Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:268325 original size:45 final size:45
Alignment explanation
Indices: 268276--268737 Score: 629
Period size: 45 Copynumber: 10.3 Consensus size: 45
268266 GGGAGCTTTT
* * * ***
268276 TGATATTTTCAAAACCTTTGGGTCATCTGTAAGCCTTTCAGTTTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
268321 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
268366 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
268411 TAATGTTTTCAAAACCTCCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
268456 TGATGTTTTCAAAACCTTCGGGTCATTTGTAAGCCCTTCAGTGCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
268501 TGATGTTTTCAAAACATTCGGGTCATCTGTAATCCCTTTAGTGCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
268546 TGATGTTTTCAAAACTTTTGGGTCATCTGCAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
268591 TGATGTTTTCAAAACC-TCTGGGTCATCTATAAGCCCTTCAATGCA
1 TGATGTTTTCAAAACCTTC-GGGTCATCTGTAAGCCCTTCAGTGCA
* * *
268636 TGATGTTTTCAAAACCTCCGGGTTATCTTTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** * * *
268681 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTCCAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
268726 GGATGTTTTCAA
1 TGATGTTTTCAA
268738 CTGAGATTTT
Statistics
Matches: 372, Mismatches: 43, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
44 1 0.00
45 370 0.99
46 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:269013 original size:3 final size:3
Alignment explanation
Indices: 269005--269038 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
268995 ATTATGTTTA
269005 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
269039 AATAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:270525 original size:24 final size:23
Alignment explanation
Indices: 270498--270592 Score: 70
Period size: 23 Copynumber: 4.1 Consensus size: 23
270488 ATTGCTTTTA
270498 ATTTCTTTAATTTTGATTATTATT
1 ATTTCTTTAATTTT-ATTATTATT
* **
270522 ATTTTGTTTTGTTTTATTATTATT
1 A-TTTCTTTAATTTTATTATTATT
** * *
270546 ATTGATAT-ATGTTTA-AATTATT
1 ATTTCTTTAAT-TTTATTATTATT
270568 ATTT-TTTATATTTTATTATTATT
1 ATTTCTTTA-ATTTTATTATTATT
270591 AT
1 AT
270593 CTTAAGTCGT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
21 2 0.04
22 14 0.25
23 18 0.33
24 11 0.20
25 10 0.18
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.67
Consensus pattern (23 bp):
ATTTCTTTAATTTTATTATTATT
Found at i:276429 original size:76 final size:76
Alignment explanation
Indices: 276296--276437 Score: 250
Period size: 76 Copynumber: 1.9 Consensus size: 76
276286 TACTAACTTG
276296 ATTGGAGCTGAACTTGTAAAGACTTCATATCACATCACAAAGAGTACCTCGAAAAAAATACTTTC
1 ATTGGAGCTGAACTTGTAAAGACTTCATATCACATCACAAAGAGTACCTCGAAAAAAATACTTTC
276361 AGACAGTAACA
66 AGACAGTAACA
* *
276372 ATTGGAGCTGAACTTGTAGAGACTTCATATCACATCACAAAGAGTA-CTCGAAGAAAAATAGTTT
1 ATTGGAGCTGAACTTGTAAAGACTTCATATCACATCACAAAGAGTACCTCGAA-AAAAATACTTT
276436 CA
65 CA
276438 AACAAAAACA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
75 6 0.10
76 57 0.90
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (76 bp):
ATTGGAGCTGAACTTGTAAAGACTTCATATCACATCACAAAGAGTACCTCGAAAAAAATACTTTC
AGACAGTAACA
Found at i:276797 original size:98 final size:97
Alignment explanation
Indices: 276669--276897 Score: 334
Period size: 98 Copynumber: 2.3 Consensus size: 97
276659 ACATATTGCA
* *
276669 AAAATAAGGTTACTAGAGAAGAAGTATCTTAATGGGAAAGGTCTACTAAGCACCCGTATTGTCAC
1 AAAATAAGGTTACTAGAGAAGAAGTATCTTAATGGG-AAGGTCTACTAAGCACCCGCATTGCCAC
** *
276734 GCTCTACAGTAGTGCTTGAACCTTATAAATAAC
65 GCTCTACAGTAGTGCTCAAACCTAATAAATAAC
* * *
276767 AAAATAAGGTTATTAGAGAA-AGAGTATCTTAATTTGGAAGGTCTACTAAGCACTCGCATTGCCA
1 AAAATAAGGTTACTAGAGAAGA-AGTATCTTAA-TGGGAAGGTCTACTAAGCACCCGCATTGCCA
*
276831 CGCTCTACTGTAGTGCTCAAACCTAATAAATAAC
64 CGCTCTACAGTAGTGCTCAAACCTAATAAATAAC
*
276865 AAAATAAGGTTACTAGAGAAGTAGTATCTTAAT
1 AAAATAAGGTTACTAGAGAAGAAGTATCTTAAT
276898 CCGAGTATTC
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
97 2 0.02
98 112 0.96
99 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (97 bp):
AAAATAAGGTTACTAGAGAAGAAGTATCTTAATGGGAAGGTCTACTAAGCACCCGCATTGCCACG
CTCTACAGTAGTGCTCAAACCTAATAAATAAC
Found at i:277300 original size:20 final size:20
Alignment explanation
Indices: 277254--277300 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
277244 TGGACCTTTT
* *
277254 TTCGATTCGGTTTTACTTGG
1 TTCGATTCGGTTTAACTTAG
*
277274 TTTGATTCGAG-TTAACTTAG
1 TTCGATTCG-GTTTAACTTAG
277294 TTCGATT
1 TTCGATT
277301 TGGGTTCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGATTCGGTTTAACTTAG
Found at i:280582 original size:17 final size:17
Alignment explanation
Indices: 280541--280590 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
280531 CTCAAAGCCT
*
280541 CTCAAACACTCTCAAAG
1 CTCAAACCCTCTCAAAG
280558 CTCAAACCCTCTCAAAG
1 CTCAAACCCTCTCAAAG
*
280575 CTCAAACCCACTCAAA
1 CTCAAACCCTCTCAAA
280591 TTCTCGCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.16
Consensus pattern (17 bp):
CTCAAACCCTCTCAAAG
Found at i:282087 original size:13 final size:13
Alignment explanation
Indices: 282071--282115 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
282061 CCATTTACCC
*
282071 GACCCGACCTGTT
1 GACCCGACCAGTT
*
282084 GACCCGACCCGTT
1 GACCCGACCAGTT
282097 GACCCGACCAGTT
1 GACCCGACCAGTT
282110 GACCCG
1 GACCCG
282116 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (13 bp):
GACCCGACCAGTT
Found at i:282105 original size:18 final size:18
Alignment explanation
Indices: 282049--282094 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
282039 ACCGGTCACA
* *
282049 ACCCGACCAGACCCATTT
1 ACCCGACCCGACCCATTG
**
282067 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCATTG
282085 ACCCGACCCG
1 ACCCGACCCG
282095 TTGACCCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.48, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:284702 original size:24 final size:24
Alignment explanation
Indices: 284648--284742 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
284638 ATTTTCGACT
* * ** *
284648 TGAATTCTATTTTGATAAATGACC
1 TGAATTCTGTTATGATATCTGATC
*
284672 TGAATTCTGTTATGATTTCTGATC
1 TGAATTCTGTTATGATATCTGATC
* * *
284696 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTATGATATCTGATC
* *
284720 TGAATTCTGTTTTGATGTCTGAT
1 TGAATTCTGTTATGATATCTGAT
284743 ATCTTCGTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTATGATATCTGATC
Found at i:284712 original size:48 final size:48
Alignment explanation
Indices: 284651--284742 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
284641 TTCGACTTGA
* *
284651 ATTCTATTTTGATAAATGACCTGAATTCTGTTATGATTTCTGATCTGG
1 ATTCTATTCTGATAAATGACCTGAATTCTGTTATGATGTCTGATCTGG
* ** ** *
284699 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTGATGTCTGAT
1 ATTCTATTCTGATAAATGACCTGAATTCTGTTATGATGTCTGAT
284743 ATCTTCGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTCTATTCTGATAAATGACCTGAATTCTGTTATGATGTCTGATCTGG
Found at i:284740 original size:12 final size:11
Alignment explanation
Indices: 284675--284740 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
284665 AATGACCTGA
*
284675 ATTCTGTTATG
1 ATTCTGTTCTG
*
284686 ATTTCTGATCTGG
1 A-TTCTGTTCT-G
284699 ATTCTGTTCTG
1 ATTCTGTTCTG
284710 ATATCTGTTCTG
1 AT-TCTGTTCTG
*
284722 AATTCTGTTTTG
1 -ATTCTGTTCTG
284734 ATGTCTG
1 AT-TCTG
284741 ATATCTTCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.13
12 36 0.78
13 4 0.09
ACGTcount: A:0.15, C:0.14, G:0.20, T:0.52
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:289427 original size:13 final size:14
Alignment explanation
Indices: 289409--289438 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
289399 CGAGCCAAAT
289409 CTGTTTTTT-TGCA
1 CTGTTTTTTCTGCA
289422 CTGTTTTTTCTGCA
1 CTGTTTTTTCTGCA
289436 CTG
1 CTG
289439 CATTGTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.07, C:0.20, G:0.17, T:0.57
Consensus pattern (14 bp):
CTGTTTTTTCTGCA
Found at i:289691 original size:21 final size:22
Alignment explanation
Indices: 289654--289699 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
289644 AAGTCCGCTG
289654 AAAATAAAACGAAAATAAAATGA
1 AAAATAAAAC-AAAATAAAATGA
*
289677 AAAATAAAA-AAAATATAATGA
1 AAAATAAAACAAAATAAAATGA
289698 AA
1 AA
289700 TGGGTTGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
23 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AAAATAAAACAAAATAAAATGA
Found at i:295177 original size:18 final size:18
Alignment explanation
Indices: 295154--295191 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
295144 TTTTCCATCG
295154 TAATTTTCATCACATACA
1 TAATTTTCATCACATACA
295172 TAATTTTCATCACATACA
1 TAATTTTCATCACATACA
295190 TA
1 TA
295192 CTTTCCCGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTTTCATCACATACA
Found at i:298098 original size:2 final size:2
Alignment explanation
Indices: 298091--298120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
298081 TCAATCTACA
298091 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
298121 TGTTGAAAAC
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):
AT
Found at i:298444 original size:64 final size:64
Alignment explanation
Indices: 298368--298554 Score: 173
Period size: 64 Copynumber: 2.9 Consensus size: 64
298358 GCATCAATCC
*
298368 ATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTTCATGCATCGATGCACTCTC
1 ATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
298431 T
64 T
** ** *** *
298432 ATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTTCATGCATCGATGCACAAGCA
1 ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
* * * ** * * *
298496 ATGCACCGATGCACTCAGG-CTATTTTCAAACATCAAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACT-TGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCAC
298555 ACTTGGTGCA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
62 2 0.02
63 6 0.06
64 93 0.90
65 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCT
Found at i:298565 original size:64 final size:63
Alignment explanation
Indices: 298396--298575 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
298386 GAATAAATTG
* * * * *
298396 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCACCGATGCACTAGGCTATTATTAA
* *
298460 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCACCGATGCACT-AGGCTATTATTA
298523 A
63 A
* * *
298524 AACATCAAATGCATTTTATGCATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCACCGATGCACTA
298576 AGTGTTACAA
Statistics
Matches: 100, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 91 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCACCGATGCACTAGGCTATTATTAA
Found at i:300012 original size:13 final size:12
Alignment explanation
Indices: 299994--300030 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
299984 GTATAATAAG
299994 AAAAAATGAAATA
1 AAAAAAT-AAATA
300007 AAAAAATAAATA
1 AAAAAATAAATA
300019 AAATAAATAAAT
1 AAA-AAATAAAT
300031 TAGGATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:300022 original size:17 final size:17
Alignment explanation
Indices: 299997--300030 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
299987 TAATAAGAAA
*
