: 400
Period size: 92 Copynumber: 2.4 Consensus size: 92
343529 AGGGTATTAG
343539 TTAGCAGAATTGGCAGCAACCGAACAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAATAC
1 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
343603 TATTCACAGTGTTAAAGAATACACAGT
66 TATTCACAGTGTTAAAGAATACACAGT
*
343630 TTAGCAGAATTGGTAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
1 TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
343695 TATTCACAGTGTTAAAGAATACACAGT
66 TATTCACAGTGTTAAAGAATACACAGT
*
343722 TTAGCAGAATTGGCAGCAACCGAA-TAATTTACT
1 TTAGCAGAATTGGCAGCAACCGAACAAATTTACT
343755 AAGCAATCTA
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
91 40 0.33
92 81 0.67
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (92 bp):
TTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
TATTCACAGTGTTAAAGAATACACAGT
Found at i:343904 original size:42 final size:42
Alignment explanation
Indices: 343856--343985 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 42
343846 GTAGAGTATG
343856 AACCTCATTCTGCAACAATACTATCATCTCACGTAGAGCGGC
1 AACCTCATTCTGCAACAATACTATCATCTCACGTAGAGCGGC
* ** * * * * **
343898 AACCTCAAATCTTAAAC-TTAC-CTCGT-T-GCGTAGAGTATG-
1 AACCTC-ATTCTGCAACAATACTATCATCTCACGTAGAG-CGGC
343937 AACCTCATTCTGCAACAATACTATCATCTCACGTAGAGCGGC
1 AACCTCATTCTGCAACAATACTATCATCTCACGTAGAGCGGC
343979 AACCTCA
1 AACCTCA
343986 CCACGTAAAG
Statistics
Matches: 63, Mismatches: 18, Indels: 14
0.66 0.19 0.15
Matches are distributed among these distances:
38 7 0.11
39 16 0.25
40 5 0.08
41 5 0.08
42 23 0.37
43 7 0.11
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (42 bp):
AACCTCATTCTGCAACAATACTATCATCTCACGTAGAGCGGC
Found at i:343941 original size:39 final size:39
Alignment explanation
Indices: 343823--343943 Score: 102
Period size: 39 Copynumber: 3.0 Consensus size: 39
343813 TAAATATGGA
343823 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTC
1 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTC
* ** * * * * **
343862 -ATTCTGCAACAATACTATCATCTCACGTAGAG-CGGCAACCTC
1 AAATCTTAAAC-TTAC-CTCGT-T-GCGTAGAGTATG-AACCTC
343904 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTC
1 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTC
343943 A
1 A
343944 TTCTGCAACA
Statistics
Matches: 57, Mismatches: 18, Indels: 14
0.64 0.20 0.16
Matches are distributed among these distances:
38 7 0.12
39 17 0.30
40 5 0.09
41 5 0.09
42 16 0.28
43 7 0.12
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (39 bp):
AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTC
Found at i:343958 original size:81 final size:81
Alignment explanation
Indices: 343823--343985 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
343813 TAAATATGGA
343823 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTCATTCTGCAACAATACTATCATCTCAC
1 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTCATTCTGCAACAATACTATCATCTCAC
343888 GTAGAGCGGCAACCTC
66 GTAGAGCGGCAACCTC
343904 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTCATTCTGCAACAATACTATCATCTCAC
1 AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTCATTCTGCAACAATACTATCATCTCAC
343969 GTAGAGCGGCAACCTC
66 GTAGAGCGGCAACCTC
343985 A
1 A
343986 CCACGTAAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (81 bp):
AAATCTTAAACTTACCTCGTTGCGTAGAGTATGAACCTCATTCTGCAACAATACTATCATCTCAC
GTAGAGCGGCAACCTC
Found at i:345402 original size:20 final size:20
Alignment explanation
Indices: 345371--345434 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
345361 TTTTGGTTGA
345371 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
345391 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
345411 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
345432 AAT
1 AAT
345435 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:345423 original size:21 final size:21
Alignment explanation
Indices: 345369--345433 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
345359 TCTTTTGGTT
345369 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
345390 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
345410 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
345431 GAA
1 GAA
345434 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:345507 original size:31 final size:33
Alignment explanation
Indices: 345469--345535 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
345459 TGCGATTTGG
345469 TTTCGCGTTGCGA-T-TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
345500 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
345533 TTT
1 TTT
345536 TTCTCGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 13 0.38
32 1 0.03
33 20 0.59
ACGTcount: A:0.09, C:0.22, G:0.21, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:345541 original size:21 final size:21
Alignment explanation
Indices: 345516--345587 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
345506 GTTGCGATTC
345516 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
345537 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
345558 TC-CGTTGTGA-TTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
345577 TCTCGTTGCGA
1 TCTCGTTGCGA
345588 CTCTTCTGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
18 3 0.07
19 6 0.15
20 12 0.29
21 14 0.34
22 6 0.15
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:345723 original size:30 final size:31
Alignment explanation
Indices: 345666--345732 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
345656 AATACTAACT
345666 TGAAAATCGCAATGAGAGATAGCAACGCGAAA
1 TGAAAATCGCAA-GAGAGATAGCAACGCGAAA
* * *
345698 TGAAAATCGCAA-CGAGATCGTAACGCGAAA
1 TGAAAATCGCAAGAGAGATAGCAACGCGAAA
345728 TGAAA
1 TGAAA
345733 TCTAAGTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 20 0.62
32 12 0.38
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.13
Consensus pattern (31 bp):
TGAAAATCGCAAGAGAGATAGCAACGCGAAA
Found at i:346137 original size:20 final size:20
Alignment explanation
Indices: 346112--346284 Score: 188
Period size: 20 Copynumber: 8.6 Consensus size: 20
346102 CTTTAAAAAT
*
346112 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
346132 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
346152 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
346173 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
346193 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
346213 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
346233 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
346253 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
346273 CGCGTTGCGATT
1 CGCGTTGCGATT
346285 CTGGAAAATC
Statistics
Matches: 129, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
20 112 0.87
21 17 0.13
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:346279 original size:60 final size:60
Alignment explanation
Indices: 346112--346284 Score: 215
Period size: 60 Copynumber: 2.9 Consensus size: 60
346102 CTTTAAAAAT
346112 CGCGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTATGGATACGCGTTGCGATTTT-CGTATTCG-CGTTGCGATTTACGGATA
* * * * * * * *
346173 CGCGTTGCGATATACGGATACGCATTGCGATTTACGGATACACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTATGGATACGCGTTGCGATTTTCGTATTCGCGTTGCGATTTACGGATA