299997 AAATGAAATAAAAAAAT
1 AAATAAAATAAAAAAAT
*
300014 AAATAAAATAAATAAAT
1 AAATAAAATAAAAAAAT
300031 TAGGATAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAAAAAAT
Found at i:300023 original size:9 final size:9
Alignment explanation
Indices: 299997--300029 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
299987 TAATAAGAAA
*
299997 AAATGAAAT
1 AAATAAAAT
300006 AAA-AAAAT
1 AAATAAAAT
300014 AAATAAAAT
1 AAATAAAAT
300023 AAATAAA
1 AAATAAA
300030 TTAGGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:300612 original size:73 final size:73
Alignment explanation
Indices: 300529--300756 Score: 269
Period size: 76 Copynumber: 3.1 Consensus size: 73
300519 TAAAACATCT
* **
300529 TAAATCCTAATTAAAACACTTAAAAATATTTAAACTAAAATACCTATAAAAAATAATATTTAAAA
1 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTATAAAAAATAATATTTAAAA
*
300594 TAATATTC
66 TAATATCC
* * *
300602 TAAATCCTAATTAAAATAC-TAAACCCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAATACTTAAA-CCTATTTAAACTAAAATACCTATAA-AAA-ATAATAT-TT
300666 AAAATAATATCC
62 AAAATAATATCC
* * ** * *
300678 TAAAACTTAATTAAAATACTTAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATAC--CTATAAAAAATAATATTTAA
*
300743 AATATTATCC
64 AATAATATCC
300753 TAAA
1 TAAA
300757 CTTGAGTTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
72 4 0.03
73 40 0.31
74 3 0.02
75 22 0.17
76 53 0.40
77 6 0.05
78 3 0.02
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTATAAAAAATAATATTTAAAA
TAATATCC
Found at i:301209 original size:3 final size:3
Alignment explanation
Indices: 301201--301242 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
301191 TATGTACTCC
*
301201 TGA TGA TGA TGA TGA TGT TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
301243 GATTGAGGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:301496 original size:25 final size:23
Alignment explanation
Indices: 301426--301497 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 23
301416 ATTACTTAAT
*
301426 TTATTTATTTTGTTAATTTTTTA
1 TTATTTATTTTTTTAATTTTTTA
* * *
301449 TTACTTAATTGTTTGAATGTTTTTA
1 TTA-TTTATTTTTTTAAT-TTTTTA
301474 TTATTTAGTGTTTTTTAATTTTTT
1 TTATTTA-T-TTTTTTAATTTTTT
301498 GGTTGTATCG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
23 3 0.08
24 13 0.34
25 15 0.39
26 7 0.18
ACGTcount: A:0.21, C:0.01, G:0.08, T:0.69
Consensus pattern (23 bp):
TTATTTATTTTTTTAATTTTTTA
Found at i:304874 original size:2 final size:2
Alignment explanation
Indices: 304867--304891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
304857 AAATCTATTA
304867 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
304892 AGATACTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:306703 original size:22 final size:23
Alignment explanation
Indices: 306678--306730 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
306668 GTATTAAAAT
* * *
306678 TAATTATTA-TAAAATAATATAA
1 TAATTAATATTAAAACAAAATAA
306700 TAA-TAATATTAAAACAAAATAA
1 TAATTAATATTAAAACAAAATAA
*
306722 TAATAAATA
1 TAATTAATA
306731 AATAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 17 0.68
23 4 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
TAATTAATATTAAAACAAAATAA
Found at i:306735 original size:14 final size:14
Alignment explanation
Indices: 306716--306751 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
306706 TATTAAAACA
306716 AAATAATAATAAAT-
1 AAATAA-AATAAATG
306730 AAATAAAATAAATG
1 AAATAAAATAAATG
306744 AAATAAAA
1 AAATAAAA
306752 AACTAGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
AAATAAAATAAATG
Found at i:306737 original size:19 final size:22
Alignment explanation
Indices: 306687--306740 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
306677 TTAATTATTA
*
306687 TAAAATAATATAATAATAATAT
1 TAAAATAAAATAATAATAATAT
*
306709 TAAAACAAAATAATAATAA-A-
1 TAAAATAAAATAATAATAATAT
306729 T-AAATAAAATAA
1 TAAAATAAAATAA
306741 ATGAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.34
20 1 0.03
21 1 0.03
22 17 0.59
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAATAAAATAATAATAATAT
Found at i:307922 original size:30 final size:31
Alignment explanation
Indices: 307867--307926 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
307857 TTATATGAGC
307867 TATGTGATAAAGGTATGGAAAATGATATGTA
1 TATGTGATAAAGGTATGGAAAATGATATGTA
307898 TATGTGATAAAGGTATGG-AAATGATATGT
1 TATGTGATAAAGGTATGGAAAATGATATGT
307927 CTACGCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (31 bp):
TATGTGATAAAGGTATGGAAAATGATATGTA
Found at i:308259 original size:24 final size:23
Alignment explanation
Indices: 308179--308256 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
308169 TATGGCGCTA
308179 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTT
*
308202 CGGTGCAATTCTACGCGGTC-CTT
1 CGGTGCAATTCTACGTGG-CACTT
*
308225 CAGG-ACAAATTCTACGTGGCACTT
1 C-GGTGC-AATTCTACGTGGCACTT
308249 CGGTGCAA
1 CGGTGCAA
308257 ATTTATACGA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
23 27 0.59
24 19 0.41
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.27
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTT
Found at i:318637 original size:118 final size:117
Alignment explanation
Indices: 318428--318734 Score: 343
Period size: 118 Copynumber: 2.6 Consensus size: 117
318418 CATTTCCAGT
* * * * *
318428 GAAGAAGTTCCTAATGAGAAGT-ACTTATTCAACGTTTCACTCGATTCCATCACAAAAGGATGTG
1 GAAGAAGTTCATAATGAGAAGTAACTTATTCAAC-CTT-AGTCAATTCCATCA-AAAAGGAGGTG
* * * **
318492 AATCAGCATTTCTAATGGAAGGGTTTGTAATGAGAAGAACTCATCTGATAAGGGA
63 AATCAACATTTCCAATAGAAGGGTTTGTAATGAGAAGAACTCATCCAATAAGGGA
* * *
318547 GAAGAAGTTCATAATGAG-AGTAACTTATTTAACCTTAAGTCAATTTCATCAAAGAAGGAGGTGG
1 GAAGAAGTTCATAATGAGAAGTAACTTATTCAACCTT-AGTCAATTCCATCAAA-AAGGAGGTGA
* * **
318611 ATTAACATTTCCAATAGAAGGGTTTGTAATGATAAGAACTCATCCAATGTGGGA
64 ATCAACATTTCCAATAGAAGGGTTTGTAATGAGAAGAACTCATCCAATAAGGGA
* *
318665 GAAGAAG-TCATAATGAGAAG-AACTTATTCAACCTTAGCTCAATTCCATCACATAAGGAGTTGA
1 GAAGAAGTTCATAATGAGAAGTAACTTATTCAACCTTAG-TCAATTCCATCA-AAAAGGAGGTGA
*
318728 AACAACA
64 ATCAACA
318735 CCTACCTTGT
Statistics
Matches: 158, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
116 2 0.01
117 50 0.32
118 79 0.50
119 27 0.17
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (117 bp):
GAAGAAGTTCATAATGAGAAGTAACTTATTCAACCTTAGTCAATTCCATCAAAAAGGAGGTGAAT
CAACATTTCCAATAGAAGGGTTTGTAATGAGAAGAACTCATCCAATAAGGGA
Found at i:319038 original size:3 final size:3
Alignment explanation
Indices: 319030--319093 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
319020 TAAACCAATA
* *
319030 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
319076 TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TA-T TAT TA
319094 CAAACCAGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 51 0.93
4 4 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:325080 original size:19 final size:19
Alignment explanation
Indices: 325056--325093 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
325046 AGTGTATGAT
325056 GTATGAAAATATTTCATAA
1 GTATGAAAATATTTCATAA
325075 GTATGAAAATATTTCATAA
1 GTATGAAAATATTTCATAA
325094 TATCTCTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (19 bp):
GTATGAAAATATTTCATAA
Found at i:325260 original size:2 final size:2
Alignment explanation
Indices: 325255--325293 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
325245 TAAAAAAATA
325255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
325294 AGTTATTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:326324 original size:21 final size:21
Alignment explanation
Indices: 326294--326867 Score: 404
Period size: 21 Copynumber: 27.6 Consensus size: 21
326284 GATTTACATA
*
326294 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326315 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
326336 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
326357 TT--CGTTGCGGTAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326376 TTCGCGTTGCGATAATCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
326397 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
326418 TT--TGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
326437 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
326460 TT--CGTTGTGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
326481 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
326502 TT--CGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
326521 TTCGCGTTACGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
326544 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326563 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326584 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
326607 -T-ACGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
326626 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
326649 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
326668 TTCGCATTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
326689 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
326708 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
326731 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
326750 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
326773 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326792 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
326813 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
326836 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
326855 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
326868 TTATTCCAAA
Statistics
Matches: 439, Mismatches: 80, Indels: 68
0.75 0.14 0.12
Matches are distributed among these distances:
19 100 0.23
20 1 0.00
21 282 0.64
22 1 0.00
23 55 0.13
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:326688 original size:187 final size:188
Alignment explanation
Indices: 326294--326880 Score: 811
Period size: 187 Copynumber: 3.1 Consensus size: 188
326284 GATTTACATA
* * *
326294 TTCGCATTGCGA--TAGTCCAAGTTCGCGTTGCGATAGTCAAAGTTCGCGTTGCGA-TT-TTCCA
1 TTCGCATTGCGATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCA
* * *
326355 AATTCGTTGCGGTAGTCCAAGTTCGCGTTGCGATAATCCAAGTTCGCATTGCGATT-TTCCAAAT
64 AATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAATCCAAGTTCGCGTTGCGATTATTCCAAGT
** * * * *
326419 TTGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTGATTTATTCCAAA
129 ACGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAG
* *
326481 TTCG--TTGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCGCGTTACGATTTATTCCAAA
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
* *
326544 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTA
66 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAATCCAAGTTCGCGTTGCGA-TTATTCCAAGTA
326609 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
130 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
326668 TTCGCATTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
* * * *
326731 TTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA-TAGTCCAAGT
66 TTCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAATCCAAGTTCGCGTTGCGATTATTCCAAG-
* *
326793 TCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
128 T-ACGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
326855 TTCGCATTGCGATTTATTCCAAATTC
1 TTCGCATTGCGATTTATTCCAAATTC
326881 ATAACGATAG
Statistics
Matches: 361, Mismatches: 25, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
185 40 0.11
186 3 0.01
187 234 0.65
188 6 0.02
189 78 0.22
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (188 bp):
TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAA
TTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAATCCAAGTTCGCGTTGCGATTATTCCAAGTAC
GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:326723 original size:124 final size:124
Alignment explanation
Indices: 326567--326804 Score: 449
Period size: 124 Copynumber: 1.9 Consensus size: 124
326557 TCCAAGTTCG
*
326567 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTACGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATACGTTGCGATAGTCGAAGTTCGCG
326632 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTTCCAAATT
66 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTTCCAAATT
*
326691 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATACGTTGCGATAGTCGAAGTTCGCG
*
326756 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGAT
66 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGAT
326805 AGTCGAAGTT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 111 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (124 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATACGTTGCGATAGTCGAAGTTCGCG
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTTCCAAATT
Found at i:326842 original size:42 final size:42
Alignment explanation
Indices: 326796--326880 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
326786 TCCAAGTTCG
*
326796 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
326838 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
326880 C
1 C
326881 ATAACGATAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
Found at i:326889 original size:42 final size:42
Alignment explanation
Indices: 326801--326892 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
326791 GTTCGCGTTG
* * **
326801 CGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 CGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCATAA
326843 CGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCATAA
1 CGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCATAA
326885 CGATAGTC
1 CGATAGTC
326893 CAAAATCGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (42 bp):
CGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCATAA
Found at i:326902 original size:42 final size:42
Alignment explanation
Indices: 326814--326902 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
326804 TAGTCGAAGT
* * ** * **
326814 TCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATTTATTCCAAATTCATAACGATAGTCCAAAA
326856 TCGCATTGCGATTTATTCCAAATTCATAACGATAGTCCAAAA
1 TCGCATTGCGATTTATTCCAAATTCATAACGATAGTCCAAAA
326898 TCGCA
1 TCGCA
326903 ACGATTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATTTATTCCAAATTCATAACGATAGTCCAAAA
Found at i:326996 original size:6 final size:6
Alignment explanation
Indices: 326985--327017 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
326975 GACACTTATT
*
326985 ACCACG ACCACG ACCACG ACCATG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
327018 CGAGACAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.48, G:0.15, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:327649 original size:21 final size:21
Alignment explanation
Indices: 327623--327778 Score: 135
Period size: 21 Copynumber: 7.4 Consensus size: 21
327613 ATTTTGGACT
*
327623 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
327644 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAACTTGGAATAA
327665 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
327686 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
* *
327707 ATTGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
327728 ATCGCAAGGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
327749 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
327770 ATCACAACG
1 ATCGCAACG
327779 CGAACTTCGA
Statistics
Matches: 108, Mismatches: 15, Indels: 24
0.73 0.10 0.16
Matches are distributed among these distances:
19 31 0.29
20 1 0.01
21 44 0.41
22 1 0.01
23 31 0.29
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:327681 original size:42 final size:42
Alignment explanation
Indices: 327619--327838 Score: 295
Period size: 42 Copynumber: 5.3 Consensus size: 42
327609 TGCGATTTTG
*
327619 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
327661 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
327703 GACTATTGCAACGAATTTGGAATAAATCGCAAGGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
327745 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* **
327787 GACTATCGCAAATC-AGTTTCCAGAT---TCGCAACGCGAACTTC
1 GACTATCGC-AA-CGAATTTGGA-ATAAATCGCAACGCGAACTTC
327828 GACTATCGCAA
1 GACTATCGCAA
327839 TGCGATAGTC
Statistics
Matches: 161, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.01
41 24 0.15
42 125 0.78
43 7 0.04
44 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:330134 original size:102 final size:102
Alignment explanation
Indices: 329940--330145 Score: 286
Period size: 102 Copynumber: 2.0 Consensus size: 102
329930 AATGCCTTCA
*** *
329940 AACAACACGAATGAAACCAACAATCAGTTAGTCTAATGGGATAAAATGTTAGATCTCTTACGCAA
1 AACAACACGAATGAAACCAACAATCAGTTAGTCTAATGGGATAAAACACTAGATCTCTTAAGCAA
* * *
330005 GGTCAGAGGTTTAAATCTTGGCATTTGTGAATGGAGC
66 GGTCAAAGGTTCAAATCTTGACATTTGTGAATGGAGC
* * *
330042 AACAACACGAATGAAACCAACAATCAGTTAGTCTAGTGGGATGAGACACTAGATCTCTTAAGCAA
1 AACAACACGAATGAAACCAACAATCAGTTAGTCTAATGGGATAAAACACTAGATCTCTTAAGCAA
* * * *
330107 GTTCAAATGTTCAAATTTTGACGTTTGTGAATGGAGC
66 GGTCAAAGGTTCAAATCTTGACATTTGTGAATGGAGC
330144 AA
1 AA
330146 ATTGGATTGA
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (102 bp):
AACAACACGAATGAAACCAACAATCAGTTAGTCTAATGGGATAAAACACTAGATCTCTTAAGCAA
GGTCAAAGGTTCAAATCTTGACATTTGTGAATGGAGC
Found at i:330461 original size:42 final size:42
Alignment explanation
Indices: 330379--330521 Score: 171
Period size: 42 Copynumber: 3.3 Consensus size: 42
330369 CAAAAACCGT
* * *
330379 CGCAATAGGTCAAGATCTATAGAGGCGTTTTTGGAACAAACGC
1 CGCAAAAGGTCAAGATCTATAGCGGC-ATTTTGGAACAAACGC
*
330422 CACAAAAGGTCGAA-ATCTATAGCGGCATTTTGGAACAAACGC
1 CGCAAAAGGTC-AAGATCTATAGCGGCATTTTGGAACAAACGC
* *
330464 CGTAAAAGGTCAAGATATATAGCGGCATTTTTTTGGATACAAACGC
1 CGCAAAAGGTCAAGATCTATAGCGGCA---TTTTGGA-ACAAACGC
330510 CGCAAAAGGTCA
1 CGCAAAAGGTCA
330522 TATCTACAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.02
42 36 0.42
43 20 0.23
44 2 0.02
45 7 0.08
46 19 0.22
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (42 bp):
CGCAAAAGGTCAAGATCTATAGCGGCATTTTGGAACAAACGC
Found at i:336226 original size:25 final size:26
Alignment explanation
Indices: 336185--336238 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
336175 TTTAACAGTG
*
336185 AAATAATCAAAGAAATGATTTAGAAT
1 AAATAATCAAAGAAATGATTAAGAAT
*
336211 AAATAAT-AAAGTAATGATTAAGAAT
1 AAATAATCAAAGAAATGATTAAGAAT
336236 AAA
1 AAA
336239 AAACTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (26 bp):
AAATAATCAAAGAAATGATTAAGAAT
Found at i:336251 original size:25 final size:23
Alignment explanation
Indices: 336197--336251 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 23
336187 ATAATCAAAG
* *
336197 AAATGATTTAGAATAAATAATAA
1 AAATGATTAAGAATAAAAAATAA
336220 AGTAATGATTAAGAATAAAAAACTAA
1 A--AATGATTAAGAATAAAAAA-TAA
336246 TAAATG
1 -AAATG
336252 GTAAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.04
25 21 0.81
26 3 0.12
27 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (23 bp):
AAATGATTAAGAATAAAAAATAA
Found at i:338315 original size:19 final size:19
Alignment explanation
Indices: 338293--338343 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
338283 CATAGTAGAG
338293 ATCAAAGATCATAACAAAA
1 ATCAAAGATCATAACAAAA
* * * *
338312 ATCAGAGATCAAAACATAT
1 ATCAAAGATCATAACAAAA
*
338331 ATCAAAGTTCATA
1 ATCAAAGATCATA
338344 GAAGAAATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.22
Consensus pattern (19 bp):
ATCAAAGATCATAACAAAA
Found at i:340086 original size:89 final size:89
Alignment explanation
Indices: 339825--340248 Score: 611
Period size: 89 Copynumber: 4.8 Consensus size: 89
339815 TCTATGACTT
* * * *
339825 GTAAGACCTTATAGTTTCCCCGGGTT-CTTATTTTGTGTGCAAGGGTAAAACCTTATAGTTTTCC
1 GTAAGACCTTATAGTTTCCCCAGGTTCCTT-TGTTATGTGCAAGGGTAAGACCTTATAGTTTTCC
339889 CCAGGTTCCTTTGTTGTGTGCAAGG
65 CCAGGTTCCTTTGTTGTGTGCAAGG
* * * *
339914 GTAAGACCTTACAGTTTTCCCCAGGTTCCTTT-TCTATGTGCTAGGGTAAGACCTTACAGTTCTC
1 GTAAGACCTTATAG-TTTCCCCAGGTTCCTTTGT-TATGTGCAAGGGTAAGACCTTATAGTTTTC
339978 CCCAGGTTCCTTTGTTGTGTGCAAGG
64 CCCAGGTTCCTTTGTTGTGTGCAAGG
** * *
340004 GTAAGACCTTATAGTTTCGTCAGGTTCCTTTGTTACGTGCAAGGGTAAGACCTTATAGTTTTCCT
1 GTAAGACCTTATAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGACCTTATAGTTTTCCC
* *
340069 CAGGTTCCTTTGCTGTGTGCAAGC
66 CAGGTTCCTTTGTTGTGTGCAAGG
* * * *
340093 ATAAGACCATATAGTTTCCCCAGGTTCTTTTGGTT-TGTGCAAGGGTAAGACCTTACAGTTTTCC
1 GTAAGACCTTATAGTTTCCCCAGGTTCCTTT-GTTATGTGCAAGGGTAAGACCTTATAGTTTTCC
*
340157 CCAGGTTCCTTTATTGTGTGCAAGG
65 CCAGGTTCCTTTGTTGTGTGCAAGG
*
340182 GTGAGACCTTATAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGACCTTATAGTTTTCCC
1 GTAAGACCTTATAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGACCTTATAGTTTTCCC
340247 CA
66 CA
340249 AGCTCCTATA
Statistics
Matches: 296, Mismatches: 33, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
88 3 0.01
89 210 0.71
90 80 0.27
91 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (89 bp):
GTAAGACCTTATAGTTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGACCTTATAGTTTTCCC
CAGGTTCCTTTGTTGTGTGCAAGG
Found at i:340267 original size:45 final size:45
Alignment explanation
Indices: 339825--340248 Score: 574
Period size: 45 Copynumber: 9.5 Consensus size: 45
339815 TCTATGACTT
* *
339825 GTAAGACCTTATAG-TTTCCCCGGGTT-CTTATTTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTT-TGTTGTGTGCAAGG
*
339869 GTAAAACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* * *
339914 GTAAGACCTTACAGTTTTCCCCAGGTTCCTTT-TCTATGTGCTAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGT-TGTGTGCAAGG
* *
339959 GTAAGACCTTACAGTTCTCCCCAGGTTCCTTTGTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
** **
340004 GTAAGACCTTATAG-TTTCGTCAGGTTCCTTTGTTACGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* * *
340048 GTAAGACCTTATAGTTTTCCTCAGGTTCCTTTGCTGTGTGCAAGC
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* * *
340093 ATAAGACCATATAG-TTTCCCCAGGTTCTTTTGGTT-TGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTT-GTTGTGTGCAAGG
* *
340137 GTAAGACCTTACAGTTTTCCCCAGGTTCCTTTATTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* *
340182 GTGAGACCTTATAG-TTTCCCCAGGTTCCTTTGTTATGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
340226 GTAAGACCTTATAGTTTTCCCCA
1 GTAAGACCTTATAGTTTTCCCCA