* *
346233 CGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGCGTTGCGATTTATG-GATACGCGTTGCGATTTTCGTATTCGCGTTGCGATT
346285 CTGGAAAATC
Statistics
Matches: 92, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
60 61 0.66
61 31 0.34
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTATGGATACGCGTTGCGATTTTCGTATTCGCGTTGCGATTTACGGATA
Found at i:346682 original size:20 final size:18
Alignment explanation
Indices: 346633--346687 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
346623 CCAGTAATCC
*
346633 TATTCCCTGGTAATCTTT
1 TATTCACTGGTAATCTTT
**
346651 TATTTTCTGGTAATCTTT
1 TATTCACTGGTAATCTTT
346669 TATTCCCACTGGTAATCTT
1 TATT--CACTGGTAATCTT
346688 ACATTCCGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 20 0.65
20 11 0.35
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTCACTGGTAATCTTT
Found at i:346693 original size:20 final size:20
Alignment explanation
Indices: 346657--346694 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
346647 CTTTTATTTT
**
346657 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
346677 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
346695 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:350391 original size:140 final size:143
Alignment explanation
Indices: 350137--350421 Score: 524
Period size: 140 Copynumber: 2.0 Consensus size: 143
350127 TTATCCAACA
350137 TTGGATAGGAATATACCTTTGGAAAGATATTTAAAGGGCACCCTTTCTACTTTATATTGAATGTG
1 TTGGATAGGAATATACCTTTGGAAAGATATTTAAAGGGCACCCTTTCTACTTTATATTGAATGTG
350202 GCTAGATAACTCCTTCGCGCACACGCGCCATCGCCATCTGTTATGGTCATTACGTGTTGTGCCAC
66 GCTAGATAACTCCTTCGCGCACACGCGCCATCGCCATCTGTTATGGTCATTACGTGTTGTGCCAC
350267 TCACATA-TATAT
131 TCACATATTATAT
350279 TTGGATAGGAATATACCTTTGG-AAGATATTTAAAGGGACACCCTTTCTACTTTATA-TG-ATGT
1 TTGGATAGGAATATACCTTTGGAAAGATATTTAAAGGG-CACCCTTTCTACTTTATATTGAATGT
*
350341 GGCTAGATAACTCCTTCGCGCACGCGCGCCATCGCCATCTGTTATGGTCATTACGTGTTGTGCCA
65 GGCTAGATAACTCCTTCGCGCACACGCGCCATCGCCATCTGTTATGGTCATTACGTGTTGTGCCA
350406 CTCACATATTATAT
130 CTCACATATTATAT
350420 TT
1 TT
350422 ATAGACACAT
Statistics
Matches: 140, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
140 76 0.54
141 24 0.17
142 40 0.29
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (143 bp):
TTGGATAGGAATATACCTTTGGAAAGATATTTAAAGGGCACCCTTTCTACTTTATATTGAATGTG
GCTAGATAACTCCTTCGCGCACACGCGCCATCGCCATCTGTTATGGTCATTACGTGTTGTGCCAC
TCACATATTATAT
Found at i:352404 original size:342 final size:342
Alignment explanation
Indices: 351774--352464 Score: 1310
Period size: 342 Copynumber: 2.0 Consensus size: 342
351764 CCCAGACCAC
* *
351774 GTAATGGGGTTAACTTCAAGAAATCGAGAAAAGACAAAGCGCAAAGAAAGCCTGTTAATTGCTAC
1 GTAAAGGGGTTAACTTCAAGAAATCGAGAAAAGACAAAGCGCAAAGAAAGCCTGTCAATTGCTAC
351839 ATGTGCGGACGAGTCAAACACAAAGCCTACCAGCTTCAACAACACCATGACCTTCAGAATGAAAA
66 ATGTGCGGACGAGTCAAACACAAAGCCTACCAGCTTCAACAACACCATGACCTTCAGAATGAAAA
*
351904 TCGACTACAACTGAATATTTCCGAGAACACGGACGAGATCATTGTTGTGGTGATTTCTGAAGTCA
131 TCGACTACAACTGAATATTTCCGAGAACACGGACGAGATAATTGTTGTGGTGATTTCTGAAGTCA
*
351969 ACCTGATAGAGAACAACGTTGAATGGGTTGTGGACACCAGAGCATCAAGGCATTTCTGCACCAAT
196 ACCTGATAGAGAACAACGTTGAATGGGTTGTGGACACCAGAGCATCAAGGAATTTCTGCACCAAT
*
352034 TGAGAGATGTTCACCTAATTCAAAAGCATGACTAAAGGTGAAAAAGTCTACATGAGTAACTCTAA
261 TGAGAGATATTCACCTAATTCAAAAGCATGACTAAAGGTGAAAAAGTCTACATGAGTAACTCTAA
352099 CAAGTCTGATGTACTAG
326 CAAGTCTGATGTACTAG
*
352116 GTAAAGGGGTTAACTTCAAGAAATCGAGAAAAGACAAAGCGCAAAGCAAGCCTGTCAATTGCTAC