340249 AGCTCCTATA
Statistics
Matches: 334, Mismatches: 37, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
44 130 0.39
45 200 0.60
46 4 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (45 bp):
GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
Found at i:347116 original size:45 final size:45
Alignment explanation
Indices: 347048--347461 Score: 552
Period size: 45 Copynumber: 9.2 Consensus size: 45
347038 TCTATGACTT
* * *
347048 GTAAGACCTTATAG-TTTCCCCAGGTTCCTTTGGTGTGTGAAAAG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* ** *
347092 GTAAAACCTTGCAGTTTTCCCCAGGTTTCTTTGTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
347137 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
** * **
347182 GTAAGACCTTGCAGTTTTCCCCAGGTTCCTTTTGCTAAGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCC-TTTGTTGTGTGCAAGG
** *
347228 GTAAGACCTTATAG-TTTCCCCAGGTTCCTTTGGAGAGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* *
347272 GTAAGACCTTAGAGTTTTCCCCAGGTTCCTTTATTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
*
347317 GTAAGACCTTAAAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
347362 GTGAA-ACCTTATAG--TTCCCCAGGTTCCTTTGTTGTGTGCAAGG
1 GT-AAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
* * *
347405 GTAAGACCTTATAGTTTTCCCCAGGCT-CTTCTGTTTTGTACACAGG
1 GTAAGACCTTATAGTTTTCCCCAGGTTCCTT-TGTTGTGTGCA-AGG
*
347451 GTAAGCCCTTA
1 GTAAGACCTTA
347462 CCGGGTGTAC
Statistics
Matches: 328, Mismatches: 33, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
42 2 0.01
43 40 0.12
44 40 0.12
45 206 0.63
46 40 0.12
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (45 bp):
GTAAGACCTTATAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGG
Found at i:349976 original size:14 final size:15
Alignment explanation
Indices: 349957--349991 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
349947 AGTCAACAGA
349957 TTGACTCAGA-CGAG
1 TTGACTCAGACCGAG
349971 TTGACTCAGACCGAG
1 TTGACTCAGACCGAG
349986 TTGACT
1 TTGACT
349992 TGATCGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (15 bp):
TTGACTCAGACCGAG
Found at i:352349 original size:61 final size:58
Alignment explanation
Indices: 352280--352421 Score: 185
Period size: 61 Copynumber: 2.4 Consensus size: 58
352270 TACCCCGTAT
* * * *
352280 AAAAATAATTTCAGTCAATAAATAGAGATATCAGAAATCAGAGAAGAGATCAGAGATTATC
1 AAAAATAATTTCAGTCAGTAAATAGAGATATAAAAAATCAAAGAAGAGATC--AGA-TATC
* * *
352341 AAAAATAATTTCAATCAGTAAATAGAGATATAAAAAATCAAAGCAGAGATCAGATGTC
1 AAAAATAATTTCAGTCAGTAAATAGAGATATAAAAAATCAAAGAAGAGATCAGATATC
*
352399 ATAAATAATTTCAGTCAGTAAAT
1 AAAAATAATTTCAGTCAGTAAAT
352422 TAGCAGACAG
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
58 24 0.33
59 3 0.04
61 45 0.62
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (58 bp):
AAAAATAATTTCAGTCAGTAAATAGAGATATAAAAAATCAAAGAAGAGATCAGATATC
Found at i:358740 original size:28 final size:29
Alignment explanation
Indices: 358708--358776 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
358698 TTAAAGTCAA
* *
358708 TGGGTTGACTCGGACGTGTTAACTCATAC
1 TGGGTTGACTCGGACGGGTTAACTCAGAC
* *
358737 -GGGTTGACT-AGACGGGTTGACTCAGAC
1 TGGGTTGACTCGGACGGGTTAACTCAGAC
*
358764 TGTGTTGACTCGG
1 TGGGTTGACTCGG
358777 TCAAGTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 14 0.44
28 17 0.53
29 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGGTTGACTCGGACGGGTTAACTCAGAC
Found at i:358753 original size:13 final size:14
Alignment explanation
Indices: 358709--358774 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 14
358699 TAAAGTCAAT
*
358709 GGGTTGACTCGGAC
1 GGGTTGACTCAGAC
* * *
358723 GTGTTAACTCATAC
1 GGGTTGACTCAGAC
358737 GGGTTGACT-AGAC
1 GGGTTGACTCAGAC
358750 GGGTTGACTCAGAC
1 GGGTTGACTCAGAC
*
358764 TGTGTTGACTC
1 -GGGTTGACTC
358775 GGTCAAGTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 12 0.29
14 21 0.50
15 9 0.21
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (14 bp):
GGGTTGACTCAGAC
Found at i:362018 original size:21 final size:20
Alignment explanation
Indices: 361992--362031 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
361982 AAATATTTAA
361992 AAATATAGATAATTTTATTTT
1 AAATAT-GATAATTTTATTTT
* *
362013 AAATATTATACTTTTATTT
1 AAATATGATAATTTTATTT
362032 AATTAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AAATATGATAATTTTATTTT
Found at i:362845 original size:20 final size:20
Alignment explanation
Indices: 362820--362865 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
362810 TCATACTAAT
362820 TTTTTTTGTAATTTTTT-GGA
1 TTTTTTTGT-ATTTTTTCGGA
*
362840 TTTTTTTGTATTTTTTCTGA
1 TTTTTTTGTATTTTTTCGGA
362860 TTTTTT
1 TTTTTT
362866 ATATTTGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.76
Consensus pattern (20 bp):
TTTTTTTGTATTTTTTCGGA
Found at i:363875 original size:22 final size:25
Alignment explanation
Indices: 363845--363895 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 25
363835 TTTTTTAGAT
*
363845 AAAATAATTA-AA-TATTATTTT-A
1 AAAACAATTATAATTATTATTTTGA
*
363867 AAAACAATTATAATTTTTATTTTGA
1 AAAACAATTATAATTATTATTTTGA
363892 AAAA
1 AAAA
363896 TTGGTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 2 0.08
24 8 0.33
25 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAACAATTATAATTATTATTTTGA
Found at i:365834 original size:30 final size:31
Alignment explanation
Indices: 365776--365835 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
365766 TTTCTCTCTT
* *
365776 CTCTTTATTTTTTTTCTGGTTTCCCCGAATC
1 CTCTCTATTTTTTTTCTGGTTTCACCGAATC
365807 CTCTCTATTTTTTTT-T-GTTCTCACCGAAT
1 CTCTCTATTTTTTTTCTGGTT-TCACCGAAT
365836 GCATCCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 9 0.35
31 14 0.54
ACGTcount: A:0.12, C:0.25, G:0.08, T:0.55
Consensus pattern (31 bp):
CTCTCTATTTTTTTTCTGGTTTCACCGAATC
Found at i:366195 original size:2 final size:2
Alignment explanation
Indices: 366188--366220 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
366178 TATGTAAGTA
366188 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
366221 CATGTATGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:366789 original size:84 final size:84
Alignment explanation
Indices: 366687--366855 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
366677 TGTACTCATC
366687 TTTTGGAAGTGTTCTCCGACTCCCAGCTCTTATGATCTTATTTAGGTTGTACGATGCCTTATCAA
1 TTTTGGAAGTGTTCTCCGACTCCCAGCTCTTATGATCTTATTTAGGTTGTACGATGCCTTATCAA
366752 GAGATTTATGCAATCGCCT
66 GAGATTTATGCAATCGCCT
366771 TTTTGGAAGTGTTCTCCGACTCCCAGCTCTTATGATCTTATTTAGGTTGTACGATGCCTTATCAA
1 TTTTGGAAGTGTTCTCCGACTCCCAGCTCTTATGATCTTATTTAGGTTGTACGATGCCTTATCAA
366836 GAGATTTATGCAATCGCCT
66 GAGATTTATGCAATCGCCT
366855 T
1 T
366856 CTATGCAATA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (84 bp):
TTTTGGAAGTGTTCTCCGACTCCCAGCTCTTATGATCTTATTTAGGTTGTACGATGCCTTATCAA
GAGATTTATGCAATCGCCT
Found at i:367359 original size:93 final size:93
Alignment explanation
Indices: 367200--367390 Score: 328
Period size: 93 Copynumber: 2.1 Consensus size: 93
367190 CAATTCTCTC
*
367200 TGATTCCTTCAATCTGGTCTTGCTCAATTTGAATCTGCTCGTATATGTCATTCTCTTGATATTCT
1 TGATTCCTTCAATATGGTCTTGCTCAATTTGAATCTGCTCGTATATGTCATTCTCTTGATATTCT
* * *
367265 ATTATCTTCGAGTAAAGTTATTCTGGAG
66 ATTATCTACGAGTAAAGTGATTATGGAG
* *
367293 TGATTCCTTCAATATGGTCTTGCTCAATTTGAATCTGCTCGTATTTGTCATTCTCTTGATGTTCT
1 TGATTCCTTCAATATGGTCTTGCTCAATTTGAATCTGCTCGTATATGTCATTCTCTTGATATTCT
367358 ATTATCTACGAGTAAAGTGATTATGGAG
66 ATTATCTACGAGTAAAGTGATTATGGAG
367386 TGATT
1 TGATT
367391 GTGTTTGATC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (93 bp):
TGATTCCTTCAATATGGTCTTGCTCAATTTGAATCTGCTCGTATATGTCATTCTCTTGATATTCT
ATTATCTACGAGTAAAGTGATTATGGAG
Found at i:367507 original size:12 final size:12
Alignment explanation
Indices: 367469--367518 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
367459 CCTTGTCTTC
367469 TTTTTCTTTG--
1 TTTTTCTTTGCT
367479 TTTTTCTTTG-T
1 TTTTTCTTTGCT
*
367490 TGTTTTCTCTGCT
1 T-TTTTCTTTGCT
367503 TTTTT-TTTGCT
1 TTTTTCTTTGCT
367514 TTTTT
1 TTTTT
367519 TTTCTCTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 10 0.29
11 11 0.31
12 12 0.34
13 2 0.06
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTGCT
Found at i:367519 original size:12 final size:12
Alignment explanation
Indices: 367469--367561 Score: 50
Period size: 13 Copynumber: 7.4 Consensus size: 12
367459 CCTTGTCTTC
*
367469 TTTT-TCTTTGT
1 TTTTCTCTTTTT
367480 TTTTCT-TTGTTGT
1 TTTTCTCTT-TT-T
367493 TTTCTCTGCTTTTT
1 TTT-TCT-CTTTTT
*
367507 TTTT-GCTTTTT
1 TTTTCTCTTTTT
367518 TTTTCTCTTTGTT
1 TTTTCTCTTT-TT
* *
367531 TTTTAT-TTGCTTC
1 TTTTCTCTT--TTT
367544 TTTTCTCTTTGTT
1 TTTTCTCTTT-TT
367557 TTTTC
1 TTTTC
367562 CGTTCTCTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
11 16 0.25
12 9 0.14
13 24 0.38
14 10 0.16
15 2 0.03
16 2 0.03
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.76
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:367519 original size:24 final size:23
Alignment explanation
Indices: 367469--367534 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
367459 CCTTGTCTTC
* *
367469 TTTTTCTTTG-TTTTTCTTTGTT
1 TTTTTCTCTGCTTTTTTTTTGTT
*
367491 GTTTTCTCTGCTTTTTTTTTGCTT
1 TTTTTCTCTGCTTTTTTTTTG-TT
*
367515 TTTTTTTCT-CTTTGTTTTTT
1 TTTTTCTCTGCTTT-TTTTTT
367535 ATTTGCTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.22
23 13 0.36
24 15 0.42
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (23 bp):
TTTTTCTCTGCTTTTTTTTTGTT
Found at i:367547 original size:26 final size:25
Alignment explanation
Indices: 367465--367560 Score: 101
Period size: 26 Copynumber: 3.8 Consensus size: 25
367455 TGCTCCTTGT
*
367465 CTTCTTTT-TCTTTGTTTTTCTTTG
1 CTTCTTTTCTCTTTGTTTTTTTTTG
*
367489 -TTGTTTTCTC--TGCTTTTTTTTTG
1 CTTCTTTTCTCTTTG-TTTTTTTTTG
*
367512 CTTTTTTTTTCTCTTTGTTTTTTATTTG
1 C--TTCTTTTCTCTTTGTTTTTT-TTTG
367540 CTTCTTTTCTCTTTGTTTTTT
1 CTTCTTTTCTCTTTGTTTTTT
367561 CCGTTCTCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
22 2 0.03
23 15 0.25
24 2 0.03
26 28 0.47
27 6 0.10
28 7 0.12
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (25 bp):
CTTCTTTTCTCTTTGTTTTTTTTTG
Found at i:367559 original size:38 final size:37
Alignment explanation
Indices: 367465--367561 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
367455 TGCTCCTTGT
*
367465 CTTCTTTTTCTTTG-TTTTTCTTTGTTGTTTTCTCTG
1 CTTCTTTTTCTTTGTTTTTTCTTTGTTGTTTTATCTG
* * *
367501 CTTTTTTTTTGCTTTTTTTTTCTCTTTGTT-TTTTATTTG
1 C-TTCTTTTT-CTTTGTTTTT-TCTTTGTTGTTTTATCTG
367540 CTTCTTTTCTCTTTGTTTTTTC
1 CTTCTTTT-TCTTTGTTTTTTC
367562 CGTTCTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
36 1 0.02
37 9 0.18
38 19 0.38
39 13 0.26
40 8 0.16
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.75
Consensus pattern (37 bp):
CTTCTTTTTCTTTGTTTTTTCTTTGTTGTTTTATCTG
Found at i:371332 original size:25 final size:24
Alignment explanation
Indices: 371304--371350 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
371294 CATAAATTCG
371304 AAGGACAAAAATAACACAAAACATA
1 AAGGACAAAAATAACA-AAAACATA
* *
371329 AAGGACTAAAATAATAAAAACA
1 AAGGACAAAAATAACAAAAACA
371351 GAAACTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.68, C:0.13, G:0.09, T:0.11
Consensus pattern (24 bp):
AAGGACAAAAATAACAAAAACATA
Found at i:371427 original size:58 final size:59
Alignment explanation
Indices: 371329--371455 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 59
371319 ACAAAACATA
* * * *
371329 AAGGACTAAAATAATAAAAACAGAAACTTAGAAGACTAAAATGGAAGAAAC-GTATATTT
1 AAGGACCAAAATAACAAAAACAGAAACTTAGAAGACTAAAATAGAAGAAACAG-AAATTT
* * * *
371388 AAGGACCAAAAT-ACAAATACAGAAGCTTA-AAGGGCTAAAATAGAAGTAACAGAAATTT
1 AAGGACCAAAATAACAAAAACAGAAACTTAGAA-GACTAAAATAGAAGAAACAGAAATTT
*
371446 AGGGACCAAA
1 AAGGACCAAA
371456 CTGGAGAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 2 0.04
58 43 0.75
59 12 0.21
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (59 bp):
AAGGACCAAAATAACAAAAACAGAAACTTAGAAGACTAAAATAGAAGAAACAGAAATTT
Found at i:372473 original size:38 final size:36
Alignment explanation
Indices: 372388--372475 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 36
372378 ACTTTATTTT
* *
372388 GTTCGGGTCGGGTCGGGTTTTTTTAGTGTGATATTCG
1 GTTC-GGTCGGGTCGAGTTTTTTTAGTGTGATATTCA
*
372425 GGTCGAGTCGGGTCGAGTTTTTTTAAGTGTGATATTCA
1 GTTCG-GTCGGGTCGAGTTTTTTT-AGTGTGATATTCA
372463 GTTCAGGTCGGGT
1 GTTC-GGTCGGGT
372476 TCGGGTTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
36 1 0.02
37 20 0.45
38 22 0.50
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.40
Consensus pattern (36 bp):
GTTCGGTCGGGTCGAGTTTTTTTAGTGTGATATTCA
Found at i:373141 original size:16 final size:18
Alignment explanation
Indices: 373120--373166 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
373110 ATATGGAATT
373120 AGATTCCAATTCC-T-AC
1 AGATTCCAATTCCTTCAC
373136 AGATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
373154 AGATTTCAATTCC
1 AGATTCCAATTCC
373167 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 13 0.46
17 1 0.04
18 14 0.50
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:373733 original size:23 final size:22
Alignment explanation
Indices: 373706--373750 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
373696 CTGGTTTCCC
*
373706 CGAATCCTCTGTGATTTTTTTTT
1 CGAATCCTCTCT-ATTTTTTTTT
*
373729 CGAATGCTCTCTATTTTTTTTT
1 CGAATCCTCTCTATTTTTTTTT
373751 GTTCTCATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.13, C:0.18, G:0.11, T:0.58
Consensus pattern (22 bp):
CGAATCCTCTCTATTTTTTTTT
Found at i:377239 original size:14 final size:14
Alignment explanation
Indices: 377220--377307 Score: 58
Period size: 14 Copynumber: 6.2 Consensus size: 14
377210 TTTTTATTTT
377220 ATTTTAGTCCTTTA
1 ATTTTAGTCCTTTA
377234 ATTTTA-TCACTTTA
1 ATTTTAGTC-CTTTA
*
377248 ATTTT-CTGCCATTT-
1 ATTTTAGT-CC-TTTA
377262 ATTTCT-GTCCTTTA
1 ATTT-TAGTCCTTTA
* **
377276 CTTTTCAGTAATTTA
1 ATTTT-AGTCCTTTA
*
377291 ATTTCAGTCCTTTA
1 ATTTTAGTCCTTTA
377305 ATT
1 ATT
377308 ATGGTACTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
13 6 0.10
14 37 0.64
15 15 0.26
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTTTAGTCCTTTA
Found at i:377274 original size:28 final size:29
Alignment explanation
Indices: 377230--377307 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
377220 ATTTTAGTCC
* * *
377230 TTTAATTTTA-TCACTTTAATTTTCTGCCA
1 TTTAATTTCAGTC-CTTTAATTTTCAGCAA
* * *
377259 TTT-ATTTCTGTCCTTTACTTTTCAGTAA
1 TTTAATTTCAGTCCTTTAATTTTCAGCAA
377287 TTTAATTTCAGTCCTTTAATT
1 TTTAATTTCAGTCCTTTAATT
377308 ATGGTACTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 19 0.49
29 20 0.51
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (29 bp):
TTTAATTTCAGTCCTTTAATTTTCAGCAA
Found at i:382089 original size:144 final size:140
Alignment explanation
Indices: 381822--382085 Score: 438
Period size: 144 Copynumber: 1.8 Consensus size: 140
381812 AGAATTTTTT
381822 TTATATTAAACCTTCTTTTAAAAAACATTTTTGTAATTACAATTATATGATTAAATATTATTTTA
1 TTATATTAAACCTTCTTTTAAAAAACATTTTTGTAATTACAATTATATGATTAAATATTATTTTA
381887 TAGTAAATGTGAACAGAATAATTGAAAATTGACAATCTTTCTATATTTTTTTTATTTATAGATTT
66 TAGTAAATGTGAACAGAATAATTGAAAATTGACAATCTTTCTATA----TTTTATTTATAGATTT
381952 TGCCTTTCTGTGAA
127 TGCCTTTCTGTGAA
381966 TTATATTAAACCTTCTTTTAAAAAACATTTTTGTAATTACAATTATATGATTATAACTATTATAT
1 TTATATTAAACCTTCTTTTAAAAAACATTTTTGTAATTACAATTATATGATTA-AA-TA-T-TAT
382031 TTTATAGTAAAATGTGAACAGAATAATTGAAAATTGACAATCTTTACTATATTTT
62 TTTATAGT-AAATGTGAACAGAATAATTGAAAATTGACAATCTTT-CTATATTTT
382086 TTATTATTTT
Statistics
Matches: 114, Mismatches: 0, Indels: 10
0.92 0.00 0.08
Matches are distributed among these distances:
144 53 0.46
145 2 0.02
146 6 0.05
147 1 0.01
148 11 0.10
149 36 0.32
150 5 0.04
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (140 bp):
TTATATTAAACCTTCTTTTAAAAAACATTTTTGTAATTACAATTATATGATTAAATATTATTTTA
TAGTAAATGTGAACAGAATAATTGAAAATTGACAATCTTTCTATATTTTATTTATAGATTTTGCC
TTTCTGTGAA
Found at i:383910 original size:17 final size:17
Alignment explanation
Indices: 383876--383910 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
383866 TGTACTTATG
*
383876 TTTATTTTATTTTATTT
1 TTTATTTTATGTTATTT
*
383893 TTTATTTTATGTTGTTT
1 TTTATTTTATGTTATTT
383910 T
1 T
383911 CACTGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTATTTTATGTTATTT
Found at i:384186 original size:16 final size:15
Alignment explanation
Indices: 384161--384190 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
384151 AACTTTAGGT
384161 ATAATAATTTAGATA
1 ATAATAATTTAGATA
384176 ATAATTAATTTAGAT
1 ATAA-TAATTTAGAT
384191 TTAGTCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
ATAATAATTTAGATA
Found at i:386402 original size:21 final size:21
Alignment explanation
Indices: 386378--386417 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
386368 TGCATCTTTG
386378 CATTAGCAT-ATATACATTGTA
1 CATTA-CATGATATACATTGTA
*
386399 CATTACATGGTATACATTG
1 CATTACATGATATACATTG
386418 CATCTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
CATTACATGATATACATTGTA
Found at i:388681 original size:76 final size:73
Alignment explanation
Indices: 388582--388778 Score: 218
Period size: 72 Copynumber: 2.7 Consensus size: 73
388572 CTTGAGATTG
* * * * * *
388582 TTTTTCTTAAAAACCATATTTGTCTCGATTGAGAGAGTTTTTACTTGAAATAAGATATTTCATTT
1 TTTTTCTT-AAAACAAGATTTGTCTCGATTGAGACAG-TTTTACTCGAAAGAAGACATTTCATTT
388647 CACTCAAGAT
64 CACTCAAGAT
*
388657 TATTTTCCTTAAAACAAGATTTGTCTC-ACTTGAGACAGTTTTACTCGAAAGAAGGCATTTCATT
1 T-TTTT-CTTAAAACAAGATTTGTCTCGA-TTGAGACAGTTTTACTCGAAAGAAGACATTTCATT
388721 TCACTCAAGAT
63 TCACTCAAGAT
* * * ** *
388732 TGTTT-TTAAAACAAGATTTATCTCGCTTGAGATTGTTTCACTCGAAA
1 TTTTTCTTAAAACAAGATTTGTCTCGATTGAGACAGTTTTACTCGAAA
388779 CAAAAGATTT
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
72 36 0.34
74 3 0.03
75 36 0.34
76 27 0.26
77 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (73 bp):
TTTTTCTTAAAACAAGATTTGTCTCGATTGAGACAGTTTTACTCGAAAGAAGACATTTCATTTCA
CTCAAGAT
Found at i:388776 original size:72 final size:74
Alignment explanation
Indices: 388638--388933 Score: 210
Period size: 78 Copynumber: 3.9 Consensus size: 74
388628 GAAATAAGAT
* * *
388638 ATTTCATTTCACTCAAGATTATTTTCCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTACTC
1 ATTTCATTTCACTCAAGATTAGTTT-CTTAAAACAAGATTTATCTCACTTGAGACAGTTTCACTC
388703 GAAAGAAGGC
65 GAAAGAAGGC
* **
388713 ATTTCATTTCACTCAAGATT-GTTT-TTAAAACAAGATTTATCTCGCTTGAGATTGTTTCACTCG
1 ATTTCATTTCACTCAAGATTAGTTTCTTAAAACAAGATTTATCTCACTTGAGACAGTTTCACTCG
* *
388776 AAACAAAAG-
66 AAA-GAAGGC
* * ** * * * *
388785 ATTTCATCTCGCTTGAGATCA-TTTCACTTGAAACATAAGATTTTATCTCGCTTGAGATAGTTTC
1 ATTTCATTTCACTCAAGATTAGTTT--CTT-AAA-ACAAGA-TTTATCTCACTTGAGACAGTTTC
*
388849 ACTCAAGACAGAA-G-
61 ACTC--GAAAGAAGGC
* * * * * *
388863 ATTTTATCTCGCTTAAGA-TAGTTTCACTTAAAACAGAAGATTTTATCTCACTTTAGATAGTTTC
1 ATTTCATTTCACTCAAGATTAGTTT--CTTAAAAC--AAGA-TTTATCTCACTTGAGACAGTTTC
388927 ACTCGAA
61 ACTCGAA
388934 CCAGAAGATT
Statistics
Matches: 184, Mismatches: 24, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
72 55 0.30
73 3 0.02
74 3 0.02
75 22 0.12
76 6 0.03
77 9 0.05
78 81 0.44
79 2 0.01
80 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (74 bp):
ATTTCATTTCACTCAAGATTAGTTTCTTAAAACAAGATTTATCTCACTTGAGACAGTTTCACTCG
AAAGAAGGC
Found at i:388796 original size:39 final size:39
Alignment explanation
Indices: 388744--389079 Score: 405
Period size: 39 Copynumber: 8.7 Consensus size: 39
388734 TTTTTAAAAC
*
388744 AAGA-TTTATCTCGCTTGAGATTGTTTCACTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* ** * *
388782 AAGATTTCATCTCGCTTGAGATCATTTCACTTGAAACAT
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
*
388821 AAGATTTTATCTCGCTTGAGATAGTTTCACTC-AAGACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAA-ACAG
* * **
388860 AAGATTTTATCTCGCTTAAGATAGTTTCACTTAAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * * *
388899 AAGATTTTATCTCACTTTAGATAGTTTCACTCGAACCAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* * *
388938 AAGATTTTATCTCGCTTGAGGTTGTTTCACTTGAAACGG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
* *
388977 AAGATTTTATCTCGCATGAGATT-ATTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
389015 AAGATTTTATCTCGCTTGAGATAT-TTTCACTCGAAACCA-
1 AAGATTTTATCTCGCTTGAGAT-TGTTTCACTCGAAA-CAG
**
389054 AAGA-TTTATCTCAATTGAGATTGTTT
1 AAGATTTTATCTCGCTTGAGATTGTTT
389080 TTCTTAAAAC
Statistics
Matches: 259, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
37 1 0.00
38 57 0.22
39 197 0.76
40 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
Found at i:389343 original size:136 final size:135
Alignment explanation
Indices: 389097--389472 Score: 500
Period size: 136 Copynumber: 2.8 Consensus size: 135
389087 AACAATCTAC
* *
389097 GCCTCGCTTGAGGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAGCTCATCCGACAGAG
1 GCCTCGCTTGAGGGATTGACATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
* ** ** * *
389162 GGAGAAGAAGTTCATAATGAGAAGAGTTTGTTCGACCTATCGCTCGAGTCACGGCATTTCGAATC
65 GGAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTATCGCTCGAGTCACAACACTTCAAATC
*
389227 AGCGAT
130 AGCAAT
* * * * *
389233 GCCTCACTTGAGGGATTGAGATTTCATATGGAGATTTCATAATGAGAAGAACTCATCCAACACAG
1 GCCTCGCTTGAGGGATTGACATTTCA-ATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
* * * * * *
389298 GGAGAGGAAGTTCTTAGTAAGAAGAACTTGTTTGACCTATTGCTCGATTCACAACACTTCAAATC
65 GGAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTATCGCTCGAGTCACAACACTTCAAATC
389363 AGCAAT
130 AGCAAT
* * * *
389369 GCCTCGCTTGAGGGATTGTCATTTCCAATGAAGAGATCATAATGAGAAGAACTCATCCGATAGAG
1 GCCTCGCTTGAGGGATTGACATTT-CAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAG
389434 GGAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTA
65 GGAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTA
389473 CTTGATTCAC
Statistics
Matches: 204, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
135 1 0.00
136 201 0.99
137 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (135 bp):
GCCTCGCTTGAGGGATTGACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGG
GAGAAGAAGTTCATAATAAGAAGAACTTGTTCGACCTATCGCTCGAGTCACAACACTTCAAATCA
GCAAT
Found at i:390278 original size:54 final size:54
Alignment explanation