1 GTAAAGGGGTTAACTTCAAGAAATCGAGAAAAGACAAAGCGCAAAGAAAGCCTGTCAATTGCTAC
*
352181 ATGTGCGGACGAGTCGAACACAAAGCCTACCAGCTTCAACAACACCATGACCTTCAGAATGAAAA
66 ATGTGCGGACGAGTCAAACACAAAGCCTACCAGCTTCAACAACACCATGACCTTCAGAATGAAAA
352246 TCGACTACAACTGAATATTTCCGAGAACACGGACGAGATAATTGTTGTGGTGATTTCTGAAGTCA
131 TCGACTACAACTGAATATTTCCGAGAACACGGACGAGATAATTGTTGTGGTGATTTCTGAAGTCA
*
352311 ACTTGATAGAGAACAACGTTGAATGGGTTGTGGACACCAGAGCATCAAGGAATTTCTGCACCAAT
196 ACCTGATAGAGAACAACGTTGAATGGGTTGTGGACACCAGAGCATCAAGGAATTTCTGCACCAAT
352376 TGAGAGATATTCACCTAATTCAAAAGCATGACTAAAGGTGAAAAAGTCTACATGAGTAACTCTAA
261 TGAGAGATATTCACCTAATTCAAAAGCATGACTAAAGGTGAAAAAGTCTACATGAGTAACTCTAA
352441 CAAGTCTGATGTACTAG
326 CAAGTCTGATGTACTAG
352458 GTAAAGG
1 GTAAAGG
352465 AAAGGTTTAA
Statistics
Matches: 341, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
342 341 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (342 bp):
GTAAAGGGGTTAACTTCAAGAAATCGAGAAAAGACAAAGCGCAAAGAAAGCCTGTCAATTGCTAC
ATGTGCGGACGAGTCAAACACAAAGCCTACCAGCTTCAACAACACCATGACCTTCAGAATGAAAA
TCGACTACAACTGAATATTTCCGAGAACACGGACGAGATAATTGTTGTGGTGATTTCTGAAGTCA
ACCTGATAGAGAACAACGTTGAATGGGTTGTGGACACCAGAGCATCAAGGAATTTCTGCACCAAT
TGAGAGATATTCACCTAATTCAAAAGCATGACTAAAGGTGAAAAAGTCTACATGAGTAACTCTAA
CAAGTCTGATGTACTAG
Found at i:353268 original size:175 final size:174
Alignment explanation
Indices: 352977--353325 Score: 689
Period size: 175 Copynumber: 2.0 Consensus size: 174
352967 TATTATATAA
352977 CCTTTGTATATGAATACTCTAGATATACAAAGGTTTATCTTCCAAGAACAAAATAAGAAGCATAA
1 CCTTTGTATATGAATACTCTAGATATACAAAGGTTTATCTTCCAAGAACAAAATAAGAAGCATAA
353042 AGTTATTTTTTACTTTATAAAGCAAAAGTAGAAAATCAATTTGATAAGCGAACATAATGACTTAA
66 AGTTATTTTTTACTTTATAAAGCAAAAGTAGAAAATCAATTTGATAAGCGAACATAATGACTTAA
353107 ATCTGATAGTGGTGAATGAATATGTCTCTGATTTTTTTTAAAGAG
131 ATCTGATAGTGGTG-ATGAATATGTCTCTGATTTTTTTTAAAGAG
353152 CCTTTGTATATGAATACTCTAGATATACAAAGGTTTATCTTCCAAGAACAAAATAAGAAGCATAA
1 CCTTTGTATATGAATACTCTAGATATACAAAGGTTTATCTTCCAAGAACAAAATAAGAAGCATAA
353217 AGTTATTTTTTACTTTATAAAGCAAAAGTAGAAAATCAATTTGATAAGCGAACATAATGACTTAA
66 AGTTATTTTTTACTTTATAAAGCAAAAGTAGAAAATCAATTTGATAAGCGAACATAATGACTTAA
353282 ATCTGATAGTGGTGATGAATATGTCTCTGATTTTTTTTAAAGAG
131 ATCTGATAGTGGTGATGAATATGTCTCTGATTTTTTTTAAAGAG
353326 GTTTGTGAAA
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
174 30 0.17
175 144 0.83
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (174 bp):
CCTTTGTATATGAATACTCTAGATATACAAAGGTTTATCTTCCAAGAACAAAATAAGAAGCATAA
AGTTATTTTTTACTTTATAAAGCAAAAGTAGAAAATCAATTTGATAAGCGAACATAATGACTTAA
ATCTGATAGTGGTGATGAATATGTCTCTGATTTTTTTTAAAGAG
Found at i:355911 original size:33 final size:33
Alignment explanation
Indices: 355869--355935 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
355859 CCTAGTACAA
355869 ATGGTGGACACGACCTTATGTGTCATACAGATT
1 ATGGTGGACACGACCTTATGTGTCATACAGATT
*
355902 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGACCTTATGTGTCATACAGATT
355935 A
1 A
355936 GTACTACGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (33 bp):
ATGGTGGACACGACCTTATGTGTCATACAGATT
Found at i:356081 original size:33 final size:33
Alignment explanation
Indices: 356037--356109 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
356027 ACAAGTGTAT
*
356037 TGGTAAAATAAGCTTACGAGCTTATGAAACAAA
1 TGGTAAGATAAGCTTACGAGCTTATGAAACAAA
** *
356070 TGGTAAGATAAGCTTACGAGCTTATGGGATAAA
1 TGGTAAGATAAGCTTACGAGCTTATGAAACAAA
356103 TGGTAAG
1 TGGTAAG
356110 TATTTTGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.26
Consensus pattern (33 bp):
TGGTAAGATAAGCTTACGAGCTTATGAAACAAA
Found at i:359232 original size:2 final size:2