Indices: 390100--390399 Score: 241
Period size: 55 Copynumber: 5.5 Consensus size: 54
390090 AAGATCGAAT
* * * * * *
390100 AAGCTCTAGCGTTTCTTTGTAACGGAGGAGTATAGGC-AAATTTTAAAGA-TCGAGT
1 AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGA-GCAAAATTTTAAA-ACT-GAGC
* * * * * * * *
390155 AAGGTTTAGCATTCCTTTGTTATGGAGGAGTATAACAAAATTTTAAAGA-TCAAAC
1 AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGAGCAAAATTTTAAA-ACT-GAGC
* *
390210 AAGCTCTAGCGTTCCTTTGCTATGGATGAGTAGAG-AAAATTCTTAAAACTGAGC
1 AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGAGCAAAATT-TTAAAACTGAGC
* * * * ** *
390264 AAGCTCTAGTGTTCCTTTTTTATGGAGGAGTAGAGTAAAATTTTTATGAC-CAGGC
1 AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGAGCAAAA-TTTTAAAACTGA-GC
* * **
390319 AAGCTCTAGCGTTCCTTTGTTATGGAAAAGTAAAGCAAAATTTTAAAGTTGGAGC
1 AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGAGCAAAATTTTAAAACT-GAGC
390374 AAGCTCTAGCGTTCCTTTGTTATGGA
1 AAGCTCTAGCGTTCCTTTGTTATGGA
390400 GCAGTATAAC
Statistics
Matches: 200, Mismatches: 37, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
54 47 0.23
55 150 0.75
56 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (54 bp):
AAGCTCTAGCGTTCCTTTGTTATGGAAGAGTAGAGCAAAATTTTAAAACTGAGC
Found at i:390414 original size:109 final size:108
Alignment explanation
Indices: 390049--390414 Score: 325
Period size: 109 Copynumber: 3.4 Consensus size: 108
390039 TGAACATGCT
* * * * * *
390049 AGCTCTAGCATTCCTTTATCATGGAGTAGAG-A-AAC-AATTTT-AAGATCGAATAAGCTCTAGC
1 AGCTCTAGCGTTCCTTTGTTATGGAG--GAGTATAACAAATTTTAAAGACCAAACAAGCTCTAGC
* * * * * *
390110 GTTTCTTTGTAACGGAGGAGTATAGGC-AAATTTTAAAGATCGAGTA
64 GTTCCTTTGTTATGGAAGAGTA-AAGCAAAATTTTAAAGAT-GAGCA
* * * *
390156 AGGTTTAGCATTCCTTTGTTATGGAGGAGTATAACAAAATTTTAAAGATCAAACAAGCTCTAGCG
1 AGCTCTAGCGTTCCTTTGTTATGGAGGAGTATAAC-AAATTTTAAAGACCAAACAAGCTCTAGCG
* * *
390221 TTCCTTTGCTATGGATGAGTAGAG-AAAATTCTTAAA-ACTGAGCA
65 TTCCTTTGTTATGGAAGAGTAAAGCAAAATT-TTAAAGA-TGAGCA
* * * * * **
390265 AGCTCTAGTGTTCCTTTTTTATGGAGGAGTAGAGTA-AAATTTTTATGACCAGGCAAGCTCTAGC
1 AGCTCTAGCGTTCCTTTGTTATGGAGGAGTATA--ACAAATTTTAAAGACCAAACAAGCTCTAGC
* *
390329 GTTCCTTTGTTATGGAAAAGTAAAGCAAAATTTTAAAGTTGGAGCA
64 GTTCCTTTGTTATGGAAGAGTAAAGCAAAATTTTAAAGAT-GAGCA
*
390375 AGCTCTAGCGTTCCTTTGTTATGGAGCAGTATAACAAATT
1 AGCTCTAGCGTTCCTTTGTTATGGAGGAGTATAACAAATT
390415 ATGTGTAAGT
Statistics
Matches: 211, Mismatches: 34, Indels: 26
0.78 0.13 0.10
Matches are distributed among these distances:
105 3 0.01
106 1 0.00
107 25 0.12
108 1 0.00
109 99 0.47
110 81 0.38
111 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (108 bp):
AGCTCTAGCGTTCCTTTGTTATGGAGGAGTATAACAAATTTTAAAGACCAAACAAGCTCTAGCGT
TCCTTTGTTATGGAAGAGTAAAGCAAAATTTTAAAGATGAGCA
Found at i:394200 original size:145 final size:145
Alignment explanation
Indices: 393944--394252 Score: 438
Period size: 145 Copynumber: 2.1 Consensus size: 145
393934 TCTTGTCGTT
* * * *
393944 GATCGGAATCTCCGATCACCATTCGGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
1 GATCGGGATCTCCGATTAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
** ** * *
394009 CTGAAAATTCAGGACGATCAGACGGTGAACGGCGGTGGATCGGAGAAAATAAGCCGAACGCTTTT
66 CTGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTT
* * *
394074 TGGTCTCTTGCCTGC
131 TAGCCTCTTGCCGGC
394089 GATCGGGATCTCCGATTAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
1 GATCGGGATCTCCGATTAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
* * * * * *
394154 CTGAAAATTCAGGGCGATTAGACGGTGGACAACGGCATATCAGAGAAAATAAGTCAAACGGTTTT
66 CTGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTT
*
394219 TAGCCTTTTGCCGGC
131 TAGCCTCTTGCCGGC
394234 GATCGGGATCTCCGATTAA
1 GATCGGGATCTCCGATTAA
394253 TACTTCAAAC
Statistics
Matches: 144, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (145 bp):
GATCGGGATCTCCGATTAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
CTGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTT
TAGCCTCTTGCCGGC
Found at i:394290 original size:145 final size:144
Alignment explanation
Indices: 393944--394300 Score: 376
Period size: 145 Copynumber: 2.5 Consensus size: 144
393934 TCTTGTCGTT
* * * ** * *
393944 GATCGGAATCTCCGATCACCATTCGGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
1 GATCGGGATCTCCGATTAACATTCCAAACAGTCAAAAGTTGCGCAAGA-CAACACGAACAACATA
** ** * *
394009 CTGAAAATTCAGGACGATCAGACGGTGAACGGCGGTGGATCGGAGAAAATAAGCCGAACGCTTTT
65 CTGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTT
* * *
394074 TGGTCTCTTGCCTGC
130 TAGCCTCTTGCCGGC
* * *
394089 GATCGGGATCTCCGATTAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
1 GATCGGGATCTCCGATTAACATTCCAAACAGTCAAAAGTTGCGCAAGA-CAACACGAACAACATA
* * * * * *
394154 CTGAAAATTCAGGGCGATTAGACGGTGGACAACGGCATATCAGAGAAAATAAGTCAAACGGTTTT
65 CTGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTT
*
394219 TAGCCTTTTGCCGGC
130 TAGCCTCTTGCCGGC
* * * * *
394234 GATCGGGATCTCCGATTAATACTT-CAAACAGTGAAAAGTTGTGTAATGTA-AACACGAACAGCA
1 GATCGGGATCTCCGATTAACA-TTCCAAACAGTCAAAAGTTGCGCAA-G-ACAACACGAACAACA
394297 TACT
63 TACT
394301 TCAATTTCAT
Statistics
Matches: 181, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
145 177 0.98
146 3 0.02
147 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (144 bp):
GATCGGGATCTCCGATTAACATTCCAAACAGTCAAAAGTTGCGCAAGACAACACGAACAACATAC
TGAAAATTCAGGACGATCAGACGGTGAACAACGGCAGATCAGAGAAAATAAGCCAAACGCTTTTT
AGCCTCTTGCCGGC
Found at i:397263 original size:55 final size:55
Alignment explanation
Indices: 397199--397340 Score: 198
Period size: 55 Copynumber: 2.6 Consensus size: 55
397189 ACATTCAAGT
* *
397199 GATTCATGAAGAATGACGTCCGATGAATGAAGAAAT-TTAAACCTGATTGAAGAAC
1 GATTCATGAAGAATGACATCCGATGAATGAAGAAATCTGAAA-CTGATTGAAGAAC
*
397254 GATTCATGAAG-ATGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGACC
1 GATTCATGAAGAAT-GACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
* * *
397309 GATCCATGAAGAAAGGCATCCGATGAATGAAG
1 GATTCATGAAGAATGACATCCGATGAATGAAG
397341 TTTGAAGTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
54 2 0.03
55 71 0.91
56 5 0.06
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAATGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
Found at i:401525 original size:32 final size:32
Alignment explanation
Indices: 401489--401562 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
401479 GCACTGTTAA
*
401489 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATTTGG
* ***
401521 AGATTTAACATTGAATATTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATTTGG
*
401553 GGATTCAACA
1 AGATTCAACA
401563 TCCTGATGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATTTGG
Found at i:402181 original size:43 final size:43
Alignment explanation
Indices: 402133--402238 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 43
402123 AAGGTGCCAA
* ***
402133 CCACGATTTCAACTCCATGACGGAGGATATCGTACCAATGGAT
1 CCACGATTTCAACTCCACGACGGAGGATATCGTACCAACACAT
* *
402176 CCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACACAT
1 CCACGATTTCAACTCCACGACGGAGGATATCGTACCAACACAT
*
402219 CCACGATTTCAACTTCACGA
1 CCACGATTTCAACTCCACGA
402239 TGAAGGGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (43 bp):
CCACGATTTCAACTCCACGACGGAGGATATCGTACCAACACAT
Found at i:402525 original size:42 final size:42
Alignment explanation
Indices: 402462--402675 Score: 304
Period size: 42 Copynumber: 5.1 Consensus size: 42
402452 TAAAGCAAGT
*
402462 TCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* * *
402504 TCATCAATAAGTCTTTTGAGCATGATGTTTAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* * *
402546 TCGTCTA-TAAGCCTTTCGAGCATGAGGCTTAAATCCTTCGGG
1 TCATC-AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
*
402588 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGG
1 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* * * *
402630 TCATCAGTAAGACTTTCAAGCATGATGATTAAATCCTCCGGG
1 TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
402672 TCAT
1 TCAT
402676 TTTAAGCCTT
Statistics
Matches: 152, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 1 0.01
42 150 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (42 bp):
TCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
Found at i:403046 original size:113 final size:113
Alignment explanation
Indices: 402743--403282 Score: 706
Period size: 112 Copynumber: 4.8 Consensus size: 113
402733 TGAAGCAAAT
* * * *
402743 CCAGATCTGATGTT-CCTTCAGAGGAAGCGGAACAGATCAT-TC-TCTTTCAAGATTTGATATTC
1 CCAGATCTGATATTCCCTTCGGAGTAAGTGGAACAGATC-TCTCTTC-TTCAAGATTTGATATTC
* * ** * *
402805 CC-T--GAGTGACAGCGGAACAAATCTGCCACGATTCAATGGATCAATTCTC
64 CCTTCAGAGT-A-AGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCC
* * * * *
402854 CCAGATCTGATATTCCCTTAGAAG-AAGCT-GAAAAGATC-CTTTTTTTTCAAGATTTGATATTC
1 CCAGATCTGATATTCCCTTCGGAGTAAG-TGGAACAGATCTC-TCTTCTTCAAGATTTGATATTC
*
402916 CCTTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATTAACTCCC
64 CCTTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCC
* * *
402966 CCATATCTTATATTCCCTTCGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCGGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
*
403031 TTCAGAGTAAGTGGAACAAGTCTGCATCGATTCAATGGATCAACTCCC
66 TTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCC
* *
403079 CCAGATCTGATATTCCCTTC-GAGTAAGTGGAACAGGTCTCTCTTCTTTAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCGGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
* *
403143 TTCAGAGTAAGTGGAACAAGTATGCTTCAATTCAATGGATCAACTCCC
66 TTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCC
* *
403191 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATCTTTCTTCTTCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCGGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
*
403256 TTCAGAGTAAGCGGAACAAGTCT-CTTC
66 TTCAGAGTAAGTGGAACAAGTCTGCTTC
403283 TCCAAGATTT
Statistics
Matches: 381, Mismatches: 36, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
111 44 0.12
112 173 0.45
113 159 0.42
114 5 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (113 bp):
CCAGATCTGATATTCCCTTCGGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCC
Found at i:403161 original size:225 final size:225
Alignment explanation
Indices: 402743--403278 Score: 750
Period size: 225 Copynumber: 2.4 Consensus size: 225
402733 TGAAGCAAAT
* * *
402743 CCAGATCTGATGTT-CCTTCAGAGGAAGCGGAACAGATCAT-TC-TCTTTCAAGATTTGATATTC
1 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATC-TCTCTTC-TTCAAGATTTGATATTC
* * *
402805 CC-T--GAGTGACAGCGGAACAAATCTGCCACGATTCAATGGATCAATTCTCCCAGATCTGATAT
64 CCTTCAGAGT-A-AGCGGAACAAGTCTGCCACGATTCAATGGATCAACTCCCCCAGATCTGATAT
* *
402867 TCCCTTAGAAGAAGCTGAAAAGATCCTTTTTTTTCAAGATTTGATATTCCCTTCAGAGTAAGTGG
127 TCCCTTAGAAGAAGCTGAAAAGATCCTCTTCTTTCAAGATTTGATATTCCCTTCAGAGTAAGTGG
* * *
402932 AACAAGTCTGCTTCGATTCAATGGATTAACTCCC
192 AACAAGTATGCTTCAATTCAATGGATCAACTCCC
* * * *
402966 CCATATCTTATATTCCCTTCGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
*
403031 TTCAGAGTAAGTGGAACAAGTCTG-CATCGATTCAATGGATCAACTCCCCCAGATCTGATATTCC
66 TTCAGAGTAAGCGGAACAAGTCTGCCA-CGATTCAATGGATCAACTCCCCCAGATCTGATATTCC
* * *
403095 CTTCG-AGTAAG-TGGAACAGGTCTCTCTTCTTT-AAGATTTGATATTCCCTTCAGAGTAAGTGG
130 CTTAGAAG-AAGCT-GAAAAGATC-CTCTTCTTTCAAGATTTGATATTCCCTTCAGAGTAAGTGG
403157 AACAAGTATGCTTCAATTCAATGGATCAACTCCC
192 AACAAGTATGCTTCAATTCAATGGATCAACTCCC
*
403191 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATCTTTCTTCTTCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
403256 TTCAGAGTAAGCGGAACAAGTCT
66 TTCAGAGTAAGCGGAACAAGTCT
403279 CTTCTCCAAG
Statistics
Matches: 278, Mismatches: 25, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
223 12 0.04
224 46 0.17
225 208 0.75
226 8 0.03
227 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (225 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGATCTCTCTTCTTCAAGATTTGATATTCCC
TTCAGAGTAAGCGGAACAAGTCTGCCACGATTCAATGGATCAACTCCCCCAGATCTGATATTCCC
TTAGAAGAAGCTGAAAAGATCCTCTTCTTTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA
AGTATGCTTCAATTCAATGGATCAACTCCC
Found at i:403304 original size:46 final size:46
Alignment explanation
Indices: 403193--403329 Score: 186
Period size: 46 Copynumber: 2.9 Consensus size: 46
403183 CAACTCCCCC
* *
403193 AGATCTGATATTCCCTTCAGAGTAAGTGGAAC-AGATCTTTCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG-TC--TCTTCTCCA
*
403241 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
* *
403287 AGATTTGATATTTCCTTCAGAGAAAGTGGAACAAGTCTGCTTC
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT-CTTC
403330 GATTCAATGG
Statistics
Matches: 81, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
46 43 0.53
47 4 0.05
48 32 0.40
49 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (46 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
Found at i:403307 original size:159 final size:159
Alignment explanation
Indices: 403081--403483 Score: 605
Period size: 159 Copynumber: 2.5 Consensus size: 159
403071 CAACTCCCCC
* * * **
403081 AGATCTGATATTCCCTTC-GAGTAAGTGGAACAGGTCTCTCTTCTTTAAGATTTGATATTCCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
403145 CAGAGTAAGTGGAACAAGTATGCTTCAATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTT
64 CAGAGTAAGTGGAACAAGTATGCTTCAATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTT
403210 CAGAGTAAGTGGAAC-AGATCT-TTCTTCTTCA
129 CAGAGTAAGTGGAACAAG-TCTCTT-TTCTTCA
*
403241 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCAAGATTTGATATTTCCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCA
* * * * *
403306 GAGAAAGTGGAACAAGTCTGCTTCGATTCAATGGATTAACTCCCCCAGATCTGATATTCCCTTCG
66 GAGTAAGTGGAACAAGTATGCTTCAATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCA
403371 GAGTAAGTGGAACAAGTCTCTTTTCTTCA
131 GAGTAAGTGGAACAAGTCTCTTTTCTTCA
*
403400 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACA-A-GTCTCTTCTCCAAGATTTGATATTCCCTT
* *
403465 CGGAGTAAGCGGAACAAGT
64 CAGAGTAAGTGGAACAAGT
403484 CTTTATTCTT
Statistics
Matches: 222, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
159 143 0.64
160 22 0.10
161 57 0.26
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (159 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCA
GAGTAAGTGGAACAAGTATGCTTCAATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCA
GAGTAAGTGGAACAAGTCTCTTTTCTTCA
Found at i:403431 original size:48 final size:48
Alignment explanation
Indices: 403352--403515 Score: 233
Period size: 48 Copynumber: 3.4 Consensus size: 48
403342 TAACTCCCCC
* * *
403352 AGATCTGATATTCCCTTCGGAGTAAGTGGAACAAGTCTCTTTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTTTCTTCA
* *
403400 AGATTTGATATTCCCTTCAGAGTAAGCGGAAC-AGATCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG-TCTCTTTTCTTCA
*
403448 AGATTTGATATTCCCTTCGGAGTAAGCGGAACAAGTCT-TTATTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTT-TTCTTCA
*
403496 AGATTTGATATACCCTTCAG
1 AGATTTGATATTCCCTTCAG
403516 CAAAAGTGGA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
47 3 0.03
48 98 0.95
49 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTTTCTTCA
Found at i:403527 original size:96 final size:96
Alignment explanation
Indices: 403352--403559 Score: 285
Period size: 96 Copynumber: 2.2 Consensus size: 96
403342 TAACTCCCCC
* *
403352 AGATCTGATATTCCCTTCGGAGTAAGTGGAACAAGTCTCTTTTCTTCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCGGAGTAAGCGGAACAAGTCTCTTTTCTTCAAGATTTGATATACCCTT
* * *
403417 CAGAGTAAGCGGAACAGATCTCTCTTCTCCA
66 CAGAGAAAGCGGAACAAATCCCTCTTCTCCA
*
403448 AGATTTGATATTCCCTTCGGAGTAAGCGGAACAAGTCT-TTATTCTTCAAGATTTGATATACCCT
1 AGATCTGATATTCCCTTCGGAGTAAGCGGAACAAGTCTCTT-TTCTTCAAGATTTGATATACCCT
* ** * *
403512 TCAGCA-AAAGTGGAACAAATCCCTCTAATGCT
65 TCAG-AGAAAGCGGAACAAATCCCTCTTCTCCA
403544 AGATCTGATATTCCCT
1 AGATCTGATATTCCCT
403560 GAGTGACAGC
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
95 2 0.02
96 95 0.97
97 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (96 bp):
AGATCTGATATTCCCTTCGGAGTAAGCGGAACAAGTCTCTTTTCTTCAAGATTTGATATACCCTT
CAGAGAAAGCGGAACAAATCCCTCTTCTCCA
Found at i:404385 original size:145 final size:145
Alignment explanation
Indices: 404149--404427 Score: 414
Period size: 145 Copynumber: 1.9 Consensus size: 145
404139 TTCGATCTCT
* *
404149 ATTCCGAACGGTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTTAGGACGATCA
1 ATTCCGAACGGTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCA
* * ** * * *
404214 GATGGTGGACGGCGGTGGATCAGAGAAAATAAGCCGAACAATTTTTGGTCTCTTGCCTGCGATCG
66 GACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCG
404279 GGATATTCGATTAAC
131 GGATATTCGATTAAC
* *
404294 ATTCCGAACGGTCAAAAGTTGCGCGAGACCATCACGAACAACATACTGAAAATTCAGGACAATCA
1 ATTCCGAACGGTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCA
* * ** *
404359 GACGGTGGACGACGGCAGATCGGAGAAAATAAGTCGAACGGTTTTTAGCCTTTTGCCGGCGATCG
66 GACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCG
404424 GGAT
131 GGAT
404428 CTCCGATCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
145 118 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (145 bp):
ATTCCGAACGGTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCA
GACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCG
GGATATTCGATTAAC
Found at i:404456 original size:145 final size:145
Alignment explanation
Indices: 404159--404665 Score: 391
Period size: 145 Copynumber: 3.5 Consensus size: 145
404149 ATTCCGAACG
* * *
404159 GTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTTAGGACGATCAGATGGTGGAC
1 GTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGGAC
* ** * * * *
404224 GGCGGTGGATCAGAGAAAATAAGCCGAACAATTTTTGGTCTCTTGCCTGCGATCGGGATATTCGA
66 GACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCGGGATATCCGA
* ** *
404289 TTAACATTCCGAACG
131 TCAACATTCAAAACA
* *
404304 GTCAAAAGTTGCGCGAGACCATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGGAC
1 GTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGGAC
* * ** * *
404369 GACGGCAGATCGGAGAAAATAAGTCGAACGGTTTTTAGCCTTTTGCCGGCGATCGGGATCTCCGA
66 GACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCGGGATATCCGA
*
404434 TCAATACTT-AAAACA
131 TCAACA-TTCAAAACA
* * * * * * * * *
404449 GTGAAAAGTTGTGTAATGTA-AA-CACGAACAGCATACTGAAATTTCATGACGATCGGACGGTAG
1 GTCAAAAGTTGCGCAA-G-ACAATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGG
** * * * * * * * * * * *
404512 ACGGTGG-TGAATCGGAGAAAACAAATCC-AGACTATATTTGGCCTCTTGCCGGTGATCTGAATC
64 ACGACGGCAG-ATCAGAGAAAA-TAAGCCGA-ACAATTTTTAGCCTCTTGCCGGCGATCGGGATA
* **
404575 TCCGATCAATATTCCGAACA
126 TCCGATCAACATTCAAAACA
* ** ** * * *
404595 GTCAAAAGTTGCGCGATGTTAA-CTTGAACAGCATACTGAAATTTCAGGACAATCGGACGGTGG-
1 GTCAAAAGTTGCGC-AAGACAATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGGA
404658 C-ACGGCAG
65 CGACGGCAG
404666 CGCAGTAACA
Statistics
Matches: 289, Mismatches: 63, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
144 3 0.01
145 187 0.65
146 97 0.34
147 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (145 bp):
GTCAAAAGTTGCGCAAGACAATCACGAACAACATACTGAAAATTCAGGACAATCAGACGGTGGAC
GACGGCAGATCAGAGAAAATAAGCCGAACAATTTTTAGCCTCTTGCCGGCGATCGGGATATCCGA
TCAACATTCAAAACA
Found at i:405311 original size:2 final size:2
Alignment explanation
Indices: 405249--405301 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
405239 TTTCGTACAT
405249 TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
405289 TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA
405302 AGGTATATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:407777 original size:29 final size:29
Alignment explanation
Indices: 407708--407769 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
407698 TGATTCGCAC
*
407708 AATTAAAATGAATTTTTAATAATATAAAA
1 AATTAAAATGAACTTTTAATAATATAAAA
407737 AATTAAAATGAACTTTTAATAATATAAAA
1 AATTAAAATGAACTTTTAATAATATAAAA
407766 AATT
1 AATT
407770 TAACTGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (29 bp):
AATTAAAATGAACTTTTAATAATATAAAA
Found at i:409265 original size:17 final size:17
Alignment explanation
Indices: 409243--409331 Score: 106
Period size: 17 Copynumber: 5.2 Consensus size: 17
409233 AATTAAGAGT
*
409243 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
409260 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
409277 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
409294 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
409311 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
409329 TAG
1 TAG
409332 ATGCATGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
17 49 0.78
18 14 0.22
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:409282 original size:34 final size:34
Alignment explanation
Indices: 409243--409344 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 34
409233 AATTAAGAGT
409243 TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
* * * *
409277 TAGTTTGATGAATGAACTAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
* * * *
409311 TAACTTTATTCAATGAACTAG-ATGCATGAATGAA
1 T-AGTTTAATAAATGAACTAGTTTG-ATGAATGAA
409345 GTGGCTTACT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 32 0.58
35 23 0.42
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (34 bp):
TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
Found at i:410040 original size:123 final size:123
Alignment explanation
Indices: 409810--410042 Score: 340
Period size: 123 Copynumber: 1.9 Consensus size: 123
409800 AAAATCCAAT
* * *
409810 TATGAAAGATTATTAAAGATTCATAAGAGTAAGTAATATGTTTTATGATCTCATTGAGTGGTCTC
1 TATGAAAGAATATAAAAGATTCATAAGAGTAAGTAATATGTTTCATGATCTCATTGAGTGGTCTC
* * ** * *
409875 GGTGATTAAAGAGAGTTTTGTTCTCCTTTGAGATCTCGGGTTCAAACACCTATAGACA
66 AGTGATTAAAAAGAACTTTGTTCTCCTTTGAGATATAGGGTTCAAACACCTATAGACA
* *
409933 TATGAAAGAATATAAAAGATTCATAAGTGTAAGTAATATGTTTCATGATCTCATTGAGTGGTCTT
1 TATGAAAGAATATAAAAGATTCATAAGAGTAAGTAATATGTTTCATGATCTCATTGAGTGGTCTC
* * *
409998 AGTGGTTAAAAAGAACTTTGTTCTCCTTTGAGGTATATGGTTCAA
66 AGTGATTAAAAAGAACTTTGTTCTCCTTTGAGATATAGGGTTCAA
410043 GCATCTGTGT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (123 bp):
TATGAAAGAATATAAAAGATTCATAAGAGTAAGTAATATGTTTCATGATCTCATTGAGTGGTCTC
AGTGATTAAAAAGAACTTTGTTCTCCTTTGAGATATAGGGTTCAAACACCTATAGACA
Found at i:411231 original size:19 final size:20
Alignment explanation