Alignment explanation
Indices: 359225--359256 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
359215 TTGTGTAGGT
359225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
359257 TGTTGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:363820 original size:7 final size:7
Alignment explanation
Indices: 363808--363841 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
363798 ATATAATTAT
363808 ATATTTA
1 ATATTTA
363815 ATATTTA
1 ATATTTA
*
363822 ATCTTTA
1 ATATTTA
363829 ATATTTA
1 ATATTTA
363836 TATATT
1 -ATATT
363842 CTATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:381148 original size:19 final size:19
Alignment explanation
Indices: 381126--381166 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
381116 TTTTTGCATC
381126 TGTATGAAATTTTATATTG
1 TGTATGAAATTTTATATTG
381145 TGTATGAAATTTTATATTG
1 TGTATGAAATTTTATATTG
381164 TGT
1 TGT
381167 GCTTATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (19 bp):
TGTATGAAATTTTATATTG
Found at i:382303 original size:129 final size:129
Alignment explanation
Indices: 382073--382330 Score: 444
Period size: 129 Copynumber: 2.0 Consensus size: 129
382063 GGATCTTTTG
* *
382073 AATGCACAATTATTTTTAAGTCCCACATTAATCACTTCCTCCACCACCTATGACTCTACTCGACC
1 AATGCACAATTATTTTTAAGGCCCACATTAATCACATCCTCCACCACCTATGACTCTACTCGACC
* *
382138 ATCCAACATGGGGAAATCTATTAAATAATCCTTCATTTCATAATTTGCACGTGCAGACTCACCA
66 ATCCAACATGGGGAAATCTATTAAATAATCATTCATTTCAAAATTTGCACGTGCAGACTCACCA
* *
382202 AATGCACAATTATTTTTAAGGGCCACATTAATCACATCCTCCACCACCTTTGACTCTACTCGACC
1 AATGCACAATTATTTTTAAGGCCCACATTAATCACATCCTCCACCACCTATGACTCTACTCGACC
* *
382267 ATCCAACATGGGGAAATCTATTAAATAATCATTCATTTCAAAATTTGCACGTGTAGTCTCACCA
66 ATCCAACATGGGGAAATCTATTAAATAATCATTCATTTCAAAATTTGCACGTGCAGACTCACCA
382331 CTTTTCATGT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (129 bp):
AATGCACAATTATTTTTAAGGCCCACATTAATCACATCCTCCACCACCTATGACTCTACTCGACC
ATCCAACATGGGGAAATCTATTAAATAATCATTCATTTCAAAATTTGCACGTGCAGACTCACCA
Found at i:382943 original size:71 final size:71
Alignment explanation
Indices: 382711--383107 Score: 317
Period size: 71 Copynumber: 5.6 Consensus size: 71
382701 TTTGCCGCAA
* * *
382711 TCTAAATTCTGTTCGTTCCCATGCATAGAATCAGTAGA--GATGAAATCTATGTCCGTGATGT-A
1 TCTAAATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGAT-TCA
*
382773 ACCGC-T
65 ACTGCAT
* * * * * * * * *
382779 TCTAAGTTCTGTCCACTCCTATGCATAGTATTAGTAGAGTGATAAATAAATATATGTCTC-T-AA
1 TCTAAATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGAT---GAAATCTATG-CCCGTGAT
**
382842 TCTTTCTGCAT
62 TC-AACTGCAT
* * *
382853 TCCACATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATTCAG
1 TCTAAATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATTCAA
382918 CTGCAT
66 CTGCAT
* * * * ** **
382924 TCTAAATTCTGCCCGTTCCCATGCATAGTATCAGTAGAGTGATGAAATCTATGTCCGCAAGGCAA
1 TCTAAATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATTCAA
382989 CTGCAT
66 CTGCAT
* * *
382995 TCTAAATTCTGAT-CATTCCCATGCATAGAATCAGTAGCGTGATGAATATCTATGTCC-TGAATC
1 TCTAAATTCTG-TCCATTCCCATGCATAGAATCAGTAGAGTGATGAA-ATCTATGCCCGTGATTC
* *
383058 TTAGTGCAT
64 -AACTGCAT
* * * **
383067 TCAAAATTATGTCCATTCACATGGTTA-ATATCAGTAGAGTG
1 TCTAAATTCTGTCCATTCCCATGCATAGA-ATCAGTAGAGTG
383108 GAAAATATTT
Statistics
Matches: 258, Mismatches: 55, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
68 31 0.12
70 5 0.02
71 121 0.47
72 51 0.20
73 12 0.05
74 38 0.15
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (71 bp):
TCTAAATTCTGTCCATTCCCATGCATAGAATCAGTAGAGTGATGAAATCTATGCCCGTGATTCAA
CTGCAT
Done.