Indices: 411204--411281 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 20
411194 ATTTGTTTTA
* *
411204 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
411223 TTTAATATTATTATTATTAT
1 TTTAATATTATTATTATTAT
* *
411243 ATT-ATATTATTATTATTAA
1 TTTAATATTATTATTATTAT
* *
411262 ATAAATAATTATTATTATTA
1 TTTAAT-ATTATTATTATTA
411282 CAAACAGGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 31 0.61
20 7 0.14
21 13 0.25
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:411231 original size:22 final size:22
Alignment explanation
Indices: 411195--411260 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
411185 TTTTATTTCA
411195 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
411218 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
411240 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
411261 AATAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:411281 original size:3 final size:3
Alignment explanation
Indices: 411205--411260 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
411195 TTTGTTTTAT
* *
411205 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
411249 TTA TTA TTA TTA
1 TTA TTA TTA TTA
411261 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:412559 original size:12 final size:12
Alignment explanation
Indices: 412542--412606 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
412532 TTAATTCCTT
412542 TTATTTTAATTA
1 TTATTTTAATTA
*
412554 TTA-TTTACAATA
1 TTATTTTA-ATTA
412566 TTATTTTATTATTA
1 TTATTTTA--ATTA
*
412580 TTACTTTTTATTA
1 TTA-TTTTAATTA
412593 TTATTCTT-ATTA
1 TTATT-TTAATTA
412605 TT
1 TT
412607 TATATAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.09
12 17 0.39
13 13 0.30
14 6 0.14
15 4 0.09
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:412570 original size:3 final size:3
Alignment explanation
Indices: 412564--412606 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
412554 TTATTTACAA
* *
412564 TAT TAT T-T TAT TAT TAT TACT TTT TAT TAT TAT TCT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
412607 TATATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:412590 original size:16 final size:15
Alignment explanation
Indices: 412569--412606 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
412559 TACAATATTA
412569 TTTTATTATTATTACT
1 TTTTATTATTATT-CT
412585 TTTTATTATTATTCT
1 TTTTATTATTATTCT
*
412600 TATTATT
1 TTTTATT
412607 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATTATTATTCT
Found at i:412609 original size:16 final size:15
Alignment explanation
Indices: 412564--412606 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 15
412554 TTATTTACAA
412564 TATTATT-TTATTAT
1 TATTATTCTTATTAT
*
412578 TATTA--CTTTTTAT
1 TATTATTCTTATTAT
412591 TATTATTCTTATTAT
1 TATTATTCTTATTAT
412606 T
1 T
412607 TATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTCTTATTAT
Found at i:412823 original size:20 final size:19
Alignment explanation
Indices: 412798--412839 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
412788 TTATTTTATA
412798 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
412818 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
412837 AAT
1 AAT
412840 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:412841 original size:120 final size:120
Alignment explanation
Indices: 412701--412931 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 120
412691 TTTTAATATA
* * * *
412701 TATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAATCTTAAAACAACTGGATGTTCATTTTCTG
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAG-TCATTTTCTG
* *
412764 ATATTTTTAAATAAAATAAATATCTTATTTTATAAAT-TATATATTAATTGTTTTAAT
65 ATATTTCTAAAT-AAATAAATATCTTA-TTTATAAATATATAAATTAATTGTTTTAAT
* ** ** * *
412821 TATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGA
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAGTCATTTTCTGA
*
412886 TATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAAT
66 TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAAT
412932 ATTTTCCATA
Statistics
Matches: 94, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
119 9 0.10
120 43 0.46
121 23 0.24
122 19 0.20
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (120 bp):
TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAATCTTAAAACAACTAGAAGTCATTTTCTGA
TATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAATTGTTTTAAT
Found at i:415108 original size:15 final size:15
Alignment explanation
Indices: 415079--415117 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
415069 AATTTACATT
415079 TTTACATTT-GCATA
1 TTTACATTTGGCATA
415093 TTTACATTTGGCATA
1 TTTACATTTGGCATA
*
415108 TTTGCATTTG
1 TTTACATTTG
415118 TATTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:421350 original size:76 final size:75
Alignment explanation
Indices: 421225--421398 Score: 222
Period size: 76 Copynumber: 2.3 Consensus size: 75
421215 ATTAACAAGA
* * *
421225 AGCAAATGTTGGGGCATACTGAAAACCCTTTTCAATTAGAATCAGGAATGTTGATGTATCCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* *
421290 TGTTTATATC
66 CGTTCATATC
* * * * **
421300 AGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCAGAATGAAGAATGTTGATGTATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
*
421365 ACGTTCGTATC
65 ACGTTCATATC
*
421376 AGCAATTGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
421399 GGCCCACATC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 21 0.25
76 63 0.75
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
CGTTCATATC
Found at i:422744 original size:22 final size:23
Alignment explanation
Indices: 422693--422748 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
422683 ATCTACACTC
* *
422693 TTCAAAGATGATAGATTCCCTTT
1 TTCAAAGATGACAAATTCCCTTT
* *
422716 TTAAAAGATGACAAATTCTC-TT
1 TTCAAAGATGACAAATTCCCTTT
422738 TTCAAAGATGA
1 TTCAAAGATGA
422749 AAGCTTTGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGACAAATTCCCTTT
Found at i:423353 original size:113 final size:113
Alignment explanation
Indices: 423184--424829 Score: 2821
Period size: 113 Copynumber: 14.6 Consensus size: 113
423174 ATTTCTAGAA
*
423184 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
423249 CAACTTTTCGCTTGAATTTATCATTCGATGGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423297 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
423362 TAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423410 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
423475 CAACTTTTCGCTTGAATTCATCATTCGATTGATCATCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423523 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
423588 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423636 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
423701 TAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423749 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
423814 CAACTTTTCGCTTGAATTCATCATTCGATTGATCAGCATTACCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423862 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
423927 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
423975 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
424040 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTGCCAAGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
*
424088 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
424153 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
*
424201 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
424266 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* *
424314 GAGTTCATAATGAGAATAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
424379 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* *
424427 GAGTTCATAATGAGAAGAAGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
424492 CAACTTTTCGCTTGAATTTATCATTTGATGGACCAGCATTGCCAGGGT-
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCA-GGTC
*
424540 GAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
424605 CAACTTTTCGCTTGAATTTATCATTCGATGGACCAGCATTGCCAGGGC
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* * * * * *
424653 GAGTTTATAATAAGAAGAACTAATCTGAAGAAAGAAGAAGAAATTCATAATGATAAGAACTTG--
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
424716 ------TT-GCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAG-A
66 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAG-GTC
* **
424757 GAGTTCATAATGAGAAGAATTCATCTGAAG-AGGAAGGGGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
424821 CAATCTTTT
66 CAA-CTTTT
424830 GCATGATTCT
Statistics
Matches: 1462, Mismatches: 59, Indels: 25
0.95 0.04 0.02
Matches are distributed among these distances:
103 27 0.02
104 55 0.04
105 3 0.00
112 4 0.00
113 1370 0.94
114 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
Found at i:424740 original size:104 final size:103
Alignment explanation
Indices: 424618--424820 Score: 244
Period size: 104 Copynumber: 2.0 Consensus size: 103
424608 CTTTTCGCTT
* * * * * *
424618 GAATTTATCATTCGATGGACCAGCATTGCCAGGGCGAGTTTATAATAAGAAGAACTAATCTGAAG
1 GAATTCATCACTCGATGGACCAACATTGCCAGAGAGAGTTCATAATAAGAAGAACTAATCTGAAG
*
424683 AAAGAAGAAGAAATTCATAATGATAAGAACTTGTTGCTC
66 -AAGAAGAAGAAATTCATAATGAGAAGAACTTGTTGCTC
* * * * * *
424722 GAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAATTCATCTGAAG
1 GAATTCATCACTCGATGGACCAACATTGCCAGAGAGAGTTCATAATAAGAAGAACTAATCTGAAG
* ** *
424787 AGGAAGGGGAAGTTCATAATGAGAAGAACTTGTT
66 AAGAAGAAGAAATTCATAATGAGAAGAACTTGTT
424821 CAATCTTTTG
Statistics
Matches: 82, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
103 29 0.35
104 53 0.65
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (103 bp):
GAATTCATCACTCGATGGACCAACATTGCCAGAGAGAGTTCATAATAAGAAGAACTAATCTGAAG
AAGAAGAAGAAATTCATAATGAGAAGAACTTGTTGCTC
Found at i:425125 original size:19 final size:20
Alignment explanation
Indices: 425098--425175 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 20
425088 ATTTGTTTTA
* *
425098 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
425117 TTTAATATTATTATTATTAT
1 TTTAATATTATTATTATTAT
* *
425137 ATT-ATATTATTATTATTAA
1 TTTAATATTATTATTATTAT
* *
425156 ATAAATAATTATTATTATTA
1 TTTAAT-ATTATTATTATTA
425176 CAAACAGGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 31 0.61
20 7 0.14
21 13 0.25
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:425125 original size:22 final size:22
Alignment explanation
Indices: 425089--425154 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
425079 TTTTATTTCA
425089 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
425112 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
425134 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
425155 AATAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:425175 original size:3 final size:3
Alignment explanation
Indices: 425099--425154 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
425089 TTTGTTTTAT
* *
425099 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
425143 TTA TTA TTA TTA
1 TTA TTA TTA TTA
425155 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Done.